3245 files found no tree given... Reading options from ./baseml.ctl.. ns = 5 ls = 898 Sequential format.. Reading seq # 1: YAL001C_Sbay Reading seq # 2: YAL001C_Scer Reading seq # 3: YAL001C_Skud Reading seq # 4: YAL001C_Smik Reading seq # 5: YAL001C_Spar Sequences read.. Counting patterns.. # site patterns = 432 Counting frequencies.. 120 bytes for distance 69120 bytes for lkl0 55296 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.800262 0.046868 0.186784 0.439734 0.646671 0.367931 0.852821 lnL0 = -5324.914375 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 5324.914375 x= 0.00006 0.80026 0.04687 0.18678 0.43973 0.64667 0.36793 0.85282 1 h-lim-p 0.0000 0.0000 639.0492 5324.021755 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0002 374.4341 5297.445319 m 0.0002 36 | 2/8 3 h-lim-p 0.0001 0.0005 1401.2952 5187.341608 7 0.0004 64 | 2/8 4 h-lim-p 0.0005 0.0037 147.1714 5108.540178 m 0.0037 76 | 2/8 5 h-lim-p -0.0000 -0.0000 133.4611 h-lim-p: -1.73159893e-19 -1.38527915e-18 1.33461056e+02 5108.540178 .. | 2/8 6 h-lim-p 0.0000 0.0058 509.8551 5027.713267 0 0.0010 102 | 2/8 7 h-lim-p 0.0001 0.0011 275.9979 4983.406595 m 0.0011 114 | 2/8 8 h-lim-p 0.0008 0.0060 60.9520 4981.496565 0 0.0011 126 | 2/8 9 h-lim-p 0.0008 0.0066 10.0509 4981.437453 0 0.0012 138 | 2/8 10 h-lim-p 0.0023 0.1956 5.3058 4981.410143 3 0.0024 156 | 2/8 11 h-lim-p 0.0130 0.6712 0.9690 4981.406754 3 0.0052 174 | 2/8 12 h-lim-p 0.1225 2.6467 0.0411 4981.209740 0 0.9802 195 | 1/8 13 h-lim-p 0.0028 0.0222 5.5777 4981.190366 5 0.0018 225 | 1/8 14 h-lim-p 0.6901 20.0000 0.0144 4981.027096 0 1.3803 238 | 1/8 15 h-lim-p 2.5000 20.0000 0.0069 4981.014693 2 1.1719 261 | 1/8 16 h-lim-p 2.5000 20.0000 0.0009 4981.014533 1 1.0938 282 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 4981.014532 0 1.0938 301 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 4981.014532 0 1.0938 320 | 1/8 19 h-lim-p 2.5000 20.0000 0.0000 4981.014532 0 1.0938 339 | 1/8 20 h-lim-p 2.5000 20.0000 0.0000 4981.014532 0 3.7500 358 | 1/8 21 h-lim-p 0.8090 20.0000 0.0000 4981.014532 0 0.8090 377 | 1/8 22 h-lim-p 0.0055 20.0000 0.0001 4981.014532 0 0.0000 411 | 1/8 23 h-lim-p 0.0000 20.0000 0.0001 | 1/8 24 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -4981.014532 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4981.014532 Node 7: lnL = -4981.014532 Node 8: lnL = -4981.014532 Node 9: lnL = -4981.014532 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 955 Sequential format.. Reading seq # 1: YAL007C_Sbay Reading seq # 2: YAL007C_Scer Reading seq # 3: YAL007C_Skud Reading seq # 4: YAL007C_Smik Reading seq # 5: YAL007C_Spar Sequences read.. Counting patterns.. # site patterns = 457 Counting frequencies.. 120 bytes for distance 73120 bytes for lkl0 58496 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.572287 0.038942 0.109104 0.296601 0.467063 0.271993 0.633162 lnL0 = -5177.466598 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 5177.466598 x= 0.00006 0.57229 0.03894 0.10910 0.29660 0.46706 0.27199 0.63316 1 h-lim-p 0.0000 0.0000 602.6254 5176.525850 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0002 405.9915 5154.384644 m 0.0002 36 | 2/8 3 h-lim-p 0.0004 0.0030 170.5673 5133.780653 0 0.0015 50 | 2/8 4 h-lim-p 0.0003 0.0021 252.3105 5110.797997 0 0.0010 64 | 2/8 5 h-lim-p 0.0046 0.0371 23.7540 5098.877952 0 0.0069 76 | 2/8 6 h-lim-p 0.0015 0.0120 55.2155 5086.791284 0 0.0045 89 | 2/8 7 h-lim-p 0.0069 0.0555 11.6731 5086.513666 2 0.0033 105 | 2/8 8 h-lim-p 0.1337 1.8489 0.2838 5072.656891 0 0.5348 119 | 1/8 9 h-lim-p 0.0002 0.0019 252.1534 5068.693365 0 0.0005 138 | 1/8 10 h-lim-p 0.7969 6.3755 0.0447 5067.743818 5 0.8336 161 | 1/8 11 h-lim-p 2.2337 17.8692 0.0096 5067.676512 3 0.9336 186 | 1/8 12 h-lim-p 2.5000 20.0000 0.0027 5067.675130 2 0.6201 210 | 1/8 13 h-lim-p 2.2357 20.0000 0.0008 5067.674962 0 1.1178 229 | 0/8 14 h-lim-p 0.0089 4.9706 0.0946 5067.674949 0 0.0039 248 | 0/8 15 h-lim-p 2.5000 20.0000 0.0001 5067.674938 1 1.2305 271 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 5067.674938 0 1.0938 291 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 5067.674938 0 1.0938 311 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 5067.674938 0 1.0938 331 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 5067.674938 0 0.1367 354 | 0/8 20 h-lim-p 0.0615 20.0000 0.0000 5067.674938 0 0.0308 374 Out... lnL = -5067.674938 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -5067.674938 Node 7: lnL = -5067.674938 Node 8: lnL = -5067.674938 Node 9: lnL = -5067.674938 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 322 Sequential format.. Reading seq # 1: YAL008W_Sbay Reading seq # 2: YAL008W_Scer Reading seq # 3: YAL008W_Skud Reading seq # 4: YAL008W_Smik Reading seq # 5: YAL008W_Spar Sequences read.. Counting patterns.. # site patterns = 112 Counting frequencies.. 120 bytes for distance 17920 bytes for lkl0 14336 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.126963 0.085205 0.095245 0.123546 0.212529 0.121845 0.263905 lnL0 = -1231.697025 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1231.697025 x= 0.00006 0.12696 0.08521 0.09525 0.12355 0.21253 0.12185 0.26390 1 h-lim-p 0.0000 0.0000 178.9090 1231.612733 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0059 59.3383 1230.120960 0 0.0013 41 | 1/8 3 h-lim-p 0.0037 0.0296 10.9285 1230.020442 6 0.0015 66 | 1/8 4 h-lim-p 0.0072 0.1712 2.2304 1229.878378 1 0.0090 80 | 1/8 5 h-lim-p 0.0115 0.0919 1.5887 1224.809044 0 0.0460 94 | 0/8 6 h-lim-p 0.0003 0.0027 63.8366 1221.439541 0 0.0010 107 | 0/8 7 h-lim-p 0.0004 0.0030 18.1726 1221.302842 0 0.0007 120 | 0/8 8 h-lim-p 0.0002 0.0016 10.0606 1221.255844 0 0.0012 134 | 0/8 9 h-lim-p 0.0137 0.2076 0.8934 1221.254148 4 0.0018 156 | 0/8 10 h-lim-p 0.0203 3.8942 0.0794 1220.959216 0 0.2430 179 | 0/8 11 h-lim-p 0.2181 1.7450 0.0099 1220.928398 0 0.6544 200 | 0/8 12 h-lim-p 0.8441 6.7524 0.0024 1220.925258 3 0.8704 226 | 0/8 13 h-lim-p 2.4616 20.0000 0.0009 1220.925114 4 0.4514 257 | 0/8 14 h-lim-p 1.7211 20.0000 0.0002 1220.925085 2 0.9059 282 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1220.925085 0 1.0938 302 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1220.925085 0 1.0938 322 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1220.925085 0 2.5000 342 | 0/8 18 h-lim-p 1.4395 20.0000 0.0000 1220.925085 0 0.0225 367 | 0/8 19 h-lim-p 0.0125 20.0000 0.0000 1220.925085 0 0.0002 392 Out... lnL = -1220.925085 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1220.925085 Node 7: lnL = -1220.925085 Node 8: lnL = -1220.925085 Node 9: lnL = -1220.925085 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 196 Sequential format.. Reading seq # 1: YAL009W_Sbay Reading seq # 2: YAL009W_Scer Reading seq # 3: YAL009W_Skud Reading seq # 4: YAL009W_Smik Reading seq # 5: YAL009W_Spar Sequences read.. Counting patterns.. # site patterns = 67 Counting frequencies.. 120 bytes for distance 10720 bytes for lkl0 8576 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.102282 0.075152 0.081297 0.094531 0.174800 0.065675 0.175621 lnL0 = -678.823941 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 678.823941 x= 0.00006 0.10228 0.07515 0.08130 0.09453 0.17480 0.06568 0.17562 1 h-lim-p 0.0000 0.0000 184.9428 678.783327 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0012 127.2003 672.771990 0 0.0009 40 | 1/8 3 h-lim-p 0.0005 0.0037 39.6183 672.303083 0 0.0007 52 | 1/8 4 h-lim-p 0.0014 0.0110 13.7950 672.203277 8 0.0010 83 | 1/8 5 h-lim-p 0.0062 0.0542 2.2802 672.085461 1 0.0077 97 | 1/8 6 h-lim-p 0.0054 0.0472 3.2638 670.132390 0 0.0215 111 | 1/8 7 h-lim-p 0.0008 0.0061 21.6459 665.650256 0 0.0031 125 | 1/8 8 h-lim-p 0.0004 0.0033 37.7937 665.032566 0 0.0008 138 | 1/8 9 h-lim-p 0.0777 0.6218 0.1691 663.399071 0 0.2332 151 | 0/8 10 h-lim-p 0.0030 0.0432 12.9522 663.361762 8 0.0005 193 | 0/8 11 h-lim-p 0.2500 12.3234 0.0239 663.229226 0 0.4999 206 | 0/8 12 h-lim-p 1.3834 15.6616 0.0087 663.215720 7 0.3804 242 | 0/8 13 h-lim-p 0.9589 20.0000 0.0034 663.210917 6 0.6576 279 | 0/8 14 h-lim-p 2.5000 20.0000 0.0008 663.210394 4 0.8855 309 | 0/8 15 h-lim-p 2.5000 20.0000 0.0001 663.210383 1 0.9961 331 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 663.210383 0 1.0938 351 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 663.210383 0 2.1875 371 | 0/8 18 h-lim-p 1.8482 20.0000 0.0000 663.210383 0 0.8086 391 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 663.210383 0 0.0002 424 Out... lnL = -663.210383 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -663.210383 Node 7: lnL = -663.210383 Node 8: lnL = -663.210383 Node 9: lnL = -663.210383 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 196 Sequential format.. Reading seq # 1: YAL010C_Sbay Reading seq # 2: YAL010C_Scer Reading seq # 3: YAL010C_Skud Reading seq # 4: YAL010C_Smik Reading seq # 5: YAL010C_Spar Sequences read.. Counting patterns.. # site patterns = 68 Counting frequencies.. 120 bytes for distance 10880 bytes for lkl0 8704 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.100132 0.075563 0.081003 0.093739 0.172269 0.065840 0.175157 lnL0 = -679.071952 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 679.071952 x= 0.00006 0.10013 0.07556 0.08100 0.09374 0.17227 0.06584 0.17516 1 h-lim-p 0.0000 0.0000 180.5365 679.030705 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0012 132.3713 672.926548 0 0.0009 40 | 1/8 3 h-lim-p 0.0003 0.0024 38.2142 672.550221 0 0.0006 53 | 1/8 4 h-lim-p 0.0015 0.0119 13.0111 672.452117 6 0.0011 77 | 1/8 5 h-lim-p 0.0078 0.0752 1.8715 672.347237 2 0.0073 93 | 1/8 6 h-lim-p 0.0057 0.0557 2.3884 668.064180 0 0.0344 107 | 1/8 7 h-lim-p 0.0005 0.0039 38.2513 665.917958 0 0.0020 121 | 1/8 8 h-lim-p 0.0075 0.0599 1.6020 665.892104 2 0.0035 137 | 0/8 9 h-lim-p 0.0001 0.0712 44.6635 665.492248 0 0.0005 151 | 0/8 10 h-lim-p 0.0152 0.1215 0.7567 664.516398 0 0.0455 164 | 0/8 11 h-lim-p 0.4883 3.9066 0.0400 664.158647 2 0.4578 188 | 0/8 12 h-lim-p 1.6904 16.5161 0.0108 664.123155 2 0.7924 212 | 0/8 13 h-lim-p 2.5000 20.0000 0.0022 664.119741 5 0.8067 244 | 0/8 14 h-lim-p 1.6232 20.0000 0.0011 664.119036 2 0.7609 268 | 0/8 15 h-lim-p 2.5000 20.0000 0.0002 664.118978 2 1.0938 292 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 664.118977 0 1.0938 312 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 664.118977 0 1.0938 332 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 664.118977 0 5.0000 353 | 0/8 19 h-lim-p 1.3158 20.0000 0.0000 664.118977 0 0.1439 375 | 0/8 20 h-lim-p 0.1771 20.0000 0.0000 664.118977 0 0.0083 399 | 0/8 21 h-lim-p 0.0088 20.0000 0.0000 664.118977 0 0.0088 419 | 0/8 22 h-lim-p 0.0094 20.0000 0.0000 664.118977 0 0.0000 459 Out... lnL = -664.118977 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -664.118977 Node 7: lnL = -664.118977 Node 8: lnL = -664.118977 Node 9: lnL = -664.118977 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 319 Sequential format.. Reading seq # 1: YAL020C_Sbay Reading seq # 2: YAL020C_Scer Reading seq # 3: YAL020C_Skud Reading seq # 4: YAL020C_Smik Reading seq # 5: YAL020C_Spar Sequences read.. Counting patterns.. # site patterns = 109 Counting frequencies.. 120 bytes for distance 17440 bytes for lkl0 13952 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.158849 0.103872 0.095779 0.122382 0.204486 0.096215 0.261321 lnL0 = -1260.680116 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1260.680116 x= 0.00006 0.15885 0.10387 0.09578 0.12238 0.20449 0.09622 0.26132 1 h-lim-p 0.0000 0.0000 222.7772 1260.585050 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0022 87.9467 1256.805700 7 0.0010 58 | 1/8 3 h-lim-p 0.0025 0.0202 15.2347 1256.662953 6 0.0011 81 | 1/8 4 h-lim-p 0.0040 0.0791 4.2133 1256.573270 7 0.0034 107 | 1/8 5 h-lim-p 0.0055 0.1269 2.6100 1255.373841 0 0.0222 121 | 1/8 6 h-lim-p 0.0021 0.0171 11.2194 1246.631600 0 0.0085 135 | 0/8 7 h-lim-p 0.0005 0.0039 56.7450 1245.390376 0 0.0007 147 | 0/8 8 h-lim-p 0.0003 0.0023 16.0676 1245.306293 0 0.0006 160 | 0/8 9 h-lim-p 0.0007 0.0055 3.2646 1245.290245 0 0.0028 174 | 0/8 10 h-lim-p 0.1146 2.1574 0.0786 1244.705667 0 0.2293 187 | 0/8 11 h-lim-p 0.7480 5.9840 0.0226 1244.616079 5 0.3629 218 | 0/8 12 h-lim-p 0.8362 6.6893 0.0043 1244.601911 2 0.7839 242 | 0/8 13 h-lim-p 1.6337 13.0696 0.0016 1244.600019 4 0.8320 271 | 0/8 14 h-lim-p 2.5000 20.0000 0.0004 1244.599979 2 0.5469 296 | 0/8 15 h-lim-p 2.5000 20.0000 0.0001 1244.599974 2 0.9644 320 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1244.599974 0 1.0938 340 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1244.599974 0 1.0938 360 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1244.599974 0 5.0000 381 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1244.599974 0 0.9375 402 | 0/8 20 h-lim-p 0.0925 20.0000 0.0000 1244.599974 0 0.0002 430 Out... lnL = -1244.599974 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1244.599974 Node 7: lnL = -1244.599974 Node 8: lnL = -1244.599974 Node 9: lnL = -1244.599974 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 654 Sequential format.. Reading seq # 1: YAL028W_Sbay Reading seq # 2: YAL028W_Scer Reading seq # 3: YAL028W_Skud Reading seq # 4: YAL028W_Smik Reading seq # 5: YAL028W_Spar Sequences read.. Counting patterns.. # site patterns = 192 Counting frequencies.. 120 bytes for distance 30720 bytes for lkl0 24576 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.088581 0.094891 0.098613 0.103929 0.191131 0.102600 0.258063 lnL0 = -2641.888644 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2641.888644 x= 0.00006 0.08858 0.09489 0.09861 0.10393 0.19113 0.10260 0.25806 1 h-lim-p 0.0000 0.0000 311.9077 2641.667666 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0033 84.3676 2640.428780 0 0.0003 39 | 1/8 3 h-lim-p 0.0012 0.0115 21.7118 2640.315462 4 0.0005 59 | 1/8 4 h-lim-p 0.0026 0.0484 3.9602 2640.291103 3 0.0011 77 | 1/8 5 h-lim-p 0.0013 0.0791 3.2643 2640.080458 0 0.0053 91 | 1/8 6 h-lim-p 0.0024 0.0246 7.1741 2637.118237 0 0.0073 104 | 0/8 7 h-lim-p 0.0003 0.0027 51.5265 2631.598378 0 0.0010 117 | 0/8 8 h-lim-p 0.0002 0.0015 59.6873 2630.617237 0 0.0006 130 | 0/8 9 h-lim-p 0.0001 0.0004 54.2931 2630.098794 m 0.0004 142 | 0/8 10 h-lim-p 0.0000 0.0000 0.0242 h-lim-p: 2.37201245e-17 1.89760996e-16 2.41878808e-02 2630.098794 .. | 0/8 11 h-lim-p 0.0000 0.0037 69.3874 2629.697784 0 0.0002 174 | 0/8 12 h-lim-p 0.0005 0.0057 23.6144 2629.652388 5 0.0002 196 | 0/8 13 h-lim-p 0.0009 0.0297 4.8387 2629.649779 5 0.0002 219 | 0/8 14 h-lim-p 0.0014 0.4271 0.7834 2629.649721 3 0.0002 239 | 0/8 15 h-lim-p 0.0008 0.5459 0.1830 2629.649717 1 0.0002 262 | 0/8 16 h-lim-p 0.0007 7.2529 0.0550 2629.649714 0 0.0010 282 | 0/8 17 h-lim-p 0.0003 1.8459 0.1715 2629.649635 0 0.0103 307 | 0/8 18 h-lim-p 0.0004 0.0693 4.7541 2629.648769 0 0.0059 331 | 0/8 19 h-lim-p 0.5845 4.6760 0.0066 2629.648669 0 1.1690 344 | 0/8 20 h-lim-p 2.5000 20.0000 0.0011 2629.648666 0 1.0938 364 | 0/8 21 h-lim-p 2.5000 20.0000 0.0001 2629.648666 0 1.0938 384 | 0/8 22 h-lim-p 2.5000 20.0000 0.0000 2629.648666 0 1.2500 404 | 0/8 23 h-lim-p 0.1191 20.0000 0.0002 2629.648666 0 0.0074 427 | 0/8 24 h-lim-p 0.0017 20.0000 0.0007 2629.648666 0 0.0000 465 | 0/8 25 h-lim-p 0.0000 20.0000 0.0000 2629.648666 0 0.0000 497 Out... lnL = -2629.648666 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2629.648666 Node 7: lnL = -2629.648666 Node 8: lnL = -2629.648666 Node 9: lnL = -2629.648666 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 503 Sequential format.. Reading seq # 1: YAL030W_Sbay Reading seq # 2: YAL030W_Scer Reading seq # 3: YAL030W_Skud Reading seq # 4: YAL030W_Smik Reading seq # 5: YAL030W_Spar Sequences read.. Counting patterns.. # site patterns = 160 Counting frequencies.. 120 bytes for distance 25600 bytes for lkl0 20480 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.128607 0.108571 0.113020 0.101044 0.204049 0.095340 0.251092 lnL0 = -1847.087716 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1847.087716 x= 0.00006 0.12861 0.10857 0.11302 0.10104 0.20405 0.09534 0.25109 1 h-lim-p 0.0000 0.0000 363.7049 1846.948625 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0041 114.8608 1843.792905 0 0.0006 40 | 1/8 3 h-lim-p 0.0010 0.0078 25.0615 1843.474596 2 0.0009 56 | 1/8 4 h-lim-p 0.0057 0.0628 4.0468 1843.210009 3 0.0051 74 | 1/8 5 h-lim-p 0.0088 0.0927 2.3738 1829.002417 0 0.0527 88 | 0/8 6 h-lim-p 0.0002 0.0017 82.8068 1823.260425 0 0.0008 102 | 0/8 7 h-lim-p 0.0000 0.0003 115.6100 1821.955659 m 0.0003 114 | 1/8 8 h-lim-p 0.0008 0.0062 22.1031 1821.800456 6 0.0004 140 | 1/8 9 h-lim-p 0.0007 0.0136 11.7435 1821.730367 5 0.0006 161 | 1/8 10 h-lim-p 0.1094 2.9721 0.0680 1819.502203 0 0.4376 175 | 0/8 11 h-lim-p 0.0100 0.4091 2.9597 1819.498737 5 0.0007 207 | 0/8 12 h-lim-p 0.0432 0.5071 0.0463 1819.185818 3 0.3161 228 | 0/8 13 h-lim-p 0.6341 5.0724 0.0031 1819.139722 0 1.2681 249 | 0/8 14 h-lim-p 0.3594 2.8748 0.0007 1819.138846 0 1.4374 271 | 0/8 15 h-lim-p 2.5000 20.0000 0.0001 1819.138820 1 1.0938 293 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1819.138820 0 1.2500 313 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1819.138820 0 1.0938 333 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1819.138820 0 1.2500 353 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1819.138820 0 0.0342 378 | 0/8 20 h-lim-p 0.0327 20.0000 0.0000 1819.138820 0 0.0327 398 | 0/8 21 h-lim-p 0.0297 20.0000 0.0000 1819.138820 0 0.0000 439 Out... lnL = -1819.138820 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1819.138820 Node 7: lnL = -1819.138820 Node 8: lnL = -1819.138820 Node 9: lnL = -1819.138820 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 207 Sequential format.. Reading seq # 1: YAL032C_Sbay Reading seq # 2: YAL032C_Scer Reading seq # 3: YAL032C_Skud Reading seq # 4: YAL032C_Smik Reading seq # 5: YAL032C_Spar Sequences read.. Counting patterns.. # site patterns = 114 Counting frequencies.. 120 bytes for distance 18240 bytes for lkl0 14592 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.213845 0.147443 0.148641 0.220518 0.355423 0.215202 0.399406 lnL0 = -955.663841 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 955.663841 x= 0.00006 0.21385 0.14744 0.14864 0.22052 0.35542 0.21520 0.39941 1 h-lim-p 0.0000 0.0000 140.7958 955.614247 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0041 83.9179 946.263462 8 0.0027 64 | 1/8 3 h-lim-p 0.0018 0.0143 26.4787 945.427631 0 0.0027 76 | 1/8 4 h-lim-p 0.0070 0.0558 4.3583 945.234547 6 0.0069 100 | 1/8 5 h-lim-p 0.0112 0.1485 2.6594 942.566459 0 0.0450 114 | 0/8 6 h-lim-p 0.0011 0.0091 32.4871 938.382398 0 0.0045 128 | 0/8 7 h-lim-p 0.0004 0.0033 52.4609 935.051141 0 0.0016 142 | 0/8 8 h-lim-p 0.0011 0.0088 16.3133 934.628606 0 0.0033 155 | 0/8 9 h-lim-p 0.0012 0.0094 11.0946 934.464137 0 0.0035 168 | 0/8 10 h-lim-p 0.1318 1.0543 0.1410 932.835168 0 0.5271 182 | 0/8 11 h-lim-p 0.0789 0.6316 0.0772 932.435747 0 0.3158 204 | 0/8 12 h-lim-p 1.1123 8.8981 0.0134 932.386568 7 0.7381 240 | 0/8 13 h-lim-p 1.9923 15.9386 0.0028 932.383673 5 1.0708 271 | 0/8 14 h-lim-p 2.5000 20.0000 0.0007 932.383533 4 0.8228 300 | 0/8 15 h-lim-p 2.5000 20.0000 0.0001 932.383530 1 0.9961 322 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 932.383530 0 1.2500 342 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 932.383530 0 2.1875 362 | 0/8 18 h-lim-p 2.3356 20.0000 0.0000 932.383530 0 1.0218 382 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 932.383530 0 2.1875 402 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 932.383530 0 0.6250 423 | 0/8 21 h-lim-p 0.4292 20.0000 0.0000 932.383530 0 0.2146 443 | 0/8 22 h-lim-p 0.0615 20.0000 0.0000 932.383530 0 0.0269 463 | 0/8 23 h-lim-p 0.0112 20.0000 0.0000 932.383530 0 0.0000 500 Out... lnL = -932.383530 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -932.383530 Node 7: lnL = -932.383530 Node 8: lnL = -932.383530 Node 9: lnL = -932.383530 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 301 Sequential format.. Reading seq # 1: YAL034W-A_Sbay Reading seq # 2: YAL034W-A_Scer Reading seq # 3: YAL034W-A_Skud Reading seq # 4: YAL034W-A_Smik Reading seq # 5: YAL034W-A_Spar Sequences read.. Counting patterns.. # site patterns = 107 Counting frequencies.. 120 bytes for distance 17120 bytes for lkl0 13696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.149136 0.105781 0.104697 0.127815 0.199572 0.094028 0.240915 lnL0 = -1162.164216 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1162.164216 x= 0.00006 0.14914 0.10578 0.10470 0.12782 0.19957 0.09403 0.24092 1 h-lim-p 0.0000 0.0000 211.5540 1162.113582 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0023 127.9554 1156.062862 5 0.0010 52 | 1/8 3 h-lim-p 0.0011 0.0091 31.6721 1155.371278 1 0.0014 66 | 1/8 4 h-lim-p 0.0035 0.0278 10.6645 1155.234650 5 0.0019 89 | 1/8 5 h-lim-p 0.0055 0.0482 3.6097 1154.963239 0 0.0083 101 | 1/8 6 h-lim-p 0.0087 0.0900 3.4421 1148.602536 0 0.0348 115 | 1/8 7 h-lim-p 0.0006 0.0045 38.1507 1143.290992 0 0.0023 129 | 1/8 8 h-lim-p 0.0011 0.0087 23.2523 1143.162307 2 0.0005 145 | 1/8 9 h-lim-p 0.1106 2.0023 0.1066 1141.297912 0 0.4424 159 | 1/8 10 h-lim-p 0.9687 7.7496 0.0231 1141.182724 7 0.5035 196 | 1/8 11 h-lim-p 2.5000 20.0000 0.0038 1141.176978 4 0.6109 225 | 1/8 12 h-lim-p 0.9329 20.0000 0.0025 1141.174980 4 0.5531 255 | 1/8 13 h-lim-p 2.2232 20.0000 0.0006 1141.174863 4 0.6038 283 | 1/8 14 h-lim-p 1.4083 20.0000 0.0003 1141.174852 2 0.4504 307 | 1/8 15 h-lim-p 2.3532 20.0000 0.0001 1141.174851 1 0.9376 328 | 0/8 16 h-lim-p -0.0000 -0.0000 0.0054 h-lim-p: -1.61363739e-19 -1.29090991e-18 5.37504883e-03 1141.174851 .. | 1/8 17 h-lim-p 0.0000 20.0000 0.0070 1141.174851 0 0.0006 369 | 1/8 18 h-lim-p 0.0017 20.0000 0.0026 1141.174851 0 0.0002 390 | 1/8 19 h-lim-p 0.0005 20.0000 0.0010 1141.174851 0 0.0010 410 | 1/8 20 h-lim-p 0.0046 20.0000 0.0002 1141.174851 0 0.0000 440 | 1/8 21 h-lim-p 0.0000 20.0000 0.0000 1141.174851 0 0.0000 463 | 1/8 22 h-lim-p 0.0000 20.0000 0.0000 1141.174851 0 0.0000 495 Out... lnL = -1141.174851 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1141.174851 Node 7: lnL = -1141.174851 Node 8: lnL = -1141.174851 Node 9: lnL = -1141.174851 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 278 Sequential format.. Reading seq # 1: YAL035W_Sbay Reading seq # 2: YAL035W_Scer Reading seq # 3: YAL035W_Skud Reading seq # 4: YAL035W_Smik Reading seq # 5: YAL035W_Spar Sequences read.. Counting patterns.. # site patterns = 83 Counting frequencies.. 120 bytes for distance 13280 bytes for lkl0 10624 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.028455 0.019215 0.058096 0.066583 0.137935 0.111088 0.183679 lnL0 = -989.295845 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 989.295845 x= 0.00006 0.02846 0.01922 0.05810 0.06658 0.13794 0.11109 0.18368 1 h-lim-p 0.0000 0.0000 106.1794 989.029642 m 0.0000 22 | 1/8 2 h-lim-p 0.0001 0.0049 19.9660 988.971045 0 0.0003 35 | 1/8 3 h-lim-p 0.0009 0.0244 5.8863 988.962608 7 0.0005 63 | 1/8 4 h-lim-p 0.0021 0.0616 1.4082 988.961532 5 0.0006 88 | 1/8 5 h-lim-p 0.0019 0.4025 0.4429 988.944419 0 0.0114 102 | 1/8 6 h-lim-p 0.0028 0.0221 0.9448 988.587351 0 0.0111 123 | 1/8 7 h-lim-p 0.0002 0.0016 22.8035 988.341525 0 0.0004 143 | 1/8 8 h-lim-p 0.0084 0.1738 1.0605 988.340981 3 0.0009 163 | 1/8 9 h-lim-p 0.2858 9.8720 0.0035 988.326420 0 0.8573 176 | 0/8 10 h-lim-p 0.2114 20.0000 0.0143 988.326416 0 0.0058 199 | 0/8 11 h-lim-p 0.0271 0.2232 0.0030 988.325982 0 0.1083 221 | 0/8 12 h-lim-p 0.0700 0.5601 0.0001 988.325960 m 0.5601 241 | 1/8 13 h-lim-p 1.5210 20.0000 0.0000 988.325957 2 0.8006 266 | 1/8 14 h-lim-p 1.8353 20.0000 0.0000 988.325957 0 1.6059 285 | 0/8 15 h-lim-p -0.0000 -0.0000 0.0040 h-lim-p: -3.31978842e-20 -2.65583074e-19 4.02586481e-03 988.325957 .. | 1/8 16 h-lim-p 0.0000 3.0174 0.0184 988.325957 0 0.0001 323 | 1/8 17 h-lim-p 0.0001 2.3065 0.0185 988.325957 0 0.0002 343 | 1/8 18 h-lim-p 0.0003 20.0000 0.0127 988.325957 0 0.0003 362 | 1/8 19 h-lim-p 0.0039 20.0000 0.0011 988.325957 0 0.0000 397 | 1/8 20 h-lim-p 0.0000 20.0000 0.0006 988.325957 0 0.0013 423 | 1/8 21 h-lim-p 0.0104 20.0000 0.0001 988.325957 0 0.0000 452 | 1/8 22 h-lim-p 0.0000 20.0000 0.0001 988.325957 0 0.0000 471 | 1/8 23 h-lim-p 0.0000 20.0000 0.0003 .. | 1/8 24 h-lim-p 0.0000 20.0000 0.0142 988.325957 0 0.0000 537 | 1/8 25 h-lim-p 0.0000 11.0931 0.0022 988.325957 0 0.0001 559 | 1/8 26 h-lim-p 0.0005 20.0000 0.0006 988.325957 0 0.0005 578 | 1/8 27 h-lim-p 0.0014 20.0000 0.0002 988.325957 0 0.0027 598 | 1/8 28 h-lim-p 0.0032 20.0000 0.0002 988.325957 0 0.0000 626 | 1/8 29 h-lim-p 0.0000 20.0000 0.0001 988.325957 0 0.0000 645 | 1/8 30 h-lim-p 0.0000 20.0000 0.0001 .. | 1/8 31 h-lim-p 0.0000 20.0000 0.0143 | 1/8 32 h-lim-p 0.0000 20.0000 0.0143 Out... lnL = -988.325957 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -988.325957 Node 7: lnL = -988.325957 Node 8: lnL = -988.325957 Node 9: lnL = -988.325957 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 320 Sequential format.. Reading seq # 1: YAL036C_Sbay Reading seq # 2: YAL036C_Scer Reading seq # 3: YAL036C_Skud Reading seq # 4: YAL036C_Smik Reading seq # 5: YAL036C_Spar Sequences read.. Counting patterns.. # site patterns = 82 Counting frequencies.. 120 bytes for distance 13120 bytes for lkl0 10496 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.047706 0.032237 0.062624 0.077588 0.142608 0.100575 0.180876 lnL0 = -1046.700482 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1046.700482 x= 0.00006 0.04771 0.03224 0.06262 0.07759 0.14261 0.10057 0.18088 1 h-lim-p 0.0000 0.0000 172.3771 1046.549588 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0067 26.0037 1046.407870 0 0.0005 38 | 1/8 3 h-lim-p 0.0022 0.0178 6.4230 1046.388563 5 0.0008 62 | 1/8 4 h-lim-p 0.0030 0.1108 1.6733 1046.357746 1 0.0037 76 | 1/8 5 h-lim-p 0.0017 0.0404 3.6604 1046.117796 0 0.0051 89 | 0/8 6 h-lim-p 0.0007 0.0056 8.7463 1044.243836 0 0.0042 103 | 0/8 7 h-lim-p 0.0003 0.0021 40.9195 1043.340375 0 0.0005 116 | 0/8 8 h-lim-p 0.0002 0.0014 22.7339 1042.942421 m 0.0014 128 | 0/8 9 h-lim-p 0.0000 0.0000 14.1333 h-lim-p: 1.41462522e-19 1.13170018e-18 1.41333447e+01 1042.942421 .. | 0/8 10 h-lim-p 0.0000 0.0025 49.3070 1042.811691 0 0.0002 152 | 0/8 11 h-lim-p 0.0002 0.0018 28.3676 1042.751390 3 0.0002 170 | 0/8 12 h-lim-p 0.0006 0.0191 8.3541 1042.738867 6 0.0004 197 | 0/8 13 h-lim-p 0.0010 0.0124 3.2515 1042.737679 4 0.0003 219 | 0/8 14 h-lim-p 0.0009 0.0073 0.6336 1042.737596 2 0.0004 235 | 0/8 15 h-lim-p 0.0020 0.0848 0.1301 1042.737580 2 0.0008 259 | 0/8 16 h-lim-p 0.0016 1.9409 0.0628 1042.737266 0 0.0094 281 | 0/8 17 h-lim-p 0.0067 0.1937 0.0882 1042.724238 0 0.0267 303 | 0/8 18 h-lim-p 2.5000 20.0000 0.0004 1042.723632 5 0.9284 335 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1042.723632 0 1.0938 355 | 0/8 20 h-lim-p 1.5106 20.0000 0.0000 1042.723632 0 0.6609 375 | 0/8 21 h-lim-p 0.3938 20.0000 0.0000 .. | 0/8 22 h-lim-p 0.0000 4.6309 0.0021 | 0/8 23 h-lim-p 0.0000 4.6309 0.0021 Out... lnL = -1042.723632 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1042.723632 Node 7: lnL = -1042.723632 Node 8: lnL = -1042.723632 Node 9: lnL = -1042.723632 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 596 Sequential format.. Reading seq # 1: YAL037W_Sbay Reading seq # 2: YAL037W_Scer Reading seq # 3: YAL037W_Skud Reading seq # 4: YAL037W_Smik Reading seq # 5: YAL037W_Spar Sequences read.. Counting patterns.. # site patterns = 273 Counting frequencies.. 120 bytes for distance 43680 bytes for lkl0 34944 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.114359 0.148930 0.137117 0.151613 0.321202 0.233731 0.445779 lnL0 = -2731.664894 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2731.664894 x= 0.00006 0.11436 0.14893 0.13712 0.15161 0.32120 0.23373 0.44578 1 h-lim-p 0.0000 0.0000 180.4869 2731.405501 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0038 70.6038 2729.409686 0 0.0013 40 | 1/8 3 h-lim-p 0.0013 0.0106 13.3891 2729.264116 1 0.0017 54 | 1/8 4 h-lim-p 0.0162 0.1924 1.3721 2729.130737 5 0.0136 77 | 1/8 5 h-lim-p 0.0093 0.1218 2.0054 2725.541777 0 0.0374 91 | 0/8 6 h-lim-p 0.0016 0.0132 30.3056 2722.882557 0 0.0025 103 | 0/8 7 h-lim-p 0.0010 0.0080 23.0014 2722.787163 6 0.0004 127 | 0/8 8 h-lim-p 0.0025 0.0202 1.8344 2722.783769 5 0.0016 151 | 0/8 9 h-lim-p 0.0018 0.3706 1.6432 2722.689267 0 0.0589 168 | 0/8 10 h-lim-p 0.1312 1.0492 0.1067 2722.544254 0 0.5246 182 | 0/8 11 h-lim-p 2.5000 20.0000 0.0144 2722.540403 4 0.6561 211 | 0/8 12 h-lim-p 2.2881 20.0000 0.0041 2722.540089 2 0.9117 235 | 0/8 13 h-lim-p 2.5000 20.0000 0.0002 2722.540084 1 0.6152 258 | 0/8 14 h-lim-p 2.0345 20.0000 0.0000 2722.540084 0 1.0172 278 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2722.540084 0 1.0938 298 | 0/8 16 h-lim-p 2.1907 20.0000 0.0000 2722.540084 0 3.2861 318 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 2722.540084 0 0.3125 340 | 0/8 18 h-lim-p 0.0204 20.0000 0.0000 2722.540084 0 0.0000 371 Out... lnL = -2722.540084 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2722.540084 Node 7: lnL = -2722.540084 Node 8: lnL = -2722.540084 Node 9: lnL = -2722.540084 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 272 Sequential format.. Reading seq # 1: YAL042W_Sbay Reading seq # 2: YAL042W_Scer Reading seq # 3: YAL042W_Skud Reading seq # 4: YAL042W_Smik Reading seq # 5: YAL042W_Spar Sequences read.. Counting patterns.. # site patterns = 128 Counting frequencies.. 120 bytes for distance 20480 bytes for lkl0 16384 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.249269 0.141545 0.141933 0.191237 0.332446 0.149576 0.367784 lnL0 = -1223.322855 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1223.322855 x= 0.00006 0.24927 0.14154 0.14193 0.19124 0.33245 0.14958 0.36778 1 h-lim-p 0.0000 0.0000 213.5686 1223.254173 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0035 99.0989 1210.609752 2 0.0025 46 | 1/8 3 h-lim-p 0.0008 0.0067 40.3188 1209.095586 0 0.0017 59 | 1/8 4 h-lim-p 0.0021 0.0168 12.1837 1208.899398 5 0.0021 82 | 1/8 5 h-lim-p 0.0070 0.0559 3.4235 1207.650959 0 0.0280 96 | 1/8 6 h-lim-p 0.0037 0.0293 5.1385 1195.550335 m 0.0293 108 | 1/8 7 h-lim-p 0.0010 0.0078 34.0145 1193.896455 0 0.0019 121 | 1/8 8 h-lim-p 0.0013 0.0102 34.3541 1192.983722 0 0.0019 133 | 1/8 9 h-lim-p 0.2206 1.7649 0.1996 1191.033347 0 0.4412 146 | 1/8 10 h-lim-p 1.2693 10.1548 0.0302 1190.956638 5 0.4855 175 | 0/8 11 h-lim-p 0.0096 0.6464 1.5197 1190.955108 5 0.0014 208 | 0/8 12 h-lim-p 0.1631 16.5254 0.0133 1190.948280 0 0.3262 221 | 0/8 13 h-lim-p 2.5000 20.0000 0.0012 1190.948032 3 0.6174 248 | 0/8 14 h-lim-p 1.7436 20.0000 0.0004 1190.948010 3 0.5112 277 | 0/8 15 h-lim-p 1.5591 20.0000 0.0001 1190.948006 1 0.6212 299 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1190.948006 0 1.0938 319 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1190.948006 0 1.0938 339 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1190.948006 0 0.0781 363 | 0/8 19 h-lim-p 0.0772 20.0000 0.0000 1190.948006 0 0.0289 384 | 0/8 20 h-lim-p 0.0250 20.0000 0.0000 1190.948006 0 0.0031 406 Out... lnL = -1190.948006 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1190.948006 Node 7: lnL = -1190.948006 Node 8: lnL = -1190.948006 Node 9: lnL = -1190.948006 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 266 Sequential format.. Reading seq # 1: YAL044C_Sbay Reading seq # 2: YAL044C_Scer Reading seq # 3: YAL044C_Skud Reading seq # 4: YAL044C_Smik Reading seq # 5: YAL044C_Spar Sequences read.. Counting patterns.. # site patterns = 116 Counting frequencies.. 120 bytes for distance 18560 bytes for lkl0 14848 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.115830 0.093499 0.071514 0.085067 0.177571 0.134676 0.297058 lnL0 = -1011.201321 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1011.201321 x= 0.00006 0.11583 0.09350 0.07151 0.08507 0.17757 0.13468 0.29706 1 h-lim-p 0.0001 0.0012 93.4012 1009.185584 0 0.0006 24 | 0/8 2 h-lim-p 0.0007 0.0057 31.0285 1008.779085 0 0.0011 36 | 0/8 3 h-lim-p 0.0007 0.0057 21.5890 1008.703508 5 0.0005 60 | 0/8 4 h-lim-p 0.0019 0.0486 5.3628 1008.694022 4 0.0007 80 | 0/8 5 h-lim-p 0.0027 0.0219 0.6339 1008.691651 0 0.0055 93 | 0/8 6 h-lim-p 0.0007 0.0052 0.6193 1008.681273 m 0.0052 113 | 0/8 7 h-lim-p -0.0000 -0.0000 4.3822 h-lim-p: -4.29747830e-21 -3.43798264e-20 4.38217968e+00 1008.681273 .. | 0/8 8 h-lim-p 0.0000 0.2558 42.8102 1008.476375 0 0.0003 146 | 0/8 9 h-lim-p 0.0019 0.0246 7.2713 1008.456222 5 0.0008 169 | 0/8 10 h-lim-p 0.0009 0.0075 2.8790 1008.452629 3 0.0010 187 | 0/8 11 h-lim-p 0.0016 0.0128 1.1066 1008.452242 3 0.0007 205 | 0/8 12 h-lim-p 0.0042 1.1766 0.1918 1008.452169 4 0.0024 228 | 0/8 13 h-lim-p 0.0143 7.5307 0.0317 1008.451290 0 0.0430 249 | 0/8 14 h-lim-p 0.0012 0.0095 0.2341 1008.440147 m 0.0095 269 | 0/8 15 h-lim-p 0.0020 0.2458 1.1328 1008.438883 3 0.0016 295 | 0/8 16 h-lim-p 0.0012 0.0093 0.0964 1008.438785 m 0.0093 307 | 1/8 17 h-lim-p 0.2280 20.0000 0.0023 1008.438387 0 0.4560 328 | 1/8 18 h-lim-p 0.5452 20.0000 0.0019 1008.438387 0 0.0000 378 | 1/8 19 h-lim-p 0.0000 0.0613 1.3024 1008.438067 0 0.0003 402 | 1/8 20 h-lim-p 0.0005 0.3843 0.8024 1008.437782 0 0.0010 415 | 1/8 21 h-lim-p 0.0020 0.5701 0.4074 1008.437717 2 0.0011 439 | 1/8 22 h-lim-p 0.0025 0.6946 0.1730 1008.437709 0 0.0006 459 | 1/8 23 h-lim-p 0.0044 5.0740 0.0247 1008.437709 0 0.0010 479 | 1/8 24 h-lim-p 0.0044 20.0000 0.0054 1008.437709 0 0.0039 498 | 1/8 25 h-lim-p 0.0423 20.0000 0.0005 1008.437703 0 0.2537 519 | 1/8 26 h-lim-p 0.0030 6.1070 0.0426 1008.437696 0 0.0030 538 | 1/8 27 h-lim-p 2.5000 20.0000 0.0000 1008.437696 0 1.0938 557 | 1/8 28 h-lim-p 2.5000 20.0000 0.0000 1008.437696 0 2.1875 576 | 1/8 29 h-lim-p 1.8425 20.0000 0.0000 1008.437696 0 0.4031 596 | 1/8 30 h-lim-p 0.6752 20.0000 0.0000 1008.437696 0 0.0000 631 Out... lnL = -1008.437696 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1008.437696 Node 7: lnL = -1008.437696 Node 8: lnL = -1008.437696 Node 9: lnL = -1008.437696 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 128 Sequential format.. Reading seq # 1: YAL046C_Sbay Reading seq # 2: YAL046C_Scer Reading seq # 3: YAL046C_Skud Reading seq # 4: YAL046C_Smik Reading seq # 5: YAL046C_Spar Sequences read.. Counting patterns.. # site patterns = 59 Counting frequencies.. 120 bytes for distance 9440 bytes for lkl0 7552 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.053403 0.064580 0.065741 0.054832 0.113982 0.137152 0.202721 lnL0 = -434.345702 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 434.345702 x= 0.00006 0.05340 0.06458 0.06574 0.05483 0.11398 0.13715 0.20272 1 h-lim-p 0.0000 0.0002 66.9552 433.695320 m 0.0002 22 | 1/8 2 h-lim-p 0.0004 0.0043 25.5661 433.369101 0 0.0016 36 | 1/8 3 h-lim-p 0.0022 0.0175 5.9667 433.341920 5 0.0014 60 | 1/8 4 h-lim-p 0.0053 0.1009 1.6193 433.325369 6 0.0045 83 | 1/8 5 h-lim-p 0.0044 0.0800 1.6476 433.220948 0 0.0133 96 | 0/8 6 h-lim-p 0.0034 0.0274 4.2890 432.574134 0 0.0137 110 | 0/8 7 h-lim-p 0.0009 0.0070 10.3515 432.436413 0 0.0017 123 | 0/8 8 h-lim-p 0.0023 0.0185 3.2154 432.426261 5 0.0019 146 | 0/8 9 h-lim-p 0.0031 0.0281 2.0033 432.337088 m 0.0281 159 | 0/8 10 h-lim-p -0.0000 -0.0000 0.0848 h-lim-p: -6.76513041e-19 -5.41210433e-18 8.48252874e-02 432.337088 .. | 0/8 11 h-lim-p 0.0000 0.0080 32.7410 432.238734 0 0.0002 191 | 0/8 12 h-lim-p 0.0005 0.0069 14.6428 432.170198 0 0.0011 204 | 0/8 13 h-lim-p 0.0039 0.0489 4.0611 432.159019 4 0.0015 224 | 0/8 14 h-lim-p 0.0045 0.0908 1.3374 432.158118 4 0.0011 247 | 0/8 15 h-lim-p 0.0022 0.0177 0.3545 432.158039 3 0.0011 266 | 0/8 16 h-lim-p 0.0023 0.0185 0.1086 432.157969 0 0.0046 287 | 0/8 17 h-lim-p 0.0025 0.0196 0.0843 432.156913 m 0.0196 307 | 0/8 18 h-lim-p 0.0000 0.0000 1.2998 h-lim-p: 1.86207596e-21 1.48966077e-20 1.29984019e+00 432.156913 .. | 0/8 19 h-lim-p 0.0000 0.0051 5.7313 432.149354 0 0.0005 340 | 0/8 20 h-lim-p 0.0006 0.3883 4.3481 432.146692 6 0.0004 367 | 0/8 21 h-lim-p 0.0026 0.1623 0.6554 432.146433 2 0.0012 383 | 0/8 22 h-lim-p 0.0030 0.0241 0.2378 432.146397 2 0.0014 407 | 0/8 23 h-lim-p 0.0059 0.0609 0.0574 432.146396 1 0.0007 431 | 0/8 24 h-lim-p 0.0089 1.2467 0.0046 432.146396 0 0.0020 452 | 0/8 25 h-lim-p 0.0094 1.2389 0.0010 432.146395 0 0.0377 474 | 0/8 26 h-lim-p 0.0074 20.0000 0.0049 432.146388 0 0.0148 495 | 0/8 27 h-lim-p 2.5000 20.0000 0.0000 432.146388 0 1.0938 515 | 0/8 28 h-lim-p 2.4274 20.0000 0.0000 432.146388 0 2.1240 535 | 0/8 29 h-lim-p 2.5000 20.0000 0.0000 432.146388 0 0.2734 557 | 0/8 30 h-lim-p 0.0428 20.0000 0.0000 432.146388 0 0.0003 583 | 0/8 31 h-lim-p 0.0002 20.0000 0.0000 432.146388 0 0.0001 603 | 0/8 32 h-lim-p 0.0001 20.0000 0.0000 432.146388 0 0.0000 638 | 0/8 33 h-lim-p 0.0000 20.0000 0.0032 | 0/8 34 h-lim-p 0.0000 20.0000 0.0032 Out... lnL = -432.146388 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -432.146388 Node 7: lnL = -432.146388 Node 8: lnL = -432.146388 Node 9: lnL = -432.146388 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 239 Sequential format.. Reading seq # 1: YAL049C_Sbay Reading seq # 2: YAL049C_Scer Reading seq # 3: YAL049C_Skud Reading seq # 4: YAL049C_Smik Reading seq # 5: YAL049C_Spar Sequences read.. Counting patterns.. # site patterns = 124 Counting frequencies.. 120 bytes for distance 19840 bytes for lkl0 15872 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.150094 0.128537 0.154358 0.160045 0.283885 0.175496 0.411061 lnL0 = -1050.401938 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1050.401938 x= 0.00006 0.15009 0.12854 0.15436 0.16004 0.28389 0.17550 0.41106 1 h-lim-p 0.0000 0.0000 86.9960 1050.352532 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0074 40.5895 1048.538540 0 0.0027 41 | 1/8 3 h-lim-p 0.0064 0.0509 8.3599 1048.416631 8 0.0032 71 | 1/8 4 h-lim-p 0.0101 0.0997 2.6353 1048.357470 7 0.0063 101 | 1/8 5 h-lim-p 0.0073 0.1856 2.2699 1047.818628 0 0.0292 115 | 0/8 6 h-lim-p 0.0055 0.0443 7.5016 1045.137028 0 0.0166 128 | 0/8 7 h-lim-p 0.0015 0.0116 12.1759 1044.841410 0 0.0029 141 | 0/8 8 h-lim-p 0.0008 0.0067 15.6370 1044.397030 m 0.0067 153 | 0/8 9 h-lim-p -0.0000 -0.0000 9.8475 h-lim-p: -2.98947630e-20 -2.39158104e-19 9.84753301e+00 1044.397030 .. | 0/8 10 h-lim-p 0.0000 0.0198 18.8416 1044.162395 0 0.0013 180 | 0/8 11 h-lim-p 0.0028 0.0224 7.7658 1044.137907 6 0.0009 205 | 0/8 12 h-lim-p 0.0036 0.2259 2.0028 1044.135454 5 0.0013 229 | 0/8 13 h-lim-p 0.0239 2.2307 0.1116 1044.135439 2 0.0023 247 | 0/8 14 h-lim-p 0.0080 4.7456 0.0323 1044.135436 2 0.0026 273 | 0/8 15 h-lim-p 0.0049 0.6466 0.0171 1044.135409 0 0.0198 295 | 0/8 16 h-lim-p 0.0067 4.4620 0.0504 1044.135135 0 0.0202 316 | 0/8 17 h-lim-p 0.0033 0.3804 0.3067 1044.134841 2 0.0031 340 | 0/8 18 h-lim-p 2.5000 20.0000 0.0001 1044.134834 1 0.9961 362 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1044.134834 0 1.0938 382 | 0/8 20 h-lim-p 1.1362 20.0000 0.0000 1044.134834 0 6.8173 404 | 0/8 21 h-lim-p 0.0922 13.9560 0.0006 1044.134834 0 0.0058 427 | 0/8 22 h-lim-p 0.0017 4.1353 0.0021 1044.134834 0 0.0000 453 | 0/8 23 h-lim-p 0.0001 20.0000 0.0003 1044.134834 0 0.0000 475 | 0/8 24 h-lim-p 0.0001 20.0000 0.0001 1044.134834 0 0.0000 504 | 0/8 25 h-lim-p 0.0000 20.0000 0.0002 | 0/8 26 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1044.134834 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1044.134834 Node 7: lnL = -1044.134834 Node 8: lnL = -1044.134834 Node 9: lnL = -1044.134834 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 872 Sequential format.. Reading seq # 1: YAL053W_Sbay Reading seq # 2: YAL053W_Scer Reading seq # 3: YAL053W_Skud Reading seq # 4: YAL053W_Smik Reading seq # 5: YAL053W_Spar Sequences read.. Counting patterns.. # site patterns = 260 Counting frequencies.. 120 bytes for distance 41600 bytes for lkl0 33280 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000848 0.028079 0.051414 0.074315 0.041779 0.128715 0.181171 0.267361 lnL0 = -3288.519034 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3288.519034 x= 0.00085 0.02808 0.05141 0.07431 0.04178 0.12872 0.18117 0.26736 1 h-lim-p 0.0021 0.7081 177.6710 3286.812535 3 0.0001 31 | 0/8 2 h-lim-p 0.0004 0.0032 32.0367 3286.728970 3 0.0002 49 | 0/8 3 h-lim-p 0.0002 0.0066 26.4237 3286.697349 6 0.0001 74 | 0/8 4 h-lim-p 0.0003 0.0073 11.7514 3286.686772 5 0.0002 98 | 0/8 5 h-lim-p 0.0007 0.0613 3.3006 3286.685291 3 0.0003 117 | 0/8 6 h-lim-p 0.0019 0.1616 0.5247 3286.685273 2 0.0001 136 | 0/8 7 h-lim-p 0.0028 9.0399 0.0240 3286.685273 0 0.0012 156 | 0/8 8 h-lim-p 0.0398 14.3029 0.0007 3286.684842 0 0.6368 180 | 0/8 9 h-lim-p 1.7607 20.0000 0.0003 3286.684825 2 0.9268 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 3286.684825 0 1.0938 225 | 0/8 11 h-lim-p 1.7483 20.0000 0.0000 3286.684825 0 1.5297 245 | 0/8 12 h-lim-p 0.4360 20.0000 0.0001 3286.684825 0 0.3815 265 | 0/8 13 h-lim-p 0.0419 3.8488 0.0012 3286.684825 0 0.0000 298 | 0/8 14 h-lim-p 0.0001 20.0000 0.0001 3286.684825 0 0.0001 318 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 3286.684825 0 0.0000 350 | 0/8 16 h-lim-p 0.0000 20.0000 0.0023 3286.684825 0 0.0001 372 | 0/8 17 h-lim-p 0.0003 20.0000 0.0006 3286.684825 0 0.0000 399 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 3286.684825 0 0.0026 427 | 0/8 19 h-lim-p 0.0066 20.0000 0.0001 3286.684825 0 0.0000 454 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 3286.684825 0 0.0000 475 | 0/8 21 h-lim-p 0.0000 6.0561 0.0008 .. | 0/8 22 h-lim-p 0.0000 20.0000 0.0048 3286.684825 0 0.0000 533 | 0/8 23 h-lim-p 0.0000 20.0000 0.0015 3286.684825 0 0.0003 558 | 0/8 24 h-lim-p 0.0010 20.0000 0.0005 3286.684825 0 0.0009 578 | 0/8 25 h-lim-p 0.0029 20.0000 0.0001 3286.684825 0 0.0000 605 | 0/8 26 h-lim-p 0.0000 20.0000 0.0001 3286.684825 0 0.0000 625 | 0/8 27 h-lim-p 0.0000 20.0000 0.0002 3286.684825 0 0.0000 645 | 0/8 28 h-lim-p 0.0000 5.9326 0.0008 3286.684825 0 0.0000 671 | 0/8 29 h-lim-p 0.0000 1.3149 0.0038 3286.684825 0 0.0000 697 | 0/8 30 h-lim-p 0.0002 20.0000 0.0000 3286.684825 0 0.0000 730 Out... lnL = -3286.684825 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3286.684825 Node 7: lnL = -3286.684825 Node 8: lnL = -3286.684825 Node 9: lnL = -3286.684825 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 866 Sequential format.. Reading seq # 1: YAL054C_Sbay Reading seq # 2: YAL054C_Scer Reading seq # 3: YAL054C_Skud Reading seq # 4: YAL054C_Smik Reading seq # 5: YAL054C_Spar Sequences read.. Counting patterns.. # site patterns = 277 Counting frequencies.. 120 bytes for distance 44320 bytes for lkl0 35456 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.008295 0.027416 0.051776 0.082735 0.045592 0.127637 0.171479 0.274307 lnL0 = -3327.415440 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3327.415440 x= 0.00829 0.02742 0.05178 0.08274 0.04559 0.12764 0.17148 0.27431 1 h-lim-p 0.0002 0.0017 301.0605 3322.942086 8 0.0001 38 | 0/8 2 h-lim-p 0.0005 0.0040 28.2989 3322.876998 5 0.0002 62 | 0/8 3 h-lim-p 0.0003 0.0240 13.8964 3322.867192 5 0.0001 86 | 0/8 4 h-lim-p 0.0002 0.0270 8.0723 3322.861500 1 0.0003 100 | 0/8 5 h-lim-p 0.0014 0.0587 1.4992 3322.861222 4 0.0003 122 | 0/8 6 h-lim-p 0.0006 0.0763 0.6445 3322.861182 2 0.0002 138 | 0/8 7 h-lim-p 0.0015 0.2580 0.1034 3322.861180 0 0.0004 159 | 0/8 8 h-lim-p 0.0941 20.0000 0.0004 3322.860521 0 1.5050 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3322.860486 1 0.9961 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3322.860486 0 1.0938 225 | 0/8 11 h-lim-p 1.1945 20.0000 0.0000 3322.860486 0 1.1945 245 | 0/8 12 h-lim-p 0.1953 20.0000 0.0002 3322.860486 0 0.0732 266 | 0/8 13 h-lim-p 0.0174 20.0000 0.0009 3322.860486 0 0.0011 289 | 0/8 14 h-lim-p 0.0005 10.4976 0.0020 3322.860486 0 0.0000 313 | 0/8 15 h-lim-p 0.0001 20.0000 0.0004 3322.860486 0 0.0000 338 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 3322.860486 0 0.0000 370 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 | 0/8 18 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -3322.860486 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3322.860486 Node 7: lnL = -3322.860486 Node 8: lnL = -3322.860486 Node 9: lnL = -3322.860486 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 422 Sequential format.. Reading seq # 1: YAL055W_Sbay Reading seq # 2: YAL055W_Scer Reading seq # 3: YAL055W_Skud Reading seq # 4: YAL055W_Smik Reading seq # 5: YAL055W_Spar Sequences read.. Counting patterns.. # site patterns = 184 Counting frequencies.. 120 bytes for distance 29440 bytes for lkl0 23552 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.038261 0.150715 0.220818 0.163699 0.257613 0.210156 0.339730 lnL0 = -1867.476085 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1867.476085 x= 0.00006 0.03826 0.15071 0.22082 0.16370 0.25761 0.21016 0.33973 1 h-lim-p 0.0000 0.0000 219.2648 1867.329005 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0024 144.3436 1860.163277 0 0.0010 40 | 1/8 3 h-lim-p 0.0017 0.0132 30.4750 1859.623556 8 0.0012 71 | 1/8 4 h-lim-p 0.0031 0.0247 7.2878 1859.552093 7 0.0017 100 | 1/8 5 h-lim-p 0.0085 0.2739 1.4495 1858.158780 0 0.0510 114 | 0/8 6 h-lim-p 0.0024 0.0193 9.9057 1848.826118 0 0.0097 128 | 0/8 7 h-lim-p 0.0009 0.0069 34.4013 1848.319575 2 0.0008 144 | 0/8 8 h-lim-p 0.0004 0.0033 12.6456 1848.071072 m 0.0033 156 | 0/8 9 h-lim-p 0.0348 0.2781 1.1286 1848.053104 6 0.0052 184 | 0/8 10 h-lim-p 0.0013 0.0103 0.6252 1847.742918 m 0.0103 196 | 0/8 11 h-lim-p -0.0000 -0.0000 0.1777 h-lim-p: -1.33157444e-19 -1.06525955e-18 1.77743135e-01 1847.742918 .. | 0/8 12 h-lim-p 0.0000 0.0012 54.0379 1846.947109 6 0.0005 252 | 0/8 13 h-lim-p 0.0014 0.0197 18.8303 1846.865519 7 0.0005 281 | 0/8 14 h-lim-p 0.0013 0.0235 7.5511 1846.853989 6 0.0005 306 | 0/8 15 h-lim-p 0.0015 0.0713 2.3561 1846.852137 3 0.0007 324 | 0/8 16 h-lim-p 0.0015 0.0182 1.1503 1846.851821 3 0.0006 342 | 0/8 17 h-lim-p 0.0102 0.3596 0.0666 1846.851819 1 0.0006 359 | 0/8 18 h-lim-p 0.0079 20.0000 0.0053 1846.851819 0 0.0009 381 | 0/8 19 h-lim-p 0.0079 13.9821 0.0006 1846.851819 0 0.5082 407 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 1846.851819 0 1.0938 427 | 0/8 21 h-lim-p 1.8970 20.0000 0.0000 1846.851819 0 0.8299 447 | 0/8 22 h-lim-p 0.6932 20.0000 0.0000 1846.851819 0 0.0027 474 | 0/8 23 h-lim-p 0.0006 20.0000 0.0001 1846.851819 0 0.0000 511 | 0/8 24 h-lim-p 0.0000 20.0000 0.0006 1846.851819 0 0.0005 536 | 0/8 25 h-lim-p 0.0012 20.0000 0.0002 1846.851819 0 0.0012 556 | 0/8 26 h-lim-p 0.0052 20.0000 0.0001 1846.851819 0 0.0000 583 | 0/8 27 h-lim-p 0.0000 20.0000 0.0001 1846.851819 0 0.0000 604 | 0/8 28 h-lim-p 0.0000 20.0000 0.0000 1846.851819 0 0.0000 624 | 0/8 29 h-lim-p 0.0000 20.0000 0.0003 1846.851819 0 0.0000 644 | 0/8 30 h-lim-p 0.0000 0.0083 0.9442 1846.851819 0 0.0000 666 | 0/8 31 h-lim-p 0.1285 20.0000 0.0000 1846.851819 0 0.0000 714 Out... lnL = -1846.851819 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1846.851819 Node 7: lnL = -1846.851819 Node 8: lnL = -1846.851819 Node 9: lnL = -1846.851819 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 229 Sequential format.. Reading seq # 1: YAL056W_Sbay Reading seq # 2: YAL056W_Scer Reading seq # 3: YAL056W_Skud Reading seq # 4: YAL056W_Smik Reading seq # 5: YAL056W_Spar Sequences read.. Counting patterns.. # site patterns = 94 Counting frequencies.. 120 bytes for distance 15040 bytes for lkl0 12032 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.005311 0.084007 0.076000 0.089051 0.050526 0.083872 0.158016 0.304065 lnL0 = -934.824785 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 934.824785 x= 0.00531 0.08401 0.07600 0.08905 0.05053 0.08387 0.15802 0.30407 1 h-lim-p 0.0255 4.4652 27.0739 934.596347 7 0.0006 42 | 0/8 2 h-lim-p 0.0026 0.0227 6.7961 934.583188 2 0.0006 59 | 0/8 3 h-lim-p 0.0013 0.0982 3.1506 934.581050 3 0.0005 77 | 0/8 4 h-lim-p 0.0010 0.1076 1.6554 934.579943 4 0.0011 98 | 0/8 5 h-lim-p 0.0064 0.1714 0.2758 934.579915 0 0.0008 112 | 0/8 6 h-lim-p 0.0030 0.3094 0.0737 934.579913 1 0.0007 135 | 0/8 7 h-lim-p 0.0028 1.0095 0.0190 934.579913 0 0.0014 155 | 0/8 8 h-lim-p 0.1000 20.0000 0.0003 934.579873 0 0.8002 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 934.579872 0 1.0938 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 934.579872 0 1.0938 218 | 0/8 11 h-lim-p 1.1852 20.0000 0.0000 934.579872 0 0.0324 242 | 0/8 12 h-lim-p 0.0069 20.0000 0.0000 934.579872 0 0.0002 266 | 0/8 13 h-lim-p 0.0001 20.0000 0.0001 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -934.579872 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -934.579872 Node 7: lnL = -934.579872 Node 8: lnL = -934.579872 Node 9: lnL = -934.579872 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 355 Sequential format.. Reading seq # 1: YAL058W_Sbay Reading seq # 2: YAL058W_Scer Reading seq # 3: YAL058W_Skud Reading seq # 4: YAL058W_Smik Reading seq # 5: YAL058W_Spar Sequences read.. Counting patterns.. # site patterns = 183 Counting frequencies.. 120 bytes for distance 29280 bytes for lkl0 23424 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.138094 0.211906 0.281902 0.298923 0.368680 0.156941 0.414726 lnL0 = -1659.327601 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1659.327601 x= 0.00006 0.13809 0.21191 0.28190 0.29892 0.36868 0.15694 0.41473 1 h-lim-p 0.0000 0.0000 183.2902 1659.281227 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0012 230.7511 1635.874542 m 0.0012 38 | 2/8 3 h-lim-p 0.0017 0.0135 31.1399 1630.897856 0 0.0051 51 | 2/8 4 h-lim-p 0.0020 0.0163 24.6046 1625.929491 0 0.0041 64 | 2/8 5 h-lim-p 0.0015 0.0121 22.8499 1625.306318 0 0.0023 76 | 1/8 6 h-lim-p 0.0011 0.0111 47.7992 1624.997882 6 0.0004 101 | 1/8 7 h-lim-p 0.0042 0.0955 4.0473 1624.984548 6 0.0015 127 | 0/8 8 h-lim-p 0.0004 0.0308 16.6350 1624.822779 0 0.0015 141 | 0/8 9 h-lim-p 0.0046 0.0787 5.3877 1624.802805 6 0.0015 167 | 0/8 10 h-lim-p 0.2047 4.4399 0.0399 1624.586158 0 0.6141 180 | 0/8 11 h-lim-p 2.5000 20.0000 0.0068 1624.574562 6 0.7998 214 | 0/8 12 h-lim-p 2.5000 20.0000 0.0011 1624.574314 3 0.8059 242 | 0/8 13 h-lim-p 2.5000 20.0000 0.0001 1624.574310 0 1.0938 262 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1624.574310 0 1.0938 282 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1624.574310 0 1.0938 302 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1624.574310 0 2.1875 322 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1624.574310 0 1.0938 342 | 0/8 18 h-lim-p 0.9410 20.0000 0.0000 1624.574310 0 0.8234 362 | 0/8 19 h-lim-p 0.0249 20.0000 0.0000 1624.574310 0 0.0000 400 Out... lnL = -1624.574310 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1624.574310 Node 7: lnL = -1624.574310 Node 8: lnL = -1624.574310 Node 9: lnL = -1624.574310 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 303 Sequential format.. Reading seq # 1: YAL059W_Sbay Reading seq # 2: YAL059W_Scer Reading seq # 3: YAL059W_Skud Reading seq # 4: YAL059W_Smik Reading seq # 5: YAL059W_Spar Sequences read.. Counting patterns.. # site patterns = 153 Counting frequencies.. 120 bytes for distance 24480 bytes for lkl0 19584 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.016903 0.133028 0.023593 0.015295 0.101608 0.211780 0.194338 0.391120 lnL0 = -1289.279356 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1289.279356 x= 0.01690 0.13303 0.02359 0.01530 0.10161 0.21178 0.19434 0.39112 1 h-lim-p 0.0007 0.5994 187.5488 1287.108853 3 0.0002 29 | 0/8 2 h-lim-p 0.0006 0.0050 41.5157 1286.606582 4 0.0006 49 | 0/8 3 h-lim-p 0.0017 0.0136 12.3422 1286.549805 2 0.0008 65 | 0/8 4 h-lim-p 0.0018 0.0489 5.3646 1286.538794 4 0.0009 85 | 0/8 5 h-lim-p 0.0043 0.2485 1.1381 1286.537919 5 0.0014 109 | 0/8 6 h-lim-p 0.0103 1.9552 0.1596 1286.537898 2 0.0017 128 | 0/8 7 h-lim-p 0.0137 5.0814 0.0198 1286.537895 0 0.0060 148 | 0/8 8 h-lim-p 0.1171 20.0000 0.0010 1286.537319 0 0.9368 171 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1286.537275 2 0.9961 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1286.537275 0 1.0938 215 | 0/8 11 h-lim-p 1.5350 20.0000 0.0000 1286.537275 0 3.0700 236 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1286.537275 0 0.6250 257 | 0/8 13 h-lim-p 0.0812 20.0000 0.0000 1286.537275 0 0.0812 277 | 0/8 14 h-lim-p 0.0216 20.0000 0.0001 1286.537275 0 0.0000 322 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1286.537275 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1286.537275 Node 7: lnL = -1286.537275 Node 8: lnL = -1286.537275 Node 9: lnL = -1286.537275 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 509 Sequential format.. Reading seq # 1: YAL060W_Sbay Reading seq # 2: YAL060W_Scer Reading seq # 3: YAL060W_Skud Reading seq # 4: YAL060W_Smik Reading seq # 5: YAL060W_Spar Sequences read.. Counting patterns.. # site patterns = 233 Counting frequencies.. 120 bytes for distance 37280 bytes for lkl0 29824 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.004493 0.113168 0.119028 0.117357 0.059318 0.201654 0.203672 0.448436 lnL0 = -2291.507015 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2291.507015 x= 0.00449 0.11317 0.11903 0.11736 0.05932 0.20165 0.20367 0.44844 1 h-lim-p 0.0017 0.0139 47.3911 2291.126216 6 0.0004 38 | 0/8 2 h-lim-p 0.0007 0.0088 24.6049 2291.036216 5 0.0004 61 | 0/8 3 h-lim-p 0.0017 0.0451 5.2313 2291.028498 4 0.0006 83 | 0/8 4 h-lim-p 0.0028 0.0684 1.1344 2291.028063 4 0.0007 104 | 0/8 5 h-lim-p 0.0013 0.0814 0.6306 2291.027882 2 0.0012 120 | 0/8 6 h-lim-p 0.0108 3.9061 0.0691 2291.027880 0 0.0012 142 | 0/8 7 h-lim-p 0.0164 20.0000 0.0050 2291.027880 0 0.0021 164 | 0/8 8 h-lim-p 0.0978 20.0000 0.0001 2291.027873 0 0.7826 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2291.027872 0 1.0938 207 | 0/8 10 h-lim-p 1.9765 20.0000 0.0000 2291.027872 0 1.7295 227 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2291.027872 0 1.0938 247 | 0/8 12 h-lim-p 0.4017 20.0000 0.0000 2291.027872 0 6.4270 271 | 0/8 13 h-lim-p 0.2528 20.0000 0.0003 2291.027872 0 0.2212 291 | 0/8 14 h-lim-p 0.0386 5.7043 0.0019 2291.027872 0 0.0048 313 | 0/8 15 h-lim-p 0.0014 1.6589 0.0066 2291.027872 0 0.0004 334 | 0/8 16 h-lim-p 0.0006 2.7099 0.0041 2291.027872 0 0.0000 358 | 0/8 17 h-lim-p 0.0001 20.0000 0.0010 2291.027872 0 0.0000 389 | 0/8 18 h-lim-p 0.0001 20.0000 0.0000 2291.027872 0 0.0000 414 Out... lnL = -2291.027872 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2291.027872 Node 7: lnL = -2291.027872 Node 8: lnL = -2291.027872 Node 9: lnL = -2291.027872 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 841 Sequential format.. Reading seq # 1: YAL062W_Sbay Reading seq # 2: YAL062W_Scer Reading seq # 3: YAL062W_Skud Reading seq # 4: YAL062W_Smik Reading seq # 5: YAL062W_Spar Sequences read.. Counting patterns.. # site patterns = 415 Counting frequencies.. 120 bytes for distance 66400 bytes for lkl0 53120 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.166027 0.276196 0.392827 0.339778 0.511712 0.342560 0.652817 lnL0 = -4683.005571 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4683.005571 x= 0.00006 0.16603 0.27620 0.39283 0.33978 0.51171 0.34256 0.65282 1 h-lim-p 0.0000 0.0000 320.2160 4682.808291 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0023 215.0418 4649.442126 0 0.0018 41 | 1/8 3 h-lim-p 0.0025 0.0203 35.2548 4647.254025 0 0.0038 53 | 1/8 4 h-lim-p 0.0022 0.0174 15.8414 4646.859211 1 0.0027 67 | 1/8 5 h-lim-p 0.0067 0.0969 6.3944 4646.369096 7 0.0074 98 | 1/8 6 h-lim-p 0.0093 0.1471 5.0744 4639.556314 0 0.0371 112 | 1/8 7 h-lim-p 0.0028 0.0221 26.3510 4627.310698 0 0.0055 125 | 1/8 8 h-lim-p 0.0006 0.0050 79.4657 4619.959605 0 0.0025 139 | 1/8 9 h-lim-p 0.9801 7.8410 0.0747 4619.164231 8 0.5412 171 | 1/8 10 h-lim-p 0.7209 11.0650 0.0561 4619.032429 2 0.3379 194 | 1/8 11 h-lim-p 2.5000 20.0000 0.0051 4619.028554 2 0.5444 218 | 1/8 12 h-lim-p 1.1695 20.0000 0.0024 4619.027934 4 0.6608 248 | 1/8 13 h-lim-p 2.5000 20.0000 0.0004 4619.027912 1 0.5469 270 | 1/8 14 h-lim-p 2.5000 20.0000 0.0001 4619.027912 0 1.0938 289 | 0/8 15 h-lim-p 0.0000 0.0000 0.0003 h-lim-p: 4.58337210e-19 3.66669768e-18 3.20543154e-04 4619.027912 .. | 1/8 16 h-lim-p 0.0000 9.6144 0.0224 4619.027911 0 0.0013 331 | 1/8 17 h-lim-p 0.0036 20.0000 0.0080 4619.027911 0 0.0016 350 | 1/8 18 h-lim-p 0.0030 20.0000 0.0042 4619.027911 0 0.0013 369 | 1/8 19 h-lim-p 0.0035 20.0000 0.0016 4619.027911 0 0.0004 390 | 1/8 20 h-lim-p 0.0025 20.0000 0.0002 4619.027911 0 0.0025 409 | 1/8 21 h-lim-p 0.0046 20.0000 0.0001 4619.027911 0 0.0137 429 | 1/8 22 h-lim-p 0.0120 20.0000 0.0002 4619.027911 0 0.0480 450 | 1/8 23 h-lim-p 0.0027 20.0000 0.0026 4619.027911 0 0.0024 469 | 1/8 24 h-lim-p 2.5000 20.0000 0.0000 4619.027911 0 1.0938 488 | 1/8 25 h-lim-p 2.5000 20.0000 0.0000 4619.027911 0 2.1875 507 | 1/8 26 h-lim-p 1.8421 20.0000 0.0000 4619.027911 0 0.9211 526 | 1/8 27 h-lim-p 2.5000 20.0000 0.0000 4619.027911 0 1.8750 545 | 1/8 28 h-lim-p 2.1414 20.0000 0.0000 4619.027911 0 0.0003 576 Out... lnL = -4619.027911 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4619.027911 Node 7: lnL = -4619.027911 Node 8: lnL = -4619.027911 Node 9: lnL = -4619.027911 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 305 Sequential format.. Reading seq # 1: YAR002C-A_Sbay Reading seq # 2: YAR002C-A_Scer Reading seq # 3: YAR002C-A_Skud Reading seq # 4: YAR002C-A_Smik Reading seq # 5: YAR002C-A_Spar Sequences read.. Counting patterns.. # site patterns = 122 Counting frequencies.. 120 bytes for distance 19520 bytes for lkl0 15616 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.109606 0.207420 0.195950 0.174777 0.307481 0.142899 0.322883 lnL0 = -1293.438460 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1293.438460 x= 0.00006 0.10961 0.20742 0.19595 0.17478 0.30748 0.14290 0.32288 1 h-lim-p 0.0000 0.0000 236.0466 1293.362558 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0026 113.8896 1282.224126 0 0.0019 41 | 1/8 3 h-lim-p 0.0003 0.0027 48.4058 1280.702124 0 0.0014 55 | 1/8 4 h-lim-p 0.0025 0.0198 20.8875 1280.303202 7 0.0018 83 | 1/8 5 h-lim-p 0.0019 0.0148 13.3161 1279.871497 0 0.0037 96 | 1/8 6 h-lim-p 0.0075 0.0628 6.5697 1278.243996 0 0.0150 109 | 1/8 7 h-lim-p 0.0054 0.0434 7.9592 1257.182392 0 0.0326 123 | 1/8 8 h-lim-p 0.0006 0.0048 34.0808 1256.367963 0 0.0012 136 | 1/8 9 h-lim-p 0.2575 2.2594 0.1587 1254.067022 0 0.5150 149 | 0/8 10 h-lim-p 0.0130 0.2946 6.2840 1254.046359 6 0.0010 184 | 0/8 11 h-lim-p 0.1352 1.2087 0.0483 1253.625853 0 0.5409 198 | 0/8 12 h-lim-p 1.1016 8.8127 0.0199 1253.474263 7 0.7501 235 | 0/8 13 h-lim-p 2.5000 20.0000 0.0022 1253.472584 3 0.8059 263 | 0/8 14 h-lim-p 2.1748 20.0000 0.0008 1253.472458 4 0.6145 294 | 0/8 15 h-lim-p 2.5000 20.0000 0.0001 1253.472456 1 0.6152 317 | 0/8 16 h-lim-p 1.8846 20.0000 0.0000 1253.472456 0 0.8245 337 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1253.472456 0 1.0938 357 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1253.472456 0 2.1875 377 | 0/8 19 h-lim-p 1.3229 20.0000 0.0000 1253.472456 0 0.5788 397 | 0/8 20 h-lim-p 1.5774 20.0000 0.0000 1253.472456 0 0.0015 426 Out... lnL = -1253.472456 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1253.472456 Node 7: lnL = -1253.472456 Node 8: lnL = -1253.472456 Node 9: lnL = -1253.472456 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 301 Sequential format.. Reading seq # 1: YAR003W_Sbay Reading seq # 2: YAR003W_Scer Reading seq # 3: YAR003W_Skud Reading seq # 4: YAR003W_Smik Reading seq # 5: YAR003W_Spar Sequences read.. Counting patterns.. # site patterns = 128 Counting frequencies.. 120 bytes for distance 20480 bytes for lkl0 16384 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.186545 0.060869 0.214616 0.155556 0.157211 0.172334 0.326343 lnL0 = -1312.844413 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1312.844413 x= 0.00006 0.18654 0.06087 0.21462 0.15556 0.15721 0.17233 0.32634 1 h-lim-p 0.0000 0.0000 215.2111 1312.747975 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0007 286.7071 1300.883290 0 0.0005 39 | 1/8 3 h-lim-p 0.0002 0.0017 93.3373 1299.703441 0 0.0004 52 | 1/8 4 h-lim-p 0.0016 0.0192 25.9282 1299.174394 7 0.0017 78 | 1/8 5 h-lim-p 0.0011 0.0092 16.9018 1299.022761 6 0.0011 105 | 1/8 6 h-lim-p 0.0059 0.0973 3.2022 1298.396986 0 0.0178 118 | 1/8 7 h-lim-p 0.0079 0.0632 2.9472 1290.669123 0 0.0316 132 | 1/8 8 h-lim-p 0.0004 0.0030 52.3805 1289.490923 0 0.0008 145 | 1/8 9 h-lim-p 0.3330 6.6300 0.1193 1285.389736 0 0.6660 158 | 1/8 10 h-lim-p 0.8492 6.7937 0.0227 1284.704067 0 1.6984 178 | 0/8 11 h-lim-p 0.0133 0.1328 2.8915 1284.697609 6 0.0017 210 | 0/8 12 h-lim-p 0.4170 20.0000 0.0116 1284.608258 0 1.2511 223 | 0/8 13 h-lim-p 2.5000 20.0000 0.0048 1284.600192 5 1.0837 252 | 0/8 14 h-lim-p 2.5000 20.0000 0.0014 1284.599433 3 1.0004 278 | 0/8 15 h-lim-p 2.5000 20.0000 0.0002 1284.599368 2 0.9961 302 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1284.599367 0 1.0938 322 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1284.599367 0 2.1875 342 | 0/8 18 h-lim-p 2.3176 20.0000 0.0000 1284.599367 0 1.0139 362 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1284.599367 0 2.1875 382 | 0/8 20 h-lim-p 2.4250 20.0000 0.0000 1284.599367 0 0.6062 403 | 0/8 21 h-lim-p 1.4691 20.0000 0.0000 1284.599367 0 0.0000 445 Out... lnL = -1284.599367 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1284.599367 Node 7: lnL = -1284.599367 Node 8: lnL = -1284.599367 Node 9: lnL = -1284.599367 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 371 Sequential format.. Reading seq # 1: YAR007C_Sbay Reading seq # 2: YAR007C_Scer Reading seq # 3: YAR007C_Skud Reading seq # 4: YAR007C_Smik Reading seq # 5: YAR007C_Spar Sequences read.. Counting patterns.. # site patterns = 133 Counting frequencies.. 120 bytes for distance 21280 bytes for lkl0 17024 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.193434 0.019581 0.205203 0.159112 0.099023 0.115460 0.260408 lnL0 = -1526.426269 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1526.426269 x= 0.00006 0.19343 0.01958 0.20520 0.15911 0.09902 0.11546 0.26041 1 h-lim-p 0.0000 0.0000 250.5762 1526.358400 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0002 393.5957 1518.588047 m 0.0002 36 | 1/8 3 h-lim-p 0.0001 0.0005 524.9666 1514.163196 0 0.0001 49 | 1/8 4 h-lim-p 0.0008 0.0067 52.0235 1513.467217 9 0.0006 82 | 1/8 5 h-lim-p 0.0020 0.0239 14.8328 1513.385995 7 0.0007 113 | 1/8 6 h-lim-p 0.0047 0.1376 2.1978 1513.238699 0 0.0094 126 | 1/8 7 h-lim-p 0.0055 0.0573 3.7563 1510.656312 0 0.0110 139 | 0/8 8 h-lim-p 0.0010 0.0087 42.7580 1503.966393 0 0.0019 152 | 0/8 9 h-lim-p 0.0003 0.0025 26.2294 1503.540363 0 0.0013 166 | 0/8 10 h-lim-p 0.1264 1.0111 0.0502 1501.709535 m 1.0111 178 | 0/8 11 h-lim-p 1.5150 12.1197 0.0205 1501.145937 5 1.3200 207 | 0/8 12 h-lim-p 2.5000 20.0000 0.0060 1501.086520 2 1.1719 231 | 0/8 13 h-lim-p 0.6565 5.2522 0.0038 1501.071314 0 1.3131 252 | 0/8 14 h-lim-p 2.5000 20.0000 0.0009 1501.068202 3 2.0898 278 | 0/8 15 h-lim-p 2.4388 20.0000 0.0008 1501.067368 5 1.3513 311 | 0/8 16 h-lim-p 2.5000 20.0000 0.0001 1501.067362 2 0.9644 335 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1501.067362 0 1.0938 355 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1501.067362 0 1.0938 375 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1501.067362 0 2.5000 395 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 1501.067362 0 0.0000 444 Out... lnL = -1501.067362 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1501.067362 Node 7: lnL = -1501.067362 Node 8: lnL = -1501.067362 Node 9: lnL = -1501.067362 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 389 Sequential format.. Reading seq # 1: YAR008W_Sbay Reading seq # 2: YAR008W_Scer Reading seq # 3: YAR008W_Skud Reading seq # 4: YAR008W_Smik Reading seq # 5: YAR008W_Spar Sequences read.. Counting patterns.. # site patterns = 134 Counting frequencies.. 120 bytes for distance 21440 bytes for lkl0 17152 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.196387 0.015248 0.209047 0.158187 0.094913 0.147433 0.286246 lnL0 = -1457.770337 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1457.770337 x= 0.00006 0.19639 0.01525 0.20905 0.15819 0.09491 0.14743 0.28625 1 h-lim-p 0.0000 0.0000 170.1846 1457.721771 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0013 167.1805 1454.067834 0 0.0005 39 | 1/8 3 h-lim-p 0.0003 0.0023 98.6938 1453.561312 7 0.0002 67 | 1/8 4 h-lim-p 0.0012 0.0228 15.1618 1453.427841 2 0.0011 83 | 1/8 5 h-lim-p 0.0078 0.0936 2.1517 1453.178977 0 0.0155 96 | 1/8 6 h-lim-p 0.0090 0.0717 3.3005 1449.171834 0 0.0179 109 | 1/8 7 h-lim-p 0.0011 0.0087 40.5983 1445.746197 0 0.0022 122 | 1/8 8 h-lim-p 0.0008 0.0064 41.3397 1445.043741 1 0.0010 136 | 1/8 9 h-lim-p 1.0968 20.0000 0.0380 1443.351029 6 1.1940 162 | 1/8 10 h-lim-p 2.1076 16.8604 0.0170 1443.000798 7 1.2393 197 | 1/8 11 h-lim-p 2.5000 20.0000 0.0073 1442.970845 6 0.8638 231 | 0/8 12 h-lim-p 0.0063 0.9278 0.9940 1442.970268 4 0.0012 259 | 0/8 13 h-lim-p 1.0898 20.0000 0.0011 1442.969152 4 1.1693 289 | 0/8 14 h-lim-p 2.5000 20.0000 0.0002 1442.969135 2 0.8246 315 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1442.969135 0 1.0938 335 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1442.969135 0 1.2500 355 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1442.969135 0 1.0938 375 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1442.969135 0 2.1875 395 | 0/8 19 h-lim-p 1.9261 20.0000 0.0000 1442.969135 0 0.8427 415 | 0/8 20 h-lim-p 2.2909 20.0000 0.0000 1442.969135 0 0.2864 437 | 0/8 21 h-lim-p 0.0907 20.0000 0.0000 1442.969135 0 0.0000 474 Out... lnL = -1442.969135 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1442.969135 Node 7: lnL = -1442.969135 Node 8: lnL = -1442.969135 Node 9: lnL = -1442.969135 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 519 Sequential format.. Reading seq # 1: YAR015W_Sbay Reading seq # 2: YAR015W_Scer Reading seq # 3: YAR015W_Skud Reading seq # 4: YAR015W_Smik Reading seq # 5: YAR015W_Spar Sequences read.. Counting patterns.. # site patterns = 157 Counting frequencies.. 120 bytes for distance 25120 bytes for lkl0 20096 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.040658 0.056519 0.085603 0.044611 0.083671 0.129763 0.211886 lnL0 = -1773.718359 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1773.718359 x= 0.00006 0.04066 0.05652 0.08560 0.04461 0.08367 0.12976 0.21189 1 h-lim-p 0.0001 0.0007 86.5569 1773.181870 0 0.0002 23 | 0/8 2 h-lim-p 0.0003 0.0025 30.5799 1773.103156 6 0.0002 50 | 0/8 3 h-lim-p 0.0004 0.0044 13.2056 1773.077471 4 0.0003 70 | 0/8 4 h-lim-p 0.0009 0.3602 5.1454 1773.073994 5 0.0003 96 | 0/8 5 h-lim-p 0.0008 0.0060 2.0825 1773.073116 5 0.0005 122 | 0/8 6 h-lim-p 0.0008 0.0070 1.3010 1773.072843 4 0.0004 143 | 0/8 7 h-lim-p 0.0008 0.0098 0.6459 1773.072237 0 0.0033 157 | 0/8 8 h-lim-p 0.0001 0.0004 8.4468 1773.069897 m 0.0004 177 | 1/8 9 h-lim-p 0.0968 20.0000 0.0275 1773.068799 0 0.0484 189 | 1/8 10 h-lim-p 0.0404 3.7450 0.0329 1773.033973 0 0.1212 209 | 0/8 11 h-lim-p 0.0000 0.0000 0.0945 h-lim-p: 4.44917907e-20 3.55934326e-19 9.44690960e-02 1773.033973 .. | 1/8 12 h-lim-p 0.0000 0.0390 3.2501 1773.032997 0 0.0002 248 | 1/8 13 h-lim-p 0.0005 0.2043 1.0406 1773.032923 3 0.0001 268 | 1/8 14 h-lim-p 0.0004 0.2995 0.4331 1773.032901 2 0.0003 284 | 1/8 15 h-lim-p 0.0005 1.3589 0.2480 1773.032891 1 0.0004 305 | 1/8 16 h-lim-p 0.0013 1.4532 0.0828 1773.032891 0 0.0003 325 | 1/8 17 h-lim-p 0.0035 20.0000 0.0067 1773.032891 0 0.0008 345 | 0/8 18 h-lim-p 0.0001 2.5969 0.0425 1773.032890 0 0.0010 367 | 0/8 19 h-lim-p 0.0078 20.0000 0.0053 1773.032888 0 0.0116 387 | 0/8 20 h-lim-p 0.0115 0.0917 0.0018 1773.032866 0 0.0688 409 | 0/8 21 h-lim-p 0.0351 0.2805 0.0001 1773.032866 m 0.2805 429 | 1/8 22 h-lim-p 0.4304 20.0000 0.0000 1773.032866 0 0.3766 449 | 0/8 23 h-lim-p 0.0004 5.8749 0.0407 1773.032866 0 0.0001 469 | 1/8 24 h-lim-p 0.0865 20.0000 0.0000 1773.032866 0 0.3458 491 | 1/8 25 h-lim-p 2.5000 20.0000 0.0000 1773.032866 0 2.1875 510 | 1/8 26 h-lim-p 2.5000 20.0000 0.0000 1773.032866 0 1.0938 529 | 1/8 27 h-lim-p 2.5000 20.0000 0.0000 1773.032866 0 2.1875 548 | 1/8 28 h-lim-p 1.7998 20.0000 0.0000 1773.032866 0 0.0984 570 | 1/8 29 h-lim-p 0.1094 20.0000 0.0000 1773.032866 0 0.0068 592 Out... lnL = -1773.032866 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1773.032866 Node 7: lnL = -1773.032866 Node 8: lnL = -1773.032866 Node 9: lnL = -1773.032866 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 348 Sequential format.. Reading seq # 1: YBL005W_Sbay Reading seq # 2: YBL005W_Scer Reading seq # 3: YBL005W_Skud Reading seq # 4: YBL005W_Smik Reading seq # 5: YBL005W_Spar Sequences read.. Counting patterns.. # site patterns = 156 Counting frequencies.. 120 bytes for distance 24960 bytes for lkl0 19968 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.025141 0.140645 0.089037 0.108784 0.085412 0.179058 0.007774 0.380680 lnL0 = -1449.487949 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1449.487949 x= 0.02514 0.14065 0.08904 0.10878 0.08541 0.17906 0.00777 0.38068 1 h-lim-p 0.0004 0.0035 279.3788 1442.518417 9 0.0003 42 | 0/8 2 h-lim-p 0.0010 0.0083 21.4159 1442.309108 5 0.0009 63 | 0/8 3 h-lim-p 0.0011 0.0109 16.9229 1442.233393 7 0.0008 93 | 0/8 4 h-lim-p 0.0012 0.0179 10.9873 1442.212097 2 0.0006 109 | 0/8 5 h-lim-p 0.0018 0.0877 3.3107 1442.204879 4 0.0016 131 | 0/8 6 h-lim-p 0.0794 6.4037 0.0652 1442.204874 2 0.0016 153 | 0/8 7 h-lim-p 0.0024 2.4055 0.0453 1442.204871 1 0.0012 176 | 0/8 8 h-lim-p 0.0222 20.0000 0.0024 1442.203833 0 0.7117 201 | 0/8 9 h-lim-p 2.3911 20.0000 0.0007 1442.203314 3 1.6939 229 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 1442.203288 2 1.1719 253 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1442.203288 0 1.0938 273 | 0/8 12 h-lim-p 1.3190 20.0000 0.0000 1442.203288 0 0.5771 293 | 0/8 13 h-lim-p 0.3410 20.0000 0.0000 1442.203288 0 0.0000 327 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 1442.203288 0 0.0000 364 Out... lnL = -1442.203288 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1442.203288 Node 7: lnL = -1442.203288 Node 8: lnL = -1442.203288 Node 9: lnL = -1442.203288 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 370 Sequential format.. Reading seq # 1: YBL006C_Sbay Reading seq # 2: YBL006C_Scer Reading seq # 3: YBL006C_Skud Reading seq # 4: YBL006C_Smik Reading seq # 5: YBL006C_Spar Sequences read.. Counting patterns.. # site patterns = 156 Counting frequencies.. 120 bytes for distance 24960 bytes for lkl0 19968 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.068000 0.066541 0.122087 0.105915 0.180193 0.127718 0.310703 lnL0 = -1464.356535 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1464.356535 x= 0.00006 0.06800 0.06654 0.12209 0.10591 0.18019 0.12772 0.31070 1 h-lim-p 0.0000 0.0001 75.4630 1463.970904 m 0.0001 22 | 1/8 2 h-lim-p 0.0003 0.0094 18.8886 1463.853982 0 0.0006 35 | 1/8 3 h-lim-p 0.0013 0.0235 8.4465 1463.837797 6 0.0005 58 | 1/8 4 h-lim-p 0.0017 0.0738 2.5944 1463.833498 5 0.0010 83 | 1/8 5 h-lim-p 0.0032 0.2758 0.8140 1463.821325 0 0.0064 96 | 0/8 6 h-lim-p 0.0009 0.0676 5.7474 1463.593340 0 0.0109 118 | 0/8 7 h-lim-p 0.0012 0.0096 45.1734 1463.221589 0 0.0024 131 | 0/8 8 h-lim-p 0.0119 0.0952 1.8075 1463.191195 6 0.0059 155 | 0/8 9 h-lim-p 0.0012 0.0183 8.8558 1462.836228 0 0.0140 170 | 0/8 10 h-lim-p 0.1584 1.2674 0.0309 1462.805792 0 0.9506 184 | 0/8 11 h-lim-p 2.5000 20.0000 0.0069 1462.803998 3 1.0449 210 | 0/8 12 h-lim-p 2.5000 20.0000 0.0005 1462.803980 2 0.9644 234 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1462.803980 0 1.0938 254 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1462.803980 0 1.0938 274 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1462.803980 0 2.1875 294 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1462.803980 0 1.0938 314 | 0/8 17 h-lim-p 1.1994 20.0000 0.0000 1462.803980 0 0.0003 345 Out... lnL = -1462.803980 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1462.803980 Node 7: lnL = -1462.803980 Node 8: lnL = -1462.803980 Node 9: lnL = -1462.803980 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 259 Sequential format.. Reading seq # 1: YBL010C_Sbay Reading seq # 2: YBL010C_Scer Reading seq # 3: YBL010C_Skud Reading seq # 4: YBL010C_Smik Reading seq # 5: YBL010C_Spar Sequences read.. Counting patterns.. # site patterns = 123 Counting frequencies.. 120 bytes for distance 19680 bytes for lkl0 15744 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.045290 0.095513 0.020532 0.058271 0.072889 0.144623 0.199124 0.384203 lnL0 = -1100.316788 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1100.316788 x= 0.04529 0.09551 0.02053 0.05827 0.07289 0.14462 0.19912 0.38420 1 h-lim-p 0.0012 0.0092 88.0680 1099.589871 5 0.0002 33 | 0/8 2 h-lim-p 0.0016 0.0132 11.9962 1099.540599 5 0.0007 54 | 0/8 3 h-lim-p 0.0011 0.0347 7.7345 1099.531421 5 0.0004 76 | 0/8 4 h-lim-p 0.0023 0.0616 1.4020 1099.530987 3 0.0005 95 | 0/8 5 h-lim-p 0.0017 0.6370 0.3983 1099.530839 0 0.0025 107 | 0/8 6 h-lim-p 0.0194 1.8348 0.0510 1099.530837 1 0.0012 132 | 0/8 7 h-lim-p 0.0034 4.7855 0.0180 1099.530837 0 0.0030 152 | 0/8 8 h-lim-p 0.1576 20.0000 0.0003 1099.530748 0 0.9458 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1099.530746 0 1.0938 194 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1099.530746 0 1.0938 214 | 0/8 11 h-lim-p 1.1330 20.0000 0.0000 1099.530746 0 0.0708 237 | 0/8 12 h-lim-p 0.0109 20.0000 0.0000 1099.530746 0 0.0000 278 | 0/8 13 h-lim-p 0.0000 20.0000 0.0002 1099.530746 0 0.0000 304 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 1099.530746 0 0.0051 333 | 0/8 15 h-lim-p 0.0125 20.0000 0.0001 1099.530746 0 0.0000 363 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 1099.530746 0 0.0000 383 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 1099.530746 0 0.0000 405 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 1099.530746 0 0.0000 428 | 0/8 19 h-lim-p 0.0000 20.0000 0.0005 1099.530746 0 0.0000 451 | 0/8 20 h-lim-p 0.0000 20.0000 0.0000 1099.530746 0 0.0000 471 | 0/8 21 h-lim-p 0.0000 20.0000 0.0000 1099.530746 0 0.0000 495 Out... lnL = -1099.530746 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1099.530746 Node 7: lnL = -1099.530746 Node 8: lnL = -1099.530746 Node 9: lnL = -1099.530746 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 376 Sequential format.. Reading seq # 1: YBL011W_Sbay Reading seq # 2: YBL011W_Scer Reading seq # 3: YBL011W_Skud Reading seq # 4: YBL011W_Smik Reading seq # 5: YBL011W_Spar Sequences read.. Counting patterns.. # site patterns = 138 Counting frequencies.. 120 bytes for distance 22080 bytes for lkl0 17664 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.034487 0.089289 0.070588 0.054864 0.044914 0.085539 0.167277 0.337578 lnL0 = -1373.363112 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1373.363112 x= 0.03449 0.08929 0.07059 0.05486 0.04491 0.08554 0.16728 0.33758 1 h-lim-p 0.0044 1.9779 79.2298 1372.188918 9 0.0004 47 | 0/8 2 h-lim-p 0.0004 0.0031 31.9049 1372.042591 5 0.0003 70 | 0/8 3 h-lim-p 0.0007 0.0080 15.2495 1371.992833 4 0.0005 90 | 0/8 4 h-lim-p 0.0017 0.0387 4.8037 1371.984201 6 0.0008 117 | 0/8 5 h-lim-p 0.0009 0.0465 4.7463 1371.980558 4 0.0006 139 | 0/8 6 h-lim-p 0.0033 0.1590 0.8185 1371.980286 3 0.0009 158 | 0/8 7 h-lim-p 0.0034 0.3680 0.2104 1371.980259 3 0.0012 185 | 0/8 8 h-lim-p 0.2798 20.0000 0.0009 1371.979348 0 1.1194 207 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1371.979345 1 0.9961 229 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1371.979345 0 0.0012 259 | 0/8 11 h-lim-p 0.0005 20.0000 0.0000 1371.979345 0 0.0000 292 | 0/8 12 h-lim-p 0.0000 20.0000 0.0020 | 0/8 13 h-lim-p 0.0000 20.0000 0.0020 Out... lnL = -1371.979345 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1371.979345 Node 7: lnL = -1371.979345 Node 8: lnL = -1371.979345 Node 9: lnL = -1371.979345 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 326 Sequential format.. Reading seq # 1: YBL013W_Sbay Reading seq # 2: YBL013W_Scer Reading seq # 3: YBL013W_Skud Reading seq # 4: YBL013W_Smik Reading seq # 5: YBL013W_Spar Sequences read.. Counting patterns.. # site patterns = 166 Counting frequencies.. 120 bytes for distance 26560 bytes for lkl0 21248 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.299108 0.045685 0.315132 0.262512 0.168127 0.298724 0.455734 lnL0 = -1602.361342 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1602.361342 x= 0.00006 0.29911 0.04568 0.31513 0.26251 0.16813 0.29872 0.45573 1 h-lim-p 0.0000 0.0000 182.5379 1602.281173 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0007 511.1995 1584.379088 0 0.0003 39 | 1/8 3 h-lim-p 0.0002 0.0019 177.5486 1579.615791 0 0.0005 52 | 1/8 4 h-lim-p 0.0032 0.0261 27.0824 1577.963250 0 0.0048 64 | 1/8 5 h-lim-p 0.0022 0.0176 16.9955 1577.705756 5 0.0017 86 | 1/8 6 h-lim-p 0.0086 0.2068 3.3678 1576.449679 0 0.0259 99 | 1/8 7 h-lim-p 0.0037 0.0293 12.9445 1571.208510 0 0.0110 112 | 0/8 8 h-lim-p 0.0016 0.0130 34.6979 1568.184343 0 0.0033 125 | 0/8 9 h-lim-p 0.0277 0.2219 0.5538 1567.085496 m 0.2219 137 | 0/8 10 h-lim-p 0.0122 0.0973 4.6750 1566.040205 0 0.0486 159 | 0/8 11 h-lim-p 0.1654 1.3236 0.1709 1565.257824 0 0.9927 173 | 0/8 12 h-lim-p 0.7921 6.3368 0.0565 1565.109495 0 1.5842 194 | 0/8 13 h-lim-p 2.2567 18.0538 0.0133 1565.085897 6 0.9680 225 | 0/8 14 h-lim-p 2.5000 20.0000 0.0027 1565.085428 2 1.0889 249 | 0/8 15 h-lim-p 2.5000 20.0000 0.0010 1565.085381 2 1.0938 273 | 0/8 16 h-lim-p 2.5000 20.0000 0.0002 1565.085380 0 1.0938 293 | 0/8 17 h-lim-p 2.5000 20.0000 0.0001 1565.085380 0 1.0938 313 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1565.085380 0 1.0938 333 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1565.085380 0 0.6250 354 | 0/8 20 h-lim-p 0.9291 20.0000 0.0000 1565.085380 0 0.0000 398 Out... lnL = -1565.085380 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1565.085380 Node 7: lnL = -1565.085380 Node 8: lnL = -1565.085380 Node 9: lnL = -1565.085380 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 320 Sequential format.. Reading seq # 1: YBL014C_Sbay Reading seq # 2: YBL014C_Scer Reading seq # 3: YBL014C_Skud Reading seq # 4: YBL014C_Smik Reading seq # 5: YBL014C_Spar Sequences read.. Counting patterns.. # site patterns = 166 Counting frequencies.. 120 bytes for distance 26560 bytes for lkl0 21248 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.251724 0.049516 0.264001 0.228221 0.157131 0.281674 0.434938 lnL0 = -1554.767074 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1554.767074 x= 0.00006 0.25172 0.04952 0.26400 0.22822 0.15713 0.28167 0.43494 1 h-lim-p 0.0000 0.0000 169.7196 1554.662067 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0006 308.9816 1546.627466 0 0.0003 39 | 1/8 3 h-lim-p 0.0003 0.0024 79.8831 1545.236117 0 0.0006 52 | 1/8 4 h-lim-p 0.0034 0.0721 14.3447 1544.679757 0 0.0050 64 | 1/8 5 h-lim-p 0.0032 0.0257 10.7980 1544.226338 0 0.0048 76 | 1/8 6 h-lim-p 0.0051 0.0405 5.7361 1542.469158 0 0.0101 89 | 1/8 7 h-lim-p 0.0023 0.0182 14.2298 1534.664568 0 0.0091 103 | 1/8 8 h-lim-p 0.0034 0.0272 15.0082 1534.181939 1 0.0043 117 | 1/8 9 h-lim-p 0.6942 8.4444 0.0920 1530.866166 2 0.6508 133 | 1/8 10 h-lim-p 1.3096 10.4772 0.0198 1530.475851 2 1.2278 156 | 1/8 11 h-lim-p 1.4842 13.4642 0.0164 1530.419534 3 0.6725 181 | 0/8 12 h-lim-p 0.0275 7.0556 0.4017 1530.419293 2 0.0030 206 | 0/8 13 h-lim-p 0.5940 20.0000 0.0020 1530.418187 0 1.1879 227 | 0/8 14 h-lim-p 2.5000 20.0000 0.0006 1530.418029 2 1.2305 252 | 0/8 15 h-lim-p 2.5000 20.0000 0.0002 1530.418000 2 1.6492 278 | 0/8 16 h-lim-p 2.5000 20.0000 0.0001 1530.417999 0 1.0938 298 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1530.417999 0 1.0938 318 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1530.417999 0 1.2500 338 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1530.417999 0 1.0938 358 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 1530.417999 m20.0000 378 | 0/8 21 h-lim-p 1.6254 20.0000 0.0000 1530.417999 0 0.0016 407 Out... lnL = -1530.417999 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1530.417999 Node 7: lnL = -1530.417999 Node 8: lnL = -1530.417999 Node 9: lnL = -1530.417999 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 700 Sequential format.. Reading seq # 1: YBL015W_Sbay Reading seq # 2: YBL015W_Scer Reading seq # 3: YBL015W_Skud Reading seq # 4: YBL015W_Smik Reading seq # 5: YBL015W_Spar Sequences read.. Counting patterns.. # site patterns = 225 Counting frequencies.. 120 bytes for distance 36000 bytes for lkl0 28800 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.055281 0.071302 0.026036 0.089483 0.064906 0.173013 0.121997 0.378802 lnL0 = -2846.290524 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2846.290524 x= 0.05528 0.07130 0.02604 0.08948 0.06491 0.17301 0.12200 0.37880 1 h-lim-p 0.0014 0.6314 200.4833 2844.000479 8 0.0001 43 | 0/8 2 h-lim-p 0.0004 0.0028 56.3055 2843.482414 3 0.0004 61 | 0/8 3 h-lim-p 0.0007 0.0065 28.6395 2843.388395 6 0.0003 87 | 0/8 4 h-lim-p 0.0004 0.0075 19.5757 2843.354033 6 0.0003 115 | 0/8 5 h-lim-p 0.0036 0.1889 1.4428 2843.353332 3 0.0007 134 | 0/8 6 h-lim-p 0.0049 0.8078 0.2016 2843.353327 0 0.0003 149 | 0/8 7 h-lim-p 0.0015 4.8988 0.0368 2843.353326 0 0.0006 169 | 0/8 8 h-lim-p 0.0655 20.0000 0.0004 2843.353096 0 1.0481 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2843.353090 0 1.0938 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2843.353090 0 1.0938 233 | 0/8 11 h-lim-p 0.6020 20.0000 0.0000 2843.353090 0 0.0188 257 | 0/8 12 h-lim-p 0.0073 20.0000 0.0000 2843.353090 0 0.0146 278 | 0/8 13 h-lim-p 0.0074 20.0000 0.0001 2843.353090 0 0.0000 315 | 0/8 14 h-lim-p 0.0000 20.0000 0.0014 | 0/8 15 h-lim-p 0.0000 20.0000 0.0014 Out... lnL = -2843.353090 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2843.353090 Node 7: lnL = -2843.353090 Node 8: lnL = -2843.353090 Node 9: lnL = -2843.353090 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 866 Sequential format.. Reading seq # 1: YBL016W_Sbay Reading seq # 2: YBL016W_Scer Reading seq # 3: YBL016W_Skud Reading seq # 4: YBL016W_Smik Reading seq # 5: YBL016W_Spar Sequences read.. Counting patterns.. # site patterns = 310 Counting frequencies.. 120 bytes for distance 49600 bytes for lkl0 39680 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.277451 0.046679 0.086833 0.106349 0.088658 0.165583 0.248443 0.162015 lnL0 = -3887.286383 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3887.286383 x= 0.27745 0.04668 0.08683 0.10635 0.08866 0.16558 0.24844 0.16202 1 h-lim-p 0.0071 1.2950 104.8299 3886.161755 4 0.0002 34 | 0/8 2 h-lim-p 0.0009 0.0073 20.1985 3886.117069 3 0.0002 53 | 0/8 3 h-lim-p 0.0006 0.0184 8.0769 3886.110145 3 0.0002 71 | 0/8 4 h-lim-p 0.0008 0.0506 2.5296 3886.108216 2 0.0007 87 | 0/8 5 h-lim-p 0.0015 0.1159 1.1699 3886.108038 2 0.0003 104 | 0/8 6 h-lim-p 0.0010 0.6166 0.3718 3886.108013 1 0.0004 118 | 0/8 7 h-lim-p 0.0037 7.1655 0.0400 3886.108012 0 0.0008 139 | 0/8 8 h-lim-p 0.0877 20.0000 0.0004 3886.107796 0 1.0522 162 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3886.107791 0 1.0938 182 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3886.107790 0 1.0938 202 | 0/8 11 h-lim-p 1.7633 20.0000 0.0000 3886.107790 0 1.7633 222 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3886.107790 0 0.1367 245 | 0/8 13 h-lim-p 0.0371 20.0000 0.0000 3886.107790 0 0.0000 279 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 3886.107790 0 0.0000 312 Out... lnL = -3886.107790 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3886.107790 Node 7: lnL = -3886.107790 Node 8: lnL = -3886.107790 Node 9: lnL = -3886.107790 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 240 Sequential format.. Reading seq # 1: YBL019W_Sbay Reading seq # 2: YBL019W_Scer Reading seq # 3: YBL019W_Skud Reading seq # 4: YBL019W_Smik Reading seq # 5: YBL019W_Spar Sequences read.. Counting patterns.. # site patterns = 99 Counting frequencies.. 120 bytes for distance 15840 bytes for lkl0 12672 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.346649 0.293109 0.181807 0.284354 3.579806 0.283434 0.290957 0.000060 lnL0 = -949.582454 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 949.582454 x= 0.34665 0.29311 0.18181 0.28435 3.57981 0.28343 0.29096 0.00006 1 h-lim-p 0.0000 0.0000 145.8824 949.371931 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0024 169.2575 927.059261 m 0.0024 39 | 1/8 3 h-lim-p 0.0007 0.0059 21.3355 926.751278 0 0.0015 52 | 1/8 4 h-lim-p 0.0039 0.0926 8.2081 926.192222 0 0.0154 66 | 1/8 5 h-lim-p 0.0088 0.0705 2.2190 925.450523 0 0.0353 80 | 1/8 6 h-lim-p 0.0104 0.0857 7.5228 918.491390 0 0.0416 94 | 0/8 7 h-lim-p 0.0195 0.1560 3.7530 918.323839 1 0.0244 108 | 0/8 8 h-lim-p 0.0339 0.2710 0.4432 917.608614 m 0.2710 120 | 0/8 9 h-lim-p -0.0000 -0.0000 0.4485 h-lim-p: -3.20321551e-18 -2.56257241e-17 4.48509016e-01 917.608614 .. | 0/8 10 h-lim-p 0.0000 0.0078 14.1065 917.456412 0 0.0013 163 | 0/8 11 h-lim-p 0.0019 15.7086 9.3100 917.425421 5 0.0010 185 | 0/8 12 h-lim-p 0.0113 0.1805 0.7909 917.424924 4 0.0016 209 | 0/8 13 h-lim-p 0.0031 0.8336 0.4102 917.424663 1 0.0038 231 | 0/8 14 h-lim-p 0.0025 0.7543 0.6307 917.423716 0 0.0100 253 | 0/8 15 h-lim-p 0.0121 0.6487 0.5195 917.423563 2 0.0028 278 | 0/8 16 h-lim-p 1.5751 20.0000 0.0009 917.423545 2 1.0391 304 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 917.423545 0 1.0938 324 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 917.423545 0 1.2500 344 | 0/8 19 h-lim-p 1.1280 20.0000 0.0000 917.423545 0 0.9870 364 | 0/8 20 h-lim-p 0.0158 20.0000 0.0006 917.423545 0 0.0001 390 | 0/8 21 h-lim-p 0.0000 10.0213 0.0052 917.423545 0 0.0000 410 | 0/8 22 h-lim-p 0.0002 20.0000 0.0003 917.423545 0 0.0000 434 | 0/8 23 h-lim-p 0.0001 20.0000 0.0000 917.423545 0 0.0001 454 | 0/8 24 h-lim-p 0.0002 20.0000 0.0000 917.423545 0 0.0000 485 | 0/8 25 h-lim-p 0.0000 20.0000 0.0001 | 0/8 26 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -917.423545 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -917.423545 Node 7: lnL = -917.423545 Node 8: lnL = -917.423545 Node 9: lnL = -917.423545 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 320 Sequential format.. Reading seq # 1: YBL020W_Sbay Reading seq # 2: YBL020W_Scer Reading seq # 3: YBL020W_Skud Reading seq # 4: YBL020W_Smik Reading seq # 5: YBL020W_Spar Sequences read.. Counting patterns.. # site patterns = 132 Counting frequencies.. 120 bytes for distance 21120 bytes for lkl0 16896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.112095 0.070134 0.076922 0.079812 0.080083 0.170981 0.161788 0.032771 lnL0 = -1212.695124 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1212.695124 x= 0.11209 0.07013 0.07692 0.07981 0.08008 0.17098 0.16179 0.03277 1 h-lim-p 0.0003 0.0021 56.5221 1211.540657 0 0.0010 24 | 0/8 2 h-lim-p 0.0020 0.0156 8.0567 1211.523285 7 0.0005 54 | 0/8 3 h-lim-p 0.0014 0.1062 3.0921 1211.521259 5 0.0005 78 | 0/8 4 h-lim-p 0.0047 0.6133 0.3005 1211.519943 2 0.0050 94 | 0/8 5 h-lim-p 0.0028 0.2190 0.5262 1211.513186 0 0.0057 115 | 0/8 6 h-lim-p 0.0016 0.0730 1.8764 1211.425005 0 0.0064 137 | 0/8 7 h-lim-p 0.0017 0.0383 7.1290 1211.347316 5 0.0014 158 | 0/8 8 h-lim-p 0.0038 0.0328 2.6834 1211.345186 5 0.0006 183 | 0/8 9 h-lim-p 1.4346 20.0000 0.0012 1211.344121 5 0.9258 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1211.344118 1 0.9961 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1211.344118 0 1.0938 249 | 0/8 12 h-lim-p 1.1964 20.0000 0.0000 1211.344118 0 2.3929 270 | 0/8 13 h-lim-p 0.4112 20.0000 0.0001 1211.344118 0 0.3598 290 | 0/8 14 h-lim-p 0.0371 20.0000 0.0010 1211.344118 0 0.0012 314 | 0/8 15 h-lim-p 0.0005 18.4493 0.0023 1211.344118 0 0.0000 346 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 1211.344118 0 0.0000 375 Out... lnL = -1211.344118 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1211.344118 Node 7: lnL = -1211.344118 Node 8: lnL = -1211.344118 Node 9: lnL = -1211.344118 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 320 Sequential format.. Reading seq # 1: YBL021C_Sbay Reading seq # 2: YBL021C_Scer Reading seq # 3: YBL021C_Skud Reading seq # 4: YBL021C_Smik Reading seq # 5: YBL021C_Spar Sequences read.. Counting patterns.. # site patterns = 137 Counting frequencies.. 120 bytes for distance 21920 bytes for lkl0 17536 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.112046 0.093341 0.058823 0.118527 0.005039 0.152574 0.157535 0.037074 lnL0 = -1248.377167 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1248.377167 x= 0.11205 0.09334 0.05882 0.11853 0.00504 0.15257 0.15753 0.03707 1 h-lim-p 0.0000 0.0686 708.1364 1240.585324 0 0.0001 23 | 0/8 2 h-lim-p 0.0007 0.0055 29.2308 1240.111133 0 0.0014 36 | 0/8 3 h-lim-p 0.0019 0.0153 6.4810 1240.097783 6 0.0007 64 | 0/8 4 h-lim-p 0.0016 0.0802 2.6672 1240.095977 5 0.0006 87 | 0/8 5 h-lim-p 0.0029 0.2729 0.5237 1240.095839 2 0.0007 104 | 0/8 6 h-lim-p 0.0028 1.1087 0.1287 1240.095081 0 0.0084 125 | 0/8 7 h-lim-p 0.0071 0.9719 0.1510 1239.935272 0 0.1142 149 | 0/8 8 h-lim-p 0.0166 0.1607 1.0379 1239.934693 2 0.0010 176 | 0/8 9 h-lim-p 0.1469 10.5059 0.0069 1239.781312 0 2.3509 192 | 0/8 10 h-lim-p 2.5000 20.0000 0.0050 1239.765149 6 0.8872 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0005 1239.764982 2 0.9961 249 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1239.764982 0 1.0938 269 | 0/8 13 h-lim-p 2.3395 20.0000 0.0000 1239.764982 0 1.0235 289 | 0/8 14 h-lim-p 0.8912 20.0000 0.0000 1239.764982 0 2.6737 310 | 0/8 15 h-lim-p 0.0077 9.8045 0.0056 1239.764982 0 0.0001 335 | 0/8 16 h-lim-p 0.0000 1.5398 0.0354 1239.764982 0 0.0000 355 | 0/8 17 h-lim-p 0.0001 20.0000 0.0053 1239.764982 0 0.0001 376 | 0/8 18 h-lim-p 0.0001 20.0000 0.0078 1239.764982 0 0.0000 406 | 0/8 19 h-lim-p 0.0002 20.0000 0.0000 1239.764982 0 0.0000 438 Out... lnL = -1239.764982 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1239.764982 Node 7: lnL = -1239.764982 Node 8: lnL = -1239.764982 Node 9: lnL = -1239.764982 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 649 Sequential format.. Reading seq # 1: YBL024W_Sbay Reading seq # 2: YBL024W_Scer Reading seq # 3: YBL024W_Skud Reading seq # 4: YBL024W_Smik Reading seq # 5: YBL024W_Spar Sequences read.. Counting patterns.. # site patterns = 265 Counting frequencies.. 120 bytes for distance 42400 bytes for lkl0 33920 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.215228 0.226721 0.054009 0.135958 0.151794 0.248324 0.273681 0.074652 lnL0 = -3196.427155 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3196.427155 x= 0.21523 0.22672 0.05401 0.13596 0.15179 0.24832 0.27368 0.07465 1 h-lim-p 0.0246 0.1967 49.9434 3196.067765 4 0.0003 35 | 0/8 2 h-lim-p 0.0019 0.0341 7.8800 3196.051007 5 0.0006 61 | 0/8 3 h-lim-p 0.0008 0.1277 5.3942 3196.044116 3 0.0006 79 | 0/8 4 h-lim-p 0.0046 0.3049 0.7543 3196.043902 4 0.0008 102 | 0/8 5 h-lim-p 0.0018 0.7880 0.3216 3196.043869 1 0.0007 124 | 0/8 6 h-lim-p 0.0163 20.0000 0.0145 3196.043869 0 0.0010 147 | 0/8 7 h-lim-p 0.0035 20.0000 0.0042 3196.043869 0 0.0008 168 | 0/8 8 h-lim-p 0.0982 20.0000 0.0000 3196.043868 0 0.7853 191 | 0/8 9 h-lim-p 1.8951 20.0000 0.0000 3196.043868 0 1.6582 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3196.043868 0 1.0938 231 | 0/8 11 h-lim-p 0.3909 20.0000 0.0000 3196.043868 0 3.1273 254 | 0/8 12 h-lim-p 1.4733 20.0000 0.0000 3196.043868 0 1.2891 274 | 0/8 13 h-lim-p 0.0382 20.0000 0.0008 3196.043868 0 0.0191 294 | 0/8 14 h-lim-p 0.0046 20.0000 0.0035 3196.043868 0 0.0040 314 | 0/8 15 h-lim-p 0.0036 20.0000 0.0039 3196.043868 0 0.0000 357 | 0/8 16 h-lim-p 0.0000 20.0000 0.0006 3196.043868 0 0.0000 389 | 0/8 17 h-lim-p 0.0000 20.0000 0.0006 | 0/8 18 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -3196.043868 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3196.043868 Node 7: lnL = -3196.043868 Node 8: lnL = -3196.043868 Node 9: lnL = -3196.043868 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 458 Sequential format.. Reading seq # 1: YBL025W_Sbay Reading seq # 2: YBL025W_Scer Reading seq # 3: YBL025W_Skud Reading seq # 4: YBL025W_Smik Reading seq # 5: YBL025W_Spar Sequences read.. Counting patterns.. # site patterns = 171 Counting frequencies.. 120 bytes for distance 27360 bytes for lkl0 21888 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.179596 0.123345 0.046519 0.093885 0.083865 0.322297 0.151372 0.072520 lnL0 = -1799.751549 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1799.751549 x= 0.17960 0.12335 0.04652 0.09389 0.08386 0.32230 0.15137 0.07252 1 h-lim-p 0.0059 0.0470 63.8016 1799.071571 2 0.0003 29 | 0/8 2 h-lim-p 0.0011 0.0087 20.1332 1798.939847 5 0.0007 53 | 0/8 3 h-lim-p 0.0005 0.0060 30.5529 1798.721943 0 0.0009 66 | 0/8 4 h-lim-p 0.0016 0.0188 18.0792 1798.635072 5 0.0010 90 | 0/8 5 h-lim-p 0.0018 0.0327 10.4511 1798.606037 5 0.0009 114 | 0/8 6 h-lim-p 0.0014 0.0459 6.6796 1798.583552 1 0.0018 128 | 0/8 7 h-lim-p 0.0048 0.0835 2.4724 1798.582275 2 0.0006 146 | 0/8 8 h-lim-p 0.7084 20.0000 0.0020 1798.578749 0 1.4168 159 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 1798.578383 3 1.0004 185 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1798.578382 0 1.0938 205 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1798.578382 0 1.0938 225 | 0/8 12 h-lim-p 1.2659 20.0000 0.0000 1798.578382 0 1.2659 245 | 0/8 13 h-lim-p 0.5589 20.0000 0.0000 1798.578382 0 0.4890 265 | 0/8 14 h-lim-p 0.0337 20.0000 0.0003 1798.578382 0 0.0337 285 | 0/8 15 h-lim-p 0.0121 20.0000 0.0009 1798.578382 0 0.0006 309 | 0/8 16 h-lim-p 0.0006 20.0000 0.0009 1798.578382 0 0.0003 329 | 0/8 17 h-lim-p 0.0005 20.0000 0.0005 1798.578382 0 0.0001 351 | 0/8 18 h-lim-p 0.0003 20.0000 0.0001 1798.578382 0 0.0000 385 | 0/8 19 h-lim-p 0.0000 20.0000 0.0002 | 0/8 20 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1798.578382 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1798.578382 Node 7: lnL = -1798.578382 Node 8: lnL = -1798.578382 Node 9: lnL = -1798.578382 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 632 Sequential format.. Reading seq # 1: YBL028C_Sbay Reading seq # 2: YBL028C_Scer Reading seq # 3: YBL028C_Skud Reading seq # 4: YBL028C_Smik Reading seq # 5: YBL028C_Spar Sequences read.. Counting patterns.. # site patterns = 234 Counting frequencies.. 120 bytes for distance 37440 bytes for lkl0 29952 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.190563 0.056340 0.056615 0.144820 0.070942 0.228978 0.259674 0.084370 lnL0 = -2871.952681 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2871.952681 x= 0.19056 0.05634 0.05662 0.14482 0.07094 0.22898 0.25967 0.08437 1 h-lim-p 0.0087 1.7779 81.4412 2871.183939 3 0.0002 32 | 0/8 2 h-lim-p 0.0006 0.0051 26.4381 2871.041121 6 0.0004 58 | 0/8 3 h-lim-p 0.0007 0.0123 16.8091 2871.012012 4 0.0003 78 | 0/8 4 h-lim-p 0.0011 0.0628 4.2990 2871.008841 5 0.0004 103 | 0/8 5 h-lim-p 0.0034 0.5818 0.4793 2871.008750 2 0.0008 120 | 0/8 6 h-lim-p 0.0051 3.4688 0.0757 2871.008749 0 0.0006 142 | 0/8 7 h-lim-p 0.0035 14.3626 0.0121 2871.008749 0 0.0008 163 | 0/8 8 h-lim-p 0.0637 20.0000 0.0001 2871.008722 0 0.7645 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2871.008722 0 1.0938 206 | 0/8 10 h-lim-p 1.7592 20.0000 0.0000 2871.008722 0 1.7592 226 | 0/8 11 h-lim-p 1.2311 20.0000 0.0000 2871.008722 0 0.1154 249 | 0/8 12 h-lim-p 0.0018 20.0000 0.0010 2871.008722 0 0.0018 269 | 0/8 13 h-lim-p 0.0002 16.0889 0.0078 2871.008722 0 0.0001 289 | 0/8 14 h-lim-p 0.0013 20.0000 0.0007 2871.008722 0 0.0000 313 | 0/8 15 h-lim-p 0.0002 20.0000 0.0001 2871.008722 0 0.0001 333 | 0/8 16 h-lim-p 0.0006 20.0000 0.0000 2871.008722 0 0.0003 353 | 0/8 17 h-lim-p 0.0006 20.0000 0.0000 2871.008722 0 0.0000 386 | 0/8 18 h-lim-p 0.0000 20.0000 0.0005 | 0/8 19 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -2871.008722 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2871.008722 Node 7: lnL = -2871.008722 Node 8: lnL = -2871.008722 Node 9: lnL = -2871.008722 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 880 Sequential format.. Reading seq # 1: YBL029C-A_Sbay Reading seq # 2: YBL029C-A_Scer Reading seq # 3: YBL029C-A_Skud Reading seq # 4: YBL029C-A_Smik Reading seq # 5: YBL029C-A_Spar Sequences read.. Counting patterns.. # site patterns = 242 Counting frequencies.. 120 bytes for distance 38720 bytes for lkl0 30976 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.150552 0.073011 0.064674 0.066539 0.057836 0.128491 0.169880 0.071826 lnL0 = -3512.760837 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3512.760837 x= 0.15055 0.07301 0.06467 0.06654 0.05784 0.12849 0.16988 0.07183 1 h-lim-p 0.0020 0.0160 152.6475 3511.106803 8 0.0001 44 | 0/8 2 h-lim-p 0.0007 0.0056 30.9868 3511.025735 4 0.0002 65 | 0/8 3 h-lim-p 0.0003 0.0127 20.2522 3511.002331 6 0.0002 94 | 0/8 4 h-lim-p 0.0004 0.0259 7.2587 3510.997118 5 0.0002 118 | 0/8 5 h-lim-p 0.0015 0.0861 1.1248 3510.997031 3 0.0001 138 | 0/8 6 h-lim-p 0.0007 1.2752 0.2319 3510.997024 1 0.0003 152 | 0/8 7 h-lim-p 0.0348 20.0000 0.0019 3510.997013 0 0.0522 172 | 0/8 8 h-lim-p 0.0023 20.0000 0.0420 3510.996730 0 0.0093 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3510.996717 1 0.9961 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3510.996717 0 1.0938 236 | 0/8 11 h-lim-p 1.9208 20.0000 0.0000 3510.996717 0 1.6807 256 | 0/8 12 h-lim-p 1.3589 20.0000 0.0000 3510.996717 0 0.0013 285 | 0/8 13 h-lim-p 0.0001 20.0000 0.0004 3510.996717 0 0.0000 320 | 0/8 14 h-lim-p 0.0000 20.0000 0.0017 | 0/8 15 h-lim-p 0.0000 20.0000 0.0017 Out... lnL = -3510.996717 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3510.996717 Node 7: lnL = -3510.996717 Node 8: lnL = -3510.996717 Node 9: lnL = -3510.996717 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 866 Sequential format.. Reading seq # 1: YBL029W_Sbay Reading seq # 2: YBL029W_Scer Reading seq # 3: YBL029W_Skud Reading seq # 4: YBL029W_Smik Reading seq # 5: YBL029W_Spar Sequences read.. Counting patterns.. # site patterns = 211 Counting frequencies.. 120 bytes for distance 33760 bytes for lkl0 27008 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.113860 0.011472 0.052302 0.060028 0.037671 0.124159 0.098560 0.059384 lnL0 = -3014.575809 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3014.575809 x= 0.11386 0.01147 0.05230 0.06003 0.03767 0.12416 0.09856 0.05938 1 h-lim-p 0.0001 0.0012 726.1790 3006.829872 8 0.0000 39 | 0/8 2 h-lim-p 0.0002 0.0019 55.8110 3006.585891 7 0.0002 68 | 0/8 3 h-lim-p 0.0003 0.0050 28.8939 3006.554282 6 0.0001 95 | 0/8 4 h-lim-p 0.0002 0.0073 11.1347 3006.549398 4 0.0001 115 | 0/8 5 h-lim-p 0.0010 0.1538 1.0310 3006.549275 2 0.0002 132 | 0/8 6 h-lim-p 0.0019 2.2440 0.1287 3006.549274 0 0.0002 146 | 0/8 7 h-lim-p 0.0045 20.0000 0.0060 3006.549274 0 0.0002 169 | 0/8 8 h-lim-p 0.0107 20.0000 0.0001 3006.549266 0 0.6858 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3006.549266 0 1.0938 215 | 0/8 10 h-lim-p 1.8912 20.0000 0.0000 3006.549266 0 1.6548 235 | 0/8 11 h-lim-p 1.2579 20.0000 0.0000 3006.549266 0 1.1006 255 | 0/8 12 h-lim-p 0.7152 20.0000 0.0000 3006.549266 0 1.4305 276 | 0/8 13 h-lim-p 0.1929 20.0000 0.0003 3006.549266 0 0.0211 298 | 0/8 14 h-lim-p 0.0056 20.0000 0.0011 3006.549266 0 0.0007 320 | 0/8 15 h-lim-p 0.0000 0.4362 0.2071 3006.549266 0 0.0000 349 | 0/8 16 h-lim-p 0.0008 20.0000 0.0000 3006.549266 0 0.0000 384 Out... lnL = -3006.549266 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3006.549266 Node 7: lnL = -3006.549266 Node 8: lnL = -3006.549266 Node 9: lnL = -3006.549266 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 525 Sequential format.. Reading seq # 1: YBL030C_Sbay Reading seq # 2: YBL030C_Scer Reading seq # 3: YBL030C_Skud Reading seq # 4: YBL030C_Smik Reading seq # 5: YBL030C_Spar Sequences read.. Counting patterns.. # site patterns = 167 Counting frequencies.. 120 bytes for distance 26720 bytes for lkl0 21376 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.116725 0.013183 0.065076 0.059808 0.042269 0.107393 0.120803 0.059091 lnL0 = -1895.791307 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1895.791307 x= 0.11673 0.01318 0.06508 0.05981 0.04227 0.10739 0.12080 0.05909 1 h-lim-p 0.0004 0.3774 298.3181 1892.211466 3 0.0001 29 | 0/8 2 h-lim-p 0.0003 0.0022 45.4220 1891.980164 3 0.0002 47 | 0/8 3 h-lim-p 0.0012 0.0210 8.5961 1891.972965 5 0.0002 71 | 0/8 4 h-lim-p 0.0004 0.0272 4.0746 1891.971684 2 0.0002 87 | 0/8 5 h-lim-p 0.0007 0.1132 1.1376 1891.971500 2 0.0003 103 | 0/8 6 h-lim-p 0.0034 0.9646 0.1030 1891.971498 1 0.0003 119 | 0/8 7 h-lim-p 0.0247 20.0000 0.0014 1891.971440 0 0.1484 141 | 0/8 8 h-lim-p 0.0019 0.3801 0.1110 1891.970897 0 0.0038 162 | 0/8 9 h-lim-p 1.0025 20.0000 0.0004 1891.970875 1 1.0338 184 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1891.970875 0 1.0938 204 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1891.970875 0 1.0938 224 | 0/8 12 h-lim-p 1.2512 20.0000 0.0000 1891.970875 010.0072 247 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1891.970875 0 0.2734 269 | 0/8 14 h-lim-p 0.0225 20.0000 0.0002 1891.970875 0 0.0028 291 | 0/8 15 h-lim-p 0.0009 20.0000 0.0006 1891.970875 0 0.0000 329 | 0/8 16 h-lim-p 0.0000 20.0000 0.0042 | 0/8 17 h-lim-p 0.0000 20.0000 0.0042 Out... lnL = -1891.970875 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1891.970875 Node 7: lnL = -1891.970875 Node 8: lnL = -1891.970875 Node 9: lnL = -1891.970875 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 399 Sequential format.. Reading seq # 1: YBL031W_Sbay Reading seq # 2: YBL031W_Scer Reading seq # 3: YBL031W_Skud Reading seq # 4: YBL031W_Smik Reading seq # 5: YBL031W_Spar Sequences read.. Counting patterns.. # site patterns = 106 Counting frequencies.. 120 bytes for distance 16960 bytes for lkl0 13568 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.111870 0.009076 0.026860 0.054198 0.033365 0.099700 0.093960 0.061465 lnL0 = -1288.229430 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1288.229430 x= 0.11187 0.00908 0.02686 0.05420 0.03336 0.09970 0.09396 0.06146 1 h-lim-p 0.0002 0.0016 124.5633 1287.577494 4 0.0001 31 | 0/8 2 h-lim-p 0.0002 0.0015 33.1680 1287.496709 7 0.0002 57 | 0/8 3 h-lim-p 0.0005 0.0151 11.3756 1287.485699 5 0.0002 82 | 0/8 4 h-lim-p 0.0005 0.0203 4.7638 1287.483925 4 0.0002 103 | 0/8 5 h-lim-p 0.0006 0.0340 1.4045 1287.483752 4 0.0002 127 | 0/8 6 h-lim-p 0.0054 3.5041 0.0508 1287.483751 0 0.0006 141 | 0/8 7 h-lim-p 0.0051 14.5177 0.0058 1287.483750 0 0.0045 161 | 0/8 8 h-lim-p 0.0152 12.1287 0.0017 1287.483609 0 0.1214 184 | 0/8 9 h-lim-p 0.4793 20.0000 0.0004 1287.483595 0 0.9586 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1287.483594 0 1.0938 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1287.483594 0 2.1875 245 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1287.483594 0 0.2734 267 | 0/8 13 h-lim-p 0.1673 20.0000 0.0000 1287.483594 0 0.0000 305 Out... lnL = -1287.483594 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1287.483594 Node 7: lnL = -1287.483594 Node 8: lnL = -1287.483594 Node 9: lnL = -1287.483594 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 547 Sequential format.. Reading seq # 1: YBL032W_Sbay Reading seq # 2: YBL032W_Scer Reading seq # 3: YBL032W_Skud Reading seq # 4: YBL032W_Smik Reading seq # 5: YBL032W_Spar Sequences read.. Counting patterns.. # site patterns = 204 Counting frequencies.. 120 bytes for distance 32640 bytes for lkl0 26112 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.258655 0.033610 0.028783 0.106131 0.074460 0.154082 0.192727 0.155990 lnL0 = -2279.969537 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2279.969537 x= 0.25866 0.03361 0.02878 0.10613 0.07446 0.15408 0.19273 0.15599 1 h-lim-p 0.0015 0.0118 151.6807 2278.423877 7 0.0002 39 | 0/8 2 h-lim-p 0.0006 0.0047 36.0817 2278.178959 7 0.0004 68 | 0/8 3 h-lim-p 0.0007 0.0119 21.0107 2278.108594 7 0.0004 101 | 0/8 4 h-lim-p 0.0008 0.0225 10.3058 2278.095419 4 0.0003 121 | 0/8 5 h-lim-p 0.0027 0.1511 1.2599 2278.095052 3 0.0005 141 | 0/8 6 h-lim-p 0.0013 0.7476 0.4516 2278.095005 2 0.0005 157 | 0/8 7 h-lim-p 0.0012 1.5394 0.1952 2278.094996 0 0.0006 177 | 0/8 8 h-lim-p 0.6074 20.0000 0.0002 2278.094908 0 1.2148 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2278.094906 0 1.0938 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2278.094906 0 1.0938 238 | 0/8 11 h-lim-p 1.2732 20.0000 0.0000 2278.094906 0 5.0929 260 | 0/8 12 h-lim-p 1.8783 20.0000 0.0000 2278.094906 0 0.4109 281 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2278.094906 0 0.0098 308 | 0/8 14 h-lim-p 0.0041 20.0000 0.0000 2278.094906 0 0.0004 331 Out... lnL = -2278.094906 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2278.094906 Node 7: lnL = -2278.094906 Node 8: lnL = -2278.094906 Node 9: lnL = -2278.094906 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 548 Sequential format.. Reading seq # 1: YBL033C_Sbay Reading seq # 2: YBL033C_Scer Reading seq # 3: YBL033C_Skud Reading seq # 4: YBL033C_Smik Reading seq # 5: YBL033C_Spar Sequences read.. Counting patterns.. # site patterns = 211 Counting frequencies.. 120 bytes for distance 33760 bytes for lkl0 27008 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.259818 0.038119 0.029086 0.112449 0.070765 0.154038 0.180562 0.157156 lnL0 = -2282.444560 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2282.444560 x= 0.25982 0.03812 0.02909 0.11245 0.07076 0.15404 0.18056 0.15716 1 h-lim-p 0.0016 0.0125 161.5068 2280.762715 8 0.0001 43 | 0/8 2 h-lim-p 0.0006 0.0049 36.4373 2280.518458 7 0.0004 72 | 0/8 3 h-lim-p 0.0007 0.0122 21.5155 2280.456708 5 0.0003 95 | 0/8 4 h-lim-p 0.0007 0.0193 10.1805 2280.442012 2 0.0004 111 | 0/8 5 h-lim-p 0.0016 0.0838 2.2600 2280.440939 5 0.0004 134 | 0/8 6 h-lim-p 0.0033 1.2487 0.3076 2280.440918 2 0.0004 152 | 0/8 7 h-lim-p 0.0010 2.0860 0.1293 2280.440913 2 0.0007 177 | 0/8 8 h-lim-p 0.3875 20.0000 0.0002 2280.440782 0 1.5501 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2280.440774 1 0.9961 221 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2280.440774 0 1.0938 241 | 0/8 11 h-lim-p 1.1355 20.0000 0.0000 2280.440774 0 1.7032 261 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2280.440774 0 0.3125 283 | 0/8 13 h-lim-p 0.0699 20.0000 0.0000 2280.440774 0 0.0699 303 | 0/8 14 h-lim-p 0.0268 20.0000 0.0000 2280.440774 0 0.0025 326 | 0/8 15 h-lim-p 0.0002 20.0000 0.0004 2280.440774 0 0.0002 346 | 0/8 16 h-lim-p 0.0013 20.0000 0.0001 2280.440774 0 0.0000 384 | 0/8 17 h-lim-p 0.0000 20.0000 0.0003 2280.440774 0 0.0000 412 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 2280.440774 0 0.0026 440 | 0/8 19 h-lim-p 0.0086 20.0000 0.0001 2280.440774 0 0.0000 472 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 2280.440774 0 0.0000 506 | 0/8 21 h-lim-p 0.0000 20.0000 0.0016 | 0/8 22 h-lim-p 0.0000 20.0000 0.0016 Out... lnL = -2280.440774 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2280.440774 Node 7: lnL = -2280.440774 Node 8: lnL = -2280.440774 Node 9: lnL = -2280.440774 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 301 Sequential format.. Reading seq # 1: YBL036C_Sbay Reading seq # 2: YBL036C_Scer Reading seq # 3: YBL036C_Skud Reading seq # 4: YBL036C_Smik Reading seq # 5: YBL036C_Spar Sequences read.. Counting patterns.. # site patterns = 154 Counting frequencies.. 120 bytes for distance 24640 bytes for lkl0 19712 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.217547 0.067542 0.089588 0.138854 0.080648 0.251604 0.148699 0.101145 lnL0 = -1294.144792 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1294.144792 x= 0.21755 0.06754 0.08959 0.13885 0.08065 0.25160 0.14870 0.10115 1 h-lim-p 0.0035 0.0276 19.5125 1294.035325 7 0.0006 41 | 0/8 2 h-lim-p 0.0022 0.0408 5.1620 1294.020325 5 0.0012 64 | 0/8 3 h-lim-p 0.0026 0.1723 2.3666 1294.019138 4 0.0005 85 | 0/8 4 h-lim-p 0.0021 0.4126 0.5569 1294.018986 2 0.0011 101 | 0/8 5 h-lim-p 0.0034 1.8438 0.1739 1294.018969 2 0.0013 125 | 0/8 6 h-lim-p 0.0035 3.3241 0.0651 1294.018967 1 0.0014 147 | 0/8 7 h-lim-p 0.0106 20.0000 0.0086 1294.018967 0 0.0013 169 | 0/8 8 h-lim-p 0.0841 20.0000 0.0001 1294.018956 0 0.6724 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1294.018956 0 1.0938 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1294.018956 0 1.0938 232 | 0/8 11 h-lim-p 1.1896 20.0000 0.0000 1294.018956 0 0.1487 254 | 0/8 12 h-lim-p 0.0538 20.0000 0.0000 1294.018956 0 0.0007 279 | 0/8 13 h-lim-p 0.0006 20.0000 0.0000 1294.018956 0 0.0000 314 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 1294.018956 0 0.0000 349 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -1294.018956 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1294.018956 Node 7: lnL = -1294.018956 Node 8: lnL = -1294.018956 Node 9: lnL = -1294.018956 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 361 Sequential format.. Reading seq # 1: YBL037W_Sbay Reading seq # 2: YBL037W_Scer Reading seq # 3: YBL037W_Skud Reading seq # 4: YBL037W_Smik Reading seq # 5: YBL037W_Spar Sequences read.. Counting patterns.. # site patterns = 153 Counting frequencies.. 120 bytes for distance 24480 bytes for lkl0 19584 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.171123 0.080383 0.067037 0.111284 0.048301 0.213393 0.168152 0.071505 lnL0 = -1540.262067 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1540.262067 x= 0.17112 0.08038 0.06704 0.11128 0.04830 0.21339 0.16815 0.07151 1 h-lim-p 0.0067 1.9049 67.7144 1539.437372 2 0.0004 29 | 0/8 2 h-lim-p 0.0005 0.0040 21.1360 1539.360850 7 0.0004 58 | 0/8 3 h-lim-p 0.0008 0.0175 9.3181 1539.336306 6 0.0007 81 | 0/8 4 h-lim-p 0.0028 0.0873 2.2129 1539.334771 2 0.0007 98 | 0/8 5 h-lim-p 0.0050 0.9721 0.2917 1539.334742 3 0.0007 118 | 0/8 6 h-lim-p 0.0026 3.0341 0.0763 1539.334740 1 0.0006 141 | 0/8 7 h-lim-p 0.0026 15.8391 0.0185 1539.334740 0 0.0011 161 | 0/8 8 h-lim-p 0.1316 20.0000 0.0002 1539.334707 0 1.0531 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1539.334705 0 1.0938 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1539.334705 0 1.2500 224 | 0/8 11 h-lim-p 1.4381 20.0000 0.0000 1539.334705 0 0.0000 258 Out... lnL = -1539.334705 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1539.334705 Node 7: lnL = -1539.334705 Node 8: lnL = -1539.334705 Node 9: lnL = -1539.334705 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 573 Sequential format.. Reading seq # 1: YBL038W_Sbay Reading seq # 2: YBL038W_Scer Reading seq # 3: YBL038W_Skud Reading seq # 4: YBL038W_Smik Reading seq # 5: YBL038W_Spar Sequences read.. Counting patterns.. # site patterns = 212 Counting frequencies.. 120 bytes for distance 33920 bytes for lkl0 27136 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.214604 0.043440 0.055365 0.130217 0.101788 0.206154 0.205995 0.104428 lnL0 = -2363.334570 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2363.334570 x= 0.21460 0.04344 0.05536 0.13022 0.10179 0.20615 0.20599 0.10443 1 h-lim-p 0.0005 0.0038 115.7122 2361.672422 8 0.0003 42 | 0/8 2 h-lim-p 0.0005 0.0042 29.2384 2361.505783 4 0.0004 62 | 0/8 3 h-lim-p 0.0014 0.0291 8.5574 2361.491220 6 0.0004 89 | 0/8 4 h-lim-p 0.0018 0.1301 2.0780 2361.490022 4 0.0006 110 | 0/8 5 h-lim-p 0.0069 0.9555 0.1778 2361.490014 2 0.0005 129 | 0/8 6 h-lim-p 0.0019 6.5105 0.0425 2361.490013 0 0.0009 149 | 0/8 7 h-lim-p 0.0065 20.0000 0.0062 2361.490011 0 0.0097 169 | 0/8 8 h-lim-p 0.0147 20.0000 0.0041 2361.489810 0 0.0883 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2361.489807 0 1.0938 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2361.489807 0 1.0938 231 | 0/8 11 h-lim-p 0.9083 20.0000 0.0000 2361.489807 0 0.7947 251 | 0/8 12 h-lim-p 0.5992 20.0000 0.0000 2361.489807 0 0.0374 274 | 0/8 13 h-lim-p 0.0100 20.0000 0.0000 2361.489807 0 0.0000 309 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 2361.489807 0 0.0000 336 Out... lnL = -2361.489807 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2361.489807 Node 7: lnL = -2361.489807 Node 8: lnL = -2361.489807 Node 9: lnL = -2361.489807 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 530 Sequential format.. Reading seq # 1: YBL039C_Sbay Reading seq # 2: YBL039C_Scer Reading seq # 3: YBL039C_Skud Reading seq # 4: YBL039C_Smik Reading seq # 5: YBL039C_Spar Sequences read.. Counting patterns.. # site patterns = 216 Counting frequencies.. 120 bytes for distance 34560 bytes for lkl0 27648 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.209628 0.048926 0.047649 0.124792 0.104164 0.199913 0.207763 0.101329 lnL0 = -2294.766496 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2294.766496 x= 0.20963 0.04893 0.04765 0.12479 0.10416 0.19991 0.20776 0.10133 1 h-lim-p 0.0005 0.0041 125.9173 2293.055187 3 0.0002 29 | 0/8 2 h-lim-p 0.0006 0.0045 26.6610 2292.922647 7 0.0004 58 | 0/8 3 h-lim-p 0.0016 0.0883 6.3376 2292.914767 5 0.0004 82 | 0/8 4 h-lim-p 0.0017 0.1822 1.5655 2292.914003 3 0.0007 100 | 0/8 5 h-lim-p 0.0037 0.8385 0.2844 2292.913976 2 0.0007 117 | 0/8 6 h-lim-p 0.0022 2.6658 0.0921 2292.913973 1 0.0005 140 | 0/8 7 h-lim-p 0.0069 20.0000 0.0072 2292.913971 0 0.0103 160 | 0/8 8 h-lim-p 0.0170 18.8464 0.0044 2292.913640 0 0.1018 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2292.913638 0 1.0938 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2292.913638 0 1.0938 222 | 0/8 11 h-lim-p 1.0567 20.0000 0.0000 2292.913638 0 0.4623 242 | 0/8 12 h-lim-p 0.2524 20.0000 0.0000 2292.913638 0 0.0158 265 | 0/8 13 h-lim-p 0.0075 20.0000 0.0000 2292.913638 0 0.0000 299 | 0/8 14 h-lim-p 0.0000 20.0000 0.0006 | 0/8 15 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -2292.913638 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2292.913638 Node 7: lnL = -2292.913638 Node 8: lnL = -2292.913638 Node 9: lnL = -2292.913638 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 847 Sequential format.. Reading seq # 1: YBL041W_Sbay Reading seq # 2: YBL041W_Scer Reading seq # 3: YBL041W_Skud Reading seq # 4: YBL041W_Smik Reading seq # 5: YBL041W_Spar Sequences read.. Counting patterns.. # site patterns = 329 Counting frequencies.. 120 bytes for distance 52640 bytes for lkl0 42112 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.222652 0.071810 0.098174 0.090924 0.156488 0.248949 0.170672 0.099331 lnL0 = -3763.117337 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3763.117337 x= 0.22265 0.07181 0.09817 0.09092 0.15649 0.24895 0.17067 0.09933 1 h-lim-p 0.0006 0.0051 117.0112 3761.175628 4 0.0003 31 | 0/8 2 h-lim-p 0.0003 0.0024 56.8196 3760.717899 6 0.0003 56 | 0/8 3 h-lim-p 0.0012 0.0178 15.6024 3760.687661 2 0.0003 73 | 0/8 4 h-lim-p 0.0021 0.1650 2.0518 3760.686727 2 0.0005 90 | 0/8 5 h-lim-p 0.0021 0.3541 0.4653 3760.686673 2 0.0005 107 | 0/8 6 h-lim-p 0.0202 19.5117 0.0116 3760.686673 0 0.0011 130 | 0/8 7 h-lim-p 0.0075 20.0000 0.0017 3760.686671 0 0.0300 152 | 0/8 8 h-lim-p 0.0022 8.0569 0.0234 3760.686618 0 0.0088 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3760.686617 0 1.0938 194 | 0/8 10 h-lim-p 2.4152 20.0000 0.0000 3760.686617 0 1.0566 214 | 0/8 11 h-lim-p 1.0675 20.0000 0.0000 3760.686617 0 4.2701 236 | 0/8 12 h-lim-p 0.7842 20.0000 0.0001 3760.686617 0 1.1763 256 | 0/8 13 h-lim-p 0.0069 13.4739 0.0115 3760.686617 0 0.0004 279 | 0/8 14 h-lim-p 0.0002 4.8143 0.0322 3760.686617 0 0.0000 313 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 3760.686617 0 0.0000 351 Out... lnL = -3760.686617 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3760.686617 Node 7: lnL = -3760.686617 Node 8: lnL = -3760.686617 Node 9: lnL = -3760.686617 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 858 Sequential format.. Reading seq # 1: YBL042C_Sbay Reading seq # 2: YBL042C_Scer Reading seq # 3: YBL042C_Skud Reading seq # 4: YBL042C_Smik Reading seq # 5: YBL042C_Spar Sequences read.. Counting patterns.. # site patterns = 298 Counting frequencies.. 120 bytes for distance 47680 bytes for lkl0 38144 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.255477 0.011484 0.000060 0.324027 0.821164 0.317506 0.148353 0.073201 lnL0 = -3730.402756 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3730.402756 x= 0.25548 0.01148 0.00006 0.32403 0.82116 0.31751 0.14835 0.07320 1 h-lim-p 0.0000 0.0000 232.9773 3730.345888 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0024 161.2186 3724.457910 0 0.0006 40 | 1/8 3 h-lim-p 0.0008 0.0066 51.6567 3724.034338 3 0.0004 58 | 1/8 4 h-lim-p 0.0022 0.0336 8.8008 3723.989212 5 0.0011 81 | 0/8 5 h-lim-p 0.0005 0.0218 20.5444 3723.858228 0 0.0007 93 | 0/8 6 h-lim-p 0.0007 0.0380 20.9332 3723.710939 0 0.0014 106 | 0/8 7 h-lim-p 0.0007 0.0059 30.9240 3723.522440 0 0.0030 120 | 0/8 8 h-lim-p 0.1168 0.9341 0.1180 3718.645695 m 0.9341 132 | 0/8 9 h-lim-p 0.0000 0.0000 0.0319 h-lim-p: 8.64175871e-19 6.91340696e-18 3.19195623e-02 3718.645695 .. | 0/8 10 h-lim-p 0.0000 0.0557 52.3112 3718.326336 0 0.0002 172 | 0/8 11 h-lim-p 0.0000 0.0001 15.2057 3718.302859 m 0.0001 184 | 1/8 12 h-lim-p 0.0001 0.0457 11.1608 3718.292314 0 0.0004 197 | 1/8 13 h-lim-p 0.0136 0.3747 0.3012 3718.292166 1 0.0014 213 | 1/8 14 h-lim-p 0.0013 1.0231 0.3195 3718.292109 1 0.0010 234 | 1/8 15 h-lim-p 0.0011 3.9181 0.2830 3718.291993 0 0.0046 255 | 1/8 16 h-lim-p 0.0012 5.9406 1.0499 3718.291820 0 0.0019 274 | 1/8 17 h-lim-p 0.8735 20.0000 0.0022 3718.288124 4 0.9511 296 | 1/8 18 h-lim-p 2.5000 20.0000 0.0001 3718.288108 1 0.9961 317 | 1/8 19 h-lim-p 2.5000 20.0000 0.0000 3718.288108 0 1.0938 336 | 1/8 20 h-lim-p 1.5400 20.0000 0.0000 3718.288108 0 1.3475 355 | 1/8 21 h-lim-p 1.3773 20.0000 0.0000 3718.288108 0 1.3773 374 | 1/8 22 h-lim-p 0.2545 20.0000 0.0000 3718.288108 0 0.2227 393 | 1/8 23 h-lim-p 0.0389 20.0000 0.0001 3718.288108 0 0.0195 412 | 1/8 24 h-lim-p 0.0104 20.0000 0.0003 3718.288108 0 0.0039 432 | 1/8 25 h-lim-p 0.0005 20.0000 0.0019 3718.288108 0 0.0000 460 | 1/8 26 h-lim-p 0.0001 20.0000 0.0000 3718.288108 0 0.0001 479 | 1/8 27 h-lim-p 0.0020 20.0000 0.0000 3718.288108 0 0.0000 511 Out... lnL = -3718.288108 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3718.288108 Node 7: lnL = -3718.288108 Node 8: lnL = -3718.288108 Node 9: lnL = -3718.288108 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 403 Sequential format.. Reading seq # 1: YBL043W_Sbay Reading seq # 2: YBL043W_Scer Reading seq # 3: YBL043W_Skud Reading seq # 4: YBL043W_Smik Reading seq # 5: YBL043W_Spar Sequences read.. Counting patterns.. # site patterns = 158 Counting frequencies.. 120 bytes for distance 25280 bytes for lkl0 20224 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.207280 0.065460 0.085967 0.100071 0.060109 0.155722 0.123816 0.109744 lnL0 = -1597.279301 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1597.279301 x= 0.20728 0.06546 0.08597 0.10007 0.06011 0.15572 0.12382 0.10974 1 h-lim-p 0.0077 0.0618 62.7924 1596.458284 2 0.0005 29 | 0/8 2 h-lim-p 0.0007 0.0053 18.0958 1596.389533 7 0.0004 60 | 0/8 3 h-lim-p 0.0011 0.0111 7.2755 1596.378703 4 0.0005 79 | 0/8 4 h-lim-p 0.0015 0.1484 2.2505 1596.377464 5 0.0005 102 | 0/8 5 h-lim-p 0.0079 1.7494 0.1553 1596.377456 2 0.0008 120 | 0/8 6 h-lim-p 0.0035 5.7285 0.0338 1596.377455 0 0.0008 141 | 0/8 7 h-lim-p 0.0465 20.0000 0.0006 1596.377451 0 0.1396 162 | 0/8 8 h-lim-p 0.0027 4.4642 0.0288 1596.377423 0 0.0054 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1596.377422 0 1.0938 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1596.377422 0 1.0938 223 | 0/8 11 h-lim-p 1.1379 20.0000 0.0000 1596.377422 0 1.7069 243 | 0/8 12 h-lim-p 1.9814 20.0000 0.0000 1596.377422 0 0.2167 265 | 0/8 13 h-lim-p 0.0381 20.0000 0.0000 1596.377422 0 0.0000 308 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -1596.377422 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1596.377422 Node 7: lnL = -1596.377422 Node 8: lnL = -1596.377422 Node 9: lnL = -1596.377422 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 754 Sequential format.. Reading seq # 1: YBL049W_Sbay Reading seq # 2: YBL049W_Scer Reading seq # 3: YBL049W_Skud Reading seq # 4: YBL049W_Smik Reading seq # 5: YBL049W_Spar Sequences read.. Counting patterns.. # site patterns = 189 Counting frequencies.. 120 bytes for distance 30240 bytes for lkl0 24192 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.124405 0.056776 0.028314 0.066606 0.068393 0.133272 0.119222 0.055504 lnL0 = -2818.146190 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2818.146190 x= 0.12440 0.05678 0.02831 0.06661 0.06839 0.13327 0.11922 0.05550 1 h-lim-p 0.0001 0.0011 146.5996 2816.844579 2 0.0001 26 | 0/8 2 h-lim-p 0.0001 0.0010 37.5168 2816.780947 7 0.0001 53 | 0/8 3 h-lim-p 0.0004 0.0401 8.9761 2816.772189 5 0.0002 78 | 0/8 4 h-lim-p 0.0011 0.0495 1.8557 2816.771971 2 0.0001 96 | 0/8 5 h-lim-p 0.0005 0.3929 0.4443 2816.771954 2 0.0002 114 | 0/8 6 h-lim-p 0.0015 2.7590 0.0537 2816.771954 0 0.0002 136 | 0/8 7 h-lim-p 0.0040 20.0000 0.0022 2816.771954 0 0.0040 156 | 0/8 8 h-lim-p 0.0066 20.0000 0.0013 2816.771919 0 0.0791 179 | 0/8 9 h-lim-p 1.8068 20.0000 0.0001 2816.771919 0 0.9034 199 | 0/8 10 h-lim-p 1.8286 20.0000 0.0000 2816.771919 0 0.8000 219 | 0/8 11 h-lim-p 0.5782 20.0000 0.0000 2816.771919 0 0.0079 244 | 0/8 12 h-lim-p 0.0017 20.0000 0.0002 2816.771919 0 0.0000 269 | 0/8 13 h-lim-p 0.0002 20.0000 0.0000 2816.771919 0 0.0000 305 | 0/8 14 h-lim-p 0.0000 20.0000 0.0009 2816.771919 0 0.0000 335 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 2816.771919 0 0.0000 370 | 0/8 16 h-lim-p 0.0000 20.0000 0.0009 | 0/8 17 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -2816.771919 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2816.771919 Node 7: lnL = -2816.771919 Node 8: lnL = -2816.771919 Node 9: lnL = -2816.771919 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 560 Sequential format.. Reading seq # 1: YBL050W_Sbay Reading seq # 2: YBL050W_Scer Reading seq # 3: YBL050W_Skud Reading seq # 4: YBL050W_Smik Reading seq # 5: YBL050W_Spar Sequences read.. Counting patterns.. # site patterns = 202 Counting frequencies.. 120 bytes for distance 32320 bytes for lkl0 25856 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.134608 0.040238 0.083236 0.125379 0.076885 0.126177 0.170925 0.043331 lnL0 = -2164.363491 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2164.363491 x= 0.13461 0.04024 0.08324 0.12538 0.07689 0.12618 0.17093 0.04333 1 h-lim-p 0.0018 0.0148 108.0222 2163.392100 7 0.0002 40 | 0/8 2 h-lim-p 0.0007 0.0053 23.5440 2163.299050 6 0.0003 66 | 0/8 3 h-lim-p 0.0013 0.0546 6.1934 2163.292111 5 0.0004 90 | 0/8 4 h-lim-p 0.0023 0.1753 1.0547 2163.291909 3 0.0004 111 | 0/8 5 h-lim-p 0.0026 0.6943 0.1533 2163.291906 0 0.0003 125 | 0/8 6 h-lim-p 0.0010 4.4027 0.0487 2163.291906 0 0.0004 145 | 0/8 7 h-lim-p 0.0226 20.0000 0.0010 2163.291906 0 0.0197 165 | 0/8 8 h-lim-p 0.0135 20.0000 0.0014 2163.291893 0 0.0539 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2163.291893 0 1.0938 207 | 0/8 10 h-lim-p 0.6900 20.0000 0.0000 2163.291893 0 1.3800 228 | 0/8 11 h-lim-p 1.1064 20.0000 0.0000 2163.291893 0 0.0692 251 | 0/8 12 h-lim-p 0.0007 18.6527 0.0032 2163.291893 0 0.0000 281 | 0/8 13 h-lim-p 0.0002 20.0000 0.0000 2163.291893 0 0.0000 306 Out... lnL = -2163.291893 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2163.291893 Node 7: lnL = -2163.291893 Node 8: lnL = -2163.291893 Node 9: lnL = -2163.291893 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 377 Sequential format.. Reading seq # 1: YBL051C_Sbay Reading seq # 2: YBL051C_Scer Reading seq # 3: YBL051C_Skud Reading seq # 4: YBL051C_Smik Reading seq # 5: YBL051C_Spar Sequences read.. Counting patterns.. # site patterns = 143 Counting frequencies.. 120 bytes for distance 22880 bytes for lkl0 18304 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.150285 0.047068 0.067201 0.126839 0.071806 0.145733 0.163540 0.056510 lnL0 = -1597.196523 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1597.196523 x= 0.15029 0.04707 0.06720 0.12684 0.07181 0.14573 0.16354 0.05651 1 h-lim-p 0.0012 0.0093 87.0012 1596.240179 3 0.0003 29 | 0/8 2 h-lim-p 0.0011 0.0086 16.8861 1596.167882 2 0.0005 45 | 0/8 3 h-lim-p 0.0011 0.0308 7.6770 1596.159612 6 0.0003 73 | 0/8 4 h-lim-p 0.0024 0.2295 1.0541 1596.159297 2 0.0006 90 | 0/8 5 h-lim-p 0.0031 1.7597 0.1917 1596.159287 2 0.0005 109 | 0/8 6 h-lim-p 0.0031 4.1689 0.0318 1596.159287 1 0.0008 132 | 0/8 7 h-lim-p 0.0097 20.0000 0.0025 1596.159237 0 0.0775 155 | 0/8 8 h-lim-p 0.0013 1.8598 0.1500 1596.158879 0 0.0039 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1596.158873 1 0.9961 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1596.158873 0 1.0938 218 | 0/8 11 h-lim-p 0.5942 20.0000 0.0000 1596.158873 0 1.1883 239 | 0/8 12 h-lim-p 0.7952 20.0000 0.0000 1596.158873 0 1.5904 260 | 0/8 13 h-lim-p 0.0344 20.0000 0.0009 1596.158873 0 0.0172 280 | 0/8 14 h-lim-p 0.0056 20.0000 0.0026 1596.158873 0 0.0007 302 | 0/8 15 h-lim-p 0.0005 20.0000 0.0034 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0005 | 0/8 17 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -1596.158873 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1596.158873 Node 7: lnL = -1596.158873 Node 8: lnL = -1596.158873 Node 9: lnL = -1596.158873 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 866 Sequential format.. Reading seq # 1: YBL052C_Sbay Reading seq # 2: YBL052C_Scer Reading seq # 3: YBL052C_Skud Reading seq # 4: YBL052C_Smik Reading seq # 5: YBL052C_Spar Sequences read.. Counting patterns.. # site patterns = 256 Counting frequencies.. 120 bytes for distance 40960 bytes for lkl0 32768 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.152342 0.046662 0.034288 0.077857 0.084310 0.158802 0.121725 0.069198 lnL0 = -3375.836800 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3375.836800 x= 0.15234 0.04666 0.03429 0.07786 0.08431 0.15880 0.12172 0.06920 1 h-lim-p 0.0010 0.5584 262.6527 3372.778056 7 0.0001 37 | 0/8 2 h-lim-p 0.0003 0.0024 39.1470 3372.633218 6 0.0002 63 | 0/8 3 h-lim-p 0.0007 0.0210 10.5788 3372.622050 6 0.0002 91 | 0/8 4 h-lim-p 0.0005 0.0398 4.8537 3372.620142 3 0.0002 109 | 0/8 5 h-lim-p 0.0037 1.0046 0.2553 3372.620132 2 0.0003 129 | 0/8 6 h-lim-p 0.0013 2.3267 0.0612 3372.620132 0 0.0003 150 | 0/8 7 h-lim-p 0.0018 14.7709 0.0097 3372.620132 0 0.0015 170 | 0/8 8 h-lim-p 0.0161 20.0000 0.0009 3372.619932 0 0.2571 194 | 0/8 9 h-lim-p 1.6427 20.0000 0.0001 3372.619928 1 0.8085 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3372.619928 0 1.0938 237 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3372.619928 0 2.1875 257 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3372.619928 0 0.5469 278 | 0/8 13 h-lim-p 0.1197 20.0000 0.0000 3372.619928 0 0.0000 317 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 3372.619928 0 0.0000 345 Out... lnL = -3372.619928 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3372.619928 Node 7: lnL = -3372.619928 Node 8: lnL = -3372.619928 Node 9: lnL = -3372.619928 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 811 Sequential format.. Reading seq # 1: YBL055C_Sbay Reading seq # 2: YBL055C_Scer Reading seq # 3: YBL055C_Skud Reading seq # 4: YBL055C_Smik Reading seq # 5: YBL055C_Spar Sequences read.. Counting patterns.. # site patterns = 250 Counting frequencies.. 120 bytes for distance 40000 bytes for lkl0 32000 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.161668 0.067285 0.049752 0.137026 0.058945 0.169461 0.162536 0.063398 lnL0 = -3218.100222 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3218.100222 x= 0.16167 0.06729 0.04975 0.13703 0.05895 0.16946 0.16254 0.06340 1 h-lim-p 0.0008 0.0062 99.5771 3217.403873 6 0.0001 35 | 0/8 2 h-lim-p 0.0005 0.0069 28.0368 3217.312418 2 0.0002 51 | 0/8 3 h-lim-p 0.0004 0.0154 15.3663 3217.299456 6 0.0001 79 | 0/8 4 h-lim-p 0.0007 0.0268 2.8861 3217.298264 3 0.0003 97 | 0/8 5 h-lim-p 0.0008 0.2655 1.1095 3217.298040 3 0.0004 116 | 0/8 6 h-lim-p 0.0081 3.1280 0.0562 3217.298040 0 0.0004 131 | 0/8 7 h-lim-p 0.0119 20.0000 0.0021 3217.298039 0 0.0104 151 | 0/8 8 h-lim-p 0.0046 20.0000 0.0048 3217.297982 0 0.0367 174 | 0/8 9 h-lim-p 0.4165 20.0000 0.0004 3217.297979 0 0.8330 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 3217.297979 0 1.0938 215 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3217.297979 0 2.1875 235 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3217.297979 0 0.6250 256 | 0/8 13 h-lim-p 0.1486 20.0000 0.0000 3217.297979 0 0.0743 276 | 0/8 14 h-lim-p 0.0315 20.0000 0.0000 3217.297979 0 0.0010 300 | 0/8 15 h-lim-p 0.0006 20.0000 0.0001 3217.297979 0 0.0000 336 | 0/8 16 h-lim-p 0.0000 20.0000 0.0021 | 0/8 17 h-lim-p 0.0000 20.0000 0.0021 Out... lnL = -3217.297979 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3217.297979 Node 7: lnL = -3217.297979 Node 8: lnL = -3217.297979 Node 9: lnL = -3217.297979 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 335 Sequential format.. Reading seq # 1: YBL056W_Sbay Reading seq # 2: YBL056W_Scer Reading seq # 3: YBL056W_Skud Reading seq # 4: YBL056W_Smik Reading seq # 5: YBL056W_Spar Sequences read.. Counting patterns.. # site patterns = 131 Counting frequencies.. 120 bytes for distance 20960 bytes for lkl0 16768 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.168179 0.106634 0.019961 0.122594 0.095307 0.192096 0.092270 0.069750 lnL0 = -1435.796708 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1435.796708 x= 0.16818 0.10663 0.01996 0.12259 0.09531 0.19210 0.09227 0.06975 1 h-lim-p 0.0017 0.8252 130.9314 1434.194916 8 0.0002 42 | 0/8 2 h-lim-p 0.0017 0.0135 16.0134 1434.102294 6 0.0007 66 | 0/8 3 h-lim-p 0.0054 0.0909 2.1838 1434.100647 4 0.0007 88 | 0/8 4 h-lim-p 0.0037 0.2824 0.4168 1434.100606 3 0.0005 108 | 0/8 5 h-lim-p 0.0048 6.0420 0.0434 1434.100605 0 0.0010 129 | 0/8 6 h-lim-p 0.0035 16.4307 0.0130 1434.100604 1 0.0017 152 | 0/8 7 h-lim-p 0.0024 12.7857 0.0094 1434.100601 0 0.0095 174 | 0/8 8 h-lim-p 0.0083 4.2910 0.0107 1434.100391 0 0.0332 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1434.100389 0 1.0938 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1434.100388 0 1.0938 236 | 0/8 11 h-lim-p 1.1288 20.0000 0.0000 1434.100388 0 2.2577 257 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1434.100388 0 0.5469 278 | 0/8 13 h-lim-p 0.0994 20.0000 0.0000 1434.100388 0 0.0373 299 | 0/8 14 h-lim-p 0.0116 20.0000 0.0001 1434.100388 0 0.0000 330 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 1434.100388 0 0.0000 359 Out... lnL = -1434.100388 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1434.100388 Node 7: lnL = -1434.100388 Node 8: lnL = -1434.100388 Node 9: lnL = -1434.100388 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 359 Sequential format.. Reading seq # 1: YBL057C_Sbay Reading seq # 2: YBL057C_Scer Reading seq # 3: YBL057C_Skud Reading seq # 4: YBL057C_Smik Reading seq # 5: YBL057C_Spar Sequences read.. Counting patterns.. # site patterns = 162 Counting frequencies.. 120 bytes for distance 25920 bytes for lkl0 20736 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.177298 0.100632 0.046652 0.107610 0.104445 0.195770 0.045329 0.078854 lnL0 = -1518.065537 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1518.065537 x= 0.17730 0.10063 0.04665 0.10761 0.10444 0.19577 0.04533 0.07885 1 h-lim-p 0.0011 0.8436 169.9675 1514.545152 5 0.0003 33 | 0/8 2 h-lim-p 0.0020 0.0161 11.5528 1514.498101 5 0.0007 57 | 0/8 3 h-lim-p 0.0026 0.0528 3.1938 1514.494840 5 0.0007 80 | 0/8 4 h-lim-p 0.0026 0.3204 0.8463 1514.494648 2 0.0006 97 | 0/8 5 h-lim-p 0.0027 1.0733 0.1809 1514.494636 3 0.0008 125 | 0/8 6 h-lim-p 0.0039 7.1937 0.0361 1514.494636 0 0.0009 146 | 0/8 7 h-lim-p 0.0954 20.0000 0.0003 1514.494635 0 0.0954 166 | 0/8 8 h-lim-p 0.0030 20.0000 0.0104 1514.494625 0 0.0120 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1514.494624 0 1.0938 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1514.494624 0 1.0938 228 | 0/8 11 h-lim-p 1.1972 20.0000 0.0000 1514.494624 0 2.3945 249 | 0/8 12 h-lim-p 2.4138 20.0000 0.0000 1514.494624 0 0.0003 281 Out... lnL = -1514.494624 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1514.494624 Node 7: lnL = -1514.494624 Node 8: lnL = -1514.494624 Node 9: lnL = -1514.494624 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 231 Sequential format.. Reading seq # 1: YBL058W_Sbay Reading seq # 2: YBL058W_Scer Reading seq # 3: YBL058W_Skud Reading seq # 4: YBL058W_Smik Reading seq # 5: YBL058W_Spar Sequences read.. Counting patterns.. # site patterns = 91 Counting frequencies.. 120 bytes for distance 14560 bytes for lkl0 11648 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.186585 0.047834 0.034589 0.142695 0.088495 0.264863 0.145697 0.077626 lnL0 = -947.513255 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 947.513255 x= 0.18658 0.04783 0.03459 0.14270 0.08849 0.26486 0.14570 0.07763 1 h-lim-p 0.0021 0.0164 39.7112 947.042910 8 0.0007 40 | 0/8 2 h-lim-p 0.0004 0.0029 18.8048 946.925411 0 0.0007 53 | 0/8 3 h-lim-p 0.0021 0.0282 6.3926 946.909018 4 0.0009 72 | 0/8 4 h-lim-p 0.0034 0.1458 1.7068 946.906977 5 0.0015 93 | 0/8 5 h-lim-p 0.0028 0.1401 0.9326 946.906664 4 0.0009 114 | 0/8 6 h-lim-p 0.0520 13.6264 0.0164 946.906658 2 0.0068 140 | 0/8 7 h-lim-p 0.0137 6.6116 0.0082 946.906164 0 0.1097 163 | 0/8 8 h-lim-p 0.0024 0.3059 0.3697 946.906042 4 0.0014 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 946.906030 2 1.0938 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 946.906030 0 1.0938 238 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 946.906030 0 0.5469 259 | 0/8 12 h-lim-p 0.3819 20.0000 0.0000 946.906030 0 0.0001 290 Out... lnL = -946.906030 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -946.906030 Node 7: lnL = -946.906030 Node 8: lnL = -946.906030 Node 9: lnL = -946.906030 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 559 Sequential format.. Reading seq # 1: YBL060W_Sbay Reading seq # 2: YBL060W_Scer Reading seq # 3: YBL060W_Skud Reading seq # 4: YBL060W_Smik Reading seq # 5: YBL060W_Spar Sequences read.. Counting patterns.. # site patterns = 202 Counting frequencies.. 120 bytes for distance 32320 bytes for lkl0 25856 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.243545 0.055437 0.042317 0.124880 0.084498 0.194662 0.222079 0.122979 lnL0 = -2551.088052 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2551.088052 x= 0.24354 0.05544 0.04232 0.12488 0.08450 0.19466 0.22208 0.12298 1 h-lim-p 0.0002 0.0013 167.1980 2547.628953 0 0.0003 23 | 0/8 2 h-lim-p 0.0002 0.0019 59.7876 2547.052875 0 0.0004 35 | 0/8 3 h-lim-p 0.0005 0.0080 40.2430 2546.864230 6 0.0003 63 | 0/8 4 h-lim-p 0.0008 0.0141 16.4515 2546.801927 6 0.0006 88 | 0/8 5 h-lim-p 0.0056 0.1117 1.6901 2546.800913 3 0.0007 109 | 0/8 6 h-lim-p 0.0023 0.4720 0.4927 2546.800699 2 0.0010 125 | 0/8 7 h-lim-p 0.0085 3.6382 0.0591 2546.790448 0 0.0678 148 | 0/8 8 h-lim-p 0.0031 0.0934 1.2816 2546.693783 0 0.0063 169 | 0/8 9 h-lim-p 2.5000 20.0000 0.0016 2546.691612 4 0.9644 189 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2546.691609 0 1.0938 209 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2546.691609 0 1.0938 229 | 0/8 12 h-lim-p 1.8256 20.0000 0.0000 2546.691609 0 1.5974 249 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2546.691609 0 0.5469 270 | 0/8 14 h-lim-p 0.2063 20.0000 0.0000 2546.691609 0 0.0516 291 | 0/8 15 h-lim-p 0.0228 20.0000 0.0000 2546.691609 0 0.0114 311 | 0/8 16 h-lim-p 0.0064 20.0000 0.0000 2546.691609 0 0.0000 340 | 0/8 17 h-lim-p 0.0005 20.0000 0.0000 2546.691609 0 0.0000 373 Out... lnL = -2546.691609 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2546.691609 Node 7: lnL = -2546.691609 Node 8: lnL = -2546.691609 Node 9: lnL = -2546.691609 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 600 Sequential format.. Reading seq # 1: YBL061C_Sbay Reading seq # 2: YBL061C_Scer Reading seq # 3: YBL061C_Skud Reading seq # 4: YBL061C_Smik Reading seq # 5: YBL061C_Spar Sequences read.. Counting patterns.. # site patterns = 195 Counting frequencies.. 120 bytes for distance 31200 bytes for lkl0 24960 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.231164 0.066051 0.045229 0.115266 0.071573 0.210393 0.224838 0.111413 lnL0 = -2586.431892 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2586.431892 x= 0.23116 0.06605 0.04523 0.11527 0.07157 0.21039 0.22484 0.11141 1 h-lim-p 0.0002 0.0016 123.1945 2584.708943 0 0.0003 22 | 0/8 2 h-lim-p 0.0004 0.0030 35.7140 2584.496993 2 0.0004 38 | 0/8 3 h-lim-p 0.0006 0.0169 22.2107 2584.444719 6 0.0003 64 | 0/8 4 h-lim-p 0.0006 0.0256 9.8460 2584.423189 2 0.0006 80 | 0/8 5 h-lim-p 0.0039 0.1489 1.4103 2584.422539 3 0.0006 101 | 0/8 6 h-lim-p 0.0024 0.6664 0.3726 2584.422426 2 0.0010 117 | 0/8 7 h-lim-p 0.0266 12.5106 0.0134 2584.381574 0 0.4251 141 | 0/8 8 h-lim-p 0.0012 0.0282 4.6120 2584.362825 3 0.0010 167 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 2584.362601 2 0.9644 183 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2584.362601 0 1.0938 203 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2584.362601 0 1.2500 223 | 0/8 12 h-lim-p 1.3775 20.0000 0.0000 2584.362601 0 0.3013 244 | 0/8 13 h-lim-p 0.1415 20.0000 0.0000 2584.362601 0 0.0044 268 | 0/8 14 h-lim-p 0.0027 20.0000 0.0000 2584.362601 0 0.0007 289 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 2584.362601 0 0.0000 324 | 0/8 16 h-lim-p 0.0000 20.0000 0.0013 | 0/8 17 h-lim-p 0.0000 20.0000 0.0013 Out... lnL = -2584.362601 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2584.362601 Node 7: lnL = -2584.362601 Node 8: lnL = -2584.362601 Node 9: lnL = -2584.362601 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 819 Sequential format.. Reading seq # 1: YBL064C_Sbay Reading seq # 2: YBL064C_Scer Reading seq # 3: YBL064C_Skud Reading seq # 4: YBL064C_Smik Reading seq # 5: YBL064C_Spar Sequences read.. Counting patterns.. # site patterns = 349 Counting frequencies.. 120 bytes for distance 55840 bytes for lkl0 44672 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.192689 0.183453 0.126595 0.159164 0.103488 0.247345 0.248773 0.038688 lnL0 = -3876.646409 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3876.646409 x= 0.19269 0.18345 0.12659 0.15916 0.10349 0.24734 0.24877 0.03869 1 h-lim-p 0.0010 0.0080 94.8649 3874.858882 3 0.0004 28 | 0/8 2 h-lim-p 0.0006 0.0045 28.9325 3874.723596 7 0.0003 60 | 0/8 3 h-lim-p 0.0008 0.0114 12.0208 3874.693542 6 0.0005 86 | 0/8 4 h-lim-p 0.0010 0.0480 6.0222 3874.686881 2 0.0005 102 | 0/8 5 h-lim-p 0.0038 0.3854 0.7287 3874.686743 3 0.0005 122 | 0/8 6 h-lim-p 0.0022 1.6670 0.1666 3874.686733 1 0.0009 144 | 0/8 7 h-lim-p 0.0181 20.0000 0.0081 3874.686733 0 0.0020 166 | 0/8 8 h-lim-p 0.1204 20.0000 0.0001 3874.686725 0 0.9636 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3874.686724 0 1.0938 209 | 0/8 10 h-lim-p 1.3059 20.0000 0.0000 3874.686724 0 1.1427 229 | 0/8 11 h-lim-p 1.0580 20.0000 0.0000 3874.686724 0 0.0083 255 | 0/8 12 h-lim-p 0.0003 20.0000 0.0007 3874.686724 0 0.0000 278 | 0/8 13 h-lim-p 0.0007 20.0000 0.0000 3874.686724 0 0.0000 309 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 3874.686724 0 0.0000 337 Out... lnL = -3874.686724 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3874.686724 Node 7: lnL = -3874.686724 Node 8: lnL = -3874.686724 Node 9: lnL = -3874.686724 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 280 Sequential format.. Reading seq # 1: YBL066C_Sbay Reading seq # 2: YBL066C_Scer Reading seq # 3: YBL066C_Skud Reading seq # 4: YBL066C_Smik Reading seq # 5: YBL066C_Spar Sequences read.. Counting patterns.. # site patterns = 129 Counting frequencies.. 120 bytes for distance 20640 bytes for lkl0 16512 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.157374 0.112313 0.076173 0.109689 0.060173 0.137862 0.172228 0.054265 lnL0 = -1179.988094 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1179.988094 x= 0.15737 0.11231 0.07617 0.10969 0.06017 0.13786 0.17223 0.05426 1 h-lim-p 0.0033 0.0267 67.5661 1178.903128 8 0.0005 44 | 0/8 2 h-lim-p 0.0009 0.0069 17.5112 1178.827844 8 0.0005 78 | 0/8 3 h-lim-p 0.0017 0.0265 5.2164 1178.814935 6 0.0010 105 | 0/8 4 h-lim-p 0.0032 0.1281 1.6659 1178.813593 5 0.0011 128 | 0/8 5 h-lim-p 0.0078 1.0960 0.2292 1178.813569 1 0.0010 144 | 0/8 6 h-lim-p 0.0037 3.6366 0.0606 1178.813567 0 0.0008 165 | 0/8 7 h-lim-p 0.0296 20.0000 0.0016 1178.813566 0 0.0296 185 | 0/8 8 h-lim-p 0.0114 20.0000 0.0043 1178.813537 0 0.0457 207 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1178.813536 0 1.0938 227 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1178.813536 0 1.0938 247 | 0/8 11 h-lim-p 1.1614 20.0000 0.0000 1178.813536 0 0.0006 277 Out... lnL = -1178.813536 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1178.813536 Node 7: lnL = -1178.813536 Node 8: lnL = -1178.813536 Node 9: lnL = -1178.813536 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 841 Sequential format.. Reading seq # 1: YBL067C_Sbay Reading seq # 2: YBL067C_Scer Reading seq # 3: YBL067C_Skud Reading seq # 4: YBL067C_Smik Reading seq # 5: YBL067C_Spar Sequences read.. Counting patterns.. # site patterns = 243 Counting frequencies.. 120 bytes for distance 38880 bytes for lkl0 31104 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.147989 0.065416 0.051046 0.081132 0.055418 0.179054 0.145715 0.058799 lnL0 = -3345.264745 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3345.264745 x= 0.14799 0.06542 0.05105 0.08113 0.05542 0.17905 0.14571 0.05880 1 h-lim-p 0.0009 0.0072 93.1862 3344.786900 6 0.0001 37 | 0/8 2 h-lim-p 0.0004 0.0060 26.8362 3344.723442 2 0.0002 53 | 0/8 3 h-lim-p 0.0004 0.0115 13.7054 3344.709191 5 0.0002 77 | 0/8 4 h-lim-p 0.0010 0.0577 2.5407 3344.708561 3 0.0002 96 | 0/8 5 h-lim-p 0.0007 0.1905 0.7348 3344.708515 2 0.0002 113 | 0/8 6 h-lim-p 0.0009 4.1662 0.1428 3344.708512 1 0.0002 136 | 0/8 7 h-lim-p 0.0012 2.7675 0.0285 3344.708512 0 0.0003 157 | 0/8 8 h-lim-p 0.0378 20.0000 0.0002 3344.708441 0 0.9083 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3344.708441 0 1.0938 201 | 0/8 10 h-lim-p 1.9262 20.0000 0.0000 3344.708441 0 1.6855 221 | 0/8 11 h-lim-p 2.4727 20.0000 0.0000 3344.708441 0 0.5409 242 | 0/8 12 h-lim-p 0.1620 20.0000 0.0001 3344.708441 0 0.0101 265 | 0/8 13 h-lim-p 0.0034 20.0000 0.0002 3344.708441 0 0.0034 285 | 0/8 14 h-lim-p 0.0016 20.0000 0.0003 3344.708441 0 0.0000 322 | 0/8 15 h-lim-p 0.0000 20.0000 0.0025 | 0/8 16 h-lim-p 0.0000 20.0000 0.0025 Out... lnL = -3344.708441 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3344.708441 Node 7: lnL = -3344.708441 Node 8: lnL = -3344.708441 Node 9: lnL = -3344.708441 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 318 Sequential format.. Reading seq # 1: YBL068W_Sbay Reading seq # 2: YBL068W_Scer Reading seq # 3: YBL068W_Skud Reading seq # 4: YBL068W_Smik Reading seq # 5: YBL068W_Spar Sequences read.. Counting patterns.. # site patterns = 135 Counting frequencies.. 120 bytes for distance 21600 bytes for lkl0 17280 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.193745 0.088672 0.084863 0.082204 0.061617 0.178748 0.213613 0.080439 lnL0 = -1381.126123 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1381.126123 x= 0.19375 0.08867 0.08486 0.08220 0.06162 0.17875 0.21361 0.08044 1 h-lim-p 0.0002 0.0016 54.1373 1380.470114 0 0.0004 23 | 0/8 2 h-lim-p 0.0017 0.0585 12.8212 1380.443646 6 0.0003 47 | 0/8 3 h-lim-p 0.0009 0.0568 4.8844 1380.435945 3 0.0008 65 | 0/8 4 h-lim-p 0.0029 0.1930 1.2725 1380.435379 4 0.0008 86 | 0/8 5 h-lim-p 0.0022 0.6946 0.4363 1380.435304 3 0.0008 105 | 0/8 6 h-lim-p 0.0029 2.4016 0.1159 1380.435254 1 0.0030 127 | 0/8 7 h-lim-p 0.0421 9.4401 0.0083 1380.426712 0 0.3369 150 | 0/8 8 h-lim-p 0.0093 0.5766 0.2988 1380.426669 2 0.0009 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1380.426667 0 1.0938 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1380.426667 0 1.0938 216 | 0/8 11 h-lim-p 1.1833 20.0000 0.0000 1380.426667 0 0.0040 243 | 0/8 12 h-lim-p 0.0018 20.0000 0.0000 1380.426667 0 0.0000 269 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 1380.426667 0 0.0000 296 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 1380.426667 0 0.0000 327 Out... lnL = -1380.426667 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1380.426667 Node 7: lnL = -1380.426667 Node 8: lnL = -1380.426667 Node 9: lnL = -1380.426667 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 262 Sequential format.. Reading seq # 1: YBL069W_Sbay Reading seq # 2: YBL069W_Scer Reading seq # 3: YBL069W_Skud Reading seq # 4: YBL069W_Smik Reading seq # 5: YBL069W_Spar Sequences read.. Counting patterns.. # site patterns = 74 Counting frequencies.. 120 bytes for distance 11840 bytes for lkl0 9472 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.118621 0.048478 0.033020 0.080085 0.074167 0.130457 0.120356 0.045454 lnL0 = -914.619748 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 914.619748 x= 0.11862 0.04848 0.03302 0.08008 0.07417 0.13046 0.12036 0.04545 1 h-lim-p 0.0005 0.0037 101.7239 912.888994 3 0.0004 28 | 0/8 2 h-lim-p 0.0005 0.0041 24.1545 912.729547 6 0.0006 54 | 0/8 3 h-lim-p 0.0020 0.0219 6.7330 912.716959 6 0.0006 82 | 0/8 4 h-lim-p 0.0024 0.1085 1.6987 912.716024 5 0.0007 106 | 0/8 5 h-lim-p 0.0040 0.5493 0.2994 912.715993 3 0.0007 126 | 0/8 6 h-lim-p 0.0027 1.9038 0.0767 912.715991 1 0.0007 149 | 0/8 7 h-lim-p 0.0103 20.0000 0.0050 912.715991 0 0.0023 170 | 0/8 8 h-lim-p 0.0366 20.0000 0.0003 912.715970 0 0.5856 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 912.715967 1 0.9961 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 912.715967 0 1.0938 236 | 0/8 11 h-lim-p 1.2624 20.0000 0.0000 912.715967 0 5.0494 258 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 912.715967 0 0.3125 280 | 0/8 13 h-lim-p 0.0887 20.0000 0.0000 912.715967 0 0.0097 302 | 0/8 14 h-lim-p 0.0030 20.0000 0.0001 912.715967 0 0.0003 324 | 0/8 15 h-lim-p 0.0002 20.0000 0.0001 912.715967 0 0.0001 344 | 0/8 16 h-lim-p 0.0000 8.1864 0.0086 912.715967 0 0.0000 371 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 912.715967 0 0.0000 400 | 0/8 18 h-lim-p 0.0000 20.0000 0.0013 912.715967 0 0.0000 427 | 0/8 19 h-lim-p 0.0000 20.0000 0.0002 912.715967 0 0.0013 454 | 0/8 20 h-lim-p 0.0098 20.0000 0.0000 912.715967 0 0.0086 474 | 0/8 21 h-lim-p 0.0222 20.0000 0.0000 912.715967 0 0.0007 498 | 0/8 22 h-lim-p 0.0002 20.0000 0.0000 912.715967 0 0.0000 525 | 0/8 23 h-lim-p 0.0000 20.0000 0.0004 .. | 0/8 24 h-lim-p 0.0000 20.0000 0.0014 | 0/8 25 h-lim-p 0.0000 20.0000 0.0014 Out... lnL = -912.715967 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -912.715967 Node 7: lnL = -912.715967 Node 8: lnL = -912.715967 Node 9: lnL = -912.715967 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 898 Sequential format.. Reading seq # 1: YBL071W-A_Sbay Reading seq # 2: YBL071W-A_Scer Reading seq # 3: YBL071W-A_Skud Reading seq # 4: YBL071W-A_Smik Reading seq # 5: YBL071W-A_Spar Sequences read.. Counting patterns.. # site patterns = 336 Counting frequencies.. 120 bytes for distance 53760 bytes for lkl0 43008 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.179242 0.115739 0.034384 0.164910 0.098639 0.320303 0.175433 0.043416 lnL0 = -3940.393260 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3940.393260 x= 0.17924 0.11574 0.03438 0.16491 0.09864 0.32030 0.17543 0.04342 1 h-lim-p 0.0040 0.9467 140.8593 3938.573732 7 0.0002 39 | 0/8 2 h-lim-p 0.0009 0.0140 29.9723 3938.354946 8 0.0005 72 | 0/8 3 h-lim-p 0.0013 0.0321 12.1159 3938.328074 6 0.0004 99 | 0/8 4 h-lim-p 0.0009 0.0244 5.6033 3938.323463 4 0.0004 119 | 0/8 5 h-lim-p 0.0016 0.0969 1.2844 3938.323104 3 0.0005 140 | 0/8 6 h-lim-p 0.0052 1.0449 0.1130 3938.323101 0 0.0006 154 | 0/8 7 h-lim-p 0.0092 20.0000 0.0070 3938.323101 0 0.0020 175 | 0/8 8 h-lim-p 0.0291 20.0000 0.0005 3938.323043 0 0.4661 199 | 0/8 9 h-lim-p 1.8903 20.0000 0.0001 3938.323042 1 0.9304 222 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3938.323042 0 1.0938 242 | 0/8 11 h-lim-p 1.0760 20.0000 0.0000 3938.323042 0 1.0760 262 | 0/8 12 h-lim-p 0.0283 20.0000 0.0011 3938.323042 0 0.0062 283 | 0/8 13 h-lim-p 0.0018 16.8472 0.0039 3938.323042 0 0.0000 321 | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -3938.323042 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3938.323042 Node 7: lnL = -3938.323042 Node 8: lnL = -3938.323042 Node 9: lnL = -3938.323042 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 871 Sequential format.. Reading seq # 1: YBL072C_Sbay Reading seq # 2: YBL072C_Scer Reading seq # 3: YBL072C_Skud Reading seq # 4: YBL072C_Smik Reading seq # 5: YBL072C_Spar Sequences read.. Counting patterns.. # site patterns = 329 Counting frequencies.. 120 bytes for distance 52640 bytes for lkl0 42112 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.255506 0.028741 0.058454 0.124080 0.122753 0.252797 0.937887 0.045203 lnL0 = -4408.899861 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4408.899861 x= 0.25551 0.02874 0.05845 0.12408 0.12275 0.25280 0.93789 0.04520 1 h-lim-p 0.0003 0.0027 154.1119 4406.322185 9 0.0002 46 | 0/8 2 h-lim-p 0.0004 0.0032 51.2285 4405.885713 3 0.0004 64 | 0/8 3 h-lim-p 0.0004 0.0030 37.9015 4405.578785 0 0.0007 77 | 0/8 4 h-lim-p 0.0004 0.0031 33.1900 4405.443577 1 0.0005 91 | 0/8 5 h-lim-p 0.0009 0.0072 11.5000 4405.412445 6 0.0006 119 | 0/8 6 h-lim-p 0.0020 0.0406 3.5209 4405.410143 3 0.0004 138 | 0/8 7 h-lim-p 0.0010 0.2172 1.5586 4405.405855 0 0.0038 152 | 0/8 8 h-lim-p 1.5485 20.0000 0.0039 4405.397215 6 1.0307 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 4405.397178 0 1.0938 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4405.397177 0 1.0938 218 | 0/8 11 h-lim-p 1.7476 20.0000 0.0000 4405.397177 0 1.5292 238 | 0/8 12 h-lim-p 1.7668 20.0000 0.0000 4405.397177 0 0.7730 258 | 0/8 13 h-lim-p 0.1536 20.0000 0.0001 4405.397177 0 0.0048 282 | 0/8 14 h-lim-p 0.0011 20.0000 0.0004 4405.397177 0 0.0003 303 | 0/8 15 h-lim-p 0.0005 20.0000 0.0002 4405.397177 0 0.0000 337 | 0/8 16 h-lim-p 0.0000 20.0000 0.0008 | 0/8 17 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -4405.397177 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4405.397177 Node 7: lnL = -4405.397177 Node 8: lnL = -4405.397177 Node 9: lnL = -4405.397177 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 827 Sequential format.. Reading seq # 1: YBL074C_Sbay Reading seq # 2: YBL074C_Scer Reading seq # 3: YBL074C_Skud Reading seq # 4: YBL074C_Smik Reading seq # 5: YBL074C_Spar Sequences read.. Counting patterns.. # site patterns = 304 Counting frequencies.. 120 bytes for distance 48640 bytes for lkl0 38912 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.176173 0.059503 0.088697 0.104312 0.085753 0.198211 0.256343 0.052856 lnL0 = -3515.328051 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3515.328051 x= 0.17617 0.05950 0.08870 0.10431 0.08575 0.19821 0.25634 0.05286 1 h-lim-p 0.0014 0.5473 226.3625 3510.478166 9 0.0002 47 | 0/8 2 h-lim-p 0.0007 0.0052 31.7241 3510.329387 2 0.0003 63 | 0/8 3 h-lim-p 0.0006 0.0080 16.5596 3510.299181 2 0.0003 79 | 0/8 4 h-lim-p 0.0021 0.0874 2.1495 3510.298381 4 0.0004 102 | 0/8 5 h-lim-p 0.0018 0.7052 0.4293 3510.298329 2 0.0006 120 | 0/8 6 h-lim-p 0.0033 2.1053 0.0774 3510.298326 0 0.0007 141 | 0/8 7 h-lim-p 0.0012 5.7019 0.0475 3510.298318 0 0.0024 162 | 0/8 8 h-lim-p 0.0213 20.0000 0.0052 3510.296065 0 0.2558 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3510.295954 2 0.9961 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3510.295954 0 1.0938 229 | 0/8 11 h-lim-p 1.3280 20.0000 0.0000 3510.295954 0 0.1660 251 | 0/8 12 h-lim-p 0.0270 20.0000 0.0001 3510.295954 0 0.0000 296 | 0/8 13 h-lim-p 0.0000 20.0000 0.0008 | 0/8 14 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -3510.295954 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3510.295954 Node 7: lnL = -3510.295954 Node 8: lnL = -3510.295954 Node 9: lnL = -3510.295954 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 174 Sequential format.. Reading seq # 1: YBL078C_Sbay Reading seq # 2: YBL078C_Scer Reading seq # 3: YBL078C_Skud Reading seq # 4: YBL078C_Smik Reading seq # 5: YBL078C_Spar Sequences read.. Counting patterns.. # site patterns = 57 Counting frequencies.. 120 bytes for distance 9120 bytes for lkl0 7296 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.081986 0.012932 0.045556 0.059978 0.058690 0.093519 0.108698 0.024074 lnL0 = -602.186641 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 602.186641 x= 0.08199 0.01293 0.04556 0.05998 0.05869 0.09352 0.10870 0.02407 1 h-lim-p 0.0003 0.0041 203.3334 599.883530 9 0.0002 43 | 0/8 2 h-lim-p 0.0003 0.0028 16.8753 599.809909 0 0.0007 56 | 0/8 3 h-lim-p 0.0024 0.1181 4.8654 599.800781 6 0.0008 82 | 0/8 4 h-lim-p 0.0029 0.0601 1.4250 599.800312 4 0.0005 105 | 0/8 5 h-lim-p 0.0031 0.2247 0.2296 599.800293 2 0.0006 122 | 0/8 6 h-lim-p 0.0017 1.3146 0.0839 599.800270 0 0.0025 142 | 0/8 7 h-lim-p 0.0078 2.3286 0.0273 599.799645 0 0.0313 164 | 0/8 8 h-lim-p 0.0016 0.2720 0.5468 599.795011 0 0.0047 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 599.794858 2 1.1719 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 599.794836 2 2.1875 233 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 599.794836 0 1.0938 253 | 0/8 12 h-lim-p 1.4300 20.0000 0.0000 599.794836 0 1.2512 273 | 0/8 13 h-lim-p 0.9993 20.0000 0.0000 599.794836 0 0.0625 296 | 0/8 14 h-lim-p 0.0006 14.4159 0.0019 599.794836 0 0.0006 316 | 0/8 15 h-lim-p 0.0002 3.9380 0.0070 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 599.794836 0 0.0000 378 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 599.794836 0 0.0000 398 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0004 | 0/8 20 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -599.794836 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -599.794836 Node 7: lnL = -599.794836 Node 8: lnL = -599.794836 Node 9: lnL = -599.794836 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 825 Sequential format.. Reading seq # 1: YBL081W_Sbay Reading seq # 2: YBL081W_Scer Reading seq # 3: YBL081W_Skud Reading seq # 4: YBL081W_Smik Reading seq # 5: YBL081W_Spar Sequences read.. Counting patterns.. # site patterns = 233 Counting frequencies.. 120 bytes for distance 37280 bytes for lkl0 29824 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.128899 0.041728 0.079771 0.095727 0.065908 0.116498 0.109526 0.045184 lnL0 = -3102.754691 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3102.754691 x= 0.12890 0.04173 0.07977 0.09573 0.06591 0.11650 0.10953 0.04518 1 h-lim-p 0.0002 0.0018 217.7522 3100.046868 8 0.0001 39 | 0/8 2 h-lim-p 0.0007 0.0052 30.8997 3099.949107 6 0.0002 65 | 0/8 3 h-lim-p 0.0012 0.0406 5.4430 3099.947077 2 0.0001 83 | 0/8 4 h-lim-p 0.0005 0.0853 1.6144 3099.946830 2 0.0002 99 | 0/8 5 h-lim-p 0.0017 0.3982 0.1930 3099.946826 0 0.0002 113 | 0/8 6 h-lim-p 0.0017 7.3070 0.0249 3099.946826 0 0.0004 134 | 0/8 7 h-lim-p 0.0082 20.0000 0.0011 3099.946826 0 0.0009 156 | 0/8 8 h-lim-p 0.0087 20.0000 0.0001 3099.946824 0 0.2781 181 | 0/8 9 h-lim-p 0.6148 20.0000 0.0001 3099.946824 0 1.2295 202 | 0/8 10 h-lim-p 2.4581 20.0000 0.0000 3099.946824 0 2.1509 222 | 0/8 11 h-lim-p 1.6381 20.0000 0.0000 3099.946824 0 1.4333 242 | 0/8 12 h-lim-p 0.1925 20.0000 0.0003 3099.946824 0 0.0007 269 | 0/8 13 h-lim-p 0.0003 20.0000 0.0006 3099.946824 0 0.0000 294 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 3099.946824 0 0.0001 314 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 3099.946824 0 0.0000 352 | 0/8 16 h-lim-p 0.0000 20.0000 0.0010 | 0/8 17 h-lim-p 0.0000 20.0000 0.0010 Out... lnL = -3099.946824 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3099.946824 Node 7: lnL = -3099.946824 Node 8: lnL = -3099.946824 Node 9: lnL = -3099.946824 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 861 Sequential format.. Reading seq # 1: YBL086C_Sbay Reading seq # 2: YBL086C_Scer Reading seq # 3: YBL086C_Skud Reading seq # 4: YBL086C_Smik Reading seq # 5: YBL086C_Spar Sequences read.. Counting patterns.. # site patterns = 382 Counting frequencies.. 120 bytes for distance 61120 bytes for lkl0 48896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.272644 0.085590 0.073013 0.226622 0.148864 0.246109 0.267567 0.103501 lnL0 = -4359.213700 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4359.213700 x= 0.27264 0.08559 0.07301 0.22662 0.14886 0.24611 0.26757 0.10350 1 h-lim-p 0.0013 0.0103 159.6737 4356.088442 3 0.0003 29 | 0/8 2 h-lim-p 0.0007 0.0057 33.0628 4355.852758 7 0.0004 59 | 0/8 3 h-lim-p 0.0011 0.0293 13.6088 4355.808232 6 0.0006 86 | 0/8 4 h-lim-p 0.0025 0.1151 3.0152 4355.805371 3 0.0007 105 | 0/8 5 h-lim-p 0.0038 0.4009 0.5311 4355.805300 3 0.0005 125 | 0/8 6 h-lim-p 0.0048 5.1736 0.0558 4355.805299 0 0.0011 146 | 0/8 7 h-lim-p 0.0131 20.0000 0.0045 4355.805299 0 0.0033 167 | 0/8 8 h-lim-p 0.0249 20.0000 0.0006 4355.805260 0 0.2990 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4355.805259 0 1.0938 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4355.805259 0 1.0938 230 | 0/8 11 h-lim-p 1.0768 20.0000 0.0000 4355.805259 0 0.0000 277 | 0/8 12 h-lim-p 0.0000 20.0000 0.0007 4355.805259 0 0.0000 299 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 4355.805259 0 0.0000 322 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 4355.805259 0 0.0000 356 | 0/8 15 h-lim-p 0.0000 20.0000 0.0007 | 0/8 16 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -4355.805259 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4355.805259 Node 7: lnL = -4355.805259 Node 8: lnL = -4355.805259 Node 9: lnL = -4355.805259 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 497 Sequential format.. Reading seq # 1: YBL087C_Sbay Reading seq # 2: YBL087C_Scer Reading seq # 3: YBL087C_Skud Reading seq # 4: YBL087C_Smik Reading seq # 5: YBL087C_Spar Sequences read.. Counting patterns.. # site patterns = 274 Counting frequencies.. 120 bytes for distance 43840 bytes for lkl0 35072 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.276643 0.081104 0.000060 0.820642 0.273398 0.327756 0.239362 0.049157 lnL0 = -2615.550044 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2615.550044 x= 0.27664 0.08110 0.00006 0.82064 0.27340 0.32776 0.23936 0.04916 1 h-lim-p 0.0000 0.0000 83.5199 2615.538129 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0118 56.5032 2614.218245 0 0.0013 41 | 1/8 3 h-lim-p 0.0021 0.0166 22.1402 2613.654447 0 0.0031 53 | 1/8 4 h-lim-p 0.0024 0.0189 25.7253 2613.362389 6 0.0018 77 | 1/8 5 h-lim-p 0.0039 0.0308 8.2470 2613.314912 5 0.0017 98 | 1/8 6 h-lim-p 0.0154 0.4512 0.9081 2613.278365 3 0.0128 116 | 1/8 7 h-lim-p 0.0075 0.2503 1.5483 2610.852328 0 0.1205 139 | 1/8 8 h-lim-p 2.0284 16.2275 0.0141 2610.811546 6 0.7413 165 | 1/8 9 h-lim-p 2.5000 20.0000 0.0035 2610.810155 5 0.9027 196 | 1/8 10 h-lim-p 2.5000 20.0000 0.0004 2610.810142 1 0.9961 217 | 1/8 11 h-lim-p 2.5000 20.0000 0.0001 2610.810141 0 1.0938 236 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 2610.810141 0 1.0938 255 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 2610.810141 0 1.0938 274 | 1/8 14 h-lim-p 1.8286 20.0000 0.0000 2610.810141 0 0.4572 294 | 1/8 15 h-lim-p 0.2198 20.0000 0.0000 2610.810141 0 0.2198 313 | 1/8 16 h-lim-p 0.1083 20.0000 0.0000 2610.810141 0 0.0000 351 Out... lnL = -2610.810141 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2610.810141 Node 7: lnL = -2610.810141 Node 8: lnL = -2610.810141 Node 9: lnL = -2610.810141 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 210 Sequential format.. Reading seq # 1: YBL090W_Sbay Reading seq # 2: YBL090W_Scer Reading seq # 3: YBL090W_Skud Reading seq # 4: YBL090W_Smik Reading seq # 5: YBL090W_Spar Sequences read.. Counting patterns.. # site patterns = 105 Counting frequencies.. 120 bytes for distance 16800 bytes for lkl0 13440 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.216938 0.130650 0.072970 0.108501 0.084416 0.110869 0.181173 0.093115 lnL0 = -923.677082 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 923.677082 x= 0.21694 0.13065 0.07297 0.10850 0.08442 0.11087 0.18117 0.09312 1 h-lim-p 0.0011 0.0084 22.2866 923.434504 2 0.0010 26 | 0/8 2 h-lim-p 0.0040 0.0324 4.5706 923.425794 5 0.0009 48 | 0/8 3 h-lim-p 0.0041 0.2305 0.9690 923.425371 2 0.0010 65 | 0/8 4 h-lim-p 0.0020 0.4430 0.4749 923.425288 2 0.0009 89 | 0/8 5 h-lim-p 0.0116 4.1838 0.0375 923.425287 1 0.0007 114 | 0/8 6 h-lim-p 0.0017 12.1546 0.0153 923.425287 0 0.0015 134 | 0/8 7 h-lim-p 0.0073 20.0000 0.0032 923.425287 0 0.0032 154 | 0/8 8 h-lim-p 0.0431 20.0000 0.0002 923.425282 0 0.5173 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 923.425282 0 1.0938 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 923.425282 0 1.0938 217 | 0/8 11 h-lim-p 1.1180 20.0000 0.0000 923.425282 0 0.2795 238 | 0/8 12 h-lim-p 0.0490 20.0000 0.0000 923.425282 0 0.0980 259 | 0/8 13 h-lim-p 0.0369 20.0000 0.0001 923.425282 0 0.0000 302 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -923.425282 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -923.425282 Node 7: lnL = -923.425282 Node 8: lnL = -923.425282 Node 9: lnL = -923.425282 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 210 Sequential format.. Reading seq # 1: YBL091C_Sbay Reading seq # 2: YBL091C_Scer Reading seq # 3: YBL091C_Skud Reading seq # 4: YBL091C_Smik Reading seq # 5: YBL091C_Spar Sequences read.. Counting patterns.. # site patterns = 106 Counting frequencies.. 120 bytes for distance 16960 bytes for lkl0 13568 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.219591 0.108733 0.103291 0.107465 0.085452 0.105392 0.165867 0.096059 lnL0 = -924.546410 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 924.546410 x= 0.21959 0.10873 0.10329 0.10746 0.08545 0.10539 0.16587 0.09606 1 h-lim-p 0.0013 0.0105 26.4139 924.201351 7 0.0010 35 | 0/8 2 h-lim-p 0.0022 0.0176 7.0499 924.179306 7 0.0009 61 | 0/8 3 h-lim-p 0.0049 0.1775 1.3562 924.178122 5 0.0013 84 | 0/8 4 h-lim-p 0.0036 0.3215 0.5026 924.178036 2 0.0008 101 | 0/8 5 h-lim-p 0.0026 2.8202 0.1497 924.178025 1 0.0010 123 | 0/8 6 h-lim-p 0.0030 3.7638 0.0526 924.178024 1 0.0007 146 | 0/8 7 h-lim-p 0.0050 20.0000 0.0076 924.178024 0 0.0022 166 | 0/8 8 h-lim-p 0.1392 20.0000 0.0001 924.178019 0 1.1134 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 924.178019 0 1.0938 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 924.178019 0 1.0938 229 | 0/8 11 h-lim-p 1.2603 20.0000 0.0000 924.178019 0 1.8904 249 | 0/8 12 h-lim-p 1.3247 20.0000 0.0000 924.178019 0 1.1591 269 | 0/8 13 h-lim-p 0.0486 20.0000 0.0001 924.178019 0 0.0015 293 | 0/8 14 h-lim-p 0.0001 20.0000 0.0014 924.178019 0 0.0001 313 | 0/8 15 h-lim-p 0.0007 20.0000 0.0003 924.178019 0 0.0002 334 | 0/8 16 h-lim-p 0.0001 20.0000 0.0007 924.178019 0 0.0001 355 | 0/8 17 h-lim-p 0.0002 20.0000 0.0005 924.178019 0 0.0001 376 | 0/8 18 h-lim-p 0.0004 20.0000 0.0001 924.178019 0 0.0002 396 | 0/8 19 h-lim-p 0.0003 20.0000 0.0000 924.178019 0 0.0000 418 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 924.178019 0 0.0000 447 | 0/8 21 h-lim-p 0.0000 20.0000 0.0001 | 0/8 22 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -924.178019 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -924.178019 Node 7: lnL = -924.178019 Node 8: lnL = -924.178019 Node 9: lnL = -924.178019 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 864 Sequential format.. Reading seq # 1: YBL093C_Sbay Reading seq # 2: YBL093C_Scer Reading seq # 3: YBL093C_Skud Reading seq # 4: YBL093C_Smik Reading seq # 5: YBL093C_Spar Sequences read.. Counting patterns.. # site patterns = 244 Counting frequencies.. 120 bytes for distance 39040 bytes for lkl0 31232 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.139149 0.028805 0.056673 0.086056 0.086248 0.130300 0.174615 0.049767 lnL0 = -3462.032588 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3462.032588 x= 0.13915 0.02881 0.05667 0.08606 0.08625 0.13030 0.17461 0.04977 1 h-lim-p 0.0008 0.0344 293.1308 3458.616734 3 0.0001 30 | 0/8 2 h-lim-p 0.0009 0.0069 19.1657 3458.575514 4 0.0002 51 | 0/8 3 h-lim-p 0.0008 0.0495 5.0591 3458.573693 4 0.0002 74 | 0/8 4 h-lim-p 0.0011 0.2519 0.6792 3458.573644 2 0.0002 91 | 0/8 5 h-lim-p 0.0005 0.8606 0.3309 3458.573633 2 0.0002 116 | 0/8 6 h-lim-p 0.0016 3.2755 0.0478 3458.573632 1 0.0004 139 | 0/8 7 h-lim-p 0.0021 16.4523 0.0094 3458.573592 0 0.0165 162 | 0/8 8 h-lim-p 0.0017 0.6578 0.0892 3458.571665 0 0.0069 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3458.571613 2 0.9961 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3458.571613 0 1.0938 228 | 0/8 11 h-lim-p 1.0597 20.0000 0.0000 3458.571613 0 0.2649 249 | 0/8 12 h-lim-p 0.0134 20.0000 0.0006 3458.571613 0 0.0134 269 | 0/8 13 h-lim-p 0.0043 20.0000 0.0018 3458.571613 0 0.0001 293 | 0/8 14 h-lim-p 0.0004 20.0000 0.0006 3458.571613 0 0.0000 317 | 0/8 15 h-lim-p 0.0000 20.0000 0.0010 3458.571613 0 0.0000 352 | 0/8 16 h-lim-p 0.0000 20.0000 0.0009 | 0/8 17 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -3458.571613 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3458.571613 Node 7: lnL = -3458.571613 Node 8: lnL = -3458.571613 Node 9: lnL = -3458.571613 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 199 Sequential format.. Reading seq # 1: YBL095W_Sbay Reading seq # 2: YBL095W_Scer Reading seq # 3: YBL095W_Skud Reading seq # 4: YBL095W_Smik Reading seq # 5: YBL095W_Spar Sequences read.. Counting patterns.. # site patterns = 89 Counting frequencies.. 120 bytes for distance 14240 bytes for lkl0 11392 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.173882 0.000060 0.099334 0.078071 0.048227 0.171323 0.144404 0.085089 lnL0 = -716.510953 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 716.510953 x= 0.17388 0.00006 0.09933 0.07807 0.04823 0.17132 0.14440 0.08509 1 h-lim-p 0.0001 0.0012 111.6326 710.966341 m 0.0012 22 | 0/8 2 h-lim-p 0.0003 0.0021 71.8487 710.491067 1 0.0003 36 | 0/8 3 h-lim-p 0.0003 0.0025 27.8808 710.304358 0 0.0006 49 | 0/8 4 h-lim-p 0.0022 0.0201 7.9342 710.271330 4 0.0011 70 | 0/8 5 h-lim-p 0.0042 0.0335 1.4086 710.269499 5 0.0014 94 | 0/8 6 h-lim-p 0.0047 0.7276 0.4053 710.259781 0 0.0188 108 | 0/8 7 h-lim-p 0.0173 0.2489 0.4408 709.908732 0 0.0691 130 | 0/8 8 h-lim-p 0.0115 0.1170 2.6486 709.901268 6 0.0021 165 | 0/8 9 h-lim-p 1.2223 18.0058 0.0045 709.864261 0 1.8334 177 | 0/8 10 h-lim-p 2.5000 20.0000 0.0028 709.858517 2 1.1719 201 | 0/8 11 h-lim-p 2.5000 20.0000 0.0006 709.858242 3 1.0004 227 | 0/8 12 h-lim-p 2.5000 20.0000 0.0001 709.858238 1 0.9961 249 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 709.858238 0 1.0938 269 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 709.858238 0 0.2734 291 | 0/8 15 h-lim-p 0.1595 20.0000 0.0000 709.858238 0 0.0050 315 | 0/8 16 h-lim-p 0.0029 20.0000 0.0000 709.858238 0 0.0000 340 Out... lnL = -709.858238 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -709.858238 Node 7: lnL = -709.858238 Node 8: lnL = -709.858238 Node 9: lnL = -709.858238 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 473 Sequential format.. Reading seq # 1: YBL098W_Sbay Reading seq # 2: YBL098W_Scer Reading seq # 3: YBL098W_Skud Reading seq # 4: YBL098W_Smik Reading seq # 5: YBL098W_Spar Sequences read.. Counting patterns.. # site patterns = 125 Counting frequencies.. 120 bytes for distance 20000 bytes for lkl0 16000 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.080754 0.000060 0.033809 0.051390 0.004846 0.075537 0.092330 0.034572 lnL0 = -1444.876923 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1444.876923 x= 0.08075 0.00006 0.03381 0.05139 0.00485 0.07554 0.09233 0.03457 1 h-lim-p 0.0000 0.0016 1162.4028 1435.866617 2 0.0000 26 | 0/8 2 h-lim-p 0.0001 0.0005 135.1731 1435.222739 1 0.0001 40 | 0/8 3 h-lim-p 0.0001 0.0011 52.6797 1435.060819 2 0.0001 56 | 0/8 4 h-lim-p 0.0013 0.0215 5.2882 1435.058598 4 0.0002 80 | 0/8 5 h-lim-p 0.0006 0.0573 1.4594 1435.058437 4 0.0002 102 | 0/8 6 h-lim-p 0.0070 3.7609 0.0344 1435.058409 1 0.0035 116 | 0/8 7 h-lim-p 0.0014 0.7016 0.0832 1435.057910 0 0.0058 138 | 0/8 8 h-lim-p 0.0015 0.0725 0.3199 1435.045803 0 0.0060 160 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 1435.041239 6 1.5246 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 1435.040787 3 1.2103 224 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1435.040787 0 1.0938 244 | 0/8 12 h-lim-p 1.0828 20.0000 0.0000 1435.040787 0 1.6242 264 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1435.040787 0 0.5469 285 | 0/8 14 h-lim-p 0.1824 20.0000 0.0001 1435.040787 0 0.0029 310 | 0/8 15 h-lim-p 0.0010 20.0000 0.0001 1435.040787 0 0.0000 352 | 0/8 16 h-lim-p 0.0000 20.0000 0.0032 | 0/8 17 h-lim-p 0.0000 20.0000 0.0032 Out... lnL = -1435.040787 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1435.040787 Node 7: lnL = -1435.040787 Node 8: lnL = -1435.040787 Node 9: lnL = -1435.040787 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 886 Sequential format.. Reading seq # 1: YBL101C_Sbay Reading seq # 2: YBL101C_Scer Reading seq # 3: YBL101C_Skud Reading seq # 4: YBL101C_Smik Reading seq # 5: YBL101C_Spar Sequences read.. Counting patterns.. # site patterns = 303 Counting frequencies.. 120 bytes for distance 48480 bytes for lkl0 38784 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.255332 0.032671 0.077190 0.091229 0.086755 0.226380 0.246608 0.114046 lnL0 = -3916.722105 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3916.722105 x= 0.25533 0.03267 0.07719 0.09123 0.08676 0.22638 0.24661 0.11405 1 h-lim-p 0.0024 0.7018 180.5798 3914.117266 9 0.0002 49 | 0/8 2 h-lim-p 0.0007 0.0053 28.9762 3914.021171 5 0.0002 73 | 0/8 3 h-lim-p 0.0004 0.0108 15.7648 3913.986236 3 0.0004 91 | 0/8 4 h-lim-p 0.0016 0.0694 3.6232 3913.984327 3 0.0003 110 | 0/8 5 h-lim-p 0.0015 0.3045 0.7662 3913.984219 2 0.0004 127 | 0/8 6 h-lim-p 0.0008 0.9362 0.3845 3913.984188 2 0.0005 152 | 0/8 7 h-lim-p 0.0076 20.0000 0.0252 3913.984188 0 0.0009 174 | 0/8 8 h-lim-p 0.0519 20.0000 0.0005 3913.983940 0 0.8300 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3913.983936 0 1.0938 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3913.983936 0 1.0938 238 | 0/8 11 h-lim-p 1.1974 20.0000 0.0000 3913.983936 0 1.1974 258 | 0/8 12 h-lim-p 0.8279 20.0000 0.0000 3913.983936 0 3.3118 280 | 0/8 13 h-lim-p 0.0226 20.0000 0.0021 3913.983936 0 0.0057 301 | 0/8 14 h-lim-p 0.0011 16.4284 0.0105 3913.983936 0 0.0000 336 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 3913.983936 0 0.0000 369 Out... lnL = -3913.983936 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3913.983936 Node 7: lnL = -3913.983936 Node 8: lnL = -3913.983936 Node 9: lnL = -3913.983936 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 584 Sequential format.. Reading seq # 1: YBL102W_Sbay Reading seq # 2: YBL102W_Scer Reading seq # 3: YBL102W_Skud Reading seq # 4: YBL102W_Smik Reading seq # 5: YBL102W_Spar Sequences read.. Counting patterns.. # site patterns = 188 Counting frequencies.. 120 bytes for distance 30080 bytes for lkl0 24064 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.185135 0.069077 0.046999 0.081407 0.086623 0.212365 0.169384 0.068589 lnL0 = -2555.471609 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2555.471609 x= 0.18513 0.06908 0.04700 0.08141 0.08662 0.21236 0.16938 0.06859 1 h-lim-p 0.0072 0.1318 84.0973 2554.952082 8 0.0002 46 | 0/8 2 h-lim-p 0.0015 0.0221 8.6280 2554.940952 5 0.0003 70 | 0/8 3 h-lim-p 0.0006 0.0487 4.6414 2554.938562 3 0.0003 88 | 0/8 4 h-lim-p 0.0016 0.4152 0.7867 2554.938438 2 0.0004 105 | 0/8 5 h-lim-p 0.0022 0.9124 0.1549 2554.938435 1 0.0003 129 | 0/8 6 h-lim-p 0.0026 10.2503 0.0157 2554.938435 0 0.0003 151 | 0/8 7 h-lim-p 0.0011 20.0000 0.0045 2554.938435 0 0.0005 171 | 0/8 8 h-lim-p 0.1214 20.0000 0.0000 2554.938434 0 0.9713 194 | 0/8 9 h-lim-p 1.0759 20.0000 0.0000 2554.938434 0 0.9414 214 | 0/8 10 h-lim-p 0.7561 20.0000 0.0000 2554.938434 0 0.0007 243 | 0/8 11 h-lim-p 0.0001 20.0000 0.0002 2554.938434 0 0.0000 263 | 0/8 12 h-lim-p 0.0001 20.0000 0.0001 2554.938434 0 0.0000 292 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 2554.938434 0 0.0000 328 Out... lnL = -2554.938434 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2554.938434 Node 7: lnL = -2554.938434 Node 8: lnL = -2554.938434 Node 9: lnL = -2554.938434 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 585 Sequential format.. Reading seq # 1: YBL103C_Sbay Reading seq # 2: YBL103C_Scer Reading seq # 3: YBL103C_Skud Reading seq # 4: YBL103C_Smik Reading seq # 5: YBL103C_Spar Sequences read.. Counting patterns.. # site patterns = 186 Counting frequencies.. 120 bytes for distance 29760 bytes for lkl0 23808 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.191927 0.067222 0.048008 0.082409 0.085621 0.212813 0.173046 0.073632 lnL0 = -2568.901262 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2568.901262 x= 0.19193 0.06722 0.04801 0.08241 0.08562 0.21281 0.17305 0.07363 1 h-lim-p 0.0055 0.0443 78.6692 2568.425990 2 0.0002 30 | 0/8 2 h-lim-p 0.0012 0.0167 10.6500 2568.408842 4 0.0003 51 | 0/8 3 h-lim-p 0.0007 0.0874 4.8720 2568.406451 5 0.0002 74 | 0/8 4 h-lim-p 0.0015 0.3196 0.7924 2568.406354 2 0.0003 91 | 0/8 5 h-lim-p 0.0011 0.9600 0.2293 2568.406343 1 0.0004 113 | 0/8 6 h-lim-p 0.0017 3.1532 0.0580 2568.406343 0 0.0004 134 | 0/8 7 h-lim-p 0.0107 20.0000 0.0021 2568.406343 0 0.0047 154 | 0/8 8 h-lim-p 0.0181 20.0000 0.0005 2568.406328 0 0.1449 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2568.406328 0 1.0938 197 | 0/8 10 h-lim-p 1.4501 20.0000 0.0000 2568.406328 0 1.4501 217 | 0/8 11 h-lim-p 1.8186 20.0000 0.0000 2568.406328 0 0.0249 242 | 0/8 12 h-lim-p 0.0069 20.0000 0.0000 2568.406328 0 0.0069 262 | 0/8 13 h-lim-p 0.0032 20.0000 0.0001 2568.406328 0 0.0000 304 | 0/8 14 h-lim-p 0.0000 20.0000 0.0018 2568.406328 0 0.0000 327 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 2568.406328 0 0.0026 355 | 0/8 16 h-lim-p 0.0059 20.0000 0.0001 2568.406328 0 0.0000 382 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 2568.406328 0 0.0000 402 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 2568.406328 0 0.0000 432 | 0/8 19 h-lim-p 0.0000 20.0000 0.0026 2568.406328 0 0.0000 459 | 0/8 20 h-lim-p 0.0000 20.0000 0.0004 2568.406328 0 0.0006 485 | 0/8 21 h-lim-p 0.0018 20.0000 0.0001 2568.406328 0 0.0001 508 | 0/8 22 h-lim-p 0.0003 20.0000 0.0001 2568.406328 0 0.0000 530 | 0/8 23 h-lim-p 0.0001 20.0000 0.0000 2568.406328 0 0.0000 552 | 0/8 24 h-lim-p 0.0000 20.0000 0.0002 2568.406328 0 0.0000 582 | 0/8 25 h-lim-p 0.0000 20.0000 0.0027 2568.406328 0 0.0000 608 | 0/8 26 h-lim-p 0.0000 20.0000 0.0001 2568.406328 0 0.0000 643 | 0/8 27 h-lim-p 0.0000 20.0000 0.0027 | 0/8 28 h-lim-p 0.0000 20.0000 0.0027 Out... lnL = -2568.406328 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2568.406328 Node 7: lnL = -2568.406328 Node 8: lnL = -2568.406328 Node 9: lnL = -2568.406328 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 863 Sequential format.. Reading seq # 1: YBL104C_Sbay Reading seq # 2: YBL104C_Scer Reading seq # 3: YBL104C_Skud Reading seq # 4: YBL104C_Smik Reading seq # 5: YBL104C_Spar Sequences read.. Counting patterns.. # site patterns = 349 Counting frequencies.. 120 bytes for distance 55840 bytes for lkl0 44672 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.287762 0.309838 0.116416 0.133050 0.129500 0.252845 0.236767 0.078237 lnL0 = -4201.998909 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4201.998909 x= 0.28776 0.30984 0.11642 0.13305 0.12950 0.25284 0.23677 0.07824 1 h-lim-p 0.0003 0.0021 81.4589 4200.728315 0 0.0004 22 | 0/8 2 h-lim-p 0.0013 0.0281 24.5267 4200.579526 5 0.0005 46 | 0/8 3 h-lim-p 0.0005 0.0177 26.5823 4200.478733 3 0.0005 64 | 0/8 4 h-lim-p 0.0029 0.0667 4.6947 4200.470165 5 0.0008 88 | 0/8 5 h-lim-p 0.0017 0.0848 2.3045 4200.468419 2 0.0008 104 | 0/8 6 h-lim-p 0.0026 2.9068 0.7166 4200.468324 2 0.0004 123 | 0/8 7 h-lim-p 0.0270 20.0000 0.0114 4200.468315 0 0.0118 143 | 0/8 8 h-lim-p 0.0195 20.0000 0.0069 4200.467730 0 0.0780 165 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4200.467721 1 0.9961 187 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4200.467721 0 1.0938 207 | 0/8 11 h-lim-p 1.0345 20.0000 0.0000 4200.467721 0 0.7758 227 | 0/8 12 h-lim-p 0.0034 20.0000 0.0029 4200.467721 0 0.0538 251 | 0/8 13 h-lim-p 0.0238 17.1625 0.0066 4200.467721 0 0.0015 274 | 0/8 14 h-lim-p 0.0001 1.5955 0.0715 4200.467721 0 0.0000 301 | 0/8 15 h-lim-p 0.0005 20.0000 0.0001 4200.467721 0 0.0000 333 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -4200.467721 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4200.467721 Node 7: lnL = -4200.467721 Node 8: lnL = -4200.467721 Node 9: lnL = -4200.467721 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 386 Sequential format.. Reading seq # 1: YBL107C_Sbay Reading seq # 2: YBL107C_Scer Reading seq # 3: YBL107C_Skud Reading seq # 4: YBL107C_Smik Reading seq # 5: YBL107C_Spar Sequences read.. Counting patterns.. # site patterns = 198 Counting frequencies.. 120 bytes for distance 31680 bytes for lkl0 25344 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.264181 0.279866 0.125366 0.130158 0.159898 0.217024 0.418976 0.044516 lnL0 = -1768.133527 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1768.133527 x= 0.26418 0.27987 0.12537 0.13016 0.15990 0.21702 0.41898 0.04452 1 h-lim-p 0.0014 0.0113 36.1664 1767.499778 8 0.0010 42 | 0/8 2 h-lim-p 0.0018 0.0146 12.7722 1767.423544 7 0.0010 72 | 0/8 3 h-lim-p 0.0019 0.0405 6.8969 1767.386028 5 0.0020 95 | 0/8 4 h-lim-p 0.0065 0.1839 2.1452 1767.383278 3 0.0014 115 | 0/8 5 h-lim-p 0.0047 0.3256 0.6195 1767.382776 4 0.0029 139 | 0/8 6 h-lim-p 0.0527 20.0000 0.0342 1767.382775 0 0.0014 163 | 0/8 7 h-lim-p 0.0060 20.0000 0.0082 1767.382775 0 0.0060 183 | 0/8 8 h-lim-p 0.1983 20.0000 0.0002 1767.382760 0 0.7933 205 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1767.382760 0 1.0938 225 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1767.382760 0 1.0938 245 | 0/8 11 h-lim-p 1.1212 20.0000 0.0000 1767.382760 0 0.0175 270 | 0/8 12 h-lim-p 0.0017 20.0000 0.0001 1767.382760 0 0.0017 290 | 0/8 13 h-lim-p 0.0008 20.0000 0.0001 1767.382760 0 0.0000 316 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 1767.382760 0 0.0000 355 Out... lnL = -1767.382760 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1767.382760 Node 7: lnL = -1767.382760 Node 8: lnL = -1767.382760 Node 9: lnL = -1767.382760 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 244 Sequential format.. Reading seq # 1: YBR002C_Sbay Reading seq # 2: YBR002C_Scer Reading seq # 3: YBR002C_Skud Reading seq # 4: YBR002C_Smik Reading seq # 5: YBR002C_Spar Sequences read.. Counting patterns.. # site patterns = 81 Counting frequencies.. 120 bytes for distance 12960 bytes for lkl0 10368 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.137154 0.038722 0.034434 0.041362 0.034710 0.108353 0.155756 0.060013 lnL0 = -899.708767 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 899.708767 x= 0.13715 0.03872 0.03443 0.04136 0.03471 0.10835 0.15576 0.06001 1 h-lim-p 0.0002 0.0014 39.2616 899.547608 0 0.0003 22 | 0/8 2 h-lim-p 0.0010 0.0376 9.9196 899.533714 6 0.0003 49 | 0/8 3 h-lim-p 0.0004 0.0135 7.1521 899.527060 4 0.0004 68 | 0/8 4 h-lim-p 0.0012 0.0474 2.1935 899.526068 3 0.0005 86 | 0/8 5 h-lim-p 0.0019 0.3075 0.5434 899.525973 3 0.0007 106 | 0/8 6 h-lim-p 0.0034 0.6241 0.1082 899.525967 2 0.0005 132 | 0/8 7 h-lim-p 0.0142 20.0000 0.0034 899.520380 0 0.4540 157 | 0/8 8 h-lim-p 0.0051 0.6467 0.3045 899.520352 2 0.0006 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 899.520346 1 0.9961 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 899.520346 0 0.6250 226 | 0/8 11 h-lim-p 0.4524 20.0000 0.0000 899.520346 0 0.0007 255 | 0/8 12 h-lim-p 0.0004 20.0000 0.0000 899.520346 0 0.0000 289 | 0/8 13 h-lim-p 0.0000 20.0000 0.0036 | 0/8 14 h-lim-p 0.0000 20.0000 0.0036 Out... lnL = -899.520346 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -899.520346 Node 7: lnL = -899.520346 Node 8: lnL = -899.520346 Node 9: lnL = -899.520346 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 245 Sequential format.. Reading seq # 1: YBR003W_Sbay Reading seq # 2: YBR003W_Scer Reading seq # 3: YBR003W_Skud Reading seq # 4: YBR003W_Smik Reading seq # 5: YBR003W_Spar Sequences read.. Counting patterns.. # site patterns = 88 Counting frequencies.. 120 bytes for distance 14080 bytes for lkl0 11264 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.127902 0.052822 0.031593 0.036594 0.039477 0.087736 0.134574 0.055385 lnL0 = -865.353706 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 865.353706 x= 0.12790 0.05282 0.03159 0.03659 0.03948 0.08774 0.13457 0.05539 1 h-lim-p 0.0002 0.0018 62.2366 864.992621 2 0.0002 26 | 0/8 2 h-lim-p 0.0020 0.0166 6.5523 864.983234 3 0.0004 45 | 0/8 3 h-lim-p 0.0007 0.0443 3.9502 864.981870 6 0.0002 73 | 0/8 4 h-lim-p 0.0008 0.1138 1.1664 864.981570 3 0.0005 93 | 0/8 5 h-lim-p 0.0008 0.2415 0.7358 864.981513 3 0.0003 111 | 0/8 6 h-lim-p 0.0014 0.6917 0.1519 864.981508 2 0.0005 137 | 0/8 7 h-lim-p 0.0073 10.2337 0.0098 864.981507 0 0.0032 157 | 0/8 8 h-lim-p 0.0169 20.0000 0.0019 864.981255 0 0.2710 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 864.981226 2 0.9961 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 864.981226 0 2.5000 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 864.981226 0 0.0005 256 Out... lnL = -864.981226 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -864.981226 Node 7: lnL = -864.981226 Node 8: lnL = -864.981226 Node 9: lnL = -864.981226 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 252 Sequential format.. Reading seq # 1: YBR004C_Sbay Reading seq # 2: YBR004C_Scer Reading seq # 3: YBR004C_Skud Reading seq # 4: YBR004C_Smik Reading seq # 5: YBR004C_Spar Sequences read.. Counting patterns.. # site patterns = 102 Counting frequencies.. 120 bytes for distance 16320 bytes for lkl0 13056 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.168873 0.030339 0.032001 0.064713 0.073290 0.158554 0.155300 0.074808 lnL0 = -1000.560890 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1000.560890 x= 0.16887 0.03034 0.03200 0.06471 0.07329 0.15855 0.15530 0.07481 1 h-lim-p 0.0029 0.1076 83.4964 999.743053 8 0.0003 45 | 0/8 2 h-lim-p 0.0015 0.0122 10.3238 999.708989 6 0.0006 72 | 0/8 3 h-lim-p 0.0010 0.0271 6.3770 999.699174 6 0.0006 100 | 0/8 4 h-lim-p 0.0022 0.0712 1.8064 999.698599 5 0.0004 124 | 0/8 5 h-lim-p 0.0115 3.7986 0.0619 999.698597 2 0.0009 143 | 0/8 6 h-lim-p 0.0096 16.1505 0.0059 999.698596 0 0.0042 163 | 0/8 7 h-lim-p 0.0052 20.0000 0.0048 999.698537 0 0.0832 187 | 0/8 8 h-lim-p 0.0027 16.6965 0.1497 999.698445 3 0.0021 213 | 0/8 9 h-lim-p 1.8780 20.0000 0.0002 999.698435 2 0.9885 238 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 999.698435 0 1.0938 258 | 0/8 11 h-lim-p 2.0908 20.0000 0.0000 999.698435 0 1.8294 278 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 999.698435 0 1.0938 298 | 0/8 13 h-lim-p 0.4802 20.0000 0.0000 999.698435 0 7.6838 322 | 0/8 14 h-lim-p 0.0713 20.0000 0.0007 999.698435 0 0.0357 342 | 0/8 15 h-lim-p 0.0097 20.0000 0.0027 999.698435 0 0.0024 363 | 0/8 16 h-lim-p 0.0011 18.3618 0.0059 999.698435 0 0.0000 392 | 0/8 17 h-lim-p 0.0001 20.0000 0.0000 999.698435 0 0.0001 412 | 0/8 18 h-lim-p 0.0001 20.0000 0.0000 999.698435 0 0.0000 439 | 0/8 19 h-lim-p 0.0000 20.0000 0.0003 | 0/8 20 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -999.698435 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -999.698435 Node 7: lnL = -999.698435 Node 8: lnL = -999.698435 Node 9: lnL = -999.698435 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 252 Sequential format.. Reading seq # 1: YBR005W_Sbay Reading seq # 2: YBR005W_Scer Reading seq # 3: YBR005W_Skud Reading seq # 4: YBR005W_Smik Reading seq # 5: YBR005W_Spar Sequences read.. Counting patterns.. # site patterns = 99 Counting frequencies.. 120 bytes for distance 15840 bytes for lkl0 12672 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.166564 0.017583 0.035246 0.061381 0.076622 0.155428 0.157845 0.074572 lnL0 = -992.495835 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 992.495835 x= 0.16656 0.01758 0.03525 0.06138 0.07662 0.15543 0.15784 0.07457 1 h-lim-p 0.0025 1.2812 88.6688 991.732053 9 0.0002 46 | 0/8 2 h-lim-p 0.0019 0.0152 4.7886 991.727226 5 0.0004 68 | 0/8 3 h-lim-p 0.0010 0.0998 1.9729 991.725974 5 0.0007 93 | 0/8 4 h-lim-p 0.0017 0.1258 0.8738 991.725815 4 0.0005 117 | 0/8 5 h-lim-p 0.0062 3.9648 0.0726 991.725813 1 0.0008 141 | 0/8 6 h-lim-p 0.0028 2.8203 0.0199 991.725813 0 0.0006 162 | 0/8 7 h-lim-p 0.0049 20.0000 0.0025 991.725813 0 0.0049 182 | 0/8 8 h-lim-p 0.0218 20.0000 0.0006 991.725793 0 0.1740 205 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 991.725792 0 1.0938 225 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 991.725792 0 2.1875 245 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 991.725792 0 1.0938 265 | 0/8 12 h-lim-p 0.4080 20.0000 0.0000 991.725792 0 3.2643 288 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 991.725792 0 0.0003 320 Out... lnL = -991.725792 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -991.725792 Node 7: lnL = -991.725792 Node 8: lnL = -991.725792 Node 9: lnL = -991.725792 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 996 Sequential format.. Reading seq # 1: YBR008C_Sbay Reading seq # 2: YBR008C_Scer Reading seq # 3: YBR008C_Skud Reading seq # 4: YBR008C_Smik Reading seq # 5: YBR008C_Spar Sequences read.. Counting patterns.. # site patterns = 420 Counting frequencies.. 120 bytes for distance 67200 bytes for lkl0 53760 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.244851 0.352973 0.075499 0.137128 0.127220 0.225815 0.296510 0.030244 lnL0 = -4768.769897 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4768.769897 x= 0.24485 0.35297 0.07550 0.13713 0.12722 0.22581 0.29651 0.03024 1 h-lim-p 0.0003 0.0024 134.4059 4765.713203 1 0.0004 24 | 0/8 2 h-lim-p 0.0006 0.0045 47.4630 4765.317203 6 0.0004 51 | 0/8 3 h-lim-p 0.0005 0.0072 39.2793 4765.090955 5 0.0005 73 | 0/8 4 h-lim-p 0.0013 0.0202 13.8559 4765.057652 6 0.0004 98 | 0/8 5 h-lim-p 0.0012 0.0509 5.1416 4765.046615 5 0.0010 119 | 0/8 6 h-lim-p 0.0365 2.2473 0.1392 4765.046596 2 0.0015 140 | 0/8 7 h-lim-p 0.0019 7.8374 0.1082 4765.046587 0 0.0010 160 | 0/8 8 h-lim-p 0.0238 20.0000 0.0044 4765.042390 0 0.3810 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 4765.042336 2 0.9961 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4765.042336 0 1.0938 228 | 0/8 11 h-lim-p 0.9076 20.0000 0.0000 4765.042336 0 0.7941 248 | 0/8 12 h-lim-p 0.1416 20.0000 0.0001 4765.042336 0 0.0089 271 | 0/8 13 h-lim-p 0.0027 20.0000 0.0004 4765.042336 0 0.0020 291 | 0/8 14 h-lim-p 0.0011 20.0000 0.0006 4765.042336 0 0.0003 312 | 0/8 15 h-lim-p 0.0003 20.0000 0.0007 4765.042336 0 0.0003 332 | 0/8 16 h-lim-p 0.0008 20.0000 0.0002 4765.042336 0 0.0001 355 | 0/8 17 h-lim-p 0.0010 20.0000 0.0000 4765.042336 0 0.0010 375 | 0/8 18 h-lim-p 0.0001 20.0000 0.0001 4765.042336 0 0.0000 407 | 0/8 19 h-lim-p 0.0000 20.0000 0.0003 | 0/8 20 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -4765.042336 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4765.042336 Node 7: lnL = -4765.042336 Node 8: lnL = -4765.042336 Node 9: lnL = -4765.042336 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 673 Sequential format.. Reading seq # 1: YBR009C_Sbay Reading seq # 2: YBR009C_Scer Reading seq # 3: YBR009C_Skud Reading seq # 4: YBR009C_Smik Reading seq # 5: YBR009C_Spar Sequences read.. Counting patterns.. # site patterns = 185 Counting frequencies.. 120 bytes for distance 29600 bytes for lkl0 23680 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.112669 0.048821 0.028350 0.071186 0.064612 0.134242 0.132783 0.029478 lnL0 = -2577.659853 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2577.659853 x= 0.11267 0.04882 0.02835 0.07119 0.06461 0.13424 0.13278 0.02948 1 h-lim-p 0.0009 0.0071 227.8316 2575.396999 5 0.0001 33 | 0/8 2 h-lim-p 0.0002 0.0020 42.1399 2575.239568 7 0.0002 61 | 0/8 3 h-lim-p 0.0007 0.0123 10.8566 2575.228941 5 0.0002 84 | 0/8 4 h-lim-p 0.0005 0.0427 4.4347 2575.227211 2 0.0002 100 | 0/8 5 h-lim-p 0.0013 0.2929 0.7036 2575.227167 3 0.0002 120 | 0/8 6 h-lim-p 0.0021 1.0236 0.0594 2575.227167 0 0.0002 142 | 0/8 7 h-lim-p 0.0011 20.0000 0.0127 2575.227167 0 0.0009 162 | 0/8 8 h-lim-p 0.0265 20.0000 0.0004 2575.227023 0 0.4236 186 | 0/8 9 h-lim-p 1.9613 20.0000 0.0001 2575.227020 1 0.9653 209 | 0/8 10 h-lim-p 1.8910 20.0000 0.0000 2575.227020 0 1.6546 229 | 0/8 11 h-lim-p 1.4391 20.0000 0.0001 2575.227020 0 1.2592 249 | 0/8 12 h-lim-p 0.0485 20.0000 0.0015 2575.227020 0 0.0002 276 | 0/8 13 h-lim-p 0.0004 20.0000 0.0007 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0021 2575.227020 0 0.0000 343 | 0/8 15 h-lim-p 0.0000 20.0000 0.0006 2575.227020 0 0.0010 369 | 0/8 16 h-lim-p 0.0058 20.0000 0.0001 2575.227020 0 0.0000 401 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 2575.227020 0 0.0000 427 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 2575.227020 0 0.0000 462 | 0/8 19 h-lim-p 0.0000 20.0000 0.0043 | 0/8 20 h-lim-p 0.0000 20.0000 0.0043 Out... lnL = -2575.227020 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2575.227020 Node 7: lnL = -2575.227020 Node 8: lnL = -2575.227020 Node 9: lnL = -2575.227020 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 862 Sequential format.. Reading seq # 1: YBR011C_Sbay Reading seq # 2: YBR011C_Scer Reading seq # 3: YBR011C_Skud Reading seq # 4: YBR011C_Smik Reading seq # 5: YBR011C_Spar Sequences read.. Counting patterns.. # site patterns = 281 Counting frequencies.. 120 bytes for distance 44960 bytes for lkl0 35968 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.421291 0.008783 0.274462 0.028720 0.016651 0.299280 0.285635 0.209071 lnL0 = -4016.786518 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4016.786518 x= 0.42129 0.00878 0.27446 0.02872 0.01665 0.29928 0.28563 0.20907 1 h-lim-p 0.0003 0.0023 103.0894 4015.399985 2 0.0003 26 | 0/8 2 h-lim-p 0.0000 0.0004 89.7505 4015.221370 0 0.0001 38 | 0/8 3 h-lim-p 0.0001 0.0017 65.5045 4015.143431 6 0.0001 65 | 0/8 4 h-lim-p 0.0001 0.0108 33.3804 4014.850474 0 0.0010 80 | 0/8 5 h-lim-p 0.0059 0.0708 5.6223 4014.837137 6 0.0009 110 | 0/8 6 h-lim-p 0.0038 0.2857 1.3219 4014.836108 4 0.0012 132 | 0/8 7 h-lim-p 0.0177 6.2269 0.0906 4014.835879 2 0.0077 148 | 0/8 8 h-lim-p 0.0152 20.0000 0.0459 4014.810426 0 0.1216 171 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 4014.809851 0 1.0938 191 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 4014.809843 0 1.0938 211 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4014.809843 0 2.1875 231 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4014.809843 0 0.6250 252 | 0/8 13 h-lim-p 0.6998 20.0000 0.0000 4014.809843 0 0.0055 278 | 0/8 14 h-lim-p 0.0033 20.0000 0.0000 4014.809843 0 0.0000 306 Out... lnL = -4014.809843 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4014.809843 Node 7: lnL = -4014.809843 Node 8: lnL = -4014.809843 Node 9: lnL = -4014.809843 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 408 Sequential format.. Reading seq # 1: YBR014C_Sbay Reading seq # 2: YBR014C_Scer Reading seq # 3: YBR014C_Skud Reading seq # 4: YBR014C_Smik Reading seq # 5: YBR014C_Spar Sequences read.. Counting patterns.. # site patterns = 188 Counting frequencies.. 120 bytes for distance 30080 bytes for lkl0 24064 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.216369 0.097156 0.041282 0.098414 0.105949 0.235195 0.296582 0.062434 lnL0 = -1789.139927 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1789.139927 x= 0.21637 0.09716 0.04128 0.09841 0.10595 0.23520 0.29658 0.06243 1 h-lim-p 0.0012 0.0093 78.1229 1788.335710 8 0.0003 42 | 0/8 2 h-lim-p 0.0013 0.0106 12.9256 1788.289515 6 0.0006 68 | 0/8 3 h-lim-p 0.0013 0.0386 5.5856 1788.281830 4 0.0006 87 | 0/8 4 h-lim-p 0.0012 0.1664 2.5914 1788.279172 4 0.0010 107 | 0/8 5 h-lim-p 0.0051 0.7485 0.4973 1788.279033 0 0.0013 120 | 0/8 6 h-lim-p 0.0055 1.5970 0.1156 1788.279029 0 0.0007 142 | 0/8 7 h-lim-p 0.0042 7.4886 0.0188 1788.279029 0 0.0009 163 | 0/8 8 h-lim-p 0.3642 20.0000 0.0000 1788.279027 0 1.0925 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1788.279027 0 1.2500 204 | 0/8 10 h-lim-p 1.5458 20.0000 0.0000 1788.279027 0 1.3526 224 | 0/8 11 h-lim-p 1.1882 20.0000 0.0000 1788.279027 0 3.5646 245 | 0/8 12 h-lim-p 0.3873 20.0000 0.0001 1788.279027 0 0.0968 266 | 0/8 13 h-lim-p 0.0102 20.0000 0.0010 1788.279027 0 0.0003 290 | 0/8 14 h-lim-p 0.0000 5.1964 0.0155 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 1788.279027 0 0.0000 346 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0005 | 0/8 18 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -1788.279027 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1788.279027 Node 7: lnL = -1788.279027 Node 8: lnL = -1788.279027 Node 9: lnL = -1788.279027 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 420 Sequential format.. Reading seq # 1: YBR022W_Sbay Reading seq # 2: YBR022W_Scer Reading seq # 3: YBR022W_Skud Reading seq # 4: YBR022W_Smik Reading seq # 5: YBR022W_Spar Sequences read.. Counting patterns.. # site patterns = 167 Counting frequencies.. 120 bytes for distance 26720 bytes for lkl0 21376 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.189012 0.093349 0.023772 0.144353 0.114627 0.182289 0.151192 0.060839 lnL0 = -1812.103642 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1812.103642 x= 0.18901 0.09335 0.02377 0.14435 0.11463 0.18229 0.15119 0.06084 1 h-lim-p 0.0022 0.0189 129.1067 1810.791197 8 0.0002 43 | 0/8 2 h-lim-p 0.0013 0.0106 18.3831 1810.694526 2 0.0006 59 | 0/8 3 h-lim-p 0.0040 0.1747 2.7388 1810.692147 5 0.0006 84 | 0/8 4 h-lim-p 0.0024 0.3071 0.7421 1810.691997 2 0.0006 101 | 0/8 5 h-lim-p 0.0070 3.7850 0.0634 1810.691996 0 0.0008 123 | 0/8 6 h-lim-p 0.0035 20.0000 0.0138 1810.691995 0 0.0015 143 | 0/8 7 h-lim-p 0.0065 20.0000 0.0033 1810.691962 0 0.0518 166 | 0/8 8 h-lim-p 0.0014 1.6962 0.1244 1810.691814 0 0.0027 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1810.691802 0 1.0938 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1810.691801 0 1.2500 227 | 0/8 11 h-lim-p 2.0582 20.0000 0.0000 1810.691801 0 0.9005 247 | 0/8 12 h-lim-p 0.6895 20.0000 0.0000 1810.691801 0 0.0002 278 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 1810.691801 0 0.0000 298 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 1810.691801 0 0.0000 323 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 1810.691801 0 0.0000 351 Out... lnL = -1810.691801 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1810.691801 Node 7: lnL = -1810.691801 Node 8: lnL = -1810.691801 Node 9: lnL = -1810.691801 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 1016 Sequential format.. Reading seq # 1: YBR024W_Sbay Reading seq # 2: YBR024W_Scer Reading seq # 3: YBR024W_Skud Reading seq # 4: YBR024W_Smik Reading seq # 5: YBR024W_Spar Sequences read.. Counting patterns.. # site patterns = 443 Counting frequencies.. 120 bytes for distance 70880 bytes for lkl0 56704 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.351560 0.095820 0.164123 0.197586 0.152919 0.160988 0.451647 0.121622 lnL0 = -4762.400522 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4762.400522 x= 0.35156 0.09582 0.16412 0.19759 0.15292 0.16099 0.45165 0.12162 1 h-lim-p 0.0029 0.0231 125.2786 4758.541235 9 0.0005 45 | 0/8 2 h-lim-p 0.0008 0.0064 39.4447 4757.802434 0 0.0012 57 | 0/8 3 h-lim-p 0.0012 0.0098 28.3861 4757.693594 7 0.0004 87 | 0/8 4 h-lim-p 0.0012 0.0566 8.9286 4757.647775 5 0.0013 110 | 0/8 5 h-lim-p 0.0086 0.2940 1.3927 4757.646683 4 0.0011 132 | 0/8 6 h-lim-p 0.0033 1.1919 0.4634 4757.646436 3 0.0018 151 | 0/8 7 h-lim-p 0.0064 2.3611 0.1293 4757.646004 1 0.0064 173 | 0/8 8 h-lim-p 0.0101 20.0000 0.0812 4757.606512 0 0.0811 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0016 4757.605206 4 1.3122 225 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 4757.605205 0 1.0938 245 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4757.605205 0 1.0938 265 | 0/8 12 h-lim-p 1.1991 20.0000 0.0000 4757.605205 0 1.7986 285 | 0/8 13 h-lim-p 0.8844 20.0000 0.0000 4757.605205 0 0.0138 310 | 0/8 14 h-lim-p 0.0003 20.0000 0.0008 4757.605205 0 0.0001 330 | 0/8 15 h-lim-p 0.0015 20.0000 0.0001 4757.605205 0 0.0000 362 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -4757.605205 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4757.605205 Node 7: lnL = -4757.605205 Node 8: lnL = -4757.605205 Node 9: lnL = -4757.605205 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 840 Sequential format.. Reading seq # 1: YBR025C_Sbay Reading seq # 2: YBR025C_Scer Reading seq # 3: YBR025C_Skud Reading seq # 4: YBR025C_Smik Reading seq # 5: YBR025C_Spar Sequences read.. Counting patterns.. # site patterns = 323 Counting frequencies.. 120 bytes for distance 51680 bytes for lkl0 41344 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.188558 0.137029 0.057907 0.152645 0.090127 0.204161 0.241604 0.036689 lnL0 = -3919.815943 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3919.815943 x= 0.18856 0.13703 0.05791 0.15265 0.09013 0.20416 0.24160 0.03669 1 h-lim-p 0.0018 0.5981 206.8696 3916.103626 3 0.0002 30 | 0/8 2 h-lim-p 0.0009 0.0074 41.0669 3915.792834 3 0.0004 48 | 0/8 3 h-lim-p 0.0007 0.0092 22.7129 3915.734625 5 0.0003 71 | 0/8 4 h-lim-p 0.0029 0.1187 2.2704 3915.733295 4 0.0005 93 | 0/8 5 h-lim-p 0.0015 0.5138 0.7839 3915.733181 3 0.0004 112 | 0/8 6 h-lim-p 0.0025 0.9022 0.1287 3915.733178 1 0.0003 136 | 0/8 7 h-lim-p 0.0016 8.9265 0.0250 3915.733178 0 0.0014 156 | 0/8 8 h-lim-p 0.0490 20.0000 0.0007 3915.732820 0 0.7845 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3915.732789 1 0.9961 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3915.732789 0 1.2500 222 | 0/8 11 h-lim-p 1.4072 20.0000 0.0000 3915.732789 0 0.6156 242 | 0/8 12 h-lim-p 0.0804 20.0000 0.0002 3915.732789 0 0.0005 268 | 0/8 13 h-lim-p 0.0004 20.0000 0.0003 3915.732789 0 0.0000 299 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 3915.732789 0 0.0000 330 Out... lnL = -3915.732789 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3915.732789 Node 7: lnL = -3915.732789 Node 8: lnL = -3915.732789 Node 9: lnL = -3915.732789 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 29 Sequential format.. Reading seq # 1: YBR026C_Sbay Reading seq # 2: YBR026C_Scer Reading seq # 3: YBR026C_Skud Reading seq # 4: YBR026C_Smik Reading seq # 5: YBR026C_Spar Sequences read.. Counting patterns.. # site patterns = 8 Counting frequencies.. 120 bytes for distance 1280 bytes for lkl0 1024 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.472156 0.476529 0.019990 0.157111 0.095501 0.179950 4.050541 0.000060 lnL0 = -47.885237 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 47.885237 x= 0.47216 0.47653 0.01999 0.15711 0.09550 0.17995 4.05054 0.00006 1 h-lim-p 0.0007 0.0055 7.6257 47.563248 m 0.0055 22 | 1/8 2 h-lim-p 0.0000 0.0002 79.3324 47.458911 m 0.0002 34 | 1/8 3 h-lim-p 0.0036 20.0000 4.5191 .. | 1/8 4 h-lim-p 0.0000 0.0167 6.8289 46.672506 m 0.0167 88 | 2/8 5 h-lim-p 0.0004 0.0034 34.9058 46.079098 m 0.0034 100 | 3/8 6 h-lim-p 0.0012 0.0095 2.9521 45.966602 m 0.0095 112 | 4/8 7 h-lim-p 0.0574 20.0000 0.2238 45.747720 m20.0000 130 | 4/8 8 h-lim-p 2.5000 20.0000 0.0000 45.747720 0 2.5000 146 Out... lnL = -45.747720 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -45.747720 Node 7: lnL = -45.747720 Node 8: lnL = -45.747720 Node 9: lnL = -45.747720 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 405 Sequential format.. Reading seq # 1: YBR028C_Sbay Reading seq # 2: YBR028C_Scer Reading seq # 3: YBR028C_Skud Reading seq # 4: YBR028C_Smik Reading seq # 5: YBR028C_Spar Sequences read.. Counting patterns.. # site patterns = 149 Counting frequencies.. 120 bytes for distance 23840 bytes for lkl0 19072 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.188330 0.002312 0.074146 0.083848 0.055808 0.146318 0.172266 0.082139 lnL0 = -1561.505057 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1561.505057 x= 0.18833 0.00231 0.07415 0.08385 0.05581 0.14632 0.17227 0.08214 1 h-lim-p 0.0013 0.0118 154.4285 1560.056597 3 0.0002 30 | 0/8 2 h-lim-p 0.0008 0.0102 29.2891 1559.797820 4 0.0006 50 | 0/8 3 h-lim-p 0.0017 0.0236 10.9043 1559.780410 4 0.0003 71 | 0/8 4 h-lim-p 0.0007 0.0292 5.3179 1559.776416 4 0.0003 92 | 0/8 5 h-lim-p 0.0008 0.1030 2.3204 1559.775219 5 0.0005 117 | 0/8 6 h-lim-p 0.0061 1.5929 0.2089 1559.775209 2 0.0004 136 | 0/8 7 h-lim-p 0.0033 8.5800 0.0255 1559.775209 0 0.0014 156 | 0/8 8 h-lim-p 0.0533 20.0000 0.0007 1559.774738 0 0.8531 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1559.774729 1 0.9961 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1559.774729 0 1.0938 222 | 0/8 11 h-lim-p 1.3755 20.0000 0.0000 1559.774729 0 0.0027 250 | 0/8 12 h-lim-p 0.0011 20.0000 0.0000 1559.774729 0 0.0000 274 | 0/8 13 h-lim-p 0.0006 20.0000 0.0000 1559.774729 0 0.0000 306 Out... lnL = -1559.774729 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1559.774729 Node 7: lnL = -1559.774729 Node 8: lnL = -1559.774729 Node 9: lnL = -1559.774729 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 573 Sequential format.. Reading seq # 1: YBR029C_Sbay Reading seq # 2: YBR029C_Scer Reading seq # 3: YBR029C_Skud Reading seq # 4: YBR029C_Smik Reading seq # 5: YBR029C_Spar Sequences read.. Counting patterns.. # site patterns = 220 Counting frequencies.. 120 bytes for distance 35200 bytes for lkl0 28160 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.210878 0.094607 0.087510 0.113439 0.073062 0.187641 0.157436 0.073720 lnL0 = -2553.067065 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2553.067065 x= 0.21088 0.09461 0.08751 0.11344 0.07306 0.18764 0.15744 0.07372 1 h-lim-p 0.0010 0.0083 103.2785 2551.393538 5 0.0003 34 | 0/8 2 h-lim-p 0.0010 0.0076 18.6208 2551.297509 6 0.0006 61 | 0/8 3 h-lim-p 0.0015 0.0352 7.0009 2551.291363 5 0.0003 84 | 0/8 4 h-lim-p 0.0006 0.0667 3.2084 2551.289894 5 0.0004 108 | 0/8 5 h-lim-p 0.0020 0.7020 0.5545 2551.289824 2 0.0005 125 | 0/8 6 h-lim-p 0.0020 1.6126 0.1305 2551.289821 0 0.0004 146 | 0/8 7 h-lim-p 0.0044 18.6545 0.0132 2551.289819 0 0.0038 166 | 0/8 8 h-lim-p 0.0202 20.0000 0.0025 2551.289415 0 0.2430 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2551.289414 0 1.0938 209 | 0/8 10 h-lim-p 1.6240 20.0000 0.0000 2551.289414 0 1.4210 229 | 0/8 11 h-lim-p 2.1439 20.0000 0.0000 2551.289414 0 1.8759 249 | 0/8 12 h-lim-p 1.8221 20.0000 0.0000 2551.289414 0 0.7972 269 | 0/8 13 h-lim-p 0.3118 20.0000 0.0000 2551.289414 0 0.0146 293 | 0/8 14 h-lim-p 0.0031 20.0000 0.0001 2551.289414 0 0.0000 323 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 2551.289414 0 0.0000 356 Out... lnL = -2551.289414 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2551.289414 Node 7: lnL = -2551.289414 Node 8: lnL = -2551.289414 Node 9: lnL = -2551.289414 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 571 Sequential format.. Reading seq # 1: YBR030W_Sbay Reading seq # 2: YBR030W_Scer Reading seq # 3: YBR030W_Skud Reading seq # 4: YBR030W_Smik Reading seq # 5: YBR030W_Spar Sequences read.. Counting patterns.. # site patterns = 223 Counting frequencies.. 120 bytes for distance 35680 bytes for lkl0 28544 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.210984 0.084755 0.087904 0.103313 0.083187 0.193330 0.167624 0.067165 lnL0 = -2553.640441 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2553.640441 x= 0.21098 0.08475 0.08790 0.10331 0.08319 0.19333 0.16762 0.06717 1 h-lim-p 0.0057 1.1629 94.5667 2552.247912 2 0.0003 29 | 0/8 2 h-lim-p 0.0008 0.0064 18.6753 2552.170812 6 0.0005 56 | 0/8 3 h-lim-p 0.0010 0.0361 8.7955 2552.161215 6 0.0003 83 | 0/8 4 h-lim-p 0.0008 0.0855 3.2783 2552.159477 2 0.0004 99 | 0/8 5 h-lim-p 0.0029 0.8961 0.4260 2552.159427 2 0.0006 116 | 0/8 6 h-lim-p 0.0026 1.7604 0.0895 2552.159426 1 0.0003 140 | 0/8 7 h-lim-p 0.0011 11.7762 0.0253 2552.159425 0 0.0011 160 | 0/8 8 h-lim-p 0.0411 20.0000 0.0007 2552.159162 0 0.6579 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2552.159162 0 1.0938 204 | 0/8 10 h-lim-p 1.9172 20.0000 0.0000 2552.159162 0 1.6776 224 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2552.159162 0 1.0938 244 | 0/8 12 h-lim-p 0.4021 20.0000 0.0000 2552.159162 0 0.4021 264 | 0/8 13 h-lim-p 0.0168 20.0000 0.0003 2552.159162 0 0.0001 291 | 0/8 14 h-lim-p 0.0006 20.0000 0.0000 2552.159162 0 0.0000 318 | 0/8 15 h-lim-p 0.0004 20.0000 0.0000 2552.159162 0 0.0000 349 Out... lnL = -2552.159162 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2552.159162 Node 7: lnL = -2552.159162 Node 8: lnL = -2552.159162 Node 9: lnL = -2552.159162 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 286 Sequential format.. Reading seq # 1: YBR031W_Sbay Reading seq # 2: YBR031W_Scer Reading seq # 3: YBR031W_Skud Reading seq # 4: YBR031W_Smik Reading seq # 5: YBR031W_Spar Sequences read.. Counting patterns.. # site patterns = 119 Counting frequencies.. 120 bytes for distance 19040 bytes for lkl0 15232 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.150688 0.128529 0.040419 0.103468 0.105533 0.354845 0.196909 0.000060 lnL0 = -1094.701225 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1094.701225 x= 0.15069 0.12853 0.04042 0.10347 0.10553 0.35485 0.19691 0.00006 1 h-lim-p 0.0000 0.0000 32.0555 1094.671253 m 0.0000 22 | 1/8 2 h-lim-p 0.0001 0.0139 10.2851 1094.612594 0 0.0015 38 | 1/8 3 h-lim-p 0.0036 0.0557 4.2099 1094.605855 2 0.0009 55 | 1/8 4 h-lim-p 0.0039 0.1803 0.9107 1094.604541 2 0.0018 71 | 0/8 5 h-lim-p 0.0008 0.2735 2.0570 1094.599645 0 0.0024 91 | 0/8 6 h-lim-p 0.0016 0.0711 3.1815 1094.590332 0 0.0032 104 | 0/8 7 h-lim-p 0.0042 0.1128 2.4049 1094.580559 2 0.0039 120 | 0/8 8 h-lim-p 0.0088 0.4365 1.0757 1094.567487 2 0.0082 136 | 0/8 9 h-lim-p 0.0126 0.1008 0.3468 1094.302395 m 0.1008 148 | 0/8 10 h-lim-p 2.5000 20.0000 0.0059 1094.290571 2 1.1719 172 | 0/8 11 h-lim-p 2.5000 20.0000 0.0015 1094.290423 2 1.0938 196 | 0/8 12 h-lim-p 2.5000 20.0000 0.0001 1094.290417 1 0.9961 218 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1094.290417 0 1.0938 238 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1094.290417 0 1.2500 258 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1094.290417 0 0.1562 281 | 0/8 16 h-lim-p 0.1029 20.0000 0.0000 1094.290417 0 0.0096 304 Out... lnL = -1094.290417 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1094.290417 Node 7: lnL = -1094.290417 Node 8: lnL = -1094.290417 Node 9: lnL = -1094.290417 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 124 Sequential format.. Reading seq # 1: YBR033W_Sbay Reading seq # 2: YBR033W_Scer Reading seq # 3: YBR033W_Skud Reading seq # 4: YBR033W_Smik Reading seq # 5: YBR033W_Spar Sequences read.. Counting patterns.. # site patterns = 70 Counting frequencies.. 120 bytes for distance 11200 bytes for lkl0 8960 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.248237 0.035186 0.105694 0.085083 0.099898 0.180814 0.218751 0.096934 lnL0 = -574.928934 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 574.928934 x= 0.24824 0.03519 0.10569 0.08508 0.09990 0.18081 0.21875 0.09693 1 h-lim-p 0.0022 0.0177 21.8156 574.669130 7 0.0012 37 | 0/8 2 h-lim-p 0.0095 0.0796 2.6842 574.660185 5 0.0025 60 | 0/8 3 h-lim-p 0.0031 0.0740 2.1555 574.658272 5 0.0012 82 | 0/8 4 h-lim-p 0.0068 0.4830 0.3801 574.658032 4 0.0036 103 | 0/8 5 h-lim-p 0.0342 4.3186 0.0397 574.658030 0 0.0019 126 | 0/8 6 h-lim-p 0.0058 16.9091 0.0127 574.658030 0 0.0025 146 | 0/8 7 h-lim-p 0.1252 20.0000 0.0003 574.658030 0 0.0548 166 | 0/8 8 h-lim-p 0.0137 20.0000 0.0010 574.658029 0 0.0548 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 574.658029 0 1.0938 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 574.658029 0 1.0938 228 | 0/8 11 h-lim-p 1.0799 20.0000 0.0000 574.658029 0 0.0675 251 | 0/8 12 h-lim-p 0.0055 20.0000 0.0000 574.658029 0 0.0021 272 | 0/8 13 h-lim-p 0.0006 20.0000 0.0001 574.658029 0 0.0006 292 | 0/8 14 h-lim-p 0.0005 20.0000 0.0001 574.658029 0 0.0000 330 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -574.658029 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -574.658029 Node 7: lnL = -574.658029 Node 8: lnL = -574.658029 Node 9: lnL = -574.658029 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 308 Sequential format.. Reading seq # 1: YBR034C_Sbay Reading seq # 2: YBR034C_Scer Reading seq # 3: YBR034C_Skud Reading seq # 4: YBR034C_Smik Reading seq # 5: YBR034C_Spar Sequences read.. Counting patterns.. # site patterns = 128 Counting frequencies.. 120 bytes for distance 20480 bytes for lkl0 16384 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.177900 0.032534 0.073546 0.074356 0.105961 0.154808 0.120204 0.064306 lnL0 = -1244.337133 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1244.337133 x= 0.17790 0.03253 0.07355 0.07436 0.10596 0.15481 0.12020 0.06431 1 h-lim-p 0.0013 0.0105 81.5804 1243.291236 5 0.0003 33 | 0/8 2 h-lim-p 0.0008 0.0063 18.0605 1243.189697 6 0.0006 59 | 0/8 3 h-lim-p 0.0020 0.0431 5.9137 1243.181981 5 0.0005 81 | 0/8 4 h-lim-p 0.0018 0.1824 1.5884 1243.181332 5 0.0006 108 | 0/8 5 h-lim-p 0.0026 0.4653 0.3414 1243.181289 3 0.0008 129 | 0/8 6 h-lim-p 0.0034 3.0601 0.0756 1243.181287 1 0.0004 153 | 0/8 7 h-lim-p 0.0063 20.0000 0.0050 1243.181287 0 0.0014 174 | 0/8 8 h-lim-p 0.0475 20.0000 0.0001 1243.181277 0 0.7593 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1243.181276 0 1.0938 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1243.181276 0 2.1875 238 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1243.181276 0 1.0938 258 | 0/8 12 h-lim-p 0.2256 20.0000 0.0000 1243.181276 0 3.6100 282 | 0/8 13 h-lim-p 2.3919 20.0000 0.0000 1243.181276 0 0.0070 310 | 0/8 14 h-lim-p 0.0007 20.0000 0.0001 1243.181276 0 0.0002 331 | 0/8 15 h-lim-p 0.0002 20.0000 0.0001 1243.181276 0 0.0000 369 | 0/8 16 h-lim-p 0.0000 20.0000 0.0008 | 0/8 17 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -1243.181276 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1243.181276 Node 7: lnL = -1243.181276 Node 8: lnL = -1243.181276 Node 9: lnL = -1243.181276 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 851 Sequential format.. Reading seq # 1: YBR035C_Sbay Reading seq # 2: YBR035C_Scer Reading seq # 3: YBR035C_Skud Reading seq # 4: YBR035C_Smik Reading seq # 5: YBR035C_Spar Sequences read.. Counting patterns.. # site patterns = 263 Counting frequencies.. 120 bytes for distance 42080 bytes for lkl0 33664 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.185051 0.079691 0.038699 0.129386 0.052635 0.187909 0.141581 0.061044 lnL0 = -3575.398865 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3575.398865 x= 0.18505 0.07969 0.03870 0.12939 0.05263 0.18791 0.14158 0.06104 1 h-lim-p 0.0001 0.0012 264.4473 3571.686174 3 0.0001 28 | 0/8 2 h-lim-p 0.0001 0.0010 60.1023 3571.412856 0 0.0002 40 | 0/8 3 h-lim-p 0.0003 0.0094 33.1458 3571.335812 4 0.0002 61 | 0/8 4 h-lim-p 0.0011 0.0462 5.1561 3571.331277 5 0.0004 87 | 0/8 5 h-lim-p 0.0019 0.3812 0.9641 3571.331150 3 0.0003 108 | 0/8 6 h-lim-p 0.0025 1.2726 0.1097 3571.331137 2 0.0008 133 | 0/8 7 h-lim-p 0.0048 12.3269 0.0180 3571.329234 0 0.0774 157 | 0/8 8 h-lim-p 0.0015 0.2106 0.9314 3571.320847 0 0.0022 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 3571.320523 2 1.1719 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 3571.320517 0 1.0938 221 | 0/8 11 h-lim-p 2.1839 20.0000 0.0000 3571.320517 0 1.9110 241 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3571.320517 0 1.0938 261 | 0/8 13 h-lim-p 0.1072 20.0000 0.0000 3571.320517 0 2.5738 285 | 0/8 14 h-lim-p 0.3821 20.0000 0.0002 3571.320517 0 0.0119 309 | 0/8 15 h-lim-p 0.0014 20.0000 0.0015 3571.320517 0 0.0011 329 | 0/8 16 h-lim-p 0.0002 8.7926 0.0095 3571.320517 0 0.0000 354 | 0/8 17 h-lim-p 0.0003 20.0000 0.0001 3571.320517 0 0.0000 388 | 0/8 18 h-lim-p 0.0000 20.0000 0.0017 | 0/8 19 h-lim-p 0.0000 20.0000 0.0017 Out... lnL = -3571.320517 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3571.320517 Node 7: lnL = -3571.320517 Node 8: lnL = -3571.320517 Node 9: lnL = -3571.320517 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 873 Sequential format.. Reading seq # 1: YBR039W_Sbay Reading seq # 2: YBR039W_Scer Reading seq # 3: YBR039W_Skud Reading seq # 4: YBR039W_Smik Reading seq # 5: YBR039W_Spar Sequences read.. Counting patterns.. # site patterns = 297 Counting frequencies.. 120 bytes for distance 47520 bytes for lkl0 38016 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.230650 0.047890 0.052627 0.161271 0.128054 0.221172 0.259778 0.068808 lnL0 = -4010.932905 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4010.932905 x= 0.23065 0.04789 0.05263 0.16127 0.12805 0.22117 0.25978 0.06881 1 h-lim-p 0.0012 0.0097 164.0575 4008.932880 5 0.0002 34 | 0/8 2 h-lim-p 0.0008 0.0060 31.0137 4008.762528 2 0.0004 50 | 0/8 3 h-lim-p 0.0021 0.0306 5.3044 4008.758627 5 0.0003 75 | 0/8 4 h-lim-p 0.0017 0.3499 0.9115 4008.758458 2 0.0004 92 | 0/8 5 h-lim-p 0.0015 0.5508 0.2557 4008.758443 2 0.0005 117 | 0/8 6 h-lim-p 0.0022 2.9716 0.0542 4008.758443 0 0.0005 138 | 0/8 7 h-lim-p 0.0014 10.6070 0.0191 4008.758442 0 0.0012 158 | 0/8 8 h-lim-p 0.0305 20.0000 0.0008 4008.758299 0 0.4873 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4008.758296 0 1.0938 202 | 0/8 10 h-lim-p 2.4120 20.0000 0.0000 4008.758296 0 1.0553 222 | 0/8 11 h-lim-p 0.9891 20.0000 0.0000 4008.758296 0 0.0039 249 | 0/8 12 h-lim-p 0.0002 20.0000 0.0005 4008.758296 0 0.0000 287 | 0/8 13 h-lim-p 0.0000 20.0000 0.0008 4008.758296 0 0.0000 309 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0008 | 0/8 16 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -4008.758296 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4008.758296 Node 7: lnL = -4008.758296 Node 8: lnL = -4008.758296 Node 9: lnL = -4008.758296 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 503 Sequential format.. Reading seq # 1: YBR040W_Sbay Reading seq # 2: YBR040W_Scer Reading seq # 3: YBR040W_Skud Reading seq # 4: YBR040W_Smik Reading seq # 5: YBR040W_Spar Sequences read.. Counting patterns.. # site patterns = 150 Counting frequencies.. 120 bytes for distance 24000 bytes for lkl0 19200 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.153946 0.027496 0.035522 0.091700 0.052545 0.161482 0.138385 0.054837 lnL0 = -1899.070999 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1899.070999 x= 0.15395 0.02750 0.03552 0.09170 0.05254 0.16148 0.13839 0.05484 1 h-lim-p 0.0006 0.0048 151.9141 1897.659570 3 0.0001 29 | 0/8 2 h-lim-p 0.0006 0.0049 20.9844 1897.598474 2 0.0003 45 | 0/8 3 h-lim-p 0.0006 0.0269 9.9605 1897.589536 6 0.0002 72 | 0/8 4 h-lim-p 0.0008 0.0667 2.7695 1897.588339 2 0.0003 88 | 0/8 5 h-lim-p 0.0016 0.1696 0.5985 1897.588280 2 0.0003 105 | 0/8 6 h-lim-p 0.0015 0.8880 0.1365 1897.588277 0 0.0004 126 | 0/8 7 h-lim-p 0.0019 9.7103 0.0270 1897.588276 0 0.0008 146 | 0/8 8 h-lim-p 0.0532 20.0000 0.0004 1897.587997 0 0.8520 170 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1897.587993 1 0.9961 192 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1897.587993 0 2.5000 212 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1897.587993 0 0.0024 241 | 0/8 12 h-lim-p 0.0004 20.0000 0.0000 1897.587993 0 0.0000 279 | 0/8 13 h-lim-p 0.0000 20.0000 0.0029 1897.587993 0 0.0000 307 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 1897.587993 0 0.0026 335 | 0/8 15 h-lim-p 0.0037 20.0000 0.0002 1897.587993 0 0.0000 365 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 1897.587993 0 0.0000 392 | 0/8 17 h-lim-p 0.0000 20.0000 0.0038 | 0/8 18 h-lim-p 0.0000 20.0000 0.0038 Out... lnL = -1897.587993 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1897.587993 Node 7: lnL = -1897.587993 Node 8: lnL = -1897.587993 Node 9: lnL = -1897.587993 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 300 Sequential format.. Reading seq # 1: YBR042C_Sbay Reading seq # 2: YBR042C_Scer Reading seq # 3: YBR042C_Skud Reading seq # 4: YBR042C_Smik Reading seq # 5: YBR042C_Spar Sequences read.. Counting patterns.. # site patterns = 142 Counting frequencies.. 120 bytes for distance 22720 bytes for lkl0 18176 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.310775 0.126331 0.050810 0.102060 0.090574 0.137525 0.177202 0.147496 lnL0 = -1334.153881 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1334.153881 x= 0.31077 0.12633 0.05081 0.10206 0.09057 0.13753 0.17720 0.14750 1 h-lim-p 0.0006 0.0046 63.0836 1333.143064 6 0.0006 35 | 0/8 2 h-lim-p 0.0009 0.0071 28.0770 1332.894838 7 0.0007 65 | 0/8 3 h-lim-p 0.0017 0.0302 11.9604 1332.847604 2 0.0008 81 | 0/8 4 h-lim-p 0.0012 0.0308 7.7982 1332.825207 4 0.0011 100 | 0/8 5 h-lim-p 0.0030 0.0841 2.7672 1332.822813 4 0.0008 121 | 0/8 6 h-lim-p 0.0141 1.5635 0.1483 1332.822802 2 0.0009 140 | 0/8 7 h-lim-p 0.0086 20.0000 0.0160 1332.822800 2 0.0055 165 | 0/8 8 h-lim-p 0.0507 20.0000 0.0017 1332.822548 0 0.4052 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1332.822529 1 0.9961 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1332.822529 0 1.0938 230 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1332.822529 0 2.5000 250 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1332.822529 0 0.1562 273 | 0/8 13 h-lim-p 0.0850 20.0000 0.0000 1332.822529 0 0.0053 296 | 0/8 14 h-lim-p 0.0024 20.0000 0.0000 1332.822529 0 0.0006 317 Out... lnL = -1332.822529 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1332.822529 Node 7: lnL = -1332.822529 Node 8: lnL = -1332.822529 Node 9: lnL = -1332.822529 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 845 Sequential format.. Reading seq # 1: YBR044C_Sbay Reading seq # 2: YBR044C_Scer Reading seq # 3: YBR044C_Skud Reading seq # 4: YBR044C_Smik Reading seq # 5: YBR044C_Spar Sequences read.. Counting patterns.. # site patterns = 302 Counting frequencies.. 120 bytes for distance 48320 bytes for lkl0 38656 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.226668 0.018118 0.193789 0.127270 0.076619 0.207735 0.203733 0.064335 lnL0 = -3947.076710 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3947.076710 x= 0.22667 0.01812 0.19379 0.12727 0.07662 0.20773 0.20373 0.06433 1 h-lim-p 0.0016 0.0346 222.5307 3943.999625 7 0.0001 39 | 0/8 2 h-lim-p 0.0010 0.0083 26.8272 3943.844420 5 0.0004 62 | 0/8 3 h-lim-p 0.0012 0.0375 9.5244 3943.833378 5 0.0003 84 | 0/8 4 h-lim-p 0.0006 0.0279 4.4112 3943.831439 3 0.0002 102 | 0/8 5 h-lim-p 0.0019 0.2472 0.5682 3943.831371 2 0.0004 119 | 0/8 6 h-lim-p 0.0018 1.1902 0.1298 3943.831368 0 0.0004 140 | 0/8 7 h-lim-p 0.0070 20.0000 0.0074 3943.831367 0 0.0031 160 | 0/8 8 h-lim-p 0.0246 20.0000 0.0009 3943.831211 0 0.2954 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3943.831210 0 1.0938 203 | 0/8 10 h-lim-p 0.6551 20.0000 0.0000 3943.831210 0 0.6551 223 | 0/8 11 h-lim-p 0.4396 20.0000 0.0000 3943.831210 0 0.3846 243 | 0/8 12 h-lim-p 0.1793 20.0000 0.0001 3943.831210 0 0.0056 267 | 0/8 13 h-lim-p 0.0021 20.0000 0.0002 3943.831210 0 0.0021 287 | 0/8 14 h-lim-p 0.0008 20.0000 0.0005 3943.831210 0 0.0000 315 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 3943.831210 0 0.0000 339 Out... lnL = -3943.831210 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3943.831210 Node 7: lnL = -3943.831210 Node 8: lnL = -3943.831210 Node 9: lnL = -3943.831210 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 432 Sequential format.. Reading seq # 1: YBR045C_Sbay Reading seq # 2: YBR045C_Scer Reading seq # 3: YBR045C_Skud Reading seq # 4: YBR045C_Smik Reading seq # 5: YBR045C_Spar Sequences read.. Counting patterns.. # site patterns = 146 Counting frequencies.. 120 bytes for distance 23360 bytes for lkl0 18688 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.166369 0.087604 0.044267 0.088172 0.050768 0.150844 0.155911 0.052074 lnL0 = -1770.222890 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1770.222890 x= 0.16637 0.08760 0.04427 0.08817 0.05077 0.15084 0.15591 0.05207 1 h-lim-p 0.0008 0.0061 73.7691 1769.707404 7 0.0002 39 | 0/8 2 h-lim-p 0.0008 0.0091 18.9464 1769.650304 5 0.0003 60 | 0/8 3 h-lim-p 0.0007 0.0294 9.1227 1769.639966 5 0.0003 81 | 0/8 4 h-lim-p 0.0007 0.0457 3.7193 1769.637684 5 0.0004 104 | 0/8 5 h-lim-p 0.0013 0.1263 1.1176 1769.637477 4 0.0004 126 | 0/8 6 h-lim-p 0.0020 2.3285 0.2074 1769.637465 2 0.0005 143 | 0/8 7 h-lim-p 0.0629 20.0000 0.0018 1769.637465 0 0.0138 164 | 0/8 8 h-lim-p 0.0092 20.0000 0.0026 1769.637427 0 0.0553 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1769.637426 0 1.0938 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1769.637426 0 2.1875 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1769.637426 0 1.0938 246 | 0/8 12 h-lim-p 0.3074 20.0000 0.0000 1769.637426 0 4.9178 270 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1769.637426 0 0.5469 291 | 0/8 14 h-lim-p 0.0387 20.0000 0.0000 1769.637426 0 0.0009 316 | 0/8 15 h-lim-p 0.0003 20.0000 0.0001 1769.637426 0 0.0001 337 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 1769.637426 0 0.0000 357 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0021 1769.637426 0 0.0000 424 | 0/8 19 h-lim-p 0.0000 20.0000 0.0021 1769.637426 0 0.0000 455 | 0/8 20 h-lim-p 0.0000 20.0000 0.0006 1769.637426 0 0.0002 479 | 0/8 21 h-lim-p 0.0007 20.0000 0.0001 1769.637426 0 0.0000 504 | 0/8 22 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 23 h-lim-p 0.0000 20.0000 0.0021 1769.637426 0 0.0000 567 | 0/8 24 h-lim-p 0.0000 20.0000 0.0006 1769.637426 0 0.0006 593 | 0/8 25 h-lim-p 0.0015 20.0000 0.0003 1769.637426 0 0.0007 613 | 0/8 26 h-lim-p 0.0042 20.0000 0.0000 1769.637426 0 0.0042 633 | 0/8 27 h-lim-p 0.0005 20.0000 0.0004 1769.637426 0 0.0001 655 | 0/8 28 h-lim-p 0.0000 9.7112 0.0082 1769.637426 0 0.0000 679 | 0/8 29 h-lim-p 0.0000 10.8768 0.0069 1769.637426 0 0.0000 705 | 0/8 30 h-lim-p 0.0000 20.0000 0.0004 .. | 0/8 31 h-lim-p 0.0000 20.0000 0.0022 | 0/8 32 h-lim-p 0.0000 20.0000 0.0022 Out... lnL = -1769.637426 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1769.637426 Node 7: lnL = -1769.637426 Node 8: lnL = -1769.637426 Node 9: lnL = -1769.637426 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 346 Sequential format.. Reading seq # 1: YBR046C_Sbay Reading seq # 2: YBR046C_Scer Reading seq # 3: YBR046C_Skud Reading seq # 4: YBR046C_Smik Reading seq # 5: YBR046C_Spar Sequences read.. Counting patterns.. # site patterns = 161 Counting frequencies.. 120 bytes for distance 25760 bytes for lkl0 20608 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.264192 0.028950 0.118662 0.192998 0.080675 0.180141 0.241546 0.094997 lnL0 = -1625.170404 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1625.170404 x= 0.26419 0.02895 0.11866 0.19300 0.08068 0.18014 0.24155 0.09500 1 h-lim-p 0.0010 0.0080 110.3197 1622.953903 8 0.0004 36 | 0/8 2 h-lim-p 0.0010 0.0077 17.1690 1622.829407 5 0.0008 58 | 0/8 3 h-lim-p 0.0011 0.0235 13.4254 1622.788664 6 0.0007 87 | 0/8 4 h-lim-p 0.0039 0.1453 2.2646 1622.785871 5 0.0011 112 | 0/8 5 h-lim-p 0.0049 0.4005 0.5306 1622.785731 2 0.0011 129 | 0/8 6 h-lim-p 0.0054 5.6280 0.1055 1622.785725 0 0.0012 150 | 0/8 7 h-lim-p 0.0125 20.0000 0.0099 1622.785721 1 0.0100 172 | 0/8 8 h-lim-p 0.0248 20.0000 0.0040 1622.785247 0 0.1981 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1622.785246 0 1.0938 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1622.785246 0 1.0938 235 | 0/8 11 h-lim-p 1.4137 20.0000 0.0000 1622.785246 0 1.2370 255 | 0/8 12 h-lim-p 0.9150 20.0000 0.0000 1622.785246 0 0.0214 280 | 0/8 13 h-lim-p 0.0004 20.0000 0.0004 1622.785246 0 0.0000 310 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 1622.785246 0 0.0000 336 Out... lnL = -1622.785246 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1622.785246 Node 7: lnL = -1622.785246 Node 8: lnL = -1622.785246 Node 9: lnL = -1622.785246 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 355 Sequential format.. Reading seq # 1: YBR047W_Sbay Reading seq # 2: YBR047W_Scer Reading seq # 3: YBR047W_Skud Reading seq # 4: YBR047W_Smik Reading seq # 5: YBR047W_Spar Sequences read.. Counting patterns.. # site patterns = 157 Counting frequencies.. 120 bytes for distance 25120 bytes for lkl0 20096 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.232846 0.144990 0.107797 0.198268 0.070832 0.178784 0.143274 0.064720 lnL0 = -1602.416612 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1602.416612 x= 0.23285 0.14499 0.10780 0.19827 0.07083 0.17878 0.14327 0.06472 1 h-lim-p 0.0019 0.0149 40.3101 1601.851231 5 0.0007 32 | 0/8 2 h-lim-p 0.0031 0.0245 7.9635 1601.819576 7 0.0010 62 | 0/8 3 h-lim-p 0.0034 0.1177 2.4446 1601.817912 5 0.0006 88 | 0/8 4 h-lim-p 0.0010 0.1372 1.5351 1601.817140 2 0.0009 104 | 0/8 5 h-lim-p 0.0113 1.4050 0.1230 1601.817132 2 0.0011 122 | 0/8 6 h-lim-p 0.0040 12.0507 0.0332 1601.817132 0 0.0018 142 | 0/8 7 h-lim-p 0.0118 20.0000 0.0050 1601.817131 0 0.0052 162 | 0/8 8 h-lim-p 0.0193 20.0000 0.0013 1601.817083 0 0.2314 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1601.817083 0 1.0938 205 | 0/8 10 h-lim-p 2.4126 20.0000 0.0000 1601.817083 0 1.0555 225 | 0/8 11 h-lim-p 1.1648 20.0000 0.0000 1601.817083 0 4.6593 247 | 0/8 12 h-lim-p 0.3541 20.0000 0.0001 1601.817083 0 0.0111 271 | 0/8 13 h-lim-p 0.0012 20.0000 0.0010 1601.817083 0 0.0000 296 | 0/8 14 h-lim-p 0.0002 20.0000 0.0001 1601.817083 0 0.0000 322 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 1601.817083 0 0.0000 345 Out... lnL = -1601.817083 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1601.817083 Node 7: lnL = -1601.817083 Node 8: lnL = -1601.817083 Node 9: lnL = -1601.817083 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 385 Sequential format.. Reading seq # 1: YBR049C_Sbay Reading seq # 2: YBR049C_Scer Reading seq # 3: YBR049C_Skud Reading seq # 4: YBR049C_Smik Reading seq # 5: YBR049C_Spar Sequences read.. Counting patterns.. # site patterns = 118 Counting frequencies.. 120 bytes for distance 18880 bytes for lkl0 15104 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.099154 0.064957 0.043378 0.048459 0.042473 0.130722 0.120455 0.016859 lnL0 = -1403.413526 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1403.413526 x= 0.09915 0.06496 0.04338 0.04846 0.04247 0.13072 0.12045 0.01686 1 h-lim-p 0.0021 1.0818 115.3245 1402.072006 3 0.0002 30 | 0/8 2 h-lim-p 0.0006 0.0045 23.4130 1402.004480 2 0.0003 46 | 0/8 3 h-lim-p 0.0005 0.0070 12.4062 1401.991547 5 0.0002 69 | 0/8 4 h-lim-p 0.0030 0.1580 0.8788 1401.991391 4 0.0004 92 | 0/8 5 h-lim-p 0.0008 0.2409 0.4745 1401.991369 3 0.0002 121 | 0/8 6 h-lim-p 0.0043 1.3532 0.0251 1401.991369 0 0.0005 143 | 0/8 7 h-lim-p 0.0039 20.0000 0.0030 1401.991360 0 0.0311 166 | 0/8 8 h-lim-p 0.0041 20.0000 0.0229 1401.991175 0 0.0123 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1401.991171 0 1.0938 207 | 0/8 10 h-lim-p 1.6869 20.0000 0.0000 1401.991171 0 1.4760 227 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1401.991171 0 1.0938 247 | 0/8 12 h-lim-p 0.4173 20.0000 0.0001 1401.991171 0 0.0012 275 | 0/8 13 h-lim-p 0.0000 0.0294 0.9503 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1401.991171 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1401.991171 Node 7: lnL = -1401.991171 Node 8: lnL = -1401.991171 Node 9: lnL = -1401.991171 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 356 Sequential format.. Reading seq # 1: YBR052C_Sbay Reading seq # 2: YBR052C_Scer Reading seq # 3: YBR052C_Skud Reading seq # 4: YBR052C_Smik Reading seq # 5: YBR052C_Spar Sequences read.. Counting patterns.. # site patterns = 172 Counting frequencies.. 120 bytes for distance 27520 bytes for lkl0 22016 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.269803 0.095360 0.060549 0.160701 0.057430 0.275294 0.220971 0.087890 lnL0 = -1632.061587 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1632.061587 x= 0.26980 0.09536 0.06055 0.16070 0.05743 0.27529 0.22097 0.08789 1 h-lim-p 0.0147 0.3564 47.1944 1631.423258 6 0.0006 38 | 0/8 2 h-lim-p 0.0008 0.0065 17.4070 1631.357270 7 0.0005 68 | 0/8 3 h-lim-p 0.0011 0.0115 7.8398 1631.344840 2 0.0005 84 | 0/8 4 h-lim-p 0.0040 0.1466 0.9763 1631.344223 4 0.0013 105 | 0/8 5 h-lim-p 0.0087 2.2538 0.1487 1631.344211 1 0.0011 129 | 0/8 6 h-lim-p 0.0026 4.6618 0.0613 1631.344208 1 0.0013 152 | 0/8 7 h-lim-p 0.0134 20.0000 0.0059 1631.344206 0 0.0134 172 | 0/8 8 h-lim-p 0.0286 20.0000 0.0028 1631.344093 0 0.1714 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1631.344087 1 0.9961 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1631.344087 0 1.0938 236 | 0/8 11 h-lim-p 1.1437 20.0000 0.0000 1631.344087 0 6.8625 258 | 0/8 12 h-lim-p 0.6221 20.0000 0.0001 1631.344087 0 0.0049 284 | 0/8 13 h-lim-p 0.0002 20.0000 0.0017 1631.344087 0 0.0000 305 | 0/8 14 h-lim-p 0.0002 20.0000 0.0003 1631.344087 0 0.0000 334 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 1631.344087 0 0.0000 366 Out... lnL = -1631.344087 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1631.344087 Node 7: lnL = -1631.344087 Node 8: lnL = -1631.344087 Node 9: lnL = -1631.344087 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 851 Sequential format.. Reading seq # 1: YBR053C_Sbay Reading seq # 2: YBR053C_Scer Reading seq # 3: YBR053C_Skud Reading seq # 4: YBR053C_Smik Reading seq # 5: YBR053C_Spar Sequences read.. Counting patterns.. # site patterns = 286 Counting frequencies.. 120 bytes for distance 45760 bytes for lkl0 36608 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.227768 0.041769 0.059494 0.144611 0.098798 0.178807 0.251358 0.071147 lnL0 = -3856.862643 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3856.862643 x= 0.22777 0.04177 0.05949 0.14461 0.09880 0.17881 0.25136 0.07115 1 h-lim-p 0.0018 0.0305 208.0573 3853.881283 8 0.0002 42 | 0/8 2 h-lim-p 0.0006 0.0051 29.6471 3853.744823 5 0.0003 64 | 0/8 3 h-lim-p 0.0006 0.0143 14.7324 3853.713272 6 0.0004 91 | 0/8 4 h-lim-p 0.0011 0.0355 4.9211 3853.710029 5 0.0003 115 | 0/8 5 h-lim-p 0.0009 0.1442 1.6466 3853.709615 4 0.0003 135 | 0/8 6 h-lim-p 0.0022 0.6482 0.2649 3853.709605 1 0.0003 151 | 0/8 7 h-lim-p 0.1162 20.0000 0.0006 3853.708778 0 0.9294 174 | 0/8 8 h-lim-p 0.0007 0.2768 0.7787 3853.708566 3 0.0005 202 | 0/8 9 h-lim-p 1.3227 20.0000 0.0003 3853.708549 2 1.0205 226 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3853.708549 0 1.0938 246 | 0/8 11 h-lim-p 1.9633 20.0000 0.0000 3853.708549 0 1.7179 266 | 0/8 12 h-lim-p 1.1385 20.0000 0.0000 3853.708549 0 1.1385 286 | 0/8 13 h-lim-p 0.0458 20.0000 0.0006 3853.708549 0 0.0057 308 | 0/8 14 h-lim-p 0.0017 20.0000 0.0020 3853.708549 0 0.0000 338 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 3853.708549 0 0.0000 372 | 0/8 16 h-lim-p 0.0000 20.0000 0.0006 | 0/8 17 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -3853.708549 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3853.708549 Node 7: lnL = -3853.708549 Node 8: lnL = -3853.708549 Node 9: lnL = -3853.708549 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 829 Sequential format.. Reading seq # 1: YBR054W_Sbay Reading seq # 2: YBR054W_Scer Reading seq # 3: YBR054W_Skud Reading seq # 4: YBR054W_Smik Reading seq # 5: YBR054W_Spar Sequences read.. Counting patterns.. # site patterns = 157 Counting frequencies.. 120 bytes for distance 25120 bytes for lkl0 20096 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.122974 0.014218 0.020378 0.037530 0.023243 0.075074 0.085515 0.059493 lnL0 = -2606.181860 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2606.181860 x= 0.12297 0.01422 0.02038 0.03753 0.02324 0.07507 0.08552 0.05949 1 h-lim-p 0.0001 0.0005 228.8865 2605.304098 7 0.0000 40 | 0/8 2 h-lim-p 0.0002 0.0018 29.0854 2605.275145 6 0.0001 70 | 0/8 3 h-lim-p 0.0001 0.0080 14.7076 2605.268749 5 0.0001 93 | 0/8 4 h-lim-p 0.0001 0.0060 8.3579 2605.267517 4 0.0000 113 | 0/8 5 h-lim-p 0.0003 0.0329 1.5232 2605.267450 0 0.0001 126 | 0/8 6 h-lim-p 0.0002 0.1558 0.6208 2605.267435 2 0.0001 143 | 0/8 7 h-lim-p 0.0014 4.7311 0.0371 2605.267435 0 0.0002 165 | 0/8 8 h-lim-p 0.0825 20.0000 0.0001 2605.267434 0 0.9896 188 | 0/8 9 h-lim-p 2.4931 20.0000 0.0000 2605.267434 0 3.7396 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2605.267434 0 0.1367 231 | 0/8 11 h-lim-p 1.6487 20.0000 0.0000 2605.267434 0 0.0129 257 | 0/8 12 h-lim-p 0.0014 20.0000 0.0000 2605.267434 0 0.0000 284 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 2605.267434 0 0.0000 305 | 0/8 14 h-lim-p 0.0000 20.0000 0.0010 2605.267434 0 0.0000 326 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 2605.267434 0 0.0000 359 | 0/8 16 h-lim-p 0.0000 20.0000 0.0407 | 0/8 17 h-lim-p 0.0000 20.0000 0.0407 Out... lnL = -2605.267434 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2605.267434 Node 7: lnL = -2605.267434 Node 8: lnL = -2605.267434 Node 9: lnL = -2605.267434 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 614 Sequential format.. Reading seq # 1: YBR055C_Sbay Reading seq # 2: YBR055C_Scer Reading seq # 3: YBR055C_Skud Reading seq # 4: YBR055C_Smik Reading seq # 5: YBR055C_Spar Sequences read.. Counting patterns.. # site patterns = 266 Counting frequencies.. 120 bytes for distance 42560 bytes for lkl0 34048 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.237040 0.035676 0.063266 0.182979 0.142704 0.300963 0.256179 0.052993 lnL0 = -2970.402460 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2970.402460 x= 0.23704 0.03568 0.06327 0.18298 0.14270 0.30096 0.25618 0.05299 1 h-lim-p 0.0018 0.6948 181.8746 2966.727602 10 0.0003 49 | 0/8 2 h-lim-p 0.0012 0.0100 30.3309 2966.352743 7 0.0008 78 | 0/8 3 h-lim-p 0.0020 0.0430 12.8336 2966.313802 5 0.0006 102 | 0/8 4 h-lim-p 0.0018 0.0706 3.9229 2966.309202 5 0.0007 125 | 0/8 5 h-lim-p 0.0039 0.2601 0.6581 2966.309018 2 0.0009 142 | 0/8 6 h-lim-p 0.0029 1.4000 0.1977 2966.309006 0 0.0007 163 | 0/8 7 h-lim-p 0.0099 9.1225 0.0144 2966.309006 0 0.0011 185 | 0/8 8 h-lim-p 0.0288 20.0000 0.0005 2966.308925 0 0.9226 210 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2966.308914 1 0.9961 232 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2966.308913 0 1.0938 252 | 0/8 11 h-lim-p 1.1974 20.0000 0.0000 2966.308913 0 1.0478 272 | 0/8 12 h-lim-p 0.3110 20.0000 0.0001 2966.308913 0 0.0024 298 | 0/8 13 h-lim-p 0.0005 20.0000 0.0002 2966.308913 0 0.0000 336 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 2966.308913 0 0.0000 356 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 2966.308913 0 0.0000 389 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -2966.308913 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2966.308913 Node 7: lnL = -2966.308913 Node 8: lnL = -2966.308913 Node 9: lnL = -2966.308913 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 405 Sequential format.. Reading seq # 1: YBR057C_Sbay Reading seq # 2: YBR057C_Scer Reading seq # 3: YBR057C_Skud Reading seq # 4: YBR057C_Smik Reading seq # 5: YBR057C_Spar Sequences read.. Counting patterns.. # site patterns = 147 Counting frequencies.. 120 bytes for distance 23520 bytes for lkl0 18816 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.219180 0.048852 0.037445 0.052041 0.079025 0.174598 0.193772 0.088694 lnL0 = -1589.105968 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1589.105968 x= 0.21918 0.04885 0.03745 0.05204 0.07903 0.17460 0.19377 0.08869 1 h-lim-p 0.0002 0.0014 125.1261 1587.240568 0 0.0003 23 | 0/8 2 h-lim-p 0.0008 0.0061 21.5514 1587.103485 6 0.0006 48 | 0/8 3 h-lim-p 0.0010 0.0181 12.9586 1587.072960 2 0.0005 64 | 0/8 4 h-lim-p 0.0006 0.0101 9.8056 1587.065230 3 0.0003 82 | 0/8 5 h-lim-p 0.0017 0.2037 1.5231 1587.064536 5 0.0006 106 | 0/8 6 h-lim-p 0.0033 0.5718 0.2745 1587.064316 4 0.0021 128 | 0/8 7 h-lim-p 0.0210 6.6405 0.0279 1587.013740 0 0.3363 152 | 0/8 8 h-lim-p 0.0019 0.0306 4.9651 1586.983019 6 0.0013 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0019 1586.979607 4 0.9643 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1586.979604 0 1.0938 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1586.979604 0 1.0938 246 | 0/8 12 h-lim-p 1.3830 20.0000 0.0000 1586.979604 0 1.3830 266 | 0/8 13 h-lim-p 1.6230 20.0000 0.0000 1586.979604 0 0.0380 291 | 0/8 14 h-lim-p 0.0092 20.0000 0.0000 1586.979604 0 0.0000 322 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 1586.979604 0 0.0001 342 Out... lnL = -1586.979604 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1586.979604 Node 7: lnL = -1586.979604 Node 8: lnL = -1586.979604 Node 9: lnL = -1586.979604 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 350 Sequential format.. Reading seq # 1: YBR058C-A_Sbay Reading seq # 2: YBR058C-A_Scer Reading seq # 3: YBR058C-A_Skud Reading seq # 4: YBR058C-A_Smik Reading seq # 5: YBR058C-A_Spar Sequences read.. Counting patterns.. # site patterns = 132 Counting frequencies.. 120 bytes for distance 21120 bytes for lkl0 16896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.207412 0.035898 0.061889 0.070035 0.086025 0.183829 0.166518 0.076844 lnL0 = -1385.127715 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1385.127715 x= 0.20741 0.03590 0.06189 0.07004 0.08602 0.18383 0.16652 0.07684 1 h-lim-p 0.0005 0.0037 98.8926 1383.602277 7 0.0004 36 | 0/8 2 h-lim-p 0.0003 0.0027 25.0098 1383.446908 0 0.0005 48 | 0/8 3 h-lim-p 0.0011 0.0173 11.8337 1383.406917 6 0.0007 74 | 0/8 4 h-lim-p 0.0020 0.0273 3.9785 1383.404235 4 0.0004 95 | 0/8 5 h-lim-p 0.0068 1.5672 0.2274 1383.404218 2 0.0007 113 | 0/8 6 h-lim-p 0.0019 1.9772 0.0794 1383.404216 1 0.0005 136 | 0/8 7 h-lim-p 0.0150 20.0000 0.0025 1383.404215 0 0.0150 156 | 0/8 8 h-lim-p 0.0135 20.0000 0.0028 1383.404150 0 0.1081 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1383.404147 1 0.9961 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1383.404147 0 1.0938 221 | 0/8 11 h-lim-p 1.4530 20.0000 0.0000 1383.404147 0 2.1795 241 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1383.404147 0 0.5469 262 | 0/8 13 h-lim-p 0.1198 20.0000 0.0000 1383.404147 0 0.0150 284 | 0/8 14 h-lim-p 0.0048 20.0000 0.0000 1383.404147 0 0.0012 305 | 0/8 15 h-lim-p 0.0005 20.0000 0.0001 1383.404147 0 0.0001 326 | 0/8 16 h-lim-p 0.0001 20.0000 0.0001 1383.404147 0 0.0000 361 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 1383.404147 0 0.0000 389 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 1383.404147 0 0.0026 417 | 0/8 19 h-lim-p 0.0034 20.0000 0.0002 1383.404147 0 0.0000 450 | 0/8 20 h-lim-p 0.0000 20.0000 0.0002 1383.404147 0 0.0000 475 | 0/8 21 h-lim-p 0.0000 20.0000 0.0006 .. | 0/8 22 h-lim-p 0.0000 20.0000 0.0009 | 0/8 23 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -1383.404147 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1383.404147 Node 7: lnL = -1383.404147 Node 8: lnL = -1383.404147 Node 9: lnL = -1383.404147 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 255 Sequential format.. Reading seq # 1: YBR058C_Sbay Reading seq # 2: YBR058C_Scer Reading seq # 3: YBR058C_Skud Reading seq # 4: YBR058C_Smik Reading seq # 5: YBR058C_Spar Sequences read.. Counting patterns.. # site patterns = 91 Counting frequencies.. 120 bytes for distance 14560 bytes for lkl0 11648 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.152394 0.056738 0.029083 0.096014 0.087133 0.149281 0.155624 0.039718 lnL0 = -1027.177660 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1027.177660 x= 0.15239 0.05674 0.02908 0.09601 0.08713 0.14928 0.15562 0.03972 1 h-lim-p 0.0032 0.0260 71.8846 1026.560925 6 0.0003 37 | 0/8 2 h-lim-p 0.0016 0.0207 11.8842 1026.508721 2 0.0008 53 | 0/8 3 h-lim-p 0.0027 0.0546 3.3123 1026.505062 5 0.0007 76 | 0/8 4 h-lim-p 0.0046 0.6653 0.5187 1026.504984 3 0.0006 96 | 0/8 5 h-lim-p 0.0057 6.3064 0.0545 1026.504983 1 0.0007 120 | 0/8 6 h-lim-p 0.0030 10.7442 0.0129 1026.504983 0 0.0013 140 | 0/8 7 h-lim-p 0.0283 20.0000 0.0006 1026.504978 0 0.1133 162 | 0/8 8 h-lim-p 0.0018 1.5846 0.0367 1026.504946 0 0.0037 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1026.504945 0 1.0938 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1026.504945 0 1.0938 223 | 0/8 11 h-lim-p 1.0433 20.0000 0.0000 1026.504945 0 3.1299 244 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1026.504945 0 0.1172 268 | 0/8 13 h-lim-p 0.0152 20.0000 0.0001 1026.504945 0 0.0004 292 | 0/8 14 h-lim-p 0.0002 20.0000 0.0002 1026.504945 0 0.0000 327 | 0/8 15 h-lim-p 0.0000 20.0000 0.0014 | 0/8 16 h-lim-p 0.0000 20.0000 0.0014 Out... lnL = -1026.504945 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1026.504945 Node 7: lnL = -1026.504945 Node 8: lnL = -1026.504945 Node 9: lnL = -1026.504945 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 482 Sequential format.. Reading seq # 1: YBR059C_Sbay Reading seq # 2: YBR059C_Scer Reading seq # 3: YBR059C_Skud Reading seq # 4: YBR059C_Smik Reading seq # 5: YBR059C_Spar Sequences read.. Counting patterns.. # site patterns = 167 Counting frequencies.. 120 bytes for distance 26720 bytes for lkl0 21376 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.217517 0.062633 0.033259 0.071016 0.035810 0.133672 0.196437 0.093320 lnL0 = -1976.206918 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1976.206918 x= 0.21752 0.06263 0.03326 0.07102 0.03581 0.13367 0.19644 0.09332 1 h-lim-p 0.0006 0.0050 93.5754 1975.242297 8 0.0002 39 | 0/8 2 h-lim-p 0.0002 0.0018 38.8354 1975.071757 1 0.0003 53 | 0/8 3 h-lim-p 0.0004 0.0029 23.0148 1975.045445 6 0.0001 77 | 0/8 4 h-lim-p 0.0008 0.0294 3.9149 1975.043108 4 0.0003 97 | 0/8 5 h-lim-p 0.0008 0.2313 1.4870 1975.042744 2 0.0004 113 | 0/8 6 h-lim-p 0.0018 0.7914 0.3109 1975.042704 1 0.0009 127 | 0/8 7 h-lim-p 0.2399 20.0000 0.0011 1975.041513 0 0.9594 149 | 0/8 8 h-lim-p 0.0016 0.4105 0.6933 1975.041260 2 0.0008 173 | 0/8 9 h-lim-p 2.1025 20.0000 0.0003 1975.041150 2 0.9856 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1975.041150 0 1.0938 217 | 0/8 11 h-lim-p 1.4182 20.0000 0.0000 1975.041150 0 0.0028 245 | 0/8 12 h-lim-p 0.0014 20.0000 0.0000 1975.041150 0 0.0014 265 | 0/8 13 h-lim-p 0.0008 20.0000 0.0000 1975.041150 0 0.0002 286 | 0/8 14 h-lim-p 0.0001 20.0000 0.0001 1975.041150 0 0.0000 323 | 0/8 15 h-lim-p 0.0000 20.0000 0.0025 | 0/8 16 h-lim-p 0.0000 20.0000 0.0025 Out... lnL = -1975.041150 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1975.041150 Node 7: lnL = -1975.041150 Node 8: lnL = -1975.041150 Node 9: lnL = -1975.041150 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 878 Sequential format.. Reading seq # 1: YBR060C_Sbay Reading seq # 2: YBR060C_Scer Reading seq # 3: YBR060C_Skud Reading seq # 4: YBR060C_Smik Reading seq # 5: YBR060C_Spar Sequences read.. Counting patterns.. # site patterns = 262 Counting frequencies.. 120 bytes for distance 41920 bytes for lkl0 33536 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.146064 0.023693 0.063368 0.182238 0.061381 0.191720 0.144561 0.023479 lnL0 = -3691.983913 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3691.983913 x= 0.14606 0.02369 0.06337 0.18224 0.06138 0.19172 0.14456 0.02348 1 h-lim-p 0.0004 0.2396 428.7313 3686.081911 4 0.0001 31 | 0/8 2 h-lim-p 0.0002 0.0017 46.5045 3685.911711 7 0.0002 61 | 0/8 3 h-lim-p 0.0004 0.0117 17.1285 3685.880871 7 0.0002 91 | 0/8 4 h-lim-p 0.0010 0.0730 4.1582 3685.879358 3 0.0002 110 | 0/8 5 h-lim-p 0.0010 0.1599 0.7864 3685.879267 3 0.0003 131 | 0/8 6 h-lim-p 0.0016 0.5583 0.1449 3685.879265 1 0.0002 155 | 0/8 7 h-lim-p 0.0009 8.5146 0.0309 3685.879264 0 0.0005 175 | 0/8 8 h-lim-p 0.0526 20.0000 0.0003 3685.878968 0 1.2626 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3685.878967 0 1.0938 219 | 0/8 10 h-lim-p 0.5726 20.0000 0.0001 3685.878967 0 1.1451 240 | 0/8 11 h-lim-p 1.0719 20.0000 0.0001 3685.878967 0 0.0167 265 | 0/8 12 h-lim-p 0.0005 20.0000 0.0018 3685.878967 0 0.0001 286 | 0/8 13 h-lim-p 0.0000 5.0302 0.0074 3685.878967 0 0.0000 309 | 0/8 14 h-lim-p 0.0001 20.0000 0.0001 3685.878967 0 0.0000 331 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 3685.878967 0 0.0000 361 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 3685.878967 0 0.0000 389 Out... lnL = -3685.878967 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3685.878967 Node 7: lnL = -3685.878967 Node 8: lnL = -3685.878967 Node 9: lnL = -3685.878967 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 276 Sequential format.. Reading seq # 1: YBR061C_Sbay Reading seq # 2: YBR061C_Scer Reading seq # 3: YBR061C_Skud Reading seq # 4: YBR061C_Smik Reading seq # 5: YBR061C_Spar Sequences read.. Counting patterns.. # site patterns = 112 Counting frequencies.. 120 bytes for distance 17920 bytes for lkl0 14336 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.190698 0.082293 0.025608 0.130360 0.087077 0.177687 0.154869 0.057034 lnL0 = -1194.384248 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1194.384248 x= 0.19070 0.08229 0.02561 0.13036 0.08708 0.17769 0.15487 0.05703 1 h-lim-p 0.0017 0.0139 80.8307 1193.709106 8 0.0002 41 | 0/8 2 h-lim-p 0.0010 0.0082 18.0932 1193.598897 7 0.0007 70 | 0/8 3 h-lim-p 0.0024 0.0529 5.2197 1193.591241 5 0.0006 94 | 0/8 4 h-lim-p 0.0032 0.3162 1.0103 1193.590819 4 0.0009 115 | 0/8 5 h-lim-p 0.0060 1.0463 0.1436 1193.590812 1 0.0007 131 | 0/8 6 h-lim-p 0.0162 20.0000 0.0059 1193.590811 1 0.0080 154 | 0/8 7 h-lim-p 0.0051 18.4569 0.0092 1193.590763 0 0.0304 176 | 0/8 8 h-lim-p 0.0030 0.6302 0.0921 1193.590604 0 0.0046 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1193.590601 1 0.9961 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1193.590601 0 2.1875 238 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1193.590601 0 1.0938 258 | 0/8 12 h-lim-p 0.1463 20.0000 0.0000 1193.590601 014.0483 284 | 0/8 13 h-lim-p 0.1163 20.0000 0.0012 1193.590601 0 0.0036 308 | 0/8 14 h-lim-p 0.0011 20.0000 0.0039 1193.590601 0 0.0000 335 | 0/8 15 h-lim-p 0.0002 20.0000 0.0001 1193.590601 0 0.0001 356 | 0/8 16 h-lim-p 0.0002 20.0000 0.0000 1193.590601 0 0.0002 376 | 0/8 17 h-lim-p 0.0001 20.0000 0.0001 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0007 | 0/8 19 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -1193.590601 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1193.590601 Node 7: lnL = -1193.590601 Node 8: lnL = -1193.590601 Node 9: lnL = -1193.590601 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 727 Sequential format.. Reading seq # 1: YBR062C_Sbay Reading seq # 2: YBR062C_Scer Reading seq # 3: YBR062C_Skud Reading seq # 4: YBR062C_Smik Reading seq # 5: YBR062C_Spar Sequences read.. Counting patterns.. # site patterns = 255 Counting frequencies.. 120 bytes for distance 40800 bytes for lkl0 32640 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.219217 0.033380 0.055831 0.134908 0.051226 0.210765 0.188248 0.077708 lnL0 = -2877.559517 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2877.559517 x= 0.21922 0.03338 0.05583 0.13491 0.05123 0.21076 0.18825 0.07771 1 h-lim-p 0.0008 0.0061 113.2741 2876.746650 8 0.0001 43 | 0/8 2 h-lim-p 0.0005 0.0060 31.4494 2876.616621 7 0.0003 73 | 0/8 3 h-lim-p 0.0006 0.0099 15.4373 2876.592105 5 0.0003 94 | 0/8 4 h-lim-p 0.0005 0.0326 7.4658 2876.579718 4 0.0006 115 | 0/8 5 h-lim-p 0.0014 0.0844 3.1166 2876.577592 3 0.0005 133 | 0/8 6 h-lim-p 0.0021 0.2464 0.7857 2876.577458 2 0.0005 150 | 0/8 7 h-lim-p 0.0057 1.1023 0.0649 2876.577457 0 0.0006 172 | 0/8 8 h-lim-p 0.5042 20.0000 0.0001 2876.577447 0 1.0084 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2876.577446 0 1.0938 213 | 0/8 10 h-lim-p 1.1550 20.0000 0.0000 2876.577446 0 2.3100 234 | 0/8 11 h-lim-p 2.2545 20.0000 0.0000 2876.577446 0 0.2114 257 | 0/8 12 h-lim-p 0.0246 20.0000 0.0001 2876.577446 0 0.0000 298 | 0/8 13 h-lim-p 0.0000 20.0000 0.0019 | 0/8 14 h-lim-p 0.0000 20.0000 0.0019 Out... lnL = -2876.577446 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2876.577446 Node 7: lnL = -2876.577446 Node 8: lnL = -2876.577446 Node 9: lnL = -2876.577446 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 455 Sequential format.. Reading seq # 1: YBR063C_Sbay Reading seq # 2: YBR063C_Scer Reading seq # 3: YBR063C_Skud Reading seq # 4: YBR063C_Smik Reading seq # 5: YBR063C_Spar Sequences read.. Counting patterns.. # site patterns = 207 Counting frequencies.. 120 bytes for distance 33120 bytes for lkl0 26496 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.280037 0.054145 0.108844 0.154518 0.095561 0.290403 0.252792 0.084679 lnL0 = -2165.617074 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2165.617074 x= 0.28004 0.05414 0.10884 0.15452 0.09556 0.29040 0.25279 0.08468 1 h-lim-p 0.0007 0.0059 56.4822 2164.784778 6 0.0006 34 | 0/8 2 h-lim-p 0.0015 0.0122 15.2150 2164.688295 7 0.0009 64 | 0/8 3 h-lim-p 0.0020 0.0453 6.7072 2164.671007 2 0.0009 80 | 0/8 4 h-lim-p 0.0022 0.0525 2.8521 2164.669693 4 0.0004 102 | 0/8 5 h-lim-p 0.0073 2.0216 0.1519 2164.669682 0 0.0009 116 | 0/8 6 h-lim-p 0.0033 10.3205 0.0418 2164.669681 0 0.0015 136 | 0/8 7 h-lim-p 0.0089 20.0000 0.0068 2164.669679 0 0.0134 156 | 0/8 8 h-lim-p 0.0176 20.0000 0.0052 2164.669480 0 0.1053 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2164.669477 0 1.0938 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2164.669477 0 1.0938 218 | 0/8 11 h-lim-p 1.5987 20.0000 0.0000 2164.669477 0 1.3989 238 | 0/8 12 h-lim-p 1.4252 20.0000 0.0000 2164.669477 0 1.2471 258 | 0/8 13 h-lim-p 0.2142 20.0000 0.0000 2164.669477 0 0.1071 278 | 0/8 14 h-lim-p 0.0224 20.0000 0.0002 2164.669477 0 0.0056 299 | 0/8 15 h-lim-p 0.0026 20.0000 0.0004 2164.669477 0 0.0000 324 | 0/8 16 h-lim-p 0.0010 20.0000 0.0000 2164.669477 0 0.0003 345 | 0/8 17 h-lim-p 0.0007 20.0000 0.0000 2164.669477 0 0.0000 372 Out... lnL = -2164.669477 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2164.669477 Node 7: lnL = -2164.669477 Node 8: lnL = -2164.669477 Node 9: lnL = -2164.669477 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 844 Sequential format.. Reading seq # 1: YBR068C_Sbay Reading seq # 2: YBR068C_Scer Reading seq # 3: YBR068C_Skud Reading seq # 4: YBR068C_Smik Reading seq # 5: YBR068C_Spar Sequences read.. Counting patterns.. # site patterns = 327 Counting frequencies.. 120 bytes for distance 52320 bytes for lkl0 41856 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.291515 0.020806 0.079155 0.139181 0.095580 0.236054 0.273459 0.110900 lnL0 = -3895.371783 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3895.371783 x= 0.29151 0.02081 0.07916 0.13918 0.09558 0.23605 0.27346 0.11090 1 h-lim-p 0.0018 0.0144 156.8533 3893.243692 3 0.0002 30 | 0/8 2 h-lim-p 0.0008 0.0086 35.2631 3892.957941 7 0.0005 59 | 0/8 3 h-lim-p 0.0008 0.0141 21.5352 3892.914591 6 0.0002 86 | 0/8 4 h-lim-p 0.0013 0.0773 3.9612 3892.910061 2 0.0006 102 | 0/8 5 h-lim-p 0.0013 0.0966 1.8807 3892.909428 3 0.0004 122 | 0/8 6 h-lim-p 0.0035 0.8584 0.2310 3892.909413 2 0.0006 140 | 0/8 7 h-lim-p 0.0028 4.8938 0.0462 3892.909412 0 0.0006 161 | 0/8 8 h-lim-p 0.0750 20.0000 0.0004 3892.909110 0 1.2000 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3892.909093 1 0.9961 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3892.909093 0 1.0938 227 | 0/8 11 h-lim-p 1.2725 20.0000 0.0000 3892.909093 0 1.2725 247 | 0/8 12 h-lim-p 0.2808 20.0000 0.0000 3892.909093 0 0.0005 275 | 0/8 13 h-lim-p 0.0003 20.0000 0.0001 3892.909093 0 0.0000 314 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -3892.909093 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3892.909093 Node 7: lnL = -3892.909093 Node 8: lnL = -3892.909093 Node 9: lnL = -3892.909093 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 822 Sequential format.. Reading seq # 1: YBR069C_Sbay Reading seq # 2: YBR069C_Scer Reading seq # 3: YBR069C_Skud Reading seq # 4: YBR069C_Smik Reading seq # 5: YBR069C_Spar Sequences read.. Counting patterns.. # site patterns = 300 Counting frequencies.. 120 bytes for distance 48000 bytes for lkl0 38400 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.291125 0.078759 0.034512 0.116435 0.100562 0.194259 0.219916 0.114901 lnL0 = -3690.606589 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3690.606589 x= 0.29113 0.07876 0.03451 0.11643 0.10056 0.19426 0.21992 0.11490 1 h-lim-p 0.0008 0.0061 225.3924 3687.489269 8 0.0001 41 | 0/8 2 h-lim-p 0.0004 0.0034 47.5975 3687.126061 4 0.0003 61 | 0/8 3 h-lim-p 0.0008 0.0180 19.7599 3687.074595 4 0.0003 81 | 0/8 4 h-lim-p 0.0006 0.0230 10.6342 3687.054732 4 0.0005 101 | 0/8 5 h-lim-p 0.0034 0.3416 1.4374 3687.054322 2 0.0004 119 | 0/8 6 h-lim-p 0.0019 0.6922 0.3150 3687.054302 1 0.0004 134 | 0/8 7 h-lim-p 0.0220 20.0000 0.0060 3687.054302 0 0.0096 154 | 0/8 8 h-lim-p 0.0179 20.0000 0.0032 3687.054132 0 0.1073 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3687.054128 0 1.0938 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3687.054128 0 2.1875 216 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3687.054128 0 1.0938 236 | 0/8 12 h-lim-p 0.4328 20.0000 0.0000 3687.054128 0 1.7311 258 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 3687.054128 0 0.0391 283 | 0/8 14 h-lim-p 0.0086 20.0000 0.0000 3687.054128 0 0.0003 307 | 0/8 15 h-lim-p 0.0004 20.0000 0.0000 3687.054128 0 0.0000 343 | 0/8 16 h-lim-p 0.0000 20.0000 0.0016 | 0/8 17 h-lim-p 0.0000 20.0000 0.0016 Out... lnL = -3687.054128 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3687.054128 Node 7: lnL = -3687.054128 Node 8: lnL = -3687.054128 Node 9: lnL = -3687.054128 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 503 Sequential format.. Reading seq # 1: YBR070C_Sbay Reading seq # 2: YBR070C_Scer Reading seq # 3: YBR070C_Skud Reading seq # 4: YBR070C_Smik Reading seq # 5: YBR070C_Spar Sequences read.. Counting patterns.. # site patterns = 165 Counting frequencies.. 120 bytes for distance 26400 bytes for lkl0 21120 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.188051 0.050011 0.065817 0.092168 0.040427 0.121704 0.105124 0.072218 lnL0 = -1959.867530 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1959.867530 x= 0.18805 0.05001 0.06582 0.09217 0.04043 0.12170 0.10512 0.07222 1 h-lim-p 0.0089 1.7586 66.4675 1959.402375 5 0.0002 36 | 0/8 2 h-lim-p 0.0006 0.0048 21.4686 1959.343153 2 0.0003 52 | 0/8 3 h-lim-p 0.0004 0.0094 15.6512 1959.328098 2 0.0002 68 | 0/8 4 h-lim-p 0.0021 0.1871 1.3175 1959.327890 2 0.0003 86 | 0/8 5 h-lim-p 0.0059 2.2895 0.0564 1959.327889 0 0.0004 101 | 0/8 6 h-lim-p 0.0015 19.0228 0.0134 1959.327889 0 0.0007 121 | 0/8 7 h-lim-p 0.0021 20.0000 0.0043 1959.327888 0 0.0062 142 | 0/8 8 h-lim-p 0.0057 20.0000 0.0047 1959.327818 0 0.0460 165 | 0/8 9 h-lim-p 0.4127 20.0000 0.0005 1959.327813 0 0.8254 186 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1959.327813 0 1.0938 206 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1959.327813 0 1.0938 226 | 0/8 12 h-lim-p 0.6120 20.0000 0.0000 1959.327813 0 0.0021 253 | 0/8 13 h-lim-p 0.0005 20.0000 0.0001 1959.327813 0 0.0000 288 | 0/8 14 h-lim-p 0.0000 20.0000 0.0006 | 0/8 15 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -1959.327813 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1959.327813 Node 7: lnL = -1959.327813 Node 8: lnL = -1959.327813 Node 9: lnL = -1959.327813 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 502 Sequential format.. Reading seq # 1: YBR071W_Sbay Reading seq # 2: YBR071W_Scer Reading seq # 3: YBR071W_Skud Reading seq # 4: YBR071W_Smik Reading seq # 5: YBR071W_Spar Sequences read.. Counting patterns.. # site patterns = 165 Counting frequencies.. 120 bytes for distance 26400 bytes for lkl0 21120 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.200400 0.051506 0.064381 0.093438 0.041705 0.128800 0.110319 0.079519 lnL0 = -1993.715071 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1993.715071 x= 0.20040 0.05151 0.06438 0.09344 0.04171 0.12880 0.11032 0.07952 1 h-lim-p 0.0015 0.0121 76.3790 1993.088507 8 0.0002 44 | 0/8 2 h-lim-p 0.0009 0.0084 20.1577 1993.006965 4 0.0004 64 | 0/8 3 h-lim-p 0.0009 0.0208 9.9860 1993.001432 5 0.0001 89 | 0/8 4 h-lim-p 0.0008 0.0979 1.7191 1993.001068 3 0.0003 109 | 0/8 5 h-lim-p 0.0026 0.8342 0.1724 1993.001062 2 0.0004 128 | 0/8 6 h-lim-p 0.0063 18.8699 0.0115 1993.001062 0 0.0014 149 | 0/8 7 h-lim-p 0.0022 20.0000 0.0072 1993.001061 0 0.0022 169 | 0/8 8 h-lim-p 0.0054 20.0000 0.0029 1993.000981 0 0.0869 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1993.000977 0 1.0938 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1993.000977 0 1.0938 233 | 0/8 11 h-lim-p 1.7513 20.0000 0.0000 1993.000977 0 2.6269 253 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1993.000977 0 0.2734 275 | 0/8 13 h-lim-p 0.0113 20.0000 0.0000 1993.000977 0 0.0227 296 | 0/8 14 h-lim-p 0.0097 20.0000 0.0000 1993.000977 0 0.0000 339 | 0/8 15 h-lim-p 0.0000 20.0000 0.0019 | 0/8 16 h-lim-p 0.0000 20.0000 0.0019 Out... lnL = -1993.000977 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1993.000977 Node 7: lnL = -1993.000977 Node 8: lnL = -1993.000977 Node 9: lnL = -1993.000977 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 848 Sequential format.. Reading seq # 1: YBR072W_Sbay Reading seq # 2: YBR072W_Scer Reading seq # 3: YBR072W_Skud Reading seq # 4: YBR072W_Smik Reading seq # 5: YBR072W_Spar Sequences read.. Counting patterns.. # site patterns = 251 Counting frequencies.. 120 bytes for distance 40160 bytes for lkl0 32128 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.189059 0.044022 0.060201 0.078014 0.070053 0.121130 0.154033 0.067059 lnL0 = -3378.601006 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3378.601006 x= 0.18906 0.04402 0.06020 0.07801 0.07005 0.12113 0.15403 0.06706 1 h-lim-p 0.0011 0.0089 171.7952 3376.882045 7 0.0001 37 | 0/8 2 h-lim-p 0.0006 0.0049 30.8110 3376.776734 6 0.0002 63 | 0/8 3 h-lim-p 0.0004 0.0114 17.0816 3376.758949 5 0.0002 85 | 0/8 4 h-lim-p 0.0009 0.0456 2.8264 3376.758166 2 0.0002 102 | 0/8 5 h-lim-p 0.0007 0.1805 0.8692 3376.758089 3 0.0002 122 | 0/8 6 h-lim-p 0.0053 3.9845 0.0386 3376.758089 0 0.0003 145 | 0/8 7 h-lim-p 0.0020 20.0000 0.0055 3376.758089 0 0.0002 167 | 0/8 8 h-lim-p 0.0418 20.0000 0.0000 3376.758087 0 1.0031 191 | 0/8 9 h-lim-p 1.2729 20.0000 0.0000 3376.758087 0 1.1138 211 | 0/8 10 h-lim-p 1.1114 20.0000 0.0000 3376.758087 0 2.2228 232 | 0/8 11 h-lim-p 0.4117 20.0000 0.0001 3376.758087 0 0.0257 255 | 0/8 12 h-lim-p 0.0035 20.0000 0.0009 3376.758087 0 0.0000 296 | 0/8 13 h-lim-p 0.0000 20.0000 0.0011 | 0/8 14 h-lim-p 0.0000 20.0000 0.0011 Out... lnL = -3376.758087 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3376.758087 Node 7: lnL = -3376.758087 Node 8: lnL = -3376.758087 Node 9: lnL = -3376.758087 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 848 Sequential format.. Reading seq # 1: YBR077C_Sbay Reading seq # 2: YBR077C_Scer Reading seq # 3: YBR077C_Skud Reading seq # 4: YBR077C_Smik Reading seq # 5: YBR077C_Spar Sequences read.. Counting patterns.. # site patterns = 207 Counting frequencies.. 120 bytes for distance 33120 bytes for lkl0 26496 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.138090 0.040119 0.028531 0.065681 0.037556 0.155223 0.106082 0.043349 lnL0 = -3005.156447 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3005.156447 x= 0.13809 0.04012 0.02853 0.06568 0.03756 0.15522 0.10608 0.04335 1 h-lim-p 0.0022 0.0448 164.1170 3004.189228 7 0.0001 40 | 0/8 2 h-lim-p 0.0002 0.0020 41.8395 3004.088287 5 0.0001 64 | 0/8 3 h-lim-p 0.0003 0.0139 16.7240 3004.076338 5 0.0001 88 | 0/8 4 h-lim-p 0.0002 0.0237 8.2317 3004.072220 4 0.0002 108 | 0/8 5 h-lim-p 0.0005 0.0734 2.3066 3004.071682 3 0.0002 126 | 0/8 6 h-lim-p 0.0015 0.4124 0.3478 3004.071671 1 0.0002 142 | 0/8 7 h-lim-p 0.0007 1.5421 0.0960 3004.071670 0 0.0001 163 | 0/8 8 h-lim-p 0.1665 20.0000 0.0001 3004.071642 0 1.3320 186 | 0/8 9 h-lim-p 2.0831 20.0000 0.0001 3004.071641 0 1.0415 206 | 0/8 10 h-lim-p 1.4573 20.0000 0.0000 3004.071641 0 0.0050 233 | 0/8 11 h-lim-p 0.0024 20.0000 0.0001 3004.071641 0 0.0024 253 | 0/8 12 h-lim-p 0.0014 20.0000 0.0001 3004.071641 0 0.0000 292 | 0/8 13 h-lim-p 0.0000 20.0000 0.0111 | 0/8 14 h-lim-p 0.0000 20.0000 0.0111 Out... lnL = -3004.071641 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3004.071641 Node 7: lnL = -3004.071641 Node 8: lnL = -3004.071641 Node 9: lnL = -3004.071641 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 357 Sequential format.. Reading seq # 1: YBR079C_Sbay Reading seq # 2: YBR079C_Scer Reading seq # 3: YBR079C_Skud Reading seq # 4: YBR079C_Smik Reading seq # 5: YBR079C_Spar Sequences read.. Counting patterns.. # site patterns = 171 Counting frequencies.. 120 bytes for distance 27360 bytes for lkl0 21888 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.232401 0.022884 0.112251 0.181134 0.040262 0.190548 0.213724 0.067662 lnL0 = -1564.103940 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1564.103940 x= 0.23240 0.02288 0.11225 0.18113 0.04026 0.19055 0.21372 0.06766 1 h-lim-p 0.0041 0.1887 87.2675 1563.036245 8 0.0003 43 | 0/8 2 h-lim-p 0.0011 0.0091 11.2363 1562.988968 6 0.0008 68 | 0/8 3 h-lim-p 0.0016 0.0507 5.3575 1562.982587 6 0.0005 94 | 0/8 4 h-lim-p 0.0039 0.2021 0.7420 1562.982348 2 0.0009 111 | 0/8 5 h-lim-p 0.0073 2.3565 0.0920 1562.982343 2 0.0012 138 | 0/8 6 h-lim-p 0.0074 10.1175 0.0150 1562.982343 0 0.0016 159 | 0/8 7 h-lim-p 0.0144 20.0000 0.0017 1562.982322 0 0.1152 182 | 0/8 8 h-lim-p 0.0042 19.4888 0.0462 1562.982220 0 0.0084 203 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1562.982217 0 1.0938 223 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1562.982217 0 1.0938 243 | 0/8 11 h-lim-p 1.2939 20.0000 0.0000 1562.982217 0 1.2939 263 | 0/8 12 h-lim-p 0.9128 20.0000 0.0000 1562.982217 0 3.6513 285 | 0/8 13 h-lim-p 0.0006 4.1033 0.0799 1562.982217 0 0.0000 326 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1562.982217 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1562.982217 Node 7: lnL = -1562.982217 Node 8: lnL = -1562.982217 Node 9: lnL = -1562.982217 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 397 Sequential format.. Reading seq # 1: YBR080C_Sbay Reading seq # 2: YBR080C_Scer Reading seq # 3: YBR080C_Skud Reading seq # 4: YBR080C_Smik Reading seq # 5: YBR080C_Spar Sequences read.. Counting patterns.. # site patterns = 153 Counting frequencies.. 120 bytes for distance 24480 bytes for lkl0 19584 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.177058 0.091363 0.073097 0.110153 0.063098 0.182776 0.197824 0.029964 lnL0 = -1714.963030 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1714.963030 x= 0.17706 0.09136 0.07310 0.11015 0.06310 0.18278 0.19782 0.02996 1 h-lim-p 0.0098 0.0896 59.0842 1714.126013 8 0.0005 43 | 0/8 2 h-lim-p 0.0005 0.0044 30.8377 1713.935568 6 0.0005 67 | 0/8 3 h-lim-p 0.0013 0.0108 10.7387 1713.915272 7 0.0004 98 | 0/8 4 h-lim-p 0.0024 0.1068 1.8363 1713.914358 2 0.0006 115 | 0/8 5 h-lim-p 0.0028 0.6872 0.3710 1713.914314 2 0.0006 132 | 0/8 6 h-lim-p 0.0075 9.4287 0.0319 1713.914312 1 0.0018 155 | 0/8 7 h-lim-p 0.0024 12.4767 0.0246 1713.914306 0 0.0036 175 | 0/8 8 h-lim-p 0.0070 20.0000 0.0127 1713.913568 0 0.0836 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1713.913558 1 0.9961 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1713.913558 0 1.0938 240 | 0/8 11 h-lim-p 1.2009 20.0000 0.0000 1713.913558 0 2.4018 261 | 0/8 12 h-lim-p 0.2435 20.0000 0.0002 1713.913558 0 0.1218 281 | 0/8 13 h-lim-p 0.0219 20.0000 0.0009 1713.913558 0 0.0014 304 | 0/8 14 h-lim-p 0.0007 20.0000 0.0018 1713.913558 0 0.0000 344 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1713.913558 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1713.913558 Node 7: lnL = -1713.913558 Node 8: lnL = -1713.913558 Node 9: lnL = -1713.913558 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 848 Sequential format.. Reading seq # 1: YBR083W_Sbay Reading seq # 2: YBR083W_Scer Reading seq # 3: YBR083W_Skud Reading seq # 4: YBR083W_Smik Reading seq # 5: YBR083W_Spar Sequences read.. Counting patterns.. # site patterns = 202 Counting frequencies.. 120 bytes for distance 32320 bytes for lkl0 25856 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.149256 0.031999 0.037300 0.078413 0.042334 0.105557 0.125951 0.053112 lnL0 = -3145.495792 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3145.495792 x= 0.14926 0.03200 0.03730 0.07841 0.04233 0.10556 0.12595 0.05311 1 h-lim-p 0.0001 0.0012 223.9799 3143.562466 9 0.0001 45 | 0/8 2 h-lim-p 0.0003 0.0024 42.7119 3143.446214 5 0.0001 66 | 0/8 3 h-lim-p 0.0003 0.0089 21.9098 3143.426858 4 0.0001 86 | 0/8 4 h-lim-p 0.0003 0.0209 7.9984 3143.423346 2 0.0001 102 | 0/8 5 h-lim-p 0.0007 0.0945 1.5242 3143.423167 2 0.0002 119 | 0/8 6 h-lim-p 0.0006 0.3752 0.3995 3143.423156 1 0.0001 134 | 0/8 7 h-lim-p 0.0042 9.9584 0.0143 3143.423156 0 0.0002 157 | 0/8 8 h-lim-p 0.0496 20.0000 0.0001 3143.423152 0 1.1895 181 | 0/8 9 h-lim-p 1.9353 20.0000 0.0000 3143.423152 0 0.8467 201 | 0/8 10 h-lim-p 0.9519 20.0000 0.0000 3143.423152 0 0.2380 222 | 0/8 11 h-lim-p 0.1283 20.0000 0.0001 3143.423152 0 0.0010 248 | 0/8 12 h-lim-p 0.0006 20.0000 0.0001 3143.423152 0 0.0000 271 | 0/8 13 h-lim-p 0.0000 20.0000 0.0013 3143.423152 0 0.0000 297 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 3143.423152 0 0.0000 325 Out... lnL = -3143.423152 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3143.423152 Node 7: lnL = -3143.423152 Node 8: lnL = -3143.423152 Node 9: lnL = -3143.423152 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 856 Sequential format.. Reading seq # 1: YBR085C-A_Sbay Reading seq # 2: YBR085C-A_Scer Reading seq # 3: YBR085C-A_Skud Reading seq # 4: YBR085C-A_Smik Reading seq # 5: YBR085C-A_Spar Sequences read.. Counting patterns.. # site patterns = 285 Counting frequencies.. 120 bytes for distance 45600 bytes for lkl0 36480 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.273661 0.051279 0.078812 0.078566 0.064726 0.122932 0.227633 0.116165 lnL0 = -3381.230778 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3381.230778 x= 0.27366 0.05128 0.07881 0.07857 0.06473 0.12293 0.22763 0.11617 1 h-lim-p 0.0010 0.0081 159.9914 3378.175857 6 0.0003 35 | 0/8 2 h-lim-p 0.0002 0.0015 73.0461 3377.288543 0 0.0004 48 | 0/8 3 h-lim-p 0.0008 0.0080 37.0013 3377.195265 2 0.0002 65 | 0/8 4 h-lim-p 0.0003 0.0108 24.6185 3377.141817 5 0.0003 87 | 0/8 5 h-lim-p 0.0026 0.0788 2.4464 3377.140896 2 0.0003 105 | 0/8 6 h-lim-p 0.0004 0.1109 1.6832 3377.140521 3 0.0004 123 | 0/8 7 h-lim-p 0.0075 6.5498 0.0809 3377.140509 1 0.0015 138 | 0/8 8 h-lim-p 0.0337 20.0000 0.0036 3377.134325 0 0.5391 162 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 3377.134022 2 0.9961 186 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3377.134022 0 1.0938 206 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3377.134022 0 1.2500 226 | 0/8 12 h-lim-p 0.7991 20.0000 0.0000 3377.134022 0 0.1998 247 | 0/8 13 h-lim-p 0.0890 20.0000 0.0000 3377.134022 0 0.0445 267 | 0/8 14 h-lim-p 0.0240 20.0000 0.0000 3377.134022 0 0.0000 295 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 3377.134022 0 0.0000 322 Out... lnL = -3377.134022 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3377.134022 Node 7: lnL = -3377.134022 Node 8: lnL = -3377.134022 Node 9: lnL = -3377.134022 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 796 Sequential format.. Reading seq # 1: YBR085W_Sbay Reading seq # 2: YBR085W_Scer Reading seq # 3: YBR085W_Skud Reading seq # 4: YBR085W_Smik Reading seq # 5: YBR085W_Spar Sequences read.. Counting patterns.. # site patterns = 192 Counting frequencies.. 120 bytes for distance 30720 bytes for lkl0 24576 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.268364 0.000060 0.196477 0.262789 0.110146 0.750296 0.204346 0.015248 lnL0 = -3003.455767 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3003.455767 x= 0.26836 0.00006 0.19648 0.26279 0.11015 0.75030 0.20435 0.01525 1 h-lim-p 0.0000 0.0000 274.5691 3003.378305 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0033 86.9907 3000.497152 0 0.0010 40 | 1/8 3 h-lim-p 0.0012 0.0093 8.1396 3000.448370 2 0.0011 56 | 1/8 4 h-lim-p 0.0011 0.0636 8.4346 3000.321961 0 0.0042 70 | 1/8 5 h-lim-p 0.0011 0.0344 33.0717 2998.983498 0 0.0086 85 | 1/8 6 h-lim-p 0.0014 0.0108 113.9370 2998.073039 1 0.0017 99 | 1/8 7 h-lim-p 0.0829 0.6633 0.9037 2988.826670 0 0.3317 113 | 1/8 8 h-lim-p 0.7376 5.9012 0.1726 2988.476751 5 0.5904 141 | 0/8 9 h-lim-p 0.0544 0.8176 1.8748 2988.476210 3 0.0005 172 | 0/8 10 h-lim-p 0.0188 0.1696 0.0454 2988.458231 m 0.1696 185 | 1/8 11 h-lim-p 0.2333 20.0000 0.0329 2988.436234 0 0.4666 206 | 1/8 12 h-lim-p 1.6651 20.0000 0.0092 2988.432202 5 1.0279 238 | 1/8 13 h-lim-p 2.5000 20.0000 0.0024 2988.432147 2 0.6580 262 | 1/8 14 h-lim-p 2.5000 20.0000 0.0002 2988.432143 1 0.6152 284 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 2988.432142 0 1.0938 303 | 1/8 16 h-lim-p 1.7966 20.0000 0.0000 2988.432142 0 1.5720 322 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 2988.432142 0 1.0938 341 | 1/8 18 h-lim-p 1.7011 20.0000 0.0000 2988.432142 0 0.7442 360 | 1/8 19 h-lim-p 0.5266 20.0000 0.0000 2988.432142 0 0.0000 404 Out... lnL = -2988.432142 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2988.432142 Node 7: lnL = -2988.432142 Node 8: lnL = -2988.432142 Node 9: lnL = -2988.432142 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 757 Sequential format.. Reading seq # 1: YBR086C_Sbay Reading seq # 2: YBR086C_Scer Reading seq # 3: YBR086C_Skud Reading seq # 4: YBR086C_Smik Reading seq # 5: YBR086C_Spar Sequences read.. Counting patterns.. # site patterns = 213 Counting frequencies.. 120 bytes for distance 34080 bytes for lkl0 27264 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.188113 0.027817 0.066110 0.118888 0.070502 0.147607 0.179175 0.051245 lnL0 = -3177.002385 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3177.002385 x= 0.18811 0.02782 0.06611 0.11889 0.07050 0.14761 0.17918 0.05124 1 h-lim-p 0.0004 0.0028 204.2843 3174.991115 9 0.0001 45 | 0/8 2 h-lim-p 0.0004 0.0034 37.0610 3174.827510 5 0.0002 69 | 0/8 3 h-lim-p 0.0005 0.0138 17.1858 3174.805531 5 0.0002 94 | 0/8 4 h-lim-p 0.0006 0.0413 5.2508 3174.802035 3 0.0003 113 | 0/8 5 h-lim-p 0.0025 0.2275 0.5960 3174.801990 1 0.0002 129 | 0/8 6 h-lim-p 0.0011 1.8272 0.1403 3174.801988 0 0.0002 150 | 0/8 7 h-lim-p 0.0013 7.4172 0.0244 3174.801988 0 0.0003 171 | 0/8 8 h-lim-p 0.1304 20.0000 0.0001 3174.801986 0 1.0435 194 | 0/8 9 h-lim-p 1.4807 20.0000 0.0000 3174.801986 0 1.2956 214 | 0/8 10 h-lim-p 1.9490 20.0000 0.0000 3174.801986 0 0.4263 235 | 0/8 11 h-lim-p 0.1805 20.0000 0.0001 3174.801986 0 0.0014 261 | 0/8 12 h-lim-p 0.0008 20.0000 0.0001 3174.801986 0 0.0001 283 | 0/8 13 h-lim-p 0.0004 20.0000 0.0000 3174.801986 0 0.0000 315 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 3174.801986 0 0.0000 349 | 0/8 15 h-lim-p 0.0000 20.0000 0.0033 | 0/8 16 h-lim-p 0.0000 20.0000 0.0033 Out... lnL = -3174.801986 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3174.801986 Node 7: lnL = -3174.801986 Node 8: lnL = -3174.801986 Node 9: lnL = -3174.801986 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 758 Sequential format.. Reading seq # 1: YBR087W_Sbay Reading seq # 2: YBR087W_Scer Reading seq # 3: YBR087W_Skud Reading seq # 4: YBR087W_Smik Reading seq # 5: YBR087W_Spar Sequences read.. Counting patterns.. # site patterns = 211 Counting frequencies.. 120 bytes for distance 33760 bytes for lkl0 27008 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.185013 0.027786 0.060089 0.116825 0.072565 0.152520 0.182871 0.049029 lnL0 = -3179.112480 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3179.112480 x= 0.18501 0.02779 0.06009 0.11683 0.07257 0.15252 0.18287 0.04903 1 h-lim-p 0.0004 0.0032 208.5014 3177.057262 5 0.0001 33 | 0/8 2 h-lim-p 0.0005 0.0041 34.7314 3176.909834 5 0.0002 56 | 0/8 3 h-lim-p 0.0005 0.0134 17.0137 3176.887139 5 0.0002 78 | 0/8 4 h-lim-p 0.0006 0.0461 5.1654 3176.883959 4 0.0003 97 | 0/8 5 h-lim-p 0.0024 0.3764 0.5710 3176.883921 2 0.0002 115 | 0/8 6 h-lim-p 0.0010 0.7036 0.1395 3176.883919 0 0.0002 136 | 0/8 7 h-lim-p 0.0015 8.1817 0.0222 3176.883919 0 0.0003 157 | 0/8 8 h-lim-p 0.1323 20.0000 0.0001 3176.883907 0 1.0585 180 | 0/8 9 h-lim-p 1.8035 20.0000 0.0000 3176.883907 0 1.5780 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3176.883906 0 1.0938 220 | 0/8 11 h-lim-p 0.6278 20.0000 0.0000 3176.883906 0 0.5493 240 | 0/8 12 h-lim-p 0.2526 20.0000 0.0001 3176.883906 0 0.0069 264 | 0/8 13 h-lim-p 0.0023 20.0000 0.0002 3176.883906 0 0.0000 302 | 0/8 14 h-lim-p 0.0000 20.0000 0.0020 3176.883906 0 0.0000 330 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 3176.883906 0 0.0013 357 | 0/8 16 h-lim-p 0.0037 20.0000 0.0001 3176.883906 0 0.0000 386 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 3176.883906 0 0.0000 407 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0033 | 0/8 20 h-lim-p 0.0000 20.0000 0.0033 Out... lnL = -3176.883906 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3176.883906 Node 7: lnL = -3176.883906 Node 8: lnL = -3176.883906 Node 9: lnL = -3176.883906 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 475 Sequential format.. Reading seq # 1: YBR088C_Sbay Reading seq # 2: YBR088C_Scer Reading seq # 3: YBR088C_Skud Reading seq # 4: YBR088C_Smik Reading seq # 5: YBR088C_Spar Sequences read.. Counting patterns.. # site patterns = 167 Counting frequencies.. 120 bytes for distance 26720 bytes for lkl0 21376 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.159058 0.126872 0.053756 0.093760 0.075403 0.142908 0.157724 0.018804 lnL0 = -1900.898101 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1900.898101 x= 0.15906 0.12687 0.05376 0.09376 0.07540 0.14291 0.15772 0.01880 1 h-lim-p 0.0036 0.0689 102.2949 1899.632055 8 0.0003 44 | 0/8 2 h-lim-p 0.0012 0.0109 23.0539 1899.501915 5 0.0005 65 | 0/8 3 h-lim-p 0.0007 0.0053 14.3254 1899.473948 7 0.0004 93 | 0/8 4 h-lim-p 0.0022 0.0178 1.9032 1899.473249 4 0.0004 115 | 0/8 5 h-lim-p 0.0054 1.8895 0.1391 1899.473243 0 0.0006 129 | 0/8 6 h-lim-p 0.0015 3.9417 0.0538 1899.473243 0 0.0007 149 | 0/8 7 h-lim-p 0.0044 20.0000 0.0081 1899.473242 0 0.0039 169 | 0/8 8 h-lim-p 0.0279 20.0000 0.0011 1899.473131 0 0.3345 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1899.473127 1 0.9961 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1899.473127 0 1.0938 234 | 0/8 11 h-lim-p 0.9303 20.0000 0.0000 1899.473127 0 0.0032 261 | 0/8 12 h-lim-p 0.0006 20.0000 0.0001 1899.473127 0 0.0000 286 | 0/8 13 h-lim-p 0.0007 20.0000 0.0000 1899.473127 0 0.0000 314 Out... lnL = -1899.473127 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1899.473127 Node 7: lnL = -1899.473127 Node 8: lnL = -1899.473127 Node 9: lnL = -1899.473127 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 694 Sequential format.. Reading seq # 1: YBR089C-A_Sbay Reading seq # 2: YBR089C-A_Scer Reading seq # 3: YBR089C-A_Skud Reading seq # 4: YBR089C-A_Smik Reading seq # 5: YBR089C-A_Spar Sequences read.. Counting patterns.. # site patterns = 199 Counting frequencies.. 120 bytes for distance 31840 bytes for lkl0 25472 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.169091 0.053230 0.061328 0.073092 0.061597 0.145386 0.148859 0.044718 lnL0 = -2786.880097 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2786.880097 x= 0.16909 0.05323 0.06133 0.07309 0.06160 0.14539 0.14886 0.04472 1 h-lim-p 0.0005 0.0039 178.1868 2784.616266 8 0.0002 40 | 0/8 2 h-lim-p 0.0006 0.0046 24.1663 2784.552439 4 0.0002 60 | 0/8 3 h-lim-p 0.0004 0.0159 13.8228 2784.539452 3 0.0002 78 | 0/8 4 h-lim-p 0.0007 0.0413 3.3230 2784.538295 5 0.0002 103 | 0/8 5 h-lim-p 0.0011 0.3084 0.7032 2784.538237 2 0.0003 120 | 0/8 6 h-lim-p 0.0013 1.4380 0.1355 2784.538234 0 0.0003 141 | 0/8 7 h-lim-p 0.0012 5.5041 0.0314 2784.538234 0 0.0005 161 | 0/8 8 h-lim-p 0.0480 20.0000 0.0004 2784.537995 0 0.7687 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2784.537990 1 0.9961 207 | 0/8 10 h-lim-p 1.7169 20.0000 0.0000 2784.537990 0 0.0000 248 | 0/8 11 h-lim-p 0.0000 20.0000 0.0000 2784.537990 0 0.0000 278 Out... lnL = -2784.537990 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2784.537990 Node 7: lnL = -2784.537990 Node 8: lnL = -2784.537990 Node 9: lnL = -2784.537990 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 263 Sequential format.. Reading seq # 1: YBR091C_Sbay Reading seq # 2: YBR091C_Scer Reading seq # 3: YBR091C_Skud Reading seq # 4: YBR091C_Smik Reading seq # 5: YBR091C_Spar Sequences read.. Counting patterns.. # site patterns = 145 Counting frequencies.. 120 bytes for distance 23200 bytes for lkl0 18560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.311565 0.000060 0.301318 0.192174 0.145982 0.376418 0.385777 0.047991 lnL0 = -1198.321451 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1198.321451 x= 0.31156 0.00006 0.30132 0.19217 0.14598 0.37642 0.38578 0.04799 1 h-lim-p 0.0003 0.0025 82.7331 1193.797149 0 0.0013 24 | 0/8 2 h-lim-p 0.0004 0.0032 22.1899 1193.296828 m 0.0032 36 | 0/8 3 h-lim-p -0.0000 -0.0000 6.5133 h-lim-p: -4.95143763e-20 -3.96115011e-19 6.51332986e+00 1193.296828 .. | 0/8 4 h-lim-p 0.0000 0.0077 17.9173 1193.176867 0 0.0006 62 | 0/8 5 h-lim-p 0.0010 0.0083 8.5086 1193.119327 0 0.0021 75 | 0/8 6 h-lim-p 0.0063 0.3522 2.7994 1193.113426 5 0.0017 98 | 0/8 7 h-lim-p 0.0035 0.0278 1.0385 1193.111533 1 0.0043 112 | 0/8 8 h-lim-p 0.0070 0.0557 0.5751 1193.111246 4 0.0022 134 | 0/8 9 h-lim-p 0.0663 10.0342 0.0193 1193.110710 0 0.1327 155 | 0/8 10 h-lim-p 0.0353 9.9189 0.0725 1193.106979 1 0.0442 177 | 0/8 11 h-lim-p 0.0161 0.4614 0.1984 1193.106871 3 0.0052 205 | 0/8 12 h-lim-p 2.5000 20.0000 0.0002 1193.106862 1 0.9961 227 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1193.106862 0 1.0938 247 | 0/8 14 h-lim-p 1.2751 20.0000 0.0000 1193.106862 0 1.1157 267 | 0/8 15 h-lim-p 0.2532 20.0000 0.0000 1193.106862 0 0.0277 289 | 0/8 16 h-lim-p 0.0057 20.0000 0.0001 1193.106862 0 0.0014 310 | 0/8 17 h-lim-p 0.0010 20.0000 0.0002 1193.106862 0 0.0001 333 | 0/8 18 h-lim-p 0.0002 20.0000 0.0001 1193.106862 0 0.0000 356 | 0/8 19 h-lim-p 0.0002 20.0000 0.0000 1193.106862 0 0.0000 387 Out... lnL = -1193.106862 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1193.106862 Node 7: lnL = -1193.106862 Node 8: lnL = -1193.106862 Node 9: lnL = -1193.106862 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 470 Sequential format.. Reading seq # 1: YBR092C_Sbay Reading seq # 2: YBR092C_Scer Reading seq # 3: YBR092C_Skud Reading seq # 4: YBR092C_Smik Reading seq # 5: YBR092C_Spar Sequences read.. Counting patterns.. # site patterns = 156 Counting frequencies.. 120 bytes for distance 24960 bytes for lkl0 19968 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.158745 0.032715 0.056485 0.087033 0.049708 0.221203 0.142666 0.032657 lnL0 = -1902.175630 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1902.175630 x= 0.15874 0.03271 0.05648 0.08703 0.04971 0.22120 0.14267 0.03266 1 h-lim-p 0.0003 0.0024 122.4934 1900.748992 7 0.0002 37 | 0/8 2 h-lim-p 0.0005 0.0036 33.9202 1900.511664 2 0.0004 53 | 0/8 3 h-lim-p 0.0007 0.0263 21.3085 1900.468531 5 0.0003 75 | 0/8 4 h-lim-p 0.0004 0.0147 12.9093 1900.451874 6 0.0003 102 | 0/8 5 h-lim-p 0.0013 0.0797 2.7869 1900.450218 5 0.0005 128 | 0/8 6 h-lim-p 0.0018 0.1471 0.7280 1900.450132 2 0.0003 145 | 0/8 7 h-lim-p 0.0101 2.8952 0.0246 1900.450132 0 0.0011 167 | 0/8 8 h-lim-p 0.0188 20.0000 0.0015 1900.449731 0 0.4506 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1900.449727 0 1.2500 211 | 0/8 10 h-lim-p 2.4565 20.0000 0.0000 1900.449727 0 1.0747 231 | 0/8 11 h-lim-p 1.0033 20.0000 0.0000 1900.449727 0 0.0157 256 | 0/8 12 h-lim-p 0.0002 20.0000 0.0022 1900.449727 0 0.0000 279 | 0/8 13 h-lim-p 0.0003 20.0000 0.0001 1900.449727 0 0.0000 306 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 1900.449727 0 0.0000 336 Out... lnL = -1900.449727 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1900.449727 Node 7: lnL = -1900.449727 Node 8: lnL = -1900.449727 Node 9: lnL = -1900.449727 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 870 Sequential format.. Reading seq # 1: YBR093C_Sbay Reading seq # 2: YBR093C_Scer Reading seq # 3: YBR093C_Skud Reading seq # 4: YBR093C_Smik Reading seq # 5: YBR093C_Spar Sequences read.. Counting patterns.. # site patterns = 271 Counting frequencies.. 120 bytes for distance 43360 bytes for lkl0 34688 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.275839 0.079282 0.074262 0.071708 0.064467 0.236448 0.167329 0.100736 lnL0 = -3766.063943 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3766.063943 x= 0.27584 0.07928 0.07426 0.07171 0.06447 0.23645 0.16733 0.10074 1 h-lim-p 0.0004 0.0030 77.3114 3765.112059 6 0.0003 35 | 0/8 2 h-lim-p 0.0006 0.0051 29.2637 3765.027728 6 0.0002 63 | 0/8 3 h-lim-p 0.0003 0.0140 20.6493 3765.000171 7 0.0002 93 | 0/8 4 h-lim-p 0.0005 0.0145 8.2211 3764.995424 4 0.0002 113 | 0/8 5 h-lim-p 0.0018 0.3017 0.8004 3764.995335 3 0.0003 134 | 0/8 6 h-lim-p 0.0005 0.3069 0.4990 3764.995304 2 0.0003 159 | 0/8 7 h-lim-p 0.0126 16.8270 0.0119 3764.995304 0 0.0007 182 | 0/8 8 h-lim-p 0.1428 20.0000 0.0001 3764.995299 0 1.1425 205 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3764.995299 0 1.0938 225 | 0/8 10 h-lim-p 1.4653 20.0000 0.0000 3764.995299 0 2.1979 245 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3764.995299 0 0.3125 267 | 0/8 12 h-lim-p 0.0358 20.0000 0.0000 3764.995299 0 0.0090 288 | 0/8 13 h-lim-p 0.0037 20.0000 0.0000 3764.995299 0 0.0009 309 | 0/8 14 h-lim-p 0.0004 20.0000 0.0001 3764.995299 0 0.0000 335 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 3764.995299 0 0.0000 370 Out... lnL = -3764.995299 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3764.995299 Node 7: lnL = -3764.995299 Node 8: lnL = -3764.995299 Node 9: lnL = -3764.995299 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 269 Sequential format.. Reading seq # 1: YBR095C_Sbay Reading seq # 2: YBR095C_Scer Reading seq # 3: YBR095C_Skud Reading seq # 4: YBR095C_Smik Reading seq # 5: YBR095C_Spar Sequences read.. Counting patterns.. # site patterns = 122 Counting frequencies.. 120 bytes for distance 19520 bytes for lkl0 15616 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.204541 0.066782 0.057523 0.103137 0.075213 0.262149 0.236464 0.035987 lnL0 = -1226.432219 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1226.432219 x= 0.20454 0.06678 0.05752 0.10314 0.07521 0.26215 0.23646 0.03599 1 h-lim-p 0.0008 0.0066 36.2997 1226.029826 4 0.0006 30 | 0/8 2 h-lim-p 0.0008 0.0065 14.7751 1225.944791 6 0.0009 56 | 0/8 3 h-lim-p 0.0024 0.0571 5.4428 1225.930610 2 0.0011 72 | 0/8 4 h-lim-p 0.0030 0.3494 2.0133 1225.929618 5 0.0006 96 | 0/8 5 h-lim-p 0.0015 0.1891 0.7603 1225.929479 3 0.0006 114 | 0/8 6 h-lim-p 0.0037 1.7988 0.1167 1225.929472 2 0.0010 139 | 0/8 7 h-lim-p 0.0022 2.9777 0.0509 1225.929470 1 0.0011 162 | 0/8 8 h-lim-p 0.0969 20.0000 0.0006 1225.929282 0 1.1632 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1225.929277 1 0.9961 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1225.929277 0 1.2500 227 | 0/8 11 h-lim-p 1.1129 20.0000 0.0000 1225.929277 0 1.1129 247 | 0/8 12 h-lim-p 0.0077 20.0000 0.0019 1225.929277 0 0.0077 267 | 0/8 13 h-lim-p 0.0024 8.1160 0.0062 1225.929277 0 0.0024 287 | 0/8 14 h-lim-p 0.0011 3.7711 0.0133 1225.929277 0 0.0000 314 | 0/8 15 h-lim-p 0.0001 20.0000 0.0004 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1225.929277 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1225.929277 Node 7: lnL = -1225.929277 Node 8: lnL = -1225.929277 Node 9: lnL = -1225.929277 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 272 Sequential format.. Reading seq # 1: YBR096W_Sbay Reading seq # 2: YBR096W_Scer Reading seq # 3: YBR096W_Skud Reading seq # 4: YBR096W_Smik Reading seq # 5: YBR096W_Spar Sequences read.. Counting patterns.. # site patterns = 125 Counting frequencies.. 120 bytes for distance 20000 bytes for lkl0 16000 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.199902 0.039337 0.067338 0.115232 0.088719 0.293778 0.200765 0.033228 lnL0 = -1238.472653 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1238.472653 x= 0.19990 0.03934 0.06734 0.11523 0.08872 0.29378 0.20077 0.03323 1 h-lim-p 0.0041 0.0330 43.5220 1238.107125 5 0.0004 33 | 0/8 2 h-lim-p 0.0010 0.0084 8.4282 1238.078047 6 0.0008 56 | 0/8 3 h-lim-p 0.0021 0.1985 3.3333 1238.073419 3 0.0010 74 | 0/8 4 h-lim-p 0.0014 0.1343 2.2425 1238.071896 5 0.0009 99 | 0/8 5 h-lim-p 0.0066 0.5150 0.2882 1238.071866 2 0.0007 117 | 0/8 6 h-lim-p 0.0340 20.0000 0.0062 1238.071866 0 0.0019 140 | 0/8 7 h-lim-p 0.0041 20.0000 0.0028 1238.071866 0 0.0041 160 | 0/8 8 h-lim-p 0.0246 20.0000 0.0005 1238.071858 0 0.1965 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1238.071858 0 1.0938 203 | 0/8 10 h-lim-p 1.7699 20.0000 0.0000 1238.071858 0 1.5487 223 | 0/8 11 h-lim-p 2.1660 20.0000 0.0000 1238.071858 0 0.5415 244 | 0/8 12 h-lim-p 0.1831 20.0000 0.0000 1238.071858 0 0.0029 269 | 0/8 13 h-lim-p 0.0010 20.0000 0.0001 1238.071858 0 0.0020 290 | 0/8 14 h-lim-p 0.0010 20.0000 0.0002 1238.071858 0 0.0000 328 | 0/8 15 h-lim-p 0.0000 20.0000 0.0007 1238.071858 0 0.0000 352 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 1238.071858 0 0.0000 386 | 0/8 17 h-lim-p 0.0000 20.0000 0.0007 | 0/8 18 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -1238.071858 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1238.071858 Node 7: lnL = -1238.071858 Node 8: lnL = -1238.071858 Node 9: lnL = -1238.071858 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 406 Sequential format.. Reading seq # 1: YBR101C_Sbay Reading seq # 2: YBR101C_Scer Reading seq # 3: YBR101C_Skud Reading seq # 4: YBR101C_Smik Reading seq # 5: YBR101C_Spar Sequences read.. Counting patterns.. # site patterns = 182 Counting frequencies.. 120 bytes for distance 29120 bytes for lkl0 23296 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.257044 0.134042 0.089913 0.133934 0.118699 0.230645 0.184417 0.056010 lnL0 = -1913.618136 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1913.618136 x= 0.25704 0.13404 0.08991 0.13393 0.11870 0.23065 0.18442 0.05601 1 h-lim-p 0.0011 0.0087 58.2671 1912.711873 8 0.0006 41 | 0/8 2 h-lim-p 0.0013 0.0101 13.7666 1912.650422 5 0.0007 64 | 0/8 3 h-lim-p 0.0016 0.0644 5.6904 1912.640324 5 0.0007 85 | 0/8 4 h-lim-p 0.0027 0.1947 1.5379 1912.639331 4 0.0009 108 | 0/8 5 h-lim-p 0.0071 0.5366 0.1967 1912.639314 2 0.0009 126 | 0/8 6 h-lim-p 0.0050 7.5338 0.0345 1912.639314 0 0.0011 147 | 0/8 7 h-lim-p 0.0062 20.0000 0.0061 1912.639314 0 0.0013 168 | 0/8 8 h-lim-p 0.0997 20.0000 0.0001 1912.639310 0 0.7975 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1912.639310 0 1.0938 211 | 0/8 10 h-lim-p 2.4493 20.0000 0.0000 1912.639310 0 1.0716 231 | 0/8 11 h-lim-p 0.9577 20.0000 0.0000 1912.639310 0 7.6612 254 | 0/8 12 h-lim-p 0.1281 20.0000 0.0007 1912.639310 0 0.0000 295 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 1912.639310 0 0.0000 330 Out... lnL = -1912.639310 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1912.639310 Node 7: lnL = -1912.639310 Node 8: lnL = -1912.639310 Node 9: lnL = -1912.639310 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 421 Sequential format.. Reading seq # 1: YBR102C_Sbay Reading seq # 2: YBR102C_Scer Reading seq # 3: YBR102C_Skud Reading seq # 4: YBR102C_Smik Reading seq # 5: YBR102C_Spar Sequences read.. Counting patterns.. # site patterns = 168 Counting frequencies.. 120 bytes for distance 26880 bytes for lkl0 21504 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.213783 0.077818 0.090279 0.168858 0.063758 0.175443 0.168803 0.047339 lnL0 = -1891.620032 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1891.620032 x= 0.21378 0.07782 0.09028 0.16886 0.06376 0.17544 0.16880 0.04734 1 h-lim-p 0.0053 0.0423 52.5236 1891.079392 8 0.0004 45 | 0/8 2 h-lim-p 0.0022 0.0173 7.2348 1891.067820 3 0.0005 64 | 0/8 3 h-lim-p 0.0010 0.0625 3.2400 1891.066259 5 0.0004 88 | 0/8 4 h-lim-p 0.0013 0.2273 0.8866 1891.066013 3 0.0007 107 | 0/8 5 h-lim-p 0.0036 1.9316 0.1726 1891.066004 2 0.0007 132 | 0/8 6 h-lim-p 0.0203 20.0000 0.0058 1891.066004 0 0.0022 154 | 0/8 7 h-lim-p 0.0135 20.0000 0.0010 1891.065997 0 0.1078 177 | 0/8 8 h-lim-p 0.0019 7.4565 0.0532 1891.065973 0 0.0039 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1891.065971 0 1.0938 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1891.065971 0 1.0938 238 | 0/8 11 h-lim-p 1.1433 20.0000 0.0000 1891.065971 0 2.2865 259 | 0/8 12 h-lim-p 1.5402 20.0000 0.0000 1891.065971 0 1.3477 279 | 0/8 13 h-lim-p 0.0860 20.0000 0.0003 1891.065971 0 0.0027 303 | 0/8 14 h-lim-p 0.0009 20.0000 0.0009 1891.065971 0 0.0005 323 | 0/8 15 h-lim-p 0.0001 10.6074 0.0065 1891.065971 0 0.0000 354 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 1891.065971 0 0.0000 388 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 | 0/8 18 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1891.065971 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1891.065971 Node 7: lnL = -1891.065971 Node 8: lnL = -1891.065971 Node 9: lnL = -1891.065971 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 421 Sequential format.. Reading seq # 1: YBR103W_Sbay Reading seq # 2: YBR103W_Scer Reading seq # 3: YBR103W_Skud Reading seq # 4: YBR103W_Smik Reading seq # 5: YBR103W_Spar Sequences read.. Counting patterns.. # site patterns = 174 Counting frequencies.. 120 bytes for distance 27840 bytes for lkl0 22272 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.213234 0.081074 0.093892 0.161763 0.060164 0.178612 0.170326 0.046365 lnL0 = -1879.445394 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1879.445394 x= 0.21323 0.08107 0.09389 0.16176 0.06016 0.17861 0.17033 0.04636 1 h-lim-p 0.0004 0.0035 53.9046 1878.862293 2 0.0004 26 | 0/8 2 h-lim-p 0.0012 0.0149 18.5663 1878.819598 2 0.0003 43 | 0/8 3 h-lim-p 0.0010 0.0310 4.9517 1878.813710 2 0.0005 59 | 0/8 4 h-lim-p 0.0014 0.1280 1.7845 1878.812904 3 0.0006 77 | 0/8 5 h-lim-p 0.0031 1.0892 0.3340 1878.812870 1 0.0006 92 | 0/8 6 h-lim-p 0.0485 20.0000 0.0042 1878.812849 2 0.0387 116 | 0/8 7 h-lim-p 0.0033 6.9574 0.0500 1878.812379 0 0.0130 138 | 0/8 8 h-lim-p 0.0015 0.5775 0.4422 1878.812261 4 0.0009 169 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1878.812257 1 0.9961 191 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1878.812257 0 2.1875 211 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1878.812257 0 1.0938 231 | 0/8 12 h-lim-p 0.2083 20.0000 0.0000 1878.812257 0 0.1562 251 | 0/8 13 h-lim-p 0.0224 20.0000 0.0003 1878.812257 0 0.0007 275 | 0/8 14 h-lim-p 0.0002 20.0000 0.0013 1878.812257 0 0.0000 298 | 0/8 15 h-lim-p 0.0002 20.0000 0.0001 1878.812257 0 0.0000 321 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 1878.812257 0 0.0000 352 Out... lnL = -1878.812257 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1878.812257 Node 7: lnL = -1878.812257 Node 8: lnL = -1878.812257 Node 9: lnL = -1878.812257 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 316 Sequential format.. Reading seq # 1: YBR107C_Sbay Reading seq # 2: YBR107C_Scer Reading seq # 3: YBR107C_Skud Reading seq # 4: YBR107C_Smik Reading seq # 5: YBR107C_Spar Sequences read.. Counting patterns.. # site patterns = 121 Counting frequencies.. 120 bytes for distance 19360 bytes for lkl0 15488 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.158571 0.112146 0.065836 0.105184 0.078851 0.205851 0.103453 0.015853 lnL0 = -1295.870692 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1295.870692 x= 0.15857 0.11215 0.06584 0.10518 0.07885 0.20585 0.10345 0.01585 1 h-lim-p 0.0020 0.0159 43.8375 1295.452315 2 0.0005 27 | 0/8 2 h-lim-p 0.0014 0.0111 12.1137 1295.409488 6 0.0006 50 | 0/8 3 h-lim-p 0.0017 0.0441 4.4086 1295.404755 4 0.0006 72 | 0/8 4 h-lim-p 0.0016 0.1340 1.5179 1295.404020 3 0.0007 90 | 0/8 5 h-lim-p 0.0031 0.2719 0.3614 1295.403980 2 0.0007 107 | 0/8 6 h-lim-p 0.0022 3.7639 0.1083 1295.403977 1 0.0006 130 | 0/8 7 h-lim-p 0.0060 6.1777 0.0099 1295.403976 0 0.0013 151 | 0/8 8 h-lim-p 0.0285 20.0000 0.0005 1295.403918 0 0.4566 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1295.403916 0 1.0938 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1295.403916 0 1.0938 215 | 0/8 11 h-lim-p 1.0299 20.0000 0.0000 1295.403916 0 2.0597 236 | 0/8 12 h-lim-p 0.6641 20.0000 0.0001 1295.403916 0 0.0000 270 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 1295.403916 0 0.0000 292 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 1295.403916 0 0.0000 323 Out... lnL = -1295.403916 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1295.403916 Node 7: lnL = -1295.403916 Node 8: lnL = -1295.403916 Node 9: lnL = -1295.403916 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 249 Sequential format.. Reading seq # 1: YBR109C_Sbay Reading seq # 2: YBR109C_Scer Reading seq # 3: YBR109C_Skud Reading seq # 4: YBR109C_Smik Reading seq # 5: YBR109C_Spar Sequences read.. Counting patterns.. # site patterns = 102 Counting frequencies.. 120 bytes for distance 16320 bytes for lkl0 13056 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.150646 0.097340 0.058513 0.127529 0.063607 0.200514 0.165816 0.000457 lnL0 = -1082.340500 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1082.340500 x= 0.15065 0.09734 0.05851 0.12753 0.06361 0.20051 0.16582 0.00046 1 h-lim-p 0.0003 0.0021 61.3741 1081.100471 0 0.0008 23 | 0/8 2 h-lim-p 0.0002 0.0014 23.0425 1080.949601 0 0.0007 37 | 0/8 3 h-lim-p 0.0002 0.0019 10.5526 1080.929901 0 0.0005 50 | 0/8 4 h-lim-p 0.0018 0.0824 2.8747 1080.925924 5 0.0011 75 | 0/8 5 h-lim-p 0.0008 0.0067 0.9712 1080.925643 2 0.0006 91 | 0/8 6 h-lim-p 0.0045 2.0006 0.1389 1080.925587 3 0.0024 118 | 0/8 7 h-lim-p 0.0061 0.2052 0.0545 1080.924796 0 0.0246 140 | 0/8 8 h-lim-p 0.0051 0.6191 0.2645 1080.911119 0 0.0203 162 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1080.911106 2 0.9961 186 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1080.911106 0 1.0938 206 | 0/8 11 h-lim-p 1.2121 20.0000 0.0000 1080.911106 0 2.4243 227 | 0/8 12 h-lim-p 0.2747 17.0629 0.0002 1080.911106 0 0.0172 250 | 0/8 13 h-lim-p 0.0028 2.7366 0.0011 1080.911106 0 0.0001 274 | 0/8 14 h-lim-p 0.0001 2.1855 0.0014 1080.911106 0 0.0000 295 | 0/8 15 h-lim-p 0.0000 20.0000 0.0034 1080.911106 0 0.0000 322 | 0/8 16 h-lim-p 0.0000 17.6958 0.0005 1080.911106 0 0.0000 348 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 1080.911106 0 0.0026 376 | 0/8 18 h-lim-p 0.0057 20.0000 0.0001 1080.911106 0 0.0000 408 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 1080.911106 0 0.0000 433 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 1080.911106 0 0.0000 456 | 0/8 21 h-lim-p 0.0000 5.4577 0.0006 1080.911106 0 0.0000 485 | 0/8 22 h-lim-p 0.0000 20.0000 0.0012 | 0/8 23 h-lim-p 0.0000 20.0000 0.0012 Out... lnL = -1080.911106 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1080.911106 Node 7: lnL = -1080.911106 Node 8: lnL = -1080.911106 Node 9: lnL = -1080.911106 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 39 Sequential format.. Reading seq # 1: YBR110W_Sbay Reading seq # 2: YBR110W_Scer Reading seq # 3: YBR110W_Skud Reading seq # 4: YBR110W_Smik Reading seq # 5: YBR110W_Spar Sequences read.. Counting patterns.. # site patterns = 32 Counting frequencies.. 120 bytes for distance 5120 bytes for lkl0 4096 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.308796 0.389951 0.320818 0.363954 0.068583 0.210884 0.295607 0.000060 lnL0 = -220.399317 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 220.399317 x= 0.30880 0.38995 0.32082 0.36395 0.06858 0.21088 0.29561 0.00006 1 h-lim-p 0.0000 0.0000 17.0873 220.395468 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0336 13.8215 219.665928 0 0.0153 44 | 1/8 3 h-lim-p 0.0111 0.0887 5.5745 219.444694 0 0.0166 56 | 1/8 4 h-lim-p 0.0163 0.1301 2.3095 219.394558 4 0.0163 76 | 1/8 5 h-lim-p 0.0237 0.1899 1.0945 219.345506 0 0.0356 88 | 0/8 6 h-lim-p 0.0064 0.0515 5.7255 219.146564 0 0.0193 101 | 0/8 7 h-lim-p 0.0233 0.1862 1.6031 219.018951 0 0.0466 114 | 0/8 8 h-lim-p 0.0197 0.1576 1.0998 218.693797 m 0.1576 126 | 0/8 9 h-lim-p 0.0000 0.0000 1.6878 h-lim-p: 4.79820818e-19 3.83856654e-18 1.68775870e+00 218.693797 .. | 0/8 10 h-lim-p 0.0000 0.1548 3.3228 218.624860 0 0.0154 156 | 0/8 11 h-lim-p 0.0013 0.0106 2.2049 218.606061 m 0.0106 168 | 0/8 12 h-lim-p 0.0169 0.2255 1.3779 218.600639 4 0.0083 188 | 0/8 13 h-lim-p 0.0205 1.1364 0.5586 218.598304 2 0.0192 204 | 0/8 14 h-lim-p 0.0814 1.3805 0.1321 218.598059 4 0.0214 233 | 0/8 15 h-lim-p 0.0471 0.3771 0.0443 218.597360 0 0.1414 254 | 0/8 16 h-lim-p 0.0733 4.0989 0.0854 218.595765 1 0.0916 276 | 0/8 17 h-lim-p 0.0384 2.3462 0.2038 218.594995 5 0.0273 307 | 0/8 18 h-lim-p 2.5000 20.0000 0.0008 218.594974 2 0.9961 331 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 218.594974 0 1.0938 351 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 218.594974 0 1.0938 371 | 0/8 21 h-lim-p 1.3005 20.0000 0.0000 218.594974 0 3.9015 392 | 0/8 22 h-lim-p 0.3920 20.0000 0.0000 218.594974 0 0.0490 414 | 0/8 23 h-lim-p 0.0050 20.0000 0.0002 218.594974 0 0.0000 442 | 0/8 24 h-lim-p 0.0000 20.0000 0.0001 218.594974 0 0.0000 464 | 0/8 25 h-lim-p 0.0001 20.0000 0.0000 218.594974 0 0.0000 487 Out... lnL = -218.594974 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -218.594974 Node 7: lnL = -218.594974 Node 8: lnL = -218.594974 Node 9: lnL = -218.594974 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 964 Sequential format.. Reading seq # 1: YBR111C_Sbay Reading seq # 2: YBR111C_Scer Reading seq # 3: YBR111C_Skud Reading seq # 4: YBR111C_Smik Reading seq # 5: YBR111C_Spar Sequences read.. Counting patterns.. # site patterns = 177 Counting frequencies.. 120 bytes for distance 28320 bytes for lkl0 22656 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.200260 0.116949 0.086549 0.105523 0.021285 0.595427 0.191992 0.000060 lnL0 = -3070.333588 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3070.333588 x= 0.20026 0.11695 0.08655 0.10552 0.02129 0.59543 0.19199 0.00006 1 h-lim-p 0.0000 0.0000 534.6786 3069.898339 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0003 523.4353 3056.624013 8 0.0001 58 | 1/8 3 h-lim-p 0.0022 0.0174 12.0189 3056.597529 7 0.0003 89 | 1/8 4 h-lim-p 0.0002 0.0153 16.7480 3056.570326 0 0.0004 101 | 1/8 5 h-lim-p 0.0004 0.0067 17.1844 3055.985692 m 0.0067 115 | 1/8 6 h-lim-p -0.0000 -0.0000 193.2624 h-lim-p: -4.26357329e-21 -3.41085863e-20 1.93262413e+02 3055.985692 .. | 1/8 7 h-lim-p 0.0000 0.0062 537.5883 3049.737285 0 0.0001 137 | 1/8 8 h-lim-p 0.0000 0.0000 59.9351 3049.621108 m 0.0000 149 | 2/8 9 h-lim-p 0.0001 0.0087 24.4852 3049.532049 0 0.0003 163 | 2/8 10 h-lim-p 0.0041 0.0930 2.0259 3049.530957 4 0.0004 187 | 2/8 11 h-lim-p 0.0006 0.3582 1.2773 3049.524560 0 0.0048 202 | 2/8 12 h-lim-p 0.0006 0.0682 10.1782 3049.476452 0 0.0036 216 | 2/8 13 h-lim-p 0.4466 12.0518 0.0826 3049.350395 0 0.6699 228 | 2/8 14 h-lim-p 0.0729 0.9951 0.7590 3049.299076 4 0.0766 254 | 2/8 15 h-lim-p 2.5000 20.0000 0.0073 3049.297686 4 0.9169 282 | 1/8 16 h-lim-p 0.0431 7.4980 0.1547 3049.297685 0 0.0006 305 | 1/8 17 h-lim-p 0.1324 1.0595 0.0005 3049.297681 m 1.0595 324 | 2/8 18 h-lim-p 2.5000 20.0000 0.0000 3049.297681 0 2.1875 343 | 2/8 19 h-lim-p 1.0214 20.0000 0.0001 3049.297681 0 0.8937 361 | 2/8 20 h-lim-p 1.3262 20.0000 0.0000 3049.297681 0 1.1604 379 | 2/8 21 h-lim-p 2.5000 20.0000 0.0000 3049.297681 0 2.1875 397 | 2/8 22 h-lim-p 1.8427 20.0000 0.0000 3049.297681 0 0.8062 415 | 2/8 23 h-lim-p 2.5000 20.0000 0.0000 3049.297681 0 0.0006 444 Out... lnL = -3049.297681 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3049.297681 Node 7: lnL = -3049.297681 Node 8: lnL = -3049.297681 Node 9: lnL = -3049.297681 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 864 Sequential format.. Reading seq # 1: YBR112C_Sbay Reading seq # 2: YBR112C_Scer Reading seq # 3: YBR112C_Skud Reading seq # 4: YBR112C_Smik Reading seq # 5: YBR112C_Spar Sequences read.. Counting patterns.. # site patterns = 216 Counting frequencies.. 120 bytes for distance 34560 bytes for lkl0 27648 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.158522 0.046945 0.031261 0.036086 0.028075 0.087897 0.045811 0.071612 lnL0 = -2823.002246 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2823.002246 x= 0.15852 0.04695 0.03126 0.03609 0.02807 0.08790 0.04581 0.07161 1 h-lim-p 0.0001 0.0009 316.2659 2820.112706 7 0.0001 39 | 0/8 2 h-lim-p 0.0001 0.0007 67.7331 2819.970131 7 0.0001 67 | 0/8 3 h-lim-p 0.0003 0.0068 14.0656 2819.961138 6 0.0001 94 | 0/8 4 h-lim-p 0.0002 0.0209 6.1060 2819.959190 5 0.0001 118 | 0/8 5 h-lim-p 0.0006 0.1167 1.3489 2819.959082 2 0.0001 135 | 0/8 6 h-lim-p 0.0004 0.2650 0.4250 2819.959069 2 0.0002 151 | 0/8 7 h-lim-p 0.0034 6.4152 0.0198 2819.959069 0 0.0004 173 | 0/8 8 h-lim-p 0.0473 20.0000 0.0002 2819.958955 0 0.7563 197 | 0/8 9 h-lim-p 0.7240 20.0000 0.0002 2819.958952 0 1.0860 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2819.958952 0 1.0938 237 | 0/8 11 h-lim-p 0.2492 20.0000 0.0000 2819.958952 0 0.2180 257 | 0/8 12 h-lim-p 0.0734 20.0000 0.0001 2819.958952 0 0.0321 277 | 0/8 13 h-lim-p 0.0141 20.0000 0.0002 2819.958952 0 0.0000 323 | 0/8 14 h-lim-p 0.0000 20.0000 0.0023 | 0/8 15 h-lim-p 0.0000 20.0000 0.0023 Out... lnL = -2819.958952 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2819.958952 Node 7: lnL = -2819.958952 Node 8: lnL = -2819.958952 Node 9: lnL = -2819.958952 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 882 Sequential format.. Reading seq # 1: YBR114W_Sbay Reading seq # 2: YBR114W_Scer Reading seq # 3: YBR114W_Skud Reading seq # 4: YBR114W_Smik Reading seq # 5: YBR114W_Spar Sequences read.. Counting patterns.. # site patterns = 394 Counting frequencies.. 120 bytes for distance 63040 bytes for lkl0 50432 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.256512 0.296789 0.095929 0.137719 0.117408 0.245136 0.278611 0.000060 lnL0 = -4154.108548 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4154.108548 x= 0.25651 0.29679 0.09593 0.13772 0.11741 0.24514 0.27861 0.00006 1 h-lim-p 0.0000 0.0001 33.7894 4153.978907 m 0.0001 22 | 1/8 2 h-lim-p 0.0003 0.0147 17.6948 4153.911569 0 0.0005 35 | 1/8 3 h-lim-p 0.0011 0.0603 8.6613 4153.891697 6 0.0007 62 | 1/8 4 h-lim-p 0.0034 0.1810 1.7293 4153.890847 4 0.0006 85 | 1/8 5 h-lim-p 0.0026 1.5947 0.3788 4153.890698 3 0.0009 104 | 0/8 6 h-lim-p 0.0002 1.3963 1.7089 4153.889126 0 0.0012 125 | 0/8 7 h-lim-p 0.0032 0.8262 0.6648 4153.887862 0 0.0032 137 | 0/8 8 h-lim-p 0.0320 0.2559 0.0606 4153.821529 0 0.1279 159 | 0/8 9 h-lim-p 0.0006 0.0049 4.5088 4153.803971 0 0.0012 180 | 0/8 10 h-lim-p 0.3605 2.8839 0.0009 4153.803303 0 1.0815 193 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4153.803302 0 1.0938 213 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4153.803302 0 1.0938 233 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 4153.803302 0 2.1875 253 | 0/8 14 h-lim-p 1.7942 20.0000 0.0000 4153.803302 0 0.7850 273 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 4153.803302 0 0.2734 295 | 0/8 16 h-lim-p 0.1947 20.0000 0.0000 4153.803302 0 0.0000 335 Out... lnL = -4153.803302 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4153.803302 Node 7: lnL = -4153.803302 Node 8: lnL = -4153.803302 Node 9: lnL = -4153.803302 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 863 Sequential format.. Reading seq # 1: YBR118W_Sbay Reading seq # 2: YBR118W_Scer Reading seq # 3: YBR118W_Skud Reading seq # 4: YBR118W_Smik Reading seq # 5: YBR118W_Spar Sequences read.. Counting patterns.. # site patterns = 297 Counting frequencies.. 120 bytes for distance 47520 bytes for lkl0 38016 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.348284 0.000060 0.244303 0.162616 0.089282 0.938429 0.226799 0.038082 lnL0 = -3698.751235 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3698.751235 x= 0.34828 0.00006 0.24430 0.16262 0.08928 0.93843 0.22680 0.03808 1 h-lim-p 0.0000 0.0000 241.8221 3698.714244 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0055 67.0312 3696.791323 0 0.0010 40 | 1/8 3 h-lim-p 0.0005 0.0037 101.7734 3695.840972 5 0.0004 61 | 1/8 4 h-lim-p 0.0010 0.0095 41.7826 3695.242877 6 0.0010 86 | 1/8 5 h-lim-p 0.0012 0.0101 37.3362 3693.765036 0 0.0046 100 | 1/8 6 h-lim-p 0.0024 0.0195 68.9710 3692.906401 7 0.0014 128 | 1/8 7 h-lim-p 0.1202 0.9616 0.4858 3682.127578 0 0.7212 142 | 0/8 8 h-lim-p 0.0002 0.0018 67.9270 3681.754874 0 0.0014 163 | 0/8 9 h-lim-p 0.2226 1.7812 0.1014 3681.268236 0 0.8906 177 | 0/8 10 h-lim-p 0.1293 1.0344 0.0387 3681.141469 m 1.0344 197 | 1/8 11 h-lim-p 0.5584 4.4671 0.0249 3681.138123 4 0.1894 228 | 0/8 12 h-lim-p 0.0051 0.1328 0.9278 3681.137857 3 0.0015 255 | 0/8 13 h-lim-p 0.0036 0.0285 0.0481 3681.133892 m 0.0285 275 | 1/8 14 h-lim-p 0.0198 7.3273 0.0587 3681.131102 0 0.0395 296 | 1/8 15 h-lim-p 0.7985 20.0000 0.0029 3681.128045 0 1.5969 316 | 1/8 16 h-lim-p 2.5000 20.0000 0.0014 3681.127670 3 1.0004 341 | 1/8 17 h-lim-p 1.8612 20.0000 0.0007 3681.127632 2 1.2277 366 | 1/8 18 h-lim-p 2.5000 20.0000 0.0001 3681.127628 0 1.2500 385 | 1/8 19 h-lim-p 2.5000 20.0000 0.0000 3681.127628 0 1.0938 404 | 1/8 20 h-lim-p 1.4092 20.0000 0.0000 3681.127628 0 0.0002 435 | 1/8 21 h-lim-p 0.0004 20.0000 0.0000 3681.127628 0 0.0000 462 Out... lnL = -3681.127628 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3681.127628 Node 7: lnL = -3681.127628 Node 8: lnL = -3681.127628 Node 9: lnL = -3681.127628 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 500 Sequential format.. Reading seq # 1: YBR120C_Sbay Reading seq # 2: YBR120C_Scer Reading seq # 3: YBR120C_Skud Reading seq # 4: YBR120C_Smik Reading seq # 5: YBR120C_Spar Sequences read.. Counting patterns.. # site patterns = 203 Counting frequencies.. 120 bytes for distance 32480 bytes for lkl0 25984 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.198754 0.121267 0.059063 0.130250 0.088017 0.233993 0.174419 0.020777 lnL0 = -2176.330309 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2176.330309 x= 0.19875 0.12127 0.05906 0.13025 0.08802 0.23399 0.17442 0.02078 1 h-lim-p 0.0120 2.1764 60.2020 2175.699818 8 0.0004 41 | 0/8 2 h-lim-p 0.0012 0.0097 15.7225 2175.635245 2 0.0006 57 | 0/8 3 h-lim-p 0.0014 0.0198 6.2607 2175.629301 4 0.0004 79 | 0/8 4 h-lim-p 0.0023 0.1918 0.9743 2175.628943 4 0.0008 101 | 0/8 5 h-lim-p 0.0041 1.1787 0.1867 2175.628935 0 0.0005 123 | 0/8 6 h-lim-p 0.0164 20.0000 0.0051 2175.628934 1 0.0081 146 | 0/8 7 h-lim-p 0.0020 19.6145 0.0203 2175.628928 0 0.0041 167 | 0/8 8 h-lim-p 0.0034 20.0000 0.0243 2175.628805 0 0.0136 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2175.628803 0 1.0938 209 | 0/8 10 h-lim-p 2.3681 20.0000 0.0000 2175.628803 0 1.0360 229 | 0/8 11 h-lim-p 0.9468 20.0000 0.0000 2175.628803 0 0.0296 253 | 0/8 12 h-lim-p 0.0006 20.0000 0.0011 2175.628803 0 0.0000 285 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 2175.628803 0 0.0000 314 Out... lnL = -2175.628803 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2175.628803 Node 7: lnL = -2175.628803 Node 8: lnL = -2175.628803 Node 9: lnL = -2175.628803 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 663 Sequential format.. Reading seq # 1: YBR121C_Sbay Reading seq # 2: YBR121C_Scer Reading seq # 3: YBR121C_Skud Reading seq # 4: YBR121C_Smik Reading seq # 5: YBR121C_Spar Sequences read.. Counting patterns.. # site patterns = 213 Counting frequencies.. 120 bytes for distance 34080 bytes for lkl0 27264 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.144621 0.098677 0.015357 0.069196 0.070057 0.167862 0.169011 0.015893 lnL0 = -2691.184184 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2691.184184 x= 0.14462 0.09868 0.01536 0.06920 0.07006 0.16786 0.16901 0.01589 1 h-lim-p 0.0003 0.0025 359.0690 2687.512485 3 0.0001 29 | 0/8 2 h-lim-p 0.0002 0.0019 59.1463 2687.157349 5 0.0002 50 | 0/8 3 h-lim-p 0.0007 0.0065 17.9669 2687.123705 6 0.0002 78 | 0/8 4 h-lim-p 0.0005 0.0071 7.8336 2687.118587 4 0.0002 98 | 0/8 5 h-lim-p 0.0024 0.3493 0.6475 2687.118501 3 0.0004 119 | 0/8 6 h-lim-p 0.0018 1.3744 0.1529 2687.118496 1 0.0004 142 | 0/8 7 h-lim-p 0.0010 2.2770 0.0523 2687.118486 0 0.0021 163 | 0/8 8 h-lim-p 0.0245 8.6836 0.0045 2687.112599 0 0.2943 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 2687.112481 3 1.0004 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2687.112481 0 1.0938 232 | 0/8 11 h-lim-p 1.3391 20.0000 0.0000 2687.112481 0 1.1717 252 | 0/8 12 h-lim-p 0.3708 20.0000 0.0001 2687.112481 0 0.0007 280 | 0/8 13 h-lim-p 0.0000 0.9412 0.0283 2687.112481 0 0.0000 302 | 0/8 14 h-lim-p 0.0000 2.6223 0.0102 2687.112481 0 0.0000 337 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 2687.112481 0 0.0013 364 | 0/8 16 h-lim-p 0.0032 20.0000 0.0001 2687.112481 0 0.0000 390 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 2687.112481 0 0.0103 418 | 0/8 18 h-lim-p 0.0063 20.0000 0.0002 2687.112481 0 0.0000 446 | 0/8 19 h-lim-p 0.0000 20.0000 0.0008 2687.112481 0 0.0000 472 | 0/8 20 h-lim-p 0.0000 20.0000 0.0002 .. | 0/8 21 h-lim-p 0.0000 20.0000 0.0031 | 0/8 22 h-lim-p 0.0000 20.0000 0.0031 Out... lnL = -2687.112481 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2687.112481 Node 7: lnL = -2687.112481 Node 8: lnL = -2687.112481 Node 9: lnL = -2687.112481 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 190 Sequential format.. Reading seq # 1: YBR122C_Sbay Reading seq # 2: YBR122C_Scer Reading seq # 3: YBR122C_Skud Reading seq # 4: YBR122C_Smik Reading seq # 5: YBR122C_Spar Sequences read.. Counting patterns.. # site patterns = 129 Counting frequencies.. 120 bytes for distance 20640 bytes for lkl0 16512 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.308443 0.075773 0.041716 0.230933 0.138035 0.230076 0.346545 0.069427 lnL0 = -937.722762 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 937.722762 x= 0.30844 0.07577 0.04172 0.23093 0.13803 0.23008 0.34655 0.06943 1 h-lim-p 0.0031 0.0247 34.6243 936.909531 4 0.0015 31 | 0/8 2 h-lim-p 0.0012 0.0099 11.4932 936.823485 1 0.0015 45 | 0/8 3 h-lim-p 0.0051 0.0496 3.5076 936.812395 4 0.0020 65 | 0/8 4 h-lim-p 0.0085 0.1747 0.8211 936.811568 5 0.0026 91 | 0/8 5 h-lim-p 0.0062 0.3891 0.3481 936.811388 4 0.0035 121 | 0/8 6 h-lim-p 0.0160 5.5440 0.0759 936.811366 2 0.0062 145 | 0/8 7 h-lim-p 0.0294 18.6092 0.0160 936.811328 1 0.0294 167 | 0/8 8 h-lim-p 0.0227 20.0000 0.0206 936.810622 0 0.0910 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 936.810540 3 1.0004 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 936.810540 0 1.2500 235 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 936.810540 0 1.0938 255 | 0/8 12 h-lim-p 1.2948 20.0000 0.0000 936.810540 0 2.5896 276 | 0/8 13 h-lim-p 1.4991 20.0000 0.0000 936.810540 0 0.1405 299 | 0/8 14 h-lim-p 0.0060 20.0000 0.0001 936.810540 0 0.0000 326 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 936.810540 0 0.0000 360 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 936.810540 0 0.0000 394 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 936.810540 0 0.0000 417 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 936.810540 0 0.0000 483 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 936.810540 0 0.0000 505 | 0/8 21 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 22 h-lim-p 0.0000 20.0000 0.0001 936.810540 0 0.0000 573 | 0/8 23 h-lim-p 0.0000 20.0000 0.0001 | 0/8 24 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -936.810540 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -936.810540 Node 7: lnL = -936.810540 Node 8: lnL = -936.810540 Node 9: lnL = -936.810540 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 570 Sequential format.. Reading seq # 1: YBR125C_Sbay Reading seq # 2: YBR125C_Scer Reading seq # 3: YBR125C_Skud Reading seq # 4: YBR125C_Smik Reading seq # 5: YBR125C_Spar Sequences read.. Counting patterns.. # site patterns = 181 Counting frequencies.. 120 bytes for distance 28960 bytes for lkl0 23168 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.204762 0.024864 0.050274 0.088622 0.061342 0.148205 0.110832 0.076748 lnL0 = -2229.890469 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2229.890469 x= 0.20476 0.02486 0.05027 0.08862 0.06134 0.14821 0.11083 0.07675 1 h-lim-p 0.0018 0.0333 158.8556 2228.472881 8 0.0001 45 | 0/8 2 h-lim-p 0.0007 0.0055 20.5616 2228.410537 5 0.0003 67 | 0/8 3 h-lim-p 0.0008 0.0217 7.8802 2228.403506 6 0.0003 93 | 0/8 4 h-lim-p 0.0020 0.1048 1.0086 2228.403381 1 0.0003 109 | 0/8 5 h-lim-p 0.0006 0.5512 0.4103 2228.403360 0 0.0003 121 | 0/8 6 h-lim-p 0.0010 0.9983 0.1118 2228.403359 1 0.0002 144 | 0/8 7 h-lim-p 0.0117 20.0000 0.0023 2228.403358 0 0.0176 164 | 0/8 8 h-lim-p 0.0080 20.0000 0.0051 2228.403240 0 0.0478 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2228.403237 0 1.0938 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2228.403237 0 1.0938 226 | 0/8 11 h-lim-p 1.5563 20.0000 0.0000 2228.403237 0 3.1126 247 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2228.403237 0 0.0195 273 | 0/8 13 h-lim-p 0.0005 20.0000 0.0000 2228.403237 0 0.0002 294 | 0/8 14 h-lim-p 0.0003 20.0000 0.0000 2228.403237 0 0.0000 316 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0031 | 0/8 17 h-lim-p 0.0000 20.0000 0.0031 Out... lnL = -2228.403237 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2228.403237 Node 7: lnL = -2228.403237 Node 8: lnL = -2228.403237 Node 9: lnL = -2228.403237 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 280 Sequential format.. Reading seq # 1: YBR127C_Sbay Reading seq # 2: YBR127C_Scer Reading seq # 3: YBR127C_Skud Reading seq # 4: YBR127C_Smik Reading seq # 5: YBR127C_Spar Sequences read.. Counting patterns.. # site patterns = 59 Counting frequencies.. 120 bytes for distance 9440 bytes for lkl0 7552 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.061762 0.016504 0.009292 0.020767 0.019030 0.026371 0.067428 0.021097 lnL0 = -721.049626 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 721.049626 x= 0.06176 0.01650 0.00929 0.02077 0.01903 0.02637 0.06743 0.02110 1 h-lim-p 0.0001 0.0012 139.4616 720.618660 6 0.0001 35 | 0/8 2 h-lim-p 0.0002 0.0014 36.4013 720.529639 5 0.0001 58 | 0/8 3 h-lim-p 0.0003 0.0068 15.6125 720.510687 7 0.0002 87 | 0/8 4 h-lim-p 0.0006 0.0085 4.8819 720.509022 5 0.0002 110 | 0/8 5 h-lim-p 0.0003 0.0220 2.4980 720.508665 2 0.0001 126 | 0/8 6 h-lim-p 0.0010 0.1012 0.3595 720.508658 1 0.0001 142 | 0/8 7 h-lim-p 0.0012 0.8973 0.0308 720.508658 0 0.0003 163 | 0/8 8 h-lim-p 0.0328 20.0000 0.0002 720.508336 0 1.0489 188 | 0/8 9 h-lim-p 0.9541 20.0000 0.0003 720.508324 1 0.9541 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 720.508324 0 1.0938 230 | 0/8 11 h-lim-p 1.5379 20.0000 0.0000 720.508324 0 1.3457 250 | 0/8 12 h-lim-p 1.5701 20.0000 0.0000 720.508324 0 1.3738 270 | 0/8 13 h-lim-p 0.4072 20.0000 0.0001 720.508324 0 0.3563 290 | 0/8 14 h-lim-p 0.0361 20.0000 0.0008 720.508324 0 0.0023 313 | 0/8 15 h-lim-p 0.0008 15.1544 0.0023 720.508324 0 0.0000 341 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 720.508324 0 0.0000 361 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 720.508324 0 0.0000 394 | 0/8 18 h-lim-p 0.0000 20.0000 0.0011 | 0/8 19 h-lim-p 0.0000 20.0000 0.0011 Out... lnL = -720.508324 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -720.508324 Node 7: lnL = -720.508324 Node 8: lnL = -720.508324 Node 9: lnL = -720.508324 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 252 Sequential format.. Reading seq # 1: YBR128C_Sbay Reading seq # 2: YBR128C_Scer Reading seq # 3: YBR128C_Skud Reading seq # 4: YBR128C_Smik Reading seq # 5: YBR128C_Spar Sequences read.. Counting patterns.. # site patterns = 113 Counting frequencies.. 120 bytes for distance 18080 bytes for lkl0 14464 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.196909 0.006311 0.136743 0.108869 0.089715 0.297271 0.143708 0.025355 lnL0 = -1110.096989 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1110.096989 x= 0.19691 0.00631 0.13674 0.10887 0.08972 0.29727 0.14371 0.02535 1 h-lim-p 0.0011 0.0086 82.2900 1109.217592 9 0.0003 46 | 0/8 2 h-lim-p 0.0017 0.0133 11.6824 1109.146444 7 0.0010 76 | 0/8 3 h-lim-p 0.0019 0.0335 6.3334 1109.136617 5 0.0006 100 | 0/8 4 h-lim-p 0.0027 0.2051 1.4411 1109.135067 5 0.0016 125 | 0/8 5 h-lim-p 0.0029 0.1933 0.7839 1109.134843 4 0.0009 148 | 0/8 6 h-lim-p 0.0405 2.5262 0.0175 1109.134843 1 0.0012 174 | 0/8 7 h-lim-p 0.0057 20.0000 0.0039 1109.134841 0 0.0226 196 | 0/8 8 h-lim-p 0.0162 20.0000 0.0054 1109.134723 0 0.0649 218 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1109.134721 0 1.0938 238 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1109.134721 0 1.0938 258 | 0/8 11 h-lim-p 1.2622 20.0000 0.0000 1109.134721 0 1.2622 278 | 0/8 12 h-lim-p 0.7576 20.0000 0.0000 1109.134721 0 0.7576 298 | 0/8 13 h-lim-p 0.0137 20.0000 0.0011 1109.134721 0 0.0000 326 | 0/8 14 h-lim-p 0.0001 20.0000 0.0003 1109.134721 0 0.0000 360 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 1109.134721 0 0.0000 390 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 1109.134721 0 0.0000 413 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 1109.134721 0 0.0051 442 | 0/8 18 h-lim-p 0.0350 20.0000 0.0000 1109.134721 0 0.0000 471 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 1109.134721 0 0.0000 491 | 0/8 20 h-lim-p 0.0000 20.0000 0.0004 1109.134721 0 0.0000 526 | 0/8 21 h-lim-p 0.0000 20.0000 0.0007 1109.134721 0 0.0000 559 | 0/8 22 h-lim-p 0.0000 20.0000 0.0007 | 0/8 23 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -1109.134721 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1109.134721 Node 7: lnL = -1109.134721 Node 8: lnL = -1109.134721 Node 9: lnL = -1109.134721 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 306 Sequential format.. Reading seq # 1: YBR129C_Sbay Reading seq # 2: YBR129C_Scer Reading seq # 3: YBR129C_Skud Reading seq # 4: YBR129C_Smik Reading seq # 5: YBR129C_Spar Sequences read.. Counting patterns.. # site patterns = 116 Counting frequencies.. 120 bytes for distance 18560 bytes for lkl0 14848 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.229605 0.052477 0.090187 0.040593 0.066733 0.230728 0.079213 0.074301 lnL0 = -1107.629197 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1107.629197 x= 0.22960 0.05248 0.09019 0.04059 0.06673 0.23073 0.07921 0.07430 1 h-lim-p 0.0003 0.0025 71.4677 1106.461094 0 0.0006 23 | 0/8 2 h-lim-p 0.0010 0.0077 28.2394 1106.356694 6 0.0003 49 | 0/8 3 h-lim-p 0.0004 0.0072 20.1215 1106.268734 0 0.0006 61 | 0/8 4 h-lim-p 0.0037 0.0942 3.5442 1106.263633 2 0.0009 78 | 0/8 5 h-lim-p 0.0020 0.1038 1.5541 1106.262962 5 0.0006 102 | 0/8 6 h-lim-p 0.0014 0.3517 0.7016 1106.262768 4 0.0008 125 | 0/8 7 h-lim-p 0.0414 10.4515 0.0143 1106.251381 0 0.3311 148 | 0/8 8 h-lim-p 0.0028 0.0605 1.7148 1106.226908 0 0.0041 168 | 0/8 9 h-lim-p 2.5000 20.0000 0.0008 1106.226616 3 0.9961 186 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1106.226616 0 1.0938 206 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1106.226616 0 1.0938 226 | 0/8 12 h-lim-p 1.2473 20.0000 0.0000 1106.226616 0 1.0914 246 | 0/8 13 h-lim-p 0.4382 20.0000 0.0000 1106.226616 0 0.0068 271 | 0/8 14 h-lim-p 0.0007 20.0000 0.0002 1106.226616 0 0.0000 302 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 1106.226616 0 0.0000 330 Out... lnL = -1106.226616 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1106.226616 Node 7: lnL = -1106.226616 Node 8: lnL = -1106.226616 Node 9: lnL = -1106.226616 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 298 Sequential format.. Reading seq # 1: YBR130C_Sbay Reading seq # 2: YBR130C_Scer Reading seq # 3: YBR130C_Skud Reading seq # 4: YBR130C_Smik Reading seq # 5: YBR130C_Spar Sequences read.. Counting patterns.. # site patterns = 119 Counting frequencies.. 120 bytes for distance 19040 bytes for lkl0 15232 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.188532 0.156318 0.061400 0.116352 0.094794 0.240739 0.101917 0.009448 lnL0 = -1324.415341 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1324.415341 x= 0.18853 0.15632 0.06140 0.11635 0.09479 0.24074 0.10192 0.00945 1 h-lim-p 0.0002 0.0012 38.3929 1324.002590 0 0.0006 24 | 0/8 2 h-lim-p 0.0003 0.0022 14.7485 1323.926497 0 0.0011 38 | 0/8 3 h-lim-p 0.0042 0.0949 3.9663 1323.922418 5 0.0006 62 | 0/8 4 h-lim-p 0.0026 0.2231 0.8425 1323.922210 2 0.0006 79 | 0/8 5 h-lim-p 0.0018 0.0622 0.2855 1323.922160 3 0.0011 107 | 0/8 6 h-lim-p 0.0019 1.5486 0.1663 1323.922119 1 0.0016 129 | 0/8 7 h-lim-p 0.0098 0.7590 0.0277 1323.919978 0 0.0784 152 | 0/8 8 h-lim-p 0.0017 0.1640 1.2565 1323.911716 0 0.0035 173 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 1323.911530 3 1.0004 191 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1323.911530 0 1.0938 211 | 0/8 11 h-lim-p 1.3163 20.0000 0.0000 1323.911530 0 1.1517 231 | 0/8 12 h-lim-p 0.6870 20.0000 0.0000 1323.911530 0 0.0429 254 | 0/8 13 h-lim-p 0.0019 7.2569 0.0008 1323.911530 0 0.0005 275 | 0/8 14 h-lim-p 0.0002 2.6984 0.0023 1323.911530 0 0.0002 295 | 0/8 15 h-lim-p 0.0001 1.8037 0.0034 1323.911530 0 0.0000 319 | 0/8 16 h-lim-p 0.0001 20.0000 0.0002 1323.911530 0 0.0000 342 | 0/8 17 h-lim-p 0.0001 20.0000 0.0000 1323.911530 0 0.0000 363 | 0/8 18 h-lim-p 0.0001 20.0000 0.0000 1323.911530 0 0.0000 387 Out... lnL = -1323.911530 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1323.911530 Node 7: lnL = -1323.911530 Node 8: lnL = -1323.911530 Node 9: lnL = -1323.911530 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 298 Sequential format.. Reading seq # 1: YBR131W_Sbay Reading seq # 2: YBR131W_Scer Reading seq # 3: YBR131W_Skud Reading seq # 4: YBR131W_Smik Reading seq # 5: YBR131W_Spar Sequences read.. Counting patterns.. # site patterns = 132 Counting frequencies.. 120 bytes for distance 21120 bytes for lkl0 16896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.184477 0.162467 0.036538 0.121766 0.089380 0.204702 0.099380 0.016040 lnL0 = -1209.337202 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1209.337202 x= 0.18448 0.16247 0.03654 0.12177 0.08938 0.20470 0.09938 0.01604 1 h-lim-p 0.0019 0.0155 26.8731 1209.170891 8 0.0005 38 | 0/8 2 h-lim-p 0.0012 0.0193 10.5477 1209.120943 6 0.0010 63 | 0/8 3 h-lim-p 0.0017 0.0525 6.1365 1209.112155 6 0.0006 90 | 0/8 4 h-lim-p 0.0022 0.0670 1.6982 1209.111274 5 0.0007 116 | 0/8 5 h-lim-p 0.0018 0.1172 0.6475 1209.111101 3 0.0010 135 | 0/8 6 h-lim-p 0.0025 1.5426 0.2490 1209.111083 3 0.0007 162 | 0/8 7 h-lim-p 0.0048 4.0873 0.0346 1209.111083 1 0.0006 186 | 0/8 8 h-lim-p 0.1776 20.0000 0.0001 1209.111078 0 1.0659 208 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1209.111078 0 1.0938 228 | 0/8 10 h-lim-p 1.3007 20.0000 0.0000 1209.111078 0 1.1381 248 | 0/8 11 h-lim-p 0.7320 20.0000 0.0000 1209.111078 0 0.0100 273 | 0/8 12 h-lim-p 0.0005 20.0000 0.0005 1209.111078 0 0.0000 301 | 0/8 13 h-lim-p 0.0002 20.0000 0.0000 1209.111078 0 0.0000 332 Out... lnL = -1209.111078 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1209.111078 Node 7: lnL = -1209.111078 Node 8: lnL = -1209.111078 Node 9: lnL = -1209.111078 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 408 Sequential format.. Reading seq # 1: YBR132C_Sbay Reading seq # 2: YBR132C_Scer Reading seq # 3: YBR132C_Skud Reading seq # 4: YBR132C_Smik Reading seq # 5: YBR132C_Spar Sequences read.. Counting patterns.. # site patterns = 128 Counting frequencies.. 120 bytes for distance 20480 bytes for lkl0 16384 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.167958 0.062644 0.044762 0.055721 0.046437 0.088494 0.142707 0.049696 lnL0 = -1452.160291 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1452.160291 x= 0.16796 0.06264 0.04476 0.05572 0.04644 0.08849 0.14271 0.04970 1 h-lim-p 0.0005 0.0040 42.7372 1451.975949 3 0.0002 28 | 0/8 2 h-lim-p 0.0012 0.0190 7.4986 1451.965224 6 0.0004 54 | 0/8 3 h-lim-p 0.0012 0.1071 2.4053 1451.964628 4 0.0002 76 | 0/8 4 h-lim-p 0.0004 0.1424 1.2270 1451.964435 4 0.0003 97 | 0/8 5 h-lim-p 0.0015 1.0021 0.2574 1451.964424 0 0.0003 110 | 0/8 6 h-lim-p 0.0007 1.0822 0.1263 1451.964422 0 0.0003 130 | 0/8 7 h-lim-p 0.0020 6.6095 0.0217 1451.964422 0 0.0004 151 | 0/8 8 h-lim-p 0.1689 20.0000 0.0001 1451.964416 0 1.3514 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1451.964416 0 1.0938 194 | 0/8 10 h-lim-p 1.8436 20.0000 0.0000 1451.964416 0 1.6131 214 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1451.964416 0 0.5469 235 | 0/8 12 h-lim-p 0.2043 20.0000 0.0000 1451.964416 0 0.0032 260 | 0/8 13 h-lim-p 0.0014 20.0000 0.0000 1451.964416 0 0.0010 280 | 0/8 14 h-lim-p 0.0007 20.0000 0.0001 1451.964416 0 0.0000 320 | 0/8 15 h-lim-p 0.0000 20.0000 0.0019 | 0/8 16 h-lim-p 0.0000 20.0000 0.0019 Out... lnL = -1451.964416 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1451.964416 Node 7: lnL = -1451.964416 Node 8: lnL = -1451.964416 Node 9: lnL = -1451.964416 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 590 Sequential format.. Reading seq # 1: YBR133C_Sbay Reading seq # 2: YBR133C_Scer Reading seq # 3: YBR133C_Skud Reading seq # 4: YBR133C_Smik Reading seq # 5: YBR133C_Spar Sequences read.. Counting patterns.. # site patterns = 179 Counting frequencies.. 120 bytes for distance 28640 bytes for lkl0 22912 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.149560 0.051094 0.061246 0.090900 0.058999 0.142426 0.121148 0.024074 lnL0 = -2270.884335 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2270.884335 x= 0.14956 0.05109 0.06125 0.09090 0.05900 0.14243 0.12115 0.02407 1 h-lim-p 0.0003 0.0023 158.6628 2268.797108 8 0.0002 40 | 0/8 2 h-lim-p 0.0007 0.0055 28.2433 2268.676527 3 0.0003 58 | 0/8 3 h-lim-p 0.0007 0.0129 12.3649 2268.665002 5 0.0002 80 | 0/8 4 h-lim-p 0.0006 0.0344 3.6028 2268.663641 3 0.0002 98 | 0/8 5 h-lim-p 0.0075 1.2473 0.1108 2268.663639 1 0.0002 116 | 0/8 6 h-lim-p 0.0016 12.9324 0.0159 2268.663639 0 0.0007 136 | 0/8 7 h-lim-p 0.0020 18.1175 0.0056 2268.663634 0 0.0119 158 | 0/8 8 h-lim-p 0.0037 20.0000 0.0184 2268.663441 0 0.0146 180 | 0/8 9 h-lim-p 0.3065 20.0000 0.0009 2268.663429 0 1.2260 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 2268.663428 0 1.0938 222 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2268.663428 0 1.0938 242 | 0/8 12 h-lim-p 0.1543 20.0000 0.0000 2268.663428 0 0.0012 268 | 0/8 13 h-lim-p 0.0000 6.8882 0.0065 2268.663428 0 0.0000 290 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 2268.663428 0 0.0000 313 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 2268.663428 0 0.0000 344 | 0/8 16 h-lim-p 0.0000 20.0000 0.0011 2268.663428 0 0.0000 370 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 2268.663428 0 0.0000 390 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 2268.663428 0 0.0000 417 | 0/8 19 h-lim-p 0.0000 20.0000 0.0002 2268.663428 0 0.0000 450 | 0/8 20 h-lim-p 0.0000 20.0000 0.0011 2268.663428 0 0.0000 479 | 0/8 21 h-lim-p 0.0000 20.0000 0.0002 2268.663428 0 0.0000 513 | 0/8 22 h-lim-p 0.0000 20.0000 0.0011 2268.663428 0 0.0000 548 | 0/8 23 h-lim-p 0.0000 20.0000 0.0011 | 0/8 24 h-lim-p 0.0000 20.0000 0.0011 Out... lnL = -2268.663428 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2268.663428 Node 7: lnL = -2268.663428 Node 8: lnL = -2268.663428 Node 9: lnL = -2268.663428 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 220 Sequential format.. Reading seq # 1: YBR135W_Sbay Reading seq # 2: YBR135W_Scer Reading seq # 3: YBR135W_Skud Reading seq # 4: YBR135W_Smik Reading seq # 5: YBR135W_Spar Sequences read.. Counting patterns.. # site patterns = 82 Counting frequencies.. 120 bytes for distance 13120 bytes for lkl0 10496 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.163203 0.034476 0.041174 0.070137 0.054502 0.150711 0.123048 0.043816 lnL0 = -837.861678 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 837.861678 x= 0.16320 0.03448 0.04117 0.07014 0.05450 0.15071 0.12305 0.04382 1 h-lim-p 0.0002 0.0020 49.8452 837.453339 0 0.0005 23 | 0/8 2 h-lim-p 0.0014 0.0112 12.3096 837.412368 6 0.0006 48 | 0/8 3 h-lim-p 0.0017 0.0400 4.2165 837.406995 5 0.0007 69 | 0/8 4 h-lim-p 0.0016 0.0406 1.7189 837.406596 4 0.0003 90 | 0/8 5 h-lim-p 0.0019 0.5148 0.2865 837.406473 3 0.0015 108 | 0/8 6 h-lim-p 0.0024 0.6682 0.1785 837.406084 0 0.0048 129 | 0/8 7 h-lim-p 0.0075 0.7032 0.1134 837.373962 0 0.0602 152 | 0/8 8 h-lim-p 0.0021 0.0445 3.3203 837.363539 6 0.0012 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0010 837.362710 4 0.9422 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 837.362709 0 1.0938 227 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 837.362709 0 1.0938 247 | 0/8 12 h-lim-p 1.2969 20.0000 0.0000 837.362709 0 0.3242 268 | 0/8 13 h-lim-p 0.1276 20.0000 0.0000 837.362709 0 0.0159 290 | 0/8 14 h-lim-p 0.0070 20.0000 0.0000 837.362709 0 0.0017 311 | 0/8 15 h-lim-p 0.0008 20.0000 0.0001 837.362709 0 0.0000 349 | 0/8 16 h-lim-p 0.0000 20.0000 0.0005 | 0/8 17 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -837.362709 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -837.362709 Node 7: lnL = -837.362709 Node 8: lnL = -837.362709 Node 9: lnL = -837.362709 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 286 Sequential format.. Reading seq # 1: YBR137W_Sbay Reading seq # 2: YBR137W_Scer Reading seq # 3: YBR137W_Skud Reading seq # 4: YBR137W_Smik Reading seq # 5: YBR137W_Spar Sequences read.. Counting patterns.. # site patterns = 134 Counting frequencies.. 120 bytes for distance 21440 bytes for lkl0 17152 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.232513 0.078705 0.069417 0.160310 0.095036 0.170163 0.223410 0.042223 lnL0 = -1321.347663 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1321.347663 x= 0.23251 0.07871 0.06942 0.16031 0.09504 0.17016 0.22341 0.04222 1 h-lim-p 0.0006 0.0049 59.8584 1320.363206 6 0.0006 36 | 0/8 2 h-lim-p 0.0012 0.0095 13.7642 1320.296244 6 0.0007 64 | 0/8 3 h-lim-p 0.0019 0.0556 5.2633 1320.288495 5 0.0006 89 | 0/8 4 h-lim-p 0.0062 0.5676 0.5392 1320.288296 2 0.0014 106 | 0/8 5 h-lim-p 0.0048 2.2712 0.1550 1320.288282 2 0.0013 131 | 0/8 6 h-lim-p 0.0055 4.1118 0.0355 1320.288281 0 0.0012 152 | 0/8 7 h-lim-p 0.1272 20.0000 0.0003 1320.288223 0 1.0174 175 | 0/8 8 h-lim-p 0.0028 0.7600 0.1216 1320.288210 2 0.0014 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1320.288209 0 1.0938 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1320.288208 0 1.0938 240 | 0/8 11 h-lim-p 1.1888 20.0000 0.0000 1320.288208 0 0.1486 262 | 0/8 12 h-lim-p 0.0480 20.0000 0.0000 1320.288208 0 0.0240 282 | 0/8 13 h-lim-p 0.0108 20.0000 0.0001 1320.288208 0 0.0000 309 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 1320.288208 0 0.0000 336 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 1320.288208 0 0.0000 368 Out... lnL = -1320.288208 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1320.288208 Node 7: lnL = -1320.288208 Node 8: lnL = -1320.288208 Node 9: lnL = -1320.288208 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 341 Sequential format.. Reading seq # 1: YBR139W_Sbay Reading seq # 2: YBR139W_Scer Reading seq # 3: YBR139W_Skud Reading seq # 4: YBR139W_Smik Reading seq # 5: YBR139W_Spar Sequences read.. Counting patterns.. # site patterns = 133 Counting frequencies.. 120 bytes for distance 21280 bytes for lkl0 17024 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.170513 0.101825 0.062378 0.125284 0.089966 0.165123 0.153688 0.010806 lnL0 = -1489.953795 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1489.953795 x= 0.17051 0.10183 0.06238 0.12528 0.08997 0.16512 0.15369 0.01081 1 h-lim-p 0.0007 0.0056 85.6195 1488.738320 5 0.0004 33 | 0/8 2 h-lim-p 0.0009 0.0069 17.7282 1488.658745 7 0.0005 65 | 0/8 3 h-lim-p 0.0020 0.1109 4.5302 1488.654491 2 0.0004 82 | 0/8 4 h-lim-p 0.0043 0.8766 0.4621 1488.654419 4 0.0007 106 | 0/8 5 h-lim-p 0.0028 0.2714 0.1115 1488.654416 1 0.0006 129 | 0/8 6 h-lim-p 0.0027 10.4276 0.0224 1488.654415 0 0.0012 149 | 0/8 7 h-lim-p 0.0187 20.0000 0.0014 1488.654338 0 0.2248 172 | 0/8 8 h-lim-p 0.0018 0.6314 0.1835 1488.654166 0 0.0026 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1488.654165 0 1.0938 212 | 0/8 10 h-lim-p 2.2059 20.0000 0.0000 1488.654165 0 1.9302 232 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1488.654165 0 1.0938 252 | 0/8 12 h-lim-p 0.2807 20.0000 0.0000 1488.654165 0 3.3683 275 | 0/8 13 h-lim-p 0.2806 20.0000 0.0003 1488.654165 0 0.0022 301 | 0/8 14 h-lim-p 0.0004 11.8351 0.0018 1488.654165 0 0.0000 328 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 1488.654165 0 0.0000 359 | 0/8 16 h-lim-p 0.0000 20.0000 0.0010 | 0/8 17 h-lim-p 0.0000 20.0000 0.0010 Out... lnL = -1488.654165 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1488.654165 Node 7: lnL = -1488.654165 Node 8: lnL = -1488.654165 Node 9: lnL = -1488.654165 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 284 Sequential format.. Reading seq # 1: YBR141C_Sbay Reading seq # 2: YBR141C_Scer Reading seq # 3: YBR141C_Skud Reading seq # 4: YBR141C_Smik Reading seq # 5: YBR141C_Spar Sequences read.. Counting patterns.. # site patterns = 129 Counting frequencies.. 120 bytes for distance 20640 bytes for lkl0 16512 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.249000 0.069446 0.060198 0.177398 0.078213 0.137249 0.218011 0.063380 lnL0 = -1307.223002 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1307.223002 x= 0.24900 0.06945 0.06020 0.17740 0.07821 0.13725 0.21801 0.06338 1 h-lim-p 0.0004 0.0035 67.1479 1306.197621 1 0.0005 24 | 0/8 2 h-lim-p 0.0022 0.0174 10.5049 1306.157802 7 0.0007 54 | 0/8 3 h-lim-p 0.0013 0.0580 6.0938 1306.149515 3 0.0006 72 | 0/8 4 h-lim-p 0.0015 0.1015 2.2686 1306.146942 4 0.0012 92 | 0/8 5 h-lim-p 0.0057 0.3572 0.4740 1306.146817 3 0.0011 111 | 0/8 6 h-lim-p 0.0110 4.6399 0.0464 1306.146690 2 0.0124 136 | 0/8 7 h-lim-p 0.0174 3.4873 0.0332 1306.138118 0 0.1391 159 | 0/8 8 h-lim-p 0.0041 0.1803 1.1327 1306.137268 4 0.0012 189 | 0/8 9 h-lim-p 1.2071 20.0000 0.0011 1306.136407 3 0.9660 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1306.136406 0 1.0938 227 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1306.136406 0 1.0938 247 | 0/8 12 h-lim-p 1.0339 20.0000 0.0000 1306.136406 0 0.0000 281 Out... lnL = -1306.136406 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1306.136406 Node 7: lnL = -1306.136406 Node 8: lnL = -1306.136406 Node 9: lnL = -1306.136406 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 326 Sequential format.. Reading seq # 1: YBR142W_Sbay Reading seq # 2: YBR142W_Scer Reading seq # 3: YBR142W_Skud Reading seq # 4: YBR142W_Smik Reading seq # 5: YBR142W_Spar Sequences read.. Counting patterns.. # site patterns = 143 Counting frequencies.. 120 bytes for distance 22880 bytes for lkl0 18304 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.239253 0.076959 0.079421 0.169782 0.085829 0.075231 0.181506 0.064730 lnL0 = -1285.389888 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1285.389888 x= 0.23925 0.07696 0.07942 0.16978 0.08583 0.07523 0.18151 0.06473 1 h-lim-p 0.0014 0.0115 72.7383 1283.961994 3 0.0006 28 | 0/8 2 h-lim-p 0.0010 0.0081 18.7507 1283.804770 2 0.0009 44 | 0/8 3 h-lim-p 0.0019 0.0355 9.3250 1283.783529 6 0.0006 72 | 0/8 4 h-lim-p 0.0065 0.4220 0.8717 1283.782978 2 0.0015 89 | 0/8 5 h-lim-p 0.0058 0.9161 0.2259 1283.782950 2 0.0012 114 | 0/8 6 h-lim-p 0.0117 9.9039 0.0225 1283.782949 0 0.0026 135 | 0/8 7 h-lim-p 0.0415 20.0000 0.0014 1283.782766 0 0.3316 158 | 0/8 8 h-lim-p 0.0018 1.6018 0.2611 1283.782680 2 0.0015 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1283.782668 0 1.0938 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1283.782668 0 1.0938 222 | 0/8 11 h-lim-p 2.0304 20.0000 0.0000 1283.782668 0 0.8883 242 | 0/8 12 h-lim-p 0.6271 20.0000 0.0000 1283.782668 0 0.0196 266 | 0/8 13 h-lim-p 0.0032 20.0000 0.0001 1283.782668 0 0.0000 303 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1283.782668 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1283.782668 Node 7: lnL = -1283.782668 Node 8: lnL = -1283.782668 Node 9: lnL = -1283.782668 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 873 Sequential format.. Reading seq # 1: YBR143C_Sbay Reading seq # 2: YBR143C_Scer Reading seq # 3: YBR143C_Skud Reading seq # 4: YBR143C_Smik Reading seq # 5: YBR143C_Spar Sequences read.. Counting patterns.. # site patterns = 236 Counting frequencies.. 120 bytes for distance 37760 bytes for lkl0 30208 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.622764 0.042826 0.192791 0.239080 0.169522 4.268763 0.360489 0.000060 lnL0 = -3746.134049 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3746.134049 x= 0.62276 0.04283 0.19279 0.23908 0.16952 4.26876 0.36049 0.00006 1 h-lim-p 0.0000 0.0000 223.8029 3746.045800 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0033 59.9876 3744.431395 0 0.0010 40 | 1/8 3 h-lim-p 0.0016 0.0174 35.6777 3743.753101 3 0.0013 58 | 1/8 4 h-lim-p 0.0066 0.0865 7.2609 3743.651812 6 0.0027 84 | 1/8 5 h-lim-p 0.0088 0.0989 2.2102 3743.277976 0 0.0176 97 | 1/8 6 h-lim-p 0.0204 0.1791 1.9121 3733.175860 0 0.0612 110 | 0/8 7 h-lim-p 0.0412 0.7555 2.8416 3733.167640 5 0.0019 137 | 0/8 8 h-lim-p 0.2157 20.0000 0.0248 3732.920694 0 0.6472 150 | 0/8 9 h-lim-p 2.5000 20.0000 0.0062 3732.909805 4 0.6161 179 | 0/8 10 h-lim-p 2.5000 20.0000 0.0006 3732.909341 4 0.9422 207 | 0/8 11 h-lim-p 2.5000 20.0000 0.0002 3732.909325 0 0.5469 228 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3732.909325 0 1.0938 248 | 0/8 13 h-lim-p 1.5146 20.0000 0.0000 3732.909325 0 1.3253 268 | 0/8 14 h-lim-p 1.9668 20.0000 0.0000 3732.909325 0 1.7210 288 | 0/8 15 h-lim-p 1.3670 20.0000 0.0000 3732.909325 0 1.1961 308 | 0/8 16 h-lim-p 0.5791 20.0000 0.0000 3732.909325 0 0.5067 328 | 0/8 17 h-lim-p 0.0076 20.0000 0.0014 3732.909325 0 0.0076 348 | 0/8 18 h-lim-p 0.0021 12.6275 0.0049 3732.909325 0 0.0000 385 | 0/8 19 h-lim-p 0.0003 20.0000 0.0000 3732.909325 0 0.0000 419 Out... lnL = -3732.909325 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3732.909325 Node 7: lnL = -3732.909325 Node 8: lnL = -3732.909325 Node 9: lnL = -3732.909325 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 220 Sequential format.. Reading seq # 1: YBR145W_Sbay Reading seq # 2: YBR145W_Scer Reading seq # 3: YBR145W_Skud Reading seq # 4: YBR145W_Smik Reading seq # 5: YBR145W_Spar Sequences read.. Counting patterns.. # site patterns = 120 Counting frequencies.. 120 bytes for distance 19200 bytes for lkl0 15360 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.263012 0.140230 0.045374 0.204515 0.145386 0.227453 0.168174 0.042269 lnL0 = -1083.121448 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1083.121448 x= 0.26301 0.14023 0.04537 0.20451 0.14539 0.22745 0.16817 0.04227 1 h-lim-p 0.0139 3.8557 39.4171 1082.544736 2 0.0008 29 | 0/8 2 h-lim-p 0.0020 0.0161 9.8132 1082.473278 4 0.0016 49 | 0/8 3 h-lim-p 0.0072 0.0603 2.1439 1082.469644 2 0.0017 66 | 0/8 4 h-lim-p 0.0073 0.6017 0.5007 1082.469406 4 0.0020 87 | 0/8 5 h-lim-p 0.0155 5.3731 0.0635 1082.469403 1 0.0015 111 | 0/8 6 h-lim-p 0.0094 20.0000 0.0105 1082.469402 1 0.0046 134 | 0/8 7 h-lim-p 0.0162 20.0000 0.0030 1082.469335 0 0.1296 157 | 0/8 8 h-lim-p 0.0036 0.9139 0.1085 1082.469259 0 0.0053 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1082.469255 1 0.9961 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1082.469255 0 1.0938 219 | 0/8 11 h-lim-p 0.9255 20.0000 0.0000 1082.469255 0 0.0578 242 | 0/8 12 h-lim-p 0.0005 20.0000 0.0010 1082.469255 0 0.0000 282 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1082.469255 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1082.469255 Node 7: lnL = -1082.469255 Node 8: lnL = -1082.469255 Node 9: lnL = -1082.469255 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 461 Sequential format.. Reading seq # 1: YBR146W_Sbay Reading seq # 2: YBR146W_Scer Reading seq # 3: YBR146W_Skud Reading seq # 4: YBR146W_Smik Reading seq # 5: YBR146W_Spar Sequences read.. Counting patterns.. # site patterns = 248 Counting frequencies.. 120 bytes for distance 39680 bytes for lkl0 31744 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.276989 0.251369 0.060216 0.155125 0.183235 0.323365 0.287196 0.000060 lnL0 = -2297.720230 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2297.720230 x= 0.27699 0.25137 0.06022 0.15513 0.18323 0.32336 0.28720 0.00006 1 h-lim-p 0.0000 0.0000 23.2802 2297.715455 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0359 6.8810 2297.695272 0 0.0009 39 | 1/8 3 h-lim-p 0.0018 0.1420 3.2462 2297.690969 5 0.0009 63 | 1/8 4 h-lim-p 0.0022 0.5074 1.3917 2297.689340 4 0.0016 85 | 1/8 5 h-lim-p 0.0092 2.0152 0.2455 2297.684205 0 0.0184 98 | 1/8 6 h-lim-p 0.0087 0.5051 0.5156 2297.639939 0 0.0175 118 | 1/8 7 h-lim-p 0.0023 0.1166 3.9469 2297.476301 0 0.0046 138 | 1/8 8 h-lim-p 0.0075 0.1876 2.3896 2297.470703 4 0.0019 159 | 1/8 9 h-lim-p 2.5000 20.0000 0.0012 2297.469505 2 1.0889 175 | 1/8 10 h-lim-p 2.5000 20.0000 0.0001 2297.469500 1 0.9961 196 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 2297.469500 0 1.0938 215 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 2297.469500 0 0.6250 235 | 1/8 13 h-lim-p 1.6698 20.0000 0.0000 2297.469500 0 0.1044 257 | 1/8 14 h-lim-p 0.1166 20.0000 0.0000 2297.469500 0 0.0001 286 Out... lnL = -2297.469500 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2297.469500 Node 7: lnL = -2297.469500 Node 8: lnL = -2297.469500 Node 9: lnL = -2297.469500 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 514 Sequential format.. Reading seq # 1: YBR147W_Sbay Reading seq # 2: YBR147W_Scer Reading seq # 3: YBR147W_Skud Reading seq # 4: YBR147W_Smik Reading seq # 5: YBR147W_Spar Sequences read.. Counting patterns.. # site patterns = 217 Counting frequencies.. 120 bytes for distance 34720 bytes for lkl0 27776 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.298166 0.020312 0.048431 0.149418 0.083774 0.220247 0.273738 0.094988 lnL0 = -2376.178010 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2376.178010 x= 0.29817 0.02031 0.04843 0.14942 0.08377 0.22025 0.27374 0.09499 1 h-lim-p 0.0038 0.0300 49.4209 2375.861504 8 0.0003 43 | 0/8 2 h-lim-p 0.0008 0.0070 15.9158 2375.820037 5 0.0004 66 | 0/8 3 h-lim-p 0.0008 0.0462 7.1431 2375.807485 6 0.0006 92 | 0/8 4 h-lim-p 0.0011 0.0888 4.0175 2375.804051 5 0.0006 115 | 0/8 5 h-lim-p 0.0017 0.0805 1.3238 2375.803721 2 0.0004 132 | 0/8 6 h-lim-p 0.0014 1.2877 0.4031 2375.803673 0 0.0007 144 | 0/8 7 h-lim-p 0.0245 20.0000 0.0115 2375.803673 0 0.0013 167 | 0/8 8 h-lim-p 0.0698 20.0000 0.0002 2375.803632 0 0.8372 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2375.803631 0 1.0938 210 | 0/8 10 h-lim-p 2.3896 20.0000 0.0000 2375.803631 0 1.0455 230 | 0/8 11 h-lim-p 0.9902 20.0000 0.0000 2375.803631 0 5.9409 252 | 0/8 12 h-lim-p 0.3130 20.0000 0.0002 2375.803631 0 0.0001 283 | 0/8 13 h-lim-p 0.0009 20.0000 0.0000 2375.803631 0 0.0000 311 | 0/8 14 h-lim-p 0.0005 20.0000 0.0000 2375.803631 0 0.0000 352 Out... lnL = -2375.803631 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2375.803631 Node 7: lnL = -2375.803631 Node 8: lnL = -2375.803631 Node 9: lnL = -2375.803631 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 430 Sequential format.. Reading seq # 1: YBR148W_Sbay Reading seq # 2: YBR148W_Scer Reading seq # 3: YBR148W_Skud Reading seq # 4: YBR148W_Smik Reading seq # 5: YBR148W_Spar Sequences read.. Counting patterns.. # site patterns = 190 Counting frequencies.. 120 bytes for distance 30400 bytes for lkl0 24320 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.260804 0.102826 0.102978 0.093922 0.083872 0.178086 0.239636 0.057739 lnL0 = -1928.329071 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1928.329071 x= 0.26080 0.10283 0.10298 0.09392 0.08387 0.17809 0.23964 0.05774 1 h-lim-p 0.0013 0.0103 25.4547 1928.162852 6 0.0005 33 | 0/8 2 h-lim-p 0.0020 0.0844 6.5819 1928.148869 6 0.0007 62 | 0/8 3 h-lim-p 0.0009 0.0446 4.8114 1928.145027 6 0.0005 86 | 0/8 4 h-lim-p 0.0009 0.0649 2.5612 1928.143365 3 0.0007 104 | 0/8 5 h-lim-p 0.0025 0.2160 0.7403 1928.143254 3 0.0005 123 | 0/8 6 h-lim-p 0.0053 3.2998 0.0647 1928.143253 1 0.0011 146 | 0/8 7 h-lim-p 0.0575 20.0000 0.0012 1928.143253 0 0.0063 168 | 0/8 8 h-lim-p 0.0254 20.0000 0.0003 1928.143250 0 0.2033 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1928.143250 0 1.0938 211 | 0/8 10 h-lim-p 1.4903 20.0000 0.0000 1928.143250 0 1.3040 231 | 0/8 11 h-lim-p 1.0266 20.0000 0.0000 1928.143250 0 0.3850 252 | 0/8 12 h-lim-p 0.0041 20.0000 0.0011 1928.143250 0 0.0001 277 | 0/8 13 h-lim-p 0.0006 20.0000 0.0001 1928.143250 0 0.0000 301 | 0/8 14 h-lim-p 0.0004 20.0000 0.0000 1928.143250 0 0.0000 333 Out... lnL = -1928.143250 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1928.143250 Node 7: lnL = -1928.143250 Node 8: lnL = -1928.143250 Node 9: lnL = -1928.143250 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 338 Sequential format.. Reading seq # 1: YBR149W_Sbay Reading seq # 2: YBR149W_Scer Reading seq # 3: YBR149W_Skud Reading seq # 4: YBR149W_Smik Reading seq # 5: YBR149W_Spar Sequences read.. Counting patterns.. # site patterns = 122 Counting frequencies.. 120 bytes for distance 19520 bytes for lkl0 15616 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.158035 0.042355 0.096546 0.096560 0.066999 0.155581 0.115319 0.016779 lnL0 = -1171.161844 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1171.161844 x= 0.15803 0.04235 0.09655 0.09656 0.06700 0.15558 0.11532 0.01678 1 h-lim-p 0.0011 0.0089 61.0326 1169.948128 9 0.0007 44 | 0/8 2 h-lim-p 0.0006 0.0046 39.6073 1169.427114 0 0.0009 56 | 0/8 3 h-lim-p 0.0018 0.0142 16.3860 1169.381284 2 0.0004 73 | 0/8 4 h-lim-p 0.0026 0.0510 2.6010 1169.379836 5 0.0004 99 | 0/8 5 h-lim-p 0.0021 0.2691 0.5357 1169.379727 3 0.0008 119 | 0/8 6 h-lim-p 0.0024 0.7355 0.1724 1169.379662 1 0.0029 141 | 0/8 7 h-lim-p 0.0035 0.8613 0.1460 1169.379615 1 0.0017 163 | 0/8 8 h-lim-p 0.0107 20.0000 0.0237 1169.367493 0 0.2569 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 1169.366885 3 1.0004 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1169.366884 0 1.0938 233 | 0/8 11 h-lim-p 1.5071 20.0000 0.0000 1169.366884 0 0.6593 253 | 0/8 12 h-lim-p 0.3988 20.0000 0.0000 1169.366884 0 0.0249 276 | 0/8 13 h-lim-p 0.0092 20.0000 0.0001 1169.366884 0 0.0001 302 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 1169.366884 0 0.0000 322 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 1169.366884 0 0.0000 356 | 0/8 16 h-lim-p 0.0000 20.0000 0.0012 | 0/8 17 h-lim-p 0.0000 20.0000 0.0012 Out... lnL = -1169.366884 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1169.366884 Node 7: lnL = -1169.366884 Node 8: lnL = -1169.366884 Node 9: lnL = -1169.366884 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 570 Sequential format.. Reading seq # 1: YBR150C_Sbay Reading seq # 2: YBR150C_Scer Reading seq # 3: YBR150C_Skud Reading seq # 4: YBR150C_Smik Reading seq # 5: YBR150C_Spar Sequences read.. Counting patterns.. # site patterns = 219 Counting frequencies.. 120 bytes for distance 35040 bytes for lkl0 28032 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.310875 0.003391 0.043347 0.136148 0.100127 0.198195 0.210684 0.113915 lnL0 = -2595.144989 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2595.144989 x= 0.31087 0.00339 0.04335 0.13615 0.10013 0.19819 0.21068 0.11391 1 h-lim-p 0.0007 0.0053 138.0770 2593.690722 6 0.0002 36 | 0/8 2 h-lim-p 0.0005 0.0036 27.8656 2593.539007 5 0.0004 57 | 0/8 3 h-lim-p 0.0007 0.0077 15.7287 2593.504211 6 0.0004 85 | 0/8 4 h-lim-p 0.0016 0.0562 3.5067 2593.501656 5 0.0004 110 | 0/8 5 h-lim-p 0.0018 0.1704 0.8708 2593.501502 2 0.0004 127 | 0/8 6 h-lim-p 0.0011 0.4200 0.3312 2593.501478 0 0.0005 147 | 0/8 7 h-lim-p 0.0059 2.3779 0.0271 2593.501477 0 0.0013 168 | 0/8 8 h-lim-p 0.2372 20.0000 0.0001 2593.501456 0 0.9487 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2593.501456 0 1.2500 210 | 0/8 10 h-lim-p 1.4020 20.0000 0.0000 2593.501456 0 0.3067 231 | 0/8 11 h-lim-p 0.1666 20.0000 0.0000 2593.501456 0 0.0000 274 | 0/8 12 h-lim-p 0.0000 20.0000 0.0013 2593.501456 0 0.0000 299 | 0/8 13 h-lim-p 0.0000 20.0000 0.0004 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0013 | 0/8 15 h-lim-p 0.0000 20.0000 0.0013 Out... lnL = -2593.501456 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2593.501456 Node 7: lnL = -2593.501456 Node 8: lnL = -2593.501456 Node 9: lnL = -2593.501456 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 567 Sequential format.. Reading seq # 1: YBR151W_Sbay Reading seq # 2: YBR151W_Scer Reading seq # 3: YBR151W_Skud Reading seq # 4: YBR151W_Smik Reading seq # 5: YBR151W_Spar Sequences read.. Counting patterns.. # site patterns = 218 Counting frequencies.. 120 bytes for distance 34880 bytes for lkl0 27904 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.288039 0.015326 0.052718 0.134946 0.101330 0.182378 0.187256 0.098881 lnL0 = -2542.809365 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2542.809365 x= 0.28804 0.01533 0.05272 0.13495 0.10133 0.18238 0.18726 0.09888 1 h-lim-p 0.0013 0.0107 111.8586 2541.719424 8 0.0002 43 | 0/8 2 h-lim-p 0.0005 0.0044 29.6196 2541.518984 6 0.0005 66 | 0/8 3 h-lim-p 0.0011 0.0116 12.6512 2541.498778 4 0.0003 87 | 0/8 4 h-lim-p 0.0019 0.1139 1.9330 2541.497999 2 0.0004 104 | 0/8 5 h-lim-p 0.0011 0.3226 0.7230 2541.497894 2 0.0005 120 | 0/8 6 h-lim-p 0.0022 1.4208 0.1474 2541.497889 1 0.0004 143 | 0/8 7 h-lim-p 0.0171 20.0000 0.0038 2541.497889 0 0.0075 163 | 0/8 8 h-lim-p 0.0217 20.0000 0.0013 2541.497835 0 0.1733 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2541.497835 0 1.0938 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2541.497835 0 1.0938 226 | 0/8 11 h-lim-p 1.0804 20.0000 0.0000 2541.497835 0 0.0338 250 | 0/8 12 h-lim-p 0.0019 20.0000 0.0002 2541.497835 0 0.0001 273 | 0/8 13 h-lim-p 0.0001 20.0000 0.0004 2541.497835 0 0.0000 303 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 2541.497835 0 0.0000 334 Out... lnL = -2541.497835 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2541.497835 Node 7: lnL = -2541.497835 Node 8: lnL = -2541.497835 Node 9: lnL = -2541.497835 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 435 Sequential format.. Reading seq # 1: YBR152W_Sbay Reading seq # 2: YBR152W_Scer Reading seq # 3: YBR152W_Skud Reading seq # 4: YBR152W_Smik Reading seq # 5: YBR152W_Spar Sequences read.. Counting patterns.. # site patterns = 207 Counting frequencies.. 120 bytes for distance 33120 bytes for lkl0 26496 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.382235 0.062810 0.065226 0.193241 0.126648 0.224343 0.305398 0.116164 lnL0 = -2126.934461 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2126.934461 x= 0.38223 0.06281 0.06523 0.19324 0.12665 0.22434 0.30540 0.11616 1 h-lim-p 0.0038 0.0304 73.9072 2125.553848 9 0.0005 47 | 0/8 2 h-lim-p 0.0011 0.0088 22.0505 2125.361311 6 0.0008 72 | 0/8 3 h-lim-p 0.0022 0.0440 8.3371 2125.334816 4 0.0009 92 | 0/8 4 h-lim-p 0.0021 0.1135 3.4728 2125.326956 5 0.0016 116 | 0/8 5 h-lim-p 0.0043 0.1831 1.2547 2125.325902 5 0.0015 141 | 0/8 6 h-lim-p 0.0075 1.7651 0.2602 2125.325865 3 0.0011 163 | 0/8 7 h-lim-p 0.0087 20.0000 0.0326 2125.325860 0 0.0038 183 | 0/8 8 h-lim-p 0.0581 20.0000 0.0021 2125.325012 0 0.4648 206 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 2125.324995 1 0.9961 228 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2125.324995 0 1.0938 248 | 0/8 11 h-lim-p 1.3514 20.0000 0.0000 2125.324995 0 2.0270 268 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2125.324995 0 0.0684 292 | 0/8 13 h-lim-p 0.0145 20.0000 0.0000 2125.324995 0 0.0005 316 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 2125.324995 0 0.0000 355 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 2125.324995 0 0.0000 382 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 2125.324995 0 0.0000 408 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 2125.324995 0 0.0000 430 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 2125.324995 0 0.0000 465 | 0/8 19 h-lim-p 0.0000 20.0000 0.0005 | 0/8 20 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -2125.324995 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2125.324995 Node 7: lnL = -2125.324995 Node 8: lnL = -2125.324995 Node 9: lnL = -2125.324995 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 228 Sequential format.. Reading seq # 1: YBR153W_Sbay Reading seq # 2: YBR153W_Scer Reading seq # 3: YBR153W_Skud Reading seq # 4: YBR153W_Smik Reading seq # 5: YBR153W_Spar Sequences read.. Counting patterns.. # site patterns = 129 Counting frequencies.. 120 bytes for distance 20640 bytes for lkl0 16512 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.347767 0.000060 0.123377 0.143739 0.116272 0.272195 0.310938 0.097866 lnL0 = -1089.239720 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1089.239720 x= 0.34777 0.00006 0.12338 0.14374 0.11627 0.27219 0.31094 0.09787 1 h-lim-p 0.0017 0.0134 45.9920 1087.698497 8 0.0012 39 | 0/8 2 h-lim-p 0.0012 0.0098 16.5528 1087.381481 0 0.0024 52 | 0/8 3 h-lim-p 0.0044 0.0471 9.1712 1087.312988 2 0.0021 68 | 0/8 4 h-lim-p 0.0036 0.0513 5.2734 1087.302375 4 0.0011 91 | 0/8 5 h-lim-p 0.0051 0.2684 1.1085 1087.301395 5 0.0017 115 | 0/8 6 h-lim-p 0.0046 0.9927 0.4162 1087.301161 4 0.0030 137 | 0/8 7 h-lim-p 0.0456 6.2372 0.0270 1087.301017 3 0.0346 163 | 0/8 8 h-lim-p 0.0273 3.1210 0.0343 1087.297073 0 0.1091 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0010 1087.296865 3 0.9644 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1087.296865 0 1.0938 231 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1087.296865 0 1.0938 251 | 0/8 12 h-lim-p 2.1308 20.0000 0.0000 1087.296865 0 0.9322 271 | 0/8 13 h-lim-p 0.6888 20.0000 0.0000 1087.296865 0 0.0000 313 Out... lnL = -1087.296865 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1087.296865 Node 7: lnL = -1087.296865 Node 8: lnL = -1087.296865 Node 9: lnL = -1087.296865 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 815 Sequential format.. Reading seq # 1: YBR154C_Sbay Reading seq # 2: YBR154C_Scer Reading seq # 3: YBR154C_Skud Reading seq # 4: YBR154C_Smik Reading seq # 5: YBR154C_Spar Sequences read.. Counting patterns.. # site patterns = 321 Counting frequencies.. 120 bytes for distance 51360 bytes for lkl0 41088 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.273851 0.062991 0.109044 0.143850 0.134889 0.208644 0.290354 0.040582 lnL0 = -3933.030075 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3933.030075 x= 0.27385 0.06299 0.10904 0.14385 0.13489 0.20864 0.29035 0.04058 1 h-lim-p 0.0015 0.0122 83.6197 3932.117909 6 0.0003 36 | 0/8 2 h-lim-p 0.0015 0.0136 15.1029 3932.068649 5 0.0004 61 | 0/8 3 h-lim-p 0.0009 0.0445 7.6187 3932.058986 2 0.0004 77 | 0/8 4 h-lim-p 0.0010 0.1003 3.0573 3932.057167 2 0.0005 93 | 0/8 5 h-lim-p 0.0032 0.1716 0.4565 3932.057118 3 0.0005 115 | 0/8 6 h-lim-p 0.0110 14.5904 0.0194 3932.057118 0 0.0006 138 | 0/8 7 h-lim-p 0.0051 20.0000 0.0023 3932.057118 0 0.0022 158 | 0/8 8 h-lim-p 0.0173 20.0000 0.0003 3932.057111 0 0.2774 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3932.057111 0 1.0938 202 | 0/8 10 h-lim-p 0.9489 20.0000 0.0000 3932.057111 0 1.8977 223 | 0/8 11 h-lim-p 0.1505 20.0000 0.0003 3932.057111 0 0.0024 248 | 0/8 12 h-lim-p 0.0016 20.0000 0.0004 3932.057111 0 0.0000 280 | 0/8 13 h-lim-p 0.0004 20.0000 0.0000 3932.057111 0 0.0000 313 Out... lnL = -3932.057111 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3932.057111 Node 7: lnL = -3932.057111 Node 8: lnL = -3932.057111 Node 9: lnL = -3932.057111 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 815 Sequential format.. Reading seq # 1: YBR155W_Sbay Reading seq # 2: YBR155W_Scer Reading seq # 3: YBR155W_Skud Reading seq # 4: YBR155W_Smik Reading seq # 5: YBR155W_Spar Sequences read.. Counting patterns.. # site patterns = 320 Counting frequencies.. 120 bytes for distance 51200 bytes for lkl0 40960 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.279731 0.066993 0.105611 0.142543 0.136196 0.199823 0.288340 0.046200 lnL0 = -3934.792907 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3934.792907 x= 0.27973 0.06699 0.10561 0.14254 0.13620 0.19982 0.28834 0.04620 1 h-lim-p 0.0025 0.0199 97.9128 3933.569535 6 0.0003 35 | 0/8 2 h-lim-p 0.0015 0.0126 17.4038 3933.496157 6 0.0005 60 | 0/8 3 h-lim-p 0.0008 0.0306 11.1839 3933.477173 4 0.0004 81 | 0/8 4 h-lim-p 0.0015 0.0782 3.1043 3933.475272 5 0.0004 108 | 0/8 5 h-lim-p 0.0038 0.4020 0.3612 3933.475238 2 0.0005 126 | 0/8 6 h-lim-p 0.0066 11.8530 0.0273 3933.475238 0 0.0007 148 | 0/8 7 h-lim-p 0.0045 20.0000 0.0044 3933.475238 0 0.0039 168 | 0/8 8 h-lim-p 0.0152 20.0000 0.0011 3933.475187 0 0.1829 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3933.475186 0 1.0938 211 | 0/8 10 h-lim-p 1.3382 20.0000 0.0000 3933.475186 0 1.1710 231 | 0/8 11 h-lim-p 1.4272 20.0000 0.0000 3933.475186 0 2.1408 251 | 0/8 12 h-lim-p 0.9433 20.0000 0.0000 3933.475186 0 2.8299 272 | 0/8 13 h-lim-p 0.0092 5.3995 0.0132 3933.475186 0 0.0000 299 | 0/8 14 h-lim-p 0.0001 20.0000 0.0093 3933.475186 0 0.0000 319 | 0/8 15 h-lim-p 0.0005 20.0000 0.0004 3933.475186 0 0.0001 340 | 0/8 16 h-lim-p 0.0005 20.0000 0.0001 3933.475186 0 0.0005 360 | 0/8 17 h-lim-p 0.0004 20.0000 0.0001 3933.475186 0 0.0000 387 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 3933.475186 0 0.0000 416 Out... lnL = -3933.475186 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3933.475186 Node 7: lnL = -3933.475186 Node 8: lnL = -3933.475186 Node 9: lnL = -3933.475186 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 822 Sequential format.. Reading seq # 1: YBR156C_Sbay Reading seq # 2: YBR156C_Scer Reading seq # 3: YBR156C_Skud Reading seq # 4: YBR156C_Smik Reading seq # 5: YBR156C_Spar Sequences read.. Counting patterns.. # site patterns = 219 Counting frequencies.. 120 bytes for distance 35040 bytes for lkl0 28032 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.114423 0.027197 0.046326 0.093265 0.067687 0.138666 0.119742 0.002687 lnL0 = -3026.322758 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3026.322758 x= 0.11442 0.02720 0.04633 0.09327 0.06769 0.13867 0.11974 0.00269 1 h-lim-p 0.0007 0.5029 294.6904 3022.547465 8 0.0001 44 | 0/8 2 h-lim-p 0.0003 0.0023 53.7278 3022.313755 8 0.0002 76 | 0/8 3 h-lim-p 0.0006 0.0123 15.0214 3022.294768 6 0.0002 105 | 0/8 4 h-lim-p 0.0004 0.0125 6.2365 3022.292000 3 0.0002 123 | 0/8 5 h-lim-p 0.0012 0.1695 0.8628 3022.291947 0 0.0002 137 | 0/8 6 h-lim-p 0.0006 0.8481 0.2170 3022.291941 0 0.0003 157 | 0/8 7 h-lim-p 0.0051 17.5534 0.0112 3022.291941 0 0.0006 179 | 0/8 8 h-lim-p 0.0110 20.0000 0.0007 3022.291718 0 0.3509 204 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3022.291716 0 1.0938 224 | 0/8 10 h-lim-p 0.7379 20.0000 0.0001 3022.291716 0 1.1068 244 | 0/8 11 h-lim-p 1.0627 20.0000 0.0001 3022.291716 0 4.2509 266 | 0/8 12 h-lim-p 0.0486 5.7964 0.0049 3022.291716 0 0.0091 288 | 0/8 13 h-lim-p 0.0022 1.4256 0.0199 3022.291716 0 0.0000 313 | 0/8 14 h-lim-p 0.0001 5.1185 0.0055 3022.291716 0 0.0000 351 | 0/8 15 h-lim-p 0.0000 20.0000 0.0014 | 0/8 16 h-lim-p 0.0000 20.0000 0.0014 Out... lnL = -3022.291716 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3022.291716 Node 7: lnL = -3022.291716 Node 8: lnL = -3022.291716 Node 9: lnL = -3022.291716 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 931 Sequential format.. Reading seq # 1: YBR157C_Sbay Reading seq # 2: YBR157C_Scer Reading seq # 3: YBR157C_Skud Reading seq # 4: YBR157C_Smik Reading seq # 5: YBR157C_Spar Sequences read.. Counting patterns.. # site patterns = 300 Counting frequencies.. 120 bytes for distance 48000 bytes for lkl0 38400 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.271308 0.056835 0.047696 0.095594 0.061107 0.205011 0.223472 0.082070 lnL0 = -3949.094620 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3949.094620 x= 0.27131 0.05684 0.04770 0.09559 0.06111 0.20501 0.22347 0.08207 1 h-lim-p 0.0001 0.0009 208.8155 3946.151765 0 0.0002 22 | 0/8 2 h-lim-p 0.0003 0.0028 36.4107 3946.020731 7 0.0002 53 | 0/8 3 h-lim-p 0.0003 0.0123 29.1184 3945.967929 6 0.0002 79 | 0/8 4 h-lim-p 0.0003 0.0146 16.1879 3945.944671 4 0.0003 99 | 0/8 5 h-lim-p 0.0019 0.1064 2.2165 3945.943839 4 0.0003 121 | 0/8 6 h-lim-p 0.0014 0.3534 0.5570 3945.943781 2 0.0004 138 | 0/8 7 h-lim-p 0.0478 20.0000 0.0042 3945.930956 0 0.7648 162 | 0/8 8 h-lim-p 0.0010 0.0544 3.1881 3945.922605 5 0.0007 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 3945.922308 2 0.9961 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3945.922308 0 1.0938 230 | 0/8 11 h-lim-p 1.7455 20.0000 0.0000 3945.922308 0 1.5273 250 | 0/8 12 h-lim-p 1.5491 20.0000 0.0000 3945.922308 0 0.1694 272 | 0/8 13 h-lim-p 0.0356 20.0000 0.0001 3945.922308 0 0.0089 293 | 0/8 14 h-lim-p 0.0027 20.0000 0.0002 3945.922308 0 0.0003 315 | 0/8 15 h-lim-p 0.0005 20.0000 0.0002 3945.922308 0 0.0001 337 | 0/8 16 h-lim-p 0.0003 20.0000 0.0000 3945.922308 0 0.0000 363 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 3945.922308 0 0.0000 390 | 0/8 18 h-lim-p 0.0000 20.0000 0.0016 3945.922308 0 0.0000 420 | 0/8 19 h-lim-p 0.0000 20.0000 0.0011 3945.922308 0 0.0006 446 | 0/8 20 h-lim-p 0.0013 20.0000 0.0005 3945.922308 0 0.0000 473 | 0/8 21 h-lim-p 0.0000 20.0000 0.0002 3945.922308 0 0.0000 494 | 0/8 22 h-lim-p 0.0000 20.0000 0.0005 3945.922308 0 0.0000 516 | 0/8 23 h-lim-p 0.0000 20.0000 0.0013 3945.922308 0 0.0000 537 | 0/8 24 h-lim-p 0.0000 20.0000 0.0009 .. | 0/8 25 h-lim-p 0.0000 20.0000 0.0034 | 0/8 26 h-lim-p 0.0000 20.0000 0.0034 Out... lnL = -3945.922308 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3945.922308 Node 7: lnL = -3945.922308 Node 8: lnL = -3945.922308 Node 9: lnL = -3945.922308 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 520 Sequential format.. Reading seq # 1: YBR159W_Sbay Reading seq # 2: YBR159W_Scer Reading seq # 3: YBR159W_Skud Reading seq # 4: YBR159W_Smik Reading seq # 5: YBR159W_Spar Sequences read.. Counting patterns.. # site patterns = 210 Counting frequencies.. 120 bytes for distance 33600 bytes for lkl0 26880 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.281900 0.084061 0.091567 0.127635 0.098222 0.216715 0.270981 0.054920 lnL0 = -2499.427370 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2499.427370 x= 0.28190 0.08406 0.09157 0.12764 0.09822 0.21672 0.27098 0.05492 1 h-lim-p 0.0003 0.0026 82.6736 2497.906981 0 0.0005 22 | 0/8 2 h-lim-p 0.0014 0.0109 15.7292 2497.831521 2 0.0006 38 | 0/8 3 h-lim-p 0.0017 0.0266 6.0091 2497.822684 6 0.0006 64 | 0/8 4 h-lim-p 0.0011 0.1367 3.0295 2497.821352 4 0.0004 85 | 0/8 5 h-lim-p 0.0013 0.3435 0.8764 2497.821056 4 0.0009 108 | 0/8 6 h-lim-p 0.0027 0.7963 0.2799 2497.821028 3 0.0008 136 | 0/8 7 h-lim-p 0.0039 3.5369 0.0564 2497.821024 1 0.0016 158 | 0/8 8 h-lim-p 0.0460 20.0000 0.0019 2497.819804 0 0.7363 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 2497.819774 2 0.9961 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2497.819774 0 2.1875 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2497.819774 0 1.0938 246 | 0/8 12 h-lim-p 0.1375 20.0000 0.0000 2497.819774 0 0.0150 268 | 0/8 13 h-lim-p 0.0002 20.0000 0.0016 2497.819774 0 0.0002 288 | 0/8 14 h-lim-p 0.0004 20.0000 0.0008 2497.819774 0 0.0000 317 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 2497.819774 0 0.0000 346 Out... lnL = -2497.819774 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2497.819774 Node 7: lnL = -2497.819774 Node 8: lnL = -2497.819774 Node 9: lnL = -2497.819774 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 396 Sequential format.. Reading seq # 1: YBR160W_Sbay Reading seq # 2: YBR160W_Scer Reading seq # 3: YBR160W_Skud Reading seq # 4: YBR160W_Smik Reading seq # 5: YBR160W_Spar Sequences read.. Counting patterns.. # site patterns = 127 Counting frequencies.. 120 bytes for distance 20320 bytes for lkl0 16256 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.672967 0.340618 0.355177 0.148461 0.246018 3.953911 0.256586 0.000060 lnL0 = -1542.649508 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1542.649508 x= 0.67297 0.34062 0.35518 0.14846 0.24602 3.95391 0.25659 0.00006 1 h-lim-p 0.0000 0.0000 274.5786 1542.584982 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0004 1593.2557 1451.655055 2 0.0003 42 | 1/8 3 h-lim-p 0.0001 0.0008 266.9108 1438.210703 0 0.0006 56 | 1/8 4 h-lim-p 0.0002 0.0017 182.4586 1430.765887 0 0.0009 70 | 1/8 5 h-lim-p 0.0030 0.0240 9.9716 1430.692954 6 0.0010 97 | 0/8 6 h-lim-p 0.0002 0.0189 65.1727 1429.291514 0 0.0006 111 | 0/8 7 h-lim-p 0.0373 0.2983 0.2777 1424.001103 m 0.2983 123 | 0/8 8 h-lim-p 0.0000 0.0000 0.0328 h-lim-p: 6.21088281e-17 4.96870624e-16 3.27948855e-02 1424.001103 .. | 0/8 9 h-lim-p 0.0000 3.4480 38.7019 1423.691124 0 0.0005 164 | 0/8 10 h-lim-p 0.0004 0.0032 7.3595 1423.678651 1 0.0005 178 | 0/8 11 h-lim-p 0.0051 0.5338 0.7229 1423.678510 2 0.0006 196 | 0/8 12 h-lim-p 0.0009 0.0076 0.2691 1423.678120 m 0.0076 216 | 1/8 13 h-lim-p 0.0001 0.0096 19.8377 1423.678091 2 0.0000 243 | 1/8 14 h-lim-p 0.0030 2.6272 0.0780 1423.678076 2 0.0023 259 | 1/8 15 h-lim-p 0.0328 20.0000 0.0055 1423.674748 0 0.3935 281 | 1/8 16 h-lim-p 2.5000 20.0000 0.0003 1423.674624 3 1.6118 308 | 1/8 17 h-lim-p 2.5000 20.0000 0.0001 1423.674564 2 2.1875 331 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 1423.674563 0 1.0938 350 | 1/8 19 h-lim-p 2.5000 20.0000 0.0000 1423.674563 0 1.0938 369 | 1/8 20 h-lim-p 1.0684 20.0000 0.0000 1423.674563 0 4.2735 390 | 1/8 21 h-lim-p 2.5000 20.0000 0.0000 1423.674563 0 0.0781 413 | 1/8 22 h-lim-p 0.0091 20.0000 0.0000 1423.674563 0 0.0003 436 | 1/8 23 h-lim-p 0.0001 20.0000 0.0000 1423.674563 0 0.0000 456 | 1/8 24 h-lim-p 0.0004 20.0000 0.0000 1423.674563 0 0.0000 487 Out... lnL = -1423.674563 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1423.674563 Node 7: lnL = -1423.674563 Node 8: lnL = -1423.674563 Node 9: lnL = -1423.674563 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 685 Sequential format.. Reading seq # 1: YBR161W_Sbay Reading seq # 2: YBR161W_Scer Reading seq # 3: YBR161W_Skud Reading seq # 4: YBR161W_Smik Reading seq # 5: YBR161W_Spar Sequences read.. Counting patterns.. # site patterns = 194 Counting frequencies.. 120 bytes for distance 31040 bytes for lkl0 24832 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.300543 0.000060 0.035755 0.184524 0.183274 0.283945 0.180049 0.084269 lnL0 = -2796.135666 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2796.135666 x= 0.30054 0.00006 0.03575 0.18452 0.18327 0.28395 0.18005 0.08427 1 h-lim-p 0.0003 0.0020 235.5351 2785.317037 0 0.0005 23 | 0/8 2 h-lim-p 0.0001 0.0007 132.9252 2782.867726 0 0.0003 37 | 0/8 3 h-lim-p 0.0005 0.0040 72.9666 2782.043105 3 0.0004 55 | 0/8 4 h-lim-p 0.0016 0.0158 19.6325 2781.823543 5 0.0013 76 | 0/8 5 h-lim-p 0.0017 0.0173 14.2595 2781.468184 0 0.0069 90 | 0/8 6 h-lim-p 0.0025 0.0201 10.7552 2781.435226 6 0.0009 117 | 0/8 7 h-lim-p 0.0039 0.1208 2.5338 2781.308165 0 0.0308 132 | 0/8 8 h-lim-p 0.2931 2.3448 0.0797 2779.380204 0 0.8793 145 | 0/8 9 h-lim-p 2.5000 20.0000 0.0117 2779.283570 6 0.7998 179 | 0/8 10 h-lim-p 2.5000 20.0000 0.0014 2779.282811 3 1.0004 205 | 0/8 11 h-lim-p 2.5000 20.0000 0.0001 2779.282804 1 0.9961 227 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2779.282804 0 1.0938 247 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2779.282804 0 1.0938 267 | 0/8 14 h-lim-p 0.9019 20.0000 0.0000 2779.282804 0 1.3528 287 | 0/8 15 h-lim-p 0.4554 20.0000 0.0000 2779.282804 0 0.1138 308 | 0/8 16 h-lim-p 0.0370 20.0000 0.0001 2779.282804 0 0.0092 329 | 0/8 17 h-lim-p 0.0045 20.0000 0.0003 2779.282804 0 0.0000 360 | 0/8 18 h-lim-p 0.0001 20.0000 0.0000 2779.282804 0 0.0000 394 Out... lnL = -2779.282804 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2779.282804 Node 7: lnL = -2779.282804 Node 8: lnL = -2779.282804 Node 9: lnL = -2779.282804 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 708 Sequential format.. Reading seq # 1: YBR162C_Sbay Reading seq # 2: YBR162C_Scer Reading seq # 3: YBR162C_Skud Reading seq # 4: YBR162C_Smik Reading seq # 5: YBR162C_Spar Sequences read.. Counting patterns.. # site patterns = 211 Counting frequencies.. 120 bytes for distance 33760 bytes for lkl0 27008 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.169901 0.039895 0.042576 0.059220 0.081188 0.152730 0.131736 0.034731 lnL0 = -2781.565116 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2781.565116 x= 0.16990 0.03990 0.04258 0.05922 0.08119 0.15273 0.13174 0.03473 1 h-lim-p 0.0016 0.7201 189.4310 2779.732162 9 0.0001 48 | 0/8 2 h-lim-p 0.0008 0.0068 23.2492 2779.674137 4 0.0002 69 | 0/8 3 h-lim-p 0.0005 0.0174 10.5076 2779.666126 6 0.0002 96 | 0/8 4 h-lim-p 0.0007 0.0628 2.6016 2779.665493 4 0.0002 118 | 0/8 5 h-lim-p 0.0031 0.4476 0.1696 2779.665490 1 0.0002 135 | 0/8 6 h-lim-p 0.0016 7.8725 0.0206 2779.665490 0 0.0003 156 | 0/8 7 h-lim-p 0.0016 20.0000 0.0044 2779.665490 0 0.0014 176 | 0/8 8 h-lim-p 0.0100 20.0000 0.0006 2779.665468 0 0.3210 201 | 0/8 9 h-lim-p 1.4959 20.0000 0.0001 2779.665468 0 1.3089 221 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2779.665468 0 1.0938 241 | 0/8 11 h-lim-p 2.2699 20.0000 0.0000 2779.665468 0 2.2699 261 | 0/8 12 h-lim-p 0.3944 20.0000 0.0002 2779.665468 0 0.0863 282 | 0/8 13 h-lim-p 0.0075 20.0000 0.0018 2779.665468 0 0.0019 303 | 0/8 14 h-lim-p 0.0007 12.2260 0.0046 2779.665468 0 0.0000 331 | 0/8 15 h-lim-p 0.0001 20.0000 0.0001 2779.665468 0 0.0000 353 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 2779.665468 0 0.0000 376 | 0/8 17 h-lim-p 0.0001 20.0000 0.0000 2779.665468 0 0.0000 411 Out... lnL = -2779.665468 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2779.665468 Node 7: lnL = -2779.665468 Node 8: lnL = -2779.665468 Node 9: lnL = -2779.665468 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 705 Sequential format.. Reading seq # 1: YBR162W-A_Sbay Reading seq # 2: YBR162W-A_Scer Reading seq # 3: YBR162W-A_Skud Reading seq # 4: YBR162W-A_Smik Reading seq # 5: YBR162W-A_Spar Sequences read.. Counting patterns.. # site patterns = 212 Counting frequencies.. 120 bytes for distance 33920 bytes for lkl0 27136 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.167109 0.026258 0.048760 0.062950 0.073791 0.150861 0.148909 0.032719 lnL0 = -2776.098074 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2776.098074 x= 0.16711 0.02626 0.04876 0.06295 0.07379 0.15086 0.14891 0.03272 1 h-lim-p 0.0010 0.5159 234.0216 2773.703525 7 0.0001 37 | 0/8 2 h-lim-p 0.0015 0.0123 14.1349 2773.680251 7 0.0002 71 | 0/8 3 h-lim-p 0.0004 0.0239 8.9178 2773.674724 4 0.0002 91 | 0/8 4 h-lim-p 0.0017 0.0815 0.9730 2773.674632 2 0.0002 109 | 0/8 5 h-lim-p 0.0018 0.6124 0.1066 2773.674631 1 0.0002 133 | 0/8 6 h-lim-p 0.0012 11.6366 0.0188 2773.674631 0 0.0005 153 | 0/8 7 h-lim-p 0.0038 20.0000 0.0027 2773.674631 0 0.0002 176 | 0/8 8 h-lim-p 0.0105 20.0000 0.0001 2773.674630 0 1.3491 203 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2773.674630 0 1.0938 223 | 0/8 10 h-lim-p 0.7178 20.0000 0.0000 2773.674630 0 4.3071 245 | 0/8 11 h-lim-p 0.7546 20.0000 0.0002 2773.674630 0 0.0118 270 | 0/8 12 h-lim-p 0.0003 5.3198 0.0094 2773.674630 0 0.0000 302 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 2773.674630 0 0.0001 322 Out... lnL = -2773.674630 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2773.674630 Node 7: lnL = -2773.674630 Node 8: lnL = -2773.674630 Node 9: lnL = -2773.674630 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 340 Sequential format.. Reading seq # 1: YBR163W_Sbay Reading seq # 2: YBR163W_Scer Reading seq # 3: YBR163W_Skud Reading seq # 4: YBR163W_Smik Reading seq # 5: YBR163W_Spar Sequences read.. Counting patterns.. # site patterns = 152 Counting frequencies.. 120 bytes for distance 24320 bytes for lkl0 19456 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.215040 0.058914 0.083822 0.116290 0.087018 0.190890 0.199036 0.026764 lnL0 = -1433.379302 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1433.379302 x= 0.21504 0.05891 0.08382 0.11629 0.08702 0.19089 0.19904 0.02676 1 h-lim-p 0.0059 1.6472 69.5777 1432.292554 8 0.0005 41 | 0/8 2 h-lim-p 0.0015 0.0122 14.1901 1432.199896 7 0.0009 73 | 0/8 3 h-lim-p 0.0018 0.0458 7.3309 1432.186627 6 0.0006 99 | 0/8 4 h-lim-p 0.0021 0.1810 2.1663 1432.184930 4 0.0008 119 | 0/8 5 h-lim-p 0.0091 1.0702 0.1930 1432.184914 2 0.0009 137 | 0/8 6 h-lim-p 0.0043 7.5247 0.0391 1432.184913 1 0.0011 160 | 0/8 7 h-lim-p 0.0919 20.0000 0.0005 1432.184735 0 1.1024 183 | 0/8 8 h-lim-p 0.0046 1.1467 0.1094 1432.184730 2 0.0008 210 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1432.184730 0 1.0938 230 | 0/8 10 h-lim-p 2.4035 20.0000 0.0000 1432.184730 0 1.0515 250 | 0/8 11 h-lim-p 1.1566 20.0000 0.0000 1432.184730 0 4.6263 272 | 0/8 12 h-lim-p 0.2956 20.0000 0.0002 1432.184730 0 0.0081 296 | 0/8 13 h-lim-p 0.0011 20.0000 0.0014 1432.184730 0 0.0001 319 | 0/8 14 h-lim-p 0.0001 20.0000 0.0017 1432.184730 0 0.0000 353 | 0/8 15 h-lim-p 0.0000 20.0000 0.0006 1432.184730 0 0.0000 373 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 1432.184730 0 0.0020 399 | 0/8 17 h-lim-p 0.0042 20.0000 0.0001 1432.184730 0 0.0002 423 | 0/8 18 h-lim-p 0.0006 20.0000 0.0000 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0008 | 0/8 20 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -1432.184730 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1432.184730 Node 7: lnL = -1432.184730 Node 8: lnL = -1432.184730 Node 9: lnL = -1432.184730 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 467 Sequential format.. Reading seq # 1: YBR164C_Sbay Reading seq # 2: YBR164C_Scer Reading seq # 3: YBR164C_Skud Reading seq # 4: YBR164C_Smik Reading seq # 5: YBR164C_Spar Sequences read.. Counting patterns.. # site patterns = 169 Counting frequencies.. 120 bytes for distance 27040 bytes for lkl0 21632 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.220911 0.130723 0.063896 0.131321 0.094906 0.205034 0.130295 0.023826 lnL0 = -2040.647627 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2040.647627 x= 0.22091 0.13072 0.06390 0.13132 0.09491 0.20503 0.13030 0.02383 1 h-lim-p 0.0016 0.0129 71.0524 2039.907721 4 0.0003 31 | 0/8 2 h-lim-p 0.0015 0.0119 9.6715 2039.888018 6 0.0004 60 | 0/8 3 h-lim-p 0.0013 0.1007 3.1890 2039.885940 5 0.0005 84 | 0/8 4 h-lim-p 0.0023 0.3866 0.6168 2039.885806 4 0.0007 106 | 0/8 5 h-lim-p 0.0036 0.3482 0.1277 2039.885802 1 0.0004 130 | 0/8 6 h-lim-p 0.0041 20.0000 0.0139 2039.885802 0 0.0009 151 | 0/8 7 h-lim-p 0.0056 20.0000 0.0022 2039.885802 0 0.0049 171 | 0/8 8 h-lim-p 0.0132 20.0000 0.0008 2039.885785 0 0.1580 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2039.885785 0 1.0938 214 | 0/8 10 h-lim-p 1.2528 20.0000 0.0000 2039.885785 0 1.0962 234 | 0/8 11 h-lim-p 0.7371 20.0000 0.0000 2039.885785 0 0.0173 259 | 0/8 12 h-lim-p 0.0005 20.0000 0.0011 2039.885785 0 0.0001 281 | 0/8 13 h-lim-p 0.0003 20.0000 0.0002 2039.885785 0 0.0000 306 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 2039.885785 0 0.0000 344 Out... lnL = -2039.885785 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2039.885785 Node 7: lnL = -2039.885785 Node 8: lnL = -2039.885785 Node 9: lnL = -2039.885785 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 487 Sequential format.. Reading seq # 1: YBR165W_Sbay Reading seq # 2: YBR165W_Scer Reading seq # 3: YBR165W_Skud Reading seq # 4: YBR165W_Smik Reading seq # 5: YBR165W_Spar Sequences read.. Counting patterns.. # site patterns = 174 Counting frequencies.. 120 bytes for distance 27840 bytes for lkl0 22272 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.256884 0.133111 0.059579 0.131141 0.095085 0.209351 0.122717 0.049789 lnL0 = -2105.661598 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2105.661598 x= 0.25688 0.13311 0.05958 0.13114 0.09509 0.20935 0.12272 0.04979 1 h-lim-p 0.0015 0.0117 87.9098 2104.558698 6 0.0003 34 | 0/8 2 h-lim-p 0.0010 0.0079 16.1875 2104.494968 3 0.0005 52 | 0/8 3 h-lim-p 0.0012 0.0551 6.5415 2104.486192 4 0.0005 72 | 0/8 4 h-lim-p 0.0018 0.1949 1.7587 2104.485257 5 0.0007 95 | 0/8 5 h-lim-p 0.0034 0.3444 0.3375 2104.485227 2 0.0006 114 | 0/8 6 h-lim-p 0.0046 3.7831 0.0413 2104.485226 0 0.0010 135 | 0/8 7 h-lim-p 0.0138 20.0000 0.0030 2104.485226 0 0.0015 157 | 0/8 8 h-lim-p 0.0822 20.0000 0.0001 2104.485225 0 0.6578 180 | 0/8 9 h-lim-p 2.1106 20.0000 0.0000 2104.485225 0 1.0553 200 | 0/8 10 h-lim-p 1.2331 20.0000 0.0000 2104.485225 0 1.0789 220 | 0/8 11 h-lim-p 0.6227 20.0000 0.0000 2104.485225 0 0.0195 244 | 0/8 12 h-lim-p 0.0037 20.0000 0.0001 2104.485225 0 0.0000 272 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 2104.485225 0 0.0000 303 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 2104.485225 0 0.0000 331 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -2104.485225 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2104.485225 Node 7: lnL = -2104.485225 Node 8: lnL = -2104.485225 Node 9: lnL = -2104.485225 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 506 Sequential format.. Reading seq # 1: YBR167C_Sbay Reading seq # 2: YBR167C_Scer Reading seq # 3: YBR167C_Skud Reading seq # 4: YBR167C_Smik Reading seq # 5: YBR167C_Spar Sequences read.. Counting patterns.. # site patterns = 197 Counting frequencies.. 120 bytes for distance 31520 bytes for lkl0 25216 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.244527 0.078658 0.077091 0.133678 0.079107 0.214343 0.216722 0.036606 lnL0 = -2322.769185 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2322.769185 x= 0.24453 0.07866 0.07709 0.13368 0.07911 0.21434 0.21672 0.03661 1 h-lim-p 0.0006 0.0050 69.0951 2321.831106 7 0.0004 39 | 0/8 2 h-lim-p 0.0008 0.0066 22.4623 2321.698613 7 0.0006 70 | 0/8 3 h-lim-p 0.0017 0.0342 7.4246 2321.685148 6 0.0005 96 | 0/8 4 h-lim-p 0.0016 0.0435 2.4866 2321.684341 4 0.0003 119 | 0/8 5 h-lim-p 0.0010 0.6409 0.7582 2321.684223 2 0.0005 135 | 0/8 6 h-lim-p 0.0111 8.8134 0.0312 2321.684222 0 0.0006 158 | 0/8 7 h-lim-p 0.0020 20.0000 0.0094 2321.684222 0 0.0009 178 | 0/8 8 h-lim-p 0.1115 20.0000 0.0001 2321.684217 0 0.8918 201 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2321.684217 0 1.0938 221 | 0/8 10 h-lim-p 1.2782 20.0000 0.0000 2321.684217 0 1.9173 241 | 0/8 11 h-lim-p 0.7586 20.0000 0.0000 2321.684217 0 0.0000 289 | 0/8 12 h-lim-p 0.0000 20.0000 0.0008 2321.684217 0 0.0000 316 | 0/8 13 h-lim-p 0.0000 20.0000 0.0002 2321.684217 0 0.0000 341 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0008 | 0/8 16 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -2321.684217 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2321.684217 Node 7: lnL = -2321.684217 Node 8: lnL = -2321.684217 Node 9: lnL = -2321.684217 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 508 Sequential format.. Reading seq # 1: YBR168W_Sbay Reading seq # 2: YBR168W_Scer Reading seq # 3: YBR168W_Skud Reading seq # 4: YBR168W_Smik Reading seq # 5: YBR168W_Spar Sequences read.. Counting patterns.. # site patterns = 200 Counting frequencies.. 120 bytes for distance 32000 bytes for lkl0 25600 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.234111 0.067177 0.080869 0.132937 0.079848 0.199286 0.194108 0.036850 lnL0 = -2288.254368 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2288.254368 x= 0.23411 0.06718 0.08087 0.13294 0.07985 0.19929 0.19411 0.03685 1 h-lim-p 0.0007 0.0055 73.5172 2287.361552 4 0.0003 31 | 0/8 2 h-lim-p 0.0012 0.0108 21.5846 2287.237459 2 0.0006 47 | 0/8 3 h-lim-p 0.0015 0.0338 8.0863 2287.228309 4 0.0003 67 | 0/8 4 h-lim-p 0.0009 0.0730 2.9108 2287.226881 2 0.0004 83 | 0/8 5 h-lim-p 0.0034 1.7265 0.3313 2287.226853 3 0.0005 105 | 0/8 6 h-lim-p 0.0042 7.1337 0.0398 2287.226853 0 0.0009 126 | 0/8 7 h-lim-p 0.0031 20.0000 0.0117 2287.226852 0 0.0027 146 | 0/8 8 h-lim-p 0.0227 20.0000 0.0014 2287.226722 0 0.3626 170 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2287.226712 1 0.9961 192 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2287.226712 0 1.0938 212 | 0/8 11 h-lim-p 0.8940 20.0000 0.0000 2287.226712 0 0.0009 241 | 0/8 12 h-lim-p 0.0001 20.0000 0.0003 2287.226712 0 0.0000 262 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 2287.226712 0 0.0001 282 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 2287.226712 0 0.0000 311 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 2287.226712 0 0.0000 343 Out... lnL = -2287.226712 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2287.226712 Node 7: lnL = -2287.226712 Node 8: lnL = -2287.226712 Node 9: lnL = -2287.226712 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 379 Sequential format.. Reading seq # 1: YBR169C_Sbay Reading seq # 2: YBR169C_Scer Reading seq # 3: YBR169C_Skud Reading seq # 4: YBR169C_Smik Reading seq # 5: YBR169C_Spar Sequences read.. Counting patterns.. # site patterns = 137 Counting frequencies.. 120 bytes for distance 21920 bytes for lkl0 17536 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.191705 0.094069 0.061364 0.122238 0.068147 0.114095 0.200047 0.021129 lnL0 = -1570.780931 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1570.780931 x= 0.19171 0.09407 0.06136 0.12224 0.06815 0.11410 0.20005 0.02113 1 h-lim-p 0.0040 0.0323 51.9292 1570.277612 6 0.0004 38 | 0/8 2 h-lim-p 0.0014 0.0111 14.0167 1570.229494 7 0.0005 64 | 0/8 3 h-lim-p 0.0010 0.0294 7.5855 1570.217661 4 0.0005 85 | 0/8 4 h-lim-p 0.0012 0.0378 3.1895 1570.215851 4 0.0004 107 | 0/8 5 h-lim-p 0.0081 0.8559 0.1719 1570.215842 2 0.0007 127 | 0/8 6 h-lim-p 0.0058 10.7492 0.0197 1570.215842 0 0.0006 149 | 0/8 7 h-lim-p 0.0043 20.0000 0.0029 1570.215842 0 0.0043 169 | 0/8 8 h-lim-p 0.0125 20.0000 0.0010 1570.215818 0 0.1496 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1570.215818 0 1.0938 212 | 0/8 10 h-lim-p 1.1858 20.0000 0.0000 1570.215818 0 1.0376 232 | 0/8 11 h-lim-p 0.9848 20.0000 0.0000 1570.215818 0 0.0308 256 | 0/8 12 h-lim-p 0.0000 1.4530 0.0294 1570.215818 0 0.0000 282 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 1570.215818 0 0.0000 303 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 1570.215818 0 0.0001 323 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 1570.215818 0 0.0000 352 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 1570.215818 0 0.0038 380 | 0/8 17 h-lim-p 0.0088 20.0000 0.0001 1570.215818 0 0.0000 409 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0013 | 0/8 20 h-lim-p 0.0000 20.0000 0.0013 Out... lnL = -1570.215818 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1570.215818 Node 7: lnL = -1570.215818 Node 8: lnL = -1570.215818 Node 9: lnL = -1570.215818 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 301 Sequential format.. Reading seq # 1: YBR170C_Sbay Reading seq # 2: YBR170C_Scer Reading seq # 3: YBR170C_Skud Reading seq # 4: YBR170C_Smik Reading seq # 5: YBR170C_Spar Sequences read.. Counting patterns.. # site patterns = 128 Counting frequencies.. 120 bytes for distance 20480 bytes for lkl0 16384 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.202860 0.089083 0.043629 0.091900 0.101363 0.154917 0.134151 0.037452 lnL0 = -1250.441782 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1250.441782 x= 0.20286 0.08908 0.04363 0.09190 0.10136 0.15492 0.13415 0.03745 1 h-lim-p 0.0012 0.0094 83.1592 1249.262727 8 0.0004 42 | 0/8 2 h-lim-p 0.0013 0.0108 21.6166 1249.098248 8 0.0007 74 | 0/8 3 h-lim-p 0.0022 0.0331 7.1969 1249.084707 6 0.0006 98 | 0/8 4 h-lim-p 0.0021 0.0876 1.9523 1249.083609 5 0.0006 123 | 0/8 5 h-lim-p 0.0046 1.0066 0.2618 1249.083581 3 0.0008 144 | 0/8 6 h-lim-p 0.0097 8.3693 0.0221 1249.083581 0 0.0011 166 | 0/8 7 h-lim-p 0.0092 20.0000 0.0025 1249.083581 0 0.0092 186 | 0/8 8 h-lim-p 0.0113 20.0000 0.0021 1249.083541 0 0.0905 209 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1249.083541 0 1.0938 229 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1249.083541 0 1.0938 249 | 0/8 11 h-lim-p 1.1082 20.0000 0.0000 1249.083541 0 0.0173 274 | 0/8 12 h-lim-p 0.0024 20.0000 0.0001 1249.083541 0 0.0003 296 | 0/8 13 h-lim-p 0.0002 20.0000 0.0001 1249.083541 0 0.0000 318 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 1249.083541 0 0.0000 349 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1249.083541 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1249.083541 Node 7: lnL = -1249.083541 Node 8: lnL = -1249.083541 Node 9: lnL = -1249.083541 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 302 Sequential format.. Reading seq # 1: YBR171W_Sbay Reading seq # 2: YBR171W_Scer Reading seq # 3: YBR171W_Skud Reading seq # 4: YBR171W_Smik Reading seq # 5: YBR171W_Spar Sequences read.. Counting patterns.. # site patterns = 127 Counting frequencies.. 120 bytes for distance 20320 bytes for lkl0 16256 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.200393 0.081816 0.041419 0.102486 0.095585 0.140747 0.149476 0.036991 lnL0 = -1242.208432 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1242.208432 x= 0.20039 0.08182 0.04142 0.10249 0.09558 0.14075 0.14948 0.03699 1 h-lim-p 0.0009 0.0069 64.4454 1241.375312 9 0.0004 42 | 0/8 2 h-lim-p 0.0008 0.0061 21.6083 1241.256622 8 0.0006 74 | 0/8 3 h-lim-p 0.0025 0.0346 4.6910 1241.250736 3 0.0006 93 | 0/8 4 h-lim-p 0.0020 0.1400 1.3717 1241.250165 4 0.0007 115 | 0/8 5 h-lim-p 0.0031 0.7762 0.3002 1241.250130 3 0.0008 134 | 0/8 6 h-lim-p 0.0311 20.0000 0.0078 1241.250130 0 0.0017 157 | 0/8 7 h-lim-p 0.0092 20.0000 0.0014 1241.250130 0 0.0139 177 | 0/8 8 h-lim-p 0.0067 20.0000 0.0030 1241.250116 0 0.0532 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1241.250115 0 1.0938 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1241.250115 0 1.0938 240 | 0/8 11 h-lim-p 1.1664 20.0000 0.0000 1241.250115 0 2.3329 261 | 0/8 12 h-lim-p 1.0649 20.0000 0.0000 1241.250115 0 0.0021 289 | 0/8 13 h-lim-p 0.0003 20.0000 0.0002 1241.250115 0 0.0000 324 | 0/8 14 h-lim-p 0.0000 20.0000 0.0007 1241.250115 0 0.0000 349 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 1241.250115 0 0.0000 369 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 1241.250115 0 0.0000 397 | 0/8 17 h-lim-p 0.0000 20.0000 0.0007 1241.250115 0 0.0000 420 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 1241.250115 0 0.0000 442 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 1241.250115 0 0.0000 469 | 0/8 20 h-lim-p 0.0000 20.0000 0.0007 | 0/8 21 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -1241.250115 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1241.250115 Node 7: lnL = -1241.250115 Node 8: lnL = -1241.250115 Node 9: lnL = -1241.250115 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 187 Sequential format.. Reading seq # 1: YBR173C_Sbay Reading seq # 2: YBR173C_Scer Reading seq # 3: YBR173C_Skud Reading seq # 4: YBR173C_Smik Reading seq # 5: YBR173C_Spar Sequences read.. Counting patterns.. # site patterns = 94 Counting frequencies.. 120 bytes for distance 15040 bytes for lkl0 12032 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.202793 0.073062 0.050552 0.104986 0.091478 0.063809 0.177459 0.046267 lnL0 = -714.390106 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 714.390106 x= 0.20279 0.07306 0.05055 0.10499 0.09148 0.06381 0.17746 0.04627 1 h-lim-p 0.0016 0.0128 65.9673 712.600419 10 0.0010 50 | 0/8 2 h-lim-p 0.0003 0.0025 24.4951 712.094802 0 0.0019 64 | 0/8 3 h-lim-p 0.0001 0.0007 25.8198 711.887613 m 0.0007 76 | 0/8 4 h-lim-p 0.0000 0.0000 14.8993 h-lim-p: 3.12318428e-21 2.49854742e-20 1.48992638e+01 711.887613 .. | 0/8 5 h-lim-p 0.0000 7.2928 15.0786 711.784272 0 0.0010 102 | 0/8 6 h-lim-p 0.0000 0.0003 9.5037 711.765295 m 0.0003 114 | 1/8 7 h-lim-p 0.0005 0.0739 3.9278 711.763013 0 0.0010 127 | 1/8 8 h-lim-p 0.0032 0.1358 1.1955 711.762095 4 0.0013 147 | 1/8 9 h-lim-p 0.0069 1.0745 0.2183 711.762048 2 0.0018 164 | 1/8 10 h-lim-p 0.0082 4.7000 0.0480 711.762008 2 0.0072 187 | 1/8 11 h-lim-p 0.0096 3.4599 0.0359 711.760774 0 0.0577 208 | 1/8 12 h-lim-p 0.0035 0.2355 0.5927 711.758667 3 0.0035 233 | 1/8 13 h-lim-p 2.5000 20.0000 0.0001 711.758662 1 0.9961 254 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 711.758662 0 1.2500 273 | 1/8 15 h-lim-p 1.6365 20.0000 0.0000 711.758662 0 0.2046 294 | 1/8 16 h-lim-p 0.0630 20.0000 0.0000 711.758662 0 0.0020 317 | 1/8 17 h-lim-p 0.0008 20.0000 0.0000 711.758662 0 0.0000 342 | 1/8 18 h-lim-p 0.0000 20.0000 0.0000 711.758662 0 0.0000 366 | 1/8 19 h-lim-p 0.0000 20.0000 0.0002 | 1/8 20 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -711.758662 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -711.758662 Node 7: lnL = -711.758662 Node 8: lnL = -711.758662 Node 9: lnL = -711.758662 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 389 Sequential format.. Reading seq # 1: YBR176W_Sbay Reading seq # 2: YBR176W_Scer Reading seq # 3: YBR176W_Skud Reading seq # 4: YBR176W_Smik Reading seq # 5: YBR176W_Spar Sequences read.. Counting patterns.. # site patterns = 226 Counting frequencies.. 120 bytes for distance 36160 bytes for lkl0 28928 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.298729 0.224035 0.068540 0.157274 0.188952 0.238723 0.257407 0.012883 lnL0 = -1832.454037 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1832.454037 x= 0.29873 0.22404 0.06854 0.15727 0.18895 0.23872 0.25741 0.01288 1 h-lim-p 0.0037 0.0298 16.5995 1832.316411 7 0.0010 38 | 0/8 2 h-lim-p 0.0025 0.0235 6.8169 1832.295834 6 0.0010 64 | 0/8 3 h-lim-p 0.0027 0.0638 2.5788 1832.291782 3 0.0014 83 | 0/8 4 h-lim-p 0.0038 0.2752 0.9566 1832.291363 4 0.0011 105 | 0/8 5 h-lim-p 0.0049 0.4347 0.2108 1832.291316 0 0.0021 125 | 0/8 6 h-lim-p 0.0062 2.2564 0.0726 1832.291313 1 0.0012 148 | 0/8 7 h-lim-p 0.0215 11.5279 0.0042 1832.291313 0 0.0024 170 | 0/8 8 h-lim-p 0.1214 20.0000 0.0001 1832.291312 0 0.9712 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1832.291312 0 1.0938 213 | 0/8 10 h-lim-p 1.3404 20.0000 0.0000 1832.291312 0 1.3404 233 | 0/8 11 h-lim-p 0.7993 20.0000 0.0000 1832.291312 0 0.0250 257 | 0/8 12 h-lim-p 0.0003 12.0163 0.0016 1832.291312 0 0.0000 283 | 0/8 13 h-lim-p 0.0002 20.0000 0.0000 1832.291312 0 0.0001 303 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 1832.291312 0 0.0000 331 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 1832.291312 0 0.0000 352 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1832.291312 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1832.291312 Node 7: lnL = -1832.291312 Node 8: lnL = -1832.291312 Node 9: lnL = -1832.291312 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 409 Sequential format.. Reading seq # 1: YBR177C_Sbay Reading seq # 2: YBR177C_Scer Reading seq # 3: YBR177C_Skud Reading seq # 4: YBR177C_Smik Reading seq # 5: YBR177C_Spar Sequences read.. Counting patterns.. # site patterns = 156 Counting frequencies.. 120 bytes for distance 24960 bytes for lkl0 19968 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.044762 0.044437 0.085188 0.060042 0.071375 0.150610 0.149991 0.239522 lnL0 = -1687.868272 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1687.868272 x= 0.04476 0.04444 0.08519 0.06004 0.07138 0.15061 0.14999 0.23952 1 h-lim-p 0.0025 0.0371 116.2777 1686.020439 4 0.0003 32 | 0/8 2 h-lim-p 0.0007 0.0059 17.6841 1685.953780 7 0.0004 61 | 0/8 3 h-lim-p 0.0005 0.0144 14.7973 1685.927193 5 0.0004 85 | 0/8 4 h-lim-p 0.0026 0.0535 2.0332 1685.926367 5 0.0004 111 | 0/8 5 h-lim-p 0.0012 0.3198 0.6789 1685.926243 2 0.0006 127 | 0/8 6 h-lim-p 0.0055 1.7074 0.0712 1685.926241 0 0.0007 149 | 0/8 7 h-lim-p 0.0193 20.0000 0.0026 1685.926019 0 0.2316 172 | 0/8 8 h-lim-p 0.0023 8.7199 0.2531 1685.925187 0 0.0035 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1685.925186 0 1.0938 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1685.925186 0 1.0938 232 | 0/8 11 h-lim-p 1.2167 20.0000 0.0000 1685.925186 0 2.4334 253 | 0/8 12 h-lim-p 1.4798 20.0000 0.0000 1685.925186 0 1.2948 273 | 0/8 13 h-lim-p 0.0680 20.0000 0.0004 1685.925186 0 0.0074 295 | 0/8 14 h-lim-p 0.0020 20.0000 0.0014 1685.925186 0 0.0000 330 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 1685.925186 0 0.0000 360 Out... lnL = -1685.925186 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1685.925186 Node 7: lnL = -1685.925186 Node 8: lnL = -1685.925186 Node 9: lnL = -1685.925186 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 883 Sequential format.. Reading seq # 1: YBR182C_Sbay Reading seq # 2: YBR182C_Scer Reading seq # 3: YBR182C_Skud Reading seq # 4: YBR182C_Smik Reading seq # 5: YBR182C_Spar Sequences read.. Counting patterns.. # site patterns = 307 Counting frequencies.. 120 bytes for distance 49120 bytes for lkl0 39296 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.019065 0.101260 0.058470 0.109477 0.091238 0.191653 0.164436 0.246073 lnL0 = -3834.851344 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3834.851344 x= 0.01907 0.10126 0.05847 0.10948 0.09124 0.19165 0.16444 0.24607 1 h-lim-p 0.0006 0.0048 137.3247 3833.149655 6 0.0002 36 | 0/8 2 h-lim-p 0.0004 0.0029 35.2522 3833.001379 7 0.0003 65 | 0/8 3 h-lim-p 0.0006 0.0048 13.0258 3832.986816 4 0.0002 86 | 0/8 4 h-lim-p 0.0009 0.0198 2.8824 3832.985748 4 0.0003 110 | 0/8 5 h-lim-p 0.0011 0.2773 0.7109 3832.985660 2 0.0004 127 | 0/8 6 h-lim-p 0.0018 1.9550 0.1375 3832.985658 1 0.0002 151 | 0/8 7 h-lim-p 0.0200 20.0000 0.0016 3832.985651 0 0.0599 172 | 0/8 8 h-lim-p 0.0033 3.9565 0.0280 3832.985512 0 0.0133 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3832.985498 1 0.9961 216 | 0/8 10 h-lim-p 2.0823 20.0000 0.0000 3832.985498 0 1.8220 236 | 0/8 11 h-lim-p 0.5930 20.0000 0.0001 3832.985498 0 0.0023 263 | 0/8 12 h-lim-p 0.0006 20.0000 0.0004 3832.985498 0 0.0000 298 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 3832.985498 0 0.0000 325 Out... lnL = -3832.985498 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3832.985498 Node 7: lnL = -3832.985498 Node 8: lnL = -3832.985498 Node 9: lnL = -3832.985498 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 920 Sequential format.. Reading seq # 1: YBR183W_Sbay Reading seq # 2: YBR183W_Scer Reading seq # 3: YBR183W_Skud Reading seq # 4: YBR183W_Smik Reading seq # 5: YBR183W_Spar Sequences read.. Counting patterns.. # site patterns = 341 Counting frequencies.. 120 bytes for distance 54560 bytes for lkl0 43648 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.223637 0.088565 0.168928 0.150303 0.143247 0.157475 0.277055 lnL0 = -4077.885973 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4077.885973 x= 0.00006 0.22364 0.08857 0.16893 0.15030 0.14325 0.15748 0.27705 1 h-lim-p 0.0000 0.0000 375.0433 4077.007580 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0009 200.7482 4073.317064 0 0.0002 38 | 1/8 3 h-lim-p 0.0011 0.0085 27.4379 4073.191941 7 0.0003 68 | 1/8 4 h-lim-p 0.0026 0.0741 3.4398 4073.157582 5 0.0015 92 | 1/8 5 h-lim-p 0.0026 0.2115 1.9363 4071.443103 0 0.0210 107 | 0/8 6 h-lim-p 0.0009 0.0114 45.6972 4066.044129 0 0.0018 120 | 0/8 7 h-lim-p 0.0004 0.0035 97.0450 4060.111110 0 0.0009 133 | 0/8 8 h-lim-p 0.0016 0.0128 16.0411 4060.025048 5 0.0006 154 | 0/8 9 h-lim-p 0.0017 0.0212 6.1126 4059.625660 m 0.0212 167 | 1/8 10 h-lim-p 0.2773 2.2184 0.1270 4059.210634 7 0.1631 195 | 0/8 11 h-lim-p 0.0006 0.0114 37.2534 4057.993087 0 0.0033 216 | 0/8 12 h-lim-p 0.1124 0.8990 0.1504 4057.573570 m 0.8990 228 | 1/8 13 h-lim-p 0.0051 0.0409 6.6801 4057.573498 3 0.0000 261 | 1/8 14 h-lim-p 0.1186 20.0000 0.0027 4057.549302 0 1.8971 277 | 1/8 15 h-lim-p 2.5000 20.0000 0.0015 4057.543993 2 1.0938 300 | 1/8 16 h-lim-p 2.5000 20.0000 0.0003 4057.543675 1 2.1875 321 | 1/8 17 h-lim-p 2.5000 20.0000 0.0001 4057.542425 010.0000 342 | 1/8 18 h-lim-p 2.1472 20.0000 0.0004 4057.542284 3 1.1541 368 | 0/8 19 h-lim-p 0.0710 20.0000 0.0057 4057.542284 0 0.0019 391 | 0/8 20 h-lim-p 0.1233 0.9862 0.0001 4057.542275 m 0.9862 411 | 1/8 21 h-lim-p 2.5000 20.0000 0.0000 4057.542275 0 1.0938 431 | 1/8 22 h-lim-p 2.5000 20.0000 0.0000 4057.542275 0 1.0938 450 | 1/8 23 h-lim-p 2.5000 20.0000 0.0000 4057.542275 0 1.0938 469 | 1/8 24 h-lim-p 2.5000 20.0000 0.0000 4057.542275 0 5.0000 489 | 1/8 25 h-lim-p 1.2507 20.0000 0.0000 4057.542275 0 0.1368 510 | 1/8 26 h-lim-p 0.1585 20.0000 0.0000 4057.542275 0 0.0000 552 Out... lnL = -4057.542275 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4057.542275 Node 7: lnL = -4057.542275 Node 8: lnL = -4057.542275 Node 9: lnL = -4057.542275 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 375 Sequential format.. Reading seq # 1: YBR184W_Sbay Reading seq # 2: YBR184W_Scer Reading seq # 3: YBR184W_Skud Reading seq # 4: YBR184W_Smik Reading seq # 5: YBR184W_Spar Sequences read.. Counting patterns.. # site patterns = 189 Counting frequencies.. 120 bytes for distance 30240 bytes for lkl0 24192 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.207480 0.117563 0.205675 0.206868 0.104480 0.214164 0.296262 lnL0 = -1708.920216 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1708.920216 x= 0.00006 0.20748 0.11756 0.20568 0.20687 0.10448 0.21416 0.29626 1 h-lim-p 0.0000 0.0000 262.4016 1708.279241 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0020 157.1023 1697.959829 5 0.0009 52 | 1/8 3 h-lim-p 0.0012 0.0096 21.7981 1697.694675 3 0.0011 70 | 1/8 4 h-lim-p 0.0022 0.0260 10.9880 1697.611984 7 0.0013 99 | 1/8 5 h-lim-p 0.0083 0.1197 1.7624 1697.467310 6 0.0091 127 | 1/8 6 h-lim-p 0.0047 0.0758 3.3973 1693.548771 0 0.0283 141 | 1/8 7 h-lim-p 0.0017 0.0140 30.7800 1685.313361 0 0.0052 154 | 0/8 8 h-lim-p 0.0005 0.0044 82.8240 1683.038166 0 0.0008 166 | 0/8 9 h-lim-p 0.1813 1.4507 0.2465 1681.840200 0 0.5440 179 | 0/8 10 h-lim-p 0.0114 0.0910 2.1656 1681.428982 m 0.0910 199 | 1/8 11 h-lim-p 0.1602 1.2820 0.2212 1681.410774 3 0.0363 218 | 0/8 12 h-lim-p 0.0035 0.1690 2.3086 1681.283318 0 0.0835 241 | 0/8 13 h-lim-p 0.1381 1.1044 0.1756 1681.084802 m 1.1044 253 | 0/8 14 h-lim-p 1.3978 11.1823 0.0359 1681.044467 2 1.3104 277 | 0/8 15 h-lim-p 2.5000 20.0000 0.0147 1681.041640 4 1.2703 307 | 0/8 16 h-lim-p 2.5000 20.0000 0.0027 1681.041449 3 1.4660 336 | 0/8 17 h-lim-p 2.5000 20.0000 0.0015 1681.041430 2 1.0938 360 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1681.041430 0 1.2500 380 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1681.041430 0 1.0938 400 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 1681.041430 0 5.0000 421 | 0/8 21 h-lim-p 0.8640 20.0000 0.0000 1681.041430 0 0.1080 443 | 0/8 22 h-lim-p 0.0311 20.0000 0.0000 1681.041430 0 0.0002 469 Out... lnL = -1681.041430 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1681.041430 Node 7: lnL = -1681.041430 Node 8: lnL = -1681.041430 Node 9: lnL = -1681.041430 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 653 Sequential format.. Reading seq # 1: YBR185C_Sbay Reading seq # 2: YBR185C_Scer Reading seq # 3: YBR185C_Skud Reading seq # 4: YBR185C_Smik Reading seq # 5: YBR185C_Spar Sequences read.. Counting patterns.. # site patterns = 285 Counting frequencies.. 120 bytes for distance 45600 bytes for lkl0 36480 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.231003 0.089805 0.225049 0.215968 0.163163 0.226859 0.329807 lnL0 = -3231.391926 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3231.391926 x= 0.00006 0.23100 0.08981 0.22505 0.21597 0.16316 0.22686 0.32981 1 h-lim-p 0.0000 0.0000 239.9490 3229.337651 m 0.0000 22 | 1/8 2 h-lim-p 0.0001 0.0022 119.4246 3226.473499 0 0.0005 36 | 1/8 3 h-lim-p 0.0022 0.0174 21.5999 3226.326992 7 0.0006 66 | 1/8 4 h-lim-p 0.0025 0.0450 5.5331 3226.289217 5 0.0016 90 | 1/8 5 h-lim-p 0.0047 0.1871 1.8858 3226.169437 0 0.0094 103 | 1/8 6 h-lim-p 0.0071 0.1912 2.4774 3221.354873 0 0.0427 117 | 0/8 7 h-lim-p 0.0018 0.0141 55.0295 3216.908487 2 0.0017 133 | 0/8 8 h-lim-p 0.0012 0.0094 39.8854 3216.422664 5 0.0006 156 | 0/8 9 h-lim-p 0.0068 0.0545 1.7187 3216.340062 0 0.0409 170 | 0/8 10 h-lim-p 1.3635 11.9231 0.0515 3215.955287 7 0.5028 198 | 0/8 11 h-lim-p 2.5000 20.0000 0.0046 3215.940138 6 1.3994 234 | 0/8 12 h-lim-p 2.5000 20.0000 0.0012 3215.939466 2 1.1719 258 | 0/8 13 h-lim-p 2.5000 20.0000 0.0001 3215.939445 2 1.6492 284 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 3215.939445 0 1.0938 304 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 3215.939445 0 1.0938 324 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 3215.939445 0 1.2500 344 | 0/8 17 h-lim-p 2.4137 20.0000 0.0000 3215.939445 0 0.9051 365 | 0/8 18 h-lim-p 0.0058 20.0000 0.0001 3215.939445 0 0.0007 387 | 0/8 19 h-lim-p 0.0004 20.0000 0.0002 3215.939445 0 0.0000 424 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 3215.939445 0 0.0000 456 | 0/8 21 h-lim-p 0.0000 20.0000 0.0001 | 0/8 22 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -3215.939445 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3215.939445 Node 7: lnL = -3215.939445 Node 8: lnL = -3215.939445 Node 9: lnL = -3215.939445 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 652 Sequential format.. Reading seq # 1: YBR186W_Sbay Reading seq # 2: YBR186W_Scer Reading seq # 3: YBR186W_Skud Reading seq # 4: YBR186W_Smik Reading seq # 5: YBR186W_Spar Sequences read.. Counting patterns.. # site patterns = 284 Counting frequencies.. 120 bytes for distance 45440 bytes for lkl0 36352 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.254077 0.084063 0.231197 0.238519 0.113610 0.229777 0.324150 lnL0 = -3214.310282 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3214.310282 x= 0.00006 0.25408 0.08406 0.23120 0.23852 0.11361 0.22978 0.32415 1 h-lim-p 0.0000 0.0000 315.0483 3213.141531 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0020 155.9851 3207.611526 0 0.0006 38 | 1/8 3 h-lim-p 0.0010 0.0083 43.4168 3207.245920 3 0.0004 56 | 1/8 4 h-lim-p 0.0018 0.0259 10.4503 3207.169527 7 0.0012 85 | 1/8 5 h-lim-p 0.0046 0.1249 2.8091 3207.120975 6 0.0030 110 | 1/8 6 h-lim-p 0.0031 0.1626 2.7411 3206.441167 0 0.0123 124 | 0/8 7 h-lim-p 0.0025 0.0279 13.6568 3198.516217 0 0.0099 138 | 0/8 8 h-lim-p 0.0012 0.0277 115.4584 3194.345206 9 0.0008 171 | 0/8 9 h-lim-p 0.0055 0.0441 4.2875 3193.822136 m 0.0441 183 | 1/8 10 h-lim-p 0.0569 0.4552 0.7246 3193.749737 6 0.0184 210 | 1/8 11 h-lim-p 0.7170 20.0000 0.0186 3193.403599 0 1.4340 230 | 1/8 12 h-lim-p 2.5000 20.0000 0.0066 3193.371784 2 1.1719 253 | 1/8 13 h-lim-p 2.5000 20.0000 0.0010 3193.370921 2 1.1719 276 | 0/8 14 h-lim-p 0.0375 20.0000 0.0303 3193.370920 0 0.0020 298 | 0/8 15 h-lim-p 0.1377 1.6419 0.0005 3193.370794 2 0.9024 326 | 0/8 16 h-lim-p 0.0593 0.4746 0.0001 3193.370789 m 0.4746 346 | 1/8 17 h-lim-p 0.3739 20.0000 0.0001 3193.370785 0 0.7478 367 | 1/8 18 h-lim-p 2.4228 20.0000 0.0000 3193.370784 1 1.1925 389 | 1/8 19 h-lim-p 2.5000 20.0000 0.0000 3193.370784 0 2.1875 408 | 0/8 20 h-lim-p -0.0000 -0.0000 0.0005 h-lim-p: -1.79509420e-19 -1.43607536e-18 4.83141172e-04 3193.370784 .. | 1/8 21 h-lim-p 0.0000 20.0000 0.0079 3193.370784 0 0.0006 449 | 1/8 22 h-lim-p 0.0011 20.0000 0.0046 3193.370784 0 0.0010 468 | 1/8 23 h-lim-p 0.0040 20.0000 0.0011 3193.370784 0 0.0009 488 | 1/8 24 h-lim-p 0.0061 20.0000 0.0002 3193.370784 0 0.0008 509 | 1/8 25 h-lim-p 0.0024 20.0000 0.0001 3193.370784 0 0.0021 528 | 1/8 26 h-lim-p 0.0052 20.0000 0.0000 3193.370784 0 0.0052 547 | 1/8 27 h-lim-p 0.0020 20.0000 0.0001 3193.370784 0 0.0078 568 | 1/8 28 h-lim-p 0.0015 20.0000 0.0003 3193.370784 0 0.0030 588 | 1/8 29 h-lim-p 2.5000 20.0000 0.0000 3193.370784 0 0.2734 609 | 1/8 30 h-lim-p 0.3764 20.0000 0.0000 3193.370784 0 0.0941 629 | 1/8 31 h-lim-p 0.1039 20.0000 0.0000 3193.370784 0 0.0032 652 Out... lnL = -3193.370784 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3193.370784 Node 7: lnL = -3193.370784 Node 8: lnL = -3193.370784 Node 9: lnL = -3193.370784 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 505 Sequential format.. Reading seq # 1: YBR187W_Sbay Reading seq # 2: YBR187W_Scer Reading seq # 3: YBR187W_Skud Reading seq # 4: YBR187W_Smik Reading seq # 5: YBR187W_Spar Sequences read.. Counting patterns.. # site patterns = 180 Counting frequencies.. 120 bytes for distance 28800 bytes for lkl0 23040 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.170012 0.074597 0.164961 0.183006 0.131367 0.156934 0.239557 lnL0 = -2324.163071 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2324.163071 x= 0.00006 0.17001 0.07460 0.16496 0.18301 0.13137 0.15693 0.23956 1 h-lim-p 0.0000 0.0000 800.6678 2322.891051 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0006 474.9357 2279.990673 1 0.0004 41 | 1/8 3 h-lim-p 0.0001 0.0007 205.1579 2277.290711 0 0.0002 54 | 1/8 4 h-lim-p 0.0001 0.0009 78.5691 2276.683322 0 0.0002 67 | 1/8 5 h-lim-p 0.0012 0.0135 14.8991 2276.587782 6 0.0006 92 | 1/8 6 h-lim-p 0.0045 0.0412 2.1316 2276.170020 0 0.0068 104 | 1/8 7 h-lim-p 0.0007 0.0200 21.6302 2264.343764 0 0.0053 119 | 1/8 8 h-lim-p 0.0011 0.0092 44.8159 2218.171217 0 0.0046 133 | 0/8 9 h-lim-p 0.0006 0.0045 105.5615 2212.884412 0 0.0011 146 | 0/8 10 h-lim-p 0.1194 0.9555 0.2190 2197.635623 m 0.9555 158 | 1/8 11 h-lim-p 1.1446 9.1566 0.0604 2192.209401 1 1.4307 180 | 1/8 12 h-lim-p 0.2244 1.7955 0.1475 2191.126907 0 0.3367 199 | 0/8 13 h-lim-p -0.0000 -0.0000 8.6964 h-lim-p: -7.36467474e-20 -5.89173979e-19 8.69636024e+00 2191.126907 .. | 0/8 14 h-lim-p 0.0000 0.0015 88.0756 2190.171828 0 0.0002 230 | 0/8 15 h-lim-p 0.0003 0.0027 51.9449 2189.327871 0 0.0007 243 | 0/8 16 h-lim-p 0.0001 0.0006 47.5311 2188.987571 m 0.0006 255 | 0/8 17 h-lim-p 0.0000 0.0000 33.3431 h-lim-p: 2.35929428e-21 1.88743542e-20 3.33431462e+01 2188.987571 .. | 0/8 18 h-lim-p 0.0000 0.0018 29.2883 2188.885694 0 0.0002 279 | 0/8 19 h-lim-p 0.0007 0.0233 9.8335 2188.856562 2 0.0007 295 | 0/8 20 h-lim-p 0.0004 0.0547 16.6393 2188.833522 3 0.0004 313 | 0/8 21 h-lim-p 0.0001 0.0009 11.6303 2188.819788 0 0.0004 327 | 0/8 22 h-lim-p 0.0005 0.0038 5.1134 2188.816576 3 0.0004 345 | 0/8 23 h-lim-p 0.0015 0.0375 1.3300 2188.816231 4 0.0005 367 | 0/8 24 h-lim-p 0.0018 0.0307 0.3403 2188.816204 3 0.0005 387 | 0/8 25 h-lim-p 0.3686 12.1267 0.0005 2188.816065 0 1.1059 408 | 0/8 26 h-lim-p 2.5000 20.0000 0.0001 2188.816064 0 1.0938 428 | 0/8 27 h-lim-p 2.1635 20.0000 0.0000 2188.816064 0 1.0817 448 | 0/8 28 h-lim-p 0.9663 20.0000 0.0000 2188.816064 0 0.8455 468 | 0/8 29 h-lim-p 0.0174 0.8317 0.0018 2188.816064 0 0.0000 507 | 0/8 30 h-lim-p 0.0000 20.0000 0.0000 2188.816064 0 0.0000 538 | 0/8 31 h-lim-p 0.0000 20.0000 0.0005 2188.816064 0 0.0000 564 | 0/8 32 h-lim-p 0.0000 20.0000 0.0002 2188.816064 0 0.0000 587 | 0/8 33 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 34 h-lim-p 0.0000 20.0000 0.0005 2188.816064 0 0.0000 652 | 0/8 35 h-lim-p 0.0000 20.0000 0.0005 | 0/8 36 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -2188.816064 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2188.816064 Node 7: lnL = -2188.816064 Node 8: lnL = -2188.816064 Node 9: lnL = -2188.816064 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 811 Sequential format.. Reading seq # 1: YBR191W_Sbay Reading seq # 2: YBR191W_Scer Reading seq # 3: YBR191W_Skud Reading seq # 4: YBR191W_Smik Reading seq # 5: YBR191W_Spar Sequences read.. Counting patterns.. # site patterns = 371 Counting frequencies.. 120 bytes for distance 59360 bytes for lkl0 47488 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.598964 0.000060 0.766916 0.492793 0.319953 0.270537 0.423593 lnL0 = -4628.149973 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4628.149973 x= 0.00006 0.59896 0.00006 0.76692 0.49279 0.31995 0.27054 0.42359 1 h-lim-p 0.0000 0.0000 415.9029 4628.065411 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0000 4740.8557 4622.283026 m 0.0000 34 | 2/8 3 h-lim-p 0.0000 0.0021 383.7464 4536.830144 1 0.0015 53 | 2/8 4 h-lim-p 0.0002 0.0014 217.6738 4518.809290 m 0.0014 65 | 2/8 5 h-lim-p 0.0017 0.0132 35.9742 4517.024070 0 0.0033 78 | 2/8 6 h-lim-p 0.0164 0.1313 4.4667 4516.865907 6 0.0082 105 | 2/8 7 h-lim-p 0.0357 1.0874 1.0315 4514.011006 0 0.1428 119 | 1/8 8 h-lim-p 0.0023 0.0186 52.7520 4513.317429 8 0.0008 151 | 1/8 9 h-lim-p 0.0022 0.0373 18.8814 4511.187939 0 0.0089 165 | 0/8 10 h-lim-p 0.0024 0.0190 34.5072 4511.040390 6 0.0008 192 | 0/8 11 h-lim-p 0.1134 0.9070 0.1563 4509.286078 m 0.9070 204 | 0/8 12 h-lim-p 0.0000 0.0000 0.0420 h-lim-p: 3.82309408e-18 3.05847526e-17 4.20096561e-02 4509.286078 .. | 0/8 13 h-lim-p 0.0000 0.0030 30.3507 4509.144040 0 0.0003 245 | 0/8 14 h-lim-p 0.0000 0.0001 14.6879 4509.129300 m 0.0001 257 | 1/8 15 h-lim-p 0.0001 0.0214 6.7419 4509.128077 0 0.0002 270 | 1/8 16 h-lim-p 0.0007 0.0689 2.1449 4509.122019 0 0.0029 284 | 1/8 17 h-lim-p 0.0042 0.3415 1.5089 4509.120340 3 0.0022 303 | 1/8 18 h-lim-p 0.0192 1.6101 0.1756 4509.120281 3 0.0028 325 | 1/8 19 h-lim-p 0.0546 20.0000 0.0090 4509.117517 0 0.4371 347 | 1/8 20 h-lim-p 0.0102 6.1240 0.3890 4509.116183 3 0.0085 372 | 1/8 21 h-lim-p 2.5000 20.0000 0.0004 4509.116120 2 0.9961 395 | 1/8 22 h-lim-p 2.5000 20.0000 0.0000 4509.116120 0 1.0938 414 | 1/8 23 h-lim-p 1.3155 20.0000 0.0000 4509.116120 0 1.1511 433 | 1/8 24 h-lim-p 0.2248 20.0000 0.0001 4509.116120 0 0.0009 459 | 1/8 25 h-lim-p 0.0004 20.0000 0.0002 4509.116120 0 0.0000 480 | 1/8 26 h-lim-p 0.0004 20.0000 0.0000 4509.116120 0 0.0000 519 | 1/8 27 h-lim-p 0.0000 20.0000 0.0000 4509.116120 0 0.0000 541 | 1/8 28 h-lim-p 0.0000 20.0000 0.0011 4509.116120 0 0.0000 572 | 1/8 29 h-lim-p 0.0000 20.0000 0.0000 4509.116120 0 0.0000 602 | 1/8 30 h-lim-p 0.0000 20.0000 0.0000 4509.116120 0 0.0000 634 | 1/8 31 h-lim-p 0.0000 20.0000 0.0000 | 1/8 32 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -4509.116120 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4509.116120 Node 7: lnL = -4509.116120 Node 8: lnL = -4509.116120 Node 9: lnL = -4509.116120 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 448 Sequential format.. Reading seq # 1: YBR192W_Sbay Reading seq # 2: YBR192W_Scer Reading seq # 3: YBR192W_Skud Reading seq # 4: YBR192W_Smik Reading seq # 5: YBR192W_Spar Sequences read.. Counting patterns.. # site patterns = 181 Counting frequencies.. 120 bytes for distance 28960 bytes for lkl0 23168 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000589 0.138623 0.017510 0.142240 0.106988 0.165503 0.158555 0.211878 lnL0 = -1974.881419 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1974.881419 x= 0.00059 0.13862 0.01751 0.14224 0.10699 0.16550 0.15856 0.21188 1 h-lim-p 0.0013 0.0107 131.6489 1973.572240 9 0.0002 45 | 0/8 2 h-lim-p 0.0008 0.0061 30.2661 1973.349872 7 0.0005 74 | 0/8 3 h-lim-p 0.0002 0.0016 9.2723 1973.329540 0 0.0006 87 | 0/8 4 h-lim-p 0.0006 0.0048 2.0976 1973.328296 2 0.0006 103 | 0/8 5 h-lim-p 0.0018 0.4920 0.7001 1973.328175 3 0.0005 124 | 0/8 6 h-lim-p 0.0034 2.4283 0.1079 1973.328170 0 0.0007 145 | 0/8 7 h-lim-p 0.0172 20.0000 0.0047 1973.328047 0 0.1033 167 | 0/8 8 h-lim-p 0.0043 0.7199 0.1141 1973.326786 0 0.0085 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1973.326747 2 1.0938 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1973.326747 0 1.0938 232 | 0/8 11 h-lim-p 1.1930 20.0000 0.0000 1973.326747 0 0.5220 252 | 0/8 12 h-lim-p 0.1955 20.0000 0.0001 1973.326747 0 0.0000 297 | 0/8 13 h-lim-p 0.0000 20.0000 0.0012 1973.326747 0 0.0000 325 | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 1973.326747 0 0.0000 345 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0012 | 0/8 17 h-lim-p 0.0000 20.0000 0.0012 Out... lnL = -1973.326747 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1973.326747 Node 7: lnL = -1973.326747 Node 8: lnL = -1973.326747 Node 9: lnL = -1973.326747 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 321 Sequential format.. Reading seq # 1: YBR193C_Sbay Reading seq # 2: YBR193C_Scer Reading seq # 3: YBR193C_Skud Reading seq # 4: YBR193C_Smik Reading seq # 5: YBR193C_Spar Sequences read.. Counting patterns.. # site patterns = 176 Counting frequencies.. 120 bytes for distance 28160 bytes for lkl0 22528 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.101315 0.157707 0.200037 0.208058 0.242081 0.313893 0.316061 lnL0 = -1540.603688 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1540.603688 x= 0.00006 0.10132 0.15771 0.20004 0.20806 0.24208 0.31389 0.31606 1 h-lim-p 0.0000 0.0000 104.7440 1540.394524 m 0.0000 22 | 1/8 2 h-lim-p 0.0001 0.0055 28.3654 1540.022885 0 0.0011 38 | 1/8 3 h-lim-p 0.0051 0.0688 6.3594 1539.947123 7 0.0028 67 | 1/8 4 h-lim-p 0.0062 0.1646 2.8744 1539.818479 0 0.0123 80 | 0/8 5 h-lim-p 0.0023 0.0646 15.7029 1539.306237 0 0.0045 93 | 0/8 6 h-lim-p 0.0043 0.0345 12.2989 1538.414257 0 0.0086 106 | 0/8 7 h-lim-p 0.0057 0.0456 5.6152 1537.187859 0 0.0114 119 | 0/8 8 h-lim-p 0.0016 0.0130 16.4610 1534.333915 0 0.0065 133 | 0/8 9 h-lim-p 0.0032 0.0259 13.7221 1534.116033 7 0.0023 163 | 0/8 10 h-lim-p 0.7871 9.0942 0.0399 1533.602187 7 0.8678 192 | 0/8 11 h-lim-p 2.5000 20.0000 0.0118 1533.551860 4 1.2732 221 | 0/8 12 h-lim-p 2.5000 20.0000 0.0058 1533.548678 4 1.2732 250 | 0/8 13 h-lim-p 2.5000 20.0000 0.0004 1533.548642 1 1.0938 272 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 1533.548640 0 1.0938 292 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1533.548640 0 1.0938 312 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1533.548640 0 1.0938 332 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1533.548640 0 0.4688 354 | 0/8 18 h-lim-p 0.1337 20.0000 0.0000 1533.548640 0 0.0010 380 Out... lnL = -1533.548640 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1533.548640 Node 7: lnL = -1533.548640 Node 8: lnL = -1533.548640 Node 9: lnL = -1533.548640 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 321 Sequential format.. Reading seq # 1: YBR194W_Sbay Reading seq # 2: YBR194W_Scer Reading seq # 3: YBR194W_Skud Reading seq # 4: YBR194W_Smik Reading seq # 5: YBR194W_Spar Sequences read.. Counting patterns.. # site patterns = 173 Counting frequencies.. 120 bytes for distance 27680 bytes for lkl0 22144 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.137017 0.198133 0.277330 0.253473 0.170263 0.276348 0.314317 lnL0 = -1535.910257 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1535.910257 x= 0.00006 0.13702 0.19813 0.27733 0.25347 0.17026 0.27635 0.31432 1 h-lim-p 0.0000 0.0000 153.9232 1535.808464 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0032 117.4891 1531.247211 0 0.0013 41 | 1/8 3 h-lim-p 0.0015 0.0121 27.1165 1530.704345 3 0.0015 59 | 1/8 4 h-lim-p 0.0032 0.0252 8.0723 1530.580294 6 0.0023 85 | 1/8 5 h-lim-p 0.0033 0.0718 5.6423 1530.257993 0 0.0066 98 | 1/8 6 h-lim-p 0.0072 0.0733 5.1443 1526.888421 0 0.0217 111 | 0/8 7 h-lim-p 0.0012 0.0098 56.2343 1520.335613 0 0.0025 124 | 0/8 8 h-lim-p 0.0007 0.0055 40.2865 1519.228438 0 0.0014 137 | 0/8 9 h-lim-p 0.0021 0.0171 8.8244 1518.742329 0 0.0085 151 | 0/8 10 h-lim-p 0.1553 1.2427 0.1368 1515.832860 0 0.6213 165 | 0/8 11 h-lim-p 1.6880 13.5041 0.0326 1515.228198 7 1.8757 202 | 0/8 12 h-lim-p 2.5000 20.0000 0.0050 1515.211355 5 1.3298 233 | 0/8 13 h-lim-p 1.4998 20.0000 0.0045 1515.209000 5 1.0214 266 | 0/8 14 h-lim-p 2.5000 20.0000 0.0012 1515.208829 4 1.5461 298 | 0/8 15 h-lim-p 2.5000 20.0000 0.0002 1515.208810 2 2.1875 322 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1515.208810 0 1.0938 342 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1515.208810 0 1.0938 362 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1515.208810 0 0.6250 383 | 0/8 19 h-lim-p 0.9924 20.0000 0.0000 1515.208810 0 0.0068 409 Out... lnL = -1515.208810 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1515.208810 Node 7: lnL = -1515.208810 Node 8: lnL = -1515.208810 Node 9: lnL = -1515.208810 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 461 Sequential format.. Reading seq # 1: YBR195C_Sbay Reading seq # 2: YBR195C_Scer Reading seq # 3: YBR195C_Skud Reading seq # 4: YBR195C_Smik Reading seq # 5: YBR195C_Spar Sequences read.. Counting patterns.. # site patterns = 149 Counting frequencies.. 120 bytes for distance 23840 bytes for lkl0 19072 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.037874 0.021476 0.013864 0.077676 0.083829 0.118164 0.159403 0.186236 lnL0 = -1709.446493 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1709.446493 x= 0.03787 0.02148 0.01386 0.07768 0.08383 0.11816 0.15940 0.18624 1 h-lim-p 0.0003 0.0353 326.0805 1704.188691 4 0.0001 30 | 0/8 2 h-lim-p 0.0001 0.0009 71.3713 1703.455561 0 0.0003 43 | 0/8 3 h-lim-p 0.0014 0.0115 14.9720 1703.419724 2 0.0003 60 | 0/8 4 h-lim-p 0.0012 0.0430 4.1035 1703.415783 4 0.0005 81 | 0/8 5 h-lim-p 0.0016 0.1271 1.2730 1703.415497 2 0.0004 98 | 0/8 6 h-lim-p 0.0016 1.0591 0.3010 1703.415465 3 0.0006 118 | 0/8 7 h-lim-p 0.0103 8.7072 0.0166 1703.414445 0 0.0825 141 | 0/8 8 h-lim-p 0.0034 0.5301 0.4063 1703.403168 0 0.0067 162 | 0/8 9 h-lim-p 2.5000 20.0000 0.0008 1703.401566 4 1.3122 191 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 1703.401444 4 1.4175 221 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1703.401444 0 1.0938 241 | 0/8 12 h-lim-p 1.6947 20.0000 0.0000 1703.401444 0 1.4828 261 | 0/8 13 h-lim-p 1.2616 20.0000 0.0000 1703.401444 0 2.5233 282 | 0/8 14 h-lim-p 0.2010 20.0000 0.0003 1703.401444 0 0.0004 310 | 0/8 15 h-lim-p 0.0000 12.9868 0.0044 1703.401444 0 0.0000 330 | 0/8 16 h-lim-p 0.0000 0.4070 0.6550 1703.401444 0 0.0000 352 | 0/8 17 h-lim-p 0.0615 20.0000 0.0004 1703.401444 0 0.0269 372 | 0/8 18 h-lim-p 0.0270 20.0000 0.0004 1703.401444 0 0.0034 394 | 0/8 19 h-lim-p 0.0033 20.0000 0.0004 .. | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 1703.401444 0 0.0051 464 | 0/8 21 h-lim-p 0.0138 20.0000 0.0000 1703.401444 0 0.0000 501 | 0/8 22 h-lim-p 0.0000 20.0000 0.0001 1703.401444 0 0.0000 525 | 0/8 23 h-lim-p 0.0000 20.0000 0.0003 1703.401444 0 0.0000 560 | 0/8 24 h-lim-p 0.0000 20.0000 0.0019 | 0/8 25 h-lim-p 0.0000 20.0000 0.0019 Out... lnL = -1703.401444 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1703.401444 Node 7: lnL = -1703.401444 Node 8: lnL = -1703.401444 Node 9: lnL = -1703.401444 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 851 Sequential format.. Reading seq # 1: YBR196C_Sbay Reading seq # 2: YBR196C_Scer Reading seq # 3: YBR196C_Skud Reading seq # 4: YBR196C_Smik Reading seq # 5: YBR196C_Spar Sequences read.. Counting patterns.. # site patterns = 404 Counting frequencies.. 120 bytes for distance 64640 bytes for lkl0 51712 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.088564 0.022466 0.142554 0.238438 0.178334 0.307275 0.301839 0.467562 lnL0 = -4591.507958 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4591.507958 x= 0.08856 0.02247 0.14255 0.23844 0.17833 0.30727 0.30184 0.46756 1 h-lim-p 0.0037 0.8106 158.5530 4587.736667 9 0.0003 48 | 0/8 2 h-lim-p 0.0010 0.0079 48.6950 4586.490590 6 0.0011 74 | 0/8 3 h-lim-p 0.0041 0.0331 9.2850 4586.448575 4 0.0010 97 | 0/8 4 h-lim-p 0.0057 0.1361 1.6569 4586.447396 4 0.0009 121 | 0/8 5 h-lim-p 0.0063 1.0247 0.2293 4586.447356 2 0.0012 138 | 0/8 6 h-lim-p 0.0055 7.2214 0.0505 4586.447283 1 0.0055 160 | 0/8 7 h-lim-p 0.0016 1.8972 0.1760 4586.446324 0 0.0063 182 | 0/8 8 h-lim-p 0.0033 20.0000 0.3332 4586.436147 0 0.0134 204 | 0/8 9 h-lim-p 2.5000 20.0000 0.0010 4586.434855 3 1.0004 230 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 4586.434854 0 1.0938 250 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4586.434854 0 1.0938 270 | 0/8 12 h-lim-p 1.4270 20.0000 0.0000 4586.434854 0 1.2486 290 | 0/8 13 h-lim-p 1.0249 20.0000 0.0000 4586.434854 0 4.0997 312 | 0/8 14 h-lim-p 0.0345 20.0000 0.0015 4586.434854 0 0.0173 332 | 0/8 15 h-lim-p 0.0053 20.0000 0.0048 4586.434854 0 0.0000 361 | 0/8 16 h-lim-p 0.0006 20.0000 0.0000 4586.434854 0 0.0000 392 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 4586.434854 0 0.0000 419 Out... lnL = -4586.434854 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4586.434854 Node 7: lnL = -4586.434854 Node 8: lnL = -4586.434854 Node 9: lnL = -4586.434854 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 350 Sequential format.. Reading seq # 1: YBR197C_Sbay Reading seq # 2: YBR197C_Scer Reading seq # 3: YBR197C_Skud Reading seq # 4: YBR197C_Smik Reading seq # 5: YBR197C_Spar Sequences read.. Counting patterns.. # site patterns = 161 Counting frequencies.. 120 bytes for distance 25760 bytes for lkl0 20608 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.058031 0.057324 0.078865 0.177770 0.123471 0.217533 0.196817 0.328701 lnL0 = -1442.908266 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1442.908266 x= 0.05803 0.05732 0.07887 0.17777 0.12347 0.21753 0.19682 0.32870 1 h-lim-p 0.0019 0.0152 64.1914 1441.232825 2 0.0009 26 | 0/8 2 h-lim-p 0.0013 0.0103 16.1187 1441.106502 4 0.0010 46 | 0/8 3 h-lim-p 0.0028 0.0299 5.8347 1441.087889 3 0.0013 64 | 0/8 4 h-lim-p 0.0022 0.0364 3.4149 1441.080127 3 0.0018 82 | 0/8 5 h-lim-p 0.0219 0.8931 0.2810 1441.080074 1 0.0014 99 | 0/8 6 h-lim-p 0.0175 18.1245 0.0220 1441.080070 2 0.0056 124 | 0/8 7 h-lim-p 0.0350 20.0000 0.0035 1441.079793 0 0.2797 147 | 0/8 8 h-lim-p 0.0043 0.6261 0.2282 1441.079596 2 0.0033 171 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1441.079589 1 0.9961 193 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1441.079589 0 1.0938 213 | 0/8 11 h-lim-p 1.1751 20.0000 0.0000 1441.079589 0 2.3503 234 | 0/8 12 h-lim-p 0.3286 20.0000 0.0000 1441.079589 0 0.3286 254 | 0/8 13 h-lim-p 0.0474 20.0000 0.0002 1441.079589 0 0.0118 275 | 0/8 14 h-lim-p 0.0045 20.0000 0.0006 1441.079589 0 0.0000 304 | 0/8 15 h-lim-p 0.0005 20.0000 0.0000 1441.079589 0 0.0000 334 Out... lnL = -1441.079589 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1441.079589 Node 7: lnL = -1441.079589 Node 8: lnL = -1441.079589 Node 9: lnL = -1441.079589 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 444 Sequential format.. Reading seq # 1: YBR198C_Sbay Reading seq # 2: YBR198C_Scer Reading seq # 3: YBR198C_Skud Reading seq # 4: YBR198C_Smik Reading seq # 5: YBR198C_Spar Sequences read.. Counting patterns.. # site patterns = 209 Counting frequencies.. 120 bytes for distance 33440 bytes for lkl0 26752 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.032909 0.083498 0.101797 0.121344 0.133918 0.238957 0.181802 0.299358 lnL0 = -2043.241074 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2043.241074 x= 0.03291 0.08350 0.10180 0.12134 0.13392 0.23896 0.18180 0.29936 1 h-lim-p 0.0092 2.1202 66.7078 2042.209762 6 0.0005 36 | 0/8 2 h-lim-p 0.0023 0.0180 12.7808 2042.138193 5 0.0009 58 | 0/8 3 h-lim-p 0.0018 0.0428 6.3508 2042.128694 6 0.0006 84 | 0/8 4 h-lim-p 0.0037 0.2290 0.9950 2042.128323 2 0.0008 101 | 0/8 5 h-lim-p 0.0056 0.6885 0.1409 2042.128313 2 0.0009 127 | 0/8 6 h-lim-p 0.0069 17.1911 0.0185 2042.128313 0 0.0030 147 | 0/8 7 h-lim-p 0.0131 20.0000 0.0042 2042.128307 0 0.0262 168 | 0/8 8 h-lim-p 0.0060 20.0000 0.0186 2042.128149 0 0.0239 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2042.128149 0 1.0938 210 | 0/8 10 h-lim-p 2.3506 20.0000 0.0000 2042.128149 0 1.0284 230 | 0/8 11 h-lim-p 0.9078 20.0000 0.0000 2042.128149 0 0.3972 250 | 0/8 12 h-lim-p 0.0003 3.4535 0.0165 2042.128149 0 0.0000 280 | 0/8 13 h-lim-p 0.0003 20.0000 0.0000 2042.128149 0 0.0000 309 Out... lnL = -2042.128149 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2042.128149 Node 7: lnL = -2042.128149 Node 8: lnL = -2042.128149 Node 9: lnL = -2042.128149 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 488 Sequential format.. Reading seq # 1: YBR199W_Sbay Reading seq # 2: YBR199W_Scer Reading seq # 3: YBR199W_Skud Reading seq # 4: YBR199W_Smik Reading seq # 5: YBR199W_Spar Sequences read.. Counting patterns.. # site patterns = 211 Counting frequencies.. 120 bytes for distance 33760 bytes for lkl0 27008 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.128913 0.140542 0.186561 0.167537 0.211596 0.218694 0.282047 lnL0 = -2138.354449 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2138.354449 x= 0.00006 0.12891 0.14054 0.18656 0.16754 0.21160 0.21869 0.28205 1 h-lim-p 0.0000 0.0000 122.5890 2138.209474 m 0.0000 22 | 1/8 2 h-lim-p 0.0001 0.0154 17.1402 2138.084836 0 0.0011 38 | 1/8 3 h-lim-p 0.0028 0.0523 6.8801 2138.049522 2 0.0013 54 | 1/8 4 h-lim-p 0.0060 0.1826 1.4904 2137.961423 0 0.0090 66 | 1/8 5 h-lim-p 0.0067 0.2285 1.9817 2135.015565 0 0.0538 81 | 0/8 6 h-lim-p 0.0012 0.0099 30.2093 2133.654819 0 0.0019 93 | 0/8 7 h-lim-p 0.0003 0.0028 14.0137 2133.572909 0 0.0010 106 | 0/8 8 h-lim-p 0.0021 0.0664 6.9672 2133.493292 0 0.0042 119 | 0/8 9 h-lim-p 0.0031 0.0389 9.3825 2133.452297 6 0.0019 147 | 0/8 10 h-lim-p 0.3745 9.4927 0.0481 2132.671034 0 0.7489 160 | 0/8 11 h-lim-p 2.5000 20.0000 0.0051 2132.664069 4 0.9802 188 | 0/8 12 h-lim-p 2.5000 20.0000 0.0008 2132.663986 2 1.1719 212 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2132.663985 0 1.0938 232 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 2132.663985 0 1.0938 252 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2132.663985 0 2.1875 272 | 0/8 16 h-lim-p 2.2668 20.0000 0.0000 2132.663985 0 0.9917 292 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 2132.663985 0 0.5469 313 | 0/8 18 h-lim-p 0.0111 20.0000 0.0000 2132.663985 0 0.0111 333 | 0/8 19 h-lim-p 0.0040 20.0000 0.0000 2132.663985 0 0.0000 374 | 0/8 20 h-lim-p 0.0000 20.0000 0.0000 | 0/8 21 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -2132.663985 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2132.663985 Node 7: lnL = -2132.663985 Node 8: lnL = -2132.663985 Node 9: lnL = -2132.663985 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 762 Sequential format.. Reading seq # 1: YBR200W_Sbay Reading seq # 2: YBR200W_Scer Reading seq # 3: YBR200W_Skud Reading seq # 4: YBR200W_Smik Reading seq # 5: YBR200W_Spar Sequences read.. Counting patterns.. # site patterns = 337 Counting frequencies.. 120 bytes for distance 53920 bytes for lkl0 43136 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.134961 0.118658 0.193450 0.049044 0.216192 0.293060 0.292079 lnL0 = -3391.262775 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3391.262775 x= 0.00006 0.13496 0.11866 0.19345 0.04904 0.21619 0.29306 0.29208 1 h-lim-p 0.0038 0.0304 116.6490 3389.569838 9 0.0003 48 | 0/8 2 h-lim-p 0.0005 0.0043 43.8825 3389.193039 7 0.0004 77 | 0/8 3 h-lim-p 0.0001 0.0007 10.0719 3389.162203 m 0.0007 89 | 0/8 4 h-lim-p 0.0049 0.2541 1.5140 3389.161431 4 0.0007 112 | 0/8 5 h-lim-p 0.0041 1.5239 0.2586 3389.161401 2 0.0009 129 | 0/8 6 h-lim-p 0.0001 0.0010 0.2107 3389.161401 0 0.0000 168 | 0/8 7 h-lim-p 0.0000 0.0001 1.4744 .. | 0/8 8 h-lim-p 0.0000 20.0000 1.8369 3389.160759 0 0.0003 218 | 0/8 9 h-lim-p 0.0008 0.1227 0.7254 3389.160687 2 0.0003 234 | 0/8 10 h-lim-p 0.0011 0.9264 0.2049 3389.160672 2 0.0007 259 | 0/8 11 h-lim-p 0.0091 12.4629 0.0160 3389.160672 0 0.0010 281 | 0/8 12 h-lim-p 0.0030 0.3899 0.0054 3389.160672 0 0.0026 301 | 0/8 13 h-lim-p 0.0062 20.0000 0.0023 3389.160670 0 0.0246 323 | 0/8 14 h-lim-p 0.0025 20.0000 0.0225 3389.160657 0 0.0049 344 | 0/8 15 h-lim-p 0.0017 6.7478 0.0658 3389.160650 0 0.0017 364 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 3389.160650 0 1.0938 384 | 0/8 17 h-lim-p 1.4241 20.0000 0.0000 3389.160650 0 1.2461 404 | 0/8 18 h-lim-p 1.1944 20.0000 0.0000 3389.160650 0 1.0451 424 | 0/8 19 h-lim-p 0.0959 3.0379 0.0003 3389.160650 0 0.0015 449 | 0/8 20 h-lim-p 0.0002 0.4160 0.0019 3389.160650 0 0.0000 482 | 0/8 21 h-lim-p 0.0001 20.0000 0.0000 3389.160650 0 0.0000 507 Out... lnL = -3389.160650 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3389.160650 Node 7: lnL = -3389.160650 Node 8: lnL = -3389.160650 Node 9: lnL = -3389.160650 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 883 Sequential format.. Reading seq # 1: YBR201W_Sbay Reading seq # 2: YBR201W_Scer Reading seq # 3: YBR201W_Skud Reading seq # 4: YBR201W_Smik Reading seq # 5: YBR201W_Spar Sequences read.. Counting patterns.. # site patterns = 344 Counting frequencies.. 120 bytes for distance 55040 bytes for lkl0 44032 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.023788 0.002508 0.084700 0.184408 0.136090 0.246688 0.398227 0.310562 lnL0 = -4243.679795 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4243.679795 x= 0.02379 0.00251 0.08470 0.18441 0.13609 0.24669 0.39823 0.31056 1 h-lim-p 0.0011 0.0088 180.2249 4241.011846 8 0.0002 40 | 0/8 2 h-lim-p 0.0003 0.0025 27.3910 4240.854995 0 0.0005 52 | 0/8 3 h-lim-p 0.0007 0.0052 9.1833 4240.842278 4 0.0003 73 | 0/8 4 h-lim-p 0.0017 0.0357 1.8512 4240.841512 4 0.0005 96 | 0/8 5 h-lim-p 0.0039 0.4843 0.2192 4240.841500 0 0.0005 110 | 0/8 6 h-lim-p 0.0020 4.9070 0.0550 4240.841497 1 0.0010 133 | 0/8 7 h-lim-p 0.0141 20.0000 0.0038 4240.840888 0 0.2252 157 | 0/8 8 h-lim-p 0.0022 0.4238 0.3937 4240.840341 1 0.0027 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 4240.840306 1 1.0938 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4240.840305 0 1.2500 221 | 0/8 11 h-lim-p 1.6176 20.0000 0.0000 4240.840305 0 1.4154 241 | 0/8 12 h-lim-p 0.6982 20.0000 0.0001 4240.840305 0 0.0218 265 | 0/8 13 h-lim-p 0.0002 6.6595 0.0047 4240.840305 0 0.0000 303 | 0/8 14 h-lim-p 0.0000 20.0000 0.0005 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -4240.840305 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4240.840305 Node 7: lnL = -4240.840305 Node 8: lnL = -4240.840305 Node 9: lnL = -4240.840305 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 847 Sequential format.. Reading seq # 1: YBR203W_Sbay Reading seq # 2: YBR203W_Scer Reading seq # 3: YBR203W_Skud Reading seq # 4: YBR203W_Smik Reading seq # 5: YBR203W_Spar Sequences read.. Counting patterns.. # site patterns = 240 Counting frequencies.. 120 bytes for distance 38400 bytes for lkl0 30720 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.044453 0.028088 0.036317 0.085418 0.038705 0.156303 0.141294 0.196698 lnL0 = -3250.552242 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3250.552242 x= 0.04445 0.02809 0.03632 0.08542 0.03871 0.15630 0.14129 0.19670 1 h-lim-p 0.0002 0.0018 193.8124 3249.000965 8 0.0001 41 | 0/8 2 h-lim-p 0.0002 0.0017 51.7011 3248.804906 6 0.0002 66 | 0/8 3 h-lim-p 0.0002 0.0066 35.3256 3248.760384 5 0.0001 87 | 0/8 4 h-lim-p 0.0003 0.0154 11.2563 3248.751653 4 0.0002 108 | 0/8 5 h-lim-p 0.0010 0.0556 1.7344 3248.751411 3 0.0002 129 | 0/8 6 h-lim-p 0.0006 0.1731 0.4878 3248.751387 2 0.0002 145 | 0/8 7 h-lim-p 0.0171 20.0000 0.0065 3248.751387 0 0.0009 168 | 0/8 8 h-lim-p 0.0452 20.0000 0.0001 3248.751362 0 0.5426 191 | 0/8 9 h-lim-p 0.9872 20.0000 0.0001 3248.751361 0 0.9872 211 | 0/8 10 h-lim-p 1.8925 20.0000 0.0000 3248.751361 0 0.8280 231 | 0/8 11 h-lim-p 0.6464 20.0000 0.0000 3248.751361 0 0.3232 251 | 0/8 12 h-lim-p 0.0835 20.0000 0.0002 3248.751361 0 0.0209 272 | 0/8 13 h-lim-p 0.0081 20.0000 0.0005 3248.751361 0 0.0020 293 | 0/8 14 h-lim-p 0.0011 20.0000 0.0009 3248.751361 0 0.0000 332 | 0/8 15 h-lim-p 0.0000 20.0000 0.0006 | 0/8 16 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -3248.751361 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3248.751361 Node 7: lnL = -3248.751361 Node 8: lnL = -3248.751361 Node 9: lnL = -3248.751361 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 259 Sequential format.. Reading seq # 1: YBR204C_Sbay Reading seq # 2: YBR204C_Scer Reading seq # 3: YBR204C_Skud Reading seq # 4: YBR204C_Smik Reading seq # 5: YBR204C_Spar Sequences read.. Counting patterns.. # site patterns = 115 Counting frequencies.. 120 bytes for distance 18400 bytes for lkl0 14720 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.179307 0.174545 0.088551 0.165830 0.170316 0.143153 0.207780 lnL0 = -1127.665598 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1127.665598 x= 0.00006 0.17931 0.17455 0.08855 0.16583 0.17032 0.14315 0.20778 1 h-lim-p 0.0000 0.0000 107.6812 1127.625036 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0021 114.1803 1125.432266 0 0.0006 40 | 1/8 3 h-lim-p 0.0010 0.0077 30.0371 1125.006869 1 0.0012 54 | 1/8 4 h-lim-p 0.0069 0.0552 4.3371 1124.964716 4 0.0027 74 | 1/8 5 h-lim-p 0.0117 0.1922 1.0015 1124.563566 0 0.0351 87 | 1/8 6 h-lim-p 0.0026 0.0207 7.2794 1123.094041 0 0.0052 100 | 1/8 7 h-lim-p 0.0009 0.0075 31.8942 1121.076041 0 0.0019 113 | 1/8 8 h-lim-p 0.0018 0.0147 17.6640 1120.882971 8 0.0013 147 | 1/8 9 h-lim-p 0.6820 14.8732 0.0328 1120.221213 0 1.0230 159 | 0/8 10 h-lim-p 0.0103 3.0773 3.2552 1120.214562 2 0.0012 184 | 0/8 11 h-lim-p 0.2301 9.4776 0.0171 1120.031770 0 0.9203 198 | 0/8 12 h-lim-p 2.5000 20.0000 0.0030 1120.026063 3 1.0449 224 | 0/8 13 h-lim-p 2.5000 20.0000 0.0005 1120.025895 2 1.0938 248 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1120.025894 0 1.0938 268 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1120.025894 0 1.0938 288 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1120.025894 0 1.0938 308 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1120.025894 0 2.1875 328 | 0/8 18 h-lim-p 1.8384 20.0000 0.0000 1120.025894 0 0.2298 350 | 0/8 19 h-lim-p 0.2590 20.0000 0.0000 1120.025894 0 0.1295 370 | 0/8 20 h-lim-p 0.1180 20.0000 0.0000 1120.025894 0 0.0074 393 Out... lnL = -1120.025894 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1120.025894 Node 7: lnL = -1120.025894 Node 8: lnL = -1120.025894 Node 9: lnL = -1120.025894 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 286 Sequential format.. Reading seq # 1: YBR205W_Sbay Reading seq # 2: YBR205W_Scer Reading seq # 3: YBR205W_Skud Reading seq # 4: YBR205W_Smik Reading seq # 5: YBR205W_Spar Sequences read.. Counting patterns.. # site patterns = 123 Counting frequencies.. 120 bytes for distance 19680 bytes for lkl0 15744 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.184709 0.198171 0.079993 0.175655 0.144502 0.137169 0.201016 lnL0 = -1096.747109 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1096.747109 x= 0.00006 0.18471 0.19817 0.07999 0.17565 0.14450 0.13717 0.20102 1 h-lim-p 0.0000 0.0000 124.4029 1096.704840 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0014 166.3254 1092.302361 0 0.0006 40 | 1/8 3 h-lim-p 0.0008 0.0066 27.7462 1091.879335 0 0.0016 53 | 1/8 4 h-lim-p 0.0077 0.0656 5.8749 1091.844375 6 0.0016 77 | 1/8 5 h-lim-p 0.0031 0.0709 2.9463 1091.804943 6 0.0032 100 | 1/8 6 h-lim-p 0.0039 0.1553 2.4386 1091.350561 0 0.0156 114 | 1/8 7 h-lim-p 0.0055 0.0438 5.6276 1088.239935 0 0.0164 127 | 0/8 8 h-lim-p 0.0008 0.0065 34.5250 1087.476213 0 0.0016 140 | 0/8 9 h-lim-p 0.0094 0.0748 2.3806 1087.453476 4 0.0072 160 | 0/8 10 h-lim-p 0.2294 3.7589 0.0749 1086.889640 0 0.4588 173 | 0/8 11 h-lim-p 1.2868 10.2945 0.0164 1086.801080 6 1.3482 207 | 0/8 12 h-lim-p 2.5000 20.0000 0.0039 1086.796730 6 0.8482 241 | 0/8 13 h-lim-p 2.5000 20.0000 0.0010 1086.796362 3 0.9961 267 | 0/8 14 h-lim-p 2.5000 20.0000 0.0002 1086.796349 2 1.0938 291 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1086.796349 0 1.0938 311 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1086.796349 0 1.0938 331 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1086.796349 0 2.5000 351 | 0/8 18 h-lim-p 1.5288 20.0000 0.0000 1086.796349 0 0.3344 372 | 0/8 19 h-lim-p 0.4371 20.0000 0.0000 1086.796349 0 0.0546 394 | 0/8 20 h-lim-p 0.0504 20.0000 0.0000 1086.796349 0 0.0504 414 | 0/8 21 h-lim-p 0.0463 20.0000 0.0000 1086.796349 0 0.0000 450 Out... lnL = -1086.796349 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1086.796349 Node 7: lnL = -1086.796349 Node 8: lnL = -1086.796349 Node 9: lnL = -1086.796349 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 238 Sequential format.. Reading seq # 1: YBR207W_Sbay Reading seq # 2: YBR207W_Scer Reading seq # 3: YBR207W_Skud Reading seq # 4: YBR207W_Smik Reading seq # 5: YBR207W_Spar Sequences read.. Counting patterns.. # site patterns = 102 Counting frequencies.. 120 bytes for distance 16320 bytes for lkl0 13056 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.170320 0.116228 0.077223 0.120601 0.184827 0.113040 0.189557 lnL0 = -985.776749 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 985.776749 x= 0.00006 0.17032 0.11623 0.07722 0.12060 0.18483 0.11304 0.18956 1 h-lim-p 0.0000 0.0000 73.1893 985.747657 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0079 27.2034 985.424939 0 0.0009 40 | 1/8 3 h-lim-p 0.0019 0.0183 12.9631 985.380541 5 0.0006 65 | 1/8 4 h-lim-p 0.0024 0.0547 3.3741 985.355777 5 0.0027 90 | 1/8 5 h-lim-p 0.0060 0.2306 1.4963 985.285152 0 0.0120 103 | 1/8 6 h-lim-p 0.0079 0.0670 2.2616 984.080608 0 0.0238 116 | 1/8 7 h-lim-p 0.0019 0.0149 20.1975 982.434006 0 0.0037 129 | 1/8 8 h-lim-p 0.0133 0.1062 1.7118 982.430278 5 0.0021 155 | 1/8 9 h-lim-p 0.1272 15.7781 0.0280 982.243324 0 0.5086 169 | 0/8 10 h-lim-p 0.0073 1.2102 1.9500 982.240904 5 0.0013 200 | 0/8 11 h-lim-p 0.5495 20.0000 0.0046 982.224593 0 1.0990 213 | 0/8 12 h-lim-p 2.5000 20.0000 0.0017 982.223554 5 0.7555 248 | 0/8 13 h-lim-p 2.5000 20.0000 0.0001 982.223545 2 0.9644 272 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 982.223545 0 1.0938 292 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 982.223545 0 1.0938 312 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 982.223545 0 2.1875 332 | 0/8 17 h-lim-p 1.9068 20.0000 0.0000 982.223545 0 0.8342 352 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 982.223545 0 0.0171 378 Out... lnL = -982.223545 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -982.223545 Node 7: lnL = -982.223545 Node 8: lnL = -982.223545 Node 9: lnL = -982.223545 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 863 Sequential format.. Reading seq # 1: YBR210W_Sbay Reading seq # 2: YBR210W_Scer Reading seq # 3: YBR210W_Skud Reading seq # 4: YBR210W_Smik Reading seq # 5: YBR210W_Spar Sequences read.. Counting patterns.. # site patterns = 417 Counting frequencies.. 120 bytes for distance 66720 bytes for lkl0 53376 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.014713 0.000060 0.328542 0.158218 0.145773 0.343684 0.437257 0.415176 lnL0 = -4676.916096 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4676.916096 x= 0.01471 0.00006 0.32854 0.15822 0.14577 0.34368 0.43726 0.41518 1 h-lim-p 0.0002 0.0019 95.2945 4673.249533 0 0.0010 24 | 0/8 2 h-lim-p 0.0000 0.0003 60.5995 4672.610713 m 0.0003 36 | 1/8 3 h-lim-p 0.0003 0.0058 49.4305 4672.189191 0 0.0006 49 | 1/8 4 h-lim-p 0.0029 0.0360 10.6047 4672.131811 6 0.0011 75 | 1/8 5 h-lim-p 0.0063 0.1937 1.7888 4672.107926 6 0.0043 102 | 1/8 6 h-lim-p 0.0037 0.1312 2.0850 4672.027029 0 0.0074 115 | 1/8 7 h-lim-p 0.0050 0.0399 1.5963 4672.022617 4 0.0026 136 | 1/8 8 h-lim-p 0.1094 5.1975 0.0382 4671.849137 0 0.4374 150 | 1/8 9 h-lim-p 0.0022 0.0818 7.6046 4671.737486 5 0.0025 180 | 1/8 10 h-lim-p 2.5000 20.0000 0.0034 4671.730908 5 0.9394 202 | 1/8 11 h-lim-p 2.5000 20.0000 0.0002 4671.730899 1 0.9961 223 | 0/8 12 h-lim-p 0.1827 20.0000 0.0010 4671.730899 0 0.0057 246 | 0/8 13 h-lim-p 0.1181 0.9444 0.0000 4671.730898 m 0.9444 266 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 4671.730898 0 1.0938 286 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 4671.730898 0 1.0938 305 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 4671.730898 0 2.1875 324 | 1/8 17 h-lim-p 1.8427 20.0000 0.0000 4671.730898 0 0.9214 343 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 4671.730898 0 0.6250 363 | 1/8 19 h-lim-p 1.6724 20.0000 0.0000 4671.730898 0 0.1829 384 Out... lnL = -4671.730898 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4671.730898 Node 7: lnL = -4671.730898 Node 8: lnL = -4671.730898 Node 9: lnL = -4671.730898 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 503 Sequential format.. Reading seq # 1: YBR213W_Sbay Reading seq # 2: YBR213W_Scer Reading seq # 3: YBR213W_Skud Reading seq # 4: YBR213W_Smik Reading seq # 5: YBR213W_Spar Sequences read.. Counting patterns.. # site patterns = 193 Counting frequencies.. 120 bytes for distance 30880 bytes for lkl0 24704 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.023267 0.000060 0.052559 0.094502 0.069032 0.187706 0.224847 0.195468 lnL0 = -2030.535058 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2030.535058 x= 0.02327 0.00006 0.05256 0.09450 0.06903 0.18771 0.22485 0.19547 1 h-lim-p 0.0009 0.0075 88.0271 2029.738371 9 0.0002 46 | 0/8 2 h-lim-p 0.0005 0.0041 16.1024 2029.707653 2 0.0002 62 | 0/8 3 h-lim-p 0.0008 0.0773 5.1535 2029.702815 4 0.0004 83 | 0/8 4 h-lim-p 0.0007 0.0459 2.9979 2029.701817 3 0.0003 102 | 0/8 5 h-lim-p 0.0017 0.1198 0.5010 2029.701759 3 0.0005 121 | 0/8 6 h-lim-p 0.0017 2.1665 0.1340 2029.701755 2 0.0006 146 | 0/8 7 h-lim-p 0.0016 2.6098 0.0463 2029.701754 0 0.0003 167 | 0/8 8 h-lim-p 0.0921 20.0000 0.0002 2029.701691 0 1.1055 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2029.701689 0 1.0938 210 | 0/8 10 h-lim-p 1.7778 20.0000 0.0000 2029.701689 0 1.5556 230 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2029.701689 0 0.5469 251 | 0/8 12 h-lim-p 0.2186 20.0000 0.0000 2029.701689 0 0.0239 273 | 0/8 13 h-lim-p 0.0107 20.0000 0.0001 2029.701689 0 0.0001 299 | 0/8 14 h-lim-p 0.0001 20.0000 0.0001 2029.701689 0 0.0000 330 | 0/8 15 h-lim-p 0.0000 20.0000 0.0041 | 0/8 16 h-lim-p 0.0000 20.0000 0.0041 Out... lnL = -2029.701689 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2029.701689 Node 7: lnL = -2029.701689 Node 8: lnL = -2029.701689 Node 9: lnL = -2029.701689 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 317 Sequential format.. Reading seq # 1: YBR214W_Sbay Reading seq # 2: YBR214W_Scer Reading seq # 3: YBR214W_Skud Reading seq # 4: YBR214W_Smik Reading seq # 5: YBR214W_Spar Sequences read.. Counting patterns.. # site patterns = 73 Counting frequencies.. 120 bytes for distance 11680 bytes for lkl0 9344 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.028185 0.007553 0.023045 0.036163 0.044997 0.116697 0.119881 0.133489 lnL0 = -909.132819 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 909.132819 x= 0.02818 0.00755 0.02305 0.03616 0.04500 0.11670 0.11988 0.13349 1 h-lim-p 0.0009 0.6081 139.0075 908.260217 8 0.0001 38 | 0/8 2 h-lim-p 0.0003 0.0026 21.9852 908.150802 0 0.0005 50 | 0/8 3 h-lim-p 0.0006 0.0127 16.8410 908.126572 4 0.0002 70 | 0/8 4 h-lim-p 0.0012 0.0181 3.6226 908.124898 2 0.0003 87 | 0/8 5 h-lim-p 0.0007 0.0491 1.3642 908.124561 4 0.0004 110 | 0/8 6 h-lim-p 0.0011 0.1028 0.5202 908.124533 2 0.0003 127 | 0/8 7 h-lim-p 0.0582 20.0000 0.0022 908.124496 0 0.1164 148 | 0/8 8 h-lim-p 0.0031 1.1308 0.0851 908.124156 0 0.0061 169 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 908.124133 2 1.2305 194 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 908.124131 1 1.2305 217 | 0/8 11 h-lim-p 2.1512 20.0000 0.0000 908.124131 0 1.8823 237 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 908.124131 0 1.0938 257 | 0/8 13 h-lim-p 0.2961 20.0000 0.0000 908.124131 0 4.7380 281 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 908.124131 0 0.0012 311 | 0/8 15 h-lim-p 0.0034 20.0000 0.0000 908.124131 0 0.0000 347 Out... lnL = -908.124131 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -908.124131 Node 7: lnL = -908.124131 Node 8: lnL = -908.124131 Node 9: lnL = -908.124131 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 250 Sequential format.. Reading seq # 1: YBR216C_Sbay Reading seq # 2: YBR216C_Scer Reading seq # 3: YBR216C_Skud Reading seq # 4: YBR216C_Smik Reading seq # 5: YBR216C_Spar Sequences read.. Counting patterns.. # site patterns = 101 Counting frequencies.. 120 bytes for distance 16160 bytes for lkl0 12928 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.071892 0.071493 0.025462 0.126487 0.064787 0.163569 0.132215 0.266521 lnL0 = -1053.293722 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1053.293722 x= 0.07189 0.07149 0.02546 0.12649 0.06479 0.16357 0.13221 0.26652 1 h-lim-p 0.0008 0.0066 49.9481 1052.915463 4 0.0003 30 | 0/8 2 h-lim-p 0.0006 0.0052 20.2900 1052.821687 4 0.0005 50 | 0/8 3 h-lim-p 0.0020 0.0272 5.1430 1052.815306 5 0.0005 74 | 0/8 4 h-lim-p 0.0019 0.1445 1.4206 1052.814484 2 0.0009 90 | 0/8 5 h-lim-p 0.0077 2.2752 0.1632 1052.814470 2 0.0010 108 | 0/8 6 h-lim-p 0.0033 1.9526 0.0494 1052.814469 0 0.0008 129 | 0/8 7 h-lim-p 0.0092 20.0000 0.0044 1052.814462 0 0.0277 150 | 0/8 8 h-lim-p 0.0120 5.1552 0.0103 1052.814253 0 0.0479 172 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1052.814240 2 0.9961 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1052.814240 0 1.0938 216 | 0/8 11 h-lim-p 1.1499 20.0000 0.0000 1052.814240 0 0.0090 242 | 0/8 12 h-lim-p 0.0031 20.0000 0.0000 1052.814240 0 0.0012 263 | 0/8 13 h-lim-p 0.0006 20.0000 0.0000 1052.814240 0 0.0006 283 | 0/8 14 h-lim-p 0.0005 20.0000 0.0000 1052.814240 0 0.0005 303 | 0/8 15 h-lim-p 0.0001 20.0000 0.0003 1052.814240 0 0.0000 340 | 0/8 16 h-lim-p 0.0000 20.0000 0.0005 | 0/8 17 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -1052.814240 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1052.814240 Node 7: lnL = -1052.814240 Node 8: lnL = -1052.814240 Node 9: lnL = -1052.814240 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 252 Sequential format.. Reading seq # 1: YBR217W_Sbay Reading seq # 2: YBR217W_Scer Reading seq # 3: YBR217W_Skud Reading seq # 4: YBR217W_Smik Reading seq # 5: YBR217W_Spar Sequences read.. Counting patterns.. # site patterns = 104 Counting frequencies.. 120 bytes for distance 16640 bytes for lkl0 13312 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.074229 0.063254 0.029231 0.116613 0.074661 0.166174 0.141764 0.271395 lnL0 = -1061.724920 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1061.724920 x= 0.07423 0.06325 0.02923 0.11661 0.07466 0.16617 0.14176 0.27140 1 h-lim-p 0.0011 0.0086 23.8792 1061.570644 4 0.0005 31 | 0/8 2 h-lim-p 0.0006 0.0046 11.7891 1061.547305 6 0.0004 59 | 0/8 3 h-lim-p 0.0011 0.0471 4.4239 1061.541508 4 0.0007 81 | 0/8 4 h-lim-p 0.0017 0.1209 1.7791 1061.540713 5 0.0006 106 | 0/8 5 h-lim-p 0.0044 1.3732 0.2414 1061.540689 2 0.0008 123 | 0/8 6 h-lim-p 0.0028 1.3644 0.0726 1061.540687 2 0.0009 148 | 0/8 7 h-lim-p 0.0090 20.0000 0.0072 1061.540687 0 0.0020 169 | 0/8 8 h-lim-p 0.2634 20.0000 0.0001 1061.540683 0 1.0535 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1061.540683 0 1.0938 211 | 0/8 10 h-lim-p 2.3992 20.0000 0.0000 1061.540683 0 2.0993 231 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1061.540683 0 0.5469 252 | 0/8 12 h-lim-p 0.0934 20.0000 0.0000 1061.540683 0 0.0000 284 Out... lnL = -1061.540683 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1061.540683 Node 7: lnL = -1061.540683 Node 8: lnL = -1061.540683 Node 9: lnL = -1061.540683 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 801 Sequential format.. Reading seq # 1: YBR218C_Sbay Reading seq # 2: YBR218C_Scer Reading seq # 3: YBR218C_Skud Reading seq # 4: YBR218C_Smik Reading seq # 5: YBR218C_Spar Sequences read.. Counting patterns.. # site patterns = 267 Counting frequencies.. 120 bytes for distance 42720 bytes for lkl0 34176 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.045686 0.041869 0.057368 0.132042 0.062694 0.179329 0.188987 0.247085 lnL0 = -3418.778601 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3418.778601 x= 0.04569 0.04187 0.05737 0.13204 0.06269 0.17933 0.18899 0.24709 1 h-lim-p 0.0005 0.0037 167.4454 3416.522743 8 0.0002 39 | 0/8 2 h-lim-p 0.0003 0.0020 48.0492 3416.260793 2 0.0002 55 | 0/8 3 h-lim-p 0.0004 0.0124 27.1940 3416.200927 6 0.0002 82 | 0/8 4 h-lim-p 0.0010 0.0432 5.6997 3416.195522 5 0.0004 105 | 0/8 5 h-lim-p 0.0017 0.1589 1.1628 3416.195261 2 0.0004 122 | 0/8 6 h-lim-p 0.0016 0.5748 0.2926 3416.195249 1 0.0003 137 | 0/8 7 h-lim-p 0.0040 9.5500 0.0236 3416.195249 0 0.0009 158 | 0/8 8 h-lim-p 0.0322 20.0000 0.0006 3416.195021 0 0.5156 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3416.195021 0 1.0938 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3416.195021 0 1.0938 222 | 0/8 11 h-lim-p 0.6412 20.0000 0.0000 3416.195021 0 0.0088 247 | 0/8 12 h-lim-p 0.0003 20.0000 0.0009 3416.195021 0 0.0000 271 | 0/8 13 h-lim-p 0.0004 20.0000 0.0000 3416.195021 0 0.0000 306 | 0/8 14 h-lim-p 0.0000 20.0000 0.0005 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -3416.195021 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3416.195021 Node 7: lnL = -3416.195021 Node 8: lnL = -3416.195021 Node 9: lnL = -3416.195021 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 339 Sequential format.. Reading seq # 1: YBR222C_Sbay Reading seq # 2: YBR222C_Scer Reading seq # 3: YBR222C_Skud Reading seq # 4: YBR222C_Smik Reading seq # 5: YBR222C_Spar Sequences read.. Counting patterns.. # site patterns = 132 Counting frequencies.. 120 bytes for distance 21120 bytes for lkl0 16896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.312133 0.161639 0.303117 0.618024 0.441041 2.880486 0.726628 lnL0 = -1436.983418 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1436.983418 x= 0.00006 0.31213 0.16164 0.30312 0.61802 0.44104 2.88049 0.72663 1 h-lim-p 0.0000 0.0000 217.9749 1436.899944 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0009 889.9675 1346.190488 1 0.0007 42 | 1/8 3 h-lim-p 0.0001 0.0011 139.7402 1340.636299 0 0.0008 56 | 1/8 4 h-lim-p 0.0001 0.0006 55.7345 1339.249652 m 0.0006 68 | 1/8 5 h-lim-p 0.0011 0.0092 29.7046 1338.928879 3 0.0010 86 | 1/8 6 h-lim-p 0.0805 1.2995 0.3539 1336.224335 0 0.2414 99 | 1/8 7 h-lim-p 0.0519 0.4155 0.0639 1335.630056 m 0.4155 118 | 2/8 8 h-lim-p 0.2045 2.0728 0.1041 1335.621066 4 0.0537 146 | 2/8 9 h-lim-p 0.0337 3.1178 0.1656 1335.449746 0 0.2025 166 | 1/8 10 h-lim-p 0.1093 3.6707 0.3067 1335.449218 5 0.0076 198 | 0/8 11 h-lim-p 0.0003 0.0022 1.4095 1335.447366 m 0.0022 217 | 0/8 12 h-lim-p 0.1010 3.3512 0.0304 1335.434316 0 0.3031 230 | 0/8 13 h-lim-p 0.0102 0.0814 0.0103 1335.433929 m 0.0814 250 | 0/8 14 h-lim-p -0.0000 -0.0000 0.0107 h-lim-p: -1.35097681e-18 -1.08078145e-17 1.07468891e-02 1335.433929 .. | 0/8 15 h-lim-p 0.0000 0.0742 1.8253 1335.432054 0 0.0013 293 | 0/8 16 h-lim-p 0.0036 1.6668 0.6441 1335.431919 2 0.0007 310 | 0/8 17 h-lim-p 0.0026 0.0206 0.0846 1335.431911 1 0.0023 332 | 0/8 18 h-lim-p 0.0008 0.0065 0.0802 1335.431907 0 0.0016 353 | 0/8 19 h-lim-p 0.0007 0.0058 0.0667 1335.431897 m 0.0058 373 | 1/8 20 h-lim-p 0.0044 20.0000 0.0504 1335.431897 0 0.0005 395 | 1/8 21 h-lim-p 0.0446 20.0000 0.0005 1335.431873 0 0.5349 417 | 1/8 22 h-lim-p 2.5000 20.0000 0.0001 1335.431868 1 1.2305 439 | 1/8 23 h-lim-p 2.5000 20.0000 0.0000 1335.431867 0 1.0938 458 | 1/8 24 h-lim-p 1.9184 20.0000 0.0000 1335.431867 0 1.6786 477 | 1/8 25 h-lim-p 1.6172 20.0000 0.0000 1335.431867 0 0.8086 496 | 1/8 26 h-lim-p 0.0946 20.0000 0.0001 1335.431867 0 0.0002 523 | 1/8 27 h-lim-p 0.0001 20.0000 0.0001 1335.431867 0 0.0001 542 | 1/8 28 h-lim-p 0.0002 20.0000 0.0001 1335.431867 0 0.0000 572 | 1/8 29 h-lim-p 0.0000 20.0000 0.0002 | 1/8 30 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1335.431867 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1335.431867 Node 7: lnL = -1335.431867 Node 8: lnL = -1335.431867 Node 9: lnL = -1335.431867 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 357 Sequential format.. Reading seq # 1: YBR223C_Sbay Reading seq # 2: YBR223C_Scer Reading seq # 3: YBR223C_Skud Reading seq # 4: YBR223C_Smik Reading seq # 5: YBR223C_Spar Sequences read.. Counting patterns.. # site patterns = 141 Counting frequencies.. 120 bytes for distance 22560 bytes for lkl0 18048 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.089567 0.052004 0.055356 0.090020 0.089943 0.126533 0.127085 0.275529 lnL0 = -1456.390725 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1456.390725 x= 0.08957 0.05200 0.05536 0.09002 0.08994 0.12653 0.12709 0.27553 1 h-lim-p 0.0040 0.0321 49.8841 1456.038697 6 0.0003 39 | 0/8 2 h-lim-p 0.0025 0.0286 5.8693 1456.026636 6 0.0007 65 | 0/8 3 h-lim-p 0.0013 0.0492 3.1473 1456.024751 5 0.0005 88 | 0/8 4 h-lim-p 0.0029 0.4173 0.5039 1456.024673 2 0.0006 105 | 0/8 5 h-lim-p 0.0027 2.4750 0.1185 1456.024669 0 0.0007 126 | 0/8 6 h-lim-p 0.0024 4.4860 0.0333 1456.024669 0 0.0011 146 | 0/8 7 h-lim-p 0.0094 20.0000 0.0038 1456.024669 0 0.0005 169 | 0/8 8 h-lim-p 0.0691 20.0000 0.0000 1456.024668 0 1.1058 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1456.024668 0 1.0938 213 | 0/8 10 h-lim-p 1.2021 20.0000 0.0000 1456.024668 0 2.4041 234 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1456.024668 0 0.6250 255 | 0/8 12 h-lim-p 0.1046 20.0000 0.0000 1456.024668 0 0.0000 287 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 1456.024668 0 0.0000 317 | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 1456.024668 0 0.0000 337 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1456.024668 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1456.024668 Node 7: lnL = -1456.024668 Node 8: lnL = -1456.024668 Node 9: lnL = -1456.024668 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 182 Sequential format.. Reading seq # 1: YBR228W_Sbay Reading seq # 2: YBR228W_Scer Reading seq # 3: YBR228W_Skud Reading seq # 4: YBR228W_Smik Reading seq # 5: YBR228W_Spar Sequences read.. Counting patterns.. # site patterns = 93 Counting frequencies.. 120 bytes for distance 14880 bytes for lkl0 11904 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.050362 0.040726 0.090058 0.133967 0.060667 0.145151 0.235684 0.260025 lnL0 = -827.248081 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 827.248081 x= 0.05036 0.04073 0.09006 0.13397 0.06067 0.14515 0.23568 0.26002 1 h-lim-p 0.0039 0.0312 28.7979 826.959661 8 0.0007 42 | 0/8 2 h-lim-p 0.0018 0.0147 8.5434 826.921559 8 0.0011 76 | 0/8 3 h-lim-p 0.0021 0.0335 4.5883 826.910025 6 0.0014 103 | 0/8 4 h-lim-p 0.0043 0.1986 1.4882 826.908628 5 0.0015 127 | 0/8 5 h-lim-p 0.0049 0.1468 0.4433 826.908489 4 0.0016 149 | 0/8 6 h-lim-p 0.0450 11.8378 0.0153 826.908489 0 0.0025 172 | 0/8 7 h-lim-p 0.0168 20.0000 0.0023 826.908489 0 0.0168 192 | 0/8 8 h-lim-p 0.0136 20.0000 0.0028 826.908468 0 0.1089 215 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 826.908467 0 1.0938 235 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 826.908467 0 1.0938 255 | 0/8 11 h-lim-p 1.3925 20.0000 0.0000 826.908467 0 1.2184 275 | 0/8 12 h-lim-p 0.7320 20.0000 0.0000 826.908467 0 0.0915 297 | 0/8 13 h-lim-p 0.0023 20.0000 0.0004 826.908467 0 0.0000 335 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -826.908467 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -826.908467 Node 7: lnL = -826.908467 Node 8: lnL = -826.908467 Node 9: lnL = -826.908467 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 355 Sequential format.. Reading seq # 1: YBR229C_Sbay Reading seq # 2: YBR229C_Scer Reading seq # 3: YBR229C_Skud Reading seq # 4: YBR229C_Smik Reading seq # 5: YBR229C_Spar Sequences read.. Counting patterns.. # site patterns = 171 Counting frequencies.. 120 bytes for distance 27360 bytes for lkl0 21888 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.076939 0.024660 0.068424 0.138035 0.154363 0.204825 0.255204 0.328315 lnL0 = -1660.249575 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1660.249575 x= 0.07694 0.02466 0.06842 0.13803 0.15436 0.20483 0.25520 0.32831 1 h-lim-p 0.0010 0.0076 62.8975 1659.135723 8 0.0006 42 | 0/8 2 h-lim-p 0.0004 0.0034 21.3097 1658.987272 0 0.0008 55 | 0/8 3 h-lim-p 0.0027 0.0396 6.6052 1658.967990 6 0.0010 81 | 0/8 4 h-lim-p 0.0046 0.1494 1.4026 1658.967221 4 0.0008 103 | 0/8 5 h-lim-p 0.0038 1.1367 0.3008 1658.967131 2 0.0018 119 | 0/8 6 h-lim-p 0.0034 1.5963 0.1570 1658.967103 0 0.0017 139 | 0/8 7 h-lim-p 0.0471 20.0000 0.0057 1658.962493 0 0.3769 162 | 0/8 8 h-lim-p 0.0039 0.2909 0.5467 1658.962238 3 0.0016 188 | 0/8 9 h-lim-p 1.8313 20.0000 0.0005 1658.962077 4 1.0384 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1658.962077 0 1.0938 238 | 0/8 11 h-lim-p 1.8826 20.0000 0.0000 1658.962077 0 0.8237 258 | 0/8 12 h-lim-p 0.5801 20.0000 0.0000 1658.962077 0 0.0023 285 | 0/8 13 h-lim-p 0.0008 20.0000 0.0000 1658.962077 0 0.0000 319 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 1658.962077 0 0.0000 340 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1658.962077 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1658.962077 Node 7: lnL = -1658.962077 Node 8: lnL = -1658.962077 Node 9: lnL = -1658.962077 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 322 Sequential format.. Reading seq # 1: YBR233W-A_Sbay Reading seq # 2: YBR233W-A_Scer Reading seq # 3: YBR233W-A_Skud Reading seq # 4: YBR233W-A_Smik Reading seq # 5: YBR233W-A_Spar Sequences read.. Counting patterns.. # site patterns = 162 Counting frequencies.. 120 bytes for distance 25920 bytes for lkl0 20736 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.095530 0.000060 0.068459 0.123099 0.135999 0.239123 0.309143 0.344371 lnL0 = -1460.820557 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1460.820557 x= 0.09553 0.00006 0.06846 0.12310 0.13600 0.23912 0.30914 0.34437 1 h-lim-p 0.0003 0.0023 69.4443 1459.070441 0 0.0006 23 | 0/8 2 h-lim-p 0.0015 0.0116 17.1826 1458.962448 5 0.0008 46 | 0/8 3 h-lim-p 0.0024 0.0752 5.5385 1458.945048 5 0.0013 69 | 0/8 4 h-lim-p 0.0011 0.0436 6.6299 1458.933859 2 0.0010 85 | 0/8 5 h-lim-p 0.0060 0.0480 0.7582 1458.933584 4 0.0009 108 | 0/8 6 h-lim-p 0.0028 2.3934 0.2426 1458.933306 0 0.0041 128 | 0/8 7 h-lim-p 0.0171 4.9702 0.0588 1458.925148 0 0.0683 150 | 0/8 8 h-lim-p 0.0037 0.1746 1.0941 1458.906479 0 0.0073 171 | 0/8 9 h-lim-p 2.5000 20.0000 0.0022 1458.904043 3 1.0004 189 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1458.904041 0 1.0938 209 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1458.904041 0 1.0938 229 | 0/8 12 h-lim-p 1.7288 20.0000 0.0000 1458.904041 0 1.5127 249 | 0/8 13 h-lim-p 1.8937 20.0000 0.0000 1458.904041 0 0.2367 271 | 0/8 14 h-lim-p 0.0580 20.0000 0.0000 1458.904041 0 0.0290 291 | 0/8 15 h-lim-p 0.0113 20.0000 0.0000 1458.904041 0 0.0113 311 | 0/8 16 h-lim-p 0.0065 20.0000 0.0001 1458.904041 0 0.0065 331 | 0/8 17 h-lim-p 0.0036 20.0000 0.0001 1458.904041 0 0.0000 375 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 | 0/8 19 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1458.904041 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1458.904041 Node 7: lnL = -1458.904041 Node 8: lnL = -1458.904041 Node 9: lnL = -1458.904041 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 358 Sequential format.. Reading seq # 1: YBR233W_Sbay Reading seq # 2: YBR233W_Scer Reading seq # 3: YBR233W_Skud Reading seq # 4: YBR233W_Smik Reading seq # 5: YBR233W_Spar Sequences read.. Counting patterns.. # site patterns = 158 Counting frequencies.. 120 bytes for distance 25280 bytes for lkl0 20224 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.056209 0.084026 0.046767 0.108239 0.092500 0.121446 0.187742 0.252932 lnL0 = -1546.974784 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1546.974784 x= 0.05621 0.08403 0.04677 0.10824 0.09250 0.12145 0.18774 0.25293 1 h-lim-p 0.0004 0.0032 91.6340 1545.258080 7 0.0004 39 | 0/8 2 h-lim-p 0.0005 0.0037 24.6722 1545.112910 6 0.0005 64 | 0/8 3 h-lim-p 0.0016 0.0429 7.7082 1545.099522 6 0.0005 92 | 0/8 4 h-lim-p 0.0010 0.0574 3.9375 1545.094556 3 0.0008 110 | 0/8 5 h-lim-p 0.0022 0.1888 1.4848 1545.093922 5 0.0007 135 | 0/8 6 h-lim-p 0.0054 0.8360 0.1869 1545.093909 2 0.0007 153 | 0/8 7 h-lim-p 0.0103 20.0000 0.0130 1545.093908 0 0.0045 173 | 0/8 8 h-lim-p 0.0329 20.0000 0.0018 1545.093643 0 0.2630 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1545.093634 1 0.9961 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1545.093634 0 1.0938 238 | 0/8 11 h-lim-p 1.4301 20.0000 0.0000 1545.093634 0 2.8602 259 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1545.093634 0 0.0781 283 | 0/8 13 h-lim-p 0.0078 20.0000 0.0000 1545.093634 0 0.0005 306 | 0/8 14 h-lim-p 0.0003 20.0000 0.0000 1545.093634 0 0.0000 328 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0012 | 0/8 17 h-lim-p 0.0000 20.0000 0.0012 Out... lnL = -1545.093634 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1545.093634 Node 7: lnL = -1545.093634 Node 8: lnL = -1545.093634 Node 9: lnL = -1545.093634 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 316 Sequential format.. Reading seq # 1: YBR234C_Sbay Reading seq # 2: YBR234C_Scer Reading seq # 3: YBR234C_Skud Reading seq # 4: YBR234C_Smik Reading seq # 5: YBR234C_Spar Sequences read.. Counting patterns.. # site patterns = 118 Counting frequencies.. 120 bytes for distance 18880 bytes for lkl0 15104 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.033795 0.084181 0.060273 0.046047 0.122888 0.106048 0.090657 0.189992 lnL0 = -1159.331906 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1159.331906 x= 0.03379 0.08418 0.06027 0.04605 0.12289 0.10605 0.09066 0.18999 1 h-lim-p 0.0002 0.0015 119.8917 1155.978579 0 0.0006 23 | 0/8 2 h-lim-p 0.0001 0.0010 64.1326 1155.441171 0 0.0003 36 | 0/8 3 h-lim-p 0.0004 0.0030 31.7205 1155.178107 0 0.0007 49 | 0/8 4 h-lim-p 0.0068 0.0570 3.4331 1155.174798 3 0.0006 71 | 0/8 5 h-lim-p 0.0021 0.1051 0.9035 1155.174444 5 0.0006 97 | 0/8 6 h-lim-p 0.0056 1.6563 0.1053 1155.168357 0 0.0222 119 | 0/8 7 h-lim-p 0.0033 0.1645 0.7176 1155.010532 0 0.0131 141 | 0/8 8 h-lim-p 0.0010 0.0078 4.7174 1155.004663 4 0.0005 170 | 0/8 9 h-lim-p 0.8209 20.0000 0.0029 1154.996918 1 1.0261 184 | 0/8 10 h-lim-p 2.5000 20.0000 0.0003 1154.996809 3 0.9482 210 | 0/8 11 h-lim-p 2.5000 20.0000 0.0001 1154.996808 1 0.6152 233 | 0/8 12 h-lim-p 1.1779 20.0000 0.0000 1154.996808 0 1.0307 253 | 0/8 13 h-lim-p 1.2861 20.0000 0.0000 1154.996808 0 0.5627 273 | 0/8 14 h-lim-p 0.0437 20.0000 0.0003 1154.996808 0 0.0055 295 | 0/8 15 h-lim-p 0.0018 20.0000 0.0009 1154.996808 0 0.0018 315 | 0/8 16 h-lim-p 0.0008 16.7069 0.0018 1154.996808 0 0.0000 344 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 1154.996808 0 0.0000 372 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 | 0/8 19 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1154.996808 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1154.996808 Node 7: lnL = -1154.996808 Node 8: lnL = -1154.996808 Node 9: lnL = -1154.996808 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 312 Sequential format.. Reading seq # 1: YBR235W_Sbay Reading seq # 2: YBR235W_Scer Reading seq # 3: YBR235W_Skud Reading seq # 4: YBR235W_Smik Reading seq # 5: YBR235W_Spar Sequences read.. Counting patterns.. # site patterns = 96 Counting frequencies.. 120 bytes for distance 15360 bytes for lkl0 12288 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.057581 0.049708 0.035707 0.074960 0.056425 0.117997 0.124241 0.205846 lnL0 = -1239.910128 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1239.910128 x= 0.05758 0.04971 0.03571 0.07496 0.05643 0.11800 0.12424 0.20585 1 h-lim-p 0.0005 0.0039 36.1504 1239.702940 8 0.0003 42 | 0/8 2 h-lim-p 0.0006 0.0048 10.7362 1239.689523 3 0.0003 60 | 0/8 3 h-lim-p 0.0014 0.1216 1.9042 1239.688874 4 0.0004 81 | 0/8 4 h-lim-p 0.0005 0.0824 1.3292 1239.688632 4 0.0004 102 | 0/8 5 h-lim-p 0.0019 0.3770 0.2657 1239.688620 2 0.0004 119 | 0/8 6 h-lim-p 0.0015 2.5194 0.0630 1239.688619 0 0.0007 139 | 0/8 7 h-lim-p 0.0202 20.0000 0.0021 1239.688619 0 0.0044 160 | 0/8 8 h-lim-p 0.0222 20.0000 0.0004 1239.688609 0 0.1774 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1239.688609 0 1.0938 203 | 0/8 10 h-lim-p 0.9391 20.0000 0.0000 1239.688609 0 0.9391 223 | 0/8 11 h-lim-p 0.7213 20.0000 0.0000 1239.688609 0 0.0225 247 | 0/8 12 h-lim-p 0.0025 20.0000 0.0001 1239.688609 0 0.0000 281 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1239.688609 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1239.688609 Node 7: lnL = -1239.688609 Node 8: lnL = -1239.688609 Node 9: lnL = -1239.688609 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 297 Sequential format.. Reading seq # 1: YBR237W_Sbay Reading seq # 2: YBR237W_Scer Reading seq # 3: YBR237W_Skud Reading seq # 4: YBR237W_Smik Reading seq # 5: YBR237W_Spar Sequences read.. Counting patterns.. # site patterns = 163 Counting frequencies.. 120 bytes for distance 26080 bytes for lkl0 20864 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.000060 0.131578 0.164060 0.183856 0.266827 1.068363 0.416202 lnL0 = -1549.275592 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1549.275592 x= 0.00006 0.00006 0.13158 0.16406 0.18386 0.26683 1.06836 0.41620 1 h-lim-p 0.0000 0.0000 82.0869 1549.247129 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0000 4621.9560 1549.203966 m 0.0000 34 | 2/8 3 h-lim-p 0.0000 0.0144 41.4433 1547.869663 0 0.0017 53 | 2/8 4 h-lim-p 0.0038 0.0306 15.9927 1547.577296 5 0.0025 77 | 2/8 5 h-lim-p 0.0031 0.0763 12.8433 1547.432846 4 0.0024 97 | 2/8 6 h-lim-p 0.0028 0.1863 11.2177 1546.862739 0 0.0167 111 | 2/8 7 h-lim-p 0.0121 0.0971 3.2066 1546.758281 7 0.0077 141 | 2/8 8 h-lim-p 0.0332 0.2913 0.7416 1542.496875 0 0.1327 155 | 2/8 9 h-lim-p 1.5470 13.7801 0.0636 1542.215529 8 0.9298 194 | 1/8 10 h-lim-p 0.0394 1.2261 1.5025 1542.213720 3 0.0021 221 | 1/8 11 h-lim-p 0.2468 20.0000 0.0125 1542.198791 0 0.9872 235 | 1/8 12 h-lim-p 2.5000 20.0000 0.0030 1542.198145 5 0.9027 266 | 1/8 13 h-lim-p 2.5000 20.0000 0.0009 1542.198108 3 0.7330 294 | 1/8 14 h-lim-p 2.5000 20.0000 0.0001 1542.198108 0 1.0938 313 | 0/8 15 h-lim-p 0.0169 20.0000 0.0033 1542.198108 0 0.0037 333 | 0/8 16 h-lim-p 0.1340 1.0720 0.0000 1542.198108 m 1.0720 353 | 1/8 17 h-lim-p 0.0932 20.0000 0.0002 1542.198107 0 0.1398 373 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 1542.198107 0 1.0938 392 | 1/8 19 h-lim-p 2.5000 20.0000 0.0000 1542.198107 0 1.2500 411 | 1/8 20 h-lim-p 2.5000 20.0000 0.0000 1542.198107 0 3.7500 430 | 1/8 21 h-lim-p 2.5000 20.0000 0.0000 1542.198107 0 5.0000 450 | 1/8 22 h-lim-p 1.2499 20.0000 0.0000 1542.198107 0 0.2734 470 | 1/8 23 h-lim-p 0.3764 20.0000 0.0000 1542.198107 0 0.0235 492 Out... lnL = -1542.198107 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1542.198107 Node 7: lnL = -1542.198107 Node 8: lnL = -1542.198107 Node 9: lnL = -1542.198107 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 831 Sequential format.. Reading seq # 1: YBR240C_Sbay Reading seq # 2: YBR240C_Scer Reading seq # 3: YBR240C_Skud Reading seq # 4: YBR240C_Smik Reading seq # 5: YBR240C_Spar Sequences read.. Counting patterns.. # site patterns = 286 Counting frequencies.. 120 bytes for distance 45760 bytes for lkl0 36608 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.050409 0.000060 0.096636 0.117119 0.098418 0.217581 0.203528 0.249956 lnL0 = -3558.865649 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3558.865649 x= 0.05041 0.00006 0.09664 0.11712 0.09842 0.21758 0.20353 0.24996 1 h-lim-p 0.0001 0.0007 215.9389 3553.867438 0 0.0002 23 | 0/8 2 h-lim-p 0.0001 0.0006 74.8817 3553.293075 0 0.0002 36 | 0/8 3 h-lim-p 0.0004 0.0069 38.0548 3553.135896 7 0.0003 66 | 0/8 4 h-lim-p 0.0008 0.0158 13.5749 3553.108722 3 0.0004 84 | 0/8 5 h-lim-p 0.0028 0.0793 1.6844 3553.108236 2 0.0003 102 | 0/8 6 h-lim-p 0.0018 0.7045 0.3118 3553.108135 3 0.0011 122 | 0/8 7 h-lim-p 0.0070 1.9615 0.0476 3553.104283 0 0.0417 144 | 0/8 8 h-lim-p 0.0020 0.1915 0.9717 3553.063276 0 0.0041 165 | 0/8 9 h-lim-p 2.5000 20.0000 0.0009 3553.062247 3 1.0004 191 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3553.062246 0 1.0938 211 | 0/8 11 h-lim-p 1.8196 20.0000 0.0000 3553.062246 0 1.5922 231 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3553.062246 0 1.0938 251 | 0/8 13 h-lim-p 0.5561 20.0000 0.0000 3553.062246 0 8.8970 275 | 0/8 14 h-lim-p 0.1061 20.0000 0.0021 3553.062246 0 0.0464 295 | 0/8 15 h-lim-p 0.0109 9.1373 0.0088 3553.062246 0 0.0012 317 | 0/8 16 h-lim-p 0.0008 6.3754 0.0126 3553.062246 0 0.0000 357 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 3553.062246 0 0.0000 386 Out... lnL = -3553.062246 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3553.062246 Node 7: lnL = -3553.062246 Node 8: lnL = -3553.062246 Node 9: lnL = -3553.062246 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 661 Sequential format.. Reading seq # 1: YBR242W_Sbay Reading seq # 2: YBR242W_Scer Reading seq # 3: YBR242W_Skud Reading seq # 4: YBR242W_Smik Reading seq # 5: YBR242W_Spar Sequences read.. Counting patterns.. # site patterns = 242 Counting frequencies.. 120 bytes for distance 38720 bytes for lkl0 30976 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.042889 0.053145 0.101312 0.132589 0.082621 0.177645 0.239825 0.271244 lnL0 = -3038.592041 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3038.592041 x= 0.04289 0.05315 0.10131 0.13259 0.08262 0.17765 0.23982 0.27124 1 h-lim-p 0.0044 1.2390 117.5200 3036.921455 2 0.0003 29 | 0/8 2 h-lim-p 0.0009 0.0072 16.8900 3036.877968 6 0.0003 58 | 0/8 3 h-lim-p 0.0007 0.0263 7.8751 3036.867405 6 0.0004 86 | 0/8 4 h-lim-p 0.0042 0.2407 0.7557 3036.867275 2 0.0005 104 | 0/8 5 h-lim-p 0.0017 1.4251 0.2062 3036.867261 1 0.0007 126 | 0/8 6 h-lim-p 0.0040 5.1123 0.0384 3036.867261 0 0.0009 147 | 0/8 7 h-lim-p 0.0094 20.0000 0.0035 3036.867259 0 0.0141 167 | 0/8 8 h-lim-p 0.0065 20.0000 0.0077 3036.867116 0 0.0518 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3036.867106 1 0.9961 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3036.867106 0 2.1875 232 | 0/8 11 h-lim-p 2.4230 20.0000 0.0000 3036.867106 0 1.2115 252 | 0/8 12 h-lim-p 0.1722 20.0000 0.0001 3036.867106 0 0.0323 274 | 0/8 13 h-lim-p 0.0065 20.0000 0.0006 3036.867106 0 0.0016 295 | 0/8 14 h-lim-p 0.0007 20.0000 0.0015 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 3036.867106 0 0.0000 362 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0005 3036.867106 0 0.0000 428 | 0/8 18 h-lim-p 0.0000 20.0000 0.0005 | 0/8 19 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -3036.867106 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3036.867106 Node 7: lnL = -3036.867106 Node 8: lnL = -3036.867106 Node 9: lnL = -3036.867106 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 815 Sequential format.. Reading seq # 1: YBR244W_Sbay Reading seq # 2: YBR244W_Scer Reading seq # 3: YBR244W_Skud Reading seq # 4: YBR244W_Smik Reading seq # 5: YBR244W_Spar Sequences read.. Counting patterns.. # site patterns = 327 Counting frequencies.. 120 bytes for distance 52320 bytes for lkl0 41856 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.047887 0.100039 0.061647 0.134438 0.135691 0.258534 0.260091 0.318761 lnL0 = -3817.267033 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3817.267033 x= 0.04789 0.10004 0.06165 0.13444 0.13569 0.25853 0.26009 0.31876 1 h-lim-p 0.0041 0.0330 89.3066 3816.359124 2 0.0002 29 | 0/8 2 h-lim-p 0.0011 0.0086 20.4755 3816.259622 2 0.0005 45 | 0/8 3 h-lim-p 0.0009 0.0141 11.0935 3816.240807 5 0.0004 68 | 0/8 4 h-lim-p 0.0013 0.0910 3.2913 3816.238233 3 0.0005 86 | 0/8 5 h-lim-p 0.0017 0.3726 1.0579 3816.237958 3 0.0006 106 | 0/8 6 h-lim-p 0.0049 1.8923 0.1208 3816.237954 0 0.0005 120 | 0/8 7 h-lim-p 0.0045 17.8177 0.0141 3816.237954 0 0.0010 141 | 0/8 8 h-lim-p 0.1284 20.0000 0.0001 3816.237938 0 1.0275 164 | 0/8 9 h-lim-p 1.0529 20.0000 0.0001 3816.237938 0 0.9213 184 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3816.237938 0 1.0938 204 | 0/8 11 h-lim-p 1.3423 20.0000 0.0000 3816.237938 0 5.3692 226 | 0/8 12 h-lim-p 0.0464 20.0000 0.0024 3816.237938 0 0.0025 249 | 0/8 13 h-lim-p 0.0000 0.0197 3.1460 3816.237938 0 0.0000 270 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 3816.237938 0 1.2500 282 | 0/8 15 h-lim-p 1.5921 20.0000 0.0000 3816.237938 0 0.0871 305 | 0/8 16 h-lim-p 0.0835 20.0000 0.0000 3816.237938 0 0.0003 332 Out... lnL = -3816.237938 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3816.237938 Node 7: lnL = -3816.237938 Node 8: lnL = -3816.237938 Node 9: lnL = -3816.237938 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 490 Sequential format.. Reading seq # 1: YBR248C_Sbay Reading seq # 2: YBR248C_Scer Reading seq # 3: YBR248C_Skud Reading seq # 4: YBR248C_Smik Reading seq # 5: YBR248C_Spar Sequences read.. Counting patterns.. # site patterns = 190 Counting frequencies.. 120 bytes for distance 30400 bytes for lkl0 24320 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.010055 0.107665 0.040421 0.126917 0.064726 0.146290 0.165853 0.189353 lnL0 = -1959.342821 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1959.342821 x= 0.01006 0.10766 0.04042 0.12692 0.06473 0.14629 0.16585 0.18935 1 h-lim-p 0.0002 0.0015 101.9573 1958.085444 0 0.0003 22 | 0/8 2 h-lim-p 0.0008 0.0066 19.4108 1958.017979 6 0.0004 45 | 0/8 3 h-lim-p 0.0007 0.0255 9.5950 1958.008664 6 0.0002 70 | 0/8 4 h-lim-p 0.0011 0.0402 2.1440 1958.007397 3 0.0006 89 | 0/8 5 h-lim-p 0.0035 1.0526 0.3586 1958.007359 3 0.0006 110 | 0/8 6 h-lim-p 0.0023 0.5679 0.0881 1958.007342 2 0.0015 135 | 0/8 7 h-lim-p 0.0129 6.3847 0.0101 1958.003181 0 0.2071 159 | 0/8 8 h-lim-p 0.0013 0.0770 1.6460 1957.999626 2 0.0011 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 1957.999558 2 0.9961 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1957.999558 0 1.0938 219 | 0/8 11 h-lim-p 1.1571 20.0000 0.0000 1957.999558 0 2.3142 240 | 0/8 12 h-lim-p 1.1284 20.0000 0.0001 1957.999558 0 0.9873 260 | 0/8 13 h-lim-p 0.0097 3.0278 0.0055 1957.999558 0 0.0048 280 | 0/8 14 h-lim-p 0.0014 0.8434 0.0198 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0014 | 0/8 16 h-lim-p 0.0000 20.0000 0.0014 Out... lnL = -1957.999558 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1957.999558 Node 7: lnL = -1957.999558 Node 8: lnL = -1957.999558 Node 9: lnL = -1957.999558 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 846 Sequential format.. Reading seq # 1: YBR249C_Sbay Reading seq # 2: YBR249C_Scer Reading seq # 3: YBR249C_Skud Reading seq # 4: YBR249C_Smik Reading seq # 5: YBR249C_Spar Sequences read.. Counting patterns.. # site patterns = 302 Counting frequencies.. 120 bytes for distance 48320 bytes for lkl0 38656 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.051673 0.062708 0.037592 0.109429 0.083421 0.165862 0.261180 0.252728 lnL0 = -3516.392965 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3516.392965 x= 0.05167 0.06271 0.03759 0.10943 0.08342 0.16586 0.26118 0.25273 1 h-lim-p 0.0023 0.0248 174.3893 3514.670640 6 0.0001 36 | 0/8 2 h-lim-p 0.0005 0.0072 39.7284 3514.431692 7 0.0003 64 | 0/8 3 h-lim-p 0.0006 0.0156 19.7942 3514.381922 5 0.0003 87 | 0/8 4 h-lim-p 0.0004 0.0158 16.6644 3514.351798 2 0.0003 103 | 0/8 5 h-lim-p 0.0015 0.0510 3.8578 3514.348186 4 0.0005 125 | 0/8 6 h-lim-p 0.0019 0.1595 1.1045 3514.347975 2 0.0004 142 | 0/8 7 h-lim-p 0.0016 0.8170 0.2705 3514.347966 2 0.0003 161 | 0/8 8 h-lim-p 0.4687 20.0000 0.0001 3514.347905 0 0.9375 182 | 0/8 9 h-lim-p 1.1799 20.0000 0.0001 3514.347903 0 1.0324 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3514.347903 0 1.0938 222 | 0/8 11 h-lim-p 1.1553 20.0000 0.0000 3514.347903 0 0.0023 250 | 0/8 12 h-lim-p 0.0000 11.9559 0.0074 3514.347903 0 0.0000 278 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 3514.347903 0 0.0000 312 Out... lnL = -3514.347903 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3514.347903 Node 7: lnL = -3514.347903 Node 8: lnL = -3514.347903 Node 9: lnL = -3514.347903 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 840 Sequential format.. Reading seq # 1: YBR250W_Sbay Reading seq # 2: YBR250W_Scer Reading seq # 3: YBR250W_Skud Reading seq # 4: YBR250W_Smik Reading seq # 5: YBR250W_Spar Sequences read.. Counting patterns.. # site patterns = 305 Counting frequencies.. 120 bytes for distance 48800 bytes for lkl0 39040 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.047390 0.045236 0.050781 0.129090 0.082435 0.193344 0.229258 0.248273 lnL0 = -3671.250958 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3671.250958 x= 0.04739 0.04524 0.05078 0.12909 0.08243 0.19334 0.22926 0.24827 1 h-lim-p 0.0002 0.0014 186.8114 3668.730972 5 0.0002 31 | 0/8 2 h-lim-p 0.0003 0.0025 44.0683 3668.534013 7 0.0002 61 | 0/8 3 h-lim-p 0.0005 0.0305 17.0703 3668.507630 4 0.0002 81 | 0/8 4 h-lim-p 0.0007 0.0460 5.3893 3668.502100 4 0.0004 103 | 0/8 5 h-lim-p 0.0017 0.1644 1.3120 3668.501789 2 0.0004 120 | 0/8 6 h-lim-p 0.0013 0.2872 0.3805 3668.501768 0 0.0003 133 | 0/8 7 h-lim-p 0.0586 20.0000 0.0021 3668.501742 1 0.0733 155 | 0/8 8 h-lim-p 0.0029 1.6316 0.0536 3668.501335 0 0.0087 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3668.501322 1 0.9961 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3668.501322 0 1.2500 218 | 0/8 11 h-lim-p 1.0873 20.0000 0.0000 3668.501322 0 0.0000 268 | 0/8 12 h-lim-p 0.0000 20.0000 0.0012 | 0/8 13 h-lim-p 0.0000 20.0000 0.0012 Out... lnL = -3668.501322 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3668.501322 Node 7: lnL = -3668.501322 Node 8: lnL = -3668.501322 Node 9: lnL = -3668.501322 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 838 Sequential format.. Reading seq # 1: YBR251W_Sbay Reading seq # 2: YBR251W_Scer Reading seq # 3: YBR251W_Skud Reading seq # 4: YBR251W_Smik Reading seq # 5: YBR251W_Spar Sequences read.. Counting patterns.. # site patterns = 365 Counting frequencies.. 120 bytes for distance 58400 bytes for lkl0 46720 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.121673 0.235173 0.103787 0.155965 0.116006 0.268955 0.375583 0.505588 lnL0 = -4365.300270 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4365.300270 x= 0.12167 0.23517 0.10379 0.15597 0.11601 0.26896 0.37558 0.50559 1 h-lim-p 0.0065 0.0522 38.8877 4364.811363 3 0.0007 30 | 0/8 2 h-lim-p 0.0012 0.0170 22.6910 4364.673789 7 0.0007 60 | 0/8 3 h-lim-p 0.0012 0.0520 13.1137 4364.650516 5 0.0004 84 | 0/8 4 h-lim-p 0.0006 0.0467 8.4892 4364.617608 0 0.0012 97 | 0/8 5 h-lim-p 0.0029 0.0941 3.4202 4364.614809 2 0.0006 114 | 0/8 6 h-lim-p 0.0014 0.1825 1.5689 4364.613632 2 0.0012 130 | 0/8 7 h-lim-p 0.0080 0.9321 0.2344 4364.613585 1 0.0018 145 | 0/8 8 h-lim-p 0.1574 20.0000 0.0026 4364.612257 0 0.9446 167 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4364.612256 0 1.0938 187 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4364.612256 0 1.0938 207 | 0/8 11 h-lim-p 1.1545 20.0000 0.0000 4364.612256 0 1.1545 227 | 0/8 12 h-lim-p 0.1932 20.0000 0.0000 4364.612256 0 0.1932 247 | 0/8 13 h-lim-p 0.0486 20.0000 0.0002 4364.612256 0 0.0015 271 | 0/8 14 h-lim-p 0.0015 20.0000 0.0002 4364.612256 0 0.0000 297 | 0/8 15 h-lim-p 0.0008 20.0000 0.0000 4364.612256 0 0.0001 319 Out... lnL = -4364.612256 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4364.612256 Node 7: lnL = -4364.612256 Node 8: lnL = -4364.612256 Node 9: lnL = -4364.612256 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 323 Sequential format.. Reading seq # 1: YBR252W_Sbay Reading seq # 2: YBR252W_Scer Reading seq # 3: YBR252W_Skud Reading seq # 4: YBR252W_Smik Reading seq # 5: YBR252W_Spar Sequences read.. Counting patterns.. # site patterns = 149 Counting frequencies.. 120 bytes for distance 23840 bytes for lkl0 19072 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.013469 0.071328 0.039195 0.127730 0.076220 0.213996 0.254144 0.212484 lnL0 = -1393.520518 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1393.520518 x= 0.01347 0.07133 0.03920 0.12773 0.07622 0.21400 0.25414 0.21248 1 h-lim-p 0.0066 2.2404 64.8263 1392.798720 5 0.0004 34 | 0/8 2 h-lim-p 0.0014 0.0112 12.9175 1392.741722 4 0.0007 55 | 0/8 3 h-lim-p 0.0025 0.0801 3.7172 1392.734415 2 0.0012 71 | 0/8 4 h-lim-p 0.0024 0.0837 1.8240 1392.733508 5 0.0007 96 | 0/8 5 h-lim-p 0.0027 0.2346 0.4441 1392.733411 2 0.0011 112 | 0/8 6 h-lim-p 0.0042 2.3241 0.1129 1392.733406 0 0.0009 133 | 0/8 7 h-lim-p 0.0048 9.0285 0.0213 1392.733405 0 0.0011 154 | 0/8 8 h-lim-p 0.2718 20.0000 0.0001 1392.733399 0 1.0872 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1392.733399 0 1.0938 196 | 0/8 10 h-lim-p 1.3171 20.0000 0.0000 1392.733399 0 2.6341 217 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1392.733399 0 1.0938 237 | 0/8 12 h-lim-p 0.1618 20.0000 0.0001 1392.733399 0 0.0013 263 | 0/8 13 h-lim-p 0.0002 20.0000 0.0004 1392.733399 0 0.0000 287 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 1392.733399 0 0.0000 316 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 1392.733399 0 0.0000 343 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 1392.733399 0 0.0000 363 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0004 | 0/8 19 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1392.733399 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1392.733399 Node 7: lnL = -1392.733399 Node 8: lnL = -1392.733399 Node 9: lnL = -1392.733399 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 244 Sequential format.. Reading seq # 1: YBR253W_Sbay Reading seq # 2: YBR253W_Scer Reading seq # 3: YBR253W_Skud Reading seq # 4: YBR253W_Smik Reading seq # 5: YBR253W_Spar Sequences read.. Counting patterns.. # site patterns = 120 Counting frequencies.. 120 bytes for distance 19200 bytes for lkl0 15360 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.028119 0.100189 0.044004 0.170737 0.100332 0.276030 0.197855 0.262266 lnL0 = -1101.848601 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1101.848601 x= 0.02812 0.10019 0.04400 0.17074 0.10033 0.27603 0.19785 0.26227 1 h-lim-p 0.0012 0.0097 18.9476 1101.724089 8 0.0007 43 | 0/8 2 h-lim-p 0.0013 0.0107 7.3661 1101.695432 5 0.0012 64 | 0/8 3 h-lim-p 0.0029 0.1366 3.0280 1101.691552 6 0.0010 92 | 0/8 4 h-lim-p 0.0035 0.5098 0.8680 1101.691103 4 0.0013 112 | 0/8 5 h-lim-p 0.0086 1.0111 0.1329 1101.691091 2 0.0014 139 | 0/8 6 h-lim-p 0.0062 10.3611 0.0307 1101.691090 1 0.0015 162 | 0/8 7 h-lim-p 0.0125 20.0000 0.0037 1101.691090 0 0.0027 183 | 0/8 8 h-lim-p 0.0557 20.0000 0.0002 1101.691084 0 0.6682 206 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1101.691083 0 1.0938 226 | 0/8 10 h-lim-p 2.1215 20.0000 0.0000 1101.691083 0 1.8563 246 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1101.691083 0 1.0938 266 | 0/8 12 h-lim-p 0.3144 20.0000 0.0000 1101.691083 010.0605 291 | 0/8 13 h-lim-p 0.0623 18.7317 0.0018 1101.691083 0 0.0273 311 | 0/8 14 h-lim-p 0.0080 5.4683 0.0061 1101.691083 0 0.0020 332 | 0/8 15 h-lim-p 0.0007 1.9013 0.0174 1101.691083 0 0.0003 352 | 0/8 16 h-lim-p 0.0002 0.8732 0.0379 1101.691083 0 0.0000 374 | 0/8 17 h-lim-p 0.0002 8.3297 0.0040 1101.691083 0 0.0000 411 | 0/8 18 h-lim-p 0.0000 20.0000 0.0005 | 0/8 19 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -1101.691083 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1101.691083 Node 7: lnL = -1101.691083 Node 8: lnL = -1101.691083 Node 9: lnL = -1101.691083 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 196 Sequential format.. Reading seq # 1: YBR254C_Sbay Reading seq # 2: YBR254C_Scer Reading seq # 3: YBR254C_Skud Reading seq # 4: YBR254C_Smik Reading seq # 5: YBR254C_Spar Sequences read.. Counting patterns.. # site patterns = 90 Counting frequencies.. 120 bytes for distance 14400 bytes for lkl0 11520 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.058296 0.100519 0.066319 0.099217 0.057419 0.195242 0.115661 0.250308 lnL0 = -855.760797 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 855.760797 x= 0.05830 0.10052 0.06632 0.09922 0.05742 0.19524 0.11566 0.25031 1 h-lim-p 0.0016 0.0130 19.8462 855.577877 7 0.0010 38 | 0/8 2 h-lim-p 0.0018 0.0140 10.1235 855.545557 5 0.0008 59 | 0/8 3 h-lim-p 0.0019 0.0379 4.0617 855.541457 6 0.0006 87 | 0/8 4 h-lim-p 0.0065 0.4364 0.3748 855.541395 4 0.0009 110 | 0/8 5 h-lim-p 0.0050 2.3571 0.0687 855.541392 0 0.0011 131 | 0/8 6 h-lim-p 0.0045 18.3012 0.0165 855.541392 0 0.0011 152 | 0/8 7 h-lim-p 0.0103 20.0000 0.0018 855.541392 0 0.0045 172 | 0/8 8 h-lim-p 0.0320 20.0000 0.0003 855.541389 0 0.3844 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 855.541389 0 1.0938 215 | 0/8 10 h-lim-p 1.7771 20.0000 0.0000 855.541389 0 1.5550 235 | 0/8 11 h-lim-p 1.9223 20.0000 0.0000 855.541389 0 1.6820 255 | 0/8 12 h-lim-p 0.5943 20.0000 0.0000 855.541389 0 0.0371 278 | 0/8 13 h-lim-p 0.0000 5.2155 0.0138 855.541389 0 0.0000 310 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 855.541389 0 0.0000 342 Out... lnL = -855.541389 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -855.541389 Node 7: lnL = -855.541389 Node 8: lnL = -855.541389 Node 9: lnL = -855.541389 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 197 Sequential format.. Reading seq # 1: YBR255W_Sbay Reading seq # 2: YBR255W_Scer Reading seq # 3: YBR255W_Skud Reading seq # 4: YBR255W_Smik Reading seq # 5: YBR255W_Spar Sequences read.. Counting patterns.. # site patterns = 91 Counting frequencies.. 120 bytes for distance 14560 bytes for lkl0 11648 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.027241 0.119967 0.048062 0.101054 0.055583 0.217809 0.107162 0.208609 lnL0 = -839.485941 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 839.485941 x= 0.02724 0.11997 0.04806 0.10105 0.05558 0.21781 0.10716 0.20861 1 h-lim-p 0.0004 0.0029 31.3605 839.131646 0 0.0007 23 | 0/8 2 h-lim-p 0.0005 0.0040 12.5887 839.082374 0 0.0008 35 | 0/8 3 h-lim-p 0.0020 0.0173 4.6763 839.077045 6 0.0006 63 | 0/8 4 h-lim-p 0.0027 0.1873 0.9820 839.076495 3 0.0012 81 | 0/8 5 h-lim-p 0.0055 1.4796 0.2174 839.076470 2 0.0011 106 | 0/8 6 h-lim-p 0.0035 1.5589 0.0661 839.076466 0 0.0017 126 | 0/8 7 h-lim-p 0.0091 18.7240 0.0127 839.076455 1 0.0114 148 | 0/8 8 h-lim-p 0.0101 20.0000 0.0144 839.075784 0 0.0603 170 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 839.075781 1 0.9961 192 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 839.075781 0 1.0938 212 | 0/8 11 h-lim-p 1.1930 20.0000 0.0000 839.075781 0 0.0746 235 | 0/8 12 h-lim-p 0.0050 20.0000 0.0002 839.075781 0 0.0050 255 | 0/8 13 h-lim-p 0.0017 20.0000 0.0005 839.075781 0 0.0000 282 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 839.075781 0 0.0000 305 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 839.075781 0 0.0000 336 Out... lnL = -839.075781 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -839.075781 Node 7: lnL = -839.075781 Node 8: lnL = -839.075781 Node 9: lnL = -839.075781 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 853 Sequential format.. Reading seq # 1: YBR256C_Sbay Reading seq # 2: YBR256C_Scer Reading seq # 3: YBR256C_Skud Reading seq # 4: YBR256C_Smik Reading seq # 5: YBR256C_Spar Sequences read.. Counting patterns.. # site patterns = 410 Counting frequencies.. 120 bytes for distance 65600 bytes for lkl0 52480 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.001982 0.288123 0.164854 0.151161 0.108177 0.268583 0.306852 0.351357 lnL0 = -4282.928061 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4282.928061 x= 0.00198 0.28812 0.16485 0.15116 0.10818 0.26858 0.30685 0.35136 1 h-lim-p 0.0093 0.0742 47.2736 4282.124011 6 0.0007 38 | 0/8 2 h-lim-p 0.0000 0.0003 32.2909 4281.973645 m 0.0003 50 | 1/8 3 h-lim-p 0.0004 0.0132 22.6510 4281.882598 0 0.0008 63 | 1/8 4 h-lim-p 0.0044 0.1076 3.9376 4281.876687 4 0.0008 86 | 1/8 5 h-lim-p 0.0028 0.2955 1.1447 4281.876131 4 0.0009 110 | 1/8 6 h-lim-p 0.0023 1.1721 0.4320 4281.875790 1 0.0029 124 | 1/8 7 h-lim-p 0.0261 20.0000 0.0475 4281.871095 0 0.0782 144 | 1/8 8 h-lim-p 0.0052 0.6067 0.7094 4281.870164 2 0.0023 167 | 1/8 9 h-lim-p 0.0816 7.7754 0.0199 4281.841560 0 0.1632 187 | 1/8 10 h-lim-p 2.5000 20.0000 0.0007 4281.840850 2 0.9961 210 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 4281.840850 0 1.0938 229 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 4281.840850 0 1.2500 248 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 4281.840850 0 0.5469 268 | 1/8 14 h-lim-p 1.2072 20.0000 0.0000 4281.840850 0 0.0566 291 | 1/8 15 h-lim-p 0.0600 20.0000 0.0000 4281.840850 0 0.0038 313 Out... lnL = -4281.840850 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4281.840850 Node 7: lnL = -4281.840850 Node 8: lnL = -4281.840850 Node 9: lnL = -4281.840850 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 861 Sequential format.. Reading seq # 1: YBR257W_Sbay Reading seq # 2: YBR257W_Scer Reading seq # 3: YBR257W_Skud Reading seq # 4: YBR257W_Smik Reading seq # 5: YBR257W_Spar Sequences read.. Counting patterns.. # site patterns = 397 Counting frequencies.. 120 bytes for distance 63520 bytes for lkl0 50816 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.007330 0.240679 0.147445 0.158445 0.099006 0.262961 0.320982 0.338303 lnL0 = -4245.903431 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4245.903431 x= 0.00733 0.24068 0.14745 0.15845 0.09901 0.26296 0.32098 0.33830 1 h-lim-p 0.0043 0.0348 56.3561 4245.030746 7 0.0006 40 | 0/8 2 h-lim-p 0.0004 0.0035 22.6231 4244.920226 4 0.0005 61 | 0/8 3 h-lim-p 0.0002 0.0019 24.7425 4244.830253 0 0.0005 74 | 0/8 4 h-lim-p 0.0034 0.0827 3.4587 4244.826416 3 0.0007 93 | 0/8 5 h-lim-p 0.0016 0.3015 1.4757 4244.825451 3 0.0010 113 | 0/8 6 h-lim-p 0.0047 0.0841 0.3308 4244.825417 2 0.0006 131 | 0/8 7 h-lim-p 0.0278 20.0000 0.0073 4244.825082 0 0.1112 153 | 0/8 8 h-lim-p 0.0034 0.2222 0.2423 4244.822816 0 0.0101 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 4244.822801 1 1.0938 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4244.822801 0 1.0938 216 | 0/8 11 h-lim-p 1.4031 20.0000 0.0000 4244.822801 0 1.2277 236 | 0/8 12 h-lim-p 0.5457 20.0000 0.0000 4244.822801 0 0.0341 259 | 0/8 13 h-lim-p 0.0029 20.0000 0.0005 4244.822801 0 0.0014 279 | 0/8 14 h-lim-p 0.0000 0.8470 0.0155 4244.822801 0 0.0000 314 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 4244.822801 0 0.0000 343 Out... lnL = -4244.822801 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4244.822801 Node 7: lnL = -4244.822801 Node 8: lnL = -4244.822801 Node 9: lnL = -4244.822801 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 235 Sequential format.. Reading seq # 1: YBR258C_Sbay Reading seq # 2: YBR258C_Scer Reading seq # 3: YBR258C_Skud Reading seq # 4: YBR258C_Smik Reading seq # 5: YBR258C_Spar Sequences read.. Counting patterns.. # site patterns = 134 Counting frequencies.. 120 bytes for distance 21440 bytes for lkl0 17152 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.092358 0.074011 0.080738 0.151915 0.101786 0.267444 0.213033 0.357235 lnL0 = -1161.810684 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1161.810684 x= 0.09236 0.07401 0.08074 0.15191 0.10179 0.26744 0.21303 0.35723 1 h-lim-p 0.0014 0.0112 43.5948 1160.860889 5 0.0011 32 | 0/8 2 h-lim-p 0.0014 0.0112 12.2225 1160.739121 0 0.0021 44 | 0/8 3 h-lim-p 0.0033 0.0348 7.7698 1160.710121 4 0.0013 64 | 0/8 4 h-lim-p 0.0028 0.0481 3.6224 1160.705624 5 0.0009 88 | 0/8 5 h-lim-p 0.0097 0.7036 0.3308 1160.705481 2 0.0024 105 | 0/8 6 h-lim-p 0.0054 1.7893 0.1477 1160.705429 3 0.0032 134 | 0/8 7 h-lim-p 0.0286 20.0000 0.0164 1160.703219 0 0.2284 157 | 0/8 8 h-lim-p 0.0071 1.6561 0.5297 1160.699757 2 0.0066 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 1160.699648 2 1.0889 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1160.699646 0 1.2500 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1160.699646 0 1.0938 245 | 0/8 12 h-lim-p 1.3267 20.0000 0.0000 1160.699646 0 1.9901 265 | 0/8 13 h-lim-p 1.0891 20.0000 0.0000 1160.699646 0 0.1361 287 | 0/8 14 h-lim-p 0.0010 20.0000 0.0008 1160.699646 0 0.0000 317 | 0/8 15 h-lim-p 0.0006 20.0000 0.0000 1160.699646 0 0.0000 343 Out... lnL = -1160.699646 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1160.699646 Node 7: lnL = -1160.699646 Node 8: lnL = -1160.699646 Node 9: lnL = -1160.699646 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 238 Sequential format.. Reading seq # 1: YBR259W_Sbay Reading seq # 2: YBR259W_Scer Reading seq # 3: YBR259W_Skud Reading seq # 4: YBR259W_Smik Reading seq # 5: YBR259W_Spar Sequences read.. Counting patterns.. # site patterns = 132 Counting frequencies.. 120 bytes for distance 21120 bytes for lkl0 16896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.093763 0.035593 0.084684 0.130182 0.123519 0.283669 0.210110 0.350448 lnL0 = -1158.507908 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1158.507908 x= 0.09376 0.03559 0.08468 0.13018 0.12352 0.28367 0.21011 0.35045 1 h-lim-p 0.0012 0.0097 65.2697 1156.887007 6 0.0009 35 | 0/8 2 h-lim-p 0.0009 0.0074 18.4404 1156.615062 0 0.0018 48 | 0/8 3 h-lim-p 0.0026 0.0210 12.1959 1156.547070 2 0.0012 64 | 0/8 4 h-lim-p 0.0025 0.0512 6.0501 1156.529610 4 0.0013 85 | 0/8 5 h-lim-p 0.0170 0.5420 0.4519 1156.529395 2 0.0020 103 | 0/8 6 h-lim-p 0.0048 1.2487 0.1851 1156.529332 3 0.0028 132 | 0/8 7 h-lim-p 0.0344 20.0000 0.0153 1156.527670 0 0.2061 154 | 0/8 8 h-lim-p 0.0094 1.4657 0.3347 1156.523625 4 0.0103 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0009 1156.523344 3 1.3437 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1156.523342 0 1.0938 230 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1156.523342 0 1.0938 250 | 0/8 12 h-lim-p 1.8581 20.0000 0.0000 1156.523342 0 1.6258 270 | 0/8 13 h-lim-p 1.7236 20.0000 0.0000 1156.523342 0 1.7236 290 | 0/8 14 h-lim-p 0.3487 20.0000 0.0000 1156.523342 0 0.1743 310 | 0/8 15 h-lim-p 0.0176 20.0000 0.0001 1156.523342 0 0.0000 356 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 1156.523342 0 0.0000 381 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1156.523342 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1156.523342 Node 7: lnL = -1156.523342 Node 8: lnL = -1156.523342 Node 9: lnL = -1156.523342 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 200 Sequential format.. Reading seq # 1: YBR260C_Sbay Reading seq # 2: YBR260C_Scer Reading seq # 3: YBR260C_Skud Reading seq # 4: YBR260C_Smik Reading seq # 5: YBR260C_Spar Sequences read.. Counting patterns.. # site patterns = 80 Counting frequencies.. 120 bytes for distance 12800 bytes for lkl0 10240 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.004072 0.061604 0.028276 0.066637 0.078040 0.139879 0.086333 0.117159 lnL0 = -722.353273 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 722.353273 x= 0.00407 0.06160 0.02828 0.06664 0.07804 0.13988 0.08633 0.11716 1 h-lim-p 0.0001 0.0004 45.8261 722.030281 m 0.0004 22 | 0/8 2 h-lim-p 0.0000 0.0000 16.2070 h-lim-p: 8.47174654e-22 6.77739724e-21 1.62069559e+01 722.030281 .. | 0/8 3 h-lim-p 0.0000 0.0023 20.2385 721.958818 0 0.0003 47 | 0/8 4 h-lim-p 0.0007 0.0060 3.7635 721.954552 4 0.0006 68 | 0/8 5 h-lim-p 0.0002 0.0012 0.4492 721.954509 0 0.0005 81 | 0/8 6 h-lim-p 0.0001 0.0011 0.1213 721.954508 0 0.0003 102 | 0/8 7 h-lim-p 0.0001 0.0004 0.1911 721.954508 0 0.0000 122 | 0/8 8 h-lim-p 0.0001 0.0028 0.0877 721.954507 0 0.0004 144 | 0/8 9 h-lim-p 0.0006 0.0050 0.0286 721.954507 0 0.0001 165 | 0/8 10 h-lim-p 0.0039 20.0000 0.0010 721.954325 0 0.4937 192 | 0/8 11 h-lim-p 0.0026 0.4554 0.1907 721.954309 2 0.0006 217 | 0/8 12 h-lim-p 0.7588 20.0000 0.0002 721.954294 0 1.1382 237 | 0/8 13 h-lim-p 2.5000 20.0000 0.0001 721.954293 0 1.0938 257 | 0/8 14 h-lim-p 1.4965 20.0000 0.0000 721.954292 0 1.3094 277 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 721.954292 0 1.0938 297 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 721.954292 0 2.1875 317 | 0/8 17 h-lim-p 2.0292 20.0000 0.0000 721.954292 0 0.4439 338 | 0/8 18 h-lim-p 0.9305 20.0000 0.0000 721.954292 0 0.0005 368 Out... lnL = -721.954292 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -721.954292 Node 7: lnL = -721.954292 Node 8: lnL = -721.954292 Node 9: lnL = -721.954292 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 195 Sequential format.. Reading seq # 1: YBR261C_Sbay Reading seq # 2: YBR261C_Scer Reading seq # 3: YBR261C_Skud Reading seq # 4: YBR261C_Smik Reading seq # 5: YBR261C_Spar Sequences read.. Counting patterns.. # site patterns = 85 Counting frequencies.. 120 bytes for distance 13600 bytes for lkl0 10880 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.096442 0.059120 0.128926 0.051014 0.141995 0.125030 0.137300 lnL0 = -769.427176 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 769.427176 x= 0.00006 0.09644 0.05912 0.12893 0.05101 0.14199 0.12503 0.13730 1 h-lim-p 0.0000 0.0000 26.3071 769.421205 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0341 7.5151 769.397945 0 0.0009 39 | 1/8 3 h-lim-p 0.0028 0.0344 2.3916 769.396271 4 0.0006 62 | 1/8 4 h-lim-p 0.0065 0.9061 0.2189 769.393775 0 0.0131 75 | 1/8 5 h-lim-p 0.0124 0.3709 0.2309 769.236802 0 0.0744 96 | 1/8 6 h-lim-p 0.0023 0.0257 7.6212 769.189256 5 0.0012 126 | 1/8 7 h-lim-p 0.0062 0.1485 1.4897 769.188165 5 0.0010 152 | 1/8 8 h-lim-p 0.0283 2.7708 0.0512 769.188117 2 0.0062 169 | 0/8 9 h-lim-p 0.0015 4.0913 0.2069 769.187909 0 0.0030 189 | 0/8 10 h-lim-p 0.0050 0.0398 0.0560 769.182583 m 0.0398 209 | 1/8 11 h-lim-p 2.5000 20.0000 0.0004 769.182495 2 0.9961 233 | 1/8 12 h-lim-p 2.5000 20.0000 0.0001 769.182493 1 0.6152 255 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 769.182493 0 1.0938 274 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 769.182493 0 2.1875 293 | 1/8 15 h-lim-p 2.1488 20.0000 0.0000 769.182493 0 0.9401 312 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 769.182493 0 0.0293 337 Out... lnL = -769.182493 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -769.182493 Node 7: lnL = -769.182493 Node 8: lnL = -769.182493 Node 9: lnL = -769.182493 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 808 Sequential format.. Reading seq # 1: YBR262C_Sbay Reading seq # 2: YBR262C_Scer Reading seq # 3: YBR262C_Skud Reading seq # 4: YBR262C_Smik Reading seq # 5: YBR262C_Spar Sequences read.. Counting patterns.. # site patterns = 162 Counting frequencies.. 120 bytes for distance 25920 bytes for lkl0 20736 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.050331 0.039108 0.047353 0.036551 0.100117 0.073927 0.085002 lnL0 = -2691.651166 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2691.651166 x= 0.00006 0.05033 0.03911 0.04735 0.03655 0.10012 0.07393 0.08500 1 h-lim-p 0.0002 0.0014 203.1337 2690.077541 3 0.0001 28 | 0/8 2 h-lim-p 0.0001 0.0012 30.9416 2690.032810 5 0.0001 53 | 0/8 3 h-lim-p 0.0002 0.0038 14.8854 2690.025486 5 0.0001 74 | 0/8 4 h-lim-p 0.0005 0.0357 2.3963 2690.025134 4 0.0001 95 | 0/8 5 h-lim-p 0.0004 0.0069 0.6920 2690.025103 2 0.0001 113 | 0/8 6 h-lim-p 0.0004 0.0940 0.2632 2690.025100 1 0.0002 135 | 0/8 7 h-lim-p 0.0002 0.0096 0.1938 2690.025091 0 0.0008 157 | 0/8 8 h-lim-p 0.0001 0.0018 1.0705 2690.024894 m 0.0018 178 | 1/8 9 h-lim-p 0.0096 0.6345 0.1407 2690.024894 0 0.0001 196 | 1/8 10 h-lim-p 0.2614 20.0000 0.0000 2690.024860 0 3.1372 218 | 1/8 11 h-lim-p 2.0620 20.0000 0.0001 2690.024783 1 2.5775 239 | 0/8 12 h-lim-p 0.0012 2.1616 0.1186 2690.024781 0 0.0003 259 | 0/8 13 h-lim-p 0.1301 1.0405 0.0001 2690.024769 m 1.0405 279 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 2690.024769 0 1.0938 299 | 1/8 15 h-lim-p 2.1260 20.0000 0.0000 2690.024769 0 0.9301 318 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 2690.024769 0 0.0000 360 Out... lnL = -2690.024769 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2690.024769 Node 7: lnL = -2690.024769 Node 8: lnL = -2690.024769 Node 9: lnL = -2690.024769 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 169 Sequential format.. Reading seq # 1: YBR264C_Sbay Reading seq # 2: YBR264C_Scer Reading seq # 3: YBR264C_Skud Reading seq # 4: YBR264C_Smik Reading seq # 5: YBR264C_Spar Sequences read.. Counting patterns.. # site patterns = 72 Counting frequencies.. 120 bytes for distance 11520 bytes for lkl0 9216 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.062476 0.021401 0.060979 0.055233 0.055824 0.103209 0.171977 0.202174 lnL0 = -637.909139 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 637.909139 x= 0.06248 0.02140 0.06098 0.05523 0.05582 0.10321 0.17198 0.20217 1 h-lim-p 0.0007 0.0059 71.4317 636.720358 9 0.0005 44 | 0/8 2 h-lim-p 0.0006 0.0048 20.5894 636.548420 0 0.0012 57 | 0/8 3 h-lim-p 0.0014 0.0118 18.3603 636.480947 2 0.0006 73 | 0/8 4 h-lim-p 0.0025 0.0274 4.6606 636.472645 7 0.0009 103 | 0/8 5 h-lim-p 0.0028 0.1067 1.4510 636.471674 5 0.0010 127 | 0/8 6 h-lim-p 0.0048 0.6349 0.3070 636.471572 4 0.0016 148 | 0/8 7 h-lim-p 0.0026 0.8001 0.1820 636.471411 0 0.0040 168 | 0/8 8 h-lim-p 0.0247 9.2033 0.0292 636.452584 0 0.1973 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 636.452437 2 1.0889 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 636.452436 0 1.0938 235 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 636.452436 0 2.1875 255 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 636.452436 0 1.0938 275 | 0/8 13 h-lim-p 0.9086 20.0000 0.0000 636.452436 0 0.0497 298 | 0/8 14 h-lim-p 0.0216 20.0000 0.0000 636.452436 0 0.0054 319 | 0/8 15 h-lim-p 0.0031 20.0000 0.0000 636.452436 0 0.0000 351 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 636.452436 0 0.0000 375 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0003 636.452436 0 0.0000 433 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 636.452436 0 0.0000 454 | 0/8 20 h-lim-p 0.0000 20.0000 0.0000 636.452436 0 0.0000 478 | 0/8 21 h-lim-p 0.0000 20.0000 0.0000 636.452436 0 0.0000 498 | 0/8 22 h-lim-p 0.0000 20.0000 0.0000 636.452436 0 0.0000 518 Out... lnL = -636.452436 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -636.452436 Node 7: lnL = -636.452436 Node 8: lnL = -636.452436 Node 9: lnL = -636.452436 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 166 Sequential format.. Reading seq # 1: YBR265W_Sbay Reading seq # 2: YBR265W_Scer Reading seq # 3: YBR265W_Skud Reading seq # 4: YBR265W_Smik Reading seq # 5: YBR265W_Spar Sequences read.. Counting patterns.. # site patterns = 81 Counting frequencies.. 120 bytes for distance 12960 bytes for lkl0 10368 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.090565 0.027597 0.118233 0.110112 0.039316 0.110321 0.161625 0.271303 lnL0 = -685.733523 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 685.733523 x= 0.09056 0.02760 0.11823 0.11011 0.03932 0.11032 0.16162 0.27130 1 h-lim-p 0.0003 0.0022 58.2193 684.687453 0 0.0008 23 | 0/8 2 h-lim-p 0.0015 0.0118 19.2453 684.485901 3 0.0012 41 | 0/8 3 h-lim-p 0.0004 0.0033 19.6066 684.422083 0 0.0006 53 | 0/8 4 h-lim-p 0.0024 0.0430 4.9890 684.408837 4 0.0012 74 | 0/8 5 h-lim-p 0.0075 0.1788 0.8160 684.408326 3 0.0016 93 | 0/8 6 h-lim-p 0.0075 1.9186 0.1695 684.408288 3 0.0019 120 | 0/8 7 h-lim-p 0.0041 3.9876 0.0758 684.408177 0 0.0083 141 | 0/8 8 h-lim-p 0.0217 4.1422 0.0289 684.399888 0 0.1738 164 | 0/8 9 h-lim-p 2.5000 20.0000 0.0010 684.399385 3 1.0449 190 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 684.399384 1 0.9961 212 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 684.399384 0 2.1875 232 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 684.399384 0 0.5469 253 | 0/8 13 h-lim-p 0.3007 20.0000 0.0000 684.399384 0 0.0047 278 | 0/8 14 h-lim-p 0.0023 20.0000 0.0000 684.399384 0 0.0006 299 Out... lnL = -684.399384 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -684.399384 Node 7: lnL = -684.399384 Node 8: lnL = -684.399384 Node 9: lnL = -684.399384 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 330 Sequential format.. Reading seq # 1: YBR267W_Sbay Reading seq # 2: YBR267W_Scer Reading seq # 3: YBR267W_Skud Reading seq # 4: YBR267W_Smik Reading seq # 5: YBR267W_Spar Sequences read.. Counting patterns.. # site patterns = 147 Counting frequencies.. 120 bytes for distance 23520 bytes for lkl0 18816 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.063727 0.137258 0.116278 0.098021 0.057445 0.115478 0.124098 0.262413 lnL0 = -1379.869388 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1379.869388 x= 0.06373 0.13726 0.11628 0.09802 0.05745 0.11548 0.12410 0.26241 1 h-lim-p 0.0003 0.0023 47.8289 1379.299006 0 0.0006 23 | 0/8 2 h-lim-p 0.0011 5.6618 25.2958 1379.211924 6 0.0003 49 | 0/8 3 h-lim-p 0.0013 0.0317 6.8824 1379.197346 5 0.0007 72 | 0/8 4 h-lim-p 0.0026 0.0605 1.8043 1379.195879 4 0.0010 92 | 0/8 5 h-lim-p 0.0041 0.5915 0.4219 1379.195821 3 0.0007 113 | 0/8 6 h-lim-p 0.0027 1.8004 0.1029 1379.195801 2 0.0024 137 | 0/8 7 h-lim-p 0.0223 15.5038 0.0110 1379.195253 0 0.0893 159 | 0/8 8 h-lim-p 0.0032 0.7441 0.3042 1379.192212 0 0.0065 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1379.192206 1 0.9961 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1379.192206 0 1.0938 222 | 0/8 11 h-lim-p 1.3162 20.0000 0.0000 1379.192206 0 2.6323 243 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1379.192206 0 0.0684 267 | 0/8 13 h-lim-p 0.0112 20.0000 0.0000 1379.192206 0 0.0112 287 | 0/8 14 h-lim-p 0.0047 20.0000 0.0000 1379.192206 0 0.0001 311 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0017 | 0/8 17 h-lim-p 0.0000 20.0000 0.0017 Out... lnL = -1379.192206 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1379.192206 Node 7: lnL = -1379.192206 Node 8: lnL = -1379.192206 Node 9: lnL = -1379.192206 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 289 Sequential format.. Reading seq # 1: YBR268W_Sbay Reading seq # 2: YBR268W_Scer Reading seq # 3: YBR268W_Skud Reading seq # 4: YBR268W_Smik Reading seq # 5: YBR268W_Spar Sequences read.. Counting patterns.. # site patterns = 144 Counting frequencies.. 120 bytes for distance 23040 bytes for lkl0 18432 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.081777 0.108270 0.040461 0.088465 0.090762 0.253577 0.199542 0.306035 lnL0 = -1280.535486 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1280.535486 x= 0.08178 0.10827 0.04046 0.08846 0.09076 0.25358 0.19954 0.30604 1 h-lim-p 0.0074 0.1272 58.6918 1279.756584 8 0.0005 42 | 0/8 2 h-lim-p 0.0015 0.0123 10.3253 1279.719528 2 0.0007 58 | 0/8 3 h-lim-p 0.0010 0.0207 7.7183 1279.694140 0 0.0014 70 | 0/8 4 h-lim-p 0.0029 0.0523 3.8661 1279.688185 5 0.0011 92 | 0/8 5 h-lim-p 0.0044 0.3281 0.9499 1279.687645 4 0.0013 115 | 0/8 6 h-lim-p 0.0089 2.6129 0.1397 1279.687625 2 0.0020 140 | 0/8 7 h-lim-p 0.0115 9.9261 0.0238 1279.687617 2 0.0073 165 | 0/8 8 h-lim-p 0.0310 20.0000 0.0056 1279.686923 0 0.2481 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1279.686914 1 1.0938 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1279.686914 0 1.0938 230 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1279.686914 0 2.1875 250 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1279.686914 0 0.5469 271 | 0/8 13 h-lim-p 0.0462 20.0000 0.0000 1279.686914 0 0.0231 291 | 0/8 14 h-lim-p 0.0077 20.0000 0.0000 1279.686914 0 0.0000 331 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1279.686914 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1279.686914 Node 7: lnL = -1279.686914 Node 8: lnL = -1279.686914 Node 9: lnL = -1279.686914 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 234 Sequential format.. Reading seq # 1: YBR269C_Sbay Reading seq # 2: YBR269C_Scer Reading seq # 3: YBR269C_Skud Reading seq # 4: YBR269C_Smik Reading seq # 5: YBR269C_Spar Sequences read.. Counting patterns.. # site patterns = 132 Counting frequencies.. 120 bytes for distance 21120 bytes for lkl0 16896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.358106 0.092896 0.199904 0.039067 0.340722 0.231440 0.268021 lnL0 = -958.146043 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 958.146043 x= 0.00006 0.35811 0.09290 0.19990 0.03907 0.34072 0.23144 0.26802 1 h-lim-p 0.0000 0.0000 79.2103 958.107654 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0044 23.2193 957.164076 0 0.0035 41 | 1/8 3 h-lim-p 0.0003 0.0022 16.9657 956.789548 m 0.0022 53 | 2/8 4 h-lim-p 0.0035 0.0412 9.2020 956.686469 6 0.0029 78 | 2/8 5 h-lim-p 0.0138 0.1101 1.4153 956.586320 0 0.0206 90 | 2/8 6 h-lim-p 0.0226 0.2116 1.2921 955.457242 0 0.0452 103 | 2/8 7 h-lim-p 0.0008 0.0067 9.5742 954.376936 m 0.0067 115 | 2/8 8 h-lim-p 0.0287 0.2293 1.3254 954.367260 2 0.0067 132 | 1/8 9 h-lim-p 0.0021 0.1107 4.1526 954.337182 0 0.0064 145 | 1/8 10 h-lim-p 0.0485 0.3878 0.1135 954.144764 m 0.3878 157 | 2/8 11 h-lim-p 0.8777 7.0220 0.0178 954.135094 5 0.4607 187 | 1/8 12 h-lim-p 0.0042 0.0998 1.9303 954.128823 0 0.0064 205 | 1/8 13 h-lim-p 1.2626 10.1006 0.0024 954.127568 6 0.7700 234 | 1/8 14 h-lim-p 1.2919 10.4077 0.0014 954.127458 3 0.9799 259 | 1/8 15 h-lim-p 2.5000 20.0000 0.0001 954.127456 0 1.0938 278 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 954.127456 0 1.0938 297 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 954.127456 0 1.0938 316 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 954.127456 0 5.0000 336 | 1/8 19 h-lim-p 1.3900 20.0000 0.0000 954.127456 0 0.3041 356 | 1/8 20 h-lim-p 0.4563 20.0000 0.0000 954.127456 0 0.0036 381 Out... lnL = -954.127456 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -954.127456 Node 7: lnL = -954.127456 Node 8: lnL = -954.127456 Node 9: lnL = -954.127456 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 465 Sequential format.. Reading seq # 1: YBR270C_Sbay Reading seq # 2: YBR270C_Scer Reading seq # 3: YBR270C_Skud Reading seq # 4: YBR270C_Smik Reading seq # 5: YBR270C_Spar Sequences read.. Counting patterns.. # site patterns = 181 Counting frequencies.. 120 bytes for distance 28960 bytes for lkl0 23168 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.025850 0.053792 0.066491 0.148489 0.093377 0.206917 0.213442 0.222676 lnL0 = -2157.627682 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2157.627682 x= 0.02585 0.05379 0.06649 0.14849 0.09338 0.20692 0.21344 0.22268 1 h-lim-p 0.0009 0.0074 121.5571 2155.682247 8 0.0003 42 | 0/8 2 h-lim-p 0.0005 0.0042 27.6350 2155.499097 2 0.0005 58 | 0/8 3 h-lim-p 0.0011 0.0231 12.3114 2155.468128 2 0.0005 74 | 0/8 4 h-lim-p 0.0024 0.1225 2.4892 2155.466571 2 0.0005 91 | 0/8 5 h-lim-p 0.0026 0.2084 0.4962 2155.466508 2 0.0005 108 | 0/8 6 h-lim-p 0.0048 4.4403 0.0549 2155.466506 0 0.0010 129 | 0/8 7 h-lim-p 0.0046 5.2317 0.0123 2155.466506 1 0.0023 152 | 0/8 8 h-lim-p 0.0162 20.0000 0.0017 2155.466224 0 0.2600 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2155.466222 0 1.0938 196 | 0/8 10 h-lim-p 2.0071 20.0000 0.0000 2155.466222 0 1.7562 216 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2155.466222 0 1.0938 236 | 0/8 12 h-lim-p 0.3565 20.0000 0.0000 2155.466222 0 2.8523 259 | 0/8 13 h-lim-p 0.1473 20.0000 0.0004 2155.466222 0 0.0046 283 | 0/8 14 h-lim-p 0.0012 20.0000 0.0016 2155.466222 0 0.0000 308 | 0/8 15 h-lim-p 0.0001 20.0000 0.0006 2155.466222 0 0.0000 338 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 2155.466222 0 0.0000 368 Out... lnL = -2155.466222 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2155.466222 Node 7: lnL = -2155.466222 Node 8: lnL = -2155.466222 Node 9: lnL = -2155.466222 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 465 Sequential format.. Reading seq # 1: YBR271W_Sbay Reading seq # 2: YBR271W_Scer Reading seq # 3: YBR271W_Skud Reading seq # 4: YBR271W_Smik Reading seq # 5: YBR271W_Spar Sequences read.. Counting patterns.. # site patterns = 181 Counting frequencies.. 120 bytes for distance 28960 bytes for lkl0 23168 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.025744 0.058848 0.074254 0.141596 0.094091 0.199672 0.215984 0.224360 lnL0 = -2158.174925 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2158.174925 x= 0.02574 0.05885 0.07425 0.14160 0.09409 0.19967 0.21598 0.22436 1 h-lim-p 0.0011 0.0085 90.9212 2156.960300 9 0.0003 44 | 0/8 2 h-lim-p 0.0008 0.0062 19.5511 2156.870287 7 0.0005 75 | 0/8 3 h-lim-p 0.0011 0.0312 8.4445 2156.856146 3 0.0005 93 | 0/8 4 h-lim-p 0.0021 0.1676 1.8553 2156.855326 2 0.0005 110 | 0/8 5 h-lim-p 0.0028 0.3532 0.3291 2156.855297 2 0.0006 127 | 0/8 6 h-lim-p 0.0033 4.3982 0.0567 2156.855295 1 0.0008 150 | 0/8 7 h-lim-p 0.0049 6.2576 0.0093 2156.855295 0 0.0021 170 | 0/8 8 h-lim-p 0.0367 20.0000 0.0005 2156.855223 0 0.5868 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2156.855219 1 0.9961 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2156.855219 0 1.0938 236 | 0/8 11 h-lim-p 0.5044 20.0000 0.0000 2156.855219 0 0.0315 259 | 0/8 12 h-lim-p 0.0039 20.0000 0.0004 2156.855219 0 0.0000 302 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -2156.855219 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2156.855219 Node 7: lnL = -2156.855219 Node 8: lnL = -2156.855219 Node 9: lnL = -2156.855219 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 262 Sequential format.. Reading seq # 1: YBR272C_Sbay Reading seq # 2: YBR272C_Scer Reading seq # 3: YBR272C_Skud Reading seq # 4: YBR272C_Smik Reading seq # 5: YBR272C_Spar Sequences read.. Counting patterns.. # site patterns = 137 Counting frequencies.. 120 bytes for distance 21920 bytes for lkl0 17536 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.029147 0.129789 0.059968 0.170652 0.071807 0.188590 0.171843 0.237301 lnL0 = -1181.662464 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1181.662464 x= 0.02915 0.12979 0.05997 0.17065 0.07181 0.18859 0.17184 0.23730 1 h-lim-p 0.0028 0.0227 39.5598 1181.147802 5 0.0007 32 | 0/8 2 h-lim-p 0.0015 0.0116 12.3685 1181.074643 7 0.0010 59 | 0/8 3 h-lim-p 0.0014 0.0276 8.9932 1181.054331 4 0.0007 80 | 0/8 4 h-lim-p 0.0045 0.1039 1.4318 1181.053138 4 0.0012 101 | 0/8 5 h-lim-p 0.0115 1.3383 0.1525 1181.053125 2 0.0011 119 | 0/8 6 h-lim-p 0.0083 3.4739 0.0204 1181.053125 0 0.0018 140 | 0/8 7 h-lim-p 0.2576 20.0000 0.0001 1181.053124 0 0.5152 161 | 0/8 8 h-lim-p 0.0046 9.4250 0.0160 1181.053123 0 0.0040 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1181.053123 0 1.0938 201 | 0/8 10 h-lim-p 2.2760 20.0000 0.0000 1181.053123 0 1.9915 221 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1181.053123 0 1.0938 241 | 0/8 12 h-lim-p 0.2623 20.0000 0.0000 1181.053123 0 0.2623 261 | 0/8 13 h-lim-p 0.0000 0.3875 0.1361 1181.053123 0 0.0000 281 | 0/8 14 h-lim-p 0.0000 0.9895 0.0533 1181.053123 0 0.0000 301 | 0/8 15 h-lim-p 0.0003 7.1677 0.0074 1181.053123 0 0.0000 323 | 0/8 16 h-lim-p 0.0004 20.0000 0.0007 1181.053123 0 0.0000 351 | 0/8 17 h-lim-p 0.0002 20.0000 0.0000 1181.053123 0 0.0001 372 Out... lnL = -1181.053123 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1181.053123 Node 7: lnL = -1181.053123 Node 8: lnL = -1181.053123 Node 9: lnL = -1181.053123 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 259 Sequential format.. Reading seq # 1: YBR278W_Sbay Reading seq # 2: YBR278W_Scer Reading seq # 3: YBR278W_Skud Reading seq # 4: YBR278W_Smik Reading seq # 5: YBR278W_Spar Sequences read.. Counting patterns.. # site patterns = 107 Counting frequencies.. 120 bytes for distance 17120 bytes for lkl0 13696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.053560 0.052832 0.060083 0.081552 0.036080 0.129197 0.212963 0.215600 lnL0 = -1072.150449 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1072.150449 x= 0.05356 0.05283 0.06008 0.08155 0.03608 0.12920 0.21296 0.21560 1 h-lim-p 0.0001 0.0011 71.8331 1071.131764 0 0.0004 23 | 0/8 2 h-lim-p 0.0012 0.0139 25.3558 1071.065379 5 0.0002 45 | 0/8 3 h-lim-p 0.0005 0.0134 11.0619 1071.030744 1 0.0007 59 | 0/8 4 h-lim-p 0.0030 0.0620 2.5183 1071.028593 3 0.0007 79 | 0/8 5 h-lim-p 0.0016 0.2138 1.1444 1071.028005 4 0.0011 101 | 0/8 6 h-lim-p 0.0179 1.4575 0.0692 1071.028003 1 0.0009 118 | 0/8 7 h-lim-p 0.0036 8.4277 0.0172 1071.028003 0 0.0016 138 | 0/8 8 h-lim-p 0.0561 20.0000 0.0005 1071.027884 0 0.6727 161 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1071.027882 0 1.0938 181 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1071.027882 0 1.2500 201 | 0/8 11 h-lim-p 1.2376 20.0000 0.0000 1071.027882 0 0.2707 222 | 0/8 12 h-lim-p 0.1301 20.0000 0.0000 1071.027882 0 0.0081 245 | 0/8 13 h-lim-p 0.0045 20.0000 0.0000 1071.027882 0 0.0000 284 | 0/8 14 h-lim-p 0.0000 20.0000 0.0012 1071.027882 0 0.0000 319 | 0/8 15 h-lim-p 0.0000 20.0000 0.0012 | 0/8 16 h-lim-p 0.0000 20.0000 0.0012 Out... lnL = -1071.027882 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1071.027882 Node 7: lnL = -1071.027882 Node 8: lnL = -1071.027882 Node 9: lnL = -1071.027882 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 664 Sequential format.. Reading seq # 1: YBR282W_Sbay Reading seq # 2: YBR282W_Scer Reading seq # 3: YBR282W_Skud Reading seq # 4: YBR282W_Smik Reading seq # 5: YBR282W_Spar Sequences read.. Counting patterns.. # site patterns = 253 Counting frequencies.. 120 bytes for distance 40480 bytes for lkl0 32384 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.035472 0.056859 0.055669 0.144568 0.125049 0.247437 0.360175 0.281291 lnL0 = -3304.525216 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3304.525216 x= 0.03547 0.05686 0.05567 0.14457 0.12505 0.24744 0.36018 0.28129 1 h-lim-p 0.0062 1.3740 103.0713 3303.340744 9 0.0002 49 | 0/8 2 h-lim-p 0.0008 0.0062 18.4049 3303.254459 7 0.0005 78 | 0/8 3 h-lim-p 0.0013 0.0101 7.5832 3303.244837 6 0.0004 106 | 0/8 4 h-lim-p 0.0019 0.1562 1.5120 3303.244261 4 0.0005 127 | 0/8 5 h-lim-p 0.0011 0.3304 0.7247 3303.244069 2 0.0009 143 | 0/8 6 h-lim-p 0.0052 2.1973 0.1228 3303.244064 1 0.0006 167 | 0/8 7 h-lim-p 0.0080 17.5357 0.0098 3303.244063 0 0.0018 188 | 0/8 8 h-lim-p 0.0293 20.0000 0.0006 3303.243962 0 0.4682 212 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3303.243961 0 1.0938 232 | 0/8 10 h-lim-p 1.6255 20.0000 0.0000 3303.243961 0 1.4223 252 | 0/8 11 h-lim-p 2.0387 20.0000 0.0000 3303.243961 0 1.7838 272 | 0/8 12 h-lim-p 1.4869 20.0000 0.0000 3303.243961 0 0.6505 292 | 0/8 13 h-lim-p 0.2094 20.0000 0.0001 3303.243961 0 0.1047 312 | 0/8 14 h-lim-p 0.0310 20.0000 0.0002 3303.243961 0 0.0077 333 | 0/8 15 h-lim-p 0.0037 20.0000 0.0004 3303.243961 0 0.0002 356 | 0/8 16 h-lim-p 0.0002 20.0000 0.0004 3303.243961 0 0.0000 388 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 3303.243961 0 0.0000 416 Out... lnL = -3303.243961 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3303.243961 Node 7: lnL = -3303.243961 Node 8: lnL = -3303.243961 Node 9: lnL = -3303.243961 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 863 Sequential format.. Reading seq # 1: YBR283C_Sbay Reading seq # 2: YBR283C_Scer Reading seq # 3: YBR283C_Skud Reading seq # 4: YBR283C_Smik Reading seq # 5: YBR283C_Spar Sequences read.. Counting patterns.. # site patterns = 267 Counting frequencies.. 120 bytes for distance 42720 bytes for lkl0 34176 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.042175 0.051261 0.082081 0.120062 0.079298 0.184149 0.215537 0.236594 lnL0 = -3838.278774 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3838.278774 x= 0.04218 0.05126 0.08208 0.12006 0.07930 0.18415 0.21554 0.23659 1 h-lim-p 0.0004 0.0030 154.8623 3836.360180 2 0.0002 26 | 0/8 2 h-lim-p 0.0008 0.0064 20.9669 3836.304449 5 0.0003 50 | 0/8 3 h-lim-p 0.0005 0.0148 9.8433 3836.296316 5 0.0002 74 | 0/8 4 h-lim-p 0.0006 0.0633 3.3963 3836.294762 3 0.0003 93 | 0/8 5 h-lim-p 0.0014 0.3955 0.7693 3836.294654 3 0.0004 112 | 0/8 6 h-lim-p 0.0033 1.9851 0.0849 3836.294652 1 0.0004 136 | 0/8 7 h-lim-p 0.0019 6.2580 0.0180 3836.294647 0 0.0029 156 | 0/8 8 h-lim-p 0.0064 10.4308 0.0082 3836.293304 0 0.1025 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3836.293295 1 0.9961 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3836.293295 0 2.5000 222 | 0/8 11 h-lim-p 0.4837 20.0000 0.0002 3836.293295 0 0.4232 242 | 0/8 12 h-lim-p 0.0347 20.0000 0.0019 3836.293295 0 0.0011 266 | 0/8 13 h-lim-p 0.0004 11.1484 0.0054 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0030 3836.293295 0 0.0000 332 | 0/8 15 h-lim-p 0.0000 20.0000 0.0006 3836.293295 0 0.0000 366 | 0/8 16 h-lim-p 0.0000 20.0000 0.0030 | 0/8 17 h-lim-p 0.0000 20.0000 0.0030 Out... lnL = -3836.293295 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3836.293295 Node 7: lnL = -3836.293295 Node 8: lnL = -3836.293295 Node 9: lnL = -3836.293295 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 868 Sequential format.. Reading seq # 1: YBR284W_Sbay Reading seq # 2: YBR284W_Scer Reading seq # 3: YBR284W_Skud Reading seq # 4: YBR284W_Smik Reading seq # 5: YBR284W_Spar Sequences read.. Counting patterns.. # site patterns = 294 Counting frequencies.. 120 bytes for distance 47040 bytes for lkl0 37632 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.030057 0.090146 0.079174 0.128051 0.075048 0.182429 0.207447 0.229682 lnL0 = -3858.729676 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3858.729676 x= 0.03006 0.09015 0.07917 0.12805 0.07505 0.18243 0.20745 0.22968 1 h-lim-p 0.0005 0.0038 123.5864 3857.182402 3 0.0002 28 | 0/8 2 h-lim-p 0.0010 0.0077 22.8396 3857.106136 7 0.0003 60 | 0/8 3 h-lim-p 0.0005 0.0224 14.3282 3857.089602 3 0.0002 78 | 0/8 4 h-lim-p 0.0007 0.0515 4.5175 3857.086892 4 0.0003 97 | 0/8 5 h-lim-p 0.0020 0.4053 0.6977 3857.086808 3 0.0003 117 | 0/8 6 h-lim-p 0.0068 7.1595 0.0354 3857.086808 0 0.0007 139 | 0/8 7 h-lim-p 0.0127 20.0000 0.0021 3857.086808 0 0.0111 159 | 0/8 8 h-lim-p 0.0056 20.0000 0.0041 3857.086752 0 0.0449 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3857.086751 0 1.0938 202 | 0/8 10 h-lim-p 0.9973 20.0000 0.0000 3857.086751 0 0.9973 222 | 0/8 11 h-lim-p 0.8227 20.0000 0.0000 3857.086751 0 0.0257 246 | 0/8 12 h-lim-p 0.0010 20.0000 0.0009 3857.086751 0 0.0000 281 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 3857.086751 0 0.0000 307 Out... lnL = -3857.086751 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3857.086751 Node 7: lnL = -3857.086751 Node 8: lnL = -3857.086751 Node 9: lnL = -3857.086751 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 307 Sequential format.. Reading seq # 1: YBR285W_Sbay Reading seq # 2: YBR285W_Scer Reading seq # 3: YBR285W_Skud Reading seq # 4: YBR285W_Smik Reading seq # 5: YBR285W_Spar Sequences read.. Counting patterns.. # site patterns = 96 Counting frequencies.. 120 bytes for distance 15360 bytes for lkl0 12288 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.045733 0.017693 0.038552 0.043387 0.042635 0.094902 0.080229 0.137586 lnL0 = -1011.437088 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1011.437088 x= 0.04573 0.01769 0.03855 0.04339 0.04264 0.09490 0.08023 0.13759 1 h-lim-p 0.0009 0.0078 147.4807 1010.149623 9 0.0001 46 | 0/8 2 h-lim-p 0.0007 0.0058 16.4858 1010.108323 6 0.0003 69 | 0/8 3 h-lim-p 0.0009 0.0173 5.7236 1010.103232 4 0.0003 89 | 0/8 4 h-lim-p 0.0012 0.0440 1.5934 1010.103021 4 0.0002 113 | 0/8 5 h-lim-p 0.0032 0.9614 0.0920 1010.103020 1 0.0003 129 | 0/8 6 h-lim-p 0.0024 7.3905 0.0120 1010.103020 0 0.0011 149 | 0/8 7 h-lim-p 0.0159 20.0000 0.0008 1010.102997 0 0.1909 172 | 0/8 8 h-lim-p 0.0015 0.5138 0.0993 1010.102919 0 0.0023 192 | 0/8 9 h-lim-p 0.9113 20.0000 0.0003 1010.102916 0 0.9113 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1010.102916 0 1.0938 232 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1010.102916 0 2.1875 252 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1010.102916 0 1.0938 272 | 0/8 13 h-lim-p 0.1050 20.0000 0.0000 1010.102916 0 0.2100 293 | 0/8 14 h-lim-p 0.0001 4.7384 0.0415 1010.102916 0 0.0000 314 | 0/8 15 h-lim-p 0.0000 0.0334 1.9785 .. | 0/8 16 h-lim-p 0.0000 2.2900 0.0310 1010.102916 0 0.0000 361 | 0/8 17 h-lim-p 0.0013 20.0000 0.0009 1010.102916 0 0.0001 384 | 0/8 18 h-lim-p 0.0002 20.0000 0.0003 1010.102916 0 0.0000 411 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 1010.102916 0 0.0000 434 | 0/8 20 h-lim-p 0.0000 20.0000 0.0000 1010.102916 0 0.0000 468 | 0/8 21 h-lim-p 0.0000 20.0000 0.0067 1010.102916 0 0.0000 490 | 0/8 22 h-lim-p 0.0003 20.0000 0.0009 1010.102916 0 0.0001 511 | 0/8 23 h-lim-p 0.0003 20.0000 0.0002 1010.102916 0 0.0012 533 | 0/8 24 h-lim-p 0.0044 20.0000 0.0001 1010.102916 0 0.0001 558 | 0/8 25 h-lim-p 0.0001 20.0000 0.0001 1010.102916 0 0.0000 578 | 0/8 26 h-lim-p 0.0000 10.7484 0.0062 .. | 0/8 27 h-lim-p 0.0000 20.0000 0.0052 | 0/8 28 h-lim-p 0.0000 20.0000 0.0052 Out... lnL = -1010.102916 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1010.102916 Node 7: lnL = -1010.102916 Node 8: lnL = -1010.102916 Node 9: lnL = -1010.102916 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 456 Sequential format.. Reading seq # 1: YBR286W_Sbay Reading seq # 2: YBR286W_Scer Reading seq # 3: YBR286W_Skud Reading seq # 4: YBR286W_Smik Reading seq # 5: YBR286W_Spar Sequences read.. Counting patterns.. # site patterns = 175 Counting frequencies.. 120 bytes for distance 28000 bytes for lkl0 22400 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.045993 0.061287 0.002711 0.078439 0.062701 0.135158 0.143856 0.173820 lnL0 = -1723.283819 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1723.283819 x= 0.04599 0.06129 0.00271 0.07844 0.06270 0.13516 0.14386 0.17382 1 h-lim-p 0.0003 0.0083 359.9079 1720.133909 9 0.0001 44 | 0/8 2 h-lim-p 0.0002 0.0013 96.0750 1718.782549 0 0.0003 57 | 0/8 3 h-lim-p 0.0012 0.0095 12.5857 1718.763385 5 0.0002 81 | 0/8 4 h-lim-p 0.0010 0.0439 3.1185 1718.760813 5 0.0006 106 | 0/8 5 h-lim-p 0.0030 0.4564 0.5780 1718.760721 3 0.0005 126 | 0/8 6 h-lim-p 0.0031 1.9191 0.0989 1718.760700 2 0.0014 150 | 0/8 7 h-lim-p 0.0226 7.9328 0.0059 1718.743238 0 0.7241 175 | 0/8 8 h-lim-p 0.0030 0.1006 1.4191 1718.742650 4 0.0005 205 | 0/8 9 h-lim-p 0.5719 20.0000 0.0013 1718.739770 0 1.1438 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1718.739728 1 1.0938 240 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1718.739728 0 1.0938 260 | 0/8 12 h-lim-p 1.3079 20.0000 0.0000 1718.739728 0 2.6158 281 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1718.739728 0 0.0006 312 Out... lnL = -1718.739728 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1718.739728 Node 7: lnL = -1718.739728 Node 8: lnL = -1718.739728 Node 9: lnL = -1718.739728 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 305 Sequential format.. Reading seq # 1: YBR287W_Sbay Reading seq # 2: YBR287W_Scer Reading seq # 3: YBR287W_Skud Reading seq # 4: YBR287W_Smik Reading seq # 5: YBR287W_Spar Sequences read.. Counting patterns.. # site patterns = 109 Counting frequencies.. 120 bytes for distance 17440 bytes for lkl0 13952 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.098827 0.025524 0.020562 0.084816 0.066121 0.103795 0.129293 0.235623 lnL0 = -1150.310917 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1150.310917 x= 0.09883 0.02552 0.02056 0.08482 0.06612 0.10379 0.12929 0.23562 1 h-lim-p 0.0013 1.0196 135.1834 1148.869675 9 0.0002 46 | 0/8 2 h-lim-p 0.0003 0.0025 31.5796 1148.660918 0 0.0005 58 | 0/8 3 h-lim-p 0.0010 0.0098 14.7244 1148.606046 7 0.0006 86 | 0/8 4 h-lim-p 0.0031 0.0312 2.8784 1148.604186 5 0.0005 113 | 0/8 5 h-lim-p 0.0016 0.2786 0.8499 1148.604003 4 0.0005 136 | 0/8 6 h-lim-p 0.0016 0.7227 0.2896 1148.603972 1 0.0008 158 | 0/8 7 h-lim-p 0.0029 1.8147 0.0785 1148.603969 2 0.0008 183 | 0/8 8 h-lim-p 0.0354 20.0000 0.0017 1148.602152 0 0.5672 207 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1148.602096 3 1.3437 234 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1148.602095 0 1.0938 254 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1148.602095 0 0.5469 275 | 0/8 12 h-lim-p 0.2741 20.0000 0.0000 1148.602095 0 0.0343 297 | 0/8 13 h-lim-p 0.0128 20.0000 0.0000 1148.602095 0 0.0016 319 | 0/8 14 h-lim-p 0.0004 20.0000 0.0001 1148.602095 0 0.0002 339 | 0/8 15 h-lim-p 0.0004 20.0000 0.0001 1148.602095 0 0.0004 359 | 0/8 16 h-lim-p 0.0001 20.0000 0.0002 1148.602095 0 0.0000 379 | 0/8 17 h-lim-p 0.0001 20.0000 0.0001 1148.602095 0 0.0003 400 | 0/8 18 h-lim-p 0.0001 20.0000 0.0002 1148.602095 0 0.0000 425 | 0/8 19 h-lim-p 0.0001 20.0000 0.0000 1148.602095 0 0.0000 450 Out... lnL = -1148.602095 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1148.602095 Node 7: lnL = -1148.602095 Node 8: lnL = -1148.602095 Node 9: lnL = -1148.602095 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 220 Sequential format.. Reading seq # 1: YBR288C_Sbay Reading seq # 2: YBR288C_Scer Reading seq # 3: YBR288C_Skud Reading seq # 4: YBR288C_Smik Reading seq # 5: YBR288C_Spar Sequences read.. Counting patterns.. # site patterns = 86 Counting frequencies.. 120 bytes for distance 13760 bytes for lkl0 11008 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.050874 0.024602 0.057123 0.080253 0.055742 0.166514 0.164265 0.196141 lnL0 = -872.487379 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 872.487379 x= 0.05087 0.02460 0.05712 0.08025 0.05574 0.16651 0.16427 0.19614 1 h-lim-p 0.0006 0.0048 90.6188 871.356458 9 0.0003 43 | 0/8 2 h-lim-p 0.0013 0.0103 12.3258 871.306511 4 0.0007 64 | 0/8 3 h-lim-p 0.0012 0.0297 6.8665 871.293868 6 0.0007 93 | 0/8 4 h-lim-p 0.0012 0.0485 3.8004 871.290691 4 0.0006 115 | 0/8 5 h-lim-p 0.0037 0.8048 0.6163 871.290498 4 0.0010 138 | 0/8 6 h-lim-p 0.0123 3.4272 0.0521 871.290497 1 0.0012 162 | 0/8 7 h-lim-p 0.0059 19.8080 0.0108 871.290497 0 0.0006 184 | 0/8 8 h-lim-p 0.1325 20.0000 0.0001 871.290493 0 1.0601 207 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 871.290492 0 1.0938 227 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 871.290492 0 1.0938 247 | 0/8 11 h-lim-p 1.1222 20.0000 0.0000 871.290492 0 8.9773 270 | 0/8 12 h-lim-p 0.3198 20.0000 0.0002 871.290492 0 0.0200 293 | 0/8 13 h-lim-p 0.0028 20.0000 0.0017 871.290492 0 0.0000 336 | 0/8 14 h-lim-p 0.0000 20.0000 0.0007 871.290492 0 0.0001 359 | 0/8 15 h-lim-p 0.0008 20.0000 0.0001 871.290492 0 0.0000 387 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 871.290492 0 0.0205 418 | 0/8 17 h-lim-p 0.0266 20.0000 0.0000 871.290492 0 0.0000 448 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 871.290492 0 0.0000 469 | 0/8 19 h-lim-p 0.0000 20.0000 0.0005 871.290492 0 0.0013 496 | 0/8 20 h-lim-p 0.0002 20.0000 0.0024 871.290492 0 0.0002 516 | 0/8 21 h-lim-p 0.0008 20.0000 0.0007 871.290492 0 0.0001 538 | 0/8 22 h-lim-p 0.0048 20.0000 0.0000 871.290492 0 0.0024 558 | 0/8 23 h-lim-p 0.0014 20.0000 0.0000 871.290492 0 0.0003 579 | 0/8 24 h-lim-p 0.0002 20.0000 0.0000 871.290492 0 0.0000 610 | 0/8 25 h-lim-p 0.0000 20.0000 0.0012 871.290492 0 0.0000 642 | 0/8 26 h-lim-p 0.0000 20.0000 0.0012 871.290492 0 0.0000 675 | 0/8 27 h-lim-p 0.0000 20.0000 0.0012 871.290492 0 0.0000 705 | 0/8 28 h-lim-p 0.0000 20.0000 0.0004 871.290492 0 0.0013 732 | 0/8 29 h-lim-p 0.0030 20.0000 0.0002 871.290492 0 0.0013 752 | 0/8 30 h-lim-p 0.0015 20.0000 0.0001 871.290492 0 0.0000 780 | 0/8 31 h-lim-p 0.0000 20.0000 0.0004 871.290492 0 0.0000 800 | 0/8 32 h-lim-p 0.0000 20.0000 0.0026 871.290492 0 0.0000 823 | 0/8 33 h-lim-p 0.0000 20.0000 0.0010 871.290492 0 0.0013 850 | 0/8 34 h-lim-p 0.0311 20.0000 0.0000 871.290492 0 0.0136 870 | 0/8 35 h-lim-p 0.0329 20.0000 0.0000 871.290492 0 0.0001 897 | 0/8 36 h-lim-p 0.0002 20.0000 0.0000 871.290492 0 0.0001 917 | 0/8 37 h-lim-p 0.0001 20.0000 0.0000 871.290492 0 0.0000 942 | 0/8 38 h-lim-p 0.0000 20.0000 0.0000 871.290492 0 0.0000 975 Out... lnL = -871.290492 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -871.290492 Node 7: lnL = -871.290492 Node 8: lnL = -871.290492 Node 9: lnL = -871.290492 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 133 Sequential format.. Reading seq # 1: YBR291C_Sbay Reading seq # 2: YBR291C_Scer Reading seq # 3: YBR291C_Skud Reading seq # 4: YBR291C_Smik Reading seq # 5: YBR291C_Spar Sequences read.. Counting patterns.. # site patterns = 62 Counting frequencies.. 120 bytes for distance 9920 bytes for lkl0 7936 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.182859 0.174877 0.214481 0.131701 3.717742 0.303881 0.651324 lnL0 = -504.174303 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 504.174303 x= 0.00006 0.18286 0.17488 0.21448 0.13170 3.71774 0.30388 0.65132 1 h-lim-p 0.0000 0.0000 78.8959 504.155391 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0086 69.7547 494.512516 9 0.0049 61 | 1/8 3 h-lim-p 0.0007 0.0054 63.4857 490.311181 0 0.0040 75 | 1/8 4 h-lim-p 0.0004 0.0028 13.0936 490.078760 m 0.0028 87 | 2/8 5 h-lim-p 0.0007 0.0098 43.0369 487.755487 0 0.0026 101 | 2/8 6 h-lim-p 0.1935 1.5480 0.2537 485.937044 0 0.3870 114 | 1/8 7 h-lim-p 0.0034 0.0269 26.7851 485.793612 6 0.0006 146 | 1/8 8 h-lim-p 0.6610 5.2883 0.0195 485.767076 2 0.6197 162 | 1/8 9 h-lim-p 1.9379 19.9406 0.0062 485.762416 5 1.0308 192 | 0/8 10 h-lim-p 0.0196 0.6658 0.3282 485.762221 4 0.0050 220 | 0/8 11 h-lim-p 1.2677 20.0000 0.0013 485.761623 1 1.5847 242 | 0/8 12 h-lim-p 2.5000 20.0000 0.0002 485.761611 2 1.0938 266 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 485.761611 1 1.2305 289 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 485.761611 0 1.0938 309 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 485.761611 0 5.0000 330 | 0/8 16 h-lim-p 1.4109 20.0000 0.0000 485.761611 0 0.0003 362 Out... lnL = -485.761611 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -485.761611 Node 7: lnL = -485.761611 Node 8: lnL = -485.761611 Node 9: lnL = -485.761611 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 864 Sequential format.. Reading seq # 1: YBR293W_Sbay Reading seq # 2: YBR293W_Scer Reading seq # 3: YBR293W_Skud Reading seq # 4: YBR293W_Smik Reading seq # 5: YBR293W_Spar Sequences read.. Counting patterns.. # site patterns = 495 Counting frequencies.. 120 bytes for distance 79200 bytes for lkl0 63360 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.120686 0.000060 0.163609 0.661362 0.340536 0.513065 0.447392 0.625405 lnL0 = -5164.945309 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 5164.945309 x= 0.12069 0.00006 0.16361 0.66136 0.34054 0.51306 0.44739 0.62541 1 h-lim-p 0.0042 0.0333 25.4351 5164.303391 3 0.0019 28 | 0/8 2 h-lim-p 0.0020 0.0262 24.3842 5164.044090 7 0.0014 60 | 0/8 3 h-lim-p 0.0033 0.0645 10.0856 5163.977156 5 0.0018 83 | 0/8 4 h-lim-p 0.0048 0.1300 3.7033 5163.965161 2 0.0021 99 | 0/8 5 h-lim-p 0.0306 1.6627 0.2523 5163.965045 2 0.0030 117 | 0/8 6 h-lim-p 0.0132 5.7883 0.0584 5163.964935 1 0.0136 139 | 0/8 7 h-lim-p 0.0322 5.3516 0.0246 5163.959475 0 0.1932 161 | 0/8 8 h-lim-p 0.0178 2.2329 0.2669 5163.959336 2 0.0039 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 5163.959287 2 0.9961 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 5163.959287 0 1.0938 230 | 0/8 11 h-lim-p 1.4246 20.0000 0.0000 5163.959287 0 1.2465 250 | 0/8 12 h-lim-p 0.9534 20.0000 0.0000 5163.959287 0 0.0596 273 | 0/8 13 h-lim-p 0.0001 20.0000 0.0045 5163.959287 0 0.0000 302 | 0/8 14 h-lim-p 0.0026 20.0000 0.0000 5163.959287 0 0.0000 333 Out... lnL = -5163.959287 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -5163.959287 Node 7: lnL = -5163.959287 Node 8: lnL = -5163.959287 Node 9: lnL = -5163.959287 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 869 Sequential format.. Reading seq # 1: YBR296C_Sbay Reading seq # 2: YBR296C_Scer Reading seq # 3: YBR296C_Skud Reading seq # 4: YBR296C_Smik Reading seq # 5: YBR296C_Spar Sequences read.. Counting patterns.. # site patterns = 345 Counting frequencies.. 120 bytes for distance 55200 bytes for lkl0 44160 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.112303 0.046233 0.092298 0.096196 0.087995 0.278799 0.252586 0.353601 lnL0 = -4092.511711 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4092.511711 x= 0.11230 0.04623 0.09230 0.09620 0.08800 0.27880 0.25259 0.35360 1 h-lim-p 0.0012 0.0092 171.8140 4089.317254 3 0.0002 29 | 0/8 2 h-lim-p 0.0006 0.0048 48.0096 4088.917606 7 0.0004 59 | 0/8 3 h-lim-p 0.0003 0.0045 57.5635 4088.648763 4 0.0003 79 | 0/8 4 h-lim-p 0.0017 0.0313 10.1498 4088.627193 5 0.0005 102 | 0/8 5 h-lim-p 0.0020 0.1088 2.3061 4088.626167 3 0.0004 121 | 0/8 6 h-lim-p 0.0007 0.2464 1.3049 4088.625849 4 0.0005 143 | 0/8 7 h-lim-p 0.0370 20.0000 0.0172 4088.625827 2 0.0122 161 | 0/8 8 h-lim-p 0.0168 20.0000 0.0125 4088.623477 0 0.1011 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 4088.623432 1 0.9961 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4088.623432 0 1.0938 225 | 0/8 11 h-lim-p 1.6923 20.0000 0.0000 4088.623432 0 0.2115 247 | 0/8 12 h-lim-p 0.0745 20.0000 0.0000 4088.623432 0 0.0000 284 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 4088.623432 0 0.0000 314 Out... lnL = -4088.623432 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4088.623432 Node 7: lnL = -4088.623432 Node 8: lnL = -4088.623432 Node 9: lnL = -4088.623432 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 860 Sequential format.. Reading seq # 1: YBR297W_Sbay Reading seq # 2: YBR297W_Scer Reading seq # 3: YBR297W_Skud Reading seq # 4: YBR297W_Smik Reading seq # 5: YBR297W_Spar Sequences read.. Counting patterns.. # site patterns = 450 Counting frequencies.. 120 bytes for distance 72000 bytes for lkl0 57600 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.199715 0.136416 0.194273 0.195423 0.177579 0.406457 0.401151 0.636094 lnL0 = -4845.491493 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4845.491493 x= 0.19972 0.13642 0.19427 0.19542 0.17758 0.40646 0.40115 0.63609 1 h-lim-p 0.0025 0.0204 34.1731 4845.054820 7 0.0008 41 | 0/8 2 h-lim-p 0.0038 0.0334 6.9003 4845.041554 6 0.0006 72 | 0/8 3 h-lim-p 0.0008 0.1086 5.0609 4845.031654 0 0.0016 85 | 0/8 4 h-lim-p 0.0026 0.2009 3.0578 4845.026031 5 0.0018 110 | 0/8 5 h-lim-p 0.0061 0.8541 0.8941 4845.025069 2 0.0029 126 | 0/8 6 h-lim-p 0.0080 1.5025 0.3202 4845.024990 2 0.0017 151 | 0/8 7 h-lim-p 0.0069 6.2762 0.0807 4845.024978 0 0.0030 171 | 0/8 8 h-lim-p 0.0884 20.0000 0.0027 4845.023889 0 0.7071 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4845.023889 0 1.0938 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4845.023889 0 1.0938 234 | 0/8 11 h-lim-p 1.2554 20.0000 0.0000 4845.023889 0 1.8832 254 | 0/8 12 h-lim-p 0.7000 20.0000 0.0000 4845.023889 0 0.0766 276 | 0/8 13 h-lim-p 0.0018 20.0000 0.0005 4845.023889 0 0.0001 300 | 0/8 14 h-lim-p 0.0001 20.0000 0.0003 4845.023889 0 0.0000 333 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 4845.023889 0 0.0000 357 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 4845.023889 0 0.0000 392 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -4845.023889 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4845.023889 Node 7: lnL = -4845.023889 Node 8: lnL = -4845.023889 Node 9: lnL = -4845.023889 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 848 Sequential format.. Reading seq # 1: YBR299W_Sbay Reading seq # 2: YBR299W_Scer Reading seq # 3: YBR299W_Skud Reading seq # 4: YBR299W_Smik Reading seq # 5: YBR299W_Spar Sequences read.. Counting patterns.. # site patterns = 348 Counting frequencies.. 120 bytes for distance 55680 bytes for lkl0 44544 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.031450 0.000060 0.006827 0.181226 0.832940 0.302512 0.218315 0.355539 lnL0 = -4346.506708 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4346.506708 x= 0.03145 0.00006 0.00683 0.18123 0.83294 0.30251 0.21831 0.35554 1 h-lim-p 0.0003 0.0021 145.3944 4338.511164 0 0.0008 23 | 0/8 2 h-lim-p 0.0006 0.0050 87.9815 4337.871235 7 0.0002 50 | 0/8 3 h-lim-p 0.0003 0.0029 69.7520 4336.915885 0 0.0006 63 | 0/8 4 h-lim-p 0.0003 0.0024 43.6316 4336.687475 0 0.0004 75 | 0/8 5 h-lim-p 0.0006 0.0089 34.5284 4336.418529 0 0.0011 88 | 0/8 6 h-lim-p 0.0010 0.0083 26.5815 4336.240779 4 0.0010 108 | 0/8 7 h-lim-p 0.0050 0.0398 1.5286 4336.240023 2 0.0006 126 | 0/8 8 h-lim-p 0.0525 7.9964 0.0170 4336.089834 0 0.8407 142 | 0/8 9 h-lim-p 2.5000 20.0000 0.0027 4336.085098 2 1.0889 166 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 4336.085070 0 1.0938 186 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4336.085070 0 1.0938 206 | 0/8 12 h-lim-p 1.8615 20.0000 0.0000 4336.085070 0 1.6288 226 | 0/8 13 h-lim-p 1.2882 20.0000 0.0000 4336.085070 0 1.9323 246 | 0/8 14 h-lim-p 0.0849 20.0000 0.0007 4336.085070 0 0.0212 267 | 0/8 15 h-lim-p 0.0059 20.0000 0.0025 4336.085070 0 0.0011 289 | 0/8 16 h-lim-p 0.0009 15.6997 0.0032 4336.085070 0 0.0004 309 | 0/8 17 h-lim-p 0.0004 20.0000 0.0034 4336.085070 0 0.0002 329 | 0/8 18 h-lim-p 0.0001 20.0000 0.0064 4336.085070 0 0.0000 355 | 0/8 19 h-lim-p 0.0002 20.0000 0.0000 4336.085070 0 0.0000 383 | 0/8 20 h-lim-p 0.0000 20.0000 0.0000 4336.085070 0 0.0000 412 Out... lnL = -4336.085070 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4336.085070 Node 7: lnL = -4336.085070 Node 8: lnL = -4336.085070 Node 9: lnL = -4336.085070 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 659 Sequential format.. Reading seq # 1: YCL001W_Sbay Reading seq # 2: YCL001W_Scer Reading seq # 3: YCL001W_Skud Reading seq # 4: YCL001W_Smik Reading seq # 5: YCL001W_Spar Sequences read.. Counting patterns.. # site patterns = 162 Counting frequencies.. 120 bytes for distance 25920 bytes for lkl0 20736 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.023679 0.075264 0.058162 0.073552 0.042878 0.135083 0.132631 0.156446 lnL0 = -2544.396586 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2544.396586 x= 0.02368 0.07526 0.05816 0.07355 0.04288 0.13508 0.13263 0.15645 1 h-lim-p 0.0006 0.0047 110.8403 2543.199518 7 0.0002 37 | 0/8 2 h-lim-p 0.0004 0.0032 25.7735 2543.133001 4 0.0002 58 | 0/8 3 h-lim-p 0.0004 0.0057 13.6790 2543.122340 5 0.0001 82 | 0/8 4 h-lim-p 0.0003 0.0303 6.2563 2543.119423 5 0.0002 109 | 0/8 5 h-lim-p 0.0011 0.2857 1.0468 2543.119287 2 0.0003 126 | 0/8 6 h-lim-p 0.0030 0.8663 0.0924 2543.119287 0 0.0002 141 | 0/8 7 h-lim-p 0.0024 20.0000 0.0063 2543.119286 0 0.0048 162 | 0/8 8 h-lim-p 0.0099 20.0000 0.0030 2543.119083 0 0.1189 185 | 0/8 9 h-lim-p 0.3207 20.0000 0.0011 2543.119079 0 0.9621 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2543.119079 0 1.0938 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2543.119079 0 1.0938 246 | 0/8 12 h-lim-p 0.1107 20.0000 0.0000 2543.119079 0 0.0017 271 | 0/8 13 h-lim-p 0.0001 20.0000 0.0009 2543.119079 0 0.0000 301 | 0/8 14 h-lim-p 0.0000 20.0000 0.0014 | 0/8 15 h-lim-p 0.0000 20.0000 0.0014 Out... lnL = -2543.119079 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2543.119079 Node 7: lnL = -2543.119079 Node 8: lnL = -2543.119079 Node 9: lnL = -2543.119079 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 329 Sequential format.. Reading seq # 1: YCL004W_Sbay Reading seq # 2: YCL004W_Scer Reading seq # 3: YCL004W_Skud Reading seq # 4: YCL004W_Smik Reading seq # 5: YCL004W_Spar Sequences read.. Counting patterns.. # site patterns = 143 Counting frequencies.. 120 bytes for distance 22880 bytes for lkl0 18304 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.034021 0.052178 0.047322 0.140511 0.072011 0.260798 0.234753 0.219529 lnL0 = -1484.479945 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1484.479945 x= 0.03402 0.05218 0.04732 0.14051 0.07201 0.26080 0.23475 0.21953 1 h-lim-p 0.0003 0.0024 62.0511 1483.687759 0 0.0005 22 | 0/8 2 h-lim-p 0.0003 0.0022 24.3134 1483.541502 0 0.0006 35 | 0/8 3 h-lim-p 0.0009 0.0075 10.1177 1483.521442 6 0.0005 59 | 0/8 4 h-lim-p 0.0012 0.1110 3.9965 1483.515370 5 0.0009 81 | 0/8 5 h-lim-p 0.0031 0.0783 1.1533 1483.514916 2 0.0007 98 | 0/8 6 h-lim-p 0.0082 2.3536 0.1033 1483.514909 0 0.0010 112 | 0/8 7 h-lim-p 0.0033 8.5874 0.0320 1483.514901 0 0.0049 132 | 0/8 8 h-lim-p 0.0368 20.0000 0.0043 1483.513696 0 0.2944 155 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1483.513687 1 0.9961 177 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1483.513687 0 2.1875 197 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1483.513687 0 1.0938 217 | 0/8 12 h-lim-p 0.1097 20.0000 0.0000 1483.513687 0 5.2643 242 | 0/8 13 h-lim-p 0.3538 20.0000 0.0003 1483.513687 0 0.0000 284 | 0/8 14 h-lim-p 0.0000 20.0000 0.0014 1483.513687 0 0.0000 310 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 1483.513687 0 0.0000 345 | 0/8 16 h-lim-p 0.0000 20.0000 0.0014 | 0/8 17 h-lim-p 0.0000 20.0000 0.0014 Out... lnL = -1483.513687 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1483.513687 Node 7: lnL = -1483.513687 Node 8: lnL = -1483.513687 Node 9: lnL = -1483.513687 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 696 Sequential format.. Reading seq # 1: YCL005W_Sbay Reading seq # 2: YCL005W_Scer Reading seq # 3: YCL005W_Skud Reading seq # 4: YCL005W_Smik Reading seq # 5: YCL005W_Spar Sequences read.. Counting patterns.. # site patterns = 158 Counting frequencies.. 120 bytes for distance 25280 bytes for lkl0 20224 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.012177 0.051997 0.021995 0.045202 0.044874 0.081718 0.074751 0.088734 lnL0 = -2222.405583 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2222.405583 x= 0.01218 0.05200 0.02199 0.04520 0.04487 0.08172 0.07475 0.08873 1 h-lim-p 0.0003 0.0021 211.3501 2220.406579 9 0.0001 42 | 0/8 2 h-lim-p 0.0001 0.0006 70.6974 2220.184427 0 0.0001 55 | 0/8 3 h-lim-p 0.0004 0.0028 12.4435 2220.176352 5 0.0001 81 | 0/8 4 h-lim-p 0.0004 0.0336 3.2916 2220.175790 4 0.0001 102 | 0/8 5 h-lim-p 0.0003 0.0994 1.1138 2220.175710 1 0.0001 116 | 0/8 6 h-lim-p 0.0018 0.9869 0.0826 2220.175632 1 0.0022 130 | 0/8 7 h-lim-p 0.0006 0.2765 0.3076 2220.175071 0 0.0012 151 | 0/8 8 h-lim-p 0.0011 0.5875 0.3325 2220.148489 0 0.0088 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 2220.146398 3 1.0483 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2220.146397 0 1.0938 221 | 0/8 11 h-lim-p 1.6925 20.0000 0.0001 2220.146397 0 1.4809 241 | 0/8 12 h-lim-p 1.0147 20.0000 0.0001 2220.146397 0 3.0440 262 | 0/8 13 h-lim-p 0.0626 3.8130 0.0051 2220.146397 0 0.0007 288 | 0/8 14 h-lim-p 0.0003 1.5760 0.0124 2220.146397 0 0.0003 308 | 0/8 15 h-lim-p 0.0000 0.0432 0.4534 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0048 | 0/8 17 h-lim-p 0.0000 20.0000 0.0048 Out... lnL = -2220.146397 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2220.146397 Node 7: lnL = -2220.146397 Node 8: lnL = -2220.146397 Node 9: lnL = -2220.146397 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 432 Sequential format.. Reading seq # 1: YCL009C_Sbay Reading seq # 2: YCL009C_Scer Reading seq # 3: YCL009C_Skud Reading seq # 4: YCL009C_Smik Reading seq # 5: YCL009C_Spar Sequences read.. Counting patterns.. # site patterns = 106 Counting frequencies.. 120 bytes for distance 16960 bytes for lkl0 13568 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.023730 0.061499 0.010378 0.056978 0.043429 0.090430 0.048193 0.102776 lnL0 = -1356.652992 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1356.652992 x= 0.02373 0.06150 0.01038 0.05698 0.04343 0.09043 0.04819 0.10278 1 h-lim-p 0.0002 0.0014 231.5579 1355.365906 8 0.0001 39 | 0/8 2 h-lim-p 0.0002 0.0015 58.8605 1355.067472 4 0.0002 59 | 0/8 3 h-lim-p 0.0005 0.0042 18.9290 1355.038608 7 0.0002 88 | 0/8 4 h-lim-p 0.0004 0.0082 8.2360 1355.031909 6 0.0002 115 | 0/8 5 h-lim-p 0.0012 0.0383 1.6763 1355.031477 4 0.0003 137 | 0/8 6 h-lim-p 0.0021 0.3518 0.2592 1355.031469 1 0.0002 153 | 0/8 7 h-lim-p 0.0314 20.0000 0.0019 1355.031226 0 0.2514 176 | 0/8 8 h-lim-p 0.0017 0.0975 0.2831 1355.029568 1 0.0021 198 | 0/8 9 h-lim-p 1.1506 20.0000 0.0005 1355.029495 2 1.0068 222 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1355.029494 0 1.0938 242 | 0/8 11 h-lim-p 0.9868 20.0000 0.0000 1355.029494 0 0.8634 262 | 0/8 12 h-lim-p 0.6960 20.0000 0.0000 1355.029494 0 0.0014 290 | 0/8 13 h-lim-p 0.0003 20.0000 0.0002 1355.029494 0 0.0000 312 | 0/8 14 h-lim-p 0.0001 20.0000 0.0001 1355.029494 0 0.0000 343 | 0/8 15 h-lim-p 0.0000 20.0000 0.0011 1355.029494 0 0.0000 373 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 1355.029494 0 0.0051 402 | 0/8 17 h-lim-p 0.0111 20.0000 0.0001 1355.029494 0 0.0000 434 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 1355.029494 0 0.0051 463 | 0/8 19 h-lim-p 0.0016 20.0000 0.0002 1355.029494 0 0.0014 483 | 0/8 20 h-lim-p 0.0007 20.0000 0.0004 1355.029494 0 0.0000 511 | 0/8 21 h-lim-p 0.0000 13.3305 0.0026 1355.029494 0 0.0006 537 | 0/8 22 h-lim-p 0.1238 20.0000 0.0000 1355.029494 0 0.0001 567 | 0/8 23 h-lim-p 0.0000 3.8415 0.0104 1355.029494 0 0.0001 590 | 0/8 24 h-lim-p 0.0328 20.0000 0.0000 1355.029494 0 0.0008 615 | 0/8 25 h-lim-p 0.0005 20.0000 0.0000 1355.029494 0 0.0001 637 | 0/8 26 h-lim-p 0.0001 20.0000 0.0000 1355.029494 0 0.0001 657 | 0/8 27 h-lim-p 0.0000 20.0000 0.0001 1355.029494 0 0.0000 691 | 0/8 28 h-lim-p 0.0000 20.0000 0.0055 | 0/8 29 h-lim-p 0.0000 20.0000 0.0055 Out... lnL = -1355.029494 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1355.029494 Node 7: lnL = -1355.029494 Node 8: lnL = -1355.029494 Node 9: lnL = -1355.029494 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 587 Sequential format.. Reading seq # 1: YCL014W_Sbay Reading seq # 2: YCL014W_Scer Reading seq # 3: YCL014W_Skud Reading seq # 4: YCL014W_Smik Reading seq # 5: YCL014W_Spar Sequences read.. Counting patterns.. # site patterns = 201 Counting frequencies.. 120 bytes for distance 32160 bytes for lkl0 25728 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.051454 0.064247 0.036064 0.135968 0.093979 0.179319 0.156724 0.215712 lnL0 = -2495.718052 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2495.718052 x= 0.05145 0.06425 0.03606 0.13597 0.09398 0.17932 0.15672 0.21571 1 h-lim-p 0.0014 0.0110 111.6264 2494.841733 3 0.0002 30 | 0/8 2 h-lim-p 0.0013 0.0114 13.3715 2494.808614 7 0.0004 60 | 0/8 3 h-lim-p 0.0020 0.0778 2.5170 2494.807681 4 0.0003 85 | 0/8 4 h-lim-p 0.0020 0.5650 0.3948 2494.807644 1 0.0005 100 | 0/8 5 h-lim-p 0.0024 2.5399 0.0792 2494.807643 0 0.0005 121 | 0/8 6 h-lim-p 0.0022 5.6771 0.0191 2494.807643 0 0.0010 141 | 0/8 7 h-lim-p 0.0061 20.0000 0.0030 2494.807637 0 0.0242 163 | 0/8 8 h-lim-p 0.0042 3.2762 0.0175 2494.807489 0 0.0169 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2494.807485 1 0.9961 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2494.807485 0 2.1875 227 | 0/8 11 h-lim-p 0.4187 20.0000 0.0001 2494.807485 0 0.0008 255 | 0/8 12 h-lim-p 0.0002 20.0000 0.0004 .. | 0/8 13 h-lim-p 0.0000 20.0000 0.0009 2494.807485 0 0.0002 317 | 0/8 14 h-lim-p 0.0014 20.0000 0.0001 2494.807485 0 0.0000 354 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 2494.807485 0 0.0000 377 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 2494.807485 0 0.0000 404 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 | 0/8 19 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -2494.807485 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2494.807485 Node 7: lnL = -2494.807485 Node 8: lnL = -2494.807485 Node 9: lnL = -2494.807485 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 584 Sequential format.. Reading seq # 1: YCL016C_Sbay Reading seq # 2: YCL016C_Scer Reading seq # 3: YCL016C_Skud Reading seq # 4: YCL016C_Smik Reading seq # 5: YCL016C_Spar Sequences read.. Counting patterns.. # site patterns = 218 Counting frequencies.. 120 bytes for distance 34880 bytes for lkl0 27904 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.030776 0.125331 0.030592 0.129867 0.102750 0.186349 0.136779 0.201412 lnL0 = -2515.779080 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2515.779080 x= 0.03078 0.12533 0.03059 0.12987 0.10275 0.18635 0.13678 0.20141 1 h-lim-p 0.0032 0.8219 124.9004 2514.703585 8 0.0002 40 | 0/8 2 h-lim-p 0.0015 0.0122 12.9095 2514.674201 2 0.0003 57 | 0/8 3 h-lim-p 0.0009 0.0580 4.9160 2514.669203 4 0.0005 78 | 0/8 4 h-lim-p 0.0070 0.8250 0.3284 2514.669182 0 0.0004 93 | 0/8 5 h-lim-p 0.0021 3.8889 0.0694 2514.669180 0 0.0005 114 | 0/8 6 h-lim-p 0.0024 5.8968 0.0132 2514.669180 0 0.0005 135 | 0/8 7 h-lim-p 0.0084 20.0000 0.0008 2514.669180 0 0.0337 157 | 0/8 8 h-lim-p 0.0023 17.5997 0.0119 2514.669161 0 0.0092 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2514.669160 0 1.0938 199 | 0/8 10 h-lim-p 1.6432 20.0000 0.0000 2514.669160 0 1.4378 219 | 0/8 11 h-lim-p 1.3201 20.0000 0.0000 2514.669160 0 1.9802 239 | 0/8 12 h-lim-p 0.2030 20.0000 0.0003 2514.669160 0 0.0014 265 | 0/8 13 h-lim-p 0.0005 20.0000 0.0008 2514.669160 0 0.0000 288 | 0/8 14 h-lim-p 0.0002 20.0000 0.0001 2514.669160 0 0.0000 319 | 0/8 15 h-lim-p 0.0000 20.0000 0.0007 2514.669160 0 0.0006 345 | 0/8 16 h-lim-p 0.0024 20.0000 0.0002 2514.669160 0 0.0000 378 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 2514.669160 0 0.0000 401 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 2514.669160 0 0.0000 421 | 0/8 19 h-lim-p 0.0000 20.0000 0.0002 2514.669160 0 0.0000 441 | 0/8 20 h-lim-p 0.0000 17.4475 0.0026 2514.669160 0 0.0000 467 | 0/8 21 h-lim-p 0.0000 20.0000 0.0019 2514.669160 0 0.0000 487 | 0/8 22 h-lim-p 0.0002 20.0000 0.0001 2514.669160 0 0.0001 507 | 0/8 23 h-lim-p 0.0013 20.0000 0.0000 2514.669160 0 0.0000 546 Out... lnL = -2514.669160 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2514.669160 Node 7: lnL = -2514.669160 Node 8: lnL = -2514.669160 Node 9: lnL = -2514.669160 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 382 Sequential format.. Reading seq # 1: YCL017C_Sbay Reading seq # 2: YCL017C_Scer Reading seq # 3: YCL017C_Skud Reading seq # 4: YCL017C_Smik Reading seq # 5: YCL017C_Spar Sequences read.. Counting patterns.. # site patterns = 173 Counting frequencies.. 120 bytes for distance 27680 bytes for lkl0 22144 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.004627 0.049558 0.112099 0.116082 0.104769 0.214239 0.196299 0.181668 lnL0 = -1663.709710 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1663.709710 x= 0.00463 0.04956 0.11210 0.11608 0.10477 0.21424 0.19630 0.18167 1 h-lim-p 0.0011 0.0086 121.7553 1661.171704 9 0.0004 42 | 0/8 2 h-lim-p 0.0001 0.0009 19.5934 1661.064939 0 0.0007 56 | 0/8 3 h-lim-p 0.0008 0.0066 3.8183 1661.060919 5 0.0006 81 | 0/8 4 h-lim-p 0.0015 0.2406 1.4040 1661.060373 3 0.0006 99 | 0/8 5 h-lim-p 0.0024 0.0298 0.3690 1661.060315 3 0.0009 117 | 0/8 6 h-lim-p 0.0044 3.2514 0.0754 1661.060306 2 0.0014 142 | 0/8 7 h-lim-p 0.0152 20.0000 0.0069 1661.058530 0 0.2438 166 | 0/8 8 h-lim-p 0.0024 1.1242 0.7107 1661.057296 2 0.0022 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1661.057255 3 1.4660 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1661.057254 0 1.0938 239 | 0/8 11 h-lim-p 2.4265 20.0000 0.0000 1661.057254 0 1.2132 259 | 0/8 12 h-lim-p 0.8199 20.0000 0.0000 1661.057254 0 0.0769 282 | 0/8 13 h-lim-p 0.0008 1.3608 0.0031 1661.057254 0 0.0007 302 | 0/8 14 h-lim-p 0.0004 0.7958 0.0054 1661.057254 0 0.0000 326 | 0/8 15 h-lim-p 0.0002 20.0000 0.0003 1661.057254 0 0.0000 349 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 1661.057254 0 0.0000 369 | 0/8 17 h-lim-p 0.0002 20.0000 0.0000 1661.057254 0 0.0002 389 | 0/8 18 h-lim-p 0.0001 20.0000 0.0000 1661.057254 0 0.0000 417 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 1661.057254 0 0.0000 445 Out... lnL = -1661.057254 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1661.057254 Node 7: lnL = -1661.057254 Node 8: lnL = -1661.057254 Node 9: lnL = -1661.057254 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 873 Sequential format.. Reading seq # 1: YCL021W-A_Sbay Reading seq # 2: YCL021W-A_Scer Reading seq # 3: YCL021W-A_Skud Reading seq # 4: YCL021W-A_Smik Reading seq # 5: YCL021W-A_Spar Sequences read.. Counting patterns.. # site patterns = 467 Counting frequencies.. 120 bytes for distance 74720 bytes for lkl0 59776 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.136849 0.000060 0.029705 0.390437 0.258308 0.442349 0.485820 0.497078 lnL0 = -4858.527349 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4858.527349 x= 0.13685 0.00006 0.02971 0.39044 0.25831 0.44235 0.48582 0.49708 1 h-lim-p 0.0029 0.0230 44.1240 4857.934696 6 0.0005 35 | 0/8 2 h-lim-p 0.0008 0.0064 27.5995 4857.698732 5 0.0008 57 | 0/8 3 h-lim-p 0.0031 0.0422 7.1166 4857.673586 5 0.0011 80 | 0/8 4 h-lim-p 0.0075 0.3685 1.0432 4857.672557 4 0.0019 101 | 0/8 5 h-lim-p 0.0063 1.8983 0.3142 4857.672458 3 0.0020 121 | 0/8 6 h-lim-p 0.0042 0.6331 0.1528 4857.672431 1 0.0018 143 | 0/8 7 h-lim-p 0.0068 6.9979 0.0414 4857.672287 0 0.0135 164 | 0/8 8 h-lim-p 0.0106 1.3557 0.0528 4857.666822 0 0.0636 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 4857.666789 1 0.9961 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4857.666789 0 1.0938 228 | 0/8 11 h-lim-p 1.2776 20.0000 0.0000 4857.666789 0 1.1179 248 | 0/8 12 h-lim-p 0.7560 20.0000 0.0000 4857.666789 0 0.0472 271 | 0/8 13 h-lim-p 0.0014 20.0000 0.0004 4857.666789 0 0.0000 305 | 0/8 14 h-lim-p 0.0003 20.0000 0.0000 4857.666789 0 0.0000 328 Out... lnL = -4857.666789 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4857.666789 Node 7: lnL = -4857.666789 Node 8: lnL = -4857.666789 Node 9: lnL = -4857.666789 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 856 Sequential format.. Reading seq # 1: YCL024W_Sbay Reading seq # 2: YCL024W_Scer Reading seq # 3: YCL024W_Skud Reading seq # 4: YCL024W_Smik Reading seq # 5: YCL024W_Spar Sequences read.. Counting patterns.. # site patterns = 337 Counting frequencies.. 120 bytes for distance 53920 bytes for lkl0 43136 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.172614 0.000060 0.100929 0.125947 0.119749 0.270993 0.312694 0.428147 lnL0 = -3914.994589 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3914.994589 x= 0.17261 0.00006 0.10093 0.12595 0.11975 0.27099 0.31269 0.42815 1 h-lim-p 0.0004 0.0035 63.8194 3914.113831 6 0.0004 33 | 0/8 2 h-lim-p 0.0010 0.0186 24.9175 3913.959354 7 0.0006 64 | 0/8 3 h-lim-p 0.0006 0.0137 22.6110 3913.902328 7 0.0004 95 | 0/8 4 h-lim-p 0.0008 0.0374 10.7897 3913.881348 6 0.0005 122 | 0/8 5 h-lim-p 0.0021 0.1541 2.6935 3913.879097 5 0.0007 146 | 0/8 6 h-lim-p 0.0009 0.2000 2.0000 3913.877890 2 0.0009 162 | 0/8 7 h-lim-p 0.0082 1.9426 0.2122 3913.877857 2 0.0011 180 | 0/8 8 h-lim-p 0.0720 20.0000 0.0032 3913.871186 0 0.8635 203 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3913.871145 1 0.9961 225 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3913.871145 0 1.0938 245 | 0/8 11 h-lim-p 1.4958 20.0000 0.0000 3913.871145 0 0.0935 268 | 0/8 12 h-lim-p 0.0388 20.0000 0.0000 3913.871145 0 0.0097 289 | 0/8 13 h-lim-p 0.0050 20.0000 0.0000 3913.871145 0 0.0012 310 | 0/8 14 h-lim-p 0.0013 20.0000 0.0000 3913.871145 0 0.0000 347 | 0/8 15 h-lim-p 0.0000 20.0000 0.0008 | 0/8 16 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -3913.871145 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3913.871145 Node 7: lnL = -3913.871145 Node 8: lnL = -3913.871145 Node 9: lnL = -3913.871145 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 972 Sequential format.. Reading seq # 1: YCL025C_Sbay Reading seq # 2: YCL025C_Scer Reading seq # 3: YCL025C_Skud Reading seq # 4: YCL025C_Smik Reading seq # 5: YCL025C_Spar Sequences read.. Counting patterns.. # site patterns = 301 Counting frequencies.. 120 bytes for distance 48160 bytes for lkl0 38528 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.177757 0.040629 0.046024 0.080088 0.094318 0.213081 0.189183 0.390688 lnL0 = -4102.071861 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4102.071861 x= 0.17776 0.04063 0.04602 0.08009 0.09432 0.21308 0.18918 0.39069 1 h-lim-p 0.0017 0.5797 221.2616 4099.085603 9 0.0001 46 | 0/8 2 h-lim-p 0.0006 0.0047 44.1071 4098.718678 7 0.0004 74 | 0/8 3 h-lim-p 0.0003 0.0048 49.3208 4098.526114 7 0.0003 99 | 0/8 4 h-lim-p 0.0017 0.0142 8.2221 4098.519282 5 0.0002 124 | 0/8 5 h-lim-p 0.0032 0.4401 0.5618 4098.519219 2 0.0004 142 | 0/8 6 h-lim-p 0.0007 0.4115 0.3120 4098.519194 1 0.0006 164 | 0/8 7 h-lim-p 0.0027 4.3615 0.0715 4098.519192 1 0.0007 187 | 0/8 8 h-lim-p 0.0448 20.0000 0.0011 4098.517609 0 0.7172 211 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4098.517581 1 0.9961 233 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4098.517581 0 1.0938 253 | 0/8 11 h-lim-p 1.1275 20.0000 0.0000 4098.517581 0 4.5100 275 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4098.517581 0 0.0000 324 Out... lnL = -4098.517581 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4098.517581 Node 7: lnL = -4098.517581 Node 8: lnL = -4098.517581 Node 9: lnL = -4098.517581 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 479 Sequential format.. Reading seq # 1: YCL027W_Sbay Reading seq # 2: YCL027W_Scer Reading seq # 3: YCL027W_Skud Reading seq # 4: YCL027W_Smik Reading seq # 5: YCL027W_Spar Sequences read.. Counting patterns.. # site patterns = 191 Counting frequencies.. 120 bytes for distance 30560 bytes for lkl0 24448 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.050445 0.047096 0.049199 0.118614 0.098541 0.216212 0.193776 0.225350 lnL0 = -2112.454196 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2112.454196 x= 0.05045 0.04710 0.04920 0.11861 0.09854 0.21621 0.19378 0.22535 1 h-lim-p 0.0021 0.9258 142.1373 2110.334086 8 0.0002 41 | 0/8 2 h-lim-p 0.0011 0.0088 20.1496 2110.205183 8 0.0006 74 | 0/8 3 h-lim-p 0.0015 0.0260 8.6840 2110.189674 6 0.0005 100 | 0/8 4 h-lim-p 0.0020 0.1022 2.0773 2110.188766 3 0.0005 119 | 0/8 5 h-lim-p 0.0045 1.2779 0.2091 2110.188752 2 0.0007 138 | 0/8 6 h-lim-p 0.0053 8.0095 0.0292 2110.188750 1 0.0013 161 | 0/8 7 h-lim-p 0.0030 18.7031 0.0129 2110.188744 0 0.0059 182 | 0/8 8 h-lim-p 0.0066 20.0000 0.0116 2110.188163 0 0.0529 205 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2110.188160 1 0.9961 227 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2110.188160 0 1.0938 247 | 0/8 11 h-lim-p 1.2010 20.0000 0.0000 2110.188160 0 4.8040 269 | 0/8 12 h-lim-p 0.0407 20.0000 0.0018 2110.188160 0 0.0204 289 | 0/8 13 h-lim-p 0.0061 13.1709 0.0061 2110.188160 0 0.0015 310 | 0/8 14 h-lim-p 0.0009 7.8550 0.0102 2110.188160 0 0.0009 330 | 0/8 15 h-lim-p 0.0002 1.4420 0.0554 2110.188160 0 0.0000 364 | 0/8 16 h-lim-p 0.0006 20.0000 0.0000 2110.188160 0 0.0000 398 Out... lnL = -2110.188160 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2110.188160 Node 7: lnL = -2110.188160 Node 8: lnL = -2110.188160 Node 9: lnL = -2110.188160 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 232 Sequential format.. Reading seq # 1: YCL028W_Sbay Reading seq # 2: YCL028W_Scer Reading seq # 3: YCL028W_Skud Reading seq # 4: YCL028W_Smik Reading seq # 5: YCL028W_Spar Sequences read.. Counting patterns.. # site patterns = 86 Counting frequencies.. 120 bytes for distance 13760 bytes for lkl0 11008 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.002881 0.073308 0.061216 0.086180 0.086881 0.175231 0.079435 0.124154 lnL0 = -914.732191 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 914.732191 x= 0.00288 0.07331 0.06122 0.08618 0.08688 0.17523 0.07943 0.12415 1 h-lim-p 0.0000 0.0002 56.5281 914.216409 m 0.0002 22 | 1/8 2 h-lim-p 0.0013 0.0235 8.8781 914.186654 7 0.0008 53 | 1/8 3 h-lim-p 0.0020 0.0659 3.4655 914.182884 4 0.0007 75 | 1/8 4 h-lim-p 0.0027 0.2990 0.8788 914.182230 4 0.0012 94 | 1/8 5 h-lim-p 0.0041 1.1949 0.2513 914.180240 0 0.0062 113 | 1/8 6 h-lim-p 0.0065 1.1245 0.2361 913.962067 0 0.0785 135 | 0/8 7 h-lim-p 0.0062 0.0882 2.9735 913.958778 2 0.0007 160 | 0/8 8 h-lim-p 0.0079 2.2673 0.2753 913.958749 2 0.0008 178 | 0/8 9 h-lim-p 0.0019 1.5881 0.1114 913.958737 2 0.0015 202 | 0/8 10 h-lim-p 0.0479 2.4841 0.0034 913.955584 0 0.7663 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0005 913.955430 2 0.9961 250 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 913.955430 0 1.0938 270 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 913.955430 0 0.0024 299 Out... lnL = -913.955430 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -913.955430 Node 7: lnL = -913.955430 Node 8: lnL = -913.955430 Node 9: lnL = -913.955430 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 230 Sequential format.. Reading seq # 1: YCL029C_Sbay Reading seq # 2: YCL029C_Scer Reading seq # 3: YCL029C_Skud Reading seq # 4: YCL029C_Smik Reading seq # 5: YCL029C_Spar Sequences read.. Counting patterns.. # site patterns = 89 Counting frequencies.. 120 bytes for distance 14240 bytes for lkl0 11392 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.026701 0.024207 0.057549 0.081835 0.091226 0.178898 0.121326 0.150657 lnL0 = -931.790020 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 931.790020 x= 0.02670 0.02421 0.05755 0.08184 0.09123 0.17890 0.12133 0.15066 1 h-lim-p 0.0010 0.0079 104.6255 930.636840 6 0.0003 36 | 0/8 2 h-lim-p 0.0004 0.0033 12.6882 930.590666 0 0.0008 49 | 0/8 3 h-lim-p 0.0042 0.0898 2.4881 930.587739 2 0.0010 66 | 0/8 4 h-lim-p 0.0049 0.2647 0.5005 930.587649 3 0.0007 88 | 0/8 5 h-lim-p 0.0023 1.1573 0.1579 930.587632 2 0.0011 112 | 0/8 6 h-lim-p 0.0028 2.2491 0.0606 930.587603 2 0.0031 137 | 0/8 7 h-lim-p 0.0078 14.3790 0.0244 930.584006 0 0.0935 160 | 0/8 8 h-lim-p 0.0014 0.0685 1.5726 930.582847 4 0.0007 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 930.582813 2 0.9961 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 930.582813 0 2.1875 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 930.582813 0 1.0938 246 | 0/8 12 h-lim-p 0.5167 20.0000 0.0000 930.582813 0 2.0670 268 | 0/8 13 h-lim-p 2.4368 20.0000 0.0000 930.582813 0 1.2184 288 | 0/8 14 h-lim-p 0.1938 20.0000 0.0001 930.582813 0 0.0003 317 | 0/8 15 h-lim-p 0.0000 4.0747 0.0074 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -930.582813 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -930.582813 Node 7: lnL = -930.582813 Node 8: lnL = -930.582813 Node 9: lnL = -930.582813 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 280 Sequential format.. Reading seq # 1: YCL030C_Sbay Reading seq # 2: YCL030C_Scer Reading seq # 3: YCL030C_Skud Reading seq # 4: YCL030C_Smik Reading seq # 5: YCL030C_Spar Sequences read.. Counting patterns.. # site patterns = 80 Counting frequencies.. 120 bytes for distance 12800 bytes for lkl0 10240 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.020669 0.034249 0.030641 0.028660 0.031614 0.103178 0.072325 0.092151 lnL0 = -873.322700 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 873.322700 x= 0.02067 0.03425 0.03064 0.02866 0.03161 0.10318 0.07233 0.09215 1 h-lim-p 0.0003 0.0020 79.9452 872.798156 9 0.0002 46 | 0/8 2 h-lim-p 0.0007 0.0056 13.2458 872.771462 5 0.0003 67 | 0/8 3 h-lim-p 0.0007 0.0239 5.5866 872.768885 4 0.0002 88 | 0/8 4 h-lim-p 0.0004 0.0290 2.4920 872.768286 5 0.0002 111 | 0/8 5 h-lim-p 0.0006 0.1688 1.0063 872.768177 2 0.0003 127 | 0/8 6 h-lim-p 0.0008 0.3337 0.3320 872.768163 2 0.0002 144 | 0/8 7 h-lim-p 0.0037 1.4930 0.0220 872.768163 0 0.0004 166 | 0/8 8 h-lim-p 0.1058 20.0000 0.0001 872.768150 0 1.2697 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 872.768150 0 1.0938 209 | 0/8 10 h-lim-p 1.5057 20.0000 0.0000 872.768150 0 3.0114 230 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 872.768150 0 0.1562 253 | 0/8 12 h-lim-p 0.0036 20.0000 0.0000 872.768150 0 0.0014 274 | 0/8 13 h-lim-p 0.0006 20.0000 0.0001 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0055 872.768150 0 0.0000 347 | 0/8 15 h-lim-p 0.0000 19.8789 0.0033 872.768150 0 0.0003 372 | 0/8 16 h-lim-p 0.0007 20.0000 0.0015 872.768150 0 0.0000 405 | 0/8 17 h-lim-p 0.0000 20.0000 0.0014 872.768150 0 0.0000 432 | 0/8 18 h-lim-p 0.0000 4.7668 0.0066 872.768150 0 0.0000 459 | 0/8 19 h-lim-p 0.0000 20.0000 0.0016 872.768150 0 0.0002 483 | 0/8 20 h-lim-p 0.0049 20.0000 0.0001 872.768150 0 0.0049 503 | 0/8 21 h-lim-p 0.0056 20.0000 0.0000 872.768150 0 0.0000 531 | 0/8 22 h-lim-p 0.0000 20.0000 0.0002 872.768150 0 0.0000 562 | 0/8 23 h-lim-p 0.0000 20.0000 0.0062 872.768150 0 0.0000 594 | 0/8 24 h-lim-p 0.0000 20.0000 0.0007 .. | 0/8 25 h-lim-p 0.0000 20.0000 0.0062 | 0/8 26 h-lim-p 0.0000 20.0000 0.0062 Out... lnL = -872.768150 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -872.768150 Node 7: lnL = -872.768150 Node 8: lnL = -872.768150 Node 9: lnL = -872.768150 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 403 Sequential format.. Reading seq # 1: YCL031C_Sbay Reading seq # 2: YCL031C_Scer Reading seq # 3: YCL031C_Skud Reading seq # 4: YCL031C_Smik Reading seq # 5: YCL031C_Spar Sequences read.. Counting patterns.. # site patterns = 160 Counting frequencies.. 120 bytes for distance 25600 bytes for lkl0 20480 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.094076 0.023461 0.090181 0.116939 0.108677 0.200862 0.159081 0.274318 lnL0 = -1735.116929 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1735.116929 x= 0.09408 0.02346 0.09018 0.11694 0.10868 0.20086 0.15908 0.27432 1 h-lim-p 0.0085 2.1331 63.7743 1734.446730 6 0.0003 38 | 0/8 2 h-lim-p 0.0005 0.0043 12.1892 1734.395028 0 0.0011 51 | 0/8 3 h-lim-p 0.0034 0.0274 3.6058 1734.390390 3 0.0008 70 | 0/8 4 h-lim-p 0.0021 0.1945 1.3037 1734.390027 2 0.0005 87 | 0/8 5 h-lim-p 0.0061 1.2494 0.0999 1734.390001 2 0.0024 103 | 0/8 6 h-lim-p 0.0088 8.1548 0.0268 1734.389559 0 0.0353 125 | 0/8 7 h-lim-p 0.0030 0.7741 0.3173 1734.384132 0 0.0119 147 | 0/8 8 h-lim-p 0.0160 1.6761 0.2364 1734.384103 2 0.0010 174 | 0/8 9 h-lim-p 0.3098 20.0000 0.0008 1734.383759 0 1.2394 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 1734.383738 2 0.9961 220 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1734.383738 0 2.1875 240 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1734.383738 0 1.0938 260 | 0/8 13 h-lim-p 0.3713 20.0000 0.0000 1734.383738 0 2.9707 283 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1734.383738 0 0.5469 304 | 0/8 15 h-lim-p 0.0508 20.0000 0.0000 1734.383738 0 0.0508 324 | 0/8 16 h-lim-p 0.0146 20.0000 0.0001 1734.383738 0 0.0000 363 | 0/8 17 h-lim-p 0.0000 20.0000 0.0005 | 0/8 18 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -1734.383738 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1734.383738 Node 7: lnL = -1734.383738 Node 8: lnL = -1734.383738 Node 9: lnL = -1734.383738 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 195 Sequential format.. Reading seq # 1: YCL032W_Sbay Reading seq # 2: YCL032W_Scer Reading seq # 3: YCL032W_Skud Reading seq # 4: YCL032W_Smik Reading seq # 5: YCL032W_Spar Sequences read.. Counting patterns.. # site patterns = 70 Counting frequencies.. 120 bytes for distance 11200 bytes for lkl0 8960 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.057237 0.052321 0.019009 0.060114 0.049420 0.077445 0.177849 0.169161 lnL0 = -676.338007 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 676.338007 x= 0.05724 0.05232 0.01901 0.06011 0.04942 0.07745 0.17785 0.16916 1 h-lim-p 0.0003 0.0028 93.9033 675.242463 6 0.0003 34 | 0/8 2 h-lim-p 0.0005 0.0039 33.8895 674.964263 1 0.0006 48 | 0/8 3 h-lim-p 0.0018 0.0232 11.6506 674.939010 5 0.0004 70 | 0/8 4 h-lim-p 0.0016 0.0252 3.1937 674.936304 5 0.0006 94 | 0/8 5 h-lim-p 0.0022 0.2394 0.8296 674.935723 4 0.0018 115 | 0/8 6 h-lim-p 0.0116 2.5522 0.1285 674.935705 3 0.0019 144 | 0/8 7 h-lim-p 0.0510 20.0000 0.0047 674.935374 0 0.2040 166 | 0/8 8 h-lim-p 0.0023 0.2751 0.4172 674.933420 0 0.0046 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 674.933260 2 1.0938 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 674.933257 0 1.0938 231 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 674.933257 0 1.0938 251 | 0/8 12 h-lim-p 1.3141 20.0000 0.0000 674.933257 0 1.9712 271 | 0/8 13 h-lim-p 1.5138 20.0000 0.0000 674.933257 0 1.3246 291 | 0/8 14 h-lim-p 0.0953 20.0000 0.0001 674.933257 0 0.0000 333 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 674.933257 0 0.0000 363 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 674.933257 0 0.0000 386 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 674.933257 0 0.0205 417 | 0/8 18 h-lim-p 0.0801 20.0000 0.0000 674.933257 0 0.0000 450 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 674.933257 0 0.0000 470 | 0/8 20 h-lim-p 0.0000 20.0000 0.0011 674.933257 0 0.0000 495 | 0/8 21 h-lim-p 0.0000 20.0000 0.0007 674.933257 0 0.0003 520 | 0/8 22 h-lim-p 0.0009 20.0000 0.0002 674.933257 0 0.0000 545 | 0/8 23 h-lim-p 0.0002 20.0000 0.0000 674.933257 0 0.0000 577 | 0/8 24 h-lim-p 0.0000 20.0000 0.0020 | 0/8 25 h-lim-p 0.0000 20.0000 0.0020 Out... lnL = -674.933257 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -674.933257 Node 7: lnL = -674.933257 Node 8: lnL = -674.933257 Node 9: lnL = -674.933257 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 536 Sequential format.. Reading seq # 1: YCL034W_Sbay Reading seq # 2: YCL034W_Scer Reading seq # 3: YCL034W_Skud Reading seq # 4: YCL034W_Smik Reading seq # 5: YCL034W_Spar Sequences read.. Counting patterns.. # site patterns = 235 Counting frequencies.. 120 bytes for distance 37600 bytes for lkl0 30080 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.032199 0.149699 0.140264 0.124837 0.084649 0.202547 0.222757 0.248705 lnL0 = -2471.720371 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2471.720371 x= 0.03220 0.14970 0.14026 0.12484 0.08465 0.20255 0.22276 0.24871 1 h-lim-p 0.0065 0.0517 46.1510 2471.138575 6 0.0006 38 | 0/8 2 h-lim-p 0.0015 0.0119 11.2580 2471.106143 6 0.0005 66 | 0/8 3 h-lim-p 0.0007 0.0187 8.6328 2471.094783 6 0.0004 93 | 0/8 4 h-lim-p 0.0029 0.2711 1.3095 2471.094215 2 0.0007 110 | 0/8 5 h-lim-p 0.0027 0.7226 0.3354 2471.094162 2 0.0010 126 | 0/8 6 h-lim-p 0.0085 4.8942 0.0405 2471.094162 0 0.0009 148 | 0/8 7 h-lim-p 0.0051 17.9355 0.0074 2471.094161 0 0.0022 168 | 0/8 8 h-lim-p 0.0406 20.0000 0.0004 2471.094131 0 0.6488 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2471.094128 0 1.0938 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2471.094128 0 1.0938 232 | 0/8 11 h-lim-p 1.1844 20.0000 0.0000 2471.094128 0 1.7767 252 | 0/8 12 h-lim-p 0.9100 20.0000 0.0000 2471.094128 0 1.8199 273 | 0/8 13 h-lim-p 0.0005 3.2374 0.1080 2471.094128 0 0.0005 293 | 0/8 14 h-lim-p 0.0003 2.1230 0.1646 2471.094128 0 0.0003 313 | 0/8 15 h-lim-p 0.0008 4.8821 0.0716 2471.094128 0 0.0000 339 | 0/8 16 h-lim-p 0.0003 20.0000 0.0017 2471.094128 0 0.0001 359 | 0/8 17 h-lim-p 0.0000 7.7227 0.0056 2471.094128 0 0.0000 387 | 0/8 18 h-lim-p 0.0004 20.0000 0.0000 2471.094128 0 0.0000 415 Out... lnL = -2471.094128 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2471.094128 Node 7: lnL = -2471.094128 Node 8: lnL = -2471.094128 Node 9: lnL = -2471.094128 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 532 Sequential format.. Reading seq # 1: YCL035C_Sbay Reading seq # 2: YCL035C_Scer Reading seq # 3: YCL035C_Skud Reading seq # 4: YCL035C_Smik Reading seq # 5: YCL035C_Spar Sequences read.. Counting patterns.. # site patterns = 234 Counting frequencies.. 120 bytes for distance 37440 bytes for lkl0 29952 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.041169 0.086405 0.241251 0.137193 0.072293 0.191781 0.204698 0.266390 lnL0 = -2481.665373 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2481.665373 x= 0.04117 0.08640 0.24125 0.13719 0.07229 0.19178 0.20470 0.26639 1 h-lim-p 0.0012 0.0095 36.7843 2481.354844 5 0.0005 32 | 0/8 2 h-lim-p 0.0009 0.0081 19.8416 2481.295413 5 0.0004 55 | 0/8 3 h-lim-p 0.0013 0.0510 5.7288 2481.283346 6 0.0008 81 | 0/8 4 h-lim-p 0.0026 0.1391 1.7669 2481.282525 2 0.0006 98 | 0/8 5 h-lim-p 0.0152 1.5999 0.0672 2481.282523 0 0.0010 113 | 0/8 6 h-lim-p 0.0036 8.4665 0.0178 2481.282523 0 0.0009 134 | 0/8 7 h-lim-p 0.0153 20.0000 0.0010 2481.282523 0 0.0134 154 | 0/8 8 h-lim-p 0.0150 20.0000 0.0009 2481.282516 0 0.0600 176 | 0/8 9 h-lim-p 0.7068 20.0000 0.0001 2481.282516 0 1.0603 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2481.282516 0 1.0938 216 | 0/8 11 h-lim-p 0.6136 20.0000 0.0000 2481.282516 0 0.1534 237 | 0/8 12 h-lim-p 0.0007 17.4582 0.0035 2481.282516 0 0.0000 271 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 2481.282516 0 0.0000 301 Out... lnL = -2481.282516 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2481.282516 Node 7: lnL = -2481.282516 Node 8: lnL = -2481.282516 Node 9: lnL = -2481.282516 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 271 Sequential format.. Reading seq # 1: YCL036W_Sbay Reading seq # 2: YCL036W_Scer Reading seq # 3: YCL036W_Skud Reading seq # 4: YCL036W_Smik Reading seq # 5: YCL036W_Spar Sequences read.. Counting patterns.. # site patterns = 50 Counting frequencies.. 120 bytes for distance 8000 bytes for lkl0 6400 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.040792 0.065799 0.064610 0.034322 0.028712 0.043471 0.038021 lnL0 = -689.708245 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 689.708245 x= 0.00006 0.04079 0.06580 0.06461 0.03432 0.02871 0.04347 0.03802 1 h-lim-p 0.0000 0.0000 215.1673 689.410027 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0005 92.5409 688.729567 0 0.0002 38 | 1/8 3 h-lim-p 0.0002 0.0018 35.0443 688.601675 4 0.0002 58 | 1/8 4 h-lim-p 0.0002 0.0015 19.7479 688.153496 m 0.0015 70 | 2/8 5 h-lim-p 0.0003 0.0286 4.0276 688.037125 0 0.0035 85 | 2/8 6 h-lim-p 0.0001 0.0012 43.8206 687.136284 m 0.0012 97 | 2/8 7 h-lim-p 0.0000 0.0000 1.6145 h-lim-p: 3.53915990e-19 2.83132792e-18 1.61448245e+00 687.136284 .. | 2/8 8 h-lim-p 0.0000 0.0038 162.3533 685.223831 0 0.0002 121 | 2/8 9 h-lim-p 0.0000 0.0002 17.6516 685.190992 m 0.0002 133 | 3/8 10 h-lim-p 0.0004 0.0084 8.4685 685.186882 6 0.0001 159 | 3/8 11 h-lim-p 0.0022 0.1854 0.5323 685.185809 5 0.0016 183 | 3/8 12 h-lim-p 0.0015 0.4326 0.5900 685.176242 0 0.0044 201 | 3/8 13 h-lim-p 0.0007 0.0377 3.6084 685.171268 5 0.0005 229 | 3/8 14 h-lim-p 2.5000 20.0000 0.0003 685.171063 2 1.0889 245 | 3/8 15 h-lim-p 2.5000 20.0000 0.0000 685.171063 0 1.0938 262 | 3/8 16 h-lim-p 2.5000 20.0000 0.0000 685.171063 0 1.0938 279 | 3/8 17 h-lim-p 2.5000 20.0000 0.0000 685.171063 0 5.0000 297 | 3/8 18 h-lim-p 1.2500 20.0000 0.0000 685.171063 0 0.2734 315 | 3/8 19 h-lim-p 0.3764 20.0000 0.0000 685.171063 0 0.0470 334 | 3/8 20 h-lim-p 0.0494 20.0000 0.0000 685.171063 0 0.0123 352 | 3/8 21 h-lim-p 0.0125 20.0000 0.0000 685.171063 0 0.0031 370 Out... lnL = -685.171063 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -685.171063 Node 7: lnL = -685.171063 Node 8: lnL = -685.171063 Node 9: lnL = -685.171063 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 839 Sequential format.. Reading seq # 1: YCL038C_Sbay Reading seq # 2: YCL038C_Scer Reading seq # 3: YCL038C_Skud Reading seq # 4: YCL038C_Smik Reading seq # 5: YCL038C_Spar Sequences read.. Counting patterns.. # site patterns = 178 Counting frequencies.. 120 bytes for distance 28480 bytes for lkl0 22784 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.042137 0.040315 0.045268 0.043812 0.031962 0.096128 0.104118 0.135424 lnL0 = -2885.277948 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2885.277948 x= 0.04214 0.04031 0.04527 0.04381 0.03196 0.09613 0.10412 0.13542 1 h-lim-p 0.0014 0.0112 121.1154 2884.676862 6 0.0001 36 | 0/8 2 h-lim-p 0.0003 0.0021 26.5836 2884.648268 5 0.0001 60 | 0/8 3 h-lim-p 0.0001 0.0077 16.1400 2884.638157 6 0.0001 86 | 0/8 4 h-lim-p 0.0008 0.0321 2.0569 2884.637967 0 0.0001 100 | 0/8 5 h-lim-p 0.0004 0.2654 0.5615 2884.637952 2 0.0001 117 | 0/8 6 h-lim-p 0.0007 1.5072 0.0728 2884.637952 0 0.0002 138 | 0/8 7 h-lim-p 0.0023 20.0000 0.0051 2884.637952 0 0.0003 160 | 0/8 8 h-lim-p 0.0185 20.0000 0.0001 2884.637951 0 1.1819 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2884.637951 0 1.0938 206 | 0/8 10 h-lim-p 0.4179 20.0000 0.0000 2884.637951 0 0.0033 232 | 0/8 11 h-lim-p 0.0008 20.0000 0.0002 2884.637951 0 0.0004 252 | 0/8 12 h-lim-p 0.0002 20.0000 0.0003 2884.637951 0 0.0000 274 | 0/8 13 h-lim-p 0.0000 20.0000 0.0027 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0047 | 0/8 15 h-lim-p 0.0000 20.0000 0.0047 Out... lnL = -2884.637951 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2884.637951 Node 7: lnL = -2884.637951 Node 8: lnL = -2884.637951 Node 9: lnL = -2884.637951 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 306 Sequential format.. Reading seq # 1: YCL039W_Sbay Reading seq # 2: YCL039W_Scer Reading seq # 3: YCL039W_Skud Reading seq # 4: YCL039W_Smik Reading seq # 5: YCL039W_Spar Sequences read.. Counting patterns.. # site patterns = 136 Counting frequencies.. 120 bytes for distance 21760 bytes for lkl0 17408 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.036856 0.120265 0.055774 0.085603 0.099198 0.238070 0.043072 0.190285 lnL0 = -1046.519600 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1046.519600 x= 0.03686 0.12026 0.05577 0.08560 0.09920 0.23807 0.04307 0.19028 1 h-lim-p 0.0010 0.7865 144.0117 1041.720337 6 0.0006 37 | 0/8 2 h-lim-p 0.0006 0.0052 18.2981 1041.510201 0 0.0013 50 | 0/8 3 h-lim-p 0.0010 0.0082 14.3318 1041.455499 5 0.0008 72 | 0/8 4 h-lim-p 0.0018 0.0953 6.2521 1041.435185 4 0.0014 92 | 0/8 5 h-lim-p 0.0088 0.1673 0.9750 1041.434374 3 0.0018 111 | 0/8 6 h-lim-p 0.0043 0.5914 0.4013 1041.434232 2 0.0020 135 | 0/8 7 h-lim-p 0.0034 0.4242 0.2369 1041.434187 3 0.0018 162 | 0/8 8 h-lim-p 0.2195 20.0000 0.0020 1041.429928 0 1.7557 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0009 1041.429504 2 1.0889 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1041.429504 0 1.0938 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1041.429504 0 1.0938 249 | 0/8 12 h-lim-p 1.2179 20.0000 0.0000 1041.429504 0 0.0381 273 | 0/8 13 h-lim-p 0.0095 20.0000 0.0000 1041.429504 0 0.0042 293 | 0/8 14 h-lim-p 0.0016 20.0000 0.0000 1041.429504 0 0.0007 313 | 0/8 15 h-lim-p 0.0005 20.0000 0.0001 1041.429504 0 0.0000 351 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1041.429504 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1041.429504 Node 7: lnL = -1041.429504 Node 8: lnL = -1041.429504 Node 9: lnL = -1041.429504 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 232 Sequential format.. Reading seq # 1: YCL040W_Sbay Reading seq # 2: YCL040W_Scer Reading seq # 3: YCL040W_Skud Reading seq # 4: YCL040W_Smik Reading seq # 5: YCL040W_Spar Sequences read.. Counting patterns.. # site patterns = 113 Counting frequencies.. 120 bytes for distance 18080 bytes for lkl0 14464 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.087910 0.064322 0.095186 0.046874 0.089150 0.205184 0.206788 0.271761 lnL0 = -966.366518 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 966.366518 x= 0.08791 0.06432 0.09519 0.04687 0.08915 0.20518 0.20679 0.27176 1 h-lim-p 0.0004 0.0034 58.1271 964.560810 0 0.0013 23 | 0/8 2 h-lim-p 0.0006 0.0051 22.0730 964.256974 0 0.0013 36 | 0/8 3 h-lim-p 0.0009 0.0097 29.9979 964.144812 7 0.0005 65 | 0/8 4 h-lim-p 0.0014 0.0169 11.2096 964.114843 2 0.0007 81 | 0/8 5 h-lim-p 0.0039 0.1391 1.9391 964.111078 6 0.0021 106 | 0/8 6 h-lim-p 0.0407 1.0247 0.1002 964.111061 3 0.0015 130 | 0/8 7 h-lim-p 0.0018 1.9322 0.0825 964.110877 0 0.0145 153 | 0/8 8 h-lim-p 0.0253 2.7991 0.0472 964.102732 0 0.1012 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0008 964.102582 4 0.9131 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 964.102582 0 1.0938 224 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 964.102582 0 1.0938 244 | 0/8 12 h-lim-p 1.5315 20.0000 0.0000 964.102582 0 0.0011 274 Out... lnL = -964.102582 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -964.102582 Node 7: lnL = -964.102582 Node 8: lnL = -964.102582 Node 9: lnL = -964.102582 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 391 Sequential format.. Reading seq # 1: YCL043C_Sbay Reading seq # 2: YCL043C_Scer Reading seq # 3: YCL043C_Skud Reading seq # 4: YCL043C_Smik Reading seq # 5: YCL043C_Spar Sequences read.. Counting patterns.. # site patterns = 165 Counting frequencies.. 120 bytes for distance 26400 bytes for lkl0 21120 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.016185 0.140249 0.030597 0.094189 0.082211 0.165819 0.142061 0.163735 lnL0 = -1444.101453 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1444.101453 x= 0.01618 0.14025 0.03060 0.09419 0.08221 0.16582 0.14206 0.16373 1 h-lim-p 0.0013 0.8627 148.8080 1440.885956 9 0.0003 43 | 0/8 2 h-lim-p 0.0006 0.0047 41.8706 1440.314608 1 0.0007 57 | 0/8 3 h-lim-p 0.0018 0.0147 17.1541 1440.204408 6 0.0009 85 | 0/8 4 h-lim-p 0.0011 0.0130 13.9537 1440.142888 3 0.0010 103 | 0/8 5 h-lim-p 0.0036 0.0291 3.6474 1440.137968 2 0.0009 120 | 0/8 6 h-lim-p 0.0033 0.2162 0.9459 1440.137560 5 0.0010 145 | 0/8 7 h-lim-p 0.0310 7.9904 0.0298 1440.137558 1 0.0019 170 | 0/8 8 h-lim-p 0.0396 20.0000 0.0014 1440.137081 0 0.6340 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1440.137065 1 1.2500 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1440.137065 0 1.0938 236 | 0/8 11 h-lim-p 2.4596 20.0000 0.0000 1440.137065 0 0.5380 257 | 0/8 12 h-lim-p 0.3393 20.0000 0.0000 1440.137065 0 0.0848 278 | 0/8 13 h-lim-p 0.0410 20.0000 0.0000 1440.137065 0 0.0102 299 | 0/8 14 h-lim-p 0.0058 20.0000 0.0000 1440.137065 0 0.0015 320 | 0/8 15 h-lim-p 0.0008 20.0000 0.0001 1440.137065 0 0.0001 342 | 0/8 16 h-lim-p 0.0000 20.0000 0.0020 1440.137065 0 0.0000 362 | 0/8 17 h-lim-p 0.0001 20.0000 0.0001 1440.137065 0 0.0000 396 | 0/8 18 h-lim-p 0.0000 20.0000 0.0005 | 0/8 19 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -1440.137065 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1440.137065 Node 7: lnL = -1440.137065 Node 8: lnL = -1440.137065 Node 9: lnL = -1440.137065 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 308 Sequential format.. Reading seq # 1: YCL044C_Sbay Reading seq # 2: YCL044C_Scer Reading seq # 3: YCL044C_Skud Reading seq # 4: YCL044C_Smik Reading seq # 5: YCL044C_Spar Sequences read.. Counting patterns.. # site patterns = 157 Counting frequencies.. 120 bytes for distance 25120 bytes for lkl0 20096 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.116469 0.001859 0.051168 0.119948 0.080148 0.209735 0.232302 0.298704 lnL0 = -1277.600747 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1277.600747 x= 0.11647 0.00186 0.05117 0.11995 0.08015 0.20973 0.23230 0.29870 1 h-lim-p 0.0012 0.0099 113.0169 1275.682773 9 0.0004 45 | 0/8 2 h-lim-p 0.0008 0.0064 19.1265 1275.533714 3 0.0008 63 | 0/8 3 h-lim-p 0.0010 0.0211 14.8299 1275.470918 4 0.0008 83 | 0/8 4 h-lim-p 0.0016 0.0319 7.3846 1275.453059 6 0.0009 108 | 0/8 5 h-lim-p 0.0072 0.2013 0.9147 1275.452427 2 0.0016 125 | 0/8 6 h-lim-p 0.0047 0.7791 0.3056 1275.452382 2 0.0010 150 | 0/8 7 h-lim-p 0.0020 1.3507 0.1543 1275.452365 2 0.0016 174 | 0/8 8 h-lim-p 0.2232 20.0000 0.0011 1275.450514 0 1.7858 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1275.450442 3 1.0004 223 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1275.450442 0 1.0938 243 | 0/8 11 h-lim-p 2.3653 20.0000 0.0000 1275.450442 0 1.0348 263 | 0/8 12 h-lim-p 0.9254 20.0000 0.0000 1275.450442 0 0.9254 283 | 0/8 13 h-lim-p 0.0014 20.0000 0.0022 1275.450442 0 0.0000 322 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1275.450442 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1275.450442 Node 7: lnL = -1275.450442 Node 8: lnL = -1275.450442 Node 9: lnL = -1275.450442 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 210 Sequential format.. Reading seq # 1: YCL047C_Sbay Reading seq # 2: YCL047C_Scer Reading seq # 3: YCL047C_Skud Reading seq # 4: YCL047C_Smik Reading seq # 5: YCL047C_Spar Sequences read.. Counting patterns.. # site patterns = 112 Counting frequencies.. 120 bytes for distance 17920 bytes for lkl0 14336 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.100750 0.000060 0.088793 0.134931 0.037443 0.074540 0.369658 0.266308 lnL0 = -843.984775 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 843.984775 x= 0.10075 0.00006 0.08879 0.13493 0.03744 0.07454 0.36966 0.26631 1 h-lim-p 0.0008 0.0064 93.9823 841.890682 6 0.0006 35 | 0/8 2 h-lim-p 0.0006 0.0045 39.5746 841.103527 0 0.0011 48 | 0/8 3 h-lim-p 0.0030 0.0242 8.1382 841.049084 7 0.0017 77 | 0/8 4 h-lim-p 0.0042 0.0593 3.2868 841.043429 6 0.0012 105 | 0/8 5 h-lim-p 0.0039 0.0887 1.0244 841.042881 5 0.0011 130 | 0/8 6 h-lim-p 0.0092 1.0583 0.1246 841.042756 4 0.0052 153 | 0/8 7 h-lim-p 0.0037 0.8089 0.1742 841.041701 0 0.0149 175 | 0/8 8 h-lim-p 0.0390 1.6201 0.0667 841.018368 0 0.1170 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0012 841.017832 2 0.9644 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 841.017830 0 1.0938 240 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 841.017830 0 1.0938 260 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 841.017830 0 1.0938 280 | 0/8 13 h-lim-p 1.0586 20.0000 0.0000 841.017830 0 0.2316 301 | 0/8 14 h-lim-p 0.0105 20.0000 0.0001 841.017830 0 0.0105 321 | 0/8 15 h-lim-p 0.0027 20.0000 0.0003 841.017830 0 0.0000 353 | 0/8 16 h-lim-p 0.0002 20.0000 0.0000 841.017830 0 0.0000 388 Out... lnL = -841.017830 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -841.017830 Node 7: lnL = -841.017830 Node 8: lnL = -841.017830 Node 9: lnL = -841.017830 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 882 Sequential format.. Reading seq # 1: YCL048W_Sbay Reading seq # 2: YCL048W_Scer Reading seq # 3: YCL048W_Skud Reading seq # 4: YCL048W_Smik Reading seq # 5: YCL048W_Spar Sequences read.. Counting patterns.. # site patterns = 221 Counting frequencies.. 120 bytes for distance 35360 bytes for lkl0 28288 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.051853 0.070270 0.056566 0.078179 0.048705 0.103088 0.109471 0.172769 lnL0 = -3233.722847 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3233.722847 x= 0.05185 0.07027 0.05657 0.07818 0.04870 0.10309 0.10947 0.17277 1 h-lim-p 0.0003 0.0024 146.0070 3232.359677 7 0.0001 35 | 0/8 2 h-lim-p 0.0006 0.0056 34.3290 3232.237933 7 0.0002 61 | 0/8 3 h-lim-p 0.0007 0.0153 10.2004 3232.232598 5 0.0001 88 | 0/8 4 h-lim-p 0.0003 0.0327 4.2067 3232.231579 2 0.0001 104 | 0/8 5 h-lim-p 0.0014 0.7788 0.4167 3232.231564 1 0.0002 120 | 0/8 6 h-lim-p 0.0008 2.0309 0.0856 3232.231563 0 0.0002 141 | 0/8 7 h-lim-p 0.0033 20.0000 0.0047 3232.231563 0 0.0029 161 | 0/8 8 h-lim-p 0.0065 20.0000 0.0021 3232.231435 0 0.1034 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3232.231434 0 1.0938 205 | 0/8 10 h-lim-p 1.9652 20.0000 0.0000 3232.231434 0 0.8598 225 | 0/8 11 h-lim-p 0.9422 20.0000 0.0000 3232.231434 0 0.0000 267 | 0/8 12 h-lim-p 0.0000 20.0000 0.0000 3232.231434 0 0.0000 290 Out... lnL = -3232.231434 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3232.231434 Node 7: lnL = -3232.231434 Node 8: lnL = -3232.231434 Node 9: lnL = -3232.231434 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 850 Sequential format.. Reading seq # 1: YCL049C_Sbay Reading seq # 2: YCL049C_Scer Reading seq # 3: YCL049C_Skud Reading seq # 4: YCL049C_Smik Reading seq # 5: YCL049C_Spar Sequences read.. Counting patterns.. # site patterns = 270 Counting frequencies.. 120 bytes for distance 43200 bytes for lkl0 34560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.070425 0.072065 0.070611 0.107397 0.066372 0.162418 0.153170 0.231587 lnL0 = -3587.036761 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3587.036761 x= 0.07043 0.07207 0.07061 0.10740 0.06637 0.16242 0.15317 0.23159 1 h-lim-p 0.0001 0.0009 165.7714 3584.247735 0 0.0002 23 | 0/8 2 h-lim-p 0.0008 0.0070 47.1357 3583.971812 7 0.0003 51 | 0/8 3 h-lim-p 0.0005 0.0046 23.0420 3583.936595 5 0.0002 76 | 0/8 4 h-lim-p 0.0004 0.0204 10.4946 3583.926992 5 0.0002 102 | 0/8 5 h-lim-p 0.0019 0.2050 1.2118 3583.926727 2 0.0004 119 | 0/8 6 h-lim-p 0.0020 0.9661 0.2199 3583.926720 1 0.0002 135 | 0/8 7 h-lim-p 0.0021 6.6658 0.0253 3583.926715 0 0.0021 155 | 0/8 8 h-lim-p 0.0085 20.0000 0.0064 3583.924891 0 0.1354 179 | 0/8 9 h-lim-p 2.0037 20.0000 0.0004 3583.924848 1 1.0019 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3583.924848 0 1.0938 221 | 0/8 11 h-lim-p 0.3100 20.0000 0.0000 3583.924848 0 0.6200 242 | 0/8 12 h-lim-p 0.4608 20.0000 0.0000 3583.924848 0 0.0576 264 | 0/8 13 h-lim-p 0.0277 20.0000 0.0001 3583.924848 0 0.0035 286 | 0/8 14 h-lim-p 0.0017 20.0000 0.0001 3583.924848 0 0.0000 329 | 0/8 15 h-lim-p 0.0000 20.0000 0.0021 | 0/8 16 h-lim-p 0.0000 20.0000 0.0021 Out... lnL = -3583.924848 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3583.924848 Node 7: lnL = -3583.924848 Node 8: lnL = -3583.924848 Node 9: lnL = -3583.924848 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 939 Sequential format.. Reading seq # 1: YCL050C_Sbay Reading seq # 2: YCL050C_Scer Reading seq # 3: YCL050C_Skud Reading seq # 4: YCL050C_Smik Reading seq # 5: YCL050C_Spar Sequences read.. Counting patterns.. # site patterns = 350 Counting frequencies.. 120 bytes for distance 56000 bytes for lkl0 44800 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.060656 0.162009 0.043152 0.144907 0.099160 0.274959 0.221218 0.272862 lnL0 = -4386.381298 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4386.381298 x= 0.06066 0.16201 0.04315 0.14491 0.09916 0.27496 0.22122 0.27286 1 h-lim-p 0.0009 0.0073 160.9127 4384.298764 8 0.0002 38 | 0/8 2 h-lim-p 0.0009 0.0069 29.2858 4384.149896 3 0.0004 56 | 0/8 3 h-lim-p 0.0006 0.0178 18.0579 4384.103514 6 0.0004 82 | 0/8 4 h-lim-p 0.0011 0.0342 6.0969 4384.097611 5 0.0004 107 | 0/8 5 h-lim-p 0.0022 0.1841 1.0398 4384.097320 3 0.0006 126 | 0/8 6 h-lim-p 0.0067 2.8626 0.0888 4384.097318 0 0.0007 140 | 0/8 7 h-lim-p 0.0027 13.4555 0.0244 4384.097318 0 0.0006 161 | 0/8 8 h-lim-p 0.0878 20.0000 0.0002 4384.097297 0 1.0535 184 | 0/8 9 h-lim-p 2.3963 20.0000 0.0001 4384.097297 0 1.0484 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4384.097297 0 1.0938 224 | 0/8 11 h-lim-p 1.4635 20.0000 0.0000 4384.097297 0 0.0000 260 | 0/8 12 h-lim-p 0.0003 20.0000 0.0000 4384.097297 0 0.0000 295 Out... lnL = -4384.097297 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4384.097297 Node 7: lnL = -4384.097297 Node 8: lnL = -4384.097297 Node 9: lnL = -4384.097297 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 498 Sequential format.. Reading seq # 1: YCL051W_Sbay Reading seq # 2: YCL051W_Scer Reading seq # 3: YCL051W_Skud Reading seq # 4: YCL051W_Smik Reading seq # 5: YCL051W_Spar Sequences read.. Counting patterns.. # site patterns = 152 Counting frequencies.. 120 bytes for distance 24320 bytes for lkl0 19456 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.044522 0.067041 0.046752 0.063919 0.067978 0.130344 0.137476 0.164200 lnL0 = -1931.250614 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1931.250614 x= 0.04452 0.06704 0.04675 0.06392 0.06798 0.13034 0.13748 0.16420 1 h-lim-p 0.0006 0.0044 54.9104 1930.920859 3 0.0002 28 | 0/8 2 h-lim-p 0.0008 0.0065 13.6019 1930.898376 6 0.0003 56 | 0/8 3 h-lim-p 0.0007 0.0321 5.0591 1930.895090 4 0.0003 78 | 0/8 4 h-lim-p 0.0008 0.0576 1.8608 1930.894746 4 0.0002 100 | 0/8 5 h-lim-p 0.0015 0.6720 0.2975 1930.894734 2 0.0003 117 | 0/8 6 h-lim-p 0.0008 1.3161 0.1039 1930.894733 1 0.0002 140 | 0/8 7 h-lim-p 0.0045 20.0000 0.0046 1930.894733 0 0.0020 160 | 0/8 8 h-lim-p 0.0239 20.0000 0.0004 1930.894705 0 0.3818 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1930.894704 0 1.0938 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1930.894704 0 2.1875 224 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1930.894704 0 1.0938 244 | 0/8 12 h-lim-p 0.1669 20.0000 0.0000 1930.894704 0 5.3392 269 | 0/8 13 h-lim-p 1.4783 20.0000 0.0001 1930.894704 0 1.2935 289 | 0/8 14 h-lim-p 0.0276 16.3742 0.0039 1930.894704 0 0.0069 310 | 0/8 15 h-lim-p 0.0020 4.7976 0.0133 1930.894704 0 0.0005 331 | 0/8 16 h-lim-p 0.0001 1.1971 0.0534 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0026 1930.894704 0 0.0000 396 | 0/8 18 h-lim-p 0.0000 20.0000 0.0006 1930.894704 0 0.0010 422 | 0/8 19 h-lim-p 0.0031 20.0000 0.0002 1930.894704 0 0.0000 453 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 1930.894704 0 0.0000 474 | 0/8 21 h-lim-p 0.0000 20.0000 0.0001 1930.894704 0 0.0000 498 | 0/8 22 h-lim-p 0.0000 18.4469 0.0036 1930.894704 0 0.0002 522 | 0/8 23 h-lim-p 0.0200 20.0000 0.0000 1930.894704 0 0.0006 546 | 0/8 24 h-lim-p 0.0010 20.0000 0.0000 1930.894704 0 0.0003 567 | 0/8 25 h-lim-p 0.0000 20.0000 0.0008 1930.894704 0 0.0000 594 | 0/8 26 h-lim-p 0.0000 20.0000 0.0000 1930.894704 0 0.0000 615 Out... lnL = -1930.894704 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1930.894704 Node 7: lnL = -1930.894704 Node 8: lnL = -1930.894704 Node 9: lnL = -1930.894704 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 498 Sequential format.. Reading seq # 1: YCL052C_Sbay Reading seq # 2: YCL052C_Scer Reading seq # 3: YCL052C_Skud Reading seq # 4: YCL052C_Smik Reading seq # 5: YCL052C_Spar Sequences read.. Counting patterns.. # site patterns = 151 Counting frequencies.. 120 bytes for distance 24160 bytes for lkl0 19328 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.043262 0.068002 0.047390 0.064073 0.067825 0.129383 0.139774 0.163161 lnL0 = -1930.580135 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1930.580135 x= 0.04326 0.06800 0.04739 0.06407 0.06782 0.12938 0.13977 0.16316 1 h-lim-p 0.0004 0.0032 55.9092 1930.213240 8 0.0002 43 | 0/8 2 h-lim-p 0.0011 0.0108 11.9692 1930.193216 4 0.0003 64 | 0/8 3 h-lim-p 0.0007 0.0360 4.5780 1930.190690 4 0.0003 86 | 0/8 4 h-lim-p 0.0007 0.0781 1.6954 1930.190430 4 0.0002 109 | 0/8 5 h-lim-p 0.0013 0.7012 0.2752 1930.190416 2 0.0004 127 | 0/8 6 h-lim-p 0.0049 5.4575 0.0241 1930.190416 0 0.0003 150 | 0/8 7 h-lim-p 0.0006 10.2597 0.0102 1930.190415 0 0.0005 170 | 0/8 8 h-lim-p 0.0397 20.0000 0.0001 1930.190399 0 0.6353 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1930.190399 0 1.0938 214 | 0/8 10 h-lim-p 1.4859 20.0000 0.0000 1930.190399 0 1.3002 234 | 0/8 11 h-lim-p 1.3214 20.0000 0.0000 1930.190399 0 1.1562 254 | 0/8 12 h-lim-p 0.2500 20.0000 0.0001 1930.190399 0 0.0234 277 | 0/8 13 h-lim-p 0.0045 20.0000 0.0005 1930.190399 0 0.0006 299 | 0/8 14 h-lim-p 0.0003 20.0000 0.0010 1930.190399 0 0.0000 322 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 1930.190399 0 0.0000 352 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 1930.190399 0 0.0000 381 Out... lnL = -1930.190399 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1930.190399 Node 7: lnL = -1930.190399 Node 8: lnL = -1930.190399 Node 9: lnL = -1930.190399 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 853 Sequential format.. Reading seq # 1: YCL054W_Sbay Reading seq # 2: YCL054W_Scer Reading seq # 3: YCL054W_Skud Reading seq # 4: YCL054W_Smik Reading seq # 5: YCL054W_Spar Sequences read.. Counting patterns.. # site patterns = 340 Counting frequencies.. 120 bytes for distance 54400 bytes for lkl0 43520 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.053629 0.070340 0.112419 0.161278 0.128276 0.186728 0.256035 0.255748 lnL0 = -4103.370790 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4103.370790 x= 0.05363 0.07034 0.11242 0.16128 0.12828 0.18673 0.25603 0.25575 1 h-lim-p 0.0028 0.6853 172.2030 4099.994087 8 0.0002 42 | 0/8 2 h-lim-p 0.0006 0.0048 31.3442 4099.784244 7 0.0004 71 | 0/8 3 h-lim-p 0.0014 0.0242 9.9273 4099.769580 2 0.0003 88 | 0/8 4 h-lim-p 0.0013 0.1370 2.4747 4099.768199 4 0.0005 108 | 0/8 5 h-lim-p 0.0034 0.9005 0.3562 4099.768157 1 0.0007 123 | 0/8 6 h-lim-p 0.0039 3.9847 0.0611 4099.768155 0 0.0009 144 | 0/8 7 h-lim-p 0.0197 20.0000 0.0027 4099.768006 0 0.1575 167 | 0/8 8 h-lim-p 0.0014 1.4946 0.3044 4099.767091 0 0.0028 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4099.767079 1 0.9961 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4099.767079 0 1.0938 230 | 0/8 11 h-lim-p 0.9584 20.0000 0.0000 4099.767079 0 0.7188 250 | 0/8 12 h-lim-p 0.0016 5.9358 0.0122 4099.767079 0 0.0008 270 | 0/8 13 h-lim-p 0.0004 2.8519 0.0255 4099.767079 0 0.0000 309 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 4099.767079 0 0.0000 336 Out... lnL = -4099.767079 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4099.767079 Node 7: lnL = -4099.767079 Node 8: lnL = -4099.767079 Node 9: lnL = -4099.767079 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 592 Sequential format.. Reading seq # 1: YCL055W_Sbay Reading seq # 2: YCL055W_Scer Reading seq # 3: YCL055W_Skud Reading seq # 4: YCL055W_Smik Reading seq # 5: YCL055W_Spar Sequences read.. Counting patterns.. # site patterns = 228 Counting frequencies.. 120 bytes for distance 36480 bytes for lkl0 29184 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.023041 0.129590 0.046788 0.195157 0.080636 0.186572 0.160147 0.192393 lnL0 = -2631.188384 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2631.188384 x= 0.02304 0.12959 0.04679 0.19516 0.08064 0.18657 0.16015 0.19239 1 h-lim-p 0.0003 0.0021 95.6313 2629.790158 0 0.0004 22 | 0/8 2 h-lim-p 0.0006 0.0047 25.9902 2629.679884 7 0.0003 50 | 0/8 3 h-lim-p 0.0007 0.0222 13.3306 2629.654664 6 0.0004 76 | 0/8 4 h-lim-p 0.0028 0.1105 1.7087 2629.653833 3 0.0006 95 | 0/8 5 h-lim-p 0.0017 0.3383 0.5880 2629.653710 3 0.0006 115 | 0/8 6 h-lim-p 0.0050 1.5564 0.0698 2629.652525 0 0.0201 137 | 0/8 7 h-lim-p 0.0062 0.4969 0.2250 2629.599880 0 0.0249 159 | 0/8 8 h-lim-p 0.0107 0.4426 0.5223 2629.599793 0 0.0006 182 | 0/8 9 h-lim-p 0.3495 20.0000 0.0009 2629.598953 0 1.0485 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2629.598947 1 0.9961 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2629.598947 0 0.5469 246 | 0/8 12 h-lim-p 0.1587 20.0000 0.0001 2629.598947 0 0.0050 270 | 0/8 13 h-lim-p 0.0014 20.0000 0.0003 2629.598947 0 0.0000 298 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 2629.598947 0 0.0000 328 Out... lnL = -2629.598947 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2629.598947 Node 7: lnL = -2629.598947 Node 8: lnL = -2629.598947 Node 9: lnL = -2629.598947 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 594 Sequential format.. Reading seq # 1: YCL056C_Sbay Reading seq # 2: YCL056C_Scer Reading seq # 3: YCL056C_Skud Reading seq # 4: YCL056C_Smik Reading seq # 5: YCL056C_Spar Sequences read.. Counting patterns.. # site patterns = 218 Counting frequencies.. 120 bytes for distance 34880 bytes for lkl0 27904 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.026539 0.121387 0.055967 0.182301 0.092487 0.179816 0.154118 0.194924 lnL0 = -2672.491423 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2672.491423 x= 0.02654 0.12139 0.05597 0.18230 0.09249 0.17982 0.15412 0.19492 1 h-lim-p 0.0003 0.0024 102.7013 2670.835118 6 0.0003 35 | 0/8 2 h-lim-p 0.0007 0.0052 33.8058 2670.654157 6 0.0003 59 | 0/8 3 h-lim-p 0.0008 0.0219 14.5888 2670.627364 5 0.0003 81 | 0/8 4 h-lim-p 0.0019 0.0807 2.2740 2670.626249 2 0.0005 98 | 0/8 5 h-lim-p 0.0015 0.4646 0.6680 2670.626155 3 0.0005 119 | 0/8 6 h-lim-p 0.0069 2.2810 0.0438 2670.626154 0 0.0008 141 | 0/8 7 h-lim-p 0.0172 20.0000 0.0019 2670.626136 0 0.0687 163 | 0/8 8 h-lim-p 0.0023 2.1118 0.0583 2670.625942 0 0.0091 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2670.625919 1 0.9961 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2670.625919 0 1.2500 227 | 0/8 11 h-lim-p 0.5993 20.0000 0.0000 2670.625919 0 0.0094 252 | 0/8 12 h-lim-p 0.0002 20.0000 0.0023 2670.625919 0 0.0000 273 | 0/8 13 h-lim-p 0.0005 20.0000 0.0002 2670.625919 0 0.0001 295 | 0/8 14 h-lim-p 0.0005 20.0000 0.0000 2670.625919 0 0.0000 325 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 2670.625919 0 0.0000 354 Out... lnL = -2670.625919 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2670.625919 Node 7: lnL = -2670.625919 Node 8: lnL = -2670.625919 Node 9: lnL = -2670.625919 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 447 Sequential format.. Reading seq # 1: YCL057C-A_Sbay Reading seq # 2: YCL057C-A_Scer Reading seq # 3: YCL057C-A_Skud Reading seq # 4: YCL057C-A_Smik Reading seq # 5: YCL057C-A_Spar Sequences read.. Counting patterns.. # site patterns = 167 Counting frequencies.. 120 bytes for distance 26720 bytes for lkl0 21376 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.074520 0.045753 0.029186 0.120241 0.086897 0.172729 0.212378 0.229449 lnL0 = -2030.985056 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2030.985056 x= 0.07452 0.04575 0.02919 0.12024 0.08690 0.17273 0.21238 0.22945 1 h-lim-p 0.0034 0.1417 109.2660 2029.940705 3 0.0002 31 | 0/8 2 h-lim-p 0.0006 0.0051 20.0932 2029.855498 7 0.0004 61 | 0/8 3 h-lim-p 0.0016 0.0307 5.4778 2029.848568 5 0.0005 87 | 0/8 4 h-lim-p 0.0012 0.0491 2.3450 2029.847623 4 0.0004 109 | 0/8 5 h-lim-p 0.0026 0.5611 0.3749 2029.847561 3 0.0009 129 | 0/8 6 h-lim-p 0.0043 2.1069 0.0794 2029.847558 1 0.0005 153 | 0/8 7 h-lim-p 0.0024 8.0153 0.0172 2029.847554 0 0.0048 174 | 0/8 8 h-lim-p 0.0180 11.0884 0.0046 2029.846699 0 0.1437 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2029.846694 1 0.9961 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2029.846694 0 2.1875 239 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2029.846694 0 1.0938 259 | 0/8 12 h-lim-p 0.1584 20.0000 0.0000 2029.846694 0 0.0173 281 | 0/8 13 h-lim-p 0.0003 20.0000 0.0011 2029.846694 0 0.0000 320 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -2029.846694 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2029.846694 Node 7: lnL = -2029.846694 Node 8: lnL = -2029.846694 Node 9: lnL = -2029.846694 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 447 Sequential format.. Reading seq # 1: YCL057W_Sbay Reading seq # 2: YCL057W_Scer Reading seq # 3: YCL057W_Skud Reading seq # 4: YCL057W_Smik Reading seq # 5: YCL057W_Spar Sequences read.. Counting patterns.. # site patterns = 166 Counting frequencies.. 120 bytes for distance 26560 bytes for lkl0 21248 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.067574 0.045556 0.034199 0.120454 0.086685 0.169019 0.206257 0.219509 lnL0 = -2020.694750 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2020.694750 x= 0.06757 0.04556 0.03420 0.12045 0.08668 0.16902 0.20626 0.21951 1 h-lim-p 0.0030 1.0682 116.9617 2019.490849 8 0.0002 43 | 0/8 2 h-lim-p 0.0010 0.0080 16.1886 2019.436840 6 0.0004 71 | 0/8 3 h-lim-p 0.0014 0.0468 4.9708 2019.431853 5 0.0004 95 | 0/8 4 h-lim-p 0.0012 0.0544 1.8354 2019.431216 4 0.0004 117 | 0/8 5 h-lim-p 0.0034 1.1159 0.2332 2019.431193 1 0.0009 132 | 0/8 6 h-lim-p 0.0031 2.3691 0.0653 2019.431192 0 0.0007 153 | 0/8 7 h-lim-p 0.0388 20.0000 0.0011 2019.431159 0 0.1553 175 | 0/8 8 h-lim-p 0.0022 0.9315 0.0806 2019.430973 0 0.0044 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2019.430971 0 1.0938 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2019.430971 0 1.0938 236 | 0/8 11 h-lim-p 0.8668 20.0000 0.0000 2019.430971 0 0.0025 264 | 0/8 12 h-lim-p 0.0007 20.0000 0.0000 2019.430971 0 0.0003 284 | 0/8 13 h-lim-p 0.0001 20.0000 0.0002 2019.430971 0 0.0000 304 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 2019.430971 0 0.0000 333 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 2019.430971 0 0.0000 353 Out... lnL = -2019.430971 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2019.430971 Node 7: lnL = -2019.430971 Node 8: lnL = -2019.430971 Node 9: lnL = -2019.430971 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 153 Sequential format.. Reading seq # 1: YCL059C_Sbay Reading seq # 2: YCL059C_Scer Reading seq # 3: YCL059C_Skud Reading seq # 4: YCL059C_Smik Reading seq # 5: YCL059C_Spar Sequences read.. Counting patterns.. # site patterns = 58 Counting frequencies.. 120 bytes for distance 9280 bytes for lkl0 7424 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.015406 0.066355 0.051626 0.041203 0.033300 0.067655 0.120535 0.100788 lnL0 = -506.532703 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 506.532703 x= 0.01541 0.06636 0.05163 0.04120 0.03330 0.06766 0.12053 0.10079 1 h-lim-p 0.0022 0.0172 36.9002 506.208693 3 0.0005 29 | 0/8 2 h-lim-p 0.0028 0.0228 4.6767 506.201704 2 0.0007 46 | 0/8 3 h-lim-p 0.0010 0.0504 3.2679 506.200101 4 0.0004 65 | 0/8 4 h-lim-p 0.0018 0.1183 0.7586 506.199912 3 0.0007 83 | 0/8 5 h-lim-p 0.0015 0.3323 0.3600 506.199868 3 0.0008 110 | 0/8 6 h-lim-p 0.0030 2.4935 0.0976 506.199865 0 0.0006 131 | 0/8 7 h-lim-p 0.0172 20.0000 0.0037 506.199865 1 0.0084 154 | 0/8 8 h-lim-p 0.0095 20.0000 0.0033 506.199781 0 0.1139 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 506.199777 1 0.9961 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 506.199777 0 2.1875 219 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 506.199777 0 0.0073 247 | 0/8 12 h-lim-p 0.0008 20.0000 0.0000 .. | 0/8 13 h-lim-p 0.0000 20.0000 0.0015 | 0/8 14 h-lim-p 0.0000 20.0000 0.0015 Out... lnL = -506.199777 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -506.199777 Node 7: lnL = -506.199777 Node 8: lnL = -506.199777 Node 9: lnL = -506.199777 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 326 Sequential format.. Reading seq # 1: YCL061C_Sbay Reading seq # 2: YCL061C_Scer Reading seq # 3: YCL061C_Skud Reading seq # 4: YCL061C_Smik Reading seq # 5: YCL061C_Spar Sequences read.. Counting patterns.. # site patterns = 124 Counting frequencies.. 120 bytes for distance 19840 bytes for lkl0 15872 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.093617 0.161780 0.086606 0.118426 0.144584 0.265866 0.244307 0.335532 lnL0 = -1228.382197 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1228.382197 x= 0.09362 0.16178 0.08661 0.11843 0.14458 0.26587 0.24431 0.33553 1 h-lim-p 0.0011 0.0091 34.8781 1227.701298 4 0.0012 30 | 0/8 2 h-lim-p 0.0015 0.0120 17.6708 1227.507263 5 0.0015 52 | 0/8 3 h-lim-p 0.0009 0.0076 23.7015 1227.295640 0 0.0019 65 | 0/8 4 h-lim-p 0.0075 0.0712 6.0072 1227.256095 7 0.0028 95 | 0/8 5 h-lim-p 0.0015 0.0124 7.5049 1227.225637 0 0.0023 107 | 0/8 6 h-lim-p 0.0577 1.1463 0.3015 1227.225254 4 0.0078 129 | 0/8 7 h-lim-p 0.2893 20.0000 0.0082 1227.223630 0 0.5785 150 | 0/8 8 h-lim-p 0.0175 1.2304 0.2693 1227.221315 4 0.0135 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0012 1227.221158 3 1.0004 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1227.221157 0 1.2500 224 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1227.221157 0 1.0938 244 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1227.221157 0 1.0938 264 | 0/8 13 h-lim-p 1.0283 20.0000 0.0000 1227.221157 0 0.1285 286 | 0/8 14 h-lim-p 0.0017 20.0000 0.0001 1227.221157 0 0.0000 323 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 1227.221157 0 0.0000 355 Out... lnL = -1227.221157 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1227.221157 Node 7: lnL = -1227.221157 Node 8: lnL = -1227.221157 Node 9: lnL = -1227.221157 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 444 Sequential format.. Reading seq # 1: YCL063W_Sbay Reading seq # 2: YCL063W_Scer Reading seq # 3: YCL063W_Skud Reading seq # 4: YCL063W_Smik Reading seq # 5: YCL063W_Spar Sequences read.. Counting patterns.. # site patterns = 146 Counting frequencies.. 120 bytes for distance 23360 bytes for lkl0 18688 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.044114 0.061851 0.069017 0.076227 0.070983 0.118370 0.134681 0.168391 lnL0 = -1753.978136 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1753.978136 x= 0.04411 0.06185 0.06902 0.07623 0.07098 0.11837 0.13468 0.16839 1 h-lim-p 0.0011 0.0085 72.8766 1753.310019 6 0.0003 34 | 0/8 2 h-lim-p 0.0023 0.0192 8.3404 1753.296463 6 0.0004 63 | 0/8 3 h-lim-p 0.0008 0.0456 3.9709 1753.294529 4 0.0003 85 | 0/8 4 h-lim-p 0.0013 0.2143 0.8945 1753.294397 3 0.0004 104 | 0/8 5 h-lim-p 0.0026 1.3844 0.1226 1753.294395 1 0.0003 128 | 0/8 6 h-lim-p 0.0012 5.5799 0.0311 1753.294395 0 0.0005 148 | 0/8 7 h-lim-p 0.0231 20.0000 0.0007 1753.294394 0 0.0202 168 | 0/8 8 h-lim-p 0.0077 20.0000 0.0019 1753.294387 0 0.0308 190 | 0/8 9 h-lim-p 2.2674 20.0000 0.0000 1753.294386 0 0.9920 210 | 0/8 10 h-lim-p 1.4288 20.0000 0.0000 1753.294386 0 0.0028 238 | 0/8 11 h-lim-p 0.0002 20.0000 0.0003 1753.294386 0 0.0000 264 | 0/8 12 h-lim-p 0.0001 20.0000 0.0000 1753.294386 0 0.0000 290 Out... lnL = -1753.294386 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1753.294386 Node 7: lnL = -1753.294386 Node 8: lnL = -1753.294386 Node 9: lnL = -1753.294386 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 442 Sequential format.. Reading seq # 1: YCL064C_Sbay Reading seq # 2: YCL064C_Scer Reading seq # 3: YCL064C_Skud Reading seq # 4: YCL064C_Smik Reading seq # 5: YCL064C_Spar Sequences read.. Counting patterns.. # site patterns = 147 Counting frequencies.. 120 bytes for distance 23520 bytes for lkl0 18816 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.040754 0.053595 0.070339 0.075996 0.071214 0.112705 0.170106 0.167325 lnL0 = -1769.638791 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1769.638791 x= 0.04075 0.05359 0.07034 0.07600 0.07121 0.11270 0.17011 0.16732 1 h-lim-p 0.0003 0.0027 98.7114 1768.449676 5 0.0003 32 | 0/8 2 h-lim-p 0.0019 0.0155 9.6609 1768.430382 5 0.0004 54 | 0/8 3 h-lim-p 0.0007 0.0367 5.6542 1768.426061 3 0.0003 73 | 0/8 4 h-lim-p 0.0010 0.0697 2.0096 1768.425516 4 0.0003 94 | 0/8 5 h-lim-p 0.0026 0.5934 0.2424 1768.425505 2 0.0004 113 | 0/8 6 h-lim-p 0.0023 2.6669 0.0464 1768.425505 0 0.0005 134 | 0/8 7 h-lim-p 0.0098 20.0000 0.0024 1768.425505 0 0.0011 156 | 0/8 8 h-lim-p 0.0700 20.0000 0.0000 1768.425503 0 0.8399 179 | 0/8 9 h-lim-p 1.6574 20.0000 0.0000 1768.425503 0 1.4502 199 | 0/8 10 h-lim-p 2.1867 20.0000 0.0000 1768.425503 0 0.9567 219 | 0/8 11 h-lim-p 0.3523 20.0000 0.0000 1768.425503 0 0.1762 239 | 0/8 12 h-lim-p 0.0267 20.0000 0.0002 1768.425503 0 0.0002 265 | 0/8 13 h-lim-p 0.0003 20.0000 0.0002 1768.425503 0 0.0000 301 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 1768.425503 0 0.0000 321 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 1768.425503 0 0.0070 349 | 0/8 16 h-lim-p 0.0121 20.0000 0.0000 1768.425503 0 0.0000 393 | 0/8 17 h-lim-p 0.0000 20.0000 0.0014 | 0/8 18 h-lim-p 0.0000 20.0000 0.0014 Out... lnL = -1768.425503 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1768.425503 Node 7: lnL = -1768.425503 Node 8: lnL = -1768.425503 Node 9: lnL = -1768.425503 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 294 Sequential format.. Reading seq # 1: YCR003W_Sbay Reading seq # 2: YCR003W_Scer Reading seq # 3: YCR003W_Skud Reading seq # 4: YCR003W_Smik Reading seq # 5: YCR003W_Spar Sequences read.. Counting patterns.. # site patterns = 124 Counting frequencies.. 120 bytes for distance 19840 bytes for lkl0 15872 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.039834 0.105671 0.029370 0.099579 0.105072 0.166473 0.172352 0.189684 lnL0 = -1284.767733 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1284.767733 x= 0.03983 0.10567 0.02937 0.09958 0.10507 0.16647 0.17235 0.18968 1 h-lim-p 0.0022 0.0175 97.9235 1283.363740 7 0.0003 41 | 0/8 2 h-lim-p 0.0008 0.0061 28.8180 1283.057509 6 0.0008 64 | 0/8 3 h-lim-p 0.0035 0.0324 6.3754 1283.041967 2 0.0008 81 | 0/8 4 h-lim-p 0.0037 0.1570 1.4390 1283.041257 3 0.0007 100 | 0/8 5 h-lim-p 0.0021 0.4199 0.4884 1283.041159 2 0.0009 116 | 0/8 6 h-lim-p 0.0164 14.5724 0.0279 1283.041158 0 0.0009 139 | 0/8 7 h-lim-p 0.0054 20.0000 0.0046 1283.041158 0 0.0108 160 | 0/8 8 h-lim-p 0.0182 20.0000 0.0027 1283.041063 0 0.1454 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1283.041054 1 0.9961 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1283.041054 0 1.0938 225 | 0/8 11 h-lim-p 1.2694 20.0000 0.0000 1283.041054 0 1.1107 245 | 0/8 12 h-lim-p 0.3250 20.0000 0.0000 1283.041054 0 0.0178 268 | 0/8 13 h-lim-p 0.0031 20.0000 0.0002 1283.041054 0 0.0016 288 | 0/8 14 h-lim-p 0.0006 20.0000 0.0005 1283.041054 0 0.0001 310 | 0/8 15 h-lim-p 0.0003 20.0000 0.0002 1283.041054 0 0.0000 335 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 1283.041054 0 0.0000 357 | 0/8 17 h-lim-p 0.0002 20.0000 0.0000 1283.041054 0 0.0002 377 Out... lnL = -1283.041054 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1283.041054 Node 7: lnL = -1283.041054 Node 8: lnL = -1283.041054 Node 9: lnL = -1283.041054 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 709 Sequential format.. Reading seq # 1: YCR004C_Sbay Reading seq # 2: YCR004C_Scer Reading seq # 3: YCR004C_Skud Reading seq # 4: YCR004C_Smik Reading seq # 5: YCR004C_Spar Sequences read.. Counting patterns.. # site patterns = 247 Counting frequencies.. 120 bytes for distance 39520 bytes for lkl0 31616 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.039010 0.017094 0.081356 0.112943 0.108249 0.203695 0.171308 0.180549 lnL0 = -3019.329074 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3019.329074 x= 0.03901 0.01709 0.08136 0.11294 0.10825 0.20369 0.17131 0.18055 1 h-lim-p 0.0018 0.0336 181.0813 3017.531232 5 0.0001 35 | 0/8 2 h-lim-p 0.0003 0.0028 33.0039 3017.388262 4 0.0003 55 | 0/8 3 h-lim-p 0.0027 0.0413 3.3507 3017.386655 2 0.0003 73 | 0/8 4 h-lim-p 0.0008 0.2247 1.2190 3017.386398 2 0.0004 89 | 0/8 5 h-lim-p 0.0033 1.2126 0.1384 3017.386395 0 0.0004 103 | 0/8 6 h-lim-p 0.0080 20.0000 0.0063 3017.386394 0 0.0070 123 | 0/8 7 h-lim-p 0.0125 18.6021 0.0035 3017.386238 0 0.1000 146 | 0/8 8 h-lim-p 0.0007 0.1330 0.4892 3017.386151 3 0.0004 175 | 0/8 9 h-lim-p 0.4674 20.0000 0.0004 3017.386129 0 0.9347 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 3017.386129 0 1.0938 216 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3017.386129 0 2.1875 236 | 0/8 12 h-lim-p 2.1938 20.0000 0.0000 3017.386129 0 1.0969 256 | 0/8 13 h-lim-p 0.1983 20.0000 0.0001 3017.386129 0 0.0002 285 | 0/8 14 h-lim-p 0.0001 20.0000 0.0005 3017.386129 0 0.0000 315 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 3017.386129 0 0.0000 345 Out... lnL = -3017.386129 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3017.386129 Node 7: lnL = -3017.386129 Node 8: lnL = -3017.386129 Node 9: lnL = -3017.386129 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 215 Sequential format.. Reading seq # 1: YCR005C_Sbay Reading seq # 2: YCR005C_Scer Reading seq # 3: YCR005C_Skud Reading seq # 4: YCR005C_Smik Reading seq # 5: YCR005C_Spar Sequences read.. Counting patterns.. # site patterns = 88 Counting frequencies.. 120 bytes for distance 14080 bytes for lkl0 11264 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.050798 0.031233 0.039745 0.122729 0.068962 0.114925 0.208695 0.175371 lnL0 = -890.872945 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 890.872945 x= 0.05080 0.03123 0.03974 0.12273 0.06896 0.11493 0.20869 0.17537 1 h-lim-p 0.0008 0.0067 71.2519 890.009991 3 0.0004 29 | 0/8 2 h-lim-p 0.0011 0.0086 13.7944 889.955452 6 0.0006 54 | 0/8 3 h-lim-p 0.0013 0.0393 6.3742 889.943546 7 0.0007 84 | 0/8 4 h-lim-p 0.0023 0.1195 1.9414 889.941646 4 0.0011 105 | 0/8 5 h-lim-p 0.0029 0.1046 0.7499 889.941493 2 0.0006 122 | 0/8 6 h-lim-p 0.0044 2.3113 0.1091 889.941488 1 0.0009 145 | 0/8 7 h-lim-p 0.0184 20.0000 0.0052 889.941488 0 0.0010 168 | 0/8 8 h-lim-p 0.0664 20.0000 0.0001 889.941483 0 1.0631 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 889.941483 0 1.0938 212 | 0/8 10 h-lim-p 1.8130 20.0000 0.0000 889.941483 0 0.7932 232 | 0/8 11 h-lim-p 0.6120 20.0000 0.0000 889.941483 0 0.0006 261 | 0/8 12 h-lim-p 0.0002 20.0000 0.0000 889.941483 0 0.0000 282 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 889.941483 0 0.0000 302 | 0/8 14 h-lim-p 0.0003 20.0000 0.0000 889.941483 0 0.0000 329 Out... lnL = -889.941483 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -889.941483 Node 7: lnL = -889.941483 Node 8: lnL = -889.941483 Node 9: lnL = -889.941483 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 907 Sequential format.. Reading seq # 1: YCR007C_Sbay Reading seq # 2: YCR007C_Scer Reading seq # 3: YCR007C_Skud Reading seq # 4: YCR007C_Smik Reading seq # 5: YCR007C_Spar Sequences read.. Counting patterns.. # site patterns = 484 Counting frequencies.. 120 bytes for distance 77440 bytes for lkl0 61952 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.208680 0.028617 0.083792 0.288389 0.120404 0.523508 0.628282 0.578340 lnL0 = -4920.818862 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4920.818862 x= 0.20868 0.02862 0.08379 0.28839 0.12040 0.52351 0.62828 0.57834 1 h-lim-p 0.0221 2.3051 66.6704 4919.896302 8 0.0004 48 | 0/8 2 h-lim-p 0.0014 0.0215 21.2643 4919.740012 7 0.0008 77 | 0/8 3 h-lim-p 0.0016 0.0140 9.8273 4919.676524 5 0.0016 101 | 0/8 4 h-lim-p 0.0038 0.1297 4.0518 4919.664066 2 0.0018 117 | 0/8 5 h-lim-p 0.0035 0.2147 2.0632 4919.659746 5 0.0026 141 | 0/8 6 h-lim-p 0.0036 0.4795 1.5033 4919.657760 3 0.0027 159 | 0/8 7 h-lim-p 0.0095 1.5895 0.4335 4919.657519 3 0.0031 179 | 0/8 8 h-lim-p 2.1392 20.0000 0.0006 4919.657302 2 1.1260 204 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4919.657301 0 1.0938 224 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4919.657301 0 1.0938 244 | 0/8 11 h-lim-p 1.2662 20.0000 0.0000 4919.657301 0 1.1079 264 | 0/8 12 h-lim-p 0.6452 20.0000 0.0000 4919.657301 0 0.6452 284 | 0/8 13 h-lim-p 0.0415 20.0000 0.0001 4919.657301 0 0.0000 322 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 4919.657301 0 0.0000 348 Out... lnL = -4919.657301 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4919.657301 Node 7: lnL = -4919.657301 Node 8: lnL = -4919.657301 Node 9: lnL = -4919.657301 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 859 Sequential format.. Reading seq # 1: YCR008W_Sbay Reading seq # 2: YCR008W_Scer Reading seq # 3: YCR008W_Skud Reading seq # 4: YCR008W_Smik Reading seq # 5: YCR008W_Spar Sequences read.. Counting patterns.. # site patterns = 212 Counting frequencies.. 120 bytes for distance 33920 bytes for lkl0 27136 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.026664 0.050108 0.030373 0.066363 0.083146 0.116370 0.099969 0.119640 lnL0 = -3142.823565 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3142.823565 x= 0.02666 0.05011 0.03037 0.06636 0.08315 0.11637 0.09997 0.11964 1 h-lim-p 0.0011 0.5058 241.4611 3140.952611 7 0.0001 38 | 0/8 2 h-lim-p 0.0004 0.0033 31.8931 3140.891113 7 0.0001 68 | 0/8 3 h-lim-p 0.0012 0.0180 3.2767 3140.890340 2 0.0001 86 | 0/8 4 h-lim-p 0.0006 0.1890 0.7568 3140.890298 2 0.0002 103 | 0/8 5 h-lim-p 0.0006 1.0351 0.1904 3140.890296 0 0.0001 124 | 0/8 6 h-lim-p 0.0067 20.0000 0.0040 3140.890295 0 0.0029 144 | 0/8 7 h-lim-p 0.0025 20.0000 0.0047 3140.890288 0 0.0099 166 | 0/8 8 h-lim-p 0.0007 0.8416 0.0691 3140.890205 0 0.0020 187 | 0/8 9 h-lim-p 1.3361 20.0000 0.0001 3140.890205 0 1.1691 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3140.890205 0 1.0938 227 | 0/8 11 h-lim-p 0.6084 20.0000 0.0001 3140.890205 0 0.0024 254 | 0/8 12 h-lim-p 0.0001 20.0000 0.0020 3140.890205 0 0.0000 278 | 0/8 13 h-lim-p 0.0002 20.0000 0.0000 3140.890205 0 0.0000 312 | 0/8 14 h-lim-p 0.0000 20.0000 0.0005 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -3140.890205 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3140.890205 Node 7: lnL = -3140.890205 Node 8: lnL = -3140.890205 Node 9: lnL = -3140.890205 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 804 Sequential format.. Reading seq # 1: YCR009C_Sbay Reading seq # 2: YCR009C_Scer Reading seq # 3: YCR009C_Skud Reading seq # 4: YCR009C_Smik Reading seq # 5: YCR009C_Spar Sequences read.. Counting patterns.. # site patterns = 289 Counting frequencies.. 120 bytes for distance 46240 bytes for lkl0 36992 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.084090 0.084119 0.062347 0.122774 0.092073 0.221791 0.215620 0.263212 lnL0 = -3665.288962 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3665.288962 x= 0.08409 0.08412 0.06235 0.12277 0.09207 0.22179 0.21562 0.26321 1 h-lim-p 0.0007 0.0057 118.2025 3663.845623 9 0.0002 48 | 0/8 2 h-lim-p 0.0008 0.0061 25.9227 3663.742454 5 0.0003 71 | 0/8 3 h-lim-p 0.0006 0.0177 13.3271 3663.721649 2 0.0003 87 | 0/8 4 h-lim-p 0.0007 0.0447 5.6976 3663.716446 5 0.0004 113 | 0/8 5 h-lim-p 0.0024 0.3436 0.9423 3663.716296 3 0.0003 135 | 0/8 6 h-lim-p 0.0022 1.6412 0.1506 3663.716291 0 0.0005 156 | 0/8 7 h-lim-p 0.0099 20.0000 0.0083 3663.716290 0 0.0011 178 | 0/8 8 h-lim-p 0.0407 20.0000 0.0002 3663.716256 0 0.6512 202 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3663.716256 0 1.0938 222 | 0/8 10 h-lim-p 1.1231 20.0000 0.0000 3663.716256 0 0.9827 242 | 0/8 11 h-lim-p 0.6915 20.0000 0.0000 3663.716256 0 0.0864 264 | 0/8 12 h-lim-p 0.0066 20.0000 0.0003 3663.716256 0 0.0017 285 | 0/8 13 h-lim-p 0.0007 20.0000 0.0006 3663.716256 0 0.0007 305 | 0/8 14 h-lim-p 0.0002 20.0000 0.0022 3663.716256 0 0.0000 340 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -3663.716256 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3663.716256 Node 7: lnL = -3663.716256 Node 8: lnL = -3663.716256 Node 9: lnL = -3663.716256 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 853 Sequential format.. Reading seq # 1: YCR012W_Sbay Reading seq # 2: YCR012W_Scer Reading seq # 3: YCR012W_Skud Reading seq # 4: YCR012W_Smik Reading seq # 5: YCR012W_Spar Sequences read.. Counting patterns.. # site patterns = 188 Counting frequencies.. 120 bytes for distance 30080 bytes for lkl0 24064 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.050555 0.024553 0.039576 0.060894 0.055450 0.102145 0.105521 0.140331 lnL0 = -3066.141122 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3066.141122 x= 0.05055 0.02455 0.03958 0.06089 0.05545 0.10214 0.10552 0.14033 1 h-lim-p 0.0006 0.0168 315.8048 3063.073734 8 0.0001 42 | 0/8 2 h-lim-p 0.0005 0.0038 42.9101 3062.897343 6 0.0002 69 | 0/8 3 h-lim-p 0.0008 0.0207 10.5795 3062.892656 3 0.0001 89 | 0/8 4 h-lim-p 0.0005 0.0620 2.0874 3062.892297 3 0.0002 107 | 0/8 5 h-lim-p 0.0016 0.4129 0.2192 3062.892294 1 0.0001 124 | 0/8 6 h-lim-p 0.0016 11.6842 0.0137 3062.892294 0 0.0004 145 | 0/8 7 h-lim-p 0.0006 16.2294 0.0080 3062.892294 0 0.0012 166 | 0/8 8 h-lim-p 0.0031 20.0000 0.0031 3062.892153 0 0.0751 190 | 0/8 9 h-lim-p 0.2963 20.0000 0.0008 3062.892144 0 1.1850 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 3062.892143 0 1.0938 232 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3062.892143 0 1.0938 252 | 0/8 12 h-lim-p 0.1267 20.0000 0.0000 3062.892143 0 0.0079 275 | 0/8 13 h-lim-p 0.0003 20.0000 0.0007 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0013 | 0/8 15 h-lim-p 0.0000 20.0000 0.0013 Out... lnL = -3062.892143 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3062.892143 Node 7: lnL = -3062.892143 Node 8: lnL = -3062.892143 Node 9: lnL = -3062.892143 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 289 Sequential format.. Reading seq # 1: YCR014C_Sbay Reading seq # 2: YCR014C_Scer Reading seq # 3: YCR014C_Skud Reading seq # 4: YCR014C_Smik Reading seq # 5: YCR014C_Spar Sequences read.. Counting patterns.. # site patterns = 147 Counting frequencies.. 120 bytes for distance 23520 bytes for lkl0 18816 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.013427 0.232650 0.112653 0.158237 0.094481 0.190981 0.209871 0.219801 lnL0 = -1415.950666 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1415.950666 x= 0.01343 0.23265 0.11265 0.15824 0.09448 0.19098 0.20987 0.21980 1 h-lim-p 0.0054 0.0436 30.3238 1415.478736 4 0.0011 31 | 0/8 2 h-lim-p 0.0009 0.0070 15.7735 1415.361722 0 0.0013 43 | 0/8 3 h-lim-p 0.0009 0.0076 8.7968 1415.337037 3 0.0009 61 | 0/8 4 h-lim-p 0.0057 0.2428 1.3333 1415.335603 4 0.0017 84 | 0/8 5 h-lim-p 0.0032 0.3635 0.6922 1415.335357 3 0.0013 102 | 0/8 6 h-lim-p 0.0062 1.1831 0.1396 1415.335329 2 0.0024 126 | 0/8 7 h-lim-p 0.0063 1.8474 0.0528 1415.335314 3 0.0037 155 | 0/8 8 h-lim-p 0.0231 20.0000 0.0085 1415.333110 0 0.2770 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 1415.333051 2 0.9961 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1415.333051 0 1.0938 222 | 0/8 11 h-lim-p 1.2652 20.0000 0.0000 1415.333051 0 0.0791 245 | 0/8 12 h-lim-p 0.0180 20.0000 0.0000 1415.333051 0 0.0000 285 | 0/8 13 h-lim-p 0.0000 20.0000 0.0004 | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1415.333051 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1415.333051 Node 7: lnL = -1415.333051 Node 8: lnL = -1415.333051 Node 9: lnL = -1415.333051 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 847 Sequential format.. Reading seq # 1: YCR015C_Sbay Reading seq # 2: YCR015C_Scer Reading seq # 3: YCR015C_Skud Reading seq # 4: YCR015C_Smik Reading seq # 5: YCR015C_Spar Sequences read.. Counting patterns.. # site patterns = 317 Counting frequencies.. 120 bytes for distance 50720 bytes for lkl0 40576 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.057244 0.088438 0.000060 0.228413 0.185537 0.234478 0.175141 0.228597 lnL0 = -4070.546583 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4070.546583 x= 0.05724 0.08844 0.00006 0.22841 0.18554 0.23448 0.17514 0.22860 1 h-lim-p 0.0014 0.0115 203.9437 4067.174845 9 0.0001 43 | 0/8 2 h-lim-p 0.0004 0.0042 70.8597 4066.063841 1 0.0005 57 | 0/8 3 h-lim-p 0.0007 0.0056 15.1555 4066.024633 4 0.0004 78 | 0/8 4 h-lim-p 0.0018 0.0558 3.0071 4066.023162 4 0.0003 99 | 0/8 5 h-lim-p 0.0016 0.3688 0.6365 4066.023083 2 0.0004 116 | 0/8 6 h-lim-p 0.0029 2.7852 0.0870 4066.023079 0 0.0006 137 | 0/8 7 h-lim-p 0.0044 19.8246 0.0124 4066.023013 0 0.0177 159 | 0/8 8 h-lim-p 0.0040 20.0000 0.0545 4066.020914 0 0.0161 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4066.020900 1 0.9961 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4066.020900 0 1.0938 223 | 0/8 11 h-lim-p 1.1457 20.0000 0.0000 4066.020900 0 3.4371 244 | 0/8 12 h-lim-p 0.0983 20.0000 0.0009 4066.020900 0 0.0123 266 | 0/8 13 h-lim-p 0.0034 20.0000 0.0032 4066.020900 0 0.0025 286 | 0/8 14 h-lim-p 0.0011 11.4898 0.0072 4066.020900 0 0.0000 323 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 4066.020900 0 0.0000 351 Out... lnL = -4066.020900 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4066.020900 Node 7: lnL = -4066.020900 Node 8: lnL = -4066.020900 Node 9: lnL = -4066.020900 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 949 Sequential format.. Reading seq # 1: YCR016W_Sbay Reading seq # 2: YCR016W_Scer Reading seq # 3: YCR016W_Skud Reading seq # 4: YCR016W_Smik Reading seq # 5: YCR016W_Spar Sequences read.. Counting patterns.. # site patterns = 458 Counting frequencies.. 120 bytes for distance 73280 bytes for lkl0 58624 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.119377 0.007660 0.078374 0.204783 0.211242 0.351233 0.610199 0.419931 lnL0 = -5116.034596 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 5116.034596 x= 0.11938 0.00766 0.07837 0.20478 0.21124 0.35123 0.61020 0.41993 1 h-lim-p 0.0037 0.8774 167.2933 5111.638803 8 0.0003 39 | 0/8 2 h-lim-p 0.0012 0.0093 37.5143 5111.042209 6 0.0009 63 | 0/8 3 h-lim-p 0.0014 0.0109 23.2975 5110.903258 4 0.0007 83 | 0/8 4 h-lim-p 0.0029 0.0444 5.3756 5110.890969 5 0.0009 108 | 0/8 5 h-lim-p 0.0049 0.1998 1.0098 5110.890368 2 0.0012 125 | 0/8 6 h-lim-p 0.0028 0.8176 0.4429 5110.890248 1 0.0014 139 | 0/8 7 h-lim-p 0.0022 2.6455 0.2762 5110.890171 1 0.0023 161 | 0/8 8 h-lim-p 0.2488 20.0000 0.0025 5110.883265 0 0.9951 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 5110.883194 1 0.9961 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 5110.883194 0 1.0938 225 | 0/8 11 h-lim-p 1.3461 20.0000 0.0000 5110.883194 0 1.3461 245 | 0/8 12 h-lim-p 1.1457 20.0000 0.0000 5110.883194 0 0.5728 265 | 0/8 13 h-lim-p 0.0296 20.0000 0.0002 5110.883194 0 0.0259 285 | 0/8 14 h-lim-p 0.0074 20.0000 0.0007 5110.883194 0 0.0000 315 | 0/8 15 h-lim-p 0.0021 20.0000 0.0000 5110.883194 0 0.0000 341 Out... lnL = -5110.883194 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -5110.883194 Node 7: lnL = -5110.883194 Node 8: lnL = -5110.883194 Node 9: lnL = -5110.883194 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 868 Sequential format.. Reading seq # 1: YCR018C_Sbay Reading seq # 2: YCR018C_Scer Reading seq # 3: YCR018C_Skud Reading seq # 4: YCR018C_Smik Reading seq # 5: YCR018C_Spar Sequences read.. Counting patterns.. # site patterns = 357 Counting frequencies.. 120 bytes for distance 57120 bytes for lkl0 45696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.061362 0.034763 0.160724 0.083542 0.125023 0.222914 0.439653 0.271266 lnL0 = -3903.620448 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3903.620448 x= 0.06136 0.03476 0.16072 0.08354 0.12502 0.22291 0.43965 0.27127 1 h-lim-p 0.0025 0.6379 175.5348 3898.785913 9 0.0004 45 | 0/8 2 h-lim-p 0.0004 0.0033 68.9774 3897.524915 0 0.0008 58 | 0/8 3 h-lim-p 0.0003 0.0025 75.1618 3897.198225 6 0.0002 85 | 0/8 4 h-lim-p 0.0020 0.0419 8.0399 3897.176832 5 0.0007 110 | 0/8 5 h-lim-p 0.0011 0.0580 5.0442 3897.171535 3 0.0005 128 | 0/8 6 h-lim-p 0.0032 0.1702 0.8586 3897.171011 4 0.0010 151 | 0/8 7 h-lim-p 0.0021 1.2678 0.4070 3897.169151 0 0.0062 172 | 0/8 8 h-lim-p 0.0290 8.8593 0.0867 3897.012648 0 0.1159 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0018 3897.005495 2 1.1719 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0005 3897.005241 3 1.3437 245 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3897.005240 0 1.0938 265 | 0/8 12 h-lim-p 1.6059 20.0000 0.0000 3897.005240 0 1.4051 285 | 0/8 13 h-lim-p 1.7695 20.0000 0.0000 3897.005240 0 1.5483 305 | 0/8 14 h-lim-p 0.5265 20.0000 0.0000 3897.005240 0 0.3949 325 | 0/8 15 h-lim-p 0.0150 20.0000 0.0010 3897.005240 0 0.0150 345 | 0/8 16 h-lim-p 0.0050 20.0000 0.0031 3897.005240 0 0.0000 373 | 0/8 17 h-lim-p 0.0003 20.0000 0.0001 3897.005240 0 0.0000 402 | 0/8 18 h-lim-p 0.0001 20.0000 0.0000 3897.005240 0 0.0000 436 Out... lnL = -3897.005240 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3897.005240 Node 7: lnL = -3897.005240 Node 8: lnL = -3897.005240 Node 9: lnL = -3897.005240 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 879 Sequential format.. Reading seq # 1: YCR019W_Sbay Reading seq # 2: YCR019W_Scer Reading seq # 3: YCR019W_Skud Reading seq # 4: YCR019W_Smik Reading seq # 5: YCR019W_Spar Sequences read.. Counting patterns.. # site patterns = 381 Counting frequencies.. 120 bytes for distance 60960 bytes for lkl0 48768 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.153782 0.097498 0.104336 0.203881 0.139701 0.290171 0.349347 0.413645 lnL0 = -4534.256897 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4534.256897 x= 0.15378 0.09750 0.10434 0.20388 0.13970 0.29017 0.34935 0.41364 1 h-lim-p 0.0030 0.0243 72.3967 4533.306652 7 0.0004 37 | 0/8 2 h-lim-p 0.0015 0.0220 18.0572 4533.196670 2 0.0007 53 | 0/8 3 h-lim-p 0.0007 0.0267 17.3052 4533.149262 6 0.0005 81 | 0/8 4 h-lim-p 0.0022 0.0983 4.1093 4533.140748 4 0.0011 102 | 0/8 5 h-lim-p 0.0034 0.2003 1.3999 4533.140095 2 0.0007 119 | 0/8 6 h-lim-p 0.0056 2.2201 0.1850 4533.140083 0 0.0007 133 | 0/8 7 h-lim-p 0.0038 6.7738 0.0336 4533.140082 0 0.0017 153 | 0/8 8 h-lim-p 0.0955 20.0000 0.0006 4533.139815 0 0.7643 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4533.139813 0 1.0938 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4533.139813 0 1.0938 216 | 0/8 11 h-lim-p 2.4064 20.0000 0.0000 4533.139813 0 1.0528 236 | 0/8 12 h-lim-p 0.7191 20.0000 0.0000 4533.139813 0 0.0112 261 | 0/8 13 h-lim-p 0.0000 16.9018 0.0130 4533.139813 0 0.0000 291 | 0/8 14 h-lim-p 0.0025 20.0000 0.0000 4533.139813 0 0.0006 312 Out... lnL = -4533.139813 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4533.139813 Node 7: lnL = -4533.139813 Node 8: lnL = -4533.139813 Node 9: lnL = -4533.139813 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 256 Sequential format.. Reading seq # 1: YCR020C-A_Sbay Reading seq # 2: YCR020C-A_Scer Reading seq # 3: YCR020C-A_Skud Reading seq # 4: YCR020C-A_Smik Reading seq # 5: YCR020C-A_Spar Sequences read.. Counting patterns.. # site patterns = 141 Counting frequencies.. 120 bytes for distance 22560 bytes for lkl0 18048 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.098674 0.092096 0.143426 0.198992 0.063103 0.218731 0.199199 0.299375 lnL0 = -1209.792691 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1209.792691 x= 0.09867 0.09210 0.14343 0.19899 0.06310 0.21873 0.19920 0.29938 1 h-lim-p 0.0157 2.2364 39.2818 1209.098201 8 0.0010 41 | 0/8 2 h-lim-p 0.0011 0.0086 13.9967 1209.012193 3 0.0010 59 | 0/8 3 h-lim-p 0.0037 0.0389 3.7362 1209.003168 5 0.0014 81 | 0/8 4 h-lim-p 0.0079 1.0745 0.6588 1209.002801 2 0.0017 98 | 0/8 5 h-lim-p 0.0081 1.0697 0.1398 1209.002777 3 0.0026 126 | 0/8 6 h-lim-p 0.0153 8.2994 0.0239 1209.002775 1 0.0038 149 | 0/8 7 h-lim-p 0.0573 20.0000 0.0016 1209.002536 0 0.4587 172 | 0/8 8 h-lim-p 0.0042 1.8813 0.1698 1209.002481 3 0.0028 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1209.002478 1 0.9961 221 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1209.002478 0 0.5469 242 | 0/8 11 h-lim-p 0.3446 20.0000 0.0000 1209.002478 0 0.0054 267 | 0/8 12 h-lim-p 0.0022 20.0000 0.0000 1209.002478 0 0.0001 290 | 0/8 13 h-lim-p 0.0002 20.0000 0.0000 1209.002478 0 0.0000 314 Out... lnL = -1209.002478 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1209.002478 Node 7: lnL = -1209.002478 Node 8: lnL = -1209.002478 Node 9: lnL = -1209.002478 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 188 Sequential format.. Reading seq # 1: YCR020C_Sbay Reading seq # 2: YCR020C_Scer Reading seq # 3: YCR020C_Skud Reading seq # 4: YCR020C_Smik Reading seq # 5: YCR020C_Spar Sequences read.. Counting patterns.. # site patterns = 90 Counting frequencies.. 120 bytes for distance 14400 bytes for lkl0 11520 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.038868 0.088576 0.105628 0.042942 0.072671 0.140877 0.127647 0.161701 lnL0 = -744.222080 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 744.222080 x= 0.03887 0.08858 0.10563 0.04294 0.07267 0.14088 0.12765 0.16170 1 h-lim-p 0.0046 0.0364 40.1751 743.586607 9 0.0008 45 | 0/8 2 h-lim-p 0.0006 0.0049 17.8988 743.496748 4 0.0006 65 | 0/8 3 h-lim-p 0.0012 0.0161 9.3516 743.463477 4 0.0010 85 | 0/8 4 h-lim-p 0.0083 0.1129 1.0971 743.462971 3 0.0009 105 | 0/8 5 h-lim-p 0.0051 0.9897 0.1873 743.462953 2 0.0010 122 | 0/8 6 h-lim-p 0.0065 8.0973 0.0288 743.462950 0 0.0033 142 | 0/8 7 h-lim-p 0.0137 20.0000 0.0069 743.462894 0 0.0546 164 | 0/8 8 h-lim-p 0.0048 9.6170 0.0780 743.462392 0 0.0145 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 743.462390 1 0.9961 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 743.462390 0 1.0938 227 | 0/8 11 h-lim-p 1.4037 20.0000 0.0000 743.462390 0 2.8075 248 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 743.462390 0 0.1562 271 | 0/8 13 h-lim-p 0.0139 20.0000 0.0000 743.462390 0 0.0030 292 | 0/8 14 h-lim-p 0.0012 20.0000 0.0000 743.462390 0 0.0000 321 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0006 743.462390 0 0.0000 389 | 0/8 17 h-lim-p 0.0000 20.0000 0.0006 | 0/8 18 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -743.462390 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -743.462390 Node 7: lnL = -743.462390 Node 8: lnL = -743.462390 Node 9: lnL = -743.462390 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 256 Sequential format.. Reading seq # 1: YCR020W-B_Sbay Reading seq # 2: YCR020W-B_Scer Reading seq # 3: YCR020W-B_Skud Reading seq # 4: YCR020W-B_Smik Reading seq # 5: YCR020W-B_Spar Sequences read.. Counting patterns.. # site patterns = 144 Counting frequencies.. 120 bytes for distance 23040 bytes for lkl0 18432 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.090871 0.141403 0.325806 0.379503 0.000060 0.196604 0.139420 0.286615 lnL0 = -1083.104911 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1083.104911 x= 0.09087 0.14140 0.32581 0.37950 0.00006 0.19660 0.13942 0.28662 1 h-lim-p 0.0000 0.0000 73.6082 1083.056128 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0052 32.3403 1082.118143 0 0.0026 41 | 1/8 3 h-lim-p 0.0055 0.0441 6.2852 1082.051101 5 0.0029 64 | 1/8 4 h-lim-p 0.0321 0.4176 0.5738 1081.487147 0 0.1285 78 | 1/8 5 h-lim-p 0.0057 0.0459 3.5987 1079.176185 0 0.0229 99 | 1/8 6 h-lim-p 0.0094 0.0749 5.7785 1079.105242 6 0.0041 123 | 1/8 7 h-lim-p 0.0091 0.2403 2.5874 1079.077611 5 0.0088 146 | 1/8 8 h-lim-p 0.5834 7.5439 0.0391 1078.954772 6 0.5005 169 | 1/8 9 h-lim-p 2.5000 20.0000 0.0046 1078.953075 2 0.5859 193 | 1/8 10 h-lim-p 2.5000 20.0000 0.0008 1078.952997 4 0.6789 221 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 1078.952997 0 1.0938 240 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 1078.952997 0 1.0938 259 | 1/8 13 h-lim-p 1.1957 20.0000 0.0000 1078.952997 0 1.1957 278 | 1/8 14 h-lim-p 0.5269 20.0000 0.0000 1078.952997 0 0.1317 298 | 1/8 15 h-lim-p 0.0096 20.0000 0.0003 1078.952997 0 0.0096 317 | 1/8 16 h-lim-p 0.0033 20.0000 0.0008 1078.952997 0 0.0000 358 | 1/8 17 h-lim-p 0.0000 20.0000 0.0001 1078.952997 0 0.0000 383 | 1/8 18 h-lim-p 0.0000 20.0000 0.0001 .. | 1/8 19 h-lim-p 0.0000 20.0000 0.0001 | 1/8 20 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1078.952997 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1078.952997 Node 7: lnL = -1078.952997 Node 8: lnL = -1078.952997 Node 9: lnL = -1078.952997 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 340 Sequential format.. Reading seq # 1: YCR021C_Sbay Reading seq # 2: YCR021C_Scer Reading seq # 3: YCR021C_Skud Reading seq # 4: YCR021C_Smik Reading seq # 5: YCR021C_Spar Sequences read.. Counting patterns.. # site patterns = 156 Counting frequencies.. 120 bytes for distance 24960 bytes for lkl0 19968 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.006521 0.071134 0.050697 0.133482 0.126003 0.247796 0.206033 0.154781 lnL0 = -1512.104928 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1512.104928 x= 0.00652 0.07113 0.05070 0.13348 0.12600 0.24780 0.20603 0.15478 1 h-lim-p 0.0065 0.0521 52.5126 1511.628586 8 0.0004 42 | 0/8 2 h-lim-p 0.0012 0.0098 9.6644 1511.594512 7 0.0007 73 | 0/8 3 h-lim-p 0.0039 0.1214 1.8503 1511.592891 5 0.0010 95 | 0/8 4 h-lim-p 0.0024 0.3124 0.7605 1511.592700 3 0.0008 115 | 0/8 5 h-lim-p 0.0079 0.6552 0.0738 1511.592698 1 0.0008 139 | 0/8 6 h-lim-p 0.0021 6.3841 0.0279 1511.592698 0 0.0009 159 | 0/8 7 h-lim-p 0.0049 10.9843 0.0052 1511.592698 0 0.0011 180 | 0/8 8 h-lim-p 0.1081 20.0000 0.0001 1511.592697 0 0.8647 203 | 0/8 9 h-lim-p 1.6916 20.0000 0.0000 1511.592697 0 1.4801 223 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1511.592697 0 1.2500 243 | 0/8 11 h-lim-p 0.6603 20.0000 0.0000 1511.592697 0 0.5778 263 | 0/8 12 h-lim-p 0.0791 20.0000 0.0002 1511.592697 0 0.0049 286 | 0/8 13 h-lim-p 0.0017 20.0000 0.0005 1511.592697 0 0.0001 309 | 0/8 14 h-lim-p 0.0000 6.1059 0.0026 1511.592697 0 0.0000 330 | 0/8 15 h-lim-p 0.0000 20.0000 0.0013 1511.592697 0 0.0000 351 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 1511.592697 0 0.0000 377 | 0/8 17 h-lim-p 0.0001 20.0000 0.0000 1511.592697 0 0.0000 410 Out... lnL = -1511.592697 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1511.592697 Node 7: lnL = -1511.592697 Node 8: lnL = -1511.592697 Node 9: lnL = -1511.592697 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 389 Sequential format.. Reading seq # 1: YCR023C_Sbay Reading seq # 2: YCR023C_Scer Reading seq # 3: YCR023C_Skud Reading seq # 4: YCR023C_Smik Reading seq # 5: YCR023C_Spar Sequences read.. Counting patterns.. # site patterns = 179 Counting frequencies.. 120 bytes for distance 28640 bytes for lkl0 22912 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.071406 0.018887 0.079127 0.138080 0.084417 0.224676 0.219488 0.227396 lnL0 = -1721.271338 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1721.271338 x= 0.07141 0.01889 0.07913 0.13808 0.08442 0.22468 0.21949 0.22740 1 h-lim-p 0.0089 0.2795 62.0585 1720.728898 6 0.0003 38 | 0/8 2 h-lim-p 0.0027 0.0229 6.9951 1720.713615 2 0.0006 55 | 0/8 3 h-lim-p 0.0034 0.1030 1.2979 1720.713072 2 0.0007 72 | 0/8 4 h-lim-p 0.0016 0.2299 0.5321 1720.713016 3 0.0005 92 | 0/8 5 h-lim-p 0.0044 4.8573 0.0594 1720.713014 0 0.0010 113 | 0/8 6 h-lim-p 0.0055 15.0877 0.0103 1720.713014 0 0.0012 134 | 0/8 7 h-lim-p 0.0032 20.0000 0.0039 1720.713013 0 0.0126 156 | 0/8 8 h-lim-p 0.0181 20.0000 0.0027 1720.712967 0 0.0726 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1720.712967 0 1.0938 198 | 0/8 10 h-lim-p 1.7435 20.0000 0.0000 1720.712967 0 0.7628 218 | 0/8 11 h-lim-p 0.5337 20.0000 0.0000 1720.712967 0 0.0021 245 | 0/8 12 h-lim-p 0.0008 20.0000 0.0000 1720.712967 0 0.0002 266 | 0/8 13 h-lim-p 0.0000 20.0000 0.0003 1720.712967 0 0.0000 287 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 | 0/8 16 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -1720.712967 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1720.712967 Node 7: lnL = -1720.712967 Node 8: lnL = -1720.712967 Node 9: lnL = -1720.712967 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 810 Sequential format.. Reading seq # 1: YCR024C_Sbay Reading seq # 2: YCR024C_Scer Reading seq # 3: YCR024C_Skud Reading seq # 4: YCR024C_Smik Reading seq # 5: YCR024C_Spar Sequences read.. Counting patterns.. # site patterns = 216 Counting frequencies.. 120 bytes for distance 34560 bytes for lkl0 27648 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.026299 0.044393 0.053521 0.079514 0.034022 0.081504 0.134284 0.112538 lnL0 = -2667.444576 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2667.444576 x= 0.02630 0.04439 0.05352 0.07951 0.03402 0.08150 0.13428 0.11254 1 h-lim-p 0.0006 0.5461 287.2273 2663.668971 9 0.0001 46 | 0/8 2 h-lim-p 0.0003 0.0021 70.3339 2663.227531 6 0.0002 71 | 0/8 3 h-lim-p 0.0005 0.0042 17.3705 2663.202106 6 0.0002 99 | 0/8 4 h-lim-p 0.0007 0.0259 4.5408 2663.200207 5 0.0002 125 | 0/8 5 h-lim-p 0.0021 0.4223 0.4177 2663.200187 1 0.0002 141 | 0/8 6 h-lim-p 0.0009 1.8857 0.1049 2663.200186 0 0.0002 162 | 0/8 7 h-lim-p 0.0037 20.0000 0.0058 2663.200179 0 0.0148 184 | 0/8 8 h-lim-p 0.0053 20.0000 0.0162 2663.199421 0 0.0318 206 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 2663.199417 0 1.0938 226 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2663.199417 0 1.0938 246 | 0/8 11 h-lim-p 1.5407 20.0000 0.0000 2663.199417 0 2.3110 266 | 0/8 12 h-lim-p 0.2276 20.0000 0.0004 2663.199417 0 0.0002 295 | 0/8 13 h-lim-p 0.0001 20.0000 0.0013 2663.199417 0 0.0001 315 | 0/8 14 h-lim-p 0.0000 4.6588 0.0083 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0014 | 0/8 16 h-lim-p 0.0000 20.0000 0.0014 Out... lnL = -2663.199417 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2663.199417 Node 7: lnL = -2663.199417 Node 8: lnL = -2663.199417 Node 9: lnL = -2663.199417 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 844 Sequential format.. Reading seq # 1: YCR026C_Sbay Reading seq # 2: YCR026C_Scer Reading seq # 3: YCR026C_Skud Reading seq # 4: YCR026C_Smik Reading seq # 5: YCR026C_Spar Sequences read.. Counting patterns.. # site patterns = 420 Counting frequencies.. 120 bytes for distance 67200 bytes for lkl0 53760 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.141999 0.134809 0.072621 0.242184 0.216819 0.343678 0.296871 0.418379 lnL0 = -4520.054537 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4520.054537 x= 0.14200 0.13481 0.07262 0.24218 0.21682 0.34368 0.29687 0.41838 1 h-lim-p 0.0104 0.0935 93.3428 4518.394502 8 0.0004 45 | 0/8 2 h-lim-p 0.0014 0.0177 27.8084 4517.976563 5 0.0012 69 | 0/8 3 h-lim-p 0.0024 0.0282 13.2343 4517.925890 6 0.0007 97 | 0/8 4 h-lim-p 0.0023 0.1228 4.1248 4517.915850 5 0.0013 122 | 0/8 5 h-lim-p 0.0085 0.5117 0.6454 4517.915682 2 0.0008 140 | 0/8 6 h-lim-p 0.0113 6.6497 0.0468 4517.915679 1 0.0014 164 | 0/8 7 h-lim-p 0.0039 20.0000 0.0167 4517.915646 0 0.0155 186 | 0/8 8 h-lim-p 0.0104 20.0000 0.0250 4517.914480 0 0.0417 208 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4517.914475 0 1.0938 228 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4517.914475 0 1.0938 248 | 0/8 11 h-lim-p 2.2480 20.0000 0.0000 4517.914475 0 0.9835 268 | 0/8 12 h-lim-p 0.8042 20.0000 0.0000 4517.914475 0 0.4021 288 | 0/8 13 h-lim-p 0.0161 20.0000 0.0002 4517.914475 0 0.0001 315 | 0/8 14 h-lim-p 0.0012 20.0000 0.0000 4517.914475 0 0.0000 342 | 0/8 15 h-lim-p 0.0029 20.0000 0.0000 4517.914475 0 0.0029 362 Out... lnL = -4517.914475 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4517.914475 Node 7: lnL = -4517.914475 Node 8: lnL = -4517.914475 Node 9: lnL = -4517.914475 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 911 Sequential format.. Reading seq # 1: YCR027C_Sbay Reading seq # 2: YCR027C_Scer Reading seq # 3: YCR027C_Skud Reading seq # 4: YCR027C_Smik Reading seq # 5: YCR027C_Spar Sequences read.. Counting patterns.. # site patterns = 417 Counting frequencies.. 120 bytes for distance 66720 bytes for lkl0 53376 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.136308 0.224943 0.000060 0.229421 0.354290 0.263030 0.305583 0.389594 lnL0 = -4773.743150 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4773.743150 x= 0.13631 0.22494 0.00006 0.22942 0.35429 0.26303 0.30558 0.38959 1 h-lim-p 0.0000 0.0000 257.5830 4773.635810 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0072 131.5694 4768.290409 0 0.0010 40 | 1/8 3 h-lim-p 0.0021 0.0166 30.1299 4767.428871 7 0.0018 65 | 1/8 4 h-lim-p 0.0046 0.0674 12.0644 4767.247501 5 0.0019 88 | 1/8 5 h-lim-p 0.0064 0.1274 3.5116 4766.680147 0 0.0128 101 | 1/8 6 h-lim-p 0.0067 0.0535 6.4752 4755.689851 0 0.0201 114 | 0/8 7 h-lim-p 0.0004 0.0028 78.2124 4749.116794 0 0.0014 128 | 0/8 8 h-lim-p 0.0262 0.2096 1.4897 4749.110703 2 0.0015 147 | 0/8 9 h-lim-p 0.0038 0.6247 0.5983 4747.044920 0 0.1223 164 | 0/8 10 h-lim-p 2.5000 20.0000 0.0210 4746.797743 6 1.0146 198 | 0/8 11 h-lim-p 2.5000 20.0000 0.0047 4746.789235 5 0.7438 231 | 0/8 12 h-lim-p 2.5000 20.0000 0.0004 4746.789158 3 0.8855 259 | 0/8 13 h-lim-p 2.5000 20.0000 0.0001 4746.789155 1 0.6152 282 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 4746.789155 0 1.0938 302 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 4746.789155 0 1.0938 322 | 0/8 16 h-lim-p 1.4123 20.0000 0.0000 4746.789155 0 1.2357 342 | 0/8 17 h-lim-p 1.2993 20.0000 0.0000 4746.789155 0 2.5985 363 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 4746.789155 0 0.6250 384 | 0/8 19 h-lim-p 0.1161 20.0000 0.0000 4746.789155 0 0.0000 422 | 0/8 20 h-lim-p 0.0000 20.0000 0.0003 | 0/8 21 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -4746.789155 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4746.789155 Node 7: lnL = -4746.789155 Node 8: lnL = -4746.789155 Node 9: lnL = -4746.789155 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 493 Sequential format.. Reading seq # 1: YCR028C-A_Sbay Reading seq # 2: YCR028C-A_Scer Reading seq # 3: YCR028C-A_Skud Reading seq # 4: YCR028C-A_Smik Reading seq # 5: YCR028C-A_Spar Sequences read.. Counting patterns.. # site patterns = 193 Counting frequencies.. 120 bytes for distance 30880 bytes for lkl0 24704 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.288679 0.089139 0.087048 0.014874 0.361753 0.259427 0.170892 0.000060 lnL0 = -2046.157878 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2046.157878 x= 0.28868 0.08914 0.08705 0.01487 0.36175 0.25943 0.17089 0.00006 1 h-lim-p 0.0000 0.0000 424.0380 2045.973214 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0013 372.9065 2006.560819 0 0.0010 40 | 1/8 3 h-lim-p 0.0001 0.0008 105.7824 2005.476979 0 0.0002 53 | 1/8 4 h-lim-p 0.0007 0.0062 31.3392 2005.265528 8 0.0005 85 | 1/8 5 h-lim-p 0.0021 0.0374 6.8882 2005.234205 6 0.0008 111 | 0/8 6 h-lim-p 0.0002 0.0173 33.9584 2004.876324 0 0.0006 125 | 0/8 7 h-lim-p 0.0019 0.0194 10.8700 2004.757819 7 0.0014 153 | 0/8 8 h-lim-p 0.0129 0.2499 1.1739 2001.578932 0 0.0517 167 | 0/8 9 h-lim-p 0.0004 0.0035 26.8646 1993.687689 m 0.0035 179 | 0/8 10 h-lim-p 0.0000 0.0000 0.0247 h-lim-p: 2.65146390e-17 2.12117112e-16 2.47327883e-02 1993.687689 .. | 0/8 11 h-lim-p 0.0000 0.0267 293.9186 1988.292923 0 0.0002 211 | 0/8 12 h-lim-p 0.0005 0.0043 30.2529 1988.065298 2 0.0005 227 | 0/8 13 h-lim-p 0.0003 0.0020 10.0950 1988.029344 0 0.0010 241 | 0/8 14 h-lim-p 0.0202 0.3064 0.4994 1988.029295 3 0.0004 266 | 0/8 15 h-lim-p 0.0020 0.3835 0.0943 1988.029288 1 0.0010 289 | 0/8 16 h-lim-p 0.0010 9.4340 0.0878 1988.029276 0 0.0016 309 | 0/8 17 h-lim-p 0.0019 3.3489 0.0721 1988.027879 0 0.1212 335 | 0/8 18 h-lim-p 0.0020 0.0504 4.2761 1988.025871 1 0.0026 357 | 0/8 19 h-lim-p 2.5000 20.0000 0.0035 1988.025485 4 1.3122 378 | 0/8 20 h-lim-p 2.4907 20.0000 0.0018 1988.025467 0 1.2453 398 | 0/8 21 h-lim-p 2.5000 20.0000 0.0001 1988.025467 0 1.0938 418 | 0/8 22 h-lim-p 2.5000 20.0000 0.0000 1988.025467 0 0.6250 439 | 0/8 23 h-lim-p 0.1417 20.0000 0.0001 1988.025467 0 0.0177 461 | 0/8 24 h-lim-p 0.0050 20.0000 0.0002 1988.025467 0 0.0000 491 | 0/8 25 h-lim-p 0.0000 20.0000 0.0000 1988.025467 0 0.0000 523 | 0/8 26 h-lim-p 0.0000 20.0000 0.0011 | 0/8 27 h-lim-p 0.0000 20.0000 0.0011 Out... lnL = -1988.025467 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1988.025467 Node 7: lnL = -1988.025467 Node 8: lnL = -1988.025467 Node 9: lnL = -1988.025467 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 1068 Sequential format.. Reading seq # 1: YCR030C_Sbay Reading seq # 2: YCR030C_Scer Reading seq # 3: YCR030C_Skud Reading seq # 4: YCR030C_Smik Reading seq # 5: YCR030C_Spar Sequences read.. Counting patterns.. # site patterns = 327 Counting frequencies.. 120 bytes for distance 52320 bytes for lkl0 41856 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.322164 0.084130 0.052001 0.147861 0.094459 0.193420 0.213068 0.007114 lnL0 = -4292.873922 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4292.873922 x= 0.32216 0.08413 0.05200 0.14786 0.09446 0.19342 0.21307 0.00711 1 h-lim-p 0.0003 0.0028 143.9611 4290.826891 9 0.0002 48 | 0/8 2 h-lim-p 0.0004 0.0032 38.2316 4290.651015 7 0.0003 76 | 0/8 3 h-lim-p 0.0006 0.0163 16.7891 4290.618243 2 0.0003 92 | 0/8 4 h-lim-p 0.0007 0.0182 6.8800 4290.611306 3 0.0003 111 | 0/8 5 h-lim-p 0.0038 0.3530 0.6319 4290.611207 3 0.0005 131 | 0/8 6 h-lim-p 0.0037 2.3355 0.0873 4290.611206 0 0.0004 153 | 0/8 7 h-lim-p 0.0028 20.0000 0.0127 4290.611206 0 0.0007 174 | 0/8 8 h-lim-p 0.0324 20.0000 0.0003 4290.611157 0 0.7776 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4290.611157 0 1.0938 218 | 0/8 10 h-lim-p 1.1563 20.0000 0.0000 4290.611157 0 1.0118 238 | 0/8 11 h-lim-p 0.7620 20.0000 0.0000 4290.611157 0 0.0060 264 | 0/8 12 h-lim-p 0.0003 20.0000 0.0008 4290.611157 0 0.0001 285 | 0/8 13 h-lim-p 0.0005 20.0000 0.0001 4290.611157 0 0.0001 306 | 0/8 14 h-lim-p 0.0000 20.0000 0.0014 4290.611157 0 0.0000 332 | 0/8 15 h-lim-p 0.0005 20.0000 0.0000 4290.611157 0 0.0000 364 Out... lnL = -4290.611157 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4290.611157 Node 7: lnL = -4290.611157 Node 8: lnL = -4290.611157 Node 9: lnL = -4290.611157 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 914 Sequential format.. Reading seq # 1: YCR032W_Sbay Reading seq # 2: YCR032W_Scer Reading seq # 3: YCR032W_Skud Reading seq # 4: YCR032W_Smik Reading seq # 5: YCR032W_Spar Sequences read.. Counting patterns.. # site patterns = 373 Counting frequencies.. 120 bytes for distance 59680 bytes for lkl0 47744 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.369424 0.113506 0.111415 0.023635 0.459221 0.332226 0.214229 0.000060 lnL0 = -4397.125455 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4397.125455 x= 0.36942 0.11351 0.11141 0.02364 0.45922 0.33223 0.21423 0.00006 1 h-lim-p 0.0000 0.0000 1003.8416 4396.186166 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0014 402.2324 4339.933654 0 0.0006 40 | 1/8 3 h-lim-p 0.0001 0.0005 535.7961 4320.283329 0 0.0002 54 | 1/8 4 h-lim-p 0.0015 0.0121 33.9042 4319.982179 6 0.0005 81 | 1/8 5 h-lim-p 0.0018 0.0286 9.8324 4319.914899 5 0.0009 104 | 0/8 6 h-lim-p 0.0003 0.0138 31.3278 4319.287356 0 0.0024 119 | 0/8 7 h-lim-p 0.0006 0.0051 61.0900 4318.831104 1 0.0008 133 | 0/8 8 h-lim-p 0.0024 0.0195 17.3547 4318.635954 7 0.0013 163 | 0/8 9 h-lim-p 0.0503 0.4023 0.3690 4285.459829 m 0.4023 175 | 1/8 10 h-lim-p 0.9448 7.5586 0.0936 4278.007271 7 1.0077 210 | 1/8 11 h-lim-p 0.1072 0.8579 0.4261 4267.559739 0 0.3217 230 | 0/8 12 h-lim-p 0.0014 0.0109 35.6189 4266.764392 0 0.0027 250 | 0/8 13 h-lim-p 0.4901 3.9212 0.0440 4265.677389 0 1.4704 263 | 0/8 14 h-lim-p 2.4347 19.4773 0.0180 4265.421964 6 1.5054 299 | 0/8 15 h-lim-p 2.5000 20.0000 0.0041 4265.391249 6 1.2615 335 | 0/8 16 h-lim-p 2.5000 20.0000 0.0007 4265.390742 2 1.3159 360 | 0/8 17 h-lim-p 2.5000 20.0000 0.0003 4265.390726 1 0.9961 382 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 4265.390726 0 1.0938 402 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 4265.390726 0 0.6250 423 | 0/8 20 h-lim-p 1.3827 20.0000 0.0000 4265.390726 0 0.0000 463 Out... lnL = -4265.390726 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4265.390726 Node 7: lnL = -4265.390726 Node 8: lnL = -4265.390726 Node 9: lnL = -4265.390726 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 482 Sequential format.. Reading seq # 1: YCR033W_Sbay Reading seq # 2: YCR033W_Scer Reading seq # 3: YCR033W_Skud Reading seq # 4: YCR033W_Smik Reading seq # 5: YCR033W_Spar Sequences read.. Counting patterns.. # site patterns = 149 Counting frequencies.. 120 bytes for distance 23840 bytes for lkl0 19072 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.186040 0.030267 0.032597 0.073803 0.061958 0.138686 0.135474 0.001661 lnL0 = -1860.469298 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1860.469298 x= 0.18604 0.03027 0.03260 0.07380 0.06196 0.13869 0.13547 0.00166 1 h-lim-p 0.0003 0.0022 184.6702 1858.443901 6 0.0001 34 | 0/8 2 h-lim-p 0.0004 0.0034 22.0801 1858.398561 4 0.0002 53 | 0/8 3 h-lim-p 0.0008 0.0060 4.6207 1858.396232 5 0.0002 80 | 0/8 4 h-lim-p 0.0006 0.0120 1.6831 1858.395846 2 0.0003 96 | 0/8 5 h-lim-p 0.0019 0.2649 0.2774 1858.395837 0 0.0002 110 | 0/8 6 h-lim-p 0.0017 4.4579 0.0392 1858.395837 0 0.0004 131 | 0/8 7 h-lim-p 0.0040 5.2000 0.0036 1858.395837 0 0.0017 151 | 0/8 8 h-lim-p 0.0511 20.0000 0.0001 1858.395827 0 0.8176 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1858.395826 0 1.0938 195 | 0/8 10 h-lim-p 0.6719 20.0000 0.0000 1858.395826 0 1.0078 215 | 0/8 11 h-lim-p 0.7751 20.0000 0.0000 1858.395826 0 0.0045 242 | 0/8 12 h-lim-p 0.0001 3.1935 0.0016 1858.395826 0 0.0000 277 | 0/8 13 h-lim-p 0.0000 20.0000 0.0004 1858.395826 0 0.0000 304 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 1858.395826 0 0.0051 333 | 0/8 15 h-lim-p 0.0160 20.0000 0.0000 1858.395826 0 0.0000 363 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 1858.395826 0 0.0000 395 | 0/8 17 h-lim-p 0.0000 20.0000 0.0026 | 0/8 18 h-lim-p 0.0000 20.0000 0.0026 Out... lnL = -1858.395826 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1858.395826 Node 7: lnL = -1858.395826 Node 8: lnL = -1858.395826 Node 9: lnL = -1858.395826 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 440 Sequential format.. Reading seq # 1: YCR034W_Sbay Reading seq # 2: YCR034W_Scer Reading seq # 3: YCR034W_Skud Reading seq # 4: YCR034W_Smik Reading seq # 5: YCR034W_Spar Sequences read.. Counting patterns.. # site patterns = 148 Counting frequencies.. 120 bytes for distance 23680 bytes for lkl0 18944 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.203695 0.060995 0.062392 0.010466 0.253752 0.184279 0.120996 0.000060 lnL0 = -1730.199510 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1730.199510 x= 0.20370 0.06099 0.06239 0.01047 0.25375 0.18428 0.12100 0.00006 1 h-lim-p 0.0000 0.0000 530.0318 1729.862717 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0008 391.6259 1699.421494 0 0.0005 39 | 1/8 3 h-lim-p 0.0001 0.0004 296.9890 1693.749644 0 0.0002 53 | 1/8 4 h-lim-p 0.0004 0.0032 48.3604 1693.301725 3 0.0004 71 | 1/8 5 h-lim-p 0.0019 0.0154 8.3110 1693.280085 7 0.0005 100 | 0/8 6 h-lim-p 0.0002 0.0221 20.8272 1693.192106 0 0.0004 113 | 0/8 7 h-lim-p 0.0009 0.0256 10.0163 1693.135646 0 0.0013 125 | 0/8 8 h-lim-p 0.0083 0.1299 1.5918 1693.058891 6 0.0062 149 | 0/8 9 h-lim-p 0.0067 0.0540 0.6941 1686.359938 m 0.0540 161 | 0/8 10 h-lim-p 0.0000 0.0000 0.0182 h-lim-p: 9.83653959e-18 7.86923167e-17 1.81930986e-02 1686.359938 .. | 0/8 11 h-lim-p 0.0000 0.0072 274.0981 1683.483347 0 0.0001 200 | 0/8 12 h-lim-p 0.0000 0.0001 40.6804 1683.393941 m 0.0001 212 | 1/8 13 h-lim-p 0.0007 0.0628 3.5250 1683.390171 4 0.0006 233 | 1/8 14 h-lim-p 0.0013 1.3701 1.6630 1683.389618 3 0.0004 253 | 1/8 15 h-lim-p 0.0030 0.6532 0.2317 1683.388605 0 0.0060 266 | 0/8 16 h-lim-p 0.0008 0.1466 1.7645 1683.383215 0 0.0024 286 | 0/8 17 h-lim-p 0.0005 0.0202 8.2164 1683.322249 0 0.0041 301 | 0/8 18 h-lim-p 0.0009 0.0076 18.3355 1683.296907 5 0.0008 322 | 0/8 19 h-lim-p 0.0073 0.0585 0.8847 1683.222981 m 0.0585 334 | 1/8 20 h-lim-p 2.0846 16.6772 0.0074 1683.221379 5 0.1636 370 | 0/8 21 h-lim-p 0.0004 0.0533 3.3349 1683.211124 0 0.0029 392 | 0/8 22 h-lim-p 0.0939 0.7514 0.0143 1683.210148 0 0.3757 406 | 0/8 23 h-lim-p 2.5000 20.0000 0.0009 1683.209963 3 0.9644 432 | 0/8 24 h-lim-p 2.5000 20.0000 0.0001 1683.209962 0 1.0938 452 | 0/8 25 h-lim-p 2.5000 20.0000 0.0000 1683.209962 0 1.0938 472 | 0/8 26 h-lim-p 2.5000 20.0000 0.0000 1683.209962 0 0.0000 509 Out... lnL = -1683.209962 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1683.209962 Node 7: lnL = -1683.209962 Node 8: lnL = -1683.209962 Node 9: lnL = -1683.209962 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 292 Sequential format.. Reading seq # 1: YCR035C_Sbay Reading seq # 2: YCR035C_Scer Reading seq # 3: YCR035C_Skud Reading seq # 4: YCR035C_Smik Reading seq # 5: YCR035C_Spar Sequences read.. Counting patterns.. # site patterns = 139 Counting frequencies.. 120 bytes for distance 22240 bytes for lkl0 17792 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.324117 0.094564 0.103087 0.040003 0.369859 0.278086 0.185468 0.000060 lnL0 = -1425.072175 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1425.072175 x= 0.32412 0.09456 0.10309 0.04000 0.36986 0.27809 0.18547 0.00006 1 h-lim-p 0.0000 0.0000 404.8211 1423.948107 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0025 159.4314 1397.518426 0 0.0017 40 | 1/8 3 h-lim-p 0.0003 0.0023 66.0900 1396.402349 0 0.0006 53 | 1/8 4 h-lim-p 0.0043 0.0520 8.6152 1396.373204 7 0.0007 87 | 1/8 5 h-lim-p 0.0023 0.0875 2.4643 1396.307605 0 0.0046 100 | 0/8 6 h-lim-p 0.0023 0.2333 5.0367 1395.400782 0 0.0180 115 | 0/8 7 h-lim-p 0.0009 0.0071 50.5141 1389.938037 m 0.0071 127 | 1/8 8 h-lim-p 0.0033 0.0268 11.9400 1389.758264 7 0.0021 156 | 1/8 9 h-lim-p 0.0127 0.1245 1.9831 1389.527976 6 0.0130 179 | 1/8 10 h-lim-p 0.0141 0.1363 1.8373 1381.826732 0 0.0563 193 | 1/8 11 h-lim-p 2.5000 20.0000 0.0193 1379.939925 5 2.5806 214 | 1/8 12 h-lim-p 1.1759 9.4072 0.0285 1379.154793 0 1.7638 233 | 1/8 13 h-lim-p 2.4097 19.2779 0.0132 1379.052035 4 1.2043 260 | 0/8 14 h-lim-p 0.0253 3.3139 0.6286 1379.051645 4 0.0020 293 | 0/8 15 h-lim-p 0.4504 20.0000 0.0027 1379.042940 0 1.8017 315 | 0/8 16 h-lim-p 2.5000 20.0000 0.0007 1379.042633 2 1.0938 339 | 0/8 17 h-lim-p 2.5000 20.0000 0.0001 1379.042622 2 1.3159 364 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1379.042622 0 1.0938 384 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1379.042622 0 2.1875 404 | 0/8 20 h-lim-p 2.0104 20.0000 0.0000 1379.042622 0 0.8795 424 | 0/8 21 h-lim-p 2.5000 20.0000 0.0000 1379.042622 0 0.0586 449 | 0/8 22 h-lim-p 0.0510 20.0000 0.0000 1379.042622 0 0.0000 489 Out... lnL = -1379.042622 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1379.042622 Node 7: lnL = -1379.042622 Node 8: lnL = -1379.042622 Node 9: lnL = -1379.042622 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 298 Sequential format.. Reading seq # 1: YCR036W_Sbay Reading seq # 2: YCR036W_Scer Reading seq # 3: YCR036W_Skud Reading seq # 4: YCR036W_Smik Reading seq # 5: YCR036W_Spar Sequences read.. Counting patterns.. # site patterns = 141 Counting frequencies.. 120 bytes for distance 22560 bytes for lkl0 18048 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.308902 0.090868 0.097419 0.027037 0.373980 0.272095 0.179247 0.000060 lnL0 = -1417.480084 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1417.480084 x= 0.30890 0.09087 0.09742 0.02704 0.37398 0.27209 0.17925 0.00006 1 h-lim-p 0.0000 0.0000 586.2635 1416.375872 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0026 159.7227 1391.426915 8 0.0017 62 | 1/8 3 h-lim-p 0.0002 0.0015 137.0146 1388.000962 0 0.0005 75 | 1/8 4 h-lim-p 0.0045 0.0357 15.6016 1387.910233 7 0.0007 104 | 1/8 5 h-lim-p 0.0020 0.0537 5.6663 1387.865680 4 0.0015 124 | 0/8 6 h-lim-p 0.0005 0.0347 16.4148 1387.290322 0 0.0042 139 | 0/8 7 h-lim-p 0.0006 0.0050 58.8742 1385.357165 m 0.0050 151 | 1/8 8 h-lim-p 0.0048 0.0381 11.0406 1385.266882 8 0.0013 184 | 1/8 9 h-lim-p 0.0121 0.2487 1.2131 1383.178039 0 0.0483 198 | 0/8 10 h-lim-p 0.0010 0.0080 49.1407 1379.765485 0 0.0040 212 | 0/8 11 h-lim-p 0.0636 0.5092 0.5465 1368.566926 m 0.5092 224 | 1/8 12 h-lim-p 0.1997 1.5972 0.1888 1366.799041 0 0.3993 245 | 0/8 13 h-lim-p 0.0010 0.0081 44.6549 1363.566727 0 0.0060 266 | 0/8 14 h-lim-p 1.6546 13.2366 0.0233 1361.665504 0 2.4819 278 | 0/8 15 h-lim-p 2.5000 20.0000 0.0188 1361.256763 7 1.2655 314 | 0/8 16 h-lim-p 0.5854 4.6830 0.0176 1361.190169 0 1.7561 335 | 0/8 17 h-lim-p 2.5000 20.0000 0.0083 1361.183889 3 1.1328 361 | 0/8 18 h-lim-p 2.5000 20.0000 0.0004 1361.183762 3 1.3437 388 | 0/8 19 h-lim-p 2.5000 20.0000 0.0002 1361.183759 1 1.2305 411 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 1361.183758 0 2.1875 431 | 0/8 21 h-lim-p 2.1612 20.0000 0.0000 1361.183758 0 1.0806 451 | 0/8 22 h-lim-p 2.5000 20.0000 0.0000 1361.183758 0 1.0938 471 | 0/8 23 h-lim-p 2.5000 20.0000 0.0000 1361.183758 0 0.6250 492 | 0/8 24 h-lim-p 0.9172 20.0000 0.0000 1361.183758 0 0.0573 515 | 0/8 25 h-lim-p 0.0363 20.0000 0.0000 1361.183758 0 0.0363 535 | 0/8 26 h-lim-p 0.0248 20.0000 0.0000 1361.183758 0 0.0000 566 Out... lnL = -1361.183758 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1361.183758 Node 7: lnL = -1361.183758 Node 8: lnL = -1361.183758 Node 9: lnL = -1361.183758 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 919 Sequential format.. Reading seq # 1: YCR038C_Sbay Reading seq # 2: YCR038C_Scer Reading seq # 3: YCR038C_Skud Reading seq # 4: YCR038C_Smik Reading seq # 5: YCR038C_Spar Sequences read.. Counting patterns.. # site patterns = 51 Counting frequencies.. 120 bytes for distance 8160 bytes for lkl0 6528 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.017087 0.005240 0.005453 0.000994 0.021489 0.015083 0.010225 0.000060 lnL0 = -1971.624858 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1971.624858 x= 0.01709 0.00524 0.00545 0.00099 0.02149 0.01508 0.01023 0.00006 1 h-lim-p 0.0000 0.0000 9213.2807 1843.987736 1 0.0000 24 | 0/8 2 h-lim-p 0.0000 0.0000 559.9297 1834.940430 m 0.0000 36 | 0/8 3 h-lim-p 0.0000 0.0000 216.5149 1833.645717 m 0.0000 48 | 1/8 4 h-lim-p 0.0000 0.0000 60388.1034 1829.263054 m 0.0000 60 | 2/8 5 h-lim-p 0.0000 0.0000 822.4375 1829.017212 m 0.0000 72 | 3/8 6 h-lim-p 0.0001 0.0038 23.5014 1828.553823 0 0.0010 87 | 3/8 7 h-lim-p 0.1084 0.8669 0.0416 1826.888403 0 0.6501 101 | 3/8 8 h-lim-p 0.0004 0.0029 3.1514 1826.768693 0 0.0014 120 | 3/8 9 h-lim-p 0.0307 0.2452 0.0221 1826.404169 m 0.2452 132 | 4/8 10 h-lim-p 0.0013 0.0107 2.7962 1826.403437 2 0.0001 155 | 4/8 11 h-lim-p 0.0675 2.5101 0.0061 1826.288145 0 1.0795 171 | 4/8 12 h-lim-p 1.8951 20.0000 0.0035 1826.273950 2 0.8883 191 | 4/8 13 h-lim-p 1.1524 9.2195 0.0005 1826.272732 3 1.2183 213 | 3/8 14 h-lim-p 0.0013 0.0615 0.4866 1826.272722 1 0.0001 234 | 3/8 15 h-lim-p 0.1374 1.0991 0.0002 1826.272685 m 1.0991 251 | 4/8 16 h-lim-p 2.5000 20.0000 0.0000 1826.272685 0 0.5469 269 | 3/8 17 h-lim-p 0.0000 0.0043 31.9157 .. | 3/8 18 h-lim-p 0.0000 0.0001 4.0288 1826.272663 2 0.0000 316 | 3/8 19 h-lim-p 0.0000 0.0323 0.3135 1826.272658 0 0.0001 329 | 3/8 20 h-lim-p 0.0000 0.0000 1.2515 1826.272658 0 0.0000 348 | 3/8 21 h-lim-p 0.0000 0.0001 0.1501 1826.272658 0 0.0000 361 | 3/8 22 h-lim-p 0.0000 0.0001 0.1248 1826.272657 m 0.0001 378 | 4/8 23 h-lim-p 0.2150 20.0000 0.0001 1826.272657 0 0.0000 413 | 4/8 24 h-lim-p 0.0000 20.0000 0.0000 1826.272657 0 0.0154 439 | 4/8 25 h-lim-p 0.0129 20.0000 0.0001 1826.272657 0 0.0000 471 | 4/8 26 h-lim-p 0.0000 20.0000 0.0000 1826.272657 0 0.0000 496 | 4/8 27 h-lim-p 0.0000 2.7831 3.4864 | 4/8 28 h-lim-p 0.0000 2.7831 3.4864 Out... lnL = -1826.272657 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1826.272657 Node 7: lnL = -1826.272657 Node 8: lnL = -1826.272657 Node 9: lnL = -1826.272657 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 240 Sequential format.. Reading seq # 1: YCR043C_Sbay Reading seq # 2: YCR043C_Scer Reading seq # 3: YCR043C_Skud Reading seq # 4: YCR043C_Smik Reading seq # 5: YCR043C_Spar Sequences read.. Counting patterns.. # site patterns = 94 Counting frequencies.. 120 bytes for distance 15040 bytes for lkl0 12032 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.256682 0.098482 0.030786 0.091856 0.040017 0.155965 0.104210 0.025378 lnL0 = -928.159441 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 928.159441 x= 0.25668 0.09848 0.03079 0.09186 0.04002 0.15596 0.10421 0.02538 1 h-lim-p 0.0006 0.0049 24.7097 927.993246 2 0.0006 26 | 0/8 2 h-lim-p 0.0007 0.0055 17.1113 927.933080 4 0.0005 46 | 0/8 3 h-lim-p 0.0029 0.0576 3.2354 927.930732 5 0.0005 71 | 0/8 4 h-lim-p 0.0008 0.0441 1.9606 927.930224 2 0.0003 87 | 0/8 5 h-lim-p 0.0029 0.7401 0.2360 927.930205 0 0.0007 100 | 0/8 6 h-lim-p 0.0048 8.6347 0.0357 927.930202 1 0.0019 122 | 0/8 7 h-lim-p 0.0183 20.0000 0.0037 927.930040 0 0.1465 145 | 0/8 8 h-lim-p 0.0027 0.4321 0.1978 927.929627 0 0.0041 165 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 927.929623 1 0.9961 187 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 927.929623 0 2.1875 207 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 927.929623 0 0.6250 228 | 0/8 12 h-lim-p 0.1053 20.0000 0.0000 927.929623 0 0.0033 252 | 0/8 13 h-lim-p 0.0014 20.0000 0.0000 927.929623 0 0.0012 272 | 0/8 14 h-lim-p 0.0007 20.0000 0.0001 927.929623 0 0.0007 292 | 0/8 15 h-lim-p 0.0005 20.0000 0.0001 927.929623 0 0.0000 318 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 927.929623 0 0.0000 351 | 0/8 17 h-lim-p 0.0000 20.0000 0.0016 | 0/8 18 h-lim-p 0.0000 20.0000 0.0016 Out... lnL = -927.929623 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -927.929623 Node 7: lnL = -927.929623 Node 8: lnL = -927.929623 Node 9: lnL = -927.929623 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 344 Sequential format.. Reading seq # 1: YCR045C_Sbay Reading seq # 2: YCR045C_Scer Reading seq # 3: YCR045C_Skud Reading seq # 4: YCR045C_Smik Reading seq # 5: YCR045C_Spar Sequences read.. Counting patterns.. # site patterns = 150 Counting frequencies.. 120 bytes for distance 24000 bytes for lkl0 19200 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.609447 0.201609 0.178669 0.028270 0.749614 0.539104 0.364709 0.000060 lnL0 = -1381.431968 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1381.431968 x= 0.60945 0.20161 0.17867 0.02827 0.74961 0.53910 0.36471 0.00006 1 h-lim-p 0.0000 0.0000 194.8172 1380.398399 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0021 384.1584 1282.469101 0 0.0019 41 | 1/8 3 h-lim-p 0.0003 0.0020 104.6739 1279.222528 0 0.0010 55 | 1/8 4 h-lim-p 0.0034 0.0271 29.7260 1277.537300 0 0.0051 67 | 1/8 5 h-lim-p 0.0034 0.0272 9.8143 1276.646490 0 0.0204 81 | 1/8 6 h-lim-p 0.0267 0.2135 2.6567 1276.597106 5 0.0130 105 | 1/8 7 h-lim-p 0.1121 0.8967 0.1383 1276.390942 0 0.4483 119 | 1/8 8 h-lim-p 0.0456 0.6481 1.3595 1276.334504 4 0.0352 146 | 1/8 9 h-lim-p 0.6528 6.6600 0.0733 1276.262704 2 0.3060 162 | 1/8 10 h-lim-p 0.6465 5.1717 0.0109 1276.260038 0 0.9697 181 | 1/8 11 h-lim-p 2.5000 20.0000 0.0007 1276.259750 4 0.8875 209 | 1/8 12 h-lim-p 1.1730 20.0000 0.0005 1276.259730 1 1.2097 230 | 0/8 13 h-lim-p 0.3594 20.0000 0.0018 1276.259730 0 0.0197 252 | 0/8 14 h-lim-p 0.1302 1.0413 0.0001 1276.259730 m 1.0413 272 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 1276.259730 0 2.1875 292 | 1/8 16 h-lim-p 2.4425 20.0000 0.0000 1276.259730 0 1.0686 311 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 1276.259730 0 1.0938 330 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 1276.259730 0 1.0938 349 | 1/8 19 h-lim-p 2.5000 20.0000 0.0000 1276.259730 0 0.3125 370 | 1/8 20 h-lim-p 0.4756 20.0000 0.0000 1276.259730 0 0.4756 389 | 1/8 21 h-lim-p 0.8983 20.0000 0.0000 1276.259730 0 0.0000 427 Out... lnL = -1276.259730 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1276.259730 Node 7: lnL = -1276.259730 Node 8: lnL = -1276.259730 Node 9: lnL = -1276.259730 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 303 Sequential format.. Reading seq # 1: YCR046C_Sbay Reading seq # 2: YCR046C_Scer Reading seq # 3: YCR046C_Skud Reading seq # 4: YCR046C_Smik Reading seq # 5: YCR046C_Spar Sequences read.. Counting patterns.. # site patterns = 179 Counting frequencies.. 120 bytes for distance 28640 bytes for lkl0 22912 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.650765 0.013395 0.034324 0.101261 0.108655 0.301584 0.364744 0.177484 lnL0 = -1402.411591 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1402.411591 x= 0.65076 0.01339 0.03432 0.10126 0.10865 0.30158 0.36474 0.17748 1 h-lim-p 0.0021 0.0167 55.2557 1401.711136 6 0.0005 34 | 0/8 2 h-lim-p 0.0015 0.0120 14.8544 1401.586914 4 0.0012 54 | 0/8 3 h-lim-p 0.0012 0.0251 14.6879 1401.522866 3 0.0010 72 | 0/8 4 h-lim-p 0.0024 0.0346 6.1142 1401.506935 2 0.0011 88 | 0/8 5 h-lim-p 0.0017 0.1293 4.0994 1401.486525 0 0.0033 101 | 0/8 6 h-lim-p 0.0032 0.0944 4.2260 1401.478769 6 0.0019 129 | 0/8 7 h-lim-p 0.0092 0.2891 0.8635 1401.477065 5 0.0053 154 | 0/8 8 h-lim-p 2.5000 20.0000 0.0015 1401.476630 2 1.0889 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1401.476619 2 1.2305 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1401.476619 0 1.0938 223 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1401.476619 0 2.1875 243 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1401.476619 0 1.0938 263 | 0/8 13 h-lim-p 0.7576 20.0000 0.0000 1401.476619 0 3.0306 285 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1401.476619 0 0.0000 326 Out... lnL = -1401.476619 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1401.476619 Node 7: lnL = -1401.476619 Node 8: lnL = -1401.476619 Node 9: lnL = -1401.476619 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 376 Sequential format.. Reading seq # 1: YCR047C_Sbay Reading seq # 2: YCR047C_Scer Reading seq # 3: YCR047C_Skud Reading seq # 4: YCR047C_Smik Reading seq # 5: YCR047C_Spar Sequences read.. Counting patterns.. # site patterns = 163 Counting frequencies.. 120 bytes for distance 26080 bytes for lkl0 20864 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.305727 0.015473 0.067237 0.105766 0.132079 0.229256 0.209041 0.002843 lnL0 = -1514.966957 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1514.966957 x= 0.30573 0.01547 0.06724 0.10577 0.13208 0.22926 0.20904 0.00284 1 h-lim-p 0.0019 0.0152 118.1984 1512.704875 6 0.0004 34 | 0/8 2 h-lim-p 0.0010 0.0081 17.5631 1512.580801 5 0.0008 56 | 0/8 3 h-lim-p 0.0024 0.0623 5.8399 1512.570281 6 0.0007 82 | 0/8 4 h-lim-p 0.0018 0.1393 2.1783 1512.568032 5 0.0011 107 | 0/8 5 h-lim-p 0.0089 0.1041 0.2661 1512.567980 3 0.0016 128 | 0/8 6 h-lim-p 0.0128 3.8584 0.0329 1512.567980 1 0.0008 153 | 0/8 7 h-lim-p 0.0047 20.0000 0.0055 1512.567979 0 0.0041 173 | 0/8 8 h-lim-p 0.0944 20.0000 0.0002 1512.567968 0 0.5664 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1512.567967 0 2.1875 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1512.567967 0 1.0938 235 | 0/8 11 h-lim-p 1.2910 20.0000 0.0000 1512.567967 0 1.1296 255 | 0/8 12 h-lim-p 1.0774 20.0000 0.0000 1512.567967 0 4.3098 277 | 0/8 13 h-lim-p 0.0488 20.0000 0.0010 1512.567967 0 0.0030 300 | 0/8 14 h-lim-p 0.0013 8.7370 0.0023 1512.567967 0 0.0006 320 | 0/8 15 h-lim-p 0.0002 2.5135 0.0080 1512.567967 0 0.0001 340 | 0/8 16 h-lim-p 0.0000 0.1874 0.1072 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1512.567967 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1512.567967 Node 7: lnL = -1512.567967 Node 8: lnL = -1512.567967 Node 9: lnL = -1512.567967 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 433 Sequential format.. Reading seq # 1: YCR048W_Sbay Reading seq # 2: YCR048W_Scer Reading seq # 3: YCR048W_Skud Reading seq # 4: YCR048W_Smik Reading seq # 5: YCR048W_Spar Sequences read.. Counting patterns.. # site patterns = 177 Counting frequencies.. 120 bytes for distance 28320 bytes for lkl0 22656 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.314259 0.123580 0.038481 0.111716 0.117909 0.141426 0.104584 0.025195 lnL0 = -1602.296406 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1602.296406 x= 0.31426 0.12358 0.03848 0.11172 0.11791 0.14143 0.10458 0.02520 1 h-lim-p 0.0005 0.0040 85.2255 1600.501234 7 0.0005 40 | 0/8 2 h-lim-p 0.0004 0.0029 39.9641 1600.196990 0 0.0005 52 | 0/8 3 h-lim-p 0.0015 0.0473 14.0967 1600.131678 6 0.0008 76 | 0/8 4 h-lim-p 0.0013 0.0272 8.5870 1600.106835 6 0.0009 103 | 0/8 5 h-lim-p 0.0018 0.0449 4.3850 1600.102607 5 0.0006 127 | 0/8 6 h-lim-p 0.0027 0.2189 0.9576 1600.101679 4 0.0022 147 | 0/8 7 h-lim-p 0.6156 20.0000 0.0033 1600.094080 0 0.9235 167 | 0/8 8 h-lim-p 0.0024 0.1539 1.2757 1600.093166 3 0.0010 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1600.093071 3 1.0004 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1600.093071 0 1.0938 231 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1600.093071 0 1.0938 251 | 0/8 12 h-lim-p 1.1629 20.0000 0.0000 1600.093071 0 0.5814 271 | 0/8 13 h-lim-p 0.0250 20.0000 0.0001 1600.093071 0 0.0016 294 | 0/8 14 h-lim-p 0.0007 20.0000 0.0003 1600.093071 0 0.0000 325 | 0/8 15 h-lim-p 0.0010 20.0000 0.0000 1600.093071 0 0.0000 357 Out... lnL = -1600.093071 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1600.093071 Node 7: lnL = -1600.093071 Node 8: lnL = -1600.093071 Node 9: lnL = -1600.093071 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 278 Sequential format.. Reading seq # 1: YCR052W_Sbay Reading seq # 2: YCR052W_Scer Reading seq # 3: YCR052W_Skud Reading seq # 4: YCR052W_Smik Reading seq # 5: YCR052W_Spar Sequences read.. Counting patterns.. # site patterns = 152 Counting frequencies.. 120 bytes for distance 24320 bytes for lkl0 19456 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.382374 0.107346 0.061352 0.169000 0.105451 0.158434 0.278102 0.011449 lnL0 = -1209.070847 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1209.070847 x= 0.38237 0.10735 0.06135 0.16900 0.10545 0.15843 0.27810 0.01145 1 h-lim-p 0.0057 0.0459 37.6087 1208.238018 5 0.0013 32 | 0/8 2 h-lim-p 0.0013 0.0108 10.7762 1208.196385 6 0.0008 58 | 0/8 3 h-lim-p 0.0026 0.1604 3.1345 1208.190327 4 0.0013 79 | 0/8 4 h-lim-p 0.0017 0.1436 2.4086 1208.186623 4 0.0019 100 | 0/8 5 h-lim-p 0.0032 0.2405 1.4359 1208.185663 3 0.0014 118 | 0/8 6 h-lim-p 0.0070 0.1613 0.2927 1208.185551 3 0.0028 136 | 0/8 7 h-lim-p 0.4145 20.0000 0.0020 1208.185540 0 0.1036 157 | 0/8 8 h-lim-p 0.0072 15.7201 0.0286 1208.185431 0 0.0287 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1208.185419 1 0.9961 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1208.185419 0 1.0938 221 | 0/8 11 h-lim-p 1.1661 20.0000 0.0000 1208.185419 0 0.5102 241 | 0/8 12 h-lim-p 0.0310 20.0000 0.0001 1208.185419 0 0.0002 267 | 0/8 13 h-lim-p 0.0004 20.0000 0.0001 1208.185419 0 0.0000 304 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 1208.185419 0 0.0000 336 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 1208.185419 0 0.0000 356 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 1208.185419 0 0.0000 379 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1208.185419 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1208.185419 Node 7: lnL = -1208.185419 Node 8: lnL = -1208.185419 Node 9: lnL = -1208.185419 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 269 Sequential format.. Reading seq # 1: YCR053W_Sbay Reading seq # 2: YCR053W_Scer Reading seq # 3: YCR053W_Skud Reading seq # 4: YCR053W_Smik Reading seq # 5: YCR053W_Spar Sequences read.. Counting patterns.. # site patterns = 113 Counting frequencies.. 120 bytes for distance 18080 bytes for lkl0 14464 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.209491 0.076682 0.092925 0.082290 0.123739 0.201220 0.152545 0.000060 lnL0 = -1034.922735 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1034.922735 x= 0.20949 0.07668 0.09292 0.08229 0.12374 0.20122 0.15254 0.00006 1 h-lim-p 0.0000 0.0000 172.6167 1034.701102 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0011 113.6603 1029.940807 0 0.0009 40 | 1/8 3 h-lim-p 0.0008 0.0063 18.8236 1029.817107 6 0.0007 63 | 1/8 4 h-lim-p 0.0008 0.0062 6.9076 1029.765332 0 0.0015 76 | 1/8 5 h-lim-p 0.0086 0.1246 1.2317 1029.408692 0 0.0346 90 | 1/8 6 h-lim-p 0.0017 0.0137 3.8840 1024.858457 m 0.0137 102 | 1/8 7 h-lim-p 0.0011 0.0088 19.5458 1024.647424 5 0.0011 124 | 1/8 8 h-lim-p 0.0053 0.0898 4.0329 1024.624219 4 0.0021 144 | 1/8 9 h-lim-p 0.0570 0.8153 0.1484 1023.502404 0 0.2278 158 | 1/8 10 h-lim-p 1.4530 12.4277 0.0233 1023.399400 6 0.7130 191 | 0/8 11 h-lim-p 0.0444 1.3358 0.3736 1023.399283 3 0.0023 219 | 0/8 12 h-lim-p 0.6230 18.2623 0.0014 1023.398623 2 0.5841 243 | 0/8 13 h-lim-p 2.5000 20.0000 0.0003 1023.398587 3 0.7330 272 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 1023.398587 1 0.6152 295 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1023.398587 0 1.0938 315 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1023.398587 0 0.0002 348 Out... lnL = -1023.398587 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1023.398587 Node 7: lnL = -1023.398587 Node 8: lnL = -1023.398587 Node 9: lnL = -1023.398587 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 444 Sequential format.. Reading seq # 1: YCR054C_Sbay Reading seq # 2: YCR054C_Scer Reading seq # 3: YCR054C_Skud Reading seq # 4: YCR054C_Smik Reading seq # 5: YCR054C_Spar Sequences read.. Counting patterns.. # site patterns = 186 Counting frequencies.. 120 bytes for distance 29760 bytes for lkl0 23808 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.274995 0.278685 0.174954 0.136404 0.315816 0.263725 0.163334 0.000060 lnL0 = -1948.956334 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1948.956334 x= 0.27500 0.27869 0.17495 0.13640 0.31582 0.26373 0.16333 0.00006 1 h-lim-p 0.0000 0.0000 288.4169 1948.856395 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0011 414.5060 1907.916425 0 0.0009 40 | 1/8 3 h-lim-p 0.0004 0.0031 67.3695 1906.227093 0 0.0008 53 | 1/8 4 h-lim-p 0.0018 0.0140 16.4308 1906.127227 5 0.0007 74 | 1/8 5 h-lim-p 0.0012 0.0314 9.3266 1906.059257 5 0.0013 97 | 1/8 6 h-lim-p 0.0062 0.1368 1.9263 1905.673627 0 0.0124 110 | 1/8 7 h-lim-p 0.0037 0.0477 6.4514 1896.432900 0 0.0223 124 | 1/8 8 h-lim-p 0.0005 0.0037 68.4187 1892.381107 0 0.0014 137 | 1/8 9 h-lim-p 0.4665 3.7323 0.0739 1891.032910 1 0.5832 151 | 0/8 10 h-lim-p 0.0079 0.1200 5.4653 1891.021578 4 0.0009 179 | 0/8 11 h-lim-p 0.3073 20.0000 0.0153 1890.949408 0 0.6145 192 | 0/8 12 h-lim-p 2.5000 20.0000 0.0028 1890.944171 6 0.9217 227 | 0/8 13 h-lim-p 2.5000 20.0000 0.0003 1890.944070 2 0.9961 251 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1890.944069 0 1.0938 271 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1890.944069 0 1.0938 291 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1890.944069 0 1.0938 311 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1890.944069 0 0.0098 338 Out... lnL = -1890.944069 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1890.944069 Node 7: lnL = -1890.944069 Node 8: lnL = -1890.944069 Node 9: lnL = -1890.944069 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 239 Sequential format.. Reading seq # 1: YCR057C_Sbay Reading seq # 2: YCR057C_Scer Reading seq # 3: YCR057C_Skud Reading seq # 4: YCR057C_Smik Reading seq # 5: YCR057C_Spar Sequences read.. Counting patterns.. # site patterns = 69 Counting frequencies.. 120 bytes for distance 11040 bytes for lkl0 8832 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 1.024387 1.099089 0.716269 0.435021 1.273539 0.971756 1.148486 0.000060 lnL0 = -1078.676018 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1078.676018 x= 1.02439 1.09909 0.71627 0.43502 1.27354 0.97176 1.14849 0.00006 1 h-lim-p 0.0000 0.0000 118.0228 1078.576206 m 0.0000 22 | 1/8 2 h-lim-p 0.0002 0.6899 4.9226 .. | 1/8 3 h-lim-p 0.0000 0.0055 117.8320 975.374233 m 0.0055 70 | 2/8 4 h-lim-p 0.0675 0.5396 4.8460 .. | 2/8 5 h-lim-p 0.0000 0.0069 146.9281 823.668885 m 0.0069 127 | 1/8 6 h-lim-p 0.0000 0.0000 7034.2245 h-lim-p: 1.05933101e-21 8.47464809e-21 7.03422452e+03 823.668885 .. | 1/8 7 h-lim-p 0.0000 0.0030 646.5478 813.089189 0 0.0001 150 | 1/8 8 h-lim-p 0.0000 0.0001 145.7850 811.157577 m 0.0001 162 | 2/8 9 h-lim-p 0.0001 0.0014 203.4408 795.136187 1 0.0012 180 | 2/8 10 h-lim-p 0.0003 0.0027 119.0487 775.899866 m 0.0027 192 | 2/8 11 h-lim-p -0.0000 -0.0000 14.8774 h-lim-p: -9.84028035e-19 -7.87222428e-18 1.48773748e+01 775.899866 .. | 2/8 12 h-lim-p 0.0000 0.0080 725.0873 769.647794 0 0.0001 214 | 2/8 13 h-lim-p 0.0004 0.0040 107.2273 750.239401 5 0.0026 241 | 2/8 14 h-lim-p 0.0001 0.0007 554.7436 742.530867 0 0.0003 255 | 2/8 15 h-lim-p 0.0001 0.0010 260.7601 736.236764 0 0.0005 269 | 1/8 16 h-lim-p 0.0000 0.0000 3549.6449 727.567476 0 0.0000 283 | 1/8 17 h-lim-p 0.4777 7.4581 0.1410 723.362442 1 0.5971 297 | 1/8 18 h-lim-p 0.7593 6.0741 0.0255 719.908121 0 3.0370 318 | 0/8 19 h-lim-p 0.0009 0.0073 25.2907 718.855726 0 0.0036 339 | 0/8 20 h-lim-p 0.1543 1.2345 0.0509 717.677582 m 1.2345 351 | 0/8 21 h-lim-p 0.0000 0.0000 0.3205 h-lim-p: 7.33357926e-19 5.86686341e-18 3.20515753e-01 717.677582 .. | 0/8 22 h-lim-p 0.0000 0.0038 45.6159 716.997112 0 0.0006 393 | 0/8 23 h-lim-p 0.0000 0.0000 20.2658 716.983704 m 0.0000 405 | 1/8 24 h-lim-p 0.0001 0.0083 14.2650 716.940916 0 0.0007 420 | 1/8 25 h-lim-p 0.0058 0.1622 1.6560 716.939937 2 0.0007 438 | 1/8 26 h-lim-p 0.0092 1.9794 0.1230 716.939230 2 0.0087 454 | 1/8 27 h-lim-p 0.0093 2.0490 0.1141 716.877950 0 0.0746 476 | 1/8 28 h-lim-p 2.2838 20.0000 0.0037 716.874146 5 0.5035 505 | 0/8 29 h-lim-p 0.0798 20.0000 0.0235 716.874144 2 0.0032 532 | 0/8 30 h-lim-p 0.0725 0.7720 0.0010 716.873873 1 0.5131 557 | 0/8 31 h-lim-p 0.0467 0.3735 0.0001 716.873873 m 0.3735 577 | 1/8 32 h-lim-p 0.1144 20.0000 0.0002 716.873873 0 0.1001 597 | 1/8 33 h-lim-p 2.4195 20.0000 0.0000 716.873873 0 2.4195 616 | 1/8 34 h-lim-p 2.1074 20.0000 0.0000 716.873873 0 1.8440 635 | 1/8 35 h-lim-p 2.5000 20.0000 0.0000 716.873873 0 1.0938 654 | 1/8 36 h-lim-p 0.6483 20.0000 0.0000 716.873873 0 0.5672 673 | 1/8 37 h-lim-p 0.2093 20.0000 0.0000 716.873873 0 0.0523 693 | 1/8 38 h-lim-p 0.0173 20.0000 0.0000 716.873873 0 0.0005 716 | 1/8 39 h-lim-p 0.0001 20.0000 0.0002 716.873873 0 0.0000 754 | 1/8 40 h-lim-p 0.0000 20.0000 0.0001 | 1/8 41 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -716.873873 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -716.873873 Node 7: lnL = -716.873873 Node 8: lnL = -716.873873 Node 9: lnL = -716.873873 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 206 Sequential format.. Reading seq # 1: YCR059C_Sbay Reading seq # 2: YCR059C_Scer Reading seq # 3: YCR059C_Skud Reading seq # 4: YCR059C_Smik Reading seq # 5: YCR059C_Spar Sequences read.. Counting patterns.. # site patterns = 74 Counting frequencies.. 120 bytes for distance 11840 bytes for lkl0 9472 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 1.024387 1.089366 0.702154 0.429347 1.254396 0.965943 1.205909 0.000060 lnL0 = -891.346053 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 891.346053 x= 1.02439 1.08937 0.70215 0.42935 1.25440 0.96594 1.20591 0.00006 1 h-lim-p 0.0000 0.0000 81.3130 891.272901 m 0.0000 22 | 1/8 2 h-lim-p 0.0002 0.9424 4.0123 .. | 1/8 3 h-lim-p 0.0000 0.0078 81.2096 822.941014 m 0.0078 71 | 2/8 4 h-lim-p 0.0589 0.4711 4.5920 .. | 2/8 5 h-lim-p 0.0000 0.0097 97.2609 736.535910 m 0.0097 128 | 1/8 6 h-lim-p 0.0000 0.0000 1394.4600 h-lim-p: 6.84065180e-21 5.47252144e-20 1.39446003e+03 736.535910 .. | 1/8 7 h-lim-p 0.0000 0.0064 272.2853 730.594851 0 0.0003 153 | 1/8 8 h-lim-p 0.0000 0.0004 84.5498 728.085876 m 0.0004 165 | 2/8 9 h-lim-p 0.0004 0.0065 87.4248 713.496998 3 0.0050 186 | 2/8 10 h-lim-p 0.0003 0.0027 144.3729 705.119371 0 0.0020 200 | 2/8 11 h-lim-p 0.0141 0.1131 3.5563 699.918519 0 0.0565 214 | 1/8 12 h-lim-p 0.0125 0.1003 3.3737 698.074349 0 0.0251 227 | 0/8 13 h-lim-p 0.0004 0.0035 21.9751 696.715805 m 0.0035 239 | 0/8 14 h-lim-p 0.0017 0.0135 41.8772 694.605701 0 0.0067 253 | 0/8 15 h-lim-p 0.0769 0.6153 0.6624 688.580897 0 0.3076 267 | 0/8 16 h-lim-p 0.3245 2.5959 0.1037 687.280000 0 1.2980 289 | 0/8 17 h-lim-p 1.8729 14.9833 0.0296 686.752548 6 1.8381 323 | 0/8 18 h-lim-p 2.5000 20.0000 0.0157 686.689712 6 1.0560 358 | 0/8 19 h-lim-p 1.8375 20.0000 0.0090 686.676543 2 0.8613 382 | 0/8 20 h-lim-p 2.5000 20.0000 0.0020 686.675887 2 1.1719 406 | 0/8 21 h-lim-p 2.5000 20.0000 0.0001 686.675886 0 1.0938 426 | 0/8 22 h-lim-p 2.5000 20.0000 0.0000 686.675886 0 2.1875 446 | 0/8 23 h-lim-p 2.5000 20.0000 0.0000 686.675886 0 1.2500 466 | 0/8 24 h-lim-p 2.5000 20.0000 0.0000 686.675886 0 0.5469 487 | 0/8 25 h-lim-p 0.3726 20.0000 0.0000 686.675886 0 0.0058 512 Out... lnL = -686.675886 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -686.675886 Node 7: lnL = -686.675886 Node 8: lnL = -686.675886 Node 9: lnL = -686.675886 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 212 Sequential format.. Reading seq # 1: YCR060W_Sbay Reading seq # 2: YCR060W_Scer Reading seq # 3: YCR060W_Skud Reading seq # 4: YCR060W_Smik Reading seq # 5: YCR060W_Spar Sequences read.. Counting patterns.. # site patterns = 112 Counting frequencies.. 120 bytes for distance 17920 bytes for lkl0 14336 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.447510 0.495754 0.305420 0.190435 0.530541 0.421675 0.311210 0.000060 lnL0 = -968.543375 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 968.543375 x= 0.44751 0.49575 0.30542 0.19044 0.53054 0.42168 0.31121 0.00006 1 h-lim-p 0.0000 0.0000 149.9292 968.455493 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0017 413.0994 908.145290 0 0.0015 41 | 1/8 3 h-lim-p 0.0007 0.0053 59.9808 904.891601 0 0.0026 55 | 1/8 4 h-lim-p 0.0011 0.0088 42.3197 903.462329 0 0.0022 68 | 1/8 5 h-lim-p 0.0078 0.0623 8.2982 903.138222 2 0.0073 84 | 1/8 6 h-lim-p 0.0140 0.1123 2.4313 902.955435 4 0.0144 104 | 1/8 7 h-lim-p 0.0057 0.0671 6.1334 902.631362 0 0.0114 117 | 0/8 8 h-lim-p 0.0051 0.0407 13.7770 902.320170 4 0.0039 137 | 0/8 9 h-lim-p 0.0047 0.0373 2.1870 902.258915 0 0.0186 151 | 0/8 10 h-lim-p 0.2133 1.7060 0.0805 902.098133 0 0.4265 164 | 0/8 11 h-lim-p 0.7181 5.7446 0.0458 902.021448 8 0.4770 203 | 0/8 12 h-lim-p 2.5000 20.0000 0.0033 902.019973 4 0.9644 231 | 0/8 13 h-lim-p 2.5000 20.0000 0.0011 902.019904 3 0.8800 258 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 902.019903 0 1.0938 278 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 902.019903 0 1.0938 298 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 902.019903 0 1.0938 318 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 902.019903 0 0.0049 346 Out... lnL = -902.019903 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -902.019903 Node 7: lnL = -902.019903 Node 8: lnL = -902.019903 Node 9: lnL = -902.019903 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 886 Sequential format.. Reading seq # 1: YCR061W_Sbay Reading seq # 2: YCR061W_Scer Reading seq # 3: YCR061W_Skud Reading seq # 4: YCR061W_Smik Reading seq # 5: YCR061W_Spar Sequences read.. Counting patterns.. # site patterns = 420 Counting frequencies.. 120 bytes for distance 67200 bytes for lkl0 53760 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.617610 0.260379 0.104867 0.136349 0.144267 0.223363 0.321640 0.057889 lnL0 = -4565.652977 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4565.652977 x= 0.61761 0.26038 0.10487 0.13635 0.14427 0.22336 0.32164 0.05789 1 h-lim-p 0.0014 0.0113 87.4086 4564.361011 7 0.0004 36 | 0/8 2 h-lim-p 0.0007 0.0060 25.8289 4564.250749 2 0.0004 52 | 0/8 3 h-lim-p 0.0008 0.0488 11.5271 4564.203758 5 0.0008 76 | 0/8 4 h-lim-p 0.0013 0.0694 7.3350 4564.183050 3 0.0011 94 | 0/8 5 h-lim-p 0.0017 0.0724 4.8153 4564.173646 5 0.0013 118 | 0/8 6 h-lim-p 0.0185 0.3495 0.3271 4564.173554 2 0.0018 136 | 0/8 7 h-lim-p 0.0132 4.8552 0.0443 4564.173553 0 0.0014 158 | 0/8 8 h-lim-p 0.1996 20.0000 0.0003 4564.173482 0 0.7984 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4564.173480 0 1.0938 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4564.173480 0 1.0938 220 | 0/8 11 h-lim-p 1.1758 20.0000 0.0000 4564.173480 0 1.0288 240 | 0/8 12 h-lim-p 0.5168 20.0000 0.0000 4564.173480 0 0.1292 261 | 0/8 13 h-lim-p 0.0182 20.0000 0.0001 4564.173480 0 0.0000 300 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 4564.173480 0 0.0000 322 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 4564.173480 0 0.0000 351 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 4564.173480 0 0.0000 373 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 4564.173480 0 0.0000 407 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -4564.173480 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4564.173480 Node 7: lnL = -4564.173480 Node 8: lnL = -4564.173480 Node 9: lnL = -4564.173480 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 877 Sequential format.. Reading seq # 1: YCR063W_Sbay Reading seq # 2: YCR063W_Scer Reading seq # 3: YCR063W_Skud Reading seq # 4: YCR063W_Smik Reading seq # 5: YCR063W_Spar Sequences read.. Counting patterns.. # site patterns = 374 Counting frequencies.. 120 bytes for distance 59840 bytes for lkl0 47872 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.469714 0.067876 0.143415 0.107163 0.096122 0.265002 0.350771 0.024414 lnL0 = -4352.960747 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4352.960747 x= 0.46971 0.06788 0.14341 0.10716 0.09612 0.26500 0.35077 0.02441 1 h-lim-p 0.0052 1.0514 128.8734 4350.117497 8 0.0004 42 | 0/8 2 h-lim-p 0.0006 0.0049 38.0417 4349.947019 3 0.0003 60 | 0/8 3 h-lim-p 0.0004 0.0096 24.2382 4349.781045 0 0.0008 73 | 0/8 4 h-lim-p 0.0028 0.0225 5.5623 4349.768616 6 0.0009 100 | 0/8 5 h-lim-p 0.0018 0.0899 2.7230 4349.766971 4 0.0006 124 | 0/8 6 h-lim-p 0.0011 0.2965 1.4013 4349.766427 4 0.0007 146 | 0/8 7 h-lim-p 0.0189 7.0891 0.0539 4349.766418 1 0.0023 162 | 0/8 8 h-lim-p 0.0379 20.0000 0.0033 4349.764204 0 0.6061 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 4349.763897 3 1.0004 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4349.763897 0 1.0938 232 | 0/8 11 h-lim-p 1.5557 20.0000 0.0000 4349.763897 0 1.3612 252 | 0/8 12 h-lim-p 1.1410 20.0000 0.0000 4349.763897 0 0.9983 272 | 0/8 13 h-lim-p 0.0882 20.0000 0.0002 4349.763897 0 0.0221 293 | 0/8 14 h-lim-p 0.0062 20.0000 0.0007 4349.763897 0 0.0000 330 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 4349.763897 0 0.0000 363 Out... lnL = -4349.763897 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4349.763897 Node 7: lnL = -4349.763897 Node 8: lnL = -4349.763897 Node 9: lnL = -4349.763897 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 540 Sequential format.. Reading seq # 1: YCR066W_Sbay Reading seq # 2: YCR066W_Scer Reading seq # 3: YCR066W_Skud Reading seq # 4: YCR066W_Smik Reading seq # 5: YCR066W_Spar Sequences read.. Counting patterns.. # site patterns = 187 Counting frequencies.. 120 bytes for distance 29920 bytes for lkl0 23936 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.215278 0.206103 0.122679 0.088427 0.219860 0.201847 0.122416 0.000060 lnL0 = -2090.851827 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2090.851827 x= 0.21528 0.20610 0.12268 0.08843 0.21986 0.20185 0.12242 0.00006 1 h-lim-p 0.0000 0.0000 411.8162 2090.609750 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0011 258.8045 2067.269664 1 0.0008 42 | 1/8 3 h-lim-p 0.0005 0.0038 44.0472 2066.633064 0 0.0007 54 | 1/8 4 h-lim-p 0.0034 0.0272 5.7959 2066.559116 2 0.0016 70 | 1/8 5 h-lim-p 0.0054 0.1829 1.7100 2061.216621 0 0.0647 85 | 0/8 6 h-lim-p -0.0000 -0.0000 35.0736 h-lim-p: -1.87443205e-22 -1.49954564e-21 3.50736284e+01 2061.216621 .. | 0/8 7 h-lim-p 0.0000 0.0007 271.3683 2047.627077 0 0.0003 110 | 0/8 8 h-lim-p 0.0002 0.0016 195.4982 2042.683082 0 0.0004 123 | 0/8 9 h-lim-p 0.0003 0.0023 81.6145 2041.981897 2 0.0003 139 | 0/8 10 h-lim-p 0.0018 0.0151 12.6814 2041.960045 6 0.0003 166 | 0/8 11 h-lim-p 0.0007 0.0054 4.1349 2041.957717 4 0.0003 188 | 0/8 12 h-lim-p 0.0019 0.0154 0.4747 2041.957232 4 0.0012 212 | 0/8 13 h-lim-p 0.0013 0.7436 0.4199 2041.950466 0 0.0054 234 | 0/8 14 h-lim-p 0.0024 0.0555 0.9292 2041.761750 0 0.0146 256 | 0/8 15 h-lim-p 2.5000 20.0000 0.0022 2041.753086 6 0.9338 290 | 0/8 16 h-lim-p 2.5000 20.0000 0.0003 2041.753010 2 0.9644 314 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 2041.753010 0 1.0938 334 | 0/8 18 h-lim-p 1.1916 20.0000 0.0000 2041.753010 0 0.0000 386 | 0/8 19 h-lim-p 0.0000 20.0000 0.0021 | 0/8 20 h-lim-p 0.0000 20.0000 0.0021 Out... lnL = -2041.753010 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2041.753010 Node 7: lnL = -2041.753010 Node 8: lnL = -2041.753010 Node 9: lnL = -2041.753010 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 890 Sequential format.. Reading seq # 1: YCR067C_Sbay Reading seq # 2: YCR067C_Scer Reading seq # 3: YCR067C_Skud Reading seq # 4: YCR067C_Smik Reading seq # 5: YCR067C_Spar Sequences read.. Counting patterns.. # site patterns = 333 Counting frequencies.. 120 bytes for distance 53280 bytes for lkl0 42624 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.385826 0.392985 0.241084 0.169930 0.418415 0.372325 0.226891 0.000060 lnL0 = -4421.584158 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4421.584158 x= 0.38583 0.39299 0.24108 0.16993 0.41841 0.37232 0.22689 0.00006 1 h-lim-p 0.0000 0.0000 596.8322 4421.297648 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0008 657.2766 4295.473533 5 0.0006 48 | 1/8 3 h-lim-p 0.0005 0.0038 100.3420 4290.816693 0 0.0010 61 | 1/8 4 h-lim-p 0.0007 0.0059 32.2763 4290.486205 5 0.0006 82 | 1/8 5 h-lim-p 0.0017 0.0459 12.1267 4290.282913 4 0.0018 102 | 1/8 6 h-lim-p 0.0128 0.2460 1.7062 4285.108261 0 0.0511 116 | 1/8 7 h-lim-p 0.0013 0.0100 32.1212 4257.997450 0 0.0050 130 | 1/8 8 h-lim-p 0.0008 0.0062 70.4376 4255.917290 6 0.0008 153 | 1/8 9 h-lim-p 0.7104 5.6828 0.0675 4255.497000 5 0.2843 174 | 0/8 10 h-lim-p 0.0068 2.3156 2.8328 4255.493880 4 0.0007 202 | 0/8 11 h-lim-p 0.0647 4.8093 0.0318 4255.368246 0 0.5179 217 | 0/8 12 h-lim-p 2.5000 20.0000 0.0045 4255.354201 5 0.9394 247 | 0/8 13 h-lim-p 2.5000 20.0000 0.0005 4255.354066 3 0.6580 274 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 4255.354060 1 0.6152 297 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 4255.354060 0 1.0938 317 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 4255.354059 0 1.0938 337 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 4255.354059 0 0.5469 358 | 0/8 18 h-lim-p 1.4550 20.0000 0.0000 4255.354059 0 0.6366 378 | 0/8 19 h-lim-p 1.4455 20.0000 0.0000 4255.354059 0 0.6324 398 | 0/8 20 h-lim-p 0.4276 20.0000 0.0000 4255.354059 0 0.0134 422 Out... lnL = -4255.354059 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4255.354059 Node 7: lnL = -4255.354059 Node 8: lnL = -4255.354059 Node 9: lnL = -4255.354059 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 292 Sequential format.. Reading seq # 1: YCR069W_Sbay Reading seq # 2: YCR069W_Scer Reading seq # 3: YCR069W_Skud Reading seq # 4: YCR069W_Smik Reading seq # 5: YCR069W_Spar Sequences read.. Counting patterns.. # site patterns = 126 Counting frequencies.. 120 bytes for distance 20160 bytes for lkl0 16128 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.299993 0.184656 0.260138 0.192931 0.043382 0.309525 0.169692 0.000060 lnL0 = -1298.859519 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1298.859519 x= 0.29999 0.18466 0.26014 0.19293 0.04338 0.30953 0.16969 0.00006 1 h-lim-p 0.0000 0.0000 200.4553 1298.786438 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0016 237.8625 1280.736624 0 0.0010 40 | 1/8 3 h-lim-p 0.0004 0.0036 42.3398 1279.917599 0 0.0009 53 | 1/8 4 h-lim-p 0.0028 0.0223 12.7359 1279.814891 2 0.0013 69 | 1/8 5 h-lim-p 0.0058 0.1035 2.8590 1279.777975 6 0.0032 94 | 1/8 6 h-lim-p 0.0193 0.3864 0.4690 1274.589648 0 0.2313 109 | 0/8 7 h-lim-p -0.0000 -0.0000 34.3852 h-lim-p: -7.44614768e-22 -5.95691814e-21 3.43851643e+01 1274.589648 .. | 0/8 8 h-lim-p 0.0000 0.0014 74.0467 1273.263448 0 0.0006 142 | 0/8 9 h-lim-p 0.0005 0.0040 97.8998 1272.339367 8 0.0004 171 | 0/8 10 h-lim-p 0.0002 0.0016 40.0632 1271.932817 0 0.0008 185 | 0/8 11 h-lim-p 0.0037 0.0296 5.7795 1271.922654 5 0.0006 211 | 0/8 12 h-lim-p 0.0016 0.1842 2.2191 1271.920513 5 0.0009 236 | 0/8 13 h-lim-p 0.0006 0.0052 0.9767 1271.920081 0 0.0010 248 | 0/8 14 h-lim-p 0.0045 1.1654 0.2104 1271.918846 0 0.0090 269 | 0/8 15 h-lim-p 0.0141 0.3904 0.1351 1271.817500 0 0.1126 292 | 0/8 16 h-lim-p 2.5000 20.0000 0.0020 1271.814487 2 1.1719 316 | 0/8 17 h-lim-p 2.5000 20.0000 0.0002 1271.814441 1 1.0938 338 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1271.814441 0 1.0938 358 | 0/8 19 h-lim-p 1.9941 20.0000 0.0000 1271.814441 0 1.7449 378 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 1271.814441 0 1.0938 398 | 0/8 21 h-lim-p 0.4707 20.0000 0.0000 1271.814441 0 3.7658 421 | 0/8 22 h-lim-p 0.3388 10.3168 0.0002 1271.814441 0 0.0000 453 | 0/8 23 h-lim-p 0.0001 20.0000 0.0002 1271.814441 0 0.0000 473 | 0/8 24 h-lim-p 0.0002 20.0000 0.0000 1271.814441 0 0.0000 505 | 0/8 25 h-lim-p 0.0000 20.0000 0.0009 | 0/8 26 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -1271.814441 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1271.814441 Node 7: lnL = -1271.814441 Node 8: lnL = -1271.814441 Node 9: lnL = -1271.814441 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 278 Sequential format.. Reading seq # 1: YCR071C_Sbay Reading seq # 2: YCR071C_Scer Reading seq # 3: YCR071C_Skud Reading seq # 4: YCR071C_Smik Reading seq # 5: YCR071C_Spar Sequences read.. Counting patterns.. # site patterns = 135 Counting frequencies.. 120 bytes for distance 21600 bytes for lkl0 17280 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.349048 0.178935 0.321009 0.264927 0.054047 0.367956 0.257106 0.000060 lnL0 = -1288.089243 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1288.089243 x= 0.34905 0.17893 0.32101 0.26493 0.05405 0.36796 0.25711 0.00006 1 h-lim-p 0.0000 0.0000 183.3640 1288.040748 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0012 349.9893 1258.712666 0 0.0009 40 | 1/8 3 h-lim-p 0.0004 0.0034 69.5723 1256.304998 0 0.0013 53 | 1/8 4 h-lim-p 0.0018 0.0148 20.8711 1255.924326 4 0.0019 73 | 1/8 5 h-lim-p 0.0056 0.0599 7.0623 1255.815897 7 0.0037 103 | 1/8 6 h-lim-p 0.0227 0.2397 1.1593 1255.466665 0 0.0340 115 | 1/8 7 h-lim-p 0.0049 0.0396 4.1512 1251.404256 0 0.0198 129 | 1/8 8 h-lim-p 0.0013 0.0106 29.4263 1249.242496 0 0.0026 142 | 1/8 9 h-lim-p 1.0488 8.3900 0.0631 1248.797160 7 0.5940 171 | 1/8 10 h-lim-p 2.5000 20.0000 0.0148 1248.765864 7 0.7226 207 | 1/8 11 h-lim-p 2.5000 20.0000 0.0011 1248.765642 4 0.7998 236 | 1/8 12 h-lim-p 1.5338 20.0000 0.0006 1248.765619 2 0.4037 260 | 1/8 13 h-lim-p 1.6238 20.0000 0.0001 1248.765615 1 0.7104 281 | 0/8 14 h-lim-p 0.0739 20.0000 0.0013 1248.765615 0 0.0040 303 | 0/8 15 h-lim-p 0.1180 0.9443 0.0000 1248.765615 0 0.7082 325 | 0/8 16 h-lim-p 0.0107 0.0858 0.0000 1248.765615 0 0.0003 350 | 0/8 17 h-lim-p 0.0000 0.0132 0.0002 1248.765615 0 0.0000 370 | 0/8 18 h-lim-p 0.0000 0.0054 0.0004 1248.765615 0 0.0000 396 | 0/8 19 h-lim-p 0.0000 0.0039 0.0005 1248.765615 0 0.0000 416 | 0/8 20 h-lim-p 0.0000 0.0018 0.0011 1248.765615 0 0.0000 442 | 0/8 21 h-lim-p 0.0000 0.0007 0.0029 1248.765615 0 0.0000 464 | 0/8 22 h-lim-p 0.0000 0.0010 0.0020 .. | 0/8 23 h-lim-p 0.0000 0.0000 0.0568 1248.765615 m 0.0000 517 | 1/8 24 h-lim-p 0.0000 20.0000 0.0037 1248.765615 0 0.0000 539 | 1/8 25 h-lim-p 0.0000 20.0000 0.0005 1248.765615 0 0.0013 565 | 1/8 26 h-lim-p 0.0060 20.0000 0.0001 1248.765615 0 0.0030 584 | 1/8 27 h-lim-p 0.0033 20.0000 0.0001 1248.765615 0 0.0029 603 | 1/8 28 h-lim-p 0.0188 20.0000 0.0000 1248.765615 0 0.0094 622 | 1/8 29 h-lim-p 0.0386 20.0000 0.0000 1248.765615 0 0.0018 645 | 1/8 30 h-lim-p 0.0000 20.0000 0.0002 1248.765615 0 0.0001 665 | 1/8 31 h-lim-p 0.0264 20.0000 0.0000 1248.765615 0 0.0008 688 Out... lnL = -1248.765615 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1248.765615 Node 7: lnL = -1248.765615 Node 8: lnL = -1248.765615 Node 9: lnL = -1248.765615 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 202 Sequential format.. Reading seq # 1: YCR076C_Sbay Reading seq # 2: YCR076C_Scer Reading seq # 3: YCR076C_Skud Reading seq # 4: YCR076C_Smik Reading seq # 5: YCR076C_Spar Sequences read.. Counting patterns.. # site patterns = 84 Counting frequencies.. 120 bytes for distance 13440 bytes for lkl0 10752 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.200179 0.076558 0.073994 0.109009 0.034649 0.103726 0.147458 0.000060 lnL0 = -751.767642 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 751.767642 x= 0.20018 0.07656 0.07399 0.10901 0.03465 0.10373 0.14746 0.00006 1 h-lim-p 0.0000 0.0000 70.0989 751.692611 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0048 33.9402 751.488818 0 0.0005 38 | 1/8 3 h-lim-p 0.0017 0.0151 9.8952 751.423658 6 0.0014 61 | 1/8 4 h-lim-p 0.0034 0.0885 4.1154 751.414062 6 0.0011 88 | 1/8 5 h-lim-p 0.0031 0.1556 1.4218 751.400781 0 0.0046 100 | 1/8 6 h-lim-p 0.0129 0.4884 0.5076 750.890921 0 0.0517 114 | 0/8 7 h-lim-p 0.0014 0.0111 15.5350 750.158258 0 0.0028 134 | 0/8 8 h-lim-p 0.0006 0.0045 9.1901 750.053957 0 0.0022 148 | 0/8 9 h-lim-p 0.0002 0.0018 9.8590 750.019635 0 0.0009 162 | 0/8 10 h-lim-p 0.1177 0.9417 0.0137 749.921792 m 0.9417 174 | 0/8 11 h-lim-p 2.5000 20.0000 0.0038 749.912315 6 0.9078 210 | 0/8 12 h-lim-p 2.0397 20.0000 0.0017 749.911395 5 0.7565 241 | 0/8 13 h-lim-p 2.5000 20.0000 0.0002 749.911381 2 0.7996 266 | 0/8 14 h-lim-p 1.9532 20.0000 0.0001 749.911380 0 0.8545 286 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 749.911380 0 1.0938 306 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 749.911380 0 2.1875 326 | 0/8 17 h-lim-p 1.9035 20.0000 0.0000 749.911380 0 0.4164 347 | 0/8 18 h-lim-p 0.7529 20.0000 0.0000 749.911380 0 0.0001 379 Out... lnL = -749.911380 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -749.911380 Node 7: lnL = -749.911380 Node 8: lnL = -749.911380 Node 9: lnL = -749.911380 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 218 Sequential format.. Reading seq # 1: YCR077C_Sbay Reading seq # 2: YCR077C_Scer Reading seq # 3: YCR077C_Skud Reading seq # 4: YCR077C_Smik Reading seq # 5: YCR077C_Spar Sequences read.. Counting patterns.. # site patterns = 85 Counting frequencies.. 120 bytes for distance 13600 bytes for lkl0 10880 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.185183 0.036362 0.042521 0.060833 0.060398 0.115999 0.092046 0.006321 lnL0 = -743.952397 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 743.952397 x= 0.18518 0.03636 0.04252 0.06083 0.06040 0.11600 0.09205 0.00632 1 h-lim-p 0.0005 0.0043 56.7838 743.189158 2 0.0005 26 | 0/8 2 h-lim-p 0.0006 0.0051 23.2638 743.075034 8 0.0005 59 | 0/8 3 h-lim-p 0.0022 0.0328 4.9033 743.067748 6 0.0006 88 | 0/8 4 h-lim-p 0.0018 0.0973 1.7026 743.067091 5 0.0005 112 | 0/8 5 h-lim-p 0.0027 0.2867 0.3198 743.067053 4 0.0008 134 | 0/8 6 h-lim-p 0.0127 5.8891 0.0195 743.067053 0 0.0014 156 | 0/8 7 h-lim-p 0.0128 20.0000 0.0021 743.067052 0 0.0112 176 | 0/8 8 h-lim-p 0.0118 20.0000 0.0020 743.067026 0 0.0947 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 743.067025 0 1.0938 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 743.067025 0 1.2500 239 | 0/8 11 h-lim-p 1.4493 20.0000 0.0000 743.067025 0 0.3170 260 | 0/8 12 h-lim-p 0.1469 20.0000 0.0000 743.067025 0 0.0001 289 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 743.067025 0 0.0000 316 | 0/8 14 h-lim-p 0.0000 20.0000 0.0014 743.067025 0 0.0000 344 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 743.067025 0 0.0000 364 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0014 | 0/8 18 h-lim-p 0.0000 20.0000 0.0014 Out... lnL = -743.067025 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -743.067025 Node 7: lnL = -743.067025 Node 8: lnL = -743.067025 Node 9: lnL = -743.067025 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 218 Sequential format.. Reading seq # 1: YCR079W_Sbay Reading seq # 2: YCR079W_Scer Reading seq # 3: YCR079W_Skud Reading seq # 4: YCR079W_Smik Reading seq # 5: YCR079W_Spar Sequences read.. Counting patterns.. # site patterns = 84 Counting frequencies.. 120 bytes for distance 13440 bytes for lkl0 10752 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.204118 0.068644 0.029060 0.073910 0.075555 0.100777 0.071175 0.012520 lnL0 = -830.410364 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 830.410364 x= 0.20412 0.06864 0.02906 0.07391 0.07556 0.10078 0.07118 0.01252 1 h-lim-p 0.0017 0.0138 30.4635 830.257950 5 0.0003 33 | 0/8 2 h-lim-p 0.0008 0.0062 12.9934 830.224127 7 0.0005 62 | 0/8 3 h-lim-p 0.0021 0.0630 2.9088 830.222055 5 0.0005 86 | 0/8 4 h-lim-p 0.0040 0.4877 0.3779 830.222018 3 0.0005 106 | 0/8 5 h-lim-p 0.0023 1.9918 0.0880 830.222016 0 0.0005 127 | 0/8 6 h-lim-p 0.0251 20.0000 0.0017 830.222016 0 0.0055 148 | 0/8 7 h-lim-p 0.0035 20.0000 0.0027 830.222012 0 0.0280 171 | 0/8 8 h-lim-p 0.0020 1.6403 0.0379 830.222001 0 0.0030 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 830.222000 0 1.0938 211 | 0/8 10 h-lim-p 1.8766 20.0000 0.0000 830.222000 0 1.6420 231 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 830.222000 0 0.5469 252 | 0/8 12 h-lim-p 0.1929 20.0000 0.0000 830.222000 0 0.0002 281 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 830.222000 0 0.0000 311 | 0/8 14 h-lim-p 0.0000 20.0000 0.0016 830.222000 0 0.0000 340 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 830.222000 0 0.0026 368 | 0/8 16 h-lim-p 0.0085 20.0000 0.0001 830.222000 0 0.0000 396 | 0/8 17 h-lim-p 0.0001 20.0000 0.0000 830.222000 0 0.0001 416 | 0/8 18 h-lim-p 0.0000 13.2636 0.0020 830.222000 0 0.0000 442 | 0/8 19 h-lim-p 0.0000 17.0515 0.0015 830.222000 0 0.0006 468 | 0/8 20 h-lim-p 0.0334 20.0000 0.0000 830.222000 0 0.0042 490 | 0/8 21 h-lim-p 0.0010 20.0000 0.0001 830.222000 0 0.0000 515 | 0/8 22 h-lim-p 0.0000 20.0000 0.0001 830.222000 0 0.0000 544 | 0/8 23 h-lim-p 0.0000 20.0000 0.0018 | 0/8 24 h-lim-p 0.0000 20.0000 0.0018 Out... lnL = -830.222000 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -830.222000 Node 7: lnL = -830.222000 Node 8: lnL = -830.222000 Node 9: lnL = -830.222000 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 239 Sequential format.. Reading seq # 1: YCR082W_Sbay Reading seq # 2: YCR082W_Scer Reading seq # 3: YCR082W_Skud Reading seq # 4: YCR082W_Smik Reading seq # 5: YCR082W_Spar Sequences read.. Counting patterns.. # site patterns = 141 Counting frequencies.. 120 bytes for distance 22560 bytes for lkl0 18048 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.287776 0.215192 0.097289 0.181929 0.123853 0.165970 0.218693 0.000060 lnL0 = -1115.982938 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1115.982938 x= 0.28778 0.21519 0.09729 0.18193 0.12385 0.16597 0.21869 0.00006 1 h-lim-p 0.0000 0.0000 21.1516 1115.978695 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0196 9.0123 1115.928634 0 0.0013 40 | 1/8 3 h-lim-p 0.0032 0.0513 3.5984 1115.920717 5 0.0014 61 | 1/8 4 h-lim-p 0.0052 0.3779 0.9422 1115.918119 6 0.0033 89 | 1/8 5 h-lim-p 0.0079 0.7403 0.3928 1115.895881 0 0.0317 110 | 1/8 6 h-lim-p 0.0161 0.4767 0.7702 1115.556016 0 0.0646 131 | 0/8 7 h-lim-p 0.0116 0.1307 4.2783 1115.534898 4 0.0023 159 | 0/8 8 h-lim-p 0.0089 0.4589 1.0973 1115.533398 5 0.0026 183 | 0/8 9 h-lim-p 0.0039 0.6834 0.7261 1115.532205 0 0.0079 196 | 0/8 10 h-lim-p 0.3189 2.5509 0.0117 1115.516028 0 0.9566 217 | 0/8 11 h-lim-p 2.5000 20.0000 0.0011 1115.515889 3 0.9961 243 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1115.515889 0 1.0938 263 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1115.515889 0 1.0938 283 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1115.515889 0 1.0938 303 | 0/8 15 h-lim-p 0.9319 20.0000 0.0000 1115.515889 0 0.9319 323 | 0/8 16 h-lim-p 0.0607 20.0000 0.0000 1115.515889 0 0.0607 343 | 0/8 17 h-lim-p 0.0198 20.0000 0.0000 1115.515889 0 0.0000 374 | 0/8 18 h-lim-p 0.0002 20.0000 0.0000 1115.515889 0 0.0000 395 Out... lnL = -1115.515889 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1115.515889 Node 7: lnL = -1115.515889 Node 8: lnL = -1115.515889 Node 9: lnL = -1115.515889 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 377 Sequential format.. Reading seq # 1: YCR083W_Sbay Reading seq # 2: YCR083W_Scer Reading seq # 3: YCR083W_Skud Reading seq # 4: YCR083W_Smik Reading seq # 5: YCR083W_Spar Sequences read.. Counting patterns.. # site patterns = 165 Counting frequencies.. 120 bytes for distance 26400 bytes for lkl0 21120 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.375384 0.066481 0.067011 0.141723 0.086361 0.232952 0.209471 0.020813 lnL0 = -1613.169021 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1613.169021 x= 0.37538 0.06648 0.06701 0.14172 0.08636 0.23295 0.20947 0.02081 1 h-lim-p 0.0035 0.0281 66.4119 1612.161131 9 0.0005 45 | 0/8 2 h-lim-p 0.0018 0.0144 12.3491 1612.104026 6 0.0008 68 | 0/8 3 h-lim-p 0.0012 0.0711 8.0105 1612.083645 7 0.0009 97 | 0/8 4 h-lim-p 0.0107 0.3826 0.6394 1612.083394 2 0.0013 115 | 0/8 5 h-lim-p 0.0028 1.3471 0.2903 1612.083341 3 0.0015 142 | 0/8 6 h-lim-p 0.0074 3.5867 0.0584 1612.083339 1 0.0009 166 | 0/8 7 h-lim-p 0.0147 20.0000 0.0036 1612.083339 0 0.0064 186 | 0/8 8 h-lim-p 0.0385 20.0000 0.0006 1612.083321 0 0.3082 209 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1612.083321 0 1.0938 229 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1612.083321 0 2.1875 249 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1612.083321 0 1.0938 269 | 0/8 12 h-lim-p 0.2625 20.0000 0.0000 1612.083321 0 3.1502 292 | 0/8 13 h-lim-p 1.5462 20.0000 0.0000 1612.083321 0 0.3382 313 | 0/8 14 h-lim-p 0.0102 20.0000 0.0006 1612.083321 0 0.0000 349 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 1612.083321 0 0.0000 377 Out... lnL = -1612.083321 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1612.083321 Node 7: lnL = -1612.083321 Node 8: lnL = -1612.083321 Node 9: lnL = -1612.083321 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 517 Sequential format.. Reading seq # 1: YCR084C_Sbay Reading seq # 2: YCR084C_Scer Reading seq # 3: YCR084C_Skud Reading seq # 4: YCR084C_Smik Reading seq # 5: YCR084C_Spar Sequences read.. Counting patterns.. # site patterns = 164 Counting frequencies.. 120 bytes for distance 26240 bytes for lkl0 20992 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.250917 0.013309 0.075994 0.062823 0.056588 0.109479 0.168959 0.024896 lnL0 = -2010.007758 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2010.007758 x= 0.25092 0.01331 0.07599 0.06282 0.05659 0.10948 0.16896 0.02490 1 h-lim-p 0.0012 0.6259 185.4185 2007.838038 8 0.0001 42 | 0/8 2 h-lim-p 0.0008 0.0061 31.7904 2007.666892 2 0.0004 58 | 0/8 3 h-lim-p 0.0013 0.0190 8.6874 2007.658453 5 0.0002 82 | 0/8 4 h-lim-p 0.0006 0.0418 3.2921 2007.657327 4 0.0002 102 | 0/8 5 h-lim-p 0.0007 0.2647 1.1418 2007.657126 2 0.0004 119 | 0/8 6 h-lim-p 0.0013 0.5719 0.3080 2007.657110 2 0.0004 136 | 0/8 7 h-lim-p 0.0019 1.2446 0.0582 2007.657109 1 0.0005 159 | 0/8 8 h-lim-p 0.0914 20.0000 0.0003 2007.656998 0 1.0970 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2007.656995 1 1.2305 205 | 0/8 10 h-lim-p 1.7469 20.0000 0.0000 2007.656995 0 1.5285 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2007.656995 0 1.0938 245 | 0/8 12 h-lim-p 0.5620 20.0000 0.0000 2007.656995 0 4.4961 268 | 0/8 13 h-lim-p 0.5678 20.0000 0.0002 2007.656995 0 0.0022 295 | 0/8 14 h-lim-p 0.0002 20.0000 0.0019 2007.656995 0 0.0001 315 | 0/8 15 h-lim-p 0.0001 20.0000 0.0016 2007.656995 0 0.0000 348 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 2007.656995 0 0.0000 382 Out... lnL = -2007.656995 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2007.656995 Node 7: lnL = -2007.656995 Node 8: lnL = -2007.656995 Node 9: lnL = -2007.656995 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 123 Sequential format.. Reading seq # 1: YCR086W_Sbay Reading seq # 2: YCR086W_Scer Reading seq # 3: YCR086W_Skud Reading seq # 4: YCR086W_Smik Reading seq # 5: YCR086W_Spar Sequences read.. Counting patterns.. # site patterns = 70 Counting frequencies.. 120 bytes for distance 11200 bytes for lkl0 8960 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.281445 0.136154 0.114655 0.207134 0.119831 0.213346 0.097885 0.000060 lnL0 = -486.474039 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 486.474039 x= 0.28145 0.13615 0.11465 0.20713 0.11983 0.21335 0.09789 0.00006 1 h-lim-p 0.0004 0.0034 45.7509 484.002296 0 0.0025 24 | 0/8 2 h-lim-p 0.0010 0.0078 22.8536 483.515822 0 0.0019 37 | 0/8 3 h-lim-p 0.0005 0.0041 6.5141 483.484991 0 0.0020 51 | 0/8 4 h-lim-p 0.0053 0.0605 2.5062 483.478484 4 0.0021 71 | 0/8 5 h-lim-p 0.0104 1.1651 0.5003 483.470969 1 0.0130 85 | 0/8 6 h-lim-p 0.0040 0.0323 0.7052 483.349287 m 0.0323 105 | 1/8 7 h-lim-p 0.0041 0.0629 4.2188 483.313303 4 0.0032 133 | 1/8 8 h-lim-p 0.0136 0.4137 0.9983 483.309573 6 0.0049 159 | 1/8 9 h-lim-p 0.0075 0.5049 0.6515 483.305042 0 0.0112 178 | 1/8 10 h-lim-p 0.2980 20.0000 0.0245 483.216485 0 0.8941 198 | 1/8 11 h-lim-p 2.5000 20.0000 0.0015 483.216097 2 1.0938 221 | 1/8 12 h-lim-p 2.5000 20.0000 0.0001 483.216093 2 1.3159 245 | 0/8 13 h-lim-p 0.1777 20.0000 0.0010 483.216093 0 0.0097 267 | 0/8 14 h-lim-p 0.1211 0.9684 0.0000 483.216093 m 0.9684 287 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 483.216093 0 1.0938 307 | 1/8 16 h-lim-p 1.8047 20.0000 0.0000 483.216093 0 1.5791 326 | 1/8 17 h-lim-p 2.1757 20.0000 0.0000 483.216093 0 0.9519 345 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 483.216093 0 0.0049 372 Out... lnL = -483.216093 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -483.216093 Node 7: lnL = -483.216093 Node 8: lnL = -483.216093 Node 9: lnL = -483.216093 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 634 Sequential format.. Reading seq # 1: YCR087C-A_Sbay Reading seq # 2: YCR087C-A_Scer Reading seq # 3: YCR087C-A_Skud Reading seq # 4: YCR087C-A_Smik Reading seq # 5: YCR087C-A_Spar Sequences read.. Counting patterns.. # site patterns = 279 Counting frequencies.. 120 bytes for distance 44640 bytes for lkl0 35712 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.383519 0.209472 0.149752 0.210084 0.113903 0.267684 0.132646 0.000060 lnL0 = -2998.865921 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2998.865921 x= 0.38352 0.20947 0.14975 0.21008 0.11390 0.26768 0.13265 0.00006 1 h-lim-p 0.0000 0.0000 185.0755 2998.618087 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0041 72.6951 2997.219383 0 0.0006 39 | 1/8 3 h-lim-p 0.0013 0.0106 32.9617 2996.892641 8 0.0007 68 | 1/8 4 h-lim-p 0.0024 0.0223 9.6373 2996.797011 7 0.0018 95 | 1/8 5 h-lim-p 0.0129 0.2728 1.3404 2996.393656 0 0.0257 108 | 1/8 6 h-lim-p 0.0039 0.0323 8.9428 2994.979475 0 0.0058 120 | 1/8 7 h-lim-p 0.0025 0.0197 18.5946 2988.865171 0 0.0049 133 | 1/8 8 h-lim-p 0.0039 0.0315 4.3342 2988.858007 5 0.0007 159 | 1/8 9 h-lim-p 0.0787 13.8772 0.0391 2988.460394 0 0.6295 174 | 0/8 10 h-lim-p 0.0506 3.5043 0.4866 2988.460204 2 0.0016 201 | 0/8 11 h-lim-p 0.1896 20.0000 0.0040 2988.454347 0 0.7584 223 | 0/8 12 h-lim-p 2.5000 20.0000 0.0007 2988.454062 3 0.8059 251 | 0/8 13 h-lim-p 2.2471 20.0000 0.0002 2988.454043 2 0.7412 277 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 2988.454043 0 1.0938 297 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2988.454043 0 1.0938 317 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 2988.454043 0 1.0938 337 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 2988.454043 0 0.6250 358 | 0/8 18 h-lim-p 1.1867 20.0000 0.0000 2988.454043 0 0.1298 380 | 0/8 19 h-lim-p 0.0880 20.0000 0.0000 2988.454043 0 0.0000 410 Out... lnL = -2988.454043 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2988.454043 Node 7: lnL = -2988.454043 Node 8: lnL = -2988.454043 Node 9: lnL = -2988.454043 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 613 Sequential format.. Reading seq # 1: YCR088W_Sbay Reading seq # 2: YCR088W_Scer Reading seq # 3: YCR088W_Skud Reading seq # 4: YCR088W_Smik Reading seq # 5: YCR088W_Spar Sequences read.. Counting patterns.. # site patterns = 234 Counting frequencies.. 120 bytes for distance 37440 bytes for lkl0 29952 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.347691 0.081834 0.063956 0.136695 0.090171 0.245924 0.176274 0.005886 lnL0 = -2840.193281 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2840.193281 x= 0.34769 0.08183 0.06396 0.13670 0.09017 0.24592 0.17627 0.00589 1 h-lim-p 0.0027 0.0219 92.9156 2839.090039 5 0.0003 34 | 0/8 2 h-lim-p 0.0011 0.0098 24.0660 2838.926596 7 0.0006 63 | 0/8 3 h-lim-p 0.0010 0.0169 14.3935 2838.905463 5 0.0003 86 | 0/8 4 h-lim-p 0.0025 0.0216 1.5630 2838.904914 4 0.0005 107 | 0/8 5 h-lim-p 0.0022 0.0788 0.3354 2838.904885 2 0.0006 124 | 0/8 6 h-lim-p 0.0037 4.6505 0.0511 2838.904884 0 0.0008 145 | 0/8 7 h-lim-p 0.0061 20.0000 0.0068 2838.904883 0 0.0053 165 | 0/8 8 h-lim-p 0.0201 20.0000 0.0018 2838.904741 0 0.1607 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2838.904740 0 1.0938 208 | 0/8 10 h-lim-p 1.4825 20.0000 0.0000 2838.904740 0 1.2972 228 | 0/8 11 h-lim-p 1.8808 20.0000 0.0000 2838.904740 0 1.6457 248 | 0/8 12 h-lim-p 0.9313 20.0000 0.0000 2838.904740 0 0.8148 268 | 0/8 13 h-lim-p 0.0268 20.0000 0.0009 2838.904740 0 0.0117 288 | 0/8 14 h-lim-p 0.0037 6.8267 0.0028 2838.904740 0 0.0000 314 | 0/8 15 h-lim-p 0.0000 0.8756 0.0219 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0005 | 0/8 17 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -2838.904740 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2838.904740 Node 7: lnL = -2838.904740 Node 8: lnL = -2838.904740 Node 9: lnL = -2838.904740 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 339 Sequential format.. Reading seq # 1: YCR094W_Sbay Reading seq # 2: YCR094W_Scer Reading seq # 3: YCR094W_Skud Reading seq # 4: YCR094W_Smik Reading seq # 5: YCR094W_Spar Sequences read.. Counting patterns.. # site patterns = 168 Counting frequencies.. 120 bytes for distance 26880 bytes for lkl0 21504 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.340925 0.218445 0.275602 0.247863 0.061454 0.357991 0.182758 0.000060 lnL0 = -1596.849067 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1596.849067 x= 0.34093 0.21844 0.27560 0.24786 0.06145 0.35799 0.18276 0.00006 1 h-lim-p 0.0000 0.0000 180.9220 1596.799692 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0010 361.1250 1572.154996 0 0.0008 40 | 1/8 3 h-lim-p 0.0003 0.0023 51.6429 1570.935853 0 0.0012 54 | 1/8 4 h-lim-p 0.0023 0.0187 19.5807 1570.722399 5 0.0012 77 | 1/8 5 h-lim-p 0.0049 0.0390 4.5177 1570.687171 3 0.0022 95 | 1/8 6 h-lim-p 0.0174 0.3354 0.5730 1569.321269 0 0.1394 110 | 1/8 7 h-lim-p 0.0016 0.0131 14.0414 1564.513189 0 0.0065 131 | 1/8 8 h-lim-p 0.0047 0.0379 10.9881 1564.393510 4 0.0019 151 | 1/8 9 h-lim-p 0.1911 3.9836 0.1070 1563.505528 0 0.5732 164 | 0/8 10 h-lim-p 0.0227 0.2957 2.7025 1563.500859 6 0.0016 199 | 0/8 11 h-lim-p 0.2242 1.7938 0.0139 1563.426204 0 0.8969 213 | 0/8 12 h-lim-p 2.5000 20.0000 0.0025 1563.423200 6 0.7907 249 | 0/8 13 h-lim-p 2.5000 20.0000 0.0006 1563.423079 3 0.8246 277 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 1563.423078 1 0.6152 300 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1563.423077 0 1.0938 320 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1563.423077 0 1.0938 340 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1563.423077 0 1.0938 360 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1563.423077 0 2.1875 380 | 0/8 19 h-lim-p 2.4736 20.0000 0.0000 1563.423077 0 0.6184 401 | 0/8 20 h-lim-p 0.2861 20.0000 0.0000 1563.423077 0 0.0358 423 | 0/8 21 h-lim-p 0.0108 20.0000 0.0000 1563.423077 0 0.0000 456 Out... lnL = -1563.423077 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1563.423077 Node 7: lnL = -1563.423077 Node 8: lnL = -1563.423077 Node 9: lnL = -1563.423077 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 880 Sequential format.. Reading seq # 1: YCR095C_Sbay Reading seq # 2: YCR095C_Scer Reading seq # 3: YCR095C_Skud Reading seq # 4: YCR095C_Smik Reading seq # 5: YCR095C_Spar Sequences read.. Counting patterns.. # site patterns = 448 Counting frequencies.. 120 bytes for distance 71680 bytes for lkl0 57344 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.727444 0.000060 0.026573 0.375169 0.207248 0.510814 0.439563 0.097576 lnL0 = -4820.034502 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4820.034502 x= 0.72744 0.00006 0.02657 0.37517 0.20725 0.51081 0.43956 0.09758 1 h-lim-p 0.0000 0.0000 98.5211 4820.017767 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0118 42.6825 4819.021148 0 0.0013 41 | 1/8 3 h-lim-p 0.0023 0.0186 7.6884 4818.990729 5 0.0010 62 | 1/8 4 h-lim-p 0.0027 0.1089 2.9568 4818.978831 5 0.0022 86 | 1/8 5 h-lim-p 0.0089 0.1841 0.7191 4818.942226 0 0.0177 99 | 1/8 6 h-lim-p 0.0080 0.1289 1.6021 4818.026248 0 0.0319 120 | 1/8 7 h-lim-p 0.0009 0.0073 16.4307 4817.465309 0 0.0037 134 | 1/8 8 h-lim-p 2.5000 20.0000 0.0161 4817.385192 4 0.9643 154 | 1/8 9 h-lim-p 2.5000 20.0000 0.0011 4817.384888 3 0.8855 181 | 1/8 10 h-lim-p 2.5000 20.0000 0.0001 4817.384885 1 0.6152 203 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 4817.384885 0 1.0938 222 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 4817.384885 0 1.0938 241 | 1/8 13 h-lim-p 1.4012 20.0000 0.0000 4817.384885 0 1.4012 260 | 1/8 14 h-lim-p 0.8423 20.0000 0.0000 4817.384885 0 0.8423 279 | 1/8 15 h-lim-p 0.0065 20.0000 0.0014 4817.384885 0 0.0033 298 | 1/8 16 h-lim-p 0.0058 20.0000 0.0008 4817.384885 0 0.0002 321 | 1/8 17 h-lim-p 0.0001 20.0000 0.0009 4817.384885 0 0.0000 352 | 1/8 18 h-lim-p 0.0001 20.0000 0.0000 4817.384885 0 0.0000 382 Out... lnL = -4817.384885 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4817.384885 Node 7: lnL = -4817.384885 Node 8: lnL = -4817.384885 Node 9: lnL = -4817.384885 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 918 Sequential format.. Reading seq # 1: YCR098C_Sbay Reading seq # 2: YCR098C_Scer Reading seq # 3: YCR098C_Skud Reading seq # 4: YCR098C_Smik Reading seq # 5: YCR098C_Spar Sequences read.. Counting patterns.. # site patterns = 288 Counting frequencies.. 120 bytes for distance 46080 bytes for lkl0 36864 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.323154 0.057551 0.072537 0.207456 0.075826 0.256946 0.310842 0.000060 lnL0 = -3851.765272 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3851.765272 x= 0.32315 0.05755 0.07254 0.20746 0.07583 0.25695 0.31084 0.00006 1 h-lim-p 0.0000 0.0000 491.3420 3851.425820 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0011 313.0436 3835.711284 0 0.0005 39 | 1/8 3 h-lim-p 0.0002 0.0017 68.1442 3835.036440 0 0.0003 51 | 1/8 4 h-lim-p 0.0018 0.0377 12.5903 3834.956761 5 0.0008 72 | 1/8 5 h-lim-p 0.0022 0.0867 4.2514 3834.800407 0 0.0033 84 | 1/8 6 h-lim-p 0.0016 0.0196 8.6941 3833.555233 0 0.0049 97 | 0/8 7 h-lim-p 0.0017 0.0136 16.5142 3813.799839 0 0.0068 111 | 0/8 8 h-lim-p 0.0002 0.0012 79.6260 3807.177071 m 0.0012 123 | 0/8 9 h-lim-p 0.0007 0.0055 50.2842 3806.471787 2 0.0006 139 | 0/8 10 h-lim-p 0.0650 0.5201 0.0213 3806.352857 0 0.3901 153 | 0/8 11 h-lim-p 2.2435 20.0000 0.0037 3806.345472 5 0.7739 186 | 0/8 12 h-lim-p 2.5000 20.0000 0.0007 3806.345125 4 0.7412 217 | 0/8 13 h-lim-p 1.9432 20.0000 0.0003 3806.345083 2 0.7496 241 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 3806.345082 0 1.0938 261 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 3806.345082 0 1.0938 281 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 3806.345082 0 2.1875 301 | 0/8 17 h-lim-p 1.9555 20.0000 0.0000 3806.345082 0 0.8555 321 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 3806.345082 0 0.0049 349 Out... lnL = -3806.345082 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3806.345082 Node 7: lnL = -3806.345082 Node 8: lnL = -3806.345082 Node 9: lnL = -3806.345082 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 428 Sequential format.. Reading seq # 1: YDL002C_Sbay Reading seq # 2: YDL002C_Scer Reading seq # 3: YDL002C_Skud Reading seq # 4: YDL002C_Smik Reading seq # 5: YDL002C_Spar Sequences read.. Counting patterns.. # site patterns = 114 Counting frequencies.. 120 bytes for distance 18240 bytes for lkl0 14592 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.163635 0.041998 0.046394 0.083170 0.036089 0.129965 0.075715 0.000060 lnL0 = -1490.583617 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1490.583617 x= 0.16363 0.04200 0.04639 0.08317 0.03609 0.12997 0.07571 0.00006 1 h-lim-p 0.0000 0.0000 161.0000 1490.462752 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0018 63.8393 1490.044713 0 0.0002 38 | 1/8 3 h-lim-p 0.0005 0.0090 24.5686 1490.000167 6 0.0002 64 | 1/8 4 h-lim-p 0.0005 0.0155 8.9606 1489.987896 6 0.0003 90 | 1/8 5 h-lim-p 0.0018 0.0476 1.7060 1489.985614 4 0.0007 110 | 1/8 6 h-lim-p 0.0006 0.1025 2.0448 1489.977641 0 0.0011 123 | 1/8 7 h-lim-p 0.0017 0.1470 1.3670 1489.859763 0 0.0066 137 | 1/8 8 h-lim-p 0.0016 0.0183 5.7341 1488.132645 0 0.0047 150 | 1/8 9 h-lim-p 2.5000 20.0000 0.0070 1487.999516 7 0.8936 179 | 0/8 10 h-lim-p 0.0182 4.2820 0.3444 1487.999480 1 0.0006 204 | 0/8 11 h-lim-p 0.1339 2.0816 0.0015 1487.992608 1 1.3238 229 | 0/8 12 h-lim-p 0.1082 0.8655 0.0004 1487.992428 m 0.8655 249 | 1/8 13 h-lim-p 2.5000 20.0000 0.0001 1487.992422 2 0.8246 275 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 1487.992422 0 1.0938 294 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 1487.992422 0 2.1875 313 | 1/8 16 h-lim-p 1.7868 20.0000 0.0000 1487.992422 0 0.3909 333 | 1/8 17 h-lim-p 0.6384 20.0000 0.0000 1487.992422 0 0.0698 354 | 1/8 18 h-lim-p 0.0752 20.0000 0.0000 1487.992422 0 0.0376 373 | 1/8 19 h-lim-p 0.0390 20.0000 0.0000 1487.992422 0 0.0003 398 Out... lnL = -1487.992422 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1487.992422 Node 7: lnL = -1487.992422 Node 8: lnL = -1487.992422 Node 9: lnL = -1487.992422 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 917 Sequential format.. Reading seq # 1: YDL003W_Sbay Reading seq # 2: YDL003W_Scer Reading seq # 3: YDL003W_Skud Reading seq # 4: YDL003W_Smik Reading seq # 5: YDL003W_Spar Sequences read.. Counting patterns.. # site patterns = 390 Counting frequencies.. 120 bytes for distance 62400 bytes for lkl0 49920 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.414351 0.032353 0.062858 0.168246 0.163776 0.273701 0.328145 0.000060 lnL0 = -4445.557214 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4445.557214 x= 0.41435 0.03235 0.06286 0.16825 0.16378 0.27370 0.32815 0.00006 1 h-lim-p 0.0006 0.0050 183.0730 4442.087427 8 0.0002 42 | 0/8 2 h-lim-p 0.0000 0.0001 44.0336 4441.866320 m 0.0001 54 | 1/8 3 h-lim-p 0.0004 0.0350 17.1209 4441.792699 0 0.0007 67 | 1/8 4 h-lim-p 0.0016 0.0460 7.4404 4441.778625 5 0.0006 91 | 1/8 5 h-lim-p 0.0033 0.1044 1.3922 4441.777707 3 0.0008 110 | 1/8 6 h-lim-p 0.0025 0.7215 0.4535 4441.777106 4 0.0019 130 | 1/8 7 h-lim-p 0.0034 2.6638 0.2471 4441.763408 0 0.0206 151 | 1/8 8 h-lim-p 0.0025 0.3019 2.0572 4441.750606 4 0.0022 177 | 1/8 9 h-lim-p 0.0721 2.8646 0.0622 4441.617021 0 0.1442 190 | 1/8 10 h-lim-p 2.5000 20.0000 0.0007 4441.616028 4 0.9644 217 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 4441.616027 0 1.0938 236 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 4441.616027 0 1.0938 255 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 4441.616027 0 1.2500 274 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 4441.616027 0 0.0002 306 Out... lnL = -4441.616027 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4441.616027 Node 7: lnL = -4441.616027 Node 8: lnL = -4441.616027 Node 9: lnL = -4441.616027 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 747 Sequential format.. Reading seq # 1: YDL004W_Sbay Reading seq # 2: YDL004W_Scer Reading seq # 3: YDL004W_Skud Reading seq # 4: YDL004W_Smik Reading seq # 5: YDL004W_Spar Sequences read.. Counting patterns.. # site patterns = 297 Counting frequencies.. 120 bytes for distance 47520 bytes for lkl0 38016 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.397838 0.101423 0.101852 0.350779 0.113077 0.358099 0.240501 0.000060 lnL0 = -3726.028391 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3726.028391 x= 0.39784 0.10142 0.10185 0.35078 0.11308 0.35810 0.24050 0.00006 1 h-lim-p 0.0000 0.0000 285.0686 3725.930901 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0021 240.2457 3710.891515 0 0.0006 40 | 1/8 3 h-lim-p 0.0012 0.0094 20.4652 3710.740098 7 0.0006 68 | 1/8 4 h-lim-p 0.0013 0.0572 10.4625 3710.691770 4 0.0006 90 | 1/8 5 h-lim-p 0.0035 0.2168 1.9174 3709.216679 0 0.0279 105 | 1/8 6 h-lim-p 0.0041 0.0328 10.5187 3692.036276 0 0.0164 119 | 0/8 7 h-lim-p 0.0012 0.0094 36.1252 3691.731504 6 0.0004 143 | 0/8 8 h-lim-p 0.0003 0.0026 2.8225 3691.715699 m 0.0026 155 | 0/8 9 h-lim-p 0.0000 0.0000 1.8242 h-lim-p: 1.30456421e-20 1.04365137e-19 1.82420976e+00 3691.715699 .. | 0/8 10 h-lim-p 0.0000 1.0521 132.9464 3689.217608 0 0.0003 180 | 0/8 11 h-lim-p 0.0006 0.0050 43.2060 3688.829981 7 0.0005 209 | 0/8 12 h-lim-p 0.0002 0.0015 9.9041 3688.811130 0 0.0004 222 | 0/8 13 h-lim-p 0.0015 0.0461 2.4594 3688.809185 2 0.0007 238 | 0/8 14 h-lim-p 0.0026 0.5720 0.6442 3688.809085 2 0.0005 255 | 0/8 15 h-lim-p 0.0023 0.0721 0.1391 3688.809069 0 0.0011 275 | 0/8 16 h-lim-p 0.0292 3.6423 0.0054 3688.806305 0 0.3501 298 | 0/8 17 h-lim-p 0.0014 0.1633 1.3500 3688.802710 2 0.0013 322 | 0/8 18 h-lim-p 2.5000 20.0000 0.0006 3688.802620 2 0.9961 338 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 3688.802620 0 1.0938 358 | 0/8 20 h-lim-p 1.4614 20.0000 0.0000 3688.802620 0 1.2787 378 | 0/8 21 h-lim-p 0.6383 20.0000 0.0001 3688.802620 0 0.3191 398 | 0/8 22 h-lim-p 0.0125 3.9115 0.0013 3688.802620 0 0.0001 424 | 0/8 23 h-lim-p 0.0008 20.0000 0.0002 3688.802620 0 0.0000 457 | 0/8 24 h-lim-p 0.0000 20.0000 0.0006 | 0/8 25 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -3688.802620 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3688.802620 Node 7: lnL = -3688.802620 Node 8: lnL = -3688.802620 Node 9: lnL = -3688.802620 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 745 Sequential format.. Reading seq # 1: YDL005C_Sbay Reading seq # 2: YDL005C_Scer Reading seq # 3: YDL005C_Skud Reading seq # 4: YDL005C_Smik Reading seq # 5: YDL005C_Spar Sequences read.. Counting patterns.. # site patterns = 294 Counting frequencies.. 120 bytes for distance 47040 bytes for lkl0 37632 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.389664 0.069732 0.101742 0.312601 0.112214 0.306591 0.255735 0.000060 lnL0 = -3703.285691 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3703.285691 x= 0.38966 0.06973 0.10174 0.31260 0.11221 0.30659 0.25573 0.00006 1 h-lim-p 0.0000 0.0000 226.9755 3703.186559 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0025 159.7984 3697.641087 0 0.0006 40 | 1/8 3 h-lim-p 0.0032 0.0366 31.6478 3697.494137 5 0.0003 64 | 1/8 4 h-lim-p 0.0010 0.0149 9.6901 3697.449125 5 0.0007 88 | 1/8 5 h-lim-p 0.0034 0.2049 2.1029 3697.147555 0 0.0136 102 | 1/8 6 h-lim-p 0.0048 0.0892 5.9360 3693.111687 0 0.0144 115 | 0/8 7 h-lim-p 0.0006 0.0049 71.5493 3685.073733 0 0.0019 128 | 0/8 8 h-lim-p 0.0007 0.0053 23.9825 3684.365155 0 0.0026 142 | 0/8 9 h-lim-p 0.0007 0.0055 15.7265 3684.302819 5 0.0006 163 | 0/8 10 h-lim-p 0.1822 1.4577 0.0508 3683.058343 0 0.7289 177 | 0/8 11 h-lim-p 2.5000 20.0000 0.0142 3682.931405 5 0.9563 207 | 0/8 12 h-lim-p 2.0841 20.0000 0.0065 3682.908985 6 0.7690 241 | 0/8 13 h-lim-p 2.5000 20.0000 0.0011 3682.907511 2 1.0938 265 | 0/8 14 h-lim-p 2.5000 20.0000 0.0004 3682.907477 2 0.9644 289 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 3682.907477 0 1.0938 309 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 3682.907477 0 1.0938 329 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 3682.907477 0 2.1875 349 | 0/8 18 h-lim-p 1.8368 20.0000 0.0000 3682.907477 0 0.8036 369 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 3682.907477 0 0.1562 392 | 0/8 20 h-lim-p 0.0955 20.0000 0.0000 3682.907477 0 0.0119 414 Out... lnL = -3682.907477 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3682.907477 Node 7: lnL = -3682.907477 Node 8: lnL = -3682.907477 Node 9: lnL = -3682.907477 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 613 Sequential format.. Reading seq # 1: YDL006W_Sbay Reading seq # 2: YDL006W_Scer Reading seq # 3: YDL006W_Skud Reading seq # 4: YDL006W_Smik Reading seq # 5: YDL006W_Spar Sequences read.. Counting patterns.. # site patterns = 200 Counting frequencies.. 120 bytes for distance 32000 bytes for lkl0 25600 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.305216 0.102961 0.075505 0.188954 0.082332 0.254753 0.162393 0.000060 lnL0 = -2651.739640 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2651.739640 x= 0.30522 0.10296 0.07550 0.18895 0.08233 0.25475 0.16239 0.00006 1 h-lim-p 0.0000 0.0000 238.6325 2651.629945 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0019 174.2504 2647.331785 0 0.0005 39 | 1/8 3 h-lim-p 0.0024 0.0193 13.5773 2647.246066 6 0.0008 67 | 1/8 4 h-lim-p 0.0016 0.0763 6.7178 2647.217302 2 0.0007 83 | 1/8 5 h-lim-p 0.0009 0.0420 5.6756 2647.106467 0 0.0018 96 | 1/8 6 h-lim-p 0.0015 0.0397 6.8186 2646.285370 0 0.0059 110 | 1/8 7 h-lim-p 0.0019 0.0149 14.2451 2640.963211 0 0.0037 123 | 1/8 8 h-lim-p 0.0006 0.0052 83.3156 2635.802170 0 0.0013 136 | 1/8 9 h-lim-p 0.3738 2.9905 0.0536 2634.342257 0 0.7476 149 | 0/8 10 h-lim-p 0.0081 1.3017 4.9548 2634.332141 4 0.0008 178 | 0/8 11 h-lim-p 0.2236 20.0000 0.0178 2634.074795 0 0.6708 191 | 0/8 12 h-lim-p 2.5000 20.0000 0.0037 2634.054931 5 0.9422 221 | 0/8 13 h-lim-p 2.5000 20.0000 0.0007 2634.054468 4 0.8228 250 | 0/8 14 h-lim-p 2.5000 20.0000 0.0002 2634.054437 1 1.0938 272 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2634.054436 0 1.0938 292 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 2634.054436 0 1.0938 312 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 2634.054436 0 1.0938 332 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 2634.054436 0 2.1875 352 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 2634.054436 0 0.6250 373 | 0/8 20 h-lim-p 0.2668 20.0000 0.0000 2634.054436 0 0.0000 418 Out... lnL = -2634.054436 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2634.054436 Node 7: lnL = -2634.054436 Node 8: lnL = -2634.054436 Node 9: lnL = -2634.054436 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 908 Sequential format.. Reading seq # 1: YDL010W_Sbay Reading seq # 2: YDL010W_Scer Reading seq # 3: YDL010W_Skud Reading seq # 4: YDL010W_Smik Reading seq # 5: YDL010W_Spar Sequences read.. Counting patterns.. # site patterns = 338 Counting frequencies.. 120 bytes for distance 54080 bytes for lkl0 43264 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.389031 0.138414 0.113650 0.146655 0.122925 0.221475 0.215639 0.000060 lnL0 = -4161.576080 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4161.576080 x= 0.38903 0.13841 0.11365 0.14666 0.12293 0.22147 0.21564 0.00006 1 h-lim-p 0.0000 0.0000 142.2133 4161.522298 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0202 41.3526 4161.199797 0 0.0005 39 | 1/8 3 h-lim-p 0.0012 0.0146 16.9170 4161.152319 6 0.0004 67 | 1/8 4 h-lim-p 0.0009 0.0640 6.6100 4161.133261 5 0.0008 92 | 1/8 5 h-lim-p 0.0023 0.1347 2.3097 4161.111765 4 0.0025 113 | 1/8 6 h-lim-p 0.0034 0.2195 1.6994 4160.896563 0 0.0134 127 | 1/8 7 h-lim-p 0.0016 0.0247 14.0170 4159.667148 0 0.0033 140 | 0/8 8 h-lim-p 0.0012 0.0094 27.4579 4157.498945 0 0.0023 153 | 0/8 9 h-lim-p 0.0003 0.0026 17.0841 4157.301447 0 0.0013 167 | 0/8 10 h-lim-p 0.1796 1.4368 0.0239 4156.864081 0 0.7184 181 | 0/8 11 h-lim-p 0.5946 4.7564 0.0034 4156.855132 0 0.8918 201 | 0/8 12 h-lim-p 2.5000 20.0000 0.0006 4156.854670 3 0.9644 227 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 4156.854670 0 1.0938 247 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 4156.854670 0 1.0938 267 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 4156.854670 0 1.0938 287 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 4156.854670 0 0.0684 311 | 0/8 17 h-lim-p 0.0469 20.0000 0.0000 4156.854670 0 0.0000 344 Out... lnL = -4156.854670 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4156.854670 Node 7: lnL = -4156.854670 Node 8: lnL = -4156.854670 Node 9: lnL = -4156.854670 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 457 Sequential format.. Reading seq # 1: YDL014W_Sbay Reading seq # 2: YDL014W_Scer Reading seq # 3: YDL014W_Skud Reading seq # 4: YDL014W_Smik Reading seq # 5: YDL014W_Spar Sequences read.. Counting patterns.. # site patterns = 131 Counting frequencies.. 120 bytes for distance 20960 bytes for lkl0 16768 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.200395 0.096650 0.064702 0.065356 0.085092 0.104619 0.129824 0.000060 lnL0 = -1766.143122 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1766.143122 x= 0.20039 0.09665 0.06470 0.06536 0.08509 0.10462 0.12982 0.00006 1 h-lim-p 0.0000 0.0000 198.3561 1766.075845 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0057 30.0102 1765.894905 0 0.0003 39 | 1/8 3 h-lim-p 0.0008 0.0154 12.7489 1765.863314 2 0.0004 55 | 1/8 4 h-lim-p 0.0016 0.0824 3.1449 1765.850976 4 0.0008 76 | 1/8 5 h-lim-p 0.0012 0.0734 2.0057 1765.659849 0 0.0050 90 | 1/8 6 h-lim-p 0.0009 0.0180 10.5961 1761.228214 0 0.0057 104 | 0/8 7 h-lim-p 0.0001 0.0008 79.6178 1759.212173 0 0.0004 118 | 0/8 8 h-lim-p 0.0012 0.0093 12.5939 1759.187442 7 0.0003 146 | 0/8 9 h-lim-p 0.0014 0.0724 2.9317 1759.101641 0 0.0220 162 | 0/8 10 h-lim-p 1.4121 11.2968 0.0229 1758.665214 7 0.7373 188 | 0/8 11 h-lim-p 0.9257 7.5519 0.0182 1758.625941 5 1.0140 222 | 0/8 12 h-lim-p 2.5000 20.0000 0.0029 1758.625566 4 0.9422 250 | 0/8 13 h-lim-p 2.5000 20.0000 0.0002 1758.625560 2 0.7996 275 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 1758.625560 0 1.0938 295 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1758.625560 0 1.0938 315 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1758.625560 0 2.1875 335 | 0/8 17 h-lim-p 1.7809 20.0000 0.0000 1758.625560 0 0.3896 356 | 0/8 18 h-lim-p 0.6065 20.0000 0.0000 1758.625560 0 0.0047 382 | 0/8 19 h-lim-p 0.0045 20.0000 0.0000 1758.625560 0 0.0006 404 Out... lnL = -1758.625560 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1758.625560 Node 7: lnL = -1758.625560 Node 8: lnL = -1758.625560 Node 9: lnL = -1758.625560 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 460 Sequential format.. Reading seq # 1: YDL015C_Sbay Reading seq # 2: YDL015C_Scer Reading seq # 3: YDL015C_Skud Reading seq # 4: YDL015C_Smik Reading seq # 5: YDL015C_Spar Sequences read.. Counting patterns.. # site patterns = 132 Counting frequencies.. 120 bytes for distance 21120 bytes for lkl0 16896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.196059 0.097732 0.069086 0.064223 0.088631 0.090889 0.130979 0.000060 lnL0 = -1761.611950 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1761.611950 x= 0.19606 0.09773 0.06909 0.06422 0.08863 0.09089 0.13098 0.00006 1 h-lim-p 0.0000 0.0000 200.5103 1761.552086 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0022 66.4183 1760.972735 0 0.0003 39 | 1/8 3 h-lim-p 0.0006 0.0048 31.0035 1760.827042 7 0.0004 69 | 1/8 4 h-lim-p 0.0015 0.0128 7.6389 1760.816123 4 0.0003 90 | 1/8 5 h-lim-p 0.0008 0.0620 2.7065 1760.782710 0 0.0017 103 | 1/8 6 h-lim-p 0.0014 0.0832 3.0972 1760.219481 0 0.0087 117 | 1/8 7 h-lim-p 0.0011 0.0085 23.5150 1757.612549 0 0.0021 130 | 0/8 8 h-lim-p 0.0002 0.0018 68.7802 1754.492776 0 0.0009 144 | 0/8 9 h-lim-p 0.0006 0.0050 9.9664 1754.427896 0 0.0019 157 | 0/8 10 h-lim-p 0.1476 1.1811 0.0413 1753.229540 0 0.8859 171 | 0/8 11 h-lim-p 1.8854 15.0833 0.0097 1753.081365 7 1.3835 206 | 0/8 12 h-lim-p 2.5000 20.0000 0.0015 1753.079138 5 0.8624 239 | 0/8 13 h-lim-p 1.1589 16.4564 0.0011 1753.078821 4 0.8139 269 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 1753.078806 2 0.7996 294 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1753.078806 0 1.0938 314 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1753.078806 0 1.0938 334 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1753.078806 0 5.0000 355 | 0/8 18 h-lim-p 1.7146 20.0000 0.0000 1753.078806 0 0.0938 378 | 0/8 19 h-lim-p 0.1373 20.0000 0.0000 1753.078806 0 0.0032 403 Out... lnL = -1753.078806 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1753.078806 Node 7: lnL = -1753.078806 Node 8: lnL = -1753.078806 Node 9: lnL = -1753.078806 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 772 Sequential format.. Reading seq # 1: YDL017W_Sbay Reading seq # 2: YDL017W_Scer Reading seq # 3: YDL017W_Skud Reading seq # 4: YDL017W_Smik Reading seq # 5: YDL017W_Spar Sequences read.. Counting patterns.. # site patterns = 281 Counting frequencies.. 120 bytes for distance 44960 bytes for lkl0 35968 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.375254 0.256494 0.188490 0.150955 0.106257 0.177256 0.172287 0.000060 lnL0 = -3571.462991 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3571.462991 x= 0.37525 0.25649 0.18849 0.15095 0.10626 0.17726 0.17229 0.00006 1 h-lim-p 0.0000 0.0000 344.7064 3571.382582 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0017 183.5703 3562.694209 0 0.0006 40 | 1/8 3 h-lim-p 0.0004 0.0035 90.6224 3560.860734 0 0.0007 52 | 1/8 4 h-lim-p 0.0019 0.0149 27.7986 3560.571794 3 0.0008 70 | 1/8 5 h-lim-p 0.0020 0.0274 10.5957 3560.502344 4 0.0008 90 | 1/8 6 h-lim-p 0.0011 0.0624 7.4226 3560.267665 0 0.0023 103 | 1/8 7 h-lim-p 0.0020 0.0496 8.2745 3558.672126 0 0.0081 117 | 1/8 8 h-lim-p 0.0020 0.0159 14.6374 3534.567769 0 0.0079 131 | 1/8 9 h-lim-p 0.2096 1.6770 0.0670 3532.294015 0 0.6289 144 | 1/8 10 h-lim-p 0.9157 7.7671 0.0460 3531.046407 6 0.6924 175 | 1/8 11 h-lim-p 1.2186 20.0000 0.0262 3530.876629 5 0.5352 203 | 1/8 12 h-lim-p 2.5000 20.0000 0.0038 3530.861863 5 1.0113 234 | 0/8 13 h-lim-p 0.0036 0.9505 1.0669 3530.861527 4 0.0006 263 | 0/8 14 h-lim-p 1.7658 20.0000 0.0004 3530.861443 2 0.7036 279 | 0/8 15 h-lim-p 2.5000 20.0000 0.0001 3530.861436 1 0.9961 301 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 3530.861436 0 1.0938 321 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 3530.861436 0 1.0938 341 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 3530.861436 0 1.2500 361 | 0/8 19 h-lim-p 1.9990 20.0000 0.0000 3530.861436 0 0.4998 382 | 0/8 20 h-lim-p 0.0215 20.0000 0.0000 3530.861436 0 0.0000 413 Out... lnL = -3530.861436 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3530.861436 Node 7: lnL = -3530.861436 Node 8: lnL = -3530.861436 Node 9: lnL = -3530.861436 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 762 Sequential format.. Reading seq # 1: YDL018C_Sbay Reading seq # 2: YDL018C_Scer Reading seq # 3: YDL018C_Skud Reading seq # 4: YDL018C_Smik Reading seq # 5: YDL018C_Spar Sequences read.. Counting patterns.. # site patterns = 209 Counting frequencies.. 120 bytes for distance 33440 bytes for lkl0 26752 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.414713 0.022084 0.164714 0.186799 0.058872 0.229036 0.296672 0.000060 lnL0 = -3150.983402 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3150.983402 x= 0.41471 0.02208 0.16471 0.18680 0.05887 0.22904 0.29667 0.00006 1 h-lim-p 0.0000 0.0000 46.3697 3150.971223 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0060 54.7573 3150.709465 0 0.0003 39 | 1/8 3 h-lim-p 0.0009 0.0174 20.2470 3150.549207 0 0.0013 51 | 1/8 4 h-lim-p 0.0017 0.0133 13.3007 3150.452950 5 0.0016 74 | 1/8 5 h-lim-p 0.0007 0.0084 29.1793 3150.373992 5 0.0007 98 | 1/8 6 h-lim-p 0.0075 0.0923 2.7867 3150.367897 4 0.0015 120 | 1/8 7 h-lim-p 0.0067 4.1827 0.6404 3150.345182 0 0.0266 134 | 1/8 8 h-lim-p 0.1473 3.8982 0.1157 3149.915926 0 0.2947 154 | 0/8 9 h-lim-p 0.0248 1.2441 1.3760 3149.914560 2 0.0015 180 | 0/8 10 h-lim-p 0.1828 3.6078 0.0109 3149.870917 0 1.0968 194 | 0/8 11 h-lim-p 2.5000 20.0000 0.0018 3149.870040 3 1.0449 220 | 0/8 12 h-lim-p 2.5000 20.0000 0.0001 3149.870038 0 1.0938 240 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 3149.870038 0 1.0938 260 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 3149.870038 0 1.0938 280 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 3149.870038 0 2.5000 300 | 0/8 16 h-lim-p 1.7196 20.0000 0.0000 3149.870038 0 1.7196 320 | 0/8 17 h-lim-p 0.0270 20.0000 0.0000 3149.870038 0 0.0135 340 | 0/8 18 h-lim-p 0.0032 20.0000 0.0000 3149.870038 0 0.0000 381 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -3149.870038 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3149.870038 Node 7: lnL = -3149.870038 Node 8: lnL = -3149.870038 Node 9: lnL = -3149.870038 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 867 Sequential format.. Reading seq # 1: YDL019C_Sbay Reading seq # 2: YDL019C_Scer Reading seq # 3: YDL019C_Skud Reading seq # 4: YDL019C_Smik Reading seq # 5: YDL019C_Spar Sequences read.. Counting patterns.. # site patterns = 286 Counting frequencies.. 120 bytes for distance 45760 bytes for lkl0 36608 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.355200 0.178583 0.181938 0.123298 0.107620 0.171359 0.180188 0.000060 lnL0 = -3980.691967 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3980.691967 x= 0.35520 0.17858 0.18194 0.12330 0.10762 0.17136 0.18019 0.00006 1 h-lim-p 0.0000 0.0000 290.4048 3980.614786 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0018 139.2705 3976.840383 0 0.0005 39 | 1/8 3 h-lim-p 0.0004 0.0031 72.1699 3976.110231 3 0.0004 57 | 1/8 4 h-lim-p 0.0011 0.0241 23.3698 3975.988003 4 0.0005 76 | 1/8 5 h-lim-p 0.0011 0.0264 9.8319 3975.948915 6 0.0006 103 | 1/8 6 h-lim-p 0.0023 0.1408 2.6860 3975.705385 0 0.0093 117 | 1/8 7 h-lim-p 0.0044 0.0650 5.7502 3972.977745 0 0.0087 130 | 1/8 8 h-lim-p 0.0007 0.0058 34.5873 3960.532614 0 0.0029 144 | 1/8 9 h-lim-p 1.7278 13.8225 0.0314 3959.657830 5 0.7454 165 | 1/8 10 h-lim-p 2.5000 20.0000 0.0086 3959.572392 5 1.0867 193 | 1/8 11 h-lim-p 2.5000 20.0000 0.0028 3959.567403 4 0.6117 223 | 1/8 12 h-lim-p 2.5000 20.0000 0.0007 3959.567185 1 0.6250 245 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 3959.567183 0 1.0938 264 | 0/8 14 h-lim-p 0.0107 20.0000 0.0049 3959.567183 0 0.0023 284 | 0/8 15 h-lim-p 0.1204 0.9634 0.0000 3959.567183 m 0.9634 304 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 3959.567183 0 1.0938 324 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 3959.567183 0 1.0938 343 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 3959.567183 0 0.1562 365 | 1/8 19 h-lim-p 0.2524 20.0000 0.0000 3959.567183 0 0.0000 411 Out... lnL = -3959.567183 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3959.567183 Node 7: lnL = -3959.567183 Node 8: lnL = -3959.567183 Node 9: lnL = -3959.567183 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 855 Sequential format.. Reading seq # 1: YDL020C_Sbay Reading seq # 2: YDL020C_Scer Reading seq # 3: YDL020C_Skud Reading seq # 4: YDL020C_Smik Reading seq # 5: YDL020C_Spar Sequences read.. Counting patterns.. # site patterns = 330 Counting frequencies.. 120 bytes for distance 52800 bytes for lkl0 42240 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.355497 0.026007 0.080267 0.113283 0.101439 0.311067 0.249728 0.000060 lnL0 = -4038.808447 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4038.808447 x= 0.35550 0.02601 0.08027 0.11328 0.10144 0.31107 0.24973 0.00006 1 h-lim-p 0.0000 0.0000 131.9283 4038.213560 m 0.0000 22 | 1/8 2 h-lim-p 0.0001 0.0160 76.1938 4037.622148 0 0.0002 36 | 1/8 3 h-lim-p 0.0010 0.0079 18.0699 4037.581066 5 0.0003 59 | 1/8 4 h-lim-p 0.0010 0.0681 4.6696 4037.576679 5 0.0003 85 | 1/8 5 h-lim-p 0.0006 0.1753 2.2674 4037.560468 0 0.0026 99 | 1/8 6 h-lim-p 0.0061 0.0747 0.9614 4037.058001 0 0.0244 113 | 1/8 7 h-lim-p 0.0010 0.0079 13.1050 4035.220996 0 0.0030 133 | 1/8 8 h-lim-p 0.0005 0.0042 49.8042 4033.635562 0 0.0011 146 | 1/8 9 h-lim-p 2.5000 20.0000 0.0130 4033.426453 4 0.9802 166 | 0/8 10 h-lim-p 0.0982 2.9620 0.1301 4033.426431 2 0.0016 194 | 0/8 11 h-lim-p 0.0474 0.5357 0.0044 4033.421470 m 0.5357 215 | 1/8 12 h-lim-p 2.5000 20.0000 0.0008 4033.421157 2 0.9644 239 | 1/8 13 h-lim-p 2.5000 20.0000 0.0001 4033.421154 1 0.6152 261 | 1/8 14 h-lim-p 1.7410 20.0000 0.0000 4033.421154 0 0.7617 280 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 4033.421154 0 1.0938 299 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 4033.421154 0 0.5469 319 | 1/8 17 h-lim-p 1.1455 20.0000 0.0000 4033.421154 0 0.0716 341 | 1/8 18 h-lim-p 0.0784 20.0000 0.0000 4033.421154 0 0.0012 365 Out... lnL = -4033.421154 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4033.421154 Node 7: lnL = -4033.421154 Node 8: lnL = -4033.421154 Node 9: lnL = -4033.421154 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 451 Sequential format.. Reading seq # 1: YDL028C_Sbay Reading seq # 2: YDL028C_Scer Reading seq # 3: YDL028C_Skud Reading seq # 4: YDL028C_Smik Reading seq # 5: YDL028C_Spar Sequences read.. Counting patterns.. # site patterns = 108 Counting frequencies.. 120 bytes for distance 17280 bytes for lkl0 13824 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 1.099691 0.742604 0.576248 0.259501 0.330978 1.829563 0.442833 0.000060 lnL0 = -1923.183252 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1923.183252 x= 1.09969 0.74260 0.57625 0.25950 0.33098 1.82956 0.44283 0.00006 1 h-lim-p 0.0000 0.0000 333.9257 1923.062721 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0000 417815.5061 1827.747058 0 0.0000 36 | 1/8 3 h-lim-p 0.0017 0.0134 33.6510 1810.718760 m 0.0134 48 | 1/8 4 h-lim-p 0.0000 0.0000 823.9455 h-lim-p: 1.70532843e-21 1.36426275e-20 8.23945477e+02 1810.718760 .. | 1/8 5 h-lim-p 0.0000 0.0007 222.4742 1777.591573 m 0.0007 72 | 2/8 6 h-lim-p 0.0000 0.0004 1485.1410 1688.852508 m 0.0004 84 | 3/8 7 h-lim-p 0.0001 0.0005 969.7199 1655.129179 0 0.0004 98 | 3/8 8 h-lim-p 0.0012 0.0097 29.4591 1653.344469 0 0.0024 111 | 2/8 9 h-lim-p 0.0000 0.0003 1270.2365 1621.817160 0 0.0001 124 | 2/8 10 h-lim-p 0.0423 0.3386 0.3844 1610.324673 m 0.3386 136 | 1/8 11 h-lim-p 0.0000 0.0000 4298.7288 h-lim-p: 1.93680020e-23 1.54944016e-22 4.29872880e+03 1610.324673 .. | 1/8 12 h-lim-p 0.0000 0.0789 1265.0978 1593.362109 0 0.0000 164 | 1/8 13 h-lim-p 0.0000 0.0000 106.1974 1592.884237 m 0.0000 176 | 2/8 14 h-lim-p 0.0002 0.0098 21.9993 1592.748385 0 0.0006 189 | 2/8 15 h-lim-p 0.0082 0.1826 1.5802 1592.724745 2 0.0039 205 | 1/8 16 h-lim-p 0.0003 0.0284 21.8879 1592.465062 0 0.0011 219 | 1/8 17 h-lim-p 0.0008 0.0118 29.9531 1590.452601 0 0.0092 234 | 1/8 18 h-lim-p 0.0580 0.4641 0.6991 1590.429660 6 0.0108 260 | 1/8 19 h-lim-p 0.2656 9.0967 0.0284 1590.261335 0 0.7968 280 | 0/8 20 h-lim-p 0.0118 0.2435 1.9108 1590.260408 2 0.0007 306 | 0/8 21 h-lim-p 0.3722 20.0000 0.0036 1590.256218 0 1.1165 319 | 0/8 22 h-lim-p 2.5000 20.0000 0.0005 1590.256063 3 1.0449 345 | 0/8 23 h-lim-p 2.5000 20.0000 0.0001 1590.256062 0 1.2500 365 | 0/8 24 h-lim-p 2.5000 20.0000 0.0000 1590.256062 0 1.0938 385 | 0/8 25 h-lim-p 2.5000 20.0000 0.0000 1590.256062 0 0.6250 406 | 0/8 26 h-lim-p 1.8458 20.0000 0.0000 1590.256062 0 0.0288 431 Out... lnL = -1590.256062 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1590.256062 Node 7: lnL = -1590.256062 Node 8: lnL = -1590.256062 Node 9: lnL = -1590.256062 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 349 Sequential format.. Reading seq # 1: YDL030W_Sbay Reading seq # 2: YDL030W_Scer Reading seq # 3: YDL030W_Skud Reading seq # 4: YDL030W_Smik Reading seq # 5: YDL030W_Spar Sequences read.. Counting patterns.. # site patterns = 168 Counting frequencies.. 120 bytes for distance 26880 bytes for lkl0 21504 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.352565 0.204327 0.157295 0.118185 0.121957 0.140544 0.184075 0.000060 lnL0 = -1614.360124 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1614.360124 x= 0.35257 0.20433 0.15729 0.11819 0.12196 0.14054 0.18408 0.00006 1 h-lim-p 0.0000 0.0000 83.9694 1614.341061 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0112 31.7572 1613.679410 0 0.0013 41 | 1/8 3 h-lim-p 0.0021 0.0167 17.6624 1613.562979 3 0.0009 59 | 1/8 4 h-lim-p 0.0020 0.0496 8.2957 1613.534899 3 0.0009 77 | 1/8 5 h-lim-p 0.0035 0.1225 2.1594 1613.498431 0 0.0053 89 | 1/8 6 h-lim-p 0.0028 0.1026 4.0972 1613.404434 0 0.0055 102 | 1/8 7 h-lim-p 0.0041 0.0448 5.5006 1612.631619 0 0.0082 115 | 1/8 8 h-lim-p 0.0030 0.0238 10.2998 1609.708954 0 0.0089 128 | 1/8 9 h-lim-p 2.1731 17.3844 0.0307 1609.507212 7 0.6454 157 | 0/8 10 h-lim-p 0.0171 0.6912 1.1568 1609.506102 3 0.0017 184 | 0/8 11 h-lim-p 0.4050 20.0000 0.0049 1609.501007 0 0.8101 197 | 0/8 12 h-lim-p 2.5000 20.0000 0.0010 1609.500425 3 1.0004 223 | 0/8 13 h-lim-p 2.5000 20.0000 0.0001 1609.500419 2 0.6580 248 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1609.500419 0 1.0938 268 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1609.500419 0 1.0938 288 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1609.500419 0 2.1875 308 | 0/8 17 h-lim-p 1.7622 20.0000 0.0000 1609.500419 0 0.7710 328 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1609.500419 0 0.2734 350 | 0/8 19 h-lim-p 0.1897 20.0000 0.0000 1609.500419 0 0.0356 372 | 0/8 20 h-lim-p 0.0204 20.0000 0.0000 1609.500419 0 0.0051 393 Out... lnL = -1609.500419 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1609.500419 Node 7: lnL = -1609.500419 Node 8: lnL = -1609.500419 Node 9: lnL = -1609.500419 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 332 Sequential format.. Reading seq # 1: YDL033C_Sbay Reading seq # 2: YDL033C_Scer Reading seq # 3: YDL033C_Skud Reading seq # 4: YDL033C_Smik Reading seq # 5: YDL033C_Spar Sequences read.. Counting patterns.. # site patterns = 147 Counting frequencies.. 120 bytes for distance 23520 bytes for lkl0 18816 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.299502 0.073708 0.144938 0.156842 0.064234 0.135106 0.141735 0.000060 lnL0 = -1394.790067 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1394.790067 x= 0.29950 0.07371 0.14494 0.15684 0.06423 0.13511 0.14174 0.00006 1 h-lim-p 0.0000 0.0000 69.6030 1394.724912 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0057 28.8585 1394.424518 0 0.0010 39 | 1/8 3 h-lim-p 0.0129 0.1035 1.7309 1394.421119 4 0.0013 61 | 1/8 4 h-lim-p 0.0021 0.4707 1.0588 1394.410830 0 0.0042 74 | 1/8 5 h-lim-p 0.0027 0.1936 1.6402 1394.285293 0 0.0108 88 | 0/8 6 h-lim-p 0.0018 0.0255 10.0852 1393.665943 0 0.0071 102 | 0/8 7 h-lim-p 0.0057 0.0459 6.4629 1393.600997 6 0.0019 128 | 0/8 8 h-lim-p 0.0008 0.0067 10.2191 1393.470427 0 0.0034 142 | 0/8 9 h-lim-p 0.0004 0.0036 10.5993 1393.447514 0 0.0009 155 | 0/8 10 h-lim-p 0.1102 0.8819 0.0317 1393.355920 m 0.8819 167 | 0/8 11 h-lim-p 2.5000 20.0000 0.0029 1393.352066 4 0.9932 195 | 0/8 12 h-lim-p 1.5916 20.0000 0.0018 1393.351819 3 0.7861 222 | 0/8 13 h-lim-p 2.5000 20.0000 0.0001 1393.351812 2 0.9644 246 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1393.351812 0 1.0938 266 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1393.351812 0 1.2500 286 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1393.351812 0 0.2734 308 | 0/8 17 h-lim-p 0.5166 20.0000 0.0000 1393.351812 0 0.0040 334 Out... lnL = -1393.351812 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1393.351812 Node 7: lnL = -1393.351812 Node 8: lnL = -1393.351812 Node 9: lnL = -1393.351812 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 359 Sequential format.. Reading seq # 1: YDL036C_Sbay Reading seq # 2: YDL036C_Scer Reading seq # 3: YDL036C_Skud Reading seq # 4: YDL036C_Smik Reading seq # 5: YDL036C_Spar Sequences read.. Counting patterns.. # site patterns = 153 Counting frequencies.. 120 bytes for distance 24480 bytes for lkl0 19584 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.404484 0.154811 0.140327 0.189774 0.130054 0.215099 0.140023 0.000060 lnL0 = -1519.885893 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1519.885893 x= 0.40448 0.15481 0.14033 0.18977 0.13005 0.21510 0.14002 0.00006 1 h-lim-p 0.0000 0.0000 62.9196 1519.835747 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0150 19.7986 1519.560266 0 0.0013 39 | 1/8 3 h-lim-p 0.0094 0.1523 2.7050 1519.549195 5 0.0020 63 | 1/8 4 h-lim-p 0.0045 0.1776 1.1886 1519.500611 0 0.0136 76 | 1/8 5 h-lim-p 0.0060 0.1140 2.6895 1519.264588 0 0.0120 89 | 1/8 6 h-lim-p 0.0076 0.0694 4.2566 1518.253911 0 0.0114 101 | 1/8 7 h-lim-p 0.0028 0.0225 15.1875 1517.933619 8 0.0021 132 | 1/8 8 h-lim-p 0.0051 0.0407 5.4765 1517.917673 5 0.0011 154 | 1/8 9 h-lim-p 0.5378 20.0000 0.0115 1517.895761 0 0.8067 166 | 0/8 10 h-lim-p 0.2669 20.0000 0.0347 1517.895756 2 0.0053 194 | 0/8 11 h-lim-p 0.0917 0.7337 0.0015 1517.895474 0 0.5503 216 | 0/8 12 h-lim-p 0.0518 0.4144 0.0002 1517.895469 m 0.4144 236 | 1/8 13 h-lim-p 0.7924 20.0000 0.0001 1517.895468 0 0.6933 256 | 1/8 14 h-lim-p 2.4404 20.0000 0.0000 1517.895467 0 1.0677 275 | 0/8 15 h-lim-p -0.0000 -0.0000 0.0019 h-lim-p: -1.53785299e-19 -1.23028239e-18 1.85792349e-03 1517.895467 .. | 1/8 16 h-lim-p 0.0000 15.6970 0.0094 1517.895467 0 0.0006 316 | 1/8 17 h-lim-p 0.0025 20.0000 0.0024 1517.895467 0 0.0011 335 | 1/8 18 h-lim-p 0.0019 20.0000 0.0014 1517.895467 0 0.0017 354 | 1/8 19 h-lim-p 0.0033 20.0000 0.0007 1517.895467 0 0.0014 373 | 1/8 20 h-lim-p 0.0069 20.0000 0.0001 1517.895467 0 0.0017 393 | 1/8 21 h-lim-p 0.0111 20.0000 0.0000 1517.895467 0 0.0097 412 | 1/8 22 h-lim-p 0.0307 20.0000 0.0000 1517.895467 0 0.1845 433 | 1/8 23 h-lim-p 0.0040 20.0000 0.0003 1517.895467 0 0.0017 452 | 1/8 24 h-lim-p 2.5000 20.0000 0.0000 1517.895467 0 0.6250 472 | 1/8 25 h-lim-p 1.6676 20.0000 0.0000 1517.895467 0 0.2084 493 | 1/8 26 h-lim-p 0.2633 20.0000 0.0000 1517.895467 0 0.0165 515 Out... lnL = -1517.895467 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1517.895467 Node 7: lnL = -1517.895467 Node 8: lnL = -1517.895467 Node 9: lnL = -1517.895467 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 802 Sequential format.. Reading seq # 1: YDL039C_Sbay Reading seq # 2: YDL039C_Scer Reading seq # 3: YDL039C_Skud Reading seq # 4: YDL039C_Smik Reading seq # 5: YDL039C_Spar Sequences read.. Counting patterns.. # site patterns = 156 Counting frequencies.. 120 bytes for distance 24960 bytes for lkl0 19968 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 1.143186 0.000060 0.683636 0.450111 0.277722 0.406155 0.290935 0.185828 lnL0 = -2705.093124 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2705.093124 x= 1.14319 0.00006 0.68364 0.45011 0.27772 0.40615 0.29094 0.18583 1 h-lim-p 0.0000 0.0000 36.1844 2705.077217 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0128 48.1106 2698.726456 0 0.0077 43 | 1/8 3 h-lim-p 0.0018 0.0146 31.9715 2697.327360 0 0.0073 57 | 1/8 4 h-lim-p 0.0269 0.2149 3.9103 2697.118252 6 0.0197 83 | 0/8 5 h-lim-p 0.0026 0.0451 29.9177 2695.906411 0 0.0051 96 | 0/8 6 h-lim-p 0.0178 0.1427 4.2791 2695.761155 2 0.0167 112 | 0/8 7 h-lim-p 0.1401 1.1728 0.5109 2695.628912 6 0.0927 137 | 0/8 8 h-lim-p 0.0239 0.2009 1.9794 2694.891196 0 0.0718 158 | 0/8 9 h-lim-p 0.2152 1.7214 0.0827 2694.595748 m 1.7214 170 | 0/8 10 h-lim-p -0.0000 -0.0000 0.0534 h-lim-p: -8.88624386e-18 -7.10899508e-17 5.34231354e-02 2694.595748 .. | 0/8 11 h-lim-p 0.0000 0.1776 4.7123 2694.553680 0 0.0051 215 | 0/8 12 h-lim-p 0.0003 0.0024 3.1918 2694.538574 m 0.0024 227 | 1/8 13 h-lim-p 0.0039 1.1700 1.6106 2694.520447 0 0.0233 241 | 1/8 14 h-lim-p 0.0465 0.4053 0.8092 2694.518957 2 0.0051 259 | 1/8 15 h-lim-p 0.0266 3.0303 0.1538 2694.518773 2 0.0131 283 | 1/8 16 h-lim-p 0.0534 11.9933 0.0377 2694.518515 2 0.0561 306 | 1/8 17 h-lim-p 0.0455 7.9586 0.0466 2694.515186 0 0.1819 327 | 1/8 18 h-lim-p 0.0531 4.9104 0.1595 2694.514830 2 0.0232 350 | 1/8 19 h-lim-p 1.4754 20.0000 0.0025 2694.514618 4 1.0062 379 | 1/8 20 h-lim-p 2.5000 20.0000 0.0001 2694.514618 0 1.0938 398 | 1/8 21 h-lim-p 2.5000 20.0000 0.0000 2694.514618 0 1.0938 417 | 1/8 22 h-lim-p 2.5000 20.0000 0.0000 2694.514618 0 2.1875 436 | 1/8 23 h-lim-p 2.5000 20.0000 0.0000 2694.514618 0 1.0938 455 | 1/8 24 h-lim-p 0.2749 20.0000 0.0000 2694.514618 0 0.2749 474 | 1/8 25 h-lim-p 0.0004 20.0000 0.0008 2694.514618 0 0.0004 493 | 1/8 26 h-lim-p 0.0034 20.0000 0.0001 2694.514618 0 0.0004 514 | 1/8 27 h-lim-p 0.0007 20.0000 0.0001 2694.514618 0 0.0000 537 | 1/8 28 h-lim-p 0.0026 20.0000 0.0000 2694.514618 0 0.0002 559 Out... lnL = -2694.514618 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2694.514618 Node 7: lnL = -2694.514618 Node 8: lnL = -2694.514618 Node 9: lnL = -2694.514618 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 600 Sequential format.. Reading seq # 1: YDL040C_Sbay Reading seq # 2: YDL040C_Scer Reading seq # 3: YDL040C_Skud Reading seq # 4: YDL040C_Smik Reading seq # 5: YDL040C_Spar Sequences read.. Counting patterns.. # site patterns = 240 Counting frequencies.. 120 bytes for distance 38400 bytes for lkl0 30720 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.395737 0.140444 0.228249 0.202915 0.139053 0.186289 0.219880 0.000060 lnL0 = -2824.341874 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2824.341874 x= 0.39574 0.14044 0.22825 0.20291 0.13905 0.18629 0.21988 0.00006 1 h-lim-p 0.0000 0.0000 206.3647 2824.276499 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0036 89.4166 2820.444271 0 0.0013 41 | 1/8 3 h-lim-p 0.0061 0.0486 8.8528 2820.348743 7 0.0018 72 | 1/8 4 h-lim-p 0.0078 0.1660 2.1019 2820.170030 1 0.0097 86 | 1/8 5 h-lim-p 0.0058 0.0577 3.4925 2816.205835 0 0.0233 100 | 1/8 6 h-lim-p 0.0012 0.0093 32.7158 2809.927522 0 0.0023 113 | 1/8 7 h-lim-p 0.0046 0.0367 6.6237 2809.915924 5 0.0005 136 | 1/8 8 h-lim-p 0.0065 0.6656 0.5222 2809.909349 4 0.0071 159 | 0/8 9 h-lim-p 0.0006 0.1987 6.0430 2809.876193 0 0.0018 179 | 0/8 10 h-lim-p 0.0122 0.0973 0.3780 2809.488447 0 0.0730 193 | 0/8 11 h-lim-p 0.4106 3.2850 0.0053 2809.469701 0 0.8213 214 | 0/8 12 h-lim-p 1.8648 14.9182 0.0010 2809.469296 4 0.6839 244 | 0/8 13 h-lim-p 2.5000 20.0000 0.0002 2809.469283 2 0.6580 269 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 2809.469283 0 1.0938 289 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2809.469283 0 1.0938 309 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 2809.469283 0 2.1875 329 | 0/8 17 h-lim-p 1.7637 20.0000 0.0000 2809.469283 0 0.7716 349 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 2809.469283 0 0.0000 385 Out... lnL = -2809.469283 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2809.469283 Node 7: lnL = -2809.469283 Node 8: lnL = -2809.469283 Node 9: lnL = -2809.469283 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 459 Sequential format.. Reading seq # 1: YDL042C_Sbay Reading seq # 2: YDL042C_Scer Reading seq # 3: YDL042C_Skud Reading seq # 4: YDL042C_Smik Reading seq # 5: YDL042C_Spar Sequences read.. Counting patterns.. # site patterns = 140 Counting frequencies.. 120 bytes for distance 22400 bytes for lkl0 17920 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.228539 0.062475 0.076567 0.106936 0.065311 0.117390 0.146757 0.000060 lnL0 = -1781.235836 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1781.235836 x= 0.22854 0.06248 0.07657 0.10694 0.06531 0.11739 0.14676 0.00006 1 h-lim-p 0.0000 0.0000 130.0868 1781.136042 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0028 38.6527 1780.875915 0 0.0003 38 | 1/8 3 h-lim-p 0.0013 0.0365 9.4002 1780.850616 5 0.0006 59 | 1/8 4 h-lim-p 0.0019 0.0854 2.8747 1780.844655 4 0.0009 80 | 1/8 5 h-lim-p 0.0019 0.3338 1.4147 1780.832524 0 0.0028 92 | 1/8 6 h-lim-p 0.0021 0.0988 1.9025 1780.627944 0 0.0084 106 | 1/8 7 h-lim-p 0.0020 0.0163 6.3862 1778.927355 0 0.0041 119 | 1/8 8 h-lim-p 0.0018 0.0142 9.7127 1778.911857 6 0.0003 146 | 1/8 9 h-lim-p 0.3442 16.6117 0.0091 1778.843528 0 0.6884 159 | 0/8 10 h-lim-p 0.0105 3.1800 0.6014 1778.843379 4 0.0008 192 | 0/8 11 h-lim-p 0.1748 6.5417 0.0028 1778.838370 0 0.6993 214 | 0/8 12 h-lim-p 2.5000 20.0000 0.0004 1778.838257 2 0.9644 238 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1778.838257 0 1.0938 258 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1778.838257 0 1.0938 278 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1778.838257 0 0.2344 301 | 0/8 16 h-lim-p 0.2674 20.0000 0.0000 1778.838257 0 0.0000 345 Out... lnL = -1778.838257 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1778.838257 Node 7: lnL = -1778.838257 Node 8: lnL = -1778.838257 Node 9: lnL = -1778.838257 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 297 Sequential format.. Reading seq # 1: YDL043C_Sbay Reading seq # 2: YDL043C_Scer Reading seq # 3: YDL043C_Skud Reading seq # 4: YDL043C_Smik Reading seq # 5: YDL043C_Spar Sequences read.. Counting patterns.. # site patterns = 95 Counting frequencies.. 120 bytes for distance 15200 bytes for lkl0 12160 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 1.124792 0.335021 0.850034 0.491386 0.410074 2.209238 0.476258 0.000060 lnL0 = -1316.619991 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1316.619991 x= 1.12479 0.33502 0.85003 0.49139 0.41007 2.20924 0.47626 0.00006 1 h-lim-p 0.0000 0.0000 212.3431 1316.517593 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0326 45.4682 1252.268024 0 0.0270 45 | 1/8 3 h-lim-p 0.0002 0.0018 235.8301 1248.444263 0 0.0009 59 | 1/8 4 h-lim-p 0.0035 0.0282 9.5705 .. | 1/8 5 h-lim-p 0.0000 0.0031 127.4655 1245.873020 0 0.0003 110 | 1/8 6 h-lim-p 0.0003 0.0023 68.0308 1238.735287 m 0.0023 122 | 2/8 7 h-lim-p 0.0050 0.0719 21.7228 1160.233584 m 0.0719 135 | 1/8 8 h-lim-p -0.0000 -0.0000 844.3559 h-lim-p: -5.00601096e-21 -4.00480877e-20 8.44355932e+02 1160.233584 .. | 1/8 9 h-lim-p 0.0000 0.0022 187.6185 1152.349128 0 0.0006 161 | 1/8 10 h-lim-p 0.0001 0.0007 177.9514 1139.555500 m 0.0007 173 | 2/8 11 h-lim-p 0.0004 0.0029 209.3763 1115.848729 0 0.0022 187 | 2/8 12 h-lim-p 0.0003 0.0023 99.5206 1113.965586 0 0.0008 200 | 2/8 13 h-lim-p 0.0033 0.0267 15.0314 1113.547812 3 0.0030 218 | 1/8 14 h-lim-p 0.0015 0.0190 30.9832 1113.055243 6 0.0013 241 | 1/8 15 h-lim-p 0.0117 0.0936 1.8731 1111.041825 0 0.0351 254 | 1/8 16 h-lim-p 0.4018 3.2142 0.0377 1110.644685 0 1.2053 267 | 0/8 17 h-lim-p 0.2433 2.5320 0.1866 1110.644429 2 0.0066 294 | 0/8 18 h-lim-p 0.0462 0.5847 0.0268 1110.625802 3 0.3352 323 | 0/8 19 h-lim-p 0.8431 6.7450 0.0027 1110.623969 3 0.8448 349 | 0/8 20 h-lim-p 2.5000 20.0000 0.0001 1110.623968 0 1.0938 369 | 0/8 21 h-lim-p 2.5000 20.0000 0.0000 1110.623968 0 1.0938 389 | 0/8 22 h-lim-p 2.5000 20.0000 0.0000 1110.623968 0 1.2500 409 | 0/8 23 h-lim-p 2.5000 20.0000 0.0000 1110.623968 0 0.3125 431 | 0/8 24 h-lim-p 0.4570 20.0000 0.0000 1110.623968 0 0.0000 467 Out... lnL = -1110.623968 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1110.623968 Node 7: lnL = -1110.623968 Node 8: lnL = -1110.623968 Node 9: lnL = -1110.623968 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 377 Sequential format.. Reading seq # 1: YDL045C_Sbay Reading seq # 2: YDL045C_Scer Reading seq # 3: YDL045C_Skud Reading seq # 4: YDL045C_Smik Reading seq # 5: YDL045C_Spar Sequences read.. Counting patterns.. # site patterns = 178 Counting frequencies.. 120 bytes for distance 28480 bytes for lkl0 22784 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.343237 0.067465 0.069672 0.182186 0.146379 0.182690 0.233380 0.000060 lnL0 = -1738.655105 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1738.655105 x= 0.34324 0.06746 0.06967 0.18219 0.14638 0.18269 0.23338 0.00006 1 h-lim-p 0.0000 0.0000 108.5776 1738.601255 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0087 25.3777 1738.355197 0 0.0009 39 | 1/8 3 h-lim-p 0.0047 0.0733 4.9997 1738.329647 7 0.0016 69 | 1/8 4 h-lim-p 0.0028 0.1477 2.8632 1738.303897 5 0.0030 91 | 1/8 5 h-lim-p 0.0069 0.1535 1.2355 1738.092579 0 0.0138 104 | 1/8 6 h-lim-p 0.0032 0.0306 5.2632 1735.988663 0 0.0097 117 | 1/8 7 h-lim-p 0.0004 0.0030 22.6981 1735.672053 0 0.0007 130 | 1/8 8 h-lim-p 0.0023 0.0402 7.4536 1735.643359 2 0.0011 146 | 1/8 9 h-lim-p 0.4757 18.7236 0.0166 1735.564096 0 0.9514 159 | 1/8 10 h-lim-p 2.5000 20.0000 0.0036 1735.555576 4 0.9802 186 | 0/8 11 h-lim-p 0.5599 20.0000 0.0063 1735.555575 0 0.0038 211 | 0/8 12 h-lim-p 0.1179 0.9436 0.0001 1735.555569 0 0.7077 233 | 0/8 13 h-lim-p 0.0285 0.2277 0.0000 1735.555569 m 0.2277 253 | 1/8 14 h-lim-p 0.0002 20.0000 0.0274 1735.555569 0 0.0002 273 | 1/8 15 h-lim-p 0.6754 20.0000 0.0000 1735.555569 0 1.3509 293 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 1735.555569 0 1.0938 312 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 1735.555569 m20.0000 331 | 1/8 18 h-lim-p 0.7013 20.0000 0.0000 1735.555569 0 1.4025 351 | 1/8 19 h-lim-p 2.5000 20.0000 0.0000 1735.555569 0 1.0938 370 | 1/8 20 h-lim-p 2.5000 20.0000 0.0000 1735.555569 0 0.0024 398 Out... lnL = -1735.555569 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1735.555569 Node 7: lnL = -1735.555569 Node 8: lnL = -1735.555569 Node 9: lnL = -1735.555569 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 570 Sequential format.. Reading seq # 1: YDL045W-A_Sbay Reading seq # 2: YDL045W-A_Scer Reading seq # 3: YDL045W-A_Skud Reading seq # 4: YDL045W-A_Smik Reading seq # 5: YDL045W-A_Spar Sequences read.. Counting patterns.. # site patterns = 234 Counting frequencies.. 120 bytes for distance 37440 bytes for lkl0 29952 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.395754 0.080349 0.162251 0.190815 0.146393 0.214326 0.199862 0.000060 lnL0 = -2584.079096 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2584.079096 x= 0.39575 0.08035 0.16225 0.19081 0.14639 0.21433 0.19986 0.00006 1 h-lim-p 0.0000 0.0000 108.6641 2584.022119 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0043 50.2156 2583.177225 0 0.0007 40 | 1/8 3 h-lim-p 0.0028 0.0225 8.7725 2583.147245 4 0.0007 61 | 1/8 4 h-lim-p 0.0025 0.1458 2.5064 2583.129577 2 0.0023 77 | 1/8 5 h-lim-p 0.0038 0.2777 1.5501 2582.927622 0 0.0152 91 | 1/8 6 h-lim-p 0.0064 0.0661 3.6641 2581.091687 0 0.0129 104 | 0/8 7 h-lim-p 0.0008 0.0065 28.5197 2580.120297 0 0.0016 117 | 0/8 8 h-lim-p 0.0003 0.0027 10.7393 2580.059641 0 0.0013 131 | 0/8 9 h-lim-p 0.0003 0.0022 3.3080 2580.051584 0 0.0016 145 | 0/8 10 h-lim-p 0.0518 0.4140 0.0184 2579.921362 m 0.4140 157 | 1/8 11 h-lim-p 1.1018 20.0000 0.0067 2579.887449 2 1.0329 181 | 1/8 12 h-lim-p 2.5000 20.0000 0.0013 2579.886661 4 0.7683 211 | 1/8 13 h-lim-p 2.4770 20.0000 0.0004 2579.886617 3 0.8774 238 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 2579.886616 0 1.0938 257 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 2579.886616 0 1.0938 276 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 2579.886616 0 1.0938 295 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 2579.886616 0 2.1875 314 | 1/8 18 h-lim-p 1.8037 20.0000 0.0000 2579.886616 0 0.1127 336 | 1/8 19 h-lim-p 0.1270 20.0000 0.0000 2579.886616 0 0.0000 379 Out... lnL = -2579.886616 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2579.886616 Node 7: lnL = -2579.886616 Node 8: lnL = -2579.886616 Node 9: lnL = -2579.886616 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 590 Sequential format.. Reading seq # 1: YDL046W_Sbay Reading seq # 2: YDL046W_Scer Reading seq # 3: YDL046W_Skud Reading seq # 4: YDL046W_Smik Reading seq # 5: YDL046W_Spar Sequences read.. Counting patterns.. # site patterns = 209 Counting frequencies.. 120 bytes for distance 33440 bytes for lkl0 26752 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.286854 0.061471 0.112537 0.075340 0.053213 0.167372 0.191895 0.000060 lnL0 = -2441.974496 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2441.974496 x= 0.28685 0.06147 0.11254 0.07534 0.05321 0.16737 0.19190 0.00006 1 h-lim-p 0.0001 0.0008 126.1807 2440.660251 0 0.0002 23 | 0/8 2 h-lim-p 0.0005 0.0054 46.9253 2440.446457 5 0.0002 46 | 0/8 3 h-lim-p 0.0001 0.0010 17.8507 2440.409436 0 0.0003 59 | 0/8 4 h-lim-p 0.0001 0.0005 6.0750 2440.402969 0 0.0004 73 | 0/8 5 h-lim-p 0.0001 0.0009 1.6863 2440.402353 0 0.0004 87 | 0/8 6 h-lim-p 0.0002 0.0015 0.5772 2440.402044 m 0.0015 99 | 1/8 7 h-lim-p 0.0046 1.0653 0.1903 2440.401485 2 0.0040 123 | 1/8 8 h-lim-p 0.0014 0.6562 0.5435 2440.400773 0 0.0021 142 | 1/8 9 h-lim-p 0.0679 8.5822 0.0170 2440.358746 0 0.2714 163 | 0/8 10 h-lim-p 0.0436 20.0000 0.1057 2440.358738 0 0.0012 186 | 0/8 11 h-lim-p 0.1301 1.4188 0.0010 2440.357446 4 0.8404 219 | 0/8 12 h-lim-p 0.0774 0.6195 0.0001 2440.357446 m 0.6195 239 | 1/8 13 h-lim-p 0.0010 6.7309 0.0412 2440.357445 0 0.0009 259 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 2440.357445 0 1.0938 278 | 0/8 15 h-lim-p 0.0000 0.0000 0.0004 h-lim-p: 1.42256039e-18 1.13804831e-17 3.78940004e-04 2440.357445 .. | 1/8 16 h-lim-p 0.0000 20.0000 0.0079 2440.357445 0 0.0002 317 | 1/8 17 h-lim-p 0.0002 17.8384 0.0059 2440.357445 0 0.0002 336 | 1/8 18 h-lim-p 0.0008 20.0000 0.0017 2440.357445 0 0.0007 355 | 1/8 19 h-lim-p 0.0009 20.0000 0.0013 2440.357445 0 0.0004 374 | 1/8 20 h-lim-p 0.0009 20.0000 0.0005 2440.357445 0 0.0002 395 | 1/8 21 h-lim-p 0.0009 20.0000 0.0001 2440.357445 0 0.0009 414 | 1/8 22 h-lim-p 0.0117 20.0000 0.0000 2440.357445 0 0.0058 433 | 1/8 23 h-lim-p 0.0006 20.0000 0.0001 2440.357445 0 0.0011 453 | 1/8 24 h-lim-p 0.1277 20.0000 0.0000 2440.357445 0 0.0279 473 | 1/8 25 h-lim-p 0.0287 20.0000 0.0000 2440.357445 0 0.0009 496 Out... lnL = -2440.357445 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2440.357445 Node 7: lnL = -2440.357445 Node 8: lnL = -2440.357445 Node 9: lnL = -2440.357445 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 874 Sequential format.. Reading seq # 1: YDL047W_Sbay Reading seq # 2: YDL047W_Scer Reading seq # 3: YDL047W_Skud Reading seq # 4: YDL047W_Smik Reading seq # 5: YDL047W_Spar Sequences read.. Counting patterns.. # site patterns = 244 Counting frequencies.. 120 bytes for distance 39040 bytes for lkl0 31232 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.252128 0.051221 0.040893 0.071802 0.052277 0.138008 0.131784 0.013016 lnL0 = -3338.386277 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3338.386277 x= 0.25213 0.05122 0.04089 0.07180 0.05228 0.13801 0.13178 0.01302 1 h-lim-p 0.0040 0.0503 128.9309 3337.556336 3 0.0001 32 | 0/8 2 h-lim-p 0.0003 0.0037 40.2998 3337.415268 7 0.0002 60 | 0/8 3 h-lim-p 0.0004 0.0097 17.4584 3337.398332 6 0.0001 88 | 0/8 4 h-lim-p 0.0005 0.0321 4.6417 3337.396811 4 0.0002 111 | 0/8 5 h-lim-p 0.0011 0.2243 0.6714 3337.396769 2 0.0002 128 | 0/8 6 h-lim-p 0.0005 0.7529 0.2660 3337.396762 0 0.0002 148 | 0/8 7 h-lim-p 0.0077 4.3395 0.0077 3337.396762 0 0.0008 170 | 0/8 8 h-lim-p 0.0305 20.0000 0.0002 3337.396719 0 0.4874 194 | 0/8 9 h-lim-p 1.2834 20.0000 0.0001 3337.396719 0 1.1230 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3337.396719 0 2.1875 234 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3337.396719 0 1.0938 254 | 0/8 12 h-lim-p 0.2957 20.0000 0.0001 3337.396719 0 0.0020 280 | 0/8 13 h-lim-p 0.0002 20.0000 0.0010 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0012 | 0/8 15 h-lim-p 0.0000 20.0000 0.0012 Out... lnL = -3337.396719 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3337.396719 Node 7: lnL = -3337.396719 Node 8: lnL = -3337.396719 Node 9: lnL = -3337.396719 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 386 Sequential format.. Reading seq # 1: YDL051W_Sbay Reading seq # 2: YDL051W_Scer Reading seq # 3: YDL051W_Skud Reading seq # 4: YDL051W_Smik Reading seq # 5: YDL051W_Spar Sequences read.. Counting patterns.. # site patterns = 142 Counting frequencies.. 120 bytes for distance 22720 bytes for lkl0 18176 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.270394 0.038204 0.099310 0.096457 0.068936 0.163072 0.153414 0.000060 lnL0 = -1605.615560 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1605.615560 x= 0.27039 0.03820 0.09931 0.09646 0.06894 0.16307 0.15341 0.00006 1 h-lim-p 0.0002 0.0016 89.0850 1604.446327 0 0.0004 23 | 0/8 2 h-lim-p 0.0005 0.0042 35.1421 1604.195072 5 0.0005 44 | 0/8 3 h-lim-p 0.0011 0.0125 14.6252 1604.160342 7 0.0004 74 | 0/8 4 h-lim-p 0.0012 0.0692 4.6934 1604.156379 5 0.0004 98 | 0/8 5 h-lim-p 0.0031 0.4884 0.6162 1604.156145 4 0.0010 119 | 0/8 6 h-lim-p 0.0009 0.0069 0.5421 1604.155558 0 0.0035 141 | 0/8 7 h-lim-p 0.0000 0.0004 4.6459 1604.154622 m 0.0004 161 | 1/8 8 h-lim-p 0.0005 0.1387 2.3574 1604.154300 4 0.0003 182 | 1/8 9 h-lim-p 0.0470 7.0046 0.0171 1604.119590 0 0.3757 197 | 1/8 10 h-lim-p 0.5098 20.0000 0.0126 .. | 1/8 11 h-lim-p 0.0000 0.0194 6.5700 1604.111367 0 0.0003 269 | 1/8 12 h-lim-p 0.0004 0.0323 4.6818 1604.107902 2 0.0004 285 | 1/8 13 h-lim-p 0.0012 0.2293 1.6638 1604.107307 2 0.0005 301 | 1/8 14 h-lim-p 0.0012 0.3620 0.7200 1604.107161 4 0.0007 323 | 1/8 15 h-lim-p 0.0019 1.7945 0.2668 1604.107146 2 0.0005 347 | 1/8 16 h-lim-p 0.0037 3.5235 0.0360 1604.107145 0 0.0008 367 | 1/8 17 h-lim-p 0.0016 17.4320 0.0183 1604.107144 0 0.0024 386 | 1/8 18 h-lim-p 0.0137 20.0000 0.0032 1604.106839 0 0.1648 408 | 1/8 19 h-lim-p 2.5000 20.0000 0.0000 1604.106839 0 1.0938 427 | 1/8 20 h-lim-p 2.5000 20.0000 0.0000 1604.106839 0 1.0938 446 | 1/8 21 h-lim-p 2.5000 20.0000 0.0000 1604.106839 0 3.7500 465 | 1/8 22 h-lim-p 1.3637 20.0000 0.0000 1604.106839 0 0.3409 485 | 1/8 23 h-lim-p 0.5172 20.0000 0.0000 1604.106839 0 0.0001 515 Out... lnL = -1604.106839 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1604.106839 Node 7: lnL = -1604.106839 Node 8: lnL = -1604.106839 Node 9: lnL = -1604.106839 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 907 Sequential format.. Reading seq # 1: YDL055C_Sbay Reading seq # 2: YDL055C_Scer Reading seq # 3: YDL055C_Skud Reading seq # 4: YDL055C_Smik Reading seq # 5: YDL055C_Spar Sequences read.. Counting patterns.. # site patterns = 217 Counting frequencies.. 120 bytes for distance 34720 bytes for lkl0 27776 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.260263 0.028793 0.017569 0.057540 0.064896 0.128242 0.103531 0.042384 lnL0 = -3337.720661 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3337.720661 x= 0.26026 0.02879 0.01757 0.05754 0.06490 0.12824 0.10353 0.04238 1 h-lim-p 0.0002 0.0049 518.3890 3332.399623 4 0.0000 31 | 0/8 2 h-lim-p 0.0003 0.0028 78.7536 3331.854640 8 0.0002 62 | 0/8 3 h-lim-p 0.0003 0.0036 49.1826 3331.721777 4 0.0001 82 | 0/8 4 h-lim-p 0.0006 0.0076 11.4440 3331.714712 5 0.0001 105 | 0/8 5 h-lim-p 0.0004 0.0420 3.4921 3331.713423 5 0.0002 131 | 0/8 6 h-lim-p 0.0011 0.1341 0.7632 3331.713386 1 0.0001 147 | 0/8 7 h-lim-p 0.0017 3.4512 0.0601 3331.713386 0 0.0004 168 | 0/8 8 h-lim-p 0.1418 20.0000 0.0002 3331.713051 0 1.7019 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3331.713044 0 1.0938 211 | 0/8 10 h-lim-p 2.1501 20.0000 0.0000 3331.713044 0 0.9407 231 | 0/8 11 h-lim-p 0.9853 20.0000 0.0000 3331.713044 0 0.0000 265 | 0/8 12 h-lim-p 0.0001 20.0000 0.0000 3331.713044 0 0.0000 292 Out... lnL = -3331.713044 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3331.713044 Node 7: lnL = -3331.713044 Node 8: lnL = -3331.713044 Node 9: lnL = -3331.713044 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 475 Sequential format.. Reading seq # 1: YDL057W_Sbay Reading seq # 2: YDL057W_Scer Reading seq # 3: YDL057W_Skud Reading seq # 4: YDL057W_Smik Reading seq # 5: YDL057W_Spar Sequences read.. Counting patterns.. # site patterns = 183 Counting frequencies.. 120 bytes for distance 29280 bytes for lkl0 23424 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.086536 0.348168 0.122310 0.143780 0.120568 0.169359 0.279185 0.250441 lnL0 = -2038.247168 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2038.247168 x= 0.08654 0.34817 0.12231 0.14378 0.12057 0.16936 0.27918 0.25044 1 h-lim-p 0.0013 0.0107 32.3268 2037.333847 0 0.0027 23 | 0/8 2 h-lim-p 0.0011 0.0089 26.5698 2037.088675 3 0.0010 41 | 0/8 3 h-lim-p 0.0007 0.0057 33.5159 2036.461288 0 0.0028 55 | 0/8 4 h-lim-p 0.0003 0.0028 25.3260 2036.241772 0 0.0014 69 | 0/8 5 h-lim-p 0.0004 0.0035 15.3695 2036.103280 0 0.0026 83 | 0/8 6 h-lim-p 0.0074 0.1344 5.4458 2036.085294 3 0.0017 102 | 0/8 7 h-lim-p 0.0047 0.0372 0.9580 2036.082878 1 0.0058 116 | 0/8 8 h-lim-p 0.3361 20.0000 0.0166 2036.050819 0 1.3443 138 | 0/8 9 h-lim-p 2.5000 20.0000 0.0024 2036.047775 4 0.9802 166 | 0/8 10 h-lim-p 2.5000 20.0000 0.0003 2036.047760 1 0.9961 188 | 0/8 11 h-lim-p 2.5000 20.0000 0.0001 2036.047759 0 1.0938 208 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2036.047759 0 1.0938 228 | 0/8 13 h-lim-p 2.1347 20.0000 0.0000 2036.047759 0 0.9339 248 | 0/8 14 h-lim-p 0.5139 20.0000 0.0000 2036.047759 0 0.0642 270 | 0/8 15 h-lim-p 0.0098 20.0000 0.0001 2036.047759 0 0.0024 291 | 0/8 16 h-lim-p 0.0010 20.0000 0.0002 2036.047759 0 0.0001 314 | 0/8 17 h-lim-p 0.0001 20.0000 0.0001 2036.047759 0 0.0000 342 | 0/8 18 h-lim-p 0.0003 20.0000 0.0000 2036.047759 0 0.0000 376 Out... lnL = -2036.047759 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2036.047759 Node 7: lnL = -2036.047759 Node 8: lnL = -2036.047759 Node 9: lnL = -2036.047759 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 741 Sequential format.. Reading seq # 1: YDL059C_Sbay Reading seq # 2: YDL059C_Scer Reading seq # 3: YDL059C_Skud Reading seq # 4: YDL059C_Smik Reading seq # 5: YDL059C_Spar Sequences read.. Counting patterns.. # site patterns = 252 Counting frequencies.. 120 bytes for distance 40320 bytes for lkl0 32256 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.091808 0.091121 0.052581 0.113253 0.109754 0.233022 0.279818 0.208687 lnL0 = -3521.408602 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3521.408602 x= 0.09181 0.09112 0.05258 0.11325 0.10975 0.23302 0.27982 0.20869 1 h-lim-p 0.0007 0.0059 60.4510 3521.026188 7 0.0002 39 | 0/8 2 h-lim-p 0.0007 0.0093 18.7512 3520.969274 3 0.0003 57 | 0/8 3 h-lim-p 0.0006 0.0314 10.7831 3520.950462 6 0.0004 84 | 0/8 4 h-lim-p 0.0011 0.0400 3.9649 3520.948625 3 0.0003 104 | 0/8 5 h-lim-p 0.0016 0.2029 0.6729 3520.948530 3 0.0004 123 | 0/8 6 h-lim-p 0.0034 2.9653 0.0861 3520.948528 0 0.0004 145 | 0/8 7 h-lim-p 0.0033 20.0000 0.0099 3520.948528 0 0.0014 165 | 0/8 8 h-lim-p 0.0728 20.0000 0.0002 3520.948496 0 0.5823 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3520.948495 0 1.0938 208 | 0/8 10 h-lim-p 2.0431 20.0000 0.0000 3520.948495 0 0.8938 228 | 0/8 11 h-lim-p 0.6887 20.0000 0.0000 3520.948495 0 0.0108 253 | 0/8 12 h-lim-p 0.0021 20.0000 0.0001 3520.948495 0 0.0001 277 | 0/8 13 h-lim-p 0.0008 20.0000 0.0000 3520.948495 0 0.0000 306 Out... lnL = -3520.948495 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3520.948495 Node 7: lnL = -3520.948495 Node 8: lnL = -3520.948495 Node 9: lnL = -3520.948495 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 836 Sequential format.. Reading seq # 1: YDL060W_Sbay Reading seq # 2: YDL060W_Scer Reading seq # 3: YDL060W_Skud Reading seq # 4: YDL060W_Smik Reading seq # 5: YDL060W_Spar Sequences read.. Counting patterns.. # site patterns = 296 Counting frequencies.. 120 bytes for distance 47360 bytes for lkl0 37888 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.092383 0.039238 0.039512 0.152601 0.110540 0.220940 0.225141 0.196606 lnL0 = -3852.843151 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3852.843151 x= 0.09238 0.03924 0.03951 0.15260 0.11054 0.22094 0.22514 0.19661 1 h-lim-p 0.0012 0.5546 249.5530 3849.251637 3 0.0001 30 | 0/8 2 h-lim-p 0.0009 0.0076 25.0589 3849.122220 5 0.0004 52 | 0/8 3 h-lim-p 0.0009 0.0284 11.6991 3849.104636 6 0.0003 79 | 0/8 4 h-lim-p 0.0019 0.1209 1.8557 3849.104101 4 0.0003 102 | 0/8 5 h-lim-p 0.0021 0.7140 0.2828 3849.104087 2 0.0003 120 | 0/8 6 h-lim-p 0.0019 6.9618 0.0506 3849.104086 0 0.0008 140 | 0/8 7 h-lim-p 0.0066 20.0000 0.0064 3849.104079 0 0.0133 161 | 0/8 8 h-lim-p 0.0059 6.0643 0.0143 3849.103509 0 0.0356 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3849.103500 1 0.9961 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3849.103500 0 1.0938 225 | 0/8 11 h-lim-p 1.1155 20.0000 0.0000 3849.103500 0 1.6733 245 | 0/8 12 h-lim-p 0.0571 20.0000 0.0004 3849.103500 0 0.0071 267 | 0/8 13 h-lim-p 0.0020 20.0000 0.0014 3849.103500 0 0.0000 309 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 3849.103500 0 0.0000 333 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 3849.103500 0 0.0000 368 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -3849.103500 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3849.103500 Node 7: lnL = -3849.103500 Node 8: lnL = -3849.103500 Node 9: lnL = -3849.103500 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 838 Sequential format.. Reading seq # 1: YDL061C_Sbay Reading seq # 2: YDL061C_Scer Reading seq # 3: YDL061C_Skud Reading seq # 4: YDL061C_Smik Reading seq # 5: YDL061C_Spar Sequences read.. Counting patterns.. # site patterns = 325 Counting frequencies.. 120 bytes for distance 52000 bytes for lkl0 41600 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.069511 0.052548 0.096623 0.167168 0.091111 0.227140 0.197362 0.177178 lnL0 = -3780.158697 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3780.158697 x= 0.06951 0.05255 0.09662 0.16717 0.09111 0.22714 0.19736 0.17718 1 h-lim-p 0.0056 1.1529 116.0767 3778.720471 7 0.0002 41 | 0/8 2 h-lim-p 0.0005 0.0040 31.6206 3778.554587 5 0.0004 65 | 0/8 3 h-lim-p 0.0019 0.0313 5.9283 3778.546888 2 0.0004 82 | 0/8 4 h-lim-p 0.0016 0.1159 1.5870 3778.546442 2 0.0004 99 | 0/8 5 h-lim-p 0.0049 1.6721 0.1251 3778.546439 1 0.0003 116 | 0/8 6 h-lim-p 0.0007 5.3200 0.0516 3778.546439 0 0.0004 136 | 0/8 7 h-lim-p 0.0076 20.0000 0.0025 3778.546434 0 0.0303 158 | 0/8 8 h-lim-p 0.0041 20.0000 0.0185 3778.546279 0 0.0164 180 | 0/8 9 h-lim-p 0.6520 20.0000 0.0005 3778.546274 0 1.3040 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 3778.546274 0 1.0938 221 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3778.546274 0 1.0938 241 | 0/8 12 h-lim-p 0.2676 20.0000 0.0000 3778.546274 0 0.2676 261 | 0/8 13 h-lim-p 0.0055 20.0000 0.0010 3778.546274 0 0.0000 304 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -3778.546274 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3778.546274 Node 7: lnL = -3778.546274 Node 8: lnL = -3778.546274 Node 9: lnL = -3778.546274 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 533 Sequential format.. Reading seq # 1: YDL063C_Sbay Reading seq # 2: YDL063C_Scer Reading seq # 3: YDL063C_Skud Reading seq # 4: YDL063C_Smik Reading seq # 5: YDL063C_Spar Sequences read.. Counting patterns.. # site patterns = 155 Counting frequencies.. 120 bytes for distance 24800 bytes for lkl0 19840 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.095244 0.095787 0.000060 0.134109 0.090372 0.000060 0.095785 0.155698 lnL0 = -1873.426658 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1873.426658 x= 0.09524 0.09579 0.00006 0.13411 0.09037 0.00006 0.09579 0.15570 1 h-lim-p 0.0000 0.0000 212.2140 1872.694906 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0003 1403.2159 1868.642635 0 0.0000 36 | 1/8 3 h-lim-p 0.0003 0.0027 60.7030 1867.831908 0 0.0005 48 | 1/8 4 h-lim-p 0.0003 0.0028 52.3035 1867.533961 5 0.0003 71 | 1/8 5 h-lim-p 0.0045 0.0616 3.9848 1867.530261 3 0.0005 91 | 1/8 6 h-lim-p 0.0102 0.7718 0.1850 1867.530155 3 0.0016 112 | 1/8 7 h-lim-p 0.0123 3.3113 0.0247 1867.462983 0 0.3935 136 | 1/8 8 h-lim-p 2.5000 20.0000 0.0009 1867.462487 3 0.9482 161 | 1/8 9 h-lim-p 2.5000 20.0000 0.0001 1867.462453 0 3.7500 180 | 1/8 10 h-lim-p 1.6790 20.0000 0.0001 1867.461411 m20.0000 200 | 1/8 11 h-lim-p 0.0744 1.2092 0.0350 1867.448035 m 1.2092 221 | 1/8 12 h-lim-p 0.3120 2.4957 0.0655 .. | 1/8 13 h-lim-p 0.0000 17.8448 7.6152 1867.441157 0 0.0002 291 | 1/8 14 h-lim-p 0.0000 0.0003 1.7005 1867.440470 m 0.0003 303 | 2/8 15 h-lim-p 0.0022 0.7195 0.2379 1867.440457 0 0.0005 316 | 2/8 16 h-lim-p 0.0042 8.2889 0.0277 1867.440456 0 0.0009 335 | 2/8 17 h-lim-p 0.0035 20.0000 0.0073 1867.440454 0 0.0035 353 | 2/8 18 h-lim-p 0.0016 10.4890 0.0156 1867.440454 0 0.0014 371 | 2/8 19 h-lim-p 0.0241 20.0000 0.0009 1867.440370 0 0.3858 393 | 2/8 20 h-lim-p 2.5000 20.0000 0.0000 1867.440369 0 1.0938 411 | 2/8 21 h-lim-p 2.5000 20.0000 0.0000 1867.440369 0 1.0938 429 | 2/8 22 h-lim-p 1.1741 20.0000 0.0000 1867.440369 0 0.5870 447 | 2/8 23 h-lim-p 0.2276 20.0000 0.0000 1867.440369 0 0.0071 469 | 2/8 24 h-lim-p 0.0028 20.0000 0.0001 1867.440369 0 0.0000 495 | 2/8 25 h-lim-p 0.0007 20.0000 0.0000 1867.440369 0 0.0000 524 Out... lnL = -1867.440369 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1867.440369 Node 7: lnL = -1867.440369 Node 8: lnL = -1867.440369 Node 9: lnL = -1867.440369 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 231 Sequential format.. Reading seq # 1: YDL065C_Sbay Reading seq # 2: YDL065C_Scer Reading seq # 3: YDL065C_Skud Reading seq # 4: YDL065C_Smik Reading seq # 5: YDL065C_Spar Sequences read.. Counting patterns.. # site patterns = 97 Counting frequencies.. 120 bytes for distance 15520 bytes for lkl0 12416 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.052660 0.037701 0.102617 0.074501 0.042239 0.203535 0.132102 0.131763 lnL0 = -792.716757 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 792.716757 x= 0.05266 0.03770 0.10262 0.07450 0.04224 0.20353 0.13210 0.13176 1 h-lim-p 0.0008 0.0062 43.8139 792.362562 4 0.0004 31 | 0/8 2 h-lim-p 0.0007 0.0059 12.4009 792.326857 5 0.0005 55 | 0/8 3 h-lim-p 0.0021 0.0208 2.9427 792.319219 3 0.0019 73 | 0/8 4 h-lim-p 0.0019 0.0983 2.8949 792.316318 6 0.0012 103 | 0/8 5 h-lim-p 0.0042 0.2324 0.7873 792.315864 3 0.0017 121 | 0/8 6 h-lim-p 0.0013 0.2443 0.9967 792.315531 3 0.0014 147 | 0/8 7 h-lim-p 0.0470 10.5509 0.0293 792.315531 0 0.0013 171 | 0/8 8 h-lim-p 0.3609 20.0000 0.0001 792.315525 0 1.4435 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 792.315524 0 1.0938 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 792.315524 0 1.0938 233 | 0/8 11 h-lim-p 1.2454 20.0000 0.0000 792.315524 0 0.0000 276 Out... lnL = -792.315524 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -792.315524 Node 7: lnL = -792.315524 Node 8: lnL = -792.315524 Node 9: lnL = -792.315524 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 451 Sequential format.. Reading seq # 1: YDL066W_Sbay Reading seq # 2: YDL066W_Scer Reading seq # 3: YDL066W_Skud Reading seq # 4: YDL066W_Smik Reading seq # 5: YDL066W_Spar Sequences read.. Counting patterns.. # site patterns = 123 Counting frequencies.. 120 bytes for distance 19680 bytes for lkl0 15744 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.061227 0.042892 0.048262 0.077700 0.051867 0.117463 0.118206 0.125528 lnL0 = -1721.794519 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1721.794519 x= 0.06123 0.04289 0.04826 0.07770 0.05187 0.11746 0.11821 0.12553 1 h-lim-p 0.0005 0.0043 57.4150 1721.495584 6 0.0002 35 | 0/8 2 h-lim-p 0.0007 0.0107 16.1466 1721.460854 5 0.0003 59 | 0/8 3 h-lim-p 0.0014 0.0828 3.2341 1721.459699 4 0.0002 82 | 0/8 4 h-lim-p 0.0007 0.0946 1.0119 1721.459603 3 0.0002 102 | 0/8 5 h-lim-p 0.0006 0.4439 0.3410 1721.459592 2 0.0002 119 | 0/8 6 h-lim-p 0.0024 7.5248 0.0289 1721.459591 0 0.0003 141 | 0/8 7 h-lim-p 0.0030 20.0000 0.0026 1721.459591 0 0.0030 161 | 0/8 8 h-lim-p 0.0080 20.0000 0.0010 1721.459564 0 0.1284 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1721.459563 0 1.0938 205 | 0/8 10 h-lim-p 2.3025 20.0000 0.0000 1721.459563 0 2.0146 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1721.459563 0 0.6250 246 | 0/8 12 h-lim-p 0.1118 20.0000 0.0000 1721.459563 0 0.0122 268 | 0/8 13 h-lim-p 0.0055 20.0000 0.0000 1721.459563 0 0.0000 297 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 1721.459563 0 0.0000 324 Out... lnL = -1721.459563 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1721.459563 Node 7: lnL = -1721.459563 Node 8: lnL = -1721.459563 Node 9: lnL = -1721.459563 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 433 Sequential format.. Reading seq # 1: YDL069C_Sbay Reading seq # 2: YDL069C_Scer Reading seq # 3: YDL069C_Skud Reading seq # 4: YDL069C_Smik Reading seq # 5: YDL069C_Spar Sequences read.. Counting patterns.. # site patterns = 166 Counting frequencies.. 120 bytes for distance 26560 bytes for lkl0 21248 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.056588 0.068203 0.067279 0.140464 0.047474 0.143104 0.228495 0.146788 lnL0 = -1839.368571 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1839.368571 x= 0.05659 0.06820 0.06728 0.14046 0.04747 0.14310 0.22849 0.14679 1 h-lim-p 0.0065 0.1316 75.4597 1838.609137 5 0.0003 37 | 0/8 2 h-lim-p 0.0006 0.0052 12.5629 1838.589978 4 0.0002 57 | 0/8 3 h-lim-p 0.0005 0.0315 5.7485 1838.583400 3 0.0005 75 | 0/8 4 h-lim-p 0.0026 0.2363 1.0566 1838.583015 4 0.0007 97 | 0/8 5 h-lim-p 0.0018 0.7256 0.4331 1838.582972 3 0.0005 118 | 0/8 6 h-lim-p 0.0075 6.3429 0.0303 1838.582972 0 0.0008 140 | 0/8 7 h-lim-p 0.0127 20.0000 0.0019 1838.582971 0 0.0127 160 | 0/8 8 h-lim-p 0.0077 20.0000 0.0032 1838.582931 0 0.0617 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1838.582930 0 1.0938 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1838.582930 0 1.0938 223 | 0/8 11 h-lim-p 1.2017 20.0000 0.0000 1838.582930 0 3.6051 244 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1838.582930 0 0.3125 266 | 0/8 13 h-lim-p 0.0095 20.0000 0.0000 1838.582930 0 0.0048 286 | 0/8 14 h-lim-p 0.0015 20.0000 0.0001 1838.582930 0 0.0000 311 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 1838.582930 0 0.0001 331 | 0/8 16 h-lim-p 0.0018 20.0000 0.0000 1838.582930 0 0.0000 359 Out... lnL = -1838.582930 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1838.582930 Node 7: lnL = -1838.582930 Node 8: lnL = -1838.582930 Node 9: lnL = -1838.582930 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 610 Sequential format.. Reading seq # 1: YDL070W_Sbay Reading seq # 2: YDL070W_Scer Reading seq # 3: YDL070W_Skud Reading seq # 4: YDL070W_Smik Reading seq # 5: YDL070W_Spar Sequences read.. Counting patterns.. # site patterns = 218 Counting frequencies.. 120 bytes for distance 34880 bytes for lkl0 27904 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.060085 0.093722 0.067778 0.099060 0.068080 0.106649 0.159641 0.142039 lnL0 = -2471.798758 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2471.798758 x= 0.06009 0.09372 0.06778 0.09906 0.06808 0.10665 0.15964 0.14204 1 h-lim-p 0.0013 0.0102 129.7810 2469.598648 5 0.0003 32 | 0/8 2 h-lim-p 0.0003 0.0025 39.0281 2469.327929 1 0.0004 46 | 0/8 3 h-lim-p 0.0017 0.0268 9.0194 2469.321127 4 0.0002 70 | 0/8 4 h-lim-p 0.0008 0.0905 1.9011 2469.320630 4 0.0003 93 | 0/8 5 h-lim-p 0.0011 0.4091 0.5078 2469.320570 2 0.0005 109 | 0/8 6 h-lim-p 0.0029 2.1296 0.0880 2469.320567 1 0.0006 132 | 0/8 7 h-lim-p 0.0021 6.9355 0.0243 2469.320549 0 0.0063 153 | 0/8 8 h-lim-p 0.0083 20.0000 0.0183 2469.318252 0 0.0667 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 2469.318182 2 0.9961 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2469.318182 0 1.0938 220 | 0/8 11 h-lim-p 1.2912 20.0000 0.0000 2469.318182 0 0.5649 240 | 0/8 12 h-lim-p 0.1253 20.0000 0.0001 2469.318182 0 0.0039 264 | 0/8 13 h-lim-p 0.0013 20.0000 0.0002 2469.318182 0 0.0002 286 | 0/8 14 h-lim-p 0.0001 20.0000 0.0003 2469.318182 0 0.0000 311 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 2469.318182 0 0.0000 347 Out... lnL = -2469.318182 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2469.318182 Node 7: lnL = -2469.318182 Node 8: lnL = -2469.318182 Node 9: lnL = -2469.318182 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 486 Sequential format.. Reading seq # 1: YDL074C_Sbay Reading seq # 2: YDL074C_Scer Reading seq # 3: YDL074C_Skud Reading seq # 4: YDL074C_Smik Reading seq # 5: YDL074C_Spar Sequences read.. Counting patterns.. # site patterns = 162 Counting frequencies.. 120 bytes for distance 25920 bytes for lkl0 20736 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.079132 0.018762 0.051490 0.085080 0.071109 0.166740 0.172118 0.157258 lnL0 = -2022.441582 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2022.441582 x= 0.07913 0.01876 0.05149 0.08508 0.07111 0.16674 0.17212 0.15726 1 h-lim-p 0.0012 0.6324 183.4210 2020.412389 3 0.0001 30 | 0/8 2 h-lim-p 0.0008 0.0066 14.6643 2020.380740 5 0.0003 53 | 0/8 3 h-lim-p 0.0008 0.0401 5.2364 2020.376320 2 0.0004 69 | 0/8 4 h-lim-p 0.0008 0.0683 2.2642 2020.375714 4 0.0003 92 | 0/8 5 h-lim-p 0.0029 1.0078 0.2167 2020.375702 2 0.0005 110 | 0/8 6 h-lim-p 0.0017 1.9355 0.0604 2020.375702 0 0.0004 131 | 0/8 7 h-lim-p 0.0018 10.9032 0.0125 2020.375702 0 0.0008 151 | 0/8 8 h-lim-p 0.1104 20.0000 0.0001 2020.375677 0 1.3251 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2020.375677 0 1.0938 194 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2020.375677 0 2.1875 214 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2020.375677 0 1.0938 234 | 0/8 12 h-lim-p 0.2049 20.0000 0.0000 2020.375677 0 6.5559 259 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2020.375677 0 0.2734 281 | 0/8 14 h-lim-p 0.0913 20.0000 0.0000 2020.375677 0 0.0228 302 | 0/8 15 h-lim-p 0.0067 20.0000 0.0001 2020.375677 0 0.0000 330 | 0/8 16 h-lim-p 0.0011 20.0000 0.0000 2020.375677 0 0.0000 366 Out... lnL = -2020.375677 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2020.375677 Node 7: lnL = -2020.375677 Node 8: lnL = -2020.375677 Node 9: lnL = -2020.375677 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 698 Sequential format.. Reading seq # 1: YDL076C_Sbay Reading seq # 2: YDL076C_Scer Reading seq # 3: YDL076C_Skud Reading seq # 4: YDL076C_Smik Reading seq # 5: YDL076C_Spar Sequences read.. Counting patterns.. # site patterns = 289 Counting frequencies.. 120 bytes for distance 46240 bytes for lkl0 36992 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.108354 0.056793 0.089951 0.136960 0.097347 0.250187 0.235746 0.227504 lnL0 = -3290.707480 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3290.707480 x= 0.10835 0.05679 0.08995 0.13696 0.09735 0.25019 0.23575 0.22750 1 h-lim-p 0.0071 0.0569 81.1182 3289.849193 8 0.0003 46 | 0/8 2 h-lim-p 0.0006 0.0048 19.1784 3289.794126 4 0.0003 67 | 0/8 3 h-lim-p 0.0013 0.0276 4.5651 3289.791081 2 0.0003 84 | 0/8 4 h-lim-p 0.0009 0.2229 1.5427 3289.790569 3 0.0005 103 | 0/8 5 h-lim-p 0.0031 0.9911 0.2374 3289.790554 2 0.0006 120 | 0/8 6 h-lim-p 0.0031 5.9990 0.0463 3289.790553 0 0.0007 141 | 0/8 7 h-lim-p 0.0030 20.0000 0.0103 3289.790553 0 0.0015 161 | 0/8 8 h-lim-p 0.0349 20.0000 0.0004 3289.790492 0 0.5581 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3289.790491 0 1.0938 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3289.790491 0 1.0938 225 | 0/8 11 h-lim-p 0.9294 20.0000 0.0000 3289.790491 0 0.0436 249 | 0/8 12 h-lim-p 0.0118 20.0000 0.0000 3289.790491 0 0.0000 294 | 0/8 13 h-lim-p 0.0000 20.0000 0.0006 | 0/8 14 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -3289.790491 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3289.790491 Node 7: lnL = -3289.790491 Node 8: lnL = -3289.790491 Node 9: lnL = -3289.790491 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 592 Sequential format.. Reading seq # 1: YDL077C_Sbay Reading seq # 2: YDL077C_Scer Reading seq # 3: YDL077C_Skud Reading seq # 4: YDL077C_Smik Reading seq # 5: YDL077C_Spar Sequences read.. Counting patterns.. # site patterns = 213 Counting frequencies.. 120 bytes for distance 34080 bytes for lkl0 27264 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.078123 0.096623 0.101348 0.135051 0.094546 0.179424 0.208313 0.188363 lnL0 = -2663.951303 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2663.951303 x= 0.07812 0.09662 0.10135 0.13505 0.09455 0.17942 0.20831 0.18836 1 h-lim-p 0.0013 0.0100 51.9827 2663.423502 8 0.0004 42 | 0/8 2 h-lim-p 0.0015 0.0139 14.0987 2663.378017 5 0.0005 66 | 0/8 3 h-lim-p 0.0031 0.1400 2.2056 2663.376547 3 0.0006 85 | 0/8 4 h-lim-p 0.0026 0.2406 0.5359 2663.376501 3 0.0003 105 | 0/8 5 h-lim-p 0.0008 1.4916 0.2266 2663.376492 0 0.0004 125 | 0/8 6 h-lim-p 0.0017 3.2884 0.0534 2663.376492 0 0.0008 145 | 0/8 7 h-lim-p 0.9014 20.0000 0.0000 2663.376489 0 0.9014 165 | 0/8 8 h-lim-p 0.0098 20.0000 0.0041 2663.376489 0 0.0005 188 | 0/8 9 h-lim-p 0.1372 20.0000 0.0000 2663.376489 0 1.0978 211 | 0/8 10 h-lim-p 1.5558 20.0000 0.0000 2663.376489 0 1.3613 231 | 0/8 11 h-lim-p 1.4052 20.0000 0.0000 2663.376489 0 0.3074 252 | 0/8 12 h-lim-p 0.0563 20.0000 0.0001 2663.376489 0 0.0281 272 | 0/8 13 h-lim-p 0.0101 20.0000 0.0002 2663.376489 0 0.0003 296 | 0/8 14 h-lim-p 0.0003 20.0000 0.0002 2663.376489 0 0.0003 316 | 0/8 15 h-lim-p 0.0000 20.0000 0.0015 2663.376489 0 0.0000 350 | 0/8 16 h-lim-p 0.0000 20.0000 0.0005 | 0/8 17 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -2663.376489 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2663.376489 Node 7: lnL = -2663.376489 Node 8: lnL = -2663.376489 Node 9: lnL = -2663.376489 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 643 Sequential format.. Reading seq # 1: YDL078C_Sbay Reading seq # 2: YDL078C_Scer Reading seq # 3: YDL078C_Skud Reading seq # 4: YDL078C_Smik Reading seq # 5: YDL078C_Spar Sequences read.. Counting patterns.. # site patterns = 288 Counting frequencies.. 120 bytes for distance 46080 bytes for lkl0 36864 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.150713 0.106367 0.058439 0.134822 0.127887 0.260223 0.301888 0.281043 lnL0 = -3149.738027 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3149.738027 x= 0.15071 0.10637 0.05844 0.13482 0.12789 0.26022 0.30189 0.28104 1 h-lim-p 0.0077 1.6815 90.5469 3148.417913 8 0.0003 41 | 0/8 2 h-lim-p 0.0013 0.0111 23.6510 3148.276226 3 0.0005 59 | 0/8 3 h-lim-p 0.0014 0.0211 9.2483 3148.255753 5 0.0006 82 | 0/8 4 h-lim-p 0.0011 0.0766 4.5127 3148.246313 3 0.0012 100 | 0/8 5 h-lim-p 0.0055 0.2748 0.9467 3148.246057 2 0.0006 118 | 0/8 6 h-lim-p 0.0034 1.1467 0.1688 3148.246043 2 0.0011 144 | 0/8 7 h-lim-p 0.0227 20.0000 0.0084 3148.246041 0 0.0099 164 | 0/8 8 h-lim-p 0.0277 20.0000 0.0030 3148.245780 0 0.1661 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3148.245775 0 1.0938 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3148.245775 0 1.0938 226 | 0/8 11 h-lim-p 1.6820 20.0000 0.0000 3148.245775 0 1.6820 246 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3148.245775 0 0.0024 275 Out... lnL = -3148.245775 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3148.245775 Node 7: lnL = -3148.245775 Node 8: lnL = -3148.245775 Node 9: lnL = -3148.245775 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 648 Sequential format.. Reading seq # 1: YDL079C_Sbay Reading seq # 2: YDL079C_Scer Reading seq # 3: YDL079C_Skud Reading seq # 4: YDL079C_Smik Reading seq # 5: YDL079C_Spar Sequences read.. Counting patterns.. # site patterns = 247 Counting frequencies.. 120 bytes for distance 39520 bytes for lkl0 31616 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.026403 1.031336 0.049155 0.052870 0.129084 0.215944 0.152299 0.237419 lnL0 = -3111.698894 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3111.698894 x= 0.02640 1.03134 0.04916 0.05287 0.12908 0.21594 0.15230 0.23742 1 h-lim-p 0.0002 0.0016 236.3017 3107.220850 2 0.0002 26 | 0/8 2 h-lim-p 0.0002 0.0013 91.3431 3106.319126 0 0.0003 39 | 0/8 3 h-lim-p 0.0010 0.0076 7.7680 3106.236187 0 0.0029 52 | 0/8 4 h-lim-p 0.0006 0.0050 19.3250 3106.208465 5 0.0005 76 | 0/8 5 h-lim-p 0.0143 0.1657 0.6145 3106.206481 2 0.0067 92 | 0/8 6 h-lim-p 0.0009 0.0391 4.4950 3106.204978 3 0.0007 118 | 0/8 7 h-lim-p 0.0054 0.4709 0.6092 3106.201254 0 0.0108 131 | 0/8 8 h-lim-p 0.1548 6.8484 0.0425 3106.122798 0 0.2322 151 | 0/8 9 h-lim-p 2.5000 20.0000 0.0011 3106.122073 4 1.3578 180 | 0/8 10 h-lim-p 2.5000 20.0000 0.0004 3106.122062 1 1.0938 202 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3106.122062 0 1.0938 222 | 0/8 12 h-lim-p 1.8365 20.0000 0.0000 3106.122062 0 1.6069 242 | 0/8 13 h-lim-p 0.8492 20.0000 0.0000 3106.122062 0 0.0000 277 | 0/8 14 h-lim-p 0.0005 20.0000 0.0000 3106.122062 0 0.0000 310 Out... lnL = -3106.122062 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3106.122062 Node 7: lnL = -3106.122062 Node 8: lnL = -3106.122062 Node 9: lnL = -3106.122062 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 499 Sequential format.. Reading seq # 1: YDL080C_Sbay Reading seq # 2: YDL080C_Scer Reading seq # 3: YDL080C_Skud Reading seq # 4: YDL080C_Smik Reading seq # 5: YDL080C_Spar Sequences read.. Counting patterns.. # site patterns = 138 Counting frequencies.. 120 bytes for distance 22080 bytes for lkl0 17664 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.058446 0.036231 0.039517 0.070496 0.049761 0.084530 0.119570 0.111099 lnL0 = -1797.083209 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1797.083209 x= 0.05845 0.03623 0.03952 0.07050 0.04976 0.08453 0.11957 0.11110 1 h-lim-p 0.0018 0.0460 140.6485 1795.989960 5 0.0001 35 | 0/8 2 h-lim-p 0.0013 0.0136 12.9052 1795.968799 4 0.0003 56 | 0/8 3 h-lim-p 0.0007 0.0361 4.6611 1795.966943 5 0.0002 79 | 0/8 4 h-lim-p 0.0008 0.1391 1.1442 1795.966784 4 0.0003 101 | 0/8 5 h-lim-p 0.0015 0.6192 0.1975 1795.966780 1 0.0002 117 | 0/8 6 h-lim-p 0.0012 4.1038 0.0312 1795.966780 0 0.0003 138 | 0/8 7 h-lim-p 0.0061 20.0000 0.0013 1795.966780 0 0.0013 159 | 0/8 8 h-lim-p 0.0120 20.0000 0.0001 1795.966778 0 0.2891 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1795.966778 0 1.0938 203 | 0/8 10 h-lim-p 0.5586 20.0000 0.0000 1795.966778 0 0.0698 225 | 0/8 11 h-lim-p 0.0318 20.0000 0.0000 1795.966778 0 0.0040 247 | 0/8 12 h-lim-p 0.0025 20.0000 0.0001 1795.966778 0 0.0006 268 | 0/8 13 h-lim-p 0.0005 20.0000 0.0001 1795.966778 0 0.0000 308 | 0/8 14 h-lim-p 0.0000 20.0000 0.0043 | 0/8 15 h-lim-p 0.0000 20.0000 0.0043 Out... lnL = -1795.966778 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1795.966778 Node 7: lnL = -1795.966778 Node 8: lnL = -1795.966778 Node 9: lnL = -1795.966778 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 738 Sequential format.. Reading seq # 1: YDL081C_Sbay Reading seq # 2: YDL081C_Scer Reading seq # 3: YDL081C_Skud Reading seq # 4: YDL081C_Smik Reading seq # 5: YDL081C_Spar Sequences read.. Counting patterns.. # site patterns = 212 Counting frequencies.. 120 bytes for distance 33920 bytes for lkl0 27136 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.068297 0.017944 0.106891 0.078311 0.089168 0.187581 0.143292 0.146318 lnL0 = -2651.798200 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2651.798200 x= 0.06830 0.01794 0.10689 0.07831 0.08917 0.18758 0.14329 0.14632 1 h-lim-p 0.0005 0.0040 211.7668 2648.775495 9 0.0002 43 | 0/8 2 h-lim-p 0.0004 0.0031 42.4644 2648.495938 3 0.0003 61 | 0/8 3 h-lim-p 0.0018 0.0223 7.7340 2648.483804 2 0.0004 78 | 0/8 4 h-lim-p 0.0014 0.0700 2.2815 2648.483208 3 0.0003 99 | 0/8 5 h-lim-p 0.0008 0.3773 0.6838 2648.483115 2 0.0004 116 | 0/8 6 h-lim-p 0.0024 1.2140 0.1238 2648.483111 1 0.0005 139 | 0/8 7 h-lim-p 0.0019 8.2453 0.0315 2648.483110 0 0.0017 159 | 0/8 8 h-lim-p 0.0339 20.0000 0.0016 2648.482043 0 0.5420 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2648.482026 1 0.9961 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2648.482026 0 2.1875 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2648.482026 0 1.0938 245 | 0/8 12 h-lim-p 0.1030 20.0000 0.0000 2648.482026 012.3899 272 | 0/8 13 h-lim-p 0.1238 20.0000 0.0017 2648.482026 0 0.0077 295 | 0/8 14 h-lim-p 0.0016 11.2308 0.0085 2648.482026 0 0.0000 336 | 0/8 15 h-lim-p 0.0000 20.0000 0.0016 | 0/8 16 h-lim-p 0.0000 20.0000 0.0016 Out... lnL = -2648.482026 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2648.482026 Node 7: lnL = -2648.482026 Node 8: lnL = -2648.482026 Node 9: lnL = -2648.482026 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 468 Sequential format.. Reading seq # 1: YDL084W_Sbay Reading seq # 2: YDL084W_Scer Reading seq # 3: YDL084W_Skud Reading seq # 4: YDL084W_Smik Reading seq # 5: YDL084W_Spar Sequences read.. Counting patterns.. # site patterns = 127 Counting frequencies.. 120 bytes for distance 20320 bytes for lkl0 16256 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.038966 0.026477 0.030339 0.050880 0.028501 0.144053 0.152195 0.090093 lnL0 = -1533.118004 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1533.118004 x= 0.03897 0.02648 0.03034 0.05088 0.02850 0.14405 0.15219 0.09009 1 h-lim-p 0.0004 0.0028 144.5282 1531.935132 8 0.0001 40 | 0/8 2 h-lim-p 0.0002 0.0016 24.1939 1531.882629 2 0.0002 56 | 0/8 3 h-lim-p 0.0004 0.0262 12.6809 1531.859224 3 0.0004 74 | 0/8 4 h-lim-p 0.0015 0.0121 2.9075 1531.858772 4 0.0001 100 | 0/8 5 h-lim-p 0.0003 0.1986 1.2033 1531.858635 2 0.0002 116 | 0/8 6 h-lim-p 0.0013 0.7811 0.2104 1531.858627 2 0.0004 134 | 0/8 7 h-lim-p 0.0008 1.5958 0.1137 1531.858626 1 0.0002 157 | 0/8 8 h-lim-p 0.1810 20.0000 0.0001 1531.858553 0 1.4479 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1531.858551 0 1.0938 200 | 0/8 10 h-lim-p 1.8597 20.0000 0.0000 1531.858551 0 0.8136 220 | 0/8 11 h-lim-p 0.7740 20.0000 0.0000 1531.858551 0 0.0001 252 | 0/8 12 h-lim-p 0.0000 20.0000 0.0004 1531.858551 0 0.0000 272 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 1531.858551 0 0.0000 294 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 1531.858551 0 0.0000 328 | 0/8 15 h-lim-p 0.0000 20.0000 0.0032 | 0/8 16 h-lim-p 0.0000 20.0000 0.0032 Out... lnL = -1531.858551 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1531.858551 Node 7: lnL = -1531.858551 Node 8: lnL = -1531.858551 Node 9: lnL = -1531.858551 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 642 Sequential format.. Reading seq # 1: YDL085C-A_Sbay Reading seq # 2: YDL085C-A_Scer Reading seq # 3: YDL085C-A_Skud Reading seq # 4: YDL085C-A_Smik Reading seq # 5: YDL085C-A_Spar Sequences read.. Counting patterns.. # site patterns = 200 Counting frequencies.. 120 bytes for distance 32000 bytes for lkl0 25600 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.116377 0.058010 0.037797 0.103915 0.078609 0.171854 0.197663 0.204485 lnL0 = -2641.892111 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2641.892111 x= 0.11638 0.05801 0.03780 0.10392 0.07861 0.17185 0.19766 0.20448 1 h-lim-p 0.0003 0.0021 134.4158 2640.597319 7 0.0002 39 | 0/8 2 h-lim-p 0.0004 0.0033 27.0611 2640.509493 6 0.0002 66 | 0/8 3 h-lim-p 0.0008 0.0356 8.2656 2640.501190 6 0.0003 92 | 0/8 4 h-lim-p 0.0010 0.0939 2.2064 2640.500271 3 0.0004 110 | 0/8 5 h-lim-p 0.0045 0.3400 0.2038 2640.500263 2 0.0004 128 | 0/8 6 h-lim-p 0.0010 6.1302 0.0850 2640.500261 1 0.0005 151 | 0/8 7 h-lim-p 0.0349 20.0000 0.0013 2640.500239 0 0.1395 173 | 0/8 8 h-lim-p 0.0030 1.0633 0.0591 2640.500036 0 0.0059 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2640.500030 1 0.9961 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2640.500030 0 2.1875 236 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2640.500030 0 1.0938 256 | 0/8 12 h-lim-p 0.2314 20.0000 0.0000 2640.500030 0 3.7027 280 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2640.500030 0 0.0195 306 | 0/8 14 h-lim-p 0.0012 20.0000 0.0000 2640.500030 0 0.0012 326 | 0/8 15 h-lim-p 0.0005 20.0000 0.0001 2640.500030 0 0.0005 346 | 0/8 16 h-lim-p 0.0002 20.0000 0.0002 2640.500030 0 0.0000 374 | 0/8 17 h-lim-p 0.0002 20.0000 0.0000 2640.500030 0 0.0000 403 Out... lnL = -2640.500030 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2640.500030 Node 7: lnL = -2640.500030 Node 8: lnL = -2640.500030 Node 9: lnL = -2640.500030 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 601 Sequential format.. Reading seq # 1: YDL085W_Sbay Reading seq # 2: YDL085W_Scer Reading seq # 3: YDL085W_Skud Reading seq # 4: YDL085W_Smik Reading seq # 5: YDL085W_Spar Sequences read.. Counting patterns.. # site patterns = 206 Counting frequencies.. 120 bytes for distance 32960 bytes for lkl0 26368 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.135378 0.023981 0.028137 0.105745 0.076779 0.196910 0.229151 0.226239 lnL0 = -2582.104129 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2582.104129 x= 0.13538 0.02398 0.02814 0.10574 0.07678 0.19691 0.22915 0.22624 1 h-lim-p 0.0007 0.0053 180.5163 2580.134116 3 0.0001 29 | 0/8 2 h-lim-p 0.0003 0.0027 36.0650 2579.963075 5 0.0003 51 | 0/8 3 h-lim-p 0.0011 0.0194 9.2705 2579.951435 6 0.0003 76 | 0/8 4 h-lim-p 0.0006 0.0788 4.4989 2579.948044 5 0.0004 102 | 0/8 5 h-lim-p 0.0028 0.2668 0.6547 2579.947961 3 0.0004 122 | 0/8 6 h-lim-p 0.0009 1.1202 0.2650 2579.947939 2 0.0007 146 | 0/8 7 h-lim-p 0.0067 13.0834 0.0288 2579.947934 0 0.0029 166 | 0/8 8 h-lim-p 0.0329 20.0000 0.0026 2579.946322 0 0.2635 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2579.946288 2 0.9961 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2579.946288 0 1.0938 233 | 0/8 11 h-lim-p 1.2194 20.0000 0.0000 2579.946288 0 4.8775 255 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2579.946288 0 0.0098 282 | 0/8 13 h-lim-p 0.0104 20.0000 0.0000 2579.946288 0 0.0052 302 | 0/8 14 h-lim-p 0.0021 20.0000 0.0000 2579.946288 0 0.0003 324 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 2579.946288 0 0.0000 359 | 0/8 16 h-lim-p 0.0000 20.0000 0.0017 | 0/8 17 h-lim-p 0.0000 20.0000 0.0017 Out... lnL = -2579.946288 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2579.946288 Node 7: lnL = -2579.946288 Node 8: lnL = -2579.946288 Node 9: lnL = -2579.946288 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 455 Sequential format.. Reading seq # 1: YDL086W_Sbay Reading seq # 2: YDL086W_Scer Reading seq # 3: YDL086W_Skud Reading seq # 4: YDL086W_Smik Reading seq # 5: YDL086W_Spar Sequences read.. Counting patterns.. # site patterns = 202 Counting frequencies.. 120 bytes for distance 32320 bytes for lkl0 25856 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.089974 0.102579 0.048890 0.209324 0.104929 0.213034 0.238019 0.201231 lnL0 = -2171.393922 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2171.393922 x= 0.08997 0.10258 0.04889 0.20932 0.10493 0.21303 0.23802 0.20123 1 h-lim-p 0.0051 1.2176 92.0323 2170.138840 7 0.0003 40 | 0/8 2 h-lim-p 0.0010 0.0081 17.7595 2170.046851 6 0.0006 67 | 0/8 3 h-lim-p 0.0018 0.0564 5.9496 2170.034441 2 0.0008 83 | 0/8 4 h-lim-p 0.0039 0.2704 1.1778 2170.033787 3 0.0010 102 | 0/8 5 h-lim-p 0.0039 0.7278 0.2960 2170.033756 2 0.0008 119 | 0/8 6 h-lim-p 0.1372 20.0000 0.0017 2170.033754 0 0.0300 140 | 0/8 7 h-lim-p 0.0083 20.0000 0.0060 2170.033702 0 0.0330 162 | 0/8 8 h-lim-p 0.0084 9.6709 0.0238 2170.033702 0 0.0009 184 | 0/8 9 h-lim-p 0.4949 20.0000 0.0000 2170.033700 0 0.9898 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2170.033700 0 1.0938 225 | 0/8 11 h-lim-p 0.9075 20.0000 0.0000 2170.033700 0 0.0009 254 | 0/8 12 h-lim-p 0.0002 20.0000 0.0000 2170.033700 0 0.0000 292 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -2170.033700 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2170.033700 Node 7: lnL = -2170.033700 Node 8: lnL = -2170.033700 Node 9: lnL = -2170.033700 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 487 Sequential format.. Reading seq # 1: YDL087C_Sbay Reading seq # 2: YDL087C_Scer Reading seq # 3: YDL087C_Skud Reading seq # 4: YDL087C_Smik Reading seq # 5: YDL087C_Spar Sequences read.. Counting patterns.. # site patterns = 205 Counting frequencies.. 120 bytes for distance 32800 bytes for lkl0 26240 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.090040 0.088009 0.072960 0.194264 0.123715 0.179487 0.231920 0.199253 lnL0 = -2152.170635 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2152.170635 x= 0.09004 0.08801 0.07296 0.19426 0.12372 0.17949 0.23192 0.19925 1 h-lim-p 0.0058 1.7720 86.4725 2150.616985 9 0.0004 48 | 0/8 2 h-lim-p 0.0015 0.0122 13.1307 2150.565768 5 0.0006 70 | 0/8 3 h-lim-p 0.0029 0.0687 2.6900 2150.562948 5 0.0008 94 | 0/8 4 h-lim-p 0.0022 0.2939 0.9935 2150.562513 2 0.0010 110 | 0/8 5 h-lim-p 0.0058 1.5945 0.1654 2150.562499 2 0.0011 135 | 0/8 6 h-lim-p 0.0105 19.0831 0.0176 2150.562499 0 0.0023 156 | 0/8 7 h-lim-p 0.0552 20.0000 0.0007 2150.562469 0 0.3310 178 | 0/8 8 h-lim-p 0.0024 5.8356 0.1004 2150.562418 1 0.0030 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2150.562417 0 1.0938 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2150.562417 0 1.0938 240 | 0/8 11 h-lim-p 1.2541 20.0000 0.0000 2150.562417 0 2.5082 261 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2150.562417 0 0.5469 282 | 0/8 13 h-lim-p 0.0423 20.0000 0.0000 2150.562417 0 0.0211 302 | 0/8 14 h-lim-p 0.0067 20.0000 0.0000 2150.562417 0 0.0001 327 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 2150.562417 0 0.0001 347 | 0/8 16 h-lim-p 0.0005 20.0000 0.0000 2150.562417 0 0.0000 378 Out... lnL = -2150.562417 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2150.562417 Node 7: lnL = -2150.562417 Node 8: lnL = -2150.562417 Node 9: lnL = -2150.562417 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 238 Sequential format.. Reading seq # 1: YDL088C_Sbay Reading seq # 2: YDL088C_Scer Reading seq # 3: YDL088C_Skud Reading seq # 4: YDL088C_Smik Reading seq # 5: YDL088C_Spar Sequences read.. Counting patterns.. # site patterns = 120 Counting frequencies.. 120 bytes for distance 19200 bytes for lkl0 15360 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.035608 0.183830 0.090189 0.097116 0.055305 0.146165 0.181406 0.126917 lnL0 = -984.963440 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 984.963440 x= 0.03561 0.18383 0.09019 0.09712 0.05531 0.14617 0.18141 0.12692 1 h-lim-p 0.0009 0.0073 28.4477 984.749024 8 0.0006 45 | 0/8 2 h-lim-p 0.0013 0.0107 10.8422 984.719199 6 0.0006 71 | 0/8 3 h-lim-p 0.0017 0.0661 3.6191 984.711978 5 0.0012 95 | 0/8 4 h-lim-p 0.0093 0.5960 0.4805 984.711813 4 0.0014 119 | 0/8 5 h-lim-p 0.0061 1.5016 0.1125 984.711808 2 0.0010 146 | 0/8 6 h-lim-p 0.0032 6.7552 0.0353 984.711807 0 0.0014 166 | 0/8 7 h-lim-p 0.0065 10.7491 0.0077 984.711806 0 0.0028 186 | 0/8 8 h-lim-p 0.0156 20.0000 0.0014 984.711721 0 0.2494 210 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 984.711719 0 1.0938 230 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 984.711719 0 1.0938 250 | 0/8 11 h-lim-p 1.1896 20.0000 0.0000 984.711719 0 0.0093 276 | 0/8 12 h-lim-p 0.0033 20.0000 0.0000 984.711719 0 0.0000 303 | 0/8 13 h-lim-p 0.0000 20.0000 0.0009 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0008 | 0/8 15 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -984.711719 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -984.711719 Node 7: lnL = -984.711719 Node 8: lnL = -984.711719 Node 9: lnL = -984.711719 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 520 Sequential format.. Reading seq # 1: YDL089W_Sbay Reading seq # 2: YDL089W_Scer Reading seq # 3: YDL089W_Skud Reading seq # 4: YDL089W_Smik Reading seq # 5: YDL089W_Spar Sequences read.. Counting patterns.. # site patterns = 191 Counting frequencies.. 120 bytes for distance 30560 bytes for lkl0 24448 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.094832 0.055118 0.066007 0.156598 0.088812 0.182104 0.222567 0.191758 lnL0 = -2386.762898 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2386.762898 x= 0.09483 0.05512 0.06601 0.15660 0.08881 0.18210 0.22257 0.19176 1 h-lim-p 0.0008 0.0063 108.6013 2385.203012 8 0.0003 41 | 0/8 2 h-lim-p 0.0006 0.0050 25.9614 2385.056487 7 0.0005 71 | 0/8 3 h-lim-p 0.0009 0.0216 12.4997 2385.029086 2 0.0004 87 | 0/8 4 h-lim-p 0.0017 0.0931 3.1867 2385.026360 5 0.0006 111 | 0/8 5 h-lim-p 0.0083 0.9180 0.2237 2385.026349 0 0.0005 126 | 0/8 6 h-lim-p 0.0074 19.6471 0.0139 2385.026349 0 0.0008 148 | 0/8 7 h-lim-p 0.0090 20.0000 0.0012 2385.026347 0 0.0360 170 | 0/8 8 h-lim-p 0.0029 12.5461 0.0152 2385.026313 0 0.0118 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2385.026313 0 1.0938 212 | 0/8 10 h-lim-p 1.9566 20.0000 0.0000 2385.026313 0 0.8560 232 | 0/8 11 h-lim-p 0.6967 20.0000 0.0000 2385.026313 0 0.0109 257 | 0/8 12 h-lim-p 0.0041 20.0000 0.0000 2385.026313 0 0.0000 300 | 0/8 13 h-lim-p 0.0000 20.0000 0.0008 | 0/8 14 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -2385.026313 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2385.026313 Node 7: lnL = -2385.026313 Node 8: lnL = -2385.026313 Node 9: lnL = -2385.026313 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 869 Sequential format.. Reading seq # 1: YDL092W_Sbay Reading seq # 2: YDL092W_Scer Reading seq # 3: YDL092W_Skud Reading seq # 4: YDL092W_Smik Reading seq # 5: YDL092W_Spar Sequences read.. Counting patterns.. # site patterns = 328 Counting frequencies.. 120 bytes for distance 52480 bytes for lkl0 41984 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.094165 0.062254 0.050732 0.283169 0.357271 0.226676 0.233002 0.232511 lnL0 = -3753.171476 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3753.171476 x= 0.09417 0.06225 0.05073 0.28317 0.35727 0.22668 0.23300 0.23251 1 h-lim-p 0.0029 0.0232 99.6498 3751.654184 2 0.0003 28 | 0/8 2 h-lim-p 0.0011 0.0093 30.3688 3751.291468 7 0.0008 56 | 0/8 3 h-lim-p 0.0093 0.1374 2.7268 3751.288964 5 0.0007 82 | 0/8 4 h-lim-p 0.0018 0.3480 1.0292 3751.288592 2 0.0008 98 | 0/8 5 h-lim-p 0.0067 4.6887 0.1204 3751.288587 0 0.0007 112 | 0/8 6 h-lim-p 0.0071 20.0000 0.0125 3751.288587 0 0.0031 132 | 0/8 7 h-lim-p 0.0047 20.0000 0.0083 3751.288585 0 0.0047 152 | 0/8 8 h-lim-p 0.0095 20.0000 0.0041 3751.288470 0 0.0761 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3751.288469 0 1.0938 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3751.288469 0 1.0938 215 | 0/8 11 h-lim-p 0.5518 20.0000 0.0000 3751.288469 0 1.1035 236 | 0/8 12 h-lim-p 0.5870 20.0000 0.0000 3751.288469 0 0.0046 262 | 0/8 13 h-lim-p 0.0001 20.0000 0.0008 3751.288469 0 0.0000 288 | 0/8 14 h-lim-p 0.0006 20.0000 0.0000 3751.288469 0 0.0000 319 Out... lnL = -3751.288469 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3751.288469 Node 7: lnL = -3751.288469 Node 8: lnL = -3751.288469 Node 9: lnL = -3751.288469 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 229 Sequential format.. Reading seq # 1: YDL098C_Sbay Reading seq # 2: YDL098C_Scer Reading seq # 3: YDL098C_Skud Reading seq # 4: YDL098C_Smik Reading seq # 5: YDL098C_Spar Sequences read.. Counting patterns.. # site patterns = 115 Counting frequencies.. 120 bytes for distance 18400 bytes for lkl0 14720 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.055578 0.131235 0.119206 0.094840 0.075114 0.152879 0.233227 0.146232 lnL0 = -928.069747 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 928.069747 x= 0.05558 0.13123 0.11921 0.09484 0.07511 0.15288 0.23323 0.14623 1 h-lim-p 0.0030 0.0237 17.5098 927.806940 8 0.0018 42 | 0/8 2 h-lim-p 0.0017 0.0139 14.3138 927.733779 8 0.0011 77 | 0/8 3 h-lim-p 0.0017 0.0176 9.0418 927.715840 6 0.0007 104 | 0/8 4 h-lim-p 0.0063 0.3110 0.9718 927.715120 2 0.0016 121 | 0/8 5 h-lim-p 0.0030 0.4627 0.5088 927.714973 2 0.0014 145 | 0/8 6 h-lim-p 0.0074 2.2623 0.0966 927.714966 2 0.0014 170 | 0/8 7 h-lim-p 0.0065 11.7969 0.0211 927.714961 0 0.0098 190 | 0/8 8 h-lim-p 0.0565 20.0000 0.0036 927.714553 0 0.4522 213 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 927.714507 2 0.9961 237 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 927.714507 0 1.0938 257 | 0/8 11 h-lim-p 1.2706 20.0000 0.0000 927.714507 0 1.1118 277 | 0/8 12 h-lim-p 0.3915 20.0000 0.0000 927.714507 0 0.0002 307 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 927.714507 0 0.0000 342 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 927.714507 0 0.0000 366 Out... lnL = -927.714507 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -927.714507 Node 7: lnL = -927.714507 Node 8: lnL = -927.714507 Node 9: lnL = -927.714507 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 250 Sequential format.. Reading seq # 1: YDL099W_Sbay Reading seq # 2: YDL099W_Scer Reading seq # 3: YDL099W_Skud Reading seq # 4: YDL099W_Smik Reading seq # 5: YDL099W_Spar Sequences read.. Counting patterns.. # site patterns = 82 Counting frequencies.. 120 bytes for distance 13120 bytes for lkl0 10496 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.123298 0.385649 0.198484 0.315082 3.962575 0.235618 0.299904 lnL0 = -913.821465 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 913.821465 x= 0.00006 0.12330 0.38565 0.19848 0.31508 3.96257 0.23562 0.29990 1 h-lim-p 0.0000 0.0000 248.3772 913.695684 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0006 392.4426 872.443839 m 0.0006 37 | 2/8 3 h-lim-p 0.0006 0.0046 86.5058 864.444860 0 0.0023 51 | 2/8 4 h-lim-p 0.0014 0.0116 11.0099 864.135938 0 0.0029 64 | 2/8 5 h-lim-p 0.0072 0.0572 4.3966 862.219114 0 0.0286 78 | 1/8 6 h-lim-p 0.0016 0.0127 18.4035 849.489979 m 0.0127 90 | 2/8 7 h-lim-p 0.0005 0.0041 47.3138 847.135589 0 0.0010 103 | 2/8 8 h-lim-p 0.1315 1.0523 0.2225 842.984731 0 0.5261 117 | 1/8 9 h-lim-p 0.0054 0.0429 13.6797 842.852931 7 0.0015 151 | 1/8 10 h-lim-p 0.5651 14.0560 0.0360 842.457486 2 0.5298 167 | 0/8 11 h-lim-p 0.0114 0.2764 1.6797 842.455822 4 0.0012 197 | 0/8 12 h-lim-p 0.0918 17.2387 0.0212 842.425835 0 0.3672 211 | 0/8 13 h-lim-p 0.2546 2.0368 0.0043 842.424840 0 0.3819 231 | 0/8 14 h-lim-p 2.5000 20.0000 0.0002 842.424811 2 1.1719 255 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 842.424811 0 1.0938 275 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 842.424811 0 1.0938 295 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 842.424811 0 0.0000 334 Out... lnL = -842.424811 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -842.424811 Node 7: lnL = -842.424811 Node 8: lnL = -842.424811 Node 9: lnL = -842.424811 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 265 Sequential format.. Reading seq # 1: YDL100C_Sbay Reading seq # 2: YDL100C_Scer Reading seq # 3: YDL100C_Skud Reading seq # 4: YDL100C_Smik Reading seq # 5: YDL100C_Spar Sequences read.. Counting patterns.. # site patterns = 122 Counting frequencies.. 120 bytes for distance 19520 bytes for lkl0 15616 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.064748 0.000060 0.151848 0.078923 0.134257 1.197650 0.130863 0.218693 lnL0 = -1206.930466 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1206.930466 x= 0.06475 0.00006 0.15185 0.07892 0.13426 1.19765 0.13086 0.21869 1 h-lim-p 0.0000 0.0000 107.7851 1206.908120 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0030 67.6017 1205.303822 0 0.0013 41 | 1/8 3 h-lim-p 0.0050 0.0397 7.3059 1205.207035 6 0.0032 68 | 1/8 4 h-lim-p 0.0020 0.0488 11.6675 1204.984050 0 0.0081 82 | 1/8 5 h-lim-p 0.0029 0.0354 32.1164 1204.638870 1 0.0037 96 | 1/8 6 h-lim-p 0.0027 0.0214 11.6857 1204.597300 2 0.0013 112 | 1/8 7 h-lim-p 0.0820 1.6522 0.1786 1201.941000 0 0.6560 127 | 0/8 8 h-lim-p 0.0000 0.0000 8.7101 h-lim-p: 9.81189073e-24 7.84951258e-23 8.71008855e+00 1201.941000 .. | 0/8 9 h-lim-p 0.0000 0.0347 56.2369 1201.476419 0 0.0003 159 | 0/8 10 h-lim-p 0.0000 0.0004 9.9437 1201.442852 m 0.0004 171 | 1/8 11 h-lim-p 0.0003 0.0474 11.2495 1201.434094 0 0.0004 183 | 1/8 12 h-lim-p 0.0029 0.1249 1.4993 1201.432573 2 0.0014 199 | 1/8 13 h-lim-p 0.0018 0.4780 1.1480 1201.428947 0 0.0071 213 | 1/8 14 h-lim-p 0.0022 0.2263 3.6768 1201.425280 1 0.0028 227 | 1/8 15 h-lim-p 0.0026 0.3537 3.8771 1201.420102 0 0.0040 239 | 1/8 16 h-lim-p 2.5000 20.0000 0.0025 1201.418669 2 1.1719 255 | 1/8 17 h-lim-p 2.5000 20.0000 0.0005 1201.418654 1 1.0938 276 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 1201.418654 0 1.0938 295 | 1/8 19 h-lim-p 2.5000 20.0000 0.0000 1201.418654 0 2.1875 314 | 1/8 20 h-lim-p 2.1851 20.0000 0.0000 1201.418654 0 0.9560 333 | 1/8 21 h-lim-p 1.6060 20.0000 0.0000 1201.418654 0 0.0031 360 Out... lnL = -1201.418654 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1201.418654 Node 7: lnL = -1201.418654 Node 8: lnL = -1201.418654 Node 9: lnL = -1201.418654 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 285 Sequential format.. Reading seq # 1: YDL101C_Sbay Reading seq # 2: YDL101C_Scer Reading seq # 3: YDL101C_Skud Reading seq # 4: YDL101C_Smik Reading seq # 5: YDL101C_Spar Sequences read.. Counting patterns.. # site patterns = 96 Counting frequencies.. 120 bytes for distance 15360 bytes for lkl0 12288 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.027558 0.066706 0.014450 0.077714 0.051593 0.210686 0.101216 0.081284 lnL0 = -1049.407287 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1049.407287 x= 0.02756 0.06671 0.01445 0.07771 0.05159 0.21069 0.10122 0.08128 1 h-lim-p 0.0004 0.0032 132.0575 1048.479676 9 0.0001 43 | 0/8 2 h-lim-p 0.0008 0.0061 13.6038 1048.441824 5 0.0004 66 | 0/8 3 h-lim-p 0.0009 0.0343 6.4399 1048.434220 4 0.0004 88 | 0/8 4 h-lim-p 0.0010 0.0718 2.6886 1048.432122 5 0.0007 112 | 0/8 5 h-lim-p 0.0022 0.2071 0.8570 1048.431968 2 0.0005 129 | 0/8 6 h-lim-p 0.0023 0.4920 0.1782 1048.431963 2 0.0003 155 | 0/8 7 h-lim-p 0.0019 3.5601 0.0290 1048.431963 0 0.0004 176 | 0/8 8 h-lim-p 0.2015 20.0000 0.0001 1048.431958 0 1.2088 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1048.431957 1 1.2305 221 | 0/8 10 h-lim-p 1.1555 20.0000 0.0000 1048.431957 0 1.1555 241 | 0/8 11 h-lim-p 1.4775 20.0000 0.0000 1048.431957 0 0.0014 270 | 0/8 12 h-lim-p 0.0001 20.0000 0.0003 1048.431957 0 0.0000 294 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0012 | 0/8 15 h-lim-p 0.0000 20.0000 0.0012 Out... lnL = -1048.431957 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1048.431957 Node 7: lnL = -1048.431957 Node 8: lnL = -1048.431957 Node 9: lnL = -1048.431957 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 313 Sequential format.. Reading seq # 1: YDL103C_Sbay Reading seq # 2: YDL103C_Scer Reading seq # 3: YDL103C_Skud Reading seq # 4: YDL103C_Smik Reading seq # 5: YDL103C_Spar Sequences read.. Counting patterns.. # site patterns = 138 Counting frequencies.. 120 bytes for distance 22080 bytes for lkl0 17664 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.098158 0.015413 0.060945 0.121314 0.071649 0.250796 0.246448 0.185176 lnL0 = -1379.555994 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1379.555994 x= 0.09816 0.01541 0.06094 0.12131 0.07165 0.25080 0.24645 0.18518 1 h-lim-p 0.0004 0.0032 133.9285 1377.236499 7 0.0003 38 | 0/8 2 h-lim-p 0.0003 0.0024 33.6335 1376.941218 0 0.0006 51 | 0/8 3 h-lim-p 0.0011 0.0139 17.5177 1376.866664 5 0.0006 74 | 0/8 4 h-lim-p 0.0009 0.0279 11.6454 1376.835812 6 0.0007 101 | 0/8 5 h-lim-p 0.0030 0.0516 2.5939 1376.833652 2 0.0007 118 | 0/8 6 h-lim-p 0.0037 0.5784 0.4984 1376.833538 3 0.0009 137 | 0/8 7 h-lim-p 0.0063 5.7471 0.0708 1376.833505 3 0.0045 164 | 0/8 8 h-lim-p 0.0463 20.0000 0.0068 1376.829731 0 0.3705 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 1376.829421 2 1.0889 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1376.829414 2 1.6492 237 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1376.829414 0 1.0938 257 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1376.829414 0 0.0073 285 | 0/8 13 h-lim-p 0.0033 20.0000 0.0000 1376.829414 0 0.0029 305 | 0/8 14 h-lim-p 0.0018 20.0000 0.0000 1376.829414 0 0.0000 337 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 1376.829414 0 0.0000 371 Out... lnL = -1376.829414 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1376.829414 Node 7: lnL = -1376.829414 Node 8: lnL = -1376.829414 Node 9: lnL = -1376.829414 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 230 Sequential format.. Reading seq # 1: YDL107W_Sbay Reading seq # 2: YDL107W_Scer Reading seq # 3: YDL107W_Skud Reading seq # 4: YDL107W_Smik Reading seq # 5: YDL107W_Spar Sequences read.. Counting patterns.. # site patterns = 122 Counting frequencies.. 120 bytes for distance 19520 bytes for lkl0 15616 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.117149 0.044094 0.059862 0.253532 0.146758 0.234088 0.237620 0.226870 lnL0 = -1157.793307 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1157.793307 x= 0.11715 0.04409 0.05986 0.25353 0.14676 0.23409 0.23762 0.22687 1 h-lim-p 0.0067 1.7697 58.7574 1156.717165 6 0.0007 37 | 0/8 2 h-lim-p 0.0011 0.0084 13.2604 1156.593446 0 0.0016 49 | 0/8 3 h-lim-p 0.0033 0.0396 6.2801 1156.568995 6 0.0015 73 | 0/8 4 h-lim-p 0.0167 0.6614 0.5577 1156.568728 3 0.0017 93 | 0/8 5 h-lim-p 0.0113 1.3435 0.0860 1156.568713 2 0.0027 118 | 0/8 6 h-lim-p 0.0069 15.3237 0.0332 1156.568656 0 0.0138 139 | 0/8 7 h-lim-p 0.0141 14.0187 0.0323 1156.566954 0 0.0565 161 | 0/8 8 h-lim-p 0.0036 0.9359 0.5086 1156.566377 3 0.0029 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 1156.566229 2 1.2402 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1156.566228 0 1.0938 231 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1156.566228 0 1.0938 251 | 0/8 12 h-lim-p 1.3453 20.0000 0.0000 1156.566228 0 2.6905 272 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1156.566228 0 0.0003 304 Out... lnL = -1156.566228 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1156.566228 Node 7: lnL = -1156.566228 Node 8: lnL = -1156.566228 Node 9: lnL = -1156.566228 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 569 Sequential format.. Reading seq # 1: YDL109C_Sbay Reading seq # 2: YDL109C_Scer Reading seq # 3: YDL109C_Skud Reading seq # 4: YDL109C_Smik Reading seq # 5: YDL109C_Spar Sequences read.. Counting patterns.. # site patterns = 238 Counting frequencies.. 120 bytes for distance 38080 bytes for lkl0 30464 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.101299 0.132922 0.102755 0.140527 0.088695 0.324293 0.219340 0.216821 lnL0 = -2651.680567 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2651.680567 x= 0.10130 0.13292 0.10276 0.14053 0.08870 0.32429 0.21934 0.21682 1 h-lim-p 0.0003 0.0026 45.0512 2651.224343 0 0.0005 22 | 0/8 2 h-lim-p 0.0014 0.0375 16.0793 2651.181908 5 0.0004 45 | 0/8 3 h-lim-p 0.0011 0.0473 5.3246 2651.170615 3 0.0009 63 | 0/8 4 h-lim-p 0.0035 0.2446 1.3662 2651.170090 4 0.0006 86 | 0/8 5 h-lim-p 0.0025 0.4617 0.3291 2651.170041 3 0.0009 105 | 0/8 6 h-lim-p 0.0028 2.4902 0.1030 2651.170029 2 0.0015 130 | 0/8 7 h-lim-p 0.0029 4.8221 0.0531 2651.169991 0 0.0058 151 | 0/8 8 h-lim-p 0.0175 18.6805 0.0177 2651.166916 0 0.1048 173 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 2651.166890 1 0.9961 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2651.166890 0 1.2500 215 | 0/8 11 h-lim-p 1.5643 20.0000 0.0000 2651.166890 0 0.1955 237 | 0/8 12 h-lim-p 0.0712 20.0000 0.0000 2651.166890 0 0.0000 267 | 0/8 13 h-lim-p 0.0013 20.0000 0.0000 2651.166890 0 0.0000 301 Out... lnL = -2651.166890 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2651.166890 Node 7: lnL = -2651.166890 Node 8: lnL = -2651.166890 Node 9: lnL = -2651.166890 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 310 Sequential format.. Reading seq # 1: YDL110C_Sbay Reading seq # 2: YDL110C_Scer Reading seq # 3: YDL110C_Skud Reading seq # 4: YDL110C_Smik Reading seq # 5: YDL110C_Spar Sequences read.. Counting patterns.. # site patterns = 116 Counting frequencies.. 120 bytes for distance 18560 bytes for lkl0 14848 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.062032 0.039540 0.090882 0.080357 0.079946 0.074933 0.154303 0.123683 lnL0 = -1208.225888 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1208.225888 x= 0.06203 0.03954 0.09088 0.08036 0.07995 0.07493 0.15430 0.12368 1 h-lim-p 0.0063 2.3408 62.1651 1207.672094 8 0.0003 40 | 0/8 2 h-lim-p 0.0023 0.0181 6.5705 1207.660279 4 0.0006 61 | 0/8 3 h-lim-p 0.0038 0.1196 0.9564 1207.660066 2 0.0005 79 | 0/8 4 h-lim-p 0.0040 1.4357 0.1124 1207.660062 2 0.0007 106 | 0/8 5 h-lim-p 0.0014 3.1428 0.0519 1207.660061 0 0.0006 126 | 0/8 6 h-lim-p 0.0030 9.0246 0.0110 1207.660061 0 0.0006 147 | 0/8 7 h-lim-p 0.0901 20.0000 0.0001 1207.660057 0 0.7205 170 | 0/8 8 h-lim-p 0.0010 1.4282 0.0550 1207.660055 1 0.0008 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1207.660055 0 1.0938 212 | 0/8 10 h-lim-p 1.2464 20.0000 0.0000 1207.660055 0 2.4929 233 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1207.660055 0 0.0001 267 Out... lnL = -1207.660055 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1207.660055 Node 7: lnL = -1207.660055 Node 8: lnL = -1207.660055 Node 9: lnL = -1207.660055 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 369 Sequential format.. Reading seq # 1: YDL112W_Sbay Reading seq # 2: YDL112W_Scer Reading seq # 3: YDL112W_Skud Reading seq # 4: YDL112W_Smik Reading seq # 5: YDL112W_Spar Sequences read.. Counting patterns.. # site patterns = 142 Counting frequencies.. 120 bytes for distance 22720 bytes for lkl0 18176 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.063013 0.024813 0.047698 0.116499 0.070189 0.197484 0.173805 0.131925 lnL0 = -1560.268628 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1560.268628 x= 0.06301 0.02481 0.04770 0.11650 0.07019 0.19748 0.17380 0.13193 1 h-lim-p 0.0003 0.0023 142.2554 1558.494311 9 0.0002 43 | 0/8 2 h-lim-p 0.0006 0.0045 24.6595 1558.380787 7 0.0004 72 | 0/8 3 h-lim-p 0.0008 0.0406 11.7233 1558.357372 6 0.0004 98 | 0/8 4 h-lim-p 0.0012 0.0732 4.1444 1558.353044 6 0.0006 122 | 0/8 5 h-lim-p 0.0025 0.0715 0.9660 1558.352866 3 0.0004 143 | 0/8 6 h-lim-p 0.0052 3.8956 0.0762 1558.352863 1 0.0006 167 | 0/8 7 h-lim-p 0.0073 15.3911 0.0068 1558.352863 0 0.0016 188 | 0/8 8 h-lim-p 0.0170 20.0000 0.0006 1558.352797 0 0.2725 212 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1558.352791 0 1.0938 232 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1558.352791 0 1.0938 252 | 0/8 11 h-lim-p 1.3107 20.0000 0.0000 1558.352791 0 0.0003 283 | 0/8 12 h-lim-p 0.0054 20.0000 0.0000 1558.352791 0 0.0000 324 Out... lnL = -1558.352791 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1558.352791 Node 7: lnL = -1558.352791 Node 8: lnL = -1558.352791 Node 9: lnL = -1558.352791 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 588 Sequential format.. Reading seq # 1: YDL114W_Sbay Reading seq # 2: YDL114W_Scer Reading seq # 3: YDL114W_Skud Reading seq # 4: YDL114W_Smik Reading seq # 5: YDL114W_Spar Sequences read.. Counting patterns.. # site patterns = 236 Counting frequencies.. 120 bytes for distance 37760 bytes for lkl0 30208 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.072020 0.110182 0.107330 0.150052 0.089526 0.148094 0.193913 0.163457 lnL0 = -2648.033376 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2648.033376 x= 0.07202 0.11018 0.10733 0.15005 0.08953 0.14809 0.19391 0.16346 1 h-lim-p 0.0073 1.5260 85.1451 2646.807384 4 0.0004 33 | 0/8 2 h-lim-p 0.0012 0.0099 22.2766 2646.703659 6 0.0004 58 | 0/8 3 h-lim-p 0.0011 0.0263 9.2224 2646.690935 4 0.0004 80 | 0/8 4 h-lim-p 0.0021 0.1590 1.5152 2646.690242 4 0.0006 102 | 0/8 5 h-lim-p 0.0031 0.6717 0.3076 2646.690222 2 0.0004 120 | 0/8 6 h-lim-p 0.0041 6.3686 0.0303 2646.690221 0 0.0009 141 | 0/8 7 h-lim-p 0.0038 20.0000 0.0072 2646.690218 0 0.0076 162 | 0/8 8 h-lim-p 0.0051 20.0000 0.0107 2646.689929 0 0.0410 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2646.689923 1 0.9961 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2646.689923 0 0.5469 228 | 0/8 11 h-lim-p 0.3599 20.0000 0.0000 2646.689923 0 0.0112 252 | 0/8 12 h-lim-p 0.0055 20.0000 0.0000 2646.689923 0 0.0055 272 | 0/8 13 h-lim-p 0.0027 20.0000 0.0001 2646.689923 0 0.0013 292 | 0/8 14 h-lim-p 0.0015 20.0000 0.0001 2646.689923 0 0.0000 316 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 2646.689923 0 0.0002 336 | 0/8 16 h-lim-p 0.0026 20.0000 0.0000 2646.689923 0 0.0000 367 Out... lnL = -2646.689923 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2646.689923 Node 7: lnL = -2646.689923 Node 8: lnL = -2646.689923 Node 9: lnL = -2646.689923 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 232 Sequential format.. Reading seq # 1: YDL115C_Sbay Reading seq # 2: YDL115C_Scer Reading seq # 3: YDL115C_Skud Reading seq # 4: YDL115C_Smik Reading seq # 5: YDL115C_Spar Sequences read.. Counting patterns.. # site patterns = 106 Counting frequencies.. 120 bytes for distance 16960 bytes for lkl0 13568 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.019224 0.061502 0.000060 0.937479 0.277507 0.178114 0.164555 0.142132 lnL0 = -1047.365342 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1047.365342 x= 0.01922 0.06150 0.00006 0.93748 0.27751 0.17811 0.16456 0.14213 1 h-lim-p 0.0000 0.0000 143.1773 1047.341583 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0027 120.6225 1039.556195 0 0.0013 41 | 1/8 3 h-lim-p 0.0003 0.0027 63.5060 1038.090581 0 0.0014 55 | 1/8 4 h-lim-p 0.0032 0.0252 13.7549 1037.641286 0 0.0047 67 | 1/8 5 h-lim-p 0.0025 0.0287 25.8528 1036.956070 0 0.0050 80 | 1/8 6 h-lim-p 0.0025 0.0198 26.4508 1036.680034 3 0.0022 98 | 1/8 7 h-lim-p 0.1084 0.8668 0.2690 1032.119843 0 0.6501 112 | 1/8 8 h-lim-p 0.6256 5.0045 0.0615 1031.658540 8 0.4285 152 | 1/8 9 h-lim-p 0.6077 7.5368 0.0434 1031.592655 8 0.3543 192 | 1/8 10 h-lim-p 0.7427 18.9336 0.0207 1031.580343 5 0.8096 223 | 1/8 11 h-lim-p 2.5000 20.0000 0.0028 1031.579971 4 0.8875 251 | 1/8 12 h-lim-p 2.5000 20.0000 0.0005 1031.579951 2 0.7996 275 | 1/8 13 h-lim-p 2.5000 20.0000 0.0001 1031.579951 0 1.0938 294 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 1031.579951 0 1.0938 313 | 1/8 15 h-lim-p 1.2459 20.0000 0.0000 1031.579951 0 1.0901 332 | 1/8 16 h-lim-p 1.1214 20.0000 0.0000 1031.579951 0 1.1214 351 | 1/8 17 h-lim-p 0.4445 20.0000 0.0000 1031.579951 0 0.0972 371 | 1/8 18 h-lim-p 0.0131 20.0000 0.0002 1031.579951 0 0.0131 390 | 1/8 19 h-lim-p 0.0051 20.0000 0.0005 1031.579951 0 0.0001 413 | 1/8 20 h-lim-p 0.0001 20.0000 0.0008 .. | 1/8 21 h-lim-p 0.0000 20.0000 0.0001 1031.579951 0 0.0000 481 | 1/8 22 h-lim-p 0.0000 20.0000 0.0001 | 1/8 23 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1031.579951 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1031.579951 Node 7: lnL = -1031.579951 Node 8: lnL = -1031.579951 Node 9: lnL = -1031.579951 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 341 Sequential format.. Reading seq # 1: YDL116W_Sbay Reading seq # 2: YDL116W_Scer Reading seq # 3: YDL116W_Skud Reading seq # 4: YDL116W_Smik Reading seq # 5: YDL116W_Spar Sequences read.. Counting patterns.. # site patterns = 145 Counting frequencies.. 120 bytes for distance 23200 bytes for lkl0 18560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.050806 0.161815 0.071408 0.122116 0.088313 0.244779 0.200657 0.147060 lnL0 = -1590.435515 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1590.435515 x= 0.05081 0.16181 0.07141 0.12212 0.08831 0.24478 0.20066 0.14706 1 h-lim-p 0.0005 0.0040 50.7139 1589.708120 1 0.0006 24 | 0/8 2 h-lim-p 0.0021 0.0165 11.9663 1589.646868 4 0.0009 43 | 0/8 3 h-lim-p 0.0020 0.0731 5.2691 1589.638751 6 0.0007 70 | 0/8 4 h-lim-p 0.0015 0.0734 2.4937 1589.637614 5 0.0005 96 | 0/8 5 h-lim-p 0.0079 1.0445 0.1446 1589.637603 1 0.0009 112 | 0/8 6 h-lim-p 0.0031 7.0710 0.0407 1589.637588 0 0.0046 132 | 0/8 7 h-lim-p 0.0218 14.3618 0.0086 1589.635374 0 0.1740 155 | 0/8 8 h-lim-p 0.0048 0.8392 0.3160 1589.635288 3 0.0017 183 | 0/8 9 h-lim-p 1.8222 20.0000 0.0003 1589.635233 3 0.9794 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1589.635233 0 1.0938 230 | 0/8 11 h-lim-p 1.4548 20.0000 0.0000 1589.635233 0 0.6365 250 | 0/8 12 h-lim-p 0.2526 20.0000 0.0000 1589.635233 0 0.0553 271 | 0/8 13 h-lim-p 0.0171 20.0000 0.0001 1589.635233 0 0.0043 292 | 0/8 14 h-lim-p 0.0022 20.0000 0.0001 1589.635233 0 0.0000 328 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 1589.635233 0 0.0000 362 Out... lnL = -1589.635233 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1589.635233 Node 7: lnL = -1589.635233 Node 8: lnL = -1589.635233 Node 9: lnL = -1589.635233 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 832 Sequential format.. Reading seq # 1: YDL119C_Sbay Reading seq # 2: YDL119C_Scer Reading seq # 3: YDL119C_Skud Reading seq # 4: YDL119C_Smik Reading seq # 5: YDL119C_Spar Sequences read.. Counting patterns.. # site patterns = 270 Counting frequencies.. 120 bytes for distance 43200 bytes for lkl0 34560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.059658 0.102202 0.076017 0.160011 0.067109 0.182827 0.173706 0.144002 lnL0 = -3736.232282 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3736.232282 x= 0.05966 0.10220 0.07602 0.16001 0.06711 0.18283 0.17371 0.14400 1 h-lim-p 0.0035 0.0282 74.7086 3735.692939 3 0.0002 31 | 0/8 2 h-lim-p 0.0006 0.0057 26.2720 3735.630115 6 0.0002 56 | 0/8 3 h-lim-p 0.0007 0.0160 7.4462 3735.624923 5 0.0002 82 | 0/8 4 h-lim-p 0.0013 0.1954 1.1572 3735.624697 3 0.0003 101 | 0/8 5 h-lim-p 0.0020 0.6377 0.1989 3735.624693 0 0.0002 115 | 0/8 6 h-lim-p 0.0037 20.0000 0.0120 3735.624693 0 0.0008 136 | 0/8 7 h-lim-p 0.0042 20.0000 0.0023 3735.624692 0 0.0125 157 | 0/8 8 h-lim-p 0.0041 20.0000 0.0070 3735.624643 0 0.0247 179 | 0/8 9 h-lim-p 1.5499 20.0000 0.0001 3735.624641 0 1.3561 199 | 0/8 10 h-lim-p 2.3823 20.0000 0.0001 3735.624641 0 1.0422 219 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3735.624641 0 2.1875 239 | 0/8 12 h-lim-p 1.3307 20.0000 0.0000 3735.624641 0 1.1644 259 | 0/8 13 h-lim-p 0.0538 20.0000 0.0008 3735.624641 0 0.0067 281 | 0/8 14 h-lim-p 0.0022 20.0000 0.0023 3735.624641 0 0.0000 314 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 3735.624641 0 0.0000 337 Out... lnL = -3735.624641 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3735.624641 Node 7: lnL = -3735.624641 Node 8: lnL = -3735.624641 Node 9: lnL = -3735.624641 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 393 Sequential format.. Reading seq # 1: YDL120W_Sbay Reading seq # 2: YDL120W_Scer Reading seq # 3: YDL120W_Skud Reading seq # 4: YDL120W_Smik Reading seq # 5: YDL120W_Spar Sequences read.. Counting patterns.. # site patterns = 173 Counting frequencies.. 120 bytes for distance 27680 bytes for lkl0 22144 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.082281 0.181531 0.025595 0.116325 0.198951 0.253254 0.210268 0.181445 lnL0 = -1799.023618 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1799.023618 x= 0.08228 0.18153 0.02559 0.11633 0.19895 0.25325 0.21027 0.18145 1 h-lim-p 0.0033 0.0265 66.1189 1798.377562 7 0.0003 40 | 0/8 2 h-lim-p 0.0015 0.0118 13.6807 1798.303907 7 0.0008 67 | 0/8 3 h-lim-p 0.0015 0.0361 7.1584 1798.283220 5 0.0010 91 | 0/8 4 h-lim-p 0.0071 0.4261 1.0081 1798.282788 2 0.0009 109 | 0/8 5 h-lim-p 0.0041 1.3415 0.2172 1798.282768 2 0.0009 126 | 0/8 6 h-lim-p 0.0057 10.5287 0.0340 1798.282767 0 0.0013 147 | 0/8 7 h-lim-p 0.0133 20.0000 0.0032 1798.282767 0 0.0029 168 | 0/8 8 h-lim-p 0.0813 20.0000 0.0001 1798.282763 0 0.6505 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1798.282763 0 1.0938 211 | 0/8 10 h-lim-p 1.9755 20.0000 0.0000 1798.282763 0 1.7286 231 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1798.282763 0 1.0938 251 | 0/8 12 h-lim-p 0.4218 20.0000 0.0000 1798.282763 0 0.1054 272 | 0/8 13 h-lim-p 0.0008 20.0000 0.0010 1798.282763 0 0.0001 294 | 0/8 14 h-lim-p 0.0001 20.0000 0.0009 1798.282763 0 0.0000 321 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 1798.282763 0 0.0001 341 Out... lnL = -1798.282763 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1798.282763 Node 7: lnL = -1798.282763 Node 8: lnL = -1798.282763 Node 9: lnL = -1798.282763 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 359 Sequential format.. Reading seq # 1: YDL121C_Sbay Reading seq # 2: YDL121C_Scer Reading seq # 3: YDL121C_Skud Reading seq # 4: YDL121C_Smik Reading seq # 5: YDL121C_Spar Sequences read.. Counting patterns.. # site patterns = 175 Counting frequencies.. 120 bytes for distance 28000 bytes for lkl0 22400 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.067242 0.202238 0.010409 0.127578 0.192217 0.273507 0.230906 0.168273 lnL0 = -1765.297680 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1765.297680 x= 0.06724 0.20224 0.01041 0.12758 0.19222 0.27351 0.23091 0.16827 1 h-lim-p 0.0021 0.0169 89.2786 1764.277587 9 0.0003 46 | 0/8 2 h-lim-p 0.0011 0.0092 16.1259 1764.177180 7 0.0008 75 | 0/8 3 h-lim-p 0.0024 0.0644 5.3227 1764.165231 5 0.0009 97 | 0/8 4 h-lim-p 0.0047 0.3742 1.0702 1764.164552 3 0.0013 116 | 0/8 5 h-lim-p 0.0057 0.6121 0.2355 1764.164529 3 0.0008 138 | 0/8 6 h-lim-p 0.0022 3.0510 0.0888 1764.164525 2 0.0015 164 | 0/8 7 h-lim-p 0.3190 20.0000 0.0004 1764.164522 1 0.2542 186 | 0/8 8 h-lim-p 0.0055 10.3815 0.0189 1764.164511 0 0.0082 206 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1764.164511 0 1.0938 226 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1764.164511 0 2.1875 246 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1764.164511 0 1.0938 266 | 0/8 12 h-lim-p 0.5134 20.0000 0.0000 1764.164511 0 2.0538 288 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1764.164511 0 0.1562 311 | 0/8 14 h-lim-p 0.0281 20.0000 0.0000 1764.164511 0 0.0004 336 | 0/8 15 h-lim-p 0.0006 20.0000 0.0000 1764.164511 0 0.0000 361 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 1764.164511 0 0.0000 382 Out... lnL = -1764.164511 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1764.164511 Node 7: lnL = -1764.164511 Node 8: lnL = -1764.164511 Node 9: lnL = -1764.164511 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 232 Sequential format.. Reading seq # 1: YDL123W_Sbay Reading seq # 2: YDL123W_Scer Reading seq # 3: YDL123W_Skud Reading seq # 4: YDL123W_Smik Reading seq # 5: YDL123W_Spar Sequences read.. Counting patterns.. # site patterns = 104 Counting frequencies.. 120 bytes for distance 16640 bytes for lkl0 13312 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.104614 0.018265 0.069904 0.105104 0.077453 0.205686 0.163793 0.175269 lnL0 = -996.985088 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 996.985088 x= 0.10461 0.01827 0.06990 0.10510 0.07745 0.20569 0.16379 0.17527 1 h-lim-p 0.0006 0.0050 75.0019 996.023949 9 0.0004 41 | 0/8 2 h-lim-p 0.0005 0.0043 18.7860 995.930258 3 0.0005 59 | 0/8 3 h-lim-p 0.0019 0.0767 5.3070 995.919427 4 0.0008 78 | 0/8 4 h-lim-p 0.0016 0.0771 2.7839 995.917042 3 0.0008 97 | 0/8 5 h-lim-p 0.0031 0.1904 0.6876 995.916890 2 0.0007 114 | 0/8 6 h-lim-p 0.0062 2.2639 0.0761 995.916886 1 0.0012 137 | 0/8 7 h-lim-p 0.0378 20.0000 0.0025 995.916849 0 0.1510 159 | 0/8 8 h-lim-p 0.0085 1.2747 0.0439 995.916508 0 0.0171 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 995.916492 2 0.9644 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 995.916492 0 1.0938 224 | 0/8 11 h-lim-p 2.0154 20.0000 0.0000 995.916492 0 1.7635 244 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 995.916492 0 1.0938 264 | 0/8 13 h-lim-p 0.4110 20.0000 0.0000 995.916492 0 0.4110 284 | 0/8 14 h-lim-p 0.0135 20.0000 0.0001 995.916492 0 0.0008 307 | 0/8 15 h-lim-p 0.0006 20.0000 0.0001 995.916492 0 0.0000 330 | 0/8 16 h-lim-p 0.0002 20.0000 0.0000 995.916492 0 0.0000 354 | 0/8 17 h-lim-p 0.0004 20.0000 0.0000 995.916492 0 0.0000 388 Out... lnL = -995.916492 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -995.916492 Node 7: lnL = -995.916492 Node 8: lnL = -995.916492 Node 9: lnL = -995.916492 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 402 Sequential format.. Reading seq # 1: YDL126C_Sbay Reading seq # 2: YDL126C_Scer Reading seq # 3: YDL126C_Skud Reading seq # 4: YDL126C_Smik Reading seq # 5: YDL126C_Spar Sequences read.. Counting patterns.. # site patterns = 103 Counting frequencies.. 120 bytes for distance 16480 bytes for lkl0 13184 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.178211 0.138175 0.196826 0.204341 4.361021 0.204757 0.274803 lnL0 = -1343.213092 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1343.213092 x= 0.00006 0.17821 0.13817 0.19683 0.20434 4.36102 0.20476 0.27480 1 h-lim-p 0.0000 0.0000 417.4154 1342.944273 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0006 449.6566 1290.209278 m 0.0006 37 | 1/8 3 h-lim-p 0.0001 0.0012 107.7779 1286.549393 0 0.0006 51 | 1/8 4 h-lim-p 0.0012 0.0095 25.9126 1286.007290 0 0.0018 63 | 1/8 5 h-lim-p 0.0024 0.0191 14.9358 1285.496605 0 0.0036 75 | 1/8 6 h-lim-p 0.0249 0.1994 1.0059 1265.835343 0 0.1496 89 | 1/8 7 h-lim-p 0.0431 0.3448 1.1013 1257.040320 0 0.1293 102 | 0/8 8 h-lim-p 0.0227 0.1819 2.1875 1257.027521 4 0.0056 123 | 0/8 9 h-lim-p 0.1573 5.1748 0.0784 1256.738058 0 0.3146 136 | 0/8 10 h-lim-p 2.2628 20.0000 0.0109 1256.726559 4 0.5635 165 | 0/8 11 h-lim-p 2.5000 20.0000 0.0022 1256.723847 5 0.7338 197 | 0/8 12 h-lim-p 1.7274 20.0000 0.0009 1256.723750 0 0.7558 217 | 0/8 13 h-lim-p 2.5000 20.0000 0.0001 1256.723748 0 1.0938 237 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1256.723748 0 1.0938 257 | 0/8 15 h-lim-p 1.2596 20.0000 0.0000 1256.723748 0 3.7788 278 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1256.723748 0 0.1367 301 | 0/8 17 h-lim-p 0.3246 20.0000 0.0000 1256.723748 0 0.0001 332 Out... lnL = -1256.723748 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1256.723748 Node 7: lnL = -1256.723748 Node 8: lnL = -1256.723748 Node 9: lnL = -1256.723748 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 898 Sequential format.. Reading seq # 1: YDL129W_Sbay Reading seq # 2: YDL129W_Scer Reading seq # 3: YDL129W_Skud Reading seq # 4: YDL129W_Smik Reading seq # 5: YDL129W_Spar Sequences read.. Counting patterns.. # site patterns = 149 Counting frequencies.. 120 bytes for distance 23840 bytes for lkl0 19072 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.084966 0.030306 0.044835 0.074014 0.045179 0.134614 0.114179 0.136415 lnL0 = -2524.134207 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2524.134207 x= 0.08497 0.03031 0.04483 0.07401 0.04518 0.13461 0.11418 0.13642 1 h-lim-p 0.0008 0.0064 172.8681 2522.512749 9 0.0001 47 | 0/8 2 h-lim-p 0.0008 0.0066 21.9943 2522.448363 6 0.0003 74 | 0/8 3 h-lim-p 0.0006 0.0330 9.3535 2522.441194 6 0.0002 103 | 0/8 4 h-lim-p 0.0006 0.0281 2.7325 2522.440542 4 0.0002 126 | 0/8 5 h-lim-p 0.0009 0.2352 0.5966 2522.440489 3 0.0003 145 | 0/8 6 h-lim-p 0.0014 1.0342 0.1336 2522.440487 1 0.0002 169 | 0/8 7 h-lim-p 0.0012 8.4654 0.0184 2522.440487 0 0.0005 189 | 0/8 8 h-lim-p 0.2077 20.0000 0.0000 2522.440482 0 1.2464 211 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2522.440482 0 1.0938 231 | 0/8 10 h-lim-p 1.3170 20.0000 0.0000 2522.440482 0 0.0823 254 | 0/8 11 h-lim-p 0.0410 20.0000 0.0000 2522.440482 0 0.0000 300 | 0/8 12 h-lim-p 0.0000 20.0000 0.0032 | 0/8 13 h-lim-p 0.0000 20.0000 0.0032 Out... lnL = -2522.440482 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2522.440482 Node 7: lnL = -2522.440482 Node 8: lnL = -2522.440482 Node 9: lnL = -2522.440482 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 491 Sequential format.. Reading seq # 1: YDL130W-A_Sbay Reading seq # 2: YDL130W-A_Scer Reading seq # 3: YDL130W-A_Skud Reading seq # 4: YDL130W-A_Smik Reading seq # 5: YDL130W-A_Spar Sequences read.. Counting patterns.. # site patterns = 217 Counting frequencies.. 120 bytes for distance 34720 bytes for lkl0 27776 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.123122 0.089549 0.058548 0.166776 0.086035 0.245823 0.286947 0.222281 lnL0 = -2334.447983 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2334.447983 x= 0.12312 0.08955 0.05855 0.16678 0.08604 0.24582 0.28695 0.22228 1 h-lim-p 0.0005 0.0037 85.2971 2333.133348 3 0.0004 28 | 0/8 2 h-lim-p 0.0012 0.0092 14.1565 2333.085631 5 0.0005 51 | 0/8 3 h-lim-p 0.0009 0.0654 7.4226 2333.075279 5 0.0005 76 | 0/8 4 h-lim-p 0.0012 0.1220 2.8483 2333.071295 2 0.0011 92 | 0/8 5 h-lim-p 0.0078 0.8448 0.4161 2333.071207 3 0.0010 112 | 0/8 6 h-lim-p 0.0394 20.0000 0.0110 2333.071207 0 0.0011 136 | 0/8 7 h-lim-p 0.0057 20.0000 0.0021 2333.071205 0 0.0227 158 | 0/8 8 h-lim-p 0.0069 14.5533 0.0069 2333.071168 0 0.0275 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2333.071167 0 1.0938 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2333.071167 0 1.0938 220 | 0/8 11 h-lim-p 1.1544 20.0000 0.0000 2333.071167 0 2.3087 241 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2333.071167 0 0.5469 262 | 0/8 13 h-lim-p 0.1037 20.0000 0.0000 2333.071167 0 0.1037 282 | 0/8 14 h-lim-p 0.0327 20.0000 0.0000 2333.071167 0 0.0082 303 | 0/8 15 h-lim-p 0.0028 20.0000 0.0001 2333.071167 0 0.0014 323 | 0/8 16 h-lim-p 0.0008 20.0000 0.0002 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 2333.071167 0 0.0000 388 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0002 | 0/8 20 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -2333.071167 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2333.071167 Node 7: lnL = -2333.071167 Node 8: lnL = -2333.071167 Node 9: lnL = -2333.071167 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 681 Sequential format.. Reading seq # 1: YDL131W_Sbay Reading seq # 2: YDL131W_Scer Reading seq # 3: YDL131W_Skud Reading seq # 4: YDL131W_Smik Reading seq # 5: YDL131W_Spar Sequences read.. Counting patterns.. # site patterns = 262 Counting frequencies.. 120 bytes for distance 41920 bytes for lkl0 33536 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.119562 0.050289 0.052942 0.135545 0.128544 0.183964 0.211273 0.202851 lnL0 = -3029.684972 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3029.684972 x= 0.11956 0.05029 0.05294 0.13554 0.12854 0.18396 0.21127 0.20285 1 h-lim-p 0.0059 1.0590 101.1204 3028.806403 6 0.0002 37 | 0/8 2 h-lim-p 0.0015 0.0120 6.2236 3028.799375 2 0.0004 54 | 0/8 3 h-lim-p 0.0015 0.2235 1.4831 3028.798774 3 0.0006 72 | 0/8 4 h-lim-p 0.0029 0.3889 0.2894 3028.798756 2 0.0005 91 | 0/8 5 h-lim-p 0.0017 4.0894 0.0821 3028.798755 0 0.0004 112 | 0/8 6 h-lim-p 0.0026 20.0000 0.0133 3028.798755 0 0.0006 133 | 0/8 7 h-lim-p 0.0243 20.0000 0.0003 3028.798752 0 0.1945 156 | 0/8 8 h-lim-p 0.0016 3.1022 0.0389 3028.798738 0 0.0031 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3028.798737 0 1.0938 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3028.798737 0 1.0938 217 | 0/8 11 h-lim-p 1.0289 20.0000 0.0000 3028.798737 0 0.9003 237 | 0/8 12 h-lim-p 0.2811 20.0000 0.0000 3028.798737 0 0.0038 262 | 0/8 13 h-lim-p 0.0005 20.0000 0.0002 3028.798737 0 0.0000 291 | 0/8 14 h-lim-p 0.0009 20.0000 0.0000 3028.798737 0 0.0000 322 Out... lnL = -3028.798737 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3028.798737 Node 7: lnL = -3028.798737 Node 8: lnL = -3028.798737 Node 9: lnL = -3028.798737 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 579 Sequential format.. Reading seq # 1: YDL132W_Sbay Reading seq # 2: YDL132W_Scer Reading seq # 3: YDL132W_Skud Reading seq # 4: YDL132W_Smik Reading seq # 5: YDL132W_Spar Sequences read.. Counting patterns.. # site patterns = 185 Counting frequencies.. 120 bytes for distance 29600 bytes for lkl0 23680 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.061992 0.067739 0.041937 0.104438 0.070348 0.144538 0.138441 0.121003 lnL0 = -2365.988003 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2365.988003 x= 0.06199 0.06774 0.04194 0.10444 0.07035 0.14454 0.13844 0.12100 1 h-lim-p 0.0056 1.2975 91.9252 2365.187772 7 0.0002 42 | 0/8 2 h-lim-p 0.0003 0.0021 29.7101 2365.084465 2 0.0002 58 | 0/8 3 h-lim-p 0.0010 0.0281 7.2808 2365.077242 6 0.0003 86 | 0/8 4 h-lim-p 0.0014 0.1510 1.5359 2365.076933 2 0.0003 103 | 0/8 5 h-lim-p 0.0014 0.3709 0.3034 2365.076922 2 0.0002 121 | 0/8 6 h-lim-p 0.0011 4.9170 0.0597 2365.076921 0 0.0005 141 | 0/8 7 h-lim-p 0.0086 20.0000 0.0034 2365.076917 0 0.0172 162 | 0/8 8 h-lim-p 0.0023 7.6387 0.0253 2365.076611 0 0.0188 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2365.076608 0 1.0938 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2365.076608 0 1.0938 225 | 0/8 11 h-lim-p 1.3652 20.0000 0.0000 2365.076608 0 0.5973 245 | 0/8 12 h-lim-p 0.1301 20.0000 0.0001 2365.076608 0 0.0003 273 | 0/8 13 h-lim-p 0.0006 20.0000 0.0000 2365.076608 0 0.0000 306 | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -2365.076608 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2365.076608 Node 7: lnL = -2365.076608 Node 8: lnL = -2365.076608 Node 9: lnL = -2365.076608 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 679 Sequential format.. Reading seq # 1: YDL133W_Sbay Reading seq # 2: YDL133W_Scer Reading seq # 3: YDL133W_Skud Reading seq # 4: YDL133W_Smik Reading seq # 5: YDL133W_Spar Sequences read.. Counting patterns.. # site patterns = 305 Counting frequencies.. 120 bytes for distance 48800 bytes for lkl0 39040 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.175802 0.046727 0.066821 0.154718 0.133565 0.248537 0.293486 0.282730 lnL0 = -3392.338198 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3392.338198 x= 0.17580 0.04673 0.06682 0.15472 0.13357 0.24854 0.29349 0.28273 1 h-lim-p 0.0024 0.8782 168.7169 3388.766628 3 0.0003 30 | 0/8 2 h-lim-p 0.0010 0.0082 30.1715 3388.484279 8 0.0006 62 | 0/8 3 h-lim-p 0.0010 0.0180 18.9373 3388.397130 7 0.0006 90 | 0/8 4 h-lim-p 0.0016 0.0467 7.4670 3388.382499 4 0.0006 110 | 0/8 5 h-lim-p 0.0026 0.1169 1.8097 3388.381235 4 0.0008 132 | 0/8 6 h-lim-p 0.0131 2.8932 0.1157 3388.381228 1 0.0008 149 | 0/8 7 h-lim-p 0.0028 12.7583 0.0329 3388.381220 1 0.0036 171 | 0/8 8 h-lim-p 0.0240 20.0000 0.0049 3388.379313 0 0.2877 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3388.379260 2 0.9961 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3388.379260 0 1.0938 238 | 0/8 11 h-lim-p 2.2609 20.0000 0.0000 3388.379260 0 0.9891 258 | 0/8 12 h-lim-p 0.8272 20.0000 0.0000 3388.379260 0 0.1034 280 | 0/8 13 h-lim-p 0.0043 20.0000 0.0001 3388.379260 0 0.0000 309 | 0/8 14 h-lim-p 0.0003 20.0000 0.0000 3388.379260 0 0.0000 341 Out... lnL = -3388.379260 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3388.379260 Node 7: lnL = -3388.379260 Node 8: lnL = -3388.379260 Node 9: lnL = -3388.379260 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 863 Sequential format.. Reading seq # 1: YDL134C_Sbay Reading seq # 2: YDL134C_Scer Reading seq # 3: YDL134C_Skud Reading seq # 4: YDL134C_Smik Reading seq # 5: YDL134C_Spar Sequences read.. Counting patterns.. # site patterns = 273 Counting frequencies.. 120 bytes for distance 43680 bytes for lkl0 34944 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.090989 0.032728 0.073940 0.110800 0.080687 0.185227 0.213900 0.157518 lnL0 = -3718.723715 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3718.723715 x= 0.09099 0.03273 0.07394 0.11080 0.08069 0.18523 0.21390 0.15752 1 h-lim-p 0.0011 0.4096 258.9818 3715.000301 3 0.0001 30 | 0/8 2 h-lim-p 0.0006 0.0050 27.9722 3714.882062 2 0.0003 46 | 0/8 3 h-lim-p 0.0005 0.0152 16.5630 3714.857349 2 0.0002 62 | 0/8 4 h-lim-p 0.0006 0.0449 6.4332 3714.853230 3 0.0002 80 | 0/8 5 h-lim-p 0.0021 0.4594 0.7387 3714.853151 3 0.0003 101 | 0/8 6 h-lim-p 0.0044 2.8456 0.0522 3714.853151 0 0.0002 124 | 0/8 7 h-lim-p 0.0012 20.0000 0.0104 3714.853151 0 0.0011 144 | 0/8 8 h-lim-p 0.0194 20.0000 0.0006 3714.853073 0 0.3106 168 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3714.853071 0 1.0938 188 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3714.853071 0 1.2500 208 | 0/8 11 h-lim-p 1.1019 20.0000 0.0000 3714.853071 0 0.0689 231 | 0/8 12 h-lim-p 0.0321 20.0000 0.0000 3714.853071 0 0.0010 255 | 0/8 13 h-lim-p 0.0001 20.0000 0.0003 3714.853071 0 0.0001 275 | 0/8 14 h-lim-p 0.0009 20.0000 0.0000 3714.853071 0 0.0009 295 | 0/8 15 h-lim-p 0.0007 20.0000 0.0000 3714.853071 0 0.0000 329 | 0/8 16 h-lim-p 0.0000 20.0000 0.0021 3714.853071 0 0.0000 355 | 0/8 17 h-lim-p 0.0000 20.0000 0.0003 3714.853071 0 0.0013 382 | 0/8 18 h-lim-p 0.0041 20.0000 0.0001 3714.853071 0 0.0000 411 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 3714.853071 0 0.0000 432 | 0/8 20 h-lim-p 0.0000 20.0000 0.0000 3714.853071 0 0.0000 457 | 0/8 21 h-lim-p 0.0000 20.0000 0.0014 .. | 0/8 22 h-lim-p 0.0000 20.0000 0.0031 | 0/8 23 h-lim-p 0.0000 20.0000 0.0031 Out... lnL = -3714.853071 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3714.853071 Node 7: lnL = -3714.853071 Node 8: lnL = -3714.853071 Node 9: lnL = -3714.853071 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 415 Sequential format.. Reading seq # 1: YDL135C_Sbay Reading seq # 2: YDL135C_Scer Reading seq # 3: YDL135C_Skud Reading seq # 4: YDL135C_Smik Reading seq # 5: YDL135C_Spar Sequences read.. Counting patterns.. # site patterns = 132 Counting frequencies.. 120 bytes for distance 21120 bytes for lkl0 16896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.055944 0.047411 0.045067 0.071376 0.041553 0.137360 0.181094 0.104595 lnL0 = -1560.379435 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1560.379435 x= 0.05594 0.04741 0.04507 0.07138 0.04155 0.13736 0.18109 0.10459 1 h-lim-p 0.0002 0.0015 113.3978 1559.048133 1 0.0002 24 | 0/8 2 h-lim-p 0.0005 0.0041 20.0488 1559.004032 3 0.0002 42 | 0/8 3 h-lim-p 0.0004 0.0069 11.3834 1558.991964 6 0.0002 70 | 0/8 4 h-lim-p 0.0005 0.0390 5.4499 1558.987421 3 0.0004 88 | 0/8 5 h-lim-p 0.0017 0.2061 1.2360 1558.987118 2 0.0004 105 | 0/8 6 h-lim-p 0.0025 0.6690 0.2150 1558.987110 2 0.0004 124 | 0/8 7 h-lim-p 0.0010 2.1978 0.0884 1558.987108 0 0.0004 144 | 0/8 8 h-lim-p 0.2577 20.0000 0.0001 1558.987071 0 1.0307 166 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1558.987070 0 1.2500 186 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1558.987070 0 2.1875 206 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1558.987070 0 1.0938 226 | 0/8 12 h-lim-p 0.1859 20.0000 0.0000 1558.987070 0 5.9475 251 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1558.987070 0 0.1367 274 | 0/8 14 h-lim-p 0.0797 20.0000 0.0000 1558.987070 0 0.0050 297 | 0/8 15 h-lim-p 0.0014 20.0000 0.0001 1558.987070 0 0.0001 320 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 1558.987070 0 0.0000 358 | 0/8 17 h-lim-p 0.0000 20.0000 0.0026 | 0/8 18 h-lim-p 0.0000 20.0000 0.0026 Out... lnL = -1558.987070 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1558.987070 Node 7: lnL = -1558.987070 Node 8: lnL = -1558.987070 Node 9: lnL = -1558.987070 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 942 Sequential format.. Reading seq # 1: YDL137W_Sbay Reading seq # 2: YDL137W_Scer Reading seq # 3: YDL137W_Skud Reading seq # 4: YDL137W_Smik Reading seq # 5: YDL137W_Spar Sequences read.. Counting patterns.. # site patterns = 297 Counting frequencies.. 120 bytes for distance 47520 bytes for lkl0 38016 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.094975 0.122481 0.072552 0.104366 0.094706 0.200007 0.137823 0.167696 lnL0 = -4035.238827 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4035.238827 x= 0.09497 0.12248 0.07255 0.10437 0.09471 0.20001 0.13782 0.16770 1 h-lim-p 0.0026 0.0206 64.5315 4034.724508 4 0.0003 32 | 0/8 2 h-lim-p 0.0006 0.0051 27.7935 4034.634915 2 0.0003 48 | 0/8 3 h-lim-p 0.0007 0.0286 10.3952 4034.625324 6 0.0002 74 | 0/8 4 h-lim-p 0.0027 0.2838 0.7873 4034.625249 3 0.0002 95 | 0/8 5 h-lim-p 0.0008 0.8310 0.2235 4034.625241 1 0.0003 117 | 0/8 6 h-lim-p 0.0020 5.4020 0.0386 4034.625241 0 0.0004 138 | 0/8 7 h-lim-p 0.0028 20.0000 0.0058 4034.625241 0 0.0025 158 | 0/8 8 h-lim-p 0.0077 20.0000 0.0019 4034.625139 0 0.1224 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4034.625135 0 1.0938 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4034.625135 0 1.0938 222 | 0/8 11 h-lim-p 1.2081 20.0000 0.0000 4034.625135 0 2.4162 243 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4034.625135 0 0.0342 268 | 0/8 13 h-lim-p 0.0057 20.0000 0.0000 4034.625135 0 0.0057 288 | 0/8 14 h-lim-p 0.0025 20.0000 0.0001 4034.625135 0 0.0001 312 | 0/8 15 h-lim-p 0.0002 20.0000 0.0001 4034.625135 0 0.0000 346 | 0/8 16 h-lim-p 0.0000 20.0000 0.0022 | 0/8 17 h-lim-p 0.0000 20.0000 0.0022 Out... lnL = -4034.625135 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4034.625135 Node 7: lnL = -4034.625135 Node 8: lnL = -4034.625135 Node 9: lnL = -4034.625135 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 859 Sequential format.. Reading seq # 1: YDL139C_Sbay Reading seq # 2: YDL139C_Scer Reading seq # 3: YDL139C_Skud Reading seq # 4: YDL139C_Smik Reading seq # 5: YDL139C_Spar Sequences read.. Counting patterns.. # site patterns = 390 Counting frequencies.. 120 bytes for distance 62400 bytes for lkl0 49920 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.248489 0.202359 0.114046 0.157632 0.207340 0.321523 0.336602 0.390783 lnL0 = -4426.958191 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4426.958191 x= 0.24849 0.20236 0.11405 0.15763 0.20734 0.32152 0.33660 0.39078 1 h-lim-p 0.0022 0.0175 71.5473 4425.711463 2 0.0005 27 | 0/8 2 h-lim-p 0.0021 0.0165 16.3237 4425.642001 4 0.0005 48 | 0/8 3 h-lim-p 0.0009 0.0459 9.5689 4425.609571 3 0.0009 66 | 0/8 4 h-lim-p 0.0035 0.1372 2.4989 4425.606542 5 0.0011 92 | 0/8 5 h-lim-p 0.0068 1.1279 0.3959 4425.606447 2 0.0013 109 | 0/8 6 h-lim-p 0.0050 4.2045 0.1036 4425.606436 1 0.0020 131 | 0/8 7 h-lim-p 0.0061 12.8397 0.0338 4425.606435 0 0.0027 151 | 0/8 8 h-lim-p 0.2315 20.0000 0.0004 4425.606322 0 0.9258 173 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4425.606321 0 1.0938 193 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4425.606321 0 1.0938 213 | 0/8 11 h-lim-p 1.4255 20.0000 0.0000 4425.606321 0 0.1782 235 | 0/8 12 h-lim-p 0.0788 20.0000 0.0000 4425.606321 0 0.0394 255 | 0/8 13 h-lim-p 0.0231 20.0000 0.0000 4425.606321 0 0.0231 275 | 0/8 14 h-lim-p 0.0137 20.0000 0.0000 4425.606321 0 0.0137 295 | 0/8 15 h-lim-p 0.0111 20.0000 0.0000 4425.606321 0 0.0000 331 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -4425.606321 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4425.606321 Node 7: lnL = -4425.606321 Node 8: lnL = -4425.606321 Node 9: lnL = -4425.606321 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 498 Sequential format.. Reading seq # 1: YDL142C_Sbay Reading seq # 2: YDL142C_Scer Reading seq # 3: YDL142C_Skud Reading seq # 4: YDL142C_Smik Reading seq # 5: YDL142C_Spar Sequences read.. Counting patterns.. # site patterns = 151 Counting frequencies.. 120 bytes for distance 24160 bytes for lkl0 19328 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.018630 0.044828 0.000060 0.265993 4.649990 0.316906 0.230073 0.268331 lnL0 = -2075.789083 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2075.789083 x= 0.01863 0.04483 0.00006 0.26599 4.64999 0.31691 0.23007 0.26833 1 h-lim-p 0.0000 0.0000 33.9152 2075.782678 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0231 17.8051 2075.696014 0 0.0006 40 | 1/8 3 h-lim-p 0.0010 0.0084 5.4974 2075.686743 4 0.0007 62 | 1/8 4 h-lim-p 0.0052 0.2460 0.7142 2075.684525 5 0.0035 86 | 1/8 5 h-lim-p 0.0138 1.1648 0.1833 2075.523387 0 0.1651 108 | 1/8 6 h-lim-p 0.0018 0.0275 16.5155 2075.290667 0 0.0037 128 | 1/8 7 h-lim-p 1.0008 8.0067 0.0159 2075.264383 2 0.9383 144 | 1/8 8 h-lim-p 2.5000 20.0000 0.0004 2075.264360 1 0.9961 165 | 1/8 9 h-lim-p 2.5000 20.0000 0.0000 2075.264360 0 1.0938 184 | 1/8 10 h-lim-p 0.7343 20.0000 0.0000 2075.264360 0 0.7343 203 | 1/8 11 h-lim-p 0.5430 20.0000 0.0000 2075.264360 0 0.1018 224 | 1/8 12 h-lim-p 0.0344 20.0000 0.0000 2075.264360 0 0.0000 268 | 1/8 13 h-lim-p 0.0000 20.0000 0.0004 | 1/8 14 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -2075.264360 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2075.264360 Node 7: lnL = -2075.264360 Node 8: lnL = -2075.264360 Node 9: lnL = -2075.264360 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 528 Sequential format.. Reading seq # 1: YDL145C_Sbay Reading seq # 2: YDL145C_Scer Reading seq # 3: YDL145C_Skud Reading seq # 4: YDL145C_Smik Reading seq # 5: YDL145C_Spar Sequences read.. Counting patterns.. # site patterns = 141 Counting frequencies.. 120 bytes for distance 22560 bytes for lkl0 18048 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.052001 0.028634 0.051476 0.078826 0.048851 0.111813 0.141698 0.095186 lnL0 = -1935.915965 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1935.915965 x= 0.05200 0.02863 0.05148 0.07883 0.04885 0.11181 0.14170 0.09519 1 h-lim-p 0.0002 0.0016 153.9368 1934.492682 7 0.0001 37 | 0/8 2 h-lim-p 0.0004 0.0032 24.5606 1934.431942 4 0.0002 58 | 0/8 3 h-lim-p 0.0005 0.0285 9.3276 1934.425182 5 0.0002 81 | 0/8 4 h-lim-p 0.0005 0.0579 3.0236 1934.423987 4 0.0003 102 | 0/8 5 h-lim-p 0.0031 0.6850 0.2876 1934.423973 0 0.0003 116 | 0/8 6 h-lim-p 0.0014 2.1676 0.0676 1934.423972 0 0.0003 137 | 0/8 7 h-lim-p 0.0102 20.0000 0.0021 1934.423969 0 0.0203 158 | 0/8 8 h-lim-p 0.0024 3.0419 0.0173 1934.423775 0 0.0147 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1934.423773 0 1.0938 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1934.423773 0 1.2500 220 | 0/8 11 h-lim-p 1.1296 20.0000 0.0000 1934.423773 0 0.2471 241 | 0/8 12 h-lim-p 0.1022 20.0000 0.0000 1934.423773 0 0.0000 284 | 0/8 13 h-lim-p 0.0000 20.0000 0.0021 | 0/8 14 h-lim-p 0.0000 20.0000 0.0021 Out... lnL = -1934.423773 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1934.423773 Node 7: lnL = -1934.423773 Node 8: lnL = -1934.423773 Node 9: lnL = -1934.423773 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 563 Sequential format.. Reading seq # 1: YDL146W_Sbay Reading seq # 2: YDL146W_Scer Reading seq # 3: YDL146W_Skud Reading seq # 4: YDL146W_Smik Reading seq # 5: YDL146W_Spar Sequences read.. Counting patterns.. # site patterns = 213 Counting frequencies.. 120 bytes for distance 34080 bytes for lkl0 27264 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.146275 0.070915 0.032084 0.105622 0.082418 0.220929 0.185561 0.220578 lnL0 = -2437.142706 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2437.142706 x= 0.14628 0.07092 0.03208 0.10562 0.08242 0.22093 0.18556 0.22058 1 h-lim-p 0.0003 0.0027 251.8599 2432.336863 9 0.0002 42 | 0/8 2 h-lim-p 0.0003 0.0022 45.6551 2431.920787 0 0.0004 54 | 0/8 3 h-lim-p 0.0008 0.0148 25.0339 2431.826004 7 0.0004 85 | 0/8 4 h-lim-p 0.0011 0.0296 8.8289 2431.806740 5 0.0006 108 | 0/8 5 h-lim-p 0.0033 0.1310 1.5263 2431.806047 4 0.0006 130 | 0/8 6 h-lim-p 0.0022 0.6871 0.4230 2431.805986 2 0.0007 148 | 0/8 7 h-lim-p 0.0569 20.0000 0.0054 2431.805956 2 0.0439 172 | 0/8 8 h-lim-p 0.0057 5.5396 0.0417 2431.805296 0 0.0227 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 2431.805240 1 1.2500 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2431.805237 1 1.2305 239 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2431.805237 0 1.0938 259 | 0/8 12 h-lim-p 1.6874 20.0000 0.0000 2431.805237 0 0.0527 283 | 0/8 13 h-lim-p 0.0239 20.0000 0.0000 2431.805237 0 0.0000 318 Out... lnL = -2431.805237 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2431.805237 Node 7: lnL = -2431.805237 Node 8: lnL = -2431.805237 Node 9: lnL = -2431.805237 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 376 Sequential format.. Reading seq # 1: YDL147W_Sbay Reading seq # 2: YDL147W_Scer Reading seq # 3: YDL147W_Skud Reading seq # 4: YDL147W_Smik Reading seq # 5: YDL147W_Spar Sequences read.. Counting patterns.. # site patterns = 167 Counting frequencies.. 120 bytes for distance 26720 bytes for lkl0 21376 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.115145 0.014974 0.087759 0.110644 0.101890 0.252214 0.202977 0.190200 lnL0 = -1729.191576 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1729.191576 x= 0.11514 0.01497 0.08776 0.11064 0.10189 0.25221 0.20298 0.19020 1 h-lim-p 0.0017 0.0134 141.3887 1726.762266 7 0.0003 42 | 0/8 2 h-lim-p 0.0017 0.0139 13.2889 1726.684042 4 0.0009 63 | 0/8 3 h-lim-p 0.0018 0.0461 6.6251 1726.673367 6 0.0006 90 | 0/8 4 h-lim-p 0.0018 0.0720 2.1877 1726.672050 4 0.0006 112 | 0/8 5 h-lim-p 0.0039 0.5441 0.3479 1726.671997 2 0.0009 129 | 0/8 6 h-lim-p 0.0065 4.1426 0.0490 1726.671996 1 0.0008 153 | 0/8 7 h-lim-p 0.0029 16.1535 0.0138 1726.671996 0 0.0013 173 | 0/8 8 h-lim-p 0.2069 20.0000 0.0001 1726.671993 0 0.8275 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1726.671993 0 1.0938 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1726.671993 0 1.2500 235 | 0/8 11 h-lim-p 1.1546 20.0000 0.0000 1726.671993 0 0.0068 262 | 0/8 12 h-lim-p 0.0034 20.0000 0.0000 1726.671993 0 0.0034 282 | 0/8 13 h-lim-p 0.0020 20.0000 0.0000 1726.671993 0 0.0002 304 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 1726.671993 0 0.0000 331 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 | 0/8 16 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -1726.671993 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1726.671993 Node 7: lnL = -1726.671993 Node 8: lnL = -1726.671993 Node 9: lnL = -1726.671993 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 298 Sequential format.. Reading seq # 1: YDL154W_Sbay Reading seq # 2: YDL154W_Scer Reading seq # 3: YDL154W_Skud Reading seq # 4: YDL154W_Smik Reading seq # 5: YDL154W_Spar Sequences read.. Counting patterns.. # site patterns = 123 Counting frequencies.. 120 bytes for distance 19680 bytes for lkl0 15744 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.101406 0.063646 0.064812 0.065926 0.070266 0.186195 0.188780 0.166085 lnL0 = -1265.508456 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1265.508456 x= 0.10141 0.06365 0.06481 0.06593 0.07027 0.18619 0.18878 0.16608 1 h-lim-p 0.0003 0.0028 72.2230 1264.333120 0 0.0005 22 | 0/8 2 h-lim-p 0.0015 0.0123 15.7764 1264.228616 7 0.0009 50 | 0/8 3 h-lim-p 0.0016 0.0291 8.8274 1264.216103 5 0.0004 73 | 0/8 4 h-lim-p 0.0008 0.0493 4.4262 1264.211362 4 0.0006 93 | 0/8 5 h-lim-p 0.0057 0.2875 0.4877 1264.211292 3 0.0006 113 | 0/8 6 h-lim-p 0.0015 1.1894 0.1913 1264.211276 3 0.0008 140 | 0/8 7 h-lim-p 0.0171 20.0000 0.0092 1264.211076 0 0.0684 162 | 0/8 8 h-lim-p 0.0053 1.1346 0.1184 1264.208590 0 0.0212 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 1264.208352 3 0.9961 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1264.208352 0 1.0938 230 | 0/8 11 h-lim-p 1.6789 20.0000 0.0000 1264.208352 0 0.0004 261 Out... lnL = -1264.208352 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1264.208352 Node 7: lnL = -1264.208352 Node 8: lnL = -1264.208352 Node 9: lnL = -1264.208352 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 317 Sequential format.. Reading seq # 1: YDL155W_Sbay Reading seq # 2: YDL155W_Scer Reading seq # 3: YDL155W_Skud Reading seq # 4: YDL155W_Smik Reading seq # 5: YDL155W_Spar Sequences read.. Counting patterns.. # site patterns = 95 Counting frequencies.. 120 bytes for distance 15200 bytes for lkl0 12160 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.057884 0.012961 0.040517 0.064003 0.042100 0.113078 0.088815 0.093836 lnL0 = -1053.804944 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1053.804944 x= 0.05788 0.01296 0.04052 0.06400 0.04210 0.11308 0.08881 0.09384 1 h-lim-p 0.0008 0.0062 116.6158 1053.168015 8 0.0001 44 | 0/8 2 h-lim-p 0.0004 0.0031 15.6927 1053.134143 7 0.0003 72 | 0/8 3 h-lim-p 0.0009 0.0614 4.9706 1053.129810 5 0.0004 93 | 0/8 4 h-lim-p 0.0020 0.1392 0.9409 1053.129658 3 0.0004 113 | 0/8 5 h-lim-p 0.0017 0.6958 0.1971 1053.129652 2 0.0003 138 | 0/8 6 h-lim-p 0.0034 17.7335 0.0194 1053.129652 0 0.0002 161 | 0/8 7 h-lim-p 0.0013 20.0000 0.0027 1053.129652 0 0.0027 182 | 0/8 8 h-lim-p 0.0135 20.0000 0.0005 1053.129624 0 0.2159 206 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1053.129623 0 1.0938 226 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1053.129623 0 2.1875 246 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1053.129623 0 1.0938 266 | 0/8 12 h-lim-p 0.3500 20.0000 0.0000 1053.129623 0 5.6007 290 | 0/8 13 h-lim-p 1.8433 20.0000 0.0000 1053.129623 0 0.4032 311 | 0/8 14 h-lim-p 2.1285 20.0000 0.0000 1053.129623 0 0.0003 343 Out... lnL = -1053.129623 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1053.129623 Node 7: lnL = -1053.129623 Node 8: lnL = -1053.129623 Node 9: lnL = -1053.129623 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 359 Sequential format.. Reading seq # 1: YDL156W_Sbay Reading seq # 2: YDL156W_Scer Reading seq # 3: YDL156W_Skud Reading seq # 4: YDL156W_Smik Reading seq # 5: YDL156W_Spar Sequences read.. Counting patterns.. # site patterns = 145 Counting frequencies.. 120 bytes for distance 23200 bytes for lkl0 18560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.072569 0.041610 0.024401 0.108731 0.087043 0.236718 0.201549 0.135217 lnL0 = -1510.935154 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1510.935154 x= 0.07257 0.04161 0.02440 0.10873 0.08704 0.23672 0.20155 0.13522 1 h-lim-p 0.0008 0.0065 93.4634 1510.210464 3 0.0002 29 | 0/8 2 h-lim-p 0.0008 0.0060 20.1848 1510.118286 6 0.0005 57 | 0/8 3 h-lim-p 0.0016 0.0396 6.0522 1510.108726 5 0.0006 81 | 0/8 4 h-lim-p 0.0012 0.0820 2.7641 1510.106652 4 0.0007 102 | 0/8 5 h-lim-p 0.0079 0.5036 0.2303 1510.106639 0 0.0005 117 | 0/8 6 h-lim-p 0.0025 13.5907 0.0451 1510.106636 2 0.0016 142 | 0/8 7 h-lim-p 0.0042 5.7837 0.0171 1510.106628 0 0.0063 162 | 0/8 8 h-lim-p 0.0133 5.1319 0.0082 1510.105768 0 0.0798 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1510.105764 1 0.9961 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1510.105764 0 1.2500 226 | 0/8 11 h-lim-p 1.4690 20.0000 0.0000 1510.105764 0 0.3213 247 | 0/8 12 h-lim-p 0.1412 20.0000 0.0000 1510.105764 0 0.0177 269 | 0/8 13 h-lim-p 0.0085 20.0000 0.0000 1510.105764 0 0.0000 311 | 0/8 14 h-lim-p 0.0000 20.0000 0.0007 | 0/8 15 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -1510.105764 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1510.105764 Node 7: lnL = -1510.105764 Node 8: lnL = -1510.105764 Node 9: lnL = -1510.105764 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 358 Sequential format.. Reading seq # 1: YDL157C_Sbay Reading seq # 2: YDL157C_Scer Reading seq # 3: YDL157C_Skud Reading seq # 4: YDL157C_Smik Reading seq # 5: YDL157C_Spar Sequences read.. Counting patterns.. # site patterns = 150 Counting frequencies.. 120 bytes for distance 24000 bytes for lkl0 19200 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.072775 0.054199 0.019419 0.110566 0.085208 0.248325 0.184522 0.135879 lnL0 = -1517.107746 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1517.107746 x= 0.07277 0.05420 0.01942 0.11057 0.08521 0.24832 0.18452 0.13588 1 h-lim-p 0.0004 0.0031 84.3301 1516.275736 5 0.0003 34 | 0/8 2 h-lim-p 0.0002 0.0019 38.5241 1515.993874 0 0.0005 47 | 0/8 3 h-lim-p 0.0010 0.0077 15.0879 1515.941176 7 0.0006 78 | 0/8 4 h-lim-p 0.0012 0.0403 7.1897 1515.928233 6 0.0006 103 | 0/8 5 h-lim-p 0.0032 0.1944 1.4138 1515.927476 3 0.0008 122 | 0/8 6 h-lim-p 0.0024 0.4503 0.4587 1515.927413 3 0.0007 141 | 0/8 7 h-lim-p 0.0048 1.9960 0.0625 1515.927409 0 0.0012 162 | 0/8 8 h-lim-p 0.0270 20.0000 0.0028 1515.925665 0 0.4324 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1515.925579 2 0.9961 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1515.925579 0 1.0938 230 | 0/8 11 h-lim-p 1.5797 20.0000 0.0000 1515.925579 0 1.3822 250 | 0/8 12 h-lim-p 1.2481 20.0000 0.0000 1515.925579 0 1.0921 270 | 0/8 13 h-lim-p 0.1030 20.0000 0.0001 1515.925579 0 0.0129 292 | 0/8 14 h-lim-p 0.0036 20.0000 0.0003 1515.925579 0 0.0000 331 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1515.925579 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1515.925579 Node 7: lnL = -1515.925579 Node 8: lnL = -1515.925579 Node 9: lnL = -1515.925579 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 255 Sequential format.. Reading seq # 1: YDL160C_Sbay Reading seq # 2: YDL160C_Scer Reading seq # 3: YDL160C_Skud Reading seq # 4: YDL160C_Smik Reading seq # 5: YDL160C_Spar Sequences read.. Counting patterns.. # site patterns = 66 Counting frequencies.. 120 bytes for distance 10560 bytes for lkl0 8448 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.055476 0.025862 0.020928 0.032177 0.019792 0.046726 0.090085 0.079043 lnL0 = -759.013822 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 759.013822 x= 0.05548 0.02586 0.02093 0.03218 0.01979 0.04673 0.09009 0.07904 1 h-lim-p 0.0001 0.0010 75.9466 758.725189 3 0.0001 28 | 0/8 2 h-lim-p 0.0003 0.0023 19.7937 758.693994 7 0.0002 58 | 0/8 3 h-lim-p 0.0003 0.0114 10.1553 758.682622 5 0.0003 81 | 0/8 4 h-lim-p 0.0009 0.0161 3.1067 758.681915 5 0.0002 105 | 0/8 5 h-lim-p 0.0006 0.1554 0.9320 758.681839 3 0.0002 125 | 0/8 6 h-lim-p 0.0004 0.2167 0.4514 758.681817 3 0.0003 153 | 0/8 7 h-lim-p 0.0043 1.7452 0.0277 758.681817 1 0.0005 177 | 0/8 8 h-lim-p 0.0162 20.0000 0.0009 758.681143 0 0.5191 202 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 758.681129 2 0.9644 226 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 758.681129 0 0.5469 247 | 0/8 11 h-lim-p 0.3899 20.0000 0.0000 758.681129 0 0.0000 287 Out... lnL = -758.681129 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -758.681129 Node 7: lnL = -758.681129 Node 8: lnL = -758.681129 Node 9: lnL = -758.681129 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 478 Sequential format.. Reading seq # 1: YDL161W_Sbay Reading seq # 2: YDL161W_Scer Reading seq # 3: YDL161W_Skud Reading seq # 4: YDL161W_Smik Reading seq # 5: YDL161W_Spar Sequences read.. Counting patterns.. # site patterns = 220 Counting frequencies.. 120 bytes for distance 35200 bytes for lkl0 28160 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.138411 0.044073 0.052312 0.148729 0.138184 0.245771 0.297100 0.218122 lnL0 = -2284.374106 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2284.374106 x= 0.13841 0.04407 0.05231 0.14873 0.13818 0.24577 0.29710 0.21812 1 h-lim-p 0.0026 0.0210 85.2236 2283.063658 6 0.0004 38 | 0/8 2 h-lim-p 0.0006 0.0052 31.9065 2282.538405 0 0.0013 51 | 0/8 3 h-lim-p 0.0023 0.0184 17.3400 2282.462955 7 0.0006 81 | 0/8 4 h-lim-p 0.0023 0.0819 4.8868 2282.453041 5 0.0009 102 | 0/8 5 h-lim-p 0.0026 0.2225 1.7656 2282.452165 2 0.0006 119 | 0/8 6 h-lim-p 0.0031 0.7248 0.3592 2282.452091 3 0.0010 139 | 0/8 7 h-lim-p 0.0042 4.1640 0.0854 2282.451992 2 0.0045 163 | 0/8 8 h-lim-p 0.0083 5.0292 0.0457 2282.439484 0 0.1331 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0010 2282.439092 3 1.0449 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2282.439091 0 1.0938 233 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2282.439091 0 1.0938 253 | 0/8 12 h-lim-p 1.4059 20.0000 0.0000 2282.439091 0 2.8117 274 | 0/8 13 h-lim-p 1.8011 20.0000 0.0000 2282.439091 0 0.9006 294 | 0/8 14 h-lim-p 0.0474 20.0000 0.0001 2282.439091 0 0.0474 314 | 0/8 15 h-lim-p 0.0140 20.0000 0.0004 2282.439091 0 0.0000 356 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 2282.439091 0 0.0000 386 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -2282.439091 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2282.439091 Node 7: lnL = -2282.439091 Node 8: lnL = -2282.439091 Node 9: lnL = -2282.439091 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 107 Sequential format.. Reading seq # 1: YDL164C_Sbay Reading seq # 2: YDL164C_Scer Reading seq # 3: YDL164C_Skud Reading seq # 4: YDL164C_Smik Reading seq # 5: YDL164C_Spar Sequences read.. Counting patterns.. # site patterns = 45 Counting frequencies.. 120 bytes for distance 7200 bytes for lkl0 5760 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.104392 0.205699 0.140460 0.095232 4.588250 0.187086 0.224600 lnL0 = -414.827949 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 414.827949 x= 0.00006 0.10439 0.20570 0.14046 0.09523 4.58825 0.18709 0.22460 1 h-lim-p 0.0000 0.0000 21.7787 414.820197 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0337 7.9143 414.766570 0 0.0028 40 | 1/8 3 h-lim-p 0.0124 0.2158 1.7856 414.754409 2 0.0058 56 | 1/8 4 h-lim-p 0.0273 0.6021 0.3803 414.711768 0 0.0545 69 | 1/8 5 h-lim-p 0.0223 0.2293 0.9286 414.256864 0 0.0446 89 | 1/8 6 h-lim-p 0.0071 0.0566 3.9283 414.234118 5 0.0028 117 | 1/8 7 h-lim-p 1.2323 20.0000 0.0090 414.224987 6 0.7961 143 | 0/8 8 h-lim-p 0.0928 8.0105 0.0774 414.224973 2 0.0054 169 | 0/8 9 h-lim-p 0.8959 20.0000 0.0005 414.224944 2 0.7804 193 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 414.224944 0 1.0938 213 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 414.224944 0 1.0938 233 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 414.224944 0 1.0938 253 | 0/8 13 h-lim-p 1.2564 20.0000 0.0000 414.224944 0 1.0994 273 | 0/8 14 h-lim-p 0.3878 20.0000 0.0000 414.224944 0 0.0106 297 | 0/8 15 h-lim-p 0.0017 20.0000 0.0000 414.224944 0 0.0000 327 | 0/8 16 h-lim-p 0.0002 20.0000 0.0000 414.224944 0 0.0000 350 Out... lnL = -414.224944 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -414.224944 Node 7: lnL = -414.224944 Node 8: lnL = -414.224944 Node 9: lnL = -414.224944 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 260 Sequential format.. Reading seq # 1: YDL165W_Sbay Reading seq # 2: YDL165W_Scer Reading seq # 3: YDL165W_Skud Reading seq # 4: YDL165W_Smik Reading seq # 5: YDL165W_Spar Sequences read.. Counting patterns.. # site patterns = 129 Counting frequencies.. 120 bytes for distance 20640 bytes for lkl0 16512 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.159340 0.046942 0.050246 0.156435 0.101288 0.188383 0.241915 0.232764 lnL0 = -1212.643767 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1212.643767 x= 0.15934 0.04694 0.05025 0.15644 0.10129 0.18838 0.24191 0.23276 1 h-lim-p 0.0008 0.0062 55.5436 1211.860917 7 0.0005 37 | 0/8 2 h-lim-p 0.0014 0.0111 17.9455 1211.733202 8 0.0009 72 | 0/8 3 h-lim-p 0.0016 0.0326 9.4968 1211.701733 6 0.0009 98 | 0/8 4 h-lim-p 0.0030 0.1202 2.8379 1211.697808 5 0.0011 122 | 0/8 5 h-lim-p 0.0038 0.2034 0.8265 1211.697433 4 0.0012 144 | 0/8 6 h-lim-p 0.0042 1.2749 0.2384 1211.697398 2 0.0014 170 | 0/8 7 h-lim-p 0.0076 6.5827 0.0431 1211.697397 1 0.0015 193 | 0/8 8 h-lim-p 0.1743 20.0000 0.0004 1211.697302 0 1.3941 216 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1211.697294 1 0.9961 238 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1211.697294 0 0.5469 259 | 0/8 11 h-lim-p 0.4133 20.0000 0.0000 1211.697294 0 0.0065 284 | 0/8 12 h-lim-p 0.0038 20.0000 0.0000 1211.697294 0 0.0000 321 Out... lnL = -1211.697294 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1211.697294 Node 7: lnL = -1211.697294 Node 8: lnL = -1211.697294 Node 9: lnL = -1211.697294 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 852 Sequential format.. Reading seq # 1: YDL169C_Sbay Reading seq # 2: YDL169C_Scer Reading seq # 3: YDL169C_Skud Reading seq # 4: YDL169C_Smik Reading seq # 5: YDL169C_Spar Sequences read.. Counting patterns.. # site patterns = 390 Counting frequencies.. 120 bytes for distance 62400 bytes for lkl0 49920 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.174961 0.000060 0.551639 0.198964 0.148659 0.247650 0.376120 0.296692 lnL0 = -4243.551242 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4243.551242 x= 0.17496 0.00006 0.55164 0.19896 0.14866 0.24765 0.37612 0.29669 1 h-lim-p 0.0000 0.0000 136.3051 4243.474746 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0128 46.7832 4242.641792 0 0.0008 40 | 1/8 3 h-lim-p 0.0013 0.2573 28.0626 4242.516426 6 0.0004 68 | 1/8 4 h-lim-p 0.0018 0.1471 6.6157 4242.423467 0 0.0035 81 | 1/8 5 h-lim-p 0.0187 0.2307 1.2447 4241.986676 0 0.0281 93 | 1/8 6 h-lim-p 0.0053 0.0558 6.6068 4237.035519 0 0.0159 106 | 1/8 7 h-lim-p 0.0031 0.0247 30.7186 4234.894986 7 0.0026 134 | 1/8 8 h-lim-p 2.5000 20.0000 0.0214 4234.751602 8 0.7611 169 | 0/8 9 h-lim-p 0.0010 0.0373 15.6270 4234.691281 7 0.0007 206 | 0/8 10 h-lim-p 1.6223 20.0000 0.0067 4234.665319 5 1.3085 227 | 0/8 11 h-lim-p 2.5000 20.0000 0.0014 4234.664802 2 1.1719 251 | 0/8 12 h-lim-p 2.5000 20.0000 0.0001 4234.664798 0 1.0938 271 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 4234.664798 0 1.0938 291 | 0/8 14 h-lim-p 1.9059 20.0000 0.0000 4234.664798 0 1.6677 311 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 4234.664798 0 1.0938 331 | 0/8 16 h-lim-p 0.4119 20.0000 0.0000 4234.664798 0 0.2059 351 | 0/8 17 h-lim-p 0.0095 20.0000 0.0002 4234.664798 0 0.0071 371 | 0/8 18 h-lim-p 0.0028 20.0000 0.0006 4234.664798 0 0.0028 391 | 0/8 19 h-lim-p 0.0002 15.8826 0.0100 4234.664798 0 0.0000 415 | 0/8 20 h-lim-p 0.0004 20.0000 0.0001 4234.664798 0 0.0000 452 | 0/8 21 h-lim-p 0.0000 20.0000 0.0000 4234.664798 0 0.0000 480 | 0/8 22 h-lim-p 0.0000 20.0000 0.0000 | 0/8 23 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -4234.664798 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4234.664798 Node 7: lnL = -4234.664798 Node 8: lnL = -4234.664798 Node 9: lnL = -4234.664798 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 747 Sequential format.. Reading seq # 1: YDL170W_Sbay Reading seq # 2: YDL170W_Scer Reading seq # 3: YDL170W_Skud Reading seq # 4: YDL170W_Smik Reading seq # 5: YDL170W_Spar Sequences read.. Counting patterns.. # site patterns = 176 Counting frequencies.. 120 bytes for distance 28160 bytes for lkl0 22528 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.071804 0.043987 0.041659 0.043601 0.031698 0.104587 0.113456 0.107826 lnL0 = -2595.991417 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2595.991417 x= 0.07180 0.04399 0.04166 0.04360 0.03170 0.10459 0.11346 0.10783 1 h-lim-p 0.0005 0.0037 169.7528 2594.372012 5 0.0001 33 | 0/8 2 h-lim-p 0.0002 0.0016 43.0515 2594.237214 5 0.0002 55 | 0/8 3 h-lim-p 0.0003 0.0045 20.7392 2594.213097 4 0.0001 74 | 0/8 4 h-lim-p 0.0004 0.0328 6.9483 2594.211706 4 0.0001 97 | 0/8 5 h-lim-p 0.0004 0.0640 1.0639 2594.211642 3 0.0001 116 | 0/8 6 h-lim-p 0.0002 0.2805 0.5435 2594.211624 2 0.0001 133 | 0/8 7 h-lim-p 0.0051 19.6584 0.0151 2594.211624 0 0.0003 156 | 0/8 8 h-lim-p 0.0849 20.0000 0.0001 2594.211616 0 1.3588 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2594.211615 0 1.0938 200 | 0/8 10 h-lim-p 1.2025 20.0000 0.0000 2594.211615 0 0.2630 221 | 0/8 11 h-lim-p 0.1503 20.0000 0.0000 2594.211615 0 0.0047 245 | 0/8 12 h-lim-p 0.0030 20.0000 0.0000 2594.211615 0 0.0000 274 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 2594.211615 0 0.0000 295 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 2594.211615 0 0.0000 327 Out... lnL = -2594.211615 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2594.211615 Node 7: lnL = -2594.211615 Node 8: lnL = -2594.211615 Node 9: lnL = -2594.211615 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 688 Sequential format.. Reading seq # 1: YDL173W_Sbay Reading seq # 2: YDL173W_Scer Reading seq # 3: YDL173W_Skud Reading seq # 4: YDL173W_Smik Reading seq # 5: YDL173W_Spar Sequences read.. Counting patterns.. # site patterns = 242 Counting frequencies.. 120 bytes for distance 38720 bytes for lkl0 30976 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.147033 0.033934 0.050298 0.113688 0.086440 0.201697 0.185120 0.211211 lnL0 = -2901.280131 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2901.280131 x= 0.14703 0.03393 0.05030 0.11369 0.08644 0.20170 0.18512 0.21121 1 h-lim-p 0.0017 0.7725 186.7941 2898.557545 3 0.0002 30 | 0/8 2 h-lim-p 0.0011 0.0098 30.8118 2898.292339 7 0.0006 57 | 0/8 3 h-lim-p 0.0014 0.0177 12.4385 2898.273819 4 0.0003 78 | 0/8 4 h-lim-p 0.0013 0.0493 2.5667 2898.272895 2 0.0003 95 | 0/8 5 h-lim-p 0.0015 0.6206 0.4945 2898.272822 1 0.0006 109 | 0/8 6 h-lim-p 0.0095 9.2081 0.0312 2898.272821 0 0.0010 131 | 0/8 7 h-lim-p 0.0019 10.0885 0.0174 2898.272819 0 0.0028 151 | 0/8 8 h-lim-p 0.0119 20.0000 0.0041 2898.272305 0 0.1429 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2898.272288 1 0.9961 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2898.272288 0 2.1875 216 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2898.272288 0 1.0938 236 | 0/8 12 h-lim-p 0.3236 20.0000 0.0000 2898.272288 0 5.1770 260 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2898.272288 0 0.0586 285 | 0/8 14 h-lim-p 0.3152 20.0000 0.0000 2898.272288 0 0.0099 309 | 0/8 15 h-lim-p 0.0025 20.0000 0.0000 2898.272288 0 0.0000 349 Out... lnL = -2898.272288 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2898.272288 Node 7: lnL = -2898.272288 Node 8: lnL = -2898.272288 Node 9: lnL = -2898.272288 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 336 Sequential format.. Reading seq # 1: YDL175C_Sbay Reading seq # 2: YDL175C_Scer Reading seq # 3: YDL175C_Skud Reading seq # 4: YDL175C_Smik Reading seq # 5: YDL175C_Spar Sequences read.. Counting patterns.. # site patterns = 183 Counting frequencies.. 120 bytes for distance 29280 bytes for lkl0 23424 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.150722 0.247962 0.137389 0.173980 0.127537 0.294400 0.280684 0.262599 lnL0 = -1721.989276 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1721.989276 x= 0.15072 0.24796 0.13739 0.17398 0.12754 0.29440 0.28068 0.26260 1 h-lim-p 0.0045 0.0363 14.6271 1721.824849 6 0.0016 38 | 0/8 2 h-lim-p 0.0022 0.0264 10.3062 1721.773361 5 0.0013 63 | 0/8 3 h-lim-p 0.0026 0.0823 5.2359 1721.757620 6 0.0016 91 | 0/8 4 h-lim-p 0.0072 0.4127 1.1228 1721.756265 4 0.0023 113 | 0/8 5 h-lim-p 0.0063 0.7661 0.4162 1721.756103 4 0.0021 136 | 0/8 6 h-lim-p 0.0170 6.6337 0.0518 1721.756101 0 0.0019 158 | 0/8 7 h-lim-p 0.0056 20.0000 0.0172 1721.756101 0 0.0025 178 | 0/8 8 h-lim-p 0.3101 20.0000 0.0001 1721.756092 0 1.2403 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1721.756091 0 1.0938 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1721.756091 0 1.0938 240 | 0/8 11 h-lim-p 2.2374 20.0000 0.0000 1721.756091 0 0.4894 261 | 0/8 12 h-lim-p 0.2948 20.0000 0.0000 1721.756091 0 0.0276 284 | 0/8 13 h-lim-p 0.0142 20.0000 0.0000 1721.756091 0 0.0071 304 | 0/8 14 h-lim-p 0.0054 20.0000 0.0000 1721.756091 0 0.0001 329 Out... lnL = -1721.756091 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1721.756091 Node 7: lnL = -1721.756091 Node 8: lnL = -1721.756091 Node 9: lnL = -1721.756091 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 390 Sequential format.. Reading seq # 1: YDL176W_Sbay Reading seq # 2: YDL176W_Scer Reading seq # 3: YDL176W_Skud Reading seq # 4: YDL176W_Smik Reading seq # 5: YDL176W_Spar Sequences read.. Counting patterns.. # site patterns = 134 Counting frequencies.. 120 bytes for distance 21440 bytes for lkl0 17152 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.074087 0.024403 0.037933 0.076078 0.090760 0.159684 0.149138 0.119788 lnL0 = -1539.084512 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1539.084512 x= 0.07409 0.02440 0.03793 0.07608 0.09076 0.15968 0.14914 0.11979 1 h-lim-p 0.0015 0.1404 141.5591 1537.703263 3 0.0002 30 | 0/8 2 h-lim-p 0.0007 0.0056 14.4859 1537.672085 6 0.0003 57 | 0/8 3 h-lim-p 0.0009 0.0450 4.8822 1537.667675 2 0.0004 73 | 0/8 4 h-lim-p 0.0014 0.1351 1.4618 1537.667301 4 0.0004 95 | 0/8 5 h-lim-p 0.0022 0.4825 0.2645 1537.667292 2 0.0003 113 | 0/8 6 h-lim-p 0.0044 14.3956 0.0160 1537.667292 0 0.0005 135 | 0/8 7 h-lim-p 0.0023 20.0000 0.0038 1537.667292 0 0.0006 156 | 0/8 8 h-lim-p 0.0718 20.0000 0.0000 1537.667291 0 1.1485 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1537.667291 0 1.0938 200 | 0/8 10 h-lim-p 1.1415 20.0000 0.0000 1537.667291 0 0.4994 220 | 0/8 11 h-lim-p 0.3100 20.0000 0.0000 1537.667291 0 0.0000 254 | 0/8 12 h-lim-p 0.0000 20.0000 0.0000 1537.667291 0 0.0000 277 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 1537.667291 0 0.0000 306 Out... lnL = -1537.667291 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1537.667291 Node 7: lnL = -1537.667291 Node 8: lnL = -1537.667291 Node 9: lnL = -1537.667291 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 385 Sequential format.. Reading seq # 1: YDL177C_Sbay Reading seq # 2: YDL177C_Scer Reading seq # 3: YDL177C_Skud Reading seq # 4: YDL177C_Smik Reading seq # 5: YDL177C_Spar Sequences read.. Counting patterns.. # site patterns = 150 Counting frequencies.. 120 bytes for distance 24000 bytes for lkl0 19200 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.073456 0.028579 0.032441 0.090186 0.043852 0.158772 0.165165 0.117824 lnL0 = -1502.960920 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1502.960920 x= 0.07346 0.02858 0.03244 0.09019 0.04385 0.15877 0.16516 0.11782 1 h-lim-p 0.0004 0.0033 200.1800 1499.572949 3 0.0002 29 | 0/8 2 h-lim-p 0.0003 0.0020 46.2043 1499.174243 0 0.0004 41 | 0/8 3 h-lim-p 0.0022 0.0302 7.8188 1499.157794 4 0.0006 62 | 0/8 4 h-lim-p 0.0012 0.0386 3.5413 1499.155404 5 0.0004 85 | 0/8 5 h-lim-p 0.0027 0.4034 0.5842 1499.155345 2 0.0004 103 | 0/8 6 h-lim-p 0.0014 0.5875 0.1478 1499.155338 1 0.0006 125 | 0/8 7 h-lim-p 0.0023 5.1296 0.0392 1499.155332 0 0.0020 145 | 0/8 8 h-lim-p 0.0223 20.0000 0.0036 1499.152704 0 0.3568 169 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1499.152672 3 0.8800 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1499.152671 0 1.0938 216 | 0/8 11 h-lim-p 1.6442 20.0000 0.0000 1499.152671 0 0.3597 237 | 0/8 12 h-lim-p 0.2058 20.0000 0.0000 1499.152671 0 0.0032 262 | 0/8 13 h-lim-p 0.0020 20.0000 0.0000 1499.152671 0 0.0015 282 | 0/8 14 h-lim-p 0.0010 20.0000 0.0000 1499.152671 0 0.0000 307 | 0/8 15 h-lim-p 0.0006 20.0000 0.0000 1499.152671 0 0.0000 345 Out... lnL = -1499.152671 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1499.152671 Node 7: lnL = -1499.152671 Node 8: lnL = -1499.152671 Node 9: lnL = -1499.152671 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 813 Sequential format.. Reading seq # 1: YDL179W_Sbay Reading seq # 2: YDL179W_Scer Reading seq # 3: YDL179W_Skud Reading seq # 4: YDL179W_Smik Reading seq # 5: YDL179W_Spar Sequences read.. Counting patterns.. # site patterns = 357 Counting frequencies.. 120 bytes for distance 57120 bytes for lkl0 45696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.103727 0.039100 0.071686 0.225108 0.224124 0.225100 0.225759 0.184874 lnL0 = -3800.007581 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3800.007581 x= 0.10373 0.03910 0.07169 0.22511 0.22412 0.22510 0.22576 0.18487 1 h-lim-p 0.0008 0.0062 165.6655 3796.852780 5 0.0003 34 | 0/8 2 h-lim-p 0.0004 0.0033 43.4089 3796.472770 3 0.0004 52 | 0/8 3 h-lim-p 0.0013 0.0229 14.6545 3796.413802 4 0.0006 72 | 0/8 4 h-lim-p 0.0052 0.1774 1.7320 3796.412938 2 0.0006 90 | 0/8 5 h-lim-p 0.0052 0.9639 0.1920 3796.412929 1 0.0005 106 | 0/8 6 h-lim-p 0.0108 20.0000 0.0091 3796.412929 0 0.0047 126 | 0/8 7 h-lim-p 0.0430 20.0000 0.0010 3796.412817 0 0.3439 149 | 0/8 8 h-lim-p 0.0019 1.4376 0.1773 3796.412799 0 0.0009 169 | 0/8 9 h-lim-p 2.0289 20.0000 0.0001 3796.412795 0 1.0145 189 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3796.412795 0 1.0938 209 | 0/8 11 h-lim-p 1.0685 20.0000 0.0000 3796.412795 0 0.2671 230 | 0/8 12 h-lim-p 0.0516 20.0000 0.0001 3796.412795 0 0.0000 270 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 3796.412795 0 0.0000 301 Out... lnL = -3796.412795 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3796.412795 Node 7: lnL = -3796.412795 Node 8: lnL = -3796.412795 Node 9: lnL = -3796.412795 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 509 Sequential format.. Reading seq # 1: YDL180W_Sbay Reading seq # 2: YDL180W_Scer Reading seq # 3: YDL180W_Skud Reading seq # 4: YDL180W_Smik Reading seq # 5: YDL180W_Spar Sequences read.. Counting patterns.. # site patterns = 148 Counting frequencies.. 120 bytes for distance 23680 bytes for lkl0 18944 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.078690 0.037254 0.049744 0.071719 0.045881 0.074295 0.155648 0.119172 lnL0 = -1836.217306 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1836.217306 x= 0.07869 0.03725 0.04974 0.07172 0.04588 0.07429 0.15565 0.11917 1 h-lim-p 0.0002 0.0016 123.3482 1835.048575 7 0.0002 38 | 0/8 2 h-lim-p 0.0010 0.0077 20.3525 1834.981683 7 0.0003 68 | 0/8 3 h-lim-p 0.0008 0.0201 7.9445 1834.974012 4 0.0003 90 | 0/8 4 h-lim-p 0.0006 0.1499 3.7637 1834.972851 5 0.0002 116 | 0/8 5 h-lim-p 0.0004 0.0950 1.8852 1834.972511 4 0.0003 140 | 0/8 6 h-lim-p 0.0020 0.4086 0.2382 1834.972504 1 0.0002 156 | 0/8 7 h-lim-p 0.0034 5.4887 0.0171 1834.972504 0 0.0004 178 | 0/8 8 h-lim-p 0.1187 20.0000 0.0001 1834.972496 0 0.9492 201 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1834.972496 0 1.0938 221 | 0/8 10 h-lim-p 1.3631 20.0000 0.0000 1834.972496 0 1.1927 241 | 0/8 11 h-lim-p 1.5115 20.0000 0.0000 1834.972496 0 1.5115 261 | 0/8 12 h-lim-p 1.0433 20.0000 0.0000 1834.972496 0 0.0020 289 | 0/8 13 h-lim-p 0.0004 20.0000 0.0001 1834.972496 0 0.0000 322 | 0/8 14 h-lim-p 0.0000 20.0000 0.0005 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -1834.972496 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1834.972496 Node 7: lnL = -1834.972496 Node 8: lnL = -1834.972496 Node 9: lnL = -1834.972496 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 519 Sequential format.. Reading seq # 1: YDL181W_Sbay Reading seq # 2: YDL181W_Scer Reading seq # 3: YDL181W_Skud Reading seq # 4: YDL181W_Smik Reading seq # 5: YDL181W_Spar Sequences read.. Counting patterns.. # site patterns = 163 Counting frequencies.. 120 bytes for distance 26080 bytes for lkl0 20864 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.086250 0.056334 0.050654 0.088266 0.056911 0.144194 0.125053 0.133866 lnL0 = -1970.851764 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1970.851764 x= 0.08625 0.05633 0.05065 0.08827 0.05691 0.14419 0.12505 0.13387 1 h-lim-p 0.0020 0.0156 76.9691 1970.274786 6 0.0002 37 | 0/8 2 h-lim-p 0.0009 0.0074 16.9712 1970.233474 5 0.0003 61 | 0/8 3 h-lim-p 0.0007 0.0193 7.7782 1970.226026 3 0.0003 79 | 0/8 4 h-lim-p 0.0009 0.0462 2.4312 1970.225464 2 0.0002 96 | 0/8 5 h-lim-p 0.0028 0.8773 0.1891 1970.225458 1 0.0004 112 | 0/8 6 h-lim-p 0.0015 6.0549 0.0441 1970.225457 0 0.0003 133 | 0/8 7 h-lim-p 0.0030 20.0000 0.0048 1970.225457 0 0.0030 153 | 0/8 8 h-lim-p 0.0105 20.0000 0.0014 1970.225380 0 0.1685 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1970.225377 0 1.0938 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1970.225377 0 1.0938 217 | 0/8 11 h-lim-p 1.7069 20.0000 0.0000 1970.225377 0 2.5604 237 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1970.225377 0 0.1562 260 | 0/8 13 h-lim-p 0.0254 20.0000 0.0000 1970.225377 0 0.0002 286 Out... lnL = -1970.225377 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1970.225377 Node 7: lnL = -1970.225377 Node 8: lnL = -1970.225377 Node 9: lnL = -1970.225377 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 897 Sequential format.. Reading seq # 1: YDL182W_Sbay Reading seq # 2: YDL182W_Scer Reading seq # 3: YDL182W_Skud Reading seq # 4: YDL182W_Smik Reading seq # 5: YDL182W_Spar Sequences read.. Counting patterns.. # site patterns = 321 Counting frequencies.. 120 bytes for distance 51360 bytes for lkl0 41088 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.108716 0.036080 0.074216 0.129765 0.119454 0.190600 0.212163 0.166864 lnL0 = -3903.345732 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3903.345732 x= 0.10872 0.03608 0.07422 0.12976 0.11945 0.19060 0.21216 0.16686 1 h-lim-p 0.0021 0.7298 193.2706 3900.681673 6 0.0002 39 | 0/8 2 h-lim-p 0.0014 0.0114 12.3180 3900.658987 4 0.0003 61 | 0/8 3 h-lim-p 0.0013 0.0457 2.7980 3900.657916 2 0.0003 78 | 0/8 4 h-lim-p 0.0010 0.3918 0.7698 3900.657805 2 0.0004 94 | 0/8 5 h-lim-p 0.0024 3.0178 0.1269 3900.657802 0 0.0005 115 | 0/8 6 h-lim-p 0.0046 13.7114 0.0147 3900.657801 0 0.0005 137 | 0/8 7 h-lim-p 0.0048 20.0000 0.0015 3900.657801 0 0.0042 157 | 0/8 8 h-lim-p 0.0115 20.0000 0.0006 3900.657790 0 0.1386 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3900.657790 0 1.0938 200 | 0/8 10 h-lim-p 1.4707 20.0000 0.0000 3900.657790 0 0.7354 220 | 0/8 11 h-lim-p 0.5333 20.0000 0.0000 3900.657790 0 0.0667 242 | 0/8 12 h-lim-p 0.0295 20.0000 0.0000 3900.657790 0 0.0258 262 | 0/8 13 h-lim-p 0.0134 20.0000 0.0000 3900.657790 0 0.0000 303 | 0/8 14 h-lim-p 0.0000 20.0000 0.0008 | 0/8 15 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -3900.657790 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3900.657790 Node 7: lnL = -3900.657790 Node 8: lnL = -3900.657790 Node 9: lnL = -3900.657790 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 899 Sequential format.. Reading seq # 1: YDL183C_Sbay Reading seq # 2: YDL183C_Scer Reading seq # 3: YDL183C_Skud Reading seq # 4: YDL183C_Smik Reading seq # 5: YDL183C_Spar Sequences read.. Counting patterns.. # site patterns = 385 Counting frequencies.. 120 bytes for distance 61600 bytes for lkl0 49280 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.127051 0.134252 0.050645 0.167168 0.126147 0.256127 0.332433 0.206464 lnL0 = -4309.737847 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4309.737847 x= 0.12705 0.13425 0.05065 0.16717 0.12615 0.25613 0.33243 0.20646 1 h-lim-p 0.0059 0.9050 121.3813 4308.317636 7 0.0002 42 | 0/8 2 h-lim-p 0.0010 0.0081 18.4734 4308.255684 6 0.0004 70 | 0/8 3 h-lim-p 0.0010 0.0610 7.1519 4308.244062 5 0.0005 93 | 0/8 4 h-lim-p 0.0014 0.1324 2.5574 4308.242245 2 0.0006 109 | 0/8 5 h-lim-p 0.0025 0.5879 0.6600 4308.242095 3 0.0007 130 | 0/8 6 h-lim-p 0.0125 9.3431 0.0379 4308.242094 0 0.0007 153 | 0/8 7 h-lim-p 0.3618 20.0000 0.0001 4308.242084 0 1.4473 175 | 0/8 8 h-lim-p 0.0039 11.7828 0.0269 4308.242084 0 0.0008 196 | 0/8 9 h-lim-p 0.9892 20.0000 0.0000 4308.242083 0 0.9892 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4308.242083 0 1.0938 236 | 0/8 11 h-lim-p 0.8724 20.0000 0.0000 4308.242083 0 0.0136 261 | 0/8 12 h-lim-p 0.0013 20.0000 0.0001 4308.242083 0 0.0000 298 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 4308.242083 0 0.0000 323 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -4308.242083 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4308.242083 Node 7: lnL = -4308.242083 Node 8: lnL = -4308.242083 Node 9: lnL = -4308.242083 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 356 Sequential format.. Reading seq # 1: YDL185W_Sbay Reading seq # 2: YDL185W_Scer Reading seq # 3: YDL185W_Skud Reading seq # 4: YDL185W_Smik Reading seq # 5: YDL185W_Spar Sequences read.. Counting patterns.. # site patterns = 78 Counting frequencies.. 120 bytes for distance 12480 bytes for lkl0 9984 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.040308 0.024653 0.020305 0.019210 0.014573 0.085838 0.054756 0.058424 lnL0 = -992.724911 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 992.724911 x= 0.04031 0.02465 0.02031 0.01921 0.01457 0.08584 0.05476 0.05842 1 h-lim-p 0.0000 0.0003 133.0729 991.968736 0 0.0001 23 | 0/8 2 h-lim-p 0.0002 0.0013 74.3363 991.852963 7 0.0001 53 | 0/8 3 h-lim-p 0.0002 0.0017 26.1600 991.814760 6 0.0001 79 | 0/8 4 h-lim-p 0.0002 0.0048 14.6974 991.804346 6 0.0001 106 | 0/8 5 h-lim-p 0.0007 0.0174 2.4968 991.803789 3 0.0002 125 | 0/8 6 h-lim-p 0.0002 0.1379 2.1640 991.803627 2 0.0001 141 | 0/8 7 h-lim-p 0.0015 0.3971 0.1550 991.803625 0 0.0002 155 | 0/8 8 h-lim-p 0.0902 20.0000 0.0003 991.803173 0 1.4427 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 991.803149 2 0.9644 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 991.803149 0 1.0938 223 | 0/8 11 h-lim-p 2.1011 20.0000 0.0000 991.803149 0 0.4596 244 | 0/8 12 h-lim-p 0.3585 20.0000 0.0000 991.803149 0 0.0000 278 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 991.803149 0 0.0000 298 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 991.803149 0 0.0000 321 Out... lnL = -991.803149 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -991.803149 Node 7: lnL = -991.803149 Node 8: lnL = -991.803149 Node 9: lnL = -991.803149 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 648 Sequential format.. Reading seq # 1: YDL186W_Sbay Reading seq # 2: YDL186W_Scer Reading seq # 3: YDL186W_Skud Reading seq # 4: YDL186W_Smik Reading seq # 5: YDL186W_Spar Sequences read.. Counting patterns.. # site patterns = 261 Counting frequencies.. 120 bytes for distance 41760 bytes for lkl0 33408 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.075566 0.104946 0.025956 0.152981 0.125715 0.220895 0.169799 0.132703 lnL0 = -2763.341439 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2763.341439 x= 0.07557 0.10495 0.02596 0.15298 0.12572 0.22090 0.16980 0.13270 1 h-lim-p 0.0010 0.4963 233.3196 2759.137820 7 0.0002 39 | 0/8 2 h-lim-p 0.0008 0.0064 29.3854 2758.877140 7 0.0006 65 | 0/8 3 h-lim-p 0.0013 0.0215 13.9371 2758.835368 6 0.0005 92 | 0/8 4 h-lim-p 0.0022 0.1009 3.1871 2758.832694 5 0.0006 114 | 0/8 5 h-lim-p 0.0021 0.2360 0.8577 2758.832505 3 0.0006 133 | 0/8 6 h-lim-p 0.0018 0.8173 0.2654 2758.832491 0 0.0004 154 | 0/8 7 h-lim-p 0.0085 20.0000 0.0124 2758.832491 0 0.0019 175 | 0/8 8 h-lim-p 0.0308 20.0000 0.0007 2758.832251 0 0.4928 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2758.832250 0 1.0938 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2758.832250 0 1.0938 239 | 0/8 11 h-lim-p 1.1622 20.0000 0.0000 2758.832250 0 1.7432 259 | 0/8 12 h-lim-p 1.1130 20.0000 0.0000 2758.832250 0 1.1130 279 | 0/8 13 h-lim-p 0.0138 20.0000 0.0011 2758.832250 0 0.0013 302 | 0/8 14 h-lim-p 0.0016 20.0000 0.0009 2758.832250 0 0.0003 324 | 0/8 15 h-lim-p 0.0012 20.0000 0.0002 2758.832250 0 0.0000 359 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -2758.832250 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2758.832250 Node 7: lnL = -2758.832250 Node 8: lnL = -2758.832250 Node 9: lnL = -2758.832250 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 557 Sequential format.. Reading seq # 1: YDL188C_Sbay Reading seq # 2: YDL188C_Scer Reading seq # 3: YDL188C_Skud Reading seq # 4: YDL188C_Smik Reading seq # 5: YDL188C_Spar Sequences read.. Counting patterns.. # site patterns = 203 Counting frequencies.. 120 bytes for distance 32480 bytes for lkl0 25984 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.091846 0.070415 0.041805 0.095186 0.106623 0.185959 0.202953 0.144817 lnL0 = -2414.564214 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2414.564214 x= 0.09185 0.07041 0.04180 0.09519 0.10662 0.18596 0.20295 0.14482 1 h-lim-p 0.0014 0.6189 188.1871 2411.582796 8 0.0002 41 | 0/8 2 h-lim-p 0.0017 0.0133 20.2118 2411.503967 2 0.0004 58 | 0/8 3 h-lim-p 0.0009 0.0410 8.8728 2411.490463 2 0.0004 74 | 0/8 4 h-lim-p 0.0016 0.1103 2.3595 2411.489317 5 0.0005 100 | 0/8 5 h-lim-p 0.0018 0.4627 0.6037 2411.489226 3 0.0005 121 | 0/8 6 h-lim-p 0.0033 2.6218 0.0938 2411.489224 1 0.0004 145 | 0/8 7 h-lim-p 0.0019 16.1360 0.0199 2411.489224 0 0.0008 165 | 0/8 8 h-lim-p 0.1176 20.0000 0.0001 2411.489193 0 0.9411 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2411.489192 1 1.2305 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2411.489192 0 1.0938 231 | 0/8 11 h-lim-p 1.3279 20.0000 0.0000 2411.489192 0 3.9837 252 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2411.489192 0 0.1367 275 | 0/8 13 h-lim-p 0.0852 20.0000 0.0000 2411.489192 0 0.0000 313 Out... lnL = -2411.489192 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2411.489192 Node 7: lnL = -2411.489192 Node 8: lnL = -2411.489192 Node 9: lnL = -2411.489192 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 585 Sequential format.. Reading seq # 1: YDL192W_Sbay Reading seq # 2: YDL192W_Scer Reading seq # 3: YDL192W_Skud Reading seq # 4: YDL192W_Smik Reading seq # 5: YDL192W_Spar Sequences read.. Counting patterns.. # site patterns = 151 Counting frequencies.. 120 bytes for distance 24160 bytes for lkl0 19328 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.055608 0.057244 0.030057 0.059096 0.051194 0.111704 0.121697 0.088527 lnL0 = -2045.075513 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2045.075513 x= 0.05561 0.05724 0.03006 0.05910 0.05119 0.11170 0.12170 0.08853 1 h-lim-p 0.0036 0.0314 106.8051 2044.532675 2 0.0001 30 | 0/8 2 h-lim-p 0.0010 0.0077 10.4811 2044.522646 5 0.0002 53 | 0/8 3 h-lim-p 0.0005 0.0518 3.7673 2044.521360 3 0.0002 71 | 0/8 4 h-lim-p 0.0006 0.0766 1.1843 2044.521253 3 0.0002 90 | 0/8 5 h-lim-p 0.0016 1.0006 0.1293 2044.521251 1 0.0002 106 | 0/8 6 h-lim-p 0.0006 5.8411 0.0397 2044.521251 0 0.0003 126 | 0/8 7 h-lim-p 0.0010 8.9501 0.0104 2044.521251 0 0.0009 146 | 0/8 8 h-lim-p 0.0186 20.0000 0.0005 2044.521143 0 0.2982 170 | 0/8 9 h-lim-p 0.4042 20.0000 0.0004 2044.521136 0 0.8085 191 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2044.521136 0 1.0938 211 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2044.521136 0 0.5469 232 | 0/8 12 h-lim-p 0.3292 20.0000 0.0000 2044.521136 0 0.0013 259 | 0/8 13 h-lim-p 0.0007 20.0000 0.0000 2044.521136 0 0.0004 279 | 0/8 14 h-lim-p 0.0003 20.0000 0.0000 2044.521136 0 0.0002 299 | 0/8 15 h-lim-p 0.0001 20.0000 0.0001 2044.521136 0 0.0001 319 | 0/8 16 h-lim-p 0.0000 20.0000 0.0031 2044.521136 0 0.0000 352 | 0/8 17 h-lim-p 0.0000 20.0000 0.0044 | 0/8 18 h-lim-p 0.0000 20.0000 0.0044 Out... lnL = -2044.521136 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2044.521136 Node 7: lnL = -2044.521136 Node 8: lnL = -2044.521136 Node 9: lnL = -2044.521136 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 510 Sequential format.. Reading seq # 1: YDL193W_Sbay Reading seq # 2: YDL193W_Scer Reading seq # 3: YDL193W_Skud Reading seq # 4: YDL193W_Smik Reading seq # 5: YDL193W_Spar Sequences read.. Counting patterns.. # site patterns = 168 Counting frequencies.. 120 bytes for distance 26880 bytes for lkl0 21504 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.102704 0.065590 0.035573 0.104500 0.059275 0.206357 0.138996 0.151379 lnL0 = -2028.518875 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2028.518875 x= 0.10270 0.06559 0.03557 0.10450 0.05927 0.20636 0.13900 0.15138 1 h-lim-p 0.0004 0.0033 92.3129 2027.700156 8 0.0002 38 | 0/8 2 h-lim-p 0.0006 0.0049 25.0048 2027.605511 7 0.0003 64 | 0/8 3 h-lim-p 0.0006 0.0151 13.0068 2027.587575 5 0.0003 85 | 0/8 4 h-lim-p 0.0009 0.0448 3.9675 2027.585010 4 0.0004 106 | 0/8 5 h-lim-p 0.0089 1.4346 0.1642 2027.585002 1 0.0005 123 | 0/8 6 h-lim-p 0.0018 3.1255 0.0499 2027.585002 1 0.0004 146 | 0/8 7 h-lim-p 0.0241 20.0000 0.0009 2027.585002 0 0.0106 166 | 0/8 8 h-lim-p 0.0119 20.0000 0.0008 2027.584995 0 0.0954 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2027.584994 0 1.0938 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2027.584994 0 2.1875 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2027.584994 0 1.0938 249 | 0/8 12 h-lim-p 0.4507 20.0000 0.0000 2027.584994 0 3.6057 272 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2027.584994 0 0.0024 301 | 0/8 14 h-lim-p 0.0183 20.0000 0.0000 2027.584994 0 0.0092 321 | 0/8 15 h-lim-p 0.0012 20.0000 0.0000 2027.584994 0 0.0001 343 Out... lnL = -2027.584994 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2027.584994 Node 7: lnL = -2027.584994 Node 8: lnL = -2027.584994 Node 9: lnL = -2027.584994 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 565 Sequential format.. Reading seq # 1: YDL194W_Sbay Reading seq # 2: YDL194W_Scer Reading seq # 3: YDL194W_Skud Reading seq # 4: YDL194W_Smik Reading seq # 5: YDL194W_Spar Sequences read.. Counting patterns.. # site patterns = 159 Counting frequencies.. 120 bytes for distance 25440 bytes for lkl0 20352 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.071063 0.082908 0.024281 0.094477 0.058870 0.102469 0.146606 0.110695 lnL0 = -2227.827226 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2227.827226 x= 0.07106 0.08291 0.02428 0.09448 0.05887 0.10247 0.14661 0.11069 1 h-lim-p 0.0009 0.0071 157.0516 2226.850171 7 0.0001 37 | 0/8 2 h-lim-p 0.0004 0.0043 37.4805 2226.698479 8 0.0002 71 | 0/8 3 h-lim-p 0.0008 0.0212 11.1390 2226.687430 4 0.0002 92 | 0/8 4 h-lim-p 0.0005 0.0373 4.4784 2226.685078 5 0.0003 117 | 0/8 5 h-lim-p 0.0026 0.7582 0.4726 2226.685048 1 0.0003 133 | 0/8 6 h-lim-p 0.0034 5.1293 0.0364 2226.685048 0 0.0004 155 | 0/8 7 h-lim-p 0.0103 20.0000 0.0013 2226.685047 0 0.0205 176 | 0/8 8 h-lim-p 0.0026 3.7236 0.0101 2226.684961 0 0.0158 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2226.684959 0 1.0938 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2226.684959 0 2.1875 238 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2226.684959 0 1.0938 258 | 0/8 12 h-lim-p 0.2682 20.0000 0.0000 2226.684959 0 4.2912 282 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2226.684959 0 0.1562 305 | 0/8 14 h-lim-p 1.7577 20.0000 0.0000 2226.684959 0 0.0069 332 | 0/8 15 h-lim-p 0.0007 20.0000 0.0000 2226.684959 0 0.0000 357 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 2226.684959 0 0.0000 392 | 0/8 17 h-lim-p 0.0000 20.0000 0.0051 | 0/8 18 h-lim-p 0.0000 20.0000 0.0051 Out... lnL = -2226.684959 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2226.684959 Node 7: lnL = -2226.684959 Node 8: lnL = -2226.684959 Node 9: lnL = -2226.684959 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 271 Sequential format.. Reading seq # 1: YDL197C_Sbay Reading seq # 2: YDL197C_Scer Reading seq # 3: YDL197C_Skud Reading seq # 4: YDL197C_Smik Reading seq # 5: YDL197C_Spar Sequences read.. Counting patterns.. # site patterns = 143 Counting frequencies.. 120 bytes for distance 22880 bytes for lkl0 18304 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.174653 0.182132 0.070460 0.119299 0.092375 0.241238 0.183178 0.251310 lnL0 = -1224.847552 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1224.847552 x= 0.17465 0.18213 0.07046 0.11930 0.09238 0.24124 0.18318 0.25131 1 h-lim-p 0.0075 0.0597 26.9831 1224.578485 6 0.0008 37 | 0/8 2 h-lim-p 0.0023 0.0349 9.1610 1224.527926 6 0.0013 64 | 0/8 3 h-lim-p 0.0021 0.0627 5.7674 1224.519138 6 0.0007 93 | 0/8 4 h-lim-p 0.0029 0.4088 1.4172 1224.517309 5 0.0020 119 | 0/8 5 h-lim-p 0.0054 0.4221 0.5285 1224.517093 4 0.0018 140 | 0/8 6 h-lim-p 0.0070 1.2350 0.1337 1224.517085 2 0.0009 166 | 0/8 7 h-lim-p 0.0186 20.0000 0.0067 1224.517085 0 0.0081 186 | 0/8 8 h-lim-p 0.1103 20.0000 0.0005 1224.517059 0 0.4412 208 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1224.517058 0 1.0938 228 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1224.517058 0 1.0938 248 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1224.517058 0 2.1875 268 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1224.517058 0 0.5469 289 | 0/8 13 h-lim-p 0.2000 20.0000 0.0000 1224.517058 0 0.2000 309 | 0/8 14 h-lim-p 0.1058 20.0000 0.0000 1224.517058 0 0.0029 333 | 0/8 15 h-lim-p 0.0019 20.0000 0.0000 1224.517058 0 0.0019 353 | 0/8 16 h-lim-p 0.0010 20.0000 0.0000 1224.517058 0 0.0005 373 Out... lnL = -1224.517058 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1224.517058 Node 7: lnL = -1224.517058 Node 8: lnL = -1224.517058 Node 9: lnL = -1224.517058 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 387 Sequential format.. Reading seq # 1: YDL198C_Sbay Reading seq # 2: YDL198C_Scer Reading seq # 3: YDL198C_Skud Reading seq # 4: YDL198C_Smik Reading seq # 5: YDL198C_Spar Sequences read.. Counting patterns.. # site patterns = 155 Counting frequencies.. 120 bytes for distance 24800 bytes for lkl0 19840 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.079551 0.043123 0.043190 0.095116 0.077881 0.149762 0.199895 0.125133 lnL0 = -1547.757389 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1547.757389 x= 0.07955 0.04312 0.04319 0.09512 0.07788 0.14976 0.19989 0.12513 1 h-lim-p 0.0023 0.0182 73.3004 1547.123826 7 0.0003 36 | 0/8 2 h-lim-p 0.0008 0.0067 12.8501 1547.090496 4 0.0004 56 | 0/8 3 h-lim-p 0.0017 0.0998 3.1768 1547.088172 5 0.0005 80 | 0/8 4 h-lim-p 0.0010 0.1278 1.5046 1547.087760 2 0.0005 96 | 0/8 5 h-lim-p 0.0024 0.9079 0.2887 1547.087728 3 0.0008 116 | 0/8 6 h-lim-p 0.0038 2.9520 0.0633 1547.087727 1 0.0005 140 | 0/8 7 h-lim-p 0.0034 13.3723 0.0089 1547.087727 0 0.0007 161 | 0/8 8 h-lim-p 0.2263 20.0000 0.0000 1547.087727 0 0.9050 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1547.087727 0 1.0938 203 | 0/8 10 h-lim-p 1.3464 20.0000 0.0000 1547.087727 0 1.3464 223 | 0/8 11 h-lim-p 0.7034 20.0000 0.0000 1547.087727 0 0.0440 246 | 0/8 12 h-lim-p 0.0013 20.0000 0.0003 1547.087727 0 0.0013 266 | 0/8 13 h-lim-p 0.0007 20.0000 0.0006 1547.087727 0 0.0007 286 | 0/8 14 h-lim-p 0.0000 1.0397 0.1165 1547.087727 0 0.0000 306 | 0/8 15 h-lim-p 0.0007 20.0000 0.0008 1547.087727 0 0.0000 342 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 1547.087727 0 0.0000 369 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 1547.087727 0 0.0000 389 | 0/8 18 h-lim-p 0.0001 20.0000 0.0000 1547.087727 0 0.0000 416 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 1547.087727 0 0.0000 446 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 1547.087727 0 0.0000 472 | 0/8 21 h-lim-p 0.0000 20.0000 0.0002 1547.087727 0 0.0000 499 | 0/8 22 h-lim-p 0.0000 20.0000 0.0001 1547.087727 0 0.0000 522 | 0/8 23 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 24 h-lim-p 0.0000 20.0000 0.0001 1547.087727 0 0.0000 582 | 0/8 25 h-lim-p 0.0000 20.0000 0.0002 .. | 0/8 26 h-lim-p 0.0000 20.0000 0.0001 | 0/8 27 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1547.087727 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1547.087727 Node 7: lnL = -1547.087727 Node 8: lnL = -1547.087727 Node 9: lnL = -1547.087727 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 313 Sequential format.. Reading seq # 1: YDL199C_Sbay Reading seq # 2: YDL199C_Scer Reading seq # 3: YDL199C_Skud Reading seq # 4: YDL199C_Smik Reading seq # 5: YDL199C_Spar Sequences read.. Counting patterns.. # site patterns = 134 Counting frequencies.. 120 bytes for distance 21440 bytes for lkl0 17152 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.097087 0.057186 0.078031 0.104953 0.054768 0.152525 0.166526 0.146295 lnL0 = -1285.403570 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1285.403570 x= 0.09709 0.05719 0.07803 0.10495 0.05477 0.15252 0.16653 0.14630 1 h-lim-p 0.0077 2.1988 57.7657 1284.733716 7 0.0004 38 | 0/8 2 h-lim-p 0.0016 0.0128 6.7428 1284.724752 2 0.0004 55 | 0/8 3 h-lim-p 0.0008 0.0536 3.2868 1284.722423 5 0.0005 79 | 0/8 4 h-lim-p 0.0029 0.4850 0.5839 1284.722309 2 0.0007 96 | 0/8 5 h-lim-p 0.0084 4.1086 0.0502 1284.722308 1 0.0005 121 | 0/8 6 h-lim-p 0.0073 20.0000 0.0035 1284.722308 0 0.0032 141 | 0/8 7 h-lim-p 0.0067 20.0000 0.0017 1284.722306 0 0.0405 163 | 0/8 8 h-lim-p 0.0062 20.0000 0.0110 1284.722291 0 0.0124 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1284.722291 0 1.0938 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1284.722291 0 1.0938 224 | 0/8 11 h-lim-p 1.1081 20.0000 0.0000 1284.722291 0 2.2162 245 | 0/8 12 h-lim-p 0.7308 20.0000 0.0000 1284.722291 0 0.1827 266 | 0/8 13 h-lim-p 0.0024 20.0000 0.0007 1284.722291 0 0.0011 286 | 0/8 14 h-lim-p 0.0002 20.0000 0.0032 1284.722291 0 0.0001 307 | 0/8 15 h-lim-p 0.0026 20.0000 0.0001 1284.722291 0 0.0000 337 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 1284.722291 0 0.0000 371 Out... lnL = -1284.722291 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1284.722291 Node 7: lnL = -1284.722291 Node 8: lnL = -1284.722291 Node 9: lnL = -1284.722291 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 242 Sequential format.. Reading seq # 1: YDL200C_Sbay Reading seq # 2: YDL200C_Scer Reading seq # 3: YDL200C_Skud Reading seq # 4: YDL200C_Smik Reading seq # 5: YDL200C_Spar Sequences read.. Counting patterns.. # site patterns = 148 Counting frequencies.. 120 bytes for distance 23680 bytes for lkl0 18944 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.185589 0.033273 0.077776 0.186851 0.084299 0.251427 0.321991 0.263260 lnL0 = -1137.024825 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1137.024825 x= 0.18559 0.03327 0.07778 0.18685 0.08430 0.25143 0.32199 0.26326 1 h-lim-p 0.0169 4.9168 36.6974 1136.412829 3 0.0010 31 | 0/8 2 h-lim-p 0.0011 0.0088 15.1035 1136.274711 0 0.0017 43 | 0/8 3 h-lim-p 0.0038 0.0304 4.9458 1136.259739 6 0.0014 71 | 0/8 4 h-lim-p 0.0047 0.1646 1.4618 1136.257160 5 0.0026 96 | 0/8 5 h-lim-p 0.0144 1.6057 0.2690 1136.257023 2 0.0034 113 | 0/8 6 h-lim-p 0.0234 5.2979 0.0388 1136.256938 4 0.0145 145 | 0/8 7 h-lim-p 0.0171 12.2599 0.0329 1136.252812 0 0.1024 167 | 0/8 8 h-lim-p 0.0114 0.7637 0.2943 1136.252696 2 0.0025 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1136.252694 0 1.0938 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1136.252694 0 1.0938 232 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1136.252694 0 1.0938 252 | 0/8 12 h-lim-p 1.1976 20.0000 0.0000 1136.252694 0 4.7905 274 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1136.252694 0 0.2734 296 | 0/8 14 h-lim-p 0.0483 20.0000 0.0000 1136.252694 0 0.0483 316 | 0/8 15 h-lim-p 0.0153 20.0000 0.0000 1136.252694 0 0.0000 352 Out... lnL = -1136.252694 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1136.252694 Node 7: lnL = -1136.252694 Node 8: lnL = -1136.252694 Node 9: lnL = -1136.252694 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 360 Sequential format.. Reading seq # 1: YDL201W_Sbay Reading seq # 2: YDL201W_Scer Reading seq # 3: YDL201W_Skud Reading seq # 4: YDL201W_Smik Reading seq # 5: YDL201W_Spar Sequences read.. Counting patterns.. # site patterns = 154 Counting frequencies.. 120 bytes for distance 24640 bytes for lkl0 19712 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.106837 0.010742 0.080961 0.067162 0.075970 0.176779 0.312907 0.154833 lnL0 = -1501.159979 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1501.159979 x= 0.10684 0.01074 0.08096 0.06716 0.07597 0.17678 0.31291 0.15483 1 h-lim-p 0.0005 0.0039 102.9512 1499.607942 9 0.0003 43 | 0/8 2 h-lim-p 0.0008 0.0065 15.1015 1499.549312 7 0.0005 73 | 0/8 3 h-lim-p 0.0007 0.0206 11.4543 1499.526461 6 0.0005 99 | 0/8 4 h-lim-p 0.0012 0.0296 4.9546 1499.521131 4 0.0006 120 | 0/8 5 h-lim-p 0.0026 0.3329 1.0554 1499.520394 4 0.0014 141 | 0/8 6 h-lim-p 0.0034 0.6095 0.4417 1499.520297 3 0.0012 161 | 0/8 7 h-lim-p 0.0065 1.3750 0.0821 1499.520294 0 0.0007 183 | 0/8 8 h-lim-p 0.2728 20.0000 0.0002 1499.520220 0 1.0913 205 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1499.520218 0 1.0938 225 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1499.520218 0 1.0938 245 | 0/8 11 h-lim-p 1.4977 20.0000 0.0000 1499.520218 0 2.9955 266 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1499.520218 0 0.0098 293 | 0/8 13 h-lim-p 0.0106 20.0000 0.0000 1499.520218 0 0.0001 319 Out... lnL = -1499.520218 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1499.520218 Node 7: lnL = -1499.520218 Node 8: lnL = -1499.520218 Node 9: lnL = -1499.520218 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 551 Sequential format.. Reading seq # 1: YDL203C_Sbay Reading seq # 2: YDL203C_Scer Reading seq # 3: YDL203C_Skud Reading seq # 4: YDL203C_Smik Reading seq # 5: YDL203C_Spar Sequences read.. Counting patterns.. # site patterns = 227 Counting frequencies.. 120 bytes for distance 36320 bytes for lkl0 29056 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.114366 0.117737 0.085540 0.088906 0.084639 0.180255 0.203310 0.167567 lnL0 = -2492.216935 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2492.216935 x= 0.11437 0.11774 0.08554 0.08891 0.08464 0.18025 0.20331 0.16757 1 h-lim-p 0.0112 2.0005 66.8022 2491.476011 6 0.0003 37 | 0/8 2 h-lim-p 0.0011 0.0097 21.3656 2491.400717 7 0.0004 67 | 0/8 3 h-lim-p 0.0007 0.0157 11.2603 2491.379398 6 0.0004 96 | 0/8 4 h-lim-p 0.0023 0.1051 2.0684 2491.378039 5 0.0007 121 | 0/8 5 h-lim-p 0.0017 0.1966 0.7992 2491.377941 3 0.0004 140 | 0/8 6 h-lim-p 0.0034 2.3595 0.0858 2491.377939 1 0.0004 164 | 0/8 7 h-lim-p 0.0032 20.0000 0.0112 2491.377938 0 0.0028 184 | 0/8 8 h-lim-p 0.0225 20.0000 0.0014 2491.377767 0 0.3600 208 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2491.377757 1 0.9961 230 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2491.377757 0 2.1875 250 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2491.377757 0 1.0938 270 | 0/8 12 h-lim-p 0.1908 20.0000 0.0000 2491.377757 0 6.1047 295 | 0/8 13 h-lim-p 0.6587 20.0000 0.0001 2491.377757 0 0.6587 315 | 0/8 14 h-lim-p 0.0167 20.0000 0.0020 2491.377757 0 0.0000 350 | 0/8 15 h-lim-p 0.0004 20.0000 0.0000 2491.377757 0 0.0000 383 Out... lnL = -2491.377757 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2491.377757 Node 7: lnL = -2491.377757 Node 8: lnL = -2491.377757 Node 9: lnL = -2491.377757 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 862 Sequential format.. Reading seq # 1: YDL204W_Sbay Reading seq # 2: YDL204W_Scer Reading seq # 3: YDL204W_Skud Reading seq # 4: YDL204W_Smik Reading seq # 5: YDL204W_Spar Sequences read.. Counting patterns.. # site patterns = 232 Counting frequencies.. 120 bytes for distance 37120 bytes for lkl0 29696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.079737 0.027030 0.043821 0.085023 0.016753 0.135628 0.139739 0.111093 lnL0 = -3225.090137 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3225.090137 x= 0.07974 0.02703 0.04382 0.08502 0.01675 0.13563 0.13974 0.11109 1 h-lim-p 0.0001 0.1605 713.7936 3217.229777 6 0.0000 36 | 0/8 2 h-lim-p 0.0001 0.0009 160.0433 3216.052713 6 0.0001 59 | 0/8 3 h-lim-p 0.0005 0.0043 21.7994 3216.018130 7 0.0001 88 | 0/8 4 h-lim-p 0.0006 0.0294 5.2238 3216.015143 4 0.0002 108 | 0/8 5 h-lim-p 0.0009 0.0569 1.4131 3216.014982 3 0.0002 127 | 0/8 6 h-lim-p 0.0058 3.7400 0.0415 3216.014976 0 0.0013 140 | 0/8 7 h-lim-p 0.0020 6.8625 0.0261 3216.014743 0 0.0162 163 | 0/8 8 h-lim-p 0.0021 0.2483 0.1996 3216.008224 0 0.0064 184 | 0/8 9 h-lim-p 1.5845 20.0000 0.0008 3216.007907 3 1.0215 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 3216.007905 0 1.0938 232 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3216.007905 0 1.2500 252 | 0/8 12 h-lim-p 1.8618 20.0000 0.0000 3216.007905 0 0.0018 281 | 0/8 13 h-lim-p 0.0010 20.0000 0.0000 3216.007905 0 0.0000 307 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 3216.007905 0 0.0000 327 Out... lnL = -3216.007905 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3216.007905 Node 7: lnL = -3216.007905 Node 8: lnL = -3216.007905 Node 9: lnL = -3216.007905 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 846 Sequential format.. Reading seq # 1: YDL205C_Sbay Reading seq # 2: YDL205C_Scer Reading seq # 3: YDL205C_Skud Reading seq # 4: YDL205C_Smik Reading seq # 5: YDL205C_Spar Sequences read.. Counting patterns.. # site patterns = 199 Counting frequencies.. 120 bytes for distance 31840 bytes for lkl0 25472 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.075166 0.022492 0.047764 0.059466 0.043073 0.113006 0.117512 0.103883 lnL0 = -3072.096169 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3072.096169 x= 0.07517 0.02249 0.04776 0.05947 0.04307 0.11301 0.11751 0.10388 1 h-lim-p 0.0009 0.0073 243.2087 3070.220259 8 0.0001 46 | 0/8 2 h-lim-p 0.0004 0.0049 38.9018 3070.096454 5 0.0002 68 | 0/8 3 h-lim-p 0.0010 0.0284 6.8532 3070.093735 2 0.0001 86 | 0/8 4 h-lim-p 0.0005 0.0968 1.7778 3070.093498 3 0.0002 106 | 0/8 5 h-lim-p 0.0004 0.0766 0.8100 3070.093480 1 0.0001 121 | 0/8 6 h-lim-p 0.0006 2.2033 0.0944 3070.093479 0 0.0001 142 | 0/8 7 h-lim-p 0.0003 4.0436 0.0375 3070.093479 0 0.0003 162 | 0/8 8 h-lim-p 0.0901 20.0000 0.0001 3070.093386 0 1.4422 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3070.093380 1 0.9961 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3070.093380 0 2.1875 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3070.093380 0 0.0098 255 | 0/8 12 h-lim-p 0.0027 20.0000 0.0000 3070.093380 0 0.0000 280 Out... lnL = -3070.093380 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3070.093380 Node 7: lnL = -3070.093380 Node 8: lnL = -3070.093380 Node 9: lnL = -3070.093380 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 331 Sequential format.. Reading seq # 1: YDL206W_Sbay Reading seq # 2: YDL206W_Scer Reading seq # 3: YDL206W_Skud Reading seq # 4: YDL206W_Smik Reading seq # 5: YDL206W_Spar Sequences read.. Counting patterns.. # site patterns = 141 Counting frequencies.. 120 bytes for distance 22560 bytes for lkl0 18048 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.124053 0.061822 0.081207 0.110487 0.069642 0.198865 0.214595 0.175570 lnL0 = -1492.342770 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1492.342770 x= 0.12405 0.06182 0.08121 0.11049 0.06964 0.19887 0.21460 0.17557 1 h-lim-p 0.0010 0.0077 62.4054 1491.474712 8 0.0005 41 | 0/8 2 h-lim-p 0.0018 0.0146 9.3362 1491.435511 4 0.0009 61 | 0/8 3 h-lim-p 0.0019 0.0642 4.4385 1491.429964 4 0.0007 83 | 0/8 4 h-lim-p 0.0011 0.0651 2.7144 1491.428724 3 0.0005 102 | 0/8 5 h-lim-p 0.0025 0.7335 0.5054 1491.428625 3 0.0008 121 | 0/8 6 h-lim-p 0.0039 2.1939 0.1063 1491.428620 1 0.0008 144 | 0/8 7 h-lim-p 0.0349 20.0000 0.0024 1491.428612 0 0.0699 165 | 0/8 8 h-lim-p 0.0088 20.0000 0.0186 1491.428449 0 0.0265 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1491.428447 0 1.0938 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1491.428447 0 1.0938 226 | 0/8 11 h-lim-p 2.0533 20.0000 0.0000 1491.428447 0 1.7967 246 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1491.428447 0 0.5469 267 | 0/8 13 h-lim-p 0.1521 20.0000 0.0000 1491.428447 0 0.0333 288 | 0/8 14 h-lim-p 0.0146 20.0000 0.0000 1491.428447 0 0.0000 323 Out... lnL = -1491.428447 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1491.428447 Node 7: lnL = -1491.428447 Node 8: lnL = -1491.428447 Node 9: lnL = -1491.428447 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 302 Sequential format.. Reading seq # 1: YDL207W_Sbay Reading seq # 2: YDL207W_Scer Reading seq # 3: YDL207W_Skud Reading seq # 4: YDL207W_Smik Reading seq # 5: YDL207W_Spar Sequences read.. Counting patterns.. # site patterns = 134 Counting frequencies.. 120 bytes for distance 21440 bytes for lkl0 17152 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.058112 0.094610 0.028230 0.086621 0.107590 0.170469 0.177076 0.099191 lnL0 = -1270.349087 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1270.349087 x= 0.05811 0.09461 0.02823 0.08662 0.10759 0.17047 0.17708 0.09919 1 h-lim-p 0.0007 0.0122 192.6630 1266.582693 5 0.0003 32 | 0/8 2 h-lim-p 0.0007 0.0057 36.3172 1266.056581 1 0.0009 46 | 0/8 3 h-lim-p 0.0037 0.0296 8.5535 1266.036408 6 0.0006 74 | 0/8 4 h-lim-p 0.0028 0.0754 1.8007 1266.035388 2 0.0007 91 | 0/8 5 h-lim-p 0.0068 1.0864 0.1716 1266.035364 3 0.0012 112 | 0/8 6 h-lim-p 0.0026 1.3664 0.0800 1266.035346 2 0.0020 136 | 0/8 7 h-lim-p 0.0018 4.6985 0.0869 1266.035197 0 0.0074 158 | 0/8 8 h-lim-p 0.0068 2.2764 0.0937 1266.030488 0 0.0273 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 1266.030263 4 1.3122 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1266.030242 3 1.3437 236 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1266.030242 0 1.0938 256 | 0/8 12 h-lim-p 1.6719 20.0000 0.0000 1266.030242 0 0.0522 280 | 0/8 13 h-lim-p 0.0223 20.0000 0.0000 1266.030242 0 0.0223 300 | 0/8 14 h-lim-p 0.0129 20.0000 0.0000 1266.030242 0 0.0000 329 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 1266.030242 0 0.0000 358 | 0/8 16 h-lim-p 0.0000 20.0000 0.0008 | 0/8 17 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -1266.030242 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1266.030242 Node 7: lnL = -1266.030242 Node 8: lnL = -1266.030242 Node 9: lnL = -1266.030242 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 296 Sequential format.. Reading seq # 1: YDL208W_Sbay Reading seq # 2: YDL208W_Scer Reading seq # 3: YDL208W_Skud Reading seq # 4: YDL208W_Smik Reading seq # 5: YDL208W_Spar Sequences read.. Counting patterns.. # site patterns = 133 Counting frequencies.. 120 bytes for distance 21280 bytes for lkl0 17024 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.096074 0.021938 0.072746 0.127148 0.082120 0.179019 0.157212 0.138979 lnL0 = -1122.141044 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1122.141044 x= 0.09607 0.02194 0.07275 0.12715 0.08212 0.17902 0.15721 0.13898 1 h-lim-p 0.0002 0.0016 86.0926 1119.360702 0 0.0008 24 | 0/8 2 h-lim-p 0.0001 0.0005 81.1701 1118.456512 0 0.0004 38 | 0/8 3 h-lim-p 0.0026 0.0349 11.5885 1118.397023 7 0.0009 66 | 0/8 4 h-lim-p 0.0017 0.0323 6.4009 1118.381028 7 0.0010 96 | 0/8 5 h-lim-p 0.0029 0.0800 2.1614 1118.379566 3 0.0007 115 | 0/8 6 h-lim-p 0.0072 0.4187 0.2175 1118.379545 0 0.0008 129 | 0/8 7 h-lim-p 0.0571 7.0203 0.0030 1118.378922 0 0.4571 152 | 0/8 8 h-lim-p 0.0020 0.0431 0.6772 1118.378304 4 0.0015 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 1118.378089 2 1.0889 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1118.378087 0 1.0938 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1118.378087 0 0.1367 248 | 0/8 12 h-lim-p 0.0734 20.0000 0.0000 1118.378087 0 0.0034 272 | 0/8 13 h-lim-p 0.0022 20.0000 0.0000 1118.378087 0 0.0001 295 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 1118.378087 0 0.0000 319 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 1118.378087 0 0.0000 352 Out... lnL = -1118.378087 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1118.378087 Node 7: lnL = -1118.378087 Node 8: lnL = -1118.378087 Node 9: lnL = -1118.378087 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 880 Sequential format.. Reading seq # 1: YDL211C_Sbay Reading seq # 2: YDL211C_Scer Reading seq # 3: YDL211C_Skud Reading seq # 4: YDL211C_Smik Reading seq # 5: YDL211C_Spar Sequences read.. Counting patterns.. # site patterns = 400 Counting frequencies.. 120 bytes for distance 64000 bytes for lkl0 51200 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.248211 0.151515 0.107106 0.178728 0.124392 0.298742 0.292158 0.334950 lnL0 = -4349.146485 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4349.146485 x= 0.24821 0.15152 0.10711 0.17873 0.12439 0.29874 0.29216 0.33495 1 h-lim-p 0.0039 0.0311 62.7516 4348.301098 2 0.0005 28 | 0/8 2 h-lim-p 0.0011 0.0147 26.3824 4348.115106 7 0.0006 56 | 0/8 3 h-lim-p 0.0006 0.0146 26.8669 4347.967727 1 0.0008 70 | 0/8 4 h-lim-p 0.0041 0.0754 4.9446 4347.956753 2 0.0010 87 | 0/8 5 h-lim-p 0.0022 0.2432 2.1292 4347.955040 3 0.0009 105 | 0/8 6 h-lim-p 0.0028 0.6686 0.6658 4347.954894 2 0.0007 122 | 0/8 7 h-lim-p 0.0059 3.3776 0.0847 4347.954889 0 0.0013 143 | 0/8 8 h-lim-p 0.1810 20.0000 0.0006 4347.954570 0 1.0861 165 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4347.954561 1 0.9961 187 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4347.954561 0 1.0938 207 | 0/8 11 h-lim-p 2.4565 20.0000 0.0000 4347.954561 0 0.9212 228 | 0/8 12 h-lim-p 0.6693 20.0000 0.0000 4347.954561 0 0.6693 248 | 0/8 13 h-lim-p 0.1046 20.0000 0.0000 4347.954561 0 0.0000 292 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -4347.954561 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4347.954561 Node 7: lnL = -4347.954561 Node 8: lnL = -4347.954561 Node 9: lnL = -4347.954561 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 544 Sequential format.. Reading seq # 1: YDL212W_Sbay Reading seq # 2: YDL212W_Scer Reading seq # 3: YDL212W_Skud Reading seq # 4: YDL212W_Smik Reading seq # 5: YDL212W_Spar Sequences read.. Counting patterns.. # site patterns = 208 Counting frequencies.. 120 bytes for distance 33280 bytes for lkl0 26624 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.082177 0.102300 0.047727 0.152375 0.142633 0.288747 0.144212 0.136675 lnL0 = -2187.786432 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2187.786432 x= 0.08218 0.10230 0.04773 0.15237 0.14263 0.28875 0.14421 0.13668 1 h-lim-p 0.0011 0.0084 54.9642 2187.051884 2 0.0005 26 | 0/8 2 h-lim-p 0.0007 0.0053 31.6881 2186.756089 6 0.0007 53 | 0/8 3 h-lim-p 0.0022 0.0237 10.7347 2186.722102 6 0.0007 79 | 0/8 4 h-lim-p 0.0023 0.0628 3.2631 2186.719280 4 0.0006 100 | 0/8 5 h-lim-p 0.0022 0.3089 0.8763 2186.718715 4 0.0016 121 | 0/8 6 h-lim-p 0.0330 10.7482 0.0418 2186.718707 1 0.0036 145 | 0/8 7 h-lim-p 0.0043 5.5934 0.0349 2186.718693 0 0.0038 165 | 0/8 8 h-lim-p 0.0065 20.0000 0.0202 2186.717391 0 0.0783 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 2186.717347 2 0.9961 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2186.717347 0 1.0938 232 | 0/8 11 h-lim-p 1.4014 20.0000 0.0000 2186.717347 0 1.2262 252 | 0/8 12 h-lim-p 0.7635 20.0000 0.0000 2186.717347 0 0.1909 273 | 0/8 13 h-lim-p 0.0032 20.0000 0.0005 2186.717347 0 0.0016 293 | 0/8 14 h-lim-p 0.0026 20.0000 0.0003 2186.717347 0 0.0026 313 | 0/8 15 h-lim-p 0.0008 20.0000 0.0009 2186.717347 0 0.0002 334 | 0/8 16 h-lim-p 0.0005 20.0000 0.0004 2186.717347 0 0.0000 357 | 0/8 17 h-lim-p 0.0000 20.0000 0.0010 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -2186.717347 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2186.717347 Node 7: lnL = -2186.717347 Node 8: lnL = -2186.717347 Node 9: lnL = -2186.717347 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 820 Sequential format.. Reading seq # 1: YDL214C_Sbay Reading seq # 2: YDL214C_Scer Reading seq # 3: YDL214C_Skud Reading seq # 4: YDL214C_Smik Reading seq # 5: YDL214C_Spar Sequences read.. Counting patterns.. # site patterns = 313 Counting frequencies.. 120 bytes for distance 50080 bytes for lkl0 40064 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.154855 0.069640 0.101694 0.109864 0.094153 0.229069 0.215116 0.214112 lnL0 = -3691.649116 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3691.649116 x= 0.15486 0.06964 0.10169 0.10986 0.09415 0.22907 0.21512 0.21411 1 h-lim-p 0.0061 1.1102 110.2212 3690.203170 8 0.0003 42 | 0/8 2 h-lim-p 0.0013 0.0106 17.8229 3690.164943 5 0.0002 67 | 0/8 3 h-lim-p 0.0006 0.0317 7.6556 3690.154706 5 0.0004 90 | 0/8 4 h-lim-p 0.0021 0.2273 1.4764 3690.154197 2 0.0005 107 | 0/8 5 h-lim-p 0.0027 0.9949 0.2715 3690.154171 2 0.0007 124 | 0/8 6 h-lim-p 0.0155 13.2240 0.0124 3690.154171 0 0.0017 146 | 0/8 7 h-lim-p 0.0020 20.0000 0.0106 3690.154166 0 0.0079 168 | 0/8 8 h-lim-p 0.0063 20.0000 0.0133 3690.153954 0 0.0253 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3690.153952 0 1.0938 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3690.153952 0 1.0938 230 | 0/8 11 h-lim-p 1.7914 20.0000 0.0000 3690.153952 0 0.7837 250 | 0/8 12 h-lim-p 0.5429 20.0000 0.0000 3690.153952 0 0.0127 275 | 0/8 13 h-lim-p 0.0054 20.0000 0.0000 3690.153952 0 0.0000 312 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -3690.153952 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3690.153952 Node 7: lnL = -3690.153952 Node 8: lnL = -3690.153952 Node 9: lnL = -3690.153952 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 588 Sequential format.. Reading seq # 1: YDL215C_Sbay Reading seq # 2: YDL215C_Scer Reading seq # 3: YDL215C_Skud Reading seq # 4: YDL215C_Smik Reading seq # 5: YDL215C_Spar Sequences read.. Counting patterns.. # site patterns = 157 Counting frequencies.. 120 bytes for distance 25120 bytes for lkl0 20096 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.079945 0.031275 0.028816 0.076135 0.044877 0.104504 0.135237 0.105270 lnL0 = -2077.619953 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2077.619953 x= 0.07995 0.03127 0.02882 0.07613 0.04488 0.10450 0.13524 0.10527 1 h-lim-p 0.0022 0.0173 136.7396 2076.618280 5 0.0001 34 | 0/8 2 h-lim-p 0.0002 0.0016 25.9967 2076.567696 7 0.0002 63 | 0/8 3 h-lim-p 0.0004 0.0186 11.0496 2076.556370 6 0.0002 91 | 0/8 4 h-lim-p 0.0007 0.0195 3.3700 2076.555675 3 0.0001 110 | 0/8 5 h-lim-p 0.0004 0.1513 1.1707 2076.555509 3 0.0003 130 | 0/8 6 h-lim-p 0.0021 1.8943 0.1586 2076.555507 0 0.0002 144 | 0/8 7 h-lim-p 0.0040 19.2030 0.0088 2076.555507 0 0.0004 166 | 0/8 8 h-lim-p 0.0283 20.0000 0.0001 2076.555475 0 0.9042 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2076.555474 0 1.0938 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2076.555474 0 1.0938 231 | 0/8 11 h-lim-p 1.1606 20.0000 0.0000 2076.555474 0 2.3211 252 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2076.555474 0 0.0000 293 Out... lnL = -2076.555474 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2076.555474 Node 7: lnL = -2076.555474 Node 8: lnL = -2076.555474 Node 9: lnL = -2076.555474 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 364 Sequential format.. Reading seq # 1: YDL216C_Sbay Reading seq # 2: YDL216C_Scer Reading seq # 3: YDL216C_Skud Reading seq # 4: YDL216C_Smik Reading seq # 5: YDL216C_Spar Sequences read.. Counting patterns.. # site patterns = 185 Counting frequencies.. 120 bytes for distance 29600 bytes for lkl0 23680 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.163779 0.157824 0.090048 0.117671 0.100884 0.340921 0.166019 0.222858 lnL0 = -1661.935954 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1661.935954 x= 0.16378 0.15782 0.09005 0.11767 0.10088 0.34092 0.16602 0.22286 1 h-lim-p 0.0037 0.0295 14.9243 1661.799752 7 0.0012 40 | 0/8 2 h-lim-p 0.0022 0.0180 8.5431 1661.779494 6 0.0007 66 | 0/8 3 h-lim-p 0.0038 0.0943 1.5658 1661.778583 3 0.0008 85 | 0/8 4 h-lim-p 0.0037 2.4541 0.3339 1661.778470 4 0.0021 108 | 0/8 5 h-lim-p 0.0066 1.4984 0.1064 1661.778466 1 0.0008 132 | 0/8 6 h-lim-p 0.0083 20.0000 0.0103 1661.778465 0 0.0018 153 | 0/8 7 h-lim-p 0.0053 20.0000 0.0036 1661.778465 0 0.0023 173 | 0/8 8 h-lim-p 0.1044 20.0000 0.0001 1661.778464 0 0.8348 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1661.778464 0 1.0938 216 | 0/8 10 h-lim-p 2.1986 20.0000 0.0000 1661.778464 0 1.9237 236 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1661.778464 0 0.2734 258 | 0/8 12 h-lim-p 0.0591 20.0000 0.0000 1661.778464 0 0.0000 298 Out... lnL = -1661.778464 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1661.778464 Node 7: lnL = -1661.778464 Node 8: lnL = -1661.778464 Node 9: lnL = -1661.778464 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 449 Sequential format.. Reading seq # 1: YDL217C_Sbay Reading seq # 2: YDL217C_Scer Reading seq # 3: YDL217C_Skud Reading seq # 4: YDL217C_Smik Reading seq # 5: YDL217C_Spar Sequences read.. Counting patterns.. # site patterns = 215 Counting frequencies.. 120 bytes for distance 34400 bytes for lkl0 27520 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.165020 0.116078 0.103931 0.165512 0.150916 0.276944 0.270183 0.228193 lnL0 = -2185.921590 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2185.921590 x= 0.16502 0.11608 0.10393 0.16551 0.15092 0.27694 0.27018 0.22819 1 h-lim-p 0.0318 3.2927 37.0559 2185.503014 6 0.0006 40 | 0/8 2 h-lim-p 0.0028 0.0490 8.4756 2185.465541 4 0.0011 60 | 0/8 3 h-lim-p 0.0023 0.0979 4.0043 2185.459614 4 0.0009 80 | 0/8 4 h-lim-p 0.0081 1.0685 0.4408 2185.459502 3 0.0012 101 | 0/8 5 h-lim-p 0.0055 2.9345 0.0967 2185.459495 2 0.0018 127 | 0/8 6 h-lim-p 0.0092 14.8006 0.0190 2185.459494 0 0.0020 148 | 0/8 7 h-lim-p 0.0188 20.0000 0.0020 2185.459493 0 0.0188 168 | 0/8 8 h-lim-p 0.0064 20.0000 0.0060 2185.459454 0 0.0509 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2185.459451 0 1.0938 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2185.459451 0 1.0938 231 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2185.459451 0 2.1875 251 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2185.459451 0 1.0938 271 | 0/8 13 h-lim-p 0.3167 20.0000 0.0000 2185.459451 0 5.0666 295 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 2185.459451 0 0.0006 326 Out... lnL = -2185.459451 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2185.459451 Node 7: lnL = -2185.459451 Node 8: lnL = -2185.459451 Node 9: lnL = -2185.459451 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 807 Sequential format.. Reading seq # 1: YDL218W_Sbay Reading seq # 2: YDL218W_Scer Reading seq # 3: YDL218W_Skud Reading seq # 4: YDL218W_Smik Reading seq # 5: YDL218W_Spar Sequences read.. Counting patterns.. # site patterns = 300 Counting frequencies.. 120 bytes for distance 48000 bytes for lkl0 38400 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.107799 0.045580 0.068584 0.100376 0.085081 0.236913 0.337458 0.155343 lnL0 = -3571.921156 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3571.921156 x= 0.10780 0.04558 0.06858 0.10038 0.08508 0.23691 0.33746 0.15534 1 h-lim-p 0.0007 0.0059 191.3480 3568.428386 8 0.0002 43 | 0/8 2 h-lim-p 0.0003 0.0027 43.5574 3568.084332 5 0.0004 68 | 0/8 3 h-lim-p 0.0006 0.0089 25.9727 3568.026492 7 0.0002 98 | 0/8 4 h-lim-p 0.0007 0.0235 8.4150 3568.016792 2 0.0003 114 | 0/8 5 h-lim-p 0.0011 0.1241 2.4986 3568.015382 2 0.0005 130 | 0/8 6 h-lim-p 0.0017 0.1508 0.7547 3568.015291 1 0.0003 145 | 0/8 7 h-lim-p 0.0026 7.0336 0.1000 3568.015277 2 0.0016 170 | 0/8 8 h-lim-p 0.0807 20.0000 0.0020 3568.010819 0 0.9686 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3568.010706 2 0.9961 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3568.010706 0 1.0938 237 | 0/8 11 h-lim-p 2.1616 20.0000 0.0000 3568.010706 0 1.8914 257 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3568.010706 0 1.0938 277 | 0/8 13 h-lim-p 0.3257 20.0000 0.0000 3568.010706 0 0.4885 297 | 0/8 14 h-lim-p 0.0425 20.0000 0.0001 3568.010706 0 0.2548 319 | 0/8 15 h-lim-p 0.0949 20.0000 0.0002 3568.010706 0 0.0830 339 | 0/8 16 h-lim-p 0.0373 20.0000 0.0004 3568.010706 0 0.0000 374 | 0/8 17 h-lim-p 0.0014 20.0000 0.0000 3568.010706 0 0.0000 407 Out... lnL = -3568.010706 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3568.010706 Node 7: lnL = -3568.010706 Node 8: lnL = -3568.010706 Node 9: lnL = -3568.010706 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 429 Sequential format.. Reading seq # 1: YDL219W_Sbay Reading seq # 2: YDL219W_Scer Reading seq # 3: YDL219W_Skud Reading seq # 4: YDL219W_Smik Reading seq # 5: YDL219W_Spar Sequences read.. Counting patterns.. # site patterns = 201 Counting frequencies.. 120 bytes for distance 32160 bytes for lkl0 25728 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.092102 0.080108 0.104692 0.296464 0.097744 0.199992 0.196543 0.144020 lnL0 = -1831.712948 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1831.712948 x= 0.09210 0.08011 0.10469 0.29646 0.09774 0.19999 0.19654 0.14402 1 h-lim-p 0.0018 0.0147 61.0675 1830.729924 9 0.0006 46 | 0/8 2 h-lim-p 0.0012 0.0124 27.5015 1830.280342 6 0.0014 74 | 0/8 3 h-lim-p 0.0020 0.0157 18.9261 1830.166164 2 0.0009 90 | 0/8 4 h-lim-p 0.0023 0.0369 7.4798 1830.148758 6 0.0008 118 | 0/8 5 h-lim-p 0.0061 0.3718 0.9621 1830.148358 4 0.0009 141 | 0/8 6 h-lim-p 0.0090 1.6365 0.0956 1830.148351 2 0.0012 167 | 0/8 7 h-lim-p 0.0299 20.0000 0.0038 1830.147996 0 0.2394 190 | 0/8 8 h-lim-p 0.0023 0.9818 0.3972 1830.147349 0 0.0034 210 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1830.147342 1 1.0938 232 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1830.147342 0 1.0938 252 | 0/8 11 h-lim-p 2.2216 20.0000 0.0000 1830.147342 0 1.9439 272 | 0/8 12 h-lim-p 2.4492 20.0000 0.0000 1830.147342 0 2.1430 292 | 0/8 13 h-lim-p 0.4933 20.0000 0.0000 1830.147342 0 0.1233 313 | 0/8 14 h-lim-p 0.0012 20.0000 0.0018 1830.147342 0 0.0001 336 | 0/8 15 h-lim-p 0.0000 20.0000 0.0055 1830.147342 0 0.0000 371 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 1830.147342 0 0.0000 391 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 1830.147342 0 0.0000 411 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1830.147342 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1830.147342 Node 7: lnL = -1830.147342 Node 8: lnL = -1830.147342 Node 9: lnL = -1830.147342 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 251 Sequential format.. Reading seq # 1: YDL220C_Sbay Reading seq # 2: YDL220C_Scer Reading seq # 3: YDL220C_Skud Reading seq # 4: YDL220C_Smik Reading seq # 5: YDL220C_Spar Sequences read.. Counting patterns.. # site patterns = 138 Counting frequencies.. 120 bytes for distance 22080 bytes for lkl0 17664 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.224305 0.033173 0.130943 0.193844 0.134285 0.208074 0.222378 0.284565 lnL0 = -1083.358654 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1083.358654 x= 0.22430 0.03317 0.13094 0.19384 0.13428 0.20807 0.22238 0.28457 1 h-lim-p 0.0035 0.0278 42.4771 1082.300352 7 0.0013 37 | 0/8 2 h-lim-p 0.0041 0.0324 9.0279 1082.201895 7 0.0025 67 | 0/8 3 h-lim-p 0.0024 0.0189 8.7746 1082.161159 7 0.0017 94 | 0/8 4 h-lim-p 0.0105 0.0838 1.1897 1082.158733 6 0.0036 123 | 0/8 5 h-lim-p 0.0087 0.2885 0.4919 1082.158374 3 0.0035 141 | 0/8 6 h-lim-p 0.0188 4.2688 0.0903 1082.158363 2 0.0031 168 | 0/8 7 h-lim-p 0.0232 16.4475 0.0121 1082.158362 0 0.0051 189 | 0/8 8 h-lim-p 0.1013 20.0000 0.0006 1082.158315 0 0.8102 212 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1082.158312 1 0.9961 234 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1082.158312 0 1.0938 254 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1082.158312 0 2.5000 274 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1082.158312 0 0.2344 297 | 0/8 13 h-lim-p 0.2274 20.0000 0.0000 1082.158312 0 0.0569 318 | 0/8 14 h-lim-p 0.0306 20.0000 0.0000 1082.158312 0 0.0306 338 | 0/8 15 h-lim-p 0.0189 20.0000 0.0000 1082.158312 0 0.0000 384 Out... lnL = -1082.158312 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1082.158312 Node 7: lnL = -1082.158312 Node 8: lnL = -1082.158312 Node 9: lnL = -1082.158312 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 277 Sequential format.. Reading seq # 1: YDL225W_Sbay Reading seq # 2: YDL225W_Scer Reading seq # 3: YDL225W_Skud Reading seq # 4: YDL225W_Smik Reading seq # 5: YDL225W_Spar Sequences read.. Counting patterns.. # site patterns = 84 Counting frequencies.. 120 bytes for distance 13440 bytes for lkl0 10752 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.085931 0.045126 0.012150 0.064689 0.052169 0.106715 0.137761 0.111601 lnL0 = -1036.212302 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1036.212302 x= 0.08593 0.04513 0.01215 0.06469 0.05217 0.10671 0.13776 0.11160 1 h-lim-p 0.0005 0.0043 171.5493 1035.192408 6 0.0001 37 | 0/8 2 h-lim-p 0.0004 0.0030 26.8941 1035.063865 2 0.0004 53 | 0/8 3 h-lim-p 0.0011 0.0149 8.9667 1035.052348 6 0.0003 80 | 0/8 4 h-lim-p 0.0015 0.0479 1.9229 1035.051792 2 0.0003 97 | 0/8 5 h-lim-p 0.0027 0.3692 0.2283 1035.051781 2 0.0004 116 | 0/8 6 h-lim-p 0.0012 2.0616 0.0865 1035.051779 0 0.0005 136 | 0/8 7 h-lim-p 0.0039 13.3744 0.0115 1035.051779 0 0.0008 157 | 0/8 8 h-lim-p 0.0981 20.0000 0.0001 1035.051757 0 1.1775 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1035.051754 0 1.2500 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1035.051754 0 2.1875 220 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1035.051754 0 1.0938 240 | 0/8 12 h-lim-p 1.2892 20.0000 0.0000 1035.051754 0 3.8675 261 | 0/8 13 h-lim-p 2.0741 20.0000 0.0000 1035.051754 0 0.2269 283 | 0/8 14 h-lim-p 0.8638 20.0000 0.0000 1035.051754 0 0.0001 316 Out... lnL = -1035.051754 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1035.051754 Node 7: lnL = -1035.051754 Node 8: lnL = -1035.051754 Node 9: lnL = -1035.051754 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 278 Sequential format.. Reading seq # 1: YDL226C_Sbay Reading seq # 2: YDL226C_Scer Reading seq # 3: YDL226C_Skud Reading seq # 4: YDL226C_Smik Reading seq # 5: YDL226C_Spar Sequences read.. Counting patterns.. # site patterns = 83 Counting frequencies.. 120 bytes for distance 13280 bytes for lkl0 10624 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.079878 0.040866 0.015857 0.067489 0.049369 0.103007 0.139013 0.104909 lnL0 = -1032.098004 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1032.098004 x= 0.07988 0.04087 0.01586 0.06749 0.04937 0.10301 0.13901 0.10491 1 h-lim-p 0.0012 0.0160 130.7101 1031.308477 7 0.0001 39 | 0/8 2 h-lim-p 0.0007 0.0054 22.2055 1031.209397 7 0.0004 69 | 0/8 3 h-lim-p 0.0015 0.0250 6.0686 1031.204656 6 0.0003 96 | 0/8 4 h-lim-p 0.0012 0.0703 1.4203 1031.204346 5 0.0003 120 | 0/8 5 h-lim-p 0.0026 0.8181 0.1818 1031.204334 3 0.0008 140 | 0/8 6 h-lim-p 0.0063 9.8880 0.0222 1031.204333 0 0.0003 163 | 0/8 7 h-lim-p 0.0020 20.0000 0.0039 1031.204333 0 0.0017 183 | 0/8 8 h-lim-p 0.0426 20.0000 0.0002 1031.204315 0 0.6811 207 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1031.204314 0 1.0938 227 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1031.204314 0 2.1875 247 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1031.204314 0 1.0938 267 | 0/8 12 h-lim-p 0.9783 20.0000 0.0000 1031.204314 0 3.9132 289 | 0/8 13 h-lim-p 2.1289 20.0000 0.0000 1031.204314 0 0.0003 321 Out... lnL = -1031.204314 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1031.204314 Node 7: lnL = -1031.204314 Node 8: lnL = -1031.204314 Node 9: lnL = -1031.204314 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 856 Sequential format.. Reading seq # 1: YDL227C_Sbay Reading seq # 2: YDL227C_Scer Reading seq # 3: YDL227C_Skud Reading seq # 4: YDL227C_Smik Reading seq # 5: YDL227C_Spar Sequences read.. Counting patterns.. # site patterns = 282 Counting frequencies.. 120 bytes for distance 45120 bytes for lkl0 36096 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.082337 0.102981 0.109874 0.101834 0.093224 0.221512 0.170682 0.126752 lnL0 = -3767.513844 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3767.513844 x= 0.08234 0.10298 0.10987 0.10183 0.09322 0.22151 0.17068 0.12675 1 h-lim-p 0.0047 0.0806 126.6544 3765.659773 3 0.0002 31 | 0/8 2 h-lim-p 0.0012 0.0093 26.9609 3765.542903 6 0.0003 59 | 0/8 3 h-lim-p 0.0005 0.0186 16.5594 3765.518932 5 0.0002 84 | 0/8 4 h-lim-p 0.0008 0.0712 4.7022 3765.516339 3 0.0003 104 | 0/8 5 h-lim-p 0.0020 0.3814 0.6366 3765.516245 1 0.0005 119 | 0/8 6 h-lim-p 0.0096 12.4723 0.0327 3765.516244 0 0.0005 142 | 0/8 7 h-lim-p 0.0027 20.0000 0.0064 3765.516243 0 0.0053 163 | 0/8 8 h-lim-p 0.0046 20.0000 0.0075 3765.515980 0 0.0550 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3765.515979 0 1.0938 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3765.515979 0 1.0938 226 | 0/8 11 h-lim-p 1.1536 20.0000 0.0000 3765.515979 0 3.4609 247 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3765.515979 0 0.5469 268 | 0/8 13 h-lim-p 0.0094 20.0000 0.0000 3765.515979 0 0.0041 288 | 0/8 14 h-lim-p 0.0010 20.0000 0.0001 3765.515979 0 0.0005 308 | 0/8 15 h-lim-p 0.0002 20.0000 0.0003 3765.515979 0 0.0000 332 | 0/8 16 h-lim-p 0.0006 20.0000 0.0000 3765.515979 0 0.0000 357 Out... lnL = -3765.515979 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3765.515979 Node 7: lnL = -3765.515979 Node 8: lnL = -3765.515979 Node 9: lnL = -3765.515979 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 388 Sequential format.. Reading seq # 1: YDL229W_Sbay Reading seq # 2: YDL229W_Scer Reading seq # 3: YDL229W_Skud Reading seq # 4: YDL229W_Smik Reading seq # 5: YDL229W_Spar Sequences read.. Counting patterns.. # site patterns = 158 Counting frequencies.. 120 bytes for distance 25280 bytes for lkl0 20224 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.050751 0.071402 0.029875 0.111169 0.048308 0.131929 0.806265 0.106770 lnL0 = -1703.752905 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1703.752905 x= 0.05075 0.07140 0.02988 0.11117 0.04831 0.13193 0.80626 0.10677 1 h-lim-p 0.0007 0.0056 181.9509 1701.049241 7 0.0002 37 | 0/8 2 h-lim-p 0.0005 0.0037 43.7036 1700.570832 7 0.0005 65 | 0/8 3 h-lim-p 0.0016 0.0137 14.0766 1700.521572 7 0.0005 94 | 0/8 4 h-lim-p 0.0008 0.0137 9.6098 1700.462342 0 0.0016 107 | 0/8 5 h-lim-p 0.0020 0.0383 7.8395 1700.451018 4 0.0006 129 | 0/8 6 h-lim-p 0.0008 0.0498 6.1473 1700.432838 0 0.0017 142 | 0/8 7 h-lim-p 0.0008 0.0223 13.2590 1700.423350 5 0.0005 166 | 0/8 8 h-lim-p 1.7057 20.0000 0.0040 1700.421172 5 1.1124 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1700.421133 3 1.4660 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1700.421133 0 1.0938 239 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1700.421133 0 2.1875 259 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1700.421133 0 1.0938 279 | 0/8 13 h-lim-p 0.2067 20.0000 0.0000 1700.421133 0 6.6133 304 | 0/8 14 h-lim-p 0.8503 20.0000 0.0001 1700.421133 0 0.2126 325 | 0/8 15 h-lim-p 0.0008 3.0166 0.0204 1700.421133 0 0.0008 345 | 0/8 16 h-lim-p 0.0000 0.0406 1.5146 .. | 0/8 17 h-lim-p 0.0000 6.5483 0.0178 1700.421133 0 0.0000 391 | 0/8 18 h-lim-p 0.0004 20.0000 0.0008 1700.421133 0 0.0004 411 | 0/8 19 h-lim-p 0.0014 20.0000 0.0002 1700.421133 0 0.0012 431 | 0/8 20 h-lim-p 0.0009 20.0000 0.0003 1700.421133 0 0.0009 451 | 0/8 21 h-lim-p 0.0015 20.0000 0.0002 1700.421133 0 0.0000 475 | 0/8 22 h-lim-p 0.0001 20.0000 0.0001 1700.421133 0 0.0001 495 | 0/8 23 h-lim-p 0.0000 20.0000 0.0002 1700.421133 0 0.0000 515 | 0/8 24 h-lim-p 0.0024 20.0000 0.0000 1700.421133 0 0.0012 535 Out... lnL = -1700.421133 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1700.421133 Node 7: lnL = -1700.421133 Node 8: lnL = -1700.421133 Node 9: lnL = -1700.421133 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 482 Sequential format.. Reading seq # 1: YDL230W_Sbay Reading seq # 2: YDL230W_Scer Reading seq # 3: YDL230W_Skud Reading seq # 4: YDL230W_Smik Reading seq # 5: YDL230W_Spar Sequences read.. Counting patterns.. # site patterns = 192 Counting frequencies.. 120 bytes for distance 30720 bytes for lkl0 24576 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.163481 0.061540 0.052624 0.108215 0.101078 0.146418 0.191615 0.206832 lnL0 = -2133.685060 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2133.685060 x= 0.16348 0.06154 0.05262 0.10822 0.10108 0.14642 0.19162 0.20683 1 h-lim-p 0.0017 0.0133 79.5438 2132.821839 7 0.0003 40 | 0/8 2 h-lim-p 0.0006 0.0048 24.2504 2132.664617 2 0.0006 56 | 0/8 3 h-lim-p 0.0011 0.0173 12.3659 2132.635687 5 0.0005 81 | 0/8 4 h-lim-p 0.0014 0.0603 4.0221 2132.632904 5 0.0004 104 | 0/8 5 h-lim-p 0.0021 0.2496 0.7632 2132.632747 3 0.0006 123 | 0/8 6 h-lim-p 0.0032 1.3027 0.1322 2132.632742 2 0.0005 150 | 0/8 7 h-lim-p 0.0025 9.1699 0.0278 2132.632741 1 0.0012 173 | 0/8 8 h-lim-p 0.0376 20.0000 0.0009 2132.632389 0 0.6015 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2132.632388 0 1.0938 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2132.632388 0 1.2500 237 | 0/8 11 h-lim-p 2.0824 20.0000 0.0000 2132.632388 0 0.4555 258 | 0/8 12 h-lim-p 0.2549 20.0000 0.0000 2132.632388 0 0.0159 281 | 0/8 13 h-lim-p 0.0082 20.0000 0.0000 2132.632388 0 0.0082 301 | 0/8 14 h-lim-p 0.0060 20.0000 0.0000 2132.632388 0 0.0000 338 Out... lnL = -2132.632388 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2132.632388 Node 7: lnL = -2132.632388 Node 8: lnL = -2132.632388 Node 9: lnL = -2132.632388 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 349 Sequential format.. Reading seq # 1: YDL235C_Sbay Reading seq # 2: YDL235C_Scer Reading seq # 3: YDL235C_Skud Reading seq # 4: YDL235C_Smik Reading seq # 5: YDL235C_Spar Sequences read.. Counting patterns.. # site patterns = 124 Counting frequencies.. 120 bytes for distance 19840 bytes for lkl0 15872 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.090363 0.064957 0.064616 0.037470 0.052941 0.135427 0.145052 0.121293 lnL0 = -1333.608044 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1333.608044 x= 0.09036 0.06496 0.06462 0.03747 0.05294 0.13543 0.14505 0.12129 1 h-lim-p 0.0001 0.0012 74.0926 1332.857825 0 0.0003 23 | 0/8 2 h-lim-p 0.0010 0.0436 20.4967 1332.823002 7 0.0002 54 | 0/8 3 h-lim-p 0.0004 0.0154 9.7691 1332.806674 5 0.0004 78 | 0/8 4 h-lim-p 0.0013 0.0670 3.2214 1332.804939 5 0.0004 105 | 0/8 5 h-lim-p 0.0017 0.2781 0.7401 1332.804797 4 0.0005 126 | 0/8 6 h-lim-p 0.0051 2.6173 0.0795 1332.804795 0 0.0006 148 | 0/8 7 h-lim-p 0.0079 20.0000 0.0056 1332.804795 0 0.0034 168 | 0/8 8 h-lim-p 0.0278 20.0000 0.0007 1332.804744 0 0.2221 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1332.804742 0 1.0938 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1332.804742 0 1.0938 231 | 0/8 11 h-lim-p 1.4688 20.0000 0.0000 1332.804742 0 0.3213 252 | 0/8 12 h-lim-p 0.1719 20.0000 0.0000 1332.804742 0 0.0430 273 | 0/8 13 h-lim-p 0.0247 20.0000 0.0000 1332.804742 0 0.0008 297 | 0/8 14 h-lim-p 0.0004 20.0000 0.0000 1332.804742 0 0.0000 319 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 1332.804742 0 0.0000 353 Out... lnL = -1332.804742 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1332.804742 Node 7: lnL = -1332.804742 Node 8: lnL = -1332.804742 Node 9: lnL = -1332.804742 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 208 Sequential format.. Reading seq # 1: YDL237W_Sbay Reading seq # 2: YDL237W_Scer Reading seq # 3: YDL237W_Skud Reading seq # 4: YDL237W_Smik Reading seq # 5: YDL237W_Spar Sequences read.. Counting patterns.. # site patterns = 88 Counting frequencies.. 120 bytes for distance 14080 bytes for lkl0 11264 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.130299 0.019995 0.065957 0.075599 0.078506 0.138956 0.248397 0.162188 lnL0 = -915.552846 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 915.552846 x= 0.13030 0.01999 0.06596 0.07560 0.07851 0.13896 0.24840 0.16219 1 h-lim-p 0.0047 0.0379 60.6742 914.848030 8 0.0004 42 | 0/8 2 h-lim-p 0.0030 0.0246 8.4148 914.797283 2 0.0014 58 | 0/8 3 h-lim-p 0.0017 0.0411 6.9231 914.784990 4 0.0008 77 | 0/8 4 h-lim-p 0.0031 0.0694 1.7205 914.784049 2 0.0007 94 | 0/8 5 h-lim-p 0.0027 0.3835 0.4623 914.783950 3 0.0010 112 | 0/8 6 h-lim-p 0.0074 1.7730 0.0636 914.783948 0 0.0008 134 | 0/8 7 h-lim-p 0.0094 20.0000 0.0055 914.783948 0 0.0021 155 | 0/8 8 h-lim-p 0.0806 20.0000 0.0001 914.783940 0 0.9670 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 914.783939 0 1.0938 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 914.783939 0 1.0938 218 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 914.783939 0 2.5000 238 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 914.783939 0 0.0098 265 | 0/8 13 h-lim-p 0.0049 20.0000 0.0000 914.783939 0 0.0025 285 Out... lnL = -914.783939 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -914.783939 Node 7: lnL = -914.783939 Node 8: lnL = -914.783939 Node 9: lnL = -914.783939 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 208 Sequential format.. Reading seq # 1: YDL238C_Sbay Reading seq # 2: YDL238C_Scer Reading seq # 3: YDL238C_Skud Reading seq # 4: YDL238C_Smik Reading seq # 5: YDL238C_Spar Sequences read.. Counting patterns.. # site patterns = 88 Counting frequencies.. 120 bytes for distance 14080 bytes for lkl0 11264 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.132467 0.018354 0.072189 0.076713 0.077392 0.136347 0.243920 0.164497 lnL0 = -917.546818 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 917.546818 x= 0.13247 0.01835 0.07219 0.07671 0.07739 0.13635 0.24392 0.16450 1 h-lim-p 0.0021 0.0168 65.8428 916.719662 8 0.0004 40 | 0/8 2 h-lim-p 0.0020 0.0160 9.6129 916.665259 6 0.0012 67 | 0/8 3 h-lim-p 0.0016 0.0377 7.0270 916.648801 7 0.0009 98 | 0/8 4 h-lim-p 0.0024 0.0517 2.7230 916.646777 6 0.0007 124 | 0/8 5 h-lim-p 0.0046 0.4235 0.3990 916.646707 2 0.0009 141 | 0/8 6 h-lim-p 0.0041 2.2755 0.0900 916.646703 0 0.0010 162 | 0/8 7 h-lim-p 0.0205 20.0000 0.0045 916.646703 0 0.0026 184 | 0/8 8 h-lim-p 0.0354 20.0000 0.0003 916.646694 0 0.5659 208 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 916.646694 0 1.0938 228 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 916.646694 0 2.1875 248 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 916.646694 0 1.0938 268 | 0/8 12 h-lim-p 1.9894 20.0000 0.0000 916.646694 0 3.9789 289 | 0/8 13 h-lim-p 2.0345 20.0000 0.0000 916.646694 0 0.4450 310 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 916.646694 0 0.0003 342 Out... lnL = -916.646694 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -916.646694 Node 7: lnL = -916.646694 Node 8: lnL = -916.646694 Node 9: lnL = -916.646694 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 867 Sequential format.. Reading seq # 1: YDL241W_Sbay Reading seq # 2: YDL241W_Scer Reading seq # 3: YDL241W_Skud Reading seq # 4: YDL241W_Smik Reading seq # 5: YDL241W_Spar Sequences read.. Counting patterns.. # site patterns = 446 Counting frequencies.. 120 bytes for distance 71360 bytes for lkl0 57088 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.319668 0.016243 0.256047 0.198880 0.143371 0.144032 0.553169 0.391161 lnL0 = -4256.983071 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4256.983071 x= 0.31967 0.01624 0.25605 0.19888 0.14337 0.14403 0.55317 0.39116 1 h-lim-p 0.0075 1.2883 106.5926 4253.744547 7 0.0006 39 | 0/8 2 h-lim-p 0.0014 0.0115 26.2923 4253.575055 5 0.0005 62 | 0/8 3 h-lim-p 0.0008 0.0172 17.8278 4253.399577 0 0.0015 75 | 0/8 4 h-lim-p 0.0062 0.1824 4.3299 4253.368133 6 0.0037 102 | 0/8 5 h-lim-p 0.0042 0.1209 3.7969 4253.362582 5 0.0012 127 | 0/8 6 h-lim-p 0.0098 0.5358 0.4711 4253.362415 3 0.0014 149 | 0/8 7 h-lim-p 0.0123 11.7260 0.0546 4253.362349 1 0.0098 171 | 0/8 8 h-lim-p 0.0461 20.0000 0.0117 4253.356310 0 0.3686 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0008 4253.355853 3 1.0004 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4253.355853 0 1.0938 240 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4253.355853 0 1.0938 260 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4253.355853 0 2.1875 280 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 4253.355853 0 0.3125 302 | 0/8 14 h-lim-p 0.0686 20.0000 0.0000 4253.355853 0 0.0038 325 Out... lnL = -4253.355853 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4253.355853 Node 7: lnL = -4253.355853 Node 8: lnL = -4253.355853 Node 9: lnL = -4253.355853 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 877 Sequential format.. Reading seq # 1: YDL244W_Sbay Reading seq # 2: YDL244W_Scer Reading seq # 3: YDL244W_Skud Reading seq # 4: YDL244W_Smik Reading seq # 5: YDL244W_Spar Sequences read.. Counting patterns.. # site patterns = 287 Counting frequencies.. 120 bytes for distance 45920 bytes for lkl0 36736 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.136628 0.336381 0.000060 0.268658 0.223853 0.139286 0.209381 0.190699 lnL0 = -3865.004832 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3865.004832 x= 0.13663 0.33638 0.00006 0.26866 0.22385 0.13929 0.20938 0.19070 1 h-lim-p 0.0004 0.0033 100.9116 3859.608710 0 0.0012 23 | 0/8 2 h-lim-p 0.0003 0.0028 33.0114 3859.153661 0 0.0010 36 | 0/8 3 h-lim-p 0.0000 0.0002 40.9521 3859.026542 m 0.0002 48 | 1/8 4 h-lim-p 0.0008 0.0483 6.5024 3859.005321 1 0.0010 62 | 1/8 5 h-lim-p 0.0017 0.0769 3.8721 3858.999657 3 0.0008 81 | 1/8 6 h-lim-p 0.0032 0.3610 0.9928 3858.999107 4 0.0011 102 | 1/8 7 h-lim-p 0.0141 5.4239 0.0807 3858.994249 0 0.0424 122 | 1/8 8 h-lim-p 0.0050 0.6299 0.6869 3858.909692 0 0.0199 143 | 1/8 9 h-lim-p 2.5000 20.0000 0.0024 3858.908032 2 0.9644 166 | 1/8 10 h-lim-p 2.5000 20.0000 0.0001 3858.908028 0 1.2500 185 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 3858.908028 0 1.0938 204 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 3858.908028 0 1.2500 223 | 1/8 13 h-lim-p 1.7535 20.0000 0.0000 3858.908028 0 0.0000 265 Out... lnL = -3858.908028 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3858.908028 Node 7: lnL = -3858.908028 Node 8: lnL = -3858.908028 Node 9: lnL = -3858.908028 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 594 Sequential format.. Reading seq # 1: YDR002W_Sbay Reading seq # 2: YDR002W_Scer Reading seq # 3: YDR002W_Skud Reading seq # 4: YDR002W_Smik Reading seq # 5: YDR002W_Spar Sequences read.. Counting patterns.. # site patterns = 187 Counting frequencies.. 120 bytes for distance 29920 bytes for lkl0 23936 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.096493 0.043282 0.025596 0.072521 0.068518 0.110702 0.137057 0.119960 lnL0 = -2234.706412 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2234.706412 x= 0.09649 0.04328 0.02560 0.07252 0.06852 0.11070 0.13706 0.11996 1 h-lim-p 0.0002 0.0018 194.2926 2232.239734 7 0.0001 39 | 0/8 2 h-lim-p 0.0001 0.0010 61.5599 2231.931615 0 0.0002 51 | 0/8 3 h-lim-p 0.0009 0.0146 13.1252 2231.911273 6 0.0002 78 | 0/8 4 h-lim-p 0.0004 0.0259 7.7084 2231.905694 6 0.0002 107 | 0/8 5 h-lim-p 0.0014 0.1446 1.3290 2231.905336 4 0.0004 130 | 0/8 6 h-lim-p 0.0035 1.3186 0.1579 2231.905330 0 0.0004 144 | 0/8 7 h-lim-p 0.0270 20.0000 0.0026 2231.905084 0 0.1079 166 | 0/8 8 h-lim-p 0.0006 0.3027 0.4777 2231.903772 0 0.0012 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2231.903730 2 0.9961 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2231.903730 0 1.0938 231 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2231.903730 0 1.0938 251 | 0/8 12 h-lim-p 0.9657 20.0000 0.0000 2231.903730 0 7.7254 274 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2231.903730 0 0.0195 300 | 0/8 14 h-lim-p 0.1366 20.0000 0.0000 2231.903730 0 0.0085 323 | 0/8 15 h-lim-p 0.0009 20.0000 0.0000 2231.903730 0 0.0000 357 | 0/8 16 h-lim-p 0.0000 20.0000 0.0016 | 0/8 17 h-lim-p 0.0000 20.0000 0.0016 Out... lnL = -2231.903730 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2231.903730 Node 7: lnL = -2231.903730 Node 8: lnL = -2231.903730 Node 9: lnL = -2231.903730 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 501 Sequential format.. Reading seq # 1: YDR003W_Sbay Reading seq # 2: YDR003W_Scer Reading seq # 3: YDR003W_Skud Reading seq # 4: YDR003W_Smik Reading seq # 5: YDR003W_Spar Sequences read.. Counting patterns.. # site patterns = 188 Counting frequencies.. 120 bytes for distance 30080 bytes for lkl0 24064 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.079578 0.013228 0.054579 0.117380 0.070649 0.243785 0.237750 0.111448 lnL0 = -2043.995005 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2043.995005 x= 0.07958 0.01323 0.05458 0.11738 0.07065 0.24379 0.23775 0.11145 1 h-lim-p 0.0006 0.0047 169.6348 2042.167360 4 0.0001 31 | 0/8 2 h-lim-p 0.0002 0.0018 42.0656 2041.911958 0 0.0003 43 | 0/8 3 h-lim-p 0.0011 0.0236 12.8584 2041.888512 6 0.0003 70 | 0/8 4 h-lim-p 0.0005 0.0340 7.4764 2041.875063 1 0.0007 84 | 0/8 5 h-lim-p 0.0015 0.0532 3.3169 2041.873531 2 0.0004 101 | 0/8 6 h-lim-p 0.0115 2.3891 0.1023 2041.873511 2 0.0015 119 | 0/8 7 h-lim-p 0.0011 2.0530 0.1390 2041.873459 0 0.0022 140 | 0/8 8 h-lim-p 0.0171 20.0000 0.0182 2041.865872 0 0.1365 163 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 2041.864934 2 1.1719 187 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2041.864898 2 1.3159 212 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2041.864898 0 1.0938 232 | 0/8 12 h-lim-p 1.3021 20.0000 0.0000 2041.864898 0 1.1393 252 | 0/8 13 h-lim-p 0.8617 20.0000 0.0000 2041.864898 0 0.4308 272 | 0/8 14 h-lim-p 0.0012 20.0000 0.0029 2041.864898 0 0.0012 292 | 0/8 15 h-lim-p 0.0010 20.0000 0.0035 2041.864898 0 0.0000 331 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -2041.864898 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2041.864898 Node 7: lnL = -2041.864898 Node 8: lnL = -2041.864898 Node 9: lnL = -2041.864898 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 532 Sequential format.. Reading seq # 1: YDR004W_Sbay Reading seq # 2: YDR004W_Scer Reading seq # 3: YDR004W_Skud Reading seq # 4: YDR004W_Smik Reading seq # 5: YDR004W_Spar Sequences read.. Counting patterns.. # site patterns = 192 Counting frequencies.. 120 bytes for distance 30720 bytes for lkl0 24576 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.092342 0.153582 0.081257 0.111863 0.066487 0.356318 0.279100 0.138608 lnL0 = -2060.343945 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2060.343945 x= 0.09234 0.15358 0.08126 0.11186 0.06649 0.35632 0.27910 0.13861 1 h-lim-p 0.0001 0.0011 128.8511 2056.059257 0 0.0005 24 | 0/8 2 h-lim-p 0.0005 0.0042 86.0178 2055.206776 8 0.0003 55 | 0/8 3 h-lim-p 0.0006 0.0052 47.1381 2054.692685 6 0.0006 78 | 0/8 4 h-lim-p 0.0020 0.0383 14.7649 2054.624906 7 0.0007 106 | 0/8 5 h-lim-p 0.0010 0.0106 10.5366 2054.436068 0 0.0062 120 | 0/8 6 h-lim-p 0.0002 0.0019 22.4698 2054.384412 0 0.0009 134 | 0/8 7 h-lim-p 0.0100 1.0474 2.1189 2054.365592 2 0.0094 150 | 0/8 8 h-lim-p 1.3626 20.0000 0.0146 2054.340134 6 0.9528 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 2054.339963 2 0.9961 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2054.339962 0 1.0938 220 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2054.339962 0 1.0938 240 | 0/8 12 h-lim-p 1.6688 20.0000 0.0000 2054.339962 0 0.2086 262 | 0/8 13 h-lim-p 0.0971 20.0000 0.0000 2054.339962 0 0.0061 285 | 0/8 14 h-lim-p 0.0034 20.0000 0.0000 2054.339962 0 0.0000 312 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 2054.339962 0 0.0000 341 Out... lnL = -2054.339962 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2054.339962 Node 7: lnL = -2054.339962 Node 8: lnL = -2054.339962 Node 9: lnL = -2054.339962 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 632 Sequential format.. Reading seq # 1: YDR006C_Sbay Reading seq # 2: YDR006C_Scer Reading seq # 3: YDR006C_Skud Reading seq # 4: YDR006C_Smik Reading seq # 5: YDR006C_Spar Sequences read.. Counting patterns.. # site patterns = 190 Counting frequencies.. 120 bytes for distance 30400 bytes for lkl0 24320 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.092806 0.047620 0.065810 0.109348 0.048834 0.132358 0.177248 0.121015 lnL0 = -2555.096505 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2555.096505 x= 0.09281 0.04762 0.06581 0.10935 0.04883 0.13236 0.17725 0.12101 1 h-lim-p 0.0020 0.0161 105.9237 2554.162427 6 0.0002 38 | 0/8 2 h-lim-p 0.0006 0.0044 20.8543 2554.110045 6 0.0002 62 | 0/8 3 h-lim-p 0.0003 0.0133 15.5905 2554.093377 4 0.0002 85 | 0/8 4 h-lim-p 0.0007 0.0686 4.2621 2554.091096 3 0.0003 103 | 0/8 5 h-lim-p 0.0017 0.2271 0.7363 2554.091023 3 0.0003 124 | 0/8 6 h-lim-p 0.0025 3.0142 0.0856 2554.091022 0 0.0003 146 | 0/8 7 h-lim-p 0.0022 18.4046 0.0107 2554.091022 0 0.0005 167 | 0/8 8 h-lim-p 0.1101 20.0000 0.0000 2554.091019 0 0.8804 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2554.091019 0 1.0938 210 | 0/8 10 h-lim-p 1.3280 20.0000 0.0000 2554.091019 0 1.3280 230 | 0/8 11 h-lim-p 1.4117 20.0000 0.0000 2554.091019 0 0.0882 253 | 0/8 12 h-lim-p 0.0103 20.0000 0.0000 2554.091019 0 0.0000 280 | 0/8 13 h-lim-p 0.0004 20.0000 0.0000 2554.091019 0 0.0000 313 Out... lnL = -2554.091019 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2554.091019 Node 7: lnL = -2554.091019 Node 8: lnL = -2554.091019 Node 9: lnL = -2554.091019 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 632 Sequential format.. Reading seq # 1: YDR007W_Sbay Reading seq # 2: YDR007W_Scer Reading seq # 3: YDR007W_Skud Reading seq # 4: YDR007W_Smik Reading seq # 5: YDR007W_Spar Sequences read.. Counting patterns.. # site patterns = 189 Counting frequencies.. 120 bytes for distance 30240 bytes for lkl0 24192 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.093811 0.044445 0.068403 0.107444 0.050739 0.135969 0.180194 0.122283 lnL0 = -2561.574510 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2561.574510 x= 0.09381 0.04445 0.06840 0.10744 0.05074 0.13597 0.18019 0.12228 1 h-lim-p 0.0002 0.0018 108.0165 2560.533269 6 0.0002 36 | 0/8 2 h-lim-p 0.0010 0.0079 20.6909 2560.467227 5 0.0003 60 | 0/8 3 h-lim-p 0.0008 0.0281 8.4357 2560.458070 5 0.0003 82 | 0/8 4 h-lim-p 0.0006 0.0840 3.9580 2560.457169 2 0.0001 99 | 0/8 5 h-lim-p 0.0006 0.2329 0.8918 2560.457071 2 0.0003 115 | 0/8 6 h-lim-p 0.0017 1.5803 0.1448 2560.457068 1 0.0003 138 | 0/8 7 h-lim-p 0.0040 12.7448 0.0118 2560.457068 0 0.0004 160 | 0/8 8 h-lim-p 0.0644 20.0000 0.0001 2560.457054 0 1.0305 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2560.457053 0 1.0938 204 | 0/8 10 h-lim-p 2.2096 20.0000 0.0000 2560.457053 0 0.5524 225 | 0/8 11 h-lim-p 0.3613 20.0000 0.0000 2560.457053 0 0.0339 248 | 0/8 12 h-lim-p 0.0190 20.0000 0.0000 2560.457053 0 0.0000 292 | 0/8 13 h-lim-p 0.0000 20.0000 0.0014 | 0/8 14 h-lim-p 0.0000 20.0000 0.0014 Out... lnL = -2560.457053 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2560.457053 Node 7: lnL = -2560.457053 Node 8: lnL = -2560.457053 Node 9: lnL = -2560.457053 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 370 Sequential format.. Reading seq # 1: YDR013W_Sbay Reading seq # 2: YDR013W_Scer Reading seq # 3: YDR013W_Skud Reading seq # 4: YDR013W_Smik Reading seq # 5: YDR013W_Spar Sequences read.. Counting patterns.. # site patterns = 185 Counting frequencies.. 120 bytes for distance 29600 bytes for lkl0 23680 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.154738 0.000060 0.413132 0.087897 0.122904 0.261831 0.307281 0.212705 lnL0 = -1616.845373 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1616.845373 x= 0.15474 0.00006 0.41313 0.08790 0.12290 0.26183 0.30728 0.21271 1 h-lim-p 0.0018 0.0147 25.8463 1616.330036 8 0.0013 43 | 0/8 2 h-lim-p 0.0016 0.0258 20.5167 1616.010944 0 0.0024 55 | 0/8 3 h-lim-p 0.0026 0.0209 11.8426 1615.967549 7 0.0009 86 | 0/8 4 h-lim-p 0.0020 0.1060 5.3993 1615.944176 5 0.0022 112 | 0/8 5 h-lim-p 0.0111 0.0886 0.8048 1615.943562 4 0.0019 135 | 0/8 6 h-lim-p 0.0038 0.2563 0.4153 1615.943281 2 0.0037 159 | 0/8 7 h-lim-p 0.0213 1.7781 0.0730 1615.943233 3 0.0063 187 | 0/8 8 h-lim-p 0.0266 6.5505 0.0174 1615.938180 0 0.4249 211 | 0/8 9 h-lim-p 2.5000 20.0000 0.0015 1615.937778 2 0.9961 235 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1615.937778 0 1.0938 255 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1615.937778 0 1.0938 275 | 0/8 12 h-lim-p 1.5671 20.0000 0.0000 1615.937778 0 3.1341 296 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1615.937778 0 0.0391 321 | 0/8 14 h-lim-p 0.0101 20.0000 0.0000 1615.937778 0 0.0025 342 Out... lnL = -1615.937778 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1615.937778 Node 7: lnL = -1615.937778 Node 8: lnL = -1615.937778 Node 9: lnL = -1615.937778 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 273 Sequential format.. Reading seq # 1: YDR014W_Sbay Reading seq # 2: YDR014W_Scer Reading seq # 3: YDR014W_Skud Reading seq # 4: YDR014W_Smik Reading seq # 5: YDR014W_Spar Sequences read.. Counting patterns.. # site patterns = 132 Counting frequencies.. 120 bytes for distance 21120 bytes for lkl0 16896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.131824 0.120017 0.105726 0.178694 0.075201 0.209849 0.200203 0.175195 lnL0 = -1325.932790 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1325.932790 x= 0.13182 0.12002 0.10573 0.17869 0.07520 0.20985 0.20020 0.17520 1 h-lim-p 0.0032 0.0257 32.2812 1325.407444 8 0.0011 40 | 0/8 2 h-lim-p 0.0033 0.0266 8.8509 1325.363600 6 0.0012 65 | 0/8 3 h-lim-p 0.0027 0.0682 3.9280 1325.359210 4 0.0007 87 | 0/8 4 h-lim-p 0.0016 0.1571 1.7011 1325.358050 5 0.0010 113 | 0/8 5 h-lim-p 0.0050 0.6134 0.3368 1325.357982 2 0.0012 130 | 0/8 6 h-lim-p 0.0086 6.5469 0.0480 1325.357980 1 0.0017 153 | 0/8 7 h-lim-p 0.0131 20.0000 0.0063 1325.357980 0 0.0057 173 | 0/8 8 h-lim-p 0.0269 20.0000 0.0013 1325.357916 0 0.3226 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1325.357915 0 1.0938 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1325.357915 0 1.0938 236 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1325.357915 0 2.1875 256 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1325.357915 0 0.5469 277 | 0/8 13 h-lim-p 0.1181 20.0000 0.0000 1325.357915 0 0.0443 298 | 0/8 14 h-lim-p 0.0206 20.0000 0.0000 1325.357915 0 0.0000 333 Out... lnL = -1325.357915 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1325.357915 Node 7: lnL = -1325.357915 Node 8: lnL = -1325.357915 Node 9: lnL = -1325.357915 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 415 Sequential format.. Reading seq # 1: YDR017C_Sbay Reading seq # 2: YDR017C_Scer Reading seq # 3: YDR017C_Skud Reading seq # 4: YDR017C_Smik Reading seq # 5: YDR017C_Spar Sequences read.. Counting patterns.. # site patterns = 131 Counting frequencies.. 120 bytes for distance 20960 bytes for lkl0 16768 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.068799 0.049046 0.044125 0.068145 0.071602 0.099921 0.170795 0.092359 lnL0 = -1608.673294 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1608.673294 x= 0.06880 0.04905 0.04412 0.06815 0.07160 0.09992 0.17080 0.09236 1 h-lim-p 0.0009 0.0069 103.8381 1607.683291 2 0.0002 27 | 0/8 2 h-lim-p 0.0008 0.0061 23.1324 1607.596318 6 0.0003 50 | 0/8 3 h-lim-p 0.0012 0.0253 6.5840 1607.590776 2 0.0003 67 | 0/8 4 h-lim-p 0.0009 0.0880 2.1241 1607.590057 3 0.0004 85 | 0/8 5 h-lim-p 0.0010 0.5026 0.7964 1607.589918 3 0.0005 104 | 0/8 6 h-lim-p 0.0078 1.8200 0.0515 1607.589917 0 0.0004 127 | 0/8 7 h-lim-p 0.0039 20.0000 0.0057 1607.589917 0 0.0017 147 | 0/8 8 h-lim-p 0.0114 20.0000 0.0008 1607.589841 0 0.2726 171 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1607.589839 0 1.0938 191 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1607.589839 0 1.2500 211 | 0/8 11 h-lim-p 1.6473 20.0000 0.0000 1607.589839 0 0.3603 232 | 0/8 12 h-lim-p 0.1854 20.0000 0.0000 1607.589839 0 0.0000 280 Out... lnL = -1607.589839 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1607.589839 Node 7: lnL = -1607.589839 Node 8: lnL = -1607.589839 Node 9: lnL = -1607.589839 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 336 Sequential format.. Reading seq # 1: YDR018C_Sbay Reading seq # 2: YDR018C_Scer Reading seq # 3: YDR018C_Skud Reading seq # 4: YDR018C_Smik Reading seq # 5: YDR018C_Spar Sequences read.. Counting patterns.. # site patterns = 192 Counting frequencies.. 120 bytes for distance 30720 bytes for lkl0 24576 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.125024 0.106448 0.365777 0.173506 0.011332 0.373353 0.253571 0.185657 lnL0 = -1619.533121 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1619.533121 x= 0.12502 0.10645 0.36578 0.17351 0.01133 0.37335 0.25357 0.18566 1 h-lim-p 0.0017 0.0136 41.8619 1618.760040 9 0.0010 42 | 0/8 2 h-lim-p 0.0002 0.0020 69.6307 1617.915188 0 0.0010 56 | 0/8 3 h-lim-p 0.0005 0.0039 32.3069 1617.441933 0 0.0015 69 | 0/8 4 h-lim-p 0.0008 0.0062 11.3352 1617.300686 0 0.0031 83 | 0/8 5 h-lim-p 0.0142 0.1180 2.4877 1617.296631 4 0.0014 105 | 0/8 6 h-lim-p 0.0056 0.1607 0.6088 1617.295093 3 0.0057 123 | 0/8 7 h-lim-p 0.0181 0.3155 0.1906 1617.292160 2 0.0170 147 | 0/8 8 h-lim-p 0.0139 1.9075 0.2323 1617.218321 0 0.0557 169 | 0/8 9 h-lim-p 2.5000 20.0000 0.0013 1617.217552 2 1.0889 193 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1617.217547 0 1.0938 213 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1617.217547 0 1.0938 233 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1617.217547 0 0.0002 266 Out... lnL = -1617.217547 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1617.217547 Node 7: lnL = -1617.217547 Node 8: lnL = -1617.217547 Node 9: lnL = -1617.217547 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 848 Sequential format.. Reading seq # 1: YDR023W_Sbay Reading seq # 2: YDR023W_Scer Reading seq # 3: YDR023W_Skud Reading seq # 4: YDR023W_Smik Reading seq # 5: YDR023W_Spar Sequences read.. Counting patterns.. # site patterns = 367 Counting frequencies.. 120 bytes for distance 58720 bytes for lkl0 46976 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.101594 0.123276 0.065023 0.478230 0.323960 0.782586 0.338253 0.184098 lnL0 = -4103.388296 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4103.388296 x= 0.10159 0.12328 0.06502 0.47823 0.32396 0.78259 0.33825 0.18410 1 h-lim-p 0.0007 0.0054 89.1754 4097.453461 0 0.0014 23 | 0/8 2 h-lim-p 0.0004 0.0035 99.2598 4095.840936 1 0.0005 37 | 0/8 3 h-lim-p 0.0030 0.0276 18.0301 4095.630317 2 0.0014 53 | 0/8 4 h-lim-p 0.0012 0.0096 18.5305 4095.469557 0 0.0018 65 | 0/8 5 h-lim-p 0.0017 0.0137 16.2196 4095.151804 0 0.0069 79 | 0/8 6 h-lim-p 0.0134 0.1072 4.3753 4095.137901 5 0.0018 103 | 0/8 7 h-lim-p 0.0028 0.1911 2.7203 4095.106770 0 0.0114 117 | 0/8 8 h-lim-p 1.1730 20.0000 0.0264 4094.916878 2 1.0997 133 | 0/8 9 h-lim-p 2.5000 20.0000 0.0032 4094.914813 4 0.9422 161 | 0/8 10 h-lim-p 2.5000 20.0000 0.0003 4094.914797 0 1.0938 181 | 0/8 11 h-lim-p 2.5000 20.0000 0.0001 4094.914796 0 1.2500 201 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4094.914796 0 1.0938 221 | 0/8 13 h-lim-p 1.1537 20.0000 0.0000 4094.914796 0 1.0095 241 | 0/8 14 h-lim-p 0.0194 20.0000 0.0003 4094.914796 0 0.0097 261 | 0/8 15 h-lim-p 0.0016 20.0000 0.0022 4094.914796 0 0.0002 283 | 0/8 16 h-lim-p 0.0023 20.0000 0.0002 4094.914796 0 0.0000 308 | 0/8 17 h-lim-p 0.0018 20.0000 0.0000 4094.914796 0 0.0000 341 Out... lnL = -4094.914796 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4094.914796 Node 7: lnL = -4094.914796 Node 8: lnL = -4094.914796 Node 9: lnL = -4094.914796 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 405 Sequential format.. Reading seq # 1: YDR026C_Sbay Reading seq # 2: YDR026C_Scer Reading seq # 3: YDR026C_Skud Reading seq # 4: YDR026C_Smik Reading seq # 5: YDR026C_Spar Sequences read.. Counting patterns.. # site patterns = 173 Counting frequencies.. 120 bytes for distance 27680 bytes for lkl0 22144 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.069549 0.126154 0.104081 0.127269 0.081281 0.236510 0.156231 0.099018 lnL0 = -1778.350925 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1778.350925 x= 0.06955 0.12615 0.10408 0.12727 0.08128 0.23651 0.15623 0.09902 1 h-lim-p 0.0006 0.0044 45.9278 1777.757057 6 0.0006 33 | 0/8 2 h-lim-p 0.0016 0.0127 13.8126 1777.708060 7 0.0006 62 | 0/8 3 h-lim-p 0.0018 0.0466 4.3176 1777.702934 6 0.0006 90 | 0/8 4 h-lim-p 0.0017 0.3217 1.5180 1777.702534 2 0.0004 107 | 0/8 5 h-lim-p 0.0016 0.8439 0.3953 1777.702473 3 0.0008 126 | 0/8 6 h-lim-p 0.0028 3.0632 0.1181 1777.702468 0 0.0007 147 | 0/8 7 h-lim-p 0.0197 20.0000 0.0042 1777.702466 1 0.0157 169 | 0/8 8 h-lim-p 0.0100 20.0000 0.0066 1777.702329 0 0.0798 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1777.702322 1 0.9961 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1777.702322 0 1.0938 234 | 0/8 11 h-lim-p 1.0586 20.0000 0.0000 1777.702322 0 0.0041 261 | 0/8 12 h-lim-p 0.0002 20.0000 0.0001 1777.702322 0 0.0000 297 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1777.702322 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1777.702322 Node 7: lnL = -1777.702322 Node 8: lnL = -1777.702322 Node 9: lnL = -1777.702322 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 235 Sequential format.. Reading seq # 1: YDR028C_Sbay Reading seq # 2: YDR028C_Scer Reading seq # 3: YDR028C_Skud Reading seq # 4: YDR028C_Smik Reading seq # 5: YDR028C_Spar Sequences read.. Counting patterns.. # site patterns = 80 Counting frequencies.. 120 bytes for distance 12800 bytes for lkl0 10240 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.086391 0.000060 0.160697 0.104235 0.066972 4.729465 0.217319 0.185484 lnL0 = -830.983646 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 830.983646 x= 0.08639 0.00006 0.16070 0.10424 0.06697 4.72946 0.21732 0.18548 1 h-lim-p 0.0000 0.0001 55.1167 830.812863 m 0.0001 22 | 1/8 2 h-lim-p 0.0001 0.0059 23.4071 830.515542 0 0.0011 37 | 1/8 3 h-lim-p 0.0065 0.0758 3.9983 830.498242 7 0.0020 66 | 1/8 4 h-lim-p 0.0080 0.1954 1.0180 830.493510 4 0.0034 88 | 1/8 5 h-lim-p 0.0283 0.5916 0.1234 829.985039 0 0.2260 103 | 0/8 6 h-lim-p 0.0015 0.0118 8.7979 829.940979 6 0.0009 136 | 0/8 7 h-lim-p 0.0005 0.0039 1.7305 829.934118 m 0.0039 148 | 0/8 8 h-lim-p 0.0000 0.0000 0.0112 h-lim-p: 1.36618306e-17 1.09294645e-16 1.11560722e-02 829.934118 .. | 0/8 9 h-lim-p 0.0000 0.0606 12.2018 829.908055 0 0.0003 181 | 0/8 10 h-lim-p 0.0008 0.0288 4.8047 829.899790 4 0.0008 201 | 0/8 11 h-lim-p 0.0004 0.0032 0.8816 829.899433 0 0.0008 214 | 0/8 12 h-lim-p 0.0020 0.6739 0.3449 829.899361 4 0.0014 244 | 0/8 13 h-lim-p 0.0041 1.8635 0.1175 829.899332 2 0.0046 269 | 0/8 14 h-lim-p 0.0017 0.7303 0.3254 829.899032 0 0.0199 292 | 0/8 15 h-lim-p 2.5000 20.0000 0.0002 829.899021 2 0.9961 316 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 829.899021 0 2.5000 336 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 829.899021 0 0.0085 363 Out... lnL = -829.899021 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -829.899021 Node 7: lnL = -829.899021 Node 8: lnL = -829.899021 Node 9: lnL = -829.899021 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 232 Sequential format.. Reading seq # 1: YDR030C_Sbay Reading seq # 2: YDR030C_Scer Reading seq # 3: YDR030C_Skud Reading seq # 4: YDR030C_Smik Reading seq # 5: YDR030C_Spar Sequences read.. Counting patterns.. # site patterns = 118 Counting frequencies.. 120 bytes for distance 18880 bytes for lkl0 15104 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.206408 0.134003 0.057886 0.138331 0.110428 0.176854 0.210569 0.242692 lnL0 = -1091.336142 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1091.336142 x= 0.20641 0.13400 0.05789 0.13833 0.11043 0.17685 0.21057 0.24269 1 h-lim-p 0.0020 0.0161 26.1529 1091.061994 7 0.0009 40 | 0/8 2 h-lim-p 0.0019 0.0252 11.8349 1090.976065 6 0.0014 64 | 0/8 3 h-lim-p 0.0032 0.0940 5.3111 1090.965605 7 0.0009 94 | 0/8 4 h-lim-p 0.0025 0.1768 1.9079 1090.963483 5 0.0014 117 | 0/8 5 h-lim-p 0.0051 0.6690 0.5041 1090.963301 4 0.0016 141 | 0/8 6 h-lim-p 0.0041 1.6130 0.1960 1090.963268 1 0.0020 163 | 0/8 7 h-lim-p 0.0224 8.5640 0.0178 1090.963267 0 0.0025 185 | 0/8 8 h-lim-p 0.0667 20.0000 0.0007 1090.963158 0 0.8002 208 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1090.963156 1 0.9961 230 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1090.963156 0 2.1875 250 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1090.963156 0 1.0938 270 | 0/8 12 h-lim-p 0.7293 20.0000 0.0000 1090.963156 0 5.8346 293 | 0/8 13 h-lim-p 2.2484 20.0000 0.0000 1090.963156 0 0.5621 314 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1090.963156 0 0.0391 339 | 0/8 15 h-lim-p 0.0059 20.0000 0.0000 1090.963156 0 0.0000 376 Out... lnL = -1090.963156 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1090.963156 Node 7: lnL = -1090.963156 Node 8: lnL = -1090.963156 Node 9: lnL = -1090.963156 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 233 Sequential format.. Reading seq # 1: YDR031W_Sbay Reading seq # 2: YDR031W_Scer Reading seq # 3: YDR031W_Skud Reading seq # 4: YDR031W_Smik Reading seq # 5: YDR031W_Spar Sequences read.. Counting patterns.. # site patterns = 136 Counting frequencies.. 120 bytes for distance 21760 bytes for lkl0 17408 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.154087 0.195715 0.038832 0.130263 0.124798 0.188647 0.235574 0.190437 lnL0 = -1100.615332 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1100.615332 x= 0.15409 0.19572 0.03883 0.13026 0.12480 0.18865 0.23557 0.19044 1 h-lim-p 0.0017 0.0136 22.4744 1100.398974 7 0.0009 36 | 0/8 2 h-lim-p 0.0017 0.0133 11.3204 1100.345885 7 0.0010 65 | 0/8 3 h-lim-p 0.0024 0.0882 4.6275 1100.333823 6 0.0014 91 | 0/8 4 h-lim-p 0.0036 0.1699 1.7271 1100.332228 5 0.0013 117 | 0/8 5 h-lim-p 0.0032 0.2711 0.6844 1100.331947 2 0.0014 133 | 0/8 6 h-lim-p 0.0083 1.7255 0.1144 1100.331933 2 0.0022 158 | 0/8 7 h-lim-p 0.0121 11.5018 0.0208 1100.331932 0 0.0026 179 | 0/8 8 h-lim-p 0.0750 20.0000 0.0007 1100.331803 0 0.5998 202 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1100.331803 0 1.0938 222 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1100.331803 0 1.0938 242 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1100.331803 0 2.1875 262 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1100.331803 0 0.5469 283 | 0/8 13 h-lim-p 0.2292 20.0000 0.0000 1100.331803 0 0.0430 305 | 0/8 14 h-lim-p 0.0213 20.0000 0.0000 1100.331803 0 0.0023 327 Out... lnL = -1100.331803 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1100.331803 Node 7: lnL = -1100.331803 Node 8: lnL = -1100.331803 Node 9: lnL = -1100.331803 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 900 Sequential format.. Reading seq # 1: YDR032C_Sbay Reading seq # 2: YDR032C_Scer Reading seq # 3: YDR032C_Skud Reading seq # 4: YDR032C_Smik Reading seq # 5: YDR032C_Spar Sequences read.. Counting patterns.. # site patterns = 468 Counting frequencies.. 120 bytes for distance 74880 bytes for lkl0 59904 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.181527 0.149580 0.098328 0.182341 0.182869 0.227647 0.546226 0.232391 lnL0 = -4658.529075 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4658.529075 x= 0.18153 0.14958 0.09833 0.18234 0.18287 0.22765 0.54623 0.23239 1 h-lim-p 0.0073 1.2654 113.2896 4655.816855 7 0.0004 38 | 0/8 2 h-lim-p 0.0013 0.0104 38.9340 4655.220259 7 0.0009 67 | 0/8 3 h-lim-p 0.0010 0.0095 33.4871 4655.002777 8 0.0006 101 | 0/8 4 h-lim-p 0.0042 0.0602 4.8921 4654.995059 4 0.0007 124 | 0/8 5 h-lim-p 0.0163 2.3164 0.2028 4654.995015 1 0.0018 140 | 0/8 6 h-lim-p 0.0017 3.6264 0.2145 4654.994976 1 0.0017 162 | 0/8 7 h-lim-p 0.0450 20.0000 0.0083 4654.992639 0 0.2702 184 | 0/8 8 h-lim-p 0.0029 0.8844 0.7861 4654.988892 1 0.0036 206 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 4654.988854 1 0.9961 228 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4654.988854 0 1.0938 248 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4654.988854 0 0.6250 269 | 0/8 12 h-lim-p 0.4307 20.0000 0.0000 4654.988854 0 0.2154 289 | 0/8 13 h-lim-p 0.1243 20.0000 0.0000 4654.988854 0 0.0311 310 | 0/8 14 h-lim-p 0.0192 20.0000 0.0000 4654.988854 0 0.0000 338 Out... lnL = -4654.988854 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4654.988854 Node 7: lnL = -4654.988854 Node 8: lnL = -4654.988854 Node 9: lnL = -4654.988854 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 832 Sequential format.. Reading seq # 1: YDR033W_Sbay Reading seq # 2: YDR033W_Scer Reading seq # 3: YDR033W_Skud Reading seq # 4: YDR033W_Smik Reading seq # 5: YDR033W_Spar Sequences read.. Counting patterns.. # site patterns = 133 Counting frequencies.. 120 bytes for distance 21280 bytes for lkl0 17024 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.063067 0.048760 0.026206 0.012847 0.023180 0.113350 0.037822 0.074623 lnL0 = -2316.886798 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2316.886798 x= 0.06307 0.04876 0.02621 0.01285 0.02318 0.11335 0.03782 0.07462 1 h-lim-p 0.0001 0.0006 88.5539 2316.757697 4 0.0000 29 | 0/8 2 h-lim-p 0.0001 0.0008 55.5115 2316.699025 2 0.0001 45 | 0/8 3 h-lim-p 0.0001 0.0025 51.7353 2316.637068 0 0.0001 58 | 0/8 4 h-lim-p 0.0001 0.0024 47.1513 2316.596627 6 0.0001 86 | 0/8 5 h-lim-p 0.0003 0.0116 12.6826 2316.589143 3 0.0001 104 | 0/8 6 h-lim-p 0.0010 0.0338 1.5300 2316.589045 3 0.0001 126 | 0/8 7 h-lim-p 0.0003 0.1190 0.4431 2316.589034 2 0.0001 142 | 0/8 8 h-lim-p 0.0377 20.0000 0.0014 2316.584567 0 0.9054 166 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 2316.584518 3 0.8800 193 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2316.584514 0 1.2500 213 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2316.584514 0 0.2734 235 | 0/8 12 h-lim-p 0.1198 20.0000 0.0000 2316.584514 0 0.0001 264 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 2316.584514 0 0.0000 285 | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 2316.584514 0 0.0000 305 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 2316.584514 0 0.0000 325 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 2316.584514 0 0.0000 345 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 2316.584514 0 0.0000 375 | 0/8 18 h-lim-p 0.0000 6.9701 0.0630 | 0/8 19 h-lim-p 0.0000 6.9701 0.0630 Out... lnL = -2316.584514 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2316.584514 Node 7: lnL = -2316.584514 Node 8: lnL = -2316.584514 Node 9: lnL = -2316.584514 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 833 Sequential format.. Reading seq # 1: YDR034C_Sbay Reading seq # 2: YDR034C_Scer Reading seq # 3: YDR034C_Skud Reading seq # 4: YDR034C_Smik Reading seq # 5: YDR034C_Spar Sequences read.. Counting patterns.. # site patterns = 348 Counting frequencies.. 120 bytes for distance 55680 bytes for lkl0 44544 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.225396 0.026608 0.160739 0.266135 0.226351 0.000060 0.375307 0.262193 lnL0 = -3960.573646 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3960.573646 x= 0.22540 0.02661 0.16074 0.26613 0.22635 0.00006 0.37531 0.26219 1 h-lim-p 0.0000 0.0093 1400.9372 3920.565571 0 0.0001 23 | 0/8 2 h-lim-p 0.0002 0.0018 70.3550 3919.243424 0 0.0005 36 | 0/8 3 h-lim-p 0.0017 0.0219 18.6539 3919.082765 7 0.0010 67 | 0/8 4 h-lim-p 0.0012 0.0094 6.2972 3919.069039 4 0.0008 88 | 0/8 5 h-lim-p 0.0025 0.0404 1.9428 3919.066901 2 0.0012 104 | 0/8 6 h-lim-p 0.0048 0.1659 0.5001 3919.066676 3 0.0016 124 | 0/8 7 h-lim-p 0.0222 1.8887 0.0351 3919.063450 0 0.0886 146 | 0/8 8 h-lim-p 0.0077 0.7069 0.4051 3919.037997 0 0.0154 167 | 0/8 9 h-lim-p 2.5000 20.0000 0.0009 3919.024288 0 5.0000 188 | 0/8 10 h-lim-p 2.2226 20.0000 0.0020 3919.018927 5 1.4167 220 | 0/8 11 h-lim-p 2.5000 20.0000 0.0003 3919.018850 1 1.0938 242 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3919.018850 0 1.0938 262 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 3919.018850 0 0.6250 283 | 0/8 14 h-lim-p 0.4465 20.0000 0.0000 3919.018850 0 0.3349 303 | 0/8 15 h-lim-p 0.2262 20.0000 0.0000 3919.018850 0 0.0000 347 Out... lnL = -3919.018850 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3919.018850 Node 7: lnL = -3919.018850 Node 8: lnL = -3919.018850 Node 9: lnL = -3919.018850 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 400 Sequential format.. Reading seq # 1: YDR035W_Sbay Reading seq # 2: YDR035W_Scer Reading seq # 3: YDR035W_Skud Reading seq # 4: YDR035W_Smik Reading seq # 5: YDR035W_Spar Sequences read.. Counting patterns.. # site patterns = 193 Counting frequencies.. 120 bytes for distance 30880 bytes for lkl0 24704 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.138944 0.046104 0.041416 0.146304 0.137304 0.213388 0.237151 0.169976 lnL0 = -1772.218909 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1772.218909 x= 0.13894 0.04610 0.04142 0.14630 0.13730 0.21339 0.23715 0.16998 1 h-lim-p 0.0032 1.3452 104.8029 1770.613374 7 0.0003 37 | 0/8 2 h-lim-p 0.0016 0.0124 9.8874 1770.573569 5 0.0008 60 | 0/8 3 h-lim-p 0.0024 0.1030 3.4005 1770.568537 4 0.0010 80 | 0/8 4 h-lim-p 0.0033 0.2530 1.0074 1770.568145 4 0.0009 101 | 0/8 5 h-lim-p 0.0037 1.4605 0.2334 1770.568122 1 0.0009 116 | 0/8 6 h-lim-p 0.0061 8.5730 0.0352 1770.568121 0 0.0013 137 | 0/8 7 h-lim-p 0.0154 20.0000 0.0031 1770.568121 0 0.0034 158 | 0/8 8 h-lim-p 0.0542 20.0000 0.0002 1770.568112 0 0.4339 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1770.568111 0 1.0938 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1770.568111 0 1.0938 221 | 0/8 11 h-lim-p 1.3994 20.0000 0.0000 1770.568111 0 4.1982 242 | 0/8 12 h-lim-p 2.1649 20.0000 0.0000 1770.568111 0 0.2368 264 | 0/8 13 h-lim-p 1.3034 20.0000 0.0000 1770.568111 0 0.0000 308 Out... lnL = -1770.568111 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1770.568111 Node 7: lnL = -1770.568111 Node 8: lnL = -1770.568111 Node 9: lnL = -1770.568111 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 781 Sequential format.. Reading seq # 1: YDR036C_Sbay Reading seq # 2: YDR036C_Scer Reading seq # 3: YDR036C_Skud Reading seq # 4: YDR036C_Smik Reading seq # 5: YDR036C_Spar Sequences read.. Counting patterns.. # site patterns = 142 Counting frequencies.. 120 bytes for distance 22720 bytes for lkl0 18176 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.208012 0.127684 0.318934 0.027616 0.015584 0.000060 0.317661 0.245383 lnL0 = -2975.695707 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2975.695707 x= 0.20801 0.12768 0.31893 0.02762 0.01558 0.00006 0.31766 0.24538 1 h-lim-p 0.0000 0.0000 891.6938 2957.390579 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0001 612.5934 2950.441405 0 0.0001 36 | 1/8 3 h-lim-p 0.0006 1.6692 63.4542 2949.367515 2 0.0006 52 | 1/8 4 h-lim-p 0.0012 0.0145 31.3756 2948.204970 0 0.0024 65 | 1/8 5 h-lim-p 0.0035 0.0282 12.5229 2948.099075 3 0.0016 83 | 1/8 6 h-lim-p 0.0046 0.0889 4.3151 2948.084059 5 0.0015 107 | 0/8 7 h-lim-p 0.0005 0.0884 12.4810 2948.083757 3 0.0000 132 | 0/8 8 h-lim-p 0.0010 0.0237 0.0731 2947.977971 m 0.0237 146 | 1/8 9 h-lim-p 0.0336 9.5177 0.0514 2945.772545 0 1.0761 171 | 1/8 10 h-lim-p 2.5000 20.0000 0.0157 2945.324476 4 1.9604 198 | 1/8 11 h-lim-p 2.5000 20.0000 0.0095 2945.227471 6 1.6962 232 | 1/8 12 h-lim-p 2.5000 20.0000 0.0047 2945.218539 5 1.3631 262 | 1/8 13 h-lim-p 2.5000 20.0000 0.0006 2945.218232 3 1.4879 289 | 1/8 14 h-lim-p 2.5000 20.0000 0.0002 2945.218221 1 0.9961 310 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 2945.218221 0 2.5000 329 | 1/8 16 h-lim-p 1.7358 20.0000 0.0000 2945.218221 0 0.0949 351 | 1/8 17 h-lim-p 0.1048 20.0000 0.0000 2945.218221 0 0.0008 376 | 1/8 18 h-lim-p 0.0008 20.0000 0.0000 2945.218221 0 0.0000 399 | 1/8 19 h-lim-p 0.0000 20.0000 0.0004 2945.218221 0 0.0000 422 | 1/8 20 h-lim-p 0.0000 20.0000 0.0003 2945.218221 0 0.0000 444 | 1/8 21 h-lim-p 0.0000 20.0000 0.0000 2945.218221 0 0.0000 476 | 1/8 22 h-lim-p 0.0000 20.0000 0.0403 | 1/8 23 h-lim-p 0.0000 20.0000 0.0403 Out... lnL = -2945.218221 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2945.218221 Node 7: lnL = -2945.218221 Node 8: lnL = -2945.218221 Node 9: lnL = -2945.218221 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 823 Sequential format.. Reading seq # 1: YDR037W_Sbay Reading seq # 2: YDR037W_Scer Reading seq # 3: YDR037W_Skud Reading seq # 4: YDR037W_Smik Reading seq # 5: YDR037W_Spar Sequences read.. Counting patterns.. # site patterns = 256 Counting frequencies.. 120 bytes for distance 40960 bytes for lkl0 32768 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.171107 0.049031 0.172052 0.003963 0.002965 0.196130 0.277849 0.202449 lnL0 = -3249.359553 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3249.359553 x= 0.17111 0.04903 0.17205 0.00396 0.00297 0.19613 0.27785 0.20245 1 h-lim-p 0.0000 0.0001 109.5884 3249.040070 0 0.0001 24 | 0/8 2 h-lim-p 0.0000 0.0021 1056.5100 3248.346362 0 0.0000 36 | 0/8 3 h-lim-p 0.0000 0.0000 690.0858 3247.762728 0 0.0000 50 | 0/8 4 h-lim-p 0.0004 0.0091 32.5994 3247.406597 0 0.0009 63 | 0/8 5 h-lim-p 0.0050 0.0593 5.5409 3247.396610 5 0.0007 87 | 0/8 6 h-lim-p 0.0043 0.3007 0.8640 3247.396305 4 0.0007 110 | 0/8 7 h-lim-p 0.0039 1.7524 0.1611 3247.395948 1 0.0040 132 | 0/8 8 h-lim-p 0.0150 6.2834 0.0432 3247.357543 0 0.0902 154 | 0/8 9 h-lim-p 2.0609 20.0000 0.0019 3247.353609 5 1.0300 184 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 3247.353464 2 1.1719 208 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3247.353463 0 0.5469 229 | 0/8 12 h-lim-p 0.6538 20.0000 0.0000 3247.353463 0 0.0000 269 | 0/8 13 h-lim-p 0.0000 20.0000 0.0005 3247.353463 0 0.0000 304 | 0/8 14 h-lim-p 0.0000 20.0000 1.2510 | 0/8 15 h-lim-p 0.0000 20.0000 1.2510 Out... lnL = -3247.353463 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3247.353463 Node 7: lnL = -3247.353463 Node 8: lnL = -3247.353463 Node 9: lnL = -3247.353463 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 882 Sequential format.. Reading seq # 1: YDR041W_Sbay Reading seq # 2: YDR041W_Scer Reading seq # 3: YDR041W_Skud Reading seq # 4: YDR041W_Smik Reading seq # 5: YDR041W_Spar Sequences read.. Counting patterns.. # site patterns = 334 Counting frequencies.. 120 bytes for distance 53440 bytes for lkl0 42752 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.336057 0.023076 0.059650 0.110153 0.097008 0.212425 0.251466 0.375881 lnL0 = -4205.496281 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4205.496281 x= 0.33606 0.02308 0.05965 0.11015 0.09701 0.21243 0.25147 0.37588 1 h-lim-p 0.0002 0.0019 222.8463 4201.141565 3 0.0002 28 | 0/8 2 h-lim-p 0.0002 0.0020 69.0312 4200.496274 1 0.0003 42 | 0/8 3 h-lim-p 0.0004 0.0059 56.0161 4200.083614 6 0.0004 65 | 0/8 4 h-lim-p 0.0006 0.0088 34.4147 4199.930078 7 0.0004 96 | 0/8 5 h-lim-p 0.0013 0.0228 11.0681 4199.908361 6 0.0004 124 | 0/8 6 h-lim-p 0.0034 0.2964 1.3853 4199.907584 2 0.0008 141 | 0/8 7 h-lim-p 0.0007 0.3740 1.6243 4199.907165 3 0.0006 159 | 0/8 8 h-lim-p 0.5332 20.0000 0.0017 4199.900894 0 1.0665 172 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 4199.900755 2 1.1719 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4199.900753 0 1.0938 216 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4199.900753 0 1.0938 236 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4199.900753 0 2.5000 256 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 4199.900753 0 0.3125 278 | 0/8 14 h-lim-p 0.1800 20.0000 0.0000 4199.900753 0 0.0000 317 Out... lnL = -4199.900753 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4199.900753 Node 7: lnL = -4199.900753 Node 8: lnL = -4199.900753 Node 9: lnL = -4199.900753 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 893 Sequential format.. Reading seq # 1: YDR042C_Sbay Reading seq # 2: YDR042C_Scer Reading seq # 3: YDR042C_Skud Reading seq # 4: YDR042C_Smik Reading seq # 5: YDR042C_Spar Sequences read.. Counting patterns.. # site patterns = 318 Counting frequencies.. 120 bytes for distance 50880 bytes for lkl0 40704 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.127067 0.039080 0.076461 0.109085 0.094747 0.172394 0.206730 0.147404 lnL0 = -3901.286128 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3901.286128 x= 0.12707 0.03908 0.07646 0.10908 0.09475 0.17239 0.20673 0.14740 1 h-lim-p 0.0015 0.5332 231.1524 3897.577841 5 0.0002 35 | 0/8 2 h-lim-p 0.0007 0.0056 23.6926 3897.512414 7 0.0002 63 | 0/8 3 h-lim-p 0.0007 0.0408 8.4872 3897.503944 4 0.0003 83 | 0/8 4 h-lim-p 0.0007 0.0724 3.1803 3897.502529 2 0.0003 99 | 0/8 5 h-lim-p 0.0020 0.7114 0.5320 3897.502475 1 0.0004 114 | 0/8 6 h-lim-p 0.0025 2.8449 0.0843 3897.502474 0 0.0003 136 | 0/8 7 h-lim-p 0.0023 20.0000 0.0114 3897.502473 0 0.0010 156 | 0/8 8 h-lim-p 0.0474 20.0000 0.0002 3897.502406 0 0.7579 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3897.502406 0 1.0938 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3897.502406 0 1.0938 220 | 0/8 11 h-lim-p 1.2802 20.0000 0.0000 3897.502406 0 3.8407 241 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3897.502406 0 0.1562 264 | 0/8 13 h-lim-p 1.2125 20.0000 0.0000 3897.502406 0 0.0095 290 | 0/8 14 h-lim-p 0.0010 20.0000 0.0000 3897.502406 0 0.0000 326 Out... lnL = -3897.502406 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3897.502406 Node 7: lnL = -3897.502406 Node 8: lnL = -3897.502406 Node 9: lnL = -3897.502406 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 882 Sequential format.. Reading seq # 1: YDR043C_Sbay Reading seq # 2: YDR043C_Scer Reading seq # 3: YDR043C_Skud Reading seq # 4: YDR043C_Smik Reading seq # 5: YDR043C_Spar Sequences read.. Counting patterns.. # site patterns = 240 Counting frequencies.. 120 bytes for distance 38400 bytes for lkl0 30720 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.075386 0.112423 0.032887 0.081457 0.064634 0.136410 0.137920 0.091270 lnL0 = -3437.359847 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3437.359847 x= 0.07539 0.11242 0.03289 0.08146 0.06463 0.13641 0.13792 0.09127 1 h-lim-p 0.0002 0.0017 251.1604 3434.393068 6 0.0001 34 | 0/8 2 h-lim-p 0.0002 0.0018 71.6010 3433.937061 6 0.0002 57 | 0/8 3 h-lim-p 0.0004 0.0073 35.7924 3433.852992 5 0.0002 78 | 0/8 4 h-lim-p 0.0004 0.0133 13.4353 3433.840108 4 0.0002 98 | 0/8 5 h-lim-p 0.0026 0.3286 0.8635 3433.840015 2 0.0003 116 | 0/8 6 h-lim-p 0.0016 1.8070 0.1360 3433.840014 0 0.0002 138 | 0/8 7 h-lim-p 0.0053 20.0000 0.0051 3433.840007 0 0.0107 159 | 0/8 8 h-lim-p 0.0037 3.8555 0.0147 3433.839415 0 0.0296 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3433.839387 1 0.9961 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3433.839387 0 1.0938 224 | 0/8 11 h-lim-p 1.7991 20.0000 0.0000 3433.839387 0 1.7991 244 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3433.839387 0 0.0098 271 | 0/8 13 h-lim-p 0.0019 20.0000 0.0000 3433.839387 0 0.0019 291 | 0/8 14 h-lim-p 0.0012 20.0000 0.0000 3433.839387 0 0.0000 317 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 3433.839387 0 0.0000 342 Out... lnL = -3433.839387 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3433.839387 Node 7: lnL = -3433.839387 Node 8: lnL = -3433.839387 Node 9: lnL = -3433.839387 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 881 Sequential format.. Reading seq # 1: YDR047W_Sbay Reading seq # 2: YDR047W_Scer Reading seq # 3: YDR047W_Skud Reading seq # 4: YDR047W_Smik Reading seq # 5: YDR047W_Spar Sequences read.. Counting patterns.. # site patterns = 348 Counting frequencies.. 120 bytes for distance 55680 bytes for lkl0 44544 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.248749 0.013594 0.116176 0.125572 0.093599 0.240005 0.387441 0.279721 lnL0 = -4160.301616 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4160.301616 x= 0.24875 0.01359 0.11618 0.12557 0.09360 0.24001 0.38744 0.27972 1 h-lim-p 0.0009 0.0071 137.6464 4157.563920 7 0.0003 39 | 0/8 2 h-lim-p 0.0007 0.0054 28.6859 4157.327653 5 0.0006 60 | 0/8 3 h-lim-p 0.0007 0.0184 23.0209 4157.271148 4 0.0003 79 | 0/8 4 h-lim-p 0.0004 0.0291 16.3600 4157.229308 1 0.0006 93 | 0/8 5 h-lim-p 0.0014 0.0785 6.4516 4157.217424 5 0.0008 116 | 0/8 6 h-lim-p 0.0014 0.0932 3.5304 4157.215164 4 0.0005 138 | 0/8 7 h-lim-p 0.0178 4.0531 0.1001 4157.215153 2 0.0014 157 | 0/8 8 h-lim-p 0.0839 20.0000 0.0017 4157.212583 0 1.0073 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 4157.212511 1 0.9961 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4157.212511 0 1.0938 222 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4157.212511 0 1.2500 242 | 0/8 12 h-lim-p 2.2645 20.0000 0.0000 4157.212511 0 0.0354 267 | 0/8 13 h-lim-p 0.0169 20.0000 0.0000 4157.212511 0 0.0042 288 | 0/8 14 h-lim-p 0.0011 20.0000 0.0000 4157.212511 0 0.0000 321 Out... lnL = -4157.212511 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4157.212511 Node 7: lnL = -4157.212511 Node 8: lnL = -4157.212511 Node 9: lnL = -4157.212511 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 383 Sequential format.. Reading seq # 1: YDR049W_Sbay Reading seq # 2: YDR049W_Scer Reading seq # 3: YDR049W_Skud Reading seq # 4: YDR049W_Smik Reading seq # 5: YDR049W_Spar Sequences read.. Counting patterns.. # site patterns = 167 Counting frequencies.. 120 bytes for distance 26720 bytes for lkl0 21376 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.150088 0.044944 0.069495 0.164781 0.086241 0.248389 0.266258 0.174997 lnL0 = -1669.622312 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1669.622312 x= 0.15009 0.04494 0.06949 0.16478 0.08624 0.24839 0.26626 0.17500 1 h-lim-p 0.0005 0.0036 74.0493 1668.248612 1 0.0006 24 | 0/8 2 h-lim-p 0.0014 0.0109 17.0360 1668.135046 6 0.0008 51 | 0/8 3 h-lim-p 0.0016 0.0516 8.8348 1668.118472 6 0.0005 77 | 0/8 4 h-lim-p 0.0019 0.1273 2.5300 1668.115149 6 0.0012 106 | 0/8 5 h-lim-p 0.0034 0.3071 0.8673 1668.114759 4 0.0012 128 | 0/8 6 h-lim-p 0.0041 0.5879 0.2476 1668.114724 3 0.0012 156 | 0/8 7 h-lim-p 0.0137 9.6151 0.0223 1668.114705 2 0.0105 180 | 0/8 8 h-lim-p 0.0233 9.0731 0.0101 1668.112877 0 0.1864 203 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1668.112826 2 0.9961 227 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1668.112826 0 1.0938 247 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1668.112826 0 0.1562 270 | 0/8 12 h-lim-p 0.0798 20.0000 0.0000 1668.112826 0 0.0199 291 | 0/8 13 h-lim-p 0.0123 20.0000 0.0000 1668.112826 0 0.0123 311 | 0/8 14 h-lim-p 0.0094 20.0000 0.0000 1668.112826 0 0.0000 347 Out... lnL = -1668.112826 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1668.112826 Node 7: lnL = -1668.112826 Node 8: lnL = -1668.112826 Node 9: lnL = -1668.112826 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 501 Sequential format.. Reading seq # 1: YDR051C_Sbay Reading seq # 2: YDR051C_Scer Reading seq # 3: YDR051C_Skud Reading seq # 4: YDR051C_Smik Reading seq # 5: YDR051C_Spar Sequences read.. Counting patterns.. # site patterns = 192 Counting frequencies.. 120 bytes for distance 30720 bytes for lkl0 24576 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.084192 0.119359 0.059498 0.122192 0.075032 0.150399 0.145141 0.102900 lnL0 = -2053.345447 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2053.345447 x= 0.08419 0.11936 0.05950 0.12219 0.07503 0.15040 0.14514 0.10290 1 h-lim-p 0.0004 0.0034 68.1723 2052.754788 9 0.0003 45 | 0/8 2 h-lim-p 0.0016 0.0185 11.3553 2052.726642 7 0.0004 75 | 0/8 3 h-lim-p 0.0011 0.1226 4.5252 2052.724188 3 0.0003 95 | 0/8 4 h-lim-p 0.0011 0.1837 1.1509 2052.723965 4 0.0004 118 | 0/8 5 h-lim-p 0.0021 0.8989 0.1981 2052.723957 1 0.0004 133 | 0/8 6 h-lim-p 0.0018 3.6253 0.0464 2052.723957 0 0.0008 153 | 0/8 7 h-lim-p 0.0088 20.0000 0.0042 2052.723957 0 0.0010 175 | 0/8 8 h-lim-p 0.0402 20.0000 0.0001 2052.723950 0 0.6429 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2052.723950 0 1.0938 219 | 0/8 10 h-lim-p 2.1177 20.0000 0.0000 2052.723950 0 1.8529 239 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2052.723950 0 0.6250 260 | 0/8 12 h-lim-p 0.1636 20.0000 0.0000 2052.723950 0 0.0000 302 Out... lnL = -2052.723950 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2052.723950 Node 7: lnL = -2052.723950 Node 8: lnL = -2052.723950 Node 9: lnL = -2052.723950 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 301 Sequential format.. Reading seq # 1: YDR056C_Sbay Reading seq # 2: YDR056C_Scer Reading seq # 3: YDR056C_Skud Reading seq # 4: YDR056C_Smik Reading seq # 5: YDR056C_Spar Sequences read.. Counting patterns.. # site patterns = 122 Counting frequencies.. 120 bytes for distance 19520 bytes for lkl0 15616 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.118237 0.086564 0.065942 0.131718 0.127381 0.130254 0.146080 0.138379 lnL0 = -1317.019091 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1317.019091 x= 0.11824 0.08656 0.06594 0.13172 0.12738 0.13025 0.14608 0.13838 1 h-lim-p 0.0071 0.0569 38.3876 1316.661726 9 0.0005 46 | 0/8 2 h-lim-p 0.0023 0.0195 8.3003 1316.639909 6 0.0007 73 | 0/8 3 h-lim-p 0.0042 0.1749 1.2842 1316.639344 4 0.0007 95 | 0/8 4 h-lim-p 0.0066 1.6899 0.1348 1316.639337 0 0.0007 109 | 0/8 5 h-lim-p 0.0044 8.7744 0.0224 1316.639337 0 0.0010 130 | 0/8 6 h-lim-p 0.0106 20.0000 0.0020 1316.639337 0 0.0026 151 | 0/8 7 h-lim-p 0.0257 20.0000 0.0002 1316.639336 0 0.2054 174 | 0/8 8 h-lim-p 0.0016 10.5222 0.0274 1316.639334 0 0.0016 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1316.639334 0 1.0938 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1316.639334 0 2.1875 234 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1316.639334 0 0.6250 255 | 0/8 12 h-lim-p 0.3728 20.0000 0.0000 1316.639334 0 0.0408 277 | 0/8 13 h-lim-p 0.0203 20.0000 0.0000 1316.639334 0 0.0013 300 Out... lnL = -1316.639334 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1316.639334 Node 7: lnL = -1316.639334 Node 8: lnL = -1316.639334 Node 9: lnL = -1316.639334 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 697 Sequential format.. Reading seq # 1: YDR061W_Sbay Reading seq # 2: YDR061W_Scer Reading seq # 3: YDR061W_Skud Reading seq # 4: YDR061W_Smik Reading seq # 5: YDR061W_Spar Sequences read.. Counting patterns.. # site patterns = 254 Counting frequencies.. 120 bytes for distance 40640 bytes for lkl0 32512 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.151560 0.124122 0.066426 0.175863 0.163454 0.483340 0.262505 0.185257 lnL0 = -2710.410730 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2710.410730 x= 0.15156 0.12412 0.06643 0.17586 0.16345 0.48334 0.26251 0.18526 1 h-lim-p 0.0161 0.1286 43.9815 2709.883236 7 0.0006 43 | 0/8 2 h-lim-p 0.0019 0.0156 12.2249 2709.810141 5 0.0010 66 | 0/8 3 h-lim-p 0.0023 0.0331 5.4773 2709.799547 5 0.0008 90 | 0/8 4 h-lim-p 0.0022 0.3338 2.0739 2709.797022 5 0.0014 115 | 0/8 5 h-lim-p 0.0037 0.4940 0.7667 2709.796672 4 0.0014 136 | 0/8 6 h-lim-p 0.0050 1.7420 0.2072 2709.796633 2 0.0019 160 | 0/8 7 h-lim-p 0.0347 20.0000 0.0116 2709.796633 0 0.0038 182 | 0/8 8 h-lim-p 0.0416 20.0000 0.0011 2709.796494 0 0.4989 205 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2709.796491 0 1.0938 225 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2709.796491 0 1.0938 245 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2709.796491 0 2.1875 265 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2709.796491 0 1.0938 285 | 0/8 13 h-lim-p 0.4389 20.0000 0.0000 2709.796491 0 3.5111 308 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 2709.796491 0 0.0195 334 | 0/8 15 h-lim-p 0.0159 20.0000 0.0000 2709.796491 0 0.0000 376 Out... lnL = -2709.796491 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2709.796491 Node 7: lnL = -2709.796491 Node 8: lnL = -2709.796491 Node 9: lnL = -2709.796491 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 738 Sequential format.. Reading seq # 1: YDR062W_Sbay Reading seq # 2: YDR062W_Scer Reading seq # 3: YDR062W_Skud Reading seq # 4: YDR062W_Smik Reading seq # 5: YDR062W_Spar Sequences read.. Counting patterns.. # site patterns = 266 Counting frequencies.. 120 bytes for distance 42560 bytes for lkl0 34048 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.138793 0.048778 0.068131 0.128480 0.060323 0.108290 0.252106 0.158965 lnL0 = -3097.482456 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3097.482456 x= 0.13879 0.04878 0.06813 0.12848 0.06032 0.10829 0.25211 0.15896 1 h-lim-p 0.0003 0.0021 151.3578 3094.582305 4 0.0003 31 | 0/8 2 h-lim-p 0.0002 0.0018 51.4971 3094.245206 1 0.0003 45 | 0/8 3 h-lim-p 0.0021 0.0238 6.9631 3094.238461 4 0.0003 67 | 0/8 4 h-lim-p 0.0004 0.1391 4.7333 3094.236899 3 0.0002 85 | 0/8 5 h-lim-p 0.0008 0.2050 1.1351 3094.236646 3 0.0004 104 | 0/8 6 h-lim-p 0.0015 0.3335 0.3291 3094.236614 1 0.0006 118 | 0/8 7 h-lim-p 0.0042 3.5253 0.0506 3094.236609 1 0.0010 141 | 0/8 8 h-lim-p 0.0136 20.0000 0.0038 3094.233640 0 0.4350 166 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 3094.233213 3 1.0004 192 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3094.233213 0 1.0938 212 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3094.233213 0 1.0938 232 | 0/8 12 h-lim-p 1.1830 20.0000 0.0000 3094.233213 0 4.7319 254 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 3094.233213 0 0.2344 277 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 3094.233213 0 0.0024 306 Out... lnL = -3094.233213 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3094.233213 Node 7: lnL = -3094.233213 Node 8: lnL = -3094.233213 Node 9: lnL = -3094.233213 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 518 Sequential format.. Reading seq # 1: YDR063W_Sbay Reading seq # 2: YDR063W_Scer Reading seq # 3: YDR063W_Skud Reading seq # 4: YDR063W_Smik Reading seq # 5: YDR063W_Spar Sequences read.. Counting patterns.. # site patterns = 238 Counting frequencies.. 120 bytes for distance 38080 bytes for lkl0 30464 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.158120 0.297586 0.192370 0.187617 0.160062 0.145222 0.232815 0.193886 lnL0 = -2427.961081 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2427.961081 x= 0.15812 0.29759 0.19237 0.18762 0.16006 0.14522 0.23281 0.19389 1 h-lim-p 0.0037 0.0293 15.4640 2427.772298 3 0.0016 28 | 0/8 2 h-lim-p 0.0022 0.0514 11.3444 2427.731673 3 0.0009 46 | 0/8 3 h-lim-p 0.0015 0.0482 6.9817 2427.706309 5 0.0015 68 | 0/8 4 h-lim-p 0.0033 0.1096 3.2583 2427.700848 4 0.0014 89 | 0/8 5 h-lim-p 0.0023 0.3707 1.9604 2427.698346 3 0.0019 107 | 0/8 6 h-lim-p 0.0080 0.4901 0.4737 2427.698079 3 0.0026 126 | 0/8 7 h-lim-p 0.0207 4.5665 0.0600 2427.698076 1 0.0013 151 | 0/8 8 h-lim-p 0.1357 20.0000 0.0006 2427.697942 0 1.0854 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2427.697940 0 1.0938 194 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2427.697940 0 1.0938 214 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2427.697940 0 1.0938 234 | 0/8 12 h-lim-p 1.1505 20.0000 0.0000 2427.697940 0 3.4516 255 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2427.697940 0 0.1562 278 | 0/8 14 h-lim-p 0.0209 20.0000 0.0000 2427.697940 0 0.0007 302 | 0/8 15 h-lim-p 0.0065 20.0000 0.0000 2427.697940 0 0.0000 335 Out... lnL = -2427.697940 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2427.697940 Node 7: lnL = -2427.697940 Node 8: lnL = -2427.697940 Node 9: lnL = -2427.697940 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 252 Sequential format.. Reading seq # 1: YDR065W_Sbay Reading seq # 2: YDR065W_Scer Reading seq # 3: YDR065W_Skud Reading seq # 4: YDR065W_Smik Reading seq # 5: YDR065W_Spar Sequences read.. Counting patterns.. # site patterns = 111 Counting frequencies.. 120 bytes for distance 17760 bytes for lkl0 14208 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.142210 0.053255 0.015162 0.186562 0.087310 0.183903 0.172567 0.162688 lnL0 = -1148.206341 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1148.206341 x= 0.14221 0.05326 0.01516 0.18656 0.08731 0.18390 0.17257 0.16269 1 h-lim-p 0.0005 0.4640 217.7721 1144.076561 7 0.0002 38 | 0/8 2 h-lim-p 0.0005 0.0043 29.3040 1143.697765 0 0.0011 51 | 0/8 3 h-lim-p 0.0027 0.0398 11.7930 1143.645520 6 0.0009 78 | 0/8 4 h-lim-p 0.0041 0.2494 2.4744 1143.643009 1 0.0008 93 | 0/8 5 h-lim-p 0.0025 0.2681 0.8263 1143.642558 4 0.0014 115 | 0/8 6 h-lim-p 0.0171 4.5946 0.0677 1143.642327 3 0.0113 143 | 0/8 7 h-lim-p 0.0105 5.6362 0.0729 1143.632595 0 0.0629 165 | 0/8 8 h-lim-p 0.0026 0.2185 1.7870 1143.625116 5 0.0023 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0009 1143.622933 3 2.2656 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0004 1143.622863 2 1.0889 236 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1143.622863 0 1.0938 256 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1143.622863 0 1.0938 276 | 0/8 13 h-lim-p 1.5172 20.0000 0.0000 1143.622863 0 1.5172 296 | 0/8 14 h-lim-p 1.5454 20.0000 0.0000 1143.622863 0 2.3181 316 | 0/8 15 h-lim-p 0.4262 20.0000 0.0000 1143.622863 0 0.1066 337 | 0/8 16 h-lim-p 0.0064 20.0000 0.0001 1143.622863 0 0.0000 376 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 1143.622863 0 0.0000 411 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 1143.622863 0 0.0000 433 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 1143.622863 0 0.0000 464 Out... lnL = -1143.622863 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1143.622863 Node 7: lnL = -1143.622863 Node 8: lnL = -1143.622863 Node 9: lnL = -1143.622863 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 273 Sequential format.. Reading seq # 1: YDR067C_Sbay Reading seq # 2: YDR067C_Scer Reading seq # 3: YDR067C_Skud Reading seq # 4: YDR067C_Smik Reading seq # 5: YDR067C_Spar Sequences read.. Counting patterns.. # site patterns = 115 Counting frequencies.. 120 bytes for distance 18400 bytes for lkl0 14720 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.101416 0.046561 0.020756 0.108135 0.030445 0.274945 0.150718 0.118888 lnL0 = -1107.203832 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1107.203832 x= 0.10142 0.04656 0.02076 0.10814 0.03044 0.27495 0.15072 0.11889 1 h-lim-p 0.0002 0.0014 58.8422 1106.598250 0 0.0004 23 | 0/8 2 h-lim-p 0.0002 0.0014 34.1331 1106.491694 0 0.0003 35 | 0/8 3 h-lim-p 0.0004 0.0032 8.9077 1106.478772 5 0.0004 56 | 0/8 4 h-lim-p 0.0003 0.0199 10.6942 1106.464329 0 0.0006 69 | 0/8 5 h-lim-p 0.0042 0.1181 1.5080 1106.463114 5 0.0011 92 | 0/8 6 h-lim-p 0.0029 0.4585 0.5888 1106.462993 3 0.0008 111 | 0/8 7 h-lim-p 0.0043 1.9096 0.1072 1106.462984 1 0.0011 134 | 0/8 8 h-lim-p 0.0552 20.0000 0.0021 1106.459761 0 0.8835 158 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 1106.459655 3 1.0004 184 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1106.459654 0 1.0938 204 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1106.459654 0 1.0938 224 | 0/8 12 h-lim-p 1.3679 20.0000 0.0000 1106.459654 010.9434 247 | 0/8 13 h-lim-p 1.3709 20.0000 0.0000 1106.459654 0 0.0003 278 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 1106.459654 0 0.0000 308 | 0/8 15 h-lim-p 0.0000 20.0000 0.0008 1106.459654 0 0.0000 334 | 0/8 16 h-lim-p 0.0000 20.0000 0.0010 1106.459654 0 0.0019 361 | 0/8 17 h-lim-p 0.0097 20.0000 0.0002 1106.459654 0 0.0000 406 | 0/8 18 h-lim-p 0.0000 20.0000 0.0036 | 0/8 19 h-lim-p 0.0000 20.0000 0.0036 Out... lnL = -1106.459654 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1106.459654 Node 7: lnL = -1106.459654 Node 8: lnL = -1106.459654 Node 9: lnL = -1106.459654 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 269 Sequential format.. Reading seq # 1: YDR068W_Sbay Reading seq # 2: YDR068W_Scer Reading seq # 3: YDR068W_Skud Reading seq # 4: YDR068W_Smik Reading seq # 5: YDR068W_Spar Sequences read.. Counting patterns.. # site patterns = 119 Counting frequencies.. 120 bytes for distance 19040 bytes for lkl0 15232 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.118953 0.039967 0.018018 0.102797 0.035783 0.280802 0.072688 0.135396 lnL0 = -1034.554078 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1034.554078 x= 0.11895 0.03997 0.01802 0.10280 0.03578 0.28080 0.07269 0.13540 1 h-lim-p 0.0001 0.0010 117.9444 1032.212481 0 0.0005 24 | 0/8 2 h-lim-p 0.0000 0.0004 60.6490 1031.895281 0 0.0002 38 | 0/8 3 h-lim-p 0.0000 0.0004 20.8504 1031.847426 0 0.0003 52 | 0/8 4 h-lim-p 0.0003 0.0207 17.1045 1031.770540 0 0.0010 65 | 0/8 5 h-lim-p 0.0006 0.0050 3.8227 1031.764183 0 0.0013 78 | 0/8 6 h-lim-p 0.0040 0.1481 1.1923 1031.763604 3 0.0008 98 | 0/8 7 h-lim-p 0.0041 0.8407 0.2477 1031.763400 4 0.0028 120 | 0/8 8 h-lim-p 0.0393 7.2656 0.0179 1031.702983 0 0.6291 144 | 0/8 9 h-lim-p 2.5000 20.0000 0.0021 1031.701344 4 1.0519 173 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1031.701335 1 0.9961 195 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1031.701335 0 1.2500 215 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1031.701335 0 0.5469 236 | 0/8 13 h-lim-p 0.7017 20.0000 0.0000 1031.701335 0 0.0014 264 Out... lnL = -1031.701335 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1031.701335 Node 7: lnL = -1031.701335 Node 8: lnL = -1031.701335 Node 9: lnL = -1031.701335 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 382 Sequential format.. Reading seq # 1: YDR069C_Sbay Reading seq # 2: YDR069C_Scer Reading seq # 3: YDR069C_Skud Reading seq # 4: YDR069C_Smik Reading seq # 5: YDR069C_Spar Sequences read.. Counting patterns.. # site patterns = 157 Counting frequencies.. 120 bytes for distance 25120 bytes for lkl0 20096 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.079640 0.142157 0.000060 0.092878 0.109143 0.273540 0.200368 0.100447 lnL0 = -1490.616375 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1490.616375 x= 0.07964 0.14216 0.00006 0.09288 0.10914 0.27354 0.20037 0.10045 1 h-lim-p 0.0076 0.0608 62.6151 1489.774156 8 0.0003 44 | 0/8 2 h-lim-p 0.0007 0.0060 30.4849 1489.280115 0 0.0013 57 | 0/8 3 h-lim-p 0.0010 0.0080 23.0869 1489.193706 7 0.0005 83 | 0/8 4 h-lim-p 0.0014 0.0320 8.4809 1489.155551 5 0.0013 106 | 0/8 5 h-lim-p 0.0010 0.0228 11.5369 1489.133038 4 0.0008 126 | 0/8 6 h-lim-p 0.1371 2.5383 0.0642 1489.132975 2 0.0040 146 | 0/8 7 h-lim-p 0.0070 1.3309 0.0368 1489.117627 0 0.1681 170 | 0/8 8 h-lim-p 0.0039 0.1344 1.5950 1489.116089 5 0.0011 202 | 0/8 9 h-lim-p 1.4058 20.0000 0.0012 1489.115562 4 0.9536 225 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1489.115562 0 1.0938 245 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1489.115562 0 1.0938 265 | 0/8 12 h-lim-p 1.8187 20.0000 0.0000 1489.115562 0 0.0995 288 | 0/8 13 h-lim-p 0.0457 20.0000 0.0000 1489.115562 0 0.0029 311 | 0/8 14 h-lim-p 0.0022 20.0000 0.0000 1489.115562 0 0.0022 331 | 0/8 15 h-lim-p 0.0010 20.0000 0.0000 1489.115562 0 0.0000 365 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 | 0/8 17 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -1489.115562 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1489.115562 Node 7: lnL = -1489.115562 Node 8: lnL = -1489.115562 Node 9: lnL = -1489.115562 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 908 Sequential format.. Reading seq # 1: YDR072C_Sbay Reading seq # 2: YDR072C_Scer Reading seq # 3: YDR072C_Skud Reading seq # 4: YDR072C_Smik Reading seq # 5: YDR072C_Spar Sequences read.. Counting patterns.. # site patterns = 313 Counting frequencies.. 120 bytes for distance 50080 bytes for lkl0 40064 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.248827 0.087774 0.060248 0.097401 0.094892 0.198009 0.244257 0.266716 lnL0 = -4057.877553 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4057.877553 x= 0.24883 0.08777 0.06025 0.09740 0.09489 0.19801 0.24426 0.26672 1 h-lim-p 0.0068 0.1176 109.3970 4056.809785 7 0.0002 40 | 0/8 2 h-lim-p 0.0009 0.0074 22.6678 4056.741480 7 0.0003 72 | 0/8 3 h-lim-p 0.0004 0.0114 14.5162 4056.717978 6 0.0003 99 | 0/8 4 h-lim-p 0.0008 0.0571 5.3158 4056.711426 5 0.0006 124 | 0/8 5 h-lim-p 0.0010 0.0978 2.8323 4056.710334 4 0.0004 147 | 0/8 6 h-lim-p 0.0017 0.6332 0.6027 4056.710218 1 0.0007 161 | 0/8 7 h-lim-p 0.0022 2.5335 0.1796 4056.710208 1 0.0005 184 | 0/8 8 h-lim-p 0.9458 20.0000 0.0001 4056.710189 1 0.9754 206 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4056.710188 0 1.0938 226 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4056.710188 0 0.5469 247 | 0/8 11 h-lim-p 0.4534 20.0000 0.0000 4056.710188 0 0.0248 270 | 0/8 12 h-lim-p 0.0201 20.0000 0.0000 4056.710188 0 0.0100 290 | 0/8 13 h-lim-p 0.0042 20.0000 0.0000 4056.710188 0 0.0000 330 Out... lnL = -4056.710188 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4056.710188 Node 7: lnL = -4056.710188 Node 8: lnL = -4056.710188 Node 9: lnL = -4056.710188 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 606 Sequential format.. Reading seq # 1: YDR075W_Sbay Reading seq # 2: YDR075W_Scer Reading seq # 3: YDR075W_Skud Reading seq # 4: YDR075W_Smik Reading seq # 5: YDR075W_Spar Sequences read.. Counting patterns.. # site patterns = 214 Counting frequencies.. 120 bytes for distance 34240 bytes for lkl0 27392 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.082925 0.105772 0.067709 0.138717 0.100292 0.208136 0.178258 0.096814 lnL0 = -2689.808805 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2689.808805 x= 0.08292 0.10577 0.06771 0.13872 0.10029 0.20814 0.17826 0.09681 1 h-lim-p 0.0185 2.2471 53.9558 2689.478132 7 0.0002 45 | 0/8 2 h-lim-p 0.0016 0.0152 8.0191 2689.464143 6 0.0004 71 | 0/8 3 h-lim-p 0.0035 0.2015 1.0096 2689.463954 2 0.0004 89 | 0/8 4 h-lim-p 0.0018 0.9906 0.2192 2689.463944 1 0.0004 104 | 0/8 5 h-lim-p 0.0022 7.3985 0.0426 2689.463943 0 0.0005 125 | 0/8 6 h-lim-p 0.0024 20.0000 0.0086 2689.463943 0 0.0005 146 | 0/8 7 h-lim-p 0.0016 20.0000 0.0029 2689.463943 0 0.0014 166 | 0/8 8 h-lim-p 0.0232 20.0000 0.0002 2689.463937 0 0.3706 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2689.463937 0 1.0938 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2689.463937 0 0.5469 231 | 0/8 11 h-lim-p 0.3863 20.0000 0.0000 2689.463937 0 0.0000 280 Out... lnL = -2689.463937 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2689.463937 Node 7: lnL = -2689.463937 Node 8: lnL = -2689.463937 Node 9: lnL = -2689.463937 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 432 Sequential format.. Reading seq # 1: YDR076W_Sbay Reading seq # 2: YDR076W_Scer Reading seq # 3: YDR076W_Skud Reading seq # 4: YDR076W_Smik Reading seq # 5: YDR076W_Spar Sequences read.. Counting patterns.. # site patterns = 202 Counting frequencies.. 120 bytes for distance 32320 bytes for lkl0 25856 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.101269 0.131440 0.068915 0.206672 0.127328 0.251335 0.226219 0.118634 lnL0 = -2000.328936 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2000.328936 x= 0.10127 0.13144 0.06891 0.20667 0.12733 0.25134 0.22622 0.11863 1 h-lim-p 0.0022 0.0177 51.9151 1999.517474 8 0.0006 42 | 0/8 2 h-lim-p 0.0012 0.0100 18.0312 1999.392616 8 0.0008 75 | 0/8 3 h-lim-p 0.0021 0.0208 7.2202 1999.375574 5 0.0008 99 | 0/8 4 h-lim-p 0.0042 0.2327 1.3113 1999.374758 2 0.0010 116 | 0/8 5 h-lim-p 0.0028 0.6289 0.4670 1999.374682 3 0.0007 135 | 0/8 6 h-lim-p 0.0035 3.0294 0.0991 1999.374676 1 0.0014 157 | 0/8 7 h-lim-p 0.0094 16.0064 0.0148 1999.374676 0 0.0020 178 | 0/8 8 h-lim-p 0.0505 20.0000 0.0006 1999.374592 0 0.8079 202 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1999.374586 1 0.9961 224 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1999.374586 0 1.0938 244 | 0/8 11 h-lim-p 1.3244 20.0000 0.0000 1999.374586 0 1.1589 264 | 0/8 12 h-lim-p 0.5522 20.0000 0.0000 1999.374586 0 0.0000 297 Out... lnL = -1999.374586 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1999.374586 Node 7: lnL = -1999.374586 Node 8: lnL = -1999.374586 Node 9: lnL = -1999.374586 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 212 Sequential format.. Reading seq # 1: YDR078C_Sbay Reading seq # 2: YDR078C_Scer Reading seq # 3: YDR078C_Skud Reading seq # 4: YDR078C_Smik Reading seq # 5: YDR078C_Spar Sequences read.. Counting patterns.. # site patterns = 101 Counting frequencies.. 120 bytes for distance 16160 bytes for lkl0 12928 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.114778 0.048811 0.051380 0.135276 0.100172 0.129785 0.247773 0.127893 lnL0 = -912.047002 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 912.047002 x= 0.11478 0.04881 0.05138 0.13528 0.10017 0.12979 0.24777 0.12789 1 h-lim-p 0.0044 0.0349 51.1811 911.292998 9 0.0006 48 | 0/8 2 h-lim-p 0.0022 0.0180 14.4554 911.175677 5 0.0012 71 | 0/8 3 h-lim-p 0.0019 0.0286 8.8609 911.139293 7 0.0012 100 | 0/8 4 h-lim-p 0.0043 0.1268 2.5207 911.136093 5 0.0011 123 | 0/8 5 h-lim-p 0.0042 0.2066 0.6830 911.135874 2 0.0010 140 | 0/8 6 h-lim-p 0.0069 2.3495 0.1021 911.135868 2 0.0013 165 | 0/8 7 h-lim-p 0.0338 20.0000 0.0040 911.135861 0 0.0296 185 | 0/8 8 h-lim-p 0.0088 20.0000 0.0136 911.135623 0 0.0350 207 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 911.135612 1 0.9961 229 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 911.135612 0 1.0938 249 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 911.135612 0 2.1875 269 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 911.135612 0 1.0938 289 | 0/8 13 h-lim-p 0.5792 20.0000 0.0000 911.135612 0 4.6337 312 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 911.135612 0 0.0000 362 Out... lnL = -911.135612 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -911.135612 Node 7: lnL = -911.135612 Node 8: lnL = -911.135612 Node 9: lnL = -911.135612 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 204 Sequential format.. Reading seq # 1: YDR079C-A_Sbay Reading seq # 2: YDR079C-A_Scer Reading seq # 3: YDR079C-A_Skud Reading seq # 4: YDR079C-A_Smik Reading seq # 5: YDR079C-A_Spar Sequences read.. Counting patterns.. # site patterns = 104 Counting frequencies.. 120 bytes for distance 16640 bytes for lkl0 13312 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.156779 0.067623 0.087485 0.148711 0.108321 0.218362 0.190293 0.172788 lnL0 = -978.502913 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 978.502913 x= 0.15678 0.06762 0.08748 0.14871 0.10832 0.21836 0.19029 0.17279 1 h-lim-p 0.0014 0.0112 36.4597 977.892282 7 0.0010 37 | 0/8 2 h-lim-p 0.0025 0.0199 9.6238 977.840313 2 0.0012 53 | 0/8 3 h-lim-p 0.0029 0.0886 3.8206 977.833360 6 0.0011 78 | 0/8 4 h-lim-p 0.0038 0.2512 1.0903 977.832635 5 0.0013 102 | 0/8 5 h-lim-p 0.0129 2.5834 0.1141 977.832625 0 0.0016 116 | 0/8 6 h-lim-p 0.0093 13.3878 0.0198 977.832625 0 0.0020 137 | 0/8 7 h-lim-p 0.0112 20.0000 0.0036 977.832625 0 0.0056 157 | 0/8 8 h-lim-p 0.0436 20.0000 0.0005 977.832612 0 0.3492 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 977.832612 0 1.0938 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 977.832612 0 1.0938 220 | 0/8 11 h-lim-p 2.1198 20.0000 0.0000 977.832612 0 0.0662 244 | 0/8 12 h-lim-p 0.0316 20.0000 0.0000 977.832612 0 0.0002 270 Out... lnL = -977.832612 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -977.832612 Node 7: lnL = -977.832612 Node 8: lnL = -977.832612 Node 9: lnL = -977.832612 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 214 Sequential format.. Reading seq # 1: YDR079W_Sbay Reading seq # 2: YDR079W_Scer Reading seq # 3: YDR079W_Skud Reading seq # 4: YDR079W_Smik Reading seq # 5: YDR079W_Spar Sequences read.. Counting patterns.. # site patterns = 105 Counting frequencies.. 120 bytes for distance 16800 bytes for lkl0 13440 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.062083 0.108816 0.056359 0.160815 0.081758 0.122009 0.266827 0.075337 lnL0 = -905.712626 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 905.712626 x= 0.06208 0.10882 0.05636 0.16082 0.08176 0.12201 0.26683 0.07534 1 h-lim-p 0.0030 0.0239 48.9434 905.115932 8 0.0005 44 | 0/8 2 h-lim-p 0.0025 0.0251 10.6118 905.038404 8 0.0014 75 | 0/8 3 h-lim-p 0.0030 0.0598 4.9828 905.026715 6 0.0011 100 | 0/8 4 h-lim-p 0.0027 0.1269 2.0727 905.024704 1 0.0011 114 | 0/8 5 h-lim-p 0.0092 0.6129 0.2420 905.024680 2 0.0009 132 | 0/8 6 h-lim-p 0.0039 4.1894 0.0556 905.024678 1 0.0010 155 | 0/8 7 h-lim-p 0.0081 20.0000 0.0065 905.024678 0 0.0036 175 | 0/8 8 h-lim-p 0.1016 20.0000 0.0002 905.024668 0 0.8127 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 905.024668 0 1.0938 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 905.024668 0 1.0938 238 | 0/8 11 h-lim-p 2.3990 20.0000 0.0000 905.024668 0 3.5985 258 | 0/8 12 h-lim-p 2.4447 20.0000 0.0000 905.024668 0 0.2674 280 | 0/8 13 h-lim-p 1.5958 20.0000 0.0000 905.024668 0 0.0249 305 | 0/8 14 h-lim-p 0.0058 20.0000 0.0000 905.024668 0 0.0004 328 Out... lnL = -905.024668 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -905.024668 Node 7: lnL = -905.024668 Node 8: lnL = -905.024668 Node 9: lnL = -905.024668 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 361 Sequential format.. Reading seq # 1: YDR081C_Sbay Reading seq # 2: YDR081C_Scer Reading seq # 3: YDR081C_Skud Reading seq # 4: YDR081C_Smik Reading seq # 5: YDR081C_Spar Sequences read.. Counting patterns.. # site patterns = 118 Counting frequencies.. 120 bytes for distance 18880 bytes for lkl0 15104 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.098345 0.037937 0.016457 0.083468 0.050763 0.167535 0.182590 0.108419 lnL0 = -1464.238180 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1464.238180 x= 0.09834 0.03794 0.01646 0.08347 0.05076 0.16754 0.18259 0.10842 1 h-lim-p 0.0013 0.0191 147.5928 1463.413592 8 0.0001 43 | 0/8 2 h-lim-p 0.0008 0.0085 17.1906 1463.343924 7 0.0005 74 | 0/8 3 h-lim-p 0.0008 0.0241 9.7099 1463.333179 6 0.0003 103 | 0/8 4 h-lim-p 0.0010 0.0382 2.9029 1463.332053 5 0.0003 129 | 0/8 5 h-lim-p 0.0012 0.0918 0.7290 1463.331940 3 0.0005 147 | 0/8 6 h-lim-p 0.0008 0.9330 0.4168 1463.331913 1 0.0004 169 | 0/8 7 h-lim-p 0.0095 6.6856 0.0176 1463.331913 0 0.0005 192 | 0/8 8 h-lim-p 0.2596 20.0000 0.0000 1463.331905 0 1.5573 214 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1463.331905 0 1.0938 234 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1463.331905 0 0.2734 256 | 0/8 11 h-lim-p 0.1762 20.0000 0.0000 1463.331905 0 0.0007 283 Out... lnL = -1463.331905 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1463.331905 Node 7: lnL = -1463.331905 Node 8: lnL = -1463.331905 Node 9: lnL = -1463.331905 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 361 Sequential format.. Reading seq # 1: YDR082W_Sbay Reading seq # 2: YDR082W_Scer Reading seq # 3: YDR082W_Skud Reading seq # 4: YDR082W_Smik Reading seq # 5: YDR082W_Spar Sequences read.. Counting patterns.. # site patterns = 117 Counting frequencies.. 120 bytes for distance 18720 bytes for lkl0 14976 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.099036 0.041850 0.014294 0.083906 0.046992 0.173387 0.181140 0.109177 lnL0 = -1466.211047 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1466.211047 x= 0.09904 0.04185 0.01429 0.08391 0.04699 0.17339 0.18114 0.10918 1 h-lim-p 0.0010 0.0098 173.3716 1465.202378 9 0.0001 46 | 0/8 2 h-lim-p 0.0004 0.0035 21.2696 1465.130479 7 0.0003 75 | 0/8 3 h-lim-p 0.0005 0.0153 13.7989 1465.108384 6 0.0003 103 | 0/8 4 h-lim-p 0.0009 0.0289 4.5161 1465.105127 4 0.0004 123 | 0/8 5 h-lim-p 0.0037 1.4925 0.4461 1465.105055 2 0.0007 140 | 0/8 6 h-lim-p 0.0034 0.5908 0.0942 1465.105053 0 0.0004 162 | 0/8 7 h-lim-p 0.0014 15.3564 0.0291 1465.105053 0 0.0003 183 | 0/8 8 h-lim-p 0.3120 20.0000 0.0000 1465.105049 0 1.2481 205 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1465.105048 0 1.2500 225 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1465.105048 0 0.0012 255 Out... lnL = -1465.105048 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1465.105048 Node 7: lnL = -1465.105048 Node 8: lnL = -1465.105048 Node 9: lnL = -1465.105048 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 295 Sequential format.. Reading seq # 1: YDR084C_Sbay Reading seq # 2: YDR084C_Scer Reading seq # 3: YDR084C_Skud Reading seq # 4: YDR084C_Smik Reading seq # 5: YDR084C_Spar Sequences read.. Counting patterns.. # site patterns = 141 Counting frequencies.. 120 bytes for distance 22560 bytes for lkl0 18048 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.117187 0.113021 0.026428 0.136573 0.070376 0.204695 0.411020 0.133913 lnL0 = -1304.669079 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1304.669079 x= 0.11719 0.11302 0.02643 0.13657 0.07038 0.20469 0.41102 0.13391 1 h-lim-p 0.0004 0.0035 49.4180 1304.158498 5 0.0005 31 | 0/8 2 h-lim-p 0.0011 0.0084 19.2804 1304.063057 7 0.0006 58 | 0/8 3 h-lim-p 0.0010 0.0276 11.5608 1304.039476 6 0.0005 82 | 0/8 4 h-lim-p 0.0013 0.0651 4.1786 1304.032223 5 0.0010 104 | 0/8 5 h-lim-p 0.0033 0.1987 1.2630 1304.031125 2 0.0015 120 | 0/8 6 h-lim-p 0.0066 0.9932 0.2960 1304.031073 2 0.0013 137 | 0/8 7 h-lim-p 0.0015 2.3279 0.2468 1304.031022 0 0.0030 158 | 0/8 8 h-lim-p 1.8306 20.0000 0.0004 1304.030842 4 1.1713 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1304.030842 0 1.0938 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1304.030842 0 1.0938 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1304.030842 0 2.1875 248 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1304.030842 0 1.0938 268 | 0/8 13 h-lim-p 0.2594 20.0000 0.0000 1304.030842 0 0.2594 288 | 0/8 14 h-lim-p 0.0173 20.0000 0.0000 1304.030842 0 0.0065 309 | 0/8 15 h-lim-p 0.0083 20.0000 0.0000 1304.030842 0 0.0000 349 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1304.030842 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1304.030842 Node 7: lnL = -1304.030842 Node 8: lnL = -1304.030842 Node 9: lnL = -1304.030842 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 834 Sequential format.. Reading seq # 1: YDR085C_Sbay Reading seq # 2: YDR085C_Scer Reading seq # 3: YDR085C_Skud Reading seq # 4: YDR085C_Smik Reading seq # 5: YDR085C_Spar Sequences read.. Counting patterns.. # site patterns = 247 Counting frequencies.. 120 bytes for distance 39520 bytes for lkl0 31616 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.135654 0.056789 0.058138 0.098942 0.071738 0.154215 0.167528 0.148019 lnL0 = -3559.652112 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3559.652112 x= 0.13565 0.05679 0.05814 0.09894 0.07174 0.15422 0.16753 0.14802 1 h-lim-p 0.0002 0.0015 184.4909 3557.195921 3 0.0002 28 | 0/8 2 h-lim-p 0.0004 0.0035 33.5013 3557.086666 3 0.0002 46 | 0/8 3 h-lim-p 0.0006 0.0256 11.2289 3557.076238 6 0.0002 74 | 0/8 4 h-lim-p 0.0003 0.0300 6.5882 3557.072132 3 0.0002 92 | 0/8 5 h-lim-p 0.0026 0.5217 0.6323 3557.072074 2 0.0003 110 | 0/8 6 h-lim-p 0.0010 0.9033 0.1784 3557.072070 0 0.0002 131 | 0/8 7 h-lim-p 0.0146 20.0000 0.0027 3557.072070 0 0.0064 151 | 0/8 8 h-lim-p 0.0116 20.0000 0.0015 3557.072018 0 0.0926 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3557.072017 0 1.0938 194 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3557.072017 0 1.0938 214 | 0/8 11 h-lim-p 1.4765 20.0000 0.0000 3557.072017 0 4.4295 235 | 0/8 12 h-lim-p 1.9858 20.0000 0.0000 3557.072017 0 0.2172 257 | 0/8 13 h-lim-p 0.7496 20.0000 0.0000 3557.072017 0 0.0000 293 Out... lnL = -3557.072017 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3557.072017 Node 7: lnL = -3557.072017 Node 8: lnL = -3557.072017 Node 9: lnL = -3557.072017 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 309 Sequential format.. Reading seq # 1: YDR086C_Sbay Reading seq # 2: YDR086C_Scer Reading seq # 3: YDR086C_Skud Reading seq # 4: YDR086C_Smik Reading seq # 5: YDR086C_Spar Sequences read.. Counting patterns.. # site patterns = 124 Counting frequencies.. 120 bytes for distance 19840 bytes for lkl0 15872 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.065151 0.063950 0.043559 0.096705 0.097675 0.178308 0.132654 0.075678 lnL0 = -1268.773223 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1268.773223 x= 0.06515 0.06395 0.04356 0.09670 0.09768 0.17831 0.13265 0.07568 1 h-lim-p 0.0009 0.0072 70.0228 1268.106600 5 0.0003 34 | 0/8 2 h-lim-p 0.0014 0.0125 14.3017 1268.053409 7 0.0005 61 | 0/8 3 h-lim-p 0.0024 0.1046 3.1772 1268.051543 4 0.0004 84 | 0/8 4 h-lim-p 0.0020 0.2808 0.6040 1268.051452 2 0.0005 101 | 0/8 5 h-lim-p 0.0017 1.2428 0.1883 1268.051441 2 0.0007 125 | 0/8 6 h-lim-p 0.0032 6.7984 0.0395 1268.051441 0 0.0008 146 | 0/8 7 h-lim-p 0.0027 13.0962 0.0118 1268.051441 0 0.0023 166 | 0/8 8 h-lim-p 0.0489 20.0000 0.0006 1268.051347 0 0.3911 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1268.051345 0 1.0938 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1268.051345 0 1.0938 229 | 0/8 11 h-lim-p 1.8935 20.0000 0.0000 1268.051345 0 1.8935 249 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1268.051345 0 0.0003 281 Out... lnL = -1268.051345 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1268.051345 Node 7: lnL = -1268.051345 Node 8: lnL = -1268.051345 Node 9: lnL = -1268.051345 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 203 Sequential format.. Reading seq # 1: YDR087C_Sbay Reading seq # 2: YDR087C_Scer Reading seq # 3: YDR087C_Skud Reading seq # 4: YDR087C_Smik Reading seq # 5: YDR087C_Spar Sequences read.. Counting patterns.. # site patterns = 97 Counting frequencies.. 120 bytes for distance 15520 bytes for lkl0 12416 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.119984 0.047362 0.105920 0.107809 0.071317 0.188478 0.181159 0.133440 lnL0 = -903.705128 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 903.705128 x= 0.11998 0.04736 0.10592 0.10781 0.07132 0.18848 0.18116 0.13344 1 h-lim-p 0.0062 2.8201 53.9191 902.759964 3 0.0007 30 | 0/8 2 h-lim-p 0.0022 0.0173 9.7494 902.718000 3 0.0009 48 | 0/8 3 h-lim-p 0.0023 0.0530 3.8778 902.710303 4 0.0012 69 | 0/8 4 h-lim-p 0.0045 0.2268 0.9996 902.709710 5 0.0013 94 | 0/8 5 h-lim-p 0.0048 0.6668 0.2625 902.709664 3 0.0014 123 | 0/8 6 h-lim-p 0.0113 6.7003 0.0331 902.709663 0 0.0014 145 | 0/8 7 h-lim-p 0.0142 20.0000 0.0033 902.709663 0 0.0062 165 | 0/8 8 h-lim-p 0.0979 20.0000 0.0002 902.709656 0 0.5875 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 902.709656 0 1.0938 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 902.709656 0 1.2500 227 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 902.709656 0 0.3125 249 | 0/8 12 h-lim-p 0.1690 20.0000 0.0000 902.709656 0 0.0000 281 Out... lnL = -902.709656 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -902.709656 Node 7: lnL = -902.709656 Node 8: lnL = -902.709656 Node 9: lnL = -902.709656 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 858 Sequential format.. Reading seq # 1: YDR088C_Sbay Reading seq # 2: YDR088C_Scer Reading seq # 3: YDR088C_Skud Reading seq # 4: YDR088C_Smik Reading seq # 5: YDR088C_Spar Sequences read.. Counting patterns.. # site patterns = 446 Counting frequencies.. 120 bytes for distance 71360 bytes for lkl0 57088 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.253710 0.074006 0.060609 0.272905 0.242730 0.441850 0.355689 0.280427 lnL0 = -4805.506879 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4805.506879 x= 0.25371 0.07401 0.06061 0.27290 0.24273 0.44185 0.35569 0.28043 1 h-lim-p 0.0029 0.6532 182.4272 4800.398388 3 0.0003 30 | 0/8 2 h-lim-p 0.0026 0.0211 22.3906 4800.133173 6 0.0011 53 | 0/8 3 h-lim-p 0.0025 0.0444 9.3467 4800.098444 6 0.0009 80 | 0/8 4 h-lim-p 0.0030 0.1083 2.8299 4800.093422 2 0.0014 96 | 0/8 5 h-lim-p 0.0053 0.6889 0.7522 4800.093103 2 0.0012 113 | 0/8 6 h-lim-p 0.0240 14.9524 0.0365 4800.092971 2 0.0186 137 | 0/8 7 h-lim-p 0.0111 9.9453 0.0609 4800.089843 0 0.0445 159 | 0/8 8 h-lim-p 0.0034 1.4901 0.7978 4800.083786 4 0.0037 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 4800.083764 1 0.9961 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4800.083764 0 1.0938 232 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4800.083764 0 1.0938 252 | 0/8 12 h-lim-p 1.4236 20.0000 0.0000 4800.083764 0 0.6228 272 | 0/8 13 h-lim-p 0.3221 20.0000 0.0000 4800.083764 0 0.0088 296 | 0/8 14 h-lim-p 0.0503 20.0000 0.0000 4800.083764 0 0.0001 324 Out... lnL = -4800.083764 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4800.083764 Node 7: lnL = -4800.083764 Node 8: lnL = -4800.083764 Node 9: lnL = -4800.083764 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 835 Sequential format.. Reading seq # 1: YDR089W_Sbay Reading seq # 2: YDR089W_Scer Reading seq # 3: YDR089W_Skud Reading seq # 4: YDR089W_Smik Reading seq # 5: YDR089W_Spar Sequences read.. Counting patterns.. # site patterns = 298 Counting frequencies.. 120 bytes for distance 47680 bytes for lkl0 38144 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.197069 0.119461 0.177012 0.121896 0.148725 0.160054 0.218185 0.206567 lnL0 = -3435.912584 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3435.912584 x= 0.19707 0.11946 0.17701 0.12190 0.14873 0.16005 0.21819 0.20657 1 h-lim-p 0.0078 0.1221 93.6160 3433.267305 6 0.0006 37 | 0/8 2 h-lim-p 0.0006 0.0046 63.2584 3432.074495 0 0.0009 49 | 0/8 3 h-lim-p 0.0013 0.0101 22.9103 3431.872556 7 0.0009 79 | 0/8 4 h-lim-p 0.0020 0.0251 10.7313 3431.822210 6 0.0011 106 | 0/8 5 h-lim-p 0.0016 0.0360 7.0880 3431.797804 5 0.0014 127 | 0/8 6 h-lim-p 0.0017 0.0494 6.0254 3431.786959 4 0.0011 148 | 0/8 7 h-lim-p 0.0093 0.3773 0.7067 3431.786601 3 0.0012 168 | 0/8 8 h-lim-p 0.0864 20.0000 0.0100 3431.716912 0 1.0373 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0033 3431.713693 2 1.1719 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 3431.713682 1 0.9961 237 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3431.713682 0 1.0938 257 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3431.713682 0 1.0938 277 | 0/8 13 h-lim-p 1.5503 20.0000 0.0000 3431.713682 0 1.3566 297 | 0/8 14 h-lim-p 1.2803 20.0000 0.0000 3431.713682 0 0.0088 323 Out... lnL = -3431.713682 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3431.713682 Node 7: lnL = -3431.713682 Node 8: lnL = -3431.713682 Node 9: lnL = -3431.713682 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 945 Sequential format.. Reading seq # 1: YDR098C_Sbay Reading seq # 2: YDR098C_Scer Reading seq # 3: YDR098C_Skud Reading seq # 4: YDR098C_Smik Reading seq # 5: YDR098C_Spar Sequences read.. Counting patterns.. # site patterns = 413 Counting frequencies.. 120 bytes for distance 66080 bytes for lkl0 52864 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.216890 0.092997 0.114583 0.109171 0.148544 0.145301 0.407384 0.226820 lnL0 = -4208.236475 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4208.236475 x= 0.21689 0.09300 0.11458 0.10917 0.14854 0.14530 0.40738 0.22682 1 h-lim-p 0.0004 0.0033 210.3387 4200.181901 8 0.0004 40 | 0/8 2 h-lim-p 0.0004 0.0033 55.3861 4199.420260 1 0.0005 54 | 0/8 3 h-lim-p 0.0003 0.0027 53.6323 4199.040248 0 0.0005 66 | 0/8 4 h-lim-p 0.0021 0.0246 13.0712 4198.979621 4 0.0008 86 | 0/8 5 h-lim-p 0.0019 0.0917 5.7298 4198.963298 5 0.0012 110 | 0/8 6 h-lim-p 0.0069 0.4240 0.9916 4198.962830 3 0.0009 130 | 0/8 7 h-lim-p 0.0038 2.4116 0.2437 4198.962713 2 0.0020 155 | 0/8 8 h-lim-p 0.0450 20.0000 0.0108 4198.929152 0 0.5403 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0020 4198.926912 2 1.1719 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 4198.926898 1 0.9961 224 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4198.926898 0 1.0938 244 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4198.926898 0 2.1875 264 | 0/8 13 h-lim-p 2.1838 20.0000 0.0000 4198.926898 0 0.9554 284 | 0/8 14 h-lim-p 1.5726 20.0000 0.0000 4198.926898 0 0.3440 305 | 0/8 15 h-lim-p 0.1977 20.0000 0.0000 4198.926898 0 0.0000 344 Out... lnL = -4198.926898 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4198.926898 Node 7: lnL = -4198.926898 Node 8: lnL = -4198.926898 Node 9: lnL = -4198.926898 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 879 Sequential format.. Reading seq # 1: YDR099W_Sbay Reading seq # 2: YDR099W_Scer Reading seq # 3: YDR099W_Skud Reading seq # 4: YDR099W_Smik Reading seq # 5: YDR099W_Spar Sequences read.. Counting patterns.. # site patterns = 229 Counting frequencies.. 120 bytes for distance 36640 bytes for lkl0 29312 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.228727 0.104888 0.231961 0.216526 0.028144 0.000060 0.179808 0.234635 lnL0 = -3375.756985 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3375.756985 x= 0.22873 0.10489 0.23196 0.21653 0.02814 0.00006 0.17981 0.23463 1 h-lim-p 0.0001 0.0009 343.2237 3338.866660 0 0.0005 24 | 0/8 2 h-lim-p 0.0001 0.0011 114.2961 3336.467038 0 0.0006 38 | 0/8 3 h-lim-p 0.0002 0.0016 69.6094 3336.050376 1 0.0002 52 | 0/8 4 h-lim-p 0.0005 0.0090 35.6221 3335.873787 6 0.0004 77 | 0/8 5 h-lim-p 0.0004 0.0030 13.9212 3335.787438 0 0.0015 91 | 0/8 6 h-lim-p 0.0003 0.0022 14.0376 3335.762378 0 0.0006 104 | 0/8 7 h-lim-p 0.0081 0.1184 0.9580 3335.760356 4 0.0013 127 | 0/8 8 h-lim-p 0.0106 1.6231 0.1176 3335.072960 0 0.1701 151 | 0/8 9 h-lim-p 2.5000 20.0000 0.0067 3335.029279 4 0.8855 181 | 0/8 10 h-lim-p 2.5000 20.0000 0.0021 3335.023437 4 1.2234 211 | 0/8 11 h-lim-p 2.5000 20.0000 0.0004 3335.023231 2 1.0938 235 | 0/8 12 h-lim-p 2.5000 20.0000 0.0001 3335.023229 0 1.0938 255 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 3335.023229 0 1.0938 275 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 3335.023229 0 1.0938 295 | 0/8 15 h-lim-p 1.3737 20.0000 0.0000 3335.023229 0 0.0859 318 | 0/8 16 h-lim-p 0.0480 20.0000 0.0000 3335.023229 0 0.0240 338 | 0/8 17 h-lim-p 0.0087 20.0000 0.0000 3335.023229 0 0.0000 380 Out... lnL = -3335.023229 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3335.023229 Node 7: lnL = -3335.023229 Node 8: lnL = -3335.023229 Node 9: lnL = -3335.023229 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 653 Sequential format.. Reading seq # 1: YDR100W_Sbay Reading seq # 2: YDR100W_Scer Reading seq # 3: YDR100W_Skud Reading seq # 4: YDR100W_Smik Reading seq # 5: YDR100W_Spar Sequences read.. Counting patterns.. # site patterns = 147 Counting frequencies.. 120 bytes for distance 23520 bytes for lkl0 18816 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.074684 0.013274 0.105222 0.089557 0.069841 4.815079 0.170137 0.098473 lnL0 = -2231.930698 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2231.930698 x= 0.07468 0.01327 0.10522 0.08956 0.06984 4.81508 0.17014 0.09847 1 h-lim-p 0.0003 0.0024 112.7636 2230.760822 8 0.0002 40 | 0/8 2 h-lim-p 0.0003 0.0025 30.6851 2230.654571 4 0.0002 60 | 0/8 3 h-lim-p 0.0008 0.0197 8.7141 2230.647741 2 0.0002 77 | 0/8 4 h-lim-p 0.0015 0.2113 1.1095 2230.647511 2 0.0004 94 | 0/8 5 h-lim-p 0.0011 0.4943 0.4017 2230.647488 2 0.0003 112 | 0/8 6 h-lim-p 1.7555 20.0000 0.0001 2230.647468 2 1.1581 138 | 0/8 7 h-lim-p 1.7843 20.0000 0.0001 2230.647468 0 1.5612 158 | 0/8 8 h-lim-p 2.5000 20.0000 0.0000 2230.647468 0 1.0938 178 | 0/8 9 h-lim-p 0.3199 20.0000 0.0000 2230.647468 0 0.6398 199 | 0/8 10 h-lim-p 0.1569 20.0000 0.0001 2230.647468 0 0.0025 224 | 0/8 11 h-lim-p 0.0007 20.0000 0.0005 2230.647468 0 0.0001 246 | 0/8 12 h-lim-p 0.0002 20.0000 0.0002 2230.647468 0 0.0000 269 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 2230.647468 0 0.0000 299 | 0/8 14 h-lim-p 0.0000 20.0000 0.0008 | 0/8 15 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -2230.647468 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2230.647468 Node 7: lnL = -2230.647468 Node 8: lnL = -2230.647468 Node 9: lnL = -2230.647468 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 182 Sequential format.. Reading seq # 1: YDR101C_Sbay Reading seq # 2: YDR101C_Scer Reading seq # 3: YDR101C_Skud Reading seq # 4: YDR101C_Smik Reading seq # 5: YDR101C_Spar Sequences read.. Counting patterns.. # site patterns = 72 Counting frequencies.. 120 bytes for distance 11520 bytes for lkl0 9216 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.069028 0.034039 0.080293 0.089781 0.045277 0.109583 0.134598 0.073425 lnL0 = -715.434270 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 715.434270 x= 0.06903 0.03404 0.08029 0.08978 0.04528 0.10958 0.13460 0.07342 1 h-lim-p 0.0015 0.0119 85.0204 714.235052 4 0.0004 31 | 0/8 2 h-lim-p 0.0014 0.0114 8.9956 714.209965 5 0.0006 52 | 0/8 3 h-lim-p 0.0013 0.0437 4.2249 714.204623 5 0.0007 75 | 0/8 4 h-lim-p 0.0033 0.1954 0.9101 714.204359 3 0.0007 94 | 0/8 5 h-lim-p 0.0109 3.1997 0.0577 714.204356 0 0.0012 116 | 0/8 6 h-lim-p 0.0046 16.1262 0.0148 714.204354 0 0.0046 136 | 0/8 7 h-lim-p 0.0076 20.0000 0.0091 714.204309 0 0.0302 158 | 0/8 8 h-lim-p 0.0028 3.4642 0.0985 714.203900 0 0.0083 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 714.203894 1 0.9961 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 714.203894 0 2.1875 221 | 0/8 11 h-lim-p 2.0839 20.0000 0.0000 714.203894 0 0.9117 241 | 0/8 12 h-lim-p 2.0236 20.0000 0.0000 714.203894 0 0.0010 271 Out... lnL = -714.203894 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -714.203894 Node 7: lnL = -714.203894 Node 8: lnL = -714.203894 Node 9: lnL = -714.203894 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 268 Sequential format.. Reading seq # 1: YDR108W_Sbay Reading seq # 2: YDR108W_Scer Reading seq # 3: YDR108W_Skud Reading seq # 4: YDR108W_Smik Reading seq # 5: YDR108W_Spar Sequences read.. Counting patterns.. # site patterns = 115 Counting frequencies.. 120 bytes for distance 18400 bytes for lkl0 14720 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.096298 0.133808 0.055964 0.106026 0.053998 0.140098 0.135365 0.102125 lnL0 = -1052.132658 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1052.132658 x= 0.09630 0.13381 0.05596 0.10603 0.05400 0.14010 0.13537 0.10213 1 h-lim-p 0.0031 0.0246 15.4132 1052.065303 7 0.0006 38 | 0/8 2 h-lim-p 0.0012 0.0177 7.0970 1052.054758 4 0.0005 58 | 0/8 3 h-lim-p 0.0015 0.0613 2.3760 1052.053046 2 0.0007 74 | 0/8 4 h-lim-p 0.0021 0.2385 0.7848 1052.052886 4 0.0006 96 | 0/8 5 h-lim-p 0.0034 1.1901 0.1355 1052.052876 2 0.0011 122 | 0/8 6 h-lim-p 0.0060 12.5185 0.0256 1052.052876 0 0.0007 144 | 0/8 7 h-lim-p 0.0038 20.0000 0.0050 1052.052876 0 0.0017 164 | 0/8 8 h-lim-p 0.0763 20.0000 0.0001 1052.052872 0 0.9159 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1052.052872 0 1.0938 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1052.052872 0 1.0938 227 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1052.052872 0 2.1875 247 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1052.052872 0 0.1562 270 | 0/8 13 h-lim-p 0.0494 20.0000 0.0000 1052.052872 0 0.0062 292 | 0/8 14 h-lim-p 0.0033 20.0000 0.0000 1052.052872 0 0.0017 312 Out... lnL = -1052.052872 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1052.052872 Node 7: lnL = -1052.052872 Node 8: lnL = -1052.052872 Node 9: lnL = -1052.052872 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 462 Sequential format.. Reading seq # 1: YDR110W_Sbay Reading seq # 2: YDR110W_Scer Reading seq # 3: YDR110W_Skud Reading seq # 4: YDR110W_Smik Reading seq # 5: YDR110W_Spar Sequences read.. Counting patterns.. # site patterns = 202 Counting frequencies.. 120 bytes for distance 32320 bytes for lkl0 25856 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.183458 0.082334 0.067181 0.154840 0.092971 0.187703 0.226266 0.191457 lnL0 = -1990.251070 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1990.251070 x= 0.18346 0.08233 0.06718 0.15484 0.09297 0.18770 0.22627 0.19146 1 h-lim-p 0.0003 0.0028 83.2971 1988.840270 0 0.0005 22 | 0/8 2 h-lim-p 0.0012 0.0093 23.9971 1988.652108 7 0.0007 51 | 0/8 3 h-lim-p 0.0017 0.0391 9.8966 1988.629678 5 0.0005 75 | 0/8 4 h-lim-p 0.0006 0.0362 8.4342 1988.612608 1 0.0008 89 | 0/8 5 h-lim-p 0.0024 0.1436 2.7286 1988.610024 5 0.0008 115 | 0/8 6 h-lim-p 0.0150 1.7542 0.1545 1988.609789 4 0.0055 137 | 0/8 7 h-lim-p 0.0130 2.7786 0.0654 1988.605528 0 0.0389 158 | 0/8 8 h-lim-p 0.0025 0.1452 1.0343 1988.572980 0 0.0049 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0013 1988.571745 4 0.9644 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1988.571744 0 1.0938 219 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1988.571744 0 1.2500 239 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1988.571744 0 0.2734 261 | 0/8 13 h-lim-p 0.2517 20.0000 0.0000 1988.571744 0 0.0039 286 Out... lnL = -1988.571744 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1988.571744 Node 7: lnL = -1988.571744 Node 8: lnL = -1988.571744 Node 9: lnL = -1988.571744 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 833 Sequential format.. Reading seq # 1: YDR111C_Sbay Reading seq # 2: YDR111C_Scer Reading seq # 3: YDR111C_Skud Reading seq # 4: YDR111C_Smik Reading seq # 5: YDR111C_Spar Sequences read.. Counting patterns.. # site patterns = 288 Counting frequencies.. 120 bytes for distance 46080 bytes for lkl0 36864 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.120289 0.061656 0.069090 0.108332 0.122757 0.188278 0.191080 0.126974 lnL0 = -3580.131672 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3580.131672 x= 0.12029 0.06166 0.06909 0.10833 0.12276 0.18828 0.19108 0.12697 1 h-lim-p 0.0025 0.0201 159.3665 3578.035833 8 0.0002 43 | 0/8 2 h-lim-p 0.0008 0.0060 23.1324 3577.953175 3 0.0003 61 | 0/8 3 h-lim-p 0.0013 0.0625 5.3930 3577.948939 2 0.0003 78 | 0/8 4 h-lim-p 0.0010 0.1444 1.7185 3577.948481 3 0.0004 98 | 0/8 5 h-lim-p 0.0030 0.9900 0.2027 3577.948474 0 0.0003 112 | 0/8 6 h-lim-p 0.0016 6.6493 0.0418 3577.948474 0 0.0007 132 | 0/8 7 h-lim-p 0.0040 20.0000 0.0071 3577.948474 0 0.0018 152 | 0/8 8 h-lim-p 0.0190 20.0000 0.0007 3577.948395 0 0.3042 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3577.948393 0 1.0938 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3577.948393 0 1.0938 216 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3577.948393 0 2.1875 236 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3577.948393 0 0.2734 258 | 0/8 13 h-lim-p 0.0723 20.0000 0.0000 3577.948393 0 0.0079 280 | 0/8 14 h-lim-p 0.0043 20.0000 0.0000 3577.948393 0 0.0000 311 Out... lnL = -3577.948393 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3577.948393 Node 7: lnL = -3577.948393 Node 8: lnL = -3577.948393 Node 9: lnL = -3577.948393 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 330 Sequential format.. Reading seq # 1: YDR113C_Sbay Reading seq # 2: YDR113C_Scer Reading seq # 3: YDR113C_Skud Reading seq # 4: YDR113C_Smik Reading seq # 5: YDR113C_Spar Sequences read.. Counting patterns.. # site patterns = 111 Counting frequencies.. 120 bytes for distance 17760 bytes for lkl0 14208 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.086626 0.058467 0.099043 0.150214 0.125203 4.763249 0.159528 0.110414 lnL0 = -1225.407106 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1225.407106 x= 0.08663 0.05847 0.09904 0.15021 0.12520 4.76325 0.15953 0.11041 1 h-lim-p 0.0055 0.0436 45.5513 1224.901577 7 0.0005 38 | 0/8 2 h-lim-p 0.0022 0.0175 10.8194 1224.846911 3 0.0010 56 | 0/8 3 h-lim-p 0.0049 0.1460 2.1672 1224.845309 5 0.0007 81 | 0/8 4 h-lim-p 0.0141 2.3678 0.1098 1224.845305 2 0.0006 101 | 0/8 5 h-lim-p 0.0187 20.0000 0.0033 1224.845305 0 0.0082 121 | 0/8 6 h-lim-p 0.0271 20.0000 0.0010 1224.845275 0 0.2165 144 | 0/8 7 h-lim-p 2.5000 20.0000 0.0000 1224.845274 0 1.0938 164 | 0/8 8 h-lim-p 2.5000 20.0000 0.0000 1224.845274 0 1.0938 184 | 0/8 9 h-lim-p 1.8563 20.0000 0.0000 1224.845274 0 1.6243 204 | 0/8 10 h-lim-p 2.2697 20.0000 0.0000 1224.845274 0 0.2482 226 | 0/8 11 h-lim-p 0.0704 20.0000 0.0000 1224.845274 0 0.0352 246 | 0/8 12 h-lim-p 0.0151 20.0000 0.0000 1224.845274 0 0.0019 268 | 0/8 13 h-lim-p 0.0009 20.0000 0.0001 1224.845274 0 0.0000 294 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 1224.845274 0 0.0000 323 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -1224.845274 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1224.845274 Node 7: lnL = -1224.845274 Node 8: lnL = -1224.845274 Node 9: lnL = -1224.845274 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 646 Sequential format.. Reading seq # 1: YDR115W_Sbay Reading seq # 2: YDR115W_Scer Reading seq # 3: YDR115W_Skud Reading seq # 4: YDR115W_Smik Reading seq # 5: YDR115W_Spar Sequences read.. Counting patterns.. # site patterns = 270 Counting frequencies.. 120 bytes for distance 43200 bytes for lkl0 34560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.118937 0.107150 0.134785 0.156833 0.100901 0.251819 0.202381 0.118478 lnL0 = -2894.008869 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2894.008869 x= 0.11894 0.10715 0.13478 0.15683 0.10090 0.25182 0.20238 0.11848 1 h-lim-p 0.0031 0.0249 93.2620 2892.213411 8 0.0004 42 | 0/8 2 h-lim-p 0.0010 0.0081 23.9550 2892.070313 4 0.0005 63 | 0/8 3 h-lim-p 0.0011 0.0288 11.0804 2892.041308 4 0.0006 84 | 0/8 4 h-lim-p 0.0012 0.0591 5.3521 2892.035969 4 0.0005 104 | 0/8 5 h-lim-p 0.0022 0.2653 1.1506 2892.035501 4 0.0007 127 | 0/8 6 h-lim-p 0.0028 1.2446 0.3007 2892.035464 3 0.0008 148 | 0/8 7 h-lim-p 0.0234 20.0000 0.0107 2892.035457 0 0.0102 168 | 0/8 8 h-lim-p 0.0100 20.0000 0.0109 2892.034642 0 0.0803 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 2892.034618 1 0.9961 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2892.034618 0 1.0938 233 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2892.034618 0 1.0938 253 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2892.034618 0 2.1875 273 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2892.034618 0 0.6250 294 | 0/8 14 h-lim-p 0.3680 20.0000 0.0000 2892.034618 0 0.0058 319 Out... lnL = -2892.034618 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2892.034618 Node 7: lnL = -2892.034618 Node 8: lnL = -2892.034618 Node 9: lnL = -2892.034618 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 373 Sequential format.. Reading seq # 1: YDR116C_Sbay Reading seq # 2: YDR116C_Scer Reading seq # 3: YDR116C_Skud Reading seq # 4: YDR116C_Smik Reading seq # 5: YDR116C_Spar Sequences read.. Counting patterns.. # site patterns = 165 Counting frequencies.. 120 bytes for distance 26400 bytes for lkl0 21120 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.157692 0.051237 0.082948 0.123746 0.081124 0.238113 0.320538 0.157244 lnL0 = -1777.673053 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1777.673053 x= 0.15769 0.05124 0.08295 0.12375 0.08112 0.23811 0.32054 0.15724 1 h-lim-p 0.0050 0.0396 53.7237 1777.052245 8 0.0005 41 | 0/8 2 h-lim-p 0.0020 0.0162 11.7858 1777.014280 7 0.0006 70 | 0/8 3 h-lim-p 0.0010 0.0231 6.9032 1776.999608 3 0.0008 88 | 0/8 4 h-lim-p 0.0023 0.1873 2.3856 1776.997313 3 0.0009 106 | 0/8 5 h-lim-p 0.0032 0.5513 0.6909 1776.997039 2 0.0013 122 | 0/8 6 h-lim-p 0.0033 0.9460 0.2609 1776.997016 0 0.0007 143 | 0/8 7 h-lim-p 0.0038 7.0984 0.0500 1776.997015 1 0.0015 165 | 0/8 8 h-lim-p 0.1881 20.0000 0.0004 1776.996852 0 1.1288 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1776.996851 0 1.0938 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1776.996851 0 1.0938 227 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1776.996851 0 2.1875 247 | 0/8 12 h-lim-p 1.8445 20.0000 0.0000 1776.996851 0 0.4035 268 | 0/8 13 h-lim-p 0.6735 20.0000 0.0000 1776.996851 0 0.0000 314 Out... lnL = -1776.996851 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1776.996851 Node 7: lnL = -1776.996851 Node 8: lnL = -1776.996851 Node 9: lnL = -1776.996851 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 269 Sequential format.. Reading seq # 1: YDR117C_Sbay Reading seq # 2: YDR117C_Scer Reading seq # 3: YDR117C_Skud Reading seq # 4: YDR117C_Smik Reading seq # 5: YDR117C_Spar Sequences read.. Counting patterns.. # site patterns = 117 Counting frequencies.. 120 bytes for distance 18720 bytes for lkl0 14976 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.199009 0.062241 0.087126 0.103149 0.065287 0.164352 0.204147 0.198604 lnL0 = -1135.631554 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1135.631554 x= 0.19901 0.06224 0.08713 0.10315 0.06529 0.16435 0.20415 0.19860 1 h-lim-p 0.0004 0.0033 38.4132 1135.063895 0 0.0008 23 | 0/8 2 h-lim-p 0.0021 0.0426 15.2790 1135.006554 7 0.0006 50 | 0/8 3 h-lim-p 0.0011 0.0246 7.8956 1134.986511 6 0.0008 77 | 0/8 4 h-lim-p 0.0039 0.1640 1.6460 1134.985304 3 0.0009 97 | 0/8 5 h-lim-p 0.0024 0.4361 0.6507 1134.985073 3 0.0013 116 | 0/8 6 h-lim-p 0.0085 1.8886 0.0963 1134.985067 2 0.0011 142 | 0/8 7 h-lim-p 0.0767 20.0000 0.0014 1134.984235 0 0.9199 165 | 0/8 8 h-lim-p 0.0086 1.9388 0.1507 1134.984216 2 0.0017 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1134.984214 0 1.0938 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1134.984214 0 1.0938 230 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1134.984214 0 0.5469 251 | 0/8 12 h-lim-p 1.2021 20.0000 0.0000 1134.984214 0 0.0164 276 Out... lnL = -1134.984214 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1134.984214 Node 7: lnL = -1134.984214 Node 8: lnL = -1134.984214 Node 9: lnL = -1134.984214 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 281 Sequential format.. Reading seq # 1: YDR118W_Sbay Reading seq # 2: YDR118W_Scer Reading seq # 3: YDR118W_Skud Reading seq # 4: YDR118W_Smik Reading seq # 5: YDR118W_Spar Sequences read.. Counting patterns.. # site patterns = 117 Counting frequencies.. 120 bytes for distance 18720 bytes for lkl0 14976 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.186325 0.069698 0.080729 0.104340 0.064096 0.171048 0.201203 0.185926 lnL0 = -1144.095992 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1144.095992 x= 0.18633 0.06970 0.08073 0.10434 0.06410 0.17105 0.20120 0.18593 1 h-lim-p 0.0003 0.0022 40.9309 1143.565898 0 0.0006 23 | 0/8 2 h-lim-p 0.0015 0.0563 14.9873 1143.511547 7 0.0005 52 | 0/8 3 h-lim-p 0.0015 0.0578 5.6451 1143.496441 6 0.0011 77 | 0/8 4 h-lim-p 0.0061 0.3607 1.0103 1143.495933 4 0.0010 99 | 0/8 5 h-lim-p 0.0019 0.4155 0.5299 1143.495807 3 0.0010 118 | 0/8 6 h-lim-p 0.0157 8.6475 0.0347 1143.495510 0 0.0314 139 | 0/8 7 h-lim-p 0.0066 0.8530 0.1653 1143.491997 0 0.0132 160 | 0/8 8 h-lim-p 0.0020 0.1117 1.1017 1143.485868 0 0.0030 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 1143.485794 2 0.9961 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1143.485794 0 1.0938 216 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1143.485794 0 2.1875 236 | 0/8 12 h-lim-p 1.8477 20.0000 0.0000 1143.485794 0 0.8084 256 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1143.485794 0 0.0012 286 Out... lnL = -1143.485794 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1143.485794 Node 7: lnL = -1143.485794 Node 8: lnL = -1143.485794 Node 9: lnL = -1143.485794 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 351 Sequential format.. Reading seq # 1: YDR121W_Sbay Reading seq # 2: YDR121W_Scer Reading seq # 3: YDR121W_Skud Reading seq # 4: YDR121W_Smik Reading seq # 5: YDR121W_Spar Sequences read.. Counting patterns.. # site patterns = 176 Counting frequencies.. 120 bytes for distance 28160 bytes for lkl0 22528 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.115838 0.074498 0.154095 0.196220 0.100837 0.276014 0.226499 0.115358 lnL0 = -1701.297070 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1701.297070 x= 0.11584 0.07450 0.15409 0.19622 0.10084 0.27601 0.22650 0.11536 1 h-lim-p 0.0017 0.0140 63.4421 1700.042612 4 0.0007 30 | 0/8 2 h-lim-p 0.0015 0.0123 13.6334 1699.969006 5 0.0008 53 | 0/8 3 h-lim-p 0.0030 0.1836 3.6950 1699.963359 5 0.0009 78 | 0/8 4 h-lim-p 0.0027 0.1202 1.2148 1699.962886 4 0.0007 99 | 0/8 5 h-lim-p 0.0046 2.1505 0.1895 1699.962856 2 0.0018 115 | 0/8 6 h-lim-p 0.0101 11.6653 0.0329 1699.962855 0 0.0022 136 | 0/8 7 h-lim-p 0.1801 20.0000 0.0004 1699.962855 0 0.0394 157 | 0/8 8 h-lim-p 0.0230 20.0000 0.0007 1699.962854 0 0.0689 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1699.962854 0 1.0938 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1699.962854 0 2.1875 218 | 0/8 11 h-lim-p 1.9820 20.0000 0.0000 1699.962854 0 0.8671 238 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1699.962854 0 0.0391 263 Out... lnL = -1699.962854 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1699.962854 Node 7: lnL = -1699.962854 Node 8: lnL = -1699.962854 Node 9: lnL = -1699.962854 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 869 Sequential format.. Reading seq # 1: YDR123C_Sbay Reading seq # 2: YDR123C_Scer Reading seq # 3: YDR123C_Skud Reading seq # 4: YDR123C_Smik Reading seq # 5: YDR123C_Spar Sequences read.. Counting patterns.. # site patterns = 252 Counting frequencies.. 120 bytes for distance 40320 bytes for lkl0 32256 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.138930 0.054448 0.020721 0.120623 0.077667 0.173800 0.144576 0.138613 lnL0 = -3613.263583 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3613.263583 x= 0.13893 0.05445 0.02072 0.12062 0.07767 0.17380 0.14458 0.13861 1 h-lim-p 0.0005 0.0037 226.5665 3610.589975 9 0.0001 41 | 0/8 2 h-lim-p 0.0001 0.0008 102.1714 3609.863679 0 0.0002 54 | 0/8 3 h-lim-p 0.0007 0.0058 30.4848 3609.767141 7 0.0002 83 | 0/8 4 h-lim-p 0.0006 0.0133 11.7625 3609.756003 6 0.0002 112 | 0/8 5 h-lim-p 0.0008 0.0628 2.7439 3609.755179 4 0.0002 134 | 0/8 6 h-lim-p 0.0017 0.6627 0.3728 3609.755127 3 0.0005 154 | 0/8 7 h-lim-p 0.0129 20.0000 0.0148 3609.746808 0 0.1549 177 | 0/8 8 h-lim-p 0.0010 0.0928 2.3671 3609.721555 0 0.0015 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 3609.721352 3 1.0004 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3609.721352 0 1.2500 235 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3609.721352 0 1.0938 255 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3609.721352 0 5.0000 276 | 0/8 13 h-lim-p 1.3029 20.0000 0.0000 3609.721352 0 0.0002 308 Out... lnL = -3609.721352 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3609.721352 Node 7: lnL = -3609.721352 Node 8: lnL = -3609.721352 Node 9: lnL = -3609.721352 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 889 Sequential format.. Reading seq # 1: YDR124W_Sbay Reading seq # 2: YDR124W_Scer Reading seq # 3: YDR124W_Skud Reading seq # 4: YDR124W_Smik Reading seq # 5: YDR124W_Spar Sequences read.. Counting patterns.. # site patterns = 288 Counting frequencies.. 120 bytes for distance 46080 bytes for lkl0 36864 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.177597 0.061854 0.041839 0.122759 0.091106 0.149867 0.145273 0.177240 lnL0 = -3729.387748 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3729.387748 x= 0.17760 0.06185 0.04184 0.12276 0.09111 0.14987 0.14527 0.17724 1 h-lim-p 0.0002 0.0015 234.8401 3723.921113 1 0.0002 24 | 0/8 2 h-lim-p 0.0001 0.0009 83.7948 3723.311036 0 0.0002 37 | 0/8 3 h-lim-p 0.0003 0.0026 56.2903 3723.099625 7 0.0002 65 | 0/8 4 h-lim-p 0.0010 0.0172 10.7769 3723.086735 4 0.0002 87 | 0/8 5 h-lim-p 0.0008 0.0436 3.0258 3723.085934 2 0.0002 104 | 0/8 6 h-lim-p 0.0008 0.5781 0.6745 3723.085843 0 0.0004 116 | 0/8 7 h-lim-p 0.0029 2.9102 0.0976 3723.085813 2 0.0015 141 | 0/8 8 h-lim-p 0.0138 20.0000 0.0106 3723.073370 0 0.2214 165 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3723.073266 1 0.9961 187 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3723.073265 0 2.1875 207 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3723.073265 0 1.0938 227 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3723.073265 0 1.2500 247 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 3723.073265 0 0.1367 270 | 0/8 14 h-lim-p 0.1567 20.0000 0.0000 3723.073265 0 0.0343 291 | 0/8 15 h-lim-p 0.0303 20.0000 0.0000 3723.073265 0 0.0076 312 Out... lnL = -3723.073265 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3723.073265 Node 7: lnL = -3723.073265 Node 8: lnL = -3723.073265 Node 9: lnL = -3723.073265 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 599 Sequential format.. Reading seq # 1: YDR125C_Sbay Reading seq # 2: YDR125C_Scer Reading seq # 3: YDR125C_Skud Reading seq # 4: YDR125C_Smik Reading seq # 5: YDR125C_Spar Sequences read.. Counting patterns.. # site patterns = 279 Counting frequencies.. 120 bytes for distance 44640 bytes for lkl0 35712 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.159650 0.179401 0.078587 0.199448 0.147131 0.311133 0.214280 0.159098 lnL0 = -2829.816361 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2829.816361 x= 0.15965 0.17940 0.07859 0.19945 0.14713 0.31113 0.21428 0.15910 1 h-lim-p 0.0024 0.0195 61.4543 2828.872463 6 0.0005 34 | 0/8 2 h-lim-p 0.0017 0.0140 14.9012 2828.783851 2 0.0008 50 | 0/8 3 h-lim-p 0.0018 0.0744 6.7761 2828.769328 4 0.0008 71 | 0/8 4 h-lim-p 0.0043 0.3560 1.1857 2828.768648 2 0.0010 88 | 0/8 5 h-lim-p 0.0029 0.6962 0.4208 2828.768580 3 0.0008 109 | 0/8 6 h-lim-p 0.0039 4.2446 0.0913 2828.768576 0 0.0010 130 | 0/8 7 h-lim-p 0.0249 20.0000 0.0035 2828.768575 0 0.0218 150 | 0/8 8 h-lim-p 0.0223 20.0000 0.0035 2828.768513 0 0.0893 172 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2828.768512 0 1.0938 192 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2828.768512 0 1.0938 212 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2828.768512 0 1.0938 232 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2828.768512 0 5.0000 253 | 0/8 13 h-lim-p 1.4933 20.0000 0.0000 2828.768512 0 0.0117 279 Out... lnL = -2828.768512 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2828.768512 Node 7: lnL = -2828.768512 Node 8: lnL = -2828.768512 Node 9: lnL = -2828.768512 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 536 Sequential format.. Reading seq # 1: YDR126W_Sbay Reading seq # 2: YDR126W_Scer Reading seq # 3: YDR126W_Skud Reading seq # 4: YDR126W_Smik Reading seq # 5: YDR126W_Spar Sequences read.. Counting patterns.. # site patterns = 253 Counting frequencies.. 120 bytes for distance 40480 bytes for lkl0 32384 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.162549 0.157316 0.077098 0.197037 0.142882 0.315163 0.234450 0.162001 lnL0 = -2652.396766 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2652.396766 x= 0.16255 0.15732 0.07710 0.19704 0.14288 0.31516 0.23445 0.16200 1 h-lim-p 0.0127 0.1355 64.6797 2651.431072 9 0.0005 48 | 0/8 2 h-lim-p 0.0022 0.0252 14.3042 2651.344604 6 0.0009 72 | 0/8 3 h-lim-p 0.0018 0.0648 7.1258 2651.328980 4 0.0008 94 | 0/8 4 h-lim-p 0.0055 0.4006 0.9826 2651.328462 3 0.0011 113 | 0/8 5 h-lim-p 0.0048 1.3808 0.2218 2651.328439 1 0.0010 136 | 0/8 6 h-lim-p 0.0076 11.6859 0.0280 2651.328439 0 0.0010 158 | 0/8 7 h-lim-p 0.0105 20.0000 0.0025 2651.328432 0 0.0632 180 | 0/8 8 h-lim-p 0.0114 20.0000 0.0141 2651.328327 0 0.0227 201 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2651.328325 0 1.0938 221 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2651.328325 0 1.0938 241 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2651.328325 0 0.6250 262 | 0/8 12 h-lim-p 1.6582 20.0000 0.0000 2651.328325 0 0.2073 284 | 0/8 13 h-lim-p 0.2271 20.0000 0.0000 2651.328325 0 0.0568 305 | 0/8 14 h-lim-p 0.0523 20.0000 0.0000 2651.328325 0 0.0001 333 Out... lnL = -2651.328325 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2651.328325 Node 7: lnL = -2651.328325 Node 8: lnL = -2651.328325 Node 9: lnL = -2651.328325 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 185 Sequential format.. Reading seq # 1: YDR130C_Sbay Reading seq # 2: YDR130C_Scer Reading seq # 3: YDR130C_Skud Reading seq # 4: YDR130C_Smik Reading seq # 5: YDR130C_Spar Sequences read.. Counting patterns.. # site patterns = 86 Counting frequencies.. 120 bytes for distance 13760 bytes for lkl0 11008 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.298371 0.000060 0.356911 0.109266 0.089234 4.178509 0.308937 0.297058 lnL0 = -727.388708 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 727.388708 x= 0.29837 0.00006 0.35691 0.10927 0.08923 4.17851 0.30894 0.29706 1 h-lim-p 0.0000 0.0000 58.9464 727.376236 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0277 23.3806 727.029732 0 0.0013 41 | 1/8 3 h-lim-p 0.0015 0.0132 19.4704 726.636555 0 0.0031 54 | 1/8 4 h-lim-p 0.0080 0.0638 6.8785 726.371758 0 0.0120 66 | 1/8 5 h-lim-p 0.0180 0.1438 2.7465 725.795468 0 0.0360 79 | 1/8 6 h-lim-p 0.0334 0.2675 1.6595 721.151049 0 0.1337 93 | 0/8 7 h-lim-p 0.0348 0.2787 1.9893 721.140918 6 0.0048 121 | 0/8 8 h-lim-p 0.1295 12.8968 0.0743 720.911466 0 0.5180 135 | 0/8 9 h-lim-p 2.5000 20.0000 0.0121 720.903367 6 0.6876 170 | 0/8 10 h-lim-p 2.5000 20.0000 0.0026 720.901697 6 0.6881 204 | 0/8 11 h-lim-p 0.8547 18.7580 0.0021 720.901552 2 0.4007 228 | 0/8 12 h-lim-p 2.5000 20.0000 0.0001 720.901550 0 1.0938 248 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 720.901550 0 1.0938 268 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 720.901550 0 1.0938 288 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 720.901550 0 5.0000 309 | 0/8 16 h-lim-p 1.6605 20.0000 0.0000 720.901550 0 0.1816 331 | 0/8 17 h-lim-p 0.0122 20.0000 0.0000 720.901550 0 0.0001 357 Out... lnL = -720.901550 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -720.901550 Node 7: lnL = -720.901550 Node 8: lnL = -720.901550 Node 9: lnL = -720.901550 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 377 Sequential format.. Reading seq # 1: YDR131C_Sbay Reading seq # 2: YDR131C_Scer Reading seq # 3: YDR131C_Skud Reading seq # 4: YDR131C_Smik Reading seq # 5: YDR131C_Spar Sequences read.. Counting patterns.. # site patterns = 207 Counting frequencies.. 120 bytes for distance 33120 bytes for lkl0 26496 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.170014 0.009178 0.208426 0.178651 0.093039 0.352461 0.343717 0.169442 lnL0 = -1917.170537 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1917.170537 x= 0.17001 0.00918 0.20843 0.17865 0.09304 0.35246 0.34372 0.16944 1 h-lim-p 0.0017 0.0136 39.0418 1916.737705 5 0.0006 33 | 0/8 2 h-lim-p 0.0033 0.0349 7.1075 1916.710179 7 0.0011 64 | 0/8 3 h-lim-p 0.0039 0.2512 2.0174 1916.709243 3 0.0005 84 | 0/8 4 h-lim-p 0.0024 0.5667 0.4017 1916.709165 1 0.0010 98 | 0/8 5 h-lim-p 0.0088 8.9288 0.0444 1916.709163 1 0.0022 121 | 0/8 6 h-lim-p 0.1147 20.0000 0.0008 1916.709163 0 0.0502 141 | 0/8 7 h-lim-p 0.0239 20.0000 0.0018 1916.709158 0 0.0479 162 | 0/8 8 h-lim-p 0.0032 20.0000 0.0264 1916.709157 0 0.0028 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1916.709157 0 1.0938 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1916.709157 0 1.0938 222 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1916.709157 0 0.3125 244 | 0/8 12 h-lim-p 0.4487 20.0000 0.0000 1916.709157 0 0.0841 266 | 0/8 13 h-lim-p 0.0826 20.0000 0.0000 1916.709157 0 0.0000 301 Out... lnL = -1916.709157 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1916.709157 Node 7: lnL = -1916.709157 Node 8: lnL = -1916.709157 Node 9: lnL = -1916.709157 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 705 Sequential format.. Reading seq # 1: YDR132C_Sbay Reading seq # 2: YDR132C_Scer Reading seq # 3: YDR132C_Skud Reading seq # 4: YDR132C_Smik Reading seq # 5: YDR132C_Spar Sequences read.. Counting patterns.. # site patterns = 266 Counting frequencies.. 120 bytes for distance 42560 bytes for lkl0 34048 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.138766 0.067734 0.060002 0.146075 0.100367 0.196193 0.200372 0.138377 lnL0 = -3213.070977 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3213.070977 x= 0.13877 0.06773 0.06000 0.14607 0.10037 0.19619 0.20037 0.13838 1 h-lim-p 0.0004 0.0035 143.0528 3210.861468 8 0.0002 38 | 0/8 2 h-lim-p 0.0005 0.0039 33.6768 3210.669722 7 0.0004 66 | 0/8 3 h-lim-p 0.0008 0.0197 14.7623 3210.641011 4 0.0003 86 | 0/8 4 h-lim-p 0.0011 0.0696 4.0467 3210.638191 4 0.0004 107 | 0/8 5 h-lim-p 0.0055 0.9480 0.2774 3210.638176 2 0.0004 126 | 0/8 6 h-lim-p 0.0058 10.3612 0.0172 3210.638176 0 0.0006 148 | 0/8 7 h-lim-p 0.0254 20.0000 0.0004 3210.638173 0 0.1521 170 | 0/8 8 h-lim-p 0.0023 6.4443 0.0290 3210.638154 0 0.0045 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3210.638154 0 1.0938 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3210.638154 0 1.0938 231 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3210.638154 0 0.0195 257 Out... lnL = -3210.638154 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3210.638154 Node 7: lnL = -3210.638154 Node 8: lnL = -3210.638154 Node 9: lnL = -3210.638154 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 161 Sequential format.. Reading seq # 1: YDR135C_Sbay Reading seq # 2: YDR135C_Scer Reading seq # 3: YDR135C_Skud Reading seq # 4: YDR135C_Smik Reading seq # 5: YDR135C_Spar Sequences read.. Counting patterns.. # site patterns = 61 Counting frequencies.. 120 bytes for distance 9760 bytes for lkl0 7808 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.134823 0.021718 0.158771 0.117863 0.084309 4.740142 0.207946 0.133510 lnL0 = -634.376224 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 634.376224 x= 0.13482 0.02172 0.15877 0.11786 0.08431 4.74014 0.20795 0.13351 1 h-lim-p 0.0007 0.0055 28.0601 633.776559 0 0.0014 23 | 0/8 2 h-lim-p 0.0021 0.0165 9.9833 633.702527 7 0.0016 50 | 0/8 3 h-lim-p 0.0073 0.1024 2.2324 633.697117 6 0.0023 79 | 0/8 4 h-lim-p 0.0068 0.9044 0.7518 633.696905 2 0.0008 97 | 0/8 5 h-lim-p 0.0058 1.3457 0.1026 633.696848 3 0.0044 123 | 0/8 6 h-lim-p 0.0352 10.5536 0.0128 633.688535 0 0.4227 146 | 0/8 7 h-lim-p 2.5000 20.0000 0.0002 633.688526 2 0.9961 170 | 0/8 8 h-lim-p 2.5000 20.0000 0.0000 633.688526 0 1.0938 190 | 0/8 9 h-lim-p 1.3062 20.0000 0.0000 633.688526 0 0.1633 212 | 0/8 10 h-lim-p 0.0590 20.0000 0.0000 633.688526 0 0.0111 234 | 0/8 11 h-lim-p 0.0053 20.0000 0.0000 633.688526 0 0.0000 276 | 0/8 12 h-lim-p 0.0000 20.0000 0.0003 | 0/8 13 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -633.688526 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -633.688526 Node 7: lnL = -633.688526 Node 8: lnL = -633.688526 Node 9: lnL = -633.688526 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 222 Sequential format.. Reading seq # 1: YDR140W_Sbay Reading seq # 2: YDR140W_Scer Reading seq # 3: YDR140W_Skud Reading seq # 4: YDR140W_Smik Reading seq # 5: YDR140W_Spar Sequences read.. Counting patterns.. # site patterns = 116 Counting frequencies.. 120 bytes for distance 18560 bytes for lkl0 14848 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.145192 0.037142 0.208093 0.070450 0.090594 0.275365 0.264229 0.144716 lnL0 = -1035.072790 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1035.072790 x= 0.14519 0.03714 0.20809 0.07045 0.09059 0.27536 0.26423 0.14472 1 h-lim-p 0.0010 0.0080 27.7387 1034.762369 6 0.0008 36 | 0/8 2 h-lim-p 0.0014 0.0111 9.4843 1034.733483 3 0.0007 54 | 0/8 3 h-lim-p 0.0012 0.0474 5.5376 1034.715921 1 0.0015 68 | 0/8 4 h-lim-p 0.0039 0.1086 2.1675 1034.713585 5 0.0012 93 | 0/8 5 h-lim-p 0.0088 1.2034 0.2983 1034.713503 2 0.0019 110 | 0/8 6 h-lim-p 0.0090 5.3762 0.0632 1034.713500 1 0.0020 133 | 0/8 7 h-lim-p 0.1342 20.0000 0.0009 1034.713496 1 0.1384 155 | 0/8 8 h-lim-p 0.0100 9.1205 0.0128 1034.713471 0 0.0200 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1034.713471 0 1.0938 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1034.713471 0 1.0938 216 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1034.713471 0 2.1875 236 | 0/8 12 h-lim-p 1.8558 20.0000 0.0000 1034.713471 0 0.8119 256 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1034.713471 0 0.0781 280 Out... lnL = -1034.713471 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1034.713471 Node 7: lnL = -1034.713471 Node 8: lnL = -1034.713471 Node 9: lnL = -1034.713471 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 485 Sequential format.. Reading seq # 1: YDR142C_Sbay Reading seq # 2: YDR142C_Scer Reading seq # 3: YDR142C_Skud Reading seq # 4: YDR142C_Smik Reading seq # 5: YDR142C_Spar Sequences read.. Counting patterns.. # site patterns = 192 Counting frequencies.. 120 bytes for distance 30720 bytes for lkl0 24576 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.129983 0.059962 0.074305 0.122381 0.089733 0.196280 0.204852 0.129607 lnL0 = -2169.677297 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2169.677297 x= 0.12998 0.05996 0.07430 0.12238 0.08973 0.19628 0.20485 0.12961 1 h-lim-p 0.0009 0.0071 98.6901 2168.242401 9 0.0003 45 | 0/8 2 h-lim-p 0.0007 0.0058 22.3624 2168.128633 6 0.0005 71 | 0/8 3 h-lim-p 0.0010 0.0261 10.8205 2168.106635 2 0.0005 87 | 0/8 4 h-lim-p 0.0017 0.0617 2.9628 2168.104567 5 0.0005 113 | 0/8 5 h-lim-p 0.0048 1.1059 0.3196 2168.104529 3 0.0008 134 | 0/8 6 h-lim-p 0.0354 20.0000 0.0070 2168.104529 0 0.0019 157 | 0/8 7 h-lim-p 0.0257 20.0000 0.0005 2168.104473 0 0.4114 181 | 0/8 8 h-lim-p 0.0025 3.0677 0.0884 2168.104470 0 0.0006 202 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2168.104470 0 1.0938 222 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2168.104470 0 1.0938 242 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2168.104470 0 1.0938 262 | 0/8 12 h-lim-p 1.9529 20.0000 0.0000 2168.104470 0 7.8115 284 | 0/8 13 h-lim-p 1.3763 20.0000 0.0000 2168.104470 0 0.0430 308 | 0/8 14 h-lim-p 0.0427 20.0000 0.0000 2168.104470 0 0.0107 329 Out... lnL = -2168.104470 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2168.104470 Node 7: lnL = -2168.104470 Node 8: lnL = -2168.104470 Node 9: lnL = -2168.104470 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 459 Sequential format.. Reading seq # 1: YDR143C_Sbay Reading seq # 2: YDR143C_Scer Reading seq # 3: YDR143C_Skud Reading seq # 4: YDR143C_Smik Reading seq # 5: YDR143C_Spar Sequences read.. Counting patterns.. # site patterns = 197 Counting frequencies.. 120 bytes for distance 31520 bytes for lkl0 25216 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.117156 0.126044 0.085164 0.123619 0.100563 0.190090 0.159128 0.109291 lnL0 = -2056.762068 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2056.762068 x= 0.11716 0.12604 0.08516 0.12362 0.10056 0.19009 0.15913 0.10929 1 h-lim-p 0.0048 0.0387 92.0952 2055.079946 8 0.0004 43 | 0/8 2 h-lim-p 0.0010 0.0080 25.7161 2054.882084 7 0.0006 72 | 0/8 3 h-lim-p 0.0014 0.0198 11.6517 2054.853583 6 0.0005 99 | 0/8 4 h-lim-p 0.0040 0.2505 1.4798 2054.853028 4 0.0005 121 | 0/8 5 h-lim-p 0.0024 0.6036 0.3158 2054.852996 3 0.0007 140 | 0/8 6 h-lim-p 0.0076 9.9565 0.0271 2054.852994 0 0.0017 161 | 0/8 7 h-lim-p 0.0063 20.0000 0.0072 2054.852901 0 0.0503 184 | 0/8 8 h-lim-p 0.0030 5.5747 0.1210 2054.852249 0 0.0060 205 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 2054.852220 2 0.9961 229 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2054.852220 0 1.0938 249 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2054.852220 0 2.1875 269 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2054.852220 0 0.0586 294 | 0/8 13 h-lim-p 0.0200 20.0000 0.0000 2054.852220 0 0.0006 318 Out... lnL = -2054.852220 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2054.852220 Node 7: lnL = -2054.852220 Node 8: lnL = -2054.852220 Node 9: lnL = -2054.852220 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 660 Sequential format.. Reading seq # 1: YDR145W_Sbay Reading seq # 2: YDR145W_Scer Reading seq # 3: YDR145W_Skud Reading seq # 4: YDR145W_Smik Reading seq # 5: YDR145W_Spar Sequences read.. Counting patterns.. # site patterns = 169 Counting frequencies.. 120 bytes for distance 27040 bytes for lkl0 21632 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.193646 0.000060 0.184036 0.121378 0.110587 4.658312 0.278180 0.167232 lnL0 = -2679.474983 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2679.474983 x= 0.19365 0.00006 0.18404 0.12138 0.11059 4.65831 0.27818 0.16723 1 h-lim-p 0.0006 0.0045 37.9283 2679.169797 7 0.0004 40 | 0/8 2 h-lim-p 0.0005 0.0094 31.8777 2678.991002 6 0.0005 63 | 0/8 3 h-lim-p 0.0023 0.0323 7.1570 2678.978689 2 0.0005 80 | 0/8 4 h-lim-p 0.0005 0.0040 1.9690 2678.977953 3 0.0004 98 | 0/8 5 h-lim-p 0.0032 0.3106 0.2546 2678.977934 2 0.0006 115 | 0/8 6 h-lim-p 0.0335 1.0971 0.0048 2678.977762 2 0.8718 143 | 0/8 7 h-lim-p 2.5000 20.0000 0.0000 2678.977762 0 1.0938 163 | 0/8 8 h-lim-p 1.0508 20.0000 0.0000 2678.977762 0 1.0508 183 | 0/8 9 h-lim-p 1.0469 20.0000 0.0000 2678.977762 0 0.0327 207 | 0/8 10 h-lim-p 0.0003 0.3296 0.0032 2678.977762 0 0.0000 229 | 0/8 11 h-lim-p 0.0003 20.0000 0.0004 2678.977762 0 0.0000 254 | 0/8 12 h-lim-p 0.0000 4.5045 0.0003 2678.977762 0 0.0000 277 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 2678.977762 0 0.0000 298 Out... lnL = -2678.977762 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2678.977762 Node 7: lnL = -2678.977762 Node 8: lnL = -2678.977762 Node 9: lnL = -2678.977762 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 855 Sequential format.. Reading seq # 1: YDR146C_Sbay Reading seq # 2: YDR146C_Scer Reading seq # 3: YDR146C_Skud Reading seq # 4: YDR146C_Smik Reading seq # 5: YDR146C_Spar Sequences read.. Counting patterns.. # site patterns = 234 Counting frequencies.. 120 bytes for distance 37440 bytes for lkl0 29952 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.151537 0.054410 0.067286 0.139922 0.090628 0.766529 0.173964 0.139950 lnL0 = -3371.009649 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3371.009649 x= 0.15154 0.05441 0.06729 0.13992 0.09063 0.76653 0.17396 0.13995 1 h-lim-p 0.0003 0.0028 130.9694 3369.406301 9 0.0002 47 | 0/8 2 h-lim-p 0.0004 0.0032 47.4790 3369.159501 8 0.0002 81 | 0/8 3 h-lim-p 0.0011 0.0102 10.4490 3369.039685 0 0.0022 94 | 0/8 4 h-lim-p 0.0003 0.0022 43.6096 3368.928087 0 0.0005 107 | 0/8 5 h-lim-p 0.0002 0.0016 36.3580 3368.872397 0 0.0004 120 | 0/8 6 h-lim-p 0.0059 0.0874 2.4093 3368.869766 5 0.0010 146 | 0/8 7 h-lim-p 0.0005 0.9623 5.2492 3368.838388 0 0.0072 162 | 0/8 8 h-lim-p 0.9801 7.8404 0.0064 3368.833758 1 1.2251 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 3368.833698 1 0.9961 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3368.833697 0 1.0938 218 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3368.833697 0 1.0938 238 | 0/8 12 h-lim-p 1.7170 20.0000 0.0000 3368.833697 0 0.3756 259 | 0/8 13 h-lim-p 0.1486 20.0000 0.0000 3368.833697 0 0.0046 283 | 0/8 14 h-lim-p 0.0043 20.0000 0.0000 3368.833697 0 0.0022 303 Out... lnL = -3368.833697 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3368.833697 Node 7: lnL = -3368.833697 Node 8: lnL = -3368.833697 Node 9: lnL = -3368.833697 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 858 Sequential format.. Reading seq # 1: YDR147W_Sbay Reading seq # 2: YDR147W_Scer Reading seq # 3: YDR147W_Skud Reading seq # 4: YDR147W_Smik Reading seq # 5: YDR147W_Spar Sequences read.. Counting patterns.. # site patterns = 283 Counting frequencies.. 120 bytes for distance 45280 bytes for lkl0 36224 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.149981 0.071903 0.047367 0.128688 0.096390 0.209482 0.181959 0.142319 lnL0 = -3855.621299 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3855.621299 x= 0.14998 0.07190 0.04737 0.12869 0.09639 0.20948 0.18196 0.14232 1 h-lim-p 0.0002 0.0020 156.4627 3853.849321 7 0.0002 41 | 0/8 2 h-lim-p 0.0004 0.0034 39.5904 3853.681214 5 0.0002 64 | 0/8 3 h-lim-p 0.0006 0.0144 14.7131 3853.658157 6 0.0002 87 | 0/8 4 h-lim-p 0.0007 0.0546 4.9254 3853.654506 2 0.0003 103 | 0/8 5 h-lim-p 0.0053 0.7170 0.3143 3853.654492 0 0.0003 118 | 0/8 6 h-lim-p 0.0016 5.4990 0.0558 3853.654491 0 0.0007 138 | 0/8 7 h-lim-p 0.0083 20.0000 0.0048 3853.654479 0 0.0166 159 | 0/8 8 h-lim-p 0.0030 2.7014 0.0267 3853.653970 0 0.0180 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3853.653954 1 0.9961 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3853.653954 0 2.1875 223 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3853.653954 0 1.0938 243 | 0/8 12 h-lim-p 1.1500 20.0000 0.0000 3853.653954 0 4.5999 265 | 0/8 13 h-lim-p 1.7755 20.0000 0.0000 3853.653954 0 0.2219 287 | 0/8 14 h-lim-p 0.5545 20.0000 0.0000 3853.653954 0 0.0347 310 | 0/8 15 h-lim-p 0.0871 20.0000 0.0000 3853.653954 0 0.0000 352 Out... lnL = -3853.653954 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3853.653954 Node 7: lnL = -3853.653954 Node 8: lnL = -3853.653954 Node 9: lnL = -3853.653954 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 541 Sequential format.. Reading seq # 1: YDR148C_Sbay Reading seq # 2: YDR148C_Scer Reading seq # 3: YDR148C_Skud Reading seq # 4: YDR148C_Smik Reading seq # 5: YDR148C_Spar Sequences read.. Counting patterns.. # site patterns = 140 Counting frequencies.. 120 bytes for distance 22400 bytes for lkl0 17920 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.207815 0.000060 0.145383 0.101232 0.079253 4.601404 0.234829 0.181400 lnL0 = -1918.960454 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1918.960454 x= 0.20781 0.00006 0.14538 0.10123 0.07925 4.60140 0.23483 0.18140 1 h-lim-p 0.0000 0.0000 204.0936 1918.919903 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0042 82.8319 1917.525226 0 0.0005 39 | 1/8 3 h-lim-p 0.0042 0.0340 9.5395 1917.475262 2 0.0010 56 | 1/8 4 h-lim-p 0.0057 0.1188 1.6460 1917.404806 1 0.0071 70 | 1/8 5 h-lim-p 0.0038 0.0843 3.0293 1916.619795 0 0.0115 83 | 1/8 6 h-lim-p 0.0020 0.0159 10.4922 1911.170379 0 0.0079 97 | 0/8 7 h-lim-p 0.0032 0.0253 7.3102 1911.158672 6 0.0005 123 | 0/8 8 h-lim-p 0.1357 11.5891 0.0282 1910.496184 0 0.5426 137 | 0/8 9 h-lim-p 0.4960 3.9682 0.0087 1910.468567 1 0.6200 159 | 0/8 10 h-lim-p 2.5000 20.0000 0.0009 1910.467778 4 0.9422 187 | 0/8 11 h-lim-p 2.5000 20.0000 0.0002 1910.467741 2 0.7996 212 | 0/8 12 h-lim-p 2.5000 20.0000 0.0001 1910.467740 0 1.0938 232 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1910.467740 0 1.0938 252 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1910.467740 0 1.2500 272 | 0/8 15 h-lim-p 2.2643 20.0000 0.0000 1910.467740 0 0.1415 295 | 0/8 16 h-lim-p 0.0652 20.0000 0.0000 1910.467740 0 0.0081 317 Out... lnL = -1910.467740 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1910.467740 Node 7: lnL = -1910.467740 Node 8: lnL = -1910.467740 Node 9: lnL = -1910.467740 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 581 Sequential format.. Reading seq # 1: YDR151C_Sbay Reading seq # 2: YDR151C_Scer Reading seq # 3: YDR151C_Skud Reading seq # 4: YDR151C_Smik Reading seq # 5: YDR151C_Spar Sequences read.. Counting patterns.. # site patterns = 214 Counting frequencies.. 120 bytes for distance 34240 bytes for lkl0 27392 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.157706 0.013244 0.082506 0.137462 0.079688 0.211912 0.197641 0.150112 lnL0 = -2620.640074 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2620.640074 x= 0.15771 0.01324 0.08251 0.13746 0.07969 0.21191 0.19764 0.15011 1 h-lim-p 0.0008 0.0063 141.6334 2619.107344 7 0.0002 38 | 0/8 2 h-lim-p 0.0010 0.0076 24.4386 2618.983029 3 0.0004 56 | 0/8 3 h-lim-p 0.0012 0.0423 9.0575 2618.973051 2 0.0003 73 | 0/8 4 h-lim-p 0.0009 0.0846 2.7788 2618.971529 3 0.0004 91 | 0/8 5 h-lim-p 0.0021 0.3294 0.5765 2618.971446 1 0.0005 106 | 0/8 6 h-lim-p 0.0019 1.9059 0.1579 2618.971441 0 0.0004 127 | 0/8 7 h-lim-p 0.0062 20.0000 0.0107 2618.971441 0 0.0014 148 | 0/8 8 h-lim-p 0.0695 20.0000 0.0002 2618.971396 0 0.8339 171 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2618.971396 0 1.0938 191 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2618.971396 0 1.0938 211 | 0/8 11 h-lim-p 2.0089 20.0000 0.0000 2618.971396 0 3.0134 231 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2618.971396 0 0.0781 255 | 0/8 13 h-lim-p 0.1396 20.0000 0.0000 2618.971396 0 0.0175 277 | 0/8 14 h-lim-p 0.0046 20.0000 0.0000 2618.971396 0 0.0000 317 Out... lnL = -2618.971396 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2618.971396 Node 7: lnL = -2618.971396 Node 8: lnL = -2618.971396 Node 9: lnL = -2618.971396 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 580 Sequential format.. Reading seq # 1: YDR152W_Sbay Reading seq # 2: YDR152W_Scer Reading seq # 3: YDR152W_Skud Reading seq # 4: YDR152W_Smik Reading seq # 5: YDR152W_Spar Sequences read.. Counting patterns.. # site patterns = 227 Counting frequencies.. 120 bytes for distance 36320 bytes for lkl0 29056 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.147877 0.004602 0.096360 0.130933 0.086216 0.213137 0.206912 0.140292 lnL0 = -2610.351029 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2610.351029 x= 0.14788 0.00460 0.09636 0.13093 0.08622 0.21314 0.20691 0.14029 1 h-lim-p 0.0007 0.0053 176.8004 2608.312157 3 0.0002 29 | 0/8 2 h-lim-p 0.0009 0.0073 25.4079 2608.166177 6 0.0005 55 | 0/8 3 h-lim-p 0.0015 0.0542 7.9593 2608.157433 3 0.0003 74 | 0/8 4 h-lim-p 0.0009 0.0816 2.7757 2608.155940 2 0.0004 90 | 0/8 5 h-lim-p 0.0020 0.4163 0.5980 2608.155844 3 0.0005 109 | 0/8 6 h-lim-p 0.0031 3.0648 0.1044 2608.155842 1 0.0004 133 | 0/8 7 h-lim-p 0.0021 13.1293 0.0194 2608.155841 0 0.0018 153 | 0/8 8 h-lim-p 0.0714 20.0000 0.0005 2608.155588 0 0.8573 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2608.155576 1 0.9961 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2608.155576 0 1.0938 218 | 0/8 11 h-lim-p 2.4731 20.0000 0.0000 2608.155576 0 4.9462 239 | 0/8 12 h-lim-p 1.7326 20.0000 0.0000 2608.155576 0 0.2166 261 | 0/8 13 h-lim-p 0.5143 20.0000 0.0000 2608.155576 0 0.0000 298 Out... lnL = -2608.155576 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2608.155576 Node 7: lnL = -2608.155576 Node 8: lnL = -2608.155576 Node 9: lnL = -2608.155576 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 569 Sequential format.. Reading seq # 1: YDR155C_Sbay Reading seq # 2: YDR155C_Scer Reading seq # 3: YDR155C_Skud Reading seq # 4: YDR155C_Smik Reading seq # 5: YDR155C_Spar Sequences read.. Counting patterns.. # site patterns = 203 Counting frequencies.. 120 bytes for distance 32480 bytes for lkl0 25984 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.202524 0.049081 0.045807 0.090767 0.078783 0.186584 0.185974 0.194904 lnL0 = -2450.430395 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2450.430395 x= 0.20252 0.04908 0.04581 0.09077 0.07878 0.18658 0.18597 0.19490 1 h-lim-p 0.0006 0.0052 144.0568 2448.124252 6 0.0002 34 | 0/8 2 h-lim-p 0.0002 0.0019 40.5310 2447.853530 0 0.0005 47 | 0/8 3 h-lim-p 0.0010 0.0122 19.9663 2447.781714 2 0.0004 63 | 0/8 4 h-lim-p 0.0008 0.0200 11.4326 2447.768239 6 0.0003 90 | 0/8 5 h-lim-p 0.0017 0.1573 1.8662 2447.767403 5 0.0005 116 | 0/8 6 h-lim-p 0.0011 0.2653 0.8557 2447.767241 2 0.0005 132 | 0/8 7 h-lim-p 0.0114 8.0125 0.0356 2447.766033 0 0.0454 154 | 0/8 8 h-lim-p 0.0073 2.0641 0.2221 2447.742315 0 0.0146 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 2447.741415 2 1.0889 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2447.741404 1 1.2305 222 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2447.741404 0 1.0938 242 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2447.741404 0 1.0938 262 | 0/8 13 h-lim-p 2.2422 20.0000 0.0000 2447.741404 0 1.9619 282 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 2447.741404 0 1.2500 302 | 0/8 15 h-lim-p 0.2738 20.0000 0.0000 2447.741404 0 0.0011 329 Out... lnL = -2447.741404 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2447.741404 Node 7: lnL = -2447.741404 Node 8: lnL = -2447.741404 Node 9: lnL = -2447.741404 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 598 Sequential format.. Reading seq # 1: YDR156W_Sbay Reading seq # 2: YDR156W_Scer Reading seq # 3: YDR156W_Skud Reading seq # 4: YDR156W_Smik Reading seq # 5: YDR156W_Spar Sequences read.. Counting patterns.. # site patterns = 216 Counting frequencies.. 120 bytes for distance 34560 bytes for lkl0 27648 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.205061 0.050846 0.063985 0.086611 0.081603 0.177058 0.177324 0.197333 lnL0 = -2508.157973 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2508.157973 x= 0.20506 0.05085 0.06399 0.08661 0.08160 0.17706 0.17732 0.19733 1 h-lim-p 0.0025 0.2281 140.7797 2505.523427 3 0.0003 30 | 0/8 2 h-lim-p 0.0003 0.0021 41.4998 2505.188832 0 0.0005 43 | 0/8 3 h-lim-p 0.0011 0.0115 20.6713 2505.122455 7 0.0004 73 | 0/8 4 h-lim-p 0.0008 0.0186 9.7079 2505.112103 6 0.0003 99 | 0/8 5 h-lim-p 0.0016 0.1767 1.7107 2505.111106 2 0.0007 115 | 0/8 6 h-lim-p 0.0023 0.2455 0.5195 2505.111048 3 0.0004 136 | 0/8 7 h-lim-p 0.0138 20.0000 0.0151 2505.103956 0 0.2208 160 | 0/8 8 h-lim-p 0.0025 0.6954 1.3634 2505.085974 1 0.0031 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 2505.085584 3 1.3437 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2505.085579 0 1.0938 221 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2505.085579 0 1.2500 241 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2505.085579 0 0.2734 263 | 0/8 13 h-lim-p 0.2221 20.0000 0.0000 2505.085579 0 0.0121 286 | 0/8 14 h-lim-p 0.0233 20.0000 0.0000 2505.085579 0 0.0000 315 Out... lnL = -2505.085579 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2505.085579 Node 7: lnL = -2505.085579 Node 8: lnL = -2505.085579 Node 9: lnL = -2505.085579 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 456 Sequential format.. Reading seq # 1: YDR159W_Sbay Reading seq # 2: YDR159W_Scer Reading seq # 3: YDR159W_Skud Reading seq # 4: YDR159W_Smik Reading seq # 5: YDR159W_Spar Sequences read.. Counting patterns.. # site patterns = 205 Counting frequencies.. 120 bytes for distance 32800 bytes for lkl0 26240 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.188845 0.012173 0.133272 0.066714 0.087950 0.238525 0.204836 0.180495 lnL0 = -1962.612938 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1962.612938 x= 0.18885 0.01217 0.13327 0.06671 0.08795 0.23852 0.20484 0.18049 1 h-lim-p 0.0007 0.0058 52.4078 1962.077215 7 0.0004 38 | 0/8 2 h-lim-p 0.0003 0.0025 18.3427 1961.934553 0 0.0013 52 | 0/8 3 h-lim-p 0.0007 0.0054 7.2013 1961.929569 5 0.0002 76 | 0/8 4 h-lim-p 0.0010 0.0229 1.6257 1961.928072 1 0.0012 90 | 0/8 5 h-lim-p 0.0073 0.7707 0.2795 1961.928039 2 0.0007 108 | 0/8 6 h-lim-p 0.0015 1.2751 0.1338 1961.928013 1 0.0013 130 | 0/8 7 h-lim-p 0.0080 19.4592 0.0213 1961.923211 0 0.1287 154 | 0/8 8 h-lim-p 0.0017 0.1949 1.6188 1961.918205 1 0.0021 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 1961.918072 3 1.0004 194 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1961.918072 0 1.0938 214 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1961.918072 0 2.1875 234 | 0/8 12 h-lim-p 1.9116 20.0000 0.0000 1961.918072 0 0.8363 254 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1961.918072 0 0.0146 281 | 0/8 14 h-lim-p 0.0053 20.0000 0.0000 1961.918072 0 0.0013 302 Out... lnL = -1961.918072 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1961.918072 Node 7: lnL = -1961.918072 Node 8: lnL = -1961.918072 Node 9: lnL = -1961.918072 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 331 Sequential format.. Reading seq # 1: YDR163W_Sbay Reading seq # 2: YDR163W_Scer Reading seq # 3: YDR163W_Skud Reading seq # 4: YDR163W_Smik Reading seq # 5: YDR163W_Spar Sequences read.. Counting patterns.. # site patterns = 128 Counting frequencies.. 120 bytes for distance 20480 bytes for lkl0 16384 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.119162 0.037341 0.058014 0.109043 0.076786 0.171920 0.159321 0.112878 lnL0 = -1417.318090 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1417.318090 x= 0.11916 0.03734 0.05801 0.10904 0.07679 0.17192 0.15932 0.11288 1 h-lim-p 0.0036 0.0285 78.5441 1416.514083 6 0.0003 38 | 0/8 2 h-lim-p 0.0011 0.0090 15.3889 1416.440605 7 0.0006 67 | 0/8 3 h-lim-p 0.0015 0.0355 6.5778 1416.432919 6 0.0004 95 | 0/8 4 h-lim-p 0.0021 0.1284 1.3289 1416.432536 2 0.0005 112 | 0/8 5 h-lim-p 0.0037 0.9333 0.1598 1416.432529 2 0.0006 131 | 0/8 6 h-lim-p 0.0032 6.6606 0.0313 1416.432529 0 0.0007 152 | 0/8 7 h-lim-p 0.0031 20.0000 0.0071 1416.432529 0 0.0027 172 | 0/8 8 h-lim-p 0.0287 20.0000 0.0007 1416.432467 0 0.4586 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1416.432460 1 0.9961 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1416.432460 0 1.0938 238 | 0/8 11 h-lim-p 1.9745 20.0000 0.0000 1416.432460 0 1.7277 258 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1416.432460 0 0.0195 284 | 0/8 13 h-lim-p 0.0047 20.0000 0.0000 1416.432460 0 0.0000 311 Out... lnL = -1416.432460 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1416.432460 Node 7: lnL = -1416.432460 Node 8: lnL = -1416.432460 Node 9: lnL = -1416.432460 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 244 Sequential format.. Reading seq # 1: YDR166C_Sbay Reading seq # 2: YDR166C_Scer Reading seq # 3: YDR166C_Skud Reading seq # 4: YDR166C_Smik Reading seq # 5: YDR166C_Spar Sequences read.. Counting patterns.. # site patterns = 126 Counting frequencies.. 120 bytes for distance 20160 bytes for lkl0 16128 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.132584 0.175082 0.024399 0.165203 0.071108 0.252649 0.231366 0.123598 lnL0 = -1128.776746 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1128.776746 x= 0.13258 0.17508 0.02440 0.16520 0.07111 0.25265 0.23137 0.12360 1 h-lim-p 0.0005 0.0043 75.8558 1127.654460 7 0.0005 36 | 0/8 2 h-lim-p 0.0005 0.0040 19.6066 1127.515527 0 0.0007 48 | 0/8 3 h-lim-p 0.0015 0.0600 9.6887 1127.481058 7 0.0009 78 | 0/8 4 h-lim-p 0.0049 0.1506 1.8148 1127.478053 4 0.0019 98 | 0/8 5 h-lim-p 0.0295 1.6012 0.1170 1127.478045 2 0.0012 119 | 0/8 6 h-lim-p 0.0109 20.0000 0.0131 1127.478044 0 0.0048 139 | 0/8 7 h-lim-p 0.0200 20.0000 0.0031 1127.478029 0 0.0801 161 | 0/8 8 h-lim-p 0.0107 3.2719 0.0232 1127.477919 0 0.0215 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1127.477911 1 0.9961 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1127.477911 0 1.0938 224 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1127.477911 0 2.1875 244 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1127.477911 0 1.0938 264 | 0/8 13 h-lim-p 0.9667 20.0000 0.0000 1127.477911 0 3.8668 286 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1127.477911 0 0.0024 315 Out... lnL = -1127.477911 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1127.477911 Node 7: lnL = -1127.477911 Node 8: lnL = -1127.477911 Node 9: lnL = -1127.477911 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 870 Sequential format.. Reading seq # 1: YDR171W_Sbay Reading seq # 2: YDR171W_Scer Reading seq # 3: YDR171W_Skud Reading seq # 4: YDR171W_Smik Reading seq # 5: YDR171W_Spar Sequences read.. Counting patterns.. # site patterns = 433 Counting frequencies.. 120 bytes for distance 69280 bytes for lkl0 55424 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.292777 0.099123 0.082361 0.284532 0.196762 0.321235 0.349509 0.278719 lnL0 = -4713.717453 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4713.717453 x= 0.29278 0.09912 0.08236 0.28453 0.19676 0.32124 0.34951 0.27872 1 h-lim-p 0.0060 0.9415 125.7777 4710.887600 8 0.0004 43 | 0/8 2 h-lim-p 0.0014 0.0114 26.1490 4710.597209 7 0.0009 74 | 0/8 3 h-lim-p 0.0019 0.0400 11.8241 4710.549765 3 0.0008 92 | 0/8 4 h-lim-p 0.0036 0.1761 2.6129 4710.544552 3 0.0016 110 | 0/8 5 h-lim-p 0.0053 0.4256 0.8081 4710.544207 2 0.0012 127 | 0/8 6 h-lim-p 0.0072 3.9512 0.1300 4710.544196 2 0.0012 153 | 0/8 7 h-lim-p 0.0066 20.0000 0.0229 4710.544175 0 0.0131 174 | 0/8 8 h-lim-p 0.0240 20.0000 0.0125 4710.542096 0 0.1443 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 4710.542031 2 0.9961 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4710.542031 0 1.0938 240 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4710.542031 0 1.0938 260 | 0/8 12 h-lim-p 1.8697 20.0000 0.0000 4710.542031 0 1.8697 280 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 4710.542031 0 0.3125 302 | 0/8 14 h-lim-p 0.0852 20.0000 0.0000 4710.542031 0 0.0001 331 Out... lnL = -4710.542031 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4710.542031 Node 7: lnL = -4710.542031 Node 8: lnL = -4710.542031 Node 9: lnL = -4710.542031 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 493 Sequential format.. Reading seq # 1: YDR174W_Sbay Reading seq # 2: YDR174W_Scer Reading seq # 3: YDR174W_Skud Reading seq # 4: YDR174W_Smik Reading seq # 5: YDR174W_Spar Sequences read.. Counting patterns.. # site patterns = 167 Counting frequencies.. 120 bytes for distance 26720 bytes for lkl0 21376 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.073404 0.049545 0.026275 0.079418 0.082422 0.166473 0.119743 0.063801 lnL0 = -1820.124833 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1820.124833 x= 0.07340 0.04954 0.02627 0.07942 0.08242 0.16647 0.11974 0.06380 1 h-lim-p 0.0005 0.0042 224.7481 1816.667431 9 0.0002 45 | 0/8 2 h-lim-p 0.0003 0.0028 74.2239 1815.658194 1 0.0004 59 | 0/8 3 h-lim-p 0.0006 0.0046 28.9959 1815.540135 7 0.0003 90 | 0/8 4 h-lim-p 0.0006 0.0102 15.6860 1815.503025 5 0.0004 114 | 0/8 5 h-lim-p 0.0013 0.0393 4.6503 1815.500112 2 0.0003 131 | 0/8 6 h-lim-p 0.0101 1.2001 0.1416 1815.500101 2 0.0008 151 | 0/8 7 h-lim-p 0.0089 11.2725 0.0133 1815.499932 0 0.0266 172 | 0/8 8 h-lim-p 0.0017 0.9674 0.2044 1815.495455 0 0.0069 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1815.495271 1 1.0938 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1815.495268 1 1.2305 239 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1815.495268 0 1.0938 259 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1815.495268 0 2.1875 279 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1815.495268 0 1.0938 299 | 0/8 14 h-lim-p 0.3359 20.0000 0.0000 1815.495268 0 5.3741 323 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1815.495268 0 0.3125 345 | 0/8 16 h-lim-p 0.6159 20.0000 0.0000 1815.495268 0 0.0012 373 Out... lnL = -1815.495268 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1815.495268 Node 7: lnL = -1815.495268 Node 8: lnL = -1815.495268 Node 9: lnL = -1815.495268 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 305 Sequential format.. Reading seq # 1: YDR175C_Sbay Reading seq # 2: YDR175C_Scer Reading seq # 3: YDR175C_Skud Reading seq # 4: YDR175C_Smik Reading seq # 5: YDR175C_Spar Sequences read.. Counting patterns.. # site patterns = 133 Counting frequencies.. 120 bytes for distance 21280 bytes for lkl0 17024 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.157880 0.018411 0.060969 0.091771 0.071545 0.209576 0.187071 0.144399 lnL0 = -1325.006814 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1325.006814 x= 0.15788 0.01841 0.06097 0.09177 0.07155 0.20958 0.18707 0.14440 1 h-lim-p 0.0021 0.0167 80.8938 1324.217987 4 0.0003 32 | 0/8 2 h-lim-p 0.0016 0.0128 8.6738 1324.197936 7 0.0005 61 | 0/8 3 h-lim-p 0.0012 0.0864 3.8132 1324.194297 2 0.0006 77 | 0/8 4 h-lim-p 0.0011 0.1087 2.0501 1324.193365 5 0.0006 100 | 0/8 5 h-lim-p 0.0067 2.1371 0.1769 1324.193351 3 0.0009 120 | 0/8 6 h-lim-p 0.0391 20.0000 0.0041 1324.193351 0 0.0021 143 | 0/8 7 h-lim-p 0.0160 20.0000 0.0005 1324.193351 0 0.0480 164 | 0/8 8 h-lim-p 0.0025 20.0000 0.0106 1324.193344 0 0.0099 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1324.193343 0 1.0938 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1324.193343 0 0.5469 227 | 0/8 11 h-lim-p 0.6356 20.0000 0.0000 1324.193343 0 0.0397 250 | 0/8 12 h-lim-p 0.0275 20.0000 0.0000 1324.193343 0 0.0120 270 | 0/8 13 h-lim-p 0.0085 20.0000 0.0000 1324.193343 0 0.0000 309 Out... lnL = -1324.193343 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1324.193343 Node 7: lnL = -1324.193343 Node 8: lnL = -1324.193343 Node 9: lnL = -1324.193343 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 348 Sequential format.. Reading seq # 1: YDR177W_Sbay Reading seq # 2: YDR177W_Scer Reading seq # 3: YDR177W_Skud Reading seq # 4: YDR177W_Smik Reading seq # 5: YDR177W_Spar Sequences read.. Counting patterns.. # site patterns = 101 Counting frequencies.. 120 bytes for distance 16160 bytes for lkl0 12928 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.066972 0.068284 0.026944 0.096775 0.047698 0.117802 0.095853 0.058368 lnL0 = -1228.121659 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1228.121659 x= 0.06697 0.06828 0.02694 0.09678 0.04770 0.11780 0.09585 0.05837 1 h-lim-p 0.0032 1.2219 87.1412 1227.579239 4 0.0002 33 | 0/8 2 h-lim-p 0.0011 0.0110 12.0373 1227.552571 6 0.0004 61 | 0/8 3 h-lim-p 0.0010 0.0286 4.3388 1227.549579 5 0.0004 86 | 0/8 4 h-lim-p 0.0018 0.1213 0.8404 1227.549469 3 0.0003 106 | 0/8 5 h-lim-p 0.0014 0.6897 0.2005 1227.549463 0 0.0003 127 | 0/8 6 h-lim-p 0.0034 7.8940 0.0199 1227.549463 0 0.0007 148 | 0/8 7 h-lim-p 0.0076 20.0000 0.0020 1227.549463 0 0.0066 168 | 0/8 8 h-lim-p 0.0097 20.0000 0.0013 1227.549433 0 0.0780 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1227.549433 0 1.0938 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1227.549433 0 0.2734 233 | 0/8 11 h-lim-p 0.1533 20.0000 0.0000 1227.549433 0 0.0096 256 | 0/8 12 h-lim-p 0.0060 20.0000 0.0000 1227.549433 0 0.0008 278 | 0/8 13 h-lim-p 0.0005 20.0000 0.0000 1227.549433 0 0.0001 299 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 1227.549433 0 0.0000 320 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 1227.549433 0 0.0000 350 Out... lnL = -1227.549433 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1227.549433 Node 7: lnL = -1227.549433 Node 8: lnL = -1227.549433 Node 9: lnL = -1227.549433 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 820 Sequential format.. Reading seq # 1: YDR179C_Sbay Reading seq # 2: YDR179C_Scer Reading seq # 3: YDR179C_Skud Reading seq # 4: YDR179C_Smik Reading seq # 5: YDR179C_Spar Sequences read.. Counting patterns.. # site patterns = 196 Counting frequencies.. 120 bytes for distance 31360 bytes for lkl0 25088 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.073718 0.076070 0.043929 0.074346 0.066908 0.146885 0.146573 0.063389 lnL0 = -3262.473398 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3262.473398 x= 0.07372 0.07607 0.04393 0.07435 0.06691 0.14689 0.14657 0.06339 1 h-lim-p 0.0010 0.0076 172.1526 3261.112626 3 0.0001 30 | 0/8 2 h-lim-p 0.0006 0.0069 28.0422 3261.042127 7 0.0002 60 | 0/8 3 h-lim-p 0.0006 0.0270 9.1240 3261.037491 4 0.0001 80 | 0/8 4 h-lim-p 0.0006 0.0808 1.9863 3261.037119 3 0.0002 99 | 0/8 5 h-lim-p 0.0006 0.4181 0.6968 3261.037080 2 0.0002 117 | 0/8 6 h-lim-p 0.0017 2.1888 0.0754 3261.037080 0 0.0002 139 | 0/8 7 h-lim-p 0.0006 15.0448 0.0254 3261.037079 0 0.0005 159 | 0/8 8 h-lim-p 0.0374 20.0000 0.0003 3261.036863 0 0.5990 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3261.036859 0 1.0938 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3261.036859 0 1.0938 223 | 0/8 11 h-lim-p 1.0741 20.0000 0.0000 3261.036859 0 2.1481 244 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3261.036859 0 0.1367 267 | 0/8 13 h-lim-p 0.0082 20.0000 0.0000 3261.036859 0 0.0001 292 Out... lnL = -3261.036859 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3261.036859 Node 7: lnL = -3261.036859 Node 8: lnL = -3261.036859 Node 9: lnL = -3261.036859 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 274 Sequential format.. Reading seq # 1: YDR181C_Sbay Reading seq # 2: YDR181C_Scer Reading seq # 3: YDR181C_Skud Reading seq # 4: YDR181C_Smik Reading seq # 5: YDR181C_Spar Sequences read.. Counting patterns.. # site patterns = 152 Counting frequencies.. 120 bytes for distance 24320 bytes for lkl0 19456 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.182384 0.065124 0.049956 0.127155 0.109156 0.274709 0.331750 0.163681 lnL0 = -1307.925530 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1307.925530 x= 0.18238 0.06512 0.04996 0.12715 0.10916 0.27471 0.33175 0.16368 1 h-lim-p 0.0266 0.7228 31.3528 1307.665283 7 0.0006 43 | 0/8 2 h-lim-p 0.0034 0.0335 5.1227 1307.650862 6 0.0011 68 | 0/8 3 h-lim-p 0.0022 0.1585 2.5567 1307.647484 6 0.0013 96 | 0/8 4 h-lim-p 0.0033 0.2349 0.9817 1307.646884 3 0.0015 114 | 0/8 5 h-lim-p 0.0090 3.2739 0.1618 1307.646854 2 0.0024 139 | 0/8 6 h-lim-p 0.0141 7.7603 0.0271 1307.646853 1 0.0017 163 | 0/8 7 h-lim-p 0.0432 20.0000 0.0011 1307.646853 0 0.0047 185 | 0/8 8 h-lim-p 0.0190 20.0000 0.0003 1307.646851 0 0.3039 209 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1307.646851 0 1.0938 229 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1307.646851 0 1.0938 249 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1307.646851 0 2.5000 269 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1307.646851 0 0.0293 295 | 0/8 13 h-lim-p 0.0228 20.0000 0.0000 1307.646851 0 0.0000 324 Out... lnL = -1307.646851 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1307.646851 Node 7: lnL = -1307.646851 Node 8: lnL = -1307.646851 Node 9: lnL = -1307.646851 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 255 Sequential format.. Reading seq # 1: YDR182W_Sbay Reading seq # 2: YDR182W_Scer Reading seq # 3: YDR182W_Skud Reading seq # 4: YDR182W_Smik Reading seq # 5: YDR182W_Spar Sequences read.. Counting patterns.. # site patterns = 140 Counting frequencies.. 120 bytes for distance 22400 bytes for lkl0 17920 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.569587 0.000060 0.554428 0.363054 0.267884 1.028711 0.335377 0.534104 lnL0 = -1165.113374 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1165.113374 x= 0.56959 0.00006 0.55443 0.36305 0.26788 1.02871 0.33538 0.53410 1 h-lim-p 0.0000 0.0000 183.8817 1165.062914 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0012 508.4075 1085.747733 m 0.0012 38 | 1/8 3 h-lim-p 0.0004 0.0033 147.9301 1077.697999 0 0.0016 52 | 1/8 4 h-lim-p 0.0007 0.0059 43.8704 1076.885844 0 0.0011 64 | 1/8 5 h-lim-p 0.0043 0.0345 4.9100 1076.844956 2 0.0020 80 | 0/8 6 h-lim-p 0.0005 0.0148 19.1833 1076.498220 0 0.0041 95 | 0/8 7 h-lim-p 0.0216 0.2588 3.6763 1073.607312 m 0.2588 108 | 1/8 8 h-lim-p 0.4178 3.3423 0.1741 1073.545773 6 0.0931 133 | 1/8 9 h-lim-p 0.0233 2.9124 0.6946 1073.099351 0 0.7468 157 | 1/8 10 h-lim-p 1.5649 12.5192 0.0626 1073.049485 6 0.4838 192 | 1/8 11 h-lim-p 0.2478 12.0681 0.1223 1073.038659 0 0.4957 212 | 1/8 12 h-lim-p 2.5000 20.0000 0.0128 1073.030631 5 0.8059 243 | 1/8 13 h-lim-p 2.4480 20.0000 0.0042 1073.030372 4 1.2849 271 | 1/8 14 h-lim-p 2.5000 20.0000 0.0012 1073.030331 3 1.4660 299 | 1/8 15 h-lim-p 2.5000 20.0000 0.0003 1073.030331 0 1.0938 318 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 1073.030331 0 1.0938 337 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 1073.030331 0 1.0938 356 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 1073.030331 0 3.7500 375 | 1/8 19 h-lim-p 0.9322 20.0000 0.0000 1073.030331 0 0.4661 394 | 1/8 20 h-lim-p 0.0004 20.0000 0.0070 1073.030331 0 0.0000 415 | 1/8 21 h-lim-p 0.0009 20.0000 0.0004 1073.030331 0 0.0000 443 | 1/8 22 h-lim-p 0.0000 20.0000 0.0000 | 1/8 23 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1073.030331 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1073.030331 Node 7: lnL = -1073.030331 Node 8: lnL = -1073.030331 Node 9: lnL = -1073.030331 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 540 Sequential format.. Reading seq # 1: YDR183W_Sbay Reading seq # 2: YDR183W_Scer Reading seq # 3: YDR183W_Skud Reading seq # 4: YDR183W_Smik Reading seq # 5: YDR183W_Spar Sequences read.. Counting patterns.. # site patterns = 217 Counting frequencies.. 120 bytes for distance 34720 bytes for lkl0 27776 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.144881 0.216905 0.047909 0.596783 0.188375 0.252894 0.273721 0.117795 lnL0 = -2224.650714 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2224.650714 x= 0.14488 0.21691 0.04791 0.59678 0.18837 0.25289 0.27372 0.11779 1 h-lim-p 0.0012 0.0100 43.5804 2223.074823 0 0.0019 22 | 0/8 2 h-lim-p 0.0020 0.0159 25.2933 2222.690974 6 0.0015 46 | 0/8 3 h-lim-p 0.0071 0.0907 5.3915 2222.644026 5 0.0035 70 | 0/8 4 h-lim-p 0.0053 20.0000 3.4970 2222.639977 5 0.0009 96 | 0/8 5 h-lim-p 0.0021 0.1257 1.5009 2222.638109 2 0.0021 112 | 0/8 6 h-lim-p 0.0121 1.3834 0.2586 2222.638012 3 0.0023 131 | 0/8 7 h-lim-p 0.0150 5.4859 0.0394 2222.637379 0 0.0451 152 | 0/8 8 h-lim-p 0.0128 2.5315 0.1392 2222.627638 0 0.0510 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0010 2222.627301 2 0.9961 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2222.627300 0 1.0938 218 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2222.627300 0 1.0938 238 | 0/8 12 h-lim-p 1.8805 20.0000 0.0000 2222.627300 0 1.6455 258 | 0/8 13 h-lim-p 1.9954 20.0000 0.0000 2222.627300 0 0.2182 280 | 0/8 14 h-lim-p 0.0445 20.0000 0.0000 2222.627300 0 0.0056 302 | 0/8 15 h-lim-p 0.0040 20.0000 0.0000 2222.627300 0 0.0003 325 Out... lnL = -2222.627300 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2222.627300 Node 7: lnL = -2222.627300 Node 8: lnL = -2222.627300 Node 9: lnL = -2222.627300 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 461 Sequential format.. Reading seq # 1: YDR184C_Sbay Reading seq # 2: YDR184C_Scer Reading seq # 3: YDR184C_Skud Reading seq # 4: YDR184C_Smik Reading seq # 5: YDR184C_Spar Sequences read.. Counting patterns.. # site patterns = 173 Counting frequencies.. 120 bytes for distance 27680 bytes for lkl0 22144 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.108292 0.046596 0.062947 0.115214 0.081293 0.190874 0.196160 0.095222 lnL0 = -1901.001901 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1901.001901 x= 0.10829 0.04660 0.06295 0.11521 0.08129 0.19087 0.19616 0.09522 1 h-lim-p 0.0026 0.0221 121.5567 1899.225852 3 0.0003 30 | 0/8 2 h-lim-p 0.0009 0.0069 18.3693 1899.141857 7 0.0005 60 | 0/8 3 h-lim-p 0.0012 0.0311 7.9156 1899.129540 4 0.0005 80 | 0/8 4 h-lim-p 0.0015 0.0875 2.4269 1899.128114 5 0.0005 105 | 0/8 5 h-lim-p 0.0090 1.7746 0.1450 1899.128110 1 0.0004 122 | 0/8 6 h-lim-p 0.0109 20.0000 0.0060 1899.128110 0 0.0012 144 | 0/8 7 h-lim-p 0.0035 20.0000 0.0020 1899.128110 0 0.0071 165 | 0/8 8 h-lim-p 0.0100 20.0000 0.0014 1899.128094 0 0.0803 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1899.128094 0 1.0938 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1899.128094 0 1.2500 228 | 0/8 11 h-lim-p 1.8341 20.0000 0.0000 1899.128094 0 0.2006 250 | 0/8 12 h-lim-p 0.1048 20.0000 0.0000 1899.128094 0 0.0262 271 | 0/8 13 h-lim-p 0.0164 20.0000 0.0000 1899.128094 0 0.0003 296 Out... lnL = -1899.128094 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1899.128094 Node 7: lnL = -1899.128094 Node 8: lnL = -1899.128094 Node 9: lnL = -1899.128094 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 461 Sequential format.. Reading seq # 1: YDR185C_Sbay Reading seq # 2: YDR185C_Scer Reading seq # 3: YDR185C_Skud Reading seq # 4: YDR185C_Smik Reading seq # 5: YDR185C_Spar Sequences read.. Counting patterns.. # site patterns = 162 Counting frequencies.. 120 bytes for distance 25920 bytes for lkl0 20736 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.157423 0.062547 0.014746 0.089033 0.051478 0.142025 0.249048 0.144382 lnL0 = -1781.725929 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1781.725929 x= 0.15742 0.06255 0.01475 0.08903 0.05148 0.14202 0.24905 0.14438 1 h-lim-p 0.0002 0.0015 115.4831 1780.644480 6 0.0002 35 | 0/8 2 h-lim-p 0.0002 0.0013 53.3129 1780.299637 0 0.0003 48 | 0/8 3 h-lim-p 0.0004 0.0035 27.0995 1780.233424 5 0.0002 71 | 0/8 4 h-lim-p 0.0006 0.0218 9.9773 1780.206084 3 0.0006 89 | 0/8 5 h-lim-p 0.0013 0.0511 5.1584 1780.199782 4 0.0006 110 | 0/8 6 h-lim-p 0.0040 0.2328 0.7901 1780.199586 3 0.0006 131 | 0/8 7 h-lim-p 0.0059 2.8390 0.0860 1780.199574 2 0.0015 156 | 0/8 8 h-lim-p 0.0359 20.0000 0.0037 1780.195320 0 0.5738 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1780.195186 3 1.0004 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1780.195186 0 1.2500 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1780.195186 0 0.2734 248 | 0/8 12 h-lim-p 0.2399 20.0000 0.0000 1780.195186 0 0.0037 273 | 0/8 13 h-lim-p 0.0020 20.0000 0.0000 1780.195186 0 0.0005 294 Out... lnL = -1780.195186 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1780.195186 Node 7: lnL = -1780.195186 Node 8: lnL = -1780.195186 Node 9: lnL = -1780.195186 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 369 Sequential format.. Reading seq # 1: YDR191W_Sbay Reading seq # 2: YDR191W_Scer Reading seq # 3: YDR191W_Skud Reading seq # 4: YDR191W_Smik Reading seq # 5: YDR191W_Spar Sequences read.. Counting patterns.. # site patterns = 147 Counting frequencies.. 120 bytes for distance 23520 bytes for lkl0 18816 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.103300 0.040052 0.077862 0.125919 0.073861 0.205900 0.139688 0.090713 lnL0 = -1533.476700 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1533.476700 x= 0.10330 0.04005 0.07786 0.12592 0.07386 0.20590 0.13969 0.09071 1 h-lim-p 0.0037 0.0296 62.9182 1532.884213 8 0.0003 45 | 0/8 2 h-lim-p 0.0012 0.0132 17.0913 1532.793022 7 0.0007 74 | 0/8 3 h-lim-p 0.0017 0.0392 6.8154 1532.782172 5 0.0005 98 | 0/8 4 h-lim-p 0.0014 0.0696 2.7172 1532.780598 5 0.0005 122 | 0/8 5 h-lim-p 0.0045 0.5137 0.3067 1532.780566 3 0.0007 144 | 0/8 6 h-lim-p 0.0052 3.0229 0.0384 1532.780566 0 0.0006 166 | 0/8 7 h-lim-p 0.0192 20.0000 0.0012 1532.780565 0 0.0288 186 | 0/8 8 h-lim-p 0.0056 12.7373 0.0059 1532.780537 0 0.0224 208 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1532.780536 0 1.0938 228 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1532.780536 0 1.0938 248 | 0/8 11 h-lim-p 1.3137 20.0000 0.0000 1532.780536 0 5.2548 270 | 0/8 12 h-lim-p 1.8037 20.0000 0.0000 1532.780536 0 0.3946 291 | 0/8 13 h-lim-p 2.0011 20.0000 0.0000 1532.780536 0 0.0156 317 | 0/8 14 h-lim-p 0.0099 20.0000 0.0000 1532.780536 0 0.0000 350 Out... lnL = -1532.780536 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1532.780536 Node 7: lnL = -1532.780536 Node 8: lnL = -1532.780536 Node 9: lnL = -1532.780536 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 867 Sequential format.. Reading seq # 1: YDR192C_Sbay Reading seq # 2: YDR192C_Scer Reading seq # 3: YDR192C_Skud Reading seq # 4: YDR192C_Smik Reading seq # 5: YDR192C_Spar Sequences read.. Counting patterns.. # site patterns = 437 Counting frequencies.. 120 bytes for distance 69920 bytes for lkl0 55936 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.392592 0.478166 0.092611 0.190012 0.209785 0.285954 0.341645 0.356427 lnL0 = -4856.636277 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4856.636277 x= 0.39259 0.47817 0.09261 0.19001 0.20978 0.28595 0.34164 0.35643 1 h-lim-p 0.0046 0.0365 44.4265 4855.979215 8 0.0007 46 | 0/8 2 h-lim-p 0.0009 0.0100 36.0286 4855.506390 1 0.0011 60 | 0/8 3 h-lim-p 0.0018 0.0165 21.0779 4855.391721 5 0.0008 83 | 0/8 4 h-lim-p 0.0020 0.0526 8.0395 4855.363157 6 0.0011 110 | 0/8 5 h-lim-p 0.0012 0.0527 7.4608 4855.323848 0 0.0024 123 | 0/8 6 h-lim-p 0.0051 0.2812 3.4738 4855.315323 4 0.0021 144 | 0/8 7 h-lim-p 0.0113 1.1617 0.6417 4855.314787 2 0.0028 161 | 0/8 8 h-lim-p 1.0163 20.0000 0.0018 4855.312290 3 1.0744 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 4855.312262 1 0.9961 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4855.312262 0 1.0938 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4855.312262 0 1.0938 249 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4855.312262 0 2.1875 269 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 4855.312262 0 1.0938 289 | 0/8 14 h-lim-p 0.2788 20.0000 0.0000 4855.312262 0 0.0697 310 | 0/8 15 h-lim-p 0.0313 20.0000 0.0000 4855.312262 0 0.0000 342 Out... lnL = -4855.312262 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4855.312262 Node 7: lnL = -4855.312262 Node 8: lnL = -4855.312262 Node 9: lnL = -4855.312262 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 252 Sequential format.. Reading seq # 1: YDR196C_Sbay Reading seq # 2: YDR196C_Scer Reading seq # 3: YDR196C_Skud Reading seq # 4: YDR196C_Smik Reading seq # 5: YDR196C_Spar Sequences read.. Counting patterns.. # site patterns = 130 Counting frequencies.. 120 bytes for distance 20800 bytes for lkl0 16640 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.102163 0.038136 0.161140 0.133255 0.140503 0.180181 0.238898 0.085954 lnL0 = -1103.083213 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1103.083213 x= 0.10216 0.03814 0.16114 0.13325 0.14050 0.18018 0.23890 0.08595 1 h-lim-p 0.0021 0.0168 44.8587 1102.536960 9 0.0006 43 | 0/8 2 h-lim-p 0.0025 0.0260 10.4004 1102.458806 6 0.0015 70 | 0/8 3 h-lim-p 0.0050 0.1143 3.1200 1102.452652 6 0.0014 97 | 0/8 4 h-lim-p 0.0042 0.1752 1.0173 1102.452151 4 0.0011 118 | 0/8 5 h-lim-p 0.0095 1.7695 0.1155 1102.452144 1 0.0009 134 | 0/8 6 h-lim-p 0.0046 12.9224 0.0236 1102.452144 0 0.0020 154 | 0/8 7 h-lim-p 0.3686 20.0000 0.0001 1102.452144 0 0.3225 174 | 0/8 8 h-lim-p 0.0051 20.0000 0.0082 1102.452143 0 0.0051 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1102.452143 0 1.0938 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1102.452143 0 1.0938 234 | 0/8 11 h-lim-p 1.5771 20.0000 0.0000 1102.452143 0 0.0123 260 | 0/8 12 h-lim-p 0.0048 20.0000 0.0000 1102.452143 0 0.0000 288 Out... lnL = -1102.452143 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1102.452143 Node 7: lnL = -1102.452143 Node 8: lnL = -1102.452143 Node 9: lnL = -1102.452143 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 293 Sequential format.. Reading seq # 1: YDR197W_Sbay Reading seq # 2: YDR197W_Scer Reading seq # 3: YDR197W_Skud Reading seq # 4: YDR197W_Smik Reading seq # 5: YDR197W_Spar Sequences read.. Counting patterns.. # site patterns = 144 Counting frequencies.. 120 bytes for distance 23040 bytes for lkl0 18432 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.105090 0.146189 0.078409 0.198432 0.055189 0.313030 0.235114 0.086811 lnL0 = -1173.878188 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1173.878188 x= 0.10509 0.14619 0.07841 0.19843 0.05519 0.31303 0.23511 0.08681 1 h-lim-p 0.0033 1.3058 84.6886 1171.901206 9 0.0007 40 | 0/8 2 h-lim-p 0.0026 0.0209 15.4247 1171.651140 3 0.0022 58 | 0/8 3 h-lim-p 0.0048 0.0384 2.8576 1171.642584 3 0.0022 76 | 0/8 4 h-lim-p 0.0043 0.1957 1.4602 1171.641079 4 0.0017 97 | 0/8 5 h-lim-p 0.0034 0.3257 0.7545 1171.640798 3 0.0013 115 | 0/8 6 h-lim-p 0.0056 1.6604 0.1747 1171.640760 2 0.0026 139 | 0/8 7 h-lim-p 0.0345 20.0000 0.0133 1171.640759 0 0.0038 161 | 0/8 8 h-lim-p 0.2258 20.0000 0.0002 1171.640746 0 0.9033 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1171.640746 1 1.2305 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1171.640746 0 1.0938 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1171.640746 0 0.5469 247 | 0/8 12 h-lim-p 0.3701 20.0000 0.0000 1171.640746 0 0.0231 270 | 0/8 13 h-lim-p 0.0141 20.0000 0.0000 1171.640746 0 0.0141 290 | 0/8 14 h-lim-p 0.0097 20.0000 0.0000 1171.640746 0 0.0002 315 Out... lnL = -1171.640746 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1171.640746 Node 7: lnL = -1171.640746 Node 8: lnL = -1171.640746 Node 9: lnL = -1171.640746 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 243 Sequential format.. Reading seq # 1: YDR200C_Sbay Reading seq # 2: YDR200C_Scer Reading seq # 3: YDR200C_Skud Reading seq # 4: YDR200C_Smik Reading seq # 5: YDR200C_Spar Sequences read.. Counting patterns.. # site patterns = 118 Counting frequencies.. 120 bytes for distance 18880 bytes for lkl0 15104 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.116348 0.133618 0.044667 0.090635 0.061141 0.130212 0.192831 0.103136 lnL0 = -980.013019 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 980.013019 x= 0.11635 0.13362 0.04467 0.09064 0.06114 0.13021 0.19283 0.10314 1 h-lim-p 0.0003 0.0027 44.2177 979.490802 0 0.0007 23 | 0/8 2 h-lim-p 0.0006 0.0045 12.1565 979.454784 3 0.0005 41 | 0/8 3 h-lim-p 0.0018 0.0629 3.4774 979.447955 5 0.0012 66 | 0/8 4 h-lim-p 0.0051 0.2416 0.8375 979.447586 1 0.0010 81 | 0/8 5 h-lim-p 0.0049 2.0864 0.1718 979.447468 4 0.0032 110 | 0/8 6 h-lim-p 0.0306 5.1901 0.0182 979.433825 0 0.2451 133 | 0/8 7 h-lim-p 0.0018 0.0733 2.5366 979.425418 5 0.0014 162 | 0/8 8 h-lim-p 0.0055 0.2948 0.6451 979.425212 3 0.0010 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 979.425205 2 0.9644 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 979.425205 0 1.0938 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 979.425205 0 0.2734 248 | 0/8 12 h-lim-p 0.1705 20.0000 0.0000 979.425205 0 0.0027 273 | 0/8 13 h-lim-p 0.0012 20.0000 0.0000 979.425205 0 0.0012 293 | 0/8 14 h-lim-p 0.0012 20.0000 0.0000 979.425205 0 0.0000 330 Out... lnL = -979.425205 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -979.425205 Node 7: lnL = -979.425205 Node 8: lnL = -979.425205 Node 9: lnL = -979.425205 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 243 Sequential format.. Reading seq # 1: YDR201W_Sbay Reading seq # 2: YDR201W_Scer Reading seq # 3: YDR201W_Skud Reading seq # 4: YDR201W_Smik Reading seq # 5: YDR201W_Spar Sequences read.. Counting patterns.. # site patterns = 94 Counting frequencies.. 120 bytes for distance 15040 bytes for lkl0 12032 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.130971 0.101545 0.053351 0.068446 0.042510 0.128546 0.178156 0.118613 lnL0 = -981.915446 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 981.915446 x= 0.13097 0.10155 0.05335 0.06845 0.04251 0.12855 0.17816 0.11861 1 h-lim-p 0.0003 0.0024 37.2417 981.619195 0 0.0004 22 | 0/8 2 h-lim-p 0.0009 0.0090 18.2189 981.559749 2 0.0004 38 | 0/8 3 h-lim-p 0.0007 0.0155 10.6370 981.537214 6 0.0005 65 | 0/8 4 h-lim-p 0.0027 0.0909 2.1106 981.535177 5 0.0010 89 | 0/8 5 h-lim-p 0.0022 0.0768 0.9458 981.534993 2 0.0005 106 | 0/8 6 h-lim-p 0.0036 1.9063 0.1269 981.534986 0 0.0009 127 | 0/8 7 h-lim-p 0.1356 20.0000 0.0008 981.534707 0 0.5425 149 | 0/8 8 h-lim-p 0.0015 0.6314 0.3119 981.534578 1 0.0015 171 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 981.534567 2 0.9961 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 981.534567 0 0.5469 216 | 0/8 11 h-lim-p 0.6247 20.0000 0.0000 981.534567 0 0.0000 249 Out... lnL = -981.534567 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -981.534567 Node 7: lnL = -981.534567 Node 8: lnL = -981.534567 Node 9: lnL = -981.534567 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 204 Sequential format.. Reading seq # 1: YDR202C_Sbay Reading seq # 2: YDR202C_Scer Reading seq # 3: YDR202C_Skud Reading seq # 4: YDR202C_Smik Reading seq # 5: YDR202C_Spar Sequences read.. Counting patterns.. # site patterns = 83 Counting frequencies.. 120 bytes for distance 13280 bytes for lkl0 10624 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.087925 0.058848 0.050375 0.101691 0.107196 0.091592 0.159082 0.077094 lnL0 = -796.489149 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 796.489149 x= 0.08792 0.05885 0.05037 0.10169 0.10720 0.09159 0.15908 0.07709 1 h-lim-p 0.0020 0.0159 36.0131 796.133264 7 0.0006 40 | 0/8 2 h-lim-p 0.0022 0.0173 9.4830 796.092519 5 0.0009 61 | 0/8 3 h-lim-p 0.0026 0.0687 3.4428 796.089560 4 0.0006 81 | 0/8 4 h-lim-p 0.0034 0.2330 0.5750 796.089437 2 0.0008 98 | 0/8 5 h-lim-p 0.0087 3.9880 0.0526 796.089435 0 0.0010 120 | 0/8 6 h-lim-p 0.0208 20.0000 0.0024 796.089435 0 0.0091 140 | 0/8 7 h-lim-p 0.0184 20.0000 0.0012 796.089415 0 0.1473 163 | 0/8 8 h-lim-p 0.0033 3.0655 0.0534 796.089414 0 0.0008 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 796.089414 0 1.0938 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 796.089414 0 1.0938 224 | 0/8 11 h-lim-p 1.9263 20.0000 0.0000 796.089414 0 3.8525 245 | 0/8 12 h-lim-p 2.2770 20.0000 0.0000 796.089414 0 0.2490 267 | 0/8 13 h-lim-p 1.3311 20.0000 0.0000 796.089414 0 0.0156 293 | 0/8 14 h-lim-p 0.0050 20.0000 0.0000 796.089414 0 0.0037 313 | 0/8 15 h-lim-p 0.0018 20.0000 0.0000 796.089414 0 0.0002 335 Out... lnL = -796.089414 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -796.089414 Node 7: lnL = -796.089414 Node 8: lnL = -796.089414 Node 9: lnL = -796.089414 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 152 Sequential format.. Reading seq # 1: YDR204W_Sbay Reading seq # 2: YDR204W_Scer Reading seq # 3: YDR204W_Skud Reading seq # 4: YDR204W_Smik Reading seq # 5: YDR204W_Spar Sequences read.. Counting patterns.. # site patterns = 64 Counting frequencies.. 120 bytes for distance 10240 bytes for lkl0 8192 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.110427 0.000060 0.046667 0.067262 0.101946 0.076764 0.177751 0.101141 lnL0 = -553.253637 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 553.253637 x= 0.11043 0.00006 0.04667 0.06726 0.10195 0.07676 0.17775 0.10114 1 h-lim-p 0.0003 0.0025 97.7527 551.852721 3 0.0003 28 | 0/8 2 h-lim-p 0.0003 0.0026 20.8135 551.724148 0 0.0006 41 | 0/8 3 h-lim-p 0.0013 0.0202 10.5168 551.678368 4 0.0010 61 | 0/8 4 h-lim-p 0.0041 0.0781 2.5491 551.674606 6 0.0012 90 | 0/8 5 h-lim-p 0.0037 0.2211 0.8490 551.674366 4 0.0007 111 | 0/8 6 h-lim-p 0.0048 0.9788 0.1289 551.674349 1 0.0012 134 | 0/8 7 h-lim-p 0.0139 10.6921 0.0112 551.673106 0 0.1111 157 | 0/8 8 h-lim-p 0.0026 0.0840 0.4758 551.666294 0 0.0052 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0008 551.665770 3 1.0004 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 551.665768 1 0.9961 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 551.665768 0 1.0938 246 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 551.665768 0 0.0073 274 | 0/8 13 h-lim-p 0.0034 20.0000 0.0000 551.665768 0 0.0013 295 Out... lnL = -551.665768 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -551.665768 Node 7: lnL = -551.665768 Node 8: lnL = -551.665768 Node 9: lnL = -551.665768 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 729 Sequential format.. Reading seq # 1: YDR208W_Sbay Reading seq # 2: YDR208W_Scer Reading seq # 3: YDR208W_Skud Reading seq # 4: YDR208W_Smik Reading seq # 5: YDR208W_Spar Sequences read.. Counting patterns.. # site patterns = 172 Counting frequencies.. 120 bytes for distance 27520 bytes for lkl0 22016 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.093023 0.043428 0.039370 0.066030 0.066126 0.098259 0.129224 0.079610 lnL0 = -2693.026423 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2693.026423 x= 0.09302 0.04343 0.03937 0.06603 0.06613 0.09826 0.12922 0.07961 1 h-lim-p 0.0022 0.8185 155.3501 2691.888788 7 0.0001 42 | 0/8 2 h-lim-p 0.0005 0.0037 24.5549 2691.845045 6 0.0001 68 | 0/8 3 h-lim-p 0.0005 0.0187 7.7349 2691.839063 2 0.0002 84 | 0/8 4 h-lim-p 0.0008 0.0525 2.0678 2691.838796 3 0.0001 104 | 0/8 5 h-lim-p 0.0006 0.3245 0.4491 2691.838778 2 0.0002 122 | 0/8 6 h-lim-p 0.0027 2.9338 0.0343 2691.838777 0 0.0002 145 | 0/8 7 h-lim-p 0.0015 20.0000 0.0039 2691.838777 0 0.0015 165 | 0/8 8 h-lim-p 0.0057 20.0000 0.0010 2691.838712 0 0.1358 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2691.838711 0 1.0938 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2691.838711 0 0.5469 230 | 0/8 11 h-lim-p 0.4037 20.0000 0.0000 2691.838711 0 0.0505 252 | 0/8 12 h-lim-p 0.0307 20.0000 0.0000 2691.838711 0 0.0000 282 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 2691.838711 0 0.0000 313 | 0/8 14 h-lim-p 0.0000 20.0000 0.0047 | 0/8 15 h-lim-p 0.0000 20.0000 0.0047 Out... lnL = -2691.838711 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2691.838711 Node 7: lnL = -2691.838711 Node 8: lnL = -2691.838711 Node 9: lnL = -2691.838711 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 535 Sequential format.. Reading seq # 1: YDR210W_Sbay Reading seq # 2: YDR210W_Scer Reading seq # 3: YDR210W_Skud Reading seq # 4: YDR210W_Smik Reading seq # 5: YDR210W_Spar Sequences read.. Counting patterns.. # site patterns = 160 Counting frequencies.. 120 bytes for distance 25600 bytes for lkl0 20480 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.135687 0.365766 0.122224 0.144024 0.094495 0.154618 0.000060 0.118174 lnL0 = -1901.618287 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1901.618287 x= 0.13569 0.36577 0.12222 0.14402 0.09449 0.15462 0.00006 0.11817 1 h-lim-p 0.0000 0.0000 587.2586 1901.502555 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0001 1212.9791 1826.140679 m 0.0001 35 | 2/8 3 h-lim-p 0.0000 0.0000 1279.0660 1820.178463 m 0.0000 47 | 3/8 4 h-lim-p 0.0001 0.0016 184.6187 1815.777071 0 0.0004 62 | 3/8 5 h-lim-p 0.0015 0.0119 17.7751 1815.563903 7 0.0011 90 | 3/8 6 h-lim-p 0.0062 0.0494 2.2915 1815.128604 0 0.0124 103 | 3/8 7 h-lim-p 0.0133 0.1067 1.4757 1799.689083 0 0.0534 117 | 3/8 8 h-lim-p 0.1614 1.2912 0.1753 1798.961088 1 0.2017 131 | 3/8 9 h-lim-p 0.2629 2.1034 0.0351 1798.751211 5 0.2952 159 | 3/8 10 h-lim-p 1.3992 11.1937 0.0049 1798.742802 6 0.4300 192 | 3/8 11 h-lim-p 1.7651 20.0000 0.0012 1798.742273 4 0.6447 218 | 3/8 12 h-lim-p 2.3657 20.0000 0.0003 1798.742179 3 0.6936 244 | 3/8 13 h-lim-p 2.5000 20.0000 0.0001 1798.742178 0 1.0938 261 | 3/8 14 h-lim-p 2.5000 20.0000 0.0000 1798.742178 0 1.0938 278 | 3/8 15 h-lim-p 2.5000 20.0000 0.0000 1798.742178 0 1.0938 295 | 3/8 16 h-lim-p 2.5000 20.0000 0.0000 1798.742178 0 5.0000 313 | 3/8 17 h-lim-p 1.2498 20.0000 0.0000 1798.742178 0 0.2734 331 | 3/8 18 h-lim-p 0.3762 20.0000 0.0000 1798.742178 0 0.0059 353 Out... lnL = -1798.742178 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1798.742178 Node 7: lnL = -1798.742178 Node 8: lnL = -1798.742178 Node 9: lnL = -1798.742178 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 403 Sequential format.. Reading seq # 1: YDR212W_Sbay Reading seq # 2: YDR212W_Scer Reading seq # 3: YDR212W_Skud Reading seq # 4: YDR212W_Smik Reading seq # 5: YDR212W_Spar Sequences read.. Counting patterns.. # site patterns = 145 Counting frequencies.. 120 bytes for distance 23200 bytes for lkl0 18560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.083287 0.150543 0.035377 0.077451 0.066300 0.160006 0.164594 0.064990 lnL0 = -1564.983883 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1564.983883 x= 0.08329 0.15054 0.03538 0.07745 0.06630 0.16001 0.16459 0.06499 1 h-lim-p 0.0002 0.0014 127.0675 1563.056990 0 0.0003 23 | 0/8 2 h-lim-p 0.0002 0.0019 39.5181 1562.840184 1 0.0003 37 | 0/8 3 h-lim-p 0.0007 0.0099 17.7208 1562.786327 7 0.0004 67 | 0/8 4 h-lim-p 0.0013 0.0345 5.5563 1562.780111 6 0.0005 95 | 0/8 5 h-lim-p 0.0045 0.7139 0.5503 1562.779748 4 0.0014 119 | 0/8 6 h-lim-p 0.0047 0.6772 0.1640 1562.778613 1 0.0059 141 | 0/8 7 h-lim-p 0.0021 0.4423 0.4560 1562.729001 0 0.0170 164 | 0/8 8 h-lim-p 0.0016 0.0240 4.7156 1562.641495 1 0.0021 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 1562.640862 4 0.9422 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1562.640861 0 1.0938 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1562.640861 0 1.0938 246 | 0/8 12 h-lim-p 1.8924 20.0000 0.0000 1562.640861 0 1.6559 266 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1562.640861 0 0.5469 287 | 0/8 14 h-lim-p 0.1865 20.0000 0.0000 1562.640861 0 0.0117 310 | 0/8 15 h-lim-p 0.0053 20.0000 0.0000 1562.640861 0 0.0000 344 | 0/8 16 h-lim-p 0.0000 20.0000 0.0005 | 0/8 17 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -1562.640861 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1562.640861 Node 7: lnL = -1562.640861 Node 8: lnL = -1562.640861 Node 9: lnL = -1562.640861 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 457 Sequential format.. Reading seq # 1: YDR214W_Sbay Reading seq # 2: YDR214W_Scer Reading seq # 3: YDR214W_Skud Reading seq # 4: YDR214W_Smik Reading seq # 5: YDR214W_Spar Sequences read.. Counting patterns.. # site patterns = 161 Counting frequencies.. 120 bytes for distance 25760 bytes for lkl0 20608 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.085567 0.036617 0.111976 0.091023 0.064490 0.169250 0.191014 0.067350 lnL0 = -1725.369726 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1725.369726 x= 0.08557 0.03662 0.11198 0.09102 0.06449 0.16925 0.19101 0.06735 1 h-lim-p 0.0003 0.0027 94.0746 1724.262678 3 0.0003 28 | 0/8 2 h-lim-p 0.0008 0.0064 20.2289 1724.180896 4 0.0004 49 | 0/8 3 h-lim-p 0.0012 0.0421 6.9767 1724.170647 4 0.0005 69 | 0/8 4 h-lim-p 0.0009 0.0316 3.5412 1724.169195 5 0.0003 94 | 0/8 5 h-lim-p 0.0012 0.3637 0.8552 1724.169015 2 0.0005 110 | 0/8 6 h-lim-p 0.0031 1.7781 0.1474 1724.169010 2 0.0005 137 | 0/8 7 h-lim-p 0.0013 4.6397 0.0564 1724.169009 0 0.0007 157 | 0/8 8 h-lim-p 0.1437 20.0000 0.0003 1724.168869 0 1.1493 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1724.168866 0 1.0938 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1724.168866 0 1.0938 220 | 0/8 11 h-lim-p 1.2721 20.0000 0.0000 1724.168866 0 0.6360 240 | 0/8 12 h-lim-p 0.3260 20.0000 0.0000 1724.168866 0 0.0045 265 | 0/8 13 h-lim-p 0.0011 20.0000 0.0000 1724.168866 0 0.0003 286 | 0/8 14 h-lim-p 0.0011 20.0000 0.0000 1724.168866 0 0.0001 308 Out... lnL = -1724.168866 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1724.168866 Node 7: lnL = -1724.168866 Node 8: lnL = -1724.168866 Node 9: lnL = -1724.168866 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 327 Sequential format.. Reading seq # 1: YDR217C_Sbay Reading seq # 2: YDR217C_Scer Reading seq # 3: YDR217C_Skud Reading seq # 4: YDR217C_Smik Reading seq # 5: YDR217C_Spar Sequences read.. Counting patterns.. # site patterns = 162 Counting frequencies.. 120 bytes for distance 25920 bytes for lkl0 20736 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.115333 0.078618 0.062452 0.126913 0.106615 0.237671 0.278164 0.091473 lnL0 = -1506.470735 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1506.470735 x= 0.11533 0.07862 0.06245 0.12691 0.10662 0.23767 0.27816 0.09147 1 h-lim-p 0.0017 0.0134 40.7677 1505.959195 4 0.0006 30 | 0/8 2 h-lim-p 0.0010 0.0082 13.7395 1505.905142 7 0.0006 62 | 0/8 3 h-lim-p 0.0021 0.0634 4.0974 1505.899649 5 0.0007 88 | 0/8 4 h-lim-p 0.0018 0.1875 1.6350 1505.898520 5 0.0010 111 | 0/8 5 h-lim-p 0.0021 0.2822 0.7762 1505.898300 2 0.0009 127 | 0/8 6 h-lim-p 0.0130 4.2806 0.0542 1505.898299 0 0.0007 150 | 0/8 7 h-lim-p 0.0051 20.0000 0.0076 1505.898298 0 0.0044 170 | 0/8 8 h-lim-p 0.0417 20.0000 0.0008 1505.898238 0 0.3338 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1505.898237 0 1.0938 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1505.898237 0 1.0938 233 | 0/8 11 h-lim-p 2.4300 20.0000 0.0000 1505.898237 0 0.6075 254 | 0/8 12 h-lim-p 0.3997 20.0000 0.0000 1505.898237 0 0.0250 277 | 0/8 13 h-lim-p 0.0127 20.0000 0.0000 1505.898237 0 0.0014 299 | 0/8 14 h-lim-p 0.0005 20.0000 0.0000 1505.898237 0 0.0000 322 | 0/8 15 h-lim-p 0.0006 20.0000 0.0000 1505.898237 0 0.0000 349 Out... lnL = -1505.898237 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1505.898237 Node 7: lnL = -1505.898237 Node 8: lnL = -1505.898237 Node 9: lnL = -1505.898237 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 477 Sequential format.. Reading seq # 1: YDR218C_Sbay Reading seq # 2: YDR218C_Scer Reading seq # 3: YDR218C_Skud Reading seq # 4: YDR218C_Smik Reading seq # 5: YDR218C_Spar Sequences read.. Counting patterns.. # site patterns = 172 Counting frequencies.. 120 bytes for distance 27520 bytes for lkl0 22016 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.271490 0.000060 0.238598 0.181736 0.105289 4.607250 0.306204 0.194873 lnL0 = -1941.666402 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1941.666402 x= 0.27149 0.00006 0.23860 0.18174 0.10529 4.60725 0.30620 0.19487 1 h-lim-p 0.0005 0.0038 40.2678 1940.536435 0 0.0014 23 | 0/8 2 h-lim-p 0.0019 0.0167 29.7997 1940.315345 6 0.0007 48 | 0/8 3 h-lim-p 0.0021 0.0282 10.1042 1940.245049 4 0.0016 68 | 0/8 4 h-lim-p 0.0046 0.1088 3.5347 1940.239478 3 0.0010 87 | 0/8 5 h-lim-p 0.0078 0.0625 0.4740 1940.239276 2 0.0018 104 | 0/8 6 h-lim-p 0.0052 0.1262 0.1653 1940.236630 m 0.1262 126 | 1/8 7 h-lim-p 0.0617 1.1944 0.2330 1940.236629 1 0.0002 155 | 1/8 8 h-lim-p 0.3031 20.0000 0.0002 1940.236380 0 4.8504 178 | 1/8 9 h-lim-p 2.5000 20.0000 0.0003 1940.236262 3 1.4660 206 | 0/8 10 h-lim-p 0.2102 20.0000 0.0023 1940.236262 0 0.0057 229 | 0/8 11 h-lim-p 0.1009 0.9051 0.0001 1940.236260 0 0.7184 252 | 0/8 12 h-lim-p 0.0239 0.1910 0.0000 1940.236260 m 0.1910 272 | 1/8 13 h-lim-p 0.0082 20.0000 0.0003 1940.236260 0 0.0246 293 | 1/8 14 h-lim-p 1.7946 20.0000 0.0000 1940.236260 0 3.5891 313 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 1940.236260 0 2.1875 332 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 1940.236260 0 1.0938 351 | 1/8 17 h-lim-p 1.3851 20.0000 0.0000 1940.236260 0 2.7702 371 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 1940.236260 0 0.2734 392 | 1/8 19 h-lim-p 0.3282 20.0000 0.0000 1940.236260 0 0.0000 427 Out... lnL = -1940.236260 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1940.236260 Node 7: lnL = -1940.236260 Node 8: lnL = -1940.236260 Node 9: lnL = -1940.236260 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 161 Sequential format.. Reading seq # 1: YDR219C_Sbay Reading seq # 2: YDR219C_Scer Reading seq # 3: YDR219C_Skud Reading seq # 4: YDR219C_Smik Reading seq # 5: YDR219C_Spar Sequences read.. Counting patterns.. # site patterns = 98 Counting frequencies.. 120 bytes for distance 15680 bytes for lkl0 12544 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.134798 0.016008 0.118498 0.069778 0.111252 0.337565 0.246656 0.110038 lnL0 = -696.156724 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 696.156724 x= 0.13480 0.01601 0.11850 0.06978 0.11125 0.33757 0.24666 0.11004 1 h-lim-p 0.0006 0.0051 30.8981 695.682943 0 0.0013 23 | 0/8 2 h-lim-p 0.0006 0.0050 12.9059 695.530811 0 0.0025 37 | 0/8 3 h-lim-p 0.0006 0.0050 7.7818 695.510327 0 0.0013 50 | 0/8 4 h-lim-p 0.0022 0.0732 4.4485 695.496147 2 0.0021 66 | 0/8 5 h-lim-p 0.0036 0.1364 2.5357 695.489761 4 0.0028 86 | 0/8 6 h-lim-p 0.0422 1.6050 0.1695 695.489544 4 0.0068 109 | 0/8 7 h-lim-p 0.0101 3.0581 0.1133 695.488851 0 0.0152 129 | 0/8 8 h-lim-p 0.0095 1.3046 0.1810 695.472466 0 0.0759 152 | 0/8 9 h-lim-p 1.6352 13.0818 0.0035 695.470265 6 0.9984 190 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 695.470262 1 0.9961 212 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 695.470262 0 1.0938 232 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 695.470262 0 1.0938 252 | 0/8 13 h-lim-p 1.4002 20.0000 0.0000 695.470262 0 0.7001 272 | 0/8 14 h-lim-p 0.3339 20.0000 0.0000 695.470262 0 0.0417 294 | 0/8 15 h-lim-p 0.0125 20.0000 0.0000 695.470262 0 0.0016 316 | 0/8 16 h-lim-p 0.0003 20.0000 0.0000 695.470262 0 0.0000 338 | 0/8 17 h-lim-p 0.0012 20.0000 0.0000 695.470262 0 0.0000 375 Out... lnL = -695.470262 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -695.470262 Node 7: lnL = -695.470262 Node 8: lnL = -695.470262 Node 9: lnL = -695.470262 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 835 Sequential format.. Reading seq # 1: YDR224C_Sbay Reading seq # 2: YDR224C_Scer Reading seq # 3: YDR224C_Skud Reading seq # 4: YDR224C_Smik Reading seq # 5: YDR224C_Spar Sequences read.. Counting patterns.. # site patterns = 219 Counting frequencies.. 120 bytes for distance 35040 bytes for lkl0 28032 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.093412 0.023390 0.058498 0.101233 0.080268 0.146128 0.135114 0.077947 lnL0 = -3384.586837 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3384.586837 x= 0.09341 0.02339 0.05850 0.10123 0.08027 0.14613 0.13511 0.07795 1 h-lim-p 0.0006 0.0055 343.0153 3380.597579 9 0.0001 46 | 0/8 2 h-lim-p 0.0004 0.0034 37.1165 3380.478849 3 0.0002 64 | 0/8 3 h-lim-p 0.0015 0.0886 4.3513 3380.477217 2 0.0002 82 | 0/8 4 h-lim-p 0.0007 0.1638 1.1106 3380.477110 3 0.0002 101 | 0/8 5 h-lim-p 0.0007 0.8019 0.2854 3380.477102 1 0.0002 116 | 0/8 6 h-lim-p 0.0016 4.2576 0.0324 3380.477102 0 0.0003 137 | 0/8 7 h-lim-p 0.0077 20.0000 0.0014 3380.477093 0 0.0617 160 | 0/8 8 h-lim-p 0.0024 1.6172 0.0365 3380.476888 0 0.0073 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3380.476884 0 1.0938 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3380.476884 0 1.0938 221 | 0/8 11 h-lim-p 0.7024 20.0000 0.0000 3380.476884 0 0.1536 242 | 0/8 12 h-lim-p 0.0803 20.0000 0.0000 3380.476884 0 0.0201 263 | 0/8 13 h-lim-p 0.0133 20.0000 0.0000 3380.476884 0 0.0000 301 | 0/8 14 h-lim-p 0.0000 20.0000 0.0025 | 0/8 15 h-lim-p 0.0000 20.0000 0.0025 Out... lnL = -3380.476884 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3380.476884 Node 7: lnL = -3380.476884 Node 8: lnL = -3380.476884 Node 9: lnL = -3380.476884 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 822 Sequential format.. Reading seq # 1: YDR225W_Sbay Reading seq # 2: YDR225W_Scer Reading seq # 3: YDR225W_Skud Reading seq # 4: YDR225W_Smik Reading seq # 5: YDR225W_Spar Sequences read.. Counting patterns.. # site patterns = 226 Counting frequencies.. 120 bytes for distance 36160 bytes for lkl0 28928 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.093336 0.017742 0.062932 0.101311 0.082321 0.147918 0.137275 0.077789 lnL0 = -3379.269407 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3379.269407 x= 0.09334 0.01774 0.06293 0.10131 0.08232 0.14792 0.13727 0.07779 1 h-lim-p 0.0004 0.0087 430.4080 3373.902512 4 0.0001 31 | 0/8 2 h-lim-p 0.0005 0.0037 35.8788 3373.780635 3 0.0002 49 | 0/8 3 h-lim-p 0.0013 0.0391 5.4740 3373.777619 3 0.0002 70 | 0/8 4 h-lim-p 0.0006 0.0975 2.0099 3373.777275 3 0.0002 90 | 0/8 5 h-lim-p 0.0012 0.7717 0.3410 3373.777265 2 0.0002 109 | 0/8 6 h-lim-p 0.0018 5.7564 0.0353 3373.777264 0 0.0004 130 | 0/8 7 h-lim-p 0.0009 12.0768 0.0158 3373.777263 0 0.0018 151 | 0/8 8 h-lim-p 0.0089 15.1758 0.0032 3373.776526 0 0.1430 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3373.776520 0 1.0938 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3373.776519 0 1.0938 215 | 0/8 11 h-lim-p 0.8121 20.0000 0.0000 3373.776519 0 0.2030 236 | 0/8 12 h-lim-p 0.1085 20.0000 0.0000 3373.776519 0 0.0136 258 | 0/8 13 h-lim-p 0.0080 20.0000 0.0000 3373.776519 0 0.0040 278 | 0/8 14 h-lim-p 0.0034 20.0000 0.0000 3373.776519 0 0.0000 319 | 0/8 15 h-lim-p 0.0000 20.0000 0.0023 | 0/8 16 h-lim-p 0.0000 20.0000 0.0023 Out... lnL = -3373.776519 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3373.776519 Node 7: lnL = -3373.776519 Node 8: lnL = -3373.776519 Node 9: lnL = -3373.776519 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 612 Sequential format.. Reading seq # 1: YDR226W_Sbay Reading seq # 2: YDR226W_Scer Reading seq # 3: YDR226W_Skud Reading seq # 4: YDR226W_Smik Reading seq # 5: YDR226W_Spar Sequences read.. Counting patterns.. # site patterns = 186 Counting frequencies.. 120 bytes for distance 29760 bytes for lkl0 23808 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.077645 0.033822 0.006059 0.081060 0.078693 0.106602 0.116309 0.065676 lnL0 = -2151.817434 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2151.817434 x= 0.07764 0.03382 0.00606 0.08106 0.07869 0.10660 0.11631 0.06568 1 h-lim-p 0.0003 0.2962 378.6923 2149.220203 9 0.0000 45 | 0/8 2 h-lim-p 0.0001 0.0011 99.3565 2148.332857 0 0.0002 57 | 0/8 3 h-lim-p 0.0006 0.0045 34.9584 2148.179151 3 0.0003 75 | 0/8 4 h-lim-p 0.0015 0.0175 6.7258 2148.173267 5 0.0003 100 | 0/8 5 h-lim-p 0.0016 0.0784 1.1322 2148.173122 4 0.0002 123 | 0/8 6 h-lim-p 0.0013 0.4589 0.2041 2148.173115 0 0.0003 136 | 0/8 7 h-lim-p 0.0013 5.0867 0.0431 2148.173094 0 0.0026 157 | 0/8 8 h-lim-p 0.0116 2.2640 0.0098 2148.162896 0 0.1393 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 2148.162756 3 1.0449 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2148.162755 0 1.0938 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2148.162755 0 1.0938 246 | 0/8 12 h-lim-p 1.1494 20.0000 0.0000 2148.162755 0 2.2988 267 | 0/8 13 h-lim-p 1.7497 20.0000 0.0000 2148.162755 0 0.0068 294 | 0/8 14 h-lim-p 0.0001 20.0000 0.0007 2148.162755 0 0.0000 314 | 0/8 15 h-lim-p 0.0012 20.0000 0.0000 2148.162755 0 0.0000 348 | 0/8 16 h-lim-p 0.0000 20.0000 0.0005 2148.162755 0 0.0000 368 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 2148.162755 0 0.0038 395 | 0/8 18 h-lim-p 0.0092 20.0000 0.0000 2148.162755 0 0.0000 425 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 2148.162755 0 0.0307 456 | 0/8 20 h-lim-p 0.0722 20.0000 0.0000 2148.162755 0 0.0001 485 | 0/8 21 h-lim-p 0.0000 20.0000 0.0006 2148.162755 0 0.0000 510 | 0/8 22 h-lim-p 0.0000 20.0000 0.0036 2148.162755 0 0.0000 530 | 0/8 23 h-lim-p 0.0002 20.0000 0.0001 2148.162755 0 0.0005 551 | 0/8 24 h-lim-p 0.0002 20.0000 0.0002 2148.162755 0 0.0002 571 | 0/8 25 h-lim-p 0.0122 20.0000 0.0000 2148.162755 0 0.0730 593 | 0/8 26 h-lim-p 0.0261 20.0000 0.0000 2148.162755 0 0.0523 614 | 0/8 27 h-lim-p 0.1161 20.0000 0.0000 2148.162755 0 0.0000 649 Out... lnL = -2148.162755 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2148.162755 Node 7: lnL = -2148.162755 Node 8: lnL = -2148.162755 Node 9: lnL = -2148.162755 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 847 Sequential format.. Reading seq # 1: YDR228C_Sbay Reading seq # 2: YDR228C_Scer Reading seq # 3: YDR228C_Skud Reading seq # 4: YDR228C_Smik Reading seq # 5: YDR228C_Spar Sequences read.. Counting patterns.. # site patterns = 336 Counting frequencies.. 120 bytes for distance 53760 bytes for lkl0 43008 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.232141 0.051709 0.121281 0.151037 0.128162 0.233395 0.279653 0.201787 lnL0 = -3821.180339 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3821.180339 x= 0.23214 0.05171 0.12128 0.15104 0.12816 0.23340 0.27965 0.20179 1 h-lim-p 0.0107 0.0855 80.2150 3820.253682 3 0.0003 32 | 0/8 2 h-lim-p 0.0012 0.0099 12.8628 3820.210833 5 0.0005 56 | 0/8 3 h-lim-p 0.0006 0.0081 11.9301 3820.190948 4 0.0004 76 | 0/8 4 h-lim-p 0.0022 0.0958 2.3706 3820.188889 5 0.0008 101 | 0/8 5 h-lim-p 0.0025 0.4601 0.7511 3820.188724 2 0.0007 118 | 0/8 6 h-lim-p 0.0033 2.2858 0.1528 3820.188716 0 0.0007 139 | 0/8 7 h-lim-p 0.0193 20.0000 0.0056 3820.188716 0 0.0042 160 | 0/8 8 h-lim-p 0.0883 20.0000 0.0003 3820.188692 0 0.5297 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3820.188691 0 1.0938 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3820.188691 0 1.0938 222 | 0/8 11 h-lim-p 1.8214 20.0000 0.0000 3820.188691 0 1.8214 242 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3820.188691 0 0.0000 280 Out... lnL = -3820.188691 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3820.188691 Node 7: lnL = -3820.188691 Node 8: lnL = -3820.188691 Node 9: lnL = -3820.188691 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 833 Sequential format.. Reading seq # 1: YDR229W_Sbay Reading seq # 2: YDR229W_Scer Reading seq # 3: YDR229W_Skud Reading seq # 4: YDR229W_Smik Reading seq # 5: YDR229W_Spar Sequences read.. Counting patterns.. # site patterns = 302 Counting frequencies.. 120 bytes for distance 48320 bytes for lkl0 38656 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.317125 0.000060 0.290335 0.187746 0.149340 0.742046 0.292264 0.264761 lnL0 = -3615.724670 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3615.724670 x= 0.31712 0.00006 0.29033 0.18775 0.14934 0.74205 0.29226 0.26476 1 h-lim-p 0.0000 0.0000 329.6609 3615.648372 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0026 178.8582 3605.638844 0 0.0006 40 | 1/8 3 h-lim-p 0.0015 0.0121 39.4253 3604.769783 7 0.0012 68 | 1/8 4 h-lim-p 0.0058 0.0465 6.2092 3604.621123 6 0.0034 96 | 1/8 5 h-lim-p 0.0155 0.2871 1.3506 3599.613176 0 0.0927 110 | 1/8 6 h-lim-p 0.0008 0.0063 58.2518 3586.284965 0 0.0032 124 | 1/8 7 h-lim-p 0.0121 0.0966 10.0170 3584.845874 0 0.0242 137 | 1/8 8 h-lim-p 1.5333 12.2661 0.0437 3584.496204 7 0.5131 165 | 1/8 9 h-lim-p 2.5000 20.0000 0.0065 3584.476025 2 0.5859 189 | 1/8 10 h-lim-p 1.0534 20.0000 0.0036 3584.475558 4 0.5529 217 | 1/8 11 h-lim-p 2.5000 20.0000 0.0003 3584.475547 1 0.6152 239 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 3584.475547 0 1.0938 258 | 1/8 13 h-lim-p 1.9514 20.0000 0.0000 3584.475546 0 0.8537 277 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 3584.475546 0 1.0938 296 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 3584.475546 0 1.0938 315 | 1/8 16 h-lim-p 1.1247 20.0000 0.0000 3584.475546 0 0.0351 338 | 1/8 17 h-lim-p 0.0120 20.0000 0.0000 3584.475546 0 0.0060 357 | 1/8 18 h-lim-p 0.0008 20.0000 0.0000 3584.475546 0 0.0000 387 | 1/8 19 h-lim-p 0.0001 20.0000 0.0000 3584.475546 0 0.0000 414 Out... lnL = -3584.475546 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3584.475546 Node 7: lnL = -3584.475546 Node 8: lnL = -3584.475546 Node 9: lnL = -3584.475546 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 553 Sequential format.. Reading seq # 1: YDR231C_Sbay Reading seq # 2: YDR231C_Scer Reading seq # 3: YDR231C_Skud Reading seq # 4: YDR231C_Smik Reading seq # 5: YDR231C_Spar Sequences read.. Counting patterns.. # site patterns = 131 Counting frequencies.. 120 bytes for distance 20960 bytes for lkl0 16768 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.074860 0.047582 0.027761 0.033154 0.025469 0.105433 0.102739 0.060876 lnL0 = -1850.098230 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1850.098230 x= 0.07486 0.04758 0.02776 0.03315 0.02547 0.10543 0.10274 0.06088 1 h-lim-p 0.0008 0.0063 104.2766 1849.405357 8 0.0001 43 | 0/8 2 h-lim-p 0.0002 0.0012 36.8759 1849.327305 3 0.0001 61 | 0/8 3 h-lim-p 0.0004 0.0085 13.1477 1849.312602 6 0.0002 86 | 0/8 4 h-lim-p 0.0004 0.0063 5.8417 1849.311726 5 0.0001 113 | 0/8 5 h-lim-p 0.0005 0.1623 0.7760 1849.311668 1 0.0002 127 | 0/8 6 h-lim-p 0.0022 0.7187 0.0653 1849.311668 0 0.0001 150 | 0/8 7 h-lim-p 0.0002 3.8305 0.0329 1849.311668 0 0.0002 170 | 0/8 8 h-lim-p 0.0521 20.0000 0.0001 1849.311602 0 0.8336 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1849.311601 0 1.0938 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1849.311601 0 1.0938 234 | 0/8 11 h-lim-p 1.2036 20.0000 0.0000 1849.311601 0 1.2036 254 | 0/8 12 h-lim-p 0.8949 20.0000 0.0000 1849.311601 0 0.0559 277 | 0/8 13 h-lim-p 0.0004 20.0000 0.0010 1849.311601 0 0.0000 305 | 0/8 14 h-lim-p 0.0003 20.0000 0.0000 1849.311601 0 0.0000 332 Out... lnL = -1849.311601 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1849.311601 Node 7: lnL = -1849.311601 Node 8: lnL = -1849.311601 Node 9: lnL = -1849.311601 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 554 Sequential format.. Reading seq # 1: YDR232W_Sbay Reading seq # 2: YDR232W_Scer Reading seq # 3: YDR232W_Skud Reading seq # 4: YDR232W_Smik Reading seq # 5: YDR232W_Spar Sequences read.. Counting patterns.. # site patterns = 132 Counting frequencies.. 120 bytes for distance 21120 bytes for lkl0 16896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.075592 0.042737 0.028266 0.033951 0.024673 0.103413 0.102171 0.061810 lnL0 = -1847.394591 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1847.394591 x= 0.07559 0.04274 0.02827 0.03395 0.02467 0.10341 0.10217 0.06181 1 h-lim-p 0.0004 0.0034 133.5480 1846.361972 8 0.0001 40 | 0/8 2 h-lim-p 0.0001 0.0012 44.4996 1846.261802 7 0.0001 68 | 0/8 3 h-lim-p 0.0002 0.0039 22.5736 1846.240466 5 0.0001 91 | 0/8 4 h-lim-p 0.0002 0.0092 12.8777 1846.232590 5 0.0001 114 | 0/8 5 h-lim-p 0.0024 0.1694 0.6862 1846.232546 3 0.0002 136 | 0/8 6 h-lim-p 0.0007 0.2273 0.1883 1846.232545 1 0.0001 160 | 0/8 7 h-lim-p 0.0044 20.0000 0.0038 1846.232544 0 0.0044 180 | 0/8 8 h-lim-p 0.0048 20.0000 0.0035 1846.232395 0 0.0771 204 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1846.232384 1 0.9961 226 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1846.232384 0 0.0195 252 | 0/8 11 h-lim-p 0.0105 20.0000 0.0000 1846.232384 0 0.0013 274 | 0/8 12 h-lim-p 0.0008 20.0000 0.0000 1846.232384 0 0.0000 311 | 0/8 13 h-lim-p 0.0000 20.0000 0.0086 | 0/8 14 h-lim-p 0.0000 20.0000 0.0086 Out... lnL = -1846.232384 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1846.232384 Node 7: lnL = -1846.232384 Node 8: lnL = -1846.232384 Node 9: lnL = -1846.232384 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 834 Sequential format.. Reading seq # 1: YDR233C_Sbay Reading seq # 2: YDR233C_Scer Reading seq # 3: YDR233C_Skud Reading seq # 4: YDR233C_Smik Reading seq # 5: YDR233C_Spar Sequences read.. Counting patterns.. # site patterns = 219 Counting frequencies.. 120 bytes for distance 35040 bytes for lkl0 28032 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.128796 0.041863 0.009364 0.096287 0.075893 0.153343 0.116936 0.108279 lnL0 = -3245.934283 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3245.934283 x= 0.12880 0.04186 0.00936 0.09629 0.07589 0.15334 0.11694 0.10828 1 h-lim-p 0.0002 0.0026 577.9363 3241.336775 7 0.0000 37 | 0/8 2 h-lim-p 0.0002 0.0016 78.9441 3240.902540 8 0.0001 67 | 0/8 3 h-lim-p 0.0007 0.0109 15.8130 3240.879968 5 0.0002 90 | 0/8 4 h-lim-p 0.0010 0.0616 3.0698 3240.879069 3 0.0002 109 | 0/8 5 h-lim-p 0.0008 0.2475 0.7465 3240.879027 2 0.0002 126 | 0/8 6 h-lim-p 0.0013 2.2468 0.0957 3240.879025 1 0.0003 149 | 0/8 7 h-lim-p 0.0238 20.0000 0.0012 3240.878186 0 0.3807 173 | 0/8 8 h-lim-p 0.0005 0.0489 0.8870 3240.876219 0 0.0008 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3240.876184 2 0.9961 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3240.876184 0 1.0938 237 | 0/8 11 h-lim-p 1.1180 20.0000 0.0000 3240.876184 0 0.9783 257 | 0/8 12 h-lim-p 0.7586 20.0000 0.0000 3240.876184 0 0.0000 303 Out... lnL = -3240.876184 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3240.876184 Node 7: lnL = -3240.876184 Node 8: lnL = -3240.876184 Node 9: lnL = -3240.876184 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 339 Sequential format.. Reading seq # 1: YDR235W_Sbay Reading seq # 2: YDR235W_Scer Reading seq # 3: YDR235W_Skud Reading seq # 4: YDR235W_Smik Reading seq # 5: YDR235W_Spar Sequences read.. Counting patterns.. # site patterns = 136 Counting frequencies.. 120 bytes for distance 21760 bytes for lkl0 17408 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.144301 0.097503 0.018039 0.099422 0.068792 0.189944 0.158406 0.118460 lnL0 = -1395.658091 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1395.658091 x= 0.14430 0.09750 0.01804 0.09942 0.06879 0.18994 0.15841 0.11846 1 h-lim-p 0.0028 0.0269 100.2383 1394.750703 9 0.0002 50 | 0/8 2 h-lim-p 0.0012 0.0097 15.3154 1394.686637 2 0.0006 66 | 0/8 3 h-lim-p 0.0014 0.0273 6.1070 1394.679633 6 0.0004 94 | 0/8 4 h-lim-p 0.0013 0.1109 1.9845 1394.678398 4 0.0007 115 | 0/8 5 h-lim-p 0.0029 0.4353 0.4826 1394.678332 1 0.0006 130 | 0/8 6 h-lim-p 0.0051 5.3836 0.0603 1394.678330 0 0.0011 151 | 0/8 7 h-lim-p 0.0093 20.0000 0.0072 1394.678327 0 0.0093 171 | 0/8 8 h-lim-p 0.0183 10.8208 0.0036 1394.678027 0 0.1462 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1394.678018 1 0.9961 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1394.678018 0 2.1875 236 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1394.678018 0 0.0006 267 Out... lnL = -1394.678018 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1394.678018 Node 7: lnL = -1394.678018 Node 8: lnL = -1394.678018 Node 9: lnL = -1394.678018 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 767 Sequential format.. Reading seq # 1: YDR236C_Sbay Reading seq # 2: YDR236C_Scer Reading seq # 3: YDR236C_Skud Reading seq # 4: YDR236C_Smik Reading seq # 5: YDR236C_Spar Sequences read.. Counting patterns.. # site patterns = 321 Counting frequencies.. 120 bytes for distance 51360 bytes for lkl0 41088 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.156886 0.175716 0.089020 0.155632 0.093834 0.254425 0.242290 0.118408 lnL0 = -3622.819900 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3622.819900 x= 0.15689 0.17572 0.08902 0.15563 0.09383 0.25443 0.24229 0.11841 1 h-lim-p 0.0104 1.2861 83.5956 3621.770163 6 0.0003 37 | 0/8 2 h-lim-p 0.0009 0.0076 20.8576 3621.689865 3 0.0004 55 | 0/8 3 h-lim-p 0.0007 0.0292 11.0797 3621.662058 5 0.0006 77 | 0/8 4 h-lim-p 0.0034 0.4671 1.8488 3621.661332 4 0.0004 99 | 0/8 5 h-lim-p 0.0025 0.6117 0.3350 3621.661285 2 0.0008 116 | 0/8 6 h-lim-p 0.0055 4.5419 0.0482 3621.661284 0 0.0007 138 | 0/8 7 h-lim-p 0.0037 20.0000 0.0088 3621.661282 0 0.0075 159 | 0/8 8 h-lim-p 0.0150 20.0000 0.0044 3621.660999 0 0.1198 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3621.660984 1 0.9961 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3621.660984 0 2.1875 224 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3621.660984 0 1.0938 244 | 0/8 12 h-lim-p 0.3233 20.0000 0.0000 3621.660984 0 3.8800 267 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 3621.660984 0 0.3125 289 | 0/8 14 h-lim-p 0.2310 20.0000 0.0000 3621.660984 0 0.0009 316 Out... lnL = -3621.660984 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3621.660984 Node 7: lnL = -3621.660984 Node 8: lnL = -3621.660984 Node 9: lnL = -3621.660984 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 256 Sequential format.. Reading seq # 1: YDR238C_Sbay Reading seq # 2: YDR238C_Scer Reading seq # 3: YDR238C_Skud Reading seq # 4: YDR238C_Smik Reading seq # 5: YDR238C_Spar Sequences read.. Counting patterns.. # site patterns = 116 Counting frequencies.. 120 bytes for distance 18560 bytes for lkl0 14848 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.108278 0.016050 0.091390 0.149834 0.082782 0.148396 0.200415 0.082949 lnL0 = -1120.307881 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1120.307881 x= 0.10828 0.01605 0.09139 0.14983 0.08278 0.14840 0.20041 0.08295 1 h-lim-p 0.0014 0.0111 123.6285 1118.088362 6 0.0004 36 | 0/8 2 h-lim-p 0.0009 0.0068 21.0438 1117.877805 1 0.0011 50 | 0/8 3 h-lim-p 0.0030 0.0331 7.3965 1117.863291 4 0.0006 71 | 0/8 4 h-lim-p 0.0035 0.1372 1.2549 1117.862634 3 0.0009 90 | 0/8 5 h-lim-p 0.0067 1.6724 0.1621 1117.862618 2 0.0011 108 | 0/8 6 h-lim-p 0.0044 6.4546 0.0398 1117.862607 0 0.0044 128 | 0/8 7 h-lim-p 0.0053 7.5547 0.0328 1117.862509 0 0.0160 149 | 0/8 8 h-lim-p 0.0058 2.7937 0.0899 1117.861005 0 0.0233 171 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1117.860956 2 1.0938 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1117.860954 1 1.2305 218 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1117.860953 0 1.0938 238 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1117.860953 0 1.0938 258 | 0/8 13 h-lim-p 1.1746 20.0000 0.0000 1117.860953 0 4.6985 280 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1117.860953 0 0.1562 303 | 0/8 15 h-lim-p 1.9112 20.0000 0.0000 1117.860953 0 0.0000 345 Out... lnL = -1117.860953 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1117.860953 Node 7: lnL = -1117.860953 Node 8: lnL = -1117.860953 Node 9: lnL = -1117.860953 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 275 Sequential format.. Reading seq # 1: YDR239C_Sbay Reading seq # 2: YDR239C_Scer Reading seq # 3: YDR239C_Skud Reading seq # 4: YDR239C_Smik Reading seq # 5: YDR239C_Spar Sequences read.. Counting patterns.. # site patterns = 142 Counting frequencies.. 120 bytes for distance 22720 bytes for lkl0 18176 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.098694 0.265299 0.216122 0.292666 0.373954 0.214951 0.436479 lnL0 = -1310.493804 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1310.493804 x= 0.00006 0.09869 0.26530 0.21612 0.29267 0.37395 0.21495 0.43648 1 h-lim-p 0.0000 0.0000 181.7239 1310.414719 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0044 113.2508 1295.623494 6 0.0026 54 | 1/8 3 h-lim-p 0.0010 0.0079 25.9856 1294.858162 0 0.0020 67 | 1/8 4 h-lim-p 0.0037 0.0298 13.3546 1294.434616 7 0.0041 96 | 1/8 5 h-lim-p 0.0127 0.1013 4.1937 1293.623937 0 0.0190 108 | 1/8 6 h-lim-p 0.0139 0.1111 4.1461 1285.443913 0 0.0556 122 | 1/8 7 h-lim-p 0.0010 0.0080 33.4740 1279.416613 0 0.0040 136 | 1/8 8 h-lim-p 0.0009 0.0068 26.9272 1278.843505 0 0.0017 149 | 1/8 9 h-lim-p 0.1604 1.2832 0.1563 1277.371547 0 0.3208 162 | 1/8 10 h-lim-p 0.4929 7.6294 0.1017 1276.835298 7 0.3609 198 | 0/8 11 h-lim-p 0.0166 4.0561 2.2164 1276.829500 6 0.0023 232 | 0/8 12 h-lim-p 0.2744 8.7262 0.0189 1276.804129 0 0.5488 245 | 0/8 13 h-lim-p 1.5603 12.4826 0.0044 1276.800003 2 0.7314 269 | 0/8 14 h-lim-p 2.0396 20.0000 0.0016 1276.799270 4 0.7241 298 | 0/8 15 h-lim-p 2.0708 20.0000 0.0006 1276.799212 3 0.7335 326 | 0/8 16 h-lim-p 2.5000 20.0000 0.0001 1276.799210 0 1.0938 346 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1276.799210 0 1.0938 366 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1276.799210 0 2.1875 386 | 0/8 19 h-lim-p 1.9147 20.0000 0.0000 1276.799210 0 0.8377 406 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 1276.799210 0 0.3125 428 | 0/8 21 h-lim-p 0.2042 20.0000 0.0000 1276.799210 0 0.0128 451 Out... lnL = -1276.799210 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1276.799210 Node 7: lnL = -1276.799210 Node 8: lnL = -1276.799210 Node 9: lnL = -1276.799210 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 844 Sequential format.. Reading seq # 1: YDR240C_Sbay Reading seq # 2: YDR240C_Scer Reading seq # 3: YDR240C_Skud Reading seq # 4: YDR240C_Smik Reading seq # 5: YDR240C_Spar Sequences read.. Counting patterns.. # site patterns = 475 Counting frequencies.. 120 bytes for distance 76000 bytes for lkl0 60800 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.226977 0.553611 0.511632 0.666899 0.831593 0.463726 0.925471 lnL0 = -5225.769559 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 5225.769559 x= 0.00006 0.22698 0.55361 0.51163 0.66690 0.83159 0.46373 0.92547 1 h-lim-p 0.0000 0.0000 242.5221 5225.699260 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0001 6820.5953 5120.585679 m 0.0001 34 | 1/8 3 h-lim-p 0.0007 0.0052 150.7311 5102.934536 0 0.0020 47 | 1/8 4 h-lim-p 0.0009 0.0073 101.3917 5098.047832 0 0.0014 59 | 1/8 5 h-lim-p 0.0044 0.0349 17.0569 5097.670928 5 0.0023 82 | 1/8 6 h-lim-p 0.0095 0.0762 2.9487 5097.173201 0 0.0190 95 | 1/8 7 h-lim-p 0.0062 0.0497 4.3096 5092.498168 0 0.0248 109 | 0/8 8 h-lim-p 0.0008 0.0064 35.5298 5090.378052 0 0.0024 122 | 0/8 9 h-lim-p 0.0009 0.0069 6.9316 5090.256110 0 0.0034 136 | 0/8 10 h-lim-p 0.0927 0.7412 0.2400 5076.334014 m 0.7412 148 | 0/8 11 h-lim-p -0.0000 -0.0000 0.0793 h-lim-p: -9.90038766e-18 -7.92031012e-17 7.93172429e-02 5076.334014 .. | 0/8 12 h-lim-p 0.0000 0.0033 43.3302 5075.093065 0 0.0013 191 | 0/8 13 h-lim-p 0.0001 0.0006 28.8189 5074.884529 m 0.0006 203 | 1/8 14 h-lim-p 0.0013 0.0962 12.1227 5074.812228 5 0.0013 228 | 1/8 15 h-lim-p 0.0102 0.5934 1.5412 5074.808671 4 0.0027 249 | 1/8 16 h-lim-p 0.0141 0.1528 0.2928 5074.807441 3 0.0074 268 | 1/8 17 h-lim-p 0.0069 0.4090 0.3123 5074.807142 3 0.0037 294 | 1/8 18 h-lim-p 0.0223 7.0528 0.0522 5074.807107 2 0.0071 318 | 1/8 19 h-lim-p 0.0138 3.1861 0.0270 5074.806464 0 0.0553 339 | 1/8 20 h-lim-p 0.0065 0.1066 0.2291 5074.803843 0 0.0130 359 | 1/8 21 h-lim-p 2.5000 20.0000 0.0002 5074.803831 1 0.9961 380 | 1/8 22 h-lim-p 2.5000 20.0000 0.0000 5074.803831 0 1.0938 399 | 1/8 23 h-lim-p 2.5000 20.0000 0.0000 5074.803831 0 1.0938 418 | 1/8 24 h-lim-p 2.5000 20.0000 0.0000 5074.803831 0 0.2344 440 Out... lnL = -5074.803831 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -5074.803831 Node 7: lnL = -5074.803831 Node 8: lnL = -5074.803831 Node 9: lnL = -5074.803831 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 459 Sequential format.. Reading seq # 1: YDR245W_Sbay Reading seq # 2: YDR245W_Scer Reading seq # 3: YDR245W_Skud Reading seq # 4: YDR245W_Smik Reading seq # 5: YDR245W_Spar Sequences read.. Counting patterns.. # site patterns = 212 Counting frequencies.. 120 bytes for distance 33920 bytes for lkl0 27136 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.105109 0.251594 0.214350 0.295246 0.368209 0.212464 0.426641 lnL0 = -2179.820524 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2179.820524 x= 0.00006 0.10511 0.25159 0.21435 0.29525 0.36821 0.21246 0.42664 1 h-lim-p 0.0000 0.0000 301.9443 2179.702775 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0017 233.0681 2147.869039 1 0.0014 43 | 1/8 3 h-lim-p 0.0013 0.0108 38.2545 2146.076103 0 0.0027 56 | 1/8 4 h-lim-p 0.0022 0.0179 22.3169 2145.847685 2 0.0010 72 | 1/8 5 h-lim-p 0.0039 0.0496 5.9174 2145.600452 0 0.0059 84 | 1/8 6 h-lim-p 0.0098 0.0783 2.3305 2139.464396 0 0.0587 98 | 1/8 7 h-lim-p 0.0016 0.0130 35.9945 2125.160712 0 0.0065 112 | 1/8 8 h-lim-p 0.0004 0.0031 52.7715 2123.666470 0 0.0008 125 | 1/8 9 h-lim-p 0.3906 6.5084 0.1057 2121.798371 7 0.4355 152 | 1/8 10 h-lim-p 0.4053 4.7130 0.1136 2121.324113 7 0.2644 188 | 1/8 11 h-lim-p 1.7211 13.7689 0.0108 2121.285302 3 0.7799 213 | 0/8 12 h-lim-p 0.0134 2.7947 0.6286 2121.285033 2 0.0013 238 | 0/8 13 h-lim-p 0.0983 0.7861 0.0058 2121.280532 0 0.3930 260 | 0/8 14 h-lim-p 0.6079 4.8633 0.0006 2121.280349 0 1.2158 281 | 0/8 15 h-lim-p 2.5000 20.0000 0.0001 2121.280338 2 0.7996 306 | 0/8 16 h-lim-p 2.4017 20.0000 0.0000 2121.280338 0 1.0507 326 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 2121.280337 0 1.0938 346 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 2121.280337 0 1.0938 366 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 2121.280337 0 2.1875 386 | 0/8 20 h-lim-p 2.1228 20.0000 0.0000 2121.280337 0 0.0663 410 | 0/8 21 h-lim-p 0.0658 20.0000 0.0000 2121.280337 0 0.0000 455 Out... lnL = -2121.280337 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2121.280337 Node 7: lnL = -2121.280337 Node 8: lnL = -2121.280337 Node 9: lnL = -2121.280337 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 353 Sequential format.. Reading seq # 1: YDR246W_Sbay Reading seq # 2: YDR246W_Scer Reading seq # 3: YDR246W_Skud Reading seq # 4: YDR246W_Smik Reading seq # 5: YDR246W_Spar Sequences read.. Counting patterns.. # site patterns = 165 Counting frequencies.. 120 bytes for distance 26400 bytes for lkl0 21120 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.109766 0.267223 0.231611 0.310618 0.388267 0.234120 0.467836 lnL0 = -1620.947640 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1620.947640 x= 0.00006 0.10977 0.26722 0.23161 0.31062 0.38827 0.23412 0.46784 1 h-lim-p 0.0000 0.0000 217.3049 1620.844133 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0033 132.2572 1600.300520 9 0.0024 60 | 1/8 3 h-lim-p 0.0038 0.0303 20.0268 1599.362656 7 0.0041 88 | 1/8 4 h-lim-p 0.0052 0.0415 6.3599 1598.952490 0 0.0078 100 | 1/8 5 h-lim-p 0.0050 0.0480 9.9554 1598.103167 0 0.0075 112 | 1/8 6 h-lim-p 0.0091 0.0730 7.0415 1589.553158 0 0.0274 125 | 1/8 7 h-lim-p 0.0010 0.0082 42.7935 1582.272238 0 0.0041 139 | 1/8 8 h-lim-p 0.0003 0.0027 60.5805 1579.599566 0 0.0013 153 | 1/8 9 h-lim-p 0.7365 6.0331 0.1107 1577.474915 9 0.4976 188 | 1/8 10 h-lim-p 0.4341 4.4494 0.1269 1577.115290 8 0.2384 226 | 0/8 11 h-lim-p 0.0132 1.4497 2.2998 1577.109360 6 0.0023 262 | 0/8 12 h-lim-p 0.3480 9.1113 0.0149 1577.072845 0 0.6960 275 | 0/8 13 h-lim-p 1.5906 20.0000 0.0065 1577.065210 4 0.6365 303 | 0/8 14 h-lim-p 2.3244 20.0000 0.0018 1577.064669 2 0.5448 328 | 0/8 15 h-lim-p 2.5000 20.0000 0.0003 1577.064623 3 0.8800 355 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1577.064622 0 1.0938 375 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1577.064621 0 1.0938 395 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1577.064621 0 1.0938 415 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1577.064621 0 1.0938 435 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 1577.064621 0 1.2500 455 | 0/8 21 h-lim-p 0.3388 20.0000 0.0000 1577.064621 0 0.0106 479 Out... lnL = -1577.064621 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1577.064621 Node 7: lnL = -1577.064621 Node 8: lnL = -1577.064621 Node 9: lnL = -1577.064621 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 875 Sequential format.. Reading seq # 1: YDR247W_Sbay Reading seq # 2: YDR247W_Scer Reading seq # 3: YDR247W_Skud Reading seq # 4: YDR247W_Smik Reading seq # 5: YDR247W_Spar Sequences read.. Counting patterns.. # site patterns = 317 Counting frequencies.. 120 bytes for distance 50720 bytes for lkl0 40576 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.071208 0.119112 0.143475 0.124877 0.230473 0.190129 0.430026 lnL0 = -3766.367113 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3766.367113 x= 0.00006 0.07121 0.11911 0.14347 0.12488 0.23047 0.19013 0.43003 1 h-lim-p 0.0001 0.0005 350.1242 3750.860003 0 0.0002 24 | 0/8 2 h-lim-p 0.0002 0.0019 71.7535 3750.264853 5 0.0002 46 | 0/8 3 h-lim-p 0.0007 0.0130 23.9352 3750.185408 4 0.0003 65 | 0/8 4 h-lim-p 0.0009 0.0266 8.3543 3750.175215 5 0.0003 88 | 0/8 5 h-lim-p 0.0009 0.0202 2.9514 3750.173508 2 0.0004 104 | 0/8 6 h-lim-p 0.0008 0.0160 1.5760 3750.172735 4 0.0005 126 | 0/8 7 h-lim-p 0.0015 0.0119 0.2044 3750.159923 m 0.0119 138 | 0/8 8 h-lim-p -0.0000 -0.0000 9.0730 h-lim-p: -1.45226827e-21 -1.16181461e-20 9.07301748e+00 3750.159923 .. | 0/8 9 h-lim-p 0.0000 2.0262 62.9351 3749.929645 0 0.0002 170 | 0/8 10 h-lim-p 0.0013 0.0191 8.0456 3749.921828 2 0.0002 187 | 0/8 11 h-lim-p 0.0008 0.0721 2.4167 3749.920662 3 0.0004 206 | 0/8 12 h-lim-p 0.0012 0.2280 0.8976 3749.920548 3 0.0003 225 | 0/8 13 h-lim-p 0.0010 0.9385 0.2711 3749.920514 2 0.0007 250 | 0/8 14 h-lim-p 0.0028 0.1043 0.0650 3749.920375 0 0.0055 271 | 0/8 15 h-lim-p 0.0011 0.0217 0.3343 3749.919539 0 0.0021 292 | 0/8 16 h-lim-p 0.0028 0.3971 0.2520 3749.905928 0 0.0114 314 | 0/8 17 h-lim-p 1.0172 8.1375 0.0008 3749.904527 2 0.9536 338 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 3749.904526 0 1.0938 358 | 0/8 19 h-lim-p 1.8695 20.0000 0.0000 3749.904526 0 1.6358 378 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 3749.904526 0 1.0938 398 | 0/8 21 h-lim-p 0.4844 20.0000 0.0000 3749.904526 m20.0000 421 | 0/8 22 h-lim-p 0.0013 0.0105 0.1302 3749.904526 m 0.0105 441 | 1/8 23 h-lim-p 0.7184 20.0000 0.0013 3749.904526 0 0.0002 472 | 1/8 24 h-lim-p 0.8865 20.0000 0.0000 3749.904526 0 0.0000 519 Out... lnL = -3749.904526 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3749.904526 Node 7: lnL = -3749.904526 Node 8: lnL = -3749.904526 Node 9: lnL = -3749.904526 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 397 Sequential format.. Reading seq # 1: YDR248C_Sbay Reading seq # 2: YDR248C_Scer Reading seq # 3: YDR248C_Skud Reading seq # 4: YDR248C_Smik Reading seq # 5: YDR248C_Spar Sequences read.. Counting patterns.. # site patterns = 108 Counting frequencies.. 120 bytes for distance 17280 bytes for lkl0 13824 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.331279 0.892236 0.681294 0.979137 1.644732 0.640922 1.373180 lnL0 = -1805.134309 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1805.134309 x= 0.00006 0.33128 0.89224 0.68129 0.97914 1.64473 0.64092 1.37318 1 h-lim-p 0.0000 0.0000 172.8016 1805.067969 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0731 20.5962 1743.093669 m 0.0731 43 | 2/8 3 h-lim-p 0.0049 0.0391 20.9944 1586.517082 m 0.0391 55 | 3/8 4 h-lim-p 0.0011 0.0089 90.9999 1573.006989 0 0.0033 68 | 3/8 5 h-lim-p 0.0164 0.1314 2.7069 1572.513298 7 0.0138 94 | 2/8 6 h-lim-p 0.0006 0.0061 66.1365 1570.653598 0 0.0023 108 | 2/8 7 h-lim-p 0.0714 0.5709 0.6053 1556.783587 m 0.5709 120 | 3/8 8 h-lim-p 0.0936 0.7485 0.8224 .. | 3/8 9 h-lim-p 0.0000 0.0173 67.2205 1522.463500 4 0.0103 199 | 2/8 10 h-lim-p 0.0000 0.0002 2402.4965 1514.065139 0 0.0001 213 | 2/8 11 h-lim-p 0.0000 0.0004 595.5714 1505.239008 m 0.0004 225 | 3/8 12 h-lim-p 0.0006 0.0050 28.7917 1493.374436 m 0.0050 237 | 2/8 13 h-lim-p 0.0000 0.0000 2951.2279 h-lim-p: 7.85318080e-22 6.28254464e-21 2.95122791e+03 1493.374436 .. | 2/8 14 h-lim-p 0.0000 0.0286 1413.6659 1425.542849 0 0.0002 261 | 2/8 15 h-lim-p 0.0002 0.0018 158.7518 1411.818835 0 0.0009 275 | 2/8 16 h-lim-p 0.0002 0.0013 249.7737 1395.410554 0 0.0010 289 | 2/8 17 h-lim-p 0.0018 0.0142 14.5060 1395.342958 7 0.0006 316 | 1/8 18 h-lim-p 0.0002 0.0637 51.8599 1394.617766 0 0.0007 330 | 1/8 19 h-lim-p 0.0187 0.1733 1.9685 1394.613256 4 0.0018 352 | 1/8 20 h-lim-p 0.0710 2.9913 0.0499 1393.870748 0 0.5678 367 | 0/8 21 h-lim-p 0.0147 0.4015 1.9340 1393.867835 2 0.0016 392 | 0/8 22 h-lim-p 1.4533 20.0000 0.0021 1393.860280 2 1.3624 408 | 0/8 23 h-lim-p 2.5000 20.0000 0.0012 1393.858481 0 3.7500 428 | 0/8 24 h-lim-p 2.5000 20.0000 0.0003 1393.858376 3 1.4660 457 | 0/8 25 h-lim-p 2.5000 20.0000 0.0001 1393.858375 0 1.0938 477 | 0/8 26 h-lim-p 2.5000 20.0000 0.0000 1393.858375 0 1.0938 497 | 0/8 27 h-lim-p 2.5000 20.0000 0.0000 1393.858375 0 0.5469 518 | 0/8 28 h-lim-p 0.7986 20.0000 0.0000 1393.858375 0 0.3993 538 | 0/8 29 h-lim-p 0.3734 20.0000 0.0000 1393.858375 0 0.0007 566 Out... lnL = -1393.858375 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1393.858375 Node 7: lnL = -1393.858375 Node 8: lnL = -1393.858375 Node 9: lnL = -1393.858375 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 299 Sequential format.. Reading seq # 1: YDR249C_Sbay Reading seq # 2: YDR249C_Scer Reading seq # 3: YDR249C_Skud Reading seq # 4: YDR249C_Smik Reading seq # 5: YDR249C_Spar Sequences read.. Counting patterns.. # site patterns = 155 Counting frequencies.. 120 bytes for distance 24800 bytes for lkl0 19840 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.129939 0.320050 0.249948 0.341131 0.444106 0.234550 0.498204 lnL0 = -1493.336800 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1493.336800 x= 0.00006 0.12994 0.32005 0.24995 0.34113 0.44411 0.23455 0.49820 1 h-lim-p 0.0000 0.0000 212.1367 1493.268733 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0026 156.4593 1468.770715 4 0.0021 49 | 1/8 3 h-lim-p 0.0009 0.0074 54.2536 1465.022656 0 0.0037 63 | 1/8 4 h-lim-p 0.0020 0.0164 23.2149 1464.415032 1 0.0026 77 | 1/8 5 h-lim-p 0.0076 0.0608 4.1751 1463.916705 0 0.0152 90 | 1/8 6 h-lim-p 0.0092 0.0739 5.1048 1457.822056 0 0.0370 104 | 1/8 7 h-lim-p 0.0027 0.0212 22.8768 1443.432187 0 0.0106 118 | 1/8 8 h-lim-p 0.0011 0.0086 26.6790 1442.747221 0 0.0021 131 | 1/8 9 h-lim-p 0.3448 2.7581 0.1455 1441.934851 2 0.3232 147 | 1/8 10 h-lim-p 0.3659 4.4353 0.1285 1441.696698 8 0.2055 185 | 0/8 11 h-lim-p 0.0195 2.0542 1.3568 1441.694537 3 0.0021 212 | 0/8 12 h-lim-p 0.0594 0.4753 0.0261 1441.624594 m 0.4753 224 | 1/8 13 h-lim-p 2.5000 20.0000 0.0043 1441.622121 3 0.6171 251 | 1/8 14 h-lim-p 2.5000 20.0000 0.0007 1441.621971 3 0.9482 276 | 0/8 15 h-lim-p 0.0189 20.0000 0.0337 1441.621970 0 0.0021 297 | 0/8 16 h-lim-p 0.1018 0.8145 0.0002 1441.621967 m 0.8145 317 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 1441.621966 0 1.0938 337 | 0/8 18 h-lim-p -0.0000 -0.0000 0.0103 h-lim-p: -6.40365534e-20 -5.12292428e-19 1.02707917e-02 1441.621966 .. | 1/8 19 h-lim-p 0.0000 20.0000 0.0131 1441.621966 0 0.0013 379 | 1/8 20 h-lim-p 0.0025 20.0000 0.0067 1441.621966 0 0.0011 398 | 1/8 21 h-lim-p 0.0033 20.0000 0.0023 1441.621966 0 0.0014 417 | 1/8 22 h-lim-p 0.0059 20.0000 0.0005 1441.621966 0 0.0013 437 | 1/8 23 h-lim-p 0.0240 20.0000 0.0000 1441.621966 0 0.0210 456 | 1/8 24 h-lim-p 0.0059 20.0000 0.0001 1441.621966 0 0.0088 475 | 1/8 25 h-lim-p 0.0058 20.0000 0.0002 1441.621966 0 0.0115 495 | 1/8 26 h-lim-p 0.0036 20.0000 0.0005 1441.621966 0 0.0031 514 | 1/8 27 h-lim-p 1.9058 20.0000 0.0000 1441.621966 0 0.8338 533 | 1/8 28 h-lim-p 2.5000 20.0000 0.0000 1441.621966 0 0.0684 556 | 1/8 29 h-lim-p 0.0734 20.0000 0.0000 1441.621966 0 0.0092 577 Out... lnL = -1441.621966 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1441.621966 Node 7: lnL = -1441.621966 Node 8: lnL = -1441.621966 Node 9: lnL = -1441.621966 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 273 Sequential format.. Reading seq # 1: YDR251W_Sbay Reading seq # 2: YDR251W_Scer Reading seq # 3: YDR251W_Skud Reading seq # 4: YDR251W_Smik Reading seq # 5: YDR251W_Spar Sequences read.. Counting patterns.. # site patterns = 130 Counting frequencies.. 120 bytes for distance 20800 bytes for lkl0 16640 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.091463 0.232970 0.194589 0.261400 0.349681 0.213336 0.408039 lnL0 = -1249.883316 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1249.883316 x= 0.00006 0.09146 0.23297 0.19459 0.26140 0.34968 0.21334 0.40804 1 h-lim-p 0.0000 0.0000 213.2021 1249.774717 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0026 157.1300 1228.686854 0 0.0019 41 | 1/8 3 h-lim-p 0.0003 0.0026 37.6061 1227.794890 0 0.0013 55 | 1/8 4 h-lim-p 0.0026 0.0208 17.6768 1227.229130 0 0.0039 67 | 1/8 5 h-lim-p 0.0120 0.0964 2.7836 1226.581530 0 0.0241 80 | 1/8 6 h-lim-p 0.0108 0.0865 4.1342 1213.124143 0 0.0433 94 | 1/8 7 h-lim-p 0.0006 0.0049 51.6125 1210.101020 0 0.0025 108 | 1/8 8 h-lim-p 0.0084 0.0673 5.6999 1210.070531 4 0.0016 129 | 1/8 9 h-lim-p 0.0453 1.4128 0.2073 1209.424319 0 0.1814 143 | 1/8 10 h-lim-p 0.7453 11.3229 0.0505 1209.178685 7 0.4435 179 | 1/8 11 h-lim-p 2.5000 20.0000 0.0034 1209.174925 6 0.8524 213 | 1/8 12 h-lim-p 2.1139 20.0000 0.0014 1209.174377 5 0.6635 246 | 1/8 13 h-lim-p 2.5000 20.0000 0.0003 1209.174369 2 0.4822 270 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 1209.174368 0 1.0938 289 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 1209.174368 0 1.0938 308 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 1209.174368 0 0.5469 328 | 1/8 17 h-lim-p 1.5503 20.0000 0.0000 1209.174368 0 1.5503 347 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 1209.174368 0 0.0049 374 Out... lnL = -1209.174368 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1209.174368 Node 7: lnL = -1209.174368 Node 8: lnL = -1209.174368 Node 9: lnL = -1209.174368 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 320 Sequential format.. Reading seq # 1: YDR252W_Sbay Reading seq # 2: YDR252W_Scer Reading seq # 3: YDR252W_Skud Reading seq # 4: YDR252W_Smik Reading seq # 5: YDR252W_Spar Sequences read.. Counting patterns.. # site patterns = 140 Counting frequencies.. 120 bytes for distance 22400 bytes for lkl0 17920 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.107409 0.265786 0.217219 0.294560 0.379807 0.222025 0.426532 lnL0 = -1526.193209 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1526.193209 x= 0.00006 0.10741 0.26579 0.21722 0.29456 0.37981 0.22202 0.42653 1 h-lim-p 0.0000 0.0000 252.9252 1526.109548 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0021 231.1729 1490.452314 0 0.0017 41 | 1/8 3 h-lim-p 0.0003 0.0024 60.1170 1488.217089 0 0.0012 55 | 1/8 4 h-lim-p 0.0008 0.0064 46.1539 1487.100347 0 0.0016 68 | 1/8 5 h-lim-p 0.0069 0.0551 5.1006 1486.484353 0 0.0138 81 | 1/8 6 h-lim-p 0.0040 0.0318 5.5054 1484.046376 0 0.0159 95 | 1/8 7 h-lim-p 0.0034 0.0269 13.9864 1467.708628 0 0.0202 109 | 1/8 8 h-lim-p 0.0240 0.1916 1.4708 1467.636813 7 0.0083 138 | 0/8 9 h-lim-p 0.0007 0.0978 18.3082 1467.306065 0 0.0013 151 | 0/8 10 h-lim-p 0.0033 0.0268 2.5918 1465.496306 m 0.0268 163 | 0/8 11 h-lim-p 0.0000 0.0000 0.1319 h-lim-p: 6.25184645e-18 5.00147716e-17 1.31888184e-01 1465.496306 .. | 0/8 12 h-lim-p 0.0000 3.2863 42.2734 1465.092881 0 0.0006 197 | 0/8 13 h-lim-p 0.0000 0.0002 16.3189 1465.051855 m 0.0002 209 | 1/8 14 h-lim-p 0.0007 0.0370 4.2205 1465.044627 4 0.0008 230 | 1/8 15 h-lim-p 0.0023 0.1345 1.5330 1465.042205 5 0.0014 255 | 1/8 16 h-lim-p 0.0041 0.3654 0.5319 1465.032964 0 0.0081 268 | 1/8 17 h-lim-p 0.0032 0.1261 1.3519 1465.011752 0 0.0048 287 | 1/8 18 h-lim-p 0.0039 0.1180 1.6449 1465.010605 3 0.0008 306 | 1/8 19 h-lim-p 0.0160 3.5533 0.0814 1465.007291 0 0.0479 319 | 1/8 20 h-lim-p 0.0109 0.5323 0.3579 1464.947542 0 0.0435 340 | 0/8 21 h-lim-p 0.1323 7.0560 0.1178 1464.947521 2 0.0020 368 | 0/8 22 h-lim-p 0.0587 1.0324 0.0041 1464.944148 0 0.7043 391 | 0/8 23 h-lim-p 0.1312 1.0499 0.0002 1464.944124 m 1.0499 411 | 1/8 24 h-lim-p 2.5000 20.0000 0.0000 1464.944124 0 1.0938 431 | 1/8 25 h-lim-p 2.5000 20.0000 0.0000 1464.944124 0 1.0938 450 | 1/8 26 h-lim-p 2.5000 20.0000 0.0000 1464.944124 0 1.2500 469 | 1/8 27 h-lim-p 2.5000 20.0000 0.0000 1464.944124 0 0.3125 490 | 1/8 28 h-lim-p 0.4545 20.0000 0.0000 1464.944124 0 0.0004 518 Out... lnL = -1464.944124 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1464.944124 Node 7: lnL = -1464.944124 Node 8: lnL = -1464.944124 Node 9: lnL = -1464.944124 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 588 Sequential format.. Reading seq # 1: YDR253C_Sbay Reading seq # 2: YDR253C_Scer Reading seq # 3: YDR253C_Skud Reading seq # 4: YDR253C_Smik Reading seq # 5: YDR253C_Spar Sequences read.. Counting patterns.. # site patterns = 223 Counting frequencies.. 120 bytes for distance 35680 bytes for lkl0 28544 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.085992 0.255677 0.198437 0.265258 0.346537 0.203199 0.392254 lnL0 = -2650.588877 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2650.588877 x= 0.00006 0.08599 0.25568 0.19844 0.26526 0.34654 0.20320 0.39225 1 h-lim-p 0.0000 0.0000 458.8832 2650.416385 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0008 387.6082 2600.038759 0 0.0007 40 | 1/8 3 h-lim-p 0.0002 0.0018 100.8177 2595.348878 0 0.0009 54 | 1/8 4 h-lim-p 0.0020 0.0158 25.9786 2594.665068 2 0.0018 70 | 1/8 5 h-lim-p 0.0036 0.0289 8.5465 2594.291778 7 0.0038 99 | 1/8 6 h-lim-p 0.0027 0.0213 4.0347 2589.787810 m 0.0213 111 | 2/8 7 h-lim-p 0.0020 0.0157 29.4140 2571.778170 0 0.0078 125 | 1/8 8 h-lim-p 0.0003 0.0026 92.9223 2567.128903 0 0.0010 138 | 1/8 9 h-lim-p 0.0006 0.0048 4.7992 2567.103999 4 0.0007 159 | 0/8 10 h-lim-p 0.0001 0.0037 29.1642 2566.629090 0 0.0009 174 | 0/8 11 h-lim-p 0.0064 0.0515 1.7497 2561.068961 m 0.0515 186 | 0/8 12 h-lim-p 1.0082 12.5766 0.0894 2559.341786 8 0.5094 218 | 0/8 13 h-lim-p 1.2470 9.9760 0.0097 2559.263269 6 0.8992 252 | 0/8 14 h-lim-p 1.3377 20.0000 0.0065 2559.249534 4 0.6813 281 | 0/8 15 h-lim-p 2.2444 20.0000 0.0020 2559.249181 2 0.2784 307 | 0/8 16 h-lim-p 1.6723 20.0000 0.0003 2559.249022 3 1.0932 334 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 2559.249021 0 1.0938 354 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 2559.249021 0 1.0938 374 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 2559.249021 0 0.0781 398 | 0/8 20 h-lim-p 0.0710 20.0000 0.0000 2559.249021 0 0.0155 419 Out... lnL = -2559.249021 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2559.249021 Node 7: lnL = -2559.249021 Node 8: lnL = -2559.249021 Node 9: lnL = -2559.249021 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 585 Sequential format.. Reading seq # 1: YDR254W_Sbay Reading seq # 2: YDR254W_Scer Reading seq # 3: YDR254W_Skud Reading seq # 4: YDR254W_Smik Reading seq # 5: YDR254W_Spar Sequences read.. Counting patterns.. # site patterns = 209 Counting frequencies.. 120 bytes for distance 33440 bytes for lkl0 26752 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.268448 0.318549 0.265983 0.259211 0.355728 0.199477 0.382634 lnL0 = -2691.367246 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2691.367246 x= 0.00006 0.26845 0.31855 0.26598 0.25921 0.35573 0.19948 0.38263 1 h-lim-p 0.0000 0.0000 523.8962 2691.137201 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0009 565.2357 2595.136872 0 0.0007 40 | 1/8 3 h-lim-p 0.0001 0.0005 256.5454 2585.717524 m 0.0005 52 | 2/8 4 h-lim-p 0.0006 0.0049 62.1041 2583.734163 0 0.0012 65 | 2/8 5 h-lim-p 0.0014 0.0116 32.2037 2581.201757 0 0.0022 77 | 2/8 6 h-lim-p 0.0013 0.0103 18.1008 2579.812566 0 0.0019 89 | 1/8 7 h-lim-p 0.0008 0.0235 44.5808 2579.498712 7 0.0003 114 | 1/8 8 h-lim-p 0.0017 0.0140 4.9833 2579.042612 0 0.0070 128 | 1/8 9 h-lim-p 0.0080 0.1205 4.3707 2545.845375 1 0.0779 145 | 1/8 10 h-lim-p 0.4114 3.2912 0.1123 2540.922110 0 0.8228 158 | 0/8 11 h-lim-p 0.0000 0.0000 6.8976 h-lim-p: 3.16146312e-24 2.52917050e-23 6.89757609e+00 2540.922110 .. | 0/8 12 h-lim-p 0.0000 0.0021 67.5748 2540.082973 0 0.0003 190 | 0/8 13 h-lim-p 0.0012 0.0165 18.0663 2540.022621 6 0.0004 215 | 0/8 14 h-lim-p 0.0008 0.0347 8.4286 2540.012987 4 0.0003 235 | 0/8 15 h-lim-p 0.0003 0.0025 4.5638 2540.010199 1 0.0004 249 | 0/8 16 h-lim-p 0.0050 0.6782 0.3629 2540.010156 2 0.0005 267 | 0/8 17 h-lim-p 0.0017 1.9585 0.1182 2540.010127 2 0.0015 291 | 0/8 18 h-lim-p 0.0019 0.1373 0.0914 2540.009883 0 0.0057 312 | 0/8 19 h-lim-p 0.0047 1.0334 0.1094 2540.000359 0 0.0189 334 | 0/8 20 h-lim-p 2.5000 20.0000 0.0005 2540.000008 2 0.9961 358 | 0/8 21 h-lim-p 2.5000 20.0000 0.0000 2540.000008 0 1.0938 378 | 0/8 22 h-lim-p 1.1181 20.0000 0.0000 2540.000008 0 2.2361 399 | 0/8 23 h-lim-p 0.7156 20.0000 0.0001 2540.000008 0 0.0196 423 | 0/8 24 h-lim-p 0.0002 0.4927 0.0078 .. | 0/8 25 h-lim-p 0.0000 17.6729 0.0017 2540.000008 0 0.0001 484 | 0/8 26 h-lim-p 0.0003 11.5746 0.0005 2540.000008 0 0.0011 506 | 0/8 27 h-lim-p 0.0025 20.0000 0.0002 2540.000008 0 0.0000 535 | 0/8 28 h-lim-p 0.0000 20.0000 0.0001 2540.000008 0 0.0000 565 | 0/8 29 h-lim-p 0.0000 20.0000 0.0020 2540.000008 0 0.0000 595 | 0/8 30 h-lim-p 0.0000 19.8577 0.0005 .. | 0/8 31 h-lim-p 0.0000 20.0000 0.0020 | 0/8 32 h-lim-p 0.0000 20.0000 0.0020 Out... lnL = -2540.000008 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2540.000008 Node 7: lnL = -2540.000008 Node 8: lnL = -2540.000008 Node 9: lnL = -2540.000008 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 320 Sequential format.. Reading seq # 1: YDR256C_Sbay Reading seq # 2: YDR256C_Scer Reading seq # 3: YDR256C_Skud Reading seq # 4: YDR256C_Smik Reading seq # 5: YDR256C_Spar Sequences read.. Counting patterns.. # site patterns = 110 Counting frequencies.. 120 bytes for distance 17600 bytes for lkl0 14080 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.064827 0.644269 0.261973 0.333999 0.816334 0.329004 0.609369 lnL0 = -1235.494069 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1235.494069 x= 0.00006 0.06483 0.64427 0.26197 0.33400 0.81633 0.32900 0.60937 1 h-lim-p 0.0000 0.0000 248.2966 1235.397950 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0000 219246.7243 1180.265814 m 0.0000 34 | 2/8 3 h-lim-p 0.0017 0.0139 53.8635 1128.810775 0 0.0104 48 | 2/8 4 h-lim-p 0.0008 0.0064 33.7341 1128.027023 0 0.0016 61 | 2/8 5 h-lim-p 0.0015 0.0196 36.4313 1126.191700 0 0.0044 74 | 2/8 6 h-lim-p 0.0039 0.0308 8.9618 1125.866015 0 0.0077 87 | 1/8 7 h-lim-p 0.0013 0.0102 36.2234 1125.298833 1 0.0016 101 | 1/8 8 h-lim-p 0.0603 0.4823 0.2990 1125.021212 0 0.1809 114 | 1/8 9 h-lim-p 0.0313 0.4191 1.7251 1124.970823 4 0.0246 141 | 1/8 10 h-lim-p 0.1604 1.2833 0.1610 1124.666301 0 0.9625 155 | 1/8 11 h-lim-p 1.3065 10.4516 0.0186 1124.652067 3 1.0921 180 | 1/8 12 h-lim-p 2.5000 20.0000 0.0025 1124.651542 4 1.3122 208 | 1/8 13 h-lim-p 2.5000 20.0000 0.0008 1124.651517 1 1.2500 229 | 1/8 14 h-lim-p 2.5000 20.0000 0.0001 1124.651517 0 1.0938 248 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 1124.651517 0 1.0938 267 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 1124.651517 0 2.1875 286 | 1/8 17 h-lim-p 2.0538 20.0000 0.0000 1124.651517 0 0.0070 312 Out... lnL = -1124.651517 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1124.651517 Node 7: lnL = -1124.651517 Node 8: lnL = -1124.651517 Node 9: lnL = -1124.651517 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 415 Sequential format.. Reading seq # 1: YDR258C_Sbay Reading seq # 2: YDR258C_Scer Reading seq # 3: YDR258C_Skud Reading seq # 4: YDR258C_Smik Reading seq # 5: YDR258C_Spar Sequences read.. Counting patterns.. # site patterns = 107 Counting frequencies.. 120 bytes for distance 17120 bytes for lkl0 13696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.415439 0.052186 0.413831 0.934735 4.173188 0.222715 0.844928 lnL0 = -1464.432958 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1464.432958 x= 0.00006 0.41544 0.05219 0.41383 0.93473 4.17319 0.22272 0.84493 1 h-lim-p 0.0000 0.0000 272.4941 1464.372354 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0009 257.1072 1429.767085 m 0.0009 38 | 2/8 3 h-lim-p 0.0087 0.1421 6.4680 .. | 2/8 4 h-lim-p 0.0000 0.0003 194.7353 1419.115024 m 0.0003 87 | 3/8 5 h-lim-p 0.0002 0.0032 261.1368 1370.824473 0 0.0023 102 | 3/8 6 h-lim-p 0.0072 0.0578 9.6173 1363.040821 m 0.0578 114 | 3/8 7 h-lim-p 0.0000 0.0003 3980.8074 1336.145753 0 0.0001 128 | 3/8 8 h-lim-p 0.0164 2.7658 35.6197 1334.335820 9 0.0093 163 | 3/8 9 h-lim-p 0.0974 0.7791 0.9820 1332.827128 0 0.1461 175 | 2/8 10 h-lim-p 0.0023 0.0185 40.2552 1332.241424 7 0.0025 208 | 2/8 11 h-lim-p 0.9796 7.8371 0.0533 1332.176045 7 0.6245 236 | 1/8 12 h-lim-p 0.0087 0.0693 2.2622 1332.174251 5 0.0015 269 | 1/8 13 h-lim-p 0.0803 9.2658 0.0422 .. | 1/8 14 h-lim-p 0.0000 0.3192 20.8233 1332.056017 0 0.0006 332 | 1/8 15 h-lim-p 0.0002 0.0013 5.8456 1332.043989 0 0.0006 346 | 1/8 16 h-lim-p 0.0010 0.0999 3.7539 1332.037728 0 0.0015 358 | 1/8 17 h-lim-p 0.0005 0.0039 5.2739 1331.993964 m 0.0039 370 | 2/8 18 h-lim-p 0.0183 0.1465 0.7141 1331.988173 6 0.0056 400 | 1/8 19 h-lim-p 0.0013 0.1390 2.9933 1331.980855 0 0.0027 419 | 1/8 20 h-lim-p 0.0013 0.0605 6.1142 1331.836161 0 0.0209 435 | 1/8 21 h-lim-p 0.0336 0.2687 2.3134 1331.642157 0 0.0672 448 | 1/8 22 h-lim-p 0.1808 1.4463 0.0356 1331.635439 0 0.7231 462 | 0/8 23 h-lim-p 0.0728 0.5827 0.2107 1331.635410 3 0.0014 493 | 0/8 24 h-lim-p 0.0686 2.4798 0.0042 1331.635200 0 1.0980 517 | 0/8 25 h-lim-p 1.2882 10.3058 0.0016 1331.635176 2 0.9938 541 | 0/8 26 h-lim-p 0.7543 6.0345 0.0002 1331.635176 0 0.6600 561 | 0/8 27 h-lim-p 0.0704 0.5629 0.0008 1331.635176 0 0.0000 601 | 0/8 28 h-lim-p 0.0000 16.7347 0.0001 1331.635176 0 0.0000 621 | 0/8 29 h-lim-p 0.0000 20.0000 0.0000 1331.635176 0 0.5966 655 | 0/8 30 h-lim-p 0.0236 0.6135 0.0006 1331.635176 0 0.0000 688 | 0/8 31 h-lim-p 0.0000 0.0994 0.0044 .. | 0/8 32 h-lim-p 0.0000 0.0168 0.0248 1331.635176 0 0.0013 748 | 0/8 33 h-lim-p 0.0002 0.0016 0.1505 1331.635176 0 0.0000 771 | 0/8 34 h-lim-p 0.0002 0.0723 0.0085 1331.635176 0 0.0000 802 | 0/8 35 h-lim-p 0.0000 0.4462 0.0051 1331.635176 0 0.0026 830 | 0/8 36 h-lim-p 0.0010 0.6018 0.0134 1331.635176 0 0.0008 850 | 0/8 37 h-lim-p 0.0427 20.0000 0.0003 1331.635176 0 0.1709 872 | 0/8 38 h-lim-p 0.0067 0.2602 0.0068 1331.635176 0 0.0000 902 | 0/8 39 h-lim-p 0.0002 11.4030 0.0002 1331.635176 0 0.4326 933 | 0/8 40 h-lim-p 0.5886 12.7862 0.0001 1331.635176 0 1.1772 954 | 0/8 41 h-lim-p 2.5000 20.0000 0.0000 1331.635176 0 1.0938 974 | 0/8 42 h-lim-p 0.2667 8.4220 0.0001 1331.635176 0 0.0000 1006 | 0/8 43 h-lim-p 0.0002 20.0000 0.0000 1331.635176 0 0.0000 1030 | 0/8 44 h-lim-p 0.0001 20.0000 0.0000 1331.635176 0 0.0000 1059 Out... lnL = -1331.635176 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1331.635176 Node 7: lnL = -1331.635176 Node 8: lnL = -1331.635176 Node 9: lnL = -1331.635176 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 896 Sequential format.. Reading seq # 1: YDR259C_Sbay Reading seq # 2: YDR259C_Scer Reading seq # 3: YDR259C_Skud Reading seq # 4: YDR259C_Smik Reading seq # 5: YDR259C_Spar Sequences read.. Counting patterns.. # site patterns = 202 Counting frequencies.. 120 bytes for distance 32320 bytes for lkl0 25856 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.253927 0.172844 0.184800 0.176176 0.278334 0.128105 0.304516 lnL0 = -3102.023144 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3102.023144 x= 0.00006 0.25393 0.17284 0.18480 0.17618 0.27833 0.12810 0.30452 1 h-lim-p 0.0000 0.0000 844.1691 3101.620713 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0004 779.2226 3012.687440 2 0.0003 42 | 1/8 3 h-lim-p 0.0000 0.0003 291.4467 3003.974789 m 0.0003 54 | 1/8 4 h-lim-p 0.0006 0.0049 75.3095 3001.821578 0 0.0009 66 | 1/8 5 h-lim-p 0.0004 0.0032 77.4945 3000.598730 0 0.0008 79 | 1/8 6 h-lim-p 0.0007 0.0054 28.8315 3000.200225 0 0.0014 92 | 1/8 7 h-lim-p 0.0019 0.0154 11.7583 2999.717243 0 0.0029 104 | 1/8 8 h-lim-p 0.0209 0.2012 1.6268 2944.427833 0 0.1256 118 | 1/8 9 h-lim-p 0.0606 0.4846 0.3450 2939.397624 0 0.1212 131 | 1/8 10 h-lim-p 0.7129 6.0473 0.0586 2938.220741 9 0.4066 174 | 0/8 11 h-lim-p 0.0036 0.1869 6.6385 2938.211466 5 0.0004 204 | 0/8 12 h-lim-p 0.1531 4.0252 0.0194 2938.026722 0 0.6125 218 | 0/8 13 h-lim-p 0.1828 1.4626 0.0099 2937.973356 0 0.7313 240 | 0/8 14 h-lim-p 2.5000 20.0000 0.0025 2937.969009 4 1.0519 269 | 0/8 15 h-lim-p 2.5000 20.0000 0.0002 2937.968984 2 0.7996 294 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 2937.968982 0 1.0938 314 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 2937.968982 0 1.0938 334 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 2937.968982 0 0.0011 364 Out... lnL = -2937.968982 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2937.968982 Node 7: lnL = -2937.968982 Node 8: lnL = -2937.968982 Node 9: lnL = -2937.968982 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 872 Sequential format.. Reading seq # 1: YDR261C_Sbay Reading seq # 2: YDR261C_Scer Reading seq # 3: YDR261C_Skud Reading seq # 4: YDR261C_Smik Reading seq # 5: YDR261C_Spar Sequences read.. Counting patterns.. # site patterns = 387 Counting frequencies.. 120 bytes for distance 61920 bytes for lkl0 49536 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.595366 0.678517 0.561469 0.583600 0.984653 0.428010 0.904441 lnL0 = -4706.534904 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4706.534904 x= 0.00006 0.59537 0.67852 0.56147 0.58360 0.98465 0.42801 0.90444 1 h-lim-p 0.0000 0.0000 419.5442 4706.262158 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0041 143.3669 4676.752881 2 0.0025 46 | 1/8 3 h-lim-p 0.0055 0.0437 33.5136 4605.161898 m 0.0437 58 | 1/8 4 h-lim-p -0.0000 -0.0000 32.1728 h-lim-p: -2.42500861e-19 -1.94000688e-18 3.21728484e+01 4605.161898 .. | 1/8 5 h-lim-p 0.0000 0.0007 352.3740 4557.780455 2 0.0006 87 | 1/8 6 h-lim-p 0.0064 0.0651 32.9656 4524.519842 m 0.0651 100 | 1/8 7 h-lim-p 0.0000 0.0000 4398.9801 h-lim-p: 1.36025983e-21 1.08820787e-20 4.39898009e+03 4524.519842 .. | 1/8 8 h-lim-p 0.0000 0.0014 223.6103 4487.657135 m 0.0014 125 | 2/8 9 h-lim-p 0.0001 0.0007 794.2455 4449.459519 0 0.0003 139 | 2/8 10 h-lim-p 0.0007 0.0058 108.3761 4433.466988 0 0.0029 153 | 2/8 11 h-lim-p 0.0004 0.0034 319.1758 4400.052488 0 0.0017 167 | 2/8 12 h-lim-p 0.0009 0.0072 142.2547 4390.987445 0 0.0018 180 | 2/8 13 h-lim-p 0.0132 0.1400 19.3653 4386.863901 0 0.0264 193 | 1/8 14 h-lim-p 0.0011 0.0088 213.3666 4384.905200 0 0.0022 206 | 1/8 15 h-lim-p 0.2329 1.8631 0.4183 4373.074812 0 0.6987 219 | 0/8 16 h-lim-p 0.0013 0.0103 71.7458 4368.142736 0 0.0039 239 | 0/8 17 h-lim-p 0.3364 2.6908 0.1116 4364.259197 0 0.6727 252 | 0/8 18 h-lim-p 0.4423 4.5752 0.1697 4364.001386 2 0.4147 276 | 0/8 19 h-lim-p 0.3054 3.0395 0.2305 4363.863055 7 0.2055 314 | 0/8 20 h-lim-p 1.3324 10.6592 0.0184 4363.814617 4 0.6786 343 | 0/8 21 h-lim-p 1.9180 20.0000 0.0065 4363.786369 0 2.8770 363 | 0/8 22 h-lim-p 2.5000 20.0000 0.0075 4363.773639 6 1.5568 399 | 0/8 23 h-lim-p 2.5000 20.0000 0.0032 4363.770934 3 1.0449 425 | 0/8 24 h-lim-p 2.5000 20.0000 0.0005 4363.770913 1 0.9961 447 | 0/8 25 h-lim-p 2.5000 20.0000 0.0000 4363.770913 0 1.0938 467 | 0/8 26 h-lim-p 2.5000 20.0000 0.0000 4363.770913 0 1.0938 487 | 0/8 27 h-lim-p 2.5000 20.0000 0.0000 4363.770913 0 1.0938 507 | 0/8 28 h-lim-p 2.5000 20.0000 0.0000 4363.770913 0 1.2500 527 | 0/8 29 h-lim-p 0.1309 20.0000 0.0000 4363.770913 0 0.0000 562 Out... lnL = -4363.770913 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4363.770913 Node 7: lnL = -4363.770913 Node 8: lnL = -4363.770913 Node 9: lnL = -4363.770913 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 885 Sequential format.. Reading seq # 1: YDR262W_Sbay Reading seq # 2: YDR262W_Scer Reading seq # 3: YDR262W_Skud Reading seq # 4: YDR262W_Smik Reading seq # 5: YDR262W_Spar Sequences read.. Counting patterns.. # site patterns = 490 Counting frequencies.. 120 bytes for distance 78400 bytes for lkl0 62720 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.300957 0.487198 0.448994 0.447380 0.592249 0.405378 0.707825 lnL0 = -4720.401843 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4720.401843 x= 0.00006 0.30096 0.48720 0.44899 0.44738 0.59225 0.40538 0.70782 1 h-lim-p 0.0000 0.0000 380.1514 4720.082185 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0003 1380.6301 4602.753002 m 0.0003 36 | 2/8 3 h-lim-p 0.0015 0.0123 62.5136 4596.071514 0 0.0031 49 | 2/8 4 h-lim-p 0.0035 0.0281 26.5240 4592.173798 0 0.0070 62 | 2/8 5 h-lim-p 0.0049 0.0392 16.9996 4591.468310 7 0.0035 91 | 2/8 6 h-lim-p 0.0194 0.1550 2.4655 4588.932228 0 0.0388 104 | 1/8 7 h-lim-p 0.0068 0.0542 13.6987 4576.666165 0 0.0136 117 | 1/8 8 h-lim-p 0.0007 0.0056 71.9338 4569.681476 0 0.0028 131 | 1/8 9 h-lim-p 0.0003 0.0025 15.2743 4569.382135 m 0.0025 143 | 2/8 10 h-lim-p 0.1248 6.2238 0.1157 4568.387103 0 0.4992 157 | 1/8 11 h-lim-p 0.0179 1.7030 3.2321 4568.372694 6 0.0027 192 | 1/8 12 h-lim-p 0.0941 0.7528 0.0388 4568.263298 0 0.5646 206 | 1/8 13 h-lim-p 1.3633 20.0000 0.0161 4568.253323 6 0.3902 242 | 1/8 14 h-lim-p 1.5182 12.1454 0.0039 4568.250860 2 0.7116 265 | 1/8 15 h-lim-p 2.5000 20.0000 0.0010 4568.250661 3 0.6580 291 | 1/8 16 h-lim-p 2.5000 20.0000 0.0001 4568.250661 0 1.0938 310 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 4568.250661 0 1.0938 329 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 4568.250661 0 1.0938 348 | 1/8 19 h-lim-p 2.5000 20.0000 0.0000 4568.250661 0 1.2500 367 | 1/8 20 h-lim-p 2.5000 20.0000 0.0000 4568.250661 0 1.0938 386 | 1/8 21 h-lim-p 2.0050 20.0000 0.0000 4568.250661 0 0.0000 427 Out... lnL = -4568.250661 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4568.250661 Node 7: lnL = -4568.250661 Node 8: lnL = -4568.250661 Node 9: lnL = -4568.250661 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 521 Sequential format.. Reading seq # 1: YDR263C_Sbay Reading seq # 2: YDR263C_Scer Reading seq # 3: YDR263C_Skud Reading seq # 4: YDR263C_Smik Reading seq # 5: YDR263C_Spar Sequences read.. Counting patterns.. # site patterns = 205 Counting frequencies.. 120 bytes for distance 32800 bytes for lkl0 26240 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.195011 0.209834 0.222924 0.210607 0.276261 0.208027 0.401386 lnL0 = -2403.114291 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2403.114291 x= 0.00006 0.19501 0.20983 0.22292 0.21061 0.27626 0.20803 0.40139 1 h-lim-p 0.0000 0.0000 389.3004 2402.752251 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0017 154.0513 2386.083145 8 0.0013 61 | 1/8 3 h-lim-p 0.0020 0.0161 21.4490 2385.393200 5 0.0023 84 | 1/8 4 h-lim-p 0.0087 0.0959 5.5356 2383.648147 0 0.0175 97 | 1/8 5 h-lim-p 0.0047 0.0377 9.3884 2366.442054 0 0.0188 111 | 1/8 6 h-lim-p 0.0006 0.0047 71.7080 2346.782057 0 0.0024 125 | 1/8 7 h-lim-p 0.0002 0.0020 128.8828 2342.236544 0 0.0005 138 | 1/8 8 h-lim-p 0.0007 0.0056 28.5255 2341.907623 1 0.0009 152 | 1/8 9 h-lim-p 0.1194 1.3075 0.2105 2339.803803 0 0.2388 165 | 0/8 10 h-lim-p 0.0031 1.4536 16.2211 2339.636076 5 0.0013 195 | 0/8 11 h-lim-p 1.0634 12.3063 0.0198 2339.407235 8 0.6735 228 | 0/8 12 h-lim-p 1.2475 20.0000 0.0107 2339.382894 5 0.5382 257 | 0/8 13 h-lim-p 1.2886 20.0000 0.0045 2339.379660 5 0.4643 290 | 0/8 14 h-lim-p 2.5000 20.0000 0.0007 2339.379582 3 0.3665 320 | 0/8 15 h-lim-p 2.5000 20.0000 0.0001 2339.379579 0 1.0938 340 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 2339.379579 0 1.0938 360 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 2339.379579 0 1.0938 380 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 2339.379579 0 2.1875 400 | 0/8 19 h-lim-p 1.5975 20.0000 0.0000 2339.379579 0 0.6989 420 | 0/8 20 h-lim-p 1.5391 20.0000 0.0000 2339.379579 0 0.0240 445 Out... lnL = -2339.379579 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2339.379579 Node 7: lnL = -2339.379579 Node 8: lnL = -2339.379579 Node 9: lnL = -2339.379579 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 571 Sequential format.. Reading seq # 1: YDR264C_Sbay Reading seq # 2: YDR264C_Scer Reading seq # 3: YDR264C_Skud Reading seq # 4: YDR264C_Smik Reading seq # 5: YDR264C_Spar Sequences read.. Counting patterns.. # site patterns = 239 Counting frequencies.. 120 bytes for distance 38240 bytes for lkl0 30592 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.300301 0.303318 0.297882 0.260516 0.357288 0.196307 0.443312 lnL0 = -2779.059741 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2779.059741 x= 0.00006 0.30030 0.30332 0.29788 0.26052 0.35729 0.19631 0.44331 1 h-lim-p 0.0000 0.0000 457.6719 2778.779697 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0013 365.9743 2715.087071 0 0.0010 40 | 1/8 3 h-lim-p 0.0004 0.0030 72.4481 2712.290836 0 0.0015 54 | 1/8 4 h-lim-p 0.0004 0.0031 56.9039 2711.148695 0 0.0012 67 | 1/8 5 h-lim-p 0.0056 0.0467 11.7248 2710.426861 4 0.0049 86 | 1/8 6 h-lim-p 0.0050 0.0396 8.9148 2708.620444 0 0.0099 99 | 1/8 7 h-lim-p 0.0065 0.0520 11.6606 2677.165517 0 0.0260 113 | 0/8 8 h-lim-p 0.0003 0.0027 150.7149 2666.602518 0 0.0010 126 | 0/8 9 h-lim-p 0.0004 0.0030 38.1849 2663.790189 m 0.0030 138 | 0/8 10 h-lim-p 0.2304 1.8428 0.2493 2661.206418 1 0.2879 152 | 0/8 11 h-lim-p 0.0595 0.4759 0.2707 2659.397306 0 0.2379 174 | 0/8 12 h-lim-p 0.0449 0.3594 0.1031 2658.985743 m 0.3594 194 | 1/8 13 h-lim-p 0.4673 5.6487 0.0613 2658.918948 5 0.1990 226 | 0/8 14 h-lim-p 0.0032 0.1698 3.7685 2658.882897 0 0.0065 246 | 0/8 15 h-lim-p 0.1005 0.8044 0.0409 2658.735500 0 0.4022 260 | 0/8 16 h-lim-p 0.4373 3.4984 0.0055 2658.719475 0 0.8746 281 | 0/8 17 h-lim-p 2.2083 20.0000 0.0022 2658.717609 5 0.6922 314 | 0/8 18 h-lim-p 2.5000 20.0000 0.0004 2658.717504 3 0.8800 341 | 0/8 19 h-lim-p 2.5000 20.0000 0.0001 2658.717499 0 1.0938 361 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 2658.717499 0 1.0938 381 | 0/8 21 h-lim-p 2.5000 20.0000 0.0000 2658.717499 0 2.1875 401 | 0/8 22 h-lim-p 2.4139 20.0000 0.0000 2658.717499 0 1.0561 421 | 0/8 23 h-lim-p 2.2580 20.0000 0.0000 2658.717499 0 4.5159 442 | 0/8 24 h-lim-p 0.6570 20.0000 0.0000 2658.717499 0 1.3140 463 | 0/8 25 h-lim-p 0.0421 20.0000 0.0001 2658.717499 0 0.0001 491 | 0/8 26 h-lim-p 0.0002 20.0000 0.0000 2658.717499 0 0.0000 525 | 0/8 27 h-lim-p 0.0000 20.0000 0.0003 2658.717499 0 0.0000 547 | 0/8 28 h-lim-p 0.0000 20.0000 0.0001 2658.717499 0 0.0000 576 | 0/8 29 h-lim-p 0.0000 20.0000 0.0003 | 0/8 30 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -2658.717499 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2658.717499 Node 7: lnL = -2658.717499 Node 8: lnL = -2658.717499 Node 9: lnL = -2658.717499 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 572 Sequential format.. Reading seq # 1: YDR265W_Sbay Reading seq # 2: YDR265W_Scer Reading seq # 3: YDR265W_Skud Reading seq # 4: YDR265W_Smik Reading seq # 5: YDR265W_Spar Sequences read.. Counting patterns.. # site patterns = 237 Counting frequencies.. 120 bytes for distance 37920 bytes for lkl0 30336 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.206711 0.079522 0.061136 0.176919 0.076807 0.206372 0.173450 0.150004 lnL0 = -2648.642123 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2648.642123 x= 0.20671 0.07952 0.06114 0.17692 0.07681 0.20637 0.17345 0.15000 1 h-lim-p 0.0123 2.1016 65.5703 2648.123387 5 0.0003 38 | 0/8 2 h-lim-p 0.0012 0.0100 13.8039 2648.084940 6 0.0004 64 | 0/8 3 h-lim-p 0.0009 0.0302 6.7480 2648.077034 4 0.0004 84 | 0/8 4 h-lim-p 0.0040 0.3553 0.7063 2648.076890 3 0.0006 105 | 0/8 5 h-lim-p 0.0031 2.2568 0.1360 2648.076885 1 0.0006 128 | 0/8 6 h-lim-p 0.0029 9.3647 0.0290 2648.076885 0 0.0006 149 | 0/8 7 h-lim-p 0.0081 20.0000 0.0023 2648.076885 0 0.0036 169 | 0/8 8 h-lim-p 0.0317 20.0000 0.0003 2648.076876 0 0.2537 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2648.076876 0 1.0938 212 | 0/8 10 h-lim-p 1.9876 20.0000 0.0000 2648.076876 0 0.4348 233 | 0/8 11 h-lim-p 0.2430 20.0000 0.0000 2648.076876 0 0.0038 258 | 0/8 12 h-lim-p 0.0014 20.0000 0.0000 2648.076876 0 0.0007 278 | 0/8 13 h-lim-p 0.0016 20.0000 0.0000 2648.076876 0 0.0001 301 Out... lnL = -2648.076876 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2648.076876 Node 7: lnL = -2648.076876 Node 8: lnL = -2648.076876 Node 9: lnL = -2648.076876 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 542 Sequential format.. Reading seq # 1: YDR266C_Sbay Reading seq # 2: YDR266C_Scer Reading seq # 3: YDR266C_Skud Reading seq # 4: YDR266C_Smik Reading seq # 5: YDR266C_Spar Sequences read.. Counting patterns.. # site patterns = 218 Counting frequencies.. 120 bytes for distance 34880 bytes for lkl0 27904 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.153592 0.022864 0.079086 0.152397 0.069588 0.167905 0.226930 0.105046 lnL0 = -2333.671190 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2333.671190 x= 0.15359 0.02286 0.07909 0.15240 0.06959 0.16790 0.22693 0.10505 1 h-lim-p 0.0021 0.0497 149.1494 2331.781868 8 0.0002 42 | 0/8 2 h-lim-p 0.0010 0.0080 23.5695 2331.644140 4 0.0005 62 | 0/8 3 h-lim-p 0.0006 0.0119 20.8354 2331.598358 7 0.0003 94 | 0/8 4 h-lim-p 0.0015 0.0488 4.4390 2331.595338 4 0.0003 114 | 0/8 5 h-lim-p 0.0030 0.3738 0.5013 2331.595268 2 0.0006 131 | 0/8 6 h-lim-p 0.0057 8.1852 0.0504 2331.595267 0 0.0006 153 | 0/8 7 h-lim-p 0.0205 20.0000 0.0015 2331.595232 0 0.1639 176 | 0/8 8 h-lim-p 0.0028 20.0000 0.0896 2331.594925 0 0.0056 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2331.594906 1 0.9961 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2331.594906 0 2.1875 239 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2331.594906 0 1.0938 259 | 0/8 12 h-lim-p 0.3858 20.0000 0.0000 2331.594906 0 6.1732 283 | 0/8 13 h-lim-p 2.0796 20.0000 0.0000 2331.594906 0 0.4549 304 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 2331.594906 0 0.0002 337 Out... lnL = -2331.594906 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2331.594906 Node 7: lnL = -2331.594906 Node 8: lnL = -2331.594906 Node 9: lnL = -2331.594906 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 528 Sequential format.. Reading seq # 1: YDR267C_Sbay Reading seq # 2: YDR267C_Scer Reading seq # 3: YDR267C_Skud Reading seq # 4: YDR267C_Smik Reading seq # 5: YDR267C_Spar Sequences read.. Counting patterns.. # site patterns = 207 Counting frequencies.. 120 bytes for distance 33120 bytes for lkl0 26496 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.137921 0.141728 0.127321 0.100480 0.113096 0.165379 0.205034 0.080969 lnL0 = -2442.391792 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2442.391792 x= 0.13792 0.14173 0.12732 0.10048 0.11310 0.16538 0.20503 0.08097 1 h-lim-p 0.0026 0.0208 22.9833 2442.260478 4 0.0005 31 | 0/8 2 h-lim-p 0.0020 0.0339 5.6985 2442.252572 4 0.0005 53 | 0/8 3 h-lim-p 0.0026 0.2656 1.1073 2442.252333 4 0.0004 78 | 0/8 4 h-lim-p 0.0010 0.6769 0.4442 2442.252294 2 0.0004 94 | 0/8 5 h-lim-p 0.0011 1.3350 0.1749 2442.252288 0 0.0005 114 | 0/8 6 h-lim-p 0.0101 19.6784 0.0086 2442.252288 0 0.0006 137 | 0/8 7 h-lim-p 0.0116 20.0000 0.0004 2442.252286 0 0.1389 160 | 0/8 8 h-lim-p 0.0023 19.5495 0.0250 2442.252275 0 0.0046 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2442.252275 0 1.0938 201 | 0/8 10 h-lim-p 1.1439 20.0000 0.0000 2442.252275 0 1.0010 221 | 0/8 11 h-lim-p 0.6851 20.0000 0.0000 2442.252275 0 0.0749 243 | 0/8 12 h-lim-p 0.0051 20.0000 0.0002 2442.252275 0 0.0001 268 | 0/8 13 h-lim-p 0.0010 20.0000 0.0000 2442.252275 0 0.0000 299 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 2442.252275 0 0.0000 337 Out... lnL = -2442.252275 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2442.252275 Node 7: lnL = -2442.252275 Node 8: lnL = -2442.252275 Node 9: lnL = -2442.252275 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 284 Sequential format.. Reading seq # 1: YDR272W_Sbay Reading seq # 2: YDR272W_Scer Reading seq # 3: YDR272W_Skud Reading seq # 4: YDR272W_Smik Reading seq # 5: YDR272W_Spar Sequences read.. Counting patterns.. # site patterns = 152 Counting frequencies.. 120 bytes for distance 24320 bytes for lkl0 19456 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.270909 0.056001 0.204365 0.185931 0.190276 0.268899 0.256632 0.188231 lnL0 = -1393.025619 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1393.025619 x= 0.27091 0.05600 0.20437 0.18593 0.19028 0.26890 0.25663 0.18823 1 h-lim-p 0.0081 0.0646 19.7623 1392.779400 7 0.0013 40 | 0/8 2 h-lim-p 0.0045 0.0529 5.7248 1392.744828 5 0.0022 62 | 0/8 3 h-lim-p 0.0105 0.3540 1.2250 1392.743601 4 0.0017 85 | 0/8 4 h-lim-p 0.0035 0.5188 0.6058 1392.743291 4 0.0021 108 | 0/8 5 h-lim-p 0.0182 3.5593 0.0690 1392.743285 1 0.0022 132 | 0/8 6 h-lim-p 0.0234 20.0000 0.0066 1392.743285 0 0.0026 154 | 0/8 7 h-lim-p 0.0226 20.0000 0.0007 1392.743285 0 0.0198 174 | 0/8 8 h-lim-p 0.0542 20.0000 0.0003 1392.743284 0 0.2168 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1392.743284 0 1.0938 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1392.743284 0 2.1875 236 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1392.743284 0 0.5469 257 | 0/8 12 h-lim-p 0.1190 20.0000 0.0000 1392.743284 0 0.1190 277 | 0/8 13 h-lim-p 0.0547 20.0000 0.0000 1392.743284 0 0.0137 298 | 0/8 14 h-lim-p 0.0089 20.0000 0.0000 1392.743284 0 0.0022 319 | 0/8 15 h-lim-p 0.0010 20.0000 0.0000 1392.743284 0 0.0002 340 | 0/8 16 h-lim-p 0.0010 20.0000 0.0000 1392.743284 0 0.0000 376 Out... lnL = -1392.743284 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1392.743284 Node 7: lnL = -1392.743284 Node 8: lnL = -1392.743284 Node 9: lnL = -1392.743284 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 362 Sequential format.. Reading seq # 1: YDR273W_Sbay Reading seq # 2: YDR273W_Scer Reading seq # 3: YDR273W_Skud Reading seq # 4: YDR273W_Smik Reading seq # 5: YDR273W_Spar Sequences read.. Counting patterns.. # site patterns = 188 Counting frequencies.. 120 bytes for distance 30080 bytes for lkl0 24064 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.198946 0.199402 0.157168 0.161118 0.112717 0.203813 0.222358 0.125345 lnL0 = -1794.972556 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1794.972556 x= 0.19895 0.19940 0.15717 0.16112 0.11272 0.20381 0.22236 0.12534 1 h-lim-p 0.0006 0.0045 32.8770 1794.490872 0 0.0011 23 | 0/8 2 h-lim-p 0.0029 0.0453 12.7045 1794.443793 2 0.0007 40 | 0/8 3 h-lim-p 0.0021 0.0648 4.2050 1794.432772 6 0.0014 67 | 0/8 4 h-lim-p 0.0081 0.9523 0.7250 1794.432284 2 0.0018 84 | 0/8 5 h-lim-p 0.0040 0.7008 0.3191 1794.432159 2 0.0017 108 | 0/8 6 h-lim-p 0.0094 8.3658 0.0594 1794.430815 0 0.0375 130 | 0/8 7 h-lim-p 0.0053 0.9955 0.4217 1794.420104 0 0.0106 151 | 0/8 8 h-lim-p 0.0021 0.2263 2.1033 1794.409530 1 0.0027 173 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 1794.409340 3 1.0004 191 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1794.409340 0 1.0938 211 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1794.409340 0 1.0938 231 | 0/8 12 h-lim-p 1.1928 20.0000 0.0000 1794.409340 0 0.1491 253 | 0/8 13 h-lim-p 0.0298 20.0000 0.0000 1794.409340 0 0.0000 282 | 0/8 14 h-lim-p 0.0003 20.0000 0.0000 1794.409340 0 0.0000 313 Out... lnL = -1794.409340 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1794.409340 Node 7: lnL = -1794.409340 Node 8: lnL = -1794.409340 Node 9: lnL = -1794.409340 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 326 Sequential format.. Reading seq # 1: YDR275W_Sbay Reading seq # 2: YDR275W_Scer Reading seq # 3: YDR275W_Skud Reading seq # 4: YDR275W_Smik Reading seq # 5: YDR275W_Spar Sequences read.. Counting patterns.. # site patterns = 129 Counting frequencies.. 120 bytes for distance 20640 bytes for lkl0 16512 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.168174 0.062904 0.036824 0.086348 0.074572 0.132581 0.150976 0.126232 lnL0 = -1283.200932 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1283.200932 x= 0.16817 0.06290 0.03682 0.08635 0.07457 0.13258 0.15098 0.12623 1 h-lim-p 0.0014 0.0113 66.6579 1282.492347 7 0.0003 36 | 0/8 2 h-lim-p 0.0007 0.0054 25.8670 1282.338500 5 0.0005 58 | 0/8 3 h-lim-p 0.0016 0.0187 8.1758 1282.318065 3 0.0007 76 | 0/8 4 h-lim-p 0.0025 0.0514 2.2364 1282.317074 5 0.0004 103 | 0/8 5 h-lim-p 0.0016 0.2000 0.5876 1282.316986 3 0.0005 122 | 0/8 6 h-lim-p 0.0092 3.4574 0.0344 1282.316986 1 0.0006 147 | 0/8 7 h-lim-p 0.0018 20.0000 0.0108 1282.316985 0 0.0036 168 | 0/8 8 h-lim-p 0.0280 20.0000 0.0014 1282.316829 0 0.2243 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1282.316826 1 0.9961 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1282.316826 0 1.0938 233 | 0/8 11 h-lim-p 1.3086 20.0000 0.0000 1282.316826 0 3.9258 254 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1282.316826 0 0.3125 276 | 0/8 13 h-lim-p 0.0980 20.0000 0.0000 1282.316826 0 0.0015 301 | 0/8 14 h-lim-p 0.0007 20.0000 0.0000 1282.316826 0 0.0001 323 Out... lnL = -1282.316826 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1282.316826 Node 7: lnL = -1282.316826 Node 8: lnL = -1282.316826 Node 9: lnL = -1282.316826 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 907 Sequential format.. Reading seq # 1: YDR276C_Sbay Reading seq # 2: YDR276C_Scer Reading seq # 3: YDR276C_Skud Reading seq # 4: YDR276C_Smik Reading seq # 5: YDR276C_Spar Sequences read.. Counting patterns.. # site patterns = 263 Counting frequencies.. 120 bytes for distance 42080 bytes for lkl0 33664 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.204078 0.042063 0.039185 0.082334 0.063829 0.174178 0.183604 0.157469 lnL0 = -3662.210693 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3662.210693 x= 0.20408 0.04206 0.03918 0.08233 0.06383 0.17418 0.18360 0.15747 1 h-lim-p 0.0005 0.0042 198.6418 3659.907802 8 0.0001 38 | 0/8 2 h-lim-p 0.0002 0.0018 55.6993 3659.548194 6 0.0002 64 | 0/8 3 h-lim-p 0.0004 0.0059 37.5453 3659.446682 7 0.0002 92 | 0/8 4 h-lim-p 0.0004 0.0108 16.8107 3659.428615 5 0.0002 116 | 0/8 5 h-lim-p 0.0014 0.1631 1.9803 3659.428157 4 0.0002 140 | 0/8 6 h-lim-p 0.0006 0.2967 0.8285 3659.428074 1 0.0003 154 | 0/8 7 h-lim-p 0.0025 2.9033 0.0947 3659.428071 0 0.0005 175 | 0/8 8 h-lim-p 0.0734 20.0000 0.0007 3659.426624 0 1.1740 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3659.426564 2 0.9961 223 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3659.426564 0 1.0938 243 | 0/8 11 h-lim-p 1.4226 20.0000 0.0000 3659.426564 0 1.2448 263 | 0/8 12 h-lim-p 1.2013 20.0000 0.0000 3659.426564 0 0.2253 285 | 0/8 13 h-lim-p 0.0322 20.0000 0.0000 3659.426564 0 0.0000 323 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 3659.426564 0 0.0000 357 Out... lnL = -3659.426564 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3659.426564 Node 7: lnL = -3659.426564 Node 8: lnL = -3659.426564 Node 9: lnL = -3659.426564 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 843 Sequential format.. Reading seq # 1: YDR277C_Sbay Reading seq # 2: YDR277C_Scer Reading seq # 3: YDR277C_Skud Reading seq # 4: YDR277C_Smik Reading seq # 5: YDR277C_Spar Sequences read.. Counting patterns.. # site patterns = 254 Counting frequencies.. 120 bytes for distance 40640 bytes for lkl0 32512 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.140062 0.048373 0.048511 0.088190 0.071855 0.162150 0.160349 0.099131 lnL0 = -3491.838929 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3491.838929 x= 0.14006 0.04837 0.04851 0.08819 0.07185 0.16215 0.16035 0.09913 1 h-lim-p 0.0017 0.0413 201.6768 3489.637636 7 0.0001 39 | 0/8 2 h-lim-p 0.0004 0.0030 30.7280 3489.545411 6 0.0002 64 | 0/8 3 h-lim-p 0.0006 0.0255 10.1414 3489.536584 5 0.0002 89 | 0/8 4 h-lim-p 0.0004 0.0354 4.9460 3489.534594 4 0.0002 110 | 0/8 5 h-lim-p 0.0017 0.5723 0.5897 3489.534554 3 0.0002 130 | 0/8 6 h-lim-p 0.0009 0.9897 0.1477 3489.534551 0 0.0002 151 | 0/8 7 h-lim-p 0.0021 15.3898 0.0140 3489.534551 0 0.0009 171 | 0/8 8 h-lim-p 0.0326 20.0000 0.0004 3489.534400 0 0.5213 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3489.534399 0 1.0938 215 | 0/8 10 h-lim-p 2.1870 20.0000 0.0000 3489.534399 0 0.9568 235 | 0/8 11 h-lim-p 0.9856 20.0000 0.0000 3489.534399 0 0.4928 255 | 0/8 12 h-lim-p 0.1048 20.0000 0.0000 3489.534399 0 0.0393 276 | 0/8 13 h-lim-p 0.0129 20.0000 0.0001 3489.534399 0 0.0000 314 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -3489.534399 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3489.534399 Node 7: lnL = -3489.534399 Node 8: lnL = -3489.534399 Node 9: lnL = -3489.534399 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 859 Sequential format.. Reading seq # 1: YDR279W_Sbay Reading seq # 2: YDR279W_Scer Reading seq # 3: YDR279W_Skud Reading seq # 4: YDR279W_Smik Reading seq # 5: YDR279W_Spar Sequences read.. Counting patterns.. # site patterns = 443 Counting frequencies.. 120 bytes for distance 70880 bytes for lkl0 56704 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.384334 0.143436 0.211877 0.256532 0.159102 0.356924 0.510807 0.267807 lnL0 = -4868.211176 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4868.211176 x= 0.38433 0.14344 0.21188 0.25653 0.15910 0.35692 0.51081 0.26781 1 h-lim-p 0.0024 0.0190 37.3743 4867.526587 5 0.0010 34 | 0/8 2 h-lim-p 0.0017 0.0133 16.8619 4867.434223 2 0.0008 50 | 0/8 3 h-lim-p 0.0011 0.0439 12.3713 4867.384727 2 0.0010 66 | 0/8 4 h-lim-p 0.0035 0.1352 3.4966 4867.378368 5 0.0012 91 | 0/8 5 h-lim-p 0.0077 1.1231 0.5454 4867.378067 3 0.0021 110 | 0/8 6 h-lim-p 0.0113 7.2319 0.0995 4867.378059 1 0.0014 134 | 0/8 7 h-lim-p 0.0051 20.0000 0.0272 4867.378054 0 0.0077 154 | 0/8 8 h-lim-p 0.1511 20.0000 0.0014 4867.377784 0 0.6043 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4867.377775 0 1.0938 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4867.377775 0 1.0938 216 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4867.377775 0 1.2500 236 | 0/8 12 h-lim-p 1.6829 20.0000 0.0000 4867.377775 0 0.2104 258 | 0/8 13 h-lim-p 0.0983 20.0000 0.0000 4867.377775 0 0.0983 278 | 0/8 14 h-lim-p 0.0542 20.0000 0.0000 4867.377775 0 0.0000 313 Out... lnL = -4867.377775 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4867.377775 Node 7: lnL = -4867.377775 Node 8: lnL = -4867.377775 Node 9: lnL = -4867.377775 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 357 Sequential format.. Reading seq # 1: YDR280W_Sbay Reading seq # 2: YDR280W_Scer Reading seq # 3: YDR280W_Skud Reading seq # 4: YDR280W_Smik Reading seq # 5: YDR280W_Spar Sequences read.. Counting patterns.. # site patterns = 181 Counting frequencies.. 120 bytes for distance 28960 bytes for lkl0 23168 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.232142 0.094457 0.136249 0.120840 0.115183 0.434719 0.228373 0.155083 lnL0 = -1750.149894 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1750.149894 x= 0.23214 0.09446 0.13625 0.12084 0.11518 0.43472 0.22837 0.15508 1 h-lim-p 0.0014 0.0111 28.2165 1749.621376 5 0.0014 33 | 0/8 2 h-lim-p 0.0010 0.0081 20.5764 1749.489734 5 0.0008 56 | 0/8 3 h-lim-p 0.0021 0.0348 8.1210 1749.469520 6 0.0008 81 | 0/8 4 h-lim-p 0.0030 0.2847 2.1006 1749.466144 5 0.0017 106 | 0/8 5 h-lim-p 0.0031 0.3365 1.1443 1749.465323 4 0.0016 127 | 0/8 6 h-lim-p 0.0035 0.7633 0.5266 1749.465188 3 0.0012 147 | 0/8 7 h-lim-p 0.0067 2.9072 0.0974 1749.465181 0 0.0015 168 | 0/8 8 h-lim-p 1.7877 20.0000 0.0001 1749.465176 1 0.8799 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1749.465176 0 1.0938 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1749.465176 0 2.1875 231 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1749.465176 0 1.0938 251 | 0/8 12 h-lim-p 0.4180 20.0000 0.0000 1749.465176 0 5.0157 274 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1749.465176 0 0.1562 297 | 0/8 14 h-lim-p 1.6347 20.0000 0.0000 1749.465176 0 0.0016 326 Out... lnL = -1749.465176 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1749.465176 Node 7: lnL = -1749.465176 Node 8: lnL = -1749.465176 Node 9: lnL = -1749.465176 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 907 Sequential format.. Reading seq # 1: YDR281C_Sbay Reading seq # 2: YDR281C_Scer Reading seq # 3: YDR281C_Skud Reading seq # 4: YDR281C_Smik Reading seq # 5: YDR281C_Spar Sequences read.. Counting patterns.. # site patterns = 338 Counting frequencies.. 120 bytes for distance 54080 bytes for lkl0 43264 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.220556 0.000060 0.168283 0.155039 0.185774 0.259724 0.212974 0.154328 lnL0 = -4246.653116 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4246.653116 x= 0.22056 0.00006 0.16828 0.15504 0.18577 0.25972 0.21297 0.15433 1 h-lim-p 0.0000 0.0000 150.6493 4246.287082 m 0.0000 22 | 1/8 2 h-lim-p 0.0001 0.0114 32.8046 4246.067555 0 0.0005 36 | 1/8 3 h-lim-p 0.0038 0.0626 3.8707 4246.057597 5 0.0007 59 | 0/8 4 h-lim-p 0.0002 0.0362 15.5569 4246.036719 2 0.0002 75 | 0/8 5 h-lim-p 0.0026 0.2876 1.1388 4245.900778 0 0.0102 89 | 0/8 6 h-lim-p 0.0016 0.0130 3.7782 4241.659505 m 0.0130 101 | 1/8 7 h-lim-p 0.0008 0.0064 57.8677 4240.700450 8 0.0005 134 | 1/8 8 h-lim-p 0.0083 0.0920 3.7948 4240.696497 4 0.0005 158 | 1/8 9 h-lim-p 0.1024 10.8375 0.0195 4240.372376 0 0.8192 173 | 1/8 10 h-lim-p 2.5000 20.0000 0.0026 4240.366876 3 1.0449 198 | 1/8 11 h-lim-p 2.5000 20.0000 0.0003 4240.366811 3 0.8800 224 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 4240.366811 0 1.0938 243 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 4240.366811 0 1.0938 262 | 1/8 14 h-lim-p 1.1055 20.0000 0.0000 4240.366811 0 0.0691 284 | 1/8 15 h-lim-p 0.0152 20.0000 0.0000 4240.366811 0 0.0303 304 | 1/8 16 h-lim-p 0.0176 20.0000 0.0000 4240.366811 0 0.0000 345 | 1/8 17 h-lim-p 0.0000 20.0000 0.0002 | 1/8 18 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -4240.366811 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4240.366811 Node 7: lnL = -4240.366811 Node 8: lnL = -4240.366811 Node 9: lnL = -4240.366811 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 336 Sequential format.. Reading seq # 1: YDR282C_Sbay Reading seq # 2: YDR282C_Scer Reading seq # 3: YDR282C_Skud Reading seq # 4: YDR282C_Smik Reading seq # 5: YDR282C_Spar Sequences read.. Counting patterns.. # site patterns = 193 Counting frequencies.. 120 bytes for distance 30880 bytes for lkl0 24704 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.265858 0.253705 0.147590 0.140030 0.100960 0.333577 0.246149 0.165905 lnL0 = -1683.150706 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1683.150706 x= 0.26586 0.25371 0.14759 0.14003 0.10096 0.33358 0.24615 0.16590 1 h-lim-p 0.0006 0.0051 22.6065 1682.891915 0 0.0013 23 | 0/8 2 h-lim-p 0.0021 0.0386 13.8787 1682.823544 3 0.0009 41 | 0/8 3 h-lim-p 0.0029 0.0693 4.5488 1682.804506 6 0.0021 68 | 0/8 4 h-lim-p 0.0104 2.3771 0.9206 1682.803448 2 0.0024 85 | 0/8 5 h-lim-p 0.0040 0.5027 0.5600 1682.803114 4 0.0024 116 | 0/8 6 h-lim-p 0.0187 6.4676 0.0713 1682.802725 2 0.0163 140 | 0/8 7 h-lim-p 0.0059 1.9901 0.1973 1682.797756 0 0.0236 162 | 0/8 8 h-lim-p 0.0075 0.7356 0.6241 1682.788235 0 0.0112 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0012 1682.787953 3 1.0004 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1682.787953 0 1.0938 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1682.787953 0 1.0938 248 | 0/8 12 h-lim-p 1.3643 20.0000 0.0000 1682.787953 0 5.4573 270 | 0/8 13 h-lim-p 2.2052 20.0000 0.0000 1682.787953 0 0.2757 292 | 0/8 14 h-lim-p 2.1480 20.0000 0.0000 1682.787953 0 0.0000 339 Out... lnL = -1682.787953 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1682.787953 Node 7: lnL = -1682.787953 Node 8: lnL = -1682.787953 Node 9: lnL = -1682.787953 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 848 Sequential format.. Reading seq # 1: YDR284C_Sbay Reading seq # 2: YDR284C_Scer Reading seq # 3: YDR284C_Skud Reading seq # 4: YDR284C_Smik Reading seq # 5: YDR284C_Spar Sequences read.. Counting patterns.. # site patterns = 373 Counting frequencies.. 120 bytes for distance 59680 bytes for lkl0 47744 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.321809 0.097480 0.213577 0.192636 0.181740 0.079689 0.494948 0.216494 lnL0 = -4200.338990 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4200.338990 x= 0.32181 0.09748 0.21358 0.19264 0.18174 0.07969 0.49495 0.21649 1 h-lim-p 0.0022 0.0234 196.0439 4192.687276 7 0.0005 39 | 0/8 2 h-lim-p 0.0008 0.0061 43.8773 4191.457004 0 0.0015 52 | 0/8 3 h-lim-p 0.0006 0.0051 50.3982 4191.119319 4 0.0005 72 | 0/8 4 h-lim-p 0.0018 0.0457 13.4394 4191.038935 7 0.0011 100 | 0/8 5 h-lim-p 0.0036 0.0990 4.0294 4191.030104 5 0.0012 125 | 0/8 6 h-lim-p 0.0051 0.5846 0.9442 4191.029229 4 0.0018 147 | 0/8 7 h-lim-p 0.0026 0.9946 0.6614 4191.028436 1 0.0032 169 | 0/8 8 h-lim-p 0.1106 20.0000 0.0191 4190.956572 0 0.4425 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0033 4190.945076 5 1.4109 223 | 0/8 10 h-lim-p 2.5000 20.0000 0.0010 4190.944422 3 1.2347 250 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4190.944421 0 1.0938 270 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4190.944421 0 1.0938 290 | 0/8 13 h-lim-p 1.6298 20.0000 0.0000 4190.944421 0 1.6298 310 | 0/8 14 h-lim-p 1.8528 20.0000 0.0000 4190.944421 0 1.3896 330 | 0/8 15 h-lim-p 0.3112 20.0000 0.0000 4190.944421 0 0.1556 350 | 0/8 16 h-lim-p 0.0202 20.0000 0.0001 4190.944421 0 0.0000 385 | 0/8 17 h-lim-p 0.0006 20.0000 0.0000 4190.944421 0 0.0000 415 Out... lnL = -4190.944421 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4190.944421 Node 7: lnL = -4190.944421 Node 8: lnL = -4190.944421 Node 9: lnL = -4190.944421 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 865 Sequential format.. Reading seq # 1: YDR285W_Sbay Reading seq # 2: YDR285W_Scer Reading seq # 3: YDR285W_Skud Reading seq # 4: YDR285W_Smik Reading seq # 5: YDR285W_Spar Sequences read.. Counting patterns.. # site patterns = 393 Counting frequencies.. 120 bytes for distance 62880 bytes for lkl0 50304 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.265718 0.182388 0.127927 0.180298 0.156307 0.189825 0.432009 0.165715 lnL0 = -4364.205082 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4364.205082 x= 0.26572 0.18239 0.12793 0.18030 0.15631 0.18983 0.43201 0.16572 1 h-lim-p 0.0019 0.0153 58.8806 4363.022140 7 0.0007 40 | 0/8 2 h-lim-p 0.0007 0.0059 30.3164 4362.719691 6 0.0008 66 | 0/8 3 h-lim-p 0.0018 0.0303 13.3117 4362.689095 2 0.0004 83 | 0/8 4 h-lim-p 0.0011 0.0622 4.9294 4362.683182 4 0.0006 105 | 0/8 5 h-lim-p 0.0025 0.4912 1.1366 4362.682625 4 0.0009 126 | 0/8 6 h-lim-p 0.0018 1.1107 0.5901 4362.682469 3 0.0011 146 | 0/8 7 h-lim-p 0.0038 1.7752 0.1757 4362.682447 2 0.0015 170 | 0/8 8 h-lim-p 0.1398 20.0000 0.0018 4362.680585 0 1.1182 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4362.680570 1 0.9961 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4362.680570 0 1.0938 235 | 0/8 11 h-lim-p 1.8125 20.0000 0.0000 4362.680570 0 1.5860 255 | 0/8 12 h-lim-p 2.1980 20.0000 0.0000 4362.680570 0 0.9616 275 | 0/8 13 h-lim-p 0.3807 20.0000 0.0000 4362.680570 0 0.1903 295 | 0/8 14 h-lim-p 0.0241 20.0000 0.0001 4362.680570 0 0.0211 315 | 0/8 15 h-lim-p 0.0050 20.0000 0.0002 4362.680570 0 0.0000 341 | 0/8 16 h-lim-p 0.0016 20.0000 0.0000 4362.680570 0 0.0016 361 | 0/8 17 h-lim-p 0.0009 20.0000 0.0000 4362.680570 0 0.0001 384 Out... lnL = -4362.680570 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4362.680570 Node 7: lnL = -4362.680570 Node 8: lnL = -4362.680570 Node 9: lnL = -4362.680570 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 522 Sequential format.. Reading seq # 1: YDR287W_Sbay Reading seq # 2: YDR287W_Scer Reading seq # 3: YDR287W_Skud Reading seq # 4: YDR287W_Smik Reading seq # 5: YDR287W_Spar Sequences read.. Counting patterns.. # site patterns = 239 Counting frequencies.. 120 bytes for distance 38240 bytes for lkl0 30592 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.215285 0.169758 0.160081 0.155945 0.144413 0.099650 0.293653 0.132485 lnL0 = -2290.826378 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2290.826378 x= 0.21529 0.16976 0.16008 0.15595 0.14441 0.09965 0.29365 0.13248 1 h-lim-p 0.0022 0.0173 54.9956 2289.694181 9 0.0008 44 | 0/8 2 h-lim-p 0.0011 0.0087 22.4249 2289.453292 6 0.0011 69 | 0/8 3 h-lim-p 0.0024 0.0447 10.0427 2289.419941 6 0.0008 95 | 0/8 4 h-lim-p 0.0020 0.0987 4.0750 2289.412172 5 0.0011 119 | 0/8 5 h-lim-p 0.0054 0.2781 0.8455 2289.411796 3 0.0011 138 | 0/8 6 h-lim-p 0.0638 20.0000 0.0150 2289.411795 0 0.0035 161 | 0/8 7 h-lim-p 0.0211 20.0000 0.0025 2289.411466 0 0.3383 185 | 0/8 8 h-lim-p 0.0061 3.7678 0.1376 2289.411450 2 0.0016 210 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2289.411449 0 1.0938 230 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2289.411449 0 1.0938 250 | 0/8 11 h-lim-p 1.8125 20.0000 0.0000 2289.411449 0 1.5859 270 | 0/8 12 h-lim-p 2.3701 20.0000 0.0000 2289.411449 0 0.0370 295 | 0/8 13 h-lim-p 0.0106 20.0000 0.0000 2289.411449 0 0.0026 316 | 0/8 14 h-lim-p 0.0009 20.0000 0.0000 2289.411449 0 0.0000 343 | 0/8 15 h-lim-p 0.0004 20.0000 0.0000 2289.411449 0 0.0000 368 Out... lnL = -2289.411449 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2289.411449 Node 7: lnL = -2289.411449 Node 8: lnL = -2289.411449 Node 9: lnL = -2289.411449 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 362 Sequential format.. Reading seq # 1: YDR288W_Sbay Reading seq # 2: YDR288W_Scer Reading seq # 3: YDR288W_Skud Reading seq # 4: YDR288W_Smik Reading seq # 5: YDR288W_Spar Sequences read.. Counting patterns.. # site patterns = 197 Counting frequencies.. 120 bytes for distance 31520 bytes for lkl0 25216 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.188545 0.194424 0.078365 0.185409 0.154499 0.278778 0.298545 0.101422 lnL0 = -1726.624892 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1726.624892 x= 0.18854 0.19442 0.07837 0.18541 0.15450 0.27878 0.29854 0.10142 1 h-lim-p 0.0171 2.5644 44.9830 1725.821069 6 0.0009 36 | 0/8 2 h-lim-p 0.0031 0.0332 12.6009 1725.695826 7 0.0017 64 | 0/8 3 h-lim-p 0.0028 0.0584 7.4259 1725.674141 7 0.0010 94 | 0/8 4 h-lim-p 0.0109 0.4614 0.7025 1725.673606 3 0.0022 113 | 0/8 5 h-lim-p 0.0053 0.7991 0.2919 1725.673551 3 0.0014 140 | 0/8 6 h-lim-p 0.0094 6.9451 0.0438 1725.673549 0 0.0021 161 | 0/8 7 h-lim-p 0.0076 20.0000 0.0119 1725.673541 0 0.0151 182 | 0/8 8 h-lim-p 0.0261 20.0000 0.0069 1725.673170 0 0.1569 204 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1725.673158 1 0.9961 226 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1725.673158 0 1.0938 246 | 0/8 11 h-lim-p 1.3824 20.0000 0.0000 1725.673158 0 0.0864 269 | 0/8 12 h-lim-p 0.0269 20.0000 0.0000 1725.673158 0 0.0202 289 | 0/8 13 h-lim-p 0.0090 20.0000 0.0000 1725.673158 0 0.0022 310 | 0/8 14 h-lim-p 0.0001 20.0000 0.0004 1725.673158 0 0.0001 330 | 0/8 15 h-lim-p 0.0021 20.0000 0.0000 1725.673158 0 0.0000 355 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 1725.673158 0 0.0000 388 Out... lnL = -1725.673158 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1725.673158 Node 7: lnL = -1725.673158 Node 8: lnL = -1725.673158 Node 9: lnL = -1725.673158 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 232 Sequential format.. Reading seq # 1: YDR289C_Sbay Reading seq # 2: YDR289C_Scer Reading seq # 3: YDR289C_Skud Reading seq # 4: YDR289C_Smik Reading seq # 5: YDR289C_Spar Sequences read.. Counting patterns.. # site patterns = 46 Counting frequencies.. 120 bytes for distance 7360 bytes for lkl0 5888 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.256256 0.671755 0.000060 0.754883 1.925732 1.903497 0.459888 0.054132 lnL0 = -793.041104 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 793.041104 x= 0.25626 0.67176 0.00006 0.75488 1.92573 1.90350 0.45989 0.05413 1 h-lim-p 0.0000 0.0000 140.3185 793.001508 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0001 1507.2665 775.055597 m 0.0001 35 | 2/8 3 h-lim-p 0.0000 0.0000 28448.9071 742.687456 m 0.0000 47 | 2/8 4 h-lim-p 0.0005 0.0040 66.5859 738.005343 0 0.0020 61 | 1/8 5 h-lim-p 0.0001 0.0011 271.1875 726.657428 0 0.0006 75 | 1/8 6 h-lim-p 0.0437 0.3500 0.1971 723.597528 m 0.3500 87 | 1/8 7 h-lim-p 0.0000 0.0000 1.2626 h-lim-p: 9.29964193e-20 7.43971354e-19 1.26256902e+00 723.597528 .. | 1/8 8 h-lim-p 0.0000 0.0037 121.2707 687.298898 0 0.0031 122 | 1/8 9 h-lim-p 0.0001 0.0008 62.4253 686.426381 m 0.0008 134 | 1/8 10 h-lim-p 0.1113 0.8906 0.2153 686.378298 2 0.0522 150 | 0/8 11 h-lim-p 0.0001 0.0010 23.9662 686.111265 m 0.0010 169 | 0/8 12 h-lim-p 1.0781 8.6245 0.0083 686.111094 2 0.1263 187 | 0/8 13 h-lim-p 0.0909 2.3485 0.0115 686.109950 0 0.1817 208 | 0/8 14 h-lim-p 2.5000 20.0000 0.0002 686.109939 2 0.9961 232 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 686.109939 0 1.0938 252 | 0/8 16 h-lim-p 1.1214 20.0000 0.0000 686.109939 0 0.9812 272 | 0/8 17 h-lim-p 0.0193 0.5395 0.0011 686.109939 0 0.0000 306 | 0/8 18 h-lim-p 0.0000 4.0928 0.0002 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 686.109939 0 0.0000 374 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 | 0/8 21 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -686.109939 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -686.109939 Node 7: lnL = -686.109939 Node 8: lnL = -686.109939 Node 9: lnL = -686.109939 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 742 Sequential format.. Reading seq # 1: YDR292C_Sbay Reading seq # 2: YDR292C_Scer Reading seq # 3: YDR292C_Skud Reading seq # 4: YDR292C_Smik Reading seq # 5: YDR292C_Spar Sequences read.. Counting patterns.. # site patterns = 272 Counting frequencies.. 120 bytes for distance 43520 bytes for lkl0 34816 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.167569 0.035944 0.053256 0.110748 0.106749 0.180127 0.199295 0.113058 lnL0 = -3126.603811 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3126.603811 x= 0.16757 0.03594 0.05326 0.11075 0.10675 0.18013 0.19929 0.11306 1 h-lim-p 0.0006 0.0051 134.7386 3125.254918 8 0.0002 38 | 0/8 2 h-lim-p 0.0006 0.0052 27.2782 3125.154779 4 0.0003 57 | 0/8 3 h-lim-p 0.0015 0.0271 5.1949 3125.151104 4 0.0003 78 | 0/8 4 h-lim-p 0.0012 0.1380 1.2236 3125.150891 2 0.0003 95 | 0/8 5 h-lim-p 0.0048 3.0815 0.0752 3125.150890 0 0.0005 109 | 0/8 6 h-lim-p 0.0012 4.6098 0.0320 3125.150890 0 0.0005 129 | 0/8 7 h-lim-p 0.0042 20.0000 0.0041 3125.150890 0 0.0037 149 | 0/8 8 h-lim-p 0.0128 20.0000 0.0012 3125.150835 0 0.1538 172 | 0/8 9 h-lim-p 1.4075 20.0000 0.0001 3125.150832 1 1.1216 194 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3125.150832 0 1.0938 214 | 0/8 11 h-lim-p 0.7079 20.0000 0.0000 3125.150832 0 0.6194 234 | 0/8 12 h-lim-p 0.4398 20.0000 0.0000 3125.150832 0 0.2199 254 | 0/8 13 h-lim-p 0.1147 20.0000 0.0000 3125.150832 0 0.0287 275 | 0/8 14 h-lim-p 0.0148 20.0000 0.0000 3125.150832 0 0.0074 295 | 0/8 15 h-lim-p 0.0055 20.0000 0.0001 3125.150832 0 0.0000 336 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 3125.150832 0 0.0000 366 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 | 0/8 18 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -3125.150832 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3125.150832 Node 7: lnL = -3125.150832 Node 8: lnL = -3125.150832 Node 9: lnL = -3125.150832 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 858 Sequential format.. Reading seq # 1: YDR293C_Sbay Reading seq # 2: YDR293C_Scer Reading seq # 3: YDR293C_Skud Reading seq # 4: YDR293C_Smik Reading seq # 5: YDR293C_Spar Sequences read.. Counting patterns.. # site patterns = 239 Counting frequencies.. 120 bytes for distance 38240 bytes for lkl0 30592 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.114751 0.058740 0.065928 0.063934 0.066346 0.103805 0.180581 0.072243 lnL0 = -3335.295113 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3335.295113 x= 0.11475 0.05874 0.06593 0.06393 0.06635 0.10381 0.18058 0.07224 1 h-lim-p 0.0005 0.0039 120.7393 3334.309372 7 0.0001 38 | 0/8 2 h-lim-p 0.0007 0.0058 24.4442 3334.266743 5 0.0001 62 | 0/8 3 h-lim-p 0.0005 0.0190 7.4114 3334.263765 3 0.0001 82 | 0/8 4 h-lim-p 0.0008 0.1517 1.1353 3334.263673 2 0.0001 99 | 0/8 5 h-lim-p 0.0008 2.1904 0.1995 3334.263666 0 0.0004 111 | 0/8 6 h-lim-p 0.0028 4.2032 0.0266 3334.263666 0 0.0002 134 | 0/8 7 h-lim-p 0.0006 19.8898 0.0068 3334.263666 0 0.0005 154 | 0/8 8 h-lim-p 0.0144 20.0000 0.0002 3334.263632 0 0.4599 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3334.263631 0 1.0938 199 | 0/8 10 h-lim-p 1.8067 20.0000 0.0000 3334.263631 0 0.7904 219 | 0/8 11 h-lim-p 0.7703 20.0000 0.0000 3334.263631 0 0.0026 246 | 0/8 12 h-lim-p 0.0013 20.0000 0.0000 3334.263631 0 0.0000 286 | 0/8 13 h-lim-p 0.0000 20.0000 0.0028 | 0/8 14 h-lim-p 0.0000 20.0000 0.0028 Out... lnL = -3334.263631 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3334.263631 Node 7: lnL = -3334.263631 Node 8: lnL = -3334.263631 Node 9: lnL = -3334.263631 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 429 Sequential format.. Reading seq # 1: YDR294C_Sbay Reading seq # 2: YDR294C_Scer Reading seq # 3: YDR294C_Skud Reading seq # 4: YDR294C_Smik Reading seq # 5: YDR294C_Spar Sequences read.. Counting patterns.. # site patterns = 180 Counting frequencies.. 120 bytes for distance 28800 bytes for lkl0 23040 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.214596 0.050204 0.107918 0.099499 0.096759 0.155292 0.220943 0.151236 lnL0 = -1919.828453 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1919.828453 x= 0.21460 0.05020 0.10792 0.09950 0.09676 0.15529 0.22094 0.15124 1 h-lim-p 0.0021 0.0171 54.8186 1919.181678 7 0.0004 39 | 0/8 2 h-lim-p 0.0020 0.0158 9.6813 1919.147139 5 0.0008 61 | 0/8 3 h-lim-p 0.0026 0.0512 2.7880 1919.145489 5 0.0005 86 | 0/8 4 h-lim-p 0.0009 0.0755 1.4509 1919.144897 3 0.0007 104 | 0/8 5 h-lim-p 0.0019 0.7444 0.5318 1919.144815 3 0.0007 123 | 0/8 6 h-lim-p 0.0022 1.3608 0.1618 1919.144808 0 0.0006 144 | 0/8 7 h-lim-p 0.0072 19.3419 0.0125 1919.144808 0 0.0016 165 | 0/8 8 h-lim-p 0.2839 20.0000 0.0001 1919.144803 0 1.1356 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1919.144803 0 1.0938 207 | 0/8 10 h-lim-p 2.1070 20.0000 0.0000 1919.144803 0 0.4609 228 | 0/8 11 h-lim-p 0.2792 20.0000 0.0000 1919.144803 0 0.0001 258 Out... lnL = -1919.144803 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1919.144803 Node 7: lnL = -1919.144803 Node 8: lnL = -1919.144803 Node 9: lnL = -1919.144803 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 589 Sequential format.. Reading seq # 1: YDR295C_Sbay Reading seq # 2: YDR295C_Scer Reading seq # 3: YDR295C_Skud Reading seq # 4: YDR295C_Smik Reading seq # 5: YDR295C_Spar Sequences read.. Counting patterns.. # site patterns = 224 Counting frequencies.. 120 bytes for distance 35840 bytes for lkl0 28672 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.218239 0.048742 0.072290 0.100492 0.082479 0.210669 0.214363 0.155536 lnL0 = -2632.569185 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2632.569185 x= 0.21824 0.04874 0.07229 0.10049 0.08248 0.21067 0.21436 0.15554 1 h-lim-p 0.0002 0.0016 123.3059 2630.541902 0 0.0003 22 | 0/8 2 h-lim-p 0.0012 0.0099 26.2373 2630.354428 3 0.0006 40 | 0/8 3 h-lim-p 0.0008 0.0223 17.4395 2630.324334 4 0.0003 62 | 0/8 4 h-lim-p 0.0007 0.0270 7.1275 2630.317760 4 0.0003 84 | 0/8 5 h-lim-p 0.0012 0.1324 1.9543 2630.316731 3 0.0006 103 | 0/8 6 h-lim-p 0.0032 0.4695 0.3592 2630.316696 2 0.0005 122 | 0/8 7 h-lim-p 0.0031 3.7731 0.0601 2630.316647 0 0.0047 142 | 0/8 8 h-lim-p 0.0177 7.1724 0.0159 2630.307182 0 0.1415 165 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 2630.306988 2 0.9961 189 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2630.306988 0 1.0938 209 | 0/8 11 h-lim-p 1.5959 20.0000 0.0000 2630.306988 0 2.3938 229 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2630.306988 0 0.2734 251 | 0/8 13 h-lim-p 0.0596 20.0000 0.0000 2630.306988 0 0.0298 271 | 0/8 14 h-lim-p 0.0140 20.0000 0.0000 2630.306988 0 0.0000 310 Out... lnL = -2630.306988 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2630.306988 Node 7: lnL = -2630.306988 Node 8: lnL = -2630.306988 Node 9: lnL = -2630.306988 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 590 Sequential format.. Reading seq # 1: YDR296W_Sbay Reading seq # 2: YDR296W_Scer Reading seq # 3: YDR296W_Skud Reading seq # 4: YDR296W_Smik Reading seq # 5: YDR296W_Spar Sequences read.. Counting patterns.. # site patterns = 221 Counting frequencies.. 120 bytes for distance 35360 bytes for lkl0 28288 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.211073 0.114857 0.074288 0.103587 0.084109 0.202412 0.164779 0.139044 lnL0 = -2642.762619 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2642.762619 x= 0.21107 0.11486 0.07429 0.10359 0.08411 0.20241 0.16478 0.13904 1 h-lim-p 0.0003 0.0027 107.0630 2641.046450 2 0.0003 26 | 0/8 2 h-lim-p 0.0007 0.0057 27.7881 2640.888812 8 0.0004 60 | 0/8 3 h-lim-p 0.0006 0.0128 21.3381 2640.841991 6 0.0003 85 | 0/8 4 h-lim-p 0.0015 0.0383 4.4164 2640.838233 5 0.0004 111 | 0/8 5 h-lim-p 0.0016 0.2338 1.1537 2640.837816 2 0.0007 127 | 0/8 6 h-lim-p 0.0212 5.7305 0.0381 2640.837815 0 0.0012 142 | 0/8 7 h-lim-p 0.0050 20.0000 0.0087 2640.837810 0 0.0101 163 | 0/8 8 h-lim-p 0.0071 20.0000 0.0125 2640.837368 0 0.0566 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 2640.837345 1 0.9961 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2640.837345 0 1.0938 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2640.837345 0 1.0938 248 | 0/8 12 h-lim-p 0.5909 20.0000 0.0000 2640.837345 0 0.0023 275 | 0/8 13 h-lim-p 0.0016 20.0000 0.0000 2640.837345 0 0.0008 295 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 2640.837345 0 0.0000 315 | 0/8 15 h-lim-p 0.0009 20.0000 0.0000 2640.837345 0 0.0000 339 Out... lnL = -2640.837345 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2640.837345 Node 7: lnL = -2640.837345 Node 8: lnL = -2640.837345 Node 9: lnL = -2640.837345 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 706 Sequential format.. Reading seq # 1: YDR297W_Sbay Reading seq # 2: YDR297W_Scer Reading seq # 3: YDR297W_Skud Reading seq # 4: YDR297W_Smik Reading seq # 5: YDR297W_Spar Sequences read.. Counting patterns.. # site patterns = 135 Counting frequencies.. 120 bytes for distance 21600 bytes for lkl0 17280 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.241132 0.000060 0.123418 0.061282 0.052976 4.819230 0.106198 0.013906 lnL0 = -2267.203362 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2267.203362 x= 0.24113 0.00006 0.12342 0.06128 0.05298 4.81923 0.10620 0.01391 1 h-lim-p 0.0001 0.0009 153.3514 2263.453450 0 0.0003 23 | 0/8 2 h-lim-p 0.0003 0.0026 70.8634 2263.172110 6 0.0001 49 | 0/8 3 h-lim-p 0.0004 0.0045 24.2144 2263.139973 7 0.0001 80 | 0/8 4 h-lim-p 0.0009 0.0071 2.9479 2263.138757 4 0.0003 102 | 0/8 5 h-lim-p 0.0067 0.0562 0.1244 2263.138722 2 0.0011 121 | 0/8 6 h-lim-p 0.0003 0.0136 0.5371 2263.133151 m 0.0136 144 | 0/8 7 h-lim-p 0.0000 0.0000 0.0964 h-lim-p: 5.52589819e-19 4.42071855e-18 9.64419434e-02 2263.133151 .. | 0/8 8 h-lim-p 0.0000 0.0106 12.7569 2263.118302 0 0.0002 184 | 0/8 9 h-lim-p 0.0000 0.0001 6.5142 2263.115602 m 0.0001 196 | 1/8 10 h-lim-p 0.0002 0.0178 3.4403 2263.114674 2 0.0002 212 | 1/8 11 h-lim-p 0.0022 0.3058 0.3133 2263.114641 3 0.0003 234 | 1/8 12 h-lim-p 0.0008 1.7262 0.1300 2263.114418 0 0.0031 255 | 1/8 13 h-lim-p 0.0023 0.7512 0.1730 2263.114411 2 0.0004 280 | 1/8 14 h-lim-p 0.1669 20.0000 0.0004 2263.114030 0 1.0011 301 | 1/8 15 h-lim-p 2.5000 20.0000 0.0001 2263.114029 0 1.0938 320 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 2263.114029 0 1.0938 339 | 1/8 17 h-lim-p 0.6795 20.0000 0.0000 2263.114029 0 0.5096 358 | 1/8 18 h-lim-p 0.0061 17.0513 0.0030 2263.114029 0 0.0000 395 | 1/8 19 h-lim-p 0.0000 20.0000 0.0000 2263.114029 0 0.0000 419 Out... lnL = -2263.114029 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2263.114029 Node 7: lnL = -2263.114029 Node 8: lnL = -2263.114029 Node 9: lnL = -2263.114029 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 825 Sequential format.. Reading seq # 1: YDR298C_Sbay Reading seq # 2: YDR298C_Scer Reading seq # 3: YDR298C_Skud Reading seq # 4: YDR298C_Smik Reading seq # 5: YDR298C_Spar Sequences read.. Counting patterns.. # site patterns = 199 Counting frequencies.. 120 bytes for distance 31840 bytes for lkl0 25472 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.174166 0.000060 0.112327 0.203978 0.057877 0.305612 0.287545 0.098389 lnL0 = -3016.174454 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3016.174454 x= 0.17417 0.00006 0.11233 0.20398 0.05788 0.30561 0.28754 0.09839 1 h-lim-p 0.0000 0.0000 175.6182 3015.949065 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0040 89.7068 3014.473277 0 0.0005 39 | 1/8 3 h-lim-p 0.0012 0.0103 35.5882 3014.249548 7 0.0004 68 | 1/8 4 h-lim-p 0.0009 0.0069 15.1811 3014.209691 2 0.0004 84 | 1/8 5 h-lim-p 0.0012 0.2806 5.0417 3013.974664 0 0.0196 100 | 1/8 6 h-lim-p 0.0019 0.0231 50.7053 3013.722544 4 0.0015 120 | 1/8 7 h-lim-p 0.4539 3.7053 0.1678 3008.272454 0 0.6809 132 | 0/8 8 h-lim-p 0.0117 10.1677 9.7367 3008.249398 6 0.0005 169 | 0/8 9 h-lim-p 0.1448 1.1581 0.0118 3008.156972 m 1.1581 181 | 1/8 10 h-lim-p 2.5000 20.0000 0.0040 3008.142384 6 1.4444 216 | 1/8 11 h-lim-p 2.5000 20.0000 0.0017 3008.142270 1 0.9961 237 | 1/8 12 h-lim-p 2.5000 20.0000 0.0002 3008.142265 1 0.9961 258 | 1/8 13 h-lim-p 2.2765 20.0000 0.0001 3008.142264 0 1.1383 277 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 3008.142264 0 1.0938 296 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 3008.142264 0 1.0938 315 | 1/8 16 h-lim-p 1.1665 20.0000 0.0000 3008.142264 0 3.4996 335 | 1/8 17 h-lim-p 0.6798 20.0000 0.0000 3008.142264 0 0.0159 359 | 1/8 18 h-lim-p 0.0024 20.0000 0.0002 3008.142264 0 0.0000 389 | 1/8 19 h-lim-p 0.0002 20.0000 0.0000 3008.142264 0 0.0000 411 Out... lnL = -3008.142264 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3008.142264 Node 7: lnL = -3008.142264 Node 8: lnL = -3008.142264 Node 9: lnL = -3008.142264 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 836 Sequential format.. Reading seq # 1: YDR299W_Sbay Reading seq # 2: YDR299W_Scer Reading seq # 3: YDR299W_Skud Reading seq # 4: YDR299W_Smik Reading seq # 5: YDR299W_Spar Sequences read.. Counting patterns.. # site patterns = 303 Counting frequencies.. 120 bytes for distance 48480 bytes for lkl0 38784 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.181766 0.121241 0.022133 0.191716 0.181885 0.314288 0.212945 0.097244 lnL0 = -3462.608231 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3462.608231 x= 0.18177 0.12124 0.02213 0.19172 0.18189 0.31429 0.21295 0.09724 1 h-lim-p 0.0006 0.0045 81.6644 3461.359471 8 0.0004 43 | 0/8 2 h-lim-p 0.0005 0.0041 55.6912 3460.874631 5 0.0004 65 | 0/8 3 h-lim-p 0.0010 0.0195 22.6546 3460.762691 6 0.0005 90 | 0/8 4 h-lim-p 0.0009 0.0238 13.9358 3460.708791 4 0.0008 109 | 0/8 5 h-lim-p 0.0028 0.0986 3.8472 3460.704289 4 0.0007 131 | 0/8 6 h-lim-p 0.0063 0.2361 0.4177 3460.704229 1 0.0007 147 | 0/8 7 h-lim-p 0.0072 5.3933 0.0403 3460.704223 2 0.0023 172 | 0/8 8 h-lim-p 0.0198 16.5409 0.0047 3460.702296 0 0.3164 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3460.702288 1 0.9961 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3460.702288 0 1.0938 238 | 0/8 11 h-lim-p 1.3151 20.0000 0.0000 3460.702288 0 1.3151 258 | 0/8 12 h-lim-p 0.8076 20.0000 0.0000 3460.702288 0 3.2305 280 | 0/8 13 h-lim-p 0.0179 20.0000 0.0034 3460.702288 0 0.0005 304 | 0/8 14 h-lim-p 0.0003 20.0000 0.0056 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0006 3460.702288 0 0.0000 366 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0006 | 0/8 18 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -3460.702288 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3460.702288 Node 7: lnL = -3460.702288 Node 8: lnL = -3460.702288 Node 9: lnL = -3460.702288 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 496 Sequential format.. Reading seq # 1: YDR303C_Sbay Reading seq # 2: YDR303C_Scer Reading seq # 3: YDR303C_Skud Reading seq # 4: YDR303C_Smik Reading seq # 5: YDR303C_Spar Sequences read.. Counting patterns.. # site patterns = 65 Counting frequencies.. 120 bytes for distance 10400 bytes for lkl0 8320 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.043175 0.130359 0.000060 0.110097 0.028323 0.061059 0.075151 0.018722 lnL0 = -1501.970963 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1501.970963 x= 0.04318 0.13036 0.00006 0.11010 0.02832 0.06106 0.07515 0.01872 1 h-lim-p 0.0000 0.0000 1029.7846 1501.743926 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0000 1304.5555 1472.556258 m 0.0000 34 | 2/8 3 h-lim-p 0.0000 0.0000 20418.2030 1454.622405 m 0.0000 46 | 3/8 4 h-lim-p 0.0005 0.0041 38.4253 1454.409364 8 0.0003 80 | 3/8 5 h-lim-p 0.0011 0.0172 8.9906 1454.239476 3 0.0010 98 | 3/8 6 h-lim-p 0.0052 0.6279 1.7634 1440.776853 0 0.0414 113 | 3/8 7 h-lim-p 0.5860 4.6877 0.0334 1438.780360 0 0.8789 125 | 3/8 8 h-lim-p 2.5000 20.0000 0.0072 1438.690030 7 0.7695 160 | 3/8 9 h-lim-p 2.5000 20.0000 0.0014 1438.674511 6 1.8676 191 | 3/8 10 h-lim-p 2.5000 20.0000 0.0005 1438.674060 5 0.8624 221 | 3/8 11 h-lim-p 2.5000 20.0000 0.0000 1438.674059 0 1.0938 238 | 3/8 12 h-lim-p 2.5000 20.0000 0.0000 1438.674059 0 1.0938 255 | 3/8 13 h-lim-p 1.0955 20.0000 0.0000 1438.674059 0 2.1909 273 | 3/8 14 h-lim-p 2.5000 20.0000 0.0000 1438.674059 0 0.3125 292 | 3/8 15 h-lim-p 0.0306 20.0000 0.0000 1438.674059 0 0.0077 310 | 3/8 16 h-lim-p 0.0030 20.0000 0.0000 1438.674059 0 0.0060 328 | 3/8 17 h-lim-p 0.0037 20.0000 0.0000 1438.674059 0 0.0000 363 | 3/8 18 h-lim-p 0.0000 20.0000 0.0006 | 3/8 19 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -1438.674059 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1438.674059 Node 7: lnL = -1438.674059 Node 8: lnL = -1438.674059 Node 9: lnL = -1438.674059 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 226 Sequential format.. Reading seq # 1: YDR304C_Sbay Reading seq # 2: YDR304C_Scer Reading seq # 3: YDR304C_Skud Reading seq # 4: YDR304C_Smik Reading seq # 5: YDR304C_Spar Sequences read.. Counting patterns.. # site patterns = 90 Counting frequencies.. 120 bytes for distance 14400 bytes for lkl0 11520 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.180746 0.036566 0.063246 0.104282 0.016669 0.152149 0.164657 0.126530 lnL0 = -869.308462 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 869.308462 x= 0.18075 0.03657 0.06325 0.10428 0.01667 0.15215 0.16466 0.12653 1 h-lim-p 0.0014 0.0115 52.9698 869.051130 7 0.0002 39 | 0/8 2 h-lim-p 0.0003 0.0046 30.7653 868.885458 0 0.0005 51 | 0/8 3 h-lim-p 0.0024 0.0191 6.2185 868.870342 7 0.0008 82 | 0/8 4 h-lim-p 0.0015 0.0620 3.4206 868.866796 4 0.0008 103 | 0/8 5 h-lim-p 0.0049 0.4573 0.5274 868.866671 4 0.0009 125 | 0/8 6 h-lim-p 0.0022 0.9588 0.2163 868.866647 0 0.0011 145 | 0/8 7 h-lim-p 0.1076 20.0000 0.0022 868.863499 0 0.8608 168 | 0/8 8 h-lim-p 0.0374 3.9020 0.0508 868.863497 1 0.0011 194 | 0/8 9 h-lim-p 0.3875 20.0000 0.0002 868.863474 0 1.1624 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 868.863474 0 1.0938 235 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 868.863474 0 2.1875 255 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 868.863474 0 1.0938 275 | 0/8 13 h-lim-p 0.8878 20.0000 0.0000 868.863474 0 3.5511 297 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 868.863474 0 0.0006 328 Out... lnL = -868.863474 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -868.863474 Node 7: lnL = -868.863474 Node 8: lnL = -868.863474 Node 9: lnL = -868.863474 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 735 Sequential format.. Reading seq # 1: YDR306C_Sbay Reading seq # 2: YDR306C_Scer Reading seq # 3: YDR306C_Skud Reading seq # 4: YDR306C_Smik Reading seq # 5: YDR306C_Spar Sequences read.. Counting patterns.. # site patterns = 303 Counting frequencies.. 120 bytes for distance 48480 bytes for lkl0 38784 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.228400 0.036714 0.076935 0.175045 0.120668 0.236931 0.240831 0.148373 lnL0 = -3587.999829 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3587.999829 x= 0.22840 0.03671 0.07694 0.17504 0.12067 0.23693 0.24083 0.14837 1 h-lim-p 0.0019 0.6500 193.4008 3584.373999 3 0.0002 30 | 0/8 2 h-lim-p 0.0020 0.0156 20.8246 3584.236787 5 0.0006 54 | 0/8 3 h-lim-p 0.0013 0.0291 10.1090 3584.218451 4 0.0004 76 | 0/8 4 h-lim-p 0.0017 0.0728 2.6297 3584.216973 4 0.0005 98 | 0/8 5 h-lim-p 0.0078 1.2396 0.1581 3584.216966 1 0.0005 115 | 0/8 6 h-lim-p 0.0028 11.0725 0.0272 3584.216965 0 0.0007 136 | 0/8 7 h-lim-p 0.0059 20.0000 0.0032 3584.216962 0 0.0238 158 | 0/8 8 h-lim-p 0.0072 20.0000 0.0105 3584.216808 0 0.0290 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3584.216804 0 1.0938 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3584.216804 0 1.0938 220 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3584.216804 0 1.0938 240 | 0/8 12 h-lim-p 0.8705 20.0000 0.0000 3584.216804 0 1.7411 261 | 0/8 13 h-lim-p 0.0146 20.0000 0.0006 3584.216804 0 0.0000 302 | 0/8 14 h-lim-p 0.0003 20.0000 0.0000 3584.216804 0 0.0000 331 Out... lnL = -3584.216804 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3584.216804 Node 7: lnL = -3584.216804 Node 8: lnL = -3584.216804 Node 9: lnL = -3584.216804 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 737 Sequential format.. Reading seq # 1: YDR307W_Sbay Reading seq # 2: YDR307W_Scer Reading seq # 3: YDR307W_Skud Reading seq # 4: YDR307W_Smik Reading seq # 5: YDR307W_Spar Sequences read.. Counting patterns.. # site patterns = 296 Counting frequencies.. 120 bytes for distance 47360 bytes for lkl0 37888 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.182511 0.107757 0.090320 0.162825 0.126051 0.220001 0.212293 0.103480 lnL0 = -3441.866787 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3441.866787 x= 0.18251 0.10776 0.09032 0.16282 0.12605 0.22000 0.21229 0.10348 1 h-lim-p 0.0038 0.0511 134.6225 3439.221306 6 0.0003 37 | 0/8 2 h-lim-p 0.0012 0.0098 27.8563 3439.030052 3 0.0005 55 | 0/8 3 h-lim-p 0.0016 0.0451 8.9107 3439.013936 6 0.0004 83 | 0/8 4 h-lim-p 0.0019 0.1530 2.1169 3439.012657 4 0.0006 105 | 0/8 5 h-lim-p 0.0042 0.9619 0.3069 3439.012632 2 0.0006 123 | 0/8 6 h-lim-p 0.0031 3.5817 0.0548 3439.012630 1 0.0008 146 | 0/8 7 h-lim-p 0.0021 20.0000 0.0195 3439.012622 0 0.0043 167 | 0/8 8 h-lim-p 0.0086 20.0000 0.0097 3439.011606 0 0.1029 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3439.011591 1 0.9961 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3439.011591 0 1.0938 232 | 0/8 11 h-lim-p 1.2548 20.0000 0.0000 3439.011591 0 1.2548 252 | 0/8 12 h-lim-p 0.2479 20.0000 0.0000 3439.011591 0 0.0620 273 | 0/8 13 h-lim-p 0.0133 20.0000 0.0002 3439.011591 0 0.0002 298 | 0/8 14 h-lim-p 0.0012 20.0000 0.0000 3439.011591 0 0.0001 321 | 0/8 15 h-lim-p 0.0021 20.0000 0.0000 3439.011591 0 0.0000 352 Out... lnL = -3439.011591 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3439.011591 Node 7: lnL = -3439.011591 Node 8: lnL = -3439.011591 Node 9: lnL = -3439.011591 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 707 Sequential format.. Reading seq # 1: YDR308C_Sbay Reading seq # 2: YDR308C_Scer Reading seq # 3: YDR308C_Skud Reading seq # 4: YDR308C_Smik Reading seq # 5: YDR308C_Spar Sequences read.. Counting patterns.. # site patterns = 250 Counting frequencies.. 120 bytes for distance 40000 bytes for lkl0 32000 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.147167 0.084599 0.117433 0.128835 0.068539 0.211217 0.188316 0.078935 lnL0 = -3037.120704 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3037.120704 x= 0.14717 0.08460 0.11743 0.12884 0.06854 0.21122 0.18832 0.07893 1 h-lim-p 0.0143 1.9112 65.2454 3036.542264 8 0.0003 46 | 0/8 2 h-lim-p 0.0009 0.0073 13.5834 3036.519800 6 0.0003 72 | 0/8 3 h-lim-p 0.0008 0.0358 4.4216 3036.517153 4 0.0003 92 | 0/8 4 h-lim-p 0.0011 0.1994 1.2122 3036.516798 2 0.0005 108 | 0/8 5 h-lim-p 0.0037 1.3764 0.1686 3036.516792 0 0.0005 122 | 0/8 6 h-lim-p 0.0019 6.1203 0.0405 3036.516792 0 0.0008 142 | 0/8 7 h-lim-p 0.0053 20.0000 0.0064 3036.516792 0 0.0023 162 | 0/8 8 h-lim-p 0.0367 20.0000 0.0004 3036.516755 0 0.4401 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3036.516754 0 1.0938 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3036.516754 0 1.0938 225 | 0/8 11 h-lim-p 1.4091 20.0000 0.0000 3036.516754 0 2.8183 246 | 0/8 12 h-lim-p 1.5605 20.0000 0.0000 3036.516754 0 0.0731 270 | 0/8 13 h-lim-p 0.0041 20.0000 0.0004 3036.516754 0 0.0041 290 | 0/8 14 h-lim-p 0.0013 20.0000 0.0011 3036.516754 0 0.0000 328 | 0/8 15 h-lim-p 0.0000 20.0000 0.0011 | 0/8 16 h-lim-p 0.0000 20.0000 0.0011 Out... lnL = -3036.516754 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3036.516754 Node 7: lnL = -3036.516754 Node 8: lnL = -3036.516754 Node 9: lnL = -3036.516754 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 883 Sequential format.. Reading seq # 1: YDR309C_Sbay Reading seq # 2: YDR309C_Scer Reading seq # 3: YDR309C_Skud Reading seq # 4: YDR309C_Smik Reading seq # 5: YDR309C_Spar Sequences read.. Counting patterns.. # site patterns = 226 Counting frequencies.. 120 bytes for distance 36160 bytes for lkl0 28928 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.130391 0.051972 0.033835 0.072241 0.057722 0.152701 0.133031 0.084389 lnL0 = -3298.451237 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3298.451237 x= 0.13039 0.05197 0.03383 0.07224 0.05772 0.15270 0.13303 0.08439 1 h-lim-p 0.0002 0.0018 176.9019 3296.852586 5 0.0001 32 | 0/8 2 h-lim-p 0.0002 0.0016 44.8116 3296.724149 6 0.0001 57 | 0/8 3 h-lim-p 0.0005 0.0135 11.6649 3296.717068 3 0.0001 76 | 0/8 4 h-lim-p 0.0004 0.0456 3.2979 3296.716061 4 0.0002 97 | 0/8 5 h-lim-p 0.0008 0.1355 0.7894 3296.716014 2 0.0002 114 | 0/8 6 h-lim-p 0.0009 2.3115 0.1396 3296.716011 1 0.0002 137 | 0/8 7 h-lim-p 0.0048 20.0000 0.0065 3296.716011 0 0.0021 157 | 0/8 8 h-lim-p 0.0238 20.0000 0.0006 3296.715928 0 0.2856 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3296.715925 0 1.0938 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3296.715925 0 1.2500 220 | 0/8 11 h-lim-p 1.3186 20.0000 0.0000 3296.715925 0 0.0824 243 | 0/8 12 h-lim-p 0.0367 20.0000 0.0000 3296.715925 0 0.0001 271 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 3296.715925 0 0.0000 294 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 3296.715925 0 0.0000 316 Out... lnL = -3296.715925 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3296.715925 Node 7: lnL = -3296.715925 Node 8: lnL = -3296.715925 Node 9: lnL = -3296.715925 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 767 Sequential format.. Reading seq # 1: YDR310C_Sbay Reading seq # 2: YDR310C_Scer Reading seq # 3: YDR310C_Skud Reading seq # 4: YDR310C_Smik Reading seq # 5: YDR310C_Spar Sequences read.. Counting patterns.. # site patterns = 200 Counting frequencies.. 120 bytes for distance 32000 bytes for lkl0 25600 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.142037 0.043282 0.058427 0.097591 0.058007 0.146659 0.133736 0.092182 lnL0 = -3150.418952 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3150.418952 x= 0.14204 0.04328 0.05843 0.09759 0.05801 0.14666 0.13374 0.09218 1 h-lim-p 0.0002 0.0019 148.3956 3149.125643 9 0.0001 41 | 0/8 2 h-lim-p 0.0009 0.0094 21.0585 3149.072553 7 0.0002 71 | 0/8 3 h-lim-p 0.0008 0.0381 6.7655 3149.069755 4 0.0001 94 | 0/8 4 h-lim-p 0.0004 0.0576 2.3259 3149.069345 2 0.0002 110 | 0/8 5 h-lim-p 0.0015 0.8577 0.2619 3149.069336 2 0.0003 127 | 0/8 6 h-lim-p 0.0025 6.7861 0.0311 3149.069336 0 0.0005 148 | 0/8 7 h-lim-p 0.0039 20.0000 0.0043 3149.069336 0 0.0004 170 | 0/8 8 h-lim-p 0.0171 20.0000 0.0001 3149.069325 0 0.5458 195 | 0/8 9 h-lim-p 2.3352 20.0000 0.0000 3149.069325 0 1.0217 215 | 0/8 10 h-lim-p 2.3424 20.0000 0.0000 3149.069325 0 2.3424 235 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3149.069325 0 0.0049 263 Out... lnL = -3149.069325 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3149.069325 Node 7: lnL = -3149.069325 Node 8: lnL = -3149.069325 Node 9: lnL = -3149.069325 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 182 Sequential format.. Reading seq # 1: YDR315C_Sbay Reading seq # 2: YDR315C_Scer Reading seq # 3: YDR315C_Skud Reading seq # 4: YDR315C_Smik Reading seq # 5: YDR315C_Spar Sequences read.. Counting patterns.. # site patterns = 108 Counting frequencies.. 120 bytes for distance 17280 bytes for lkl0 13824 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.139478 0.177115 0.126186 0.168054 0.074026 0.228240 0.117754 0.063951 lnL0 = -824.412355 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 824.412355 x= 0.13948 0.17711 0.12619 0.16805 0.07403 0.22824 0.11775 0.06395 1 h-lim-p 0.0076 0.0608 28.3070 823.890988 9 0.0014 44 | 0/8 2 h-lim-p 0.0028 0.0221 10.2631 823.814967 8 0.0016 76 | 0/8 3 h-lim-p 0.0022 0.0213 7.5204 823.784392 7 0.0016 106 | 0/8 4 h-lim-p 0.0048 0.0785 2.4479 823.780331 6 0.0016 132 | 0/8 5 h-lim-p 0.0124 0.9518 0.3178 823.780202 1 0.0027 147 | 0/8 6 h-lim-p 0.0092 2.5598 0.0938 823.780188 2 0.0029 172 | 0/8 7 h-lim-p 0.0094 14.5447 0.0293 823.780181 2 0.0073 196 | 0/8 8 h-lim-p 0.0635 20.0000 0.0034 823.779643 0 0.5077 219 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 823.779633 1 0.9961 241 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 823.779633 0 1.0938 261 | 0/8 11 h-lim-p 1.4561 20.0000 0.0000 823.779633 0 0.3640 282 | 0/8 12 h-lim-p 0.1125 20.0000 0.0000 823.779633 0 0.0281 303 | 0/8 13 h-lim-p 0.0113 20.0000 0.0000 823.779633 0 0.0113 323 | 0/8 14 h-lim-p 0.0050 20.0000 0.0001 823.779633 0 0.0000 359 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 823.779633 0 0.0000 382 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -823.779633 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -823.779633 Node 7: lnL = -823.779633 Node 8: lnL = -823.779633 Node 9: lnL = -823.779633 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 822 Sequential format.. Reading seq # 1: YDR318W_Sbay Reading seq # 2: YDR318W_Scer Reading seq # 3: YDR318W_Skud Reading seq # 4: YDR318W_Smik Reading seq # 5: YDR318W_Spar Sequences read.. Counting patterns.. # site patterns = 336 Counting frequencies.. 120 bytes for distance 53760 bytes for lkl0 43008 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.165412 0.115585 0.000060 0.966318 0.197949 0.234710 0.173876 0.047132 lnL0 = -3889.180815 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3889.180815 x= 0.16541 0.11559 0.00006 0.96632 0.19795 0.23471 0.17388 0.04713 1 h-lim-p 0.0000 0.0000 262.1088 3889.124318 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0065 64.0157 3888.059791 0 0.0006 40 | 1/8 3 h-lim-p 0.0012 0.0168 33.6222 3887.524446 2 0.0011 56 | 1/8 4 h-lim-p 0.0010 0.0279 39.9738 3886.710679 0 0.0019 69 | 1/8 5 h-lim-p 0.0026 0.0211 24.7364 3886.580082 7 0.0007 99 | 1/8 6 h-lim-p 0.0105 0.1439 1.7491 3886.503551 7 0.0063 129 | 1/8 7 h-lim-p 0.0070 0.1427 1.5756 3877.665433 9 0.0946 166 | 0/8 8 h-lim-p 0.0008 0.0067 15.7833 3877.644450 5 0.0004 189 | 0/8 9 h-lim-p 0.2567 2.0537 0.0170 3877.582687 0 0.5134 202 | 0/8 10 h-lim-p 0.2822 2.2577 0.0073 3877.576386 0 1.1288 224 | 0/8 11 h-lim-p 2.5000 20.0000 0.0013 3877.575808 3 0.9482 250 | 0/8 12 h-lim-p 2.5000 20.0000 0.0004 3877.575787 0 1.0938 270 | 0/8 13 h-lim-p 2.5000 20.0000 0.0001 3877.575785 0 1.0938 290 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 3877.575785 0 1.0938 310 | 0/8 15 h-lim-p 1.5511 20.0000 0.0000 3877.575785 0 1.3572 330 | 0/8 16 h-lim-p 1.1474 20.0000 0.0000 3877.575785 0 1.0040 350 | 0/8 17 h-lim-p 0.6842 20.0000 0.0000 3877.575785 0 0.0374 373 | 0/8 18 h-lim-p 0.0015 20.0000 0.0007 3877.575785 0 0.0008 393 | 0/8 19 h-lim-p 0.0001 15.1527 0.0051 3877.575785 0 0.0001 413 | 0/8 20 h-lim-p 0.0007 20.0000 0.0007 3877.575785 0 0.0000 440 | 0/8 21 h-lim-p 0.0001 20.0000 0.0000 3877.575785 0 0.0000 474 | 0/8 22 h-lim-p 0.0000 20.0000 0.0003 3877.575785 0 0.0000 502 | 0/8 23 h-lim-p 0.0000 20.0000 0.0004 .. | 0/8 24 h-lim-p 0.0000 20.0000 0.0003 | 0/8 25 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -3877.575785 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3877.575785 Node 7: lnL = -3877.575785 Node 8: lnL = -3877.575785 Node 9: lnL = -3877.575785 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 281 Sequential format.. Reading seq # 1: YDR319C_Sbay Reading seq # 2: YDR319C_Scer Reading seq # 3: YDR319C_Skud Reading seq # 4: YDR319C_Smik Reading seq # 5: YDR319C_Spar Sequences read.. Counting patterns.. # site patterns = 135 Counting frequencies.. 120 bytes for distance 21600 bytes for lkl0 17280 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.272632 0.034314 0.021569 0.143263 0.052648 0.315486 0.307445 0.181347 lnL0 = -1329.236349 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1329.236349 x= 0.27263 0.03431 0.02157 0.14326 0.05265 0.31549 0.30744 0.18135 1 h-lim-p 0.0003 0.0023 46.4843 1328.520306 0 0.0006 23 | 0/8 2 h-lim-p 0.0002 0.0018 29.1112 1328.370861 0 0.0004 36 | 0/8 3 h-lim-p 0.0004 0.0033 11.7302 1328.311052 0 0.0012 49 | 0/8 4 h-lim-p 0.0007 0.0215 21.0472 1328.275576 6 0.0004 76 | 0/8 5 h-lim-p 0.0029 0.0277 3.2381 1328.271306 5 0.0009 100 | 0/8 6 h-lim-p 0.0034 0.5101 0.8935 1328.270352 4 0.0024 122 | 0/8 7 h-lim-p 0.0196 4.4480 0.1090 1328.269744 5 0.0139 153 | 0/8 8 h-lim-p 0.0260 1.3358 0.0584 1328.229443 0 0.1562 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 1328.229295 3 1.0004 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1328.229295 0 1.0938 221 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1328.229295 0 0.6250 242 | 0/8 12 h-lim-p 0.5055 20.0000 0.0000 1328.229295 0 0.0948 264 | 0/8 13 h-lim-p 0.0575 20.0000 0.0000 1328.229295 0 0.0000 304 Out... lnL = -1328.229295 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1328.229295 Node 7: lnL = -1328.229295 Node 8: lnL = -1328.229295 Node 9: lnL = -1328.229295 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 238 Sequential format.. Reading seq # 1: YDR320C-A_Sbay Reading seq # 2: YDR320C-A_Scer Reading seq # 3: YDR320C-A_Skud Reading seq # 4: YDR320C-A_Smik Reading seq # 5: YDR320C-A_Spar Sequences read.. Counting patterns.. # site patterns = 108 Counting frequencies.. 120 bytes for distance 17280 bytes for lkl0 13824 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.216738 0.000060 0.037774 0.116704 0.085057 0.186500 0.219905 0.148593 lnL0 = -983.527769 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 983.527769 x= 0.21674 0.00006 0.03777 0.11670 0.08506 0.18650 0.21991 0.14859 1 h-lim-p 0.0008 0.0063 78.8959 982.363162 8 0.0004 40 | 0/8 2 h-lim-p 0.0002 0.0014 19.8228 982.173806 0 0.0011 54 | 0/8 3 h-lim-p 0.0005 0.0040 9.2346 982.138057 0 0.0010 67 | 0/8 4 h-lim-p 0.0001 0.0009 3.6256 982.132243 m 0.0009 79 | 1/8 5 h-lim-p 0.0032 0.9424 0.9118 982.131511 4 0.0017 100 | 1/8 6 h-lim-p 0.0099 2.1152 0.1575 982.131403 3 0.0032 127 | 1/8 7 h-lim-p 0.0057 5.0846 0.0876 982.131381 1 0.0029 148 | 1/8 8 h-lim-p 0.1841 20.0000 0.0014 982.130594 0 1.1049 169 | 1/8 9 h-lim-p 2.5000 20.0000 0.0003 982.130568 2 0.9961 192 | 1/8 10 h-lim-p 2.5000 20.0000 0.0000 982.130567 0 1.0938 211 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 982.130567 0 1.0938 230 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 982.130567 0 0.5469 250 | 1/8 13 h-lim-p 0.3620 20.0000 0.0000 982.130567 0 0.0396 271 | 1/8 14 h-lim-p 0.0228 20.0000 0.0000 982.130567 0 0.0000 311 Out... lnL = -982.130567 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -982.130567 Node 7: lnL = -982.130567 Node 8: lnL = -982.130567 Node 9: lnL = -982.130567 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 236 Sequential format.. Reading seq # 1: YDR321W_Sbay Reading seq # 2: YDR321W_Scer Reading seq # 3: YDR321W_Skud Reading seq # 4: YDR321W_Smik Reading seq # 5: YDR321W_Spar Sequences read.. Counting patterns.. # site patterns = 111 Counting frequencies.. 120 bytes for distance 17760 bytes for lkl0 14208 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.118304 0.073563 0.049848 0.090846 0.100944 0.166833 0.205291 0.056165 lnL0 = -950.043522 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 950.043522 x= 0.11830 0.07356 0.04985 0.09085 0.10094 0.16683 0.20529 0.05616 1 h-lim-p 0.0010 0.0083 42.5204 949.510374 9 0.0006 44 | 0/8 2 h-lim-p 0.0010 0.0081 11.0753 949.464388 4 0.0008 64 | 0/8 3 h-lim-p 0.0029 0.0505 2.9905 949.461548 2 0.0007 81 | 0/8 4 h-lim-p 0.0039 0.2641 0.5162 949.461452 3 0.0007 100 | 0/8 5 h-lim-p 0.0076 2.9593 0.0506 949.461450 1 0.0009 124 | 0/8 6 h-lim-p 0.0019 11.6397 0.0245 949.461450 0 0.0017 144 | 0/8 7 h-lim-p 0.0118 20.0000 0.0035 949.461442 0 0.0471 166 | 0/8 8 h-lim-p 0.0097 20.0000 0.0171 949.461321 0 0.0291 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 949.461321 0 1.0938 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 949.461321 0 1.0938 227 | 0/8 11 h-lim-p 1.2585 20.0000 0.0000 949.461321 0 2.5171 248 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 949.461321 0 0.1367 271 | 0/8 13 h-lim-p 0.0168 20.0000 0.0000 949.461321 0 0.0084 291 | 0/8 14 h-lim-p 0.0035 20.0000 0.0000 949.461321 0 0.0003 314 | 0/8 15 h-lim-p 0.0002 20.0000 0.0001 949.461321 0 0.0001 334 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 949.461321 0 0.0000 362 | 0/8 17 h-lim-p 0.0000 20.0000 0.0005 949.461321 0 0.0000 385 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 949.461321 0 0.0000 405 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 20 h-lim-p 0.0000 20.0000 0.0005 949.461321 0 0.0000 464 | 0/8 21 h-lim-p 0.0000 20.0000 0.0001 949.461321 0 0.0000 485 | 0/8 22 h-lim-p 0.0000 20.0000 0.0000 949.461321 0 0.0000 517 | 0/8 23 h-lim-p 0.0000 20.0000 0.0005 | 0/8 24 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -949.461321 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -949.461321 Node 7: lnL = -949.461321 Node 8: lnL = -949.461321 Node 9: lnL = -949.461321 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 217 Sequential format.. Reading seq # 1: YDR322C-A_Sbay Reading seq # 2: YDR322C-A_Scer Reading seq # 3: YDR322C-A_Skud Reading seq # 4: YDR322C-A_Smik Reading seq # 5: YDR322C-A_Spar Sequences read.. Counting patterns.. # site patterns = 80 Counting frequencies.. 120 bytes for distance 12800 bytes for lkl0 10240 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.079790 0.032791 0.034079 0.054208 0.061853 0.115115 0.115438 0.041553 lnL0 = -769.826557 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 769.826557 x= 0.07979 0.03279 0.03408 0.05421 0.06185 0.11512 0.11544 0.04155 1 h-lim-p 0.0004 0.0032 125.6033 767.991235 9 0.0003 46 | 0/8 2 h-lim-p 0.0005 0.0036 19.0177 767.915809 2 0.0004 62 | 0/8 3 h-lim-p 0.0036 0.0595 2.2688 767.914764 2 0.0004 80 | 0/8 4 h-lim-p 0.0025 0.4290 0.3725 767.914732 3 0.0005 99 | 0/8 5 h-lim-p 0.0032 2.9932 0.0566 767.914730 1 0.0008 122 | 0/8 6 h-lim-p 0.0060 9.1938 0.0074 767.914730 1 0.0029 145 | 0/8 7 h-lim-p 0.0037 20.0000 0.0059 767.914609 0 0.0590 169 | 0/8 8 h-lim-p 0.0016 0.6034 0.2184 767.914469 0 0.0024 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 767.914456 2 0.9961 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 767.914456 0 1.0938 233 | 0/8 11 h-lim-p 1.3855 20.0000 0.0000 767.914456 0 2.0783 253 | 0/8 12 h-lim-p 1.0801 20.0000 0.0000 767.914456 0 0.5401 273 | 0/8 13 h-lim-p 0.0050 20.0000 0.0018 767.914456 0 0.0000 317 | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -767.914456 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -767.914456 Node 7: lnL = -767.914456 Node 8: lnL = -767.914456 Node 9: lnL = -767.914456 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 345 Sequential format.. Reading seq # 1: YDR325W_Sbay Reading seq # 2: YDR325W_Scer Reading seq # 3: YDR325W_Skud Reading seq # 4: YDR325W_Smik Reading seq # 5: YDR325W_Spar Sequences read.. Counting patterns.. # site patterns = 127 Counting frequencies.. 120 bytes for distance 20320 bytes for lkl0 16256 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.252327 0.103381 0.054045 0.371302 4.313730 0.288436 0.275598 0.000060 lnL0 = -1351.609508 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1351.609508 x= 0.25233 0.10338 0.05405 0.37130 4.31373 0.28844 0.27560 0.00006 1 h-lim-p 0.0000 0.0000 144.7248 1351.569649 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0019 48.5780 1349.269323 m 0.0019 39 | 2/8 3 h-lim-p 0.0015 0.0124 20.3157 1339.625523 0 0.0062 53 | 2/8 4 h-lim-p 0.0018 0.0146 20.8522 1339.317162 6 0.0015 77 | 2/8 5 h-lim-p 0.0202 0.3117 1.5005 1339.313453 2 0.0027 95 | 2/8 6 h-lim-p 0.0253 1.6996 0.1581 1339.284613 0 0.0505 108 | 2/8 7 h-lim-p 0.0049 0.0877 1.6372 1339.088395 0 0.0098 127 | 2/8 8 h-lim-p 2.5000 20.0000 0.0037 1339.081582 6 0.8741 153 | 1/8 9 h-lim-p 0.0164 5.3024 0.1979 1339.081551 2 0.0016 177 | 1/8 10 h-lim-p 1.1567 15.9076 0.0003 1339.081529 2 0.8924 200 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 1339.081529 0 1.0938 219 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 1339.081529 0 1.0938 238 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 1339.081529 0 2.1875 257 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 1339.081529 0 0.3125 278 Out... lnL = -1339.081529 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1339.081529 Node 7: lnL = -1339.081529 Node 8: lnL = -1339.081529 Node 9: lnL = -1339.081529 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 286 Sequential format.. Reading seq # 1: YDR328C_Sbay Reading seq # 2: YDR328C_Scer Reading seq # 3: YDR328C_Skud Reading seq # 4: YDR328C_Smik Reading seq # 5: YDR328C_Spar Sequences read.. Counting patterns.. # site patterns = 128 Counting frequencies.. 120 bytes for distance 20480 bytes for lkl0 16384 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.144391 0.091619 0.035173 0.097375 0.127393 0.238071 0.142421 0.076036 lnL0 = -1120.863801 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1120.863801 x= 0.14439 0.09162 0.03517 0.09738 0.12739 0.23807 0.14242 0.07604 1 h-lim-p 0.0013 0.0105 40.0916 1120.385542 2 0.0006 26 | 0/8 2 h-lim-p 0.0007 0.0058 15.0260 1120.284487 0 0.0015 39 | 0/8 3 h-lim-p 0.0033 0.0599 6.7196 1120.271201 5 0.0007 61 | 0/8 4 h-lim-p 0.0026 0.1419 1.8178 1120.269939 5 0.0008 86 | 0/8 5 h-lim-p 0.0029 0.4118 0.5255 1120.269702 4 0.0017 109 | 0/8 6 h-lim-p 0.0086 1.5325 0.1037 1120.269652 3 0.0031 137 | 0/8 7 h-lim-p 0.0181 16.3081 0.0176 1120.259390 0 0.2890 161 | 0/8 8 h-lim-p 0.0143 0.7055 0.3544 1120.259259 4 0.0020 193 | 0/8 9 h-lim-p 2.4251 20.0000 0.0003 1120.259192 2 1.0562 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1120.259192 0 1.0938 237 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1120.259192 0 1.0938 257 | 0/8 12 h-lim-p 1.0452 20.0000 0.0000 1120.259192 0 0.7839 277 | 0/8 13 h-lim-p 0.0079 20.0000 0.0004 1120.259192 0 0.0059 297 | 0/8 14 h-lim-p 0.0014 20.0000 0.0016 1120.259192 0 0.0007 317 | 0/8 15 h-lim-p 0.0006 20.0000 0.0019 1120.259192 0 0.0000 346 | 0/8 16 h-lim-p 0.0004 20.0000 0.0000 1120.259192 0 0.0000 372 Out... lnL = -1120.259192 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1120.259192 Node 7: lnL = -1120.259192 Node 8: lnL = -1120.259192 Node 9: lnL = -1120.259192 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 293 Sequential format.. Reading seq # 1: YDR329C_Sbay Reading seq # 2: YDR329C_Scer Reading seq # 3: YDR329C_Skud Reading seq # 4: YDR329C_Smik Reading seq # 5: YDR329C_Spar Sequences read.. Counting patterns.. # site patterns = 102 Counting frequencies.. 120 bytes for distance 16320 bytes for lkl0 13056 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.252327 0.075668 0.143932 0.247469 0.110369 4.435465 0.227588 0.000060 lnL0 = -1005.868862 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1005.868862 x= 0.25233 0.07567 0.14393 0.24747 0.11037 4.43546 0.22759 0.00006 1 h-lim-p 0.0000 0.0000 152.3790 1005.799031 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0061 47.6408 1003.005819 0 0.0026 42 | 1/8 3 h-lim-p 0.0036 0.0286 7.1780 1002.919420 7 0.0023 69 | 1/8 4 h-lim-p 0.0115 0.1610 1.4652 1002.329204 0 0.0459 83 | 1/8 5 h-lim-p 0.0045 0.0359 5.3750 996.811892 0 0.0179 97 | 1/8 6 h-lim-p 0.0014 0.0109 30.6406 994.214946 0 0.0027 110 | 1/8 7 h-lim-p 0.2163 1.7302 0.0765 993.832893 0 0.4325 123 | 0/8 8 h-lim-p 0.0000 0.0000 3.0205 h-lim-p: 4.49249146e-23 3.59399316e-22 3.02048015e+00 993.832893 .. | 0/8 9 h-lim-p 0.0000 0.0093 14.1066 993.774343 0 0.0006 156 | 0/8 10 h-lim-p 0.0000 0.0002 3.1724 993.772825 m 0.0002 168 | 1/8 11 h-lim-p 0.0005 0.4489 0.9339 993.772322 0 0.0010 181 | 1/8 12 h-lim-p 0.0052 0.4299 0.1886 993.772281 2 0.0013 205 | 1/8 13 h-lim-p 0.0014 1.4733 0.1747 993.772192 0 0.0028 225 | 1/8 14 h-lim-p 0.0042 0.9796 0.1149 993.771859 0 0.0085 245 | 1/8 15 h-lim-p 0.3369 20.0000 0.0029 993.768791 0 1.3477 266 | 0/8 16 h-lim-p -0.0000 -0.0000 0.0130 h-lim-p: -6.74477144e-21 -5.39581716e-20 1.30454685e-02 993.768791 .. | 0/8 17 h-lim-p 0.0000 0.5654 0.4893 993.768631 0 0.0013 308 | 0/8 18 h-lim-p 0.0005 0.0043 0.1502 993.768619 0 0.0011 329 | 0/8 19 h-lim-p 0.0003 0.0025 0.0587 993.768619 0 0.0006 350 | 0/8 20 h-lim-p 0.0001 0.0008 0.0910 993.768619 0 0.0000 385 | 0/8 21 h-lim-p 0.0000 0.0001 1.0167 .. | 0/8 22 h-lim-p 0.0000 11.9709 0.0174 993.768619 0 0.0013 437 | 0/8 23 h-lim-p 0.0012 0.0129 0.0186 993.768619 0 0.0000 476 | 0/8 24 h-lim-p 0.0000 0.0293 0.0101 993.768619 0 0.0000 511 | 0/8 25 h-lim-p 0.0000 0.0017 0.0459 993.768619 0 0.0002 535 | 0/8 26 h-lim-p 0.0000 0.0005 0.1513 993.768619 0 0.0000 570 | 0/8 27 h-lim-p 0.0000 0.0000 47.2123 .. | 0/8 28 h-lim-p 0.0000 20.0000 0.0042 993.768619 0 0.0003 615 | 0/8 29 h-lim-p 0.0000 0.0071 0.0929 993.768619 0 0.0000 645 | 0/8 30 h-lim-p 0.0000 20.0000 0.0011 993.768619 0 0.0026 673 | 0/8 31 h-lim-p 0.0105 5.6532 0.0003 993.768619 0 0.0000 708 | 0/8 32 h-lim-p 0.0000 20.0000 0.0002 993.768619 0 0.0038 736 | 0/8 33 h-lim-p 0.0035 18.1673 0.0003 993.768619 0 0.0139 758 | 0/8 34 h-lim-p 0.0007 0.5728 0.0053 993.768619 0 0.0000 789 | 0/8 35 h-lim-p 0.0000 20.0000 0.0001 993.768619 0 0.0000 823 | 0/8 36 h-lim-p 0.0000 0.0016 0.0433 | 0/8 37 h-lim-p 0.0000 0.0016 0.0433 Out... lnL = -993.768619 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -993.768619 Node 7: lnL = -993.768619 Node 8: lnL = -993.768619 Node 9: lnL = -993.768619 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 295 Sequential format.. Reading seq # 1: YDR330W_Sbay Reading seq # 2: YDR330W_Scer Reading seq # 3: YDR330W_Skud Reading seq # 4: YDR330W_Smik Reading seq # 5: YDR330W_Spar Sequences read.. Counting patterns.. # site patterns = 137 Counting frequencies.. 120 bytes for distance 21920 bytes for lkl0 17536 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.154408 0.014522 0.096764 0.130663 0.072361 0.331113 0.192487 0.078605 lnL0 = -1208.774997 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1208.774997 x= 0.15441 0.01452 0.09676 0.13066 0.07236 0.33111 0.19249 0.07860 1 h-lim-p 0.0026 0.0204 62.8698 1208.044781 6 0.0004 37 | 0/8 2 h-lim-p 0.0012 0.0100 20.5998 1207.776992 7 0.0013 65 | 0/8 3 h-lim-p 0.0016 0.0137 17.1084 1207.721033 7 0.0006 95 | 0/8 4 h-lim-p 0.0013 0.0603 8.0055 1207.679562 0 0.0019 107 | 0/8 5 h-lim-p 0.0033 0.0328 4.6124 1207.669684 4 0.0013 127 | 0/8 6 h-lim-p 0.0030 0.0714 2.0721 1207.667761 3 0.0012 145 | 0/8 7 h-lim-p 0.0300 2.3371 0.0819 1207.667754 2 0.0012 165 | 0/8 8 h-lim-p 0.0374 20.0000 0.0026 1207.664947 0 0.8978 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1207.664916 1 0.9961 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1207.664916 0 1.0938 231 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1207.664916 0 1.0938 251 | 0/8 12 h-lim-p 1.1867 20.0000 0.0000 1207.664916 0 3.5601 272 | 0/8 13 h-lim-p 0.4832 20.0000 0.0000 1207.664916 0 0.0000 311 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 1207.664916 0 0.0000 335 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 1207.664916 0 0.0000 355 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 1207.664916 0 0.0000 376 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 1207.664916 0 0.0000 408 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 | 0/8 19 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1207.664916 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1207.664916 Node 7: lnL = -1207.664916 Node 8: lnL = -1207.664916 Node 9: lnL = -1207.664916 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 237 Sequential format.. Reading seq # 1: YDR331W_Sbay Reading seq # 2: YDR331W_Scer Reading seq # 3: YDR331W_Skud Reading seq # 4: YDR331W_Smik Reading seq # 5: YDR331W_Spar Sequences read.. Counting patterns.. # site patterns = 130 Counting frequencies.. 120 bytes for distance 20800 bytes for lkl0 16640 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.174059 0.052989 0.070263 0.119285 0.111976 0.276451 0.215405 0.094867 lnL0 = -1065.140616 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1065.140616 x= 0.17406 0.05299 0.07026 0.11929 0.11198 0.27645 0.21540 0.09487 1 h-lim-p 0.0073 0.0828 54.0946 1064.316687 8 0.0006 44 | 0/8 2 h-lim-p 0.0024 0.0189 9.2530 1064.265968 6 0.0012 70 | 0/8 3 h-lim-p 0.0046 0.1503 2.4371 1064.263066 2 0.0011 87 | 0/8 4 h-lim-p 0.0024 0.3418 1.0798 1064.262259 4 0.0016 110 | 0/8 5 h-lim-p 0.0095 1.1294 0.1856 1064.262239 2 0.0013 128 | 0/8 6 h-lim-p 0.0115 15.8739 0.0202 1064.262238 0 0.0025 149 | 0/8 7 h-lim-p 0.0136 20.0000 0.0037 1064.262237 0 0.0136 169 | 0/8 8 h-lim-p 0.0116 20.0000 0.0044 1064.262160 0 0.0929 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1064.262159 0 1.0938 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1064.262159 0 1.0938 232 | 0/8 11 h-lim-p 1.8296 20.0000 0.0000 1064.262159 0 1.6009 252 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1064.262159 0 0.3125 274 | 0/8 13 h-lim-p 0.0972 20.0000 0.0000 1064.262159 0 0.0243 295 | 0/8 14 h-lim-p 0.0106 20.0000 0.0000 1064.262159 0 0.0000 334 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1064.262159 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1064.262159 Node 7: lnL = -1064.262159 Node 8: lnL = -1064.262159 Node 9: lnL = -1064.262159 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 514 Sequential format.. Reading seq # 1: YDR333C_Sbay Reading seq # 2: YDR333C_Scer Reading seq # 3: YDR333C_Skud Reading seq # 4: YDR333C_Smik Reading seq # 5: YDR333C_Spar Sequences read.. Counting patterns.. # site patterns = 164 Counting frequencies.. 120 bytes for distance 26240 bytes for lkl0 20992 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.093781 0.077575 0.039565 0.086857 0.071981 0.147891 0.116874 0.044172 lnL0 = -2043.578916 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2043.578916 x= 0.09378 0.07757 0.03956 0.08686 0.07198 0.14789 0.11687 0.04417 1 h-lim-p 0.0002 0.0018 182.7174 2041.182626 8 0.0002 40 | 0/8 2 h-lim-p 0.0003 0.0024 35.3836 2041.033655 6 0.0002 63 | 0/8 3 h-lim-p 0.0009 0.0305 9.5532 2041.024112 5 0.0002 88 | 0/8 4 h-lim-p 0.0015 0.1418 1.4156 2041.023762 2 0.0004 105 | 0/8 5 h-lim-p 0.0026 1.3106 0.1928 2041.023756 0 0.0003 119 | 0/8 6 h-lim-p 0.0013 3.1456 0.0472 2041.023756 0 0.0006 139 | 0/8 7 h-lim-p 0.0027 19.8318 0.0103 2041.023748 0 0.0080 160 | 0/8 8 h-lim-p 0.0060 4.7976 0.0138 2041.022993 0 0.0477 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 2041.022966 2 0.9644 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2041.022966 0 1.0938 227 | 0/8 11 h-lim-p 1.3686 20.0000 0.0000 2041.022966 0 1.3686 247 | 0/8 12 h-lim-p 0.7307 20.0000 0.0000 2041.022966 0 1.4615 268 | 0/8 13 h-lim-p 0.0293 20.0000 0.0017 2041.022966 0 0.0009 292 | 0/8 14 h-lim-p 0.0003 15.2636 0.0044 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0011 2041.022966 0 0.0001 353 | 0/8 16 h-lim-p 0.0009 20.0000 0.0001 2041.022966 0 0.0000 381 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 2041.022966 0 0.0000 401 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 2041.022966 0 0.0000 423 | 0/8 19 h-lim-p 0.0000 20.0000 0.0002 .. | 0/8 20 h-lim-p 0.0000 20.0000 0.0007 | 0/8 21 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -2041.022966 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2041.022966 Node 7: lnL = -2041.022966 Node 8: lnL = -2041.022966 Node 9: lnL = -2041.022966 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 375 Sequential format.. Reading seq # 1: YDR339C_Sbay Reading seq # 2: YDR339C_Scer Reading seq # 3: YDR339C_Skud Reading seq # 4: YDR339C_Smik Reading seq # 5: YDR339C_Spar Sequences read.. Counting patterns.. # site patterns = 146 Counting frequencies.. 120 bytes for distance 23360 bytes for lkl0 18688 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.220173 0.043854 0.082727 0.210050 0.203545 1.535686 0.227993 0.043174 lnL0 = -1608.588688 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1608.588688 x= 0.22017 0.04385 0.08273 0.21005 0.20355 1.53569 0.22799 0.04317 1 h-lim-p 0.0053 0.0424 43.8108 1608.165023 7 0.0005 41 | 0/8 2 h-lim-p 0.0023 0.0202 8.8400 1608.123029 2 0.0011 57 | 0/8 3 h-lim-p 0.0041 0.1876 2.3285 1608.120396 4 0.0010 79 | 0/8 4 h-lim-p 0.0028 0.3054 0.8793 1608.119228 1 0.0035 93 | 0/8 5 h-lim-p 0.0012 0.8987 2.4601 1608.107685 0 0.0148 116 | 0/8 6 h-lim-p 0.0019 0.4035 19.3477 1608.049202 0 0.0151 131 | 0/8 7 h-lim-p 2.5000 20.0000 0.0315 1608.041894 4 1.0947 150 | 0/8 8 h-lim-p 2.5000 20.0000 0.0076 1608.041796 3 1.4660 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 1608.041795 0 1.0938 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1608.041795 0 1.0938 219 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1608.041795 0 1.0938 239 | 0/8 12 h-lim-p 0.2954 20.0000 0.0000 1608.041795 0 0.0023 265 | 0/8 13 h-lim-p 0.0003 20.0000 0.0003 1608.041795 0 0.0000 302 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1608.041795 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1608.041795 Node 7: lnL = -1608.041795 Node 8: lnL = -1608.041795 Node 9: lnL = -1608.041795 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 845 Sequential format.. Reading seq # 1: YDR345C_Sbay Reading seq # 2: YDR345C_Scer Reading seq # 3: YDR345C_Skud Reading seq # 4: YDR345C_Smik Reading seq # 5: YDR345C_Spar Sequences read.. Counting patterns.. # site patterns = 179 Counting frequencies.. 120 bytes for distance 28640 bytes for lkl0 22912 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.108567 0.072080 0.000060 0.241687 0.657917 0.140209 0.161717 0.023770 lnL0 = -2794.048786 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2794.048786 x= 0.10857 0.07208 0.00006 0.24169 0.65792 0.14021 0.16172 0.02377 1 h-lim-p 0.0000 0.0000 593.0311 2793.944973 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0008 379.8728 2777.323064 0 0.0003 39 | 1/8 3 h-lim-p 0.0001 0.0011 165.2040 2773.561618 0 0.0003 52 | 1/8 4 h-lim-p 0.0016 0.0129 21.5250 2773.219119 4 0.0013 72 | 1/8 5 h-lim-p 0.0004 0.0245 60.4663 2771.183860 0 0.0036 87 | 1/8 6 h-lim-p 0.0005 0.0043 163.3629 2769.926514 0 0.0008 99 | 1/8 7 h-lim-p 0.0259 0.2073 0.9166 2752.748369 m 0.2073 111 | 2/8 8 h-lim-p 0.0000 0.0002 908.2327 2749.543421 0 0.0001 131 | 2/8 9 h-lim-p 0.4107 3.2855 0.0948 2743.293640 0 1.2321 144 | 2/8 10 h-lim-p 0.6224 4.9795 0.0311 2739.557919 0 1.2449 163 | 2/8 11 h-lim-p 0.5418 4.3348 0.0171 2739.202142 1 0.6773 183 | 2/8 12 h-lim-p 1.1061 16.4381 0.0105 2739.170002 5 0.4659 212 | 2/8 13 h-lim-p 0.9931 20.0000 0.0049 2739.165987 5 0.6763 243 | 1/8 14 h-lim-p 0.0076 4.6654 0.4392 2739.165967 2 0.0002 269 | 1/8 15 h-lim-p 0.0446 1.6801 0.0025 2739.165759 0 1.0696 292 | 1/8 16 h-lim-p 0.0406 0.3251 0.0006 2739.165747 m 0.3251 311 | 2/8 17 h-lim-p 0.5511 20.0000 0.0004 2739.165741 2 0.3525 335 | 2/8 18 h-lim-p 2.5000 20.0000 0.0000 2739.165737 1 0.9961 355 | 2/8 19 h-lim-p 0.7196 20.0000 0.0001 2739.165737 0 1.4392 374 | 2/8 20 h-lim-p 2.5000 20.0000 0.0000 2739.165737 0 1.2500 392 | 2/8 21 h-lim-p 2.5000 20.0000 0.0000 2739.165737 0 0.2734 412 | 2/8 22 h-lim-p 0.3715 20.0000 0.0000 2739.165737 0 0.0058 435 | 2/8 23 h-lim-p 0.0058 20.0000 0.0000 2739.165737 0 0.0058 453 | 2/8 24 h-lim-p 0.0059 20.0000 0.0000 2739.165737 0 0.0000 487 Out... lnL = -2739.165737 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2739.165737 Node 7: lnL = -2739.165737 Node 8: lnL = -2739.165737 Node 9: lnL = -2739.165737 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 583 Sequential format.. Reading seq # 1: YDR346C_Sbay Reading seq # 2: YDR346C_Scer Reading seq # 3: YDR346C_Skud Reading seq # 4: YDR346C_Smik Reading seq # 5: YDR346C_Spar Sequences read.. Counting patterns.. # site patterns = 178 Counting frequencies.. 120 bytes for distance 28480 bytes for lkl0 22784 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.120880 0.050120 0.065555 0.112317 0.058185 0.119264 0.149965 0.066976 lnL0 = -2246.085233 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2246.085233 x= 0.12088 0.05012 0.06556 0.11232 0.05818 0.11926 0.14996 0.06698 1 h-lim-p 0.0002 0.0015 109.5743 2244.902237 7 0.0002 39 | 0/8 2 h-lim-p 0.0010 0.0077 19.7053 2244.849391 7 0.0003 67 | 0/8 3 h-lim-p 0.0014 0.2312 3.9521 2244.847903 4 0.0002 90 | 0/8 4 h-lim-p 0.0005 0.0998 1.5348 2244.847616 4 0.0003 111 | 0/8 5 h-lim-p 0.0011 0.5172 0.3852 2244.847592 2 0.0004 129 | 0/8 6 h-lim-p 0.0036 5.5718 0.0394 2244.847592 0 0.0004 151 | 0/8 7 h-lim-p 0.0030 20.0000 0.0051 2244.847592 0 0.0026 171 | 0/8 8 h-lim-p 0.0184 20.0000 0.0007 2244.847537 0 0.2212 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2244.847537 0 1.0938 214 | 0/8 10 h-lim-p 2.3585 20.0000 0.0000 2244.847537 0 2.0637 234 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2244.847537 0 0.5469 255 | 0/8 12 h-lim-p 0.1100 20.0000 0.0000 2244.847537 0 0.0138 277 | 0/8 13 h-lim-p 0.0056 20.0000 0.0000 2244.847537 0 0.0000 315 | 0/8 14 h-lim-p 0.0000 20.0000 0.0018 | 0/8 15 h-lim-p 0.0000 20.0000 0.0018 Out... lnL = -2244.847537 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2244.847537 Node 7: lnL = -2244.847537 Node 8: lnL = -2244.847537 Node 9: lnL = -2244.847537 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 860 Sequential format.. Reading seq # 1: YDR349C_Sbay Reading seq # 2: YDR349C_Scer Reading seq # 3: YDR349C_Skud Reading seq # 4: YDR349C_Smik Reading seq # 5: YDR349C_Spar Sequences read.. Counting patterns.. # site patterns = 470 Counting frequencies.. 120 bytes for distance 75200 bytes for lkl0 60160 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.383649 0.000060 0.054907 0.360130 1.017125 0.396195 0.478671 0.174673 lnL0 = -4561.219830 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4561.219830 x= 0.38365 0.00006 0.05491 0.36013 1.01713 0.39620 0.47867 0.17467 1 h-lim-p 0.0002 0.0017 84.4065 4556.387168 0 0.0012 24 | 0/8 2 h-lim-p 0.0014 0.0109 27.5708 4555.789420 1 0.0017 38 | 0/8 3 h-lim-p 0.0008 0.0065 12.5441 4555.695392 0 0.0016 51 | 0/8 4 h-lim-p 0.0001 0.0011 13.4471 4555.649065 m 0.0011 63 | 0/8 5 h-lim-p 0.0000 0.0000 3.4739 h-lim-p: 4.69144999e-20 3.75315999e-19 3.47391682e+00 4555.649065 .. | 0/8 6 h-lim-p 0.0000 0.0083 21.3648 4555.461118 0 0.0010 89 | 0/8 7 h-lim-p 0.0003 0.0025 4.6978 4555.453070 0 0.0009 102 | 0/8 8 h-lim-p 0.0004 0.0030 3.4203 4555.442926 m 0.0030 114 | 1/8 9 h-lim-p 0.0043 0.2007 2.0963 4555.439426 5 0.0026 141 | 1/8 10 h-lim-p 0.0032 0.6005 1.6912 4555.435246 0 0.0064 154 | 1/8 11 h-lim-p 0.0169 1.3224 0.6453 4555.434828 4 0.0026 178 | 1/8 12 h-lim-p 0.1317 20.0000 0.0127 4555.434226 3 0.1054 203 | 1/8 13 h-lim-p 0.0029 1.9419 0.4581 4555.429846 0 0.0117 224 | 1/8 14 h-lim-p 2.5000 20.0000 0.0003 4555.429806 2 0.9644 247 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 4555.429806 0 1.0938 266 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 4555.429806 0 1.0938 285 | 1/8 17 h-lim-p 1.2641 20.0000 0.0000 4555.429806 0 1.8962 304 | 1/8 18 h-lim-p 0.7761 20.0000 0.0000 4555.429806 0 0.7761 323 | 1/8 19 h-lim-p 0.0068 20.0000 0.0014 4555.429806 0 0.0000 363 | 1/8 20 h-lim-p 0.0000 20.0000 0.0000 4555.429806 0 0.0000 392 Out... lnL = -4555.429806 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4555.429806 Node 7: lnL = -4555.429806 Node 8: lnL = -4555.429806 Node 9: lnL = -4555.429806 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 507 Sequential format.. Reading seq # 1: YDR350C_Sbay Reading seq # 2: YDR350C_Scer Reading seq # 3: YDR350C_Skud Reading seq # 4: YDR350C_Smik Reading seq # 5: YDR350C_Spar Sequences read.. Counting patterns.. # site patterns = 185 Counting frequencies.. 120 bytes for distance 29600 bytes for lkl0 23680 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.135796 0.111740 0.039458 0.094020 0.069594 0.168046 0.128472 0.069769 lnL0 = -2094.705103 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2094.705103 x= 0.13580 0.11174 0.03946 0.09402 0.06959 0.16805 0.12847 0.06977 1 h-lim-p 0.0046 0.0369 92.5692 2093.983817 8 0.0002 45 | 0/8 2 h-lim-p 0.0013 0.0121 12.9387 2093.953422 6 0.0004 72 | 0/8 3 h-lim-p 0.0007 0.0491 7.2729 2093.947958 4 0.0003 92 | 0/8 4 h-lim-p 0.0020 0.1592 0.9612 2093.947761 2 0.0004 109 | 0/8 5 h-lim-p 0.0021 1.2861 0.1971 2093.947755 2 0.0003 136 | 0/8 6 h-lim-p 0.0035 12.1477 0.0198 2093.947755 0 0.0008 157 | 0/8 7 h-lim-p 0.0024 20.0000 0.0063 2093.947755 0 0.0005 178 | 0/8 8 h-lim-p 0.0437 20.0000 0.0001 2093.947747 0 0.6992 202 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2093.947747 0 1.0938 222 | 0/8 10 h-lim-p 1.8827 20.0000 0.0000 2093.947747 0 0.8237 242 | 0/8 11 h-lim-p 0.5957 20.0000 0.0000 2093.947747 0 0.0020 269 | 0/8 12 h-lim-p 0.0005 20.0000 0.0001 2093.947747 0 0.0005 289 | 0/8 13 h-lim-p 0.0006 20.0000 0.0001 2093.947747 0 0.0000 313 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 2093.947747 0 0.0000 344 Out... lnL = -2093.947747 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2093.947747 Node 7: lnL = -2093.947747 Node 8: lnL = -2093.947747 Node 9: lnL = -2093.947747 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 509 Sequential format.. Reading seq # 1: YDR351W_Sbay Reading seq # 2: YDR351W_Scer Reading seq # 3: YDR351W_Skud Reading seq # 4: YDR351W_Smik Reading seq # 5: YDR351W_Spar Sequences read.. Counting patterns.. # site patterns = 186 Counting frequencies.. 120 bytes for distance 29760 bytes for lkl0 23808 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.135132 0.110291 0.035894 0.096458 0.067157 0.170128 0.140406 0.068749 lnL0 = -2102.783528 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2102.783528 x= 0.13513 0.11029 0.03589 0.09646 0.06716 0.17013 0.14041 0.06875 1 h-lim-p 0.0026 0.0205 120.0021 2101.699431 7 0.0002 38 | 0/8 2 h-lim-p 0.0009 0.0072 14.2052 2101.667230 6 0.0003 63 | 0/8 3 h-lim-p 0.0005 0.0268 8.3623 2101.658771 5 0.0003 88 | 0/8 4 h-lim-p 0.0019 0.1149 1.3349 2101.658438 3 0.0004 107 | 0/8 5 h-lim-p 0.0016 0.6606 0.3200 2101.658418 2 0.0004 124 | 0/8 6 h-lim-p 0.0063 16.2980 0.0215 2101.658418 0 0.0007 146 | 0/8 7 h-lim-p 0.0025 20.0000 0.0061 2101.658418 0 0.0005 167 | 0/8 8 h-lim-p 0.1973 20.0000 0.0000 2101.658418 0 1.1837 189 | 0/8 9 h-lim-p 1.6629 20.0000 0.0000 2101.658418 0 1.4550 209 | 0/8 10 h-lim-p 1.9700 20.0000 0.0000 2101.658418 0 1.7237 229 | 0/8 11 h-lim-p 1.8959 20.0000 0.0000 2101.658418 0 0.4147 250 | 0/8 12 h-lim-p 0.1564 20.0000 0.0000 2101.658418 0 0.0171 272 | 0/8 13 h-lim-p 0.0077 20.0000 0.0000 2101.658418 0 0.0001 298 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 2101.658418 0 0.0000 318 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 2101.658418 0 0.0000 340 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 2101.658418 0 0.0000 373 Out... lnL = -2101.658418 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2101.658418 Node 7: lnL = -2101.658418 Node 8: lnL = -2101.658418 Node 9: lnL = -2101.658418 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 582 Sequential format.. Reading seq # 1: YDR352W_Sbay Reading seq # 2: YDR352W_Scer Reading seq # 3: YDR352W_Skud Reading seq # 4: YDR352W_Smik Reading seq # 5: YDR352W_Spar Sequences read.. Counting patterns.. # site patterns = 206 Counting frequencies.. 120 bytes for distance 32960 bytes for lkl0 26368 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.178558 0.069105 0.062984 0.132041 0.062941 0.191899 0.155625 0.102939 lnL0 = -2477.995442 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2477.995442 x= 0.17856 0.06910 0.06298 0.13204 0.06294 0.19190 0.15563 0.10294 1 h-lim-p 0.0002 0.0014 111.5123 2476.394002 0 0.0004 23 | 0/8 2 h-lim-p 0.0015 0.0120 23.2189 2476.286789 6 0.0004 50 | 0/8 3 h-lim-p 0.0018 0.0215 5.2793 2476.282182 4 0.0003 71 | 0/8 4 h-lim-p 0.0004 0.0560 4.5998 2476.280512 5 0.0002 97 | 0/8 5 h-lim-p 0.0066 1.4550 0.1674 2476.280142 4 0.0038 119 | 0/8 6 h-lim-p 0.0027 0.8018 0.2367 2476.273205 0 0.0106 141 | 0/8 7 h-lim-p 0.0017 0.1404 1.5174 2476.213682 0 0.0050 162 | 0/8 8 h-lim-p 0.0011 0.0203 6.5647 2476.184167 5 0.0009 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0008 2476.183375 4 0.9802 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2476.183374 0 1.0938 224 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2476.183374 0 1.0938 244 | 0/8 12 h-lim-p 1.1620 20.0000 0.0000 2476.183374 0 1.0167 264 | 0/8 13 h-lim-p 0.4647 20.0000 0.0000 2476.183374 0 0.0218 288 | 0/8 14 h-lim-p 0.0036 20.0000 0.0001 2476.183374 0 0.0002 311 | 0/8 15 h-lim-p 0.0003 20.0000 0.0001 2476.183374 0 0.0001 331 | 0/8 16 h-lim-p 0.0008 20.0000 0.0000 2476.183374 0 0.0000 355 | 0/8 17 h-lim-p 0.0007 20.0000 0.0000 2476.183374 0 0.0000 379 Out... lnL = -2476.183374 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2476.183374 Node 7: lnL = -2476.183374 Node 8: lnL = -2476.183374 Node 9: lnL = -2476.183374 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 539 Sequential format.. Reading seq # 1: YDR354W_Sbay Reading seq # 2: YDR354W_Scer Reading seq # 3: YDR354W_Skud Reading seq # 4: YDR354W_Smik Reading seq # 5: YDR354W_Spar Sequences read.. Counting patterns.. # site patterns = 210 Counting frequencies.. 120 bytes for distance 33600 bytes for lkl0 26880 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.175052 0.155209 0.094791 0.117242 0.090487 0.195354 0.336258 0.074174 lnL0 = -2181.447177 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2181.447177 x= 0.17505 0.15521 0.09479 0.11724 0.09049 0.19535 0.33626 0.07417 1 h-lim-p 0.0003 0.0027 47.5475 2180.936715 0 0.0005 22 | 0/8 2 h-lim-p 0.0014 0.0258 17.4093 2180.844229 6 0.0007 46 | 0/8 3 h-lim-p 0.0004 0.0131 27.6000 2180.668214 0 0.0013 59 | 0/8 4 h-lim-p 0.0065 0.0518 4.0011 2180.660181 5 0.0011 85 | 0/8 5 h-lim-p 0.0012 0.0982 3.6974 2180.655761 3 0.0011 103 | 0/8 6 h-lim-p 0.0027 0.3775 1.4297 2180.655328 3 0.0005 122 | 0/8 7 h-lim-p 0.0070 1.9115 0.1109 2180.655245 2 0.0037 139 | 0/8 8 h-lim-p 0.0128 11.5810 0.0319 2180.640287 0 0.2048 163 | 0/8 9 h-lim-p 2.5000 20.0000 0.0009 2180.639961 3 1.0004 189 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2180.639960 0 1.0938 209 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2180.639960 0 1.2500 229 | 0/8 12 h-lim-p 1.5704 20.0000 0.0000 2180.639960 0 0.3926 250 | 0/8 13 h-lim-p 0.1865 20.0000 0.0000 2180.639960 0 0.0117 273 | 0/8 14 h-lim-p 0.0054 20.0000 0.0000 2180.639960 0 0.0027 293 | 0/8 15 h-lim-p 0.0014 20.0000 0.0000 2180.639960 0 0.0000 330 | 0/8 16 h-lim-p 0.0000 20.0000 0.0005 | 0/8 17 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -2180.639960 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2180.639960 Node 7: lnL = -2180.639960 Node 8: lnL = -2180.639960 Node 9: lnL = -2180.639960 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 231 Sequential format.. Reading seq # 1: YDR356W_Sbay Reading seq # 2: YDR356W_Scer Reading seq # 3: YDR356W_Skud Reading seq # 4: YDR356W_Smik Reading seq # 5: YDR356W_Spar Sequences read.. Counting patterns.. # site patterns = 100 Counting frequencies.. 120 bytes for distance 16000 bytes for lkl0 12800 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.125679 0.033583 0.076688 0.123653 0.069786 0.242894 0.226259 0.051328 lnL0 = -1018.649645 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1018.649645 x= 0.12568 0.03358 0.07669 0.12365 0.06979 0.24289 0.22626 0.05133 1 h-lim-p 0.0011 0.0087 54.5739 1018.048760 6 0.0004 35 | 0/8 2 h-lim-p 0.0013 0.0108 12.6572 1017.985800 7 0.0008 66 | 0/8 3 h-lim-p 0.0016 0.0423 6.6493 1017.972485 4 0.0008 87 | 0/8 4 h-lim-p 0.0016 0.0924 3.1554 1017.969407 4 0.0008 107 | 0/8 5 h-lim-p 0.0054 0.3325 0.4586 1017.969329 4 0.0008 131 | 0/8 6 h-lim-p 0.0307 20.0000 0.0114 1017.969329 0 0.0019 154 | 0/8 7 h-lim-p 0.0807 20.0000 0.0003 1017.969327 0 0.1613 175 | 0/8 8 h-lim-p 0.0021 3.3152 0.0212 1017.969320 0 0.0062 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1017.969320 0 1.0938 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1017.969320 0 1.0938 236 | 0/8 11 h-lim-p 1.1289 20.0000 0.0000 1017.969320 0 0.0617 259 | 0/8 12 h-lim-p 0.0086 20.0000 0.0001 1017.969320 0 0.0000 287 | 0/8 13 h-lim-p 0.0002 20.0000 0.0000 1017.969320 0 0.0000 311 Out... lnL = -1017.969320 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1017.969320 Node 7: lnL = -1017.969320 Node 8: lnL = -1017.969320 Node 9: lnL = -1017.969320 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 536 Sequential format.. Reading seq # 1: YDR357C_Sbay Reading seq # 2: YDR357C_Scer Reading seq # 3: YDR357C_Skud Reading seq # 4: YDR357C_Smik Reading seq # 5: YDR357C_Spar Sequences read.. Counting patterns.. # site patterns = 263 Counting frequencies.. 120 bytes for distance 42080 bytes for lkl0 33664 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.266709 0.090446 0.080644 0.152510 0.143097 0.324583 0.368972 0.144148 lnL0 = -2725.479598 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2725.479598 x= 0.26671 0.09045 0.08064 0.15251 0.14310 0.32458 0.36897 0.14415 1 h-lim-p 0.0044 0.0354 53.2945 2724.820840 6 0.0005 35 | 0/8 2 h-lim-p 0.0025 0.0251 10.5085 2724.756357 5 0.0012 58 | 0/8 3 h-lim-p 0.0013 0.0384 9.9816 2724.738591 3 0.0006 76 | 0/8 4 h-lim-p 0.0029 0.1938 1.9594 2724.735783 5 0.0016 99 | 0/8 5 h-lim-p 0.0060 0.5397 0.5184 2724.735682 3 0.0008 119 | 0/8 6 h-lim-p 0.0051 5.1936 0.0824 2724.735678 0 0.0011 140 | 0/8 7 h-lim-p 0.0038 15.4202 0.0243 2724.735678 0 0.0017 160 | 0/8 8 h-lim-p 0.4899 20.0000 0.0001 2724.735671 0 0.9798 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2724.735671 0 1.0938 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2724.735671 0 1.0938 221 | 0/8 11 h-lim-p 1.0750 20.0000 0.0000 2724.735671 0 0.5375 241 | 0/8 12 h-lim-p 0.0733 20.0000 0.0000 2724.735671 0 0.0367 261 | 0/8 13 h-lim-p 0.0120 20.0000 0.0001 2724.735671 0 0.0015 283 | 0/8 14 h-lim-p 0.0011 20.0000 0.0001 2724.735671 0 0.0008 303 | 0/8 15 h-lim-p 0.0010 20.0000 0.0001 2724.735671 0 0.0000 340 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -2724.735671 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2724.735671 Node 7: lnL = -2724.735671 Node 8: lnL = -2724.735671 Node 9: lnL = -2724.735671 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 539 Sequential format.. Reading seq # 1: YDR358W_Sbay Reading seq # 2: YDR358W_Scer Reading seq # 3: YDR358W_Skud Reading seq # 4: YDR358W_Smik Reading seq # 5: YDR358W_Spar Sequences read.. Counting patterns.. # site patterns = 280 Counting frequencies.. 120 bytes for distance 44800 bytes for lkl0 35840 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.194087 0.225428 0.120661 0.175487 0.123197 0.292062 0.235154 0.074695 lnL0 = -2682.024189 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2682.024189 x= 0.19409 0.22543 0.12066 0.17549 0.12320 0.29206 0.23515 0.07470 1 h-lim-p 0.0036 0.0285 35.4926 2681.641165 7 0.0006 41 | 0/8 2 h-lim-p 0.0029 0.0268 7.5227 2681.609867 4 0.0012 61 | 0/8 3 h-lim-p 0.0020 0.0751 4.2514 2681.604852 5 0.0007 86 | 0/8 4 h-lim-p 0.0017 0.1424 1.7776 2681.604110 4 0.0006 109 | 0/8 5 h-lim-p 0.0022 0.5828 0.4501 2681.603992 3 0.0013 129 | 0/8 6 h-lim-p 0.0172 7.2575 0.0350 2681.603992 0 0.0009 152 | 0/8 7 h-lim-p 0.0037 20.0000 0.0088 2681.603992 0 0.0033 172 | 0/8 8 h-lim-p 0.1133 20.0000 0.0003 2681.603975 0 0.9067 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2681.603974 0 1.0938 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2681.603974 0 1.0938 235 | 0/8 11 h-lim-p 1.2374 20.0000 0.0000 2681.603974 0 1.2374 255 | 0/8 12 h-lim-p 0.7240 20.0000 0.0000 2681.603974 0 1.0860 275 | 0/8 13 h-lim-p 0.0292 20.0000 0.0005 2681.603974 0 0.0000 316 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 2681.603974 0 0.0000 341 Out... lnL = -2681.603974 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2681.603974 Node 7: lnL = -2681.603974 Node 8: lnL = -2681.603974 Node 9: lnL = -2681.603974 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 543 Sequential format.. Reading seq # 1: YDR359C_Sbay Reading seq # 2: YDR359C_Scer Reading seq # 3: YDR359C_Skud Reading seq # 4: YDR359C_Smik Reading seq # 5: YDR359C_Spar Sequences read.. Counting patterns.. # site patterns = 183 Counting frequencies.. 120 bytes for distance 29280 bytes for lkl0 23424 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.136348 0.045100 0.065527 0.102037 0.078705 0.191153 0.126044 0.071832 lnL0 = -2307.081556 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2307.081556 x= 0.13635 0.04510 0.06553 0.10204 0.07870 0.19115 0.12604 0.07183 1 h-lim-p 0.0012 0.0097 117.4970 2305.830092 6 0.0002 37 | 0/8 2 h-lim-p 0.0008 0.0065 25.1413 2305.710507 2 0.0004 53 | 0/8 3 h-lim-p 0.0014 0.0325 6.6785 2305.703537 2 0.0003 70 | 0/8 4 h-lim-p 0.0008 0.0606 2.8961 2305.702422 3 0.0003 88 | 0/8 5 h-lim-p 0.0013 0.1752 0.6984 2305.702344 3 0.0003 107 | 0/8 6 h-lim-p 0.0028 1.4371 0.0838 2305.702343 0 0.0004 129 | 0/8 7 h-lim-p 0.0149 20.0000 0.0020 2305.702340 0 0.0299 150 | 0/8 8 h-lim-p 0.0028 5.2979 0.0210 2305.702190 0 0.0114 172 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2305.702185 0 1.0938 192 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2305.702185 0 1.0938 212 | 0/8 11 h-lim-p 1.0866 20.0000 0.0000 2305.702185 0 2.1732 233 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2305.702185 0 0.0043 261 | 0/8 13 h-lim-p 0.0008 20.0000 0.0000 2305.702185 0 0.0003 282 | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 2305.702185 0 0.0000 318 | 0/8 15 h-lim-p 0.0000 20.0000 0.0015 | 0/8 16 h-lim-p 0.0000 20.0000 0.0015 Out... lnL = -2305.702185 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2305.702185 Node 7: lnL = -2305.702185 Node 8: lnL = -2305.702185 Node 9: lnL = -2305.702185 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 450 Sequential format.. Reading seq # 1: YDR361C_Sbay Reading seq # 2: YDR361C_Scer Reading seq # 3: YDR361C_Skud Reading seq # 4: YDR361C_Smik Reading seq # 5: YDR361C_Spar Sequences read.. Counting patterns.. # site patterns = 259 Counting frequencies.. 120 bytes for distance 41440 bytes for lkl0 33152 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.277497 0.051010 0.071535 0.256667 0.203623 0.210791 0.453825 0.149115 lnL0 = -2328.049237 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2328.049237 x= 0.27750 0.05101 0.07154 0.25667 0.20362 0.21079 0.45382 0.14912 1 h-lim-p 0.0129 0.1683 59.9982 2326.915720 3 0.0007 31 | 0/8 2 h-lim-p 0.0021 0.0171 16.2475 2326.783777 4 0.0011 51 | 0/8 3 h-lim-p 0.0025 0.0770 6.8479 2326.748222 6 0.0018 76 | 0/8 4 h-lim-p 0.0039 0.1577 3.1278 2326.740684 4 0.0019 98 | 0/8 5 h-lim-p 0.0052 0.2240 1.1535 2326.739832 5 0.0015 122 | 0/8 6 h-lim-p 0.0078 1.6003 0.2227 2326.739796 2 0.0015 139 | 0/8 7 h-lim-p 0.0158 14.3114 0.0213 2326.739793 1 0.0039 162 | 0/8 8 h-lim-p 0.0390 20.0000 0.0021 2326.739299 0 0.4683 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2326.739295 0 1.0938 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2326.739295 0 1.0938 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2326.739295 0 1.2500 245 | 0/8 12 h-lim-p 1.4904 20.0000 0.0000 2326.739295 0 0.0000 292 Out... lnL = -2326.739295 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2326.739295 Node 7: lnL = -2326.739295 Node 8: lnL = -2326.739295 Node 9: lnL = -2326.739295 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 512 Sequential format.. Reading seq # 1: YDR362C_Sbay Reading seq # 2: YDR362C_Scer Reading seq # 3: YDR362C_Skud Reading seq # 4: YDR362C_Smik Reading seq # 5: YDR362C_Spar Sequences read.. Counting patterns.. # site patterns = 190 Counting frequencies.. 120 bytes for distance 30400 bytes for lkl0 24320 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.180314 0.144301 0.076599 0.136571 0.066218 0.259391 0.188992 0.087792 lnL0 = -2406.990345 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2406.990345 x= 0.18031 0.14430 0.07660 0.13657 0.06622 0.25939 0.18899 0.08779 1 h-lim-p 0.0002 0.0017 64.4229 2406.285461 0 0.0004 23 | 0/8 2 h-lim-p 0.0014 0.0892 20.2767 2406.240317 5 0.0002 48 | 0/8 3 h-lim-p 0.0010 0.0396 4.8315 2406.235020 2 0.0005 64 | 0/8 4 h-lim-p 0.0015 0.3671 1.5611 2406.233940 3 0.0009 84 | 0/8 5 h-lim-p 0.0147 2.5035 0.1008 2406.233746 3 0.0061 102 | 0/8 6 h-lim-p 0.0092 2.6757 0.0670 2406.225360 0 0.0555 124 | 0/8 7 h-lim-p 0.0021 0.1222 1.8001 2406.206357 1 0.0026 146 | 0/8 8 h-lim-p 0.0074 0.2570 0.6294 2406.206260 3 0.0005 167 | 0/8 9 h-lim-p 0.6578 20.0000 0.0005 2406.206041 0 0.9867 187 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2406.206041 0 1.0938 207 | 0/8 11 h-lim-p 1.6073 20.0000 0.0000 2406.206041 0 0.8037 227 | 0/8 12 h-lim-p 0.5711 20.0000 0.0000 2406.206041 0 0.0312 250 | 0/8 13 h-lim-p 0.0089 20.0000 0.0000 2406.206041 0 0.0000 285 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -2406.206041 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2406.206041 Node 7: lnL = -2406.206041 Node 8: lnL = -2406.206041 Node 9: lnL = -2406.206041 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 860 Sequential format.. Reading seq # 1: YDR363W-A_Sbay Reading seq # 2: YDR363W-A_Scer Reading seq # 3: YDR363W-A_Skud Reading seq # 4: YDR363W-A_Smik Reading seq # 5: YDR363W-A_Spar Sequences read.. Counting patterns.. # site patterns = 438 Counting frequencies.. 120 bytes for distance 70080 bytes for lkl0 56064 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.406750 0.106364 0.071218 0.258268 0.256455 0.387472 0.352065 0.232502 lnL0 = -4857.066049 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4857.066049 x= 0.40675 0.10636 0.07122 0.25827 0.25646 0.38747 0.35207 0.23250 1 h-lim-p 0.0068 1.0720 119.9615 4854.315099 7 0.0004 38 | 0/8 2 h-lim-p 0.0040 0.0318 11.9527 4854.249240 2 0.0009 55 | 0/8 3 h-lim-p 0.0018 0.0670 6.1008 4854.225204 4 0.0016 74 | 0/8 4 h-lim-p 0.0040 0.1610 2.4066 4854.222184 5 0.0012 99 | 0/8 5 h-lim-p 0.0208 3.2129 0.1440 4854.222171 0 0.0013 114 | 0/8 6 h-lim-p 0.0065 8.6621 0.0286 4854.222170 0 0.0029 134 | 0/8 7 h-lim-p 0.0500 20.0000 0.0016 4854.222130 0 0.2001 156 | 0/8 8 h-lim-p 0.0049 15.3280 0.0661 4854.221990 0 0.0074 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4854.221990 0 1.0938 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4854.221990 0 1.0938 216 | 0/8 11 h-lim-p 1.9361 20.0000 0.0000 4854.221990 0 1.6941 236 | 0/8 12 h-lim-p 2.4134 20.0000 0.0000 4854.221990 0 1.0558 256 | 0/8 13 h-lim-p 0.3558 20.0000 0.0000 4854.221990 0 0.0003 285 Out... lnL = -4854.221990 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4854.221990 Node 7: lnL = -4854.221990 Node 8: lnL = -4854.221990 Node 9: lnL = -4854.221990 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 512 Sequential format.. Reading seq # 1: YDR363W_Sbay Reading seq # 2: YDR363W_Scer Reading seq # 3: YDR363W_Skud Reading seq # 4: YDR363W_Smik Reading seq # 5: YDR363W_Spar Sequences read.. Counting patterns.. # site patterns = 191 Counting frequencies.. 120 bytes for distance 30560 bytes for lkl0 24448 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.201206 0.108663 0.084720 0.136316 0.066473 0.255122 0.204706 0.100045 lnL0 = -2416.065839 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2416.065839 x= 0.20121 0.10866 0.08472 0.13632 0.06647 0.25512 0.20471 0.10004 1 h-lim-p 0.0002 0.0019 68.7462 2415.259080 0 0.0005 23 | 0/8 2 h-lim-p 0.0018 0.0242 18.6134 2415.217846 7 0.0003 53 | 0/8 3 h-lim-p 0.0007 0.0210 7.0813 2415.207707 6 0.0005 80 | 0/8 4 h-lim-p 0.0015 0.1180 2.1113 2415.206154 3 0.0007 99 | 0/8 5 h-lim-p 0.0062 1.6005 0.2545 2415.206024 3 0.0017 118 | 0/8 6 h-lim-p 0.0044 1.7567 0.0960 2415.204175 0 0.0176 140 | 0/8 7 h-lim-p 0.0031 0.3838 0.5484 2415.172677 0 0.0124 162 | 0/8 8 h-lim-p 0.0019 0.0628 3.6451 2415.155690 4 0.0014 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0008 2415.155262 2 0.9644 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2415.155261 0 1.0938 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2415.155261 0 1.2500 246 | 0/8 12 h-lim-p 1.4090 20.0000 0.0000 2415.155261 0 0.3082 267 | 0/8 13 h-lim-p 0.1264 20.0000 0.0000 2415.155261 0 0.0000 300 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 2415.155261 0 0.0000 332 Out... lnL = -2415.155261 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2415.155261 Node 7: lnL = -2415.155261 Node 8: lnL = -2415.155261 Node 9: lnL = -2415.155261 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 317 Sequential format.. Reading seq # 1: YDR364C_Sbay Reading seq # 2: YDR364C_Scer Reading seq # 3: YDR364C_Skud Reading seq # 4: YDR364C_Smik Reading seq # 5: YDR364C_Spar Sequences read.. Counting patterns.. # site patterns = 152 Counting frequencies.. 120 bytes for distance 24320 bytes for lkl0 19456 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.179742 0.164396 0.067330 0.168445 0.078664 0.212123 0.193673 0.078217 lnL0 = -1484.736430 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1484.736430 x= 0.17974 0.16440 0.06733 0.16845 0.07866 0.21212 0.19367 0.07822 1 h-lim-p 0.0010 0.0078 43.7983 1484.053070 5 0.0007 32 | 0/8 2 h-lim-p 0.0019 0.0152 12.1040 1483.991647 2 0.0009 48 | 0/8 3 h-lim-p 0.0014 0.0646 7.6167 1483.978184 4 0.0006 67 | 0/8 4 h-lim-p 0.0018 0.1290 2.6259 1483.975052 4 0.0011 90 | 0/8 5 h-lim-p 0.0046 0.5159 0.6112 1483.974851 3 0.0011 109 | 0/8 6 h-lim-p 0.0053 2.2074 0.1304 1483.974842 1 0.0012 132 | 0/8 7 h-lim-p 0.0125 20.0000 0.0121 1483.974842 0 0.0027 153 | 0/8 8 h-lim-p 0.1145 20.0000 0.0003 1483.974814 0 0.9164 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1483.974814 0 1.0938 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1483.974814 0 1.0938 216 | 0/8 11 h-lim-p 1.1614 20.0000 0.0000 1483.974814 0 0.2903 237 | 0/8 12 h-lim-p 0.0687 20.0000 0.0000 1483.974814 0 0.0003 264 | 0/8 13 h-lim-p 0.0008 20.0000 0.0000 1483.974814 0 0.0001 286 Out... lnL = -1483.974814 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1483.974814 Node 7: lnL = -1483.974814 Node 8: lnL = -1483.974814 Node 9: lnL = -1483.974814 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 170 Sequential format.. Reading seq # 1: YDR367W_Sbay Reading seq # 2: YDR367W_Scer Reading seq # 3: YDR367W_Skud Reading seq # 4: YDR367W_Smik Reading seq # 5: YDR367W_Spar Sequences read.. Counting patterns.. # site patterns = 70 Counting frequencies.. 120 bytes for distance 11200 bytes for lkl0 8960 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.134013 0.033312 0.035743 0.265919 0.073070 0.184389 0.146105 0.056293 lnL0 = -621.741473 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 621.741473 x= 0.13401 0.03331 0.03574 0.26592 0.07307 0.18439 0.14611 0.05629 1 h-lim-p 0.0014 0.0347 92.7046 619.943022 9 0.0005 43 | 0/8 2 h-lim-p 0.0006 0.0051 20.3356 619.677863 0 0.0013 56 | 0/8 3 h-lim-p 0.0011 0.0086 15.1991 619.533044 0 0.0022 69 | 0/8 4 h-lim-p 0.0005 0.0037 15.2960 619.268344 m 0.0037 81 | 1/8 5 h-lim-p 0.0003 0.0221 132.2098 619.256278 6 0.0000 109 | 1/8 6 h-lim-p 0.0037 0.3392 1.5249 619.243431 0 0.0110 122 | 1/8 7 h-lim-p 0.0033 0.5449 5.0619 619.218782 0 0.0066 135 | 1/8 8 h-lim-p 0.6816 5.4530 0.0238 619.180423 6 0.4392 161 | 1/8 9 h-lim-p 2.5000 20.0000 0.0036 619.173833 4 2.4902 188 | 1/8 10 h-lim-p 2.5000 20.0000 0.0022 619.173409 5 1.5673 220 | 1/8 11 h-lim-p 2.5000 20.0000 0.0005 619.173385 3 1.3437 246 | 1/8 12 h-lim-p 2.5000 20.0000 0.0001 619.173385 0 1.0938 265 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 619.173385 0 1.0938 284 | 1/8 14 h-lim-p 1.2631 20.0000 0.0000 619.173385 0 0.0789 306 | 1/8 15 h-lim-p 0.0040 20.0000 0.0001 619.173385 0 0.0020 325 | 1/8 16 h-lim-p 0.0007 20.0000 0.0003 619.173385 0 0.0007 344 | 1/8 17 h-lim-p 0.0004 20.0000 0.0004 619.173385 0 0.0001 364 | 1/8 18 h-lim-p 0.0001 20.0000 0.0006 619.173385 0 0.0000 386 | 1/8 19 h-lim-p 0.0001 20.0000 0.0000 619.173385 0 0.0000 418 | 1/8 20 h-lim-p 0.0000 20.0000 0.0001 | 1/8 21 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -619.173385 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -619.173385 Node 7: lnL = -619.173385 Node 8: lnL = -619.173385 Node 9: lnL = -619.173385 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 332 Sequential format.. Reading seq # 1: YDR368W_Sbay Reading seq # 2: YDR368W_Scer Reading seq # 3: YDR368W_Skud Reading seq # 4: YDR368W_Smik Reading seq # 5: YDR368W_Spar Sequences read.. Counting patterns.. # site patterns = 149 Counting frequencies.. 120 bytes for distance 23840 bytes for lkl0 19072 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.230419 0.015738 0.102796 0.128160 0.092245 0.247822 0.288053 0.126286 lnL0 = -1518.860127 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1518.860127 x= 0.23042 0.01574 0.10280 0.12816 0.09225 0.24782 0.28805 0.12629 1 h-lim-p 0.0008 0.0062 50.4572 1518.141002 7 0.0006 37 | 0/8 2 h-lim-p 0.0010 0.0079 19.7835 1517.977972 2 0.0009 53 | 0/8 3 h-lim-p 0.0025 0.0672 7.4396 1517.959411 6 0.0008 79 | 0/8 4 h-lim-p 0.0017 0.0448 3.4168 1517.956570 5 0.0006 103 | 0/8 5 h-lim-p 0.0025 0.1545 0.8104 1517.956233 2 0.0011 119 | 0/8 6 h-lim-p 0.0047 0.7884 0.1885 1517.956218 2 0.0009 144 | 0/8 7 h-lim-p 0.0135 10.8814 0.0128 1517.956218 1 0.0033 167 | 0/8 8 h-lim-p 0.1190 20.0000 0.0004 1517.956171 0 0.7138 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1517.956170 0 1.0938 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1517.956170 0 1.0938 229 | 0/8 11 h-lim-p 1.2487 20.0000 0.0000 1517.956170 0 0.0098 255 | 0/8 12 h-lim-p 0.0026 20.0000 0.0000 1517.956170 0 0.0003 277 | 0/8 13 h-lim-p 0.0000 20.0000 0.0074 1517.956170 0 0.0000 300 | 0/8 14 h-lim-p 0.0006 20.0000 0.0000 1517.956170 0 0.0000 334 Out... lnL = -1517.956170 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1517.956170 Node 7: lnL = -1517.956170 Node 8: lnL = -1517.956170 Node 9: lnL = -1517.956170 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 251 Sequential format.. Reading seq # 1: YDR369C_Sbay Reading seq # 2: YDR369C_Scer Reading seq # 3: YDR369C_Skud Reading seq # 4: YDR369C_Smik Reading seq # 5: YDR369C_Spar Sequences read.. Counting patterns.. # site patterns = 152 Counting frequencies.. 120 bytes for distance 24320 bytes for lkl0 19456 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.215379 0.045678 0.174042 0.172090 0.095416 0.188167 0.500509 0.087237 lnL0 = -1196.725755 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1196.725755 x= 0.21538 0.04568 0.17404 0.17209 0.09542 0.18817 0.50051 0.08724 1 h-lim-p 0.0016 0.0131 35.5656 1196.107342 9 0.0010 42 | 0/8 2 h-lim-p 0.0043 0.0345 7.6488 1196.045029 4 0.0022 63 | 0/8 3 h-lim-p 0.0047 0.0946 3.5612 1196.038978 5 0.0011 88 | 0/8 4 h-lim-p 0.0022 0.1499 1.8580 1196.036817 5 0.0016 111 | 0/8 5 h-lim-p 0.0048 0.8630 0.6292 1196.036062 2 0.0045 127 | 0/8 6 h-lim-p 0.0212 1.6536 0.1327 1196.036039 2 0.0028 153 | 0/8 7 h-lim-p 0.0086 6.0155 0.0431 1196.036036 1 0.0021 176 | 0/8 8 h-lim-p 0.1162 20.0000 0.0008 1196.035820 0 0.9293 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1196.035819 0 1.0938 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1196.035818 0 1.0938 239 | 0/8 11 h-lim-p 2.4638 20.0000 0.0000 1196.035818 0 1.0779 259 | 0/8 12 h-lim-p 0.9641 20.0000 0.0000 1196.035818 015.4256 283 | 0/8 13 h-lim-p 0.0399 20.0000 0.0013 1196.035818 0 0.0003 309 | 0/8 14 h-lim-p 0.0004 20.0000 0.0010 1196.035818 0 0.0000 333 | 0/8 15 h-lim-p 0.0002 20.0000 0.0001 1196.035818 0 0.0000 366 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1196.035818 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1196.035818 Node 7: lnL = -1196.035818 Node 8: lnL = -1196.035818 Node 9: lnL = -1196.035818 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 319 Sequential format.. Reading seq # 1: YDR371W_Sbay Reading seq # 2: YDR371W_Scer Reading seq # 3: YDR371W_Skud Reading seq # 4: YDR371W_Smik Reading seq # 5: YDR371W_Spar Sequences read.. Counting patterns.. # site patterns = 110 Counting frequencies.. 120 bytes for distance 17600 bytes for lkl0 14080 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.515777 0.759539 0.000060 0.662753 2.091864 0.870298 0.554198 0.213247 lnL0 = -1500.802331 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1500.802331 x= 0.51578 0.75954 0.00006 0.66275 2.09186 0.87030 0.55420 0.21325 1 h-lim-p 0.0000 0.0000 210.2108 1500.752934 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0111 63.8845 1474.186791 3 0.0094 49 | 1/8 3 h-lim-p 0.0014 0.0108 44.4899 1458.348808 m 0.0108 61 | 2/8 4 h-lim-p 0.0011 0.0087 35.9494 1455.919374 0 0.0044 75 | 2/8 5 h-lim-p 0.0310 0.2479 4.9865 .. | 1/8 6 h-lim-p 0.0000 0.0033 140.9990 1415.088682 m 0.0033 130 | 2/8 7 h-lim-p 0.0004 0.0035 214.6082 1396.456147 0 0.0018 144 | 2/8 8 h-lim-p 0.0013 0.0100 101.4610 1364.422198 0 0.0075 158 | 1/8 9 h-lim-p 0.0000 0.0000 9655.4919 1354.849627 0 0.0000 172 | 1/8 10 h-lim-p 0.0010 0.0083 22.0574 1354.537954 1 0.0013 186 | 0/8 11 h-lim-p 0.0007 0.0244 42.1381 1353.224682 0 0.0014 199 | 0/8 12 h-lim-p 0.0156 0.1245 0.6535 1336.280730 m 0.1245 211 | 0/8 13 h-lim-p 0.0000 0.0000 0.5856 h-lim-p: 5.11238257e-18 4.08990605e-17 5.85596167e-01 1336.280730 .. | 0/8 14 h-lim-p 0.0000 0.0010 1009.0831 1286.404429 0 0.0002 251 | 0/8 15 h-lim-p 0.0000 0.0000 130.6145 1286.007409 m 0.0000 263 | 1/8 16 h-lim-p 0.0001 0.0014 45.8294 1284.563597 m 0.0014 277 | 2/8 17 h-lim-p 0.0014 0.0114 18.5117 1278.729610 0 0.0057 291 | 2/8 18 h-lim-p 0.0012 0.0097 21.3244 1278.505112 5 0.0010 314 | 2/8 19 h-lim-p 0.0198 0.2311 1.0990 1278.503864 5 0.0017 340 | 1/8 20 h-lim-p 0.0007 1.6475 2.7291 1278.498406 0 0.0014 353 | 1/8 21 h-lim-p 0.0950 1.8886 0.0401 1278.463966 0 0.2849 366 | 1/8 22 h-lim-p 2.5000 20.0000 0.0042 1278.460221 4 0.6366 394 | 0/8 23 h-lim-p 0.0065 0.6237 0.4122 1278.460142 3 0.0011 422 | 0/8 24 h-lim-p 1.3126 20.0000 0.0003 1278.460105 3 0.9241 449 | 0/8 25 h-lim-p 2.5000 20.0000 0.0000 1278.460105 0 1.0938 469 | 0/8 26 h-lim-p 2.5000 20.0000 0.0000 1278.460105 0 1.0938 489 | 0/8 27 h-lim-p 2.5000 20.0000 0.0000 1278.460105 0 2.1875 509 | 0/8 28 h-lim-p 2.5000 20.0000 0.0000 1278.460105 0 0.1562 532 Out... lnL = -1278.460105 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1278.460105 Node 7: lnL = -1278.460105 Node 8: lnL = -1278.460105 Node 9: lnL = -1278.460105 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 631 Sequential format.. Reading seq # 1: YDR372C_Sbay Reading seq # 2: YDR372C_Scer Reading seq # 3: YDR372C_Skud Reading seq # 4: YDR372C_Smik Reading seq # 5: YDR372C_Spar Sequences read.. Counting patterns.. # site patterns = 192 Counting frequencies.. 120 bytes for distance 30720 bytes for lkl0 24576 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.116139 0.091631 0.043688 0.100680 0.078516 0.162531 0.133504 0.048169 lnL0 = -2610.244854 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2610.244854 x= 0.11614 0.09163 0.04369 0.10068 0.07852 0.16253 0.13350 0.04817 1 h-lim-p 0.0020 0.6471 162.5631 2608.604965 9 0.0001 49 | 0/8 2 h-lim-p 0.0012 0.0131 18.2954 2608.552944 4 0.0003 70 | 0/8 3 h-lim-p 0.0007 0.0260 8.4569 2608.545913 5 0.0002 95 | 0/8 4 h-lim-p 0.0020 0.1787 0.9748 2608.545765 3 0.0003 116 | 0/8 5 h-lim-p 0.0041 1.3295 0.0769 2608.545765 0 0.0003 139 | 0/8 6 h-lim-p 0.0012 20.0000 0.0169 2608.545765 0 0.0005 159 | 0/8 7 h-lim-p 0.0027 20.0000 0.0032 2608.545765 0 0.0007 180 | 0/8 8 h-lim-p 0.0182 20.0000 0.0001 2608.545758 0 0.5829 205 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2608.545758 0 1.0938 225 | 0/8 10 h-lim-p 1.2047 20.0000 0.0000 2608.545758 0 1.0542 245 | 0/8 11 h-lim-p 0.3623 20.0000 0.0001 2608.545758 0 0.0057 270 | 0/8 12 h-lim-p 0.0012 20.0000 0.0003 2608.545758 0 0.0000 295 | 0/8 13 h-lim-p 0.0001 20.0000 0.0001 2608.545758 0 0.0001 315 | 0/8 14 h-lim-p 0.0004 20.0000 0.0000 2608.545758 0 0.0004 335 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 2608.545758 0 0.0000 355 | 0/8 16 h-lim-p 0.0003 20.0000 0.0000 2608.545758 0 0.0000 386 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -2608.545758 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2608.545758 Node 7: lnL = -2608.545758 Node 8: lnL = -2608.545758 Node 9: lnL = -2608.545758 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 631 Sequential format.. Reading seq # 1: YDR373W_Sbay Reading seq # 2: YDR373W_Scer Reading seq # 3: YDR373W_Skud Reading seq # 4: YDR373W_Smik Reading seq # 5: YDR373W_Spar Sequences read.. Counting patterns.. # site patterns = 194 Counting frequencies.. 120 bytes for distance 31040 bytes for lkl0 24832 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.114491 0.096724 0.042632 0.103677 0.077653 0.163785 0.134861 0.045961 lnL0 = -2622.088038 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2622.088038 x= 0.11449 0.09672 0.04263 0.10368 0.07765 0.16378 0.13486 0.04596 1 h-lim-p 0.0016 0.5703 181.5454 2620.064284 8 0.0001 44 | 0/8 2 h-lim-p 0.0009 0.0069 15.3066 2620.035994 6 0.0002 72 | 0/8 3 h-lim-p 0.0007 0.0386 5.6559 2620.031716 2 0.0003 88 | 0/8 4 h-lim-p 0.0017 0.1711 1.0420 2620.031552 3 0.0003 107 | 0/8 5 h-lim-p 0.0016 0.5062 0.2056 2620.031548 1 0.0002 123 | 0/8 6 h-lim-p 0.0012 5.9506 0.0350 2620.031548 0 0.0005 143 | 0/8 7 h-lim-p 0.0061 20.0000 0.0029 2620.031548 0 0.0013 164 | 0/8 8 h-lim-p 0.0147 20.0000 0.0003 2620.031536 0 0.4705 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2620.031535 0 1.0938 209 | 0/8 10 h-lim-p 1.8153 20.0000 0.0000 2620.031535 0 1.5884 229 | 0/8 11 h-lim-p 1.9091 20.0000 0.0000 2620.031535 0 1.6705 249 | 0/8 12 h-lim-p 1.2094 20.0000 0.0000 2620.031535 0 1.0582 269 | 0/8 13 h-lim-p 0.3253 20.0000 0.0001 2620.031535 0 0.0003 298 | 0/8 14 h-lim-p 0.0003 20.0000 0.0001 2620.031535 0 0.0000 320 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 2620.031535 0 0.0000 344 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 2620.031535 0 0.0000 374 Out... lnL = -2620.031535 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2620.031535 Node 7: lnL = -2620.031535 Node 8: lnL = -2620.031535 Node 9: lnL = -2620.031535 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 800 Sequential format.. Reading seq # 1: YDR374C_Sbay Reading seq # 2: YDR374C_Scer Reading seq # 3: YDR374C_Skud Reading seq # 4: YDR374C_Smik Reading seq # 5: YDR374C_Spar Sequences read.. Counting patterns.. # site patterns = 244 Counting frequencies.. 120 bytes for distance 39040 bytes for lkl0 31232 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.153762 0.018371 0.050576 0.131498 0.081184 0.174902 0.190354 0.079940 lnL0 = -3416.986468 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3416.986468 x= 0.15376 0.01837 0.05058 0.13150 0.08118 0.17490 0.19035 0.07994 1 h-lim-p 0.0008 0.0149 287.6121 3413.497520 3 0.0001 30 | 0/8 2 h-lim-p 0.0005 0.0038 28.0997 3413.412739 2 0.0002 46 | 0/8 3 h-lim-p 0.0006 0.0297 10.0366 3413.402697 5 0.0002 70 | 0/8 4 h-lim-p 0.0009 0.0971 2.4065 3413.401699 3 0.0004 88 | 0/8 5 h-lim-p 0.0028 0.4105 0.3139 3413.401686 2 0.0003 106 | 0/8 6 h-lim-p 0.0007 2.5514 0.1183 3413.401684 0 0.0004 126 | 0/8 7 h-lim-p 0.0075 20.0000 0.0057 3413.401671 0 0.0151 147 | 0/8 8 h-lim-p 0.0038 20.0000 0.0230 3413.400666 0 0.0300 170 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3413.400593 2 0.9961 194 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3413.400593 0 1.0938 214 | 0/8 11 h-lim-p 1.3763 20.0000 0.0000 3413.400593 0 1.2043 234 | 0/8 12 h-lim-p 0.6143 20.0000 0.0000 3413.400593 0 0.0006 263 | 0/8 13 h-lim-p 0.0001 20.0000 0.0003 3413.400593 0 0.0000 287 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 3413.400593 0 0.0000 319 Out... lnL = -3413.400593 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3413.400593 Node 7: lnL = -3413.400593 Node 8: lnL = -3413.400593 Node 9: lnL = -3413.400593 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 340 Sequential format.. Reading seq # 1: YDR376W_Sbay Reading seq # 2: YDR376W_Scer Reading seq # 3: YDR376W_Skud Reading seq # 4: YDR376W_Smik Reading seq # 5: YDR376W_Spar Sequences read.. Counting patterns.. # site patterns = 163 Counting frequencies.. 120 bytes for distance 26080 bytes for lkl0 20864 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.207013 0.084974 0.100531 0.149812 0.107559 0.190414 0.255946 0.102798 lnL0 = -1541.497265 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1541.497265 x= 0.20701 0.08497 0.10053 0.14981 0.10756 0.19041 0.25595 0.10280 1 h-lim-p 0.0030 0.0240 43.2242 1540.828769 8 0.0008 42 | 0/8 2 h-lim-p 0.0021 0.0168 15.0960 1540.727773 2 0.0010 58 | 0/8 3 h-lim-p 0.0027 0.0626 5.5385 1540.716447 6 0.0008 86 | 0/8 4 h-lim-p 0.0024 0.1699 1.9410 1540.714322 4 0.0013 107 | 0/8 5 h-lim-p 0.0086 1.4628 0.2892 1540.714279 1 0.0011 123 | 0/8 6 h-lim-p 0.0134 8.2531 0.0231 1540.714279 0 0.0015 145 | 0/8 7 h-lim-p 0.0092 20.0000 0.0037 1540.714277 0 0.0184 166 | 0/8 8 h-lim-p 0.0106 20.0000 0.0064 1540.714203 0 0.0423 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1540.714200 1 0.9961 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1540.714200 0 1.0938 230 | 0/8 11 h-lim-p 1.7371 20.0000 0.0000 1540.714200 0 2.6056 250 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1540.714200 0 0.1562 273 | 0/8 13 h-lim-p 0.0112 20.0000 0.0000 1540.714200 0 0.0000 300 Out... lnL = -1540.714200 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1540.714200 Node 7: lnL = -1540.714200 Node 8: lnL = -1540.714200 Node 9: lnL = -1540.714200 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 333 Sequential format.. Reading seq # 1: YDR377W_Sbay Reading seq # 2: YDR377W_Scer Reading seq # 3: YDR377W_Skud Reading seq # 4: YDR377W_Smik Reading seq # 5: YDR377W_Spar Sequences read.. Counting patterns.. # site patterns = 124 Counting frequencies.. 120 bytes for distance 19840 bytes for lkl0 15872 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.144975 0.040021 0.087048 0.065108 0.072129 0.134343 0.149444 0.077670 lnL0 = -1327.806709 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1327.806709 x= 0.14498 0.04002 0.08705 0.06511 0.07213 0.13434 0.14944 0.07767 1 h-lim-p 0.0005 0.0038 96.6540 1326.491287 8 0.0003 42 | 0/8 2 h-lim-p 0.0008 0.0064 11.9760 1326.466907 5 0.0003 63 | 0/8 3 h-lim-p 0.0011 0.0628 3.7816 1326.463461 4 0.0005 85 | 0/8 4 h-lim-p 0.0016 0.1156 1.2637 1326.463076 4 0.0005 108 | 0/8 5 h-lim-p 0.0025 0.9034 0.2712 1326.463056 0 0.0006 121 | 0/8 6 h-lim-p 0.0075 12.8269 0.0226 1326.463055 0 0.0008 143 | 0/8 7 h-lim-p 0.0069 20.0000 0.0027 1326.463055 0 0.0030 163 | 0/8 8 h-lim-p 0.0707 20.0000 0.0001 1326.463050 0 0.5657 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1326.463050 0 1.0938 206 | 0/8 10 h-lim-p 2.3019 20.0000 0.0000 1326.463050 0 2.0141 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1326.463050 0 1.0938 246 | 0/8 12 h-lim-p 0.2394 20.0000 0.0000 1326.463050 0 7.6620 271 | 0/8 13 h-lim-p 0.2789 20.0000 0.0002 1326.463050 0 0.0174 294 | 0/8 14 h-lim-p 0.0023 20.0000 0.0015 1326.463050 0 0.0001 317 | 0/8 15 h-lim-p 0.0002 20.0000 0.0011 1326.463050 0 0.0000 347 | 0/8 16 h-lim-p 0.0006 20.0000 0.0000 1326.463050 0 0.0003 367 Out... lnL = -1326.463050 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1326.463050 Node 7: lnL = -1326.463050 Node 8: lnL = -1326.463050 Node 9: lnL = -1326.463050 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 804 Sequential format.. Reading seq # 1: YDR380W_Sbay Reading seq # 2: YDR380W_Scer Reading seq # 3: YDR380W_Skud Reading seq # 4: YDR380W_Smik Reading seq # 5: YDR380W_Spar Sequences read.. Counting patterns.. # site patterns = 257 Counting frequencies.. 120 bytes for distance 41120 bytes for lkl0 32896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.244003 0.357596 0.000060 0.267206 0.231383 0.620782 0.247824 0.106708 lnL0 = -3197.827830 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3197.827830 x= 0.24400 0.35760 0.00006 0.26721 0.23138 0.62078 0.24782 0.10671 1 h-lim-p 0.0000 0.0000 442.0105 3197.689903 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0025 149.1729 3188.110499 0 0.0010 40 | 1/8 3 h-lim-p 0.0017 0.0133 33.3547 3186.667664 0 0.0025 52 | 1/8 4 h-lim-p 0.0036 0.0660 23.1699 3183.769237 0 0.0107 65 | 1/8 5 h-lim-p 0.0015 0.0121 66.1189 3180.846668 0 0.0045 78 | 1/8 6 h-lim-p 0.0016 0.0128 48.7966 3179.029383 0 0.0032 91 | 1/8 7 h-lim-p 0.0567 0.4538 1.4680 3139.038643 0 0.2269 105 | 1/8 8 h-lim-p 0.1726 1.3811 0.6110 3135.367063 0 0.3453 118 | 0/8 9 h-lim-p 0.0000 0.0000 1.2902 h-lim-p: 2.02569314e-23 1.62055452e-22 1.29017492e+00 3135.367063 .. | 0/8 10 h-lim-p 0.0000 0.0127 37.7460 3135.103346 0 0.0003 150 | 0/8 11 h-lim-p 0.0008 0.0138 14.4752 3135.059285 7 0.0005 178 | 0/8 12 h-lim-p 0.0013 0.0758 5.4233 3135.046486 3 0.0010 196 | 0/8 13 h-lim-p 0.0004 0.0638 13.6159 3134.966787 0 0.0032 211 | 0/8 14 h-lim-p 0.0005 0.0096 85.7146 3134.858496 0 0.0008 223 | 0/8 15 h-lim-p 0.0219 0.1749 1.7110 3134.857298 4 0.0009 249 | 0/8 16 h-lim-p 0.0007 0.1284 2.1548 3134.852402 0 0.0044 263 | 0/8 17 h-lim-p 0.5058 9.0229 0.0188 3134.838592 0 1.0115 276 | 0/8 18 h-lim-p 2.5000 20.0000 0.0030 3134.838334 3 1.0004 302 | 0/8 19 h-lim-p 2.5000 20.0000 0.0001 3134.838334 0 1.0938 322 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 3134.838334 0 1.0938 342 | 0/8 21 h-lim-p 2.5000 20.0000 0.0000 3134.838334 0 2.1875 362 | 0/8 22 h-lim-p 2.5000 20.0000 0.0000 3134.838334 0 0.6250 383 | 0/8 23 h-lim-p 0.1195 20.0000 0.0000 3134.838334 0 0.1793 403 | 0/8 24 h-lim-p 0.0646 20.0000 0.0000 3134.838334 0 0.0000 447 | 0/8 25 h-lim-p 0.0000 20.0000 0.0002 | 0/8 26 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -3134.838334 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3134.838334 Node 7: lnL = -3134.838334 Node 8: lnL = -3134.838334 Node 9: lnL = -3134.838334 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 741 Sequential format.. Reading seq # 1: YDR382W_Sbay Reading seq # 2: YDR382W_Scer Reading seq # 3: YDR382W_Skud Reading seq # 4: YDR382W_Smik Reading seq # 5: YDR382W_Spar Sequences read.. Counting patterns.. # site patterns = 291 Counting frequencies.. 120 bytes for distance 46560 bytes for lkl0 37248 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.175487 0.087945 0.067114 0.109631 0.104825 0.231229 0.233598 0.074020 lnL0 = -3361.957193 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3361.957193 x= 0.17549 0.08794 0.06711 0.10963 0.10483 0.23123 0.23360 0.07402 1 h-lim-p 0.0014 0.0110 171.4829 3358.662409 6 0.0002 36 | 0/8 2 h-lim-p 0.0005 0.0041 34.4970 3358.469085 6 0.0003 63 | 0/8 3 h-lim-p 0.0008 0.0117 14.3649 3358.437702 5 0.0004 84 | 0/8 4 h-lim-p 0.0015 0.0580 3.3175 3358.435487 5 0.0004 108 | 0/8 5 h-lim-p 0.0020 0.4207 0.7076 3358.435328 3 0.0007 127 | 0/8 6 h-lim-p 0.0172 5.8888 0.0272 3358.435328 0 0.0009 150 | 0/8 7 h-lim-p 0.0024 20.0000 0.0109 3358.435327 0 0.0035 170 | 0/8 8 h-lim-p 0.0160 20.0000 0.0024 3358.435132 0 0.1925 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3358.435123 1 0.9961 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3358.435123 0 2.1875 235 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3358.435123 0 1.0938 255 | 0/8 12 h-lim-p 0.1510 20.0000 0.0000 3358.435123 0 0.0000 295 | 0/8 13 h-lim-p 0.0000 20.0000 0.0002 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -3358.435123 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3358.435123 Node 7: lnL = -3358.435123 Node 8: lnL = -3358.435123 Node 9: lnL = -3358.435123 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 557 Sequential format.. Reading seq # 1: YDR383C_Sbay Reading seq # 2: YDR383C_Scer Reading seq # 3: YDR383C_Skud Reading seq # 4: YDR383C_Smik Reading seq # 5: YDR383C_Spar Sequences read.. Counting patterns.. # site patterns = 289 Counting frequencies.. 120 bytes for distance 46240 bytes for lkl0 36992 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.365561 0.068823 0.112690 0.197442 0.129517 0.257985 0.525374 0.195728 lnL0 = -2913.564085 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2913.564085 x= 0.36556 0.06882 0.11269 0.19744 0.12952 0.25799 0.52537 0.19573 1 h-lim-p 0.0110 1.6550 72.6899 2912.181763 7 0.0006 38 | 0/8 2 h-lim-p 0.0013 0.0106 19.7684 2912.034539 7 0.0008 69 | 0/8 3 h-lim-p 0.0018 0.0331 8.8170 2911.998838 6 0.0011 99 | 0/8 4 h-lim-p 0.0038 0.1534 2.5329 2911.994768 5 0.0014 123 | 0/8 5 h-lim-p 0.0036 0.5596 1.0048 2911.993407 2 0.0031 139 | 0/8 6 h-lim-p 0.0078 1.5327 0.3992 2911.993222 3 0.0028 159 | 0/8 7 h-lim-p 0.0067 1.9805 0.1646 2911.993202 0 0.0017 180 | 0/8 8 h-lim-p 0.2035 20.0000 0.0014 2911.991761 0 1.2210 202 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 2911.991740 1 0.9961 224 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2911.991740 0 1.0938 244 | 0/8 11 h-lim-p 1.7222 20.0000 0.0000 2911.991740 0 0.7534 264 | 0/8 12 h-lim-p 0.4604 20.0000 0.0000 2911.991740 0 0.0575 286 | 0/8 13 h-lim-p 0.0147 20.0000 0.0000 2911.991740 0 0.0005 310 | 0/8 14 h-lim-p 0.0006 20.0000 0.0000 2911.991740 0 0.0002 331 | 0/8 15 h-lim-p 0.0023 20.0000 0.0000 2911.991740 0 0.0003 353 Out... lnL = -2911.991740 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2911.991740 Node 7: lnL = -2911.991740 Node 8: lnL = -2911.991740 Node 9: lnL = -2911.991740 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 920 Sequential format.. Reading seq # 1: YDR384C_Sbay Reading seq # 2: YDR384C_Scer Reading seq # 3: YDR384C_Skud Reading seq # 4: YDR384C_Smik Reading seq # 5: YDR384C_Spar Sequences read.. Counting patterns.. # site patterns = 268 Counting frequencies.. 120 bytes for distance 42880 bytes for lkl0 34304 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.246504 0.019077 0.066615 0.082213 0.053390 0.117718 0.148709 0.164261 lnL0 = -3515.428651 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3515.428651 x= 0.24650 0.01908 0.06661 0.08221 0.05339 0.11772 0.14871 0.16426 1 h-lim-p 0.0004 0.0035 183.3658 3513.291359 8 0.0001 44 | 0/8 2 h-lim-p 0.0003 0.0027 54.8019 3512.936949 6 0.0003 68 | 0/8 3 h-lim-p 0.0003 0.0055 40.1130 3512.862258 4 0.0001 88 | 0/8 4 h-lim-p 0.0004 0.0094 13.8054 3512.846208 5 0.0002 112 | 0/8 5 h-lim-p 0.0006 0.0406 4.6212 3512.842847 5 0.0004 137 | 0/8 6 h-lim-p 0.0048 0.1311 0.3467 3512.842831 0 0.0003 152 | 0/8 7 h-lim-p 0.0012 1.2760 0.0765 3512.842830 0 0.0005 172 | 0/8 8 h-lim-p 0.1728 20.0000 0.0002 3512.842749 0 1.0368 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3512.842749 0 1.0938 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3512.842749 0 2.1875 234 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3512.842749 0 1.0938 254 | 0/8 12 h-lim-p 0.2576 20.0000 0.0000 3512.842749 0 4.1222 278 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 3512.842749 0 0.0098 305 | 0/8 14 h-lim-p 0.0153 20.0000 0.0000 3512.842749 0 0.0076 325 | 0/8 15 h-lim-p 0.0018 20.0000 0.0000 3512.842749 0 0.0000 360 | 0/8 16 h-lim-p 0.0000 20.0000 0.0019 3512.842749 0 0.0000 384 | 0/8 17 h-lim-p 0.0000 20.0000 0.0007 3512.842749 0 0.0010 410 | 0/8 18 h-lim-p 0.0015 20.0000 0.0004 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0046 | 0/8 20 h-lim-p 0.0000 20.0000 0.0046 Out... lnL = -3512.842749 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3512.842749 Node 7: lnL = -3512.842749 Node 8: lnL = -3512.842749 Node 9: lnL = -3512.842749 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 407 Sequential format.. Reading seq # 1: YDR387C_Sbay Reading seq # 2: YDR387C_Scer Reading seq # 3: YDR387C_Skud Reading seq # 4: YDR387C_Smik Reading seq # 5: YDR387C_Spar Sequences read.. Counting patterns.. # site patterns = 156 Counting frequencies.. 120 bytes for distance 24960 bytes for lkl0 19968 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.193523 0.083458 0.042776 0.115300 0.070207 0.171327 0.143534 0.107007 lnL0 = -1711.762913 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1711.762913 x= 0.19352 0.08346 0.04278 0.11530 0.07021 0.17133 0.14353 0.10701 1 h-lim-p 0.0007 0.0056 110.3728 1710.341009 9 0.0003 43 | 0/8 2 h-lim-p 0.0009 0.0069 31.7946 1710.059806 8 0.0006 74 | 0/8 3 h-lim-p 0.0016 0.0237 11.4050 1710.034977 5 0.0004 97 | 0/8 4 h-lim-p 0.0020 0.0400 2.5215 1710.033906 5 0.0004 123 | 0/8 5 h-lim-p 0.0024 0.5682 0.3679 1710.033864 2 0.0006 140 | 0/8 6 h-lim-p 0.0034 3.7067 0.0690 1710.033863 1 0.0004 164 | 0/8 7 h-lim-p 0.0135 20.0000 0.0021 1710.033862 0 0.0135 184 | 0/8 8 h-lim-p 0.0095 20.0000 0.0031 1710.033808 0 0.0757 207 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1710.033808 0 1.0938 227 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1710.033808 0 1.0938 247 | 0/8 11 h-lim-p 1.1773 20.0000 0.0000 1710.033808 0 0.0023 275 | 0/8 12 h-lim-p 0.0012 20.0000 0.0000 1710.033808 0 0.0000 301 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 1710.033808 0 0.0000 333 Out... lnL = -1710.033808 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1710.033808 Node 7: lnL = -1710.033808 Node 8: lnL = -1710.033808 Node 9: lnL = -1710.033808 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 676 Sequential format.. Reading seq # 1: YDR391C_Sbay Reading seq # 2: YDR391C_Scer Reading seq # 3: YDR391C_Skud Reading seq # 4: YDR391C_Smik Reading seq # 5: YDR391C_Spar Sequences read.. Counting patterns.. # site patterns = 274 Counting frequencies.. 120 bytes for distance 43840 bytes for lkl0 35072 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.250010 0.200328 0.086585 0.132745 0.100305 0.191329 0.244434 0.121516 lnL0 = -3306.447093 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3306.447093 x= 0.25001 0.20033 0.08659 0.13274 0.10030 0.19133 0.24443 0.12152 1 h-lim-p 0.0003 0.0027 67.4754 3305.600411 5 0.0004 33 | 0/8 2 h-lim-p 0.0009 0.0102 27.2362 3305.446978 4 0.0005 54 | 0/8 3 h-lim-p 0.0008 0.0198 15.5956 3305.414617 5 0.0004 79 | 0/8 4 h-lim-p 0.0009 0.0579 5.8971 3305.405883 4 0.0006 101 | 0/8 5 h-lim-p 0.0012 0.0855 3.0701 3305.404006 2 0.0005 117 | 0/8 6 h-lim-p 0.0036 0.8335 0.4340 3305.403947 3 0.0006 138 | 0/8 7 h-lim-p 0.0142 19.6384 0.0197 3305.403945 0 0.0031 159 | 0/8 8 h-lim-p 0.0314 20.0000 0.0019 3305.403475 0 0.3769 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3305.403461 1 0.9961 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3305.403461 0 2.1875 224 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3305.403461 0 1.0938 244 | 0/8 12 h-lim-p 0.1076 20.0000 0.0000 3305.403461 0 0.1076 264 | 0/8 13 h-lim-p 0.0027 20.0000 0.0003 3305.403461 0 0.0000 301 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -3305.403461 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3305.403461 Node 7: lnL = -3305.403461 Node 8: lnL = -3305.403461 Node 9: lnL = -3305.403461 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 260 Sequential format.. Reading seq # 1: YDR393W_Sbay Reading seq # 2: YDR393W_Scer Reading seq # 3: YDR393W_Skud Reading seq # 4: YDR393W_Smik Reading seq # 5: YDR393W_Spar Sequences read.. Counting patterns.. # site patterns = 99 Counting frequencies.. 120 bytes for distance 15840 bytes for lkl0 12672 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.132560 0.152950 0.118034 0.116772 0.023168 0.206741 0.106834 0.042160 lnL0 = -964.273467 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 964.273467 x= 0.13256 0.15295 0.11803 0.11677 0.02317 0.20674 0.10683 0.04216 1 h-lim-p 0.0111 0.0887 12.1818 964.228560 3 0.0006 31 | 0/8 2 h-lim-p 0.0006 0.0050 13.3968 964.197712 3 0.0006 49 | 0/8 3 h-lim-p 0.0029 0.0568 2.6447 964.194447 5 0.0010 73 | 0/8 4 h-lim-p 0.0021 0.1630 1.2775 964.193884 3 0.0008 91 | 0/8 5 h-lim-p 0.0084 2.1934 0.1296 964.193871 2 0.0016 108 | 0/8 6 h-lim-p 0.0083 6.6491 0.0251 964.193871 1 0.0010 132 | 0/8 7 h-lim-p 0.0066 20.0000 0.0039 964.193871 0 0.0015 153 | 0/8 8 h-lim-p 0.0581 20.0000 0.0001 964.193869 0 0.9302 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 964.193869 0 1.0938 197 | 0/8 10 h-lim-p 1.8586 20.0000 0.0000 964.193869 0 1.6263 217 | 0/8 11 h-lim-p 2.4793 20.0000 0.0000 964.193869 0 0.1356 240 | 0/8 12 h-lim-p 0.0375 20.0000 0.0000 964.193869 0 0.0094 261 | 0/8 13 h-lim-p 0.0043 20.0000 0.0000 964.193869 0 0.0001 285 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 964.193869 0 0.0000 318 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 964.193869 0 0.0000 344 | 0/8 16 h-lim-p 0.0000 20.0000 0.0005 964.193869 0 0.0026 372 | 0/8 17 h-lim-p 0.0109 20.0000 0.0001 964.193869 0 0.0000 402 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 964.193869 0 0.0000 425 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 964.193869 0 0.0000 451 | 0/8 20 h-lim-p 0.0000 20.0000 0.0021 | 0/8 21 h-lim-p 0.0000 20.0000 0.0021 Out... lnL = -964.193869 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -964.193869 Node 7: lnL = -964.193869 Node 8: lnL = -964.193869 Node 9: lnL = -964.193869 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 423 Sequential format.. Reading seq # 1: YDR394W_Sbay Reading seq # 2: YDR394W_Scer Reading seq # 3: YDR394W_Skud Reading seq # 4: YDR394W_Smik Reading seq # 5: YDR394W_Spar Sequences read.. Counting patterns.. # site patterns = 156 Counting frequencies.. 120 bytes for distance 24960 bytes for lkl0 19968 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.117196 0.080272 0.056844 0.131945 0.057597 0.165959 0.110005 0.044434 lnL0 = -1715.532089 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1715.532089 x= 0.11720 0.08027 0.05684 0.13194 0.05760 0.16596 0.11000 0.04443 1 h-lim-p 0.0002 0.0018 88.4315 1714.557866 1 0.0003 24 | 0/8 2 h-lim-p 0.0013 0.0101 12.2880 1714.524275 7 0.0005 53 | 0/8 3 h-lim-p 0.0011 0.0828 4.8887 1714.521961 4 0.0002 74 | 0/8 4 h-lim-p 0.0009 0.1735 1.1482 1714.521627 4 0.0006 96 | 0/8 5 h-lim-p 0.0030 1.2807 0.2090 1714.521617 2 0.0004 114 | 0/8 6 h-lim-p 0.0034 4.3306 0.0242 1714.521598 0 0.0069 135 | 0/8 7 h-lim-p 0.0051 5.9842 0.0324 1714.520287 0 0.0411 158 | 0/8 8 h-lim-p 0.0014 0.1234 0.9761 1714.518324 2 0.0013 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1714.518253 2 0.9961 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1714.518253 0 1.0938 226 | 0/8 11 h-lim-p 1.0161 20.0000 0.0000 1714.518253 0 0.1111 248 | 0/8 12 h-lim-p 0.0408 20.0000 0.0000 1714.518253 0 0.0408 268 | 0/8 13 h-lim-p 0.0201 20.0000 0.0001 1714.518253 0 0.0001 295 | 0/8 14 h-lim-p 0.0001 20.0000 0.0001 1714.518253 0 0.0000 316 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 1714.518253 0 0.0000 344 | 0/8 16 h-lim-p 0.0000 20.0000 0.0013 1714.518253 0 0.0000 377 | 0/8 17 h-lim-p 0.0000 20.0000 0.0013 1714.518253 0 0.0000 408 | 0/8 18 h-lim-p 0.0000 20.0000 0.0015 1714.518253 0 0.0000 428 | 0/8 19 h-lim-p 0.0001 20.0000 0.0003 1714.518253 0 0.0005 451 | 0/8 20 h-lim-p 0.0003 20.0000 0.0004 1714.518253 0 0.0000 479 | 0/8 21 h-lim-p 0.0000 20.0000 0.0001 1714.518253 0 0.0000 502 | 0/8 22 h-lim-p 0.0000 20.0000 0.0000 1714.518253 0 0.0000 534 | 0/8 23 h-lim-p 0.0000 20.0000 0.0012 | 0/8 24 h-lim-p 0.0000 20.0000 0.0012 Out... lnL = -1714.518253 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1714.518253 Node 7: lnL = -1714.518253 Node 8: lnL = -1714.518253 Node 9: lnL = -1714.518253 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 743 Sequential format.. Reading seq # 1: YDR397C_Sbay Reading seq # 2: YDR397C_Scer Reading seq # 3: YDR397C_Skud Reading seq # 4: YDR397C_Smik Reading seq # 5: YDR397C_Spar Sequences read.. Counting patterns.. # site patterns = 248 Counting frequencies.. 120 bytes for distance 39680 bytes for lkl0 31744 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.140758 0.059947 0.063252 0.095025 0.073891 0.137615 0.165906 0.065331 lnL0 = -2972.054132 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2972.054132 x= 0.14076 0.05995 0.06325 0.09503 0.07389 0.13762 0.16591 0.06533 1 h-lim-p 0.0003 0.0020 98.1045 2971.213018 7 0.0002 37 | 0/8 2 h-lim-p 0.0005 0.0042 25.6247 2971.155636 4 0.0002 58 | 0/8 3 h-lim-p 0.0012 0.0644 3.8873 2971.154020 5 0.0002 84 | 0/8 4 h-lim-p 0.0007 0.1721 1.1480 2971.153833 1 0.0003 98 | 0/8 5 h-lim-p 0.0025 1.5992 0.1338 2971.153830 0 0.0003 112 | 0/8 6 h-lim-p 0.0024 14.1777 0.0155 2971.153830 0 0.0005 133 | 0/8 7 h-lim-p 0.0016 20.0000 0.0052 2971.153829 0 0.0062 155 | 0/8 8 h-lim-p 0.0035 10.2513 0.0093 2971.153699 0 0.0280 178 | 0/8 9 h-lim-p 1.1049 20.0000 0.0002 2971.153696 0 0.9668 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2971.153696 0 1.0938 218 | 0/8 11 h-lim-p 1.5295 20.0000 0.0000 2971.153696 0 1.3383 238 | 0/8 12 h-lim-p 1.1918 20.0000 0.0000 2971.153696 0 4.7673 260 | 0/8 13 h-lim-p 0.1330 20.0000 0.0008 2971.153696 0 0.1164 280 | 0/8 14 h-lim-p 0.0265 20.0000 0.0036 2971.153696 0 0.0000 312 | 0/8 15 h-lim-p 0.0005 20.0000 0.0000 2971.153696 0 0.0000 347 | 0/8 16 h-lim-p 0.0000 20.0000 0.0015 | 0/8 17 h-lim-p 0.0000 20.0000 0.0015 Out... lnL = -2971.153696 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2971.153696 Node 7: lnL = -2971.153696 Node 8: lnL = -2971.153696 Node 9: lnL = -2971.153696 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 600 Sequential format.. Reading seq # 1: YDR398W_Sbay Reading seq # 2: YDR398W_Scer Reading seq # 3: YDR398W_Skud Reading seq # 4: YDR398W_Smik Reading seq # 5: YDR398W_Spar Sequences read.. Counting patterns.. # site patterns = 136 Counting frequencies.. 120 bytes for distance 21760 bytes for lkl0 17408 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.327632 0.066094 0.163771 0.238963 0.187343 4.390246 0.251607 0.000060 lnL0 = -2226.469439 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2226.469439 x= 0.32763 0.06609 0.16377 0.23896 0.18734 4.39025 0.25161 0.00006 1 h-lim-p 0.0000 0.0000 480.4287 2226.265993 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0025 147.0085 2215.920864 0 0.0010 40 | 1/8 3 h-lim-p 0.0033 0.0262 14.2330 2215.391713 7 0.0028 69 | 1/8 4 h-lim-p 0.0054 0.0430 5.4226 2212.601834 0 0.0161 82 | 1/8 5 h-lim-p 0.0033 0.0265 11.8039 2177.219519 0 0.0198 96 | 1/8 6 h-lim-p 0.0003 0.0028 96.9377 2170.112893 0 0.0010 109 | 1/8 7 h-lim-p 0.1320 1.0561 0.3317 2162.003323 0 0.2640 122 | 1/8 8 h-lim-p 0.5988 4.7907 0.0952 2161.059957 8 0.2233 161 | 0/8 9 h-lim-p 0.0028 0.3156 7.5476 2161.038784 5 0.0008 191 | 0/8 10 h-lim-p 0.3385 10.9044 0.0171 2160.870022 0 0.6770 204 | 0/8 11 h-lim-p 0.1757 1.4052 0.0213 2160.803037 0 0.3513 225 | 0/8 12 h-lim-p 0.7281 5.8246 0.0029 2160.798345 1 0.9101 247 | 0/8 13 h-lim-p 2.5000 20.0000 0.0002 2160.798311 1 0.9961 269 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 2160.798311 0 1.2500 289 | 0/8 15 h-lim-p 1.5196 20.0000 0.0000 2160.798311 0 0.6648 309 | 0/8 16 h-lim-p 0.3995 20.0000 0.0000 2160.798311 0 0.0027 335 | 0/8 17 h-lim-p 0.0010 20.0000 0.0000 2160.798311 0 0.0000 374 | 0/8 18 h-lim-p 0.0000 20.0000 0.0009 2160.798311 0 0.0000 399 | 0/8 19 h-lim-p 0.0000 20.0000 0.0004 2160.798311 0 0.0000 419 | 0/8 20 h-lim-p 0.0001 20.0000 0.0001 2160.798311 0 0.0001 439 | 0/8 21 h-lim-p 0.0001 20.0000 0.0001 2160.798311 0 0.0000 475 | 0/8 22 h-lim-p 0.0000 20.0000 0.0009 | 0/8 23 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -2160.798311 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2160.798311 Node 7: lnL = -2160.798311 Node 8: lnL = -2160.798311 Node 9: lnL = -2160.798311 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 737 Sequential format.. Reading seq # 1: YDR399W_Sbay Reading seq # 2: YDR399W_Scer Reading seq # 3: YDR399W_Skud Reading seq # 4: YDR399W_Smik Reading seq # 5: YDR399W_Spar Sequences read.. Counting patterns.. # site patterns = 191 Counting frequencies.. 120 bytes for distance 30560 bytes for lkl0 24448 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.135727 0.042401 0.037276 0.067365 0.060604 0.108131 0.167392 0.071893 lnL0 = -2686.403144 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2686.403144 x= 0.13573 0.04240 0.03728 0.06737 0.06060 0.10813 0.16739 0.07189 1 h-lim-p 0.0003 0.0022 171.8492 2684.777229 7 0.0001 40 | 0/8 2 h-lim-p 0.0004 0.0030 34.0468 2684.686530 7 0.0002 65 | 0/8 3 h-lim-p 0.0006 0.0188 9.8439 2684.678316 5 0.0002 88 | 0/8 4 h-lim-p 0.0004 0.0406 4.7648 2684.676457 4 0.0002 109 | 0/8 5 h-lim-p 0.0009 0.2210 1.0641 2684.676264 3 0.0004 127 | 0/8 6 h-lim-p 0.0065 1.8000 0.0582 2684.676263 0 0.0002 143 | 0/8 7 h-lim-p 0.0025 20.0000 0.0042 2684.676263 0 0.0011 163 | 0/8 8 h-lim-p 0.0139 20.0000 0.0003 2684.676238 0 0.3328 187 | 0/8 9 h-lim-p 0.1620 20.0000 0.0007 2684.676234 0 0.6481 209 | 0/8 10 h-lim-p 1.8846 20.0000 0.0002 2684.676234 0 1.6490 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0001 2684.676234 0 1.0938 249 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2684.676234 0 0.2734 271 | 0/8 13 h-lim-p 0.0578 20.0000 0.0000 2684.676234 0 0.0005 297 | 0/8 14 h-lim-p 0.0001 20.0000 0.0001 2684.676234 0 0.0000 317 | 0/8 15 h-lim-p 0.0004 20.0000 0.0000 2684.676234 0 0.0000 346 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 2684.676234 0 0.0000 378 Out... lnL = -2684.676234 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2684.676234 Node 7: lnL = -2684.676234 Node 8: lnL = -2684.676234 Node 9: lnL = -2684.676234 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 244 Sequential format.. Reading seq # 1: YDR400W_Sbay Reading seq # 2: YDR400W_Scer Reading seq # 3: YDR400W_Skud Reading seq # 4: YDR400W_Smik Reading seq # 5: YDR400W_Spar Sequences read.. Counting patterns.. # site patterns = 132 Counting frequencies.. 120 bytes for distance 21120 bytes for lkl0 16896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.267237 0.133195 0.146446 0.151975 0.096166 0.176379 0.253232 0.136133 lnL0 = -1150.619906 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1150.619906 x= 0.26724 0.13319 0.14645 0.15197 0.09617 0.17638 0.25323 0.13613 1 h-lim-p 0.0038 0.0301 21.4544 1150.354229 8 0.0012 43 | 0/8 2 h-lim-p 0.0038 0.0317 6.6653 1150.334768 4 0.0009 64 | 0/8 3 h-lim-p 0.0031 0.1471 2.0376 1150.331413 6 0.0018 93 | 0/8 4 h-lim-p 0.0084 0.8106 0.4325 1150.331181 4 0.0026 116 | 0/8 5 h-lim-p 0.0072 2.3571 0.1536 1150.331158 3 0.0021 145 | 0/8 6 h-lim-p 0.0067 8.0088 0.0489 1150.331156 1 0.0016 168 | 0/8 7 h-lim-p 0.0353 20.0000 0.0023 1150.331156 0 0.0039 190 | 0/8 8 h-lim-p 0.1724 20.0000 0.0001 1150.331155 0 0.6894 212 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1150.331155 0 1.0938 232 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1150.331155 0 1.0938 252 | 0/8 11 h-lim-p 1.1010 20.0000 0.0000 1150.331155 0 6.6060 274 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1150.331155 0 0.3125 296 | 0/8 13 h-lim-p 0.0303 20.0000 0.0000 1150.331155 0 0.0114 317 | 0/8 14 h-lim-p 0.0039 20.0000 0.0001 1150.331155 0 0.0005 339 | 0/8 15 h-lim-p 0.0001 20.0000 0.0004 1150.331155 0 0.0000 361 | 0/8 16 h-lim-p 0.0005 20.0000 0.0000 1150.331155 0 0.0000 388 Out... lnL = -1150.331155 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1150.331155 Node 7: lnL = -1150.331155 Node 8: lnL = -1150.331155 Node 9: lnL = -1150.331155 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 507 Sequential format.. Reading seq # 1: YDR404C_Sbay Reading seq # 2: YDR404C_Scer Reading seq # 3: YDR404C_Skud Reading seq # 4: YDR404C_Smik Reading seq # 5: YDR404C_Spar Sequences read.. Counting patterns.. # site patterns = 192 Counting frequencies.. 120 bytes for distance 30720 bytes for lkl0 24576 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.228786 0.000060 0.246445 0.110626 0.220522 0.058144 0.226419 0.124486 lnL0 = -2108.330509 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2108.330509 x= 0.22879 0.00006 0.24644 0.11063 0.22052 0.05814 0.22642 0.12449 1 h-lim-p 0.0001 0.0011 339.0690 2075.907636 0 0.0008 24 | 0/8 2 h-lim-p 0.0001 0.0009 183.1070 2070.764518 0 0.0005 38 | 0/8 3 h-lim-p 0.0004 0.0036 61.1115 2070.268123 8 0.0003 70 | 0/8 4 h-lim-p 0.0007 0.0055 26.9699 2070.125548 7 0.0005 101 | 0/8 5 h-lim-p 0.0012 0.0225 10.8046 2070.083602 6 0.0008 127 | 0/8 6 h-lim-p 0.0042 0.1008 2.1536 2070.077514 5 0.0015 152 | 0/8 7 h-lim-p 0.0087 0.6843 0.3770 2069.931837 0 0.0522 166 | 0/8 8 h-lim-p 0.0037 0.0546 5.2863 2067.229370 0 0.0149 188 | 0/8 9 h-lim-p 0.6780 5.4244 0.0359 2066.842987 1 0.8476 202 | 0/8 10 h-lim-p 1.8283 14.6266 0.0084 2066.811855 4 0.8852 231 | 0/8 11 h-lim-p 2.5000 20.0000 0.0011 2066.811180 2 0.9644 255 | 0/8 12 h-lim-p 2.5000 20.0000 0.0001 2066.811167 2 0.9644 279 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2066.811166 0 1.2500 299 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 2066.811166 0 1.0938 319 | 0/8 15 h-lim-p 1.4052 20.0000 0.0000 2066.811166 0 0.6148 339 | 0/8 16 h-lim-p 0.2498 20.0000 0.0000 2066.811166 0 0.1249 359 | 0/8 17 h-lim-p 0.0406 20.0000 0.0000 2066.811166 0 0.0000 394 | 0/8 18 h-lim-p 0.0001 20.0000 0.0000 2066.811166 0 0.0001 414 Out... lnL = -2066.811166 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2066.811166 Node 7: lnL = -2066.811166 Node 8: lnL = -2066.811166 Node 9: lnL = -2066.811166 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 517 Sequential format.. Reading seq # 1: YDR405W_Sbay Reading seq # 2: YDR405W_Scer Reading seq # 3: YDR405W_Skud Reading seq # 4: YDR405W_Smik Reading seq # 5: YDR405W_Spar Sequences read.. Counting patterns.. # site patterns = 150 Counting frequencies.. 120 bytes for distance 24000 bytes for lkl0 19200 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.336883 0.000060 0.425301 0.136702 0.435636 0.148033 0.347797 0.174983 lnL0 = -1978.679539 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1978.679539 x= 0.33688 0.00006 0.42530 0.13670 0.43564 0.14803 0.34780 0.17498 1 h-lim-p 0.0000 0.0000 273.3167 1978.609556 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0009 607.3688 1881.920226 m 0.0009 38 | 1/8 3 h-lim-p 0.0003 0.0026 83.5517 1878.850164 0 0.0013 52 | 1/8 4 h-lim-p 0.0002 0.0013 95.7986 1878.037043 0 0.0003 65 | 1/8 5 h-lim-p 0.0012 0.2260 27.5279 1873.005400 0 0.0187 81 | 1/8 6 h-lim-p 0.0028 0.0220 30.9733 1872.364801 5 0.0023 104 | 1/8 7 h-lim-p 0.1224 1.4972 0.5828 1870.807283 0 0.2448 117 | 1/8 8 h-lim-p 0.7637 6.1096 0.0943 1870.143529 2 0.7160 140 | 0/8 9 h-lim-p 0.2013 12.8732 0.3353 1870.143444 3 0.0010 172 | 0/8 10 h-lim-p 0.0062 0.0499 0.0336 1870.140069 m 0.0499 192 | 1/8 11 h-lim-p 0.0234 9.3527 0.0701 1870.119376 0 0.2811 215 | 1/8 12 h-lim-p 1.2388 20.0000 0.0159 1870.111790 0 2.4775 235 | 1/8 13 h-lim-p 2.5000 20.0000 0.0033 1870.110554 2 1.1719 258 | 1/8 14 h-lim-p 2.0422 20.0000 0.0019 1870.110518 2 1.0750 282 | 1/8 15 h-lim-p 2.5000 20.0000 0.0001 1870.110517 0 1.0938 301 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 1870.110517 0 1.2500 320 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 1870.110517 0 2.1875 339 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 1870.110517 0 2.1875 358 | 1/8 19 h-lim-p 2.4587 20.0000 0.0000 1870.110517 0 0.5378 378 | 1/8 20 h-lim-p 0.1977 20.0000 0.0000 1870.110517 0 0.0062 401 | 1/8 21 h-lim-p 0.0029 20.0000 0.0000 1870.110517 0 0.0000 429 | 1/8 22 h-lim-p 0.0001 20.0000 0.0000 1870.110517 0 0.0000 460 Out... lnL = -1870.110517 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1870.110517 Node 7: lnL = -1870.110517 Node 8: lnL = -1870.110517 Node 9: lnL = -1870.110517 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 298 Sequential format.. Reading seq # 1: YDR410C_Sbay Reading seq # 2: YDR410C_Scer Reading seq # 3: YDR410C_Skud Reading seq # 4: YDR410C_Smik Reading seq # 5: YDR410C_Spar Sequences read.. Counting patterns.. # site patterns = 133 Counting frequencies.. 120 bytes for distance 21280 bytes for lkl0 17024 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.192411 0.148109 0.061213 0.157049 0.085736 0.193935 0.100616 0.086134 lnL0 = -1195.369960 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1195.369960 x= 0.19241 0.14811 0.06121 0.15705 0.08574 0.19393 0.10062 0.08613 1 h-lim-p 0.0036 0.0285 62.6297 1194.296725 8 0.0006 44 | 0/8 2 h-lim-p 0.0014 0.0109 22.3444 1194.011849 2 0.0013 60 | 0/8 3 h-lim-p 0.0029 0.0259 9.9554 1193.975250 7 0.0009 91 | 0/8 4 h-lim-p 0.0023 0.0442 3.8352 1193.961828 2 0.0022 107 | 0/8 5 h-lim-p 0.0046 0.1639 1.7848 1193.959986 5 0.0014 132 | 0/8 6 h-lim-p 0.0066 0.3137 0.3901 1193.959762 2 0.0031 148 | 0/8 7 h-lim-p 0.0184 2.9442 0.0650 1193.959756 1 0.0018 172 | 0/8 8 h-lim-p 0.0572 20.0000 0.0021 1193.958174 0 0.9155 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 1193.957947 3 1.0004 222 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1193.957947 0 1.0938 242 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1193.957947 0 1.0938 262 | 0/8 12 h-lim-p 1.1223 20.0000 0.0000 1193.957947 0 4.4892 284 | 0/8 13 h-lim-p 1.7467 20.0000 0.0000 1193.957947 0 0.0136 310 | 0/8 14 h-lim-p 0.0009 20.0000 0.0001 1193.957947 0 0.0000 341 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 1193.957947 0 0.0000 364 Out... lnL = -1193.957947 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1193.957947 Node 7: lnL = -1193.957947 Node 8: lnL = -1193.957947 Node 9: lnL = -1193.957947 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 310 Sequential format.. Reading seq # 1: YDR411C_Sbay Reading seq # 2: YDR411C_Scer Reading seq # 3: YDR411C_Skud Reading seq # 4: YDR411C_Smik Reading seq # 5: YDR411C_Spar Sequences read.. Counting patterns.. # site patterns = 127 Counting frequencies.. 120 bytes for distance 20320 bytes for lkl0 16256 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.162112 0.029892 0.070147 0.124407 0.094469 0.192149 0.163377 0.071951 lnL0 = -1346.816218 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1346.816218 x= 0.16211 0.02989 0.07015 0.12441 0.09447 0.19215 0.16338 0.07195 1 h-lim-p 0.0022 0.0178 60.3751 1346.295133 8 0.0003 42 | 0/8 2 h-lim-p 0.0025 0.0229 7.5662 1346.274607 5 0.0007 67 | 0/8 3 h-lim-p 0.0028 0.1233 1.9815 1346.273530 3 0.0006 87 | 0/8 4 h-lim-p 0.0020 0.3392 0.5842 1346.273436 4 0.0006 111 | 0/8 5 h-lim-p 0.0102 4.2126 0.0347 1346.273436 0 0.0006 134 | 0/8 6 h-lim-p 0.0084 20.0000 0.0026 1346.273436 0 0.0018 155 | 0/8 7 h-lim-p 0.0060 20.0000 0.0008 1346.273436 0 0.0060 175 | 0/8 8 h-lim-p 0.0192 20.0000 0.0003 1346.273434 0 0.1534 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1346.273434 0 1.0938 218 | 0/8 10 h-lim-p 1.3968 20.0000 0.0000 1346.273434 0 1.3968 238 | 0/8 11 h-lim-p 1.1577 20.0000 0.0000 1346.273434 0 0.0045 265 | 0/8 12 h-lim-p 0.0000 20.0000 0.0011 1346.273434 0 0.0000 293 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 1346.273434 0 0.0000 314 Out... lnL = -1346.273434 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1346.273434 Node 7: lnL = -1346.273434 Node 8: lnL = -1346.273434 Node 9: lnL = -1346.273434 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 382 Sequential format.. Reading seq # 1: YDR414C_Sbay Reading seq # 2: YDR414C_Scer Reading seq # 3: YDR414C_Skud Reading seq # 4: YDR414C_Smik Reading seq # 5: YDR414C_Spar Sequences read.. Counting patterns.. # site patterns = 168 Counting frequencies.. 120 bytes for distance 26880 bytes for lkl0 21504 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.185269 0.121761 0.017718 0.156484 0.121791 0.201027 0.162253 0.080267 lnL0 = -1511.103864 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1511.103864 x= 0.18527 0.12176 0.01772 0.15648 0.12179 0.20103 0.16225 0.08027 1 h-lim-p 0.0073 0.0986 64.1569 1510.423213 7 0.0004 40 | 0/8 2 h-lim-p 0.0014 0.0177 16.1621 1510.320479 8 0.0008 74 | 0/8 3 h-lim-p 0.0052 0.0934 2.5957 1510.317656 5 0.0009 99 | 0/8 4 h-lim-p 0.0025 0.2111 0.9133 1510.317178 4 0.0013 120 | 0/8 5 h-lim-p 0.0045 0.8599 0.2610 1510.317146 2 0.0010 145 | 0/8 6 h-lim-p 0.0037 2.4914 0.0705 1510.317142 0 0.0016 165 | 0/8 7 h-lim-p 0.0048 6.4638 0.0235 1510.317142 0 0.0011 186 | 0/8 8 h-lim-p 0.0760 20.0000 0.0003 1510.317048 0 1.2152 210 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1510.317039 1 0.9961 232 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1510.317039 0 2.1875 252 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1510.317039 0 0.6250 273 | 0/8 12 h-lim-p 0.0821 20.0000 0.0000 1510.317039 0 0.0000 317 Out... lnL = -1510.317039 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1510.317039 Node 7: lnL = -1510.317039 Node 8: lnL = -1510.317039 Node 9: lnL = -1510.317039 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 294 Sequential format.. Reading seq # 1: YDR416W_Sbay Reading seq # 2: YDR416W_Scer Reading seq # 3: YDR416W_Skud Reading seq # 4: YDR416W_Smik Reading seq # 5: YDR416W_Spar Sequences read.. Counting patterns.. # site patterns = 152 Counting frequencies.. 120 bytes for distance 24320 bytes for lkl0 19456 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.240099 0.133629 0.047416 0.136587 0.137479 0.238227 0.285926 0.106839 lnL0 = -1410.973641 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1410.973641 x= 0.24010 0.13363 0.04742 0.13659 0.13748 0.23823 0.28593 0.10684 1 h-lim-p 0.0019 0.0153 43.8329 1410.432219 8 0.0006 44 | 0/8 2 h-lim-p 0.0027 0.0217 9.6139 1410.381208 6 0.0011 71 | 0/8 3 h-lim-p 0.0021 0.0478 5.3664 1410.366526 6 0.0013 98 | 0/8 4 h-lim-p 0.0027 0.1330 2.5789 1410.362585 5 0.0015 122 | 0/8 5 h-lim-p 0.0088 0.7239 0.4446 1410.362469 4 0.0013 145 | 0/8 6 h-lim-p 0.0115 7.1770 0.0484 1410.362467 1 0.0014 169 | 0/8 7 h-lim-p 0.0401 20.0000 0.0017 1410.362462 0 0.0802 190 | 0/8 8 h-lim-p 0.0128 7.6941 0.0107 1410.362405 0 0.0256 211 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1410.362405 0 1.0938 231 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1410.362405 0 1.0938 251 | 0/8 11 h-lim-p 1.2038 20.0000 0.0000 1410.362405 0 2.4076 272 | 0/8 12 h-lim-p 1.2758 20.0000 0.0000 1410.362405 0 0.0399 296 | 0/8 13 h-lim-p 0.0010 20.0000 0.0003 1410.362405 0 0.0000 322 | 0/8 14 h-lim-p 0.0003 20.0000 0.0000 1410.362405 0 0.0000 355 Out... lnL = -1410.362405 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1410.362405 Node 7: lnL = -1410.362405 Node 8: lnL = -1410.362405 Node 9: lnL = -1410.362405 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 650 Sequential format.. Reading seq # 1: YDR418W_Sbay Reading seq # 2: YDR418W_Scer Reading seq # 3: YDR418W_Skud Reading seq # 4: YDR418W_Smik Reading seq # 5: YDR418W_Spar Sequences read.. Counting patterns.. # site patterns = 253 Counting frequencies.. 120 bytes for distance 40480 bytes for lkl0 32384 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.211683 0.131535 0.045140 0.133612 0.114233 0.205367 0.833993 0.041832 lnL0 = -3282.897590 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3282.897590 x= 0.21168 0.13154 0.04514 0.13361 0.11423 0.20537 0.83399 0.04183 1 h-lim-p 0.0005 0.0036 187.1053 3278.714874 8 0.0003 43 | 0/8 2 h-lim-p 0.0004 0.0028 71.2576 3277.641721 0 0.0005 55 | 0/8 3 h-lim-p 0.0006 0.0051 33.6580 3277.466799 6 0.0004 82 | 0/8 4 h-lim-p 0.0009 0.0101 14.8826 3277.381765 6 0.0009 109 | 0/8 5 h-lim-p 0.0008 0.0065 15.1012 3277.315561 0 0.0012 121 | 0/8 6 h-lim-p 0.0065 0.3964 2.8101 3277.304533 2 0.0031 137 | 0/8 7 h-lim-p 0.0012 0.0466 7.0243 3277.299755 4 0.0006 158 | 0/8 8 h-lim-p 0.7553 20.0000 0.0058 3277.271388 1 0.9441 172 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 3277.271013 2 1.0889 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 3277.271006 1 1.2305 219 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3277.271006 0 1.0938 239 | 0/8 12 h-lim-p 1.7157 20.0000 0.0000 3277.271006 0 1.5013 259 | 0/8 13 h-lim-p 1.9006 20.0000 0.0000 3277.271006 0 0.8315 279 | 0/8 14 h-lim-p 0.2824 20.0000 0.0000 3277.271006 0 0.0530 301 | 0/8 15 h-lim-p 0.0110 20.0000 0.0001 3277.271006 0 0.0000 342 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 | 0/8 17 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -3277.271006 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3277.271006 Node 7: lnL = -3277.271006 Node 8: lnL = -3277.271006 Node 9: lnL = -3277.271006 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 807 Sequential format.. Reading seq # 1: YDR419W_Sbay Reading seq # 2: YDR419W_Scer Reading seq # 3: YDR419W_Skud Reading seq # 4: YDR419W_Smik Reading seq # 5: YDR419W_Spar Sequences read.. Counting patterns.. # site patterns = 105 Counting frequencies.. 120 bytes for distance 16800 bytes for lkl0 13440 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.491214 0.000060 0.598212 0.184656 0.687371 0.063306 0.465378 0.272365 lnL0 = -2450.757694 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2450.757694 x= 0.49121 0.00006 0.59821 0.18466 0.68737 0.06331 0.46538 0.27237 1 h-lim-p 0.0000 0.0000 61.9612 2450.715309 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0056 73.2655 2444.948243 6 0.0044 55 | 1/8 3 h-lim-p 0.0028 0.0225 13.0999 2444.185448 0 0.0113 69 | 1/8 4 h-lim-p 0.0122 0.0975 5.8492 2443.389453 0 0.0488 83 | 1/8 5 h-lim-p 0.0126 0.1011 3.8078 2443.009071 0 0.0506 97 | 1/8 6 h-lim-p 0.1879 1.5030 0.6595 2441.762720 0 0.3758 110 | 1/8 7 h-lim-p 0.0826 0.6605 0.8719 2441.527204 0 0.3303 131 | 1/8 8 h-lim-p 0.3490 2.7923 0.2976 2441.321166 0 0.5236 150 | 1/8 9 h-lim-p 1.3535 10.8281 0.0324 2441.291230 6 0.8367 184 | 1/8 10 h-lim-p 2.5000 20.0000 0.0082 2441.290697 4 0.9169 213 | 1/8 11 h-lim-p 2.5000 20.0000 0.0018 2441.290675 2 0.8246 238 | 1/8 12 h-lim-p 2.5000 20.0000 0.0002 2441.290672 1 1.2305 260 | 1/8 13 h-lim-p 1.6482 20.0000 0.0002 2441.290672 0 1.4422 279 | 1/8 14 h-lim-p 2.4263 20.0000 0.0001 2441.290672 0 1.0615 298 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 2441.290672 0 1.0938 317 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 2441.290672 0 1.0938 336 | 1/8 17 h-lim-p 1.2180 20.0000 0.0000 2441.290672 0 4.8720 357 | 1/8 18 h-lim-p 0.1165 20.0000 0.0001 2441.290672 0 0.0036 380 | 1/8 19 h-lim-p 0.0003 20.0000 0.0010 2441.290672 0 0.0000 405 | 1/8 20 h-lim-p 0.0035 20.0000 0.0000 2441.290672 0 0.0001 429 Out... lnL = -2441.290672 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2441.290672 Node 7: lnL = -2441.290672 Node 8: lnL = -2441.290672 Node 9: lnL = -2441.290672 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 869 Sequential format.. Reading seq # 1: YDR420W_Sbay Reading seq # 2: YDR420W_Scer Reading seq # 3: YDR420W_Skud Reading seq # 4: YDR420W_Smik Reading seq # 5: YDR420W_Spar Sequences read.. Counting patterns.. # site patterns = 293 Counting frequencies.. 120 bytes for distance 46880 bytes for lkl0 37504 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.373801 0.000060 0.389233 0.167011 0.410833 0.305944 0.332136 0.192166 lnL0 = -3898.001270 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3898.001270 x= 0.37380 0.00006 0.38923 0.16701 0.41083 0.30594 0.33214 0.19217 1 h-lim-p 0.0000 0.0000 477.5252 3897.869679 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0009 682.8458 3778.931927 1 0.0007 42 | 1/8 3 h-lim-p 0.0009 0.0073 80.0857 3774.283038 0 0.0018 55 | 1/8 4 h-lim-p 0.0012 0.0095 77.6694 3772.207809 4 0.0012 75 | 1/8 5 h-lim-p 0.0013 0.0152 68.5198 3771.198531 8 0.0009 107 | 1/8 6 h-lim-p 0.0096 0.0770 3.5344 3771.088722 5 0.0041 130 | 1/8 7 h-lim-p 0.0138 0.4339 1.0393 3751.094534 9 0.1884 170 | 0/8 8 h-lim-p 0.0082 0.0659 17.6886 3751.042178 6 0.0004 200 | 0/8 9 h-lim-p 0.0705 9.6133 0.0893 3750.694719 0 0.5639 215 | 0/8 10 h-lim-p 0.9083 7.2663 0.0365 3750.380760 0 1.3624 235 | 0/8 11 h-lim-p 1.4460 11.5677 0.0162 3750.299059 5 1.1572 264 | 0/8 12 h-lim-p 2.5000 20.0000 0.0057 3750.278487 5 1.6959 297 | 0/8 13 h-lim-p 1.2753 20.0000 0.0075 3750.271547 3 1.2348 324 | 0/8 14 h-lim-p 2.3990 20.0000 0.0039 3750.270258 3 1.0870 350 | 0/8 15 h-lim-p 2.5000 20.0000 0.0008 3750.270196 2 0.9644 374 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 3750.270196 0 1.0938 394 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 3750.270196 0 1.0938 414 | 0/8 18 h-lim-p 2.3379 20.0000 0.0000 3750.270196 0 1.0228 434 | 0/8 19 h-lim-p 0.8960 20.0000 0.0000 3750.270196 0 0.8960 454 | 0/8 20 h-lim-p 0.0057 20.0000 0.0004 3750.270196 0 0.0002 478 | 0/8 21 h-lim-p 0.0014 20.0000 0.0001 3750.270196 0 0.0014 498 | 0/8 22 h-lim-p 0.0019 20.0000 0.0000 3750.270196 0 0.0000 529 | 0/8 23 h-lim-p 0.0002 20.0000 0.0000 3750.270196 0 0.0000 560 Out... lnL = -3750.270196 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3750.270196 Node 7: lnL = -3750.270196 Node 8: lnL = -3750.270196 Node 9: lnL = -3750.270196 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 399 Sequential format.. Reading seq # 1: YDR421W_Sbay Reading seq # 2: YDR421W_Scer Reading seq # 3: YDR421W_Skud Reading seq # 4: YDR421W_Smik Reading seq # 5: YDR421W_Spar Sequences read.. Counting patterns.. # site patterns = 171 Counting frequencies.. 120 bytes for distance 27360 bytes for lkl0 21888 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.140280 0.091985 0.075013 0.123046 0.108065 0.171111 0.157968 0.046460 lnL0 = -1752.127174 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1752.127174 x= 0.14028 0.09198 0.07501 0.12305 0.10806 0.17111 0.15797 0.04646 1 h-lim-p 0.0023 0.0187 51.4006 1751.623976 7 0.0004 41 | 0/8 2 h-lim-p 0.0016 0.0128 12.4515 1751.580667 6 0.0006 67 | 0/8 3 h-lim-p 0.0021 0.0686 3.4954 1751.577721 5 0.0005 89 | 0/8 4 h-lim-p 0.0024 0.2333 0.7641 1751.577573 2 0.0005 106 | 0/8 5 h-lim-p 0.0074 2.4607 0.0539 1751.577573 1 0.0005 131 | 0/8 6 h-lim-p 0.0024 14.7423 0.0102 1751.577573 0 0.0011 151 | 0/8 7 h-lim-p 0.0109 20.0000 0.0010 1751.577572 0 0.0217 172 | 0/8 8 h-lim-p 0.0064 20.0000 0.0034 1751.577561 0 0.0382 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1751.577560 0 1.0938 214 | 0/8 10 h-lim-p 1.9513 20.0000 0.0000 1751.577560 0 0.8537 234 | 0/8 11 h-lim-p 0.6889 20.0000 0.0000 1751.577560 0 0.0753 256 | 0/8 12 h-lim-p 0.0232 20.0000 0.0001 1751.577560 0 0.0000 288 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 1751.577560 0 0.0000 318 Out... lnL = -1751.577560 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1751.577560 Node 7: lnL = -1751.577560 Node 8: lnL = -1751.577560 Node 9: lnL = -1751.577560 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 233 Sequential format.. Reading seq # 1: YDR425W_Sbay Reading seq # 2: YDR425W_Scer Reading seq # 3: YDR425W_Skud Reading seq # 4: YDR425W_Smik Reading seq # 5: YDR425W_Spar Sequences read.. Counting patterns.. # site patterns = 101 Counting frequencies.. 120 bytes for distance 16160 bytes for lkl0 12928 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.134936 0.044703 0.055887 0.096262 0.065435 0.173505 0.191668 0.053464 lnL0 = -970.340431 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 970.340431 x= 0.13494 0.04470 0.05589 0.09626 0.06544 0.17351 0.19167 0.05346 1 h-lim-p 0.0004 0.0033 59.0609 969.562356 0 0.0006 22 | 0/8 2 h-lim-p 0.0006 0.0049 13.6128 969.506037 3 0.0006 40 | 0/8 3 h-lim-p 0.0014 0.0269 6.2115 969.494978 6 0.0007 68 | 0/8 4 h-lim-p 0.0024 0.0923 1.8095 969.493795 5 0.0008 93 | 0/8 5 h-lim-p 0.0018 0.6394 0.8020 969.493651 4 0.0005 114 | 0/8 6 h-lim-p 0.0028 1.5134 0.1402 969.493541 0 0.0042 134 | 0/8 7 h-lim-p 0.0024 1.3513 0.2462 969.493218 0 0.0035 154 | 0/8 8 h-lim-p 0.0121 1.1522 0.0723 969.465293 0 0.0966 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 969.464974 4 0.9422 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 969.464974 0 1.0938 225 | 0/8 11 h-lim-p 1.4707 20.0000 0.0000 969.464974 0 1.2868 245 | 0/8 12 h-lim-p 0.8161 20.0000 0.0000 969.464974 0 0.1785 266 | 0/8 13 h-lim-p 0.0009 20.0000 0.0022 969.464974 0 0.0000 294 | 0/8 14 h-lim-p 0.0000 20.0000 0.0013 969.464974 0 0.0000 329 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -969.464974 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -969.464974 Node 7: lnL = -969.464974 Node 8: lnL = -969.464974 Node 9: lnL = -969.464974 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 248 Sequential format.. Reading seq # 1: YDR427W_Sbay Reading seq # 2: YDR427W_Scer Reading seq # 3: YDR427W_Skud Reading seq # 4: YDR427W_Smik Reading seq # 5: YDR427W_Spar Sequences read.. Counting patterns.. # site patterns = 92 Counting frequencies.. 120 bytes for distance 14720 bytes for lkl0 11776 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.151370 0.103341 0.064749 0.139206 0.089071 0.140920 0.152122 0.058844 lnL0 = -923.287340 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 923.287340 x= 0.15137 0.10334 0.06475 0.13921 0.08907 0.14092 0.15212 0.05884 1 h-lim-p 0.0013 0.0101 48.2592 922.305223 8 0.0009 40 | 0/8 2 h-lim-p 0.0013 0.0101 16.2393 922.191895 7 0.0009 68 | 0/8 3 h-lim-p 0.0031 0.0450 4.7557 922.183288 5 0.0008 91 | 0/8 4 h-lim-p 0.0029 0.1310 1.3647 922.182011 4 0.0015 112 | 0/8 5 h-lim-p 0.0334 3.0655 0.0606 922.182008 1 0.0010 130 | 0/8 6 h-lim-p 0.0053 10.5055 0.0118 922.182008 1 0.0026 153 | 0/8 7 h-lim-p 0.0273 20.0000 0.0011 922.181909 0 0.4370 177 | 0/8 8 h-lim-p 0.0038 1.3203 0.1299 922.181896 2 0.0015 201 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 922.181895 0 1.0938 221 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 922.181895 0 1.0938 241 | 0/8 11 h-lim-p 0.7431 20.0000 0.0000 922.181895 0 1.1147 261 | 0/8 12 h-lim-p 0.5954 20.0000 0.0000 922.181895 0 0.0093 286 | 0/8 13 h-lim-p 0.0010 20.0000 0.0001 922.181895 0 0.0000 315 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 922.181895 0 0.0001 335 Out... lnL = -922.181895 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -922.181895 Node 7: lnL = -922.181895 Node 8: lnL = -922.181895 Node 9: lnL = -922.181895 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 253 Sequential format.. Reading seq # 1: YDR428C_Sbay Reading seq # 2: YDR428C_Scer Reading seq # 3: YDR428C_Skud Reading seq # 4: YDR428C_Smik Reading seq # 5: YDR428C_Spar Sequences read.. Counting patterns.. # site patterns = 101 Counting frequencies.. 120 bytes for distance 16160 bytes for lkl0 12928 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.207990 0.056493 0.019163 0.063421 0.070782 0.123017 0.107819 0.131085 lnL0 = -994.965990 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 994.965990 x= 0.20799 0.05649 0.01916 0.06342 0.07078 0.12302 0.10782 0.13109 1 h-lim-p 0.0018 1.2025 105.4131 993.732773 9 0.0003 47 | 0/8 2 h-lim-p 0.0005 0.0043 31.0399 993.473110 5 0.0006 70 | 0/8 3 h-lim-p 0.0039 0.0309 4.3780 993.465028 3 0.0009 89 | 0/8 4 h-lim-p 0.0011 0.0347 3.5353 993.462806 2 0.0005 105 | 0/8 5 h-lim-p 0.0041 0.3837 0.4338 993.462737 3 0.0007 125 | 0/8 6 h-lim-p 0.0018 1.4524 0.1727 993.462726 0 0.0008 145 | 0/8 7 h-lim-p 0.0036 7.6564 0.0388 993.462724 0 0.0018 165 | 0/8 8 h-lim-p 0.1081 20.0000 0.0006 993.462256 0 0.8649 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 993.462252 1 1.0938 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 993.462252 0 1.0938 230 | 0/8 11 h-lim-p 1.6874 20.0000 0.0000 993.462252 0 1.4764 250 | 0/8 12 h-lim-p 2.0673 20.0000 0.0000 993.462252 0 1.8088 270 | 0/8 13 h-lim-p 1.1847 20.0000 0.0000 993.462252 0 1.1847 290 | 0/8 14 h-lim-p 0.2750 20.0000 0.0000 993.462252 0 0.0344 312 | 0/8 15 h-lim-p 0.0058 20.0000 0.0001 993.462252 0 0.0058 332 | 0/8 16 h-lim-p 0.0019 20.0000 0.0002 993.462252 0 0.0000 370 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -993.462252 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -993.462252 Node 7: lnL = -993.462252 Node 8: lnL = -993.462252 Node 9: lnL = -993.462252 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 207 Sequential format.. Reading seq # 1: YDR429C_Sbay Reading seq # 2: YDR429C_Scer Reading seq # 3: YDR429C_Skud Reading seq # 4: YDR429C_Smik Reading seq # 5: YDR429C_Spar Sequences read.. Counting patterns.. # site patterns = 72 Counting frequencies.. 120 bytes for distance 11520 bytes for lkl0 9216 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.096364 0.008739 0.017856 0.093016 0.033193 0.164254 0.112112 0.041753 lnL0 = -737.824813 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 737.824813 x= 0.09636 0.00874 0.01786 0.09302 0.03319 0.16425 0.11211 0.04175 1 h-lim-p 0.0008 0.0062 51.1456 737.639600 6 0.0002 36 | 0/8 2 h-lim-p 0.0004 0.0033 19.9391 737.564761 6 0.0004 62 | 0/8 3 h-lim-p 0.0006 0.0063 15.0463 737.541869 6 0.0003 87 | 0/8 4 h-lim-p 0.0009 0.0276 5.1603 737.534954 5 0.0006 110 | 0/8 5 h-lim-p 0.0022 0.0190 1.4812 737.534621 4 0.0003 135 | 0/8 6 h-lim-p 0.0014 0.2273 0.3516 737.534591 3 0.0005 155 | 0/8 7 h-lim-p 0.0064 7.1490 0.0279 737.534591 1 0.0008 179 | 0/8 8 h-lim-p 0.0738 20.0000 0.0003 737.534453 0 0.8857 202 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 737.534451 0 1.0938 222 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 737.534451 0 2.1875 242 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 737.534451 0 0.5469 263 | 0/8 12 h-lim-p 0.1347 20.0000 0.0000 737.534451 0 0.0008 290 | 0/8 13 h-lim-p 0.0003 20.0000 0.0000 737.534451 0 0.0000 324 | 0/8 14 h-lim-p 0.0000 20.0000 0.0026 737.534451 0 0.0000 356 | 0/8 15 h-lim-p 0.0000 20.0000 0.0010 737.534451 0 0.0019 383 | 0/8 16 h-lim-p 0.0023 20.0000 0.0008 737.534451 0 0.0000 420 | 0/8 17 h-lim-p 0.0000 20.0000 0.0003 737.534451 0 0.0013 447 | 0/8 18 h-lim-p 0.0031 20.0000 0.0001 737.534451 0 0.0004 469 | 0/8 19 h-lim-p 0.0003 20.0000 0.0001 .. | 0/8 20 h-lim-p 0.0000 20.0000 0.0055 | 0/8 21 h-lim-p 0.0000 20.0000 0.0055 Out... lnL = -737.534451 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -737.534451 Node 7: lnL = -737.534451 Node 8: lnL = -737.534451 Node 9: lnL = -737.534451 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 834 Sequential format.. Reading seq # 1: YDR434W_Sbay Reading seq # 2: YDR434W_Scer Reading seq # 3: YDR434W_Skud Reading seq # 4: YDR434W_Smik Reading seq # 5: YDR434W_Spar Sequences read.. Counting patterns.. # site patterns = 271 Counting frequencies.. 120 bytes for distance 43360 bytes for lkl0 34688 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.204372 0.066861 0.075203 0.103081 0.063321 0.235767 0.183183 0.100584 lnL0 = -3728.937986 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3728.937986 x= 0.20437 0.06686 0.07520 0.10308 0.06332 0.23577 0.18318 0.10058 1 h-lim-p 0.0003 0.0022 115.8904 3727.655159 8 0.0002 40 | 0/8 2 h-lim-p 0.0007 0.0053 21.9967 3727.592822 3 0.0003 58 | 0/8 3 h-lim-p 0.0005 0.0110 11.7924 3727.582975 5 0.0002 81 | 0/8 4 h-lim-p 0.0003 0.0419 6.3031 3727.578964 4 0.0003 102 | 0/8 5 h-lim-p 0.0016 0.1656 1.0947 3727.578833 3 0.0002 124 | 0/8 6 h-lim-p 0.0040 6.8184 0.0617 3727.578832 0 0.0004 138 | 0/8 7 h-lim-p 0.0100 20.0000 0.0027 3727.578825 0 0.0401 160 | 0/8 8 h-lim-p 0.0061 14.1171 0.0179 3727.578634 0 0.0243 182 | 0/8 9 h-lim-p 0.8033 20.0000 0.0005 3727.578606 1 1.0041 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 3727.578606 0 1.0938 224 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3727.578606 0 1.0938 244 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3727.578606 0 0.0003 276 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0028 | 0/8 15 h-lim-p 0.0000 20.0000 0.0028 Out... lnL = -3727.578606 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3727.578606 Node 7: lnL = -3727.578606 Node 8: lnL = -3727.578606 Node 9: lnL = -3727.578606 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 839 Sequential format.. Reading seq # 1: YDR435C_Sbay Reading seq # 2: YDR435C_Scer Reading seq # 3: YDR435C_Skud Reading seq # 4: YDR435C_Smik Reading seq # 5: YDR435C_Spar Sequences read.. Counting patterns.. # site patterns = 253 Counting frequencies.. 120 bytes for distance 40480 bytes for lkl0 32384 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.200780 0.068365 0.048163 0.116818 0.103887 0.193968 0.135560 0.097660 lnL0 = -3761.237078 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3761.237078 x= 0.20078 0.06836 0.04816 0.11682 0.10389 0.19397 0.13556 0.09766 1 h-lim-p 0.0021 0.0624 188.3011 3759.236987 3 0.0001 31 | 0/8 2 h-lim-p 0.0008 0.0067 26.2643 3759.131563 7 0.0003 60 | 0/8 3 h-lim-p 0.0010 0.0386 8.1445 3759.125226 3 0.0002 80 | 0/8 4 h-lim-p 0.0014 0.2119 1.2011 3759.125028 2 0.0003 97 | 0/8 5 h-lim-p 0.0012 0.4819 0.2941 3759.125018 0 0.0003 110 | 0/8 6 h-lim-p 0.0019 6.7517 0.0385 3759.125018 0 0.0004 131 | 0/8 7 h-lim-p 0.0112 20.0000 0.0014 3759.125018 0 0.0098 151 | 0/8 8 h-lim-p 0.0052 20.0000 0.0027 3759.124982 0 0.0418 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3759.124982 0 1.0938 194 | 0/8 10 h-lim-p 1.6196 20.0000 0.0000 3759.124982 0 1.4172 214 | 0/8 11 h-lim-p 2.0625 20.0000 0.0000 3759.124982 0 1.8047 234 | 0/8 12 h-lim-p 0.6209 20.0000 0.0000 3759.124982 0 0.0024 261 | 0/8 13 h-lim-p 0.0003 20.0000 0.0002 3759.124982 0 0.0000 293 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 3759.124982 0 0.0000 326 Out... lnL = -3759.124982 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3759.124982 Node 7: lnL = -3759.124982 Node 8: lnL = -3759.124982 Node 9: lnL = -3759.124982 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 841 Sequential format.. Reading seq # 1: YDR436W_Sbay Reading seq # 2: YDR436W_Scer Reading seq # 3: YDR436W_Skud Reading seq # 4: YDR436W_Smik Reading seq # 5: YDR436W_Spar Sequences read.. Counting patterns.. # site patterns = 255 Counting frequencies.. 120 bytes for distance 40800 bytes for lkl0 32640 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.198803 0.071882 0.047873 0.125141 0.099607 0.197459 0.124245 0.095948 lnL0 = -3748.995628 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3748.995628 x= 0.19880 0.07188 0.04787 0.12514 0.09961 0.19746 0.12425 0.09595 1 h-lim-p 0.0010 0.0077 159.6682 3747.442821 6 0.0001 36 | 0/8 2 h-lim-p 0.0005 0.0044 35.6212 3747.262808 5 0.0003 59 | 0/8 3 h-lim-p 0.0015 0.0499 7.1938 3747.257848 5 0.0002 83 | 0/8 4 h-lim-p 0.0011 0.1872 1.3017 3747.257599 4 0.0003 105 | 0/8 5 h-lim-p 0.0014 0.5300 0.2983 3747.257590 2 0.0002 123 | 0/8 6 h-lim-p 0.0014 6.6752 0.0448 3747.257590 0 0.0003 144 | 0/8 7 h-lim-p 0.0028 20.0000 0.0050 3747.257590 0 0.0006 165 | 0/8 8 h-lim-p 0.0553 20.0000 0.0001 3747.257587 0 0.8846 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3747.257587 0 1.0938 209 | 0/8 10 h-lim-p 0.3885 20.0000 0.0000 3747.257587 0 1.5539 231 | 0/8 11 h-lim-p 1.0682 20.0000 0.0000 3747.257587 0 0.1335 253 | 0/8 12 h-lim-p 0.0001 3.0049 0.0468 3747.257587 0 0.0000 290 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 3747.257587 0 0.0000 325 Out... lnL = -3747.257587 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3747.257587 Node 7: lnL = -3747.257587 Node 8: lnL = -3747.257587 Node 9: lnL = -3747.257587 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 473 Sequential format.. Reading seq # 1: YDR437W_Sbay Reading seq # 2: YDR437W_Scer Reading seq # 3: YDR437W_Skud Reading seq # 4: YDR437W_Smik Reading seq # 5: YDR437W_Spar Sequences read.. Counting patterns.. # site patterns = 182 Counting frequencies.. 120 bytes for distance 29120 bytes for lkl0 23296 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.223725 0.131125 0.081465 0.117860 0.066799 0.197510 0.244575 0.096212 lnL0 = -2064.038995 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2064.038995 x= 0.22373 0.13112 0.08146 0.11786 0.06680 0.19751 0.24458 0.09621 1 h-lim-p 0.0004 0.0036 24.9776 2063.915833 6 0.0004 35 | 0/8 2 h-lim-p 0.0012 0.0645 8.3660 2063.905538 6 0.0003 62 | 0/8 3 h-lim-p 0.0014 0.0814 2.0052 2063.903827 5 0.0009 86 | 0/8 4 h-lim-p 0.0030 0.4905 0.6074 2063.903722 3 0.0006 105 | 0/8 5 h-lim-p 0.0020 1.4082 0.1895 2063.903709 1 0.0008 127 | 0/8 6 h-lim-p 0.0029 3.6970 0.0527 2063.903708 1 0.0007 150 | 0/8 7 h-lim-p 0.0064 20.0000 0.0058 2063.903708 0 0.0028 170 | 0/8 8 h-lim-p 0.0425 20.0000 0.0004 2063.903683 0 0.3402 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2063.903683 0 1.0938 213 | 0/8 10 h-lim-p 2.4039 20.0000 0.0000 2063.903683 0 1.0517 233 | 0/8 11 h-lim-p 0.9796 20.0000 0.0000 2063.903683 0 7.8370 256 | 0/8 12 h-lim-p 0.4193 20.0000 0.0001 2063.903683 0 0.0004 285 | 0/8 13 h-lim-p 0.0009 20.0000 0.0001 2063.903683 0 0.0001 308 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 2063.903683 0 0.0000 334 | 0/8 15 h-lim-p 0.0007 20.0000 0.0000 2063.903683 0 0.0000 365 Out... lnL = -2063.903683 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2063.903683 Node 7: lnL = -2063.903683 Node 8: lnL = -2063.903683 Node 9: lnL = -2063.903683 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 328 Sequential format.. Reading seq # 1: YDR439W_Sbay Reading seq # 2: YDR439W_Scer Reading seq # 3: YDR439W_Skud Reading seq # 4: YDR439W_Smik Reading seq # 5: YDR439W_Spar Sequences read.. Counting patterns.. # site patterns = 174 Counting frequencies.. 120 bytes for distance 27840 bytes for lkl0 22272 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.214393 0.160332 0.095261 0.108649 0.105940 0.298235 0.228691 0.072178 lnL0 = -1513.190806 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1513.190806 x= 0.21439 0.16033 0.09526 0.10865 0.10594 0.29823 0.22869 0.07218 1 h-lim-p 0.0421 5.0719 26.8123 1512.885668 8 0.0009 46 | 0/8 2 h-lim-p 0.0024 0.0240 9.7865 1512.849831 7 0.0008 75 | 0/8 3 h-lim-p 0.0013 0.0325 6.2067 1512.832816 2 0.0012 91 | 0/8 4 h-lim-p 0.0076 0.1909 1.0035 1512.832238 4 0.0012 114 | 0/8 5 h-lim-p 0.0043 1.3076 0.2831 1512.832153 3 0.0023 133 | 0/8 6 h-lim-p 0.0275 12.5669 0.0234 1512.832152 1 0.0017 158 | 0/8 7 h-lim-p 0.0041 20.0000 0.0098 1512.832152 0 0.0035 178 | 0/8 8 h-lim-p 0.0507 20.0000 0.0007 1512.832106 0 0.4053 201 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1512.832106 0 1.0938 221 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1512.832106 0 1.0938 241 | 0/8 11 h-lim-p 1.1815 20.0000 0.0000 1512.832106 0 0.0738 264 | 0/8 12 h-lim-p 0.0178 20.0000 0.0000 1512.832106 0 0.0045 285 | 0/8 13 h-lim-p 0.0019 20.0000 0.0001 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 1512.832106 0 0.0000 346 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1512.832106 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1512.832106 Node 7: lnL = -1512.832106 Node 8: lnL = -1512.832106 Node 9: lnL = -1512.832106 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 673 Sequential format.. Reading seq # 1: YDR441C_Sbay Reading seq # 2: YDR441C_Scer Reading seq # 3: YDR441C_Skud Reading seq # 4: YDR441C_Smik Reading seq # 5: YDR441C_Spar Sequences read.. Counting patterns.. # site patterns = 195 Counting frequencies.. 120 bytes for distance 31200 bytes for lkl0 24960 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.177418 0.053108 0.040698 0.070128 0.056508 0.149054 0.136670 0.094314 lnL0 = -2543.617579 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2543.617579 x= 0.17742 0.05311 0.04070 0.07013 0.05651 0.14905 0.13667 0.09431 1 h-lim-p 0.0002 0.0014 120.9242 2542.337117 8 0.0002 43 | 0/8 2 h-lim-p 0.0002 0.0020 43.5726 2542.127656 5 0.0002 65 | 0/8 3 h-lim-p 0.0006 0.0092 19.3136 2542.097093 6 0.0002 90 | 0/8 4 h-lim-p 0.0008 0.0503 4.9365 2542.095454 4 0.0001 111 | 0/8 5 h-lim-p 0.0006 0.1143 1.2392 2542.095326 4 0.0002 134 | 0/8 6 h-lim-p 0.0008 0.7670 0.2843 2542.095311 0 0.0004 146 | 0/8 7 h-lim-p 0.0120 20.0000 0.0092 2542.095309 0 0.0053 166 | 0/8 8 h-lim-p 0.0100 20.0000 0.0048 2542.094806 0 0.0797 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2542.094786 1 0.9961 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2542.094786 0 0.5469 232 | 0/8 11 h-lim-p 0.3618 20.0000 0.0000 2542.094786 0 0.0000 271 | 0/8 12 h-lim-p 0.0000 20.0000 0.0000 2542.094786 0 0.0000 294 Out... lnL = -2542.094786 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2542.094786 Node 7: lnL = -2542.094786 Node 8: lnL = -2542.094786 Node 9: lnL = -2542.094786 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 371 Sequential format.. Reading seq # 1: YDR443C_Sbay Reading seq # 2: YDR443C_Scer Reading seq # 3: YDR443C_Skud Reading seq # 4: YDR443C_Smik Reading seq # 5: YDR443C_Spar Sequences read.. Counting patterns.. # site patterns = 140 Counting frequencies.. 120 bytes for distance 22400 bytes for lkl0 17920 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.201017 0.047872 0.075014 0.082341 0.093433 0.178297 0.170284 0.099350 lnL0 = -1635.713574 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1635.713574 x= 0.20102 0.04787 0.07501 0.08234 0.09343 0.17830 0.17028 0.09935 1 h-lim-p 0.0013 0.0102 61.7885 1635.097949 6 0.0003 35 | 0/8 2 h-lim-p 0.0020 0.0198 10.5714 1635.062742 6 0.0006 61 | 0/8 3 h-lim-p 0.0012 0.0375 5.6190 1635.057362 5 0.0004 85 | 0/8 4 h-lim-p 0.0016 0.0932 1.4566 1635.056951 4 0.0004 106 | 0/8 5 h-lim-p 0.0107 3.0171 0.0581 1635.056950 0 0.0007 121 | 0/8 6 h-lim-p 0.0030 14.0811 0.0132 1635.056949 0 0.0013 141 | 0/8 7 h-lim-p 0.0502 20.0000 0.0003 1635.056890 0 0.8029 165 | 0/8 8 h-lim-p 0.0034 2.4247 0.0792 1635.056887 1 0.0008 188 | 0/8 9 h-lim-p 0.5704 20.0000 0.0001 1635.056884 0 1.1408 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1635.056884 0 1.0938 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1635.056884 0 2.1875 249 | 0/8 12 h-lim-p 2.1327 20.0000 0.0000 1635.056884 0 0.9331 269 | 0/8 13 h-lim-p 0.4461 20.0000 0.0000 1635.056884 0 0.0035 295 | 0/8 14 h-lim-p 0.0008 20.0000 0.0000 1635.056884 0 0.0012 315 | 0/8 15 h-lim-p 0.0005 20.0000 0.0001 1635.056884 0 0.0000 352 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1635.056884 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1635.056884 Node 7: lnL = -1635.056884 Node 8: lnL = -1635.056884 Node 9: lnL = -1635.056884 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 392 Sequential format.. Reading seq # 1: YDR444W_Sbay Reading seq # 2: YDR444W_Scer Reading seq # 3: YDR444W_Skud Reading seq # 4: YDR444W_Smik Reading seq # 5: YDR444W_Spar Sequences read.. Counting patterns.. # site patterns = 143 Counting frequencies.. 120 bytes for distance 22880 bytes for lkl0 18304 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.200014 0.055001 0.077536 0.084681 0.091092 0.171905 0.165194 0.098256 lnL0 = -1662.158777 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1662.158777 x= 0.20001 0.05500 0.07754 0.08468 0.09109 0.17191 0.16519 0.09826 1 h-lim-p 0.0008 0.0062 50.5520 1661.703435 4 0.0004 31 | 0/8 2 h-lim-p 0.0023 0.0210 8.1136 1661.685693 2 0.0005 48 | 0/8 3 h-lim-p 0.0011 0.0521 3.9204 1661.682634 5 0.0005 69 | 0/8 4 h-lim-p 0.0014 0.1039 1.3518 1661.682296 4 0.0004 93 | 0/8 5 h-lim-p 0.0074 2.1219 0.0786 1661.682294 1 0.0007 109 | 0/8 6 h-lim-p 0.0034 10.3774 0.0171 1661.682293 0 0.0007 130 | 0/8 7 h-lim-p 0.0241 20.0000 0.0005 1661.682286 0 0.1932 153 | 0/8 8 h-lim-p 0.0021 5.3417 0.0475 1661.682259 0 0.0043 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1661.682258 0 1.0938 194 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1661.682258 0 1.0938 214 | 0/8 11 h-lim-p 1.2902 20.0000 0.0000 1661.682258 0 1.2902 234 | 0/8 12 h-lim-p 0.7850 20.0000 0.0000 1661.682258 0 0.0123 259 | 0/8 13 h-lim-p 0.0000 3.5913 0.0402 1661.682258 0 0.0000 286 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 1661.682258 0 0.0002 306 Out... lnL = -1661.682258 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1661.682258 Node 7: lnL = -1661.682258 Node 8: lnL = -1661.682258 Node 9: lnL = -1661.682258 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 866 Sequential format.. Reading seq # 1: YDR446W_Sbay Reading seq # 2: YDR446W_Scer Reading seq # 3: YDR446W_Skud Reading seq # 4: YDR446W_Smik Reading seq # 5: YDR446W_Spar Sequences read.. Counting patterns.. # site patterns = 482 Counting frequencies.. 120 bytes for distance 77120 bytes for lkl0 61696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.568707 0.645783 0.000060 0.512095 0.823645 0.226743 0.488055 0.304646 lnL0 = -5106.886919 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 5106.886919 x= 0.56871 0.64578 0.00006 0.51209 0.82365 0.22674 0.48806 0.30465 1 h-lim-p 0.0000 0.0000 245.0290 5106.708950 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0008 980.4361 5021.372117 9 0.0006 60 | 1/8 3 h-lim-p 0.0004 0.0033 153.1567 5013.020149 0 0.0008 73 | 1/8 4 h-lim-p 0.0061 0.0489 17.4246 5012.719707 7 0.0018 102 | 0/8 5 h-lim-p 0.0002 0.0061 141.7066 5009.588885 0 0.0007 115 | 0/8 6 h-lim-p 0.0067 0.0678 14.2234 5009.409008 7 0.0020 146 | 0/8 7 h-lim-p 0.0061 0.0650 4.7503 5009.265929 6 0.0066 174 | 0/8 8 h-lim-p 0.0553 0.4425 0.4291 4997.052570 m 0.4425 186 | 0/8 9 h-lim-p -0.0000 -0.0000 0.0884 h-lim-p: -9.01244858e-18 -7.20995887e-17 8.83881425e-02 4997.052570 .. | 0/8 10 h-lim-p 0.0000 0.2625 52.0073 4995.831305 0 0.0010 228 | 0/8 11 h-lim-p 0.0000 0.0001 44.4817 4995.690071 m 0.0001 240 | 1/8 12 h-lim-p 0.0002 0.0159 18.1414 4995.615347 0 0.0009 254 | 1/8 13 h-lim-p 0.0024 0.0610 6.5463 4995.578177 6 0.0016 283 | 1/8 14 h-lim-p 0.0055 0.9548 1.9380 4995.575746 4 0.0014 304 | 1/8 15 h-lim-p 0.0039 0.7388 0.6944 4995.574168 1 0.0049 318 | 1/8 16 h-lim-p 0.0655 7.1785 0.0518 4995.500577 0 0.3929 339 | 1/8 17 h-lim-p 0.0067 0.1690 3.0396 4995.362457 1 0.0084 360 | 1/8 18 h-lim-p 2.5000 20.0000 0.0026 4995.360435 4 0.9644 380 | 1/8 19 h-lim-p 2.5000 20.0000 0.0001 4995.360433 0 1.0938 399 | 1/8 20 h-lim-p 2.5000 20.0000 0.0000 4995.360433 0 1.0938 418 | 1/8 21 h-lim-p 1.3953 20.0000 0.0000 4995.360433 0 1.2209 437 | 1/8 22 h-lim-p 0.7635 20.0000 0.0000 4995.360433 0 0.7635 456 | 1/8 23 h-lim-p 0.0138 20.0000 0.0006 4995.360433 0 0.0000 496 | 1/8 24 h-lim-p 0.0000 20.0000 0.0001 | 1/8 25 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -4995.360433 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4995.360433 Node 7: lnL = -4995.360433 Node 8: lnL = -4995.360433 Node 9: lnL = -4995.360433 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 549 Sequential format.. Reading seq # 1: YDR448W_Sbay Reading seq # 2: YDR448W_Scer Reading seq # 3: YDR448W_Skud Reading seq # 4: YDR448W_Smik Reading seq # 5: YDR448W_Spar Sequences read.. Counting patterns.. # site patterns = 217 Counting frequencies.. 120 bytes for distance 34720 bytes for lkl0 27776 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.196472 0.003644 0.039645 0.169655 0.122725 0.248729 0.301114 0.077469 lnL0 = -2587.454062 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2587.454062 x= 0.19647 0.00364 0.03964 0.16966 0.12272 0.24873 0.30111 0.07747 1 h-lim-p 0.0018 0.0145 169.2356 2585.460727 8 0.0002 42 | 0/8 2 h-lim-p 0.0006 0.0045 31.2695 2585.196128 6 0.0006 66 | 0/8 3 h-lim-p 0.0012 0.0108 14.5008 2585.157524 6 0.0004 93 | 0/8 4 h-lim-p 0.0019 0.0411 3.4067 2585.154454 5 0.0006 120 | 0/8 5 h-lim-p 0.0028 0.1292 0.6871 2585.154358 3 0.0004 142 | 0/8 6 h-lim-p 0.0020 1.1362 0.1421 2585.154347 2 0.0010 167 | 0/8 7 h-lim-p 0.0091 8.2826 0.0163 2585.154347 0 0.0010 189 | 0/8 8 h-lim-p 0.0249 20.0000 0.0007 2585.154239 0 0.5984 213 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2585.154238 1 1.2305 236 | 0/8 10 h-lim-p 2.2914 20.0000 0.0000 2585.154237 0 1.0025 256 | 0/8 11 h-lim-p 1.0785 20.0000 0.0000 2585.154237 0 0.4718 276 | 0/8 12 h-lim-p 0.1984 20.0000 0.0000 2585.154237 0 0.0016 302 | 0/8 13 h-lim-p 0.0007 20.0000 0.0001 2585.154237 0 0.0000 337 | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -2585.154237 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2585.154237 Node 7: lnL = -2585.154237 Node 8: lnL = -2585.154237 Node 9: lnL = -2585.154237 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 883 Sequential format.. Reading seq # 1: YDR449C_Sbay Reading seq # 2: YDR449C_Scer Reading seq # 3: YDR449C_Skud Reading seq # 4: YDR449C_Smik Reading seq # 5: YDR449C_Spar Sequences read.. Counting patterns.. # site patterns = 393 Counting frequencies.. 120 bytes for distance 62880 bytes for lkl0 50304 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.376425 0.060018 0.096633 0.181357 0.136907 0.307284 0.377496 0.194195 lnL0 = -4463.543922 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4463.543922 x= 0.37643 0.06002 0.09663 0.18136 0.13691 0.30728 0.37750 0.19419 1 h-lim-p 0.0007 0.0058 98.3633 4461.785834 6 0.0004 35 | 0/8 2 h-lim-p 0.0008 0.0068 23.1634 4461.677318 4 0.0004 55 | 0/8 3 h-lim-p 0.0008 0.0499 11.6790 4461.644450 6 0.0006 80 | 0/8 4 h-lim-p 0.0010 0.0708 6.9871 4461.626887 3 0.0010 98 | 0/8 5 h-lim-p 0.0034 0.2937 2.0104 4461.624927 4 0.0011 120 | 0/8 6 h-lim-p 0.0042 0.4163 0.5283 4461.624830 3 0.0007 140 | 0/8 7 h-lim-p 0.0070 5.3465 0.0562 4461.624828 0 0.0015 161 | 0/8 8 h-lim-p 0.3690 20.0000 0.0002 4461.624761 0 1.4760 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4461.624755 0 1.0938 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4461.624754 0 1.0938 223 | 0/8 11 h-lim-p 2.0043 20.0000 0.0000 4461.624754 0 1.7537 243 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4461.624754 0 1.0938 263 | 0/8 13 h-lim-p 0.3874 20.0000 0.0000 4461.624754 0 0.3874 283 | 0/8 14 h-lim-p 0.0069 20.0000 0.0003 4461.624754 0 0.0000 327 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -4461.624754 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4461.624754 Node 7: lnL = -4461.624754 Node 8: lnL = -4461.624754 Node 9: lnL = -4461.624754 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 733 Sequential format.. Reading seq # 1: YDR451C_Sbay Reading seq # 2: YDR451C_Scer Reading seq # 3: YDR451C_Skud Reading seq # 4: YDR451C_Smik Reading seq # 5: YDR451C_Spar Sequences read.. Counting patterns.. # site patterns = 196 Counting frequencies.. 120 bytes for distance 31360 bytes for lkl0 25088 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.133427 0.028320 0.043075 0.092868 0.051948 0.114927 0.138680 0.058488 lnL0 = -2820.243271 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2820.243271 x= 0.13343 0.02832 0.04307 0.09287 0.05195 0.11493 0.13868 0.05849 1 h-lim-p 0.0013 0.6653 207.1921 2818.539061 6 0.0001 36 | 0/8 2 h-lim-p 0.0005 0.0037 21.1918 2818.500905 6 0.0002 62 | 0/8 3 h-lim-p 0.0004 0.0175 9.6170 2818.494225 2 0.0002 78 | 0/8 4 h-lim-p 0.0007 0.0680 2.4285 2818.493708 4 0.0002 99 | 0/8 5 h-lim-p 0.0012 0.3494 0.3904 2818.493696 2 0.0002 117 | 0/8 6 h-lim-p 0.0012 3.5508 0.0486 2818.493696 0 0.0003 138 | 0/8 7 h-lim-p 0.0039 20.0000 0.0034 2818.493696 0 0.0017 158 | 0/8 8 h-lim-p 0.0090 20.0000 0.0006 2818.493658 0 0.1433 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2818.493657 0 1.0938 202 | 0/8 10 h-lim-p 0.9884 20.0000 0.0000 2818.493657 0 0.9884 222 | 0/8 11 h-lim-p 0.7248 20.0000 0.0000 2818.493657 0 0.0227 246 | 0/8 12 h-lim-p 0.0035 20.0000 0.0002 2818.493657 0 0.0001 271 | 0/8 13 h-lim-p 0.0004 20.0000 0.0000 2818.493657 0 0.0000 297 | 0/8 14 h-lim-p 0.0006 20.0000 0.0000 2818.493657 0 0.0000 323 Out... lnL = -2818.493657 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2818.493657 Node 7: lnL = -2818.493657 Node 8: lnL = -2818.493657 Node 9: lnL = -2818.493657 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 687 Sequential format.. Reading seq # 1: YDR453C_Sbay Reading seq # 2: YDR453C_Scer Reading seq # 3: YDR453C_Skud Reading seq # 4: YDR453C_Smik Reading seq # 5: YDR453C_Spar Sequences read.. Counting patterns.. # site patterns = 278 Counting frequencies.. 120 bytes for distance 44480 bytes for lkl0 35584 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.198022 0.114028 0.063806 0.197356 0.125502 0.293143 0.164630 0.057975 lnL0 = -3228.087666 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3228.087666 x= 0.19802 0.11403 0.06381 0.19736 0.12550 0.29314 0.16463 0.05797 1 h-lim-p 0.0068 1.4985 97.2873 3226.838573 6 0.0003 38 | 0/8 2 h-lim-p 0.0014 0.0139 19.5657 3226.731624 3 0.0006 56 | 0/8 3 h-lim-p 0.0022 0.0346 5.2296 3226.725748 4 0.0005 79 | 0/8 4 h-lim-p 0.0041 0.6456 0.5916 3226.725624 3 0.0007 99 | 0/8 5 h-lim-p 0.0024 1.6723 0.1753 3226.725616 0 0.0005 120 | 0/8 6 h-lim-p 0.0015 4.4735 0.0637 3226.725615 0 0.0006 140 | 0/8 7 h-lim-p 0.0107 20.0000 0.0038 3226.725614 0 0.0093 160 | 0/8 8 h-lim-p 0.0085 20.0000 0.0042 3226.725490 0 0.0682 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3226.725490 0 1.0938 203 | 0/8 10 h-lim-p 1.6015 20.0000 0.0000 3226.725490 0 1.4014 223 | 0/8 11 h-lim-p 1.8388 20.0000 0.0000 3226.725490 0 1.6089 243 | 0/8 12 h-lim-p 0.8478 20.0000 0.0000 3226.725490 0 0.8478 263 | 0/8 13 h-lim-p 0.0212 20.0000 0.0010 3226.725490 0 0.0212 283 | 0/8 14 h-lim-p 0.0068 20.0000 0.0032 3226.725490 0 0.0000 323 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 3226.725490 0 0.0000 352 Out... lnL = -3226.725490 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3226.725490 Node 7: lnL = -3226.725490 Node 8: lnL = -3226.725490 Node 9: lnL = -3226.725490 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 567 Sequential format.. Reading seq # 1: YDR454C_Sbay Reading seq # 2: YDR454C_Scer Reading seq # 3: YDR454C_Skud Reading seq # 4: YDR454C_Smik Reading seq # 5: YDR454C_Spar Sequences read.. Counting patterns.. # site patterns = 263 Counting frequencies.. 120 bytes for distance 42080 bytes for lkl0 33664 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.330121 0.092175 0.120665 0.131317 0.158710 0.239947 0.240350 0.160345 lnL0 = -2834.159182 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2834.159182 x= 0.33012 0.09217 0.12066 0.13132 0.15871 0.23995 0.24035 0.16035 1 h-lim-p 0.0052 0.0417 67.1096 2832.997784 6 0.0005 37 | 0/8 2 h-lim-p 0.0013 0.0107 14.4677 2832.912751 7 0.0008 67 | 0/8 3 h-lim-p 0.0017 0.0483 7.2601 2832.896257 2 0.0008 83 | 0/8 4 h-lim-p 0.0012 0.0647 4.9054 2832.891287 4 0.0006 104 | 0/8 5 h-lim-p 0.0038 0.5365 0.7878 2832.890915 4 0.0012 125 | 0/8 6 h-lim-p 0.0116 2.4942 0.0843 2832.890912 1 0.0007 150 | 0/8 7 h-lim-p 0.0053 20.0000 0.0114 2832.890905 0 0.0106 171 | 0/8 8 h-lim-p 0.0153 20.0000 0.0079 2832.890329 0 0.1227 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2832.890324 0 1.0938 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2832.890324 0 1.0938 234 | 0/8 11 h-lim-p 2.3752 20.0000 0.0000 2832.890324 0 1.0391 254 | 0/8 12 h-lim-p 0.9512 20.0000 0.0000 2832.890324 0 0.9512 274 | 0/8 13 h-lim-p 0.0017 20.0000 0.0026 2832.890324 0 0.0000 298 | 0/8 14 h-lim-p 0.0012 20.0000 0.0001 2832.890324 0 0.0000 329 | 0/8 15 h-lim-p 0.0020 20.0000 0.0000 2832.890324 0 0.0000 361 Out... lnL = -2832.890324 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2832.890324 Node 7: lnL = -2832.890324 Node 8: lnL = -2832.890324 Node 9: lnL = -2832.890324 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 690 Sequential format.. Reading seq # 1: YDR456W_Sbay Reading seq # 2: YDR456W_Scer Reading seq # 3: YDR456W_Skud Reading seq # 4: YDR456W_Smik Reading seq # 5: YDR456W_Spar Sequences read.. Counting patterns.. # site patterns = 284 Counting frequencies.. 120 bytes for distance 45440 bytes for lkl0 36352 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.279370 0.119843 0.086594 0.130902 0.142814 0.249154 0.192137 0.125742 lnL0 = -3348.545238 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3348.545238 x= 0.27937 0.11984 0.08659 0.13090 0.14281 0.24915 0.19214 0.12574 1 h-lim-p 0.0094 0.0748 70.5846 3347.565940 7 0.0004 41 | 0/8 2 h-lim-p 0.0008 0.0064 22.5693 3347.418036 4 0.0006 61 | 0/8 3 h-lim-p 0.0013 0.0223 11.1388 3347.394957 6 0.0005 88 | 0/8 4 h-lim-p 0.0011 0.0560 4.4609 3347.391448 5 0.0004 112 | 0/8 5 h-lim-p 0.0040 0.7789 0.4778 3347.391356 1 0.0008 127 | 0/8 6 h-lim-p 0.0026 1.6891 0.1454 3347.391350 0 0.0006 148 | 0/8 7 h-lim-p 0.0066 19.6187 0.0126 3347.391343 0 0.0098 168 | 0/8 8 h-lim-p 0.0137 20.0000 0.0091 3347.390524 0 0.1092 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3347.390508 1 0.9961 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3347.390508 0 1.0938 233 | 0/8 11 h-lim-p 1.2137 20.0000 0.0000 3347.390508 0 1.8206 253 | 0/8 12 h-lim-p 0.2660 20.0000 0.0000 3347.390508 0 0.0000 300 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 3347.390508 0 0.0000 321 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 3347.390508 0 0.0000 356 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -3347.390508 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3347.390508 Node 7: lnL = -3347.390508 Node 8: lnL = -3347.390508 Node 9: lnL = -3347.390508 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 302 Sequential format.. Reading seq # 1: YDR458C_Sbay Reading seq # 2: YDR458C_Scer Reading seq # 3: YDR458C_Skud Reading seq # 4: YDR458C_Smik Reading seq # 5: YDR458C_Spar Sequences read.. Counting patterns.. # site patterns = 152 Counting frequencies.. 120 bytes for distance 24320 bytes for lkl0 19456 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.266744 0.057542 0.081197 0.195301 0.100386 0.213824 0.219674 0.124042 lnL0 = -1399.591639 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1399.591639 x= 0.26674 0.05754 0.08120 0.19530 0.10039 0.21382 0.21967 0.12404 1 h-lim-p 0.0006 0.0050 65.7121 1398.031124 1 0.0008 24 | 0/8 2 h-lim-p 0.0008 0.0064 18.2059 1397.875968 1 0.0010 38 | 0/8 3 h-lim-p 0.0017 0.0427 10.8175 1397.834248 7 0.0009 67 | 0/8 4 h-lim-p 0.0041 0.1178 2.4861 1397.828989 3 0.0019 85 | 0/8 5 h-lim-p 0.0134 0.5210 0.3434 1397.828902 2 0.0015 103 | 0/8 6 h-lim-p 0.0053 3.7553 0.0947 1397.828895 2 0.0014 128 | 0/8 7 h-lim-p 0.0435 20.0000 0.0031 1397.828893 1 0.0346 150 | 0/8 8 h-lim-p 0.0133 20.0000 0.0079 1397.828823 0 0.0534 172 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1397.828823 0 1.2500 192 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1397.828823 0 1.0938 212 | 0/8 11 h-lim-p 2.0552 20.0000 0.0000 1397.828823 0 0.8991 232 | 0/8 12 h-lim-p 0.6012 20.0000 0.0000 1397.828823 0 0.4509 252 | 0/8 13 h-lim-p 0.0733 20.0000 0.0000 1397.828823 0 0.0001 280 | 0/8 14 h-lim-p 0.0001 20.0000 0.0001 1397.828823 0 0.0000 318 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 1397.828823 0 0.0000 338 Out... lnL = -1397.828823 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1397.828823 Node 7: lnL = -1397.828823 Node 8: lnL = -1397.828823 Node 9: lnL = -1397.828823 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 388 Sequential format.. Reading seq # 1: YDR459C_Sbay Reading seq # 2: YDR459C_Scer Reading seq # 3: YDR459C_Skud Reading seq # 4: YDR459C_Smik Reading seq # 5: YDR459C_Spar Sequences read.. Counting patterns.. # site patterns = 168 Counting frequencies.. 120 bytes for distance 26880 bytes for lkl0 21504 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.227333 0.014636 0.099022 0.160457 0.127337 0.181134 0.228398 0.099020 lnL0 = -1821.163874 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1821.163874 x= 0.22733 0.01464 0.09902 0.16046 0.12734 0.18113 0.22840 0.09902 1 h-lim-p 0.0023 0.0837 125.6142 1819.344712 3 0.0003 30 | 0/8 2 h-lim-p 0.0035 0.0350 9.5339 1819.300916 5 0.0010 53 | 0/8 3 h-lim-p 0.0026 0.0911 3.4586 1819.297308 4 0.0007 74 | 0/8 4 h-lim-p 0.0026 0.2339 0.9085 1819.296998 4 0.0008 96 | 0/8 5 h-lim-p 0.0031 0.7300 0.2395 1819.296976 2 0.0008 121 | 0/8 6 h-lim-p 0.0050 6.4895 0.0395 1819.296974 1 0.0012 144 | 0/8 7 h-lim-p 0.0071 20.0000 0.0068 1819.296935 0 0.0428 166 | 0/8 8 h-lim-p 0.0065 20.0000 0.0447 1819.296151 0 0.0259 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1819.296075 2 0.9961 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1819.296075 0 1.0938 232 | 0/8 11 h-lim-p 1.3821 20.0000 0.0000 1819.296075 0 0.3023 253 | 0/8 12 h-lim-p 0.1374 20.0000 0.0000 1819.296075 0 0.0344 274 | 0/8 13 h-lim-p 0.0167 20.0000 0.0000 1819.296075 0 0.0000 315 | 0/8 14 h-lim-p 0.0000 20.0000 0.0005 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -1819.296075 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1819.296075 Node 7: lnL = -1819.296075 Node 8: lnL = -1819.296075 Node 9: lnL = -1819.296075 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 421 Sequential format.. Reading seq # 1: YDR460W_Sbay Reading seq # 2: YDR460W_Scer Reading seq # 3: YDR460W_Skud Reading seq # 4: YDR460W_Smik Reading seq # 5: YDR460W_Spar Sequences read.. Counting patterns.. # site patterns = 167 Counting frequencies.. 120 bytes for distance 26720 bytes for lkl0 21376 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.220232 0.033522 0.088012 0.162784 0.125010 0.210263 0.208359 0.091269 lnL0 = -1866.693563 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1866.693563 x= 0.22023 0.03352 0.08801 0.16278 0.12501 0.21026 0.20836 0.09127 1 h-lim-p 0.0016 0.0131 76.5684 1865.774084 6 0.0003 38 | 0/8 2 h-lim-p 0.0019 0.0150 12.9041 1865.719448 6 0.0007 63 | 0/8 3 h-lim-p 0.0026 0.0674 3.2729 1865.716628 4 0.0006 86 | 0/8 4 h-lim-p 0.0050 0.6397 0.3692 1865.716556 2 0.0011 103 | 0/8 5 h-lim-p 0.0057 2.1559 0.0705 1865.716554 1 0.0007 127 | 0/8 6 h-lim-p 0.0050 20.0000 0.0098 1865.716554 0 0.0011 148 | 0/8 7 h-lim-p 0.0077 20.0000 0.0014 1865.716554 0 0.0067 168 | 0/8 8 h-lim-p 0.0391 20.0000 0.0002 1865.716550 0 0.3124 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1865.716550 0 1.0938 211 | 0/8 10 h-lim-p 1.7906 20.0000 0.0000 1865.716550 0 0.7834 231 | 0/8 11 h-lim-p 0.5751 20.0000 0.0000 1865.716550 0 0.0045 257 | 0/8 12 h-lim-p 0.0015 20.0000 0.0000 1865.716550 0 0.0000 295 | 0/8 13 h-lim-p 0.0000 20.0000 0.0004 1865.716550 0 0.0000 330 | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1865.716550 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1865.716550 Node 7: lnL = -1865.716550 Node 8: lnL = -1865.716550 Node 9: lnL = -1865.716550 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 574 Sequential format.. Reading seq # 1: YDR465C_Sbay Reading seq # 2: YDR465C_Scer Reading seq # 3: YDR465C_Skud Reading seq # 4: YDR465C_Smik Reading seq # 5: YDR465C_Spar Sequences read.. Counting patterns.. # site patterns = 193 Counting frequencies.. 120 bytes for distance 30880 bytes for lkl0 24704 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.165283 0.090800 0.045851 0.138355 0.096281 0.156921 0.179213 0.057944 lnL0 = -2535.353206 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2535.353206 x= 0.16528 0.09080 0.04585 0.13835 0.09628 0.15692 0.17921 0.05794 1 h-lim-p 0.0009 0.0071 87.0150 2534.529045 4 0.0002 31 | 0/8 2 h-lim-p 0.0005 0.0042 23.2497 2534.452144 7 0.0003 63 | 0/8 3 h-lim-p 0.0010 0.0367 6.7614 2534.444816 5 0.0003 88 | 0/8 4 h-lim-p 0.0012 0.1014 2.0343 2534.444076 4 0.0004 111 | 0/8 5 h-lim-p 0.0015 0.6437 0.5204 2534.444023 3 0.0004 130 | 0/8 6 h-lim-p 0.0060 6.0378 0.0360 2534.444023 0 0.0007 152 | 0/8 7 h-lim-p 0.0029 20.0000 0.0082 2534.444018 0 0.0115 174 | 0/8 8 h-lim-p 0.0069 20.0000 0.0136 2534.443590 0 0.0414 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2534.443579 1 0.9961 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2534.443579 0 1.0938 238 | 0/8 11 h-lim-p 0.9107 20.0000 0.0000 2534.443579 0 3.6427 260 | 0/8 12 h-lim-p 0.0385 20.0000 0.0021 2534.443579 0 0.0042 282 | 0/8 13 h-lim-p 0.0011 11.0401 0.0077 2534.443579 0 0.0000 317 | 0/8 14 h-lim-p 0.0003 20.0000 0.0000 2534.443579 0 0.0003 337 Out... lnL = -2534.443579 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2534.443579 Node 7: lnL = -2534.443579 Node 8: lnL = -2534.443579 Node 9: lnL = -2534.443579 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 574 Sequential format.. Reading seq # 1: YDR466W_Sbay Reading seq # 2: YDR466W_Scer Reading seq # 3: YDR466W_Skud Reading seq # 4: YDR466W_Smik Reading seq # 5: YDR466W_Spar Sequences read.. Counting patterns.. # site patterns = 185 Counting frequencies.. 120 bytes for distance 29600 bytes for lkl0 23680 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.155484 0.108981 0.046199 0.140406 0.094229 0.155123 0.162426 0.049153 lnL0 = -2518.595050 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2518.595050 x= 0.15548 0.10898 0.04620 0.14041 0.09423 0.15512 0.16243 0.04915 1 h-lim-p 0.0019 0.0149 77.7264 2517.972704 2 0.0002 28 | 0/8 2 h-lim-p 0.0007 0.0058 22.9897 2517.888320 2 0.0003 44 | 0/8 3 h-lim-p 0.0015 0.0299 5.0951 2517.884577 4 0.0003 65 | 0/8 4 h-lim-p 0.0014 0.1616 1.1180 2517.884312 3 0.0004 85 | 0/8 5 h-lim-p 0.0015 1.0816 0.3406 2517.884293 0 0.0004 98 | 0/8 6 h-lim-p 0.0112 13.8369 0.0111 2517.884293 0 0.0006 121 | 0/8 7 h-lim-p 0.0054 20.0000 0.0013 2517.884292 0 0.0215 143 | 0/8 8 h-lim-p 0.0037 9.0320 0.0073 2517.884267 0 0.0150 165 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2517.884267 0 1.0938 185 | 0/8 10 h-lim-p 2.0515 20.0000 0.0000 2517.884267 0 0.8975 205 | 0/8 11 h-lim-p 0.5020 20.0000 0.0000 2517.884267 0 0.0020 232 | 0/8 12 h-lim-p 0.0005 20.0000 0.0001 2517.884267 0 0.0000 269 | 0/8 13 h-lim-p 0.0000 20.0000 0.0004 | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -2517.884267 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2517.884267 Node 7: lnL = -2517.884267 Node 8: lnL = -2517.884267 Node 9: lnL = -2517.884267 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 335 Sequential format.. Reading seq # 1: YDR468C_Sbay Reading seq # 2: YDR468C_Scer Reading seq # 3: YDR468C_Skud Reading seq # 4: YDR468C_Smik Reading seq # 5: YDR468C_Spar Sequences read.. Counting patterns.. # site patterns = 148 Counting frequencies.. 120 bytes for distance 23680 bytes for lkl0 18944 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.218678 0.030920 0.069650 0.149885 0.090114 0.214531 0.211960 0.096942 lnL0 = -1508.655897 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1508.655897 x= 0.21868 0.03092 0.06965 0.14988 0.09011 0.21453 0.21196 0.09694 1 h-lim-p 0.0006 0.0052 37.0245 1508.365905 8 0.0004 42 | 0/8 2 h-lim-p 0.0013 0.0107 10.9636 1508.337032 4 0.0005 62 | 0/8 3 h-lim-p 0.0014 0.0657 3.9546 1508.332600 3 0.0006 80 | 0/8 4 h-lim-p 0.0020 0.1535 1.2587 1508.332088 4 0.0007 101 | 0/8 5 h-lim-p 0.0024 0.5465 0.3748 1508.332042 3 0.0007 122 | 0/8 6 h-lim-p 0.0053 10.4316 0.0504 1508.332041 1 0.0011 145 | 0/8 7 h-lim-p 0.0266 20.0000 0.0020 1508.332039 0 0.0266 165 | 0/8 8 h-lim-p 0.0100 16.2797 0.0053 1508.331991 0 0.0401 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1508.331991 0 1.0938 207 | 0/8 10 h-lim-p 2.1879 20.0000 0.0000 1508.331991 0 0.9572 227 | 0/8 11 h-lim-p 0.7576 20.0000 0.0000 1508.331991 0 0.0059 253 | 0/8 12 h-lim-p 0.0004 20.0000 0.0001 1508.331991 0 0.0004 273 | 0/8 13 h-lim-p 0.0005 20.0000 0.0001 1508.331991 0 0.0005 293 | 0/8 14 h-lim-p 0.0003 20.0000 0.0001 1508.331991 0 0.0000 318 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 1508.331991 0 0.0000 348 Out... lnL = -1508.331991 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1508.331991 Node 7: lnL = -1508.331991 Node 8: lnL = -1508.331991 Node 9: lnL = -1508.331991 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 384 Sequential format.. Reading seq # 1: YDR469W_Sbay Reading seq # 2: YDR469W_Scer Reading seq # 3: YDR469W_Skud Reading seq # 4: YDR469W_Smik Reading seq # 5: YDR469W_Spar Sequences read.. Counting patterns.. # site patterns = 153 Counting frequencies.. 120 bytes for distance 24480 bytes for lkl0 19584 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.176429 0.060357 0.075919 0.150237 0.089761 0.213983 0.229088 0.056085 lnL0 = -1575.316189 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1575.316189 x= 0.17643 0.06036 0.07592 0.15024 0.08976 0.21398 0.22909 0.05609 1 h-lim-p 0.0014 0.0115 27.8536 1575.124178 6 0.0005 35 | 0/8 2 h-lim-p 0.0021 0.0186 6.7374 1575.109184 6 0.0007 60 | 0/8 3 h-lim-p 0.0018 0.1234 2.6073 1575.107352 5 0.0006 86 | 0/8 4 h-lim-p 0.0015 0.3144 1.0490 1575.106936 5 0.0009 111 | 0/8 5 h-lim-p 0.0106 1.9785 0.0878 1575.106933 1 0.0007 128 | 0/8 6 h-lim-p 0.0029 12.6406 0.0196 1575.106933 0 0.0013 148 | 0/8 7 h-lim-p 0.2618 20.0000 0.0001 1575.106933 0 0.0573 169 | 0/8 8 h-lim-p 0.0035 20.0000 0.0016 1575.106933 0 0.0279 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1575.106933 0 1.0938 212 | 0/8 10 h-lim-p 0.7667 20.0000 0.0000 1575.106933 0 1.5334 233 | 0/8 11 h-lim-p 1.8711 20.0000 0.0000 1575.106933 0 0.0877 257 | 0/8 12 h-lim-p 0.0148 20.0000 0.0000 1575.106933 0 0.0018 279 | 0/8 13 h-lim-p 0.0007 20.0000 0.0001 1575.106933 0 0.0000 305 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 1575.106933 0 0.0000 337 Out... lnL = -1575.106933 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1575.106933 Node 7: lnL = -1575.106933 Node 8: lnL = -1575.106933 Node 9: lnL = -1575.106933 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 594 Sequential format.. Reading seq # 1: YDR470C_Sbay Reading seq # 2: YDR470C_Scer Reading seq # 3: YDR470C_Skud Reading seq # 4: YDR470C_Smik Reading seq # 5: YDR470C_Spar Sequences read.. Counting patterns.. # site patterns = 251 Counting frequencies.. 120 bytes for distance 40160 bytes for lkl0 32128 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.215085 0.074038 0.096301 0.126476 0.102626 0.279804 0.271369 0.072852 lnL0 = -2892.179909 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2892.179909 x= 0.21509 0.07404 0.09630 0.12648 0.10263 0.27980 0.27137 0.07285 1 h-lim-p 0.0125 1.9509 67.9340 2891.468853 3 0.0003 32 | 0/8 2 h-lim-p 0.0020 0.0190 11.3178 2891.442254 5 0.0004 54 | 0/8 3 h-lim-p 0.0008 0.0360 6.0041 2891.433462 5 0.0006 76 | 0/8 4 h-lim-p 0.0040 0.2593 0.9096 2891.433154 3 0.0008 95 | 0/8 5 h-lim-p 0.0131 3.9609 0.0536 2891.433153 0 0.0007 118 | 0/8 6 h-lim-p 0.0017 20.0000 0.0222 2891.433153 0 0.0015 138 | 0/8 7 h-lim-p 0.0089 20.0000 0.0038 2891.433149 0 0.0178 159 | 0/8 8 h-lim-p 0.0042 8.3189 0.0161 2891.433015 0 0.0167 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2891.433011 0 1.0938 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2891.433011 0 1.0938 221 | 0/8 11 h-lim-p 1.1273 20.0000 0.0000 2891.433011 0 2.2546 242 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2891.433011 0 0.6250 263 | 0/8 13 h-lim-p 0.1228 20.0000 0.0000 2891.433011 0 0.0614 283 | 0/8 14 h-lim-p 0.0173 20.0000 0.0001 2891.433011 0 0.0000 323 | 0/8 15 h-lim-p 0.0000 20.0000 0.0007 | 0/8 16 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -2891.433011 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2891.433011 Node 7: lnL = -2891.433011 Node 8: lnL = -2891.433011 Node 9: lnL = -2891.433011 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 797 Sequential format.. Reading seq # 1: YDR472W_Sbay Reading seq # 2: YDR472W_Scer Reading seq # 3: YDR472W_Skud Reading seq # 4: YDR472W_Smik Reading seq # 5: YDR472W_Spar Sequences read.. Counting patterns.. # site patterns = 260 Counting frequencies.. 120 bytes for distance 41600 bytes for lkl0 33280 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.132847 0.065433 0.045477 0.103586 0.094730 0.138362 0.165051 0.037181 lnL0 = -3344.580290 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3344.580290 x= 0.13285 0.06543 0.04548 0.10359 0.09473 0.13836 0.16505 0.03718 1 h-lim-p 0.0010 0.0226 256.4282 3340.671615 4 0.0001 32 | 0/8 2 h-lim-p 0.0005 0.0040 45.5209 3340.442578 2 0.0002 48 | 0/8 3 h-lim-p 0.0012 0.0104 9.0872 3340.434766 5 0.0002 74 | 0/8 4 h-lim-p 0.0011 0.1221 1.5686 3340.434433 2 0.0003 91 | 0/8 5 h-lim-p 0.0015 0.7340 0.3033 3340.434418 0 0.0003 104 | 0/8 6 h-lim-p 0.0013 1.3916 0.0738 3340.434417 1 0.0003 127 | 0/8 7 h-lim-p 0.0010 6.0720 0.0234 3340.434414 0 0.0015 147 | 0/8 8 h-lim-p 0.0087 20.0000 0.0041 3340.433254 0 0.1396 171 | 0/8 9 h-lim-p 2.0032 20.0000 0.0003 3340.433231 2 1.0544 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 3340.433231 0 1.0938 216 | 0/8 11 h-lim-p 2.1743 20.0000 0.0000 3340.433231 0 1.9025 236 | 0/8 12 h-lim-p 0.5593 20.0000 0.0001 3340.433231 0 0.0087 261 | 0/8 13 h-lim-p 0.0002 14.5506 0.0039 3340.433231 0 0.0000 287 | 0/8 14 h-lim-p 0.0000 20.0000 0.0005 3340.433231 0 0.0000 318 | 0/8 15 h-lim-p 0.0000 20.0000 0.0013 3340.433231 0 0.0000 338 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 3340.433231 0 0.0009 363 | 0/8 17 h-lim-p 0.0025 20.0000 0.0001 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0017 | 0/8 19 h-lim-p 0.0000 20.0000 0.0017 Out... lnL = -3340.433231 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3340.433231 Node 7: lnL = -3340.433231 Node 8: lnL = -3340.433231 Node 9: lnL = -3340.433231 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 386 Sequential format.. Reading seq # 1: YDR475C_Sbay Reading seq # 2: YDR475C_Scer Reading seq # 3: YDR475C_Skud Reading seq # 4: YDR475C_Smik Reading seq # 5: YDR475C_Spar Sequences read.. Counting patterns.. # site patterns = 118 Counting frequencies.. 120 bytes for distance 18880 bytes for lkl0 15104 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.293094 0.116842 0.074166 0.071895 0.071959 0.116869 0.000060 0.180127 lnL0 = -1402.086928 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1402.086928 x= 0.29309 0.11684 0.07417 0.07190 0.07196 0.11687 0.00006 0.18013 1 h-lim-p 0.0006 0.0052 101.8702 1399.209336 5 0.0005 33 | 0/8 2 h-lim-p 0.0007 0.0057 30.1811 1398.982023 7 0.0005 62 | 0/8 3 h-lim-p 0.0006 0.0051 28.8553 1398.771273 0 0.0008 74 | 0/8 4 h-lim-p 0.0006 0.0046 26.6384 1398.652022 1 0.0007 88 | 0/8 5 h-lim-p 0.0013 0.0101 14.7413 1398.585644 6 0.0011 115 | 0/8 6 h-lim-p 0.0032 0.0528 4.9799 1398.577763 4 0.0008 136 | 0/8 7 h-lim-p 0.0010 0.0495 4.0859 1398.574223 5 0.0007 160 | 0/8 8 h-lim-p 0.8676 20.0000 0.0033 1398.571267 4 0.8491 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1398.571203 3 1.6342 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1398.571198 0 1.0938 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1398.571198 0 1.0938 249 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1398.571198 0 1.0938 269 | 0/8 13 h-lim-p 1.1649 20.0000 0.0000 1398.571198 0 1.0193 289 | 0/8 14 h-lim-p 0.3075 20.0000 0.0000 1398.571198 0 0.0084 313 | 0/8 15 h-lim-p 0.0028 20.0000 0.0000 1398.571198 0 0.0002 336 | 0/8 16 h-lim-p 0.0012 20.0000 0.0000 1398.571198 0 0.0000 361 Out... lnL = -1398.571198 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1398.571198 Node 7: lnL = -1398.571198 Node 8: lnL = -1398.571198 Node 9: lnL = -1398.571198 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 869 Sequential format.. Reading seq # 1: YDR476C_Sbay Reading seq # 2: YDR476C_Scer Reading seq # 3: YDR476C_Skud Reading seq # 4: YDR476C_Smik Reading seq # 5: YDR476C_Spar Sequences read.. Counting patterns.. # site patterns = 381 Counting frequencies.. 120 bytes for distance 60960 bytes for lkl0 48768 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.367703 0.138463 0.106562 0.140116 0.123433 0.253703 0.228152 0.178341 lnL0 = -4323.880304 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4323.880304 x= 0.36770 0.13846 0.10656 0.14012 0.12343 0.25370 0.22815 0.17834 1 h-lim-p 0.0021 0.0165 102.0446 4321.697342 6 0.0004 37 | 0/8 2 h-lim-p 0.0006 0.0045 44.3364 4321.169202 6 0.0006 64 | 0/8 3 h-lim-p 0.0007 0.0053 39.0529 4321.010874 4 0.0003 85 | 0/8 4 h-lim-p 0.0013 0.0264 9.9217 4320.978601 5 0.0008 110 | 0/8 5 h-lim-p 0.0019 0.1036 4.0180 4320.973989 5 0.0007 135 | 0/8 6 h-lim-p 0.0026 0.3456 1.0500 4320.973706 2 0.0006 152 | 0/8 7 h-lim-p 0.0095 4.6884 0.0615 4320.973676 1 0.0038 166 | 0/8 8 h-lim-p 0.0258 20.0000 0.0091 4320.967233 0 0.3098 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 4320.967133 2 0.9961 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4320.967133 0 1.0938 233 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4320.967133 0 1.0938 253 | 0/8 12 h-lim-p 0.9118 20.0000 0.0000 4320.967133 0 0.4559 273 | 0/8 13 h-lim-p 0.0007 20.0000 0.0042 4320.967133 0 0.0007 293 | 0/8 14 h-lim-p 0.0025 20.0000 0.0011 4320.967133 0 0.0000 328 | 0/8 15 h-lim-p 0.0014 20.0000 0.0000 4320.967133 0 0.0000 365 Out... lnL = -4320.967133 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4320.967133 Node 7: lnL = -4320.967133 Node 8: lnL = -4320.967133 Node 9: lnL = -4320.967133 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 592 Sequential format.. Reading seq # 1: YDR480W_Sbay Reading seq # 2: YDR480W_Scer Reading seq # 3: YDR480W_Skud Reading seq # 4: YDR480W_Smik Reading seq # 5: YDR480W_Spar Sequences read.. Counting patterns.. # site patterns = 180 Counting frequencies.. 120 bytes for distance 28800 bytes for lkl0 23040 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.189515 0.074832 0.020776 0.126683 0.086665 0.182448 0.137475 0.081358 lnL0 = -2447.700055 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2447.700055 x= 0.18951 0.07483 0.02078 0.12668 0.08666 0.18245 0.13748 0.08136 1 h-lim-p 0.0013 0.0104 125.2770 2446.884616 8 0.0001 44 | 0/8 2 h-lim-p 0.0006 0.0053 25.8329 2446.767757 6 0.0004 69 | 0/8 3 h-lim-p 0.0020 0.0406 4.7087 2446.763672 5 0.0004 92 | 0/8 4 h-lim-p 0.0014 0.1772 1.2590 2446.763449 1 0.0003 107 | 0/8 5 h-lim-p 0.0019 1.8118 0.2063 2446.763440 0 0.0004 120 | 0/8 6 h-lim-p 0.0023 3.0464 0.0370 2446.763440 0 0.0006 141 | 0/8 7 h-lim-p 0.0022 18.2088 0.0099 2446.763438 0 0.0043 162 | 0/8 8 h-lim-p 0.0122 9.7559 0.0035 2446.763089 0 0.0977 185 | 0/8 9 h-lim-p 2.4188 20.0000 0.0001 2446.763083 1 0.9638 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2446.763083 0 1.0938 227 | 0/8 11 h-lim-p 1.2621 20.0000 0.0000 2446.763083 0 3.7862 248 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2446.763083 0 0.3125 270 | 0/8 13 h-lim-p 0.0402 20.0000 0.0001 2446.763083 0 0.0402 290 | 0/8 14 h-lim-p 0.0133 20.0000 0.0002 2446.763083 0 0.0000 329 | 0/8 15 h-lim-p 0.0000 20.0000 0.0020 2446.763083 0 0.0000 359 | 0/8 16 h-lim-p 0.0000 20.0000 0.0009 2446.763083 0 0.0006 385 | 0/8 17 h-lim-p 0.0031 20.0000 0.0002 2446.763083 0 0.0000 415 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 2446.763083 0 0.0000 436 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 20 h-lim-p 0.0000 20.0000 0.0025 2446.763083 0 0.0000 499 | 0/8 21 h-lim-p 0.0000 20.0000 0.0005 2446.763083 0 0.0005 524 | 0/8 22 h-lim-p 0.0028 20.0000 0.0001 2446.763083 0 0.0003 546 | 0/8 23 h-lim-p 0.0003 20.0000 0.0001 2446.763083 0 0.0001 567 | 0/8 24 h-lim-p 0.0000 20.0000 0.0005 2446.763083 0 0.0000 595 | 0/8 25 h-lim-p 0.0000 20.0000 0.0057 .. | 0/8 26 h-lim-p 0.0000 20.0000 0.0025 | 0/8 27 h-lim-p 0.0000 20.0000 0.0025 Out... lnL = -2446.763083 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2446.763083 Node 7: lnL = -2446.763083 Node 8: lnL = -2446.763083 Node 9: lnL = -2446.763083 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 193 Sequential format.. Reading seq # 1: YDR481C_Sbay Reading seq # 2: YDR481C_Scer Reading seq # 3: YDR481C_Skud Reading seq # 4: YDR481C_Smik Reading seq # 5: YDR481C_Spar Sequences read.. Counting patterns.. # site patterns = 86 Counting frequencies.. 120 bytes for distance 13760 bytes for lkl0 11008 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.094901 0.090453 0.054066 0.063777 0.049986 0.166316 0.128191 0.011420 lnL0 = -710.944608 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 710.944608 x= 0.09490 0.09045 0.05407 0.06378 0.04999 0.16632 0.12819 0.01142 1 h-lim-p 0.0006 0.0047 44.1321 710.453308 2 0.0006 26 | 0/8 2 h-lim-p 0.0012 0.0098 12.5908 710.395658 8 0.0008 57 | 0/8 3 h-lim-p 0.0010 0.0251 9.7951 710.377122 7 0.0006 87 | 0/8 4 h-lim-p 0.0035 0.0513 1.5939 710.376504 5 0.0005 113 | 0/8 5 h-lim-p 0.0074 0.5824 0.1092 710.376499 1 0.0008 129 | 0/8 6 h-lim-p 0.0028 3.9226 0.0322 710.376497 2 0.0018 155 | 0/8 7 h-lim-p 0.0210 20.0000 0.0028 710.376292 0 0.2514 178 | 0/8 8 h-lim-p 0.0034 0.3632 0.2048 710.376025 3 0.0035 204 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 710.376021 1 0.9961 226 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 710.376021 0 1.0938 246 | 0/8 11 h-lim-p 1.0244 20.0000 0.0000 710.376021 0 0.0560 269 | 0/8 12 h-lim-p 0.0002 6.1792 0.0037 710.376021 0 0.0000 293 | 0/8 13 h-lim-p 0.0000 20.0000 0.0009 710.376021 0 0.0000 318 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 710.376021 0 0.0000 338 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 710.376021 0 0.0000 370 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 710.376021 0 0.0000 400 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -710.376021 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -710.376021 Node 7: lnL = -710.376021 Node 8: lnL = -710.376021 Node 9: lnL = -710.376021 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 362 Sequential format.. Reading seq # 1: YDR482C_Sbay Reading seq # 2: YDR482C_Scer Reading seq # 3: YDR482C_Skud Reading seq # 4: YDR482C_Smik Reading seq # 5: YDR482C_Spar Sequences read.. Counting patterns.. # site patterns = 164 Counting frequencies.. 120 bytes for distance 26240 bytes for lkl0 20992 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.183690 0.021912 0.045552 0.111851 0.084204 0.240309 0.269264 0.063394 lnL0 = -1533.030218 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1533.030218 x= 0.18369 0.02191 0.04555 0.11185 0.08420 0.24031 0.26926 0.06339 1 h-lim-p 0.0033 0.0278 95.8949 1531.821624 7 0.0003 39 | 0/8 2 h-lim-p 0.0004 0.0035 18.4882 1531.727225 0 0.0007 51 | 0/8 3 h-lim-p 0.0017 0.0333 7.1688 1531.709282 2 0.0008 67 | 0/8 4 h-lim-p 0.0011 0.0497 5.1230 1531.704035 4 0.0006 88 | 0/8 5 h-lim-p 0.0069 0.7672 0.4320 1531.703924 4 0.0012 112 | 0/8 6 h-lim-p 0.0020 1.2513 0.2515 1531.703901 2 0.0008 136 | 0/8 7 h-lim-p 0.0196 10.5529 0.0103 1531.703684 0 0.0588 157 | 0/8 8 h-lim-p 0.0047 4.4451 0.1284 1531.700939 0 0.0141 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 1531.700787 2 1.1719 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1531.700784 0 1.2500 222 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1531.700784 0 1.2500 242 | 0/8 12 h-lim-p 1.5889 20.0000 0.0000 1531.700784 0 0.0993 265 | 0/8 13 h-lim-p 0.0388 20.0000 0.0000 1531.700784 0 0.0000 312 | 0/8 14 h-lim-p 0.0000 20.0000 0.0010 1531.700784 0 0.0000 334 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 1531.700784 0 0.0000 354 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0010 | 0/8 18 h-lim-p 0.0000 20.0000 0.0010 Out... lnL = -1531.700784 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1531.700784 Node 7: lnL = -1531.700784 Node 8: lnL = -1531.700784 Node 9: lnL = -1531.700784 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 362 Sequential format.. Reading seq # 1: YDR483W_Sbay Reading seq # 2: YDR483W_Scer Reading seq # 3: YDR483W_Skud Reading seq # 4: YDR483W_Smik Reading seq # 5: YDR483W_Spar Sequences read.. Counting patterns.. # site patterns = 166 Counting frequencies.. 120 bytes for distance 26560 bytes for lkl0 21248 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.189220 0.034580 0.044156 0.107833 0.088222 0.247084 0.239875 0.068375 lnL0 = -1534.718754 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1534.718754 x= 0.18922 0.03458 0.04416 0.10783 0.08822 0.24708 0.23988 0.06838 1 h-lim-p 0.0009 0.0074 105.9663 1532.922526 6 0.0004 33 | 0/8 2 h-lim-p 0.0002 0.0017 33.9677 1532.607848 0 0.0007 46 | 0/8 3 h-lim-p 0.0014 0.0260 15.6663 1532.524165 7 0.0008 76 | 0/8 4 h-lim-p 0.0016 0.0218 7.9975 1532.512586 6 0.0005 105 | 0/8 5 h-lim-p 0.0035 0.3708 1.0537 1532.512146 2 0.0008 122 | 0/8 6 h-lim-p 0.0078 1.8435 0.1123 1532.512122 2 0.0015 139 | 0/8 7 h-lim-p 0.0031 14.3616 0.0551 1532.511537 0 0.0244 162 | 0/8 8 h-lim-p 0.0104 3.7921 0.1298 1532.503427 0 0.0208 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 1532.502961 4 1.4126 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1532.502958 0 1.0938 234 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1532.502958 0 1.0938 254 | 0/8 12 h-lim-p 1.0071 20.0000 0.0000 1532.502958 0 0.8812 274 | 0/8 13 h-lim-p 0.5049 20.0000 0.0000 1532.502958 0 0.0035 300 | 0/8 14 h-lim-p 0.0006 20.0000 0.0001 1532.502958 0 0.0006 320 | 0/8 15 h-lim-p 0.0000 20.0000 0.0013 1532.502958 0 0.0000 356 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 1532.502958 0 0.0000 379 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1532.502958 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1532.502958 Node 7: lnL = -1532.502958 Node 8: lnL = -1532.502958 Node 9: lnL = -1532.502958 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 315 Sequential format.. Reading seq # 1: YDR484W_Sbay Reading seq # 2: YDR484W_Scer Reading seq # 3: YDR484W_Skud Reading seq # 4: YDR484W_Smik Reading seq # 5: YDR484W_Spar Sequences read.. Counting patterns.. # site patterns = 136 Counting frequencies.. 120 bytes for distance 21760 bytes for lkl0 17408 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.234719 0.030542 0.072379 0.096216 0.093836 0.258376 0.243243 0.099948 lnL0 = -1404.410022 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1404.410022 x= 0.23472 0.03054 0.07238 0.09622 0.09384 0.25838 0.24324 0.09995 1 h-lim-p 0.0008 0.0067 66.2533 1403.516937 5 0.0004 33 | 0/8 2 h-lim-p 0.0012 0.0094 14.1671 1403.441338 7 0.0008 60 | 0/8 3 h-lim-p 0.0014 0.0443 7.9704 1403.421875 5 0.0008 85 | 0/8 4 h-lim-p 0.0016 0.0438 3.7779 1403.418051 3 0.0007 103 | 0/8 5 h-lim-p 0.0034 0.3303 0.7672 1403.417710 4 0.0012 125 | 0/8 6 h-lim-p 0.0070 1.0533 0.1359 1403.417702 2 0.0009 151 | 0/8 7 h-lim-p 0.0041 10.2050 0.0307 1403.417701 0 0.0018 171 | 0/8 8 h-lim-p 0.5078 20.0000 0.0001 1403.417686 0 1.0156 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1403.417686 0 1.0938 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1403.417686 0 1.0938 232 | 0/8 11 h-lim-p 1.1864 20.0000 0.0000 1403.417686 0 0.0093 258 | 0/8 12 h-lim-p 0.0033 20.0000 0.0000 1403.417686 0 0.0049 278 | 0/8 13 h-lim-p 0.0025 20.0000 0.0000 1403.417686 0 0.0000 311 | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1403.417686 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1403.417686 Node 7: lnL = -1403.417686 Node 8: lnL = -1403.417686 Node 9: lnL = -1403.417686 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 195 Sequential format.. Reading seq # 1: YDR485C_Sbay Reading seq # 2: YDR485C_Scer Reading seq # 3: YDR485C_Skud Reading seq # 4: YDR485C_Smik Reading seq # 5: YDR485C_Spar Sequences read.. Counting patterns.. # site patterns = 111 Counting frequencies.. 120 bytes for distance 17760 bytes for lkl0 14208 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.244402 0.063078 0.080384 0.151193 0.142146 0.283684 0.205618 0.092097 lnL0 = -945.540931 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 945.540931 x= 0.24440 0.06308 0.08038 0.15119 0.14215 0.28368 0.20562 0.09210 1 h-lim-p 0.0030 0.0242 43.2675 944.669095 9 0.0010 45 | 0/8 2 h-lim-p 0.0034 0.0275 7.2161 944.626810 2 0.0016 61 | 0/8 3 h-lim-p 0.0046 0.1357 2.5363 944.620852 3 0.0021 79 | 0/8 4 h-lim-p 0.0043 0.2519 1.2254 944.619546 2 0.0022 95 | 0/8 5 h-lim-p 0.0190 1.2319 0.1391 944.619528 2 0.0019 113 | 0/8 6 h-lim-p 0.0184 20.0000 0.0143 944.619528 0 0.0040 134 | 0/8 7 h-lim-p 0.0170 20.0000 0.0034 944.619527 0 0.0255 154 | 0/8 8 h-lim-p 0.0277 20.0000 0.0031 944.619497 0 0.1108 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 944.619496 0 1.0938 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 944.619496 0 1.0938 216 | 0/8 11 h-lim-p 1.6882 20.0000 0.0000 944.619496 0 2.5324 236 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 944.619496 0 0.3125 258 | 0/8 13 h-lim-p 0.0482 20.0000 0.0000 944.619496 0 0.0724 278 | 0/8 14 h-lim-p 0.0245 20.0000 0.0000 944.619496 0 0.0061 299 | 0/8 15 h-lim-p 0.0032 20.0000 0.0001 944.619496 0 0.0032 319 | 0/8 16 h-lim-p 0.0019 20.0000 0.0001 944.619496 0 0.0000 359 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -944.619496 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -944.619496 Node 7: lnL = -944.619496 Node 8: lnL = -944.619496 Node 9: lnL = -944.619496 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 234 Sequential format.. Reading seq # 1: YDR487C_Sbay Reading seq # 2: YDR487C_Scer Reading seq # 3: YDR487C_Skud Reading seq # 4: YDR487C_Smik Reading seq # 5: YDR487C_Spar Sequences read.. Counting patterns.. # site patterns = 118 Counting frequencies.. 120 bytes for distance 18880 bytes for lkl0 15104 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.189298 0.267292 0.122402 0.079596 0.000060 0.183248 0.220350 0.083061 lnL0 = -904.543830 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 904.543830 x= 0.18930 0.26729 0.12240 0.07960 0.00006 0.18325 0.22035 0.08306 1 h-lim-p 0.0001 0.0017 358.2831 898.757550 8 0.0001 42 | 0/8 2 h-lim-p 0.0002 0.0015 94.1639 892.041871 m 0.0015 54 | 0/8 3 h-lim-p -0.0000 -0.0000 44.5623 h-lim-p: -3.11285266e-19 -2.49028213e-18 4.45623115e+01 892.041871 .. | 0/8 4 h-lim-p 0.0000 0.0027 57.2334 890.855374 0 0.0006 80 | 0/8 5 h-lim-p 0.0002 0.0017 26.0825 890.425948 0 0.0013 94 | 0/8 6 h-lim-p 0.0005 0.0038 12.0260 890.395447 1 0.0006 108 | 0/8 7 h-lim-p 0.0007 0.0055 3.8991 890.388554 0 0.0010 120 | 0/8 8 h-lim-p 0.0015 0.1413 2.6423 890.384765 4 0.0015 140 | 0/8 9 h-lim-p 0.0136 0.2396 0.2928 890.384331 4 0.0048 161 | 0/8 10 h-lim-p 0.0186 0.5323 0.0760 890.376644 0 0.0746 183 | 0/8 11 h-lim-p 0.0086 0.2950 0.6590 890.332102 0 0.0172 204 | 0/8 12 h-lim-p 2.5000 20.0000 0.0005 890.331926 4 0.9131 233 | 0/8 13 h-lim-p 2.5000 20.0000 0.0001 890.331923 2 0.8246 259 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 890.331923 0 1.0938 279 | 0/8 15 h-lim-p 1.8783 20.0000 0.0000 890.331923 0 1.6435 299 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 890.331923 0 1.0938 319 | 0/8 17 h-lim-p 0.4825 20.0000 0.0000 890.331923 0 0.1206 340 | 0/8 18 h-lim-p 0.0011 12.4779 0.0013 890.331923 0 0.0000 364 | 0/8 19 h-lim-p 0.0001 20.0000 0.0006 890.331923 0 0.0000 393 | 0/8 20 h-lim-p 0.0002 20.0000 0.0000 890.331923 0 0.0000 426 Out... lnL = -890.331923 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -890.331923 Node 7: lnL = -890.331923 Node 8: lnL = -890.331923 Node 9: lnL = -890.331923 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 242 Sequential format.. Reading seq # 1: YDR489W_Sbay Reading seq # 2: YDR489W_Scer Reading seq # 3: YDR489W_Skud Reading seq # 4: YDR489W_Smik Reading seq # 5: YDR489W_Spar Sequences read.. Counting patterns.. # site patterns = 110 Counting frequencies.. 120 bytes for distance 17600 bytes for lkl0 14080 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.254323 0.066392 0.001465 0.120573 0.087093 0.151702 0.202337 0.134239 lnL0 = -1053.443052 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1053.443052 x= 0.25432 0.06639 0.00147 0.12057 0.08709 0.15170 0.20234 0.13424 1 h-lim-p 0.0002 0.2673 373.8774 1049.602074 9 0.0001 45 | 0/8 2 h-lim-p 0.0005 0.0043 28.5005 1049.196712 0 0.0011 58 | 0/8 3 h-lim-p 0.0030 0.0246 10.1319 1049.167058 5 0.0006 83 | 0/8 4 h-lim-p 0.0068 0.2723 0.9678 1049.166391 3 0.0014 103 | 0/8 5 h-lim-p 0.0030 0.7423 0.4578 1049.166252 2 0.0015 127 | 0/8 6 h-lim-p 0.0151 3.2678 0.0453 1049.166199 0 0.0075 147 | 0/8 7 h-lim-p 0.0116 9.7165 0.0295 1049.161434 0 0.0926 170 | 0/8 8 h-lim-p 0.0038 0.5355 0.7153 1049.160867 2 0.0019 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1049.160443 2 2.1875 218 | 0/8 10 h-lim-p 2.3222 20.0000 0.0003 1049.160311 3 1.6451 246 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1049.160311 0 1.0938 266 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1049.160311 0 0.2734 288 | 0/8 13 h-lim-p 0.1551 20.0000 0.0000 1049.160311 0 0.0024 313 | 0/8 14 h-lim-p 0.0016 20.0000 0.0000 1049.160311 0 0.0000 338 Out... lnL = -1049.160311 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1049.160311 Node 7: lnL = -1049.160311 Node 8: lnL = -1049.160311 Node 9: lnL = -1049.160311 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 362 Sequential format.. Reading seq # 1: YDR493W_Sbay Reading seq # 2: YDR493W_Scer Reading seq # 3: YDR493W_Skud Reading seq # 4: YDR493W_Smik Reading seq # 5: YDR493W_Spar Sequences read.. Counting patterns.. # site patterns = 175 Counting frequencies.. 120 bytes for distance 28000 bytes for lkl0 22400 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.358199 0.090176 0.144942 0.120470 0.053516 0.294806 0.195782 0.180588 lnL0 = -1593.124284 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1593.124284 x= 0.35820 0.09018 0.14494 0.12047 0.05352 0.29481 0.19578 0.18059 1 h-lim-p 0.0017 0.0136 20.6572 1592.900256 8 0.0011 42 | 0/8 2 h-lim-p 0.0017 0.1055 13.3531 1592.846750 2 0.0008 58 | 0/8 3 h-lim-p 0.0005 0.0203 19.3498 1592.789168 0 0.0008 70 | 0/8 4 h-lim-p 0.0108 0.1915 1.4444 1592.787747 4 0.0014 92 | 0/8 5 h-lim-p 0.0024 0.2677 0.8590 1592.787444 2 0.0010 108 | 0/8 6 h-lim-p 0.0045 1.3191 0.1971 1592.787394 3 0.0027 137 | 0/8 7 h-lim-p 0.0216 13.5319 0.0243 1592.787389 2 0.0071 163 | 0/8 8 h-lim-p 0.0706 20.0000 0.0025 1592.786872 0 0.2823 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1592.786850 1 0.9961 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1592.786850 0 1.0938 227 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1592.786850 0 2.1875 247 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1592.786850 0 0.1562 270 | 0/8 13 h-lim-p 0.0201 20.0000 0.0000 1592.786850 0 0.0000 315 Out... lnL = -1592.786850 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1592.786850 Node 7: lnL = -1592.786850 Node 8: lnL = -1592.786850 Node 9: lnL = -1592.786850 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 371 Sequential format.. Reading seq # 1: YDR494W_Sbay Reading seq # 2: YDR494W_Scer Reading seq # 3: YDR494W_Skud Reading seq # 4: YDR494W_Smik Reading seq # 5: YDR494W_Spar Sequences read.. Counting patterns.. # site patterns = 179 Counting frequencies.. 120 bytes for distance 28640 bytes for lkl0 22912 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.251983 0.030849 0.065030 0.190434 0.101452 0.199213 0.202689 0.107349 lnL0 = -1711.766520 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1711.766520 x= 0.25198 0.03085 0.06503 0.19043 0.10145 0.19921 0.20269 0.10735 1 h-lim-p 0.0019 0.0382 133.6241 1708.908538 4 0.0004 31 | 0/8 2 h-lim-p 0.0008 0.0067 29.8061 1708.501798 1 0.0010 45 | 0/8 3 h-lim-p 0.0016 0.0134 19.8858 1708.410782 5 0.0006 66 | 0/8 4 h-lim-p 0.0044 0.0987 2.8001 1708.407158 4 0.0010 86 | 0/8 5 h-lim-p 0.0039 0.1824 0.6769 1708.406976 3 0.0008 105 | 0/8 6 h-lim-p 0.0117 6.6876 0.0477 1708.406889 2 0.0093 129 | 0/8 7 h-lim-p 0.0091 4.8107 0.0490 1708.403252 0 0.0727 152 | 0/8 8 h-lim-p 0.0031 1.0179 1.1327 1708.398980 5 0.0024 182 | 0/8 9 h-lim-p 2.3298 20.0000 0.0012 1708.398227 4 1.1865 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 1708.398198 2 1.2305 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1708.398198 0 1.0938 248 | 0/8 12 h-lim-p 2.2004 20.0000 0.0000 1708.398198 0 1.9254 268 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1708.398198 0 1.0938 288 | 0/8 14 h-lim-p 0.2788 20.0000 0.0000 1708.398198 0 0.2788 308 | 0/8 15 h-lim-p 0.0015 20.0000 0.0010 1708.398198 0 0.0000 345 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 1708.398198 0 0.0000 380 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1708.398198 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1708.398198 Node 7: lnL = -1708.398198 Node 8: lnL = -1708.398198 Node 9: lnL = -1708.398198 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 353 Sequential format.. Reading seq # 1: YDR496C_Sbay Reading seq # 2: YDR496C_Scer Reading seq # 3: YDR496C_Skud Reading seq # 4: YDR496C_Smik Reading seq # 5: YDR496C_Spar Sequences read.. Counting patterns.. # site patterns = 145 Counting frequencies.. 120 bytes for distance 23200 bytes for lkl0 18560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.166837 0.025630 0.071590 0.116710 0.100954 0.268021 0.203367 0.040855 lnL0 = -1547.843156 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1547.843156 x= 0.16684 0.02563 0.07159 0.11671 0.10095 0.26802 0.20337 0.04086 1 h-lim-p 0.0017 0.7976 134.3607 1545.614902 9 0.0003 44 | 0/8 2 h-lim-p 0.0008 0.0061 16.8059 1545.520691 5 0.0007 65 | 0/8 3 h-lim-p 0.0024 0.0466 4.5680 1545.514967 2 0.0006 82 | 0/8 4 h-lim-p 0.0018 0.1576 1.4865 1545.514140 2 0.0008 98 | 0/8 5 h-lim-p 0.0036 0.9895 0.3360 1545.514102 2 0.0007 115 | 0/8 6 h-lim-p 0.0060 7.1718 0.0391 1545.514096 2 0.0032 140 | 0/8 7 h-lim-p 0.0229 20.0000 0.0054 1545.513805 0 0.0917 162 | 0/8 8 h-lim-p 0.0014 1.1552 0.3526 1545.512358 0 0.0042 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1545.512309 2 0.9961 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1545.512309 0 1.0938 227 | 0/8 11 h-lim-p 1.4339 20.0000 0.0000 1545.512309 0 1.2546 247 | 0/8 12 h-lim-p 0.7907 20.0000 0.0000 1545.512309 0 0.3953 267 | 0/8 13 h-lim-p 0.0019 19.5496 0.0035 1545.512309 0 0.0005 288 | 0/8 14 h-lim-p 0.0001 5.2776 0.0128 1545.512309 0 0.0000 314 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 1545.512309 0 0.0000 339 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 1545.512309 0 0.0000 373 Out... lnL = -1545.512309 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1545.512309 Node 7: lnL = -1545.512309 Node 8: lnL = -1545.512309 Node 9: lnL = -1545.512309 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 417 Sequential format.. Reading seq # 1: YDR497C_Sbay Reading seq # 2: YDR497C_Scer Reading seq # 3: YDR497C_Skud Reading seq # 4: YDR497C_Smik Reading seq # 5: YDR497C_Spar Sequences read.. Counting patterns.. # site patterns = 171 Counting frequencies.. 120 bytes for distance 27360 bytes for lkl0 21888 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.240679 0.053336 0.081572 0.127291 0.053764 0.196386 0.213562 0.103252 lnL0 = -1840.764102 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1840.764102 x= 0.24068 0.05334 0.08157 0.12729 0.05376 0.19639 0.21356 0.10325 1 h-lim-p 0.0003 0.0021 95.9430 1838.880371 0 0.0005 23 | 0/8 2 h-lim-p 0.0009 0.0071 33.8804 1838.493423 3 0.0007 41 | 0/8 3 h-lim-p 0.0006 0.0046 16.0944 1838.463924 2 0.0003 57 | 0/8 4 h-lim-p 0.0006 0.0316 7.6183 1838.450635 3 0.0006 75 | 0/8 5 h-lim-p 0.0025 0.1761 1.7357 1838.449512 5 0.0008 101 | 0/8 6 h-lim-p 0.0229 2.8874 0.0601 1838.449220 2 0.0100 117 | 0/8 7 h-lim-p 0.0034 0.9566 0.1790 1838.440505 0 0.0269 140 | 0/8 8 h-lim-p 0.0026 0.0771 1.8214 1838.416422 1 0.0033 162 | 0/8 9 h-lim-p 2.5000 20.0000 0.0011 1838.415755 3 0.9961 180 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1838.415755 0 1.0938 200 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1838.415755 0 1.0938 220 | 0/8 12 h-lim-p 1.3456 20.0000 0.0000 1838.415755 0 1.1774 240 | 0/8 13 h-lim-p 0.8130 20.0000 0.0000 1838.415755 0 0.0000 275 Out... lnL = -1838.415755 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1838.415755 Node 7: lnL = -1838.415755 Node 8: lnL = -1838.415755 Node 9: lnL = -1838.415755 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 870 Sequential format.. Reading seq # 1: YDR499W_Sbay Reading seq # 2: YDR499W_Scer Reading seq # 3: YDR499W_Skud Reading seq # 4: YDR499W_Smik Reading seq # 5: YDR499W_Spar Sequences read.. Counting patterns.. # site patterns = 402 Counting frequencies.. 120 bytes for distance 64320 bytes for lkl0 51456 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.491427 0.048631 0.183964 0.154208 0.166976 0.437986 0.419083 0.220825 lnL0 = -4830.216511 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4830.216511 x= 0.49143 0.04863 0.18396 0.15421 0.16698 0.43799 0.41908 0.22082 1 h-lim-p 0.0022 0.0176 52.9721 4828.755086 8 0.0011 40 | 0/8 2 h-lim-p 0.0008 0.0065 38.7628 4828.240373 1 0.0010 54 | 0/8 3 h-lim-p 0.0023 0.0343 17.1644 4828.187529 3 0.0005 73 | 0/8 4 h-lim-p 0.0007 0.0401 11.4658 4828.143003 0 0.0014 86 | 0/8 5 h-lim-p 0.0042 0.1462 3.8743 4828.131250 3 0.0019 104 | 0/8 6 h-lim-p 0.0073 0.3366 1.0072 4828.130754 4 0.0010 127 | 0/8 7 h-lim-p 0.0022 0.7668 0.4853 4828.130598 2 0.0014 145 | 0/8 8 h-lim-p 0.1094 20.0000 0.0063 4828.117953 0 0.8751 168 | 0/8 9 h-lim-p 2.5000 20.0000 0.0009 4828.117713 2 1.0938 192 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 4828.117711 0 1.0938 212 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4828.117711 0 1.0938 232 | 0/8 12 h-lim-p 1.6439 20.0000 0.0000 4828.117711 0 1.4384 252 | 0/8 13 h-lim-p 1.0801 20.0000 0.0000 4828.117711 0 4.3204 274 | 0/8 14 h-lim-p 0.0615 20.0000 0.0004 4828.117711 0 0.0000 315 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 4828.117711 0 0.0000 343 Out... lnL = -4828.117711 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4828.117711 Node 7: lnL = -4828.117711 Node 8: lnL = -4828.117711 Node 9: lnL = -4828.117711 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 559 Sequential format.. Reading seq # 1: YDR501W_Sbay Reading seq # 2: YDR501W_Scer Reading seq # 3: YDR501W_Skud Reading seq # 4: YDR501W_Smik Reading seq # 5: YDR501W_Spar Sequences read.. Counting patterns.. # site patterns = 189 Counting frequencies.. 120 bytes for distance 30240 bytes for lkl0 24192 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.150964 0.075752 0.028310 0.130512 0.082071 0.157051 0.174449 0.042928 lnL0 = -2374.669579 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2374.669579 x= 0.15096 0.07575 0.02831 0.13051 0.08207 0.15705 0.17445 0.04293 1 h-lim-p 0.0016 0.0126 108.6299 2373.880639 7 0.0001 40 | 0/8 2 h-lim-p 0.0005 0.0049 30.7831 2373.736137 6 0.0003 66 | 0/8 3 h-lim-p 0.0011 0.0212 9.5641 2373.722219 6 0.0003 94 | 0/8 4 h-lim-p 0.0022 0.1406 1.4892 2373.721861 4 0.0003 118 | 0/8 5 h-lim-p 0.0016 0.8625 0.3177 2373.721845 1 0.0003 133 | 0/8 6 h-lim-p 0.0021 2.2181 0.0519 2373.721844 0 0.0005 154 | 0/8 7 h-lim-p 0.0045 20.0000 0.0052 2373.721843 0 0.0045 174 | 0/8 8 h-lim-p 0.0090 20.0000 0.0026 2373.721693 0 0.1079 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2373.721690 0 1.0938 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2373.721690 0 1.0938 237 | 0/8 11 h-lim-p 0.7940 20.0000 0.0000 2373.721690 0 0.0008 266 | 0/8 12 h-lim-p 0.0001 20.0000 0.0003 2373.721690 0 0.0000 288 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 2373.721690 0 0.0000 310 | 0/8 14 h-lim-p 0.0005 20.0000 0.0000 2373.721690 0 0.0000 334 Out... lnL = -2373.721690 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2373.721690 Node 7: lnL = -2373.721690 Node 8: lnL = -2373.721690 Node 9: lnL = -2373.721690 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 636 Sequential format.. Reading seq # 1: YDR502C_Sbay Reading seq # 2: YDR502C_Scer Reading seq # 3: YDR502C_Skud Reading seq # 4: YDR502C_Smik Reading seq # 5: YDR502C_Spar Sequences read.. Counting patterns.. # site patterns = 191 Counting frequencies.. 120 bytes for distance 30560 bytes for lkl0 24448 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.149542 0.045210 0.064091 0.067036 0.049594 0.184728 0.189579 0.046695 lnL0 = -2552.660786 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2552.660786 x= 0.14954 0.04521 0.06409 0.06704 0.04959 0.18473 0.18958 0.04670 1 h-lim-p 0.0005 0.0043 114.1056 2551.563907 7 0.0002 39 | 0/8 2 h-lim-p 0.0009 0.0070 13.9246 2551.539412 6 0.0003 66 | 0/8 3 h-lim-p 0.0003 0.0162 13.8173 2551.526694 5 0.0002 89 | 0/8 4 h-lim-p 0.0009 0.0512 3.2645 2551.525444 5 0.0003 114 | 0/8 5 h-lim-p 0.0012 0.2034 0.6980 2551.525381 2 0.0003 131 | 0/8 6 h-lim-p 0.0007 1.1095 0.2588 2551.525370 1 0.0004 154 | 0/8 7 h-lim-p 0.0020 2.0271 0.0472 2551.525369 0 0.0004 175 | 0/8 8 h-lim-p 0.1425 20.0000 0.0001 2551.525313 0 1.1399 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2551.525313 0 1.0938 218 | 0/8 10 h-lim-p 1.8079 20.0000 0.0000 2551.525313 0 1.5819 238 | 0/8 11 h-lim-p 2.1609 20.0000 0.0000 2551.525313 0 0.1351 261 | 0/8 12 h-lim-p 0.0388 20.0000 0.0000 2551.525313 0 0.0194 281 | 0/8 13 h-lim-p 0.0090 20.0000 0.0001 2551.525313 0 0.0000 324 | 0/8 14 h-lim-p 0.0000 20.0000 0.0028 | 0/8 15 h-lim-p 0.0000 20.0000 0.0028 Out... lnL = -2551.525313 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2551.525313 Node 7: lnL = -2551.525313 Node 8: lnL = -2551.525313 Node 9: lnL = -2551.525313 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 556 Sequential format.. Reading seq # 1: YDR503C_Sbay Reading seq # 2: YDR503C_Scer Reading seq # 3: YDR503C_Skud Reading seq # 4: YDR503C_Smik Reading seq # 5: YDR503C_Spar Sequences read.. Counting patterns.. # site patterns = 195 Counting frequencies.. 120 bytes for distance 31200 bytes for lkl0 24960 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.189565 0.046779 0.065667 0.074033 0.049569 0.194020 0.251394 0.069162 lnL0 = -2139.310549 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2139.310549 x= 0.18956 0.04678 0.06567 0.07403 0.04957 0.19402 0.25139 0.06916 1 h-lim-p 0.0063 1.4373 82.1343 2138.473043 8 0.0003 43 | 0/8 2 h-lim-p 0.0008 0.0067 16.5690 2138.437402 5 0.0003 67 | 0/8 3 h-lim-p 0.0004 0.0119 11.5496 2138.419671 2 0.0004 83 | 0/8 4 h-lim-p 0.0008 0.0511 5.1962 2138.414439 5 0.0005 109 | 0/8 5 h-lim-p 0.0020 0.1276 1.3207 2138.414053 2 0.0005 126 | 0/8 6 h-lim-p 0.0008 0.3783 0.7836 2138.413934 4 0.0005 149 | 0/8 7 h-lim-p 0.0083 2.8485 0.0478 2138.413934 0 0.0009 171 | 0/8 8 h-lim-p 0.1282 20.0000 0.0003 2138.413747 0 1.0257 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2138.413747 0 1.0938 214 | 0/8 10 h-lim-p 2.0235 20.0000 0.0000 2138.413747 0 1.7706 234 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2138.413747 0 1.0938 254 | 0/8 12 h-lim-p 0.3423 20.0000 0.0000 2138.413747 0 2.0535 276 | 0/8 13 h-lim-p 0.1889 20.0000 0.0001 2138.413747 0 0.0413 297 | 0/8 14 h-lim-p 0.0090 20.0000 0.0006 2138.413747 0 0.0000 336 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 2138.413747 0 0.0000 364 Out... lnL = -2138.413747 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2138.413747 Node 7: lnL = -2138.413747 Node 8: lnL = -2138.413747 Node 9: lnL = -2138.413747 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 567 Sequential format.. Reading seq # 1: YDR505C_Sbay Reading seq # 2: YDR505C_Scer Reading seq # 3: YDR505C_Skud Reading seq # 4: YDR505C_Smik Reading seq # 5: YDR505C_Spar Sequences read.. Counting patterns.. # site patterns = 143 Counting frequencies.. 120 bytes for distance 22880 bytes for lkl0 18304 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.084509 0.042483 0.057206 0.065421 0.033950 0.087172 0.079196 0.021517 lnL0 = -1882.908542 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1882.908542 x= 0.08451 0.04248 0.05721 0.06542 0.03395 0.08717 0.07920 0.02152 1 h-lim-p 0.0002 0.0015 130.3318 1881.831199 7 0.0001 37 | 0/8 2 h-lim-p 0.0006 0.0049 26.3593 1881.768879 7 0.0002 68 | 0/8 3 h-lim-p 0.0010 0.0319 5.0758 1881.767335 4 0.0001 90 | 0/8 4 h-lim-p 0.0003 0.0390 1.9368 1881.767141 4 0.0001 110 | 0/8 5 h-lim-p 0.0009 0.2163 0.2533 1881.767136 2 0.0001 128 | 0/8 6 h-lim-p 0.0016 7.2238 0.0228 1881.767136 0 0.0002 150 | 0/8 7 h-lim-p 0.0032 20.0000 0.0013 1881.767136 0 0.0028 170 | 0/8 8 h-lim-p 0.0029 20.0000 0.0012 1881.767125 0 0.0921 195 | 0/8 9 h-lim-p 1.3177 20.0000 0.0001 1881.767125 0 1.3177 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1881.767125 0 1.2500 235 | 0/8 11 h-lim-p 0.3648 20.0000 0.0001 1881.767125 0 0.0007 263 | 0/8 12 h-lim-p 0.0001 20.0000 0.0007 1881.767125 0 0.0000 294 | 0/8 13 h-lim-p 0.0000 20.0000 0.0009 | 0/8 14 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -1881.767125 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1881.767125 Node 7: lnL = -1881.767125 Node 8: lnL = -1881.767125 Node 9: lnL = -1881.767125 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 896 Sequential format.. Reading seq # 1: YDR510W_Sbay Reading seq # 2: YDR510W_Scer Reading seq # 3: YDR510W_Skud Reading seq # 4: YDR510W_Smik Reading seq # 5: YDR510W_Spar Sequences read.. Counting patterns.. # site patterns = 293 Counting frequencies.. 120 bytes for distance 46880 bytes for lkl0 37504 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.305480 0.000060 0.071886 0.095916 0.063480 0.204945 0.197967 0.168386 lnL0 = -3905.111870 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3905.111870 x= 0.30548 0.00006 0.07189 0.09592 0.06348 0.20495 0.19797 0.16839 1 h-lim-p 0.0004 0.0035 174.6987 3902.633302 8 0.0001 42 | 0/8 2 h-lim-p 0.0004 0.0034 52.8105 3902.327156 8 0.0002 75 | 0/8 3 h-lim-p 0.0003 0.0048 44.3092 3902.156881 2 0.0003 91 | 0/8 4 h-lim-p 0.0014 0.0195 8.0601 3902.150318 6 0.0002 120 | 0/8 5 h-lim-p 0.0008 0.1407 2.2732 3902.149252 5 0.0004 146 | 0/8 6 h-lim-p 0.0022 0.3269 0.4630 3902.149211 2 0.0004 165 | 0/8 7 h-lim-p 0.0008 1.0123 0.2107 3902.149177 1 0.0008 187 | 0/8 8 h-lim-p 0.0326 13.1864 0.0053 3902.130343 0 0.5214 211 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 3902.130006 2 0.9644 235 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3902.130006 0 1.0938 255 | 0/8 11 h-lim-p 1.5432 20.0000 0.0000 3902.130006 0 1.5432 275 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3902.130006 0 0.0098 302 | 0/8 13 h-lim-p 0.0026 20.0000 0.0000 3902.130006 0 0.0000 339 | 0/8 14 h-lim-p 0.0000 20.0000 0.0024 | 0/8 15 h-lim-p 0.0000 20.0000 0.0024 Out... lnL = -3902.130006 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3902.130006 Node 7: lnL = -3902.130006 Node 8: lnL = -3902.130006 Node 9: lnL = -3902.130006 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 348 Sequential format.. Reading seq # 1: YDR511W_Sbay Reading seq # 2: YDR511W_Scer Reading seq # 3: YDR511W_Skud Reading seq # 4: YDR511W_Smik Reading seq # 5: YDR511W_Spar Sequences read.. Counting patterns.. # site patterns = 148 Counting frequencies.. 120 bytes for distance 23680 bytes for lkl0 18944 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.265812 0.073520 0.045838 0.127286 0.098280 0.184520 0.184637 0.118165 lnL0 = -1499.584512 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1499.584512 x= 0.26581 0.07352 0.04584 0.12729 0.09828 0.18452 0.18464 0.11816 1 h-lim-p 0.0004 0.0030 81.2930 1498.026370 0 0.0006 22 | 0/8 2 h-lim-p 0.0007 0.0057 30.5384 1497.708019 4 0.0007 42 | 0/8 3 h-lim-p 0.0012 0.0119 18.8770 1497.634132 2 0.0006 58 | 0/8 4 h-lim-p 0.0017 0.0346 6.0705 1497.622155 4 0.0008 77 | 0/8 5 h-lim-p 0.0128 0.4687 0.3544 1497.622083 4 0.0010 102 | 0/8 6 h-lim-p 0.0033 2.1513 0.1060 1497.622029 1 0.0034 124 | 0/8 7 h-lim-p 0.0288 14.6374 0.0125 1497.613746 0 0.2306 147 | 0/8 8 h-lim-p 0.0020 0.0870 1.4625 1497.611620 5 0.0015 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0008 1497.611309 2 0.9644 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1497.611309 0 1.0938 215 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1497.611309 0 1.0938 235 | 0/8 12 h-lim-p 1.3170 20.0000 0.0000 1497.611309 0 1.3170 255 | 0/8 13 h-lim-p 1.2445 20.0000 0.0000 1497.611309 0 0.0049 282 | 0/8 14 h-lim-p 0.0008 20.0000 0.0000 1497.611309 0 0.0002 304 | 0/8 15 h-lim-p 0.0005 20.0000 0.0000 1497.611309 0 0.0000 330 Out... lnL = -1497.611309 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1497.611309 Node 7: lnL = -1497.611309 Node 8: lnL = -1497.611309 Node 9: lnL = -1497.611309 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 629 Sequential format.. Reading seq # 1: YDR513W_Sbay Reading seq # 2: YDR513W_Scer Reading seq # 3: YDR513W_Skud Reading seq # 4: YDR513W_Smik Reading seq # 5: YDR513W_Spar Sequences read.. Counting patterns.. # site patterns = 169 Counting frequencies.. 120 bytes for distance 27040 bytes for lkl0 21632 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.129223 0.030649 0.040161 0.083808 0.057983 0.124108 0.108068 0.045680 lnL0 = -2359.282667 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2359.282667 x= 0.12922 0.03065 0.04016 0.08381 0.05798 0.12411 0.10807 0.04568 1 h-lim-p 0.0003 0.0027 254.2080 2356.150556 8 0.0001 41 | 0/8 2 h-lim-p 0.0004 0.0029 33.7254 2356.043786 6 0.0002 65 | 0/8 3 h-lim-p 0.0005 0.0198 12.2536 2356.031424 5 0.0002 88 | 0/8 4 h-lim-p 0.0007 0.0439 3.3967 2356.030293 4 0.0002 110 | 0/8 5 h-lim-p 0.0010 0.0930 0.7398 2356.030248 3 0.0002 131 | 0/8 6 h-lim-p 0.0022 4.9084 0.0582 2356.030248 0 0.0002 153 | 0/8 7 h-lim-p 0.0019 19.9836 0.0076 2356.030248 0 0.0016 173 | 0/8 8 h-lim-p 0.0283 20.0000 0.0004 2356.030161 0 0.4527 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2356.030157 0 1.0938 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2356.030157 0 2.1875 237 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2356.030157 0 1.0938 257 | 0/8 12 h-lim-p 0.1215 20.0000 0.0000 2356.030157 0 3.8866 282 | 0/8 13 h-lim-p 1.8151 20.0000 0.0001 2356.030157 0 0.4538 303 | 0/8 14 h-lim-p 0.0210 20.0000 0.0013 2356.030157 0 0.0007 327 | 0/8 15 h-lim-p 0.0002 13.7353 0.0049 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0040 2356.030157 0 0.0000 393 | 0/8 17 h-lim-p 0.0000 20.0000 0.0009 2356.030157 0 0.0006 419 | 0/8 18 h-lim-p 0.0040 20.0000 0.0001 2356.030157 0 0.0004 441 | 0/8 19 h-lim-p 0.0008 20.0000 0.0001 2356.030157 0 0.0011 461 | 0/8 20 h-lim-p 0.0006 20.0000 0.0002 2356.030157 0 0.0000 486 | 0/8 21 h-lim-p 0.0000 20.0000 0.0016 2356.030157 0 0.0000 507 | 0/8 22 h-lim-p 0.0000 2.3737 0.0278 .. | 0/8 23 h-lim-p 0.0000 20.0000 0.0051 | 0/8 24 h-lim-p 0.0000 20.0000 0.0051 Out... lnL = -2356.030157 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2356.030157 Node 7: lnL = -2356.030157 Node 8: lnL = -2356.030157 Node 9: lnL = -2356.030157 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 455 Sequential format.. Reading seq # 1: YDR515W_Sbay Reading seq # 2: YDR515W_Scer Reading seq # 3: YDR515W_Skud Reading seq # 4: YDR515W_Smik Reading seq # 5: YDR515W_Spar Sequences read.. Counting patterns.. # site patterns = 198 Counting frequencies.. 120 bytes for distance 31680 bytes for lkl0 25344 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.225457 0.078234 0.095892 0.104816 0.095841 0.214836 0.270600 0.067312 lnL0 = -2147.378581 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2147.378581 x= 0.22546 0.07823 0.09589 0.10482 0.09584 0.21484 0.27060 0.06731 1 h-lim-p 0.0010 0.0078 66.4981 2146.473145 7 0.0004 36 | 0/8 2 h-lim-p 0.0011 0.0089 13.3761 2146.435976 4 0.0004 56 | 0/8 3 h-lim-p 0.0008 0.0279 7.0155 2146.422962 4 0.0007 76 | 0/8 4 h-lim-p 0.0028 0.1183 1.6502 2146.422140 0 0.0007 89 | 0/8 5 h-lim-p 0.0026 0.3554 0.4414 2146.422044 2 0.0010 105 | 0/8 6 h-lim-p 0.0041 1.5880 0.1116 2146.422039 1 0.0008 128 | 0/8 7 h-lim-p 0.0038 8.1367 0.0241 2146.422039 0 0.0008 149 | 0/8 8 h-lim-p 0.1736 20.0000 0.0001 2146.422027 0 1.3890 172 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2146.422025 0 1.0938 192 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2146.422025 0 1.0938 212 | 0/8 11 h-lim-p 1.1898 20.0000 0.0000 2146.422025 0 1.1898 232 | 0/8 12 h-lim-p 0.5019 20.0000 0.0000 2146.422025 0 0.5019 252 | 0/8 13 h-lim-p 0.0530 20.0000 0.0002 2146.422025 0 0.0530 272 | 0/8 14 h-lim-p 0.0192 20.0000 0.0006 2146.422025 0 0.0000 315 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 2146.422025 0 0.0000 336 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 2146.422025 0 0.0000 368 | 0/8 17 h-lim-p 0.0000 20.0000 0.0003 2146.422025 0 0.0000 395 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 2146.422025 0 0.0000 415 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 20 h-lim-p 0.0000 20.0000 0.0003 | 0/8 21 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -2146.422025 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2146.422025 Node 7: lnL = -2146.422025 Node 8: lnL = -2146.422025 Node 9: lnL = -2146.422025 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 846 Sequential format.. Reading seq # 1: YDR516C_Sbay Reading seq # 2: YDR516C_Scer Reading seq # 3: YDR516C_Skud Reading seq # 4: YDR516C_Smik Reading seq # 5: YDR516C_Spar Sequences read.. Counting patterns.. # site patterns = 234 Counting frequencies.. 120 bytes for distance 37440 bytes for lkl0 29952 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.156614 0.048929 0.065890 0.088087 0.039325 0.104351 0.118901 0.062044 lnL0 = -3125.795761 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3125.795761 x= 0.15661 0.04893 0.06589 0.08809 0.03932 0.10435 0.11890 0.06204 1 h-lim-p 0.0001 0.0009 177.1865 3123.993503 1 0.0001 24 | 0/8 2 h-lim-p 0.0007 0.0063 33.3481 3123.944888 4 0.0001 46 | 0/8 3 h-lim-p 0.0002 0.0075 17.7995 3123.926233 5 0.0001 67 | 0/8 4 h-lim-p 0.0008 0.0553 3.0899 3123.925275 2 0.0002 84 | 0/8 5 h-lim-p 0.0010 0.2639 0.6762 3123.925219 2 0.0002 101 | 0/8 6 h-lim-p 0.0016 2.1207 0.0969 3123.925208 0 0.0007 121 | 0/8 7 h-lim-p 0.0013 2.2833 0.0522 3123.924952 0 0.0053 143 | 0/8 8 h-lim-p 0.0015 0.4723 0.1843 3123.912389 0 0.0120 166 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 3123.912208 2 0.9961 190 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3123.912208 0 1.2500 210 | 0/8 11 h-lim-p 1.2396 20.0000 0.0000 3123.912208 0 0.5423 230 | 0/8 12 h-lim-p 0.2978 20.0000 0.0000 3123.912208 0 0.0000 262 | 0/8 13 h-lim-p 0.0000 20.0000 0.0006 3123.912208 0 0.0000 282 | 0/8 14 h-lim-p 0.0001 20.0000 0.0001 3123.912208 0 0.0000 321 | 0/8 15 h-lim-p 0.0000 20.0000 0.0039 | 0/8 16 h-lim-p 0.0000 20.0000 0.0039 Out... lnL = -3123.912208 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3123.912208 Node 7: lnL = -3123.912208 Node 8: lnL = -3123.912208 Node 9: lnL = -3123.912208 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 847 Sequential format.. Reading seq # 1: YDR517W_Sbay Reading seq # 2: YDR517W_Scer Reading seq # 3: YDR517W_Skud Reading seq # 4: YDR517W_Smik Reading seq # 5: YDR517W_Spar Sequences read.. Counting patterns.. # site patterns = 233 Counting frequencies.. 120 bytes for distance 37280 bytes for lkl0 29824 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.158287 0.058969 0.068176 0.084820 0.042591 0.113055 0.110131 0.061255 lnL0 = -3142.142905 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3142.142905 x= 0.15829 0.05897 0.06818 0.08482 0.04259 0.11306 0.11013 0.06125 1 h-lim-p 0.0002 0.0019 152.9496 3140.548596 9 0.0001 47 | 0/8 2 h-lim-p 0.0005 0.0036 37.7866 3140.406728 2 0.0002 63 | 0/8 3 h-lim-p 0.0004 0.0032 18.9344 3140.394200 5 0.0001 85 | 0/8 4 h-lim-p 0.0006 0.0726 2.5724 3140.393631 4 0.0002 107 | 0/8 5 h-lim-p 0.0011 0.4332 0.4268 3140.393613 2 0.0002 124 | 0/8 6 h-lim-p 0.0018 2.2965 0.0499 3140.393613 0 0.0002 146 | 0/8 7 h-lim-p 0.0191 20.0000 0.0006 3140.393524 0 0.3058 170 | 0/8 8 h-lim-p 0.0005 0.4712 0.3555 3140.393375 0 0.0007 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3140.393367 1 0.9961 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3140.393367 0 1.0938 232 | 0/8 11 h-lim-p 1.0254 20.0000 0.0000 3140.393367 0 2.0509 253 | 0/8 12 h-lim-p 0.4338 20.0000 0.0001 3140.393367 0 0.3796 273 | 0/8 13 h-lim-p 0.0392 20.0000 0.0011 3140.393367 0 0.0049 295 | 0/8 14 h-lim-p 0.0017 20.0000 0.0031 3140.393367 0 0.0008 315 | 0/8 15 h-lim-p 0.0002 8.9578 0.0107 3140.393367 0 0.0000 337 | 0/8 16 h-lim-p 0.0001 20.0000 0.0034 3140.393367 0 0.0000 375 | 0/8 17 h-lim-p 0.0000 20.0000 0.0016 3140.393367 0 0.0000 410 | 0/8 18 h-lim-p 0.0000 20.0000 0.0016 3140.393367 0 0.0000 444 | 0/8 19 h-lim-p 0.0000 20.0000 0.0016 | 0/8 20 h-lim-p 0.0000 20.0000 0.0016 Out... lnL = -3140.393367 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3140.393367 Node 7: lnL = -3140.393367 Node 8: lnL = -3140.393367 Node 9: lnL = -3140.393367 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 302 Sequential format.. Reading seq # 1: YDR518W_Sbay Reading seq # 2: YDR518W_Scer Reading seq # 3: YDR518W_Skud Reading seq # 4: YDR518W_Smik Reading seq # 5: YDR518W_Spar Sequences read.. Counting patterns.. # site patterns = 125 Counting frequencies.. 120 bytes for distance 20000 bytes for lkl0 16000 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.217732 0.008284 0.013686 0.091572 0.060507 0.217248 0.240646 0.095759 lnL0 = -1084.768038 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1084.768038 x= 0.21773 0.00828 0.01369 0.09157 0.06051 0.21725 0.24065 0.09576 1 h-lim-p 0.0005 0.0165 217.2930 1082.264239 8 0.0001 42 | 0/8 2 h-lim-p 0.0014 0.0111 13.7841 1082.028090 0 0.0028 55 | 0/8 3 h-lim-p 0.0011 0.0089 16.0146 1081.986032 6 0.0006 80 | 0/8 4 h-lim-p 0.0018 0.0181 5.0898 1081.980676 6 0.0005 107 | 0/8 5 h-lim-p 0.0024 0.3037 1.0804 1081.980018 3 0.0012 126 | 0/8 6 h-lim-p 0.0063 1.2672 0.1996 1081.979985 3 0.0012 145 | 0/8 7 h-lim-p 0.0016 1.8112 0.1504 1081.979902 0 0.0032 166 | 0/8 8 h-lim-p 0.0188 5.8386 0.0256 1081.971902 0 0.2253 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1081.971872 1 1.0938 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1081.971872 0 2.1875 231 | 0/8 11 h-lim-p 2.3873 20.0000 0.0000 1081.971872 0 1.0444 251 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1081.971872 0 2.1875 271 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1081.971872 0 1.0938 291 | 0/8 14 h-lim-p 0.7163 20.0000 0.0000 1081.971872 0 5.7300 314 | 0/8 15 h-lim-p 1.7626 20.0000 0.0000 1081.971872 0 0.3856 335 | 0/8 16 h-lim-p 1.5616 20.0000 0.0000 1081.971872 0 0.0000 370 Out... lnL = -1081.971872 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1081.971872 Node 7: lnL = -1081.971872 Node 8: lnL = -1081.971872 Node 9: lnL = -1081.971872 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 301 Sequential format.. Reading seq # 1: YDR519W_Sbay Reading seq # 2: YDR519W_Scer Reading seq # 3: YDR519W_Skud Reading seq # 4: YDR519W_Smik Reading seq # 5: YDR519W_Spar Sequences read.. Counting patterns.. # site patterns = 154 Counting frequencies.. 120 bytes for distance 24640 bytes for lkl0 19712 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.250935 0.014505 0.023357 0.161747 0.143779 0.243592 0.304877 0.091155 lnL0 = -1413.195776 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1413.195776 x= 0.25094 0.01450 0.02336 0.16175 0.14378 0.24359 0.30488 0.09116 1 h-lim-p 0.0024 0.0188 100.8484 1411.431123 9 0.0004 47 | 0/8 2 h-lim-p 0.0007 0.0058 22.5144 1411.200885 0 0.0011 59 | 0/8 3 h-lim-p 0.0052 0.0415 4.0973 1411.192878 5 0.0010 82 | 0/8 4 h-lim-p 0.0062 0.2963 0.6558 1411.192549 2 0.0015 99 | 0/8 5 h-lim-p 0.0043 0.3743 0.2338 1411.192511 3 0.0013 128 | 0/8 6 h-lim-p 0.0048 4.5914 0.0616 1411.192424 0 0.0096 149 | 0/8 7 h-lim-p 0.0117 3.8693 0.0507 1411.191337 0 0.0466 171 | 0/8 8 h-lim-p 0.0062 0.4662 0.3836 1411.187758 0 0.0092 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 1411.187561 3 1.0449 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1411.187559 1 1.2305 240 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1411.187559 0 1.0938 260 | 0/8 12 h-lim-p 1.9367 20.0000 0.0000 1411.187559 0 0.4237 281 | 0/8 13 h-lim-p 0.2351 20.0000 0.0000 1411.187559 0 0.0000 325 Out... lnL = -1411.187559 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1411.187559 Node 7: lnL = -1411.187559 Node 8: lnL = -1411.187559 Node 9: lnL = -1411.187559 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 572 Sequential format.. Reading seq # 1: YDR523C_Sbay Reading seq # 2: YDR523C_Scer Reading seq # 3: YDR523C_Skud Reading seq # 4: YDR523C_Smik Reading seq # 5: YDR523C_Spar Sequences read.. Counting patterns.. # site patterns = 151 Counting frequencies.. 120 bytes for distance 24160 bytes for lkl0 19328 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.478240 0.094298 0.209422 0.208991 0.155665 4.191714 0.233428 0.000060 lnL0 = -2041.693312 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2041.693312 x= 0.47824 0.09430 0.20942 0.20899 0.15567 4.19171 0.23343 0.00006 1 h-lim-p 0.0000 0.0000 445.6465 2041.567870 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0014 226.4333 2006.310877 2 0.0013 44 | 1/8 3 h-lim-p 0.0006 0.0046 76.5186 2004.548323 1 0.0007 58 | 1/8 4 h-lim-p 0.0015 0.0116 33.9742 2003.755569 3 0.0015 76 | 1/8 5 h-lim-p 0.0177 0.1412 1.7443 2000.515808 0 0.0530 89 | 1/8 6 h-lim-p 0.0025 0.0200 17.4499 1963.048788 0 0.0150 103 | 0/8 7 h-lim-p 0.0021 0.0172 21.6328 1962.919917 6 0.0006 128 | 0/8 8 h-lim-p 0.1480 3.1936 0.0853 1961.866971 0 0.2961 141 | 0/8 9 h-lim-p 1.0389 8.3114 0.0195 1961.806634 6 0.3477 175 | 0/8 10 h-lim-p 1.7292 20.0000 0.0039 1961.804846 5 0.2983 209 | 0/8 11 h-lim-p 1.1398 20.0000 0.0010 1961.803977 4 0.7731 240 | 0/8 12 h-lim-p 1.9030 20.0000 0.0004 1961.803864 3 0.7217 266 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1961.803863 0 1.0938 286 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1961.803863 0 1.0938 306 | 0/8 15 h-lim-p 1.6673 20.0000 0.0000 1961.803863 0 0.0261 331 | 0/8 16 h-lim-p 0.0104 20.0000 0.0000 1961.803863 0 0.0000 367 Out... lnL = -1961.803863 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1961.803863 Node 7: lnL = -1961.803863 Node 8: lnL = -1961.803863 Node 9: lnL = -1961.803863 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 452 Sequential format.. Reading seq # 1: YDR524C_Sbay Reading seq # 2: YDR524C_Scer Reading seq # 3: YDR524C_Skud Reading seq # 4: YDR524C_Smik Reading seq # 5: YDR524C_Spar Sequences read.. Counting patterns.. # site patterns = 129 Counting frequencies.. 120 bytes for distance 20640 bytes for lkl0 16512 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.157884 0.063078 0.066950 0.078863 0.062516 0.120954 0.000060 0.082877 lnL0 = -1519.736538 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1519.736538 x= 0.15788 0.06308 0.06695 0.07886 0.06252 0.12095 0.00006 0.08288 1 h-lim-p 0.0001 0.0007 578.1658 1509.279053 1 0.0001 24 | 0/8 2 h-lim-p 0.0001 0.0008 93.3426 1508.290475 0 0.0002 37 | 0/8 3 h-lim-p 0.0005 0.0042 27.1855 1508.180955 6 0.0003 65 | 0/8 4 h-lim-p 0.0005 0.0049 17.2165 1508.129431 2 0.0005 81 | 0/8 5 h-lim-p 0.0008 0.0101 10.1398 1508.105627 3 0.0007 99 | 0/8 6 h-lim-p 0.0021 0.0256 3.2808 1508.104295 5 0.0003 124 | 0/8 7 h-lim-p 0.0021 0.2103 0.4463 1508.104205 3 0.0006 145 | 0/8 8 h-lim-p 0.0577 15.5370 0.0049 1508.004261 0 1.8450 170 | 0/8 9 h-lim-p 2.1877 18.0256 0.0041 1507.943052 6 1.3468 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0007 1507.942672 4 0.9169 236 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1507.942671 0 1.0938 256 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1507.942671 0 1.0938 276 | 0/8 13 h-lim-p 1.5869 20.0000 0.0000 1507.942671 0 1.3885 296 | 0/8 14 h-lim-p 1.5977 20.0000 0.0000 1507.942671 0 0.0999 319 | 0/8 15 h-lim-p 0.0226 20.0000 0.0000 1507.942671 0 0.0085 340 | 0/8 16 h-lim-p 0.0039 20.0000 0.0001 1507.942671 0 0.0000 382 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 1507.942671 0 0.0000 406 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 1507.942671 0 0.0000 429 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 1507.942671 0 0.0000 463 | 0/8 20 h-lim-p 0.0000 20.0000 0.0004 | 0/8 21 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1507.942671 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1507.942671 Node 7: lnL = -1507.942671 Node 8: lnL = -1507.942671 Node 9: lnL = -1507.942671 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 394 Sequential format.. Reading seq # 1: YDR525W-A_Sbay Reading seq # 2: YDR525W-A_Scer Reading seq # 3: YDR525W-A_Skud Reading seq # 4: YDR525W-A_Smik Reading seq # 5: YDR525W-A_Spar Sequences read.. Counting patterns.. # site patterns = 129 Counting frequencies.. 120 bytes for distance 20640 bytes for lkl0 16512 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.165858 0.044954 0.078933 0.091833 0.056340 0.156711 0.111717 0.060200 lnL0 = -1561.118645 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1561.118645 x= 0.16586 0.04495 0.07893 0.09183 0.05634 0.15671 0.11172 0.06020 1 h-lim-p 0.0005 0.0042 99.7271 1559.894303 4 0.0003 31 | 0/8 2 h-lim-p 0.0011 0.0085 21.7377 1559.766960 7 0.0006 59 | 0/8 3 h-lim-p 0.0032 0.0444 3.7436 1559.764435 2 0.0004 77 | 0/8 4 h-lim-p 0.0018 0.0805 0.8004 1559.764364 3 0.0002 97 | 0/8 5 h-lim-p 0.0008 1.0305 0.2445 1559.764354 0 0.0004 117 | 0/8 6 h-lim-p 0.0021 5.4311 0.0439 1559.764353 0 0.0005 138 | 0/8 7 h-lim-p 0.0176 20.0000 0.0013 1559.764341 0 0.0703 160 | 0/8 8 h-lim-p 0.0020 9.0002 0.0472 1559.764188 0 0.0079 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1559.764186 0 1.0938 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1559.764186 0 1.0938 222 | 0/8 11 h-lim-p 1.2183 20.0000 0.0000 1559.764186 0 1.2183 242 | 0/8 12 h-lim-p 0.7720 20.0000 0.0000 1559.764186 0 3.0881 264 | 0/8 13 h-lim-p 0.0489 20.0000 0.0011 1559.764186 0 0.0031 287 | 0/8 14 h-lim-p 0.0008 20.0000 0.0042 1559.764186 0 0.0008 307 | 0/8 15 h-lim-p 0.0005 15.9994 0.0060 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0006 1559.764186 0 0.0000 379 | 0/8 17 h-lim-p 0.0000 20.0000 0.0006 1559.764186 0 0.0002 403 | 0/8 18 h-lim-p 0.0006 20.0000 0.0002 1559.764186 0 0.0000 431 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 1559.764186 0 0.0000 452 | 0/8 20 h-lim-p 0.0000 20.0000 0.0000 1559.764186 0 0.0000 488 | 0/8 21 h-lim-p 0.0000 20.0000 0.0003 | 0/8 22 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -1559.764186 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1559.764186 Node 7: lnL = -1559.764186 Node 8: lnL = -1559.764186 Node 9: lnL = -1559.764186 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 271 Sequential format.. Reading seq # 1: YDR527W_Sbay Reading seq # 2: YDR527W_Scer Reading seq # 3: YDR527W_Skud Reading seq # 4: YDR527W_Smik Reading seq # 5: YDR527W_Spar Sequences read.. Counting patterns.. # site patterns = 115 Counting frequencies.. 120 bytes for distance 18400 bytes for lkl0 14720 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.225398 0.000060 0.083686 0.131289 0.084225 0.246068 0.133192 0.105886 lnL0 = -1132.480116 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1132.480116 x= 0.22540 0.00006 0.08369 0.13129 0.08422 0.24607 0.13319 0.10589 1 h-lim-p 0.0006 0.0047 64.8889 1131.093727 7 0.0006 36 | 0/8 2 h-lim-p 0.0003 0.0025 53.0793 1130.633399 0 0.0005 48 | 0/8 3 h-lim-p 0.0012 0.0190 19.7709 1130.540877 2 0.0006 64 | 0/8 4 h-lim-p 0.0014 0.0122 8.3668 1130.512663 6 0.0010 91 | 0/8 5 h-lim-p 0.0038 0.0673 2.1559 1130.510950 3 0.0008 111 | 0/8 6 h-lim-p 0.0119 0.6824 0.1453 1130.510933 2 0.0012 129 | 0/8 7 h-lim-p 0.0026 4.2494 0.0662 1130.510911 1 0.0033 151 | 0/8 8 h-lim-p 0.0231 3.2799 0.0093 1130.507403 0 0.1849 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1130.507378 2 0.9644 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1130.507377 0 1.0938 218 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1130.507377 0 0.5469 239 | 0/8 12 h-lim-p 0.3751 20.0000 0.0000 1130.507377 0 0.0059 264 | 0/8 13 h-lim-p 0.0033 20.0000 0.0000 1130.507377 0 0.0002 287 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 1130.507377 0 0.0000 322 Out... lnL = -1130.507377 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1130.507377 Node 7: lnL = -1130.507377 Node 8: lnL = -1130.507377 Node 9: lnL = -1130.507377 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 870 Sequential format.. Reading seq # 1: YDR528W_Sbay Reading seq # 2: YDR528W_Scer Reading seq # 3: YDR528W_Skud Reading seq # 4: YDR528W_Smik Reading seq # 5: YDR528W_Spar Sequences read.. Counting patterns.. # site patterns = 263 Counting frequencies.. 120 bytes for distance 42080 bytes for lkl0 33664 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.219231 0.036585 0.055965 0.083845 0.072177 0.137900 0.200362 0.098030 lnL0 = -3651.175046 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3651.175046 x= 0.21923 0.03659 0.05596 0.08385 0.07218 0.13790 0.20036 0.09803 1 h-lim-p 0.0005 0.0040 205.3097 3648.649717 6 0.0001 34 | 0/8 2 h-lim-p 0.0004 0.0036 33.3471 3648.552994 4 0.0002 54 | 0/8 3 h-lim-p 0.0004 0.0138 13.6032 3648.538848 3 0.0002 72 | 0/8 4 h-lim-p 0.0006 0.0503 4.0108 3648.537246 5 0.0002 97 | 0/8 5 h-lim-p 0.0008 0.2732 1.0422 3648.537096 3 0.0003 117 | 0/8 6 h-lim-p 0.0008 0.4868 0.3869 3648.537081 2 0.0003 135 | 0/8 7 h-lim-p 0.0012 2.4835 0.0861 3648.537079 0 0.0005 155 | 0/8 8 h-lim-p 0.3529 20.0000 0.0001 3648.537010 0 1.4114 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3648.537007 0 1.0938 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3648.537007 0 1.0938 217 | 0/8 11 h-lim-p 0.9478 20.0000 0.0000 3648.537007 0 0.8294 237 | 0/8 12 h-lim-p 0.3036 20.0000 0.0000 3648.537007 0 0.0380 259 | 0/8 13 h-lim-p 0.0093 20.0000 0.0002 3648.537007 0 0.0000 300 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 3648.537007 0 0.0000 321 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 3648.537007 0 0.0000 341 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 3648.537007 0 0.0000 363 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 3648.537007 0 0.0000 390 | 0/8 18 h-lim-p 0.0000 20.0000 0.0003 | 0/8 19 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -3648.537007 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3648.537007 Node 7: lnL = -3648.537007 Node 8: lnL = -3648.537007 Node 9: lnL = -3648.537007 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 259 Sequential format.. Reading seq # 1: YDR529C_Sbay Reading seq # 2: YDR529C_Scer Reading seq # 3: YDR529C_Skud Reading seq # 4: YDR529C_Smik Reading seq # 5: YDR529C_Spar Sequences read.. Counting patterns.. # site patterns = 109 Counting frequencies.. 120 bytes for distance 17440 bytes for lkl0 13952 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.148356 0.054574 0.043140 0.093684 0.109105 0.150273 0.211381 0.029102 lnL0 = -1086.652682 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1086.652682 x= 0.14836 0.05457 0.04314 0.09368 0.10911 0.15027 0.21138 0.02910 1 h-lim-p 0.0048 1.8901 67.1769 1085.915375 6 0.0004 39 | 0/8 2 h-lim-p 0.0039 0.0355 6.0389 1085.903607 6 0.0007 65 | 0/8 3 h-lim-p 0.0027 0.0680 1.4747 1085.902783 5 0.0008 90 | 0/8 4 h-lim-p 0.0034 0.5881 0.3421 1085.902745 2 0.0007 107 | 0/8 5 h-lim-p 0.0041 4.6078 0.0569 1085.902743 0 0.0009 128 | 0/8 6 h-lim-p 0.0029 12.8012 0.0176 1085.902743 0 0.0013 148 | 0/8 7 h-lim-p 0.0077 20.0000 0.0029 1085.902743 0 0.0017 169 | 0/8 8 h-lim-p 0.0468 20.0000 0.0001 1085.902739 0 0.7489 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1085.902739 0 1.0938 213 | 0/8 10 h-lim-p 1.1630 20.0000 0.0000 1085.902739 0 0.5815 233 | 0/8 11 h-lim-p 0.3429 20.0000 0.0000 1085.902739 0 0.0107 257 | 0/8 12 h-lim-p 0.0044 20.0000 0.0000 1085.902739 0 0.0006 279 | 0/8 13 h-lim-p 0.0003 20.0000 0.0001 1085.902739 0 0.0000 301 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 1085.902739 0 0.0000 332 | 0/8 15 h-lim-p 0.0000 20.0000 0.0007 | 0/8 16 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -1085.902739 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1085.902739 Node 7: lnL = -1085.902739 Node 8: lnL = -1085.902739 Node 9: lnL = -1085.902739 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 487 Sequential format.. Reading seq # 1: YDR531W_Sbay Reading seq # 2: YDR531W_Scer Reading seq # 3: YDR531W_Skud Reading seq # 4: YDR531W_Smik Reading seq # 5: YDR531W_Spar Sequences read.. Counting patterns.. # site patterns = 182 Counting frequencies.. 120 bytes for distance 29120 bytes for lkl0 23296 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.182632 0.126668 0.048224 0.091756 0.067916 0.157266 0.193482 0.047958 lnL0 = -2100.081325 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2100.081325 x= 0.18263 0.12667 0.04822 0.09176 0.06792 0.15727 0.19348 0.04796 1 h-lim-p 0.0018 0.0143 56.5548 2099.674282 6 0.0003 38 | 0/8 2 h-lim-p 0.0008 0.0112 19.6255 2099.603907 5 0.0004 61 | 0/8 3 h-lim-p 0.0010 0.0406 7.9086 2099.597178 5 0.0003 85 | 0/8 4 h-lim-p 0.0011 0.0903 1.8024 2099.596585 4 0.0004 107 | 0/8 5 h-lim-p 0.0011 0.3621 0.6554 2099.596480 2 0.0006 124 | 0/8 6 h-lim-p 0.0023 2.4733 0.1628 2099.596475 1 0.0005 147 | 0/8 7 h-lim-p 0.0033 11.2811 0.0221 2099.596475 0 0.0007 168 | 0/8 8 h-lim-p 0.3707 20.0000 0.0000 2099.596471 0 1.1120 189 | 0/8 9 h-lim-p 2.4841 20.0000 0.0000 2099.596471 0 1.0868 209 | 0/8 10 h-lim-p 1.2348 20.0000 0.0000 2099.596471 0 4.9394 231 | 0/8 11 h-lim-p 0.5543 20.0000 0.0002 2099.596471 0 0.0003 261 | 0/8 12 h-lim-p 0.0001 20.0000 0.0004 2099.596471 0 0.0002 281 | 0/8 13 h-lim-p 0.0001 20.0000 0.0006 2099.596471 0 0.0000 303 | 0/8 14 h-lim-p 0.0002 20.0000 0.0001 2099.596471 0 0.0000 334 | 0/8 15 h-lim-p 0.0000 20.0000 0.0015 2099.596471 0 0.0000 361 | 0/8 16 h-lim-p 0.0000 20.0000 0.0007 2099.596471 0 0.0010 387 | 0/8 17 h-lim-p 0.0034 20.0000 0.0002 2099.596471 0 0.0007 408 | 0/8 18 h-lim-p 0.0019 20.0000 0.0001 2099.596471 0 0.0000 438 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 2099.596471 0 0.0000 464 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 2099.596471 0 0.0000 485 | 0/8 21 h-lim-p 0.0000 20.0000 0.0010 .. | 0/8 22 h-lim-p 0.0000 20.0000 0.0021 | 0/8 23 h-lim-p 0.0000 20.0000 0.0021 Out... lnL = -2099.596471 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2099.596471 Node 7: lnL = -2099.596471 Node 8: lnL = -2099.596471 Node 9: lnL = -2099.596471 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 881 Sequential format.. Reading seq # 1: YDR532C_Sbay Reading seq # 2: YDR532C_Scer Reading seq # 3: YDR532C_Skud Reading seq # 4: YDR532C_Smik Reading seq # 5: YDR532C_Spar Sequences read.. Counting patterns.. # site patterns = 440 Counting frequencies.. 120 bytes for distance 70400 bytes for lkl0 56320 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.521519 0.016411 0.193282 0.184325 0.113578 0.348385 0.547080 0.219640 lnL0 = -4679.822062 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4679.822062 x= 0.52152 0.01641 0.19328 0.18433 0.11358 0.34838 0.54708 0.21964 1 h-lim-p 0.0014 0.0109 104.1995 4677.096992 7 0.0005 37 | 0/8 2 h-lim-p 0.0006 0.0045 46.8778 4676.692618 7 0.0004 63 | 0/8 3 h-lim-p 0.0027 0.0697 7.3501 4676.662347 5 0.0012 84 | 0/8 4 h-lim-p 0.0019 0.1503 4.4553 4676.646963 4 0.0020 104 | 0/8 5 h-lim-p 0.0028 0.1849 3.2256 4676.641045 5 0.0018 128 | 0/8 6 h-lim-p 0.0051 0.5047 1.1323 4676.639790 2 0.0024 144 | 0/8 7 h-lim-p 0.0417 10.5088 0.0644 4676.639781 1 0.0026 161 | 0/8 8 h-lim-p 0.1289 20.0000 0.0013 4676.638860 0 1.0316 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 4676.638838 1 0.9961 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4676.638838 0 1.0938 226 | 0/8 11 h-lim-p 2.0028 20.0000 0.0000 4676.638838 0 1.7525 246 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4676.638838 0 1.0938 266 | 0/8 13 h-lim-p 0.4587 20.0000 0.0000 4676.638838 0 0.4587 286 | 0/8 14 h-lim-p 0.0007 20.0000 0.0031 4676.638838 0 0.0000 309 | 0/8 15 h-lim-p 0.0022 20.0000 0.0001 4676.638838 0 0.0000 341 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 4676.638838 0 0.0000 362 Out... lnL = -4676.638838 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4676.638838 Node 7: lnL = -4676.638838 Node 8: lnL = -4676.638838 Node 9: lnL = -4676.638838 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 867 Sequential format.. Reading seq # 1: YDR533C_Sbay Reading seq # 2: YDR533C_Scer Reading seq # 3: YDR533C_Skud Reading seq # 4: YDR533C_Smik Reading seq # 5: YDR533C_Spar Sequences read.. Counting patterns.. # site patterns = 472 Counting frequencies.. 120 bytes for distance 75520 bytes for lkl0 60416 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.519532 0.061614 0.084282 0.240998 0.284610 0.633074 0.432875 0.182326 lnL0 = -5038.656338 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 5038.656338 x= 0.51953 0.06161 0.08428 0.24100 0.28461 0.63307 0.43287 0.18233 1 h-lim-p 0.0079 0.0631 78.6908 5037.141921 6 0.0005 37 | 0/8 2 h-lim-p 0.0019 0.0152 18.9969 5036.948626 7 0.0011 66 | 0/8 3 h-lim-p 0.0020 0.0180 10.4050 5036.906471 5 0.0010 89 | 0/8 4 h-lim-p 0.0043 0.1343 2.3566 5036.901997 3 0.0017 107 | 0/8 5 h-lim-p 0.0065 1.0545 0.6289 5036.901557 4 0.0024 128 | 0/8 6 h-lim-p 0.0109 1.3303 0.1370 5036.901537 1 0.0022 151 | 0/8 7 h-lim-p 0.0140 5.3409 0.0212 5036.901525 0 0.0140 171 | 0/8 8 h-lim-p 0.0811 20.0000 0.0037 5036.900793 0 0.3244 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 5036.900780 1 0.9961 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 5036.900780 0 1.0938 235 | 0/8 11 h-lim-p 1.2732 20.0000 0.0000 5036.900780 0 1.9098 255 | 0/8 12 h-lim-p 0.8498 20.0000 0.0000 5036.900780 0 0.0002 286 | 0/8 13 h-lim-p 0.0004 20.0000 0.0000 5036.900780 0 0.0000 321 Out... lnL = -5036.900780 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -5036.900780 Node 7: lnL = -5036.900780 Node 8: lnL = -5036.900780 Node 9: lnL = -5036.900780 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 860 Sequential format.. Reading seq # 1: YDR538W_Sbay Reading seq # 2: YDR538W_Scer Reading seq # 3: YDR538W_Skud Reading seq # 4: YDR538W_Smik Reading seq # 5: YDR538W_Spar Sequences read.. Counting patterns.. # site patterns = 396 Counting frequencies.. 120 bytes for distance 63360 bytes for lkl0 50688 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.465984 0.035910 0.166112 0.185811 0.117314 0.304327 0.303900 0.211984 lnL0 = -4527.095092 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4527.095092 x= 0.46598 0.03591 0.16611 0.18581 0.11731 0.30433 0.30390 0.21198 1 h-lim-p 0.0013 0.0107 86.6050 4525.613947 9 0.0004 45 | 0/8 2 h-lim-p 0.0012 0.0121 30.6740 4525.142917 2 0.0011 61 | 0/8 3 h-lim-p 0.0011 0.0117 31.0017 4525.047172 7 0.0003 91 | 0/8 4 h-lim-p 0.0012 0.0289 9.2193 4525.027744 2 0.0005 107 | 0/8 5 h-lim-p 0.0020 0.1458 2.4747 4525.024085 4 0.0013 129 | 0/8 6 h-lim-p 0.0131 1.9062 0.2467 4525.024045 2 0.0013 147 | 0/8 7 h-lim-p 0.0536 20.0000 0.0058 4525.023375 0 0.2145 169 | 0/8 8 h-lim-p 0.0027 3.1890 0.4564 4525.019798 0 0.0055 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0008 4525.019286 3 1.0004 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4525.019286 0 1.0938 236 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4525.019286 0 1.0938 256 | 0/8 12 h-lim-p 1.0912 20.0000 0.0000 4525.019286 0 4.3647 278 | 0/8 13 h-lim-p 0.8560 20.0000 0.0000 4525.019286 0 5.1358 300 | 0/8 14 h-lim-p 0.0055 13.2162 0.0238 4525.019286 0 0.0000 338 | 0/8 15 h-lim-p 0.0004 20.0000 0.0000 4525.019286 0 0.0000 371 Out... lnL = -4525.019286 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4525.019286 Node 7: lnL = -4525.019286 Node 8: lnL = -4525.019286 Node 9: lnL = -4525.019286 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 491 Sequential format.. Reading seq # 1: YDR539W_Sbay Reading seq # 2: YDR539W_Scer Reading seq # 3: YDR539W_Skud Reading seq # 4: YDR539W_Smik Reading seq # 5: YDR539W_Spar Sequences read.. Counting patterns.. # site patterns = 195 Counting frequencies.. 120 bytes for distance 31200 bytes for lkl0 24960 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.323442 0.083751 0.089796 0.090860 0.079779 0.172031 0.272403 0.143296 lnL0 = -2281.556602 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2281.556602 x= 0.32344 0.08375 0.08980 0.09086 0.07978 0.17203 0.27240 0.14330 1 h-lim-p 0.0034 0.0271 47.7559 2280.966743 7 0.0005 39 | 0/8 2 h-lim-p 0.0009 0.0074 22.4672 2280.887834 6 0.0004 64 | 0/8 3 h-lim-p 0.0008 0.0169 10.5249 2280.857323 2 0.0007 80 | 0/8 4 h-lim-p 0.0011 0.0543 6.7573 2280.847455 6 0.0006 106 | 0/8 5 h-lim-p 0.0024 0.1589 1.7741 2280.846331 4 0.0008 128 | 0/8 6 h-lim-p 0.0019 0.2808 0.7526 2280.846232 2 0.0004 145 | 0/8 7 h-lim-p 0.0017 3.0887 0.1821 2280.846215 2 0.0011 171 | 0/8 8 h-lim-p 0.4077 20.0000 0.0005 2280.845931 0 1.2232 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2280.845929 0 1.0938 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2280.845929 0 1.0938 232 | 0/8 11 h-lim-p 1.4884 20.0000 0.0000 2280.845929 0 2.2327 252 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2280.845929 0 0.1562 275 | 0/8 13 h-lim-p 0.0156 20.0000 0.0000 2280.845929 0 0.0156 295 | 0/8 14 h-lim-p 0.0074 20.0000 0.0000 2280.845929 0 0.0005 318 | 0/8 15 h-lim-p 0.0001 20.0000 0.0001 2280.845929 0 0.0000 339 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 2280.845929 0 0.0000 374 | 0/8 17 h-lim-p 0.0000 20.0000 0.0008 | 0/8 18 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -2280.845929 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2280.845929 Node 7: lnL = -2280.845929 Node 8: lnL = -2280.845929 Node 9: lnL = -2280.845929 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 882 Sequential format.. Reading seq # 1: YEL001C_Sbay Reading seq # 2: YEL001C_Scer Reading seq # 3: YEL001C_Skud Reading seq # 4: YEL001C_Smik Reading seq # 5: YEL001C_Spar Sequences read.. Counting patterns.. # site patterns = 441 Counting frequencies.. 120 bytes for distance 70560 bytes for lkl0 56448 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.441598 0.000060 0.168471 0.208893 0.167827 0.327460 0.602582 0.156252 lnL0 = -4778.772454 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4778.772454 x= 0.44160 0.00006 0.16847 0.20889 0.16783 0.32746 0.60258 0.15625 1 h-lim-p 0.0325 2.1614 54.1991 4777.910996 8 0.0006 44 | 0/8 2 h-lim-p 0.0018 0.0173 16.6155 4777.830590 7 0.0006 75 | 0/8 3 h-lim-p 0.0010 0.0411 10.5786 4777.786436 5 0.0011 100 | 0/8 4 h-lim-p 0.0039 0.1842 2.8719 4777.777555 5 0.0024 126 | 0/8 5 h-lim-p 0.0040 0.2786 1.7353 4777.776160 4 0.0012 149 | 0/8 6 h-lim-p 0.0041 1.6446 0.5232 4777.775987 3 0.0014 169 | 0/8 7 h-lim-p 0.0141 0.6899 0.0536 4777.775976 1 0.0028 192 | 0/8 8 h-lim-p 0.0233 20.0000 0.0065 4777.772601 0 0.3725 216 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4777.772591 1 0.9961 238 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4777.772591 0 1.0938 258 | 0/8 11 h-lim-p 1.1800 20.0000 0.0000 4777.772591 0 1.7700 278 | 0/8 12 h-lim-p 0.2785 20.0000 0.0000 4777.772591 0 0.0696 299 | 0/8 13 h-lim-p 0.0134 20.0000 0.0002 4777.772591 0 0.0002 325 | 0/8 14 h-lim-p 0.0009 20.0000 0.0000 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -4777.772591 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4777.772591 Node 7: lnL = -4777.772591 Node 8: lnL = -4777.772591 Node 9: lnL = -4777.772591 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 229 Sequential format.. Reading seq # 1: YEL004W_Sbay Reading seq # 2: YEL004W_Scer Reading seq # 3: YEL004W_Skud Reading seq # 4: YEL004W_Smik Reading seq # 5: YEL004W_Spar Sequences read.. Counting patterns.. # site patterns = 123 Counting frequencies.. 120 bytes for distance 19680 bytes for lkl0 15744 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.230050 0.148811 0.079641 0.166668 0.094338 0.243710 0.260819 0.044456 lnL0 = -1060.440886 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1060.440886 x= 0.23005 0.14881 0.07964 0.16667 0.09434 0.24371 0.26082 0.04446 1 h-lim-p 0.0026 0.0210 27.9236 1060.032817 5 0.0011 33 | 0/8 2 h-lim-p 0.0028 0.0314 11.0259 1059.953968 7 0.0015 59 | 0/8 3 h-lim-p 0.0033 0.0548 4.8731 1059.940752 4 0.0013 80 | 0/8 4 h-lim-p 0.0071 0.2295 0.9208 1059.940146 3 0.0015 100 | 0/8 5 h-lim-p 0.0058 1.1987 0.2377 1059.940082 1 0.0025 122 | 0/8 6 h-lim-p 0.0139 5.3479 0.0434 1059.940081 1 0.0017 146 | 0/8 7 h-lim-p 0.0050 7.6960 0.0147 1059.940080 0 0.0022 166 | 0/8 8 h-lim-p 0.1732 20.0000 0.0002 1059.940065 0 1.0393 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1059.940065 0 1.0938 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1059.940065 0 1.0938 228 | 0/8 11 h-lim-p 1.0999 20.0000 0.0000 1059.940065 0 4.3995 250 | 0/8 12 h-lim-p 1.2974 20.0000 0.0000 1059.940065 0 1.2974 270 | 0/8 13 h-lim-p 0.0233 20.0000 0.0011 1059.940065 0 0.0025 292 | 0/8 14 h-lim-p 0.0009 20.0000 0.0032 1059.940065 0 0.0009 312 | 0/8 15 h-lim-p 0.0001 2.8492 0.0225 1059.940065 0 0.0000 335 | 0/8 16 h-lim-p 0.0001 20.0000 0.0030 1059.940065 0 0.0000 357 | 0/8 17 h-lim-p 0.0001 20.0000 0.0002 1059.940065 0 0.0000 378 | 0/8 18 h-lim-p 0.0001 20.0000 0.0000 1059.940065 0 0.0000 408 | 0/8 19 h-lim-p 0.0000 20.0000 0.0003 | 0/8 20 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -1059.940065 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1059.940065 Node 7: lnL = -1059.940065 Node 8: lnL = -1059.940065 Node 9: lnL = -1059.940065 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 228 Sequential format.. Reading seq # 1: YEL005C_Sbay Reading seq # 2: YEL005C_Scer Reading seq # 3: YEL005C_Skud Reading seq # 4: YEL005C_Smik Reading seq # 5: YEL005C_Spar Sequences read.. Counting patterns.. # site patterns = 108 Counting frequencies.. 120 bytes for distance 17280 bytes for lkl0 13824 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.528443 0.177640 0.013736 0.345153 4.145632 0.445949 0.342501 0.000060 lnL0 = -969.907596 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 969.907596 x= 0.52844 0.17764 0.01374 0.34515 4.14563 0.44595 0.34250 0.00006 1 h-lim-p 0.0000 0.0000 80.8922 969.891301 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0148 52.8892 962.767245 0 0.0051 43 | 1/8 3 h-lim-p 0.0036 0.0285 19.7727 961.767652 0 0.0071 56 | 1/8 4 h-lim-p 0.0173 0.1385 2.7641 961.657528 7 0.0112 86 | 1/8 5 h-lim-p 0.0455 0.8442 0.6813 957.151910 0 0.3637 101 | 0/8 6 h-lim-p 0.0030 0.0238 8.6945 957.032239 3 0.0030 126 | 0/8 7 h-lim-p 0.1455 1.6066 0.1806 956.766958 0 0.2183 138 | 0/8 8 h-lim-p 0.0016 0.0130 7.2690 956.306027 0 0.0065 160 | 0/8 9 h-lim-p 0.9266 20.0000 0.0511 956.206930 6 0.4106 183 | 0/8 10 h-lim-p 0.6413 5.1307 0.0091 956.197587 0 0.9620 203 | 0/8 11 h-lim-p 2.5000 20.0000 0.0029 956.197076 5 0.6815 234 | 0/8 12 h-lim-p 2.5000 20.0000 0.0003 956.197057 1 1.0938 256 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 956.197057 0 1.0938 276 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 956.197057 0 1.0938 296 | 0/8 15 h-lim-p 1.0799 20.0000 0.0000 956.197057 0 2.1597 317 | 0/8 16 h-lim-p 0.6504 20.0000 0.0000 956.197057 0 0.0813 339 | 0/8 17 h-lim-p 0.0048 20.0000 0.0002 956.197057 0 0.0012 360 | 0/8 18 h-lim-p 0.0002 20.0000 0.0012 956.197057 0 0.0001 380 | 0/8 19 h-lim-p 0.0002 20.0000 0.0006 956.197057 0 0.0000 408 | 0/8 20 h-lim-p 0.0002 20.0000 0.0000 956.197057 0 0.0000 435 Out... lnL = -956.197057 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -956.197057 Node 7: lnL = -956.197057 Node 8: lnL = -956.197057 Node 9: lnL = -956.197057 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 485 Sequential format.. Reading seq # 1: YEL006W_Sbay Reading seq # 2: YEL006W_Scer Reading seq # 3: YEL006W_Skud Reading seq # 4: YEL006W_Smik Reading seq # 5: YEL006W_Spar Sequences read.. Counting patterns.. # site patterns = 148 Counting frequencies.. 120 bytes for distance 23680 bytes for lkl0 18944 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.159844 0.074946 0.066569 0.076511 0.060578 0.152246 0.160741 0.038550 lnL0 = -1923.153642 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1923.153642 x= 0.15984 0.07495 0.06657 0.07651 0.06058 0.15225 0.16074 0.03855 1 h-lim-p 0.0009 0.0076 61.0016 1922.632540 7 0.0003 40 | 0/8 2 h-lim-p 0.0012 0.0100 15.1437 1922.593420 7 0.0004 70 | 0/8 3 h-lim-p 0.0006 0.0186 8.4764 1922.586587 4 0.0002 90 | 0/8 4 h-lim-p 0.0012 0.0763 1.7714 1922.585830 2 0.0005 106 | 0/8 5 h-lim-p 0.0025 0.5283 0.3622 1922.585808 3 0.0003 126 | 0/8 6 h-lim-p 0.0013 2.1705 0.0946 1922.585807 1 0.0003 149 | 0/8 7 h-lim-p 0.0012 3.4337 0.0240 1922.585806 0 0.0005 169 | 0/8 8 h-lim-p 0.1661 20.0000 0.0001 1922.585800 0 1.3291 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1922.585799 0 1.0938 212 | 0/8 10 h-lim-p 0.9882 20.0000 0.0000 1922.585799 0 0.8647 232 | 0/8 11 h-lim-p 0.6677 20.0000 0.0000 1922.585799 0 0.0000 265 | 0/8 12 h-lim-p 0.0000 20.0000 0.0000 1922.585799 0 0.0000 288 | 0/8 13 h-lim-p 0.0000 20.0000 0.0006 | 0/8 14 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -1922.585799 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1922.585799 Node 7: lnL = -1922.585799 Node 8: lnL = -1922.585799 Node 9: lnL = -1922.585799 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 854 Sequential format.. Reading seq # 1: YEL009C_Sbay Reading seq # 2: YEL009C_Scer Reading seq # 3: YEL009C_Skud Reading seq # 4: YEL009C_Smik Reading seq # 5: YEL009C_Spar Sequences read.. Counting patterns.. # site patterns = 176 Counting frequencies.. 120 bytes for distance 28160 bytes for lkl0 22528 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.072154 0.015909 0.021737 0.056368 0.039047 0.070859 0.091221 0.015551 lnL0 = -2575.811898 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2575.811898 x= 0.07215 0.01591 0.02174 0.05637 0.03905 0.07086 0.09122 0.01555 1 h-lim-p 0.0001 0.0010 613.2755 2570.168068 9 0.0000 45 | 0/8 2 h-lim-p 0.0000 0.0004 82.0984 2569.827532 0 0.0001 58 | 0/8 3 h-lim-p 0.0002 0.0022 33.6348 2569.773609 5 0.0001 80 | 0/8 4 h-lim-p 0.0004 0.0169 9.3261 2569.770641 4 0.0001 101 | 0/8 5 h-lim-p 0.0005 0.0529 1.5236 2569.770512 2 0.0001 118 | 0/8 6 h-lim-p 0.0006 0.3947 0.2950 2569.770506 1 0.0001 133 | 0/8 7 h-lim-p 0.0006 1.1737 0.0603 2569.770501 0 0.0005 153 | 0/8 8 h-lim-p 0.0050 4.3316 0.0063 2569.764445 0 0.1612 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 2569.764248 4 1.4126 209 | 0/8 10 h-lim-p 1.4358 20.0000 0.0004 2569.764228 0 1.2563 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0001 2569.764228 0 1.0938 249 | 0/8 12 h-lim-p 1.0404 20.0000 0.0001 2569.764228 0 0.0009 278 | 0/8 13 h-lim-p 0.0001 10.2140 0.0015 2569.764228 0 0.0000 313 | 0/8 14 h-lim-p 0.0000 20.0000 0.0064 | 0/8 15 h-lim-p 0.0000 20.0000 0.0064 Out... lnL = -2569.764228 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2569.764228 Node 7: lnL = -2569.764228 Node 8: lnL = -2569.764228 Node 9: lnL = -2569.764228 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 1007 Sequential format.. Reading seq # 1: YEL012W_Sbay Reading seq # 2: YEL012W_Scer Reading seq # 3: YEL012W_Skud Reading seq # 4: YEL012W_Smik Reading seq # 5: YEL012W_Spar Sequences read.. Counting patterns.. # site patterns = 486 Counting frequencies.. 120 bytes for distance 77760 bytes for lkl0 62208 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.346595 0.000060 0.209443 0.303868 0.206983 0.305453 0.390148 0.080769 lnL0 = -5163.614985 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 5163.614985 x= 0.34660 0.00006 0.20944 0.30387 0.20698 0.30545 0.39015 0.08077 1 h-lim-p 0.0012 0.0098 67.8637 5161.333982 6 0.0009 34 | 0/8 2 h-lim-p 0.0004 0.0036 72.7148 5160.533047 6 0.0005 61 | 0/8 3 h-lim-p 0.0025 0.0411 14.6236 5160.450769 7 0.0009 90 | 0/8 4 h-lim-p 0.0025 0.0589 4.8837 5160.444650 3 0.0006 109 | 0/8 5 h-lim-p 0.0046 0.1826 0.6081 5160.444465 1 0.0009 124 | 0/8 6 h-lim-p 0.0067 4.9828 0.0835 5160.444426 0 0.0029 144 | 0/8 7 h-lim-p 0.0076 2.7006 0.0325 5160.442869 0 0.0605 167 | 0/8 8 h-lim-p 0.0020 0.1629 0.9846 5160.435512 0 0.0040 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 5160.435358 2 0.9961 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 5160.435358 0 1.0938 232 | 0/8 11 h-lim-p 1.5603 20.0000 0.0000 5160.435358 0 1.3652 252 | 0/8 12 h-lim-p 1.3921 20.0000 0.0000 5160.435358 0 1.2181 272 | 0/8 13 h-lim-p 0.3670 20.0000 0.0000 5160.435358 0 0.0115 296 | 0/8 14 h-lim-p 0.0027 20.0000 0.0002 5160.435358 0 0.0014 316 | 0/8 15 h-lim-p 0.0007 20.0000 0.0004 5160.435358 0 0.0000 350 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 5160.435358 0 0.0000 376 Out... lnL = -5160.435358 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -5160.435358 Node 7: lnL = -5160.435358 Node 8: lnL = -5160.435358 Node 9: lnL = -5160.435358 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 809 Sequential format.. Reading seq # 1: YEL017W_Sbay Reading seq # 2: YEL017W_Scer Reading seq # 3: YEL017W_Skud Reading seq # 4: YEL017W_Smik Reading seq # 5: YEL017W_Spar Sequences read.. Counting patterns.. # site patterns = 222 Counting frequencies.. 120 bytes for distance 35520 bytes for lkl0 28416 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.227949 0.008388 0.055857 0.064909 0.058430 0.149336 0.205936 0.100623 lnL0 = -2914.846886 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2914.846886 x= 0.22795 0.00839 0.05586 0.06491 0.05843 0.14934 0.20594 0.10062 1 h-lim-p 0.0009 0.0069 166.6741 2913.046450 9 0.0001 46 | 0/8 2 h-lim-p 0.0005 0.0055 44.0386 2912.344777 0 0.0008 58 | 0/8 3 h-lim-p 0.0003 0.0021 93.2457 2912.098171 7 0.0002 88 | 0/8 4 h-lim-p 0.0004 0.0052 38.9185 2912.008241 7 0.0002 117 | 0/8 5 h-lim-p 0.0009 0.0140 9.3186 2911.996777 6 0.0003 145 | 0/8 6 h-lim-p 0.0020 0.0784 1.4341 2911.996323 2 0.0004 162 | 0/8 7 h-lim-p 0.0012 0.1766 0.5037 2911.996300 2 0.0002 180 | 0/8 8 h-lim-p 0.0122 20.0000 0.0067 2911.976269 0 0.7795 206 | 0/8 9 h-lim-p 2.5000 20.0000 0.0009 2911.975750 0 1.2500 226 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2911.975737 0 1.0938 246 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2911.975737 0 1.0938 266 | 0/8 12 h-lim-p 1.5557 20.0000 0.0000 2911.975737 0 1.5557 286 | 0/8 13 h-lim-p 1.6662 20.0000 0.0000 2911.975737 0 0.0114 312 | 0/8 14 h-lim-p 0.0014 20.0000 0.0001 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0012 | 0/8 16 h-lim-p 0.0000 20.0000 0.0012 Out... lnL = -2911.975737 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2911.975737 Node 7: lnL = -2911.975737 Node 8: lnL = -2911.975737 Node 9: lnL = -2911.975737 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 170 Sequential format.. Reading seq # 1: YEL019C_Sbay Reading seq # 2: YEL019C_Scer Reading seq # 3: YEL019C_Skud Reading seq # 4: YEL019C_Smik Reading seq # 5: YEL019C_Spar Sequences read.. Counting patterns.. # site patterns = 71 Counting frequencies.. 120 bytes for distance 11360 bytes for lkl0 9088 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.528443 0.222595 0.089697 0.159473 0.141013 0.306749 4.275473 0.000060 lnL0 = -645.649650 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 645.649650 x= 0.52844 0.22259 0.08970 0.15947 0.14101 0.30675 4.27547 0.00006 1 h-lim-p 0.0000 0.0000 78.9648 645.613914 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0072 41.7759 642.405172 9 0.0043 66 | 1/8 3 h-lim-p 0.0019 0.0151 21.8599 641.542229 0 0.0038 79 | 1/8 4 h-lim-p 0.0057 0.0457 4.3137 641.462218 6 0.0056 103 | 1/8 5 h-lim-p 0.0098 0.0979 2.4673 641.255856 0 0.0196 116 | 1/8 6 h-lim-p 0.0363 0.2905 1.1710 637.811639 0 0.1089 129 | 0/8 7 h-lim-p 0.0437 0.3493 2.6962 637.771482 3 0.0099 148 | 0/8 8 h-lim-p 0.2221 1.7769 0.0791 637.595638 0 0.3332 160 | 0/8 9 h-lim-p 2.2395 20.0000 0.0118 637.576370 7 0.6831 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0015 637.575969 5 0.7576 234 | 0/8 11 h-lim-p 1.3091 20.0000 0.0009 637.575879 2 0.5727 258 | 0/8 12 h-lim-p 2.5000 20.0000 0.0001 637.575879 1 0.6152 281 | 0/8 13 h-lim-p 2.0660 20.0000 0.0000 637.575879 0 1.0330 301 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 637.575879 0 1.0938 321 | 0/8 15 h-lim-p 1.4886 20.0000 0.0000 637.575879 0 2.9772 342 | 0/8 16 h-lim-p 1.2511 20.0000 0.0000 637.575879 0 0.6256 362 | 0/8 17 h-lim-p 0.0113 20.0000 0.0003 637.575879 0 0.0001 388 | 0/8 18 h-lim-p 0.0003 20.0000 0.0001 637.575879 0 0.0003 408 | 0/8 19 h-lim-p 0.0002 20.0000 0.0002 637.575879 0 0.0002 428 | 0/8 20 h-lim-p 0.0004 20.0000 0.0001 637.575879 0 0.0000 459 | 0/8 21 h-lim-p 0.0000 20.0000 0.0001 637.575879 0 0.0000 487 | 0/8 22 h-lim-p 0.0000 20.0000 0.0001 637.575879 0 0.0000 513 | 0/8 23 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 24 h-lim-p 0.0000 20.0000 0.0001 | 0/8 25 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -637.575879 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -637.575879 Node 7: lnL = -637.575879 Node 8: lnL = -637.575879 Node 9: lnL = -637.575879 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 253 Sequential format.. Reading seq # 1: YEL020W-A_Sbay Reading seq # 2: YEL020W-A_Scer Reading seq # 3: YEL020W-A_Skud Reading seq # 4: YEL020W-A_Smik Reading seq # 5: YEL020W-A_Spar Sequences read.. Counting patterns.. # site patterns = 102 Counting frequencies.. 120 bytes for distance 16320 bytes for lkl0 13056 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.158151 0.021528 0.074135 0.112837 0.049442 0.177172 0.154176 0.040391 lnL0 = -1029.776700 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1029.776700 x= 0.15815 0.02153 0.07414 0.11284 0.04944 0.17717 0.15418 0.04039 1 h-lim-p 0.0006 0.0052 78.4703 1028.952311 3 0.0003 29 | 0/8 2 h-lim-p 0.0011 0.0085 13.0618 1028.898095 8 0.0006 65 | 0/8 3 h-lim-p 0.0011 0.0365 7.3937 1028.889284 6 0.0004 92 | 0/8 4 h-lim-p 0.0015 0.1112 2.0435 1028.887828 4 0.0008 113 | 0/8 5 h-lim-p 0.0128 0.9728 0.1247 1028.887821 2 0.0008 132 | 0/8 6 h-lim-p 0.0035 9.4190 0.0298 1028.887821 0 0.0009 153 | 0/8 7 h-lim-p 0.0108 20.0000 0.0024 1028.887821 0 0.0047 173 | 0/8 8 h-lim-p 0.0213 20.0000 0.0005 1028.887802 0 0.2557 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1028.887802 0 1.0938 216 | 0/8 10 h-lim-p 1.8952 20.0000 0.0000 1028.887802 0 0.8291 236 | 0/8 11 h-lim-p 0.7373 20.0000 0.0000 1028.887802 0 0.0007 265 | 0/8 12 h-lim-p 0.0002 20.0000 0.0001 1028.887802 0 0.0000 287 | 0/8 13 h-lim-p 0.0002 20.0000 0.0000 1028.887802 0 0.0001 307 Out... lnL = -1028.887802 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1028.887802 Node 7: lnL = -1028.887802 Node 8: lnL = -1028.887802 Node 9: lnL = -1028.887802 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 416 Sequential format.. Reading seq # 1: YEL021W_Sbay Reading seq # 2: YEL021W_Scer Reading seq # 3: YEL021W_Skud Reading seq # 4: YEL021W_Smik Reading seq # 5: YEL021W_Spar Sequences read.. Counting patterns.. # site patterns = 187 Counting frequencies.. 120 bytes for distance 29920 bytes for lkl0 23936 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.418060 0.055260 0.058560 0.171106 0.119754 0.207697 0.217281 0.205286 lnL0 = -1995.367517 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1995.367517 x= 0.41806 0.05526 0.05856 0.17111 0.11975 0.20770 0.21728 0.20529 1 h-lim-p 0.0050 0.0517 89.2595 1994.027403 7 0.0004 41 | 0/8 2 h-lim-p 0.0019 0.0155 15.6977 1993.915343 2 0.0009 57 | 0/8 3 h-lim-p 0.0032 0.0915 4.4805 1993.907323 5 0.0009 80 | 0/8 4 h-lim-p 0.0018 0.1511 2.1370 1993.904751 4 0.0014 100 | 0/8 5 h-lim-p 0.0034 0.2745 0.8591 1993.904525 2 0.0007 117 | 0/8 6 h-lim-p 0.0059 3.1043 0.1079 1993.904514 2 0.0020 143 | 0/8 7 h-lim-p 0.0036 6.6657 0.0588 1993.904512 1 0.0014 165 | 0/8 8 h-lim-p 0.1399 20.0000 0.0006 1993.904209 0 1.1191 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1993.904206 1 0.9961 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1993.904206 0 1.0938 230 | 0/8 11 h-lim-p 1.2429 20.0000 0.0000 1993.904206 0 0.0194 255 | 0/8 12 h-lim-p 0.0055 20.0000 0.0000 1993.904206 0 0.0003 278 Out... lnL = -1993.904206 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1993.904206 Node 7: lnL = -1993.904206 Node 8: lnL = -1993.904206 Node 9: lnL = -1993.904206 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 832 Sequential format.. Reading seq # 1: YEL022W_Sbay Reading seq # 2: YEL022W_Scer Reading seq # 3: YEL022W_Skud Reading seq # 4: YEL022W_Smik Reading seq # 5: YEL022W_Spar Sequences read.. Counting patterns.. # site patterns = 341 Counting frequencies.. 120 bytes for distance 54560 bytes for lkl0 43648 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.376920 0.036573 0.056601 0.174777 0.118951 0.282345 0.302950 0.157978 lnL0 = -4146.592798 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4146.592798 x= 0.37692 0.03657 0.05660 0.17478 0.11895 0.28234 0.30295 0.15798 1 h-lim-p 0.0043 0.0815 138.5677 4144.751812 4 0.0002 33 | 0/8 2 h-lim-p 0.0010 0.0081 16.4125 4144.710999 7 0.0003 64 | 0/8 3 h-lim-p 0.0007 0.0192 6.9085 4144.697010 2 0.0007 80 | 0/8 4 h-lim-p 0.0013 0.0253 3.6043 4144.693555 4 0.0007 101 | 0/8 5 h-lim-p 0.0025 0.1813 1.0021 4144.693086 2 0.0011 117 | 0/8 6 h-lim-p 0.0054 0.2774 0.1981 4144.693077 1 0.0005 133 | 0/8 7 h-lim-p 0.0065 17.9994 0.0165 4144.693077 0 0.0008 155 | 0/8 8 h-lim-p 0.1889 20.0000 0.0001 4144.693073 0 1.1335 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4144.693073 0 1.0938 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4144.693073 0 2.1875 217 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4144.693073 0 1.0938 237 | 0/8 12 h-lim-p 0.1490 20.0000 0.0000 4144.693073 0 7.1526 262 | 0/8 13 h-lim-p 0.9302 20.0000 0.0001 4144.693073 0 0.9302 282 | 0/8 14 h-lim-p 0.0001 0.3011 0.7809 4144.693073 0 0.0000 305 | 0/8 15 h-lim-p 0.0020 20.0000 0.0018 4144.693073 0 0.0010 325 | 0/8 16 h-lim-p 0.0030 20.0000 0.0006 4144.693073 0 0.0004 347 | 0/8 17 h-lim-p 0.0019 20.0000 0.0001 4144.693073 0 0.0000 378 | 0/8 18 h-lim-p 0.0004 20.0000 0.0000 4144.693073 0 0.0000 409 Out... lnL = -4144.693073 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4144.693073 Node 7: lnL = -4144.693073 Node 8: lnL = -4144.693073 Node 9: lnL = -4144.693073 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 839 Sequential format.. Reading seq # 1: YEL023C_Sbay Reading seq # 2: YEL023C_Scer Reading seq # 3: YEL023C_Skud Reading seq # 4: YEL023C_Smik Reading seq # 5: YEL023C_Spar Sequences read.. Counting patterns.. # site patterns = 353 Counting frequencies.. 120 bytes for distance 56480 bytes for lkl0 45184 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.492824 0.043207 0.088311 0.169022 0.121869 0.248054 0.274695 0.246223 lnL0 = -4208.073604 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4208.073604 x= 0.49282 0.04321 0.08831 0.16902 0.12187 0.24805 0.27469 0.24622 1 h-lim-p 0.0008 0.0068 89.6531 4206.569075 2 0.0004 26 | 0/8 2 h-lim-p 0.0005 0.0042 29.8583 4206.322134 1 0.0007 40 | 0/8 3 h-lim-p 0.0012 0.0257 16.7762 4206.243805 6 0.0007 68 | 0/8 4 h-lim-p 0.0015 0.0253 8.3389 4206.231631 6 0.0005 96 | 0/8 5 h-lim-p 0.0006 0.0841 5.9737 4206.225987 4 0.0005 116 | 0/8 6 h-lim-p 0.0015 0.1568 2.0209 4206.224934 2 0.0006 132 | 0/8 7 h-lim-p 0.0016 0.1423 0.7934 4206.224415 1 0.0020 146 | 0/8 8 h-lim-p 1.1810 20.0000 0.0014 4206.222895 3 0.9451 172 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4206.222894 0 1.0938 192 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4206.222894 0 1.0938 212 | 0/8 11 h-lim-p 1.3267 20.0000 0.0000 4206.222894 0 0.0726 235 | 0/8 12 h-lim-p 0.0287 20.0000 0.0000 4206.222894 0 0.0004 260 Out... lnL = -4206.222894 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4206.222894 Node 7: lnL = -4206.222894 Node 8: lnL = -4206.222894 Node 9: lnL = -4206.222894 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 905 Sequential format.. Reading seq # 1: YEL024W_Sbay Reading seq # 2: YEL024W_Scer Reading seq # 3: YEL024W_Skud Reading seq # 4: YEL024W_Smik Reading seq # 5: YEL024W_Spar Sequences read.. Counting patterns.. # site patterns = 292 Counting frequencies.. 120 bytes for distance 46720 bytes for lkl0 37376 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.231406 0.103109 0.084532 0.121817 0.078119 0.204047 0.226543 0.061600 lnL0 = -4077.284445 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4077.284445 x= 0.23141 0.10311 0.08453 0.12182 0.07812 0.20405 0.22654 0.06160 1 h-lim-p 0.0012 0.0096 103.2903 4076.126738 6 0.0002 35 | 0/8 2 h-lim-p 0.0007 0.0056 20.7533 4076.076234 6 0.0002 63 | 0/8 3 h-lim-p 0.0004 0.0230 13.3562 4076.055147 4 0.0003 84 | 0/8 4 h-lim-p 0.0009 0.0575 4.6686 4076.052092 4 0.0003 105 | 0/8 5 h-lim-p 0.0029 0.4765 0.5334 4076.052050 1 0.0003 121 | 0/8 6 h-lim-p 0.0035 8.2066 0.0439 4076.052050 0 0.0008 142 | 0/8 7 h-lim-p 0.0106 20.0000 0.0032 4076.052050 0 0.0023 163 | 0/8 8 h-lim-p 0.0233 20.0000 0.0003 4076.052036 0 0.3730 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4076.052036 0 1.0938 207 | 0/8 10 h-lim-p 0.9263 20.0000 0.0000 4076.052036 0 0.9263 227 | 0/8 11 h-lim-p 0.7586 20.0000 0.0000 4076.052036 0 0.0474 250 | 0/8 12 h-lim-p 0.0054 20.0000 0.0002 4076.052036 0 0.0027 270 | 0/8 13 h-lim-p 0.0014 20.0000 0.0004 4076.052036 0 0.0001 292 | 0/8 14 h-lim-p 0.0000 0.9694 0.1001 4076.052036 0 0.0000 316 | 0/8 15 h-lim-p 0.0001 20.0000 0.0004 4076.052036 0 0.0000 348 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 4076.052036 0 0.0000 378 Out... lnL = -4076.052036 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4076.052036 Node 7: lnL = -4076.052036 Node 8: lnL = -4076.052036 Node 9: lnL = -4076.052036 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 713 Sequential format.. Reading seq # 1: YEL026W_Sbay Reading seq # 2: YEL026W_Scer Reading seq # 3: YEL026W_Skud Reading seq # 4: YEL026W_Smik Reading seq # 5: YEL026W_Spar Sequences read.. Counting patterns.. # site patterns = 172 Counting frequencies.. 120 bytes for distance 27520 bytes for lkl0 22016 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.107402 0.039351 0.067221 0.043664 0.041129 0.119258 0.106321 0.019290 lnL0 = -2572.117786 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2572.117786 x= 0.10740 0.03935 0.06722 0.04366 0.04113 0.11926 0.10632 0.01929 1 h-lim-p 0.0016 0.0135 180.6601 2570.557937 7 0.0001 40 | 0/8 2 h-lim-p 0.0003 0.0027 31.5217 2570.507980 7 0.0001 72 | 0/8 3 h-lim-p 0.0002 0.0091 14.6424 2570.493801 5 0.0002 95 | 0/8 4 h-lim-p 0.0006 0.0466 3.8551 2570.492738 4 0.0002 116 | 0/8 5 h-lim-p 0.0007 0.1581 0.8190 2570.492678 2 0.0002 133 | 0/8 6 h-lim-p 0.0008 0.2527 0.1977 2570.492676 1 0.0002 156 | 0/8 7 h-lim-p 0.0018 11.2735 0.0169 2570.492676 0 0.0004 177 | 0/8 8 h-lim-p 0.0692 20.0000 0.0001 2570.492667 0 1.1065 201 | 0/8 9 h-lim-p 1.5161 20.0000 0.0001 2570.492667 0 1.3266 221 | 0/8 10 h-lim-p 1.8575 20.0000 0.0000 2570.492667 0 1.6253 241 | 0/8 11 h-lim-p 1.4099 20.0000 0.0001 2570.492667 0 0.6168 261 | 0/8 12 h-lim-p 0.1496 20.0000 0.0002 2570.492667 0 0.0001 290 | 0/8 13 h-lim-p 0.0000 5.8367 0.0049 2570.492667 0 0.0000 313 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 2570.492667 0 0.0000 348 | 0/8 15 h-lim-p 0.0000 20.0000 0.0050 | 0/8 16 h-lim-p 0.0000 20.0000 0.0050 Out... lnL = -2570.492667 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2570.492667 Node 7: lnL = -2570.492667 Node 8: lnL = -2570.492667 Node 9: lnL = -2570.492667 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 884 Sequential format.. Reading seq # 1: YEL029C_Sbay Reading seq # 2: YEL029C_Scer Reading seq # 3: YEL029C_Skud Reading seq # 4: YEL029C_Smik Reading seq # 5: YEL029C_Spar Sequences read.. Counting patterns.. # site patterns = 398 Counting frequencies.. 120 bytes for distance 63680 bytes for lkl0 50944 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.505520 0.000060 0.086463 0.323624 0.202639 0.266790 0.311859 0.236773 lnL0 = -4594.019922 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4594.019922 x= 0.50552 0.00006 0.08646 0.32362 0.20264 0.26679 0.31186 0.23677 1 h-lim-p 0.0002 0.0019 116.5440 4589.636921 0 0.0007 23 | 0/8 2 h-lim-p 0.0011 0.0087 60.9629 4588.879222 2 0.0005 39 | 0/8 3 h-lim-p 0.0007 0.0062 45.5331 4588.499194 7 0.0006 64 | 0/8 4 h-lim-p 0.0012 0.0122 20.6135 4588.410120 2 0.0006 80 | 0/8 5 h-lim-p 0.0023 0.0958 5.2069 4588.396764 2 0.0011 96 | 0/8 6 h-lim-p 0.0036 0.2488 1.5523 4588.394624 3 0.0015 115 | 0/8 7 h-lim-p 0.0695 8.9589 0.0333 4588.243877 0 0.4173 129 | 0/8 8 h-lim-p 0.0016 0.0363 8.8542 4588.167152 7 0.0012 166 | 0/8 9 h-lim-p 2.5000 20.0000 0.0010 4588.166500 3 1.0004 184 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 4588.166498 0 1.0938 204 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4588.166498 0 1.0938 224 | 0/8 12 h-lim-p 1.6199 20.0000 0.0000 4588.166498 0 1.4175 244 | 0/8 13 h-lim-p 1.6941 20.0000 0.0000 4588.166498 0 0.8470 264 | 0/8 14 h-lim-p 0.2557 20.0000 0.0000 4588.166498 0 0.0160 287 | 0/8 15 h-lim-p 0.0038 20.0000 0.0001 4588.166498 0 0.0000 326 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -4588.166498 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4588.166498 Node 7: lnL = -4588.166498 Node 8: lnL = -4588.166498 Node 9: lnL = -4588.166498 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 136 Sequential format.. Reading seq # 1: YEL034W_Sbay Reading seq # 2: YEL034W_Scer Reading seq # 3: YEL034W_Skud Reading seq # 4: YEL034W_Smik Reading seq # 5: YEL034W_Spar Sequences read.. Counting patterns.. # site patterns = 66 Counting frequencies.. 120 bytes for distance 10560 bytes for lkl0 8448 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.218511 0.004032 0.027460 0.077384 0.066312 0.106382 0.163422 0.103037 lnL0 = -524.346839 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 524.346839 x= 0.21851 0.00403 0.02746 0.07738 0.06631 0.10638 0.16342 0.10304 1 h-lim-p 0.0019 0.0155 69.8839 523.632873 9 0.0004 45 | 0/8 2 h-lim-p 0.0002 0.0013 13.8775 523.500775 m 0.0013 57 | 0/8 3 h-lim-p 0.0028 0.1016 6.7194 523.483447 7 0.0009 85 | 0/8 4 h-lim-p 0.0001 0.0005 3.3491 523.479987 m 0.0005 97 | 1/8 5 h-lim-p 0.0023 0.1917 0.6486 523.479236 4 0.0018 117 | 1/8 6 h-lim-p 0.0120 1.1651 0.0955 523.479223 2 0.0020 143 | 1/8 7 h-lim-p 0.0111 9.0037 0.0170 523.479126 0 0.0446 164 | 1/8 8 h-lim-p 0.0092 3.4828 0.0821 523.477896 0 0.0368 185 | 1/8 9 h-lim-p 2.5000 20.0000 0.0007 523.477741 2 1.0889 208 | 1/8 10 h-lim-p 2.5000 20.0000 0.0001 523.477737 2 1.3159 232 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 523.477737 0 1.0938 251 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 523.477737 0 0.1367 273 | 1/8 13 h-lim-p 0.0689 20.0000 0.0000 523.477737 0 0.0172 293 | 1/8 14 h-lim-p 0.0111 20.0000 0.0000 523.477737 0 0.0000 337 Out... lnL = -523.477737 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -523.477737 Node 7: lnL = -523.477737 Node 8: lnL = -523.477737 Node 9: lnL = -523.477737 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 558 Sequential format.. Reading seq # 1: YEL036C_Sbay Reading seq # 2: YEL036C_Scer Reading seq # 3: YEL036C_Skud Reading seq # 4: YEL036C_Smik Reading seq # 5: YEL036C_Spar Sequences read.. Counting patterns.. # site patterns = 248 Counting frequencies.. 120 bytes for distance 39680 bytes for lkl0 31744 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.455211 0.029941 0.099758 0.082484 0.067660 0.172086 0.302535 0.232723 lnL0 = -2433.265856 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2433.265856 x= 0.45521 0.02994 0.09976 0.08248 0.06766 0.17209 0.30253 0.23272 1 h-lim-p 0.0002 0.0016 90.0398 2431.665921 0 0.0004 23 | 0/8 2 h-lim-p 0.0017 0.0187 21.4559 2431.539030 7 0.0006 52 | 0/8 3 h-lim-p 0.0005 0.0096 27.8238 2431.466265 5 0.0004 74 | 0/8 4 h-lim-p 0.0008 0.0263 13.3026 2431.414785 1 0.0010 88 | 0/8 5 h-lim-p 0.0017 0.0564 7.4013 2431.404656 5 0.0006 112 | 0/8 6 h-lim-p 0.0021 0.1410 1.9307 2431.402866 4 0.0011 134 | 0/8 7 h-lim-p 0.0022 0.4705 0.9437 2431.402060 2 0.0022 150 | 0/8 8 h-lim-p 1.5130 20.0000 0.0014 2431.399793 5 1.1090 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 2431.399781 1 0.9961 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2431.399781 0 1.0938 223 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2431.399781 0 2.1875 243 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2431.399781 0 0.3125 265 | 0/8 13 h-lim-p 0.0991 20.0000 0.0000 2431.399781 0 0.0000 309 Out... lnL = -2431.399781 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2431.399781 Node 7: lnL = -2431.399781 Node 8: lnL = -2431.399781 Node 9: lnL = -2431.399781 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 487 Sequential format.. Reading seq # 1: YEL037C_Sbay Reading seq # 2: YEL037C_Scer Reading seq # 3: YEL037C_Skud Reading seq # 4: YEL037C_Smik Reading seq # 5: YEL037C_Spar Sequences read.. Counting patterns.. # site patterns = 170 Counting frequencies.. 120 bytes for distance 27200 bytes for lkl0 21760 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.149998 0.067444 0.062015 0.091979 0.076081 0.143356 0.155214 0.026413 lnL0 = -1977.255445 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1977.255445 x= 0.15000 0.06744 0.06202 0.09198 0.07608 0.14336 0.15521 0.02641 1 h-lim-p 0.0010 0.0080 85.9562 1976.429455 2 0.0002 27 | 0/8 2 h-lim-p 0.0025 0.0197 6.8077 1976.422037 5 0.0003 51 | 0/8 3 h-lim-p 0.0008 0.0699 2.6721 1976.421063 4 0.0003 71 | 0/8 4 h-lim-p 0.0014 0.3864 0.5791 1976.420993 3 0.0005 91 | 0/8 5 h-lim-p 0.0021 1.7911 0.1272 1976.420991 1 0.0004 114 | 0/8 6 h-lim-p 0.0060 20.0000 0.0089 1976.420991 0 0.0013 135 | 0/8 7 h-lim-p 0.0028 20.0000 0.0042 1976.420990 0 0.0042 155 | 0/8 8 h-lim-p 0.0053 20.0000 0.0033 1976.420944 0 0.0426 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1976.420943 0 1.0938 198 | 0/8 10 h-lim-p 1.5141 20.0000 0.0000 1976.420943 0 1.3249 218 | 0/8 11 h-lim-p 1.5409 20.0000 0.0000 1976.420943 0 0.6742 238 | 0/8 12 h-lim-p 0.2220 20.0000 0.0001 1976.420943 0 0.0017 264 | 0/8 13 h-lim-p 0.0005 20.0000 0.0003 1976.420943 0 0.0000 293 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 1976.420943 0 0.0000 320 Out... lnL = -1976.420943 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1976.420943 Node 7: lnL = -1976.420943 Node 8: lnL = -1976.420943 Node 9: lnL = -1976.420943 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 517 Sequential format.. Reading seq # 1: YEL038W_Sbay Reading seq # 2: YEL038W_Scer Reading seq # 3: YEL038W_Skud Reading seq # 4: YEL038W_Smik Reading seq # 5: YEL038W_Spar Sequences read.. Counting patterns.. # site patterns = 185 Counting frequencies.. 120 bytes for distance 29600 bytes for lkl0 23680 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.184793 0.004556 0.062675 0.087319 0.078044 0.155514 0.127901 0.066559 lnL0 = -2039.391866 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2039.391866 x= 0.18479 0.00456 0.06267 0.08732 0.07804 0.15551 0.12790 0.06656 1 h-lim-p 0.0006 0.4078 266.5698 2036.661765 7 0.0001 40 | 0/8 2 h-lim-p 0.0006 0.0049 43.0833 2036.335351 8 0.0004 73 | 0/8 3 h-lim-p 0.0010 0.0107 15.7659 2036.301855 7 0.0003 105 | 0/8 4 h-lim-p 0.0015 0.0333 3.1911 2036.300257 2 0.0003 122 | 0/8 5 h-lim-p 0.0034 0.9721 0.3029 2036.300236 2 0.0005 140 | 0/8 6 h-lim-p 0.0024 3.5623 0.0577 2036.300235 0 0.0005 161 | 0/8 7 h-lim-p 0.0130 20.0000 0.0023 2036.300209 0 0.0782 183 | 0/8 8 h-lim-p 0.0039 0.7337 0.0456 2036.299676 0 0.0118 204 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2036.299657 2 0.9961 228 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2036.299657 0 2.1875 248 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2036.299657 0 1.0938 268 | 0/8 12 h-lim-p 0.1505 20.0000 0.0000 2036.299657 0 4.8174 293 | 0/8 13 h-lim-p 0.9833 20.0000 0.0001 2036.299657 0 0.7374 313 | 0/8 14 h-lim-p 0.0007 4.2729 0.0652 2036.299657 0 0.0000 337 | 0/8 15 h-lim-p 0.0001 15.1465 0.0184 2036.299657 0 0.0000 358 | 0/8 16 h-lim-p 0.0001 20.0000 0.0033 2036.299657 0 0.0000 396 | 0/8 17 h-lim-p 0.0000 20.0000 0.0014 | 0/8 18 h-lim-p 0.0000 20.0000 0.0014 Out... lnL = -2036.299657 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2036.299657 Node 7: lnL = -2036.299657 Node 8: lnL = -2036.299657 Node 9: lnL = -2036.299657 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 477 Sequential format.. Reading seq # 1: YEL039C_Sbay Reading seq # 2: YEL039C_Scer Reading seq # 3: YEL039C_Skud Reading seq # 4: YEL039C_Smik Reading seq # 5: YEL039C_Spar Sequences read.. Counting patterns.. # site patterns = 165 Counting frequencies.. 120 bytes for distance 26400 bytes for lkl0 21120 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.223658 0.000536 0.061370 0.098911 0.066451 0.147672 0.123824 0.097987 lnL0 = -1908.188371 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1908.188371 x= 0.22366 0.00054 0.06137 0.09891 0.06645 0.14767 0.12382 0.09799 1 h-lim-p 0.0002 0.2320 442.0652 1902.557093 4 0.0001 31 | 0/8 2 h-lim-p 0.0003 0.0026 55.9408 1901.818982 0 0.0005 43 | 0/8 3 h-lim-p 0.0007 0.0059 25.5331 1901.736308 5 0.0003 64 | 0/8 4 h-lim-p 0.0011 0.0184 6.6163 1901.729309 6 0.0003 94 | 0/8 5 h-lim-p 0.0011 0.1038 2.1418 1901.728272 2 0.0005 110 | 0/8 6 h-lim-p 0.0044 0.8284 0.2462 1901.728248 3 0.0006 132 | 0/8 7 h-lim-p 0.0041 3.0781 0.0382 1901.728214 1 0.0041 154 | 0/8 8 h-lim-p 0.0058 7.0895 0.0273 1901.721930 0 0.0929 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 1901.720113 5 1.6985 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0003 1901.719871 3 1.3437 237 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1901.719871 0 1.0938 257 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1901.719871 0 2.1875 277 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1901.719871 0 1.0938 297 | 0/8 14 h-lim-p 0.2430 20.0000 0.0000 1901.719871 0 5.8309 321 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1901.719871 0 0.2734 343 | 0/8 16 h-lim-p 0.2113 20.0000 0.0000 1901.719871 0 0.0066 367 | 0/8 17 h-lim-p 0.0017 20.0000 0.0000 1901.719871 0 0.0000 393 | 0/8 18 h-lim-p 0.0002 20.0000 0.0000 1901.719871 0 0.0000 419 Out... lnL = -1901.719871 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1901.719871 Node 7: lnL = -1901.719871 Node 8: lnL = -1901.719871 Node 9: lnL = -1901.719871 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 446 Sequential format.. Reading seq # 1: YEL042W_Sbay Reading seq # 2: YEL042W_Scer Reading seq # 3: YEL042W_Skud Reading seq # 4: YEL042W_Smik Reading seq # 5: YEL042W_Spar Sequences read.. Counting patterns.. # site patterns = 190 Counting frequencies.. 120 bytes for distance 30400 bytes for lkl0 24320 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.194950 0.097898 0.055432 0.114808 0.083192 0.218226 0.193838 0.036746 lnL0 = -1852.998984 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1852.998984 x= 0.19495 0.09790 0.05543 0.11481 0.08319 0.21823 0.19384 0.03675 1 h-lim-p 0.0169 0.1351 42.4425 1852.701509 8 0.0003 43 | 0/8 2 h-lim-p 0.0013 0.0230 10.8863 1852.667518 2 0.0006 59 | 0/8 3 h-lim-p 0.0010 0.0254 7.0010 1852.658478 4 0.0005 80 | 0/8 4 h-lim-p 0.0018 0.0478 1.8972 1852.657540 4 0.0006 102 | 0/8 5 h-lim-p 0.0025 0.5467 0.4514 1852.657449 2 0.0009 118 | 0/8 6 h-lim-p 0.0048 1.9300 0.0893 1852.657447 1 0.0006 142 | 0/8 7 h-lim-p 0.0021 6.2592 0.0251 1852.657447 0 0.0009 162 | 0/8 8 h-lim-p 0.1637 20.0000 0.0001 1852.657431 0 0.9824 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1852.657430 0 1.0938 204 | 0/8 10 h-lim-p 1.1174 20.0000 0.0000 1852.657430 0 0.2794 225 | 0/8 11 h-lim-p 0.0828 20.0000 0.0001 1852.657430 0 0.0000 273 | 0/8 12 h-lim-p 0.0000 20.0000 0.0007 | 0/8 13 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -1852.657430 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1852.657430 Node 7: lnL = -1852.657430 Node 8: lnL = -1852.657430 Node 9: lnL = -1852.657430 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 236 Sequential format.. Reading seq # 1: YEL043W_Sbay Reading seq # 2: YEL043W_Scer Reading seq # 3: YEL043W_Skud Reading seq # 4: YEL043W_Smik Reading seq # 5: YEL043W_Spar Sequences read.. Counting patterns.. # site patterns = 99 Counting frequencies.. 120 bytes for distance 15840 bytes for lkl0 12672 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.553544 0.035980 0.238484 0.207359 0.187433 4.284071 0.291447 0.000060 lnL0 = -928.025964 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 928.025964 x= 0.55354 0.03598 0.23848 0.20736 0.18743 4.28407 0.29145 0.00006 1 h-lim-p 0.0000 0.0000 88.8396 927.989610 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0144 22.7255 926.620309 0 0.0045 42 | 1/8 3 h-lim-p 0.0203 0.1622 3.9641 926.454152 3 0.0103 60 | 1/8 4 h-lim-p 0.0139 0.1732 2.9368 926.005182 0 0.0278 73 | 1/8 5 h-lim-p 0.0034 0.0271 6.1747 923.963194 0 0.0203 87 | 0/8 6 h-lim-p 0.0012 0.0098 14.5974 921.612442 m 0.0098 99 | 0/8 7 h-lim-p 0.0016 0.0129 10.3133 921.127834 0 0.0096 113 | 0/8 8 h-lim-p 0.1157 0.9255 0.0982 920.616837 0 0.4627 127 | 0/8 9 h-lim-p 1.0079 15.7166 0.0451 920.445723 2 0.4725 151 | 0/8 10 h-lim-p 2.5000 20.0000 0.0081 920.440431 5 0.8152 183 | 0/8 11 h-lim-p 2.3302 20.0000 0.0028 920.439470 4 0.6115 212 | 0/8 12 h-lim-p 2.5000 20.0000 0.0005 920.439404 3 1.0004 238 | 0/8 13 h-lim-p 2.5000 20.0000 0.0001 920.439403 1 0.9961 260 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 920.439403 0 1.0938 280 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 920.439403 0 1.2500 300 | 0/8 16 h-lim-p 1.2568 20.0000 0.0000 920.439403 0 0.5498 320 | 0/8 17 h-lim-p 0.0528 20.0000 0.0001 920.439403 0 0.0132 341 | 0/8 18 h-lim-p 0.0043 20.0000 0.0002 920.439403 0 0.0000 380 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -920.439403 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -920.439403 Node 7: lnL = -920.439403 Node 8: lnL = -920.439403 Node 9: lnL = -920.439403 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 48 Sequential format.. Reading seq # 1: YEL046C_Sbay Reading seq # 2: YEL046C_Scer Reading seq # 3: YEL046C_Skud Reading seq # 4: YEL046C_Smik Reading seq # 5: YEL046C_Spar Sequences read.. Counting patterns.. # site patterns = 25 Counting frequencies.. 120 bytes for distance 4000 bytes for lkl0 3200 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.553544 0.069952 0.194592 0.209334 0.268886 3.796505 0.299460 0.000060 lnL0 = -149.520158 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 149.520158 x= 0.55354 0.06995 0.19459 0.20933 0.26889 3.79650 0.29946 0.00006 1 h-lim-p 0.0000 0.0000 58.6637 149.498353 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0001 1979.4090 133.736539 m 0.0001 35 | 2/8 3 h-lim-p 0.0000 0.0001 50.1496 133.549767 m 0.0001 47 | 3/8 4 h-lim-p 0.0001 0.0100 46.9159 126.881955 5 0.0091 75 | 3/8 5 h-lim-p 0.0111 0.0887 2.0965 126.125404 0 0.0443 89 | 2/8 6 h-lim-p 0.0016 0.0132 10.9362 126.015603 1 0.0021 103 | 2/8 7 h-lim-p 0.0026 0.0211 1.4253 125.948242 m 0.0211 115 | 1/8 8 h-lim-p 0.0000 0.0000 49.3255 h-lim-p: 1.65170260e-21 1.32136208e-20 4.93254903e+01 125.948242 .. | 1/8 9 h-lim-p 0.0000 0.0578 17.5189 125.854695 0 0.0006 141 | 1/8 10 h-lim-p 0.0003 0.0023 5.3050 125.803378 m 0.0023 153 | 1/8 11 h-lim-p 0.0014 0.0133 8.7970 125.760296 0 0.0028 166 | 1/8 12 h-lim-p 0.0267 0.2135 0.3300 125.760028 4 0.0028 190 | 1/8 13 h-lim-p 0.0215 1.6863 0.0437 125.724153 0 0.5153 213 | 1/8 14 h-lim-p 1.5561 12.4490 0.0033 125.723587 6 0.9751 248 | 1/8 15 h-lim-p 2.5000 20.0000 0.0001 125.723583 2 1.2402 271 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 125.723583 0 1.0938 290 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 125.723583 0 0.5469 310 | 1/8 18 h-lim-p 0.3717 20.0000 0.0000 125.723583 0 0.0029 335 | 1/8 19 h-lim-p 0.0014 20.0000 0.0000 125.723583 0 0.0014 354 | 1/8 20 h-lim-p 0.0009 20.0000 0.0000 125.723583 0 0.0000 395 | 1/8 21 h-lim-p 0.0000 20.0000 0.0005 | 1/8 22 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -125.723583 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -125.723583 Node 7: lnL = -125.723583 Node 8: lnL = -125.723583 Node 9: lnL = -125.723583 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 861 Sequential format.. Reading seq # 1: YEL047C_Sbay Reading seq # 2: YEL047C_Scer Reading seq # 3: YEL047C_Skud Reading seq # 4: YEL047C_Smik Reading seq # 5: YEL047C_Spar Sequences read.. Counting patterns.. # site patterns = 185 Counting frequencies.. 120 bytes for distance 29600 bytes for lkl0 23680 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.121098 0.021159 0.034073 0.051789 0.043428 0.076575 0.107012 0.043428 lnL0 = -2890.041550 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2890.041550 x= 0.12110 0.02116 0.03407 0.05179 0.04343 0.07657 0.10701 0.04343 1 h-lim-p 0.0001 0.0012 357.0497 2886.957165 8 0.0001 36 | 0/8 2 h-lim-p 0.0004 0.0033 35.5093 2886.872510 5 0.0001 60 | 0/8 3 h-lim-p 0.0004 0.0154 13.1892 2886.865767 2 0.0001 77 | 0/8 4 h-lim-p 0.0003 0.0281 3.7445 2886.865124 4 0.0001 98 | 0/8 5 h-lim-p 0.0002 0.0956 1.5071 2886.865000 3 0.0001 117 | 0/8 6 h-lim-p 0.0021 1.1855 0.0940 2886.864999 0 0.0002 131 | 0/8 7 h-lim-p 0.0044 11.8871 0.0049 2886.864999 0 0.0005 153 | 0/8 8 h-lim-p 0.0037 20.0000 0.0006 2886.864947 0 0.3565 179 | 0/8 9 h-lim-p 0.3343 20.0000 0.0007 2886.864943 0 1.0028 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2886.864943 0 1.0938 220 | 0/8 11 h-lim-p 0.5320 20.0000 0.0001 2886.864943 0 1.0640 241 | 0/8 12 h-lim-p 1.2888 20.0000 0.0000 2886.864943 0 3.8663 262 | 0/8 13 h-lim-p 0.4937 20.0000 0.0004 2886.864943 0 0.0019 289 | 0/8 14 h-lim-p 0.0001 13.3506 0.0051 2886.864943 0 0.0000 311 | 0/8 15 h-lim-p 0.0000 3.7724 0.0182 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0060 2886.864943 0 0.0000 373 | 0/8 17 h-lim-p 0.0000 20.0000 0.0023 2886.864943 0 0.0005 398 | 0/8 18 h-lim-p 0.0016 20.0000 0.0007 2886.864943 0 0.0000 425 | 0/8 19 h-lim-p 0.0000 20.0000 0.0002 2886.864943 0 0.0000 448 | 0/8 20 h-lim-p 0.0000 20.0000 0.0002 .. | 0/8 21 h-lim-p 0.0000 20.0000 0.0129 | 0/8 22 h-lim-p 0.0000 20.0000 0.0129 Out... lnL = -2886.864943 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2886.864943 Node 7: lnL = -2886.864943 Node 8: lnL = -2886.864943 Node 9: lnL = -2886.864943 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 228 Sequential format.. Reading seq # 1: YEL048C_Sbay Reading seq # 2: YEL048C_Scer Reading seq # 3: YEL048C_Skud Reading seq # 4: YEL048C_Smik Reading seq # 5: YEL048C_Spar Sequences read.. Counting patterns.. # site patterns = 119 Counting frequencies.. 120 bytes for distance 19040 bytes for lkl0 15232 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.256374 0.064501 0.056013 0.089312 0.158156 0.305474 0.189140 0.071720 lnL0 = -1035.386731 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1035.386731 x= 0.25637 0.06450 0.05601 0.08931 0.15816 0.30547 0.18914 0.07172 1 h-lim-p 0.0019 0.0150 24.1389 1035.139208 2 0.0009 26 | 0/8 2 h-lim-p 0.0014 0.0109 7.2548 1035.113374 4 0.0010 46 | 0/8 3 h-lim-p 0.0030 0.1243 2.5542 1035.109476 2 0.0014 62 | 0/8 4 h-lim-p 0.0022 0.0923 1.5859 1035.108702 5 0.0008 85 | 0/8 5 h-lim-p 0.0049 0.7076 0.2678 1035.108630 2 0.0021 101 | 0/8 6 h-lim-p 0.0102 5.8207 0.0564 1035.108627 2 0.0016 127 | 0/8 7 h-lim-p 0.0043 10.0151 0.0214 1035.108627 1 0.0021 150 | 0/8 8 h-lim-p 0.0625 20.0000 0.0007 1035.108509 0 0.7500 173 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1035.108508 0 1.0938 193 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1035.108508 0 1.0938 213 | 0/8 11 h-lim-p 1.4348 20.0000 0.0000 1035.108508 0 0.6277 233 | 0/8 12 h-lim-p 0.3433 20.0000 0.0000 1035.108508 0 0.0375 255 | 0/8 13 h-lim-p 0.0133 20.0000 0.0000 1035.108508 0 0.0133 275 | 0/8 14 h-lim-p 0.0067 20.0000 0.0000 1035.108508 0 0.0004 298 | 0/8 15 h-lim-p 0.0002 20.0000 0.0001 1035.108508 0 0.0002 318 | 0/8 16 h-lim-p 0.0001 20.0000 0.0001 1035.108508 0 0.0000 355 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 1035.108508 0 0.0000 378 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1035.108508 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1035.108508 Node 7: lnL = -1035.108508 Node 8: lnL = -1035.108508 Node 9: lnL = -1035.108508 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 862 Sequential format.. Reading seq # 1: YEL050C_Sbay Reading seq # 2: YEL050C_Scer Reading seq # 3: YEL050C_Skud Reading seq # 4: YEL050C_Smik Reading seq # 5: YEL050C_Spar Sequences read.. Counting patterns.. # site patterns = 267 Counting frequencies.. 120 bytes for distance 42720 bytes for lkl0 34176 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.142426 0.062454 0.052273 0.104823 0.066106 0.142876 0.122088 0.027585 lnL0 = -3373.448435 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3373.448435 x= 0.14243 0.06245 0.05227 0.10482 0.06611 0.14288 0.12209 0.02758 1 h-lim-p 0.0010 0.4835 259.8767 3369.886354 3 0.0001 30 | 0/8 2 h-lim-p 0.0004 0.0030 26.8314 3369.828638 6 0.0002 53 | 0/8 3 h-lim-p 0.0006 0.0161 7.5746 3369.823407 5 0.0002 79 | 0/8 4 h-lim-p 0.0015 0.1899 0.9877 3369.823282 3 0.0003 100 | 0/8 5 h-lim-p 0.0011 0.3344 0.2483 3369.823276 1 0.0002 123 | 0/8 6 h-lim-p 0.0034 9.5055 0.0153 3369.823276 0 0.0004 145 | 0/8 7 h-lim-p 0.0051 20.0000 0.0011 3369.823274 0 0.0303 167 | 0/8 8 h-lim-p 0.0023 13.5393 0.0150 3369.823216 0 0.0092 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3369.823216 0 1.0938 209 | 0/8 10 h-lim-p 1.1186 20.0000 0.0000 3369.823216 0 1.6779 229 | 0/8 11 h-lim-p 0.9919 20.0000 0.0001 3369.823216 0 2.9758 250 | 0/8 12 h-lim-p 0.0042 0.7829 0.0530 3369.823216 0 0.0000 280 | 0/8 13 h-lim-p 0.0002 20.0000 0.0005 3369.823216 0 0.0000 305 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 3369.823216 0 0.0000 334 Out... lnL = -3369.823216 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3369.823216 Node 7: lnL = -3369.823216 Node 8: lnL = -3369.823216 Node 9: lnL = -3369.823216 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 372 Sequential format.. Reading seq # 1: YEL051W_Sbay Reading seq # 2: YEL051W_Scer Reading seq # 3: YEL051W_Skud Reading seq # 4: YEL051W_Smik Reading seq # 5: YEL051W_Spar Sequences read.. Counting patterns.. # site patterns = 102 Counting frequencies.. 120 bytes for distance 16320 bytes for lkl0 13056 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.128380 0.088741 0.015563 0.034046 0.046491 0.130082 0.089391 0.036641 lnL0 = -1164.857181 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1164.857181 x= 0.12838 0.08874 0.01556 0.03405 0.04649 0.13008 0.08939 0.03664 1 h-lim-p 0.0001 0.0007 75.2818 1164.244548 0 0.0003 23 | 0/8 2 h-lim-p 0.0004 0.0034 34.4855 1164.102376 7 0.0003 52 | 0/8 3 h-lim-p 0.0001 0.0010 23.6258 1164.058051 0 0.0003 65 | 0/8 4 h-lim-p 0.0008 0.0306 7.7440 1164.053627 2 0.0002 82 | 0/8 5 h-lim-p 0.0006 0.0389 2.5096 1164.052701 5 0.0003 107 | 0/8 6 h-lim-p 0.0040 0.9337 0.2075 1164.052682 2 0.0006 125 | 0/8 7 h-lim-p 0.0037 5.9547 0.0357 1164.052610 0 0.0074 146 | 0/8 8 h-lim-p 0.0089 2.2238 0.0297 1164.046344 0 0.0714 169 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1164.046115 3 1.0004 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1164.046114 0 1.2500 215 | 0/8 11 h-lim-p 1.8747 20.0000 0.0000 1164.046114 0 0.4101 236 | 0/8 12 h-lim-p 0.2342 20.0000 0.0000 1164.046114 0 0.0005 264 | 0/8 13 h-lim-p 0.0002 20.0000 0.0001 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0075 | 0/8 15 h-lim-p 0.0000 20.0000 0.0075 Out... lnL = -1164.046114 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1164.046114 Node 7: lnL = -1164.046114 Node 8: lnL = -1164.046114 Node 9: lnL = -1164.046114 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 880 Sequential format.. Reading seq # 1: YEL056W_Sbay Reading seq # 2: YEL056W_Scer Reading seq # 3: YEL056W_Skud Reading seq # 4: YEL056W_Smik Reading seq # 5: YEL056W_Spar Sequences read.. Counting patterns.. # site patterns = 395 Counting frequencies.. 120 bytes for distance 63200 bytes for lkl0 50560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.422738 0.366914 0.451811 0.382038 0.198272 0.289727 0.397284 lnL0 = -4433.042287 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4433.042287 x= 0.00006 0.42274 0.36691 0.45181 0.38204 0.19827 0.28973 0.39728 1 h-lim-p 0.0000 0.0000 467.4614 4432.824623 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0003 1975.7795 4288.579556 0 0.0002 38 | 1/8 3 h-lim-p 0.0003 0.0021 190.3959 4273.705528 0 0.0011 52 | 1/8 4 h-lim-p 0.0011 0.0088 48.5646 4272.780868 7 0.0008 80 | 1/8 5 h-lim-p 0.0018 0.0211 23.2732 4272.560691 5 0.0009 103 | 1/8 6 h-lim-p 0.0043 0.0353 5.1134 4272.530763 6 0.0014 129 | 1/8 7 h-lim-p 0.0078 0.4731 0.9460 4271.990707 0 0.0313 143 | 1/8 8 h-lim-p 0.0036 0.0633 8.2339 4265.139994 0 0.0144 164 | 1/8 9 h-lim-p 1.3554 10.8428 0.0367 4264.824184 5 0.5184 187 | 1/8 10 h-lim-p 0.9612 20.0000 0.0198 4264.776168 3 0.4008 213 | 0/8 11 h-lim-p 0.0123 5.7378 0.6428 4264.775987 3 0.0008 241 | 0/8 12 h-lim-p 0.2593 6.9680 0.0021 4264.773647 0 1.0373 263 | 0/8 13 h-lim-p 2.5000 20.0000 0.0004 4264.773573 3 0.8800 290 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 4264.773572 0 1.0938 310 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 4264.773572 0 1.0938 330 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 4264.773572 0 1.0938 350 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 4264.773572 0 1.0938 370 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 4264.773572 0 0.0391 395 Out... lnL = -4264.773572 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4264.773572 Node 7: lnL = -4264.773572 Node 8: lnL = -4264.773572 Node 9: lnL = -4264.773572 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 941 Sequential format.. Reading seq # 1: YEL057C_Sbay Reading seq # 2: YEL057C_Scer Reading seq # 3: YEL057C_Skud Reading seq # 4: YEL057C_Smik Reading seq # 5: YEL057C_Spar Sequences read.. Counting patterns.. # site patterns = 348 Counting frequencies.. 120 bytes for distance 55680 bytes for lkl0 44544 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.309765 0.276004 0.365389 0.288376 0.158932 0.271070 0.343873 lnL0 = -4452.603329 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4452.603329 x= 0.00006 0.30976 0.27600 0.36539 0.28838 0.15893 0.27107 0.34387 1 h-lim-p 0.0000 0.0000 519.4442 4452.207542 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0006 715.5477 4373.938167 0 0.0005 39 | 1/8 3 h-lim-p 0.0003 0.0020 159.8103 4364.535384 0 0.0008 52 | 1/8 4 h-lim-p 0.0025 0.0196 18.3116 4364.366920 7 0.0009 82 | 1/8 5 h-lim-p 0.0078 0.1214 2.0002 4363.183150 0 0.0312 96 | 1/8 6 h-lim-p 0.0031 0.0250 11.0161 4354.053190 0 0.0125 110 | 1/8 7 h-lim-p 0.0007 0.0056 73.2459 4341.679442 0 0.0014 123 | 1/8 8 h-lim-p 0.0029 0.0230 18.4408 4341.464188 6 0.0012 148 | 1/8 9 h-lim-p 0.0927 1.5032 0.2326 4336.983112 0 0.3707 162 | 1/8 10 h-lim-p 0.6308 5.0466 0.0901 4335.979954 9 0.3544 203 | 0/8 11 h-lim-p 0.0033 0.1733 9.5996 4335.942692 7 0.0009 236 | 0/8 12 h-lim-p 0.5051 4.2976 0.0165 4335.832821 0 0.7577 248 | 0/8 13 h-lim-p 2.5000 20.0000 0.0035 4335.820300 5 0.9482 278 | 0/8 14 h-lim-p 2.5000 20.0000 0.0005 4335.820196 2 0.8246 304 | 0/8 15 h-lim-p 2.5000 20.0000 0.0001 4335.820193 1 0.9961 326 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 4335.820193 0 1.0938 346 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 4335.820193 0 1.0938 366 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 4335.820193 0 0.1562 389 | 0/8 19 h-lim-p 0.2003 20.0000 0.0000 4335.820193 0 0.0016 415 Out... lnL = -4335.820193 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4335.820193 Node 7: lnL = -4335.820193 Node 8: lnL = -4335.820193 Node 9: lnL = -4335.820193 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 329 Sequential format.. Reading seq # 1: YEL058W_Sbay Reading seq # 2: YEL058W_Scer Reading seq # 3: YEL058W_Skud Reading seq # 4: YEL058W_Smik Reading seq # 5: YEL058W_Spar Sequences read.. Counting patterns.. # site patterns = 160 Counting frequencies.. 120 bytes for distance 25600 bytes for lkl0 20480 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.056326 0.162653 0.023921 0.148953 0.131250 0.231650 0.260056 0.435604 lnL0 = -1553.989117 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1553.989117 x= 0.05633 0.16265 0.02392 0.14895 0.13125 0.23165 0.26006 0.43560 1 h-lim-p 0.0027 0.0220 88.2119 1552.611560 9 0.0004 48 | 0/8 2 h-lim-p 0.0015 0.0121 20.4110 1552.336595 3 0.0014 66 | 0/8 3 h-lim-p 0.0045 0.0777 6.2890 1552.317812 2 0.0010 83 | 0/8 4 h-lim-p 0.0022 0.1100 3.0241 1552.311168 3 0.0018 101 | 0/8 5 h-lim-p 0.0033 0.1907 1.6664 1552.309185 5 0.0019 126 | 0/8 6 h-lim-p 0.0090 0.6189 0.3514 1552.309056 2 0.0022 143 | 0/8 7 h-lim-p 0.0104 1.7390 0.0756 1552.309051 1 0.0021 166 | 0/8 8 h-lim-p 1.2155 20.0000 0.0001 1552.309045 1 0.9686 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1552.309045 0 1.0938 208 | 0/8 10 h-lim-p 0.9755 20.0000 0.0000 1552.309045 0 0.8535 228 | 0/8 11 h-lim-p 0.8019 20.0000 0.0000 1552.309045 0 0.0002 259 Out... lnL = -1552.309045 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1552.309045 Node 7: lnL = -1552.309045 Node 8: lnL = -1552.309045 Node 9: lnL = -1552.309045 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 27 Sequential format.. Reading seq # 1: YEL059C-A_Sbay Reading seq # 2: YEL059C-A_Scer Reading seq # 3: YEL059C-A_Skud Reading seq # 4: YEL059C-A_Smik Reading seq # 5: YEL059C-A_Spar Sequences read.. Counting patterns.. # site patterns = 16 Counting frequencies.. 120 bytes for distance 2560 bytes for lkl0 2048 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.181927 0.159203 0.188728 0.159749 0.064063 0.130626 0.151994 lnL0 = -102.559170 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 102.559170 x= 0.00006 0.18193 0.15920 0.18873 0.15975 0.06406 0.13063 0.15199 1 h-lim-p 0.0000 0.0000 38.4589 102.538442 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0007 309.0417 94.744932 m 0.0007 38 | 2/8 3 h-lim-p 0.0044 0.0352 5.9455 94.593495 0 0.0088 51 | 2/8 4 h-lim-p 0.0051 0.0405 2.3690 94.519954 0 0.0101 64 | 2/8 5 h-lim-p 0.0071 0.0566 1.6755 94.369568 0 0.0212 77 | 2/8 6 h-lim-p 0.0068 0.0545 3.3653 93.951690 0 0.0272 91 | 2/8 7 h-lim-p 0.0088 0.0704 2.3555 93.934422 7 0.0058 119 | 1/8 8 h-lim-p 0.0032 0.1115 4.2885 93.893490 0 0.0064 132 | 1/8 9 h-lim-p 0.3974 12.3796 0.0692 93.851364 7 0.2446 162 | 1/8 10 h-lim-p 0.8259 6.6072 0.0127 93.843636 4 0.7185 188 | 1/8 11 h-lim-p 2.2101 17.6807 0.0034 93.842814 6 0.8209 220 | 1/8 12 h-lim-p 2.5000 20.0000 0.0002 93.842809 2 1.1719 243 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 93.842809 0 1.0938 262 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 93.842809 0 2.1875 281 | 1/8 15 h-lim-p 2.1238 20.0000 0.0000 93.842809 0 0.9291 300 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 93.842809 0 0.0003 331 Out... lnL = -93.842809 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -93.842809 Node 7: lnL = -93.842809 Node 8: lnL = -93.842809 Node 9: lnL = -93.842809 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 462 Sequential format.. Reading seq # 1: YEL060C_Sbay Reading seq # 2: YEL060C_Scer Reading seq # 3: YEL060C_Skud Reading seq # 4: YEL060C_Smik Reading seq # 5: YEL060C_Spar Sequences read.. Counting patterns.. # site patterns = 146 Counting frequencies.. 120 bytes for distance 23360 bytes for lkl0 18688 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.042149 0.053720 0.019244 0.063861 0.058760 0.126310 0.127069 0.227727 lnL0 = -1833.288328 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1833.288328 x= 0.04215 0.05372 0.01924 0.06386 0.05876 0.12631 0.12707 0.22773 1 h-lim-p 0.0006 0.4258 249.7244 1830.976217 9 0.0001 47 | 0/8 2 h-lim-p 0.0005 0.0059 43.7351 1830.678680 8 0.0003 77 | 0/8 3 h-lim-p 0.0012 0.0140 12.0880 1830.649883 5 0.0004 101 | 0/8 4 h-lim-p 0.0012 0.0207 4.1923 1830.648453 5 0.0002 127 | 0/8 5 h-lim-p 0.0012 0.2121 0.6383 1830.648354 1 0.0005 141 | 0/8 6 h-lim-p 0.0019 0.5967 0.1739 1830.648349 2 0.0003 168 | 0/8 7 h-lim-p 0.0022 5.5924 0.0245 1830.648348 1 0.0018 190 | 0/8 8 h-lim-p 0.0329 20.0000 0.0013 1830.647239 0 0.5270 214 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1830.647189 2 0.9961 238 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1830.647189 0 1.0938 258 | 0/8 11 h-lim-p 1.2063 20.0000 0.0000 1830.647189 0 9.6503 281 | 0/8 12 h-lim-p 0.5468 20.0000 0.0003 1830.647189 0 0.0171 305 | 0/8 13 h-lim-p 0.0009 11.9604 0.0062 1830.647189 0 0.0000 347 | 0/8 14 h-lim-p 0.0000 20.0000 0.0029 | 0/8 15 h-lim-p 0.0000 20.0000 0.0029 Out... lnL = -1830.647189 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1830.647189 Node 7: lnL = -1830.647189 Node 8: lnL = -1830.647189 Node 9: lnL = -1830.647189 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 484 Sequential format.. Reading seq # 1: YEL061C_Sbay Reading seq # 2: YEL061C_Scer Reading seq # 3: YEL061C_Skud Reading seq # 4: YEL061C_Smik Reading seq # 5: YEL061C_Spar Sequences read.. Counting patterns.. # site patterns = 184 Counting frequencies.. 120 bytes for distance 29440 bytes for lkl0 23552 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.032306 0.015616 0.047264 0.097338 0.082758 0.213145 0.194003 0.275353 lnL0 = -1942.044154 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1942.044154 x= 0.03231 0.01562 0.04726 0.09734 0.08276 0.21315 0.19400 0.27535 1 h-lim-p 0.0029 1.2121 115.4896 1940.761585 8 0.0002 44 | 0/8 2 h-lim-p 0.0008 0.0066 16.6200 1940.677027 5 0.0006 66 | 0/8 3 h-lim-p 0.0015 0.0270 7.1635 1940.669384 2 0.0003 83 | 0/8 4 h-lim-p 0.0018 0.1166 1.3233 1940.668985 4 0.0005 104 | 0/8 5 h-lim-p 0.0012 0.2318 0.5164 1940.668901 3 0.0007 125 | 0/8 6 h-lim-p 0.0149 2.1080 0.0244 1940.668900 0 0.0016 147 | 0/8 7 h-lim-p 0.0028 12.4176 0.0144 1940.668900 0 0.0024 167 | 0/8 8 h-lim-p 0.0404 20.0000 0.0009 1940.668760 0 0.3231 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1940.668759 0 1.0938 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1940.668759 0 1.0938 230 | 0/8 11 h-lim-p 1.0451 20.0000 0.0000 1940.668759 0 4.1805 252 | 0/8 12 h-lim-p 0.3515 20.0000 0.0002 1940.668759 0 0.1758 272 | 0/8 13 h-lim-p 0.0204 20.0000 0.0015 1940.668759 0 0.0006 296 | 0/8 14 h-lim-p 0.0005 20.0000 0.0018 1940.668759 0 0.0000 332 | 0/8 15 h-lim-p 0.0000 20.0000 0.0010 | 0/8 16 h-lim-p 0.0000 20.0000 0.0010 Out... lnL = -1940.668759 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1940.668759 Node 7: lnL = -1940.668759 Node 8: lnL = -1940.668759 Node 9: lnL = -1940.668759 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 863 Sequential format.. Reading seq # 1: YEL062W_Sbay Reading seq # 2: YEL062W_Scer Reading seq # 3: YEL062W_Skud Reading seq # 4: YEL062W_Smik Reading seq # 5: YEL062W_Spar Sequences read.. Counting patterns.. # site patterns = 324 Counting frequencies.. 120 bytes for distance 51840 bytes for lkl0 41472 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.018077 0.025183 0.040851 0.182726 0.139306 0.290135 0.266793 0.348413 lnL0 = -4150.999580 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4150.999580 x= 0.01808 0.02518 0.04085 0.18273 0.13931 0.29013 0.26679 0.34841 1 h-lim-p 0.0025 0.7896 180.8065 4148.901765 5 0.0001 34 | 0/8 2 h-lim-p 0.0016 0.0145 15.4831 4148.827802 5 0.0006 56 | 0/8 3 h-lim-p 0.0013 0.0144 7.5815 4148.819700 5 0.0003 79 | 0/8 4 h-lim-p 0.0034 0.2748 0.7611 4148.819568 3 0.0005 99 | 0/8 5 h-lim-p 0.0017 0.6544 0.2035 4148.819559 1 0.0004 122 | 0/8 6 h-lim-p 0.0018 1.0215 0.0470 4148.819559 0 0.0008 142 | 0/8 7 h-lim-p 0.0073 13.2611 0.0051 4148.819557 0 0.0073 162 | 0/8 8 h-lim-p 0.0070 20.0000 0.0053 4148.819310 0 0.0561 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4148.819310 0 1.0938 205 | 0/8 10 h-lim-p 0.8205 20.0000 0.0000 4148.819310 0 1.2308 225 | 0/8 11 h-lim-p 1.1586 20.0000 0.0000 4148.819310 0 1.0137 245 | 0/8 12 h-lim-p 0.0400 20.0000 0.0008 4148.819310 0 0.0011 269 | 0/8 13 h-lim-p 0.0000 0.1748 0.1560 4148.819310 0 0.0000 289 | 0/8 14 h-lim-p 0.0013 20.0000 0.0012 4148.819310 0 0.0013 309 | 0/8 15 h-lim-p 0.0005 9.0794 0.0030 4148.819310 0 0.0005 329 | 0/8 16 h-lim-p 0.0003 5.6413 0.0048 4148.819310 0 0.0000 354 | 0/8 17 h-lim-p 0.0000 20.0000 0.0007 4148.819310 0 0.0000 377 | 0/8 18 h-lim-p 0.0004 20.0000 0.0000 4148.819310 0 0.0000 409 Out... lnL = -4148.819310 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4148.819310 Node 7: lnL = -4148.819310 Node 8: lnL = -4148.819310 Node 9: lnL = -4148.819310 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 869 Sequential format.. Reading seq # 1: YEL066W_Sbay Reading seq # 2: YEL066W_Scer Reading seq # 3: YEL066W_Skud Reading seq # 4: YEL066W_Smik Reading seq # 5: YEL066W_Spar Sequences read.. Counting patterns.. # site patterns = 367 Counting frequencies.. 120 bytes for distance 58720 bytes for lkl0 46976 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.208084 0.000060 0.189941 0.280158 0.243194 0.357527 0.435012 0.710791 lnL0 = -3715.180999 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3715.180999 x= 0.20808 0.00006 0.18994 0.28016 0.24319 0.35753 0.43501 0.71079 1 h-lim-p 0.0000 0.0000 328.5546 3715.098354 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0091 65.3083 3709.279882 0 0.0026 42 | 1/8 3 h-lim-p 0.0043 0.0347 8.6381 3708.609986 0 0.0087 55 | 1/8 4 h-lim-p 0.0052 0.0413 4.4651 3704.542617 0 0.0206 69 | 1/8 5 h-lim-p 0.0016 0.0125 28.8421 3694.195663 0 0.0047 82 | 1/8 6 h-lim-p 0.0007 0.0052 75.7007 3679.846944 0 0.0026 96 | 1/8 7 h-lim-p 0.0047 0.0375 38.0931 3677.687022 9 0.0029 133 | 1/8 8 h-lim-p 0.3878 3.1021 0.1855 3674.746311 3 0.3938 151 | 1/8 9 h-lim-p 1.2652 12.4098 0.0577 3674.370799 7 0.4510 185 | 1/8 10 h-lim-p 2.5000 20.0000 0.0067 3674.363743 5 0.7695 218 | 1/8 11 h-lim-p 1.5905 20.0000 0.0032 3674.362487 2 0.7890 241 | 1/8 12 h-lim-p 2.5000 20.0000 0.0008 3674.362410 2 0.5444 265 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 3674.362410 0 1.0938 284 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 3674.362410 0 1.0938 303 | 1/8 15 h-lim-p 2.4299 20.0000 0.0000 3674.362410 0 1.0631 322 | 1/8 16 h-lim-p 1.7422 20.0000 0.0000 3674.362410 0 0.3811 342 | 1/8 17 h-lim-p 0.2037 20.0000 0.0000 3674.362410 0 0.2037 361 | 1/8 18 h-lim-p 0.1162 20.0000 0.0000 3674.362410 0 0.0036 384 | 1/8 19 h-lim-p 0.0004 20.0000 0.0001 .. | 1/8 20 h-lim-p 0.0000 20.0000 0.0001 3674.362410 0 0.0000 449 | 1/8 21 h-lim-p 0.0000 20.0000 0.0001 | 1/8 22 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -3674.362410 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3674.362410 Node 7: lnL = -3674.362410 Node 8: lnL = -3674.362410 Node 9: lnL = -3674.362410 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 871 Sequential format.. Reading seq # 1: YEL069C_Sbay Reading seq # 2: YEL069C_Scer Reading seq # 3: YEL069C_Skud Reading seq # 4: YEL069C_Smik Reading seq # 5: YEL069C_Spar Sequences read.. Counting patterns.. # site patterns = 416 Counting frequencies.. 120 bytes for distance 66560 bytes for lkl0 53248 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.068914 0.026262 0.070775 0.211833 0.085134 0.260917 0.344866 0.441433 lnL0 = -4263.237335 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4263.237335 x= 0.06891 0.02626 0.07078 0.21183 0.08513 0.26092 0.34487 0.44143 1 h-lim-p 0.0014 0.5569 249.2507 4257.148679 8 0.0002 41 | 0/8 2 h-lim-p 0.0014 0.0113 28.4309 4256.900084 4 0.0006 60 | 0/8 3 h-lim-p 0.0017 0.0408 10.6403 4256.866429 5 0.0007 81 | 0/8 4 h-lim-p 0.0015 0.0714 4.8225 4256.859400 2 0.0007 97 | 0/8 5 h-lim-p 0.0017 0.0837 2.1390 4256.858037 2 0.0007 113 | 0/8 6 h-lim-p 0.0053 0.7117 0.2901 4256.858009 0 0.0007 127 | 0/8 7 h-lim-p 0.0059 3.7514 0.0330 4256.858003 1 0.0029 150 | 0/8 8 h-lim-p 0.0354 20.0000 0.0027 4256.856230 0 0.4243 173 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4256.856216 1 0.9961 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4256.856216 0 1.0938 215 | 0/8 11 h-lim-p 1.1678 20.0000 0.0000 4256.856216 0 0.5839 235 | 0/8 12 h-lim-p 0.0301 20.0000 0.0003 4256.856216 0 0.0301 255 | 0/8 13 h-lim-p 0.0089 20.0000 0.0008 4256.856216 0 0.0000 284 | 0/8 14 h-lim-p 0.0010 20.0000 0.0000 4256.856216 0 0.0010 304 | 0/8 15 h-lim-p 0.0005 20.0000 0.0000 4256.856216 0 0.0000 339 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -4256.856216 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4256.856216 Node 7: lnL = -4256.856216 Node 8: lnL = -4256.856216 Node 9: lnL = -4256.856216 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 902 Sequential format.. Reading seq # 1: YEL071W_Sbay Reading seq # 2: YEL071W_Scer Reading seq # 3: YEL071W_Skud Reading seq # 4: YEL071W_Smik Reading seq # 5: YEL071W_Spar Sequences read.. Counting patterns.. # site patterns = 427 Counting frequencies.. 120 bytes for distance 68320 bytes for lkl0 54656 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.141950 0.176468 0.000060 0.252849 0.502822 0.362422 0.339108 0.643391 lnL0 = -4828.690108 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4828.690108 x= 0.14195 0.17647 0.00006 0.25285 0.50282 0.36242 0.33911 0.64339 1 h-lim-p 0.0000 0.0000 432.9739 4828.589703 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0009 409.7168 4802.095367 0 0.0005 39 | 1/8 3 h-lim-p 0.0004 0.0028 119.5788 4790.637914 m 0.0028 51 | 2/8 4 h-lim-p 0.0007 0.0053 86.8887 4765.954451 0 0.0027 65 | 2/8 5 h-lim-p 0.0008 0.0068 66.2769 4764.249700 3 0.0009 83 | 2/8 6 h-lim-p 0.0068 0.0721 8.3687 4764.008490 6 0.0029 109 | 1/8 7 h-lim-p 0.0004 0.0270 62.2519 4763.759262 7 0.0001 138 | 1/8 8 h-lim-p 0.0043 0.0829 2.0717 4745.117787 m 0.0829 152 | 2/8 9 h-lim-p 0.2437 1.9492 0.3857 4731.686120 0 0.9746 166 | 2/8 10 h-lim-p 1.4468 20.0000 0.2598 4725.869106 8 0.6186 199 | 2/8 11 h-lim-p 0.7434 5.9476 0.0743 4724.794350 2 0.6970 221 | 2/8 12 h-lim-p 1.6394 15.0885 0.0316 4724.542853 3 1.6650 245 | 2/8 13 h-lim-p 2.5000 20.0000 0.0017 4724.538438 5 1.4675 275 | 2/8 14 h-lim-p 2.5000 20.0000 0.0004 4724.538345 1 0.9961 295 | 2/8 15 h-lim-p 2.5000 20.0000 0.0001 4724.538344 0 1.2500 313 | 2/8 16 h-lim-p 2.5000 20.0000 0.0000 4724.538344 0 1.0938 331 | 2/8 17 h-lim-p 1.7153 20.0000 0.0000 4724.538344 0 0.8576 349 | 2/8 18 h-lim-p 0.4658 20.0000 0.0000 4724.538344 0 0.0582 369 | 2/8 19 h-lim-p 0.0148 20.0000 0.0000 4724.538344 0 0.0000 402 | 2/8 20 h-lim-p 0.0000 20.0000 0.0001 4724.538344 0 0.0000 423 | 2/8 21 h-lim-p 0.0000 20.0000 0.0000 4724.538344 0 0.0000 452 | 2/8 22 h-lim-p 0.0000 20.0000 0.0001 | 2/8 23 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -4724.538344 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4724.538344 Node 7: lnL = -4724.538344 Node 8: lnL = -4724.538344 Node 9: lnL = -4724.538344 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 851 Sequential format.. Reading seq # 1: YER001W_Sbay Reading seq # 2: YER001W_Scer Reading seq # 3: YER001W_Skud Reading seq # 4: YER001W_Smik Reading seq # 5: YER001W_Spar Sequences read.. Counting patterns.. # site patterns = 330 Counting frequencies.. 120 bytes for distance 52800 bytes for lkl0 42240 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.020218 0.081745 0.067696 0.115539 0.095804 0.269944 0.243574 0.330969 lnL0 = -3950.264336 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3950.264336 x= 0.02022 0.08174 0.06770 0.11554 0.09580 0.26994 0.24357 0.33097 1 h-lim-p 0.0053 0.9635 122.5398 3948.484786 5 0.0003 36 | 0/8 2 h-lim-p 0.0004 0.0034 35.1250 3948.245492 5 0.0004 59 | 0/8 3 h-lim-p 0.0007 0.0080 22.1246 3948.198551 4 0.0003 79 | 0/8 4 h-lim-p 0.0006 0.0132 8.8352 3948.185191 4 0.0004 101 | 0/8 5 h-lim-p 0.0093 1.1484 0.4031 3948.185146 0 0.0006 116 | 0/8 6 h-lim-p 0.0021 1.7689 0.1092 3948.185143 0 0.0005 137 | 0/8 7 h-lim-p 0.0019 5.5433 0.0265 3948.185136 0 0.0039 158 | 0/8 8 h-lim-p 0.0183 20.0000 0.0056 3948.183681 0 0.1461 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3948.183635 2 0.9961 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3948.183635 0 1.0938 225 | 0/8 11 h-lim-p 1.2756 20.0000 0.0000 3948.183635 0 5.1025 247 | 0/8 12 h-lim-p 0.4132 20.0000 0.0003 3948.183635 0 0.0000 291 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 3948.183635 0 0.0000 313 Out... lnL = -3948.183635 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3948.183635 Node 7: lnL = -3948.183635 Node 8: lnL = -3948.183635 Node 9: lnL = -3948.183635 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 935 Sequential format.. Reading seq # 1: YER002W_Sbay Reading seq # 2: YER002W_Scer Reading seq # 3: YER002W_Skud Reading seq # 4: YER002W_Smik Reading seq # 5: YER002W_Spar Sequences read.. Counting patterns.. # site patterns = 434 Counting frequencies.. 120 bytes for distance 69440 bytes for lkl0 55552 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.178812 0.134372 0.157285 0.355770 0.369761 0.508943 0.518466 lnL0 = -4999.951297 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4999.951297 x= 0.00006 0.17881 0.13437 0.15728 0.35577 0.36976 0.50894 0.51847 1 h-lim-p 0.0000 0.0000 183.1391 4999.806933 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0051 103.4713 4996.100031 0 0.0013 41 | 1/8 3 h-lim-p 0.0011 0.0091 27.2611 4995.864893 8 0.0007 76 | 1/8 4 h-lim-p 0.0017 0.1168 10.2908 4995.728341 0 0.0026 88 | 1/8 5 h-lim-p 0.0050 0.0539 5.3627 4995.596592 4 0.0039 108 | 1/8 6 h-lim-p 0.0091 0.1616 2.2994 4993.396070 0 0.0365 122 | 1/8 7 h-lim-p 0.0040 0.0318 14.4837 4984.968701 0 0.0080 135 | 1/8 8 h-lim-p 0.0051 0.0405 17.3573 4984.378170 8 0.0035 168 | 1/8 9 h-lim-p 0.9507 7.6052 0.0492 4983.767465 7 0.6778 195 | 0/8 10 h-lim-p 0.0676 6.6768 0.4934 4983.767144 3 0.0023 224 | 0/8 11 h-lim-p 0.1346 20.0000 0.0083 4983.751293 0 0.8073 246 | 0/8 12 h-lim-p 1.5075 12.0597 0.0015 4983.750107 4 0.9323 278 | 0/8 13 h-lim-p 2.5000 20.0000 0.0003 4983.750081 2 0.9644 302 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 4983.750081 0 1.0938 322 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 4983.750081 0 1.0938 342 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 4983.750081 0 1.8750 362 | 0/8 17 h-lim-p 2.1643 20.0000 0.0000 4983.750081 0 0.9469 382 | 0/8 18 h-lim-p 2.3718 20.0000 0.0000 4983.750081 0 0.0093 409 Out... lnL = -4983.750081 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4983.750081 Node 7: lnL = -4983.750081 Node 8: lnL = -4983.750081 Node 9: lnL = -4983.750081 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 243 Sequential format.. Reading seq # 1: YER007W_Sbay Reading seq # 2: YER007W_Scer Reading seq # 3: YER007W_Skud Reading seq # 4: YER007W_Smik Reading seq # 5: YER007W_Spar Sequences read.. Counting patterns.. # site patterns = 108 Counting frequencies.. 120 bytes for distance 17280 bytes for lkl0 13824 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.097360 0.081947 0.080399 0.191129 0.178710 0.151571 0.223379 lnL0 = -946.647423 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 946.647423 x= 0.00006 0.09736 0.08195 0.08040 0.19113 0.17871 0.15157 0.22338 1 h-lim-p 0.0000 0.0000 109.8176 946.585589 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0023 91.3317 944.175907 0 0.0006 40 | 1/8 3 h-lim-p 0.0007 0.0059 36.2607 943.811862 6 0.0007 67 | 1/8 4 h-lim-p 0.0076 0.0970 3.3964 943.783605 6 0.0024 93 | 1/8 5 h-lim-p 0.0045 0.0661 1.8596 943.650702 0 0.0089 106 | 1/8 6 h-lim-p 0.0058 0.1148 2.8638 940.938725 0 0.0348 120 | 0/8 7 h-lim-p 0.0014 0.0113 24.0950 940.216272 1 0.0018 134 | 0/8 8 h-lim-p 0.0010 0.0077 16.5326 940.010237 0 0.0019 147 | 0/8 9 h-lim-p 0.0040 0.0321 0.9407 939.906952 m 0.0321 159 | 0/8 10 h-lim-p -0.0000 -0.0000 10.3988 h-lim-p: -1.84559394e-20 -1.47647515e-19 1.03987945e+01 939.906952 .. | 0/8 11 h-lim-p 0.0000 0.1417 56.6256 939.158009 0 0.0006 193 | 0/8 12 h-lim-p 0.0015 0.0120 16.4546 939.017451 7 0.0011 219 | 0/8 13 h-lim-p 0.0009 0.0070 5.3757 939.003457 1 0.0011 233 | 0/8 14 h-lim-p 0.0057 0.2623 1.0327 939.002943 4 0.0010 256 | 0/8 15 h-lim-p 0.0035 0.9039 0.2851 939.002742 2 0.0033 272 | 0/8 16 h-lim-p 0.0067 0.1550 0.1388 939.002465 3 0.0056 298 | 0/8 17 h-lim-p 0.0150 1.0221 0.0522 938.974377 0 0.1197 321 | 0/8 18 h-lim-p 0.0062 0.1532 1.0080 938.973600 2 0.0015 346 | 0/8 19 h-lim-p 2.5000 20.0000 0.0006 938.973492 2 0.9961 362 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 938.973492 0 1.0938 382 | 0/8 21 h-lim-p 1.5559 20.0000 0.0000 938.973492 0 1.3614 402 | 0/8 22 h-lim-p 1.4949 20.0000 0.0000 938.973492 0 1.3081 422 | 0/8 23 h-lim-p 0.4111 20.0000 0.0000 938.973492 0 0.0016 449 | 0/8 24 h-lim-p 0.0002 20.0000 0.0003 938.973492 0 0.0001 470 | 0/8 25 h-lim-p 0.0001 20.0000 0.0003 938.973492 0 0.0001 490 | 0/8 26 h-lim-p 0.0001 20.0000 0.0006 938.973492 0 0.0000 527 | 0/8 27 h-lim-p 0.0000 20.0000 0.0000 938.973492 0 0.0000 548 | 0/8 28 h-lim-p 0.0000 20.0000 0.0000 938.973492 0 0.0000 581 | 0/8 29 h-lim-p 0.0000 20.0000 0.0000 | 0/8 30 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -938.973492 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -938.973492 Node 7: lnL = -938.973492 Node 8: lnL = -938.973492 Node 9: lnL = -938.973492 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 303 Sequential format.. Reading seq # 1: YER009W_Sbay Reading seq # 2: YER009W_Scer Reading seq # 3: YER009W_Skud Reading seq # 4: YER009W_Smik Reading seq # 5: YER009W_Spar Sequences read.. Counting patterns.. # site patterns = 133 Counting frequencies.. 120 bytes for distance 21280 bytes for lkl0 17024 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.019591 0.083504 0.006883 0.113411 0.078036 0.218269 0.132287 0.236487 lnL0 = -1255.491111 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1255.491111 x= 0.01959 0.08350 0.00688 0.11341 0.07804 0.21827 0.13229 0.23649 1 h-lim-p 0.0006 0.0046 138.2899 1254.412129 7 0.0001 36 | 0/8 2 h-lim-p 0.0005 0.0042 17.9841 1254.312348 1 0.0006 50 | 0/8 3 h-lim-p 0.0013 0.0125 8.8628 1254.296736 5 0.0005 74 | 0/8 4 h-lim-p 0.0024 0.1528 1.7497 1254.295576 4 0.0008 96 | 0/8 5 h-lim-p 0.0021 0.5647 0.6788 1254.295349 4 0.0011 117 | 0/8 6 h-lim-p 0.0069 0.2820 0.1108 1254.295344 1 0.0007 141 | 0/8 7 h-lim-p 0.0062 9.8569 0.0123 1254.295343 0 0.0027 161 | 0/8 8 h-lim-p 0.0141 20.0000 0.0024 1254.295086 0 0.2250 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1254.295074 2 1.5991 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1254.295074 0 1.0938 230 | 0/8 11 h-lim-p 1.5004 20.0000 0.0000 1254.295074 0 1.5004 250 | 0/8 12 h-lim-p 1.1733 20.0000 0.0000 1254.295074 0 0.0046 277 | 0/8 13 h-lim-p 0.0001 16.2104 0.0014 1254.295074 0 0.0000 305 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 1254.295074 0 0.0000 327 Out... lnL = -1254.295074 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1254.295074 Node 7: lnL = -1254.295074 Node 8: lnL = -1254.295074 Node 9: lnL = -1254.295074 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 875 Sequential format.. Reading seq # 1: YER010C_Sbay Reading seq # 2: YER010C_Scer Reading seq # 3: YER010C_Skud Reading seq # 4: YER010C_Smik Reading seq # 5: YER010C_Spar Sequences read.. Counting patterns.. # site patterns = 382 Counting frequencies.. 120 bytes for distance 61120 bytes for lkl0 48896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.087030 0.207507 0.240393 0.094073 0.348425 0.255997 0.396567 lnL0 = -4497.436720 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4497.436720 x= 0.00006 0.08703 0.20751 0.24039 0.09407 0.34842 0.25600 0.39657 1 h-lim-p 0.0000 0.0000 94.3926 4497.409159 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0054 67.3891 4496.678129 0 0.0005 39 | 1/8 3 h-lim-p 0.0013 0.0165 25.4508 4496.574905 7 0.0004 70 | 1/8 4 h-lim-p 0.0024 0.0808 4.0267 4496.565752 4 0.0009 90 | 1/8 5 h-lim-p 0.0032 0.3793 1.1674 4496.550896 0 0.0049 102 | 1/8 6 h-lim-p 0.0194 3.3435 0.2925 4494.770293 0 0.1551 117 | 1/8 7 h-lim-p 0.0020 0.0269 23.0032 4494.493707 5 0.0009 145 | 1/8 8 h-lim-p 0.0045 0.1146 4.3640 4494.483822 2 0.0011 162 | 1/8 9 h-lim-p 1.0262 20.0000 0.0045 4494.474132 4 0.8636 183 | 1/8 10 h-lim-p 2.5000 20.0000 0.0001 4494.474115 0 1.0938 202 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 4494.474114 0 1.2500 221 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 4494.474114 0 1.0938 240 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 4494.474114 0 1.0938 259 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 4494.474114 m20.0000 278 | 1/8 15 h-lim-p 1.0584 20.0000 0.0000 4494.474114 0 0.2646 298 | 1/8 16 h-lim-p 0.3598 20.0000 0.0000 4494.474114 0 0.1799 317 | 1/8 17 h-lim-p 0.2194 20.0000 0.0000 4494.474114 0 0.0000 354 Out... lnL = -4494.474114 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4494.474114 Node 7: lnL = -4494.474114 Node 8: lnL = -4494.474114 Node 9: lnL = -4494.474114 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 857 Sequential format.. Reading seq # 1: YER011W_Sbay Reading seq # 2: YER011W_Scer Reading seq # 3: YER011W_Skud Reading seq # 4: YER011W_Smik Reading seq # 5: YER011W_Spar Sequences read.. Counting patterns.. # site patterns = 211 Counting frequencies.. 120 bytes for distance 33760 bytes for lkl0 27008 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.027834 0.034103 0.054232 0.043083 0.050204 0.097859 0.150705 0.188221 lnL0 = -3172.866707 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3172.866707 x= 0.02783 0.03410 0.05423 0.04308 0.05020 0.09786 0.15071 0.18822 1 h-lim-p 0.0007 0.0057 171.5458 3171.617005 4 0.0001 32 | 0/8 2 h-lim-p 0.0008 0.0095 19.5592 3171.581655 2 0.0002 49 | 0/8 3 h-lim-p 0.0003 0.0167 13.9407 3171.575487 5 0.0001 73 | 0/8 4 h-lim-p 0.0003 0.0553 3.7050 3171.574590 2 0.0001 89 | 0/8 5 h-lim-p 0.0005 0.0741 1.1279 3171.574480 2 0.0002 105 | 0/8 6 h-lim-p 0.0006 0.2076 0.3549 3171.574476 1 0.0001 121 | 0/8 7 h-lim-p 0.0245 20.0000 0.0011 3171.574476 0 0.0054 142 | 0/8 8 h-lim-p 0.0012 10.7318 0.0049 3171.574457 0 0.0373 167 | 0/8 9 h-lim-p 1.4555 20.0000 0.0001 3171.574457 0 1.2735 187 | 0/8 10 h-lim-p 2.2533 20.0000 0.0001 3171.574457 0 0.9858 207 | 0/8 11 h-lim-p 1.6020 20.0000 0.0000 3171.574457 0 0.0031 235 | 0/8 12 h-lim-p 0.0003 20.0000 0.0004 3171.574457 0 0.0000 258 | 0/8 13 h-lim-p 0.0000 20.0000 0.0003 3171.574457 0 0.0000 280 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 3171.574457 0 0.0000 314 | 0/8 15 h-lim-p 0.0000 20.0000 0.0027 | 0/8 16 h-lim-p 0.0000 20.0000 0.0027 Out... lnL = -3171.574457 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3171.574457 Node 7: lnL = -3171.574457 Node 8: lnL = -3171.574457 Node 9: lnL = -3171.574457 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 879 Sequential format.. Reading seq # 1: YER012W_Sbay Reading seq # 2: YER012W_Scer Reading seq # 3: YER012W_Skud Reading seq # 4: YER012W_Smik Reading seq # 5: YER012W_Spar Sequences read.. Counting patterns.. # site patterns = 366 Counting frequencies.. 120 bytes for distance 58560 bytes for lkl0 46848 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.116763 0.135724 0.191952 0.087927 0.261140 0.251289 0.323774 lnL0 = -4220.849920 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4220.849920 x= 0.00006 0.11676 0.13572 0.19195 0.08793 0.26114 0.25129 0.32377 1 h-lim-p 0.0000 0.0000 199.4604 4220.782340 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0026 132.2777 4218.337720 0 0.0003 39 | 1/8 3 h-lim-p 0.0007 0.0053 48.9540 4217.930112 7 0.0004 70 | 1/8 4 h-lim-p 0.0012 0.0208 15.7624 4217.869322 5 0.0005 95 | 1/8 5 h-lim-p 0.0031 0.1626 2.7253 4217.851014 5 0.0020 119 | 1/8 6 h-lim-p 0.0055 0.2543 0.9689 4217.607384 0 0.0165 132 | 1/8 7 h-lim-p 0.0025 0.1110 6.3837 4212.708052 0 0.0100 153 | 1/8 8 h-lim-p 0.0010 0.0084 38.8296 4211.735296 2 0.0010 169 | 1/8 9 h-lim-p 2.5000 20.0000 0.0078 4211.648137 3 1.1328 187 | 1/8 10 h-lim-p 2.5000 20.0000 0.0023 4211.642358 2 1.0889 210 | 0/8 11 h-lim-p 0.0988 20.0000 0.0255 4211.642357 0 0.0027 233 | 0/8 12 h-lim-p 0.1326 1.0612 0.0004 4211.642238 m 1.0612 253 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 4211.642236 0 1.0938 273 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 4211.642236 0 1.0938 292 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 4211.642236 0 1.0938 311 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 4211.642236 0 1.2500 330 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 4211.642236 0 0.0098 356 Out... lnL = -4211.642236 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4211.642236 Node 7: lnL = -4211.642236 Node 8: lnL = -4211.642236 Node 9: lnL = -4211.642236 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 481 Sequential format.. Reading seq # 1: YER013W_Sbay Reading seq # 2: YER013W_Scer Reading seq # 3: YER013W_Skud Reading seq # 4: YER013W_Smik Reading seq # 5: YER013W_Spar Sequences read.. Counting patterns.. # site patterns = 203 Counting frequencies.. 120 bytes for distance 32480 bytes for lkl0 25984 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.006453 0.161837 0.026220 0.154039 0.094149 0.210712 0.261133 0.313604 lnL0 = -2232.166852 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2232.166852 x= 0.00645 0.16184 0.02622 0.15404 0.09415 0.21071 0.26113 0.31360 1 h-lim-p 0.0008 0.0066 101.5810 2230.861313 8 0.0003 40 | 0/8 2 h-lim-p 0.0008 0.0067 29.4655 2230.591138 6 0.0007 65 | 0/8 3 h-lim-p 0.0011 0.0087 9.3740 2230.555805 3 0.0009 83 | 0/8 4 h-lim-p 0.0018 0.0148 4.8739 2230.550844 6 0.0005 111 | 0/8 5 h-lim-p 0.0028 0.3046 0.9105 2230.550419 3 0.0011 129 | 0/8 6 h-lim-p 0.0045 3.6075 0.2157 2230.550402 2 0.0007 155 | 0/8 7 h-lim-p 0.0100 7.3765 0.0155 2230.550396 2 0.0064 180 | 0/8 8 h-lim-p 0.0249 12.3336 0.0040 2230.549673 0 0.1994 203 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2230.549651 1 0.9961 225 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2230.549650 0 1.0938 245 | 0/8 11 h-lim-p 1.2876 20.0000 0.0000 2230.549650 0 1.2876 265 | 0/8 12 h-lim-p 0.5229 20.0000 0.0000 2230.549650 0 0.1144 286 | 0/8 13 h-lim-p 0.0105 20.0000 0.0004 2230.549650 0 0.0000 314 | 0/8 14 h-lim-p 0.0002 20.0000 0.0001 2230.549650 0 0.0003 335 | 0/8 15 h-lim-p 0.0003 20.0000 0.0001 2230.549650 0 0.0000 367 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -2230.549650 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2230.549650 Node 7: lnL = -2230.549650 Node 8: lnL = -2230.549650 Node 9: lnL = -2230.549650 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 351 Sequential format.. Reading seq # 1: YER015W_Sbay Reading seq # 2: YER015W_Scer Reading seq # 3: YER015W_Skud Reading seq # 4: YER015W_Smik Reading seq # 5: YER015W_Spar Sequences read.. Counting patterns.. # site patterns = 125 Counting frequencies.. 120 bytes for distance 20000 bytes for lkl0 16000 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.017816 0.043154 0.032029 0.098275 0.073288 0.142467 0.196145 0.217106 lnL0 = -1407.391671 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1407.391671 x= 0.01782 0.04315 0.03203 0.09827 0.07329 0.14247 0.19615 0.21711 1 h-lim-p 0.0031 0.0286 95.0720 1406.478191 9 0.0002 48 | 0/8 2 h-lim-p 0.0008 0.0066 17.7157 1406.418042 2 0.0004 64 | 0/8 3 h-lim-p 0.0018 0.0525 3.8594 1406.413143 4 0.0007 84 | 0/8 4 h-lim-p 0.0020 0.0913 1.3448 1406.412720 3 0.0005 103 | 0/8 5 h-lim-p 0.0012 0.4134 0.5944 1406.412633 1 0.0006 117 | 0/8 6 h-lim-p 0.0027 0.7767 0.1274 1406.412630 2 0.0004 143 | 0/8 7 h-lim-p 0.0047 2.9760 0.0119 1406.412630 0 0.0010 164 | 0/8 8 h-lim-p 0.0695 20.0000 0.0002 1406.412607 0 0.8341 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1406.412607 0 1.0938 207 | 0/8 10 h-lim-p 1.1430 20.0000 0.0000 1406.412607 0 1.0001 227 | 0/8 11 h-lim-p 1.0274 20.0000 0.0000 1406.412607 0 0.0005 257 | 0/8 12 h-lim-p 0.0002 20.0000 0.0001 1406.412607 0 0.0002 277 | 0/8 13 h-lim-p 0.0001 20.0000 0.0002 1406.412607 0 0.0000 305 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 1406.412607 0 0.0000 336 Out... lnL = -1406.412607 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1406.412607 Node 7: lnL = -1406.412607 Node 8: lnL = -1406.412607 Node 9: lnL = -1406.412607 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 898 Sequential format.. Reading seq # 1: YER016W_Sbay Reading seq # 2: YER016W_Scer Reading seq # 3: YER016W_Skud Reading seq # 4: YER016W_Smik Reading seq # 5: YER016W_Spar Sequences read.. Counting patterns.. # site patterns = 475 Counting frequencies.. 120 bytes for distance 76000 bytes for lkl0 60800 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.124117 0.062375 0.469580 0.718217 0.360761 0.351190 0.594290 lnL0 = -5013.769464 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 5013.769464 x= 0.00006 0.12412 0.06238 0.46958 0.71822 0.36076 0.35119 0.59429 1 h-lim-p 0.0000 0.0000 280.1355 5013.701869 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0005 349.1573 4987.366134 m 0.0005 37 | 2/8 3 h-lim-p 0.0012 0.0098 85.8973 4956.841186 0 0.0037 50 | 2/8 4 h-lim-p 0.0006 0.0050 66.7085 4953.294616 0 0.0012 63 | 2/8 5 h-lim-p 0.0083 0.0738 9.9876 4953.214759 6 0.0014 91 | 2/8 6 h-lim-p 0.0030 0.1926 4.8025 4953.159708 5 0.0029 115 | 2/8 7 h-lim-p 0.0026 0.6148 5.4441 4953.024274 0 0.0051 128 | 2/8 8 h-lim-p 0.0214 0.5960 1.3084 4948.527937 0 0.0857 142 | 2/8 9 h-lim-p 2.5000 20.0000 0.0299 4948.399053 2 1.1719 158 | 1/8 10 h-lim-p 0.0129 0.6095 2.7053 4948.396389 2 0.0014 182 | 1/8 11 h-lim-p 2.5000 20.0000 0.0006 4948.396208 2 1.0938 198 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 4948.396207 0 1.0938 217 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 4948.396207 0 1.0938 236 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 4948.396207 0 1.0938 255 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 4948.396207 0 2.1875 274 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 4948.396207 0 0.0012 303 Out... lnL = -4948.396207 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4948.396207 Node 7: lnL = -4948.396207 Node 8: lnL = -4948.396207 Node 9: lnL = -4948.396207 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 218 Sequential format.. Reading seq # 1: YER018C_Sbay Reading seq # 2: YER018C_Scer Reading seq # 3: YER018C_Skud Reading seq # 4: YER018C_Smik Reading seq # 5: YER018C_Spar Sequences read.. Counting patterns.. # site patterns = 92 Counting frequencies.. 120 bytes for distance 14720 bytes for lkl0 11776 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.083224 0.000060 0.082753 0.116797 0.050279 0.159123 0.167450 0.294807 lnL0 = -778.125442 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 778.125442 x= 0.08322 0.00006 0.08275 0.11680 0.05028 0.15912 0.16745 0.29481 1 h-lim-p 0.0000 0.0000 78.2691 778.112828 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0016 78.0165 777.343663 0 0.0005 39 | 1/8 3 h-lim-p 0.0030 0.0680 12.5895 777.224887 5 0.0016 62 | 1/8 4 h-lim-p 0.0134 0.1074 1.3466 777.210825 7 0.0038 91 | 1/8 5 h-lim-p 0.0032 0.1594 1.6235 776.992847 0 0.0190 105 | 1/8 6 h-lim-p 0.0038 0.0301 4.6326 775.546195 0 0.0150 119 | 1/8 7 h-lim-p 0.0038 0.0306 4.6683 775.530786 7 0.0013 149 | 1/8 8 h-lim-p 0.2359 18.2299 0.0261 775.254661 0 0.7078 162 | 1/8 9 h-lim-p 2.5000 20.0000 0.0059 775.235945 3 1.1328 187 | 1/8 10 h-lim-p 2.5000 20.0000 0.0024 775.233463 3 1.1328 212 | 1/8 11 h-lim-p 2.5000 20.0000 0.0003 775.233429 3 0.9482 237 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 775.233428 0 1.0938 256 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 775.233428 0 1.2500 275 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 775.233428 0 1.0938 294 | 1/8 15 h-lim-p 1.2397 20.0000 0.0000 775.233428 0 9.9175 316 | 1/8 16 h-lim-p 1.6427 20.0000 0.0000 775.233428 0 0.0000 354 | 1/8 17 h-lim-p 0.0000 20.0000 0.0000 775.233428 0 0.0000 386 Out... lnL = -775.233428 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -775.233428 Node 7: lnL = -775.233428 Node 8: lnL = -775.233428 Node 9: lnL = -775.233428 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 697 Sequential format.. Reading seq # 1: YER019C-A_Sbay Reading seq # 2: YER019C-A_Scer Reading seq # 3: YER019C-A_Skud Reading seq # 4: YER019C-A_Smik Reading seq # 5: YER019C-A_Spar Sequences read.. Counting patterns.. # site patterns = 256 Counting frequencies.. 120 bytes for distance 40960 bytes for lkl0 32768 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.021623 0.082655 0.046215 0.118192 0.113978 0.199907 0.217403 0.289740 lnL0 = -3090.993728 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3090.993728 x= 0.02162 0.08266 0.04621 0.11819 0.11398 0.19991 0.21740 0.28974 1 h-lim-p 0.0021 0.1153 170.8174 3088.685753 8 0.0002 43 | 0/8 2 h-lim-p 0.0011 0.0094 26.4464 3088.537145 6 0.0004 67 | 0/8 3 h-lim-p 0.0011 0.0247 10.5912 3088.521977 6 0.0003 95 | 0/8 4 h-lim-p 0.0017 0.0436 1.9475 3088.521197 2 0.0004 112 | 0/8 5 h-lim-p 0.0020 0.7163 0.4293 3088.521136 3 0.0007 132 | 0/8 6 h-lim-p 0.0084 7.0982 0.0366 3088.521135 0 0.0005 155 | 0/8 7 h-lim-p 0.0021 20.0000 0.0092 3088.521135 0 0.0018 175 | 0/8 8 h-lim-p 0.0447 20.0000 0.0004 3088.521065 0 0.5363 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3088.521063 0 1.0938 218 | 0/8 10 h-lim-p 1.8505 20.0000 0.0000 3088.521063 0 0.9252 238 | 0/8 11 h-lim-p 0.8187 20.0000 0.0000 3088.521063 0 0.0256 262 | 0/8 12 h-lim-p 0.0039 20.0000 0.0002 3088.521063 0 0.0000 290 | 0/8 13 h-lim-p 0.0002 20.0000 0.0000 3088.521063 0 0.0002 310 Out... lnL = -3088.521063 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3088.521063 Node 7: lnL = -3088.521063 Node 8: lnL = -3088.521063 Node 9: lnL = -3088.521063 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 295 Sequential format.. Reading seq # 1: YER019W_Sbay Reading seq # 2: YER019W_Scer Reading seq # 3: YER019W_Skud Reading seq # 4: YER019W_Smik Reading seq # 5: YER019W_Spar Sequences read.. Counting patterns.. # site patterns = 145 Counting frequencies.. 120 bytes for distance 23200 bytes for lkl0 18560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.101302 0.023129 0.000060 0.045290 0.097019 0.239362 0.193579 0.342786 lnL0 = -1192.650382 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1192.650382 x= 0.10130 0.02313 0.00006 0.04529 0.09702 0.23936 0.19358 0.34279 1 h-lim-p 0.0003 0.0052 270.4832 1186.462271 10 0.0002 46 | 0/8 2 h-lim-p 0.0002 0.0017 68.0107 1184.816278 0 0.0009 60 | 0/8 3 h-lim-p 0.0028 0.0228 13.2874 1184.702096 2 0.0013 76 | 0/8 4 h-lim-p 0.0037 0.0299 4.2210 1184.695646 3 0.0008 95 | 0/8 5 h-lim-p 0.0034 0.2309 0.9757 1184.694554 5 0.0019 120 | 0/8 6 h-lim-p 0.0048 0.4626 0.3792 1184.693875 5 0.0030 154 | 0/8 7 h-lim-p 0.0039 0.6052 0.2896 1184.680004 0 0.0311 177 | 0/8 8 h-lim-p 0.0106 0.2772 0.8484 1184.598482 1 0.0133 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0027 1184.586571 6 1.8541 233 | 0/8 10 h-lim-p 2.5000 20.0000 0.0012 1184.584972 6 1.3762 267 | 0/8 11 h-lim-p 2.5000 20.0000 0.0001 1184.584969 0 1.0938 287 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1184.584969 0 1.0938 307 | 0/8 13 h-lim-p 1.3909 20.0000 0.0000 1184.584969 0 0.3042 328 | 0/8 14 h-lim-p 0.1148 20.0000 0.0000 1184.584969 0 0.0018 353 | 0/8 15 h-lim-p 0.0009 20.0000 0.0000 1184.584969 0 0.0005 373 | 0/8 16 h-lim-p 0.0005 20.0000 0.0000 1184.584969 0 0.0000 408 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1184.584969 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1184.584969 Node 7: lnL = -1184.584969 Node 8: lnL = -1184.584969 Node 9: lnL = -1184.584969 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 696 Sequential format.. Reading seq # 1: YER020W_Sbay Reading seq # 2: YER020W_Scer Reading seq # 3: YER020W_Skud Reading seq # 4: YER020W_Smik Reading seq # 5: YER020W_Spar Sequences read.. Counting patterns.. # site patterns = 257 Counting frequencies.. 120 bytes for distance 41120 bytes for lkl0 32896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.021846 0.085636 0.046924 0.117106 0.115063 0.203250 0.234596 0.297987 lnL0 = -3112.799066 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3112.799066 x= 0.02185 0.08564 0.04692 0.11711 0.11506 0.20325 0.23460 0.29799 1 h-lim-p 0.0026 0.0205 155.7826 3110.786483 7 0.0002 42 | 0/8 2 h-lim-p 0.0011 0.0090 27.1244 3110.625072 5 0.0004 65 | 0/8 3 h-lim-p 0.0010 0.0208 12.5011 3110.604676 4 0.0003 87 | 0/8 4 h-lim-p 0.0018 0.0606 2.1472 3110.603652 4 0.0005 108 | 0/8 5 h-lim-p 0.0015 0.4259 0.6799 3110.603516 2 0.0006 124 | 0/8 6 h-lim-p 0.0029 1.8220 0.1513 3110.603512 1 0.0004 148 | 0/8 7 h-lim-p 0.0087 6.8417 0.0061 3110.603512 0 0.0038 168 | 0/8 8 h-lim-p 0.0257 20.0000 0.0009 3110.603414 0 0.2052 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3110.603409 0 1.0938 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3110.603409 0 1.0938 231 | 0/8 11 h-lim-p 1.1164 20.0000 0.0000 3110.603409 0 0.2791 252 | 0/8 12 h-lim-p 0.0630 20.0000 0.0001 3110.603409 0 0.0009 277 | 0/8 13 h-lim-p 0.0003 20.0000 0.0002 3110.603409 0 0.0000 312 | 0/8 14 h-lim-p 0.0000 20.0000 0.0010 | 0/8 15 h-lim-p 0.0000 20.0000 0.0010 Out... lnL = -3110.603409 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3110.603409 Node 7: lnL = -3110.603409 Node 8: lnL = -3110.603409 Node 9: lnL = -3110.603409 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 447 Sequential format.. Reading seq # 1: YER021W_Sbay Reading seq # 2: YER021W_Scer Reading seq # 3: YER021W_Skud Reading seq # 4: YER021W_Smik Reading seq # 5: YER021W_Spar Sequences read.. Counting patterns.. # site patterns = 177 Counting frequencies.. 120 bytes for distance 28320 bytes for lkl0 22656 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.069650 0.022480 0.059250 0.079462 0.096339 0.136810 0.232654 0.304811 lnL0 = -1833.200975 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1833.200975 x= 0.06965 0.02248 0.05925 0.07946 0.09634 0.13681 0.23265 0.30481 1 h-lim-p 0.0039 0.0389 96.4994 1831.952448 7 0.0003 41 | 0/8 2 h-lim-p 0.0010 0.0082 16.7505 1831.878218 5 0.0005 64 | 0/8 3 h-lim-p 0.0009 0.0314 10.4567 1831.859164 5 0.0005 87 | 0/8 4 h-lim-p 0.0013 0.0499 3.5720 1831.856406 4 0.0005 107 | 0/8 5 h-lim-p 0.0015 0.1796 1.2296 1831.855939 2 0.0007 123 | 0/8 6 h-lim-p 0.0029 0.8388 0.2961 1831.855911 1 0.0007 138 | 0/8 7 h-lim-p 0.0014 1.1940 0.1496 1831.855903 2 0.0009 164 | 0/8 8 h-lim-p 0.7066 20.0000 0.0002 1831.855835 0 1.4133 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1831.855834 0 1.0938 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1831.855834 0 1.0938 225 | 0/8 11 h-lim-p 1.1936 20.0000 0.0000 1831.855834 0 1.7905 245 | 0/8 12 h-lim-p 1.2048 20.0000 0.0000 1831.855834 0 0.9036 265 | 0/8 13 h-lim-p 0.0228 20.0000 0.0005 1831.855834 0 0.0000 306 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 1831.855834 0 0.0000 328 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 1831.855834 0 0.0000 387 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 1831.855834 0 0.0000 421 | 0/8 18 h-lim-p 0.0000 20.0000 0.0003 1831.855834 0 0.0000 447 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 20 h-lim-p 0.0000 20.0000 0.0003 | 0/8 21 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -1831.855834 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1831.855834 Node 7: lnL = -1831.855834 Node 8: lnL = -1831.855834 Node 9: lnL = -1831.855834 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 247 Sequential format.. Reading seq # 1: YER023W_Sbay Reading seq # 2: YER023W_Scer Reading seq # 3: YER023W_Skud Reading seq # 4: YER023W_Smik Reading seq # 5: YER023W_Spar Sequences read.. Counting patterns.. # site patterns = 117 Counting frequencies.. 120 bytes for distance 18720 bytes for lkl0 14976 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.154199 0.088277 0.237113 0.020494 0.247432 0.199263 0.269955 lnL0 = -995.775316 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 995.775316 x= 0.00006 0.15420 0.08828 0.23711 0.02049 0.24743 0.19926 0.26995 1 h-lim-p 0.0000 0.0000 78.5143 995.689000 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0104 22.5940 995.254728 0 0.0016 39 | 1/8 3 h-lim-p 0.0048 0.0555 7.5434 995.215265 6 0.0015 65 | 1/8 4 h-lim-p 0.0092 0.1636 1.2482 995.209878 5 0.0037 89 | 1/8 5 h-lim-p 0.0112 0.5565 0.4169 995.169096 0 0.0335 102 | 1/8 6 h-lim-p 0.0138 0.3688 1.0107 994.480310 0 0.0414 122 | 1/8 7 h-lim-p 0.0043 0.0357 9.7137 994.202815 6 0.0037 148 | 1/8 8 h-lim-p 0.0256 0.2546 1.3930 994.199778 2 0.0030 166 | 1/8 9 h-lim-p 0.5609 20.0000 0.0075 994.177615 0 1.1218 179 | 1/8 10 h-lim-p 2.5000 20.0000 0.0020 994.175112 4 1.3159 207 | 0/8 11 h-lim-p 0.0299 20.0000 0.0895 994.175101 2 0.0024 233 | 0/8 12 h-lim-p 0.4009 6.7461 0.0005 994.175026 0 1.2027 254 | 0/8 13 h-lim-p 0.4203 3.3625 0.0001 994.175025 0 0.8406 275 | 0/8 14 h-lim-p 0.0902 0.7217 0.0003 994.175025 0 0.0395 295 | 0/8 15 h-lim-p 0.0039 0.0716 0.0026 994.175025 0 0.0034 315 | 0/8 16 h-lim-p 0.0972 20.0000 0.0001 994.175024 0 0.1945 336 | 0/8 17 h-lim-p 0.3669 4.0843 0.0000 994.175024 0 0.0000 372 | 0/8 18 h-lim-p 0.0000 0.7185 0.0002 994.175024 0 0.0000 397 | 0/8 19 h-lim-p 0.0000 0.2774 0.0006 .. | 0/8 20 h-lim-p 0.0000 0.0106 0.0206 994.175024 0 0.0026 458 | 0/8 21 h-lim-p 0.0001 0.0005 0.2527 .. | 0/8 22 h-lim-p 0.0000 0.0051 0.0238 994.175024 0 0.0002 518 | 0/8 23 h-lim-p 0.0000 0.0007 0.1506 .. | 0/8 24 h-lim-p 0.0000 0.0049 0.0227 | 0/8 25 h-lim-p 0.0000 0.0049 0.0227 Out... lnL = -994.175024 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -994.175024 Node 7: lnL = -994.175024 Node 8: lnL = -994.175024 Node 9: lnL = -994.175024 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 265 Sequential format.. Reading seq # 1: YER024W_Sbay Reading seq # 2: YER024W_Scer Reading seq # 3: YER024W_Skud Reading seq # 4: YER024W_Smik Reading seq # 5: YER024W_Spar Sequences read.. Counting patterns.. # site patterns = 113 Counting frequencies.. 120 bytes for distance 18080 bytes for lkl0 14464 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.006712 0.134263 0.095274 0.089778 0.045682 0.085690 0.118797 0.209976 lnL0 = -1072.388761 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1072.388761 x= 0.00671 0.13426 0.09527 0.08978 0.04568 0.08569 0.11880 0.20998 1 h-lim-p 0.0052 0.0413 45.7400 1071.866884 6 0.0005 37 | 0/8 2 h-lim-p 0.0006 0.0047 25.4959 1071.731096 5 0.0005 58 | 0/8 3 h-lim-p 0.0015 0.0123 8.0966 1071.711434 5 0.0007 79 | 0/8 4 h-lim-p 0.0021 0.0372 2.5745 1071.708979 4 0.0008 99 | 0/8 5 h-lim-p 0.0062 1.0373 0.3479 1071.708940 1 0.0006 115 | 0/8 6 h-lim-p 0.0030 2.8797 0.0707 1071.708938 1 0.0007 138 | 0/8 7 h-lim-p 0.0046 5.7412 0.0114 1071.708936 0 0.0040 158 | 0/8 8 h-lim-p 0.0105 20.0000 0.0044 1071.708588 0 0.1676 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1071.708587 0 1.0938 202 | 0/8 10 h-lim-p 1.6023 20.0000 0.0000 1071.708587 0 1.4020 222 | 0/8 11 h-lim-p 2.2985 20.0000 0.0000 1071.708587 0 2.0112 242 | 0/8 12 h-lim-p 2.0048 20.0000 0.0000 1071.708587 0 0.8771 262 | 0/8 13 h-lim-p 0.3317 20.0000 0.0000 1071.708587 0 0.0000 299 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 1071.708587 0 0.0000 322 Out... lnL = -1071.708587 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1071.708587 Node 7: lnL = -1071.708587 Node 8: lnL = -1071.708587 Node 9: lnL = -1071.708587 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 296 Sequential format.. Reading seq # 1: YER025W_Sbay Reading seq # 2: YER025W_Scer Reading seq # 3: YER025W_Skud Reading seq # 4: YER025W_Smik Reading seq # 5: YER025W_Spar Sequences read.. Counting patterns.. # site patterns = 107 Counting frequencies.. 120 bytes for distance 17120 bytes for lkl0 13696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.029570 0.019391 0.071928 0.063187 0.033721 0.106956 0.131075 0.184292 lnL0 = -1077.543827 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1077.543827 x= 0.02957 0.01939 0.07193 0.06319 0.03372 0.10696 0.13108 0.18429 1 h-lim-p 0.0005 0.0042 56.6169 1077.199092 6 0.0002 33 | 0/8 2 h-lim-p 0.0011 0.0149 11.7050 1077.181940 2 0.0003 50 | 0/8 3 h-lim-p 0.0004 0.0097 8.0592 1077.174671 6 0.0003 73 | 0/8 4 h-lim-p 0.0011 0.0835 2.2896 1077.173638 3 0.0005 91 | 0/8 5 h-lim-p 0.0012 0.1325 0.8926 1077.173499 3 0.0004 110 | 0/8 6 h-lim-p 0.0017 0.3373 0.2139 1077.173485 2 0.0007 134 | 0/8 7 h-lim-p 0.0206 16.8392 0.0068 1077.173485 0 0.0011 157 | 0/8 8 h-lim-p 0.0950 20.0000 0.0001 1077.173476 0 0.7599 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1077.173476 0 1.0938 200 | 0/8 10 h-lim-p 1.7805 20.0000 0.0000 1077.173476 0 0.7790 220 | 0/8 11 h-lim-p 0.5295 20.0000 0.0000 1077.173476 0 0.0004 250 | 0/8 12 h-lim-p 0.0001 20.0000 0.0001 1077.173476 0 0.0000 286 | 0/8 13 h-lim-p 0.0000 20.0000 0.0009 1077.173476 0 0.0000 321 | 0/8 14 h-lim-p 0.0000 20.0000 0.0009 1077.173476 0 0.0000 343 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0009 1077.173476 0 0.0000 396 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 1077.173476 0 0.0000 432 | 0/8 18 h-lim-p 0.0000 20.0000 0.0009 1077.173476 0 0.0000 467 | 0/8 19 h-lim-p 0.0000 20.0000 0.0009 | 0/8 20 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -1077.173476 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1077.173476 Node 7: lnL = -1077.173476 Node 8: lnL = -1077.173476 Node 9: lnL = -1077.173476 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 518 Sequential format.. Reading seq # 1: YER027C_Sbay Reading seq # 2: YER027C_Scer Reading seq # 3: YER027C_Skud Reading seq # 4: YER027C_Smik Reading seq # 5: YER027C_Spar Sequences read.. Counting patterns.. # site patterns = 216 Counting frequencies.. 120 bytes for distance 34560 bytes for lkl0 27648 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.004860 0.040717 0.096591 0.162420 0.093892 0.189173 0.275168 0.277656 lnL0 = -2330.207391 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2330.207391 x= 0.00486 0.04072 0.09659 0.16242 0.09389 0.18917 0.27517 0.27766 1 h-lim-p 0.0042 0.0339 100.2359 2328.724275 7 0.0003 43 | 0/8 2 h-lim-p 0.0001 0.0007 22.4210 2328.589008 m 0.0007 55 | 0/8 3 h-lim-p -0.0000 -0.0000 7.9712 h-lim-p: -4.73916932e-21 -3.79133546e-20 7.97118891e+00 2328.589008 .. | 0/8 4 h-lim-p 0.0000 0.2783 9.9838 2328.574069 0 0.0003 80 | 0/8 5 h-lim-p 0.0023 0.0996 1.3669 2328.573449 5 0.0007 105 | 0/8 6 h-lim-p 0.0021 1.1710 0.4403 2328.573395 3 0.0006 125 | 0/8 7 h-lim-p 0.0011 0.0086 0.1913 2328.573382 2 0.0008 149 | 0/8 8 h-lim-p 0.0018 0.0142 0.0464 2328.573382 0 0.0008 169 | 0/8 9 h-lim-p 0.0025 0.0260 0.0146 2328.573382 0 0.0037 189 | 0/8 10 h-lim-p 0.0000 0.0001 2.3502 2328.573382 0 0.0000 209 | 0/8 11 h-lim-p 0.0016 12.5129 0.0119 2328.573381 0 0.0016 221 | 0/8 12 h-lim-p 0.0277 0.7473 0.0007 2328.573338 0 0.2213 244 | 0/8 13 h-lim-p 0.5365 4.2921 0.0001 2328.573336 0 0.8048 264 | 0/8 14 h-lim-p 1.0760 8.6077 0.0000 2328.573336 0 0.9415 284 | 0/8 15 h-lim-p 0.2951 2.3610 0.0001 2328.573336 0 0.0000 319 | 0/8 16 h-lim-p 0.0000 0.5351 0.0003 2328.573336 0 0.0000 349 | 0/8 17 h-lim-p 0.0000 0.0017 0.0724 2328.573336 0 0.0003 374 | 0/8 18 h-lim-p 0.0001 0.0008 0.1003 2328.573336 0 0.0000 411 | 0/8 19 h-lim-p 0.0000 0.0003 0.2993 2328.573336 0 0.0000 442 | 0/8 20 h-lim-p 0.0000 0.0008 0.1452 .. | 0/8 21 h-lim-p 0.0000 0.0016 0.0511 2328.573336 0 0.0000 508 | 0/8 22 h-lim-p 0.0000 0.0002 0.4584 .. | 0/8 23 h-lim-p 0.0000 0.0016 0.0511 | 0/8 24 h-lim-p 0.0000 0.0016 0.0511 Out... lnL = -2328.573336 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2328.573336 Node 7: lnL = -2328.573336 Node 8: lnL = -2328.573336 Node 9: lnL = -2328.573336 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 787 Sequential format.. Reading seq # 1: YER028C_Sbay Reading seq # 2: YER028C_Scer Reading seq # 3: YER028C_Skud Reading seq # 4: YER028C_Smik Reading seq # 5: YER028C_Spar Sequences read.. Counting patterns.. # site patterns = 287 Counting frequencies.. 120 bytes for distance 45920 bytes for lkl0 36736 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.045977 0.027506 0.074472 0.098636 0.082137 0.216221 0.236056 0.301770 lnL0 = -3454.854046 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3454.854046 x= 0.04598 0.02751 0.07447 0.09864 0.08214 0.21622 0.23606 0.30177 1 h-lim-p 0.0015 0.0119 190.4068 3452.110394 3 0.0002 30 | 0/8 2 h-lim-p 0.0006 0.0048 25.8000 3452.019002 2 0.0003 46 | 0/8 3 h-lim-p 0.0005 0.0134 14.7963 3451.992308 6 0.0003 73 | 0/8 4 h-lim-p 0.0006 0.0286 7.6729 3451.984827 5 0.0003 97 | 0/8 5 h-lim-p 0.0019 0.2259 1.3289 3451.984520 3 0.0004 116 | 0/8 6 h-lim-p 0.0010 0.4427 0.4691 3451.984478 1 0.0004 130 | 0/8 7 h-lim-p 0.0080 8.7013 0.0245 3451.984478 0 0.0009 152 | 0/8 8 h-lim-p 0.0811 20.0000 0.0003 3451.984408 0 0.9727 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3451.984405 0 1.2500 195 | 0/8 10 h-lim-p 1.7162 20.0000 0.0000 3451.984405 0 1.5017 215 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3451.984405 0 1.0938 235 | 0/8 12 h-lim-p 0.5963 20.0000 0.0000 3451.984405 0 0.5963 255 | 0/8 13 h-lim-p 0.0530 20.0000 0.0002 3451.984405 0 0.0265 275 | 0/8 14 h-lim-p 0.0090 20.0000 0.0007 3451.984405 0 0.0090 295 | 0/8 15 h-lim-p 0.0043 20.0000 0.0015 3451.984405 0 0.0000 325 | 0/8 16 h-lim-p 0.0006 20.0000 0.0000 3451.984405 0 0.0000 360 Out... lnL = -3451.984405 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3451.984405 Node 7: lnL = -3451.984405 Node 8: lnL = -3451.984405 Node 9: lnL = -3451.984405 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 253 Sequential format.. Reading seq # 1: YER029C_Sbay Reading seq # 2: YER029C_Scer Reading seq # 3: YER029C_Skud Reading seq # 4: YER029C_Smik Reading seq # 5: YER029C_Spar Sequences read.. Counting patterns.. # site patterns = 133 Counting frequencies.. 120 bytes for distance 21280 bytes for lkl0 17024 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.068605 0.000060 0.061350 0.158229 0.088160 0.251828 0.339241 0.365376 lnL0 = -1218.364730 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1218.364730 x= 0.06860 0.00006 0.06135 0.15823 0.08816 0.25183 0.33924 0.36538 1 h-lim-p 0.0047 0.0375 29.3219 1218.016171 8 0.0008 42 | 0/8 2 h-lim-p 0.0005 0.0036 14.0387 1217.912941 0 0.0018 56 | 0/8 3 h-lim-p 0.0003 0.0023 6.5882 1217.898264 0 0.0012 70 | 0/8 4 h-lim-p 0.0043 0.0899 1.7741 1217.896954 4 0.0009 92 | 0/8 5 h-lim-p 0.0016 0.0127 0.3578 1217.896814 1 0.0020 106 | 0/8 6 h-lim-p 0.0039 0.8854 0.1800 1217.896699 2 0.0037 130 | 0/8 7 h-lim-p 0.0203 0.2062 0.0326 1217.889615 m 0.2062 151 | 0/8 8 h-lim-p 0.0095 0.3458 0.7100 1217.883682 2 0.0089 175 | 0/8 9 h-lim-p 1.9611 15.6887 0.0005 1217.883638 0 0.9805 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1217.883636 2 0.7996 220 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1217.883636 0 1.0938 240 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1217.883636 0 1.0938 260 | 0/8 13 h-lim-p 1.0307 20.0000 0.0000 1217.883636 0 1.0307 280 | 0/8 14 h-lim-p 0.0383 20.0000 0.0001 1217.883636 0 0.0024 303 | 0/8 15 h-lim-p 0.0007 20.0000 0.0005 1217.883636 0 0.0000 333 | 0/8 16 h-lim-p 0.0003 20.0000 0.0000 1217.883636 0 0.0001 354 Out... lnL = -1217.883636 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1217.883636 Node 7: lnL = -1217.883636 Node 8: lnL = -1217.883636 Node 9: lnL = -1217.883636 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 275 Sequential format.. Reading seq # 1: YER030W_Sbay Reading seq # 2: YER030W_Scer Reading seq # 3: YER030W_Skud Reading seq # 4: YER030W_Smik Reading seq # 5: YER030W_Spar Sequences read.. Counting patterns.. # site patterns = 144 Counting frequencies.. 120 bytes for distance 23040 bytes for lkl0 18432 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.057592 0.055796 0.016985 0.170487 0.076007 0.251104 0.286693 0.351456 lnL0 = -1286.673461 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1286.673461 x= 0.05759 0.05580 0.01698 0.17049 0.07601 0.25110 0.28669 0.35146 1 h-lim-p 0.0068 0.0767 61.5276 1285.973165 4 0.0004 33 | 0/8 2 h-lim-p 0.0007 0.0054 18.9203 1285.741411 0 0.0013 46 | 0/8 3 h-lim-p 0.0017 0.0137 7.5943 1285.723044 4 0.0007 65 | 0/8 4 h-lim-p 0.0021 0.0777 2.7237 1285.718689 5 0.0014 89 | 0/8 5 h-lim-p 0.0083 0.4036 0.4434 1285.718446 4 0.0026 113 | 0/8 6 h-lim-p 0.0084 1.7268 0.1359 1285.718431 2 0.0016 138 | 0/8 7 h-lim-p 0.0051 11.4605 0.0431 1285.718421 1 0.0045 160 | 0/8 8 h-lim-p 0.0419 9.8336 0.0046 1285.717304 0 0.3351 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1285.717301 1 0.9961 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1285.717301 0 2.1875 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1285.717301 0 1.0938 245 | 0/8 12 h-lim-p 0.2046 20.0000 0.0000 1285.717301 0 6.5478 270 | 0/8 13 h-lim-p 0.1419 20.0000 0.0003 1285.717301 0 0.0000 319 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1285.717301 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1285.717301 Node 7: lnL = -1285.717301 Node 8: lnL = -1285.717301 Node 9: lnL = -1285.717301 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 171 Sequential format.. Reading seq # 1: YER031C_Sbay Reading seq # 2: YER031C_Scer Reading seq # 3: YER031C_Skud Reading seq # 4: YER031C_Smik Reading seq # 5: YER031C_Spar Sequences read.. Counting patterns.. # site patterns = 59 Counting frequencies.. 120 bytes for distance 9440 bytes for lkl0 7552 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.002633 0.022746 0.020754 0.079778 0.056963 0.102682 0.116336 0.126827 lnL0 = -615.323108 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 615.323108 x= 0.00263 0.02275 0.02075 0.07978 0.05696 0.10268 0.11634 0.12683 1 h-lim-p 0.0003 0.0022 95.3631 614.448914 3 0.0002 28 | 0/8 2 h-lim-p 0.0003 0.0028 25.8626 614.302965 0 0.0005 40 | 0/8 3 h-lim-p 0.0014 0.0148 9.5878 614.281198 5 0.0005 62 | 0/8 4 h-lim-p 0.0018 0.0146 1.9556 614.280009 5 0.0007 85 | 0/8 5 h-lim-p 0.0053 0.2660 0.2416 614.279990 2 0.0006 103 | 0/8 6 h-lim-p 0.0017 1.6665 0.0832 614.279982 3 0.0010 131 | 0/8 7 h-lim-p 0.0150 5.8637 0.0055 614.276088 0 0.4798 156 | 0/8 8 h-lim-p 0.0341 4.9216 0.0779 614.276085 1 0.0009 182 | 0/8 9 h-lim-p 0.0903 20.0000 0.0008 614.275562 0 1.0830 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 614.275540 1 1.0938 227 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 614.275539 0 1.2500 247 | 0/8 12 h-lim-p 1.7934 20.0000 0.0000 614.275539 0 0.7846 267 | 0/8 13 h-lim-p 0.5177 20.0000 0.0000 614.275539 0 0.0004 297 | 0/8 14 h-lim-p 0.0001 20.0000 0.0001 614.275539 0 0.0000 334 | 0/8 15 h-lim-p 0.0000 20.0000 0.0009 | 0/8 16 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -614.275539 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -614.275539 Node 7: lnL = -614.275539 Node 8: lnL = -614.275539 Node 9: lnL = -614.275539 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 267 Sequential format.. Reading seq # 1: YER035W_Sbay Reading seq # 2: YER035W_Scer Reading seq # 3: YER035W_Skud Reading seq # 4: YER035W_Smik Reading seq # 5: YER035W_Spar Sequences read.. Counting patterns.. # site patterns = 123 Counting frequencies.. 120 bytes for distance 19680 bytes for lkl0 15744 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.285475 0.208007 0.218971 0.041496 0.136173 0.195873 0.248273 lnL0 = -974.620724 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 974.620724 x= 0.00006 0.28547 0.20801 0.21897 0.04150 0.13617 0.19587 0.24827 1 h-lim-p 0.0000 0.0000 125.1702 974.581852 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0046 80.2815 969.221543 8 0.0020 61 | 1/8 3 h-lim-p 0.0010 0.0081 23.2663 968.566777 0 0.0030 74 | 1/8 4 h-lim-p 0.0021 0.0167 10.7257 968.405377 0 0.0031 86 | 1/8 5 h-lim-p 0.0075 0.0873 4.4629 968.343005 7 0.0043 116 | 1/8 6 h-lim-p 0.0070 0.0559 2.5328 968.234742 0 0.0105 128 | 1/8 7 h-lim-p 0.0145 0.1156 1.4622 965.078726 0 0.0578 142 | 1/8 8 h-lim-p 0.0011 0.0087 21.3275 963.381441 0 0.0043 156 | 1/8 9 h-lim-p 1.3399 10.7190 0.0391 963.140541 6 0.4725 182 | 0/8 10 h-lim-p 0.0531 10.1332 0.3479 963.139797 5 0.0045 216 | 0/8 11 h-lim-p 0.0171 0.1370 0.0710 963.093402 m 0.1370 236 | 1/8 12 h-lim-p 2.2147 20.0000 0.0043 963.089824 5 0.8931 265 | 1/8 13 h-lim-p 2.5000 20.0000 0.0012 963.089615 4 0.6789 293 | 1/8 14 h-lim-p 2.5000 20.0000 0.0003 963.089605 3 0.7439 320 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 963.089605 0 1.0938 339 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 963.089605 0 1.0938 358 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 963.089605 0 1.0938 377 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 963.089605 0 2.1875 396 | 1/8 19 h-lim-p 1.7582 20.0000 0.0000 963.089605 0 0.7692 415 | 1/8 20 h-lim-p 2.5000 20.0000 0.0000 963.089605 0 0.0002 447 Out... lnL = -963.089605 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -963.089605 Node 7: lnL = -963.089605 Node 8: lnL = -963.089605 Node 9: lnL = -963.089605 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 207 Sequential format.. Reading seq # 1: YER042W_Sbay Reading seq # 2: YER042W_Scer Reading seq # 3: YER042W_Skud Reading seq # 4: YER042W_Smik Reading seq # 5: YER042W_Spar Sequences read.. Counting patterns.. # site patterns = 107 Counting frequencies.. 120 bytes for distance 17120 bytes for lkl0 13696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.122346 0.116935 0.108316 0.064518 0.241295 0.198895 0.239737 lnL0 = -898.537231 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 898.537231 x= 0.00006 0.12235 0.11693 0.10832 0.06452 0.24130 0.19890 0.23974 1 h-lim-p 0.0000 0.0000 42.6062 898.496145 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0071 22.2779 898.251271 0 0.0014 39 | 1/8 3 h-lim-p 0.0211 0.1685 1.3230 898.246029 6 0.0036 67 | 1/8 4 h-lim-p 0.0117 0.7131 0.4023 898.216747 0 0.0234 80 | 0/8 5 h-lim-p 0.0039 0.1505 2.4298 897.854483 0 0.0309 102 | 0/8 6 h-lim-p 0.0045 0.0358 8.5131 897.772893 2 0.0021 118 | 0/8 7 h-lim-p 0.0097 0.3287 1.8452 897.770917 2 0.0011 136 | 0/8 8 h-lim-p 0.0085 0.3761 0.2452 897.768805 0 0.0342 150 | 0/8 9 h-lim-p 0.0040 0.0354 2.0714 897.752613 6 0.0251 184 | 0/8 10 h-lim-p 0.4132 3.3059 0.0887 897.727370 7 0.2491 216 | 0/8 11 h-lim-p 2.5000 20.0000 0.0007 897.727294 3 0.9482 242 | 0/8 12 h-lim-p 2.5000 20.0000 0.0002 897.727293 1 0.9961 264 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 897.727293 0 1.0938 284 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 897.727293 0 1.0938 304 | 0/8 15 h-lim-p 0.4323 20.0000 0.0000 897.727293 m20.0000 327 | 0/8 16 h-lim-p 0.0344 20.0000 0.0008 897.727293 0 0.0172 347 | 0/8 17 h-lim-p 0.0055 16.0508 0.0026 897.727293 0 0.0000 389 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -897.727293 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -897.727293 Node 7: lnL = -897.727293 Node 8: lnL = -897.727293 Node 9: lnL = -897.727293 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 480 Sequential format.. Reading seq # 1: YER043C_Sbay Reading seq # 2: YER043C_Scer Reading seq # 3: YER043C_Skud Reading seq # 4: YER043C_Smik Reading seq # 5: YER043C_Spar Sequences read.. Counting patterns.. # site patterns = 149 Counting frequencies.. 120 bytes for distance 23840 bytes for lkl0 19072 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.001636 0.051901 0.035009 0.073831 0.054917 0.174178 0.171945 0.178921 lnL0 = -1922.237557 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1922.237557 x= 0.00164 0.05190 0.03501 0.07383 0.05492 0.17418 0.17195 0.17892 1 h-lim-p 0.0002 0.0013 157.9987 1920.424447 5 0.0002 32 | 0/8 2 h-lim-p 0.0002 0.0017 31.8341 1920.297894 1 0.0003 46 | 0/8 3 h-lim-p 0.0002 0.0014 14.1960 1920.281888 1 0.0002 60 | 0/8 4 h-lim-p 0.0002 0.0020 4.3786 1920.279056 0 0.0004 72 | 0/8 5 h-lim-p 0.0013 0.1034 1.2531 1920.278756 4 0.0004 94 | 0/8 6 h-lim-p 0.0025 1.4643 0.2129 1920.278749 1 0.0003 110 | 0/8 7 h-lim-p 0.0017 0.4940 0.0386 1920.278747 0 0.0015 130 | 0/8 8 h-lim-p 0.0364 20.0000 0.0015 1920.277992 0 0.5826 154 | 0/8 9 h-lim-p 1.8514 14.8109 0.0002 1920.277962 3 1.1018 182 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1920.277962 0 1.0938 202 | 0/8 11 h-lim-p 1.6377 20.0000 0.0000 1920.277962 0 2.4565 222 | 0/8 12 h-lim-p 0.3761 9.5407 0.0003 1920.277962 0 0.0002 252 | 0/8 13 h-lim-p 0.0006 20.0000 0.0001 1920.277962 0 0.0003 272 | 0/8 14 h-lim-p 0.0000 4.9512 0.0005 1920.277962 0 0.0000 292 | 0/8 15 h-lim-p 0.0000 3.5771 0.0007 1920.277962 0 0.0000 312 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 1920.277962 0 0.0000 341 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 18 h-lim-p 0.0000 10.6513 0.0025 | 0/8 19 h-lim-p 0.0000 10.6513 0.0025 Out... lnL = -1920.277962 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1920.277962 Node 7: lnL = -1920.277962 Node 8: lnL = -1920.277962 Node 9: lnL = -1920.277962 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 520 Sequential format.. Reading seq # 1: YER044C_Sbay Reading seq # 2: YER044C_Scer Reading seq # 3: YER044C_Skud Reading seq # 4: YER044C_Smik Reading seq # 5: YER044C_Spar Sequences read.. Counting patterns.. # site patterns = 168 Counting frequencies.. 120 bytes for distance 26880 bytes for lkl0 21504 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.024413 0.058733 0.027080 0.070566 0.055657 0.141955 0.192228 0.210277 lnL0 = -1954.360836 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1954.360836 x= 0.02441 0.05873 0.02708 0.07057 0.05566 0.14195 0.19223 0.21028 1 h-lim-p 0.0010 0.5790 200.5990 1951.752314 8 0.0002 43 | 0/8 2 h-lim-p 0.0005 0.0040 39.6795 1951.484321 7 0.0004 71 | 0/8 3 h-lim-p 0.0008 0.0154 16.8028 1951.459504 5 0.0002 96 | 0/8 4 h-lim-p 0.0007 0.0141 4.8755 1951.454354 5 0.0005 121 | 0/8 5 h-lim-p 0.0025 0.2269 0.9401 1951.454039 4 0.0007 144 | 0/8 6 h-lim-p 0.0031 0.5058 0.2239 1951.454032 1 0.0003 168 | 0/8 7 h-lim-p 0.0030 2.8560 0.0228 1951.454032 0 0.0007 189 | 0/8 8 h-lim-p 0.1267 20.0000 0.0001 1951.454001 0 1.0132 212 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1951.454000 1 1.2305 235 | 0/8 10 h-lim-p 1.5561 20.0000 0.0000 1951.454000 0 1.3616 255 | 0/8 11 h-lim-p 2.3007 20.0000 0.0000 1951.454000 0 2.0131 275 | 0/8 12 h-lim-p 1.9062 20.0000 0.0000 1951.454000 0 1.6679 295 | 0/8 13 h-lim-p 0.7962 20.0000 0.0000 1951.454000 0 2.3886 316 | 0/8 14 h-lim-p 0.2221 20.0000 0.0003 1951.454000 0 0.0069 340 | 0/8 15 h-lim-p 0.0011 18.1934 0.0021 1951.454000 0 0.0000 372 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 1951.454000 0 0.0000 410 Out... lnL = -1951.454000 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1951.454000 Node 7: lnL = -1951.454000 Node 8: lnL = -1951.454000 Node 9: lnL = -1951.454000 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 951 Sequential format.. Reading seq # 1: YER046W_Sbay Reading seq # 2: YER046W_Scer Reading seq # 3: YER046W_Skud Reading seq # 4: YER046W_Smik Reading seq # 5: YER046W_Spar Sequences read.. Counting patterns.. # site patterns = 349 Counting frequencies.. 120 bytes for distance 55840 bytes for lkl0 44672 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.050464 0.119974 0.074957 0.156756 0.082440 0.256623 0.197964 0.367188 lnL0 = -4311.722084 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4311.722084 x= 0.05046 0.11997 0.07496 0.15676 0.08244 0.25662 0.19796 0.36719 1 h-lim-p 0.0003 0.0023 103.4745 4310.221159 4 0.0003 30 | 0/8 2 h-lim-p 0.0011 0.0087 25.6913 4310.088106 4 0.0004 50 | 0/8 3 h-lim-p 0.0011 0.0298 9.9809 4310.067743 5 0.0005 71 | 0/8 4 h-lim-p 0.0008 0.0212 5.7405 4310.065364 2 0.0002 88 | 0/8 5 h-lim-p 0.0008 0.1508 1.4483 4310.064910 4 0.0005 111 | 0/8 6 h-lim-p 0.0017 0.4899 0.3993 4310.064870 2 0.0006 129 | 0/8 7 h-lim-p 0.1340 20.0000 0.0017 4310.064867 1 0.0330 152 | 0/8 8 h-lim-p 0.0040 16.1717 0.0138 4310.064775 0 0.0159 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4310.064774 0 1.0938 194 | 0/8 10 h-lim-p 1.9304 20.0000 0.0000 4310.064774 0 1.6891 214 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4310.064774 0 1.0938 234 | 0/8 12 h-lim-p 0.4071 20.0000 0.0000 4310.064774 0 1.6286 256 | 0/8 13 h-lim-p 0.0646 20.0000 0.0005 4310.064774 0 0.0565 276 | 0/8 14 h-lim-p 0.0158 20.0000 0.0017 4310.064774 0 0.0000 306 | 0/8 15 h-lim-p 0.0001 20.0000 0.0001 4310.064774 0 0.0000 339 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 4310.064774 0 0.0000 371 | 0/8 17 h-lim-p 0.0000 20.0000 0.0003 | 0/8 18 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -4310.064774 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4310.064774 Node 7: lnL = -4310.064774 Node 8: lnL = -4310.064774 Node 9: lnL = -4310.064774 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 851 Sequential format.. Reading seq # 1: YER048W-A_Sbay Reading seq # 2: YER048W-A_Scer Reading seq # 3: YER048W-A_Skud Reading seq # 4: YER048W-A_Smik Reading seq # 5: YER048W-A_Spar Sequences read.. Counting patterns.. # site patterns = 410 Counting frequencies.. 120 bytes for distance 65600 bytes for lkl0 52480 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.078236 0.111957 0.000060 0.213398 0.249120 0.454231 0.341800 0.458051 lnL0 = -4627.693044 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4627.693044 x= 0.07824 0.11196 0.00006 0.21340 0.24912 0.45423 0.34180 0.45805 1 h-lim-p 0.0001 0.0011 311.1298 4602.474477 0 0.0005 24 | 0/8 2 h-lim-p 0.0000 0.0001 50.3867 4602.261726 m 0.0001 36 | 1/8 3 h-lim-p 0.0002 0.0049 20.3157 4602.116624 0 0.0009 50 | 1/8 4 h-lim-p 0.0036 0.1060 5.0466 4602.101236 6 0.0011 78 | 1/8 5 h-lim-p 0.0192 1.4831 0.3000 4602.018049 0 0.0384 91 | 1/8 6 h-lim-p 0.0026 0.0287 4.4297 4601.998325 5 0.0014 121 | 1/8 7 h-lim-p 0.0087 0.2210 0.7037 4601.997731 3 0.0017 140 | 1/8 8 h-lim-p 0.0890 7.0620 0.0131 4601.856854 0 0.7118 162 | 1/8 9 h-lim-p 2.5000 20.0000 0.0019 4601.853767 4 0.9644 189 | 0/8 10 h-lim-p 0.0014 0.1570 1.2785 4601.853566 3 0.0004 215 | 0/8 11 h-lim-p 0.9501 20.0000 0.0005 4601.853557 0 0.9501 227 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4601.853557 0 1.0938 247 | 0/8 13 h-lim-p 1.4989 20.0000 0.0000 4601.853557 0 1.3116 267 | 0/8 14 h-lim-p 0.9989 20.0000 0.0000 4601.853557 0 0.8741 287 | 0/8 15 h-lim-p 0.0214 20.0000 0.0009 4601.853557 0 0.0000 326 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 4601.853557 0 0.0000 350 Out... lnL = -4601.853557 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4601.853557 Node 7: lnL = -4601.853557 Node 8: lnL = -4601.853557 Node 9: lnL = -4601.853557 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 786 Sequential format.. Reading seq # 1: YER049W_Sbay Reading seq # 2: YER049W_Scer Reading seq # 3: YER049W_Skud Reading seq # 4: YER049W_Smik Reading seq # 5: YER049W_Spar Sequences read.. Counting patterns.. # site patterns = 298 Counting frequencies.. 120 bytes for distance 47680 bytes for lkl0 38144 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.010815 0.070690 0.043689 0.146245 0.108817 0.216402 0.094281 0.223530 lnL0 = -3345.021454 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3345.021454 x= 0.01081 0.07069 0.04369 0.14624 0.10882 0.21640 0.09428 0.22353 1 h-lim-p 0.0012 0.0172 238.4743 3340.548355 9 0.0002 45 | 0/8 2 h-lim-p 0.0002 0.0017 49.6539 3340.271803 6 0.0002 71 | 0/8 3 h-lim-p 0.0006 0.0044 10.6398 3340.254351 6 0.0003 98 | 0/8 4 h-lim-p 0.0016 0.0641 2.1498 3340.253631 3 0.0003 117 | 0/8 5 h-lim-p 0.0010 0.4311 0.6844 3340.253560 2 0.0003 135 | 0/8 6 h-lim-p 0.0029 2.6418 0.0805 3340.253559 0 0.0006 156 | 0/8 7 h-lim-p 0.0046 18.6738 0.0113 3340.253556 0 0.0046 176 | 0/8 8 h-lim-p 0.0090 20.0000 0.0057 3340.252859 0 0.1080 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3340.252857 0 1.0938 219 | 0/8 10 h-lim-p 0.9984 20.0000 0.0000 3340.252857 0 0.8736 239 | 0/8 11 h-lim-p 0.7587 20.0000 0.0000 3340.252857 0 0.0059 265 | 0/8 12 h-lim-p 0.0015 20.0000 0.0002 3340.252857 0 0.0000 303 | 0/8 13 h-lim-p 0.0000 20.0000 0.0020 | 0/8 14 h-lim-p 0.0000 20.0000 0.0020 Out... lnL = -3340.252857 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3340.252857 Node 7: lnL = -3340.252857 Node 8: lnL = -3340.252857 Node 9: lnL = -3340.252857 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 280 Sequential format.. Reading seq # 1: YER050C_Sbay Reading seq # 2: YER050C_Scer Reading seq # 3: YER050C_Skud Reading seq # 4: YER050C_Smik Reading seq # 5: YER050C_Spar Sequences read.. Counting patterns.. # site patterns = 170 Counting frequencies.. 120 bytes for distance 27200 bytes for lkl0 21760 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.108394 0.322431 0.000060 0.278680 0.256599 0.522696 0.390183 0.592827 lnL0 = -1280.508882 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1280.508882 x= 0.10839 0.32243 0.00006 0.27868 0.25660 0.52270 0.39018 0.59283 1 h-lim-p 0.0000 0.0000 93.8989 1280.482337 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0031 67.0070 1272.160862 m 0.0031 40 | 2/8 3 h-lim-p 0.0045 0.0361 11.9002 1268.309536 0 0.0180 54 | 2/8 4 h-lim-p 0.0037 0.0299 21.5371 1261.286438 0 0.0150 68 | 2/8 5 h-lim-p 0.0065 0.0518 15.6799 1257.457141 0 0.0194 81 | 2/8 6 h-lim-p 0.0061 0.0491 13.3184 1257.168749 7 0.0040 110 | 1/8 7 h-lim-p 0.0020 0.1670 26.1373 1256.726230 7 0.0014 137 | 1/8 8 h-lim-p 0.0288 0.5283 1.3058 1256.707855 6 0.0116 160 | 1/8 9 h-lim-p 0.0826 0.8843 0.1838 1256.261733 0 0.3303 174 | 0/8 10 h-lim-p 0.0101 0.0805 3.1341 1256.242358 5 0.0045 202 | 0/8 11 h-lim-p 0.1426 1.1405 0.0544 1256.055713 m 1.1405 214 | 1/8 12 h-lim-p 1.4024 11.2191 0.0146 1256.041277 4 1.0819 242 | 0/8 13 h-lim-p 0.0160 0.2804 0.9883 1256.040600 2 0.0020 267 | 0/8 14 h-lim-p 0.2918 2.3344 0.0050 1256.039606 0 1.1672 289 | 0/8 15 h-lim-p 2.5000 20.0000 0.0009 1256.039578 2 1.0889 313 | 0/8 16 h-lim-p 2.5000 20.0000 0.0001 1256.039577 1 1.2305 336 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1256.039577 0 1.0938 356 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1256.039577 0 1.0938 376 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1256.039577 0 0.6250 397 | 0/8 20 h-lim-p 0.6400 20.0000 0.0000 1256.039577 0 0.0000 432 Out... lnL = -1256.039577 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1256.039577 Node 7: lnL = -1256.039577 Node 8: lnL = -1256.039577 Node 9: lnL = -1256.039577 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 80 Sequential format.. Reading seq # 1: YER051W_Sbay Reading seq # 2: YER051W_Scer Reading seq # 3: YER051W_Skud Reading seq # 4: YER051W_Smik Reading seq # 5: YER051W_Spar Sequences read.. Counting patterns.. # site patterns = 66 Counting frequencies.. 120 bytes for distance 10560 bytes for lkl0 8448 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.257483 0.096265 0.302724 0.281953 0.395018 0.560539 0.514242 lnL0 = -457.307563 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 457.307563 x= 0.00006 0.25748 0.09626 0.30272 0.28195 0.39502 0.56054 0.51424 1 h-lim-p 0.0000 0.0000 18.8947 457.303070 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0621 7.4170 456.988726 0 0.0152 43 | 1/8 3 h-lim-p 0.0075 0.0602 8.3709 456.604476 0 0.0150 56 | 1/8 4 h-lim-p 0.0065 0.0522 2.5668 456.427736 m 0.0522 68 | 2/8 5 h-lim-p 0.0011 0.0089 77.3382 456.339721 6 0.0008 94 | 2/8 6 h-lim-p 0.0224 0.1794 2.1203 456.273098 8 0.0155 126 | 2/8 7 h-lim-p 0.0409 0.5626 0.8053 455.851593 0 0.1636 140 | 1/8 8 h-lim-p 0.0275 0.3926 4.7885 455.737568 8 0.0081 176 | 1/8 9 h-lim-p 0.0116 0.1056 3.3325 455.454263 0 0.0348 189 | 1/8 10 h-lim-p 0.6538 5.2302 0.0823 455.314128 0 0.9807 201 | 1/8 11 h-lim-p 1.9234 16.0208 0.0420 455.244222 7 1.3882 237 | 1/8 12 h-lim-p 2.5000 20.0000 0.0162 455.233240 2 1.1719 260 | 0/8 13 h-lim-p 0.1220 8.2254 0.1555 455.233048 4 0.0187 291 | 0/8 14 h-lim-p 2.1316 20.0000 0.0014 455.232882 4 1.5571 320 | 0/8 15 h-lim-p 2.5000 20.0000 0.0002 455.232881 1 0.9961 342 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 455.232881 0 1.0938 362 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 455.232881 0 1.2500 382 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 455.232881 0 1.0938 402 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 455.232881 0 1.8750 422 | 0/8 20 h-lim-p 0.7093 20.0000 0.0000 455.232881 0 0.1773 443 | 0/8 21 h-lim-p 0.0359 20.0000 0.0000 455.232881 0 0.0045 465 Out... lnL = -455.232881 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -455.232881 Node 7: lnL = -455.232881 Node 8: lnL = -455.232881 Node 9: lnL = -455.232881 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 838 Sequential format.. Reading seq # 1: YER052C_Sbay Reading seq # 2: YER052C_Scer Reading seq # 3: YER052C_Skud Reading seq # 4: YER052C_Smik Reading seq # 5: YER052C_Spar Sequences read.. Counting patterns.. # site patterns = 326 Counting frequencies.. 120 bytes for distance 52160 bytes for lkl0 41728 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.148411 0.048000 0.152687 0.070886 0.235885 0.213374 0.260511 lnL0 = -3783.422385 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3783.422385 x= 0.00006 0.14841 0.04800 0.15269 0.07089 0.23589 0.21337 0.26051 1 h-lim-p 0.0000 0.0000 195.3375 3783.265220 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0072 57.6268 3782.525231 0 0.0005 39 | 1/8 3 h-lim-p 0.0018 0.0248 14.7083 3782.494012 6 0.0003 67 | 1/8 4 h-lim-p 0.0006 0.0257 7.7422 3782.485330 6 0.0003 94 | 1/8 5 h-lim-p 0.0015 0.1804 1.6535 3782.476154 0 0.0022 106 | 1/8 6 h-lim-p 0.0023 0.1378 1.6098 3782.422725 0 0.0046 119 | 1/8 7 h-lim-p 0.0045 0.2593 1.6420 3779.472389 0 0.0271 133 | 1/8 8 h-lim-p 0.0014 0.0143 32.4948 3779.053246 2 0.0006 149 | 1/8 9 h-lim-p 2.5000 20.0000 0.0042 3779.009591 6 1.3053 173 | 0/8 10 h-lim-p 0.0193 15.6075 0.2822 3779.009565 2 0.0006 200 | 0/8 11 h-lim-p 0.3074 2.4595 0.0005 3779.008843 0 1.2298 222 | 0/8 12 h-lim-p 0.1095 0.8760 0.0002 3779.008823 m 0.8760 242 | 1/8 13 h-lim-p 1.0708 20.0000 0.0001 3779.008820 0 0.4685 262 | 0/8 14 h-lim-p 0.0055 20.0000 0.0108 3779.008820 0 0.0003 284 | 0/8 15 h-lim-p 0.1253 1.0020 0.0000 3779.008820 m 1.0020 304 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 3779.008820 0 1.0938 324 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 3779.008820 0 1.0938 343 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 3779.008820 0 0.0342 367 Out... lnL = -3779.008820 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3779.008820 Node 7: lnL = -3779.008820 Node 8: lnL = -3779.008820 Node 9: lnL = -3779.008820 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 868 Sequential format.. Reading seq # 1: YER053C_Sbay Reading seq # 2: YER053C_Scer Reading seq # 3: YER053C_Skud Reading seq # 4: YER053C_Smik Reading seq # 5: YER053C_Spar Sequences read.. Counting patterns.. # site patterns = 304 Counting frequencies.. 120 bytes for distance 48640 bytes for lkl0 38912 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.118442 0.033060 0.098476 0.119118 0.218823 0.157229 0.218221 lnL0 = -3768.593922 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3768.593922 x= 0.00006 0.11844 0.03306 0.09848 0.11912 0.21882 0.15723 0.21822 1 h-lim-p 0.0000 0.0000 270.6460 3768.483165 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0027 78.1658 3767.779835 0 0.0003 39 | 1/8 3 h-lim-p 0.0006 0.0061 42.3862 3767.596896 5 0.0003 60 | 1/8 4 h-lim-p 0.0016 0.0321 6.6257 3767.589197 4 0.0003 81 | 1/8 5 h-lim-p 0.0051 0.7554 0.4055 3767.534119 0 0.0205 95 | 0/8 6 h-lim-p 0.0015 0.0926 5.7380 3766.789452 0 0.0044 115 | 0/8 7 h-lim-p 0.0009 0.0170 26.5782 3765.236722 7 0.0010 145 | 0/8 8 h-lim-p 0.0001 0.0009 42.0109 3763.856090 m 0.0009 157 | 0/8 9 h-lim-p -0.0000 -0.0000 11.0290 h-lim-p: -8.42241849e-20 -6.73793479e-19 1.10290141e+01 3763.856090 .. | 0/8 10 h-lim-p 0.0000 0.0132 38.3716 3763.730142 0 0.0002 181 | 0/8 11 h-lim-p 0.0000 0.0001 10.9379 3763.723667 m 0.0001 193 | 1/8 12 h-lim-p 0.0002 0.0575 3.3682 3763.722293 1 0.0003 207 | 1/8 13 h-lim-p 0.0021 0.5673 0.4352 3763.722256 2 0.0003 226 | 1/8 14 h-lim-p 0.0034 5.9455 0.0448 3763.722153 0 0.0067 246 | 1/8 15 h-lim-p 0.0027 1.5007 0.1135 3763.719630 0 0.0106 267 | 1/8 16 h-lim-p 0.0006 0.1343 1.9752 3763.717537 2 0.0006 290 | 1/8 17 h-lim-p 0.0031 0.6143 0.3696 3763.717501 2 0.0005 309 | 1/8 18 h-lim-p 0.0666 20.0000 0.0028 3763.713529 0 0.5330 331 | 0/8 19 h-lim-p 0.0143 10.6682 0.1039 3763.713527 0 0.0004 354 | 0/8 20 h-lim-p 0.1345 1.0761 0.0002 3763.713435 m 1.0761 374 | 1/8 21 h-lim-p 2.5000 20.0000 0.0000 3763.713434 0 1.0938 394 | 0/8 22 h-lim-p -0.0000 -0.0000 0.0094 h-lim-p: -2.63757757e-20 -2.11006205e-19 9.35281693e-03 3763.713434 .. | 1/8 23 h-lim-p 0.0000 20.0000 0.0112 3763.713434 0 0.0003 434 | 1/8 24 h-lim-p 0.0007 20.0000 0.0050 3763.713434 0 0.0003 453 | 1/8 25 h-lim-p 0.0015 20.0000 0.0011 3763.713434 0 0.0003 473 | 1/8 26 h-lim-p 0.0061 20.0000 0.0001 3763.713434 0 0.0015 493 | 1/8 27 h-lim-p 0.0029 20.0000 0.0000 3763.713434 0 0.0000 519 | 1/8 28 h-lim-p 0.0000 20.0000 0.0000 3763.713434 0 0.0000 541 | 1/8 29 h-lim-p 0.0000 20.0000 0.0001 3763.713434 0 0.0000 560 | 1/8 30 h-lim-p 0.0000 20.0000 0.0003 3763.713434 0 0.0000 580 | 1/8 31 h-lim-p 0.0010 20.0000 0.0000 3763.713434 0 0.0002 600 Out... lnL = -3763.713434 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3763.713434 Node 7: lnL = -3763.713434 Node 8: lnL = -3763.713434 Node 9: lnL = -3763.713434 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 853 Sequential format.. Reading seq # 1: YER054C_Sbay Reading seq # 2: YER054C_Scer Reading seq # 3: YER054C_Skud Reading seq # 4: YER054C_Smik Reading seq # 5: YER054C_Spar Sequences read.. Counting patterns.. # site patterns = 275 Counting frequencies.. 120 bytes for distance 44000 bytes for lkl0 35200 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.018920 0.050034 0.066010 0.094055 0.070700 0.146019 0.235439 0.231404 lnL0 = -3582.104376 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3582.104376 x= 0.01892 0.05003 0.06601 0.09406 0.07070 0.14602 0.23544 0.23140 1 h-lim-p 0.0002 0.0016 124.7255 3580.848393 3 0.0002 28 | 0/8 2 h-lim-p 0.0003 0.0026 28.4151 3580.713252 6 0.0004 54 | 0/8 3 h-lim-p 0.0007 0.0120 14.5211 3580.690848 5 0.0003 76 | 0/8 4 h-lim-p 0.0007 0.0259 5.8097 3580.687615 5 0.0002 100 | 0/8 5 h-lim-p 0.0003 0.0373 3.9066 3580.686667 3 0.0002 119 | 0/8 6 h-lim-p 0.0030 0.8447 0.2379 3580.686661 1 0.0002 136 | 0/8 7 h-lim-p 0.0111 20.0000 0.0039 3580.686660 0 0.0097 156 | 0/8 8 h-lim-p 0.0067 5.9644 0.0056 3580.686494 0 0.0538 179 | 0/8 9 h-lim-p 0.9015 20.0000 0.0003 3580.686491 0 0.9015 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 3580.686491 0 1.0938 219 | 0/8 11 h-lim-p 1.5608 20.0000 0.0000 3580.686491 0 0.6828 239 | 0/8 12 h-lim-p 0.2075 20.0000 0.0001 3580.686491 0 0.0778 260 | 0/8 13 h-lim-p 0.0226 20.0000 0.0004 3580.686491 0 0.0000 293 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 3580.686491 0 0.0000 328 Out... lnL = -3580.686491 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3580.686491 Node 7: lnL = -3580.686491 Node 8: lnL = -3580.686491 Node 9: lnL = -3580.686491 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 763 Sequential format.. Reading seq # 1: YER055C_Sbay Reading seq # 2: YER055C_Scer Reading seq # 3: YER055C_Skud Reading seq # 4: YER055C_Smik Reading seq # 5: YER055C_Spar Sequences read.. Counting patterns.. # site patterns = 301 Counting frequencies.. 120 bytes for distance 48160 bytes for lkl0 38528 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.006660 0.064708 0.088098 0.141806 0.087975 0.180514 0.245271 0.258376 lnL0 = -3426.627820 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3426.627820 x= 0.00666 0.06471 0.08810 0.14181 0.08797 0.18051 0.24527 0.25838 1 h-lim-p 0.0029 0.9047 152.4624 3424.239405 8 0.0002 43 | 0/8 2 h-lim-p 0.0002 0.0019 21.5632 3424.171753 1 0.0003 57 | 0/8 3 h-lim-p 0.0003 0.0027 7.7805 3424.160463 0 0.0005 69 | 0/8 4 h-lim-p 0.0018 0.2152 2.1594 3424.159433 3 0.0005 88 | 0/8 5 h-lim-p 0.0018 0.2247 0.5859 3424.159342 2 0.0006 106 | 0/8 6 h-lim-p 0.0049 0.4033 0.0695 3424.159340 0 0.0006 128 | 0/8 7 h-lim-p 0.0029 4.6919 0.0148 3424.159338 0 0.0029 148 | 0/8 8 h-lim-p 0.0078 20.0000 0.0054 3424.158801 0 0.1254 172 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3424.158797 0 1.0938 192 | 0/8 10 h-lim-p 1.6829 20.0000 0.0000 3424.158797 0 1.4725 212 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3424.158797 0 2.1875 232 | 0/8 12 h-lim-p 1.9082 20.0000 0.0000 3424.158797 0 0.8349 252 | 0/8 13 h-lim-p 0.3137 20.0000 0.0001 3424.158797 0 0.1373 272 | 0/8 14 h-lim-p 0.0270 20.0000 0.0003 3424.158797 0 0.0000 317 | 0/8 15 h-lim-p 0.0000 20.0000 0.0010 3424.158797 0 0.0000 340 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0010 | 0/8 18 h-lim-p 0.0000 20.0000 0.0010 Out... lnL = -3424.158797 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3424.158797 Node 7: lnL = -3424.158797 Node 8: lnL = -3424.158797 Node 9: lnL = -3424.158797 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 716 Sequential format.. Reading seq # 1: YER058W_Sbay Reading seq # 2: YER058W_Scer Reading seq # 3: YER058W_Skud Reading seq # 4: YER058W_Smik Reading seq # 5: YER058W_Spar Sequences read.. Counting patterns.. # site patterns = 298 Counting frequencies.. 120 bytes for distance 47680 bytes for lkl0 38144 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.189630 0.118440 0.178519 0.144535 0.330924 0.226686 0.325857 lnL0 = -3529.115290 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3529.115290 x= 0.00006 0.18963 0.11844 0.17852 0.14454 0.33092 0.22669 0.32586 1 h-lim-p 0.0000 0.0000 121.6193 3529.090037 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0151 60.1186 3528.251608 0 0.0006 40 | 1/8 3 h-lim-p 0.0051 0.0434 7.6047 3528.217651 5 0.0010 62 | 1/8 4 h-lim-p 0.0040 0.2584 1.9273 3528.182627 1 0.0050 76 | 1/8 5 h-lim-p 0.0070 0.1439 1.3740 3527.784663 0 0.0141 89 | 1/8 6 h-lim-p 0.0017 0.0252 11.5500 3523.868007 0 0.0067 103 | 1/8 7 h-lim-p 0.0011 0.0090 39.7721 3523.259617 7 0.0007 133 | 1/8 8 h-lim-p 0.0087 0.1351 3.1407 3523.253639 6 0.0012 160 | 1/8 9 h-lim-p 0.3764 20.0000 0.0100 3523.193426 0 0.7529 173 | 1/8 10 h-lim-p 2.5000 20.0000 0.0011 3523.192877 3 0.8855 200 | 1/8 11 h-lim-p 2.5000 20.0000 0.0001 3523.192871 1 0.9961 221 | 0/8 12 h-lim-p 0.0297 20.0000 0.0027 3523.192871 0 0.0032 242 | 0/8 13 h-lim-p 0.1205 0.9637 0.0000 3523.192871 m 0.9637 262 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 3523.192871 0 1.0938 282 | 1/8 15 h-lim-p 1.6783 20.0000 0.0000 3523.192871 0 0.7343 301 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 3523.192871 0 2.1875 320 | 1/8 17 h-lim-p 1.7415 20.0000 0.0000 3523.192871 0 0.3265 341 | 1/8 18 h-lim-p 0.4856 20.0000 0.0000 .. | 1/8 19 h-lim-p 0.0000 20.0000 0.0006 3523.192871 0 0.0000 408 | 1/8 20 h-lim-p 0.0000 20.0000 0.0001 .. | 1/8 21 h-lim-p 0.0000 20.0000 0.0005 | 1/8 22 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -3523.192871 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3523.192871 Node 7: lnL = -3523.192871 Node 8: lnL = -3523.192871 Node 9: lnL = -3523.192871 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 553 Sequential format.. Reading seq # 1: YER059W_Sbay Reading seq # 2: YER059W_Scer Reading seq # 3: YER059W_Skud Reading seq # 4: YER059W_Smik Reading seq # 5: YER059W_Spar Sequences read.. Counting patterns.. # site patterns = 191 Counting frequencies.. 120 bytes for distance 30560 bytes for lkl0 24448 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.052183 0.047202 0.064703 0.137991 0.068392 0.185945 0.190406 0.282508 lnL0 = -2514.160431 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2514.160431 x= 0.05218 0.04720 0.06470 0.13799 0.06839 0.18594 0.19041 0.28251 1 h-lim-p 0.0010 0.0081 91.9284 2513.275038 6 0.0002 34 | 0/8 2 h-lim-p 0.0015 0.0129 13.5266 2513.236868 6 0.0004 62 | 0/8 3 h-lim-p 0.0006 0.0324 9.8731 2513.227499 2 0.0003 78 | 0/8 4 h-lim-p 0.0013 0.1278 2.0670 2513.226721 5 0.0004 105 | 0/8 5 h-lim-p 0.0018 0.4917 0.4413 2513.226669 3 0.0005 126 | 0/8 6 h-lim-p 0.0051 6.0672 0.0466 2513.226669 0 0.0006 148 | 0/8 7 h-lim-p 0.0159 20.0000 0.0016 2513.226668 0 0.0319 169 | 0/8 8 h-lim-p 0.0077 20.0000 0.0067 2513.226607 0 0.0309 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2513.226606 0 1.0938 211 | 0/8 10 h-lim-p 1.7614 20.0000 0.0000 2513.226606 0 1.5413 231 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2513.226606 0 1.2500 251 | 0/8 12 h-lim-p 0.6397 20.0000 0.0000 2513.226606 0 0.0075 277 | 0/8 13 h-lim-p 0.0017 20.0000 0.0001 2513.226606 0 0.0001 300 | 0/8 14 h-lim-p 0.0001 20.0000 0.0001 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0011 2513.226606 0 0.0000 362 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0011 | 0/8 18 h-lim-p 0.0000 20.0000 0.0011 Out... lnL = -2513.226606 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2513.226606 Node 7: lnL = -2513.226606 Node 8: lnL = -2513.226606 Node 9: lnL = -2513.226606 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 854 Sequential format.. Reading seq # 1: YER062C_Sbay Reading seq # 2: YER062C_Scer Reading seq # 3: YER062C_Skud Reading seq # 4: YER062C_Smik Reading seq # 5: YER062C_Spar Sequences read.. Counting patterns.. # site patterns = 355 Counting frequencies.. 120 bytes for distance 56800 bytes for lkl0 45440 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.050648 0.053702 0.064553 0.128125 0.117692 0.251125 0.299726 0.340347 lnL0 = -4148.982402 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4148.982402 x= 0.05065 0.05370 0.06455 0.12812 0.11769 0.25113 0.29973 0.34035 1 h-lim-p 0.0023 0.0444 189.7982 4145.325834 6 0.0002 35 | 0/8 2 h-lim-p 0.0005 0.0038 35.0398 4145.106581 5 0.0004 57 | 0/8 3 h-lim-p 0.0007 0.0126 17.8240 4145.058773 4 0.0004 78 | 0/8 4 h-lim-p 0.0006 0.0182 10.5054 4145.038642 6 0.0005 101 | 0/8 5 h-lim-p 0.0039 0.3619 1.3417 4145.038040 3 0.0007 122 | 0/8 6 h-lim-p 0.0018 0.4450 0.5213 4145.037993 1 0.0004 137 | 0/8 7 h-lim-p 0.0033 2.7891 0.0619 4145.037987 0 0.0014 157 | 0/8 8 h-lim-p 0.0398 20.0000 0.0022 4145.035077 0 0.6367 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4145.035064 1 0.9961 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4145.035064 0 1.0938 223 | 0/8 11 h-lim-p 1.3474 20.0000 0.0000 4145.035064 0 2.6948 244 | 0/8 12 h-lim-p 0.3366 20.0000 0.0001 4145.035064 0 0.0421 266 | 0/8 13 h-lim-p 0.0049 20.0000 0.0012 4145.035064 0 0.0000 295 | 0/8 14 h-lim-p 0.0004 20.0000 0.0000 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0007 4145.035064 0 0.0000 367 | 0/8 16 h-lim-p 0.0000 20.0000 0.0007 4145.035064 0 0.0000 397 | 0/8 17 h-lim-p 0.0000 20.0000 0.0023 4145.035064 0 0.0001 420 | 0/8 18 h-lim-p 0.0007 20.0000 0.0003 4145.035064 0 0.0006 440 | 0/8 19 h-lim-p 0.0010 20.0000 0.0002 4145.035064 0 0.0003 461 | 0/8 20 h-lim-p 0.0004 20.0000 0.0001 4145.035064 0 0.0000 487 | 0/8 21 h-lim-p 0.0000 20.0000 0.0002 4145.035064 0 0.0000 512 | 0/8 22 h-lim-p 0.0000 20.0000 0.0005 4145.035064 0 0.0000 537 | 0/8 23 h-lim-p 0.0000 20.0000 0.0001 4145.035064 0 0.0000 568 | 0/8 24 h-lim-p 0.0000 20.0000 0.0003 4145.035064 0 0.0000 594 | 0/8 25 h-lim-p 0.0000 20.0000 0.0002 4145.035064 0 0.0000 614 | 0/8 26 h-lim-p 0.0000 20.0000 0.0001 4145.035064 0 0.0000 641 | 0/8 27 h-lim-p 0.0000 20.0000 0.0002 .. | 0/8 28 h-lim-p 0.0000 20.0000 0.0003 | 0/8 29 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -4145.035064 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4145.035064 Node 7: lnL = -4145.035064 Node 8: lnL = -4145.035064 Node 9: lnL = -4145.035064 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 868 Sequential format.. Reading seq # 1: YER063W_Sbay Reading seq # 2: YER063W_Scer Reading seq # 3: YER063W_Skud Reading seq # 4: YER063W_Smik Reading seq # 5: YER063W_Spar Sequences read.. Counting patterns.. # site patterns = 329 Counting frequencies.. 120 bytes for distance 52640 bytes for lkl0 42112 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.025060 0.067022 0.094981 0.139565 0.082765 0.206196 0.268167 0.291717 lnL0 = -4091.791282 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4091.791282 x= 0.02506 0.06702 0.09498 0.13957 0.08277 0.20620 0.26817 0.29172 1 h-lim-p 0.0026 0.6529 178.9274 4088.470503 7 0.0002 40 | 0/8 2 h-lim-p 0.0006 0.0045 36.2509 4088.288896 6 0.0003 66 | 0/8 3 h-lim-p 0.0004 0.0081 23.3493 4088.210080 2 0.0004 82 | 0/8 4 h-lim-p 0.0014 0.0489 6.6150 4088.201884 6 0.0004 111 | 0/8 5 h-lim-p 0.0020 0.4032 1.3887 4088.201445 2 0.0005 128 | 0/8 6 h-lim-p 0.0031 0.9108 0.2109 4088.201436 0 0.0004 142 | 0/8 7 h-lim-p 0.0017 4.0734 0.0492 4088.201431 0 0.0017 162 | 0/8 8 h-lim-p 0.0246 20.0000 0.0033 4088.198653 0 0.3933 186 | 0/8 9 h-lim-p 2.3188 20.0000 0.0006 4088.198640 1 0.9239 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4088.198640 0 1.0938 228 | 0/8 11 h-lim-p 0.2310 20.0000 0.0000 4088.198640 0 1.8478 251 | 0/8 12 h-lim-p 0.3561 20.0000 0.0001 4088.198640 0 0.0012 278 | 0/8 13 h-lim-p 0.0001 20.0000 0.0012 4088.198640 0 0.0000 317 | 0/8 14 h-lim-p 0.0000 20.0000 0.0008 | 0/8 15 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -4088.198640 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4088.198640 Node 7: lnL = -4088.198640 Node 8: lnL = -4088.198640 Node 9: lnL = -4088.198640 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 839 Sequential format.. Reading seq # 1: YER064C_Sbay Reading seq # 2: YER064C_Scer Reading seq # 3: YER064C_Skud Reading seq # 4: YER064C_Smik Reading seq # 5: YER064C_Spar Sequences read.. Counting patterns.. # site patterns = 232 Counting frequencies.. 120 bytes for distance 37120 bytes for lkl0 29696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.014760 0.011175 0.059158 0.100234 0.080209 0.165222 0.172310 0.190677 lnL0 = -3311.968545 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3311.968545 x= 0.01476 0.01118 0.05916 0.10023 0.08021 0.16522 0.17231 0.19068 1 h-lim-p 0.0005 0.0322 374.1474 3308.301891 8 0.0001 41 | 0/8 2 h-lim-p 0.0001 0.0008 40.1189 3308.146732 0 0.0002 54 | 0/8 3 h-lim-p 0.0005 0.0040 9.1596 3308.139458 5 0.0002 79 | 0/8 4 h-lim-p 0.0007 0.1742 2.3250 3308.138744 2 0.0003 95 | 0/8 5 h-lim-p 0.0016 0.4032 0.4212 3308.138726 2 0.0002 113 | 0/8 6 h-lim-p 0.0067 7.9510 0.0130 3308.138726 0 0.0002 137 | 0/8 7 h-lim-p 0.0048 20.0000 0.0006 3308.138725 0 0.0380 160 | 0/8 8 h-lim-p 0.0023 1.3502 0.0095 3308.138711 0 0.0091 182 | 0/8 9 h-lim-p 0.8748 20.0000 0.0001 3308.138710 0 1.3122 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 3308.138710 0 1.2500 222 | 0/8 11 h-lim-p 1.0839 20.0000 0.0001 3308.138710 0 3.2517 243 | 0/8 12 h-lim-p 0.3388 20.0000 0.0006 3308.138710 0 0.0000 278 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 3308.138710 0 0.0000 310 | 0/8 14 h-lim-p 0.0000 20.0000 0.0053 3308.138710 0 0.0000 330 | 0/8 15 h-lim-p 0.0001 20.0000 0.0009 3308.138710 0 0.0004 352 | 0/8 16 h-lim-p 0.0012 20.0000 0.0003 3308.138710 0 0.0000 379 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 3308.138710 0 0.0000 410 | 0/8 18 h-lim-p 0.0000 20.0000 0.0048 3308.138710 0 0.0000 433 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 20 h-lim-p 0.0000 20.0000 0.0048 | 0/8 21 h-lim-p 0.0000 20.0000 0.0048 Out... lnL = -3308.138710 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3308.138710 Node 7: lnL = -3308.138710 Node 8: lnL = -3308.138710 Node 9: lnL = -3308.138710 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 915 Sequential format.. Reading seq # 1: YER065C_Sbay Reading seq # 2: YER065C_Scer Reading seq # 3: YER065C_Skud Reading seq # 4: YER065C_Smik Reading seq # 5: YER065C_Spar Sequences read.. Counting patterns.. # site patterns = 347 Counting frequencies.. 120 bytes for distance 55520 bytes for lkl0 44416 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.046112 0.052178 0.049274 0.165839 0.160938 0.183850 0.279042 0.313631 lnL0 = -4305.896894 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4305.896894 x= 0.04611 0.05218 0.04927 0.16584 0.16094 0.18385 0.27904 0.31363 1 h-lim-p 0.0012 0.5337 264.8915 4300.486824 8 0.0002 41 | 0/8 2 h-lim-p 0.0008 0.0061 38.6588 4300.196835 7 0.0004 69 | 0/8 3 h-lim-p 0.0011 0.0085 12.2567 4300.165165 4 0.0005 88 | 0/8 4 h-lim-p 0.0016 0.0911 3.6134 4300.161802 5 0.0006 113 | 0/8 5 h-lim-p 0.0018 0.2552 1.1118 4300.161575 2 0.0004 130 | 0/8 6 h-lim-p 0.0036 2.3654 0.1232 4300.161570 1 0.0004 146 | 0/8 7 h-lim-p 0.0051 20.0000 0.0106 4300.161543 0 0.0154 167 | 0/8 8 h-lim-p 0.0058 20.0000 0.0284 4300.159678 0 0.0462 190 | 0/8 9 h-lim-p 0.9953 20.0000 0.0013 4300.159475 1 0.9953 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 4300.159475 0 1.0938 232 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4300.159475 0 1.0938 252 | 0/8 12 h-lim-p 0.5073 20.0000 0.0000 4300.159475 0 0.0277 275 | 0/8 13 h-lim-p 0.0000 0.0820 0.7769 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -4300.159475 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4300.159475 Node 7: lnL = -4300.159475 Node 8: lnL = -4300.159475 Node 9: lnL = -4300.159475 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 632 Sequential format.. Reading seq # 1: YER069W_Sbay Reading seq # 2: YER069W_Scer Reading seq # 3: YER069W_Skud Reading seq # 4: YER069W_Smik Reading seq # 5: YER069W_Spar Sequences read.. Counting patterns.. # site patterns = 241 Counting frequencies.. 120 bytes for distance 38560 bytes for lkl0 30848 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.013947 0.023069 0.044374 0.123916 0.085968 0.177453 0.206934 0.201076 lnL0 = -2616.639595 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2616.639595 x= 0.01395 0.02307 0.04437 0.12392 0.08597 0.17745 0.20693 0.20108 1 h-lim-p 0.0005 0.0038 244.2654 2613.135078 9 0.0001 44 | 0/8 2 h-lim-p 0.0002 0.0019 36.6316 2612.955443 1 0.0003 58 | 0/8 3 h-lim-p 0.0006 0.0047 10.4946 2612.942356 2 0.0003 74 | 0/8 4 h-lim-p 0.0013 0.1960 2.0474 2612.941391 4 0.0005 96 | 0/8 5 h-lim-p 0.0047 0.4765 0.2118 2612.941383 1 0.0003 113 | 0/8 6 h-lim-p 0.0009 3.6871 0.0659 2612.941381 1 0.0005 136 | 0/8 7 h-lim-p 0.0009 2.1948 0.0321 2612.941375 0 0.0037 158 | 0/8 8 h-lim-p 0.0173 20.0000 0.0069 2612.940299 0 0.1386 181 | 0/8 9 h-lim-p 2.0153 20.0000 0.0005 2612.940205 3 1.0608 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2612.940203 1 1.2305 231 | 0/8 11 h-lim-p 1.3828 20.0000 0.0000 2612.940203 0 1.2100 251 | 0/8 12 h-lim-p 1.2854 20.0000 0.0000 2612.940203 0 1.2854 271 | 0/8 13 h-lim-p 0.8862 20.0000 0.0000 2612.940203 0 0.2215 292 | 0/8 14 h-lim-p 0.0005 1.0095 0.0204 2612.940203 0 0.0002 312 | 0/8 15 h-lim-p 0.0002 10.6687 0.0267 2612.940203 0 0.0000 341 | 0/8 16 h-lim-p 0.0000 20.0000 0.0005 2612.940203 0 0.0000 373 | 0/8 17 h-lim-p 0.0000 20.0000 0.0012 2612.940203 0 0.0000 401 | 0/8 18 h-lim-p 0.0000 20.0000 0.0003 2612.940203 0 0.0013 428 | 0/8 19 h-lim-p 0.0033 20.0000 0.0001 2612.940203 0 0.0000 460 | 0/8 20 h-lim-p 0.0000 20.0000 0.0000 2612.940203 0 0.0000 480 | 0/8 21 h-lim-p 0.0000 20.0000 0.0000 2612.940203 0 0.0000 500 | 0/8 22 h-lim-p 0.0000 16.0536 0.0013 2612.940203 0 0.0000 522 | 0/8 23 h-lim-p 0.0000 3.5367 0.0061 .. | 0/8 24 h-lim-p 0.0000 20.0000 0.0017 2612.940203 0 0.0000 580 | 0/8 25 h-lim-p 0.0000 20.0000 0.0003 .. | 0/8 26 h-lim-p 0.0000 20.0000 0.0017 | 0/8 27 h-lim-p 0.0000 20.0000 0.0017 Out... lnL = -2612.940203 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2612.940203 Node 7: lnL = -2612.940203 Node 8: lnL = -2612.940203 Node 9: lnL = -2612.940203 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 824 Sequential format.. Reading seq # 1: YER070W_Sbay Reading seq # 2: YER070W_Scer Reading seq # 3: YER070W_Skud Reading seq # 4: YER070W_Smik Reading seq # 5: YER070W_Spar Sequences read.. Counting patterns.. # site patterns = 213 Counting frequencies.. 120 bytes for distance 34080 bytes for lkl0 27264 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.006082 0.083123 0.026136 0.093601 0.054327 0.133691 0.121123 0.155819 lnL0 = -3243.291707 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3243.291707 x= 0.00608 0.08312 0.02614 0.09360 0.05433 0.13369 0.12112 0.15582 1 h-lim-p 0.0008 0.0063 217.7153 3241.538863 3 0.0001 30 | 0/8 2 h-lim-p 0.0003 0.0021 60.8186 3241.270461 8 0.0002 65 | 0/8 3 h-lim-p 0.0005 0.0038 19.3345 3241.249224 5 0.0001 88 | 0/8 4 h-lim-p 0.0004 0.0054 5.6699 3241.246733 3 0.0002 106 | 0/8 5 h-lim-p 0.0011 0.2269 0.9059 3241.246656 3 0.0002 126 | 0/8 6 h-lim-p 0.0017 2.1837 0.1005 3241.246654 1 0.0002 150 | 0/8 7 h-lim-p 0.0139 20.0000 0.0015 3241.246225 0 0.3324 174 | 0/8 8 h-lim-p 0.0008 0.0858 0.6466 3241.245147 1 0.0010 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3241.245109 2 0.9961 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 3241.245109 0 1.0938 240 | 0/8 11 h-lim-p 0.9009 20.0000 0.0001 3241.245109 0 0.0123 265 | 0/8 12 h-lim-p 0.0003 3.0630 0.0042 3241.245109 0 0.0003 285 | 0/8 13 h-lim-p 0.0000 0.0175 0.7292 3241.245109 0 0.0000 309 | 0/8 14 h-lim-p 0.0001 3.8443 0.0033 3241.245109 0 0.0000 332 | 0/8 15 h-lim-p 0.0000 15.4045 0.0008 3241.245109 0 0.0000 365 | 0/8 16 h-lim-p 0.0000 20.0000 0.0011 3241.245109 0 0.0005 390 | 0/8 17 h-lim-p 0.0012 20.0000 0.0004 3241.245109 0 0.0000 420 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 3241.245109 0 0.0000 440 | 0/8 19 h-lim-p 0.0000 20.0000 0.0002 3241.245109 0 0.0000 461 | 0/8 20 h-lim-p 0.0000 15.1506 0.0009 3241.245109 0 0.0000 483 | 0/8 21 h-lim-p 0.0000 0.4582 0.0276 3241.245109 0 0.0006 509 | 0/8 22 h-lim-p 0.0001 0.0870 0.1465 3241.245109 0 0.0001 529 | 0/8 23 h-lim-p 0.0584 20.0000 0.0003 3241.245109 0 0.0000 559 | 0/8 24 h-lim-p 0.0000 3.5491 0.0036 3241.245109 0 0.0000 583 | 0/8 25 h-lim-p 0.0000 20.0000 0.0001 3241.245109 0 0.0000 603 | 0/8 26 h-lim-p 0.0000 20.0000 0.0000 3241.245109 0 0.0000 633 | 0/8 27 h-lim-p 0.0000 20.0000 0.0026 | 0/8 28 h-lim-p 0.0000 20.0000 0.0026 Out... lnL = -3241.245109 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3241.245109 Node 7: lnL = -3241.245109 Node 8: lnL = -3241.245109 Node 9: lnL = -3241.245109 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 527 Sequential format.. Reading seq # 1: YER071C_Sbay Reading seq # 2: YER071C_Scer Reading seq # 3: YER071C_Skud Reading seq # 4: YER071C_Smik Reading seq # 5: YER071C_Spar Sequences read.. Counting patterns.. # site patterns = 210 Counting frequencies.. 120 bytes for distance 33600 bytes for lkl0 26880 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.021306 0.115313 0.070187 0.103031 0.088207 0.215201 0.155912 0.249797 lnL0 = -2314.175001 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2314.175001 x= 0.02131 0.11531 0.07019 0.10303 0.08821 0.21520 0.15591 0.24980 1 h-lim-p 0.0056 0.0448 80.8319 2312.958902 8 0.0004 42 | 0/8 2 h-lim-p 0.0007 0.0059 27.0420 2312.748608 5 0.0006 66 | 0/8 3 h-lim-p 0.0014 0.0183 12.4303 2312.730894 3 0.0003 85 | 0/8 4 h-lim-p 0.0029 0.1448 1.2153 2312.730465 3 0.0006 104 | 0/8 5 h-lim-p 0.0019 0.6557 0.3797 2312.730416 2 0.0007 120 | 0/8 6 h-lim-p 0.0044 0.9501 0.0625 2312.730414 0 0.0010 141 | 0/8 7 h-lim-p 0.0074 16.9331 0.0080 2312.730403 0 0.0149 162 | 0/8 8 h-lim-p 0.0041 20.0000 0.0292 2312.729636 0 0.0328 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2312.729615 1 0.9961 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2312.729615 0 1.0938 227 | 0/8 11 h-lim-p 1.2349 20.0000 0.0000 2312.729615 0 2.4698 248 | 0/8 12 h-lim-p 0.1312 20.0000 0.0004 2312.729615 0 0.1148 268 | 0/8 13 h-lim-p 0.0288 20.0000 0.0015 2312.729615 0 0.0018 291 | 0/8 14 h-lim-p 0.0009 13.8064 0.0030 2312.729615 0 0.0000 317 | 0/8 15 h-lim-p 0.0001 20.0000 0.0003 2312.729615 0 0.0000 339 | 0/8 16 h-lim-p 0.0004 20.0000 0.0000 2312.729615 0 0.0000 361 Out... lnL = -2312.729615 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2312.729615 Node 7: lnL = -2312.729615 Node 8: lnL = -2312.729615 Node 9: lnL = -2312.729615 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 526 Sequential format.. Reading seq # 1: YER072W_Sbay Reading seq # 2: YER072W_Scer Reading seq # 3: YER072W_Skud Reading seq # 4: YER072W_Smik Reading seq # 5: YER072W_Spar Sequences read.. Counting patterns.. # site patterns = 193 Counting frequencies.. 120 bytes for distance 30880 bytes for lkl0 24704 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.009038 0.102325 0.076628 0.106711 0.084994 0.212779 0.162250 0.229775 lnL0 = -2305.221109 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2305.221109 x= 0.00904 0.10233 0.07663 0.10671 0.08499 0.21278 0.16225 0.22977 1 h-lim-p 0.0077 0.1839 77.2719 2304.253449 6 0.0003 38 | 0/8 2 h-lim-p 0.0015 0.0140 17.4221 2304.171526 7 0.0006 66 | 0/8 3 h-lim-p 0.0011 0.0294 8.7038 2304.162535 4 0.0003 87 | 0/8 4 h-lim-p 0.0027 0.2451 0.9354 2304.162308 2 0.0005 104 | 0/8 5 h-lim-p 0.0024 1.6130 0.2095 2304.162296 0 0.0005 125 | 0/8 6 h-lim-p 0.0026 1.3165 0.0415 2304.162295 0 0.0011 145 | 0/8 7 h-lim-p 0.0183 20.0000 0.0026 2304.162289 0 0.0274 165 | 0/8 8 h-lim-p 0.0024 20.0000 0.0302 2304.162076 0 0.0142 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2304.162075 0 1.0938 207 | 0/8 10 h-lim-p 1.4438 20.0000 0.0000 2304.162075 0 1.2634 227 | 0/8 11 h-lim-p 1.3948 20.0000 0.0000 2304.162075 0 2.0922 247 | 0/8 12 h-lim-p 0.8894 20.0000 0.0001 2304.162075 0 0.8894 267 | 0/8 13 h-lim-p 0.0024 1.1797 0.0184 2304.162075 0 0.0000 294 | 0/8 14 h-lim-p 0.0001 18.7971 0.0012 2304.162075 0 0.0000 330 | 0/8 15 h-lim-p 0.0000 20.0000 0.0012 | 0/8 16 h-lim-p 0.0000 20.0000 0.0012 Out... lnL = -2304.162075 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2304.162075 Node 7: lnL = -2304.162075 Node 8: lnL = -2304.162075 Node 9: lnL = -2304.162075 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 890 Sequential format.. Reading seq # 1: YER073W_Sbay Reading seq # 2: YER073W_Scer Reading seq # 3: YER073W_Skud Reading seq # 4: YER073W_Smik Reading seq # 5: YER073W_Spar Sequences read.. Counting patterns.. # site patterns = 301 Counting frequencies.. 120 bytes for distance 48160 bytes for lkl0 38528 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.030615 0.018464 0.083399 0.114215 0.062990 0.195464 0.151816 0.221671 lnL0 = -3689.262148 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3689.262148 x= 0.03061 0.01846 0.08340 0.11422 0.06299 0.19546 0.15182 0.22167 1 h-lim-p 0.0005 0.0042 365.3880 3683.891000 7 0.0001 39 | 0/8 2 h-lim-p 0.0003 0.0024 48.6537 3683.596525 6 0.0003 64 | 0/8 3 h-lim-p 0.0006 0.0137 20.8151 3683.566297 6 0.0002 90 | 0/8 4 h-lim-p 0.0004 0.0286 7.8588 3683.558899 5 0.0003 114 | 0/8 5 h-lim-p 0.0060 0.3245 0.3678 3683.558880 2 0.0003 133 | 0/8 6 h-lim-p 0.0020 3.5443 0.0541 3683.558879 0 0.0005 154 | 0/8 7 h-lim-p 0.0030 20.0000 0.0089 3683.558874 0 0.0059 175 | 0/8 8 h-lim-p 0.0052 4.7540 0.0102 3683.558031 0 0.0416 198 | 0/8 9 h-lim-p 1.4983 20.0000 0.0003 3683.557985 2 0.9584 223 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3683.557985 0 1.0938 243 | 0/8 11 h-lim-p 1.5820 20.0000 0.0000 3683.557985 0 0.6921 263 | 0/8 12 h-lim-p 0.2237 20.0000 0.0001 3683.557985 0 0.0000 302 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 3683.557985 0 0.0000 324 Out... lnL = -3683.557985 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3683.557985 Node 7: lnL = -3683.557985 Node 8: lnL = -3683.557985 Node 9: lnL = -3683.557985 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 641 Sequential format.. Reading seq # 1: YER078C_Sbay Reading seq # 2: YER078C_Scer Reading seq # 3: YER078C_Skud Reading seq # 4: YER078C_Smik Reading seq # 5: YER078C_Spar Sequences read.. Counting patterns.. # site patterns = 235 Counting frequencies.. 120 bytes for distance 37600 bytes for lkl0 30080 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.037091 0.075041 0.064635 0.113769 0.073160 0.180827 0.188046 0.245444 lnL0 = -2678.878382 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2678.878382 x= 0.03709 0.07504 0.06463 0.11377 0.07316 0.18083 0.18805 0.24544 1 h-lim-p 0.0007 0.0054 72.3364 2678.249232 6 0.0002 36 | 0/8 2 h-lim-p 0.0012 0.0098 13.6922 2678.216335 6 0.0004 63 | 0/8 3 h-lim-p 0.0008 0.0485 6.0961 2678.212076 5 0.0003 87 | 0/8 4 h-lim-p 0.0007 0.0561 2.4971 2678.211079 5 0.0004 113 | 0/8 5 h-lim-p 0.0019 0.3413 0.5047 2678.211021 2 0.0005 130 | 0/8 6 h-lim-p 0.0016 2.2658 0.1505 2678.211016 2 0.0005 155 | 0/8 7 h-lim-p 0.0148 20.0000 0.0051 2678.211016 0 0.0016 177 | 0/8 8 h-lim-p 0.0252 20.0000 0.0003 2678.210989 0 0.4029 201 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2678.210989 0 1.0938 221 | 0/8 10 h-lim-p 1.5664 20.0000 0.0000 2678.210989 0 1.3706 241 | 0/8 11 h-lim-p 1.4443 20.0000 0.0000 2678.210989 0 0.0903 264 | 0/8 12 h-lim-p 0.0175 20.0000 0.0001 2678.210989 0 0.0044 285 | 0/8 13 h-lim-p 0.0020 20.0000 0.0002 2678.210989 0 0.0010 305 | 0/8 14 h-lim-p 0.0003 20.0000 0.0007 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0015 2678.210989 0 0.0000 374 | 0/8 16 h-lim-p 0.0000 20.0000 0.0021 2678.210989 0 0.0000 395 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0015 | 0/8 19 h-lim-p 0.0000 20.0000 0.0015 Out... lnL = -2678.210989 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2678.210989 Node 7: lnL = -2678.210989 Node 8: lnL = -2678.210989 Node 9: lnL = -2678.210989 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 635 Sequential format.. Reading seq # 1: YER079W_Sbay Reading seq # 2: YER079W_Scer Reading seq # 3: YER079W_Skud Reading seq # 4: YER079W_Smik Reading seq # 5: YER079W_Spar Sequences read.. Counting patterns.. # site patterns = 234 Counting frequencies.. 120 bytes for distance 37440 bytes for lkl0 29952 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.028067 0.092372 0.072420 0.116165 0.068435 0.180825 0.241939 0.254088 lnL0 = -2740.146037 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2740.146037 x= 0.02807 0.09237 0.07242 0.11616 0.06844 0.18083 0.24194 0.25409 1 h-lim-p 0.0022 0.0177 48.7090 2739.780426 8 0.0003 44 | 0/8 2 h-lim-p 0.0008 0.0071 19.5697 2739.732036 5 0.0003 68 | 0/8 3 h-lim-p 0.0008 0.0142 7.2920 2739.724573 4 0.0003 89 | 0/8 4 h-lim-p 0.0010 0.0671 2.2631 2739.723489 3 0.0005 107 | 0/8 5 h-lim-p 0.0019 0.5094 0.5507 2739.723409 3 0.0006 127 | 0/8 6 h-lim-p 0.0012 1.2485 0.2725 2739.723396 1 0.0005 149 | 0/8 7 h-lim-p 0.0042 2.0106 0.0305 2739.723395 0 0.0009 170 | 0/8 8 h-lim-p 0.1631 20.0000 0.0002 2739.723360 0 1.3048 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2739.723356 0 1.0938 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2739.723356 0 1.0938 233 | 0/8 11 h-lim-p 1.1500 20.0000 0.0000 2739.723356 0 2.3000 254 | 0/8 12 h-lim-p 1.3494 20.0000 0.0000 2739.723356 0 0.5904 274 | 0/8 13 h-lim-p 0.0208 20.0000 0.0010 2739.723356 0 0.0000 308 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 2739.723356 0 0.0000 338 Out... lnL = -2739.723356 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2739.723356 Node 7: lnL = -2739.723356 Node 8: lnL = -2739.723356 Node 9: lnL = -2739.723356 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 438 Sequential format.. Reading seq # 1: YER080W_Sbay Reading seq # 2: YER080W_Scer Reading seq # 3: YER080W_Skud Reading seq # 4: YER080W_Smik Reading seq # 5: YER080W_Spar Sequences read.. Counting patterns.. # site patterns = 175 Counting frequencies.. 120 bytes for distance 28000 bytes for lkl0 22400 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.001220 0.072760 0.072298 0.098041 0.072928 0.232833 0.175627 0.199635 lnL0 = -1871.253808 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1871.253808 x= 0.00122 0.07276 0.07230 0.09804 0.07293 0.23283 0.17563 0.19963 1 h-lim-p 0.0009 0.0072 55.1448 1870.753593 6 0.0003 34 | 0/8 2 h-lim-p 0.0001 0.0007 10.0256 1870.728962 m 0.0007 46 | 0/8 3 h-lim-p -0.0000 -0.0000 4.7925 h-lim-p: -7.06131860e-21 -5.64905488e-20 4.79245565e+00 1870.728962 .. | 0/8 4 h-lim-p 0.0000 17.4906 6.1179 1870.724393 0 0.0003 71 | 0/8 5 h-lim-p 0.0012 0.1119 1.6173 1870.723791 3 0.0005 89 | 0/8 6 h-lim-p 0.0013 0.0129 0.6248 1870.723674 3 0.0007 108 | 0/8 7 h-lim-p 0.0024 0.0480 0.1742 1870.723667 1 0.0005 131 | 0/8 8 h-lim-p 0.0015 0.0551 0.0568 1870.723665 0 0.0006 151 | 0/8 9 h-lim-p 0.0039 20.0000 0.0095 1870.723664 0 0.0039 171 | 0/8 10 h-lim-p 0.0015 0.3368 0.0247 1870.723647 0 0.0059 193 | 0/8 11 h-lim-p 0.0043 0.0733 0.0339 1870.723409 0 0.0130 214 | 0/8 12 h-lim-p 2.5000 20.0000 0.0001 1870.723404 1 0.9961 236 | 0/8 13 h-lim-p 2.3740 20.0000 0.0000 1870.723404 0 2.0772 256 | 0/8 14 h-lim-p 0.0242 0.2801 0.0025 1870.723404 0 0.0045 278 | 0/8 15 h-lim-p 0.0015 0.0923 0.0076 1870.723404 0 0.0000 313 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 1870.723404 0 0.0000 347 Out... lnL = -1870.723404 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1870.723404 Node 7: lnL = -1870.723404 Node 8: lnL = -1870.723404 Node 9: lnL = -1870.723404 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 880 Sequential format.. Reading seq # 1: YER081W_Sbay Reading seq # 2: YER081W_Scer Reading seq # 3: YER081W_Skud Reading seq # 4: YER081W_Smik Reading seq # 5: YER081W_Spar Sequences read.. Counting patterns.. # site patterns = 281 Counting frequencies.. 120 bytes for distance 44960 bytes for lkl0 35968 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.043747 0.070408 0.044644 0.088326 0.094216 0.202993 0.204198 0.254658 lnL0 = -3801.593879 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3801.593879 x= 0.04375 0.07041 0.04464 0.08833 0.09422 0.20299 0.20420 0.25466 1 h-lim-p 0.0005 0.0044 187.1188 3799.281971 7 0.0001 36 | 0/8 2 h-lim-p 0.0005 0.0042 35.1327 3799.139902 3 0.0002 54 | 0/8 3 h-lim-p 0.0006 0.0094 14.9368 3799.118452 4 0.0002 74 | 0/8 4 h-lim-p 0.0006 0.0446 5.4164 3799.114417 4 0.0003 95 | 0/8 5 h-lim-p 0.0016 0.1544 1.0457 3799.114270 3 0.0003 116 | 0/8 6 h-lim-p 0.0015 1.5017 0.2041 3799.114260 2 0.0005 133 | 0/8 7 h-lim-p 0.0074 18.6889 0.0131 3799.114260 0 0.0016 154 | 0/8 8 h-lim-p 0.0173 20.0000 0.0012 3799.113933 0 0.2762 178 | 0/8 9 h-lim-p 1.3712 20.0000 0.0002 3799.113931 0 1.1998 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3799.113931 0 1.0938 218 | 0/8 11 h-lim-p 0.8993 20.0000 0.0000 3799.113931 0 0.8993 238 | 0/8 12 h-lim-p 0.4518 20.0000 0.0001 3799.113931 0 0.0565 260 | 0/8 13 h-lim-p 0.0106 20.0000 0.0003 3799.113931 0 0.0000 298 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 3799.113931 0 0.0000 323 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -3799.113931 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3799.113931 Node 7: lnL = -3799.113931 Node 8: lnL = -3799.113931 Node 9: lnL = -3799.113931 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 995 Sequential format.. Reading seq # 1: YER084W_Sbay Reading seq # 2: YER084W_Scer Reading seq # 3: YER084W_Skud Reading seq # 4: YER084W_Smik Reading seq # 5: YER084W_Spar Sequences read.. Counting patterns.. # site patterns = 198 Counting frequencies.. 120 bytes for distance 31680 bytes for lkl0 25344 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.019386 0.022038 0.007527 0.074689 0.068076 0.103224 0.140751 0.136000 lnL0 = -3210.195760 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3210.195760 x= 0.01939 0.02204 0.00753 0.07469 0.06808 0.10322 0.14075 0.13600 1 h-lim-p 0.0002 0.0015 639.6753 3205.573353 6 0.0000 35 | 0/8 2 h-lim-p 0.0001 0.0005 166.0495 3204.397221 0 0.0001 48 | 0/8 3 h-lim-p 0.0001 0.0010 44.3370 3204.262417 0 0.0002 60 | 0/8 4 h-lim-p 0.0005 0.0086 16.7258 3204.236255 5 0.0002 81 | 0/8 5 h-lim-p 0.0007 0.0182 4.7717 3204.235135 5 0.0001 108 | 0/8 6 h-lim-p 0.0006 0.0996 0.8839 3204.235041 3 0.0002 127 | 0/8 7 h-lim-p 0.0033 2.2302 0.0545 3204.234095 0 0.0133 149 | 0/8 8 h-lim-p 0.0019 0.1822 0.3858 3204.145911 0 0.0150 172 | 0/8 9 h-lim-p 2.5000 20.0000 0.0009 3204.141017 2 1.1719 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0003 3204.140661 4 1.3578 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0001 3204.140661 0 1.0938 245 | 0/8 12 h-lim-p 1.9263 20.0000 0.0001 3204.140661 0 0.9632 265 | 0/8 13 h-lim-p 0.5190 20.0000 0.0001 3204.140661 0 0.0020 292 | 0/8 14 h-lim-p 0.0003 20.0000 0.0008 3204.140661 0 0.0000 316 | 0/8 15 h-lim-p 0.0001 20.0000 0.0001 3204.140661 0 0.0000 346 | 0/8 16 h-lim-p 0.0000 20.0000 0.0012 3204.140661 0 0.0000 376 | 0/8 17 h-lim-p 0.0000 20.0000 0.0015 3204.140661 0 0.0010 402 | 0/8 18 h-lim-p 0.0053 20.0000 0.0003 3204.140661 0 0.0000 431 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 3204.140661 0 0.0000 451 | 0/8 20 h-lim-p 0.0000 20.0000 0.0005 3204.140661 0 0.0000 476 | 0/8 21 h-lim-p 0.0000 12.0593 0.0153 .. | 0/8 22 h-lim-p 0.0000 20.0000 0.0165 | 0/8 23 h-lim-p 0.0000 20.0000 0.0165 Out... lnL = -3204.140661 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3204.140661 Node 7: lnL = -3204.140661 Node 8: lnL = -3204.140661 Node 9: lnL = -3204.140661 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 377 Sequential format.. Reading seq # 1: YER085C_Sbay Reading seq # 2: YER085C_Scer Reading seq # 3: YER085C_Skud Reading seq # 4: YER085C_Smik Reading seq # 5: YER085C_Spar Sequences read.. Counting patterns.. # site patterns = 158 Counting frequencies.. 120 bytes for distance 25280 bytes for lkl0 20224 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.036432 0.026208 0.051613 0.100092 0.070069 0.120470 0.194716 0.203945 lnL0 = -1429.499329 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1429.499329 x= 0.03643 0.02621 0.05161 0.10009 0.07007 0.12047 0.19472 0.20395 1 h-lim-p 0.0005 0.0038 152.3613 1426.862448 10 0.0003 46 | 0/8 2 h-lim-p 0.0002 0.0017 41.4327 1426.445223 0 0.0004 59 | 0/8 3 h-lim-p 0.0010 0.0156 16.8509 1426.395206 6 0.0004 85 | 0/8 4 h-lim-p 0.0009 0.0322 7.9352 1426.381976 4 0.0005 108 | 0/8 5 h-lim-p 0.0030 0.1957 1.3759 1426.381338 2 0.0007 125 | 0/8 6 h-lim-p 0.0020 0.4434 0.4754 1426.381253 3 0.0007 144 | 0/8 7 h-lim-p 0.0100 2.0138 0.0343 1426.380774 0 0.0200 165 | 0/8 8 h-lim-p 0.0037 0.3570 0.1839 1426.366222 0 0.0298 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0012 1426.363731 2 1.1719 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0003 1426.363602 3 1.3159 239 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1426.363602 0 1.0938 259 | 0/8 12 h-lim-p 1.2219 20.0000 0.0000 1426.363602 0 1.2219 279 | 0/8 13 h-lim-p 1.1795 20.0000 0.0000 1426.363602 0 0.0040 306 | 0/8 14 h-lim-p 0.0003 20.0000 0.0002 1426.363602 0 0.0000 340 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 | 0/8 16 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -1426.363602 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1426.363602 Node 7: lnL = -1426.363602 Node 8: lnL = -1426.363602 Node 9: lnL = -1426.363602 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 377 Sequential format.. Reading seq # 1: YER086W_Sbay Reading seq # 2: YER086W_Scer Reading seq # 3: YER086W_Skud Reading seq # 4: YER086W_Smik Reading seq # 5: YER086W_Spar Sequences read.. Counting patterns.. # site patterns = 145 Counting frequencies.. 120 bytes for distance 23200 bytes for lkl0 18560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.041979 0.019581 0.036584 0.104331 0.065830 0.147165 0.203406 0.212965 lnL0 = -1507.824319 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1507.824319 x= 0.04198 0.01958 0.03658 0.10433 0.06583 0.14717 0.20341 0.21297 1 h-lim-p 0.0004 0.0028 219.2205 1503.929730 9 0.0002 45 | 0/8 2 h-lim-p 0.0005 0.0040 21.8218 1503.802302 6 0.0005 70 | 0/8 3 h-lim-p 0.0008 0.0064 12.1657 1503.782328 6 0.0003 93 | 0/8 4 h-lim-p 0.0016 0.0598 2.5734 1503.780972 5 0.0004 116 | 0/8 5 h-lim-p 0.0017 0.1050 0.6595 1503.780875 4 0.0005 138 | 0/8 6 h-lim-p 0.0014 1.1830 0.2206 1503.780860 0 0.0007 158 | 0/8 7 h-lim-p 0.0044 6.6273 0.0360 1503.780859 0 0.0011 179 | 0/8 8 h-lim-p 0.4083 20.0000 0.0001 1503.780824 0 1.6331 201 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1503.780823 0 1.0938 221 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1503.780823 0 1.0938 241 | 0/8 11 h-lim-p 1.1095 20.0000 0.0000 1503.780823 0 1.1095 261 | 0/8 12 h-lim-p 0.1350 20.0000 0.0001 1503.780823 0 0.1013 281 | 0/8 13 h-lim-p 0.0277 20.0000 0.0004 1503.780823 0 0.0000 312 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 1503.780823 0 0.0001 332 | 0/8 15 h-lim-p 0.0004 20.0000 0.0000 1503.780823 0 0.0000 361 Out... lnL = -1503.780823 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1503.780823 Node 7: lnL = -1503.780823 Node 8: lnL = -1503.780823 Node 9: lnL = -1503.780823 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 413 Sequential format.. Reading seq # 1: YER087W_Sbay Reading seq # 2: YER087W_Scer Reading seq # 3: YER087W_Skud Reading seq # 4: YER087W_Smik Reading seq # 5: YER087W_Spar Sequences read.. Counting patterns.. # site patterns = 153 Counting frequencies.. 120 bytes for distance 24480 bytes for lkl0 19584 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.062918 0.048938 0.059100 0.115163 0.087101 0.151218 0.193964 0.270239 lnL0 = -1742.802032 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1742.802032 x= 0.06292 0.04894 0.05910 0.11516 0.08710 0.15122 0.19396 0.27024 1 h-lim-p 0.0004 0.0036 69.6838 1741.874674 3 0.0004 28 | 0/8 2 h-lim-p 0.0006 0.0051 16.5990 1741.804563 3 0.0005 46 | 0/8 3 h-lim-p 0.0013 0.0480 7.0569 1741.794443 5 0.0005 68 | 0/8 4 h-lim-p 0.0014 0.0633 2.4076 1741.793275 4 0.0005 90 | 0/8 5 h-lim-p 0.0012 0.2733 0.9681 1741.792999 4 0.0007 113 | 0/8 6 h-lim-p 0.0036 1.3846 0.1813 1741.792990 2 0.0006 140 | 0/8 7 h-lim-p 0.0083 7.3354 0.0131 1741.792990 0 0.0018 161 | 0/8 8 h-lim-p 0.0650 20.0000 0.0004 1741.792927 0 0.7801 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1741.792926 0 1.0938 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1741.792926 0 1.0938 224 | 0/8 11 h-lim-p 1.1222 20.0000 0.0000 1741.792926 0 0.5611 244 | 0/8 12 h-lim-p 0.1339 20.0000 0.0000 1741.792926 0 0.0042 268 | 0/8 13 h-lim-p 0.0016 20.0000 0.0001 1741.792926 0 0.0000 293 | 0/8 14 h-lim-p 0.0003 20.0000 0.0000 1741.792926 0 0.0000 323 Out... lnL = -1741.792926 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1741.792926 Node 7: lnL = -1741.792926 Node 8: lnL = -1741.792926 Node 9: lnL = -1741.792926 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 672 Sequential format.. Reading seq # 1: YER089C_Sbay Reading seq # 2: YER089C_Scer Reading seq # 3: YER089C_Skud Reading seq # 4: YER089C_Smik Reading seq # 5: YER089C_Spar Sequences read.. Counting patterns.. # site patterns = 202 Counting frequencies.. 120 bytes for distance 32320 bytes for lkl0 25856 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.049230 0.054853 0.034344 0.067266 0.049949 0.144631 0.166786 0.213254 lnL0 = -2603.082625 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2603.082625 x= 0.04923 0.05485 0.03434 0.06727 0.04995 0.14463 0.16679 0.21325 1 h-lim-p 0.0002 0.0016 150.8952 2601.514870 7 0.0001 36 | 0/8 2 h-lim-p 0.0002 0.0017 37.6451 2601.379453 2 0.0002 52 | 0/8 3 h-lim-p 0.0007 0.0290 10.4269 2601.371579 3 0.0002 71 | 0/8 4 h-lim-p 0.0003 0.0289 5.7744 2601.368664 4 0.0002 91 | 0/8 5 h-lim-p 0.0005 0.0885 2.4904 2601.368073 2 0.0002 107 | 0/8 6 h-lim-p 0.0013 0.4608 0.4494 2601.368033 2 0.0004 125 | 0/8 7 h-lim-p 0.0083 14.0561 0.0241 2601.368032 0 0.0009 147 | 0/8 8 h-lim-p 0.0671 20.0000 0.0003 2601.367850 0 0.8049 170 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2601.367849 0 1.0938 190 | 0/8 10 h-lim-p 1.2017 20.0000 0.0000 2601.367849 0 1.0515 210 | 0/8 11 h-lim-p 1.0704 20.0000 0.0000 2601.367849 0 8.5628 233 | 0/8 12 h-lim-p 0.6231 20.0000 0.0003 2601.367849 0 0.0097 258 | 0/8 13 h-lim-p 0.0000 0.1810 0.4138 2601.367849 0 0.0000 291 | 0/8 14 h-lim-p 0.0004 20.0000 0.0000 2601.367849 0 0.0000 323 Out... lnL = -2601.367849 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2601.367849 Node 7: lnL = -2601.367849 Node 8: lnL = -2601.367849 Node 9: lnL = -2601.367849 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 657 Sequential format.. Reading seq # 1: YER090W_Sbay Reading seq # 2: YER090W_Scer Reading seq # 3: YER090W_Skud Reading seq # 4: YER090W_Smik Reading seq # 5: YER090W_Spar Sequences read.. Counting patterns.. # site patterns = 204 Counting frequencies.. 120 bytes for distance 32640 bytes for lkl0 26112 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.078338 0.038221 0.044499 0.066672 0.046649 0.143886 0.176125 0.255566 lnL0 = -2643.304270 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2643.304270 x= 0.07834 0.03822 0.04450 0.06667 0.04665 0.14389 0.17612 0.25557 1 h-lim-p 0.0002 0.0017 160.5119 2641.344713 4 0.0002 30 | 0/8 2 h-lim-p 0.0003 0.0020 33.9457 2641.194937 5 0.0003 52 | 0/8 3 h-lim-p 0.0006 0.0146 14.8004 2641.163655 7 0.0003 82 | 0/8 4 h-lim-p 0.0010 0.0197 5.1930 2641.161130 3 0.0002 101 | 0/8 5 h-lim-p 0.0004 0.0972 2.5379 2641.160576 2 0.0002 117 | 0/8 6 h-lim-p 0.0003 0.0805 2.0063 2641.160361 3 0.0002 136 | 0/8 7 h-lim-p 0.0238 8.4714 0.0145 2641.160347 2 0.0076 153 | 0/8 8 h-lim-p 0.0085 20.0000 0.0130 2641.158335 0 0.0678 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 2641.158259 2 0.9961 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2641.158258 0 1.0938 220 | 0/8 11 h-lim-p 1.2253 20.0000 0.0000 2641.158258 0 2.4506 241 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2641.158258 0 0.0171 267 | 0/8 13 h-lim-p 0.0015 20.0000 0.0000 2641.158258 0 0.0008 287 | 0/8 14 h-lim-p 0.0005 20.0000 0.0000 2641.158258 0 0.0000 310 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 2641.158258 0 0.0000 330 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 2641.158258 0 0.0000 351 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 2641.158258 0 0.0000 379 | 0/8 18 h-lim-p 0.0000 20.0000 0.0042 | 0/8 19 h-lim-p 0.0000 20.0000 0.0042 Out... lnL = -2641.158258 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2641.158258 Node 7: lnL = -2641.158258 Node 8: lnL = -2641.158258 Node 9: lnL = -2641.158258 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 562 Sequential format.. Reading seq # 1: YER093C-A_Sbay Reading seq # 2: YER093C-A_Scer Reading seq # 3: YER093C-A_Skud Reading seq # 4: YER093C-A_Smik Reading seq # 5: YER093C-A_Spar Sequences read.. Counting patterns.. # site patterns = 220 Counting frequencies.. 120 bytes for distance 35200 bytes for lkl0 28160 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.007044 0.113651 0.082776 0.165049 0.040209 0.078203 0.164142 0.194757 lnL0 = -2239.590967 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2239.590967 x= 0.00704 0.11365 0.08278 0.16505 0.04021 0.07820 0.16414 0.19476 1 h-lim-p 0.0005 0.0037 184.7361 2237.225146 9 0.0002 46 | 0/8 2 h-lim-p 0.0004 0.0030 61.8880 2236.301898 0 0.0006 58 | 0/8 3 h-lim-p 0.0013 0.0105 16.5441 2236.249154 7 0.0004 89 | 0/8 4 h-lim-p 0.0050 0.1531 1.3812 2236.248869 2 0.0003 108 | 0/8 5 h-lim-p 0.0017 0.8549 0.2374 2236.248840 1 0.0007 122 | 0/8 6 h-lim-p 0.0021 0.2084 0.0768 2236.248750 0 0.0042 143 | 0/8 7 h-lim-p 0.0016 0.9955 0.1991 2236.247709 0 0.0064 165 | 0/8 8 h-lim-p 0.0019 0.4589 0.6736 2236.236813 0 0.0057 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 2236.236316 3 1.0449 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2236.236313 1 1.2305 235 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2236.236312 0 1.0938 255 | 0/8 12 h-lim-p 1.2482 20.0000 0.0000 2236.236312 0 0.0073 282 | 0/8 13 h-lim-p 0.0004 12.1276 0.0007 2236.236312 0 0.0000 308 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 2236.236312 0 0.0000 329 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 2236.236312 0 0.0000 361 Out... lnL = -2236.236312 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2236.236312 Node 7: lnL = -2236.236312 Node 8: lnL = -2236.236312 Node 9: lnL = -2236.236312 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 693 Sequential format.. Reading seq # 1: YER094C_Sbay Reading seq # 2: YER094C_Scer Reading seq # 3: YER094C_Skud Reading seq # 4: YER094C_Smik Reading seq # 5: YER094C_Spar Sequences read.. Counting patterns.. # site patterns = 217 Counting frequencies.. 120 bytes for distance 34720 bytes for lkl0 27776 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.015113 0.020875 0.073017 0.115812 0.088060 0.131202 0.235102 0.199079 lnL0 = -2558.941354 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2558.941354 x= 0.01511 0.02088 0.07302 0.11581 0.08806 0.13120 0.23510 0.19908 1 h-lim-p 0.0019 0.0220 165.8848 2556.662274 4 0.0002 32 | 0/8 2 h-lim-p 0.0003 0.0027 52.3893 2555.816432 0 0.0007 45 | 0/8 3 h-lim-p 0.0004 0.0035 29.1350 2555.675093 2 0.0004 61 | 0/8 4 h-lim-p 0.0009 0.0070 12.1513 2555.658189 5 0.0003 85 | 0/8 5 h-lim-p 0.0014 0.0791 2.4932 2555.656353 2 0.0006 101 | 0/8 6 h-lim-p 0.0028 0.3198 0.5805 2555.656257 2 0.0006 118 | 0/8 7 h-lim-p 0.0012 0.5214 0.2574 2555.656221 2 0.0010 142 | 0/8 8 h-lim-p 0.0876 20.0000 0.0028 2555.644297 0 1.0515 165 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 2555.643532 3 1.0449 191 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2555.643532 0 1.0938 211 | 0/8 11 h-lim-p 1.7265 20.0000 0.0000 2555.643532 0 1.5107 231 | 0/8 12 h-lim-p 1.7512 20.0000 0.0000 2555.643532 0 0.7661 251 | 0/8 13 h-lim-p 0.2077 20.0000 0.0001 2555.643532 0 0.0049 276 | 0/8 14 h-lim-p 0.0013 20.0000 0.0003 2555.643532 0 0.0000 312 | 0/8 15 h-lim-p 0.0000 20.0000 0.0011 | 0/8 16 h-lim-p 0.0000 20.0000 0.0011 Out... lnL = -2555.643532 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2555.643532 Node 7: lnL = -2555.643532 Node 8: lnL = -2555.643532 Node 9: lnL = -2555.643532 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 656 Sequential format.. Reading seq # 1: YER095W_Sbay Reading seq # 2: YER095W_Scer Reading seq # 3: YER095W_Skud Reading seq # 4: YER095W_Smik Reading seq # 5: YER095W_Spar Sequences read.. Counting patterns.. # site patterns = 148 Counting frequencies.. 120 bytes for distance 23680 bytes for lkl0 18944 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.394520 0.259586 0.190000 0.349773 3.586184 0.358776 0.720544 lnL0 = -2603.343068 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2603.343068 x= 0.00006 0.39452 0.25959 0.19000 0.34977 3.58618 0.35878 0.72054 1 h-lim-p 0.0000 0.0000 561.1348 2603.172253 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0002 2103.6006 2386.143691 m 0.0002 36 | 2/8 3 h-lim-p 0.0001 0.0008 344.5931 2357.847939 0 0.0006 50 | 2/8 4 h-lim-p 0.0001 0.0012 281.4492 2347.447628 0 0.0004 63 | 2/8 5 h-lim-p 0.0020 0.0160 21.7864 2347.260958 7 0.0007 93 | 2/8 6 h-lim-p 0.0147 0.2084 1.1003 2347.162331 6 0.0081 120 | 1/8 7 h-lim-p 0.0003 0.0191 35.4579 2346.803797 0 0.0008 133 | 1/8 8 h-lim-p 0.0681 0.5444 0.1444 2344.549052 0 0.4083 147 | 0/8 9 h-lim-p 0.0011 0.0088 8.3586 2344.532715 2 0.0005 170 | 0/8 10 h-lim-p 0.1107 0.8854 0.0201 2344.370940 m 0.8854 182 | 1/8 11 h-lim-p 2.5000 20.0000 0.0040 2344.356629 6 0.8872 215 | 0/8 12 h-lim-p 0.0014 0.2567 2.5904 2344.354927 4 0.0006 244 | 0/8 13 h-lim-p 2.5000 20.0000 0.0003 2344.354854 3 0.8800 263 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 2344.354854 0 1.0938 283 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2344.354854 0 1.2500 303 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 2344.354854 0 0.0012 333 Out... lnL = -2344.354854 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2344.354854 Node 7: lnL = -2344.354854 Node 8: lnL = -2344.354854 Node 9: lnL = -2344.354854 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 565 Sequential format.. Reading seq # 1: YER096W_Sbay Reading seq # 2: YER096W_Scer Reading seq # 3: YER096W_Skud Reading seq # 4: YER096W_Smik Reading seq # 5: YER096W_Spar Sequences read.. Counting patterns.. # site patterns = 162 Counting frequencies.. 120 bytes for distance 25920 bytes for lkl0 20736 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.005756 0.043297 0.055057 0.096982 0.045998 0.163503 0.116676 0.144231 lnL0 = -2138.123916 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2138.123916 x= 0.00576 0.04330 0.05506 0.09698 0.04600 0.16350 0.11668 0.14423 1 h-lim-p 0.0032 0.8937 116.5023 2137.208046 8 0.0001 43 | 0/8 2 h-lim-p 0.0003 0.0026 14.6341 2137.188887 6 0.0002 70 | 0/8 3 h-lim-p 0.0005 0.0071 4.8664 2137.187068 5 0.0002 96 | 0/8 4 h-lim-p 0.0009 0.1862 0.9473 2137.186912 1 0.0003 110 | 0/8 5 h-lim-p 0.0023 1.2255 0.1461 2137.186909 1 0.0003 134 | 0/8 6 h-lim-p 0.0011 0.5271 0.0379 2137.186908 0 0.0005 154 | 0/8 7 h-lim-p 0.0046 20.0000 0.0039 2137.186908 0 0.0040 174 | 0/8 8 h-lim-p 0.0078 13.4357 0.0020 2137.186826 0 0.1242 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2137.186823 0 1.0938 218 | 0/8 10 h-lim-p 0.8435 20.0000 0.0001 2137.186823 0 0.8435 238 | 0/8 11 h-lim-p 0.6436 20.0000 0.0001 2137.186823 0 0.0402 261 | 0/8 12 h-lim-p 0.0094 20.0000 0.0003 2137.186823 0 0.0023 282 | 0/8 13 h-lim-p 0.0010 13.1000 0.0007 2137.186823 0 0.0000 324 | 0/8 14 h-lim-p 0.0000 20.0000 0.0024 2137.186823 0 0.0000 356 | 0/8 15 h-lim-p 0.0000 20.0000 0.0010 2137.186823 0 0.0000 385 | 0/8 16 h-lim-p 0.0000 20.0000 0.0006 2137.186823 0 0.0013 412 | 0/8 17 h-lim-p 0.0050 20.0000 0.0002 2137.186823 0 0.0000 440 | 0/8 18 h-lim-p 0.0000 20.0000 0.0003 2137.186823 0 0.0000 463 | 0/8 19 h-lim-p 0.0000 9.7237 0.0008 2137.186823 0 0.0000 483 | 0/8 20 h-lim-p 0.0006 20.0000 0.0000 2137.186823 0 0.0095 507 | 0/8 21 h-lim-p 0.0042 20.0000 0.0000 2137.186823 0 0.0000 534 | 0/8 22 h-lim-p 0.0000 20.0000 0.0004 2137.186823 0 0.0000 569 | 0/8 23 h-lim-p 0.0000 20.0000 0.0045 | 0/8 24 h-lim-p 0.0000 20.0000 0.0045 Out... lnL = -2137.186823 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2137.186823 Node 7: lnL = -2137.186823 Node 8: lnL = -2137.186823 Node 9: lnL = -2137.186823 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 847 Sequential format.. Reading seq # 1: YER098W_Sbay Reading seq # 2: YER098W_Scer Reading seq # 3: YER098W_Skud Reading seq # 4: YER098W_Smik Reading seq # 5: YER098W_Spar Sequences read.. Counting patterns.. # site patterns = 341 Counting frequencies.. 120 bytes for distance 54560 bytes for lkl0 43648 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.019241 0.058880 0.003587 0.168258 0.203526 0.214611 0.279061 0.256524 lnL0 = -4167.990592 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4167.990592 x= 0.01924 0.05888 0.00359 0.16826 0.20353 0.21461 0.27906 0.25652 1 h-lim-p 0.0002 0.1767 615.8113 4157.002030 7 0.0001 39 | 0/8 2 h-lim-p 0.0004 0.0033 98.0733 4155.154166 7 0.0004 68 | 0/8 3 h-lim-p 0.0003 0.0021 29.1535 4155.004197 0 0.0004 80 | 0/8 4 h-lim-p 0.0045 0.1839 2.5159 4155.003018 4 0.0004 103 | 0/8 5 h-lim-p 0.0025 0.6804 0.3762 4155.002988 2 0.0004 121 | 0/8 6 h-lim-p 0.0021 2.6137 0.0726 4155.002985 0 0.0009 141 | 0/8 7 h-lim-p 0.0034 18.8222 0.0195 4155.002983 0 0.0029 161 | 0/8 8 h-lim-p 0.0124 20.0000 0.0046 4155.002367 0 0.1987 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4155.002316 3 1.4879 213 | 0/8 10 h-lim-p 2.4433 20.0000 0.0001 4155.002308 1 1.2025 236 | 0/8 11 h-lim-p 1.9262 20.0000 0.0000 4155.002308 0 1.6854 256 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4155.002308 0 1.0938 276 | 0/8 13 h-lim-p 0.2873 20.0000 0.0000 4155.002308 0 1.7240 298 | 0/8 14 h-lim-p 1.2264 20.0000 0.0000 4155.002308 0 1.2264 318 | 0/8 15 h-lim-p 0.0159 8.3213 0.0035 4155.002308 0 0.0159 338 | 0/8 16 h-lim-p 0.0049 2.5753 0.0113 4155.002308 0 0.0003 361 | 0/8 17 h-lim-p 0.0001 0.8066 0.0361 4155.002308 0 0.0000 398 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 4155.002308 0 0.0000 426 Out... lnL = -4155.002308 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4155.002308 Node 7: lnL = -4155.002308 Node 8: lnL = -4155.002308 Node 9: lnL = -4155.002308 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 547 Sequential format.. Reading seq # 1: YER099C_Sbay Reading seq # 2: YER099C_Scer Reading seq # 3: YER099C_Skud Reading seq # 4: YER099C_Smik Reading seq # 5: YER099C_Spar Sequences read.. Counting patterns.. # site patterns = 186 Counting frequencies.. 120 bytes for distance 29760 bytes for lkl0 23808 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.034071 0.044200 0.048686 0.128711 0.082399 0.161775 0.200554 0.219807 lnL0 = -2332.371062 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2332.371062 x= 0.03407 0.04420 0.04869 0.12871 0.08240 0.16178 0.20055 0.21981 1 h-lim-p 0.0005 0.0041 153.4441 2330.364270 7 0.0002 39 | 0/8 2 h-lim-p 0.0006 0.0048 25.8250 2330.254234 7 0.0003 67 | 0/8 3 h-lim-p 0.0008 0.0116 11.3135 2330.235858 4 0.0003 86 | 0/8 4 h-lim-p 0.0013 0.0860 2.8278 2330.234032 4 0.0005 107 | 0/8 5 h-lim-p 0.0021 0.2660 0.6593 2330.233946 2 0.0004 124 | 0/8 6 h-lim-p 0.0019 1.7316 0.1468 2330.233941 0 0.0004 145 | 0/8 7 h-lim-p 0.0038 4.7811 0.0157 2330.233941 0 0.0008 166 | 0/8 8 h-lim-p 0.0997 20.0000 0.0001 2330.233906 0 1.1962 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2330.233906 0 1.0938 209 | 0/8 10 h-lim-p 1.1568 20.0000 0.0000 2330.233906 0 1.0122 229 | 0/8 11 h-lim-p 0.8204 20.0000 0.0000 2330.233906 0 0.0016 257 | 0/8 12 h-lim-p 0.0000 9.3342 0.0049 2330.233906 0 0.0000 281 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 2330.233906 0 0.0000 313 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -2330.233906 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2330.233906 Node 7: lnL = -2330.233906 Node 8: lnL = -2330.233906 Node 9: lnL = -2330.233906 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 597 Sequential format.. Reading seq # 1: YER100W_Sbay Reading seq # 2: YER100W_Scer Reading seq # 3: YER100W_Skud Reading seq # 4: YER100W_Smik Reading seq # 5: YER100W_Spar Sequences read.. Counting patterns.. # site patterns = 185 Counting frequencies.. 120 bytes for distance 29600 bytes for lkl0 23680 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.028360 0.039146 0.052337 0.133918 0.079846 0.158399 0.202533 0.211178 lnL0 = -2393.232199 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2393.232199 x= 0.02836 0.03915 0.05234 0.13392 0.07985 0.15840 0.20253 0.21118 1 h-lim-p 0.0005 0.0039 174.1264 2390.734793 6 0.0002 34 | 0/8 2 h-lim-p 0.0005 0.0037 25.8960 2390.626184 6 0.0003 60 | 0/8 3 h-lim-p 0.0008 0.0096 10.3041 2390.611947 5 0.0003 82 | 0/8 4 h-lim-p 0.0015 0.1339 2.0577 2390.610832 5 0.0006 106 | 0/8 5 h-lim-p 0.0026 0.5833 0.4434 2390.610789 3 0.0005 126 | 0/8 6 h-lim-p 0.0016 1.1495 0.1234 2390.610786 0 0.0004 147 | 0/8 7 h-lim-p 0.0071 7.3909 0.0071 2390.610786 0 0.0009 169 | 0/8 8 h-lim-p 0.0317 20.0000 0.0002 2390.610754 0 0.7601 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2390.610753 0 1.0938 213 | 0/8 10 h-lim-p 0.8801 20.0000 0.0000 2390.610753 0 0.8801 233 | 0/8 11 h-lim-p 0.6114 20.0000 0.0000 2390.610753 0 0.5350 253 | 0/8 12 h-lim-p 0.0958 20.0000 0.0002 2390.610753 0 0.0026 277 | 0/8 13 h-lim-p 0.0008 20.0000 0.0006 2390.610753 0 0.0000 304 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 2390.610753 0 0.0000 338 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 2390.610753 0 0.0000 359 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 2390.610753 0 0.0000 392 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -2390.610753 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2390.610753 Node 7: lnL = -2390.610753 Node 8: lnL = -2390.610753 Node 9: lnL = -2390.610753 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 909 Sequential format.. Reading seq # 1: YER101C_Sbay Reading seq # 2: YER101C_Scer Reading seq # 3: YER101C_Skud Reading seq # 4: YER101C_Smik Reading seq # 5: YER101C_Spar Sequences read.. Counting patterns.. # site patterns = 397 Counting frequencies.. 120 bytes for distance 63520 bytes for lkl0 50816 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.258871 0.092901 0.221286 0.154248 0.260146 0.326634 0.336144 lnL0 = -4501.900558 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4501.900558 x= 0.00006 0.25887 0.09290 0.22129 0.15425 0.26015 0.32663 0.33614 1 h-lim-p 0.0000 0.0000 76.9097 4501.874455 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0354 22.5623 4501.752327 0 0.0005 39 | 1/8 3 h-lim-p 0.0016 0.0581 6.4128 4501.730101 5 0.0011 64 | 1/8 4 h-lim-p 0.0021 0.1329 3.3196 4501.725865 5 0.0007 89 | 1/8 5 h-lim-p 0.0047 0.3663 0.5132 4501.702263 0 0.0187 103 | 1/8 6 h-lim-p 0.0069 0.3291 1.4004 4501.161044 0 0.0206 123 | 0/8 7 h-lim-p 0.0018 0.0143 14.4368 4500.640568 5 0.0016 144 | 0/8 8 h-lim-p 0.0003 0.0021 9.9295 4500.574105 0 0.0015 158 | 0/8 9 h-lim-p 0.0001 0.0007 3.4435 4500.569166 m 0.0007 170 | 1/8 10 h-lim-p 0.0192 8.1826 0.0752 4500.567509 1 0.0240 184 | 1/8 11 h-lim-p 0.4849 20.0000 0.0037 4500.561198 0 0.9698 204 | 1/8 12 h-lim-p 2.5000 20.0000 0.0005 4500.559580 0 5.0000 224 | 1/8 13 h-lim-p 2.5000 20.0000 0.0006 4500.559140 2 1.2500 247 | 1/8 14 h-lim-p 2.5000 20.0000 0.0001 4500.559135 0 1.0938 266 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 4500.559135 0 1.0938 285 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 4500.559135 0 1.0938 304 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 4500.559135 0 0.6250 324 | 1/8 18 h-lim-p 1.6561 20.0000 0.0000 4500.559135 0 0.0000 369 Out... lnL = -4500.559135 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4500.559135 Node 7: lnL = -4500.559135 Node 8: lnL = -4500.559135 Node 9: lnL = -4500.559135 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 843 Sequential format.. Reading seq # 1: YER103W_Sbay Reading seq # 2: YER103W_Scer Reading seq # 3: YER103W_Skud Reading seq # 4: YER103W_Smik Reading seq # 5: YER103W_Spar Sequences read.. Counting patterns.. # site patterns = 250 Counting frequencies.. 120 bytes for distance 40000 bytes for lkl0 32000 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.003681 0.152647 0.072323 0.114098 0.073573 0.184205 0.141803 0.207871 lnL0 = -3701.913048 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3701.913048 x= 0.00368 0.15265 0.07232 0.11410 0.07357 0.18421 0.14180 0.20787 1 h-lim-p 0.0006 0.0051 114.0579 3700.468925 8 0.0002 41 | 0/8 2 h-lim-p 0.0006 0.0046 33.1936 3700.256178 7 0.0004 70 | 0/8 3 h-lim-p 0.0013 0.0262 10.8864 3700.248168 2 0.0001 88 | 0/8 4 h-lim-p 0.0006 0.0520 2.6509 3700.247433 4 0.0002 109 | 0/8 5 h-lim-p 0.0014 0.4610 0.4195 3700.247403 1 0.0004 124 | 0/8 6 h-lim-p 0.0049 0.7578 0.0303 3700.247402 0 0.0005 146 | 0/8 7 h-lim-p 0.0012 14.7349 0.0139 3700.247398 0 0.0047 168 | 0/8 8 h-lim-p 0.0073 20.0000 0.0089 3700.246926 0 0.0584 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3700.246925 0 1.0938 211 | 0/8 10 h-lim-p 1.3047 20.0000 0.0001 3700.246925 0 1.1416 231 | 0/8 11 h-lim-p 1.3684 20.0000 0.0000 3700.246925 0 2.7369 252 | 0/8 12 h-lim-p 0.1286 13.9591 0.0010 3700.246925 0 0.0563 272 | 0/8 13 h-lim-p 0.0136 3.3664 0.0040 3700.246925 0 0.0003 297 | 0/8 14 h-lim-p 0.0003 2.7954 0.0048 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0013 3700.246925 0 0.0000 364 | 0/8 16 h-lim-p 0.0000 20.0000 0.0009 3700.246925 0 0.0005 389 | 0/8 17 h-lim-p 0.0013 20.0000 0.0003 3700.246925 0 0.0006 409 | 0/8 18 h-lim-p 0.0006 20.0000 0.0003 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0014 3700.246925 0 0.0000 472 | 0/8 20 h-lim-p 0.0000 20.0000 0.0003 .. | 0/8 21 h-lim-p 0.0000 20.0000 0.0014 | 0/8 22 h-lim-p 0.0000 20.0000 0.0014 Out... lnL = -3700.246925 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3700.246925 Node 7: lnL = -3700.246925 Node 8: lnL = -3700.246925 Node 9: lnL = -3700.246925 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 316 Sequential format.. Reading seq # 1: YER104W_Sbay Reading seq # 2: YER104W_Scer Reading seq # 3: YER104W_Skud Reading seq # 4: YER104W_Smik Reading seq # 5: YER104W_Spar Sequences read.. Counting patterns.. # site patterns = 169 Counting frequencies.. 120 bytes for distance 27040 bytes for lkl0 21632 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.018266 0.159356 0.036095 0.201388 0.124452 0.252199 0.265254 0.297259 lnL0 = -1532.385182 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1532.385182 x= 0.01827 0.15936 0.03609 0.20139 0.12445 0.25220 0.26525 0.29726 1 h-lim-p 0.0050 0.0396 29.6313 1531.962240 7 0.0010 36 | 0/8 2 h-lim-p 0.0004 0.0035 17.5469 1531.847713 0 0.0009 49 | 0/8 3 h-lim-p 0.0015 0.0121 5.1684 1531.834310 6 0.0011 74 | 0/8 4 h-lim-p 0.0031 0.1181 1.8886 1531.832308 3 0.0013 92 | 0/8 5 h-lim-p 0.0030 0.2254 0.8092 1531.831879 4 0.0016 113 | 0/8 6 h-lim-p 0.0228 1.4996 0.0561 1531.831872 1 0.0028 137 | 0/8 7 h-lim-p 0.0063 17.7311 0.0250 1531.831850 0 0.0126 158 | 0/8 8 h-lim-p 0.0146 4.3732 0.0216 1531.830807 0 0.1169 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 1531.830733 2 0.9961 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1531.830733 0 1.0938 225 | 0/8 11 h-lim-p 1.5785 20.0000 0.0000 1531.830733 0 0.6906 245 | 0/8 12 h-lim-p 0.4257 20.0000 0.0000 1531.830733 0 0.0532 267 | 0/8 13 h-lim-p 0.0196 20.0000 0.0000 1531.830733 0 0.0000 311 | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 1531.830733 0 0.0000 340 | 0/8 15 h-lim-p 0.0000 20.0000 0.0024 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1531.830733 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1531.830733 Node 7: lnL = -1531.830733 Node 8: lnL = -1531.830733 Node 9: lnL = -1531.830733 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 331 Sequential format.. Reading seq # 1: YER106W_Sbay Reading seq # 2: YER106W_Scer Reading seq # 3: YER106W_Skud Reading seq # 4: YER106W_Smik Reading seq # 5: YER106W_Spar Sequences read.. Counting patterns.. # site patterns = 176 Counting frequencies.. 120 bytes for distance 28160 bytes for lkl0 22528 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.041784 0.081508 0.074526 0.156155 0.129841 0.299057 0.189440 0.301538 lnL0 = -1575.533759 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1575.533759 x= 0.04178 0.08151 0.07453 0.15616 0.12984 0.29906 0.18944 0.30154 1 h-lim-p 0.0019 0.0150 72.0293 1573.405173 4 0.0009 31 | 0/8 2 h-lim-p 0.0006 0.0047 20.8596 1573.217967 0 0.0012 44 | 0/8 3 h-lim-p 0.0023 0.0184 8.2082 1573.190376 3 0.0010 62 | 0/8 4 h-lim-p 0.0022 0.0629 3.6560 1573.184320 4 0.0011 84 | 0/8 5 h-lim-p 0.0060 0.2231 0.6721 1573.183783 4 0.0023 104 | 0/8 6 h-lim-p 0.0419 10.5168 0.0376 1573.183374 4 0.0259 136 | 0/8 7 h-lim-p 0.0031 1.0875 0.3178 1573.178416 0 0.0123 158 | 0/8 8 h-lim-p 0.0054 0.4643 0.7265 1573.170745 1 0.0067 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 1573.170605 2 1.1719 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1573.170602 0 1.2500 224 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1573.170602 0 1.0938 244 | 0/8 12 h-lim-p 1.7298 20.0000 0.0000 1573.170602 0 1.5135 264 | 0/8 13 h-lim-p 1.3860 20.0000 0.0000 1573.170602 0 1.3860 284 | 0/8 14 h-lim-p 0.1256 20.0000 0.0001 1573.170602 0 0.0628 304 | 0/8 15 h-lim-p 0.0155 20.0000 0.0003 1573.170602 0 0.0008 327 | 0/8 16 h-lim-p 0.0010 20.0000 0.0003 1573.170602 0 0.0005 347 | 0/8 17 h-lim-p 0.0002 20.0000 0.0006 1573.170602 0 0.0000 374 | 0/8 18 h-lim-p 0.0004 20.0000 0.0000 1573.170602 0 0.0000 397 Out... lnL = -1573.170602 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1573.170602 Node 7: lnL = -1573.170602 Node 8: lnL = -1573.170602 Node 9: lnL = -1573.170602 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 738 Sequential format.. Reading seq # 1: YER107C_Sbay Reading seq # 2: YER107C_Scer Reading seq # 3: YER107C_Skud Reading seq # 4: YER107C_Smik Reading seq # 5: YER107C_Spar Sequences read.. Counting patterns.. # site patterns = 271 Counting frequencies.. 120 bytes for distance 43360 bytes for lkl0 34688 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.037768 0.079093 0.065077 0.147000 0.109427 0.209777 0.206630 0.257389 lnL0 = -3348.774874 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3348.774874 x= 0.03777 0.07909 0.06508 0.14700 0.10943 0.20978 0.20663 0.25739 1 h-lim-p 0.0054 0.0556 111.4221 3347.419780 9 0.0002 50 | 0/8 2 h-lim-p 0.0010 0.0077 25.0214 3347.277018 6 0.0005 75 | 0/8 3 h-lim-p 0.0011 0.0221 11.1150 3347.259271 6 0.0003 101 | 0/8 4 h-lim-p 0.0018 0.1339 2.1406 3347.258403 2 0.0004 118 | 0/8 5 h-lim-p 0.0024 0.5102 0.3449 3347.258376 2 0.0005 135 | 0/8 6 h-lim-p 0.0026 2.2791 0.0622 3347.258375 0 0.0006 156 | 0/8 7 h-lim-p 0.0250 20.0000 0.0014 3347.258350 0 0.1002 178 | 0/8 8 h-lim-p 0.0016 13.9545 0.0863 3347.258116 0 0.0049 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3347.258108 1 0.9961 221 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3347.258108 0 1.0938 241 | 0/8 11 h-lim-p 0.8521 20.0000 0.0000 3347.258108 0 0.0266 265 | 0/8 12 h-lim-p 0.0010 20.0000 0.0010 3347.258108 0 0.0004 286 | 0/8 13 h-lim-p 0.0001 12.6170 0.0046 3347.258108 0 0.0000 311 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 3347.258108 0 0.0000 337 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 3347.258108 0 0.0000 359 Out... lnL = -3347.258108 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3347.258108 Node 7: lnL = -3347.258108 Node 8: lnL = -3347.258108 Node 9: lnL = -3347.258108 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 835 Sequential format.. Reading seq # 1: YER109C_Sbay Reading seq # 2: YER109C_Scer Reading seq # 3: YER109C_Skud Reading seq # 4: YER109C_Smik Reading seq # 5: YER109C_Spar Sequences read.. Counting patterns.. # site patterns = 261 Counting frequencies.. 120 bytes for distance 41760 bytes for lkl0 33408 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.084682 0.041101 0.051934 0.129265 0.068739 0.139099 0.204218 0.278259 lnL0 = -3703.929003 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3703.929003 x= 0.08468 0.04110 0.05193 0.12926 0.06874 0.13910 0.20422 0.27826 1 h-lim-p 0.0017 0.0250 205.9128 3701.404412 8 0.0001 44 | 0/8 2 h-lim-p 0.0007 0.0057 33.3576 3701.278534 5 0.0002 68 | 0/8 3 h-lim-p 0.0004 0.0144 17.8240 3701.244857 6 0.0003 97 | 0/8 4 h-lim-p 0.0005 0.0254 8.9636 3701.236699 5 0.0003 122 | 0/8 5 h-lim-p 0.0024 0.2322 0.9854 3701.236554 2 0.0003 140 | 0/8 6 h-lim-p 0.0009 0.4593 0.3272 3701.236537 1 0.0004 162 | 0/8 7 h-lim-p 0.0033 4.5162 0.0354 3701.236536 0 0.0007 183 | 0/8 8 h-lim-p 0.0543 20.0000 0.0005 3701.236113 0 0.8690 207 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3701.236109 0 1.0938 227 | 0/8 10 h-lim-p 2.3607 20.0000 0.0000 3701.236109 0 1.0328 247 | 0/8 11 h-lim-p 1.1089 20.0000 0.0000 3701.236109 0 4.4355 269 | 0/8 12 h-lim-p 0.4702 20.0000 0.0002 3701.236109 0 0.4114 289 | 0/8 13 h-lim-p 0.0298 20.0000 0.0022 3701.236109 0 0.0131 309 | 0/8 14 h-lim-p 0.0055 20.0000 0.0053 3701.236109 0 0.0000 350 | 0/8 15 h-lim-p 0.0000 20.0000 0.0025 3701.236109 0 0.0000 374 | 0/8 16 h-lim-p 0.0000 20.0000 0.0006 3701.236109 0 0.0006 400 | 0/8 17 h-lim-p 0.0012 20.0000 0.0003 3701.236109 0 0.0000 432 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 3701.236109 0 0.0000 453 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 3701.236109 0 0.0000 486 | 0/8 20 h-lim-p 0.0000 20.0000 0.0031 | 0/8 21 h-lim-p 0.0000 20.0000 0.0031 Out... lnL = -3701.236109 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3701.236109 Node 7: lnL = -3701.236109 Node 8: lnL = -3701.236109 Node 9: lnL = -3701.236109 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 944 Sequential format.. Reading seq # 1: YER112W_Sbay Reading seq # 2: YER112W_Scer Reading seq # 3: YER112W_Skud Reading seq # 4: YER112W_Smik Reading seq # 5: YER112W_Spar Sequences read.. Counting patterns.. # site patterns = 420 Counting frequencies.. 120 bytes for distance 67200 bytes for lkl0 53760 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.343783 0.073095 0.220140 0.169423 0.321781 0.416398 0.378431 lnL0 = -4832.664802 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4832.664802 x= 0.00006 0.34378 0.07309 0.22014 0.16942 0.32178 0.41640 0.37843 1 h-lim-p 0.0000 0.0000 62.0559 4832.641903 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0393 12.8209 4832.558256 0 0.0009 39 | 1/8 3 h-lim-p 0.0014 0.0159 8.0842 4832.535192 6 0.0009 66 | 1/8 4 h-lim-p 0.0017 0.1435 4.3146 4832.526435 5 0.0011 90 | 1/8 5 h-lim-p 0.0034 0.2051 1.4526 4832.523601 2 0.0016 106 | 1/8 6 h-lim-p 0.0095 2.2911 0.2441 4832.395868 0 0.0761 121 | 1/8 7 h-lim-p 0.0052 0.0416 3.0690 4831.897945 0 0.0104 141 | 1/8 8 h-lim-p 0.0067 0.1424 4.7767 4831.873447 5 0.0020 168 | 1/8 9 h-lim-p 1.2618 20.0000 0.0077 4831.828034 5 0.9255 192 | 1/8 10 h-lim-p 2.5000 20.0000 0.0001 4831.828023 1 0.9961 213 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 4831.828023 0 1.0938 232 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 4831.828023 0 1.0938 251 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 4831.828023 0 1.0938 270 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 4831.828023 0 1.8750 289 | 1/8 15 h-lim-p 2.1416 20.0000 0.0000 4831.828023 0 2.1416 308 | 1/8 16 h-lim-p 1.8768 20.0000 0.0000 4831.828023 0 0.0001 341 Out... lnL = -4831.828023 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4831.828023 Node 7: lnL = -4831.828023 Node 8: lnL = -4831.828023 Node 9: lnL = -4831.828023 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 633 Sequential format.. Reading seq # 1: YER114C_Sbay Reading seq # 2: YER114C_Scer Reading seq # 3: YER114C_Skud Reading seq # 4: YER114C_Smik Reading seq # 5: YER114C_Spar Sequences read.. Counting patterns.. # site patterns = 270 Counting frequencies.. 120 bytes for distance 43200 bytes for lkl0 34560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.037729 0.113069 0.045586 0.113427 0.125468 0.253831 0.217026 0.270682 lnL0 = -2945.200581 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2945.200581 x= 0.03773 0.11307 0.04559 0.11343 0.12547 0.25383 0.21703 0.27068 1 h-lim-p 0.0026 0.0206 84.8622 2944.474749 8 0.0002 43 | 0/8 2 h-lim-p 0.0017 0.0152 10.8253 2944.453496 4 0.0004 63 | 0/8 3 h-lim-p 0.0010 0.1282 3.8008 2944.450635 3 0.0004 82 | 0/8 4 h-lim-p 0.0013 0.1625 1.3066 2944.450225 2 0.0006 98 | 0/8 5 h-lim-p 0.0027 0.3336 0.2719 2944.450207 2 0.0005 115 | 0/8 6 h-lim-p 0.0022 5.6764 0.0637 2944.450206 1 0.0005 138 | 0/8 7 h-lim-p 0.0032 16.8276 0.0109 2944.450206 0 0.0008 159 | 0/8 8 h-lim-p 0.3264 20.0000 0.0000 2944.450205 0 1.3056 181 | 0/8 9 h-lim-p 1.6732 20.0000 0.0000 2944.450205 0 1.4641 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2944.450205 0 1.0938 221 | 0/8 11 h-lim-p 0.6504 20.0000 0.0000 2944.450205 0 0.6504 241 | 0/8 12 h-lim-p 0.0529 20.0000 0.0002 2944.450205 0 0.0066 263 | 0/8 13 h-lim-p 0.0021 20.0000 0.0007 2944.450205 0 0.0003 285 | 0/8 14 h-lim-p 0.0000 0.3525 0.1675 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 2944.450205 0 0.0000 343 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -2944.450205 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2944.450205 Node 7: lnL = -2944.450205 Node 8: lnL = -2944.450205 Node 9: lnL = -2944.450205 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 538 Sequential format.. Reading seq # 1: YER115C_Sbay Reading seq # 2: YER115C_Scer Reading seq # 3: YER115C_Skud Reading seq # 4: YER115C_Smik Reading seq # 5: YER115C_Spar Sequences read.. Counting patterns.. # site patterns = 226 Counting frequencies.. 120 bytes for distance 36160 bytes for lkl0 28928 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.020041 0.106995 0.068150 0.145732 0.112606 0.196512 0.220678 0.242780 lnL0 = -2435.840397 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2435.840397 x= 0.02004 0.10699 0.06815 0.14573 0.11261 0.19651 0.22068 0.24278 1 h-lim-p 0.0021 0.0170 77.2307 2434.908780 9 0.0003 46 | 0/8 2 h-lim-p 0.0005 0.0044 17.1968 2434.828513 3 0.0006 64 | 0/8 3 h-lim-p 0.0014 0.0162 6.9676 2434.818478 6 0.0005 92 | 0/8 4 h-lim-p 0.0036 0.2660 0.9185 2434.818251 4 0.0005 116 | 0/8 5 h-lim-p 0.0033 0.6423 0.1509 2434.818244 1 0.0007 139 | 0/8 6 h-lim-p 0.0036 11.3079 0.0275 2434.818244 0 0.0008 160 | 0/8 7 h-lim-p 0.0030 9.1504 0.0072 2434.818244 0 0.0026 180 | 0/8 8 h-lim-p 0.0429 20.0000 0.0004 2434.818210 0 0.5142 203 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2434.818209 0 1.0938 223 | 0/8 10 h-lim-p 1.7921 20.0000 0.0000 2434.818209 0 1.5681 243 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2434.818209 0 1.0938 263 | 0/8 12 h-lim-p 0.4692 20.0000 0.0000 2434.818209 0 0.0037 289 | 0/8 13 h-lim-p 0.0000 8.6273 0.0028 2434.818209 0 0.0000 325 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 2434.818209 0 0.0000 359 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -2434.818209 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2434.818209 Node 7: lnL = -2434.818209 Node 8: lnL = -2434.818209 Node 9: lnL = -2434.818209 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 630 Sequential format.. Reading seq # 1: YER116C_Sbay Reading seq # 2: YER116C_Scer Reading seq # 3: YER116C_Skud Reading seq # 4: YER116C_Smik Reading seq # 5: YER116C_Spar Sequences read.. Counting patterns.. # site patterns = 258 Counting frequencies.. 120 bytes for distance 41280 bytes for lkl0 33024 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.043991 0.029329 0.094618 0.146049 0.100685 0.204032 0.312991 0.280239 lnL0 = -2996.969329 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2996.969329 x= 0.04399 0.02933 0.09462 0.14605 0.10069 0.20403 0.31299 0.28024 1 h-lim-p 0.0033 0.0266 96.4006 2995.911209 9 0.0002 45 | 0/8 2 h-lim-p 0.0020 0.0162 8.2077 2995.897133 3 0.0004 64 | 0/8 3 h-lim-p 0.0007 0.0381 5.3307 2995.891048 2 0.0006 80 | 0/8 4 h-lim-p 0.0013 0.1176 2.2920 2995.889927 3 0.0005 98 | 0/8 5 h-lim-p 0.0042 0.8402 0.2896 2995.889902 3 0.0006 119 | 0/8 6 h-lim-p 0.0042 2.5429 0.0430 2995.889902 0 0.0005 141 | 0/8 7 h-lim-p 0.0038 20.0000 0.0052 2995.889902 0 0.0017 161 | 0/8 8 h-lim-p 0.0436 20.0000 0.0002 2995.889886 0 0.6977 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2995.889884 0 1.0938 205 | 0/8 10 h-lim-p 2.1847 20.0000 0.0000 2995.889884 0 0.9558 225 | 0/8 11 h-lim-p 0.8731 20.0000 0.0000 2995.889884 0 0.0001 258 | 0/8 12 h-lim-p 0.0002 20.0000 0.0000 2995.889884 0 0.0000 291 Out... lnL = -2995.889884 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2995.889884 Node 7: lnL = -2995.889884 Node 8: lnL = -2995.889884 Node 9: lnL = -2995.889884 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 523 Sequential format.. Reading seq # 1: YER118C_Sbay Reading seq # 2: YER118C_Scer Reading seq # 3: YER118C_Skud Reading seq # 4: YER118C_Smik Reading seq # 5: YER118C_Spar Sequences read.. Counting patterns.. # site patterns = 127 Counting frequencies.. 120 bytes for distance 20320 bytes for lkl0 16256 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.027086 0.019435 0.043142 0.066941 0.043011 0.138425 0.127315 0.146326 lnL0 = -1824.415632 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1824.415632 x= 0.02709 0.01944 0.04314 0.06694 0.04301 0.13842 0.12732 0.14633 1 h-lim-p 0.0001 0.0006 236.2529 1822.058983 0 0.0001 23 | 0/8 2 h-lim-p 0.0003 0.0028 37.6304 1821.914244 7 0.0002 55 | 0/8 3 h-lim-p 0.0004 0.0088 20.3612 1821.890655 6 0.0001 81 | 0/8 4 h-lim-p 0.0003 0.0159 9.7214 1821.881927 4 0.0002 101 | 0/8 5 h-lim-p 0.0016 0.0395 1.4119 1821.881698 4 0.0002 123 | 0/8 6 h-lim-p 0.0111 1.9876 0.0271 1821.866391 0 0.1327 138 | 0/8 7 h-lim-p 0.0013 0.0219 2.8122 1821.723171 0 0.0026 159 | 0/8 8 h-lim-p 0.0007 0.0129 10.4810 1821.684771 7 0.0005 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0013 1821.681870 4 0.9802 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1821.681856 2 0.9644 231 | 0/8 11 h-lim-p 2.4002 20.0000 0.0000 1821.681856 0 1.0501 251 | 0/8 12 h-lim-p 1.0880 20.0000 0.0000 1821.681856 0 2.1760 272 | 0/8 13 h-lim-p 0.5202 20.0000 0.0001 1821.681856 0 0.0041 298 | 0/8 14 h-lim-p 0.0002 20.0000 0.0022 1821.681856 0 0.0000 321 | 0/8 15 h-lim-p 0.0001 20.0000 0.0003 1821.681856 0 0.0000 341 | 0/8 16 h-lim-p 0.0000 20.0000 0.0035 1821.681856 0 0.0000 362 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 1821.681856 0 0.0000 383 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 1821.681856 0 0.0000 415 | 0/8 19 h-lim-p 0.0000 20.0000 0.0017 | 0/8 20 h-lim-p 0.0000 20.0000 0.0017 Out... lnL = -1821.681856 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1821.681856 Node 7: lnL = -1821.681856 Node 8: lnL = -1821.681856 Node 9: lnL = -1821.681856 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 478 Sequential format.. Reading seq # 1: YER123W_Sbay Reading seq # 2: YER123W_Scer Reading seq # 3: YER123W_Skud Reading seq # 4: YER123W_Smik Reading seq # 5: YER123W_Spar Sequences read.. Counting patterns.. # site patterns = 144 Counting frequencies.. 120 bytes for distance 23040 bytes for lkl0 18432 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.038327 0.037880 0.043034 0.068188 0.057304 0.147594 0.125525 0.174166 lnL0 = -1841.186097 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1841.186097 x= 0.03833 0.03788 0.04303 0.06819 0.05730 0.14759 0.12552 0.17417 1 h-lim-p 0.0026 0.0205 90.5453 1840.579368 7 0.0002 39 | 0/8 2 h-lim-p 0.0008 0.0072 17.1136 1840.533423 4 0.0003 59 | 0/8 3 h-lim-p 0.0008 0.0208 7.1086 1840.528388 5 0.0002 84 | 0/8 4 h-lim-p 0.0012 0.0812 1.3892 1840.528214 3 0.0002 105 | 0/8 5 h-lim-p 0.0052 2.8569 0.0506 1840.528214 0 0.0003 120 | 0/8 6 h-lim-p 0.0010 12.5831 0.0149 1840.528214 0 0.0004 140 | 0/8 7 h-lim-p 0.0649 20.0000 0.0001 1840.528198 0 1.0391 164 | 0/8 8 h-lim-p 0.0019 1.2087 0.0544 1840.528197 0 0.0004 185 | 0/8 9 h-lim-p 0.0267 20.0000 0.0008 1840.528194 0 0.8529 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1840.528194 0 1.0938 230 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1840.528194 0 0.2734 252 | 0/8 12 h-lim-p 0.1156 20.0000 0.0000 1840.528194 0 0.0072 275 | 0/8 13 h-lim-p 0.0039 20.0000 0.0001 1840.528194 0 0.0010 296 | 0/8 14 h-lim-p 0.0006 20.0000 0.0001 1840.528194 0 0.0000 322 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 1840.528194 0 0.0000 342 | 0/8 16 h-lim-p 0.0000 5.8682 0.0099 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0038 | 0/8 18 h-lim-p 0.0000 20.0000 0.0038 Out... lnL = -1840.528194 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1840.528194 Node 7: lnL = -1840.528194 Node 8: lnL = -1840.528194 Node 9: lnL = -1840.528194 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 844 Sequential format.. Reading seq # 1: YER124C_Sbay Reading seq # 2: YER124C_Scer Reading seq # 3: YER124C_Skud Reading seq # 4: YER124C_Smik Reading seq # 5: YER124C_Spar Sequences read.. Counting patterns.. # site patterns = 231 Counting frequencies.. 120 bytes for distance 36960 bytes for lkl0 29568 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.034188 0.058608 0.041465 0.087186 0.066761 0.158936 0.138010 0.186588 lnL0 = -3427.391064 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3427.391064 x= 0.03419 0.05861 0.04146 0.08719 0.06676 0.15894 0.13801 0.18659 1 h-lim-p 0.0008 0.3921 297.0013 3423.568529 8 0.0001 43 | 0/8 2 h-lim-p 0.0009 0.0076 31.6786 3423.467262 6 0.0002 68 | 0/8 3 h-lim-p 0.0004 0.0164 14.5600 3423.451349 3 0.0002 86 | 0/8 4 h-lim-p 0.0007 0.0564 3.6515 3423.450124 4 0.0002 108 | 0/8 5 h-lim-p 0.0022 0.8303 0.3287 3423.450112 1 0.0002 124 | 0/8 6 h-lim-p 0.0021 3.6247 0.0379 3423.450112 0 0.0002 146 | 0/8 7 h-lim-p 0.0014 16.2799 0.0063 3423.450111 0 0.0006 166 | 0/8 8 h-lim-p 0.0361 20.0000 0.0001 3423.450090 0 0.8662 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3423.450090 0 1.0938 210 | 0/8 10 h-lim-p 0.4654 20.0000 0.0000 3423.450090 0 0.6981 230 | 0/8 11 h-lim-p 0.4950 20.0000 0.0001 3423.450090 0 0.0019 257 | 0/8 12 h-lim-p 0.0008 20.0000 0.0001 3423.450090 0 0.0000 282 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 3423.450090 0 0.0000 303 | 0/8 14 h-lim-p 0.0006 20.0000 0.0000 3423.450090 0 0.0000 342 Out... lnL = -3423.450090 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3423.450090 Node 7: lnL = -3423.450090 Node 8: lnL = -3423.450090 Node 9: lnL = -3423.450090 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 854 Sequential format.. Reading seq # 1: YER125W_Sbay Reading seq # 2: YER125W_Scer Reading seq # 3: YER125W_Skud Reading seq # 4: YER125W_Smik Reading seq # 5: YER125W_Spar Sequences read.. Counting patterns.. # site patterns = 189 Counting frequencies.. 120 bytes for distance 30240 bytes for lkl0 24192 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.028316 0.036211 0.039387 0.058109 0.046872 0.107997 0.128583 0.144791 lnL0 = -3093.724063 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3093.724063 x= 0.02832 0.03621 0.03939 0.05811 0.04687 0.10800 0.12858 0.14479 1 h-lim-p 0.0008 0.0134 278.4783 3090.900877 7 0.0001 38 | 0/8 2 h-lim-p 0.0005 0.0037 43.5116 3090.748688 6 0.0002 64 | 0/8 3 h-lim-p 0.0003 0.0059 25.2143 3090.720739 4 0.0001 84 | 0/8 4 h-lim-p 0.0004 0.0213 7.6446 3090.717762 5 0.0001 110 | 0/8 5 h-lim-p 0.0011 0.0824 0.7834 3090.717713 3 0.0002 131 | 0/8 6 h-lim-p 0.0012 0.7286 0.1097 3090.717712 0 0.0001 153 | 0/8 7 h-lim-p 0.0008 16.4509 0.0177 3090.717712 0 0.0004 173 | 0/8 8 h-lim-p 0.0219 20.0000 0.0003 3090.717540 0 0.7004 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3090.717537 0 1.0938 218 | 0/8 10 h-lim-p 0.6659 20.0000 0.0001 3090.717537 0 0.6659 238 | 0/8 11 h-lim-p 0.4763 20.0000 0.0001 3090.717537 0 0.4168 258 | 0/8 12 h-lim-p 0.2129 20.0000 0.0001 3090.717537 0 0.0033 283 | 0/8 13 h-lim-p 0.0015 20.0000 0.0003 3090.717537 0 0.0000 309 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 3090.717537 0 0.0000 340 | 0/8 15 h-lim-p 0.0000 20.0000 0.0029 3090.717537 0 0.0000 367 | 0/8 16 h-lim-p 0.0000 20.0000 0.0016 3090.717537 0 0.0005 392 | 0/8 17 h-lim-p 0.0019 20.0000 0.0004 3090.717537 0 0.0004 413 | 0/8 18 h-lim-p 0.0011 20.0000 0.0002 3090.717537 0 0.0000 439 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 3090.717537 0 0.0000 464 | 0/8 20 h-lim-p 0.0000 19.1091 0.0028 3090.717537 0 0.0000 484 | 0/8 21 h-lim-p 0.0001 20.0000 0.0001 3090.717537 0 0.0000 505 | 0/8 22 h-lim-p 0.0003 20.0000 0.0000 3090.717537 0 0.0000 527 Out... lnL = -3090.717537 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3090.717537 Node 7: lnL = -3090.717537 Node 8: lnL = -3090.717537 Node 9: lnL = -3090.717537 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 315 Sequential format.. Reading seq # 1: YER126C_Sbay Reading seq # 2: YER126C_Scer Reading seq # 3: YER126C_Skud Reading seq # 4: YER126C_Smik Reading seq # 5: YER126C_Spar Sequences read.. Counting patterns.. # site patterns = 132 Counting frequencies.. 120 bytes for distance 21120 bytes for lkl0 16896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.238318 0.119673 0.062745 0.128498 0.078123 0.131922 0.213069 0.002468 lnL0 = -1397.172236 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1397.172236 x= 0.23832 0.11967 0.06275 0.12850 0.07812 0.13192 0.21307 0.00247 1 h-lim-p 0.0129 0.1035 42.2795 1396.624340 7 0.0006 41 | 0/8 2 h-lim-p 0.0004 0.0029 17.0442 1396.559579 0 0.0007 54 | 0/8 3 h-lim-p 0.0002 0.0016 5.0401 1396.551233 0 0.0008 68 | 0/8 4 h-lim-p 0.0006 0.0051 1.3619 1396.550779 3 0.0005 86 | 0/8 5 h-lim-p 0.0024 0.3886 0.3004 1396.550719 2 0.0012 103 | 0/8 6 h-lim-p 0.0046 2.1109 0.0776 1396.550666 2 0.0052 128 | 0/8 7 h-lim-p 0.0347 20.0000 0.0115 1396.544586 0 0.2780 151 | 0/8 8 h-lim-p 0.0647 1.1093 0.0496 1396.544584 0 0.0009 176 | 0/8 9 h-lim-p 0.0599 18.4024 0.0007 1396.544292 0 0.9588 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1396.544282 1 0.9961 222 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1396.544282 0 0.0000 258 | 0/8 12 h-lim-p 0.0001 20.0000 0.0000 1396.544282 0 0.0000 280 Out... lnL = -1396.544282 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1396.544282 Node 7: lnL = -1396.544282 Node 8: lnL = -1396.544282 Node 9: lnL = -1396.544282 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 317 Sequential format.. Reading seq # 1: YER127W_Sbay Reading seq # 2: YER127W_Scer Reading seq # 3: YER127W_Skud Reading seq # 4: YER127W_Smik Reading seq # 5: YER127W_Spar Sequences read.. Counting patterns.. # site patterns = 136 Counting frequencies.. 120 bytes for distance 21760 bytes for lkl0 17408 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.218200 0.103923 0.046617 0.272401 0.278422 0.185249 0.197617 0.000060 lnL0 = -1389.644064 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1389.644064 x= 0.21820 0.10392 0.04662 0.27240 0.27842 0.18525 0.19762 0.00006 1 h-lim-p 0.0000 0.0000 209.7414 1389.439640 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0010 383.1763 1362.367457 6 0.0007 52 | 1/8 3 h-lim-p 0.0085 0.0679 11.9892 1362.310546 7 0.0007 83 | 1/8 4 h-lim-p 0.0020 0.0483 4.3168 1362.276426 5 0.0020 106 | 1/8 5 h-lim-p 0.0100 0.2979 0.8436 1361.397854 0 0.0399 120 | 1/8 6 h-lim-p 0.0016 0.0131 15.2702 1355.254114 0 0.0066 141 | 0/8 7 h-lim-p 0.0004 0.0035 45.6330 1354.729925 1 0.0005 155 | 0/8 8 h-lim-p 0.0024 0.0193 4.1023 1354.720500 4 0.0009 175 | 0/8 9 h-lim-p 0.0127 0.8919 0.2998 1354.293022 0 0.2033 191 | 0/8 10 h-lim-p 0.0032 0.0258 3.1519 1354.144296 0 0.0129 213 | 0/8 11 h-lim-p 1.1452 10.8230 0.0355 1353.894100 5 0.4989 234 | 0/8 12 h-lim-p 1.1842 15.2262 0.0150 1353.841738 4 1.1796 262 | 0/8 13 h-lim-p 2.5000 20.0000 0.0007 1353.841688 1 1.0938 284 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1353.841687 0 1.0938 304 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1353.841687 0 1.0938 324 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1353.841687 0 1.0938 344 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1353.841687 0 2.1875 364 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1353.841687 0 0.1562 387 | 0/8 19 h-lim-p 0.2951 20.0000 0.0000 1353.841687 0 0.0023 413 Out... lnL = -1353.841687 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1353.841687 Node 7: lnL = -1353.841687 Node 8: lnL = -1353.841687 Node 9: lnL = -1353.841687 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 360 Sequential format.. Reading seq # 1: YER128W_Sbay Reading seq # 2: YER128W_Scer Reading seq # 3: YER128W_Skud Reading seq # 4: YER128W_Smik Reading seq # 5: YER128W_Spar Sequences read.. Counting patterns.. # site patterns = 175 Counting frequencies.. 120 bytes for distance 28000 bytes for lkl0 22400 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.348945 0.102335 0.085583 0.168304 0.110464 0.216061 0.279040 0.031253 lnL0 = -1603.457993 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1603.457993 x= 0.34894 0.10233 0.08558 0.16830 0.11046 0.21606 0.27904 0.03125 1 h-lim-p 0.0023 0.0182 26.5946 1603.194151 7 0.0008 39 | 0/8 2 h-lim-p 0.0027 0.0336 7.5893 1603.163165 5 0.0011 62 | 0/8 3 h-lim-p 0.0021 0.0872 4.1701 1603.155774 5 0.0011 86 | 0/8 4 h-lim-p 0.0028 0.1421 1.5965 1603.154660 5 0.0010 110 | 0/8 5 h-lim-p 0.0060 0.9510 0.2808 1603.154608 0 0.0013 123 | 0/8 6 h-lim-p 0.0129 3.2030 0.0283 1603.154608 0 0.0014 145 | 0/8 7 h-lim-p 0.1086 20.0000 0.0004 1603.154600 0 0.4342 167 | 0/8 8 h-lim-p 0.0038 1.6150 0.0425 1603.154587 1 0.0039 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1603.154587 0 1.0938 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1603.154587 0 1.0938 229 | 0/8 11 h-lim-p 1.0926 20.0000 0.0000 1603.154587 0 2.1852 250 | 0/8 12 h-lim-p 0.2289 20.0000 0.0001 1603.154587 0 0.0143 273 | 0/8 13 h-lim-p 0.0029 20.0000 0.0004 1603.154587 0 0.0000 311 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 1603.154587 0 0.0000 346 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1603.154587 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1603.154587 Node 7: lnL = -1603.154587 Node 8: lnL = -1603.154587 Node 9: lnL = -1603.154587 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 837 Sequential format.. Reading seq # 1: YER132C_Sbay Reading seq # 2: YER132C_Scer Reading seq # 3: YER132C_Skud Reading seq # 4: YER132C_Smik Reading seq # 5: YER132C_Spar Sequences read.. Counting patterns.. # site patterns = 295 Counting frequencies.. 120 bytes for distance 47200 bytes for lkl0 37760 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.274256 0.071031 0.062791 0.140075 0.085581 0.170372 0.166230 0.036662 lnL0 = -3696.338641 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3696.338641 x= 0.27426 0.07103 0.06279 0.14007 0.08558 0.17037 0.16623 0.03666 1 h-lim-p 0.0055 1.1516 115.5415 3695.163943 5 0.0002 36 | 0/8 2 h-lim-p 0.0006 0.0050 25.0011 3695.096068 7 0.0002 66 | 0/8 3 h-lim-p 0.0007 0.0285 7.7299 3695.088927 5 0.0003 90 | 0/8 4 h-lim-p 0.0006 0.0567 3.3026 3695.087443 4 0.0003 111 | 0/8 5 h-lim-p 0.0025 0.3346 0.4236 3695.087414 2 0.0003 129 | 0/8 6 h-lim-p 0.0016 0.9393 0.0852 3695.087413 0 0.0004 150 | 0/8 7 h-lim-p 0.1703 20.0000 0.0002 3695.087357 0 1.0217 172 | 0/8 8 h-lim-p 0.0009 1.2037 0.1949 3695.087346 0 0.0005 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3695.087345 0 1.0938 212 | 0/8 10 h-lim-p 0.7434 20.0000 0.0000 3695.087345 0 0.7434 232 | 0/8 11 h-lim-p 0.5434 20.0000 0.0000 3695.087345 0 0.1358 253 | 0/8 12 h-lim-p 0.0479 20.0000 0.0001 3695.087345 0 0.0000 282 | 0/8 13 h-lim-p 0.0002 20.0000 0.0000 3695.087345 0 0.0000 318 | 0/8 14 h-lim-p 0.0000 20.0000 0.0016 | 0/8 15 h-lim-p 0.0000 20.0000 0.0016 Out... lnL = -3695.087345 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3695.087345 Node 7: lnL = -3695.087345 Node 8: lnL = -3695.087345 Node 9: lnL = -3695.087345 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 161 Sequential format.. Reading seq # 1: YER134C_Sbay Reading seq # 2: YER134C_Scer Reading seq # 3: YER134C_Skud Reading seq # 4: YER134C_Smik Reading seq # 5: YER134C_Spar Sequences read.. Counting patterns.. # site patterns = 96 Counting frequencies.. 120 bytes for distance 15360 bytes for lkl0 12288 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.422579 0.000060 0.056607 0.296733 0.239612 0.235766 0.325002 0.102165 lnL0 = -776.270504 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 776.270504 x= 0.42258 0.00006 0.05661 0.29673 0.23961 0.23577 0.32500 0.10217 1 h-lim-p 0.0000 0.0000 78.9059 776.212723 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0066 48.7437 773.227380 7 0.0030 58 | 1/8 3 h-lim-p 0.0097 0.0778 3.4552 773.099066 5 0.0095 82 | 1/8 4 h-lim-p 0.0214 0.3294 1.5359 772.147065 0 0.0643 95 | 1/8 5 h-lim-p 0.0028 0.0223 6.5392 768.526337 m 0.0223 107 | 1/8 6 h-lim-p 0.0000 0.0000 8.5655 h-lim-p: 1.77798382e-18 1.42238706e-17 8.56548565e+00 768.526337 .. | 1/8 7 h-lim-p 0.0000 0.0361 28.7928 768.238856 0 0.0006 133 | 1/8 8 h-lim-p 0.0013 0.0104 12.4118 768.024310 0 0.0039 146 | 1/8 9 h-lim-p 0.0031 0.0249 8.0164 767.989869 2 0.0015 162 | 1/8 10 h-lim-p 0.0064 0.1768 1.8231 767.984529 6 0.0035 187 | 1/8 11 h-lim-p 0.0422 0.4220 0.1496 767.984329 3 0.0075 208 | 0/8 12 h-lim-p 0.0005 1.0836 2.4000 767.980942 0 0.0014 228 | 0/8 13 h-lim-p 0.0548 0.4381 0.0358 767.979459 0 0.1095 241 | 0/8 14 h-lim-p 0.0015 0.0120 0.4995 767.970159 m 0.0120 261 | 1/8 15 h-lim-p 1.9503 20.0000 0.0028 767.969106 4 0.7522 289 | 1/8 16 h-lim-p 1.9797 20.0000 0.0011 767.969003 3 0.7922 314 | 1/8 17 h-lim-p 2.5000 20.0000 0.0001 767.969002 0 1.0938 333 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 767.969002 0 1.0938 352 | 1/8 19 h-lim-p 2.3103 20.0000 0.0000 767.969002 0 2.3103 371 | 1/8 20 h-lim-p 2.5000 20.0000 0.0000 767.969002 0 0.0024 399 Out... lnL = -767.969002 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -767.969002 Node 7: lnL = -767.969002 Node 8: lnL = -767.969002 Node 9: lnL = -767.969002 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 903 Sequential format.. Reading seq # 1: YER136W_Sbay Reading seq # 2: YER136W_Scer Reading seq # 3: YER136W_Skud Reading seq # 4: YER136W_Smik Reading seq # 5: YER136W_Spar Sequences read.. Counting patterns.. # site patterns = 379 Counting frequencies.. 120 bytes for distance 60640 bytes for lkl0 48512 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.303561 0.138639 0.069907 0.362521 0.343083 0.284331 0.269520 0.000060 lnL0 = -4199.769004 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4199.769004 x= 0.30356 0.13864 0.06991 0.36252 0.34308 0.28433 0.26952 0.00006 1 h-lim-p 0.0000 0.0000 416.3316 4199.337000 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0002 2594.2162 4096.091991 10 0.0001 59 | 1/8 3 h-lim-p 0.0008 0.0065 46.1099 4095.490646 7 0.0006 90 | 1/8 4 h-lim-p 0.0033 0.0854 7.7949 4095.464354 5 0.0008 114 | 1/8 5 h-lim-p 0.0020 0.0670 3.0540 4095.454980 6 0.0012 140 | 1/8 6 h-lim-p 0.0045 0.4224 0.8176 4095.360223 0 0.0179 154 | 1/8 7 h-lim-p 0.0048 0.0687 3.0709 4091.820147 0 0.0287 175 | 0/8 8 h-lim-p 0.0025 0.0204 17.4855 4091.714260 6 0.0006 201 | 0/8 9 h-lim-p 0.0001 0.0008 7.7865 4091.681696 m 0.0008 213 | 0/8 10 h-lim-p 0.0000 0.0000 0.0269 h-lim-p: 1.86212741e-17 1.48970193e-16 2.68870868e-02 4091.681696 .. | 0/8 11 h-lim-p 0.0000 0.0182 37.1334 4091.429447 0 0.0003 246 | 0/8 12 h-lim-p 0.0014 0.0171 8.2487 4091.418450 2 0.0003 263 | 0/8 13 h-lim-p 0.0004 0.0402 6.3206 4091.412621 2 0.0004 279 | 0/8 14 h-lim-p 0.0019 0.3649 1.4022 4091.412245 2 0.0004 296 | 0/8 15 h-lim-p 0.0014 0.8932 0.4214 4091.412081 0 0.0020 308 | 0/8 16 h-lim-p 0.0008 0.3342 1.1345 4091.411391 0 0.0030 330 | 0/8 17 h-lim-p 0.0006 0.0706 5.3031 4091.406017 0 0.0052 345 | 0/8 18 h-lim-p 0.1476 1.6196 0.1857 4091.406003 0 0.0010 363 | 0/8 19 h-lim-p 0.0383 20.0000 0.0049 4091.405889 0 1.2260 388 | 0/8 20 h-lim-p 2.5000 20.0000 0.0011 4091.405884 0 1.0938 408 | 0/8 21 h-lim-p 2.5000 20.0000 0.0001 4091.405884 0 1.0938 428 | 0/8 22 h-lim-p 2.5000 20.0000 0.0000 4091.405884 0 1.0938 448 | 0/8 23 h-lim-p 2.5000 20.0000 0.0000 4091.405884 0 0.0000 490 Out... lnL = -4091.405884 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4091.405884 Node 7: lnL = -4091.405884 Node 8: lnL = -4091.405884 Node 9: lnL = -4091.405884 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 856 Sequential format.. Reading seq # 1: YER137C_Sbay Reading seq # 2: YER137C_Scer Reading seq # 3: YER137C_Skud Reading seq # 4: YER137C_Smik Reading seq # 5: YER137C_Spar Sequences read.. Counting patterns.. # site patterns = 258 Counting frequencies.. 120 bytes for distance 41280 bytes for lkl0 33024 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.139510 0.019315 0.001502 0.125171 0.106749 0.145852 0.136670 0.000060 lnL0 = -3279.908837 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3279.908837 x= 0.13951 0.01932 0.00150 0.12517 0.10675 0.14585 0.13667 0.00006 1 h-lim-p 0.0001 0.0021 689.5150 3272.863228 9 0.0000 44 | 0/8 2 h-lim-p 0.0001 0.0006 139.7536 3271.290464 0 0.0001 57 | 0/8 3 h-lim-p 0.0001 0.0006 43.6366 3271.111212 0 0.0002 70 | 0/8 4 h-lim-p 0.0009 0.0114 12.4359 3271.097498 2 0.0002 87 | 0/8 5 h-lim-p 0.0003 0.0027 2.1762 3271.096985 4 0.0002 109 | 0/8 6 h-lim-p 0.0004 0.0046 1.1973 3271.094578 0 0.0039 124 | 0/8 7 h-lim-p 0.0000 0.0001 15.7640 3271.093755 m 0.0001 136 | 0/8 8 h-lim-p 0.0000 0.0000 4.2281 h-lim-p: 2.71419008e-22 2.17135206e-21 4.22814180e+00 3271.093755 .. | 0/8 9 h-lim-p 0.0000 0.0006 35.8959 3271.035045 0 0.0001 159 | 0/8 10 h-lim-p 0.0003 0.0356 11.4789 3271.027953 2 0.0001 175 | 0/8 11 h-lim-p 0.0001 0.0012 2.7279 3271.027071 0 0.0003 188 | 0/8 12 h-lim-p 0.0014 0.1793 0.5908 3271.027039 2 0.0002 206 | 0/8 13 h-lim-p 0.0007 0.0648 0.1427 3271.027036 0 0.0003 226 | 0/8 14 h-lim-p 0.0031 7.7304 0.0153 3271.027034 1 0.0015 249 | 0/8 15 h-lim-p 0.0032 1.3721 0.0072 3271.026426 0 0.0514 273 | 0/8 16 h-lim-p 0.0004 0.0223 0.9500 3271.026145 2 0.0003 297 | 0/8 17 h-lim-p 0.2890 2.3118 0.0004 3271.026135 0 1.1559 319 | 0/8 18 h-lim-p 0.0116 0.0928 0.0042 3271.026135 0 0.0000 352 | 0/8 19 h-lim-p 0.0002 20.0000 0.0000 3271.026135 0 0.8887 384 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 3271.026135 0 0.5469 405 | 0/8 21 h-lim-p 1.2213 20.0000 0.0000 3271.026135 0 0.0009 435 Out... lnL = -3271.026135 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3271.026135 Node 7: lnL = -3271.026135 Node 8: lnL = -3271.026135 Node 9: lnL = -3271.026135 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 354 Sequential format.. Reading seq # 1: YER139C_Sbay Reading seq # 2: YER139C_Scer Reading seq # 3: YER139C_Skud Reading seq # 4: YER139C_Smik Reading seq # 5: YER139C_Spar Sequences read.. Counting patterns.. # site patterns = 145 Counting frequencies.. 120 bytes for distance 23200 bytes for lkl0 18560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.290560 0.059029 0.139837 0.116220 0.061494 0.134415 0.160772 0.045571 lnL0 = -1539.481752 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1539.481752 x= 0.29056 0.05903 0.13984 0.11622 0.06149 0.13442 0.16077 0.04557 1 h-lim-p 0.0003 0.0025 63.1495 1538.642612 0 0.0005 22 | 0/8 2 h-lim-p 0.0018 0.0195 16.7535 1538.585267 7 0.0004 52 | 0/8 3 h-lim-p 0.0007 0.0181 10.6949 1538.560204 6 0.0006 78 | 0/8 4 h-lim-p 0.0036 0.0969 1.7343 1538.559272 5 0.0007 103 | 0/8 5 h-lim-p 0.0034 0.6258 0.3285 1538.559220 3 0.0010 123 | 0/8 6 h-lim-p 0.0233 20.0000 0.0144 1538.559217 0 0.0051 144 | 0/8 7 h-lim-p 0.0185 20.0000 0.0040 1538.558814 0 0.2223 167 | 0/8 8 h-lim-p 0.0022 0.4716 0.4097 1538.558722 2 0.0009 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1538.558710 1 0.9961 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1538.558710 0 1.0938 233 | 0/8 11 h-lim-p 0.8148 20.0000 0.0000 1538.558710 0 0.0000 276 | 0/8 12 h-lim-p 0.0000 20.0000 0.0001 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1538.558710 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1538.558710 Node 7: lnL = -1538.558710 Node 8: lnL = -1538.558710 Node 9: lnL = -1538.558710 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 297 Sequential format.. Reading seq # 1: YER142C_Sbay Reading seq # 2: YER142C_Scer Reading seq # 3: YER142C_Skud Reading seq # 4: YER142C_Smik Reading seq # 5: YER142C_Spar Sequences read.. Counting patterns.. # site patterns = 159 Counting frequencies.. 120 bytes for distance 25440 bytes for lkl0 20352 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.293132 0.137108 0.031392 0.181569 0.112878 0.203571 0.163265 0.021336 lnL0 = -1239.326640 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1239.326640 x= 0.29313 0.13711 0.03139 0.18157 0.11288 0.20357 0.16326 0.02134 1 h-lim-p 0.0044 1.5914 75.1488 1237.824021 9 0.0006 43 | 0/8 2 h-lim-p 0.0019 0.0155 20.8272 1237.527514 7 0.0015 69 | 0/8 3 h-lim-p 0.0011 0.0089 6.6797 1237.495116 0 0.0017 81 | 0/8 4 h-lim-p 0.0031 0.0246 2.0763 1237.492194 4 0.0015 103 | 0/8 5 h-lim-p 0.0051 0.2945 0.6116 1237.491900 4 0.0017 124 | 0/8 6 h-lim-p 0.0102 2.4491 0.1004 1237.491883 3 0.0028 151 | 0/8 7 h-lim-p 0.0070 6.5675 0.0394 1237.491870 1 0.0056 173 | 0/8 8 h-lim-p 0.0454 20.0000 0.0048 1237.490190 0 0.3634 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1237.490171 1 0.9961 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1237.490170 0 1.0938 238 | 0/8 11 h-lim-p 2.0221 20.0000 0.0000 1237.490170 0 1.7694 258 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1237.490170 0 1.0938 278 | 0/8 13 h-lim-p 0.3481 20.0000 0.0000 1237.490170 0 0.1305 299 | 0/8 14 h-lim-p 0.0114 20.0000 0.0002 1237.490170 0 0.0000 332 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 1237.490170 0 0.0000 365 Out... lnL = -1237.490170 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1237.490170 Node 7: lnL = -1237.490170 Node 8: lnL = -1237.490170 Node 9: lnL = -1237.490170 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 293 Sequential format.. Reading seq # 1: YER143W_Sbay Reading seq # 2: YER143W_Scer Reading seq # 3: YER143W_Skud Reading seq # 4: YER143W_Smik Reading seq # 5: YER143W_Spar Sequences read.. Counting patterns.. # site patterns = 155 Counting frequencies.. 120 bytes for distance 24800 bytes for lkl0 19840 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.388484 0.025215 0.003513 0.278146 0.239381 0.160857 0.201144 0.072998 lnL0 = -1194.371691 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1194.371691 x= 0.38848 0.02521 0.00351 0.27815 0.23938 0.16086 0.20114 0.07300 1 h-lim-p 0.0019 0.0154 58.4541 1193.426994 8 0.0006 40 | 0/8 2 h-lim-p 0.0013 0.0107 25.1508 1192.632614 0 0.0027 53 | 0/8 3 h-lim-p 0.0013 0.0101 14.5523 1192.494346 0 0.0019 65 | 0/8 4 h-lim-p 0.0075 0.0863 3.6571 1192.485710 4 0.0014 86 | 0/8 5 h-lim-p 0.0066 0.1234 0.7947 1192.485098 5 0.0020 113 | 0/8 6 h-lim-p 0.0245 3.4633 0.0646 1192.484997 4 0.0133 142 | 0/8 7 h-lim-p 0.0274 15.3410 0.0313 1192.483204 0 0.1097 164 | 0/8 8 h-lim-p 0.0053 0.1493 0.6520 1192.480627 4 0.0057 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 1192.480402 2 1.0889 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1192.480400 1 0.9961 240 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1192.480400 0 1.0938 260 | 0/8 12 h-lim-p 1.5514 20.0000 0.0000 1192.480400 0 1.3574 280 | 0/8 13 h-lim-p 0.8357 20.0000 0.0000 1192.480400 0 0.2089 301 | 0/8 14 h-lim-p 0.0006 20.0000 0.0029 1192.480400 0 0.0000 331 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 1192.480400 0 0.0001 352 Out... lnL = -1192.480400 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1192.480400 Node 7: lnL = -1192.480400 Node 8: lnL = -1192.480400 Node 9: lnL = -1192.480400 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 364 Sequential format.. Reading seq # 1: YER144C_Sbay Reading seq # 2: YER144C_Scer Reading seq # 3: YER144C_Skud Reading seq # 4: YER144C_Smik Reading seq # 5: YER144C_Spar Sequences read.. Counting patterns.. # site patterns = 166 Counting frequencies.. 120 bytes for distance 26560 bytes for lkl0 21248 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.297874 0.000060 0.089485 0.095156 0.048044 0.218408 0.292194 0.041207 lnL0 = -1479.844473 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1479.844473 x= 0.29787 0.00006 0.08949 0.09516 0.04804 0.21841 0.29219 0.04121 1 h-lim-p 0.0025 0.0204 37.4587 1479.305287 3 0.0006 29 | 0/8 2 h-lim-p 0.0009 0.0075 11.4813 1479.261477 5 0.0007 51 | 0/8 3 h-lim-p 0.0018 0.0163 4.5686 1479.257481 3 0.0004 70 | 0/8 4 h-lim-p 0.0006 0.0220 3.5144 1479.255574 4 0.0005 91 | 0/8 5 h-lim-p 0.0039 0.4968 0.4297 1479.255465 4 0.0012 114 | 0/8 6 h-lim-p 0.0025 0.5938 0.2065 1479.255455 1 0.0005 137 | 0/8 7 h-lim-p 0.0037 11.3352 0.0302 1479.255438 0 0.0111 158 | 0/8 8 h-lim-p 0.0618 6.8131 0.0054 1479.254231 0 0.2473 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1479.254223 1 0.9961 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1479.254223 0 2.1875 222 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1479.254223 0 0.5469 243 | 0/8 12 h-lim-p 0.0445 20.0000 0.0000 1479.254223 0 0.0222 263 | 0/8 13 h-lim-p 0.0086 20.0000 0.0000 1479.254223 0 0.0129 283 | 0/8 14 h-lim-p 0.0070 20.0000 0.0001 1479.254223 0 0.0000 323 | 0/8 15 h-lim-p 0.0000 20.0000 0.0009 | 0/8 16 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -1479.254223 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1479.254223 Node 7: lnL = -1479.254223 Node 8: lnL = -1479.254223 Node 9: lnL = -1479.254223 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 1006 Sequential format.. Reading seq # 1: YER145C_Sbay Reading seq # 2: YER145C_Scer Reading seq # 3: YER145C_Skud Reading seq # 4: YER145C_Smik Reading seq # 5: YER145C_Spar Sequences read.. Counting patterns.. # site patterns = 260 Counting frequencies.. 120 bytes for distance 41600 bytes for lkl0 33280 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.367587 0.033450 0.080351 0.099956 0.046852 0.191048 0.248409 0.090607 lnL0 = -3556.178049 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3556.178049 x= 0.36759 0.03345 0.08035 0.09996 0.04685 0.19105 0.24841 0.09061 1 h-lim-p 0.0019 0.0453 195.8735 3552.087121 8 0.0002 43 | 0/8 2 h-lim-p 0.0005 0.0037 27.1889 3552.000855 4 0.0002 64 | 0/8 3 h-lim-p 0.0002 0.0047 25.8672 3551.947130 4 0.0003 84 | 0/8 4 h-lim-p 0.0007 0.0368 9.0324 3551.926525 5 0.0006 105 | 0/8 5 h-lim-p 0.0025 0.1644 2.2966 3551.925112 2 0.0006 122 | 0/8 6 h-lim-p 0.0008 0.1245 1.6865 3551.924757 2 0.0004 138 | 0/8 7 h-lim-p 0.0140 20.0000 0.0444 3551.924750 1 0.0028 153 | 0/8 8 h-lim-p 0.0457 20.0000 0.0027 3551.922162 0 0.5484 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 3551.922153 1 0.9961 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3551.922153 0 1.0938 218 | 0/8 11 h-lim-p 2.2778 20.0000 0.0000 3551.922153 0 1.9931 238 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3551.922153 0 0.0391 263 | 0/8 13 h-lim-p 0.0091 20.0000 0.0000 3551.922153 0 0.0011 285 | 0/8 14 h-lim-p 0.0004 20.0000 0.0001 3551.922153 0 0.0000 311 | 0/8 15 h-lim-p 0.0004 20.0000 0.0000 3551.922153 0 0.0001 332 Out... lnL = -3551.922153 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3551.922153 Node 7: lnL = -3551.922153 Node 8: lnL = -3551.922153 Node 9: lnL = -3551.922153 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 487 Sequential format.. Reading seq # 1: YER148W_Sbay Reading seq # 2: YER148W_Scer Reading seq # 3: YER148W_Skud Reading seq # 4: YER148W_Smik Reading seq # 5: YER148W_Spar Sequences read.. Counting patterns.. # site patterns = 164 Counting frequencies.. 120 bytes for distance 26240 bytes for lkl0 20992 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.177145 0.151921 0.071243 0.083490 0.041375 0.164700 0.161789 0.000060 lnL0 = -1912.006236 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1912.006236 x= 0.17714 0.15192 0.07124 0.08349 0.04138 0.16470 0.16179 0.00006 1 h-lim-p 0.0000 0.0000 282.7358 1911.813997 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0003 307.6400 1906.667295 0 0.0002 38 | 1/8 3 h-lim-p 0.0002 0.0016 99.5774 1905.684361 1 0.0002 52 | 1/8 4 h-lim-p 0.0003 0.0021 59.8133 1905.324583 7 0.0003 81 | 1/8 5 h-lim-p 0.0015 0.0170 10.9440 1905.287750 4 0.0006 101 | 1/8 6 h-lim-p 0.0085 0.3019 0.7531 1905.164445 0 0.0170 114 | 1/8 7 h-lim-p 0.0049 0.0431 2.6143 1902.204904 0 0.0196 135 | 0/8 8 h-lim-p 0.0003 0.0021 73.1850 1900.399232 0 0.0005 148 | 0/8 9 h-lim-p 0.0004 0.0030 14.8874 1900.139076 0 0.0023 162 | 0/8 10 h-lim-p 1.1968 20.0000 0.0284 1899.491885 6 0.5194 186 | 0/8 11 h-lim-p 0.2929 2.3431 0.0080 1899.430917 0 1.1715 208 | 0/8 12 h-lim-p 1.6534 13.2271 0.0018 1899.421493 3 1.3821 234 | 0/8 13 h-lim-p 2.5000 20.0000 0.0008 1899.420781 4 1.2732 263 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 1899.420766 2 0.9644 287 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1899.420766 0 1.0938 307 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1899.420766 0 2.1875 327 | 0/8 17 h-lim-p 2.2006 20.0000 0.0000 1899.420766 0 0.9628 347 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1899.420766 0 0.0012 377 Out... lnL = -1899.420766 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1899.420766 Node 7: lnL = -1899.420766 Node 8: lnL = -1899.420766 Node 9: lnL = -1899.420766 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 877 Sequential format.. Reading seq # 1: YER149C_Sbay Reading seq # 2: YER149C_Scer Reading seq # 3: YER149C_Skud Reading seq # 4: YER149C_Smik Reading seq # 5: YER149C_Spar Sequences read.. Counting patterns.. # site patterns = 313 Counting frequencies.. 120 bytes for distance 50080 bytes for lkl0 40064 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.284744 0.069206 0.056325 0.128800 0.076179 0.194870 0.181559 0.036156 lnL0 = -3886.968059 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3886.968059 x= 0.28474 0.06921 0.05632 0.12880 0.07618 0.19487 0.18156 0.03616 1 h-lim-p 0.0007 0.0053 189.0368 3884.382329 3 0.0002 29 | 0/8 2 h-lim-p 0.0004 0.0030 40.3950 3884.180503 7 0.0003 57 | 0/8 3 h-lim-p 0.0004 0.0113 24.2552 3884.127240 7 0.0002 88 | 0/8 4 h-lim-p 0.0009 0.0314 6.5707 3884.120870 5 0.0003 110 | 0/8 5 h-lim-p 0.0029 0.1518 0.7472 3884.120759 3 0.0004 131 | 0/8 6 h-lim-p 0.0026 1.5624 0.1240 3884.120756 0 0.0003 153 | 0/8 7 h-lim-p 0.0024 17.7886 0.0144 3884.120756 0 0.0011 173 | 0/8 8 h-lim-p 0.0212 20.0000 0.0007 3884.120552 0 0.5098 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3884.120545 0 1.0938 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3884.120545 0 1.0938 237 | 0/8 11 h-lim-p 1.0733 20.0000 0.0000 3884.120545 0 1.0733 257 | 0/8 12 h-lim-p 0.3892 20.0000 0.0001 3884.120545 0 0.0851 278 | 0/8 13 h-lim-p 0.0139 20.0000 0.0004 3884.120545 0 0.0004 302 | 0/8 14 h-lim-p 0.0006 20.0000 0.0003 3884.120545 0 0.0000 332 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 3884.120545 0 0.0000 355 Out... lnL = -3884.120545 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3884.120545 Node 7: lnL = -3884.120545 Node 8: lnL = -3884.120545 Node 9: lnL = -3884.120545 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 903 Sequential format.. Reading seq # 1: YER150W_Sbay Reading seq # 2: YER150W_Scer Reading seq # 3: YER150W_Skud Reading seq # 4: YER150W_Smik Reading seq # 5: YER150W_Spar Sequences read.. Counting patterns.. # site patterns = 314 Counting frequencies.. 120 bytes for distance 50240 bytes for lkl0 40192 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.263615 0.122354 0.054491 0.124715 0.074898 0.210884 0.189181 0.005192 lnL0 = -3985.812665 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3985.812665 x= 0.26362 0.12235 0.05449 0.12472 0.07490 0.21088 0.18918 0.00519 1 h-lim-p 0.0033 0.7558 155.6421 3983.931035 7 0.0002 40 | 0/8 2 h-lim-p 0.0005 0.0043 28.5400 3983.826543 5 0.0003 65 | 0/8 3 h-lim-p 0.0004 0.0101 19.6573 3983.789020 5 0.0003 89 | 0/8 4 h-lim-p 0.0021 0.0391 2.4727 3983.788164 4 0.0003 111 | 0/8 5 h-lim-p 0.0059 2.6495 0.1198 3983.788161 1 0.0004 128 | 0/8 6 h-lim-p 0.0105 5.6827 0.0042 3983.788159 0 0.0105 148 | 0/8 7 h-lim-p 0.0012 5.3813 0.0357 3983.788137 0 0.0037 169 | 0/8 8 h-lim-p 0.0018 0.2133 0.0742 3983.787932 0 0.0035 190 | 0/8 9 h-lim-p 0.2462 9.2679 0.0011 3983.787918 0 0.9847 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3983.787918 0 1.0938 232 | 0/8 11 h-lim-p 1.0345 20.0000 0.0000 3983.787918 0 0.9052 252 | 0/8 12 h-lim-p 0.6486 20.0000 0.0001 3983.787918 0 0.0089 277 | 0/8 13 h-lim-p 0.0016 20.0000 0.0004 3983.787918 0 0.0000 302 | 0/8 14 h-lim-p 0.0001 20.0000 0.0001 3983.787918 0 0.0001 322 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 3983.787918 0 0.0000 344 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 3983.787918 0 0.0001 364 | 0/8 17 h-lim-p 0.0005 20.0000 0.0000 3983.787918 0 0.0000 396 Out... lnL = -3983.787918 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3983.787918 Node 7: lnL = -3983.787918 Node 8: lnL = -3983.787918 Node 9: lnL = -3983.787918 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 506 Sequential format.. Reading seq # 1: YER155C_Sbay Reading seq # 2: YER155C_Scer Reading seq # 3: YER155C_Skud Reading seq # 4: YER155C_Smik Reading seq # 5: YER155C_Spar Sequences read.. Counting patterns.. # site patterns = 134 Counting frequencies.. 120 bytes for distance 21440 bytes for lkl0 17152 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.159385 0.051311 0.033286 0.046697 0.029545 0.108726 0.113477 0.021259 lnL0 = -1747.831809 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1747.831809 x= 0.15938 0.05131 0.03329 0.04670 0.02955 0.10873 0.11348 0.02126 1 h-lim-p 0.0001 0.0012 114.5946 1747.112672 7 0.0001 39 | 0/8 2 h-lim-p 0.0008 0.0103 16.1589 1747.085224 4 0.0002 60 | 0/8 3 h-lim-p 0.0005 0.0076 6.5071 1747.083101 2 0.0001 77 | 0/8 4 h-lim-p 0.0002 0.0398 3.7083 1747.082154 3 0.0002 95 | 0/8 5 h-lim-p 0.0005 0.1005 1.3089 1747.082034 3 0.0002 115 | 0/8 6 h-lim-p 0.0022 2.3090 0.0986 1747.082033 1 0.0003 131 | 0/8 7 h-lim-p 0.0168 20.0000 0.0016 1747.082033 0 0.0037 152 | 0/8 8 h-lim-p 0.0039 20.0000 0.0015 1747.082020 0 0.1257 177 | 0/8 9 h-lim-p 2.2547 20.0000 0.0001 1747.082020 0 1.9728 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1747.082020 0 1.0938 217 | 0/8 11 h-lim-p 0.3819 20.0000 0.0000 1747.082020 0 3.0554 240 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1747.082020 0 0.2734 262 | 0/8 13 h-lim-p 0.0142 20.0000 0.0001 1747.082020 0 0.0854 284 | 0/8 14 h-lim-p 0.0324 20.0000 0.0001 1747.082020 0 0.0015 308 | 0/8 15 h-lim-p 0.0008 20.0000 0.0003 1747.082020 0 0.0000 346 | 0/8 16 h-lim-p 0.0000 20.0000 0.0076 | 0/8 17 h-lim-p 0.0000 20.0000 0.0076 Out... lnL = -1747.082020 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1747.082020 Node 7: lnL = -1747.082020 Node 8: lnL = -1747.082020 Node 9: lnL = -1747.082020 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 522 Sequential format.. Reading seq # 1: YER156C_Sbay Reading seq # 2: YER156C_Scer Reading seq # 3: YER156C_Skud Reading seq # 4: YER156C_Smik Reading seq # 5: YER156C_Spar Sequences read.. Counting patterns.. # site patterns = 232 Counting frequencies.. 120 bytes for distance 37120 bytes for lkl0 29696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.402275 0.026387 0.035269 0.253460 0.132669 0.228918 0.306521 0.064696 lnL0 = -2461.443713 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2461.443713 x= 0.40227 0.02639 0.03527 0.25346 0.13267 0.22892 0.30652 0.06470 1 h-lim-p 0.0012 0.0094 114.6340 2459.500839 9 0.0003 46 | 0/8 2 h-lim-p 0.0005 0.0041 46.6399 2458.833404 0 0.0008 58 | 0/8 3 h-lim-p 0.0021 0.0185 16.8786 2458.747787 6 0.0007 85 | 0/8 4 h-lim-p 0.0033 0.0965 3.5682 2458.741642 6 0.0010 112 | 0/8 5 h-lim-p 0.0019 0.1304 1.9472 2458.739778 5 0.0012 135 | 0/8 6 h-lim-p 0.0065 0.4633 0.3646 2458.739679 2 0.0013 152 | 0/8 7 h-lim-p 0.0079 2.4030 0.0602 2458.739438 0 0.0158 173 | 0/8 8 h-lim-p 0.0171 4.5042 0.0558 2458.727134 0 0.0682 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 2458.727007 3 1.3159 222 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2458.727005 0 1.0938 242 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2458.727005 0 1.2500 262 | 0/8 12 h-lim-p 1.3917 20.0000 0.0000 2458.727005 0 0.6959 282 | 0/8 13 h-lim-p 0.1342 20.0000 0.0000 2458.727005 0 0.0073 305 | 0/8 14 h-lim-p 0.0019 20.0000 0.0002 2458.727005 0 0.0000 332 | 0/8 15 h-lim-p 0.0007 20.0000 0.0000 2458.727005 0 0.0000 362 Out... lnL = -2458.727005 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2458.727005 Node 7: lnL = -2458.727005 Node 8: lnL = -2458.727005 Node 9: lnL = -2458.727005 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 485 Sequential format.. Reading seq # 1: YER157W_Sbay Reading seq # 2: YER157W_Scer Reading seq # 3: YER157W_Skud Reading seq # 4: YER157W_Smik Reading seq # 5: YER157W_Spar Sequences read.. Counting patterns.. # site patterns = 222 Counting frequencies.. 120 bytes for distance 35520 bytes for lkl0 28416 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.421111 0.024132 0.027025 0.253686 0.132442 0.233000 0.325532 0.066948 lnL0 = -2446.578428 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2446.578428 x= 0.42111 0.02413 0.02702 0.25369 0.13244 0.23300 0.32553 0.06695 1 h-lim-p 0.0016 0.0124 114.0120 2445.049244 8 0.0003 43 | 0/8 2 h-lim-p 0.0006 0.0051 36.7711 2444.611877 5 0.0007 67 | 0/8 3 h-lim-p 0.0017 0.0278 14.8769 2444.540851 6 0.0008 90 | 0/8 4 h-lim-p 0.0036 0.0749 3.0860 2444.536147 5 0.0010 116 | 0/8 5 h-lim-p 0.0024 0.1936 1.3635 2444.535365 3 0.0010 135 | 0/8 6 h-lim-p 0.0025 0.3034 0.5458 2444.535191 4 0.0014 157 | 0/8 7 h-lim-p 0.0076 3.8327 0.1009 2444.535185 1 0.0009 181 | 0/8 8 h-lim-p 0.1196 20.0000 0.0008 2444.534531 0 1.4355 204 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 2444.534492 2 0.9961 228 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2444.534492 0 1.0938 248 | 0/8 11 h-lim-p 1.2479 20.0000 0.0000 2444.534492 0 1.8718 268 | 0/8 12 h-lim-p 1.7467 20.0000 0.0000 2444.534492 0 0.3821 289 | 0/8 13 h-lim-p 0.0431 20.0000 0.0001 2444.534492 0 0.0216 309 | 0/8 14 h-lim-p 0.0063 20.0000 0.0003 2444.534492 0 0.0000 347 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 2444.534492 0 0.0000 369 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 2444.534492 0 0.0000 398 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 | 0/8 18 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -2444.534492 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2444.534492 Node 7: lnL = -2444.534492 Node 8: lnL = -2444.534492 Node 9: lnL = -2444.534492 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 865 Sequential format.. Reading seq # 1: YER158C_Sbay Reading seq # 2: YER158C_Scer Reading seq # 3: YER158C_Skud Reading seq # 4: YER158C_Smik Reading seq # 5: YER158C_Spar Sequences read.. Counting patterns.. # site patterns = 229 Counting frequencies.. 120 bytes for distance 36640 bytes for lkl0 29312 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.176172 0.068943 0.044737 0.087013 0.040853 0.151097 0.144730 0.000060 lnL0 = -3290.891789 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3290.891789 x= 0.17617 0.06894 0.04474 0.08701 0.04085 0.15110 0.14473 0.00006 1 h-lim-p 0.0001 0.0006 130.6068 3289.902660 0 0.0001 23 | 0/8 2 h-lim-p 0.0001 0.0006 64.7313 3289.756570 0 0.0001 35 | 0/8 3 h-lim-p 0.0000 0.0001 11.1605 3289.748343 m 0.0001 47 | 1/8 4 h-lim-p 0.0006 0.0742 2.4167 3289.747139 2 0.0003 63 | 1/8 5 h-lim-p 0.0007 0.2599 0.9705 3289.744526 0 0.0011 75 | 1/8 6 h-lim-p 0.0008 0.0758 1.3487 3289.724574 0 0.0024 95 | 1/8 7 h-lim-p 0.0071 0.3980 0.4483 3289.724545 2 0.0003 116 | 1/8 8 h-lim-p 0.0062 14.9696 0.0212 3289.724545 0 0.0014 136 | 0/8 9 h-lim-p 0.0001 3.8320 0.1957 3289.724536 0 0.0006 157 | 0/8 10 h-lim-p 0.0751 0.6005 0.0013 3289.724128 0 0.3003 179 | 0/8 11 h-lim-p 0.0752 0.6013 0.0001 3289.724126 m 0.6013 199 | 1/8 12 h-lim-p 0.0212 20.0000 0.0019 3289.724126 0 0.0046 220 | 1/8 13 h-lim-p 1.3570 20.0000 0.0000 3289.724125 0 1.1874 239 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 3289.724125 0 2.1875 258 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 3289.724125 0 5.0000 278 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 3289.724125 0 2.1875 297 | 1/8 17 h-lim-p 1.8481 20.0000 0.0000 3289.724125 0 0.8086 316 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 3289.724125 0 0.3125 337 | 1/8 19 h-lim-p 0.4543 20.0000 0.0000 3289.724125 0 0.0018 363 Out... lnL = -3289.724125 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3289.724125 Node 7: lnL = -3289.724125 Node 8: lnL = -3289.724125 Node 9: lnL = -3289.724125 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 866 Sequential format.. Reading seq # 1: YER159C_Sbay Reading seq # 2: YER159C_Scer Reading seq # 3: YER159C_Skud Reading seq # 4: YER159C_Smik Reading seq # 5: YER159C_Spar Sequences read.. Counting patterns.. # site patterns = 374 Counting frequencies.. 120 bytes for distance 59840 bytes for lkl0 47872 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.335987 0.064225 0.026215 0.209306 0.250210 0.210770 0.290929 0.000060 lnL0 = -4407.978997 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4407.978997 x= 0.33599 0.06423 0.02622 0.20931 0.25021 0.21077 0.29093 0.00006 1 h-lim-p 0.0006 0.3370 387.2556 4396.488733 9 0.0002 44 | 0/8 2 h-lim-p 0.0007 0.0054 68.6943 4395.192551 3 0.0006 62 | 0/8 3 h-lim-p 0.0003 0.0022 23.2867 4395.050763 0 0.0006 75 | 0/8 4 h-lim-p 0.0029 0.0791 4.4451 4395.043585 4 0.0007 96 | 0/8 5 h-lim-p 0.0048 0.5831 0.6878 4395.043369 2 0.0009 113 | 0/8 6 h-lim-p 0.0017 1.4132 0.3707 4395.041872 0 0.0276 137 | 0/8 7 h-lim-p 0.0007 0.0336 14.4223 4395.034935 0 0.0028 159 | 0/8 8 h-lim-p 0.0502 0.4535 0.8132 4395.034864 1 0.0007 178 | 0/8 9 h-lim-p 0.6250 20.0000 0.0009 4395.034731 0 1.2500 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 4395.034720 1 0.9961 221 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4395.034720 0 1.0938 241 | 0/8 12 h-lim-p 1.4000 20.0000 0.0000 4395.034720 0 1.4000 261 | 0/8 13 h-lim-p 0.0202 20.0000 0.0002 4395.034720 0 0.0000 300 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 4395.034720 0 0.0000 330 Out... lnL = -4395.034720 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4395.034720 Node 7: lnL = -4395.034720 Node 8: lnL = -4395.034720 Node 9: lnL = -4395.034720 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 297 Sequential format.. Reading seq # 1: YER161C_Sbay Reading seq # 2: YER161C_Scer Reading seq # 3: YER161C_Skud Reading seq # 4: YER161C_Smik Reading seq # 5: YER161C_Spar Sequences read.. Counting patterns.. # site patterns = 145 Counting frequencies.. 120 bytes for distance 23200 bytes for lkl0 18560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.297666 0.060583 0.044716 0.078834 0.079648 0.280700 0.254295 0.022723 lnL0 = -1356.418413 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1356.418413 x= 0.29767 0.06058 0.04472 0.07883 0.07965 0.28070 0.25430 0.02272 1 h-lim-p 0.0007 0.0055 66.8632 1355.507760 6 0.0004 36 | 0/8 2 h-lim-p 0.0009 0.0075 14.8181 1355.436140 7 0.0007 63 | 0/8 3 h-lim-p 0.0010 0.0107 10.1444 1355.411854 7 0.0007 92 | 0/8 4 h-lim-p 0.0014 0.0425 4.7005 1355.404226 4 0.0009 114 | 0/8 5 h-lim-p 0.0024 0.1101 1.7893 1355.403049 5 0.0009 137 | 0/8 6 h-lim-p 0.0113 2.4554 0.1399 1355.403037 1 0.0012 153 | 0/8 7 h-lim-p 0.0515 20.0000 0.0034 1355.403037 0 0.0113 174 | 0/8 8 h-lim-p 0.0536 20.0000 0.0007 1355.403015 0 0.3218 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1355.403014 0 1.0938 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1355.403014 0 1.0938 236 | 0/8 11 h-lim-p 1.0880 20.0000 0.0000 1355.403014 0 0.2380 257 | 0/8 12 h-lim-p 0.0645 20.0000 0.0000 1355.403014 0 0.0000 299 | 0/8 13 h-lim-p 0.0000 20.0000 0.0004 | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1355.403014 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1355.403014 Node 7: lnL = -1355.403014 Node 8: lnL = -1355.403014 Node 9: lnL = -1355.403014 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 853 Sequential format.. Reading seq # 1: YER163C_Sbay Reading seq # 2: YER163C_Scer Reading seq # 3: YER163C_Skud Reading seq # 4: YER163C_Smik Reading seq # 5: YER163C_Spar Sequences read.. Counting patterns.. # site patterns = 318 Counting frequencies.. 120 bytes for distance 50880 bytes for lkl0 40704 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.341161 0.209714 0.177978 0.206468 0.107850 0.316129 0.228983 0.000060 lnL0 = -4220.349196 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4220.349196 x= 0.34116 0.20971 0.17798 0.20647 0.10785 0.31613 0.22898 0.00006 1 h-lim-p 0.0000 0.0000 251.2787 4220.257692 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0021 124.7543 4217.673021 0 0.0005 39 | 1/8 3 h-lim-p 0.0006 0.0049 45.2432 4217.094770 7 0.0006 64 | 1/8 4 h-lim-p 0.0036 0.0447 8.1866 4217.007067 4 0.0018 84 | 1/8 5 h-lim-p 0.0078 0.1560 1.8407 4216.626669 0 0.0156 97 | 1/8 6 h-lim-p 0.0028 0.0372 10.3099 4213.183896 0 0.0056 110 | 1/8 7 h-lim-p 0.0011 0.0090 32.3387 4204.833403 0 0.0034 123 | 1/8 8 h-lim-p 0.0016 0.0125 28.1973 4204.530185 4 0.0008 143 | 1/8 9 h-lim-p 0.4563 5.6216 0.0480 4203.483217 0 0.6844 155 | 0/8 10 h-lim-p 0.0125 0.7045 2.6314 4203.480587 2 0.0007 181 | 0/8 11 h-lim-p 0.1851 1.4940 0.0104 4203.444455 0 0.7404 195 | 0/8 12 h-lim-p 2.5000 20.0000 0.0026 4203.440399 5 0.8067 227 | 0/8 13 h-lim-p 2.5000 20.0000 0.0006 4203.440243 3 0.8059 255 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 4203.440242 0 1.0938 275 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 4203.440242 0 1.0938 295 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 4203.440242 0 1.0938 315 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 4203.440242 0 1.2500 335 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 4203.440242 0 0.1562 358 | 0/8 19 h-lim-p 0.1775 20.0000 0.0000 4203.440242 0 0.0000 389 Out... lnL = -4203.440242 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4203.440242 Node 7: lnL = -4203.440242 Node 8: lnL = -4203.440242 Node 9: lnL = -4203.440242 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 838 Sequential format.. Reading seq # 1: YER164W_Sbay Reading seq # 2: YER164W_Scer Reading seq # 3: YER164W_Skud Reading seq # 4: YER164W_Smik Reading seq # 5: YER164W_Spar Sequences read.. Counting patterns.. # site patterns = 242 Counting frequencies.. 120 bytes for distance 38720 bytes for lkl0 30976 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.229969 0.058931 0.066936 0.103739 0.062991 0.195377 0.153537 0.008689 lnL0 = -3588.973077 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3588.973077 x= 0.22997 0.05893 0.06694 0.10374 0.06299 0.19538 0.15354 0.00869 1 h-lim-p 0.0002 0.0016 152.3795 3587.308350 4 0.0002 30 | 0/8 2 h-lim-p 0.0003 0.0021 24.7558 3587.246613 5 0.0002 52 | 0/8 3 h-lim-p 0.0005 0.0043 4.9834 3587.244473 5 0.0002 77 | 0/8 4 h-lim-p 0.0004 0.0106 2.5098 3587.244096 3 0.0001 95 | 0/8 5 h-lim-p 0.0010 0.4710 0.3881 3587.244074 2 0.0003 113 | 0/8 6 h-lim-p 0.0017 2.7774 0.0734 3587.244074 0 0.0004 134 | 0/8 7 h-lim-p 0.0038 20.0000 0.0071 3587.244071 0 0.0076 155 | 0/8 8 h-lim-p 0.0083 20.0000 0.0064 3587.243642 0 0.0668 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3587.243640 0 1.0938 198 | 0/8 10 h-lim-p 0.9974 20.0000 0.0001 3587.243640 0 0.8727 218 | 0/8 11 h-lim-p 0.7358 20.0000 0.0001 3587.243640 0 0.1839 239 | 0/8 12 h-lim-p 0.0342 20.0000 0.0003 .. | 0/8 13 h-lim-p 0.0000 20.0000 0.0013 3587.243640 0 0.0000 313 | 0/8 14 h-lim-p 0.0000 20.0000 0.0005 3587.243640 0 0.0000 348 | 0/8 15 h-lim-p 0.0000 20.0000 0.0013 | 0/8 16 h-lim-p 0.0000 20.0000 0.0013 Out... lnL = -3587.243640 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3587.243640 Node 7: lnL = -3587.243640 Node 8: lnL = -3587.243640 Node 9: lnL = -3587.243640 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 769 Sequential format.. Reading seq # 1: YER167W_Sbay Reading seq # 2: YER167W_Scer Reading seq # 3: YER167W_Skud Reading seq # 4: YER167W_Smik Reading seq # 5: YER167W_Spar Sequences read.. Counting patterns.. # site patterns = 159 Counting frequencies.. 120 bytes for distance 25440 bytes for lkl0 20352 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.170900 0.029654 0.028341 0.062617 0.031163 0.086561 0.111345 0.033980 lnL0 = -2710.678585 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2710.678585 x= 0.17090 0.02965 0.02834 0.06262 0.03116 0.08656 0.11135 0.03398 1 h-lim-p 0.0001 0.0006 248.0444 2708.395418 4 0.0001 30 | 0/8 2 h-lim-p 0.0001 0.0009 47.8552 2708.270108 2 0.0001 46 | 0/8 3 h-lim-p 0.0003 0.0038 20.7295 2708.249329 4 0.0001 65 | 0/8 4 h-lim-p 0.0003 0.0440 7.4662 2708.247857 4 0.0001 86 | 0/8 5 h-lim-p 0.0004 0.0803 1.1450 2708.247771 3 0.0001 106 | 0/8 6 h-lim-p 0.0004 0.5823 0.3722 2708.247758 0 0.0002 118 | 0/8 7 h-lim-p 0.0048 16.6197 0.0167 2708.247758 0 0.0005 140 | 0/8 8 h-lim-p 0.0421 20.0000 0.0002 2708.247670 0 0.6739 164 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2708.247667 0 1.0938 184 | 0/8 10 h-lim-p 0.9452 20.0000 0.0000 2708.247667 0 0.8270 204 | 0/8 11 h-lim-p 0.6569 20.0000 0.0001 2708.247667 0 0.0010 233 | 0/8 12 h-lim-p 0.0003 20.0000 0.0002 2708.247667 0 0.0000 257 | 0/8 13 h-lim-p 0.0003 20.0000 0.0000 2708.247667 0 0.0000 291 Out... lnL = -2708.247667 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2708.247667 Node 7: lnL = -2708.247667 Node 8: lnL = -2708.247667 Node 9: lnL = -2708.247667 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 789 Sequential format.. Reading seq # 1: YER168C_Sbay Reading seq # 2: YER168C_Scer Reading seq # 3: YER168C_Skud Reading seq # 4: YER168C_Smik Reading seq # 5: YER168C_Spar Sequences read.. Counting patterns.. # site patterns = 228 Counting frequencies.. 120 bytes for distance 36480 bytes for lkl0 29184 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.196430 0.020025 0.040683 0.120171 0.076130 0.139740 0.176183 0.007122 lnL0 = -3097.096858 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3097.096858 x= 0.19643 0.02002 0.04068 0.12017 0.07613 0.13974 0.17618 0.00712 1 h-lim-p 0.0007 0.3700 288.3384 3094.053649 3 0.0001 30 | 0/8 2 h-lim-p 0.0001 0.0007 24.4576 3093.984202 0 0.0003 43 | 0/8 3 h-lim-p 0.0005 0.0038 7.6978 3093.979581 5 0.0002 67 | 0/8 4 h-lim-p 0.0006 0.1128 2.0959 3093.979053 3 0.0003 85 | 0/8 5 h-lim-p 0.0018 0.3483 0.2991 3093.979038 2 0.0004 102 | 0/8 6 h-lim-p 0.0009 0.3026 0.1178 3093.979036 1 0.0002 125 | 0/8 7 h-lim-p 0.0012 3.8613 0.0217 3093.979030 0 0.0024 146 | 0/8 8 h-lim-p 0.0049 11.6497 0.0106 3093.977466 0 0.0791 170 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3093.977428 3 1.3437 197 | 0/8 10 h-lim-p 0.6845 20.0000 0.0001 3093.977428 0 1.3689 218 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3093.977428 0 1.0938 238 | 0/8 12 h-lim-p 0.1866 20.0000 0.0001 3093.977428 0 2.2390 261 | 0/8 13 h-lim-p 0.2632 15.9644 0.0005 3093.977428 0 0.0001 292 | 0/8 14 h-lim-p 0.0001 17.3226 0.0004 3093.977428 0 0.0000 324 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 3093.977428 0 0.0000 350 Out... lnL = -3093.977428 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3093.977428 Node 7: lnL = -3093.977428 Node 8: lnL = -3093.977428 Node 9: lnL = -3093.977428 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 220 Sequential format.. Reading seq # 1: YER170W_Sbay Reading seq # 2: YER170W_Scer Reading seq # 3: YER170W_Skud Reading seq # 4: YER170W_Smik Reading seq # 5: YER170W_Spar Sequences read.. Counting patterns.. # site patterns = 117 Counting frequencies.. 120 bytes for distance 18720 bytes for lkl0 14976 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.312336 0.094819 0.028895 0.196400 0.098780 0.192452 0.148658 0.037436 lnL0 = -992.438545 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 992.438545 x= 0.31234 0.09482 0.02890 0.19640 0.09878 0.19245 0.14866 0.03744 1 h-lim-p 0.0002 0.0016 25.5580 992.238287 0 0.0006 23 | 0/8 2 h-lim-p 0.0009 0.0180 17.8603 992.139319 3 0.0009 41 | 0/8 3 h-lim-p 0.0033 0.0308 4.6723 992.130912 5 0.0009 65 | 0/8 4 h-lim-p 0.0049 0.2035 0.8140 992.130646 4 0.0008 88 | 0/8 5 h-lim-p 0.0085 2.7580 0.0799 992.130641 2 0.0016 113 | 0/8 6 h-lim-p 0.0354 20.0000 0.0037 992.130638 2 0.0226 138 | 0/8 7 h-lim-p 0.0193 5.3540 0.0044 992.130552 0 0.0773 160 | 0/8 8 h-lim-p 0.0077 5.3309 0.0435 992.130551 1 0.0015 183 | 0/8 9 h-lim-p 0.8458 20.0000 0.0001 992.130544 1 1.0572 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 992.130544 0 1.0938 225 | 0/8 11 h-lim-p 1.3809 20.0000 0.0000 992.130544 0 0.0001 259 Out... lnL = -992.130544 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -992.130544 Node 7: lnL = -992.130544 Node 8: lnL = -992.130544 Node 9: lnL = -992.130544 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 298 Sequential format.. Reading seq # 1: YER173W_Sbay Reading seq # 2: YER173W_Scer Reading seq # 3: YER173W_Skud Reading seq # 4: YER173W_Smik Reading seq # 5: YER173W_Spar Sequences read.. Counting patterns.. # site patterns = 152 Counting frequencies.. 120 bytes for distance 24320 bytes for lkl0 19456 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.293953 0.151375 0.204324 0.167665 0.101784 0.252129 0.256985 0.000060 lnL0 = -1344.800279 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1344.800279 x= 0.29395 0.15137 0.20432 0.16767 0.10178 0.25213 0.25699 0.00006 1 h-lim-p 0.0000 0.0000 91.8526 1344.772841 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0061 49.8441 1343.468759 0 0.0013 41 | 1/8 3 h-lim-p 0.0010 0.0082 30.0145 1342.984756 0 0.0020 54 | 1/8 4 h-lim-p 0.0071 0.0571 5.5534 1342.886273 7 0.0048 83 | 1/8 5 h-lim-p 0.0530 0.4435 0.4983 1341.881326 0 0.1059 96 | 1/8 6 h-lim-p 0.0022 0.0172 15.1908 1339.680705 0 0.0043 116 | 1/8 7 h-lim-p 0.0014 0.0110 28.0011 1338.224774 0 0.0027 129 | 1/8 8 h-lim-p 0.0223 0.1781 2.1899 1338.218057 5 0.0025 152 | 1/8 9 h-lim-p 0.1381 10.3304 0.0392 1338.020019 0 0.5525 166 | 1/8 10 h-lim-p 2.5000 20.0000 0.0056 1338.016345 5 0.5350 195 | 1/8 11 h-lim-p 2.5000 20.0000 0.0011 1338.016095 3 0.6718 221 | 1/8 12 h-lim-p 2.5000 20.0000 0.0001 1338.016093 1 0.6152 243 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 1338.016093 0 1.0938 262 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 1338.016093 0 1.0938 281 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 1338.016093 0 0.5469 301 | 1/8 16 h-lim-p 1.2113 20.0000 0.0000 1338.016093 0 0.1514 322 | 1/8 17 h-lim-p 0.1788 20.0000 0.0000 1338.016093 0 0.0000 363 Out... lnL = -1338.016093 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1338.016093 Node 7: lnL = -1338.016093 Node 8: lnL = -1338.016093 Node 9: lnL = -1338.016093 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 317 Sequential format.. Reading seq # 1: YER174C_Sbay Reading seq # 2: YER174C_Scer Reading seq # 3: YER174C_Skud Reading seq # 4: YER174C_Smik Reading seq # 5: YER174C_Spar Sequences read.. Counting patterns.. # site patterns = 135 Counting frequencies.. 120 bytes for distance 21600 bytes for lkl0 17280 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.258554 0.080935 0.071652 0.100912 0.053965 0.217499 0.211887 0.005752 lnL0 = -1390.211585 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1390.211585 x= 0.25855 0.08093 0.07165 0.10091 0.05396 0.21750 0.21189 0.00575 1 h-lim-p 0.0004 0.0028 42.9498 1389.766633 0 0.0005 22 | 0/8 2 h-lim-p 0.0007 0.0056 25.8329 1389.686827 3 0.0003 40 | 0/8 3 h-lim-p 0.0014 0.0137 5.7734 1389.674552 6 0.0008 68 | 0/8 4 h-lim-p 0.0015 0.0122 3.0157 1389.671908 2 0.0007 84 | 0/8 5 h-lim-p 0.0037 0.5550 0.5795 1389.671778 2 0.0008 101 | 0/8 6 h-lim-p 0.0016 0.8084 0.2894 1389.671752 2 0.0007 125 | 0/8 7 h-lim-p 0.0048 0.8580 0.0425 1389.671726 1 0.0060 147 | 0/8 8 h-lim-p 0.0236 5.3672 0.0108 1389.668443 0 0.1885 170 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1389.668430 1 0.9961 192 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1389.668430 0 1.0938 212 | 0/8 11 h-lim-p 1.1018 20.0000 0.0000 1389.668430 0 0.0258 237 | 0/8 12 h-lim-p 0.0028 20.0000 0.0001 1389.668430 0 0.0003 259 | 0/8 13 h-lim-p 0.0001 20.0000 0.0004 1389.668430 0 0.0001 279 | 0/8 14 h-lim-p 0.0000 7.2059 0.0019 1389.668430 0 0.0000 306 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 1389.668430 0 0.0001 326 Out... lnL = -1389.668430 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1389.668430 Node 7: lnL = -1389.668430 Node 8: lnL = -1389.668430 Node 9: lnL = -1389.668430 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 857 Sequential format.. Reading seq # 1: YER175C_Sbay Reading seq # 2: YER175C_Scer Reading seq # 3: YER175C_Skud Reading seq # 4: YER175C_Smik Reading seq # 5: YER175C_Spar Sequences read.. Counting patterns.. # site patterns = 374 Counting frequencies.. 120 bytes for distance 59840 bytes for lkl0 47872 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.513446 0.031830 0.076219 0.167925 0.116595 0.358329 0.324316 0.103693 lnL0 = -4417.575080 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4417.575080 x= 0.51345 0.03183 0.07622 0.16793 0.11660 0.35833 0.32432 0.10369 1 h-lim-p 0.0003 0.0027 124.9468 4415.293461 2 0.0003 26 | 0/8 2 h-lim-p 0.0006 0.0048 38.1543 4414.943062 6 0.0005 49 | 0/8 3 h-lim-p 0.0007 0.0151 29.4657 4414.822185 7 0.0004 80 | 0/8 4 h-lim-p 0.0007 0.0221 18.1011 4414.756024 2 0.0006 96 | 0/8 5 h-lim-p 0.0039 0.0710 2.9516 4414.749948 4 0.0015 116 | 0/8 6 h-lim-p 0.0125 0.4710 0.3471 4414.749914 2 0.0006 135 | 0/8 7 h-lim-p 0.0078 15.5593 0.0269 4414.749914 0 0.0017 156 | 0/8 8 h-lim-p 0.1086 20.0000 0.0004 4414.749833 0 0.8691 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4414.749833 0 1.0938 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4414.749832 0 1.0938 219 | 0/8 11 h-lim-p 1.2820 20.0000 0.0000 4414.749832 0 2.5640 240 | 0/8 12 h-lim-p 0.4557 20.0000 0.0001 4414.749832 0 0.0570 262 | 0/8 13 h-lim-p 0.0051 20.0000 0.0006 4414.749832 0 0.0000 304 | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -4414.749832 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4414.749832 Node 7: lnL = -4414.749832 Node 8: lnL = -4414.749832 Node 9: lnL = -4414.749832 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 821 Sequential format.. Reading seq # 1: YER180C_Sbay Reading seq # 2: YER180C_Scer Reading seq # 3: YER180C_Skud Reading seq # 4: YER180C_Smik Reading seq # 5: YER180C_Spar Sequences read.. Counting patterns.. # site patterns = 247 Counting frequencies.. 120 bytes for distance 39520 bytes for lkl0 31616 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.277189 0.049355 0.012848 0.153929 0.109006 0.182286 0.168601 0.031942 lnL0 = -3673.961544 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3673.961544 x= 0.27719 0.04935 0.01285 0.15393 0.10901 0.18229 0.16860 0.03194 1 h-lim-p 0.0006 0.0280 340.6916 3670.098377 7 0.0001 38 | 0/8 2 h-lim-p 0.0002 0.0014 71.3810 3669.477069 0 0.0003 50 | 0/8 3 h-lim-p 0.0010 0.0122 19.3067 3669.421008 6 0.0003 77 | 0/8 4 h-lim-p 0.0016 0.0532 4.0129 3669.419019 5 0.0003 102 | 0/8 5 h-lim-p 0.0012 0.2168 0.8763 3669.418898 3 0.0003 121 | 0/8 6 h-lim-p 0.0028 1.7184 0.0997 3669.418893 0 0.0006 142 | 0/8 7 h-lim-p 0.0131 20.0000 0.0047 3669.418192 0 0.1578 165 | 0/8 8 h-lim-p 0.0013 0.1310 0.5871 3669.414951 0 0.0025 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 3669.414801 3 1.0449 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3669.414801 0 1.0938 232 | 0/8 11 h-lim-p 1.1186 20.0000 0.0000 3669.414801 0 0.2097 254 | 0/8 12 h-lim-p 0.0725 20.0000 0.0001 3669.414801 0 0.0000 286 | 0/8 13 h-lim-p 0.0004 20.0000 0.0000 3669.414801 0 0.0000 310 Out... lnL = -3669.414801 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3669.414801 Node 7: lnL = -3669.414801 Node 8: lnL = -3669.414801 Node 9: lnL = -3669.414801 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 806 Sequential format.. Reading seq # 1: YER182W_Sbay Reading seq # 2: YER182W_Scer Reading seq # 3: YER182W_Skud Reading seq # 4: YER182W_Smik Reading seq # 5: YER182W_Spar Sequences read.. Counting patterns.. # site patterns = 410 Counting frequencies.. 120 bytes for distance 65600 bytes for lkl0 52480 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.629687 0.196165 0.181855 0.287747 0.143893 0.368503 0.483915 0.024987 lnL0 = -4633.948582 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4633.948582 x= 0.62969 0.19617 0.18186 0.28775 0.14389 0.36850 0.48392 0.02499 1 h-lim-p 0.0585 3.8295 39.7969 4633.310258 2 0.0009 31 | 0/8 2 h-lim-p 0.0016 0.0132 18.5303 4633.197635 2 0.0008 47 | 0/8 3 h-lim-p 0.0012 0.0487 11.9330 4633.117858 0 0.0018 59 | 0/8 4 h-lim-p 0.0036 0.0398 5.9109 4633.092909 5 0.0019 82 | 0/8 5 h-lim-p 0.0079 0.4264 1.4511 4633.090867 4 0.0021 103 | 0/8 6 h-lim-p 0.0055 0.5944 0.5609 4633.090610 3 0.0018 122 | 0/8 7 h-lim-p 0.0242 1.4668 0.0420 4633.090595 2 0.0064 147 | 0/8 8 h-lim-p 0.0442 20.0000 0.0060 4633.089213 0 0.3536 170 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4633.089208 0 1.0938 190 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4633.089208 0 1.0938 210 | 0/8 11 h-lim-p 1.7287 20.0000 0.0000 4633.089208 0 1.5126 230 | 0/8 12 h-lim-p 1.6347 20.0000 0.0000 4633.089208 0 1.6347 250 | 0/8 13 h-lim-p 0.3110 20.0000 0.0000 4633.089208 0 0.0000 294 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 4633.089208 0 0.0000 320 | 0/8 15 h-lim-p 0.0000 20.0000 0.0010 4633.089208 0 0.0000 340 | 0/8 16 h-lim-p 0.0002 20.0000 0.0000 4633.089208 0 0.0000 378 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 4633.089208 0 0.0000 413 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -4633.089208 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4633.089208 Node 7: lnL = -4633.089208 Node 8: lnL = -4633.089208 Node 9: lnL = -4633.089208 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 902 Sequential format.. Reading seq # 1: YER183C_Sbay Reading seq # 2: YER183C_Scer Reading seq # 3: YER183C_Skud Reading seq # 4: YER183C_Smik Reading seq # 5: YER183C_Spar Sequences read.. Counting patterns.. # site patterns = 470 Counting frequencies.. 120 bytes for distance 75200 bytes for lkl0 60160 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.635398 0.173878 0.000060 0.355467 0.272322 0.521052 0.472362 0.078132 lnL0 = -5048.757013 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 5048.757013 x= 0.63540 0.17388 0.00006 0.35547 0.27232 0.52105 0.47236 0.07813 1 h-lim-p 0.0000 0.0000 162.9393 5048.711859 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0059 134.9028 5042.709279 0 0.0013 41 | 1/8 3 h-lim-p 0.0024 0.0194 13.8200 5042.336788 0 0.0036 53 | 1/8 4 h-lim-p 0.0055 0.0980 9.1052 5042.142465 5 0.0039 77 | 1/8 5 h-lim-p 0.0166 0.2951 2.1428 5041.430343 0 0.0332 90 | 1/8 6 h-lim-p 0.0075 0.0776 9.5206 5036.664504 0 0.0149 103 | 1/8 7 h-lim-p 0.0014 0.0114 41.0800 5032.193932 0 0.0028 116 | 1/8 8 h-lim-p 0.6633 5.3067 0.0978 5030.676369 3 0.6737 134 | 0/8 9 h-lim-p 0.0032 0.1847 20.2704 5030.599501 5 0.0004 167 | 0/8 10 h-lim-p 0.5304 20.0000 0.0152 5030.534827 0 1.0608 180 | 0/8 11 h-lim-p 2.5000 20.0000 0.0044 5030.531435 4 0.9131 209 | 0/8 12 h-lim-p 2.5000 20.0000 0.0005 5030.531388 3 0.6718 236 | 0/8 13 h-lim-p 2.4714 20.0000 0.0001 5030.531385 1 0.6082 259 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 5030.531384 0 1.0938 279 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 5030.531384 0 1.0938 299 | 0/8 16 h-lim-p 1.1705 20.0000 0.0000 5030.531384 0 1.1705 319 | 0/8 17 h-lim-p 0.6135 20.0000 0.0000 5030.531384 0 0.3067 339 | 0/8 18 h-lim-p 0.0162 20.0000 0.0002 5030.531384 0 0.0000 374 | 0/8 19 h-lim-p 0.0005 20.0000 0.0000 5030.531384 0 0.0000 398 Out... lnL = -5030.531384 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -5030.531384 Node 7: lnL = -5030.531384 Node 8: lnL = -5030.531384 Node 9: lnL = -5030.531384 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 293 Sequential format.. Reading seq # 1: YFL001W_Sbay Reading seq # 2: YFL001W_Scer Reading seq # 3: YFL001W_Skud Reading seq # 4: YFL001W_Smik Reading seq # 5: YFL001W_Spar Sequences read.. Counting patterns.. # site patterns = 108 Counting frequencies.. 120 bytes for distance 17280 bytes for lkl0 13824 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.243765 0.018947 0.123327 0.057768 0.085249 0.249084 0.137007 0.004634 lnL0 = -1056.269360 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1056.269360 x= 0.24377 0.01895 0.12333 0.05777 0.08525 0.24908 0.13701 0.00463 1 h-lim-p 0.0024 0.0191 57.8562 1055.676418 9 0.0004 44 | 0/8 2 h-lim-p 0.0019 0.0155 10.9917 1055.618885 4 0.0010 64 | 0/8 3 h-lim-p 0.0019 0.0526 5.4838 1055.605885 5 0.0011 87 | 0/8 4 h-lim-p 0.0032 0.0678 1.8214 1055.604734 2 0.0008 104 | 0/8 5 h-lim-p 0.0011 0.1188 1.2534 1055.604211 3 0.0010 122 | 0/8 6 h-lim-p 0.0223 0.2406 0.0539 1055.604209 1 0.0011 139 | 0/8 7 h-lim-p 0.0183 20.0000 0.0033 1055.604209 0 0.0080 159 | 0/8 8 h-lim-p 0.0424 20.0000 0.0006 1055.604183 0 0.3392 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1055.604183 0 1.0938 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1055.604183 0 1.0938 222 | 0/8 11 h-lim-p 1.4013 20.0000 0.0000 1055.604183 0 4.2040 243 | 0/8 12 h-lim-p 0.7502 20.0000 0.0001 1055.604183 0 0.0234 267 | 0/8 13 h-lim-p 0.0001 0.7235 0.0172 1055.604183 0 0.0000 287 | 0/8 14 h-lim-p 0.0001 20.0000 0.0077 1055.604183 0 0.0000 308 | 0/8 15 h-lim-p 0.0000 20.0000 0.0066 1055.604183 0 0.0000 328 | 0/8 16 h-lim-p 0.0001 20.0000 0.0008 1055.604183 0 0.0001 348 | 0/8 17 h-lim-p 0.0001 7.8423 0.0016 1055.604183 0 0.0000 376 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 1055.604183 0 0.0000 396 | 0/8 19 h-lim-p 0.0002 20.0000 0.0000 1055.604183 0 0.0000 424 Out... lnL = -1055.604183 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1055.604183 Node 7: lnL = -1055.604183 Node 8: lnL = -1055.604183 Node 9: lnL = -1055.604183 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 259 Sequential format.. Reading seq # 1: YFL002C_Sbay Reading seq # 2: YFL002C_Scer Reading seq # 3: YFL002C_Skud Reading seq # 4: YFL002C_Smik Reading seq # 5: YFL002C_Spar Sequences read.. Counting patterns.. # site patterns = 109 Counting frequencies.. 120 bytes for distance 17440 bytes for lkl0 13952 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.240689 0.026559 0.111635 0.074287 0.082501 0.271465 0.146651 0.000060 lnL0 = -1014.731956 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1014.731956 x= 0.24069 0.02656 0.11164 0.07429 0.08250 0.27146 0.14665 0.00006 1 h-lim-p 0.0008 0.0062 38.6002 1014.396701 8 0.0005 41 | 0/8 2 h-lim-p 0.0005 0.0043 6.6991 1014.375351 0 0.0011 54 | 0/8 3 h-lim-p 0.0021 0.0874 3.3763 1014.371325 4 0.0009 75 | 0/8 4 h-lim-p 0.0018 0.0779 1.6648 1014.370412 2 0.0008 91 | 0/8 5 h-lim-p 0.0016 0.3142 0.8506 1014.370089 4 0.0012 113 | 0/8 6 h-lim-p 0.0017 0.0137 0.1681 1014.370075 3 0.0010 142 | 0/8 7 h-lim-p 0.0069 0.5641 0.0246 1014.370074 1 0.0017 165 | 0/8 8 h-lim-p 0.0029 0.1327 0.0145 1014.369984 m 0.1327 188 | 1/8 9 h-lim-p 0.1517 20.0000 0.0090 1014.369981 2 0.0121 215 | 1/8 10 h-lim-p 0.1039 20.0000 0.0011 1014.369889 0 0.4155 236 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 1014.369886 1 1.2305 258 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 1014.369886 0 1.0938 277 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 1014.369886 0 0.5469 297 | 1/8 14 h-lim-p 1.2072 20.0000 0.0000 1014.369886 0 0.0000 337 Out... lnL = -1014.369886 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1014.369886 Node 7: lnL = -1014.369886 Node 8: lnL = -1014.369886 Node 9: lnL = -1014.369886 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 892 Sequential format.. Reading seq # 1: YFL004W_Sbay Reading seq # 2: YFL004W_Scer Reading seq # 3: YFL004W_Skud Reading seq # 4: YFL004W_Smik Reading seq # 5: YFL004W_Spar Sequences read.. Counting patterns.. # site patterns = 272 Counting frequencies.. 120 bytes for distance 43520 bytes for lkl0 34816 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.247274 0.022187 0.067421 0.086079 0.060834 0.205337 0.231696 0.011475 lnL0 = -3697.233059 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3697.233059 x= 0.24727 0.02219 0.06742 0.08608 0.06083 0.20534 0.23170 0.01148 1 h-lim-p 0.0011 0.4255 259.2748 3693.715206 6 0.0001 35 | 0/8 2 h-lim-p 0.0002 0.0013 44.2866 3693.448462 0 0.0003 48 | 0/8 3 h-lim-p 0.0002 0.0015 36.2917 3693.379066 5 0.0002 69 | 0/8 4 h-lim-p 0.0007 0.0265 7.6466 3693.371446 5 0.0003 91 | 0/8 5 h-lim-p 0.0011 0.1249 1.9948 3693.371018 2 0.0002 108 | 0/8 6 h-lim-p 0.0013 0.3464 0.3607 3693.371002 1 0.0003 123 | 0/8 7 h-lim-p 0.0015 1.7588 0.0631 3693.370988 1 0.0019 145 | 0/8 8 h-lim-p 0.0187 20.0000 0.0063 3693.366119 0 0.2996 169 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 3693.365911 2 1.0889 193 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 3693.365907 1 1.2305 216 | 0/8 11 h-lim-p 1.4187 20.0000 0.0000 3693.365907 0 1.2414 236 | 0/8 12 h-lim-p 1.6000 20.0000 0.0000 3693.365907 0 1.4000 256 | 0/8 13 h-lim-p 0.6774 20.0000 0.0001 3693.365907 0 0.2964 276 | 0/8 14 h-lim-p 0.0027 1.9872 0.0078 3693.365907 0 0.0000 319 | 0/8 15 h-lim-p 0.0000 20.0000 0.0015 | 0/8 16 h-lim-p 0.0000 20.0000 0.0015 Out... lnL = -3693.365907 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3693.365907 Node 7: lnL = -3693.365907 Node 8: lnL = -3693.365907 Node 9: lnL = -3693.365907 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 454 Sequential format.. Reading seq # 1: YFL005W_Sbay Reading seq # 2: YFL005W_Scer Reading seq # 3: YFL005W_Skud Reading seq # 4: YFL005W_Smik Reading seq # 5: YFL005W_Spar Sequences read.. Counting patterns.. # site patterns = 162 Counting frequencies.. 120 bytes for distance 25920 bytes for lkl0 20736 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.238987 0.145011 0.035442 0.132638 0.075051 0.221488 0.162523 0.000060 lnL0 = -1902.522702 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1902.522702 x= 0.23899 0.14501 0.03544 0.13264 0.07505 0.22149 0.16252 0.00006 1 h-lim-p 0.0000 0.0000 151.0580 1902.415586 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0014 77.9433 1901.459331 0 0.0003 39 | 1/8 3 h-lim-p 0.0006 0.0151 38.9451 1901.324615 8 0.0002 70 | 1/8 4 h-lim-p 0.0011 0.0339 7.9834 1901.294960 6 0.0008 96 | 1/8 5 h-lim-p 0.0077 0.4012 0.8623 1901.207102 0 0.0154 109 | 1/8 6 h-lim-p 0.0039 0.0537 3.3810 1899.652910 0 0.0157 130 | 1/8 7 h-lim-p 0.0010 0.0082 31.8062 1897.263441 0 0.0015 142 | 1/8 8 h-lim-p 0.0093 0.0747 3.1051 1897.256857 4 0.0011 166 | 1/8 9 h-lim-p 0.0890 9.8206 0.0398 1896.638183 0 0.7123 181 | 1/8 10 h-lim-p 2.4478 19.5827 0.0079 1896.567618 7 0.9073 216 | 0/8 11 h-lim-p 0.5203 20.0000 0.0138 1896.566448 2 0.1037 240 | 0/8 12 h-lim-p 0.0010 0.0082 0.3125 1896.557862 m 0.0082 260 | 1/8 13 h-lim-p 2.5000 20.0000 0.0008 1896.557464 3 0.9644 286 | 0/8 14 h-lim-p 0.0043 6.1237 0.1768 1896.557450 1 0.0009 308 | 0/8 15 h-lim-p 0.2623 2.0987 0.0001 1896.557437 0 1.0493 330 | 0/8 16 h-lim-p 0.0789 0.6314 0.0002 1896.557437 0 0.0000 377 | 0/8 17 h-lim-p 0.0000 0.0015 0.0812 1896.557437 0 0.0002 401 | 0/8 18 h-lim-p 0.0001 0.0006 0.1489 .. | 0/8 19 h-lim-p 0.0000 0.0014 0.0629 | 0/8 20 h-lim-p 0.0000 0.0014 0.0629 Out... lnL = -1896.557437 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1896.557437 Node 7: lnL = -1896.557437 Node 8: lnL = -1896.557437 Node 9: lnL = -1896.557437 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 893 Sequential format.. Reading seq # 1: YFL008W_Sbay Reading seq # 2: YFL008W_Scer Reading seq # 3: YFL008W_Skud Reading seq # 4: YFL008W_Smik Reading seq # 5: YFL008W_Spar Sequences read.. Counting patterns.. # site patterns = 420 Counting frequencies.. 120 bytes for distance 67200 bytes for lkl0 53760 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.733460 0.000060 0.390010 0.206817 0.195429 0.346013 0.266109 0.166696 lnL0 = -4663.120340 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4663.120340 x= 0.73346 0.00006 0.39001 0.20682 0.19543 0.34601 0.26611 0.16670 1 h-lim-p 0.0000 0.0000 220.6779 4663.058236 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0072 112.1700 4657.595057 0 0.0013 41 | 1/8 3 h-lim-p 0.0015 0.0123 38.9644 4656.804601 4 0.0012 61 | 1/8 4 h-lim-p 0.0081 0.1412 5.6752 4656.624304 6 0.0055 88 | 1/8 5 h-lim-p 0.0138 0.1606 2.2821 4655.460197 0 0.0276 101 | 1/8 6 h-lim-p 0.0078 0.0627 7.6079 4646.103829 0 0.0157 114 | 1/8 7 h-lim-p 0.0009 0.0070 50.0281 4643.516666 0 0.0018 127 | 1/8 8 h-lim-p 1.1264 9.0112 0.0457 4643.134501 7 0.7428 154 | 0/8 9 h-lim-p 0.0009 0.0242 36.1335 4642.871180 6 0.0005 186 | 0/8 10 h-lim-p 0.6112 12.7473 0.0302 4642.491640 0 1.2223 199 | 0/8 11 h-lim-p 2.0365 16.2919 0.0163 4642.432464 4 1.0371 228 | 0/8 12 h-lim-p 2.5000 20.0000 0.0011 4642.431864 3 0.8855 256 | 0/8 13 h-lim-p 2.5000 20.0000 0.0003 4642.431812 2 0.8246 282 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 4642.431811 0 1.0938 302 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 4642.431811 0 1.0938 322 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 4642.431811 0 1.0938 342 | 0/8 17 h-lim-p 1.1937 20.0000 0.0000 4642.431811 0 1.0445 362 | 0/8 18 h-lim-p 0.5456 20.0000 0.0000 4642.431811 0 0.0043 388 | 0/8 19 h-lim-p 0.0000 20.0000 0.0011 4642.431811 0 0.0000 408 | 0/8 20 h-lim-p 0.0000 20.0000 0.0018 4642.431811 0 0.0000 434 | 0/8 21 h-lim-p 0.0013 20.0000 0.0000 4642.431811 0 0.0000 472 Out... lnL = -4642.431811 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4642.431811 Node 7: lnL = -4642.431811 Node 8: lnL = -4642.431811 Node 9: lnL = -4642.431811 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 422 Sequential format.. Reading seq # 1: YFL009W_Sbay Reading seq # 2: YFL009W_Scer Reading seq # 3: YFL009W_Skud Reading seq # 4: YFL009W_Smik Reading seq # 5: YFL009W_Spar Sequences read.. Counting patterns.. # site patterns = 131 Counting frequencies.. 120 bytes for distance 20960 bytes for lkl0 16768 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.200189 0.018767 0.040978 0.068532 0.043801 0.139098 0.153300 0.022381 lnL0 = -1603.306749 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1603.306749 x= 0.20019 0.01877 0.04098 0.06853 0.04380 0.13910 0.15330 0.02238 1 h-lim-p 0.0061 1.7055 72.4363 1602.939352 4 0.0001 34 | 0/8 2 h-lim-p 0.0007 0.0097 15.0053 1602.897336 5 0.0004 57 | 0/8 3 h-lim-p 0.0007 0.0100 8.9652 1602.889711 5 0.0002 79 | 0/8 4 h-lim-p 0.0007 0.0354 2.9672 1602.888943 4 0.0002 100 | 0/8 5 h-lim-p 0.0011 0.3681 0.5538 1602.888876 2 0.0005 116 | 0/8 6 h-lim-p 0.0022 0.5924 0.1202 1602.888874 0 0.0003 138 | 0/8 7 h-lim-p 0.0016 1.9306 0.0208 1602.888874 0 0.0007 158 | 0/8 8 h-lim-p 0.0734 20.0000 0.0002 1602.888793 0 0.8812 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1602.888792 0 1.0938 201 | 0/8 10 h-lim-p 1.9812 20.0000 0.0000 1602.888792 0 1.7335 221 | 0/8 11 h-lim-p 2.3975 20.0000 0.0000 1602.888792 0 0.0749 245 | 0/8 12 h-lim-p 0.0179 20.0000 0.0001 1602.888792 0 0.0008 269 | 0/8 13 h-lim-p 0.0004 20.0000 0.0001 1602.888792 0 0.0000 298 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 1602.888792 0 0.0000 322 Out... lnL = -1602.888792 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1602.888792 Node 7: lnL = -1602.888792 Node 8: lnL = -1602.888792 Node 9: lnL = -1602.888792 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 422 Sequential format.. Reading seq # 1: YFL010C_Sbay Reading seq # 2: YFL010C_Scer Reading seq # 3: YFL010C_Skud Reading seq # 4: YFL010C_Smik Reading seq # 5: YFL010C_Spar Sequences read.. Counting patterns.. # site patterns = 131 Counting frequencies.. 120 bytes for distance 20960 bytes for lkl0 16768 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.199973 0.013360 0.043177 0.069163 0.043171 0.140526 0.152893 0.023004 lnL0 = -1601.785558 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1601.785558 x= 0.19997 0.01336 0.04318 0.06916 0.04317 0.14053 0.15289 0.02300 1 h-lim-p 0.0028 1.0134 106.9722 1601.141648 8 0.0001 43 | 0/8 2 h-lim-p 0.0009 0.0072 13.8468 1601.103125 3 0.0004 61 | 0/8 3 h-lim-p 0.0007 0.0104 7.9991 1601.096321 4 0.0003 81 | 0/8 4 h-lim-p 0.0009 0.0274 2.4847 1601.095831 3 0.0002 100 | 0/8 5 h-lim-p 0.0008 0.3293 0.5781 1601.095765 3 0.0004 119 | 0/8 6 h-lim-p 0.0037 3.0763 0.0645 1601.095765 0 0.0004 141 | 0/8 7 h-lim-p 0.0013 3.5552 0.0200 1601.095765 0 0.0006 161 | 0/8 8 h-lim-p 0.1530 20.0000 0.0001 1601.095749 0 1.2236 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1601.095749 0 1.0938 204 | 0/8 10 h-lim-p 1.3416 20.0000 0.0000 1601.095749 0 2.6832 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1601.095749 0 0.5469 246 | 0/8 12 h-lim-p 0.0122 20.0000 0.0000 1601.095749 0 0.0000 276 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 1601.095749 0 0.0000 299 Out... lnL = -1601.095749 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1601.095749 Node 7: lnL = -1601.095749 Node 8: lnL = -1601.095749 Node 9: lnL = -1601.095749 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 875 Sequential format.. Reading seq # 1: YFL011W_Sbay Reading seq # 2: YFL011W_Scer Reading seq # 3: YFL011W_Skud Reading seq # 4: YFL011W_Smik Reading seq # 5: YFL011W_Spar Sequences read.. Counting patterns.. # site patterns = 388 Counting frequencies.. 120 bytes for distance 62080 bytes for lkl0 49664 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.574248 0.000060 0.094148 0.151958 0.121569 0.279973 0.304734 0.152533 lnL0 = -4257.905027 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4257.905027 x= 0.57425 0.00006 0.09415 0.15196 0.12157 0.27997 0.30473 0.15253 1 h-lim-p 0.0008 0.0065 45.7237 4257.496779 2 0.0004 26 | 0/8 2 h-lim-p 0.0009 0.0227 18.5381 4257.388456 4 0.0007 46 | 0/8 3 h-lim-p 0.0007 0.0294 20.4978 4257.346081 7 0.0004 76 | 0/8 4 h-lim-p 0.0016 0.0487 4.9888 4257.342457 2 0.0003 93 | 0/8 5 h-lim-p 0.0010 0.2644 1.7346 4257.341325 2 0.0009 109 | 0/8 6 h-lim-p 0.0021 0.5293 0.7138 4257.341085 3 0.0011 128 | 0/8 7 h-lim-p 0.0016 0.7010 0.5128 4257.341028 1 0.0006 150 | 0/8 8 h-lim-p 0.6555 20.0000 0.0005 4257.340743 0 1.3110 171 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4257.340728 1 0.9961 193 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4257.340728 0 2.1875 213 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4257.340728 0 1.2500 233 | 0/8 12 h-lim-p 0.2584 20.0000 0.0000 4257.340728 0 0.0000 275 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 4257.340728 0 0.0000 299 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 4257.340728 0 0.0000 361 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 4257.340728 0 0.0000 389 | 0/8 17 h-lim-p 0.0000 20.0000 0.0006 4257.340728 0 0.0000 412 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 4257.340728 0 0.0000 432 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 4257.340728 0 0.0000 464 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 | 0/8 21 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -4257.340728 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4257.340728 Node 7: lnL = -4257.340728 Node 8: lnL = -4257.340728 Node 9: lnL = -4257.340728 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 763 Sequential format.. Reading seq # 1: YFL013C_Sbay Reading seq # 2: YFL013C_Scer Reading seq # 3: YFL013C_Skud Reading seq # 4: YFL013C_Smik Reading seq # 5: YFL013C_Spar Sequences read.. Counting patterns.. # site patterns = 316 Counting frequencies.. 120 bytes for distance 50560 bytes for lkl0 40448 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.340862 0.125941 0.049853 0.171362 0.136511 0.242409 0.276673 0.000060 lnL0 = -3724.709966 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3724.709966 x= 0.34086 0.12594 0.04985 0.17136 0.13651 0.24241 0.27667 0.00006 1 h-lim-p 0.0000 0.0000 73.3460 3724.670423 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0033 20.1075 3724.624448 0 0.0002 37 | 1/8 3 h-lim-p 0.0006 0.0567 7.0379 3724.608619 1 0.0008 51 | 1/8 4 h-lim-p 0.0030 0.2336 1.7797 3724.605722 4 0.0011 72 | 1/8 5 h-lim-p 0.0018 0.2207 1.1166 3724.600994 3 0.0018 90 | 1/8 6 h-lim-p 0.0015 0.1574 1.3684 3724.538522 0 0.0060 104 | 1/8 7 h-lim-p 0.0022 0.0805 3.6858 3723.680745 0 0.0089 118 | 0/8 8 h-lim-p 0.0018 0.0168 18.7522 3723.525988 5 0.0007 140 | 0/8 9 h-lim-p 0.0004 0.0030 3.8883 3723.504057 m 0.0030 152 | 0/8 10 h-lim-p 2.5000 20.0000 0.0030 3723.491816 5 0.9027 176 | 0/8 11 h-lim-p 1.2247 9.7976 0.0003 3723.491747 2 1.0716 200 | 0/8 12 h-lim-p 0.3193 2.5546 0.0001 3723.491747 0 0.0000 233 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 3723.491747 0 0.8329 268 | 0/8 14 h-lim-p 0.1774 1.4193 0.0003 3723.491747 0 0.0388 289 | 0/8 15 h-lim-p 0.5642 20.0000 0.0000 3723.491747 0 1.1284 310 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 3723.491747 0 0.5469 331 | 0/8 17 h-lim-p 0.8264 20.0000 0.0000 3723.491747 0 1.6528 352 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 3723.491747 0 1.0938 372 | 0/8 19 h-lim-p 2.3244 20.0000 0.0000 3723.491747 0 0.8717 393 | 0/8 20 h-lim-p 1.1909 20.0000 0.0000 3723.491747 0 0.8932 413 | 0/8 21 h-lim-p 0.0103 20.0000 0.0000 3723.491747 0 0.0000 443 | 0/8 22 h-lim-p 0.0005 20.0000 0.0000 3723.491747 0 0.0000 479 Out... lnL = -3723.491747 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3723.491747 Node 7: lnL = -3723.491747 Node 8: lnL = -3723.491747 Node 9: lnL = -3723.491747 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 307 Sequential format.. Reading seq # 1: YFL014W_Sbay Reading seq # 2: YFL014W_Scer Reading seq # 3: YFL014W_Skud Reading seq # 4: YFL014W_Smik Reading seq # 5: YFL014W_Spar Sequences read.. Counting patterns.. # site patterns = 131 Counting frequencies.. 120 bytes for distance 20960 bytes for lkl0 16768 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.254074 0.000060 0.101745 0.075218 0.058062 0.164610 0.282758 0.015328 lnL0 = -1310.424904 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1310.424904 x= 0.25407 0.00006 0.10174 0.07522 0.05806 0.16461 0.28276 0.01533 1 h-lim-p 0.0000 0.0000 47.1448 1310.340423 m 0.0000 22 | 1/8 2 h-lim-p 0.0001 0.0028 14.4106 1310.281551 0 0.0005 36 | 1/8 3 h-lim-p 0.0017 0.0202 4.3332 1310.278356 3 0.0004 55 | 1/8 4 h-lim-p 0.0011 0.1052 1.4247 1310.276883 3 0.0011 73 | 1/8 5 h-lim-p 0.0018 1.6107 0.8897 1310.274513 0 0.0027 85 | 1/8 6 h-lim-p 0.0034 0.0377 0.7080 1310.261629 0 0.0068 105 | 1/8 7 h-lim-p 0.0076 0.1562 0.6316 1309.896587 0 0.0303 126 | 1/8 8 h-lim-p 2.5000 20.0000 0.0021 1309.890023 6 0.8692 161 | 1/8 9 h-lim-p 2.5000 20.0000 0.0002 1309.889946 2 1.0889 184 | 1/8 10 h-lim-p 2.5000 20.0000 0.0000 1309.889945 0 1.0938 203 | 1/8 11 h-lim-p 1.5045 20.0000 0.0000 1309.889945 0 0.7522 222 | 1/8 12 h-lim-p 0.4282 20.0000 0.0000 1309.889945 0 0.0535 243 | 1/8 13 h-lim-p 0.0148 20.0000 0.0001 1309.889945 0 0.0016 264 | 1/8 14 h-lim-p 0.0007 20.0000 0.0003 1309.889945 0 0.0001 285 | 1/8 15 h-lim-p 0.0000 14.7022 0.0010 1309.889945 0 0.0000 305 | 1/8 16 h-lim-p 0.0001 20.0000 0.0001 1309.889945 0 0.0000 338 | 1/8 17 h-lim-p 0.0000 20.0000 0.0004 | 1/8 18 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1309.889945 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1309.889945 Node 7: lnL = -1309.889945 Node 8: lnL = -1309.889945 Node 9: lnL = -1309.889945 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 289 Sequential format.. Reading seq # 1: YFL017C_Sbay Reading seq # 2: YFL017C_Scer Reading seq # 3: YFL017C_Skud Reading seq # 4: YFL017C_Smik Reading seq # 5: YFL017C_Spar Sequences read.. Counting patterns.. # site patterns = 126 Counting frequencies.. 120 bytes for distance 20160 bytes for lkl0 16128 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.223761 0.163194 0.051467 0.057571 0.046735 0.127768 0.168018 0.000060 lnL0 = -1083.618584 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1083.618584 x= 0.22376 0.16319 0.05147 0.05757 0.04674 0.12777 0.16802 0.00006 1 h-lim-p 0.0003 0.0023 42.7963 1083.031183 0 0.0006 23 | 0/8 2 h-lim-p 0.0005 0.0039 48.6879 1082.753741 5 0.0004 44 | 0/8 3 h-lim-p 0.0002 0.0016 10.9562 1082.726938 0 0.0006 57 | 0/8 4 h-lim-p 0.0003 0.0027 5.8633 1082.714038 0 0.0010 70 | 0/8 5 h-lim-p 0.0050 0.5011 1.1892 1082.713394 4 0.0010 91 | 0/8 6 h-lim-p 0.0036 0.6483 0.3162 1082.713302 2 0.0016 107 | 0/8 7 h-lim-p 0.0022 1.0962 0.2237 1082.713254 3 0.0013 135 | 0/8 8 h-lim-p 0.0008 0.8301 0.3855 1082.697455 0 0.1946 163 | 0/8 9 h-lim-p 2.5000 20.0000 0.0040 1082.697405 2 0.9961 187 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1082.697405 0 1.0938 207 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1082.697405 0 5.0000 228 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1082.697405 0 0.2734 250 | 0/8 13 h-lim-p 0.1194 20.0000 0.0000 1082.697405 0 0.0005 277 Out... lnL = -1082.697405 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1082.697405 Node 7: lnL = -1082.697405 Node 8: lnL = -1082.697405 Node 9: lnL = -1082.697405 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 646 Sequential format.. Reading seq # 1: YFL017W-A_Sbay Reading seq # 2: YFL017W-A_Scer Reading seq # 3: YFL017W-A_Skud Reading seq # 4: YFL017W-A_Smik Reading seq # 5: YFL017W-A_Spar Sequences read.. Counting patterns.. # site patterns = 246 Counting frequencies.. 120 bytes for distance 39360 bytes for lkl0 31488 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.330085 0.096431 0.126584 0.129018 0.108160 0.235370 0.276904 0.000060 lnL0 = -2903.714870 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2903.714870 x= 0.33008 0.09643 0.12658 0.12902 0.10816 0.23537 0.27690 0.00006 1 h-lim-p 0.0000 0.0000 79.4619 2903.666639 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0093 18.1696 2903.548871 0 0.0008 38 | 1/8 3 h-lim-p 0.0019 0.0426 7.4625 2903.538731 4 0.0004 60 | 1/8 4 h-lim-p 0.0008 0.0920 3.5625 2903.531215 0 0.0012 72 | 1/8 5 h-lim-p 0.0050 0.3377 0.8830 2903.516147 5 0.0055 97 | 1/8 6 h-lim-p 0.0021 0.0484 2.3296 2903.425927 0 0.0042 117 | 1/8 7 h-lim-p 0.0028 0.0627 3.4577 2901.981631 0 0.0113 131 | 1/8 8 h-lim-p 0.0452 0.4212 0.8659 2901.981101 2 0.0013 151 | 1/8 9 h-lim-p 0.2761 20.0000 0.0042 2901.959019 0 1.1045 172 | 1/8 10 h-lim-p 2.5000 20.0000 0.0010 2901.958059 2 0.9961 195 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 2901.958057 0 1.0938 214 | 0/8 12 h-lim-p 0.0000 0.0000 0.0011 h-lim-p: 5.38410699e-19 4.30728559e-18 1.11138026e-03 2901.958057 .. | 1/8 13 h-lim-p 0.0000 11.3378 0.0141 2901.958057 0 0.0005 254 | 1/8 14 h-lim-p 0.0017 20.0000 0.0040 2901.958057 0 0.0004 274 | 1/8 15 h-lim-p 0.0011 20.0000 0.0014 2901.958057 0 0.0009 293 | 1/8 16 h-lim-p 0.0027 20.0000 0.0005 2901.958057 0 0.0007 313 | 1/8 17 h-lim-p 0.0026 20.0000 0.0001 2901.958057 0 0.0011 332 | 1/8 18 h-lim-p 0.0060 20.0000 0.0000 2901.958057 0 0.0030 351 | 1/8 19 h-lim-p 0.0146 20.0000 0.0000 2901.958057 0 0.1168 373 | 1/8 20 h-lim-p 0.0022 20.0000 0.0003 2901.958057 0 0.0022 392 | 1/8 21 h-lim-p 2.5000 20.0000 0.0000 2901.958057 0 0.0012 421 Out... lnL = -2901.958057 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2901.958057 Node 7: lnL = -2901.958057 Node 8: lnL = -2901.958057 Node 9: lnL = -2901.958057 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 608 Sequential format.. Reading seq # 1: YFL018C_Sbay Reading seq # 2: YFL018C_Scer Reading seq # 3: YFL018C_Skud Reading seq # 4: YFL018C_Smik Reading seq # 5: YFL018C_Spar Sequences read.. Counting patterns.. # site patterns = 249 Counting frequencies.. 120 bytes for distance 39840 bytes for lkl0 31872 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.333610 0.209012 0.194374 0.106278 0.130706 0.180339 0.258601 0.000060 lnL0 = -2827.757157 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2827.757157 x= 0.33361 0.20901 0.19437 0.10628 0.13071 0.18034 0.25860 0.00006 1 h-lim-p 0.0000 0.0000 223.6081 2827.693628 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0014 194.4664 2823.413393 0 0.0003 39 | 1/8 3 h-lim-p 0.0003 0.0027 86.3529 2822.043170 0 0.0007 52 | 1/8 4 h-lim-p 0.0016 0.0125 23.5635 2821.824647 5 0.0008 75 | 1/8 5 h-lim-p 0.0018 0.0314 11.2002 2821.756989 6 0.0010 102 | 1/8 6 h-lim-p 0.0066 0.2034 1.7101 2821.407430 0 0.0198 115 | 1/8 7 h-lim-p 0.0062 0.0800 5.4723 2817.713199 0 0.0124 128 | 0/8 8 h-lim-p 0.0011 0.0091 53.3510 2810.473236 0 0.0023 141 | 0/8 9 h-lim-p 0.0004 0.0035 30.0589 2809.383778 0 0.0027 155 | 0/8 10 h-lim-p 0.4559 3.6471 0.0417 2808.481576 0 0.9118 168 | 0/8 11 h-lim-p 2.2908 18.3260 0.0123 2808.346187 7 1.3884 207 | 0/8 12 h-lim-p 2.5000 20.0000 0.0028 2808.335028 6 1.3762 241 | 0/8 13 h-lim-p 2.5000 20.0000 0.0015 2808.333669 3 0.9961 267 | 0/8 14 h-lim-p 2.5000 20.0000 0.0002 2808.333618 1 1.2500 289 | 0/8 15 h-lim-p 2.5000 20.0000 0.0001 2808.333616 1 0.9961 311 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 2808.333616 0 1.0938 331 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 2808.333616 0 2.1875 351 | 0/8 18 h-lim-p 1.9058 20.0000 0.0000 2808.333616 0 0.8338 371 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 2808.333616 0 0.0586 396 | 0/8 20 h-lim-p 0.0470 20.0000 0.0000 2808.333616 0 0.0059 418 Out... lnL = -2808.333616 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2808.333616 Node 7: lnL = -2808.333616 Node 8: lnL = -2808.333616 Node 9: lnL = -2808.333616 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 674 Sequential format.. Reading seq # 1: YFL024C_Sbay Reading seq # 2: YFL024C_Scer Reading seq # 3: YFL024C_Skud Reading seq # 4: YFL024C_Smik Reading seq # 5: YFL024C_Spar Sequences read.. Counting patterns.. # site patterns = 196 Counting frequencies.. 120 bytes for distance 31360 bytes for lkl0 25088 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.172791 0.052330 0.086148 0.073348 0.066807 0.116377 0.126386 0.000060 lnL0 = -2548.094524 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2548.094524 x= 0.17279 0.05233 0.08615 0.07335 0.06681 0.11638 0.12639 0.00006 1 h-lim-p 0.0001 0.0007 174.8543 2544.901912 0 0.0002 23 | 0/8 2 h-lim-p 0.0006 0.0048 42.3844 2544.715640 7 0.0002 52 | 0/8 3 h-lim-p 0.0005 0.0096 17.2234 2544.693712 6 0.0002 78 | 0/8 4 h-lim-p 0.0007 0.0363 4.2414 2544.691518 5 0.0003 101 | 0/8 5 h-lim-p 0.0006 0.1706 1.9794 2544.690854 4 0.0004 123 | 0/8 6 h-lim-p 0.0003 0.1070 2.5863 2544.683992 0 0.0048 139 | 0/8 7 h-lim-p 0.0004 0.0071 34.3027 2544.607781 0 0.0029 154 | 0/8 8 h-lim-p 0.0008 0.0063 20.0625 2544.604719 5 0.0002 180 | 0/8 9 h-lim-p 0.2280 6.4448 0.0214 2544.601546 0 0.9119 194 | 0/8 10 h-lim-p 2.5000 20.0000 0.0024 2544.601505 2 0.9961 218 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2544.601505 0 1.2500 238 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2544.601505 0 0.1172 262 | 0/8 13 h-lim-p 0.1524 20.0000 0.0000 2544.601505 0 0.0001 291 Out... lnL = -2544.601505 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2544.601505 Node 7: lnL = -2544.601505 Node 8: lnL = -2544.601505 Node 9: lnL = -2544.601505 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 719 Sequential format.. Reading seq # 1: YFL027C_Sbay Reading seq # 2: YFL027C_Scer Reading seq # 3: YFL027C_Skud Reading seq # 4: YFL027C_Smik Reading seq # 5: YFL027C_Spar Sequences read.. Counting patterns.. # site patterns = 245 Counting frequencies.. 120 bytes for distance 39200 bytes for lkl0 31360 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.273001 0.168527 0.121446 0.103574 0.084392 0.155059 0.202528 0.000060 lnL0 = -3231.124866 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3231.124866 x= 0.27300 0.16853 0.12145 0.10357 0.08439 0.15506 0.20253 0.00006 1 h-lim-p 0.0000 0.0000 250.3360 3231.056977 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0021 96.1301 3229.770203 0 0.0003 39 | 1/8 3 h-lim-p 0.0004 0.0033 68.5140 3229.335477 6 0.0003 64 | 1/8 4 h-lim-p 0.0011 0.0301 16.9463 3229.260285 5 0.0005 86 | 1/8 5 h-lim-p 0.0014 0.0412 6.6058 3229.240252 2 0.0006 102 | 1/8 6 h-lim-p 0.0021 0.1593 1.8614 3229.008257 0 0.0085 116 | 1/8 7 h-lim-p 0.0018 0.0314 8.7148 3226.716335 0 0.0073 130 | 0/8 8 h-lim-p 0.0005 0.0043 36.4548 3218.910183 0 0.0021 144 | 0/8 9 h-lim-p 0.0004 0.0030 15.7031 3218.722890 m 0.0030 156 | 0/8 10 h-lim-p 1.6670 20.0000 0.0278 3217.605467 2 0.7814 172 | 0/8 11 h-lim-p 1.5941 12.7530 0.0093 3217.485932 7 0.9836 210 | 0/8 12 h-lim-p 2.5000 20.0000 0.0029 3217.480253 4 0.8855 240 | 0/8 13 h-lim-p 2.5000 20.0000 0.0004 3217.480011 2 1.0938 264 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 3217.479996 0 1.0938 284 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 3217.479995 0 1.0938 304 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 3217.479995 0 1.0938 324 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 3217.479995 0 2.5000 344 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 3217.479995 0 0.2344 367 | 0/8 19 h-lim-p 0.0746 20.0000 0.0000 3217.479995 0 0.0186 388 | 0/8 20 h-lim-p 0.0076 20.0000 0.0000 3217.479995 0 0.0000 425 Out... lnL = -3217.479995 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3217.479995 Node 7: lnL = -3217.479995 Node 8: lnL = -3217.479995 Node 9: lnL = -3217.479995 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 201 Sequential format.. Reading seq # 1: YFL029C_Sbay Reading seq # 2: YFL029C_Scer Reading seq # 3: YFL029C_Skud Reading seq # 4: YFL029C_Smik Reading seq # 5: YFL029C_Spar Sequences read.. Counting patterns.. # site patterns = 85 Counting frequencies.. 120 bytes for distance 13600 bytes for lkl0 10880 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.222483 0.181871 0.104838 0.054896 0.105024 0.118430 0.183283 0.000060 lnL0 = -811.030014 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 811.030014 x= 0.22248 0.18187 0.10484 0.05490 0.10502 0.11843 0.18328 0.00006 1 h-lim-p 0.0000 0.0000 127.4405 810.999157 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0016 141.8526 807.331187 0 0.0006 40 | 1/8 3 h-lim-p 0.0003 0.0025 71.2846 806.385908 0 0.0006 53 | 1/8 4 h-lim-p 0.0009 0.0070 30.1221 806.137069 6 0.0007 79 | 1/8 5 h-lim-p 0.0031 0.0498 6.8651 806.082813 7 0.0020 109 | 1/8 6 h-lim-p 0.0102 0.0814 1.1336 806.020246 7 0.0075 136 | 1/8 7 h-lim-p 0.0033 0.0737 2.5640 803.483632 0 0.0264 151 | 1/8 8 h-lim-p 0.0012 0.0095 27.9806 800.738105 0 0.0024 164 | 1/8 9 h-lim-p 2.5000 20.0000 0.0202 800.241453 8 1.4099 194 | 1/8 10 h-lim-p 1.6211 12.9691 0.0150 800.163208 4 0.8102 221 | 0/8 11 h-lim-p 0.0040 0.1104 3.0627 800.156352 6 0.0021 255 | 0/8 12 h-lim-p 1.9128 20.0000 0.0033 800.144781 2 1.7933 271 | 0/8 13 h-lim-p 2.5000 20.0000 0.0017 800.143057 5 1.3438 302 | 0/8 14 h-lim-p 2.5000 20.0000 0.0004 800.142966 2 1.1719 326 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 800.142965 1 1.2305 349 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 800.142965 0 1.0938 369 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 800.142965 0 2.1875 389 | 0/8 18 h-lim-p 2.2946 20.0000 0.0000 800.142965 0 1.0039 409 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 800.142965 m20.0000 429 | 0/8 20 h-lim-p 0.1912 20.0000 0.0000 800.142965 0 0.0239 451 | 0/8 21 h-lim-p 0.0049 20.0000 0.0000 800.142965 0 0.0049 471 | 0/8 22 h-lim-p 0.0021 20.0000 0.0001 800.142965 0 0.0000 499 | 0/8 23 h-lim-p 0.0001 20.0000 0.0000 800.142965 0 0.0000 532 Out... lnL = -800.142965 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -800.142965 Node 7: lnL = -800.142965 Node 8: lnL = -800.142965 Node 9: lnL = -800.142965 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 736 Sequential format.. Reading seq # 1: YFL030W_Sbay Reading seq # 2: YFL030W_Scer Reading seq # 3: YFL030W_Skud Reading seq # 4: YFL030W_Smik Reading seq # 5: YFL030W_Spar Sequences read.. Counting patterns.. # site patterns = 243 Counting frequencies.. 120 bytes for distance 38880 bytes for lkl0 31104 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.206750 0.026710 0.053222 0.093684 0.050708 0.193730 0.138723 0.001667 lnL0 = -2745.637927 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2745.637927 x= 0.20675 0.02671 0.05322 0.09368 0.05071 0.19373 0.13872 0.00167 1 h-lim-p 0.0002 0.0016 225.0059 2742.962889 9 0.0001 47 | 0/8 2 h-lim-p 0.0005 0.0036 28.5454 2742.855126 6 0.0003 74 | 0/8 3 h-lim-p 0.0004 0.0048 18.1846 2742.834893 4 0.0002 94 | 0/8 4 h-lim-p 0.0004 0.0191 8.3638 2742.829163 6 0.0002 122 | 0/8 5 h-lim-p 0.0025 0.2103 0.7125 2742.829071 3 0.0004 144 | 0/8 6 h-lim-p 0.0009 0.0737 0.2890 2742.829060 2 0.0003 170 | 0/8 7 h-lim-p 0.0015 0.1279 0.0582 2742.829060 0 0.0003 191 | 0/8 8 h-lim-p 0.1310 20.0000 0.0001 2742.828972 0 1.5717 214 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2742.828971 0 1.0938 234 | 0/8 10 h-lim-p 0.8462 20.0000 0.0000 2742.828971 0 0.8462 254 | 0/8 11 h-lim-p 0.5985 20.0000 0.0001 2742.828971 0 0.0094 279 | 0/8 12 h-lim-p 0.0020 19.4483 0.0003 2742.828971 0 0.0030 299 | 0/8 13 h-lim-p 0.0011 7.2899 0.0008 2742.828971 0 0.0000 330 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 2742.828971 0 0.0000 362 Out... lnL = -2742.828971 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2742.828971 Node 7: lnL = -2742.828971 Node 8: lnL = -2742.828971 Node 9: lnL = -2742.828971 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 843 Sequential format.. Reading seq # 1: YFL031W_Sbay Reading seq # 2: YFL031W_Scer Reading seq # 3: YFL031W_Skud Reading seq # 4: YFL031W_Smik Reading seq # 5: YFL031W_Spar Sequences read.. Counting patterns.. # site patterns = 323 Counting frequencies.. 120 bytes for distance 51680 bytes for lkl0 41344 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.278981 0.137533 0.081630 0.146394 0.112959 0.196242 0.167956 0.000060 lnL0 = -3517.382438 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3517.382438 x= 0.27898 0.13753 0.08163 0.14639 0.11296 0.19624 0.16796 0.00006 1 h-lim-p 0.0000 0.0000 150.1948 3517.323828 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0321 49.7396 3516.914543 0 0.0003 39 | 1/8 3 h-lim-p 0.0019 0.0336 8.5449 3516.889713 6 0.0006 65 | 1/8 4 h-lim-p 0.0046 0.2162 1.1597 3516.860009 1 0.0057 79 | 1/8 5 h-lim-p 0.0026 0.1073 2.5282 3516.562631 0 0.0053 92 | 1/8 6 h-lim-p 0.0013 0.0173 10.2942 3513.335663 0 0.0052 106 | 1/8 7 h-lim-p 0.0002 0.0019 45.2682 3512.905796 0 0.0004 118 | 1/8 8 h-lim-p 0.0052 0.1301 3.0693 3512.902635 5 0.0007 141 | 1/8 9 h-lim-p 0.2692 20.0000 0.0075 3512.841306 0 1.0767 155 | 1/8 10 h-lim-p 2.5000 20.0000 0.0021 3512.833392 3 1.0449 180 | 1/8 11 h-lim-p 2.5000 20.0000 0.0001 3512.833380 2 0.9644 203 | 0/8 12 h-lim-p 0.0316 20.0000 0.0039 3512.833380 0 0.0017 225 | 0/8 13 h-lim-p 0.1204 0.9631 0.0000 3512.833379 m 0.9631 245 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 3512.833379 0 1.0938 265 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 3512.833379 0 1.0938 284 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 3512.833379 0 5.0000 304 | 1/8 17 h-lim-p 1.2266 20.0000 0.0000 3512.833379 0 0.0767 326 | 1/8 18 h-lim-p 0.0828 20.0000 0.0000 3512.833379 0 0.0414 345 | 1/8 19 h-lim-p 0.0432 20.0000 0.0000 3512.833379 0 0.0027 367 Out... lnL = -3512.833379 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3512.833379 Node 7: lnL = -3512.833379 Node 8: lnL = -3512.833379 Node 9: lnL = -3512.833379 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 355 Sequential format.. Reading seq # 1: YFL037W_Sbay Reading seq # 2: YFL037W_Scer Reading seq # 3: YFL037W_Skud Reading seq # 4: YFL037W_Smik Reading seq # 5: YFL037W_Spar Sequences read.. Counting patterns.. # site patterns = 82 Counting frequencies.. 120 bytes for distance 13120 bytes for lkl0 10496 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.164818 0.045007 0.022396 0.027010 0.030018 0.081510 0.097635 0.029432 lnL0 = -1200.104229 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1200.104229 x= 0.16482 0.04501 0.02240 0.02701 0.03002 0.08151 0.09763 0.02943 1 h-lim-p 0.0003 0.0022 94.2866 1199.626309 5 0.0001 31 | 0/8 2 h-lim-p 0.0003 0.0025 29.4659 1199.551496 7 0.0002 60 | 0/8 3 h-lim-p 0.0009 0.0212 6.0245 1199.549503 2 0.0001 78 | 0/8 4 h-lim-p 0.0003 0.0243 2.4479 1199.548894 1 0.0002 92 | 0/8 5 h-lim-p 0.0004 0.0449 1.4948 1199.548759 2 0.0002 108 | 0/8 6 h-lim-p 0.0039 2.1193 0.0626 1199.548758 0 0.0004 122 | 0/8 7 h-lim-p 0.0028 20.0000 0.0093 1199.548758 0 0.0006 143 | 0/8 8 h-lim-p 0.0577 20.0000 0.0001 1199.548744 0 0.9234 167 | 0/8 9 h-lim-p 0.1924 20.0000 0.0005 1199.548741 0 0.7695 189 | 0/8 10 h-lim-p 2.4000 20.0000 0.0002 1199.548741 0 1.0500 209 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1199.548741 0 2.5000 229 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1199.548741 0 0.0073 257 | 0/8 13 h-lim-p 0.0190 20.0000 0.0000 1199.548741 0 0.0000 292 Out... lnL = -1199.548741 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1199.548741 Node 7: lnL = -1199.548741 Node 8: lnL = -1199.548741 Node 9: lnL = -1199.548741 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 356 Sequential format.. Reading seq # 1: YFL038C_Sbay Reading seq # 2: YFL038C_Scer Reading seq # 3: YFL038C_Skud Reading seq # 4: YFL038C_Smik Reading seq # 5: YFL038C_Spar Sequences read.. Counting patterns.. # site patterns = 88 Counting frequencies.. 120 bytes for distance 14080 bytes for lkl0 11264 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.149179 0.065065 0.019988 0.025198 0.031830 0.082191 0.078002 0.018615 lnL0 = -1180.276710 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1180.276710 x= 0.14918 0.06507 0.01999 0.02520 0.03183 0.08219 0.07800 0.01862 1 h-lim-p 0.0002 0.0013 135.5055 1179.586470 8 0.0001 40 | 0/8 2 h-lim-p 0.0003 0.0025 25.9754 1179.521027 6 0.0002 66 | 0/8 3 h-lim-p 0.0004 0.0122 12.8961 1179.511558 6 0.0001 93 | 0/8 4 h-lim-p 0.0005 0.0086 3.7753 1179.510851 2 0.0001 110 | 0/8 5 h-lim-p 0.0007 0.1767 0.5867 1179.510802 1 0.0003 124 | 0/8 6 h-lim-p 0.0018 1.8581 0.0929 1179.510801 1 0.0004 147 | 0/8 7 h-lim-p 0.0080 9.4165 0.0042 1179.510800 0 0.0070 167 | 0/8 8 h-lim-p 0.0097 10.7620 0.0030 1179.510607 0 0.0780 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1179.510605 1 0.9961 212 | 0/8 10 h-lim-p 1.8413 20.0000 0.0000 1179.510605 0 1.6112 232 | 0/8 11 h-lim-p 1.4785 20.0000 0.0000 1179.510605 0 1.4785 252 | 0/8 12 h-lim-p 0.0709 20.0000 0.0007 1179.510605 0 0.0044 275 | 0/8 13 h-lim-p 0.0012 11.8813 0.0025 1179.510605 0 0.0000 307 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 1179.510605 0 0.0000 327 Out... lnL = -1179.510605 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1179.510605 Node 7: lnL = -1179.510605 Node 8: lnL = -1179.510605 Node 9: lnL = -1179.510605 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 1097 Sequential format.. Reading seq # 1: YFL039C_Sbay Reading seq # 2: YFL039C_Scer Reading seq # 3: YFL039C_Skud Reading seq # 4: YFL039C_Smik Reading seq # 5: YFL039C_Spar Sequences read.. Counting patterns.. # site patterns = 302 Counting frequencies.. 120 bytes for distance 48320 bytes for lkl0 38656 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.176512 0.040434 0.065160 0.065203 0.046472 0.094785 0.162815 0.000060 lnL0 = -3870.674447 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3870.674447 x= 0.17651 0.04043 0.06516 0.06520 0.04647 0.09479 0.16282 0.00006 1 h-lim-p 0.0002 0.0014 252.0843 3868.058225 4 0.0001 31 | 0/8 2 h-lim-p 0.0000 0.0002 35.9593 3867.993740 0 0.0001 45 | 0/8 3 h-lim-p 0.0000 0.0001 14.0603 3867.984729 m 0.0001 57 | 0/8 4 h-lim-p 0.0006 0.1550 1.9447 3867.984403 4 0.0002 81 | 0/8 5 h-lim-p 0.0008 0.5014 0.4111 3867.984384 2 0.0002 98 | 0/8 6 h-lim-p 0.0002 0.0013 0.1996 3867.984383 0 0.0001 118 | 0/8 7 h-lim-p 0.0003 0.0023 0.0714 3867.984383 0 0.0003 138 | 0/8 8 h-lim-p 0.0000 0.0002 0.9875 3867.984383 0 0.0000 158 | 0/8 9 h-lim-p 0.0076 20.0000 0.0024 3867.981311 0 0.2440 183 | 0/8 10 h-lim-p 0.0208 0.1660 0.0009 3867.981288 m 0.1660 203 | 1/8 11 h-lim-p 0.4222 20.0000 0.0003 3867.981220 0 0.6333 223 | 0/8 12 h-lim-p 0.0006 2.2095 0.2908 3867.981210 1 0.0003 245 | 0/8 13 h-lim-p 0.0440 0.3521 0.0005 3867.981206 0 0.1760 267 | 0/8 14 h-lim-p 0.0395 0.3158 0.0002 3867.981205 m 0.3158 287 | 1/8 15 h-lim-p 1.5386 20.0000 0.0000 3867.981204 0 0.6731 307 | 0/8 16 h-lim-p 0.0023 18.3286 0.0083 3867.981204 0 0.0003 328 | 1/8 17 h-lim-p 0.0346 20.0000 0.0001 3867.981204 0 0.2770 351 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 3867.981204 0 2.1875 370 | 0/8 19 h-lim-p 0.0000 0.0002 0.0049 3867.981204 0 0.0000 395 | 1/8 20 h-lim-p 0.0000 8.8860 0.0277 3867.981204 0 0.0001 418 | 1/8 21 h-lim-p 2.0430 20.0000 0.0000 3867.981204 0 1.7877 437 | 1/8 22 h-lim-p 2.5000 20.0000 0.0000 3867.981204 0 1.0938 456 | 1/8 23 h-lim-p 2.5000 20.0000 0.0000 3867.981204 010.0000 477 | 1/8 24 h-lim-p 2.3210 20.0000 0.0000 3867.981204 0 2.0309 496 | 1/8 25 h-lim-p 2.5000 20.0000 0.0000 3867.981204 0 5.0000 516 | 1/8 26 h-lim-p 0.9010 20.0000 0.0000 3867.981204 0 0.4505 535 | 1/8 27 h-lim-p 0.6854 20.0000 0.0000 3867.981204 0 0.1499 555 | 1/8 28 h-lim-p 0.1754 20.0000 0.0000 3867.981204 0 0.0000 586 Out... lnL = -3867.981204 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3867.981204 Node 7: lnL = -3867.981204 Node 8: lnL = -3867.981204 Node 9: lnL = -3867.981204 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 347 Sequential format.. Reading seq # 1: YFL040W_Sbay Reading seq # 2: YFL040W_Scer Reading seq # 3: YFL040W_Skud Reading seq # 4: YFL040W_Smik Reading seq # 5: YFL040W_Spar Sequences read.. Counting patterns.. # site patterns = 100 Counting frequencies.. 120 bytes for distance 16000 bytes for lkl0 12800 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.955167 0.389781 0.671817 0.329188 0.428330 0.186856 2.671203 0.000060 lnL0 = -1446.648353 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1446.648353 x= 0.95517 0.38978 0.67182 0.32919 0.42833 0.18686 2.67120 0.00006 1 h-lim-p 0.0000 0.0000 332.9266 1446.475939 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0012 322.4840 1385.717268 m 0.0012 38 | 2/8 3 h-lim-p 0.0010 0.0081 34.6759 1378.406194 m 0.0081 50 | 3/8 4 h-lim-p 0.0015 0.0123 59.9687 1355.972932 0 0.0062 64 | 2/8 5 h-lim-p 0.0000 0.0002 1768.1582 1349.358372 0 0.0001 78 | 2/8 6 h-lim-p 0.1662 1.3298 0.8928 .. | 1/8 7 h-lim-p 0.0000 0.0018 247.4116 1332.472518 0 0.0010 141 | 1/8 8 h-lim-p 0.0001 0.0006 260.6420 1322.580201 0 0.0004 155 | 1/8 9 h-lim-p 0.0003 0.0025 67.5799 1311.824578 m 0.0025 167 | 2/8 10 h-lim-p 0.0004 0.0029 168.7787 1306.593609 0 0.0011 180 | 2/8 11 h-lim-p 0.0023 0.0184 13.1461 1305.429709 0 0.0046 193 | 1/8 12 h-lim-p 0.0003 0.0027 144.1975 1302.037519 0 0.0005 205 | 1/8 13 h-lim-p 0.0643 0.8143 1.1413 .. | 1/8 14 h-lim-p 0.0000 0.0027 276.2337 1296.028404 0 0.0003 260 | 1/8 15 h-lim-p 0.0002 0.0016 141.8104 1286.958618 0 0.0008 274 | 1/8 16 h-lim-p 0.0003 0.0023 235.7218 1237.728484 m 0.0023 286 | 2/8 17 h-lim-p 0.0001 0.0006 316.8213 1234.491657 0 0.0003 300 | 2/8 18 h-lim-p 0.0002 0.0019 267.4531 1231.334107 0 0.0005 313 | 2/8 19 h-lim-p 0.0298 0.2387 1.9221 1228.227369 1 0.0373 327 | 1/8 20 h-lim-p 0.0017 0.0262 42.6305 1226.438709 0 0.0034 340 | 1/8 21 h-lim-p 0.1737 1.3894 0.1684 1219.898725 0 0.6947 354 | 1/8 22 h-lim-p 0.7373 5.8987 0.0501 1218.510714 0 1.4747 374 | 1/8 23 h-lim-p 1.7963 14.3705 0.0140 1218.395842 8 0.9935 413 | 1/8 24 h-lim-p 2.5000 20.0000 0.0049 1218.336316 6 2.0097 443 | 1/8 25 h-lim-p 2.5000 20.0000 0.0014 1218.335594 3 1.0483 469 | 1/8 26 h-lim-p 2.5000 20.0000 0.0001 1218.335589 2 1.6492 494 | 0/8 27 h-lim-p 0.0199 20.0000 0.0094 1218.335589 0 0.0043 514 | 0/8 28 h-lim-p 0.1345 1.0763 0.0000 1218.335588 m 1.0763 534 | 1/8 29 h-lim-p 2.5000 20.0000 0.0000 1218.335588 0 0.5469 555 | 1/8 30 h-lim-p 0.7413 20.0000 0.0000 1218.335588 0 1.1120 574 | 1/8 31 h-lim-p 2.5000 20.0000 0.0000 1218.335588 0 1.0938 593 | 1/8 32 h-lim-p 2.5000 20.0000 0.0000 1218.335588 0 2.5000 612 | 1/8 33 h-lim-p 2.3226 20.0000 0.0000 1218.335588 0 0.0000 649 Out... lnL = -1218.335588 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1218.335588 Node 7: lnL = -1218.335588 Node 8: lnL = -1218.335588 Node 9: lnL = -1218.335588 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 890 Sequential format.. Reading seq # 1: YFL041W_Sbay Reading seq # 2: YFL041W_Scer Reading seq # 3: YFL041W_Skud Reading seq # 4: YFL041W_Smik Reading seq # 5: YFL041W_Spar Sequences read.. Counting patterns.. # site patterns = 358 Counting frequencies.. 120 bytes for distance 57280 bytes for lkl0 45824 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.775733 0.091614 0.007604 0.176143 0.101474 0.281888 0.115395 0.293560 lnL0 = -4061.801697 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4061.801697 x= 0.77573 0.09161 0.00760 0.17614 0.10147 0.28189 0.11540 0.29356 1 h-lim-p 0.0001 0.0010 247.0644 4058.207267 1 0.0002 24 | 0/8 2 h-lim-p 0.0001 0.0009 119.3174 4056.966046 0 0.0002 37 | 0/8 3 h-lim-p 0.0006 0.0078 48.4508 4056.654252 8 0.0003 69 | 0/8 4 h-lim-p 0.0008 0.0318 20.0546 4056.429031 0 0.0016 82 | 0/8 5 h-lim-p 0.0014 0.0195 22.7955 4056.285755 6 0.0011 108 | 0/8 6 h-lim-p 0.0021 0.0192 11.6964 4056.265412 2 0.0005 125 | 0/8 7 h-lim-p 0.0030 0.0568 1.9655 4056.258391 0 0.0044 137 | 0/8 8 h-lim-p 1.3147 11.7350 0.0066 4056.166001 2 1.2325 153 | 0/8 9 h-lim-p 2.5000 20.0000 0.0012 4056.161574 3 1.0449 179 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 4056.161550 1 0.9961 201 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4056.161550 0 1.0938 221 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4056.161550 0 0.1562 244 | 0/8 13 h-lim-p 0.0784 20.0000 0.0000 4056.161550 0 0.0000 289 Out... lnL = -4056.161550 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4056.161550 Node 7: lnL = -4056.161550 Node 8: lnL = -4056.161550 Node 9: lnL = -4056.161550 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 261 Sequential format.. Reading seq # 1: YFL046W_Sbay Reading seq # 2: YFL046W_Scer Reading seq # 3: YFL046W_Skud Reading seq # 4: YFL046W_Smik Reading seq # 5: YFL046W_Spar Sequences read.. Counting patterns.. # site patterns = 125 Counting frequencies.. 120 bytes for distance 20000 bytes for lkl0 16000 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.304618 0.114841 0.177482 0.130848 0.128415 0.231839 0.249701 0.000060 lnL0 = -1189.884030 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1189.884030 x= 0.30462 0.11484 0.17748 0.13085 0.12842 0.23184 0.24970 0.00006 1 h-lim-p 0.0000 0.0000 108.6044 1189.852261 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0049 52.6819 1187.725723 0 0.0019 41 | 1/8 3 h-lim-p 0.0043 0.0346 14.7513 1187.526475 2 0.0020 57 | 1/8 4 h-lim-p 0.0081 0.0883 3.6869 1187.470277 7 0.0042 83 | 1/8 5 h-lim-p 0.0132 0.2463 1.1872 1186.959554 0 0.0527 97 | 1/8 6 h-lim-p 0.0036 0.0291 6.7693 1184.025833 0 0.0109 110 | 1/8 7 h-lim-p 0.0014 0.0115 28.5305 1182.462721 0 0.0029 123 | 1/8 8 h-lim-p 0.0026 0.0205 10.4052 1182.384757 7 0.0014 152 | 1/8 9 h-lim-p 0.3497 9.9218 0.0424 1182.097335 0 0.6994 165 | 0/8 10 h-lim-p 0.0091 0.8926 3.2515 1182.088186 5 0.0017 195 | 0/8 11 h-lim-p 0.5127 5.8309 0.0111 1182.071137 0 0.7690 207 | 0/8 12 h-lim-p 2.5000 20.0000 0.0019 1182.070146 5 0.7228 241 | 0/8 13 h-lim-p 2.5000 20.0000 0.0003 1182.070096 3 0.7330 270 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 1182.070095 1 0.9961 292 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1182.070095 0 1.0938 312 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1182.070095 0 1.0938 332 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1182.070095 0 1.0938 352 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1182.070095 0 5.0000 373 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1182.070095 0 0.3125 395 | 0/8 20 h-lim-p 0.2532 20.0000 0.0000 1182.070095 0 0.0079 419 Out... lnL = -1182.070095 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1182.070095 Node 7: lnL = -1182.070095 Node 8: lnL = -1182.070095 Node 9: lnL = -1182.070095 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 717 Sequential format.. Reading seq # 1: YFR001W_Sbay Reading seq # 2: YFR001W_Scer Reading seq # 3: YFR001W_Skud Reading seq # 4: YFR001W_Smik Reading seq # 5: YFR001W_Spar Sequences read.. Counting patterns.. # site patterns = 375 Counting frequencies.. 120 bytes for distance 60000 bytes for lkl0 48000 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.517391 0.073159 0.086423 0.284763 0.224124 0.323244 0.558190 0.000060 lnL0 = -3925.230511 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3925.230511 x= 0.51739 0.07316 0.08642 0.28476 0.22412 0.32324 0.55819 0.00006 1 h-lim-p 0.0000 0.0000 40.3612 3925.200066 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0210 19.7629 3925.062155 0 0.0012 39 | 1/8 3 h-lim-p 0.0039 0.0897 6.2019 3925.028378 4 0.0019 60 | 1/8 4 h-lim-p 0.0039 0.1878 2.9843 3925.020795 3 0.0018 78 | 1/8 5 h-lim-p 0.0031 0.3245 1.6959 3925.016521 5 0.0023 103 | 1/8 6 h-lim-p 0.0038 0.5944 1.0044 3925.004680 0 0.0077 116 | 1/8 7 h-lim-p 0.0043 0.1139 1.7704 3924.965216 0 0.0087 129 | 1/8 8 h-lim-p 0.0148 0.1187 1.0280 3924.459220 0 0.0297 142 | 1/8 9 h-lim-p 2.5000 20.0000 0.0054 3924.446249 6 0.8687 169 | 1/8 10 h-lim-p 2.5000 20.0000 0.0004 3924.446214 2 0.9644 192 | 0/8 11 h-lim-p 0.3831 20.0000 0.0009 3924.446214 0 0.0052 216 | 0/8 12 h-lim-p 0.1184 0.9469 0.0000 3924.446214 m 0.9469 236 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 3924.446214 0 1.0938 256 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 3924.446214 0 1.0938 275 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 3924.446214 0 1.2500 294 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 3924.446214 0 2.1875 313 | 1/8 17 h-lim-p 1.8417 20.0000 0.0000 3924.446214 0 0.0000 354 Out... lnL = -3924.446214 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3924.446214 Node 7: lnL = -3924.446214 Node 8: lnL = -3924.446214 Node 9: lnL = -3924.446214 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 309 Sequential format.. Reading seq # 1: YFR002W_Sbay Reading seq # 2: YFR002W_Scer Reading seq # 3: YFR002W_Skud Reading seq # 4: YFR002W_Smik Reading seq # 5: YFR002W_Spar Sequences read.. Counting patterns.. # site patterns = 162 Counting frequencies.. 120 bytes for distance 25920 bytes for lkl0 20736 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.344889 0.000844 0.122714 0.135585 0.123434 0.244949 0.320541 0.000060 lnL0 = -1344.928265 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1344.928265 x= 0.34489 0.00084 0.12271 0.13558 0.12343 0.24495 0.32054 0.00006 1 h-lim-p 0.0000 0.0000 85.7253 1344.680916 m 0.0000 22 | 1/8 2 h-lim-p 0.0001 0.0040 37.9315 1344.128171 0 0.0013 38 | 1/8 3 h-lim-p 0.0019 0.0152 25.2820 1343.897227 7 0.0010 65 | 1/8 4 h-lim-p 0.0027 0.0395 9.5291 1343.835743 7 0.0016 94 | 0/8 5 h-lim-p 0.0006 0.0314 24.0937 1343.272150 0 0.0025 108 | 0/8 6 h-lim-p 0.0033 0.0262 15.0327 1343.113235 7 0.0022 137 | 0/8 7 h-lim-p 0.0045 0.0357 5.9726 1343.065379 6 0.0034 161 | 0/8 8 h-lim-p 0.0068 0.0541 2.7043 1343.060717 6 0.0012 188 | 0/8 9 h-lim-p 0.0466 4.8832 0.0704 1341.873059 0 1.1172 204 | 0/8 10 h-lim-p 1.7349 13.8795 0.0262 1341.798691 7 1.2126 240 | 0/8 11 h-lim-p 2.5000 20.0000 0.0069 1341.793128 3 1.2500 266 | 0/8 12 h-lim-p 2.5000 20.0000 0.0008 1341.792964 3 1.2347 293 | 0/8 13 h-lim-p 2.5000 20.0000 0.0001 1341.792963 0 1.0938 313 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1341.792963 0 1.0938 333 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1341.792963 0 2.1875 353 | 0/8 16 h-lim-p 1.8415 20.0000 0.0000 1341.792963 0 0.8057 373 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1341.792963 0 0.0049 401 Out... lnL = -1341.792963 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1341.792963 Node 7: lnL = -1341.792963 Node 8: lnL = -1341.792963 Node 9: lnL = -1341.792963 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 312 Sequential format.. Reading seq # 1: YFR003C_Sbay Reading seq # 2: YFR003C_Scer Reading seq # 3: YFR003C_Skud Reading seq # 4: YFR003C_Smik Reading seq # 5: YFR003C_Spar Sequences read.. Counting patterns.. # site patterns = 128 Counting frequencies.. 120 bytes for distance 20480 bytes for lkl0 16384 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.278366 0.049814 0.112779 0.146573 0.099185 0.165543 0.212447 0.000060 lnL0 = -1291.787184 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1291.787184 x= 0.27837 0.04981 0.11278 0.14657 0.09919 0.16554 0.21245 0.00006 1 h-lim-p 0.0000 0.0000 96.4538 1291.745294 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0026 42.0893 1291.320363 0 0.0006 40 | 1/8 3 h-lim-p 0.0020 0.0227 13.9405 1291.210113 7 0.0012 71 | 1/8 4 h-lim-p 0.0035 0.0424 4.8447 1291.194657 6 0.0011 97 | 1/8 5 h-lim-p 0.0035 0.1499 1.5649 1291.172208 1 0.0044 111 | 1/8 6 h-lim-p 0.0063 0.3202 1.0850 1290.453371 0 0.0380 125 | 0/8 7 h-lim-p 0.0024 0.0190 12.8019 1288.910810 0 0.0048 138 | 0/8 8 h-lim-p 0.0004 0.0029 13.3309 1288.689369 0 0.0022 152 | 0/8 9 h-lim-p 0.0183 0.1460 0.2354 1288.684755 5 0.0139 174 | 0/8 10 h-lim-p 0.0146 0.1165 0.2160 1288.463645 0 0.0582 196 | 0/8 11 h-lim-p 2.5000 20.0000 0.0049 1288.448985 4 1.2218 225 | 0/8 12 h-lim-p 2.5000 20.0000 0.0014 1288.447607 4 1.2703 255 | 0/8 13 h-lim-p 2.5000 20.0000 0.0003 1288.447545 3 0.9482 281 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1288.447544 0 1.0938 301 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1288.447544 0 1.0938 321 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1288.447544 0 2.1875 341 | 0/8 17 h-lim-p 2.1139 20.0000 0.0000 1288.447544 0 0.9248 361 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1288.447544 0 0.0391 386 Out... lnL = -1288.447544 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1288.447544 Node 7: lnL = -1288.447544 Node 8: lnL = -1288.447544 Node 9: lnL = -1288.447544 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 280 Sequential format.. Reading seq # 1: YFR005C_Sbay Reading seq # 2: YFR005C_Scer Reading seq # 3: YFR005C_Skud Reading seq # 4: YFR005C_Smik Reading seq # 5: YFR005C_Spar Sequences read.. Counting patterns.. # site patterns = 105 Counting frequencies.. 120 bytes for distance 16800 bytes for lkl0 13440 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.209710 0.050550 0.000060 0.126882 0.078939 0.156186 0.140705 0.016107 lnL0 = -1095.965114 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1095.965114 x= 0.20971 0.05055 0.00006 0.12688 0.07894 0.15619 0.14070 0.01611 1 h-lim-p 0.0001 0.0008 133.6364 1092.532706 0 0.0004 24 | 0/8 2 h-lim-p 0.0000 0.0003 91.2059 1091.909638 0 0.0002 38 | 0/8 3 h-lim-p 0.0001 0.0009 32.6253 1091.682689 0 0.0005 52 | 0/8 4 h-lim-p 0.0018 0.0222 8.2015 1091.663239 6 0.0006 80 | 0/8 5 h-lim-p 0.0019 0.0154 1.7915 1091.662174 5 0.0006 105 | 0/8 6 h-lim-p 0.0045 0.1176 0.2571 1091.661472 2 0.0042 121 | 0/8 7 h-lim-p 0.0176 0.2029 0.0616 1091.593281 0 0.1054 143 | 0/8 8 h-lim-p 0.0007 0.0053 4.0958 1091.586017 4 0.0007 171 | 0/8 9 h-lim-p 1.0854 20.0000 0.0026 1091.579358 6 0.7883 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0003 1091.579254 4 0.9169 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1091.579254 0 1.0938 249 | 0/8 12 h-lim-p 1.6271 20.0000 0.0000 1091.579254 0 1.4237 269 | 0/8 13 h-lim-p 1.6467 20.0000 0.0000 1091.579254 0 1.6467 289 | 0/8 14 h-lim-p 0.5850 20.0000 0.0000 1091.579254 0 0.2925 309 | 0/8 15 h-lim-p 0.0046 3.0226 0.0030 1091.579254 0 0.0000 338 | 0/8 16 h-lim-p 0.0001 20.0000 0.0001 1091.579254 0 0.0000 373 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 1091.579254 0 0.0051 402 | 0/8 18 h-lim-p 0.0062 20.0000 0.0004 1091.579254 0 0.0000 442 | 0/8 19 h-lim-p 0.0000 5.8091 0.0041 1091.579254 0 0.0000 474 | 0/8 20 h-lim-p 0.0000 3.3862 0.0044 1091.579254 0 0.0006 500 | 0/8 21 h-lim-p 0.0021 20.0000 0.0013 1091.579254 0 0.0000 542 | 0/8 22 h-lim-p 0.0000 20.0000 0.0099 | 0/8 23 h-lim-p 0.0000 20.0000 0.0099 Out... lnL = -1091.579254 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1091.579254 Node 7: lnL = -1091.579254 Node 8: lnL = -1091.579254 Node 9: lnL = -1091.579254 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 280 Sequential format.. Reading seq # 1: YFR006W_Sbay Reading seq # 2: YFR006W_Scer Reading seq # 3: YFR006W_Skud Reading seq # 4: YFR006W_Smik Reading seq # 5: YFR006W_Spar Sequences read.. Counting patterns.. # site patterns = 99 Counting frequencies.. 120 bytes for distance 15840 bytes for lkl0 12672 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.208949 0.041884 0.000060 0.131866 0.089147 0.156387 0.151204 0.017969 lnL0 = -1091.302160 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1091.302160 x= 0.20895 0.04188 0.00006 0.13187 0.08915 0.15639 0.15120 0.01797 1 h-lim-p 0.0001 0.0008 133.4623 1087.000962 0 0.0004 24 | 0/8 2 h-lim-p 0.0000 0.0002 122.7480 1086.266571 0 0.0001 38 | 0/8 3 h-lim-p 0.0001 0.0009 20.2698 1086.158897 0 0.0005 52 | 0/8 4 h-lim-p 0.0024 0.0464 3.9469 1086.154318 5 0.0006 77 | 0/8 5 h-lim-p 0.0013 0.0104 0.9609 1086.154067 4 0.0005 99 | 0/8 6 h-lim-p 0.0035 0.1806 0.1307 1086.152669 0 0.0140 121 | 0/8 7 h-lim-p 0.0056 0.0760 0.3282 1086.125716 0 0.0168 142 | 0/8 8 h-lim-p 0.0013 0.0318 4.3976 1086.098800 1 0.0016 164 | 0/8 9 h-lim-p 1.0743 8.5946 0.0016 1086.096072 4 0.8536 184 | 0/8 10 h-lim-p 2.5000 20.0000 0.0003 1086.095958 3 0.8800 211 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1086.095956 0 1.2500 231 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1086.095956 0 0.5469 252 | 0/8 13 h-lim-p 0.3178 20.0000 0.0000 1086.095956 0 0.0099 276 | 0/8 14 h-lim-p 0.0055 20.0000 0.0001 1086.095956 0 0.0055 296 | 0/8 15 h-lim-p 0.0037 20.0000 0.0001 1086.095956 0 0.0000 333 | 0/8 16 h-lim-p 0.0000 1.2072 0.0058 | 0/8 17 h-lim-p 0.0000 1.2072 0.0058 Out... lnL = -1086.095956 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1086.095956 Node 7: lnL = -1086.095956 Node 8: lnL = -1086.095956 Node 9: lnL = -1086.095956 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 848 Sequential format.. Reading seq # 1: YFR007W_Sbay Reading seq # 2: YFR007W_Scer Reading seq # 3: YFR007W_Skud Reading seq # 4: YFR007W_Smik Reading seq # 5: YFR007W_Spar Sequences read.. Counting patterns.. # site patterns = 432 Counting frequencies.. 120 bytes for distance 69120 bytes for lkl0 55296 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.624578 0.094605 0.000060 0.360626 0.281186 0.308483 0.473101 0.042151 lnL0 = -4875.748072 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4875.748072 x= 0.62458 0.09461 0.00006 0.36063 0.28119 0.30848 0.47310 0.04215 1 h-lim-p 0.0015 0.0122 128.5383 4870.896656 9 0.0005 45 | 0/8 2 h-lim-p 0.0006 0.0051 76.6241 4869.048396 1 0.0008 59 | 0/8 3 h-lim-p 0.0024 0.0196 18.2415 4868.883913 5 0.0011 80 | 0/8 4 h-lim-p 0.0037 0.1083 5.2343 4868.848482 6 0.0028 104 | 0/8 5 h-lim-p 0.0068 0.0709 2.1597 4868.846500 5 0.0010 129 | 0/8 6 h-lim-p 0.0033 0.1289 0.6490 4868.846215 2 0.0015 145 | 0/8 7 h-lim-p 0.0079 1.3306 0.1191 4868.846189 2 0.0021 170 | 0/8 8 h-lim-p 0.0429 20.0000 0.0058 4868.841882 0 0.5152 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 4868.841832 1 0.9961 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4868.841831 0 1.2500 235 | 0/8 11 h-lim-p 1.6296 20.0000 0.0000 4868.841831 0 1.4259 255 | 0/8 12 h-lim-p 1.8162 20.0000 0.0000 4868.841831 0 1.8162 275 | 0/8 13 h-lim-p 0.7953 20.0000 0.0000 4868.841831 0 0.0000 315 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 4868.841831 0 0.0000 346 Out... lnL = -4868.841831 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4868.841831 Node 7: lnL = -4868.841831 Node 8: lnL = -4868.841831 Node 9: lnL = -4868.841831 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 192 Sequential format.. Reading seq # 1: YFR008W_Sbay Reading seq # 2: YFR008W_Scer Reading seq # 3: YFR008W_Skud Reading seq # 4: YFR008W_Smik Reading seq # 5: YFR008W_Spar Sequences read.. Counting patterns.. # site patterns = 108 Counting frequencies.. 120 bytes for distance 17280 bytes for lkl0 13824 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.369211 0.153484 0.088207 0.243257 0.186530 0.132049 0.361309 0.000060 lnL0 = -918.885478 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 918.885478 x= 0.36921 0.15348 0.08821 0.24326 0.18653 0.13205 0.36131 0.00006 1 h-lim-p 0.0000 0.0000 85.4234 918.861047 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0066 63.1032 916.430813 0 0.0019 41 | 1/8 3 h-lim-p 0.0038 0.0302 11.9089 916.127737 6 0.0039 67 | 1/8 4 h-lim-p 0.0093 0.1037 5.0307 916.007207 7 0.0061 97 | 1/8 5 h-lim-p 0.0389 0.4009 0.7844 913.721688 0 0.1556 111 | 0/8 6 h-lim-p 0.0000 0.0000 20.3217 h-lim-p: 6.65807260e-23 5.32645808e-22 2.03216706e+01 913.721688 .. | 0/8 7 h-lim-p 0.0000 0.0042 61.9443 910.371945 0 0.0013 145 | 0/8 8 h-lim-p 0.0004 0.0035 25.8271 910.014834 0 0.0018 159 | 0/8 9 h-lim-p 0.0007 0.0060 7.0321 909.976950 0 0.0015 172 | 0/8 10 h-lim-p 0.0002 0.0014 2.1201 909.972242 m 0.0014 184 | 0/8 11 h-lim-p -0.0000 -0.0000 0.4828 h-lim-p: -3.08384883e-20 -2.46707906e-19 4.82807087e-01 909.972242 .. | 0/8 12 h-lim-p 0.0000 0.0080 17.9935 909.816067 0 0.0010 218 | 0/8 13 h-lim-p 0.0025 0.0198 3.7540 909.805804 6 0.0015 245 | 0/8 14 h-lim-p 0.0000 0.0003 0.8377 909.805619 m 0.0003 257 | 1/8 15 h-lim-p 0.0004 0.6806 0.5420 909.805435 0 0.0016 279 | 1/8 16 h-lim-p 0.0061 1.4747 0.1393 909.805422 0 0.0015 299 | 1/8 17 h-lim-p 0.0064 12.7422 0.0334 909.805412 0 0.0096 318 | 1/8 18 h-lim-p 0.0109 10.3456 0.0295 909.805395 2 0.0084 341 | 1/8 19 h-lim-p 0.0109 14.6913 0.0227 909.804943 0 0.0653 362 | 1/8 20 h-lim-p 0.1881 20.0000 0.0079 909.804682 4 0.1336 390 | 1/8 21 h-lim-p 2.5000 20.0000 0.0004 909.804626 2 1.1719 413 | 1/8 22 h-lim-p 2.5000 20.0000 0.0000 909.804626 0 1.0938 432 | 1/8 23 h-lim-p 2.5000 20.0000 0.0000 909.804626 0 1.0938 451 | 1/8 24 h-lim-p 2.5000 20.0000 0.0000 909.804626 0 0.0293 476 | 1/8 25 h-lim-p 0.0302 20.0000 0.0000 909.804626 0 0.0000 510 Out... lnL = -909.804626 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -909.804626 Node 7: lnL = -909.804626 Node 8: lnL = -909.804626 Node 9: lnL = -909.804626 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 352 Sequential format.. Reading seq # 1: YFR010W_Sbay Reading seq # 2: YFR010W_Scer Reading seq # 3: YFR010W_Skud Reading seq # 4: YFR010W_Smik Reading seq # 5: YFR010W_Spar Sequences read.. Counting patterns.. # site patterns = 158 Counting frequencies.. 120 bytes for distance 25280 bytes for lkl0 20224 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.234666 0.119050 0.035184 0.167775 0.069189 0.193839 0.172864 0.000060 lnL0 = -1542.825872 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1542.825872 x= 0.23467 0.11905 0.03518 0.16778 0.06919 0.19384 0.17286 0.00006 1 h-lim-p 0.0000 0.0000 75.5733 1542.805566 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0032 37.4879 1542.547675 0 0.0006 40 | 1/8 3 h-lim-p 0.0012 0.0127 20.8301 1542.461956 2 0.0005 56 | 1/8 4 h-lim-p 0.0027 0.0632 4.1543 1542.453552 6 0.0009 83 | 1/8 5 h-lim-p 0.0083 0.5031 0.4660 1542.444542 3 0.0085 101 | 1/8 6 h-lim-p 0.0058 2.7716 0.6764 1542.207387 0 0.0233 122 | 1/8 7 h-lim-p 0.0019 0.0413 8.1848 1541.555523 0 0.0039 142 | 1/8 8 h-lim-p 0.0220 0.2161 1.4344 1541.554512 5 0.0009 170 | 0/8 9 h-lim-p 0.0002 1.8275 5.5436 1541.539330 0 0.0010 184 | 0/8 10 h-lim-p 0.6115 20.0000 0.0086 1541.501140 0 1.2230 197 | 0/8 11 h-lim-p 2.5000 20.0000 0.0023 1541.497786 3 1.0449 223 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1541.497785 0 1.0938 243 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1541.497785 0 1.0938 263 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1541.497785 0 0.0000 310 Out... lnL = -1541.497785 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1541.497785 Node 7: lnL = -1541.497785 Node 8: lnL = -1541.497785 Node 9: lnL = -1541.497785 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 697 Sequential format.. Reading seq # 1: YFR011C_Sbay Reading seq # 2: YFR011C_Scer Reading seq # 3: YFR011C_Skud Reading seq # 4: YFR011C_Smik Reading seq # 5: YFR011C_Spar Sequences read.. Counting patterns.. # site patterns = 293 Counting frequencies.. 120 bytes for distance 46880 bytes for lkl0 37504 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.336166 0.115278 0.087933 0.179415 0.179327 0.213920 0.238205 0.000060 lnL0 = -3308.704753 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3308.704753 x= 0.33617 0.11528 0.08793 0.17941 0.17933 0.21392 0.23820 0.00006 1 h-lim-p 0.0000 0.0000 269.1331 3308.624263 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0020 141.4030 3305.695966 0 0.0003 39 | 1/8 3 h-lim-p 0.0009 0.0084 49.3767 3305.054861 5 0.0006 63 | 1/8 4 h-lim-p 0.0012 0.0095 21.6180 3304.934766 2 0.0006 79 | 1/8 5 h-lim-p 0.0018 0.0652 6.7581 3304.876920 6 0.0013 105 | 1/8 6 h-lim-p 0.0037 0.1311 2.3750 3304.232506 0 0.0147 119 | 1/8 7 h-lim-p 0.0030 0.0240 8.7272 3291.719107 0 0.0120 133 | 1/8 8 h-lim-p 0.0005 0.0043 69.3611 3289.896308 1 0.0007 147 | 1/8 9 h-lim-p 1.0573 20.0000 0.0442 3287.768744 6 0.8401 171 | 0/8 10 h-lim-p 0.0101 0.5612 3.6975 3287.763423 5 0.0008 207 | 0/8 11 h-lim-p 0.2114 4.2886 0.0133 3287.526985 0 1.6915 222 | 0/8 12 h-lim-p 2.5000 20.0000 0.0053 3287.488132 4 1.1078 249 | 0/8 13 h-lim-p 2.5000 20.0000 0.0010 3287.486387 5 1.5673 282 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 3287.486373 1 1.0938 304 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 3287.486373 0 1.0938 324 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 3287.486373 0 1.0938 344 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 3287.486373 0 0.5469 365 | 0/8 18 h-lim-p 0.8598 20.0000 0.0000 3287.486373 0 0.1075 387 | 0/8 19 h-lim-p 0.0957 20.0000 0.0000 3287.486373 0 0.0957 407 | 0/8 20 h-lim-p 0.0873 20.0000 0.0000 3287.486373 0 0.0873 427 | 0/8 21 h-lim-p 0.0786 20.0000 0.0000 3287.486373 0 0.0000 466 Out... lnL = -3287.486373 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3287.486373 Node 7: lnL = -3287.486373 Node 8: lnL = -3287.486373 Node 9: lnL = -3287.486373 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 697 Sequential format.. Reading seq # 1: YFR012W_Sbay Reading seq # 2: YFR012W_Scer Reading seq # 3: YFR012W_Skud Reading seq # 4: YFR012W_Smik Reading seq # 5: YFR012W_Spar Sequences read.. Counting patterns.. # site patterns = 298 Counting frequencies.. 120 bytes for distance 47680 bytes for lkl0 38144 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.256831 0.160515 0.078421 0.127471 0.129644 0.230635 0.201238 0.000060 lnL0 = -3301.703774 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3301.703774 x= 0.25683 0.16052 0.07842 0.12747 0.12964 0.23063 0.20124 0.00006 1 h-lim-p 0.0054 1.3318 110.2042 3299.808957 8 0.0003 40 | 0/8 2 h-lim-p 0.0000 0.0000 29.8012 3299.775002 m 0.0000 52 | 1/8 3 h-lim-p 0.0001 0.0186 11.6756 3299.747048 0 0.0004 66 | 1/8 4 h-lim-p 0.0042 0.2247 1.1760 3299.746377 3 0.0008 85 | 1/8 5 h-lim-p 0.0027 0.8636 0.3448 3299.745465 0 0.0041 97 | 1/8 6 h-lim-p 0.0045 1.6676 0.3132 3299.734413 0 0.0134 117 | 1/8 7 h-lim-p 0.0025 0.1850 1.6595 3299.574550 0 0.0101 138 | 1/8 8 h-lim-p 0.0159 0.2501 1.0595 3299.573941 2 0.0010 157 | 1/8 9 h-lim-p 0.0390 4.8039 0.0267 3299.570378 0 0.0781 170 | 0/8 10 h-lim-p 0.0074 4.1901 0.2818 3299.570343 0 0.0008 191 | 0/8 11 h-lim-p 0.1680 4.9065 0.0014 3299.568610 0 1.0078 213 | 0/8 12 h-lim-p 0.4243 3.3947 0.0002 3299.568583 0 0.8487 234 | 0/8 13 h-lim-p 0.1586 1.2689 0.0001 3299.568583 0 0.3172 255 | 0/8 14 h-lim-p 0.0001 0.0008 0.1744 3299.568583 0 0.0000 288 | 0/8 15 h-lim-p 0.0000 0.0873 0.0015 3299.568583 0 0.0026 316 | 0/8 16 h-lim-p 0.0050 0.1665 0.0008 3299.568583 0 0.0044 336 | 0/8 17 h-lim-p 0.0081 0.3068 0.0004 3299.568583 0 0.0071 356 | 0/8 18 h-lim-p 0.0125 0.5455 0.0002 3299.568583 0 0.0109 376 | 0/8 19 h-lim-p 0.0194 1.0100 0.0001 3299.568583 0 0.0170 396 | 0/8 20 h-lim-p 0.0318 2.1500 0.0001 3299.568583 0 0.0278 416 | 0/8 21 h-lim-p 0.0567 6.8143 0.0000 3299.568583 0 0.0496 436 | 0/8 22 h-lim-p 0.1145 20.0000 0.0000 3299.568583 0 0.1002 456 | 0/8 23 h-lim-p 0.6570 20.0000 0.0000 3299.568583 0 0.0006 485 Out... lnL = -3299.568583 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3299.568583 Node 7: lnL = -3299.568583 Node 8: lnL = -3299.568583 Node 9: lnL = -3299.568583 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 343 Sequential format.. Reading seq # 1: YFR017C_Sbay Reading seq # 2: YFR017C_Scer Reading seq # 3: YFR017C_Skud Reading seq # 4: YFR017C_Smik Reading seq # 5: YFR017C_Spar Sequences read.. Counting patterns.. # site patterns = 135 Counting frequencies.. 120 bytes for distance 21600 bytes for lkl0 17280 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.273576 0.080780 0.002452 0.073165 0.107367 0.122811 0.120772 0.041837 lnL0 = -1287.819942 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1287.819942 x= 0.27358 0.08078 0.00245 0.07317 0.10737 0.12281 0.12077 0.04184 1 h-lim-p 0.0001 0.0234 507.1399 1283.595237 7 0.0001 39 | 0/8 2 h-lim-p 0.0008 0.0064 33.3164 1283.305804 8 0.0005 72 | 0/8 3 h-lim-p 0.0017 0.0229 10.4714 1283.275004 7 0.0006 101 | 0/8 4 h-lim-p 0.0023 0.0873 2.7679 1283.272735 5 0.0006 125 | 0/8 5 h-lim-p 0.0059 0.4528 0.2986 1283.272712 3 0.0005 147 | 0/8 6 h-lim-p 0.0068 7.4702 0.0232 1283.272712 0 0.0015 168 | 0/8 7 h-lim-p 0.0042 20.0000 0.0083 1283.272711 0 0.0042 188 | 0/8 8 h-lim-p 0.0135 20.0000 0.0026 1283.272569 0 0.1619 211 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1283.272518 1 2.5781 233 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1283.272513 0 1.0938 253 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1283.272513 0 1.2500 273 | 0/8 12 h-lim-p 1.8419 20.0000 0.0000 1283.272513 0 0.0063 300 | 0/8 13 h-lim-p 0.0025 20.0000 0.0000 1283.272513 0 0.0000 339 | 0/8 14 h-lim-p 0.0000 20.0000 0.0020 | 0/8 15 h-lim-p 0.0000 20.0000 0.0020 Out... lnL = -1283.272513 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1283.272513 Node 7: lnL = -1283.272513 Node 8: lnL = -1283.272513 Node 9: lnL = -1283.272513 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 863 Sequential format.. Reading seq # 1: YFR021W_Sbay Reading seq # 2: YFR021W_Scer Reading seq # 3: YFR021W_Skud Reading seq # 4: YFR021W_Smik Reading seq # 5: YFR021W_Spar Sequences read.. Counting patterns.. # site patterns = 370 Counting frequencies.. 120 bytes for distance 59200 bytes for lkl0 47360 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.484659 0.050830 0.169811 0.117391 0.133442 0.336654 0.268281 0.028832 lnL0 = -4477.000142 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4477.000142 x= 0.48466 0.05083 0.16981 0.11739 0.13344 0.33665 0.26828 0.02883 1 h-lim-p 0.0044 0.8261 142.1553 4473.926183 8 0.0003 43 | 0/8 2 h-lim-p 0.0012 0.0094 32.0833 4473.648946 2 0.0006 59 | 0/8 3 h-lim-p 0.0004 0.0071 42.0796 4473.441640 5 0.0005 83 | 0/8 4 h-lim-p 0.0058 0.0593 3.2882 4473.438848 5 0.0005 110 | 0/8 5 h-lim-p 0.0018 0.0970 0.9467 4473.438519 2 0.0008 126 | 0/8 6 h-lim-p 0.0081 0.8927 0.0931 4473.438508 2 0.0013 152 | 0/8 7 h-lim-p 0.0348 20.0000 0.0035 4473.434493 0 0.5571 176 | 0/8 8 h-lim-p 0.0023 0.9840 0.8525 4473.433905 4 0.0013 207 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 4473.433832 2 0.9961 231 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4473.433832 0 1.0938 251 | 0/8 11 h-lim-p 1.3545 20.0000 0.0000 4473.433832 0 1.1852 271 | 0/8 12 h-lim-p 0.6235 20.0000 0.0000 4473.433832 0 0.5455 291 | 0/8 13 h-lim-p 0.0300 20.0000 0.0005 4473.433832 0 0.0038 313 | 0/8 14 h-lim-p 0.0009 20.0000 0.0022 4473.433832 0 0.0001 335 | 0/8 15 h-lim-p 0.0002 20.0000 0.0013 4473.433832 0 0.0000 368 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 4473.433832 0 0.0000 397 Out... lnL = -4473.433832 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4473.433832 Node 7: lnL = -4473.433832 Node 8: lnL = -4473.433832 Node 9: lnL = -4473.433832 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 858 Sequential format.. Reading seq # 1: YFR027W_Sbay Reading seq # 2: YFR027W_Scer Reading seq # 3: YFR027W_Skud Reading seq # 4: YFR027W_Smik Reading seq # 5: YFR027W_Spar Sequences read.. Counting patterns.. # site patterns = 468 Counting frequencies.. 120 bytes for distance 74880 bytes for lkl0 59904 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.633400 0.331068 0.122822 0.722273 0.486040 0.589609 0.456638 0.000060 lnL0 = -5060.226466 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 5060.226466 x= 0.63340 0.33107 0.12282 0.72227 0.48604 0.58961 0.45664 0.00006 1 h-lim-p 0.0000 0.0000 347.9409 5060.145703 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0000 68165.0702 4984.478232 m 0.0000 34 | 2/8 3 h-lim-p 0.0006 0.0049 115.0564 4963.100594 0 0.0024 48 | 2/8 4 h-lim-p 0.0016 0.0131 48.7334 4951.122086 0 0.0033 61 | 2/8 5 h-lim-p 0.0008 0.0061 50.1792 4934.807805 0 0.0045 75 | 2/8 6 h-lim-p 0.0013 0.0100 39.0959 4933.788527 7 0.0014 106 | 2/8 7 h-lim-p 0.0024 0.0193 8.3524 4933.724323 6 0.0018 133 | 1/8 8 h-lim-p 0.0004 0.0088 41.8537 4933.102399 0 0.0011 146 | 1/8 9 h-lim-p 0.7201 5.7611 0.0261 4932.951699 2 0.6751 162 | 1/8 10 h-lim-p 1.8228 14.5823 0.0041 4932.945069 5 1.0124 193 | 1/8 11 h-lim-p 2.5000 20.0000 0.0014 4932.944878 3 0.6580 219 | 1/8 12 h-lim-p 2.5000 20.0000 0.0002 4932.944867 0 1.0938 238 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 4932.944867 0 1.0938 257 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 4932.944867 0 1.0938 276 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 4932.944867 0 2.5000 295 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 4932.944867 0 0.0000 337 Out... lnL = -4932.944867 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4932.944867 Node 7: lnL = -4932.944867 Node 8: lnL = -4932.944867 Node 9: lnL = -4932.944867 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 365 Sequential format.. Reading seq # 1: YFR030W_Sbay Reading seq # 2: YFR030W_Scer Reading seq # 3: YFR030W_Skud Reading seq # 4: YFR030W_Smik Reading seq # 5: YFR030W_Spar Sequences read.. Counting patterns.. # site patterns = 150 Counting frequencies.. 120 bytes for distance 24000 bytes for lkl0 19200 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.248135 0.011706 0.042692 0.107141 0.101441 0.181362 0.151130 0.011571 lnL0 = -1484.293885 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1484.293885 x= 0.24814 0.01171 0.04269 0.10714 0.10144 0.18136 0.15113 0.01157 1 h-lim-p 0.0014 0.9360 147.7179 1482.353836 8 0.0002 44 | 0/8 2 h-lim-p 0.0010 0.0082 17.3704 1482.242632 7 0.0008 72 | 0/8 3 h-lim-p 0.0051 0.1127 2.5581 1482.240969 4 0.0005 95 | 0/8 4 h-lim-p 0.0020 0.1853 0.6850 1482.240830 3 0.0006 115 | 0/8 5 h-lim-p 0.0022 0.4575 0.1977 1482.240821 0 0.0005 136 | 0/8 6 h-lim-p 0.0037 5.4572 0.0259 1482.240820 0 0.0008 157 | 0/8 7 h-lim-p 0.0025 20.0000 0.0084 1482.240820 0 0.0022 177 | 0/8 8 h-lim-p 0.0762 20.0000 0.0002 1482.240779 0 0.6093 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1482.240778 0 1.0938 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1482.240778 0 1.0938 240 | 0/8 11 h-lim-p 1.0155 20.0000 0.0000 1482.240778 0 4.0620 262 | 0/8 12 h-lim-p 1.0978 20.0000 0.0001 1482.240778 0 0.8234 282 | 0/8 13 h-lim-p 0.0036 2.8791 0.0122 1482.240778 0 0.0005 304 | 0/8 14 h-lim-p 0.0000 0.0029 11.9156 .. | 0/8 15 h-lim-p 0.0000 4.3835 0.0147 1482.240778 0 0.0000 349 | 0/8 16 h-lim-p 0.0002 20.0000 0.0008 1482.240778 0 0.0003 369 | 0/8 17 h-lim-p 0.0012 20.0000 0.0002 1482.240778 0 0.0000 394 | 0/8 18 h-lim-p 0.0001 20.0000 0.0001 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0016 | 0/8 20 h-lim-p 0.0000 20.0000 0.0016 Out... lnL = -1482.240778 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1482.240778 Node 7: lnL = -1482.240778 Node 8: lnL = -1482.240778 Node 9: lnL = -1482.240778 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 829 Sequential format.. Reading seq # 1: YFR032C-A_Sbay Reading seq # 2: YFR032C-A_Scer Reading seq # 3: YFR032C-A_Skud Reading seq # 4: YFR032C-A_Smik Reading seq # 5: YFR032C-A_Spar Sequences read.. Counting patterns.. # site patterns = 310 Counting frequencies.. 120 bytes for distance 49600 bytes for lkl0 39680 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.365999 0.068047 0.050145 0.126133 0.103611 0.193690 0.206876 0.040501 lnL0 = -3704.249753 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3704.249753 x= 0.36600 0.06805 0.05014 0.12613 0.10361 0.19369 0.20688 0.04050 1 h-lim-p 0.0026 0.7436 170.1803 3701.863212 9 0.0002 47 | 0/8 2 h-lim-p 0.0008 0.0091 37.2837 3701.584589 4 0.0004 68 | 0/8 3 h-lim-p 0.0007 0.0077 20.8737 3701.523749 2 0.0003 84 | 0/8 4 h-lim-p 0.0006 0.0077 11.9939 3701.500277 5 0.0005 108 | 0/8 5 h-lim-p 0.0056 0.1477 0.9621 3701.500031 3 0.0005 128 | 0/8 6 h-lim-p 0.0017 0.4300 0.3060 3701.500014 0 0.0004 149 | 0/8 7 h-lim-p 0.0021 2.3391 0.0552 3701.500013 0 0.0009 169 | 0/8 8 h-lim-p 0.0556 20.0000 0.0009 3701.499466 0 0.8899 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3701.499453 1 0.9961 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3701.499453 0 1.2500 235 | 0/8 11 h-lim-p 1.4989 20.0000 0.0000 3701.499453 0 1.3116 255 | 0/8 12 h-lim-p 0.8668 20.0000 0.0000 3701.499453 0 1.7337 276 | 0/8 13 h-lim-p 0.0029 4.8791 0.0153 3701.499453 0 0.0029 296 | 0/8 14 h-lim-p 0.0008 1.3684 0.0545 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0006 | 0/8 16 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -3701.499453 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3701.499453 Node 7: lnL = -3701.499453 Node 8: lnL = -3701.499453 Node 9: lnL = -3701.499453 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 333 Sequential format.. Reading seq # 1: YFR032C_Sbay Reading seq # 2: YFR032C_Scer Reading seq # 3: YFR032C_Skud Reading seq # 4: YFR032C_Smik Reading seq # 5: YFR032C_Spar Sequences read.. Counting patterns.. # site patterns = 148 Counting frequencies.. 120 bytes for distance 23680 bytes for lkl0 18944 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.312122 0.033975 0.071990 0.123741 0.056403 0.173678 0.163185 0.037237 lnL0 = -1392.504693 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1392.504693 x= 0.31212 0.03397 0.07199 0.12374 0.05640 0.17368 0.16318 0.03724 1 h-lim-p 0.0003 0.0025 110.9161 1390.593937 1 0.0004 24 | 0/8 2 h-lim-p 0.0014 0.0111 19.4531 1390.424731 6 0.0009 49 | 0/8 3 h-lim-p 0.0027 0.0321 6.6116 1390.410714 5 0.0007 72 | 0/8 4 h-lim-p 0.0016 0.1340 2.9778 1390.409598 4 0.0003 93 | 0/8 5 h-lim-p 0.0016 0.1744 0.5558 1390.409505 2 0.0006 109 | 0/8 6 h-lim-p 0.0039 5.7860 0.0886 1390.409490 0 0.0020 129 | 0/8 7 h-lim-p 0.0413 19.3975 0.0042 1390.404050 0 0.6605 153 | 0/8 8 h-lim-p 0.0033 0.0789 0.8460 1390.403503 3 0.0013 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1390.403496 2 0.9644 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1390.403496 0 1.0938 223 | 0/8 11 h-lim-p 1.2832 20.0000 0.0000 1390.403496 0 2.5664 244 | 0/8 12 h-lim-p 0.8944 20.0000 0.0000 1390.403496 0 0.8944 264 | 0/8 13 h-lim-p 0.0003 5.4349 0.0833 1390.403496 0 0.0000 304 | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1390.403496 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1390.403496 Node 7: lnL = -1390.403496 Node 8: lnL = -1390.403496 Node 9: lnL = -1390.403496 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 303 Sequential format.. Reading seq # 1: YFR033C_Sbay Reading seq # 2: YFR033C_Scer Reading seq # 3: YFR033C_Skud Reading seq # 4: YFR033C_Smik Reading seq # 5: YFR033C_Spar Sequences read.. Counting patterns.. # site patterns = 113 Counting frequencies.. 120 bytes for distance 18080 bytes for lkl0 14464 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.235257 0.036382 0.014773 0.147382 0.079800 0.133861 0.132686 0.015176 lnL0 = -1095.552919 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1095.552919 x= 0.23526 0.03638 0.01477 0.14738 0.07980 0.13386 0.13269 0.01518 1 h-lim-p 0.0007 0.6208 174.5193 1093.273464 9 0.0002 41 | 0/8 2 h-lim-p 0.0006 0.0047 29.7790 1092.972330 1 0.0007 55 | 0/8 3 h-lim-p 0.0020 0.0207 10.8078 1092.932464 6 0.0008 79 | 0/8 4 h-lim-p 0.0087 0.1455 0.9520 1092.932163 4 0.0007 104 | 0/8 5 h-lim-p 0.0020 0.6911 0.3107 1092.932123 2 0.0009 128 | 0/8 6 h-lim-p 0.0102 5.1628 0.0273 1092.932119 2 0.0034 154 | 0/8 7 h-lim-p 0.0183 8.1330 0.0050 1092.931525 0 0.2193 177 | 0/8 8 h-lim-p 0.0023 0.2173 0.4699 1092.931031 2 0.0020 201 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1092.930911 4 1.4823 232 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1092.930910 0 1.0938 252 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1092.930910 0 1.0938 272 | 0/8 12 h-lim-p 1.0600 20.0000 0.0000 1092.930910 0 4.2400 294 | 0/8 13 h-lim-p 1.5546 20.0000 0.0000 1092.930910 0 0.3886 315 | 0/8 14 h-lim-p 0.0151 20.0000 0.0007 1092.930910 0 0.0009 338 | 0/8 15 h-lim-p 0.0003 16.8505 0.0021 1092.930910 0 0.0003 358 | 0/8 16 h-lim-p 0.0002 9.7706 0.0037 1092.930910 0 0.0000 385 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 1092.930910 0 0.0000 418 | 0/8 18 h-lim-p 0.0000 20.0000 0.0009 | 0/8 19 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -1092.930910 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1092.930910 Node 7: lnL = -1092.930910 Node 8: lnL = -1092.930910 Node 9: lnL = -1092.930910 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 231 Sequential format.. Reading seq # 1: YFR041C_Sbay Reading seq # 2: YFR041C_Scer Reading seq # 3: YFR041C_Skud Reading seq # 4: YFR041C_Smik Reading seq # 5: YFR041C_Spar Sequences read.. Counting patterns.. # site patterns = 94 Counting frequencies.. 120 bytes for distance 15040 bytes for lkl0 12032 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.254513 0.026709 0.080209 0.116928 0.109848 0.200358 0.230197 0.000060 lnL0 = -937.573141 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 937.573141 x= 0.25451 0.02671 0.08021 0.11693 0.10985 0.20036 0.23020 0.00006 1 h-lim-p 0.0000 0.0000 62.8778 937.539088 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0100 16.9672 937.424913 0 0.0010 39 | 1/8 3 h-lim-p 0.0045 0.0585 3.8149 937.411674 6 0.0016 67 | 1/8 4 h-lim-p 0.0084 0.3574 0.7152 937.378602 0 0.0167 80 | 1/8 5 h-lim-p 0.0064 0.0512 0.8718 936.800127 0 0.0384 101 | 1/8 6 h-lim-p 0.0011 0.0087 17.5659 936.188077 0 0.0016 120 | 1/8 7 h-lim-p 0.0018 0.0147 4.7827 936.168043 2 0.0017 136 | 1/8 8 h-lim-p 0.1519 4.8222 0.0541 936.164995 4 0.0573 156 | 0/8 9 h-lim-p 0.0007 0.1179 4.3911 936.139003 0 0.0028 177 | 0/8 10 h-lim-p 0.0199 0.1594 0.0939 936.135431 m 0.1594 189 | 0/8 11 h-lim-p -0.0000 -0.0000 0.0245 h-lim-p: -4.19507872e-18 -3.35606298e-17 2.44517342e-02 936.135431 .. | 0/8 12 h-lim-p 0.0000 0.1430 1.3915 936.134876 0 0.0006 231 | 0/8 13 h-lim-p 0.0015 0.0386 0.6036 936.134791 3 0.0006 249 | 0/8 14 h-lim-p 0.0017 1.2767 0.1942 936.134776 2 0.0009 274 | 0/8 15 h-lim-p 0.0005 0.0038 0.1233 936.134770 0 0.0009 295 | 0/8 16 h-lim-p 0.0003 0.0021 0.0454 936.134770 0 0.0016 317 | 0/8 17 h-lim-p 0.0000 0.0000 1.4328 936.134770 m 0.0000 337 | 0/8 18 h-lim-p 0.0011 10.5166 0.0220 936.134770 0 0.0011 349 | 1/8 19 h-lim-p 0.0181 20.0000 0.0014 936.134769 0 0.0159 369 | 1/8 20 h-lim-p 0.0181 20.0000 0.0012 936.134763 0 0.0724 390 | 0/8 21 h-lim-p 0.0391 20.0000 0.0022 936.134763 0 0.0043 411 | 0/8 22 h-lim-p 0.1088 0.8707 0.0000 936.134763 0 0.6530 433 | 0/8 23 h-lim-p 0.0205 0.1640 0.0000 936.134763 m 0.1640 453 | 1/8 24 h-lim-p 0.5081 20.0000 0.0000 936.134763 0 1.5242 474 | 1/8 25 h-lim-p 1.1533 20.0000 0.0000 936.134763 0 1.0091 493 | 1/8 26 h-lim-p 1.8613 20.0000 0.0000 936.134763 0 1.6286 512 | 1/8 27 h-lim-p 2.5000 20.0000 0.0000 936.134763 0 2.1875 531 | 1/8 28 h-lim-p 1.9474 20.0000 0.0000 936.134763 0 0.8520 550 | 1/8 29 h-lim-p 2.5000 20.0000 0.0000 936.134763 0 0.0049 577 Out... lnL = -936.134763 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -936.134763 Node 7: lnL = -936.134763 Node 8: lnL = -936.134763 Node 9: lnL = -936.134763 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 210 Sequential format.. Reading seq # 1: YFR042W_Sbay Reading seq # 2: YFR042W_Scer Reading seq # 3: YFR042W_Skud Reading seq # 4: YFR042W_Smik Reading seq # 5: YFR042W_Spar Sequences read.. Counting patterns.. # site patterns = 95 Counting frequencies.. 120 bytes for distance 15200 bytes for lkl0 12160 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.260191 0.049721 0.086830 0.135301 0.124329 0.188751 0.236048 0.000060 lnL0 = -917.351951 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 917.351951 x= 0.26019 0.04972 0.08683 0.13530 0.12433 0.18875 0.23605 0.00006 1 h-lim-p 0.0000 0.0000 84.4969 917.317190 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0069 19.5088 917.123623 0 0.0013 40 | 1/8 3 h-lim-p 0.0032 0.0257 3.1031 917.092836 4 0.0036 61 | 1/8 4 h-lim-p 0.0060 0.1414 1.8577 917.037483 5 0.0065 86 | 1/8 5 h-lim-p 0.0065 0.0520 1.1771 915.250024 m 0.0520 98 | 1/8 6 h-lim-p 0.0012 0.0095 19.6803 914.628840 0 0.0024 111 | 1/8 7 h-lim-p 0.0022 0.0173 15.9442 914.488256 8 0.0013 142 | 1/8 8 h-lim-p 0.6982 8.1531 0.0294 914.312659 7 0.5004 170 | 0/8 9 h-lim-p 0.0051 0.0742 2.8923 914.305702 7 0.0015 210 | 0/8 10 h-lim-p 0.0007 0.0055 0.1444 914.305510 m 0.0055 222 | 0/8 11 h-lim-p 0.0354 7.2044 0.0223 914.292257 0 0.2126 244 | 0/8 12 h-lim-p 0.0713 0.5703 0.0026 914.291561 m 0.5703 264 | 0/8 13 h-lim-p 0.0000 0.0000 0.0006 h-lim-p: 1.09398475e-16 8.75187804e-16 5.96231036e-04 914.291561 .. | 0/8 14 h-lim-p 0.0000 0.0888 0.5188 914.291452 0 0.0010 306 | 0/8 15 h-lim-p 0.0025 2.7949 0.2019 914.291440 2 0.0006 331 | 0/8 16 h-lim-p 0.0002 0.0019 0.0929 914.291438 0 0.0009 353 | 0/8 17 h-lim-p 0.0001 0.0005 0.0757 914.291437 m 0.0005 373 | 1/8 18 h-lim-p 0.0017 5.4953 0.0201 914.291437 0 0.0015 393 | 1/8 19 h-lim-p 0.0097 20.0000 0.0030 914.291437 0 0.0043 412 | 1/8 20 h-lim-p 0.0035 17.8487 0.0037 914.291437 0 0.0052 431 | 1/8 21 h-lim-p 0.0040 20.0000 0.0048 914.291437 0 0.0035 450 | 1/8 22 h-lim-p 0.1115 20.0000 0.0002 914.291433 0 0.4460 471 | 1/8 23 h-lim-p 2.5000 20.0000 0.0000 914.291433 0 1.0938 490 | 1/8 24 h-lim-p 2.5000 20.0000 0.0000 914.291433 0 1.0938 509 | 1/8 25 h-lim-p 2.5000 20.0000 0.0000 914.291433 0 0.1172 532 | 1/8 26 h-lim-p 0.1351 20.0000 0.0000 914.291433 0 0.0000 575 Out... lnL = -914.291433 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -914.291433 Node 7: lnL = -914.291433 Node 8: lnL = -914.291433 Node 9: lnL = -914.291433 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 171 Sequential format.. Reading seq # 1: YFR043C_Sbay Reading seq # 2: YFR043C_Scer Reading seq # 3: YFR043C_Skud Reading seq # 4: YFR043C_Smik Reading seq # 5: YFR043C_Spar Sequences read.. Counting patterns.. # site patterns = 60 Counting frequencies.. 120 bytes for distance 9600 bytes for lkl0 7680 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.273307 0.071970 0.205928 0.085416 0.135684 0.131739 0.158437 0.000060 lnL0 = -537.822233 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 537.822233 x= 0.27331 0.07197 0.20593 0.08542 0.13568 0.13174 0.15844 0.00006 1 h-lim-p 0.0003 0.0027 57.5001 535.937700 0 0.0010 23 | 0/8 2 h-lim-p 0.0007 0.0056 23.4229 535.587045 0 0.0014 36 | 0/8 3 h-lim-p 0.0012 0.0096 7.4414 535.337849 m 0.0096 48 | 0/8 4 h-lim-p 0.0028 0.0226 9.9669 535.271419 5 0.0028 70 | 0/8 5 h-lim-p 0.0016 0.0128 4.0592 535.139710 m 0.0128 82 | 1/8 6 h-lim-p 0.0238 0.1901 0.4116 535.138982 4 0.0092 102 | 1/8 7 h-lim-p 0.0015 0.0122 2.4065 535.131660 m 0.0122 121 | 2/8 8 h-lim-p 0.0212 0.2609 1.0794 535.131629 3 0.0008 145 | 2/8 9 h-lim-p 0.0043 1.9582 0.1954 535.116241 0 0.1375 162 | 2/8 10 h-lim-p 1.7950 20.0000 0.0150 535.114937 2 0.4207 185 | 2/8 11 h-lim-p 0.5136 20.0000 0.0123 535.114149 1 0.6420 205 | 2/8 12 h-lim-p 2.5000 20.0000 0.0005 535.114141 3 1.3437 230 | 2/8 13 h-lim-p 2.5000 20.0000 0.0002 535.114135 0 5.0000 249 | 2/8 14 h-lim-p 2.5000 20.0000 0.0002 535.114132 0 2.5000 267 | 2/8 15 h-lim-p 2.0303 20.0000 0.0002 535.114132 1 0.9993 288 | 2/8 16 h-lim-p 2.5000 20.0000 0.0000 535.114131 0 1.0938 306 | 2/8 17 h-lim-p 2.5000 20.0000 0.0000 535.114131 0 2.1875 324 | 2/8 18 h-lim-p 1.8421 20.0000 0.0000 535.114131 0 0.8059 342 | 2/8 19 h-lim-p 2.5000 20.0000 0.0000 535.114131 0 0.0049 368 Out... lnL = -535.114131 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -535.114131 Node 7: lnL = -535.114131 Node 8: lnL = -535.114131 Node 9: lnL = -535.114131 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 836 Sequential format.. Reading seq # 1: YFR044C_Sbay Reading seq # 2: YFR044C_Scer Reading seq # 3: YFR044C_Skud Reading seq # 4: YFR044C_Smik Reading seq # 5: YFR044C_Spar Sequences read.. Counting patterns.. # site patterns = 267 Counting frequencies.. 120 bytes for distance 42720 bytes for lkl0 34176 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.267061 0.095230 0.083460 0.159191 0.100862 0.190421 0.153912 0.000060 lnL0 = -3505.885611 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3505.885611 x= 0.26706 0.09523 0.08346 0.15919 0.10086 0.19042 0.15391 0.00006 1 h-lim-p 0.0000 0.0000 209.2989 3505.793797 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0086 46.7763 3505.485080 0 0.0003 39 | 1/8 3 h-lim-p 0.0009 0.0182 16.8197 3505.430242 2 0.0004 55 | 1/8 4 h-lim-p 0.0012 0.0650 5.7728 3505.418276 2 0.0006 71 | 1/8 5 h-lim-p 0.0012 0.0708 2.6434 3505.397970 0 0.0019 83 | 1/8 6 h-lim-p 0.0076 0.3239 0.6526 3504.063145 0 0.0605 98 | 1/8 7 h-lim-p 0.0004 0.0033 36.0385 3501.315808 0 0.0008 118 | 1/8 8 h-lim-p 0.0007 0.0065 40.4415 3500.914330 8 0.0004 149 | 1/8 9 h-lim-p 1.1080 19.1986 0.0158 3500.632232 7 0.8172 177 | 1/8 10 h-lim-p 2.5000 20.0000 0.0010 3500.630959 4 0.9169 206 | 1/8 11 h-lim-p 2.5000 20.0000 0.0001 3500.630954 1 0.9961 227 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 3500.630953 0 1.0938 246 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 3500.630953 0 1.0938 265 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 3500.630953 0 1.0938 284 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 3500.630953 0 2.1875 303 | 1/8 16 h-lim-p 1.7961 20.0000 0.0000 3500.630953 0 0.0070 329 Out... lnL = -3500.630953 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3500.630953 Node 7: lnL = -3500.630953 Node 8: lnL = -3500.630953 Node 9: lnL = -3500.630953 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 1162 Sequential format.. Reading seq # 1: YFR045W_Sbay Reading seq # 2: YFR045W_Scer Reading seq # 3: YFR045W_Skud Reading seq # 4: YFR045W_Smik Reading seq # 5: YFR045W_Spar Sequences read.. Counting patterns.. # site patterns = 275 Counting frequencies.. 120 bytes for distance 44000 bytes for lkl0 35200 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.070162 0.064721 0.064298 0.133361 0.072599 0.204328 0.151568 0.198363 lnL0 = -4074.765797 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4074.765797 x= 0.07016 0.06472 0.06430 0.13336 0.07260 0.20433 0.15157 0.19836 1 h-lim-p 0.0008 0.0062 162.9737 4072.839195 7 0.0002 36 | 0/8 2 h-lim-p 0.0007 0.0056 34.6595 4072.673716 7 0.0003 61 | 0/8 3 h-lim-p 0.0006 0.0177 15.6100 4072.656563 3 0.0002 80 | 0/8 4 h-lim-p 0.0011 0.0877 2.2756 4072.655751 4 0.0003 103 | 0/8 5 h-lim-p 0.0015 0.3061 0.4889 4072.655714 1 0.0003 118 | 0/8 6 h-lim-p 0.0021 3.5977 0.0772 4072.655713 0 0.0005 139 | 0/8 7 h-lim-p 0.0020 10.3784 0.0172 4072.655713 0 0.0004 160 | 0/8 8 h-lim-p 0.0543 20.0000 0.0001 4072.655668 0 0.8680 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4072.655667 0 1.0938 204 | 0/8 10 h-lim-p 2.0543 20.0000 0.0000 4072.655667 0 0.8987 224 | 0/8 11 h-lim-p 0.5980 20.0000 0.0000 4072.655667 0 0.0000 264 | 0/8 12 h-lim-p 0.0000 20.0000 0.0000 4072.655667 0 0.0000 289 Out... lnL = -4072.655667 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4072.655667 Node 7: lnL = -4072.655667 Node 8: lnL = -4072.655667 Node 9: lnL = -4072.655667 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 122 Sequential format.. Reading seq # 1: YFR046C_Sbay Reading seq # 2: YFR046C_Scer Reading seq # 3: YFR046C_Skud Reading seq # 4: YFR046C_Smik Reading seq # 5: YFR046C_Spar Sequences read.. Counting patterns.. # site patterns = 66 Counting frequencies.. 120 bytes for distance 10560 bytes for lkl0 8448 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.025573 0.030501 0.119694 0.080302 0.067870 0.155471 0.181388 0.134561 lnL0 = -483.704812 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 483.704812 x= 0.02557 0.03050 0.11969 0.08030 0.06787 0.15547 0.18139 0.13456 1 h-lim-p 0.0020 0.0162 11.7422 483.598138 6 0.0015 35 | 0/8 2 h-lim-p 0.0018 0.0145 5.8013 483.578516 4 0.0014 55 | 0/8 3 h-lim-p 0.0050 0.1004 1.6054 483.576985 5 0.0013 79 | 0/8 4 h-lim-p 0.0032 0.1158 0.6627 483.576697 3 0.0016 97 | 0/8 5 h-lim-p 0.0040 0.2622 0.2570 483.576669 2 0.0010 122 | 0/8 6 h-lim-p 0.0045 1.9271 0.0574 483.576667 0 0.0011 143 | 0/8 7 h-lim-p 0.0049 13.0153 0.0130 483.576667 0 0.0025 163 | 0/8 8 h-lim-p 0.2091 20.0000 0.0002 483.576661 0 0.8363 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 483.576661 0 1.0938 205 | 0/8 10 h-lim-p 2.1321 20.0000 0.0000 483.576661 0 1.0660 225 | 0/8 11 h-lim-p 0.8558 20.0000 0.0000 483.576661 0 0.2139 246 | 0/8 12 h-lim-p 0.0012 20.0000 0.0017 483.576661 0 0.0006 266 | 0/8 13 h-lim-p 0.0002 9.4842 0.0039 483.576661 0 0.0000 290 | 0/8 14 h-lim-p 0.0000 20.0000 0.0016 483.576661 0 0.0000 314 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 483.576661 0 0.0000 336 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 483.576661 0 0.0001 356 Out... lnL = -483.576661 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -483.576661 Node 7: lnL = -483.576661 Node 8: lnL = -483.576661 Node 9: lnL = -483.576661 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 829 Sequential format.. Reading seq # 1: YFR047C_Sbay Reading seq # 2: YFR047C_Scer Reading seq # 3: YFR047C_Skud Reading seq # 4: YFR047C_Smik Reading seq # 5: YFR047C_Spar Sequences read.. Counting patterns.. # site patterns = 310 Counting frequencies.. 120 bytes for distance 49600 bytes for lkl0 39680 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.095421 0.104463 0.120500 0.163732 0.103231 0.272972 0.223135 0.280251 lnL0 = -4166.447843 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4166.447843 x= 0.09542 0.10446 0.12050 0.16373 0.10323 0.27297 0.22314 0.28025 1 h-lim-p 0.0007 0.0055 63.8656 4165.764169 7 0.0003 36 | 0/8 2 h-lim-p 0.0015 0.0189 14.3439 4165.703122 5 0.0006 57 | 0/8 3 h-lim-p 0.0016 0.0479 5.4946 4165.697227 5 0.0004 81 | 0/8 4 h-lim-p 0.0018 0.5439 1.3602 4165.697030 3 0.0002 101 | 0/8 5 h-lim-p 0.0011 1.1380 0.2885 4165.697008 2 0.0006 118 | 0/8 6 h-lim-p 0.0057 9.3136 0.0279 4165.697007 0 0.0013 139 | 0/8 7 h-lim-p 0.0055 20.0000 0.0064 4165.697007 0 0.0027 159 | 0/8 8 h-lim-p 0.0115 20.0000 0.0015 4165.696924 0 0.1840 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4165.696923 0 1.0938 203 | 0/8 10 h-lim-p 2.1874 20.0000 0.0000 4165.696923 0 0.9570 223 | 0/8 11 h-lim-p 0.9590 20.0000 0.0000 4165.696923 0 0.0599 246 | 0/8 12 h-lim-p 0.0075 20.0000 0.0001 4165.696923 0 0.0019 267 | 0/8 13 h-lim-p 0.0001 20.0000 0.0017 4165.696923 0 0.0000 288 | 0/8 14 h-lim-p 0.0020 20.0000 0.0000 4165.696923 0 0.0000 327 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -4165.696923 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4165.696923 Node 7: lnL = -4165.696923 Node 8: lnL = -4165.696923 Node 9: lnL = -4165.696923 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 833 Sequential format.. Reading seq # 1: YFR048W_Sbay Reading seq # 2: YFR048W_Scer Reading seq # 3: YFR048W_Skud Reading seq # 4: YFR048W_Smik Reading seq # 5: YFR048W_Spar Sequences read.. Counting patterns.. # site patterns = 322 Counting frequencies.. 120 bytes for distance 51520 bytes for lkl0 41216 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.116770 0.100234 0.104631 0.185237 0.101126 0.273100 0.260973 0.311607 lnL0 = -4272.587301 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4272.587301 x= 0.11677 0.10023 0.10463 0.18524 0.10113 0.27310 0.26097 0.31161 1 h-lim-p 0.0003 0.0027 90.8772 4271.204797 7 0.0003 35 | 0/8 2 h-lim-p 0.0017 0.0253 18.2660 4271.118624 7 0.0005 66 | 0/8 3 h-lim-p 0.0013 0.0437 7.3132 4271.102304 6 0.0007 90 | 0/8 4 h-lim-p 0.0014 0.1823 3.5876 4271.101173 4 0.0002 115 | 0/8 5 h-lim-p 0.0025 0.6551 0.3184 4271.101143 0 0.0006 128 | 0/8 6 h-lim-p 0.0030 5.6561 0.0658 4271.101142 0 0.0007 149 | 0/8 7 h-lim-p 0.0127 20.0000 0.0034 4271.101142 0 0.0055 169 | 0/8 8 h-lim-p 0.0280 20.0000 0.0007 4271.101116 0 0.2238 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4271.101115 0 1.0938 212 | 0/8 10 h-lim-p 2.2836 20.0000 0.0000 4271.101115 0 0.9991 232 | 0/8 11 h-lim-p 0.9029 20.0000 0.0000 4271.101115 0 0.2257 253 | 0/8 12 h-lim-p 0.0029 20.0000 0.0009 4271.101115 0 0.0029 273 | 0/8 13 h-lim-p 0.0004 20.0000 0.0057 4271.101115 0 0.0000 310 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 4271.101115 0 0.0000 339 Out... lnL = -4271.101115 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4271.101115 Node 7: lnL = -4271.101115 Node 8: lnL = -4271.101115 Node 9: lnL = -4271.101115 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 448 Sequential format.. Reading seq # 1: YFR049W_Sbay Reading seq # 2: YFR049W_Scer Reading seq # 3: YFR049W_Skud Reading seq # 4: YFR049W_Smik Reading seq # 5: YFR049W_Spar Sequences read.. Counting patterns.. # site patterns = 130 Counting frequencies.. 120 bytes for distance 20800 bytes for lkl0 16640 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.025348 0.031282 0.061511 0.087748 0.063907 0.116323 0.132117 0.109791 lnL0 = -1629.251288 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1629.251288 x= 0.02535 0.03128 0.06151 0.08775 0.06391 0.11632 0.13212 0.10979 1 h-lim-p 0.0031 0.0245 59.8920 1628.898499 5 0.0002 35 | 0/8 2 h-lim-p 0.0005 0.0037 13.5072 1628.878004 5 0.0002 59 | 0/8 3 h-lim-p 0.0024 0.1188 1.3415 1628.877637 4 0.0004 82 | 0/8 4 h-lim-p 0.0026 0.3043 0.2173 1628.877632 1 0.0003 98 | 0/8 5 h-lim-p 0.0022 3.5537 0.0252 1628.877632 0 0.0002 120 | 0/8 6 h-lim-p 0.0016 20.0000 0.0037 1628.877632 0 0.0016 140 | 0/8 7 h-lim-p 0.0035 20.0000 0.0017 1628.877627 0 0.0421 163 | 0/8 8 h-lim-p 0.0015 6.7037 0.0470 1628.877605 0 0.0031 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1628.877603 0 1.0938 204 | 0/8 10 h-lim-p 1.2370 20.0000 0.0000 1628.877603 0 1.0824 224 | 0/8 11 h-lim-p 1.1465 20.0000 0.0000 1628.877603 0 4.5860 246 | 0/8 12 h-lim-p 0.1927 20.0000 0.0007 1628.877603 0 0.0843 266 | 0/8 13 h-lim-p 0.0168 10.4983 0.0037 1628.877603 0 0.0016 289 | 0/8 14 h-lim-p 0.0005 3.3431 0.0117 1628.877603 0 0.0001 310 | 0/8 15 h-lim-p 0.0002 4.4144 0.0089 1628.877603 0 0.0000 345 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 1628.877603 0 0.0000 380 Out... lnL = -1628.877603 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1628.877603 Node 7: lnL = -1628.877603 Node 8: lnL = -1628.877603 Node 9: lnL = -1628.877603 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 321 Sequential format.. Reading seq # 1: YFR050C_Sbay Reading seq # 2: YFR050C_Scer Reading seq # 3: YFR050C_Skud Reading seq # 4: YFR050C_Smik Reading seq # 5: YFR050C_Spar Sequences read.. Counting patterns.. # site patterns = 156 Counting frequencies.. 120 bytes for distance 24960 bytes for lkl0 19968 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.132865 0.007801 0.071600 0.135274 0.115056 0.196470 0.234449 0.285451 lnL0 = -1482.791471 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1482.791471 x= 0.13286 0.00780 0.07160 0.13527 0.11506 0.19647 0.23445 0.28545 1 h-lim-p 0.0015 0.0120 91.9824 1481.317317 9 0.0004 40 | 0/8 2 h-lim-p 0.0017 0.0134 12.4014 1481.256650 2 0.0008 56 | 0/8 3 h-lim-p 0.0034 0.0998 2.8529 1481.251599 5 0.0013 78 | 0/8 4 h-lim-p 0.0019 0.1229 1.9276 1481.250440 4 0.0009 97 | 0/8 5 h-lim-p 0.0071 0.9326 0.2318 1481.250408 3 0.0013 118 | 0/8 6 h-lim-p 0.0058 2.6700 0.0500 1481.250407 1 0.0007 142 | 0/8 7 h-lim-p 0.0124 20.0000 0.0029 1481.250407 0 0.0054 162 | 0/8 8 h-lim-p 0.0454 20.0000 0.0003 1481.250397 0 0.3628 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1481.250396 0 1.0938 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1481.250396 0 1.0938 225 | 0/8 11 h-lim-p 1.1669 20.0000 0.0000 1481.250396 0 7.0016 247 | 0/8 12 h-lim-p 2.0120 20.0000 0.0000 1481.250396 0 0.2201 269 | 0/8 13 h-lim-p 0.0139 20.0000 0.0002 1481.250396 0 0.0000 300 | 0/8 14 h-lim-p 0.0011 20.0000 0.0000 1481.250396 0 0.0011 320 Out... lnL = -1481.250396 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1481.250396 Node 7: lnL = -1481.250396 Node 8: lnL = -1481.250396 Node 9: lnL = -1481.250396 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 750 Sequential format.. Reading seq # 1: YFR052W_Sbay Reading seq # 2: YFR052W_Scer Reading seq # 3: YFR052W_Skud Reading seq # 4: YFR052W_Smik Reading seq # 5: YFR052W_Spar Sequences read.. Counting patterns.. # site patterns = 336 Counting frequencies.. 120 bytes for distance 53760 bytes for lkl0 43008 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.094110 0.067130 0.074036 0.193712 0.157543 0.248874 0.360424 0.288840 lnL0 = -3854.653820 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3854.653820 x= 0.09411 0.06713 0.07404 0.19371 0.15754 0.24887 0.36042 0.28884 1 h-lim-p 0.0030 0.0237 147.5176 3851.610264 3 0.0003 30 | 0/8 2 h-lim-p 0.0015 0.0123 28.3669 3851.369557 5 0.0006 52 | 0/8 3 h-lim-p 0.0012 0.0312 14.6624 3851.303286 5 0.0008 76 | 0/8 4 h-lim-p 0.0016 0.0522 6.9241 3851.291004 5 0.0006 97 | 0/8 5 h-lim-p 0.0042 0.1941 1.0744 3851.290570 3 0.0008 116 | 0/8 6 h-lim-p 0.0056 1.9884 0.1528 3851.290562 0 0.0006 130 | 0/8 7 h-lim-p 0.0153 20.0000 0.0061 3851.290562 0 0.0067 150 | 0/8 8 h-lim-p 0.0210 20.0000 0.0019 3851.290416 0 0.1677 173 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3851.290415 0 1.0938 193 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3851.290415 0 1.0938 213 | 0/8 11 h-lim-p 2.1698 20.0000 0.0000 3851.290415 0 1.8986 233 | 0/8 12 h-lim-p 1.8553 20.0000 0.0000 3851.290415 0 1.6234 253 | 0/8 13 h-lim-p 0.3538 20.0000 0.0000 3851.290415 0 0.0083 278 | 0/8 14 h-lim-p 0.0003 20.0000 0.0011 3851.290415 0 0.0004 298 | 0/8 15 h-lim-p 0.0005 20.0000 0.0010 3851.290415 0 0.0000 334 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -3851.290415 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3851.290415 Node 7: lnL = -3851.290415 Node 8: lnL = -3851.290415 Node 9: lnL = -3851.290415 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 923 Sequential format.. Reading seq # 1: YFR053C_Sbay Reading seq # 2: YFR053C_Scer Reading seq # 3: YFR053C_Skud Reading seq # 4: YFR053C_Smik Reading seq # 5: YFR053C_Spar Sequences read.. Counting patterns.. # site patterns = 226 Counting frequencies.. 120 bytes for distance 36160 bytes for lkl0 28928 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.079728 0.035440 0.113434 0.063086 0.028098 0.159855 0.166796 0.194317 lnL0 = -3531.456628 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3531.456628 x= 0.07973 0.03544 0.11343 0.06309 0.02810 0.15986 0.16680 0.19432 1 h-lim-p 0.0043 0.9264 128.2782 3530.405464 7 0.0001 43 | 0/8 2 h-lim-p 0.0001 0.0012 31.2075 3530.375176 5 0.0001 64 | 0/8 3 h-lim-p 0.0002 0.0201 9.1747 3530.365132 1 0.0003 78 | 0/8 4 h-lim-p 0.0016 0.0712 1.6124 3530.364882 2 0.0002 96 | 0/8 5 h-lim-p 0.0004 0.2089 0.8314 3530.364826 2 0.0002 113 | 0/8 6 h-lim-p 0.0039 3.0045 0.0421 3530.364826 0 0.0004 135 | 0/8 7 h-lim-p 0.0087 20.0000 0.0021 3530.364826 0 0.0076 155 | 0/8 8 h-lim-p 0.0063 20.0000 0.0025 3530.364792 0 0.0504 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3530.364791 0 1.0938 198 | 0/8 10 h-lim-p 1.7710 20.0000 0.0000 3530.364791 0 1.5496 218 | 0/8 11 h-lim-p 1.9964 20.0000 0.0000 3530.364791 0 1.7468 238 | 0/8 12 h-lim-p 0.9047 20.0000 0.0000 3530.364791 0 1.8094 259 | 0/8 13 h-lim-p 0.1484 20.0000 0.0003 3530.364791 0 0.0000 292 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 3530.364791 0 0.0001 312 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 3530.364791 0 0.0000 342 Out... lnL = -3530.364791 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3530.364791 Node 7: lnL = -3530.364791 Node 8: lnL = -3530.364791 Node 9: lnL = -3530.364791 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 676 Sequential format.. Reading seq # 1: YGL001C_Sbay Reading seq # 2: YGL001C_Scer Reading seq # 3: YGL001C_Skud Reading seq # 4: YGL001C_Smik Reading seq # 5: YGL001C_Spar Sequences read.. Counting patterns.. # site patterns = 309 Counting frequencies.. 120 bytes for distance 49440 bytes for lkl0 39552 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.067798 0.000060 0.164554 0.146973 0.153521 0.267287 0.264304 0.239810 lnL0 = -3263.664094 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3263.664094 x= 0.06780 0.00006 0.16455 0.14697 0.15352 0.26729 0.26430 0.23981 1 h-lim-p 0.0020 0.1068 178.6755 3258.365263 8 0.0003 43 | 0/8 2 h-lim-p 0.0008 0.0066 48.8923 3257.320737 1 0.0010 57 | 0/8 3 h-lim-p 0.0059 0.0474 5.9670 3257.306612 5 0.0008 81 | 0/8 4 h-lim-p 0.0070 0.5548 0.6874 3257.306432 1 0.0008 97 | 0/8 5 h-lim-p 0.0022 1.1255 0.2400 3257.306400 2 0.0007 122 | 0/8 6 h-lim-p 0.0033 3.0461 0.0516 3257.306111 0 0.0130 144 | 0/8 7 h-lim-p 0.0039 2.6037 0.1728 3257.295381 0 0.0311 167 | 0/8 8 h-lim-p 0.0031 0.2129 1.7456 3257.293513 5 0.0010 200 | 0/8 9 h-lim-p 1.4977 20.0000 0.0012 3257.292734 4 1.0213 222 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3257.292733 0 1.2500 242 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3257.292733 0 1.0938 262 | 0/8 12 h-lim-p 1.1587 20.0000 0.0000 3257.292733 0 0.5793 282 | 0/8 13 h-lim-p 0.0735 20.0000 0.0001 3257.292733 0 0.0184 303 | 0/8 14 h-lim-p 0.0060 20.0000 0.0003 3257.292733 0 0.0060 323 | 0/8 15 h-lim-p 0.0025 20.0000 0.0007 3257.292733 0 0.0012 343 | 0/8 16 h-lim-p 0.0010 20.0000 0.0009 3257.292733 0 0.0000 382 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -3257.292733 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3257.292733 Node 7: lnL = -3257.292733 Node 8: lnL = -3257.292733 Node 9: lnL = -3257.292733 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 364 Sequential format.. Reading seq # 1: YGL002W_Sbay Reading seq # 2: YGL002W_Scer Reading seq # 3: YGL002W_Skud Reading seq # 4: YGL002W_Smik Reading seq # 5: YGL002W_Spar Sequences read.. Counting patterns.. # site patterns = 181 Counting frequencies.. 120 bytes for distance 28960 bytes for lkl0 23168 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.062483 0.110012 0.032622 0.121672 0.115786 0.255537 0.168859 0.205722 lnL0 = -1629.021120 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1629.021120 x= 0.06248 0.11001 0.03262 0.12167 0.11579 0.25554 0.16886 0.20572 1 h-lim-p 0.0039 1.1283 91.1666 1627.911991 8 0.0003 46 | 0/8 2 h-lim-p 0.0031 0.0270 9.0032 1627.882185 2 0.0007 63 | 0/8 3 h-lim-p 0.0019 0.0813 3.3234 1627.879362 4 0.0006 86 | 0/8 4 h-lim-p 0.0050 0.8869 0.3869 1627.879297 3 0.0009 107 | 0/8 5 h-lim-p 0.0026 1.6986 0.1306 1627.879288 1 0.0011 129 | 0/8 6 h-lim-p 0.0083 15.1907 0.0179 1627.879288 0 0.0018 150 | 0/8 7 h-lim-p 0.0044 20.0000 0.0073 1627.879287 0 0.0044 170 | 0/8 8 h-lim-p 0.0149 20.0000 0.0022 1627.879193 0 0.1793 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1627.879188 0 1.0938 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1627.879188 0 1.0938 233 | 0/8 11 h-lim-p 1.1715 20.0000 0.0000 1627.879188 0 1.1715 253 | 0/8 12 h-lim-p 0.4688 20.0000 0.0000 1627.879188 0 0.0586 275 | 0/8 13 h-lim-p 0.0073 20.0000 0.0002 1627.879188 0 0.0000 302 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 1627.879188 0 0.0000 325 | 0/8 15 h-lim-p 0.0006 20.0000 0.0000 1627.879188 0 0.0000 355 Out... lnL = -1627.879188 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1627.879188 Node 7: lnL = -1627.879188 Node 8: lnL = -1627.879188 Node 9: lnL = -1627.879188 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 359 Sequential format.. Reading seq # 1: YGL003C_Sbay Reading seq # 2: YGL003C_Scer Reading seq # 3: YGL003C_Skud Reading seq # 4: YGL003C_Smik Reading seq # 5: YGL003C_Spar Sequences read.. Counting patterns.. # site patterns = 173 Counting frequencies.. 120 bytes for distance 27680 bytes for lkl0 22144 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.042214 0.161567 0.020537 0.117620 0.119839 0.235440 0.220976 0.192707 lnL0 = -1641.621204 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1641.621204 x= 0.04221 0.16157 0.02054 0.11762 0.11984 0.23544 0.22098 0.19271 1 h-lim-p 0.0015 0.0420 149.4557 1639.276246 8 0.0003 40 | 0/8 2 h-lim-p 0.0014 0.0113 20.4618 1639.095440 8 0.0009 75 | 0/8 3 h-lim-p 0.0016 0.0196 11.2888 1639.062524 3 0.0007 93 | 0/8 4 h-lim-p 0.0030 0.0998 2.4172 1639.060734 4 0.0007 113 | 0/8 5 h-lim-p 0.0036 0.3113 0.4428 1639.060643 3 0.0010 132 | 0/8 6 h-lim-p 0.0033 1.9168 0.1288 1639.060635 2 0.0009 157 | 0/8 7 h-lim-p 0.0976 20.0000 0.0011 1639.060321 0 0.7805 180 | 0/8 8 h-lim-p 0.0034 1.6671 0.2607 1639.059933 2 0.0032 204 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1639.059901 2 0.9961 228 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1639.059901 0 1.0938 248 | 0/8 11 h-lim-p 1.3010 20.0000 0.0000 1639.059901 0 1.1383 268 | 0/8 12 h-lim-p 0.2736 20.0000 0.0001 1639.059901 0 0.0150 291 | 0/8 13 h-lim-p 0.0030 20.0000 0.0003 1639.059901 0 0.0000 317 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 1639.059901 0 0.0000 355 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 1639.059901 0 0.0000 379 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 1639.059901 0 0.0000 446 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1639.059901 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1639.059901 Node 7: lnL = -1639.059901 Node 8: lnL = -1639.059901 Node 9: lnL = -1639.059901 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 592 Sequential format.. Reading seq # 1: YGL004C_Sbay Reading seq # 2: YGL004C_Scer Reading seq # 3: YGL004C_Skud Reading seq # 4: YGL004C_Smik Reading seq # 5: YGL004C_Spar Sequences read.. Counting patterns.. # site patterns = 282 Counting frequencies.. 120 bytes for distance 45120 bytes for lkl0 36096 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.069538 0.203271 0.108413 0.173082 0.142921 0.223368 0.280359 0.261306 lnL0 = -2832.448793 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2832.448793 x= 0.06954 0.20327 0.10841 0.17308 0.14292 0.22337 0.28036 0.26131 1 h-lim-p 0.0020 0.0160 51.7744 2831.660807 9 0.0006 47 | 0/8 2 h-lim-p 0.0022 0.0200 14.6121 2831.575709 4 0.0008 67 | 0/8 3 h-lim-p 0.0013 0.0294 9.3328 2831.554118 6 0.0007 93 | 0/8 4 h-lim-p 0.0042 0.2153 1.5019 2831.552985 3 0.0010 112 | 0/8 5 h-lim-p 0.0022 0.4802 0.6910 2831.552724 3 0.0013 132 | 0/8 6 h-lim-p 0.0190 5.0059 0.0484 2831.552723 0 0.0010 155 | 0/8 7 h-lim-p 0.0038 20.0000 0.0133 2831.552722 0 0.0017 175 | 0/8 8 h-lim-p 0.0595 20.0000 0.0004 2831.552689 0 0.9516 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2831.552687 0 1.0938 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2831.552687 0 1.0938 239 | 0/8 11 h-lim-p 1.3856 20.0000 0.0000 2831.552687 0 1.2124 259 | 0/8 12 h-lim-p 0.8680 20.0000 0.0000 2831.552687 0 0.8680 279 | 0/8 13 h-lim-p 0.0016 13.2623 0.0071 2831.552687 0 0.0000 304 | 0/8 14 h-lim-p 0.0005 20.0000 0.0003 2831.552687 0 0.0000 328 | 0/8 15 h-lim-p 0.0004 20.0000 0.0000 2831.552687 0 0.0000 363 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 2831.552687 0 0.0000 387 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 2831.552687 0 0.0000 447 | 0/8 19 h-lim-p 0.0000 20.0000 0.0009 .. | 0/8 20 h-lim-p 0.0000 20.0000 0.0002 | 0/8 21 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -2831.552687 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2831.552687 Node 7: lnL = -2831.552687 Node 8: lnL = -2831.552687 Node 9: lnL = -2831.552687 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 205 Sequential format.. Reading seq # 1: YGL005C_Sbay Reading seq # 2: YGL005C_Scer Reading seq # 3: YGL005C_Skud Reading seq # 4: YGL005C_Smik Reading seq # 5: YGL005C_Spar Sequences read.. Counting patterns.. # site patterns = 96 Counting frequencies.. 120 bytes for distance 15360 bytes for lkl0 12288 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.088973 0.095614 0.102678 0.167635 0.105260 0.131570 0.218012 0.236579 lnL0 = -823.735949 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 823.735949 x= 0.08897 0.09561 0.10268 0.16763 0.10526 0.13157 0.21801 0.23658 1 h-lim-p 0.0027 0.0218 7.8780 823.686718 7 0.0016 39 | 0/8 2 h-lim-p 0.0043 0.0869 2.8988 823.678638 5 0.0022 64 | 0/8 3 h-lim-p 0.0075 0.2017 0.8341 823.678085 2 0.0018 81 | 0/8 4 h-lim-p 0.0080 1.5074 0.1828 823.678060 2 0.0016 106 | 0/8 5 h-lim-p 0.0043 3.8510 0.0672 823.678058 2 0.0014 132 | 0/8 6 h-lim-p 0.0073 15.1560 0.0131 823.678058 0 0.0016 153 | 0/8 7 h-lim-p 0.0233 20.0000 0.0009 823.678057 0 0.0204 173 | 0/8 8 h-lim-p 0.0140 20.0000 0.0013 823.678054 0 0.1124 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 823.678054 0 1.0938 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 823.678054 0 1.0938 236 | 0/8 11 h-lim-p 1.6019 20.0000 0.0000 823.678054 0 1.4017 256 | 0/8 12 h-lim-p 1.2564 20.0000 0.0000 823.678054 0 2.5128 277 | 0/8 13 h-lim-p 0.1841 20.0000 0.0000 823.678054 0 0.0000 326 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 823.678054 0 0.0000 358 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -823.678054 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -823.678054 Node 7: lnL = -823.678054 Node 8: lnL = -823.678054 Node 9: lnL = -823.678054 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 317 Sequential format.. Reading seq # 1: YGL010W_Sbay Reading seq # 2: YGL010W_Scer Reading seq # 3: YGL010W_Skud Reading seq # 4: YGL010W_Smik Reading seq # 5: YGL010W_Spar Sequences read.. Counting patterns.. # site patterns = 157 Counting frequencies.. 120 bytes for distance 25120 bytes for lkl0 20096 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.045841 0.157509 0.112969 0.168996 0.040470 0.222766 0.219930 0.200398 lnL0 = -1483.963436 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1483.963436 x= 0.04584 0.15751 0.11297 0.16900 0.04047 0.22277 0.21993 0.20040 1 h-lim-p 0.0013 0.0104 97.1171 1482.538438 8 0.0003 41 | 0/8 2 h-lim-p 0.0007 0.0058 34.2851 1482.115569 6 0.0008 67 | 0/8 3 h-lim-p 0.0037 0.0296 6.8895 1482.083878 5 0.0014 89 | 0/8 4 h-lim-p 0.0042 0.1740 2.2609 1482.081363 4 0.0011 110 | 0/8 5 h-lim-p 0.0059 0.6063 0.4112 1482.081250 0 0.0013 123 | 0/8 6 h-lim-p 0.0036 2.0289 0.1498 1482.081238 2 0.0011 148 | 0/8 7 h-lim-p 0.0392 20.0000 0.0044 1482.081221 0 0.0588 168 | 0/8 8 h-lim-p 0.0180 6.0598 0.0143 1482.080875 0 0.0359 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1482.080863 1 0.9961 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1482.080863 0 1.0938 231 | 0/8 11 h-lim-p 1.2558 20.0000 0.0000 1482.080863 0 1.0988 251 | 0/8 12 h-lim-p 0.2611 20.0000 0.0000 1482.080863 0 0.1305 271 | 0/8 13 h-lim-p 0.0282 20.0000 0.0001 1482.080863 0 0.0004 296 | 0/8 14 h-lim-p 0.0004 20.0000 0.0002 1482.080863 0 0.0000 325 | 0/8 15 h-lim-p 0.0004 20.0000 0.0000 1482.080863 0 0.0000 356 Out... lnL = -1482.080863 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1482.080863 Node 7: lnL = -1482.080863 Node 8: lnL = -1482.080863 Node 9: lnL = -1482.080863 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 401 Sequential format.. Reading seq # 1: YGL011C_Sbay Reading seq # 2: YGL011C_Scer Reading seq # 3: YGL011C_Skud Reading seq # 4: YGL011C_Smik Reading seq # 5: YGL011C_Spar Sequences read.. Counting patterns.. # site patterns = 162 Counting frequencies.. 120 bytes for distance 25920 bytes for lkl0 20736 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.047168 0.149541 0.074021 0.168984 0.040482 0.242767 0.292903 0.205120 lnL0 = -1616.068698 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1616.068698 x= 0.04717 0.14954 0.07402 0.16898 0.04048 0.24277 0.29290 0.20512 1 h-lim-p 0.0139 0.1238 48.1473 1615.638139 2 0.0004 30 | 0/8 2 h-lim-p 0.0009 0.0126 22.8898 1615.444158 3 0.0009 48 | 0/8 3 h-lim-p 0.0014 0.0112 9.8175 1615.400420 4 0.0011 68 | 0/8 4 h-lim-p 0.0047 0.0507 2.2932 1615.398031 3 0.0010 87 | 0/8 5 h-lim-p 0.0123 3.6941 0.1824 1615.398003 2 0.0016 105 | 0/8 6 h-lim-p 0.0043 1.9385 0.0684 1615.397999 2 0.0014 131 | 0/8 7 h-lim-p 0.0064 18.3409 0.0153 1615.397988 0 0.0127 152 | 0/8 8 h-lim-p 0.0374 11.5217 0.0052 1615.397471 0 0.1497 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1615.397442 2 0.9961 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1615.397442 0 1.0938 218 | 0/8 11 h-lim-p 1.4112 20.0000 0.0000 1615.397442 0 5.6450 240 | 0/8 12 h-lim-p 0.2487 20.0000 0.0002 1615.397442 0 0.2487 260 | 0/8 13 h-lim-p 0.0446 20.0000 0.0010 1615.397442 0 0.0003 286 | 0/8 14 h-lim-p 0.0001 20.0000 0.0028 1615.397442 0 0.0000 307 | 0/8 15 h-lim-p 0.0011 20.0000 0.0001 1615.397442 0 0.0000 344 | 0/8 16 h-lim-p 0.0000 20.0000 0.0006 | 0/8 17 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -1615.397442 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1615.397442 Node 7: lnL = -1615.397442 Node 8: lnL = -1615.397442 Node 9: lnL = -1615.397442 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 752 Sequential format.. Reading seq # 1: YGL015C_Sbay Reading seq # 2: YGL015C_Scer Reading seq # 3: YGL015C_Skud Reading seq # 4: YGL015C_Smik Reading seq # 5: YGL015C_Spar Sequences read.. Counting patterns.. # site patterns = 212 Counting frequencies.. 120 bytes for distance 33920 bytes for lkl0 27136 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.046948 0.063881 0.044927 0.092039 0.064929 0.112903 0.152432 0.138293 lnL0 = -2935.489108 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2935.489108 x= 0.04695 0.06388 0.04493 0.09204 0.06493 0.11290 0.15243 0.13829 1 h-lim-p 0.0003 0.0022 206.0784 2932.907479 3 0.0001 29 | 0/8 2 h-lim-p 0.0004 0.0028 50.2953 2932.676553 6 0.0002 54 | 0/8 3 h-lim-p 0.0007 0.0132 13.3789 2932.664563 6 0.0001 78 | 0/8 4 h-lim-p 0.0005 0.0375 3.5509 2932.663541 4 0.0002 100 | 0/8 5 h-lim-p 0.0016 0.4772 0.3994 2932.663515 1 0.0003 115 | 0/8 6 h-lim-p 0.0011 1.3806 0.1261 2932.663513 0 0.0003 136 | 0/8 7 h-lim-p 0.0019 8.7245 0.0181 2932.663510 0 0.0019 156 | 0/8 8 h-lim-p 0.0072 20.0000 0.0047 2932.662279 0 0.1148 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2932.662245 2 0.9961 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2932.662245 0 1.0938 224 | 0/8 11 h-lim-p 1.3398 20.0000 0.0000 2932.662245 0 2.6796 245 | 0/8 12 h-lim-p 1.1551 20.0000 0.0001 2932.662245 0 0.0002 276 | 0/8 13 h-lim-p 0.0004 20.0000 0.0000 2932.662245 0 0.0001 297 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 2932.662245 0 0.0000 318 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 2932.662245 0 0.0000 349 Out... lnL = -2932.662245 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2932.662245 Node 7: lnL = -2932.662245 Node 8: lnL = -2932.662245 Node 9: lnL = -2932.662245 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 334 Sequential format.. Reading seq # 1: YGL016W_Sbay Reading seq # 2: YGL016W_Scer Reading seq # 3: YGL016W_Skud Reading seq # 4: YGL016W_Smik Reading seq # 5: YGL016W_Spar Sequences read.. Counting patterns.. # site patterns = 124 Counting frequencies.. 120 bytes for distance 19840 bytes for lkl0 15872 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.066494 0.072659 0.075115 0.128235 0.075557 0.212928 0.105665 0.184409 lnL0 = -1405.745916 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1405.745916 x= 0.06649 0.07266 0.07511 0.12824 0.07556 0.21293 0.10566 0.18441 1 h-lim-p 0.0032 0.0253 47.7247 1405.226725 8 0.0005 45 | 0/8 2 h-lim-p 0.0014 0.0109 12.4259 1405.176623 5 0.0007 69 | 0/8 3 h-lim-p 0.0025 0.0569 3.4173 1405.174250 4 0.0004 91 | 0/8 4 h-lim-p 0.0014 0.2580 1.0738 1405.173774 3 0.0009 111 | 0/8 5 h-lim-p 0.0030 0.7120 0.3284 1405.173740 2 0.0007 128 | 0/8 6 h-lim-p 0.0070 4.2795 0.0325 1405.173739 0 0.0009 150 | 0/8 7 h-lim-p 0.0089 20.0000 0.0032 1405.173738 0 0.0134 170 | 0/8 8 h-lim-p 0.0073 20.0000 0.0059 1405.173647 0 0.0581 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1405.173647 0 1.0938 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1405.173647 0 1.0938 233 | 0/8 11 h-lim-p 1.1919 20.0000 0.0000 1405.173647 0 3.5758 254 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1405.173647 0 0.3125 276 | 0/8 13 h-lim-p 0.0414 20.0000 0.0000 1405.173647 0 0.0052 298 | 0/8 14 h-lim-p 0.0017 20.0000 0.0001 1405.173647 0 0.0000 330 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 1405.173647 0 0.0000 351 Out... lnL = -1405.173647 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1405.173647 Node 7: lnL = -1405.173647 Node 8: lnL = -1405.173647 Node 9: lnL = -1405.173647 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 207 Sequential format.. Reading seq # 1: YGL017W_Sbay Reading seq # 2: YGL017W_Scer Reading seq # 3: YGL017W_Skud Reading seq # 4: YGL017W_Smik Reading seq # 5: YGL017W_Spar Sequences read.. Counting patterns.. # site patterns = 111 Counting frequencies.. 120 bytes for distance 17760 bytes for lkl0 14208 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.058016 0.143635 0.089769 0.128721 0.090672 0.168036 0.211147 0.201165 lnL0 = -908.073465 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 908.073465 x= 0.05802 0.14363 0.08977 0.12872 0.09067 0.16804 0.21115 0.20116 1 h-lim-p 0.0005 0.0040 40.1092 907.124757 0 0.0010 23 | 0/8 2 h-lim-p 0.0028 0.0223 11.6402 907.028184 8 0.0015 55 | 0/8 3 h-lim-p 0.0027 0.0403 6.7129 907.007883 5 0.0012 76 | 0/8 4 h-lim-p 0.0027 0.1067 2.8752 907.004122 3 0.0011 94 | 0/8 5 h-lim-p 0.0053 0.3780 0.6146 907.003604 2 0.0023 110 | 0/8 6 h-lim-p 0.0523 20.0000 0.0272 906.991873 0 0.2091 132 | 0/8 7 h-lim-p 0.0034 0.0857 1.6977 906.962993 0 0.0067 153 | 0/8 8 h-lim-p 0.0074 0.3180 1.5368 906.960178 6 0.0022 182 | 0/8 9 h-lim-p 1.5704 20.0000 0.0022 906.958181 5 0.9845 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 906.958177 1 0.9961 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 906.958177 0 1.0938 249 | 0/8 12 h-lim-p 1.6828 20.0000 0.0000 906.958177 0 1.6828 269 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 906.958177 0 0.0000 305 Out... lnL = -906.958177 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -906.958177 Node 7: lnL = -906.958177 Node 8: lnL = -906.958177 Node 9: lnL = -906.958177 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 203 Sequential format.. Reading seq # 1: YGL018C_Sbay Reading seq # 2: YGL018C_Scer Reading seq # 3: YGL018C_Skud Reading seq # 4: YGL018C_Smik Reading seq # 5: YGL018C_Spar Sequences read.. Counting patterns.. # site patterns = 113 Counting frequencies.. 120 bytes for distance 18080 bytes for lkl0 14464 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.042307 0.146591 0.096564 0.119856 0.099538 0.165944 0.221489 0.184308 lnL0 = -905.163697 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 905.163697 x= 0.04231 0.14659 0.09656 0.11986 0.09954 0.16594 0.22149 0.18431 1 h-lim-p 0.0006 0.0049 41.2072 904.094068 0 0.0012 23 | 0/8 2 h-lim-p 0.0021 0.0169 12.4453 903.983800 7 0.0015 50 | 0/8 3 h-lim-p 0.0024 0.0401 7.8676 903.962956 4 0.0009 70 | 0/8 4 h-lim-p 0.0031 0.1131 2.3398 903.959767 4 0.0013 89 | 0/8 5 h-lim-p 0.0066 0.5925 0.4695 903.959507 4 0.0023 110 | 0/8 6 h-lim-p 0.0314 8.1947 0.0350 903.959359 3 0.0207 138 | 0/8 7 h-lim-p 0.0058 4.0102 0.1251 903.958026 0 0.0174 159 | 0/8 8 h-lim-p 0.0043 0.4026 0.5007 903.952445 0 0.0087 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 903.952434 1 0.9961 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 903.952434 0 1.0938 222 | 0/8 11 h-lim-p 1.5146 20.0000 0.0000 903.952434 0 1.5146 242 | 0/8 12 h-lim-p 1.2766 20.0000 0.0000 903.952434 0 0.0100 268 | 0/8 13 h-lim-p 0.0007 20.0000 0.0001 903.952434 0 0.0000 306 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 903.952434 0 0.0000 332 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 903.952434 0 0.0000 352 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 903.952434 0 0.0000 372 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 903.952434 0 0.0000 405 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 903.952434 0 0.0000 436 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -903.952434 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -903.952434 Node 7: lnL = -903.952434 Node 8: lnL = -903.952434 Node 9: lnL = -903.952434 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 295 Sequential format.. Reading seq # 1: YGL019W_Sbay Reading seq # 2: YGL019W_Scer Reading seq # 3: YGL019W_Skud Reading seq # 4: YGL019W_Smik Reading seq # 5: YGL019W_Spar Sequences read.. Counting patterns.. # site patterns = 98 Counting frequencies.. 120 bytes for distance 15680 bytes for lkl0 12544 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.041548 0.062742 0.045333 0.067511 0.042674 0.105835 0.099782 0.116974 lnL0 = -1072.406500 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1072.406500 x= 0.04155 0.06274 0.04533 0.06751 0.04267 0.10583 0.09978 0.11697 1 h-lim-p 0.0003 0.0023 54.4165 1071.994354 5 0.0003 32 | 0/8 2 h-lim-p 0.0013 0.0104 8.5968 1071.979625 6 0.0004 59 | 0/8 3 h-lim-p 0.0017 0.0791 2.0231 1071.978618 5 0.0005 84 | 0/8 4 h-lim-p 0.0030 0.3262 0.3523 1071.978592 3 0.0004 106 | 0/8 5 h-lim-p 0.0010 1.6027 0.1494 1071.978590 0 0.0002 127 | 0/8 6 h-lim-p 0.0009 5.9438 0.0357 1071.978590 0 0.0005 147 | 0/8 7 h-lim-p 0.0033 15.9686 0.0051 1071.978590 0 0.0007 168 | 0/8 8 h-lim-p 0.0412 20.0000 0.0001 1071.978583 0 0.6587 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1071.978583 0 1.0938 212 | 0/8 10 h-lim-p 1.8042 20.0000 0.0000 1071.978583 0 0.7893 232 | 0/8 11 h-lim-p 0.5024 20.0000 0.0000 1071.978583 0 0.0039 258 | 0/8 12 h-lim-p 0.0010 20.0000 0.0001 1071.978583 0 0.0003 279 | 0/8 13 h-lim-p 0.0002 20.0000 0.0001 1071.978583 0 0.0000 316 | 0/8 14 h-lim-p 0.0000 20.0000 0.0005 1071.978583 0 0.0000 348 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 | 0/8 16 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -1071.978583 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1071.978583 Node 7: lnL = -1071.978583 Node 8: lnL = -1071.978583 Node 9: lnL = -1071.978583 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 295 Sequential format.. Reading seq # 1: YGL020C_Sbay Reading seq # 2: YGL020C_Scer Reading seq # 3: YGL020C_Skud Reading seq # 4: YGL020C_Smik Reading seq # 5: YGL020C_Spar Sequences read.. Counting patterns.. # site patterns = 88 Counting frequencies.. 120 bytes for distance 14080 bytes for lkl0 11264 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.054430 0.032129 0.037536 0.066156 0.044029 0.118393 0.093324 0.126395 lnL0 = -1058.038133 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1058.038133 x= 0.05443 0.03213 0.03754 0.06616 0.04403 0.11839 0.09332 0.12639 1 h-lim-p 0.0004 0.0035 61.0498 1057.622570 6 0.0002 35 | 0/8 2 h-lim-p 0.0008 0.0062 16.2131 1057.576762 2 0.0004 51 | 0/8 3 h-lim-p 0.0007 0.0219 8.1093 1057.568798 3 0.0003 69 | 0/8 4 h-lim-p 0.0009 0.0320 2.8613 1057.567633 4 0.0003 89 | 0/8 5 h-lim-p 0.0030 0.1669 0.3113 1057.567614 2 0.0004 107 | 0/8 6 h-lim-p 0.0016 2.3676 0.0794 1057.567613 0 0.0004 128 | 0/8 7 h-lim-p 0.0144 20.0000 0.0022 1057.567611 0 0.0144 148 | 0/8 8 h-lim-p 0.0039 7.1357 0.0079 1057.567528 0 0.0313 171 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1057.567524 1 0.9961 193 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1057.567524 0 1.0938 213 | 0/8 11 h-lim-p 1.1055 20.0000 0.0000 1057.567524 0 8.8437 236 | 0/8 12 h-lim-p 0.2398 20.0000 0.0004 1057.567524 0 0.0262 258 | 0/8 13 h-lim-p 0.0045 20.0000 0.0025 1057.567524 0 0.0045 278 | 0/8 14 h-lim-p 0.0017 12.0513 0.0066 1057.567524 0 0.0000 307 | 0/8 15 h-lim-p 0.0001 20.0000 0.0002 1057.567524 0 0.0000 340 | 0/8 16 h-lim-p 0.0000 20.0000 0.0013 | 0/8 17 h-lim-p 0.0000 20.0000 0.0013 Out... lnL = -1057.567524 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1057.567524 Node 7: lnL = -1057.567524 Node 8: lnL = -1057.567524 Node 9: lnL = -1057.567524 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 326 Sequential format.. Reading seq # 1: YGL021W_Sbay Reading seq # 2: YGL021W_Scer Reading seq # 3: YGL021W_Skud Reading seq # 4: YGL021W_Smik Reading seq # 5: YGL021W_Spar Sequences read.. Counting patterns.. # site patterns = 124 Counting frequencies.. 120 bytes for distance 19840 bytes for lkl0 15872 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.042825 0.053249 0.055009 0.046270 0.048794 0.154940 0.143048 0.129018 lnL0 = -1200.852690 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1200.852690 x= 0.04282 0.05325 0.05501 0.04627 0.04879 0.15494 0.14305 0.12902 1 h-lim-p 0.0001 0.0006 160.8601 1196.548014 0 0.0004 24 | 0/8 2 h-lim-p 0.0002 0.0016 16.5392 1196.510107 0 0.0003 36 | 0/8 3 h-lim-p 0.0002 0.0170 20.7318 1196.488622 4 0.0002 56 | 0/8 4 h-lim-p 0.0024 0.1026 1.6164 1196.487658 5 0.0007 79 | 0/8 5 h-lim-p 0.0019 0.4841 0.5609 1196.487131 4 0.0015 99 | 0/8 6 h-lim-p 0.0048 0.5498 0.1726 1196.475946 0 0.0193 121 | 0/8 7 h-lim-p 0.0021 0.0864 1.6281 1196.312385 0 0.0082 143 | 0/8 8 h-lim-p 0.0016 0.0238 8.3868 1196.253834 6 0.0011 170 | 0/8 9 h-lim-p 2.5000 20.0000 0.0009 1196.251627 2 1.1719 186 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 1196.251555 2 0.9961 210 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1196.251555 0 1.0938 230 | 0/8 12 h-lim-p 2.3147 20.0000 0.0000 1196.251555 0 1.1574 250 | 0/8 13 h-lim-p 1.1039 20.0000 0.0000 1196.251555 0 0.2415 271 | 0/8 14 h-lim-p 0.0927 20.0000 0.0000 1196.251555 0 0.0463 291 | 0/8 15 h-lim-p 0.0219 20.0000 0.0001 1196.251555 0 0.0048 312 | 0/8 16 h-lim-p 0.0026 20.0000 0.0001 1196.251555 0 0.0000 353 | 0/8 17 h-lim-p 0.0000 20.0000 0.0007 | 0/8 18 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -1196.251555 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1196.251555 Node 7: lnL = -1196.251555 Node 8: lnL = -1196.251555 Node 9: lnL = -1196.251555 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 245 Sequential format.. Reading seq # 1: YGL026C_Sbay Reading seq # 2: YGL026C_Scer Reading seq # 3: YGL026C_Skud Reading seq # 4: YGL026C_Smik Reading seq # 5: YGL026C_Spar Sequences read.. Counting patterns.. # site patterns = 112 Counting frequencies.. 120 bytes for distance 17920 bytes for lkl0 14336 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.056366 0.093902 0.035810 0.067773 0.030086 0.263082 0.152188 0.166671 lnL0 = -977.791355 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 977.791355 x= 0.05637 0.09390 0.03581 0.06777 0.03009 0.26308 0.15219 0.16667 1 h-lim-p 0.0001 0.0012 58.3815 977.232568 0 0.0003 23 | 0/8 2 h-lim-p 0.0010 1.5206 16.8360 977.206190 6 0.0002 47 | 0/8 3 h-lim-p 0.0010 0.0535 3.5688 977.200996 5 0.0009 68 | 0/8 4 h-lim-p 0.0016 0.0779 1.8982 977.199931 3 0.0007 86 | 0/8 5 h-lim-p 0.0018 0.2127 0.7805 977.199621 3 0.0012 106 | 0/8 6 h-lim-p 0.0046 1.1796 0.1971 977.199535 2 0.0024 131 | 0/8 7 h-lim-p 0.0098 2.4824 0.0490 977.197961 0 0.0392 153 | 0/8 8 h-lim-p 0.0082 0.3238 0.2354 977.179689 0 0.0163 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 977.179389 3 1.0449 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 977.179389 0 1.0938 220 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 977.179389 0 2.1875 240 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 977.179389 0 0.3125 262 | 0/8 13 h-lim-p 0.0685 20.0000 0.0000 977.179389 0 0.0021 286 | 0/8 14 h-lim-p 0.0010 20.0000 0.0000 977.179389 0 0.0010 306 | 0/8 15 h-lim-p 0.0007 20.0000 0.0000 977.179389 0 0.0000 340 | 0/8 16 h-lim-p 0.0000 20.0000 0.0051 | 0/8 17 h-lim-p 0.0000 20.0000 0.0051 Out... lnL = -977.179389 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -977.179389 Node 7: lnL = -977.179389 Node 8: lnL = -977.179389 Node 9: lnL = -977.179389 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 297 Sequential format.. Reading seq # 1: YGL027C_Sbay Reading seq # 2: YGL027C_Scer Reading seq # 3: YGL027C_Skud Reading seq # 4: YGL027C_Smik Reading seq # 5: YGL027C_Spar Sequences read.. Counting patterns.. # site patterns = 128 Counting frequencies.. 120 bytes for distance 20480 bytes for lkl0 16384 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.109808 0.035950 0.081289 0.115143 0.046820 0.217775 0.163124 0.235965 lnL0 = -1234.766165 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1234.766165 x= 0.10981 0.03595 0.08129 0.11514 0.04682 0.21777 0.16312 0.23597 1 h-lim-p 0.0066 0.0525 22.8433 1234.604437 4 0.0006 32 | 0/8 2 h-lim-p 0.0008 0.0083 17.5933 1234.536784 7 0.0006 58 | 0/8 3 h-lim-p 0.0015 0.0150 7.1695 1234.527454 6 0.0005 87 | 0/8 4 h-lim-p 0.0126 0.7800 0.2601 1234.527413 2 0.0012 105 | 0/8 5 h-lim-p 0.0078 5.6830 0.0408 1234.527413 0 0.0008 127 | 0/8 6 h-lim-p 0.0052 17.0079 0.0067 1234.527412 0 0.0052 147 | 0/8 7 h-lim-p 0.0053 15.5430 0.0065 1234.527408 0 0.0107 168 | 0/8 8 h-lim-p 0.0026 20.0000 0.0272 1234.527340 0 0.0102 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1234.527338 1 0.9961 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1234.527338 0 0.0024 241 | 0/8 11 h-lim-p 0.0008 20.0000 0.0000 1234.527338 0 0.0000 277 | 0/8 12 h-lim-p 0.0000 20.0000 0.0007 1234.527338 0 0.0000 301 | 0/8 13 h-lim-p 0.0000 20.0000 0.0002 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0007 | 0/8 15 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -1234.527338 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1234.527338 Node 7: lnL = -1234.527338 Node 8: lnL = -1234.527338 Node 9: lnL = -1234.527338 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 781 Sequential format.. Reading seq # 1: YGL028C_Sbay Reading seq # 2: YGL028C_Scer Reading seq # 3: YGL028C_Skud Reading seq # 4: YGL028C_Smik Reading seq # 5: YGL028C_Spar Sequences read.. Counting patterns.. # site patterns = 263 Counting frequencies.. 120 bytes for distance 42080 bytes for lkl0 33664 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.061637 0.044022 0.075601 0.108052 0.085197 0.190479 0.223139 0.183928 lnL0 = -3395.498699 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3395.498699 x= 0.06164 0.04402 0.07560 0.10805 0.08520 0.19048 0.22314 0.18393 1 h-lim-p 0.0035 0.0281 110.3763 3394.574065 8 0.0002 44 | 0/8 2 h-lim-p 0.0008 0.0122 21.0885 3394.481331 4 0.0004 65 | 0/8 3 h-lim-p 0.0008 0.0250 11.4100 3394.469724 5 0.0002 90 | 0/8 4 h-lim-p 0.0012 0.0598 2.0613 3394.469253 3 0.0002 109 | 0/8 5 h-lim-p 0.0015 0.6540 0.3156 3394.469238 1 0.0003 124 | 0/8 6 h-lim-p 0.0041 11.4963 0.0232 3394.469238 0 0.0005 146 | 0/8 7 h-lim-p 0.0037 20.0000 0.0032 3394.469238 0 0.0033 166 | 0/8 8 h-lim-p 0.0059 20.0000 0.0018 3394.469183 0 0.0940 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3394.469181 0 1.0938 210 | 0/8 10 h-lim-p 1.7850 20.0000 0.0000 3394.469181 0 0.8925 230 | 0/8 11 h-lim-p 0.9380 20.0000 0.0000 3394.469181 0 0.0009 259 | 0/8 12 h-lim-p 0.0001 20.0000 0.0002 3394.469181 0 0.0000 294 | 0/8 13 h-lim-p 0.0000 20.0000 0.0014 | 0/8 14 h-lim-p 0.0000 20.0000 0.0014 Out... lnL = -3394.469181 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3394.469181 Node 7: lnL = -3394.469181 Node 8: lnL = -3394.469181 Node 9: lnL = -3394.469181 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 471 Sequential format.. Reading seq # 1: YGL029W_Sbay Reading seq # 2: YGL029W_Scer Reading seq # 3: YGL029W_Skud Reading seq # 4: YGL029W_Smik Reading seq # 5: YGL029W_Spar Sequences read.. Counting patterns.. # site patterns = 187 Counting frequencies.. 120 bytes for distance 29920 bytes for lkl0 23936 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.042839 0.114326 0.073022 0.111071 0.091419 0.210567 0.173521 0.171005 lnL0 = -2077.369178 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2077.369178 x= 0.04284 0.11433 0.07302 0.11107 0.09142 0.21057 0.17352 0.17101 1 h-lim-p 0.0058 0.0466 68.2471 2076.600028 3 0.0003 31 | 0/8 2 h-lim-p 0.0018 0.0208 12.6894 2076.559650 6 0.0005 58 | 0/8 3 h-lim-p 0.0010 0.0402 6.3715 2076.552112 5 0.0005 79 | 0/8 4 h-lim-p 0.0030 0.2455 0.9600 2076.551831 1 0.0007 94 | 0/8 5 h-lim-p 0.0034 1.1505 0.1887 2076.551821 2 0.0005 120 | 0/8 6 h-lim-p 0.0118 10.8051 0.0086 2076.551814 1 0.0094 142 | 0/8 7 h-lim-p 0.0040 20.0000 0.0203 2076.551340 0 0.0318 165 | 0/8 8 h-lim-p 0.0014 0.8499 0.4603 2076.551068 2 0.0013 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2076.551060 1 0.9961 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2076.551060 0 1.0938 231 | 0/8 11 h-lim-p 0.7489 20.0000 0.0000 2076.551060 0 0.0007 260 | 0/8 12 h-lim-p 0.0002 20.0000 0.0001 2076.551060 0 0.0000 294 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -2076.551060 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2076.551060 Node 7: lnL = -2076.551060 Node 8: lnL = -2076.551060 Node 9: lnL = -2076.551060 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 824 Sequential format.. Reading seq # 1: YGL031C_Sbay Reading seq # 2: YGL031C_Scer Reading seq # 3: YGL031C_Skud Reading seq # 4: YGL031C_Smik Reading seq # 5: YGL031C_Spar Sequences read.. Counting patterns.. # site patterns = 276 Counting frequencies.. 120 bytes for distance 44160 bytes for lkl0 35328 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.087759 0.075467 0.065893 0.141019 0.081512 0.207928 0.209609 0.217135 lnL0 = -3812.770665 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3812.770665 x= 0.08776 0.07547 0.06589 0.14102 0.08151 0.20793 0.20961 0.21714 1 h-lim-p 0.0003 0.0023 100.8131 3811.733991 7 0.0002 39 | 0/8 2 h-lim-p 0.0007 0.0055 19.3338 3811.685206 4 0.0003 59 | 0/8 3 h-lim-p 0.0009 0.0945 5.6748 3811.681863 3 0.0002 78 | 0/8 4 h-lim-p 0.0004 0.0999 3.2414 3811.680574 3 0.0003 96 | 0/8 5 h-lim-p 0.0028 0.7492 0.3633 3811.680543 2 0.0005 114 | 0/8 6 h-lim-p 0.0028 5.5647 0.0585 3811.680543 0 0.0006 135 | 0/8 7 h-lim-p 0.0029 13.0507 0.0126 3811.680543 0 0.0006 156 | 0/8 8 h-lim-p 0.1011 20.0000 0.0001 3811.680533 0 0.8088 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3811.680532 0 1.0938 199 | 0/8 10 h-lim-p 1.4558 20.0000 0.0000 3811.680532 0 1.2738 219 | 0/8 11 h-lim-p 1.3252 20.0000 0.0000 3811.680532 0 1.1595 239 | 0/8 12 h-lim-p 0.2740 20.0000 0.0001 3811.680532 0 0.0000 273 | 0/8 13 h-lim-p 0.0002 20.0000 0.0000 3811.680532 0 0.0000 306 Out... lnL = -3811.680532 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3811.680532 Node 7: lnL = -3811.680532 Node 8: lnL = -3811.680532 Node 9: lnL = -3811.680532 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 683 Sequential format.. Reading seq # 1: YGL032C_Sbay Reading seq # 2: YGL032C_Scer Reading seq # 3: YGL032C_Skud Reading seq # 4: YGL032C_Smik Reading seq # 5: YGL032C_Spar Sequences read.. Counting patterns.. # site patterns = 271 Counting frequencies.. 120 bytes for distance 43360 bytes for lkl0 34688 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.054409 0.096618 0.088837 0.128636 0.113215 0.166640 0.160413 0.174756 lnL0 = -3065.354484 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3065.354484 x= 0.05441 0.09662 0.08884 0.12864 0.11321 0.16664 0.16041 0.17476 1 h-lim-p 0.0034 0.2486 133.8352 3063.150616 8 0.0003 46 | 0/8 2 h-lim-p 0.0015 0.0122 20.6761 3063.065331 5 0.0004 69 | 0/8 3 h-lim-p 0.0011 0.0313 7.6154 3063.056555 6 0.0003 96 | 0/8 4 h-lim-p 0.0015 0.2004 1.7365 3063.056017 2 0.0004 113 | 0/8 5 h-lim-p 0.0019 0.7706 0.3656 3063.055991 1 0.0004 128 | 0/8 6 h-lim-p 0.0024 3.3942 0.0633 3063.055990 0 0.0006 149 | 0/8 7 h-lim-p 0.0218 20.0000 0.0017 3063.055962 0 0.0872 171 | 0/8 8 h-lim-p 0.0015 8.1524 0.0970 3063.055669 0 0.0062 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3063.055645 1 0.9961 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3063.055645 0 1.0938 235 | 0/8 11 h-lim-p 0.9321 20.0000 0.0000 3063.055645 0 0.9321 255 | 0/8 12 h-lim-p 0.0069 20.0000 0.0033 3063.055645 0 0.0002 279 | 0/8 13 h-lim-p 0.0001 5.8807 0.0140 3063.055645 0 0.0000 314 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 3063.055645 0 0.0000 348 Out... lnL = -3063.055645 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3063.055645 Node 7: lnL = -3063.055645 Node 8: lnL = -3063.055645 Node 9: lnL = -3063.055645 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 167 Sequential format.. Reading seq # 1: YGL035C_Sbay Reading seq # 2: YGL035C_Scer Reading seq # 3: YGL035C_Skud Reading seq # 4: YGL035C_Smik Reading seq # 5: YGL035C_Spar Sequences read.. Counting patterns.. # site patterns = 69 Counting frequencies.. 120 bytes for distance 11040 bytes for lkl0 8832 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.096822 0.046847 0.013742 0.102231 0.022446 0.195702 0.130511 0.189409 lnL0 = -639.759096 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 639.759096 x= 0.09682 0.04685 0.01374 0.10223 0.02245 0.19570 0.13051 0.18941 1 h-lim-p 0.0023 0.0187 34.7328 639.638615 8 0.0002 42 | 0/8 2 h-lim-p 0.0007 0.0085 10.8052 639.591151 1 0.0009 56 | 0/8 3 h-lim-p 0.0009 0.0075 10.1812 639.580182 6 0.0004 80 | 0/8 4 h-lim-p 0.0008 0.0423 4.4532 639.575243 5 0.0007 101 | 0/8 5 h-lim-p 0.0041 0.5990 0.7435 639.574939 5 0.0011 126 | 0/8 6 h-lim-p 0.0033 0.6756 0.2567 639.574908 3 0.0011 154 | 0/8 7 h-lim-p 0.0212 11.6038 0.0129 639.574907 0 0.0023 176 | 0/8 8 h-lim-p 0.1949 20.0000 0.0002 639.574870 0 0.7797 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 639.574869 0 1.0938 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 639.574869 0 0.5469 239 | 0/8 11 h-lim-p 0.4036 20.0000 0.0000 639.574869 0 0.0000 274 Out... lnL = -639.574869 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -639.574869 Node 7: lnL = -639.574869 Node 8: lnL = -639.574869 Node 9: lnL = -639.574869 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 726 Sequential format.. Reading seq # 1: YGL036W_Sbay Reading seq # 2: YGL036W_Scer Reading seq # 3: YGL036W_Skud Reading seq # 4: YGL036W_Smik Reading seq # 5: YGL036W_Spar Sequences read.. Counting patterns.. # site patterns = 276 Counting frequencies.. 120 bytes for distance 44160 bytes for lkl0 35328 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.035439 0.104454 0.070913 0.105996 0.107066 0.169239 0.231783 0.154792 lnL0 = -3098.953394 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3098.953394 x= 0.03544 0.10445 0.07091 0.10600 0.10707 0.16924 0.23178 0.15479 1 h-lim-p 0.0036 0.9724 132.1244 3097.126686 7 0.0002 41 | 0/8 2 h-lim-p 0.0011 0.0092 17.8162 3097.077421 7 0.0003 69 | 0/8 3 h-lim-p 0.0008 0.0197 7.3193 3097.069042 2 0.0004 85 | 0/8 4 h-lim-p 0.0018 0.1974 1.4480 3097.068705 4 0.0003 107 | 0/8 5 h-lim-p 0.0014 0.7225 0.3457 3097.068675 2 0.0006 123 | 0/8 6 h-lim-p 0.0017 1.9126 0.1107 3097.068673 0 0.0004 144 | 0/8 7 h-lim-p 0.0119 20.0000 0.0035 3097.068672 0 0.0052 164 | 0/8 8 h-lim-p 0.0154 20.0000 0.0012 3097.068623 0 0.1233 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3097.068621 0 1.0938 207 | 0/8 10 h-lim-p 1.6696 20.0000 0.0000 3097.068621 0 1.4609 227 | 0/8 11 h-lim-p 2.2146 20.0000 0.0000 3097.068621 0 0.9689 247 | 0/8 12 h-lim-p 0.4853 20.0000 0.0000 3097.068621 0 0.0227 271 | 0/8 13 h-lim-p 0.0016 20.0000 0.0004 3097.068621 0 0.0000 298 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 3097.068621 0 0.0000 327 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -3097.068621 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3097.068621 Node 7: lnL = -3097.068621 Node 8: lnL = -3097.068621 Node 9: lnL = -3097.068621 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 738 Sequential format.. Reading seq # 1: YGL037C_Sbay Reading seq # 2: YGL037C_Scer Reading seq # 3: YGL037C_Skud Reading seq # 4: YGL037C_Smik Reading seq # 5: YGL037C_Spar Sequences read.. Counting patterns.. # site patterns = 270 Counting frequencies.. 120 bytes for distance 43200 bytes for lkl0 34560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.068991 0.024504 0.064793 0.095388 0.115623 0.160203 0.250784 0.181535 lnL0 = -3100.306491 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3100.306491 x= 0.06899 0.02450 0.06479 0.09539 0.11562 0.16020 0.25078 0.18154 1 h-lim-p 0.0009 0.0080 267.9404 3095.221914 9 0.0002 45 | 0/8 2 h-lim-p 0.0005 0.0041 38.0006 3094.980321 7 0.0003 72 | 0/8 3 h-lim-p 0.0014 0.0264 9.0550 3094.969329 3 0.0003 91 | 0/8 4 h-lim-p 0.0007 0.0601 3.4450 3094.967539 2 0.0003 107 | 0/8 5 h-lim-p 0.0018 0.4567 0.6742 3094.967435 3 0.0005 126 | 0/8 6 h-lim-p 0.0013 1.3251 0.2435 3094.967422 1 0.0005 148 | 0/8 7 h-lim-p 0.0053 4.9821 0.0243 3094.967421 0 0.0012 169 | 0/8 8 h-lim-p 0.0349 20.0000 0.0008 3094.966898 0 0.5590 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3094.966889 1 0.9961 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3094.966889 0 0.2734 237 | 0/8 11 h-lim-p 0.1275 20.0000 0.0000 3094.966889 0 0.0239 259 | 0/8 12 h-lim-p 0.0118 20.0000 0.0001 3094.966889 0 0.0000 302 | 0/8 13 h-lim-p 0.0000 20.0000 0.0017 3094.966889 0 0.0000 329 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0017 | 0/8 16 h-lim-p 0.0000 20.0000 0.0017 Out... lnL = -3094.966889 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3094.966889 Node 7: lnL = -3094.966889 Node 8: lnL = -3094.966889 Node 9: lnL = -3094.966889 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 529 Sequential format.. Reading seq # 1: YGL038C_Sbay Reading seq # 2: YGL038C_Scer Reading seq # 3: YGL038C_Skud Reading seq # 4: YGL038C_Smik Reading seq # 5: YGL038C_Spar Sequences read.. Counting patterns.. # site patterns = 180 Counting frequencies.. 120 bytes for distance 28800 bytes for lkl0 23040 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.084065 0.105580 0.064151 0.102368 0.054623 0.169580 0.137167 0.195670 lnL0 = -2171.392097 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2171.392097 x= 0.08407 0.10558 0.06415 0.10237 0.05462 0.16958 0.13717 0.19567 1 h-lim-p 0.0001 0.0012 74.5122 2170.727024 0 0.0003 23 | 0/8 2 h-lim-p 0.0009 0.0320 22.6861 2170.684488 3 0.0002 42 | 0/8 3 h-lim-p 0.0008 0.0338 5.5278 2170.678308 6 0.0004 70 | 0/8 4 h-lim-p 0.0015 0.1204 1.5665 2170.677888 2 0.0004 87 | 0/8 5 h-lim-p 0.0039 1.2117 0.1433 2170.677849 2 0.0015 103 | 0/8 6 h-lim-p 0.0049 4.2853 0.0437 2170.676898 0 0.0197 125 | 0/8 7 h-lim-p 0.0019 0.4274 0.4604 2170.667415 0 0.0075 147 | 0/8 8 h-lim-p 0.0012 0.0949 2.8484 2170.662416 5 0.0007 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0008 2170.661484 3 1.0004 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2170.661484 0 1.0938 219 | 0/8 11 h-lim-p 1.3245 20.0000 0.0000 2170.661484 0 1.1589 239 | 0/8 12 h-lim-p 1.2228 20.0000 0.0000 2170.661484 0 2.4456 260 | 0/8 13 h-lim-p 0.3011 20.0000 0.0001 2170.661484 0 0.2634 280 | 0/8 14 h-lim-p 0.0398 20.0000 0.0006 2170.661484 0 0.0050 302 | 0/8 15 h-lim-p 0.0016 20.0000 0.0017 2170.661484 0 0.0001 325 | 0/8 16 h-lim-p 0.0004 20.0000 0.0005 2170.661484 0 0.0004 345 | 0/8 17 h-lim-p 0.0002 20.0000 0.0009 2170.661484 0 0.0000 368 | 0/8 18 h-lim-p 0.0003 20.0000 0.0000 2170.661484 0 0.0000 401 | 0/8 19 h-lim-p 0.0000 20.0000 0.0005 | 0/8 20 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -2170.661484 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2170.661484 Node 7: lnL = -2170.661484 Node 8: lnL = -2170.661484 Node 9: lnL = -2170.661484 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 873 Sequential format.. Reading seq # 1: YGL039W_Sbay Reading seq # 2: YGL039W_Scer Reading seq # 3: YGL039W_Skud Reading seq # 4: YGL039W_Smik Reading seq # 5: YGL039W_Spar Sequences read.. Counting patterns.. # site patterns = 398 Counting frequencies.. 120 bytes for distance 63680 bytes for lkl0 50944 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.313208 0.099535 0.022077 0.179992 0.123590 0.329584 0.317096 0.534676 lnL0 = -4382.912510 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4382.912510 x= 0.31321 0.09953 0.02208 0.17999 0.12359 0.32958 0.31710 0.53468 1 h-lim-p 0.0007 0.0055 197.1621 4379.245711 6 0.0002 36 | 0/8 2 h-lim-p 0.0004 0.0035 58.4243 4378.349332 0 0.0006 48 | 0/8 3 h-lim-p 0.0007 0.0078 55.2110 4377.883307 8 0.0005 79 | 0/8 4 h-lim-p 0.0015 0.0213 18.7483 4377.780330 4 0.0007 99 | 0/8 5 h-lim-p 0.0016 0.0710 8.6504 4377.742249 3 0.0013 117 | 0/8 6 h-lim-p 0.0047 0.1494 2.4271 4377.740547 4 0.0006 139 | 0/8 7 h-lim-p 0.0033 1.1151 0.4705 4377.739990 1 0.0041 153 | 0/8 8 h-lim-p 0.2643 20.0000 0.0073 4377.708008 0 0.7929 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0012 4377.706886 2 1.3159 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 4377.706838 0 1.2500 219 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4377.706838 0 1.0938 239 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4377.706838 0 1.0938 259 | 0/8 13 h-lim-p 1.2677 20.0000 0.0000 4377.706838 0 1.1092 279 | 0/8 14 h-lim-p 0.5921 20.0000 0.0000 4377.706838 0 0.2961 299 | 0/8 15 h-lim-p 0.0261 20.0000 0.0000 4377.706838 0 0.0523 320 | 0/8 16 h-lim-p 0.0136 20.0000 0.0002 4377.706838 0 0.0000 359 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 4377.706838 0 0.0000 382 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 4377.706838 0 0.0000 407 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 20 h-lim-p 0.0000 20.0000 0.0000 4377.706838 0 0.0000 461 | 0/8 21 h-lim-p 0.0000 20.0000 0.0000 4377.706838 0 0.0000 496 | 0/8 22 h-lim-p 0.0000 20.0000 0.0000 | 0/8 23 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -4377.706838 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4377.706838 Node 7: lnL = -4377.706838 Node 8: lnL = -4377.706838 Node 9: lnL = -4377.706838 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 861 Sequential format.. Reading seq # 1: YGL040C_Sbay Reading seq # 2: YGL040C_Scer Reading seq # 3: YGL040C_Skud Reading seq # 4: YGL040C_Smik Reading seq # 5: YGL040C_Spar Sequences read.. Counting patterns.. # site patterns = 367 Counting frequencies.. 120 bytes for distance 58720 bytes for lkl0 46976 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.041813 0.265502 0.184017 0.134728 0.132050 0.336485 0.229504 0.228679 lnL0 = -4453.527664 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4453.527664 x= 0.04181 0.26550 0.18402 0.13473 0.13205 0.33649 0.22950 0.22868 1 h-lim-p 0.0015 0.0122 82.4297 4451.669900 7 0.0006 36 | 0/8 2 h-lim-p 0.0006 0.0044 42.1853 4451.369417 7 0.0004 63 | 0/8 3 h-lim-p 0.0007 0.0061 23.2172 4451.268506 6 0.0005 89 | 0/8 4 h-lim-p 0.0009 0.0377 12.3810 4451.234825 4 0.0006 111 | 0/8 5 h-lim-p 0.0124 0.4664 0.5995 4451.234632 3 0.0011 133 | 0/8 6 h-lim-p 0.0040 1.8304 0.1659 4451.234619 0 0.0009 154 | 0/8 7 h-lim-p 0.0025 6.8059 0.0581 4451.234609 1 0.0031 176 | 0/8 8 h-lim-p 0.0439 20.0000 0.0041 4451.232610 0 0.5270 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 4451.232540 2 0.9961 223 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4451.232540 0 1.0938 243 | 0/8 11 h-lim-p 1.1589 20.0000 0.0000 4451.232540 0 1.0141 263 | 0/8 12 h-lim-p 0.0622 20.0000 0.0003 4451.232540 0 0.0156 284 | 0/8 13 h-lim-p 0.0047 20.0000 0.0010 4451.232540 0 0.0001 308 | 0/8 14 h-lim-p 0.0003 20.0000 0.0005 4451.232540 0 0.0000 331 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 4451.232540 0 0.0000 362 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -4451.232540 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4451.232540 Node 7: lnL = -4451.232540 Node 8: lnL = -4451.232540 Node 9: lnL = -4451.232540 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 479 Sequential format.. Reading seq # 1: YGL043W_Sbay Reading seq # 2: YGL043W_Scer Reading seq # 3: YGL043W_Skud Reading seq # 4: YGL043W_Smik Reading seq # 5: YGL043W_Spar Sequences read.. Counting patterns.. # site patterns = 201 Counting frequencies.. 120 bytes for distance 32160 bytes for lkl0 25728 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.080622 0.058118 0.098455 0.136501 0.065594 0.177020 0.201948 0.195417 lnL0 = -2124.670157 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2124.670157 x= 0.08062 0.05812 0.09846 0.13650 0.06559 0.17702 0.20195 0.19542 1 h-lim-p 0.0002 0.0019 101.5440 2122.870074 0 0.0005 23 | 0/8 2 h-lim-p 0.0015 0.0123 23.0019 2122.723862 4 0.0006 43 | 0/8 3 h-lim-p 0.0026 0.0276 5.1394 2122.717748 5 0.0005 67 | 0/8 4 h-lim-p 0.0006 0.0673 4.2108 2122.716030 3 0.0003 86 | 0/8 5 h-lim-p 0.0023 0.5936 0.5238 2122.715871 3 0.0009 104 | 0/8 6 h-lim-p 0.0089 4.8468 0.0513 2122.713007 0 0.0356 126 | 0/8 7 h-lim-p 0.0042 0.2463 0.4394 2122.656190 0 0.0166 148 | 0/8 8 h-lim-p 0.0057 0.1550 1.2867 2122.655750 4 0.0005 178 | 0/8 9 h-lim-p 0.9109 20.0000 0.0008 2122.655255 3 0.9629 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2122.655254 0 1.0938 216 | 0/8 11 h-lim-p 2.4321 20.0000 0.0000 2122.655254 0 2.1281 236 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2122.655254 0 1.0938 256 | 0/8 13 h-lim-p 0.2314 20.0000 0.0000 2122.655254 0 3.7021 280 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 2122.655254 0 0.0001 314 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 2122.655254 0 0.0000 338 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 2122.655254 0 0.0000 370 Out... lnL = -2122.655254 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2122.655254 Node 7: lnL = -2122.655254 Node 8: lnL = -2122.655254 Node 9: lnL = -2122.655254 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 151 Sequential format.. Reading seq # 1: YGL045W_Sbay Reading seq # 2: YGL045W_Scer Reading seq # 3: YGL045W_Skud Reading seq # 4: YGL045W_Smik Reading seq # 5: YGL045W_Spar Sequences read.. Counting patterns.. # site patterns = 83 Counting frequencies.. 120 bytes for distance 13280 bytes for lkl0 10624 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.087256 0.000060 0.056015 0.097687 0.079906 0.190089 0.281781 0.191166 lnL0 = -624.353153 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 624.353153 x= 0.08726 0.00006 0.05601 0.09769 0.07991 0.19009 0.28178 0.19117 1 h-lim-p 0.0036 0.0292 50.1977 623.286050 6 0.0007 35 | 0/8 2 h-lim-p 0.0028 0.0223 11.6615 623.173862 7 0.0017 67 | 0/8 3 h-lim-p 0.0032 0.0359 6.1534 623.157178 7 0.0011 99 | 0/8 4 h-lim-p 0.0030 0.0867 2.2779 623.154371 5 0.0013 120 | 0/8 5 h-lim-p 0.0039 0.3965 0.7546 623.153527 3 0.0033 138 | 0/8 6 h-lim-p 0.0163 1.1075 0.1542 623.153507 2 0.0016 164 | 0/8 7 h-lim-p 0.0104 7.2668 0.0233 623.153476 0 0.0208 185 | 0/8 8 h-lim-p 0.0396 4.2373 0.0123 623.151557 0 0.1582 207 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 623.151555 1 0.9961 229 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 623.151555 0 1.0938 249 | 0/8 11 h-lim-p 1.5911 20.0000 0.0000 623.151555 0 1.3922 269 | 0/8 12 h-lim-p 1.2551 20.0000 0.0000 623.151555 0 2.5103 290 | 0/8 13 h-lim-p 0.3483 20.0000 0.0000 623.151555 0 0.0007 318 | 0/8 14 h-lim-p 0.0000 1.8772 0.0612 623.151555 0 0.0000 338 | 0/8 15 h-lim-p 0.0056 20.0000 0.0001 623.151555 0 0.0000 370 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -623.151555 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -623.151555 Node 7: lnL = -623.151555 Node 8: lnL = -623.151555 Node 9: lnL = -623.151555 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 283 Sequential format.. Reading seq # 1: YGL047W_Sbay Reading seq # 2: YGL047W_Scer Reading seq # 3: YGL047W_Skud Reading seq # 4: YGL047W_Smik Reading seq # 5: YGL047W_Spar Sequences read.. Counting patterns.. # site patterns = 138 Counting frequencies.. 120 bytes for distance 22080 bytes for lkl0 17664 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.234988 0.024971 0.070762 0.105107 0.106418 0.168442 0.097455 0.363155 lnL0 = -1187.376884 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1187.376884 x= 0.23499 0.02497 0.07076 0.10511 0.10642 0.16844 0.09746 0.36315 1 h-lim-p 0.0004 0.0034 108.7038 1184.465898 0 0.0006 22 | 0/8 2 h-lim-p 0.0005 0.0041 28.4006 1184.175155 0 0.0008 34 | 0/8 3 h-lim-p 0.0016 0.0155 13.9062 1184.106884 8 0.0009 66 | 0/8 4 h-lim-p 0.0022 0.0601 5.3902 1184.093159 6 0.0011 94 | 0/8 5 h-lim-p 0.0053 0.3180 1.1534 1184.091649 4 0.0023 113 | 0/8 6 h-lim-p 0.0043 0.3616 0.6287 1184.091435 4 0.0012 135 | 0/8 7 h-lim-p 0.0049 0.8327 0.1569 1184.091094 0 0.0097 156 | 0/8 8 h-lim-p 0.0797 5.0789 0.0191 1184.062008 0 0.3186 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0016 1184.060520 4 0.9422 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1184.060517 1 0.9961 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1184.060517 0 1.0938 248 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1184.060517 0 1.0938 268 | 0/8 13 h-lim-p 1.2692 20.0000 0.0000 1184.060517 0 3.8077 289 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1184.060517 0 0.4688 311 | 0/8 15 h-lim-p 0.2848 20.0000 0.0000 1184.060517 0 0.0001 342 Out... lnL = -1184.060517 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1184.060517 Node 7: lnL = -1184.060517 Node 8: lnL = -1184.060517 Node 9: lnL = -1184.060517 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 299 Sequential format.. Reading seq # 1: YGL048C_Sbay Reading seq # 2: YGL048C_Scer Reading seq # 3: YGL048C_Skud Reading seq # 4: YGL048C_Smik Reading seq # 5: YGL048C_Spar Sequences read.. Counting patterns.. # site patterns = 137 Counting frequencies.. 120 bytes for distance 21920 bytes for lkl0 17536 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.194110 0.182490 0.082921 0.114064 0.097461 0.174470 0.139475 0.348217 lnL0 = -1333.500949 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1333.500949 x= 0.19411 0.18249 0.08292 0.11406 0.09746 0.17447 0.13948 0.34822 1 h-lim-p 0.0007 0.0053 51.6316 1332.298143 0 0.0010 22 | 0/8 2 h-lim-p 0.0022 0.0174 16.4169 1332.138282 7 0.0013 50 | 0/8 3 h-lim-p 0.0015 0.0317 14.0288 1332.084200 7 0.0009 80 | 0/8 4 h-lim-p 0.0015 0.0230 8.3329 1332.046705 1 0.0018 94 | 0/8 5 h-lim-p 0.0046 0.0581 3.3085 1332.041714 4 0.0012 115 | 0/8 6 h-lim-p 0.0049 0.2672 0.7912 1332.041154 2 0.0020 131 | 0/8 7 h-lim-p 0.0124 6.2926 0.1246 1332.041126 2 0.0033 156 | 0/8 8 h-lim-p 0.2052 20.0000 0.0020 1332.039811 0 0.8206 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1332.039790 1 1.0938 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1332.039789 0 1.0938 220 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1332.039789 0 1.2500 240 | 0/8 12 h-lim-p 1.8092 20.0000 0.0000 1332.039789 0 0.3958 261 | 0/8 13 h-lim-p 0.1991 20.0000 0.0000 1332.039789 0 0.0000 305 Out... lnL = -1332.039789 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1332.039789 Node 7: lnL = -1332.039789 Node 8: lnL = -1332.039789 Node 9: lnL = -1332.039789 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 860 Sequential format.. Reading seq # 1: YGL055W_Sbay Reading seq # 2: YGL055W_Scer Reading seq # 3: YGL055W_Skud Reading seq # 4: YGL055W_Smik Reading seq # 5: YGL055W_Spar Sequences read.. Counting patterns.. # site patterns = 194 Counting frequencies.. 120 bytes for distance 31040 bytes for lkl0 24832 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.055524 0.028459 0.014740 0.053205 0.047672 0.112125 0.126709 0.116089 lnL0 = -3034.606226 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3034.606226 x= 0.05552 0.02846 0.01474 0.05321 0.04767 0.11212 0.12671 0.11609 1 h-lim-p 0.0002 0.0019 620.7592 3029.186263 3 0.0000 29 | 0/8 2 h-lim-p 0.0002 0.0014 91.1726 3028.782176 8 0.0001 62 | 0/8 3 h-lim-p 0.0005 0.0116 19.9137 3028.755483 7 0.0001 93 | 0/8 4 h-lim-p 0.0003 0.0107 10.7642 3028.750921 4 0.0001 113 | 0/8 5 h-lim-p 0.0005 0.0878 2.1883 3028.750561 3 0.0002 133 | 0/8 6 h-lim-p 0.0005 0.1635 0.7511 3028.750530 2 0.0001 150 | 0/8 7 h-lim-p 0.0010 3.7750 0.0903 3028.750528 1 0.0003 173 | 0/8 8 h-lim-p 0.0282 20.0000 0.0008 3028.745316 0 0.9037 198 | 0/8 9 h-lim-p 2.2455 20.0000 0.0003 3028.745182 2 0.9824 222 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3028.745181 0 1.0938 242 | 0/8 11 h-lim-p 1.4981 20.0000 0.0000 3028.745181 0 0.0015 271 | 0/8 12 h-lim-p 0.0004 20.0000 0.0001 3028.745181 0 0.0000 306 | 0/8 13 h-lim-p 0.0000 20.0000 0.0048 | 0/8 14 h-lim-p 0.0000 20.0000 0.0048 Out... lnL = -3028.745181 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3028.745181 Node 7: lnL = -3028.745181 Node 8: lnL = -3028.745181 Node 9: lnL = -3028.745181 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 366 Sequential format.. Reading seq # 1: YGL060W_Sbay Reading seq # 2: YGL060W_Scer Reading seq # 3: YGL060W_Skud Reading seq # 4: YGL060W_Smik Reading seq # 5: YGL060W_Spar Sequences read.. Counting patterns.. # site patterns = 147 Counting frequencies.. 120 bytes for distance 23520 bytes for lkl0 18816 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.064392 0.089859 0.086566 0.167014 0.117007 0.290938 0.268814 0.209733 lnL0 = -1460.732418 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1460.732418 x= 0.06439 0.08986 0.08657 0.16701 0.11701 0.29094 0.26881 0.20973 1 h-lim-p 0.0015 0.0121 33.9584 1460.156216 7 0.0011 38 | 0/8 2 h-lim-p 0.0011 0.0085 12.3693 1460.080248 4 0.0011 58 | 0/8 3 h-lim-p 0.0025 0.0549 5.4589 1460.065864 2 0.0012 74 | 0/8 4 h-lim-p 0.0030 0.1498 2.0767 1460.063884 5 0.0011 97 | 0/8 5 h-lim-p 0.0039 0.5508 0.5751 1460.063678 3 0.0014 117 | 0/8 6 h-lim-p 0.0064 3.8312 0.1234 1460.063666 2 0.0017 142 | 0/8 7 h-lim-p 0.0049 6.8639 0.0426 1460.063664 0 0.0021 162 | 0/8 8 h-lim-p 0.2392 20.0000 0.0004 1460.063612 0 0.9569 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1460.063610 0 1.0938 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1460.063610 0 1.0938 224 | 0/8 11 h-lim-p 1.4881 20.0000 0.0000 1460.063610 0 0.6510 244 | 0/8 12 h-lim-p 0.3660 20.0000 0.0000 1460.063610 0 0.1830 264 | 0/8 13 h-lim-p 0.0660 20.0000 0.0000 1460.063610 0 0.0165 285 | 0/8 14 h-lim-p 0.0074 20.0000 0.0001 1460.063610 0 0.0000 323 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 1460.063610 0 0.0000 345 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 1460.063610 0 0.0000 407 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1460.063610 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1460.063610 Node 7: lnL = -1460.063610 Node 8: lnL = -1460.063610 Node 9: lnL = -1460.063610 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 368 Sequential format.. Reading seq # 1: YGL061C_Sbay Reading seq # 2: YGL061C_Scer Reading seq # 3: YGL061C_Skud Reading seq # 4: YGL061C_Smik Reading seq # 5: YGL061C_Spar Sequences read.. Counting patterns.. # site patterns = 156 Counting frequencies.. 120 bytes for distance 24960 bytes for lkl0 19968 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.063990 0.063808 0.063395 0.140085 0.091754 0.239647 0.187928 0.178906 lnL0 = -1713.381419 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1713.381419 x= 0.06399 0.06381 0.06340 0.14009 0.09175 0.23965 0.18793 0.17891 1 h-lim-p 0.0008 0.0065 85.8392 1711.949492 8 0.0004 41 | 0/8 2 h-lim-p 0.0007 0.0058 23.4609 1711.796290 7 0.0006 67 | 0/8 3 h-lim-p 0.0013 0.0255 10.3870 1711.771626 3 0.0005 85 | 0/8 4 h-lim-p 0.0022 0.0946 2.5799 1711.769223 4 0.0008 107 | 0/8 5 h-lim-p 0.0084 0.7337 0.2388 1711.769198 1 0.0008 123 | 0/8 6 h-lim-p 0.0022 4.1343 0.0922 1711.769195 0 0.0009 143 | 0/8 7 h-lim-p 0.0098 18.0043 0.0089 1711.769194 0 0.0043 163 | 0/8 8 h-lim-p 0.0218 20.0000 0.0018 1711.769017 0 0.2615 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1711.769016 0 1.0938 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1711.769016 0 1.0938 226 | 0/8 11 h-lim-p 1.2065 20.0000 0.0000 1711.769016 0 1.2065 246 | 0/8 12 h-lim-p 0.2626 20.0000 0.0000 1711.769016 0 0.0036 271 | 0/8 13 h-lim-p 0.0008 20.0000 0.0002 1711.769016 0 0.0000 308 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 1711.769016 0 0.0000 343 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1711.769016 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1711.769016 Node 7: lnL = -1711.769016 Node 8: lnL = -1711.769016 Node 9: lnL = -1711.769016 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 464 Sequential format.. Reading seq # 1: YGL062W_Sbay Reading seq # 2: YGL062W_Scer Reading seq # 3: YGL062W_Skud Reading seq # 4: YGL062W_Smik Reading seq # 5: YGL062W_Spar Sequences read.. Counting patterns.. # site patterns = 155 Counting frequencies.. 120 bytes for distance 24800 bytes for lkl0 19840 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.138793 0.000060 0.081883 0.059023 0.055392 0.133699 0.211556 0.231187 lnL0 = -1817.947416 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1817.947416 x= 0.13879 0.00006 0.08188 0.05902 0.05539 0.13370 0.21156 0.23119 1 h-lim-p 0.0001 0.0009 163.2662 1813.512299 0 0.0003 23 | 0/8 2 h-lim-p 0.0004 0.0028 62.1578 1813.228312 4 0.0002 44 | 0/8 3 h-lim-p 0.0003 0.0067 31.5542 1813.094699 4 0.0003 64 | 0/8 4 h-lim-p 0.0007 0.0105 15.1256 1813.057534 6 0.0004 91 | 0/8 5 h-lim-p 0.0009 0.0166 7.0978 1813.051107 6 0.0003 118 | 0/8 6 h-lim-p 0.0024 6.5924 0.9654 1813.050914 4 0.0003 140 | 0/8 7 h-lim-p 0.0025 0.4161 0.1147 1813.042385 0 0.0407 164 | 0/8 8 h-lim-p 0.0086 0.3183 0.5439 1812.916715 0 0.0172 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0008 1812.915855 3 1.0449 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1812.915848 1 0.9961 233 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1812.915848 0 1.0938 253 | 0/8 12 h-lim-p 1.7517 20.0000 0.0000 1812.915848 0 0.7664 273 | 0/8 13 h-lim-p 0.5609 20.0000 0.0000 1812.915848 0 0.2805 293 | 0/8 14 h-lim-p 0.1031 20.0000 0.0000 1812.915848 0 0.0226 314 | 0/8 15 h-lim-p 0.0091 20.0000 0.0000 1812.915848 0 0.0046 334 | 0/8 16 h-lim-p 0.0033 20.0000 0.0000 1812.915848 0 0.0000 365 | 0/8 17 h-lim-p 0.0001 20.0000 0.0000 1812.915848 0 0.0000 394 Out... lnL = -1812.915848 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1812.915848 Node 7: lnL = -1812.915848 Node 8: lnL = -1812.915848 Node 9: lnL = -1812.915848 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 497 Sequential format.. Reading seq # 1: YGL063W_Sbay Reading seq # 2: YGL063W_Scer Reading seq # 3: YGL063W_Skud Reading seq # 4: YGL063W_Smik Reading seq # 5: YGL063W_Spar Sequences read.. Counting patterns.. # site patterns = 209 Counting frequencies.. 120 bytes for distance 33440 bytes for lkl0 26752 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.151169 0.109438 0.029277 0.108200 0.094382 0.270621 0.232647 0.294051 lnL0 = -2105.088062 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2105.088062 x= 0.15117 0.10944 0.02928 0.10820 0.09438 0.27062 0.23265 0.29405 1 h-lim-p 0.0011 0.0086 64.3790 2104.395512 7 0.0004 37 | 0/8 2 h-lim-p 0.0007 0.0057 19.2091 2104.285182 3 0.0006 55 | 0/8 3 h-lim-p 0.0009 0.0078 13.1264 2104.255167 4 0.0005 76 | 0/8 4 h-lim-p 0.0012 0.0389 5.2550 2104.247563 6 0.0007 103 | 0/8 5 h-lim-p 0.0016 0.1284 2.2022 2104.245748 5 0.0009 127 | 0/8 6 h-lim-p 0.0038 0.4920 0.5375 2104.245575 3 0.0013 147 | 0/8 7 h-lim-p 0.0402 9.3642 0.0179 2104.245574 0 0.0022 170 | 0/8 8 h-lim-p 0.6189 20.0000 0.0001 2104.245570 0 1.2378 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2104.245569 0 1.0938 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2104.245569 0 1.0938 231 | 0/8 11 h-lim-p 1.1650 20.0000 0.0000 2104.245569 0 4.6599 253 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2104.245569 0 0.2734 275 | 0/8 13 h-lim-p 2.0382 20.0000 0.0000 2104.245569 0 0.0318 300 | 0/8 14 h-lim-p 0.0038 20.0000 0.0000 2104.245569 0 0.0058 320 | 0/8 15 h-lim-p 0.0030 20.0000 0.0000 2104.245569 0 0.0004 342 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 2104.245569 0 0.0000 368 | 0/8 17 h-lim-p 0.0002 20.0000 0.0000 2104.245569 0 0.0000 391 Out... lnL = -2104.245569 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2104.245569 Node 7: lnL = -2104.245569 Node 8: lnL = -2104.245569 Node 9: lnL = -2104.245569 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 465 Sequential format.. Reading seq # 1: YGL064C_Sbay Reading seq # 2: YGL064C_Scer Reading seq # 3: YGL064C_Skud Reading seq # 4: YGL064C_Smik Reading seq # 5: YGL064C_Spar Sequences read.. Counting patterns.. # site patterns = 200 Counting frequencies.. 120 bytes for distance 32000 bytes for lkl0 25600 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.151119 0.078028 0.058811 0.090510 0.103790 0.207195 0.187744 0.270860 lnL0 = -2056.761689 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2056.761689 x= 0.15112 0.07803 0.05881 0.09051 0.10379 0.20719 0.18774 0.27086 1 h-lim-p 0.0019 0.0152 69.8234 2055.516989 9 0.0006 44 | 0/8 2 h-lim-p 0.0004 0.0028 25.1106 2055.383029 0 0.0005 56 | 0/8 3 h-lim-p 0.0010 0.0195 13.1771 2055.338401 5 0.0007 80 | 0/8 4 h-lim-p 0.0017 0.0385 4.9756 2055.334783 3 0.0003 99 | 0/8 5 h-lim-p 0.0011 0.1845 1.5276 2055.333801 3 0.0009 117 | 0/8 6 h-lim-p 0.0048 0.4903 0.3007 2055.333780 2 0.0005 135 | 0/8 7 h-lim-p 0.0060 20.0000 0.0231 2055.333730 0 0.0181 156 | 0/8 8 h-lim-p 0.0199 20.0000 0.0210 2055.331047 0 0.0795 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 2055.330958 2 1.0889 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2055.330957 0 1.0938 222 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2055.330957 0 1.0938 242 | 0/8 12 h-lim-p 1.5779 20.0000 0.0000 2055.330957 0 1.5779 262 | 0/8 13 h-lim-p 1.8628 20.0000 0.0000 2055.330957 0 0.1164 285 | 0/8 14 h-lim-p 0.0246 20.0000 0.0000 2055.330957 0 0.0062 306 | 0/8 15 h-lim-p 0.0025 20.0000 0.0000 2055.330957 0 0.0006 327 | 0/8 16 h-lim-p 0.0003 20.0000 0.0001 2055.330957 0 0.0000 365 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 2055.330957 0 0.0000 397 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 2055.330957 0 0.0000 431 | 0/8 19 h-lim-p 0.0000 20.0000 0.0002 | 0/8 20 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -2055.330957 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2055.330957 Node 7: lnL = -2055.330957 Node 8: lnL = -2055.330957 Node 9: lnL = -2055.330957 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 486 Sequential format.. Reading seq # 1: YGL067W_Sbay Reading seq # 2: YGL067W_Scer Reading seq # 3: YGL067W_Skud Reading seq # 4: YGL067W_Smik Reading seq # 5: YGL067W_Spar Sequences read.. Counting patterns.. # site patterns = 191 Counting frequencies.. 120 bytes for distance 30560 bytes for lkl0 24448 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.082561 0.070536 0.060195 0.090082 0.097389 0.194418 0.198194 0.185333 lnL0 = -2088.301835 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2088.301835 x= 0.08256 0.07054 0.06020 0.09008 0.09739 0.19442 0.19819 0.18533 1 h-lim-p 0.0018 0.0147 92.2871 2087.224874 6 0.0003 38 | 0/8 2 h-lim-p 0.0018 0.0146 14.0852 2087.176850 7 0.0005 66 | 0/8 3 h-lim-p 0.0010 0.0588 6.8452 2087.169535 5 0.0004 90 | 0/8 4 h-lim-p 0.0015 0.1365 1.7797 2087.168718 4 0.0006 110 | 0/8 5 h-lim-p 0.0020 0.6786 0.4976 2087.168658 3 0.0005 129 | 0/8 6 h-lim-p 0.0029 2.5177 0.0919 2087.168656 1 0.0004 153 | 0/8 7 h-lim-p 0.0036 20.0000 0.0090 2087.168656 0 0.0016 173 | 0/8 8 h-lim-p 0.1227 20.0000 0.0001 2087.168640 0 0.9819 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2087.168640 0 1.0938 216 | 0/8 10 h-lim-p 1.3627 20.0000 0.0000 2087.168640 0 0.5962 236 | 0/8 11 h-lim-p 0.3758 20.0000 0.0000 2087.168640 0 0.0470 258 | 0/8 12 h-lim-p 0.0220 20.0000 0.0000 2087.168640 0 0.0880 280 | 0/8 13 h-lim-p 0.0527 20.0000 0.0001 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0007 2087.168640 0 0.0000 352 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0007 | 0/8 17 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -2087.168640 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2087.168640 Node 7: lnL = -2087.168640 Node 8: lnL = -2087.168640 Node 9: lnL = -2087.168640 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 264 Sequential format.. Reading seq # 1: YGL070C_Sbay Reading seq # 2: YGL070C_Scer Reading seq # 3: YGL070C_Skud Reading seq # 4: YGL070C_Smik Reading seq # 5: YGL070C_Spar Sequences read.. Counting patterns.. # site patterns = 98 Counting frequencies.. 120 bytes for distance 15680 bytes for lkl0 12544 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.023719 0.105874 0.109987 0.064067 0.053822 0.009213 0.128632 0.092171 lnL0 = -909.694097 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 909.694097 x= 0.02372 0.10587 0.10999 0.06407 0.05382 0.00921 0.12863 0.09217 1 h-lim-p 0.0001 0.0094 391.4888 902.670662 0 0.0002 23 | 0/8 2 h-lim-p 0.0012 0.0098 15.5179 902.561924 8 0.0009 57 | 0/8 3 h-lim-p 0.0009 0.0092 14.6955 902.497550 4 0.0009 77 | 0/8 4 h-lim-p 0.0011 0.0129 12.5513 902.462109 4 0.0009 97 | 0/8 5 h-lim-p 0.0021 0.0181 5.1616 902.457479 2 0.0005 114 | 0/8 6 h-lim-p 0.0014 0.0563 1.8608 902.456733 3 0.0005 132 | 0/8 7 h-lim-p 0.0182 3.1393 0.0527 902.456511 3 0.0128 151 | 0/8 8 h-lim-p 0.0182 2.8852 0.0370 902.366392 0 0.4378 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0013 902.365168 4 0.9802 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 902.365166 1 0.9961 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 902.365166 0 1.0938 245 | 0/8 12 h-lim-p 1.2769 20.0000 0.0000 902.365166 0 1.1173 265 | 0/8 13 h-lim-p 0.3077 20.0000 0.0001 902.365166 0 0.0096 289 | 0/8 14 h-lim-p 0.0018 20.0000 0.0003 902.365166 0 0.0000 326 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -902.365166 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -902.365166 Node 7: lnL = -902.365166 Node 8: lnL = -902.365166 Node 9: lnL = -902.365166 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 670 Sequential format.. Reading seq # 1: YGL071W_Sbay Reading seq # 2: YGL071W_Scer Reading seq # 3: YGL071W_Skud Reading seq # 4: YGL071W_Smik Reading seq # 5: YGL071W_Spar Sequences read.. Counting patterns.. # site patterns = 180 Counting frequencies.. 120 bytes for distance 28800 bytes for lkl0 23040 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.034198 0.036581 0.041885 0.062612 0.043642 0.139753 0.100598 0.092358 lnL0 = -2403.203919 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2403.203919 x= 0.03420 0.03658 0.04188 0.06261 0.04364 0.13975 0.10060 0.09236 1 h-lim-p 0.0020 0.8179 153.5269 2402.182822 8 0.0001 46 | 0/8 2 h-lim-p 0.0008 0.0066 16.8289 2402.160393 4 0.0002 67 | 0/8 3 h-lim-p 0.0003 0.0199 8.5023 2402.155899 2 0.0001 83 | 0/8 4 h-lim-p 0.0006 0.0612 2.2079 2402.155556 3 0.0002 102 | 0/8 5 h-lim-p 0.0006 0.3562 0.5462 2402.155523 2 0.0002 118 | 0/8 6 h-lim-p 0.0053 5.5573 0.0247 2402.155523 0 0.0001 142 | 0/8 7 h-lim-p 0.0015 20.0000 0.0025 2402.155523 0 0.0007 162 | 0/8 8 h-lim-p 0.0069 20.0000 0.0003 2402.155509 0 0.2211 187 | 0/8 9 h-lim-p 2.2301 20.0000 0.0000 2402.155509 0 0.9757 207 | 0/8 10 h-lim-p 0.6486 20.0000 0.0000 2402.155509 0 1.2971 228 | 0/8 11 h-lim-p 0.1281 20.0000 0.0004 2402.155509 0 0.0035 252 | 0/8 12 h-lim-p 0.0010 20.0000 0.0013 2402.155509 0 0.0009 272 | 0/8 13 h-lim-p 0.0003 12.6733 0.0043 2402.155509 0 0.0000 300 | 0/8 14 h-lim-p 0.0000 20.0000 0.0010 2402.155509 0 0.0000 328 | 0/8 15 h-lim-p 0.0000 20.0000 0.0007 2402.155509 0 0.0000 360 | 0/8 16 h-lim-p 0.0000 20.0000 0.0007 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0007 | 0/8 18 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -2402.155509 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2402.155509 Node 7: lnL = -2402.155509 Node 8: lnL = -2402.155509 Node 9: lnL = -2402.155509 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 687 Sequential format.. Reading seq # 1: YGL073W_Sbay Reading seq # 2: YGL073W_Scer Reading seq # 3: YGL073W_Skud Reading seq # 4: YGL073W_Smik Reading seq # 5: YGL073W_Spar Sequences read.. Counting patterns.. # site patterns = 253 Counting frequencies.. 120 bytes for distance 40480 bytes for lkl0 32384 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.051609 0.122488 0.082251 0.151574 0.079337 0.221498 0.206709 0.168371 lnL0 = -3198.145626 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3198.145626 x= 0.05161 0.12249 0.08225 0.15157 0.07934 0.22150 0.20671 0.16837 1 h-lim-p 0.0025 0.0197 96.5009 3196.987091 7 0.0003 40 | 0/8 2 h-lim-p 0.0009 0.0068 28.6975 3196.848200 6 0.0004 67 | 0/8 3 h-lim-p 0.0007 0.0153 14.9034 3196.815455 6 0.0004 92 | 0/8 4 h-lim-p 0.0026 0.1937 2.0978 3196.814555 4 0.0004 115 | 0/8 5 h-lim-p 0.0017 0.6552 0.5076 3196.814501 2 0.0005 132 | 0/8 6 h-lim-p 0.0031 2.3191 0.0752 3196.814499 0 0.0007 153 | 0/8 7 h-lim-p 0.0022 12.0026 0.0230 3196.814499 0 0.0010 173 | 0/8 8 h-lim-p 0.0511 20.0000 0.0004 3196.814358 0 0.8177 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3196.814354 0 1.0938 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3196.814354 0 1.0938 237 | 0/8 11 h-lim-p 1.1769 20.0000 0.0000 3196.814354 0 2.3537 258 | 0/8 12 h-lim-p 1.4962 20.0000 0.0000 3196.814354 0 1.3092 278 | 0/8 13 h-lim-p 0.0739 20.0000 0.0005 3196.814354 0 0.0023 302 | 0/8 14 h-lim-p 0.0011 20.0000 0.0010 3196.814354 0 0.0000 327 | 0/8 15 h-lim-p 0.0004 20.0000 0.0000 3196.814354 0 0.0000 358 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 3196.814354 0 0.0000 385 Out... lnL = -3196.814354 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3196.814354 Node 7: lnL = -3196.814354 Node 8: lnL = -3196.814354 Node 9: lnL = -3196.814354 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 526 Sequential format.. Reading seq # 1: YGL075C_Sbay Reading seq # 2: YGL075C_Scer Reading seq # 3: YGL075C_Skud Reading seq # 4: YGL075C_Smik Reading seq # 5: YGL075C_Spar Sequences read.. Counting patterns.. # site patterns = 223 Counting frequencies.. 120 bytes for distance 35680 bytes for lkl0 28544 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.069397 0.170908 0.094065 0.179715 0.087063 0.217760 0.217989 0.204647 lnL0 = -2568.292364 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2568.292364 x= 0.06940 0.17091 0.09407 0.17971 0.08706 0.21776 0.21799 0.20465 1 h-lim-p 0.0021 0.0165 66.2735 2567.519713 7 0.0004 38 | 0/8 2 h-lim-p 0.0011 0.0129 21.8258 2567.377768 8 0.0007 69 | 0/8 3 h-lim-p 0.0014 0.0244 10.0181 2567.349654 2 0.0007 85 | 0/8 4 h-lim-p 0.0058 0.4388 1.1528 2567.349141 4 0.0008 107 | 0/8 5 h-lim-p 0.0038 0.7296 0.2395 2567.349122 2 0.0007 124 | 0/8 6 h-lim-p 0.0059 5.5284 0.0298 2567.349121 0 0.0006 146 | 0/8 7 h-lim-p 0.0036 20.0000 0.0053 2567.349121 0 0.0016 166 | 0/8 8 h-lim-p 0.0505 20.0000 0.0002 2567.349114 0 0.8078 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2567.349114 0 1.0938 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2567.349114 0 1.0938 230 | 0/8 11 h-lim-p 1.0840 20.0000 0.0000 2567.349114 0 1.0840 250 | 0/8 12 h-lim-p 0.1895 20.0000 0.0001 2567.349114 0 0.1895 270 | 0/8 13 h-lim-p 0.0493 20.0000 0.0002 2567.349114 0 0.0000 302 | 0/8 14 h-lim-p 0.0006 20.0000 0.0000 2567.349114 0 0.0001 323 Out... lnL = -2567.349114 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2567.349114 Node 7: lnL = -2567.349114 Node 8: lnL = -2567.349114 Node 9: lnL = -2567.349114 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 455 Sequential format.. Reading seq # 1: YGL077C_Sbay Reading seq # 2: YGL077C_Scer Reading seq # 3: YGL077C_Skud Reading seq # 4: YGL077C_Smik Reading seq # 5: YGL077C_Spar Sequences read.. Counting patterns.. # site patterns = 159 Counting frequencies.. 120 bytes for distance 25440 bytes for lkl0 20352 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.082046 0.041403 0.038712 0.094932 0.050685 0.134119 0.083349 0.152723 lnL0 = -1675.111356 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1675.111356 x= 0.08205 0.04140 0.03871 0.09493 0.05068 0.13412 0.08335 0.15272 1 h-lim-p 0.0003 0.0020 86.3720 1674.331420 7 0.0002 36 | 0/8 2 h-lim-p 0.0004 0.0034 28.8431 1674.215268 7 0.0003 65 | 0/8 3 h-lim-p 0.0008 0.0205 11.2757 1674.204332 4 0.0002 86 | 0/8 4 h-lim-p 0.0007 0.0451 3.3194 1674.202923 3 0.0003 105 | 0/8 5 h-lim-p 0.0013 0.1329 0.7173 1674.202853 2 0.0003 122 | 0/8 6 h-lim-p 0.0018 1.2628 0.1128 1674.202850 0 0.0005 143 | 0/8 7 h-lim-p 0.0084 20.0000 0.0061 1674.202850 0 0.0009 165 | 0/8 8 h-lim-p 0.0669 20.0000 0.0001 1674.202845 0 0.8027 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1674.202845 0 1.0938 208 | 0/8 10 h-lim-p 1.1074 20.0000 0.0000 1674.202845 0 2.2148 229 | 0/8 11 h-lim-p 1.9134 20.0000 0.0000 1674.202845 0 0.0037 257 | 0/8 12 h-lim-p 0.0003 20.0000 0.0001 1674.202845 0 0.0000 280 | 0/8 13 h-lim-p 0.0002 20.0000 0.0000 1674.202845 0 0.0001 300 | 0/8 14 h-lim-p 0.0051 20.0000 0.0000 1674.202845 0 0.0002 324 Out... lnL = -1674.202845 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1674.202845 Node 7: lnL = -1674.202845 Node 8: lnL = -1674.202845 Node 9: lnL = -1674.202845 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 401 Sequential format.. Reading seq # 1: YGL078C_Sbay Reading seq # 2: YGL078C_Scer Reading seq # 3: YGL078C_Skud Reading seq # 4: YGL078C_Smik Reading seq # 5: YGL078C_Spar Sequences read.. Counting patterns.. # site patterns = 159 Counting frequencies.. 120 bytes for distance 25440 bytes for lkl0 20352 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.045102 0.103365 0.036909 0.104176 0.074231 0.188482 0.199222 0.139731 lnL0 = -1720.118798 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1720.118798 x= 0.04510 0.10337 0.03691 0.10418 0.07423 0.18848 0.19922 0.13973 1 h-lim-p 0.0005 0.0039 118.5955 1718.189965 9 0.0003 43 | 0/8 2 h-lim-p 0.0004 0.0031 31.4728 1718.005230 5 0.0004 66 | 0/8 3 h-lim-p 0.0009 0.0183 13.3799 1717.965957 6 0.0005 93 | 0/8 4 h-lim-p 0.0013 0.0450 5.2784 1717.959084 5 0.0006 114 | 0/8 5 h-lim-p 0.0066 0.4158 0.4627 1717.959030 3 0.0005 137 | 0/8 6 h-lim-p 0.0037 2.6921 0.0608 1717.959028 0 0.0008 158 | 0/8 7 h-lim-p 0.0558 20.0000 0.0009 1717.958835 0 0.6698 181 | 0/8 8 h-lim-p 0.0021 0.7709 0.2743 1717.958661 3 0.0017 207 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1717.958652 1 0.9961 229 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1717.958652 0 1.0938 249 | 0/8 11 h-lim-p 1.1395 20.0000 0.0000 1717.958652 0 0.9970 269 | 0/8 12 h-lim-p 0.1819 20.0000 0.0001 1717.958652 0 0.0057 293 | 0/8 13 h-lim-p 0.0015 20.0000 0.0002 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1717.958652 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1717.958652 Node 7: lnL = -1717.958652 Node 8: lnL = -1717.958652 Node 9: lnL = -1717.958652 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 447 Sequential format.. Reading seq # 1: YGL079W_Sbay Reading seq # 2: YGL079W_Scer Reading seq # 3: YGL079W_Skud Reading seq # 4: YGL079W_Smik Reading seq # 5: YGL079W_Spar Sequences read.. Counting patterns.. # site patterns = 184 Counting frequencies.. 120 bytes for distance 29440 bytes for lkl0 23552 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.085530 0.008160 0.091973 0.126556 0.081668 0.204954 0.205794 0.188185 lnL0 = -1981.083211 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1981.083211 x= 0.08553 0.00816 0.09197 0.12656 0.08167 0.20495 0.20579 0.18818 1 h-lim-p 0.0006 0.0049 208.7123 1978.121192 8 0.0002 41 | 0/8 2 h-lim-p 0.0008 0.0064 27.6357 1977.887836 6 0.0006 66 | 0/8 3 h-lim-p 0.0009 0.0132 18.1033 1977.841905 6 0.0004 89 | 0/8 4 h-lim-p 0.0016 0.0373 4.3476 1977.837766 6 0.0005 118 | 0/8 5 h-lim-p 0.0084 1.0067 0.2472 1977.837740 2 0.0008 136 | 0/8 6 h-lim-p 0.0043 4.0229 0.0478 1977.837740 0 0.0009 157 | 0/8 7 h-lim-p 0.0066 20.0000 0.0068 1977.837739 0 0.0058 177 | 0/8 8 h-lim-p 0.0207 20.0000 0.0019 1977.837569 0 0.1659 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1977.837550 0 1.0938 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1977.837550 0 1.0938 240 | 0/8 11 h-lim-p 2.0913 20.0000 0.0000 1977.837550 0 1.0457 260 | 0/8 12 h-lim-p 0.9349 20.0000 0.0000 1977.837550 m20.0000 282 | 0/8 13 h-lim-p 0.0141 9.6396 0.0131 1977.837550 0 0.0564 304 | 0/8 14 h-lim-p 0.0138 2.3437 0.0535 1977.837550 0 0.0030 325 | 0/8 15 h-lim-p 0.0010 0.7944 0.1577 1977.837550 0 0.0000 351 | 0/8 16 h-lim-p 0.0001 19.1120 0.0143 1977.837550 0 0.0000 377 | 0/8 17 h-lim-p 0.0004 20.0000 0.0000 1977.837550 0 0.0000 410 | 0/8 18 h-lim-p 0.0000 20.0000 0.0012 1977.837550 0 0.0000 442 | 0/8 19 h-lim-p 0.0000 20.0000 0.0012 | 0/8 20 h-lim-p 0.0000 20.0000 0.0012 Out... lnL = -1977.837550 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1977.837550 Node 7: lnL = -1977.837550 Node 8: lnL = -1977.837550 Node 9: lnL = -1977.837550 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 305 Sequential format.. Reading seq # 1: YGL080W_Sbay Reading seq # 2: YGL080W_Scer Reading seq # 3: YGL080W_Skud Reading seq # 4: YGL080W_Smik Reading seq # 5: YGL080W_Spar Sequences read.. Counting patterns.. # site patterns = 127 Counting frequencies.. 120 bytes for distance 20320 bytes for lkl0 16256 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.073745 0.101733 0.065650 0.099940 0.021230 0.137806 0.103544 0.156840 lnL0 = -1204.441825 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1204.441825 x= 0.07374 0.10173 0.06565 0.09994 0.02123 0.13781 0.10354 0.15684 1 h-lim-p 0.0010 0.0089 156.1105 1202.540313 4 0.0002 31 | 0/8 2 h-lim-p 0.0008 0.0062 27.9668 1202.272150 2 0.0007 47 | 0/8 3 h-lim-p 0.0033 0.0332 6.2191 1202.259523 5 0.0007 71 | 0/8 4 h-lim-p 0.0024 0.0627 1.7809 1202.258705 2 0.0006 88 | 0/8 5 h-lim-p 0.0026 1.8874 0.3875 1202.258663 2 0.0006 105 | 0/8 6 h-lim-p 0.0026 1.8698 0.0836 1202.258660 1 0.0006 128 | 0/8 7 h-lim-p 0.0154 20.0000 0.0035 1202.258604 0 0.0925 150 | 0/8 8 h-lim-p 0.0035 1.1174 0.0923 1202.257776 0 0.0140 172 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 1202.257613 2 1.2500 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1202.257609 0 1.0938 216 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1202.257609 0 2.1875 236 | 0/8 12 h-lim-p 0.3613 20.0000 0.0001 1202.257609 0 0.0056 261 | 0/8 13 h-lim-p 0.0008 20.0000 0.0004 1202.257609 0 0.0001 283 | 0/8 14 h-lim-p 0.0001 20.0000 0.0007 1202.257609 0 0.0000 306 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 1202.257609 0 0.0001 326 | 0/8 16 h-lim-p 0.0005 20.0000 0.0000 1202.257609 0 0.0000 351 Out... lnL = -1202.257609 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1202.257609 Node 7: lnL = -1202.257609 Node 8: lnL = -1202.257609 Node 9: lnL = -1202.257609 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 440 Sequential format.. Reading seq # 1: YGL081W_Sbay Reading seq # 2: YGL081W_Scer Reading seq # 3: YGL081W_Skud Reading seq # 4: YGL081W_Smik Reading seq # 5: YGL081W_Spar Sequences read.. Counting patterns.. # site patterns = 190 Counting frequencies.. 120 bytes for distance 30400 bytes for lkl0 24320 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.090398 0.045451 0.132859 0.119569 0.069468 0.209951 0.202947 0.205058 lnL0 = -1949.717725 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1949.717725 x= 0.09040 0.04545 0.13286 0.11957 0.06947 0.20995 0.20295 0.20506 1 h-lim-p 0.0020 0.0160 67.4438 1948.947374 9 0.0004 47 | 0/8 2 h-lim-p 0.0017 0.0136 10.1817 1948.928023 6 0.0004 72 | 0/8 3 h-lim-p 0.0008 0.0475 4.6497 1948.920738 2 0.0008 88 | 0/8 4 h-lim-p 0.0029 0.1528 1.2370 1948.920313 3 0.0006 107 | 0/8 5 h-lim-p 0.0039 1.5836 0.1962 1948.920299 2 0.0007 124 | 0/8 6 h-lim-p 0.0055 13.9737 0.0267 1948.920299 0 0.0012 145 | 0/8 7 h-lim-p 0.0059 20.0000 0.0054 1948.920298 0 0.0051 165 | 0/8 8 h-lim-p 0.0189 20.0000 0.0015 1948.920230 0 0.1513 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1948.920227 0 1.0938 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1948.920227 0 1.0938 228 | 0/8 11 h-lim-p 1.4257 20.0000 0.0000 1948.920227 0 0.3119 249 | 0/8 12 h-lim-p 0.1460 20.0000 0.0000 1948.920227 0 0.0730 269 | 0/8 13 h-lim-p 0.0369 20.0000 0.0000 1948.920227 0 0.0006 294 | 0/8 14 h-lim-p 0.0002 20.0000 0.0001 1948.920227 0 0.0000 319 | 0/8 15 h-lim-p 0.0004 20.0000 0.0000 1948.920227 0 0.0000 341 Out... lnL = -1948.920227 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1948.920227 Node 7: lnL = -1948.920227 Node 8: lnL = -1948.920227 Node 9: lnL = -1948.920227 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 380 Sequential format.. Reading seq # 1: YGL082W_Sbay Reading seq # 2: YGL082W_Scer Reading seq # 3: YGL082W_Skud Reading seq # 4: YGL082W_Smik Reading seq # 5: YGL082W_Spar Sequences read.. Counting patterns.. # site patterns = 172 Counting frequencies.. 120 bytes for distance 27520 bytes for lkl0 22016 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.083694 0.102101 0.054197 0.118903 0.094207 0.226054 0.133273 0.190065 lnL0 = -1691.653809 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1691.653809 x= 0.08369 0.10210 0.05420 0.11890 0.09421 0.22605 0.13327 0.19006 1 h-lim-p 0.0005 0.0039 39.9084 1691.187987 1 0.0006 24 | 0/8 2 h-lim-p 0.0013 0.0133 18.6063 1691.122888 6 0.0004 51 | 0/8 3 h-lim-p 0.0017 0.0256 4.8889 1691.117410 6 0.0005 78 | 0/8 4 h-lim-p 0.0017 0.2151 1.4216 1691.116974 5 0.0005 102 | 0/8 5 h-lim-p 0.0012 0.2869 0.5843 1691.116865 3 0.0007 122 | 0/8 6 h-lim-p 0.0148 7.2884 0.0295 1691.116864 1 0.0009 147 | 0/8 7 h-lim-p 0.0084 20.0000 0.0032 1691.116717 0 0.1349 171 | 0/8 8 h-lim-p 0.0015 0.5766 0.2898 1691.116385 0 0.0030 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1691.116362 2 0.9961 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1691.116362 0 2.1875 236 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1691.116362 0 1.0938 256 | 0/8 12 h-lim-p 0.0896 20.0000 0.0000 1691.116362 0 0.0112 278 | 0/8 13 h-lim-p 0.0002 20.0000 0.0007 1691.116362 0 0.0002 298 | 0/8 14 h-lim-p 0.0001 20.0000 0.0017 1691.116362 0 0.0000 319 | 0/8 15 h-lim-p 0.0002 20.0000 0.0001 1691.116362 0 0.0000 357 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 1691.116362 0 0.0000 389 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1691.116362 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1691.116362 Node 7: lnL = -1691.116362 Node 8: lnL = -1691.116362 Node 9: lnL = -1691.116362 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 808 Sequential format.. Reading seq # 1: YGL083W_Sbay Reading seq # 2: YGL083W_Scer Reading seq # 3: YGL083W_Skud Reading seq # 4: YGL083W_Smik Reading seq # 5: YGL083W_Spar Sequences read.. Counting patterns.. # site patterns = 331 Counting frequencies.. 120 bytes for distance 52960 bytes for lkl0 42368 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.082191 0.078481 0.125206 0.159130 0.128664 0.255024 0.296888 0.225174 lnL0 = -4030.339273 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4030.339273 x= 0.08219 0.07848 0.12521 0.15913 0.12866 0.25502 0.29689 0.22517 1 h-lim-p 0.0080 1.1534 100.2024 4028.932730 6 0.0003 40 | 0/8 2 h-lim-p 0.0016 0.0214 17.9708 4028.843422 7 0.0006 72 | 0/8 3 h-lim-p 0.0009 0.0348 11.2246 4028.824815 5 0.0004 93 | 0/8 4 h-lim-p 0.0017 0.1542 2.5556 4028.822923 4 0.0006 114 | 0/8 5 h-lim-p 0.0062 1.2547 0.2581 4028.822904 2 0.0006 132 | 0/8 6 h-lim-p 0.0027 4.1365 0.0576 4028.822903 0 0.0012 152 | 0/8 7 h-lim-p 0.0106 20.0000 0.0063 4028.822895 0 0.0159 172 | 0/8 8 h-lim-p 0.0052 20.0000 0.0196 4028.822423 0 0.0412 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 4028.822365 2 0.9961 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4028.822365 0 1.0938 239 | 0/8 11 h-lim-p 1.3563 20.0000 0.0000 4028.822365 0 1.3563 259 | 0/8 12 h-lim-p 0.2497 20.0000 0.0001 4028.822365 0 0.0068 283 | 0/8 13 h-lim-p 0.0010 20.0000 0.0004 4028.822365 0 0.0000 322 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -4028.822365 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4028.822365 Node 7: lnL = -4028.822365 Node 8: lnL = -4028.822365 Node 9: lnL = -4028.822365 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 277 Sequential format.. Reading seq # 1: YGL085W_Sbay Reading seq # 2: YGL085W_Scer Reading seq # 3: YGL085W_Skud Reading seq # 4: YGL085W_Smik Reading seq # 5: YGL085W_Spar Sequences read.. Counting patterns.. # site patterns = 142 Counting frequencies.. 120 bytes for distance 22720 bytes for lkl0 18176 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.106545 0.057419 0.107146 0.170257 0.080843 0.206961 0.509181 0.250697 lnL0 = -1185.376745 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1185.376745 x= 0.10654 0.05742 0.10715 0.17026 0.08084 0.20696 0.50918 0.25070 1 h-lim-p 0.0027 0.0217 35.0124 1184.916872 8 0.0008 40 | 0/8 2 h-lim-p 0.0019 0.0155 12.6047 1184.841534 5 0.0010 63 | 0/8 3 h-lim-p 0.0028 0.0630 4.7791 1184.804801 0 0.0041 75 | 0/8 4 h-lim-p 0.0026 0.0825 7.4696 1184.776491 2 0.0025 91 | 0/8 5 h-lim-p 0.0056 0.1694 3.3029 1184.767181 6 0.0028 119 | 0/8 6 h-lim-p 0.0050 0.3225 1.8657 1184.764502 2 0.0023 135 | 0/8 7 h-lim-p 0.0054 0.1828 0.8166 1184.763806 4 0.0028 156 | 0/8 8 h-lim-p 0.6686 20.0000 0.0034 1184.762843 0 1.0029 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1184.762836 1 0.9961 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1184.762836 0 1.2500 218 | 0/8 11 h-lim-p 2.2551 20.0000 0.0000 1184.762836 0 0.9866 238 | 0/8 12 h-lim-p 0.8380 20.0000 0.0000 1184.762836 0 0.0016 266 Out... lnL = -1184.762836 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1184.762836 Node 7: lnL = -1184.762836 Node 8: lnL = -1184.762836 Node 9: lnL = -1184.762836 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 347 Sequential format.. Reading seq # 1: YGL086W_Sbay Reading seq # 2: YGL086W_Scer Reading seq # 3: YGL086W_Skud Reading seq # 4: YGL086W_Smik Reading seq # 5: YGL086W_Spar Sequences read.. Counting patterns.. # site patterns = 160 Counting frequencies.. 120 bytes for distance 25600 bytes for lkl0 20480 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.098278 0.000060 0.024639 0.170105 0.168786 0.211512 0.311478 0.207286 lnL0 = -1504.738209 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1504.738209 x= 0.09828 0.00006 0.02464 0.17010 0.16879 0.21151 0.31148 0.20729 1 h-lim-p 0.0040 1.6631 87.0861 1503.190853 7 0.0004 37 | 0/8 2 h-lim-p 0.0009 0.0072 30.7004 1502.745151 1 0.0011 51 | 0/8 3 h-lim-p 0.0011 0.0092 5.4324 1502.735900 6 0.0006 77 | 0/8 4 h-lim-p 0.0023 0.0730 1.5555 1502.734422 5 0.0013 102 | 0/8 5 h-lim-p 0.0056 0.6184 0.3597 1502.734250 2 0.0026 118 | 0/8 6 h-lim-p 0.0136 1.7986 0.0699 1502.734209 3 0.0048 146 | 0/8 7 h-lim-p 0.0175 4.6437 0.0193 1502.731080 0 0.1396 169 | 0/8 8 h-lim-p 0.0026 0.0893 1.0439 1502.727343 2 0.0027 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 1502.727260 2 0.9961 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1502.727260 0 1.0938 229 | 0/8 11 h-lim-p 2.3864 20.0000 0.0000 1502.727260 0 1.1932 249 | 0/8 12 h-lim-p 1.2308 20.0000 0.0000 1502.727260 0 0.5385 269 | 0/8 13 h-lim-p 0.1394 20.0000 0.0000 1502.727260 0 0.0044 293 | 0/8 14 h-lim-p 0.0022 20.0000 0.0000 1502.727260 0 0.0000 323 | 0/8 15 h-lim-p 0.0005 20.0000 0.0000 1502.727260 0 0.0001 345 Out... lnL = -1502.727260 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1502.727260 Node 7: lnL = -1502.727260 Node 8: lnL = -1502.727260 Node 9: lnL = -1502.727260 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 335 Sequential format.. Reading seq # 1: YGL091C_Sbay Reading seq # 2: YGL091C_Scer Reading seq # 3: YGL091C_Skud Reading seq # 4: YGL091C_Smik Reading seq # 5: YGL091C_Spar Sequences read.. Counting patterns.. # site patterns = 159 Counting frequencies.. 120 bytes for distance 25440 bytes for lkl0 20352 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.064171 0.202307 0.051944 0.179794 0.114820 0.242386 0.215056 0.191617 lnL0 = -1577.035726 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1577.035726 x= 0.06417 0.20231 0.05194 0.17979 0.11482 0.24239 0.21506 0.19162 1 h-lim-p 0.0023 0.0187 19.1389 1576.868555 5 0.0009 32 | 0/8 2 h-lim-p 0.0019 0.0208 9.1880 1576.840698 5 0.0008 53 | 0/8 3 h-lim-p 0.0024 0.1009 2.9444 1576.837779 5 0.0008 79 | 0/8 4 h-lim-p 0.0028 0.3439 0.8036 1576.837439 3 0.0012 97 | 0/8 5 h-lim-p 0.0062 4.3081 0.1514 1576.837424 1 0.0014 120 | 0/8 6 h-lim-p 0.0090 5.2168 0.0230 1576.837424 0 0.0020 141 | 0/8 7 h-lim-p 0.0064 20.0000 0.0070 1576.837423 0 0.0056 161 | 0/8 8 h-lim-p 0.0215 20.0000 0.0018 1576.837360 0 0.1721 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1576.837360 0 1.0938 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1576.837360 0 1.0938 224 | 0/8 11 h-lim-p 1.1800 20.0000 0.0000 1576.837360 0 1.7700 244 | 0/8 12 h-lim-p 1.1463 20.0000 0.0000 1576.837360 0 0.8597 264 | 0/8 13 h-lim-p 0.0138 20.0000 0.0007 1576.837360 0 0.0001 291 | 0/8 14 h-lim-p 0.0000 20.0000 0.0021 1576.837360 0 0.0000 317 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 1576.837360 0 0.0000 341 Out... lnL = -1576.837360 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1576.837360 Node 7: lnL = -1576.837360 Node 8: lnL = -1576.837360 Node 9: lnL = -1576.837360 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 556 Sequential format.. Reading seq # 1: YGL095C_Sbay Reading seq # 2: YGL095C_Scer Reading seq # 3: YGL095C_Skud Reading seq # 4: YGL095C_Smik Reading seq # 5: YGL095C_Spar Sequences read.. Counting patterns.. # site patterns = 273 Counting frequencies.. 120 bytes for distance 43680 bytes for lkl0 34944 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.066053 0.198630 0.009751 0.237625 0.136369 0.224405 0.203429 0.191957 lnL0 = -2638.137901 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2638.137901 x= 0.06605 0.19863 0.00975 0.23763 0.13637 0.22441 0.20343 0.19196 1 h-lim-p 0.0032 0.8715 128.7157 2636.589930 6 0.0002 37 | 0/8 2 h-lim-p 0.0010 0.0080 15.8447 2636.483853 5 0.0009 58 | 0/8 3 h-lim-p 0.0025 0.0312 5.4038 2636.475607 4 0.0006 80 | 0/8 4 h-lim-p 0.0023 0.1833 1.4514 2636.474648 2 0.0010 96 | 0/8 5 h-lim-p 0.0067 1.9524 0.2173 2636.474626 2 0.0009 114 | 0/8 6 h-lim-p 0.0025 2.3924 0.0765 2636.474624 1 0.0010 136 | 0/8 7 h-lim-p 0.0106 20.0000 0.0072 2636.474607 0 0.0213 157 | 0/8 8 h-lim-p 0.0097 1.9678 0.0159 2636.473890 0 0.0388 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2636.473881 1 0.9961 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2636.473881 0 1.0938 221 | 0/8 11 h-lim-p 1.2589 20.0000 0.0000 2636.473881 0 0.6295 241 | 0/8 12 h-lim-p 0.0148 20.0000 0.0005 2636.473881 0 0.0000 282 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -2636.473881 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2636.473881 Node 7: lnL = -2636.473881 Node 8: lnL = -2636.473881 Node 9: lnL = -2636.473881 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 870 Sequential format.. Reading seq # 1: YGL096W_Sbay Reading seq # 2: YGL096W_Scer Reading seq # 3: YGL096W_Skud Reading seq # 4: YGL096W_Smik Reading seq # 5: YGL096W_Spar Sequences read.. Counting patterns.. # site patterns = 279 Counting frequencies.. 120 bytes for distance 44640 bytes for lkl0 35712 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.127905 0.086986 0.076991 0.096270 0.065427 0.160514 0.147223 0.226003 lnL0 = -3673.614701 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3673.614701 x= 0.12791 0.08699 0.07699 0.09627 0.06543 0.16051 0.14722 0.22600 1 h-lim-p 0.0003 0.0027 117.9074 3672.247734 8 0.0002 42 | 0/8 2 h-lim-p 0.0008 0.0071 30.5437 3672.116074 7 0.0003 68 | 0/8 3 h-lim-p 0.0005 0.0133 20.1337 3672.092564 5 0.0002 92 | 0/8 4 h-lim-p 0.0005 0.0254 6.8910 3672.086854 5 0.0003 118 | 0/8 5 h-lim-p 0.0011 0.1125 1.7195 3672.086428 4 0.0003 139 | 0/8 6 h-lim-p 0.0012 0.4793 0.4318 3672.086405 1 0.0003 154 | 0/8 7 h-lim-p 0.0016 3.2019 0.0739 3672.086403 1 0.0004 177 | 0/8 8 h-lim-p 0.1653 20.0000 0.0002 3672.086337 0 1.3224 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3672.086334 0 1.0938 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3672.086334 0 1.0938 240 | 0/8 11 h-lim-p 1.2867 20.0000 0.0000 3672.086334 0 1.2867 260 | 0/8 12 h-lim-p 1.0360 20.0000 0.0000 3672.086334 0 0.2590 281 | 0/8 13 h-lim-p 0.0038 20.0000 0.0007 3672.086334 0 0.0001 305 | 0/8 14 h-lim-p 0.0014 20.0000 0.0001 3672.086334 0 0.0000 336 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 3672.086334 0 0.0001 356 Out... lnL = -3672.086334 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3672.086334 Node 7: lnL = -3672.086334 Node 8: lnL = -3672.086334 Node 9: lnL = -3672.086334 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 891 Sequential format.. Reading seq # 1: YGL097W_Sbay Reading seq # 2: YGL097W_Scer Reading seq # 3: YGL097W_Skud Reading seq # 4: YGL097W_Smik Reading seq # 5: YGL097W_Spar Sequences read.. Counting patterns.. # site patterns = 438 Counting frequencies.. 120 bytes for distance 70080 bytes for lkl0 56064 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.042157 0.296485 0.068116 0.496024 0.233836 0.555658 0.328500 0.268938 lnL0 = -5031.068744 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 5031.068744 x= 0.04216 0.29649 0.06812 0.49602 0.23384 0.55566 0.32850 0.26894 1 h-lim-p 0.0053 0.0426 48.7236 5030.248306 6 0.0007 36 | 0/8 2 h-lim-p 0.0019 0.0233 19.0059 5030.007596 7 0.0015 61 | 0/8 3 h-lim-p 0.0022 0.0466 13.1157 5029.966446 6 0.0007 87 | 0/8 4 h-lim-p 0.0020 0.0855 4.5454 5029.954632 5 0.0014 112 | 0/8 5 h-lim-p 0.0067 0.2994 0.9368 5029.953968 2 0.0016 129 | 0/8 6 h-lim-p 0.0094 2.0029 0.1562 5029.953941 0 0.0020 150 | 0/8 7 h-lim-p 0.0087 7.2063 0.0368 5029.953928 1 0.0069 172 | 0/8 8 h-lim-p 0.0737 20.0000 0.0035 5029.952798 0 0.4421 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 5029.952784 1 0.9961 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 5029.952784 0 1.0938 236 | 0/8 11 h-lim-p 1.1101 20.0000 0.0000 5029.952784 0 2.2201 257 | 0/8 12 h-lim-p 0.0483 20.0000 0.0007 5029.952784 0 0.0121 278 | 0/8 13 h-lim-p 0.0050 20.0000 0.0018 5029.952784 0 0.0000 304 | 0/8 14 h-lim-p 0.0026 20.0000 0.0000 5029.952784 0 0.0007 325 | 0/8 15 h-lim-p 0.0023 20.0000 0.0000 5029.952784 0 0.0000 355 Out... lnL = -5029.952784 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -5029.952784 Node 7: lnL = -5029.952784 Node 8: lnL = -5029.952784 Node 9: lnL = -5029.952784 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 872 Sequential format.. Reading seq # 1: YGL098W_Sbay Reading seq # 2: YGL098W_Scer Reading seq # 3: YGL098W_Skud Reading seq # 4: YGL098W_Smik Reading seq # 5: YGL098W_Spar Sequences read.. Counting patterns.. # site patterns = 288 Counting frequencies.. 120 bytes for distance 46080 bytes for lkl0 36864 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.046705 0.099305 0.072045 0.116606 0.096706 0.193438 0.142349 0.137562 lnL0 = -3687.952048 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3687.952048 x= 0.04670 0.09931 0.07204 0.11661 0.09671 0.19344 0.14235 0.13756 1 h-lim-p 0.0014 0.0110 173.4851 3685.168134 9 0.0002 46 | 0/8 2 h-lim-p 0.0004 0.0033 39.7108 3684.960217 6 0.0003 74 | 0/8 3 h-lim-p 0.0008 0.0147 12.8841 3684.943181 5 0.0002 97 | 0/8 4 h-lim-p 0.0011 0.0638 2.6948 3684.942347 2 0.0002 114 | 0/8 5 h-lim-p 0.0015 0.4932 0.4276 3684.942317 1 0.0003 129 | 0/8 6 h-lim-p 0.0010 1.4129 0.1351 3684.942314 1 0.0004 151 | 0/8 7 h-lim-p 0.0067 20.0000 0.0084 3684.942312 0 0.0058 171 | 0/8 8 h-lim-p 0.0090 20.0000 0.0055 3684.941865 0 0.1075 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3684.941847 1 0.9961 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3684.941847 0 1.0938 236 | 0/8 11 h-lim-p 0.8271 20.0000 0.0000 3684.941847 0 0.0012 265 | 0/8 12 h-lim-p 0.0002 20.0000 0.0002 3684.941847 0 0.0000 289 | 0/8 13 h-lim-p 0.0008 20.0000 0.0000 3684.941847 0 0.0000 325 Out... lnL = -3684.941847 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3684.941847 Node 7: lnL = -3684.941847 Node 8: lnL = -3684.941847 Node 9: lnL = -3684.941847 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 431 Sequential format.. Reading seq # 1: YGL100W_Sbay Reading seq # 2: YGL100W_Scer Reading seq # 3: YGL100W_Skud Reading seq # 4: YGL100W_Smik Reading seq # 5: YGL100W_Spar Sequences read.. Counting patterns.. # site patterns = 206 Counting frequencies.. 120 bytes for distance 32960 bytes for lkl0 26368 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.067656 0.185595 0.014640 0.132333 0.143460 0.188513 0.278950 0.186733 lnL0 = -2001.018334 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2001.018334 x= 0.06766 0.18560 0.01464 0.13233 0.14346 0.18851 0.27895 0.18673 1 h-lim-p 0.0054 0.3538 85.9075 2000.285091 6 0.0002 38 | 0/8 2 h-lim-p 0.0010 0.0118 18.2941 2000.157416 7 0.0008 65 | 0/8 3 h-lim-p 0.0028 0.0481 5.1498 2000.149625 2 0.0007 82 | 0/8 4 h-lim-p 0.0028 0.1431 1.2045 2000.149094 4 0.0008 104 | 0/8 5 h-lim-p 0.0019 1.0735 0.4894 2000.148977 3 0.0012 124 | 0/8 6 h-lim-p 0.0103 3.5579 0.0551 2000.148974 1 0.0013 148 | 0/8 7 h-lim-p 0.0090 20.0000 0.0078 2000.148972 0 0.0079 168 | 0/8 8 h-lim-p 0.0140 20.0000 0.0044 2000.148618 0 0.1117 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2000.148614 0 1.0938 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2000.148614 0 1.0938 231 | 0/8 11 h-lim-p 1.5331 20.0000 0.0000 2000.148614 0 1.3414 251 | 0/8 12 h-lim-p 1.3664 20.0000 0.0000 2000.148614 0 0.5978 271 | 0/8 13 h-lim-p 0.0888 20.0000 0.0001 2000.148614 0 0.0888 291 | 0/8 14 h-lim-p 0.0280 20.0000 0.0002 2000.148614 0 0.0017 314 | 0/8 15 h-lim-p 0.0007 20.0000 0.0004 2000.148614 0 0.0000 352 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -2000.148614 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2000.148614 Node 7: lnL = -2000.148614 Node 8: lnL = -2000.148614 Node 9: lnL = -2000.148614 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 281 Sequential format.. Reading seq # 1: YGL101W_Sbay Reading seq # 2: YGL101W_Scer Reading seq # 3: YGL101W_Skud Reading seq # 4: YGL101W_Smik Reading seq # 5: YGL101W_Spar Sequences read.. Counting patterns.. # site patterns = 106 Counting frequencies.. 120 bytes for distance 16960 bytes for lkl0 13568 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.024887 0.074713 0.083402 0.107504 0.085982 0.105086 0.118006 0.095947 lnL0 = -1111.365410 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1111.365410 x= 0.02489 0.07471 0.08340 0.10750 0.08598 0.10509 0.11801 0.09595 1 h-lim-p 0.0008 0.0067 40.1393 1111.018783 7 0.0005 37 | 0/8 2 h-lim-p 0.0022 0.0178 4.9578 1111.012980 4 0.0005 57 | 0/8 3 h-lim-p 0.0019 0.1752 1.2646 1111.012684 1 0.0004 72 | 0/8 4 h-lim-p 0.0019 0.4467 0.2558 1111.012668 2 0.0005 89 | 0/8 5 h-lim-p 0.0026 4.8109 0.0471 1111.012668 0 0.0007 110 | 0/8 6 h-lim-p 0.0062 20.0000 0.0050 1111.012668 0 0.0008 132 | 0/8 7 h-lim-p 0.0077 20.0000 0.0005 1111.012668 0 0.0067 152 | 0/8 8 h-lim-p 0.0161 20.0000 0.0002 1111.012667 0 0.1290 175 | 0/8 9 h-lim-p 1.1339 20.0000 0.0000 1111.012667 0 0.9922 195 | 0/8 10 h-lim-p 0.9781 20.0000 0.0000 1111.012667 0 0.0000 231 | 0/8 11 h-lim-p 0.0001 20.0000 0.0000 1111.012667 0 0.0000 263 Out... lnL = -1111.012667 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1111.012667 Node 7: lnL = -1111.012667 Node 8: lnL = -1111.012667 Node 9: lnL = -1111.012667 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 799 Sequential format.. Reading seq # 1: YGL103W_Sbay Reading seq # 2: YGL103W_Scer Reading seq # 3: YGL103W_Skud Reading seq # 4: YGL103W_Smik Reading seq # 5: YGL103W_Spar Sequences read.. Counting patterns.. # site patterns = 221 Counting frequencies.. 120 bytes for distance 35360 bytes for lkl0 28288 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.052331 0.030294 0.891074 0.135918 0.134118 0.129157 0.130347 lnL0 = -3468.526502 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3468.526502 x= 0.00006 0.05233 0.03029 0.89107 0.13592 0.13412 0.12916 0.13035 1 h-lim-p 0.0000 0.0000 334.4530 3468.449505 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0015 93.0385 3467.394496 0 0.0003 39 | 1/8 3 h-lim-p 0.0012 0.0119 25.6309 3467.117350 6 0.0009 63 | 1/8 4 h-lim-p 0.0005 0.0039 41.6441 3466.668775 0 0.0010 76 | 1/8 5 h-lim-p 0.0007 0.0074 55.4802 3466.522773 5 0.0003 97 | 1/8 6 h-lim-p 0.0071 0.0610 2.5392 3466.503699 5 0.0015 121 | 1/8 7 h-lim-p 0.0022 0.1037 1.6594 3464.822718 0 0.0356 137 | 1/8 8 h-lim-p 0.0009 0.0074 9.9124 3458.041426 m 0.0074 149 | 0/8 9 h-lim-p 0.0000 0.0000 7.1329 h-lim-p: 4.38979375e-20 3.51183500e-19 7.13293673e+00 3458.041426 .. | 0/8 10 h-lim-p 0.0000 0.0053 32.9604 3457.979508 0 0.0002 173 | 0/8 11 h-lim-p 0.0001 0.0009 14.4149 3457.963946 0 0.0002 186 | 0/8 12 h-lim-p 0.0004 0.0100 7.9473 3457.958766 4 0.0002 207 | 0/8 13 h-lim-p 0.0004 0.0285 4.6171 3457.955559 1 0.0005 221 | 0/8 14 h-lim-p 0.0003 0.0039 6.1267 3457.954280 2 0.0002 237 | 0/8 15 h-lim-p 0.0027 0.0476 0.3693 3457.954250 2 0.0004 256 | 0/8 16 h-lim-p 0.0003 2.0987 0.4704 3457.954045 0 0.0028 279 | 0/8 17 h-lim-p 0.4729 3.7830 0.0018 3457.947958 0 0.9458 300 | 0/8 18 h-lim-p 2.5000 20.0000 0.0003 3457.947850 2 0.9961 324 | 0/8 19 h-lim-p 2.1492 17.1939 0.0001 3457.947850 0 1.8806 344 | 0/8 20 h-lim-p 1.2476 10.1941 0.0002 3457.947850 0 2.4952 365 | 0/8 21 h-lim-p 0.0159 0.1274 0.0106 3457.947850 0 0.0005 389 | 0/8 22 h-lim-p 0.0001 0.0159 0.0844 .. | 0/8 23 h-lim-p 0.0000 20.0000 0.0055 3457.947850 0 0.0000 447 | 0/8 24 h-lim-p 0.0001 2.9317 0.0020 3457.947850 0 0.0003 468 | 0/8 25 h-lim-p 0.0011 20.0000 0.0006 3457.947850 0 0.0005 488 | 0/8 26 h-lim-p 0.0008 5.0507 0.0004 3457.947850 0 0.0000 512 | 0/8 27 h-lim-p 0.0000 4.9184 0.0005 3457.947850 0 0.0000 535 | 0/8 28 h-lim-p 0.0000 2.8744 0.0008 .. | 0/8 29 h-lim-p 0.0000 20.0000 0.0047 3457.947850 0 0.0000 593 | 0/8 30 h-lim-p 0.0000 2.8860 0.0006 3457.947850 0 0.0000 613 | 0/8 31 h-lim-p 0.0000 20.0000 0.0003 .. | 0/8 32 h-lim-p 0.0000 20.0000 0.0047 3457.947850 0 0.0000 671 | 0/8 33 h-lim-p 0.0000 2.9459 0.0006 3457.947850 0 0.0000 698 | 0/8 34 h-lim-p 0.0000 20.0000 0.0003 3457.947850 0 0.0000 719 | 0/8 35 h-lim-p 0.0000 6.1148 0.0003 .. | 0/8 36 h-lim-p 0.0000 20.0000 0.0047 | 0/8 37 h-lim-p 0.0000 20.0000 0.0047 Out... lnL = -3457.947850 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3457.947850 Node 7: lnL = -3457.947850 Node 8: lnL = -3457.947850 Node 9: lnL = -3457.947850 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 823 Sequential format.. Reading seq # 1: YGL104C_Sbay Reading seq # 2: YGL104C_Scer Reading seq # 3: YGL104C_Skud Reading seq # 4: YGL104C_Smik Reading seq # 5: YGL104C_Spar Sequences read.. Counting patterns.. # site patterns = 321 Counting frequencies.. 120 bytes for distance 51360 bytes for lkl0 41088 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.072254 0.114370 0.116897 0.212464 0.133673 0.313649 0.230055 0.200642 lnL0 = -3902.408550 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3902.408550 x= 0.07225 0.11437 0.11690 0.21246 0.13367 0.31365 0.23006 0.20064 1 h-lim-p 0.0104 1.5269 86.5981 3901.023955 9 0.0004 48 | 0/8 2 h-lim-p 0.0011 0.0090 24.9774 3900.855972 6 0.0006 74 | 0/8 3 h-lim-p 0.0012 0.0360 12.3475 3900.822888 2 0.0005 90 | 0/8 4 h-lim-p 0.0021 0.1524 3.1818 3900.820186 5 0.0006 114 | 0/8 5 h-lim-p 0.0017 0.3127 1.1019 3900.819823 3 0.0007 132 | 0/8 6 h-lim-p 0.0051 2.5577 0.1448 3900.819815 1 0.0006 148 | 0/8 7 h-lim-p 0.0058 20.0000 0.0158 3900.819810 0 0.0058 168 | 0/8 8 h-lim-p 0.0149 20.0000 0.0062 3900.818955 0 0.1786 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 3900.818915 1 0.9961 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3900.818915 0 1.0938 233 | 0/8 11 h-lim-p 2.0603 20.0000 0.0000 3900.818915 0 1.8028 253 | 0/8 12 h-lim-p 1.9228 20.0000 0.0000 3900.818915 0 1.6824 273 | 0/8 13 h-lim-p 0.6537 20.0000 0.0000 3900.818915 010.3442 297 | 0/8 14 h-lim-p 0.0291 11.6428 0.0091 3900.818915 0 0.0008 321 | 0/8 15 h-lim-p 0.0006 9.2933 0.0114 3900.818915 0 0.0001 342 | 0/8 16 h-lim-p 0.0004 20.0000 0.0035 3900.818915 0 0.0000 366 | 0/8 17 h-lim-p 0.0003 20.0000 0.0002 3900.818915 0 0.0001 386 | 0/8 18 h-lim-p 0.0002 20.0000 0.0001 3900.818915 0 0.0000 414 | 0/8 19 h-lim-p 0.0003 20.0000 0.0000 3900.818915 0 0.0000 446 Out... lnL = -3900.818915 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3900.818915 Node 7: lnL = -3900.818915 Node 8: lnL = -3900.818915 Node 9: lnL = -3900.818915 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 304 Sequential format.. Reading seq # 1: YGL106W_Sbay Reading seq # 2: YGL106W_Scer Reading seq # 3: YGL106W_Skud Reading seq # 4: YGL106W_Smik Reading seq # 5: YGL106W_Spar Sequences read.. Counting patterns.. # site patterns = 121 Counting frequencies.. 120 bytes for distance 19360 bytes for lkl0 15488 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.072190 0.034499 0.084156 0.131091 0.092016 0.159928 0.159550 0.152588 lnL0 = -1311.245537 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1311.245537 x= 0.07219 0.03450 0.08416 0.13109 0.09202 0.15993 0.15955 0.15259 1 h-lim-p 0.0016 0.0129 104.2600 1309.658116 8 0.0003 43 | 0/8 2 h-lim-p 0.0009 0.0069 29.0094 1309.313747 6 0.0008 69 | 0/8 3 h-lim-p 0.0039 0.0449 6.2923 1309.304437 5 0.0005 94 | 0/8 4 h-lim-p 0.0025 0.1458 1.2477 1309.304009 2 0.0006 111 | 0/8 5 h-lim-p 0.0065 1.3163 0.1123 1309.304005 1 0.0006 127 | 0/8 6 h-lim-p 0.0062 20.0000 0.0118 1309.304005 0 0.0014 148 | 0/8 7 h-lim-p 0.0232 20.0000 0.0007 1309.304003 0 0.0695 169 | 0/8 8 h-lim-p 0.0024 8.4044 0.0198 1309.303987 0 0.0097 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1309.303986 0 1.2500 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1309.303986 0 1.0938 231 | 0/8 11 h-lim-p 2.0152 20.0000 0.0000 1309.303986 0 4.0304 252 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1309.303986 0 0.3125 274 | 0/8 13 h-lim-p 0.6309 20.0000 0.0000 1309.303986 0 0.0002 305 Out... lnL = -1309.303986 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1309.303986 Node 7: lnL = -1309.303986 Node 8: lnL = -1309.303986 Node 9: lnL = -1309.303986 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 254 Sequential format.. Reading seq # 1: YGL111W_Sbay Reading seq # 2: YGL111W_Scer Reading seq # 3: YGL111W_Skud Reading seq # 4: YGL111W_Smik Reading seq # 5: YGL111W_Spar Sequences read.. Counting patterns.. # site patterns = 98 Counting frequencies.. 120 bytes for distance 15680 bytes for lkl0 12544 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.062616 0.067169 0.055934 0.093840 0.058239 0.168592 0.180434 0.137998 lnL0 = -1082.171927 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1082.171927 x= 0.06262 0.06717 0.05593 0.09384 0.05824 0.16859 0.18043 0.13800 1 h-lim-p 0.0004 0.0033 52.8296 1081.509931 1 0.0005 24 | 0/8 2 h-lim-p 0.0010 0.0084 14.9410 1081.437034 7 0.0007 53 | 0/8 3 h-lim-p 0.0044 0.0731 2.3602 1081.434950 5 0.0008 78 | 0/8 4 h-lim-p 0.0025 0.3541 0.7410 1081.434786 3 0.0006 97 | 0/8 5 h-lim-p 0.0008 0.1826 0.5675 1081.434735 3 0.0005 124 | 0/8 6 h-lim-p 0.0044 4.6267 0.0591 1081.434733 1 0.0011 147 | 0/8 7 h-lim-p 0.0081 13.4361 0.0078 1081.434732 1 0.0040 170 | 0/8 8 h-lim-p 0.0064 20.0000 0.0049 1081.434485 0 0.1027 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1081.434483 1 0.9961 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1081.434483 0 1.2500 236 | 0/8 11 h-lim-p 1.2551 20.0000 0.0000 1081.434483 0 0.0098 262 | 0/8 12 h-lim-p 0.0004 20.0000 0.0002 1081.434483 0 0.0001 283 | 0/8 13 h-lim-p 0.0001 20.0000 0.0003 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 1081.434483 0 0.0000 349 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 1081.434483 0 0.0000 376 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1081.434483 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1081.434483 Node 7: lnL = -1081.434483 Node 8: lnL = -1081.434483 Node 9: lnL = -1081.434483 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 254 Sequential format.. Reading seq # 1: YGL112C_Sbay Reading seq # 2: YGL112C_Scer Reading seq # 3: YGL112C_Skud Reading seq # 4: YGL112C_Smik Reading seq # 5: YGL112C_Spar Sequences read.. Counting patterns.. # site patterns = 99 Counting frequencies.. 120 bytes for distance 15840 bytes for lkl0 12672 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.072608 0.042027 0.060271 0.091520 0.060560 0.164255 0.182669 0.146751 lnL0 = -1079.440440 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1079.440440 x= 0.07261 0.04203 0.06027 0.09152 0.06056 0.16425 0.18267 0.14675 1 h-lim-p 0.0003 0.0028 76.1189 1078.335527 1 0.0004 24 | 0/8 2 h-lim-p 0.0010 0.0082 16.0601 1078.260578 7 0.0006 52 | 0/8 3 h-lim-p 0.0019 0.0421 5.1573 1078.256331 4 0.0004 73 | 0/8 4 h-lim-p 0.0011 0.1062 1.5829 1078.255569 5 0.0007 97 | 0/8 5 h-lim-p 0.0024 0.4811 0.4460 1078.255475 2 0.0010 113 | 0/8 6 h-lim-p 0.0067 1.6937 0.0699 1078.255472 2 0.0011 140 | 0/8 7 h-lim-p 0.0023 6.7996 0.0329 1078.255467 0 0.0035 160 | 0/8 8 h-lim-p 0.0269 19.1134 0.0043 1078.254340 0 0.3224 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1078.254294 2 0.9961 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1078.254294 0 2.1875 227 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1078.254294 0 1.0938 247 | 0/8 12 h-lim-p 0.2884 20.0000 0.0000 1078.254294 0 4.6151 271 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1078.254294 0 0.3125 293 | 0/8 14 h-lim-p 0.0257 20.0000 0.0000 1078.254294 0 0.0032 315 | 0/8 15 h-lim-p 0.0009 20.0000 0.0002 1078.254294 0 0.0002 336 | 0/8 16 h-lim-p 0.0002 20.0000 0.0001 1078.254294 0 0.0000 362 | 0/8 17 h-lim-p 0.0001 20.0000 0.0000 1078.254294 0 0.0000 396 Out... lnL = -1078.254294 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1078.254294 Node 7: lnL = -1078.254294 Node 8: lnL = -1078.254294 Node 9: lnL = -1078.254294 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 349 Sequential format.. Reading seq # 1: YGL113W_Sbay Reading seq # 2: YGL113W_Scer Reading seq # 3: YGL113W_Skud Reading seq # 4: YGL113W_Smik Reading seq # 5: YGL113W_Spar Sequences read.. Counting patterns.. # site patterns = 163 Counting frequencies.. 120 bytes for distance 26080 bytes for lkl0 20864 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.110864 0.103420 0.040848 0.101213 0.122058 0.197114 0.179278 0.207328 lnL0 = -1503.472267 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1503.472267 x= 0.11086 0.10342 0.04085 0.10121 0.12206 0.19711 0.17928 0.20733 1 h-lim-p 0.0029 0.0234 90.8231 1502.002407 9 0.0004 45 | 0/8 2 h-lim-p 0.0011 0.0089 26.3275 1501.732051 8 0.0008 78 | 0/8 3 h-lim-p 0.0024 0.0388 8.9995 1501.703711 6 0.0008 105 | 0/8 4 h-lim-p 0.0031 0.0705 2.2876 1501.701911 2 0.0007 122 | 0/8 5 h-lim-p 0.0024 0.4059 0.7055 1501.701663 0 0.0010 134 | 0/8 6 h-lim-p 0.0068 2.1024 0.1059 1501.701656 2 0.0011 160 | 0/8 7 h-lim-p 0.0202 20.0000 0.0057 1501.701656 0 0.0022 182 | 0/8 8 h-lim-p 0.0386 20.0000 0.0003 1501.701636 0 0.6184 206 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1501.701635 0 1.0938 226 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1501.701635 0 1.0938 246 | 0/8 11 h-lim-p 1.2754 20.0000 0.0000 1501.701635 0 1.2754 266 | 0/8 12 h-lim-p 0.5520 20.0000 0.0000 1501.701635 0 0.1380 287 | 0/8 13 h-lim-p 0.0099 20.0000 0.0001 1501.701635 0 0.0025 308 | 0/8 14 h-lim-p 0.0009 20.0000 0.0003 1501.701635 0 0.0000 343 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 1501.701635 0 0.0000 369 Out... lnL = -1501.701635 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1501.701635 Node 7: lnL = -1501.701635 Node 8: lnL = -1501.701635 Node 9: lnL = -1501.701635 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 480 Sequential format.. Reading seq # 1: YGL114W_Sbay Reading seq # 2: YGL114W_Scer Reading seq # 3: YGL114W_Skud Reading seq # 4: YGL114W_Smik Reading seq # 5: YGL114W_Spar Sequences read.. Counting patterns.. # site patterns = 153 Counting frequencies.. 120 bytes for distance 24480 bytes for lkl0 19584 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.080455 0.032263 0.047429 0.066052 0.067040 0.133017 0.147106 0.144931 lnL0 = -1873.655852 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1873.655852 x= 0.08045 0.03226 0.04743 0.06605 0.06704 0.13302 0.14711 0.14493 1 h-lim-p 0.0024 0.0406 125.2391 1872.533735 5 0.0002 35 | 0/8 2 h-lim-p 0.0009 0.0078 21.8055 1872.431536 2 0.0004 51 | 0/8 3 h-lim-p 0.0010 0.0220 9.3171 1872.423175 3 0.0002 70 | 0/8 4 h-lim-p 0.0013 0.0692 1.6851 1872.422862 4 0.0002 92 | 0/8 5 h-lim-p 0.0008 0.2853 0.5043 1872.422822 2 0.0003 108 | 0/8 6 h-lim-p 0.0057 3.5321 0.0298 1872.422822 0 0.0003 131 | 0/8 7 h-lim-p 0.0125 20.0000 0.0007 1872.422814 0 0.1002 154 | 0/8 8 h-lim-p 0.0013 4.1994 0.0559 1872.422754 0 0.0040 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1872.422752 0 1.0938 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1872.422752 0 1.0938 215 | 0/8 11 h-lim-p 1.1139 20.0000 0.0000 1872.422752 0 4.4555 237 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1872.422752 0 0.1367 260 | 0/8 13 h-lim-p 0.0945 20.0000 0.0000 1872.422752 0 0.0177 282 | 0/8 14 h-lim-p 0.0055 20.0000 0.0000 1872.422752 0 0.0000 320 | 0/8 15 h-lim-p 0.0000 20.0000 0.0023 1872.422752 0 0.0000 348 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 1872.422752 0 0.0013 375 | 0/8 17 h-lim-p 0.0025 20.0000 0.0002 1872.422752 0 0.0000 403 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0027 | 0/8 20 h-lim-p 0.0000 20.0000 0.0027 Out... lnL = -1872.422752 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1872.422752 Node 7: lnL = -1872.422752 Node 8: lnL = -1872.422752 Node 9: lnL = -1872.422752 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 428 Sequential format.. Reading seq # 1: YGL115W_Sbay Reading seq # 2: YGL115W_Scer Reading seq # 3: YGL115W_Skud Reading seq # 4: YGL115W_Smik Reading seq # 5: YGL115W_Spar Sequences read.. Counting patterns.. # site patterns = 168 Counting frequencies.. 120 bytes for distance 26880 bytes for lkl0 21504 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.080938 0.110288 0.080211 0.113286 0.076305 0.174929 0.174338 0.172633 lnL0 = -1849.199463 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1849.199463 x= 0.08094 0.11029 0.08021 0.11329 0.07631 0.17493 0.17434 0.17263 1 h-lim-p 0.0024 0.0194 42.9572 1848.880998 7 0.0004 39 | 0/8 2 h-lim-p 0.0015 0.0150 10.2613 1848.861045 5 0.0004 62 | 0/8 3 h-lim-p 0.0014 0.0527 2.9320 1848.858485 2 0.0007 78 | 0/8 4 h-lim-p 0.0034 0.3132 0.5666 1848.858403 3 0.0005 99 | 0/8 5 h-lim-p 0.0042 1.7953 0.0732 1848.858401 0 0.0009 120 | 0/8 6 h-lim-p 0.0049 20.0000 0.0138 1848.858401 0 0.0011 141 | 0/8 7 h-lim-p 0.0053 20.0000 0.0028 1848.858401 0 0.0012 162 | 0/8 8 h-lim-p 0.0362 20.0000 0.0001 1848.858397 0 0.5795 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1848.858397 0 1.0938 206 | 0/8 10 h-lim-p 1.3889 20.0000 0.0000 1848.858397 0 2.0834 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1848.858397 0 0.1562 249 | 0/8 12 h-lim-p 0.0303 20.0000 0.0000 1848.858397 0 0.0000 283 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 1848.858397 0 0.0000 315 Out... lnL = -1848.858397 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1848.858397 Node 7: lnL = -1848.858397 Node 8: lnL = -1848.858397 Node 9: lnL = -1848.858397 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 67 Sequential format.. Reading seq # 1: YGL117W_Sbay Reading seq # 2: YGL117W_Scer Reading seq # 3: YGL117W_Skud Reading seq # 4: YGL117W_Smik Reading seq # 5: YGL117W_Spar Sequences read.. Counting patterns.. # site patterns = 47 Counting frequencies.. 120 bytes for distance 7520 bytes for lkl0 6016 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.108023 0.110676 0.184050 0.206180 0.049515 0.487860 0.162529 0.253418 lnL0 = -335.342179 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 335.342179 x= 0.10802 0.11068 0.18405 0.20618 0.04952 0.48786 0.16253 0.25342 1 h-lim-p 0.0058 0.0466 11.1292 335.169570 7 0.0030 38 | 0/8 2 h-lim-p 0.0050 0.0425 6.7763 335.083852 2 0.0047 54 | 0/8 3 h-lim-p 0.0062 0.0498 2.4527 335.062284 0 0.0093 66 | 0/8 4 h-lim-p 0.0222 0.4677 1.0293 335.059085 6 0.0073 91 | 0/8 5 h-lim-p 0.0130 0.3856 0.5785 335.057673 4 0.0112 110 | 0/8 6 h-lim-p 0.0232 1.9850 0.2805 335.057294 4 0.0126 139 | 0/8 7 h-lim-p 0.0250 3.5912 0.1411 335.057211 2 0.0109 163 | 0/8 8 h-lim-p 0.6773 20.0000 0.0023 335.056953 0 1.0159 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 335.056950 1 0.9961 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 335.056950 0 1.0938 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 335.056950 0 2.1875 245 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 335.056950 0 0.1562 268 | 0/8 13 h-lim-p 0.0646 20.0000 0.0000 335.056950 0 0.0000 298 Out... lnL = -335.056950 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -335.056950 Node 7: lnL = -335.056950 Node 8: lnL = -335.056950 Node 9: lnL = -335.056950 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 526 Sequential format.. Reading seq # 1: YGL119W_Sbay Reading seq # 2: YGL119W_Scer Reading seq # 3: YGL119W_Skud Reading seq # 4: YGL119W_Smik Reading seq # 5: YGL119W_Spar Sequences read.. Counting patterns.. # site patterns = 239 Counting frequencies.. 120 bytes for distance 38240 bytes for lkl0 30592 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.085499 0.099123 0.084210 0.147771 0.125960 0.269489 0.216263 0.197549 lnL0 = -2583.592208 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2583.592208 x= 0.08550 0.09912 0.08421 0.14777 0.12596 0.26949 0.21626 0.19755 1 h-lim-p 0.0078 1.6526 81.3114 2582.375059 7 0.0004 41 | 0/8 2 h-lim-p 0.0016 0.0131 15.0479 2582.299955 3 0.0007 59 | 0/8 3 h-lim-p 0.0014 0.0272 7.1663 2582.287274 3 0.0006 77 | 0/8 4 h-lim-p 0.0027 0.1734 1.5931 2582.286402 4 0.0007 98 | 0/8 5 h-lim-p 0.0038 0.9164 0.3128 2582.286365 1 0.0007 113 | 0/8 6 h-lim-p 0.0049 10.8480 0.0480 2582.286364 0 0.0012 134 | 0/8 7 h-lim-p 0.1024 20.0000 0.0006 2582.286252 0 0.8196 157 | 0/8 8 h-lim-p 0.0015 3.1199 0.3021 2582.286174 3 0.0009 186 | 0/8 9 h-lim-p 2.2663 20.0000 0.0001 2582.286160 0 0.9915 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2582.286160 0 1.0938 226 | 0/8 11 h-lim-p 1.1839 20.0000 0.0000 2582.286160 0 0.0740 249 | 0/8 12 h-lim-p 0.0064 20.0000 0.0001 2582.286160 0 0.0008 271 | 0/8 13 h-lim-p 0.0001 20.0000 0.0006 2582.286160 0 0.0000 310 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -2582.286160 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2582.286160 Node 7: lnL = -2582.286160 Node 8: lnL = -2582.286160 Node 9: lnL = -2582.286160 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 527 Sequential format.. Reading seq # 1: YGL120C_Sbay Reading seq # 2: YGL120C_Scer Reading seq # 3: YGL120C_Skud Reading seq # 4: YGL120C_Smik Reading seq # 5: YGL120C_Spar Sequences read.. Counting patterns.. # site patterns = 250 Counting frequencies.. 120 bytes for distance 40000 bytes for lkl0 32000 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.086530 0.084659 0.081811 0.146591 0.130121 0.256697 0.237423 0.197475 lnL0 = -2594.348316 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2594.348316 x= 0.08653 0.08466 0.08181 0.14659 0.13012 0.25670 0.23742 0.19748 1 h-lim-p 0.0037 1.0791 117.9299 2591.962736 6 0.0004 36 | 0/8 2 h-lim-p 0.0014 0.0114 18.0943 2591.852136 5 0.0007 59 | 0/8 3 h-lim-p 0.0016 0.0231 7.6194 2591.838321 6 0.0006 86 | 0/8 4 h-lim-p 0.0029 0.3102 1.4495 2591.837282 4 0.0010 107 | 0/8 5 h-lim-p 0.0099 1.3286 0.1515 2591.837274 1 0.0006 124 | 0/8 6 h-lim-p 0.0065 20.0000 0.0141 2591.837269 0 0.0065 144 | 0/8 7 h-lim-p 0.0104 20.0000 0.0088 2591.837020 0 0.0626 166 | 0/8 8 h-lim-p 0.0014 1.1111 0.3936 2591.836575 0 0.0021 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 2591.836559 1 0.9961 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2591.836559 0 1.0938 228 | 0/8 11 h-lim-p 1.2128 20.0000 0.0000 2591.836559 0 1.0612 248 | 0/8 12 h-lim-p 0.1863 20.0000 0.0000 2591.836559 0 0.1863 268 | 0/8 13 h-lim-p 0.0484 20.0000 0.0002 2591.836559 0 0.0061 290 | 0/8 14 h-lim-p 0.0026 20.0000 0.0004 2591.836559 0 0.0013 310 | 0/8 15 h-lim-p 0.0010 20.0000 0.0005 2591.836559 0 0.0002 331 | 0/8 16 h-lim-p 0.0014 20.0000 0.0001 2591.836559 0 0.0000 366 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -2591.836559 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2591.836559 Node 7: lnL = -2591.836559 Node 8: lnL = -2591.836559 Node 9: lnL = -2591.836559 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 524 Sequential format.. Reading seq # 1: YGL121C_Sbay Reading seq # 2: YGL121C_Scer Reading seq # 3: YGL121C_Skud Reading seq # 4: YGL121C_Smik Reading seq # 5: YGL121C_Spar Sequences read.. Counting patterns.. # site patterns = 205 Counting frequencies.. 120 bytes for distance 32800 bytes for lkl0 26240 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.107692 0.069205 0.092962 0.106407 0.096440 0.161124 0.259776 0.208300 lnL0 = -2295.893510 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2295.893510 x= 0.10769 0.06921 0.09296 0.10641 0.09644 0.16112 0.25978 0.20830 1 h-lim-p 0.0009 0.0075 86.6744 2294.559440 7 0.0004 35 | 0/8 2 h-lim-p 0.0019 0.0158 17.3417 2294.493290 2 0.0004 52 | 0/8 3 h-lim-p 0.0008 0.0333 9.8538 2294.471742 6 0.0006 79 | 0/8 4 h-lim-p 0.0012 0.0649 4.6427 2294.466529 4 0.0006 100 | 0/8 5 h-lim-p 0.0027 0.1641 1.0468 2294.466158 3 0.0007 119 | 0/8 6 h-lim-p 0.0028 0.6310 0.2755 2294.466143 2 0.0005 138 | 0/8 7 h-lim-p 0.0226 20.0000 0.0055 2294.466135 0 0.0198 158 | 0/8 8 h-lim-p 0.0083 20.0000 0.0133 2294.465745 0 0.0661 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 2294.465715 2 0.9961 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2294.465715 0 1.0938 225 | 0/8 11 h-lim-p 0.9718 20.0000 0.0000 2294.465715 0 0.0304 249 | 0/8 12 h-lim-p 0.0107 20.0000 0.0000 2294.465715 0 0.0000 278 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 2294.465715 0 0.0000 305 Out... lnL = -2294.465715 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2294.465715 Node 7: lnL = -2294.465715 Node 8: lnL = -2294.465715 Node 9: lnL = -2294.465715 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 303 Sequential format.. Reading seq # 1: YGL122C_Sbay Reading seq # 2: YGL122C_Scer Reading seq # 3: YGL122C_Skud Reading seq # 4: YGL122C_Smik Reading seq # 5: YGL122C_Spar Sequences read.. Counting patterns.. # site patterns = 150 Counting frequencies.. 120 bytes for distance 24000 bytes for lkl0 19200 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.116309 0.083138 0.038777 0.159670 0.129577 0.221277 0.327311 0.232807 lnL0 = -1422.615762 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1422.615762 x= 0.11631 0.08314 0.03878 0.15967 0.12958 0.22128 0.32731 0.23281 1 h-lim-p 0.0079 0.1172 60.0232 1421.858371 3 0.0005 31 | 0/8 2 h-lim-p 0.0033 0.0263 8.4636 1421.809967 3 0.0014 50 | 0/8 3 h-lim-p 0.0033 0.1286 3.4687 1421.803225 4 0.0013 70 | 0/8 4 h-lim-p 0.0031 0.1881 1.4154 1421.802006 2 0.0015 86 | 0/8 5 h-lim-p 0.0045 0.7198 0.4679 1421.801853 3 0.0016 105 | 0/8 6 h-lim-p 0.0216 6.8192 0.0341 1421.801851 1 0.0013 130 | 0/8 7 h-lim-p 0.0138 20.0000 0.0033 1421.801787 0 0.1106 153 | 0/8 8 h-lim-p 0.0050 8.6460 0.0727 1421.801427 0 0.0100 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1421.801423 1 0.9961 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1421.801423 0 0.6250 217 | 0/8 11 h-lim-p 0.4576 20.0000 0.0000 1421.801423 0 0.0000 261 Out... lnL = -1421.801423 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1421.801423 Node 7: lnL = -1421.801423 Node 8: lnL = -1421.801423 Node 9: lnL = -1421.801423 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 893 Sequential format.. Reading seq # 1: YGL123W_Sbay Reading seq # 2: YGL123W_Scer Reading seq # 3: YGL123W_Skud Reading seq # 4: YGL123W_Smik Reading seq # 5: YGL123W_Spar Sequences read.. Counting patterns.. # site patterns = 336 Counting frequencies.. 120 bytes for distance 53760 bytes for lkl0 43008 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.067280 0.147359 0.078472 0.151321 0.132563 0.267632 0.217006 0.182709 lnL0 = -4288.466848 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4288.466848 x= 0.06728 0.14736 0.07847 0.15132 0.13256 0.26763 0.21701 0.18271 1 h-lim-p 0.0067 1.2777 113.3195 4286.842573 7 0.0003 41 | 0/8 2 h-lim-p 0.0011 0.0108 27.4147 4286.686803 5 0.0004 63 | 0/8 3 h-lim-p 0.0010 0.0153 12.2314 4286.664656 6 0.0004 89 | 0/8 4 h-lim-p 0.0017 0.1454 2.5692 4286.663354 2 0.0004 106 | 0/8 5 h-lim-p 0.0013 0.3476 0.8298 4286.663221 3 0.0004 125 | 0/8 6 h-lim-p 0.0021 2.0660 0.1663 4286.663215 0 0.0005 146 | 0/8 7 h-lim-p 0.0020 11.2928 0.0382 4286.663214 0 0.0009 166 | 0/8 8 h-lim-p 0.1108 20.0000 0.0003 4286.663089 0 0.8865 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4286.663088 0 1.0938 209 | 0/8 10 h-lim-p 2.4692 20.0000 0.0000 4286.663088 0 1.0803 229 | 0/8 11 h-lim-p 1.0645 20.0000 0.0000 4286.663088 0 0.0004 260 | 0/8 12 h-lim-p 0.0003 20.0000 0.0000 4286.663088 0 0.0003 280 | 0/8 13 h-lim-p 0.0004 20.0000 0.0000 4286.663088 0 0.0000 316 | 0/8 14 h-lim-p 0.0000 20.0000 0.0007 | 0/8 15 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -4286.663088 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4286.663088 Node 7: lnL = -4286.663088 Node 8: lnL = -4286.663088 Node 9: lnL = -4286.663088 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 445 Sequential format.. Reading seq # 1: YGL125W_Sbay Reading seq # 2: YGL125W_Scer Reading seq # 3: YGL125W_Skud Reading seq # 4: YGL125W_Smik Reading seq # 5: YGL125W_Spar Sequences read.. Counting patterns.. # site patterns = 148 Counting frequencies.. 120 bytes for distance 23680 bytes for lkl0 18944 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.071438 0.054322 0.026337 0.053727 0.040683 0.096734 0.143978 0.122360 lnL0 = -1552.573741 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1552.573741 x= 0.07144 0.05432 0.02634 0.05373 0.04068 0.09673 0.14398 0.12236 1 h-lim-p 0.0001 0.0008 167.4799 1550.723596 0 0.0002 23 | 0/8 2 h-lim-p 0.0004 0.0034 46.0200 1550.400256 4 0.0003 43 | 0/8 3 h-lim-p 0.0014 0.0114 6.9610 1550.395588 6 0.0002 71 | 0/8 4 h-lim-p 0.0003 0.0336 4.6494 1550.394001 5 0.0002 94 | 0/8 5 h-lim-p 0.0004 0.0392 2.3717 1550.392997 1 0.0005 108 | 0/8 6 h-lim-p 0.0016 0.5450 0.7070 1550.392657 4 0.0009 130 | 0/8 7 h-lim-p 0.0024 0.4204 0.2802 1550.391854 0 0.0035 150 | 0/8 8 h-lim-p 0.0112 0.6406 0.0889 1550.222467 0 0.0894 173 | 0/8 9 h-lim-p 2.5000 20.0000 0.0011 1550.220614 4 0.9644 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1550.220611 1 0.9961 223 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1550.220611 0 1.0938 243 | 0/8 12 h-lim-p 1.3280 20.0000 0.0000 1550.220611 0 5.3118 265 | 0/8 13 h-lim-p 1.9089 20.0000 0.0000 1550.220611 0 0.2386 287 | 0/8 14 h-lim-p 0.8031 20.0000 0.0000 1550.220611 0 0.0063 313 | 0/8 15 h-lim-p 0.0087 20.0000 0.0000 1550.220611 0 0.0000 341 Out... lnL = -1550.220611 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1550.220611 Node 7: lnL = -1550.220611 Node 8: lnL = -1550.220611 Node 9: lnL = -1550.220611 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 250 Sequential format.. Reading seq # 1: YGL126W_Sbay Reading seq # 2: YGL126W_Scer Reading seq # 3: YGL126W_Skud Reading seq # 4: YGL126W_Smik Reading seq # 5: YGL126W_Spar Sequences read.. Counting patterns.. # site patterns = 124 Counting frequencies.. 120 bytes for distance 19840 bytes for lkl0 15872 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.208884 0.038592 0.046154 0.091058 0.079780 0.113949 0.218788 0.298016 lnL0 = -1040.548454 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1040.548454 x= 0.20888 0.03859 0.04615 0.09106 0.07978 0.11395 0.21879 0.29802 1 h-lim-p 0.0005 0.0040 46.6123 1039.815604 0 0.0008 22 | 0/8 2 h-lim-p 0.0007 0.0059 14.6578 1039.748672 3 0.0007 40 | 0/8 3 h-lim-p 0.0013 0.0722 7.7473 1039.726504 6 0.0009 66 | 0/8 4 h-lim-p 0.0011 0.0172 6.4876 1039.711398 5 0.0012 89 | 0/8 5 h-lim-p 0.0020 0.0177 3.8210 1039.707008 2 0.0010 105 | 0/8 6 h-lim-p 0.0050 0.2990 0.7328 1039.706709 2 0.0012 122 | 0/8 7 h-lim-p 0.0039 0.7231 0.2210 1039.706633 3 0.0029 148 | 0/8 8 h-lim-p 0.2551 20.0000 0.0025 1039.702840 0 1.0203 170 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1039.702789 2 0.9961 194 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1039.702789 0 1.0938 214 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1039.702789 0 0.0195 240 | 0/8 12 h-lim-p 0.0097 20.0000 0.0000 1039.702789 0 0.0002 265 Out... lnL = -1039.702789 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1039.702789 Node 7: lnL = -1039.702789 Node 8: lnL = -1039.702789 Node 9: lnL = -1039.702789 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 248 Sequential format.. Reading seq # 1: YGL127C_Sbay Reading seq # 2: YGL127C_Scer Reading seq # 3: YGL127C_Skud Reading seq # 4: YGL127C_Smik Reading seq # 5: YGL127C_Spar Sequences read.. Counting patterns.. # site patterns = 125 Counting frequencies.. 120 bytes for distance 20000 bytes for lkl0 16000 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.131013 0.075794 0.031067 0.092086 0.078752 0.152245 0.262324 0.216683 lnL0 = -1057.052799 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1057.052799 x= 0.13101 0.07579 0.03107 0.09209 0.07875 0.15225 0.26232 0.21668 1 h-lim-p 0.0003 0.0026 105.2723 1055.161689 1 0.0004 24 | 0/8 2 h-lim-p 0.0004 0.0029 30.9734 1054.857550 0 0.0007 37 | 0/8 3 h-lim-p 0.0016 0.0253 14.6596 1054.798169 5 0.0007 58 | 0/8 4 h-lim-p 0.0021 0.0467 4.6590 1054.788263 2 0.0010 74 | 0/8 5 h-lim-p 0.0047 0.1910 0.9964 1054.787550 4 0.0015 96 | 0/8 6 h-lim-p 0.0137 2.5413 0.1093 1054.787524 3 0.0024 124 | 0/8 7 h-lim-p 0.0088 6.3154 0.0300 1054.786947 0 0.0701 147 | 0/8 8 h-lim-p 0.0195 2.4774 0.1082 1054.782494 0 0.0389 168 | 0/8 9 h-lim-p 2.5000 20.0000 0.0011 1054.781611 2 1.0889 192 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1054.781601 0 1.0938 212 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1054.781601 0 1.0938 232 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1054.781601 0 0.5469 253 | 0/8 13 h-lim-p 0.3566 20.0000 0.0000 1054.781601 0 0.0111 277 | 0/8 14 h-lim-p 0.0062 20.0000 0.0000 1054.781601 0 0.0008 299 | 0/8 15 h-lim-p 0.0005 20.0000 0.0000 1054.781601 0 0.0000 334 Out... lnL = -1054.781601 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1054.781601 Node 7: lnL = -1054.781601 Node 8: lnL = -1054.781601 Node 9: lnL = -1054.781601 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 211 Sequential format.. Reading seq # 1: YGL129C_Sbay Reading seq # 2: YGL129C_Scer Reading seq # 3: YGL129C_Skud Reading seq # 4: YGL129C_Smik Reading seq # 5: YGL129C_Spar Sequences read.. Counting patterns.. # site patterns = 100 Counting frequencies.. 120 bytes for distance 16000 bytes for lkl0 12800 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.174443 0.051824 0.109957 0.068555 0.023397 0.265636 0.186028 0.270948 lnL0 = -793.691391 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 793.691391 x= 0.17444 0.05182 0.10996 0.06856 0.02340 0.26564 0.18603 0.27095 1 h-lim-p 0.0014 0.0113 34.4636 793.407127 6 0.0005 35 | 0/8 2 h-lim-p 0.0008 0.0061 16.7366 793.321200 2 0.0007 51 | 0/8 3 h-lim-p 0.0026 0.0627 4.5035 793.289757 0 0.0040 63 | 0/8 4 h-lim-p 0.0090 0.1149 1.9800 793.286164 4 0.0022 85 | 0/8 5 h-lim-p 0.0052 0.3033 0.8323 793.285610 5 0.0019 109 | 0/8 6 h-lim-p 0.0071 0.4733 0.2262 793.285575 3 0.0014 136 | 0/8 7 h-lim-p 0.0099 7.9849 0.0326 793.285556 0 0.0197 157 | 0/8 8 h-lim-p 0.1074 20.0000 0.0060 793.284773 0 0.4295 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 793.284721 2 0.9961 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 793.284721 0 1.0938 223 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 793.284721 0 0.2734 245 | 0/8 12 h-lim-p 0.2016 20.0000 0.0000 793.284721 0 0.0028 270 Out... lnL = -793.284721 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -793.284721 Node 7: lnL = -793.284721 Node 8: lnL = -793.284721 Node 9: lnL = -793.284721 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 803 Sequential format.. Reading seq # 1: YGL135W_Sbay Reading seq # 2: YGL135W_Scer Reading seq # 3: YGL135W_Skud Reading seq # 4: YGL135W_Smik Reading seq # 5: YGL135W_Spar Sequences read.. Counting patterns.. # site patterns = 236 Counting frequencies.. 120 bytes for distance 37760 bytes for lkl0 30208 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.423876 0.000060 0.132390 0.162622 0.210610 0.233223 0.143239 0.550793 lnL0 = -3421.297436 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3421.297436 x= 0.42388 0.00006 0.13239 0.16262 0.21061 0.23322 0.14324 0.55079 1 h-lim-p 0.0000 0.0000 153.0636 3421.105931 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0050 81.6404 3419.223411 0 0.0010 40 | 1/8 3 h-lim-p 0.0008 0.0065 35.7409 3418.520562 0 0.0016 53 | 1/8 4 h-lim-p 0.0012 0.0099 37.6809 3418.138118 6 0.0010 78 | 1/8 5 h-lim-p 0.0112 0.0895 2.6064 3418.023899 4 0.0113 99 | 1/8 6 h-lim-p 0.0078 0.0621 1.9976 3417.208475 0 0.0310 113 | 0/8 7 h-lim-p 0.0004 0.0036 26.2566 3415.117214 m 0.0036 125 | 0/8 8 h-lim-p 0.0019 0.0153 6.9671 3414.162327 m 0.0153 137 | 0/8 9 h-lim-p 0.7890 6.3123 0.0397 3412.927269 3 0.8014 155 | 0/8 10 h-lim-p 0.0337 0.2697 0.0360 3412.901802 m 0.2697 175 | 0/8 11 h-lim-p -0.0000 -0.0000 6.7405 h-lim-p: -5.37950585e-21 -4.30360468e-20 6.74049769e+00 3412.901802 .. | 0/8 12 h-lim-p 0.0000 0.0903 6.5286 3412.882650 0 0.0010 209 | 0/8 13 h-lim-p 0.0008 0.0572 7.9599 3412.871555 4 0.0006 230 | 0/8 14 h-lim-p 0.0012 0.4622 4.2298 3412.868013 4 0.0006 251 | 0/8 15 h-lim-p 0.0011 0.0119 2.4108 3412.864508 0 0.0022 264 | 0/8 16 h-lim-p 0.0016 0.0125 1.0544 3412.864180 2 0.0008 281 | 0/8 17 h-lim-p 0.0012 0.0130 0.6469 3412.860824 m 0.0130 294 | 1/8 18 h-lim-p 0.0004 0.8426 16.8967 3412.860288 4 0.0001 323 | 1/8 19 h-lim-p 1.6777 20.0000 0.0013 3412.860083 3 0.9017 342 | 1/8 20 h-lim-p 2.5000 20.0000 0.0001 3412.860082 0 1.0938 361 | 1/8 21 h-lim-p 2.5000 20.0000 0.0000 3412.860082 0 1.0938 380 | 1/8 22 h-lim-p 2.5000 20.0000 0.0000 3412.860082 0 1.0938 399 | 1/8 23 h-lim-p 1.2192 20.0000 0.0000 3412.860082 0 4.8770 420 | 1/8 24 h-lim-p 2.5000 20.0000 0.0000 3412.860082 0 0.0000 462 Out... lnL = -3412.860082 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3412.860082 Node 7: lnL = -3412.860082 Node 8: lnL = -3412.860082 Node 9: lnL = -3412.860082 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 803 Sequential format.. Reading seq # 1: YGL136C_Sbay Reading seq # 2: YGL136C_Scer Reading seq # 3: YGL136C_Skud Reading seq # 4: YGL136C_Smik Reading seq # 5: YGL136C_Spar Sequences read.. Counting patterns.. # site patterns = 303 Counting frequencies.. 120 bytes for distance 48480 bytes for lkl0 38784 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.135251 0.170233 0.067286 0.207654 0.124338 0.253790 0.076693 0.244854 lnL0 = -3403.163313 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3403.163313 x= 0.13525 0.17023 0.06729 0.20765 0.12434 0.25379 0.07669 0.24485 1 h-lim-p 0.0042 0.1564 127.1117 3400.108164 4 0.0004 32 | 0/8 2 h-lim-p 0.0009 0.0075 56.4368 3399.014819 7 0.0008 59 | 0/8 3 h-lim-p 0.0016 0.0128 26.5443 3398.835628 4 0.0006 79 | 0/8 4 h-lim-p 0.0015 0.0294 10.8643 3398.796967 4 0.0008 100 | 0/8 5 h-lim-p 0.0019 0.0452 4.3787 3398.788575 4 0.0011 121 | 0/8 6 h-lim-p 0.0059 0.4638 0.7838 3398.787384 4 0.0038 143 | 0/8 7 h-lim-p 0.4942 20.0000 0.0060 3398.758887 0 1.4825 164 | 0/8 8 h-lim-p 0.0066 0.2074 1.3487 3398.758295 2 0.0007 190 | 0/8 9 h-lim-p 1.1629 20.0000 0.0008 3398.757732 2 1.0175 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3398.757732 0 1.0938 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3398.757732 0 1.0938 246 | 0/8 12 h-lim-p 1.1005 20.0000 0.0000 3398.757732 0 2.2009 267 | 0/8 13 h-lim-p 0.2573 20.0000 0.0000 3398.757732 0 0.0020 293 | 0/8 14 h-lim-p 0.0018 20.0000 0.0000 3398.757732 0 0.0000 325 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 3398.757732 0 0.0000 353 Out... lnL = -3398.757732 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3398.757732 Node 7: lnL = -3398.757732 Node 8: lnL = -3398.757732 Node 9: lnL = -3398.757732 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 342 Sequential format.. Reading seq # 1: YGL137W_Sbay Reading seq # 2: YGL137W_Scer Reading seq # 3: YGL137W_Skud Reading seq # 4: YGL137W_Smik Reading seq # 5: YGL137W_Spar Sequences read.. Counting patterns.. # site patterns = 64 Counting frequencies.. 120 bytes for distance 10240 bytes for lkl0 8192 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.068913 0.041371 0.949685 0.054195 0.081109 0.088445 0.101620 lnL0 = -1261.649243 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1261.649243 x= 0.00006 0.06891 0.04137 0.94968 0.05419 0.08111 0.08844 0.10162 1 h-lim-p 0.0000 0.0000 408.9772 1261.533234 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0006 143.4793 1256.645943 0 0.0005 39 | 1/8 3 h-lim-p 0.0002 0.0013 60.5426 1255.084000 0 0.0010 53 | 1/8 4 h-lim-p 0.0000 0.0001 175.3097 1254.387728 m 0.0001 65 | 2/8 5 h-lim-p 0.0000 0.0000 21126.6675 1246.677447 0 0.0000 79 | 2/8 6 h-lim-p 0.0001 0.0011 118.9726 1238.861441 0 0.0005 93 | 2/8 7 h-lim-p 0.0062 0.0623 10.3507 1238.580677 7 0.0052 120 | 2/8 8 h-lim-p 0.0467 0.3733 1.0712 1237.725022 0 0.0700 132 | 2/8 9 h-lim-p 0.1663 1.3302 0.0576 1236.747569 0 0.4988 145 | 2/8 10 h-lim-p 2.1696 20.0000 0.0132 1236.187844 8 1.4911 185 | 1/8 11 h-lim-p 0.0025 0.1332 7.9239 1236.182058 6 0.0002 221 | 1/8 12 h-lim-p 0.0650 0.6921 0.0240 1235.904024 2 0.5416 240 | 1/8 13 h-lim-p 0.0248 0.1986 0.0158 1235.854782 m 0.1986 259 | 2/8 14 h-lim-p 0.3116 7.3663 0.0100 1235.776323 0 0.9347 279 | 2/8 15 h-lim-p 2.5000 20.0000 0.0015 1235.774103 4 0.9802 305 | 1/8 16 h-lim-p 0.0044 1.6410 0.3401 1235.774093 2 0.0002 330 | 1/8 17 h-lim-p 0.1644 1.3154 0.0004 1235.774007 m 1.3154 349 | 2/8 18 h-lim-p 2.5000 20.0000 0.0001 1235.773994 2 1.0938 372 | 2/8 19 h-lim-p 2.5000 20.0000 0.0000 1235.773994 0 0.5469 391 | 2/8 20 h-lim-p 0.6931 20.0000 0.0000 1235.773994 0 0.6065 409 | 2/8 21 h-lim-p 2.5000 20.0000 0.0000 1235.773994 0 0.0001 441 Out... lnL = -1235.773994 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1235.773994 Node 7: lnL = -1235.773994 Node 8: lnL = -1235.773994 Node 9: lnL = -1235.773994 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 246 Sequential format.. Reading seq # 1: YGL141W_Sbay Reading seq # 2: YGL141W_Scer Reading seq # 3: YGL141W_Skud Reading seq # 4: YGL141W_Smik Reading seq # 5: YGL141W_Spar Sequences read.. Counting patterns.. # site patterns = 106 Counting frequencies.. 120 bytes for distance 16960 bytes for lkl0 13568 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.073833 0.087068 0.067580 0.136910 0.052496 0.242797 0.197001 0.159598 lnL0 = -1108.899079 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1108.899079 x= 0.07383 0.08707 0.06758 0.13691 0.05250 0.24280 0.19700 0.15960 1 h-lim-p 0.0011 0.0084 39.1246 1108.313775 4 0.0008 30 | 0/8 2 h-lim-p 0.0013 0.0101 8.5238 1108.287354 5 0.0008 55 | 0/8 3 h-lim-p 0.0020 0.0777 3.1535 1108.283486 3 0.0009 73 | 0/8 4 h-lim-p 0.0016 0.0480 1.7507 1108.282918 5 0.0005 99 | 0/8 5 h-lim-p 0.0013 0.3448 0.6750 1108.282749 3 0.0009 118 | 0/8 6 h-lim-p 0.0119 6.2158 0.0502 1108.282747 0 0.0015 140 | 0/8 7 h-lim-p 0.0034 20.0000 0.0218 1108.282747 0 0.0015 160 | 0/8 8 h-lim-p 0.2694 20.0000 0.0001 1108.282737 0 1.0777 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1108.282736 0 1.0938 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1108.282736 0 1.0938 222 | 0/8 11 h-lim-p 1.1038 20.0000 0.0000 1108.282736 0 1.1038 242 | 0/8 12 h-lim-p 0.2274 20.0000 0.0000 1108.282736 0 0.1137 262 | 0/8 13 h-lim-p 0.0263 20.0000 0.0001 1108.282736 0 0.0131 282 | 0/8 14 h-lim-p 0.0054 20.0000 0.0003 1108.282736 0 0.0000 321 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1108.282736 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1108.282736 Node 7: lnL = -1108.282736 Node 8: lnL = -1108.282736 Node 9: lnL = -1108.282736 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 246 Sequential format.. Reading seq # 1: YGL142C_Sbay Reading seq # 2: YGL142C_Scer Reading seq # 3: YGL142C_Skud Reading seq # 4: YGL142C_Smik Reading seq # 5: YGL142C_Spar Sequences read.. Counting patterns.. # site patterns = 106 Counting frequencies.. 120 bytes for distance 16960 bytes for lkl0 13568 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.072874 0.084845 0.073906 0.138315 0.051091 0.240418 0.198624 0.158934 lnL0 = -1109.413480 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1109.413480 x= 0.07287 0.08485 0.07391 0.13832 0.05109 0.24042 0.19862 0.15893 1 h-lim-p 0.0013 0.0107 37.1573 1108.892418 9 0.0008 46 | 0/8 2 h-lim-p 0.0015 0.0120 8.3795 1108.865104 5 0.0008 69 | 0/8 3 h-lim-p 0.0020 0.0677 3.3825 1108.860770 3 0.0009 87 | 0/8 4 h-lim-p 0.0014 0.0393 2.0629 1108.860083 4 0.0004 111 | 0/8 5 h-lim-p 0.0017 0.7087 0.5254 1108.859965 4 0.0009 132 | 0/8 6 h-lim-p 0.0136 5.7060 0.0364 1108.859964 1 0.0008 157 | 0/8 7 h-lim-p 0.0020 20.0000 0.0149 1108.859964 0 0.0018 177 | 0/8 8 h-lim-p 0.6716 20.0000 0.0000 1108.859963 0 1.3433 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1108.859963 0 1.0938 218 | 0/8 10 h-lim-p 1.8751 20.0000 0.0000 1108.859963 0 0.8203 238 | 0/8 11 h-lim-p 0.5931 20.0000 0.0000 1108.859963 0 0.0371 261 | 0/8 12 h-lim-p 0.0095 20.0000 0.0000 1108.859963 0 0.0284 282 | 0/8 13 h-lim-p 0.0126 20.0000 0.0001 1108.859963 0 0.0000 313 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 1108.859963 0 0.0000 346 Out... lnL = -1108.859963 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1108.859963 Node 7: lnL = -1108.859963 Node 8: lnL = -1108.859963 Node 9: lnL = -1108.859963 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 380 Sequential format.. Reading seq # 1: YGL143C_Sbay Reading seq # 2: YGL143C_Scer Reading seq # 3: YGL143C_Skud Reading seq # 4: YGL143C_Smik Reading seq # 5: YGL143C_Spar Sequences read.. Counting patterns.. # site patterns = 204 Counting frequencies.. 120 bytes for distance 32640 bytes for lkl0 26112 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.104313 0.140467 0.068691 0.174202 0.117741 0.255749 0.257463 0.217169 lnL0 = -1717.702717 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1717.702717 x= 0.10431 0.14047 0.06869 0.17420 0.11774 0.25575 0.25746 0.21717 1 h-lim-p 0.0017 0.0134 45.4612 1716.974461 3 0.0008 28 | 0/8 2 h-lim-p 0.0022 0.0175 12.4522 1716.897237 2 0.0010 44 | 0/8 3 h-lim-p 0.0018 0.0474 7.2350 1716.876912 7 0.0010 75 | 0/8 4 h-lim-p 0.0026 0.1414 2.7656 1716.873720 5 0.0010 97 | 0/8 5 h-lim-p 0.0078 0.9735 0.3579 1716.873639 3 0.0013 117 | 0/8 6 h-lim-p 0.0042 3.7343 0.1097 1716.873630 1 0.0017 139 | 0/8 7 h-lim-p 0.0162 20.0000 0.0112 1716.873630 0 0.0035 160 | 0/8 8 h-lim-p 0.1153 20.0000 0.0003 1716.873598 0 0.6921 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1716.873598 0 1.0938 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1716.873598 0 1.0938 222 | 0/8 11 h-lim-p 1.2341 20.0000 0.0000 1716.873598 0 0.3085 243 | 0/8 12 h-lim-p 0.0245 20.0000 0.0001 1716.873598 0 0.0003 269 | 0/8 13 h-lim-p 0.0000 20.0000 0.0004 1716.873598 0 0.0000 301 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 1716.873598 0 0.0000 321 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1716.873598 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1716.873598 Node 7: lnL = -1716.873598 Node 8: lnL = -1716.873598 Node 9: lnL = -1716.873598 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 219 Sequential format.. Reading seq # 1: YGL144C_Sbay Reading seq # 2: YGL144C_Scer Reading seq # 3: YGL144C_Skud Reading seq # 4: YGL144C_Smik Reading seq # 5: YGL144C_Spar Sequences read.. Counting patterns.. # site patterns = 104 Counting frequencies.. 120 bytes for distance 16640 bytes for lkl0 13312 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.055711 0.061696 0.083108 0.097520 0.064517 0.078359 0.156930 0.117426 lnL0 = -831.302443 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 831.302443 x= 0.05571 0.06170 0.08311 0.09752 0.06452 0.07836 0.15693 0.11743 1 h-lim-p 0.0006 0.0045 79.4999 829.586806 8 0.0006 39 | 0/8 2 h-lim-p 0.0014 0.0108 12.0237 829.532896 7 0.0008 68 | 0/8 3 h-lim-p 0.0015 0.0223 5.8360 829.522100 4 0.0008 88 | 0/8 4 h-lim-p 0.0015 0.0466 3.0839 829.519337 4 0.0008 109 | 0/8 5 h-lim-p 0.0048 0.3338 0.4865 829.519237 4 0.0009 132 | 0/8 6 h-lim-p 0.0055 2.2662 0.0789 829.519233 0 0.0012 153 | 0/8 7 h-lim-p 0.2699 20.0000 0.0003 829.519112 0 1.0795 175 | 0/8 8 h-lim-p 0.0077 4.3366 0.0492 829.519110 2 0.0012 201 | 0/8 9 h-lim-p 0.6378 20.0000 0.0001 829.519106 0 1.2756 222 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 829.519106 0 1.0938 242 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 829.519106 0 1.0938 262 | 0/8 12 h-lim-p 1.1779 20.0000 0.0000 829.519106 0 2.3559 283 | 0/8 13 h-lim-p 1.1336 20.0000 0.0000 829.519106 0 2.2673 304 | 0/8 14 h-lim-p 0.0232 20.0000 0.0013 829.519106 0 0.0058 325 | 0/8 15 h-lim-p 0.0019 18.2405 0.0041 829.519106 0 0.0000 358 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 829.519106 0 0.0000 390 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -829.519106 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -829.519106 Node 7: lnL = -829.519106 Node 8: lnL = -829.519106 Node 9: lnL = -829.519106 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 590 Sequential format.. Reading seq # 1: YGL145W_Sbay Reading seq # 2: YGL145W_Scer Reading seq # 3: YGL145W_Skud Reading seq # 4: YGL145W_Smik Reading seq # 5: YGL145W_Spar Sequences read.. Counting patterns.. # site patterns = 277 Counting frequencies.. 120 bytes for distance 44320 bytes for lkl0 35456 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.137911 0.060905 0.069862 0.129310 0.150550 0.248080 0.246621 0.243882 lnL0 = -2796.051830 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2796.051830 x= 0.13791 0.06091 0.06986 0.12931 0.15055 0.24808 0.24662 0.24388 1 h-lim-p 0.0059 1.5222 97.5923 2794.627660 6 0.0003 36 | 0/8 2 h-lim-p 0.0013 0.0104 19.4841 2794.493782 6 0.0007 62 | 0/8 3 h-lim-p 0.0015 0.0309 9.5790 2794.472517 5 0.0006 84 | 0/8 4 h-lim-p 0.0019 0.1065 2.8999 2794.470115 5 0.0006 110 | 0/8 5 h-lim-p 0.0045 1.0275 0.4120 2794.470032 2 0.0010 127 | 0/8 6 h-lim-p 0.0091 9.7050 0.0449 2794.470031 0 0.0010 149 | 0/8 7 h-lim-p 0.0215 20.0000 0.0021 2794.470029 0 0.0215 169 | 0/8 8 h-lim-p 0.0047 20.0000 0.0096 2794.469949 0 0.0373 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2794.469942 1 0.9961 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2794.469942 0 2.1875 234 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2794.469942 0 1.0938 254 | 0/8 12 h-lim-p 0.1343 20.0000 0.0000 2794.469942 0 0.0671 274 | 0/8 13 h-lim-p 0.0001 20.0000 0.0036 2794.469942 0 0.0000 296 | 0/8 14 h-lim-p 0.0022 20.0000 0.0000 2794.469942 0 0.0000 337 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -2794.469942 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2794.469942 Node 7: lnL = -2794.469942 Node 8: lnL = -2794.469942 Node 9: lnL = -2794.469942 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 592 Sequential format.. Reading seq # 1: YGL146C_Sbay Reading seq # 2: YGL146C_Scer Reading seq # 3: YGL146C_Skud Reading seq # 4: YGL146C_Smik Reading seq # 5: YGL146C_Spar Sequences read.. Counting patterns.. # site patterns = 259 Counting frequencies.. 120 bytes for distance 41440 bytes for lkl0 33152 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.129333 0.082223 0.047361 0.140484 0.142808 0.265489 0.193039 0.221564 lnL0 = -2809.367551 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2809.367551 x= 0.12933 0.08222 0.04736 0.14048 0.14281 0.26549 0.19304 0.22156 1 h-lim-p 0.0074 1.4955 86.9885 2808.460353 8 0.0003 44 | 0/8 2 h-lim-p 0.0013 0.0165 16.5521 2808.384243 6 0.0006 67 | 0/8 3 h-lim-p 0.0022 0.0781 4.3412 2808.378270 6 0.0007 94 | 0/8 4 h-lim-p 0.0022 0.1596 1.3299 2808.377889 2 0.0005 111 | 0/8 5 h-lim-p 0.0027 0.9155 0.2402 2808.377872 0 0.0007 124 | 0/8 6 h-lim-p 0.0043 8.4930 0.0375 2808.377871 0 0.0009 145 | 0/8 7 h-lim-p 0.0051 20.0000 0.0069 2808.377871 0 0.0011 166 | 0/8 8 h-lim-p 0.2313 20.0000 0.0000 2808.377869 0 0.9252 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2808.377869 0 1.0938 208 | 0/8 10 h-lim-p 1.5721 20.0000 0.0000 2808.377869 0 1.5721 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2808.377869 0 0.0391 253 | 0/8 12 h-lim-p 0.0124 20.0000 0.0000 2808.377869 0 0.0000 295 | 0/8 13 h-lim-p 0.0000 20.0000 0.0009 2808.377869 0 0.0000 326 | 0/8 14 h-lim-p 0.0000 20.0000 0.0048 2808.377869 0 0.0000 350 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 2808.377869 0 0.0000 377 | 0/8 16 h-lim-p 0.0000 20.0000 0.0031 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0009 2808.377869 0 0.0000 433 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 2808.377869 0 0.0000 456 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 2808.377869 0 0.0000 484 | 0/8 20 h-lim-p 0.0000 20.0000 0.0009 | 0/8 21 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -2808.377869 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2808.377869 Node 7: lnL = -2808.377869 Node 8: lnL = -2808.377869 Node 9: lnL = -2808.377869 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 187 Sequential format.. Reading seq # 1: YGL153W_Sbay Reading seq # 2: YGL153W_Scer Reading seq # 3: YGL153W_Skud Reading seq # 4: YGL153W_Smik Reading seq # 5: YGL153W_Spar Sequences read.. Counting patterns.. # site patterns = 103 Counting frequencies.. 120 bytes for distance 16480 bytes for lkl0 13184 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.077443 0.200347 0.073642 0.149265 0.150535 0.141171 0.158175 0.167370 lnL0 = -877.453337 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 877.453337 x= 0.07744 0.20035 0.07364 0.14927 0.15054 0.14117 0.15817 0.16737 1 h-lim-p 0.0055 0.0438 17.8629 877.251634 2 0.0013 27 | 0/8 2 h-lim-p 0.0032 0.0266 7.2416 877.212010 6 0.0017 52 | 0/8 3 h-lim-p 0.0043 0.0959 2.8823 877.206621 4 0.0015 74 | 0/8 4 h-lim-p 0.0078 0.4500 0.5666 877.206355 2 0.0017 91 | 0/8 5 h-lim-p 0.0083 1.9157 0.1159 877.206342 0 0.0021 112 | 0/8 6 h-lim-p 0.0392 20.0000 0.0062 877.206340 1 0.0156 134 | 0/8 7 h-lim-p 0.0149 20.0000 0.0064 877.206280 0 0.0596 156 | 0/8 8 h-lim-p 0.0023 1.2720 0.1682 877.206211 1 0.0029 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 877.206210 0 1.0938 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 877.206210 0 1.0938 218 | 0/8 11 h-lim-p 1.9158 20.0000 0.0000 877.206210 0 0.8382 238 | 0/8 12 h-lim-p 0.5898 20.0000 0.0000 877.206210 0 0.1475 259 | 0/8 13 h-lim-p 0.0330 20.0000 0.0000 877.206210 0 0.0000 299 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -877.206210 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -877.206210 Node 7: lnL = -877.206210 Node 8: lnL = -877.206210 Node 9: lnL = -877.206210 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 187 Sequential format.. Reading seq # 1: YGL154C_Sbay Reading seq # 2: YGL154C_Scer Reading seq # 3: YGL154C_Skud Reading seq # 4: YGL154C_Smik Reading seq # 5: YGL154C_Spar Sequences read.. Counting patterns.. # site patterns = 103 Counting frequencies.. 120 bytes for distance 16480 bytes for lkl0 13184 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.087341 0.123025 0.072935 0.140033 0.159768 0.141878 0.216034 0.174282 lnL0 = -873.745464 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 873.745464 x= 0.08734 0.12303 0.07293 0.14003 0.15977 0.14188 0.21603 0.17428 1 h-lim-p 0.0066 0.0525 16.3740 873.580059 4 0.0013 31 | 0/8 2 h-lim-p 0.0031 0.0328 6.7067 873.554382 3 0.0013 49 | 0/8 3 h-lim-p 0.0066 0.1929 1.3307 873.553008 4 0.0016 70 | 0/8 4 h-lim-p 0.0052 0.7056 0.4192 873.552848 3 0.0020 88 | 0/8 5 h-lim-p 0.0596 20.0000 0.0140 873.552847 0 0.0016 112 | 0/8 6 h-lim-p 0.0109 20.0000 0.0021 873.552847 0 0.0048 132 | 0/8 7 h-lim-p 0.0207 20.0000 0.0005 873.552844 0 0.1652 155 | 0/8 8 h-lim-p 0.0030 16.0141 0.0269 873.552843 0 0.0026 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 873.552843 0 1.0938 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 873.552843 0 2.1875 215 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 873.552843 0 1.0938 235 | 0/8 12 h-lim-p 0.2899 20.0000 0.0000 873.552843 0 4.6387 259 | 0/8 13 h-lim-p 1.3595 20.0000 0.0000 873.552843 0 0.3399 280 | 0/8 14 h-lim-p 0.0043 20.0000 0.0009 873.552843 0 0.0043 300 | 0/8 15 h-lim-p 0.0020 20.0000 0.0019 873.552843 0 0.0000 343 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -873.552843 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -873.552843 Node 7: lnL = -873.552843 Node 8: lnL = -873.552843 Node 9: lnL = -873.552843 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 439 Sequential format.. Reading seq # 1: YGL155W_Sbay Reading seq # 2: YGL155W_Scer Reading seq # 3: YGL155W_Skud Reading seq # 4: YGL155W_Smik Reading seq # 5: YGL155W_Spar Sequences read.. Counting patterns.. # site patterns = 198 Counting frequencies.. 120 bytes for distance 31680 bytes for lkl0 25344 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.091937 0.159469 0.075003 0.110549 0.105418 0.263456 0.197007 0.185491 lnL0 = -2002.950474 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2002.950474 x= 0.09194 0.15947 0.07500 0.11055 0.10542 0.26346 0.19701 0.18549 1 h-lim-p 0.0024 0.0193 38.3538 2002.508365 4 0.0006 31 | 0/8 2 h-lim-p 0.0013 0.0103 13.3982 2002.419247 5 0.0011 52 | 0/8 3 h-lim-p 0.0042 0.1303 3.5310 2002.416338 2 0.0005 70 | 0/8 4 h-lim-p 0.0008 0.1498 2.0405 2002.415137 2 0.0007 86 | 0/8 5 h-lim-p 0.0023 0.3226 0.6495 2002.414980 4 0.0008 107 | 0/8 6 h-lim-p 0.0068 2.2204 0.0814 2002.414978 0 0.0007 129 | 0/8 7 h-lim-p 0.0029 20.0000 0.0207 2002.414977 0 0.0025 149 | 0/8 8 h-lim-p 0.0624 20.0000 0.0008 2002.414822 0 0.4989 172 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2002.414818 0 1.0938 192 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2002.414818 0 1.0938 212 | 0/8 11 h-lim-p 1.9282 20.0000 0.0000 2002.414818 0 0.8436 232 | 0/8 12 h-lim-p 0.6157 20.0000 0.0000 2002.414818 0 0.0000 269 Out... lnL = -2002.414818 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2002.414818 Node 7: lnL = -2002.414818 Node 8: lnL = -2002.414818 Node 9: lnL = -2002.414818 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 406 Sequential format.. Reading seq # 1: YGL156W_Sbay Reading seq # 2: YGL156W_Scer Reading seq # 3: YGL156W_Skud Reading seq # 4: YGL156W_Smik Reading seq # 5: YGL156W_Spar Sequences read.. Counting patterns.. # site patterns = 177 Counting frequencies.. 120 bytes for distance 28320 bytes for lkl0 22656 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.081095 0.086446 0.054671 0.123910 0.144493 0.190613 0.186382 0.159772 lnL0 = -1792.589324 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1792.589324 x= 0.08110 0.08645 0.05467 0.12391 0.14449 0.19061 0.18638 0.15977 1 h-lim-p 0.0026 0.0207 72.7215 1791.661436 8 0.0004 43 | 0/8 2 h-lim-p 0.0016 0.0153 16.5911 1791.562189 2 0.0008 59 | 0/8 3 h-lim-p 0.0027 0.0504 4.8043 1791.555062 6 0.0007 83 | 0/8 4 h-lim-p 0.0036 0.1862 0.8793 1791.554830 4 0.0006 107 | 0/8 5 h-lim-p 0.0067 4.6036 0.0816 1791.554827 0 0.0007 129 | 0/8 6 h-lim-p 0.0048 20.0000 0.0124 1791.554827 0 0.0021 149 | 0/8 7 h-lim-p 0.0050 20.0000 0.0052 1791.554821 0 0.0202 171 | 0/8 8 h-lim-p 0.0045 13.5268 0.0232 1791.554713 0 0.0179 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1791.554709 0 1.0938 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1791.554709 0 1.0938 233 | 0/8 11 h-lim-p 1.3090 20.0000 0.0000 1791.554709 0 1.1454 253 | 0/8 12 h-lim-p 0.8693 20.0000 0.0000 1791.554709 0 0.0000 293 Out... lnL = -1791.554709 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1791.554709 Node 7: lnL = -1791.554709 Node 8: lnL = -1791.554709 Node 9: lnL = -1791.554709 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 502 Sequential format.. Reading seq # 1: YGL157W_Sbay Reading seq # 2: YGL157W_Scer Reading seq # 3: YGL157W_Skud Reading seq # 4: YGL157W_Smik Reading seq # 5: YGL157W_Spar Sequences read.. Counting patterns.. # site patterns = 243 Counting frequencies.. 120 bytes for distance 38880 bytes for lkl0 31104 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.260661 0.168731 0.094537 0.187797 0.104810 0.241108 0.272841 0.393641 lnL0 = -2334.703327 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2334.703327 x= 0.26066 0.16873 0.09454 0.18780 0.10481 0.24111 0.27284 0.39364 1 h-lim-p 0.0007 0.0052 29.7015 2334.361686 1 0.0008 24 | 0/8 2 h-lim-p 0.0012 0.0152 20.4623 2334.250046 7 0.0007 53 | 0/8 3 h-lim-p 0.0028 0.0413 5.3780 2334.237223 6 0.0010 78 | 0/8 4 h-lim-p 0.0113 1.2972 0.4696 2334.236966 3 0.0024 97 | 0/8 5 h-lim-p 0.0017 0.3039 0.6331 2334.236860 3 0.0010 125 | 0/8 6 h-lim-p 0.0049 2.2680 0.1336 2334.236847 2 0.0016 151 | 0/8 7 h-lim-p 0.0071 13.5098 0.0304 2334.236837 1 0.0074 173 | 0/8 8 h-lim-p 0.0579 20.0000 0.0039 2334.236084 0 0.2317 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 2334.236056 1 0.9961 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2334.236056 0 1.0938 237 | 0/8 11 h-lim-p 1.7422 20.0000 0.0000 2334.236056 0 3.4845 258 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2334.236056 0 0.2734 280 | 0/8 13 h-lim-p 1.2164 20.0000 0.0000 2334.236056 0 0.0012 309 Out... lnL = -2334.236056 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2334.236056 Node 7: lnL = -2334.236056 Node 8: lnL = -2334.236056 Node 9: lnL = -2334.236056 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 964 Sequential format.. Reading seq # 1: YGL158W_Sbay Reading seq # 2: YGL158W_Scer Reading seq # 3: YGL158W_Skud Reading seq # 4: YGL158W_Smik Reading seq # 5: YGL158W_Spar Sequences read.. Counting patterns.. # site patterns = 324 Counting frequencies.. 120 bytes for distance 51840 bytes for lkl0 41472 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.170065 0.054011 0.095703 0.116388 0.104935 0.249476 0.207621 0.266021 lnL0 = -4113.037152 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4113.037152 x= 0.17007 0.05401 0.09570 0.11639 0.10494 0.24948 0.20762 0.26602 1 h-lim-p 0.0004 0.0032 126.3370 4111.200543 8 0.0002 44 | 0/8 2 h-lim-p 0.0007 0.0054 28.0292 4111.069106 4 0.0003 66 | 0/8 3 h-lim-p 0.0005 0.0125 19.4552 4111.021559 6 0.0003 92 | 0/8 4 h-lim-p 0.0009 0.0250 7.8010 4111.013425 4 0.0003 112 | 0/8 5 h-lim-p 0.0064 0.4468 0.4079 4111.013391 2 0.0004 131 | 0/8 6 h-lim-p 0.0025 4.4937 0.0687 4111.013389 1 0.0006 154 | 0/8 7 h-lim-p 0.0373 20.0000 0.0011 4111.013389 0 0.0163 174 | 0/8 8 h-lim-p 0.0078 20.0000 0.0024 4111.013371 0 0.0470 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4111.013371 0 1.0938 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4111.013371 0 1.0938 236 | 0/8 11 h-lim-p 1.2180 20.0000 0.0000 4111.013371 0 3.6539 257 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4111.013371 0 0.2734 279 | 0/8 13 h-lim-p 0.0755 20.0000 0.0000 4111.013371 0 0.0142 301 | 0/8 14 h-lim-p 0.0058 20.0000 0.0000 4111.013371 0 0.0000 336 | 0/8 15 h-lim-p 0.0000 20.0000 0.0009 | 0/8 16 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -4111.013371 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4111.013371 Node 7: lnL = -4111.013371 Node 8: lnL = -4111.013371 Node 9: lnL = -4111.013371 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 484 Sequential format.. Reading seq # 1: YGL159W_Sbay Reading seq # 2: YGL159W_Scer Reading seq # 3: YGL159W_Skud Reading seq # 4: YGL159W_Smik Reading seq # 5: YGL159W_Spar Sequences read.. Counting patterns.. # site patterns = 251 Counting frequencies.. 120 bytes for distance 40160 bytes for lkl0 32128 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.088847 0.247781 0.115241 0.145540 0.146774 0.248811 0.287699 0.208572 lnL0 = -2292.312879 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2292.312879 x= 0.08885 0.24778 0.11524 0.14554 0.14677 0.24881 0.28770 0.20857 1 h-lim-p 0.0048 0.0387 32.8757 2291.712612 2 0.0011 27 | 0/8 2 h-lim-p 0.0011 0.0089 18.1969 2291.498662 0 0.0022 40 | 0/8 3 h-lim-p 0.0041 0.0330 5.6538 2291.491001 4 0.0005 62 | 0/8 4 h-lim-p 0.0016 0.3488 1.9453 2291.488467 2 0.0015 78 | 0/8 5 h-lim-p 0.0031 0.2393 0.9156 2291.488018 2 0.0012 94 | 0/8 6 h-lim-p 0.0118 3.6379 0.0934 2291.487591 1 0.0148 116 | 0/8 7 h-lim-p 0.0072 1.2620 0.1926 2291.485669 0 0.0108 136 | 0/8 8 h-lim-p 0.0032 0.8196 0.6509 2291.466039 0 0.0127 158 | 0/8 9 h-lim-p 2.5000 20.0000 0.0011 2291.465685 3 1.0004 184 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2291.465685 0 1.0938 204 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2291.465685 0 1.0938 224 | 0/8 12 h-lim-p 1.1293 20.0000 0.0000 2291.465685 0 4.5174 246 | 0/8 13 h-lim-p 0.3043 20.0000 0.0001 2291.465685 0 0.0024 272 | 0/8 14 h-lim-p 0.0003 20.0000 0.0007 2291.465685 0 0.0000 294 | 0/8 15 h-lim-p 0.0009 20.0000 0.0000 2291.465685 0 0.0001 316 | 0/8 16 h-lim-p 0.0004 20.0000 0.0000 2291.465685 0 0.0000 351 Out... lnL = -2291.465685 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2291.465685 Node 7: lnL = -2291.465685 Node 8: lnL = -2291.465685 Node 9: lnL = -2291.465685 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 439 Sequential format.. Reading seq # 1: YGL160W_Sbay Reading seq # 2: YGL160W_Scer Reading seq # 3: YGL160W_Skud Reading seq # 4: YGL160W_Smik Reading seq # 5: YGL160W_Spar Sequences read.. Counting patterns.. # site patterns = 224 Counting frequencies.. 120 bytes for distance 35840 bytes for lkl0 28672 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.215268 0.474537 0.000060 0.323986 0.698804 0.354557 0.296082 0.369042 lnL0 = -2161.798215 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2161.798215 x= 0.21527 0.47454 0.00006 0.32399 0.69880 0.35456 0.29608 0.36904 1 h-lim-p 0.0000 0.0000 191.8843 2161.760937 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0025 203.3609 2127.204325 0 0.0019 41 | 1/8 3 h-lim-p 0.0006 0.0049 66.8325 2123.840587 0 0.0018 54 | 1/8 4 h-lim-p 0.0050 0.0399 13.6311 2123.180774 0 0.0075 66 | 1/8 5 h-lim-p 0.0062 0.0494 10.8289 2122.996998 6 0.0033 91 | 1/8 6 h-lim-p 0.0607 1.3063 0.5980 2118.197839 0 0.3640 105 | 1/8 7 h-lim-p 0.0054 0.0435 11.7158 2117.098833 0 0.0109 125 | 1/8 8 h-lim-p 0.4539 3.6312 0.1136 2116.262170 1 0.5674 139 | 1/8 9 h-lim-p 2.5000 20.0000 0.0223 2116.212362 5 0.5291 172 | 1/8 10 h-lim-p 0.7926 20.0000 0.0149 2116.208014 5 0.4500 204 | 1/8 11 h-lim-p 2.5000 20.0000 0.0011 2116.207809 3 0.8855 231 | 1/8 12 h-lim-p 2.5000 20.0000 0.0002 2116.207808 1 0.6152 253 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 2116.207808 0 1.0938 272 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 2116.207808 0 1.0938 291 | 1/8 15 h-lim-p 1.0800 20.0000 0.0000 2116.207808 0 0.0169 315 | 1/8 16 h-lim-p 0.0033 20.0000 0.0000 2116.207808 0 0.0017 334 | 1/8 17 h-lim-p 0.0000 20.0000 0.0075 2116.207808 0 0.0000 360 | 1/8 18 h-lim-p 0.0004 20.0000 0.0000 2116.207808 0 0.0000 390 Out... lnL = -2116.207808 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2116.207808 Node 7: lnL = -2116.207808 Node 8: lnL = -2116.207808 Node 9: lnL = -2116.207808 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 439 Sequential format.. Reading seq # 1: YGL161C_Sbay Reading seq # 2: YGL161C_Scer Reading seq # 3: YGL161C_Skud Reading seq # 4: YGL161C_Smik Reading seq # 5: YGL161C_Spar Sequences read.. Counting patterns.. # site patterns = 208 Counting frequencies.. 120 bytes for distance 33280 bytes for lkl0 26624 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.125470 0.083597 0.121192 0.105303 0.123342 0.214629 0.226888 0.210809 lnL0 = -1936.422468 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1936.422468 x= 0.12547 0.08360 0.12119 0.10530 0.12334 0.21463 0.22689 0.21081 1 h-lim-p 0.0019 0.0154 43.2376 1935.852863 6 0.0006 35 | 0/8 2 h-lim-p 0.0016 0.0206 16.7535 1935.728256 7 0.0010 66 | 0/8 3 h-lim-p 0.0011 0.0212 15.7577 1935.687105 6 0.0006 91 | 0/8 4 h-lim-p 0.0026 0.0824 3.3816 1935.681598 3 0.0011 109 | 0/8 5 h-lim-p 0.0029 0.2347 1.2818 1935.680905 4 0.0010 131 | 0/8 6 h-lim-p 0.0073 1.1309 0.1724 1935.680887 2 0.0012 150 | 0/8 7 h-lim-p 0.0036 3.3348 0.0570 1935.680885 0 0.0016 170 | 0/8 8 h-lim-p 0.1327 20.0000 0.0007 1935.680671 0 1.0614 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1935.680670 0 1.0938 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1935.680670 0 1.0938 233 | 0/8 11 h-lim-p 1.8414 20.0000 0.0000 1935.680670 0 1.6112 253 | 0/8 12 h-lim-p 2.3823 20.0000 0.0000 1935.680670 0 0.5211 274 | 0/8 13 h-lim-p 0.1634 20.0000 0.0000 1935.680670 0 0.0204 296 | 0/8 14 h-lim-p 0.0070 20.0000 0.0000 1935.680670 0 0.0000 332 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 1935.680670 0 0.0000 363 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 1935.680670 0 0.0000 391 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1935.680670 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1935.680670 Node 7: lnL = -1935.680670 Node 8: lnL = -1935.680670 Node 9: lnL = -1935.680670 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 876 Sequential format.. Reading seq # 1: YGL162W_Sbay Reading seq # 2: YGL162W_Scer Reading seq # 3: YGL162W_Skud Reading seq # 4: YGL162W_Smik Reading seq # 5: YGL162W_Spar Sequences read.. Counting patterns.. # site patterns = 220 Counting frequencies.. 120 bytes for distance 35200 bytes for lkl0 28160 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.128271 0.032419 0.030282 0.079913 0.049648 0.118821 0.139296 0.179565 lnL0 = -3314.027132 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3314.027132 x= 0.12827 0.03242 0.03028 0.07991 0.04965 0.11882 0.13930 0.17957 1 h-lim-p 0.0016 0.0128 189.5891 3312.950568 6 0.0001 38 | 0/8 2 h-lim-p 0.0005 0.0066 26.9247 3312.864984 6 0.0002 65 | 0/8 3 h-lim-p 0.0004 0.0137 16.3754 3312.854236 4 0.0001 86 | 0/8 4 h-lim-p 0.0006 0.0348 2.7835 3312.853693 2 0.0001 103 | 0/8 5 h-lim-p 0.0007 0.2506 0.5803 3312.853663 2 0.0002 120 | 0/8 6 h-lim-p 0.0008 0.3811 0.1247 3312.853661 0 0.0002 141 | 0/8 7 h-lim-p 0.0004 9.0626 0.0514 3312.853661 0 0.0004 161 | 0/8 8 h-lim-p 0.3347 20.0000 0.0001 3312.853632 0 1.3389 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3312.853631 0 1.0938 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3312.853631 0 2.1875 223 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3312.853631 0 0.3125 245 | 0/8 12 h-lim-p 0.0414 20.0000 0.0000 3312.853631 0 0.0003 271 Out... lnL = -3312.853631 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3312.853631 Node 7: lnL = -3312.853631 Node 8: lnL = -3312.853631 Node 9: lnL = -3312.853631 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 870 Sequential format.. Reading seq # 1: YGL163C_Sbay Reading seq # 2: YGL163C_Scer Reading seq # 3: YGL163C_Skud Reading seq # 4: YGL163C_Smik Reading seq # 5: YGL163C_Spar Sequences read.. Counting patterns.. # site patterns = 365 Counting frequencies.. 120 bytes for distance 58400 bytes for lkl0 46720 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.164417 0.089425 0.124743 0.138146 0.088186 0.228839 0.258278 0.259153 lnL0 = -4135.310652 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4135.310652 x= 0.16442 0.08942 0.12474 0.13815 0.08819 0.22884 0.25828 0.25915 1 h-lim-p 0.0020 0.0161 115.0050 4133.322659 7 0.0003 41 | 0/8 2 h-lim-p 0.0007 0.0057 23.2324 4133.235205 2 0.0003 57 | 0/8 3 h-lim-p 0.0004 0.0157 19.7519 4133.181955 4 0.0004 77 | 0/8 4 h-lim-p 0.0016 0.0461 5.1285 4133.176062 4 0.0005 99 | 0/8 5 h-lim-p 0.0017 0.2305 1.5783 4133.175267 2 0.0007 115 | 0/8 6 h-lim-p 0.0084 1.9361 0.1347 4133.175262 1 0.0005 132 | 0/8 7 h-lim-p 0.0038 13.2158 0.0185 4133.175260 0 0.0033 152 | 0/8 8 h-lim-p 0.0269 20.0000 0.0023 4133.174703 0 0.3223 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4133.174692 1 0.9961 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4133.174692 0 1.0938 217 | 0/8 11 h-lim-p 2.4037 20.0000 0.0000 4133.174692 0 2.1033 237 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4133.174692 0 1.0938 257 | 0/8 13 h-lim-p 0.2637 20.0000 0.0000 4133.174692 0 6.3282 281 | 0/8 14 h-lim-p 0.6901 20.0000 0.0000 4133.174692 0 0.3450 301 | 0/8 15 h-lim-p 0.0089 20.0000 0.0019 4133.174692 0 0.0000 340 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 4133.174692 0 0.0000 368 Out... lnL = -4133.174692 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4133.174692 Node 7: lnL = -4133.174692 Node 8: lnL = -4133.174692 Node 9: lnL = -4133.174692 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 751 Sequential format.. Reading seq # 1: YGL169W_Sbay Reading seq # 2: YGL169W_Scer Reading seq # 3: YGL169W_Skud Reading seq # 4: YGL169W_Smik Reading seq # 5: YGL169W_Spar Sequences read.. Counting patterns.. # site patterns = 311 Counting frequencies.. 120 bytes for distance 49760 bytes for lkl0 39808 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.146454 0.043281 0.104719 0.140524 0.108741 0.230233 0.260683 0.233655 lnL0 = -3524.084726 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3524.084726 x= 0.14645 0.04328 0.10472 0.14052 0.10874 0.23023 0.26068 0.23365 1 h-lim-p 0.0020 0.7050 186.4510 3519.792352 8 0.0003 41 | 0/8 2 h-lim-p 0.0011 0.0087 23.6164 3519.660568 5 0.0005 62 | 0/8 3 h-lim-p 0.0006 0.0211 18.4918 3519.603697 4 0.0005 82 | 0/8 4 h-lim-p 0.0029 0.1121 3.0819 3519.600764 2 0.0007 99 | 0/8 5 h-lim-p 0.0019 0.3024 1.0965 3519.600408 3 0.0007 118 | 0/8 6 h-lim-p 0.0043 1.1688 0.1673 3519.600400 0 0.0005 132 | 0/8 7 h-lim-p 0.0104 20.0000 0.0087 3519.600375 0 0.0208 153 | 0/8 8 h-lim-p 0.0072 20.0000 0.0251 3519.599124 0 0.0577 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 3519.598971 2 0.9961 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3519.598971 0 1.0938 220 | 0/8 11 h-lim-p 2.1381 20.0000 0.0000 3519.598971 0 1.0691 240 | 0/8 12 h-lim-p 0.9115 20.0000 0.0000 3519.598971 0 0.4557 260 | 0/8 13 h-lim-p 0.0108 20.0000 0.0002 3519.598971 0 0.0000 291 | 0/8 14 h-lim-p 0.0013 20.0000 0.0000 3519.598971 0 0.0007 311 Out... lnL = -3519.598971 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3519.598971 Node 7: lnL = -3519.598971 Node 8: lnL = -3519.598971 Node 9: lnL = -3519.598971 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 727 Sequential format.. Reading seq # 1: YGL170C_Sbay Reading seq # 2: YGL170C_Scer Reading seq # 3: YGL170C_Skud Reading seq # 4: YGL170C_Smik Reading seq # 5: YGL170C_Spar Sequences read.. Counting patterns.. # site patterns = 313 Counting frequencies.. 120 bytes for distance 50080 bytes for lkl0 40064 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.130948 0.061579 0.132702 0.131279 0.113681 0.211352 0.238156 0.217642 lnL0 = -3468.827119 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3468.827119 x= 0.13095 0.06158 0.13270 0.13128 0.11368 0.21135 0.23816 0.21764 1 h-lim-p 0.0024 0.7749 171.4999 3464.518282 9 0.0003 43 | 0/8 2 h-lim-p 0.0011 0.0085 44.9409 3463.863226 7 0.0007 71 | 0/8 3 h-lim-p 0.0009 0.0103 32.2017 3463.748029 7 0.0003 100 | 0/8 4 h-lim-p 0.0025 0.0829 4.0702 3463.742638 5 0.0007 123 | 0/8 5 h-lim-p 0.0028 0.2853 0.9781 3463.742366 2 0.0006 140 | 0/8 6 h-lim-p 0.0048 2.1940 0.1232 3463.742356 2 0.0008 166 | 0/8 7 h-lim-p 0.0053 20.0000 0.0180 3463.742048 0 0.0421 189 | 0/8 8 h-lim-p 0.0047 15.5358 0.1603 3463.735903 0 0.0189 211 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 3463.735362 3 1.0004 237 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3463.735362 0 1.0938 257 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3463.735362 0 1.0938 277 | 0/8 12 h-lim-p 1.2100 20.0000 0.0000 3463.735362 0 1.0587 297 | 0/8 13 h-lim-p 0.5680 20.0000 0.0000 3463.735362 0 0.2840 317 | 0/8 14 h-lim-p 0.0265 20.0000 0.0001 3463.735362 0 0.0000 349 | 0/8 15 h-lim-p 0.0015 20.0000 0.0000 3463.735362 0 0.0000 379 Out... lnL = -3463.735362 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3463.735362 Node 7: lnL = -3463.735362 Node 8: lnL = -3463.735362 Node 9: lnL = -3463.735362 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 292 Sequential format.. Reading seq # 1: YGL171W_Sbay Reading seq # 2: YGL171W_Scer Reading seq # 3: YGL171W_Skud Reading seq # 4: YGL171W_Smik Reading seq # 5: YGL171W_Spar Sequences read.. Counting patterns.. # site patterns = 129 Counting frequencies.. 120 bytes for distance 20640 bytes for lkl0 16512 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.074279 0.040831 0.056029 0.129470 0.097132 0.171781 0.173173 0.134406 lnL0 = -1252.518871 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1252.518871 x= 0.07428 0.04083 0.05603 0.12947 0.09713 0.17178 0.17317 0.13441 1 h-lim-p 0.0008 0.0066 111.7358 1250.429578 3 0.0004 29 | 0/8 2 h-lim-p 0.0007 0.0058 21.9637 1250.278703 5 0.0006 50 | 0/8 3 h-lim-p 0.0021 0.0473 6.6831 1250.264983 5 0.0007 74 | 0/8 4 h-lim-p 0.0026 0.1501 1.7084 1250.263701 5 0.0009 98 | 0/8 5 h-lim-p 0.0117 0.8400 0.1378 1250.263695 0 0.0006 113 | 0/8 6 h-lim-p 0.0209 20.0000 0.0042 1250.263658 0 0.0628 134 | 0/8 7 h-lim-p 0.0032 3.8257 0.0820 1250.263242 0 0.0129 156 | 0/8 8 h-lim-p 0.0024 0.8369 0.4438 1250.262824 3 0.0019 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1250.262797 2 0.9961 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1250.262797 0 1.0938 226 | 0/8 11 h-lim-p 1.1553 20.0000 0.0000 1250.262797 0 1.0109 246 | 0/8 12 h-lim-p 0.9074 20.0000 0.0000 1250.262797 0 0.0142 271 | 0/8 13 h-lim-p 0.0004 20.0000 0.0002 1250.262797 0 0.0000 293 | 0/8 14 h-lim-p 0.0005 20.0000 0.0000 1250.262797 0 0.0001 315 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 1250.262797 0 0.0001 335 | 0/8 16 h-lim-p 0.0002 20.0000 0.0000 1250.262797 0 0.0002 355 Out... lnL = -1250.262797 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1250.262797 Node 7: lnL = -1250.262797 Node 8: lnL = -1250.262797 Node 9: lnL = -1250.262797 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 613 Sequential format.. Reading seq # 1: YGL172W_Sbay Reading seq # 2: YGL172W_Scer Reading seq # 3: YGL172W_Skud Reading seq # 4: YGL172W_Smik Reading seq # 5: YGL172W_Spar Sequences read.. Counting patterns.. # site patterns = 179 Counting frequencies.. 120 bytes for distance 28640 bytes for lkl0 22912 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.066770 0.060267 0.015492 0.086233 0.047624 0.166636 0.177022 0.117121 lnL0 = -2404.046836 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2404.046836 x= 0.06677 0.06027 0.01549 0.08623 0.04762 0.16664 0.17702 0.11712 1 h-lim-p 0.0002 0.0012 180.6638 2402.828357 8 0.0001 43 | 0/8 2 h-lim-p 0.0002 0.0015 58.3315 2402.572667 6 0.0002 66 | 0/8 3 h-lim-p 0.0004 0.0059 22.9147 2402.540967 5 0.0001 91 | 0/8 4 h-lim-p 0.0005 0.0319 6.0655 2402.535819 5 0.0003 116 | 0/8 5 h-lim-p 0.0011 0.1334 1.7131 2402.535370 4 0.0003 139 | 0/8 6 h-lim-p 0.0047 1.7503 0.1207 2402.535367 1 0.0005 155 | 0/8 7 h-lim-p 0.0012 3.8888 0.0466 2402.535365 0 0.0006 175 | 0/8 8 h-lim-p 0.0242 20.0000 0.0012 2402.534052 0 0.3878 199 | 0/8 9 h-lim-p 0.9967 20.0000 0.0005 2402.533992 1 1.0278 221 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2402.533991 0 1.0938 241 | 0/8 11 h-lim-p 1.4635 20.0000 0.0000 2402.533991 0 1.2806 261 | 0/8 12 h-lim-p 1.7573 20.0000 0.0000 2402.533991 0 3.5146 282 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2402.533991 0 0.2734 304 | 0/8 14 h-lim-p 0.0445 20.0000 0.0001 2402.533991 0 0.0000 349 | 0/8 15 h-lim-p 0.0000 20.0000 0.0021 2402.533991 0 0.0000 382 | 0/8 16 h-lim-p 0.0000 20.0000 0.0021 | 0/8 17 h-lim-p 0.0000 20.0000 0.0021 Out... lnL = -2402.533991 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2402.533991 Node 7: lnL = -2402.533991 Node 8: lnL = -2402.533991 Node 9: lnL = -2402.533991 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 658 Sequential format.. Reading seq # 1: YGL173C_Sbay Reading seq # 2: YGL173C_Scer Reading seq # 3: YGL173C_Skud Reading seq # 4: YGL173C_Smik Reading seq # 5: YGL173C_Spar Sequences read.. Counting patterns.. # site patterns = 183 Counting frequencies.. 120 bytes for distance 29280 bytes for lkl0 23424 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.072169 0.035611 0.014481 0.085053 0.048804 0.164559 0.193259 0.121578 lnL0 = -2454.304076 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2454.304076 x= 0.07217 0.03561 0.01448 0.08505 0.04880 0.16456 0.19326 0.12158 1 h-lim-p 0.0002 0.0017 220.7107 2452.777237 7 0.0001 39 | 0/8 2 h-lim-p 0.0001 0.0012 64.4311 2452.481035 5 0.0002 62 | 0/8 3 h-lim-p 0.0005 0.0080 19.3445 2452.451354 6 0.0002 89 | 0/8 4 h-lim-p 0.0003 0.0204 10.4635 2452.439892 3 0.0003 107 | 0/8 5 h-lim-p 0.0008 0.0620 3.4137 2452.438543 4 0.0003 129 | 0/8 6 h-lim-p 0.0014 0.2927 0.6558 2452.438490 3 0.0002 149 | 0/8 7 h-lim-p 0.0016 1.8082 0.0991 2452.438488 1 0.0004 172 | 0/8 8 h-lim-p 0.1488 20.0000 0.0003 2452.437944 0 1.1908 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2452.437934 1 1.0938 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2452.437934 0 2.1875 237 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2452.437934 0 1.0938 257 | 0/8 12 h-lim-p 0.2814 20.0000 0.0000 2452.437934 0 4.5021 281 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2452.437934 0 0.2734 303 | 0/8 14 h-lim-p 1.2974 20.0000 0.0000 2452.437934 0 0.0089 329 | 0/8 15 h-lim-p 0.0014 20.0000 0.0000 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0042 | 0/8 17 h-lim-p 0.0000 20.0000 0.0042 Out... lnL = -2452.437934 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2452.437934 Node 7: lnL = -2452.437934 Node 8: lnL = -2452.437934 Node 9: lnL = -2452.437934 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 241 Sequential format.. Reading seq # 1: YGL174W_Sbay Reading seq # 2: YGL174W_Scer Reading seq # 3: YGL174W_Skud Reading seq # 4: YGL174W_Smik Reading seq # 5: YGL174W_Spar Sequences read.. Counting patterns.. # site patterns = 136 Counting frequencies.. 120 bytes for distance 21760 bytes for lkl0 17408 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.087480 0.072679 0.090379 0.155828 0.112831 0.216613 0.226264 0.166066 lnL0 = -1067.104987 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1067.104987 x= 0.08748 0.07268 0.09038 0.15583 0.11283 0.21661 0.22626 0.16607 1 h-lim-p 0.0008 0.0060 43.5401 1066.266119 1 0.0009 24 | 0/8 2 h-lim-p 0.0026 0.0208 10.0117 1066.203086 5 0.0013 46 | 0/8 3 h-lim-p 0.0030 0.0911 4.3473 1066.195076 6 0.0010 73 | 0/8 4 h-lim-p 0.0026 0.1726 1.6674 1066.193343 6 0.0015 100 | 0/8 5 h-lim-p 0.0089 1.1167 0.2724 1066.193265 2 0.0021 117 | 0/8 6 h-lim-p 0.0049 1.4067 0.1164 1066.193255 2 0.0016 142 | 0/8 7 h-lim-p 0.0162 12.2569 0.0113 1066.193250 1 0.0129 164 | 0/8 8 h-lim-p 0.0278 20.0000 0.0052 1066.192930 0 0.2223 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1066.192892 2 0.9961 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1066.192892 0 2.1875 231 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1066.192892 0 1.0938 251 | 0/8 12 h-lim-p 0.3389 20.0000 0.0000 1066.192892 0 5.4220 275 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1066.192892 0 0.3125 297 | 0/8 14 h-lim-p 0.0313 20.0000 0.0000 1066.192892 0 0.0020 320 | 0/8 15 h-lim-p 0.0002 20.0000 0.0003 1066.192892 0 0.0001 341 | 0/8 16 h-lim-p 0.0006 20.0000 0.0000 1066.192892 0 0.0000 374 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1066.192892 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1066.192892 Node 7: lnL = -1066.192892 Node 8: lnL = -1066.192892 Node 9: lnL = -1066.192892 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 240 Sequential format.. Reading seq # 1: YGL175C_Sbay Reading seq # 2: YGL175C_Scer Reading seq # 3: YGL175C_Skud Reading seq # 4: YGL175C_Smik Reading seq # 5: YGL175C_Spar Sequences read.. Counting patterns.. # site patterns = 126 Counting frequencies.. 120 bytes for distance 20160 bytes for lkl0 16128 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.083448 0.100306 0.102609 0.166158 0.102502 0.219931 0.271074 0.168971 lnL0 = -1130.333239 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1130.333239 x= 0.08345 0.10031 0.10261 0.16616 0.10250 0.21993 0.27107 0.16897 1 h-lim-p 0.0009 0.0071 30.6913 1129.890694 7 0.0010 37 | 0/8 2 h-lim-p 0.0047 0.0679 6.2233 1129.864386 7 0.0014 67 | 0/8 3 h-lim-p 0.0023 0.0682 3.9042 1129.857621 4 0.0012 88 | 0/8 4 h-lim-p 0.0029 0.2203 1.5265 1129.856412 4 0.0013 107 | 0/8 5 h-lim-p 0.0120 1.7007 0.1613 1129.856392 2 0.0016 125 | 0/8 6 h-lim-p 0.0072 8.1015 0.0352 1129.856391 0 0.0018 146 | 0/8 7 h-lim-p 0.0147 20.0000 0.0043 1129.856389 0 0.0295 167 | 0/8 8 h-lim-p 0.0262 20.0000 0.0049 1129.856307 0 0.1047 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1129.856301 1 0.9961 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1129.856301 0 1.0938 231 | 0/8 11 h-lim-p 1.0915 20.0000 0.0000 1129.856301 0 0.8186 251 | 0/8 12 h-lim-p 0.0270 20.0000 0.0001 1129.856301 0 0.0001 279 | 0/8 13 h-lim-p 0.0002 20.0000 0.0000 1129.856301 0 0.0000 301 | 0/8 14 h-lim-p 0.0003 20.0000 0.0000 1129.856301 0 0.0000 324 Out... lnL = -1129.856301 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1129.856301 Node 7: lnL = -1129.856301 Node 8: lnL = -1129.856301 Node 9: lnL = -1129.856301 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 242 Sequential format.. Reading seq # 1: YGL176C_Sbay Reading seq # 2: YGL176C_Scer Reading seq # 3: YGL176C_Skud Reading seq # 4: YGL176C_Smik Reading seq # 5: YGL176C_Spar Sequences read.. Counting patterns.. # site patterns = 137 Counting frequencies.. 120 bytes for distance 21920 bytes for lkl0 17536 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.090028 0.297857 0.072858 0.194352 0.147603 0.193583 0.315316 0.200289 lnL0 = -1133.856471 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1133.856471 x= 0.09003 0.29786 0.07286 0.19435 0.14760 0.19358 0.31532 0.20029 1 h-lim-p 0.0024 0.0189 8.9202 1133.770779 3 0.0021 28 | 0/8 2 h-lim-p 0.0034 0.0596 5.5903 1133.743519 6 0.0023 54 | 0/8 3 h-lim-p 0.0057 20.0000 2.2350 1133.740663 4 0.0014 76 | 0/8 4 h-lim-p 0.0166 0.5588 0.1879 1133.740613 3 0.0029 97 | 0/8 5 h-lim-p 0.0046 4.2497 0.1198 1133.740600 2 0.0023 122 | 0/8 6 h-lim-p 0.0109 13.3123 0.0248 1133.740599 1 0.0027 145 | 0/8 7 h-lim-p 0.0112 20.0000 0.0059 1133.740599 0 0.0049 165 | 0/8 8 h-lim-p 0.0833 20.0000 0.0004 1133.740591 0 0.6663 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1133.740591 0 1.0938 208 | 0/8 10 h-lim-p 2.4542 20.0000 0.0000 1133.740591 0 1.0737 228 | 0/8 11 h-lim-p 0.9649 20.0000 0.0000 1133.740591 015.4387 252 | 0/8 12 h-lim-p 0.0732 20.0000 0.0007 1133.740591 0 0.0183 273 | 0/8 13 h-lim-p 0.0055 20.0000 0.0023 1133.740591 0 0.0003 296 | 0/8 14 h-lim-p 0.0000 3.7202 0.0298 1133.740591 0 0.0000 326 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 1133.740591 0 0.0000 351 Out... lnL = -1133.740591 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1133.740591 Node 7: lnL = -1133.740591 Node 8: lnL = -1133.740591 Node 9: lnL = -1133.740591 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 863 Sequential format.. Reading seq # 1: YGL179C_Sbay Reading seq # 2: YGL179C_Scer Reading seq # 3: YGL179C_Skud Reading seq # 4: YGL179C_Smik Reading seq # 5: YGL179C_Spar Sequences read.. Counting patterns.. # site patterns = 295 Counting frequencies.. 120 bytes for distance 47200 bytes for lkl0 37760 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.140215 0.026860 0.071990 0.138005 0.087360 0.205364 0.172090 0.211883 lnL0 = -3897.912650 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3897.912650 x= 0.14022 0.02686 0.07199 0.13800 0.08736 0.20536 0.17209 0.21188 1 h-lim-p 0.0007 0.0054 232.7762 3894.381960 6 0.0001 36 | 0/8 2 h-lim-p 0.0003 0.0025 57.7764 3893.828414 6 0.0003 61 | 0/8 3 h-lim-p 0.0007 0.0110 26.9396 3893.766488 7 0.0002 91 | 0/8 4 h-lim-p 0.0008 0.0295 6.5520 3893.762198 4 0.0002 113 | 0/8 5 h-lim-p 0.0018 0.1955 0.7963 3893.762105 3 0.0003 133 | 0/8 6 h-lim-p 0.0012 1.3732 0.1869 3893.762098 2 0.0004 158 | 0/8 7 h-lim-p 0.0210 20.0000 0.0035 3893.762061 0 0.0630 179 | 0/8 8 h-lim-p 0.0040 7.8945 0.0558 3893.761207 0 0.0159 201 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3893.761135 2 0.9961 225 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3893.761135 0 1.0938 245 | 0/8 11 h-lim-p 1.1846 20.0000 0.0000 3893.761135 0 0.0185 270 | 0/8 12 h-lim-p 0.0075 20.0000 0.0000 3893.761135 0 0.0000 301 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 3893.761135 0 0.0000 331 Out... lnL = -3893.761135 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3893.761135 Node 7: lnL = -3893.761135 Node 8: lnL = -3893.761135 Node 9: lnL = -3893.761135 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 493 Sequential format.. Reading seq # 1: YGL183C_Sbay Reading seq # 2: YGL183C_Scer Reading seq # 3: YGL183C_Skud Reading seq # 4: YGL183C_Smik Reading seq # 5: YGL183C_Spar Sequences read.. Counting patterns.. # site patterns = 183 Counting frequencies.. 120 bytes for distance 29280 bytes for lkl0 23424 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.082860 0.067632 0.120121 0.244366 0.030883 0.183866 0.143813 0.147848 lnL0 = -1941.379976 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1941.379976 x= 0.08286 0.06763 0.12012 0.24437 0.03088 0.18387 0.14381 0.14785 1 h-lim-p 0.0008 0.0067 172.3602 1937.408881 9 0.0003 44 | 0/8 2 h-lim-p 0.0003 0.0021 69.7845 1936.198745 0 0.0005 57 | 0/8 3 h-lim-p 0.0011 0.0085 30.3814 1935.933500 5 0.0007 81 | 0/8 4 h-lim-p 0.0012 0.0135 17.4142 1935.831830 7 0.0009 110 | 0/8 5 h-lim-p 0.0037 0.0511 4.2137 1935.826230 6 0.0007 137 | 0/8 6 h-lim-p 0.0035 0.2543 0.8253 1935.826000 2 0.0007 154 | 0/8 7 h-lim-p 0.0071 2.3279 0.0822 1935.825991 1 0.0014 177 | 0/8 8 h-lim-p 0.0354 20.0000 0.0033 1935.823282 0 0.5666 201 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 1935.823012 2 1.2402 225 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1935.823007 0 1.0938 245 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1935.823007 0 1.0938 265 | 0/8 12 h-lim-p 1.3255 20.0000 0.0000 1935.823007 0 2.6510 286 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1935.823007 0 0.0781 310 | 0/8 14 h-lim-p 0.0112 20.0000 0.0000 1935.823007 0 0.0000 338 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 1935.823007 0 0.0000 362 Out... lnL = -1935.823007 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1935.823007 Node 7: lnL = -1935.823007 Node 8: lnL = -1935.823007 Node 9: lnL = -1935.823007 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 621 Sequential format.. Reading seq # 1: YGL184C_Sbay Reading seq # 2: YGL184C_Scer Reading seq # 3: YGL184C_Skud Reading seq # 4: YGL184C_Smik Reading seq # 5: YGL184C_Spar Sequences read.. Counting patterns.. # site patterns = 260 Counting frequencies.. 120 bytes for distance 41600 bytes for lkl0 33280 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.175251 0.035334 0.063228 0.126462 0.096694 0.184083 0.272415 0.248141 lnL0 = -2668.272880 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2668.272880 x= 0.17525 0.03533 0.06323 0.12646 0.09669 0.18408 0.27241 0.24814 1 h-lim-p 0.0009 0.0074 120.0833 2666.415285 8 0.0003 44 | 0/8 2 h-lim-p 0.0008 0.0061 28.7213 2666.230645 7 0.0005 75 | 0/8 3 h-lim-p 0.0010 0.0266 13.4289 2666.200273 3 0.0004 93 | 0/8 4 h-lim-p 0.0013 0.0639 4.2749 2666.195197 2 0.0006 109 | 0/8 5 h-lim-p 0.0019 0.1932 1.3888 2666.194573 3 0.0007 127 | 0/8 6 h-lim-p 0.0028 1.1200 0.3655 2666.194501 1 0.0012 141 | 0/8 7 h-lim-p 0.0114 6.5305 0.0387 2666.194501 0 0.0006 164 | 0/8 8 h-lim-p 0.1742 20.0000 0.0001 2666.194470 0 1.0454 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2666.194469 0 1.0938 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2666.194469 0 1.0938 226 | 0/8 11 h-lim-p 1.3771 20.0000 0.0000 2666.194469 0 5.5083 248 | 0/8 12 h-lim-p 2.2043 20.0000 0.0000 2666.194469 0 0.0043 276 | 0/8 13 h-lim-p 0.0046 20.0000 0.0000 2666.194469 0 0.0000 314 Out... lnL = -2666.194469 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2666.194469 Node 7: lnL = -2666.194469 Node 8: lnL = -2666.194469 Node 9: lnL = -2666.194469 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 324 Sequential format.. Reading seq # 1: YGL185C_Sbay Reading seq # 2: YGL185C_Scer Reading seq # 3: YGL185C_Skud Reading seq # 4: YGL185C_Smik Reading seq # 5: YGL185C_Spar Sequences read.. Counting patterns.. # site patterns = 188 Counting frequencies.. 120 bytes for distance 30080 bytes for lkl0 24064 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.186250 0.055326 0.123228 0.204836 0.135106 0.262928 0.311754 0.282465 lnL0 = -1650.127560 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1650.127560 x= 0.18625 0.05533 0.12323 0.20484 0.13511 0.26293 0.31175 0.28246 1 h-lim-p 0.0136 0.1401 49.2589 1649.139256 8 0.0009 43 | 0/8 2 h-lim-p 0.0036 0.0329 12.1922 1649.004268 5 0.0019 66 | 0/8 3 h-lim-p 0.0021 0.0315 11.2029 1648.951220 5 0.0014 90 | 0/8 4 h-lim-p 0.0060 0.1785 2.5377 1648.947356 3 0.0014 109 | 0/8 5 h-lim-p 0.0175 3.2887 0.1963 1648.947306 3 0.0023 129 | 0/8 6 h-lim-p 0.0108 7.4405 0.0426 1648.947296 1 0.0043 151 | 0/8 7 h-lim-p 0.0198 20.0000 0.0093 1648.946667 0 0.1585 174 | 0/8 8 h-lim-p 0.0053 2.0180 0.2750 1648.945622 0 0.0080 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 1648.945559 2 0.9961 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1648.945559 0 1.0938 238 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1648.945559 0 1.0938 258 | 0/8 12 h-lim-p 1.1690 20.0000 0.0000 1648.945559 0 4.6760 280 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1648.945559 0 0.0000 326 Out... lnL = -1648.945559 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1648.945559 Node 7: lnL = -1648.945559 Node 8: lnL = -1648.945559 Node 9: lnL = -1648.945559 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 438 Sequential format.. Reading seq # 1: YGL186C_Sbay Reading seq # 2: YGL186C_Scer Reading seq # 3: YGL186C_Skud Reading seq # 4: YGL186C_Smik Reading seq # 5: YGL186C_Spar Sequences read.. Counting patterns.. # site patterns = 193 Counting frequencies.. 120 bytes for distance 30880 bytes for lkl0 24704 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.124914 0.134155 0.058156 0.138780 0.121106 0.199666 0.196826 0.198836 lnL0 = -1960.510525 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1960.510525 x= 0.12491 0.13416 0.05816 0.13878 0.12111 0.19967 0.19683 0.19884 1 h-lim-p 0.0008 0.0061 68.1943 1959.298190 7 0.0006 38 | 0/8 2 h-lim-p 0.0012 0.0098 29.6600 1959.017332 7 0.0007 67 | 0/8 3 h-lim-p 0.0015 0.0198 14.1698 1958.966753 3 0.0006 85 | 0/8 4 h-lim-p 0.0018 0.0563 5.0089 1958.958737 3 0.0008 103 | 0/8 5 h-lim-p 0.0030 0.1916 1.2780 1958.958037 5 0.0009 129 | 0/8 6 h-lim-p 0.0079 3.2992 0.1497 1958.958028 1 0.0008 145 | 0/8 7 h-lim-p 0.0177 20.0000 0.0067 1958.958028 0 0.0019 167 | 0/8 8 h-lim-p 0.0540 20.0000 0.0002 1958.958014 0 0.6482 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1958.958014 0 1.0938 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1958.958014 0 2.1875 230 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1958.958014 0 1.0938 250 | 0/8 12 h-lim-p 0.2936 20.0000 0.0000 1958.958014 0 4.6973 274 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1958.958014 0 0.0171 300 | 0/8 14 h-lim-p 0.0018 20.0000 0.0000 1958.958014 0 0.0000 341 Out... lnL = -1958.958014 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1958.958014 Node 7: lnL = -1958.958014 Node 8: lnL = -1958.958014 Node 9: lnL = -1958.958014 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 835 Sequential format.. Reading seq # 1: YGL187C_Sbay Reading seq # 2: YGL187C_Scer Reading seq # 3: YGL187C_Skud Reading seq # 4: YGL187C_Smik Reading seq # 5: YGL187C_Spar Sequences read.. Counting patterns.. # site patterns = 323 Counting frequencies.. 120 bytes for distance 51680 bytes for lkl0 41344 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.079162 0.056721 0.071903 0.153184 0.111880 0.229043 0.237928 0.146192 lnL0 = -3787.593186 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3787.593186 x= 0.07916 0.05672 0.07190 0.15318 0.11188 0.22904 0.23793 0.14619 1 h-lim-p 0.0017 0.0144 211.0643 3783.984875 5 0.0002 35 | 0/8 2 h-lim-p 0.0007 0.0059 36.0348 3783.723104 7 0.0004 64 | 0/8 3 h-lim-p 0.0010 0.0227 14.8699 3783.691150 6 0.0003 91 | 0/8 4 h-lim-p 0.0011 0.0626 4.5074 3783.687664 5 0.0004 117 | 0/8 5 h-lim-p 0.0015 0.2144 1.1347 3783.687426 3 0.0004 136 | 0/8 6 h-lim-p 0.0013 0.8437 0.3577 3783.687395 1 0.0005 150 | 0/8 7 h-lim-p 0.0074 6.0254 0.0245 3783.687395 0 0.0008 172 | 0/8 8 h-lim-p 0.0392 20.0000 0.0005 3783.687133 0 0.6270 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3783.687123 1 0.9961 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3783.687123 0 0.5469 239 | 0/8 11 h-lim-p 0.3107 20.0000 0.0000 3783.687123 0 0.0036 265 | 0/8 12 h-lim-p 0.0020 20.0000 0.0000 3783.687123 0 0.0000 304 | 0/8 13 h-lim-p 0.0000 20.0000 0.0010 3783.687123 0 0.0000 328 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0010 3783.687123 0 0.0000 387 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0010 | 0/8 18 h-lim-p 0.0000 20.0000 0.0010 Out... lnL = -3783.687123 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3783.687123 Node 7: lnL = -3783.687123 Node 8: lnL = -3783.687123 Node 9: lnL = -3783.687123 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 811 Sequential format.. Reading seq # 1: YGL189C_Sbay Reading seq # 2: YGL189C_Scer Reading seq # 3: YGL189C_Skud Reading seq # 4: YGL189C_Smik Reading seq # 5: YGL189C_Spar Sequences read.. Counting patterns.. # site patterns = 314 Counting frequencies.. 120 bytes for distance 50240 bytes for lkl0 40192 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.074620 0.134142 0.075430 0.173457 0.130642 0.264274 0.253982 0.154190 lnL0 = -3964.043804 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3964.043804 x= 0.07462 0.13414 0.07543 0.17346 0.13064 0.26427 0.25398 0.15419 1 h-lim-p 0.0070 0.0602 106.5091 3962.541581 7 0.0003 41 | 0/8 2 h-lim-p 0.0011 0.0094 25.8838 3962.400603 4 0.0004 61 | 0/8 3 h-lim-p 0.0014 0.0229 8.1582 3962.388688 6 0.0004 87 | 0/8 4 h-lim-p 0.0015 0.1152 2.1530 3962.387800 5 0.0004 111 | 0/8 5 h-lim-p 0.0014 0.4556 0.6403 3962.387708 3 0.0005 130 | 0/8 6 h-lim-p 0.0019 2.4593 0.1696 3962.387701 1 0.0005 153 | 0/8 7 h-lim-p 0.0048 19.3067 0.0163 3962.387700 0 0.0021 173 | 0/8 8 h-lim-p 0.0323 20.0000 0.0011 3962.387449 0 0.5166 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3962.387435 1 0.9961 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3962.387435 0 2.1875 239 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3962.387435 0 1.0938 259 | 0/8 12 h-lim-p 0.1166 20.0000 0.0000 3962.387435 0 0.0009 285 | 0/8 13 h-lim-p 0.0002 20.0000 0.0001 3962.387435 0 0.0001 305 | 0/8 14 h-lim-p 0.0001 20.0000 0.0001 3962.387435 0 0.0001 325 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 3962.387435 0 0.0000 355 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 3962.387435 0 0.0000 385 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 3962.387435 0 0.0000 410 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 3962.387435 0 0.0000 438 | 0/8 19 h-lim-p 0.0000 20.0000 0.0003 .. | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 3962.387435 0 0.0000 506 | 0/8 21 h-lim-p 0.0000 20.0000 0.0001 | 0/8 22 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -3962.387435 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3962.387435 Node 7: lnL = -3962.387435 Node 8: lnL = -3962.387435 Node 9: lnL = -3962.387435 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 821 Sequential format.. Reading seq # 1: YGL190C_Sbay Reading seq # 2: YGL190C_Scer Reading seq # 3: YGL190C_Skud Reading seq # 4: YGL190C_Smik Reading seq # 5: YGL190C_Spar Sequences read.. Counting patterns.. # site patterns = 236 Counting frequencies.. 120 bytes for distance 37760 bytes for lkl0 30208 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.044989 0.036726 0.054976 0.102942 0.082477 0.179364 0.107607 0.088297 lnL0 = -3232.194600 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3232.194600 x= 0.04499 0.03673 0.05498 0.10294 0.08248 0.17936 0.10761 0.08830 1 h-lim-p 0.0012 0.4866 229.2186 3230.006747 9 0.0001 46 | 0/8 2 h-lim-p 0.0008 0.0061 26.8306 3229.931734 7 0.0002 76 | 0/8 3 h-lim-p 0.0008 0.0425 7.0427 3229.926911 5 0.0002 100 | 0/8 4 h-lim-p 0.0005 0.0667 2.9232 3229.926045 2 0.0002 116 | 0/8 5 h-lim-p 0.0014 0.2771 0.4737 3229.926030 1 0.0001 132 | 0/8 6 h-lim-p 0.0009 3.9373 0.0767 3229.926029 0 0.0002 153 | 0/8 7 h-lim-p 0.0095 20.0000 0.0016 3229.926029 0 0.0041 173 | 0/8 8 h-lim-p 0.0041 20.0000 0.0016 3229.925996 0 0.0651 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3229.925996 0 1.0938 217 | 0/8 10 h-lim-p 0.3767 20.0000 0.0000 3229.925996 0 0.7534 238 | 0/8 11 h-lim-p 0.3694 20.0000 0.0001 3229.925996 0 0.0058 263 | 0/8 12 h-lim-p 0.0014 20.0000 0.0002 3229.925996 0 0.0006 283 | 0/8 13 h-lim-p 0.0000 1.8844 0.0362 3229.925996 0 0.0000 304 | 0/8 14 h-lim-p 0.0006 20.0000 0.0002 3229.925996 0 0.0001 326 | 0/8 15 h-lim-p 0.0000 20.0000 0.0009 3229.925996 0 0.0000 358 | 0/8 16 h-lim-p 0.0000 20.0000 0.0010 3229.925996 0 0.0000 390 | 0/8 17 h-lim-p 0.0000 20.0000 0.0016 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0010 | 0/8 19 h-lim-p 0.0000 20.0000 0.0010 Out... lnL = -3229.925996 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3229.925996 Node 7: lnL = -3229.925996 Node 8: lnL = -3229.925996 Node 9: lnL = -3229.925996 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 18 Sequential format.. Reading seq # 1: YGL192W_Sbay Reading seq # 2: YGL192W_Scer Reading seq # 3: YGL192W_Skud Reading seq # 4: YGL192W_Smik Reading seq # 5: YGL192W_Spar Sequences read.. Counting patterns.. # site patterns = 8 Counting frequencies.. 120 bytes for distance 1280 bytes for lkl0 1024 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 1.381306 0.000060 0.776034 0.205191 0.774047 2.482957 0.900393 1.599821 lnL0 = -62.838083 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 62.838083 x= 1.38131 0.00006 0.77603 0.20519 0.77405 2.48296 0.90039 1.59982 1 h-lim-p 0.0000 0.0000 14.4674 62.832290 m 0.0000 22 | 1/8 2 h-lim-p 0.0002 20.0000 1.9680 .. | 1/8 3 h-lim-p 0.0000 0.0204 14.3055 58.270579 m 0.0204 71 | 2/8 4 h-lim-p 0.0793 1.2337 2.6283 .. | 2/8 5 h-lim-p 0.0000 0.0588 11.8815 52.052494 0 0.0499 133 | 2/8 6 h-lim-p 0.0057 0.0457 13.3235 49.622410 0 0.0342 147 | 1/8 7 h-lim-p 0.0002 0.0019 92.3541 49.373486 0 0.0010 161 | 1/8 8 h-lim-p 0.0044 0.0355 3.7798 48.926570 0 0.0177 175 | 1/8 9 h-lim-p 0.4317 20.0000 0.1554 48.131842 0 0.6475 187 | 1/8 10 h-lim-p 0.4247 3.3978 0.0525 47.668796 0 1.6989 208 | 0/8 11 h-lim-p 0.0099 0.0790 1.9744 47.483074 m 0.0790 227 | 1/8 12 h-lim-p 0.0032 0.0254 0.3569 47.474770 m 0.0254 239 | 1/8 13 h-lim-p 0.0000 0.0000 1.7572 h-lim-p: 7.00502973e-21 5.60402379e-20 1.75721868e+00 47.474770 .. | 1/8 14 h-lim-p 0.0000 13.7889 7.1746 47.358671 0 0.0051 275 | 1/8 15 h-lim-p 1.5774 20.0000 0.0233 47.358669 3 0.0066 300 | 1/8 16 h-lim-p 0.7713 20.0000 0.0002 47.358663 0 1.5425 320 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 47.358663 0 1.0938 339 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 47.358663 0 1.0938 358 | 1/8 19 h-lim-p 2.5000 20.0000 0.0000 47.358663 0 2.5000 377 | 1/8 20 h-lim-p 2.5000 20.0000 0.0000 47.358663 0 0.0049 404 Out... lnL = -47.358663 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -47.358663 Node 7: lnL = -47.358663 Node 8: lnL = -47.358663 Node 9: lnL = -47.358663 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 190 Sequential format.. Reading seq # 1: YGL194C_Sbay Reading seq # 2: YGL194C_Scer Reading seq # 3: YGL194C_Skud Reading seq # 4: YGL194C_Smik Reading seq # 5: YGL194C_Spar Sequences read.. Counting patterns.. # site patterns = 89 Counting frequencies.. 120 bytes for distance 14240 bytes for lkl0 11392 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.087693 0.084658 0.109848 0.121008 0.073229 0.103064 0.155338 0.144606 lnL0 = -835.128565 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 835.128565 x= 0.08769 0.08466 0.10985 0.12101 0.07323 0.10306 0.15534 0.14461 1 h-lim-p 0.0006 0.0051 28.0003 834.781642 0 0.0010 22 | 0/8 2 h-lim-p 0.0032 0.0258 7.1155 834.764482 3 0.0007 41 | 0/8 3 h-lim-p 0.0025 0.0722 2.1030 834.762978 6 0.0007 69 | 0/8 4 h-lim-p 0.0039 0.6138 0.4029 834.762894 4 0.0011 90 | 0/8 5 h-lim-p 0.0058 3.4726 0.0737 834.762888 2 0.0015 115 | 0/8 6 h-lim-p 0.0082 18.7940 0.0136 834.762868 0 0.0164 136 | 0/8 7 h-lim-p 0.0081 7.9572 0.0277 834.762030 0 0.0644 159 | 0/8 8 h-lim-p 0.0063 0.4477 0.2854 834.761977 2 0.0012 184 | 0/8 9 h-lim-p 0.8437 20.0000 0.0004 834.761900 1 1.0547 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 834.761900 0 1.0938 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 834.761900 0 1.0938 246 | 0/8 12 h-lim-p 1.3683 20.0000 0.0000 834.761900 0 1.3683 266 | 0/8 13 h-lim-p 1.0750 20.0000 0.0000 834.761900 0 0.5375 286 | 0/8 14 h-lim-p 0.0080 20.0000 0.0003 834.761900 0 0.0000 316 | 0/8 15 h-lim-p 0.0007 20.0000 0.0000 834.761900 0 0.0000 357 Out... lnL = -834.761900 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -834.761900 Node 7: lnL = -834.761900 Node 8: lnL = -834.761900 Node 9: lnL = -834.761900 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 377 Sequential format.. Reading seq # 1: YGL197W_Sbay Reading seq # 2: YGL197W_Scer Reading seq # 3: YGL197W_Skud Reading seq # 4: YGL197W_Smik Reading seq # 5: YGL197W_Spar Sequences read.. Counting patterns.. # site patterns = 113 Counting frequencies.. 120 bytes for distance 18080 bytes for lkl0 14464 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.095823 0.009837 0.062640 0.050232 0.054197 0.105551 0.168236 0.137811 lnL0 = -1344.348899 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1344.348899 x= 0.09582 0.00984 0.06264 0.05023 0.05420 0.10555 0.16824 0.13781 1 h-lim-p 0.0015 0.0119 119.5287 1343.529748 9 0.0001 47 | 0/8 2 h-lim-p 0.0009 0.0072 15.7982 1343.484577 6 0.0004 74 | 0/8 3 h-lim-p 0.0005 0.0173 10.5923 1343.466316 4 0.0004 94 | 0/8 4 h-lim-p 0.0020 0.0594 2.3600 1343.465560 5 0.0003 121 | 0/8 5 h-lim-p 0.0007 0.1643 1.0032 1343.465432 2 0.0003 137 | 0/8 6 h-lim-p 0.0010 0.3635 0.3172 1343.465419 2 0.0003 155 | 0/8 7 h-lim-p 0.0035 4.9563 0.0288 1343.465419 0 0.0008 176 | 0/8 8 h-lim-p 0.2104 20.0000 0.0001 1343.465388 0 1.6828 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1343.465382 1 0.9961 221 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1343.465382 0 1.0938 241 | 0/8 11 h-lim-p 1.5674 20.0000 0.0000 1343.465382 0 0.0061 268 | 0/8 12 h-lim-p 0.0028 20.0000 0.0000 1343.465382 0 0.0000 309 Out... lnL = -1343.465382 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1343.465382 Node 7: lnL = -1343.465382 Node 8: lnL = -1343.465382 Node 9: lnL = -1343.465382 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 287 Sequential format.. Reading seq # 1: YGL200C_Sbay Reading seq # 2: YGL200C_Scer Reading seq # 3: YGL200C_Skud Reading seq # 4: YGL200C_Smik Reading seq # 5: YGL200C_Spar Sequences read.. Counting patterns.. # site patterns = 106 Counting frequencies.. 120 bytes for distance 16960 bytes for lkl0 13568 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.055014 0.029251 0.060900 0.111400 0.042328 0.102993 0.148016 0.095233 lnL0 = -1067.714444 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1067.714444 x= 0.05501 0.02925 0.06090 0.11140 0.04233 0.10299 0.14802 0.09523 1 h-lim-p 0.0001 0.0008 126.9976 1065.992500 0 0.0003 23 | 0/8 2 h-lim-p 0.0013 0.0103 20.2698 1065.900470 7 0.0005 53 | 0/8 3 h-lim-p 0.0004 0.0035 12.6257 1065.887034 4 0.0002 73 | 0/8 4 h-lim-p 0.0017 0.1110 1.6549 1065.886052 4 0.0007 92 | 0/8 5 h-lim-p 0.0024 0.2956 0.4858 1065.885929 3 0.0008 111 | 0/8 6 h-lim-p 0.0100 2.8819 0.0387 1065.883065 0 0.0400 133 | 0/8 7 h-lim-p 0.0021 0.0960 0.7511 1065.843804 0 0.0082 155 | 0/8 8 h-lim-p 0.0010 0.0231 6.1365 1065.824522 6 0.0007 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 1065.824077 4 0.9169 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1065.824077 0 1.0938 232 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1065.824077 0 1.0938 252 | 0/8 12 h-lim-p 1.1253 20.0000 0.0000 1065.824077 0 0.4923 272 | 0/8 13 h-lim-p 0.1589 20.0000 0.0000 1065.824077 0 0.0012 298 | 0/8 14 h-lim-p 0.0003 20.0000 0.0001 1065.824077 0 0.0000 333 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1065.824077 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1065.824077 Node 7: lnL = -1065.824077 Node 8: lnL = -1065.824077 Node 9: lnL = -1065.824077 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 695 Sequential format.. Reading seq # 1: YGL205W_Sbay Reading seq # 2: YGL205W_Scer Reading seq # 3: YGL205W_Skud Reading seq # 4: YGL205W_Smik Reading seq # 5: YGL205W_Spar Sequences read.. Counting patterns.. # site patterns = 227 Counting frequencies.. 120 bytes for distance 36320 bytes for lkl0 29056 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.085568 0.081814 0.019851 0.110381 0.087045 0.210687 0.140145 0.139517 lnL0 = -2958.622004 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2958.622004 x= 0.08557 0.08181 0.01985 0.11038 0.08705 0.21069 0.14015 0.13952 1 h-lim-p 0.0007 0.3717 290.2260 2955.186068 8 0.0001 42 | 0/8 2 h-lim-p 0.0006 0.0046 35.9736 2954.997842 4 0.0003 63 | 0/8 3 h-lim-p 0.0009 0.0231 11.9685 2954.981137 6 0.0003 90 | 0/8 4 h-lim-p 0.0009 0.0661 3.4665 2954.979408 4 0.0003 111 | 0/8 5 h-lim-p 0.0013 0.3436 0.8159 2954.979290 3 0.0004 130 | 0/8 6 h-lim-p 0.0020 1.8140 0.1458 2954.979286 1 0.0004 153 | 0/8 7 h-lim-p 0.0033 14.0967 0.0178 2954.979286 0 0.0007 174 | 0/8 8 h-lim-p 0.0455 20.0000 0.0003 2954.979153 0 0.7286 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2954.979146 0 1.0938 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2954.979146 0 1.0938 238 | 0/8 11 h-lim-p 1.3997 20.0000 0.0000 2954.979146 0 0.6124 258 | 0/8 12 h-lim-p 0.3227 20.0000 0.0000 2954.979146 0 0.0202 281 | 0/8 13 h-lim-p 0.0077 20.0000 0.0001 2954.979146 0 0.0077 301 | 0/8 14 h-lim-p 0.0042 20.0000 0.0001 2954.979146 0 0.0003 324 | 0/8 15 h-lim-p 0.0006 20.0000 0.0000 2954.979146 0 0.0000 359 | 0/8 16 h-lim-p 0.0000 20.0000 0.0006 2954.979146 0 0.0000 392 | 0/8 17 h-lim-p 0.0000 20.0000 0.0006 | 0/8 18 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -2954.979146 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2954.979146 Node 7: lnL = -2954.979146 Node 8: lnL = -2954.979146 Node 9: lnL = -2954.979146 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 891 Sequential format.. Reading seq # 1: YGL209W_Sbay Reading seq # 2: YGL209W_Scer Reading seq # 3: YGL209W_Skud Reading seq # 4: YGL209W_Smik Reading seq # 5: YGL209W_Spar Sequences read.. Counting patterns.. # site patterns = 251 Counting frequencies.. 120 bytes for distance 40160 bytes for lkl0 32128 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.103255 0.037897 0.052846 0.094074 0.049881 0.166573 0.181334 0.148636 lnL0 = -3616.311686 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3616.311686 x= 0.10326 0.03790 0.05285 0.09407 0.04988 0.16657 0.18133 0.14864 1 h-lim-p 0.0003 0.0020 237.5800 3613.378331 3 0.0001 28 | 0/8 2 h-lim-p 0.0004 0.0035 23.8431 3613.330740 5 0.0002 50 | 0/8 3 h-lim-p 0.0004 0.0221 10.8527 3613.323884 5 0.0001 73 | 0/8 4 h-lim-p 0.0002 0.0401 6.0770 3613.320814 3 0.0002 91 | 0/8 5 h-lim-p 0.0026 0.5004 0.5114 3613.320770 2 0.0003 109 | 0/8 6 h-lim-p 0.0015 1.1933 0.1185 3613.320769 1 0.0002 133 | 0/8 7 h-lim-p 0.0027 20.0000 0.0081 3613.320769 0 0.0003 155 | 0/8 8 h-lim-p 0.0777 20.0000 0.0000 3613.320765 0 1.2438 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3613.320765 0 1.2500 199 | 0/8 10 h-lim-p 1.3941 20.0000 0.0000 3613.320765 0 0.0654 223 | 0/8 11 h-lim-p 0.0285 20.0000 0.0000 3613.320765 0 0.0002 249 | 0/8 12 h-lim-p 0.0000 20.0000 0.0001 3613.320765 0 0.0000 279 | 0/8 13 h-lim-p 0.0000 20.0000 0.0034 | 0/8 14 h-lim-p 0.0000 20.0000 0.0034 Out... lnL = -3613.320765 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3613.320765 Node 7: lnL = -3613.320765 Node 8: lnL = -3613.320765 Node 9: lnL = -3613.320765 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 156 Sequential format.. Reading seq # 1: YGL211W_Sbay Reading seq # 2: YGL211W_Scer Reading seq # 3: YGL211W_Skud Reading seq # 4: YGL211W_Smik Reading seq # 5: YGL211W_Spar Sequences read.. Counting patterns.. # site patterns = 86 Counting frequencies.. 120 bytes for distance 13760 bytes for lkl0 11008 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.064192 0.058721 0.119827 0.116470 0.150759 0.182730 0.240434 0.123283 lnL0 = -688.789121 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 688.789121 x= 0.06419 0.05872 0.11983 0.11647 0.15076 0.18273 0.24043 0.12328 1 h-lim-p 0.0152 5.0883 30.1241 688.285390 8 0.0012 43 | 0/8 2 h-lim-p 0.0056 0.0445 5.4644 688.254310 4 0.0021 63 | 0/8 3 h-lim-p 0.0071 0.1864 1.6625 688.252065 6 0.0018 87 | 0/8 4 h-lim-p 0.0094 0.7250 0.3107 688.251953 2 0.0023 104 | 0/8 5 h-lim-p 0.0086 3.4428 0.0843 688.251946 0 0.0021 125 | 0/8 6 h-lim-p 0.0328 20.0000 0.0055 688.251943 2 0.0253 149 | 0/8 7 h-lim-p 0.0263 20.0000 0.0053 688.251805 0 0.1053 171 | 0/8 8 h-lim-p 0.0309 14.7124 0.0180 688.251804 0 0.0034 193 | 0/8 9 h-lim-p 0.5492 20.0000 0.0001 688.251801 0 1.0983 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 688.251801 0 1.0938 234 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 688.251801 0 1.0938 254 | 0/8 12 h-lim-p 1.1926 20.0000 0.0000 688.251801 0 4.7705 276 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 688.251801 0 0.5469 297 | 0/8 14 h-lim-p 0.0146 20.0000 0.0000 688.251801 0 0.0146 317 | 0/8 15 h-lim-p 0.0039 20.0000 0.0000 688.251801 0 0.0000 347 | 0/8 16 h-lim-p 0.0002 20.0000 0.0000 688.251801 0 0.0000 370 Out... lnL = -688.251801 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -688.251801 Node 7: lnL = -688.251801 Node 8: lnL = -688.251801 Node 9: lnL = -688.251801 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 203 Sequential format.. Reading seq # 1: YGL213C_Sbay Reading seq # 2: YGL213C_Scer Reading seq # 3: YGL213C_Skud Reading seq # 4: YGL213C_Smik Reading seq # 5: YGL213C_Spar Sequences read.. Counting patterns.. # site patterns = 99 Counting frequencies.. 120 bytes for distance 15840 bytes for lkl0 12672 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.095830 0.017049 0.040939 0.121017 0.107017 0.219201 0.279124 0.150483 lnL0 = -885.777545 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 885.777545 x= 0.09583 0.01705 0.04094 0.12102 0.10702 0.21920 0.27912 0.15048 1 h-lim-p 0.0020 0.0158 89.2302 884.386233 7 0.0004 37 | 0/8 2 h-lim-p 0.0016 0.0129 14.7044 884.247925 6 0.0013 61 | 0/8 3 h-lim-p 0.0036 0.0634 5.2874 884.228821 5 0.0015 82 | 0/8 4 h-lim-p 0.0025 0.0814 3.2989 884.223484 4 0.0013 103 | 0/8 5 h-lim-p 0.0176 1.0063 0.2474 884.223445 3 0.0013 125 | 0/8 6 h-lim-p 0.0139 2.8997 0.0234 884.223444 0 0.0017 147 | 0/8 7 h-lim-p 0.0075 20.0000 0.0054 884.223424 0 0.0598 170 | 0/8 8 h-lim-p 0.0173 20.0000 0.0188 884.223119 0 0.0346 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 884.223115 1 0.9961 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 884.223115 0 1.0938 233 | 0/8 11 h-lim-p 1.2931 20.0000 0.0000 884.223115 0 2.5861 254 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 884.223115 0 0.1562 277 | 0/8 13 h-lim-p 0.0254 20.0000 0.0000 884.223115 0 0.0032 299 | 0/8 14 h-lim-p 0.0012 20.0000 0.0000 884.223115 0 0.0012 319 | 0/8 15 h-lim-p 0.0005 20.0000 0.0000 884.223115 0 0.0003 339 | 0/8 16 h-lim-p 0.0005 20.0000 0.0000 884.223115 0 0.0000 373 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -884.223115 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -884.223115 Node 7: lnL = -884.223115 Node 8: lnL = -884.223115 Node 9: lnL = -884.223115 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 736 Sequential format.. Reading seq # 1: YGL215W_Sbay Reading seq # 2: YGL215W_Scer Reading seq # 3: YGL215W_Skud Reading seq # 4: YGL215W_Smik Reading seq # 5: YGL215W_Spar Sequences read.. Counting patterns.. # site patterns = 153 Counting frequencies.. 120 bytes for distance 24480 bytes for lkl0 19584 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.068005 0.019242 0.023090 0.044778 0.044547 0.068188 0.086955 0.092149 lnL0 = -2098.212307 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2098.212307 x= 0.06800 0.01924 0.02309 0.04478 0.04455 0.06819 0.08696 0.09215 1 h-lim-p 0.0011 0.6783 196.5562 2097.127561 3 0.0001 31 | 0/8 2 h-lim-p 0.0003 0.0022 34.7963 2097.051034 2 0.0001 47 | 0/8 3 h-lim-p 0.0002 0.0044 20.9754 2097.021155 3 0.0002 65 | 0/8 4 h-lim-p 0.0007 0.0333 5.3191 2097.019485 5 0.0001 90 | 0/8 5 h-lim-p 0.0005 0.0709 1.3755 2097.019405 3 0.0001 111 | 0/8 6 h-lim-p 0.0011 1.2310 0.1145 2097.019404 0 0.0002 124 | 0/8 7 h-lim-p 0.0002 1.1566 0.1312 2097.019403 0 0.0002 144 | 0/8 8 h-lim-p 0.0570 20.0000 0.0004 2097.018593 0 0.9115 168 | 0/8 9 h-lim-p 1.0060 20.0000 0.0004 2097.018540 2 0.9431 192 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2097.018536 0 1.0938 212 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2097.018536 0 1.0938 232 | 0/8 12 h-lim-p 1.0223 20.0000 0.0000 2097.018536 0 0.0000 279 Out... lnL = -2097.018536 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2097.018536 Node 7: lnL = -2097.018536 Node 8: lnL = -2097.018536 Node 9: lnL = -2097.018536 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 91 Sequential format.. Reading seq # 1: YGL221C_Sbay Reading seq # 2: YGL221C_Scer Reading seq # 3: YGL221C_Skud Reading seq # 4: YGL221C_Smik Reading seq # 5: YGL221C_Spar Sequences read.. Counting patterns.. # site patterns = 47 Counting frequencies.. 120 bytes for distance 7520 bytes for lkl0 6016 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.072178 0.130621 0.041665 0.060265 0.074627 0.127732 0.080698 0.112753 lnL0 = -333.567848 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 333.567848 x= 0.07218 0.13062 0.04166 0.06026 0.07463 0.12773 0.08070 0.11275 1 h-lim-p 0.0006 0.0045 42.7180 332.731922 0 0.0011 23 | 0/8 2 h-lim-p 0.0013 0.0102 12.7253 332.603252 0 0.0019 35 | 0/8 3 h-lim-p 0.0026 0.0209 6.5298 332.588229 7 0.0009 64 | 0/8 4 h-lim-p 0.0035 0.0722 1.6544 332.585953 5 0.0018 88 | 0/8 5 h-lim-p 0.0100 2.0678 0.2966 332.585730 3 0.0042 106 | 0/8 6 h-lim-p 0.0314 2.7005 0.0394 332.585250 2 0.0314 130 | 0/8 7 h-lim-p 0.0087 1.1576 0.1426 332.573298 0 0.0520 152 | 0/8 8 h-lim-p 0.0164 0.2559 0.4511 332.573081 4 0.0021 183 | 0/8 9 h-lim-p 0.5197 20.0000 0.0018 332.572033 0 1.0395 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 332.572031 1 0.9961 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 332.572031 0 1.2500 246 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 332.572031 0 1.0938 266 | 0/8 13 h-lim-p 1.0879 20.0000 0.0000 332.572031 0 4.3516 288 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 332.572031 0 0.0391 313 | 0/8 15 h-lim-p 0.0044 20.0000 0.0000 332.572031 0 0.0000 346 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 332.572031 0 0.0000 378 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -332.572031 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -332.572031 Node 7: lnL = -332.572031 Node 8: lnL = -332.572031 Node 9: lnL = -332.572031 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 273 Sequential format.. Reading seq # 1: YGL222C_Sbay Reading seq # 2: YGL222C_Scer Reading seq # 3: YGL222C_Skud Reading seq # 4: YGL222C_Smik Reading seq # 5: YGL222C_Spar Sequences read.. Counting patterns.. # site patterns = 132 Counting frequencies.. 120 bytes for distance 21120 bytes for lkl0 16896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.147198 0.129411 0.081661 0.145608 0.064149 0.274147 0.157364 0.215299 lnL0 = -1190.116966 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1190.116966 x= 0.14720 0.12941 0.08166 0.14561 0.06415 0.27415 0.15736 0.21530 1 h-lim-p 0.0005 0.0043 19.6807 1189.969743 0 0.0008 22 | 0/8 2 h-lim-p 0.0018 0.1344 9.0204 1189.949150 6 0.0006 49 | 0/8 3 h-lim-p 0.0037 0.1293 1.4727 1189.947802 5 0.0013 73 | 0/8 4 h-lim-p 0.0027 0.5381 0.6921 1189.947539 2 0.0013 89 | 0/8 5 h-lim-p 0.0147 5.2817 0.0604 1189.947535 0 0.0018 111 | 0/8 6 h-lim-p 0.0074 15.5583 0.0150 1189.947528 0 0.0111 131 | 0/8 7 h-lim-p 0.0082 9.3245 0.0203 1189.947394 0 0.0329 153 | 0/8 8 h-lim-p 0.0054 2.4253 0.1244 1189.947073 0 0.0080 173 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1189.947067 1 0.9961 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1189.947067 0 2.1875 215 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1189.947067 0 0.5469 236 | 0/8 12 h-lim-p 0.2333 20.0000 0.0000 1189.947067 0 0.0146 259 | 0/8 13 h-lim-p 0.0070 20.0000 0.0000 1189.947067 0 0.0000 293 Out... lnL = -1189.947067 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1189.947067 Node 7: lnL = -1189.947067 Node 8: lnL = -1189.947067 Node 9: lnL = -1189.947067 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 333 Sequential format.. Reading seq # 1: YGL223C_Sbay Reading seq # 2: YGL223C_Scer Reading seq # 3: YGL223C_Skud Reading seq # 4: YGL223C_Smik Reading seq # 5: YGL223C_Spar Sequences read.. Counting patterns.. # site patterns = 124 Counting frequencies.. 120 bytes for distance 19840 bytes for lkl0 15872 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.053807 0.091697 0.053944 0.083394 0.077526 0.163703 0.114828 0.095438 lnL0 = -1288.438936 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1288.438936 x= 0.05381 0.09170 0.05394 0.08339 0.07753 0.16370 0.11483 0.09544 1 h-lim-p 0.0010 0.0080 77.2418 1287.393891 7 0.0004 35 | 0/8 2 h-lim-p 0.0006 0.0048 22.4273 1287.252208 5 0.0006 58 | 0/8 3 h-lim-p 0.0020 0.0277 6.7354 1287.242476 2 0.0005 75 | 0/8 4 h-lim-p 0.0017 0.2050 1.8495 1287.241307 2 0.0007 91 | 0/8 5 h-lim-p 0.0057 0.8149 0.2387 1287.241291 1 0.0006 107 | 0/8 6 h-lim-p 0.0083 10.4524 0.0165 1287.241291 0 0.0009 129 | 0/8 7 h-lim-p 0.0040 20.0000 0.0037 1287.241291 0 0.0018 149 | 0/8 8 h-lim-p 0.0208 20.0000 0.0003 1287.241278 0 0.3325 173 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1287.241277 0 1.0938 193 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1287.241277 0 2.1875 213 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1287.241277 0 1.0938 233 | 0/8 12 h-lim-p 0.2659 20.0000 0.0000 1287.241277 0 4.2548 257 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1287.241277 0 0.5469 278 | 0/8 14 h-lim-p 0.0575 20.0000 0.0001 1287.241277 0 0.0072 300 | 0/8 15 h-lim-p 0.0020 20.0000 0.0002 1287.241277 0 0.0030 320 | 0/8 16 h-lim-p 0.0013 20.0000 0.0005 1287.241277 0 0.0000 362 | 0/8 17 h-lim-p 0.0000 20.0000 0.0008 | 0/8 18 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -1287.241277 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1287.241277 Node 7: lnL = -1287.241277 Node 8: lnL = -1287.241277 Node 9: lnL = -1287.241277 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 255 Sequential format.. Reading seq # 1: YGL224C_Sbay Reading seq # 2: YGL224C_Scer Reading seq # 3: YGL224C_Skud Reading seq # 4: YGL224C_Smik Reading seq # 5: YGL224C_Spar Sequences read.. Counting patterns.. # site patterns = 111 Counting frequencies.. 120 bytes for distance 17760 bytes for lkl0 14208 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.143322 0.106373 0.029964 0.151808 0.090931 0.180085 0.112383 0.199138 lnL0 = -1019.333885 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1019.333885 x= 0.14332 0.10637 0.02996 0.15181 0.09093 0.18009 0.11238 0.19914 1 h-lim-p 0.0019 0.0153 50.7479 1018.599271 5 0.0006 34 | 0/8 2 h-lim-p 0.0008 0.0066 18.6548 1018.436208 1 0.0010 48 | 0/8 3 h-lim-p 0.0021 0.0209 9.0936 1018.399882 4 0.0011 69 | 0/8 4 h-lim-p 0.0024 0.0320 4.1376 1018.391971 4 0.0012 90 | 0/8 5 h-lim-p 0.0090 0.3546 0.5317 1018.391807 3 0.0012 110 | 0/8 6 h-lim-p 0.0076 4.0617 0.0825 1018.391801 1 0.0017 133 | 0/8 7 h-lim-p 0.0501 20.0000 0.0027 1018.391786 0 0.1003 154 | 0/8 8 h-lim-p 0.0083 10.9410 0.0333 1018.391580 0 0.0248 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1018.391577 1 0.9961 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1018.391577 0 2.1875 217 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1018.391577 0 0.5469 238 | 0/8 12 h-lim-p 0.3873 20.0000 0.0000 1018.391577 0 0.0968 259 | 0/8 13 h-lim-p 0.0503 20.0000 0.0000 1018.391577 0 0.0000 299 Out... lnL = -1018.391577 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1018.391577 Node 7: lnL = -1018.391577 Node 8: lnL = -1018.391577 Node 9: lnL = -1018.391577 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 866 Sequential format.. Reading seq # 1: YGL225W_Sbay Reading seq # 2: YGL225W_Scer Reading seq # 3: YGL225W_Skud Reading seq # 4: YGL225W_Smik Reading seq # 5: YGL225W_Spar Sequences read.. Counting patterns.. # site patterns = 348 Counting frequencies.. 120 bytes for distance 55680 bytes for lkl0 44544 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.045224 0.130530 0.273703 0.244984 0.193560 0.222712 0.111863 0.125161 lnL0 = -4204.236304 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4204.236304 x= 0.04522 0.13053 0.27370 0.24498 0.19356 0.22271 0.11186 0.12516 1 h-lim-p 0.0040 0.0321 45.8341 4203.767103 2 0.0005 28 | 0/8 2 h-lim-p 0.0010 0.0116 22.2836 4203.677806 5 0.0004 49 | 0/8 3 h-lim-p 0.0004 0.0127 23.1080 4203.635304 6 0.0003 74 | 0/8 4 h-lim-p 0.0015 0.0347 4.6093 4203.631784 4 0.0004 96 | 0/8 5 h-lim-p 0.0030 0.6772 0.5694 4203.631645 3 0.0009 116 | 0/8 6 h-lim-p 0.0070 4.5796 0.0738 4203.631645 0 0.0008 138 | 0/8 7 h-lim-p 0.0057 20.0000 0.0098 4203.631644 0 0.0029 158 | 0/8 8 h-lim-p 0.0300 20.0000 0.0009 4203.631544 0 0.3597 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4203.631542 0 1.0938 201 | 0/8 10 h-lim-p 1.8114 20.0000 0.0000 4203.631542 0 1.5850 221 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4203.631542 0 1.0938 241 | 0/8 12 h-lim-p 0.5023 20.0000 0.0000 4203.631542 0 0.0235 265 | 0/8 13 h-lim-p 0.0000 2.9182 0.0215 4203.631542 0 0.0000 302 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 4203.631542 0 0.0000 329 Out... lnL = -4203.631542 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4203.631542 Node 7: lnL = -4203.631542 Node 8: lnL = -4203.631542 Node 9: lnL = -4203.631542 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 210 Sequential format.. Reading seq # 1: YGL226W_Sbay Reading seq # 2: YGL226W_Scer Reading seq # 3: YGL226W_Skud Reading seq # 4: YGL226W_Smik Reading seq # 5: YGL226W_Spar Sequences read.. Counting patterns.. # site patterns = 112 Counting frequencies.. 120 bytes for distance 17920 bytes for lkl0 14336 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.103622 0.144171 0.024443 0.137169 0.144232 0.145935 0.163892 0.160799 lnL0 = -937.522727 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 937.522727 x= 0.10362 0.14417 0.02444 0.13717 0.14423 0.14594 0.16389 0.16080 1 h-lim-p 0.0024 0.0772 88.7589 936.075089 8 0.0005 38 | 0/8 2 h-lim-p 0.0015 0.0120 18.5396 935.788602 1 0.0019 52 | 0/8 3 h-lim-p 0.0084 0.0910 4.1349 935.777018 6 0.0014 79 | 0/8 4 h-lim-p 0.0043 0.2200 1.3665 935.775765 5 0.0015 104 | 0/8 5 h-lim-p 0.0120 1.9047 0.1672 935.775731 2 0.0020 123 | 0/8 6 h-lim-p 0.0112 8.3346 0.0297 935.775671 1 0.0140 145 | 0/8 7 h-lim-p 0.0102 8.8247 0.0408 935.772537 0 0.0813 168 | 0/8 8 h-lim-p 0.0080 0.4187 0.4153 935.772418 4 0.0014 199 | 0/8 9 h-lim-p 0.8161 20.0000 0.0007 935.772203 0 1.6322 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 935.772179 2 1.0938 244 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 935.772178 0 1.0938 264 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 935.772178 0 1.0938 284 | 0/8 13 h-lim-p 1.4437 20.0000 0.0000 935.772178 0 2.8874 305 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 935.772178 0 0.0098 332 | 0/8 15 h-lim-p 0.0010 20.0000 0.0000 935.772178 0 0.0010 352 | 0/8 16 h-lim-p 0.0006 20.0000 0.0000 935.772178 0 0.0000 380 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 935.772178 0 0.0000 400 Out... lnL = -935.772178 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -935.772178 Node 7: lnL = -935.772178 Node 8: lnL = -935.772178 Node 9: lnL = -935.772178 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 682 Sequential format.. Reading seq # 1: YGL228W_Sbay Reading seq # 2: YGL228W_Scer Reading seq # 3: YGL228W_Skud Reading seq # 4: YGL228W_Smik Reading seq # 5: YGL228W_Spar Sequences read.. Counting patterns.. # site patterns = 256 Counting frequencies.. 120 bytes for distance 40960 bytes for lkl0 32768 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.127925 0.029323 0.033545 0.145314 0.075733 0.154617 0.233771 0.180109 lnL0 = -2903.506998 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2903.506998 x= 0.12792 0.02932 0.03354 0.14531 0.07573 0.15462 0.23377 0.18011 1 h-lim-p 0.0015 0.7677 197.6942 2900.781396 3 0.0002 30 | 0/8 2 h-lim-p 0.0004 0.0034 37.8389 2900.549232 4 0.0003 50 | 0/8 3 h-lim-p 0.0012 0.0276 10.3815 2900.526639 6 0.0004 75 | 0/8 4 h-lim-p 0.0013 0.0778 3.5759 2900.523888 5 0.0005 99 | 0/8 5 h-lim-p 0.0017 0.2247 0.9968 2900.523724 3 0.0004 118 | 0/8 6 h-lim-p 0.0014 0.8976 0.2579 2900.523714 0 0.0003 139 | 0/8 7 h-lim-p 0.0024 7.3608 0.0334 2900.523714 0 0.0005 160 | 0/8 8 h-lim-p 0.0914 20.0000 0.0002 2900.523613 0 1.4622 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2900.523606 1 0.9961 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2900.523606 0 2.1875 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2900.523606 0 0.1172 250 | 0/8 12 h-lim-p 0.0174 20.0000 0.0000 2900.523606 0 0.0262 270 | 0/8 13 h-lim-p 0.0119 20.0000 0.0000 2900.523606 0 0.0001 297 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 2900.523606 0 0.0000 331 Out... lnL = -2900.523606 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2900.523606 Node 7: lnL = -2900.523606 Node 8: lnL = -2900.523606 Node 9: lnL = -2900.523606 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 673 Sequential format.. Reading seq # 1: YGL229C_Sbay Reading seq # 2: YGL229C_Scer Reading seq # 3: YGL229C_Skud Reading seq # 4: YGL229C_Smik Reading seq # 5: YGL229C_Spar Sequences read.. Counting patterns.. # site patterns = 233 Counting frequencies.. 120 bytes for distance 37280 bytes for lkl0 29824 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.118169 0.024397 0.055957 0.112728 0.103565 0.188442 0.231676 0.172185 lnL0 = -2990.881005 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2990.881005 x= 0.11817 0.02440 0.05596 0.11273 0.10356 0.18844 0.23168 0.17219 1 h-lim-p 0.0033 1.1526 135.2169 2989.383131 8 0.0002 42 | 0/8 2 h-lim-p 0.0008 0.0065 23.7282 2989.261087 7 0.0004 73 | 0/8 3 h-lim-p 0.0032 0.0257 3.1940 2989.259906 4 0.0002 97 | 0/8 4 h-lim-p 0.0020 0.7260 0.3736 2989.259869 3 0.0005 116 | 0/8 5 h-lim-p 0.0011 0.8868 0.1850 2989.259863 1 0.0004 138 | 0/8 6 h-lim-p 0.0048 13.8453 0.0169 2989.259863 0 0.0010 159 | 0/8 7 h-lim-p 0.0046 20.0000 0.0039 2989.259863 0 0.0023 179 | 0/8 8 h-lim-p 0.0101 20.0000 0.0009 2989.259825 0 0.1617 203 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2989.259825 0 1.0938 223 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2989.259825 0 2.1875 243 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2989.259825 0 1.0938 263 | 0/8 12 h-lim-p 0.3489 20.0000 0.0000 2989.259825 0 4.1864 286 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2989.259825 0 0.1367 309 | 0/8 14 h-lim-p 2.1255 20.0000 0.0000 2989.259825 0 0.0000 357 Out... lnL = -2989.259825 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2989.259825 Node 7: lnL = -2989.259825 Node 8: lnL = -2989.259825 Node 9: lnL = -2989.259825 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 337 Sequential format.. Reading seq # 1: YGL230C_Sbay Reading seq # 2: YGL230C_Scer Reading seq # 3: YGL230C_Skud Reading seq # 4: YGL230C_Smik Reading seq # 5: YGL230C_Spar Sequences read.. Counting patterns.. # site patterns = 164 Counting frequencies.. 120 bytes for distance 26240 bytes for lkl0 20992 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.131603 0.046129 0.083175 0.189906 0.129018 0.339925 0.273431 0.207164 lnL0 = -1601.904573 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1601.904573 x= 0.13160 0.04613 0.08317 0.18991 0.12902 0.33993 0.27343 0.20716 1 h-lim-p 0.0107 2.7346 54.6606 1601.065683 3 0.0006 31 | 0/8 2 h-lim-p 0.0039 0.0550 8.4544 1601.003440 2 0.0018 47 | 0/8 3 h-lim-p 0.0031 0.0741 4.9713 1600.991985 5 0.0012 69 | 0/8 4 h-lim-p 0.0040 0.1562 1.4918 1600.990828 4 0.0012 92 | 0/8 5 h-lim-p 0.0254 1.6247 0.0687 1600.990822 2 0.0020 111 | 0/8 6 h-lim-p 0.0084 20.0000 0.0165 1600.990822 0 0.0037 131 | 0/8 7 h-lim-p 0.0148 20.0000 0.0041 1600.990813 0 0.0443 152 | 0/8 8 h-lim-p 0.0076 5.0667 0.0241 1600.990689 0 0.0228 173 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1600.990688 0 1.0938 193 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1600.990688 0 1.0938 213 | 0/8 11 h-lim-p 1.6667 20.0000 0.0000 1600.990688 0 0.7292 233 | 0/8 12 h-lim-p 0.4540 20.0000 0.0000 1600.990688 0 0.0035 259 | 0/8 13 h-lim-p 0.0006 20.0000 0.0000 1600.990688 0 0.0011 280 | 0/8 14 h-lim-p 0.0016 20.0000 0.0000 1600.990688 0 0.0016 300 | 0/8 15 h-lim-p 0.0000 12.6761 0.0153 1600.990688 0 0.0000 323 | 0/8 16 h-lim-p 0.0015 20.0000 0.0000 1600.990688 0 0.0001 346 Out... lnL = -1600.990688 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1600.990688 Node 7: lnL = -1600.990688 Node 8: lnL = -1600.990688 Node 9: lnL = -1600.990688 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 170 Sequential format.. Reading seq # 1: YGL231C_Sbay Reading seq # 2: YGL231C_Scer Reading seq # 3: YGL231C_Skud Reading seq # 4: YGL231C_Smik Reading seq # 5: YGL231C_Spar Sequences read.. Counting patterns.. # site patterns = 75 Counting frequencies.. 120 bytes for distance 12000 bytes for lkl0 9600 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.055371 0.045748 0.040291 0.090764 0.066526 0.144199 0.194994 0.095411 lnL0 = -653.635134 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 653.635134 x= 0.05537 0.04575 0.04029 0.09076 0.06653 0.14420 0.19499 0.09541 1 h-lim-p 0.0030 0.0239 47.3182 653.050196 6 0.0006 35 | 0/8 2 h-lim-p 0.0014 0.0111 8.8959 653.014510 6 0.0009 60 | 0/8 3 h-lim-p 0.0046 0.0700 1.7687 653.013165 4 0.0009 81 | 0/8 4 h-lim-p 0.0035 0.3655 0.4512 653.013049 3 0.0012 101 | 0/8 5 h-lim-p 0.0046 1.3619 0.1207 653.013041 1 0.0012 124 | 0/8 6 h-lim-p 0.0043 6.3382 0.0324 653.013040 1 0.0011 147 | 0/8 7 h-lim-p 0.0029 20.0000 0.0118 653.013040 0 0.0025 167 | 0/8 8 h-lim-p 0.0937 20.0000 0.0003 653.013001 0 0.7498 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 653.013001 0 1.0938 210 | 0/8 10 h-lim-p 2.2766 20.0000 0.0000 653.013001 0 1.9920 230 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 653.013001 0 0.3125 252 | 0/8 12 h-lim-p 0.0577 20.0000 0.0000 653.013001 0 0.0036 275 | 0/8 13 h-lim-p 0.0017 20.0000 0.0000 653.013001 0 0.0002 298 Out... lnL = -653.013001 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -653.013001 Node 7: lnL = -653.013001 Node 8: lnL = -653.013001 Node 9: lnL = -653.013001 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 246 Sequential format.. Reading seq # 1: YGL237C_Sbay Reading seq # 2: YGL237C_Scer Reading seq # 3: YGL237C_Skud Reading seq # 4: YGL237C_Smik Reading seq # 5: YGL237C_Spar Sequences read.. Counting patterns.. # site patterns = 99 Counting frequencies.. 120 bytes for distance 15840 bytes for lkl0 12672 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.045382 0.137984 0.027964 0.107329 0.054269 0.201374 0.118756 0.090052 lnL0 = -980.879740 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 980.879740 x= 0.04538 0.13798 0.02796 0.10733 0.05427 0.20137 0.11876 0.09005 1 h-lim-p 0.0034 0.0274 20.5033 980.790074 4 0.0004 32 | 0/8 2 h-lim-p 0.0009 0.0094 10.4427 980.755468 3 0.0008 50 | 0/8 3 h-lim-p 0.0023 0.0201 3.5513 980.751748 5 0.0007 75 | 0/8 4 h-lim-p 0.0015 0.0780 1.6032 980.751154 4 0.0006 95 | 0/8 5 h-lim-p 0.0021 0.4464 0.4239 980.751099 4 0.0007 118 | 0/8 6 h-lim-p 0.0031 2.8594 0.0904 980.751097 0 0.0007 139 | 0/8 7 h-lim-p 0.0016 5.5534 0.0375 980.751096 1 0.0008 162 | 0/8 8 h-lim-p 0.8552 20.0000 0.0000 980.751095 0 0.8552 182 | 0/8 9 h-lim-p 2.4238 20.0000 0.0000 980.751095 0 1.0604 202 | 0/8 10 h-lim-p 1.5788 20.0000 0.0000 980.751095 0 3.1576 223 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 980.751095 0 0.2734 245 | 0/8 12 h-lim-p 0.0952 20.0000 0.0000 980.751095 0 0.0004 272 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 980.751095 0 0.0000 306 | 0/8 14 h-lim-p 0.0000 20.0000 0.0012 | 0/8 15 h-lim-p 0.0000 20.0000 0.0012 Out... lnL = -980.751095 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -980.751095 Node 7: lnL = -980.751095 Node 8: lnL = -980.751095 Node 9: lnL = -980.751095 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 259 Sequential format.. Reading seq # 1: YGL242C_Sbay Reading seq # 2: YGL242C_Scer Reading seq # 3: YGL242C_Skud Reading seq # 4: YGL242C_Smik Reading seq # 5: YGL242C_Spar Sequences read.. Counting patterns.. # site patterns = 134 Counting frequencies.. 120 bytes for distance 21440 bytes for lkl0 17152 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.128356 0.068960 0.074402 0.133732 0.118211 0.226736 0.201591 0.191006 lnL0 = -1208.189417 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1208.189417 x= 0.12836 0.06896 0.07440 0.13373 0.11821 0.22674 0.20159 0.19101 1 h-lim-p 0.0018 0.0145 46.1559 1207.453544 7 0.0007 37 | 0/8 2 h-lim-p 0.0014 0.0115 10.1548 1207.404742 7 0.0010 66 | 0/8 3 h-lim-p 0.0030 0.0667 3.3133 1207.398870 4 0.0012 86 | 0/8 4 h-lim-p 0.0027 0.1674 1.4776 1207.397877 3 0.0011 104 | 0/8 5 h-lim-p 0.0097 1.7574 0.1694 1207.397858 3 0.0013 124 | 0/8 6 h-lim-p 0.0071 7.0087 0.0309 1207.397857 0 0.0016 145 | 0/8 7 h-lim-p 0.0165 20.0000 0.0029 1207.397848 0 0.0662 167 | 0/8 8 h-lim-p 0.0112 20.0000 0.0173 1207.397719 0 0.0335 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1207.397717 0 1.0938 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1207.397717 0 1.0938 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1207.397717 0 2.1875 248 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1207.397717 0 0.5469 269 | 0/8 13 h-lim-p 0.1509 20.0000 0.0000 1207.397717 0 0.0021 294 Out... lnL = -1207.397717 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1207.397717 Node 7: lnL = -1207.397717 Node 8: lnL = -1207.397717 Node 9: lnL = -1207.397717 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 189 Sequential format.. Reading seq # 1: YGL243W_Sbay Reading seq # 2: YGL243W_Scer Reading seq # 3: YGL243W_Skud Reading seq # 4: YGL243W_Smik Reading seq # 5: YGL243W_Spar Sequences read.. Counting patterns.. # site patterns = 101 Counting frequencies.. 120 bytes for distance 16160 bytes for lkl0 12928 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.064287 0.090055 0.017588 0.084717 0.094819 0.200907 0.264215 0.108211 lnL0 = -742.047374 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 742.047374 x= 0.06429 0.09006 0.01759 0.08472 0.09482 0.20091 0.26421 0.10821 1 h-lim-p 0.0020 1.2798 86.9693 740.534692 9 0.0005 46 | 0/8 2 h-lim-p 0.0014 0.0114 14.9952 740.352758 1 0.0018 60 | 0/8 3 h-lim-p 0.0037 0.0475 7.2206 740.313900 5 0.0018 83 | 0/8 4 h-lim-p 0.0093 0.1168 1.4034 740.312571 6 0.0014 113 | 0/8 5 h-lim-p 0.0031 0.4119 0.6438 740.312167 4 0.0023 133 | 0/8 6 h-lim-p 0.0290 3.6165 0.0515 740.312159 0 0.0036 155 | 0/8 7 h-lim-p 0.0064 5.5713 0.0291 740.312144 1 0.0066 177 | 0/8 8 h-lim-p 0.0123 20.0000 0.0156 740.311106 0 0.0987 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 740.311038 3 1.4660 229 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 740.311036 0 1.0938 249 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 740.311036 0 1.0938 269 | 0/8 12 h-lim-p 1.5276 20.0000 0.0000 740.311036 0 0.0239 294 | 0/8 13 h-lim-p 0.0093 20.0000 0.0000 740.311036 0 0.0069 314 | 0/8 14 h-lim-p 0.0036 20.0000 0.0000 740.311036 0 0.0000 353 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -740.311036 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -740.311036 Node 7: lnL = -740.311036 Node 8: lnL = -740.311036 Node 9: lnL = -740.311036 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 214 Sequential format.. Reading seq # 1: YGL246C_Sbay Reading seq # 2: YGL246C_Scer Reading seq # 3: YGL246C_Skud Reading seq # 4: YGL246C_Smik Reading seq # 5: YGL246C_Spar Sequences read.. Counting patterns.. # site patterns = 93 Counting frequencies.. 120 bytes for distance 14880 bytes for lkl0 11904 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.082763 0.039994 0.064712 0.139597 0.048889 0.101414 0.140268 0.118137 lnL0 = -839.555159 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 839.555159 x= 0.08276 0.03999 0.06471 0.13960 0.04889 0.10141 0.14027 0.11814 1 h-lim-p 0.0015 0.0120 69.2130 838.534523 6 0.0005 36 | 0/8 2 h-lim-p 0.0009 0.0074 20.4969 838.359148 2 0.0009 52 | 0/8 3 h-lim-p 0.0017 0.0173 10.2760 838.339014 7 0.0005 81 | 0/8 4 h-lim-p 0.0017 0.0600 2.9069 838.336462 3 0.0007 99 | 0/8 5 h-lim-p 0.0039 0.2158 0.5041 838.336372 3 0.0007 118 | 0/8 6 h-lim-p 0.0092 4.2424 0.0408 838.336371 0 0.0010 140 | 0/8 7 h-lim-p 0.1739 20.0000 0.0002 838.336307 0 1.3910 163 | 0/8 8 h-lim-p 0.0040 1.9805 0.0813 838.336304 0 0.0010 184 | 0/8 9 h-lim-p 2.4027 20.0000 0.0000 838.336303 0 1.0512 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 838.336303 0 1.0938 224 | 0/8 11 h-lim-p 1.4485 20.0000 0.0000 838.336303 0 2.8969 245 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 838.336303 0 0.0012 275 Out... lnL = -838.336303 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -838.336303 Node 7: lnL = -838.336303 Node 8: lnL = -838.336303 Node 9: lnL = -838.336303 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 215 Sequential format.. Reading seq # 1: YGL247W_Sbay Reading seq # 2: YGL247W_Scer Reading seq # 3: YGL247W_Skud Reading seq # 4: YGL247W_Smik Reading seq # 5: YGL247W_Spar Sequences read.. Counting patterns.. # site patterns = 129 Counting frequencies.. 120 bytes for distance 20640 bytes for lkl0 16512 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.126701 0.172186 0.092074 0.177245 0.115840 0.239333 0.147112 0.189169 lnL0 = -930.397471 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 930.397471 x= 0.12670 0.17219 0.09207 0.17725 0.11584 0.23933 0.14711 0.18917 1 h-lim-p 0.0013 0.0103 30.5229 929.686976 0 0.0019 22 | 0/8 2 h-lim-p 0.0021 0.0170 10.8957 929.619514 7 0.0012 51 | 0/8 3 h-lim-p 0.0045 0.0611 3.0159 929.609224 6 0.0024 76 | 0/8 4 h-lim-p 0.0127 0.3642 0.5824 929.608786 4 0.0022 98 | 0/8 5 h-lim-p 0.0072 4.4480 0.1814 929.608359 1 0.0090 120 | 0/8 6 h-lim-p 0.0082 0.6576 0.1993 929.606795 0 0.0123 140 | 0/8 7 h-lim-p 0.0087 0.6438 0.2813 929.576412 0 0.0349 162 | 0/8 8 h-lim-p 1.3884 20.0000 0.0071 929.576411 0 0.0095 188 | 0/8 9 h-lim-p 0.0482 20.0000 0.0014 929.576363 0 0.3859 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 929.576361 1 0.9961 233 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 929.576361 0 2.1875 253 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 929.576361 0 0.5469 274 | 0/8 13 h-lim-p 0.3161 20.0000 0.0000 929.576361 0 0.0000 321 Out... lnL = -929.576361 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -929.576361 Node 7: lnL = -929.576361 Node 8: lnL = -929.576361 Node 9: lnL = -929.576361 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 494 Sequential format.. Reading seq # 1: YGL248W_Sbay Reading seq # 2: YGL248W_Scer Reading seq # 3: YGL248W_Skud Reading seq # 4: YGL248W_Smik Reading seq # 5: YGL248W_Spar Sequences read.. Counting patterns.. # site patterns = 201 Counting frequencies.. 120 bytes for distance 32160 bytes for lkl0 25728 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.106019 0.081016 0.059250 0.156629 0.078494 0.209336 0.220892 0.157137 lnL0 = -2220.179135 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2220.179135 x= 0.10602 0.08102 0.05925 0.15663 0.07849 0.20934 0.22089 0.15714 1 h-lim-p 0.0008 0.0064 85.8634 2218.997900 7 0.0003 38 | 0/8 2 h-lim-p 0.0008 0.0064 19.8101 2218.910264 7 0.0005 67 | 0/8 3 h-lim-p 0.0011 0.0268 8.4952 2218.901016 6 0.0003 95 | 0/8 4 h-lim-p 0.0024 0.2262 1.0788 2218.900680 2 0.0006 112 | 0/8 5 h-lim-p 0.0021 0.9044 0.3003 2218.900644 2 0.0008 128 | 0/8 6 h-lim-p 0.0073 11.3026 0.0347 2218.900643 0 0.0008 150 | 0/8 7 h-lim-p 0.0620 20.0000 0.0004 2218.900521 0 0.9915 174 | 0/8 8 h-lim-p 0.0021 1.1384 0.2122 2218.900490 1 0.0010 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2218.900483 1 0.9961 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2218.900483 0 1.0938 238 | 0/8 11 h-lim-p 1.1723 20.0000 0.0000 2218.900483 0 4.6892 260 | 0/8 12 h-lim-p 0.6084 20.0000 0.0000 2218.900483 0 0.3042 280 | 0/8 13 h-lim-p 0.0074 20.0000 0.0015 2218.900483 0 0.0009 302 | 0/8 14 h-lim-p 0.0007 20.0000 0.0022 2218.900483 0 0.0000 343 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 2218.900483 0 0.0000 375 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -2218.900483 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2218.900483 Node 7: lnL = -2218.900483 Node 8: lnL = -2218.900483 Node 9: lnL = -2218.900483 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 480 Sequential format.. Reading seq # 1: YGL249W_Sbay Reading seq # 2: YGL249W_Scer Reading seq # 3: YGL249W_Skud Reading seq # 4: YGL249W_Smik Reading seq # 5: YGL249W_Spar Sequences read.. Counting patterns.. # site patterns = 141 Counting frequencies.. 120 bytes for distance 22560 bytes for lkl0 18048 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.092152 0.109081 0.069786 0.204017 0.157179 0.229838 4.647384 0.260464 lnL0 = -2009.136855 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2009.136855 x= 0.09215 0.10908 0.06979 0.20402 0.15718 0.22984 4.64738 0.26046 1 h-lim-p 0.0010 0.0077 43.4590 2008.494301 8 0.0007 40 | 0/8 2 h-lim-p 0.0017 0.0149 18.1165 2008.387254 5 0.0007 62 | 0/8 3 h-lim-p 0.0019 0.0451 7.0731 2008.372112 5 0.0007 84 | 0/8 4 h-lim-p 0.0025 0.1297 2.0256 2008.370493 5 0.0009 108 | 0/8 5 h-lim-p 0.0362 6.9946 0.0487 2008.370492 0 0.0010 124 | 0/8 6 h-lim-p 0.1809 20.0000 0.0003 2008.370455 0 1.0855 146 | 0/8 7 h-lim-p 2.5000 20.0000 0.0000 2008.370455 0 1.0938 166 | 0/8 8 h-lim-p 2.5000 20.0000 0.0000 2008.370455 0 1.0938 186 | 0/8 9 h-lim-p 2.1903 20.0000 0.0000 2008.370455 0 1.9165 206 | 0/8 10 h-lim-p 1.8696 20.0000 0.0000 2008.370455 0 0.4090 227 | 0/8 11 h-lim-p 0.0741 20.0000 0.0000 2008.370455 0 0.0001 256 | 0/8 12 h-lim-p 0.0004 20.0000 0.0000 2008.370455 0 0.0000 294 Out... lnL = -2008.370455 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2008.370455 Node 7: lnL = -2008.370455 Node 8: lnL = -2008.370455 Node 9: lnL = -2008.370455 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 839 Sequential format.. Reading seq # 1: YGL250W_Sbay Reading seq # 2: YGL250W_Scer Reading seq # 3: YGL250W_Skud Reading seq # 4: YGL250W_Smik Reading seq # 5: YGL250W_Spar Sequences read.. Counting patterns.. # site patterns = 243 Counting frequencies.. 120 bytes for distance 38880 bytes for lkl0 31104 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.093428 0.044811 0.065986 0.107205 0.084534 0.171813 0.147174 0.134019 lnL0 = -3627.133606 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3627.133606 x= 0.09343 0.04481 0.06599 0.10721 0.08453 0.17181 0.14717 0.13402 1 h-lim-p 0.0008 0.0064 243.9307 3623.815495 9 0.0001 46 | 0/8 2 h-lim-p 0.0009 0.0069 19.3940 3623.773377 6 0.0002 73 | 0/8 3 h-lim-p 0.0007 0.0297 6.3459 3623.769314 5 0.0002 97 | 0/8 4 h-lim-p 0.0008 0.0809 1.6994 3623.769013 3 0.0002 116 | 0/8 5 h-lim-p 0.0032 1.4521 0.1162 3623.769012 0 0.0004 130 | 0/8 6 h-lim-p 0.0016 9.3502 0.0261 3623.769012 0 0.0003 151 | 0/8 7 h-lim-p 0.0044 20.0000 0.0020 3623.769011 0 0.0066 171 | 0/8 8 h-lim-p 0.0044 20.0000 0.0031 3623.768956 0 0.0531 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3623.768955 0 1.0938 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3623.768955 0 1.0938 234 | 0/8 11 h-lim-p 1.9053 20.0000 0.0000 3623.768955 0 1.6671 254 | 0/8 12 h-lim-p 1.6396 20.0000 0.0000 3623.768955 0 0.0769 278 | 0/8 13 h-lim-p 0.0140 20.0000 0.0000 3623.768955 0 0.0001 304 | 0/8 14 h-lim-p 0.0007 20.0000 0.0000 3623.768955 0 0.0000 328 Out... lnL = -3623.768955 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3623.768955 Node 7: lnL = -3623.768955 Node 8: lnL = -3623.768955 Node 9: lnL = -3623.768955 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 465 Sequential format.. Reading seq # 1: YGL252C_Sbay Reading seq # 2: YGL252C_Scer Reading seq # 3: YGL252C_Skud Reading seq # 4: YGL252C_Smik Reading seq # 5: YGL252C_Spar Sequences read.. Counting patterns.. # site patterns = 175 Counting frequencies.. 120 bytes for distance 28000 bytes for lkl0 22400 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.166900 0.036402 0.039259 0.153819 0.078165 0.199627 0.227855 0.218909 lnL0 = -1841.700425 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1841.700425 x= 0.16690 0.03640 0.03926 0.15382 0.07816 0.19963 0.22785 0.21891 1 h-lim-p 0.0002 0.0019 78.2093 1840.705108 0 0.0003 22 | 0/8 2 h-lim-p 0.0007 0.0056 25.4428 1840.548152 7 0.0005 48 | 0/8 3 h-lim-p 0.0007 0.0252 19.4133 1840.494844 7 0.0004 80 | 0/8 4 h-lim-p 0.0007 0.0290 11.4054 1840.459545 1 0.0009 94 | 0/8 5 h-lim-p 0.0089 0.1120 1.1546 1840.459004 4 0.0008 116 | 0/8 6 h-lim-p 0.0025 0.4872 0.3793 1840.458958 3 0.0007 135 | 0/8 7 h-lim-p 0.0121 11.9446 0.0214 1840.458950 2 0.0080 161 | 0/8 8 h-lim-p 0.0230 15.1566 0.0074 1840.457915 0 0.1839 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1840.457908 1 0.9961 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1840.457908 0 1.0938 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1840.457908 0 2.1875 246 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1840.457908 0 0.1562 269 | 0/8 13 h-lim-p 0.0337 20.0000 0.0000 1840.457908 0 0.0168 289 | 0/8 14 h-lim-p 0.0084 20.0000 0.0000 1840.457908 0 0.0084 309 | 0/8 15 h-lim-p 0.0051 20.0000 0.0000 1840.457908 0 0.0001 333 Out... lnL = -1840.457908 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1840.457908 Node 7: lnL = -1840.457908 Node 8: lnL = -1840.457908 Node 9: lnL = -1840.457908 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 812 Sequential format.. Reading seq # 1: YGL253W_Sbay Reading seq # 2: YGL253W_Scer Reading seq # 3: YGL253W_Skud Reading seq # 4: YGL253W_Smik Reading seq # 5: YGL253W_Spar Sequences read.. Counting patterns.. # site patterns = 262 Counting frequencies.. 120 bytes for distance 41920 bytes for lkl0 33536 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.071505 0.089428 0.059501 0.098355 0.075620 0.146675 0.168598 0.111715 lnL0 = -3295.858949 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3295.858949 x= 0.07151 0.08943 0.05950 0.09836 0.07562 0.14667 0.16860 0.11171 1 h-lim-p 0.0032 0.0427 144.3273 3294.356254 4 0.0002 33 | 0/8 2 h-lim-p 0.0008 0.0071 26.5379 3294.269968 7 0.0003 62 | 0/8 3 h-lim-p 0.0006 0.0180 10.8417 3294.259036 6 0.0002 89 | 0/8 4 h-lim-p 0.0018 0.1014 1.3195 3294.258838 3 0.0002 109 | 0/8 5 h-lim-p 0.0019 1.0439 0.1619 3294.258835 1 0.0002 125 | 0/8 6 h-lim-p 0.0015 14.7944 0.0244 3294.258835 0 0.0003 146 | 0/8 7 h-lim-p 0.0044 20.0000 0.0019 3294.258834 0 0.0019 166 | 0/8 8 h-lim-p 0.0150 20.0000 0.0002 3294.258828 0 0.2396 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3294.258828 0 1.0938 210 | 0/8 10 h-lim-p 1.9243 20.0000 0.0000 3294.258828 0 1.6838 230 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3294.258828 0 1.0938 250 | 0/8 12 h-lim-p 0.4643 20.0000 0.0000 3294.258828 0 0.0000 291 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 3294.258828 0 0.0000 318 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -3294.258828 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3294.258828 Node 7: lnL = -3294.258828 Node 8: lnL = -3294.258828 Node 9: lnL = -3294.258828 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 262 Sequential format.. Reading seq # 1: YGL254W_Sbay Reading seq # 2: YGL254W_Scer Reading seq # 3: YGL254W_Skud Reading seq # 4: YGL254W_Smik Reading seq # 5: YGL254W_Spar Sequences read.. Counting patterns.. # site patterns = 120 Counting frequencies.. 120 bytes for distance 19200 bytes for lkl0 15360 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.130800 0.045362 0.048682 0.182921 0.105982 0.146338 0.234038 0.181174 lnL0 = -1035.705913 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1035.705913 x= 0.13080 0.04536 0.04868 0.18292 0.10598 0.14634 0.23404 0.18117 1 h-lim-p 0.0109 3.3261 43.5289 1035.136534 3 0.0006 31 | 0/8 2 h-lim-p 0.0017 0.0138 9.4953 1035.088055 6 0.0011 57 | 0/8 3 h-lim-p 0.0045 0.1694 2.3629 1035.084271 5 0.0014 81 | 0/8 4 h-lim-p 0.0082 0.3492 0.4141 1035.084159 3 0.0014 102 | 0/8 5 h-lim-p 0.0037 1.4627 0.1510 1035.084139 2 0.0018 127 | 0/8 6 h-lim-p 0.0126 14.0375 0.0219 1035.084138 0 0.0028 148 | 0/8 7 h-lim-p 0.0203 20.0000 0.0030 1035.084098 0 0.1622 171 | 0/8 8 h-lim-p 0.0072 20.0000 0.0672 1035.083912 1 0.0090 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1035.083908 1 0.9961 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1035.083908 0 1.0938 235 | 0/8 11 h-lim-p 1.4513 20.0000 0.0000 1035.083908 0 0.7257 255 | 0/8 12 h-lim-p 0.3431 20.0000 0.0000 1035.083908 0 0.1716 275 | 0/8 13 h-lim-p 0.0480 20.0000 0.0000 1035.083908 0 0.0008 300 | 0/8 14 h-lim-p 0.0000 20.0000 0.0028 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1035.083908 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1035.083908 Node 7: lnL = -1035.083908 Node 8: lnL = -1035.083908 Node 9: lnL = -1035.083908 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 950 Sequential format.. Reading seq # 1: YGL256W_Sbay Reading seq # 2: YGL256W_Scer Reading seq # 3: YGL256W_Skud Reading seq # 4: YGL256W_Smik Reading seq # 5: YGL256W_Spar Sequences read.. Counting patterns.. # site patterns = 312 Counting frequencies.. 120 bytes for distance 49920 bytes for lkl0 39936 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.118451 0.051961 0.033455 0.097729 0.097944 0.200856 0.144553 0.161031 lnL0 = -3954.896400 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3954.896400 x= 0.11845 0.05196 0.03345 0.09773 0.09794 0.20086 0.14455 0.16103 1 h-lim-p 0.0007 0.0057 300.2964 3950.941929 9 0.0001 48 | 0/8 2 h-lim-p 0.0002 0.0019 72.4293 3950.371579 2 0.0002 64 | 0/8 3 h-lim-p 0.0008 0.0103 19.4046 3950.329150 7 0.0002 94 | 0/8 4 h-lim-p 0.0008 0.0280 5.7496 3950.325651 4 0.0002 117 | 0/8 5 h-lim-p 0.0031 0.7171 0.4261 3950.325626 2 0.0003 135 | 0/8 6 h-lim-p 0.0016 1.4802 0.0785 3950.325625 0 0.0004 156 | 0/8 7 h-lim-p 0.0030 20.0000 0.0092 3950.325625 0 0.0015 176 | 0/8 8 h-lim-p 0.0156 20.0000 0.0009 3950.325407 0 0.2495 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3950.325404 0 1.0938 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3950.325404 0 1.0938 240 | 0/8 11 h-lim-p 1.5346 20.0000 0.0000 3950.325404 0 0.6714 260 | 0/8 12 h-lim-p 0.4105 20.0000 0.0000 3950.325404 0 0.0225 283 | 0/8 13 h-lim-p 0.0082 20.0000 0.0000 3950.325404 0 0.0000 316 | 0/8 14 h-lim-p 0.0000 20.0000 0.0005 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -3950.325404 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3950.325404 Node 7: lnL = -3950.325404 Node 8: lnL = -3950.325404 Node 9: lnL = -3950.325404 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 855 Sequential format.. Reading seq # 1: YGL257C_Sbay Reading seq # 2: YGL257C_Scer Reading seq # 3: YGL257C_Skud Reading seq # 4: YGL257C_Smik Reading seq # 5: YGL257C_Spar Sequences read.. Counting patterns.. # site patterns = 250 Counting frequencies.. 120 bytes for distance 40000 bytes for lkl0 32000 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.119717 0.033730 0.043153 0.109366 0.084575 0.190762 0.169485 0.162430 lnL0 = -3536.734440 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3536.734440 x= 0.11972 0.03373 0.04315 0.10937 0.08458 0.19076 0.16948 0.16243 1 h-lim-p 0.0005 0.0041 210.0815 3534.480698 6 0.0001 34 | 0/8 2 h-lim-p 0.0004 0.0036 34.9574 3534.339355 6 0.0002 58 | 0/8 3 h-lim-p 0.0006 0.0162 14.0809 3534.319291 3 0.0002 76 | 0/8 4 h-lim-p 0.0007 0.0388 4.4717 3534.317007 5 0.0003 100 | 0/8 5 h-lim-p 0.0021 0.2882 0.5516 3534.316965 2 0.0003 118 | 0/8 6 h-lim-p 0.0009 1.3923 0.1622 3534.316962 1 0.0002 141 | 0/8 7 h-lim-p 0.0370 20.0000 0.0010 3534.316962 0 0.0323 161 | 0/8 8 h-lim-p 0.0064 20.0000 0.0051 3534.316928 0 0.0256 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3534.316927 0 1.0938 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3534.316927 0 1.0938 223 | 0/8 11 h-lim-p 1.1921 20.0000 0.0000 3534.316927 0 2.3841 244 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3534.316927 0 0.2344 267 | 0/8 13 h-lim-p 0.0318 20.0000 0.0000 3534.316927 0 0.0001 294 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 3534.316927 0 0.0000 327 | 0/8 15 h-lim-p 0.0000 20.0000 0.0010 3534.316927 0 0.0000 358 | 0/8 16 h-lim-p 0.0000 20.0000 0.0017 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0010 | 0/8 18 h-lim-p 0.0000 20.0000 0.0010 Out... lnL = -3534.316927 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3534.316927 Node 7: lnL = -3534.316927 Node 8: lnL = -3534.316927 Node 9: lnL = -3534.316927 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 853 Sequential format.. Reading seq # 1: YGL258W_Sbay Reading seq # 2: YGL258W_Scer Reading seq # 3: YGL258W_Skud Reading seq # 4: YGL258W_Smik Reading seq # 5: YGL258W_Spar Sequences read.. Counting patterns.. # site patterns = 302 Counting frequencies.. 120 bytes for distance 48320 bytes for lkl0 38656 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.151266 0.100243 0.170719 0.136921 0.098490 0.869647 0.222819 0.232141 lnL0 = -3698.248980 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3698.248980 x= 0.15127 0.10024 0.17072 0.13692 0.09849 0.86965 0.22282 0.23214 1 h-lim-p 0.0023 0.0188 69.5223 3697.332814 7 0.0004 40 | 0/8 2 h-lim-p 0.0009 0.0072 31.3307 3697.203977 7 0.0003 70 | 0/8 3 h-lim-p 0.0006 0.0193 15.8190 3697.143342 3 0.0006 88 | 0/8 4 h-lim-p 0.0015 0.0523 6.4395 3697.122734 6 0.0012 111 | 0/8 5 h-lim-p 0.0010 0.0676 7.4720 3697.020008 0 0.0084 126 | 0/8 6 h-lim-p 0.0034 0.0294 18.1980 3697.000598 6 0.0006 154 | 0/8 7 h-lim-p 0.0440 1.1362 0.2623 3696.999926 2 0.0193 170 | 0/8 8 h-lim-p 1.4896 20.0000 0.0034 3696.999206 4 1.0576 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3696.999204 0 1.0938 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3696.999204 0 1.0938 239 | 0/8 11 h-lim-p 2.2891 20.0000 0.0000 3696.999204 0 1.0015 259 | 0/8 12 h-lim-p 0.5786 20.0000 0.0000 3696.999204 0 0.5786 279 | 0/8 13 h-lim-p 0.0744 20.0000 0.0001 3696.999204 0 0.0035 303 | 0/8 14 h-lim-p 0.0006 20.0000 0.0004 3696.999204 0 0.0000 339 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -3696.999204 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3696.999204 Node 7: lnL = -3696.999204 Node 8: lnL = -3696.999204 Node 9: lnL = -3696.999204 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 240 Sequential format.. Reading seq # 1: YGR002C_Sbay Reading seq # 2: YGR002C_Scer Reading seq # 3: YGR002C_Skud Reading seq # 4: YGR002C_Smik Reading seq # 5: YGR002C_Spar Sequences read.. Counting patterns.. # site patterns = 155 Counting frequencies.. 120 bytes for distance 24800 bytes for lkl0 19840 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.210390 0.014742 0.108756 0.176576 0.200396 0.343949 0.365214 0.277579 lnL0 = -1189.097266 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1189.097266 x= 0.21039 0.01474 0.10876 0.17658 0.20040 0.34395 0.36521 0.27758 1 h-lim-p 0.0033 0.0264 28.2350 1188.573969 6 0.0014 33 | 0/8 2 h-lim-p 0.0012 0.0100 13.2694 1188.381384 0 0.0025 46 | 0/8 3 h-lim-p 0.0053 0.0806 6.2925 1188.339755 6 0.0026 73 | 0/8 4 h-lim-p 0.0063 0.1297 2.6405 1188.333981 5 0.0020 97 | 0/8 5 h-lim-p 0.0061 0.6407 0.8783 1188.332671 5 0.0039 121 | 0/8 6 h-lim-p 0.0165 1.3728 0.2068 1188.332626 3 0.0022 149 | 0/8 7 h-lim-p 0.0199 13.9984 0.0230 1188.332614 2 0.0127 174 | 0/8 8 h-lim-p 0.0612 20.0000 0.0048 1188.331858 0 0.4893 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 1188.331804 2 0.9961 221 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1188.331804 0 1.0938 241 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1188.331804 0 1.0938 261 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1188.331804 0 0.1562 284 | 0/8 13 h-lim-p 0.0788 20.0000 0.0000 1188.331804 0 0.0788 304 | 0/8 14 h-lim-p 0.0508 20.0000 0.0000 1188.331804 0 0.0008 329 Out... lnL = -1188.331804 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1188.331804 Node 7: lnL = -1188.331804 Node 8: lnL = -1188.331804 Node 9: lnL = -1188.331804 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 240 Sequential format.. Reading seq # 1: YGR003W_Sbay Reading seq # 2: YGR003W_Scer Reading seq # 3: YGR003W_Skud Reading seq # 4: YGR003W_Smik Reading seq # 5: YGR003W_Spar Sequences read.. Counting patterns.. # site patterns = 144 Counting frequencies.. 120 bytes for distance 23040 bytes for lkl0 18432 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.117865 0.084550 0.145171 0.204488 0.172484 0.335302 0.281289 0.180357 lnL0 = -1235.122594 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1235.122594 x= 0.11786 0.08455 0.14517 0.20449 0.17248 0.33530 0.28129 0.18036 1 h-lim-p 0.0145 0.1162 16.1500 1234.945467 4 0.0014 32 | 0/8 2 h-lim-p 0.0035 0.0537 6.5311 1234.898917 7 0.0025 61 | 0/8 3 h-lim-p 0.0087 0.1668 1.8600 1234.895959 4 0.0019 81 | 0/8 4 h-lim-p 0.0126 0.9263 0.2758 1234.895846 2 0.0030 98 | 0/8 5 h-lim-p 0.0159 6.6305 0.0513 1234.895844 1 0.0016 122 | 0/8 6 h-lim-p 0.0090 20.0000 0.0091 1234.895844 0 0.0039 142 | 0/8 7 h-lim-p 0.0517 20.0000 0.0007 1234.895824 0 0.4135 165 | 0/8 8 h-lim-p 0.0046 6.0807 0.0624 1234.895812 2 0.0035 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1234.895812 0 1.0938 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1234.895812 0 1.0938 229 | 0/8 11 h-lim-p 1.4000 20.0000 0.0000 1234.895812 0 2.8001 250 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1234.895812 0 0.1562 273 | 0/8 13 h-lim-p 0.0128 20.0000 0.0000 1234.895812 0 0.0000 314 Out... lnL = -1234.895812 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1234.895812 Node 7: lnL = -1234.895812 Node 8: lnL = -1234.895812 Node 9: lnL = -1234.895812 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 221 Sequential format.. Reading seq # 1: YGR005C_Sbay Reading seq # 2: YGR005C_Scer Reading seq # 3: YGR005C_Skud Reading seq # 4: YGR005C_Smik Reading seq # 5: YGR005C_Spar Sequences read.. Counting patterns.. # site patterns = 126 Counting frequencies.. 120 bytes for distance 20160 bytes for lkl0 16128 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.062280 0.132977 0.096194 0.171964 0.122483 0.344776 0.215787 0.114824 lnL0 = -1078.245343 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1078.245343 x= 0.06228 0.13298 0.09619 0.17196 0.12248 0.34478 0.21579 0.11482 1 h-lim-p 0.0010 0.0077 21.2234 1077.961039 0 0.0014 22 | 0/8 2 h-lim-p 0.0026 0.0208 7.0546 1077.937409 5 0.0010 43 | 0/8 3 h-lim-p 0.0048 0.5216 1.5351 1077.936126 2 0.0011 60 | 0/8 4 h-lim-p 0.0033 0.7002 0.5256 1077.935897 4 0.0018 81 | 0/8 5 h-lim-p 0.0029 1.3435 0.3227 1077.935808 4 0.0020 112 | 0/8 6 h-lim-p 0.0155 5.8979 0.0409 1077.935666 1 0.0194 134 | 0/8 7 h-lim-p 0.0195 6.8190 0.0407 1077.930595 0 0.0778 156 | 0/8 8 h-lim-p 0.0214 1.2153 0.1480 1077.930571 2 0.0021 182 | 0/8 9 h-lim-p 0.7059 20.0000 0.0004 1077.930496 0 1.0588 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1077.930496 0 1.0938 222 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1077.930496 0 1.0938 242 | 0/8 12 h-lim-p 1.3100 20.0000 0.0000 1077.930496 0 1.1463 262 | 0/8 13 h-lim-p 0.6096 20.0000 0.0000 1077.930496 0 0.1524 283 | 0/8 14 h-lim-p 0.0106 20.0000 0.0001 1077.930496 0 0.0000 325 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1077.930496 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1077.930496 Node 7: lnL = -1077.930496 Node 8: lnL = -1077.930496 Node 9: lnL = -1077.930496 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 250 Sequential format.. Reading seq # 1: YGR007W_Sbay Reading seq # 2: YGR007W_Scer Reading seq # 3: YGR007W_Skud Reading seq # 4: YGR007W_Smik Reading seq # 5: YGR007W_Spar Sequences read.. Counting patterns.. # site patterns = 86 Counting frequencies.. 120 bytes for distance 13760 bytes for lkl0 11008 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.060617 0.080352 0.027945 0.087462 0.062100 0.154805 0.086878 0.087416 lnL0 = -963.658838 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 963.658838 x= 0.06062 0.08035 0.02794 0.08746 0.06210 0.15481 0.08688 0.08742 1 h-lim-p 0.0009 0.0074 116.4395 962.424405 3 0.0002 29 | 0/8 2 h-lim-p 0.0008 0.0062 15.9263 962.351705 7 0.0006 56 | 0/8 3 h-lim-p 0.0014 0.0207 6.4755 962.343751 6 0.0004 84 | 0/8 4 h-lim-p 0.0035 0.1970 0.8062 962.343564 4 0.0006 107 | 0/8 5 h-lim-p 0.0013 1.3989 0.3644 962.343526 2 0.0007 132 | 0/8 6 h-lim-p 0.0041 1.7507 0.0616 962.343525 1 0.0008 155 | 0/8 7 h-lim-p 0.0191 20.0000 0.0026 962.343525 0 0.0084 175 | 0/8 8 h-lim-p 0.0136 20.0000 0.0016 962.343469 0 0.1086 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 962.343467 0 1.0938 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 962.343467 0 1.0938 238 | 0/8 11 h-lim-p 1.2603 20.0000 0.0000 962.343467 0 3.7810 259 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 962.343467 0 0.2734 281 | 0/8 13 h-lim-p 1.2902 20.0000 0.0000 962.343467 0 0.0101 307 | 0/8 14 h-lim-p 0.0018 20.0000 0.0000 962.343467 0 0.0000 340 Out... lnL = -962.343467 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -962.343467 Node 7: lnL = -962.343467 Node 8: lnL = -962.343467 Node 9: lnL = -962.343467 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 719 Sequential format.. Reading seq # 1: YGR008C_Sbay Reading seq # 2: YGR008C_Scer Reading seq # 3: YGR008C_Skud Reading seq # 4: YGR008C_Smik Reading seq # 5: YGR008C_Spar Sequences read.. Counting patterns.. # site patterns = 335 Counting frequencies.. 120 bytes for distance 53600 bytes for lkl0 42880 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.210252 0.074817 0.112332 0.175409 0.134995 0.270224 0.275817 0.272101 lnL0 = -3593.480273 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3593.480273 x= 0.21025 0.07482 0.11233 0.17541 0.13499 0.27022 0.27582 0.27210 1 h-lim-p 0.0012 0.0092 71.2142 3592.489711 7 0.0004 37 | 0/8 2 h-lim-p 0.0015 0.0122 14.3418 3592.436687 7 0.0005 68 | 0/8 3 h-lim-p 0.0011 0.0518 7.2381 3592.426430 2 0.0005 84 | 0/8 4 h-lim-p 0.0019 0.1578 1.8846 3592.425373 4 0.0006 107 | 0/8 5 h-lim-p 0.0239 7.0806 0.0507 3592.425372 0 0.0013 122 | 0/8 6 h-lim-p 0.0066 20.0000 0.0100 3592.425372 0 0.0029 142 | 0/8 7 h-lim-p 0.0048 20.0000 0.0060 3592.425372 0 0.0042 162 | 0/8 8 h-lim-p 0.0249 20.0000 0.0010 3592.425341 0 0.1990 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3592.425339 0 1.0938 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3592.425339 0 1.0938 225 | 0/8 11 h-lim-p 1.8988 20.0000 0.0000 3592.425339 0 0.9494 245 | 0/8 12 h-lim-p 0.7627 20.0000 0.0000 3592.425339 0 0.1907 266 | 0/8 13 h-lim-p 0.0338 20.0000 0.0000 3592.425339 0 0.0003 292 | 0/8 14 h-lim-p 0.0038 20.0000 0.0000 3592.425339 0 0.0019 312 Out... lnL = -3592.425339 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3592.425339 Node 7: lnL = -3592.425339 Node 8: lnL = -3592.425339 Node 9: lnL = -3592.425339 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 569 Sequential format.. Reading seq # 1: YGR010W_Sbay Reading seq # 2: YGR010W_Scer Reading seq # 3: YGR010W_Skud Reading seq # 4: YGR010W_Smik Reading seq # 5: YGR010W_Spar Sequences read.. Counting patterns.. # site patterns = 203 Counting frequencies.. 120 bytes for distance 32480 bytes for lkl0 25984 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.142819 0.137218 0.054616 0.123735 0.107348 0.195203 0.148883 0.188423 lnL0 = -2646.849358 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2646.849358 x= 0.14282 0.13722 0.05462 0.12374 0.10735 0.19520 0.14888 0.18842 1 h-lim-p 0.0006 0.0050 51.7993 2646.438914 7 0.0003 39 | 0/8 2 h-lim-p 0.0009 0.0078 17.7042 2646.372828 6 0.0005 66 | 0/8 3 h-lim-p 0.0010 0.0303 8.4788 2646.362254 6 0.0004 90 | 0/8 4 h-lim-p 0.0016 0.0806 1.9082 2646.361679 2 0.0004 107 | 0/8 5 h-lim-p 0.0030 1.5878 0.2246 2646.361664 1 0.0006 122 | 0/8 6 h-lim-p 0.0051 16.6940 0.0264 2646.361664 0 0.0006 144 | 0/8 7 h-lim-p 0.0063 20.0000 0.0023 2646.361664 0 0.0014 165 | 0/8 8 h-lim-p 0.0487 20.0000 0.0001 2646.361662 0 0.7799 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2646.361662 0 1.0938 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2646.361662 0 1.0938 229 | 0/8 11 h-lim-p 1.1962 20.0000 0.0000 2646.361662 0 0.0748 252 | 0/8 12 h-lim-p 0.0247 20.0000 0.0000 2646.361662 0 0.0123 272 | 0/8 13 h-lim-p 0.0058 20.0000 0.0000 2646.361662 0 0.0029 292 | 0/8 14 h-lim-p 0.0019 20.0000 0.0000 2646.361662 0 0.0009 312 | 0/8 15 h-lim-p 0.0005 20.0000 0.0001 2646.361662 0 0.0000 349 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 | 0/8 17 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -2646.361662 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2646.361662 Node 7: lnL = -2646.361662 Node 8: lnL = -2646.361662 Node 9: lnL = -2646.361662 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 393 Sequential format.. Reading seq # 1: YGR012W_Sbay Reading seq # 2: YGR012W_Scer Reading seq # 3: YGR012W_Skud Reading seq # 4: YGR012W_Smik Reading seq # 5: YGR012W_Spar Sequences read.. Counting patterns.. # site patterns = 176 Counting frequencies.. 120 bytes for distance 28160 bytes for lkl0 22528 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.262379 0.038560 0.063137 0.159337 0.106122 0.216391 0.318196 0.321039 lnL0 = -1872.107341 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1872.107341 x= 0.26238 0.03856 0.06314 0.15934 0.10612 0.21639 0.31820 0.32104 1 h-lim-p 0.0005 0.0039 70.9870 1870.656480 0 0.0007 22 | 0/8 2 h-lim-p 0.0017 0.0139 23.4441 1870.366647 7 0.0011 51 | 0/8 3 h-lim-p 0.0017 0.0231 15.2409 1870.243158 3 0.0015 69 | 0/8 4 h-lim-p 0.0030 0.0244 7.3280 1870.229909 5 0.0007 91 | 0/8 5 h-lim-p 0.0012 0.0755 4.0832 1870.224165 3 0.0010 109 | 0/8 6 h-lim-p 0.0040 0.5052 0.9902 1870.223304 2 0.0019 125 | 0/8 7 h-lim-p 0.0034 0.9283 0.5482 1870.223145 3 0.0012 152 | 0/8 8 h-lim-p 0.1257 20.0000 0.0052 1870.206685 0 1.0056 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 1870.206543 2 0.9644 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1870.206543 0 1.0938 219 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1870.206543 0 1.0938 239 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1870.206543 0 1.0938 259 | 0/8 13 h-lim-p 1.0860 20.0000 0.0000 1870.206543 0 0.5430 279 | 0/8 14 h-lim-p 0.0485 20.0000 0.0000 1870.206543 0 0.0485 299 | 0/8 15 h-lim-p 0.0180 20.0000 0.0000 1870.206543 0 0.0180 319 | 0/8 16 h-lim-p 0.0073 20.0000 0.0001 1870.206543 0 0.0000 360 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1870.206543 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1870.206543 Node 7: lnL = -1870.206543 Node 8: lnL = -1870.206543 Node 9: lnL = -1870.206543 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 209 Sequential format.. Reading seq # 1: YGR016W_Sbay Reading seq # 2: YGR016W_Scer Reading seq # 3: YGR016W_Skud Reading seq # 4: YGR016W_Smik Reading seq # 5: YGR016W_Spar Sequences read.. Counting patterns.. # site patterns = 93 Counting frequencies.. 120 bytes for distance 14880 bytes for lkl0 11904 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.133497 0.059320 0.029219 0.136073 0.063026 0.181399 0.274406 0.175375 lnL0 = -904.235391 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 904.235391 x= 0.13350 0.05932 0.02922 0.13607 0.06303 0.18140 0.27441 0.17538 1 h-lim-p 0.0013 0.0107 47.3439 903.783482 8 0.0005 42 | 0/8 2 h-lim-p 0.0011 0.0086 16.6343 903.671093 3 0.0009 60 | 0/8 3 h-lim-p 0.0014 0.0356 11.0723 903.637983 7 0.0008 90 | 0/8 4 h-lim-p 0.0020 0.0690 4.1343 903.627808 5 0.0014 113 | 0/8 5 h-lim-p 0.0042 0.1918 1.4083 903.626500 5 0.0015 136 | 0/8 6 h-lim-p 0.0092 1.0594 0.2303 903.626465 3 0.0014 158 | 0/8 7 h-lim-p 0.0071 5.4549 0.0439 903.626463 0 0.0016 179 | 0/8 8 h-lim-p 0.0845 20.0000 0.0008 903.626127 0 1.0134 202 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 903.626123 1 0.9961 224 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 903.626123 0 1.0938 244 | 0/8 11 h-lim-p 1.9613 20.0000 0.0000 903.626123 0 3.9226 265 | 0/8 12 h-lim-p 2.3782 20.0000 0.0000 903.626123 0 0.1486 288 | 0/8 13 h-lim-p 0.6475 20.0000 0.0000 903.626123 0 0.0202 312 | 0/8 14 h-lim-p 0.0064 20.0000 0.0000 903.626123 0 0.0000 351 Out... lnL = -903.626123 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -903.626123 Node 7: lnL = -903.626123 Node 8: lnL = -903.626123 Node 9: lnL = -903.626123 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 851 Sequential format.. Reading seq # 1: YGR017W_Sbay Reading seq # 2: YGR017W_Scer Reading seq # 3: YGR017W_Skud Reading seq # 4: YGR017W_Smik Reading seq # 5: YGR017W_Spar Sequences read.. Counting patterns.. # site patterns = 311 Counting frequencies.. 120 bytes for distance 49760 bytes for lkl0 39808 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.216769 0.055475 0.084579 0.134958 0.085270 0.175252 0.212066 0.266448 lnL0 = -3932.404261 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3932.404261 x= 0.21677 0.05548 0.08458 0.13496 0.08527 0.17525 0.21207 0.26645 1 h-lim-p 0.0028 0.0226 100.1474 3931.170194 6 0.0003 38 | 0/8 2 h-lim-p 0.0005 0.0038 29.0960 3931.064452 6 0.0003 64 | 0/8 3 h-lim-p 0.0007 0.0312 11.7301 3931.046365 2 0.0003 80 | 0/8 4 h-lim-p 0.0006 0.0460 5.7082 3931.042337 3 0.0003 99 | 0/8 5 h-lim-p 0.0012 0.1907 1.5245 3931.041788 2 0.0005 115 | 0/8 6 h-lim-p 0.0207 5.2488 0.0371 3931.041788 0 0.0006 131 | 0/8 7 h-lim-p 0.0010 15.2021 0.0201 3931.041788 0 0.0009 151 | 0/8 8 h-lim-p 0.0909 20.0000 0.0002 3931.041743 0 0.7268 174 | 0/8 9 h-lim-p 1.9585 20.0000 0.0001 3931.041741 1 0.9639 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3931.041741 0 1.0938 217 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3931.041741 0 1.0938 237 | 0/8 12 h-lim-p 0.6736 20.0000 0.0000 3931.041741 0 0.0105 262 | 0/8 13 h-lim-p 0.0072 20.0000 0.0000 3931.041741 0 0.0000 299 Out... lnL = -3931.041741 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3931.041741 Node 7: lnL = -3931.041741 Node 8: lnL = -3931.041741 Node 9: lnL = -3931.041741 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 314 Sequential format.. Reading seq # 1: YGR020C_Sbay Reading seq # 2: YGR020C_Scer Reading seq # 3: YGR020C_Skud Reading seq # 4: YGR020C_Smik Reading seq # 5: YGR020C_Spar Sequences read.. Counting patterns.. # site patterns = 108 Counting frequencies.. 120 bytes for distance 17280 bytes for lkl0 13824 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.058752 0.033456 0.043995 0.102994 0.070491 0.117117 0.175684 0.081515 lnL0 = -1229.730394 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1229.730394 x= 0.05875 0.03346 0.04399 0.10299 0.07049 0.11712 0.17568 0.08152 1 h-lim-p 0.0024 0.0193 65.4289 1229.286077 7 0.0002 40 | 0/8 2 h-lim-p 0.0029 0.0419 4.9764 1229.279136 4 0.0006 61 | 0/8 3 h-lim-p 0.0013 0.0777 2.1936 1229.278131 3 0.0005 79 | 0/8 4 h-lim-p 0.0015 0.2281 0.7031 1229.278032 3 0.0004 100 | 0/8 5 h-lim-p 0.0015 0.8054 0.2083 1229.278024 2 0.0005 126 | 0/8 6 h-lim-p 0.0024 2.7693 0.0430 1229.278023 0 0.0005 147 | 0/8 7 h-lim-p 0.0040 20.0000 0.0056 1229.278023 0 0.0009 168 | 0/8 8 h-lim-p 0.0751 20.0000 0.0001 1229.278017 0 0.9012 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1229.278017 0 1.0938 211 | 0/8 10 h-lim-p 1.6276 20.0000 0.0000 1229.278017 0 2.4413 231 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1229.278017 0 0.2734 253 | 0/8 12 h-lim-p 0.0358 20.0000 0.0000 1229.278017 0 0.0089 274 | 0/8 13 h-lim-p 0.0037 20.0000 0.0000 1229.278017 0 0.0032 294 | 0/8 14 h-lim-p 0.0021 20.0000 0.0000 1229.278017 0 0.0000 324 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 1229.278017 0 0.0000 354 Out... lnL = -1229.278017 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1229.278017 Node 7: lnL = -1229.278017 Node 8: lnL = -1229.278017 Node 9: lnL = -1229.278017 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 44 Sequential format.. Reading seq # 1: YGR024C_Sbay Reading seq # 2: YGR024C_Scer Reading seq # 3: YGR024C_Skud Reading seq # 4: YGR024C_Smik Reading seq # 5: YGR024C_Spar Sequences read.. Counting patterns.. # site patterns = 37 Counting frequencies.. 120 bytes for distance 5920 bytes for lkl0 4736 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.078500 0.067105 0.239953 0.130503 0.155948 0.225498 0.683075 0.137447 lnL0 = -231.955932 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 231.955932 x= 0.07850 0.06710 0.23995 0.13050 0.15595 0.22550 0.68307 0.13745 1 h-lim-p 0.0048 0.0382 4.4820 231.898166 1 0.0060 24 | 0/8 2 h-lim-p 0.0104 0.1257 2.5826 231.873981 5 0.0090 45 | 0/8 3 h-lim-p 0.0205 0.6362 1.1346 231.864414 3 0.0186 63 | 0/8 4 h-lim-p 0.0118 0.2752 1.7925 231.858674 5 0.0089 85 | 0/8 5 h-lim-p 0.0366 1.2271 0.4370 231.858203 5 0.0063 111 | 0/8 6 h-lim-p 0.1249 10.7994 0.0221 231.858179 3 0.0336 138 | 0/8 7 h-lim-p 0.0981 20.0000 0.0076 231.857784 0 0.3922 160 | 0/8 8 h-lim-p 0.6694 20.0000 0.0044 231.857783 2 0.0412 187 | 0/8 9 h-lim-p 0.0823 20.0000 0.0022 231.857760 0 0.3291 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 231.857760 0 1.0938 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 231.857760 0 1.0938 249 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 231.857760 0 0.5469 270 | 0/8 13 h-lim-p 0.5018 20.0000 0.0000 231.857760 0 0.0157 294 | 0/8 14 h-lim-p 0.0091 20.0000 0.0000 231.857760 0 0.0091 314 | 0/8 15 h-lim-p 0.0062 20.0000 0.0000 231.857760 0 0.0001 339 Out... lnL = -231.857760 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -231.857760 Node 7: lnL = -231.857760 Node 8: lnL = -231.857760 Node 9: lnL = -231.857760 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 871 Sequential format.. Reading seq # 1: YGR027C_Sbay Reading seq # 2: YGR027C_Scer Reading seq # 3: YGR027C_Skud Reading seq # 4: YGR027C_Smik Reading seq # 5: YGR027C_Spar Sequences read.. Counting patterns.. # site patterns = 329 Counting frequencies.. 120 bytes for distance 52640 bytes for lkl0 42112 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.192607 0.111196 0.052179 0.195179 0.153137 0.167585 0.247273 0.237923 lnL0 = -3956.513656 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3956.513656 x= 0.19261 0.11120 0.05218 0.19518 0.15314 0.16758 0.24727 0.23792 1 h-lim-p 0.0046 1.2729 131.3319 3954.153109 6 0.0003 38 | 0/8 2 h-lim-p 0.0009 0.0069 37.8484 3953.560021 6 0.0009 61 | 0/8 3 h-lim-p 0.0006 0.0047 27.5444 3953.431926 3 0.0005 79 | 0/8 4 h-lim-p 0.0017 0.0140 7.9082 3953.406275 6 0.0009 104 | 0/8 5 h-lim-p 0.0031 0.0930 2.3890 3953.404127 4 0.0008 125 | 0/8 6 h-lim-p 0.0044 0.6690 0.4511 3953.404037 1 0.0009 140 | 0/8 7 h-lim-p 0.0180 9.2142 0.0221 3953.404021 2 0.0069 164 | 0/8 8 h-lim-p 0.0110 20.0000 0.0139 3953.401432 0 0.1319 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3953.401345 2 0.9961 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3953.401345 0 1.0938 231 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3953.401345 0 0.5469 252 | 0/8 12 h-lim-p 0.3533 20.0000 0.0000 3953.401345 0 0.0883 273 | 0/8 13 h-lim-p 0.0510 20.0000 0.0000 3953.401345 0 0.0255 293 | 0/8 14 h-lim-p 0.0184 20.0000 0.0000 3953.401345 0 0.0092 313 | 0/8 15 h-lim-p 0.0044 20.0000 0.0000 3953.401345 0 0.0022 333 | 0/8 16 h-lim-p 0.0020 20.0000 0.0000 3953.401345 0 0.0000 375 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 | 0/8 18 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -3953.401345 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3953.401345 Node 7: lnL = -3953.401345 Node 8: lnL = -3953.401345 Node 9: lnL = -3953.401345 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 863 Sequential format.. Reading seq # 1: YGR028W_Sbay Reading seq # 2: YGR028W_Scer Reading seq # 3: YGR028W_Skud Reading seq # 4: YGR028W_Smik Reading seq # 5: YGR028W_Spar Sequences read.. Counting patterns.. # site patterns = 444 Counting frequencies.. 120 bytes for distance 71040 bytes for lkl0 56832 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.255612 0.046983 0.000060 0.343887 0.238077 0.442848 0.881110 0.330344 lnL0 = -4853.354489 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4853.354489 x= 0.25561 0.04698 0.00006 0.34389 0.23808 0.44285 0.88111 0.33034 1 h-lim-p 0.0000 0.0000 88.4403 4853.312734 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0237 24.1108 4853.063464 0 0.0012 40 | 1/8 3 h-lim-p 0.0030 0.0569 9.8852 4852.985150 7 0.0017 71 | 1/8 4 h-lim-p 0.0037 0.2770 4.6390 4852.938840 5 0.0039 93 | 1/8 5 h-lim-p 0.0044 0.0352 2.2215 4852.841930 0 0.0176 107 | 1/8 6 h-lim-p 0.0010 0.0078 5.6543 4852.782417 0 0.0039 121 | 1/8 7 h-lim-p 0.0153 0.1227 0.5986 4850.640887 m 0.1227 133 | 0/8 8 h-lim-p -0.0000 -0.0000 26.7237 h-lim-p: -8.86551911e-21 -7.09241528e-20 2.67237214e+01 4850.640887 .. | 0/8 9 h-lim-p 0.0000 0.4897 42.0783 4850.407435 0 0.0003 165 | 0/8 10 h-lim-p 0.0016 0.0669 8.5495 4850.373129 5 0.0010 191 | 0/8 11 h-lim-p 0.0007 0.0056 4.8886 4850.363757 0 0.0014 204 | 0/8 12 h-lim-p 0.0100 0.0988 0.6871 4850.363059 4 0.0030 227 | 0/8 13 h-lim-p 0.0023 0.0691 0.8993 4850.362681 2 0.0018 251 | 0/8 14 h-lim-p 0.0034 1.2793 0.4633 4850.362524 3 0.0022 279 | 0/8 15 h-lim-p 0.0032 0.5477 0.3201 4850.362450 2 0.0021 305 | 0/8 16 h-lim-p 0.2179 6.2971 0.0031 4850.357366 0 0.8715 327 | 0/8 17 h-lim-p 2.5000 20.0000 0.0002 4850.357346 1 0.9961 349 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 4850.357346 0 1.0938 369 | 0/8 19 h-lim-p 1.9446 20.0000 0.0000 4850.357346 0 0.9723 389 | 0/8 20 h-lim-p 0.7841 20.0000 0.0000 4850.357346 0 0.0000 427 Out... lnL = -4850.357346 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4850.357346 Node 7: lnL = -4850.357346 Node 8: lnL = -4850.357346 Node 9: lnL = -4850.357346 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 312 Sequential format.. Reading seq # 1: YGR030C_Sbay Reading seq # 2: YGR030C_Scer Reading seq # 3: YGR030C_Skud Reading seq # 4: YGR030C_Smik Reading seq # 5: YGR030C_Spar Sequences read.. Counting patterns.. # site patterns = 177 Counting frequencies.. 120 bytes for distance 28320 bytes for lkl0 22656 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.118104 0.181517 0.096275 0.183477 0.305767 0.237730 0.294461 0.172553 lnL0 = -1431.017471 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1431.017471 x= 0.11810 0.18152 0.09628 0.18348 0.30577 0.23773 0.29446 0.17255 1 h-lim-p 0.0020 0.0164 15.1252 1430.691446 0 0.0041 23 | 0/8 2 h-lim-p 0.0054 0.0434 6.2310 1430.658306 6 0.0019 48 | 0/8 3 h-lim-p 0.0029 0.0940 4.1658 1430.646774 5 0.0019 72 | 0/8 4 h-lim-p 0.0064 0.1094 1.2230 1430.645846 3 0.0013 92 | 0/8 5 h-lim-p 0.0070 2.9558 0.2337 1430.645315 1 0.0070 106 | 0/8 6 h-lim-p 0.0077 1.6043 0.2121 1430.642460 0 0.0154 127 | 0/8 7 h-lim-p 0.0074 0.8190 0.4410 1430.612929 0 0.0296 149 | 0/8 8 h-lim-p 0.0075 0.2026 1.7390 1430.603664 6 0.0046 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0008 1430.603541 2 0.9961 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1430.603541 0 1.0938 221 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1430.603541 0 1.0938 241 | 0/8 12 h-lim-p 1.6851 20.0000 0.0000 1430.603541 0 0.6319 262 | 0/8 13 h-lim-p 0.2708 20.0000 0.0000 1430.603541 0 0.1354 282 | 0/8 14 h-lim-p 0.0439 20.0000 0.0000 1430.603541 0 0.0000 326 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1430.603541 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1430.603541 Node 7: lnL = -1430.603541 Node 8: lnL = -1430.603541 Node 9: lnL = -1430.603541 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 329 Sequential format.. Reading seq # 1: YGR031W_Sbay Reading seq # 2: YGR031W_Scer Reading seq # 3: YGR031W_Skud Reading seq # 4: YGR031W_Smik Reading seq # 5: YGR031W_Spar Sequences read.. Counting patterns.. # site patterns = 194 Counting frequencies.. 120 bytes for distance 31040 bytes for lkl0 24832 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.242783 0.070073 0.093077 0.216824 0.092204 0.220837 0.371952 0.295859 lnL0 = -1586.992551 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1586.992551 x= 0.24278 0.07007 0.09308 0.21682 0.09220 0.22084 0.37195 0.29586 1 h-lim-p 0.0155 3.4961 45.3081 1586.156341 3 0.0009 31 | 0/8 2 h-lim-p 0.0012 0.0095 15.7194 1585.991440 0 0.0018 43 | 0/8 3 h-lim-p 0.0063 0.0993 4.4845 1585.968455 5 0.0025 65 | 0/8 4 h-lim-p 0.0052 0.2209 2.1584 1585.962829 6 0.0029 92 | 0/8 5 h-lim-p 0.0135 0.7459 0.4684 1585.962585 3 0.0022 113 | 0/8 6 h-lim-p 0.0101 4.4180 0.1037 1585.962535 2 0.0040 137 | 0/8 7 h-lim-p 0.0044 4.6740 0.0957 1585.962290 0 0.0131 158 | 0/8 8 h-lim-p 0.0198 3.1323 0.0630 1585.956394 0 0.0794 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 1585.956231 3 1.0004 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1585.956231 0 1.0938 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1585.956230 0 1.0938 246 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1585.956230 0 0.1367 269 | 0/8 13 h-lim-p 0.0672 20.0000 0.0000 1585.956230 0 0.0084 291 | 0/8 14 h-lim-p 0.0041 20.0000 0.0000 1585.956230 0 0.0000 327 Out... lnL = -1585.956230 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1585.956230 Node 7: lnL = -1585.956230 Node 8: lnL = -1585.956230 Node 9: lnL = -1585.956230 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 934 Sequential format.. Reading seq # 1: YGR033C_Sbay Reading seq # 2: YGR033C_Scer Reading seq # 3: YGR033C_Skud Reading seq # 4: YGR033C_Smik Reading seq # 5: YGR033C_Spar Sequences read.. Counting patterns.. # site patterns = 366 Counting frequencies.. 120 bytes for distance 58560 bytes for lkl0 46848 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.180454 0.070736 0.065346 0.170966 0.161623 0.253970 0.325132 0.228477 lnL0 = -4511.720998 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4511.720998 x= 0.18045 0.07074 0.06535 0.17097 0.16162 0.25397 0.32513 0.22848 1 h-lim-p 0.0012 0.0096 167.4059 4508.403604 8 0.0003 38 | 0/8 2 h-lim-p 0.0008 0.0065 36.1814 4508.116052 7 0.0005 66 | 0/8 3 h-lim-p 0.0014 0.0307 11.4176 4508.090028 6 0.0004 94 | 0/8 4 h-lim-p 0.0014 0.1069 3.7199 4508.085899 3 0.0007 112 | 0/8 5 h-lim-p 0.0028 0.4435 0.8933 4508.085559 3 0.0009 132 | 0/8 6 h-lim-p 0.0044 1.7061 0.1854 4508.085551 0 0.0005 154 | 0/8 7 h-lim-p 0.0137 20.0000 0.0066 4508.085545 0 0.0137 174 | 0/8 8 h-lim-p 0.0108 20.0000 0.0083 4508.085120 0 0.0866 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4508.085091 1 0.9961 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4508.085091 0 1.0938 239 | 0/8 11 h-lim-p 1.3275 20.0000 0.0000 4508.085091 0 0.5808 259 | 0/8 12 h-lim-p 0.2807 20.0000 0.0000 4508.085091 0 0.0044 284 | 0/8 13 h-lim-p 0.0002 20.0000 0.0001 4508.085091 0 0.0000 307 | 0/8 14 h-lim-p 0.0008 20.0000 0.0000 4508.085091 0 0.0000 341 Out... lnL = -4508.085091 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4508.085091 Node 7: lnL = -4508.085091 Node 8: lnL = -4508.085091 Node 9: lnL = -4508.085091 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 764 Sequential format.. Reading seq # 1: YGR035C_Sbay Reading seq # 2: YGR035C_Scer Reading seq # 3: YGR035C_Skud Reading seq # 4: YGR035C_Smik Reading seq # 5: YGR035C_Spar Sequences read.. Counting patterns.. # site patterns = 257 Counting frequencies.. 120 bytes for distance 41120 bytes for lkl0 32896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.181968 0.024794 0.098095 0.107491 0.077668 0.159624 0.215741 0.218026 lnL0 = -3467.134145 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3467.134145 x= 0.18197 0.02479 0.09810 0.10749 0.07767 0.15962 0.21574 0.21803 1 h-lim-p 0.0020 0.6273 186.6718 3464.465444 6 0.0002 39 | 0/8 2 h-lim-p 0.0009 0.0072 29.3115 3464.281447 2 0.0004 55 | 0/8 3 h-lim-p 0.0006 0.0122 22.0091 3464.244501 4 0.0002 75 | 0/8 4 h-lim-p 0.0007 0.0313 6.4918 3464.238134 2 0.0003 91 | 0/8 5 h-lim-p 0.0015 0.2340 1.4568 3464.237767 2 0.0004 108 | 0/8 6 h-lim-p 0.0023 1.1538 0.2308 3464.237757 2 0.0004 127 | 0/8 7 h-lim-p 0.0014 5.1141 0.0601 3464.237756 0 0.0006 147 | 0/8 8 h-lim-p 0.0639 20.0000 0.0006 3464.237220 0 1.0225 171 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3464.237213 0 1.0938 191 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3464.237213 0 1.0938 211 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3464.237213 0 0.5469 232 | 0/8 12 h-lim-p 0.3806 20.0000 0.0000 3464.237213 0 0.0238 255 | 0/8 13 h-lim-p 0.0151 20.0000 0.0000 3464.237213 0 0.0000 293 Out... lnL = -3464.237213 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3464.237213 Node 7: lnL = -3464.237213 Node 8: lnL = -3464.237213 Node 9: lnL = -3464.237213 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 858 Sequential format.. Reading seq # 1: YGR036C_Sbay Reading seq # 2: YGR036C_Scer Reading seq # 3: YGR036C_Skud Reading seq # 4: YGR036C_Smik Reading seq # 5: YGR036C_Spar Sequences read.. Counting patterns.. # site patterns = 305 Counting frequencies.. 120 bytes for distance 48800 bytes for lkl0 39040 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.140124 0.107202 0.084920 0.151704 0.115258 0.224003 0.200923 0.181110 lnL0 = -4083.001146 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4083.001146 x= 0.14012 0.10720 0.08492 0.15170 0.11526 0.22400 0.20092 0.18111 1 h-lim-p 0.0045 0.0357 124.9643 4081.211849 6 0.0002 37 | 0/8 2 h-lim-p 0.0013 0.0110 24.0531 4081.083170 7 0.0005 68 | 0/8 3 h-lim-p 0.0007 0.0176 15.1146 4081.058470 4 0.0003 88 | 0/8 4 h-lim-p 0.0071 0.5739 0.6104 4081.058382 3 0.0005 109 | 0/8 5 h-lim-p 0.0035 2.4802 0.0832 4081.058380 0 0.0004 131 | 0/8 6 h-lim-p 0.0026 20.0000 0.0123 4081.058380 0 0.0011 151 | 0/8 7 h-lim-p 0.0066 20.0000 0.0021 4081.058380 0 0.0058 171 | 0/8 8 h-lim-p 0.0058 20.0000 0.0021 4081.058354 0 0.0699 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4081.058353 0 1.0938 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4081.058353 0 1.0938 234 | 0/8 11 h-lim-p 1.3051 20.0000 0.0000 4081.058353 0 2.6102 255 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4081.058353 0 0.1367 278 | 0/8 13 h-lim-p 0.0414 20.0000 0.0000 4081.058353 0 0.0621 298 | 0/8 14 h-lim-p 0.0266 20.0000 0.0000 4081.058353 0 0.0017 321 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 4081.058353 0 0.0000 355 | 0/8 16 h-lim-p 0.0000 20.0000 0.0011 | 0/8 17 h-lim-p 0.0000 20.0000 0.0011 Out... lnL = -4081.058353 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4081.058353 Node 7: lnL = -4081.058353 Node 8: lnL = -4081.058353 Node 9: lnL = -4081.058353 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 730 Sequential format.. Reading seq # 1: YGR037C_Sbay Reading seq # 2: YGR037C_Scer Reading seq # 3: YGR037C_Skud Reading seq # 4: YGR037C_Smik Reading seq # 5: YGR037C_Spar Sequences read.. Counting patterns.. # site patterns = 239 Counting frequencies.. 120 bytes for distance 38240 bytes for lkl0 30592 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.101893 0.119130 0.065055 0.125431 0.104350 0.173987 0.162658 0.135925 lnL0 = -3286.318458 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3286.318458 x= 0.10189 0.11913 0.06505 0.12543 0.10435 0.17399 0.16266 0.13592 1 h-lim-p 0.0051 1.0304 113.8891 3285.096601 8 0.0002 44 | 0/8 2 h-lim-p 0.0009 0.0074 18.6000 3285.043798 7 0.0003 72 | 0/8 3 h-lim-p 0.0011 0.0612 5.1252 3285.039987 5 0.0003 96 | 0/8 4 h-lim-p 0.0014 0.1880 1.1146 3285.039750 4 0.0004 118 | 0/8 5 h-lim-p 0.0051 2.5120 0.0896 3285.039749 0 0.0006 132 | 0/8 6 h-lim-p 0.0038 20.0000 0.0130 3285.039749 0 0.0004 154 | 0/8 7 h-lim-p 0.0023 20.0000 0.0024 3285.039749 0 0.0010 174 | 0/8 8 h-lim-p 0.0142 20.0000 0.0002 3285.039742 0 0.4532 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3285.039742 0 1.0938 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3285.039742 0 1.0938 239 | 0/8 11 h-lim-p 1.2021 20.0000 0.0000 3285.039742 0 3.6063 260 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3285.039742 0 0.2734 282 | 0/8 13 h-lim-p 0.0203 20.0000 0.0000 3285.039742 0 0.0003 307 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 3285.039742 0 0.0000 343 | 0/8 15 h-lim-p 0.0000 20.0000 0.0009 | 0/8 16 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -3285.039742 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3285.039742 Node 7: lnL = -3285.039742 Node 8: lnL = -3285.039742 Node 9: lnL = -3285.039742 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 731 Sequential format.. Reading seq # 1: YGR038W_Sbay Reading seq # 2: YGR038W_Scer Reading seq # 3: YGR038W_Skud Reading seq # 4: YGR038W_Smik Reading seq # 5: YGR038W_Spar Sequences read.. Counting patterns.. # site patterns = 241 Counting frequencies.. 120 bytes for distance 38560 bytes for lkl0 30848 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.117592 0.070120 0.053819 0.128729 0.101052 0.185213 0.185894 0.143584 lnL0 = -3276.730751 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3276.730751 x= 0.11759 0.07012 0.05382 0.12873 0.10105 0.18521 0.18589 0.14358 1 h-lim-p 0.0031 0.0348 144.5725 3275.069465 6 0.0002 36 | 0/8 2 h-lim-p 0.0008 0.0063 20.7052 3275.007931 6 0.0003 61 | 0/8 3 h-lim-p 0.0013 0.0849 4.7174 3275.004961 2 0.0003 78 | 0/8 4 h-lim-p 0.0012 0.2196 1.0587 3275.004698 2 0.0005 94 | 0/8 5 h-lim-p 0.0050 2.2047 0.1054 3275.004696 1 0.0003 111 | 0/8 6 h-lim-p 0.0047 20.0000 0.0068 3275.004696 0 0.0005 133 | 0/8 7 h-lim-p 0.0029 20.0000 0.0012 3275.004696 0 0.0026 153 | 0/8 8 h-lim-p 0.0255 20.0000 0.0001 3275.004694 0 0.3066 176 | 0/8 9 h-lim-p 2.4694 20.0000 0.0000 3275.004694 0 1.0804 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3275.004694 0 2.1875 216 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3275.004694 0 0.6250 237 | 0/8 12 h-lim-p 0.1527 20.0000 0.0000 3275.004694 0 0.0382 258 | 0/8 13 h-lim-p 0.0188 20.0000 0.0000 3275.004694 0 0.0012 281 | 0/8 14 h-lim-p 0.0009 20.0000 0.0000 3275.004694 0 0.0001 303 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 3275.004694 0 0.0000 323 | 0/8 16 h-lim-p 0.0003 20.0000 0.0000 3275.004694 0 0.0000 354 Out... lnL = -3275.004694 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3275.004694 Node 7: lnL = -3275.004694 Node 8: lnL = -3275.004694 Node 9: lnL = -3275.004694 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 219 Sequential format.. Reading seq # 1: YGR040W_Sbay Reading seq # 2: YGR040W_Scer Reading seq # 3: YGR040W_Skud Reading seq # 4: YGR040W_Smik Reading seq # 5: YGR040W_Spar Sequences read.. Counting patterns.. # site patterns = 93 Counting frequencies.. 120 bytes for distance 14880 bytes for lkl0 11904 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.079946 0.084133 0.060484 0.064697 0.044987 0.213279 0.212283 0.103143 lnL0 = -878.613396 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 878.613396 x= 0.07995 0.08413 0.06048 0.06470 0.04499 0.21328 0.21228 0.10314 1 h-lim-p 0.0002 0.0013 44.7988 878.179815 0 0.0005 23 | 0/8 2 h-lim-p 0.0013 0.9173 17.2351 878.127901 7 0.0004 53 | 0/8 3 h-lim-p 0.0011 0.0383 6.4673 878.112372 6 0.0009 76 | 0/8 4 h-lim-p 0.0034 0.0724 1.6544 878.111458 4 0.0007 99 | 0/8 5 h-lim-p 0.0043 0.6788 0.2777 878.111408 2 0.0010 116 | 0/8 6 h-lim-p 0.0029 3.0710 0.0975 878.111267 0 0.0086 137 | 0/8 7 h-lim-p 0.0332 5.8566 0.0252 878.102205 0 0.1329 159 | 0/8 8 h-lim-p 0.0032 0.2505 1.0416 878.100730 4 0.0021 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 878.100698 2 1.0889 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 878.100698 0 1.0938 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 878.100698 0 2.1875 245 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 878.100698 0 0.5469 266 | 0/8 13 h-lim-p 0.3095 20.0000 0.0000 878.100698 0 0.0006 294 Out... lnL = -878.100698 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -878.100698 Node 7: lnL = -878.100698 Node 8: lnL = -878.100698 Node 9: lnL = -878.100698 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 859 Sequential format.. Reading seq # 1: YGR041W_Sbay Reading seq # 2: YGR041W_Scer Reading seq # 3: YGR041W_Skud Reading seq # 4: YGR041W_Smik Reading seq # 5: YGR041W_Spar Sequences read.. Counting patterns.. # site patterns = 241 Counting frequencies.. 120 bytes for distance 38560 bytes for lkl0 30848 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.067292 0.102895 0.048762 0.090196 0.068286 0.194524 0.153580 0.089384 lnL0 = -3551.210504 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3551.210504 x= 0.06729 0.10289 0.04876 0.09020 0.06829 0.19452 0.15358 0.08938 1 h-lim-p 0.0002 0.0014 121.5466 3550.192203 5 0.0001 32 | 0/8 2 h-lim-p 0.0006 0.0049 22.0060 3550.148485 6 0.0002 62 | 0/8 3 h-lim-p 0.0004 0.0312 9.3709 3550.142166 4 0.0002 82 | 0/8 4 h-lim-p 0.0004 0.0417 3.7274 3550.141083 2 0.0002 98 | 0/8 5 h-lim-p 0.0008 0.2950 0.8105 3550.140994 3 0.0003 118 | 0/8 6 h-lim-p 0.0010 1.2413 0.2436 3550.140990 1 0.0002 141 | 0/8 7 h-lim-p 0.0192 20.0000 0.0025 3550.140989 0 0.0084 161 | 0/8 8 h-lim-p 0.0055 19.7686 0.0038 3550.140904 0 0.0442 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3550.140904 0 1.0938 204 | 0/8 10 h-lim-p 1.8934 20.0000 0.0000 3550.140904 0 1.6567 224 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3550.140904 0 0.5469 245 | 0/8 12 h-lim-p 0.1950 20.0000 0.0000 3550.140904 0 0.0015 271 | 0/8 13 h-lim-p 0.0005 20.0000 0.0000 3550.140904 0 0.0000 295 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 3550.140904 0 0.0000 317 Out... lnL = -3550.140904 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3550.140904 Node 7: lnL = -3550.140904 Node 8: lnL = -3550.140904 Node 9: lnL = -3550.140904 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 356 Sequential format.. Reading seq # 1: YGR042W_Sbay Reading seq # 2: YGR042W_Scer Reading seq # 3: YGR042W_Skud Reading seq # 4: YGR042W_Smik Reading seq # 5: YGR042W_Spar Sequences read.. Counting patterns.. # site patterns = 201 Counting frequencies.. 120 bytes for distance 32160 bytes for lkl0 25728 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.135451 0.139795 0.149635 0.126422 0.107810 0.465252 0.383767 0.180932 lnL0 = -1857.210070 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1857.210070 x= 0.13545 0.13980 0.14964 0.12642 0.10781 0.46525 0.38377 0.18093 1 h-lim-p 0.0056 0.0447 28.7500 1856.786606 6 0.0011 36 | 0/8 2 h-lim-p 0.0013 0.0104 15.2219 1856.718870 6 0.0007 61 | 0/8 3 h-lim-p 0.0014 0.0318 7.8209 1856.677847 0 0.0021 73 | 0/8 4 h-lim-p 0.0040 0.1151 4.0212 1856.667377 4 0.0017 92 | 0/8 5 h-lim-p 0.0073 0.2471 0.9541 1856.666747 3 0.0015 111 | 0/8 6 h-lim-p 0.0051 1.7965 0.2858 1856.666642 3 0.0027 138 | 0/8 7 h-lim-p 0.0602 20.0000 0.0127 1856.666522 1 0.0752 160 | 0/8 8 h-lim-p 0.0186 19.6862 0.0515 1856.665141 0 0.0372 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 1856.665086 2 0.9961 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1856.665086 0 1.0938 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1856.665086 0 1.0938 245 | 0/8 12 h-lim-p 1.5385 20.0000 0.0000 1856.665086 0 0.3846 266 | 0/8 13 h-lim-p 0.1086 20.0000 0.0000 1856.665086 0 0.0407 287 | 0/8 14 h-lim-p 0.0138 20.0000 0.0000 1856.665086 0 0.0017 309 | 0/8 15 h-lim-p 0.0016 20.0000 0.0000 1856.665086 0 0.0000 344 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1856.665086 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1856.665086 Node 7: lnL = -1856.665086 Node 8: lnL = -1856.665086 Node 9: lnL = -1856.665086 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 868 Sequential format.. Reading seq # 1: YGR043C_Sbay Reading seq # 2: YGR043C_Scer Reading seq # 3: YGR043C_Skud Reading seq # 4: YGR043C_Smik Reading seq # 5: YGR043C_Spar Sequences read.. Counting patterns.. # site patterns = 305 Counting frequencies.. 120 bytes for distance 48800 bytes for lkl0 39040 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.143664 0.069839 0.056844 0.127344 0.096354 0.146314 0.174796 0.169661 lnL0 = -3613.380376 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3613.380376 x= 0.14366 0.06984 0.05684 0.12734 0.09635 0.14631 0.17480 0.16966 1 h-lim-p 0.0031 0.8492 151.7236 3611.412546 2 0.0002 29 | 0/8 2 h-lim-p 0.0004 0.0032 34.3611 3611.239217 5 0.0003 51 | 0/8 3 h-lim-p 0.0007 0.0165 14.0045 3611.214323 4 0.0003 71 | 0/8 4 h-lim-p 0.0008 0.0426 5.0212 3611.211260 5 0.0003 96 | 0/8 5 h-lim-p 0.0027 0.3636 0.5243 3611.211208 3 0.0004 117 | 0/8 6 h-lim-p 0.0039 3.2708 0.0531 3611.211207 0 0.0004 139 | 0/8 7 h-lim-p 0.0043 20.0000 0.0053 3611.211207 0 0.0037 159 | 0/8 8 h-lim-p 0.0218 20.0000 0.0009 3611.211133 0 0.1741 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3611.211131 0 1.0938 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3611.211131 0 1.0938 222 | 0/8 11 h-lim-p 1.7607 20.0000 0.0000 3611.211131 0 0.3852 243 | 0/8 12 h-lim-p 0.2185 20.0000 0.0000 3611.211131 0 0.0239 265 | 0/8 13 h-lim-p 0.0126 20.0000 0.0000 3611.211131 0 0.0000 295 Out... lnL = -3611.211131 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3611.211131 Node 7: lnL = -3611.211131 Node 8: lnL = -3611.211131 Node 9: lnL = -3611.211131 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 43 Sequential format.. Reading seq # 1: YGR044C_Sbay Reading seq # 2: YGR044C_Scer Reading seq # 3: YGR044C_Skud Reading seq # 4: YGR044C_Smik Reading seq # 5: YGR044C_Spar Sequences read.. Counting patterns.. # site patterns = 38 Counting frequencies.. 120 bytes for distance 6080 bytes for lkl0 4864 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.564956 0.000060 0.354767 0.222244 0.361123 0.398791 0.499964 0.627794 lnL0 = -251.392520 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 251.392520 x= 0.56496 0.00006 0.35477 0.22224 0.36112 0.39879 0.49996 0.62779 1 h-lim-p 0.0000 0.0000 15.2310 251.389487 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0234 16.8266 249.279167 9 0.0185 65 | 1/8 3 h-lim-p 0.0550 0.4400 2.7296 249.124513 9 0.0378 103 | 1/8 4 h-lim-p 0.1690 1.3518 0.5881 248.887022 0 0.2535 115 | 1/8 5 h-lim-p 0.0320 0.2559 1.1056 248.638521 0 0.0640 135 | 1/8 6 h-lim-p 0.0201 0.1609 2.3690 248.561337 7 0.0222 165 | 1/8 7 h-lim-p 0.3809 4.6336 0.1383 248.559517 5 0.0621 190 | 1/8 8 h-lim-p 0.0739 15.0838 0.1163 248.541894 0 0.2954 211 | 1/8 9 h-lim-p 2.5000 20.0000 0.0063 248.541660 5 0.3984 243 | 1/8 10 h-lim-p 1.3006 20.0000 0.0019 248.541604 4 0.7660 272 | 1/8 11 h-lim-p 2.5000 20.0000 0.0003 248.541603 2 0.8246 297 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 248.541603 0 1.0938 316 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 248.541603 0 1.0938 335 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 248.541603 0 1.0938 354 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 248.541603 0 2.1875 373 | 1/8 16 h-lim-p 1.8683 20.0000 0.0000 248.541603 0 0.0073 399 Out... lnL = -248.541603 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -248.541603 Node 7: lnL = -248.541603 Node 8: lnL = -248.541603 Node 9: lnL = -248.541603 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 751 Sequential format.. Reading seq # 1: YGR046W_Sbay Reading seq # 2: YGR046W_Scer Reading seq # 3: YGR046W_Skud Reading seq # 4: YGR046W_Smik Reading seq # 5: YGR046W_Spar Sequences read.. Counting patterns.. # site patterns = 349 Counting frequencies.. 120 bytes for distance 55840 bytes for lkl0 44672 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.222936 0.069804 0.066104 0.105068 0.148133 0.324956 0.304427 0.261907 lnL0 = -3754.440450 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3754.440450 x= 0.22294 0.06980 0.06610 0.10507 0.14813 0.32496 0.30443 0.26191 1 h-lim-p 0.0025 0.0299 172.9636 3750.652157 6 0.0003 35 | 0/8 2 h-lim-p 0.0005 0.0038 46.7187 3750.131175 4 0.0005 55 | 0/8 3 h-lim-p 0.0014 0.0258 16.1764 3750.035315 7 0.0008 87 | 0/8 4 h-lim-p 0.0017 0.0313 7.7490 3750.022149 6 0.0005 114 | 0/8 5 h-lim-p 0.0020 0.1945 2.1114 3750.019997 4 0.0011 135 | 0/8 6 h-lim-p 0.0620 6.2761 0.0363 3750.019989 1 0.0031 152 | 0/8 7 h-lim-p 0.0033 8.8558 0.0338 3750.019881 0 0.0133 174 | 0/8 8 h-lim-p 0.0063 7.4424 0.0713 3750.017350 0 0.0251 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3750.017292 2 0.9961 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3750.017292 0 1.0938 240 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3750.017292 0 0.5469 261 | 0/8 12 h-lim-p 0.3842 20.0000 0.0000 3750.017292 0 0.0060 286 | 0/8 13 h-lim-p 0.0096 20.0000 0.0000 3750.017292 0 0.0006 309 Out... lnL = -3750.017292 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3750.017292 Node 7: lnL = -3750.017292 Node 8: lnL = -3750.017292 Node 9: lnL = -3750.017292 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 373 Sequential format.. Reading seq # 1: YGR048W_Sbay Reading seq # 2: YGR048W_Scer Reading seq # 3: YGR048W_Skud Reading seq # 4: YGR048W_Smik Reading seq # 5: YGR048W_Spar Sequences read.. Counting patterns.. # site patterns = 158 Counting frequencies.. 120 bytes for distance 25280 bytes for lkl0 20224 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.097003 0.082864 0.075659 0.081527 0.063425 0.203275 0.199813 0.121923 lnL0 = -1612.822619 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1612.822619 x= 0.09700 0.08286 0.07566 0.08153 0.06343 0.20328 0.19981 0.12192 1 h-lim-p 0.0007 0.0058 71.0669 1611.814894 9 0.0004 42 | 0/8 2 h-lim-p 0.0018 0.0145 12.3616 1611.777592 6 0.0005 68 | 0/8 3 h-lim-p 0.0007 0.0303 9.1531 1611.766055 6 0.0004 96 | 0/8 4 h-lim-p 0.0010 0.0667 3.5357 1611.762854 5 0.0006 122 | 0/8 5 h-lim-p 0.0036 0.2430 0.6229 1611.762768 2 0.0005 140 | 0/8 6 h-lim-p 0.0020 1.3818 0.1444 1611.762760 2 0.0008 164 | 0/8 7 h-lim-p 0.0198 20.0000 0.0058 1611.762759 0 0.0086 184 | 0/8 8 h-lim-p 0.0204 20.0000 0.0024 1611.762628 0 0.1635 207 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1611.762626 0 1.0938 227 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1611.762626 0 1.0938 247 | 0/8 11 h-lim-p 2.2033 20.0000 0.0000 1611.762626 0 2.2033 267 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1611.762626 0 0.0781 291 | 0/8 13 h-lim-p 0.0152 20.0000 0.0000 1611.762626 0 0.0152 311 | 0/8 14 h-lim-p 0.0071 20.0000 0.0000 1611.762626 0 0.0018 332 | 0/8 15 h-lim-p 0.0011 20.0000 0.0000 1611.762626 0 0.0000 359 Out... lnL = -1611.762626 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1611.762626 Node 7: lnL = -1611.762626 Node 8: lnL = -1611.762626 Node 9: lnL = -1611.762626 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 454 Sequential format.. Reading seq # 1: YGR049W_Sbay Reading seq # 2: YGR049W_Scer Reading seq # 3: YGR049W_Skud Reading seq # 4: YGR049W_Smik Reading seq # 5: YGR049W_Spar Sequences read.. Counting patterns.. # site patterns = 175 Counting frequencies.. 120 bytes for distance 28000 bytes for lkl0 22400 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.130477 0.083110 0.073131 0.106983 0.067633 0.169790 0.167717 0.156099 lnL0 = -1935.962066 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1935.962066 x= 0.13048 0.08311 0.07313 0.10698 0.06763 0.16979 0.16772 0.15610 1 h-lim-p 0.0017 0.0133 95.4170 1934.573649 4 0.0003 31 | 0/8 2 h-lim-p 0.0011 0.0084 17.4166 1934.522208 5 0.0003 54 | 0/8 3 h-lim-p 0.0008 0.0385 7.1694 1934.507424 5 0.0007 77 | 0/8 4 h-lim-p 0.0025 0.1142 1.8938 1934.506398 2 0.0006 94 | 0/8 5 h-lim-p 0.0035 0.5022 0.3394 1934.506371 3 0.0005 115 | 0/8 6 h-lim-p 0.0024 4.3815 0.0723 1934.506369 1 0.0006 138 | 0/8 7 h-lim-p 0.0843 20.0000 0.0005 1934.506349 0 0.3374 160 | 0/8 8 h-lim-p 0.0020 4.4295 0.0849 1934.506296 0 0.0031 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1934.506295 0 1.0938 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1934.506295 0 1.0938 220 | 0/8 11 h-lim-p 1.4658 20.0000 0.0000 1934.506295 0 0.0458 244 | 0/8 12 h-lim-p 0.0196 20.0000 0.0000 1934.506295 0 0.0074 265 | 0/8 13 h-lim-p 0.0056 20.0000 0.0000 1934.506295 0 0.0007 287 Out... lnL = -1934.506295 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1934.506295 Node 7: lnL = -1934.506295 Node 8: lnL = -1934.506295 Node 9: lnL = -1934.506295 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 412 Sequential format.. Reading seq # 1: YGR052W_Sbay Reading seq # 2: YGR052W_Scer Reading seq # 3: YGR052W_Skud Reading seq # 4: YGR052W_Smik Reading seq # 5: YGR052W_Spar Sequences read.. Counting patterns.. # site patterns = 209 Counting frequencies.. 120 bytes for distance 33440 bytes for lkl0 26752 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.198829 0.033806 0.000060 0.223103 0.297588 0.164760 0.252701 0.233351 lnL0 = -1960.070345 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1960.070345 x= 0.19883 0.03381 0.00006 0.22310 0.29759 0.16476 0.25270 0.23335 1 h-lim-p 0.0014 0.0113 71.3837 1958.959765 6 0.0004 35 | 0/8 2 h-lim-p 0.0009 0.0071 30.7641 1958.613973 2 0.0008 51 | 0/8 3 h-lim-p 0.0020 0.0209 12.6657 1958.545497 4 0.0010 71 | 0/8 4 h-lim-p 0.0010 0.0079 5.3386 1958.538836 6 0.0006 99 | 0/8 5 h-lim-p 0.0070 0.6417 0.4329 1958.538720 3 0.0012 119 | 0/8 6 h-lim-p 0.0100 7.2876 0.0534 1958.538717 1 0.0012 143 | 0/8 7 h-lim-p 0.0672 20.0000 0.0010 1958.538654 0 0.4031 165 | 0/8 8 h-lim-p 0.0029 3.8106 0.1374 1958.538561 1 0.0029 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1958.538558 0 1.0938 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1958.538558 0 1.0938 227 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1958.538558 0 1.0938 247 | 0/8 12 h-lim-p 1.2077 20.0000 0.0000 1958.538558 0 2.4155 268 | 0/8 13 h-lim-p 1.6351 20.0000 0.0000 1958.538558 0 0.8175 288 | 0/8 14 h-lim-p 0.0571 20.0000 0.0000 1958.538558 0 0.0018 312 | 0/8 15 h-lim-p 0.0008 20.0000 0.0000 1958.538558 0 0.0000 348 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 1958.538558 0 0.0000 383 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1958.538558 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1958.538558 Node 7: lnL = -1958.538558 Node 8: lnL = -1958.538558 Node 9: lnL = -1958.538558 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 874 Sequential format.. Reading seq # 1: YGR053C_Sbay Reading seq # 2: YGR053C_Scer Reading seq # 3: YGR053C_Skud Reading seq # 4: YGR053C_Smik Reading seq # 5: YGR053C_Spar Sequences read.. Counting patterns.. # site patterns = 298 Counting frequencies.. 120 bytes for distance 47680 bytes for lkl0 38144 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.135388 0.049668 0.049974 0.136664 0.074150 0.203072 0.216684 0.162114 lnL0 = -3890.124241 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3890.124241 x= 0.13539 0.04967 0.04997 0.13666 0.07415 0.20307 0.21668 0.16211 1 h-lim-p 0.0019 0.6855 202.6450 3887.508769 9 0.0001 45 | 0/8 2 h-lim-p 0.0004 0.0029 36.0853 3887.369531 6 0.0002 72 | 0/8 3 h-lim-p 0.0004 0.0132 17.7786 3887.335588 6 0.0003 99 | 0/8 4 h-lim-p 0.0008 0.0410 5.9166 3887.330283 4 0.0003 118 | 0/8 5 h-lim-p 0.0030 0.5330 0.6932 3887.330206 2 0.0003 136 | 0/8 6 h-lim-p 0.0017 1.2848 0.1336 3887.330204 0 0.0004 157 | 0/8 7 h-lim-p 0.0035 15.6488 0.0142 3887.330203 0 0.0015 177 | 0/8 8 h-lim-p 0.0240 20.0000 0.0009 3887.329910 0 0.3842 201 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3887.329910 0 1.0938 221 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3887.329910 0 1.0938 241 | 0/8 11 h-lim-p 1.2515 20.0000 0.0000 3887.329910 0 2.5030 262 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3887.329910 0 0.0098 289 Out... lnL = -3887.329910 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3887.329910 Node 7: lnL = -3887.329910 Node 8: lnL = -3887.329910 Node 9: lnL = -3887.329910 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 873 Sequential format.. Reading seq # 1: YGR054W_Sbay Reading seq # 2: YGR054W_Scer Reading seq # 3: YGR054W_Skud Reading seq # 4: YGR054W_Smik Reading seq # 5: YGR054W_Spar Sequences read.. Counting patterns.. # site patterns = 282 Counting frequencies.. 120 bytes for distance 45120 bytes for lkl0 36096 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.120680 0.053493 0.053929 0.127398 0.083725 0.177352 0.228597 0.146611 lnL0 = -3840.489519 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3840.489519 x= 0.12068 0.05349 0.05393 0.12740 0.08372 0.17735 0.22860 0.14661 1 h-lim-p 0.0019 0.6324 203.0770 3837.696523 8 0.0001 44 | 0/8 2 h-lim-p 0.0006 0.0046 32.1898 3837.582180 4 0.0002 64 | 0/8 3 h-lim-p 0.0007 0.0274 10.9844 3837.569409 5 0.0002 88 | 0/8 4 h-lim-p 0.0008 0.1125 3.3757 3837.567805 3 0.0003 106 | 0/8 5 h-lim-p 0.0013 0.3547 0.8089 3837.567673 3 0.0004 125 | 0/8 6 h-lim-p 0.0022 2.0575 0.1527 3837.567670 1 0.0003 149 | 0/8 7 h-lim-p 0.0012 5.8429 0.0337 3837.567669 0 0.0011 169 | 0/8 8 h-lim-p 0.0441 20.0000 0.0008 3837.567031 0 0.7057 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3837.567023 1 0.9961 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3837.567023 0 2.1875 235 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3837.567023 0 1.0938 255 | 0/8 12 h-lim-p 0.2456 20.0000 0.0000 3837.567023 0 3.9297 279 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 3837.567023 0 0.6250 300 | 0/8 14 h-lim-p 0.0725 20.0000 0.0000 3837.567023 0 0.0362 320 | 0/8 15 h-lim-p 0.0081 20.0000 0.0001 3837.567023 0 0.0000 350 | 0/8 16 h-lim-p 0.0022 20.0000 0.0000 3837.567023 0 0.0003 372 Out... lnL = -3837.567023 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3837.567023 Node 7: lnL = -3837.567023 Node 8: lnL = -3837.567023 Node 9: lnL = -3837.567023 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 856 Sequential format.. Reading seq # 1: YGR055W_Sbay Reading seq # 2: YGR055W_Scer Reading seq # 3: YGR055W_Skud Reading seq # 4: YGR055W_Smik Reading seq # 5: YGR055W_Spar Sequences read.. Counting patterns.. # site patterns = 302 Counting frequencies.. 120 bytes for distance 48320 bytes for lkl0 38656 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.144407 0.014863 0.087911 0.111035 0.075791 0.233534 0.168840 0.163443 lnL0 = -3739.593785 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3739.593785 x= 0.14441 0.01486 0.08791 0.11104 0.07579 0.23353 0.16884 0.16344 1 h-lim-p 0.0003 0.0021 238.0444 3736.348471 7 0.0001 36 | 0/8 2 h-lim-p 0.0003 0.0021 62.5573 3735.876544 4 0.0003 56 | 0/8 3 h-lim-p 0.0007 0.0114 21.9044 3735.836865 4 0.0002 77 | 0/8 4 h-lim-p 0.0005 0.0257 7.9346 3735.829507 4 0.0003 98 | 0/8 5 h-lim-p 0.0020 0.1251 1.0564 3735.829319 3 0.0004 119 | 0/8 6 h-lim-p 0.0020 2.3383 0.1831 3735.829311 0 0.0004 132 | 0/8 7 h-lim-p 0.0024 4.2483 0.0339 3735.829310 0 0.0011 152 | 0/8 8 h-lim-p 0.0483 20.0000 0.0007 3735.828645 0 0.7736 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3735.828607 2 0.9961 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3735.828607 0 1.2500 220 | 0/8 11 h-lim-p 1.9702 20.0000 0.0000 3735.828607 0 0.4310 241 | 0/8 12 h-lim-p 0.2523 20.0000 0.0000 3735.828607 0 0.0079 265 | 0/8 13 h-lim-p 0.0062 20.0000 0.0000 3735.828607 0 0.0092 285 | 0/8 14 h-lim-p 0.0059 20.0000 0.0000 3735.828607 0 0.0007 307 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 3735.828607 0 0.0000 345 | 0/8 16 h-lim-p 0.0000 20.0000 0.0021 | 0/8 17 h-lim-p 0.0000 20.0000 0.0021 Out... lnL = -3735.828607 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3735.828607 Node 7: lnL = -3735.828607 Node 8: lnL = -3735.828607 Node 9: lnL = -3735.828607 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 554 Sequential format.. Reading seq # 1: YGR056W_Sbay Reading seq # 2: YGR056W_Scer Reading seq # 3: YGR056W_Skud Reading seq # 4: YGR056W_Smik Reading seq # 5: YGR056W_Spar Sequences read.. Counting patterns.. # site patterns = 220 Counting frequencies.. 120 bytes for distance 35200 bytes for lkl0 28160 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.151651 0.063091 0.113129 0.076259 0.068481 0.231004 0.191210 0.172575 lnL0 = -2507.518184 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2507.518184 x= 0.15165 0.06309 0.11313 0.07626 0.06848 0.23100 0.19121 0.17258 1 h-lim-p 0.0022 0.0172 109.3624 2505.477310 8 0.0004 44 | 0/8 2 h-lim-p 0.0010 0.0077 31.9421 2505.142752 7 0.0007 72 | 0/8 3 h-lim-p 0.0011 0.0149 19.7744 2505.116350 5 0.0002 97 | 0/8 4 h-lim-p 0.0012 0.1132 3.1026 2505.114002 2 0.0005 113 | 0/8 5 h-lim-p 0.0036 0.4117 0.4393 2505.113961 0 0.0004 127 | 0/8 6 h-lim-p 0.0010 1.0892 0.2026 2505.113953 0 0.0005 147 | 0/8 7 h-lim-p 0.0079 20.0000 0.0125 2505.113938 0 0.0158 168 | 0/8 8 h-lim-p 0.0154 20.0000 0.0128 2505.112688 0 0.0923 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2505.112669 1 0.9961 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2505.112669 0 1.0938 232 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2505.112669 0 2.1875 252 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2505.112669 0 1.0938 272 | 0/8 13 h-lim-p 0.6370 20.0000 0.0000 2505.112669 0 5.0959 295 | 0/8 14 h-lim-p 2.0052 20.0000 0.0000 2505.112669 0 0.1253 318 | 0/8 15 h-lim-p 0.3311 20.0000 0.0000 2505.112669 0 0.0045 343 | 0/8 16 h-lim-p 0.0088 20.0000 0.0000 2505.112669 0 0.0044 363 Out... lnL = -2505.112669 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2505.112669 Node 7: lnL = -2505.112669 Node 8: lnL = -2505.112669 Node 9: lnL = -2505.112669 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 677 Sequential format.. Reading seq # 1: YGR057C_Sbay Reading seq # 2: YGR057C_Scer Reading seq # 3: YGR057C_Skud Reading seq # 4: YGR057C_Smik Reading seq # 5: YGR057C_Spar Sequences read.. Counting patterns.. # site patterns = 248 Counting frequencies.. 120 bytes for distance 39680 bytes for lkl0 31744 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.135254 0.080486 0.134505 0.101746 0.097801 0.203469 0.220002 0.157680 lnL0 = -3121.855971 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3121.855971 x= 0.13525 0.08049 0.13450 0.10175 0.09780 0.20347 0.22000 0.15768 1 h-lim-p 0.0003 0.0025 106.1254 3120.023467 7 0.0003 39 | 0/8 2 h-lim-p 0.0019 0.0152 17.9330 3119.942899 5 0.0005 62 | 0/8 3 h-lim-p 0.0008 0.0305 10.7500 3119.930364 6 0.0003 87 | 0/8 4 h-lim-p 0.0008 0.0555 3.6432 3119.928188 2 0.0004 103 | 0/8 5 h-lim-p 0.0016 0.3135 0.9072 3119.928007 3 0.0005 124 | 0/8 6 h-lim-p 0.0067 8.2432 0.0623 3119.928006 0 0.0007 146 | 0/8 7 h-lim-p 0.0033 13.6254 0.0137 3119.928006 0 0.0015 166 | 0/8 8 h-lim-p 0.0739 20.0000 0.0003 3119.927954 0 0.8873 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3119.927953 0 1.0938 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3119.927953 0 1.0938 229 | 0/8 11 h-lim-p 2.0125 20.0000 0.0000 3119.927953 0 2.0125 249 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3119.927953 0 0.0049 277 Out... lnL = -3119.927953 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3119.927953 Node 7: lnL = -3119.927953 Node 8: lnL = -3119.927953 Node 9: lnL = -3119.927953 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 679 Sequential format.. Reading seq # 1: YGR058W_Sbay Reading seq # 2: YGR058W_Scer Reading seq # 3: YGR058W_Skud Reading seq # 4: YGR058W_Smik Reading seq # 5: YGR058W_Spar Sequences read.. Counting patterns.. # site patterns = 246 Counting frequencies.. 120 bytes for distance 39360 bytes for lkl0 31488 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.134248 0.090504 0.133083 0.101199 0.095005 0.212771 0.215332 0.156898 lnL0 = -3139.120624 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3139.120624 x= 0.13425 0.09050 0.13308 0.10120 0.09500 0.21277 0.21533 0.15690 1 h-lim-p 0.0004 0.0029 106.2701 3137.179284 4 0.0004 30 | 0/8 2 h-lim-p 0.0014 0.0115 22.9929 3137.031103 6 0.0006 53 | 0/8 3 h-lim-p 0.0009 0.0206 15.2626 3137.010795 5 0.0002 76 | 0/8 4 h-lim-p 0.0011 0.0834 3.3071 3137.008559 3 0.0004 94 | 0/8 5 h-lim-p 0.0017 0.2802 0.8660 3137.008412 2 0.0004 111 | 0/8 6 h-lim-p 0.0040 5.3221 0.0894 3137.008410 0 0.0005 133 | 0/8 7 h-lim-p 0.0039 20.0000 0.0115 3137.008410 0 0.0034 153 | 0/8 8 h-lim-p 0.0446 20.0000 0.0009 3137.008264 0 0.3571 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3137.008262 0 1.0938 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3137.008262 0 1.0938 216 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3137.008262 0 1.0938 236 | 0/8 12 h-lim-p 1.0902 20.0000 0.0000 3137.008262 0 1.0902 256 | 0/8 13 h-lim-p 0.2013 20.0000 0.0000 3137.008262 0 0.0000 292 | 0/8 14 h-lim-p 0.0027 20.0000 0.0000 3137.008262 0 0.0000 324 Out... lnL = -3137.008262 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3137.008262 Node 7: lnL = -3137.008262 Node 8: lnL = -3137.008262 Node 9: lnL = -3137.008262 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 462 Sequential format.. Reading seq # 1: YGR059W_Sbay Reading seq # 2: YGR059W_Scer Reading seq # 3: YGR059W_Skud Reading seq # 4: YGR059W_Smik Reading seq # 5: YGR059W_Spar Sequences read.. Counting patterns.. # site patterns = 219 Counting frequencies.. 120 bytes for distance 35040 bytes for lkl0 28032 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.214815 0.079666 0.027598 0.137013 0.158879 0.209217 0.306787 0.240679 lnL0 = -2232.328461 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2232.328461 x= 0.21481 0.07967 0.02760 0.13701 0.15888 0.20922 0.30679 0.24068 1 h-lim-p 0.0020 0.0162 93.3929 2231.316872 4 0.0003 32 | 0/8 2 h-lim-p 0.0013 0.0111 18.3408 2231.208017 3 0.0007 50 | 0/8 3 h-lim-p 0.0058 0.1325 2.1158 2231.206450 3 0.0007 70 | 0/8 4 h-lim-p 0.0020 0.3402 0.7546 2231.206242 3 0.0008 88 | 0/8 5 h-lim-p 0.0024 0.5198 0.2620 2231.206194 2 0.0015 113 | 0/8 6 h-lim-p 0.0065 3.8474 0.0622 2231.206192 1 0.0008 137 | 0/8 7 h-lim-p 0.0036 20.0000 0.0139 2231.206192 0 0.0016 157 | 0/8 8 h-lim-p 0.1928 20.0000 0.0001 2231.206181 0 1.1569 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2231.206181 0 1.0938 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2231.206181 0 2.1875 219 | 0/8 11 h-lim-p 2.3034 20.0000 0.0000 2231.206181 0 1.0078 239 | 0/8 12 h-lim-p 1.6965 20.0000 0.0000 2231.206181 m20.0000 260 | 0/8 13 h-lim-p 1.6579 20.0000 0.0000 2231.206181 0 0.0000 301 Out... lnL = -2231.206181 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2231.206181 Node 7: lnL = -2231.206181 Node 8: lnL = -2231.206181 Node 9: lnL = -2231.206181 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 830 Sequential format.. Reading seq # 1: YGR060W_Sbay Reading seq # 2: YGR060W_Scer Reading seq # 3: YGR060W_Skud Reading seq # 4: YGR060W_Smik Reading seq # 5: YGR060W_Spar Sequences read.. Counting patterns.. # site patterns = 203 Counting frequencies.. 120 bytes for distance 32480 bytes for lkl0 25984 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.097748 0.018311 0.046077 0.039349 0.057560 0.101522 0.110914 0.108839 lnL0 = -2989.394197 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2989.394197 x= 0.09775 0.01831 0.04608 0.03935 0.05756 0.10152 0.11091 0.10884 1 h-lim-p 0.0001 0.0005 390.8254 2984.686955 1 0.0001 24 | 0/8 2 h-lim-p 0.0001 0.0011 53.7164 2984.512701 6 0.0001 50 | 0/8 3 h-lim-p 0.0002 0.0091 27.4376 2984.486621 6 0.0001 75 | 0/8 4 h-lim-p 0.0002 0.0120 9.9137 2984.480610 5 0.0001 102 | 0/8 5 h-lim-p 0.0013 0.0762 1.1076 2984.480500 3 0.0002 122 | 0/8 6 h-lim-p 0.0006 0.4715 0.2942 2984.480468 2 0.0004 140 | 0/8 7 h-lim-p 0.0028 3.0590 0.0448 2984.478951 0 0.0223 163 | 0/8 8 h-lim-p 0.0021 0.0963 0.4856 2984.420677 0 0.0082 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 2984.420117 3 0.9644 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2984.420117 0 1.0938 231 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2984.420117 0 1.0938 251 | 0/8 12 h-lim-p 1.0874 20.0000 0.0000 2984.420117 0 2.1748 272 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2984.420117 0 0.2734 294 | 0/8 14 h-lim-p 0.0316 20.0000 0.0000 2984.420117 0 0.0316 314 | 0/8 15 h-lim-p 0.0132 20.0000 0.0000 2984.420117 0 0.0016 336 | 0/8 16 h-lim-p 0.0016 20.0000 0.0000 2984.420117 0 0.0004 357 | 0/8 17 h-lim-p 0.0001 20.0000 0.0001 2984.420117 0 0.0000 391 | 0/8 18 h-lim-p 0.0000 20.0000 0.0006 | 0/8 19 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -2984.420117 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2984.420117 Node 7: lnL = -2984.420117 Node 8: lnL = -2984.420117 Node 9: lnL = -2984.420117 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 315 Sequential format.. Reading seq # 1: YGR063C_Sbay Reading seq # 2: YGR063C_Scer Reading seq # 3: YGR063C_Skud Reading seq # 4: YGR063C_Smik Reading seq # 5: YGR063C_Spar Sequences read.. Counting patterns.. # site patterns = 118 Counting frequencies.. 120 bytes for distance 18880 bytes for lkl0 15104 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.242715 0.284047 0.000060 0.296068 4.251090 0.333627 0.277046 0.310622 lnL0 = -1273.056965 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1273.056965 x= 0.24271 0.28405 0.00006 0.29607 4.25109 0.33363 0.27705 0.31062 1 h-lim-p 0.0000 0.0000 132.6890 1273.007024 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0060 84.0812 1263.176407 0 0.0038 42 | 1/8 3 h-lim-p 0.0008 0.0063 36.9449 1261.114233 0 0.0032 56 | 1/8 4 h-lim-p 0.0058 0.0463 7.0929 1260.893963 6 0.0064 83 | 1/8 5 h-lim-p 0.0315 0.3882 1.4484 1259.610941 0 0.0945 96 | 1/8 6 h-lim-p 0.0131 0.1045 5.8913 1251.717846 0 0.0523 110 | 0/8 7 h-lim-p 0.0131 0.1049 5.5431 1251.688746 7 0.0023 138 | 0/8 8 h-lim-p 0.1772 20.0000 0.0732 1250.961105 0 0.7086 152 | 0/8 9 h-lim-p 0.8402 6.7213 0.0181 1250.911701 3 0.7023 178 | 0/8 10 h-lim-p 0.5839 20.0000 0.0218 1250.893079 5 0.4724 210 | 0/8 11 h-lim-p 2.5000 20.0000 0.0012 1250.892983 1 0.5469 233 | 0/8 12 h-lim-p 2.5000 20.0000 0.0001 1250.892981 0 1.0938 253 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1250.892981 0 1.0938 273 | 0/8 14 h-lim-p 2.3992 20.0000 0.0000 1250.892981 0 1.0496 293 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1250.892981 0 1.0938 313 | 0/8 16 h-lim-p 1.1913 20.0000 0.0000 1250.892981 0 4.7652 335 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1250.892981 0 0.6250 356 | 0/8 18 h-lim-p 0.0717 20.0000 0.0000 1250.892981 0 0.0717 376 | 0/8 19 h-lim-p 0.0207 20.0000 0.0001 1250.892981 0 0.0052 397 | 0/8 20 h-lim-p 0.0027 20.0000 0.0002 1250.892981 0 0.0002 420 | 0/8 21 h-lim-p 0.0003 20.0000 0.0001 1250.892981 0 0.0003 440 | 0/8 22 h-lim-p 0.0001 20.0000 0.0003 1250.892981 0 0.0000 469 | 0/8 23 h-lim-p 0.0004 20.0000 0.0000 1250.892981 0 0.0000 502 Out... lnL = -1250.892981 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1250.892981 Node 7: lnL = -1250.892981 Node 8: lnL = -1250.892981 Node 9: lnL = -1250.892981 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 679 Sequential format.. Reading seq # 1: YGR066C_Sbay Reading seq # 2: YGR066C_Scer Reading seq # 3: YGR066C_Skud Reading seq # 4: YGR066C_Smik Reading seq # 5: YGR066C_Spar Sequences read.. Counting patterns.. # site patterns = 316 Counting frequencies.. 120 bytes for distance 50560 bytes for lkl0 40448 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.204975 0.084898 0.060630 0.150246 0.113039 0.235949 0.289301 0.231104 lnL0 = -3283.286373 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3283.286373 x= 0.20497 0.08490 0.06063 0.15025 0.11304 0.23595 0.28930 0.23110 1 h-lim-p 0.0055 1.1402 109.3036 3281.759473 5 0.0003 35 | 0/8 2 h-lim-p 0.0011 0.0089 20.2846 3281.671449 5 0.0004 58 | 0/8 3 h-lim-p 0.0009 0.0353 9.6168 3281.650426 6 0.0005 85 | 0/8 4 h-lim-p 0.0013 0.0791 4.0717 3281.644228 5 0.0009 109 | 0/8 5 h-lim-p 0.0050 0.4690 0.7358 3281.644057 3 0.0007 129 | 0/8 6 h-lim-p 0.0026 1.1041 0.1847 3281.644046 2 0.0007 154 | 0/8 7 h-lim-p 0.0095 20.0000 0.0135 3281.644045 0 0.0021 175 | 0/8 8 h-lim-p 0.0550 20.0000 0.0005 3281.643935 0 0.6596 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3281.643934 0 1.0938 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3281.643934 0 1.0938 238 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3281.643934 0 1.0938 258 | 0/8 12 h-lim-p 1.1141 20.0000 0.0000 3281.643934 0 0.0696 281 | 0/8 13 h-lim-p 0.0202 20.0000 0.0000 3281.643934 0 0.0000 314 Out... lnL = -3281.643934 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3281.643934 Node 7: lnL = -3281.643934 Node 8: lnL = -3281.643934 Node 9: lnL = -3281.643934 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 762 Sequential format.. Reading seq # 1: YGR068C_Sbay Reading seq # 2: YGR068C_Scer Reading seq # 3: YGR068C_Skud Reading seq # 4: YGR068C_Smik Reading seq # 5: YGR068C_Spar Sequences read.. Counting patterns.. # site patterns = 299 Counting frequencies.. 120 bytes for distance 47840 bytes for lkl0 38272 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.093744 0.167392 0.038262 0.160992 0.095987 0.215753 0.223268 0.115727 lnL0 = -3323.671704 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3323.671704 x= 0.09374 0.16739 0.03826 0.16099 0.09599 0.21575 0.22327 0.11573 1 h-lim-p 0.0017 0.0136 84.2260 3323.017621 2 0.0002 28 | 0/8 2 h-lim-p 0.0008 0.0146 19.9592 3322.925837 7 0.0005 59 | 0/8 3 h-lim-p 0.0007 0.0179 14.5782 3322.899647 5 0.0003 82 | 0/8 4 h-lim-p 0.0016 0.0586 3.1686 3322.898009 2 0.0004 99 | 0/8 5 h-lim-p 0.0036 0.4915 0.3116 3322.897995 2 0.0003 119 | 0/8 6 h-lim-p 0.0032 14.0873 0.0283 3322.897995 0 0.0007 140 | 0/8 7 h-lim-p 0.0120 20.0000 0.0017 3322.897995 0 0.0052 160 | 0/8 8 h-lim-p 0.0118 20.0000 0.0007 3322.897985 0 0.1415 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3322.897985 0 1.0938 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3322.897985 0 1.0938 223 | 0/8 11 h-lim-p 1.1137 20.0000 0.0000 3322.897985 0 0.4873 243 | 0/8 12 h-lim-p 0.1429 20.0000 0.0000 3322.897985 0 0.1429 263 | 0/8 13 h-lim-p 0.0545 20.0000 0.0000 3322.897985 0 0.0009 288 | 0/8 14 h-lim-p 0.0010 20.0000 0.0000 3322.897985 0 0.0001 311 | 0/8 15 h-lim-p 0.0012 20.0000 0.0000 3322.897985 0 0.0000 336 Out... lnL = -3322.897985 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3322.897985 Node 7: lnL = -3322.897985 Node 8: lnL = -3322.897985 Node 9: lnL = -3322.897985 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 406 Sequential format.. Reading seq # 1: YGR070W_Sbay Reading seq # 2: YGR070W_Scer Reading seq # 3: YGR070W_Skud Reading seq # 4: YGR070W_Smik Reading seq # 5: YGR070W_Spar Sequences read.. Counting patterns.. # site patterns = 108 Counting frequencies.. 120 bytes for distance 17280 bytes for lkl0 13824 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.146801 0.000060 0.118713 0.106007 0.132720 4.648352 0.249800 0.214708 lnL0 = -1523.059831 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1523.059831 x= 0.14680 0.00006 0.11871 0.10601 0.13272 4.64835 0.24980 0.21471 1 h-lim-p 0.0000 0.0000 133.2911 1523.033958 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0103 40.1169 1522.567642 0 0.0006 40 | 1/8 3 h-lim-p 0.0021 0.0289 12.4488 1522.479203 8 0.0012 72 | 1/8 4 h-lim-p 0.0046 0.0922 3.1706 1522.457284 5 0.0022 95 | 1/8 5 h-lim-p 0.0045 0.2211 1.5907 1522.342426 0 0.0089 108 | 1/8 6 h-lim-p 0.0081 0.0996 1.7480 1518.137214 0 0.0488 122 | 0/8 7 h-lim-p 0.0018 0.0143 10.1179 1518.086298 5 0.0016 143 | 0/8 8 h-lim-p 0.4015 3.2123 0.0251 1517.869824 0 0.8031 156 | 0/8 9 h-lim-p 2.5000 20.0000 0.0041 1517.862352 4 0.9802 184 | 0/8 10 h-lim-p 2.5000 20.0000 0.0010 1517.862134 4 0.7412 215 | 0/8 11 h-lim-p 2.5000 20.0000 0.0001 1517.862131 1 0.6152 238 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1517.862131 0 1.0938 258 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1517.862131 0 1.0938 278 | 0/8 14 h-lim-p 1.1635 20.0000 0.0000 1517.862131 0 0.0091 304 Out... lnL = -1517.862131 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1517.862131 Node 7: lnL = -1517.862131 Node 8: lnL = -1517.862131 Node 9: lnL = -1517.862131 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 254 Sequential format.. Reading seq # 1: YGR071C_Sbay Reading seq # 2: YGR071C_Scer Reading seq # 3: YGR071C_Skud Reading seq # 4: YGR071C_Smik Reading seq # 5: YGR071C_Spar Sequences read.. Counting patterns.. # site patterns = 92 Counting frequencies.. 120 bytes for distance 14720 bytes for lkl0 11776 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.145559 0.095770 0.025653 0.070042 0.062318 0.204631 0.077809 0.161937 lnL0 = -1028.533351 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1028.533351 x= 0.14556 0.09577 0.02565 0.07004 0.06232 0.20463 0.07781 0.16194 1 h-lim-p 0.0003 0.0027 37.2205 1028.305287 5 0.0003 32 | 0/8 2 h-lim-p 0.0006 0.0052 9.7921 1028.286793 7 0.0004 62 | 0/8 3 h-lim-p 0.0010 0.1045 4.0703 1028.282660 6 0.0006 89 | 0/8 4 h-lim-p 0.0011 0.0684 2.2371 1028.281753 3 0.0005 107 | 0/8 5 h-lim-p 0.0024 0.2252 0.4407 1028.281701 2 0.0006 124 | 0/8 6 h-lim-p 0.0046 4.7435 0.0548 1028.281699 0 0.0010 145 | 0/8 7 h-lim-p 0.0148 20.0000 0.0037 1028.281699 0 0.0130 165 | 0/8 8 h-lim-p 0.0333 20.0000 0.0014 1028.281652 0 0.1334 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1028.281651 0 1.0938 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1028.281651 0 2.1875 227 | 0/8 11 h-lim-p 1.9371 20.0000 0.0000 1028.281651 0 0.8475 247 | 0/8 12 h-lim-p 2.4738 20.0000 0.0000 1028.281651 0 0.0009 278 Out... lnL = -1028.281651 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1028.281651 Node 7: lnL = -1028.281651 Node 8: lnL = -1028.281651 Node 9: lnL = -1028.281651 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 259 Sequential format.. Reading seq # 1: YGR074W_Sbay Reading seq # 2: YGR074W_Scer Reading seq # 3: YGR074W_Skud Reading seq # 4: YGR074W_Smik Reading seq # 5: YGR074W_Spar Sequences read.. Counting patterns.. # site patterns = 114 Counting frequencies.. 120 bytes for distance 18240 bytes for lkl0 14592 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.085028 0.085101 0.077794 0.242862 0.055369 0.140536 0.158258 0.103681 lnL0 = -1021.583085 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1021.583085 x= 0.08503 0.08510 0.07779 0.24286 0.05537 0.14054 0.15826 0.10368 1 h-lim-p 0.0072 2.9388 53.1165 1020.743029 9 0.0006 48 | 0/8 2 h-lim-p 0.0011 0.0087 13.9673 1020.638032 4 0.0011 68 | 0/8 3 h-lim-p 0.0028 0.0557 5.5488 1020.622463 3 0.0012 86 | 0/8 4 h-lim-p 0.0036 0.1397 1.8143 1020.620678 5 0.0012 111 | 0/8 5 h-lim-p 0.0053 0.5786 0.4165 1020.620572 2 0.0013 128 | 0/8 6 h-lim-p 0.0108 11.2602 0.0505 1020.620570 1 0.0013 152 | 0/8 7 h-lim-p 0.0315 20.0000 0.0021 1020.620562 0 0.0631 173 | 0/8 8 h-lim-p 0.0064 20.0000 0.0210 1020.620460 0 0.0256 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1020.620458 0 1.0938 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1020.620458 0 1.0938 235 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1020.620458 0 1.0938 255 | 0/8 12 h-lim-p 1.1757 20.0000 0.0000 1020.620458 0 1.1757 275 | 0/8 13 h-lim-p 0.3740 20.0000 0.0000 1020.620458 0 0.0029 301 | 0/8 14 h-lim-p 0.0002 20.0000 0.0001 1020.620458 0 0.0000 331 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 1020.620458 0 0.0000 351 Out... lnL = -1020.620458 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1020.620458 Node 7: lnL = -1020.620458 Node 8: lnL = -1020.620458 Node 9: lnL = -1020.620458 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 242 Sequential format.. Reading seq # 1: YGR075C_Sbay Reading seq # 2: YGR075C_Scer Reading seq # 3: YGR075C_Skud Reading seq # 4: YGR075C_Smik Reading seq # 5: YGR075C_Spar Sequences read.. Counting patterns.. # site patterns = 121 Counting frequencies.. 120 bytes for distance 19360 bytes for lkl0 15488 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.073566 0.074115 0.110397 0.222241 0.078547 0.142523 0.211600 0.093462 lnL0 = -1098.043149 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1098.043149 x= 0.07357 0.07412 0.11040 0.22224 0.07855 0.14252 0.21160 0.09346 1 h-lim-p 0.0008 0.0067 42.4657 1097.336432 6 0.0008 34 | 0/8 2 h-lim-p 0.0014 0.0113 13.4660 1097.260716 7 0.0009 64 | 0/8 3 h-lim-p 0.0020 0.0205 6.1208 1097.246320 2 0.0009 80 | 0/8 4 h-lim-p 0.0034 0.0668 1.6490 1097.245430 3 0.0007 99 | 0/8 5 h-lim-p 0.0033 0.8377 0.3638 1097.245349 2 0.0013 115 | 0/8 6 h-lim-p 0.0110 8.9133 0.0414 1097.245348 1 0.0022 138 | 0/8 7 h-lim-p 0.0343 20.0000 0.0027 1097.245342 0 0.0515 158 | 0/8 8 h-lim-p 0.0085 17.8112 0.0160 1097.245228 0 0.0341 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1097.245225 1 0.9961 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1097.245225 0 1.0938 222 | 0/8 11 h-lim-p 1.3653 20.0000 0.0000 1097.245225 0 2.7307 243 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1097.245225 0 0.0781 267 | 0/8 13 h-lim-p 0.0101 20.0000 0.0000 1097.245225 0 0.0101 287 | 0/8 14 h-lim-p 0.0045 20.0000 0.0000 1097.245225 0 0.0000 325 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1097.245225 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1097.245225 Node 7: lnL = -1097.245225 Node 8: lnL = -1097.245225 Node 9: lnL = -1097.245225 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 201 Sequential format.. Reading seq # 1: YGR076C_Sbay Reading seq # 2: YGR076C_Scer Reading seq # 3: YGR076C_Skud Reading seq # 4: YGR076C_Smik Reading seq # 5: YGR076C_Spar Sequences read.. Counting patterns.. # site patterns = 111 Counting frequencies.. 120 bytes for distance 17760 bytes for lkl0 14208 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.108188 0.097947 0.077447 0.174194 0.105015 0.137598 0.327719 0.122320 lnL0 = -847.836949 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 847.836949 x= 0.10819 0.09795 0.07745 0.17419 0.10502 0.13760 0.32772 0.12232 1 h-lim-p 0.0047 0.0376 33.8423 847.170609 5 0.0013 33 | 0/8 2 h-lim-p 0.0018 0.0142 14.2560 846.999179 7 0.0019 63 | 0/8 3 h-lim-p 0.0028 0.0378 9.6856 846.948939 7 0.0015 91 | 0/8 4 h-lim-p 0.0031 0.0703 4.7922 846.928003 5 0.0025 113 | 0/8 5 h-lim-p 0.0104 0.4275 1.1424 846.926953 4 0.0018 137 | 0/8 6 h-lim-p 0.0091 0.9346 0.2213 846.926921 3 0.0013 159 | 0/8 7 h-lim-p 0.0204 9.1931 0.0145 846.926917 0 0.0089 179 | 0/8 8 h-lim-p 0.0321 20.0000 0.0040 846.926609 0 0.2570 202 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 846.926600 2 1.0938 226 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 846.926600 0 1.0938 246 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 846.926600 0 1.2500 266 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 846.926600 0 0.3125 288 | 0/8 13 h-lim-p 0.1725 20.0000 0.0000 846.926600 0 0.0013 314 Out... lnL = -846.926600 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -846.926600 Node 7: lnL = -846.926600 Node 8: lnL = -846.926600 Node 9: lnL = -846.926600 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 378 Sequential format.. Reading seq # 1: YGR078C_Sbay Reading seq # 2: YGR078C_Scer Reading seq # 3: YGR078C_Skud Reading seq # 4: YGR078C_Smik Reading seq # 5: YGR078C_Spar Sequences read.. Counting patterns.. # site patterns = 142 Counting frequencies.. 120 bytes for distance 22720 bytes for lkl0 18176 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.114926 0.025113 0.044725 0.078059 0.085741 0.142136 0.120319 0.123712 lnL0 = -1454.209644 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1454.209644 x= 0.11493 0.02511 0.04472 0.07806 0.08574 0.14214 0.12032 0.12371 1 h-lim-p 0.0021 0.1076 118.6902 1452.690936 3 0.0002 30 | 0/8 2 h-lim-p 0.0007 0.0056 29.1807 1452.454206 6 0.0006 55 | 0/8 3 h-lim-p 0.0026 0.0323 6.6432 1452.445938 6 0.0004 84 | 0/8 4 h-lim-p 0.0017 0.0758 1.5956 1452.445417 4 0.0004 105 | 0/8 5 h-lim-p 0.0013 0.1451 0.5366 1452.445353 2 0.0005 121 | 0/8 6 h-lim-p 0.0083 8.3533 0.0325 1452.445352 0 0.0009 143 | 0/8 7 h-lim-p 0.0027 4.7089 0.0110 1452.445350 0 0.0053 164 | 0/8 8 h-lim-p 0.0100 12.6216 0.0059 1452.444965 0 0.0802 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1452.444962 0 1.0938 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1452.444962 0 1.2500 227 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1452.444962 0 0.2734 249 | 0/8 12 h-lim-p 0.1882 20.0000 0.0000 1452.444962 0 0.0000 280 Out... lnL = -1452.444962 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1452.444962 Node 7: lnL = -1452.444962 Node 8: lnL = -1452.444962 Node 9: lnL = -1452.444962 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 538 Sequential format.. Reading seq # 1: YGR079W_Sbay Reading seq # 2: YGR079W_Scer Reading seq # 3: YGR079W_Skud Reading seq # 4: YGR079W_Smik Reading seq # 5: YGR079W_Spar Sequences read.. Counting patterns.. # site patterns = 168 Counting frequencies.. 120 bytes for distance 26880 bytes for lkl0 21504 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.098256 0.060925 0.026136 0.090826 0.102904 0.126767 0.118991 0.107107 lnL0 = -1808.131401 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1808.131401 x= 0.09826 0.06092 0.02614 0.09083 0.10290 0.12677 0.11899 0.10711 1 h-lim-p 0.0013 0.0136 164.1985 1805.814595 8 0.0002 44 | 0/8 2 h-lim-p 0.0004 0.0033 56.1125 1805.190481 6 0.0004 68 | 0/8 3 h-lim-p 0.0012 0.0098 13.5123 1805.145642 5 0.0005 93 | 0/8 4 h-lim-p 0.0024 0.0552 2.9379 1805.143665 3 0.0005 112 | 0/8 5 h-lim-p 0.0032 0.2982 0.4443 1805.143621 3 0.0005 133 | 0/8 6 h-lim-p 0.0298 20.0000 0.0070 1805.143620 1 0.0037 157 | 0/8 7 h-lim-p 0.0084 20.0000 0.0031 1805.143375 0 0.1348 181 | 0/8 8 h-lim-p 0.0024 1.5057 0.1719 1805.143365 2 0.0006 206 | 0/8 9 h-lim-p 1.6803 20.0000 0.0001 1805.143359 2 1.1084 232 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1805.143358 0 1.0938 252 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1805.143358 0 0.2734 274 | 0/8 12 h-lim-p 0.1797 20.0000 0.0000 1805.143358 0 0.0225 296 | 0/8 13 h-lim-p 0.0154 20.0000 0.0000 1805.143358 0 0.0000 336 Out... lnL = -1805.143358 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1805.143358 Node 7: lnL = -1805.143358 Node 8: lnL = -1805.143358 Node 9: lnL = -1805.143358 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 195 Sequential format.. Reading seq # 1: YGR080W_Sbay Reading seq # 2: YGR080W_Scer Reading seq # 3: YGR080W_Skud Reading seq # 4: YGR080W_Smik Reading seq # 5: YGR080W_Spar Sequences read.. Counting patterns.. # site patterns = 106 Counting frequencies.. 120 bytes for distance 16960 bytes for lkl0 13568 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.193964 0.011654 0.094013 0.089591 0.063808 0.229042 0.226580 0.207305 lnL0 = -876.425556 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 876.425556 x= 0.19396 0.01165 0.09401 0.08959 0.06381 0.22904 0.22658 0.20731 1 h-lim-p 0.0108 0.2703 40.2068 875.897853 4 0.0007 33 | 0/8 2 h-lim-p 0.0021 0.0175 13.5204 875.790232 8 0.0013 66 | 0/8 3 h-lim-p 0.0007 0.0057 9.5223 875.757752 0 0.0011 78 | 0/8 4 h-lim-p 0.0043 0.0342 1.5121 875.755420 6 0.0021 102 | 0/8 5 h-lim-p 0.0037 0.0803 0.8635 875.755049 4 0.0013 125 | 0/8 6 h-lim-p 0.0057 0.9020 0.1917 875.755021 3 0.0015 152 | 0/8 7 h-lim-p 0.0078 7.5313 0.0378 875.755019 2 0.0025 177 | 0/8 8 h-lim-p 0.1720 20.0000 0.0005 875.754885 0 0.6878 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 875.754879 1 0.9961 221 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 875.754879 0 1.0938 241 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 875.754879 0 0.0684 265 | 0/8 12 h-lim-p 0.0389 20.0000 0.0000 875.754879 0 0.0006 290 Out... lnL = -875.754879 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -875.754879 Node 7: lnL = -875.754879 Node 8: lnL = -875.754879 Node 9: lnL = -875.754879 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 276 Sequential format.. Reading seq # 1: YGR081C_Sbay Reading seq # 2: YGR081C_Scer Reading seq # 3: YGR081C_Skud Reading seq # 4: YGR081C_Smik Reading seq # 5: YGR081C_Spar Sequences read.. Counting patterns.. # site patterns = 121 Counting frequencies.. 120 bytes for distance 19360 bytes for lkl0 15488 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.130034 0.079101 0.052836 0.163089 0.074790 0.212060 0.146045 0.142203 lnL0 = -1256.638771 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1256.638771 x= 0.13003 0.07910 0.05284 0.16309 0.07479 0.21206 0.14604 0.14220 1 h-lim-p 0.0009 0.0068 56.8093 1255.794905 9 0.0006 45 | 0/8 2 h-lim-p 0.0007 0.0059 16.2757 1255.698465 4 0.0008 65 | 0/8 3 h-lim-p 0.0019 0.0271 6.4327 1255.688102 6 0.0006 94 | 0/8 4 h-lim-p 0.0018 0.0554 2.0871 1255.686999 4 0.0006 116 | 0/8 5 h-lim-p 0.0025 0.4623 0.4841 1255.686889 3 0.0010 134 | 0/8 6 h-lim-p 0.0058 4.2420 0.0822 1255.686884 1 0.0012 157 | 0/8 7 h-lim-p 0.1609 20.0000 0.0006 1255.686564 0 1.2869 180 | 0/8 8 h-lim-p 0.0482 13.2896 0.0158 1255.686564 0 0.0013 204 | 0/8 9 h-lim-p 0.4608 20.0000 0.0000 1255.686563 0 0.9215 225 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1255.686563 0 1.0938 245 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1255.686563 0 1.0938 265 | 0/8 12 h-lim-p 1.2437 20.0000 0.0000 1255.686563 0 2.4875 286 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1255.686563 0 0.1562 309 | 0/8 14 h-lim-p 0.0214 20.0000 0.0000 1255.686563 0 0.0027 331 | 0/8 15 h-lim-p 0.0068 20.0000 0.0000 1255.686563 0 0.0034 351 Out... lnL = -1255.686563 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1255.686563 Node 7: lnL = -1255.686563 Node 8: lnL = -1255.686563 Node 9: lnL = -1255.686563 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 277 Sequential format.. Reading seq # 1: YGR082W_Sbay Reading seq # 2: YGR082W_Scer Reading seq # 3: YGR082W_Skud Reading seq # 4: YGR082W_Smik Reading seq # 5: YGR082W_Spar Sequences read.. Counting patterns.. # site patterns = 121 Counting frequencies.. 120 bytes for distance 19360 bytes for lkl0 15488 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.142124 0.068613 0.048933 0.151668 0.086212 0.221875 0.135299 0.154313 lnL0 = -1259.082430 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1259.082430 x= 0.14212 0.06861 0.04893 0.15167 0.08621 0.22187 0.13530 0.15431 1 h-lim-p 0.0007 0.0057 72.1923 1257.812372 5 0.0005 32 | 0/8 2 h-lim-p 0.0005 0.0040 24.3825 1257.609223 0 0.0008 44 | 0/8 3 h-lim-p 0.0018 0.0153 10.4736 1257.583410 6 0.0006 70 | 0/8 4 h-lim-p 0.0025 0.0783 2.3891 1257.581333 6 0.0008 97 | 0/8 5 h-lim-p 0.0021 0.1517 0.8774 1257.581057 3 0.0008 115 | 0/8 6 h-lim-p 0.0046 2.5895 0.1534 1257.581043 2 0.0012 140 | 0/8 7 h-lim-p 0.0148 17.1250 0.0125 1257.581032 2 0.0114 164 | 0/8 8 h-lim-p 0.0129 20.0000 0.0111 1257.580271 0 0.1033 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 1257.580164 2 1.0889 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1257.580164 0 1.0938 231 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1257.580164 0 1.0938 251 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1257.580164 0 0.5469 272 | 0/8 13 h-lim-p 0.3713 20.0000 0.0000 1257.580164 0 0.0116 296 | 0/8 14 h-lim-p 0.0063 20.0000 0.0000 1257.580164 0 0.0000 330 Out... lnL = -1257.580164 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1257.580164 Node 7: lnL = -1257.580164 Node 8: lnL = -1257.580164 Node 9: lnL = -1257.580164 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 322 Sequential format.. Reading seq # 1: YGR083C_Sbay Reading seq # 2: YGR083C_Scer Reading seq # 3: YGR083C_Skud Reading seq # 4: YGR083C_Smik Reading seq # 5: YGR083C_Spar Sequences read.. Counting patterns.. # site patterns = 133 Counting frequencies.. 120 bytes for distance 21280 bytes for lkl0 17024 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.105528 0.094293 0.018494 0.105696 0.056300 0.234849 0.234553 0.117209 lnL0 = -1404.249183 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1404.249183 x= 0.10553 0.09429 0.01849 0.10570 0.05630 0.23485 0.23455 0.11721 1 h-lim-p 0.0015 0.0121 78.1582 1403.688739 7 0.0002 38 | 0/8 2 h-lim-p 0.0008 0.0065 18.3635 1403.589519 4 0.0006 58 | 0/8 3 h-lim-p 0.0010 0.0137 11.1388 1403.568723 5 0.0004 79 | 0/8 4 h-lim-p 0.0009 0.0534 5.7181 1403.560179 6 0.0007 102 | 0/8 5 h-lim-p 0.0035 0.1990 1.1491 1403.559682 2 0.0008 119 | 0/8 6 h-lim-p 0.0048 1.0709 0.1936 1403.559669 3 0.0007 140 | 0/8 7 h-lim-p 0.0063 14.0653 0.0223 1403.559667 1 0.0031 163 | 0/8 8 h-lim-p 0.0583 20.0000 0.0012 1403.559136 0 0.4666 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1403.559131 1 0.9961 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1403.559131 0 1.0938 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1403.559131 0 2.1875 248 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1403.559131 0 0.3125 270 | 0/8 13 h-lim-p 0.1008 20.0000 0.0000 1403.559131 0 0.0000 307 Out... lnL = -1403.559131 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1403.559131 Node 7: lnL = -1403.559131 Node 8: lnL = -1403.559131 Node 9: lnL = -1403.559131 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 346 Sequential format.. Reading seq # 1: YGR084C_Sbay Reading seq # 2: YGR084C_Scer Reading seq # 3: YGR084C_Skud Reading seq # 4: YGR084C_Smik Reading seq # 5: YGR084C_Spar Sequences read.. Counting patterns.. # site patterns = 180 Counting frequencies.. 120 bytes for distance 28800 bytes for lkl0 23040 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.115341 0.115743 0.034329 0.115501 0.113612 0.278329 0.158114 0.128288 lnL0 = -1497.877459 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1497.877459 x= 0.11534 0.11574 0.03433 0.11550 0.11361 0.27833 0.15811 0.12829 1 h-lim-p 0.0008 0.0066 62.5975 1496.815687 6 0.0006 35 | 0/8 2 h-lim-p 0.0005 0.0041 27.2522 1496.597457 0 0.0008 47 | 0/8 3 h-lim-p 0.0013 0.0103 10.7024 1496.555656 7 0.0009 77 | 0/8 4 h-lim-p 0.0026 0.0693 3.5494 1496.550172 4 0.0010 97 | 0/8 5 h-lim-p 0.0042 0.4435 0.8367 1496.549801 3 0.0011 116 | 0/8 6 h-lim-p 0.0039 1.3741 0.2396 1496.549773 1 0.0010 139 | 0/8 7 h-lim-p 0.0082 8.9325 0.0281 1496.549724 0 0.0123 159 | 0/8 8 h-lim-p 0.0099 15.5888 0.0350 1496.546330 0 0.0792 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 1496.546181 3 1.0449 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1496.546180 0 1.0938 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1496.546180 0 2.1875 248 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1496.546180 0 1.0938 268 | 0/8 13 h-lim-p 1.1586 20.0000 0.0000 1496.546180 0 4.6343 290 | 0/8 14 h-lim-p 1.7998 20.0000 0.0000 1496.546180 0 0.0281 315 | 0/8 15 h-lim-p 0.0495 20.0000 0.0000 1496.546180 0 0.0248 335 | 0/8 16 h-lim-p 0.0715 20.0000 0.0000 1496.546180 0 0.0000 379 Out... lnL = -1496.546180 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1496.546180 Node 7: lnL = -1496.546180 Node 8: lnL = -1496.546180 Node 9: lnL = -1496.546180 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 685 Sequential format.. Reading seq # 1: YGR086C_Sbay Reading seq # 2: YGR086C_Scer Reading seq # 3: YGR086C_Skud Reading seq # 4: YGR086C_Smik Reading seq # 5: YGR086C_Spar Sequences read.. Counting patterns.. # site patterns = 174 Counting frequencies.. 120 bytes for distance 27840 bytes for lkl0 22272 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.090791 0.023229 0.037450 0.067093 0.044161 0.103735 0.127993 0.097899 lnL0 = -2488.719726 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2488.719726 x= 0.09079 0.02323 0.03745 0.06709 0.04416 0.10373 0.12799 0.09790 1 h-lim-p 0.0001 0.0011 149.8983 2487.731593 7 0.0001 38 | 0/8 2 h-lim-p 0.0004 0.0035 33.5138 2487.639636 3 0.0002 56 | 0/8 3 h-lim-p 0.0004 0.0136 13.7090 2487.630045 6 0.0001 83 | 0/8 4 h-lim-p 0.0003 0.0191 5.3562 2487.628370 2 0.0001 99 | 0/8 5 h-lim-p 0.0007 0.2372 1.0676 2487.628240 3 0.0002 118 | 0/8 6 h-lim-p 0.0010 0.2280 0.2407 2487.628236 1 0.0001 134 | 0/8 7 h-lim-p 0.0010 6.7362 0.0315 2487.628236 0 0.0004 154 | 0/8 8 h-lim-p 0.0577 20.0000 0.0002 2487.628073 0 0.9226 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2487.628069 0 1.0938 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2487.628069 0 1.0938 218 | 0/8 11 h-lim-p 2.0797 20.0000 0.0000 2487.628069 0 0.9099 238 | 0/8 12 h-lim-p 0.9418 20.0000 0.0000 2487.628069 0 1.8835 259 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2487.628069 0 1.0938 279 | 0/8 14 h-lim-p 0.2018 20.0000 0.0000 2487.628069 0 0.0252 301 | 0/8 15 h-lim-p 0.0004 20.0000 0.0002 2487.628069 0 0.0004 321 | 0/8 16 h-lim-p 0.0016 20.0000 0.0001 2487.628069 0 0.0000 359 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 2487.628069 0 0.0000 381 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 2487.628069 0 0.0000 401 Out... lnL = -2487.628069 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2487.628069 Node 7: lnL = -2487.628069 Node 8: lnL = -2487.628069 Node 9: lnL = -2487.628069 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 315 Sequential format.. Reading seq # 1: YGR091W_Sbay Reading seq # 2: YGR091W_Scer Reading seq # 3: YGR091W_Skud Reading seq # 4: YGR091W_Smik Reading seq # 5: YGR091W_Spar Sequences read.. Counting patterns.. # site patterns = 149 Counting frequencies.. 120 bytes for distance 23840 bytes for lkl0 19072 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.114274 0.023314 0.081518 0.170901 0.072951 0.284231 0.230175 0.127484 lnL0 = -1333.040159 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1333.040159 x= 0.11427 0.02331 0.08152 0.17090 0.07295 0.28423 0.23017 0.12748 1 h-lim-p 0.0004 0.0028 50.1016 1332.352858 0 0.0007 23 | 0/8 2 h-lim-p 0.0019 0.0151 15.7489 1332.264781 3 0.0008 41 | 0/8 3 h-lim-p 0.0014 0.0113 8.2978 1332.247863 5 0.0006 62 | 0/8 4 h-lim-p 0.0014 0.0691 3.5708 1332.242541 5 0.0010 87 | 0/8 5 h-lim-p 0.0049 0.2180 0.7527 1332.242151 5 0.0014 111 | 0/8 6 h-lim-p 0.0101 3.1329 0.1009 1332.241947 4 0.0069 141 | 0/8 7 h-lim-p 0.0105 0.8666 0.0663 1332.226955 0 0.0840 164 | 0/8 8 h-lim-p 0.0038 0.1807 1.4804 1332.217084 4 0.0037 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0011 1332.216683 2 0.9644 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1332.216682 0 1.0938 230 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1332.216682 0 1.0938 250 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1332.216682 0 0.0146 277 | 0/8 13 h-lim-p 0.0083 20.0000 0.0000 1332.216682 0 0.0000 313 Out... lnL = -1332.216682 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1332.216682 Node 7: lnL = -1332.216682 Node 8: lnL = -1332.216682 Node 9: lnL = -1332.216682 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 533 Sequential format.. Reading seq # 1: YGR093W_Sbay Reading seq # 2: YGR093W_Scer Reading seq # 3: YGR093W_Skud Reading seq # 4: YGR093W_Smik Reading seq # 5: YGR093W_Spar Sequences read.. Counting patterns.. # site patterns = 280 Counting frequencies.. 120 bytes for distance 44800 bytes for lkl0 35840 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.145644 0.193539 0.181735 0.140044 0.143036 0.232150 0.293270 0.164842 lnL0 = -2457.216673 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2457.216673 x= 0.14564 0.19354 0.18174 0.14004 0.14304 0.23215 0.29327 0.16484 1 h-lim-p 0.0016 0.0125 21.6347 2456.949141 7 0.0011 37 | 0/8 2 h-lim-p 0.0031 0.0468 8.1333 2456.909149 3 0.0014 55 | 0/8 3 h-lim-p 0.0011 0.0251 10.5381 2456.890406 4 0.0007 77 | 0/8 4 h-lim-p 0.0039 0.1219 1.8377 2456.888667 5 0.0012 101 | 0/8 5 h-lim-p 0.0032 1.2333 0.6698 2456.888371 2 0.0015 117 | 0/8 6 h-lim-p 0.0030 1.1485 0.3289 2456.888328 2 0.0010 142 | 0/8 7 h-lim-p 0.0045 10.6334 0.0706 2456.888323 0 0.0020 162 | 0/8 8 h-lim-p 0.3179 20.0000 0.0004 2456.888239 0 1.2718 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2456.888231 1 0.9961 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2456.888231 0 1.0938 226 | 0/8 11 h-lim-p 1.3194 20.0000 0.0000 2456.888231 0 1.3194 246 | 0/8 12 h-lim-p 0.6480 20.0000 0.0000 2456.888231 0 0.3240 266 | 0/8 13 h-lim-p 0.0157 20.0000 0.0000 2456.888231 0 0.0001 292 | 0/8 14 h-lim-p 0.0084 20.0000 0.0000 2456.888231 0 0.0000 320 Out... lnL = -2456.888231 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2456.888231 Node 7: lnL = -2456.888231 Node 8: lnL = -2456.888231 Node 9: lnL = -2456.888231 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 280 Sequential format.. Reading seq # 1: YGR094W_Sbay Reading seq # 2: YGR094W_Scer Reading seq # 3: YGR094W_Skud Reading seq # 4: YGR094W_Smik Reading seq # 5: YGR094W_Spar Sequences read.. Counting patterns.. # site patterns = 109 Counting frequencies.. 120 bytes for distance 17440 bytes for lkl0 13952 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.081752 0.035073 0.045798 0.105630 0.075503 0.154156 0.149937 0.090643 lnL0 = -1109.620469 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1109.620469 x= 0.08175 0.03507 0.04580 0.10563 0.07550 0.15416 0.14994 0.09064 1 h-lim-p 0.0025 0.0206 94.3661 1108.144571 7 0.0004 41 | 0/8 2 h-lim-p 0.0003 0.0024 29.8298 1107.875344 0 0.0006 54 | 0/8 3 h-lim-p 0.0015 0.0206 11.8689 1107.841488 5 0.0006 76 | 0/8 4 h-lim-p 0.0023 0.0658 2.9425 1107.839067 4 0.0006 97 | 0/8 5 h-lim-p 0.0027 0.2551 0.6480 1107.838970 3 0.0005 118 | 0/8 6 h-lim-p 0.0034 3.0644 0.0935 1107.838957 2 0.0018 143 | 0/8 7 h-lim-p 0.0165 15.4276 0.0100 1107.838648 0 0.0659 165 | 0/8 8 h-lim-p 0.0019 0.1789 0.3545 1107.836233 0 0.0056 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1107.836200 2 1.0889 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1107.836199 1 1.2305 233 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1107.836199 0 1.0938 253 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1107.836199 0 2.1875 273 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1107.836199 0 0.3125 295 | 0/8 14 h-lim-p 0.0986 20.0000 0.0000 1107.836199 0 0.0123 317 | 0/8 15 h-lim-p 0.0059 20.0000 0.0000 1107.836199 0 0.0000 343 Out... lnL = -1107.836199 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1107.836199 Node 7: lnL = -1107.836199 Node 8: lnL = -1107.836199 Node 9: lnL = -1107.836199 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 192 Sequential format.. Reading seq # 1: YGR096W_Sbay Reading seq # 2: YGR096W_Scer Reading seq # 3: YGR096W_Skud Reading seq # 4: YGR096W_Smik Reading seq # 5: YGR096W_Spar Sequences read.. Counting patterns.. # site patterns = 106 Counting frequencies.. 120 bytes for distance 16960 bytes for lkl0 13568 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.101602 0.233255 0.000060 0.153185 0.098737 0.224184 0.128124 0.114815 lnL0 = -843.956537 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 843.956537 x= 0.10160 0.23326 0.00006 0.15318 0.09874 0.22418 0.12812 0.11482 1 h-lim-p 0.0003 0.0026 66.0950 842.241684 0 0.0007 23 | 0/8 2 h-lim-p 0.0003 0.0024 40.0719 841.818320 0 0.0006 36 | 0/8 3 h-lim-p 0.0017 0.0183 13.9346 841.719187 7 0.0012 65 | 0/8 4 h-lim-p 0.0039 0.0742 4.3654 841.701757 5 0.0020 88 | 0/8 5 h-lim-p 0.0060 0.0809 1.4906 841.700144 5 0.0016 111 | 0/8 6 h-lim-p 0.0046 0.1507 0.5323 841.699864 2 0.0021 127 | 0/8 7 h-lim-p 0.0215 3.9760 0.0530 841.699739 3 0.0142 155 | 0/8 8 h-lim-p 0.0286 3.6713 0.0263 841.693099 0 0.1713 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 841.692806 4 0.9482 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 841.692805 0 1.0938 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 841.692805 0 1.0938 245 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 841.692805 0 2.1875 265 | 0/8 13 h-lim-p 2.3566 20.0000 0.0000 841.692805 0 0.5155 286 | 0/8 14 h-lim-p 0.6058 20.0000 0.0000 841.692805 0 0.0041 312 Out... lnL = -841.692805 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -841.692805 Node 7: lnL = -841.692805 Node 8: lnL = -841.692805 Node 9: lnL = -841.692805 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 898 Sequential format.. Reading seq # 1: YGR097W_Sbay Reading seq # 2: YGR097W_Scer Reading seq # 3: YGR097W_Skud Reading seq # 4: YGR097W_Smik Reading seq # 5: YGR097W_Spar Sequences read.. Counting patterns.. # site patterns = 223 Counting frequencies.. 120 bytes for distance 35680 bytes for lkl0 28544 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.096672 0.034059 0.058962 0.053274 0.053906 0.116742 0.109284 0.104363 lnL0 = -3218.183605 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3218.183605 x= 0.09667 0.03406 0.05896 0.05327 0.05391 0.11674 0.10928 0.10436 1 h-lim-p 0.0029 0.0230 146.5037 3217.207027 5 0.0001 36 | 0/8 2 h-lim-p 0.0006 0.0044 23.5518 3217.172431 2 0.0001 53 | 0/8 3 h-lim-p 0.0003 0.0133 9.0274 3217.168416 5 0.0001 76 | 0/8 4 h-lim-p 0.0004 0.0971 2.2606 3217.168066 4 0.0001 97 | 0/8 5 h-lim-p 0.0008 0.3772 0.4008 3217.168055 2 0.0001 115 | 0/8 6 h-lim-p 0.0005 1.3690 0.1081 3217.168055 0 0.0002 135 | 0/8 7 h-lim-p 0.0101 20.0000 0.0023 3217.168055 0 0.0011 157 | 0/8 8 h-lim-p 0.0186 20.0000 0.0001 3217.168048 0 0.2978 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3217.168048 0 1.0938 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3217.168048 0 0.0024 230 | 0/8 11 h-lim-p 0.0008 20.0000 0.0000 3217.168048 0 0.0000 270 Out... lnL = -3217.168048 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3217.168048 Node 7: lnL = -3217.168048 Node 8: lnL = -3217.168048 Node 9: lnL = -3217.168048 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 494 Sequential format.. Reading seq # 1: YGR098C_Sbay Reading seq # 2: YGR098C_Scer Reading seq # 3: YGR098C_Skud Reading seq # 4: YGR098C_Smik Reading seq # 5: YGR098C_Spar Sequences read.. Counting patterns.. # site patterns = 131 Counting frequencies.. 120 bytes for distance 20960 bytes for lkl0 16768 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 1.482296 1.248661 1.220716 0.953563 1.506788 1.325362 0.812310 0.000060 lnL0 = -2472.149620 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2472.149620 x= 1.48230 1.24866 1.22072 0.95356 1.50679 1.32536 0.81231 0.00006 1 h-lim-p 0.0000 0.0000 73.9757 2472.135301 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.2646 7.6194 2276.975368 m 0.2646 45 | 2/8 3 h-lim-p 0.0661 0.5288 4.8090 2102.231370 0 0.3966 59 | 2/8 4 h-lim-p 0.0015 0.0120 25.6817 2102.152393 6 0.0009 87 | 2/8 5 h-lim-p 0.0041 0.0826 5.3789 .. | 2/8 6 h-lim-p 0.0000 0.0014 249.2553 2051.192695 2 0.0012 143 | 2/8 7 h-lim-p 0.0002 0.0015 444.9158 1972.147891 0 0.0012 157 | 2/8 8 h-lim-p 0.0001 0.0008 321.1368 1951.931040 m 0.0008 169 | 2/8 9 h-lim-p 0.0001 0.0007 461.3919 1944.442166 0 0.0003 182 | 2/8 10 h-lim-p 0.0003 0.0022 124.0413 1942.393419 0 0.0004 194 | 1/8 11 h-lim-p 0.0001 0.0011 373.0063 1930.582127 0 0.0003 207 | 1/8 12 h-lim-p 0.0226 0.3242 4.5714 1900.215306 m 0.3242 220 | 2/8 13 h-lim-p 0.7970 6.3757 0.0778 1896.197407 5 0.8243 241 | 2/8 14 h-lim-p 0.5727 4.5812 0.0517 1894.367241 0 1.1453 260 | 1/8 15 h-lim-p 0.0041 0.0329 8.0670 1894.308999 5 0.0033 288 | 1/8 16 h-lim-p 0.6905 5.5238 0.0105 1893.778283 m 5.5238 300 | 2/8 17 h-lim-p 0.9776 7.8209 0.0255 1893.772711 3 0.1022 327 | 2/8 18 h-lim-p 0.1422 11.0178 0.0183 .. | 2/8 19 h-lim-p 0.0000 0.0156 13.7391 1893.705388 0 0.0006 396 | 2/8 20 h-lim-p 0.0007 0.0054 3.5747 1893.703180 4 0.0004 417 | 2/8 21 h-lim-p 0.0015 0.1175 0.8744 1893.702985 3 0.0005 436 | 2/8 22 h-lim-p 0.0024 1.7427 0.1906 1893.702964 1 0.0012 456 | 2/8 23 h-lim-p 0.0110 6.7953 0.0212 1893.702961 1 0.0027 477 | 2/8 24 h-lim-p 0.0110 20.0000 0.0052 1893.702211 0 0.1760 499 | 2/8 25 h-lim-p 2.5000 20.0000 0.0001 1893.702201 1 0.9961 519 | 2/8 26 h-lim-p 2.5000 20.0000 0.0000 1893.702201 0 0.5469 538 | 2/8 27 h-lim-p 0.0729 20.0000 0.0002 1893.702201 0 0.0001 565 | 2/8 28 h-lim-p 0.0002 20.0000 0.0001 1893.702201 0 0.0000 590 | 2/8 29 h-lim-p 0.0002 20.0000 0.0000 1893.702201 0 0.0000 617 Out... lnL = -1893.702201 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1893.702201 Node 7: lnL = -1893.702201 Node 8: lnL = -1893.702201 Node 9: lnL = -1893.702201 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 447 Sequential format.. Reading seq # 1: YGR099W_Sbay Reading seq # 2: YGR099W_Scer Reading seq # 3: YGR099W_Skud Reading seq # 4: YGR099W_Smik Reading seq # 5: YGR099W_Spar Sequences read.. Counting patterns.. # site patterns = 164 Counting frequencies.. 120 bytes for distance 26240 bytes for lkl0 20992 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.342093 0.306844 0.299004 0.215267 0.300477 0.309069 0.205637 0.000060 lnL0 = -2028.104588 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2028.104588 x= 0.34209 0.30684 0.29900 0.21527 0.30048 0.30907 0.20564 0.00006 1 h-lim-p 0.0000 0.0000 464.8126 2027.954348 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0006 648.2216 1917.542089 9 0.0006 57 | 1/8 3 h-lim-p 0.0002 0.0014 130.0630 1913.606654 0 0.0007 71 | 1/8 4 h-lim-p 0.0002 0.0016 69.8048 1912.774431 0 0.0004 84 | 1/8 5 h-lim-p 0.0014 0.0147 21.1331 1912.278724 0 0.0020 96 | 1/8 6 h-lim-p 0.0192 0.1615 2.2474 1909.881737 0 0.0383 109 | 1/8 7 h-lim-p 0.0026 0.0211 20.2877 1893.335598 0 0.0105 123 | 1/8 8 h-lim-p 0.0002 0.0020 141.0249 1880.835644 0 0.0010 137 | 1/8 9 h-lim-p 0.0881 0.7050 0.2632 1877.402766 0 0.1762 150 | 0/8 10 h-lim-p 0.0011 0.0517 40.5768 1876.999075 2 0.0005 173 | 0/8 11 h-lim-p 0.2854 8.2039 0.0762 1875.709996 0 0.5708 186 | 0/8 12 h-lim-p 0.4799 3.8391 0.0185 1875.502816 0 0.9598 207 | 0/8 13 h-lim-p 2.5000 20.0000 0.0057 1875.489776 6 0.7967 241 | 0/8 14 h-lim-p 2.2987 20.0000 0.0020 1875.488482 3 0.5677 268 | 0/8 15 h-lim-p 2.5000 20.0000 0.0002 1875.488458 2 0.9644 292 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1875.488457 0 1.0938 312 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1875.488457 0 1.0938 332 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1875.488457 0 2.1875 352 | 0/8 19 h-lim-p 1.8551 20.0000 0.0000 1875.488457 0 0.4638 373 | 0/8 20 h-lim-p 0.8543 20.0000 0.0000 1875.488457 0 0.0002 404 Out... lnL = -1875.488457 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1875.488457 Node 7: lnL = -1875.488457 Node 8: lnL = -1875.488457 Node 9: lnL = -1875.488457 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 286 Sequential format.. Reading seq # 1: YGR101W_Sbay Reading seq # 2: YGR101W_Scer Reading seq # 3: YGR101W_Skud Reading seq # 4: YGR101W_Smik Reading seq # 5: YGR101W_Spar Sequences read.. Counting patterns.. # site patterns = 122 Counting frequencies.. 120 bytes for distance 19520 bytes for lkl0 15616 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.410591 0.369120 0.360981 0.257147 0.359552 0.369547 0.245168 0.000060 lnL0 = -1346.023633 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1346.023633 x= 0.41059 0.36912 0.36098 0.25715 0.35955 0.36955 0.24517 0.00006 1 h-lim-p 0.0000 0.0000 285.4438 1345.922305 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0009 550.2654 1260.059449 m 0.0009 38 | 1/8 3 h-lim-p 0.0001 0.0010 136.4089 1255.740525 0 0.0005 52 | 1/8 4 h-lim-p 0.0005 0.0037 45.5922 1254.200825 0 0.0018 66 | 1/8 5 h-lim-p 0.0044 0.0355 11.6820 1253.659703 7 0.0043 95 | 1/8 6 h-lim-p 0.0086 0.0732 5.8861 1251.859045 0 0.0172 108 | 1/8 7 h-lim-p 0.0040 0.0317 14.5661 1241.713793 0 0.0158 122 | 0/8 8 h-lim-p 0.0006 0.0051 51.3850 1237.545467 0 0.0025 136 | 0/8 9 h-lim-p 0.0002 0.0015 34.1253 1236.347332 m 0.0015 148 | 1/8 10 h-lim-p 0.0001 0.0010 542.9765 1235.814931 0 0.0001 160 | 1/8 11 h-lim-p 0.3076 2.4605 0.1470 1231.655495 0 0.6151 173 | 1/8 12 h-lim-p 1.9257 15.4057 0.0176 1231.313948 6 1.5580 206 | 1/8 13 h-lim-p 1.8813 20.0000 0.0145 1230.746535 0 2.8219 225 | 1/8 14 h-lim-p 1.1769 9.4149 0.0211 1229.872826 0 2.3537 245 | 1/8 15 h-lim-p 2.2063 17.6506 0.0169 1229.533176 8 1.5348 283 | 1/8 16 h-lim-p 1.3184 10.5471 0.0089 1229.421573 5 1.3019 312 | 0/8 17 h-lim-p 0.0043 0.1181 2.7037 1229.416229 5 0.0016 342 | 0/8 18 h-lim-p 1.8554 20.0000 0.0023 1229.414317 3 0.7755 360 | 0/8 19 h-lim-p 2.5000 20.0000 0.0002 1229.414308 2 0.9644 384 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 1229.414307 0 1.0938 404 | 0/8 21 h-lim-p 2.5000 20.0000 0.0000 1229.414307 0 1.0938 424 | 0/8 22 h-lim-p 2.5000 20.0000 0.0000 1229.414307 0 2.1875 444 | 0/8 23 h-lim-p 1.8537 20.0000 0.0000 1229.414307 0 0.8110 464 | 0/8 24 h-lim-p 2.5000 20.0000 0.0000 1229.414307 0 0.0391 489 | 0/8 25 h-lim-p 0.0302 20.0000 0.0000 1229.414307 0 0.0000 530 Out... lnL = -1229.414307 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1229.414307 Node 7: lnL = -1229.414307 Node 8: lnL = -1229.414307 Node 9: lnL = -1229.414307 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 294 Sequential format.. Reading seq # 1: YGR102C_Sbay Reading seq # 2: YGR102C_Scer Reading seq # 3: YGR102C_Skud Reading seq # 4: YGR102C_Smik Reading seq # 5: YGR102C_Spar Sequences read.. Counting patterns.. # site patterns = 132 Counting frequencies.. 120 bytes for distance 21120 bytes for lkl0 16896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.407822 0.365757 0.358871 0.256094 0.361151 0.367055 0.247363 0.000060 lnL0 = -1448.480372 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1448.480372 x= 0.40782 0.36576 0.35887 0.25609 0.36115 0.36705 0.24736 0.00006 1 h-lim-p 0.0000 0.0000 270.5755 1448.394423 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0014 418.6829 1366.806790 3 0.0013 46 | 1/8 3 h-lim-p 0.0003 0.0022 85.3689 1362.716400 0 0.0011 60 | 1/8 4 h-lim-p 0.0012 0.0098 33.7543 1361.406842 0 0.0024 73 | 1/8 5 h-lim-p 0.0027 0.0218 13.2324 1361.283361 5 0.0013 96 | 1/8 6 h-lim-p 0.0061 0.0978 2.8810 1361.041874 0 0.0121 109 | 1/8 7 h-lim-p 0.0085 0.1299 4.1110 1347.325967 6 0.0632 133 | 0/8 8 h-lim-p 0.0007 0.0056 42.3248 1346.235398 0 0.0014 146 | 0/8 9 h-lim-p 0.0011 0.0087 4.0798 1346.224428 0 0.0016 158 | 0/8 10 h-lim-p 0.0883 2.7779 0.0752 1345.967770 0 0.2650 171 | 0/8 11 h-lim-p 0.2722 2.1777 0.0201 1345.900314 0 0.8166 192 | 0/8 12 h-lim-p 2.5000 20.0000 0.0030 1345.897850 5 0.8900 223 | 0/8 13 h-lim-p 2.5000 20.0000 0.0007 1345.897796 2 0.5859 248 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 1345.897793 1 0.6152 271 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1345.897793 0 1.0938 291 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1345.897793 0 1.0938 311 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1345.897793 0 2.1875 331 | 0/8 18 h-lim-p 1.7784 20.0000 0.0000 1345.897793 0 0.7781 351 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1345.897793 0 0.0049 379 Out... lnL = -1345.897793 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1345.897793 Node 7: lnL = -1345.897793 Node 8: lnL = -1345.897793 Node 9: lnL = -1345.897793 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 298 Sequential format.. Reading seq # 1: YGR103W_Sbay Reading seq # 2: YGR103W_Scer Reading seq # 3: YGR103W_Skud Reading seq # 4: YGR103W_Smik Reading seq # 5: YGR103W_Spar Sequences read.. Counting patterns.. # site patterns = 131 Counting frequencies.. 120 bytes for distance 20960 bytes for lkl0 16768 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.207379 0.052096 0.055681 0.129261 0.126349 0.194183 0.227852 0.000060 lnL0 = -1348.423508 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1348.423508 x= 0.20738 0.05210 0.05568 0.12926 0.12635 0.19418 0.22785 0.00006 1 h-lim-p 0.0000 0.0000 96.1679 1348.379623 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0080 29.0640 1347.939364 0 0.0010 40 | 1/8 3 h-lim-p 0.0030 0.0244 8.8502 1347.907580 7 0.0008 71 | 1/8 4 h-lim-p 0.0036 0.0435 2.1063 1347.903637 6 0.0010 97 | 1/8 5 h-lim-p 0.0023 0.3332 0.9187 1347.872520 0 0.0092 111 | 1/8 6 h-lim-p 0.0032 0.0785 2.6495 1347.591673 0 0.0096 131 | 1/8 7 h-lim-p 0.0031 0.2465 8.2133 1346.071767 0 0.0062 144 | 1/8 8 h-lim-p 0.0028 0.0221 15.4539 1345.839188 7 0.0016 175 | 1/8 9 h-lim-p 2.5000 20.0000 0.0062 1345.807785 5 1.2671 199 | 1/8 10 h-lim-p 2.5000 20.0000 0.0016 1345.806015 5 1.3886 230 | 0/8 11 h-lim-p 0.0154 3.5489 0.1439 1345.806003 2 0.0012 256 | 0/8 12 h-lim-p 0.4099 3.2792 0.0003 1345.805971 0 1.2297 277 | 0/8 13 h-lim-p 0.1491 1.1930 0.0001 1345.805971 0 0.0000 311 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 1345.805970 0 0.9830 347 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1345.805970 0 1.0938 367 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1345.805970 0 1.2500 387 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1345.805970 0 0.2734 409 | 0/8 18 h-lim-p 0.3288 20.0000 0.0000 1345.805970 0 0.0154 433 | 0/8 19 h-lim-p 0.0128 20.0000 0.0000 1345.805970 0 0.0016 455 Out... lnL = -1345.805970 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1345.805970 Node 7: lnL = -1345.805970 Node 8: lnL = -1345.805970 Node 9: lnL = -1345.805970 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 303 Sequential format.. Reading seq # 1: YGR104C_Sbay Reading seq # 2: YGR104C_Scer Reading seq # 3: YGR104C_Skud Reading seq # 4: YGR104C_Smik Reading seq # 5: YGR104C_Spar Sequences read.. Counting patterns.. # site patterns = 143 Counting frequencies.. 120 bytes for distance 22880 bytes for lkl0 18304 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.614300 0.534307 0.523138 0.377738 0.525319 0.546388 0.373661 0.000060 lnL0 = -1455.866286 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1455.866286 x= 0.61430 0.53431 0.52314 0.37774 0.52532 0.54639 0.37366 0.00006 1 h-lim-p 0.0000 0.0000 181.0033 1455.731989 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0008 757.8004 1392.902107 0 0.0007 40 | 1/8 3 h-lim-p 0.0013 0.0102 49.9075 1390.873726 0 0.0025 53 | 1/8 4 h-lim-p 0.0011 0.0085 40.6621 1389.677876 0 0.0021 66 | 1/8 5 h-lim-p 0.0056 0.0460 15.3075 1389.598944 6 0.0023 93 | 0/8 6 h-lim-p 0.0007 0.0203 48.9165 1386.679720 0 0.0057 108 | 0/8 7 h-lim-p 0.0024 0.0189 23.2895 1384.193939 m 0.0189 120 | 1/8 8 h-lim-p 0.0603 0.4825 1.3751 .. | 1/8 9 h-lim-p 0.0000 0.0031 127.5826 1359.597496 3 0.0023 184 | 1/8 10 h-lim-p 0.0001 0.0005 320.2967 1352.904489 0 0.0004 198 | 1/8 11 h-lim-p 0.0002 0.0018 152.6625 1345.520607 0 0.0009 212 | 1/8 12 h-lim-p 0.0002 0.0017 135.4699 1342.106025 0 0.0008 226 | 1/8 13 h-lim-p 0.0008 0.0065 28.2058 1341.315149 0 0.0024 239 | 1/8 14 h-lim-p 0.0058 0.0814 11.8237 1341.078448 8 0.0034 271 | 1/8 15 h-lim-p 0.0347 1.1370 1.1522 1339.211280 0 0.1387 285 | 1/8 16 h-lim-p 0.0104 0.0831 7.6554 1333.567998 0 0.0312 298 | 1/8 17 h-lim-p 0.5786 4.6287 0.0751 1333.180061 0 0.8679 310 | 1/8 18 h-lim-p 2.5000 20.0000 0.0101 1333.135878 7 1.5259 348 | 0/8 19 h-lim-p 0.0437 5.0741 0.3527 1333.135546 3 0.0059 375 | 0/8 20 h-lim-p 0.8580 20.0000 0.0024 1333.133388 0 1.7159 396 | 0/8 21 h-lim-p 1.0248 8.1985 0.0014 1333.132670 3 1.1462 423 | 0/8 22 h-lim-p 2.5000 20.0000 0.0002 1333.132653 1 1.2500 445 | 0/8 23 h-lim-p 2.5000 20.0000 0.0000 1333.132653 0 1.2500 465 | 0/8 24 h-lim-p 2.5000 20.0000 0.0000 1333.132653 0 2.1875 485 | 0/8 25 h-lim-p 2.5000 20.0000 0.0000 1333.132653 0 1.2500 505 | 0/8 26 h-lim-p 2.5000 20.0000 0.0000 1333.132653 0 0.5469 526 | 0/8 27 h-lim-p 1.0236 20.0000 0.0000 1333.132653 0 0.0280 550 | 0/8 28 h-lim-p 0.0236 20.0000 0.0000 1333.132653 0 0.0007 574 Out... lnL = -1333.132653 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1333.132653 Node 7: lnL = -1333.132653 Node 8: lnL = -1333.132653 Node 9: lnL = -1333.132653 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 292 Sequential format.. Reading seq # 1: YGR105W_Sbay Reading seq # 2: YGR105W_Scer Reading seq # 3: YGR105W_Skud Reading seq # 4: YGR105W_Smik Reading seq # 5: YGR105W_Spar Sequences read.. Counting patterns.. # site patterns = 136 Counting frequencies.. 120 bytes for distance 21760 bytes for lkl0 17408 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.478521 0.432652 0.420411 0.301247 0.420740 0.432161 0.284798 0.000060 lnL0 = -1342.292948 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1342.292948 x= 0.47852 0.43265 0.42041 0.30125 0.42074 0.43216 0.28480 0.00006 1 h-lim-p 0.0000 0.0000 243.7034 1342.224675 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0010 645.0628 1248.012329 m 0.0010 38 | 1/8 3 h-lim-p -0.0000 -0.0000 90.9707 h-lim-p: -1.02677213e-19 -8.21417702e-19 9.09706716e+01 1248.012329 .. | 1/8 4 h-lim-p 0.0000 0.0050 613.0044 1234.205087 0 0.0002 62 | 1/8 5 h-lim-p 0.0004 0.0035 110.4121 1224.438967 0 0.0017 76 | 1/8 6 h-lim-p 0.0006 0.0051 65.2304 1223.223743 1 0.0008 90 | 1/8 7 h-lim-p 0.0024 0.0190 14.9275 1223.120497 3 0.0010 108 | 0/8 8 h-lim-p 0.0006 0.0254 24.8019 1222.846109 0 0.0012 121 | 0/8 9 h-lim-p 0.0024 0.0287 12.3136 1222.728078 3 0.0020 139 | 0/8 10 h-lim-p 0.0031 0.0247 7.1274 1222.699379 4 0.0015 159 | 0/8 11 h-lim-p 0.0190 0.2981 0.5756 1222.697374 2 0.0044 176 | 0/8 12 h-lim-p 0.0416 1.5496 0.0616 1222.334306 0 0.4990 199 | 0/8 13 h-lim-p 2.5000 20.0000 0.0046 1222.222680 1 3.1250 221 | 0/8 14 h-lim-p 2.5000 20.0000 0.0039 1222.215185 4 1.0875 248 | 0/8 15 h-lim-p 2.5000 20.0000 0.0004 1222.215138 3 0.8855 276 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1222.215138 0 1.0938 296 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1222.215138 0 1.0938 316 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1222.215138 0 0.0146 343 | 0/8 19 h-lim-p 0.0131 20.0000 0.0000 1222.215138 0 0.0001 369 Out... lnL = -1222.215138 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1222.215138 Node 7: lnL = -1222.215138 Node 8: lnL = -1222.215138 Node 9: lnL = -1222.215138 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 924 Sequential format.. Reading seq # 1: YGR106C_Sbay Reading seq # 2: YGR106C_Scer Reading seq # 3: YGR106C_Skud Reading seq # 4: YGR106C_Smik Reading seq # 5: YGR106C_Spar Sequences read.. Counting patterns.. # site patterns = 350 Counting frequencies.. 120 bytes for distance 56000 bytes for lkl0 44800 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.544641 0.405540 0.419055 0.312467 0.416233 0.411136 0.322423 0.000060 lnL0 = -4144.710705 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4144.710705 x= 0.54464 0.40554 0.41905 0.31247 0.41623 0.41114 0.32242 0.00006 1 h-lim-p 0.0000 0.0000 549.5342 4143.863411 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0005 1536.9365 3924.221847 0 0.0004 39 | 1/8 3 h-lim-p 0.0004 0.0029 95.5861 3919.328949 0 0.0014 53 | 1/8 4 h-lim-p 0.0002 0.0016 36.0181 3919.034435 0 0.0006 66 | 1/8 5 h-lim-p 0.0005 0.0041 13.1490 3918.920188 0 0.0010 79 | 1/8 6 h-lim-p 0.0022 0.0525 6.0936 3918.791719 0 0.0044 92 | 1/8 7 h-lim-p 0.0036 0.0702 7.4534 3918.317890 0 0.0054 104 | 1/8 8 h-lim-p 0.0053 0.0829 7.4923 3909.740651 0 0.0214 118 | 0/8 9 h-lim-p 0.0094 0.0749 14.1573 3909.538318 5 0.0025 141 | 0/8 10 h-lim-p 0.6373 5.0981 0.0242 3909.376489 3 0.6472 159 | 0/8 11 h-lim-p 0.7779 20.0000 0.0202 3909.340791 5 0.3430 188 | 0/8 12 h-lim-p 2.1458 20.0000 0.0032 3909.336918 5 0.7184 221 | 0/8 13 h-lim-p 2.5000 20.0000 0.0005 3909.336799 3 0.8171 248 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 3909.336798 0 1.0938 268 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 3909.336798 0 1.0938 288 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 3909.336798 0 1.0938 308 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 3909.336798 0 1.0938 328 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 3909.336798 0 5.0000 349 | 0/8 19 h-lim-p 1.4800 20.0000 0.0000 3909.336798 0 0.1850 371 | 0/8 20 h-lim-p 0.0115 20.0000 0.0000 3909.336798 0 0.0115 391 | 0/8 21 h-lim-p 0.0040 20.0000 0.0000 3909.336798 0 0.0005 413 | 0/8 22 h-lim-p 0.0002 20.0000 0.0000 3909.336798 0 0.0000 451 | 0/8 23 h-lim-p 0.0000 20.0000 0.0001 | 0/8 24 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -3909.336798 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3909.336798 Node 7: lnL = -3909.336798 Node 8: lnL = -3909.336798 Node 9: lnL = -3909.336798 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 551 Sequential format.. Reading seq # 1: YGR108W_Sbay Reading seq # 2: YGR108W_Scer Reading seq # 3: YGR108W_Skud Reading seq # 4: YGR108W_Smik Reading seq # 5: YGR108W_Spar Sequences read.. Counting patterns.. # site patterns = 145 Counting frequencies.. 120 bytes for distance 23200 bytes for lkl0 18560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.265724 0.203162 0.199603 0.144453 0.206100 0.219279 0.151292 0.000060 lnL0 = -2184.323100 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2184.323100 x= 0.26572 0.20316 0.19960 0.14445 0.20610 0.21928 0.15129 0.00006 1 h-lim-p 0.0000 0.0000 672.6224 2183.159969 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0007 475.2154 2108.592388 4 0.0006 47 | 1/8 3 h-lim-p 0.0001 0.0006 121.2523 2105.983096 0 0.0004 61 | 1/8 4 h-lim-p 0.0002 0.0020 52.3222 2104.863338 0 0.0010 75 | 1/8 5 h-lim-p 0.0011 0.0088 22.5266 2104.661662 6 0.0005 99 | 1/8 6 h-lim-p 0.0015 0.0434 8.1805 2100.821774 0 0.0120 114 | 1/8 7 h-lim-p 0.0014 0.0112 20.7616 2083.325506 0 0.0056 128 | 1/8 8 h-lim-p 0.0004 0.0029 98.6881 2057.263166 0 0.0014 142 | 1/8 9 h-lim-p 0.0284 0.2276 1.1105 2038.989912 0 0.1138 156 | 1/8 10 h-lim-p 0.4338 3.4705 0.0989 2037.803217 8 0.3053 187 | 1/8 11 h-lim-p 0.8535 6.8281 0.0303 2037.541618 7 0.3642 221 | 1/8 12 h-lim-p 0.5550 15.4134 0.0199 2037.416530 6 0.4227 253 | 0/8 13 h-lim-p 0.0039 0.6756 2.1647 2037.414714 3 0.0008 279 | 0/8 14 h-lim-p 0.2020 1.6156 0.0035 2037.407914 0 0.4039 292 | 0/8 15 h-lim-p 2.5000 20.0000 0.0005 2037.407291 4 0.8479 323 | 0/8 16 h-lim-p 1.9272 20.0000 0.0002 2037.407232 3 0.6827 351 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 2037.407232 0 1.0938 371 | 0/8 18 h-lim-p 2.0063 20.0000 0.0000 2037.407232 0 0.8778 391 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 2037.407232 0 1.2500 411 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 2037.407232 0 0.0684 435 | 0/8 21 h-lim-p 0.0795 20.0000 0.0000 2037.407232 0 0.0397 455 | 0/8 22 h-lim-p 0.0448 20.0000 0.0000 2037.407232 0 0.0000 497 Out... lnL = -2037.407232 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2037.407232 Node 7: lnL = -2037.407232 Node 8: lnL = -2037.407232 Node 9: lnL = -2037.407232 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 865 Sequential format.. Reading seq # 1: YGR110W_Sbay Reading seq # 2: YGR110W_Scer Reading seq # 3: YGR110W_Skud Reading seq # 4: YGR110W_Smik Reading seq # 5: YGR110W_Spar Sequences read.. Counting patterns.. # site patterns = 413 Counting frequencies.. 120 bytes for distance 66080 bytes for lkl0 52864 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.276351 0.166725 0.170333 0.237865 0.191961 0.340337 0.385844 0.271992 lnL0 = -4557.158687 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4557.158687 x= 0.27635 0.16672 0.17033 0.23786 0.19196 0.34034 0.38584 0.27199 1 h-lim-p 0.0187 0.1498 55.1216 4556.111432 7 0.0007 43 | 0/8 2 h-lim-p 0.0023 0.0188 16.8712 4555.993198 5 0.0009 65 | 0/8 3 h-lim-p 0.0013 0.0336 11.7421 4555.948628 6 0.0009 90 | 0/8 4 h-lim-p 0.0065 0.2947 1.6271 4555.947011 4 0.0013 111 | 0/8 5 h-lim-p 0.0056 1.5638 0.3654 4555.946845 2 0.0026 127 | 0/8 6 h-lim-p 0.0322 13.2998 0.0299 4555.946843 1 0.0020 152 | 0/8 7 h-lim-p 0.0215 20.0000 0.0027 4555.946392 0 0.3446 176 | 0/8 8 h-lim-p 0.0030 2.3251 0.3122 4555.946204 2 0.0023 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4555.946202 0 1.0938 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4555.946202 0 1.0938 240 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4555.946202 0 1.0938 260 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4555.946202 0 2.5000 280 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 4555.946202 0 0.2734 302 | 0/8 14 h-lim-p 0.2015 20.0000 0.0000 4555.946202 0 0.0002 331 Out... lnL = -4555.946202 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4555.946202 Node 7: lnL = -4555.946202 Node 8: lnL = -4555.946202 Node 9: lnL = -4555.946202 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 363 Sequential format.. Reading seq # 1: YGR112W_Sbay Reading seq # 2: YGR112W_Scer Reading seq # 3: YGR112W_Skud Reading seq # 4: YGR112W_Smik Reading seq # 5: YGR112W_Spar Sequences read.. Counting patterns.. # site patterns = 168 Counting frequencies.. 120 bytes for distance 26880 bytes for lkl0 21504 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.110447 0.107444 0.033880 0.172620 0.114263 0.186929 0.259059 0.108152 lnL0 = -1693.480832 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1693.480832 x= 0.11045 0.10744 0.03388 0.17262 0.11426 0.18693 0.25906 0.10815 1 h-lim-p 0.0026 0.9720 114.0796 1691.662548 5 0.0003 33 | 0/8 2 h-lim-p 0.0027 0.0262 13.7330 1691.576350 6 0.0009 59 | 0/8 3 h-lim-p 0.0029 0.0795 4.3668 1691.570245 2 0.0007 76 | 0/8 4 h-lim-p 0.0047 0.5232 0.6426 1691.569974 4 0.0013 99 | 0/8 5 h-lim-p 0.0037 1.0031 0.2293 1691.569958 2 0.0007 124 | 0/8 6 h-lim-p 0.0066 15.4257 0.0248 1691.569958 0 0.0014 145 | 0/8 7 h-lim-p 0.0274 20.0000 0.0013 1691.569958 0 0.0137 165 | 0/8 8 h-lim-p 0.0111 20.0000 0.0016 1691.569946 0 0.0885 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1691.569946 0 1.2500 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1691.569946 0 2.1875 228 | 0/8 11 h-lim-p 1.9044 20.0000 0.0000 1691.569946 0 0.8332 248 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1691.569946 0 0.0195 274 | 0/8 13 h-lim-p 0.0105 20.0000 0.0000 1691.569946 0 0.0007 297 Out... lnL = -1691.569946 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1691.569946 Node 7: lnL = -1691.569946 Node 8: lnL = -1691.569946 Node 9: lnL = -1691.569946 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 380 Sequential format.. Reading seq # 1: YGR113W_Sbay Reading seq # 2: YGR113W_Scer Reading seq # 3: YGR113W_Skud Reading seq # 4: YGR113W_Smik Reading seq # 5: YGR113W_Spar Sequences read.. Counting patterns.. # site patterns = 169 Counting frequencies.. 120 bytes for distance 27040 bytes for lkl0 21632 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.155836 0.087139 0.103702 0.192375 0.075634 0.237881 0.239472 0.153191 lnL0 = -1849.420710 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1849.420710 x= 0.15584 0.08714 0.10370 0.19238 0.07563 0.23788 0.23947 0.15319 1 h-lim-p 0.0197 0.5652 43.3314 1848.906179 2 0.0006 30 | 0/8 2 h-lim-p 0.0020 0.0163 9.6262 1848.869898 5 0.0008 52 | 0/8 3 h-lim-p 0.0009 0.0344 8.2626 1848.855544 5 0.0006 77 | 0/8 4 h-lim-p 0.0063 0.3699 0.8466 1848.855221 3 0.0009 99 | 0/8 5 h-lim-p 0.0076 4.3733 0.1025 1848.855217 0 0.0009 121 | 0/8 6 h-lim-p 0.0122 20.0000 0.0080 1848.855217 0 0.0027 142 | 0/8 7 h-lim-p 0.0124 20.0000 0.0017 1848.855212 0 0.0746 164 | 0/8 8 h-lim-p 0.0064 20.0000 0.0199 1848.855177 0 0.0128 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1848.855176 0 1.0938 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1848.855176 0 1.0938 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1848.855176 0 2.1875 245 | 0/8 12 h-lim-p 2.0256 20.0000 0.0000 1848.855176 0 0.0633 269 | 0/8 13 h-lim-p 0.0596 20.0000 0.0000 1848.855176 0 0.0149 290 | 0/8 14 h-lim-p 0.0088 20.0000 0.0000 1848.855176 0 0.0011 312 Out... lnL = -1848.855176 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1848.855176 Node 7: lnL = -1848.855176 Node 8: lnL = -1848.855176 Node 9: lnL = -1848.855176 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 518 Sequential format.. Reading seq # 1: YGR117C_Sbay Reading seq # 2: YGR117C_Scer Reading seq # 3: YGR117C_Skud Reading seq # 4: YGR117C_Smik Reading seq # 5: YGR117C_Spar Sequences read.. Counting patterns.. # site patterns = 246 Counting frequencies.. 120 bytes for distance 39360 bytes for lkl0 31488 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.122107 0.107125 0.116524 0.147736 0.117347 0.273353 0.228908 0.119455 lnL0 = -2491.344252 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2491.344252 x= 0.12211 0.10713 0.11652 0.14774 0.11735 0.27335 0.22891 0.11945 1 h-lim-p 0.0269 3.4341 43.0061 2490.941963 5 0.0004 37 | 0/8 2 h-lim-p 0.0020 0.0240 9.6080 2490.911456 7 0.0007 69 | 0/8 3 h-lim-p 0.0030 0.0987 2.2451 2490.910314 4 0.0005 92 | 0/8 4 h-lim-p 0.0039 0.9063 0.2773 2490.910289 2 0.0006 110 | 0/8 5 h-lim-p 0.0026 5.1375 0.0651 2490.910287 0 0.0011 130 | 0/8 6 h-lim-p 0.0104 20.0000 0.0072 2490.910287 0 0.0011 152 | 0/8 7 h-lim-p 0.0041 20.0000 0.0020 2490.910287 0 0.0082 173 | 0/8 8 h-lim-p 0.0141 20.0000 0.0012 2490.910277 0 0.1129 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2490.910276 0 1.0938 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2490.910276 0 1.0938 236 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2490.910276 0 2.1875 256 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2490.910276 0 0.3125 278 | 0/8 13 h-lim-p 0.2838 20.0000 0.0000 2490.910276 0 0.0006 306 Out... lnL = -2490.910276 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2490.910276 Node 7: lnL = -2490.910276 Node 8: lnL = -2490.910276 Node 9: lnL = -2490.910276 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 388 Sequential format.. Reading seq # 1: YGR119C_Sbay Reading seq # 2: YGR119C_Scer Reading seq # 3: YGR119C_Skud Reading seq # 4: YGR119C_Smik Reading seq # 5: YGR119C_Spar Sequences read.. Counting patterns.. # site patterns = 169 Counting frequencies.. 120 bytes for distance 27040 bytes for lkl0 21632 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.151112 0.033043 0.102538 0.104990 0.081105 0.237172 0.202065 0.148885 lnL0 = -1768.054313 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1768.054313 x= 0.15111 0.03304 0.10254 0.10499 0.08111 0.23717 0.20206 0.14889 1 h-lim-p 0.0006 0.0049 99.0144 1766.409940 7 0.0004 40 | 0/8 2 h-lim-p 0.0010 0.0081 17.3491 1766.298056 8 0.0008 72 | 0/8 3 h-lim-p 0.0022 0.0567 5.9065 1766.288599 6 0.0006 97 | 0/8 4 h-lim-p 0.0011 0.0477 3.3173 1766.286784 3 0.0004 115 | 0/8 5 h-lim-p 0.0019 0.6126 0.7686 1766.286646 3 0.0005 134 | 0/8 6 h-lim-p 0.0043 2.6123 0.0881 1766.286643 0 0.0010 155 | 0/8 7 h-lim-p 0.0077 20.0000 0.0109 1766.286642 1 0.0038 178 | 0/8 8 h-lim-p 0.0305 20.0000 0.0014 1766.286450 0 0.4883 202 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1766.286427 2 0.9961 226 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1766.286427 0 1.0938 246 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1766.286427 0 0.3125 268 | 0/8 12 h-lim-p 0.2563 20.0000 0.0000 1766.286427 0 0.0641 289 | 0/8 13 h-lim-p 0.0386 20.0000 0.0000 1766.286427 0 0.0000 326 Out... lnL = -1766.286427 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1766.286427 Node 7: lnL = -1766.286427 Node 8: lnL = -1766.286427 Node 9: lnL = -1766.286427 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 671 Sequential format.. Reading seq # 1: YGR120C_Sbay Reading seq # 2: YGR120C_Scer Reading seq # 3: YGR120C_Skud Reading seq # 4: YGR120C_Smik Reading seq # 5: YGR120C_Spar Sequences read.. Counting patterns.. # site patterns = 301 Counting frequencies.. 120 bytes for distance 48160 bytes for lkl0 38528 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.159544 0.142900 0.011688 0.159772 0.106248 0.734461 0.199534 0.156096 lnL0 = -3342.860503 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3342.860503 x= 0.15954 0.14290 0.01169 0.15977 0.10625 0.73446 0.19953 0.15610 1 h-lim-p 0.0020 0.0800 183.1150 3339.399257 3 0.0002 30 | 0/8 2 h-lim-p 0.0009 0.0074 31.5135 3338.997736 6 0.0008 53 | 0/8 3 h-lim-p 0.0006 0.0048 33.6194 3338.785322 6 0.0006 77 | 0/8 4 h-lim-p 0.0017 0.0196 12.3238 3338.754784 7 0.0005 109 | 0/8 5 h-lim-p 0.0025 0.2463 2.5502 3338.748551 3 0.0020 127 | 0/8 6 h-lim-p 0.0016 0.1464 3.2289 3338.745600 5 0.0011 151 | 0/8 7 h-lim-p 0.0056 0.6821 0.6269 3338.745435 3 0.0008 173 | 0/8 8 h-lim-p 0.1789 20.0000 0.0029 3338.722854 0 1.4309 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0014 3338.721935 3 1.0004 222 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3338.721934 0 1.0938 242 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3338.721934 0 1.0938 262 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3338.721934 0 2.1875 282 | 0/8 13 h-lim-p 2.3282 20.0000 0.0000 3338.721934 0 0.5093 303 | 0/8 14 h-lim-p 0.5953 20.0000 0.0000 3338.721934 0 0.0023 330 Out... lnL = -3338.721934 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3338.721934 Node 7: lnL = -3338.721934 Node 8: lnL = -3338.721934 Node 9: lnL = -3338.721934 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 873 Sequential format.. Reading seq # 1: YGR121C_Sbay Reading seq # 2: YGR121C_Scer Reading seq # 3: YGR121C_Skud Reading seq # 4: YGR121C_Smik Reading seq # 5: YGR121C_Spar Sequences read.. Counting patterns.. # site patterns = 299 Counting frequencies.. 120 bytes for distance 47840 bytes for lkl0 38272 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.225992 0.029666 0.090972 0.106222 0.080889 0.169674 0.211691 0.223627 lnL0 = -3883.477282 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3883.477282 x= 0.22599 0.02967 0.09097 0.10622 0.08089 0.16967 0.21169 0.22363 1 h-lim-p 0.0014 0.0599 235.6285 3879.089512 4 0.0002 32 | 0/8 2 h-lim-p 0.0004 0.0032 38.1198 3878.866644 4 0.0003 52 | 0/8 3 h-lim-p 0.0005 0.0107 24.7951 3878.798529 7 0.0003 83 | 0/8 4 h-lim-p 0.0005 0.0182 14.1667 3878.777789 6 0.0003 109 | 0/8 5 h-lim-p 0.0019 0.1240 2.1311 3878.776830 2 0.0005 126 | 0/8 6 h-lim-p 0.0016 0.3482 0.6112 3878.776783 2 0.0003 144 | 0/8 7 h-lim-p 0.0010 2.2649 0.1520 3878.776770 1 0.0009 166 | 0/8 8 h-lim-p 0.0795 20.0000 0.0017 3878.771035 0 1.2719 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 3878.770741 3 1.0004 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3878.770741 0 1.0938 236 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3878.770741 0 1.0938 256 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3878.770741 0 0.0391 281 | 0/8 13 h-lim-p 0.0313 20.0000 0.0000 3878.770741 0 0.0005 306 Out... lnL = -3878.770741 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3878.770741 Node 7: lnL = -3878.770741 Node 8: lnL = -3878.770741 Node 9: lnL = -3878.770741 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 875 Sequential format.. Reading seq # 1: YGR123C_Sbay Reading seq # 2: YGR123C_Scer Reading seq # 3: YGR123C_Skud Reading seq # 4: YGR123C_Smik Reading seq # 5: YGR123C_Spar Sequences read.. Counting patterns.. # site patterns = 393 Counting frequencies.. 120 bytes for distance 62880 bytes for lkl0 50304 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.285935 0.043748 0.000060 0.372583 0.309505 0.622265 0.471278 0.281230 lnL0 = -4428.633027 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4428.633027 x= 0.28593 0.04375 0.00006 0.37258 0.30950 0.62227 0.47128 0.28123 1 h-lim-p 0.0006 0.0051 67.3051 4424.475852 0 0.0019 23 | 0/8 2 h-lim-p 0.0001 0.0010 44.3215 4424.064348 0 0.0005 37 | 0/8 3 h-lim-p 0.0002 0.0017 35.5659 4423.359672 m 0.0017 49 | 1/8 4 h-lim-p 0.0037 0.0299 13.9097 4423.179096 7 0.0025 78 | 1/8 5 h-lim-p 0.0013 0.0107 9.7459 4423.133024 5 0.0015 101 | 1/8 6 h-lim-p 0.0083 0.0754 1.7718 4423.130534 5 0.0014 125 | 1/8 7 h-lim-p 0.0647 16.0662 0.0374 4423.129242 2 0.0563 141 | 0/8 8 h-lim-p 0.0005 0.2443 4.1303 4423.123305 0 0.0010 161 | 0/8 9 h-lim-p 0.0042 0.0339 0.3422 4423.107359 m 0.0339 173 | 1/8 10 h-lim-p 2.5000 20.0000 0.0013 4423.107221 3 0.7330 202 | 1/8 11 h-lim-p 1.2397 20.0000 0.0008 4423.107186 0 0.6199 221 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 4423.107186 0 1.0938 240 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 4423.107186 0 1.0938 259 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 4423.107186 0 0.3125 280 | 1/8 15 h-lim-p 0.2587 20.0000 0.0000 4423.107186 0 0.2587 299 | 1/8 16 h-lim-p 0.2307 20.0000 0.0000 4423.107186 0 0.0018 324 Out... lnL = -4423.107186 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4423.107186 Node 7: lnL = -4423.107186 Node 8: lnL = -4423.107186 Node 9: lnL = -4423.107186 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 918 Sequential format.. Reading seq # 1: YGR124W_Sbay Reading seq # 2: YGR124W_Scer Reading seq # 3: YGR124W_Skud Reading seq # 4: YGR124W_Smik Reading seq # 5: YGR124W_Spar Sequences read.. Counting patterns.. # site patterns = 336 Counting frequencies.. 120 bytes for distance 53760 bytes for lkl0 43008 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.124778 0.132270 0.017115 0.150942 0.122882 0.204365 0.162104 0.122585 lnL0 = -4083.716983 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4083.716983 x= 0.12478 0.13227 0.01712 0.15094 0.12288 0.20436 0.16210 0.12258 1 h-lim-p 0.0009 0.3622 308.5402 4079.528029 9 0.0001 41 | 0/8 2 h-lim-p 0.0005 0.0041 60.6436 4078.947249 6 0.0003 67 | 0/8 3 h-lim-p 0.0010 0.0149 20.4169 4078.882427 6 0.0003 93 | 0/8 4 h-lim-p 0.0021 0.0656 3.4256 4078.880687 5 0.0003 119 | 0/8 5 h-lim-p 0.0014 0.4855 0.7537 4078.880604 2 0.0003 136 | 0/8 6 h-lim-p 0.0020 2.2249 0.1145 4078.880602 0 0.0004 157 | 0/8 7 h-lim-p 0.0102 20.0000 0.0049 4078.880596 0 0.0204 178 | 0/8 8 h-lim-p 0.0095 4.4439 0.0104 4078.880098 0 0.0382 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4078.880084 0 1.0938 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4078.880083 0 1.0938 240 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4078.880083 0 1.0938 260 | 0/8 12 h-lim-p 2.1160 20.0000 0.0000 4078.880083 0 4.2320 281 | 0/8 13 h-lim-p 1.9760 20.0000 0.0000 4078.880083 0 0.0617 305 | 0/8 14 h-lim-p 0.1298 20.0000 0.0000 4078.880083 0 0.0324 326 | 0/8 15 h-lim-p 0.0409 20.0000 0.0000 4078.880083 0 0.0179 346 | 0/8 16 h-lim-p 0.0096 20.0000 0.0000 4078.880083 0 0.0006 369 Out... lnL = -4078.880083 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4078.880083 Node 7: lnL = -4078.880083 Node 8: lnL = -4078.880083 Node 9: lnL = -4078.880083 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 717 Sequential format.. Reading seq # 1: YGR125W_Sbay Reading seq # 2: YGR125W_Scer Reading seq # 3: YGR125W_Skud Reading seq # 4: YGR125W_Smik Reading seq # 5: YGR125W_Spar Sequences read.. Counting patterns.. # site patterns = 251 Counting frequencies.. 120 bytes for distance 40160 bytes for lkl0 32128 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.145617 0.070065 0.095470 0.107787 0.090166 0.206292 0.152725 0.143458 lnL0 = -3071.738725 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3071.738725 x= 0.14562 0.07007 0.09547 0.10779 0.09017 0.20629 0.15272 0.14346 1 h-lim-p 0.0037 0.3237 128.5780 3069.819900 6 0.0002 37 | 0/8 2 h-lim-p 0.0008 0.0065 26.7650 3069.691178 2 0.0004 53 | 0/8 3 h-lim-p 0.0007 0.0141 13.9434 3069.669287 5 0.0003 75 | 0/8 4 h-lim-p 0.0020 0.0901 1.9763 3069.668612 4 0.0004 98 | 0/8 5 h-lim-p 0.0041 0.9012 0.1746 3069.668605 0 0.0004 112 | 0/8 6 h-lim-p 0.0035 14.0084 0.0222 3069.668604 0 0.0018 132 | 0/8 7 h-lim-p 0.0028 20.0000 0.0137 3069.668582 0 0.0114 154 | 0/8 8 h-lim-p 0.0047 20.0000 0.0333 3069.668010 0 0.0188 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3069.667991 1 0.9961 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3069.667991 0 1.0938 218 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3069.667991 0 0.6250 239 | 0/8 12 h-lim-p 0.8427 20.0000 0.0000 3069.667991 0 0.0016 267 Out... lnL = -3069.667991 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3069.667991 Node 7: lnL = -3069.667991 Node 8: lnL = -3069.667991 Node 9: lnL = -3069.667991 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 288 Sequential format.. Reading seq # 1: YGR127W_Sbay Reading seq # 2: YGR127W_Scer Reading seq # 3: YGR127W_Skud Reading seq # 4: YGR127W_Smik Reading seq # 5: YGR127W_Spar Sequences read.. Counting patterns.. # site patterns = 137 Counting frequencies.. 120 bytes for distance 21920 bytes for lkl0 17536 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.153306 0.080495 0.081339 0.131241 0.106850 0.161286 0.246213 0.143039 lnL0 = -1297.842481 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1297.842481 x= 0.15331 0.08049 0.08134 0.13124 0.10685 0.16129 0.24621 0.14304 1 h-lim-p 0.0157 0.3196 40.6453 1297.262576 6 0.0007 37 | 0/8 2 h-lim-p 0.0022 0.0173 7.3849 1297.241323 6 0.0008 64 | 0/8 3 h-lim-p 0.0021 0.0975 2.7931 1297.236502 6 0.0014 90 | 0/8 4 h-lim-p 0.0026 0.2077 1.5174 1297.235727 4 0.0009 112 | 0/8 5 h-lim-p 0.0050 1.4257 0.2645 1297.235691 2 0.0011 129 | 0/8 6 h-lim-p 0.0033 3.1977 0.0880 1297.235687 2 0.0011 155 | 0/8 7 h-lim-p 0.0161 20.0000 0.0060 1297.235687 0 0.0070 175 | 0/8 8 h-lim-p 0.0315 20.0000 0.0013 1297.235617 0 0.2521 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1297.235617 0 1.0938 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1297.235617 0 1.0938 238 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1297.235617 0 0.3125 260 | 0/8 12 h-lim-p 0.2050 20.0000 0.0000 1297.235617 0 0.1025 280 | 0/8 13 h-lim-p 0.0705 20.0000 0.0000 1297.235617 0 0.0001 308 Out... lnL = -1297.235617 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1297.235617 Node 7: lnL = -1297.235617 Node 8: lnL = -1297.235617 Node 9: lnL = -1297.235617 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 893 Sequential format.. Reading seq # 1: YGR131W_Sbay Reading seq # 2: YGR131W_Scer Reading seq # 3: YGR131W_Skud Reading seq # 4: YGR131W_Smik Reading seq # 5: YGR131W_Spar Sequences read.. Counting patterns.. # site patterns = 298 Counting frequencies.. 120 bytes for distance 47680 bytes for lkl0 38144 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.097266 0.104217 0.072005 0.118258 0.062353 0.206840 0.163406 0.088591 lnL0 = -3750.170251 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3750.170251 x= 0.09727 0.10422 0.07200 0.11826 0.06235 0.20684 0.16341 0.08859 1 h-lim-p 0.0001 0.0012 138.1319 3748.262827 0 0.0002 22 | 0/8 2 h-lim-p 0.0008 0.0066 34.5287 3748.138274 6 0.0002 47 | 0/8 3 h-lim-p 0.0004 0.0059 19.3343 3748.115755 4 0.0002 67 | 0/8 4 h-lim-p 0.0006 0.0465 4.9508 3748.112629 2 0.0003 83 | 0/8 5 h-lim-p 0.0016 0.2245 0.8880 3748.112504 1 0.0003 98 | 0/8 6 h-lim-p 0.0028 1.6760 0.1098 3748.112501 0 0.0003 120 | 0/8 7 h-lim-p 0.0032 20.0000 0.0106 3748.112405 0 0.0253 143 | 0/8 8 h-lim-p 0.0029 1.8266 0.0909 3748.109799 0 0.0117 165 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3748.109770 1 0.9961 187 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3748.109770 0 2.1875 207 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3748.109770 0 0.5469 228 | 0/8 12 h-lim-p 0.1329 20.0000 0.0000 3748.109770 0 0.0001 257 Out... lnL = -3748.109770 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3748.109770 Node 7: lnL = -3748.109770 Node 8: lnL = -3748.109770 Node 9: lnL = -3748.109770 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 477 Sequential format.. Reading seq # 1: YGR132C_Sbay Reading seq # 2: YGR132C_Scer Reading seq # 3: YGR132C_Skud Reading seq # 4: YGR132C_Smik Reading seq # 5: YGR132C_Spar Sequences read.. Counting patterns.. # site patterns = 209 Counting frequencies.. 120 bytes for distance 33440 bytes for lkl0 26752 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.141441 0.140333 0.079612 0.164351 0.122740 0.223922 0.235119 0.129765 lnL0 = -2280.666693 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2280.666693 x= 0.14144 0.14033 0.07961 0.16435 0.12274 0.22392 0.23512 0.12977 1 h-lim-p 0.0045 0.0360 35.7636 2280.356328 7 0.0005 38 | 0/8 2 h-lim-p 0.0019 0.0270 9.3804 2280.327139 6 0.0007 64 | 0/8 3 h-lim-p 0.0019 0.0760 3.5175 2280.324271 5 0.0005 88 | 0/8 4 h-lim-p 0.0039 0.8694 0.4775 2280.324186 2 0.0008 105 | 0/8 5 h-lim-p 0.0022 1.5503 0.1645 2280.324175 1 0.0009 127 | 0/8 6 h-lim-p 0.0077 16.2477 0.0187 2280.324175 0 0.0008 149 | 0/8 7 h-lim-p 0.0096 20.0000 0.0016 2280.324175 0 0.0021 170 | 0/8 8 h-lim-p 0.1310 20.0000 0.0000 2280.324175 0 1.0481 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2280.324175 0 1.0938 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2280.324175 0 1.0938 233 | 0/8 11 h-lim-p 1.2916 20.0000 0.0000 2280.324175 0 0.3229 254 | 0/8 12 h-lim-p 0.1387 20.0000 0.0000 2280.324175 0 0.0005 281 Out... lnL = -2280.324175 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2280.324175 Node 7: lnL = -2280.324175 Node 8: lnL = -2280.324175 Node 9: lnL = -2280.324175 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 532 Sequential format.. Reading seq # 1: YGR133W_Sbay Reading seq # 2: YGR133W_Scer Reading seq # 3: YGR133W_Skud Reading seq # 4: YGR133W_Smik Reading seq # 5: YGR133W_Spar Sequences read.. Counting patterns.. # site patterns = 239 Counting frequencies.. 120 bytes for distance 38240 bytes for lkl0 30592 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.169098 0.084293 0.071488 0.158843 0.124892 0.228398 0.282134 0.157361 lnL0 = -2540.292778 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2540.292778 x= 0.16910 0.08429 0.07149 0.15884 0.12489 0.22840 0.28213 0.15736 1 h-lim-p 0.0023 0.0183 70.6774 2539.260669 7 0.0004 36 | 0/8 2 h-lim-p 0.0011 0.0090 20.3865 2539.146845 4 0.0006 57 | 0/8 3 h-lim-p 0.0015 0.0552 7.8954 2539.131071 4 0.0006 77 | 0/8 4 h-lim-p 0.0018 0.1272 2.5001 2539.128727 2 0.0009 93 | 0/8 5 h-lim-p 0.0027 0.3181 0.7883 2539.128529 3 0.0007 112 | 0/8 6 h-lim-p 0.0076 4.8066 0.0745 2539.128526 0 0.0008 134 | 0/8 7 h-lim-p 0.0041 12.8105 0.0151 2539.128525 0 0.0036 154 | 0/8 8 h-lim-p 0.0182 20.0000 0.0030 2539.128137 0 0.2917 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2539.128124 1 0.9961 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2539.128124 0 1.2500 220 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2539.128124 0 0.2344 243 | 0/8 12 h-lim-p 0.1214 20.0000 0.0000 2539.128124 0 0.0076 266 | 0/8 13 h-lim-p 0.0046 20.0000 0.0000 2539.128124 0 0.0000 302 Out... lnL = -2539.128124 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2539.128124 Node 7: lnL = -2539.128124 Node 8: lnL = -2539.128124 Node 9: lnL = -2539.128124 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 282 Sequential format.. Reading seq # 1: YGR136W_Sbay Reading seq # 2: YGR136W_Scer Reading seq # 3: YGR136W_Skud Reading seq # 4: YGR136W_Smik Reading seq # 5: YGR136W_Spar Sequences read.. Counting patterns.. # site patterns = 111 Counting frequencies.. 120 bytes for distance 17760 bytes for lkl0 14208 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.110038 0.024248 0.047267 0.110483 0.066284 0.164848 0.188088 0.102674 lnL0 = -1151.937426 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1151.937426 x= 0.11004 0.02425 0.04727 0.11048 0.06628 0.16485 0.18809 0.10267 1 h-lim-p 0.0003 0.0027 146.7271 1149.524872 7 0.0003 36 | 0/8 2 h-lim-p 0.0005 0.0043 20.2643 1149.413758 5 0.0005 59 | 0/8 3 h-lim-p 0.0016 0.0540 6.9862 1149.404680 5 0.0004 82 | 0/8 4 h-lim-p 0.0026 0.1359 1.1132 1149.404140 4 0.0009 105 | 0/8 5 h-lim-p 0.0026 0.7833 0.3855 1149.404096 2 0.0007 122 | 0/8 6 h-lim-p 0.0049 4.2593 0.0533 1149.404094 2 0.0016 148 | 0/8 7 h-lim-p 0.0098 19.8854 0.0087 1149.404089 0 0.0086 168 | 0/8 8 h-lim-p 0.0115 10.1091 0.0065 1149.403570 0 0.0917 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1149.403552 2 0.9961 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1149.403552 0 1.0938 235 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1149.403552 0 3.7500 255 | 0/8 12 h-lim-p 2.1792 20.0000 0.0000 1149.403552 0 0.2384 277 | 0/8 13 h-lim-p 0.7961 20.0000 0.0000 1149.403552 0 0.0062 303 Out... lnL = -1149.403552 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1149.403552 Node 7: lnL = -1149.403552 Node 8: lnL = -1149.403552 Node 9: lnL = -1149.403552 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 308 Sequential format.. Reading seq # 1: YGR141W_Sbay Reading seq # 2: YGR141W_Scer Reading seq # 3: YGR141W_Skud Reading seq # 4: YGR141W_Smik Reading seq # 5: YGR141W_Spar Sequences read.. Counting patterns.. # site patterns = 173 Counting frequencies.. 120 bytes for distance 27680 bytes for lkl0 22144 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.162013 0.063538 0.097154 0.172713 0.129993 0.246114 0.289483 0.149955 lnL0 = -1476.759565 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1476.759565 x= 0.16201 0.06354 0.09715 0.17271 0.12999 0.24611 0.28948 0.14996 1 h-lim-p 0.0020 0.0162 34.5204 1476.316511 5 0.0008 32 | 0/8 2 h-lim-p 0.0036 0.0291 5.5487 1476.302466 4 0.0009 53 | 0/8 3 h-lim-p 0.0030 0.1031 1.7284 1476.300992 5 0.0011 77 | 0/8 4 h-lim-p 0.0029 0.2222 0.6388 1476.300634 4 0.0020 100 | 0/8 5 h-lim-p 0.0100 2.1210 0.1270 1476.300622 2 0.0017 127 | 0/8 6 h-lim-p 0.0132 17.8306 0.0159 1476.300622 0 0.0017 149 | 0/8 7 h-lim-p 0.0579 20.0000 0.0005 1476.300601 0 0.4632 172 | 0/8 8 h-lim-p 0.0032 2.6380 0.0664 1476.300585 1 0.0033 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1476.300585 0 1.0938 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1476.300585 0 1.0938 234 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1476.300585 0 2.1875 254 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1476.300585 0 0.6250 275 | 0/8 13 h-lim-p 0.3605 20.0000 0.0000 1476.300585 0 0.0901 296 | 0/8 14 h-lim-p 0.0441 20.0000 0.0000 1476.300585 0 0.0055 318 Out... lnL = -1476.300585 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1476.300585 Node 7: lnL = -1476.300585 Node 8: lnL = -1476.300585 Node 9: lnL = -1476.300585 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 530 Sequential format.. Reading seq # 1: YGR142W_Sbay Reading seq # 2: YGR142W_Scer Reading seq # 3: YGR142W_Skud Reading seq # 4: YGR142W_Smik Reading seq # 5: YGR142W_Spar Sequences read.. Counting patterns.. # site patterns = 246 Counting frequencies.. 120 bytes for distance 39360 bytes for lkl0 31488 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.139759 0.074302 0.096292 0.134697 0.135925 0.262532 0.333133 0.127716 lnL0 = -2578.919276 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2578.919276 x= 0.13976 0.07430 0.09629 0.13470 0.13592 0.26253 0.33313 0.12772 1 h-lim-p 0.0042 1.0034 110.3381 2576.405658 7 0.0005 37 | 0/8 2 h-lim-p 0.0007 0.0058 32.5647 2575.941064 0 0.0011 49 | 0/8 3 h-lim-p 0.0018 0.0143 15.1793 2575.890199 7 0.0005 80 | 0/8 4 h-lim-p 0.0013 0.0618 6.2508 2575.871619 5 0.0011 101 | 0/8 5 h-lim-p 0.0074 0.3602 0.9738 2575.871222 2 0.0008 119 | 0/8 6 h-lim-p 0.0020 1.2813 0.3934 2575.871082 2 0.0016 143 | 0/8 7 h-lim-p 0.0109 3.8145 0.0576 2575.870765 2 0.0108 167 | 0/8 8 h-lim-p 0.0054 17.9662 0.1157 2575.851319 0 0.0430 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0011 2575.850586 3 1.2347 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2575.850577 0 1.0938 237 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2575.850577 0 1.0938 257 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2575.850577 0 0.0781 281 | 0/8 13 h-lim-p 0.0392 20.0000 0.0000 2575.850577 0 0.0000 311 Out... lnL = -2575.850577 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2575.850577 Node 7: lnL = -2575.850577 Node 8: lnL = -2575.850577 Node 9: lnL = -2575.850577 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 884 Sequential format.. Reading seq # 1: YGR143W_Sbay Reading seq # 2: YGR143W_Scer Reading seq # 3: YGR143W_Skud Reading seq # 4: YGR143W_Smik Reading seq # 5: YGR143W_Spar Sequences read.. Counting patterns.. # site patterns = 237 Counting frequencies.. 120 bytes for distance 37920 bytes for lkl0 30336 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.087462 0.044221 0.025520 0.091887 0.085907 0.155238 0.147153 0.080934 lnL0 = -3466.038822 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3466.038822 x= 0.08746 0.04422 0.02552 0.09189 0.08591 0.15524 0.14715 0.08093 1 h-lim-p 0.0007 0.0187 314.1816 3463.136558 5 0.0001 34 | 0/8 2 h-lim-p 0.0005 0.0037 42.7985 3462.990177 6 0.0002 61 | 0/8 3 h-lim-p 0.0006 0.0198 10.9044 3462.979367 5 0.0002 88 | 0/8 4 h-lim-p 0.0007 0.0554 3.0829 3462.978502 5 0.0002 113 | 0/8 5 h-lim-p 0.0103 3.0283 0.0588 3462.978502 0 0.0003 129 | 0/8 6 h-lim-p 0.0006 7.1109 0.0264 3462.978502 0 0.0003 149 | 0/8 7 h-lim-p 0.0010 20.0000 0.0070 3462.978502 0 0.0010 169 | 0/8 8 h-lim-p 0.0078 20.0000 0.0009 3462.978396 0 0.1860 193 | 0/8 9 h-lim-p 1.2658 20.0000 0.0001 3462.978385 0 1.1075 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3462.978384 0 1.0938 233 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3462.978384 0 2.1875 253 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3462.978384 0 0.1367 276 | 0/8 13 h-lim-p 0.0899 20.0000 0.0000 3462.978384 0 0.0098 298 | 0/8 14 h-lim-p 0.0038 20.0000 0.0000 3462.978384 0 0.0058 318 | 0/8 15 h-lim-p 0.0034 20.0000 0.0000 3462.978384 0 0.0001 343 Out... lnL = -3462.978384 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3462.978384 Node 7: lnL = -3462.978384 Node 8: lnL = -3462.978384 Node 9: lnL = -3462.978384 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 937 Sequential format.. Reading seq # 1: YGR144W_Sbay Reading seq # 2: YGR144W_Scer Reading seq # 3: YGR144W_Skud Reading seq # 4: YGR144W_Smik Reading seq # 5: YGR144W_Spar Sequences read.. Counting patterns.. # site patterns = 321 Counting frequencies.. 120 bytes for distance 51360 bytes for lkl0 41088 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.114220 0.091733 0.097747 0.144025 0.053258 0.231858 0.215031 0.104281 lnL0 = -3740.177001 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3740.177001 x= 0.11422 0.09173 0.09775 0.14403 0.05326 0.23186 0.21503 0.10428 1 h-lim-p 0.0052 1.1973 119.8480 3738.342027 3 0.0003 31 | 0/8 2 h-lim-p 0.0008 0.0062 35.9044 3738.061442 8 0.0005 65 | 0/8 3 h-lim-p 0.0011 0.0115 15.7583 3738.014526 5 0.0004 88 | 0/8 4 h-lim-p 0.0009 0.0376 7.6135 3738.001654 5 0.0006 115 | 0/8 5 h-lim-p 0.0022 0.1044 1.9866 3738.000467 4 0.0007 139 | 0/8 6 h-lim-p 0.0085 2.4156 0.1554 3738.000459 1 0.0005 156 | 0/8 7 h-lim-p 0.0555 20.0000 0.0015 3738.000453 0 0.0555 176 | 0/8 8 h-lim-p 0.0036 20.0000 0.0226 3738.000348 0 0.0144 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3738.000339 1 0.9961 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3738.000339 0 1.2500 240 | 0/8 11 h-lim-p 1.4940 20.0000 0.0000 3738.000339 0 0.5603 261 | 0/8 12 h-lim-p 0.3174 20.0000 0.0000 3738.000339 0 0.0000 293 Out... lnL = -3738.000339 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3738.000339 Node 7: lnL = -3738.000339 Node 8: lnL = -3738.000339 Node 9: lnL = -3738.000339 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 874 Sequential format.. Reading seq # 1: YGR146C_Sbay Reading seq # 2: YGR146C_Scer Reading seq # 3: YGR146C_Skud Reading seq # 4: YGR146C_Smik Reading seq # 5: YGR146C_Spar Sequences read.. Counting patterns.. # site patterns = 235 Counting frequencies.. 120 bytes for distance 37600 bytes for lkl0 30080 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.100735 0.006103 0.053189 0.052982 0.050724 0.217006 0.120424 0.094449 lnL0 = -3203.066396 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3203.066396 x= 0.10073 0.00610 0.05319 0.05298 0.05072 0.21701 0.12042 0.09445 1 h-lim-p 0.0002 0.0012 503.5507 3197.992839 7 0.0001 37 | 0/8 2 h-lim-p 0.0002 0.0013 86.4777 3197.238156 0 0.0002 49 | 0/8 3 h-lim-p 0.0003 0.0026 73.5493 3196.950205 8 0.0002 84 | 0/8 4 h-lim-p 0.0002 0.0026 49.6030 3196.846215 7 0.0001 112 | 0/8 5 h-lim-p 0.0004 0.0071 18.1245 3196.825993 5 0.0002 135 | 0/8 6 h-lim-p 0.0014 0.0805 2.0624 3196.825530 4 0.0002 158 | 0/8 7 h-lim-p 0.0026 0.8507 0.1761 3196.825519 2 0.0004 177 | 0/8 8 h-lim-p 0.0168 20.0000 0.0045 3196.809295 0 0.5369 202 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 3196.808297 4 1.8338 232 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 3196.808281 1 1.0938 254 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3196.808281 0 1.0938 274 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3196.808281 0 0.0005 305 Out... lnL = -3196.808281 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3196.808281 Node 7: lnL = -3196.808281 Node 8: lnL = -3196.808281 Node 9: lnL = -3196.808281 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 411 Sequential format.. Reading seq # 1: YGR147C_Sbay Reading seq # 2: YGR147C_Scer Reading seq # 3: YGR147C_Skud Reading seq # 4: YGR147C_Smik Reading seq # 5: YGR147C_Spar Sequences read.. Counting patterns.. # site patterns = 181 Counting frequencies.. 120 bytes for distance 28960 bytes for lkl0 23168 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.112940 0.093780 0.101262 0.112399 0.129435 0.214114 0.165689 0.103144 lnL0 = -1878.547454 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1878.547454 x= 0.11294 0.09378 0.10126 0.11240 0.12943 0.21411 0.16569 0.10314 1 h-lim-p 0.0013 0.0101 65.7997 1877.559619 5 0.0005 32 | 0/8 2 h-lim-p 0.0016 0.0126 13.4293 1877.508533 7 0.0006 60 | 0/8 3 h-lim-p 0.0018 0.0733 4.3187 1877.503496 4 0.0006 82 | 0/8 4 h-lim-p 0.0017 0.1964 1.5512 1877.502729 2 0.0007 98 | 0/8 5 h-lim-p 0.0026 0.4486 0.4318 1877.502683 1 0.0006 113 | 0/8 6 h-lim-p 0.0759 20.0000 0.0032 1877.502683 0 0.0010 138 | 0/8 7 h-lim-p 0.0114 20.0000 0.0003 1877.502683 0 0.0457 160 | 0/8 8 h-lim-p 0.0055 20.0000 0.0024 1877.502681 0 0.0221 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1877.502681 0 1.0938 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1877.502681 0 1.0938 222 | 0/8 11 h-lim-p 1.3970 20.0000 0.0000 1877.502681 0 2.7940 243 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1877.502681 0 0.0002 276 Out... lnL = -1877.502681 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1877.502681 Node 7: lnL = -1877.502681 Node 8: lnL = -1877.502681 Node 9: lnL = -1877.502681 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 888 Sequential format.. Reading seq # 1: YGR149W_Sbay Reading seq # 2: YGR149W_Scer Reading seq # 3: YGR149W_Skud Reading seq # 4: YGR149W_Smik Reading seq # 5: YGR149W_Spar Sequences read.. Counting patterns.. # site patterns = 324 Counting frequencies.. 120 bytes for distance 51840 bytes for lkl0 41472 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.147872 0.041504 0.066862 0.155271 0.105667 0.217850 0.258431 0.137601 lnL0 = -4011.917351 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4011.917351 x= 0.14787 0.04150 0.06686 0.15527 0.10567 0.21785 0.25843 0.13760 1 h-lim-p 0.0025 0.1179 179.0194 4009.382260 9 0.0002 46 | 0/8 2 h-lim-p 0.0006 0.0051 31.2688 4009.236789 2 0.0003 62 | 0/8 3 h-lim-p 0.0007 0.0287 12.7429 4009.212253 2 0.0003 78 | 0/8 4 h-lim-p 0.0009 0.0623 4.9874 4009.208080 4 0.0004 97 | 0/8 5 h-lim-p 0.0021 0.3328 0.9295 4009.207920 3 0.0004 116 | 0/8 6 h-lim-p 0.0015 1.4665 0.2417 4009.207909 1 0.0004 139 | 0/8 7 h-lim-p 0.0020 6.9379 0.0446 4009.207908 0 0.0009 159 | 0/8 8 h-lim-p 0.0625 20.0000 0.0006 4009.207310 0 0.9998 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4009.207297 1 0.9961 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4009.207297 0 2.1875 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4009.207297 0 1.0938 245 | 0/8 12 h-lim-p 0.6669 20.0000 0.0000 4009.207297 0 5.3356 268 | 0/8 13 h-lim-p 1.6724 20.0000 0.0000 4009.207297 0 0.3658 289 | 0/8 14 h-lim-p 1.2330 20.0000 0.0000 4009.207297 0 0.0006 319 Out... lnL = -4009.207297 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4009.207297 Node 7: lnL = -4009.207297 Node 8: lnL = -4009.207297 Node 9: lnL = -4009.207297 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 827 Sequential format.. Reading seq # 1: YGR150C_Sbay Reading seq # 2: YGR150C_Scer Reading seq # 3: YGR150C_Skud Reading seq # 4: YGR150C_Smik Reading seq # 5: YGR150C_Spar Sequences read.. Counting patterns.. # site patterns = 382 Counting frequencies.. 120 bytes for distance 61120 bytes for lkl0 48896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.245780 0.000060 0.558207 0.278220 0.381629 0.185703 0.637684 0.221492 lnL0 = -4481.491281 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4481.491281 x= 0.24578 0.00006 0.55821 0.27822 0.38163 0.18570 0.63768 0.22149 1 h-lim-p 0.0000 0.0000 226.5321 4481.354030 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0121 74.7185 4474.269791 0 0.0026 42 | 1/8 3 h-lim-p 0.0011 0.0086 74.2412 4472.149680 1 0.0013 56 | 1/8 4 h-lim-p 0.0062 0.0514 16.2391 4471.798797 3 0.0026 74 | 1/8 5 h-lim-p 0.0141 0.1430 2.9725 4471.349748 1 0.0176 88 | 1/8 6 h-lim-p 0.0098 0.1224 5.3532 4466.864655 0 0.0293 101 | 1/8 7 h-lim-p 0.0106 0.0957 14.8014 4445.638986 0 0.0212 114 | 1/8 8 h-lim-p 1.1176 8.9411 0.0538 4444.945346 6 1.1574 137 | 1/8 9 h-lim-p 2.5000 20.0000 0.0248 4444.794549 6 1.6332 171 | 1/8 10 h-lim-p 2.5000 20.0000 0.0071 4444.770727 5 1.5934 202 | 1/8 11 h-lim-p 2.5000 20.0000 0.0018 4444.769945 2 1.1719 225 | 1/8 12 h-lim-p 2.5000 20.0000 0.0006 4444.769841 3 1.3437 251 | 1/8 13 h-lim-p 2.5000 20.0000 0.0001 4444.769837 1 1.2305 273 | 1/8 14 h-lim-p 2.5000 20.0000 0.0001 4444.769837 0 2.1875 292 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 4444.769837 0 1.0938 311 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 4444.769837 0 2.1875 330 | 1/8 17 h-lim-p 2.3586 20.0000 0.0000 4444.769837 0 1.0319 349 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 4444.769837 0 1.2500 368 | 1/8 19 h-lim-p 2.5000 20.0000 0.0000 4444.769837 0 1.2500 387 | 1/8 20 h-lim-p 1.2063 20.0000 0.0000 4444.769837 0 0.0000 423 Out... lnL = -4444.769837 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4444.769837 Node 7: lnL = -4444.769837 Node 8: lnL = -4444.769837 Node 9: lnL = -4444.769837 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 642 Sequential format.. Reading seq # 1: YGR153W_Sbay Reading seq # 2: YGR153W_Scer Reading seq # 3: YGR153W_Skud Reading seq # 4: YGR153W_Smik Reading seq # 5: YGR153W_Spar Sequences read.. Counting patterns.. # site patterns = 230 Counting frequencies.. 120 bytes for distance 36800 bytes for lkl0 29440 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.203586 0.103190 0.047370 0.123020 0.096174 0.202720 0.145059 0.185433 lnL0 = -2895.018977 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2895.018977 x= 0.20359 0.10319 0.04737 0.12302 0.09617 0.20272 0.14506 0.18543 1 h-lim-p 0.0075 0.0602 67.7722 2894.494424 7 0.0002 43 | 0/8 2 h-lim-p 0.0007 0.0056 20.6460 2894.422097 5 0.0004 66 | 0/8 3 h-lim-p 0.0010 0.0279 7.8708 2894.410749 2 0.0004 82 | 0/8 4 h-lim-p 0.0009 0.0549 3.5166 2894.409055 4 0.0003 103 | 0/8 5 h-lim-p 0.0026 0.8038 0.4527 2894.409019 3 0.0003 123 | 0/8 6 h-lim-p 0.0018 4.3471 0.0856 2894.409016 0 0.0008 143 | 0/8 7 h-lim-p 0.0442 20.0000 0.0016 2894.409016 0 0.0097 164 | 0/8 8 h-lim-p 0.0088 20.0000 0.0017 2894.408997 0 0.0703 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2894.408997 0 1.0938 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2894.408997 0 2.1875 227 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2894.408997 0 0.6250 248 | 0/8 12 h-lim-p 0.2324 20.0000 0.0000 2894.408997 0 0.1162 268 | 0/8 13 h-lim-p 0.0551 20.0000 0.0000 2894.408997 0 0.0000 304 Out... lnL = -2894.408997 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2894.408997 Node 7: lnL = -2894.408997 Node 8: lnL = -2894.408997 Node 9: lnL = -2894.408997 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 492 Sequential format.. Reading seq # 1: YGR156W_Sbay Reading seq # 2: YGR156W_Scer Reading seq # 3: YGR156W_Skud Reading seq # 4: YGR156W_Smik Reading seq # 5: YGR156W_Spar Sequences read.. Counting patterns.. # site patterns = 172 Counting frequencies.. 120 bytes for distance 27520 bytes for lkl0 22016 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.154590 0.053518 0.062648 0.078387 0.060357 0.141423 0.180785 0.140304 lnL0 = -2042.000679 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2042.000679 x= 0.15459 0.05352 0.06265 0.07839 0.06036 0.14142 0.18079 0.14030 1 h-lim-p 0.0005 0.0044 129.7957 2040.002448 3 0.0003 29 | 0/8 2 h-lim-p 0.0005 0.0043 22.3316 2039.931652 5 0.0003 52 | 0/8 3 h-lim-p 0.0005 0.0190 13.1123 2039.911257 6 0.0003 81 | 0/8 4 h-lim-p 0.0010 0.0546 3.9918 2039.907696 4 0.0005 103 | 0/8 5 h-lim-p 0.0020 0.2585 1.0289 2039.907479 2 0.0004 120 | 0/8 6 h-lim-p 0.0013 0.5991 0.3479 2039.907452 2 0.0005 136 | 0/8 7 h-lim-p 0.0044 6.5645 0.0393 2039.907451 0 0.0010 157 | 0/8 8 h-lim-p 0.0560 20.0000 0.0007 2039.906985 0 0.8955 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2039.906984 0 1.0938 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2039.906984 0 1.0938 221 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2039.906984 0 2.1875 241 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2039.906984 0 0.0781 265 | 0/8 13 h-lim-p 0.0238 20.0000 0.0000 2039.906984 0 0.0000 306 Out... lnL = -2039.906984 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2039.906984 Node 7: lnL = -2039.906984 Node 8: lnL = -2039.906984 Node 9: lnL = -2039.906984 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 452 Sequential format.. Reading seq # 1: YGR158C_Sbay Reading seq # 2: YGR158C_Scer Reading seq # 3: YGR158C_Skud Reading seq # 4: YGR158C_Smik Reading seq # 5: YGR158C_Spar Sequences read.. Counting patterns.. # site patterns = 156 Counting frequencies.. 120 bytes for distance 24960 bytes for lkl0 19968 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.126474 0.029250 0.031675 0.119152 0.090620 0.152294 0.225037 0.112383 lnL0 = -1827.050584 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1827.050584 x= 0.12647 0.02925 0.03167 0.11915 0.09062 0.15229 0.22504 0.11238 1 h-lim-p 0.0004 0.0031 182.8326 1823.998725 7 0.0002 37 | 0/8 2 h-lim-p 0.0004 0.0028 40.9988 1823.686563 7 0.0004 65 | 0/8 3 h-lim-p 0.0016 0.0404 9.4484 1823.669358 6 0.0004 89 | 0/8 4 h-lim-p 0.0024 0.0980 1.5992 1823.668755 3 0.0005 108 | 0/8 5 h-lim-p 0.0021 0.5543 0.3691 1823.668722 1 0.0005 123 | 0/8 6 h-lim-p 0.0030 2.5497 0.0639 1823.668720 1 0.0012 145 | 0/8 7 h-lim-p 0.0065 17.8042 0.0119 1823.668720 0 0.0014 166 | 0/8 8 h-lim-p 0.0431 20.0000 0.0004 1823.668647 0 0.6900 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1823.668635 1 1.0938 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1823.668635 0 1.2500 232 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1823.668635 0 0.5469 253 | 0/8 12 h-lim-p 0.4166 20.0000 0.0000 1823.668635 0 0.0065 278 | 0/8 13 h-lim-p 0.0036 20.0000 0.0000 1823.668635 0 0.0036 298 | 0/8 14 h-lim-p 0.0037 20.0000 0.0000 1823.668635 0 0.0000 340 Out... lnL = -1823.668635 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1823.668635 Node 7: lnL = -1823.668635 Node 8: lnL = -1823.668635 Node 9: lnL = -1823.668635 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 869 Sequential format.. Reading seq # 1: YGR159C_Sbay Reading seq # 2: YGR159C_Scer Reading seq # 3: YGR159C_Skud Reading seq # 4: YGR159C_Smik Reading seq # 5: YGR159C_Spar Sequences read.. Counting patterns.. # site patterns = 271 Counting frequencies.. 120 bytes for distance 43360 bytes for lkl0 34688 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.128481 0.047497 0.036528 0.153370 0.120231 0.168873 0.025348 0.115610 lnL0 = -3370.399111 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3370.399111 x= 0.12848 0.04750 0.03653 0.15337 0.12023 0.16887 0.02535 0.11561 1 h-lim-p 0.0001 0.0083 937.7559 3340.745564 0 0.0002 23 | 0/8 2 h-lim-p 0.0002 0.0019 70.3238 3340.104202 6 0.0003 48 | 0/8 3 h-lim-p 0.0004 0.0035 23.4843 3339.991361 4 0.0005 68 | 0/8 4 h-lim-p 0.0005 0.0043 19.5286 3339.900516 0 0.0008 80 | 0/8 5 h-lim-p 0.0012 0.0096 7.8054 3339.892016 6 0.0004 107 | 0/8 6 h-lim-p 0.0013 0.0854 2.0852 3339.891353 2 0.0003 124 | 0/8 7 h-lim-p 0.0020 0.5454 0.3203 3339.891210 2 0.0010 141 | 0/8 8 h-lim-p 0.0185 10.5060 0.0174 3339.520957 0 1.7769 167 | 0/8 9 h-lim-p 0.9544 7.6351 0.0093 3339.477463 2 0.9544 191 | 0/8 10 h-lim-p 2.5000 20.0000 0.0004 3339.477338 3 0.8800 218 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3339.477337 0 1.0938 238 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3339.477337 0 1.0938 258 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 3339.477337 0 2.1875 278 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 3339.477337 0 0.6250 299 | 0/8 15 h-lim-p 0.2008 20.0000 0.0000 3339.477337 0 0.0125 322 | 0/8 16 h-lim-p 0.0050 20.0000 0.0000 3339.477337 0 0.0000 349 Out... lnL = -3339.477337 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3339.477337 Node 7: lnL = -3339.477337 Node 8: lnL = -3339.477337 Node 9: lnL = -3339.477337 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 885 Sequential format.. Reading seq # 1: YGR161C_Sbay Reading seq # 2: YGR161C_Scer Reading seq # 3: YGR161C_Skud Reading seq # 4: YGR161C_Smik Reading seq # 5: YGR161C_Spar Sequences read.. Counting patterns.. # site patterns = 241 Counting frequencies.. 120 bytes for distance 38560 bytes for lkl0 30848 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.122071 0.037413 0.026224 0.072166 0.055804 0.128852 0.133999 0.111021 lnL0 = -3282.983248 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3282.983248 x= 0.12207 0.03741 0.02622 0.07217 0.05580 0.12885 0.13400 0.11102 1 h-lim-p 0.0009 0.5058 268.4936 3280.159862 7 0.0001 37 | 0/8 2 h-lim-p 0.0001 0.0009 80.2208 3279.674866 0 0.0002 49 | 0/8 3 h-lim-p 0.0005 0.0058 27.7184 3279.610990 6 0.0002 74 | 0/8 4 h-lim-p 0.0006 0.0098 8.7617 3279.607284 4 0.0001 97 | 0/8 5 h-lim-p 0.0006 0.1370 1.6725 3279.606942 2 0.0003 113 | 0/8 6 h-lim-p 0.0016 0.5117 0.2786 3279.606936 1 0.0002 129 | 0/8 7 h-lim-p 0.0042 20.0000 0.0105 3279.606903 0 0.0126 150 | 0/8 8 h-lim-p 0.0034 10.3662 0.0394 3279.604603 0 0.0202 172 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3279.604556 2 1.0938 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3279.604555 0 1.0938 216 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3279.604555 0 1.0938 236 | 0/8 12 h-lim-p 1.3661 20.0000 0.0000 3279.604555 0 4.0982 257 | 0/8 13 h-lim-p 2.0789 20.0000 0.0000 3279.604555 0 0.0162 283 | 0/8 14 h-lim-p 0.0292 20.0000 0.0000 3279.604555 0 0.0001 310 Out... lnL = -3279.604555 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3279.604555 Node 7: lnL = -3279.604555 Node 8: lnL = -3279.604555 Node 9: lnL = -3279.604555 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 871 Sequential format.. Reading seq # 1: YGR162W_Sbay Reading seq # 2: YGR162W_Scer Reading seq # 3: YGR162W_Skud Reading seq # 4: YGR162W_Smik Reading seq # 5: YGR162W_Spar Sequences read.. Counting patterns.. # site patterns = 332 Counting frequencies.. 120 bytes for distance 53120 bytes for lkl0 42496 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.132737 0.022030 0.012138 0.151418 0.194994 0.254840 0.205801 0.115737 lnL0 = -4064.494478 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4064.494478 x= 0.13274 0.02203 0.01214 0.15142 0.19499 0.25484 0.20580 0.11574 1 h-lim-p 0.0002 0.1898 695.3365 4050.076978 3 0.0001 29 | 0/8 2 h-lim-p 0.0003 0.0021 61.4730 4049.483269 0 0.0004 41 | 0/8 3 h-lim-p 0.0012 0.0153 20.6715 4049.399887 7 0.0004 70 | 0/8 4 h-lim-p 0.0022 0.0901 3.9965 4049.397083 4 0.0004 93 | 0/8 5 h-lim-p 0.0016 0.4237 0.9147 4049.396874 4 0.0005 116 | 0/8 6 h-lim-p 0.0028 1.1850 0.1599 4049.396831 1 0.0011 138 | 0/8 7 h-lim-p 0.0020 1.5185 0.0894 4049.396160 0 0.0080 160 | 0/8 8 h-lim-p 0.0029 0.5500 0.2451 4049.374197 0 0.0176 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 4049.373816 2 1.0889 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4049.373799 2 1.9287 230 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4049.373798 0 1.0938 250 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4049.373798 0 1.0938 270 | 0/8 13 h-lim-p 1.1788 20.0000 0.0000 4049.373798 0 2.3576 291 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 4049.373798 0 0.3125 313 | 0/8 15 h-lim-p 0.0475 20.0000 0.0000 4049.373798 0 0.0119 334 | 0/8 16 h-lim-p 0.0035 20.0000 0.0001 4049.373798 0 0.0000 370 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 4049.373798 0 0.0000 402 Out... lnL = -4049.373798 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4049.373798 Node 7: lnL = -4049.373798 Node 8: lnL = -4049.373798 Node 9: lnL = -4049.373798 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 726 Sequential format.. Reading seq # 1: YGR163W_Sbay Reading seq # 2: YGR163W_Scer Reading seq # 3: YGR163W_Skud Reading seq # 4: YGR163W_Smik Reading seq # 5: YGR163W_Spar Sequences read.. Counting patterns.. # site patterns = 188 Counting frequencies.. 120 bytes for distance 30080 bytes for lkl0 24064 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.072697 0.110640 0.025294 0.099297 0.092620 0.123874 0.100535 0.061115 lnL0 = -2720.430966 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2720.430966 x= 0.07270 0.11064 0.02529 0.09930 0.09262 0.12387 0.10053 0.06112 1 h-lim-p 0.0040 0.9844 117.2679 2719.805760 4 0.0001 34 | 0/8 2 h-lim-p 0.0004 0.0053 25.8976 2719.731567 5 0.0002 57 | 0/8 3 h-lim-p 0.0007 0.0152 9.2306 2719.724260 5 0.0002 81 | 0/8 4 h-lim-p 0.0017 0.1395 1.0148 2719.724157 0 0.0002 95 | 0/8 5 h-lim-p 0.0024 1.4407 0.0928 2719.724156 0 0.0003 109 | 0/8 6 h-lim-p 0.0036 20.0000 0.0067 2719.724156 0 0.0004 131 | 0/8 7 h-lim-p 0.0078 20.0000 0.0003 2719.724156 0 0.0313 153 | 0/8 8 h-lim-p 0.0013 5.0819 0.0080 2719.724149 0 0.0053 175 | 0/8 9 h-lim-p 1.1083 20.0000 0.0000 2719.724148 0 1.1083 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2719.724148 0 1.2500 215 | 0/8 11 h-lim-p 1.5745 20.0000 0.0000 2719.724148 0 0.3444 236 | 0/8 12 h-lim-p 0.1751 20.0000 0.0000 2719.724148 0 0.0014 262 | 0/8 13 h-lim-p 0.0013 20.0000 0.0000 2719.724148 0 0.0001 285 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 2719.724148 0 0.0000 312 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 2719.724148 0 0.0000 347 Out... lnL = -2719.724148 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2719.724148 Node 7: lnL = -2719.724148 Node 8: lnL = -2719.724148 Node 9: lnL = -2719.724148 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 156 Sequential format.. Reading seq # 1: YGR165W_Sbay Reading seq # 2: YGR165W_Scer Reading seq # 3: YGR165W_Skud Reading seq # 4: YGR165W_Smik Reading seq # 5: YGR165W_Spar Sequences read.. Counting patterns.. # site patterns = 63 Counting frequencies.. 120 bytes for distance 10080 bytes for lkl0 8064 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.105853 0.046230 0.103269 0.098857 0.051268 0.075715 0.155579 0.093488 lnL0 = -627.534273 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 627.534273 x= 0.10585 0.04623 0.10327 0.09886 0.05127 0.07572 0.15558 0.09349 1 h-lim-p 0.0028 0.0227 34.8861 627.240990 6 0.0005 36 | 0/8 2 h-lim-p 0.0022 0.0180 7.3794 627.217360 5 0.0009 57 | 0/8 3 h-lim-p 0.0036 0.0506 1.8662 627.215453 4 0.0012 79 | 0/8 4 h-lim-p 0.0040 0.7834 0.5523 627.215301 4 0.0011 100 | 0/8 5 h-lim-p 0.0056 1.2312 0.1050 627.215296 2 0.0009 126 | 0/8 6 h-lim-p 0.0041 13.3863 0.0231 627.215296 0 0.0009 147 | 0/8 7 h-lim-p 0.0104 20.0000 0.0020 627.215295 0 0.0208 168 | 0/8 8 h-lim-p 0.0122 20.0000 0.0034 627.215261 0 0.0735 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 627.215260 1 0.9961 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 627.215260 0 0.0049 240 | 0/8 11 h-lim-p 0.0024 20.0000 0.0000 627.215260 0 0.0006 261 Out... lnL = -627.215260 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -627.215260 Node 7: lnL = -627.215260 Node 8: lnL = -627.215260 Node 9: lnL = -627.215260 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 885 Sequential format.. Reading seq # 1: YGR169C_Sbay Reading seq # 2: YGR169C_Scer Reading seq # 3: YGR169C_Skud Reading seq # 4: YGR169C_Smik Reading seq # 5: YGR169C_Spar Sequences read.. Counting patterns.. # site patterns = 273 Counting frequencies.. 120 bytes for distance 43680 bytes for lkl0 34944 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.099341 0.229125 0.000060 0.092374 0.135731 0.280036 0.162973 0.081450 lnL0 = -3387.884922 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3387.884922 x= 0.09934 0.22912 0.00006 0.09237 0.13573 0.28004 0.16297 0.08145 1 h-lim-p 0.0013 0.0102 143.5018 3385.400188 9 0.0002 48 | 0/8 2 h-lim-p 0.0004 0.0039 78.5233 3383.109048 0 0.0008 61 | 0/8 3 h-lim-p 0.0007 0.0052 66.3357 3382.210332 5 0.0007 84 | 0/8 4 h-lim-p 0.0011 0.0086 27.7761 3381.938528 5 0.0009 105 | 0/8 5 h-lim-p 0.0008 0.0068 27.4537 3381.861746 2 0.0004 121 | 0/8 6 h-lim-p 0.0019 0.0518 5.8094 3381.857109 5 0.0003 145 | 0/8 7 h-lim-p 0.0012 0.1199 1.5675 3381.856699 4 0.0003 167 | 0/8 8 h-lim-p 0.0648 19.6142 0.0079 3381.702910 0 1.0362 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0022 3381.700718 4 0.9169 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 3381.700694 2 0.7996 238 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3381.700694 0 1.0938 258 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3381.700694 0 1.0938 278 | 0/8 13 h-lim-p 1.1694 20.0000 0.0000 3381.700694 0 0.5847 298 | 0/8 14 h-lim-p 0.2567 20.0000 0.0000 3381.700694 0 0.0001 329 | 0/8 15 h-lim-p 0.0010 20.0000 0.0000 3381.700694 0 0.0000 360 Out... lnL = -3381.700694 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3381.700694 Node 7: lnL = -3381.700694 Node 8: lnL = -3381.700694 Node 9: lnL = -3381.700694 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 846 Sequential format.. Reading seq # 1: YGR170W_Sbay Reading seq # 2: YGR170W_Scer Reading seq # 3: YGR170W_Skud Reading seq # 4: YGR170W_Smik Reading seq # 5: YGR170W_Spar Sequences read.. Counting patterns.. # site patterns = 231 Counting frequencies.. 120 bytes for distance 36960 bytes for lkl0 29568 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.092122 0.065895 0.077803 0.086305 0.065258 0.179062 0.136790 0.079003 lnL0 = -3500.180215 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3500.180215 x= 0.09212 0.06590 0.07780 0.08631 0.06526 0.17906 0.13679 0.07900 1 h-lim-p 0.0019 0.5494 193.3216 3497.716259 8 0.0001 44 | 0/8 2 h-lim-p 0.0009 0.0072 26.4047 3497.647769 5 0.0002 66 | 0/8 3 h-lim-p 0.0005 0.0203 10.3695 3497.640848 5 0.0001 91 | 0/8 4 h-lim-p 0.0005 0.0746 2.9471 3497.640006 3 0.0002 109 | 0/8 5 h-lim-p 0.0014 0.7808 0.4646 3497.639985 2 0.0002 128 | 0/8 6 h-lim-p 0.0015 2.8016 0.0692 3497.639984 1 0.0004 151 | 0/8 7 h-lim-p 0.0029 20.0000 0.0090 3497.639983 0 0.0025 171 | 0/8 8 h-lim-p 0.0064 20.0000 0.0035 3497.639567 0 0.1020 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3497.639562 0 1.0938 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3497.639562 0 1.0938 235 | 0/8 11 h-lim-p 1.8172 20.0000 0.0000 3497.639562 0 1.5900 255 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3497.639562 0 1.2500 275 | 0/8 13 h-lim-p 0.6420 20.0000 0.0000 3497.639562 0 0.6420 295 | 0/8 14 h-lim-p 0.0661 20.0000 0.0001 3497.639562 0 0.0496 315 | 0/8 15 h-lim-p 0.0183 20.0000 0.0001 3497.639562 0 0.0183 335 | 0/8 16 h-lim-p 0.0060 20.0000 0.0004 3497.639562 0 0.0000 362 | 0/8 17 h-lim-p 0.0029 20.0000 0.0000 3497.639562 0 0.0001 386 Out... lnL = -3497.639562 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3497.639562 Node 7: lnL = -3497.639562 Node 8: lnL = -3497.639562 Node 9: lnL = -3497.639562 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 323 Sequential format.. Reading seq # 1: YGR171C_Sbay Reading seq # 2: YGR171C_Scer Reading seq # 3: YGR171C_Skud Reading seq # 4: YGR171C_Smik Reading seq # 5: YGR171C_Spar Sequences read.. Counting patterns.. # site patterns = 153 Counting frequencies.. 120 bytes for distance 24480 bytes for lkl0 19584 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.113961 0.139609 0.104813 0.139017 0.087900 0.311344 0.169168 0.094265 lnL0 = -1490.369967 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1490.369967 x= 0.11396 0.13961 0.10481 0.13902 0.08790 0.31134 0.16917 0.09426 1 h-lim-p 0.0017 0.0132 22.6724 1490.118952 8 0.0010 46 | 0/8 2 h-lim-p 0.0020 0.0157 10.8628 1490.084085 6 0.0007 71 | 0/8 3 h-lim-p 0.0020 0.0687 3.7209 1490.079319 4 0.0008 91 | 0/8 4 h-lim-p 0.0028 0.4174 1.0434 1490.078810 4 0.0010 113 | 0/8 5 h-lim-p 0.0022 0.5210 0.4794 1490.078724 3 0.0009 131 | 0/8 6 h-lim-p 0.0028 1.6895 0.1558 1490.078713 2 0.0009 156 | 0/8 7 h-lim-p 0.0098 11.6913 0.0139 1490.078713 0 0.0022 177 | 0/8 8 h-lim-p 0.0220 20.0000 0.0014 1490.078565 0 0.3524 201 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1490.078562 1 0.9961 223 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1490.078562 0 0.6250 244 | 0/8 11 h-lim-p 0.4458 20.0000 0.0000 1490.078562 0 0.2229 264 | 0/8 12 h-lim-p 0.1141 20.0000 0.0000 1490.078562 0 0.0285 285 | 0/8 13 h-lim-p 0.0149 20.0000 0.0000 1490.078562 0 0.0001 312 | 0/8 14 h-lim-p 0.0007 20.0000 0.0000 1490.078562 0 0.0000 342 Out... lnL = -1490.078562 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1490.078562 Node 7: lnL = -1490.078562 Node 8: lnL = -1490.078562 Node 9: lnL = -1490.078562 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 270 Sequential format.. Reading seq # 1: YGR172C_Sbay Reading seq # 2: YGR172C_Scer Reading seq # 3: YGR172C_Skud Reading seq # 4: YGR172C_Smik Reading seq # 5: YGR172C_Spar Sequences read.. Counting patterns.. # site patterns = 108 Counting frequencies.. 120 bytes for distance 17280 bytes for lkl0 13824 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.137365 0.029489 0.057106 0.093747 0.102164 0.220436 0.134752 0.122907 lnL0 = -1181.995323 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1181.995323 x= 0.13737 0.02949 0.05711 0.09375 0.10216 0.22044 0.13475 0.12291 1 h-lim-p 0.0016 0.0132 58.5538 1181.440633 7 0.0003 38 | 0/8 2 h-lim-p 0.0010 0.0082 13.0759 1181.390002 8 0.0006 72 | 0/8 3 h-lim-p 0.0026 0.0884 3.1296 1181.385261 3 0.0010 90 | 0/8 4 h-lim-p 0.0049 0.4142 0.6514 1181.385101 3 0.0008 111 | 0/8 5 h-lim-p 0.0025 0.7305 0.2099 1181.385089 0 0.0006 132 | 0/8 6 h-lim-p 0.0040 5.8296 0.0324 1181.385089 0 0.0009 153 | 0/8 7 h-lim-p 0.0038 11.2051 0.0075 1181.385089 0 0.0016 173 | 0/8 8 h-lim-p 0.1801 20.0000 0.0001 1181.385083 0 1.0807 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1181.385083 0 1.0938 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1181.385083 0 0.1562 238 | 0/8 11 h-lim-p 0.0934 20.0000 0.0000 1181.385083 0 0.0013 263 Out... lnL = -1181.385083 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1181.385083 Node 7: lnL = -1181.385083 Node 8: lnL = -1181.385083 Node 9: lnL = -1181.385083 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 309 Sequential format.. Reading seq # 1: YGR173W_Sbay Reading seq # 2: YGR173W_Scer Reading seq # 3: YGR173W_Skud Reading seq # 4: YGR173W_Smik Reading seq # 5: YGR173W_Spar Sequences read.. Counting patterns.. # site patterns = 113 Counting frequencies.. 120 bytes for distance 18080 bytes for lkl0 14464 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.144592 0.035487 0.060880 0.096396 0.099516 0.223059 0.127363 0.129766 lnL0 = -1245.125419 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1245.125419 x= 0.14459 0.03549 0.06088 0.09640 0.09952 0.22306 0.12736 0.12977 1 h-lim-p 0.0019 0.0154 45.7842 1244.741426 5 0.0004 32 | 0/8 2 h-lim-p 0.0015 0.0121 9.8627 1244.710860 5 0.0007 53 | 0/8 3 h-lim-p 0.0028 0.0744 2.3335 1244.708563 5 0.0009 77 | 0/8 4 h-lim-p 0.0033 0.3336 0.6253 1244.708440 3 0.0007 96 | 0/8 5 h-lim-p 0.0017 1.2587 0.2568 1244.708418 0 0.0008 116 | 0/8 6 h-lim-p 0.0088 5.2835 0.0247 1244.708417 0 0.0010 138 | 0/8 7 h-lim-p 0.0041 20.0000 0.0059 1244.708417 0 0.0018 158 | 0/8 8 h-lim-p 0.1838 20.0000 0.0001 1244.708414 0 1.1026 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1244.708414 0 1.0938 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1244.708414 0 2.1875 220 | 0/8 11 h-lim-p 2.4469 20.0000 0.0000 1244.708414 0 0.5353 241 | 0/8 12 h-lim-p 0.5919 20.0000 0.0000 1244.708414 0 0.0370 264 | 0/8 13 h-lim-p 0.0200 20.0000 0.0000 1244.708414 0 0.0000 305 Out... lnL = -1244.708414 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1244.708414 Node 7: lnL = -1244.708414 Node 8: lnL = -1244.708414 Node 9: lnL = -1244.708414 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 314 Sequential format.. Reading seq # 1: YGR175C_Sbay Reading seq # 2: YGR175C_Scer Reading seq # 3: YGR175C_Skud Reading seq # 4: YGR175C_Smik Reading seq # 5: YGR175C_Spar Sequences read.. Counting patterns.. # site patterns = 98 Counting frequencies.. 120 bytes for distance 15680 bytes for lkl0 12544 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.073405 0.027396 0.009329 0.039666 0.035397 0.099666 0.095014 0.063228 lnL0 = -997.978667 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 997.978667 x= 0.07340 0.02740 0.00933 0.03967 0.03540 0.09967 0.09501 0.06323 1 h-lim-p 0.0002 0.0019 101.8125 997.594998 7 0.0001 37 | 0/8 2 h-lim-p 0.0002 0.0013 57.0203 997.326266 0 0.0002 49 | 0/8 3 h-lim-p 0.0005 0.0038 21.9998 997.280038 5 0.0002 72 | 0/8 4 h-lim-p 0.0010 0.0168 5.2434 997.276904 4 0.0002 94 | 0/8 5 h-lim-p 0.0004 0.0615 2.8664 997.276126 5 0.0002 117 | 0/8 6 h-lim-p 0.0033 0.1504 0.2086 997.276122 1 0.0002 134 | 0/8 7 h-lim-p 0.0216 20.0000 0.0020 997.274640 0 0.6916 159 | 0/8 8 h-lim-p 0.0011 0.1019 1.1843 997.273320 5 0.0008 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 997.273185 3 1.0449 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 997.273184 0 1.0938 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 997.273184 0 2.5000 248 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 997.273184 0 0.1367 271 | 0/8 13 h-lim-p 0.1719 20.0000 0.0000 997.273184 0 0.0003 299 Out... lnL = -997.273184 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -997.273184 Node 7: lnL = -997.273184 Node 8: lnL = -997.273184 Node 9: lnL = -997.273184 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 622 Sequential format.. Reading seq # 1: YGR177C_Sbay Reading seq # 2: YGR177C_Scer Reading seq # 3: YGR177C_Skud Reading seq # 4: YGR177C_Smik Reading seq # 5: YGR177C_Spar Sequences read.. Counting patterns.. # site patterns = 212 Counting frequencies.. 120 bytes for distance 33920 bytes for lkl0 27136 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.093016 0.060345 0.074098 0.120533 0.095079 0.231227 0.158482 0.071589 lnL0 = -2515.040389 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2515.040389 x= 0.09302 0.06035 0.07410 0.12053 0.09508 0.23123 0.15848 0.07159 1 h-lim-p 0.0013 0.0105 122.9176 2513.424086 9 0.0002 45 | 0/8 2 h-lim-p 0.0009 0.0074 18.2666 2513.367444 7 0.0003 73 | 0/8 3 h-lim-p 0.0012 0.0347 5.1645 2513.363080 5 0.0004 98 | 0/8 4 h-lim-p 0.0011 0.1530 1.7219 2513.362476 2 0.0005 114 | 0/8 5 h-lim-p 0.0011 0.2647 0.7203 2513.362396 3 0.0004 133 | 0/8 6 h-lim-p 0.0066 5.2431 0.0394 2513.362395 0 0.0007 155 | 0/8 7 h-lim-p 0.0057 20.0000 0.0050 2513.362394 0 0.0050 175 | 0/8 8 h-lim-p 0.0080 20.0000 0.0031 2513.362254 0 0.0965 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2513.362254 0 1.0938 218 | 0/8 10 h-lim-p 2.2838 20.0000 0.0000 2513.362254 0 0.9992 238 | 0/8 11 h-lim-p 0.9448 20.0000 0.0000 2513.362254 0 0.1181 260 | 0/8 12 h-lim-p 0.0002 20.0000 0.0040 2513.362254 0 0.0000 292 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 2513.362254 0 0.0000 324 Out... lnL = -2513.362254 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2513.362254 Node 7: lnL = -2513.362254 Node 8: lnL = -2513.362254 Node 9: lnL = -2513.362254 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 477 Sequential format.. Reading seq # 1: YGR178C_Sbay Reading seq # 2: YGR178C_Scer Reading seq # 3: YGR178C_Skud Reading seq # 4: YGR178C_Smik Reading seq # 5: YGR178C_Spar Sequences read.. Counting patterns.. # site patterns = 153 Counting frequencies.. 120 bytes for distance 24480 bytes for lkl0 19584 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.105845 0.067674 0.046494 0.078988 0.042999 0.171652 0.203347 0.086858 lnL0 = -1926.997752 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1926.997752 x= 0.10585 0.06767 0.04649 0.07899 0.04300 0.17165 0.20335 0.08686 1 h-lim-p 0.0002 0.0016 45.1739 1926.804384 2 0.0002 26 | 0/8 2 h-lim-p 0.0007 0.0324 12.6844 1926.791287 5 0.0002 49 | 0/8 3 h-lim-p 0.0004 0.0221 5.7389 1926.786887 3 0.0003 67 | 0/8 4 h-lim-p 0.0011 0.0841 1.7032 1926.786523 2 0.0003 84 | 0/8 5 h-lim-p 0.0011 0.4914 0.4356 1926.786485 1 0.0004 98 | 0/8 6 h-lim-p 0.0035 3.9318 0.0519 1926.786485 0 0.0004 120 | 0/8 7 h-lim-p 0.0010 8.5191 0.0194 1926.786485 0 0.0009 140 | 0/8 8 h-lim-p 0.1091 20.0000 0.0002 1926.786444 0 0.8727 163 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1926.786443 0 1.0938 183 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1926.786443 0 1.0938 203 | 0/8 11 h-lim-p 1.2009 20.0000 0.0000 1926.786443 0 1.2009 223 | 0/8 12 h-lim-p 0.9405 20.0000 0.0000 1926.786443 0 0.4702 243 | 0/8 13 h-lim-p 0.0000 0.9780 0.1297 1926.786443 0 0.0000 263 | 0/8 14 h-lim-p 0.0012 20.0000 0.0016 1926.786443 0 0.0000 302 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1926.786443 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1926.786443 Node 7: lnL = -1926.786443 Node 8: lnL = -1926.786443 Node 9: lnL = -1926.786443 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 446 Sequential format.. Reading seq # 1: YGR179C_Sbay Reading seq # 2: YGR179C_Scer Reading seq # 3: YGR179C_Skud Reading seq # 4: YGR179C_Smik Reading seq # 5: YGR179C_Spar Sequences read.. Counting patterns.. # site patterns = 198 Counting frequencies.. 120 bytes for distance 31680 bytes for lkl0 25344 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.203656 0.007047 0.055713 0.156802 0.093594 0.271644 0.216697 0.176895 lnL0 = -1916.977184 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1916.977184 x= 0.20366 0.00705 0.05571 0.15680 0.09359 0.27164 0.21670 0.17690 1 h-lim-p 0.0015 0.0232 160.2210 1913.918630 8 0.0003 38 | 0/8 2 h-lim-p 0.0008 0.0061 22.6983 1913.746812 5 0.0007 59 | 0/8 3 h-lim-p 0.0015 0.0258 10.1490 1913.718661 5 0.0006 80 | 0/8 4 h-lim-p 0.0018 0.0677 3.7031 1913.713869 2 0.0008 96 | 0/8 5 h-lim-p 0.0043 0.1311 0.7231 1913.713674 4 0.0008 118 | 0/8 6 h-lim-p 0.0037 3.6964 0.1506 1913.713659 2 0.0014 142 | 0/8 7 h-lim-p 0.0546 20.0000 0.0040 1913.713659 0 0.0119 163 | 0/8 8 h-lim-p 0.0319 20.0000 0.0015 1913.713613 0 0.1275 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1913.713610 0 1.2500 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1913.713610 0 2.1875 225 | 0/8 11 h-lim-p 2.4865 20.0000 0.0000 1913.713610 0 1.0878 245 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1913.713610 0 1.0938 265 | 0/8 13 h-lim-p 1.7819 20.0000 0.0000 1913.713610 0 2.6729 285 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1913.713610 0 0.2344 308 | 0/8 15 h-lim-p 0.1285 20.0000 0.0000 1913.713610 0 0.0161 330 | 0/8 16 h-lim-p 0.0066 20.0000 0.0000 1913.713610 0 0.0000 366 Out... lnL = -1913.713610 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1913.713610 Node 7: lnL = -1913.713610 Node 8: lnL = -1913.713610 Node 9: lnL = -1913.713610 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 891 Sequential format.. Reading seq # 1: YGR180C_Sbay Reading seq # 2: YGR180C_Scer Reading seq # 3: YGR180C_Skud Reading seq # 4: YGR180C_Smik Reading seq # 5: YGR180C_Spar Sequences read.. Counting patterns.. # site patterns = 160 Counting frequencies.. 120 bytes for distance 25600 bytes for lkl0 20480 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.088418 0.025065 0.026183 0.054179 0.021785 0.091573 0.096454 0.077247 lnL0 = -2855.061857 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2855.061857 x= 0.08842 0.02506 0.02618 0.05418 0.02178 0.09157 0.09645 0.07725 1 h-lim-p 0.0002 0.0016 249.0554 2853.640172 4 0.0000 31 | 0/8 2 h-lim-p 0.0002 0.0018 34.7035 2853.581287 3 0.0001 49 | 0/8 3 h-lim-p 0.0002 0.0068 22.9295 2853.570153 4 0.0001 69 | 0/8 4 h-lim-p 0.0001 0.0064 11.2917 2853.567121 5 0.0001 92 | 0/8 5 h-lim-p 0.0009 0.1063 0.8035 2853.567088 0 0.0001 106 | 0/8 6 h-lim-p 0.0003 0.7592 0.2665 2853.567085 1 0.0001 128 | 0/8 7 h-lim-p 0.0032 14.8484 0.0112 2853.567085 0 0.0004 150 | 0/8 8 h-lim-p 0.0173 20.0000 0.0003 2853.566961 0 0.5523 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2853.566959 0 1.0938 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2853.566959 0 0.2734 217 | 0/8 11 h-lim-p 0.1598 20.0000 0.0000 2853.566959 0 0.0025 242 | 0/8 12 h-lim-p 0.0016 20.0000 0.0000 2853.566959 0 0.0004 263 | 0/8 13 h-lim-p 0.0006 20.0000 0.0000 2853.566959 0 0.0001 284 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 2853.566959 0 0.0000 304 | 0/8 15 h-lim-p 0.0013 20.0000 0.0000 2853.566959 0 0.0000 343 Out... lnL = -2853.566959 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2853.566959 Node 7: lnL = -2853.566959 Node 8: lnL = -2853.566959 Node 9: lnL = -2853.566959 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 878 Sequential format.. Reading seq # 1: YGR181W_Sbay Reading seq # 2: YGR181W_Scer Reading seq # 3: YGR181W_Skud Reading seq # 4: YGR181W_Smik Reading seq # 5: YGR181W_Spar Sequences read.. Counting patterns.. # site patterns = 456 Counting frequencies.. 120 bytes for distance 72960 bytes for lkl0 58368 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.421601 0.020997 0.226669 0.224666 0.151261 0.386140 0.495543 0.368254 lnL0 = -4839.995665 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4839.995665 x= 0.42160 0.02100 0.22667 0.22467 0.15126 0.38614 0.49554 0.36825 1 h-lim-p 0.0058 0.0465 71.2606 4838.090598 8 0.0008 42 | 0/8 2 h-lim-p 0.0009 0.0071 38.7901 4837.577473 2 0.0008 58 | 0/8 3 h-lim-p 0.0009 0.0160 36.3699 4837.246601 5 0.0009 80 | 0/8 4 h-lim-p 0.0033 0.0614 9.6654 4837.171177 6 0.0019 107 | 0/8 5 h-lim-p 0.0027 0.1083 6.7262 4837.136630 5 0.0022 130 | 0/8 6 h-lim-p 0.0102 0.4544 1.4652 4837.134222 2 0.0024 147 | 0/8 7 h-lim-p 0.0111 0.8825 0.3176 4837.134139 3 0.0015 167 | 0/8 8 h-lim-p 0.1333 20.0000 0.0035 4837.125491 0 1.0661 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0008 4837.125392 2 0.9644 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4837.125392 0 1.0938 234 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4837.125392 0 1.0938 254 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4837.125392 0 2.1875 274 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 4837.125392 0 1.0938 294 | 0/8 14 h-lim-p 0.2335 20.0000 0.0000 4837.125392 0 0.0000 330 Out... lnL = -4837.125392 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4837.125392 Node 7: lnL = -4837.125392 Node 8: lnL = -4837.125392 Node 9: lnL = -4837.125392 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 273 Sequential format.. Reading seq # 1: YGR185C_Sbay Reading seq # 2: YGR185C_Scer Reading seq # 3: YGR185C_Skud Reading seq # 4: YGR185C_Smik Reading seq # 5: YGR185C_Spar Sequences read.. Counting patterns.. # site patterns = 125 Counting frequencies.. 120 bytes for distance 20000 bytes for lkl0 16000 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.099809 0.112754 0.072172 0.082323 0.062866 0.264273 0.211864 0.076109 lnL0 = -1198.616265 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1198.616265 x= 0.09981 0.11275 0.07217 0.08232 0.06287 0.26427 0.21186 0.07611 1 h-lim-p 0.0020 0.0161 35.7092 1198.271662 9 0.0006 45 | 0/8 2 h-lim-p 0.0014 0.0111 8.3689 1198.254479 6 0.0005 72 | 0/8 3 h-lim-p 0.0009 0.0441 4.9220 1198.246128 3 0.0009 90 | 0/8 4 h-lim-p 0.0037 0.1206 1.1879 1198.245582 2 0.0009 107 | 0/8 5 h-lim-p 0.0027 1.0212 0.3774 1198.245492 2 0.0013 124 | 0/8 6 h-lim-p 0.0061 1.7052 0.0831 1198.245490 0 0.0007 146 | 0/8 7 h-lim-p 0.0038 20.0000 0.0147 1198.245490 0 0.0017 166 | 0/8 8 h-lim-p 0.2415 20.0000 0.0001 1198.245483 0 0.9661 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1198.245483 0 1.0938 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1198.245483 0 2.1875 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1198.245483 0 0.5469 249 | 0/8 12 h-lim-p 0.0759 20.0000 0.0000 1198.245483 0 0.0095 271 | 0/8 13 h-lim-p 0.0043 20.0000 0.0000 1198.245483 0 0.0000 306 Out... lnL = -1198.245483 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1198.245483 Node 7: lnL = -1198.245483 Node 8: lnL = -1198.245483 Node 9: lnL = -1198.245483 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 847 Sequential format.. Reading seq # 1: YGR188C_Sbay Reading seq # 2: YGR188C_Scer Reading seq # 3: YGR188C_Skud Reading seq # 4: YGR188C_Smik Reading seq # 5: YGR188C_Spar Sequences read.. Counting patterns.. # site patterns = 468 Counting frequencies.. 120 bytes for distance 74880 bytes for lkl0 59904 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.292539 0.000060 0.197772 0.518670 0.341492 0.319697 0.498879 0.243063 lnL0 = -4615.868529 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4615.868529 x= 0.29254 0.00006 0.19777 0.51867 0.34149 0.31970 0.49888 0.24306 1 h-lim-p 0.0000 0.0000 118.7307 4615.849651 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0083 109.6330 4609.856877 0 0.0019 41 | 1/8 3 h-lim-p 0.0027 0.0220 30.0801 4609.302025 5 0.0014 63 | 1/8 4 h-lim-p 0.0024 0.0274 17.0603 4609.075124 4 0.0019 83 | 1/8 5 h-lim-p 0.0063 0.2059 5.1350 4608.969785 3 0.0053 101 | 1/8 6 h-lim-p 0.0185 0.3597 1.4678 4608.600900 0 0.0277 113 | 1/8 7 h-lim-p 0.0078 0.1512 5.2280 4601.806104 0 0.0311 127 | 1/8 8 h-lim-p 0.9325 7.4603 0.0651 4601.127232 5 0.7254 149 | 1/8 9 h-lim-p 2.5000 20.0000 0.0119 4601.108628 6 0.7509 184 | 1/8 10 h-lim-p 2.5000 20.0000 0.0032 4601.106035 4 0.9422 211 | 1/8 11 h-lim-p 2.5000 20.0000 0.0009 4601.105923 3 0.7330 239 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 4601.105923 0 1.0938 258 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 4601.105923 0 1.0938 277 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 4601.105923 0 1.0938 296 | 1/8 15 h-lim-p 1.8634 20.0000 0.0000 4601.105923 0 0.4659 316 | 1/8 16 h-lim-p 0.2718 20.0000 0.0000 4601.105923 0 0.1359 335 | 1/8 17 h-lim-p 0.0787 20.0000 0.0000 4601.105923 0 0.0000 365 Out... lnL = -4601.105923 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4601.105923 Node 7: lnL = -4601.105923 Node 8: lnL = -4601.105923 Node 9: lnL = -4601.105923 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 840 Sequential format.. Reading seq # 1: YGR189C_Sbay Reading seq # 2: YGR189C_Scer Reading seq # 3: YGR189C_Skud Reading seq # 4: YGR189C_Smik Reading seq # 5: YGR189C_Spar Sequences read.. Counting patterns.. # site patterns = 311 Counting frequencies.. 120 bytes for distance 49760 bytes for lkl0 39808 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.155236 0.014174 0.036355 0.142375 0.106793 0.191499 0.221213 0.132620 lnL0 = -3833.856414 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3833.856414 x= 0.15524 0.01417 0.03635 0.14238 0.10679 0.19150 0.22121 0.13262 1 h-lim-p 0.0005 0.2853 409.5443 3826.776086 6 0.0001 35 | 0/8 2 h-lim-p 0.0004 0.0032 34.2331 3826.596189 4 0.0003 55 | 0/8 3 h-lim-p 0.0008 0.0201 12.6741 3826.576172 6 0.0003 82 | 0/8 4 h-lim-p 0.0009 0.0665 4.1604 3826.573587 3 0.0003 100 | 0/8 5 h-lim-p 0.0012 0.2200 1.1709 3826.573404 2 0.0003 117 | 0/8 6 h-lim-p 0.0014 1.0061 0.2339 3826.573396 0 0.0003 130 | 0/8 7 h-lim-p 0.0039 15.3294 0.0187 3826.573395 0 0.0008 151 | 0/8 8 h-lim-p 0.0457 20.0000 0.0003 3826.573152 0 0.7308 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3826.573143 1 0.9961 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3826.573143 0 1.0938 217 | 0/8 11 h-lim-p 1.1138 20.0000 0.0000 3826.573143 0 4.4554 239 | 0/8 12 h-lim-p 2.0936 20.0000 0.0000 3826.573143 0 0.2290 261 | 0/8 13 h-lim-p 1.0221 20.0000 0.0000 3826.573143 0 0.0000 297 Out... lnL = -3826.573143 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3826.573143 Node 7: lnL = -3826.573143 Node 8: lnL = -3826.573143 Node 9: lnL = -3826.573143 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 378 Sequential format.. Reading seq # 1: YGR193C_Sbay Reading seq # 2: YGR193C_Scer Reading seq # 3: YGR193C_Skud Reading seq # 4: YGR193C_Smik Reading seq # 5: YGR193C_Spar Sequences read.. Counting patterns.. # site patterns = 161 Counting frequencies.. 120 bytes for distance 25760 bytes for lkl0 20608 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.106147 0.043711 0.037689 0.130336 0.077138 0.227005 0.214044 0.078680 lnL0 = -1520.637843 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1520.637843 x= 0.10615 0.04371 0.03769 0.13034 0.07714 0.22700 0.21404 0.07868 1 h-lim-p 0.0061 1.9225 70.4304 1519.988858 9 0.0003 48 | 0/8 2 h-lim-p 0.0009 0.0074 11.3475 1519.959027 4 0.0005 69 | 0/8 3 h-lim-p 0.0019 0.0538 2.8213 1519.956796 5 0.0006 94 | 0/8 4 h-lim-p 0.0015 0.2348 1.1035 1519.956425 2 0.0007 110 | 0/8 5 h-lim-p 0.0024 0.5725 0.3332 1519.956391 3 0.0006 129 | 0/8 6 h-lim-p 0.0101 5.9685 0.0208 1519.956391 0 0.0011 151 | 0/8 7 h-lim-p 0.0030 20.0000 0.0078 1519.956391 0 0.0015 171 | 0/8 8 h-lim-p 0.0577 20.0000 0.0002 1519.956371 0 0.6925 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1519.956370 0 1.0938 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1519.956370 0 1.0938 234 | 0/8 11 h-lim-p 1.1828 20.0000 0.0000 1519.956370 0 3.5483 255 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1519.956370 0 0.3125 277 | 0/8 13 h-lim-p 0.0364 20.0000 0.0000 1519.956370 0 0.0000 314 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 1519.956370 0 0.0000 342 Out... lnL = -1519.956370 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1519.956370 Node 7: lnL = -1519.956370 Node 8: lnL = -1519.956370 Node 9: lnL = -1519.956370 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 925 Sequential format.. Reading seq # 1: YGR194C_Sbay Reading seq # 2: YGR194C_Scer Reading seq # 3: YGR194C_Skud Reading seq # 4: YGR194C_Smik Reading seq # 5: YGR194C_Spar Sequences read.. Counting patterns.. # site patterns = 514 Counting frequencies.. 120 bytes for distance 82240 bytes for lkl0 65792 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.233758 0.413759 0.000060 0.290201 0.462551 0.449550 0.333705 0.163067 lnL0 = -5130.767477 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 5130.767477 x= 0.23376 0.41376 0.00006 0.29020 0.46255 0.44955 0.33370 0.16307 1 h-lim-p 0.0000 0.0000 60.8228 5130.758205 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0261 35.2229 5130.147037 0 0.0013 41 | 1/8 3 h-lim-p 0.0049 0.0599 9.2420 5130.084886 6 0.0016 67 | 1/8 4 h-lim-p 0.0035 0.1499 4.1439 5130.070961 2 0.0016 83 | 1/8 5 h-lim-p 0.0131 0.7885 0.5158 5130.026517 0 0.0261 96 | 1/8 6 h-lim-p 0.0136 0.3446 0.9903 5128.795633 0 0.0544 117 | 1/8 7 h-lim-p 0.0052 0.0666 10.3125 5128.679822 5 0.0020 146 | 1/8 8 h-lim-p 2.5000 20.0000 0.0062 5128.667679 5 0.9136 170 | 1/8 9 h-lim-p 2.5000 20.0000 0.0005 5128.667616 2 0.9961 193 | 1/8 10 h-lim-p 2.5000 20.0000 0.0000 5128.667616 0 1.0938 212 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 5128.667616 0 1.0938 231 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 5128.667616 0 1.0938 250 | 1/8 13 h-lim-p 1.4527 20.0000 0.0000 5128.667616 0 2.1791 269 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 5128.667616 0 1.2500 288 | 1/8 15 h-lim-p 0.2215 20.0000 0.0000 5128.667616 0 0.1107 307 | 1/8 16 h-lim-p 0.0000 0.4443 0.5432 5128.667616 0 0.0000 329 | 1/8 17 h-lim-p 0.0043 20.0000 0.0001 5128.667616 0 0.0004 351 | 1/8 18 h-lim-p 0.0106 20.0000 0.0000 5128.667616 0 0.0000 379 Out... lnL = -5128.667616 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -5128.667616 Node 7: lnL = -5128.667616 Node 8: lnL = -5128.667616 Node 9: lnL = -5128.667616 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 858 Sequential format.. Reading seq # 1: YGR195W_Sbay Reading seq # 2: YGR195W_Scer Reading seq # 3: YGR195W_Skud Reading seq # 4: YGR195W_Smik Reading seq # 5: YGR195W_Spar Sequences read.. Counting patterns.. # site patterns = 457 Counting frequencies.. 120 bytes for distance 73120 bytes for lkl0 58496 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.318337 0.288447 0.000060 0.272333 0.373712 0.376297 0.338375 0.252507 lnL0 = -4784.956064 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4784.956064 x= 0.31834 0.28845 0.00006 0.27233 0.37371 0.37630 0.33838 0.25251 1 h-lim-p 0.0000 0.0000 47.4208 4784.942340 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0340 14.1487 4784.801233 0 0.0012 40 | 1/8 3 h-lim-p 0.0024 0.0964 7.3081 4784.773185 2 0.0012 57 | 1/8 4 h-lim-p 0.0043 0.4508 2.0114 4784.766257 2 0.0020 73 | 1/8 5 h-lim-p 0.0051 0.6308 0.7973 4784.720647 0 0.0153 86 | 1/8 6 h-lim-p 0.0082 0.3258 1.4923 4783.365232 0 0.0491 107 | 1/8 7 h-lim-p 0.0097 0.0846 7.5411 4783.326016 6 0.0014 136 | 1/8 8 h-lim-p 0.7731 20.0000 0.0133 4783.263571 1 0.9664 150 | 1/8 9 h-lim-p 2.5000 20.0000 0.0013 4783.262889 2 1.0889 173 | 1/8 10 h-lim-p 2.5000 20.0000 0.0001 4783.262887 0 1.0938 192 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 4783.262887 0 1.0938 211 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 4783.262887 0 0.1562 233 | 1/8 13 h-lim-p 0.0725 20.0000 0.0000 4783.262887 0 0.0091 254 | 1/8 14 h-lim-p 0.0082 20.0000 0.0000 4783.262887 0 0.0001 279 Out... lnL = -4783.262887 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4783.262887 Node 7: lnL = -4783.262887 Node 8: lnL = -4783.262887 Node 9: lnL = -4783.262887 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 560 Sequential format.. Reading seq # 1: YGR203W_Sbay Reading seq # 2: YGR203W_Scer Reading seq # 3: YGR203W_Skud Reading seq # 4: YGR203W_Smik Reading seq # 5: YGR203W_Spar Sequences read.. Counting patterns.. # site patterns = 199 Counting frequencies.. 120 bytes for distance 31840 bytes for lkl0 25472 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.169926 0.051960 0.083964 0.067835 0.069225 0.167503 0.198678 0.140669 lnL0 = -2199.919068 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2199.919068 x= 0.16993 0.05196 0.08396 0.06783 0.06922 0.16750 0.19868 0.14067 1 h-lim-p 0.0028 0.0719 125.3172 2197.758684 6 0.0003 35 | 0/8 2 h-lim-p 0.0011 0.0092 13.5256 2197.735748 3 0.0003 54 | 0/8 3 h-lim-p 0.0005 0.0227 7.4195 2197.727878 4 0.0004 74 | 0/8 4 h-lim-p 0.0018 0.1738 1.4417 2197.727034 2 0.0009 90 | 0/8 5 h-lim-p 0.0029 0.3077 0.4233 2197.727002 2 0.0004 108 | 0/8 6 h-lim-p 0.0010 2.4126 0.1630 2197.726994 2 0.0007 134 | 0/8 7 h-lim-p 0.0482 20.0000 0.0022 2197.726983 1 0.0603 156 | 0/8 8 h-lim-p 0.0050 20.0000 0.0267 2197.726756 0 0.0200 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2197.726749 1 0.9961 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2197.726749 0 1.0938 220 | 0/8 11 h-lim-p 1.2877 20.0000 0.0000 2197.726749 0 3.8630 241 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2197.726749 0 0.0781 265 | 0/8 13 h-lim-p 0.0885 20.0000 0.0000 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -2197.726749 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2197.726749 Node 7: lnL = -2197.726749 Node 8: lnL = -2197.726749 Node 9: lnL = -2197.726749 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 455 Sequential format.. Reading seq # 1: YGR205W_Sbay Reading seq # 2: YGR205W_Scer Reading seq # 3: YGR205W_Skud Reading seq # 4: YGR205W_Smik Reading seq # 5: YGR205W_Spar Sequences read.. Counting patterns.. # site patterns = 152 Counting frequencies.. 120 bytes for distance 24320 bytes for lkl0 19456 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.131465 0.068802 0.045800 0.066203 0.064672 0.159489 0.113893 0.108018 lnL0 = -1793.434695 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1793.434695 x= 0.13147 0.06880 0.04580 0.06620 0.06467 0.15949 0.11389 0.10802 1 h-lim-p 0.0005 0.0041 86.5127 1792.613967 3 0.0002 28 | 0/8 2 h-lim-p 0.0008 0.0068 20.7604 1792.550457 7 0.0003 58 | 0/8 3 h-lim-p 0.0007 0.0211 8.9287 1792.541227 5 0.0003 80 | 0/8 4 h-lim-p 0.0007 0.0642 3.5883 1792.539364 2 0.0003 97 | 0/8 5 h-lim-p 0.0073 0.9439 0.1638 1792.539361 1 0.0002 115 | 0/8 6 h-lim-p 0.0013 19.4931 0.0280 1792.539361 0 0.0006 135 | 0/8 7 h-lim-p 0.0144 20.0000 0.0011 1792.539358 0 0.0576 157 | 0/8 8 h-lim-p 0.0040 5.8680 0.0160 1792.539306 0 0.0121 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1792.539306 0 1.0938 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1792.539305 0 1.2500 218 | 0/8 11 h-lim-p 1.3747 20.0000 0.0000 1792.539305 0 0.1718 240 | 0/8 12 h-lim-p 0.0894 20.0000 0.0000 1792.539305 0 0.0056 263 | 0/8 13 h-lim-p 0.0036 20.0000 0.0000 1792.539305 0 0.0009 284 | 0/8 14 h-lim-p 0.0006 20.0000 0.0000 1792.539305 0 0.0000 312 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 1792.539305 0 0.0000 332 Out... lnL = -1792.539305 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1792.539305 Node 7: lnL = -1792.539305 Node 8: lnL = -1792.539305 Node 9: lnL = -1792.539305 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 373 Sequential format.. Reading seq # 1: YGR206W_Sbay Reading seq # 2: YGR206W_Scer Reading seq # 3: YGR206W_Skud Reading seq # 4: YGR206W_Smik Reading seq # 5: YGR206W_Spar Sequences read.. Counting patterns.. # site patterns = 166 Counting frequencies.. 120 bytes for distance 26560 bytes for lkl0 21248 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.199957 0.099909 0.073432 0.135815 0.099428 0.176893 0.248322 0.163060 lnL0 = -1649.687623 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1649.687623 x= 0.19996 0.09991 0.07343 0.13581 0.09943 0.17689 0.24832 0.16306 1 h-lim-p 0.0006 0.0045 74.3251 1648.029310 1 0.0007 24 | 0/8 2 h-lim-p 0.0013 0.0101 15.5003 1647.927735 7 0.0009 56 | 0/8 3 h-lim-p 0.0016 0.0364 8.6528 1647.906709 2 0.0007 72 | 0/8 4 h-lim-p 0.0013 0.0681 4.7726 1647.897475 3 0.0011 90 | 0/8 5 h-lim-p 0.0056 0.3239 0.9456 1647.896998 3 0.0011 109 | 0/8 6 h-lim-p 0.0061 3.3661 0.1736 1647.896956 2 0.0019 134 | 0/8 7 h-lim-p 0.0527 20.0000 0.0064 1647.892837 0 0.4214 157 | 0/8 8 h-lim-p 0.0026 0.2169 1.0363 1647.889793 4 0.0026 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 1647.889695 2 0.9644 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1647.889695 0 1.0938 221 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1647.889695 0 1.2500 241 | 0/8 12 h-lim-p 2.1944 20.0000 0.0000 1647.889695 0 0.4800 262 | 0/8 13 h-lim-p 0.2764 20.0000 0.0000 1647.889695 0 0.0086 286 | 0/8 14 h-lim-p 0.0057 20.0000 0.0000 1647.889695 0 0.0000 313 Out... lnL = -1647.889695 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1647.889695 Node 7: lnL = -1647.889695 Node 8: lnL = -1647.889695 Node 9: lnL = -1647.889695 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 263 Sequential format.. Reading seq # 1: YGR207C_Sbay Reading seq # 2: YGR207C_Scer Reading seq # 3: YGR207C_Skud Reading seq # 4: YGR207C_Smik Reading seq # 5: YGR207C_Spar Sequences read.. Counting patterns.. # site patterns = 125 Counting frequencies.. 120 bytes for distance 20000 bytes for lkl0 16000 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.122299 0.135140 0.014010 0.101233 0.147067 0.224152 0.179532 0.090993 lnL0 = -1206.920153 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1206.920153 x= 0.12230 0.13514 0.01401 0.10123 0.14707 0.22415 0.17953 0.09099 1 h-lim-p 0.0056 1.9444 65.9122 1206.123953 7 0.0004 40 | 0/8 2 h-lim-p 0.0008 0.0068 13.6470 1206.015825 0 0.0013 52 | 0/8 3 h-lim-p 0.0022 0.0174 6.5449 1205.997079 5 0.0011 75 | 0/8 4 h-lim-p 0.0061 0.2015 1.1410 1205.996496 4 0.0009 100 | 0/8 5 h-lim-p 0.0035 1.0613 0.3034 1205.996448 4 0.0011 123 | 0/8 6 h-lim-p 0.0063 3.6389 0.0524 1205.996444 2 0.0021 149 | 0/8 7 h-lim-p 0.0055 11.3300 0.0197 1205.996428 0 0.0110 170 | 0/8 8 h-lim-p 0.0217 5.2732 0.0100 1205.995577 0 0.1303 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1205.995542 2 0.9961 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1205.995542 0 2.1875 236 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1205.995542 0 1.0938 256 | 0/8 12 h-lim-p 0.7711 20.0000 0.0000 1205.995542 0 4.6266 278 | 0/8 13 h-lim-p 2.1179 20.0000 0.0000 1205.995542 0 0.2316 300 | 0/8 14 h-lim-p 1.0015 20.0000 0.0000 1205.995542 0 0.0020 328 Out... lnL = -1205.995542 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1205.995542 Node 7: lnL = -1205.995542 Node 8: lnL = -1205.995542 Node 9: lnL = -1205.995542 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 264 Sequential format.. Reading seq # 1: YGR208W_Sbay Reading seq # 2: YGR208W_Scer Reading seq # 3: YGR208W_Skud Reading seq # 4: YGR208W_Smik Reading seq # 5: YGR208W_Spar Sequences read.. Counting patterns.. # site patterns = 121 Counting frequencies.. 120 bytes for distance 19360 bytes for lkl0 15488 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.119455 0.129110 0.000060 0.112022 0.130619 0.219717 0.185311 0.089475 lnL0 = -1190.301833 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1190.301833 x= 0.11945 0.12911 0.00006 0.11202 0.13062 0.21972 0.18531 0.08948 1 h-lim-p 0.0057 2.1543 64.5927 1189.407097 8 0.0004 40 | 0/8 2 h-lim-p 0.0003 0.0023 18.1609 1189.225081 0 0.0011 54 | 0/8 3 h-lim-p 0.0012 0.0098 5.8372 1189.211878 6 0.0009 81 | 0/8 4 h-lim-p 0.0047 0.1769 1.0534 1189.211301 2 0.0011 98 | 0/8 5 h-lim-p 0.0037 0.1778 0.3130 1189.211255 2 0.0009 115 | 0/8 6 h-lim-p 0.0031 2.6619 0.0919 1189.211226 1 0.0032 137 | 0/8 7 h-lim-p 0.0068 4.5260 0.0437 1189.211101 0 0.0135 158 | 0/8 8 h-lim-p 0.0089 18.3787 0.0668 1189.206792 0 0.0354 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 1189.206737 2 0.9644 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1189.206737 0 1.0938 224 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1189.206737 0 1.0938 244 | 0/8 12 h-lim-p 1.1125 20.0000 0.0000 1189.206737 0 0.2781 265 | 0/8 13 h-lim-p 0.0516 20.0000 0.0000 1189.206737 0 0.0129 286 | 0/8 14 h-lim-p 0.0052 20.0000 0.0000 1189.206737 0 0.0000 324 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 1189.206737 0 0.0000 349 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1189.206737 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1189.206737 Node 7: lnL = -1189.206737 Node 8: lnL = -1189.206737 Node 9: lnL = -1189.206737 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 307 Sequential format.. Reading seq # 1: YGR209C_Sbay Reading seq # 2: YGR209C_Scer Reading seq # 3: YGR209C_Skud Reading seq # 4: YGR209C_Smik Reading seq # 5: YGR209C_Spar Sequences read.. Counting patterns.. # site patterns = 123 Counting frequencies.. 120 bytes for distance 19680 bytes for lkl0 15744 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.220328 0.055745 0.061776 0.066350 0.097340 0.143096 0.201797 0.188876 lnL0 = -1302.764134 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1302.764134 x= 0.22033 0.05574 0.06178 0.06635 0.09734 0.14310 0.20180 0.18888 1 h-lim-p 0.0007 0.0057 44.9012 1302.229236 4 0.0006 30 | 0/8 2 h-lim-p 0.0014 0.0161 17.7428 1302.096442 7 0.0010 60 | 0/8 3 h-lim-p 0.0017 0.0221 9.8974 1302.070369 6 0.0007 86 | 0/8 4 h-lim-p 0.0017 0.0783 4.1004 1302.067658 2 0.0004 103 | 0/8 5 h-lim-p 0.0015 0.1406 1.0726 1302.067266 3 0.0007 122 | 0/8 6 h-lim-p 0.0029 0.7431 0.2759 1302.067235 3 0.0008 143 | 0/8 7 h-lim-p 0.0016 2.2955 0.1456 1302.067226 2 0.0011 169 | 0/8 8 h-lim-p 0.2315 20.0000 0.0007 1302.066791 0 0.9259 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1302.066777 1 0.9961 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1302.066777 0 1.0938 233 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1302.066777 0 3.7500 253 | 0/8 12 h-lim-p 2.1824 20.0000 0.0000 1302.066777 0 0.1364 276 | 0/8 13 h-lim-p 0.3185 20.0000 0.0000 1302.066777 0 0.0199 299 | 0/8 14 h-lim-p 0.0133 20.0000 0.0000 1302.066777 0 0.0000 339 Out... lnL = -1302.066777 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1302.066777 Node 7: lnL = -1302.066777 Node 8: lnL = -1302.066777 Node 9: lnL = -1302.066777 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 584 Sequential format.. Reading seq # 1: YGR210C_Sbay Reading seq # 2: YGR210C_Scer Reading seq # 3: YGR210C_Skud Reading seq # 4: YGR210C_Smik Reading seq # 5: YGR210C_Spar Sequences read.. Counting patterns.. # site patterns = 245 Counting frequencies.. 120 bytes for distance 39200 bytes for lkl0 31360 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.182637 0.009448 0.130666 0.141839 0.090216 0.232296 0.262239 0.146253 lnL0 = -2589.192733 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2589.192733 x= 0.18264 0.00945 0.13067 0.14184 0.09022 0.23230 0.26224 0.14625 1 h-lim-p 0.0018 0.0152 170.9959 2586.267855 6 0.0002 36 | 0/8 2 h-lim-p 0.0008 0.0065 29.2906 2585.975069 6 0.0007 63 | 0/8 3 h-lim-p 0.0010 0.0184 19.3329 2585.913707 6 0.0004 86 | 0/8 4 h-lim-p 0.0010 0.0356 8.8162 2585.894614 5 0.0006 110 | 0/8 5 h-lim-p 0.0034 0.2269 1.6582 2585.893710 3 0.0007 129 | 0/8 6 h-lim-p 0.0032 0.9895 0.3585 2585.893656 3 0.0009 148 | 0/8 7 h-lim-p 0.0051 4.7283 0.0613 2585.893654 0 0.0011 169 | 0/8 8 h-lim-p 0.0779 20.0000 0.0009 2585.892526 0 1.2463 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2585.892518 1 0.9961 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2585.892518 0 1.0938 235 | 0/8 11 h-lim-p 1.7136 20.0000 0.0000 2585.892518 0 0.7497 255 | 0/8 12 h-lim-p 0.5156 20.0000 0.0000 2585.892518 0 0.0644 277 | 0/8 13 h-lim-p 0.0219 20.0000 0.0000 2585.892518 0 0.0014 300 | 0/8 14 h-lim-p 0.0004 20.0000 0.0000 2585.892518 0 0.0004 320 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 2585.892518 0 0.0000 354 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -2585.892518 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2585.892518 Node 7: lnL = -2585.892518 Node 8: lnL = -2585.892518 Node 9: lnL = -2585.892518 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 553 Sequential format.. Reading seq # 1: YGR211W_Sbay Reading seq # 2: YGR211W_Scer Reading seq # 3: YGR211W_Skud Reading seq # 4: YGR211W_Smik Reading seq # 5: YGR211W_Spar Sequences read.. Counting patterns.. # site patterns = 258 Counting frequencies.. 120 bytes for distance 41280 bytes for lkl0 33024 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.296296 0.021710 0.084997 0.138404 0.096461 0.254642 0.265099 0.244706 lnL0 = -2653.430922 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2653.430922 x= 0.29630 0.02171 0.08500 0.13840 0.09646 0.25464 0.26510 0.24471 1 h-lim-p 0.0009 0.0072 110.0009 2651.165946 3 0.0004 29 | 0/8 2 h-lim-p 0.0004 0.0034 47.2024 2650.434766 0 0.0009 42 | 0/8 3 h-lim-p 0.0013 0.0111 30.3779 2650.287516 6 0.0005 69 | 0/8 4 h-lim-p 0.0011 0.0227 12.3554 2650.259864 3 0.0005 87 | 0/8 5 h-lim-p 0.0021 0.1509 2.6690 2650.255537 6 0.0013 115 | 0/8 6 h-lim-p 0.0071 0.4268 0.4856 2650.255397 3 0.0011 136 | 0/8 7 h-lim-p 0.0018 1.7274 0.2834 2650.255288 0 0.0016 156 | 0/8 8 h-lim-p 0.0351 20.0000 0.0128 2650.231953 0 0.4210 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0010 2650.231313 4 1.2732 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2650.231299 0 1.0938 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2650.231299 0 1.0938 248 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2650.231299 0 1.0938 268 | 0/8 13 h-lim-p 1.1356 20.0000 0.0000 2650.231299 0 0.0000 311 Out... lnL = -2650.231299 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2650.231299 Node 7: lnL = -2650.231299 Node 8: lnL = -2650.231299 Node 9: lnL = -2650.231299 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 369 Sequential format.. Reading seq # 1: YGR212W_Sbay Reading seq # 2: YGR212W_Scer Reading seq # 3: YGR212W_Skud Reading seq # 4: YGR212W_Smik Reading seq # 5: YGR212W_Spar Sequences read.. Counting patterns.. # site patterns = 203 Counting frequencies.. 120 bytes for distance 32480 bytes for lkl0 25984 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.208475 0.034869 0.050835 0.190336 0.106251 0.341350 0.248101 0.159476 lnL0 = -1752.425920 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1752.425920 x= 0.20847 0.03487 0.05084 0.19034 0.10625 0.34135 0.24810 0.15948 1 h-lim-p 0.0027 1.1072 113.4156 1749.944119 8 0.0004 41 | 0/8 2 h-lim-p 0.0009 0.0075 18.5532 1749.785441 5 0.0009 63 | 0/8 3 h-lim-p 0.0017 0.0140 9.4688 1749.743232 7 0.0012 90 | 0/8 4 h-lim-p 0.0031 0.1322 3.5895 1749.735478 2 0.0014 106 | 0/8 5 h-lim-p 0.0136 1.0989 0.3787 1749.735375 2 0.0015 124 | 0/8 6 h-lim-p 0.0171 7.7983 0.0327 1749.735371 1 0.0034 147 | 0/8 7 h-lim-p 0.0085 20.0000 0.0131 1749.735297 0 0.0341 169 | 0/8 8 h-lim-p 0.0093 19.3368 0.0478 1749.734343 0 0.0373 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 1749.734284 2 0.9961 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1749.734284 0 1.0938 235 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1749.734284 0 0.5469 256 | 0/8 12 h-lim-p 0.3559 20.0000 0.0000 1749.734284 0 0.1779 276 | 0/8 13 h-lim-p 0.1080 20.0000 0.0000 1749.734284 0 0.0540 296 | 0/8 14 h-lim-p 0.0358 20.0000 0.0000 1749.734284 0 0.0000 329 Out... lnL = -1749.734284 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1749.734284 Node 7: lnL = -1749.734284 Node 8: lnL = -1749.734284 Node 9: lnL = -1749.734284 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 402 Sequential format.. Reading seq # 1: YGR215W_Sbay Reading seq # 2: YGR215W_Scer Reading seq # 3: YGR215W_Skud Reading seq # 4: YGR215W_Smik Reading seq # 5: YGR215W_Spar Sequences read.. Counting patterns.. # site patterns = 159 Counting frequencies.. 120 bytes for distance 25440 bytes for lkl0 20352 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.115832 0.052400 0.063338 0.097761 0.090160 0.192174 0.232269 0.081001 lnL0 = -1751.412548 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1751.412548 x= 0.11583 0.05240 0.06334 0.09776 0.09016 0.19217 0.23227 0.08100 1 h-lim-p 0.0013 0.0102 93.4037 1750.101459 4 0.0003 31 | 0/8 2 h-lim-p 0.0008 0.0061 15.1221 1750.047230 7 0.0005 62 | 0/8 3 h-lim-p 0.0012 0.0662 5.9994 1750.038313 2 0.0006 78 | 0/8 4 h-lim-p 0.0013 0.0714 2.6223 1750.036983 5 0.0005 103 | 0/8 5 h-lim-p 0.0018 0.4609 0.6934 1750.036834 3 0.0007 121 | 0/8 6 h-lim-p 0.0032 2.0076 0.1486 1750.036825 2 0.0008 146 | 0/8 7 h-lim-p 0.0039 5.4686 0.0319 1750.036824 0 0.0009 167 | 0/8 8 h-lim-p 0.0292 20.0000 0.0009 1750.036397 0 0.9333 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1750.036349 2 0.9961 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1750.036349 0 1.0938 236 | 0/8 11 h-lim-p 1.3403 20.0000 0.0000 1750.036349 0 0.0002 268 Out... lnL = -1750.036349 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1750.036349 Node 7: lnL = -1750.036349 Node 8: lnL = -1750.036349 Node 9: lnL = -1750.036349 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 254 Sequential format.. Reading seq # 1: YGR216C_Sbay Reading seq # 2: YGR216C_Scer Reading seq # 3: YGR216C_Skud Reading seq # 4: YGR216C_Smik Reading seq # 5: YGR216C_Spar Sequences read.. Counting patterns.. # site patterns = 127 Counting frequencies.. 120 bytes for distance 20320 bytes for lkl0 16256 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.123043 0.099152 0.085392 0.133305 0.099312 0.214656 0.160470 0.084343 lnL0 = -1142.746144 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1142.746144 x= 0.12304 0.09915 0.08539 0.13330 0.09931 0.21466 0.16047 0.08434 1 h-lim-p 0.0025 0.0198 32.3454 1142.383018 8 0.0007 41 | 0/8 2 h-lim-p 0.0027 0.0217 8.5104 1142.352413 6 0.0009 66 | 0/8 3 h-lim-p 0.0046 0.0766 1.6428 1142.351126 4 0.0010 86 | 0/8 4 h-lim-p 0.0039 0.8536 0.4203 1142.351029 4 0.0012 110 | 0/8 5 h-lim-p 0.0037 2.4962 0.1374 1142.351022 0 0.0008 131 | 0/8 6 h-lim-p 0.0081 13.6681 0.0137 1142.351021 0 0.0018 152 | 0/8 7 h-lim-p 0.0222 20.0000 0.0011 1142.351021 0 0.0097 172 | 0/8 8 h-lim-p 0.0216 20.0000 0.0005 1142.351018 0 0.1725 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1142.351018 0 1.0938 215 | 0/8 10 h-lim-p 2.2018 20.0000 0.0000 1142.351018 0 0.4817 236 | 0/8 11 h-lim-p 0.2879 20.0000 0.0000 1142.351018 0 0.0360 258 | 0/8 12 h-lim-p 0.0194 20.0000 0.0000 1142.351018 0 0.0049 279 | 0/8 13 h-lim-p 0.0034 20.0000 0.0000 1142.351018 0 0.0000 305 | 0/8 14 h-lim-p 0.0011 20.0000 0.0000 1142.351018 0 0.0000 329 Out... lnL = -1142.351018 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1142.351018 Node 7: lnL = -1142.351018 Node 8: lnL = -1142.351018 Node 9: lnL = -1142.351018 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 287 Sequential format.. Reading seq # 1: YGR220C_Sbay Reading seq # 2: YGR220C_Scer Reading seq # 3: YGR220C_Skud Reading seq # 4: YGR220C_Smik Reading seq # 5: YGR220C_Spar Sequences read.. Counting patterns.. # site patterns = 148 Counting frequencies.. 120 bytes for distance 23680 bytes for lkl0 18944 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.192503 0.000060 0.091176 0.126418 0.119687 0.225355 0.330345 0.148839 lnL0 = -1259.477277 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1259.477277 x= 0.19250 0.00006 0.09118 0.12642 0.11969 0.22536 0.33034 0.14884 1 h-lim-p 0.0000 0.0001 26.9509 1259.432267 m 0.0001 22 | 1/8 2 h-lim-p 0.0001 0.0186 12.8930 1259.344412 0 0.0011 37 | 1/8 3 h-lim-p 0.0020 0.0561 6.7990 1259.323960 7 0.0011 66 | 1/8 4 h-lim-p 0.0045 0.1656 1.6981 1259.321670 5 0.0014 92 | 0/8 5 h-lim-p 0.0006 0.2999 3.9235 1259.317036 5 0.0006 117 | 0/8 6 h-lim-p 0.0027 0.2937 0.9242 1259.315135 3 0.0023 135 | 0/8 7 h-lim-p 0.0137 0.1337 0.1537 1259.188638 m 0.1337 156 | 0/8 8 h-lim-p 0.0000 0.0000 5.8924 h-lim-p: 3.29875064e-20 2.63900051e-19 5.89241857e+00 1259.188638 .. | 0/8 9 h-lim-p 0.0000 0.0246 19.8047 1259.008118 0 0.0013 191 | 0/8 10 h-lim-p 0.0000 0.0002 9.7709 1258.996327 m 0.0002 203 | 1/8 11 h-lim-p 0.0005 0.0580 2.5102 1258.982333 0 0.0029 217 | 1/8 12 h-lim-p 0.0038 0.1475 1.9060 1258.977902 2 0.0018 233 | 1/8 13 h-lim-p 0.0063 0.7535 0.5463 1258.977742 4 0.0010 255 | 1/8 14 h-lim-p 0.0075 3.1784 0.0747 1258.977680 3 0.0053 281 | 1/8 15 h-lim-p 0.0039 3.9482 0.1002 1258.977006 0 0.0158 302 | 1/8 16 h-lim-p 0.0092 1.6137 0.1727 1258.966131 0 0.0367 323 | 1/8 17 h-lim-p 2.5000 20.0000 0.0008 1258.965910 2 0.9961 346 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 1258.965909 0 1.0938 365 | 1/8 19 h-lim-p 2.5000 20.0000 0.0000 1258.965909 0 1.0938 384 | 1/8 20 h-lim-p 1.9963 20.0000 0.0000 1258.965909 0 1.7468 403 | 1/8 21 h-lim-p 2.5000 20.0000 0.0000 1258.965909 0 0.0195 428 | 1/8 22 h-lim-p 0.0050 20.0000 0.0000 1258.965909 0 0.0000 464 Out... lnL = -1258.965909 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1258.965909 Node 7: lnL = -1258.965909 Node 8: lnL = -1258.965909 Node 9: lnL = -1258.965909 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 861 Sequential format.. Reading seq # 1: YGR222W_Sbay Reading seq # 2: YGR222W_Scer Reading seq # 3: YGR222W_Skud Reading seq # 4: YGR222W_Smik Reading seq # 5: YGR222W_Spar Sequences read.. Counting patterns.. # site patterns = 235 Counting frequencies.. 120 bytes for distance 37600 bytes for lkl0 30080 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.099565 0.044916 0.049598 0.087306 0.059605 0.121372 0.163076 0.073132 lnL0 = -3375.928476 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3375.928476 x= 0.09957 0.04492 0.04960 0.08731 0.05961 0.12137 0.16308 0.07313 1 h-lim-p 0.0003 0.0021 250.2919 3372.909020 3 0.0001 28 | 0/8 2 h-lim-p 0.0003 0.0027 30.5729 3372.846676 6 0.0001 51 | 0/8 3 h-lim-p 0.0005 0.0295 8.6752 3372.842398 4 0.0001 72 | 0/8 4 h-lim-p 0.0017 0.2243 0.6288 3372.842363 1 0.0002 88 | 0/8 5 h-lim-p 0.0010 1.6802 0.1182 3372.842361 1 0.0002 111 | 0/8 6 h-lim-p 0.0006 4.2010 0.0484 3372.842360 0 0.0005 131 | 0/8 7 h-lim-p 0.0047 20.0000 0.0054 3372.842267 0 0.0375 154 | 0/8 8 h-lim-p 0.0011 0.4590 0.1797 3372.841078 0 0.0034 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3372.841073 0 1.0938 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3372.841073 0 1.0938 215 | 0/8 11 h-lim-p 0.8059 20.0000 0.0000 3372.841073 0 0.0126 240 | 0/8 12 h-lim-p 0.0057 20.0000 0.0000 3372.841073 0 0.0000 266 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 3372.841073 0 0.0000 287 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 3372.841073 0 0.0000 319 Out... lnL = -3372.841073 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3372.841073 Node 7: lnL = -3372.841073 Node 8: lnL = -3372.841073 Node 9: lnL = -3372.841073 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 528 Sequential format.. Reading seq # 1: YGR225W_Sbay Reading seq # 2: YGR225W_Scer Reading seq # 3: YGR225W_Skud Reading seq # 4: YGR225W_Smik Reading seq # 5: YGR225W_Spar Sequences read.. Counting patterns.. # site patterns = 217 Counting frequencies.. 120 bytes for distance 34720 bytes for lkl0 27776 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.157503 0.018937 0.093750 0.100584 0.125342 0.163290 0.225996 0.119877 lnL0 = -2311.361658 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2311.361658 x= 0.15750 0.01894 0.09375 0.10058 0.12534 0.16329 0.22600 0.11988 1 h-lim-p 0.0023 0.0193 141.9077 2309.332669 8 0.0002 41 | 0/8 2 h-lim-p 0.0016 0.0126 18.4314 2309.238047 7 0.0006 70 | 0/8 3 h-lim-p 0.0017 0.0527 6.1778 2309.227686 6 0.0006 96 | 0/8 4 h-lim-p 0.0021 0.0904 1.7685 2309.227096 2 0.0004 113 | 0/8 5 h-lim-p 0.0010 0.4436 0.7597 2309.226954 3 0.0006 134 | 0/8 6 h-lim-p 0.0042 1.6063 0.1026 2309.226951 0 0.0005 156 | 0/8 7 h-lim-p 0.0045 20.0000 0.0106 2309.226951 0 0.0010 177 | 0/8 8 h-lim-p 0.4047 20.0000 0.0000 2309.226950 0 1.2142 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2309.226950 0 1.2500 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2309.226950 0 0.5469 239 | 0/8 11 h-lim-p 0.3512 20.0000 0.0000 2309.226950 0 0.0439 261 | 0/8 12 h-lim-p 0.0245 20.0000 0.0000 2309.226950 0 0.0023 284 | 0/8 13 h-lim-p 0.0016 20.0000 0.0000 2309.226950 0 0.0000 323 | 0/8 14 h-lim-p 0.0000 20.0000 0.0005 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -2309.226950 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2309.226950 Node 7: lnL = -2309.226950 Node 8: lnL = -2309.226950 Node 9: lnL = -2309.226950 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 441 Sequential format.. Reading seq # 1: YGR227W_Sbay Reading seq # 2: YGR227W_Scer Reading seq # 3: YGR227W_Skud Reading seq # 4: YGR227W_Smik Reading seq # 5: YGR227W_Spar Sequences read.. Counting patterns.. # site patterns = 165 Counting frequencies.. 120 bytes for distance 26400 bytes for lkl0 21120 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.139478 0.078155 0.063862 0.120744 0.059466 0.217060 0.200644 0.102173 lnL0 = -1944.812010 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1944.812010 x= 0.13948 0.07815 0.06386 0.12074 0.05947 0.21706 0.20064 0.10217 1 h-lim-p 0.0002 0.0016 99.2264 1942.963299 0 0.0004 23 | 0/8 2 h-lim-p 0.0006 0.0045 31.2452 1942.820503 7 0.0003 52 | 0/8 3 h-lim-p 0.0007 0.0056 14.8722 1942.794193 5 0.0003 76 | 0/8 4 h-lim-p 0.0013 0.1069 3.3385 1942.790707 4 0.0007 97 | 0/8 5 h-lim-p 0.0019 0.2126 1.1773 1942.790306 4 0.0006 120 | 0/8 6 h-lim-p 0.0132 3.9383 0.0578 1942.790305 0 0.0007 135 | 0/8 7 h-lim-p 0.0029 20.0000 0.0145 1942.790303 0 0.0043 155 | 0/8 8 h-lim-p 0.0298 20.0000 0.0021 1942.789959 0 0.2381 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1942.789956 0 1.0938 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1942.789956 0 1.0938 218 | 0/8 11 h-lim-p 2.0168 20.0000 0.0000 1942.789956 0 0.8823 238 | 0/8 12 h-lim-p 0.9062 20.0000 0.0000 1942.789956 0 0.0000 275 Out... lnL = -1942.789956 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1942.789956 Node 7: lnL = -1942.789956 Node 8: lnL = -1942.789956 Node 9: lnL = -1942.789956 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 908 Sequential format.. Reading seq # 1: YGR230W_Sbay Reading seq # 2: YGR230W_Scer Reading seq # 3: YGR230W_Skud Reading seq # 4: YGR230W_Smik Reading seq # 5: YGR230W_Spar Sequences read.. Counting patterns.. # site patterns = 318 Counting frequencies.. 120 bytes for distance 50880 bytes for lkl0 40704 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.168461 0.051677 0.051309 0.151147 0.110215 0.208770 0.231465 0.127627 lnL0 = -4054.909308 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4054.909308 x= 0.16846 0.05168 0.05131 0.15115 0.11021 0.20877 0.23147 0.12763 1 h-lim-p 0.0042 0.0497 138.1413 4053.554851 7 0.0002 42 | 0/8 2 h-lim-p 0.0008 0.0064 23.0618 4053.489210 6 0.0003 68 | 0/8 3 h-lim-p 0.0008 0.0383 7.4213 4053.479615 4 0.0004 90 | 0/8 4 h-lim-p 0.0010 0.1056 2.8152 4053.478553 4 0.0003 114 | 0/8 5 h-lim-p 0.0019 0.6816 0.4676 4053.478516 2 0.0004 131 | 0/8 6 h-lim-p 0.0019 3.0464 0.0898 4053.478515 0 0.0004 152 | 0/8 7 h-lim-p 0.0055 20.0000 0.0067 4053.478515 0 0.0006 174 | 0/8 8 h-lim-p 0.0521 20.0000 0.0001 4053.478504 0 0.8332 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4053.478504 0 1.0938 218 | 0/8 10 h-lim-p 1.3669 20.0000 0.0000 4053.478504 0 1.3669 238 | 0/8 11 h-lim-p 1.5739 20.0000 0.0000 4053.478504 0 0.0046 266 | 0/8 12 h-lim-p 0.0006 20.0000 0.0000 4053.478504 0 0.0000 298 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 4053.478504 0 0.0000 327 Out... lnL = -4053.478504 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4053.478504 Node 7: lnL = -4053.478504 Node 8: lnL = -4053.478504 Node 9: lnL = -4053.478504 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 512 Sequential format.. Reading seq # 1: YGR231C_Sbay Reading seq # 2: YGR231C_Scer Reading seq # 3: YGR231C_Skud Reading seq # 4: YGR231C_Smik Reading seq # 5: YGR231C_Spar Sequences read.. Counting patterns.. # site patterns = 246 Counting frequencies.. 120 bytes for distance 39360 bytes for lkl0 31488 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.243970 0.095884 0.069717 0.187055 0.146839 0.295820 0.355460 0.185046 lnL0 = -2675.166446 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2675.166446 x= 0.24397 0.09588 0.06972 0.18705 0.14684 0.29582 0.35546 0.18505 1 h-lim-p 0.0017 0.0138 58.7882 2674.452245 4 0.0004 31 | 0/8 2 h-lim-p 0.0020 0.0159 10.1411 2674.420546 6 0.0006 58 | 0/8 3 h-lim-p 0.0016 0.1048 4.0422 2674.414344 5 0.0009 83 | 0/8 4 h-lim-p 0.0027 0.2975 1.3057 2674.413444 2 0.0012 99 | 0/8 5 h-lim-p 0.0047 1.3464 0.3251 2674.413358 3 0.0018 117 | 0/8 6 h-lim-p 0.0378 19.9804 0.0154 2674.413358 0 0.0021 140 | 0/8 7 h-lim-p 0.0103 20.0000 0.0031 2674.413358 0 0.0013 162 | 0/8 8 h-lim-p 0.0842 20.0000 0.0000 2674.413357 0 1.0109 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2674.413356 0 1.0938 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2674.413356 0 1.0938 225 | 0/8 11 h-lim-p 1.1386 20.0000 0.0000 2674.413356 0 0.2846 246 | 0/8 12 h-lim-p 0.0591 20.0000 0.0000 2674.413356 0 0.0148 267 | 0/8 13 h-lim-p 0.0044 20.0000 0.0000 2674.413356 0 0.0019 287 | 0/8 14 h-lim-p 0.0038 20.0000 0.0000 2674.413356 0 0.0000 322 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 2674.413356 0 0.0000 348 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -2674.413356 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2674.413356 Node 7: lnL = -2674.413356 Node 8: lnL = -2674.413356 Node 9: lnL = -2674.413356 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 542 Sequential format.. Reading seq # 1: YGR232W_Sbay Reading seq # 2: YGR232W_Scer Reading seq # 3: YGR232W_Skud Reading seq # 4: YGR232W_Smik Reading seq # 5: YGR232W_Spar Sequences read.. Counting patterns.. # site patterns = 244 Counting frequencies.. 120 bytes for distance 39040 bytes for lkl0 31232 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.242230 0.099757 0.079236 0.180312 0.153581 0.286301 0.341150 0.183553 lnL0 = -2713.977733 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2713.977733 x= 0.24223 0.09976 0.07924 0.18031 0.15358 0.28630 0.34115 0.18355 1 h-lim-p 0.0016 0.0127 60.0078 2713.165456 8 0.0005 45 | 0/8 2 h-lim-p 0.0019 0.0155 12.8496 2713.103942 5 0.0008 68 | 0/8 3 h-lim-p 0.0015 0.0618 6.6158 2713.089455 6 0.0008 94 | 0/8 4 h-lim-p 0.0026 0.1575 2.0870 2713.087308 4 0.0011 113 | 0/8 5 h-lim-p 0.0038 0.7828 0.6202 2713.087049 2 0.0015 129 | 0/8 6 h-lim-p 0.0307 9.7618 0.0302 2713.087049 0 0.0008 153 | 0/8 7 h-lim-p 0.0161 20.0000 0.0016 2713.087049 0 0.0070 173 | 0/8 8 h-lim-p 0.0352 20.0000 0.0003 2713.087043 0 0.2819 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2713.087043 0 1.0938 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2713.087043 0 1.0938 236 | 0/8 11 h-lim-p 1.2699 20.0000 0.0000 2713.087043 0 1.2699 256 | 0/8 12 h-lim-p 0.9431 20.0000 0.0000 2713.087043 0 0.9431 276 | 0/8 13 h-lim-p 0.0000 4.7033 0.0559 2713.087043 0 0.0000 297 | 0/8 14 h-lim-p 0.0040 20.0000 0.0002 2713.087043 0 0.0000 323 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 2713.087043 0 0.0000 355 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -2713.087043 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2713.087043 Node 7: lnL = -2713.087043 Node 8: lnL = -2713.087043 Node 9: lnL = -2713.087043 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 867 Sequential format.. Reading seq # 1: YGR233C_Sbay Reading seq # 2: YGR233C_Scer Reading seq # 3: YGR233C_Skud Reading seq # 4: YGR233C_Smik Reading seq # 5: YGR233C_Spar Sequences read.. Counting patterns.. # site patterns = 302 Counting frequencies.. 120 bytes for distance 48320 bytes for lkl0 38656 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.220249 0.038942 0.059211 0.124525 0.098463 0.218765 0.244615 0.176639 lnL0 = -4015.540898 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4015.540898 x= 0.22025 0.03894 0.05921 0.12452 0.09846 0.21876 0.24461 0.17664 1 h-lim-p 0.0007 0.0059 192.0771 4012.502476 8 0.0002 38 | 0/8 2 h-lim-p 0.0005 0.0039 45.0802 4012.204016 6 0.0003 66 | 0/8 3 h-lim-p 0.0006 0.0120 24.2078 4012.125498 6 0.0003 93 | 0/8 4 h-lim-p 0.0007 0.0214 10.8734 4012.110788 3 0.0003 111 | 0/8 5 h-lim-p 0.0019 0.2186 1.8021 4012.109927 4 0.0006 133 | 0/8 6 h-lim-p 0.0027 0.6884 0.3662 4012.109905 0 0.0003 147 | 0/8 7 h-lim-p 0.0025 4.7799 0.0510 4012.109904 0 0.0011 167 | 0/8 8 h-lim-p 0.0914 20.0000 0.0006 4012.109294 0 1.0973 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4012.109267 1 0.9961 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4012.109267 0 1.0938 232 | 0/8 11 h-lim-p 1.4845 20.0000 0.0000 4012.109267 0 1.4845 252 | 0/8 12 h-lim-p 1.8494 20.0000 0.0000 4012.109267 0 0.2312 274 | 0/8 13 h-lim-p 0.0687 20.0000 0.0000 4012.109267 0 0.0687 294 | 0/8 14 h-lim-p 0.0296 20.0000 0.0000 4012.109267 0 0.0074 315 | 0/8 15 h-lim-p 0.0054 20.0000 0.0000 4012.109267 0 0.0000 354 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -4012.109267 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4012.109267 Node 7: lnL = -4012.109267 Node 8: lnL = -4012.109267 Node 9: lnL = -4012.109267 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 846 Sequential format.. Reading seq # 1: YGR234W_Sbay Reading seq # 2: YGR234W_Scer Reading seq # 3: YGR234W_Skud Reading seq # 4: YGR234W_Smik Reading seq # 5: YGR234W_Spar Sequences read.. Counting patterns.. # site patterns = 321 Counting frequencies.. 120 bytes for distance 51360 bytes for lkl0 41088 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.229438 0.065985 0.088440 0.130961 0.093370 0.212002 0.245481 0.173953 lnL0 = -4009.657007 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4009.657007 x= 0.22944 0.06598 0.08844 0.13096 0.09337 0.21200 0.24548 0.17395 1 h-lim-p 0.0010 0.0079 156.3181 4007.012264 2 0.0002 27 | 0/8 2 h-lim-p 0.0006 0.0050 37.5117 4006.828479 4 0.0003 46 | 0/8 3 h-lim-p 0.0008 0.0229 12.9412 4006.798741 5 0.0004 71 | 0/8 4 h-lim-p 0.0009 0.0575 5.8565 4006.792034 4 0.0005 92 | 0/8 5 h-lim-p 0.0018 0.2146 1.5726 4006.791535 3 0.0004 111 | 0/8 6 h-lim-p 0.0015 0.4939 0.4535 4006.791491 2 0.0005 129 | 0/8 7 h-lim-p 0.0081 16.4503 0.0278 4006.791490 0 0.0018 150 | 0/8 8 h-lim-p 0.0366 20.0000 0.0014 4006.790795 0 0.5851 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4006.790770 1 0.9961 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4006.790770 0 1.0938 216 | 0/8 11 h-lim-p 1.3139 20.0000 0.0000 4006.790770 0 0.9854 236 | 0/8 12 h-lim-p 0.5164 20.0000 0.0000 4006.790770 0 0.0010 264 | 0/8 13 h-lim-p 0.0010 20.0000 0.0000 4006.790770 0 0.0000 292 Out... lnL = -4006.790770 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4006.790770 Node 7: lnL = -4006.790770 Node 8: lnL = -4006.790770 Node 9: lnL = -4006.790770 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 426 Sequential format.. Reading seq # 1: YGR235C_Sbay Reading seq # 2: YGR235C_Scer Reading seq # 3: YGR235C_Skud Reading seq # 4: YGR235C_Smik Reading seq # 5: YGR235C_Spar Sequences read.. Counting patterns.. # site patterns = 211 Counting frequencies.. 120 bytes for distance 33760 bytes for lkl0 27008 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.163939 0.146855 0.071755 0.123764 0.154805 0.267529 0.347031 0.101314 lnL0 = -2032.235577 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2032.235577 x= 0.16394 0.14686 0.07176 0.12376 0.15480 0.26753 0.34703 0.10131 1 h-lim-p 0.0025 0.0196 83.7285 2030.446008 2 0.0006 27 | 0/8 2 h-lim-p 0.0011 0.0091 20.3807 2030.254548 3 0.0010 45 | 0/8 3 h-lim-p 0.0018 0.0410 11.0581 2030.204883 7 0.0010 74 | 0/8 4 h-lim-p 0.0035 0.0966 3.2738 2030.199124 5 0.0012 98 | 0/8 5 h-lim-p 0.0048 0.4557 0.8270 2030.198662 4 0.0015 122 | 0/8 6 h-lim-p 0.0032 1.0390 0.3805 2030.198589 3 0.0012 148 | 0/8 7 h-lim-p 0.1314 20.0000 0.0035 2030.198586 0 0.0329 169 | 0/8 8 h-lim-p 0.0184 20.0000 0.0063 2030.198449 0 0.0736 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2030.198449 0 1.0938 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2030.198449 0 1.0938 231 | 0/8 11 h-lim-p 1.6973 20.0000 0.0000 2030.198449 0 0.7426 251 | 0/8 12 h-lim-p 0.4781 20.0000 0.0000 2030.198449 0 0.4781 271 | 0/8 13 h-lim-p 0.1662 20.0000 0.0000 2030.198449 0 0.0416 292 | 0/8 14 h-lim-p 0.0169 20.0000 0.0000 2030.198449 0 0.0000 325 | 0/8 15 h-lim-p 0.0014 20.0000 0.0000 2030.198449 0 0.0000 353 Out... lnL = -2030.198449 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2030.198449 Node 7: lnL = -2030.198449 Node 8: lnL = -2030.198449 Node 9: lnL = -2030.198449 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 506 Sequential format.. Reading seq # 1: YGR236C_Sbay Reading seq # 2: YGR236C_Scer Reading seq # 3: YGR236C_Skud Reading seq # 4: YGR236C_Smik Reading seq # 5: YGR236C_Spar Sequences read.. Counting patterns.. # site patterns = 264 Counting frequencies.. 120 bytes for distance 42240 bytes for lkl0 33792 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.167531 0.058031 0.063849 0.194763 0.170291 0.355253 0.195947 0.109547 lnL0 = -2477.058749 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2477.058749 x= 0.16753 0.05803 0.06385 0.19476 0.17029 0.35525 0.19595 0.10955 1 h-lim-p 0.0027 1.0245 136.7141 2474.378077 4 0.0003 32 | 0/8 2 h-lim-p 0.0021 0.0166 14.4375 2474.295165 4 0.0008 52 | 0/8 3 h-lim-p 0.0027 0.0686 4.3181 2474.288176 6 0.0008 82 | 0/8 4 h-lim-p 0.0070 0.6570 0.5059 2474.288092 2 0.0007 100 | 0/8 5 h-lim-p 0.0027 3.4986 0.1275 2474.288081 0 0.0013 120 | 0/8 6 h-lim-p 0.0040 11.1937 0.0422 2474.288078 1 0.0020 143 | 0/8 7 h-lim-p 0.0672 20.0000 0.0012 2474.287248 0 0.8067 166 | 0/8 8 h-lim-p 0.0452 7.5673 0.0222 2474.287248 0 0.0012 190 | 0/8 9 h-lim-p 0.1875 20.0000 0.0001 2474.287227 0 0.7501 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2474.287227 0 1.0938 232 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2474.287227 0 1.0938 252 | 0/8 12 h-lim-p 1.2517 20.0000 0.0000 2474.287227 0 2.5035 273 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2474.287227 0 0.5469 294 | 0/8 14 h-lim-p 0.0392 20.0000 0.0000 2474.287227 0 0.0024 317 | 0/8 15 h-lim-p 0.0008 20.0000 0.0000 2474.287227 0 0.0000 351 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 2474.287227 0 0.0000 382 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 2474.287227 0 0.0000 407 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 2474.287227 0 0.0000 433 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 2474.287227 0 0.0000 456 | 0/8 20 h-lim-p 0.0000 20.0000 0.0000 2474.287227 0 0.0000 491 | 0/8 21 h-lim-p 0.0000 20.0000 0.0004 | 0/8 22 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -2474.287227 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2474.287227 Node 7: lnL = -2474.287227 Node 8: lnL = -2474.287227 Node 9: lnL = -2474.287227 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 407 Sequential format.. Reading seq # 1: YGR237C_Sbay Reading seq # 2: YGR237C_Scer Reading seq # 3: YGR237C_Skud Reading seq # 4: YGR237C_Smik Reading seq # 5: YGR237C_Spar Sequences read.. Counting patterns.. # site patterns = 154 Counting frequencies.. 120 bytes for distance 24640 bytes for lkl0 19712 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.152817 0.062192 0.021852 0.102224 0.075068 0.233050 0.198604 0.110743 lnL0 = -1769.739897 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1769.739897 x= 0.15282 0.06219 0.02185 0.10222 0.07507 0.23305 0.19860 0.11074 1 h-lim-p 0.0005 0.0041 70.6245 1768.971704 9 0.0003 43 | 0/8 2 h-lim-p 0.0001 0.0010 35.6018 1768.810019 0 0.0003 56 | 0/8 3 h-lim-p 0.0009 0.0140 10.0436 1768.789601 6 0.0005 80 | 0/8 4 h-lim-p 0.0007 0.0432 6.3662 1768.782480 6 0.0005 108 | 0/8 5 h-lim-p 0.0032 0.3354 0.9415 1768.782194 3 0.0006 127 | 0/8 6 h-lim-p 0.0181 9.9039 0.0338 1768.782125 3 0.0107 155 | 0/8 7 h-lim-p 0.0043 0.6308 0.0845 1768.781519 0 0.0086 176 | 0/8 8 h-lim-p 0.0014 0.0746 0.5173 1768.776662 0 0.0042 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1768.776541 2 1.0938 221 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1768.776540 0 1.0938 241 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1768.776540 0 1.0938 261 | 0/8 12 h-lim-p 1.2303 20.0000 0.0000 1768.776540 0 4.9214 283 | 0/8 13 h-lim-p 2.3899 20.0000 0.0000 1768.776540 0 0.5228 304 | 0/8 14 h-lim-p 2.1593 20.0000 0.0000 1768.776540 0 0.0169 330 | 0/8 15 h-lim-p 0.0036 20.0000 0.0000 1768.776540 0 0.0000 363 Out... lnL = -1768.776540 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1768.776540 Node 7: lnL = -1768.776540 Node 8: lnL = -1768.776540 Node 9: lnL = -1768.776540 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 540 Sequential format.. Reading seq # 1: YGR238C_Sbay Reading seq # 2: YGR238C_Scer Reading seq # 3: YGR238C_Skud Reading seq # 4: YGR238C_Smik Reading seq # 5: YGR238C_Spar Sequences read.. Counting patterns.. # site patterns = 163 Counting frequencies.. 120 bytes for distance 26080 bytes for lkl0 20864 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.106827 0.010919 0.068983 0.061774 0.068894 0.135212 0.157145 0.076239 lnL0 = -2039.152169 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2039.152169 x= 0.10683 0.01092 0.06898 0.06177 0.06889 0.13521 0.15715 0.07624 1 h-lim-p 0.0006 0.0123 265.6039 2036.644172 9 0.0001 47 | 0/8 2 h-lim-p 0.0010 0.0078 16.0208 2036.613622 4 0.0002 68 | 0/8 3 h-lim-p 0.0010 0.0481 3.7588 2036.611279 5 0.0003 93 | 0/8 4 h-lim-p 0.0008 0.1312 1.6270 2036.611041 3 0.0002 112 | 0/8 5 h-lim-p 0.0007 0.3150 0.4595 2036.611017 2 0.0002 129 | 0/8 6 h-lim-p 0.0008 1.3445 0.1345 2036.611014 0 0.0004 149 | 0/8 7 h-lim-p 0.0050 20.0000 0.0109 2036.611014 0 0.0006 171 | 0/8 8 h-lim-p 0.0634 20.0000 0.0001 2036.610972 0 1.5228 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2036.610970 0 1.0938 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2036.610970 0 2.1875 235 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2036.610970 0 1.0938 255 | 0/8 12 h-lim-p 0.4480 20.0000 0.0000 2036.610970 0 3.5838 278 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2036.610970 0 0.1367 301 | 0/8 14 h-lim-p 1.8478 20.0000 0.0000 2036.610970 0 0.0000 345 Out... lnL = -2036.610970 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2036.610970 Node 7: lnL = -2036.610970 Node 8: lnL = -2036.610970 Node 9: lnL = -2036.610970 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 776 Sequential format.. Reading seq # 1: YGR239C_Sbay Reading seq # 2: YGR239C_Scer Reading seq # 3: YGR239C_Skud Reading seq # 4: YGR239C_Smik Reading seq # 5: YGR239C_Spar Sequences read.. Counting patterns.. # site patterns = 241 Counting frequencies.. 120 bytes for distance 38560 bytes for lkl0 30848 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.125051 0.038271 0.030493 0.098285 0.071404 0.127790 0.200772 0.090624 lnL0 = -3154.950505 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3154.950505 x= 0.12505 0.03827 0.03049 0.09829 0.07140 0.12779 0.20077 0.09062 1 h-lim-p 0.0001 0.0012 320.2333 3150.220397 6 0.0001 36 | 0/8 2 h-lim-p 0.0002 0.0012 73.8477 3149.828942 2 0.0001 52 | 0/8 3 h-lim-p 0.0006 0.0121 18.8078 3149.798974 6 0.0002 78 | 0/8 4 h-lim-p 0.0005 0.0295 6.6278 3149.794565 2 0.0002 94 | 0/8 5 h-lim-p 0.0007 0.1489 2.2916 3149.793810 3 0.0003 113 | 0/8 6 h-lim-p 0.0009 0.2197 0.7943 3149.793741 2 0.0002 130 | 0/8 7 h-lim-p 0.0176 17.0405 0.0110 3149.793741 0 0.0019 152 | 0/8 8 h-lim-p 0.0130 20.0000 0.0016 3149.793439 0 0.2086 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3149.793425 0 1.2500 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3149.793425 0 1.0938 216 | 0/8 11 h-lim-p 0.9712 20.0000 0.0000 3149.793425 0 0.0038 243 | 0/8 12 h-lim-p 0.0013 20.0000 0.0000 3149.793425 0 0.0002 265 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 3149.793425 0 0.0000 291 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 3149.793425 0 0.0000 317 Out... lnL = -3149.793425 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3149.793425 Node 7: lnL = -3149.793425 Node 8: lnL = -3149.793425 Node 9: lnL = -3149.793425 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 739 Sequential format.. Reading seq # 1: YGR243W_Sbay Reading seq # 2: YGR243W_Scer Reading seq # 3: YGR243W_Skud Reading seq # 4: YGR243W_Smik Reading seq # 5: YGR243W_Spar Sequences read.. Counting patterns.. # site patterns = 247 Counting frequencies.. 120 bytes for distance 39520 bytes for lkl0 31616 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.130413 0.083111 0.061445 0.068350 0.073246 0.175342 0.105447 0.094023 lnL0 = -2824.406831 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2824.406831 x= 0.13041 0.08311 0.06145 0.06835 0.07325 0.17534 0.10545 0.09402 1 h-lim-p 0.0022 0.8387 161.3299 2822.039462 8 0.0002 41 | 0/8 2 h-lim-p 0.0005 0.0041 38.6959 2821.861602 6 0.0002 67 | 0/8 3 h-lim-p 0.0005 0.0070 19.4198 2821.822106 5 0.0003 91 | 0/8 4 h-lim-p 0.0018 0.0664 2.7591 2821.821059 5 0.0003 118 | 0/8 5 h-lim-p 0.0010 0.3270 0.7870 2821.820958 3 0.0004 138 | 0/8 6 h-lim-p 0.0011 0.6603 0.2538 2821.820950 0 0.0003 159 | 0/8 7 h-lim-p 0.0483 20.0000 0.0014 2821.820773 0 0.2896 181 | 0/8 8 h-lim-p 0.0011 2.6210 0.3619 2821.820113 0 0.0023 202 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 2821.820047 2 0.9961 226 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2821.820047 0 1.0938 246 | 0/8 11 h-lim-p 1.3093 20.0000 0.0000 2821.820047 0 0.1432 268 | 0/8 12 h-lim-p 0.0495 20.0000 0.0000 2821.820047 0 0.0000 298 | 0/8 13 h-lim-p 0.0011 20.0000 0.0000 2821.820047 0 0.0000 325 Out... lnL = -2821.820047 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2821.820047 Node 7: lnL = -2821.820047 Node 8: lnL = -2821.820047 Node 9: lnL = -2821.820047 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 754 Sequential format.. Reading seq # 1: YGR246C_Sbay Reading seq # 2: YGR246C_Scer Reading seq # 3: YGR246C_Skud Reading seq # 4: YGR246C_Smik Reading seq # 5: YGR246C_Spar Sequences read.. Counting patterns.. # site patterns = 189 Counting frequencies.. 120 bytes for distance 30240 bytes for lkl0 24192 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.277014 0.000060 0.205255 0.180006 0.102957 4.617387 0.301137 0.119008 lnL0 = -3067.626323 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3067.626323 x= 0.27701 0.00006 0.20526 0.18001 0.10296 4.61739 0.30114 0.11901 1 h-lim-p 0.0000 0.0000 121.2041 3067.568843 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0111 39.3873 3067.089793 0 0.0008 40 | 1/8 3 h-lim-p 0.0031 0.0415 9.6290 3067.037539 5 0.0011 64 | 1/8 4 h-lim-p 0.0067 0.1207 1.6464 3067.029481 6 0.0020 93 | 1/8 5 h-lim-p 0.0045 0.2424 0.7251 3066.821744 0 0.0273 107 | 1/8 6 h-lim-p 0.0043 0.0375 4.6380 3064.939338 0 0.0085 127 | 1/8 7 h-lim-p 2.5000 20.0000 0.0100 3064.893744 7 0.7246 158 | 1/8 8 h-lim-p 2.5000 20.0000 0.0005 3064.893640 3 0.8800 184 | 1/8 9 h-lim-p 2.5000 20.0000 0.0000 3064.893640 0 1.0938 203 | 1/8 10 h-lim-p 2.5000 20.0000 0.0000 3064.893640 0 1.0938 222 | 1/8 11 h-lim-p 0.9986 20.0000 0.0000 3064.893640 0 0.8738 241 | 1/8 12 h-lim-p 0.4844 20.0000 0.0000 3064.893640 0 0.0303 263 | 1/8 13 h-lim-p 0.0048 20.0000 0.0001 3064.893640 0 0.0001 287 | 1/8 14 h-lim-p 0.0009 20.0000 0.0000 3064.893640 0 0.0000 316 Out... lnL = -3064.893640 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3064.893640 Node 7: lnL = -3064.893640 Node 8: lnL = -3064.893640 Node 9: lnL = -3064.893640 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 757 Sequential format.. Reading seq # 1: YGR247W_Sbay Reading seq # 2: YGR247W_Scer Reading seq # 3: YGR247W_Skud Reading seq # 4: YGR247W_Smik Reading seq # 5: YGR247W_Spar Sequences read.. Counting patterns.. # site patterns = 295 Counting frequencies.. 120 bytes for distance 47200 bytes for lkl0 37760 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.273869 0.051005 0.074075 0.159071 0.094760 0.233171 0.257468 0.214038 lnL0 = -3616.564994 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3616.564994 x= 0.27387 0.05101 0.07408 0.15907 0.09476 0.23317 0.25747 0.21404 1 h-lim-p 0.0003 0.0021 94.3500 3615.337236 7 0.0003 39 | 0/8 2 h-lim-p 0.0010 0.0083 23.3418 3615.239453 7 0.0004 67 | 0/8 3 h-lim-p 0.0010 0.0634 8.5279 3615.230285 6 0.0003 93 | 0/8 4 h-lim-p 0.0005 0.0988 4.4667 3615.225909 3 0.0006 111 | 0/8 5 h-lim-p 0.0030 0.5583 0.8337 3615.225672 2 0.0007 128 | 0/8 6 h-lim-p 0.0021 0.7783 0.2783 3615.225657 0 0.0005 149 | 0/8 7 h-lim-p 0.0093 20.0000 0.0137 3615.225656 0 0.0020 170 | 0/8 8 h-lim-p 0.0765 20.0000 0.0004 3615.225576 0 0.6121 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3615.225576 0 1.0938 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3615.225576 0 2.1875 233 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3615.225576 0 0.6250 254 | 0/8 12 h-lim-p 0.1764 20.0000 0.0000 3615.225576 0 0.0000 300 Out... lnL = -3615.225576 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3615.225576 Node 7: lnL = -3615.225576 Node 8: lnL = -3615.225576 Node 9: lnL = -3615.225576 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 318 Sequential format.. Reading seq # 1: YGR248W_Sbay Reading seq # 2: YGR248W_Scer Reading seq # 3: YGR248W_Skud Reading seq # 4: YGR248W_Smik Reading seq # 5: YGR248W_Spar Sequences read.. Counting patterns.. # site patterns = 130 Counting frequencies.. 120 bytes for distance 20800 bytes for lkl0 16640 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.151948 0.004946 0.029590 0.186587 0.090818 0.150164 0.073768 0.117297 lnL0 = -1220.520758 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1220.520758 x= 0.15195 0.00495 0.02959 0.18659 0.09082 0.15016 0.07377 0.11730 1 h-lim-p 0.0001 0.0011 138.7182 1217.688844 0 0.0004 23 | 0/8 2 h-lim-p 0.0001 0.0010 45.7110 1217.128184 0 0.0005 37 | 0/8 3 h-lim-p 0.0001 0.0007 39.9833 1216.981470 0 0.0003 51 | 0/8 4 h-lim-p 0.0004 0.0032 9.0254 1216.955497 0 0.0008 64 | 0/8 5 h-lim-p 0.0038 0.0505 1.8537 1216.954308 5 0.0007 87 | 0/8 6 h-lim-p 0.0148 0.2722 0.0906 1216.954232 4 0.0042 110 | 0/8 7 h-lim-p 0.0232 2.5776 0.0163 1216.938305 0 0.2790 133 | 0/8 8 h-lim-p 0.0094 0.0864 0.4820 1216.938173 2 0.0011 159 | 0/8 9 h-lim-p 0.3013 20.0000 0.0018 1216.936609 0 1.2053 181 | 0/8 10 h-lim-p 1.8091 14.4725 0.0006 1216.936284 4 1.0222 212 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1216.936283 0 1.0938 232 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1216.936283 0 0.5469 253 | 0/8 13 h-lim-p 0.5897 20.0000 0.0000 1216.936283 0 0.0369 276 | 0/8 14 h-lim-p 0.0236 20.0000 0.0000 1216.936283 0 0.0000 312 Out... lnL = -1216.936283 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1216.936283 Node 7: lnL = -1216.936283 Node 8: lnL = -1216.936283 Node 9: lnL = -1216.936283 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 867 Sequential format.. Reading seq # 1: YGR249W_Sbay Reading seq # 2: YGR249W_Scer Reading seq # 3: YGR249W_Skud Reading seq # 4: YGR249W_Smik Reading seq # 5: YGR249W_Spar Sequences read.. Counting patterns.. # site patterns = 193 Counting frequencies.. 120 bytes for distance 30880 bytes for lkl0 24704 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.094885 0.025252 0.024701 0.070736 0.032641 0.111809 0.093521 0.071701 lnL0 = -2990.823958 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2990.823958 x= 0.09488 0.02525 0.02470 0.07074 0.03264 0.11181 0.09352 0.07170 1 h-lim-p 0.0001 0.0005 260.0025 2988.904119 7 0.0001 38 | 0/8 2 h-lim-p 0.0001 0.0010 60.0367 2988.730315 3 0.0001 56 | 0/8 3 h-lim-p 0.0002 0.0062 30.3980 2988.703525 6 0.0001 83 | 0/8 4 h-lim-p 0.0002 0.0057 13.0967 2988.697023 6 0.0001 110 | 0/8 5 h-lim-p 0.0004 0.0330 2.7451 2988.696604 3 0.0001 129 | 0/8 6 h-lim-p 0.0009 0.4130 0.3523 2988.696594 2 0.0001 147 | 0/8 7 h-lim-p 0.0027 5.8371 0.0194 2988.696594 0 0.0006 168 | 0/8 8 h-lim-p 0.0252 20.0000 0.0005 2988.696278 0 0.4033 192 | 0/8 9 h-lim-p 1.6167 20.0000 0.0001 2988.696265 2 1.0665 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2988.696265 0 1.0938 238 | 0/8 11 h-lim-p 0.5103 20.0000 0.0000 2988.696265 0 0.2232 258 | 0/8 12 h-lim-p 0.1270 20.0000 0.0000 2988.696265 0 0.1111 278 | 0/8 13 h-lim-p 0.0747 20.0000 0.0000 2988.696265 0 0.0000 310 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 2988.696265 0 0.0000 344 Out... lnL = -2988.696265 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2988.696265 Node 7: lnL = -2988.696265 Node 8: lnL = -2988.696265 Node 9: lnL = -2988.696265 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 843 Sequential format.. Reading seq # 1: YGR250C_Sbay Reading seq # 2: YGR250C_Scer Reading seq # 3: YGR250C_Skud Reading seq # 4: YGR250C_Smik Reading seq # 5: YGR250C_Spar Sequences read.. Counting patterns.. # site patterns = 214 Counting frequencies.. 120 bytes for distance 34240 bytes for lkl0 27392 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.098519 0.018103 0.068873 0.062563 0.049272 0.119774 0.112340 0.067259 lnL0 = -2830.878607 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2830.878607 x= 0.09852 0.01810 0.06887 0.06256 0.04927 0.11977 0.11234 0.06726 1 h-lim-p 0.0002 0.0013 311.9633 2827.688066 3 0.0001 29 | 0/8 2 h-lim-p 0.0003 0.0021 63.5537 2827.315825 7 0.0002 56 | 0/8 3 h-lim-p 0.0006 0.0111 20.1590 2827.297324 6 0.0001 84 | 0/8 4 h-lim-p 0.0003 0.0145 6.6100 2827.294745 4 0.0001 103 | 0/8 5 h-lim-p 0.0003 0.0425 2.9736 2827.293716 2 0.0003 119 | 0/8 6 h-lim-p 0.0008 0.1860 1.0736 2827.293628 0 0.0002 132 | 0/8 7 h-lim-p 0.0039 3.5800 0.0456 2827.293628 0 0.0004 146 | 0/8 8 h-lim-p 0.0282 20.0000 0.0007 2827.292318 0 0.9010 171 | 0/8 9 h-lim-p 0.3906 20.0000 0.0016 2827.292231 0 0.7812 192 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 2827.292224 0 1.0938 212 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2827.292224 0 1.0938 232 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2827.292224 0 0.0000 272 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 2827.292224 0 0.0000 295 Out... lnL = -2827.292224 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2827.292224 Node 7: lnL = -2827.292224 Node 8: lnL = -2827.292224 Node 9: lnL = -2827.292224 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 925 Sequential format.. Reading seq # 1: YGR251W_Sbay Reading seq # 2: YGR251W_Scer Reading seq # 3: YGR251W_Skud Reading seq # 4: YGR251W_Smik Reading seq # 5: YGR251W_Spar Sequences read.. Counting patterns.. # site patterns = 397 Counting frequencies.. 120 bytes for distance 63520 bytes for lkl0 50816 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.241751 0.122835 0.163613 0.155183 0.162499 0.251573 0.369930 0.155514 lnL0 = -4662.315035 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4662.315035 x= 0.24175 0.12283 0.16361 0.15518 0.16250 0.25157 0.36993 0.15551 1 h-lim-p 0.0018 0.0144 82.7849 4660.836019 8 0.0005 38 | 0/8 2 h-lim-p 0.0012 0.0093 27.1256 4660.656857 3 0.0005 56 | 0/8 3 h-lim-p 0.0008 0.0206 17.5723 4660.592668 6 0.0006 84 | 0/8 4 h-lim-p 0.0027 0.0878 3.6788 4660.587854 5 0.0008 108 | 0/8 5 h-lim-p 0.0021 0.3408 1.3239 4660.587157 2 0.0009 124 | 0/8 6 h-lim-p 0.0550 14.3115 0.0223 4660.587154 0 0.0030 139 | 0/8 7 h-lim-p 0.0076 20.0000 0.0088 4660.587100 0 0.0306 161 | 0/8 8 h-lim-p 0.0026 15.7726 0.1045 4660.586512 0 0.0077 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 4660.586506 0 1.0938 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4660.586506 0 1.0938 222 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4660.586506 0 1.0938 242 | 0/8 12 h-lim-p 0.6433 20.0000 0.0000 4660.586506 0 0.0804 264 | 0/8 13 h-lim-p 0.0184 20.0000 0.0000 4660.586506 0 0.0000 294 | 0/8 14 h-lim-p 0.0004 20.0000 0.0000 4660.586506 0 0.0000 318 Out... lnL = -4660.586506 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4660.586506 Node 7: lnL = -4660.586506 Node 8: lnL = -4660.586506 Node 9: lnL = -4660.586506 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 676 Sequential format.. Reading seq # 1: YGR252W_Sbay Reading seq # 2: YGR252W_Scer Reading seq # 3: YGR252W_Skud Reading seq # 4: YGR252W_Smik Reading seq # 5: YGR252W_Spar Sequences read.. Counting patterns.. # site patterns = 306 Counting frequencies.. 120 bytes for distance 48960 bytes for lkl0 39168 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.212518 0.069171 0.108340 0.189965 0.119150 0.294913 0.270125 0.139638 lnL0 = -3340.284382 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3340.284382 x= 0.21252 0.06917 0.10834 0.18997 0.11915 0.29491 0.27012 0.13964 1 h-lim-p 0.0069 1.1904 98.3893 3338.674555 3 0.0004 31 | 0/8 2 h-lim-p 0.0019 0.0157 18.9133 3338.564079 7 0.0006 60 | 0/8 3 h-lim-p 0.0010 0.0319 11.9912 3338.532891 7 0.0006 92 | 0/8 4 h-lim-p 0.0025 0.1195 2.7081 3338.530447 4 0.0007 115 | 0/8 5 h-lim-p 0.0039 0.6511 0.5040 3338.530352 2 0.0008 132 | 0/8 6 h-lim-p 0.0063 5.7978 0.0621 3338.530350 0 0.0014 153 | 0/8 7 h-lim-p 0.0420 20.0000 0.0020 3338.530338 0 0.0630 173 | 0/8 8 h-lim-p 0.0034 20.0000 0.0372 3338.530128 0 0.0137 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3338.530122 0 1.0938 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3338.530122 0 1.0938 235 | 0/8 11 h-lim-p 2.1619 20.0000 0.0000 3338.530122 0 1.8916 255 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3338.530122 0 0.5469 276 | 0/8 13 h-lim-p 0.1241 20.0000 0.0000 3338.530122 0 0.0620 296 | 0/8 14 h-lim-p 0.0292 20.0000 0.0000 3338.530122 0 0.0000 327 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 3338.530122 0 0.0000 362 Out... lnL = -3338.530122 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3338.530122 Node 7: lnL = -3338.530122 Node 8: lnL = -3338.530122 Node 9: lnL = -3338.530122 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 817 Sequential format.. Reading seq # 1: YGR253C_Sbay Reading seq # 2: YGR253C_Scer Reading seq # 3: YGR253C_Skud Reading seq # 4: YGR253C_Smik Reading seq # 5: YGR253C_Spar Sequences read.. Counting patterns.. # site patterns = 408 Counting frequencies.. 120 bytes for distance 65280 bytes for lkl0 52224 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.300050 0.155969 0.088541 0.194962 0.166558 0.293176 0.383015 0.206726 lnL0 = -4177.998337 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4177.998337 x= 0.30005 0.15597 0.08854 0.19496 0.16656 0.29318 0.38301 0.20673 1 h-lim-p 0.0031 0.0247 60.8148 4177.184332 7 0.0005 40 | 0/8 2 h-lim-p 0.0016 0.0186 17.3909 4177.084700 5 0.0007 61 | 0/8 3 h-lim-p 0.0009 0.0342 12.9979 4177.041641 4 0.0007 81 | 0/8 4 h-lim-p 0.0013 0.0593 7.6402 4177.019201 3 0.0011 99 | 0/8 5 h-lim-p 0.0053 0.2233 1.6374 4177.018284 4 0.0008 122 | 0/8 6 h-lim-p 0.0153 4.3190 0.0809 4177.018279 0 0.0017 136 | 0/8 7 h-lim-p 0.0308 20.0000 0.0044 4177.018277 1 0.0151 159 | 0/8 8 h-lim-p 0.0133 20.0000 0.0050 4177.018161 0 0.1065 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4177.018149 1 0.9961 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4177.018149 0 1.0938 224 | 0/8 11 h-lim-p 1.1025 20.0000 0.0000 4177.018149 0 1.1025 244 | 0/8 12 h-lim-p 0.3837 20.0000 0.0000 4177.018149 0 0.0001 275 Out... lnL = -4177.018149 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4177.018149 Node 7: lnL = -4177.018149 Node 8: lnL = -4177.018149 Node 9: lnL = -4177.018149 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 860 Sequential format.. Reading seq # 1: YGR254W_Sbay Reading seq # 2: YGR254W_Scer Reading seq # 3: YGR254W_Skud Reading seq # 4: YGR254W_Smik Reading seq # 5: YGR254W_Spar Sequences read.. Counting patterns.. # site patterns = 254 Counting frequencies.. 120 bytes for distance 40640 bytes for lkl0 32512 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.111605 0.036172 0.048447 0.076541 0.055992 0.134492 0.137314 0.076480 lnL0 = -3264.239643 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3264.239643 x= 0.11160 0.03617 0.04845 0.07654 0.05599 0.13449 0.13731 0.07648 1 h-lim-p 0.0013 0.0667 220.9580 3262.107482 8 0.0001 42 | 0/8 2 h-lim-p 0.0007 0.0057 19.9947 3262.081488 6 0.0001 70 | 0/8 3 h-lim-p 0.0005 0.0367 5.3691 3262.079247 4 0.0002 93 | 0/8 4 h-lim-p 0.0005 0.0828 1.7350 3262.079003 3 0.0002 113 | 0/8 5 h-lim-p 0.0011 0.6048 0.2904 3262.078995 1 0.0002 128 | 0/8 6 h-lim-p 0.0020 5.8491 0.0309 3262.078995 0 0.0002 150 | 0/8 7 h-lim-p 0.0008 20.0000 0.0088 3262.078995 0 0.0003 170 | 0/8 8 h-lim-p 0.0752 20.0000 0.0000 3262.078989 0 1.2026 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3262.078989 0 1.0938 214 | 0/8 10 h-lim-p 0.7029 20.0000 0.0000 3262.078989 0 0.0096 239 | 0/8 11 h-lim-p 0.0046 20.0000 0.0000 3262.078989 0 0.0035 259 | 0/8 12 h-lim-p 0.0022 20.0000 0.0000 3262.078989 0 0.0003 281 | 0/8 13 h-lim-p 0.0001 20.0000 0.0001 3262.078989 0 0.0000 309 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 3262.078989 0 0.0000 340 Out... lnL = -3262.078989 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3262.078989 Node 7: lnL = -3262.078989 Node 8: lnL = -3262.078989 Node 9: lnL = -3262.078989 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 732 Sequential format.. Reading seq # 1: YGR255C_Sbay Reading seq # 2: YGR255C_Scer Reading seq # 3: YGR255C_Skud Reading seq # 4: YGR255C_Smik Reading seq # 5: YGR255C_Spar Sequences read.. Counting patterns.. # site patterns = 298 Counting frequencies.. 120 bytes for distance 47680 bytes for lkl0 38144 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.404098 0.078707 0.092213 0.128462 0.073453 0.243903 0.197597 0.324582 lnL0 = -3504.482702 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3504.482702 x= 0.40410 0.07871 0.09221 0.12846 0.07345 0.24390 0.19760 0.32458 1 h-lim-p 0.0035 0.0282 66.2763 3503.894373 7 0.0003 42 | 0/8 2 h-lim-p 0.0006 0.0075 28.8672 3503.765504 6 0.0004 69 | 0/8 3 h-lim-p 0.0006 0.0104 18.5269 3503.703642 3 0.0005 87 | 0/8 4 h-lim-p 0.0017 0.0427 5.4799 3503.692372 5 0.0009 112 | 0/8 5 h-lim-p 0.0013 0.1262 3.4913 3503.689556 2 0.0006 128 | 0/8 6 h-lim-p 0.0033 0.3283 0.6603 3503.689479 2 0.0004 146 | 0/8 7 h-lim-p 0.0032 6.1230 0.0755 3503.689473 1 0.0016 169 | 0/8 8 h-lim-p 0.2994 20.0000 0.0004 3503.689266 0 1.1977 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3503.689259 1 0.9961 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3503.689259 0 1.2500 233 | 0/8 11 h-lim-p 1.7732 20.0000 0.0000 3503.689259 0 0.8866 253 | 0/8 12 h-lim-p 0.5758 20.0000 0.0000 3503.689259 0 0.0022 280 Out... lnL = -3503.689259 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3503.689259 Node 7: lnL = -3503.689259 Node 8: lnL = -3503.689259 Node 9: lnL = -3503.689259 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 765 Sequential format.. Reading seq # 1: YGR256W_Sbay Reading seq # 2: YGR256W_Scer Reading seq # 3: YGR256W_Skud Reading seq # 4: YGR256W_Smik Reading seq # 5: YGR256W_Spar Sequences read.. Counting patterns.. # site patterns = 292 Counting frequencies.. 120 bytes for distance 46720 bytes for lkl0 37376 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.243492 0.087525 0.041361 0.113099 0.088816 0.272908 0.228498 0.179077 lnL0 = -3469.277329 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3469.277329 x= 0.24349 0.08752 0.04136 0.11310 0.08882 0.27291 0.22850 0.17908 1 h-lim-p 0.0021 0.7040 179.8056 3466.306486 5 0.0002 34 | 0/8 2 h-lim-p 0.0007 0.0058 38.4868 3465.986844 8 0.0005 68 | 0/8 3 h-lim-p 0.0006 0.0084 29.3322 3465.887137 6 0.0003 95 | 0/8 4 h-lim-p 0.0010 0.0245 9.5945 3465.864631 6 0.0006 121 | 0/8 5 h-lim-p 0.0026 0.1145 2.1638 3465.863565 4 0.0005 142 | 0/8 6 h-lim-p 0.0013 0.5077 0.8369 3465.863383 2 0.0006 158 | 0/8 7 h-lim-p 0.0229 12.0040 0.0216 3465.863382 0 0.0025 180 | 0/8 8 h-lim-p 0.0851 20.0000 0.0006 3465.863181 0 0.6811 203 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3465.863177 0 1.2500 223 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3465.863177 0 1.0938 243 | 0/8 11 h-lim-p 1.7453 20.0000 0.0000 3465.863177 0 0.0954 266 | 0/8 12 h-lim-p 0.0452 20.0000 0.0000 3465.863177 0 0.0001 295 Out... lnL = -3465.863177 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3465.863177 Node 7: lnL = -3465.863177 Node 8: lnL = -3465.863177 Node 9: lnL = -3465.863177 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 219 Sequential format.. Reading seq # 1: YGR262C_Sbay Reading seq # 2: YGR262C_Scer Reading seq # 3: YGR262C_Skud Reading seq # 4: YGR262C_Smik Reading seq # 5: YGR262C_Spar Sequences read.. Counting patterns.. # site patterns = 95 Counting frequencies.. 120 bytes for distance 15200 bytes for lkl0 12160 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.189072 0.027959 0.072080 0.133431 0.051863 0.186264 0.199394 0.137900 lnL0 = -954.024341 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 954.024341 x= 0.18907 0.02796 0.07208 0.13343 0.05186 0.18626 0.19939 0.13790 1 h-lim-p 0.0005 0.0040 50.4768 953.447408 7 0.0005 39 | 0/8 2 h-lim-p 0.0026 0.0244 9.6731 953.398036 6 0.0011 65 | 0/8 3 h-lim-p 0.0046 0.0935 2.3101 953.395248 2 0.0011 82 | 0/8 4 h-lim-p 0.0032 0.0876 0.7640 953.395129 4 0.0005 105 | 0/8 5 h-lim-p 0.0012 0.9150 0.2870 953.395098 3 0.0009 132 | 0/8 6 h-lim-p 0.0034 3.2399 0.0738 953.395094 0 0.0015 152 | 0/8 7 h-lim-p 0.0169 20.0000 0.0064 953.395094 0 0.0074 172 | 0/8 8 h-lim-p 0.0463 20.0000 0.0010 953.395026 0 0.3706 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 953.395022 1 0.9961 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 953.395022 0 2.5000 237 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 953.395022 0 0.1367 260 | 0/8 12 h-lim-p 0.1204 20.0000 0.0000 953.395022 0 0.0009 286 Out... lnL = -953.395022 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -953.395022 Node 7: lnL = -953.395022 Node 8: lnL = -953.395022 Node 9: lnL = -953.395022 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 379 Sequential format.. Reading seq # 1: YGR263C_Sbay Reading seq # 2: YGR263C_Scer Reading seq # 3: YGR263C_Skud Reading seq # 4: YGR263C_Smik Reading seq # 5: YGR263C_Spar Sequences read.. Counting patterns.. # site patterns = 177 Counting frequencies.. 120 bytes for distance 28320 bytes for lkl0 22656 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.183159 0.042160 0.088780 0.131293 0.145453 0.244144 0.218564 0.122536 lnL0 = -1754.280671 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1754.280671 x= 0.18316 0.04216 0.08878 0.13129 0.14545 0.24414 0.21856 0.12254 1 h-lim-p 0.0022 0.0180 42.8633 1753.895015 4 0.0004 31 | 0/8 2 h-lim-p 0.0016 0.0165 11.4998 1753.849589 5 0.0007 52 | 0/8 3 h-lim-p 0.0040 0.2389 2.0659 1753.848330 5 0.0006 80 | 0/8 4 h-lim-p 0.0020 0.5519 0.6205 1753.848141 3 0.0011 99 | 0/8 5 h-lim-p 0.0052 2.2736 0.1275 1753.848135 2 0.0009 126 | 0/8 6 h-lim-p 0.0100 20.0000 0.0109 1753.848135 0 0.0022 147 | 0/8 7 h-lim-p 0.1211 20.0000 0.0002 1753.848135 0 0.1060 167 | 0/8 8 h-lim-p 0.0029 20.0000 0.0073 1753.848132 0 0.0086 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1753.848132 0 1.0938 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1753.848132 0 1.0938 228 | 0/8 11 h-lim-p 1.0959 20.0000 0.0000 1753.848132 0 6.5757 250 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1753.848132 0 0.3125 272 | 0/8 13 h-lim-p 0.0185 20.0000 0.0000 1753.848132 0 0.0012 295 | 0/8 14 h-lim-p 0.0006 20.0000 0.0000 1753.848132 0 0.0000 329 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 | 0/8 16 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -1753.848132 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1753.848132 Node 7: lnL = -1753.848132 Node 8: lnL = -1753.848132 Node 9: lnL = -1753.848132 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 856 Sequential format.. Reading seq # 1: YGR264C_Sbay Reading seq # 2: YGR264C_Scer Reading seq # 3: YGR264C_Skud Reading seq # 4: YGR264C_Smik Reading seq # 5: YGR264C_Spar Sequences read.. Counting patterns.. # site patterns = 327 Counting frequencies.. 120 bytes for distance 52320 bytes for lkl0 41856 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.205690 0.091769 0.076074 0.134495 0.104743 0.243248 0.213258 0.142427 lnL0 = -4050.466392 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4050.466392 x= 0.20569 0.09177 0.07607 0.13449 0.10474 0.24325 0.21326 0.14243 1 h-lim-p 0.0100 1.5527 90.1270 4049.562104 8 0.0002 43 | 0/8 2 h-lim-p 0.0010 0.0092 20.0202 4049.486072 5 0.0004 65 | 0/8 3 h-lim-p 0.0007 0.0254 11.7235 4049.471036 3 0.0003 84 | 0/8 4 h-lim-p 0.0010 0.0749 3.4538 4049.469087 3 0.0004 102 | 0/8 5 h-lim-p 0.0051 1.2601 0.2506 4049.469074 2 0.0004 121 | 0/8 6 h-lim-p 0.0014 2.8673 0.0742 4049.469073 0 0.0006 141 | 0/8 7 h-lim-p 0.0068 20.0000 0.0066 4049.469073 0 0.0030 161 | 0/8 8 h-lim-p 0.0294 20.0000 0.0007 4049.469008 0 0.2351 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4049.469006 0 1.0938 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4049.469006 0 1.0938 224 | 0/8 11 h-lim-p 1.6035 20.0000 0.0000 4049.469006 0 0.7015 244 | 0/8 12 h-lim-p 0.4400 20.0000 0.0000 4049.469006 0 0.2200 264 | 0/8 13 h-lim-p 0.0840 20.0000 0.0000 4049.469006 0 0.0000 297 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 4049.469006 0 0.0000 321 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 4049.469006 0 0.0000 345 Out... lnL = -4049.469006 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4049.469006 Node 7: lnL = -4049.469006 Node 8: lnL = -4049.469006 Node 9: lnL = -4049.469006 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 745 Sequential format.. Reading seq # 1: YGR268C_Sbay Reading seq # 2: YGR268C_Scer Reading seq # 3: YGR268C_Skud Reading seq # 4: YGR268C_Smik Reading seq # 5: YGR268C_Spar Sequences read.. Counting patterns.. # site patterns = 228 Counting frequencies.. 120 bytes for distance 36480 bytes for lkl0 29184 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.134972 0.078062 0.043815 0.095671 0.079651 0.153196 0.238650 0.087489 lnL0 = -2933.480542 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2933.480542 x= 0.13497 0.07806 0.04382 0.09567 0.07965 0.15320 0.23865 0.08749 1 h-lim-p 0.0016 0.0128 97.6475 2932.883452 8 0.0001 43 | 0/8 2 h-lim-p 0.0006 0.0123 20.9049 2932.740756 6 0.0007 70 | 0/8 3 h-lim-p 0.0004 0.0065 37.8451 2932.674320 7 0.0002 100 | 0/8 4 h-lim-p 0.0022 0.0376 3.8770 2932.672601 2 0.0002 118 | 0/8 5 h-lim-p 0.0009 0.1957 1.0890 2932.672411 2 0.0003 134 | 0/8 6 h-lim-p 0.0019 0.7156 0.1962 2932.672402 0 0.0005 147 | 0/8 7 h-lim-p 0.0043 5.6051 0.0219 2932.672402 0 0.0005 169 | 0/8 8 h-lim-p 0.0146 20.0000 0.0007 2932.672270 0 0.6986 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2932.672265 0 1.0938 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2932.672265 0 1.0938 234 | 0/8 11 h-lim-p 1.8167 20.0000 0.0000 2932.672265 0 1.8167 254 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2932.672265 0 0.0098 281 | 0/8 13 h-lim-p 0.0024 20.0000 0.0000 2932.672265 0 0.0003 303 | 0/8 14 h-lim-p 0.0009 20.0000 0.0000 2932.672265 0 0.0001 326 Out... lnL = -2932.672265 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2932.672265 Node 7: lnL = -2932.672265 Node 8: lnL = -2932.672265 Node 9: lnL = -2932.672265 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 791 Sequential format.. Reading seq # 1: YGR273C_Sbay Reading seq # 2: YGR273C_Scer Reading seq # 3: YGR273C_Skud Reading seq # 4: YGR273C_Smik Reading seq # 5: YGR273C_Spar Sequences read.. Counting patterns.. # site patterns = 385 Counting frequencies.. 120 bytes for distance 61600 bytes for lkl0 49280 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.381166 0.142410 0.106020 0.153184 0.234369 0.265006 0.279649 0.272428 lnL0 = -4021.911348 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4021.911348 x= 0.38117 0.14241 0.10602 0.15318 0.23437 0.26501 0.27965 0.27243 1 h-lim-p 0.0215 2.2815 61.1938 4021.068717 8 0.0005 46 | 0/8 2 h-lim-p 0.0020 0.0226 14.6381 4020.973380 2 0.0009 62 | 0/8 3 h-lim-p 0.0009 0.0254 14.8677 4020.903716 1 0.0011 76 | 0/8 4 h-lim-p 0.0118 0.3540 1.4177 4020.902556 3 0.0012 96 | 0/8 5 h-lim-p 0.0045 1.1114 0.3768 4020.902485 1 0.0011 111 | 0/8 6 h-lim-p 0.0064 4.7311 0.0651 4020.902481 0 0.0016 132 | 0/8 7 h-lim-p 0.0140 20.0000 0.0075 4020.902471 1 0.0175 154 | 0/8 8 h-lim-p 0.0071 18.3220 0.0185 4020.902078 0 0.0566 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 4020.902032 1 0.9961 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4020.902032 0 1.0938 219 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4020.902032 0 1.0938 239 | 0/8 12 h-lim-p 0.8810 20.0000 0.0000 4020.902032 0 0.2203 260 | 0/8 13 h-lim-p 0.0000 0.9933 0.3988 4020.902032 0 0.0000 280 | 0/8 14 h-lim-p 0.0364 20.0000 0.0001 4020.902032 0 0.0000 318 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 4020.902032 0 0.0000 349 Out... lnL = -4020.902032 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4020.902032 Node 7: lnL = -4020.902032 Node 8: lnL = -4020.902032 Node 9: lnL = -4020.902032 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 168 Sequential format.. Reading seq # 1: YGR276C_Sbay Reading seq # 2: YGR276C_Scer Reading seq # 3: YGR276C_Skud Reading seq # 4: YGR276C_Smik Reading seq # 5: YGR276C_Spar Sequences read.. Counting patterns.. # site patterns = 66 Counting frequencies.. 120 bytes for distance 10560 bytes for lkl0 8448 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.080408 0.000060 0.080028 0.070261 0.058896 0.074109 0.168784 0.047807 lnL0 = -601.481243 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 601.481243 x= 0.08041 0.00006 0.08003 0.07026 0.05890 0.07411 0.16878 0.04781 1 h-lim-p 0.0003 0.0023 165.9385 599.361285 8 0.0002 38 | 0/8 2 h-lim-p 0.0003 0.0024 36.9480 599.009818 0 0.0006 51 | 0/8 3 h-lim-p 0.0029 0.0240 7.5558 598.982528 7 0.0010 81 | 0/8 4 h-lim-p 0.0015 0.0378 5.0974 598.976903 3 0.0006 99 | 0/8 5 h-lim-p 0.0080 0.2419 0.3771 598.976851 4 0.0006 123 | 0/8 6 h-lim-p 0.0041 2.9730 0.0582 598.976733 0 0.0083 144 | 0/8 7 h-lim-p 0.0107 1.8827 0.0448 598.963979 0 0.0857 167 | 0/8 8 h-lim-p 0.0111 0.2430 0.3447 598.963944 3 0.0006 196 | 0/8 9 h-lim-p 0.2503 20.0000 0.0008 598.962165 0 1.5019 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 598.962117 2 1.0889 242 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 598.962117 0 1.0938 262 | 0/8 12 h-lim-p 1.8561 20.0000 0.0000 598.962117 0 2.7841 282 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 598.962117 0 0.1367 305 | 0/8 14 h-lim-p 0.1290 20.0000 0.0000 598.962117 0 0.0010 331 | 0/8 15 h-lim-p 0.0004 20.0000 0.0000 598.962117 0 0.0000 370 Out... lnL = -598.962117 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -598.962117 Node 7: lnL = -598.962117 Node 8: lnL = -598.962117 Node 9: lnL = -598.962117 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 672 Sequential format.. Reading seq # 1: YGR283C_Sbay Reading seq # 2: YGR283C_Scer Reading seq # 3: YGR283C_Skud Reading seq # 4: YGR283C_Smik Reading seq # 5: YGR283C_Spar Sequences read.. Counting patterns.. # site patterns = 155 Counting frequencies.. 120 bytes for distance 24800 bytes for lkl0 19840 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.265954 0.100172 0.084249 0.155651 0.126148 0.220284 4.676300 0.057745 lnL0 = -2675.818599 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2675.818599 x= 0.26595 0.10017 0.08425 0.15565 0.12615 0.22028 4.67630 0.05775 1 h-lim-p 0.0015 0.0124 39.2909 2675.489430 7 0.0004 39 | 0/8 2 h-lim-p 0.0012 0.0175 14.0409 2675.440982 5 0.0005 60 | 0/8 3 h-lim-p 0.0012 0.0458 6.5892 2675.433283 5 0.0004 82 | 0/8 4 h-lim-p 0.0017 0.1122 1.7244 2675.432677 4 0.0004 103 | 0/8 5 h-lim-p 0.0775 20.0000 0.0099 2675.432677 0 0.0005 121 | 0/8 6 h-lim-p 0.0705 20.0000 0.0001 2675.432675 0 0.5640 144 | 0/8 7 h-lim-p 0.0261 20.0000 0.0016 2675.432673 0 0.6260 168 | 0/8 8 h-lim-p 2.5000 20.0000 0.0000 2675.432673 0 1.2500 188 | 0/8 9 h-lim-p 1.1952 20.0000 0.0000 2675.432673 0 1.0458 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2675.432673 0 0.2734 230 | 0/8 11 h-lim-p 0.0165 20.0000 0.0000 2675.432673 0 0.0002 255 | 0/8 12 h-lim-p 0.0001 20.0000 0.0000 2675.432673 0 0.0000 289 | 0/8 13 h-lim-p 0.0000 20.0000 0.0006 | 0/8 14 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -2675.432673 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2675.432673 Node 7: lnL = -2675.432673 Node 8: lnL = -2675.432673 Node 9: lnL = -2675.432673 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 313 Sequential format.. Reading seq # 1: YGR284C_Sbay Reading seq # 2: YGR284C_Scer Reading seq # 3: YGR284C_Skud Reading seq # 4: YGR284C_Smik Reading seq # 5: YGR284C_Spar Sequences read.. Counting patterns.. # site patterns = 105 Counting frequencies.. 120 bytes for distance 16800 bytes for lkl0 13440 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.169180 0.041578 0.059442 0.080171 0.058881 0.145932 0.136077 0.121263 lnL0 = -1176.145947 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1176.145947 x= 0.16918 0.04158 0.05944 0.08017 0.05888 0.14593 0.13608 0.12126 1 h-lim-p 0.0002 0.0015 98.5156 1174.269895 0 0.0004 23 | 0/8 2 h-lim-p 0.0011 0.0089 25.0589 1173.999947 7 0.0009 53 | 0/8 3 h-lim-p 0.0019 0.0152 10.7380 1173.971022 6 0.0006 80 | 0/8 4 h-lim-p 0.0056 0.2194 1.1293 1173.970728 4 0.0004 104 | 0/8 5 h-lim-p 0.0007 0.1553 0.7209 1173.970630 3 0.0005 124 | 0/8 6 h-lim-p 0.0024 0.9535 0.1358 1173.970572 3 0.0020 150 | 0/8 7 h-lim-p 0.0056 5.2602 0.0488 1173.966518 0 0.0673 173 | 0/8 8 h-lim-p 0.0039 0.2201 0.8418 1173.948766 0 0.0078 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0015 1173.946474 4 1.0199 223 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1173.946473 0 1.0938 243 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1173.946473 0 1.0938 263 | 0/8 12 h-lim-p 2.4131 20.0000 0.0000 1173.946473 0 2.4131 283 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1173.946473 0 0.0098 310 | 0/8 14 h-lim-p 0.0048 20.0000 0.0000 1173.946473 0 0.0000 350 Out... lnL = -1173.946473 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1173.946473 Node 7: lnL = -1173.946473 Node 8: lnL = -1173.946473 Node 9: lnL = -1173.946473 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 865 Sequential format.. Reading seq # 1: YGR285C_Sbay Reading seq # 2: YGR285C_Scer Reading seq # 3: YGR285C_Skud Reading seq # 4: YGR285C_Smik Reading seq # 5: YGR285C_Spar Sequences read.. Counting patterns.. # site patterns = 350 Counting frequencies.. 120 bytes for distance 56000 bytes for lkl0 44800 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.196022 0.168924 0.095891 0.214175 0.159954 0.332334 0.263973 0.103458 lnL0 = -3999.429634 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3999.429634 x= 0.19602 0.16892 0.09589 0.21418 0.15995 0.33233 0.26397 0.10346 1 h-lim-p 0.0093 1.4891 92.8641 3997.637913 8 0.0004 40 | 0/8 2 h-lim-p 0.0015 0.0118 20.9757 3997.513474 5 0.0006 62 | 0/8 3 h-lim-p 0.0019 0.0345 6.3310 3997.496026 4 0.0010 84 | 0/8 4 h-lim-p 0.0054 0.3724 1.1273 3997.495515 4 0.0008 108 | 0/8 5 h-lim-p 0.0017 0.7772 0.5578 3997.495437 3 0.0006 127 | 0/8 6 h-lim-p 0.0025 3.7079 0.1307 3997.495429 1 0.0010 149 | 0/8 7 h-lim-p 0.0066 20.0000 0.0198 3997.495429 0 0.0029 169 | 0/8 8 h-lim-p 0.1051 20.0000 0.0005 3997.495297 0 0.8410 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3997.495295 0 1.0938 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3997.495295 0 1.0938 232 | 0/8 11 h-lim-p 1.3759 20.0000 0.0000 3997.495295 0 1.3759 252 | 0/8 12 h-lim-p 1.2439 20.0000 0.0000 3997.495295 0 0.0389 276 | 0/8 13 h-lim-p 0.0029 20.0000 0.0001 3997.495295 0 0.0029 296 | 0/8 14 h-lim-p 0.0001 20.0000 0.0025 3997.495295 0 0.0000 319 | 0/8 15 h-lim-p 0.0016 20.0000 0.0000 3997.495295 0 0.0000 353 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 | 0/8 17 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -3997.495295 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3997.495295 Node 7: lnL = -3997.495295 Node 8: lnL = -3997.495295 Node 9: lnL = -3997.495295 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 860 Sequential format.. Reading seq # 1: YGR286C_Sbay Reading seq # 2: YGR286C_Scer Reading seq # 3: YGR286C_Skud Reading seq # 4: YGR286C_Smik Reading seq # 5: YGR286C_Spar Sequences read.. Counting patterns.. # site patterns = 364 Counting frequencies.. 120 bytes for distance 58240 bytes for lkl0 46592 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.288718 0.036885 0.088685 0.115590 0.126792 0.310246 0.254379 0.205986 lnL0 = -4282.694928 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4282.694928 x= 0.28872 0.03688 0.08868 0.11559 0.12679 0.31025 0.25438 0.20599 1 h-lim-p 0.0016 0.0125 159.6028 4279.885658 8 0.0002 45 | 0/8 2 h-lim-p 0.0006 0.0044 38.6062 4279.621380 8 0.0004 76 | 0/8 3 h-lim-p 0.0006 0.0175 22.3300 4279.530990 7 0.0005 104 | 0/8 4 h-lim-p 0.0016 0.0313 6.6928 4279.523353 3 0.0004 123 | 0/8 5 h-lim-p 0.0020 0.3304 1.2579 4279.522588 2 0.0010 139 | 0/8 6 h-lim-p 0.0059 1.0038 0.2182 4279.522576 2 0.0005 158 | 0/8 7 h-lim-p 0.0051 16.4649 0.0200 4279.522574 1 0.0025 181 | 0/8 8 h-lim-p 0.0298 20.0000 0.0017 4279.522114 0 0.4773 205 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 4279.522071 1 0.9961 227 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4279.522071 0 1.0938 247 | 0/8 11 h-lim-p 1.1227 20.0000 0.0000 4279.522071 0 0.5614 267 | 0/8 12 h-lim-p 0.3366 20.0000 0.0000 4279.522071 0 0.0013 294 | 0/8 13 h-lim-p 0.0073 20.0000 0.0000 4279.522071 0 0.0037 314 Out... lnL = -4279.522071 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4279.522071 Node 7: lnL = -4279.522071 Node 8: lnL = -4279.522071 Node 9: lnL = -4279.522071 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 39 Sequential format.. Reading seq # 1: YHL006C_Sbay Reading seq # 2: YHL006C_Scer Reading seq # 3: YHL006C_Skud Reading seq # 4: YHL006C_Smik Reading seq # 5: YHL006C_Spar Sequences read.. Counting patterns.. # site patterns = 15 Counting frequencies.. 120 bytes for distance 2400 bytes for lkl0 1920 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 1.354104 0.000060 2.289134 0.210865 0.210866 2.499999 2.499999 1.145895 lnL0 = -84.544384 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 84.544384 x= 1.35410 0.00006 2.28913 0.21087 0.21087 2.50000 2.50000 1.14590 1 h-lim-p 2.5000 20.0000 0.0000 84.544384 0 0.0171 28 | 0/8 2 h-lim-p 2.5000 20.0000 0.0000 84.544384 0 1.0938 48 | 0/8 3 h-lim-p 2.5000 20.0000 0.0000 84.544384 0 5.0000 69 | 0/8 4 h-lim-p 1.2500 20.0000 0.0000 84.544384 0 0.1563 91 Out... lnL = -84.544384 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -84.544384 Node 7: lnL = -84.544384 Node 8: lnL = -84.544384 Node 9: lnL = -84.544384 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 419 Sequential format.. Reading seq # 1: YHL007C_Sbay Reading seq # 2: YHL007C_Scer Reading seq # 3: YHL007C_Skud Reading seq # 4: YHL007C_Smik Reading seq # 5: YHL007C_Spar Sequences read.. Counting patterns.. # site patterns = 106 Counting frequencies.. 120 bytes for distance 16960 bytes for lkl0 13568 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.246363 0.084077 0.049233 0.070556 0.055348 0.104032 0.043041 0.195567 lnL0 = -1238.596429 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1238.596429 x= 0.24636 0.08408 0.04923 0.07056 0.05535 0.10403 0.04304 0.19557 1 h-lim-p 0.0004 0.0031 86.4824 1237.799638 8 0.0002 41 | 0/8 2 h-lim-p 0.0006 0.0046 15.4029 1237.766178 4 0.0003 61 | 0/8 3 h-lim-p 0.0004 0.0056 10.1516 1237.720581 0 0.0017 75 | 0/8 4 h-lim-p 0.0001 0.0009 48.1748 1237.451328 m 0.0009 87 | 1/8 5 h-lim-p 0.0031 0.0393 11.1242 1237.410524 7 0.0005 118 | 1/8 6 h-lim-p 0.0018 0.0387 3.2200 1237.408111 3 0.0004 137 | 1/8 7 h-lim-p 0.0112 12.7453 0.1185 1237.406456 0 0.0447 151 | 1/8 8 h-lim-p 0.0559 5.1592 0.0948 1237.396773 1 0.0698 172 | 1/8 9 h-lim-p 0.7333 20.0000 0.0090 1237.389704 3 0.6130 197 | 1/8 10 h-lim-p 2.5000 20.0000 0.0002 1237.389621 2 1.0889 220 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 1237.389620 0 1.0938 239 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 1237.389620 0 0.5469 259 | 1/8 13 h-lim-p 1.1517 20.0000 0.0000 1237.389620 0 0.0000 298 Out... lnL = -1237.389620 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1237.389620 Node 7: lnL = -1237.389620 Node 8: lnL = -1237.389620 Node 9: lnL = -1237.389620 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 876 Sequential format.. Reading seq # 1: YHL008C_Sbay Reading seq # 2: YHL008C_Scer Reading seq # 3: YHL008C_Skud Reading seq # 4: YHL008C_Smik Reading seq # 5: YHL008C_Spar Sequences read.. Counting patterns.. # site patterns = 365 Counting frequencies.. 120 bytes for distance 58400 bytes for lkl0 46720 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.191428 0.086085 0.021752 0.613881 0.134281 0.172356 0.198156 0.103936 lnL0 = -4128.762514 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4128.762514 x= 0.19143 0.08608 0.02175 0.61388 0.13428 0.17236 0.19816 0.10394 1 h-lim-p 0.0009 0.0068 139.2273 4126.462507 8 0.0003 44 | 0/8 2 h-lim-p 0.0003 0.0024 66.8219 4125.956338 6 0.0003 68 | 0/8 3 h-lim-p 0.0005 0.0073 34.8968 4125.750765 5 0.0004 89 | 0/8 4 h-lim-p 0.0011 0.0217 13.5629 4125.698911 6 0.0007 117 | 0/8 5 h-lim-p 0.0009 0.0405 10.1383 4125.658436 0 0.0014 129 | 0/8 6 h-lim-p 0.0034 0.0492 4.1273 4125.654837 5 0.0006 154 | 0/8 7 h-lim-p 0.0030 0.2462 0.7593 4125.654728 3 0.0004 174 | 0/8 8 h-lim-p 0.2193 20.0000 0.0014 4125.653469 0 1.3156 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 4125.653410 1 0.9961 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4125.653409 0 1.0938 238 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4125.653409 0 1.0938 258 | 0/8 12 h-lim-p 1.0812 20.0000 0.0000 4125.653409 0 0.1183 280 | 0/8 13 h-lim-p 0.0060 20.0000 0.0002 4125.653409 0 0.0000 317 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 4125.653409 0 0.0000 345 Out... lnL = -4125.653409 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4125.653409 Node 7: lnL = -4125.653409 Node 8: lnL = -4125.653409 Node 9: lnL = -4125.653409 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 847 Sequential format.. Reading seq # 1: YHL009C_Sbay Reading seq # 2: YHL009C_Scer Reading seq # 3: YHL009C_Skud Reading seq # 4: YHL009C_Smik Reading seq # 5: YHL009C_Spar Sequences read.. Counting patterns.. # site patterns = 422 Counting frequencies.. 120 bytes for distance 67520 bytes for lkl0 54016 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.227916 0.000060 0.091606 0.332061 0.213044 0.334373 0.466227 0.129387 lnL0 = -4360.245159 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4360.245159 x= 0.22792 0.00006 0.09161 0.33206 0.21304 0.33437 0.46623 0.12939 1 h-lim-p 0.0004 0.0028 129.5748 4351.144606 0 0.0014 24 | 0/8 2 h-lim-p 0.0003 0.0024 81.9079 4349.954647 0 0.0006 37 | 0/8 3 h-lim-p 0.0013 0.0403 38.5759 4349.669446 6 0.0005 62 | 0/8 4 h-lim-p 0.0007 0.0060 23.0357 4349.583716 7 0.0005 94 | 0/8 5 h-lim-p 0.0013 0.0178 7.9782 4349.558696 5 0.0009 118 | 0/8 6 h-lim-p 0.0054 0.1738 1.3570 4349.554779 2 0.0023 134 | 0/8 7 h-lim-p 0.0066 0.6155 0.4838 4349.521235 0 0.0263 148 | 0/8 8 h-lim-p 0.0103 0.1502 1.2422 4348.811232 0 0.0410 170 | 0/8 9 h-lim-p 2.5000 20.0000 0.0070 4348.792347 6 0.9078 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0004 4348.792218 2 0.9961 222 | 0/8 11 h-lim-p 2.5000 20.0000 0.0001 4348.792217 0 1.0938 242 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4348.792217 0 1.0938 262 | 0/8 13 h-lim-p 1.1497 20.0000 0.0000 4348.792217 0 1.0060 282 | 0/8 14 h-lim-p 0.2727 20.0000 0.0000 4348.792217 0 0.0043 307 | 0/8 15 h-lim-p 0.0023 20.0000 0.0001 4348.792217 0 0.0000 332 | 0/8 16 h-lim-p 0.0009 20.0000 0.0000 4348.792217 0 0.0000 362 Out... lnL = -4348.792217 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4348.792217 Node 7: lnL = -4348.792217 Node 8: lnL = -4348.792217 Node 9: lnL = -4348.792217 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 373 Sequential format.. Reading seq # 1: YHL010C_Sbay Reading seq # 2: YHL010C_Scer Reading seq # 3: YHL010C_Skud Reading seq # 4: YHL010C_Smik Reading seq # 5: YHL010C_Spar Sequences read.. Counting patterns.. # site patterns = 183 Counting frequencies.. 120 bytes for distance 29280 bytes for lkl0 23424 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.245944 0.097784 0.077634 0.126045 0.165085 0.213434 0.317719 0.153559 lnL0 = -1858.340878 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1858.340878 x= 0.24594 0.09778 0.07763 0.12604 0.16509 0.21343 0.31772 0.15356 1 h-lim-p 0.0035 0.0279 41.1283 1857.774918 8 0.0007 38 | 0/8 2 h-lim-p 0.0020 0.0159 11.4023 1857.722296 5 0.0009 59 | 0/8 3 h-lim-p 0.0021 0.0907 4.7580 1857.712694 2 0.0010 75 | 0/8 4 h-lim-p 0.0017 0.1681 2.6278 1857.709973 5 0.0010 100 | 0/8 5 h-lim-p 0.0041 0.6129 0.6657 1857.709662 3 0.0016 118 | 0/8 6 h-lim-p 0.0042 1.1410 0.2448 1857.709633 2 0.0011 143 | 0/8 7 h-lim-p 0.0283 20.0000 0.0096 1857.709632 0 0.0062 164 | 0/8 8 h-lim-p 0.0251 20.0000 0.0024 1857.709446 0 0.3017 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1857.709440 1 0.9961 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1857.709440 0 2.1875 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1857.709440 0 1.0938 249 | 0/8 12 h-lim-p 0.4599 20.0000 0.0000 1857.709440 0 3.6795 272 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1857.709440 0 0.1562 295 | 0/8 14 h-lim-p 0.0158 20.0000 0.0000 1857.709440 0 0.0010 318 | 0/8 15 h-lim-p 0.0001 20.0000 0.0001 1857.709440 0 0.0000 353 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1857.709440 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1857.709440 Node 7: lnL = -1857.709440 Node 8: lnL = -1857.709440 Node 9: lnL = -1857.709440 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 359 Sequential format.. Reading seq # 1: YHL011C_Sbay Reading seq # 2: YHL011C_Scer Reading seq # 3: YHL011C_Skud Reading seq # 4: YHL011C_Smik Reading seq # 5: YHL011C_Spar Sequences read.. Counting patterns.. # site patterns = 107 Counting frequencies.. 120 bytes for distance 17120 bytes for lkl0 13696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.107280 0.028610 0.026186 0.062734 0.040100 0.112786 0.126988 0.069831 lnL0 = -1281.772211 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1281.772211 x= 0.10728 0.02861 0.02619 0.06273 0.04010 0.11279 0.12699 0.06983 1 h-lim-p 0.0001 0.0011 63.2813 1281.443208 1 0.0002 24 | 0/8 2 h-lim-p 0.0005 0.0040 14.9885 1281.419437 3 0.0002 42 | 0/8 3 h-lim-p 0.0006 0.0222 5.4471 1281.416707 5 0.0002 67 | 0/8 4 h-lim-p 0.0004 0.0347 2.5848 1281.416130 3 0.0002 85 | 0/8 5 h-lim-p 0.0010 0.1756 0.5774 1281.416090 3 0.0003 104 | 0/8 6 h-lim-p 0.0009 0.9375 0.1683 1281.416085 0 0.0004 124 | 0/8 7 h-lim-p 0.0033 7.6637 0.0221 1281.416084 0 0.0014 144 | 0/8 8 h-lim-p 0.0238 20.0000 0.0013 1281.415602 0 0.3815 168 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1281.415578 2 0.9961 192 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1281.415578 0 2.1875 212 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1281.415578 0 0.0195 238 | 0/8 12 h-lim-p 0.0043 20.0000 0.0000 1281.415578 0 0.0043 258 | 0/8 13 h-lim-p 0.0020 20.0000 0.0000 1281.415578 0 0.0003 280 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 1281.415578 0 0.0000 302 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 1281.415578 0 0.0000 334 | 0/8 16 h-lim-p 0.0000 20.0000 0.0073 | 0/8 17 h-lim-p 0.0000 20.0000 0.0073 Out... lnL = -1281.415578 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1281.415578 Node 7: lnL = -1281.415578 Node 8: lnL = -1281.415578 Node 9: lnL = -1281.415578 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 638 Sequential format.. Reading seq # 1: YHL012W_Sbay Reading seq # 2: YHL012W_Scer Reading seq # 3: YHL012W_Skud Reading seq # 4: YHL012W_Smik Reading seq # 5: YHL012W_Spar Sequences read.. Counting patterns.. # site patterns = 317 Counting frequencies.. 120 bytes for distance 50720 bytes for lkl0 40576 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.331066 0.000060 0.241359 0.276046 0.104619 0.656425 0.316007 0.203611 lnL0 = -3314.288985 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3314.288985 x= 0.33107 0.00006 0.24136 0.27605 0.10462 0.65642 0.31601 0.20361 1 h-lim-p 0.0000 0.0000 173.9553 3314.251106 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0038 180.3998 3306.266567 0 0.0010 40 | 1/8 3 h-lim-p 0.0011 0.0089 52.0627 3304.616693 0 0.0017 52 | 1/8 4 h-lim-p 0.0026 0.0209 28.9272 3304.018442 7 0.0019 81 | 1/8 5 h-lim-p 0.0064 0.0837 8.4129 3303.871258 5 0.0035 104 | 1/8 6 h-lim-p 0.0075 0.0822 3.8779 3303.682505 6 0.0080 130 | 1/8 7 h-lim-p 0.0350 0.5832 0.8912 3293.762375 0 0.1400 144 | 1/8 8 h-lim-p 0.5927 4.7416 0.0402 3293.264003 6 0.6601 176 | 1/8 9 h-lim-p 1.9696 20.0000 0.0135 3293.242319 4 1.0031 204 | 1/8 10 h-lim-p 2.5000 20.0000 0.0046 3293.240728 4 0.7063 234 | 1/8 11 h-lim-p 2.5000 20.0000 0.0004 3293.240686 3 0.6718 260 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 3293.240686 0 0.6250 280 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 3293.240686 0 1.0938 299 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 3293.240686 0 1.0938 318 | 1/8 15 h-lim-p 1.3982 20.0000 0.0000 3293.240686 0 1.2234 337 | 1/8 16 h-lim-p 1.5251 20.0000 0.0000 3293.240686 0 0.7625 356 | 1/8 17 h-lim-p 0.3871 20.0000 0.0000 3293.240686 0 0.3871 375 | 1/8 18 h-lim-p 0.1053 20.0000 0.0000 3293.240686 0 0.0000 412 Out... lnL = -3293.240686 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3293.240686 Node 7: lnL = -3293.240686 Node 8: lnL = -3293.240686 Node 9: lnL = -3293.240686 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 660 Sequential format.. Reading seq # 1: YHL013C_Sbay Reading seq # 2: YHL013C_Scer Reading seq # 3: YHL013C_Skud Reading seq # 4: YHL013C_Smik Reading seq # 5: YHL013C_Spar Sequences read.. Counting patterns.. # site patterns = 284 Counting frequencies.. 120 bytes for distance 45440 bytes for lkl0 36352 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.241443 0.000060 0.098714 0.203858 0.121718 0.313397 0.291822 0.150461 lnL0 = -3146.298581 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3146.298581 x= 0.24144 0.00006 0.09871 0.20386 0.12172 0.31340 0.29182 0.15046 1 h-lim-p 0.0014 0.0115 98.4935 3144.560675 7 0.0003 35 | 0/8 2 h-lim-p 0.0016 0.0139 19.3956 3144.452764 7 0.0006 63 | 0/8 3 h-lim-p 0.0012 0.0375 9.9051 3144.424527 7 0.0007 94 | 0/8 4 h-lim-p 0.0024 0.1102 2.9672 3144.421576 5 0.0008 118 | 0/8 5 h-lim-p 0.0108 1.1742 0.2076 3144.421554 2 0.0009 138 | 0/8 6 h-lim-p 0.0060 10.1340 0.0307 3144.421474 0 0.0120 159 | 0/8 7 h-lim-p 0.0043 1.0192 0.0861 3144.419788 0 0.0171 181 | 0/8 8 h-lim-p 0.0023 0.5519 0.6420 3144.416138 0 0.0046 202 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 3144.415851 2 0.9961 226 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3144.415851 0 1.0938 246 | 0/8 11 h-lim-p 1.3269 20.0000 0.0000 3144.415851 0 1.1610 266 | 0/8 12 h-lim-p 1.0263 20.0000 0.0000 3144.415851 0 8.2106 289 | 0/8 13 h-lim-p 0.1483 20.0000 0.0003 3144.415851 0 0.0162 311 | 0/8 14 h-lim-p 0.0042 20.0000 0.0010 3144.415851 0 0.0000 349 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 3144.415851 0 0.0001 369 Out... lnL = -3144.415851 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3144.415851 Node 7: lnL = -3144.415851 Node 8: lnL = -3144.415851 Node 9: lnL = -3144.415851 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 119 Sequential format.. Reading seq # 1: YHL014C_Sbay Reading seq # 2: YHL014C_Scer Reading seq # 3: YHL014C_Skud Reading seq # 4: YHL014C_Smik Reading seq # 5: YHL014C_Spar Sequences read.. Counting patterns.. # site patterns = 44 Counting frequencies.. 120 bytes for distance 7040 bytes for lkl0 5632 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.085434 0.011273 0.000232 0.063326 0.039000 0.210268 0.151979 0.047204 lnL0 = -433.715805 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 433.715805 x= 0.08543 0.01127 0.00023 0.06333 0.03900 0.21027 0.15198 0.04720 1 h-lim-p 0.0000 0.1427 703.0864 430.362318 0 0.0000 23 | 0/8 2 h-lim-p 0.0004 0.0034 16.7443 430.275474 0 0.0008 36 | 0/8 3 h-lim-p 0.0013 0.0141 10.9955 430.229586 4 0.0010 56 | 0/8 4 h-lim-p 0.0023 0.0263 4.8459 430.220202 6 0.0010 79 | 0/8 5 h-lim-p 0.0028 0.0227 1.5017 430.219641 3 0.0006 98 | 0/8 6 h-lim-p 0.0009 0.2853 0.9334 430.219230 0 0.0014 110 | 0/8 7 h-lim-p 0.0207 1.1253 0.0615 430.219171 2 0.0048 135 | 0/8 8 h-lim-p 0.0125 2.1365 0.0239 430.210491 0 0.1496 158 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 430.210392 2 1.1719 182 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 430.210312 0 7.5000 203 | 0/8 11 h-lim-p 2.5000 20.0000 0.0001 430.210305 1 1.0938 225 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 430.210305 0 2.1875 245 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 430.210305 0 1.0938 265 | 0/8 14 h-lim-p 0.9214 20.0000 0.0000 430.210305 0 3.6858 287 | 0/8 15 h-lim-p 2.4025 20.0000 0.0000 430.210305 0 0.1314 310 | 0/8 16 h-lim-p 0.6410 20.0000 0.0000 430.210305 0 0.0013 338 Out... lnL = -430.210305 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -430.210305 Node 7: lnL = -430.210305 Node 8: lnL = -430.210305 Node 9: lnL = -430.210305 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 871 Sequential format.. Reading seq # 1: YHL015W_Sbay Reading seq # 2: YHL015W_Scer Reading seq # 3: YHL015W_Skud Reading seq # 4: YHL015W_Smik Reading seq # 5: YHL015W_Spar Sequences read.. Counting patterns.. # site patterns = 341 Counting frequencies.. 120 bytes for distance 54560 bytes for lkl0 43648 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.194265 0.043803 0.174109 0.128730 0.105614 0.259554 0.236509 0.109582 lnL0 = -4214.398338 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4214.398338 x= 0.19427 0.04380 0.17411 0.12873 0.10561 0.25955 0.23651 0.10958 1 h-lim-p 0.0018 0.0354 218.1956 4209.683146 6 0.0002 37 | 0/8 2 h-lim-p 0.0006 0.0049 33.1505 4209.491321 6 0.0004 65 | 0/8 3 h-lim-p 0.0010 0.0328 11.8482 4209.476209 4 0.0002 86 | 0/8 4 h-lim-p 0.0010 0.1035 2.8473 4209.473833 5 0.0006 111 | 0/8 5 h-lim-p 0.0049 0.7168 0.3639 4209.473803 2 0.0005 129 | 0/8 6 h-lim-p 0.0029 5.9680 0.0596 4209.473802 0 0.0006 150 | 0/8 7 h-lim-p 0.0035 20.0000 0.0107 4209.473802 0 0.0031 170 | 0/8 8 h-lim-p 0.0285 20.0000 0.0011 4209.473585 0 0.3418 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4209.473584 0 1.0938 213 | 0/8 10 h-lim-p 1.6313 20.0000 0.0000 4209.473584 0 1.4274 233 | 0/8 11 h-lim-p 2.1545 20.0000 0.0000 4209.473584 0 0.9426 253 | 0/8 12 h-lim-p 0.4881 20.0000 0.0000 4209.473584 0 0.0153 277 | 0/8 13 h-lim-p 0.0017 20.0000 0.0001 4209.473584 0 0.0035 298 | 0/8 14 h-lim-p 0.0007 20.0000 0.0006 4209.473584 0 0.0000 323 | 0/8 15 h-lim-p 0.0017 20.0000 0.0000 4209.473584 0 0.0004 344 Out... lnL = -4209.473584 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4209.473584 Node 7: lnL = -4209.473584 Node 8: lnL = -4209.473584 Node 9: lnL = -4209.473584 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 176 Sequential format.. Reading seq # 1: YHL019C_Sbay Reading seq # 2: YHL019C_Scer Reading seq # 3: YHL019C_Skud Reading seq # 4: YHL019C_Smik Reading seq # 5: YHL019C_Spar Sequences read.. Counting patterns.. # site patterns = 86 Counting frequencies.. 120 bytes for distance 13760 bytes for lkl0 11008 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.170544 0.058439 0.010459 0.092305 0.093473 1.258191 0.106154 0.053719 lnL0 = -742.594967 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 742.594967 x= 0.17054 0.05844 0.01046 0.09231 0.09347 1.25819 0.10615 0.05372 1 h-lim-p 0.0025 0.0196 65.6171 741.163972 9 0.0008 44 | 0/8 2 h-lim-p 0.0003 0.0024 28.1447 740.714259 0 0.0012 58 | 0/8 3 h-lim-p 0.0004 0.0029 6.8882 740.667972 0 0.0022 72 | 0/8 4 h-lim-p 0.0001 0.0004 11.7841 740.645626 m 0.0004 84 | 1/8 5 h-lim-p 0.0002 0.0350 14.5205 740.627700 0 0.0005 97 | 1/8 6 h-lim-p 0.0151 0.1974 0.4446 740.627422 4 0.0024 120 | 1/8 7 h-lim-p 0.0034 9.7338 0.3139 740.624381 0 0.0551 143 | 1/8 8 h-lim-p 1.4668 15.7180 0.0118 740.610952 2 0.6875 166 | 1/8 9 h-lim-p 2.5000 20.0000 0.0025 740.610842 3 0.4400 193 | 1/8 10 h-lim-p 2.5000 20.0000 0.0002 740.610839 1 0.9961 214 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 740.610839 0 1.0938 233 | 1/8 12 h-lim-p 1.5064 20.0000 0.0000 740.610839 0 1.3181 252 | 1/8 13 h-lim-p 1.4285 20.0000 0.0000 740.610839 0 5.7140 273 | 1/8 14 h-lim-p 0.3274 20.0000 0.0001 740.610839 0 0.0003 301 | 1/8 15 h-lim-p 0.0000 20.0000 0.0011 740.610839 0 0.0000 324 | 1/8 16 h-lim-p 0.0002 20.0000 0.0000 740.610839 0 0.0000 354 Out... lnL = -740.610839 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -740.610839 Node 7: lnL = -740.610839 Node 8: lnL = -740.610839 Node 9: lnL = -740.610839 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 275 Sequential format.. Reading seq # 1: YHL020C_Sbay Reading seq # 2: YHL020C_Scer Reading seq # 3: YHL020C_Skud Reading seq # 4: YHL020C_Smik Reading seq # 5: YHL020C_Spar Sequences read.. Counting patterns.. # site patterns = 75 Counting frequencies.. 120 bytes for distance 12000 bytes for lkl0 9600 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.115661 0.023803 0.021169 0.043322 0.019476 0.053585 0.062109 0.087707 lnL0 = -836.677713 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 836.677713 x= 0.11566 0.02380 0.02117 0.04332 0.01948 0.05359 0.06211 0.08771 1 h-lim-p 0.0005 0.0036 73.5669 836.291153 8 0.0002 42 | 0/8 2 h-lim-p 0.0004 0.0031 26.6506 836.214866 8 0.0002 76 | 0/8 3 h-lim-p 0.0006 0.0082 10.6998 836.208888 3 0.0001 95 | 0/8 4 h-lim-p 0.0003 0.0510 4.1691 836.206455 3 0.0003 113 | 0/8 5 h-lim-p 0.0008 0.0277 1.6519 836.206168 5 0.0003 139 | 0/8 6 h-lim-p 0.0012 0.2538 0.3393 836.206148 3 0.0004 159 | 0/8 7 h-lim-p 0.0027 1.1474 0.0459 836.206148 0 0.0003 181 | 0/8 8 h-lim-p 0.1016 20.0000 0.0001 836.206089 0 1.2196 204 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 836.206089 0 1.0938 224 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 836.206089 0 2.1875 244 | 0/8 11 h-lim-p 2.4352 20.0000 0.0000 836.206089 0 0.5327 265 | 0/8 12 h-lim-p 0.4142 20.0000 0.0000 836.206089 0 0.0004 294 Out... lnL = -836.206089 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -836.206089 Node 7: lnL = -836.206089 Node 8: lnL = -836.206089 Node 9: lnL = -836.206089 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 346 Sequential format.. Reading seq # 1: YHL022C_Sbay Reading seq # 2: YHL022C_Scer Reading seq # 3: YHL022C_Skud Reading seq # 4: YHL022C_Smik Reading seq # 5: YHL022C_Spar Sequences read.. Counting patterns.. # site patterns = 201 Counting frequencies.. 120 bytes for distance 32160 bytes for lkl0 25728 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.256487 0.060056 0.043177 0.259815 0.164981 0.225125 0.360903 0.158166 lnL0 = -1715.412708 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1715.412708 x= 0.25649 0.06006 0.04318 0.25982 0.16498 0.22513 0.36090 0.15817 1 h-lim-p 0.0045 1.3122 87.5005 1713.585915 4 0.0005 32 | 0/8 2 h-lim-p 0.0024 0.0194 13.2273 1713.455659 6 0.0015 60 | 0/8 3 h-lim-p 0.0064 0.1167 3.0953 1713.450029 4 0.0012 81 | 0/8 4 h-lim-p 0.0236 1.3802 0.1622 1713.450007 2 0.0016 100 | 0/8 5 h-lim-p 0.0050 8.4730 0.0499 1713.449995 1 0.0052 122 | 0/8 6 h-lim-p 0.0279 20.0000 0.0093 1713.449831 0 0.1117 144 | 0/8 7 h-lim-p 0.0111 9.7988 0.0938 1713.448600 0 0.0166 164 | 0/8 8 h-lim-p 0.0291 6.7938 0.0536 1713.448597 1 0.0018 189 | 0/8 9 h-lim-p 0.4525 20.0000 0.0002 1713.448584 0 0.9049 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1713.448584 0 1.0938 230 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1713.448584 0 1.0938 250 | 0/8 12 h-lim-p 1.4270 20.0000 0.0000 1713.448584 0 2.1405 270 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1713.448584 0 0.4688 292 | 0/8 14 h-lim-p 0.0916 20.0000 0.0000 1713.448584 0 0.0229 313 | 0/8 15 h-lim-p 0.0072 20.0000 0.0000 1713.448584 0 0.0000 351 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 1713.448584 0 0.0000 371 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1713.448584 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1713.448584 Node 7: lnL = -1713.448584 Node 8: lnL = -1713.448584 Node 9: lnL = -1713.448584 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 418 Sequential format.. Reading seq # 1: YHL023C_Sbay Reading seq # 2: YHL023C_Scer Reading seq # 3: YHL023C_Skud Reading seq # 4: YHL023C_Smik Reading seq # 5: YHL023C_Spar Sequences read.. Counting patterns.. # site patterns = 193 Counting frequencies.. 120 bytes for distance 30880 bytes for lkl0 24704 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.202393 0.081834 0.047103 0.147346 0.131909 0.232337 0.243825 0.123110 lnL0 = -2016.411597 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2016.411597 x= 0.20239 0.08183 0.04710 0.14735 0.13191 0.23234 0.24383 0.12311 1 h-lim-p 0.0028 0.0224 104.8166 2014.561568 5 0.0004 34 | 0/8 2 h-lim-p 0.0011 0.0091 22.2321 2014.358702 8 0.0008 66 | 0/8 3 h-lim-p 0.0019 0.0330 9.6710 2014.328431 4 0.0008 86 | 0/8 4 h-lim-p 0.0023 0.0926 3.1581 2014.324498 5 0.0009 108 | 0/8 5 h-lim-p 0.0060 0.8391 0.4685 2014.324377 3 0.0011 127 | 0/8 6 h-lim-p 0.0076 4.8755 0.0702 2014.324375 1 0.0009 151 | 0/8 7 h-lim-p 0.0051 20.0000 0.0130 2014.324375 0 0.0022 171 | 0/8 8 h-lim-p 0.0609 20.0000 0.0005 2014.324289 0 0.4876 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2014.324285 0 1.0938 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2014.324285 0 1.0938 234 | 0/8 11 h-lim-p 1.9196 20.0000 0.0000 2014.324285 0 1.6797 254 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2014.324285 0 0.0781 278 | 0/8 13 h-lim-p 0.0225 20.0000 0.0000 2014.324285 0 0.0014 301 | 0/8 14 h-lim-p 0.0005 20.0000 0.0000 2014.324285 0 0.0000 335 | 0/8 15 h-lim-p 0.0000 20.0000 0.0006 2014.324285 0 0.0000 359 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 2014.324285 0 0.0000 382 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 2014.324285 0 0.0000 416 | 0/8 18 h-lim-p 0.0000 20.0000 0.0006 | 0/8 19 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -2014.324285 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2014.324285 Node 7: lnL = -2014.324285 Node 8: lnL = -2014.324285 Node 9: lnL = -2014.324285 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 919 Sequential format.. Reading seq # 1: YHL024W_Sbay Reading seq # 2: YHL024W_Scer Reading seq # 3: YHL024W_Skud Reading seq # 4: YHL024W_Smik Reading seq # 5: YHL024W_Spar Sequences read.. Counting patterns.. # site patterns = 271 Counting frequencies.. 120 bytes for distance 43360 bytes for lkl0 34688 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.182433 0.023650 0.071971 0.076309 0.050322 0.103109 0.152285 0.125036 lnL0 = -3542.545164 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3542.545164 x= 0.18243 0.02365 0.07197 0.07631 0.05032 0.10311 0.15228 0.12504 1 h-lim-p 0.0011 0.5526 251.6963 3539.282433 7 0.0001 37 | 0/8 2 h-lim-p 0.0003 0.0025 60.2285 3538.863740 4 0.0002 57 | 0/8 3 h-lim-p 0.0003 0.0059 42.3614 3538.790088 7 0.0001 86 | 0/8 4 h-lim-p 0.0005 0.0132 9.0258 3538.782519 5 0.0002 110 | 0/8 5 h-lim-p 0.0017 0.2265 1.0461 3538.782364 3 0.0003 130 | 0/8 6 h-lim-p 0.0009 0.4643 0.3357 3538.782353 1 0.0002 145 | 0/8 7 h-lim-p 0.0007 1.4513 0.1003 3538.782352 0 0.0003 165 | 0/8 8 h-lim-p 0.1156 20.0000 0.0003 3538.782105 0 1.3873 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3538.782096 1 0.9961 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3538.782096 0 1.0938 230 | 0/8 11 h-lim-p 0.5422 20.0000 0.0000 3538.782096 0 0.0085 255 | 0/8 12 h-lim-p 0.0027 20.0000 0.0000 3538.782096 0 0.0014 275 | 0/8 13 h-lim-p 0.0011 20.0000 0.0000 3538.782096 0 0.0000 300 | 0/8 14 h-lim-p 0.0008 20.0000 0.0000 3538.782096 0 0.0000 334 Out... lnL = -3538.782096 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3538.782096 Node 7: lnL = -3538.782096 Node 8: lnL = -3538.782096 Node 9: lnL = -3538.782096 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 894 Sequential format.. Reading seq # 1: YHL025W_Sbay Reading seq # 2: YHL025W_Scer Reading seq # 3: YHL025W_Skud Reading seq # 4: YHL025W_Smik Reading seq # 5: YHL025W_Spar Sequences read.. Counting patterns.. # site patterns = 232 Counting frequencies.. 120 bytes for distance 37120 bytes for lkl0 29696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.155878 0.038926 0.037902 0.069041 0.050724 0.108343 0.134351 0.104984 lnL0 = -3300.241621 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3300.241621 x= 0.15588 0.03893 0.03790 0.06904 0.05072 0.10834 0.13435 0.10498 1 h-lim-p 0.0014 0.0116 178.3146 3298.947533 4 0.0001 33 | 0/8 2 h-lim-p 0.0003 0.0023 44.0818 3298.794143 6 0.0002 60 | 0/8 3 h-lim-p 0.0004 0.0075 20.6652 3298.767794 3 0.0001 79 | 0/8 4 h-lim-p 0.0003 0.0112 8.8890 3298.764408 5 0.0001 106 | 0/8 5 h-lim-p 0.0015 0.2926 0.6094 3298.764368 3 0.0002 127 | 0/8 6 h-lim-p 0.0009 0.6727 0.1600 3298.764366 0 0.0002 148 | 0/8 7 h-lim-p 0.0007 6.1453 0.0437 3298.764366 0 0.0003 168 | 0/8 8 h-lim-p 0.0538 20.0000 0.0002 3298.764114 0 0.8604 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3298.764111 0 1.0938 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3298.764111 0 1.0938 232 | 0/8 11 h-lim-p 1.3298 20.0000 0.0000 3298.764111 0 0.0052 259 | 0/8 12 h-lim-p 0.0021 20.0000 0.0000 3298.764111 0 0.0000 299 | 0/8 13 h-lim-p 0.0000 20.0000 0.0019 | 0/8 14 h-lim-p 0.0000 20.0000 0.0019 Out... lnL = -3298.764111 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3298.764111 Node 7: lnL = -3298.764111 Node 8: lnL = -3298.764111 Node 9: lnL = -3298.764111 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 885 Sequential format.. Reading seq # 1: YHL026C_Sbay Reading seq # 2: YHL026C_Scer Reading seq # 3: YHL026C_Skud Reading seq # 4: YHL026C_Smik Reading seq # 5: YHL026C_Spar Sequences read.. Counting patterns.. # site patterns = 232 Counting frequencies.. 120 bytes for distance 37120 bytes for lkl0 29696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.157333 0.030774 0.041846 0.088098 0.050707 0.121053 0.150715 0.103556 lnL0 = -3141.335787 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3141.335787 x= 0.15733 0.03077 0.04185 0.08810 0.05071 0.12105 0.15072 0.10356 1 h-lim-p 0.0001 0.0011 186.0459 3139.611886 5 0.0001 32 | 0/8 2 h-lim-p 0.0003 0.0028 29.6024 3139.541703 2 0.0002 48 | 0/8 3 h-lim-p 0.0003 0.0159 14.1265 3139.528853 3 0.0002 66 | 0/8 4 h-lim-p 0.0003 0.0279 6.3306 3139.525307 5 0.0002 91 | 0/8 5 h-lim-p 0.0013 0.1712 1.0935 3139.525141 2 0.0003 108 | 0/8 6 h-lim-p 0.0015 1.0638 0.2124 3139.525137 1 0.0002 124 | 0/8 7 h-lim-p 0.0022 9.1928 0.0182 3139.525137 0 0.0005 145 | 0/8 8 h-lim-p 0.2223 20.0000 0.0000 3139.525134 0 0.8893 167 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3139.525134 0 1.0938 187 | 0/8 10 h-lim-p 0.5194 20.0000 0.0000 3139.525134 0 0.1136 208 | 0/8 11 h-lim-p 0.0570 20.0000 0.0000 3139.525134 0 0.0570 228 | 0/8 12 h-lim-p 0.0369 20.0000 0.0000 3139.525134 0 0.0000 265 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 3139.525134 0 0.0000 293 Out... lnL = -3139.525134 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3139.525134 Node 7: lnL = -3139.525134 Node 8: lnL = -3139.525134 Node 9: lnL = -3139.525134 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 662 Sequential format.. Reading seq # 1: YHL031C_Sbay Reading seq # 2: YHL031C_Scer Reading seq # 3: YHL031C_Skud Reading seq # 4: YHL031C_Smik Reading seq # 5: YHL031C_Spar Sequences read.. Counting patterns.. # site patterns = 303 Counting frequencies.. 120 bytes for distance 48480 bytes for lkl0 38784 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.236309 0.196994 0.108765 0.154882 0.091852 0.243252 0.279863 0.126644 lnL0 = -3289.468787 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3289.468787 x= 0.23631 0.19699 0.10876 0.15488 0.09185 0.24325 0.27986 0.12664 1 h-lim-p 0.0005 0.0043 112.6928 3287.299695 8 0.0004 43 | 0/8 2 h-lim-p 0.0005 0.0037 46.3821 3286.918621 6 0.0004 66 | 0/8 3 h-lim-p 0.0012 0.0259 15.4082 3286.808337 6 0.0011 89 | 0/8 4 h-lim-p 0.0031 0.0696 5.2922 3286.798081 5 0.0008 112 | 0/8 5 h-lim-p 0.0038 0.2330 1.1567 3286.797515 2 0.0009 129 | 0/8 6 h-lim-p 0.0022 1.1128 0.4552 3286.797456 3 0.0007 149 | 0/8 7 h-lim-p 0.0172 18.5825 0.0177 3286.797451 1 0.0069 171 | 0/8 8 h-lim-p 0.0409 20.0000 0.0030 3286.796798 0 0.2451 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3286.796777 1 0.9961 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3286.796777 0 1.0938 235 | 0/8 11 h-lim-p 2.1122 20.0000 0.0000 3286.796777 0 1.8481 255 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3286.796777 0 1.0938 275 | 0/8 13 h-lim-p 0.3273 20.0000 0.0000 3286.796777 0 0.0000 313 Out... lnL = -3286.796777 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3286.796777 Node 7: lnL = -3286.796777 Node 8: lnL = -3286.796777 Node 9: lnL = -3286.796777 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 322 Sequential format.. Reading seq # 1: YHL032C_Sbay Reading seq # 2: YHL032C_Scer Reading seq # 3: YHL032C_Skud Reading seq # 4: YHL032C_Smik Reading seq # 5: YHL032C_Spar Sequences read.. Counting patterns.. # site patterns = 104 Counting frequencies.. 120 bytes for distance 16640 bytes for lkl0 13312 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.081870 0.019734 0.032952 0.072904 0.051316 0.088717 0.148863 0.042895 lnL0 = -1066.556313 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1066.556313 x= 0.08187 0.01973 0.03295 0.07290 0.05132 0.08872 0.14886 0.04290 1 h-lim-p 0.0010 0.0217 148.3731 1065.042166 8 0.0002 40 | 0/8 2 h-lim-p 0.0011 0.0088 20.9078 1064.925348 5 0.0005 63 | 0/8 3 h-lim-p 0.0011 0.0177 10.1456 1064.909754 6 0.0004 88 | 0/8 4 h-lim-p 0.0009 0.0396 3.9229 1064.907536 5 0.0003 113 | 0/8 5 h-lim-p 0.0015 0.1316 0.8951 1064.907420 3 0.0003 132 | 0/8 6 h-lim-p 0.0023 0.9782 0.1208 1064.907418 1 0.0003 156 | 0/8 7 h-lim-p 0.0045 8.9911 0.0076 1064.907417 0 0.0020 176 | 0/8 8 h-lim-p 0.0164 20.0000 0.0009 1064.907280 0 0.2620 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1064.907272 1 0.9961 222 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1064.907272 0 1.0938 242 | 0/8 11 h-lim-p 1.3933 20.0000 0.0000 1064.907272 0 2.7866 263 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1064.907272 0 0.3125 285 | 0/8 13 h-lim-p 0.0309 20.0000 0.0000 1064.907272 0 0.0154 305 | 0/8 14 h-lim-p 0.0061 20.0000 0.0000 1064.907272 0 0.0000 337 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 1064.907272 0 0.0000 371 Out... lnL = -1064.907272 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1064.907272 Node 7: lnL = -1064.907272 Node 8: lnL = -1064.907272 Node 9: lnL = -1064.907272 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 833 Sequential format.. Reading seq # 1: YHL034C_Sbay Reading seq # 2: YHL034C_Scer Reading seq # 3: YHL034C_Skud Reading seq # 4: YHL034C_Smik Reading seq # 5: YHL034C_Spar Sequences read.. Counting patterns.. # site patterns = 272 Counting frequencies.. 120 bytes for distance 43520 bytes for lkl0 34816 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.167792 0.075086 0.073426 0.106018 0.075322 0.171031 0.170440 0.098093 lnL0 = -3702.745257 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3702.745257 x= 0.16779 0.07509 0.07343 0.10602 0.07532 0.17103 0.17044 0.09809 1 h-lim-p 0.0030 0.9806 156.4343 3700.767508 3 0.0002 31 | 0/8 2 h-lim-p 0.0005 0.0041 30.5616 3700.660983 2 0.0002 47 | 0/8 3 h-lim-p 0.0004 0.0120 17.7893 3700.630910 6 0.0002 74 | 0/8 4 h-lim-p 0.0017 0.0591 2.6105 3700.630096 4 0.0002 98 | 0/8 5 h-lim-p 0.0031 1.3631 0.2071 3700.630090 1 0.0003 114 | 0/8 6 h-lim-p 0.0014 4.7464 0.0464 3700.630089 0 0.0003 135 | 0/8 7 h-lim-p 0.0132 20.0000 0.0012 3700.630089 0 0.0263 156 | 0/8 8 h-lim-p 0.0041 20.0000 0.0078 3700.630044 0 0.0165 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3700.630043 0 1.0938 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3700.630043 0 1.0938 218 | 0/8 11 h-lim-p 1.3289 20.0000 0.0000 3700.630043 0 3.9866 239 | 0/8 12 h-lim-p 0.2993 20.0000 0.0001 3700.630043 0 0.0000 272 | 0/8 13 h-lim-p 0.0007 20.0000 0.0000 3700.630043 0 0.0000 295 Out... lnL = -3700.630043 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3700.630043 Node 7: lnL = -3700.630043 Node 8: lnL = -3700.630043 Node 9: lnL = -3700.630043 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 206 Sequential format.. Reading seq # 1: YHL038C_Sbay Reading seq # 2: YHL038C_Scer Reading seq # 3: YHL038C_Skud Reading seq # 4: YHL038C_Smik Reading seq # 5: YHL038C_Spar Sequences read.. Counting patterns.. # site patterns = 120 Counting frequencies.. 120 bytes for distance 19200 bytes for lkl0 15360 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.171238 0.067526 0.167204 0.152696 0.167533 0.082868 0.199646 0.087604 lnL0 = -913.499973 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 913.499973 x= 0.17124 0.06753 0.16720 0.15270 0.16753 0.08287 0.19965 0.08760 1 h-lim-p 0.0016 0.0129 36.2262 912.852766 8 0.0011 41 | 0/8 2 h-lim-p 0.0029 0.0229 5.3712 912.837103 4 0.0011 61 | 0/8 3 h-lim-p 0.0074 0.3052 0.7975 912.836504 4 0.0019 82 | 0/8 4 h-lim-p 0.0097 1.7389 0.1550 912.836484 3 0.0017 110 | 0/8 5 h-lim-p 0.0057 5.4842 0.0469 912.836482 1 0.0023 132 | 0/8 6 h-lim-p 0.0571 20.0000 0.0019 912.836481 0 0.0250 152 | 0/8 7 h-lim-p 0.0262 20.0000 0.0018 912.836471 0 0.1049 174 | 0/8 8 h-lim-p 0.0041 3.8291 0.0449 912.836467 2 0.0026 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 912.836467 0 1.0938 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 912.836467 0 1.0938 239 | 0/8 11 h-lim-p 1.2171 20.0000 0.0000 912.836467 0 1.0650 259 | 0/8 12 h-lim-p 0.3481 20.0000 0.0000 912.836467 0 0.0109 283 | 0/8 13 h-lim-p 0.0020 20.0000 0.0001 912.836467 0 0.0020 303 | 0/8 14 h-lim-p 0.0006 20.0000 0.0002 912.836467 0 0.0000 342 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -912.836467 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -912.836467 Node 7: lnL = -912.836467 Node 8: lnL = -912.836467 Node 9: lnL = -912.836467 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 904 Sequential format.. Reading seq # 1: YHL039W_Sbay Reading seq # 2: YHL039W_Scer Reading seq # 3: YHL039W_Skud Reading seq # 4: YHL039W_Smik Reading seq # 5: YHL039W_Spar Sequences read.. Counting patterns.. # site patterns = 302 Counting frequencies.. 120 bytes for distance 48320 bytes for lkl0 38656 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.187861 0.105115 0.030039 0.127537 0.098540 0.223246 0.229694 0.106795 lnL0 = -4045.520025 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4045.520025 x= 0.18786 0.10511 0.03004 0.12754 0.09854 0.22325 0.22969 0.10680 1 h-lim-p 0.0019 0.5176 206.0922 4043.359006 4 0.0001 33 | 0/8 2 h-lim-p 0.0010 0.0082 24.5273 4043.272827 7 0.0003 64 | 0/8 3 h-lim-p 0.0007 0.0375 10.5872 4043.259613 3 0.0003 82 | 0/8 4 h-lim-p 0.0009 0.0878 3.4212 4043.257791 3 0.0003 100 | 0/8 5 h-lim-p 0.0018 0.4194 0.6650 4043.257702 0 0.0004 113 | 0/8 6 h-lim-p 0.0014 1.4132 0.2167 4043.257694 1 0.0003 136 | 0/8 7 h-lim-p 0.0028 9.3530 0.0266 4043.257694 0 0.0006 157 | 0/8 8 h-lim-p 0.2512 20.0000 0.0001 4043.257684 0 1.0046 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4043.257684 0 1.0938 199 | 0/8 10 h-lim-p 1.3365 20.0000 0.0000 4043.257684 0 2.6729 220 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4043.257684 0 0.5469 241 | 0/8 12 h-lim-p 0.0829 20.0000 0.0001 4043.257684 0 0.0414 261 | 0/8 13 h-lim-p 0.0118 20.0000 0.0002 4043.257684 0 0.0002 286 | 0/8 14 h-lim-p 0.0004 20.0000 0.0001 4043.257684 0 0.0000 315 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 4043.257684 0 0.0000 343 Out... lnL = -4043.257684 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4043.257684 Node 7: lnL = -4043.257684 Node 8: lnL = -4043.257684 Node 9: lnL = -4043.257684 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 886 Sequential format.. Reading seq # 1: YHL040C_Sbay Reading seq # 2: YHL040C_Scer Reading seq # 3: YHL040C_Skud Reading seq # 4: YHL040C_Smik Reading seq # 5: YHL040C_Spar Sequences read.. Counting patterns.. # site patterns = 287 Counting frequencies.. 120 bytes for distance 45920 bytes for lkl0 36736 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.160935 0.180608 0.035987 0.123027 0.097928 0.216390 0.198571 0.078244 lnL0 = -3955.022841 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3955.022841 x= 0.16093 0.18061 0.03599 0.12303 0.09793 0.21639 0.19857 0.07824 1 h-lim-p 0.0032 0.6425 157.8042 3953.529294 8 0.0001 43 | 0/8 2 h-lim-p 0.0008 0.0106 25.9829 3953.392387 4 0.0004 64 | 0/8 3 h-lim-p 0.0008 0.0249 13.8227 3953.376025 5 0.0002 89 | 0/8 4 h-lim-p 0.0022 0.2433 1.3109 3953.375665 3 0.0004 108 | 0/8 5 h-lim-p 0.0009 0.3856 0.5966 3953.375608 2 0.0004 124 | 0/8 6 h-lim-p 0.0101 10.2886 0.0220 3953.375608 0 0.0006 147 | 0/8 7 h-lim-p 0.0021 20.0000 0.0057 3953.375608 0 0.0032 167 | 0/8 8 h-lim-p 0.0127 20.0000 0.0014 3953.375523 0 0.1529 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3953.375522 0 1.0938 210 | 0/8 10 h-lim-p 2.1023 20.0000 0.0000 3953.375522 0 1.8396 230 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3953.375522 0 1.0938 250 | 0/8 12 h-lim-p 0.3185 20.0000 0.0000 3953.375522 0 5.0957 274 | 0/8 13 h-lim-p 0.0930 20.0000 0.0010 3953.375522 0 0.0465 294 | 0/8 14 h-lim-p 0.0126 20.0000 0.0035 3953.375522 0 0.0032 315 | 0/8 15 h-lim-p 0.0020 19.0022 0.0057 3953.375522 0 0.0000 357 | 0/8 16 h-lim-p 0.0000 20.0000 0.0009 | 0/8 17 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -3953.375522 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3953.375522 Node 7: lnL = -3953.375522 Node 8: lnL = -3953.375522 Node 9: lnL = -3953.375522 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 772 Sequential format.. Reading seq # 1: YHR002W_Sbay Reading seq # 2: YHR002W_Scer Reading seq # 3: YHR002W_Skud Reading seq # 4: YHR002W_Smik Reading seq # 5: YHR002W_Spar Sequences read.. Counting patterns.. # site patterns = 254 Counting frequencies.. 120 bytes for distance 40640 bytes for lkl0 32512 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.137396 0.057737 0.084945 0.092332 0.089212 0.182776 0.188601 0.070238 lnL0 = -3284.221953 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3284.221953 x= 0.13740 0.05774 0.08494 0.09233 0.08921 0.18278 0.18860 0.07024 1 h-lim-p 0.0012 0.0092 102.0126 3283.295797 7 0.0002 38 | 0/8 2 h-lim-p 0.0009 0.0075 21.2714 3283.243642 5 0.0002 61 | 0/8 3 h-lim-p 0.0007 0.0394 7.0318 3283.236910 3 0.0003 80 | 0/8 4 h-lim-p 0.0008 0.0791 2.7175 3283.236207 4 0.0002 103 | 0/8 5 h-lim-p 0.0055 1.3282 0.1082 3283.236205 0 0.0003 118 | 0/8 6 h-lim-p 0.0010 9.2879 0.0326 3283.236204 0 0.0004 138 | 0/8 7 h-lim-p 0.0028 20.0000 0.0051 3283.236204 0 0.0007 159 | 0/8 8 h-lim-p 0.0154 20.0000 0.0002 3283.236184 0 0.4912 184 | 0/8 9 h-lim-p 0.5580 20.0000 0.0002 3283.236183 0 1.1160 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3283.236183 0 1.0938 225 | 0/8 11 h-lim-p 1.0867 20.0000 0.0000 3283.236183 0 0.9509 245 | 0/8 12 h-lim-p 0.6569 20.0000 0.0000 3283.236183 0 0.0411 268 | 0/8 13 h-lim-p 0.0053 20.0000 0.0002 3283.236183 0 0.0000 294 | 0/8 14 h-lim-p 0.0006 20.0000 0.0000 3283.236183 0 0.0001 315 | 0/8 15 h-lim-p 0.0006 20.0000 0.0000 3283.236183 0 0.0000 341 Out... lnL = -3283.236183 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3283.236183 Node 7: lnL = -3283.236183 Node 8: lnL = -3283.236183 Node 9: lnL = -3283.236183 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 463 Sequential format.. Reading seq # 1: YHR003C_Sbay Reading seq # 2: YHR003C_Scer Reading seq # 3: YHR003C_Skud Reading seq # 4: YHR003C_Smik Reading seq # 5: YHR003C_Spar Sequences read.. Counting patterns.. # site patterns = 201 Counting frequencies.. 120 bytes for distance 32160 bytes for lkl0 25728 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.197603 0.082301 0.090719 0.107195 0.072393 0.151738 0.227858 0.119345 lnL0 = -2017.656834 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2017.656834 x= 0.19760 0.08230 0.09072 0.10720 0.07239 0.15174 0.22786 0.11934 1 h-lim-p 0.0088 2.5033 67.7857 2016.845689 8 0.0004 45 | 0/8 2 h-lim-p 0.0008 0.0066 20.6675 2016.769703 2 0.0004 61 | 0/8 3 h-lim-p 0.0012 0.0422 6.9092 2016.755741 6 0.0007 88 | 0/8 4 h-lim-p 0.0020 0.1116 2.2507 2016.753686 2 0.0009 104 | 0/8 5 h-lim-p 0.0033 0.4235 0.6351 2016.753541 2 0.0008 121 | 0/8 6 h-lim-p 0.0017 1.0843 0.2863 2016.753521 2 0.0006 146 | 0/8 7 h-lim-p 0.0134 17.5260 0.0118 2016.753520 0 0.0029 167 | 0/8 8 h-lim-p 0.0363 20.0000 0.0010 2016.753370 0 0.4358 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2016.753364 1 0.9961 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2016.753364 0 2.1875 232 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2016.753364 0 0.2734 254 | 0/8 12 h-lim-p 0.0562 20.0000 0.0000 2016.753364 0 0.0141 275 | 0/8 13 h-lim-p 0.0066 20.0000 0.0000 2016.753364 0 0.0066 295 | 0/8 14 h-lim-p 0.0042 20.0000 0.0000 2016.753364 0 0.0001 320 | 0/8 15 h-lim-p 0.0000 20.0000 0.0028 2016.753364 0 0.0000 351 | 0/8 16 h-lim-p 0.0000 20.0000 0.0012 | 0/8 17 h-lim-p 0.0000 20.0000 0.0012 Out... lnL = -2016.753364 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2016.753364 Node 7: lnL = -2016.753364 Node 8: lnL = -2016.753364 Node 9: lnL = -2016.753364 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 418 Sequential format.. Reading seq # 1: YHR004C_Sbay Reading seq # 2: YHR004C_Scer Reading seq # 3: YHR004C_Skud Reading seq # 4: YHR004C_Smik Reading seq # 5: YHR004C_Spar Sequences read.. Counting patterns.. # site patterns = 121 Counting frequencies.. 120 bytes for distance 19360 bytes for lkl0 15488 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.084514 0.056693 0.040617 0.062052 0.040349 0.074980 0.092064 0.046837 lnL0 = -1448.717712 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1448.717712 x= 0.08451 0.05669 0.04062 0.06205 0.04035 0.07498 0.09206 0.04684 1 h-lim-p 0.0004 0.0030 140.9735 1447.194778 6 0.0002 34 | 0/8 2 h-lim-p 0.0004 0.0035 32.6029 1447.089492 2 0.0002 50 | 0/8 3 h-lim-p 0.0007 0.0116 8.8184 1447.081320 6 0.0002 79 | 0/8 4 h-lim-p 0.0010 0.0678 1.9508 1447.080819 4 0.0003 100 | 0/8 5 h-lim-p 0.0013 0.3252 0.4225 1447.080798 2 0.0003 117 | 0/8 6 h-lim-p 0.0014 1.9724 0.0756 1447.080798 0 0.0003 138 | 0/8 7 h-lim-p 0.0045 20.0000 0.0052 1447.080797 0 0.0020 158 | 0/8 8 h-lim-p 0.0118 20.0000 0.0009 1447.080741 0 0.1882 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1447.080740 0 1.0938 202 | 0/8 10 h-lim-p 2.1059 20.0000 0.0000 1447.080740 0 0.9213 222 | 0/8 11 h-lim-p 0.7400 20.0000 0.0000 1447.080740 0 0.0011 251 | 0/8 12 h-lim-p 0.0004 20.0000 0.0000 .. | 0/8 13 h-lim-p 0.0000 20.0000 0.0011 | 0/8 14 h-lim-p 0.0000 20.0000 0.0011 Out... lnL = -1447.080740 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1447.080740 Node 7: lnL = -1447.080740 Node 8: lnL = -1447.080740 Node 9: lnL = -1447.080740 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 916 Sequential format.. Reading seq # 1: YHR005C-A_Sbay Reading seq # 2: YHR005C-A_Scer Reading seq # 3: YHR005C-A_Skud Reading seq # 4: YHR005C-A_Smik Reading seq # 5: YHR005C-A_Spar Sequences read.. Counting patterns.. # site patterns = 399 Counting frequencies.. 120 bytes for distance 63840 bytes for lkl0 51072 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.310994 0.000060 0.082618 0.196219 0.240172 0.422352 0.301049 0.184061 lnL0 = -4698.687604 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4698.687604 x= 0.31099 0.00006 0.08262 0.19622 0.24017 0.42235 0.30105 0.18406 1 h-lim-p 0.0005 0.0042 105.8064 4694.398575 0 0.0008 22 | 0/8 2 h-lim-p 0.0002 0.0018 93.3685 4693.401995 0 0.0003 34 | 0/8 3 h-lim-p 0.0009 0.0111 33.7390 4693.139972 8 0.0006 69 | 0/8 4 h-lim-p 0.0016 0.0377 12.2672 4693.100011 4 0.0006 89 | 0/8 5 h-lim-p 0.0034 0.0720 2.2047 4693.098125 2 0.0008 106 | 0/8 6 h-lim-p 0.0025 0.0904 0.7124 4693.097897 3 0.0009 125 | 0/8 7 h-lim-p 0.0053 1.0602 0.1176 4693.097781 3 0.0037 152 | 0/8 8 h-lim-p 0.0143 4.9010 0.0308 4693.074451 0 0.2288 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 4693.074374 2 0.9644 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4693.074374 0 1.0938 220 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4693.074374 0 1.0938 240 | 0/8 12 h-lim-p 1.0328 20.0000 0.0000 4693.074374 0 0.1130 262 | 0/8 13 h-lim-p 0.0407 20.0000 0.0000 4693.074374 0 0.0051 284 | 0/8 14 h-lim-p 0.0030 20.0000 0.0000 4693.074374 0 0.0000 309 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 4693.074374 0 0.0000 345 Out... lnL = -4693.074374 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4693.074374 Node 7: lnL = -4693.074374 Node 8: lnL = -4693.074374 Node 9: lnL = -4693.074374 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 731 Sequential format.. Reading seq # 1: YHR005C_Sbay Reading seq # 2: YHR005C_Scer Reading seq # 3: YHR005C_Skud Reading seq # 4: YHR005C_Smik Reading seq # 5: YHR005C_Spar Sequences read.. Counting patterns.. # site patterns = 238 Counting frequencies.. 120 bytes for distance 38080 bytes for lkl0 30464 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.140805 0.054313 0.033152 0.131371 0.086699 0.149955 0.135026 0.076430 lnL0 = -3017.481149 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3017.481149 x= 0.14080 0.05431 0.03315 0.13137 0.08670 0.14996 0.13503 0.07643 1 h-lim-p 0.0008 0.3862 277.7496 3014.185646 8 0.0001 41 | 0/8 2 h-lim-p 0.0006 0.0051 36.8516 3014.033380 7 0.0002 70 | 0/8 3 h-lim-p 0.0009 0.0192 8.9896 3014.024390 5 0.0002 95 | 0/8 4 h-lim-p 0.0013 0.0777 1.5989 3014.024090 3 0.0003 114 | 0/8 5 h-lim-p 0.0011 1.0443 0.3575 3014.024071 2 0.0003 131 | 0/8 6 h-lim-p 0.0025 2.6038 0.0427 3014.024071 0 0.0005 152 | 0/8 7 h-lim-p 0.0135 20.0000 0.0017 3014.024065 0 0.0270 173 | 0/8 8 h-lim-p 0.0021 2.7727 0.0221 3014.023862 0 0.0125 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3014.023859 0 1.0938 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3014.023859 0 1.0938 235 | 0/8 11 h-lim-p 0.8041 20.0000 0.0000 3014.023859 0 0.0047 262 | 0/8 12 h-lim-p 0.0019 20.0000 0.0000 3014.023859 0 0.0002 284 | 0/8 13 h-lim-p 0.0000 20.0000 0.0009 3014.023859 0 0.0000 306 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 3014.023859 0 0.0000 329 Out... lnL = -3014.023859 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3014.023859 Node 7: lnL = -3014.023859 Node 8: lnL = -3014.023859 Node 9: lnL = -3014.023859 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 857 Sequential format.. Reading seq # 1: YHR006W_Sbay Reading seq # 2: YHR006W_Scer Reading seq # 3: YHR006W_Skud Reading seq # 4: YHR006W_Smik Reading seq # 5: YHR006W_Spar Sequences read.. Counting patterns.. # site patterns = 427 Counting frequencies.. 120 bytes for distance 68320 bytes for lkl0 54656 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.325836 0.135108 0.019706 0.336349 0.259388 0.274678 0.362891 0.177020 lnL0 = -4782.120311 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4782.120311 x= 0.32584 0.13511 0.01971 0.33635 0.25939 0.27468 0.36289 0.17702 1 h-lim-p 0.0036 0.7444 162.4862 4778.688862 6 0.0003 38 | 0/8 2 h-lim-p 0.0014 0.0160 34.1568 4778.203392 7 0.0009 67 | 0/8 3 h-lim-p 0.0030 0.0545 9.8390 4778.151958 5 0.0011 89 | 0/8 4 h-lim-p 0.0034 0.1263 3.2953 4778.145355 3 0.0014 107 | 0/8 5 h-lim-p 0.0096 0.4171 0.4660 4778.145259 2 0.0009 125 | 0/8 6 h-lim-p 0.0089 10.0928 0.0483 4778.145252 1 0.0022 148 | 0/8 7 h-lim-p 0.0298 20.0000 0.0036 4778.143904 0 0.4774 172 | 0/8 8 h-lim-p 0.0027 1.3231 0.6347 4778.143243 4 0.0017 204 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 4778.143190 1 0.9961 226 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4778.143190 0 1.0938 246 | 0/8 11 h-lim-p 1.5490 20.0000 0.0000 4778.143190 0 0.6777 266 | 0/8 12 h-lim-p 0.3791 20.0000 0.0000 4778.143190 0 0.3791 286 | 0/8 13 h-lim-p 0.1383 20.0000 0.0000 4778.143190 0 0.0002 315 | 0/8 14 h-lim-p 0.0033 20.0000 0.0000 4778.143190 0 0.0001 339 Out... lnL = -4778.143190 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4778.143190 Node 7: lnL = -4778.143190 Node 8: lnL = -4778.143190 Node 9: lnL = -4778.143190 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 869 Sequential format.. Reading seq # 1: YHR007C_Sbay Reading seq # 2: YHR007C_Scer Reading seq # 3: YHR007C_Skud Reading seq # 4: YHR007C_Smik Reading seq # 5: YHR007C_Spar Sequences read.. Counting patterns.. # site patterns = 178 Counting frequencies.. 120 bytes for distance 28480 bytes for lkl0 22784 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.099029 0.043258 0.033459 0.042891 0.036520 0.081993 0.082951 0.059844 lnL0 = -2815.160415 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2815.160415 x= 0.09903 0.04326 0.03346 0.04289 0.03652 0.08199 0.08295 0.05984 1 h-lim-p 0.0001 0.0010 207.8697 2813.734005 8 0.0001 43 | 0/8 2 h-lim-p 0.0003 0.0025 44.4397 2813.639479 7 0.0001 73 | 0/8 3 h-lim-p 0.0002 0.0065 20.1400 2813.625783 5 0.0001 97 | 0/8 4 h-lim-p 0.0004 0.0235 4.6243 2813.624763 4 0.0001 119 | 0/8 5 h-lim-p 0.0016 0.3004 0.3064 2813.624760 1 0.0001 136 | 0/8 6 h-lim-p 0.0006 2.0672 0.0427 2813.624760 0 0.0001 157 | 0/8 7 h-lim-p 0.0061 20.0000 0.0010 2813.624760 0 0.0003 180 | 0/8 8 h-lim-p 0.0168 20.0000 0.0000 2813.624759 0 0.5361 205 | 0/8 9 h-lim-p 0.3140 20.0000 0.0000 2813.624759 0 0.9420 226 | 0/8 10 h-lim-p 1.2105 20.0000 0.0000 2813.624759 0 2.4209 247 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2813.624759 0 0.5469 268 | 0/8 12 h-lim-p 0.0439 20.0000 0.0000 2813.624759 0 0.0877 289 | 0/8 13 h-lim-p 0.0262 20.0000 0.0001 2813.624759 0 0.0262 309 | 0/8 14 h-lim-p 0.0120 20.0000 0.0002 2813.624759 0 0.0000 346 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 2813.624759 0 0.0000 381 Out... lnL = -2813.624759 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2813.624759 Node 7: lnL = -2813.624759 Node 8: lnL = -2813.624759 Node 9: lnL = -2813.624759 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 546 Sequential format.. Reading seq # 1: YHR008C_Sbay Reading seq # 2: YHR008C_Scer Reading seq # 3: YHR008C_Skud Reading seq # 4: YHR008C_Smik Reading seq # 5: YHR008C_Spar Sequences read.. Counting patterns.. # site patterns = 201 Counting frequencies.. 120 bytes for distance 32160 bytes for lkl0 25728 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.189191 0.064683 0.054413 0.077460 0.073044 0.188680 0.210802 0.111380 lnL0 = -2257.203630 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2257.203630 x= 0.18919 0.06468 0.05441 0.07746 0.07304 0.18868 0.21080 0.11138 1 h-lim-p 0.0005 0.0041 146.7499 2254.665394 7 0.0003 38 | 0/8 2 h-lim-p 0.0005 0.0041 31.0076 2254.501599 8 0.0003 71 | 0/8 3 h-lim-p 0.0006 0.0135 19.5319 2254.462713 5 0.0003 95 | 0/8 4 h-lim-p 0.0008 0.0404 6.3440 2254.452705 6 0.0006 123 | 0/8 5 h-lim-p 0.0018 0.1003 2.0397 2254.451823 3 0.0005 142 | 0/8 6 h-lim-p 0.0014 0.4170 0.6890 2254.451682 2 0.0007 158 | 0/8 7 h-lim-p 0.0544 20.0000 0.0083 2254.451679 1 0.0067 182 | 0/8 8 h-lim-p 0.0125 20.0000 0.0045 2254.451253 0 0.1497 205 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2254.451242 1 0.9961 227 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2254.451242 0 1.0938 247 | 0/8 11 h-lim-p 1.2063 20.0000 0.0000 2254.451242 0 2.4126 268 | 0/8 12 h-lim-p 0.6698 20.0000 0.0000 2254.451242 0 0.3349 288 | 0/8 13 h-lim-p 0.0068 20.0000 0.0009 2254.451242 0 0.0025 309 | 0/8 14 h-lim-p 0.0000 0.0294 5.4312 2254.451242 0 0.0000 339 | 0/8 15 h-lim-p 0.0005 20.0000 0.0000 2254.451242 0 0.0000 358 | 0/8 16 h-lim-p 0.0000 20.0000 0.0041 2254.451242 0 0.0000 381 | 0/8 17 h-lim-p 0.0005 20.0000 0.0000 2254.451242 0 0.0000 405 Out... lnL = -2254.451242 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2254.451242 Node 7: lnL = -2254.451242 Node 8: lnL = -2254.451242 Node 9: lnL = -2254.451242 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 843 Sequential format.. Reading seq # 1: YHR009C_Sbay Reading seq # 2: YHR009C_Scer Reading seq # 3: YHR009C_Skud Reading seq # 4: YHR009C_Smik Reading seq # 5: YHR009C_Spar Sequences read.. Counting patterns.. # site patterns = 267 Counting frequencies.. 120 bytes for distance 42720 bytes for lkl0 34176 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.119303 0.137371 0.078799 0.113664 0.056905 0.153118 0.163082 0.045525 lnL0 = -3522.445967 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3522.445967 x= 0.11930 0.13737 0.07880 0.11366 0.05691 0.15312 0.16308 0.04553 1 h-lim-p 0.0003 0.0025 105.1461 3521.479192 8 0.0002 43 | 0/8 2 h-lim-p 0.0010 0.0093 19.5222 3521.426202 7 0.0003 73 | 0/8 3 h-lim-p 0.0006 0.0098 8.9907 3521.421988 3 0.0001 92 | 0/8 4 h-lim-p 0.0005 0.0756 2.1315 3521.421521 2 0.0002 108 | 0/8 5 h-lim-p 0.0014 0.7213 0.3439 3521.421501 0 0.0004 121 | 0/8 6 h-lim-p 0.0026 5.4393 0.0474 3521.421501 0 0.0003 143 | 0/8 7 h-lim-p 0.0007 9.0656 0.0210 3521.421501 0 0.0003 163 | 0/8 8 h-lim-p 0.0703 20.0000 0.0001 3521.421479 0 1.1244 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3521.421479 0 1.0938 207 | 0/8 10 h-lim-p 0.8763 20.0000 0.0000 3521.421479 0 0.8763 227 | 0/8 11 h-lim-p 0.6324 20.0000 0.0000 3521.421479 0 0.6324 247 | 0/8 12 h-lim-p 0.1209 20.0000 0.0002 3521.421479 0 0.0038 271 | 0/8 13 h-lim-p 0.0010 20.0000 0.0007 3521.421479 0 0.0000 307 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 3521.421479 0 0.0000 339 Out... lnL = -3521.421479 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3521.421479 Node 7: lnL = -3521.421479 Node 8: lnL = -3521.421479 Node 9: lnL = -3521.421479 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 297 Sequential format.. Reading seq # 1: YHR011W_Sbay Reading seq # 2: YHR011W_Scer Reading seq # 3: YHR011W_Skud Reading seq # 4: YHR011W_Smik Reading seq # 5: YHR011W_Spar Sequences read.. Counting patterns.. # site patterns = 100 Counting frequencies.. 120 bytes for distance 16000 bytes for lkl0 12800 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.096290 0.055273 0.005930 0.076624 0.054141 0.169105 0.175728 0.042872 lnL0 = -1139.487693 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1139.487693 x= 0.09629 0.05527 0.00593 0.07662 0.05414 0.16910 0.17573 0.04287 1 h-lim-p 0.0009 0.0071 91.6049 1139.177959 4 0.0001 32 | 0/8 2 h-lim-p 0.0004 0.0048 21.7110 1139.092694 4 0.0004 52 | 0/8 3 h-lim-p 0.0009 0.0209 9.2178 1139.075359 5 0.0005 75 | 0/8 4 h-lim-p 0.0010 0.0309 4.3983 1139.072554 5 0.0004 100 | 0/8 5 h-lim-p 0.0045 0.3173 0.3536 1139.072531 2 0.0004 120 | 0/8 6 h-lim-p 0.0021 1.7704 0.0620 1139.072530 1 0.0005 143 | 0/8 7 h-lim-p 0.0012 9.1245 0.0260 1139.072530 0 0.0011 163 | 0/8 8 h-lim-p 0.0648 20.0000 0.0004 1139.072216 0 0.7779 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1139.072200 2 0.9644 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1139.072200 0 1.0938 230 | 0/8 11 h-lim-p 1.3925 20.0000 0.0000 1139.072200 0 5.5700 252 | 0/8 12 h-lim-p 2.4967 20.0000 0.0000 1139.072200 0 0.1365 275 | 0/8 13 h-lim-p 1.3709 20.0000 0.0000 1139.072200 0 0.0003 306 Out... lnL = -1139.072200 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1139.072200 Node 7: lnL = -1139.072200 Node 8: lnL = -1139.072200 Node 9: lnL = -1139.072200 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 689 Sequential format.. Reading seq # 1: YHR013C_Sbay Reading seq # 2: YHR013C_Scer Reading seq # 3: YHR013C_Skud Reading seq # 4: YHR013C_Smik Reading seq # 5: YHR013C_Spar Sequences read.. Counting patterns.. # site patterns = 283 Counting frequencies.. 120 bytes for distance 45280 bytes for lkl0 36224 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.310499 0.139218 0.040329 0.192150 0.170660 0.250705 0.209910 0.190041 lnL0 = -3400.634295 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3400.634295 x= 0.31050 0.13922 0.04033 0.19215 0.17066 0.25071 0.20991 0.19004 1 h-lim-p 0.0024 0.0192 101.5488 3399.241489 6 0.0003 35 | 0/8 2 h-lim-p 0.0008 0.0098 38.5016 3398.691925 6 0.0008 59 | 0/8 3 h-lim-p 0.0031 0.0293 10.3034 3398.646470 7 0.0009 89 | 0/8 4 h-lim-p 0.0023 0.0801 4.2327 3398.641760 5 0.0006 112 | 0/8 5 h-lim-p 0.0036 0.6166 0.7320 3398.641550 2 0.0008 129 | 0/8 6 h-lim-p 0.0032 1.8349 0.1924 3398.641536 0 0.0008 150 | 0/8 7 h-lim-p 0.0136 20.0000 0.0112 3398.641536 0 0.0015 172 | 0/8 8 h-lim-p 0.0141 20.0000 0.0012 3398.641420 0 0.4524 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3398.641417 0 1.0938 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3398.641417 0 1.0938 237 | 0/8 11 h-lim-p 1.8773 20.0000 0.0000 3398.641417 0 0.9386 257 | 0/8 12 h-lim-p 0.6531 20.0000 0.0000 3398.641417 0 0.3265 277 | 0/8 13 h-lim-p 0.0395 20.0000 0.0000 3398.641417 0 0.0395 297 | 0/8 14 h-lim-p 0.0144 20.0000 0.0001 3398.641417 0 0.0000 335 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 3398.641417 0 0.0000 358 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 3398.641417 0 0.0000 392 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 3398.641417 0 0.0000 427 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -3398.641417 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3398.641417 Node 7: lnL = -3398.641417 Node 8: lnL = -3398.641417 Node 9: lnL = -3398.641417 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 648 Sequential format.. Reading seq # 1: YHR014W_Sbay Reading seq # 2: YHR014W_Scer Reading seq # 3: YHR014W_Skud Reading seq # 4: YHR014W_Smik Reading seq # 5: YHR014W_Spar Sequences read.. Counting patterns.. # site patterns = 284 Counting frequencies.. 120 bytes for distance 45440 bytes for lkl0 36352 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.285795 0.134463 0.036043 0.192436 0.170375 0.261347 0.211610 0.168896 lnL0 = -3325.564821 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3325.564821 x= 0.28580 0.13446 0.03604 0.19244 0.17037 0.26135 0.21161 0.16890 1 h-lim-p 0.0039 0.0314 104.9836 3324.192737 8 0.0003 43 | 0/8 2 h-lim-p 0.0009 0.0121 33.4148 3323.736442 6 0.0009 69 | 0/8 3 h-lim-p 0.0041 0.0334 7.2030 3323.715268 3 0.0009 88 | 0/8 4 h-lim-p 0.0023 0.1336 2.7330 3323.713167 4 0.0006 111 | 0/8 5 h-lim-p 0.0049 0.5688 0.3578 3323.713129 1 0.0006 127 | 0/8 6 h-lim-p 0.0039 5.4062 0.0566 3323.713128 0 0.0008 148 | 0/8 7 h-lim-p 0.0065 20.0000 0.0074 3323.713127 0 0.0057 168 | 0/8 8 h-lim-p 0.0170 20.0000 0.0025 3323.712958 0 0.2038 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3323.712953 0 1.0938 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3323.712953 0 1.0938 231 | 0/8 11 h-lim-p 2.4334 20.0000 0.0000 3323.712953 0 2.1293 251 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3323.712953 0 1.0938 271 | 0/8 13 h-lim-p 0.1987 20.0000 0.0000 3323.712953 0 6.3568 296 | 0/8 14 h-lim-p 2.0610 20.0000 0.0000 3323.712953 0 0.1127 319 | 0/8 15 h-lim-p 0.0065 20.0000 0.0002 3323.712953 0 0.0008 341 | 0/8 16 h-lim-p 0.0002 20.0000 0.0010 3323.712953 0 0.0000 367 | 0/8 17 h-lim-p 0.0003 20.0000 0.0000 3323.712953 0 0.0000 398 Out... lnL = -3323.712953 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3323.712953 Node 7: lnL = -3323.712953 Node 8: lnL = -3323.712953 Node 9: lnL = -3323.712953 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 930 Sequential format.. Reading seq # 1: YHR015W_Sbay Reading seq # 2: YHR015W_Scer Reading seq # 3: YHR015W_Skud Reading seq # 4: YHR015W_Smik Reading seq # 5: YHR015W_Spar Sequences read.. Counting patterns.. # site patterns = 441 Counting frequencies.. 120 bytes for distance 70560 bytes for lkl0 56448 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.316588 0.007886 0.002039 0.238382 0.346307 0.529285 0.295955 0.171933 lnL0 = -4979.621192 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4979.621192 x= 0.31659 0.00789 0.00204 0.23838 0.34631 0.52928 0.29595 0.17193 1 h-lim-p 0.0011 0.0090 227.6776 4974.792655 5 0.0002 33 | 0/8 2 h-lim-p 0.0003 0.0026 130.3986 4969.014878 0 0.0010 46 | 0/8 3 h-lim-p 0.0006 0.0048 32.3845 4968.482758 0 0.0012 59 | 0/8 4 h-lim-p 0.0004 0.0033 20.3882 4968.397438 0 0.0008 72 | 0/8 5 h-lim-p 0.0023 0.0181 6.3941 4968.380187 5 0.0010 95 | 0/8 6 h-lim-p 0.0043 0.0358 1.4135 4968.378872 3 0.0010 115 | 0/8 7 h-lim-p 0.0320 2.4680 0.0462 4968.263857 0 0.2562 130 | 0/8 8 h-lim-p 0.0018 0.0944 6.6905 4968.144290 1 0.0022 152 | 0/8 9 h-lim-p 2.5000 20.0000 0.0025 4968.138168 2 1.1719 168 | 0/8 10 h-lim-p 2.5000 20.0000 0.0005 4968.138035 1 1.2500 190 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4968.138034 0 1.0938 210 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4968.138034 0 1.2500 230 | 0/8 13 h-lim-p 1.5685 20.0000 0.0000 4968.138034 0 0.3431 251 | 0/8 14 h-lim-p 0.1405 20.0000 0.0000 4968.138034 0 0.0351 272 | 0/8 15 h-lim-p 0.0158 20.0000 0.0000 4968.138034 0 0.0001 298 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 4968.138034 0 0.0000 331 | 0/8 17 h-lim-p 0.0000 20.0000 0.0003 4968.138034 0 0.0000 352 | 0/8 18 h-lim-p 0.0000 20.0000 0.0003 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0003 | 0/8 20 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -4968.138034 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4968.138034 Node 7: lnL = -4968.138034 Node 8: lnL = -4968.138034 Node 9: lnL = -4968.138034 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 264 Sequential format.. Reading seq # 1: YHR017W_Sbay Reading seq # 2: YHR017W_Scer Reading seq # 3: YHR017W_Skud Reading seq # 4: YHR017W_Smik Reading seq # 5: YHR017W_Spar Sequences read.. Counting patterns.. # site patterns = 129 Counting frequencies.. 120 bytes for distance 20640 bytes for lkl0 16512 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.147403 0.134818 0.087929 0.120220 0.056199 0.154980 0.164070 0.061905 lnL0 = -1068.616323 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1068.616323 x= 0.14740 0.13482 0.08793 0.12022 0.05620 0.15498 0.16407 0.06191 1 h-lim-p 0.0006 0.0050 39.7664 1068.043998 0 0.0009 22 | 0/8 2 h-lim-p 0.0022 0.0178 10.9417 1068.002207 7 0.0008 51 | 0/8 3 h-lim-p 0.0010 0.0165 8.0939 1067.989613 5 0.0005 74 | 0/8 4 h-lim-p 0.0030 0.1596 1.4577 1067.988462 5 0.0011 96 | 0/8 5 h-lim-p 0.0037 0.6371 0.4531 1067.988306 2 0.0014 112 | 0/8 6 h-lim-p 0.0257 7.8176 0.0249 1067.986988 0 0.0772 133 | 0/8 7 h-lim-p 0.0054 0.3903 0.3573 1067.973032 0 0.0161 154 | 0/8 8 h-lim-p 0.0028 0.0510 2.0495 1067.970417 5 0.0011 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 1067.970303 2 0.9644 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1067.970303 0 1.0938 220 | 0/8 11 h-lim-p 2.2178 20.0000 0.0000 1067.970303 0 1.9406 240 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1067.970303 0 0.5469 261 | 0/8 13 h-lim-p 0.1339 20.0000 0.0000 1067.970303 0 0.0335 282 | 0/8 14 h-lim-p 0.0155 20.0000 0.0000 1067.970303 0 0.0310 303 | 0/8 15 h-lim-p 0.0188 20.0000 0.0000 1067.970303 0 0.0000 344 | 0/8 16 h-lim-p 0.0000 20.0000 0.0005 1067.970303 0 0.0000 367 | 0/8 17 h-lim-p 0.0000 20.0000 0.0003 1067.970303 0 0.0019 394 | 0/8 18 h-lim-p 0.0160 20.0000 0.0000 1067.970303 0 0.0017 416 | 0/8 19 h-lim-p 0.0045 20.0000 0.0000 1067.970303 0 0.0000 447 | 0/8 20 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 21 h-lim-p 0.0000 20.0000 0.0010 | 0/8 22 h-lim-p 0.0000 20.0000 0.0010 Out... lnL = -1067.970303 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1067.970303 Node 7: lnL = -1067.970303 Node 8: lnL = -1067.970303 Node 9: lnL = -1067.970303 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 530 Sequential format.. Reading seq # 1: YHR018C_Sbay Reading seq # 2: YHR018C_Scer Reading seq # 3: YHR018C_Skud Reading seq # 4: YHR018C_Smik Reading seq # 5: YHR018C_Spar Sequences read.. Counting patterns.. # site patterns = 212 Counting frequencies.. 120 bytes for distance 33920 bytes for lkl0 27136 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.180643 0.079615 0.080139 0.141829 0.075664 0.159093 0.171336 0.093286 lnL0 = -2258.812795 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2258.812795 x= 0.18064 0.07961 0.08014 0.14183 0.07566 0.15909 0.17134 0.09329 1 h-lim-p 0.0004 0.0031 68.7241 2258.039069 5 0.0003 31 | 0/8 2 h-lim-p 0.0023 0.0224 9.9260 2258.018574 6 0.0004 58 | 0/8 3 h-lim-p 0.0010 0.0279 4.2524 2258.016147 5 0.0003 84 | 0/8 4 h-lim-p 0.0009 0.1731 1.4875 2258.015650 4 0.0005 107 | 0/8 5 h-lim-p 0.0032 1.0021 0.2377 2258.015630 1 0.0007 122 | 0/8 6 h-lim-p 0.0043 4.2240 0.0385 2258.015630 0 0.0005 144 | 0/8 7 h-lim-p 0.0062 20.0000 0.0033 2258.015630 0 0.0027 164 | 0/8 8 h-lim-p 0.0215 20.0000 0.0004 2258.015614 0 0.3441 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2258.015613 0 1.0938 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2258.015613 0 1.0938 228 | 0/8 11 h-lim-p 1.2456 20.0000 0.0000 2258.015613 0 1.2456 248 | 0/8 12 h-lim-p 0.8427 20.0000 0.0000 2258.015613 0 1.6853 269 | 0/8 13 h-lim-p 0.0065 20.0000 0.0027 2258.015613 0 0.0008 291 | 0/8 14 h-lim-p 0.0001 3.2316 0.0418 2258.015613 0 0.0000 311 | 0/8 15 h-lim-p 0.0005 20.0000 0.0019 2258.015613 0 0.0000 346 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 2258.015613 0 0.0000 379 Out... lnL = -2258.015613 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2258.015613 Node 7: lnL = -2258.015613 Node 8: lnL = -2258.015613 Node 9: lnL = -2258.015613 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 248 Sequential format.. Reading seq # 1: YHR025W_Sbay Reading seq # 2: YHR025W_Scer Reading seq # 3: YHR025W_Skud Reading seq # 4: YHR025W_Smik Reading seq # 5: YHR025W_Spar Sequences read.. Counting patterns.. # site patterns = 95 Counting frequencies.. 120 bytes for distance 15200 bytes for lkl0 12160 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.120234 0.028009 0.049080 0.074666 0.065168 0.179689 0.141704 0.058085 lnL0 = -999.869298 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 999.869298 x= 0.12023 0.02801 0.04908 0.07467 0.06517 0.17969 0.14170 0.05808 1 h-lim-p 0.0054 0.0433 43.6680 999.599228 7 0.0003 38 | 0/8 2 h-lim-p 0.0011 0.0114 12.3617 999.554168 6 0.0006 65 | 0/8 3 h-lim-p 0.0017 0.0606 4.6165 999.548761 6 0.0006 93 | 0/8 4 h-lim-p 0.0023 0.0956 1.1821 999.548380 4 0.0006 114 | 0/8 5 h-lim-p 0.0023 0.4182 0.3048 999.548354 2 0.0006 131 | 0/8 6 h-lim-p 0.0016 1.5678 0.1159 999.548351 2 0.0005 156 | 0/8 7 h-lim-p 0.0027 11.6384 0.0217 999.548350 0 0.0006 177 | 0/8 8 h-lim-p 0.1905 20.0000 0.0001 999.548342 0 1.1428 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 999.548342 0 1.0938 219 | 0/8 10 h-lim-p 2.1814 20.0000 0.0000 999.548342 0 1.9087 239 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 999.548342 0 0.0000 275 Out... lnL = -999.548342 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -999.548342 Node 7: lnL = -999.548342 Node 8: lnL = -999.548342 Node 9: lnL = -999.548342 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 344 Sequential format.. Reading seq # 1: YHR029C_Sbay Reading seq # 2: YHR029C_Scer Reading seq # 3: YHR029C_Skud Reading seq # 4: YHR029C_Smik Reading seq # 5: YHR029C_Spar Sequences read.. Counting patterns.. # site patterns = 194 Counting frequencies.. 120 bytes for distance 31040 bytes for lkl0 24832 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.273523 0.057379 0.035383 0.170719 0.129817 0.272546 0.240448 0.159485 lnL0 = -1567.217635 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1567.217635 x= 0.27352 0.05738 0.03538 0.17072 0.12982 0.27255 0.24045 0.15949 1 h-lim-p 0.0040 0.0323 57.7455 1566.429792 8 0.0005 43 | 0/8 2 h-lim-p 0.0008 0.0061 20.8692 1566.208596 0 0.0015 56 | 0/8 3 h-lim-p 0.0034 0.0272 8.7914 1566.169546 6 0.0012 82 | 0/8 4 h-lim-p 0.0040 0.0751 2.6382 1566.166750 3 0.0009 101 | 0/8 5 h-lim-p 0.0028 0.1972 0.8314 1566.166201 5 0.0017 125 | 0/8 6 h-lim-p 0.0076 1.3618 0.1823 1566.166115 4 0.0023 156 | 0/8 7 h-lim-p 0.0259 14.9845 0.0165 1566.149370 0 0.4141 180 | 0/8 8 h-lim-p 0.0086 0.3807 0.7925 1566.148642 3 0.0021 207 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 1566.148457 3 1.0449 233 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1566.148456 0 1.0938 253 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1566.148456 0 1.0938 273 | 0/8 12 h-lim-p 1.8707 20.0000 0.0000 1566.148456 0 0.0018 302 Out... lnL = -1566.148456 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1566.148456 Node 7: lnL = -1566.148456 Node 8: lnL = -1566.148456 Node 9: lnL = -1566.148456 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 518 Sequential format.. Reading seq # 1: YHR030C_Sbay Reading seq # 2: YHR030C_Scer Reading seq # 3: YHR030C_Skud Reading seq # 4: YHR030C_Smik Reading seq # 5: YHR030C_Spar Sequences read.. Counting patterns.. # site patterns = 170 Counting frequencies.. 120 bytes for distance 27200 bytes for lkl0 21760 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.151893 0.034079 0.077579 0.095517 0.058231 0.146312 0.186737 0.079042 lnL0 = -2054.317919 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2054.317919 x= 0.15189 0.03408 0.07758 0.09552 0.05823 0.14631 0.18674 0.07904 1 h-lim-p 0.0036 0.9992 106.9382 2053.285099 6 0.0002 37 | 0/8 2 h-lim-p 0.0010 0.0082 15.3943 2053.244736 6 0.0003 65 | 0/8 3 h-lim-p 0.0008 0.0268 6.4044 2053.240704 6 0.0002 91 | 0/8 4 h-lim-p 0.0011 0.1081 1.3252 2053.240411 4 0.0004 113 | 0/8 5 h-lim-p 0.0016 0.8872 0.2984 2053.240391 2 0.0005 131 | 0/8 6 h-lim-p 0.0022 5.5658 0.0713 2053.240390 1 0.0005 154 | 0/8 7 h-lim-p 0.0077 18.9350 0.0050 2053.240390 0 0.0005 177 | 0/8 8 h-lim-p 0.0435 20.0000 0.0001 2053.240385 0 1.0428 201 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2053.240385 0 1.0938 221 | 0/8 10 h-lim-p 1.6346 20.0000 0.0000 2053.240385 0 0.7151 241 | 0/8 11 h-lim-p 0.3994 20.0000 0.0000 2053.240385 0 0.0499 263 | 0/8 12 h-lim-p 0.0150 20.0000 0.0001 2053.240385 0 0.0150 283 | 0/8 13 h-lim-p 0.0061 20.0000 0.0001 2053.240385 0 0.0000 313 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 2053.240385 0 0.0001 334 Out... lnL = -2053.240385 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2053.240385 Node 7: lnL = -2053.240385 Node 8: lnL = -2053.240385 Node 9: lnL = -2053.240385 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 420 Sequential format.. Reading seq # 1: YHR031C_Sbay Reading seq # 2: YHR031C_Scer Reading seq # 3: YHR031C_Skud Reading seq # 4: YHR031C_Smik Reading seq # 5: YHR031C_Spar Sequences read.. Counting patterns.. # site patterns = 131 Counting frequencies.. 120 bytes for distance 20960 bytes for lkl0 16768 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.124437 0.041480 0.059824 0.069137 0.071460 0.104415 0.109419 0.067007 lnL0 = -1517.372870 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1517.372870 x= 0.12444 0.04148 0.05982 0.06914 0.07146 0.10441 0.10942 0.06701 1 h-lim-p 0.0015 0.0122 66.7051 1516.923179 7 0.0002 39 | 0/8 2 h-lim-p 0.0010 0.0087 14.0295 1516.883434 6 0.0004 64 | 0/8 3 h-lim-p 0.0030 0.1568 1.9721 1516.882940 4 0.0003 88 | 0/8 4 h-lim-p 0.0013 0.4029 0.3930 1516.882916 2 0.0003 105 | 0/8 5 h-lim-p 0.0027 3.7939 0.0503 1516.882916 0 0.0003 127 | 0/8 6 h-lim-p 0.0173 20.0000 0.0009 1516.882916 0 0.0076 147 | 0/8 7 h-lim-p 0.0033 20.0000 0.0020 1516.882915 0 0.0131 169 | 0/8 8 h-lim-p 0.0010 2.8510 0.0269 1516.882910 0 0.0019 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1516.882910 0 1.0938 210 | 0/8 10 h-lim-p 1.6708 20.0000 0.0000 1516.882910 0 0.3655 231 | 0/8 11 h-lim-p 0.1799 20.0000 0.0000 1516.882910 0 0.0169 254 | 0/8 12 h-lim-p 0.0081 20.0000 0.0000 1516.882910 0 0.0041 274 | 0/8 13 h-lim-p 0.0024 20.0000 0.0001 1516.882910 0 0.0012 294 | 0/8 14 h-lim-p 0.0009 20.0000 0.0001 1516.882910 0 0.0000 324 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 1516.882910 0 0.0000 350 Out... lnL = -1516.882910 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1516.882910 Node 7: lnL = -1516.882910 Node 8: lnL = -1516.882910 Node 9: lnL = -1516.882910 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 420 Sequential format.. Reading seq # 1: YHR032W_Sbay Reading seq # 2: YHR032W_Scer Reading seq # 3: YHR032W_Skud Reading seq # 4: YHR032W_Smik Reading seq # 5: YHR032W_Spar Sequences read.. Counting patterns.. # site patterns = 138 Counting frequencies.. 120 bytes for distance 22080 bytes for lkl0 17664 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.125648 0.040470 0.041482 0.076703 0.077767 0.156450 0.096177 0.066237 lnL0 = -1551.498383 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1551.498383 x= 0.12565 0.04047 0.04148 0.07670 0.07777 0.15645 0.09618 0.06624 1 h-lim-p 0.0012 0.0099 84.8150 1550.826531 8 0.0002 40 | 0/8 2 h-lim-p 0.0008 0.0066 18.7857 1550.767943 5 0.0003 63 | 0/8 3 h-lim-p 0.0016 0.0420 4.0167 1550.765608 4 0.0003 84 | 0/8 4 h-lim-p 0.0016 0.3017 0.7657 1550.765469 4 0.0005 108 | 0/8 5 h-lim-p 0.0015 1.1483 0.2516 1550.765460 1 0.0003 131 | 0/8 6 h-lim-p 0.0037 5.4016 0.0223 1550.765460 0 0.0004 153 | 0/8 7 h-lim-p 0.0026 20.0000 0.0035 1550.765460 0 0.0006 174 | 0/8 8 h-lim-p 0.0623 20.0000 0.0000 1550.765458 0 0.9968 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1550.765458 0 2.1875 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1550.765458 0 1.0938 238 | 0/8 11 h-lim-p 0.2311 20.0000 0.0000 1550.765458 0 3.6981 262 | 0/8 12 h-lim-p 0.9280 20.0000 0.0000 1550.765458 0 5.5680 284 | 0/8 13 h-lim-p 0.0030 1.3309 0.0767 1550.765458 0 0.0007 305 | 0/8 14 h-lim-p 0.0003 0.5678 0.1796 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0012 | 0/8 16 h-lim-p 0.0000 20.0000 0.0012 Out... lnL = -1550.765458 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1550.765458 Node 7: lnL = -1550.765458 Node 8: lnL = -1550.765458 Node 9: lnL = -1550.765458 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 543 Sequential format.. Reading seq # 1: YHR033W_Sbay Reading seq # 2: YHR033W_Scer Reading seq # 3: YHR033W_Skud Reading seq # 4: YHR033W_Smik Reading seq # 5: YHR033W_Spar Sequences read.. Counting patterns.. # site patterns = 186 Counting frequencies.. 120 bytes for distance 29760 bytes for lkl0 23808 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.180019 0.014241 0.046646 0.089860 0.040905 0.092106 0.322339 0.104239 lnL0 = -2038.250339 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2038.250339 x= 0.18002 0.01424 0.04665 0.08986 0.04091 0.09211 0.32234 0.10424 1 h-lim-p 0.0001 0.0011 150.3779 2036.496519 0 0.0002 22 | 0/8 2 h-lim-p 0.0006 0.0044 24.5574 2036.408883 5 0.0003 45 | 0/8 3 h-lim-p 0.0016 0.0615 4.4875 2036.405678 3 0.0003 64 | 0/8 4 h-lim-p 0.0002 0.0232 6.5141 2036.402960 1 0.0003 78 | 0/8 5 h-lim-p 0.0005 0.0165 4.1535 2036.400208 0 0.0007 90 | 0/8 6 h-lim-p 0.0093 0.6160 0.3044 2036.400127 2 0.0011 108 | 0/8 7 h-lim-p 0.0027 1.5634 0.1208 2036.400029 3 0.0021 134 | 0/8 8 h-lim-p 0.0070 2.2712 0.0360 2036.364362 0 0.1116 158 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 2036.364254 2 0.9644 182 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2036.364254 0 1.0938 202 | 0/8 11 h-lim-p 1.6120 20.0000 0.0000 2036.364254 0 1.6120 222 | 0/8 12 h-lim-p 2.2818 20.0000 0.0000 2036.364254 0 0.0022 251 | 0/8 13 h-lim-p 0.0006 20.0000 0.0000 2036.364254 0 0.0000 278 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 2036.364254 0 0.0000 307 Out... lnL = -2036.364254 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2036.364254 Node 7: lnL = -2036.364254 Node 8: lnL = -2036.364254 Node 9: lnL = -2036.364254 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 232 Sequential format.. Reading seq # 1: YHR034C_Sbay Reading seq # 2: YHR034C_Scer Reading seq # 3: YHR034C_Skud Reading seq # 4: YHR034C_Smik Reading seq # 5: YHR034C_Spar Sequences read.. Counting patterns.. # site patterns = 137 Counting frequencies.. 120 bytes for distance 21920 bytes for lkl0 17536 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.242970 0.075232 0.169048 0.204524 0.077029 0.240983 0.386995 0.108997 lnL0 = -1171.190685 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1171.190685 x= 0.24297 0.07523 0.16905 0.20452 0.07703 0.24098 0.38700 0.10900 1 h-lim-p 0.0093 0.0745 37.7904 1170.382812 7 0.0012 39 | 0/8 2 h-lim-p 0.0021 0.0168 10.8733 1170.312727 8 0.0013 71 | 0/8 3 h-lim-p 0.0020 0.0399 6.8978 1170.277586 4 0.0020 91 | 0/8 4 h-lim-p 0.0084 0.2661 1.6272 1170.274295 5 0.0027 115 | 0/8 5 h-lim-p 0.0067 0.7018 0.6624 1170.273639 4 0.0035 136 | 0/8 6 h-lim-p 0.0129 2.3340 0.1803 1170.273592 0 0.0028 157 | 0/8 7 h-lim-p 0.0061 4.0332 0.0831 1170.273581 2 0.0030 182 | 0/8 8 h-lim-p 0.1536 20.0000 0.0016 1170.272758 0 1.2284 205 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1170.272724 2 0.9961 229 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1170.272724 0 1.0938 249 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1170.272724 0 1.0938 269 | 0/8 12 h-lim-p 1.0624 20.0000 0.0000 1170.272724 0 4.2494 291 | 0/8 13 h-lim-p 0.3399 20.0000 0.0000 1170.272724 0 0.0425 313 | 0/8 14 h-lim-p 0.0053 20.0000 0.0002 1170.272724 0 0.0000 340 | 0/8 15 h-lim-p 0.0007 20.0000 0.0000 1170.272724 0 0.0000 366 Out... lnL = -1170.272724 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1170.272724 Node 7: lnL = -1170.272724 Node 8: lnL = -1170.272724 Node 9: lnL = -1170.272724 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 392 Sequential format.. Reading seq # 1: YHR038W_Sbay Reading seq # 2: YHR038W_Scer Reading seq # 3: YHR038W_Skud Reading seq # 4: YHR038W_Smik Reading seq # 5: YHR038W_Spar Sequences read.. Counting patterns.. # site patterns = 176 Counting frequencies.. 120 bytes for distance 28160 bytes for lkl0 22528 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.197486 0.034266 0.080415 0.103743 0.092169 0.203959 0.234820 0.106111 lnL0 = -1730.983096 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1730.983096 x= 0.19749 0.03427 0.08041 0.10374 0.09217 0.20396 0.23482 0.10611 1 h-lim-p 0.0065 0.0524 51.5162 1730.563872 3 0.0003 31 | 0/8 2 h-lim-p 0.0017 0.0262 10.2458 1730.517766 6 0.0009 55 | 0/8 3 h-lim-p 0.0017 0.0591 5.3570 1730.512622 4 0.0004 76 | 0/8 4 h-lim-p 0.0015 0.2054 1.5805 1730.511773 4 0.0008 97 | 0/8 5 h-lim-p 0.0038 0.5065 0.3139 1730.511748 3 0.0005 117 | 0/8 6 h-lim-p 0.0104 13.6109 0.0154 1730.511747 0 0.0023 138 | 0/8 7 h-lim-p 0.0346 20.0000 0.0010 1730.511736 0 0.1385 160 | 0/8 8 h-lim-p 0.0021 1.1591 0.0672 1730.511668 0 0.0042 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1730.511666 0 1.0938 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1730.511666 0 1.0938 221 | 0/8 11 h-lim-p 1.4222 20.0000 0.0000 1730.511666 0 0.6222 241 | 0/8 12 h-lim-p 0.3704 20.0000 0.0000 1730.511666 0 0.0116 265 | 0/8 13 h-lim-p 0.0045 20.0000 0.0000 1730.511666 0 0.0045 285 | 0/8 14 h-lim-p 0.0026 20.0000 0.0000 1730.511666 0 0.0001 309 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 1730.511666 0 0.0000 329 | 0/8 16 h-lim-p 0.0003 20.0000 0.0000 1730.511666 0 0.0000 356 | 0/8 17 h-lim-p 0.0001 20.0000 0.0000 1730.511666 0 0.0000 383 Out... lnL = -1730.511666 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1730.511666 Node 7: lnL = -1730.511666 Node 8: lnL = -1730.511666 Node 9: lnL = -1730.511666 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 541 Sequential format.. Reading seq # 1: YHR043C_Sbay Reading seq # 2: YHR043C_Scer Reading seq # 3: YHR043C_Skud Reading seq # 4: YHR043C_Smik Reading seq # 5: YHR043C_Spar Sequences read.. Counting patterns.. # site patterns = 239 Counting frequencies.. 120 bytes for distance 38240 bytes for lkl0 30592 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.262709 0.358755 0.057992 0.173837 0.068542 0.166869 0.219680 0.127399 lnL0 = -2601.456519 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2601.456519 x= 0.26271 0.35875 0.05799 0.17384 0.06854 0.16687 0.21968 0.12740 1 h-lim-p 0.0050 0.0403 69.4378 2600.802175 2 0.0003 29 | 0/8 2 h-lim-p 0.0008 0.0114 26.6742 2600.561688 4 0.0008 49 | 0/8 3 h-lim-p 0.0015 0.0183 13.3526 2600.521882 6 0.0006 74 | 0/8 4 h-lim-p 0.0012 0.0646 6.3713 2600.503118 3 0.0012 92 | 0/8 5 h-lim-p 0.0018 0.0537 4.2420 2600.497606 4 0.0009 113 | 0/8 6 h-lim-p 0.0037 0.7703 1.0329 2600.497089 4 0.0011 135 | 0/8 7 h-lim-p 0.0037 0.8251 0.3055 2600.497032 3 0.0013 154 | 0/8 8 h-lim-p 1.3825 20.0000 0.0003 2600.496990 2 1.0666 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2600.496990 0 1.0938 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2600.496990 0 1.0938 218 | 0/8 11 h-lim-p 1.1288 20.0000 0.0000 2600.496990 0 0.0705 241 | 0/8 12 h-lim-p 0.0169 20.0000 0.0000 2600.496990 0 0.0000 270 | 0/8 13 h-lim-p 0.0008 20.0000 0.0000 2600.496990 0 0.0000 297 Out... lnL = -2600.496990 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2600.496990 Node 7: lnL = -2600.496990 Node 8: lnL = -2600.496990 Node 9: lnL = -2600.496990 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 486 Sequential format.. Reading seq # 1: YHR046C_Sbay Reading seq # 2: YHR046C_Scer Reading seq # 3: YHR046C_Skud Reading seq # 4: YHR046C_Smik Reading seq # 5: YHR046C_Spar Sequences read.. Counting patterns.. # site patterns = 192 Counting frequencies.. 120 bytes for distance 30720 bytes for lkl0 24576 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.139107 0.101503 0.106914 0.110504 0.086035 0.230829 0.213665 0.045436 lnL0 = -2150.766551 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2150.766551 x= 0.13911 0.10150 0.10691 0.11050 0.08604 0.23083 0.21366 0.04544 1 h-lim-p 0.0011 0.0086 66.2907 2149.873341 5 0.0004 32 | 0/8 2 h-lim-p 0.0010 0.0081 11.4567 2149.847640 4 0.0004 52 | 0/8 3 h-lim-p 0.0011 0.0536 4.1475 2149.843757 2 0.0005 68 | 0/8 4 h-lim-p 0.0010 0.1539 2.0766 2149.842948 2 0.0005 84 | 0/8 5 h-lim-p 0.0035 1.1512 0.2844 2149.842913 2 0.0009 101 | 0/8 6 h-lim-p 0.0049 3.4968 0.0507 2149.842912 0 0.0006 123 | 0/8 7 h-lim-p 0.0024 20.0000 0.0131 2149.842912 0 0.0010 143 | 0/8 8 h-lim-p 0.0697 20.0000 0.0002 2149.842887 0 1.1148 167 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2149.842885 0 1.0938 187 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2149.842885 0 1.0938 207 | 0/8 11 h-lim-p 1.1791 20.0000 0.0000 2149.842885 0 1.1791 227 | 0/8 12 h-lim-p 0.4525 20.0000 0.0000 2149.842885 0 0.3959 247 | 0/8 13 h-lim-p 0.0505 20.0000 0.0003 2149.842885 0 0.0000 291 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -2149.842885 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2149.842885 Node 7: lnL = -2149.842885 Node 8: lnL = -2149.842885 Node 9: lnL = -2149.842885 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 946 Sequential format.. Reading seq # 1: YHR048W_Sbay Reading seq # 2: YHR048W_Scer Reading seq # 3: YHR048W_Skud Reading seq # 4: YHR048W_Smik Reading seq # 5: YHR048W_Spar Sequences read.. Counting patterns.. # site patterns = 337 Counting frequencies.. 120 bytes for distance 53920 bytes for lkl0 43136 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.378521 0.234372 0.286154 0.166563 0.183063 0.056065 0.414220 0.199240 lnL0 = -4429.119188 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4429.119188 x= 0.37852 0.23437 0.28615 0.16656 0.18306 0.05607 0.41422 0.19924 1 h-lim-p 0.0049 0.0391 86.2485 4425.716562 6 0.0011 35 | 0/8 2 h-lim-p 0.0006 0.0050 55.0089 4425.134795 4 0.0005 55 | 0/8 3 h-lim-p 0.0012 0.0191 21.6209 4424.804616 0 0.0019 67 | 0/8 4 h-lim-p 0.0031 0.0300 12.8055 4424.616846 4 0.0032 87 | 0/8 5 h-lim-p 0.0038 0.0439 10.6463 4424.481585 6 0.0042 115 | 0/8 6 h-lim-p 0.0794 0.6349 0.5013 4424.481111 3 0.0024 137 | 0/8 7 h-lim-p 0.0063 2.4260 0.1937 4424.479081 0 0.0254 159 | 0/8 8 h-lim-p 0.0385 20.0000 0.1275 4424.368591 0 0.1541 181 | 0/8 9 h-lim-p 1.6794 20.0000 0.0117 4424.355785 4 1.1897 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0003 4424.355762 1 0.9961 233 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4424.355762 0 1.0938 253 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4424.355762 0 1.0938 273 | 0/8 13 h-lim-p 1.1813 20.0000 0.0000 4424.355762 0 1.7719 293 | 0/8 14 h-lim-p 0.3587 20.0000 0.0000 4424.355762 0 0.0897 314 | 0/8 15 h-lim-p 0.0120 20.0000 0.0001 4424.355762 0 0.0120 334 | 0/8 16 h-lim-p 0.0037 20.0000 0.0004 4424.355762 0 0.0005 356 | 0/8 17 h-lim-p 0.0019 20.0000 0.0001 4424.355762 0 0.0000 392 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 4424.355762 0 0.0000 423 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 4424.355762 0 0.0000 457 | 0/8 20 h-lim-p 0.0000 20.0000 0.0000 | 0/8 21 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -4424.355762 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4424.355762 Node 7: lnL = -4424.355762 Node 8: lnL = -4424.355762 Node 9: lnL = -4424.355762 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 348 Sequential format.. Reading seq # 1: YHR049W_Sbay Reading seq # 2: YHR049W_Scer Reading seq # 3: YHR049W_Skud Reading seq # 4: YHR049W_Smik Reading seq # 5: YHR049W_Spar Sequences read.. Counting patterns.. # site patterns = 130 Counting frequencies.. 120 bytes for distance 20800 bytes for lkl0 16640 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.186590 0.031102 0.039783 0.089537 0.070682 0.154955 0.178391 0.107072 lnL0 = -1416.481349 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1416.481349 x= 0.18659 0.03110 0.03978 0.08954 0.07068 0.15495 0.17839 0.10707 1 h-lim-p 0.0006 0.0049 90.8737 1415.601363 7 0.0002 35 | 0/8 2 h-lim-p 0.0007 0.0055 16.4457 1415.547223 6 0.0004 62 | 0/8 3 h-lim-p 0.0012 0.0581 5.4865 1415.540684 5 0.0005 85 | 0/8 4 h-lim-p 0.0012 0.0525 2.1498 1415.539520 2 0.0006 101 | 0/8 5 h-lim-p 0.0036 0.1283 0.3439 1415.539488 3 0.0005 123 | 0/8 6 h-lim-p 0.0012 2.0632 0.1542 1415.539481 2 0.0008 149 | 0/8 7 h-lim-p 0.0120 19.0313 0.0100 1415.539481 1 0.0030 172 | 0/8 8 h-lim-p 0.0264 20.0000 0.0011 1415.539286 0 0.3169 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1415.539285 0 1.0938 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1415.539285 0 1.0938 235 | 0/8 11 h-lim-p 1.2349 20.0000 0.0000 1415.539285 0 0.0003 266 Out... lnL = -1415.539285 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1415.539285 Node 7: lnL = -1415.539285 Node 8: lnL = -1415.539285 Node 9: lnL = -1415.539285 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 424 Sequential format.. Reading seq # 1: YHR051W_Sbay Reading seq # 2: YHR051W_Scer Reading seq # 3: YHR051W_Skud Reading seq # 4: YHR051W_Smik Reading seq # 5: YHR051W_Spar Sequences read.. Counting patterns.. # site patterns = 137 Counting frequencies.. 120 bytes for distance 21920 bytes for lkl0 17536 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.108590 0.023068 0.026030 0.102691 0.050048 0.126600 0.171601 0.047974 lnL0 = -1619.407445 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1619.407445 x= 0.10859 0.02307 0.02603 0.10269 0.05005 0.12660 0.17160 0.04797 1 h-lim-p 0.0002 0.0015 197.7645 1617.331197 4 0.0001 31 | 0/8 2 h-lim-p 0.0003 0.0022 31.0825 1617.215969 5 0.0002 52 | 0/8 3 h-lim-p 0.0005 0.0160 16.4274 1617.187408 7 0.0003 81 | 0/8 4 h-lim-p 0.0016 0.0408 2.7780 1617.186228 3 0.0003 100 | 0/8 5 h-lim-p 0.0010 0.1105 0.8960 1617.186118 3 0.0003 121 | 0/8 6 h-lim-p 0.0032 2.1652 0.0840 1617.186116 0 0.0007 142 | 0/8 7 h-lim-p 0.0031 7.9499 0.0185 1617.186115 0 0.0016 162 | 0/8 8 h-lim-p 0.0154 20.0000 0.0019 1617.185436 0 0.2465 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1617.185424 1 0.9961 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1617.185424 0 1.0938 228 | 0/8 11 h-lim-p 1.2427 20.0000 0.0000 1617.185424 0 2.4855 249 | 0/8 12 h-lim-p 1.2180 20.0000 0.0000 1617.185424 0 1.0657 269 | 0/8 13 h-lim-p 0.0199 20.0000 0.0016 1617.185424 0 0.0025 291 | 0/8 14 h-lim-p 0.0008 14.6176 0.0050 1617.185424 0 0.0006 311 | 0/8 15 h-lim-p 0.0004 10.4070 0.0070 1617.185424 0 0.0001 333 | 0/8 16 h-lim-p 0.0002 20.0000 0.0023 1617.185424 0 0.0000 359 | 0/8 17 h-lim-p 0.0000 20.0000 0.0014 1617.185424 0 0.0000 390 | 0/8 18 h-lim-p 0.0000 20.0000 0.0010 | 0/8 19 h-lim-p 0.0000 20.0000 0.0010 Out... lnL = -1617.185424 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1617.185424 Node 7: lnL = -1617.185424 Node 8: lnL = -1617.185424 Node 9: lnL = -1617.185424 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 755 Sequential format.. Reading seq # 1: YHR052W_Sbay Reading seq # 2: YHR052W_Scer Reading seq # 3: YHR052W_Skud Reading seq # 4: YHR052W_Smik Reading seq # 5: YHR052W_Spar Sequences read.. Counting patterns.. # site patterns = 191 Counting frequencies.. 120 bytes for distance 30560 bytes for lkl0 24448 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.098379 0.035353 0.054982 0.074467 0.035045 0.143200 0.164243 0.037154 lnL0 = -2827.946677 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2827.946677 x= 0.09838 0.03535 0.05498 0.07447 0.03504 0.14320 0.16424 0.03715 1 h-lim-p 0.0003 0.0025 196.0513 2826.131971 5 0.0001 34 | 0/8 2 h-lim-p 0.0002 0.0017 31.1578 2826.072922 6 0.0001 60 | 0/8 3 h-lim-p 0.0002 0.0092 15.5420 2826.061236 2 0.0001 76 | 0/8 4 h-lim-p 0.0003 0.0385 6.3879 2826.057610 5 0.0002 98 | 0/8 5 h-lim-p 0.0019 0.1426 0.7285 2826.057568 2 0.0001 117 | 0/8 6 h-lim-p 0.0006 2.4431 0.1877 2826.057563 1 0.0003 140 | 0/8 7 h-lim-p 0.0033 5.3718 0.0163 2826.057563 0 0.0004 162 | 0/8 8 h-lim-p 0.0153 20.0000 0.0004 2826.057399 0 0.4881 187 | 0/8 9 h-lim-p 1.9120 20.0000 0.0001 2826.057391 1 0.9411 210 | 0/8 10 h-lim-p 1.9347 20.0000 0.0000 2826.057391 0 1.6928 230 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2826.057391 0 1.0938 250 | 0/8 12 h-lim-p 0.2860 20.0000 0.0000 2826.057391 m20.0000 274 | 0/8 13 h-lim-p 0.0016 0.0823 0.6009 2826.057391 0 0.0014 294 | 0/8 14 h-lim-p 0.0795 4.7073 0.0103 2826.057391 0 0.0009 320 | 0/8 15 h-lim-p 0.0019 20.0000 0.0051 2826.057391 0 0.0000 359 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 2826.057391 0 0.0000 392 Out... lnL = -2826.057391 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2826.057391 Node 7: lnL = -2826.057391 Node 8: lnL = -2826.057391 Node 9: lnL = -2826.057391 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 175 Sequential format.. Reading seq # 1: YHR057C_Sbay Reading seq # 2: YHR057C_Scer Reading seq # 3: YHR057C_Skud Reading seq # 4: YHR057C_Smik Reading seq # 5: YHR057C_Spar Sequences read.. Counting patterns.. # site patterns = 85 Counting frequencies.. 120 bytes for distance 13600 bytes for lkl0 10880 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.148238 0.101676 0.063460 0.072864 0.078729 0.161483 0.154715 0.065541 lnL0 = -719.786625 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 719.786625 x= 0.14824 0.10168 0.06346 0.07286 0.07873 0.16148 0.15472 0.06554 1 h-lim-p 0.0021 0.0167 33.4743 719.398112 8 0.0007 40 | 0/8 2 h-lim-p 0.0017 0.0135 7.2519 719.376948 5 0.0008 63 | 0/8 3 h-lim-p 0.0021 0.0682 2.8181 719.372588 5 0.0012 88 | 0/8 4 h-lim-p 0.0082 0.3133 0.4274 719.372507 2 0.0009 106 | 0/8 5 h-lim-p 0.0105 7.7043 0.0367 719.372506 1 0.0013 130 | 0/8 6 h-lim-p 0.0078 20.0000 0.0060 719.372506 0 0.0017 151 | 0/8 7 h-lim-p 0.0061 20.0000 0.0017 719.372506 0 0.0053 171 | 0/8 8 h-lim-p 0.0489 20.0000 0.0002 719.372504 0 0.3911 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 719.372504 0 1.0938 214 | 0/8 10 h-lim-p 1.8886 20.0000 0.0000 719.372504 0 2.8328 234 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 719.372504 0 0.2734 256 | 0/8 12 h-lim-p 0.0838 20.0000 0.0000 719.372504 0 0.0419 276 | 0/8 13 h-lim-p 0.0163 20.0000 0.0000 719.372504 0 0.0008 300 | 0/8 14 h-lim-p 0.0005 20.0000 0.0000 719.372504 0 0.0005 320 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 719.372504 0 0.0002 340 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 719.372504 0 0.0000 360 | 0/8 17 h-lim-p 0.0002 20.0000 0.0000 719.372504 0 0.0000 381 | 0/8 18 h-lim-p 0.0001 20.0000 0.0000 719.372504 0 0.0001 401 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 719.372504 0 0.0000 422 | 0/8 20 h-lim-p 0.0002 20.0000 0.0000 719.372504 0 0.0000 455 Out... lnL = -719.372504 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -719.372504 Node 7: lnL = -719.372504 Node 8: lnL = -719.372504 Node 9: lnL = -719.372504 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 238 Sequential format.. Reading seq # 1: YHR058C_Sbay Reading seq # 2: YHR058C_Scer Reading seq # 3: YHR058C_Skud Reading seq # 4: YHR058C_Smik Reading seq # 5: YHR058C_Spar Sequences read.. Counting patterns.. # site patterns = 124 Counting frequencies.. 120 bytes for distance 19840 bytes for lkl0 15872 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.165401 0.175509 0.074260 0.101500 0.093804 0.279943 0.171940 0.054864 lnL0 = -1086.628119 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1086.628119 x= 0.16540 0.17551 0.07426 0.10150 0.09380 0.27994 0.17194 0.05486 1 h-lim-p 0.0042 0.0338 29.3208 1086.247303 5 0.0009 32 | 0/8 2 h-lim-p 0.0034 0.0279 8.0629 1086.192911 5 0.0018 55 | 0/8 3 h-lim-p 0.0028 0.0760 5.1751 1086.185446 6 0.0008 80 | 0/8 4 h-lim-p 0.0020 0.1484 1.9690 1086.183350 6 0.0013 106 | 0/8 5 h-lim-p 0.0048 0.2795 0.5462 1086.183196 2 0.0011 123 | 0/8 6 h-lim-p 0.0761 20.0000 0.0080 1086.183195 0 0.0042 146 | 0/8 7 h-lim-p 0.0136 20.0000 0.0024 1086.183195 0 0.0119 166 | 0/8 8 h-lim-p 0.0115 20.0000 0.0025 1086.183178 0 0.0921 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1086.183178 0 1.0938 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1086.183178 0 1.0938 229 | 0/8 11 h-lim-p 1.1794 20.0000 0.0000 1086.183178 0 2.3588 250 | 0/8 12 h-lim-p 0.9735 20.0000 0.0000 1086.183178 0 1.4602 270 | 0/8 13 h-lim-p 0.0008 4.2842 0.0233 1086.183178 0 0.0002 291 | 0/8 14 h-lim-p 0.0004 20.0000 0.0104 1086.183178 0 0.0001 313 | 0/8 15 h-lim-p 0.0002 20.0000 0.0036 1086.183178 0 0.0001 333 | 0/8 16 h-lim-p 0.0007 20.0000 0.0004 1086.183178 0 0.0007 353 | 0/8 17 h-lim-p 0.0004 20.0000 0.0008 1086.183178 0 0.0000 389 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 1086.183178 0 0.0000 423 | 0/8 19 h-lim-p 0.0000 20.0000 0.0002 | 0/8 20 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1086.183178 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1086.183178 Node 7: lnL = -1086.183178 Node 8: lnL = -1086.183178 Node 9: lnL = -1086.183178 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 248 Sequential format.. Reading seq # 1: YHR059W_Sbay Reading seq # 2: YHR059W_Scer Reading seq # 3: YHR059W_Skud Reading seq # 4: YHR059W_Smik Reading seq # 5: YHR059W_Spar Sequences read.. Counting patterns.. # site patterns = 120 Counting frequencies.. 120 bytes for distance 19200 bytes for lkl0 15360 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.182331 0.126470 0.100320 0.112590 0.082714 0.206525 0.187657 0.076560 lnL0 = -1094.618145 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1094.618145 x= 0.18233 0.12647 0.10032 0.11259 0.08271 0.20653 0.18766 0.07656 1 h-lim-p 0.0015 0.0122 26.5987 1094.328316 7 0.0008 39 | 0/8 2 h-lim-p 0.0030 0.0237 7.1451 1094.311966 2 0.0007 56 | 0/8 3 h-lim-p 0.0020 0.1157 2.4849 1094.308234 5 0.0014 81 | 0/8 4 h-lim-p 0.0047 0.3787 0.7191 1094.307923 4 0.0013 103 | 0/8 5 h-lim-p 0.0065 1.8326 0.1470 1094.307905 3 0.0017 130 | 0/8 6 h-lim-p 0.0121 7.3656 0.0213 1094.307905 0 0.0013 152 | 0/8 7 h-lim-p 0.0050 20.0000 0.0056 1094.307905 0 0.0022 172 | 0/8 8 h-lim-p 0.0622 20.0000 0.0002 1094.307897 0 0.7459 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1094.307897 0 1.0938 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1094.307897 0 1.0938 235 | 0/8 11 h-lim-p 1.1887 20.0000 0.0000 1094.307897 0 2.3774 256 | 0/8 12 h-lim-p 1.7670 20.0000 0.0000 1094.307897 0 0.2209 278 | 0/8 13 h-lim-p 0.0185 20.0000 0.0001 1094.307897 0 0.0012 301 | 0/8 14 h-lim-p 0.0010 20.0000 0.0001 1094.307897 0 0.0000 326 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 1094.307897 0 0.0000 359 Out... lnL = -1094.307897 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1094.307897 Node 7: lnL = -1094.307897 Node 8: lnL = -1094.307897 Node 9: lnL = -1094.307897 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 276 Sequential format.. Reading seq # 1: YHR060W_Sbay Reading seq # 2: YHR060W_Scer Reading seq # 3: YHR060W_Skud Reading seq # 4: YHR060W_Smik Reading seq # 5: YHR060W_Spar Sequences read.. Counting patterns.. # site patterns = 128 Counting frequencies.. 120 bytes for distance 20480 bytes for lkl0 16384 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.121777 0.190274 0.066292 0.150073 0.072823 0.210415 0.183542 0.020017 lnL0 = -1083.323746 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1083.323746 x= 0.12178 0.19027 0.06629 0.15007 0.07282 0.21041 0.18354 0.02002 1 h-lim-p 0.0002 0.0014 29.3754 1083.045388 0 0.0007 24 | 0/8 2 h-lim-p 0.0017 0.0137 7.6733 1083.016719 6 0.0010 53 | 0/8 3 h-lim-p 0.0026 0.2237 3.0086 1083.012993 6 0.0009 80 | 0/8 4 h-lim-p 0.0023 0.0220 1.2510 1083.012507 3 0.0007 100 | 0/8 5 h-lim-p 0.0030 1.0401 0.3041 1083.012430 4 0.0017 123 | 0/8 6 h-lim-p 0.0104 3.7719 0.0499 1083.012418 2 0.0033 148 | 0/8 7 h-lim-p 0.0185 20.0000 0.0089 1083.011376 0 0.1484 171 | 0/8 8 h-lim-p 0.0030 0.6232 0.4367 1083.010430 1 0.0038 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 1083.010386 2 0.9961 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1083.010386 0 1.0938 237 | 0/8 11 h-lim-p 1.1157 20.0000 0.0000 1083.010386 0 4.4626 259 | 0/8 12 h-lim-p 0.0790 14.2957 0.0010 1083.010386 0 0.0395 279 | 0/8 13 h-lim-p 0.0108 3.8861 0.0036 1083.010386 0 0.0003 303 | 0/8 14 h-lim-p 0.0000 0.3659 0.0383 1083.010386 0 0.0000 323 | 0/8 15 h-lim-p 0.0003 3.4821 0.0040 1083.010386 0 0.0000 346 | 0/8 16 h-lim-p 0.0001 20.0000 0.0011 1083.010386 0 0.0000 382 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 | 0/8 18 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1083.010386 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1083.010386 Node 7: lnL = -1083.010386 Node 8: lnL = -1083.010386 Node 9: lnL = -1083.010386 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 498 Sequential format.. Reading seq # 1: YHR061C_Sbay Reading seq # 2: YHR061C_Scer Reading seq # 3: YHR061C_Skud Reading seq # 4: YHR061C_Smik Reading seq # 5: YHR061C_Spar Sequences read.. Counting patterns.. # site patterns = 150 Counting frequencies.. 120 bytes for distance 24000 bytes for lkl0 19200 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.180570 0.000060 0.057917 0.083454 0.069280 0.149728 0.189377 0.103951 lnL0 = -1825.758050 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1825.758050 x= 0.18057 0.00006 0.05792 0.08345 0.06928 0.14973 0.18938 0.10395 1 h-lim-p 0.0008 0.0060 180.8604 1822.072870 9 0.0002 45 | 0/8 2 h-lim-p 0.0004 0.0032 40.6242 1821.684505 1 0.0005 59 | 0/8 3 h-lim-p 0.0008 0.0091 25.6680 1821.590742 2 0.0004 75 | 0/8 4 h-lim-p 0.0010 0.0143 9.6550 1821.578239 5 0.0003 99 | 0/8 5 h-lim-p 0.0019 0.1366 1.6371 1821.577363 5 0.0007 122 | 0/8 6 h-lim-p 0.0036 0.6471 0.3042 1821.577346 2 0.0004 140 | 0/8 7 h-lim-p 0.0117 14.4309 0.0091 1821.577230 0 0.0467 162 | 0/8 8 h-lim-p 0.0046 0.9656 0.0936 1821.574555 0 0.0182 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1821.574421 2 1.1719 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1821.574420 0 1.0938 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1821.574420 0 1.0938 248 | 0/8 12 h-lim-p 1.1465 20.0000 0.0000 1821.574420 0 0.5016 268 | 0/8 13 h-lim-p 0.1673 20.0000 0.0000 1821.574420 0 0.0000 314 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 1821.574420 0 0.0000 349 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1821.574420 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1821.574420 Node 7: lnL = -1821.574420 Node 8: lnL = -1821.574420 Node 9: lnL = -1821.574420 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 304 Sequential format.. Reading seq # 1: YHR062C_Sbay Reading seq # 2: YHR062C_Scer Reading seq # 3: YHR062C_Skud Reading seq # 4: YHR062C_Smik Reading seq # 5: YHR062C_Spar Sequences read.. Counting patterns.. # site patterns = 145 Counting frequencies.. 120 bytes for distance 23200 bytes for lkl0 18560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.212058 0.027107 0.070104 0.141689 0.151299 0.237030 0.159379 0.109148 lnL0 = -1373.534008 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1373.534008 x= 0.21206 0.02711 0.07010 0.14169 0.15130 0.23703 0.15938 0.10915 1 h-lim-p 0.0054 0.0908 71.1104 1372.535507 7 0.0004 40 | 0/8 2 h-lim-p 0.0009 0.0075 10.6620 1372.488446 3 0.0008 58 | 0/8 3 h-lim-p 0.0055 0.1785 1.6531 1372.487124 5 0.0010 84 | 0/8 4 h-lim-p 0.0059 0.2712 0.2778 1372.487092 3 0.0009 106 | 0/8 5 h-lim-p 0.0035 1.6247 0.0673 1372.487089 1 0.0014 128 | 0/8 6 h-lim-p 0.0159 20.0000 0.0060 1372.487089 0 0.0070 148 | 0/8 7 h-lim-p 0.0211 20.0000 0.0020 1372.487079 0 0.0844 170 | 0/8 8 h-lim-p 0.0041 8.3407 0.0408 1372.487039 0 0.0061 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1372.487038 0 1.0938 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1372.487038 0 1.0938 230 | 0/8 11 h-lim-p 1.4794 20.0000 0.0000 1372.487038 0 2.2191 250 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1372.487038 0 0.1367 273 | 0/8 13 h-lim-p 0.0181 20.0000 0.0000 1372.487038 0 0.0000 311 Out... lnL = -1372.487038 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1372.487038 Node 7: lnL = -1372.487038 Node 8: lnL = -1372.487038 Node 9: lnL = -1372.487038 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 355 Sequential format.. Reading seq # 1: YHR063C_Sbay Reading seq # 2: YHR063C_Scer Reading seq # 3: YHR063C_Skud Reading seq # 4: YHR063C_Smik Reading seq # 5: YHR063C_Spar Sequences read.. Counting patterns.. # site patterns = 162 Counting frequencies.. 120 bytes for distance 25920 bytes for lkl0 20736 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.212432 0.075552 0.042803 0.144797 0.113506 0.337608 0.261435 0.093144 lnL0 = -1543.234560 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1543.234560 x= 0.21243 0.07555 0.04280 0.14480 0.11351 0.33761 0.26144 0.09314 1 h-lim-p 0.0067 0.0676 67.7579 1542.055220 9 0.0006 46 | 0/8 2 h-lim-p 0.0012 0.0093 18.9576 1541.869090 2 0.0011 62 | 0/8 3 h-lim-p 0.0020 0.0163 9.2486 1541.827917 7 0.0012 91 | 0/8 4 h-lim-p 0.0033 0.0712 3.3049 1541.822969 5 0.0011 115 | 0/8 5 h-lim-p 0.0098 0.8972 0.3552 1541.822848 2 0.0019 132 | 0/8 6 h-lim-p 0.0045 1.1186 0.1525 1541.822834 2 0.0015 158 | 0/8 7 h-lim-p 0.0144 12.5169 0.0159 1541.822833 0 0.0031 179 | 0/8 8 h-lim-p 0.0740 20.0000 0.0007 1541.822720 0 0.5917 202 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1541.822716 1 0.9961 224 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1541.822716 0 1.0938 244 | 0/8 11 h-lim-p 1.2333 20.0000 0.0000 1541.822716 0 0.6166 264 | 0/8 12 h-lim-p 0.1064 20.0000 0.0000 1541.822716 0 0.0000 302 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1541.822716 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1541.822716 Node 7: lnL = -1541.822716 Node 8: lnL = -1541.822716 Node 9: lnL = -1541.822716 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 307 Sequential format.. Reading seq # 1: YHR064C_Sbay Reading seq # 2: YHR064C_Scer Reading seq # 3: YHR064C_Skud Reading seq # 4: YHR064C_Smik Reading seq # 5: YHR064C_Spar Sequences read.. Counting patterns.. # site patterns = 119 Counting frequencies.. 120 bytes for distance 19040 bytes for lkl0 15232 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.121988 0.052851 0.061087 0.094267 0.097243 0.153386 0.161157 0.046730 lnL0 = -1278.854317 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1278.854317 x= 0.12199 0.05285 0.06109 0.09427 0.09724 0.15339 0.16116 0.04673 1 h-lim-p 0.0023 0.0183 67.1830 1278.132023 8 0.0003 42 | 0/8 2 h-lim-p 0.0018 0.0140 8.3977 1278.112398 6 0.0006 68 | 0/8 3 h-lim-p 0.0023 0.1229 2.0040 1278.111261 4 0.0006 90 | 0/8 4 h-lim-p 0.0023 0.2951 0.5204 1278.111186 3 0.0006 109 | 0/8 5 h-lim-p 0.0075 2.2387 0.0419 1278.111185 1 0.0005 134 | 0/8 6 h-lim-p 0.0022 20.0000 0.0089 1278.111185 0 0.0009 154 | 0/8 7 h-lim-p 0.1715 20.0000 0.0000 1278.111182 0 1.3717 177 | 0/8 8 h-lim-p 0.0554 20.0000 0.0012 1278.111182 0 0.0009 202 | 0/8 9 h-lim-p 0.0493 20.0000 0.0000 1278.111182 0 0.7884 226 | 0/8 10 h-lim-p 1.4523 20.0000 0.0000 1278.111182 0 2.1784 246 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1278.111182 0 0.1562 269 | 0/8 12 h-lim-p 0.0268 20.0000 0.0000 1278.111182 0 0.0000 314 | 0/8 13 h-lim-p 0.0000 20.0000 0.0010 | 0/8 14 h-lim-p 0.0000 20.0000 0.0010 Out... lnL = -1278.111182 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1278.111182 Node 7: lnL = -1278.111182 Node 8: lnL = -1278.111182 Node 9: lnL = -1278.111182 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 179 Sequential format.. Reading seq # 1: YHR065C_Sbay Reading seq # 2: YHR065C_Scer Reading seq # 3: YHR065C_Skud Reading seq # 4: YHR065C_Smik Reading seq # 5: YHR065C_Spar Sequences read.. Counting patterns.. # site patterns = 82 Counting frequencies.. 120 bytes for distance 13120 bytes for lkl0 10496 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.142324 0.000060 0.108528 0.169162 0.051559 0.225241 0.234686 0.056163 lnL0 = -790.117057 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 790.117057 x= 0.14232 0.00006 0.10853 0.16916 0.05156 0.22524 0.23469 0.05616 1 h-lim-p 0.0004 0.0035 32.8412 789.716558 0 0.0007 22 | 0/8 2 h-lim-p 0.0018 0.0145 6.3328 789.695740 7 0.0011 50 | 0/8 3 h-lim-p 0.0026 0.0946 2.6145 789.693925 2 0.0006 67 | 0/8 4 h-lim-p 0.0016 0.0755 0.9649 789.693159 1 0.0020 81 | 0/8 5 h-lim-p 0.0390 1.1953 0.0506 789.693062 4 0.0115 111 | 0/8 6 h-lim-p 0.0104 1.8233 0.0556 789.690682 0 0.0418 133 | 0/8 7 h-lim-p 0.0045 0.0868 0.5181 789.686271 0 0.0067 153 | 0/8 8 h-lim-p 0.0220 1.1688 0.1586 789.686254 1 0.0014 178 | 0/8 9 h-lim-p 0.3412 20.0000 0.0006 789.686153 0 1.0236 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 789.686153 0 1.0938 219 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 789.686153 0 1.2500 239 | 0/8 12 h-lim-p 1.5254 20.0000 0.0000 789.686153 0 0.1907 261 | 0/8 13 h-lim-p 0.0720 20.0000 0.0000 789.686153 0 0.0000 300 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 789.686153 0 0.0000 333 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 789.686153 0 0.0000 359 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 789.686153 0 0.0038 387 | 0/8 17 h-lim-p 0.0113 20.0000 0.0001 789.686153 0 0.0000 414 | 0/8 18 h-lim-p 0.0001 20.0000 0.0000 789.686153 0 0.0145 441 | 0/8 19 h-lim-p 0.0261 20.0000 0.0000 789.686153 0 0.0000 470 | 0/8 20 h-lim-p 0.0000 20.0000 0.0002 789.686153 0 0.0000 498 | 0/8 21 h-lim-p 0.0000 20.0000 0.0009 | 0/8 22 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -789.686153 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -789.686153 Node 7: lnL = -789.686153 Node 8: lnL = -789.686153 Node 9: lnL = -789.686153 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 252 Sequential format.. Reading seq # 1: YHR069C_Sbay Reading seq # 2: YHR069C_Scer Reading seq # 3: YHR069C_Skud Reading seq # 4: YHR069C_Smik Reading seq # 5: YHR069C_Spar Sequences read.. Counting patterns.. # site patterns = 136 Counting frequencies.. 120 bytes for distance 21760 bytes for lkl0 17408 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.187956 0.110257 0.132311 0.174317 0.124567 0.169356 0.323129 0.054244 lnL0 = -1150.572073 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1150.572073 x= 0.18796 0.11026 0.13231 0.17432 0.12457 0.16936 0.32313 0.05424 1 h-lim-p 0.0008 0.0063 19.0782 1150.388428 0 0.0012 22 | 0/8 2 h-lim-p 0.0046 0.0371 3.9198 1150.378327 5 0.0014 47 | 0/8 3 h-lim-p 0.0056 0.4714 0.9545 1150.377825 3 0.0012 66 | 0/8 4 h-lim-p 0.0054 1.1702 0.2046 1150.377789 3 0.0015 93 | 0/8 5 h-lim-p 0.0058 7.0667 0.0512 1150.377731 0 0.0117 114 | 0/8 6 h-lim-p 0.0126 5.6305 0.0474 1150.377189 0 0.0252 135 | 0/8 7 h-lim-p 0.0051 0.7337 0.2333 1150.374562 0 0.0103 156 | 0/8 8 h-lim-p 0.0046 0.4585 0.5256 1150.374238 2 0.0021 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1150.374207 2 0.9961 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1150.374207 0 1.0938 224 | 0/8 11 h-lim-p 1.3410 20.0000 0.0000 1150.374207 0 1.3410 244 | 0/8 12 h-lim-p 0.5423 20.0000 0.0000 1150.374207 0 0.5423 264 | 0/8 13 h-lim-p 0.0414 20.0000 0.0002 1150.374207 0 0.0000 302 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 1150.374207 0 0.0000 332 Out... lnL = -1150.374207 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1150.374207 Node 7: lnL = -1150.374207 Node 8: lnL = -1150.374207 Node 9: lnL = -1150.374207 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 845 Sequential format.. Reading seq # 1: YHR072W_Sbay Reading seq # 2: YHR072W_Scer Reading seq # 3: YHR072W_Skud Reading seq # 4: YHR072W_Smik Reading seq # 5: YHR072W_Spar Sequences read.. Counting patterns.. # site patterns = 385 Counting frequencies.. 120 bytes for distance 61600 bytes for lkl0 49280 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.308280 0.086490 0.151157 0.191554 0.183932 0.318261 0.273409 0.138846 lnL0 = -4526.549681 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4526.549681 x= 0.30828 0.08649 0.15116 0.19155 0.18393 0.31826 0.27341 0.13885 1 h-lim-p 0.0051 0.8940 132.6878 4523.353129 9 0.0004 49 | 0/8 2 h-lim-p 0.0017 0.0139 27.6748 4523.022785 4 0.0009 70 | 0/8 3 h-lim-p 0.0012 0.0174 19.8019 4522.954009 4 0.0005 90 | 0/8 4 h-lim-p 0.0043 0.2548 2.2532 4522.951902 3 0.0009 109 | 0/8 5 h-lim-p 0.0041 1.1974 0.4744 4522.951784 2 0.0011 126 | 0/8 6 h-lim-p 0.0074 3.1100 0.0690 4522.951774 1 0.0018 149 | 0/8 7 h-lim-p 0.0052 13.6828 0.0243 4522.951658 0 0.0206 171 | 0/8 8 h-lim-p 0.0060 20.0000 0.0835 4522.948002 0 0.0240 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 4522.947990 1 0.9961 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4522.947990 0 1.0938 235 | 0/8 11 h-lim-p 1.4726 20.0000 0.0000 4522.947990 0 1.4726 255 | 0/8 12 h-lim-p 1.1977 20.0000 0.0000 4522.947990 0 0.5988 275 | 0/8 13 h-lim-p 0.0262 20.0000 0.0002 4522.947990 0 0.0000 319 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 4522.947990 0 0.0000 347 | 0/8 15 h-lim-p 0.0000 20.0000 0.0045 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -4522.947990 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4522.947990 Node 7: lnL = -4522.947990 Node 8: lnL = -4522.947990 Node 9: lnL = -4522.947990 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 821 Sequential format.. Reading seq # 1: YHR073W_Sbay Reading seq # 2: YHR073W_Scer Reading seq # 3: YHR073W_Skud Reading seq # 4: YHR073W_Smik Reading seq # 5: YHR073W_Spar Sequences read.. Counting patterns.. # site patterns = 251 Counting frequencies.. 120 bytes for distance 40160 bytes for lkl0 32128 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.187984 0.062789 0.081986 0.091204 0.053695 0.188506 0.196062 0.089949 lnL0 = -3470.743278 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3470.743278 x= 0.18798 0.06279 0.08199 0.09120 0.05369 0.18851 0.19606 0.08995 1 h-lim-p 0.0027 0.7505 159.6014 3468.486987 9 0.0002 48 | 0/8 2 h-lim-p 0.0004 0.0028 29.4267 3468.414707 4 0.0002 69 | 0/8 3 h-lim-p 0.0002 0.0113 20.4955 3468.368613 0 0.0004 81 | 0/8 4 h-lim-p 0.0017 0.0620 4.3352 3468.365922 5 0.0003 105 | 0/8 5 h-lim-p 0.0029 0.5536 0.4646 3468.365884 1 0.0004 121 | 0/8 6 h-lim-p 0.0007 0.8182 0.2306 3468.365876 0 0.0003 141 | 0/8 7 h-lim-p 0.0101 20.0000 0.0073 3468.365798 0 0.0403 163 | 0/8 8 h-lim-p 0.0026 2.3834 0.1114 3468.363810 0 0.0105 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3468.363790 0 1.2500 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3468.363789 0 1.0938 225 | 0/8 11 h-lim-p 1.6606 20.0000 0.0000 3468.363789 0 1.4531 245 | 0/8 12 h-lim-p 1.7617 20.0000 0.0000 3468.363789 0 0.7708 265 | 0/8 13 h-lim-p 0.2427 20.0000 0.0000 3468.363789 0 0.0607 286 | 0/8 14 h-lim-p 0.0154 20.0000 0.0001 3468.363789 0 0.0001 313 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 3468.363789 0 0.0001 334 | 0/8 16 h-lim-p 0.0002 20.0000 0.0000 3468.363789 0 0.0000 358 | 0/8 17 h-lim-p 0.0004 20.0000 0.0000 3468.363789 0 0.0002 378 Out... lnL = -3468.363789 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3468.363789 Node 7: lnL = -3468.363789 Node 8: lnL = -3468.363789 Node 9: lnL = -3468.363789 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 808 Sequential format.. Reading seq # 1: YHR074W_Sbay Reading seq # 2: YHR074W_Scer Reading seq # 3: YHR074W_Skud Reading seq # 4: YHR074W_Smik Reading seq # 5: YHR074W_Spar Sequences read.. Counting patterns.. # site patterns = 325 Counting frequencies.. 120 bytes for distance 52000 bytes for lkl0 41600 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.277499 0.076662 0.084081 0.149506 0.147872 0.281872 0.713788 0.095057 lnL0 = -3640.776534 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3640.776534 x= 0.27750 0.07666 0.08408 0.14951 0.14787 0.28187 0.71379 0.09506 1 h-lim-p 0.0482 4.0941 38.8723 3640.472368 7 0.0004 42 | 0/8 2 h-lim-p 0.0015 0.0325 10.9797 3640.437120 5 0.0006 63 | 0/8 3 h-lim-p 0.0011 0.0371 6.5465 3640.422193 4 0.0009 82 | 0/8 4 h-lim-p 0.0015 0.0456 4.0442 3640.417187 5 0.0009 107 | 0/8 5 h-lim-p 0.0154 1.4875 0.2324 3640.417130 3 0.0021 127 | 0/8 6 h-lim-p 0.0013 0.6520 0.3821 3640.417091 0 0.0011 147 | 0/8 7 h-lim-p 0.0034 2.3097 0.1238 3640.417083 0 0.0015 167 | 0/8 8 h-lim-p 0.7470 20.0000 0.0002 3640.417028 0 1.1205 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3640.417028 0 1.0938 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3640.417028 0 1.0938 227 | 0/8 11 h-lim-p 1.1250 20.0000 0.0000 3640.417028 0 3.3749 248 | 0/8 12 h-lim-p 0.5320 20.0000 0.0000 3640.417028 0 0.1995 269 | 0/8 13 h-lim-p 0.0093 20.0000 0.0010 3640.417028 0 0.0093 289 | 0/8 14 h-lim-p 0.0030 20.0000 0.0030 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -3640.417028 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3640.417028 Node 7: lnL = -3640.417028 Node 8: lnL = -3640.417028 Node 9: lnL = -3640.417028 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 648 Sequential format.. Reading seq # 1: YHR078W_Sbay Reading seq # 2: YHR078W_Scer Reading seq # 3: YHR078W_Skud Reading seq # 4: YHR078W_Smik Reading seq # 5: YHR078W_Spar Sequences read.. Counting patterns.. # site patterns = 284 Counting frequencies.. 120 bytes for distance 45440 bytes for lkl0 36352 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.210461 0.054709 0.075701 0.165985 0.116951 0.281008 0.236300 0.086736 lnL0 = -3002.605833 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3002.605833 x= 0.21046 0.05471 0.07570 0.16598 0.11695 0.28101 0.23630 0.08674 1 h-lim-p 0.0045 0.0487 115.0011 3000.931777 4 0.0003 33 | 0/8 2 h-lim-p 0.0007 0.0059 21.9326 3000.812077 7 0.0005 63 | 0/8 3 h-lim-p 0.0014 0.0234 8.2015 3000.801130 5 0.0004 86 | 0/8 4 h-lim-p 0.0026 0.2120 1.1797 3000.800732 2 0.0006 103 | 0/8 5 h-lim-p 0.0023 0.9410 0.3105 3000.800699 2 0.0008 121 | 0/8 6 h-lim-p 0.0066 7.2327 0.0356 3000.800695 1 0.0016 144 | 0/8 7 h-lim-p 0.0023 11.6741 0.0251 3000.800625 0 0.0184 167 | 0/8 8 h-lim-p 0.0118 20.0000 0.0390 3000.799107 0 0.0236 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3000.799047 2 0.9961 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3000.799047 0 1.0938 232 | 0/8 11 h-lim-p 1.3570 20.0000 0.0000 3000.799047 0 2.0355 252 | 0/8 12 h-lim-p 1.6375 20.0000 0.0000 3000.799047 0 0.1023 275 | 0/8 13 h-lim-p 0.0104 20.0000 0.0001 3000.799047 0 0.0003 299 | 0/8 14 h-lim-p 0.0012 20.0000 0.0000 3000.799047 0 0.0000 332 | 0/8 15 h-lim-p 0.0000 20.0000 0.0008 | 0/8 16 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -3000.799047 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3000.799047 Node 7: lnL = -3000.799047 Node 8: lnL = -3000.799047 Node 9: lnL = -3000.799047 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 787 Sequential format.. Reading seq # 1: YHR080C_Sbay Reading seq # 2: YHR080C_Scer Reading seq # 3: YHR080C_Skud Reading seq # 4: YHR080C_Smik Reading seq # 5: YHR080C_Spar Sequences read.. Counting patterns.. # site patterns = 269 Counting frequencies.. 120 bytes for distance 43040 bytes for lkl0 34432 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.217371 0.060750 0.054225 0.133706 0.099698 0.188014 0.178451 0.105270 lnL0 = -3443.180920 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3443.180920 x= 0.21737 0.06075 0.05423 0.13371 0.09970 0.18801 0.17845 0.10527 1 h-lim-p 0.0006 0.0052 135.0603 3441.413074 7 0.0002 37 | 0/8 2 h-lim-p 0.0004 0.0031 38.9984 3441.204975 7 0.0003 66 | 0/8 3 h-lim-p 0.0006 0.0105 18.3369 3441.161947 3 0.0003 84 | 0/8 4 h-lim-p 0.0013 0.0498 4.2497 3441.159813 3 0.0003 103 | 0/8 5 h-lim-p 0.0016 0.2400 0.6568 3441.159749 2 0.0003 120 | 0/8 6 h-lim-p 0.0016 1.4485 0.1331 3441.159745 1 0.0004 143 | 0/8 7 h-lim-p 0.0908 20.0000 0.0006 3441.159501 0 0.7261 166 | 0/8 8 h-lim-p 0.0009 2.8925 0.4707 3441.159336 2 0.0008 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3441.159336 0 1.0938 210 | 0/8 10 h-lim-p 2.3571 20.0000 0.0000 3441.159336 0 1.0312 230 | 0/8 11 h-lim-p 1.0732 20.0000 0.0000 3441.159336 0 4.2926 252 | 0/8 12 h-lim-p 0.4830 20.0000 0.0001 3441.159336 0 0.2113 272 | 0/8 13 h-lim-p 0.0148 20.0000 0.0014 3441.159336 0 0.0018 294 | 0/8 14 h-lim-p 0.0001 8.2952 0.0196 3441.159336 0 0.0001 314 | 0/8 15 h-lim-p 0.0010 20.0000 0.0013 3441.159336 0 0.0000 353 | 0/8 16 h-lim-p 0.0000 20.0000 0.0010 | 0/8 17 h-lim-p 0.0000 20.0000 0.0010 Out... lnL = -3441.159336 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3441.159336 Node 7: lnL = -3441.159336 Node 8: lnL = -3441.159336 Node 9: lnL = -3441.159336 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 786 Sequential format.. Reading seq # 1: YHR081W_Sbay Reading seq # 2: YHR081W_Scer Reading seq # 3: YHR081W_Skud Reading seq # 4: YHR081W_Smik Reading seq # 5: YHR081W_Spar Sequences read.. Counting patterns.. # site patterns = 268 Counting frequencies.. 120 bytes for distance 42880 bytes for lkl0 34304 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.219081 0.047032 0.064331 0.134868 0.098536 0.186921 0.180676 0.107060 lnL0 = -3452.192766 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3452.192766 x= 0.21908 0.04703 0.06433 0.13487 0.09854 0.18692 0.18068 0.10706 1 h-lim-p 0.0004 0.0034 171.4984 3449.577970 3 0.0002 29 | 0/8 2 h-lim-p 0.0006 0.0047 38.7937 3449.363250 4 0.0003 49 | 0/8 3 h-lim-p 0.0007 0.0123 17.5618 3449.323904 2 0.0003 65 | 0/8 4 h-lim-p 0.0010 0.0400 5.5537 3449.319518 5 0.0003 88 | 0/8 5 h-lim-p 0.0021 0.1255 0.8465 3449.319414 3 0.0003 109 | 0/8 6 h-lim-p 0.0015 1.2210 0.1768 3449.319408 1 0.0004 132 | 0/8 7 h-lim-p 0.0280 20.0000 0.0023 3449.319404 0 0.0245 152 | 0/8 8 h-lim-p 0.0043 20.0000 0.0133 3449.319221 0 0.0257 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3449.319219 0 1.0938 194 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3449.319219 0 1.0938 214 | 0/8 11 h-lim-p 1.1085 20.0000 0.0000 3449.319219 0 1.1085 234 | 0/8 12 h-lim-p 0.5918 20.0000 0.0000 3449.319219 0 0.2959 254 | 0/8 13 h-lim-p 0.0241 20.0000 0.0002 3449.319219 0 0.0000 285 | 0/8 14 h-lim-p 0.0003 20.0000 0.0000 3449.319219 0 0.0003 305 Out... lnL = -3449.319219 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3449.319219 Node 7: lnL = -3449.319219 Node 8: lnL = -3449.319219 Node 9: lnL = -3449.319219 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 560 Sequential format.. Reading seq # 1: YHR085W_Sbay Reading seq # 2: YHR085W_Scer Reading seq # 3: YHR085W_Skud Reading seq # 4: YHR085W_Smik Reading seq # 5: YHR085W_Spar Sequences read.. Counting patterns.. # site patterns = 183 Counting frequencies.. 120 bytes for distance 29280 bytes for lkl0 23424 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.147062 0.052426 0.049073 0.077957 0.062336 0.171371 0.192520 0.058783 lnL0 = -2295.484938 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2295.484938 x= 0.14706 0.05243 0.04907 0.07796 0.06234 0.17137 0.19252 0.05878 1 h-lim-p 0.0027 0.8827 129.5407 2293.984039 8 0.0002 44 | 0/8 2 h-lim-p 0.0004 0.0033 29.3636 2293.846434 6 0.0003 69 | 0/8 3 h-lim-p 0.0006 0.0184 16.3050 2293.818885 5 0.0003 90 | 0/8 4 h-lim-p 0.0007 0.0335 6.6005 2293.814137 4 0.0003 111 | 0/8 5 h-lim-p 0.0014 0.2644 1.2203 2293.813886 2 0.0004 128 | 0/8 6 h-lim-p 0.0017 0.7890 0.2520 2293.813874 0 0.0004 141 | 0/8 7 h-lim-p 0.0011 1.9644 0.0900 2293.813873 1 0.0003 164 | 0/8 8 h-lim-p 0.0692 20.0000 0.0003 2293.813580 0 1.1072 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2293.813578 0 1.0938 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2293.813578 0 1.0938 228 | 0/8 11 h-lim-p 1.4789 20.0000 0.0000 2293.813578 0 1.2941 248 | 0/8 12 h-lim-p 0.5052 20.0000 0.0000 2293.813578 0 0.0158 272 | 0/8 13 h-lim-p 0.0015 20.0000 0.0004 2293.813578 0 0.0015 292 | 0/8 14 h-lim-p 0.0002 20.0000 0.0031 2293.813578 0 0.0001 312 | 0/8 15 h-lim-p 0.0005 20.0000 0.0006 2293.813578 0 0.0000 346 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -2293.813578 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2293.813578 Node 7: lnL = -2293.813578 Node 8: lnL = -2293.813578 Node 9: lnL = -2293.813578 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 877 Sequential format.. Reading seq # 1: YHR087W_Sbay Reading seq # 2: YHR087W_Scer Reading seq # 3: YHR087W_Skud Reading seq # 4: YHR087W_Smik Reading seq # 5: YHR087W_Spar Sequences read.. Counting patterns.. # site patterns = 293 Counting frequencies.. 120 bytes for distance 46880 bytes for lkl0 37504 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.189339 0.095517 0.072668 0.111998 0.054404 0.183090 0.259367 0.074197 lnL0 = -3781.420431 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3781.420431 x= 0.18934 0.09552 0.07267 0.11200 0.05440 0.18309 0.25937 0.07420 1 h-lim-p 0.0002 0.0016 97.2008 3780.440532 7 0.0002 39 | 0/8 2 h-lim-p 0.0006 0.0214 36.8611 3780.361972 2 0.0001 56 | 0/8 3 h-lim-p 0.0003 0.0088 15.9461 3780.336842 4 0.0002 76 | 0/8 4 h-lim-p 0.0010 0.0353 3.7845 3780.334711 4 0.0003 98 | 0/8 5 h-lim-p 0.0015 0.3405 0.7871 3780.334633 3 0.0003 119 | 0/8 6 h-lim-p 0.0008 1.3461 0.2668 3780.334613 1 0.0006 141 | 0/8 7 h-lim-p 0.0414 20.0000 0.0041 3780.334599 2 0.0273 167 | 0/8 8 h-lim-p 0.0039 7.4708 0.0291 3780.334078 0 0.0155 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3780.334064 1 0.9961 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3780.334064 0 1.0938 231 | 0/8 11 h-lim-p 0.8194 20.0000 0.0000 3780.334064 0 0.0024 259 | 0/8 12 h-lim-p 0.0000 20.0000 0.0037 3780.334064 0 0.0000 283 | 0/8 13 h-lim-p 0.0002 20.0000 0.0000 3780.334064 0 0.0000 315 Out... lnL = -3780.334064 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3780.334064 Node 7: lnL = -3780.334064 Node 8: lnL = -3780.334064 Node 9: lnL = -3780.334064 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 383 Sequential format.. Reading seq # 1: YHR088W_Sbay Reading seq # 2: YHR088W_Scer Reading seq # 3: YHR088W_Skud Reading seq # 4: YHR088W_Smik Reading seq # 5: YHR088W_Spar Sequences read.. Counting patterns.. # site patterns = 156 Counting frequencies.. 120 bytes for distance 24960 bytes for lkl0 19968 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.220149 0.205518 0.054716 0.081473 0.066060 0.157381 0.261006 0.090449 lnL0 = -1718.977971 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1718.977971 x= 0.22015 0.20552 0.05472 0.08147 0.06606 0.15738 0.26101 0.09045 1 h-lim-p 0.0004 0.0035 51.8704 1718.358079 7 0.0005 41 | 0/8 2 h-lim-p 0.0012 0.0161 20.2478 1718.162232 3 0.0011 59 | 0/8 3 h-lim-p 0.0030 0.0399 7.4211 1718.136093 7 0.0011 88 | 0/8 4 h-lim-p 0.0012 0.0620 6.6636 1718.132068 3 0.0003 107 | 0/8 5 h-lim-p 0.0016 0.1850 1.2520 1718.131455 3 0.0009 126 | 0/8 6 h-lim-p 0.0009 0.2948 1.1932 1718.131134 3 0.0008 144 | 0/8 7 h-lim-p 0.0541 11.5477 0.0166 1718.131133 0 0.0030 159 | 0/8 8 h-lim-p 0.0340 20.0000 0.0014 1718.130910 0 0.5439 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1718.130888 2 0.9961 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1718.130888 0 1.0938 227 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1718.130888 0 1.2500 247 | 0/8 12 h-lim-p 0.5152 20.0000 0.0000 1718.130888 0 0.0040 273 | 0/8 13 h-lim-p 0.0018 20.0000 0.0000 1718.130888 0 0.0000 303 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0006 1718.130888 0 0.0000 367 | 0/8 16 h-lim-p 0.0000 20.0000 0.0006 | 0/8 17 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -1718.130888 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1718.130888 Node 7: lnL = -1718.130888 Node 8: lnL = -1718.130888 Node 9: lnL = -1718.130888 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 517 Sequential format.. Reading seq # 1: YHR089C_Sbay Reading seq # 2: YHR089C_Scer Reading seq # 3: YHR089C_Skud Reading seq # 4: YHR089C_Smik Reading seq # 5: YHR089C_Spar Sequences read.. Counting patterns.. # site patterns = 216 Counting frequencies.. 120 bytes for distance 34560 bytes for lkl0 27648 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.202843 0.043910 0.035598 0.137233 0.117027 0.182620 0.218286 0.093245 lnL0 = -2308.239595 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2308.239595 x= 0.20284 0.04391 0.03560 0.13723 0.11703 0.18262 0.21829 0.09325 1 h-lim-p 0.0023 0.9744 140.1931 2306.498725 9 0.0002 46 | 0/8 2 h-lim-p 0.0008 0.0061 27.4360 2306.326623 8 0.0005 79 | 0/8 3 h-lim-p 0.0014 0.0252 9.5711 2306.302657 6 0.0006 102 | 0/8 4 h-lim-p 0.0025 0.1515 2.2190 2306.301283 2 0.0006 119 | 0/8 5 h-lim-p 0.0018 0.2017 0.7195 2306.301178 2 0.0004 136 | 0/8 6 h-lim-p 0.0066 3.9577 0.0488 2306.301178 0 0.0007 158 | 0/8 7 h-lim-p 0.0158 20.0000 0.0022 2306.301176 0 0.0237 178 | 0/8 8 h-lim-p 0.0076 20.0000 0.0070 2306.301069 0 0.0304 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2306.301068 0 1.0938 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2306.301068 0 1.0938 240 | 0/8 11 h-lim-p 1.1916 20.0000 0.0000 2306.301068 0 0.0093 266 | 0/8 12 h-lim-p 0.0036 20.0000 0.0000 2306.301068 0 0.0009 287 | 0/8 13 h-lim-p 0.0004 20.0000 0.0000 2306.301068 0 0.0004 307 | 0/8 14 h-lim-p 0.0001 20.0000 0.0002 2306.301068 0 0.0000 330 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 2306.301068 0 0.0000 358 | 0/8 16 h-lim-p 0.0000 20.0000 0.0007 | 0/8 17 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -2306.301068 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2306.301068 Node 7: lnL = -2306.301068 Node 8: lnL = -2306.301068 Node 9: lnL = -2306.301068 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 353 Sequential format.. Reading seq # 1: YHR092C_Sbay Reading seq # 2: YHR092C_Scer Reading seq # 3: YHR092C_Skud Reading seq # 4: YHR092C_Smik Reading seq # 5: YHR092C_Spar Sequences read.. Counting patterns.. # site patterns = 108 Counting frequencies.. 120 bytes for distance 17280 bytes for lkl0 13824 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.133206 0.039123 0.063520 0.050028 0.058002 0.088665 0.114865 0.065231 lnL0 = -1293.057087 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1293.057087 x= 0.13321 0.03912 0.06352 0.05003 0.05800 0.08867 0.11487 0.06523 1 h-lim-p 0.0012 0.0098 69.0870 1292.491616 3 0.0003 29 | 0/8 2 h-lim-p 0.0011 0.0094 16.4508 1292.444524 7 0.0004 58 | 0/8 3 h-lim-p 0.0011 0.0318 5.5211 1292.441055 2 0.0003 75 | 0/8 4 h-lim-p 0.0008 0.0766 1.7754 1292.440601 3 0.0003 93 | 0/8 5 h-lim-p 0.0026 0.6330 0.2281 1292.440591 2 0.0003 111 | 0/8 6 h-lim-p 0.0081 8.3204 0.0095 1292.440591 0 0.0018 132 | 0/8 7 h-lim-p 0.0045 20.0000 0.0037 1292.440462 0 0.0726 156 | 0/8 8 h-lim-p 0.0008 0.3347 0.3417 1292.440313 1 0.0010 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1292.440309 1 0.9961 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1292.440309 0 2.1875 220 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1292.440309 0 1.0938 240 | 0/8 12 h-lim-p 0.2833 20.0000 0.0000 1292.440309 0 4.5335 264 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1292.440309 0 0.0024 293 | 0/8 14 h-lim-p 0.0032 20.0000 0.0000 1292.440309 0 0.0000 319 Out... lnL = -1292.440309 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1292.440309 Node 7: lnL = -1292.440309 Node 8: lnL = -1292.440309 Node 9: lnL = -1292.440309 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 327 Sequential format.. Reading seq # 1: YHR094C_Sbay Reading seq # 2: YHR094C_Scer Reading seq # 3: YHR094C_Skud Reading seq # 4: YHR094C_Smik Reading seq # 5: YHR094C_Spar Sequences read.. Counting patterns.. # site patterns = 112 Counting frequencies.. 120 bytes for distance 17920 bytes for lkl0 14336 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.127188 0.073044 0.028702 0.058508 0.051025 0.211618 0.167822 0.043979 lnL0 = -1302.123889 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1302.123889 x= 0.12719 0.07304 0.02870 0.05851 0.05103 0.21162 0.16782 0.04398 1 h-lim-p 0.0008 0.0063 42.8034 1301.924881 7 0.0002 38 | 0/8 2 h-lim-p 0.0007 0.0114 14.8823 1301.855348 6 0.0007 62 | 0/8 3 h-lim-p 0.0010 0.0331 10.0135 1301.845223 6 0.0003 87 | 0/8 4 h-lim-p 0.0010 0.0293 2.8182 1301.844294 4 0.0003 108 | 0/8 5 h-lim-p 0.0010 0.1193 0.7737 1301.844169 0 0.0005 120 | 0/8 6 h-lim-p 0.0019 1.1417 0.1957 1301.844159 3 0.0006 148 | 0/8 7 h-lim-p 0.0022 1.9263 0.0512 1301.844158 1 0.0005 171 | 0/8 8 h-lim-p 0.2044 20.0000 0.0001 1301.844122 0 1.2266 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1301.844121 0 1.0938 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1301.844121 0 2.1875 233 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1301.844121 0 1.0938 253 | 0/8 12 h-lim-p 0.2312 20.0000 0.0000 1301.844121 0 3.6989 277 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1301.844121 0 0.0684 301 | 0/8 14 h-lim-p 0.0011 20.0000 0.0000 1301.844121 0 0.0000 329 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 1301.844121 0 0.0000 352 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 1301.844121 0 0.0000 372 | 0/8 17 h-lim-p 0.0001 20.0000 0.0000 1301.844121 0 0.0001 392 Out... lnL = -1301.844121 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1301.844121 Node 7: lnL = -1301.844121 Node 8: lnL = -1301.844121 Node 9: lnL = -1301.844121 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 221 Sequential format.. Reading seq # 1: YHR100C_Sbay Reading seq # 2: YHR100C_Scer Reading seq # 3: YHR100C_Skud Reading seq # 4: YHR100C_Smik Reading seq # 5: YHR100C_Spar Sequences read.. Counting patterns.. # site patterns = 118 Counting frequencies.. 120 bytes for distance 18880 bytes for lkl0 15104 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.181475 0.086227 0.044081 0.133128 0.054282 0.292016 0.339103 0.053598 lnL0 = -942.529624 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 942.529624 x= 0.18147 0.08623 0.04408 0.13313 0.05428 0.29202 0.33910 0.05360 1 h-lim-p 0.0004 0.0035 31.9132 942.147557 0 0.0009 23 | 0/8 2 h-lim-p 0.0032 0.0469 8.6232 942.121278 2 0.0008 40 | 0/8 3 h-lim-p 0.0014 0.0193 4.7491 942.114866 6 0.0007 64 | 0/8 4 h-lim-p 0.0024 0.3475 1.4174 942.112601 3 0.0025 82 | 0/8 5 h-lim-p 0.0094 0.3689 0.3826 942.112457 2 0.0020 99 | 0/8 6 h-lim-p 0.0059 1.7532 0.1334 942.112410 4 0.0036 130 | 0/8 7 h-lim-p 0.0084 6.0885 0.0572 942.112253 0 0.0168 151 | 0/8 8 h-lim-p 0.0342 3.1927 0.0281 942.107974 0 0.1369 173 | 0/8 9 h-lim-p 2.5000 20.0000 0.0009 942.107568 3 0.9961 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 942.107568 0 1.0938 219 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 942.107568 0 1.0938 239 | 0/8 12 h-lim-p 1.1815 20.0000 0.0000 942.107568 0 4.7259 261 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 942.107568 0 0.1562 284 | 0/8 14 h-lim-p 0.1772 20.0000 0.0000 942.107568 0 0.0000 319 Out... lnL = -942.107568 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -942.107568 Node 7: lnL = -942.107568 Node 8: lnL = -942.107568 Node 9: lnL = -942.107568 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 490 Sequential format.. Reading seq # 1: YHR104W_Sbay Reading seq # 2: YHR104W_Scer Reading seq # 3: YHR104W_Skud Reading seq # 4: YHR104W_Smik Reading seq # 5: YHR104W_Spar Sequences read.. Counting patterns.. # site patterns = 200 Counting frequencies.. 120 bytes for distance 32000 bytes for lkl0 25600 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.219912 0.052394 0.062450 0.116550 0.141876 0.183482 0.228679 0.100790 lnL0 = -2115.763479 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2115.763479 x= 0.21991 0.05239 0.06245 0.11655 0.14188 0.18348 0.22868 0.10079 1 h-lim-p 0.0076 1.5286 74.5648 2114.842979 8 0.0004 43 | 0/8 2 h-lim-p 0.0007 0.0055 16.5910 2114.757246 2 0.0006 59 | 0/8 3 h-lim-p 0.0018 0.0712 6.0535 2114.747311 6 0.0006 86 | 0/8 4 h-lim-p 0.0020 0.1164 1.8598 2114.746423 5 0.0006 112 | 0/8 5 h-lim-p 0.0021 0.5785 0.5084 2114.746309 2 0.0010 128 | 0/8 6 h-lim-p 0.0099 3.7108 0.0505 2114.746308 1 0.0006 153 | 0/8 7 h-lim-p 0.0030 17.5958 0.0104 2114.746304 0 0.0059 174 | 0/8 8 h-lim-p 0.0110 20.0000 0.0056 2114.745912 0 0.1314 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2114.745897 1 0.9961 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2114.745897 0 1.0938 239 | 0/8 11 h-lim-p 1.2214 20.0000 0.0000 2114.745897 0 1.2214 259 | 0/8 12 h-lim-p 0.2599 20.0000 0.0000 2114.745897 0 0.0001 289 | 0/8 13 h-lim-p 0.0005 20.0000 0.0000 2114.745897 0 0.0000 312 Out... lnL = -2114.745897 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2114.745897 Node 7: lnL = -2114.745897 Node 8: lnL = -2114.745897 Node 9: lnL = -2114.745897 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 406 Sequential format.. Reading seq # 1: YHR105W_Sbay Reading seq # 2: YHR105W_Scer Reading seq # 3: YHR105W_Skud Reading seq # 4: YHR105W_Smik Reading seq # 5: YHR105W_Spar Sequences read.. Counting patterns.. # site patterns = 169 Counting frequencies.. 120 bytes for distance 27040 bytes for lkl0 21632 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.216675 0.073648 0.051151 0.129878 0.065667 0.225540 0.193988 0.101922 lnL0 = -1762.698052 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1762.698052 x= 0.21668 0.07365 0.05115 0.12988 0.06567 0.22554 0.19399 0.10192 1 h-lim-p 0.0031 0.0248 31.1843 1762.533919 2 0.0004 28 | 0/8 2 h-lim-p 0.0010 0.0125 11.6536 1762.500149 7 0.0006 59 | 0/8 3 h-lim-p 0.0013 0.0599 5.0536 1762.496399 6 0.0004 86 | 0/8 4 h-lim-p 0.0011 0.2038 1.5844 1762.495762 2 0.0006 103 | 0/8 5 h-lim-p 0.0030 0.9524 0.2926 1762.495724 3 0.0009 124 | 0/8 6 h-lim-p 0.0079 9.4212 0.0326 1762.495723 0 0.0009 146 | 0/8 7 h-lim-p 0.0054 20.0000 0.0052 1762.495708 0 0.0432 169 | 0/8 8 h-lim-p 0.0098 3.0538 0.0229 1762.495416 0 0.0196 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1762.495413 0 1.0938 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1762.495413 0 1.0938 230 | 0/8 11 h-lim-p 1.4230 20.0000 0.0000 1762.495413 0 1.4230 250 | 0/8 12 h-lim-p 1.6449 20.0000 0.0000 1762.495413 0 0.0001 284 Out... lnL = -1762.495413 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1762.495413 Node 7: lnL = -1762.495413 Node 8: lnL = -1762.495413 Node 9: lnL = -1762.495413 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 200 Sequential format.. Reading seq # 1: YHR106W_Sbay Reading seq # 2: YHR106W_Scer Reading seq # 3: YHR106W_Skud Reading seq # 4: YHR106W_Smik Reading seq # 5: YHR106W_Spar Sequences read.. Counting patterns.. # site patterns = 96 Counting frequencies.. 120 bytes for distance 15360 bytes for lkl0 12288 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.142159 0.098750 0.074446 0.082008 0.065234 0.144721 0.136080 0.051874 lnL0 = -804.523682 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 804.523682 x= 0.14216 0.09875 0.07445 0.08201 0.06523 0.14472 0.13608 0.05187 1 h-lim-p 0.0011 0.0086 13.5124 804.453635 7 0.0008 37 | 0/8 2 h-lim-p 0.0021 0.0694 4.9922 804.447418 6 0.0006 62 | 0/8 3 h-lim-p 0.0019 0.1385 1.4965 804.446542 2 0.0009 78 | 0/8 4 h-lim-p 0.0043 0.4375 0.3060 804.446511 3 0.0007 99 | 0/8 5 h-lim-p 0.0053 3.2526 0.0397 804.446510 0 0.0012 120 | 0/8 6 h-lim-p 0.0044 20.0000 0.0105 804.446510 0 0.0010 141 | 0/8 7 h-lim-p 0.0032 20.0000 0.0032 804.446510 0 0.0028 161 | 0/8 8 h-lim-p 0.0610 20.0000 0.0001 804.446507 0 0.4878 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 804.446507 0 1.0938 204 | 0/8 10 h-lim-p 1.3076 20.0000 0.0000 804.446507 0 0.0026 232 | 0/8 11 h-lim-p 0.0008 20.0000 0.0000 804.446507 0 0.0008 252 | 0/8 12 h-lim-p 0.0003 20.0000 0.0001 804.446507 0 0.0000 289 | 0/8 13 h-lim-p 0.0000 20.0000 0.0003 804.446507 0 0.0000 318 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -804.446507 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -804.446507 Node 7: lnL = -804.446507 Node 8: lnL = -804.446507 Node 9: lnL = -804.446507 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 278 Sequential format.. Reading seq # 1: YHR107C_Sbay Reading seq # 2: YHR107C_Scer Reading seq # 3: YHR107C_Skud Reading seq # 4: YHR107C_Smik Reading seq # 5: YHR107C_Spar Sequences read.. Counting patterns.. # site patterns = 118 Counting frequencies.. 120 bytes for distance 18880 bytes for lkl0 15104 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.136156 0.090096 0.049208 0.077500 0.076997 0.193557 0.156627 0.044590 lnL0 = -1179.389464 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1179.389464 x= 0.13616 0.09010 0.04921 0.07750 0.07700 0.19356 0.15663 0.04459 1 h-lim-p 0.0027 0.0215 84.6440 1178.263863 5 0.0004 34 | 0/8 2 h-lim-p 0.0008 0.0066 15.6020 1178.181714 3 0.0007 52 | 0/8 3 h-lim-p 0.0015 0.0172 7.2828 1178.170345 6 0.0005 78 | 0/8 4 h-lim-p 0.0017 0.1016 2.2285 1178.168829 4 0.0007 99 | 0/8 5 h-lim-p 0.0020 0.1465 0.7492 1178.168656 4 0.0007 122 | 0/8 6 h-lim-p 0.0053 2.1728 0.0971 1178.168652 2 0.0009 148 | 0/8 7 h-lim-p 0.0037 6.3755 0.0225 1178.168651 0 0.0008 169 | 0/8 8 h-lim-p 0.1398 20.0000 0.0001 1178.168632 0 1.1182 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1178.168631 0 1.2500 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1178.168631 0 1.0938 232 | 0/8 11 h-lim-p 1.1504 20.0000 0.0000 1178.168631 0 2.3008 253 | 0/8 12 h-lim-p 0.6670 20.0000 0.0000 1178.168631 0 1.0005 273 | 0/8 13 h-lim-p 0.0236 20.0000 0.0017 1178.168631 0 0.0007 297 | 0/8 14 h-lim-p 0.0001 5.2713 0.0120 1178.168631 0 0.0000 322 | 0/8 15 h-lim-p 0.0001 20.0000 0.0002 1178.168631 0 0.0001 342 | 0/8 16 h-lim-p 0.0001 20.0000 0.0002 1178.168631 0 0.0000 364 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 1178.168631 0 0.0000 392 | 0/8 18 h-lim-p 0.0000 20.0000 0.0006 | 0/8 19 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -1178.168631 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1178.168631 Node 7: lnL = -1178.168631 Node 8: lnL = -1178.168631 Node 9: lnL = -1178.168631 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 280 Sequential format.. Reading seq # 1: YHR108W_Sbay Reading seq # 2: YHR108W_Scer Reading seq # 3: YHR108W_Skud Reading seq # 4: YHR108W_Smik Reading seq # 5: YHR108W_Spar Sequences read.. Counting patterns.. # site patterns = 117 Counting frequencies.. 120 bytes for distance 18720 bytes for lkl0 14976 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.147212 0.101198 0.042084 0.069969 0.084528 0.206530 0.129957 0.054311 lnL0 = -1179.322992 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1179.322992 x= 0.14721 0.10120 0.04208 0.06997 0.08453 0.20653 0.12996 0.05431 1 h-lim-p 0.0018 0.0142 62.0375 1178.758869 8 0.0003 41 | 0/8 2 h-lim-p 0.0017 0.0138 11.1560 1178.716511 6 0.0007 64 | 0/8 3 h-lim-p 0.0014 0.0404 5.4647 1178.709428 5 0.0006 88 | 0/8 4 h-lim-p 0.0015 0.0825 2.0869 1178.708384 4 0.0006 108 | 0/8 5 h-lim-p 0.0025 0.6168 0.4727 1178.708288 4 0.0009 129 | 0/8 6 h-lim-p 0.0083 4.7611 0.0522 1178.708287 1 0.0005 154 | 0/8 7 h-lim-p 0.0040 20.0000 0.0066 1178.708287 0 0.0009 175 | 0/8 8 h-lim-p 0.1162 20.0000 0.0000 1178.708285 0 0.9297 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1178.708285 0 1.0938 218 | 0/8 10 h-lim-p 1.4224 20.0000 0.0000 1178.708285 0 1.2446 238 | 0/8 11 h-lim-p 0.9862 20.0000 0.0000 1178.708285 0 0.0308 262 | 0/8 12 h-lim-p 0.0002 20.0000 0.0019 1178.708285 0 0.0001 282 | 0/8 13 h-lim-p 0.0002 20.0000 0.0009 1178.708285 0 0.0001 303 | 0/8 14 h-lim-p 0.0002 20.0000 0.0004 1178.708285 0 0.0000 334 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1178.708285 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1178.708285 Node 7: lnL = -1178.708285 Node 8: lnL = -1178.708285 Node 9: lnL = -1178.708285 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 260 Sequential format.. Reading seq # 1: YHR109W_Sbay Reading seq # 2: YHR109W_Scer Reading seq # 3: YHR109W_Skud Reading seq # 4: YHR109W_Smik Reading seq # 5: YHR109W_Spar Sequences read.. Counting patterns.. # site patterns = 128 Counting frequencies.. 120 bytes for distance 20480 bytes for lkl0 16384 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.246087 0.107676 0.056981 0.125615 0.035719 0.174156 0.242979 0.123719 lnL0 = -1145.095334 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1145.095334 x= 0.24609 0.10768 0.05698 0.12562 0.03572 0.17416 0.24298 0.12372 1 h-lim-p 0.0015 0.0118 87.6206 1143.978113 3 0.0003 29 | 0/8 2 h-lim-p 0.0009 0.0075 24.6744 1143.704963 3 0.0010 47 | 0/8 3 h-lim-p 0.0036 0.0301 6.5088 1143.675761 3 0.0015 65 | 0/8 4 h-lim-p 0.0036 0.1075 2.7477 1143.671585 6 0.0013 93 | 0/8 5 h-lim-p 0.0031 0.1652 1.1569 1143.671116 4 0.0008 114 | 0/8 6 h-lim-p 0.0059 4.0377 0.1643 1143.671092 3 0.0018 134 | 0/8 7 h-lim-p 0.0252 18.1788 0.0115 1143.671088 1 0.0100 156 | 0/8 8 h-lim-p 0.0321 20.0000 0.0036 1143.670669 0 0.1926 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1143.670653 0 1.2500 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1143.670653 0 1.0938 218 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1143.670653 0 1.0938 238 | 0/8 12 h-lim-p 1.1447 20.0000 0.0000 1143.670653 0 4.5787 260 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1143.670653 0 0.3125 282 | 0/8 14 h-lim-p 0.0368 20.0000 0.0000 1143.670653 0 0.0009 307 | 0/8 15 h-lim-p 0.0009 20.0000 0.0000 1143.670653 0 0.0000 341 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1143.670653 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1143.670653 Node 7: lnL = -1143.670653 Node 8: lnL = -1143.670653 Node 9: lnL = -1143.670653 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 257 Sequential format.. Reading seq # 1: YHR110W_Sbay Reading seq # 2: YHR110W_Scer Reading seq # 3: YHR110W_Skud Reading seq # 4: YHR110W_Smik Reading seq # 5: YHR110W_Spar Sequences read.. Counting patterns.. # site patterns = 122 Counting frequencies.. 120 bytes for distance 19520 bytes for lkl0 15616 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.218573 0.124970 0.062548 0.142477 0.104291 0.156975 0.238818 0.084726 lnL0 = -1145.639620 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1145.639620 x= 0.21857 0.12497 0.06255 0.14248 0.10429 0.15698 0.23882 0.08473 1 h-lim-p 0.0024 0.0194 47.3997 1144.981783 9 0.0006 40 | 0/8 2 h-lim-p 0.0026 0.0207 11.1856 1144.901320 7 0.0013 68 | 0/8 3 h-lim-p 0.0053 0.1242 2.8110 1144.896557 2 0.0013 85 | 0/8 4 h-lim-p 0.0034 0.2042 1.0340 1144.895923 3 0.0014 103 | 0/8 5 h-lim-p 0.0048 0.6795 0.2902 1144.895855 3 0.0018 121 | 0/8 6 h-lim-p 0.0419 12.0648 0.0127 1144.895855 0 0.0013 145 | 0/8 7 h-lim-p 0.0310 20.0000 0.0005 1144.895854 0 0.0929 166 | 0/8 8 h-lim-p 0.0050 17.6285 0.0101 1144.895848 0 0.0198 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1144.895847 0 1.0938 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1144.895847 0 1.0938 228 | 0/8 11 h-lim-p 1.4780 20.0000 0.0000 1144.895847 0 1.2933 248 | 0/8 12 h-lim-p 0.9161 20.0000 0.0000 1144.895847 0 0.0573 271 | 0/8 13 h-lim-p 0.0006 20.0000 0.0006 1144.895847 0 0.0002 292 | 0/8 14 h-lim-p 0.0000 6.4249 0.0167 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 1144.895847 0 0.0000 347 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1144.895847 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1144.895847 Node 7: lnL = -1144.895847 Node 8: lnL = -1144.895847 Node 9: lnL = -1144.895847 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 172 Sequential format.. Reading seq # 1: YHR111W_Sbay Reading seq # 2: YHR111W_Scer Reading seq # 3: YHR111W_Skud Reading seq # 4: YHR111W_Smik Reading seq # 5: YHR111W_Spar Sequences read.. Counting patterns.. # site patterns = 77 Counting frequencies.. 120 bytes for distance 12320 bytes for lkl0 9856 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.250700 0.000060 0.085241 0.108161 0.106031 0.162487 0.135269 0.141292 lnL0 = -623.291290 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 623.291290 x= 0.25070 0.00006 0.08524 0.10816 0.10603 0.16249 0.13527 0.14129 1 h-lim-p 0.0026 0.0208 30.3172 622.772338 3 0.0012 29 | 0/8 2 h-lim-p 0.0001 0.0010 6.7570 622.739245 m 0.0010 41 | 0/8 3 h-lim-p 0.0025 0.1048 2.6146 622.735371 4 0.0013 62 | 0/8 4 h-lim-p 0.0028 0.2862 1.2059 622.734238 5 0.0019 87 | 0/8 5 h-lim-p 0.0037 0.5094 0.5989 622.732018 0 0.0150 101 | 0/8 6 h-lim-p 0.0304 0.6053 0.2950 622.730517 2 0.0285 125 | 0/8 7 h-lim-p 0.0030 0.0574 2.8279 622.727946 0 0.0060 146 | 0/8 8 h-lim-p 0.2286 1.8290 0.0219 622.717499 0 0.4573 159 | 0/8 9 h-lim-p 1.0926 8.7409 0.0032 622.717016 2 1.0243 183 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 622.717012 0 1.2500 203 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 622.717012 0 1.0938 223 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 622.717012 0 1.0938 243 | 0/8 13 h-lim-p 1.5260 20.0000 0.0000 622.717012 0 0.0954 266 | 0/8 14 h-lim-p 0.0214 20.0000 0.0000 622.717012 0 0.0000 295 Out... lnL = -622.717012 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -622.717012 Node 7: lnL = -622.717012 Node 8: lnL = -622.717012 Node 9: lnL = -622.717012 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 711 Sequential format.. Reading seq # 1: YHR112C_Sbay Reading seq # 2: YHR112C_Scer Reading seq # 3: YHR112C_Skud Reading seq # 4: YHR112C_Smik Reading seq # 5: YHR112C_Spar Sequences read.. Counting patterns.. # site patterns = 313 Counting frequencies.. 120 bytes for distance 50080 bytes for lkl0 40064 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.249935 0.146289 0.107525 0.207620 0.105652 0.244639 0.231245 0.085723 lnL0 = -3407.022572 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3407.022572 x= 0.24993 0.14629 0.10752 0.20762 0.10565 0.24464 0.23124 0.08572 1 h-lim-p 0.0015 0.0122 36.3404 3406.665005 7 0.0006 40 | 0/8 2 h-lim-p 0.0009 0.0094 23.1944 3406.566707 5 0.0005 63 | 0/8 3 h-lim-p 0.0020 0.0609 5.5652 3406.560701 4 0.0004 83 | 0/8 4 h-lim-p 0.0037 0.3748 0.6366 3406.560537 2 0.0008 100 | 0/8 5 h-lim-p 0.0032 1.9433 0.1634 3406.560527 0 0.0007 121 | 0/8 6 h-lim-p 0.0052 13.5953 0.0215 3406.560527 0 0.0011 142 | 0/8 7 h-lim-p 0.0062 20.0000 0.0040 3406.560527 0 0.0054 162 | 0/8 8 h-lim-p 0.0074 20.0000 0.0029 3406.560477 0 0.1176 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3406.560472 0 1.0938 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3406.560472 0 1.0938 226 | 0/8 11 h-lim-p 1.3311 20.0000 0.0000 3406.560472 0 1.1647 246 | 0/8 12 h-lim-p 0.8084 20.0000 0.0000 3406.560472 0 0.0003 276 | 0/8 13 h-lim-p 0.0010 20.0000 0.0000 3406.560472 0 0.0000 306 Out... lnL = -3406.560472 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3406.560472 Node 7: lnL = -3406.560472 Node 8: lnL = -3406.560472 Node 9: lnL = -3406.560472 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 699 Sequential format.. Reading seq # 1: YHR113W_Sbay Reading seq # 2: YHR113W_Scer Reading seq # 3: YHR113W_Skud Reading seq # 4: YHR113W_Smik Reading seq # 5: YHR113W_Spar Sequences read.. Counting patterns.. # site patterns = 284 Counting frequencies.. 120 bytes for distance 45440 bytes for lkl0 36352 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.254482 0.090163 0.072888 0.228238 0.142054 0.200969 0.301945 0.094499 lnL0 = -3565.927060 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3565.927060 x= 0.25448 0.09016 0.07289 0.22824 0.14205 0.20097 0.30195 0.09450 1 h-lim-p 0.0125 1.4501 75.6862 3565.166258 7 0.0003 42 | 0/8 2 h-lim-p 0.0013 0.0129 16.8813 3565.097117 4 0.0005 62 | 0/8 3 h-lim-p 0.0017 0.0730 4.9153 3565.091412 5 0.0005 87 | 0/8 4 h-lim-p 0.0019 0.2885 1.3240 3565.090690 2 0.0009 103 | 0/8 5 h-lim-p 0.0046 0.6326 0.2588 3565.090673 0 0.0006 117 | 0/8 6 h-lim-p 0.0032 16.6799 0.0464 3565.090673 0 0.0007 138 | 0/8 7 h-lim-p 0.0508 20.0000 0.0006 3565.090662 0 0.2032 160 | 0/8 8 h-lim-p 0.0024 14.3825 0.0545 3565.090606 0 0.0047 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3565.090604 0 1.0938 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3565.090604 0 1.0938 221 | 0/8 11 h-lim-p 1.2153 20.0000 0.0000 3565.090604 0 1.8229 241 | 0/8 12 h-lim-p 1.4098 20.0000 0.0000 3565.090604 0 0.7049 261 | 0/8 13 h-lim-p 0.0437 20.0000 0.0002 3565.090604 0 0.0003 287 | 0/8 14 h-lim-p 0.0013 20.0000 0.0001 3565.090604 0 0.0000 319 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 3565.090604 0 0.0000 349 Out... lnL = -3565.090604 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3565.090604 Node 7: lnL = -3565.090604 Node 8: lnL = -3565.090604 Node 9: lnL = -3565.090604 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 284 Sequential format.. Reading seq # 1: YHR114W_Sbay Reading seq # 2: YHR114W_Scer Reading seq # 3: YHR114W_Skud Reading seq # 4: YHR114W_Smik Reading seq # 5: YHR114W_Spar Sequences read.. Counting patterns.. # site patterns = 129 Counting frequencies.. 120 bytes for distance 20640 bytes for lkl0 16512 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.182986 0.063368 0.088811 0.079505 0.088323 0.210295 0.139417 0.073648 lnL0 = -1247.947457 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1247.947457 x= 0.18299 0.06337 0.08881 0.07950 0.08832 0.21030 0.13942 0.07365 1 h-lim-p 0.0025 0.0200 52.4688 1247.230677 3 0.0006 29 | 0/8 2 h-lim-p 0.0012 0.0100 17.5243 1247.122539 8 0.0008 64 | 0/8 3 h-lim-p 0.0020 0.0256 6.6776 1247.113189 2 0.0005 81 | 0/8 4 h-lim-p 0.0045 0.2147 0.6979 1247.113024 4 0.0007 106 | 0/8 5 h-lim-p 0.0048 3.3961 0.1008 1247.113019 1 0.0011 129 | 0/8 6 h-lim-p 0.0028 3.9964 0.0378 1247.113019 0 0.0012 149 | 0/8 7 h-lim-p 0.0133 20.0000 0.0035 1247.113019 0 0.0058 169 | 0/8 8 h-lim-p 0.0353 20.0000 0.0006 1247.112999 0 0.2824 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1247.112998 0 1.0938 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1247.112998 0 1.0938 232 | 0/8 11 h-lim-p 1.2059 20.0000 0.0000 1247.112998 0 2.4119 253 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1247.112998 0 0.5469 274 | 0/8 13 h-lim-p 0.0629 20.0000 0.0000 1247.112998 0 0.0039 297 | 0/8 14 h-lim-p 0.0010 20.0000 0.0000 1247.112998 0 0.0003 318 | 0/8 15 h-lim-p 0.0002 20.0000 0.0001 1247.112998 0 0.0002 338 | 0/8 16 h-lim-p 0.0000 20.0000 0.0007 1247.112998 0 0.0000 358 | 0/8 17 h-lim-p 0.0002 20.0000 0.0000 1247.112998 0 0.0000 391 | 0/8 18 h-lim-p 0.0000 20.0000 0.0004 | 0/8 19 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1247.112998 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1247.112998 Node 7: lnL = -1247.112998 Node 8: lnL = -1247.112998 Node 9: lnL = -1247.112998 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 320 Sequential format.. Reading seq # 1: YHR115C_Sbay Reading seq # 2: YHR115C_Scer Reading seq # 3: YHR115C_Skud Reading seq # 4: YHR115C_Smik Reading seq # 5: YHR115C_Spar Sequences read.. Counting patterns.. # site patterns = 105 Counting frequencies.. 120 bytes for distance 16800 bytes for lkl0 13440 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.228342 0.052368 0.050829 0.113105 0.023636 0.110657 0.103382 0.133708 lnL0 = -1111.282619 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1111.282619 x= 0.22834 0.05237 0.05083 0.11310 0.02364 0.11066 0.10338 0.13371 1 h-lim-p 0.0061 0.0485 45.1114 1111.066054 7 0.0002 41 | 0/8 2 h-lim-p 0.0003 0.0025 28.6581 1110.976626 3 0.0003 59 | 0/8 3 h-lim-p 0.0006 0.0095 14.6482 1110.918216 0 0.0008 71 | 0/8 4 h-lim-p 0.0011 0.0159 11.4427 1110.881214 5 0.0009 92 | 0/8 5 h-lim-p 0.0027 0.0576 4.0383 1110.878299 5 0.0005 118 | 0/8 6 h-lim-p 0.0038 0.2725 0.4807 1110.878146 3 0.0013 138 | 0/8 7 h-lim-p 0.0011 0.2772 0.5875 1110.878069 3 0.0008 164 | 0/8 8 h-lim-p 0.4784 20.0000 0.0010 1110.877176 0 0.9569 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1110.877174 0 1.0938 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1110.877174 0 1.0938 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1110.877174 0 0.0006 256 Out... lnL = -1110.877174 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1110.877174 Node 7: lnL = -1110.877174 Node 8: lnL = -1110.877174 Node 9: lnL = -1110.877174 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 237 Sequential format.. Reading seq # 1: YHR117W_Sbay Reading seq # 2: YHR117W_Scer Reading seq # 3: YHR117W_Skud Reading seq # 4: YHR117W_Smik Reading seq # 5: YHR117W_Spar Sequences read.. Counting patterns.. # site patterns = 99 Counting frequencies.. 120 bytes for distance 15840 bytes for lkl0 12672 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.115866 0.056287 0.043453 0.115300 0.058167 0.122780 0.137015 0.035754 lnL0 = -909.721403 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 909.721403 x= 0.11587 0.05629 0.04345 0.11530 0.05817 0.12278 0.13701 0.03575 1 h-lim-p 0.0002 0.0019 96.6485 908.098331 0 0.0005 23 | 0/8 2 h-lim-p 0.0005 0.0041 20.0140 907.973106 1 0.0006 37 | 0/8 3 h-lim-p 0.0011 0.0196 11.5304 907.953532 6 0.0004 66 | 0/8 4 h-lim-p 0.0032 0.1149 1.3708 907.952611 5 0.0010 92 | 0/8 5 h-lim-p 0.0055 1.2467 0.2404 907.952490 3 0.0018 112 | 0/8 6 h-lim-p 0.0056 0.9513 0.0767 907.949800 0 0.0224 134 | 0/8 7 h-lim-p 0.0024 0.1496 0.7023 907.918692 0 0.0098 156 | 0/8 8 h-lim-p 0.0019 0.0483 3.6515 907.899042 3 0.0016 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 907.898795 3 0.9482 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 907.898795 0 1.0938 220 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 907.898795 0 1.0938 240 | 0/8 12 h-lim-p 1.1044 20.0000 0.0000 907.898795 0 0.9664 260 | 0/8 13 h-lim-p 0.3107 20.0000 0.0000 907.898795 0 0.0002 290 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 907.898795 0 0.0000 310 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 907.898795 0 0.0000 338 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -907.898795 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -907.898795 Node 7: lnL = -907.898795 Node 8: lnL = -907.898795 Node 9: lnL = -907.898795 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 303 Sequential format.. Reading seq # 1: YHR120W_Sbay Reading seq # 2: YHR120W_Scer Reading seq # 3: YHR120W_Skud Reading seq # 4: YHR120W_Smik Reading seq # 5: YHR120W_Spar Sequences read.. Counting patterns.. # site patterns = 144 Counting frequencies.. 120 bytes for distance 23040 bytes for lkl0 18432 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.194013 0.221880 0.031859 0.088009 0.096026 0.208639 0.146851 0.065362 lnL0 = -1364.645598 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1364.645598 x= 0.19401 0.22188 0.03186 0.08801 0.09603 0.20864 0.14685 0.06536 1 h-lim-p 0.0005 0.0043 64.9702 1363.786538 3 0.0005 28 | 0/8 2 h-lim-p 0.0008 0.0066 18.5691 1363.675714 3 0.0007 46 | 0/8 3 h-lim-p 0.0010 0.0289 12.2539 1363.630446 5 0.0008 68 | 0/8 4 h-lim-p 0.0019 0.0356 5.2211 1363.623019 5 0.0007 91 | 0/8 5 h-lim-p 0.0029 0.1636 1.2395 1363.622048 2 0.0014 107 | 0/8 6 h-lim-p 0.0050 0.7104 0.3392 1363.621998 3 0.0009 126 | 0/8 7 h-lim-p 0.0052 2.7496 0.0616 1363.621994 2 0.0017 152 | 0/8 8 h-lim-p 0.0829 20.0000 0.0013 1363.621040 0 0.9952 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1363.621009 2 0.9961 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1363.621009 0 1.0938 219 | 0/8 11 h-lim-p 1.2528 20.0000 0.0000 1363.621009 0 2.5057 240 | 0/8 12 h-lim-p 0.4303 20.0000 0.0000 1363.621009 0 0.0538 262 | 0/8 13 h-lim-p 0.0046 20.0000 0.0005 1363.621009 0 0.0000 295 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 1363.621009 0 0.0000 323 Out... lnL = -1363.621009 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1363.621009 Node 7: lnL = -1363.621009 Node 8: lnL = -1363.621009 Node 9: lnL = -1363.621009 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 394 Sequential format.. Reading seq # 1: YHR121W_Sbay Reading seq # 2: YHR121W_Scer Reading seq # 3: YHR121W_Skud Reading seq # 4: YHR121W_Smik Reading seq # 5: YHR121W_Spar Sequences read.. Counting patterns.. # site patterns = 136 Counting frequencies.. 120 bytes for distance 21760 bytes for lkl0 17408 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.169857 0.068462 0.060194 0.142056 0.058103 0.209178 0.157074 0.061765 lnL0 = -1513.876327 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1513.876327 x= 0.16986 0.06846 0.06019 0.14206 0.05810 0.20918 0.15707 0.06176 1 h-lim-p 0.0002 0.0018 69.8192 1512.855077 0 0.0004 23 | 0/8 2 h-lim-p 0.0022 0.0224 14.2615 1512.785143 7 0.0007 53 | 0/8 3 h-lim-p 0.0027 0.0214 3.3304 1512.783063 4 0.0004 77 | 0/8 4 h-lim-p 0.0006 0.0891 2.0635 1512.782163 2 0.0006 93 | 0/8 5 h-lim-p 0.0044 0.7321 0.2614 1512.782141 3 0.0006 115 | 0/8 6 h-lim-p 0.0065 9.0664 0.0259 1512.782141 0 0.0016 136 | 0/8 7 h-lim-p 0.0116 20.0000 0.0036 1512.782137 0 0.0232 157 | 0/8 8 h-lim-p 0.0060 8.7172 0.0141 1512.781995 0 0.0239 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1512.781991 1 0.9961 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1512.781991 0 2.5000 221 | 0/8 11 h-lim-p 1.6734 20.0000 0.0000 1512.781991 0 0.1046 244 | 0/8 12 h-lim-p 0.0046 20.0000 0.0003 1512.781991 0 0.0000 272 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 1512.781991 0 0.0000 293 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 1512.781991 0 0.0001 313 Out... lnL = -1512.781991 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1512.781991 Node 7: lnL = -1512.781991 Node 8: lnL = -1512.781991 Node 9: lnL = -1512.781991 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 341 Sequential format.. Reading seq # 1: YHR122W_Sbay Reading seq # 2: YHR122W_Scer Reading seq # 3: YHR122W_Skud Reading seq # 4: YHR122W_Smik Reading seq # 5: YHR122W_Spar Sequences read.. Counting patterns.. # site patterns = 183 Counting frequencies.. 120 bytes for distance 29280 bytes for lkl0 23424 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.252485 0.055212 0.115718 0.155247 0.104117 0.257028 0.361170 0.091305 lnL0 = -1587.825204 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1587.825204 x= 0.25249 0.05521 0.11572 0.15525 0.10412 0.25703 0.36117 0.09130 1 h-lim-p 0.0015 0.0122 26.8995 1587.536334 5 0.0008 33 | 0/8 2 h-lim-p 0.0032 0.0255 6.5581 1587.506758 2 0.0015 49 | 0/8 3 h-lim-p 0.0031 0.1480 3.1094 1587.501381 5 0.0013 70 | 0/8 4 h-lim-p 0.0020 0.1148 2.0724 1587.500256 4 0.0008 90 | 0/8 5 h-lim-p 0.0020 0.2608 0.7708 1587.499800 2 0.0019 106 | 0/8 6 h-lim-p 0.0034 0.2410 0.4354 1587.499689 0 0.0017 126 | 0/8 7 h-lim-p 0.0092 3.4934 0.0802 1587.499683 1 0.0018 149 | 0/8 8 h-lim-p 0.4387 20.0000 0.0003 1587.499618 0 0.8775 170 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1587.499617 0 1.0938 190 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1587.499617 0 1.0938 210 | 0/8 11 h-lim-p 1.4132 20.0000 0.0000 1587.499617 0 1.2366 230 | 0/8 12 h-lim-p 1.0295 20.0000 0.0000 1587.499617 0 8.2361 253 | 0/8 13 h-lim-p 0.1021 20.0000 0.0005 1587.499617 0 0.0255 274 | 0/8 14 h-lim-p 0.0073 20.0000 0.0017 1587.499617 0 0.0018 295 | 0/8 15 h-lim-p 0.0009 20.0000 0.0035 1587.499617 0 0.0005 315 | 0/8 16 h-lim-p 0.0006 20.0000 0.0027 1587.499617 0 0.0003 335 | 0/8 17 h-lim-p 0.0003 20.0000 0.0029 1587.499617 0 0.0000 370 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 | 0/8 19 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1587.499617 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1587.499617 Node 7: lnL = -1587.499617 Node 8: lnL = -1587.499617 Node 9: lnL = -1587.499617 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 507 Sequential format.. Reading seq # 1: YHR124W_Sbay Reading seq # 2: YHR124W_Scer Reading seq # 3: YHR124W_Skud Reading seq # 4: YHR124W_Smik Reading seq # 5: YHR124W_Spar Sequences read.. Counting patterns.. # site patterns = 150 Counting frequencies.. 120 bytes for distance 24000 bytes for lkl0 19200 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.111514 0.065378 0.046347 0.063712 0.059572 0.135345 0.108750 0.036969 lnL0 = -1917.075076 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1917.075076 x= 0.11151 0.06538 0.04635 0.06371 0.05957 0.13534 0.10875 0.03697 1 h-lim-p 0.0004 0.0035 121.9952 1915.877361 4 0.0002 30 | 0/8 2 h-lim-p 0.0006 0.0051 21.2529 1915.825624 7 0.0002 59 | 0/8 3 h-lim-p 0.0005 0.0224 9.1657 1915.817774 5 0.0002 80 | 0/8 4 h-lim-p 0.0010 0.0634 1.9596 1915.817302 4 0.0003 101 | 0/8 5 h-lim-p 0.0012 0.3539 0.4245 1915.817278 0 0.0003 114 | 0/8 6 h-lim-p 0.0021 4.1629 0.0541 1915.817278 0 0.0005 135 | 0/8 7 h-lim-p 0.0186 20.0000 0.0013 1915.817278 0 0.0005 159 | 0/8 8 h-lim-p 0.0095 20.0000 0.0001 1915.817277 0 0.9102 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1915.817277 0 1.0938 205 | 0/8 10 h-lim-p 0.7871 20.0000 0.0000 1915.817277 0 6.2968 228 | 0/8 11 h-lim-p 0.4256 20.0000 0.0004 1915.817277 0 0.0033 254 | 0/8 12 h-lim-p 0.0004 13.5750 0.0039 1915.817277 0 0.0000 281 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 1915.817277 0 0.0000 313 | 0/8 14 h-lim-p 0.0000 20.0000 0.0034 1915.817277 0 0.0000 334 | 0/8 15 h-lim-p 0.0002 20.0000 0.0006 1915.817277 0 0.0010 356 | 0/8 16 h-lim-p 0.0034 20.0000 0.0002 1915.817277 0 0.0000 386 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0042 | 0/8 19 h-lim-p 0.0000 20.0000 0.0042 Out... lnL = -1915.817277 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1915.817277 Node 7: lnL = -1915.817277 Node 8: lnL = -1915.817277 Node 9: lnL = -1915.817277 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 816 Sequential format.. Reading seq # 1: YHR127W_Sbay Reading seq # 2: YHR127W_Scer Reading seq # 3: YHR127W_Skud Reading seq # 4: YHR127W_Smik Reading seq # 5: YHR127W_Spar Sequences read.. Counting patterns.. # site patterns = 307 Counting frequencies.. 120 bytes for distance 49120 bytes for lkl0 39296 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.234297 0.093495 0.087278 0.164282 0.107766 0.225100 0.198024 0.093179 lnL0 = -3816.822907 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3816.822907 x= 0.23430 0.09349 0.08728 0.16428 0.10777 0.22510 0.19802 0.09318 1 h-lim-p 0.0008 0.0065 113.4190 3815.195556 8 0.0003 39 | 0/8 2 h-lim-p 0.0006 0.0048 25.7149 3815.090738 6 0.0003 64 | 0/8 3 h-lim-p 0.0009 0.0403 9.1722 3815.077803 5 0.0003 86 | 0/8 4 h-lim-p 0.0019 0.1853 1.6603 3815.077086 4 0.0005 109 | 0/8 5 h-lim-p 0.0056 2.0505 0.1605 3815.077078 0 0.0006 123 | 0/8 6 h-lim-p 0.0044 14.2349 0.0225 3815.077078 0 0.0010 144 | 0/8 7 h-lim-p 0.0106 20.0000 0.0020 3815.077078 0 0.0023 165 | 0/8 8 h-lim-p 0.0155 20.0000 0.0003 3815.077070 0 0.2474 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3815.077070 0 1.0938 209 | 0/8 10 h-lim-p 0.5252 20.0000 0.0000 3815.077070 0 2.1008 231 | 0/8 11 h-lim-p 1.8587 20.0000 0.0000 3815.077070 0 0.1162 254 | 0/8 12 h-lim-p 0.0122 20.0000 0.0001 3815.077070 0 0.0061 274 | 0/8 13 h-lim-p 0.0017 20.0000 0.0005 3815.077070 0 0.0000 301 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 3815.077070 0 0.0000 330 | 0/8 15 h-lim-p 0.0000 20.0000 0.0011 3815.077070 0 0.0000 365 | 0/8 16 h-lim-p 0.0000 20.0000 0.0011 | 0/8 17 h-lim-p 0.0000 20.0000 0.0011 Out... lnL = -3815.077070 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3815.077070 Node 7: lnL = -3815.077070 Node 8: lnL = -3815.077070 Node 9: lnL = -3815.077070 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 866 Sequential format.. Reading seq # 1: YHR129C_Sbay Reading seq # 2: YHR129C_Scer Reading seq # 3: YHR129C_Skud Reading seq # 4: YHR129C_Smik Reading seq # 5: YHR129C_Spar Sequences read.. Counting patterns.. # site patterns = 390 Counting frequencies.. 120 bytes for distance 62400 bytes for lkl0 49920 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.298873 0.116865 0.120074 0.185781 0.136391 0.307128 0.406424 0.103276 lnL0 = -4546.290833 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4546.290833 x= 0.29887 0.11686 0.12007 0.18578 0.13639 0.30713 0.40642 0.10328 1 h-lim-p 0.0021 0.0167 61.2135 4545.553225 4 0.0004 31 | 0/8 2 h-lim-p 0.0018 0.0146 13.8379 4545.505149 6 0.0005 59 | 0/8 3 h-lim-p 0.0007 0.0477 10.3618 4545.484332 4 0.0006 79 | 0/8 4 h-lim-p 0.0015 0.0977 3.8830 4545.479810 2 0.0007 95 | 0/8 5 h-lim-p 0.0033 0.4882 0.8743 4545.479467 3 0.0010 115 | 0/8 6 h-lim-p 0.0037 1.0541 0.2327 4545.479450 2 0.0007 140 | 0/8 7 h-lim-p 0.0123 20.0000 0.0134 4545.479450 0 0.0014 162 | 0/8 8 h-lim-p 0.0971 20.0000 0.0002 4545.479421 0 0.7766 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4545.479420 0 1.0938 205 | 0/8 10 h-lim-p 2.4682 20.0000 0.0000 4545.479420 0 1.0799 225 | 0/8 11 h-lim-p 1.0296 20.0000 0.0000 4545.479420 0 0.0161 250 | 0/8 12 h-lim-p 0.0030 20.0000 0.0001 4545.479420 0 0.0000 283 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 4545.479420 0 0.0000 311 Out... lnL = -4545.479420 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4545.479420 Node 7: lnL = -4545.479420 Node 8: lnL = -4545.479420 Node 9: lnL = -4545.479420 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 321 Sequential format.. Reading seq # 1: YHR132C_Sbay Reading seq # 2: YHR132C_Scer Reading seq # 3: YHR132C_Skud Reading seq # 4: YHR132C_Smik Reading seq # 5: YHR132C_Spar Sequences read.. Counting patterns.. # site patterns = 126 Counting frequencies.. 120 bytes for distance 20160 bytes for lkl0 16128 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.247829 0.071345 0.061955 0.140174 0.100980 0.174050 0.200843 0.111739 lnL0 = -1354.091764 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1354.091764 x= 0.24783 0.07134 0.06195 0.14017 0.10098 0.17405 0.20084 0.11174 1 h-lim-p 0.0036 0.0287 44.7873 1353.600411 9 0.0005 47 | 0/8 2 h-lim-p 0.0027 0.0288 8.6694 1353.568453 6 0.0009 74 | 0/8 3 h-lim-p 0.0030 0.1291 2.5036 1353.565981 5 0.0009 98 | 0/8 4 h-lim-p 0.0023 0.2598 0.9415 1353.565533 3 0.0011 117 | 0/8 5 h-lim-p 0.0051 1.2616 0.2084 1353.565504 3 0.0014 144 | 0/8 6 h-lim-p 0.0086 6.1017 0.0330 1353.565504 0 0.0009 166 | 0/8 7 h-lim-p 0.0053 20.0000 0.0059 1353.565504 0 0.0023 186 | 0/8 8 h-lim-p 0.2653 20.0000 0.0001 1353.565502 0 1.0611 208 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1353.565502 0 1.0938 228 | 0/8 10 h-lim-p 1.5965 20.0000 0.0000 1353.565502 0 0.7983 248 | 0/8 11 h-lim-p 0.3950 20.0000 0.0000 1353.565502 0 0.0002 278 Out... lnL = -1353.565502 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1353.565502 Node 7: lnL = -1353.565502 Node 8: lnL = -1353.565502 Node 9: lnL = -1353.565502 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 272 Sequential format.. Reading seq # 1: YHR132W-A_Sbay Reading seq # 2: YHR132W-A_Scer Reading seq # 3: YHR132W-A_Skud Reading seq # 4: YHR132W-A_Smik Reading seq # 5: YHR132W-A_Spar Sequences read.. Counting patterns.. # site patterns = 117 Counting frequencies.. 120 bytes for distance 18720 bytes for lkl0 14976 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.236793 0.058905 0.059514 0.141370 0.099785 0.170162 0.213825 0.104365 lnL0 = -1264.305214 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1264.305214 x= 0.23679 0.05891 0.05951 0.14137 0.09978 0.17016 0.21383 0.10437 1 h-lim-p 0.0099 0.0796 47.4074 1263.831056 8 0.0005 44 | 0/8 2 h-lim-p 0.0035 0.0429 6.0729 1263.815295 4 0.0009 65 | 0/8 3 h-lim-p 0.0025 0.1496 2.0890 1263.813728 5 0.0008 90 | 0/8 4 h-lim-p 0.0036 0.3463 0.4552 1263.813621 3 0.0011 111 | 0/8 5 h-lim-p 0.0038 2.8235 0.1289 1263.813611 2 0.0012 136 | 0/8 6 h-lim-p 0.0057 3.9494 0.0271 1263.813611 0 0.0012 157 | 0/8 7 h-lim-p 0.0056 20.0000 0.0061 1263.813610 0 0.0012 178 | 0/8 8 h-lim-p 0.2512 20.0000 0.0000 1263.813610 0 1.0047 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1263.813610 0 1.0938 220 | 0/8 10 h-lim-p 1.0895 20.0000 0.0000 1263.813610 0 0.0074 246 | 0/8 11 h-lim-p 0.0021 20.0000 0.0000 1263.813610 0 0.0005 267 | 0/8 12 h-lim-p 0.0002 20.0000 0.0001 1263.813610 0 0.0000 288 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 1263.813610 0 0.0000 319 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1263.813610 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1263.813610 Node 7: lnL = -1263.813610 Node 8: lnL = -1263.813610 Node 9: lnL = -1263.813610 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 386 Sequential format.. Reading seq # 1: YHR135C_Sbay Reading seq # 2: YHR135C_Scer Reading seq # 3: YHR135C_Skud Reading seq # 4: YHR135C_Smik Reading seq # 5: YHR135C_Spar Sequences read.. Counting patterns.. # site patterns = 117 Counting frequencies.. 120 bytes for distance 18720 bytes for lkl0 14976 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.252234 0.025514 0.053887 0.055527 0.038053 0.130744 0.169947 0.146628 lnL0 = -1325.506833 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1325.506833 x= 0.25223 0.02551 0.05389 0.05553 0.03805 0.13074 0.16995 0.14663 1 h-lim-p 0.0020 0.0162 69.5342 1324.892656 8 0.0003 43 | 0/8 2 h-lim-p 0.0005 0.0039 31.8712 1324.742251 6 0.0003 68 | 0/8 3 h-lim-p 0.0003 0.0095 32.1637 1324.492666 0 0.0010 81 | 0/8 4 h-lim-p 0.0013 0.0110 26.1735 1324.394481 2 0.0006 97 | 0/8 5 h-lim-p 0.0021 0.0166 6.6616 1324.388079 5 0.0004 123 | 0/8 6 h-lim-p 0.0011 0.1338 2.1478 1324.384753 0 0.0016 135 | 0/8 7 h-lim-p 0.0012 0.0733 2.9618 1324.381815 1 0.0015 149 | 0/8 8 h-lim-p 2.0661 20.0000 0.0021 1324.375445 4 1.0498 171 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1324.375429 2 1.0938 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1324.375429 0 1.0938 215 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1324.375429 0 2.5000 235 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1324.375429 0 0.0781 259 | 0/8 13 h-lim-p 0.0770 20.0000 0.0000 1324.375429 0 0.0096 281 | 0/8 14 h-lim-p 0.0059 20.0000 0.0000 1324.375429 0 0.0000 310 Out... lnL = -1324.375429 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1324.375429 Node 7: lnL = -1324.375429 Node 8: lnL = -1324.375429 Node 9: lnL = -1324.375429 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 660 Sequential format.. Reading seq # 1: YHR137W_Sbay Reading seq # 2: YHR137W_Scer Reading seq # 3: YHR137W_Skud Reading seq # 4: YHR137W_Smik Reading seq # 5: YHR137W_Spar Sequences read.. Counting patterns.. # site patterns = 302 Counting frequencies.. 120 bytes for distance 48320 bytes for lkl0 38656 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.314639 0.063905 0.115118 0.107874 0.133011 0.244596 0.226195 0.147647 lnL0 = -3099.400604 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3099.400604 x= 0.31464 0.06390 0.11512 0.10787 0.13301 0.24460 0.22620 0.14765 1 h-lim-p 0.0017 0.0133 85.9075 3098.071551 2 0.0004 27 | 0/8 2 h-lim-p 0.0012 0.0126 27.1451 3097.794511 6 0.0008 52 | 0/8 3 h-lim-p 0.0010 0.0144 23.1325 3097.737924 7 0.0003 82 | 0/8 4 h-lim-p 0.0020 0.0760 3.8987 3097.731495 2 0.0009 98 | 0/8 5 h-lim-p 0.0028 0.2430 1.2684 3097.731029 2 0.0007 115 | 0/8 6 h-lim-p 0.0019 0.7394 0.4468 3097.730968 2 0.0007 131 | 0/8 7 h-lim-p 0.0028 2.8306 0.1159 3097.730964 0 0.0007 152 | 0/8 8 h-lim-p 0.3901 20.0000 0.0002 3097.730897 0 1.1704 173 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3097.730896 0 1.0938 193 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3097.730896 0 1.0938 213 | 0/8 11 h-lim-p 1.2930 20.0000 0.0000 3097.730896 0 1.9395 233 | 0/8 12 h-lim-p 1.2770 20.0000 0.0000 3097.730896 0 1.2770 253 | 0/8 13 h-lim-p 0.0425 20.0000 0.0002 3097.730896 0 0.0001 281 | 0/8 14 h-lim-p 0.0007 20.0000 0.0000 3097.730896 0 0.0000 305 | 0/8 15 h-lim-p 0.0007 20.0000 0.0000 3097.730896 0 0.0001 327 Out... lnL = -3097.730896 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3097.730896 Node 7: lnL = -3097.730896 Node 8: lnL = -3097.730896 Node 9: lnL = -3097.730896 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 577 Sequential format.. Reading seq # 1: YHR138C_Sbay Reading seq # 2: YHR138C_Scer Reading seq # 3: YHR138C_Skud Reading seq # 4: YHR138C_Smik Reading seq # 5: YHR138C_Spar Sequences read.. Counting patterns.. # site patterns = 221 Counting frequencies.. 120 bytes for distance 35360 bytes for lkl0 28288 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.218325 0.097878 0.056762 0.134903 0.080134 0.150293 0.214413 0.088802 lnL0 = -2277.455225 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2277.455225 x= 0.21832 0.09788 0.05676 0.13490 0.08013 0.15029 0.21441 0.08880 1 h-lim-p 0.0014 0.0109 43.3666 2277.096670 8 0.0004 42 | 0/8 2 h-lim-p 0.0007 0.0054 18.0461 2277.030345 7 0.0005 73 | 0/8 3 h-lim-p 0.0015 0.0247 5.7345 2277.025089 4 0.0004 95 | 0/8 4 h-lim-p 0.0012 0.0983 1.7081 2277.024398 2 0.0005 111 | 0/8 5 h-lim-p 0.0016 0.4810 0.5452 2277.024290 1 0.0008 125 | 0/8 6 h-lim-p 0.0044 3.3997 0.1016 2277.024287 1 0.0005 149 | 0/8 7 h-lim-p 0.0137 20.0000 0.0040 2277.024287 0 0.0060 169 | 0/8 8 h-lim-p 0.0125 20.0000 0.0019 2277.024224 0 0.0999 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2277.024222 0 1.0938 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2277.024222 0 1.0938 232 | 0/8 11 h-lim-p 1.2521 20.0000 0.0000 2277.024222 0 0.5478 252 | 0/8 12 h-lim-p 0.2631 20.0000 0.0000 2277.024222 0 0.0164 275 | 0/8 13 h-lim-p 0.0055 20.0000 0.0001 2277.024222 0 0.0001 300 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 2277.024222 0 0.0000 323 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 2277.024222 0 0.0000 346 Out... lnL = -2277.024222 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2277.024222 Node 7: lnL = -2277.024222 Node 8: lnL = -2277.024222 Node 9: lnL = -2277.024222 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 870 Sequential format.. Reading seq # 1: YHR139C_Sbay Reading seq # 2: YHR139C_Scer Reading seq # 3: YHR139C_Skud Reading seq # 4: YHR139C_Smik Reading seq # 5: YHR139C_Spar Sequences read.. Counting patterns.. # site patterns = 320 Counting frequencies.. 120 bytes for distance 51200 bytes for lkl0 40960 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.247017 0.051270 0.062244 0.096536 0.075133 0.199414 0.248675 0.113789 lnL0 = -3831.331120 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3831.331120 x= 0.24702 0.05127 0.06224 0.09654 0.07513 0.19941 0.24868 0.11379 1 h-lim-p 0.0030 0.7750 159.4080 3829.237416 2 0.0002 29 | 0/8 2 h-lim-p 0.0005 0.0042 38.4990 3829.034118 7 0.0003 59 | 0/8 3 h-lim-p 0.0004 0.0056 29.2161 3828.960522 6 0.0002 84 | 0/8 4 h-lim-p 0.0009 0.0387 8.3084 3828.950204 4 0.0003 104 | 0/8 5 h-lim-p 0.0014 0.1428 2.0131 3828.949224 4 0.0005 126 | 0/8 6 h-lim-p 0.0029 0.3712 0.3591 3828.949209 2 0.0002 145 | 0/8 7 h-lim-p 0.0009 3.8143 0.0963 3828.949207 1 0.0004 168 | 0/8 8 h-lim-p 0.1005 20.0000 0.0004 3828.948726 0 1.2054 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3828.948718 1 0.9961 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3828.948718 0 1.0938 233 | 0/8 11 h-lim-p 1.2808 20.0000 0.0000 3828.948718 0 1.2808 253 | 0/8 12 h-lim-p 0.1702 20.0000 0.0001 3828.948718 0 0.0851 273 | 0/8 13 h-lim-p 0.0197 20.0000 0.0004 3828.948718 0 0.0049 294 | 0/8 14 h-lim-p 0.0023 20.0000 0.0008 3828.948718 0 0.0000 322 | 0/8 15 h-lim-p 0.0007 20.0000 0.0000 3828.948718 0 0.0000 352 Out... lnL = -3828.948718 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3828.948718 Node 7: lnL = -3828.948718 Node 8: lnL = -3828.948718 Node 9: lnL = -3828.948718 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 169 Sequential format.. Reading seq # 1: YHR140W_Sbay Reading seq # 2: YHR140W_Scer Reading seq # 3: YHR140W_Skud Reading seq # 4: YHR140W_Smik Reading seq # 5: YHR140W_Spar Sequences read.. Counting patterns.. # site patterns = 86 Counting frequencies.. 120 bytes for distance 13760 bytes for lkl0 11008 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.213056 0.055799 0.082377 0.197623 0.064633 0.217669 0.129525 0.084107 lnL0 = -675.972867 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 675.972867 x= 0.21306 0.05580 0.08238 0.19762 0.06463 0.21767 0.12953 0.08411 1 h-lim-p 0.0109 0.0873 32.2707 675.455904 5 0.0011 33 | 0/8 2 h-lim-p 0.0025 0.0201 10.5383 675.319036 5 0.0026 55 | 0/8 3 h-lim-p 0.0055 0.0442 2.8728 675.311594 5 0.0020 79 | 0/8 4 h-lim-p 0.0036 0.1379 1.5521 675.310451 5 0.0012 103 | 0/8 5 h-lim-p 0.0057 0.4635 0.3299 675.310337 2 0.0022 119 | 0/8 6 h-lim-p 0.0214 3.1619 0.0339 675.310336 1 0.0021 143 | 0/8 7 h-lim-p 0.1166 20.0000 0.0006 675.310309 0 0.6995 165 | 0/8 8 h-lim-p 0.0060 5.0902 0.0721 675.310294 3 0.0043 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 675.310293 0 1.0938 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 675.310293 0 1.0938 233 | 0/8 11 h-lim-p 1.9613 20.0000 0.0000 675.310293 0 1.9613 253 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 675.310293 0 0.0012 283 Out... lnL = -675.310293 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -675.310293 Node 7: lnL = -675.310293 Node 8: lnL = -675.310293 Node 9: lnL = -675.310293 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 843 Sequential format.. Reading seq # 1: YHR142W_Sbay Reading seq # 2: YHR142W_Scer Reading seq # 3: YHR142W_Skud Reading seq # 4: YHR142W_Smik Reading seq # 5: YHR142W_Spar Sequences read.. Counting patterns.. # site patterns = 284 Counting frequencies.. 120 bytes for distance 45440 bytes for lkl0 36352 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.200214 0.049081 0.067916 0.125475 0.097663 0.258254 0.216537 0.068046 lnL0 = -3911.736578 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3911.736578 x= 0.20021 0.04908 0.06792 0.12547 0.09766 0.25825 0.21654 0.06805 1 h-lim-p 0.0004 0.0034 206.2053 3908.312334 3 0.0002 28 | 0/8 2 h-lim-p 0.0003 0.0027 45.9138 3908.046766 5 0.0003 50 | 0/8 3 h-lim-p 0.0008 0.0133 14.6629 3908.023501 6 0.0002 77 | 0/8 4 h-lim-p 0.0009 0.0725 3.8431 3908.020544 2 0.0004 93 | 0/8 5 h-lim-p 0.0022 0.3229 0.7523 3908.020440 3 0.0004 114 | 0/8 6 h-lim-p 0.0038 1.9036 0.0761 3908.020439 0 0.0004 136 | 0/8 7 h-lim-p 0.0013 12.5275 0.0253 3908.020439 0 0.0006 156 | 0/8 8 h-lim-p 0.0866 20.0000 0.0002 3908.020395 0 1.3863 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3908.020390 0 1.0938 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3908.020390 0 1.0938 220 | 0/8 11 h-lim-p 1.1053 20.0000 0.0000 3908.020390 0 0.9672 240 | 0/8 12 h-lim-p 0.3725 20.0000 0.0001 3908.020390 0 0.0233 263 | 0/8 13 h-lim-p 0.0040 20.0000 0.0003 3908.020390 0 0.0001 287 | 0/8 14 h-lim-p 0.0012 20.0000 0.0000 3908.020390 0 0.0000 317 | 0/8 15 h-lim-p 0.0007 20.0000 0.0000 3908.020390 0 0.0000 343 Out... lnL = -3908.020390 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3908.020390 Node 7: lnL = -3908.020390 Node 8: lnL = -3908.020390 Node 9: lnL = -3908.020390 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 822 Sequential format.. Reading seq # 1: YHR143W-A_Sbay Reading seq # 2: YHR143W-A_Scer Reading seq # 3: YHR143W-A_Skud Reading seq # 4: YHR143W-A_Smik Reading seq # 5: YHR143W-A_Spar Sequences read.. Counting patterns.. # site patterns = 356 Counting frequencies.. 120 bytes for distance 56960 bytes for lkl0 45568 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.495383 0.206974 0.037638 0.195453 0.120491 0.230147 0.254048 0.271499 lnL0 = -4204.467607 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4204.467607 x= 0.49538 0.20697 0.03764 0.19545 0.12049 0.23015 0.25405 0.27150 1 h-lim-p 0.0025 0.0201 173.8641 4201.109902 6 0.0002 36 | 0/8 2 h-lim-p 0.0006 0.0045 56.3317 4200.143640 1 0.0007 50 | 0/8 3 h-lim-p 0.0028 0.0242 14.1908 4200.104659 7 0.0004 81 | 0/8 4 h-lim-p 0.0014 0.0555 4.2392 4200.100401 5 0.0005 105 | 0/8 5 h-lim-p 0.0018 0.2883 1.2280 4200.099830 2 0.0008 121 | 0/8 6 h-lim-p 0.0015 0.9635 0.6661 4200.099511 2 0.0017 138 | 0/8 7 h-lim-p 0.0101 4.1966 0.1144 4200.099360 3 0.0071 165 | 0/8 8 h-lim-p 0.0656 20.0000 0.0124 4200.087181 0 0.2624 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 4200.086706 3 1.3437 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4200.086705 0 1.0938 234 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4200.086705 0 1.0938 254 | 0/8 12 h-lim-p 1.2288 20.0000 0.0000 4200.086705 0 2.4576 275 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 4200.086705 0 0.0391 300 | 0/8 14 h-lim-p 0.0051 20.0000 0.0000 4200.086705 0 0.0013 321 | 0/8 15 h-lim-p 0.0004 20.0000 0.0000 4200.086705 0 0.0000 355 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 4200.086705 0 0.0000 384 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 | 0/8 18 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -4200.086705 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4200.086705 Node 7: lnL = -4200.086705 Node 8: lnL = -4200.086705 Node 9: lnL = -4200.086705 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 873 Sequential format.. Reading seq # 1: YHR143W_Sbay Reading seq # 2: YHR143W_Scer Reading seq # 3: YHR143W_Skud Reading seq # 4: YHR143W_Smik Reading seq # 5: YHR143W_Spar Sequences read.. Counting patterns.. # site patterns = 258 Counting frequencies.. 120 bytes for distance 41280 bytes for lkl0 33024 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.161700 0.060268 0.032715 0.103144 0.083185 0.154091 0.184385 0.059224 lnL0 = -3651.225196 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3651.225196 x= 0.16170 0.06027 0.03271 0.10314 0.08319 0.15409 0.18439 0.05922 1 h-lim-p 0.0021 0.7652 185.6593 3649.618016 6 0.0001 37 | 0/8 2 h-lim-p 0.0003 0.0025 40.1943 3649.472642 7 0.0002 67 | 0/8 3 h-lim-p 0.0007 0.0201 10.3636 3649.459101 5 0.0003 91 | 0/8 4 h-lim-p 0.0008 0.0662 3.3984 3649.458009 4 0.0002 112 | 0/8 5 h-lim-p 0.0008 0.4501 0.8583 3649.457941 0 0.0002 125 | 0/8 6 h-lim-p 0.0020 2.2578 0.0882 3649.457940 0 0.0002 147 | 0/8 7 h-lim-p 0.0012 11.3345 0.0162 3649.457940 0 0.0003 168 | 0/8 8 h-lim-p 0.0953 20.0000 0.0000 3649.457930 0 1.1440 191 | 0/8 9 h-lim-p 1.8503 20.0000 0.0000 3649.457930 0 1.6190 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3649.457930 0 1.0938 231 | 0/8 11 h-lim-p 0.5669 20.0000 0.0000 3649.457930 0 2.2676 253 | 0/8 12 h-lim-p 0.7988 20.0000 0.0001 3649.457930 0 0.0250 277 | 0/8 13 h-lim-p 0.0047 20.0000 0.0004 3649.457930 0 0.0003 300 | 0/8 14 h-lim-p 0.0114 20.0000 0.0000 3649.457930 0 0.0114 320 | 0/8 15 h-lim-p 0.0000 0.2576 0.3266 3649.457930 0 0.0000 340 | 0/8 16 h-lim-p 0.0024 20.0000 0.0010 3649.457930 0 0.0024 360 | 0/8 17 h-lim-p 0.0021 20.0000 0.0011 3649.457930 0 0.0000 401 | 0/8 18 h-lim-p 0.0000 20.0000 0.0021 | 0/8 19 h-lim-p 0.0000 20.0000 0.0021 Out... lnL = -3649.457930 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3649.457930 Node 7: lnL = -3649.457930 Node 8: lnL = -3649.457930 Node 9: lnL = -3649.457930 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 283 Sequential format.. Reading seq # 1: YHR144C_Sbay Reading seq # 2: YHR144C_Scer Reading seq # 3: YHR144C_Skud Reading seq # 4: YHR144C_Smik Reading seq # 5: YHR144C_Spar Sequences read.. Counting patterns.. # site patterns = 135 Counting frequencies.. 120 bytes for distance 21600 bytes for lkl0 17280 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.134424 0.088387 0.070163 0.153428 0.060923 0.146813 0.194489 0.024203 lnL0 = -1181.614849 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1181.614849 x= 0.13442 0.08839 0.07016 0.15343 0.06092 0.14681 0.19449 0.02420 1 h-lim-p 0.0020 0.0160 83.6690 1179.794944 9 0.0006 45 | 0/8 2 h-lim-p 0.0004 0.0032 22.1958 1179.649689 0 0.0008 58 | 0/8 3 h-lim-p 0.0026 0.0252 6.8265 1179.636186 4 0.0006 79 | 0/8 4 h-lim-p 0.0036 0.2157 1.2054 1179.635774 4 0.0006 102 | 0/8 5 h-lim-p 0.0019 0.2017 0.3761 1179.635682 4 0.0013 124 | 0/8 6 h-lim-p 0.0070 6.8744 0.0685 1179.635594 2 0.0069 148 | 0/8 7 h-lim-p 0.0194 20.0000 0.0243 1179.628611 0 0.1555 171 | 0/8 8 h-lim-p 0.0031 0.2039 1.2260 1179.627266 2 0.0014 195 | 0/8 9 h-lim-p 2.0531 20.0000 0.0009 1179.626767 2 1.0807 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1179.626761 1 1.2305 235 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1179.626761 0 1.0938 255 | 0/8 12 h-lim-p 1.4608 20.0000 0.0000 1179.626761 0 1.2782 275 | 0/8 13 h-lim-p 0.6167 20.0000 0.0000 1179.626761 0 0.1349 296 | 0/8 14 h-lim-p 0.0079 20.0000 0.0005 1179.626761 0 0.0040 316 | 0/8 15 h-lim-p 0.0014 17.3371 0.0015 1179.626761 0 0.0014 336 | 0/8 16 h-lim-p 0.0006 7.5570 0.0035 1179.626761 0 0.0000 376 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1179.626761 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1179.626761 Node 7: lnL = -1179.626761 Node 8: lnL = -1179.626761 Node 9: lnL = -1179.626761 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 284 Sequential format.. Reading seq # 1: YHR147C_Sbay Reading seq # 2: YHR147C_Scer Reading seq # 3: YHR147C_Skud Reading seq # 4: YHR147C_Smik Reading seq # 5: YHR147C_Spar Sequences read.. Counting patterns.. # site patterns = 141 Counting frequencies.. 120 bytes for distance 22560 bytes for lkl0 18048 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.175930 0.132586 0.095452 0.117936 0.093173 0.182198 0.195254 0.042867 lnL0 = -1277.948227 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1277.948227 x= 0.17593 0.13259 0.09545 0.11794 0.09317 0.18220 0.19525 0.04287 1 h-lim-p 0.0069 0.0555 41.3901 1277.430105 7 0.0006 40 | 0/8 2 h-lim-p 0.0025 0.0204 9.0078 1277.399203 7 0.0008 70 | 0/8 3 h-lim-p 0.0018 0.0435 4.0203 1277.391724 6 0.0011 97 | 0/8 4 h-lim-p 0.0063 0.7110 0.6951 1277.391538 3 0.0008 117 | 0/8 5 h-lim-p 0.0045 1.8189 0.1211 1277.391527 2 0.0014 142 | 0/8 6 h-lim-p 0.0121 13.5528 0.0143 1277.391527 0 0.0027 163 | 0/8 7 h-lim-p 0.0166 20.0000 0.0023 1277.391525 0 0.0332 184 | 0/8 8 h-lim-p 0.0071 20.0000 0.0107 1277.391469 0 0.0284 206 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1277.391469 0 1.0938 226 | 0/8 10 h-lim-p 1.6514 20.0000 0.0000 1277.391469 0 1.4450 246 | 0/8 11 h-lim-p 1.6978 20.0000 0.0000 1277.391469 0 0.7428 266 | 0/8 12 h-lim-p 0.1882 20.0000 0.0000 1277.391469 0 0.0118 289 | 0/8 13 h-lim-p 0.0032 20.0000 0.0001 1277.391469 0 0.0000 328 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 1277.391469 0 0.0000 351 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 1277.391469 0 0.0000 385 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1277.391469 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1277.391469 Node 7: lnL = -1277.391469 Node 8: lnL = -1277.391469 Node 9: lnL = -1277.391469 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 616 Sequential format.. Reading seq # 1: YHR150W_Sbay Reading seq # 2: YHR150W_Scer Reading seq # 3: YHR150W_Skud Reading seq # 4: YHR150W_Smik Reading seq # 5: YHR150W_Spar Sequences read.. Counting patterns.. # site patterns = 227 Counting frequencies.. 120 bytes for distance 36320 bytes for lkl0 29056 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.054563 0.117765 0.127787 0.065026 0.180048 0.271866 0.312112 lnL0 = -2818.731468 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2818.731468 x= 0.00006 0.05456 0.11777 0.12779 0.06503 0.18005 0.27187 0.31211 1 h-lim-p 0.0000 0.0000 257.6151 2818.613733 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0017 97.5115 2816.840684 0 0.0005 39 | 1/8 3 h-lim-p 0.0010 0.0085 48.4580 2816.302731 6 0.0006 66 | 1/8 4 h-lim-p 0.0016 0.0131 14.1985 2816.259719 6 0.0005 93 | 1/8 5 h-lim-p 0.0018 0.0688 3.6235 2816.252196 3 0.0007 111 | 1/8 6 h-lim-p 0.0015 0.1260 1.7772 2816.234477 0 0.0029 124 | 1/8 7 h-lim-p 0.0025 0.1385 2.0615 2815.580751 0 0.0200 139 | 0/8 8 h-lim-p 0.0020 0.0481 20.7658 2813.074998 0 0.0030 151 | 0/8 9 h-lim-p 0.0003 0.0028 27.9719 2810.968216 m 0.0028 163 | 0/8 10 h-lim-p 2.5000 20.0000 0.0072 2810.928938 2 1.1719 179 | 0/8 11 h-lim-p 0.9669 7.7354 0.0012 2810.926836 1 1.2087 201 | 0/8 12 h-lim-p 2.5000 20.0000 0.0002 2810.926788 2 1.1719 225 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2810.926787 0 1.0938 245 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 2810.926787 0 1.0938 265 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2810.926787 0 1.2500 285 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 2810.926787 0 0.0000 328 Out... lnL = -2810.926787 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2810.926787 Node 7: lnL = -2810.926787 Node 8: lnL = -2810.926787 Node 9: lnL = -2810.926787 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 621 Sequential format.. Reading seq # 1: YHR151C_Sbay Reading seq # 2: YHR151C_Scer Reading seq # 3: YHR151C_Skud Reading seq # 4: YHR151C_Smik Reading seq # 5: YHR151C_Spar Sequences read.. Counting patterns.. # site patterns = 192 Counting frequencies.. 120 bytes for distance 30720 bytes for lkl0 24576 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.004837 0.053214 0.038245 0.085653 0.069813 0.144758 0.180754 0.246028 lnL0 = -2598.359138 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2598.359138 x= 0.00484 0.05321 0.03825 0.08565 0.06981 0.14476 0.18075 0.24603 1 h-lim-p 0.0026 1.0075 141.6686 2596.869809 7 0.0002 39 | 0/8 2 h-lim-p 0.0003 0.0024 37.8030 2596.707070 5 0.0002 61 | 0/8 3 h-lim-p 0.0008 0.0206 10.8509 2596.689472 4 0.0003 81 | 0/8 4 h-lim-p 0.0006 0.0263 5.8748 2596.686308 4 0.0002 101 | 0/8 5 h-lim-p 0.0011 0.0342 1.2158 2596.686015 3 0.0004 119 | 0/8 6 h-lim-p 0.0060 1.1916 0.0856 2596.686014 0 0.0003 134 | 0/8 7 h-lim-p 0.0033 5.9918 0.0084 2596.686014 0 0.0015 154 | 0/8 8 h-lim-p 0.0142 20.0000 0.0009 2596.685925 0 0.4543 179 | 0/8 9 h-lim-p 0.7766 20.0000 0.0005 2596.685913 0 1.1649 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2596.685913 0 1.0938 219 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2596.685912 0 1.2500 239 | 0/8 12 h-lim-p 0.1029 20.0000 0.0000 2596.685912 0 0.4115 261 | 0/8 13 h-lim-p 0.0920 20.0000 0.0001 2596.685912 0 0.0029 285 | 0/8 14 h-lim-p 0.0012 20.0000 0.0003 2596.685912 0 0.0000 315 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 2596.685912 0 0.0000 341 Out... lnL = -2596.685912 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2596.685912 Node 7: lnL = -2596.685912 Node 8: lnL = -2596.685912 Node 9: lnL = -2596.685912 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 620 Sequential format.. Reading seq # 1: YHR152W_Sbay Reading seq # 2: YHR152W_Scer Reading seq # 3: YHR152W_Skud Reading seq # 4: YHR152W_Smik Reading seq # 5: YHR152W_Spar Sequences read.. Counting patterns.. # site patterns = 197 Counting frequencies.. 120 bytes for distance 31520 bytes for lkl0 25216 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.007826 0.053912 0.035786 0.087288 0.068178 0.146011 0.183312 0.251763 lnL0 = -2603.648451 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2603.648451 x= 0.00783 0.05391 0.03579 0.08729 0.06818 0.14601 0.18331 0.25176 1 h-lim-p 0.0028 1.0128 136.0081 2602.281956 3 0.0002 31 | 0/8 2 h-lim-p 0.0003 0.0021 40.0674 2602.107656 3 0.0002 49 | 0/8 3 h-lim-p 0.0008 0.0188 11.9389 2602.085781 5 0.0003 73 | 0/8 4 h-lim-p 0.0006 0.0203 6.7283 2602.081847 4 0.0002 93 | 0/8 5 h-lim-p 0.0011 0.0351 1.3484 2602.081502 4 0.0004 115 | 0/8 6 h-lim-p 0.0017 0.2516 0.3303 2602.081490 2 0.0002 133 | 0/8 7 h-lim-p 0.0030 2.1331 0.0243 2602.081490 0 0.0007 154 | 0/8 8 h-lim-p 0.1010 20.0000 0.0002 2602.081452 0 0.8077 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2602.081452 0 1.0938 197 | 0/8 10 h-lim-p 0.9055 20.0000 0.0000 2602.081452 0 0.9055 217 | 0/8 11 h-lim-p 0.6458 20.0000 0.0000 2602.081452 0 0.6458 237 | 0/8 12 h-lim-p 0.1866 20.0000 0.0002 2602.081452 0 0.0933 257 | 0/8 13 h-lim-p 0.0302 20.0000 0.0005 2602.081452 0 0.0000 291 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 2602.081452 0 0.0000 313 Out... lnL = -2602.081452 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2602.081452 Node 7: lnL = -2602.081452 Node 8: lnL = -2602.081452 Node 9: lnL = -2602.081452 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 313 Sequential format.. Reading seq # 1: YHR153C_Sbay Reading seq # 2: YHR153C_Scer Reading seq # 3: YHR153C_Skud Reading seq # 4: YHR153C_Smik Reading seq # 5: YHR153C_Spar Sequences read.. Counting patterns.. # site patterns = 150 Counting frequencies.. 120 bytes for distance 24000 bytes for lkl0 19200 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.086112 0.140300 0.127567 0.045657 0.193999 0.278102 0.335213 lnL0 = -1414.081845 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1414.081845 x= 0.00006 0.08611 0.14030 0.12757 0.04566 0.19400 0.27810 0.33521 1 h-lim-p 0.0000 0.0000 143.8016 1414.020991 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0011 176.6120 1410.826679 0 0.0003 39 | 1/8 3 h-lim-p 0.0006 0.0046 77.9046 1408.623869 0 0.0011 52 | 1/8 4 h-lim-p 0.0009 0.0075 35.7491 1408.302300 8 0.0007 83 | 1/8 5 h-lim-p 0.0043 0.0609 5.6113 1408.272043 7 0.0015 115 | 1/8 6 h-lim-p 0.0029 0.1017 2.8162 1408.239853 4 0.0030 135 | 0/8 7 h-lim-p 0.0010 0.0858 8.8811 1408.066988 0 0.0038 149 | 0/8 8 h-lim-p 0.0111 0.1894 3.0454 1407.685698 2 0.0104 165 | 0/8 9 h-lim-p 0.0027 0.0213 4.4399 1403.056560 m 0.0213 177 | 0/8 10 h-lim-p 2.5000 20.0000 0.0116 1402.928705 7 0.8513 206 | 0/8 11 h-lim-p 2.2687 20.0000 0.0044 1402.903259 7 1.5346 243 | 0/8 12 h-lim-p 0.6735 5.3881 0.0013 1402.902030 0 2.0206 264 | 0/8 13 h-lim-p 2.5000 20.0000 0.0004 1402.901933 2 1.1719 288 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 1402.901931 0 1.2500 308 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1402.901931 0 2.1875 328 | 0/8 16 h-lim-p 2.3563 20.0000 0.0000 1402.901931 0 1.0309 348 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1402.901931 0 2.1875 368 | 0/8 18 h-lim-p 1.8475 20.0000 0.0000 1402.901931 0 0.4041 389 | 0/8 19 h-lim-p 0.5807 20.0000 0.0000 1402.901931 0 0.0181 413 Out... lnL = -1402.901931 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1402.901931 Node 7: lnL = -1402.901931 Node 8: lnL = -1402.901931 Node 9: lnL = -1402.901931 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 560 Sequential format.. Reading seq # 1: YHR157W_Sbay Reading seq # 2: YHR157W_Scer Reading seq # 3: YHR157W_Skud Reading seq # 4: YHR157W_Smik Reading seq # 5: YHR157W_Spar Sequences read.. Counting patterns.. # site patterns = 257 Counting frequencies.. 120 bytes for distance 41120 bytes for lkl0 32896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.110751 0.166150 0.183134 0.046402 0.256163 0.361600 0.426769 lnL0 = -2552.948498 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2552.948498 x= 0.00006 0.11075 0.16615 0.18313 0.04640 0.25616 0.36160 0.42677 1 h-lim-p 0.0000 0.0000 127.2659 2552.918481 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0016 361.9774 2544.235188 0 0.0005 39 | 1/8 3 h-lim-p 0.0013 0.0106 33.4544 2543.719083 8 0.0010 71 | 1/8 4 h-lim-p 0.0055 0.0808 5.9139 2543.684675 7 0.0015 100 | 1/8 5 h-lim-p 0.0030 0.0997 3.0216 2543.648671 4 0.0029 120 | 1/8 6 h-lim-p 0.0054 0.1506 1.6593 2543.207046 0 0.0214 134 | 1/8 7 h-lim-p 0.0029 0.0235 8.5461 2538.365099 0 0.0117 148 | 0/8 8 h-lim-p 0.0004 0.0030 51.4430 2537.122462 0 0.0007 161 | 0/8 9 h-lim-p 0.0019 0.0155 2.8134 2537.093617 0 0.0078 175 | 0/8 10 h-lim-p 0.7952 20.0000 0.0274 2536.857977 7 0.5966 201 | 0/8 11 h-lim-p 2.5000 20.0000 0.0035 2536.847981 5 0.8900 232 | 0/8 12 h-lim-p 1.8257 20.0000 0.0017 2536.847206 2 0.7952 256 | 0/8 13 h-lim-p 2.5000 20.0000 0.0001 2536.847203 1 0.9961 278 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 2536.847203 0 1.0938 298 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2536.847203 0 1.0938 318 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 2536.847203 0 1.0938 338 | 0/8 17 h-lim-p 0.6537 20.0000 0.0000 2536.847203 0 0.3269 358 | 0/8 18 h-lim-p 0.0319 20.0000 0.0000 2536.847203 0 0.0001 386 Out... lnL = -2536.847203 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2536.847203 Node 7: lnL = -2536.847203 Node 8: lnL = -2536.847203 Node 9: lnL = -2536.847203 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 375 Sequential format.. Reading seq # 1: YHR158C_Sbay Reading seq # 2: YHR158C_Scer Reading seq # 3: YHR158C_Skud Reading seq # 4: YHR158C_Smik Reading seq # 5: YHR158C_Spar Sequences read.. Counting patterns.. # site patterns = 101 Counting frequencies.. 120 bytes for distance 16160 bytes for lkl0 12928 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.049101 0.059281 0.063704 0.030013 0.105061 0.149789 0.178464 lnL0 = -1389.236226 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1389.236226 x= 0.00006 0.04910 0.05928 0.06370 0.03001 0.10506 0.14979 0.17846 1 h-lim-p 0.0000 0.0000 186.6715 1389.137622 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0007 138.4328 1388.123460 0 0.0002 38 | 1/8 3 h-lim-p 0.0003 0.0022 59.0786 1387.763433 2 0.0003 54 | 1/8 4 h-lim-p 0.0005 0.0067 31.8249 1387.658188 8 0.0003 88 | 1/8 5 h-lim-p 0.0023 0.0419 3.7808 1387.651357 5 0.0007 112 | 1/8 6 h-lim-p 0.0028 0.2552 0.9174 1387.631012 0 0.0057 125 | 0/8 7 h-lim-p 0.0012 0.0252 4.4615 1387.525353 0 0.0023 145 | 0/8 8 h-lim-p 0.0007 0.0216 15.2890 1386.845851 0 0.0027 159 | 0/8 9 h-lim-p 0.0005 0.0038 14.0839 1384.650907 m 0.0038 171 | 0/8 10 h-lim-p 2.5000 20.0000 0.0039 1384.604213 2 1.1719 187 | 0/8 11 h-lim-p 2.5000 20.0000 0.0013 1384.595840 6 1.4543 222 | 0/8 12 h-lim-p 0.6352 5.0813 0.0005 1384.595485 0 1.2703 243 | 0/8 13 h-lim-p 2.5000 20.0000 0.0001 1384.595462 0 1.0938 263 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1384.595462 0 1.0938 283 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1384.595462 0 0.2734 305 | 0/8 16 h-lim-p 0.4043 20.0000 0.0000 1384.595462 0 0.0063 330 | 0/8 17 h-lim-p 0.0066 20.0000 0.0000 1384.595462 0 0.0000 357 Out... lnL = -1384.595462 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1384.595462 Node 7: lnL = -1384.595462 Node 8: lnL = -1384.595462 Node 9: lnL = -1384.595462 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 375 Sequential format.. Reading seq # 1: YHR159W_Sbay Reading seq # 2: YHR159W_Scer Reading seq # 3: YHR159W_Skud Reading seq # 4: YHR159W_Smik Reading seq # 5: YHR159W_Spar Sequences read.. Counting patterns.. # site patterns = 101 Counting frequencies.. 120 bytes for distance 16160 bytes for lkl0 12928 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.049036 0.059339 0.064655 0.029211 0.105887 0.150559 0.178222 lnL0 = -1387.371394 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1387.371394 x= 0.00006 0.04904 0.05934 0.06466 0.02921 0.10589 0.15056 0.17822 1 h-lim-p 0.0000 0.0000 200.6967 1387.271023 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0006 154.1234 1386.062290 0 0.0002 38 | 1/8 3 h-lim-p 0.0002 0.0019 66.1110 1385.633684 3 0.0002 56 | 1/8 4 h-lim-p 0.0004 0.0059 36.9421 1385.493228 6 0.0003 82 | 1/8 5 h-lim-p 0.0025 0.0405 4.0905 1385.485531 5 0.0007 105 | 1/8 6 h-lim-p 0.0021 0.0675 1.3278 1385.476806 4 0.0016 125 | 1/8 7 h-lim-p 0.0007 0.0685 3.1601 1385.385617 0 0.0027 139 | 0/8 8 h-lim-p 0.0013 0.0586 6.7877 1384.271812 0 0.0051 153 | 0/8 9 h-lim-p 0.0003 0.0020 19.3688 1382.316678 m 0.0020 165 | 0/8 10 h-lim-p 0.0000 0.0000 0.0063 h-lim-p: 5.10922994e-16 4.08738395e-15 6.28605311e-03 1382.316678 .. | 0/8 11 h-lim-p 0.0000 1.7808 58.4821 1382.101665 0 0.0002 197 | 0/8 12 h-lim-p 0.0000 0.0002 12.6955 1382.084387 m 0.0002 209 | 1/8 13 h-lim-p 0.0006 0.0513 3.9515 1382.082409 3 0.0003 227 | 1/8 14 h-lim-p 0.0030 0.5456 0.3640 1382.082373 3 0.0005 247 | 1/8 15 h-lim-p 0.0013 2.3699 0.1368 1382.082368 2 0.0003 271 | 1/8 16 h-lim-p 0.0012 5.5696 0.0395 1382.082219 0 0.0095 293 | 0/8 17 h-lim-p 0.0009 0.6134 0.4413 1382.081098 0 0.0034 314 | 0/8 18 h-lim-p 0.0008 0.0061 0.3584 1382.077546 m 0.0061 334 | 1/8 19 h-lim-p 0.0011 0.0954 1.5657 1382.076645 3 0.0005 361 | 1/8 20 h-lim-p 0.6255 20.0000 0.0014 1382.076370 4 0.3868 385 | 0/8 21 h-lim-p 0.0015 0.9970 0.3569 1382.076320 3 0.0011 410 | 0/8 22 h-lim-p 0.7951 6.3606 0.0002 1382.076282 1 0.9938 432 | 0/8 23 h-lim-p 2.5000 20.0000 0.0000 1382.076282 0 1.2500 452 | 0/8 24 h-lim-p 2.5000 20.0000 0.0000 1382.076282 0 1.0938 472 | 0/8 25 h-lim-p 2.5000 20.0000 0.0000 1382.076282 0 3.7500 492 | 0/8 26 h-lim-p 1.6160 20.0000 0.0000 1382.076282 0 0.0884 515 | 0/8 27 h-lim-p 0.0890 20.0000 0.0000 1382.076282 0 0.0056 538 Out... lnL = -1382.076282 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1382.076282 Node 7: lnL = -1382.076282 Node 8: lnL = -1382.076282 Node 9: lnL = -1382.076282 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 321 Sequential format.. Reading seq # 1: YHR160C_Sbay Reading seq # 2: YHR160C_Scer Reading seq # 3: YHR160C_Skud Reading seq # 4: YHR160C_Smik Reading seq # 5: YHR160C_Spar Sequences read.. Counting patterns.. # site patterns = 153 Counting frequencies.. 120 bytes for distance 24480 bytes for lkl0 19584 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.018001 0.086577 0.032817 0.144474 0.084441 0.222232 0.204307 0.352431 lnL0 = -1474.850663 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1474.850663 x= 0.01800 0.08658 0.03282 0.14447 0.08444 0.22223 0.20431 0.35243 1 h-lim-p 0.0006 0.0051 46.9722 1474.401030 7 0.0004 39 | 0/8 2 h-lim-p 0.0009 0.0071 17.7792 1474.319845 6 0.0006 65 | 0/8 3 h-lim-p 0.0013 0.0259 7.8022 1474.305282 3 0.0006 83 | 0/8 4 h-lim-p 0.0021 0.1438 2.2103 1474.302943 4 0.0011 104 | 0/8 5 h-lim-p 0.0107 0.4545 0.2178 1474.302916 1 0.0012 120 | 0/8 6 h-lim-p 0.0030 4.4188 0.0860 1474.302911 1 0.0015 143 | 0/8 7 h-lim-p 0.0343 20.0000 0.0037 1474.302894 0 0.0687 164 | 0/8 8 h-lim-p 0.0114 2.2739 0.0221 1474.302618 0 0.0228 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1474.302617 0 1.0938 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1474.302617 0 1.0938 225 | 0/8 11 h-lim-p 1.0275 20.0000 0.0000 1474.302617 0 0.4495 245 | 0/8 12 h-lim-p 0.1839 20.0000 0.0000 1474.302617 0 0.0029 270 | 0/8 13 h-lim-p 0.0010 20.0000 0.0001 1474.302617 0 0.0000 297 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 1474.302617 0 0.0001 317 Out... lnL = -1474.302617 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1474.302617 Node 7: lnL = -1474.302617 Node 8: lnL = -1474.302617 Node 9: lnL = -1474.302617 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 814 Sequential format.. Reading seq # 1: YHR161C_Sbay Reading seq # 2: YHR161C_Scer Reading seq # 3: YHR161C_Skud Reading seq # 4: YHR161C_Smik Reading seq # 5: YHR161C_Spar Sequences read.. Counting patterns.. # site patterns = 211 Counting frequencies.. 120 bytes for distance 33760 bytes for lkl0 27008 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.013356 0.046437 0.021180 0.084460 0.042034 0.142144 0.150136 0.223458 lnL0 = -3119.846031 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3119.846031 x= 0.01336 0.04644 0.02118 0.08446 0.04203 0.14214 0.15014 0.22346 1 h-lim-p 0.0005 0.0039 246.5526 3118.350729 3 0.0001 30 | 0/8 2 h-lim-p 0.0002 0.0016 41.5133 3118.239992 7 0.0001 57 | 0/8 3 h-lim-p 0.0003 0.0045 18.8768 3118.223250 4 0.0001 77 | 0/8 4 h-lim-p 0.0004 0.0071 5.9205 3118.219527 5 0.0002 102 | 0/8 5 h-lim-p 0.0014 0.2398 0.9759 3118.219431 3 0.0002 123 | 0/8 6 h-lim-p 0.0007 0.4497 0.3056 3118.219423 1 0.0002 146 | 0/8 7 h-lim-p 0.0141 8.0513 0.0036 3118.219422 0 0.0062 166 | 0/8 8 h-lim-p 0.0073 12.1439 0.0031 3118.219229 0 0.0581 189 | 0/8 9 h-lim-p 1.8073 20.0000 0.0001 3118.219226 1 0.8895 212 | 0/8 10 h-lim-p 1.3431 20.0000 0.0001 3118.219226 0 1.1752 232 | 0/8 11 h-lim-p 1.8048 20.0000 0.0000 3118.219226 0 1.5792 252 | 0/8 12 h-lim-p 0.6349 20.0000 0.0001 3118.219226 0 0.0099 277 | 0/8 13 h-lim-p 0.0001 1.6262 0.0105 3118.219226 0 0.0000 304 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 3118.219226 0 0.0000 330 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 3118.219226 0 0.0000 354 Out... lnL = -3118.219226 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3118.219226 Node 7: lnL = -3118.219226 Node 8: lnL = -3118.219226 Node 9: lnL = -3118.219226 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 307 Sequential format.. Reading seq # 1: YHR163W_Sbay Reading seq # 2: YHR163W_Scer Reading seq # 3: YHR163W_Skud Reading seq # 4: YHR163W_Smik Reading seq # 5: YHR163W_Spar Sequences read.. Counting patterns.. # site patterns = 109 Counting frequencies.. 120 bytes for distance 17440 bytes for lkl0 13952 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.028272 0.075002 0.076180 0.032658 0.105507 0.164380 0.177639 lnL0 = -1036.051891 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1036.051891 x= 0.00006 0.02827 0.07500 0.07618 0.03266 0.10551 0.16438 0.17764 1 h-lim-p 0.0000 0.0000 301.9684 1035.860783 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0036 67.3051 1033.988952 0 0.0013 41 | 1/8 3 h-lim-p 0.0004 0.0035 38.4252 1033.598540 0 0.0006 53 | 1/8 4 h-lim-p 0.0023 0.0186 5.9439 1033.586237 2 0.0005 70 | 0/8 5 h-lim-p 0.0002 0.0377 15.0718 1033.483429 0 0.0009 84 | 0/8 6 h-lim-p 0.0019 0.0151 6.6734 1033.457283 4 0.0010 105 | 0/8 7 h-lim-p 0.0016 0.0509 4.0031 1033.430151 2 0.0015 121 | 0/8 8 h-lim-p 0.0027 0.0579 2.2081 1032.979612 0 0.0163 135 | 0/8 9 h-lim-p 0.0025 0.0203 3.7285 1025.749672 m 0.0203 147 | 0/8 10 h-lim-p 0.0000 0.0000 0.0236 h-lim-p: 2.03219077e-17 1.62575262e-16 2.35862192e-02 1025.749672 .. | 0/8 11 h-lim-p 0.0000 0.0182 59.8382 1024.724457 0 0.0006 181 | 0/8 12 h-lim-p 0.0001 0.0004 36.0926 1024.385740 m 0.0004 193 | 1/8 13 h-lim-p 0.0015 0.0201 10.1418 1024.352273 2 0.0007 209 | 1/8 14 h-lim-p 0.0022 0.0213 3.2913 1024.348198 5 0.0008 233 | 1/8 15 h-lim-p 0.0037 0.3112 0.7272 1024.347611 3 0.0015 251 | 1/8 16 h-lim-p 0.0213 2.5404 0.0526 1024.317673 0 0.1707 273 | 1/8 17 h-lim-p 0.0022 0.0244 4.0082 1024.244312 0 0.0034 292 | 1/8 18 h-lim-p 1.8896 18.9451 0.0071 1024.241668 6 0.3283 320 | 1/8 19 h-lim-p 0.0047 0.2293 0.4983 1024.241557 4 0.0009 349 | 1/8 20 h-lim-p 0.1938 20.0000 0.0022 1024.240296 0 0.7752 370 | 0/8 21 h-lim-p 0.0480 20.0000 0.0356 1024.240295 0 0.0013 393 | 0/8 22 h-lim-p 0.1061 0.9644 0.0004 1024.240192 1 0.8485 417 | 0/8 23 h-lim-p 0.0239 0.1909 0.0000 1024.240192 m 0.1909 437 | 1/8 24 h-lim-p 0.0928 20.0000 0.0001 1024.240192 0 0.0406 457 | 1/8 25 h-lim-p 0.9725 20.0000 0.0000 1024.240192 0 1.9451 477 | 1/8 26 h-lim-p 2.5000 20.0000 0.0000 1024.240192 0 2.1875 496 | 1/8 27 h-lim-p 2.4048 20.0000 0.0000 1024.240192 0 1.0521 515 | 1/8 28 h-lim-p 2.5000 20.0000 0.0000 1024.240192 0 5.0000 535 | 1/8 29 h-lim-p 1.2474 20.0000 0.0000 1024.240192 0 0.0097 560 Out... lnL = -1024.240192 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1024.240192 Node 7: lnL = -1024.240192 Node 8: lnL = -1024.240192 Node 9: lnL = -1024.240192 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 316 Sequential format.. Reading seq # 1: YHR166C_Sbay Reading seq # 2: YHR166C_Scer Reading seq # 3: YHR166C_Skud Reading seq # 4: YHR166C_Smik Reading seq # 5: YHR166C_Spar Sequences read.. Counting patterns.. # site patterns = 147 Counting frequencies.. 120 bytes for distance 23520 bytes for lkl0 18816 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.096271 0.132090 0.188530 0.059017 0.221759 0.305061 0.385710 lnL0 = -1526.703339 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1526.703339 x= 0.00006 0.09627 0.13209 0.18853 0.05902 0.22176 0.30506 0.38571 1 h-lim-p 0.0000 0.0000 126.8010 1526.640752 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0019 102.9206 1522.499001 8 0.0010 61 | 1/8 3 h-lim-p 0.0010 0.0082 47.9425 1521.452254 1 0.0013 75 | 1/8 4 h-lim-p 0.0081 0.0675 7.5029 1521.407436 7 0.0015 105 | 1/8 5 h-lim-p 0.0043 0.1659 2.5674 1521.385380 2 0.0033 121 | 1/8 6 h-lim-p 0.0050 0.3275 1.7183 1521.322482 0 0.0100 134 | 1/8 7 h-lim-p 0.0050 0.0650 3.4643 1520.766882 0 0.0099 147 | 0/8 8 h-lim-p 0.0024 0.0294 14.0265 1519.193278 0 0.0049 160 | 0/8 9 h-lim-p 0.0008 0.0065 12.3056 1518.247684 m 0.0065 172 | 1/8 10 h-lim-p 1.1995 9.6629 0.0415 1518.178650 7 0.3969 199 | 0/8 11 h-lim-p 0.0056 0.2338 2.9311 1518.164584 6 0.0046 232 | 0/8 12 h-lim-p 0.1429 1.1432 0.0180 1518.073353 m 1.1432 244 | 1/8 13 h-lim-p 2.5000 20.0000 0.0047 1518.068062 6 0.7907 280 | 0/8 14 h-lim-p 0.0044 0.3964 0.8555 1518.067206 5 0.0025 312 | 0/8 15 h-lim-p 2.5000 20.0000 0.0006 1518.067067 2 0.9644 336 | 0/8 16 h-lim-p 2.5000 20.0000 0.0001 1518.067065 0 1.2500 356 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1518.067065 0 1.0938 376 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1518.067065 0 1.0938 396 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1518.067065 0 0.9375 417 | 0/8 20 h-lim-p 0.5073 20.0000 0.0000 1518.067065 0 0.0079 442 Out... lnL = -1518.067065 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1518.067065 Node 7: lnL = -1518.067065 Node 8: lnL = -1518.067065 Node 9: lnL = -1518.067065 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 314 Sequential format.. Reading seq # 1: YHR167W_Sbay Reading seq # 2: YHR167W_Scer Reading seq # 3: YHR167W_Skud Reading seq # 4: YHR167W_Smik Reading seq # 5: YHR167W_Spar Sequences read.. Counting patterns.. # site patterns = 154 Counting frequencies.. 120 bytes for distance 24640 bytes for lkl0 19712 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.101625 0.153133 0.182663 0.060595 0.219507 0.318202 0.396198 lnL0 = -1532.780796 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1532.780796 x= 0.00006 0.10163 0.15313 0.18266 0.06059 0.21951 0.31820 0.39620 1 h-lim-p 0.0000 0.0000 147.2213 1532.713079 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0022 122.7455 1525.395243 3 0.0013 46 | 1/8 3 h-lim-p 0.0006 0.0050 68.0806 1523.984217 0 0.0012 59 | 1/8 4 h-lim-p 0.0067 0.0539 7.1955 1523.938411 2 0.0016 76 | 1/8 5 h-lim-p 0.0028 0.0995 4.0591 1523.916829 6 0.0019 104 | 0/8 6 h-lim-p 0.0011 0.1143 7.2483 1523.818668 0 0.0044 118 | 0/8 7 h-lim-p 0.0071 0.0636 4.4340 1523.768375 7 0.0030 144 | 0/8 8 h-lim-p 0.0088 0.1510 1.5336 1523.366120 0 0.0264 157 | 0/8 9 h-lim-p 0.0025 0.0200 4.7280 1520.077757 m 0.0200 169 | 1/8 10 h-lim-p 1.7302 13.8416 0.0314 1519.919916 5 0.7499 191 | 0/8 11 h-lim-p 0.0038 0.1373 6.2407 1519.875361 5 0.0030 220 | 0/8 12 h-lim-p 2.5000 20.0000 0.0052 1519.861296 7 1.3704 249 | 0/8 13 h-lim-p 2.5000 20.0000 0.0012 1519.860580 2 1.1719 273 | 0/8 14 h-lim-p 2.5000 20.0000 0.0004 1519.860502 2 1.0938 297 | 0/8 15 h-lim-p 2.5000 20.0000 0.0001 1519.860500 0 1.0938 317 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1519.860500 0 1.0938 337 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1519.860500 0 1.2500 357 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1519.860500 0 0.0195 383 Out... lnL = -1519.860500 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1519.860500 Node 7: lnL = -1519.860500 Node 8: lnL = -1519.860500 Node 9: lnL = -1519.860500 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 378 Sequential format.. Reading seq # 1: YHR169W_Sbay Reading seq # 2: YHR169W_Scer Reading seq # 3: YHR169W_Skud Reading seq # 4: YHR169W_Smik Reading seq # 5: YHR169W_Spar Sequences read.. Counting patterns.. # site patterns = 136 Counting frequencies.. 120 bytes for distance 21760 bytes for lkl0 17408 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.101128 0.081015 0.159619 0.062758 0.181684 0.165790 0.252743 lnL0 = -1432.551398 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1432.551398 x= 0.00006 0.10113 0.08101 0.15962 0.06276 0.18168 0.16579 0.25274 1 h-lim-p 0.0000 0.0000 89.3538 1432.444804 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0048 29.2145 1432.140797 0 0.0007 38 | 1/8 3 h-lim-p 0.0028 0.0262 6.9581 1432.115716 6 0.0010 64 | 1/8 4 h-lim-p 0.0026 0.1015 2.6952 1432.106177 6 0.0018 91 | 1/8 5 h-lim-p 0.0071 0.4174 0.6843 1432.047241 0 0.0142 104 | 1/8 6 h-lim-p 0.0077 0.0761 1.2643 1430.626129 0 0.0307 125 | 1/8 7 h-lim-p 0.0034 0.0272 7.8897 1430.593337 7 0.0010 157 | 1/8 8 h-lim-p 0.0518 1.0087 0.1565 1430.592846 3 0.0052 177 | 1/8 9 h-lim-p 0.0119 4.3820 0.0678 1430.538395 0 0.0956 199 | 1/8 10 h-lim-p 2.5000 20.0000 0.0013 1430.537327 5 0.7837 231 | 1/8 11 h-lim-p 2.5000 20.0000 0.0002 1430.537295 2 0.9961 254 | 0/8 12 h-lim-p -0.0000 -0.0000 0.0000 h-lim-p: -7.91777708e-18 -6.33422166e-17 2.26473439e-05 1430.537295 .. | 1/8 13 h-lim-p 0.0000 20.0000 0.0124 1430.537295 0 0.0006 295 | 1/8 14 h-lim-p 0.0021 20.0000 0.0037 1430.537295 0 0.0009 314 | 1/8 15 h-lim-p 0.0032 20.0000 0.0011 1430.537295 0 0.0001 337 | 1/8 16 h-lim-p 0.0002 20.0000 0.0006 1430.537295 0 0.0012 359 | 1/8 17 h-lim-p 0.0049 20.0000 0.0002 1430.537295 0 0.0000 385 | 1/8 18 h-lim-p 0.0001 20.0000 0.0000 1430.537295 0 0.0001 404 | 1/8 19 h-lim-p 0.0003 20.0000 0.0000 1430.537295 0 0.0328 429 | 1/8 20 h-lim-p 0.0015 20.0000 0.0003 1430.537295 0 0.0023 448 | 1/8 21 h-lim-p 1.3043 20.0000 0.0000 1430.537295 0 0.0051 474 Out... lnL = -1430.537295 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1430.537295 Node 7: lnL = -1430.537295 Node 8: lnL = -1430.537295 Node 9: lnL = -1430.537295 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 396 Sequential format.. Reading seq # 1: YHR170W_Sbay Reading seq # 2: YHR170W_Scer Reading seq # 3: YHR170W_Skud Reading seq # 4: YHR170W_Smik Reading seq # 5: YHR170W_Spar Sequences read.. Counting patterns.. # site patterns = 184 Counting frequencies.. 120 bytes for distance 29440 bytes for lkl0 23552 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.207987 0.172589 0.194972 0.068968 0.198139 0.223408 0.283985 lnL0 = -1748.328270 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1748.328270 x= 0.00006 0.20799 0.17259 0.19497 0.06897 0.19814 0.22341 0.28398 1 h-lim-p 0.0000 0.0000 196.6528 1748.266238 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0025 131.6474 1742.133926 0 0.0010 40 | 1/8 3 h-lim-p 0.0011 0.0090 25.4216 1741.758566 5 0.0012 62 | 1/8 4 h-lim-p 0.0066 0.0681 4.6314 1741.706686 4 0.0025 82 | 1/8 5 h-lim-p 0.0141 0.4038 0.8317 1740.156089 0 0.0848 96 | 0/8 6 h-lim-p -0.0000 -0.0000 15.0423 h-lim-p: -1.55616131e-21 -1.24492905e-20 1.50422697e+01 1740.156089 .. | 0/8 7 h-lim-p 0.0000 0.0009 154.9648 1733.142697 9 0.0005 149 | 0/8 8 h-lim-p 0.0007 0.0058 58.3541 1732.203586 5 0.0006 170 | 0/8 9 h-lim-p 0.0016 0.0124 20.3303 1732.090739 6 0.0006 195 | 0/8 10 h-lim-p 0.0032 0.1108 3.9497 1732.085775 4 0.0007 217 | 0/8 11 h-lim-p 0.0017 0.0135 1.3096 1732.085296 4 0.0006 238 | 0/8 12 h-lim-p 0.0056 1.4168 0.1435 1732.085287 1 0.0007 254 | 0/8 13 h-lim-p 0.0099 20.0000 0.0100 1732.085239 0 0.0297 275 | 0/8 14 h-lim-p 0.0054 1.9998 0.0546 1732.084187 0 0.0218 297 | 0/8 15 h-lim-p 2.5000 20.0000 0.0003 1732.084107 3 0.8171 324 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1732.084107 0 1.0938 344 | 0/8 17 h-lim-p 2.2015 20.0000 0.0000 1732.084107 0 0.9632 364 | 0/8 18 h-lim-p 0.5407 20.0000 0.0000 1732.084107 0 0.0037 390 | 0/8 19 h-lim-p 0.0006 20.0000 0.0002 1732.084107 0 0.0006 410 | 0/8 20 h-lim-p 0.0002 13.1432 0.0008 1732.084107 0 0.0000 436 | 0/8 21 h-lim-p 0.0002 20.0000 0.0000 1732.084107 0 0.0000 471 Out... lnL = -1732.084107 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1732.084107 Node 7: lnL = -1732.084107 Node 8: lnL = -1732.084107 Node 9: lnL = -1732.084107 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 371 Sequential format.. Reading seq # 1: YHR171W_Sbay Reading seq # 2: YHR171W_Scer Reading seq # 3: YHR171W_Skud Reading seq # 4: YHR171W_Smik Reading seq # 5: YHR171W_Spar Sequences read.. Counting patterns.. # site patterns = 142 Counting frequencies.. 120 bytes for distance 22720 bytes for lkl0 18176 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.206314 0.163072 0.178532 0.067547 0.158287 0.228508 0.254501 lnL0 = -1547.735691 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1547.735691 x= 0.00006 0.20631 0.16307 0.17853 0.06755 0.15829 0.22851 0.25450 1 h-lim-p 0.0000 0.0000 221.9439 1547.662341 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0017 160.9564 1540.554864 0 0.0006 40 | 1/8 3 h-lim-p 0.0007 0.0054 34.5398 1539.911000 0 0.0014 53 | 1/8 4 h-lim-p 0.0084 0.0672 5.0938 1539.842458 7 0.0026 85 | 1/8 5 h-lim-p 0.0054 0.1480 2.3946 1539.319259 0 0.0163 98 | 1/8 6 h-lim-p 0.0029 0.0231 5.5128 1534.857018 0 0.0115 112 | 1/8 7 h-lim-p 0.0007 0.0055 59.0130 1528.400211 0 0.0014 125 | 1/8 8 h-lim-p 0.0115 0.0922 3.4698 1528.391950 4 0.0011 147 | 1/8 9 h-lim-p 0.0587 1.5212 0.0657 1527.762947 0 0.3521 161 | 1/8 10 h-lim-p 1.6382 20.0000 0.0141 1527.699651 7 0.5903 196 | 1/8 11 h-lim-p 2.5000 20.0000 0.0028 1527.697683 2 0.5859 220 | 1/8 12 h-lim-p 2.5000 20.0000 0.0006 1527.697594 2 0.5859 244 | 0/8 13 h-lim-p 0.0031 7.8090 0.1068 1527.697588 2 0.0010 269 | 0/8 14 h-lim-p 0.1840 1.4723 0.0001 1527.697586 0 0.7361 291 | 0/8 15 h-lim-p 0.0217 0.1739 0.0004 1527.697586 0 0.0000 326 | 0/8 16 h-lim-p 0.0000 0.0004 0.1561 .. | 0/8 17 h-lim-p 0.0000 0.0008 0.0720 | 0/8 18 h-lim-p 0.0000 0.0008 0.0720 Out... lnL = -1527.697586 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1527.697586 Node 7: lnL = -1527.697586 Node 8: lnL = -1527.697586 Node 9: lnL = -1527.697586 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 356 Sequential format.. Reading seq # 1: YHR175W_Sbay Reading seq # 2: YHR175W_Scer Reading seq # 3: YHR175W_Skud Reading seq # 4: YHR175W_Smik Reading seq # 5: YHR175W_Spar Sequences read.. Counting patterns.. # site patterns = 154 Counting frequencies.. 120 bytes for distance 24640 bytes for lkl0 19712 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.022335 0.078718 0.000060 0.014799 0.136635 0.124545 0.148350 0.238403 lnL0 = -1385.250183 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1385.250183 x= 0.02233 0.07872 0.00006 0.01480 0.13664 0.12454 0.14835 0.23840 1 h-lim-p 0.0001 0.2279 508.0585 1374.962144 1 0.0001 24 | 0/8 2 h-lim-p 0.0003 0.0024 86.9069 1372.714526 0 0.0006 37 | 0/8 3 h-lim-p 0.0013 0.0105 23.6049 1372.522324 8 0.0008 70 | 0/8 4 h-lim-p 0.0015 0.0122 11.1298 1372.493460 7 0.0006 99 | 0/8 5 h-lim-p 0.0019 0.0534 3.2833 1372.489395 4 0.0008 118 | 0/8 6 h-lim-p 0.0201 0.5485 0.1375 1372.489378 2 0.0013 137 | 0/8 7 h-lim-p 0.0047 4.4388 0.0383 1372.489349 1 0.0059 159 | 0/8 8 h-lim-p 0.0118 4.0953 0.0192 1372.485182 0 0.1416 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 1372.484418 5 1.7288 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0003 1372.484176 4 1.7557 246 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1372.484176 0 1.0938 266 | 0/8 12 h-lim-p 1.5477 20.0000 0.0000 1372.484176 0 1.5477 286 | 0/8 13 h-lim-p 2.0167 20.0000 0.0000 1372.484176 0 0.1103 309 | 0/8 14 h-lim-p 0.0327 20.0000 0.0000 1372.484176 0 0.0327 329 | 0/8 15 h-lim-p 0.0158 20.0000 0.0000 1372.484176 0 0.0020 351 | 0/8 16 h-lim-p 0.0012 20.0000 0.0001 1372.484176 0 0.0012 371 | 0/8 17 h-lim-p 0.0004 20.0000 0.0002 1372.484176 0 0.0000 395 | 0/8 18 h-lim-p 0.0003 20.0000 0.0000 1372.484176 0 0.0000 425 | 0/8 19 h-lim-p 0.0000 20.0000 0.0010 1372.484176 0 0.0000 452 | 0/8 20 h-lim-p 0.0000 20.0000 0.0002 1372.484176 0 0.0000 472 | 0/8 21 h-lim-p 0.0000 20.0000 0.0001 1372.484176 0 0.0000 508 | 0/8 22 h-lim-p 0.0000 20.0000 0.0010 | 0/8 23 h-lim-p 0.0000 20.0000 0.0010 Out... lnL = -1372.484176 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1372.484176 Node 7: lnL = -1372.484176 Node 8: lnL = -1372.484176 Node 9: lnL = -1372.484176 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 875 Sequential format.. Reading seq # 1: YHR178W_Sbay Reading seq # 2: YHR178W_Scer Reading seq # 3: YHR178W_Skud Reading seq # 4: YHR178W_Smik Reading seq # 5: YHR178W_Spar Sequences read.. Counting patterns.. # site patterns = 280 Counting frequencies.. 120 bytes for distance 44800 bytes for lkl0 35840 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.007758 0.084285 0.077459 0.140269 0.069481 0.183787 0.195682 0.322511 lnL0 = -3924.857990 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3924.857990 x= 0.00776 0.08429 0.07746 0.14027 0.06948 0.18379 0.19568 0.32251 1 h-lim-p 0.0035 0.0276 115.7116 3923.588321 2 0.0002 29 | 0/8 2 h-lim-p 0.0004 0.0035 24.8763 3923.517828 6 0.0002 54 | 0/8 3 h-lim-p 0.0004 0.0039 15.3188 3923.493935 5 0.0003 78 | 0/8 4 h-lim-p 0.0010 0.0574 4.0615 3923.491290 4 0.0004 100 | 0/8 5 h-lim-p 0.0025 1.1879 0.5756 3923.491224 2 0.0004 119 | 0/8 6 h-lim-p 0.0079 12.0253 0.0303 3923.491224 0 0.0009 141 | 0/8 7 h-lim-p 0.0059 20.0000 0.0044 3923.491222 0 0.0059 161 | 0/8 8 h-lim-p 0.0033 5.1175 0.0079 3923.491043 0 0.0397 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3923.491041 0 1.0938 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3923.491041 0 1.0938 224 | 0/8 11 h-lim-p 0.8983 20.0000 0.0000 3923.491041 0 0.0140 249 | 0/8 12 h-lim-p 0.0011 20.0000 0.0004 3923.491041 0 0.0000 274 | 0/8 13 h-lim-p 0.0004 20.0000 0.0000 3923.491041 0 0.0000 307 | 0/8 14 h-lim-p 0.0000 20.0000 0.0014 | 0/8 15 h-lim-p 0.0000 20.0000 0.0014 Out... lnL = -3923.491041 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3923.491041 Node 7: lnL = -3923.491041 Node 8: lnL = -3923.491041 Node 9: lnL = -3923.491041 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 861 Sequential format.. Reading seq # 1: YHR179W_Sbay Reading seq # 2: YHR179W_Scer Reading seq # 3: YHR179W_Skud Reading seq # 4: YHR179W_Smik Reading seq # 5: YHR179W_Spar Sequences read.. Counting patterns.. # site patterns = 368 Counting frequencies.. 120 bytes for distance 58880 bytes for lkl0 47104 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.034108 0.139076 0.131944 0.110975 0.264278 0.266167 0.378386 lnL0 = -4193.238128 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4193.238128 x= 0.00006 0.03411 0.13908 0.13194 0.11097 0.26428 0.26617 0.37839 1 h-lim-p 0.0005 0.0044 174.1102 4189.660888 3 0.0003 29 | 0/8 2 h-lim-p 0.0007 0.0053 27.1350 4189.527807 5 0.0004 52 | 0/8 3 h-lim-p 0.0006 0.0245 17.4617 4189.481041 6 0.0004 78 | 0/8 4 h-lim-p 0.0009 0.0318 7.9912 4189.470021 3 0.0004 96 | 0/8 5 h-lim-p 0.0055 0.6404 0.6447 4189.469854 3 0.0008 118 | 0/8 6 h-lim-p 0.0028 3.0746 0.1861 4189.469830 2 0.0014 143 | 0/8 7 h-lim-p 0.0007 1.4944 0.3763 4189.468877 0 0.0434 169 | 0/8 8 h-lim-p 0.0153 0.4013 1.0692 4189.468830 2 0.0006 197 | 0/8 9 h-lim-p 0.2432 9.4532 0.0027 4189.468785 0 0.9726 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 4189.468785 0 1.0938 231 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4189.468785 0 1.0938 251 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4189.468785 0 0.0781 275 | 0/8 13 h-lim-p 0.0098 20.0000 0.0000 4189.468785 0 0.0098 295 | 0/8 14 h-lim-p 0.0032 20.0000 0.0001 4189.468785 0 0.0008 316 | 0/8 15 h-lim-p 0.0006 20.0000 0.0001 4189.468785 0 0.0000 351 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 | 0/8 17 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -4189.468785 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4189.468785 Node 7: lnL = -4189.468785 Node 8: lnL = -4189.468785 Node 9: lnL = -4189.468785 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 895 Sequential format.. Reading seq # 1: YHR181W_Sbay Reading seq # 2: YHR181W_Scer Reading seq # 3: YHR181W_Skud Reading seq # 4: YHR181W_Smik Reading seq # 5: YHR181W_Spar Sequences read.. Counting patterns.. # site patterns = 443 Counting frequencies.. 120 bytes for distance 70880 bytes for lkl0 56704 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.415001 0.308714 0.349469 0.148052 0.383933 0.536897 0.522181 lnL0 = -4672.047679 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4672.047679 x= 0.00006 0.41500 0.30871 0.34947 0.14805 0.38393 0.53690 0.52218 1 h-lim-p 0.0000 0.0000 390.7297 4671.905025 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0013 329.3531 4620.784527 m 0.0013 38 | 1/8 3 h-lim-p -0.0000 -0.0000 101.7786 h-lim-p: -7.49945703e-19 -5.99956563e-18 1.01778622e+02 4620.784527 .. | 1/8 4 h-lim-p 0.0000 0.0013 296.3278 4587.485117 0 0.0006 64 | 1/8 5 h-lim-p 0.0003 0.0023 47.4999 4587.026190 0 0.0004 76 | 1/8 6 h-lim-p 0.0009 0.0225 22.5917 4586.830872 4 0.0009 96 | 1/8 7 h-lim-p 0.0017 0.0535 12.2770 4586.763737 7 0.0012 125 | 1/8 8 h-lim-p 0.0025 0.1508 5.8266 4586.751402 5 0.0009 147 | 1/8 9 h-lim-p 0.0309 1.8478 0.1780 4586.751024 2 0.0072 164 | 0/8 10 h-lim-p 0.0014 0.4941 0.9373 4586.750231 2 0.0015 188 | 0/8 11 h-lim-p 0.0036 1.5681 0.4061 4586.749031 0 0.0072 209 | 0/8 12 h-lim-p 0.0114 0.0912 0.0800 4586.729333 0 0.0456 231 | 0/8 13 h-lim-p 0.2910 2.3281 0.0012 4586.728092 0 1.1641 253 | 0/8 14 h-lim-p 2.5000 20.0000 0.0002 4586.728043 1 0.9961 275 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 4586.728043 0 1.0938 295 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 4586.728043 0 1.0938 315 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 4586.728043 0 0.1562 338 | 0/8 18 h-lim-p 0.0860 20.0000 0.0000 4586.728043 0 0.0430 358 Out... lnL = -4586.728043 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4586.728043 Node 7: lnL = -4586.728043 Node 8: lnL = -4586.728043 Node 9: lnL = -4586.728043 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 329 Sequential format.. Reading seq # 1: YHR182W_Sbay Reading seq # 2: YHR182W_Scer Reading seq # 3: YHR182W_Skud Reading seq # 4: YHR182W_Smik Reading seq # 5: YHR182W_Spar Sequences read.. Counting patterns.. # site patterns = 134 Counting frequencies.. 120 bytes for distance 21440 bytes for lkl0 17152 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.050054 0.172790 0.053220 0.013902 0.194806 0.238565 0.277273 lnL0 = -1346.717600 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1346.717600 x= 0.00006 0.05005 0.17279 0.05322 0.01390 0.19481 0.23856 0.27727 1 h-lim-p 0.0000 0.0001 161.0880 1345.461138 0 0.0001 24 | 0/8 2 h-lim-p 0.0001 0.0006 51.9833 1345.208353 0 0.0002 37 | 0/8 3 h-lim-p 0.0000 0.0001 22.1658 1345.171420 m 0.0001 49 | 1/8 4 h-lim-p 0.0003 0.0165 8.3130 1345.151557 0 0.0008 62 | 1/8 5 h-lim-p 0.0034 0.1966 1.8739 1345.149346 5 0.0012 86 | 1/8 6 h-lim-p 0.0067 0.8598 0.3479 1345.148418 4 0.0046 108 | 0/8 7 h-lim-p 0.0008 0.3897 2.0955 1345.141665 0 0.0030 129 | 0/8 8 h-lim-p 0.0017 0.1052 3.6619 1345.120148 0 0.0070 143 | 0/8 9 h-lim-p 0.0352 0.2813 0.1253 1345.025328 0 0.2110 157 | 0/8 10 h-lim-p 2.3870 19.0962 0.0019 1345.022151 4 0.4680 186 | 0/8 11 h-lim-p 1.1007 20.0000 0.0008 1345.021925 3 0.8771 212 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1345.021925 0 1.0938 232 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1345.021925 0 0.0000 269 Out... lnL = -1345.021925 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1345.021925 Node 7: lnL = -1345.021925 Node 8: lnL = -1345.021925 Node 9: lnL = -1345.021925 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 824 Sequential format.. Reading seq # 1: YHR183W_Sbay Reading seq # 2: YHR183W_Scer Reading seq # 3: YHR183W_Skud Reading seq # 4: YHR183W_Smik Reading seq # 5: YHR183W_Spar Sequences read.. Counting patterns.. # site patterns = 122 Counting frequencies.. 120 bytes for distance 19520 bytes for lkl0 15616 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.034054 0.102639 0.105546 0.054815 0.120443 0.137742 0.141875 lnL0 = -1982.014055 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1982.014055 x= 0.00006 0.03405 0.10264 0.10555 0.05482 0.12044 0.13774 0.14187 1 h-lim-p 0.0000 0.0000 235.4964 1981.873748 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0008 167.9033 1977.772941 0 0.0003 39 | 1/8 3 h-lim-p 0.0005 0.0040 28.1929 1977.598695 3 0.0005 57 | 1/8 4 h-lim-p 0.0019 0.0401 6.6541 1977.581015 6 0.0006 83 | 1/8 5 h-lim-p 0.0048 0.2388 0.8593 1977.359592 0 0.0191 97 | 1/8 6 h-lim-p 0.0026 0.0206 4.3123 1974.280792 0 0.0103 118 | 1/8 7 h-lim-p 0.0002 0.0013 67.8348 1972.338909 0 0.0005 131 | 1/8 8 h-lim-p 0.0010 0.0077 23.9864 1972.210535 2 0.0005 147 | 1/8 9 h-lim-p 0.2905 2.7370 0.0375 1971.613252 0 0.4357 159 | 0/8 10 h-lim-p 0.0061 2.7047 2.6833 1971.611469 5 0.0005 194 | 0/8 11 h-lim-p 0.1355 2.3900 0.0095 1971.538933 0 0.5419 208 | 0/8 12 h-lim-p 0.3263 2.6108 0.0016 1971.536562 0 0.6527 229 | 0/8 13 h-lim-p 2.5000 20.0000 0.0004 1971.536297 4 0.8875 258 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1971.536294 1 0.9961 280 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1971.536294 0 1.0938 300 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1971.536294 0 1.0938 320 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1971.536294 0 1.0938 340 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1971.536294 0 0.0391 365 | 0/8 19 h-lim-p 0.0037 20.0000 0.0000 1971.536294 0 0.0000 403 Out... lnL = -1971.536294 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1971.536294 Node 7: lnL = -1971.536294 Node 8: lnL = -1971.536294 Node 9: lnL = -1971.536294 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 338 Sequential format.. Reading seq # 1: YHR184W_Sbay Reading seq # 2: YHR184W_Scer Reading seq # 3: YHR184W_Skud Reading seq # 4: YHR184W_Smik Reading seq # 5: YHR184W_Spar Sequences read.. Counting patterns.. # site patterns = 153 Counting frequencies.. 120 bytes for distance 24480 bytes for lkl0 19584 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.008379 0.058212 0.066654 0.074028 0.054860 0.215571 0.165540 0.264710 lnL0 = -1390.542086 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1390.542086 x= 0.00838 0.05821 0.06665 0.07403 0.05486 0.21557 0.16554 0.26471 1 h-lim-p 0.0103 0.1606 52.0604 1390.034833 9 0.0004 51 | 0/8 2 h-lim-p 0.0007 0.0055 16.5205 1389.981487 7 0.0004 81 | 0/8 3 h-lim-p 0.0006 0.0127 11.2237 1389.950422 1 0.0008 95 | 0/8 4 h-lim-p 0.0041 0.0332 1.1928 1389.950030 4 0.0006 117 | 0/8 5 h-lim-p 0.0018 0.0792 0.3712 1389.949986 2 0.0007 133 | 0/8 6 h-lim-p 0.0033 0.6851 0.0790 1389.949984 0 0.0008 154 | 0/8 7 h-lim-p 0.0082 20.0000 0.0079 1389.949974 0 0.0164 175 | 0/8 8 h-lim-p 0.0093 5.3478 0.0140 1389.949618 0 0.0740 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1389.949580 2 0.9961 222 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1389.949580 0 2.1875 242 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1389.949580 0 1.0938 262 | 0/8 12 h-lim-p 0.0999 20.0000 0.0000 1389.949580 0 6.3948 288 | 0/8 13 h-lim-p 0.1656 20.0000 0.0006 1389.949580 0 0.0725 308 | 0/8 14 h-lim-p 0.0163 8.0437 0.0026 1389.949580 0 0.0020 330 | 0/8 15 h-lim-p 0.0006 2.2575 0.0093 1389.949580 0 0.0003 350 | 0/8 16 h-lim-p 0.0003 2.2571 0.0093 1389.949580 0 0.0000 390 | 0/8 17 h-lim-p 0.0000 20.0000 0.0011 1389.949580 0 0.0000 413 | 0/8 18 h-lim-p 0.0000 20.0000 0.0003 1389.949580 0 0.0013 440 | 0/8 19 h-lim-p 0.0076 20.0000 0.0001 1389.949580 0 0.0001 465 | 0/8 20 h-lim-p 0.0002 20.0000 0.0000 1389.949580 0 0.0069 490 | 0/8 21 h-lim-p 0.0026 20.0000 0.0001 1389.949580 0 0.0006 511 | 0/8 22 h-lim-p 0.0000 17.9124 0.0012 1389.949580 0 0.0000 531 | 0/8 23 h-lim-p 0.0000 17.3169 0.0014 1389.949580 0 0.0000 565 | 0/8 24 h-lim-p 0.0000 20.0000 0.0017 | 0/8 25 h-lim-p 0.0000 20.0000 0.0017 Out... lnL = -1389.949580 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1389.949580 Node 7: lnL = -1389.949580 Node 8: lnL = -1389.949580 Node 9: lnL = -1389.949580 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 700 Sequential format.. Reading seq # 1: YHR185C_Sbay Reading seq # 2: YHR185C_Scer Reading seq # 3: YHR185C_Skud Reading seq # 4: YHR185C_Smik Reading seq # 5: YHR185C_Spar Sequences read.. Counting patterns.. # site patterns = 287 Counting frequencies.. 120 bytes for distance 45920 bytes for lkl0 36736 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.105822 0.141052 0.394003 0.190495 0.510882 0.269734 0.416486 lnL0 = -3667.118625 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3667.118625 x= 0.00006 0.10582 0.14105 0.39400 0.19049 0.51088 0.26973 0.41649 1 h-lim-p 0.0000 0.0000 456.0621 3666.722390 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0003 696.2411 3606.097048 m 0.0003 36 | 2/8 3 h-lim-p 0.0002 0.0017 179.2791 3597.874321 0 0.0008 50 | 2/8 4 h-lim-p 0.0010 0.0077 40.2137 3596.578537 1 0.0012 64 | 2/8 5 h-lim-p 0.0006 0.0085 84.6408 3594.766081 0 0.0009 76 | 2/8 6 h-lim-p 0.0047 0.0525 15.4717 3593.780585 3 0.0039 94 | 2/8 7 h-lim-p 0.0047 0.0444 12.7694 3593.664579 6 0.0014 122 | 2/8 8 h-lim-p 0.1426 1.1408 0.0859 3592.087993 0 0.5704 136 | 1/8 9 h-lim-p 0.0003 0.0025 30.6876 3592.048827 2 0.0001 158 | 1/8 10 h-lim-p 0.2410 1.9494 0.0187 3591.797723 0 0.7231 171 | 0/8 11 h-lim-p 0.0290 1.1348 0.4659 3591.797563 2 0.0014 197 | 0/8 12 h-lim-p 0.1299 1.7053 0.0050 3591.793127 0 0.7794 219 | 0/8 13 h-lim-p 2.5000 20.0000 0.0010 3591.792853 1 1.0938 241 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 3591.792852 0 1.0938 261 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 3591.792852 0 1.0938 281 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 3591.792852 0 0.3125 303 | 0/8 17 h-lim-p 0.4462 20.0000 0.0000 3591.792852 0 0.0030 329 Out... lnL = -3591.792852 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3591.792852 Node 7: lnL = -3591.792852 Node 8: lnL = -3591.792852 Node 9: lnL = -3591.792852 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 341 Sequential format.. Reading seq # 1: YHR187W_Sbay Reading seq # 2: YHR187W_Scer Reading seq # 3: YHR187W_Skud Reading seq # 4: YHR187W_Smik Reading seq # 5: YHR187W_Spar Sequences read.. Counting patterns.. # site patterns = 147 Counting frequencies.. 120 bytes for distance 23520 bytes for lkl0 18816 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.157285 0.166405 0.183801 0.075440 0.136624 0.181211 0.259375 lnL0 = -1425.489668 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1425.489668 x= 0.00006 0.15728 0.16640 0.18380 0.07544 0.13662 0.18121 0.25938 1 h-lim-p 0.0000 0.0000 167.0431 1425.391547 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0025 82.3104 1421.300655 7 0.0013 52 | 1/8 3 h-lim-p 0.0029 0.0235 20.3551 1421.050075 7 0.0013 76 | 1/8 4 h-lim-p 0.0047 0.0578 5.6382 1421.006451 6 0.0019 99 | 1/8 5 h-lim-p 0.0089 0.2087 1.1965 1420.744282 0 0.0178 112 | 1/8 6 h-lim-p 0.0044 0.0435 4.8372 1416.828324 0 0.0176 126 | 1/8 7 h-lim-p 0.0004 0.0030 40.2639 1415.482273 0 0.0008 139 | 1/8 8 h-lim-p 0.0011 0.0115 27.2485 1414.909061 0 0.0017 151 | 1/8 9 h-lim-p 1.0508 8.5834 0.0433 1414.296743 5 0.6853 175 | 0/8 10 h-lim-p 0.0092 0.3895 3.2207 1414.289874 5 0.0014 209 | 0/8 11 h-lim-p 0.4888 5.3066 0.0094 1414.269248 3 0.5045 227 | 0/8 12 h-lim-p 1.3630 20.0000 0.0035 1414.264640 5 0.7133 258 | 0/8 13 h-lim-p 2.5000 20.0000 0.0006 1414.264530 4 0.7998 288 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 1414.264524 2 0.8246 314 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1414.264524 0 1.0938 334 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1414.264524 0 1.0938 354 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1414.264524 0 1.0938 374 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1414.264524 0 1.2500 394 | 0/8 19 h-lim-p 0.8970 20.0000 0.0000 1414.264524 0 0.0000 435 Out... lnL = -1414.264524 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1414.264524 Node 7: lnL = -1414.264524 Node 8: lnL = -1414.264524 Node 9: lnL = -1414.264524 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 207 Sequential format.. Reading seq # 1: YHR188C_Sbay Reading seq # 2: YHR188C_Scer Reading seq # 3: YHR188C_Skud Reading seq # 4: YHR188C_Smik Reading seq # 5: YHR188C_Spar Sequences read.. Counting patterns.. # site patterns = 85 Counting frequencies.. 120 bytes for distance 13600 bytes for lkl0 10880 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.082708 0.130584 0.127711 0.066666 0.161871 0.141211 0.187767 lnL0 = -769.520017 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 769.520017 x= 0.00006 0.08271 0.13058 0.12771 0.06667 0.16187 0.14121 0.18777 1 h-lim-p 0.0000 0.0000 125.5780 769.467900 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0022 94.5090 765.998502 8 0.0010 57 | 1/8 3 h-lim-p 0.0146 0.1169 5.2059 765.961764 5 0.0020 81 | 1/8 4 h-lim-p 0.0062 0.0806 1.6418 765.898629 1 0.0078 95 | 1/8 5 h-lim-p 0.0072 0.1150 1.7807 763.706989 0 0.0430 109 | 0/8 6 h-lim-p 0.0005 0.0038 43.5634 762.122747 0 0.0009 122 | 0/8 7 h-lim-p 0.0009 0.0074 14.0134 761.995538 0 0.0014 134 | 0/8 8 h-lim-p 0.0006 0.0047 6.3254 761.931288 m 0.0047 146 | 0/8 9 h-lim-p 0.0000 0.0000 10.8442 h-lim-p: 1.36702657e-20 1.09362126e-19 1.08441606e+01 761.931288 .. | 0/8 10 h-lim-p 0.0000 0.0038 50.2749 761.391381 0 0.0005 171 | 0/8 11 h-lim-p 0.0011 0.0087 13.1586 761.349402 2 0.0005 187 | 0/8 12 h-lim-p 0.0013 0.0307 5.3546 761.341792 4 0.0006 207 | 0/8 13 h-lim-p 0.0032 0.0794 1.0165 761.341380 4 0.0008 228 | 0/8 14 h-lim-p 0.0021 0.2155 0.4003 761.341334 3 0.0006 249 | 0/8 15 h-lim-p 0.0074 4.1306 0.0333 761.341323 0 0.0037 269 | 0/8 16 h-lim-p 0.0024 1.0712 0.0511 761.341092 0 0.0145 291 | 0/8 17 h-lim-p 0.0061 0.2498 0.1217 761.338451 0 0.0121 312 | 0/8 18 h-lim-p 2.5000 20.0000 0.0003 761.338386 2 0.9961 336 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 761.338386 0 1.0938 356 | 0/8 20 h-lim-p 1.0795 20.0000 0.0000 761.338386 0 8.6362 379 | 0/8 21 h-lim-p 0.3214 20.0000 0.0005 761.338386 0 0.0013 406 | 0/8 22 h-lim-p 0.0001 2.8457 0.0054 .. | 0/8 23 h-lim-p 0.0000 20.0000 0.0015 761.338386 0 0.0000 465 | 0/8 24 h-lim-p 0.0002 20.0000 0.0003 761.338386 0 0.0022 488 | 0/8 25 h-lim-p 0.0056 20.0000 0.0001 761.338386 0 0.0004 511 | 0/8 26 h-lim-p 0.0012 20.0000 0.0000 761.338386 0 0.0000 549 | 0/8 27 h-lim-p 0.0000 20.0000 0.0019 761.338386 0 0.0000 570 | 0/8 28 h-lim-p 0.0003 20.0000 0.0001 761.338386 0 0.0000 593 | 0/8 29 h-lim-p 0.0000 20.0000 0.0001 761.338386 0 0.0039 619 | 0/8 30 h-lim-p 0.0054 20.0000 0.0000 761.338386 0 0.0002 643 | 0/8 31 h-lim-p 0.0000 20.0000 0.0002 761.338386 0 0.0081 671 | 0/8 32 h-lim-p 0.0004 3.6121 0.0043 761.338386 0 0.0000 697 | 0/8 33 h-lim-p 0.0000 6.6389 0.0025 761.338386 0 0.0002 721 | 0/8 34 h-lim-p 0.0008 20.0000 0.0005 761.338386 0 0.0000 747 | 0/8 35 h-lim-p 0.0001 20.0000 0.0000 761.338386 0 0.0000 768 | 0/8 36 h-lim-p 0.0000 20.0000 0.0001 761.338386 0 0.0000 798 | 0/8 37 h-lim-p 0.0000 20.0000 0.0016 | 0/8 38 h-lim-p 0.0000 20.0000 0.0016 Out... lnL = -761.338386 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -761.338386 Node 7: lnL = -761.338386 Node 8: lnL = -761.338386 Node 9: lnL = -761.338386 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 207 Sequential format.. Reading seq # 1: YHR189W_Sbay Reading seq # 2: YHR189W_Scer Reading seq # 3: YHR189W_Skud Reading seq # 4: YHR189W_Smik Reading seq # 5: YHR189W_Spar Sequences read.. Counting patterns.. # site patterns = 79 Counting frequencies.. 120 bytes for distance 12640 bytes for lkl0 10112 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.107796 0.120268 0.128125 0.065458 0.168263 0.125046 0.197700 lnL0 = -791.312942 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 791.312942 x= 0.00006 0.10780 0.12027 0.12813 0.06546 0.16826 0.12505 0.19770 1 h-lim-p 0.0000 0.0000 123.7055 791.245203 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0025 72.2953 788.761353 9 0.0011 62 | 1/8 3 h-lim-p 0.0024 0.0191 7.8751 788.715624 5 0.0013 85 | 1/8 4 h-lim-p 0.0050 0.1099 2.0121 788.668566 1 0.0062 99 | 1/8 5 h-lim-p 0.0125 0.1960 0.9976 787.044237 0 0.0501 113 | 1/8 6 h-lim-p 0.0010 0.0082 21.9831 784.478394 0 0.0031 133 | 1/8 7 h-lim-p 0.0011 0.0085 18.2735 784.316854 5 0.0009 154 | 1/8 8 h-lim-p 0.0136 0.1625 1.2471 784.314691 5 0.0018 179 | 0/8 9 h-lim-p 0.0007 0.1017 3.2575 784.299608 0 0.0040 193 | 0/8 10 h-lim-p 0.0975 0.7800 0.0755 784.157102 0 0.1950 206 | 0/8 11 h-lim-p 0.8067 6.4533 0.0067 784.142653 7 0.5625 244 | 0/8 12 h-lim-p 2.3818 20.0000 0.0016 784.141828 5 0.6721 276 | 0/8 13 h-lim-p 2.5000 20.0000 0.0003 784.141821 2 0.7996 301 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 784.141821 0 1.0938 321 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 784.141821 0 1.0938 341 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 784.141821 0 2.1875 361 | 0/8 17 h-lim-p 1.7384 20.0000 0.0000 784.141821 0 0.7605 381 | 0/8 18 h-lim-p 2.2785 20.0000 0.0000 784.141821 0 0.0356 406 | 0/8 19 h-lim-p 0.0263 20.0000 0.0000 784.141821 0 0.0001 433 Out... lnL = -784.141821 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -784.141821 Node 7: lnL = -784.141821 Node 8: lnL = -784.141821 Node 9: lnL = -784.141821 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 247 Sequential format.. Reading seq # 1: YHR190W_Sbay Reading seq # 2: YHR190W_Scer Reading seq # 3: YHR190W_Skud Reading seq # 4: YHR190W_Smik Reading seq # 5: YHR190W_Spar Sequences read.. Counting patterns.. # site patterns = 91 Counting frequencies.. 120 bytes for distance 14560 bytes for lkl0 11648 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.020945 0.102773 0.045820 0.124790 0.063839 0.110906 0.000060 0.185907 lnL0 = -899.502560 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 899.502560 x= 0.02095 0.10277 0.04582 0.12479 0.06384 0.11091 0.00006 0.18591 1 h-lim-p 0.0001 0.0008 244.1766 894.347318 0 0.0002 23 | 0/8 2 h-lim-p 0.0002 0.0015 55.4647 893.855073 0 0.0004 36 | 0/8 3 h-lim-p 0.0007 0.0057 25.2995 893.715067 7 0.0005 64 | 0/8 4 h-lim-p 0.0030 0.0279 4.3987 893.708469 2 0.0007 81 | 0/8 5 h-lim-p 0.0009 0.0201 3.4776 893.706672 2 0.0004 97 | 0/8 6 h-lim-p 0.0017 0.0750 0.8442 893.706145 3 0.0014 115 | 0/8 7 h-lim-p 0.0222 3.3009 0.0547 893.704439 0 0.0334 135 | 0/8 8 h-lim-p 0.0082 0.2998 0.2222 893.639343 0 0.0328 157 | 0/8 9 h-lim-p 2.3707 18.9658 0.0023 893.627965 4 1.2074 186 | 0/8 10 h-lim-p 2.5000 20.0000 0.0003 893.627882 3 1.0004 212 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 893.627882 0 1.0938 232 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 893.627882 0 1.0938 252 | 0/8 13 h-lim-p 1.0718 20.0000 0.0000 893.627882 0 2.1435 273 | 0/8 14 h-lim-p 0.7234 20.0000 0.0000 893.627882 0 1.4468 294 | 0/8 15 h-lim-p 0.0225 20.0000 0.0017 893.627882 0 0.0056 315 | 0/8 16 h-lim-p 0.0017 8.7869 0.0055 893.627882 0 0.0000 348 | 0/8 17 h-lim-p 0.0001 20.0000 0.0000 893.627882 0 0.0000 369 Out... lnL = -893.627882 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -893.627882 Node 7: lnL = -893.627882 Node 8: lnL = -893.627882 Node 9: lnL = -893.627882 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 201 Sequential format.. Reading seq # 1: YHR191C_Sbay Reading seq # 2: YHR191C_Scer Reading seq # 3: YHR191C_Skud Reading seq # 4: YHR191C_Smik Reading seq # 5: YHR191C_Spar Sequences read.. Counting patterns.. # site patterns = 117 Counting frequencies.. 120 bytes for distance 18720 bytes for lkl0 14976 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.005771 0.215370 0.196422 0.240188 0.000060 0.268309 0.239077 0.356720 lnL0 = -921.651678 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 921.651678 x= 0.00577 0.21537 0.19642 0.24019 0.00006 0.26831 0.23908 0.35672 1 h-lim-p 0.0000 0.0000 72.4865 921.608554 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0244 17.4338 921.100778 0 0.0043 41 | 1/8 3 h-lim-p 0.0075 0.0602 4.1140 920.991750 2 0.0071 57 | 1/8 4 h-lim-p 0.0127 0.2360 2.2826 920.628744 0 0.0254 70 | 0/8 5 h-lim-p 0.0019 0.0153 30.1089 920.566336 8 0.0003 104 | 0/8 6 h-lim-p 0.0016 0.0371 5.5251 917.146885 2 0.0241 124 | 0/8 7 h-lim-p 0.0018 0.0143 16.7961 915.187094 0 0.0054 137 | 0/8 8 h-lim-p 0.0022 0.0179 5.5381 915.135557 0 0.0045 150 | 0/8 9 h-lim-p 0.0603 0.4823 0.0759 914.863327 m 0.4823 162 | 0/8 10 h-lim-p -0.0000 -0.0000 0.2700 h-lim-p: -6.04248519e-19 -4.83398815e-18 2.69970077e-01 914.863327 .. | 0/8 11 h-lim-p 0.0000 0.0035 5.0201 914.860211 0 0.0003 203 | 0/8 12 h-lim-p 0.0007 0.1406 2.2306 914.855785 0 0.0022 216 | 0/8 13 h-lim-p 0.0051 0.1767 0.9402 914.855239 5 0.0015 241 | 0/8 14 h-lim-p 0.0015 0.0119 0.2616 914.855164 0 0.0030 262 | 0/8 15 h-lim-p 0.0022 0.0179 0.1247 914.855135 0 0.0045 283 | 0/8 16 h-lim-p 0.0012 0.0096 0.1184 914.855075 m 0.0096 303 | 0/8 17 h-lim-p -0.0000 -0.0000 7960.2751 h-lim-p: -1.20543122e-24 -9.64344976e-24 7.96027511e+03 914.855075 .. | 0/8 18 h-lim-p 0.0000 20.0000 1.2662 914.854904 0 0.0002 335 | 0/8 19 h-lim-p 0.0016 1.0808 0.1960 914.854871 2 0.0017 352 | 0/8 20 h-lim-p 0.0035 0.0477 0.0991 914.854861 2 0.0027 376 | 0/8 21 h-lim-p 0.0010 0.0078 0.0495 914.854860 0 0.0019 397 | 0/8 22 h-lim-p 0.0014 0.0113 0.0157 914.854860 0 0.0056 419 | 0/8 23 h-lim-p 0.0001 0.0006 0.1075 .. | 0/8 24 h-lim-p 0.0000 0.0026 0.1422 914.854858 0 0.0002 479 | 0/8 25 h-lim-p 0.0003 0.0023 0.0220 914.854858 0 0.0009 500 | 0/8 26 h-lim-p 0.0001 0.0005 0.0675 914.854858 0 0.0001 521 | 0/8 27 h-lim-p 0.0000 0.0000 0.9017 914.854858 0 0.0000 541 | 0/8 28 h-lim-p 0.0000 0.0000 37.4380 .. | 0/8 29 h-lim-p 0.0000 20.0000 0.0123 914.854857 0 0.0026 587 | 0/8 30 h-lim-p 0.0014 0.0111 0.0126 914.854857 0 0.0002 609 | 0/8 31 h-lim-p 0.0001 0.0031 0.0300 914.854857 0 0.0001 630 | 0/8 32 h-lim-p 0.0009 0.0285 0.0043 .. | 0/8 33 h-lim-p 0.0000 0.0016 0.0214 914.854857 0 0.0002 694 | 0/8 34 h-lim-p 0.0000 0.0002 0.1270 914.854857 0 0.0001 715 | 0/8 35 h-lim-p 0.0000 0.0003 0.0794 914.854857 0 0.0000 748 | 0/8 36 h-lim-p 0.0000 0.0000 3.8791 .. | 0/8 37 h-lim-p 0.0000 1.0232 0.0143 914.854857 0 0.0000 791 | 0/8 38 h-lim-p 0.0000 0.0018 0.0164 914.854857 0 0.0000 821 | 0/8 39 h-lim-p 0.0000 3.4663 0.0018 914.854857 0 0.0038 849 | 0/8 40 h-lim-p 0.0053 0.1531 0.0013 914.854857 0 0.0000 885 | 0/8 41 h-lim-p 0.0000 5.1157 0.0001 914.854857 0 0.0000 906 | 0/8 42 h-lim-p 0.0000 0.5505 0.0002 914.854857 0 0.0000 932 | 0/8 43 h-lim-p 0.0000 0.0821 0.0007 914.854857 0 0.0000 955 | 0/8 44 h-lim-p 0.0000 1.4800 0.0005 914.854857 0 0.0026 983 | 0/8 45 h-lim-p 0.0036 0.7850 0.0004 914.854857 0 0.0000 1013 | 0/8 46 h-lim-p 0.0000 1.2227 0.0000 914.854857 0 0.0000 1038 | 0/8 47 h-lim-p 0.0000 2.2114 0.0000 914.854857 0 0.0000 1059 | 0/8 48 h-lim-p 0.0000 1.9852 0.0000 914.854857 0 0.0000 1092 | 0/8 49 h-lim-p 0.0000 0.0011 0.0205 914.854857 0 0.0000 1113 | 0/8 50 h-lim-p 0.0000 0.0002 0.1072 914.854857 0 0.0000 1147 | 0/8 51 h-lim-p 0.0000 0.0001 0.2094 .. | 0/8 52 h-lim-p 0.0000 0.0011 0.0202 914.854857 0 0.0000 1200 | 0/8 53 h-lim-p 0.0000 0.0002 0.1205 .. | 0/8 54 h-lim-p 0.0000 0.0011 0.0201 914.854857 0 0.0000 1264 | 0/8 55 h-lim-p 0.0000 0.0002 0.1339 914.854857 0 0.0000 1293 | 0/8 56 h-lim-p 0.0000 0.0001 0.1538 914.854857 0 0.0000 1314 | 0/8 57 h-lim-p 0.0000 0.0000 1.1186 .. | 0/8 58 h-lim-p 0.0000 0.0531 0.0119 914.854857 0 0.0000 1364 | 0/8 59 h-lim-p 0.0000 0.0015 0.0190 .. | 0/8 60 h-lim-p 0.0000 0.0010 0.0201 | 0/8 61 h-lim-p 0.0000 0.0010 0.0201 Out... lnL = -914.854857 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -914.854857 Node 7: lnL = -914.854857 Node 8: lnL = -914.854857 Node 9: lnL = -914.854857 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 437 Sequential format.. Reading seq # 1: YHR193C_Sbay Reading seq # 2: YHR193C_Scer Reading seq # 3: YHR193C_Skud Reading seq # 4: YHR193C_Smik Reading seq # 5: YHR193C_Spar Sequences read.. Counting patterns.. # site patterns = 192 Counting frequencies.. 120 bytes for distance 30720 bytes for lkl0 24576 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.034940 0.007593 0.079704 0.146873 0.108651 0.193835 0.276390 0.367560 lnL0 = -2103.147688 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2103.147688 x= 0.03494 0.00759 0.07970 0.14687 0.10865 0.19383 0.27639 0.36756 1 h-lim-p 0.0013 0.0102 114.1938 2101.398723 3 0.0003 29 | 0/8 2 h-lim-p 0.0012 0.0098 14.0586 2101.347004 6 0.0005 52 | 0/8 3 h-lim-p 0.0017 0.0822 4.3496 2101.341930 5 0.0006 78 | 0/8 4 h-lim-p 0.0013 0.1579 1.9759 2101.339981 2 0.0012 94 | 0/8 5 h-lim-p 0.0072 0.5103 0.3339 2101.339948 2 0.0006 113 | 0/8 6 h-lim-p 0.0027 3.7814 0.0707 2101.339945 0 0.0012 133 | 0/8 7 h-lim-p 0.0146 10.5044 0.0057 2101.339884 0 0.0586 155 | 0/8 8 h-lim-p 0.0066 18.1618 0.0507 2101.338935 0 0.0198 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2101.338931 0 1.0938 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2101.338931 0 1.0938 216 | 0/8 11 h-lim-p 1.5638 20.0000 0.0000 2101.338931 0 1.3683 236 | 0/8 12 h-lim-p 0.9251 20.0000 0.0000 2101.338931 0 2.7752 257 | 0/8 13 h-lim-p 0.0023 2.7556 0.0199 2101.338931 0 0.0023 277 | 0/8 14 h-lim-p 0.0001 0.0765 0.7174 2101.338931 0 0.0000 302 | 0/8 15 h-lim-p 0.0003 20.0000 0.0023 2101.338931 0 0.0000 324 | 0/8 16 h-lim-p 0.0002 20.0000 0.0004 2101.338931 0 0.0000 360 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 2101.338931 0 0.0000 388 | 0/8 18 h-lim-p 0.0000 20.0000 0.0003 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0002 | 0/8 20 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -2101.338931 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2101.338931 Node 7: lnL = -2101.338931 Node 8: lnL = -2101.338931 Node 9: lnL = -2101.338931 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 442 Sequential format.. Reading seq # 1: YHR194W_Sbay Reading seq # 2: YHR194W_Scer Reading seq # 3: YHR194W_Skud Reading seq # 4: YHR194W_Smik Reading seq # 5: YHR194W_Spar Sequences read.. Counting patterns.. # site patterns = 194 Counting frequencies.. 120 bytes for distance 31040 bytes for lkl0 24832 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.009851 0.034920 0.063880 0.142621 0.113356 0.212433 0.309554 0.349398 lnL0 = -2142.760826 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2142.760826 x= 0.00985 0.03492 0.06388 0.14262 0.11336 0.21243 0.30955 0.34940 1 h-lim-p 0.0019 0.0151 104.5426 2140.989530 6 0.0004 35 | 0/8 2 h-lim-p 0.0011 0.0085 17.6947 2140.900421 6 0.0006 60 | 0/8 3 h-lim-p 0.0010 0.0081 7.2511 2140.882431 4 0.0008 80 | 0/8 4 h-lim-p 0.0013 0.0197 4.3219 2140.876560 5 0.0008 104 | 0/8 5 h-lim-p 0.0042 0.1806 0.8792 2140.876237 2 0.0009 121 | 0/8 6 h-lim-p 0.0029 0.8721 0.2795 2140.876209 3 0.0008 148 | 0/8 7 h-lim-p 0.1067 20.0000 0.0020 2140.876159 0 0.1600 168 | 0/8 8 h-lim-p 0.0042 1.5088 0.0769 2140.875773 0 0.0084 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2140.875772 0 1.0938 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2140.875772 0 1.0938 229 | 0/8 11 h-lim-p 1.0814 20.0000 0.0000 2140.875772 0 0.0169 254 | 0/8 12 h-lim-p 0.0021 20.0000 0.0001 2140.875772 0 0.0003 276 | 0/8 13 h-lim-p 0.0003 20.0000 0.0001 2140.875772 0 0.0000 305 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 2140.875772 0 0.0000 334 Out... lnL = -2140.875772 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2140.875772 Node 7: lnL = -2140.875772 Node 8: lnL = -2140.875772 Node 9: lnL = -2140.875772 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 379 Sequential format.. Reading seq # 1: YHR195W_Sbay Reading seq # 2: YHR195W_Scer Reading seq # 3: YHR195W_Skud Reading seq # 4: YHR195W_Smik Reading seq # 5: YHR195W_Spar Sequences read.. Counting patterns.. # site patterns = 162 Counting frequencies.. 120 bytes for distance 25920 bytes for lkl0 20736 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.048229 0.049457 0.028303 0.091093 0.077720 0.162028 0.236620 0.328433 lnL0 = -1584.493206 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1584.493206 x= 0.04823 0.04946 0.02830 0.09109 0.07772 0.16203 0.23662 0.32843 1 h-lim-p 0.0009 0.0068 69.0068 1583.994901 5 0.0002 33 | 0/8 2 h-lim-p 0.0007 0.0064 21.2453 1583.879812 7 0.0006 59 | 0/8 3 h-lim-p 0.0008 0.0061 14.3622 1583.833802 6 0.0006 85 | 0/8 4 h-lim-p 0.0011 0.0118 7.7516 1583.823849 5 0.0005 106 | 0/8 5 h-lim-p 0.0023 0.1363 1.5535 1583.823267 2 0.0005 123 | 0/8 6 h-lim-p 0.0015 0.5822 0.5406 1583.823140 4 0.0010 145 | 0/8 7 h-lim-p 0.0642 19.9289 0.0083 1583.823139 0 0.0035 168 | 0/8 8 h-lim-p 0.0229 20.0000 0.0013 1583.823023 0 0.3656 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1583.823011 1 0.9961 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1583.823011 0 0.0000 261 | 0/8 11 h-lim-p 0.0000 20.0000 0.0007 | 0/8 12 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -1583.823011 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1583.823011 Node 7: lnL = -1583.823011 Node 8: lnL = -1583.823011 Node 9: lnL = -1583.823011 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 231 Sequential format.. Reading seq # 1: YHR196W_Sbay Reading seq # 2: YHR196W_Scer Reading seq # 3: YHR196W_Skud Reading seq # 4: YHR196W_Smik Reading seq # 5: YHR196W_Spar Sequences read.. Counting patterns.. # site patterns = 81 Counting frequencies.. 120 bytes for distance 12960 bytes for lkl0 10368 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.005231 0.029247 0.047459 0.091431 0.029433 0.117494 0.141181 0.186537 lnL0 = -856.978409 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 856.978409 x= 0.00523 0.02925 0.04746 0.09143 0.02943 0.11749 0.14118 0.18654 1 h-lim-p 0.0002 0.0014 56.6812 856.612773 0 0.0004 23 | 0/8 2 h-lim-p 0.0012 0.0232 16.4470 856.589219 7 0.0002 54 | 0/8 3 h-lim-p 0.0005 0.0258 6.6325 856.577656 0 0.0007 66 | 0/8 4 h-lim-p 0.0023 0.0870 2.0218 856.576516 4 0.0006 87 | 0/8 5 h-lim-p 0.0028 0.2656 0.4489 856.576406 3 0.0009 107 | 0/8 6 h-lim-p 0.0045 0.5628 0.0888 856.576191 1 0.0056 129 | 0/8 7 h-lim-p 0.0081 0.3025 0.0620 856.549325 0 0.0647 152 | 0/8 8 h-lim-p 0.0012 0.0250 3.3631 856.543807 5 0.0008 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0008 856.543027 3 0.9961 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 856.543023 1 1.0938 223 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 856.543023 0 1.0938 243 | 0/8 12 h-lim-p 1.0614 20.0000 0.0000 856.543023 0 0.9287 263 | 0/8 13 h-lim-p 0.2557 20.0000 0.0001 856.543023 0 0.0040 288 | 0/8 14 h-lim-p 0.0008 20.0000 0.0003 856.543023 0 0.0000 314 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 856.543023 0 0.0000 337 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 856.543023 0 0.0000 357 Out... lnL = -856.543023 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -856.543023 Node 7: lnL = -856.543023 Node 8: lnL = -856.543023 Node 9: lnL = -856.543023 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 256 Sequential format.. Reading seq # 1: YHR197W_Sbay Reading seq # 2: YHR197W_Scer Reading seq # 3: YHR197W_Skud Reading seq # 4: YHR197W_Smik Reading seq # 5: YHR197W_Spar Sequences read.. Counting patterns.. # site patterns = 106 Counting frequencies.. 120 bytes for distance 16960 bytes for lkl0 13568 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.118002 0.137365 0.151077 0.086355 0.168021 0.185703 0.247038 lnL0 = -1068.822155 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1068.822155 x= 0.00006 0.11800 0.13737 0.15108 0.08635 0.16802 0.18570 0.24704 1 h-lim-p 0.0000 0.0000 120.1842 1068.714385 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0025 68.0909 1066.292934 0 0.0013 40 | 1/8 3 h-lim-p 0.0040 0.0321 11.2553 1066.195772 8 0.0015 69 | 1/8 4 h-lim-p 0.0099 0.1686 1.7128 1066.148090 7 0.0066 98 | 1/8 5 h-lim-p 0.0056 0.1788 2.0270 1065.398419 0 0.0223 112 | 0/8 6 h-lim-p 0.0021 0.0171 12.5208 1062.815043 0 0.0064 125 | 0/8 7 h-lim-p 0.0008 0.0063 25.7014 1062.283375 0 0.0012 137 | 0/8 8 h-lim-p 0.0005 0.0038 14.8812 1062.086230 0 0.0019 151 | 0/8 9 h-lim-p 0.0006 0.0052 9.8693 1062.008886 0 0.0026 165 | 0/8 10 h-lim-p 0.1129 0.9032 0.0346 1061.792734 0 0.6774 179 | 0/8 11 h-lim-p 0.0861 0.6889 0.0107 1061.775525 0 0.5167 201 | 0/8 12 h-lim-p 1.9706 20.0000 0.0028 1061.772075 2 0.9237 225 | 0/8 13 h-lim-p 0.6244 4.9955 0.0005 1061.772025 0 1.2489 246 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 1061.772019 1 0.9961 268 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1061.772019 0 1.0938 288 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1061.772019 0 1.0938 308 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1061.772019 0 1.0938 328 | 0/8 18 h-lim-p 0.9925 20.0000 0.0000 1061.772019 0 0.2481 349 | 0/8 19 h-lim-p 0.0021 20.0000 0.0000 1061.772019 0 0.0000 380 | 0/8 20 h-lim-p 0.0000 20.0000 0.0000 1061.772019 0 0.0000 408 | 0/8 21 h-lim-p 0.0000 20.0000 0.0000 1061.772019 0 0.0000 438 | 0/8 22 h-lim-p 0.0000 20.0000 0.0000 | 0/8 23 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1061.772019 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1061.772019 Node 7: lnL = -1061.772019 Node 8: lnL = -1061.772019 Node 9: lnL = -1061.772019 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 740 Sequential format.. Reading seq # 1: YHR199C_Sbay Reading seq # 2: YHR199C_Scer Reading seq # 3: YHR199C_Skud Reading seq # 4: YHR199C_Smik Reading seq # 5: YHR199C_Spar Sequences read.. Counting patterns.. # site patterns = 213 Counting frequencies.. 120 bytes for distance 34080 bytes for lkl0 27264 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.071864 0.071128 0.112274 0.082365 0.152940 0.128510 0.209376 lnL0 = -2771.657302 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2771.657302 x= 0.00006 0.07186 0.07113 0.11227 0.08236 0.15294 0.12851 0.20938 1 h-lim-p 0.0000 0.0000 189.8204 2771.590423 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0037 61.7617 2770.972366 0 0.0003 39 | 1/8 3 h-lim-p 0.0020 0.0312 9.8392 2770.952853 5 0.0004 64 | 1/8 4 h-lim-p 0.0008 0.0480 4.8222 2770.944158 5 0.0005 88 | 1/8 5 h-lim-p 0.0014 0.0911 1.8435 2770.924017 1 0.0018 102 | 1/8 6 h-lim-p 0.0029 0.2339 1.1348 2768.115813 0 0.0458 118 | 1/8 7 h-lim-p 0.0002 0.0018 74.5534 2766.638560 0 0.0004 131 | 1/8 8 h-lim-p 0.0004 0.0028 53.8801 2766.127862 3 0.0004 149 | 1/8 9 h-lim-p 1.2102 16.4991 0.0158 2765.659274 6 0.8537 175 | 0/8 10 h-lim-p 0.0054 0.3634 2.5130 2765.657835 4 0.0005 207 | 0/8 11 h-lim-p 0.4587 4.9731 0.0025 2765.652091 0 0.9174 220 | 0/8 12 h-lim-p 2.5000 20.0000 0.0007 2765.651200 3 1.0004 246 | 0/8 13 h-lim-p 2.5000 20.0000 0.0001 2765.651190 1 1.2305 269 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 2765.651190 0 1.0938 289 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2765.651190 0 1.0938 309 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 2765.651190 0 0.0195 335 | 0/8 17 h-lim-p 0.0196 20.0000 0.0000 2765.651190 0 0.0003 360 Out... lnL = -2765.651190 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2765.651190 Node 7: lnL = -2765.651190 Node 8: lnL = -2765.651190 Node 9: lnL = -2765.651190 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 689 Sequential format.. Reading seq # 1: YHR200W_Sbay Reading seq # 2: YHR200W_Scer Reading seq # 3: YHR200W_Skud Reading seq # 4: YHR200W_Smik Reading seq # 5: YHR200W_Spar Sequences read.. Counting patterns.. # site patterns = 198 Counting frequencies.. 120 bytes for distance 31680 bytes for lkl0 25344 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.078677 0.072318 0.107089 0.087863 0.160709 0.129325 0.208746 lnL0 = -2772.732468 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2772.732468 x= 0.00006 0.07868 0.07232 0.10709 0.08786 0.16071 0.12932 0.20875 1 h-lim-p 0.0000 0.0000 252.3504 2772.664494 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0033 76.1574 2771.859737 0 0.0003 39 | 1/8 3 h-lim-p 0.0011 0.0194 22.4088 2771.806151 3 0.0002 58 | 1/8 4 h-lim-p 0.0011 0.0298 4.5286 2771.793934 5 0.0006 82 | 1/8 5 h-lim-p 0.0011 0.0819 2.3689 2771.715478 0 0.0045 96 | 1/8 6 h-lim-p 0.0010 0.0262 10.4059 2771.336820 0 0.0015 108 | 1/8 7 h-lim-p 0.0010 0.0144 16.2158 2766.113558 0 0.0039 122 | 0/8 8 h-lim-p 0.0002 0.0017 106.0212 2762.728587 0 0.0004 135 | 0/8 9 h-lim-p 0.0002 0.0015 20.4935 2762.601140 0 0.0007 149 | 0/8 10 h-lim-p 0.8807 20.0000 0.0172 2762.000855 2 0.8256 165 | 0/8 11 h-lim-p 2.4909 20.0000 0.0057 2761.954190 6 0.9237 199 | 0/8 12 h-lim-p 2.4613 20.0000 0.0021 2761.948795 5 0.8643 231 | 0/8 13 h-lim-p 2.5000 20.0000 0.0001 2761.948733 1 1.2500 253 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 2761.948726 1 0.9961 275 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2761.948726 0 1.0938 295 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 2761.948726 0 0.5469 316 | 0/8 17 h-lim-p 0.9106 20.0000 0.0000 2761.948726 0 0.1138 338 | 0/8 18 h-lim-p 0.1024 20.0000 0.0000 2761.948726 0 0.0032 362 Out... lnL = -2761.948726 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2761.948726 Node 7: lnL = -2761.948726 Node 8: lnL = -2761.948726 Node 9: lnL = -2761.948726 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 912 Sequential format.. Reading seq # 1: YHR201C_Sbay Reading seq # 2: YHR201C_Scer Reading seq # 3: YHR201C_Skud Reading seq # 4: YHR201C_Smik Reading seq # 5: YHR201C_Spar Sequences read.. Counting patterns.. # site patterns = 413 Counting frequencies.. 120 bytes for distance 66080 bytes for lkl0 52864 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.070125 0.085198 0.121525 0.231189 0.147100 0.250011 0.439764 0.596595 lnL0 = -4738.492080 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4738.492080 x= 0.07012 0.08520 0.12152 0.23119 0.14710 0.25001 0.43976 0.59660 1 h-lim-p 0.0035 0.0283 65.3647 4737.364875 8 0.0006 44 | 0/8 2 h-lim-p 0.0015 0.0120 21.9735 4737.239559 6 0.0006 68 | 0/8 3 h-lim-p 0.0010 0.0462 12.5108 4737.188119 5 0.0009 89 | 0/8 4 h-lim-p 0.0008 0.0355 13.3286 4737.135473 0 0.0012 101 | 0/8 5 h-lim-p 0.0214 0.1713 0.7299 4737.135113 2 0.0013 120 | 0/8 6 h-lim-p 0.0038 0.6991 0.2559 4737.135084 2 0.0009 145 | 0/8 7 h-lim-p 0.0039 4.8311 0.0607 4737.135079 0 0.0017 165 | 0/8 8 h-lim-p 0.0502 20.0000 0.0021 4737.133878 0 0.8036 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 4737.133816 2 0.9961 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4737.133816 0 1.0938 233 | 0/8 11 h-lim-p 1.2059 20.0000 0.0000 4737.133816 0 1.0552 253 | 0/8 12 h-lim-p 0.1740 20.0000 0.0001 4737.133816 0 0.0190 275 | 0/8 13 h-lim-p 0.0069 20.0000 0.0002 4737.133816 0 0.0004 298 | 0/8 14 h-lim-p 0.0020 20.0000 0.0000 4737.133816 0 0.0000 334 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 4737.133816 0 0.0000 366 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 4737.133816 0 0.0000 400 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -4737.133816 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4737.133816 Node 7: lnL = -4737.133816 Node 8: lnL = -4737.133816 Node 9: lnL = -4737.133816 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 850 Sequential format.. Reading seq # 1: YHR202W_Sbay Reading seq # 2: YHR202W_Scer Reading seq # 3: YHR202W_Skud Reading seq # 4: YHR202W_Smik Reading seq # 5: YHR202W_Spar Sequences read.. Counting patterns.. # site patterns = 415 Counting frequencies.. 120 bytes for distance 66400 bytes for lkl0 53120 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.091866 0.230060 0.174812 0.234992 0.601035 0.384165 0.514315 lnL0 = -4544.397438 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4544.397438 x= 0.00006 0.09187 0.23006 0.17481 0.23499 0.60104 0.38416 0.51431 1 h-lim-p 0.0000 0.0000 214.9227 4544.361032 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0023 299.2252 4524.021305 0 0.0010 40 | 1/8 3 h-lim-p 0.0022 0.0178 37.6725 4522.826865 3 0.0019 58 | 1/8 4 h-lim-p 0.0023 0.0184 14.3117 4522.673590 6 0.0015 84 | 1/8 5 h-lim-p 0.0038 0.1093 5.6286 4522.583060 3 0.0034 102 | 1/8 6 h-lim-p 0.0184 0.9444 1.0428 4519.484673 0 0.1474 117 | 1/8 7 h-lim-p 0.0029 0.0236 14.3370 4514.489536 0 0.0059 130 | 1/8 8 h-lim-p 0.0008 0.0065 46.0601 4512.603096 0 0.0016 143 | 1/8 9 h-lim-p 0.8352 7.3495 0.0897 4511.895555 8 0.5613 175 | 1/8 10 h-lim-p 2.5000 20.0000 0.0156 4511.851894 5 0.6069 206 | 0/8 11 h-lim-p 0.0287 4.4381 0.3301 4511.851839 2 0.0012 234 | 0/8 12 h-lim-p 0.1306 1.5769 0.0030 4511.850471 0 0.7839 256 | 0/8 13 h-lim-p 0.3470 2.7761 0.0003 4511.850445 0 0.6940 277 | 0/8 14 h-lim-p 0.0960 0.7681 0.0002 4511.850445 0 0.3840 299 | 0/8 15 h-lim-p 0.0005 0.0040 0.0247 4511.850445 0 0.0000 332 | 0/8 16 h-lim-p 0.0000 0.2226 0.0005 4511.850445 0 0.0102 362 | 0/8 17 h-lim-p 0.0309 1.3641 0.0002 4511.850445 0 0.0926 383 | 0/8 18 h-lim-p 0.2748 20.0000 0.0001 4511.850445 0 0.2748 403 | 0/8 19 h-lim-p 0.1148 0.9187 0.0001 4511.850445 0 0.0000 435 | 0/8 20 h-lim-p 0.0000 0.1708 0.0006 .. | 0/8 21 h-lim-p 0.0000 0.0016 0.0768 4511.850444 0 0.0010 494 | 0/8 22 h-lim-p 0.0000 0.0001 0.2876 4511.850444 0 0.0000 529 | 0/8 23 h-lim-p 0.0000 0.0002 0.2224 4511.850444 0 0.0000 562 | 0/8 24 h-lim-p 0.0000 0.0005 0.0913 .. | 0/8 25 h-lim-p 0.0000 0.0004 0.0729 | 0/8 26 h-lim-p 0.0000 0.0004 0.0729 Out... lnL = -4511.850444 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4511.850444 Node 7: lnL = -4511.850444 Node 8: lnL = -4511.850444 Node 9: lnL = -4511.850444 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 871 Sequential format.. Reading seq # 1: YHR204W_Sbay Reading seq # 2: YHR204W_Scer Reading seq # 3: YHR204W_Skud Reading seq # 4: YHR204W_Smik Reading seq # 5: YHR204W_Spar Sequences read.. Counting patterns.. # site patterns = 301 Counting frequencies.. 120 bytes for distance 48160 bytes for lkl0 38528 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.081979 0.098176 0.127993 0.118349 0.260483 0.228520 0.299041 lnL0 = -3974.712417 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3974.712417 x= 0.00006 0.08198 0.09818 0.12799 0.11835 0.26048 0.22852 0.29904 1 h-lim-p 0.0000 0.0000 213.7304 3974.660887 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0028 90.6524 3973.545686 0 0.0003 39 | 1/8 3 h-lim-p 0.0007 0.0105 43.6707 3973.272127 5 0.0004 62 | 1/8 4 h-lim-p 0.0017 0.0165 9.0886 3973.256813 6 0.0003 90 | 1/8 5 h-lim-p 0.0008 0.1246 3.4413 3973.227451 0 0.0017 103 | 1/8 6 h-lim-p 0.0052 0.2541 1.0981 3972.326031 0 0.0209 117 | 1/8 7 h-lim-p 0.0009 0.0111 26.3484 3967.078959 0 0.0035 131 | 1/8 8 h-lim-p 0.0005 0.0041 60.5292 3965.514884 0 0.0008 143 | 1/8 9 h-lim-p 1.5102 20.0000 0.0305 3964.278609 5 0.8033 166 | 0/8 10 h-lim-p 0.0065 0.1392 3.7738 3964.274385 4 0.0006 195 | 0/8 11 h-lim-p 0.4260 3.4082 0.0052 3964.255830 0 0.8521 208 | 0/8 12 h-lim-p 2.5000 20.0000 0.0009 3964.255046 2 1.0889 232 | 0/8 13 h-lim-p 2.5000 20.0000 0.0001 3964.255035 1 1.2305 255 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 3964.255035 0 1.0938 275 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 3964.255035 0 1.0938 295 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 3964.255035 0 0.0391 320 Out... lnL = -3964.255035 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3964.255035 Node 7: lnL = -3964.255035 Node 8: lnL = -3964.255035 Node 9: lnL = -3964.255035 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 689 Sequential format.. Reading seq # 1: YHR205W_Sbay Reading seq # 2: YHR205W_Scer Reading seq # 3: YHR205W_Skud Reading seq # 4: YHR205W_Smik Reading seq # 5: YHR205W_Spar Sequences read.. Counting patterns.. # site patterns = 153 Counting frequencies.. 120 bytes for distance 24480 bytes for lkl0 19584 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.002334 0.031312 0.020032 0.045856 0.056331 0.104162 0.116032 0.142435 lnL0 = -2377.541445 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2377.541445 x= 0.00233 0.03131 0.02003 0.04586 0.05633 0.10416 0.11603 0.14243 1 h-lim-p 0.0000 0.0002 288.5255 2375.724799 0 0.0001 23 | 0/8 2 h-lim-p 0.0000 0.0002 34.6983 2375.656044 0 0.0001 37 | 0/8 3 h-lim-p 0.0001 0.0007 6.9178 2375.652195 0 0.0002 50 | 0/8 4 h-lim-p 0.0004 0.0109 3.2086 2375.651622 4 0.0001 71 | 0/8 5 h-lim-p 0.0007 0.2851 0.5573 2375.651593 2 0.0002 88 | 0/8 6 h-lim-p 0.0008 1.3186 0.1090 2375.651576 2 0.0006 114 | 0/8 7 h-lim-p 0.0008 0.1012 0.0762 2375.650092 0 0.0126 138 | 0/8 8 h-lim-p 0.0012 0.0096 0.5341 2375.619328 0 0.0048 160 | 0/8 9 h-lim-p 0.0324 0.2589 0.0021 2375.618744 m 0.2589 180 | 0/8 10 h-lim-p 0.0000 0.0000 9.6877 h-lim-p: 5.33293343e-22 4.26634674e-21 9.68767254e+00 2375.618744 .. | 0/8 11 h-lim-p 0.0000 0.0325 3.7131 2375.618107 0 0.0001 211 | 0/8 12 h-lim-p 0.0003 0.0792 1.0030 2375.618060 2 0.0001 228 | 0/8 13 h-lim-p 0.0005 0.6213 0.1979 2375.618058 1 0.0001 243 | 0/8 14 h-lim-p 0.0001 0.0022 0.1655 2375.618058 0 0.0000 264 | 0/8 15 h-lim-p 0.0001 0.0049 0.1160 2375.618058 0 0.0000 284 | 0/8 16 h-lim-p 0.0001 0.0188 0.0425 2375.618058 0 0.0000 320 | 0/8 17 h-lim-p 0.0000 2.7827 0.0006 2375.618058 0 0.0205 351 | 0/8 18 h-lim-p 0.0007 0.0650 0.0190 2375.618056 0 0.0013 372 | 0/8 19 h-lim-p 0.0002 0.0032 0.1285 2375.618046 0 0.0008 394 | 0/8 20 h-lim-p 0.4764 3.8108 0.0000 2375.618046 0 0.9527 415 | 0/8 21 h-lim-p 0.0009 0.0069 0.0176 2375.618046 0 0.0008 435 | 0/8 22 h-lim-p 0.0253 0.2094 0.0005 2375.618046 0 0.0222 455 | 0/8 23 h-lim-p 0.1204 1.2911 0.0001 2375.618046 0 0.0301 476 | 0/8 24 h-lim-p 0.0857 20.0000 0.0000 2375.618046 0 0.0750 496 | 0/8 25 h-lim-p 0.0218 0.8052 0.0001 2375.618046 0 0.0000 527 | 0/8 26 h-lim-p 0.0000 0.1579 0.0006 2375.618046 0 0.0000 558 | 0/8 27 h-lim-p 0.0000 0.0002 0.3294 2375.618044 0 0.0001 581 | 0/8 28 h-lim-p 0.0000 0.0001 0.4493 .. | 0/8 29 h-lim-p 0.0000 0.0002 0.2371 2375.618044 0 0.0000 648 | 0/8 30 h-lim-p 0.0000 0.0000 1.1970 .. | 0/8 31 h-lim-p 0.0000 0.8533 0.0706 2375.618044 0 0.0001 694 | 0/8 32 h-lim-p 0.0000 0.0005 0.2837 2375.618044 0 0.0000 727 | 0/8 33 h-lim-p 0.0000 20.0000 0.0285 2375.618044 0 0.0003 752 | 0/8 34 h-lim-p 0.0012 0.0934 0.0076 2375.618044 0 0.0000 787 | 0/8 35 h-lim-p 0.0000 0.3451 0.0028 .. | 0/8 36 h-lim-p 0.0000 0.0002 0.2460 2375.618044 0 0.0000 840 | 0/8 37 h-lim-p 0.0000 0.0000 0.9293 2375.618044 0 0.0000 871 | 0/8 38 h-lim-p 0.0000 0.0000 88.3872 .. | 0/8 39 h-lim-p 0.0000 0.0066 0.0487 | 0/8 40 h-lim-p 0.0000 0.0002 0.2413 2375.618044 0 0.0000 944 | 0/8 41 h-lim-p 0.0000 0.0000 1.0828 2375.618044 0 0.0000 978 | 0/8 42 h-lim-p 0.0000 0.0000 34.0583 .. | 0/8 43 h-lim-p 0.0000 0.0002 0.2408 2375.618044 0 0.0000 1039 | 0/8 44 h-lim-p 0.0000 0.0000 1.1222 2375.618044 0 0.0000 1073 | 0/8 45 h-lim-p 0.0000 0.0000 100.3718 .. | 0/8 46 h-lim-p 0.0000 0.0002 0.2408 2375.618044 0 0.0000 1128 | 0/8 47 h-lim-p 0.0000 0.0000 1.1058 .. | 0/8 48 h-lim-p 0.0000 0.0002 0.2408 Out... lnL = -2375.618044 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2375.618044 Node 7: lnL = -2375.618044 Node 8: lnL = -2375.618044 Node 9: lnL = -2375.618044 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 869 Sequential format.. Reading seq # 1: YHR206W_Sbay Reading seq # 2: YHR206W_Scer Reading seq # 3: YHR206W_Skud Reading seq # 4: YHR206W_Smik Reading seq # 5: YHR206W_Spar Sequences read.. Counting patterns.. # site patterns = 251 Counting frequencies.. 120 bytes for distance 40160 bytes for lkl0 32128 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.013993 0.039881 0.034147 0.106749 0.079297 0.154218 0.210109 0.253029 lnL0 = -3705.302626 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3705.302626 x= 0.01399 0.03988 0.03415 0.10675 0.07930 0.15422 0.21011 0.25303 1 h-lim-p 0.0004 0.0031 335.3413 3700.418974 4 0.0001 31 | 0/8 2 h-lim-p 0.0003 0.0021 56.4092 3700.138732 6 0.0002 57 | 0/8 3 h-lim-p 0.0004 0.0031 14.6351 3700.119409 4 0.0002 77 | 0/8 4 h-lim-p 0.0005 0.0058 5.6153 3700.115768 4 0.0003 98 | 0/8 5 h-lim-p 0.0010 0.1841 1.4594 3700.115423 4 0.0003 121 | 0/8 6 h-lim-p 0.0013 0.6203 0.3773 3700.115406 1 0.0003 136 | 0/8 7 h-lim-p 0.0063 10.1675 0.0160 3700.115405 0 0.0014 157 | 0/8 8 h-lim-p 0.0210 20.0000 0.0010 3700.114905 0 0.3363 181 | 0/8 9 h-lim-p 2.3745 20.0000 0.0001 3700.114897 0 1.0389 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 3700.114897 0 1.0938 221 | 0/8 11 h-lim-p 1.3073 20.0000 0.0000 3700.114897 0 3.9218 242 | 0/8 12 h-lim-p 0.0921 10.9715 0.0018 3700.114897 0 0.0086 265 | 0/8 13 h-lim-p 0.0021 2.7060 0.0073 3700.114897 0 0.0001 288 | 0/8 14 h-lim-p 0.0002 3.3815 0.0058 3700.114897 0 0.0000 311 | 0/8 15 h-lim-p 0.0002 20.0000 0.0002 3700.114897 0 0.0000 339 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 3700.114897 0 0.0000 372 Out... lnL = -3700.114897 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3700.114897 Node 7: lnL = -3700.114897 Node 8: lnL = -3700.114897 Node 9: lnL = -3700.114897 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 873 Sequential format.. Reading seq # 1: YHR207C_Sbay Reading seq # 2: YHR207C_Scer Reading seq # 3: YHR207C_Skud Reading seq # 4: YHR207C_Smik Reading seq # 5: YHR207C_Spar Sequences read.. Counting patterns.. # site patterns = 394 Counting frequencies.. 120 bytes for distance 63040 bytes for lkl0 50432 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.013630 0.029501 0.156969 0.141373 0.133019 0.342574 0.440050 0.470149 lnL0 = -4569.597213 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4569.597213 x= 0.01363 0.02950 0.15697 0.14137 0.13302 0.34257 0.44005 0.47015 1 h-lim-p 0.0007 0.0058 102.4954 4567.628849 9 0.0004 45 | 0/8 2 h-lim-p 0.0006 0.0049 24.0616 4567.395362 0 0.0009 57 | 0/8 3 h-lim-p 0.0006 0.0049 17.0071 4567.351471 6 0.0004 84 | 0/8 4 h-lim-p 0.0007 0.0068 11.0571 4567.331120 4 0.0005 104 | 0/8 5 h-lim-p 0.0014 0.0354 4.1455 4567.326207 4 0.0007 125 | 0/8 6 h-lim-p 0.0018 0.3758 1.6541 4567.325068 4 0.0010 147 | 0/8 7 h-lim-p 0.0121 0.2148 0.1398 4567.325048 0 0.0015 161 | 0/8 8 h-lim-p 0.0769 20.0000 0.0028 4567.321549 0 0.6149 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 4567.321388 1 1.0938 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 4567.321387 0 1.0938 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4567.321387 0 1.0938 246 | 0/8 12 h-lim-p 1.0667 20.0000 0.0000 4567.321387 0 2.1334 267 | 0/8 13 h-lim-p 0.0147 8.4669 0.0026 4567.321387 0 0.0000 313 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 4567.321387 0 0.0000 346 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 4567.321387 0 0.0000 371 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 4567.321387 0 0.0000 438 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -4567.321387 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4567.321387 Node 7: lnL = -4567.321387 Node 8: lnL = -4567.321387 Node 9: lnL = -4567.321387 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 772 Sequential format.. Reading seq # 1: YHR209W_Sbay Reading seq # 2: YHR209W_Scer Reading seq # 3: YHR209W_Skud Reading seq # 4: YHR209W_Smik Reading seq # 5: YHR209W_Spar Sequences read.. Counting patterns.. # site patterns = 398 Counting frequencies.. 120 bytes for distance 63680 bytes for lkl0 50944 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.081841 0.000060 0.323655 0.155534 0.104830 0.590811 0.381036 0.693441 lnL0 = -4241.027134 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4241.027134 x= 0.08184 0.00006 0.32366 0.15553 0.10483 0.59081 0.38104 0.69344 1 h-lim-p 0.0051 0.0405 29.6199 4240.704657 5 0.0007 36 | 0/8 2 h-lim-p 0.0005 0.0109 49.0576 4240.197981 0 0.0009 49 | 0/8 3 h-lim-p 0.0024 0.0190 15.3965 4240.104849 2 0.0011 65 | 0/8 4 h-lim-p 0.0085 0.1254 2.0189 4240.098171 4 0.0034 85 | 0/8 5 h-lim-p 0.0102 1.4895 0.6642 4240.097824 4 0.0017 108 | 0/8 6 h-lim-p 0.0017 0.6268 0.6638 4240.097655 3 0.0013 134 | 0/8 7 h-lim-p 0.0204 14.9706 0.0430 4240.097640 2 0.0067 160 | 0/8 8 h-lim-p 0.0541 20.0000 0.0054 4240.096160 0 0.4325 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 4240.096139 1 0.9961 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4240.096139 0 1.0938 225 | 0/8 11 h-lim-p 1.1030 20.0000 0.0000 4240.096139 0 8.8242 248 | 0/8 12 h-lim-p 0.0849 20.0000 0.0007 4240.096139 0 0.0001 278 | 0/8 13 h-lim-p 0.0002 20.0000 0.0003 4240.096139 0 0.0000 310 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -4240.096139 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4240.096139 Node 7: lnL = -4240.096139 Node 8: lnL = -4240.096139 Node 9: lnL = -4240.096139 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 542 Sequential format.. Reading seq # 1: YIL002C_Sbay Reading seq # 2: YIL002C_Scer Reading seq # 3: YIL002C_Skud Reading seq # 4: YIL002C_Smik Reading seq # 5: YIL002C_Spar Sequences read.. Counting patterns.. # site patterns = 228 Counting frequencies.. 120 bytes for distance 36480 bytes for lkl0 29184 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.178858 0.200622 0.165851 0.154775 0.324231 0.305505 0.332825 lnL0 = -2586.513426 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2586.513426 x= 0.00006 0.17886 0.20062 0.16585 0.15478 0.32423 0.30551 0.33282 1 h-lim-p 0.0000 0.0000 273.8778 2586.438599 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0053 82.6211 2582.923129 0 0.0013 41 | 1/8 3 h-lim-p 0.0017 0.0134 27.7886 2582.252421 6 0.0018 67 | 1/8 4 h-lim-p 0.0138 0.1523 3.6667 2582.008491 4 0.0070 88 | 1/8 5 h-lim-p 0.0054 0.0480 4.7585 2579.578657 0 0.0217 102 | 1/8 6 h-lim-p 0.0027 0.0212 15.1050 2563.458825 0 0.0106 116 | 0/8 7 h-lim-p 0.0013 0.0106 15.0265 2563.406951 7 0.0004 146 | 0/8 8 h-lim-p 0.0009 0.0451 7.5539 2563.385945 4 0.0008 165 | 0/8 9 h-lim-p 0.0030 0.0242 1.1328 2563.336457 0 0.0091 178 | 0/8 10 h-lim-p 0.0100 0.2658 1.0303 2561.373454 0 0.0399 192 | 0/8 11 h-lim-p 0.6041 4.8330 0.0270 2561.207743 3 0.5050 210 | 0/8 12 h-lim-p 2.5000 20.0000 0.0040 2561.200434 5 0.9273 241 | 0/8 13 h-lim-p 2.5000 20.0000 0.0006 2561.200057 3 1.0004 267 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 2561.200054 0 1.2500 287 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2561.200054 0 1.0938 307 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 2561.200054 0 1.0938 327 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 2561.200054 0 2.1875 347 | 0/8 18 h-lim-p 1.9174 20.0000 0.0000 2561.200054 0 0.8389 367 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 2561.200054 0 0.0586 392 | 0/8 20 h-lim-p 0.0492 20.0000 0.0000 2561.200054 0 0.0046 415 Out... lnL = -2561.200054 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2561.200054 Node 7: lnL = -2561.200054 Node 8: lnL = -2561.200054 Node 9: lnL = -2561.200054 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 670 Sequential format.. Reading seq # 1: YIL003W_Sbay Reading seq # 2: YIL003W_Scer Reading seq # 3: YIL003W_Skud Reading seq # 4: YIL003W_Smik Reading seq # 5: YIL003W_Spar Sequences read.. Counting patterns.. # site patterns = 252 Counting frequencies.. 120 bytes for distance 40320 bytes for lkl0 32256 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.001425 0.107312 0.051555 0.152456 0.100062 0.230737 0.196686 0.309710 lnL0 = -3162.559236 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3162.559236 x= 0.00142 0.10731 0.05155 0.15246 0.10006 0.23074 0.19669 0.30971 1 h-lim-p 0.0006 0.0047 120.2456 3160.935213 5 0.0002 33 | 0/8 2 h-lim-p 0.0006 0.0047 33.1363 3160.749781 8 0.0004 68 | 0/8 3 h-lim-p 0.0008 0.0217 15.1515 3160.715451 2 0.0004 84 | 0/8 4 h-lim-p 0.0013 0.0134 4.2859 3160.711445 5 0.0005 106 | 0/8 5 h-lim-p 0.0049 0.7015 0.4266 3160.711381 3 0.0007 127 | 0/8 6 h-lim-p 0.0081 6.4223 0.0379 3160.711381 0 0.0004 150 | 0/8 7 h-lim-p 0.0059 5.4125 0.0029 3160.711381 0 0.0052 170 | 0/8 8 h-lim-p 0.0244 20.0000 0.0006 3160.711361 0 0.1954 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3160.711361 0 1.0938 213 | 0/8 10 h-lim-p 1.4209 20.0000 0.0000 3160.711361 0 1.4209 233 | 0/8 11 h-lim-p 1.2059 20.0000 0.0000 3160.711361 0 1.2059 253 | 0/8 12 h-lim-p 0.0116 3.8183 0.0034 3160.711361 0 0.0011 276 | 0/8 13 h-lim-p 0.0004 1.3994 0.0093 3160.711361 0 0.0000 312 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 3160.711361 0 0.0000 345 Out... lnL = -3160.711361 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3160.711361 Node 7: lnL = -3160.711361 Node 8: lnL = -3160.711361 Node 9: lnL = -3160.711361 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 419 Sequential format.. Reading seq # 1: YIL006W_Sbay Reading seq # 2: YIL006W_Scer Reading seq # 3: YIL006W_Skud Reading seq # 4: YIL006W_Smik Reading seq # 5: YIL006W_Spar Sequences read.. Counting patterns.. # site patterns = 172 Counting frequencies.. 120 bytes for distance 27520 bytes for lkl0 22016 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.087556 0.062120 0.113606 0.123141 0.187787 0.199601 0.246381 lnL0 = -1788.506690 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1788.506690 x= 0.00006 0.08756 0.06212 0.11361 0.12314 0.18779 0.19960 0.24638 1 h-lim-p 0.0000 0.0000 66.9245 1788.477558 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0081 30.0262 1788.235385 0 0.0007 39 | 1/8 3 h-lim-p 0.0038 0.0346 5.3670 1788.224466 4 0.0007 60 | 1/8 4 h-lim-p 0.0030 0.2252 1.3335 1788.220696 5 0.0020 85 | 1/8 5 h-lim-p 0.0029 0.1850 0.9406 1788.211233 0 0.0043 97 | 1/8 6 h-lim-p 0.0065 0.3023 0.6182 1787.532591 0 0.0523 119 | 0/8 7 h-lim-p 0.0014 0.0110 14.6625 1787.375554 7 0.0009 155 | 0/8 8 h-lim-p 0.0003 0.0023 9.2321 1787.352150 0 0.0006 168 | 0/8 9 h-lim-p 0.0002 0.0019 2.9850 1787.346068 m 0.0019 180 | 0/8 10 h-lim-p 0.9070 20.0000 0.0062 1787.317505 2 0.8503 196 | 0/8 11 h-lim-p 2.5000 20.0000 0.0002 1787.317477 2 0.9644 220 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1787.317476 0 1.0938 240 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1787.317476 0 1.0938 260 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1787.317476 0 0.5469 281 | 0/8 15 h-lim-p 1.2116 20.0000 0.0000 1787.317476 0 0.0663 304 | 0/8 16 h-lim-p 0.0632 20.0000 0.0000 1787.317476 0 0.0010 329 Out... lnL = -1787.317476 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1787.317476 Node 7: lnL = -1787.317476 Node 8: lnL = -1787.317476 Node 9: lnL = -1787.317476 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 419 Sequential format.. Reading seq # 1: YIL007C_Sbay Reading seq # 2: YIL007C_Scer Reading seq # 3: YIL007C_Skud Reading seq # 4: YIL007C_Smik Reading seq # 5: YIL007C_Spar Sequences read.. Counting patterns.. # site patterns = 168 Counting frequencies.. 120 bytes for distance 26880 bytes for lkl0 21504 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.074020 0.043205 0.107442 0.120440 0.181938 0.202051 0.254441 lnL0 = -1865.015911 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1865.015911 x= 0.00006 0.07402 0.04321 0.10744 0.12044 0.18194 0.20205 0.25444 1 h-lim-p 0.0015 0.0116 53.7595 1864.570378 5 0.0003 32 | 0/8 2 h-lim-p 0.0008 0.0094 22.2004 1864.469776 7 0.0005 61 | 0/8 3 h-lim-p 0.0008 0.0065 6.2301 1864.461275 5 0.0005 85 | 0/8 4 h-lim-p 0.0013 0.0102 1.5485 1864.460709 3 0.0005 103 | 0/8 5 h-lim-p 0.0016 0.1136 0.4897 1864.460626 2 0.0008 119 | 0/8 6 h-lim-p 0.0055 0.2552 0.0667 1864.460624 1 0.0007 143 | 0/8 7 h-lim-p 0.0007 0.0806 0.0676 1864.460589 0 0.0214 168 | 0/8 8 h-lim-p 0.0003 0.0025 1.3805 1864.460548 0 0.0013 190 | 0/8 9 h-lim-p 0.6328 5.0620 0.0004 1864.460545 0 1.2655 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1864.460544 0 1.0938 223 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1864.460544 0 1.0938 243 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1864.460544 0 2.5000 263 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1864.460544 0 0.0073 291 | 0/8 14 h-lim-p 0.0012 20.0000 0.0000 1864.460544 0 0.0012 311 | 0/8 15 h-lim-p 0.0005 20.0000 0.0000 1864.460544 0 0.0001 332 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 1864.460544 0 0.0000 352 | 0/8 17 h-lim-p 0.0000 1.3686 0.0011 1864.460544 0 0.0000 380 | 0/8 18 h-lim-p 0.0001 20.0000 0.0000 1864.460544 0 0.0000 408 Out... lnL = -1864.460544 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1864.460544 Node 7: lnL = -1864.460544 Node 8: lnL = -1864.460544 Node 9: lnL = -1864.460544 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 855 Sequential format.. Reading seq # 1: YIL008W_Sbay Reading seq # 2: YIL008W_Scer Reading seq # 3: YIL008W_Skud Reading seq # 4: YIL008W_Smik Reading seq # 5: YIL008W_Spar Sequences read.. Counting patterns.. # site patterns = 453 Counting frequencies.. 120 bytes for distance 72480 bytes for lkl0 57984 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.217354 0.272808 0.210588 0.402103 0.394765 0.542889 0.577106 lnL0 = -4815.077859 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4815.077859 x= 0.00006 0.21735 0.27281 0.21059 0.40210 0.39476 0.54289 0.57711 1 h-lim-p 0.0000 0.0000 199.8353 4814.997324 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0127 58.4694 4812.710589 0 0.0013 41 | 1/8 3 h-lim-p 0.0040 0.0317 15.7411 4812.195765 6 0.0039 67 | 1/8 4 h-lim-p 0.0148 0.1698 4.1198 4811.893759 7 0.0092 98 | 1/8 5 h-lim-p 0.0149 0.1979 2.5536 4806.143065 0 0.0596 112 | 1/8 6 h-lim-p 0.0016 0.0125 27.1364 4799.639273 0 0.0063 126 | 1/8 7 h-lim-p 0.0024 0.0190 29.5012 4798.544256 2 0.0022 142 | 1/8 8 h-lim-p 0.0091 0.0729 3.5760 4798.510510 6 0.0037 165 | 0/8 9 h-lim-p 0.0015 2.5598 8.8519 4798.417129 0 0.0022 177 | 0/8 10 h-lim-p 0.1470 5.3603 0.1342 4796.874031 0 0.4410 190 | 0/8 11 h-lim-p 2.3450 20.0000 0.0252 4796.805878 5 0.6237 221 | 0/8 12 h-lim-p 2.5000 20.0000 0.0048 4796.798244 4 0.8855 251 | 0/8 13 h-lim-p 2.5000 20.0000 0.0010 4796.797927 4 0.7063 282 | 0/8 14 h-lim-p 2.5000 20.0000 0.0002 4796.797916 2 0.8246 308 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 4796.797916 0 1.0938 328 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 4796.797916 0 1.0938 348 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 4796.797916 0 2.1875 368 | 0/8 18 h-lim-p 1.8558 20.0000 0.0000 4796.797916 0 0.8119 388 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 4796.797916 0 0.3125 410 | 0/8 20 h-lim-p 0.2591 20.0000 0.0000 4796.797916 0 0.0005 438 Out... lnL = -4796.797916 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4796.797916 Node 7: lnL = -4796.797916 Node 8: lnL = -4796.797916 Node 9: lnL = -4796.797916 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 843 Sequential format.. Reading seq # 1: YIL009C-A_Sbay Reading seq # 2: YIL009C-A_Scer Reading seq # 3: YIL009C-A_Skud Reading seq # 4: YIL009C-A_Smik Reading seq # 5: YIL009C-A_Spar Sequences read.. Counting patterns.. # site patterns = 398 Counting frequencies.. 120 bytes for distance 63680 bytes for lkl0 50944 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.200674 0.157296 0.219313 0.199006 0.164176 0.279968 0.463148 lnL0 = -4153.720719 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4153.720719 x= 0.00006 0.20067 0.15730 0.21931 0.19901 0.16418 0.27997 0.46315 1 h-lim-p 0.0043 0.0598 138.7444 4147.754744 9 0.0007 46 | 0/8 2 h-lim-p 0.0010 0.0079 43.3742 4146.843694 4 0.0010 66 | 0/8 3 h-lim-p 0.0008 0.0063 38.3795 4146.483231 5 0.0008 88 | 0/8 4 h-lim-p 0.0024 0.0251 12.5997 4146.397275 6 0.0013 116 | 0/8 5 h-lim-p 0.0013 0.0102 5.2816 4146.382977 4 0.0012 138 | 0/8 6 h-lim-p 0.0122 1.1212 0.5419 4146.382473 2 0.0030 155 | 0/8 7 h-lim-p 0.0023 1.0515 0.7245 4146.379620 0 0.0180 178 | 0/8 8 h-lim-p 0.0016 0.0839 7.9844 4146.347844 0 0.0196 201 | 0/8 9 h-lim-p 1.1787 9.4294 0.0204 4146.346933 2 1.0267 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4146.346932 0 1.0938 237 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4146.346932 0 1.0938 257 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4146.346932 0 1.0938 277 | 0/8 13 h-lim-p 1.2349 20.0000 0.0000 4146.346932 0 1.2349 297 | 0/8 14 h-lim-p 0.0051 20.0000 0.0007 4146.346932 0 0.0002 321 | 0/8 15 h-lim-p 0.0007 20.0000 0.0002 4146.346932 0 0.0001 343 | 0/8 16 h-lim-p 0.0001 20.0000 0.0001 4146.346932 0 0.0001 363 | 0/8 17 h-lim-p 0.0001 20.0000 0.0001 4146.346932 0 0.0000 395 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -4146.346932 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4146.346932 Node 7: lnL = -4146.346932 Node 8: lnL = -4146.346932 Node 9: lnL = -4146.346932 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 365 Sequential format.. Reading seq # 1: YIL010W_Sbay Reading seq # 2: YIL010W_Scer Reading seq # 3: YIL010W_Skud Reading seq # 4: YIL010W_Smik Reading seq # 5: YIL010W_Spar Sequences read.. Counting patterns.. # site patterns = 145 Counting frequencies.. 120 bytes for distance 23200 bytes for lkl0 18560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.030901 0.024171 0.062139 0.119434 0.083131 0.123028 0.145135 0.244644 lnL0 = -1500.987534 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1500.987534 x= 0.03090 0.02417 0.06214 0.11943 0.08313 0.12303 0.14514 0.24464 1 h-lim-p 0.0026 0.0207 75.2862 1500.357502 8 0.0002 42 | 0/8 2 h-lim-p 0.0015 0.0125 11.9748 1500.323634 7 0.0005 70 | 0/8 3 h-lim-p 0.0027 0.1305 2.1266 1500.322694 5 0.0004 96 | 0/8 4 h-lim-p 0.0017 0.3483 0.5276 1500.322626 3 0.0005 117 | 0/8 5 h-lim-p 0.0016 1.0611 0.1668 1500.322620 2 0.0004 142 | 0/8 6 h-lim-p 0.0038 8.7822 0.0187 1500.322620 0 0.0008 163 | 0/8 7 h-lim-p 0.0055 20.0000 0.0028 1500.322620 0 0.0048 183 | 0/8 8 h-lim-p 0.0397 20.0000 0.0003 1500.322606 0 0.3180 206 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1500.322606 0 1.0938 226 | 0/8 10 h-lim-p 1.2071 20.0000 0.0000 1500.322606 0 1.2071 246 | 0/8 11 h-lim-p 1.1465 20.0000 0.0000 1500.322606 0 0.0003 277 | 0/8 12 h-lim-p 0.0000 6.2216 0.0080 .. | 0/8 13 h-lim-p 0.0000 20.0000 0.0006 | 0/8 14 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -1500.322606 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1500.322606 Node 7: lnL = -1500.322606 Node 8: lnL = -1500.322606 Node 9: lnL = -1500.322606 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 590 Sequential format.. Reading seq # 1: YIL013C_Sbay Reading seq # 2: YIL013C_Scer Reading seq # 3: YIL013C_Skud Reading seq # 4: YIL013C_Smik Reading seq # 5: YIL013C_Spar Sequences read.. Counting patterns.. # site patterns = 199 Counting frequencies.. 120 bytes for distance 31840 bytes for lkl0 25472 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.042225 0.038728 0.118924 0.075828 0.104115 0.189814 0.184299 lnL0 = -2370.370797 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2370.370797 x= 0.00006 0.04222 0.03873 0.11892 0.07583 0.10412 0.18981 0.18430 1 h-lim-p 0.0003 0.0027 209.8726 2367.460044 5 0.0001 31 | 0/8 2 h-lim-p 0.0004 0.0034 38.4690 2367.303834 4 0.0002 51 | 0/8 3 h-lim-p 0.0007 0.0157 11.3536 2367.289614 6 0.0002 76 | 0/8 4 h-lim-p 0.0010 0.0152 2.8157 2367.287806 4 0.0005 98 | 0/8 5 h-lim-p 0.0029 0.5002 0.4802 2367.287764 2 0.0004 116 | 0/8 6 h-lim-p 0.0021 0.0464 0.0852 2367.287756 0 0.0021 136 | 0/8 7 h-lim-p 0.0003 0.0057 0.5867 2367.287612 m 0.0057 158 | 0/8 8 h-lim-p -0.0000 -0.0000 1.4640 h-lim-p: -3.99208097e-21 -3.19366477e-20 1.46401028e+00 2367.287612 .. | 0/8 9 h-lim-p 0.0000 0.0362 2.3360 2367.287088 0 0.0002 190 | 0/8 10 h-lim-p 0.0013 0.6499 0.4156 2367.287064 1 0.0003 205 | 0/8 11 h-lim-p 0.0008 0.0063 0.1074 2367.287063 0 0.0003 225 | 0/8 12 h-lim-p 0.0004 0.0029 0.0905 2367.287063 0 0.0002 245 | 0/8 13 h-lim-p 0.0000 0.0008 0.3022 2367.287063 0 0.0001 266 | 0/8 14 h-lim-p 0.0000 0.0001 2.2682 2367.287063 0 0.0000 301 | 0/8 15 h-lim-p 0.0000 0.1524 0.0259 2367.287063 0 0.0003 318 | 0/8 16 h-lim-p 0.0089 20.0000 0.0009 2367.287062 0 0.0178 339 | 0/8 17 h-lim-p 0.0029 20.0000 0.0056 2367.287043 0 0.0236 362 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 2367.287042 0 1.0938 382 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 2367.287042 0 2.1875 402 | 0/8 20 h-lim-p 1.9283 20.0000 0.0000 2367.287042 0 0.0527 426 | 0/8 21 h-lim-p 0.0560 20.0000 0.0000 2367.287042 0 0.0000 456 Out... lnL = -2367.287042 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2367.287042 Node 7: lnL = -2367.287042 Node 8: lnL = -2367.287042 Node 9: lnL = -2367.287042 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 646 Sequential format.. Reading seq # 1: YIL014W_Sbay Reading seq # 2: YIL014W_Scer Reading seq # 3: YIL014W_Skud Reading seq # 4: YIL014W_Smik Reading seq # 5: YIL014W_Spar Sequences read.. Counting patterns.. # site patterns = 343 Counting frequencies.. 120 bytes for distance 54880 bytes for lkl0 43904 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.040121 0.000060 0.163017 0.256233 0.209648 0.265492 0.394514 0.452619 lnL0 = -3359.689991 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3359.689991 x= 0.04012 0.00006 0.16302 0.25623 0.20965 0.26549 0.39451 0.45262 1 h-lim-p 0.0000 0.0000 147.6502 3359.602788 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0110 31.3381 3359.267003 0 0.0006 39 | 1/8 3 h-lim-p 0.0014 0.0416 13.8141 3359.138948 4 0.0014 59 | 1/8 4 h-lim-p 0.0056 0.1959 3.3989 3359.081511 5 0.0032 83 | 1/8 5 h-lim-p 0.0062 0.1869 1.7575 3357.699727 0 0.0369 97 | 1/8 6 h-lim-p 0.0023 0.0184 17.8527 3350.207094 0 0.0069 110 | 1/8 7 h-lim-p 0.0050 0.0397 3.6728 3350.200029 4 0.0010 131 | 1/8 8 h-lim-p 0.1103 20.0000 0.0319 3349.505244 0 0.8825 146 | 1/8 9 h-lim-p 2.4672 20.0000 0.0114 3349.449453 2 1.1565 169 | 1/8 10 h-lim-p 2.5000 20.0000 0.0010 3349.448930 2 1.0889 192 | 1/8 11 h-lim-p 2.5000 20.0000 0.0002 3349.448907 1 0.9961 213 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 3349.448907 0 1.0938 232 | 1/8 13 h-lim-p 2.2707 20.0000 0.0000 3349.448907 0 0.9935 251 | 1/8 14 h-lim-p 1.0047 20.0000 0.0000 3349.448907 0 0.8791 270 | 1/8 15 h-lim-p 0.1276 20.0000 0.0001 3349.448907 0 0.0005 296 | 1/8 16 h-lim-p 0.0005 20.0000 0.0001 3349.448907 0 0.0000 318 | 1/8 17 h-lim-p 0.0005 20.0000 0.0000 3349.448907 0 0.0000 348 Out... lnL = -3349.448907 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3349.448907 Node 7: lnL = -3349.448907 Node 8: lnL = -3349.448907 Node 9: lnL = -3349.448907 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 432 Sequential format.. Reading seq # 1: YIL015W_Sbay Reading seq # 2: YIL015W_Scer Reading seq # 3: YIL015W_Skud Reading seq # 4: YIL015W_Smik Reading seq # 5: YIL015W_Spar Sequences read.. Counting patterns.. # site patterns = 200 Counting frequencies.. 120 bytes for distance 32000 bytes for lkl0 25600 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.122421 0.045517 0.153523 0.118650 0.169570 0.125871 0.242324 lnL0 = -1846.264920 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1846.264920 x= 0.00006 0.12242 0.04552 0.15352 0.11865 0.16957 0.12587 0.24232 1 h-lim-p 0.0000 0.0000 133.5722 1846.157422 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0019 77.9721 1845.231833 0 0.0003 39 | 1/8 3 h-lim-p 0.0018 0.0186 14.4781 1845.154280 5 0.0008 63 | 1/8 4 h-lim-p 0.0050 0.1500 2.2008 1845.146434 5 0.0015 88 | 1/8 5 h-lim-p 0.0026 0.2040 1.2358 1845.091561 0 0.0106 102 | 0/8 6 h-lim-p 0.0018 0.0518 7.0673 1844.272914 0 0.0148 117 | 0/8 7 h-lim-p 0.0012 0.0098 35.4082 1843.659729 7 0.0013 147 | 0/8 8 h-lim-p 0.0018 0.0140 10.7221 1842.659632 0 0.0070 161 | 0/8 9 h-lim-p 0.0003 0.0027 32.2474 1842.394624 0 0.0010 174 | 0/8 10 h-lim-p 0.2579 2.0632 0.0217 1842.287500 0 1.0316 188 | 0/8 11 h-lim-p 2.2858 18.2863 0.0023 1842.283448 2 1.0715 212 | 0/8 12 h-lim-p 2.5000 20.0000 0.0003 1842.283391 2 1.1719 236 | 0/8 13 h-lim-p 2.3961 20.0000 0.0001 1842.283389 1 1.1793 259 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1842.283389 0 1.0938 279 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1842.283389 0 1.0938 299 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1842.283389 0 2.5000 319 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1842.283389 0 0.0684 343 | 0/8 18 h-lim-p 0.0116 20.0000 0.0000 1842.283389 0 0.0000 384 Out... lnL = -1842.283389 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1842.283389 Node 7: lnL = -1842.283389 Node 8: lnL = -1842.283389 Node 9: lnL = -1842.283389 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 521 Sequential format.. Reading seq # 1: YIL016W_Sbay Reading seq # 2: YIL016W_Scer Reading seq # 3: YIL016W_Skud Reading seq # 4: YIL016W_Smik Reading seq # 5: YIL016W_Spar Sequences read.. Counting patterns.. # site patterns = 206 Counting frequencies.. 120 bytes for distance 32960 bytes for lkl0 26368 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.158479 0.074176 0.185771 0.124635 0.159459 0.167980 0.280433 lnL0 = -2361.870509 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2361.870509 x= 0.00006 0.15848 0.07418 0.18577 0.12464 0.15946 0.16798 0.28043 1 h-lim-p 0.0000 0.0000 204.4909 2361.809484 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0014 103.3285 2360.537099 0 0.0003 39 | 1/8 3 h-lim-p 0.0014 0.0124 23.2974 2360.372918 5 0.0006 60 | 1/8 4 h-lim-p 0.0015 0.0240 9.4438 2360.334338 4 0.0008 81 | 1/8 5 h-lim-p 0.0031 0.1105 2.3810 2360.261173 0 0.0046 93 | 1/8 6 h-lim-p 0.0029 0.0620 3.7894 2359.410038 0 0.0116 107 | 1/8 7 h-lim-p 0.0025 0.0203 13.1187 2353.859675 0 0.0051 120 | 1/8 8 h-lim-p 0.0004 0.0032 67.6234 2352.221248 0 0.0006 132 | 1/8 9 h-lim-p 1.5690 20.0000 0.0261 2351.526039 5 0.8346 155 | 1/8 10 h-lim-p 2.5000 20.0000 0.0065 2351.463902 4 1.0889 181 | 1/8 11 h-lim-p 2.4760 20.0000 0.0029 2351.457541 5 0.8694 212 | 0/8 12 h-lim-p 0.0126 3.0592 0.1974 2351.457521 2 0.0012 237 | 0/8 13 h-lim-p 0.4645 20.0000 0.0005 2351.457151 0 1.8581 259 | 0/8 14 h-lim-p 1.1535 9.2277 0.0002 2351.457107 0 1.1535 279 | 0/8 15 h-lim-p 0.3933 3.1465 0.0001 2351.457106 0 1.1799 300 | 0/8 16 h-lim-p 0.0493 0.3947 0.0006 2351.457106 0 0.0216 320 | 0/8 17 h-lim-p 0.1331 20.0000 0.0001 2351.457106 0 0.5326 342 | 0/8 18 h-lim-p 0.0002 0.0019 0.1143 2351.457106 0 0.0001 362 | 0/8 19 h-lim-p 0.0001 1.9286 0.1976 2351.457106 0 0.0000 384 | 0/8 20 h-lim-p 0.0000 0.0006 0.3588 2351.457106 0 0.0000 409 | 0/8 21 h-lim-p 0.0000 0.0159 0.0130 2351.457106 0 0.0000 430 | 0/8 22 h-lim-p 0.0001 0.0737 0.0028 2351.457106 0 0.0003 451 | 0/8 23 h-lim-p 0.0007 0.1862 0.0011 2351.457106 0 0.0014 472 | 0/8 24 h-lim-p 0.0028 0.3770 0.0006 2351.457106 0 0.0024 492 | 0/8 25 h-lim-p 0.0044 0.6984 0.0003 2351.457106 0 0.0066 512 | 0/8 26 h-lim-p 0.0115 1.2714 0.0002 2351.457106 0 0.0101 532 | 0/8 27 h-lim-p 0.0176 2.4396 0.0001 2351.457106 0 0.0176 552 | 0/8 28 h-lim-p 0.0316 5.5041 0.0001 2351.457106 0 0.0316 572 | 0/8 29 h-lim-p 0.0602 20.0000 0.0000 2351.457106 0 0.0527 592 | 0/8 30 h-lim-p 0.1249 20.0000 0.0000 2351.457106 0 0.1249 612 | 0/8 31 h-lim-p 0.2484 20.0000 0.0000 2351.457106 0 0.0000 644 Out... lnL = -2351.457106 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2351.457106 Node 7: lnL = -2351.457106 Node 8: lnL = -2351.457106 Node 9: lnL = -2351.457106 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 507 Sequential format.. Reading seq # 1: YIL017C_Sbay Reading seq # 2: YIL017C_Scer Reading seq # 3: YIL017C_Skud Reading seq # 4: YIL017C_Smik Reading seq # 5: YIL017C_Spar Sequences read.. Counting patterns.. # site patterns = 194 Counting frequencies.. 120 bytes for distance 31040 bytes for lkl0 24832 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.152944 0.054563 0.179754 0.117004 0.166667 0.162516 0.270087 lnL0 = -2303.849482 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2303.849482 x= 0.00006 0.15294 0.05456 0.17975 0.11700 0.16667 0.16252 0.27009 1 h-lim-p 0.0000 0.0000 180.6905 2303.789454 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0010 109.4013 2302.642879 0 0.0002 38 | 1/8 3 h-lim-p 0.0013 0.0199 20.2050 2302.499473 7 0.0007 65 | 1/8 4 h-lim-p 0.0025 0.0340 5.7062 2302.479468 6 0.0009 90 | 1/8 5 h-lim-p 0.0030 0.1816 1.6794 2302.404136 0 0.0061 103 | 1/8 6 h-lim-p 0.0022 0.0547 4.6460 2301.722042 0 0.0066 116 | 1/8 7 h-lim-p 0.0021 0.0164 11.5949 2297.211813 0 0.0041 129 | 1/8 8 h-lim-p 0.0012 0.0094 27.3396 2297.028089 6 0.0005 155 | 1/8 9 h-lim-p 0.8556 20.0000 0.0152 2296.542734 0 1.7113 168 | 1/8 10 h-lim-p 2.5000 20.0000 0.0077 2296.479031 5 1.0721 196 | 0/8 11 h-lim-p 0.0282 3.2674 0.2924 2296.478991 3 0.0009 225 | 0/8 12 h-lim-p 0.2072 20.0000 0.0013 2296.477570 0 0.8287 247 | 0/8 13 h-lim-p 2.5000 20.0000 0.0003 2296.477409 4 1.4126 278 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 2296.477407 0 1.0938 298 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2296.477407 0 1.0938 318 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 2296.477407 0 1.2500 338 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 2296.477407 0 0.0049 366 Out... lnL = -2296.477407 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2296.477407 Node 7: lnL = -2296.477407 Node 8: lnL = -2296.477407 Node 9: lnL = -2296.477407 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 477 Sequential format.. Reading seq # 1: YIL021W_Sbay Reading seq # 2: YIL021W_Scer Reading seq # 3: YIL021W_Skud Reading seq # 4: YIL021W_Smik Reading seq # 5: YIL021W_Spar Sequences read.. Counting patterns.. # site patterns = 156 Counting frequencies.. 120 bytes for distance 24960 bytes for lkl0 19968 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.018044 0.026946 0.046073 0.085763 0.061229 0.123750 0.159116 0.203852 lnL0 = -1813.479296 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1813.479296 x= 0.01804 0.02695 0.04607 0.08576 0.06123 0.12375 0.15912 0.20385 1 h-lim-p 0.0023 0.0372 125.8600 1812.295098 9 0.0002 48 | 0/8 2 h-lim-p 0.0006 0.0046 24.4514 1812.166854 4 0.0004 68 | 0/8 3 h-lim-p 0.0008 0.0144 12.8742 1812.148683 5 0.0003 93 | 0/8 4 h-lim-p 0.0017 0.0269 2.0372 1812.148011 2 0.0003 110 | 0/8 5 h-lim-p 0.0008 0.0544 0.8950 1812.147914 3 0.0003 128 | 0/8 6 h-lim-p 0.0058 3.2144 0.0444 1812.147914 0 0.0006 150 | 0/8 7 h-lim-p 0.0031 12.2743 0.0090 1812.147913 0 0.0027 170 | 0/8 8 h-lim-p 0.0145 20.0000 0.0017 1812.147699 0 0.2328 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1812.147683 1 0.9961 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1812.147683 0 2.1875 236 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1812.147683 0 1.0938 256 | 0/8 12 h-lim-p 0.1205 20.0000 0.0000 1812.147683 0 0.0075 279 | 0/8 13 h-lim-p 0.0002 20.0000 0.0012 1812.147683 0 0.0000 316 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -1812.147683 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1812.147683 Node 7: lnL = -1812.147683 Node 8: lnL = -1812.147683 Node 9: lnL = -1812.147683 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 844 Sequential format.. Reading seq # 1: YIL023C_Sbay Reading seq # 2: YIL023C_Scer Reading seq # 3: YIL023C_Skud Reading seq # 4: YIL023C_Smik Reading seq # 5: YIL023C_Spar Sequences read.. Counting patterns.. # site patterns = 355 Counting frequencies.. 120 bytes for distance 56800 bytes for lkl0 45440 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.200120 0.088168 0.239986 0.183488 0.191416 0.292476 0.370764 lnL0 = -3982.551209 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3982.551209 x= 0.00006 0.20012 0.08817 0.23999 0.18349 0.19142 0.29248 0.37076 1 h-lim-p 0.0000 0.0000 306.4381 3982.455542 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0011 248.3316 3975.823489 0 0.0003 39 | 1/8 3 h-lim-p 0.0009 0.0075 56.5721 3974.609414 8 0.0008 69 | 1/8 4 h-lim-p 0.0011 0.0086 25.6378 3974.436604 6 0.0006 94 | 1/8 5 h-lim-p 0.0030 0.0866 5.0205 3974.355036 6 0.0022 119 | 1/8 6 h-lim-p 0.0026 0.1147 4.1992 3973.606791 0 0.0105 133 | 1/8 7 h-lim-p 0.0041 0.0328 8.2178 3965.918832 0 0.0082 146 | 0/8 8 h-lim-p 0.0007 0.0056 85.6184 3959.319737 0 0.0011 158 | 0/8 9 h-lim-p 0.0003 0.0027 18.0294 3959.121368 0 0.0014 172 | 0/8 10 h-lim-p 0.6186 20.0000 0.0394 3957.135003 0 0.9279 184 | 0/8 11 h-lim-p 1.8243 14.5940 0.0191 3956.641170 7 1.3711 218 | 0/8 12 h-lim-p 2.5000 20.0000 0.0038 3956.623712 4 1.2732 247 | 0/8 13 h-lim-p 2.5000 20.0000 0.0014 3956.621240 5 1.4194 280 | 0/8 14 h-lim-p 2.5000 20.0000 0.0005 3956.621012 2 1.0938 304 | 0/8 15 h-lim-p 2.5000 20.0000 0.0001 3956.621007 0 1.0938 324 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 3956.621007 0 1.0938 344 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 3956.621007 0 2.1875 364 | 0/8 18 h-lim-p 2.0339 20.0000 0.0000 3956.621007 0 0.8898 384 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 3956.621007 0 0.0684 408 | 0/8 20 h-lim-p 0.0558 20.0000 0.0000 3956.621007 0 0.0017 432 Out... lnL = -3956.621007 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3956.621007 Node 7: lnL = -3956.621007 Node 8: lnL = -3956.621007 Node 9: lnL = -3956.621007 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 227 Sequential format.. Reading seq # 1: YIL024C_Sbay Reading seq # 2: YIL024C_Scer Reading seq # 3: YIL024C_Skud Reading seq # 4: YIL024C_Smik Reading seq # 5: YIL024C_Spar Sequences read.. Counting patterns.. # site patterns = 93 Counting frequencies.. 120 bytes for distance 14880 bytes for lkl0 11904 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.048015 0.032699 0.052682 0.072853 0.055445 0.111337 0.185555 0.257656 lnL0 = -923.026391 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 923.026391 x= 0.04801 0.03270 0.05268 0.07285 0.05544 0.11134 0.18556 0.25766 1 h-lim-p 0.0010 0.0079 88.8206 921.515110 5 0.0004 31 | 0/8 2 h-lim-p 0.0008 0.0065 16.1350 921.410718 5 0.0008 53 | 0/8 3 h-lim-p 0.0011 0.0232 12.1434 921.381664 5 0.0006 76 | 0/8 4 h-lim-p 0.0014 0.0431 5.0707 921.373834 6 0.0008 104 | 0/8 5 h-lim-p 0.0037 0.2011 1.0611 921.373223 5 0.0012 130 | 0/8 6 h-lim-p 0.0043 0.4425 0.2885 921.373175 3 0.0013 150 | 0/8 7 h-lim-p 0.0066 2.4700 0.0554 921.373174 1 0.0008 174 | 0/8 8 h-lim-p 0.0753 20.0000 0.0006 921.372830 0 1.2052 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 921.372826 1 0.9961 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 921.372826 0 1.0938 240 | 0/8 11 h-lim-p 1.2467 20.0000 0.0000 921.372826 0 3.7400 261 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 921.372826 0 0.2734 283 | 0/8 13 h-lim-p 0.3657 20.0000 0.0000 921.372826 0 0.0004 312 Out... lnL = -921.372826 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -921.372826 Node 7: lnL = -921.372826 Node 8: lnL = -921.372826 Node 9: lnL = -921.372826 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 284 Sequential format.. Reading seq # 1: YIL026C_Sbay Reading seq # 2: YIL026C_Scer Reading seq # 3: YIL026C_Skud Reading seq # 4: YIL026C_Smik Reading seq # 5: YIL026C_Spar Sequences read.. Counting patterns.. # site patterns = 137 Counting frequencies.. 120 bytes for distance 21920 bytes for lkl0 17536 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.049305 0.082726 0.182748 0.129952 0.165786 0.215381 0.272028 lnL0 = -1306.722699 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1306.722699 x= 0.00006 0.04930 0.08273 0.18275 0.12995 0.16579 0.21538 0.27203 1 h-lim-p 0.0000 0.0000 81.9005 1306.480527 m 0.0000 22 | 1/8 2 h-lim-p 0.0001 0.0126 21.9489 1306.264557 0 0.0011 37 | 1/8 3 h-lim-p 0.0035 0.0467 7.1114 1306.237383 5 0.0011 61 | 1/8 4 h-lim-p 0.0039 0.0932 2.0513 1306.232903 5 0.0014 86 | 0/8 5 h-lim-p 0.0005 0.1100 5.9265 1306.157690 0 0.0056 101 | 0/8 6 h-lim-p 0.0021 0.0217 15.9205 1306.009762 0 0.0042 114 | 0/8 7 h-lim-p 0.0141 0.1131 3.1402 1305.998824 4 0.0018 136 | 0/8 8 h-lim-p 0.0091 0.3419 0.6220 1305.938448 0 0.0182 149 | 0/8 9 h-lim-p 0.0036 0.0390 3.1347 1304.714128 8 0.0222 191 | 0/8 10 h-lim-p 2.5000 20.0000 0.0172 1304.696955 2 1.1719 207 | 0/8 11 h-lim-p 2.5000 20.0000 0.0020 1304.696240 2 1.1719 231 | 0/8 12 h-lim-p 2.5000 20.0000 0.0001 1304.696237 1 1.2305 254 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1304.696237 0 2.1875 274 | 0/8 14 h-lim-p 2.4645 20.0000 0.0000 1304.696237 0 1.0782 294 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1304.696237 0 1.0938 314 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1304.696237 0 0.0586 339 | 0/8 17 h-lim-p 0.0270 20.0000 0.0000 1304.696237 0 0.0008 363 Out... lnL = -1304.696237 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1304.696237 Node 7: lnL = -1304.696237 Node 8: lnL = -1304.696237 Node 9: lnL = -1304.696237 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 388 Sequential format.. Reading seq # 1: YIL027C_Sbay Reading seq # 2: YIL027C_Scer Reading seq # 3: YIL027C_Skud Reading seq # 4: YIL027C_Smik Reading seq # 5: YIL027C_Spar Sequences read.. Counting patterns.. # site patterns = 175 Counting frequencies.. 120 bytes for distance 28000 bytes for lkl0 22400 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.077643 0.087624 0.171557 0.133523 0.227874 0.214839 0.267139 lnL0 = -1760.042474 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1760.042474 x= 0.00006 0.07764 0.08762 0.17156 0.13352 0.22787 0.21484 0.26714 1 h-lim-p 0.0000 0.0000 120.2450 1760.009362 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0124 22.1782 1759.796729 0 0.0008 40 | 1/8 3 h-lim-p 0.0014 0.0115 12.2222 1759.726434 4 0.0011 60 | 1/8 4 h-lim-p 0.0035 0.0425 3.6498 1759.704523 2 0.0017 76 | 1/8 5 h-lim-p 0.0031 0.0787 1.9565 1759.482640 0 0.0123 90 | 1/8 6 h-lim-p 0.0044 0.0488 5.4519 1757.550550 0 0.0133 103 | 1/8 7 h-lim-p 0.0004 0.0032 28.6559 1755.216347 0 0.0024 117 | 1/8 8 h-lim-p 0.0007 0.0054 36.5703 1754.717347 1 0.0008 131 | 1/8 9 h-lim-p 0.6564 7.3778 0.0469 1754.197325 6 0.4999 156 | 0/8 10 h-lim-p 0.0035 0.2484 6.7063 1754.173154 5 0.0011 187 | 0/8 11 h-lim-p 1.2094 11.1629 0.0063 1754.154375 4 0.9484 207 | 0/8 12 h-lim-p 2.5000 20.0000 0.0009 1754.153846 3 1.0004 233 | 0/8 13 h-lim-p 2.5000 20.0000 0.0001 1754.153840 1 0.9961 255 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1754.153840 0 1.0938 275 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1754.153840 0 1.0938 295 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1754.153840 0 0.6250 316 | 0/8 17 h-lim-p 0.4042 20.0000 0.0000 1754.153840 0 0.0095 341 Out... lnL = -1754.153840 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1754.153840 Node 7: lnL = -1754.153840 Node 8: lnL = -1754.153840 Node 9: lnL = -1754.153840 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 343 Sequential format.. Reading seq # 1: YIL031W_Sbay Reading seq # 2: YIL031W_Scer Reading seq # 3: YIL031W_Skud Reading seq # 4: YIL031W_Smik Reading seq # 5: YIL031W_Spar Sequences read.. Counting patterns.. # site patterns = 129 Counting frequencies.. 120 bytes for distance 20640 bytes for lkl0 16512 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.044418 0.013512 0.095018 0.068695 0.142289 0.169735 0.173266 lnL0 = -1309.630955 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1309.630955 x= 0.00006 0.04442 0.01351 0.09502 0.06869 0.14229 0.16973 0.17327 1 h-lim-p 0.0021 0.9471 111.4359 1309.052584 3 0.0001 31 | 0/8 2 h-lim-p 0.0000 0.0000 14.5932 1309.044045 m 0.0000 43 | 1/8 3 h-lim-p 0.0002 0.0321 4.1110 1309.040279 0 0.0006 57 | 1/8 4 h-lim-p 0.0035 0.1359 0.7056 1309.040142 4 0.0005 80 | 1/8 5 h-lim-p 0.0011 0.7991 0.3227 1309.040059 2 0.0010 103 | 1/8 6 h-lim-p 0.0015 0.6574 0.2083 1309.039836 0 0.0030 123 | 0/8 7 h-lim-p 0.0011 0.6754 0.5539 1309.037346 0 0.0045 144 | 0/8 8 h-lim-p 0.0013 0.1534 1.8850 1309.032284 0 0.0026 165 | 0/8 9 h-lim-p 0.0018 0.0142 0.5306 1309.005883 m 0.0142 177 | 0/8 10 h-lim-p 0.0000 0.0000 0.0019 h-lim-p: 3.82271830e-19 3.05817464e-18 1.89787365e-03 1309.005883 .. | 0/8 11 h-lim-p 0.0000 0.4422 3.4012 1309.005006 0 0.0002 217 | 0/8 12 h-lim-p 0.0009 0.4263 0.6008 1309.004913 3 0.0005 238 | 0/8 13 h-lim-p 0.0003 0.0024 0.2251 1309.004903 0 0.0006 259 | 0/8 14 h-lim-p 0.0002 0.0018 0.1169 1309.004902 0 0.0003 279 | 0/8 15 h-lim-p 0.0002 0.0013 0.1180 1309.004902 0 0.0006 301 | 0/8 16 h-lim-p 0.0000 0.0000 308.4069 1309.004902 0 0.0000 321 | 0/8 17 h-lim-p 0.0029 20.0000 0.0029 1309.004902 0 0.0025 333 | 0/8 18 h-lim-p 0.0052 1.2196 0.0014 1309.004901 0 0.0052 353 | 0/8 19 h-lim-p 0.0037 0.1313 0.0020 1309.004898 0 0.0296 376 | 0/8 20 h-lim-p 1.8838 20.0000 0.0000 1309.004897 0 0.8242 396 | 0/8 21 h-lim-p 0.6953 13.3541 0.0000 1309.004897 0 0.1738 417 | 0/8 22 h-lim-p 0.6709 17.5144 0.0000 1309.004897 0 0.2935 437 | 0/8 23 h-lim-p 0.2412 8.9936 0.0000 1309.004897 0 0.0000 471 | 0/8 24 h-lim-p 0.0000 3.8738 0.0000 .. | 0/8 25 h-lim-p 0.0000 0.0005 0.0840 1309.004897 0 0.0000 526 | 0/8 26 h-lim-p 0.0000 0.0001 0.3127 .. | 0/8 27 h-lim-p 0.0000 0.0005 0.0803 1309.004897 0 0.0000 593 | 0/8 28 h-lim-p 0.0000 0.0001 0.3785 .. | 0/8 29 h-lim-p 0.0000 0.0005 0.0803 | 0/8 30 h-lim-p 0.0000 0.0005 0.0803 Out... lnL = -1309.004897 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1309.004897 Node 7: lnL = -1309.004897 Node 8: lnL = -1309.004897 Node 9: lnL = -1309.004897 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 306 Sequential format.. Reading seq # 1: YIL033C_Sbay Reading seq # 2: YIL033C_Scer Reading seq # 3: YIL033C_Skud Reading seq # 4: YIL033C_Smik Reading seq # 5: YIL033C_Spar Sequences read.. Counting patterns.. # site patterns = 122 Counting frequencies.. 120 bytes for distance 19520 bytes for lkl0 15616 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.027082 0.146343 0.096396 0.067603 0.036009 0.144397 0.107889 0.268055 lnL0 = -1247.295549 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1247.295549 x= 0.02708 0.14634 0.09640 0.06760 0.03601 0.14440 0.10789 0.26805 1 h-lim-p 0.0011 0.0090 30.3804 1246.831772 2 0.0011 26 | 0/8 2 h-lim-p 0.0003 0.0027 19.0238 1246.802133 7 0.0002 56 | 0/8 3 h-lim-p 0.0012 0.0749 3.2207 1246.797758 5 0.0009 79 | 0/8 4 h-lim-p 0.0016 0.0658 1.8135 1246.797159 4 0.0005 102 | 0/8 5 h-lim-p 0.0015 0.3594 0.5785 1246.797082 3 0.0005 121 | 0/8 6 h-lim-p 0.0044 1.6866 0.0678 1246.797081 1 0.0005 145 | 0/8 7 h-lim-p 0.0028 20.0000 0.0128 1246.797081 0 0.0025 165 | 0/8 8 h-lim-p 0.0385 20.0000 0.0008 1246.796999 0 0.6159 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1246.796996 1 0.9961 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1246.796996 0 2.5000 231 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1246.796996 0 0.0011 261 Out... lnL = -1246.796996 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1246.796996 Node 7: lnL = -1246.796996 Node 8: lnL = -1246.796996 Node 9: lnL = -1246.796996 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 356 Sequential format.. Reading seq # 1: YIL034C_Sbay Reading seq # 2: YIL034C_Scer Reading seq # 3: YIL034C_Skud Reading seq # 4: YIL034C_Smik Reading seq # 5: YIL034C_Spar Sequences read.. Counting patterns.. # site patterns = 156 Counting frequencies.. 120 bytes for distance 24960 bytes for lkl0 19968 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.115890 0.081889 0.105146 0.115896 0.151303 0.245852 0.239731 lnL0 = -1465.081148 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1465.081148 x= 0.00006 0.11589 0.08189 0.10515 0.11590 0.15130 0.24585 0.23973 1 h-lim-p 0.0000 0.0000 66.5338 1465.056683 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0080 21.5096 1464.922901 0 0.0005 39 | 1/8 3 h-lim-p 0.0018 0.0294 6.4248 1464.904686 7 0.0009 66 | 1/8 4 h-lim-p 0.0013 0.0556 4.4581 1464.896014 5 0.0010 90 | 1/8 5 h-lim-p 0.0020 0.1685 2.0995 1464.887608 4 0.0021 110 | 1/8 6 h-lim-p 0.0207 0.9166 0.2145 1464.032768 0 0.1659 125 | 1/8 7 h-lim-p 0.0021 0.0174 17.0634 1463.550771 3 0.0017 150 | 1/8 8 h-lim-p 0.0026 0.0227 11.5676 1463.467887 5 0.0013 173 | 1/8 9 h-lim-p 2.5000 20.0000 0.0058 1463.440806 5 0.9487 195 | 0/8 10 h-lim-p 0.0135 20.0000 0.4103 1463.440686 3 0.0014 222 | 0/8 11 h-lim-p 0.3862 3.0896 0.0012 1463.439496 0 0.7724 243 | 0/8 12 h-lim-p 2.5000 20.0000 0.0003 1463.439447 2 0.9961 267 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1463.439447 0 1.0938 287 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1463.439447 0 1.0938 307 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1463.439447 0 1.0938 327 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1463.439447 0 5.0000 348 | 0/8 17 h-lim-p 1.9954 20.0000 0.0000 1463.439447 0 0.1247 371 | 0/8 18 h-lim-p 0.1485 20.0000 0.0000 1463.439447 0 0.0023 396 Out... lnL = -1463.439447 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1463.439447 Node 7: lnL = -1463.439447 Node 8: lnL = -1463.439447 Node 9: lnL = -1463.439447 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 409 Sequential format.. Reading seq # 1: YIL035C_Sbay Reading seq # 2: YIL035C_Scer Reading seq # 3: YIL035C_Skud Reading seq # 4: YIL035C_Smik Reading seq # 5: YIL035C_Spar Sequences read.. Counting patterns.. # site patterns = 150 Counting frequencies.. 120 bytes for distance 24000 bytes for lkl0 19200 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.010891 0.049900 0.061983 0.153391 0.080094 0.249767 0.175861 0.275069 lnL0 = -1664.537807 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1664.537807 x= 0.01089 0.04990 0.06198 0.15339 0.08009 0.24977 0.17586 0.27507 1 h-lim-p 0.0013 0.0108 104.5190 1662.598305 6 0.0004 37 | 0/8 2 h-lim-p 0.0006 0.0051 27.1652 1662.341088 1 0.0008 51 | 0/8 3 h-lim-p 0.0017 0.0167 13.0516 1662.306766 6 0.0005 78 | 0/8 4 h-lim-p 0.0041 0.1471 1.5619 1662.305631 2 0.0010 95 | 0/8 5 h-lim-p 0.0098 1.5618 0.1534 1662.305614 2 0.0012 113 | 0/8 6 h-lim-p 0.0030 2.5044 0.0624 1662.305599 0 0.0026 133 | 0/8 7 h-lim-p 0.0130 20.0000 0.0124 1662.304582 0 0.1040 156 | 0/8 8 h-lim-p 0.0019 0.0651 0.6882 1662.302963 1 0.0023 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1662.302941 1 1.2500 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1662.302940 0 1.0938 220 | 0/8 11 h-lim-p 2.3213 20.0000 0.0000 1662.302940 0 1.0156 240 | 0/8 12 h-lim-p 0.9408 20.0000 0.0000 1662.302940 0 0.0441 264 | 0/8 13 h-lim-p 0.0014 20.0000 0.0005 1662.302940 0 0.0000 295 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 1662.302940 0 0.0000 327 Out... lnL = -1662.302940 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1662.302940 Node 7: lnL = -1662.302940 Node 8: lnL = -1662.302940 Node 9: lnL = -1662.302940 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 386 Sequential format.. Reading seq # 1: YIL038C_Sbay Reading seq # 2: YIL038C_Scer Reading seq # 3: YIL038C_Skud Reading seq # 4: YIL038C_Smik Reading seq # 5: YIL038C_Spar Sequences read.. Counting patterns.. # site patterns = 108 Counting frequencies.. 120 bytes for distance 17280 bytes for lkl0 13824 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.098823 0.038746 0.062947 0.077451 0.085774 0.099373 0.142793 lnL0 = -1398.476719 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1398.476719 x= 0.00006 0.09882 0.03875 0.06295 0.07745 0.08577 0.09937 0.14279 1 h-lim-p 0.0000 0.0000 106.3121 1398.453483 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0034 22.5455 1398.406845 0 0.0002 38 | 1/8 3 h-lim-p 0.0011 0.0545 3.3200 1398.403560 4 0.0005 60 | 1/8 4 h-lim-p 0.0005 0.0271 2.9695 1398.401198 3 0.0004 78 | 1/8 5 h-lim-p 0.0014 0.3601 0.8882 1398.383056 0 0.0043 91 | 1/8 6 h-lim-p 0.0028 0.0835 1.3861 1397.597511 0 0.0167 112 | 1/8 7 h-lim-p 0.0006 0.0046 34.1727 1396.740945 1 0.0007 126 | 1/8 8 h-lim-p 0.0019 0.0191 12.8097 1396.711770 6 0.0004 153 | 1/8 9 h-lim-p 1.1162 20.0000 0.0041 1396.683664 5 0.9107 176 | 1/8 10 h-lim-p 2.5000 20.0000 0.0009 1396.682197 4 0.9802 203 | 1/8 11 h-lim-p 2.5000 20.0000 0.0002 1396.682165 3 0.8855 230 | 0/8 12 h-lim-p 0.0232 20.0000 0.0061 1396.682165 0 0.0015 252 | 0/8 13 h-lim-p 0.1178 0.9423 0.0000 1396.682165 m 0.9423 272 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 1396.682165 0 0.5469 293 | 1/8 15 h-lim-p 1.8644 20.0000 0.0000 1396.682165 0 0.4078 313 | 1/8 16 h-lim-p 1.0427 20.0000 0.0000 1396.682165 0 0.0041 339 Out... lnL = -1396.682165 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1396.682165 Node 7: lnL = -1396.682165 Node 8: lnL = -1396.682165 Node 9: lnL = -1396.682165 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 300 Sequential format.. Reading seq # 1: YIL039W_Sbay Reading seq # 2: YIL039W_Scer Reading seq # 3: YIL039W_Skud Reading seq # 4: YIL039W_Smik Reading seq # 5: YIL039W_Spar Sequences read.. Counting patterns.. # site patterns = 120 Counting frequencies.. 120 bytes for distance 19200 bytes for lkl0 15360 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.098428 0.063131 0.084516 0.109070 0.188871 0.190271 0.208984 lnL0 = -1264.564392 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1264.564392 x= 0.00006 0.09843 0.06313 0.08452 0.10907 0.18887 0.19027 0.20898 1 h-lim-p 0.0000 0.0000 88.6693 1264.546056 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0245 15.1440 1264.442331 0 0.0008 40 | 1/8 3 h-lim-p 0.0014 0.0168 8.6484 1264.412257 7 0.0009 69 | 1/8 4 h-lim-p 0.0050 0.1920 1.5946 1264.394949 4 0.0038 89 | 1/8 5 h-lim-p 0.0037 0.0664 1.6623 1264.333197 1 0.0046 103 | 1/8 6 h-lim-p 0.0012 0.0393 6.4025 1263.402088 0 0.0072 117 | 1/8 7 h-lim-p 0.0010 0.0077 20.4589 1261.815509 0 0.0019 130 | 1/8 8 h-lim-p 0.0011 0.0088 11.8939 1261.750844 4 0.0009 150 | 1/8 9 h-lim-p 0.6171 16.0407 0.0166 1261.653806 0 0.9256 162 | 1/8 10 h-lim-p 2.5000 20.0000 0.0042 1261.645466 6 0.8912 194 | 1/8 11 h-lim-p 2.5000 20.0000 0.0006 1261.645280 4 0.8228 222 | 1/8 12 h-lim-p 2.5000 20.0000 0.0001 1261.645275 2 0.9644 245 | 0/8 13 h-lim-p 0.0512 20.0000 0.0018 1261.645275 0 0.0028 267 | 0/8 14 h-lim-p 0.1203 0.9628 0.0000 1261.645275 m 0.9628 287 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 1261.645275 0 1.0938 307 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 1261.645275 0 1.0938 326 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 1261.645275 0 0.0085 352 Out... lnL = -1261.645275 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1261.645275 Node 7: lnL = -1261.645275 Node 8: lnL = -1261.645275 Node 9: lnL = -1261.645275 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 234 Sequential format.. Reading seq # 1: YIL040W_Sbay Reading seq # 2: YIL040W_Scer Reading seq # 3: YIL040W_Skud Reading seq # 4: YIL040W_Smik Reading seq # 5: YIL040W_Spar Sequences read.. Counting patterns.. # site patterns = 113 Counting frequencies.. 120 bytes for distance 18080 bytes for lkl0 14464 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.009563 0.072206 0.154168 0.120178 0.019510 0.159823 0.184063 0.271731 lnL0 = -974.416326 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 974.416326 x= 0.00956 0.07221 0.15417 0.12018 0.01951 0.15982 0.18406 0.27173 1 h-lim-p 0.0048 0.0384 33.0015 974.141906 3 0.0005 30 | 0/8 2 h-lim-p 0.0002 0.0019 32.9982 973.992049 0 0.0005 43 | 0/8 3 h-lim-p 0.0020 0.0251 7.8203 973.954502 6 0.0014 70 | 0/8 4 h-lim-p 0.0091 0.0759 1.1748 973.953858 3 0.0010 91 | 0/8 5 h-lim-p 0.0050 0.3138 0.2240 973.953826 1 0.0013 106 | 0/8 6 h-lim-p 0.0102 6.1416 0.0275 973.953794 2 0.0115 131 | 0/8 7 h-lim-p 0.0224 11.0074 0.0141 973.952282 0 0.0897 153 | 0/8 8 h-lim-p 0.0023 0.0647 0.5406 973.951903 4 0.0018 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 973.951901 1 0.9961 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 973.951900 0 1.2500 223 | 0/8 11 h-lim-p 1.4682 20.0000 0.0000 973.951900 0 0.0014 252 | 0/8 12 h-lim-p 0.0005 20.0000 0.0000 973.951900 0 0.0000 275 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 973.951900 0 0.0000 295 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 973.951900 0 0.0000 332 Out... lnL = -973.951900 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -973.951900 Node 7: lnL = -973.951900 Node 8: lnL = -973.951900 Node 9: lnL = -973.951900 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 234 Sequential format.. Reading seq # 1: YIL041W_Sbay Reading seq # 2: YIL041W_Scer Reading seq # 3: YIL041W_Skud Reading seq # 4: YIL041W_Smik Reading seq # 5: YIL041W_Spar Sequences read.. Counting patterns.. # site patterns = 95 Counting frequencies.. 120 bytes for distance 15200 bytes for lkl0 12160 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.027328 0.047447 0.017123 0.098318 0.134298 0.156274 0.166233 0.247279 lnL0 = -1038.558531 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1038.558531 x= 0.02733 0.04745 0.01712 0.09832 0.13430 0.15627 0.16623 0.24728 1 h-lim-p 0.0019 0.0289 104.2649 1037.612566 4 0.0002 32 | 0/8 2 h-lim-p 0.0017 0.0155 12.4931 1037.545312 4 0.0009 52 | 0/8 3 h-lim-p 0.0034 0.0314 3.2192 1037.542032 3 0.0007 71 | 0/8 4 h-lim-p 0.0048 0.4404 0.4474 1037.541926 2 0.0011 88 | 0/8 5 h-lim-p 0.0046 1.4756 0.1031 1037.541923 2 0.0008 115 | 0/8 6 h-lim-p 0.0054 3.9245 0.0145 1037.541923 0 0.0012 136 | 0/8 7 h-lim-p 0.0169 20.0000 0.0010 1037.541922 0 0.0339 157 | 0/8 8 h-lim-p 0.0102 18.1104 0.0033 1037.541903 0 0.0409 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1037.541902 0 1.0938 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1037.541902 0 0.5469 220 | 0/8 11 h-lim-p 0.3358 20.0000 0.0000 1037.541902 0 0.0420 242 | 0/8 12 h-lim-p 0.0202 20.0000 0.0000 1037.541902 0 0.0202 262 | 0/8 13 h-lim-p 0.0119 20.0000 0.0001 1037.541902 0 0.0000 300 | 0/8 14 h-lim-p 0.0000 20.0000 0.0009 | 0/8 15 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -1037.541902 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1037.541902 Node 7: lnL = -1037.541902 Node 8: lnL = -1037.541902 Node 9: lnL = -1037.541902 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 246 Sequential format.. Reading seq # 1: YIL042C_Sbay Reading seq # 2: YIL042C_Scer Reading seq # 3: YIL042C_Skud Reading seq # 4: YIL042C_Smik Reading seq # 5: YIL042C_Spar Sequences read.. Counting patterns.. # site patterns = 96 Counting frequencies.. 120 bytes for distance 15360 bytes for lkl0 12288 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.027328 0.047447 0.017123 0.098318 0.134298 0.156274 0.166233 0.247279 lnL0 = -1055.194063 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1055.194063 x= 0.02733 0.04745 0.01712 0.09832 0.13430 0.15627 0.16623 0.24728 1 h-lim-p 0.0019 0.0289 104.2649 1054.248099 4 0.0002 32 | 0/8 2 h-lim-p 0.0017 0.0155 12.4928 1054.180844 4 0.0009 52 | 0/8 3 h-lim-p 0.0034 0.0314 3.2188 1054.177565 3 0.0007 71 | 0/8 4 h-lim-p 0.0048 0.4404 0.4474 1054.177460 2 0.0011 88 | 0/8 5 h-lim-p 0.0046 1.4755 0.1031 1054.177456 2 0.0008 115 | 0/8 6 h-lim-p 0.0054 3.9237 0.0145 1054.177456 0 0.0012 136 | 0/8 7 h-lim-p 0.0168 20.0000 0.0010 1054.177456 0 0.0336 157 | 0/8 8 h-lim-p 0.0095 16.7217 0.0036 1054.177435 0 0.0379 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1054.177434 0 1.0938 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1054.177434 0 0.5469 220 | 0/8 11 h-lim-p 0.3433 20.0000 0.0000 1054.177434 0 0.0858 241 | 0/8 12 h-lim-p 0.0450 20.0000 0.0000 1054.177434 0 0.0112 262 | 0/8 13 h-lim-p 0.0068 20.0000 0.0001 1054.177434 0 0.0004 285 | 0/8 14 h-lim-p 0.0002 20.0000 0.0001 1054.177434 0 0.0000 309 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 1054.177434 0 0.0000 341 | 0/8 16 h-lim-p 0.0000 20.0000 0.0012 1054.177434 0 0.0000 371 | 0/8 17 h-lim-p 0.0000 20.0000 0.0003 1054.177434 0 0.0019 398 | 0/8 18 h-lim-p 0.0069 20.0000 0.0001 1054.177434 0 0.0000 424 | 0/8 19 h-lim-p 0.0000 20.0000 0.0002 1054.177434 0 0.0000 456 | 0/8 20 h-lim-p 0.0000 20.0000 0.0013 | 0/8 21 h-lim-p 0.0000 20.0000 0.0013 Out... lnL = -1054.177434 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1054.177434 Node 7: lnL = -1054.177434 Node 8: lnL = -1054.177434 Node 9: lnL = -1054.177434 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 437 Sequential format.. Reading seq # 1: YIL049W_Sbay Reading seq # 2: YIL049W_Scer Reading seq # 3: YIL049W_Skud Reading seq # 4: YIL049W_Smik Reading seq # 5: YIL049W_Spar Sequences read.. Counting patterns.. # site patterns = 207 Counting frequencies.. 120 bytes for distance 33120 bytes for lkl0 26496 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.102277 0.078267 0.018167 0.153442 0.099436 0.281677 0.248142 0.454600 lnL0 = -2114.193899 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2114.193899 x= 0.10228 0.07827 0.01817 0.15344 0.09944 0.28168 0.24814 0.45460 1 h-lim-p 0.0035 0.0710 109.2150 2113.006186 4 0.0002 33 | 0/8 2 h-lim-p 0.0022 0.0216 11.1853 2112.948986 3 0.0009 51 | 0/8 3 h-lim-p 0.0017 0.0652 6.0495 2112.933613 6 0.0010 80 | 0/8 4 h-lim-p 0.0022 0.0567 2.8223 2112.931694 5 0.0006 103 | 0/8 5 h-lim-p 0.0017 0.3173 1.0342 2112.931153 4 0.0012 125 | 0/8 6 h-lim-p 0.0049 0.6820 0.2566 2112.931125 2 0.0009 142 | 0/8 7 h-lim-p 0.0041 2.5003 0.0590 2112.931121 0 0.0021 162 | 0/8 8 h-lim-p 0.2335 20.0000 0.0005 2112.930593 0 1.4009 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2112.930577 1 0.9961 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2112.930577 0 1.2500 226 | 0/8 11 h-lim-p 1.8571 20.0000 0.0000 2112.930577 0 0.0871 250 | 0/8 12 h-lim-p 0.0333 20.0000 0.0000 2112.930577 0 0.0042 272 | 0/8 13 h-lim-p 0.0023 20.0000 0.0000 2112.930577 0 0.0000 311 | 0/8 14 h-lim-p 0.0000 20.0000 0.0008 2112.930577 0 0.0000 344 | 0/8 15 h-lim-p 0.0000 20.0000 0.0008 2112.930577 0 0.0000 374 | 0/8 16 h-lim-p 0.0000 20.0000 0.0011 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0008 | 0/8 18 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -2112.930577 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2112.930577 Node 7: lnL = -2112.930577 Node 8: lnL = -2112.930577 Node 9: lnL = -2112.930577 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 668 Sequential format.. Reading seq # 1: YIL051C_Sbay Reading seq # 2: YIL051C_Scer Reading seq # 3: YIL051C_Skud Reading seq # 4: YIL051C_Smik Reading seq # 5: YIL051C_Spar Sequences read.. Counting patterns.. # site patterns = 238 Counting frequencies.. 120 bytes for distance 38080 bytes for lkl0 30464 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.020129 0.015175 0.077751 0.126137 0.073564 0.217929 0.225607 0.276265 lnL0 = -2974.661038 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2974.661038 x= 0.02013 0.01518 0.07775 0.12614 0.07356 0.21793 0.22561 0.27626 1 h-lim-p 0.0018 0.5756 183.2913 2972.582224 7 0.0001 40 | 0/8 2 h-lim-p 0.0013 0.0106 17.9828 2972.483997 2 0.0006 56 | 0/8 3 h-lim-p 0.0018 0.0577 6.1696 2972.478154 5 0.0003 79 | 0/8 4 h-lim-p 0.0017 0.0707 1.2640 2972.477997 3 0.0002 99 | 0/8 5 h-lim-p 0.0006 0.7467 0.4111 2972.477956 1 0.0006 113 | 0/8 6 h-lim-p 0.0042 0.7522 0.0537 2972.477955 1 0.0005 137 | 0/8 7 h-lim-p 0.0027 9.1923 0.0102 2972.477954 0 0.0024 157 | 0/8 8 h-lim-p 0.0075 20.0000 0.0033 2972.477561 0 0.1201 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2972.477544 1 1.0938 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2972.477544 0 1.0938 223 | 0/8 11 h-lim-p 1.2600 20.0000 0.0000 2972.477544 0 0.1575 245 | 0/8 12 h-lim-p 0.0324 20.0000 0.0001 2972.477544 0 0.0162 265 | 0/8 13 h-lim-p 0.0066 20.0000 0.0003 2972.477544 0 0.0000 304 | 0/8 14 h-lim-p 0.0000 20.0000 0.0015 2972.477544 0 0.0000 330 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 2972.477544 0 0.0000 363 | 0/8 16 h-lim-p 0.0000 20.0000 0.0015 2972.477544 0 0.0000 389 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0015 | 0/8 19 h-lim-p 0.0000 20.0000 0.0015 Out... lnL = -2972.477544 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2972.477544 Node 7: lnL = -2972.477544 Node 8: lnL = -2972.477544 Node 9: lnL = -2972.477544 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 877 Sequential format.. Reading seq # 1: YIL057C_Sbay Reading seq # 2: YIL057C_Scer Reading seq # 3: YIL057C_Skud Reading seq # 4: YIL057C_Smik Reading seq # 5: YIL057C_Spar Sequences read.. Counting patterns.. # site patterns = 317 Counting frequencies.. 120 bytes for distance 50720 bytes for lkl0 40576 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.054603 0.000060 0.098351 0.106000 0.111402 0.206048 0.295712 0.340596 lnL0 = -3897.255106 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3897.255106 x= 0.05460 0.00006 0.09835 0.10600 0.11140 0.20605 0.29571 0.34060 1 h-lim-p 0.0002 0.0013 134.0909 3894.882354 0 0.0003 23 | 0/8 2 h-lim-p 0.0007 0.0059 23.9400 3894.782856 5 0.0004 46 | 0/8 3 h-lim-p 0.0007 0.0207 11.7244 3894.762458 4 0.0004 66 | 0/8 4 h-lim-p 0.0010 0.1690 4.0443 3894.760753 3 0.0002 85 | 0/8 5 h-lim-p 0.0005 0.1114 1.9665 3894.759865 3 0.0005 103 | 0/8 6 h-lim-p 0.0009 0.2856 1.1211 3894.759439 3 0.0006 122 | 0/8 7 h-lim-p 0.0028 0.3498 0.2563 3894.757620 0 0.0055 135 | 0/8 8 h-lim-p 0.0101 0.3655 0.1406 3894.608258 0 0.0808 158 | 0/8 9 h-lim-p 2.5000 20.0000 0.0024 3894.596924 4 0.9802 186 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 3894.596910 1 0.9961 208 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3894.596910 0 1.0938 228 | 0/8 12 h-lim-p 1.3262 20.0000 0.0000 3894.596910 0 1.1604 248 | 0/8 13 h-lim-p 0.7248 20.0000 0.0000 3894.596910 0 0.0170 273 | 0/8 14 h-lim-p 0.0000 4.1457 0.0196 3894.596910 0 0.0000 293 | 0/8 15 h-lim-p 0.0006 20.0000 0.0006 3894.596910 0 0.0000 328 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 | 0/8 17 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -3894.596910 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3894.596910 Node 7: lnL = -3894.596910 Node 8: lnL = -3894.596910 Node 9: lnL = -3894.596910 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 884 Sequential format.. Reading seq # 1: YIL061C_Sbay Reading seq # 2: YIL061C_Scer Reading seq # 3: YIL061C_Skud Reading seq # 4: YIL061C_Smik Reading seq # 5: YIL061C_Spar Sequences read.. Counting patterns.. # site patterns = 346 Counting frequencies.. 120 bytes for distance 55360 bytes for lkl0 44288 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.002727 0.392215 0.000060 0.391785 0.245700 0.428147 0.264263 0.434836 lnL0 = -4562.699317 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4562.699317 x= 0.00273 0.39221 0.00006 0.39178 0.24570 0.42815 0.26426 0.43484 1 h-lim-p 0.0000 0.0000 490.7106 4562.563754 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0001 441.9752 4547.662860 m 0.0001 35 | 2/8 3 h-lim-p 0.0001 0.0006 597.0188 4497.089632 0 0.0004 49 | 2/8 4 h-lim-p 0.0002 0.0012 197.0106 4482.495036 0 0.0006 63 | 2/8 5 h-lim-p 0.0003 0.0028 159.9679 4462.972481 0 0.0014 77 | 2/8 6 h-lim-p 0.0010 0.0080 23.7088 4462.829648 5 0.0004 98 | 1/8 7 h-lim-p 0.0001 0.0043 147.7825 4458.703682 0 0.0006 113 | 1/8 8 h-lim-p 0.0028 0.0223 28.2581 4458.224289 5 0.0012 136 | 0/8 9 h-lim-p 0.0007 0.0371 49.8466 4458.011493 6 0.0002 163 | 0/8 10 h-lim-p 0.0263 0.7764 0.3480 4445.981359 4 0.4475 186 | 0/8 11 h-lim-p 0.0293 0.2343 0.1032 4444.226008 m 0.2343 206 | 0/8 12 h-lim-p 0.0000 0.0000 0.0518 h-lim-p: 2.02802073e-18 1.62241659e-17 5.17934639e-02 4444.226008 .. | 0/8 13 h-lim-p 0.0000 0.0385 64.8314 4443.801439 0 0.0002 246 | 0/8 14 h-lim-p 0.0000 0.0001 47.1050 4443.698729 m 0.0001 258 | 1/8 15 h-lim-p 0.0001 3.5542 33.4735 4443.642476 0 0.0003 272 | 1/8 16 h-lim-p 0.0008 0.0218 13.3213 4443.580501 2 0.0007 288 | 1/8 17 h-lim-p 0.0014 0.0459 6.7456 4443.573017 5 0.0005 312 | 1/8 18 h-lim-p 0.0031 0.2691 1.0543 4443.572378 2 0.0008 329 | 1/8 19 h-lim-p 0.0016 1.1274 0.5360 4443.569338 0 0.0064 343 | 1/8 20 h-lim-p 0.0262 1.1159 0.1310 4443.332228 0 0.1569 364 | 1/8 21 h-lim-p 2.5000 20.0000 0.0007 4443.331433 3 0.9482 389 | 1/8 22 h-lim-p 2.5000 20.0000 0.0000 4443.331432 0 1.0938 408 | 1/8 23 h-lim-p 2.3903 20.0000 0.0000 4443.331432 0 1.0458 427 | 1/8 24 h-lim-p 0.9449 20.0000 0.0000 4443.331432 0 1.8897 447 | 1/8 25 h-lim-p 0.3096 20.0000 0.0001 4443.331432 0 0.0085 470 | 1/8 26 h-lim-p 0.0018 20.0000 0.0005 4443.331432 0 0.0000 496 | 1/8 27 h-lim-p 0.0003 20.0000 0.0000 4443.331432 0 0.0000 521 | 1/8 28 h-lim-p 0.0002 20.0000 0.0000 4443.331432 0 0.0000 551 Out... lnL = -4443.331432 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4443.331432 Node 7: lnL = -4443.331432 Node 8: lnL = -4443.331432 Node 9: lnL = -4443.331432 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 207 Sequential format.. Reading seq # 1: YIL062C_Sbay Reading seq # 2: YIL062C_Scer Reading seq # 3: YIL062C_Skud Reading seq # 4: YIL062C_Smik Reading seq # 5: YIL062C_Spar Sequences read.. Counting patterns.. # site patterns = 102 Counting frequencies.. 120 bytes for distance 16320 bytes for lkl0 13056 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.043999 0.145795 0.000060 0.152414 0.132664 0.138741 0.194114 0.296772 lnL0 = -908.842247 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 908.842247 x= 0.04400 0.14580 0.00006 0.15241 0.13266 0.13874 0.19411 0.29677 1 h-lim-p 0.0004 0.0035 44.6630 907.572984 0 0.0013 23 | 0/8 2 h-lim-p 0.0004 0.0031 11.9650 907.513707 0 0.0008 36 | 0/8 3 h-lim-p 0.0007 0.0345 13.0868 907.498074 2 0.0003 52 | 0/8 4 h-lim-p 0.0011 0.0202 3.8718 907.488471 0 0.0022 65 | 0/8 5 h-lim-p 0.0143 0.3985 0.6060 907.488171 3 0.0014 85 | 0/8 6 h-lim-p 0.0106 3.2323 0.0814 907.487557 0 0.0212 106 | 0/8 7 h-lim-p 0.0093 0.8677 0.1862 907.476441 0 0.0371 128 | 0/8 8 h-lim-p 0.0037 0.0298 1.5991 907.465702 2 0.0035 152 | 0/8 9 h-lim-p 2.5000 20.0000 0.0015 907.464870 3 1.0004 170 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 907.464869 0 1.0938 190 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 907.464869 0 1.0938 210 | 0/8 12 h-lim-p 1.2104 20.0000 0.0000 907.464869 0 1.2104 230 | 0/8 13 h-lim-p 0.5357 20.0000 0.0000 907.464869 0 0.5357 250 | 0/8 14 h-lim-p 0.0491 20.0000 0.0001 907.464869 0 0.0491 270 | 0/8 15 h-lim-p 0.0171 20.0000 0.0004 907.464869 0 0.0171 290 | 0/8 16 h-lim-p 0.0084 20.0000 0.0009 907.464869 0 0.0000 334 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -907.464869 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -907.464869 Node 7: lnL = -907.464869 Node 8: lnL = -907.464869 Node 9: lnL = -907.464869 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 280 Sequential format.. Reading seq # 1: YIL063C_Sbay Reading seq # 2: YIL063C_Scer Reading seq # 3: YIL063C_Skud Reading seq # 4: YIL063C_Smik Reading seq # 5: YIL063C_Spar Sequences read.. Counting patterns.. # site patterns = 126 Counting frequencies.. 120 bytes for distance 20160 bytes for lkl0 16128 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.062205 0.063673 0.071785 0.104959 0.065668 0.135094 0.205840 0.313834 lnL0 = -1214.263852 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1214.263852 x= 0.06221 0.06367 0.07179 0.10496 0.06567 0.13509 0.20584 0.31383 1 h-lim-p 0.0497 6.9595 22.1088 1214.153478 7 0.0005 44 | 0/8 2 h-lim-p 0.0015 0.0236 6.6307 1214.142446 5 0.0005 68 | 0/8 3 h-lim-p 0.0030 0.0749 1.2130 1214.142002 3 0.0006 88 | 0/8 4 h-lim-p 0.0022 0.4270 0.3436 1214.141932 3 0.0013 108 | 0/8 5 h-lim-p 0.0044 2.0513 0.1029 1214.141927 0 0.0011 129 | 0/8 6 h-lim-p 0.0049 10.2470 0.0229 1214.141926 0 0.0011 150 | 0/8 7 h-lim-p 0.0022 13.0473 0.0113 1214.141926 0 0.0010 170 | 0/8 8 h-lim-p 0.3211 20.0000 0.0000 1214.141925 0 1.2843 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1214.141925 0 1.0938 212 | 0/8 10 h-lim-p 1.6803 20.0000 0.0000 1214.141925 0 0.3676 233 | 0/8 11 h-lim-p 0.2053 20.0000 0.0000 1214.141925 0 0.0224 255 | 0/8 12 h-lim-p 0.0128 20.0000 0.0000 1214.141925 0 0.0000 293 | 0/8 13 h-lim-p 0.0000 20.0000 0.0011 | 0/8 14 h-lim-p 0.0000 20.0000 0.0011 Out... lnL = -1214.141925 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1214.141925 Node 7: lnL = -1214.141925 Node 8: lnL = -1214.141925 Node 9: lnL = -1214.141925 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 173 Sequential format.. Reading seq # 1: YIL065C_Sbay Reading seq # 2: YIL065C_Scer Reading seq # 3: YIL065C_Skud Reading seq # 4: YIL065C_Smik Reading seq # 5: YIL065C_Spar Sequences read.. Counting patterns.. # site patterns = 91 Counting frequencies.. 120 bytes for distance 14560 bytes for lkl0 11648 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.124602 0.008926 0.049554 0.110562 0.044699 0.143310 0.195595 0.373809 lnL0 = -738.979705 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 738.979705 x= 0.12460 0.00893 0.04955 0.11056 0.04470 0.14331 0.19559 0.37381 1 h-lim-p 0.0006 0.0047 48.5980 738.416778 2 0.0005 26 | 0/8 2 h-lim-p 0.0009 0.0072 11.5660 738.347950 1 0.0011 40 | 0/8 3 h-lim-p 0.0012 0.0229 10.7106 738.317348 6 0.0009 65 | 0/8 4 h-lim-p 0.0028 0.0385 3.3362 738.312295 5 0.0011 88 | 0/8 5 h-lim-p 0.0012 0.0904 3.1395 738.310596 5 0.0006 112 | 0/8 6 h-lim-p 0.0028 0.2321 0.6694 738.310359 2 0.0012 128 | 0/8 7 h-lim-p 0.0026 0.5843 0.3149 738.310257 2 0.0024 152 | 0/8 8 h-lim-p 0.8411 20.0000 0.0009 738.309921 1 1.0514 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 738.309915 0 1.0938 194 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 738.309914 0 1.2500 214 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 738.309914 0 1.0938 234 | 0/8 12 h-lim-p 1.4455 20.0000 0.0000 738.309914 0 2.1682 254 | 0/8 13 h-lim-p 1.4407 20.0000 0.0000 738.309914 0 0.3602 275 | 0/8 14 h-lim-p 0.0165 20.0000 0.0001 738.309914 0 0.0010 298 | 0/8 15 h-lim-p 0.0002 20.0000 0.0004 738.309914 0 0.0002 318 | 0/8 16 h-lim-p 0.0004 20.0000 0.0002 738.309914 0 0.0004 338 | 0/8 17 h-lim-p 0.0002 20.0000 0.0003 738.309914 0 0.0000 377 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -738.309914 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -738.309914 Node 7: lnL = -738.309914 Node 8: lnL = -738.309914 Node 9: lnL = -738.309914 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 603 Sequential format.. Reading seq # 1: YIL066C_Sbay Reading seq # 2: YIL066C_Scer Reading seq # 3: YIL066C_Skud Reading seq # 4: YIL066C_Smik Reading seq # 5: YIL066C_Spar Sequences read.. Counting patterns.. # site patterns = 134 Counting frequencies.. 120 bytes for distance 21440 bytes for lkl0 17152 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.018281 0.027453 0.040659 0.041680 0.039804 0.123884 0.065763 0.141180 lnL0 = -1949.675679 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1949.675679 x= 0.01828 0.02745 0.04066 0.04168 0.03980 0.12388 0.06576 0.14118 1 h-lim-p 0.0002 0.0016 148.6697 1948.797182 7 0.0001 40 | 0/8 2 h-lim-p 0.0005 0.0042 19.3396 1948.766716 7 0.0002 69 | 0/8 3 h-lim-p 0.0005 0.0237 6.6774 1948.764229 4 0.0001 90 | 0/8 4 h-lim-p 0.0003 0.0457 2.8981 1948.763600 4 0.0002 113 | 0/8 5 h-lim-p 0.0004 0.1250 1.1365 1948.763523 3 0.0001 133 | 0/8 6 h-lim-p 0.0012 0.3032 0.1410 1948.763522 1 0.0001 149 | 0/8 7 h-lim-p 0.0012 1.8639 0.0168 1948.763522 0 0.0003 170 | 0/8 8 h-lim-p 0.0342 20.0000 0.0001 1948.763507 0 1.0956 195 | 0/8 9 h-lim-p 0.2376 20.0000 0.0006 1948.763506 0 0.9503 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1948.763506 0 1.2500 237 | 0/8 11 h-lim-p 0.1225 20.0000 0.0001 1948.763506 0 0.4901 259 | 0/8 12 h-lim-p 0.2167 20.0000 0.0001 1948.763506 0 0.0948 279 | 0/8 13 h-lim-p 0.0373 20.0000 0.0003 1948.763506 0 0.0005 304 | 0/8 14 h-lim-p 0.0003 20.0000 0.0005 1948.763506 0 0.0000 331 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 1948.763506 0 0.0000 369 Out... lnL = -1948.763506 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1948.763506 Node 7: lnL = -1948.763506 Node 8: lnL = -1948.763506 Node 9: lnL = -1948.763506 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 366 Sequential format.. Reading seq # 1: YIL067C_Sbay Reading seq # 2: YIL067C_Scer Reading seq # 3: YIL067C_Skud Reading seq # 4: YIL067C_Smik Reading seq # 5: YIL067C_Spar Sequences read.. Counting patterns.. # site patterns = 146 Counting frequencies.. 120 bytes for distance 23360 bytes for lkl0 18688 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.058341 0.086212 0.091528 0.086874 0.206849 0.154539 0.211137 lnL0 = -1509.587198 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1509.587198 x= 0.00006 0.05834 0.08621 0.09153 0.08687 0.20685 0.15454 0.21114 1 h-lim-p 0.0000 0.0000 59.9901 1509.563205 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0149 15.9198 1509.507284 0 0.0004 38 | 1/8 3 h-lim-p 0.0013 0.0513 4.6581 1509.498774 6 0.0008 64 | 1/8 4 h-lim-p 0.0017 0.0532 2.1558 1509.497211 4 0.0006 86 | 1/8 5 h-lim-p 0.0028 0.7914 0.4268 1509.481766 0 0.0111 100 | 1/8 6 h-lim-p 0.0035 0.0854 1.3665 1509.267503 0 0.0139 121 | 1/8 7 h-lim-p 0.0011 0.0089 12.6837 1508.762246 0 0.0017 133 | 1/8 8 h-lim-p 0.0067 0.1459 3.1615 1508.757045 6 0.0010 162 | 1/8 9 h-lim-p 0.5468 20.0000 0.0060 1508.725947 0 1.0936 175 | 0/8 10 h-lim-p 0.0150 20.0000 0.4356 1508.725855 3 0.0009 203 | 0/8 11 h-lim-p 0.2976 20.0000 0.0014 1508.723784 0 1.1906 225 | 0/8 12 h-lim-p 2.5000 20.0000 0.0003 1508.723707 2 0.9961 249 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1508.723707 0 1.2500 269 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1508.723707 0 1.0938 289 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1508.723707 0 2.5000 309 | 0/8 16 h-lim-p 1.8058 20.0000 0.0000 1508.723707 0 0.0564 333 | 0/8 17 h-lim-p 0.0573 20.0000 0.0000 1508.723707 0 0.0001 362 Out... lnL = -1508.723707 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1508.723707 Node 7: lnL = -1508.723707 Node 8: lnL = -1508.723707 Node 9: lnL = -1508.723707 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 495 Sequential format.. Reading seq # 1: YIL070C_Sbay Reading seq # 2: YIL070C_Scer Reading seq # 3: YIL070C_Skud Reading seq # 4: YIL070C_Smik Reading seq # 5: YIL070C_Spar Sequences read.. Counting patterns.. # site patterns = 197 Counting frequencies.. 120 bytes for distance 31520 bytes for lkl0 25216 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.133429 0.086371 0.136716 0.101605 0.197444 0.169910 0.220766 lnL0 = -2121.487359 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2121.487359 x= 0.00006 0.13343 0.08637 0.13672 0.10161 0.19744 0.16991 0.22077 1 h-lim-p 0.0000 0.0000 163.0467 2121.454240 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0068 47.7256 2120.731546 0 0.0006 40 | 1/8 3 h-lim-p 0.0028 0.0228 7.1277 2120.704879 6 0.0009 69 | 1/8 4 h-lim-p 0.0042 0.2071 1.4559 2120.640113 0 0.0084 82 | 1/8 5 h-lim-p 0.0043 0.1148 2.8388 2119.778397 0 0.0129 95 | 1/8 6 h-lim-p 0.0009 0.0075 18.1270 2116.112054 0 0.0028 108 | 1/8 7 h-lim-p 0.0005 0.0043 53.2518 2115.144631 7 0.0006 137 | 1/8 8 h-lim-p 0.0080 0.0638 3.6282 2115.140120 5 0.0007 163 | 0/8 9 h-lim-p 0.0002 0.1413 14.7162 2115.085191 0 0.0007 177 | 0/8 10 h-lim-p 0.6506 5.2044 0.0120 2115.006314 5 0.7168 202 | 0/8 11 h-lim-p 1.5488 12.3901 0.0028 2115.002355 5 0.8238 233 | 0/8 12 h-lim-p 2.5000 20.0000 0.0005 2115.002193 3 0.8059 261 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2115.002193 0 1.0938 281 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 2115.002193 0 1.0938 301 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2115.002193 0 2.1875 321 | 0/8 16 h-lim-p 1.6543 20.0000 0.0000 2115.002193 0 0.7237 341 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 2115.002193 0 0.0049 369 Out... lnL = -2115.002193 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2115.002193 Node 7: lnL = -2115.002193 Node 8: lnL = -2115.002193 Node 9: lnL = -2115.002193 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 282 Sequential format.. Reading seq # 1: YIL071C_Sbay Reading seq # 2: YIL071C_Scer Reading seq # 3: YIL071C_Skud Reading seq # 4: YIL071C_Smik Reading seq # 5: YIL071C_Spar Sequences read.. Counting patterns.. # site patterns = 128 Counting frequencies.. 120 bytes for distance 20480 bytes for lkl0 16384 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.091679 0.080261 0.149383 0.101425 0.150849 0.279665 0.269264 lnL0 = -1319.778720 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1319.778720 x= 0.00006 0.09168 0.08026 0.14938 0.10142 0.15085 0.27966 0.26926 1 h-lim-p 0.0000 0.0000 39.7895 1319.735027 m 0.0000 22 | 1/8 2 h-lim-p 0.0001 0.0160 9.6766 1319.683159 0 0.0014 37 | 1/8 3 h-lim-p 0.0036 0.0783 3.7359 1319.674536 5 0.0013 62 | 1/8 4 h-lim-p 0.0034 0.2418 1.4079 1319.671904 4 0.0018 83 | 0/8 5 h-lim-p 0.0008 0.1587 3.2005 1319.657644 0 0.0032 97 | 0/8 6 h-lim-p 0.0073 0.3637 1.3896 1319.653635 5 0.0020 120 | 0/8 7 h-lim-p 0.0030 0.1972 0.9100 1319.633565 0 0.0061 133 | 0/8 8 h-lim-p 0.0025 0.0676 2.2207 1319.367956 0 0.0099 155 | 0/8 9 h-lim-p 0.0011 0.0091 7.3212 1319.152041 0 0.0046 169 | 0/8 10 h-lim-p 2.5000 20.0000 0.0095 1319.115531 5 1.0181 192 | 0/8 11 h-lim-p 2.5000 20.0000 0.0014 1319.114877 4 0.9644 220 | 0/8 12 h-lim-p 2.5000 20.0000 0.0001 1319.114869 1 1.0938 242 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1319.114869 0 1.0938 262 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1319.114869 0 2.1875 282 | 0/8 15 h-lim-p 1.8586 20.0000 0.0000 1319.114869 0 0.8131 302 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1319.114869 0 0.0781 326 | 0/8 17 h-lim-p 0.0541 20.0000 0.0000 1319.114869 0 0.0000 357 Out... lnL = -1319.114869 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1319.114869 Node 7: lnL = -1319.114869 Node 8: lnL = -1319.114869 Node 9: lnL = -1319.114869 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 884 Sequential format.. Reading seq # 1: YIL072W_Sbay Reading seq # 2: YIL072W_Scer Reading seq # 3: YIL072W_Skud Reading seq # 4: YIL072W_Smik Reading seq # 5: YIL072W_Spar Sequences read.. Counting patterns.. # site patterns = 359 Counting frequencies.. 120 bytes for distance 57440 bytes for lkl0 45952 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.016621 0.121890 0.073273 0.114682 0.150471 0.241352 0.268705 0.346822 lnL0 = -4203.446987 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4203.446987 x= 0.01662 0.12189 0.07327 0.11468 0.15047 0.24135 0.26870 0.34682 1 h-lim-p 0.0034 0.0274 106.4972 4202.017719 8 0.0003 44 | 0/8 2 h-lim-p 0.0010 0.0080 26.4520 4201.883203 6 0.0004 67 | 0/8 3 h-lim-p 0.0006 0.0220 17.7765 4201.834069 6 0.0004 92 | 0/8 4 h-lim-p 0.0011 0.0193 7.0182 4201.823977 2 0.0005 108 | 0/8 5 h-lim-p 0.0036 0.0632 0.9999 4201.823764 2 0.0004 126 | 0/8 6 h-lim-p 0.0023 0.3570 0.1893 4201.823753 2 0.0006 151 | 0/8 7 h-lim-p 0.0144 20.0000 0.0081 4201.823752 0 0.0032 172 | 0/8 8 h-lim-p 0.0180 20.0000 0.0014 4201.823610 0 0.2875 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4201.823602 1 0.9961 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4201.823602 0 1.0938 238 | 0/8 11 h-lim-p 0.4200 20.0000 0.0001 4201.823602 0 0.0263 261 | 0/8 12 h-lim-p 0.0047 20.0000 0.0003 4201.823602 0 0.0000 287 | 0/8 13 h-lim-p 0.0004 20.0000 0.0000 4201.823602 0 0.0002 307 | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 4201.823602 0 0.0000 338 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 4201.823602 0 0.0000 361 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 4201.823602 0 0.0000 387 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 | 0/8 19 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -4201.823602 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4201.823602 Node 7: lnL = -4201.823602 Node 8: lnL = -4201.823602 Node 9: lnL = -4201.823602 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 858 Sequential format.. Reading seq # 1: YIL073C_Sbay Reading seq # 2: YIL073C_Scer Reading seq # 3: YIL073C_Skud Reading seq # 4: YIL073C_Smik Reading seq # 5: YIL073C_Spar Sequences read.. Counting patterns.. # site patterns = 393 Counting frequencies.. 120 bytes for distance 62880 bytes for lkl0 50304 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.164352 0.050310 0.000060 0.702445 0.481234 0.270137 0.469149 0.687846 lnL0 = -4745.681601 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4745.681601 x= 0.16435 0.05031 0.00006 0.70244 0.48123 0.27014 0.46915 0.68785 1 h-lim-p 0.0000 0.0000 412.4383 4745.602469 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0032 196.9226 4706.993890 0 0.0019 41 | 1/8 3 h-lim-p 0.0011 0.0086 76.8140 4700.323360 0 0.0032 54 | 1/8 4 h-lim-p 0.0013 0.0106 54.1405 4698.211667 0 0.0026 67 | 1/8 5 h-lim-p 0.0033 0.0262 12.1680 4697.286645 0 0.0066 80 | 1/8 6 h-lim-p 0.0139 0.1632 5.7386 4694.780284 0 0.0278 93 | 1/8 7 h-lim-p 0.0091 0.0729 6.3512 4672.304173 m 0.0729 105 | 1/8 8 h-lim-p 0.4387 3.5093 0.2495 4668.678085 0 0.6580 117 | 1/8 9 h-lim-p 0.1594 1.2751 0.3094 4667.279117 0 0.3188 137 | 1/8 10 h-lim-p 0.3550 2.8400 0.0472 4667.121662 0 0.7100 157 | 1/8 11 h-lim-p 1.0180 8.1438 0.0116 4667.089497 6 0.6776 190 | 1/8 12 h-lim-p 2.4573 20.0000 0.0032 4667.088016 5 0.7426 224 | 1/8 13 h-lim-p 2.5000 20.0000 0.0005 4667.087958 1 0.5469 246 | 1/8 14 h-lim-p 2.5000 20.0000 0.0001 4667.087957 0 0.5469 266 | 1/8 15 h-lim-p 1.4258 20.0000 0.0000 4667.087957 0 0.6238 285 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 4667.087957 0 1.0938 304 | 1/8 17 h-lim-p 2.3765 20.0000 0.0000 4667.087957 0 2.0794 323 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 4667.087957 0 0.5469 343 | 1/8 19 h-lim-p 0.1423 20.0000 0.0000 4667.087957 0 0.1423 362 | 1/8 20 h-lim-p 0.0671 20.0000 0.0000 4667.087957 0 0.0587 381 | 1/8 21 h-lim-p 0.0303 20.0000 0.0000 4667.087957 0 0.0152 400 | 1/8 22 h-lim-p 0.0140 20.0000 0.0000 4667.087957 0 0.0140 419 | 1/8 23 h-lim-p 0.0060 20.0000 0.0000 4667.087957 0 0.0015 439 | 1/8 24 h-lim-p 0.0008 20.0000 0.0001 4667.087957 0 0.0008 458 | 1/8 25 h-lim-p 0.0039 20.0000 0.0000 4667.087957 0 0.0000 483 Out... lnL = -4667.087957 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4667.087957 Node 7: lnL = -4667.087957 Node 8: lnL = -4667.087957 Node 9: lnL = -4667.087957 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 605 Sequential format.. Reading seq # 1: YIL077C_Sbay Reading seq # 2: YIL077C_Scer Reading seq # 3: YIL077C_Skud Reading seq # 4: YIL077C_Smik Reading seq # 5: YIL077C_Spar Sequences read.. Counting patterns.. # site patterns = 297 Counting frequencies.. 120 bytes for distance 47520 bytes for lkl0 38016 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.142069 0.142328 0.053988 0.211952 0.132197 0.210970 0.276317 0.564882 lnL0 = -3067.667126 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3067.667126 x= 0.14207 0.14233 0.05399 0.21195 0.13220 0.21097 0.27632 0.56488 1 h-lim-p 0.0252 2.8644 49.3170 3067.186770 8 0.0004 42 | 0/8 2 h-lim-p 0.0010 0.0171 20.3949 3067.065415 7 0.0007 72 | 0/8 3 h-lim-p 0.0019 0.0601 7.0537 3067.036574 6 0.0013 100 | 0/8 4 h-lim-p 0.0012 0.0425 7.8890 3067.019422 5 0.0010 121 | 0/8 5 h-lim-p 0.0084 0.2550 0.9634 3067.019024 2 0.0009 139 | 0/8 6 h-lim-p 0.0044 1.2460 0.1979 3067.018995 2 0.0014 164 | 0/8 7 h-lim-p 0.0029 2.5776 0.0969 3067.018989 0 0.0013 184 | 0/8 8 h-lim-p 0.2478 20.0000 0.0005 3067.018771 0 0.9913 206 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3067.018770 0 1.0938 226 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3067.018770 0 1.0938 246 | 0/8 11 h-lim-p 1.4236 20.0000 0.0000 3067.018770 0 0.3559 267 | 0/8 12 h-lim-p 0.1671 20.0000 0.0000 3067.018770 0 0.0005 295 | 0/8 13 h-lim-p 0.0017 20.0000 0.0000 3067.018770 0 0.0000 331 Out... lnL = -3067.018770 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3067.018770 Node 7: lnL = -3067.018770 Node 8: lnL = -3067.018770 Node 9: lnL = -3067.018770 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 837 Sequential format.. Reading seq # 1: YIL083C_Sbay Reading seq # 2: YIL083C_Scer Reading seq # 3: YIL083C_Skud Reading seq # 4: YIL083C_Smik Reading seq # 5: YIL083C_Spar Sequences read.. Counting patterns.. # site patterns = 449 Counting frequencies.. 120 bytes for distance 71840 bytes for lkl0 57472 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.428323 0.092853 0.072476 0.233107 0.252042 0.296025 0.326029 0.097285 lnL0 = -4401.944585 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4401.944585 x= 0.42832 0.09285 0.07248 0.23311 0.25204 0.29602 0.32603 0.09728 1 h-lim-p 0.0047 1.1299 137.4830 4398.296419 8 0.0004 43 | 0/8 2 h-lim-p 0.0017 0.0160 33.8945 4397.835329 5 0.0008 65 | 0/8 3 h-lim-p 0.0023 0.0186 12.2797 4397.775738 4 0.0009 85 | 0/8 4 h-lim-p 0.0030 0.0684 3.6461 4397.769897 4 0.0010 107 | 0/8 5 h-lim-p 0.0024 0.1773 1.4616 4397.768280 4 0.0018 129 | 0/8 6 h-lim-p 0.0080 1.1929 0.3226 4397.768228 2 0.0010 147 | 0/8 7 h-lim-p 0.0099 11.9243 0.0321 4397.768211 2 0.0066 173 | 0/8 8 h-lim-p 0.0284 20.0000 0.0074 4397.765648 0 0.2270 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 4397.765631 1 0.9961 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4397.765631 0 1.0938 238 | 0/8 11 h-lim-p 1.1384 20.0000 0.0000 4397.765631 0 2.2768 259 | 0/8 12 h-lim-p 0.2157 20.0000 0.0001 4397.765631 0 0.2157 279 | 0/8 13 h-lim-p 0.0457 20.0000 0.0005 4397.765631 0 0.0057 301 | 0/8 14 h-lim-p 0.0014 20.0000 0.0019 4397.765631 0 0.0002 323 | 0/8 15 h-lim-p 0.0001 20.0000 0.0023 4397.765631 0 0.0001 343 | 0/8 16 h-lim-p 0.0014 20.0000 0.0001 4397.765631 0 0.0000 376 | 0/8 17 h-lim-p 0.0002 20.0000 0.0000 4397.765631 0 0.0000 402 Out... lnL = -4397.765631 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4397.765631 Node 7: lnL = -4397.765631 Node 8: lnL = -4397.765631 Node 9: lnL = -4397.765631 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 310 Sequential format.. Reading seq # 1: YIL084C_Sbay Reading seq # 2: YIL084C_Scer Reading seq # 3: YIL084C_Skud Reading seq # 4: YIL084C_Smik Reading seq # 5: YIL084C_Spar Sequences read.. Counting patterns.. # site patterns = 124 Counting frequencies.. 120 bytes for distance 19840 bytes for lkl0 15872 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.147180 0.082017 0.036498 0.081755 0.086040 0.155241 0.105699 0.012351 lnL0 = -1203.725239 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1203.725239 x= 0.14718 0.08202 0.03650 0.08175 0.08604 0.15524 0.10570 0.01235 1 h-lim-p 0.0027 1.2230 94.0691 1202.675619 4 0.0003 32 | 0/8 2 h-lim-p 0.0020 0.0170 12.4892 1202.629349 7 0.0006 62 | 0/8 3 h-lim-p 0.0018 0.0188 4.2437 1202.625901 2 0.0004 79 | 0/8 4 h-lim-p 0.0047 0.0849 0.3753 1202.625863 0 0.0005 93 | 0/8 5 h-lim-p 0.0016 1.8146 0.1230 1202.625859 1 0.0006 115 | 0/8 6 h-lim-p 0.0021 5.4878 0.0374 1202.625858 0 0.0009 135 | 0/8 7 h-lim-p 0.0134 20.0000 0.0025 1202.625853 0 0.0268 156 | 0/8 8 h-lim-p 0.0041 3.7194 0.0165 1202.625688 0 0.0246 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1202.625684 1 0.9961 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1202.625684 0 1.0938 220 | 0/8 11 h-lim-p 0.2533 20.0000 0.0001 1202.625684 0 0.0059 245 | 0/8 12 h-lim-p 0.0013 20.0000 0.0005 1202.625684 0 0.0000 286 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1202.625684 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1202.625684 Node 7: lnL = -1202.625684 Node 8: lnL = -1202.625684 Node 9: lnL = -1202.625684 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 33 Sequential format.. Reading seq # 1: YIL087C_Sbay Reading seq # 2: YIL087C_Scer Reading seq # 3: YIL087C_Skud Reading seq # 4: YIL087C_Smik Reading seq # 5: YIL087C_Spar Sequences read.. Counting patterns.. # site patterns = 27 Counting frequencies.. 120 bytes for distance 0 bytes for lkl0 3456 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: 41.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.377717 0.208169 0.000060 0.535587 0.750122 0.358665 0.518063 0.029979 lnL0 = -194.012997 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 194.012997 x= 0.37772 0.20817 0.00006 0.53559 0.75012 0.35867 0.51806 0.02998 1 h-lim-p 0.0000 0.0000 24.7899 194.008653 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0005 1623.7734 180.038675 m 0.0005 37 | 1/8 3 h-lim-p 0.0017 0.0140 20.6810 178.855584 0 0.0070 51 | 1/8 4 h-lim-p 0.0165 0.1321 3.0120 178.704384 1 0.0206 65 | 1/8 5 h-lim-p 0.0458 1.0169 1.3582 178.509194 1 0.0572 79 | 1/8 6 h-lim-p 0.0043 0.0341 2.1300 178.398453 0 0.0255 93 | 1/8 7 h-lim-p 0.0344 0.4828 1.5793 178.359463 4 0.0270 113 | 1/8 8 h-lim-p 0.1003 0.8027 0.0746 178.289649 m 0.8027 125 | 1/8 9 h-lim-p 0.0000 0.0000 0.2733 h-lim-p: 1.17974934e-20 9.43799469e-20 2.73314915e-01 178.289649 .. | 1/8 10 h-lim-p 0.0000 0.0401 6.7694 177.924349 7 0.0159 184 | 1/8 11 h-lim-p 0.0167 0.1338 5.5881 177.544525 0 0.0334 197 | 1/8 12 h-lim-p 0.0057 0.0454 5.6087 177.514938 8 0.0040 229 | 1/8 13 h-lim-p 0.0041 0.0325 1.0724 177.506069 0 0.0162 243 | 1/8 14 h-lim-p 0.0385 1.2162 0.4526 177.503747 7 0.0221 274 | 1/8 15 h-lim-p 0.0513 0.4100 0.0782 177.497769 0 0.2050 295 | 1/8 16 h-lim-p 0.0010 0.0082 0.5975 177.494959 m 0.0082 314 | 2/8 17 h-lim-p 0.0396 11.4012 0.0780 177.494706 4 0.0425 342 | 2/8 18 h-lim-p 0.2471 20.0000 0.0134 177.490059 0 0.9882 362 | 2/8 19 h-lim-p 2.5000 20.0000 0.0032 177.489851 5 0.9162 391 | 2/8 20 h-lim-p 2.5000 20.0000 0.0004 177.489842 2 0.9961 413 | 2/8 21 h-lim-p 2.5000 20.0000 0.0000 177.489842 0 1.0938 431 | 2/8 22 h-lim-p 2.5000 20.0000 0.0000 177.489842 0 1.0938 449 | 2/8 23 h-lim-p 2.5000 20.0000 0.0000 177.489842 0 2.1875 467 | 2/8 24 h-lim-p 1.8420 20.0000 0.0000 177.489842 0 0.2303 487 | 2/8 25 h-lim-p 0.2992 20.0000 0.0000 177.489842 0 0.0374 507 | 2/8 26 h-lim-p 0.0389 20.0000 0.0000 177.489842 0 0.0049 527 Out... lnL = -177.489842 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -177.489842 Node 7: lnL = -177.489842 Node 8: lnL = -177.489842 Node 9: lnL = -177.489842 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 248 Sequential format.. Reading seq # 1: YIL088C_Sbay Reading seq # 2: YIL088C_Scer Reading seq # 3: YIL088C_Skud Reading seq # 4: YIL088C_Smik Reading seq # 5: YIL088C_Spar Sequences read.. Counting patterns.. # site patterns = 113 Counting frequencies.. 120 bytes for distance 18080 bytes for lkl0 14464 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.287191 0.070328 0.059647 0.097491 0.069866 0.181121 0.180596 0.092862 lnL0 = -1124.517595 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1124.517595 x= 0.28719 0.07033 0.05965 0.09749 0.06987 0.18112 0.18060 0.09286 1 h-lim-p 0.0059 1.6392 61.9133 1123.710600 8 0.0005 42 | 0/8 2 h-lim-p 0.0012 0.0099 11.6879 1123.660381 7 0.0008 75 | 0/8 3 h-lim-p 0.0014 0.0167 6.4037 1123.649198 3 0.0007 93 | 0/8 4 h-lim-p 0.0021 0.2465 2.0812 1123.646983 5 0.0012 118 | 0/8 5 h-lim-p 0.0055 0.2600 0.4425 1123.646850 3 0.0014 137 | 0/8 6 h-lim-p 0.0057 1.2243 0.1116 1123.646845 2 0.0009 164 | 0/8 7 h-lim-p 0.0047 8.3259 0.0225 1123.646845 0 0.0021 184 | 0/8 8 h-lim-p 0.1775 20.0000 0.0003 1123.646782 0 1.4197 207 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1123.646776 1 0.9961 229 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1123.646776 0 2.1875 249 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1123.646776 0 1.0938 269 | 0/8 12 h-lim-p 0.2192 20.0000 0.0000 1123.646776 0 5.2601 293 | 0/8 13 h-lim-p 0.3709 20.0000 0.0001 1123.646776 0 0.0927 314 | 0/8 14 h-lim-p 0.0108 20.0000 0.0007 1123.646776 0 0.0000 348 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 1123.646776 0 0.0000 381 Out... lnL = -1123.646776 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1123.646776 Node 7: lnL = -1123.646776 Node 8: lnL = -1123.646776 Node 9: lnL = -1123.646776 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 461 Sequential format.. Reading seq # 1: YIL090W_Sbay Reading seq # 2: YIL090W_Scer Reading seq # 3: YIL090W_Skud Reading seq # 4: YIL090W_Smik Reading seq # 5: YIL090W_Spar Sequences read.. Counting patterns.. # site patterns = 148 Counting frequencies.. 120 bytes for distance 23680 bytes for lkl0 18944 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.293985 0.148197 0.020231 0.371601 0.521214 0.248197 0.598882 0.000060 lnL0 = -2129.220277 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2129.220277 x= 0.29398 0.14820 0.02023 0.37160 0.52121 0.24820 0.59888 0.00006 1 h-lim-p 0.0000 0.0000 447.3056 2129.062321 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0008 796.6205 1951.295349 0 0.0007 40 | 1/8 3 h-lim-p 0.0001 0.0005 250.8908 1943.312850 0 0.0003 54 | 1/8 4 h-lim-p 0.0011 0.0086 46.8541 1941.426074 0 0.0022 67 | 1/8 5 h-lim-p 0.0021 0.0167 43.0387 1940.580948 9 0.0014 102 | 1/8 6 h-lim-p 0.0028 0.0227 8.4052 1940.425166 7 0.0023 127 | 1/8 7 h-lim-p 0.0164 0.1398 1.1676 1928.086321 m 0.1398 140 | 0/8 8 h-lim-p 0.0008 0.0066 54.1421 1925.023328 0 0.0017 153 | 0/8 9 h-lim-p 0.0002 0.0019 69.2153 1920.862346 m 0.0019 165 | 0/8 10 h-lim-p 0.0000 0.0000 0.2745 h-lim-p: 5.10731994e-18 4.08585595e-17 2.74487956e-01 1920.862346 .. | 0/8 11 h-lim-p 0.0000 0.0015 220.6980 1918.491916 0 0.0002 197 | 0/8 12 h-lim-p 0.0002 0.0019 45.5382 1918.201066 1 0.0003 211 | 0/8 13 h-lim-p 0.0007 0.0143 18.7250 1918.058798 0 0.0014 224 | 0/8 14 h-lim-p 0.0007 0.0053 32.6602 1917.892370 1 0.0008 238 | 0/8 15 h-lim-p 0.0013 0.0169 21.5370 1917.849012 6 0.0004 265 | 0/8 16 h-lim-p 0.0017 0.0219 5.4354 1917.739242 0 0.0102 279 | 0/8 17 h-lim-p 0.0034 0.0271 0.6661 1917.738933 2 0.0008 296 | 0/8 18 h-lim-p 0.0005 0.0122 1.1528 1917.721930 m 0.0122 318 | 1/8 19 h-lim-p 0.0151 0.1458 0.6569 1917.721884 1 0.0004 336 | 1/8 20 h-lim-p 0.0227 14.3720 0.0108 1917.500420 0 1.4549 361 | 1/8 21 h-lim-p 2.5000 20.0000 0.0038 1917.498519 4 1.0199 389 | 0/8 22 h-lim-p 0.2324 20.0000 0.0165 1917.498519 0 0.0016 414 | 0/8 23 h-lim-p 0.0513 0.9735 0.0005 1917.498501 1 0.8202 439 | 0/8 24 h-lim-p 0.0170 0.1363 0.0000 1917.498501 m 0.1363 459 | 1/8 25 h-lim-p 0.1452 20.0000 0.0000 1917.498501 0 0.2179 479 | 1/8 26 h-lim-p 0.6025 20.0000 0.0000 1917.498501 0 1.2050 499 | 1/8 27 h-lim-p 2.5000 20.0000 0.0000 1917.498501 0 1.2500 518 | 1/8 28 h-lim-p 2.5000 20.0000 0.0000 1917.498501 0 2.1875 537 | 1/8 29 h-lim-p 2.4706 20.0000 0.0000 1917.498501 0 0.6177 557 | 1/8 30 h-lim-p 1.6200 20.0000 0.0000 1917.498501 0 0.0506 580 | 1/8 31 h-lim-p 0.0534 20.0000 0.0000 1917.498501 0 0.0001 607 Out... lnL = -1917.498501 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1917.498501 Node 7: lnL = -1917.498501 Node 8: lnL = -1917.498501 Node 9: lnL = -1917.498501 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 435 Sequential format.. Reading seq # 1: YIL091C_Sbay Reading seq # 2: YIL091C_Scer Reading seq # 3: YIL091C_Skud Reading seq # 4: YIL091C_Smik Reading seq # 5: YIL091C_Spar Sequences read.. Counting patterns.. # site patterns = 124 Counting frequencies.. 120 bytes for distance 19840 bytes for lkl0 15872 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.141774 0.059244 0.044912 0.060566 0.050850 0.125460 0.124392 0.021884 lnL0 = -1606.898409 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1606.898409 x= 0.14177 0.05924 0.04491 0.06057 0.05085 0.12546 0.12439 0.02188 1 h-lim-p 0.0025 0.0897 112.5744 1605.470630 4 0.0002 32 | 0/8 2 h-lim-p 0.0003 0.0027 22.4387 1605.400496 6 0.0003 59 | 0/8 3 h-lim-p 0.0008 0.0074 7.8272 1605.393460 6 0.0003 86 | 0/8 4 h-lim-p 0.0006 0.0355 3.6189 1605.391915 4 0.0003 107 | 0/8 5 h-lim-p 0.0010 0.1062 1.0694 1605.391756 4 0.0003 130 | 0/8 6 h-lim-p 0.0036 1.6502 0.0890 1605.391754 0 0.0005 144 | 0/8 7 h-lim-p 0.0009 2.4512 0.0442 1605.391754 0 0.0004 164 | 0/8 8 h-lim-p 0.0496 20.0000 0.0004 1605.391546 0 1.1912 188 | 0/8 9 h-lim-p 0.9380 20.0000 0.0005 1605.391540 0 0.9380 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1605.391540 0 1.0938 228 | 0/8 11 h-lim-p 1.8240 20.0000 0.0000 1605.391540 0 1.5960 248 | 0/8 12 h-lim-p 1.2859 20.0000 0.0000 1605.391540 0 1.1252 268 | 0/8 13 h-lim-p 0.3390 20.0000 0.0001 1605.391540 0 0.0013 295 | 0/8 14 h-lim-p 0.0002 20.0000 0.0005 1605.391540 0 0.0004 315 | 0/8 15 h-lim-p 0.0016 20.0000 0.0001 1605.391540 0 0.0000 356 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 | 0/8 17 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -1605.391540 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1605.391540 Node 7: lnL = -1605.391540 Node 8: lnL = -1605.391540 Node 9: lnL = -1605.391540 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 336 Sequential format.. Reading seq # 1: YIL092W_Sbay Reading seq # 2: YIL092W_Scer Reading seq # 3: YIL092W_Skud Reading seq # 4: YIL092W_Smik Reading seq # 5: YIL092W_Spar Sequences read.. Counting patterns.. # site patterns = 163 Counting frequencies.. 120 bytes for distance 26080 bytes for lkl0 20864 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.242072 0.060206 0.116819 0.110071 0.150633 0.236491 0.185044 0.027762 lnL0 = -1538.225181 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1538.225181 x= 0.24207 0.06021 0.11682 0.11007 0.15063 0.23649 0.18504 0.02776 1 h-lim-p 0.0227 3.3901 36.8379 1537.862362 4 0.0006 34 | 0/8 2 h-lim-p 0.0028 0.0220 5.5073 1537.846170 4 0.0011 54 | 0/8 3 h-lim-p 0.0050 0.2685 1.1809 1537.845618 4 0.0008 76 | 0/8 4 h-lim-p 0.0032 0.3827 0.3085 1537.845572 2 0.0010 94 | 0/8 5 h-lim-p 0.0054 3.4346 0.0598 1537.845570 0 0.0012 115 | 0/8 6 h-lim-p 0.0077 20.0000 0.0091 1537.845570 0 0.0017 136 | 0/8 7 h-lim-p 0.0082 20.0000 0.0019 1537.845570 0 0.0082 156 | 0/8 8 h-lim-p 0.0118 20.0000 0.0013 1537.845558 0 0.0947 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1537.845558 0 1.0938 199 | 0/8 10 h-lim-p 1.4880 20.0000 0.0000 1537.845558 0 1.3020 219 | 0/8 11 h-lim-p 1.2402 20.0000 0.0000 1537.845558 0 0.0388 243 | 0/8 12 h-lim-p 0.0035 20.0000 0.0001 1537.845558 0 0.0004 265 | 0/8 13 h-lim-p 0.0001 20.0000 0.0010 1537.845558 0 0.0000 289 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 1537.845558 0 0.0000 323 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 1537.845558 0 0.0000 357 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1537.845558 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1537.845558 Node 7: lnL = -1537.845558 Node 8: lnL = -1537.845558 Node 9: lnL = -1537.845558 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 311 Sequential format.. Reading seq # 1: YIL093C_Sbay Reading seq # 2: YIL093C_Scer Reading seq # 3: YIL093C_Skud Reading seq # 4: YIL093C_Smik Reading seq # 5: YIL093C_Spar Sequences read.. Counting patterns.. # site patterns = 149 Counting frequencies.. 120 bytes for distance 23840 bytes for lkl0 19072 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.237968 0.080019 0.073822 0.134875 0.121840 0.244503 0.191949 0.028455 lnL0 = -1421.030763 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1421.030763 x= 0.23797 0.08002 0.07382 0.13487 0.12184 0.24450 0.19195 0.02846 1 h-lim-p 0.0033 0.0261 32.2771 1420.729409 8 0.0006 43 | 0/8 2 h-lim-p 0.0026 0.0278 7.3824 1420.707565 6 0.0008 69 | 0/8 3 h-lim-p 0.0039 0.1551 1.5897 1420.706445 2 0.0009 86 | 0/8 4 h-lim-p 0.0026 0.4311 0.5482 1420.706321 3 0.0009 106 | 0/8 5 h-lim-p 0.0062 1.7377 0.0821 1420.706317 2 0.0010 132 | 0/8 6 h-lim-p 0.0060 13.8198 0.0137 1420.706317 0 0.0026 152 | 0/8 7 h-lim-p 0.0224 20.0000 0.0016 1420.706317 0 0.0049 173 | 0/8 8 h-lim-p 0.0210 20.0000 0.0004 1420.706312 0 0.2518 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1420.706312 0 1.0938 216 | 0/8 10 h-lim-p 1.6359 20.0000 0.0000 1420.706312 0 1.4314 236 | 0/8 11 h-lim-p 1.7661 20.0000 0.0000 1420.706312 0 0.7727 256 | 0/8 12 h-lim-p 0.2423 20.0000 0.0000 1420.706312 0 0.0019 282 | 0/8 13 h-lim-p 0.0007 20.0000 0.0001 1420.706312 0 0.0000 312 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 1420.706312 0 0.0000 339 Out... lnL = -1420.706312 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1420.706312 Node 7: lnL = -1420.706312 Node 8: lnL = -1420.706312 Node 9: lnL = -1420.706312 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 376 Sequential format.. Reading seq # 1: YIL094C_Sbay Reading seq # 2: YIL094C_Scer Reading seq # 3: YIL094C_Skud Reading seq # 4: YIL094C_Smik Reading seq # 5: YIL094C_Spar Sequences read.. Counting patterns.. # site patterns = 141 Counting frequencies.. 120 bytes for distance 22560 bytes for lkl0 18048 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.172584 0.045233 0.045082 0.086491 0.070947 0.153951 0.159659 0.030149 lnL0 = -1498.888661 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1498.888661 x= 0.17258 0.04523 0.04508 0.08649 0.07095 0.15395 0.15966 0.03015 1 h-lim-p 0.0027 0.3226 105.7067 1497.675096 6 0.0002 37 | 0/8 2 h-lim-p 0.0012 0.0096 11.5999 1497.644683 5 0.0005 59 | 0/8 3 h-lim-p 0.0010 0.0391 5.1188 1497.639711 5 0.0004 80 | 0/8 4 h-lim-p 0.0021 0.1203 1.0596 1497.639482 3 0.0004 99 | 0/8 5 h-lim-p 0.0055 0.7488 0.0833 1497.639481 1 0.0005 115 | 0/8 6 h-lim-p 0.0043 18.8962 0.0104 1497.639481 0 0.0005 137 | 0/8 7 h-lim-p 0.0026 20.0000 0.0022 1497.639481 0 0.0011 157 | 0/8 8 h-lim-p 0.1991 20.0000 0.0000 1497.639481 0 1.1949 179 | 0/8 9 h-lim-p 0.8713 20.0000 0.0000 1497.639481 0 0.7624 199 | 0/8 10 h-lim-p 0.4617 20.0000 0.0000 1497.639481 0 0.2020 219 | 0/8 11 h-lim-p 0.0673 20.0000 0.0001 1497.639481 0 0.0126 241 | 0/8 12 h-lim-p 0.0055 20.0000 0.0002 1497.639481 0 0.0000 270 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0006 1497.639481 0 0.0000 336 | 0/8 15 h-lim-p 0.0000 20.0000 0.0006 | 0/8 16 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -1497.639481 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1497.639481 Node 7: lnL = -1497.639481 Node 8: lnL = -1497.639481 Node 9: lnL = -1497.639481 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 869 Sequential format.. Reading seq # 1: YIL096C_Sbay Reading seq # 2: YIL096C_Scer Reading seq # 3: YIL096C_Skud Reading seq # 4: YIL096C_Smik Reading seq # 5: YIL096C_Spar Sequences read.. Counting patterns.. # site patterns = 343 Counting frequencies.. 120 bytes for distance 54880 bytes for lkl0 43904 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.252179 0.005694 0.146990 0.179250 0.118165 0.248599 0.202385 0.030406 lnL0 = -4133.488667 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4133.488667 x= 0.25218 0.00569 0.14699 0.17925 0.11817 0.24860 0.20238 0.03041 1 h-lim-p 0.0008 0.3357 319.0953 4128.299344 9 0.0001 48 | 0/8 2 h-lim-p 0.0011 0.0088 30.7409 4128.054154 2 0.0005 64 | 0/8 3 h-lim-p 0.0030 0.0969 5.2928 4128.048177 5 0.0004 89 | 0/8 4 h-lim-p 0.0020 0.1126 1.1829 4128.047886 2 0.0004 106 | 0/8 5 h-lim-p 0.0014 0.4606 0.3760 4128.047867 0 0.0003 119 | 0/8 6 h-lim-p 0.0012 4.6114 0.0906 4128.047865 0 0.0005 139 | 0/8 7 h-lim-p 0.0092 20.0000 0.0053 4128.047865 0 0.0023 160 | 0/8 8 h-lim-p 0.0158 20.0000 0.0008 4128.047797 0 0.2532 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4128.047791 0 1.0938 204 | 0/8 10 h-lim-p 2.1589 20.0000 0.0000 4128.047791 0 1.0795 224 | 0/8 11 h-lim-p 0.8898 20.0000 0.0000 4128.047791 010.6781 247 | 0/8 12 h-lim-p 0.0201 3.1461 0.0163 4128.047791 0 0.0006 271 | 0/8 13 h-lim-p 0.0010 5.1486 0.0100 4128.047791 0 0.0000 295 | 0/8 14 h-lim-p 0.0002 20.0000 0.0020 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0012 | 0/8 16 h-lim-p 0.0000 20.0000 0.0012 Out... lnL = -4128.047791 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4128.047791 Node 7: lnL = -4128.047791 Node 8: lnL = -4128.047791 Node 9: lnL = -4128.047791 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 207 Sequential format.. Reading seq # 1: YIL097W_Sbay Reading seq # 2: YIL097W_Scer Reading seq # 3: YIL097W_Skud Reading seq # 4: YIL097W_Smik Reading seq # 5: YIL097W_Spar Sequences read.. Counting patterns.. # site patterns = 119 Counting frequencies.. 120 bytes for distance 19040 bytes for lkl0 15232 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.239734 0.149514 0.000060 0.297989 0.386670 0.228795 0.294315 0.019870 lnL0 = -962.115098 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 962.115098 x= 0.23973 0.14951 0.00006 0.29799 0.38667 0.22879 0.29431 0.01987 1 h-lim-p 0.0000 0.0000 118.4916 962.057921 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0007 148.4937 954.891909 m 0.0007 38 | 1/8 3 h-lim-p 0.0002 0.0013 237.0314 944.715112 0 0.0010 52 | 1/8 4 h-lim-p 0.0007 0.0053 16.6887 944.416774 0 0.0027 66 | 0/8 5 h-lim-p 0.0005 0.0069 84.8006 943.626400 8 0.0004 98 | 0/8 6 h-lim-p 0.0039 0.0311 4.0327 943.110740 0 0.0155 112 | 0/8 7 h-lim-p 0.0051 0.0408 7.6288 941.198805 0 0.0102 125 | 0/8 8 h-lim-p 0.0028 0.0227 17.6270 933.031802 0 0.0113 139 | 0/8 9 h-lim-p 0.1023 0.8188 0.1958 932.018201 0 0.3070 152 | 0/8 10 h-lim-p 0.3994 3.1953 0.0518 931.571307 0 0.7988 173 | 0/8 11 h-lim-p 1.5406 12.3247 0.0197 931.496796 2 0.7222 197 | 0/8 12 h-lim-p 2.5000 20.0000 0.0037 931.493671 3 1.0449 223 | 0/8 13 h-lim-p 2.5000 20.0000 0.0007 931.493535 3 0.9644 249 | 0/8 14 h-lim-p 2.5000 20.0000 0.0002 931.493518 1 1.0938 271 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 931.493518 0 1.0938 291 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 931.493518 0 1.0938 311 | 0/8 17 h-lim-p 2.1495 20.0000 0.0000 931.493518 0 1.8808 331 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 931.493518 0 0.0049 359 | 0/8 19 h-lim-p 0.0010 20.0000 0.0000 931.493518 0 0.0003 380 Out... lnL = -931.493518 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -931.493518 Node 7: lnL = -931.493518 Node 8: lnL = -931.493518 Node 9: lnL = -931.493518 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 203 Sequential format.. Reading seq # 1: YIL098C_Sbay Reading seq # 2: YIL098C_Scer Reading seq # 3: YIL098C_Skud Reading seq # 4: YIL098C_Smik Reading seq # 5: YIL098C_Spar Sequences read.. Counting patterns.. # site patterns = 110 Counting frequencies.. 120 bytes for distance 17600 bytes for lkl0 14080 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.300349 0.202554 0.018072 0.129148 0.109356 0.241627 0.205863 0.058244 lnL0 = -959.662084 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 959.662084 x= 0.30035 0.20255 0.01807 0.12915 0.10936 0.24163 0.20586 0.05824 1 h-lim-p 0.0008 0.0066 65.1525 958.533648 8 0.0006 37 | 0/8 2 h-lim-p 0.0008 0.0061 19.4748 958.326705 0 0.0011 49 | 0/8 3 h-lim-p 0.0039 0.0487 5.6753 958.312072 4 0.0010 70 | 0/8 4 h-lim-p 0.0072 0.6934 0.7915 958.311449 4 0.0020 93 | 0/8 5 h-lim-p 0.0135 2.3823 0.1187 958.311429 2 0.0026 118 | 0/8 6 h-lim-p 0.0162 14.5046 0.0191 958.311408 0 0.0243 138 | 0/8 7 h-lim-p 0.0304 16.3421 0.0152 958.311074 0 0.0912 159 | 0/8 8 h-lim-p 0.0078 0.3989 0.1787 958.310368 1 0.0097 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 958.310349 2 0.9644 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 958.310349 0 1.0938 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 958.310349 0 1.0938 245 | 0/8 12 h-lim-p 1.0559 20.0000 0.0000 958.310349 0 2.1117 266 | 0/8 13 h-lim-p 0.7196 20.0000 0.0000 958.310349 0 0.0450 289 | 0/8 14 h-lim-p 0.0010 20.0000 0.0005 958.310349 0 0.0005 309 | 0/8 15 h-lim-p 0.0000 0.9687 0.1002 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 958.310349 0 0.0000 362 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 958.310349 0 0.0000 416 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 958.310349 0 0.0000 438 | 0/8 20 h-lim-p 0.0000 20.0000 0.0000 958.310349 0 0.0000 471 | 0/8 21 h-lim-p 0.0000 20.0000 0.0001 958.310349 0 0.0000 500 | 0/8 22 h-lim-p 0.0000 20.0000 0.0001 | 0/8 23 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -958.310349 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -958.310349 Node 7: lnL = -958.310349 Node 8: lnL = -958.310349 Node 9: lnL = -958.310349 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 263 Sequential format.. Reading seq # 1: YIL103W_Sbay Reading seq # 2: YIL103W_Scer Reading seq # 3: YIL103W_Skud Reading seq # 4: YIL103W_Smik Reading seq # 5: YIL103W_Spar Sequences read.. Counting patterns.. # site patterns = 136 Counting frequencies.. 120 bytes for distance 21760 bytes for lkl0 17408 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.254992 0.163225 0.013107 0.201625 0.146790 0.246211 0.268774 0.009856 lnL0 = -1249.739423 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1249.739423 x= 0.25499 0.16323 0.01311 0.20163 0.14679 0.24621 0.26877 0.00986 1 h-lim-p 0.0020 0.0159 86.0241 1248.472144 3 0.0004 29 | 0/8 2 h-lim-p 0.0015 0.0123 21.7111 1248.087222 6 0.0017 54 | 0/8 3 h-lim-p 0.0012 0.0099 4.6698 1248.071369 0 0.0019 66 | 0/8 4 h-lim-p 0.0079 0.1012 1.0997 1248.070648 4 0.0013 89 | 0/8 5 h-lim-p 0.0085 1.1634 0.1628 1248.070616 3 0.0023 108 | 0/8 6 h-lim-p 0.0077 0.5720 0.0484 1248.070612 2 0.0025 134 | 0/8 7 h-lim-p 0.0059 15.3493 0.0209 1248.070594 0 0.0177 155 | 0/8 8 h-lim-p 0.0259 14.9870 0.0142 1248.069959 0 0.1037 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1248.069941 3 1.4879 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1248.069941 0 1.0938 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1248.069941 0 1.0938 245 | 0/8 12 h-lim-p 1.0622 20.0000 0.0000 1248.069941 0 4.2489 267 | 0/8 13 h-lim-p 0.0902 20.0000 0.0004 1248.069941 0 0.0902 287 | 0/8 14 h-lim-p 0.0243 10.6211 0.0016 1248.069941 0 0.0013 310 | 0/8 15 h-lim-p 0.0006 4.7703 0.0035 1248.069941 0 0.0001 332 | 0/8 16 h-lim-p 0.0000 0.1735 0.0976 1248.069941 0 0.0000 357 | 0/8 17 h-lim-p 0.0002 20.0000 0.0001 1248.069941 0 0.0000 383 | 0/8 18 h-lim-p 0.0002 20.0000 0.0000 1248.069941 0 0.0000 413 Out... lnL = -1248.069941 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1248.069941 Node 7: lnL = -1248.069941 Node 8: lnL = -1248.069941 Node 9: lnL = -1248.069941 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 263 Sequential format.. Reading seq # 1: YIL104C_Sbay Reading seq # 2: YIL104C_Scer Reading seq # 3: YIL104C_Skud Reading seq # 4: YIL104C_Smik Reading seq # 5: YIL104C_Spar Sequences read.. Counting patterns.. # site patterns = 139 Counting frequencies.. 120 bytes for distance 22240 bytes for lkl0 17792 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.260779 0.110630 0.028253 0.199237 0.149179 0.247212 0.236668 0.026973 lnL0 = -1232.984556 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1232.984556 x= 0.26078 0.11063 0.02825 0.19924 0.14918 0.24721 0.23667 0.02697 1 h-lim-p 0.0032 0.0259 42.5813 1232.608518 8 0.0005 42 | 0/8 2 h-lim-p 0.0021 0.0242 9.1254 1232.556475 7 0.0013 74 | 0/8 3 h-lim-p 0.0067 0.1294 1.7490 1232.554636 5 0.0012 98 | 0/8 4 h-lim-p 0.0050 0.4991 0.4321 1232.554504 4 0.0015 121 | 0/8 5 h-lim-p 0.0235 10.7558 0.0275 1232.554503 0 0.0013 144 | 0/8 6 h-lim-p 0.0124 20.0000 0.0028 1232.554503 0 0.0124 164 | 0/8 7 h-lim-p 0.0111 20.0000 0.0032 1232.554499 0 0.0444 186 | 0/8 8 h-lim-p 0.0087 4.7384 0.0163 1232.554481 0 0.0130 206 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1232.554480 0 1.0938 226 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1232.554480 0 1.0938 246 | 0/8 11 h-lim-p 1.2009 20.0000 0.0000 1232.554480 0 0.0000 286 Out... lnL = -1232.554480 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1232.554480 Node 7: lnL = -1232.554480 Node 8: lnL = -1232.554480 Node 9: lnL = -1232.554480 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 362 Sequential format.. Reading seq # 1: YIL105C_Sbay Reading seq # 2: YIL105C_Scer Reading seq # 3: YIL105C_Skud Reading seq # 4: YIL105C_Smik Reading seq # 5: YIL105C_Spar Sequences read.. Counting patterns.. # site patterns = 125 Counting frequencies.. 120 bytes for distance 20000 bytes for lkl0 16000 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.166325 0.016262 0.086159 0.088773 0.057546 0.120694 0.172943 0.023240 lnL0 = -1424.726055 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1424.726055 x= 0.16632 0.01626 0.08616 0.08877 0.05755 0.12069 0.17294 0.02324 1 h-lim-p 0.0019 0.8814 122.4930 1423.645551 8 0.0002 44 | 0/8 2 h-lim-p 0.0012 0.0125 16.6495 1423.584875 7 0.0005 72 | 0/8 3 h-lim-p 0.0011 0.0163 6.5632 1423.578315 6 0.0003 100 | 0/8 4 h-lim-p 0.0012 0.1216 1.9115 1423.577441 2 0.0005 116 | 0/8 5 h-lim-p 0.0023 0.5334 0.4297 1423.577390 2 0.0006 133 | 0/8 6 h-lim-p 0.0039 2.4978 0.0629 1423.577389 0 0.0005 155 | 0/8 7 h-lim-p 0.0093 20.0000 0.0033 1423.577389 0 0.0082 175 | 0/8 8 h-lim-p 0.0152 20.0000 0.0018 1423.577305 0 0.1212 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1423.577305 0 1.0938 218 | 0/8 10 h-lim-p 1.8502 20.0000 0.0000 1423.577305 0 1.6189 238 | 0/8 11 h-lim-p 1.9425 20.0000 0.0000 1423.577305 0 0.8499 258 | 0/8 12 h-lim-p 0.2320 20.0000 0.0001 1423.577305 0 0.0290 280 | 0/8 13 h-lim-p 0.0064 20.0000 0.0003 1423.577305 0 0.0000 307 | 0/8 14 h-lim-p 0.0000 20.0000 0.0018 1423.577305 0 0.0000 341 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 | 0/8 16 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -1423.577305 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1423.577305 Node 7: lnL = -1423.577305 Node 8: lnL = -1423.577305 Node 9: lnL = -1423.577305 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 466 Sequential format.. Reading seq # 1: YIL115C_Sbay Reading seq # 2: YIL115C_Scer Reading seq # 3: YIL115C_Skud Reading seq # 4: YIL115C_Smik Reading seq # 5: YIL115C_Spar Sequences read.. Counting patterns.. # site patterns = 223 Counting frequencies.. 120 bytes for distance 35680 bytes for lkl0 28544 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.381029 0.122543 0.068052 0.137406 0.104227 0.248023 0.253027 0.104414 lnL0 = -2209.313934 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2209.313934 x= 0.38103 0.12254 0.06805 0.13741 0.10423 0.24802 0.25303 0.10441 1 h-lim-p 0.0055 0.0437 27.3730 2209.126914 6 0.0005 36 | 0/8 2 h-lim-p 0.0012 0.0224 11.4146 2209.080104 6 0.0008 61 | 0/8 3 h-lim-p 0.0013 0.0578 7.0882 2209.070476 3 0.0005 79 | 0/8 4 h-lim-p 0.0015 0.1140 2.4249 2209.067587 4 0.0012 99 | 0/8 5 h-lim-p 0.0027 0.4047 1.0477 2209.067187 3 0.0009 119 | 0/8 6 h-lim-p 0.0028 0.7277 0.3340 2209.067142 2 0.0009 137 | 0/8 7 h-lim-p 0.0063 3.1743 0.0492 2209.067141 0 0.0016 158 | 0/8 8 h-lim-p 1.1245 20.0000 0.0001 2209.067136 0 1.1245 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2209.067136 0 1.0938 198 | 0/8 10 h-lim-p 1.1290 20.0000 0.0000 2209.067136 0 0.0309 222 | 0/8 11 h-lim-p 0.0084 20.0000 0.0000 2209.067136 0 0.0005 245 | 0/8 12 h-lim-p 0.0001 20.0000 0.0001 2209.067136 0 0.0000 278 | 0/8 13 h-lim-p 0.0000 20.0000 0.0003 2209.067136 0 0.0000 312 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -2209.067136 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2209.067136 Node 7: lnL = -2209.067136 Node 8: lnL = -2209.067136 Node 9: lnL = -2209.067136 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 856 Sequential format.. Reading seq # 1: YIL116W_Sbay Reading seq # 2: YIL116W_Scer Reading seq # 3: YIL116W_Skud Reading seq # 4: YIL116W_Smik Reading seq # 5: YIL116W_Spar Sequences read.. Counting patterns.. # site patterns = 381 Counting frequencies.. 120 bytes for distance 60960 bytes for lkl0 48768 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.387983 0.136965 0.037502 0.204339 0.190530 0.298732 0.304978 0.073426 lnL0 = -4457.829271 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4457.829271 x= 0.38798 0.13696 0.03750 0.20434 0.19053 0.29873 0.30498 0.07343 1 h-lim-p 0.0043 0.1132 143.2178 4455.285837 7 0.0003 38 | 0/8 2 h-lim-p 0.0011 0.0097 36.9396 4454.852980 7 0.0007 66 | 0/8 3 h-lim-p 0.0017 0.0311 14.9118 4454.783792 4 0.0007 85 | 0/8 4 h-lim-p 0.0015 0.0484 7.2812 4454.768820 2 0.0007 101 | 0/8 5 h-lim-p 0.0041 0.2263 1.2447 4454.768162 2 0.0009 118 | 0/8 6 h-lim-p 0.0083 2.6910 0.1332 4454.768156 1 0.0005 135 | 0/8 7 h-lim-p 0.0107 20.0000 0.0063 4454.768124 0 0.0428 157 | 0/8 8 h-lim-p 0.0091 20.0000 0.0299 4454.767249 0 0.0363 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 4454.767219 1 0.9961 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4454.767219 0 1.0938 221 | 0/8 11 h-lim-p 1.0956 20.0000 0.0000 4454.767219 0 1.0956 241 | 0/8 12 h-lim-p 0.6411 20.0000 0.0000 4454.767219 0 0.6411 261 | 0/8 13 h-lim-p 0.0231 20.0000 0.0005 4454.767219 0 0.0029 283 | 0/8 14 h-lim-p 0.0019 20.0000 0.0008 4454.767219 0 0.0037 304 | 0/8 15 h-lim-p 0.0000 0.1174 0.9363 4454.767219 0 0.0000 332 | 0/8 16 h-lim-p 0.0007 20.0000 0.0000 4454.767219 0 0.0000 362 | 0/8 17 h-lim-p 0.0001 20.0000 0.0000 4454.767219 0 0.0000 391 Out... lnL = -4454.767219 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4454.767219 Node 7: lnL = -4454.767219 Node 8: lnL = -4454.767219 Node 9: lnL = -4454.767219 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 853 Sequential format.. Reading seq # 1: YIL117C_Sbay Reading seq # 2: YIL117C_Scer Reading seq # 3: YIL117C_Skud Reading seq # 4: YIL117C_Smik Reading seq # 5: YIL117C_Spar Sequences read.. Counting patterns.. # site patterns = 307 Counting frequencies.. 120 bytes for distance 49120 bytes for lkl0 39296 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.317191 0.043037 0.097240 0.161969 0.105218 0.255775 0.241293 0.068626 lnL0 = -4109.779256 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4109.779256 x= 0.31719 0.04304 0.09724 0.16197 0.10522 0.25578 0.24129 0.06863 1 h-lim-p 0.0105 0.3668 88.2766 4108.935238 8 0.0002 46 | 0/8 2 h-lim-p 0.0009 0.0113 21.0695 4108.852528 3 0.0004 64 | 0/8 3 h-lim-p 0.0010 0.0448 8.4530 4108.841630 6 0.0004 91 | 0/8 4 h-lim-p 0.0009 0.0647 3.3761 4108.839778 2 0.0004 107 | 0/8 5 h-lim-p 0.0036 0.9279 0.3613 4108.839745 2 0.0006 126 | 0/8 6 h-lim-p 0.0033 5.0051 0.0648 4108.839744 0 0.0007 147 | 0/8 7 h-lim-p 0.0030 8.9824 0.0155 4108.839744 0 0.0007 168 | 0/8 8 h-lim-p 0.1770 20.0000 0.0001 4108.839741 0 1.0621 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4108.839741 0 1.0938 210 | 0/8 10 h-lim-p 1.1632 20.0000 0.0000 4108.839741 0 0.0363 234 | 0/8 11 h-lim-p 0.0059 20.0000 0.0001 4108.839741 0 0.0004 257 | 0/8 12 h-lim-p 0.0004 20.0000 0.0001 4108.839741 0 0.0004 277 | 0/8 13 h-lim-p 0.0002 20.0000 0.0002 4108.839741 0 0.0000 313 | 0/8 14 h-lim-p 0.0000 20.0000 0.0010 4108.839741 0 0.0000 338 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 4108.839741 0 0.0000 370 | 0/8 16 h-lim-p 0.0000 20.0000 0.0010 4108.839741 0 0.0000 399 | 0/8 17 h-lim-p 0.0000 20.0000 0.0011 4108.839741 0 0.0000 426 | 0/8 18 h-lim-p 0.0000 20.0000 0.0003 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0010 | 0/8 20 h-lim-p 0.0000 20.0000 0.0010 Out... lnL = -4108.839741 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4108.839741 Node 7: lnL = -4108.839741 Node 8: lnL = -4108.839741 Node 9: lnL = -4108.839741 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 865 Sequential format.. Reading seq # 1: YIL118W_Sbay Reading seq # 2: YIL118W_Scer Reading seq # 3: YIL118W_Skud Reading seq # 4: YIL118W_Smik Reading seq # 5: YIL118W_Spar Sequences read.. Counting patterns.. # site patterns = 261 Counting frequencies.. 120 bytes for distance 41760 bytes for lkl0 33408 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.222847 0.078437 0.071266 0.078378 0.054566 0.154667 0.194770 0.044790 lnL0 = -3618.183664 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3618.183664 x= 0.22285 0.07844 0.07127 0.07838 0.05457 0.15467 0.19477 0.04479 1 h-lim-p 0.0002 0.0015 151.9633 3616.257351 2 0.0002 26 | 0/8 2 h-lim-p 0.0010 0.0085 25.7338 3616.168217 5 0.0003 49 | 0/8 3 h-lim-p 0.0011 0.0339 6.5546 3616.160753 5 0.0004 74 | 0/8 4 h-lim-p 0.0005 0.0610 4.7196 3616.159936 3 0.0001 93 | 0/8 5 h-lim-p 0.0005 0.2137 0.8875 3616.159826 3 0.0003 112 | 0/8 6 h-lim-p 0.0009 0.4383 0.2866 3616.159818 0 0.0002 133 | 0/8 7 h-lim-p 0.0069 10.8836 0.0082 3616.159796 0 0.0138 154 | 0/8 8 h-lim-p 0.0036 7.3815 0.0315 3616.158234 0 0.0289 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3616.158209 1 0.9961 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3616.158209 0 1.0938 219 | 0/8 11 h-lim-p 0.8530 20.0000 0.0000 3616.158209 0 0.0533 242 | 0/8 12 h-lim-p 0.0009 20.0000 0.0020 3616.158209 0 0.0001 265 | 0/8 13 h-lim-p 0.0000 20.0000 0.0029 3616.158209 0 0.0000 302 | 0/8 14 h-lim-p 0.0000 20.0000 0.0005 3616.158209 0 0.0006 328 | 0/8 15 h-lim-p 0.0012 20.0000 0.0003 3616.158209 0 0.0000 361 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 3616.158209 0 0.0000 381 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 3616.158209 0 0.0000 402 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0018 | 0/8 20 h-lim-p 0.0000 20.0000 0.0018 Out... lnL = -3616.158209 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3616.158209 Node 7: lnL = -3616.158209 Node 8: lnL = -3616.158209 Node 9: lnL = -3616.158209 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 883 Sequential format.. Reading seq # 1: YIL119C_Sbay Reading seq # 2: YIL119C_Scer Reading seq # 3: YIL119C_Skud Reading seq # 4: YIL119C_Smik Reading seq # 5: YIL119C_Spar Sequences read.. Counting patterns.. # site patterns = 179 Counting frequencies.. 120 bytes for distance 28640 bytes for lkl0 22912 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.176752 0.019447 0.027923 0.048467 0.044591 0.085838 0.134803 0.062707 lnL0 = -3048.235387 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3048.235387 x= 0.17675 0.01945 0.02792 0.04847 0.04459 0.08584 0.13480 0.06271 1 h-lim-p 0.0011 0.0099 230.4758 3046.823822 3 0.0001 31 | 0/8 2 h-lim-p 0.0002 0.0017 25.6098 3046.800148 5 0.0001 55 | 0/8 3 h-lim-p 0.0003 0.0169 5.7301 3046.798147 3 0.0001 73 | 0/8 4 h-lim-p 0.0005 0.0547 1.4215 3046.798064 3 0.0001 94 | 0/8 5 h-lim-p 0.0002 0.2818 0.6622 3046.798028 1 0.0002 108 | 0/8 6 h-lim-p 0.0015 1.0503 0.0888 3046.798028 0 0.0002 130 | 0/8 7 h-lim-p 0.0004 3.7422 0.0342 3046.798028 0 0.0004 150 | 0/8 8 h-lim-p 0.0836 20.0000 0.0001 3046.797883 0 1.3377 174 | 0/8 9 h-lim-p 2.2742 20.0000 0.0001 3046.797873 0 0.9949 194 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3046.797873 0 2.1875 214 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3046.797873 0 0.2734 236 | 0/8 12 h-lim-p 0.0229 20.0000 0.0000 3046.797873 0 0.0029 258 | 0/8 13 h-lim-p 0.0012 20.0000 0.0001 3046.797873 0 0.0001 280 | 0/8 14 h-lim-p 0.0004 20.0000 0.0000 3046.797873 0 0.0000 316 | 0/8 15 h-lim-p 0.0000 13.3205 0.0087 | 0/8 16 h-lim-p 0.0000 13.3205 0.0087 Out... lnL = -3046.797873 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3046.797873 Node 7: lnL = -3046.797873 Node 8: lnL = -3046.797873 Node 9: lnL = -3046.797873 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 822 Sequential format.. Reading seq # 1: YIL122W_Sbay Reading seq # 2: YIL122W_Scer Reading seq # 3: YIL122W_Skud Reading seq # 4: YIL122W_Smik Reading seq # 5: YIL122W_Spar Sequences read.. Counting patterns.. # site patterns = 192 Counting frequencies.. 120 bytes for distance 30720 bytes for lkl0 24576 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.160347 0.046125 0.027154 0.063258 0.050938 0.099326 0.094554 0.046235 lnL0 = -2991.360132 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2991.360132 x= 0.16035 0.04613 0.02715 0.06326 0.05094 0.09933 0.09455 0.04624 1 h-lim-p 0.0001 0.0011 253.4364 2989.579681 3 0.0001 28 | 0/8 2 h-lim-p 0.0002 0.0016 47.5756 2989.466084 5 0.0001 51 | 0/8 3 h-lim-p 0.0005 0.0247 10.3390 2989.461265 3 0.0001 70 | 0/8 4 h-lim-p 0.0004 0.0514 2.6419 2989.460735 2 0.0002 86 | 0/8 5 h-lim-p 0.0024 0.7199 0.1794 2989.460732 1 0.0001 103 | 0/8 6 h-lim-p 0.0005 3.2424 0.0570 2989.460731 0 0.0004 123 | 0/8 7 h-lim-p 0.0030 20.0000 0.0076 2989.460681 0 0.0242 146 | 0/8 8 h-lim-p 0.0020 0.5175 0.0926 2989.459039 0 0.0060 167 | 0/8 9 h-lim-p 0.1674 19.8005 0.0033 2989.458965 0 1.0046 189 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2989.458961 0 1.0938 209 | 0/8 11 h-lim-p 1.2923 20.0000 0.0001 2989.458961 0 1.1308 229 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2989.458961 0 1.0938 249 | 0/8 13 h-lim-p 0.0684 20.0000 0.0006 2989.458961 0 0.0086 271 | 0/8 14 h-lim-p 0.0023 20.0000 0.0022 2989.458961 0 0.0000 310 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 2989.458961 0 0.0000 344 Out... lnL = -2989.458961 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2989.458961 Node 7: lnL = -2989.458961 Node 8: lnL = -2989.458961 Node 9: lnL = -2989.458961 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 836 Sequential format.. Reading seq # 1: YIL123W_Sbay Reading seq # 2: YIL123W_Scer Reading seq # 3: YIL123W_Skud Reading seq # 4: YIL123W_Smik Reading seq # 5: YIL123W_Spar Sequences read.. Counting patterns.. # site patterns = 202 Counting frequencies.. 120 bytes for distance 32320 bytes for lkl0 25856 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.139847 0.036345 0.041144 0.091509 0.056120 0.161184 0.122461 0.012061 lnL0 = -3249.084447 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3249.084447 x= 0.13985 0.03634 0.04114 0.09151 0.05612 0.16118 0.12246 0.01206 1 h-lim-p 0.0013 0.5564 223.8289 3247.283646 4 0.0001 33 | 0/8 2 h-lim-p 0.0004 0.0034 20.6040 3247.255847 6 0.0001 61 | 0/8 3 h-lim-p 0.0004 0.0483 6.1859 3247.253050 5 0.0002 86 | 0/8 4 h-lim-p 0.0005 0.0865 2.0271 3247.252693 3 0.0002 104 | 0/8 5 h-lim-p 0.0008 0.0867 0.5197 3247.252673 1 0.0002 119 | 0/8 6 h-lim-p 0.0009 2.8960 0.0983 3247.252672 0 0.0002 140 | 0/8 7 h-lim-p 0.0047 5.4212 0.0045 3247.252672 0 0.0010 161 | 0/8 8 h-lim-p 0.0067 20.0000 0.0007 3247.252604 0 0.2145 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3247.252602 0 1.0938 206 | 0/8 10 h-lim-p 0.4284 20.0000 0.0001 3247.252602 0 0.6426 226 | 0/8 11 h-lim-p 0.3420 20.0000 0.0002 3247.252602 0 0.0107 250 | 0/8 12 h-lim-p 0.0034 20.0000 0.0005 .. | 0/8 13 h-lim-p 0.0000 20.0000 0.0050 | 0/8 14 h-lim-p 0.0000 20.0000 0.0050 Out... lnL = -3247.252602 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3247.252602 Node 7: lnL = -3247.252602 Node 8: lnL = -3247.252602 Node 9: lnL = -3247.252602 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 524 Sequential format.. Reading seq # 1: YIL124W_Sbay Reading seq # 2: YIL124W_Scer Reading seq # 3: YIL124W_Skud Reading seq # 4: YIL124W_Smik Reading seq # 5: YIL124W_Spar Sequences read.. Counting patterns.. # site patterns = 223 Counting frequencies.. 120 bytes for distance 35680 bytes for lkl0 28544 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.234521 0.146954 0.085763 0.120936 0.095590 0.187807 0.246593 0.007585 lnL0 = -2334.838354 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2334.838354 x= 0.23452 0.14695 0.08576 0.12094 0.09559 0.18781 0.24659 0.00758 1 h-lim-p 0.0064 0.0514 64.5841 2333.967857 8 0.0004 42 | 0/8 2 h-lim-p 0.0015 0.0125 18.3911 2333.872625 4 0.0006 62 | 0/8 3 h-lim-p 0.0009 0.0073 11.4882 2333.850292 6 0.0005 86 | 0/8 4 h-lim-p 0.0026 0.0691 1.9953 2333.848673 4 0.0009 108 | 0/8 5 h-lim-p 0.0021 0.4548 0.8305 2333.848488 4 0.0006 131 | 0/8 6 h-lim-p 0.0113 7.5283 0.0452 2333.848487 0 0.0012 153 | 0/8 7 h-lim-p 0.0030 3.3053 0.0183 2333.848486 0 0.0027 173 | 0/8 8 h-lim-p 0.0380 20.0000 0.0013 2333.848258 0 0.3039 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2333.848249 1 0.9961 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2333.848249 0 1.0938 238 | 0/8 11 h-lim-p 0.5207 20.0000 0.0000 2333.848249 0 0.0081 263 | 0/8 12 h-lim-p 0.0009 20.0000 0.0004 2333.848249 0 0.0003 284 | 0/8 13 h-lim-p 0.0003 20.0000 0.0005 2333.848249 0 0.0000 315 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 2333.848249 0 0.0001 335 Out... lnL = -2333.848249 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2333.848249 Node 7: lnL = -2333.848249 Node 8: lnL = -2333.848249 Node 9: lnL = -2333.848249 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 651 Sequential format.. Reading seq # 1: YIL125W_Sbay Reading seq # 2: YIL125W_Scer Reading seq # 3: YIL125W_Skud Reading seq # 4: YIL125W_Smik Reading seq # 5: YIL125W_Spar Sequences read.. Counting patterns.. # site patterns = 181 Counting frequencies.. 120 bytes for distance 28960 bytes for lkl0 23168 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.171256 0.013079 0.049828 0.115123 0.069131 0.093471 0.105306 0.044598 lnL0 = -2462.682781 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2462.682781 x= 0.17126 0.01308 0.04983 0.11512 0.06913 0.09347 0.10531 0.04460 1 h-lim-p 0.0002 0.0012 382.3479 2458.867217 8 0.0001 41 | 0/8 2 h-lim-p 0.0002 0.0013 69.0383 2458.421887 1 0.0002 55 | 0/8 3 h-lim-p 0.0008 0.0141 18.8516 2458.392226 2 0.0002 72 | 0/8 4 h-lim-p 0.0011 0.0221 2.8935 2458.391579 5 0.0002 97 | 0/8 5 h-lim-p 0.0009 0.8787 0.4927 2458.391551 1 0.0002 112 | 0/8 6 h-lim-p 0.0035 15.4533 0.0329 2458.391546 0 0.0015 132 | 0/8 7 h-lim-p 0.0074 20.0000 0.0068 2458.389546 0 0.1184 156 | 0/8 8 h-lim-p 0.0005 0.1189 1.5644 2458.388992 4 0.0003 186 | 0/8 9 h-lim-p 1.0619 20.0000 0.0005 2458.388854 0 1.5928 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2458.388841 0 1.0938 218 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2458.388841 0 1.2500 238 | 0/8 12 h-lim-p 1.5394 20.0000 0.0000 2458.388841 0 0.6735 258 | 0/8 13 h-lim-p 0.3854 20.0000 0.0000 2458.388841 0 0.0030 284 | 0/8 14 h-lim-p 0.0011 20.0000 0.0001 2458.388841 0 0.0000 309 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 2458.388841 0 0.0000 329 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 2458.388841 0 0.0000 349 | 0/8 17 h-lim-p 0.0004 20.0000 0.0000 2458.388841 0 0.0001 370 Out... lnL = -2458.388841 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2458.388841 Node 7: lnL = -2458.388841 Node 8: lnL = -2458.388841 Node 9: lnL = -2458.388841 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 594 Sequential format.. Reading seq # 1: YIL126W_Sbay Reading seq # 2: YIL126W_Scer Reading seq # 3: YIL126W_Skud Reading seq # 4: YIL126W_Smik Reading seq # 5: YIL126W_Spar Sequences read.. Counting patterns.. # site patterns = 142 Counting frequencies.. 120 bytes for distance 22720 bytes for lkl0 18176 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.148320 0.062705 0.092311 0.118536 0.057152 0.149694 0.140728 0.000060 lnL0 = -1816.610069 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1816.610069 x= 0.14832 0.06270 0.09231 0.11854 0.05715 0.14969 0.14073 0.00006 1 h-lim-p 0.0002 0.0017 73.6756 1815.409258 0 0.0004 23 | 0/8 2 h-lim-p 0.0002 0.0019 26.7849 1815.282201 0 0.0005 36 | 0/8 3 h-lim-p 0.0012 0.0119 10.1509 1815.266702 6 0.0003 63 | 0/8 4 h-lim-p 0.0012 0.0890 2.9240 1815.264870 4 0.0005 83 | 0/8 5 h-lim-p 0.0013 0.0103 0.9243 1815.264707 3 0.0004 103 | 0/8 6 h-lim-p 0.0022 1.2634 0.1704 1815.264168 0 0.0360 127 | 0/8 7 h-lim-p 0.0008 0.0285 7.4761 1815.259699 0 0.0066 150 | 0/8 8 h-lim-p 0.3256 2.6050 0.0642 1815.259692 2 0.0017 174 | 0/8 9 h-lim-p 0.0021 1.1721 0.0510 1815.257149 0 0.2701 201 | 0/8 10 h-lim-p 1.1117 8.8938 0.0051 1815.257041 2 0.9728 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0001 1815.257041 0 1.0938 245 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1815.257041 0 0.5469 266 | 0/8 13 h-lim-p 0.1430 20.0000 0.0000 1815.257041 0 0.0626 286 | 0/8 14 h-lim-p 0.0273 20.0000 0.0000 1815.257041 0 0.0239 306 | 0/8 15 h-lim-p 0.0136 20.0000 0.0000 1815.257041 0 0.0000 347 | 0/8 16 h-lim-p 0.0000 20.0000 0.0011 | 0/8 17 h-lim-p 0.0000 20.0000 0.0011 Out... lnL = -1815.257041 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1815.257041 Node 7: lnL = -1815.257041 Node 8: lnL = -1815.257041 Node 9: lnL = -1815.257041 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 368 Sequential format.. Reading seq # 1: YIL127C_Sbay Reading seq # 2: YIL127C_Scer Reading seq # 3: YIL127C_Skud Reading seq # 4: YIL127C_Smik Reading seq # 5: YIL127C_Spar Sequences read.. Counting patterns.. # site patterns = 142 Counting frequencies.. 120 bytes for distance 22720 bytes for lkl0 18176 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.148163 0.069540 0.102672 0.116482 0.058327 0.146154 0.144215 0.000060 lnL0 = -1494.730392 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1494.730392 x= 0.14816 0.06954 0.10267 0.11648 0.05833 0.14615 0.14422 0.00006 1 h-lim-p 0.0001 0.0010 78.7017 1493.529368 0 0.0005 24 | 0/8 2 h-lim-p 0.0007 0.0052 47.9389 1493.248381 6 0.0003 49 | 0/8 3 h-lim-p 0.0025 0.0385 6.1232 1493.238167 4 0.0006 69 | 0/8 4 h-lim-p 0.0003 0.0023 2.3528 1493.237219 0 0.0004 81 | 0/8 5 h-lim-p 0.0018 0.0144 0.2607 1493.236070 0 0.0072 95 | 0/8 6 h-lim-p 0.0001 0.0006 2.4483 1493.233671 m 0.0006 115 | 0/8 7 h-lim-p -0.0000 -0.0000 75.5138 h-lim-p: -1.29883290e-22 -1.03906632e-21 7.55137735e+01 1493.233671 .. | 0/8 8 h-lim-p 0.0000 0.0282 29.5091 1493.149661 0 0.0002 139 | 0/8 9 h-lim-p 0.0007 0.0186 9.4432 1493.128183 6 0.0005 165 | 0/8 10 h-lim-p 0.0000 0.0002 1.1839 1493.127983 m 0.0002 177 | 1/8 11 h-lim-p 0.0004 0.5210 0.4435 1493.127938 1 0.0005 191 | 1/8 12 h-lim-p 0.0037 1.3380 0.0645 1493.127931 2 0.0014 214 | 1/8 13 h-lim-p 0.0031 5.5008 0.0297 1493.127814 0 0.0125 235 | 1/8 14 h-lim-p 0.0013 0.6842 0.2810 1493.127407 0 0.0026 255 | 1/8 15 h-lim-p 0.0056 1.0702 0.1321 1493.127397 2 0.0009 281 | 1/8 16 h-lim-p 0.0418 17.4085 0.0029 1493.125556 0 0.3347 303 | 1/8 17 h-lim-p 2.5000 20.0000 0.0001 1493.125545 0 1.0938 322 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 1493.125544 1 1.2305 344 | 1/8 19 h-lim-p 2.5000 20.0000 0.0000 1493.125544 0 2.1875 363 | 1/8 20 h-lim-p 1.8499 20.0000 0.0000 1493.125544 0 0.8093 382 | 1/8 21 h-lim-p 2.5000 20.0000 0.0000 1493.125544 0 0.0001 415 Out... lnL = -1493.125544 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1493.125544 Node 7: lnL = -1493.125544 Node 8: lnL = -1493.125544 Node 9: lnL = -1493.125544 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 592 Sequential format.. Reading seq # 1: YIL128W_Sbay Reading seq # 2: YIL128W_Scer Reading seq # 3: YIL128W_Skud Reading seq # 4: YIL128W_Smik Reading seq # 5: YIL128W_Spar Sequences read.. Counting patterns.. # site patterns = 267 Counting frequencies.. 120 bytes for distance 42720 bytes for lkl0 34176 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.249063 0.075229 0.054614 0.206515 0.087948 0.251054 0.299475 0.004174 lnL0 = -2877.451057 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2877.451057 x= 0.24906 0.07523 0.05461 0.20651 0.08795 0.25105 0.29948 0.00417 1 h-lim-p 0.0025 1.0620 152.6067 2874.546094 6 0.0003 36 | 0/8 2 h-lim-p 0.0001 0.0009 20.5013 2874.395633 m 0.0009 48 | 0/8 3 h-lim-p 0.0046 0.1127 4.1518 2874.391388 3 0.0005 68 | 0/8 4 h-lim-p 0.0016 0.0575 1.3523 2874.390805 2 0.0007 84 | 0/8 5 h-lim-p 0.0027 0.0407 0.3434 2874.390760 2 0.0007 101 | 0/8 6 h-lim-p 0.0022 0.2491 0.1119 2874.390727 1 0.0022 123 | 0/8 7 h-lim-p 0.0079 15.2520 0.0314 2874.389845 0 0.0316 145 | 0/8 8 h-lim-p 0.0021 0.6160 0.4690 2874.383357 0 0.0085 167 | 0/8 9 h-lim-p 1.4472 11.5773 0.0008 2874.382930 4 1.0163 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2874.382930 0 1.2500 217 | 0/8 11 h-lim-p 1.1118 20.0000 0.0000 2874.382930 0 0.9728 237 | 0/8 12 h-lim-p 0.7468 20.0000 0.0000 2874.382930 0 0.1867 258 | 0/8 13 h-lim-p 0.0259 11.8005 0.0003 2874.382930 0 0.0000 298 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -2874.382930 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2874.382930 Node 7: lnL = -2874.382930 Node 8: lnL = -2874.382930 Node 9: lnL = -2874.382930 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 564 Sequential format.. Reading seq # 1: YIL131C_Sbay Reading seq # 2: YIL131C_Scer Reading seq # 3: YIL131C_Skud Reading seq # 4: YIL131C_Smik Reading seq # 5: YIL131C_Spar Sequences read.. Counting patterns.. # site patterns = 194 Counting frequencies.. 120 bytes for distance 31040 bytes for lkl0 24832 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.199781 0.091770 0.048701 0.116657 0.076248 0.196826 0.198732 0.008898 lnL0 = -2480.821254 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2480.821254 x= 0.19978 0.09177 0.04870 0.11666 0.07625 0.19683 0.19873 0.00890 1 h-lim-p 0.0032 0.0259 109.3429 2479.673138 4 0.0002 33 | 0/8 2 h-lim-p 0.0003 0.0026 20.9512 2479.601212 6 0.0003 56 | 0/8 3 h-lim-p 0.0005 0.0040 8.5183 2479.592547 5 0.0003 79 | 0/8 4 h-lim-p 0.0022 0.0469 1.0634 2479.592331 3 0.0004 99 | 0/8 5 h-lim-p 0.0021 1.3747 0.1942 2479.592320 2 0.0006 116 | 0/8 6 h-lim-p 0.0041 0.5596 0.0267 2479.592320 0 0.0004 138 | 0/8 7 h-lim-p 0.0024 20.0000 0.0050 2479.592320 0 0.0010 158 | 0/8 8 h-lim-p 0.0251 20.0000 0.0002 2479.592309 0 0.6016 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2479.592309 0 1.0938 202 | 0/8 10 h-lim-p 0.7565 20.0000 0.0000 2479.592309 0 0.6619 222 | 0/8 11 h-lim-p 0.1542 20.0000 0.0001 2479.592309 0 0.0024 247 | 0/8 12 h-lim-p 0.0007 20.0000 0.0005 2479.592309 0 0.0003 267 | 0/8 13 h-lim-p 0.0002 12.7114 0.0008 2479.592309 0 0.0000 292 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 2479.592309 0 0.0000 322 | 0/8 15 h-lim-p 0.0000 20.0000 0.0006 | 0/8 16 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -2479.592309 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2479.592309 Node 7: lnL = -2479.592309 Node 8: lnL = -2479.592309 Node 9: lnL = -2479.592309 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 287 Sequential format.. Reading seq # 1: YIL132C_Sbay Reading seq # 2: YIL132C_Scer Reading seq # 3: YIL132C_Skud Reading seq # 4: YIL132C_Smik Reading seq # 5: YIL132C_Spar Sequences read.. Counting patterns.. # site patterns = 133 Counting frequencies.. 120 bytes for distance 21280 bytes for lkl0 17024 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.242234 0.013148 0.084582 0.124541 0.043736 0.066572 0.204949 0.071713 lnL0 = -1173.458873 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1173.458873 x= 0.24223 0.01315 0.08458 0.12454 0.04374 0.06657 0.20495 0.07171 1 h-lim-p 0.0001 0.0008 166.9438 1169.796745 0 0.0004 24 | 0/8 2 h-lim-p 0.0010 0.0079 35.0613 1169.378355 8 0.0007 54 | 0/8 3 h-lim-p 0.0002 0.0016 31.5134 1169.290140 0 0.0003 66 | 0/8 4 h-lim-p 0.0008 0.0190 11.6060 1169.245615 5 0.0008 89 | 0/8 5 h-lim-p 0.0047 0.0759 2.0598 1169.244011 5 0.0008 113 | 0/8 6 h-lim-p 0.0039 0.3667 0.4045 1169.243776 2 0.0018 129 | 0/8 7 h-lim-p 0.0080 1.6156 0.0931 1169.242273 0 0.0160 150 | 0/8 8 h-lim-p 0.0063 0.3503 0.2377 1169.156965 0 0.0501 173 | 0/8 9 h-lim-p 2.5000 20.0000 0.0012 1169.156262 4 0.9644 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1169.156261 0 1.0938 221 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1169.156261 0 1.0938 241 | 0/8 12 h-lim-p 1.2301 20.0000 0.0000 1169.156261 0 1.2301 261 | 0/8 13 h-lim-p 0.9636 20.0000 0.0000 1169.156261 m20.0000 283 | 0/8 14 h-lim-p 0.0642 20.0000 0.0024 1169.156261 0 0.0020 307 | 0/8 15 h-lim-p 0.0009 20.0000 0.0052 1169.156261 0 0.0000 343 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 1169.156261 0 0.0000 374 Out... lnL = -1169.156261 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1169.156261 Node 7: lnL = -1169.156261 Node 8: lnL = -1169.156261 Node 9: lnL = -1169.156261 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 848 Sequential format.. Reading seq # 1: YIL134W_Sbay Reading seq # 2: YIL134W_Scer Reading seq # 3: YIL134W_Skud Reading seq # 4: YIL134W_Smik Reading seq # 5: YIL134W_Spar Sequences read.. Counting patterns.. # site patterns = 299 Counting frequencies.. 120 bytes for distance 47840 bytes for lkl0 38272 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.229045 0.049506 0.038776 0.123698 0.094048 0.202080 0.220245 0.033090 lnL0 = -3752.756013 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3752.756013 x= 0.22904 0.04951 0.03878 0.12370 0.09405 0.20208 0.22025 0.03309 1 h-lim-p 0.0014 0.5965 231.9774 3749.482164 8 0.0001 43 | 0/8 2 h-lim-p 0.0002 0.0019 51.5495 3749.130150 1 0.0003 57 | 0/8 3 h-lim-p 0.0007 0.0052 18.0309 3749.093955 3 0.0003 75 | 0/8 4 h-lim-p 0.0008 0.0198 5.6281 3749.090572 5 0.0002 99 | 0/8 5 h-lim-p 0.0014 0.2522 0.9689 3749.090383 3 0.0004 120 | 0/8 6 h-lim-p 0.0105 7.2791 0.0371 3749.090380 1 0.0013 144 | 0/8 7 h-lim-p 0.0009 4.6594 0.0562 3749.090362 0 0.0026 165 | 0/8 8 h-lim-p 0.0084 10.5444 0.0172 3749.088851 0 0.0672 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 3749.088717 2 0.9961 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3749.088717 0 1.2500 232 | 0/8 11 h-lim-p 1.2969 20.0000 0.0000 3749.088717 0 0.5674 252 | 0/8 12 h-lim-p 0.2051 20.0000 0.0001 3749.088717 0 0.0000 284 | 0/8 13 h-lim-p 0.0000 3.6432 0.0132 3749.088717 0 0.0000 308 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 3749.088717 0 0.0000 344 | 0/8 15 h-lim-p 0.0000 20.0000 0.0017 | 0/8 16 h-lim-p 0.0000 20.0000 0.0017 Out... lnL = -3749.088717 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3749.088717 Node 7: lnL = -3749.088717 Node 8: lnL = -3749.088717 Node 9: lnL = -3749.088717 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 858 Sequential format.. Reading seq # 1: YIL137C_Sbay Reading seq # 2: YIL137C_Scer Reading seq # 3: YIL137C_Skud Reading seq # 4: YIL137C_Smik Reading seq # 5: YIL137C_Spar Sequences read.. Counting patterns.. # site patterns = 322 Counting frequencies.. 120 bytes for distance 51520 bytes for lkl0 41216 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.233367 0.083946 0.052140 0.139152 0.078501 0.205437 0.237110 0.021412 lnL0 = -3760.686528 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3760.686528 x= 0.23337 0.08395 0.05214 0.13915 0.07850 0.20544 0.23711 0.02141 1 h-lim-p 0.0002 0.0014 169.3762 3758.200978 7 0.0002 35 | 0/8 2 h-lim-p 0.0003 0.0023 39.3713 3758.016724 5 0.0002 56 | 0/8 3 h-lim-p 0.0005 0.0046 20.0902 3757.984628 3 0.0002 74 | 0/8 4 h-lim-p 0.0007 0.0330 5.8617 3757.978694 5 0.0004 99 | 0/8 5 h-lim-p 0.0030 0.3604 0.7524 3757.978543 3 0.0005 119 | 0/8 6 h-lim-p 0.0023 2.0177 0.1732 3757.978538 1 0.0003 143 | 0/8 7 h-lim-p 0.0010 1.2860 0.0505 3757.978537 0 0.0008 163 | 0/8 8 h-lim-p 0.0803 20.0000 0.0005 3757.978083 0 0.9633 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3757.978069 1 0.9961 208 | 0/8 10 h-lim-p 2.2589 20.0000 0.0000 3757.978069 0 0.9882 228 | 0/8 11 h-lim-p 0.6110 20.0000 0.0001 3757.978069 0 0.0024 255 | 0/8 12 h-lim-p 0.0000 2.4399 0.0107 3757.978069 0 0.0000 279 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 3757.978069 0 0.0000 307 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 3757.978069 0 0.0000 329 Out... lnL = -3757.978069 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3757.978069 Node 7: lnL = -3757.978069 Node 8: lnL = -3757.978069 Node 9: lnL = -3757.978069 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 251 Sequential format.. Reading seq # 1: YIL138C_Sbay Reading seq # 2: YIL138C_Scer Reading seq # 3: YIL138C_Skud Reading seq # 4: YIL138C_Smik Reading seq # 5: YIL138C_Spar Sequences read.. Counting patterns.. # site patterns = 123 Counting frequencies.. 120 bytes for distance 19680 bytes for lkl0 15744 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.208923 0.063901 0.102151 0.120312 0.086878 0.213265 0.169874 0.008721 lnL0 = -1120.747831 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1120.747831 x= 0.20892 0.06390 0.10215 0.12031 0.08688 0.21326 0.16987 0.00872 1 h-lim-p 0.0037 0.0293 41.7700 1120.171610 8 0.0007 38 | 0/8 2 h-lim-p 0.0010 0.0079 10.8679 1120.116051 4 0.0010 58 | 0/8 3 h-lim-p 0.0024 0.0752 4.4373 1120.109585 6 0.0008 85 | 0/8 4 h-lim-p 0.0022 0.1334 1.5375 1120.108586 2 0.0010 101 | 0/8 5 h-lim-p 0.0052 0.4323 0.2864 1120.108535 1 0.0013 116 | 0/8 6 h-lim-p 0.0050 2.3494 0.0743 1120.108532 0 0.0012 137 | 0/8 7 h-lim-p 0.0089 2.1105 0.0105 1120.108532 0 0.0019 158 | 0/8 8 h-lim-p 0.0317 20.0000 0.0006 1120.108462 0 0.5068 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1120.108460 0 1.0938 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1120.108460 0 1.0938 222 | 0/8 11 h-lim-p 1.1318 20.0000 0.0000 1120.108460 0 0.5659 242 | 0/8 12 h-lim-p 0.1235 20.0000 0.0001 1120.108460 0 0.0001 272 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 1120.108460 0 0.0000 302 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 1120.108460 0 0.0000 326 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 1120.108460 0 0.0000 355 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1120.108460 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1120.108460 Node 7: lnL = -1120.108460 Node 8: lnL = -1120.108460 Node 9: lnL = -1120.108460 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 533 Sequential format.. Reading seq # 1: YIL140W_Sbay Reading seq # 2: YIL140W_Scer Reading seq # 3: YIL140W_Skud Reading seq # 4: YIL140W_Smik Reading seq # 5: YIL140W_Spar Sequences read.. Counting patterns.. # site patterns = 174 Counting frequencies.. 120 bytes for distance 27840 bytes for lkl0 22272 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.168351 0.031947 0.049833 0.064137 0.053662 0.143007 0.160141 0.028171 lnL0 = -2019.997885 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2019.997885 x= 0.16835 0.03195 0.04983 0.06414 0.05366 0.14301 0.16014 0.02817 1 h-lim-p 0.0009 0.0069 106.6664 2019.176979 9 0.0002 44 | 0/8 2 h-lim-p 0.0008 0.0065 14.5697 2019.152914 5 0.0002 69 | 0/8 3 h-lim-p 0.0005 0.0476 6.6039 2019.148995 3 0.0002 88 | 0/8 4 h-lim-p 0.0006 0.0483 2.2249 2019.148442 3 0.0003 106 | 0/8 5 h-lim-p 0.0007 0.1489 0.7512 2019.148353 2 0.0004 122 | 0/8 6 h-lim-p 0.0016 0.5317 0.1695 2019.148350 1 0.0002 146 | 0/8 7 h-lim-p 0.0066 20.0000 0.0049 2019.148350 0 0.0007 168 | 0/8 8 h-lim-p 0.0691 20.0000 0.0001 2019.148348 0 1.1055 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2019.148348 0 1.0938 212 | 0/8 10 h-lim-p 0.9062 20.0000 0.0000 2019.148348 0 1.8123 233 | 0/8 11 h-lim-p 1.5943 20.0000 0.0000 2019.148348 0 0.0004 264 | 0/8 12 h-lim-p 0.0000 20.0000 0.0018 2019.148348 0 0.0000 294 | 0/8 13 h-lim-p 0.0000 20.0000 0.0024 | 0/8 14 h-lim-p 0.0000 20.0000 0.0024 Out... lnL = -2019.148348 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2019.148348 Node 7: lnL = -2019.148348 Node 8: lnL = -2019.148348 Node 9: lnL = -2019.148348 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 273 Sequential format.. Reading seq # 1: YIL142W_Sbay Reading seq # 2: YIL142W_Scer Reading seq # 3: YIL142W_Skud Reading seq # 4: YIL142W_Smik Reading seq # 5: YIL142W_Spar Sequences read.. Counting patterns.. # site patterns = 106 Counting frequencies.. 120 bytes for distance 16960 bytes for lkl0 13568 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.182390 0.036961 0.056081 0.145675 0.052844 0.125121 0.135202 0.029015 lnL0 = -1103.386056 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1103.386056 x= 0.18239 0.03696 0.05608 0.14568 0.05284 0.12512 0.13520 0.02902 1 h-lim-p 0.0022 0.0180 52.6895 1102.990995 8 0.0003 43 | 0/8 2 h-lim-p 0.0017 0.0136 9.2923 1102.966861 6 0.0006 70 | 0/8 3 h-lim-p 0.0016 0.0329 3.2196 1102.964733 5 0.0005 95 | 0/8 4 h-lim-p 0.0024 0.2101 0.6114 1102.964642 2 0.0005 112 | 0/8 5 h-lim-p 0.0013 0.8566 0.2403 1102.964628 1 0.0005 134 | 0/8 6 h-lim-p 0.0034 1.9351 0.0375 1102.964628 0 0.0007 155 | 0/8 7 h-lim-p 0.0329 20.0000 0.0008 1102.964628 0 0.0018 178 | 0/8 8 h-lim-p 0.0320 20.0000 0.0000 1102.964627 0 0.5121 202 | 0/8 9 h-lim-p 1.4518 20.0000 0.0000 1102.964627 0 1.2703 222 | 0/8 10 h-lim-p 1.6628 20.0000 0.0000 1102.964627 0 1.4550 242 | 0/8 11 h-lim-p 0.8940 20.0000 0.0000 1102.964627 0 0.8940 262 | 0/8 12 h-lim-p 0.0100 20.0000 0.0019 1102.964627 0 0.0100 282 | 0/8 13 h-lim-p 0.0032 6.6951 0.0059 1102.964627 0 0.0004 304 | 0/8 14 h-lim-p 0.0001 1.6279 0.0242 1102.964627 0 0.0000 326 | 0/8 15 h-lim-p 0.0002 20.0000 0.0018 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 1102.964627 0 0.0000 384 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0003 | 0/8 19 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -1102.964627 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1102.964627 Node 7: lnL = -1102.964627 Node 8: lnL = -1102.964627 Node 9: lnL = -1102.964627 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 179 Sequential format.. Reading seq # 1: YIL143C_Sbay Reading seq # 2: YIL143C_Scer Reading seq # 3: YIL143C_Skud Reading seq # 4: YIL143C_Smik Reading seq # 5: YIL143C_Spar Sequences read.. Counting patterns.. # site patterns = 74 Counting frequencies.. 120 bytes for distance 11840 bytes for lkl0 9472 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.147785 0.021352 0.083111 0.111435 0.042781 0.092130 0.038827 0.030358 lnL0 = -616.196254 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 616.196254 x= 0.14779 0.02135 0.08311 0.11143 0.04278 0.09213 0.03883 0.03036 1 h-lim-p 0.0002 0.0018 142.3429 611.947117 0 0.0007 23 | 0/8 2 h-lim-p 0.0002 0.0016 34.8755 611.688912 0 0.0006 36 | 0/8 3 h-lim-p 0.0001 0.0008 28.1161 611.427639 m 0.0008 48 | 1/8 4 h-lim-p 0.0002 0.0021 37.3591 611.378167 1 0.0002 62 | 1/8 5 h-lim-p 0.0030 0.0448 2.9930 611.372345 6 0.0010 91 | 1/8 6 h-lim-p 0.0038 0.1987 0.7975 611.372001 3 0.0010 110 | 1/8 7 h-lim-p 0.1102 20.0000 0.0073 611.306180 0 1.7637 133 | 1/8 8 h-lim-p 0.0023 0.0522 5.4949 611.283050 7 0.0013 169 | 1/8 9 h-lim-p 2.5000 20.0000 0.0029 611.275040 4 1.9286 189 | 1/8 10 h-lim-p 2.5000 20.0000 0.0006 611.274311 2 1.1719 212 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 611.274310 0 1.0938 231 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 611.274310 0 0.5469 251 | 1/8 13 h-lim-p 0.3431 20.0000 0.0000 611.274310 0 0.0001 281 | 1/8 14 h-lim-p 0.0001 20.0000 0.0000 611.274310 0 0.0000 300 | 1/8 15 h-lim-p 0.0000 20.0000 0.0000 611.274310 0 0.0000 319 | 1/8 16 h-lim-p 0.0000 20.0000 0.0000 611.274310 0 0.0000 338 | 1/8 17 h-lim-p 0.0000 20.0000 0.0000 611.274310 0 0.0000 370 Out... lnL = -611.274310 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -611.274310 Node 7: lnL = -611.274310 Node 8: lnL = -611.274310 Node 9: lnL = -611.274310 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 616 Sequential format.. Reading seq # 1: YIL146C_Sbay Reading seq # 2: YIL146C_Scer Reading seq # 3: YIL146C_Skud Reading seq # 4: YIL146C_Smik Reading seq # 5: YIL146C_Spar Sequences read.. Counting patterns.. # site patterns = 180 Counting frequencies.. 120 bytes for distance 28800 bytes for lkl0 23040 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.192195 0.079093 0.056083 0.072626 0.053626 0.159451 0.163321 0.022321 lnL0 = -2506.946514 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2506.946514 x= 0.19220 0.07909 0.05608 0.07263 0.05363 0.15945 0.16332 0.02232 1 h-lim-p 0.0002 0.0017 91.5351 2506.083667 7 0.0002 39 | 0/8 2 h-lim-p 0.0007 0.0054 26.5531 2506.018816 6 0.0002 66 | 0/8 3 h-lim-p 0.0004 0.0062 15.0045 2506.002243 5 0.0002 89 | 0/8 4 h-lim-p 0.0006 0.0192 4.3645 2505.999586 2 0.0003 105 | 0/8 5 h-lim-p 0.0024 0.4989 0.5559 2505.999529 3 0.0004 126 | 0/8 6 h-lim-p 0.0013 1.3158 0.1642 2505.999526 1 0.0003 149 | 0/8 7 h-lim-p 0.0009 4.7005 0.0449 2505.999526 0 0.0008 169 | 0/8 8 h-lim-p 0.0532 20.0000 0.0007 2505.999018 0 0.8510 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2505.998999 1 0.9961 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2505.998999 0 1.0938 235 | 0/8 11 h-lim-p 0.5227 20.0000 0.0001 2505.998999 0 0.0041 261 | 0/8 12 h-lim-p 0.0005 20.0000 0.0005 2505.998999 0 0.0000 287 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 2505.998999 0 0.0000 317 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -2505.998999 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2505.998999 Node 7: lnL = -2505.998999 Node 8: lnL = -2505.998999 Node 9: lnL = -2505.998999 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 342 Sequential format.. Reading seq # 1: YIL150C_Sbay Reading seq # 2: YIL150C_Scer Reading seq # 3: YIL150C_Skud Reading seq # 4: YIL150C_Smik Reading seq # 5: YIL150C_Spar Sequences read.. Counting patterns.. # site patterns = 168 Counting frequencies.. 120 bytes for distance 26880 bytes for lkl0 21504 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.286009 0.175300 0.094844 0.199287 0.102527 0.237231 0.247252 0.000060 lnL0 = -1618.406084 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1618.406084 x= 0.28601 0.17530 0.09484 0.19929 0.10253 0.23723 0.24725 0.00006 1 h-lim-p 0.0036 0.0290 33.0854 1617.809747 8 0.0011 43 | 0/8 2 h-lim-p 0.0001 0.0011 14.4787 1617.700224 m 0.0011 55 | 1/8 3 h-lim-p 0.0036 0.1511 4.2359 1617.695130 6 0.0006 83 | 1/8 4 h-lim-p 0.0030 0.3984 0.8883 1617.694331 4 0.0021 105 | 1/8 5 h-lim-p 0.0129 4.3945 0.1460 1617.694307 3 0.0019 134 | 1/8 6 h-lim-p 0.0077 11.7845 0.0360 1617.694292 1 0.0061 155 | 1/8 7 h-lim-p 0.0133 17.2943 0.0165 1617.693845 0 0.0797 176 | 1/8 8 h-lim-p 0.0026 0.8220 0.5026 1617.693197 3 0.0028 203 | 1/8 9 h-lim-p 0.1734 17.7328 0.0082 1617.692864 4 0.0942 231 | 0/8 10 h-lim-p 0.0355 20.0000 0.0218 1617.692863 1 0.0022 255 | 0/8 11 h-lim-p 0.1427 1.1416 0.0002 1617.692855 m 1.1416 275 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 1617.692855 0 1.0938 295 | 0/8 13 h-lim-p 0.0075 20.0000 0.0040 1617.692855 0 0.0008 316 | 0/8 14 h-lim-p 0.1199 0.9591 0.0000 1617.692855 m 0.9591 336 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 1617.692855 0 1.0938 356 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 1617.692855 0 0.6250 376 | 1/8 17 h-lim-p 1.6731 20.0000 0.0000 1617.692855 0 0.0261 400 Out... lnL = -1617.692855 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1617.692855 Node 7: lnL = -1617.692855 Node 8: lnL = -1617.692855 Node 9: lnL = -1617.692855 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 218 Sequential format.. Reading seq # 1: YIL153W_Sbay Reading seq # 2: YIL153W_Scer Reading seq # 3: YIL153W_Skud Reading seq # 4: YIL153W_Smik Reading seq # 5: YIL153W_Spar Sequences read.. Counting patterns.. # site patterns = 83 Counting frequencies.. 120 bytes for distance 13280 bytes for lkl0 10624 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.735339 0.092394 0.124409 0.448447 0.270685 3.212767 0.581733 0.000060 lnL0 = -852.314286 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 852.314286 x= 0.73534 0.09239 0.12441 0.44845 0.27069 3.21277 0.58173 0.00006 1 h-lim-p 0.0000 0.0000 146.4181 852.243243 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0032 167.2575 821.434261 5 0.0025 51 | 1/8 3 h-lim-p 0.0008 0.0068 47.5602 815.547241 0 0.0051 65 | 1/8 4 h-lim-p 0.0006 0.0051 54.5528 813.120209 0 0.0025 79 | 1/8 5 h-lim-p 0.0577 0.4615 0.7629 802.589323 0 0.3461 93 | 1/8 6 h-lim-p 0.0038 0.0306 20.3015 801.643217 0 0.0077 113 | 1/8 7 h-lim-p 0.1189 0.9515 0.1865 801.225553 0 0.2379 126 | 0/8 8 h-lim-p 0.0133 20.0000 3.3296 801.193567 3 0.0056 151 | 0/8 9 h-lim-p 0.3393 4.6701 0.0546 801.067978 1 0.4241 165 | 0/8 10 h-lim-p 1.3013 12.6351 0.0178 801.029600 5 0.6519 195 | 0/8 11 h-lim-p 2.5000 20.0000 0.0038 801.028021 5 0.7412 228 | 0/8 12 h-lim-p 2.5000 20.0000 0.0001 801.028014 1 1.0938 250 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 801.028014 0 1.0938 270 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 801.028014 0 1.0938 290 | 0/8 15 h-lim-p 1.3700 20.0000 0.0000 801.028014 0 0.0749 313 | 0/8 16 h-lim-p 0.0259 20.0000 0.0000 801.028014 0 0.0016 336 Out... lnL = -801.028014 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -801.028014 Node 7: lnL = -801.028014 Node 8: lnL = -801.028014 Node 9: lnL = -801.028014 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 223 Sequential format.. Reading seq # 1: YIL154C_Sbay Reading seq # 2: YIL154C_Scer Reading seq # 3: YIL154C_Skud Reading seq # 4: YIL154C_Smik Reading seq # 5: YIL154C_Spar Sequences read.. Counting patterns.. # site patterns = 103 Counting frequencies.. 120 bytes for distance 16480 bytes for lkl0 13184 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.413446 0.005354 0.058670 0.121869 0.093892 0.114413 0.150766 0.183292 lnL0 = -918.865640 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 918.865640 x= 0.41345 0.00535 0.05867 0.12187 0.09389 0.11441 0.15077 0.18329 1 h-lim-p 0.0009 0.0073 100.3476 916.860552 8 0.0005 41 | 0/8 2 h-lim-p 0.0003 0.0026 31.2953 916.397773 0 0.0010 54 | 0/8 3 h-lim-p 0.0010 0.0081 21.6174 916.187195 1 0.0013 68 | 0/8 4 h-lim-p 0.0035 0.0280 7.4188 916.153912 3 0.0015 86 | 0/8 5 h-lim-p 0.0061 0.2075 1.7682 916.151580 5 0.0016 110 | 0/8 6 h-lim-p 0.0017 0.1571 1.6609 916.150354 4 0.0014 131 | 0/8 7 h-lim-p 0.0049 0.3518 0.4787 916.150249 3 0.0010 150 | 0/8 8 h-lim-p 0.1471 20.0000 0.0032 916.134770 0 1.7652 173 | 0/8 9 h-lim-p 2.3060 20.0000 0.0025 916.132810 3 1.0449 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 916.132806 1 0.9961 221 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 916.132806 0 1.0938 241 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 916.132806 0 2.5000 261 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 916.132806 0 0.0049 289 Out... lnL = -916.132806 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -916.132806 Node 7: lnL = -916.132806 Node 8: lnL = -916.132806 Node 9: lnL = -916.132806 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 571 Sequential format.. Reading seq # 1: YIL157C_Sbay Reading seq # 2: YIL157C_Scer Reading seq # 3: YIL157C_Skud Reading seq # 4: YIL157C_Smik Reading seq # 5: YIL157C_Spar Sequences read.. Counting patterns.. # site patterns = 128 Counting frequencies.. 120 bytes for distance 20480 bytes for lkl0 16384 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.100954 0.032598 0.023956 0.050357 0.055494 0.107325 0.082440 0.005481 lnL0 = -1936.771876 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1936.771876 x= 0.10095 0.03260 0.02396 0.05036 0.05549 0.10732 0.08244 0.00548 1 h-lim-p 0.0003 0.0023 209.9621 1935.168764 7 0.0001 39 | 0/8 2 h-lim-p 0.0002 0.0013 39.4884 1935.065872 5 0.0001 62 | 0/8 3 h-lim-p 0.0005 0.0167 9.7574 1935.056325 4 0.0002 82 | 0/8 4 h-lim-p 0.0007 0.0282 2.9049 1935.055782 2 0.0001 99 | 0/8 5 h-lim-p 0.0012 0.0545 0.3340 1935.055774 0 0.0002 113 | 0/8 6 h-lim-p 0.0007 2.7195 0.0678 1935.055773 0 0.0002 134 | 0/8 7 h-lim-p 0.0097 7.7860 0.0013 1935.055773 0 0.0021 155 | 0/8 8 h-lim-p 0.0034 13.7637 0.0008 1935.055762 0 0.1086 180 | 0/8 9 h-lim-p 0.4583 20.0000 0.0002 1935.055761 0 0.9166 201 | 0/8 10 h-lim-p 1.6574 20.0000 0.0001 1935.055761 0 0.7251 221 | 0/8 11 h-lim-p 0.4623 20.0000 0.0002 1935.055761 0 0.0007 250 | 0/8 12 h-lim-p 0.0002 12.9296 0.0006 1935.055761 0 0.0002 270 | 0/8 13 h-lim-p 0.0001 5.2125 0.0014 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0043 | 0/8 15 h-lim-p 0.0000 20.0000 0.0043 Out... lnL = -1935.055761 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1935.055761 Node 7: lnL = -1935.055761 Node 8: lnL = -1935.055761 Node 9: lnL = -1935.055761 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 266 Sequential format.. Reading seq # 1: YIL158W_Sbay Reading seq # 2: YIL158W_Scer Reading seq # 3: YIL158W_Skud Reading seq # 4: YIL158W_Smik Reading seq # 5: YIL158W_Spar Sequences read.. Counting patterns.. # site patterns = 150 Counting frequencies.. 120 bytes for distance 24000 bytes for lkl0 19200 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.245980 0.009852 0.059442 0.198592 0.130933 0.195836 0.362985 0.002649 lnL0 = -1255.041783 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1255.041783 x= 0.24598 0.00985 0.05944 0.19859 0.13093 0.19584 0.36299 0.00265 1 h-lim-p 0.0031 0.0307 90.3897 1253.618870 9 0.0004 45 | 0/8 2 h-lim-p 0.0002 0.0015 15.5668 1253.480851 m 0.0015 57 | 0/8 3 h-lim-p -0.0000 -0.0000 3.1418 h-lim-p: -3.50619681e-20 -2.80495745e-19 3.14182726e+00 1253.480851 .. | 0/8 4 h-lim-p 0.0000 20.0000 6.2501 1253.468614 0 0.0006 83 | 0/8 5 h-lim-p 0.0026 0.0471 1.5656 1253.467495 4 0.0010 103 | 0/8 6 h-lim-p 0.0027 0.6844 0.5618 1253.467350 3 0.0010 121 | 0/8 7 h-lim-p 0.0027 0.1108 0.2153 1253.467312 3 0.0019 149 | 0/8 8 h-lim-p 0.0029 0.6358 0.1417 1253.467303 1 0.0013 171 | 0/8 9 h-lim-p 0.0113 0.1909 0.0160 1253.467303 0 0.0012 193 | 0/8 10 h-lim-p 0.0491 17.9534 0.0004 1253.467303 0 0.0429 213 | 0/8 11 h-lim-p 0.0086 1.8290 0.0020 1253.467300 0 0.0343 235 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1253.467300 0 1.0938 255 | 0/8 13 h-lim-p 1.2945 20.0000 0.0000 1253.467300 0 1.2945 275 | 0/8 14 h-lim-p 1.1451 20.0000 0.0000 1253.467300 0 0.0039 302 | 0/8 15 h-lim-p 0.0001 4.1641 0.0004 1253.467300 0 0.0001 322 | 0/8 16 h-lim-p 0.0000 1.2461 0.0014 1253.467300 0 0.0000 343 | 0/8 17 h-lim-p 0.0002 20.0000 0.0001 1253.467300 0 0.0000 382 | 0/8 18 h-lim-p 0.0000 20.0000 0.0004 | 0/8 19 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1253.467300 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1253.467300 Node 7: lnL = -1253.467300 Node 8: lnL = -1253.467300 Node 9: lnL = -1253.467300 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 447 Sequential format.. Reading seq # 1: YIL160C_Sbay Reading seq # 2: YIL160C_Scer Reading seq # 3: YIL160C_Skud Reading seq # 4: YIL160C_Smik Reading seq # 5: YIL160C_Spar Sequences read.. Counting patterns.. # site patterns = 146 Counting frequencies.. 120 bytes for distance 23360 bytes for lkl0 18688 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.238445 0.053233 0.015809 0.086527 0.078520 0.170080 0.110939 0.070155 lnL0 = -1721.307689 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1721.307689 x= 0.23845 0.05323 0.01581 0.08653 0.07852 0.17008 0.11094 0.07015 1 h-lim-p 0.0009 0.0201 195.1017 1719.365307 9 0.0001 45 | 0/8 2 h-lim-p 0.0004 0.0031 45.0125 1718.979385 4 0.0004 65 | 0/8 3 h-lim-p 0.0015 0.0186 12.3627 1718.934662 6 0.0006 91 | 0/8 4 h-lim-p 0.0050 0.0622 1.5532 1718.934270 3 0.0003 112 | 0/8 5 h-lim-p 0.0013 0.8748 0.4094 1718.934233 3 0.0004 131 | 0/8 6 h-lim-p 0.0014 1.5555 0.1296 1718.934225 2 0.0007 156 | 0/8 7 h-lim-p 0.0129 19.0987 0.0074 1718.933833 0 0.1028 179 | 0/8 8 h-lim-p 0.0047 0.2618 0.1625 1718.930231 0 0.0094 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1718.930118 2 0.9961 224 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1718.930118 0 1.0938 244 | 0/8 11 h-lim-p 1.8786 20.0000 0.0000 1718.930118 0 0.0073 271 | 0/8 12 h-lim-p 0.0028 20.0000 0.0000 1718.930118 0 0.0000 314 | 0/8 13 h-lim-p 0.0000 20.0000 0.0010 | 0/8 14 h-lim-p 0.0000 20.0000 0.0010 Out... lnL = -1718.930118 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1718.930118 Node 7: lnL = -1718.930118 Node 8: lnL = -1718.930118 Node 9: lnL = -1718.930118 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 633 Sequential format.. Reading seq # 1: YIL161W_Sbay Reading seq # 2: YIL161W_Scer Reading seq # 3: YIL161W_Skud Reading seq # 4: YIL161W_Smik Reading seq # 5: YIL161W_Spar Sequences read.. Counting patterns.. # site patterns = 269 Counting frequencies.. 120 bytes for distance 43040 bytes for lkl0 34432 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.483562 0.118206 0.125220 0.116597 0.156952 0.181248 0.228406 0.153141 lnL0 = -2704.124565 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2704.124565 x= 0.48356 0.11821 0.12522 0.11660 0.15695 0.18125 0.22841 0.15314 1 h-lim-p 0.0077 0.1764 84.0262 2701.877841 7 0.0007 39 | 0/8 2 h-lim-p 0.0007 0.0058 35.4910 2701.390626 1 0.0009 53 | 0/8 3 h-lim-p 0.0009 0.0070 23.5238 2701.238562 6 0.0008 76 | 0/8 4 h-lim-p 0.0020 0.0373 9.1439 2701.179597 5 0.0018 97 | 0/8 5 h-lim-p 0.0041 0.0700 3.8991 2701.174111 5 0.0009 119 | 0/8 6 h-lim-p 0.0189 1.5872 0.1823 2701.174067 3 0.0017 141 | 0/8 7 h-lim-p 0.0502 20.0000 0.0061 2701.164261 0 0.8027 165 | 0/8 8 h-lim-p 0.0051 0.9898 0.9553 2701.162988 2 0.0022 189 | 0/8 9 h-lim-p 1.8014 20.0000 0.0012 2701.162117 4 1.0179 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2701.162116 0 1.0938 240 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2701.162116 0 1.0938 260 | 0/8 12 h-lim-p 1.1638 20.0000 0.0000 2701.162116 0 2.3276 281 | 0/8 13 h-lim-p 0.9063 20.0000 0.0000 2701.162116 0 0.4532 301 | 0/8 14 h-lim-p 0.0018 20.0000 0.0029 2701.162116 0 0.0018 321 | 0/8 15 h-lim-p 0.0017 20.0000 0.0031 2701.162116 0 0.0051 342 | 0/8 16 h-lim-p 0.0020 20.0000 0.0077 2701.162116 0 0.0000 381 | 0/8 17 h-lim-p 0.0001 20.0000 0.0000 2701.162116 0 0.0001 401 Out... lnL = -2701.162116 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2701.162116 Node 7: lnL = -2701.162116 Node 8: lnL = -2701.162116 Node 9: lnL = -2701.162116 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 886 Sequential format.. Reading seq # 1: YIL162W_Sbay Reading seq # 2: YIL162W_Scer Reading seq # 3: YIL162W_Skud Reading seq # 4: YIL162W_Smik Reading seq # 5: YIL162W_Spar Sequences read.. Counting patterns.. # site patterns = 300 Counting frequencies.. 120 bytes for distance 48000 bytes for lkl0 38400 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.299953 0.093167 0.038201 0.100243 0.106617 0.196587 0.182484 0.073239 lnL0 = -3959.702544 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3959.702544 x= 0.29995 0.09317 0.03820 0.10024 0.10662 0.19659 0.18248 0.07324 1 h-lim-p 0.0022 0.0178 152.8339 3958.353569 3 0.0001 31 | 0/8 2 h-lim-p 0.0007 0.0061 28.1589 3958.252129 4 0.0003 51 | 0/8 3 h-lim-p 0.0013 0.0395 5.6698 3958.248907 4 0.0002 74 | 0/8 4 h-lim-p 0.0009 0.1453 1.3405 3958.248662 3 0.0003 94 | 0/8 5 h-lim-p 0.0009 0.6982 0.4186 3958.248636 2 0.0003 111 | 0/8 6 h-lim-p 0.0035 8.8867 0.0362 3958.248635 0 0.0008 132 | 0/8 7 h-lim-p 0.0042 20.0000 0.0065 3958.248632 0 0.0085 153 | 0/8 8 h-lim-p 0.0087 9.8071 0.0063 3958.248332 0 0.0523 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3958.248331 0 1.0938 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3958.248331 0 1.0938 215 | 0/8 11 h-lim-p 0.6742 20.0000 0.0000 3958.248331 0 0.0053 241 | 0/8 12 h-lim-p 0.0005 20.0000 0.0002 3958.248331 0 0.0003 261 | 0/8 13 h-lim-p 0.0001 20.0000 0.0004 3958.248331 0 0.0000 283 | 0/8 14 h-lim-p 0.0003 20.0000 0.0000 3958.248331 0 0.0003 303 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 3958.248331 0 0.0000 335 | 0/8 16 h-lim-p 0.0000 20.0000 0.0009 | 0/8 17 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -3958.248331 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3958.248331 Node 7: lnL = -3958.248331 Node 8: lnL = -3958.248331 Node 9: lnL = -3958.248331 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 863 Sequential format.. Reading seq # 1: YIL166C_Sbay Reading seq # 2: YIL166C_Scer Reading seq # 3: YIL166C_Skud Reading seq # 4: YIL166C_Smik Reading seq # 5: YIL166C_Spar Sequences read.. Counting patterns.. # site patterns = 353 Counting frequencies.. 120 bytes for distance 56480 bytes for lkl0 45184 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.434341 0.076770 0.124602 0.118071 0.098227 0.374347 0.273401 0.100753 lnL0 = -4354.822087 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4354.822087 x= 0.43434 0.07677 0.12460 0.11807 0.09823 0.37435 0.27340 0.10075 1 h-lim-p 0.0007 0.0057 74.4196 4353.691485 6 0.0004 37 | 0/8 2 h-lim-p 0.0009 0.0072 30.4872 4353.324966 5 0.0009 59 | 0/8 3 h-lim-p 0.0017 0.0294 16.0163 4353.300515 5 0.0002 86 | 0/8 4 h-lim-p 0.0005 0.0429 8.3134 4353.287310 4 0.0005 108 | 0/8 5 h-lim-p 0.0017 0.1175 2.4454 4353.286045 5 0.0005 133 | 0/8 6 h-lim-p 0.0011 0.3507 1.0841 4353.285645 3 0.0008 151 | 0/8 7 h-lim-p 0.0097 7.0329 0.0913 4353.285637 1 0.0012 167 | 0/8 8 h-lim-p 0.0623 20.0000 0.0018 4353.283810 0 0.9962 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 4353.283716 2 0.9961 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4353.283716 0 1.0938 235 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4353.283716 0 2.1875 255 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4353.283716 0 1.0938 275 | 0/8 13 h-lim-p 0.3247 20.0000 0.0000 4353.283716 010.3892 300 | 0/8 14 h-lim-p 0.0360 20.0000 0.0036 4353.283716 0 0.0270 320 | 0/8 15 h-lim-p 0.0078 12.4199 0.0127 4353.283716 0 0.0010 342 | 0/8 16 h-lim-p 0.0004 4.6048 0.0342 4353.283716 0 0.0000 364 | 0/8 17 h-lim-p 0.0001 20.0000 0.0238 4353.283716 0 0.0000 394 | 0/8 18 h-lim-p 0.0012 20.0000 0.0000 4353.283716 0 0.0000 431 Out... lnL = -4353.283716 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4353.283716 Node 7: lnL = -4353.283716 Node 8: lnL = -4353.283716 Node 9: lnL = -4353.283716 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 542 Sequential format.. Reading seq # 1: YIR001C_Sbay Reading seq # 2: YIR001C_Scer Reading seq # 3: YIR001C_Skud Reading seq # 4: YIR001C_Smik Reading seq # 5: YIR001C_Spar Sequences read.. Counting patterns.. # site patterns = 200 Counting frequencies.. 120 bytes for distance 32000 bytes for lkl0 25600 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.255715 0.010012 0.068829 0.123653 0.099361 0.183923 0.183109 0.055748 lnL0 = -2391.666702 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2391.666702 x= 0.25571 0.01001 0.06883 0.12365 0.09936 0.18392 0.18311 0.05575 1 h-lim-p 0.0026 0.0208 132.5733 2390.393530 8 0.0002 40 | 0/8 2 h-lim-p 0.0010 0.0120 20.7366 2390.290262 2 0.0005 56 | 0/8 3 h-lim-p 0.0014 0.0230 7.4147 2390.282857 4 0.0003 76 | 0/8 4 h-lim-p 0.0033 0.3599 0.6814 2390.282759 3 0.0004 96 | 0/8 5 h-lim-p 0.0012 0.6719 0.2532 2390.282745 1 0.0005 118 | 0/8 6 h-lim-p 0.0049 8.0740 0.0262 2390.282745 0 0.0005 140 | 0/8 7 h-lim-p 0.0024 20.0000 0.0058 2390.282745 0 0.0011 160 | 0/8 8 h-lim-p 0.0258 20.0000 0.0002 2390.282730 0 0.4136 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2390.282730 0 1.0938 204 | 0/8 10 h-lim-p 2.0502 20.0000 0.0000 2390.282730 0 1.7939 224 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2390.282730 0 1.2500 244 | 0/8 12 h-lim-p 0.6368 20.0000 0.0000 2390.282730 0 0.5572 264 | 0/8 13 h-lim-p 0.0831 20.0000 0.0001 2390.282730 0 0.0091 286 | 0/8 14 h-lim-p 0.0027 20.0000 0.0004 2390.282730 0 0.0013 306 | 0/8 15 h-lim-p 0.0012 20.0000 0.0004 2390.282730 0 0.0003 327 | 0/8 16 h-lim-p 0.0000 20.0000 0.0041 2390.282730 0 0.0000 355 | 0/8 17 h-lim-p 0.0001 20.0000 0.0000 2390.282730 0 0.0000 382 Out... lnL = -2390.282730 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2390.282730 Node 7: lnL = -2390.282730 Node 8: lnL = -2390.282730 Node 9: lnL = -2390.282730 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 528 Sequential format.. Reading seq # 1: YIR002C_Sbay Reading seq # 2: YIR002C_Scer Reading seq # 3: YIR002C_Skud Reading seq # 4: YIR002C_Smik Reading seq # 5: YIR002C_Spar Sequences read.. Counting patterns.. # site patterns = 228 Counting frequencies.. 120 bytes for distance 36480 bytes for lkl0 29184 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.324212 0.072111 0.042733 0.148284 0.095783 0.222130 0.278389 0.067597 lnL0 = -2350.197599 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2350.197599 x= 0.32421 0.07211 0.04273 0.14828 0.09578 0.22213 0.27839 0.06760 1 h-lim-p 0.0014 0.0109 81.3648 2349.306670 7 0.0003 41 | 0/8 2 h-lim-p 0.0009 0.0079 26.5818 2349.074370 7 0.0007 66 | 0/8 3 h-lim-p 0.0010 0.0076 18.6738 2349.008099 7 0.0005 95 | 0/8 4 h-lim-p 0.0012 0.0173 8.7277 2348.988456 6 0.0007 122 | 0/8 5 h-lim-p 0.0038 0.1707 1.5836 2348.987362 3 0.0009 141 | 0/8 6 h-lim-p 0.0029 0.5148 0.5065 2348.987283 0 0.0007 154 | 0/8 7 h-lim-p 0.0024 2.4235 0.1538 2348.987274 2 0.0008 179 | 0/8 8 h-lim-p 0.4429 20.0000 0.0003 2348.987211 0 0.8858 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2348.987208 0 1.0938 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2348.987208 0 1.0938 240 | 0/8 11 h-lim-p 1.2175 20.0000 0.0000 2348.987208 0 0.0095 266 | 0/8 12 h-lim-p 0.0028 20.0000 0.0000 2348.987208 0 0.0000 295 | 0/8 13 h-lim-p 0.0004 20.0000 0.0000 2348.987208 0 0.0000 318 Out... lnL = -2348.987208 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2348.987208 Node 7: lnL = -2348.987208 Node 8: lnL = -2348.987208 Node 9: lnL = -2348.987208 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 431 Sequential format.. Reading seq # 1: YIR005W_Sbay Reading seq # 2: YIR005W_Scer Reading seq # 3: YIR005W_Skud Reading seq # 4: YIR005W_Smik Reading seq # 5: YIR005W_Spar Sequences read.. Counting patterns.. # site patterns = 185 Counting frequencies.. 120 bytes for distance 29600 bytes for lkl0 23680 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.267262 0.127216 0.159999 0.091403 0.072598 0.241837 0.185092 0.004881 lnL0 = -1836.092568 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1836.092568 x= 0.26726 0.12722 0.16000 0.09140 0.07260 0.24184 0.18509 0.00488 1 h-lim-p 0.0266 4.2581 37.1821 1835.718682 8 0.0006 44 | 0/8 2 h-lim-p 0.0010 0.0076 18.6303 1835.658888 5 0.0004 65 | 0/8 3 h-lim-p 0.0007 0.0057 4.7392 1835.648502 0 0.0011 77 | 0/8 4 h-lim-p 0.0031 0.1669 1.6261 1835.647468 4 0.0009 99 | 0/8 5 h-lim-p 0.0032 0.4797 0.4559 1835.647401 2 0.0007 116 | 0/8 6 h-lim-p 0.0060 1.9809 0.0520 1835.647398 1 0.0015 139 | 0/8 7 h-lim-p 0.1338 20.0000 0.0006 1835.647229 0 1.0707 162 | 0/8 8 h-lim-p 0.0043 0.2981 0.1438 1835.647214 2 0.0014 188 | 0/8 9 h-lim-p 1.6510 20.0000 0.0001 1835.647203 2 1.0891 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1835.647203 0 1.0938 234 | 0/8 11 h-lim-p 1.4234 20.0000 0.0000 1835.647203 0 1.2454 254 | 0/8 12 h-lim-p 0.9988 20.0000 0.0000 1835.647203 0 0.3746 275 | 0/8 13 h-lim-p 0.0029 4.6907 0.0024 1835.647203 0 0.0000 303 | 0/8 14 h-lim-p 0.0003 20.0000 0.0000 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -1835.647203 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1835.647203 Node 7: lnL = -1835.647203 Node 8: lnL = -1835.647203 Node 9: lnL = -1835.647203 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 869 Sequential format.. Reading seq # 1: YIR007W_Sbay Reading seq # 2: YIR007W_Scer Reading seq # 3: YIR007W_Skud Reading seq # 4: YIR007W_Smik Reading seq # 5: YIR007W_Spar Sequences read.. Counting patterns.. # site patterns = 314 Counting frequencies.. 120 bytes for distance 50240 bytes for lkl0 40192 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.294953 0.058402 0.053546 0.139509 0.108454 0.282203 0.229872 0.039048 lnL0 = -4088.431510 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4088.431510 x= 0.29495 0.05840 0.05355 0.13951 0.10845 0.28220 0.22987 0.03905 1 h-lim-p 0.0019 0.6589 209.4800 4084.916542 7 0.0002 39 | 0/8 2 h-lim-p 0.0007 0.0055 32.0807 4084.736190 6 0.0004 66 | 0/8 3 h-lim-p 0.0007 0.0125 15.7177 4084.700332 4 0.0004 87 | 0/8 4 h-lim-p 0.0010 0.0566 5.5232 4084.694720 4 0.0004 109 | 0/8 5 h-lim-p 0.0029 0.5143 0.8130 4084.694568 2 0.0005 128 | 0/8 6 h-lim-p 0.0089 4.7634 0.0438 4084.694567 0 0.0010 150 | 0/8 7 h-lim-p 0.0028 14.0588 0.0154 4084.694567 0 0.0012 170 | 0/8 8 h-lim-p 0.0565 20.0000 0.0003 4084.694487 0 0.9032 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4084.694480 0 1.0938 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4084.694480 0 1.0938 234 | 0/8 11 h-lim-p 1.1271 20.0000 0.0000 4084.694480 0 1.1271 254 | 0/8 12 h-lim-p 0.4600 20.0000 0.0001 4084.694480 0 0.2013 274 | 0/8 13 h-lim-p 0.0256 20.0000 0.0005 4084.694480 0 0.0064 295 | 0/8 14 h-lim-p 0.0027 20.0000 0.0011 4084.694480 0 0.0000 324 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 4084.694480 0 0.0000 357 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -4084.694480 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4084.694480 Node 7: lnL = -4084.694480 Node 8: lnL = -4084.694480 Node 9: lnL = -4084.694480 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 279 Sequential format.. Reading seq # 1: YIR008C_Sbay Reading seq # 2: YIR008C_Scer Reading seq # 3: YIR008C_Skud Reading seq # 4: YIR008C_Smik Reading seq # 5: YIR008C_Spar Sequences read.. Counting patterns.. # site patterns = 116 Counting frequencies.. 120 bytes for distance 18560 bytes for lkl0 14848 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.202950 0.034519 0.039668 0.134487 0.132691 0.177995 0.237175 0.000715 lnL0 = -1127.995615 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1127.995615 x= 0.20295 0.03452 0.03967 0.13449 0.13269 0.17799 0.23717 0.00072 1 h-lim-p 0.0043 0.1082 72.1966 1127.164135 6 0.0004 37 | 0/8 2 h-lim-p 0.0013 0.0102 7.4217 1127.133343 5 0.0011 58 | 0/8 3 h-lim-p 0.0017 0.0136 3.4256 1127.128516 6 0.0010 86 | 0/8 4 h-lim-p 0.0042 0.1766 0.7952 1127.128289 4 0.0008 108 | 0/8 5 h-lim-p 0.0055 0.6075 0.1102 1127.128282 1 0.0012 131 | 0/8 6 h-lim-p 0.0180 17.7744 0.0074 1127.128282 0 0.0011 154 | 0/8 7 h-lim-p 0.0367 20.0000 0.0002 1127.128281 0 0.0733 175 | 0/8 8 h-lim-p 0.0028 2.7463 0.0060 1127.128279 0 0.0112 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1127.128279 0 1.0938 217 | 0/8 10 h-lim-p 1.2961 20.0000 0.0000 1127.128279 0 0.0000 256 | 0/8 11 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 12 h-lim-p 0.0000 20.0000 0.0005 | 0/8 13 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -1127.128279 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1127.128279 Node 7: lnL = -1127.128279 Node 8: lnL = -1127.128279 Node 9: lnL = -1127.128279 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 240 Sequential format.. Reading seq # 1: YIR009W_Sbay Reading seq # 2: YIR009W_Scer Reading seq # 3: YIR009W_Skud Reading seq # 4: YIR009W_Smik Reading seq # 5: YIR009W_Spar Sequences read.. Counting patterns.. # site patterns = 107 Counting frequencies.. 120 bytes for distance 17120 bytes for lkl0 13696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.194875 0.041721 0.036645 0.100049 0.110379 0.202074 0.207907 0.004748 lnL0 = -1040.861404 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1040.861404 x= 0.19487 0.04172 0.03665 0.10005 0.11038 0.20207 0.20791 0.00475 1 h-lim-p 0.0042 0.0540 70.4022 1040.128665 8 0.0003 44 | 0/8 2 h-lim-p 0.0028 0.0249 8.3887 1040.093163 7 0.0010 73 | 0/8 3 h-lim-p 0.0021 0.0220 4.0543 1040.087566 4 0.0008 93 | 0/8 4 h-lim-p 0.0061 0.3185 0.5435 1040.087461 2 0.0008 111 | 0/8 5 h-lim-p 0.0191 9.5512 0.0214 1040.087460 0 0.0010 134 | 0/8 6 h-lim-p 0.0075 20.0000 0.0030 1040.087460 0 0.0019 155 | 0/8 7 h-lim-p 0.0045 20.0000 0.0012 1040.087460 0 0.0270 177 | 0/8 8 h-lim-p 0.0083 8.6879 0.0041 1040.087454 0 0.0332 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1040.087454 0 1.0938 219 | 0/8 10 h-lim-p 2.4868 20.0000 0.0000 1040.087454 0 1.2434 239 | 0/8 11 h-lim-p 1.3744 20.0000 0.0000 1040.087454 0 1.2026 259 | 0/8 12 h-lim-p 0.3376 20.0000 0.0001 1040.087454 0 0.0026 285 | 0/8 13 h-lim-p 0.0004 20.0000 0.0004 1040.087454 0 0.0001 306 | 0/8 14 h-lim-p 0.0001 20.0000 0.0004 1040.087454 0 0.0000 339 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1040.087454 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1040.087454 Node 7: lnL = -1040.087454 Node 8: lnL = -1040.087454 Node 9: lnL = -1040.087454 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 591 Sequential format.. Reading seq # 1: YIR010W_Sbay Reading seq # 2: YIR010W_Scer Reading seq # 3: YIR010W_Skud Reading seq # 4: YIR010W_Smik Reading seq # 5: YIR010W_Spar Sequences read.. Counting patterns.. # site patterns = 239 Counting frequencies.. 120 bytes for distance 38240 bytes for lkl0 30592 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.361252 0.115111 0.038206 0.120955 0.108750 0.234773 0.310800 0.069960 lnL0 = -2902.291470 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2902.291470 x= 0.36125 0.11511 0.03821 0.12095 0.10875 0.23477 0.31080 0.06996 1 h-lim-p 0.0007 0.0057 119.6463 2900.696156 8 0.0002 41 | 0/8 2 h-lim-p 0.0009 0.0070 24.9810 2900.549077 6 0.0005 68 | 0/8 3 h-lim-p 0.0008 0.0275 14.6856 2900.509678 7 0.0005 99 | 0/8 4 h-lim-p 0.0010 0.0338 6.9484 2900.497877 6 0.0006 126 | 0/8 5 h-lim-p 0.0015 0.1126 2.9970 2900.494717 5 0.0009 152 | 0/8 6 h-lim-p 0.0044 0.5102 0.6069 2900.494573 3 0.0008 171 | 0/8 7 h-lim-p 0.0153 9.4591 0.0327 2900.494573 0 0.0017 193 | 0/8 8 h-lim-p 0.4234 20.0000 0.0001 2900.494557 0 0.8469 214 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2900.494556 0 1.0938 234 | 0/8 10 h-lim-p 2.4750 20.0000 0.0000 2900.494556 0 1.0828 254 | 0/8 11 h-lim-p 0.9399 20.0000 0.0000 2900.494556 0 0.0147 279 | 0/8 12 h-lim-p 0.0037 20.0000 0.0001 2900.494556 0 0.0016 299 | 0/8 13 h-lim-p 0.0005 20.0000 0.0002 2900.494556 0 0.0001 320 | 0/8 14 h-lim-p 0.0009 20.0000 0.0000 2900.494556 0 0.0000 359 | 0/8 15 h-lim-p 0.0000 20.0000 0.0006 2900.494556 0 0.0000 386 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0006 | 0/8 18 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -2900.494556 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2900.494556 Node 7: lnL = -2900.494556 Node 8: lnL = -2900.494556 Node 9: lnL = -2900.494556 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 245 Sequential format.. Reading seq # 1: YIR012W_Sbay Reading seq # 2: YIR012W_Scer Reading seq # 3: YIR012W_Skud Reading seq # 4: YIR012W_Smik Reading seq # 5: YIR012W_Spar Sequences read.. Counting patterns.. # site patterns = 95 Counting frequencies.. 120 bytes for distance 15200 bytes for lkl0 12160 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.133842 0.116127 0.060453 0.111515 0.064881 0.161039 0.181240 0.000060 lnL0 = -868.983394 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 868.983394 x= 0.13384 0.11613 0.06045 0.11151 0.06488 0.16104 0.18124 0.00006 1 h-lim-p 0.0000 0.0000 145.4568 868.949382 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0046 42.6837 867.680916 0 0.0019 41 | 1/8 3 h-lim-p 0.0042 0.0334 7.9977 867.626161 7 0.0015 70 | 1/8 4 h-lim-p 0.0080 0.0777 1.4867 867.554777 3 0.0082 88 | 1/8 5 h-lim-p 0.0029 0.0461 4.1941 867.011414 0 0.0116 102 | 1/8 6 h-lim-p 0.0020 0.0156 9.2711 863.119788 0 0.0078 116 | 1/8 7 h-lim-p 0.0006 0.0047 31.7795 862.426966 0 0.0012 129 | 1/8 8 h-lim-p 0.0022 0.0175 10.9101 862.347977 7 0.0013 161 | 0/8 9 h-lim-p 0.0006 0.3289 24.3789 862.198756 3 0.0005 179 | 0/8 10 h-lim-p 0.4713 7.5402 0.0277 862.039888 0 0.7069 191 | 0/8 11 h-lim-p 2.5000 20.0000 0.0058 862.032850 3 0.5225 218 | 0/8 12 h-lim-p 1.1087 20.0000 0.0027 862.031103 6 0.6453 254 | 0/8 13 h-lim-p 2.5000 20.0000 0.0004 862.031070 3 0.5225 281 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 862.031067 1 0.9961 303 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 862.031067 0 1.0938 323 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 862.031067 0 1.0938 343 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 862.031067 0 0.2734 365 | 0/8 18 h-lim-p 0.4303 20.0000 0.0000 862.031067 0 0.0000 400 Out... lnL = -862.031067 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -862.031067 Node 7: lnL = -862.031067 Node 8: lnL = -862.031067 Node 9: lnL = -862.031067 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 653 Sequential format.. Reading seq # 1: YIR013C_Sbay Reading seq # 2: YIR013C_Scer Reading seq # 3: YIR013C_Skud Reading seq # 4: YIR013C_Smik Reading seq # 5: YIR013C_Spar Sequences read.. Counting patterns.. # site patterns = 291 Counting frequencies.. 120 bytes for distance 46560 bytes for lkl0 37248 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.363952 0.094128 0.059752 0.274132 0.000060 0.360796 0.339980 0.084022 lnL0 = -3014.159863 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3014.159863 x= 0.36395 0.09413 0.05975 0.27413 0.00006 0.36080 0.33998 0.08402 1 h-lim-p 0.0004 0.0035 369.6521 3006.637853 2 0.0001 27 | 0/8 2 h-lim-p 0.0003 0.0024 128.4497 2999.680438 0 0.0009 40 | 0/8 3 h-lim-p 0.0006 0.0045 70.2055 2998.574990 6 0.0006 66 | 0/8 4 h-lim-p 0.0037 0.0310 11.5789 2998.517227 5 0.0009 90 | 0/8 5 h-lim-p 0.0040 0.1315 2.6075 2998.512961 4 0.0013 112 | 0/8 6 h-lim-p 0.0035 0.4400 0.9570 2998.512091 2 0.0016 128 | 0/8 7 h-lim-p 0.0308 9.5103 0.0505 2998.489385 0 0.1232 150 | 0/8 8 h-lim-p 0.0028 0.0966 2.2460 2998.428012 0 0.0055 171 | 0/8 9 h-lim-p 2.5000 20.0000 0.0027 2998.424265 4 1.0721 190 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 2998.424033 2 2.3438 214 | 0/8 11 h-lim-p 2.5000 20.0000 0.0002 2998.424011 2 1.3159 239 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2998.424011 0 1.0938 259 | 0/8 13 h-lim-p 2.1742 20.0000 0.0000 2998.424011 0 0.9512 279 | 0/8 14 h-lim-p 0.7655 20.0000 0.0000 2998.424011 0 0.0957 301 | 0/8 15 h-lim-p 0.0085 20.0000 0.0001 2998.424011 0 0.0011 323 | 0/8 16 h-lim-p 0.0002 20.0000 0.0008 2998.424011 0 0.0000 357 | 0/8 17 h-lim-p 0.0001 20.0000 0.0000 2998.424011 0 0.0000 387 Out... lnL = -2998.424011 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2998.424011 Node 7: lnL = -2998.424011 Node 8: lnL = -2998.424011 Node 9: lnL = -2998.424011 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 146 Sequential format.. Reading seq # 1: YIR015W_Sbay Reading seq # 2: YIR015W_Scer Reading seq # 3: YIR015W_Skud Reading seq # 4: YIR015W_Smik Reading seq # 5: YIR015W_Spar Sequences read.. Counting patterns.. # site patterns = 87 Counting frequencies.. 120 bytes for distance 13920 bytes for lkl0 11136 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.372125 0.230416 0.266421 0.029034 0.155766 0.027452 0.340626 0.027788 lnL0 = -644.761866 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 644.761866 x= 0.37213 0.23042 0.26642 0.02903 0.15577 0.02745 0.34063 0.02779 1 h-lim-p 0.0096 0.1277 36.5976 643.418353 9 0.0026 43 | 0/8 2 h-lim-p 0.0007 0.0052 15.9877 643.206520 0 0.0020 56 | 0/8 3 h-lim-p 0.0012 0.0123 25.2557 642.561857 0 0.0050 70 | 0/8 4 h-lim-p 0.0089 0.0715 3.1327 642.535065 6 0.0058 97 | 0/8 5 h-lim-p 0.0078 0.0665 2.3335 642.527308 6 0.0041 123 | 0/8 6 h-lim-p 0.0149 0.5225 0.6380 642.526171 5 0.0056 145 | 0/8 7 h-lim-p 0.0178 2.0956 0.2018 642.525288 1 0.0223 167 | 0/8 8 h-lim-p 0.1303 20.0000 0.0345 642.507922 0 0.5211 189 | 0/8 9 h-lim-p 1.9169 20.0000 0.0094 642.501711 6 1.3467 223 | 0/8 10 h-lim-p 2.5000 20.0000 0.0017 642.501241 5 1.4416 256 | 0/8 11 h-lim-p 2.5000 20.0000 0.0001 642.501241 0 1.0938 276 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 642.501241 0 1.0938 296 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 642.501241 0 1.0938 316 | 0/8 14 h-lim-p 0.8456 20.0000 0.0000 642.501241 0 0.0264 340 | 0/8 15 h-lim-p 0.0001 20.0000 0.0006 642.501241 0 0.0001 360 | 0/8 16 h-lim-p 0.0005 20.0000 0.0001 642.501241 0 0.0000 396 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 642.501241 0 0.0000 431 Out... lnL = -642.501241 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -642.501241 Node 7: lnL = -642.501241 Node 8: lnL = -642.501241 Node 9: lnL = -642.501241 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 853 Sequential format.. Reading seq # 1: YIR021W_Sbay Reading seq # 2: YIR021W_Scer Reading seq # 3: YIR021W_Skud Reading seq # 4: YIR021W_Smik Reading seq # 5: YIR021W_Spar Sequences read.. Counting patterns.. # site patterns = 296 Counting frequencies.. 120 bytes for distance 47360 bytes for lkl0 37888 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.385042 0.076805 0.112938 0.115962 0.080905 0.188806 0.229680 0.103479 lnL0 = -4092.634451 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4092.634451 x= 0.38504 0.07680 0.11294 0.11596 0.08091 0.18881 0.22968 0.10348 1 h-lim-p 0.0023 0.0182 69.6070 4092.000884 2 0.0003 28 | 0/8 2 h-lim-p 0.0015 0.0155 12.0578 4091.968960 6 0.0005 54 | 0/8 3 h-lim-p 0.0010 0.0470 5.6383 4091.961605 6 0.0006 83 | 0/8 4 h-lim-p 0.0013 0.1676 2.4825 4091.961172 4 0.0002 105 | 0/8 5 h-lim-p 0.0006 0.2913 0.6539 4091.961095 3 0.0004 126 | 0/8 6 h-lim-p 0.0006 0.4730 0.4200 4091.961065 1 0.0005 148 | 0/8 7 h-lim-p 0.0170 20.0000 0.0116 4091.961064 0 0.0037 169 | 0/8 8 h-lim-p 0.0159 20.0000 0.0027 4091.960686 0 0.1905 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4091.960685 0 1.0938 212 | 0/8 10 h-lim-p 2.2728 20.0000 0.0000 4091.960685 0 0.9944 232 | 0/8 11 h-lim-p 1.0194 20.0000 0.0000 4091.960685 0 0.0319 256 | 0/8 12 h-lim-p 0.0011 20.0000 0.0004 4091.960685 0 0.0000 282 | 0/8 13 h-lim-p 0.0018 20.0000 0.0000 4091.960685 0 0.0000 316 Out... lnL = -4091.960685 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4091.960685 Node 7: lnL = -4091.960685 Node 8: lnL = -4091.960685 Node 9: lnL = -4091.960685 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 565 Sequential format.. Reading seq # 1: YIR023W_Sbay Reading seq # 2: YIR023W_Scer Reading seq # 3: YIR023W_Skud Reading seq # 4: YIR023W_Smik Reading seq # 5: YIR023W_Spar Sequences read.. Counting patterns.. # site patterns = 214 Counting frequencies.. 120 bytes for distance 34240 bytes for lkl0 27392 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.245906 0.063387 0.100442 0.109290 0.094221 0.233737 0.176923 0.018011 lnL0 = -2337.247889 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2337.247889 x= 0.24591 0.06339 0.10044 0.10929 0.09422 0.23374 0.17692 0.01801 1 h-lim-p 0.0005 0.0040 77.5364 2336.062942 3 0.0004 28 | 0/8 2 h-lim-p 0.0002 0.0016 21.6812 2335.893948 0 0.0008 42 | 0/8 3 h-lim-p 0.0007 0.0059 10.1262 2335.879035 2 0.0003 58 | 0/8 4 h-lim-p 0.0008 0.0379 4.6321 2335.875576 4 0.0004 79 | 0/8 5 h-lim-p 0.0013 0.1964 1.4817 2335.874569 3 0.0010 97 | 0/8 6 h-lim-p 0.0025 0.1131 0.6166 2335.874469 1 0.0006 112 | 0/8 7 h-lim-p 0.0022 1.7662 0.1755 2335.874455 1 0.0010 134 | 0/8 8 h-lim-p 0.2319 20.0000 0.0007 2335.873847 0 0.9274 156 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2335.873839 0 1.0938 176 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2335.873839 0 1.0938 196 | 0/8 11 h-lim-p 1.2186 20.0000 0.0000 2335.873839 0 0.2666 217 | 0/8 12 h-lim-p 0.0229 20.0000 0.0002 2335.873839 0 0.0229 237 | 0/8 13 h-lim-p 0.0078 20.0000 0.0007 2335.873839 0 0.0000 279 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -2335.873839 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2335.873839 Node 7: lnL = -2335.873839 Node 8: lnL = -2335.873839 Node 9: lnL = -2335.873839 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 220 Sequential format.. Reading seq # 1: YIR024C_Sbay Reading seq # 2: YIR024C_Scer Reading seq # 3: YIR024C_Skud Reading seq # 4: YIR024C_Smik Reading seq # 5: YIR024C_Spar Sequences read.. Counting patterns.. # site patterns = 88 Counting frequencies.. 120 bytes for distance 14080 bytes for lkl0 11264 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.250318 0.084233 0.074841 0.091886 0.054923 0.220911 0.251142 0.021347 lnL0 = -860.336720 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 860.336720 x= 0.25032 0.08423 0.07484 0.09189 0.05492 0.22091 0.25114 0.02135 1 h-lim-p 0.0030 0.0237 15.3899 860.206559 5 0.0011 32 | 0/8 2 h-lim-p 0.0015 0.0123 8.2013 860.186129 2 0.0007 48 | 0/8 3 h-lim-p 0.0017 0.0199 3.5397 860.181150 6 0.0010 74 | 0/8 4 h-lim-p 0.0019 0.0601 1.8747 860.179433 5 0.0013 98 | 0/8 5 h-lim-p 0.0054 0.8954 0.4528 860.179284 3 0.0016 119 | 0/8 6 h-lim-p 0.0209 2.5013 0.0342 860.179283 0 0.0011 142 | 0/8 7 h-lim-p 0.0028 20.0000 0.0139 860.179283 0 0.0025 162 | 0/8 8 h-lim-p 0.0952 20.0000 0.0004 860.179256 0 0.7615 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 860.179256 0 1.0938 205 | 0/8 10 h-lim-p 2.0376 20.0000 0.0000 860.179256 0 1.7829 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 860.179256 0 0.5469 246 | 0/8 12 h-lim-p 0.1546 20.0000 0.0000 860.179256 0 0.0048 270 | 0/8 13 h-lim-p 0.0018 20.0000 0.0000 860.179256 0 0.0000 295 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 860.179256 0 0.0000 315 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 860.179256 0 0.0000 346 | 0/8 16 h-lim-p 0.0000 20.0000 0.0005 | 0/8 17 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -860.179256 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -860.179256 Node 7: lnL = -860.179256 Node 8: lnL = -860.179256 Node 9: lnL = -860.179256 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 185 Sequential format.. Reading seq # 1: YIR025W_Sbay Reading seq # 2: YIR025W_Scer Reading seq # 3: YIR025W_Skud Reading seq # 4: YIR025W_Smik Reading seq # 5: YIR025W_Spar Sequences read.. Counting patterns.. # site patterns = 102 Counting frequencies.. 120 bytes for distance 16320 bytes for lkl0 13056 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.282829 0.036650 0.116636 0.143614 0.010985 0.187019 0.324119 0.036457 lnL0 = -792.272387 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 792.272387 x= 0.28283 0.03665 0.11664 0.14361 0.01099 0.18702 0.32412 0.03646 1 h-lim-p 0.0007 0.6938 150.2921 790.447598 6 0.0002 35 | 0/8 2 h-lim-p 0.0009 0.0113 37.0293 789.535334 0 0.0019 48 | 0/8 3 h-lim-p 0.0012 0.0093 14.0535 789.327672 0 0.0023 61 | 0/8 4 h-lim-p 0.0069 0.0980 4.6892 789.312420 2 0.0016 78 | 0/8 5 h-lim-p 0.0047 0.2198 1.6240 789.309071 5 0.0028 105 | 0/8 6 h-lim-p 0.0103 0.7975 0.4475 789.308766 5 0.0030 131 | 0/8 7 h-lim-p 0.0144 1.0848 0.0925 789.308584 2 0.0115 155 | 0/8 8 h-lim-p 0.0372 4.4183 0.0286 789.293917 0 0.2979 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 789.293643 5 1.3886 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 789.293599 3 1.4660 239 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 789.293599 0 1.0938 259 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 789.293599 0 1.0938 279 | 0/8 13 h-lim-p 1.2004 20.0000 0.0000 789.293599 0 2.4008 300 | 0/8 14 h-lim-p 1.3976 20.0000 0.0000 789.293599 0 1.3976 320 | 0/8 15 h-lim-p 0.0685 20.0000 0.0002 789.293599 0 0.0514 340 | 0/8 16 h-lim-p 0.0146 20.0000 0.0006 789.293599 0 0.0002 365 | 0/8 17 h-lim-p 0.0001 20.0000 0.0015 789.293599 0 0.0000 390 | 0/8 18 h-lim-p 0.0002 20.0000 0.0000 789.293599 0 0.0000 425 Out... lnL = -789.293599 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -789.293599 Node 7: lnL = -789.293599 Node 8: lnL = -789.293599 Node 9: lnL = -789.293599 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 351 Sequential format.. Reading seq # 1: YIR026C_Sbay Reading seq # 2: YIR026C_Scer Reading seq # 3: YIR026C_Skud Reading seq # 4: YIR026C_Smik Reading seq # 5: YIR026C_Spar Sequences read.. Counting patterns.. # site patterns = 139 Counting frequencies.. 120 bytes for distance 22240 bytes for lkl0 17792 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.256294 0.018009 0.058145 0.143555 0.077744 0.221940 0.156196 0.049553 lnL0 = -1435.648882 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1435.648882 x= 0.25629 0.01801 0.05815 0.14356 0.07774 0.22194 0.15620 0.04955 1 h-lim-p 0.0003 0.0028 89.6234 1434.646126 8 0.0003 41 | 0/8 2 h-lim-p 0.0005 0.0043 22.5650 1434.526759 3 0.0005 59 | 0/8 3 h-lim-p 0.0011 0.0248 10.4496 1434.502555 6 0.0005 86 | 0/8 4 h-lim-p 0.0035 0.1374 1.5720 1434.501509 3 0.0009 105 | 0/8 5 h-lim-p 0.0047 0.6476 0.2901 1434.501483 3 0.0006 125 | 0/8 6 h-lim-p 0.0019 2.6038 0.0981 1434.501478 0 0.0009 145 | 0/8 7 h-lim-p 0.0255 20.0000 0.0036 1434.501473 0 0.0255 165 | 0/8 8 h-lim-p 0.0095 4.6835 0.0098 1434.501234 0 0.0379 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1434.501229 1 0.9961 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1434.501229 0 2.1875 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1434.501229 0 1.0938 249 | 0/8 12 h-lim-p 0.0902 20.0000 0.0000 1434.501229 0 0.0113 271 | 0/8 13 h-lim-p 0.0000 6.8841 0.0102 1434.501229 0 0.0000 291 | 0/8 14 h-lim-p 0.0002 20.0000 0.0004 1434.501229 0 0.0000 313 | 0/8 15 h-lim-p 0.0001 20.0000 0.0001 1434.501229 0 0.0000 334 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 1434.501229 0 0.0000 368 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 1434.501229 0 0.0000 391 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 | 0/8 20 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1434.501229 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1434.501229 Node 7: lnL = -1434.501229 Node 8: lnL = -1434.501229 Node 9: lnL = -1434.501229 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 880 Sequential format.. Reading seq # 1: YIR027C_Sbay Reading seq # 2: YIR027C_Scer Reading seq # 3: YIR027C_Skud Reading seq # 4: YIR027C_Smik Reading seq # 5: YIR027C_Spar Sequences read.. Counting patterns.. # site patterns = 206 Counting frequencies.. 120 bytes for distance 32960 bytes for lkl0 26368 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.172974 0.030065 0.047807 0.057141 0.034165 0.128222 0.148736 0.029044 lnL0 = -3193.398146 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3193.398146 x= 0.17297 0.03006 0.04781 0.05714 0.03416 0.12822 0.14874 0.02904 1 h-lim-p 0.0001 0.0010 204.7791 3191.820145 7 0.0001 37 | 0/8 2 h-lim-p 0.0006 0.0051 12.7877 3191.807606 2 0.0002 54 | 0/8 3 h-lim-p 0.0003 0.0081 7.4103 3191.805776 3 0.0001 74 | 0/8 4 h-lim-p 0.0002 0.0508 3.8152 3191.805095 4 0.0001 94 | 0/8 5 h-lim-p 0.0005 0.2396 0.9711 3191.805030 3 0.0001 115 | 0/8 6 h-lim-p 0.0004 0.4684 0.3402 3191.805022 1 0.0002 137 | 0/8 7 h-lim-p 0.0022 5.3404 0.0250 3191.805022 0 0.0002 159 | 0/8 8 h-lim-p 0.0633 20.0000 0.0001 3191.805017 0 1.0121 183 | 0/8 9 h-lim-p 2.2020 20.0000 0.0000 3191.805017 0 1.9267 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3191.805017 0 0.6250 224 | 0/8 11 h-lim-p 0.1717 20.0000 0.0001 3191.805017 0 0.0027 249 | 0/8 12 h-lim-p 0.0009 20.0000 0.0003 3191.805017 0 0.0001 271 | 0/8 13 h-lim-p 0.0000 0.6671 0.0597 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0064 | 0/8 15 h-lim-p 0.0000 20.0000 0.0064 Out... lnL = -3191.805017 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3191.805017 Node 7: lnL = -3191.805017 Node 8: lnL = -3191.805017 Node 9: lnL = -3191.805017 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 879 Sequential format.. Reading seq # 1: YIR028W_Sbay Reading seq # 2: YIR028W_Scer Reading seq # 3: YIR028W_Skud Reading seq # 4: YIR028W_Smik Reading seq # 5: YIR028W_Spar Sequences read.. Counting patterns.. # site patterns = 205 Counting frequencies.. 120 bytes for distance 32800 bytes for lkl0 26240 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.186254 0.025674 0.044832 0.059289 0.037751 0.128005 0.155499 0.037511 lnL0 = -3239.930338 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3239.930338 x= 0.18625 0.02567 0.04483 0.05929 0.03775 0.12800 0.15550 0.03751 1 h-lim-p 0.0002 0.0014 229.8720 3238.018793 5 0.0001 31 | 0/8 2 h-lim-p 0.0007 0.0055 13.8263 3238.006191 4 0.0001 52 | 0/8 3 h-lim-p 0.0002 0.0082 9.1795 3238.003074 3 0.0001 70 | 0/8 4 h-lim-p 0.0002 0.0264 3.6938 3238.002448 2 0.0001 86 | 0/8 5 h-lim-p 0.0006 0.1936 0.6909 3238.002406 3 0.0002 107 | 0/8 6 h-lim-p 0.0004 0.6123 0.3028 3238.002399 0 0.0002 127 | 0/8 7 h-lim-p 0.0027 7.0877 0.0200 3238.002399 0 0.0003 149 | 0/8 8 h-lim-p 0.0789 20.0000 0.0001 3238.002398 0 1.2619 173 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3238.002398 0 1.2500 193 | 0/8 10 h-lim-p 0.8680 20.0000 0.0000 3238.002398 0 0.7595 213 | 0/8 11 h-lim-p 0.3212 20.0000 0.0001 3238.002398 0 0.0050 238 | 0/8 12 h-lim-p 0.0012 20.0000 0.0004 3238.002398 0 0.0012 258 | 0/8 13 h-lim-p 0.0009 20.0000 0.0005 3238.002398 0 0.0001 280 | 0/8 14 h-lim-p 0.0001 20.0000 0.0007 3238.002398 0 0.0000 300 | 0/8 15 h-lim-p 0.0000 20.0000 0.0008 3238.002398 0 0.0000 327 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 3238.002398 0 0.0000 354 | 0/8 17 h-lim-p 0.0000 20.0000 0.0017 | 0/8 18 h-lim-p 0.0000 20.0000 0.0017 Out... lnL = -3238.002398 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3238.002398 Node 7: lnL = -3238.002398 Node 8: lnL = -3238.002398 Node 9: lnL = -3238.002398 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 502 Sequential format.. Reading seq # 1: YIR029W_Sbay Reading seq # 2: YIR029W_Scer Reading seq # 3: YIR029W_Skud Reading seq # 4: YIR029W_Smik Reading seq # 5: YIR029W_Spar Sequences read.. Counting patterns.. # site patterns = 168 Counting frequencies.. 120 bytes for distance 26880 bytes for lkl0 21504 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.283818 0.013477 0.092891 0.108188 0.056534 0.235281 0.169262 0.059277 lnL0 = -2113.109506 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2113.109506 x= 0.28382 0.01348 0.09289 0.10819 0.05653 0.23528 0.16926 0.05928 1 h-lim-p 0.0013 0.0172 179.1807 2110.464870 9 0.0002 48 | 0/8 2 h-lim-p 0.0004 0.0033 40.2587 2110.094837 1 0.0005 62 | 0/8 3 h-lim-p 0.0007 0.0066 31.9883 2110.007242 4 0.0003 82 | 0/8 4 h-lim-p 0.0012 0.0347 6.9800 2109.997186 4 0.0005 102 | 0/8 5 h-lim-p 0.0029 0.3093 1.0850 2109.996757 2 0.0007 119 | 0/8 6 h-lim-p 0.0018 0.3671 0.4303 2109.996711 3 0.0005 139 | 0/8 7 h-lim-p 0.0169 6.8593 0.0136 2109.996208 0 0.0678 161 | 0/8 8 h-lim-p 0.0044 2.8567 0.2077 2109.989386 0 0.0089 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 2109.988575 3 1.2347 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 2109.988537 2 1.2305 234 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2109.988536 0 1.0938 254 | 0/8 12 h-lim-p 1.5016 20.0000 0.0000 2109.988536 0 0.0022 283 | 0/8 13 h-lim-p 0.0007 20.0000 0.0000 2109.988536 0 0.0003 303 | 0/8 14 h-lim-p 0.0005 20.0000 0.0000 2109.988536 0 0.0005 323 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 2109.988536 0 0.0001 344 | 0/8 16 h-lim-p 0.0000 0.6234 0.1453 2109.988536 0 0.0000 365 | 0/8 17 h-lim-p 0.0062 20.0000 0.0001 2109.988536 0 0.0000 409 | 0/8 18 h-lim-p 0.0000 20.0000 0.0018 2109.988536 0 0.0000 438 | 0/8 19 h-lim-p 0.0000 20.0000 0.0004 2109.988536 0 0.0010 464 | 0/8 20 h-lim-p 0.0027 20.0000 0.0001 2109.988536 0 0.0014 484 | 0/8 21 h-lim-p 0.0017 20.0000 0.0001 2109.988536 0 0.0000 518 | 0/8 22 h-lim-p 0.0000 20.0000 0.0020 | 0/8 23 h-lim-p 0.0000 20.0000 0.0020 Out... lnL = -2109.988536 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2109.988536 Node 7: lnL = -2109.988536 Node 8: lnL = -2109.988536 Node 9: lnL = -2109.988536 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 163 Sequential format.. Reading seq # 1: YIR030C_Sbay Reading seq # 2: YIR030C_Scer Reading seq # 3: YIR030C_Skud Reading seq # 4: YIR030C_Smik Reading seq # 5: YIR030C_Spar Sequences read.. Counting patterns.. # site patterns = 99 Counting frequencies.. 120 bytes for distance 15840 bytes for lkl0 12672 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.548890 0.260364 0.037762 0.214965 0.068953 0.295740 0.372345 0.116423 lnL0 = -755.968319 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 755.968319 x= 0.54889 0.26036 0.03776 0.21496 0.06895 0.29574 0.37234 0.11642 1 h-lim-p 0.0077 0.0617 30.4694 755.305168 5 0.0016 34 | 0/8 2 h-lim-p 0.0025 0.0201 9.3935 755.188227 1 0.0031 48 | 0/8 3 h-lim-p 0.0037 0.0385 8.0462 755.109014 3 0.0037 66 | 0/8 4 h-lim-p 0.0209 0.4441 1.4356 755.098804 6 0.0106 94 | 0/8 5 h-lim-p 0.0136 0.3299 1.1135 755.096812 6 0.0047 122 | 0/8 6 h-lim-p 0.0178 3.0475 0.2928 755.096339 5 0.0111 147 | 0/8 7 h-lim-p 0.0211 3.1864 0.1548 755.096009 3 0.0230 174 | 0/8 8 h-lim-p 0.6197 20.0000 0.0057 755.091308 1 0.7746 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0017 755.090965 2 1.1719 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 755.090959 1 1.0938 242 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 755.090959 0 1.0938 262 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 755.090959 0 2.1875 282 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 755.090959 0 1.0938 302 | 0/8 14 h-lim-p 0.7682 20.0000 0.0000 755.090959 0 4.6090 324 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 755.090959 0 0.0684 348 | 0/8 16 h-lim-p 0.1131 20.0000 0.0000 755.090959 0 0.0009 374 Out... lnL = -755.090959 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -755.090959 Node 7: lnL = -755.090959 Node 8: lnL = -755.090959 Node 9: lnL = -755.090959 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 554 Sequential format.. Reading seq # 1: YIR032C_Sbay Reading seq # 2: YIR032C_Scer Reading seq # 3: YIR032C_Skud Reading seq # 4: YIR032C_Smik Reading seq # 5: YIR032C_Spar Sequences read.. Counting patterns.. # site patterns = 211 Counting frequencies.. 120 bytes for distance 33760 bytes for lkl0 27008 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.200099 0.089236 0.148418 0.095144 0.090727 0.168272 0.157554 0.000060 lnL0 = -2290.184624 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2290.184624 x= 0.20010 0.08924 0.14842 0.09514 0.09073 0.16827 0.15755 0.00006 1 h-lim-p 0.0000 0.0000 145.9706 2290.140523 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0127 23.8777 2290.040567 0 0.0004 39 | 1/8 3 h-lim-p 0.0009 0.0187 9.7800 2290.015129 6 0.0005 68 | 1/8 4 h-lim-p 0.0015 0.3965 3.6240 2290.005017 6 0.0009 96 | 1/8 5 h-lim-p 0.0020 0.1110 1.6331 2289.933507 0 0.0078 110 | 1/8 6 h-lim-p 0.0061 0.0489 2.0631 2288.015906 0 0.0244 124 | 1/8 7 h-lim-p 0.0007 0.0056 51.9121 2285.522522 0 0.0011 136 | 1/8 8 h-lim-p 0.0114 0.0911 3.8305 2285.516486 5 0.0008 161 | 1/8 9 h-lim-p 0.1488 20.0000 0.0195 2285.131929 0 0.5951 175 | 0/8 10 h-lim-p 0.0069 0.8424 1.6925 2285.131130 4 0.0006 206 | 0/8 11 h-lim-p 0.2569 20.0000 0.0036 2285.116134 0 1.0275 220 | 0/8 12 h-lim-p 2.5000 20.0000 0.0006 2285.115881 3 0.9644 246 | 0/8 13 h-lim-p 2.5000 20.0000 0.0001 2285.115878 0 1.0938 266 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 2285.115878 0 1.0938 286 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2285.115878 0 2.1875 306 | 0/8 16 h-lim-p 1.9202 20.0000 0.0000 2285.115878 0 0.8401 326 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 2285.115878 0 0.0391 351 | 0/8 18 h-lim-p 0.0256 20.0000 0.0000 2285.115878 0 0.0000 381 Out... lnL = -2285.115878 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2285.115878 Node 7: lnL = -2285.115878 Node 8: lnL = -2285.115878 Node 9: lnL = -2285.115878 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 323 Sequential format.. Reading seq # 1: YIR035C_Sbay Reading seq # 2: YIR035C_Scer Reading seq # 3: YIR035C_Skud Reading seq # 4: YIR035C_Smik Reading seq # 5: YIR035C_Spar Sequences read.. Counting patterns.. # site patterns = 155 Counting frequencies.. 120 bytes for distance 24800 bytes for lkl0 19840 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.332978 0.078309 0.065879 0.086919 0.097021 0.174676 0.197795 0.083808 lnL0 = -1372.557327 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1372.557327 x= 0.33298 0.07831 0.06588 0.08692 0.09702 0.17468 0.19779 0.08381 1 h-lim-p 0.0005 0.0037 78.6836 1370.925841 0 0.0007 22 | 0/8 2 h-lim-p 0.0006 0.0051 23.3096 1370.768009 2 0.0006 38 | 0/8 3 h-lim-p 0.0009 0.0150 15.1380 1370.699565 6 0.0008 61 | 0/8 4 h-lim-p 0.0025 0.0522 5.0085 1370.686401 3 0.0012 79 | 0/8 5 h-lim-p 0.0027 0.0987 2.2876 1370.684111 4 0.0011 99 | 0/8 6 h-lim-p 0.0042 0.4516 0.5804 1370.683826 4 0.0015 120 | 0/8 7 h-lim-p 0.0086 1.3466 0.1030 1370.683374 0 0.0173 141 | 0/8 8 h-lim-p 0.0349 2.8782 0.0510 1370.648008 0 0.1397 163 | 0/8 9 h-lim-p 2.5000 20.0000 0.0008 1370.647769 3 0.9644 189 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1370.647769 0 1.0938 209 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1370.647769 0 1.0938 229 | 0/8 12 h-lim-p 1.2305 20.0000 0.0000 1370.647769 0 1.0767 249 | 0/8 13 h-lim-p 0.4736 20.0000 0.0000 1370.647769 0 0.0074 274 | 0/8 14 h-lim-p 0.0015 20.0000 0.0001 1370.647769 0 0.0007 294 | 0/8 15 h-lim-p 0.0001 20.0000 0.0004 1370.647769 0 0.0000 316 | 0/8 16 h-lim-p 0.0004 20.0000 0.0000 1370.647769 0 0.0001 337 | 0/8 17 h-lim-p 0.0002 20.0000 0.0000 1370.647769 0 0.0000 375 Out... lnL = -1370.647769 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1370.647769 Node 7: lnL = -1370.647769 Node 8: lnL = -1370.647769 Node 9: lnL = -1370.647769 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 737 Sequential format.. Reading seq # 1: YJL001W_Sbay Reading seq # 2: YJL001W_Scer Reading seq # 3: YJL001W_Skud Reading seq # 4: YJL001W_Smik Reading seq # 5: YJL001W_Spar Sequences read.. Counting patterns.. # site patterns = 275 Counting frequencies.. 120 bytes for distance 44000 bytes for lkl0 35200 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.214714 0.069137 0.057199 0.222501 0.075621 0.182909 0.154734 0.000060 lnL0 = -3156.782154 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3156.782154 x= 0.21471 0.06914 0.05720 0.22250 0.07562 0.18291 0.15473 0.00006 1 h-lim-p 0.0020 0.0159 132.0753 3155.239778 8 0.0002 43 | 0/8 2 h-lim-p 0.0004 0.0031 30.1905 3155.128440 6 0.0003 70 | 0/8 3 h-lim-p 0.0003 0.0022 11.9688 3155.102996 0 0.0004 82 | 0/8 4 h-lim-p 0.0013 0.0734 3.7680 3155.100588 5 0.0004 107 | 0/8 5 h-lim-p 0.0023 0.0504 0.6215 3155.100502 2 0.0005 124 | 0/8 6 h-lim-p 0.0031 3.7569 0.0926 3155.100438 0 0.0123 146 | 0/8 7 h-lim-p 0.0003 0.0834 3.6513 3155.100217 0 0.0012 168 | 0/8 8 h-lim-p 0.0052 0.3741 0.8669 3155.100197 2 0.0005 186 | 0/8 9 h-lim-p 1.2997 20.0000 0.0003 3155.100178 2 1.0027 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3155.100178 0 1.0938 230 | 0/8 11 h-lim-p 1.7365 20.0000 0.0000 3155.100178 0 0.3799 251 | 0/8 12 h-lim-p 0.1760 20.0000 0.0000 3155.100178 0 0.0000 282 Out... lnL = -3155.100178 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3155.100178 Node 7: lnL = -3155.100178 Node 8: lnL = -3155.100178 Node 9: lnL = -3155.100178 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 546 Sequential format.. Reading seq # 1: YJL002C_Sbay Reading seq # 2: YJL002C_Scer Reading seq # 3: YJL002C_Skud Reading seq # 4: YJL002C_Smik Reading seq # 5: YJL002C_Spar Sequences read.. Counting patterns.. # site patterns = 214 Counting frequencies.. 120 bytes for distance 34240 bytes for lkl0 27392 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.263400 0.072400 0.064466 0.166529 0.087021 0.208387 0.218946 0.018676 lnL0 = -2533.054602 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2533.054602 x= 0.26340 0.07240 0.06447 0.16653 0.08702 0.20839 0.21895 0.01868 1 h-lim-p 0.0004 0.0032 92.6276 2531.763849 4 0.0003 30 | 0/8 2 h-lim-p 0.0008 0.0063 18.9369 2531.675090 5 0.0005 54 | 0/8 3 h-lim-p 0.0010 0.0322 9.4970 2531.661219 6 0.0004 81 | 0/8 4 h-lim-p 0.0009 0.0658 4.0271 2531.658201 4 0.0005 102 | 0/8 5 h-lim-p 0.0030 0.6725 0.6122 2531.658102 3 0.0006 121 | 0/8 6 h-lim-p 0.0041 3.3672 0.0851 2531.658099 1 0.0008 144 | 0/8 7 h-lim-p 0.0056 4.8850 0.0122 2531.658099 0 0.0025 164 | 0/8 8 h-lim-p 0.0402 20.0000 0.0007 2531.657962 0 0.4820 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2531.657959 0 1.0938 207 | 0/8 10 h-lim-p 2.4312 20.0000 0.0000 2531.657959 0 1.0636 227 | 0/8 11 h-lim-p 1.0528 20.0000 0.0000 2531.657959 0 2.1056 248 | 0/8 12 h-lim-p 0.3089 20.0000 0.0001 2531.657959 0 0.1158 269 | 0/8 13 h-lim-p 0.0179 20.0000 0.0009 2531.657959 0 0.0011 292 | 0/8 14 h-lim-p 0.0007 20.0000 0.0014 2531.657959 0 0.0000 332 | 0/8 15 h-lim-p 0.0000 20.0000 0.0008 | 0/8 16 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -2531.657959 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2531.657959 Node 7: lnL = -2531.657959 Node 8: lnL = -2531.657959 Node 9: lnL = -2531.657959 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 494 Sequential format.. Reading seq # 1: YJL003W_Sbay Reading seq # 2: YJL003W_Scer Reading seq # 3: YJL003W_Skud Reading seq # 4: YJL003W_Smik Reading seq # 5: YJL003W_Spar Sequences read.. Counting patterns.. # site patterns = 204 Counting frequencies.. 120 bytes for distance 32640 bytes for lkl0 26112 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.319601 0.075058 0.053782 0.126080 0.101572 0.234644 0.248969 0.052232 lnL0 = -2313.613687 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2313.613687 x= 0.31960 0.07506 0.05378 0.12608 0.10157 0.23464 0.24897 0.05223 1 h-lim-p 0.0006 0.0046 106.5541 2311.703711 6 0.0004 36 | 0/8 2 h-lim-p 0.0008 0.0060 34.0746 2311.384005 4 0.0006 56 | 0/8 3 h-lim-p 0.0010 0.0150 20.9781 2311.293845 7 0.0006 87 | 0/8 4 h-lim-p 0.0012 0.0303 9.2971 2311.274398 2 0.0006 103 | 0/8 5 h-lim-p 0.0038 0.1701 1.4106 2311.273573 2 0.0008 120 | 0/8 6 h-lim-p 0.0034 0.5429 0.3458 2311.273537 2 0.0007 137 | 0/8 7 h-lim-p 0.0326 15.3985 0.0070 2311.273535 0 0.0082 158 | 0/8 8 h-lim-p 0.0191 20.0000 0.0030 2311.273331 0 0.1526 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2311.273326 0 1.0938 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2311.273326 0 1.0938 221 | 0/8 11 h-lim-p 1.4512 20.0000 0.0000 2311.273326 0 1.4512 241 | 0/8 12 h-lim-p 0.9443 20.0000 0.0000 2311.273326 0 0.2361 262 | 0/8 13 h-lim-p 0.0002 6.0258 0.0151 2311.273326 0 0.0001 283 | 0/8 14 h-lim-p 0.0001 20.0000 0.0105 2311.273326 0 0.0000 304 | 0/8 15 h-lim-p 0.0006 20.0000 0.0004 2311.273326 0 0.0000 331 | 0/8 16 h-lim-p 0.0004 20.0000 0.0000 2311.273326 0 0.0000 360 Out... lnL = -2311.273326 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2311.273326 Node 7: lnL = -2311.273326 Node 8: lnL = -2311.273326 Node 9: lnL = -2311.273326 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 492 Sequential format.. Reading seq # 1: YJL004C_Sbay Reading seq # 2: YJL004C_Scer Reading seq # 3: YJL004C_Skud Reading seq # 4: YJL004C_Smik Reading seq # 5: YJL004C_Spar Sequences read.. Counting patterns.. # site patterns = 220 Counting frequencies.. 120 bytes for distance 35200 bytes for lkl0 28160 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.304339 0.036753 0.045606 0.123875 0.103776 0.242691 0.335865 0.037889 lnL0 = -2222.145511 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2222.145511 x= 0.30434 0.03675 0.04561 0.12388 0.10378 0.24269 0.33586 0.03789 1 h-lim-p 0.0012 0.0092 126.4756 2220.004737 4 0.0003 31 | 0/8 2 h-lim-p 0.0007 0.0058 27.9966 2219.758588 3 0.0007 49 | 0/8 3 h-lim-p 0.0009 0.0186 20.9348 2219.633837 2 0.0008 65 | 0/8 4 h-lim-p 0.0011 0.0221 15.2770 2219.582248 6 0.0007 92 | 0/8 5 h-lim-p 0.0052 0.1332 2.1307 2219.580205 5 0.0010 117 | 0/8 6 h-lim-p 0.0035 0.2746 0.5725 2219.580106 3 0.0006 137 | 0/8 7 h-lim-p 0.1219 20.0000 0.0029 2219.579779 0 0.2439 158 | 0/8 8 h-lim-p 0.0029 1.4362 0.2437 2219.578685 0 0.0059 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 2219.578584 3 1.0004 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2219.578584 0 1.0938 225 | 0/8 11 h-lim-p 1.6284 20.0000 0.0000 2219.578584 0 1.4248 245 | 0/8 12 h-lim-p 1.3809 20.0000 0.0000 2219.578584 0 1.3809 265 | 0/8 13 h-lim-p 0.1560 20.0000 0.0001 2219.578584 0 0.1560 285 | 0/8 14 h-lim-p 0.0378 20.0000 0.0005 2219.578584 0 0.0012 309 | 0/8 15 h-lim-p 0.0010 20.0000 0.0005 2219.578584 0 0.0000 346 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 2219.578584 0 0.0000 379 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -2219.578584 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2219.578584 Node 7: lnL = -2219.578584 Node 8: lnL = -2219.578584 Node 9: lnL = -2219.578584 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 915 Sequential format.. Reading seq # 1: YJL006C_Sbay Reading seq # 2: YJL006C_Scer Reading seq # 3: YJL006C_Skud Reading seq # 4: YJL006C_Smik Reading seq # 5: YJL006C_Spar Sequences read.. Counting patterns.. # site patterns = 425 Counting frequencies.. 120 bytes for distance 68000 bytes for lkl0 54400 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.415141 0.000060 0.152043 0.187721 0.170722 0.376979 0.303777 0.068095 lnL0 = -4421.998103 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4421.998103 x= 0.41514 0.00006 0.15204 0.18772 0.17072 0.37698 0.30378 0.06809 1 h-lim-p 0.0005 0.0042 96.7951 4418.668147 0 0.0008 22 | 0/8 2 h-lim-p 0.0005 0.0038 66.4158 4417.542494 0 0.0007 34 | 0/8 3 h-lim-p 0.0026 0.0242 17.7977 4417.430894 6 0.0008 61 | 0/8 4 h-lim-p 0.0035 0.0583 3.9527 4417.426493 5 0.0006 87 | 0/8 5 h-lim-p 0.0009 0.1621 2.6436 4417.425197 4 0.0005 109 | 0/8 6 h-lim-p 0.0019 0.3592 0.6898 4417.424892 3 0.0011 130 | 0/8 7 h-lim-p 0.0094 1.7779 0.0822 4417.423532 0 0.0189 151 | 0/8 8 h-lim-p 0.0059 0.5860 0.2629 4417.365897 0 0.0473 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0012 4417.365376 2 0.9644 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4417.365375 0 1.0938 218 | 0/8 11 h-lim-p 1.7746 20.0000 0.0000 4417.365375 0 1.5528 238 | 0/8 12 h-lim-p 2.3463 20.0000 0.0000 4417.365375 0 2.0531 258 | 0/8 13 h-lim-p 1.6790 20.0000 0.0000 4417.365375 0 1.4691 278 | 0/8 14 h-lim-p 0.7247 20.0000 0.0000 4417.365375 0 2.8989 300 | 0/8 15 h-lim-p 0.1162 20.0000 0.0005 4417.365375 0 0.0000 339 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 4417.365375 0 0.0000 367 Out... lnL = -4417.365375 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4417.365375 Node 7: lnL = -4417.365375 Node 8: lnL = -4417.365375 Node 9: lnL = -4417.365375 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 853 Sequential format.. Reading seq # 1: YJL008C_Sbay Reading seq # 2: YJL008C_Scer Reading seq # 3: YJL008C_Skud Reading seq # 4: YJL008C_Smik Reading seq # 5: YJL008C_Spar Sequences read.. Counting patterns.. # site patterns = 480 Counting frequencies.. 120 bytes for distance 76800 bytes for lkl0 61440 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.763836 0.010478 0.198033 0.329560 0.289807 0.449628 0.405341 0.174643 lnL0 = -5097.815569 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 5097.815569 x= 0.76384 0.01048 0.19803 0.32956 0.28981 0.44963 0.40534 0.17464 1 h-lim-p 0.0047 0.0374 68.5439 5095.699444 3 0.0010 29 | 0/8 2 h-lim-p 0.0012 0.0096 37.3321 5094.845027 1 0.0015 43 | 0/8 3 h-lim-p 0.0040 0.0453 14.1448 5094.743003 6 0.0012 71 | 0/8 4 h-lim-p 0.0023 0.0783 7.4832 5094.691351 4 0.0024 91 | 0/8 5 h-lim-p 0.0054 0.2192 3.3133 5094.678869 4 0.0029 112 | 0/8 6 h-lim-p 0.0127 0.3964 0.7454 5094.677942 4 0.0034 133 | 0/8 7 h-lim-p 0.0210 1.9106 0.1223 5094.677895 2 0.0035 160 | 0/8 8 h-lim-p 0.0708 20.0000 0.0060 5094.670465 0 0.5665 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0011 5094.670195 1 1.0938 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 5094.670194 0 1.0938 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 5094.670194 0 1.0938 245 | 0/8 12 h-lim-p 1.7023 20.0000 0.0000 5094.670194 0 0.8512 265 | 0/8 13 h-lim-p 0.4898 20.0000 0.0000 5094.670194 0 0.0612 287 | 0/8 14 h-lim-p 0.0108 20.0000 0.0000 5094.670194 0 0.0005 311 | 0/8 15 h-lim-p 0.0002 20.0000 0.0001 5094.670194 0 0.0000 342 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 5094.670194 0 0.0000 376 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 5094.670194 0 0.0000 396 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 5094.670194 0 0.0000 416 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 5094.670194 0 0.0000 440 Out... lnL = -5094.670194 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -5094.670194 Node 7: lnL = -5094.670194 Node 8: lnL = -5094.670194 Node 9: lnL = -5094.670194 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 883 Sequential format.. Reading seq # 1: YJL011C_Sbay Reading seq # 2: YJL011C_Scer Reading seq # 3: YJL011C_Skud Reading seq # 4: YJL011C_Smik Reading seq # 5: YJL011C_Spar Sequences read.. Counting patterns.. # site patterns = 395 Counting frequencies.. 120 bytes for distance 63200 bytes for lkl0 50560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.442013 0.027024 0.196175 0.162239 0.141382 0.471104 0.296763 0.034916 lnL0 = -4618.402821 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4618.402821 x= 0.44201 0.02702 0.19618 0.16224 0.14138 0.47110 0.29676 0.03492 1 h-lim-p 0.0007 0.0052 96.7186 4616.550331 6 0.0004 36 | 0/8 2 h-lim-p 0.0008 0.0061 27.1946 4616.366508 6 0.0005 64 | 0/8 3 h-lim-p 0.0008 0.0094 17.8137 4616.313231 7 0.0005 95 | 0/8 4 h-lim-p 0.0014 0.0821 5.6880 4616.301440 5 0.0009 120 | 0/8 5 h-lim-p 0.0037 0.1675 1.3122 4616.300377 4 0.0013 141 | 0/8 6 h-lim-p 0.0120 0.7863 0.1429 4616.300366 2 0.0010 160 | 0/8 7 h-lim-p 0.0041 2.4270 0.0332 4616.300365 0 0.0018 180 | 0/8 8 h-lim-p 0.5027 20.0000 0.0001 4616.300354 0 1.0054 201 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4616.300354 0 1.0938 221 | 0/8 10 h-lim-p 1.2819 20.0000 0.0000 4616.300354 0 1.1216 241 | 0/8 11 h-lim-p 0.8210 20.0000 0.0000 4616.300354 0 0.0128 266 | 0/8 12 h-lim-p 0.0007 20.0000 0.0004 4616.300354 0 0.0003 286 | 0/8 13 h-lim-p 0.0017 20.0000 0.0001 4616.300354 0 0.0000 321 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -4616.300354 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4616.300354 Node 7: lnL = -4616.300354 Node 8: lnL = -4616.300354 Node 9: lnL = -4616.300354 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 864 Sequential format.. Reading seq # 1: YJL012C_Sbay Reading seq # 2: YJL012C_Scer Reading seq # 3: YJL012C_Skud Reading seq # 4: YJL012C_Smik Reading seq # 5: YJL012C_Spar Sequences read.. Counting patterns.. # site patterns = 332 Counting frequencies.. 120 bytes for distance 53120 bytes for lkl0 42496 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.426125 0.097497 0.078574 0.139311 0.109004 0.319057 0.183314 0.094263 lnL0 = -4093.768842 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4093.768842 x= 0.42612 0.09750 0.07857 0.13931 0.10900 0.31906 0.18331 0.09426 1 h-lim-p 0.0008 0.0063 96.5335 4092.480362 6 0.0003 34 | 0/8 2 h-lim-p 0.0007 0.0093 40.7693 4092.058181 3 0.0006 52 | 0/8 3 h-lim-p 0.0010 0.0144 25.0834 4091.984251 6 0.0003 79 | 0/8 4 h-lim-p 0.0007 0.0303 11.6584 4091.968020 3 0.0003 97 | 0/8 5 h-lim-p 0.0026 0.2122 1.4029 4091.967639 4 0.0004 122 | 0/8 6 h-lim-p 0.0020 0.4973 0.2898 4091.967608 2 0.0008 138 | 0/8 7 h-lim-p 0.0131 9.0300 0.0167 4091.967605 0 0.0057 158 | 0/8 8 h-lim-p 0.0181 20.0000 0.0053 4091.967045 0 0.1447 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4091.967027 1 0.9961 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4091.967027 0 1.0938 223 | 0/8 11 h-lim-p 1.3362 20.0000 0.0000 4091.967027 0 1.3362 243 | 0/8 12 h-lim-p 0.9324 20.0000 0.0000 4091.967027 0 3.7295 265 | 0/8 13 h-lim-p 0.0326 20.0000 0.0024 4091.967027 0 0.0003 291 | 0/8 14 h-lim-p 0.0000 7.7100 0.0181 4091.967027 0 0.0000 322 | 0/8 15 h-lim-p 0.0011 20.0000 0.0000 4091.967027 0 0.0000 358 Out... lnL = -4091.967027 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4091.967027 Node 7: lnL = -4091.967027 Node 8: lnL = -4091.967027 Node 9: lnL = -4091.967027 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 259 Sequential format.. Reading seq # 1: YJL013C_Sbay Reading seq # 2: YJL013C_Scer Reading seq # 3: YJL013C_Skud Reading seq # 4: YJL013C_Smik Reading seq # 5: YJL013C_Spar Sequences read.. Counting patterns.. # site patterns = 116 Counting frequencies.. 120 bytes for distance 18560 bytes for lkl0 14848 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.243873 0.171849 0.013415 0.123413 0.076559 0.245090 0.042491 0.021121 lnL0 = -942.803588 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 942.803588 x= 0.24387 0.17185 0.01341 0.12341 0.07656 0.24509 0.04249 0.02112 1 h-lim-p 0.0012 0.0098 69.0192 941.885040 7 0.0005 38 | 0/8 2 h-lim-p 0.0005 0.0037 19.4589 941.770408 0 0.0009 51 | 0/8 3 h-lim-p 0.0015 0.0365 11.6092 941.703192 5 0.0013 72 | 0/8 4 h-lim-p 0.0021 0.0172 7.1873 941.668065 2 0.0020 88 | 0/8 5 h-lim-p 0.0042 0.0365 3.4430 941.664914 5 0.0007 115 | 0/8 6 h-lim-p 0.0015 0.1025 1.6300 941.663004 1 0.0019 129 | 0/8 7 h-lim-p 0.0044 0.2600 0.7052 941.662676 4 0.0015 151 | 0/8 8 h-lim-p 0.2669 20.0000 0.0041 941.651838 0 1.0678 173 | 0/8 9 h-lim-p 2.5000 20.0000 0.0008 941.651375 2 1.1719 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 941.651354 3 1.4660 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 941.651354 0 1.0938 246 | 0/8 12 h-lim-p 2.4390 20.0000 0.0000 941.651354 0 1.0671 266 | 0/8 13 h-lim-p 0.9072 20.0000 0.0000 941.651354 0 0.0071 292 | 0/8 14 h-lim-p 0.0001 20.0000 0.0009 941.651354 0 0.0000 314 | 0/8 15 h-lim-p 0.0001 20.0000 0.0001 941.651354 0 0.0001 334 | 0/8 16 h-lim-p 0.0001 20.0000 0.0001 941.651354 0 0.0001 354 | 0/8 17 h-lim-p 0.0001 20.0000 0.0001 941.651354 0 0.0001 374 | 0/8 18 h-lim-p 0.0001 20.0000 0.0001 941.651354 0 0.0000 394 | 0/8 19 h-lim-p 0.0001 20.0000 0.0000 941.651354 0 0.0000 424 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 941.651354 0 0.0000 445 | 0/8 21 h-lim-p 0.0000 20.0000 0.0000 941.651354 0 0.0000 468 | 0/8 22 h-lim-p 0.0000 20.0000 0.0000 941.651354 0 0.0000 488 | 0/8 23 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 24 h-lim-p 0.0000 20.0000 0.0001 941.651354 0 0.0000 543 | 0/8 25 h-lim-p 0.0000 20.0000 0.0000 941.651354 0 0.0000 563 | 0/8 26 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 27 h-lim-p 0.0000 20.0000 0.0001 941.651354 0 0.0000 616 | 0/8 28 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 29 h-lim-p 0.0000 20.0000 0.0001 | 0/8 30 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -941.651354 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -941.651354 Node 7: lnL = -941.651354 Node 8: lnL = -941.651354 Node 9: lnL = -941.651354 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 206 Sequential format.. Reading seq # 1: YJL016W_Sbay Reading seq # 2: YJL016W_Scer Reading seq # 3: YJL016W_Skud Reading seq # 4: YJL016W_Smik Reading seq # 5: YJL016W_Spar Sequences read.. Counting patterns.. # site patterns = 101 Counting frequencies.. 120 bytes for distance 16160 bytes for lkl0 12928 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.191458 0.091263 0.046764 0.119658 0.086407 0.159563 0.133303 0.000060 lnL0 = -852.638218 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 852.638218 x= 0.19146 0.09126 0.04676 0.11966 0.08641 0.15956 0.13330 0.00006 1 h-lim-p 0.0000 0.0000 67.9216 852.569001 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0052 23.7932 852.365842 0 0.0007 38 | 1/8 3 h-lim-p 0.0025 0.0455 6.6680 852.344997 6 0.0010 64 | 1/8 4 h-lim-p 0.0033 0.1103 2.0044 852.340100 5 0.0018 87 | 1/8 5 h-lim-p 0.0071 1.0542 0.4929 852.316192 0 0.0143 100 | 0/8 6 h-lim-p 0.0047 0.2234 1.4970 851.952646 0 0.0188 121 | 0/8 7 h-lim-p 0.0008 0.0066 8.9452 851.471047 0 0.0033 135 | 0/8 8 h-lim-p 0.0002 0.0020 9.2936 851.336035 m 0.0020 147 | 0/8 9 h-lim-p 0.0210 0.2820 0.8802 851.335598 4 0.0010 170 | 0/8 10 h-lim-p 0.0141 0.1128 0.0097 851.323971 m 0.1128 190 | 0/8 11 h-lim-p 0.0000 0.0000 0.0172 h-lim-p: 3.90096769e-20 3.12077415e-19 1.71782792e-02 851.323971 .. | 0/8 12 h-lim-p 0.0000 0.4635 12.1877 851.275484 0 0.0006 232 | 0/8 13 h-lim-p 0.0001 0.0009 2.6499 851.272407 m 0.0009 244 | 0/8 14 h-lim-p 0.0018 0.1343 1.3579 851.271761 2 0.0008 260 | 0/8 15 h-lim-p 0.0046 1.8137 0.2454 851.271731 2 0.0011 277 | 0/8 16 h-lim-p 0.0001 0.0010 0.0914 851.271729 0 0.0007 299 | 0/8 17 h-lim-p 0.0001 0.0004 0.0483 851.271729 0 0.0000 334 | 0/8 18 h-lim-p 0.0000 0.0000 35.7885 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.6043 851.271606 0 0.0006 378 | 0/8 20 h-lim-p 0.0001 0.0007 0.1280 851.271602 m 0.0007 398 | 1/8 21 h-lim-p 0.0018 4.5317 0.0423 851.271601 1 0.0015 420 | 1/8 22 h-lim-p 0.0096 20.0000 0.0065 851.271601 0 0.0021 440 | 1/8 23 h-lim-p 0.0118 20.0000 0.0012 851.271600 0 0.0118 459 | 1/8 24 h-lim-p 0.0030 20.0000 0.0046 851.271600 0 0.0026 478 | 1/8 25 h-lim-p 0.0263 20.0000 0.0005 851.271600 0 0.0029 499 | 1/8 26 h-lim-p 0.0100 20.0000 0.0001 851.271600 0 0.0100 518 | 1/8 27 h-lim-p 0.0096 20.0000 0.0001 851.271600 0 0.0770 540 | 1/8 28 h-lim-p 2.5000 20.0000 0.0000 851.271600 0 0.5469 560 | 1/8 29 h-lim-p 1.1578 20.0000 0.0000 851.271600 0 0.0000 609 Out... lnL = -851.271600 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -851.271600 Node 7: lnL = -851.271600 Node 8: lnL = -851.271600 Node 9: lnL = -851.271600 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 581 Sequential format.. Reading seq # 1: YJL023C_Sbay Reading seq # 2: YJL023C_Scer Reading seq # 3: YJL023C_Skud Reading seq # 4: YJL023C_Smik Reading seq # 5: YJL023C_Spar Sequences read.. Counting patterns.. # site patterns = 278 Counting frequencies.. 120 bytes for distance 44480 bytes for lkl0 35584 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.459566 0.145646 0.000060 0.266700 0.167344 0.333327 0.657071 0.022816 lnL0 = -2842.747076 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2842.747076 x= 0.45957 0.14565 0.00006 0.26670 0.16734 0.33333 0.65707 0.02282 1 h-lim-p 0.0002 0.0019 120.1905 2836.751523 0 0.0007 23 | 0/8 2 h-lim-p 0.0002 0.0013 34.7394 2836.103288 m 0.0013 35 | 0/8 3 h-lim-p 0.0000 0.0000 21.7723 h-lim-p: 2.41090481e-20 1.92872385e-19 2.17722650e+01 2836.103288 .. | 0/8 4 h-lim-p 0.0000 0.0040 24.8582 2835.911789 0 0.0006 61 | 0/8 5 h-lim-p 0.0014 0.0579 11.3912 2835.869727 6 0.0008 88 | 0/8 6 h-lim-p 0.0011 0.0390 8.1807 2835.846911 2 0.0010 104 | 0/8 7 h-lim-p 0.0010 0.0170 8.0764 2835.826118 0 0.0015 116 | 0/8 8 h-lim-p 0.0030 0.1107 4.1125 2835.815668 6 0.0020 143 | 0/8 9 h-lim-p 0.0040 0.0763 2.1219 2835.813260 3 0.0016 161 | 0/8 10 h-lim-p 0.0013 0.0108 1.3212 2835.811826 0 0.0027 174 | 0/8 11 h-lim-p 1.5720 20.0000 0.0023 2835.810731 5 0.9502 201 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2835.810730 0 1.0938 221 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2835.810730 0 1.0938 241 | 0/8 14 h-lim-p 1.0848 20.0000 0.0000 2835.810730 0 1.0848 261 | 0/8 15 h-lim-p 0.1928 20.0000 0.0001 2835.810730 0 0.0723 282 | 0/8 16 h-lim-p 0.0182 20.0000 0.0003 2835.810730 0 0.0182 302 | 0/8 17 h-lim-p 0.0073 10.9940 0.0006 2835.810730 0 0.0000 345 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 2835.810730 0 0.0000 369 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 | 0/8 21 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -2835.810730 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2835.810730 Node 7: lnL = -2835.810730 Node 8: lnL = -2835.810730 Node 9: lnL = -2835.810730 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 375 Sequential format.. Reading seq # 1: YJL025W_Sbay Reading seq # 2: YJL025W_Scer Reading seq # 3: YJL025W_Skud Reading seq # 4: YJL025W_Smik Reading seq # 5: YJL025W_Spar Sequences read.. Counting patterns.. # site patterns = 196 Counting frequencies.. 120 bytes for distance 31360 bytes for lkl0 25088 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.349382 0.000060 0.181998 0.149278 0.022295 0.204871 0.266233 0.070998 lnL0 = -1633.103573 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1633.103573 x= 0.34938 0.00006 0.18200 0.14928 0.02230 0.20487 0.26623 0.07100 1 h-lim-p 0.0012 0.0095 119.3020 1629.964161 8 0.0005 43 | 0/8 2 h-lim-p 0.0003 0.0027 84.3703 1627.702276 0 0.0010 56 | 0/8 3 h-lim-p 0.0004 0.0029 30.5198 1627.288549 0 0.0011 69 | 0/8 4 h-lim-p 0.0026 0.0206 8.7921 1627.251426 3 0.0011 87 | 0/8 5 h-lim-p 0.0066 0.2257 1.4349 1627.248981 5 0.0021 113 | 0/8 6 h-lim-p 0.0068 0.7429 0.4358 1627.246976 2 0.0064 129 | 0/8 7 h-lim-p 0.0213 0.6603 0.1306 1627.178069 0 0.0854 151 | 0/8 8 h-lim-p 0.0029 0.0432 3.8149 1627.109602 1 0.0037 173 | 0/8 9 h-lim-p 2.5000 20.0000 0.0027 1627.105578 3 1.1328 191 | 0/8 10 h-lim-p 2.5000 20.0000 0.0007 1627.105388 2 1.2402 215 | 0/8 11 h-lim-p 2.5000 20.0000 0.0001 1627.105382 1 1.0938 237 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1627.105382 0 1.0938 257 | 0/8 13 h-lim-p 1.8932 20.0000 0.0000 1627.105382 0 0.4733 278 | 0/8 14 h-lim-p 0.2460 20.0000 0.0000 1627.105382 0 0.0000 323 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -1627.105382 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1627.105382 Node 7: lnL = -1627.105382 Node 8: lnL = -1627.105382 Node 9: lnL = -1627.105382 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 158 Sequential format.. Reading seq # 1: YJL026W_Sbay Reading seq # 2: YJL026W_Scer Reading seq # 3: YJL026W_Skud Reading seq # 4: YJL026W_Smik Reading seq # 5: YJL026W_Spar Sequences read.. Counting patterns.. # site patterns = 55 Counting frequencies.. 120 bytes for distance 8800 bytes for lkl0 7040 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.810643 0.227796 0.047452 0.302894 0.385145 0.213952 3.363724 0.000060 lnL0 = -614.225186 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 614.225186 x= 0.81064 0.22780 0.04745 0.30289 0.38514 0.21395 3.36372 0.00006 1 h-lim-p 0.0000 0.0000 147.6848 614.108141 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0006 734.5416 573.393825 m 0.0006 37 | 2/8 3 h-lim-p 0.0001 0.0005 109.2766 572.734480 0 0.0001 50 | 2/8 4 h-lim-p 0.0004 0.0078 33.0012 568.155980 5 0.0059 76 | 2/8 5 h-lim-p 0.0010 0.0077 8.2211 567.738410 m 0.0077 88 | 2/8 6 h-lim-p 0.0511 20.0000 1.2332 564.834137 0 0.0766 100 | 2/8 7 h-lim-p 0.2804 2.2431 0.0462 563.962112 0 1.6823 114 | 1/8 8 h-lim-p 0.0008 0.0068 5.7311 563.952507 1 0.0011 134 | 1/8 9 h-lim-p 0.1027 0.8214 0.0257 563.567302 m 0.8214 146 | 1/8 10 h-lim-p 0.0000 0.0000 1.8139 h-lim-p: 1.13504899e-22 9.08039196e-22 1.81390843e+00 563.567302 .. | 1/8 11 h-lim-p 0.0000 0.0049 45.0774 563.172117 0 0.0005 178 | 1/8 12 h-lim-p 0.0010 0.0078 9.4743 563.145555 7 0.0006 207 | 1/8 13 h-lim-p 0.0012 0.6231 4.9391 563.131942 0 0.0017 219 | 1/8 14 h-lim-p 0.0086 0.5475 0.9946 563.130656 6 0.0027 246 | 1/8 15 h-lim-p 1.1495 12.1093 0.0024 563.125194 5 1.2409 277 | 1/8 16 h-lim-p 2.5000 20.0000 0.0003 563.125158 1 1.0938 298 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 563.125158 0 1.0938 317 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 563.125158 0 1.0938 336 | 1/8 19 h-lim-p 1.0767 20.0000 0.0000 563.125158 0 4.3070 357 | 1/8 20 h-lim-p 1.1226 20.0000 0.0000 563.125158 0 3.3677 377 | 1/8 21 h-lim-p 0.0202 4.9198 0.0027 563.125158 0 0.0000 408 | 1/8 22 h-lim-p 0.0001 20.0000 0.0000 563.125158 0 0.0000 438 | 1/8 23 h-lim-p 0.0000 20.0000 0.0002 | 1/8 24 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -563.125158 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -563.125158 Node 7: lnL = -563.125158 Node 8: lnL = -563.125158 Node 9: lnL = -563.125158 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 437 Sequential format.. Reading seq # 1: YJL030W_Sbay Reading seq # 2: YJL030W_Scer Reading seq # 3: YJL030W_Skud Reading seq # 4: YJL030W_Smik Reading seq # 5: YJL030W_Spar Sequences read.. Counting patterns.. # site patterns = 155 Counting frequencies.. 120 bytes for distance 24800 bytes for lkl0 19840 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.198550 0.101987 0.060198 0.073462 0.111261 0.149084 0.195759 0.000060 lnL0 = -1835.766141 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1835.766141 x= 0.19855 0.10199 0.06020 0.07346 0.11126 0.14908 0.19576 0.00006 1 h-lim-p 0.0000 0.0000 167.3062 1835.701664 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0019 66.0361 1835.049040 0 0.0003 39 | 1/8 3 h-lim-p 0.0007 0.0088 31.0579 1834.881544 8 0.0004 70 | 1/8 4 h-lim-p 0.0015 0.0263 9.1316 1834.855683 5 0.0006 93 | 1/8 5 h-lim-p 0.0047 0.1518 1.2020 1834.825495 5 0.0050 115 | 1/8 6 h-lim-p 0.0022 0.6426 2.6897 1834.378289 0 0.0088 129 | 1/8 7 h-lim-p 0.0018 0.0147 9.8744 1832.019619 0 0.0037 142 | 1/8 8 h-lim-p 0.0008 0.0070 44.3948 1830.701997 7 0.0009 171 | 1/8 9 h-lim-p 2.5000 20.0000 0.0100 1830.461894 2 1.1719 187 | 1/8 10 h-lim-p 2.5000 20.0000 0.0036 1830.442218 6 1.0092 217 | 1/8 11 h-lim-p 2.5000 20.0000 0.0005 1830.442006 3 0.8855 244 | 0/8 12 h-lim-p 0.0086 13.6450 0.0547 1830.442005 0 0.0009 265 | 0/8 13 h-lim-p 0.1411 1.1287 0.0001 1830.442000 m 1.1287 285 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 1830.441999 0 1.0938 305 | 1/8 15 h-lim-p 2.2649 20.0000 0.0000 1830.441999 0 0.9909 324 | 0/8 16 h-lim-p 0.0000 0.0000 0.0030 h-lim-p: 9.41410265e-20 7.53128212e-19 3.00600503e-03 1830.441999 .. | 1/8 17 h-lim-p 0.0000 20.0000 0.0075 1830.441999 0 0.0003 364 | 1/8 18 h-lim-p 0.0009 20.0000 0.0028 1830.441999 0 0.0007 383 | 1/8 19 h-lim-p 0.0012 20.0000 0.0018 1830.441999 0 0.0001 405 | 1/8 20 h-lim-p 0.0004 20.0000 0.0003 1830.441999 0 0.0018 426 | 1/8 21 h-lim-p 0.0100 20.0000 0.0001 1830.441999 0 0.0001 451 | 1/8 22 h-lim-p 0.0001 20.0000 0.0000 1830.441999 0 0.0001 470 | 1/8 23 h-lim-p 0.0004 20.0000 0.0000 1830.441999 0 0.0225 495 | 1/8 24 h-lim-p 0.0006 20.0000 0.0007 1830.441999 0 0.0005 514 | 1/8 25 h-lim-p 0.6516 20.0000 0.0000 1830.441999 0 0.1425 534 | 1/8 26 h-lim-p 0.1664 20.0000 0.0000 1830.441999 0 0.0104 556 | 1/8 27 h-lim-p 0.0105 20.0000 0.0000 1830.441999 0 0.0000 591 Out... lnL = -1830.441999 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1830.441999 Node 7: lnL = -1830.441999 Node 8: lnL = -1830.441999 Node 9: lnL = -1830.441999 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 513 Sequential format.. Reading seq # 1: YJL033W_Sbay Reading seq # 2: YJL033W_Scer Reading seq # 3: YJL033W_Skud Reading seq # 4: YJL033W_Smik Reading seq # 5: YJL033W_Spar Sequences read.. Counting patterns.. # site patterns = 182 Counting frequencies.. 120 bytes for distance 29120 bytes for lkl0 23296 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.181243 0.094448 0.063272 0.093847 0.063090 0.121738 0.169454 0.000060 lnL0 = -2013.388231 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2013.388231 x= 0.18124 0.09445 0.06327 0.09385 0.06309 0.12174 0.16945 0.00006 1 h-lim-p 0.0000 0.0000 112.5164 2013.334716 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0061 24.9738 2013.230040 0 0.0003 38 | 1/8 3 h-lim-p 0.0006 0.0186 11.9575 2013.210473 4 0.0003 59 | 1/8 4 h-lim-p 0.0009 0.0305 4.3326 2013.206836 4 0.0004 80 | 1/8 5 h-lim-p 0.0025 0.4069 0.6581 2013.196420 0 0.0049 93 | 1/8 6 h-lim-p 0.0016 0.1716 2.0490 2013.098211 0 0.0047 113 | 1/8 7 h-lim-p 0.0020 0.0372 4.8753 2012.142448 0 0.0060 126 | 1/8 8 h-lim-p 0.0008 0.0067 33.0107 2011.669477 8 0.0006 156 | 1/8 9 h-lim-p 2.5000 20.0000 0.0069 2011.581328 7 0.8293 185 | 0/8 10 h-lim-p 0.0068 1.2305 0.8395 2011.581123 4 0.0006 217 | 0/8 11 h-lim-p 0.6796 20.0000 0.0007 2011.580398 0 1.0193 237 | 0/8 12 h-lim-p 2.5000 20.0000 0.0001 2011.580372 1 0.9961 259 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2011.580372 0 1.0938 279 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 2011.580372 0 1.0938 299 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2011.580372 0 0.0000 341 Out... lnL = -2011.580372 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2011.580372 Node 7: lnL = -2011.580372 Node 8: lnL = -2011.580372 Node 9: lnL = -2011.580372 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 348 Sequential format.. Reading seq # 1: YJL035C_Sbay Reading seq # 2: YJL035C_Scer Reading seq # 3: YJL035C_Skud Reading seq # 4: YJL035C_Smik Reading seq # 5: YJL035C_Spar Sequences read.. Counting patterns.. # site patterns = 89 Counting frequencies.. 120 bytes for distance 14240 bytes for lkl0 11392 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.233357 0.050302 0.037741 0.118260 0.107329 0.118496 0.556112 0.000060 lnL0 = -1117.169868 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1117.169868 x= 0.23336 0.05030 0.03774 0.11826 0.10733 0.11850 0.55611 0.00006 1 h-lim-p 0.0000 0.0000 216.6938 1117.112089 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0012 121.5465 1114.216442 9 0.0005 64 | 1/8 3 h-lim-p 0.0003 0.0023 20.2027 1114.064853 0 0.0009 77 | 1/8 4 h-lim-p 0.0010 0.0080 8.2254 1113.754969 m 0.0080 89 | 2/8 5 h-lim-p 0.0008 0.0068 47.7884 1112.591768 0 0.0017 102 | 2/8 6 h-lim-p 0.0027 0.0357 29.5247 1111.965027 0 0.0041 114 | 2/8 7 h-lim-p 0.0013 0.0104 64.0178 1111.578191 5 0.0014 136 | 2/8 8 h-lim-p 0.1220 0.9759 0.1333 1105.383749 0 0.4880 150 | 1/8 9 h-lim-p 0.0141 1.1323 4.6263 1105.375261 5 0.0008 180 | 1/8 10 h-lim-p 0.0541 1.9386 0.0660 1105.149575 0 0.4328 195 | 1/8 11 h-lim-p 0.7453 19.8818 0.0383 1105.106604 0 1.1179 214 | 1/8 12 h-lim-p 2.5000 20.0000 0.0024 1105.104697 5 0.9394 243 | 1/8 13 h-lim-p 2.5000 20.0000 0.0005 1105.104682 2 0.6580 267 | 1/8 14 h-lim-p 1.6738 20.0000 0.0002 1105.104681 0 0.7323 286 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 1105.104681 0 0.6250 306 | 1/8 16 h-lim-p 1.1313 20.0000 0.0000 1105.104681 0 0.4949 325 | 1/8 17 h-lim-p 1.1779 20.0000 0.0000 1105.104681 0 0.0081 350 | 1/8 18 h-lim-p 0.0080 20.0000 0.0000 1105.104681 0 0.0000 379 Out... lnL = -1105.104681 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1105.104681 Node 7: lnL = -1105.104681 Node 8: lnL = -1105.104681 Node 9: lnL = -1105.104681 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 873 Sequential format.. Reading seq # 1: YJL036W_Sbay Reading seq # 2: YJL036W_Scer Reading seq # 3: YJL036W_Skud Reading seq # 4: YJL036W_Smik Reading seq # 5: YJL036W_Spar Sequences read.. Counting patterns.. # site patterns = 385 Counting frequencies.. 120 bytes for distance 61600 bytes for lkl0 49280 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.328803 0.021620 0.137260 0.169943 0.088205 0.278448 0.355669 0.002908 lnL0 = -4250.760158 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4250.760158 x= 0.32880 0.02162 0.13726 0.16994 0.08821 0.27845 0.35567 0.00291 1 h-lim-p 0.0014 0.7107 250.8609 4243.830776 8 0.0002 42 | 0/8 2 h-lim-p 0.0007 0.0057 52.6043 4242.848423 3 0.0007 60 | 0/8 3 h-lim-p 0.0006 0.0051 31.9393 4242.650776 5 0.0005 82 | 0/8 4 h-lim-p 0.0011 0.0244 14.2269 4242.591020 6 0.0007 108 | 0/8 5 h-lim-p 0.0036 0.0987 2.9904 4242.588098 4 0.0007 129 | 0/8 6 h-lim-p 0.0076 0.1546 0.2751 4242.588059 1 0.0008 145 | 0/8 7 h-lim-p 0.0030 4.7686 0.0760 4242.587992 0 0.0045 165 | 0/8 8 h-lim-p 0.0193 20.0000 0.0178 4242.573915 0 0.2316 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 4242.573361 3 1.0004 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4242.573360 0 1.0938 234 | 0/8 11 h-lim-p 2.0032 20.0000 0.0000 4242.573360 0 1.0016 254 | 0/8 12 h-lim-p 0.8030 20.0000 0.0000 4242.573360 0 0.0004 284 | 0/8 13 h-lim-p 0.0001 20.0000 0.0001 4242.573360 0 0.0000 314 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 4242.573360 0 0.0000 342 Out... lnL = -4242.573360 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4242.573360 Node 7: lnL = -4242.573360 Node 8: lnL = -4242.573360 Node 9: lnL = -4242.573360 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 839 Sequential format.. Reading seq # 1: YJL039C_Sbay Reading seq # 2: YJL039C_Scer Reading seq # 3: YJL039C_Skud Reading seq # 4: YJL039C_Smik Reading seq # 5: YJL039C_Spar Sequences read.. Counting patterns.. # site patterns = 304 Counting frequencies.. 120 bytes for distance 48640 bytes for lkl0 38912 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.238402 0.111446 0.076547 0.151428 0.103952 0.192920 0.194109 0.000060 lnL0 = -3788.410677 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3788.410677 x= 0.23840 0.11145 0.07655 0.15143 0.10395 0.19292 0.19411 0.00006 1 h-lim-p 0.0000 0.0000 163.9689 3788.310525 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0064 27.2632 3788.182190 0 0.0004 38 | 1/8 3 h-lim-p 0.0011 0.0411 9.0900 3788.170760 5 0.0003 62 | 1/8 4 h-lim-p 0.0007 0.0801 3.6170 3788.164415 2 0.0007 78 | 1/8 5 h-lim-p 0.0032 1.0289 0.7386 3788.067027 0 0.0128 92 | 1/8 6 h-lim-p 0.0024 0.0350 3.9653 3786.737396 0 0.0072 112 | 0/8 7 h-lim-p 0.0006 0.0046 44.3132 3785.043395 1 0.0007 126 | 0/8 8 h-lim-p 0.0001 0.0005 20.6816 3784.936976 m 0.0005 138 | 0/8 9 h-lim-p -0.0000 -0.0000 3.9323 h-lim-p: -4.26727684e-20 -3.41382147e-19 3.93227211e+00 3784.936976 .. | 0/8 10 h-lim-p 0.0000 0.0651 39.4995 3784.819550 0 0.0002 162 | 0/8 11 h-lim-p 0.0007 0.0085 9.1173 3784.804508 6 0.0004 189 | 0/8 12 h-lim-p 0.0000 0.0004 2.7040 3784.803637 0 0.0003 203 | 0/8 13 h-lim-p 0.0016 0.5969 0.5164 3784.803591 0 0.0003 216 | 0/8 14 h-lim-p 0.0002 0.0019 0.1201 3784.803590 0 0.0002 236 | 0/8 15 h-lim-p 0.0001 0.0007 0.2815 3784.803589 0 0.0003 258 | 0/8 16 h-lim-p 0.0000 0.0000 111.9293 3784.803589 0 0.0000 278 | 0/8 17 h-lim-p 0.0006 0.1114 0.0192 3784.803589 0 0.0012 291 | 0/8 18 h-lim-p 0.0329 0.5790 0.0007 3784.803378 2 0.4193 318 | 0/8 19 h-lim-p 0.2822 2.2573 0.0003 3784.803370 0 0.2469 338 | 0/8 20 h-lim-p 0.4121 3.2966 0.0000 3784.803370 0 0.0000 372 | 0/8 21 h-lim-p 0.0000 1.0985 0.0000 3784.803370 0 0.0000 392 | 0/8 22 h-lim-p 0.0000 0.5060 0.0001 3784.803370 0 0.0000 418 | 0/8 23 h-lim-p 0.0000 20.0000 0.0000 3784.803370 0 0.3277 453 | 0/8 24 h-lim-p 0.8380 7.8845 0.0000 3784.803370 0 0.0917 475 | 0/8 25 h-lim-p 0.0684 4.6520 0.0000 3784.803370 0 0.0000 522 Out... lnL = -3784.803370 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3784.803370 Node 7: lnL = -3784.803370 Node 8: lnL = -3784.803370 Node 9: lnL = -3784.803370 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 382 Sequential format.. Reading seq # 1: YJL041W_Sbay Reading seq # 2: YJL041W_Scer Reading seq # 3: YJL041W_Skud Reading seq # 4: YJL041W_Smik Reading seq # 5: YJL041W_Spar Sequences read.. Counting patterns.. # site patterns = 215 Counting frequencies.. 120 bytes for distance 34400 bytes for lkl0 27520 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.658683 0.234115 0.000060 0.938716 0.592466 0.539981 0.517376 0.077869 lnL0 = -2243.675247 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2243.675247 x= 0.65868 0.23412 0.00006 0.93872 0.59247 0.53998 0.51738 0.07787 1 h-lim-p 0.0000 0.0000 197.1672 2243.637402 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0007 183.8447 2229.582486 m 0.0007 38 | 2/8 3 h-lim-p 0.0008 0.0063 42.6916 2206.675751 m 0.0063 50 | 3/8 4 h-lim-p 0.0017 0.0134 62.2527 2152.215772 0 0.0101 64 | 3/8 5 h-lim-p 0.0003 0.0028 102.4655 2147.784178 0 0.0014 78 | 3/8 6 h-lim-p 0.0053 0.0426 19.3550 2147.066223 9 0.0031 112 | 2/8 7 h-lim-p 0.0004 0.0083 142.2334 2121.185317 8 0.0056 148 | 2/8 8 h-lim-p 0.0220 0.1762 1.5483 2112.333015 0 0.0881 162 | 2/8 9 h-lim-p 0.0699 0.5594 0.5744 2106.816360 m 0.5594 174 | 3/8 10 h-lim-p 0.7913 6.3306 0.2076 2106.100454 8 0.5370 210 | 3/8 11 h-lim-p 1.7329 17.4097 0.0643 2104.723121 1 2.1661 229 | 2/8 12 h-lim-p 0.0255 0.2974 5.4575 2104.581362 6 0.0145 261 | 2/8 13 h-lim-p 0.7229 11.0405 0.1094 2103.819741 0 1.4459 274 | 2/8 14 h-lim-p 2.5000 20.0000 0.0496 2103.706353 3 1.0449 298 | 2/8 15 h-lim-p 2.5000 20.0000 0.0149 2103.698931 6 0.7833 332 | 2/8 16 h-lim-p 2.2153 20.0000 0.0053 2103.698400 2 0.9692 354 | 2/8 17 h-lim-p 2.5000 20.0000 0.0013 2103.698359 1 0.9961 374 | 2/8 18 h-lim-p 2.5000 20.0000 0.0001 2103.698359 0 1.0938 392 | 2/8 19 h-lim-p 2.5000 20.0000 0.0000 2103.698359 0 1.0938 410 | 2/8 20 h-lim-p 2.5000 20.0000 0.0000 2103.698359 0 2.1875 428 | 2/8 21 h-lim-p 1.7271 20.0000 0.0000 2103.698359 0 0.7556 446 | 2/8 22 h-lim-p 2.2019 20.0000 0.0000 2103.698359 0 0.0688 468 | 2/8 23 h-lim-p 0.0494 20.0000 0.0000 2103.698359 0 0.0124 487 Out... lnL = -2103.698359 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2103.698359 Node 7: lnL = -2103.698359 Node 8: lnL = -2103.698359 Node 9: lnL = -2103.698359 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 510 Sequential format.. Reading seq # 1: YJL043W_Sbay Reading seq # 2: YJL043W_Scer Reading seq # 3: YJL043W_Skud Reading seq # 4: YJL043W_Smik Reading seq # 5: YJL043W_Spar Sequences read.. Counting patterns.. # site patterns = 216 Counting frequencies.. 120 bytes for distance 34560 bytes for lkl0 27648 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.465578 0.054776 0.049682 0.121100 0.096584 0.226829 0.244394 0.141768 lnL0 = -2159.801774 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2159.801774 x= 0.46558 0.05478 0.04968 0.12110 0.09658 0.22683 0.24439 0.14177 1 h-lim-p 0.0041 0.1039 102.1438 2158.278602 8 0.0003 44 | 0/8 2 h-lim-p 0.0013 0.0106 12.8098 2158.239175 6 0.0005 70 | 0/8 3 h-lim-p 0.0009 0.0506 6.9299 2158.223089 2 0.0008 86 | 0/8 4 h-lim-p 0.0015 0.0840 3.8843 2158.216136 3 0.0012 104 | 0/8 5 h-lim-p 0.0040 0.2175 1.2199 2158.215612 3 0.0008 123 | 0/8 6 h-lim-p 0.0055 1.5702 0.1848 2158.215589 1 0.0014 138 | 0/8 7 h-lim-p 0.0085 15.1056 0.0297 2158.215588 0 0.0021 159 | 0/8 8 h-lim-p 0.2327 20.0000 0.0003 2158.215499 0 0.9307 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2158.215495 0 1.0938 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2158.215495 0 1.0938 221 | 0/8 11 h-lim-p 1.7388 20.0000 0.0000 2158.215495 0 0.7607 241 | 0/8 12 h-lim-p 0.5289 20.0000 0.0000 2158.215495 0 0.0000 276 Out... lnL = -2158.215495 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2158.215495 Node 7: lnL = -2158.215495 Node 8: lnL = -2158.215495 Node 9: lnL = -2158.215495 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 522 Sequential format.. Reading seq # 1: YJL044C_Sbay Reading seq # 2: YJL044C_Scer Reading seq # 3: YJL044C_Skud Reading seq # 4: YJL044C_Smik Reading seq # 5: YJL044C_Spar Sequences read.. Counting patterns.. # site patterns = 221 Counting frequencies.. 120 bytes for distance 35360 bytes for lkl0 28288 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.450314 0.076604 0.029418 0.114987 0.099624 0.232222 0.304547 0.120255 lnL0 = -2247.525976 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2247.525976 x= 0.45031 0.07660 0.02942 0.11499 0.09962 0.23222 0.30455 0.12026 1 h-lim-p 0.0005 0.0037 76.5594 2246.518679 5 0.0004 31 | 0/8 2 h-lim-p 0.0005 0.0039 27.8964 2246.357375 2 0.0005 47 | 0/8 3 h-lim-p 0.0012 0.0096 9.7654 2246.337398 4 0.0005 67 | 0/8 4 h-lim-p 0.0010 0.0515 4.4838 2246.330423 4 0.0008 88 | 0/8 5 h-lim-p 0.0028 0.0837 1.3390 2246.329147 5 0.0016 113 | 0/8 6 h-lim-p 0.0027 0.3508 0.7937 2246.328763 4 0.0016 137 | 0/8 7 h-lim-p 0.0103 2.8666 0.1267 2246.328745 1 0.0021 160 | 0/8 8 h-lim-p 0.3299 20.0000 0.0008 2246.327986 0 1.3196 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 2246.327913 2 0.9961 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2246.327913 0 1.0938 226 | 0/8 11 h-lim-p 1.4861 20.0000 0.0000 2246.327913 0 0.3251 247 | 0/8 12 h-lim-p 0.1661 20.0000 0.0000 2246.327913 0 0.0208 269 | 0/8 13 h-lim-p 0.0113 20.0000 0.0000 2246.327913 0 0.0004 293 | 0/8 14 h-lim-p 0.0004 20.0000 0.0000 2246.327913 0 0.0000 321 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 2246.327913 0 0.0000 344 Out... lnL = -2246.327913 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2246.327913 Node 7: lnL = -2246.327913 Node 8: lnL = -2246.327913 Node 9: lnL = -2246.327913 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 1089 Sequential format.. Reading seq # 1: YJL045W_Sbay Reading seq # 2: YJL045W_Scer Reading seq # 3: YJL045W_Skud Reading seq # 4: YJL045W_Smik Reading seq # 5: YJL045W_Spar Sequences read.. Counting patterns.. # site patterns = 436 Counting frequencies.. 120 bytes for distance 69760 bytes for lkl0 55808 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.284192 0.106000 0.083484 0.168546 0.230555 0.285181 0.227087 0.000060 lnL0 = -4780.875528 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4780.875528 x= 0.28419 0.10600 0.08348 0.16855 0.23056 0.28518 0.22709 0.00006 1 h-lim-p 0.0000 0.0000 132.2519 4780.841985 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0045 59.6872 4780.320011 0 0.0003 39 | 1/8 3 h-lim-p 0.0019 0.0181 10.0156 4780.292346 6 0.0005 65 | 1/8 4 h-lim-p 0.0040 0.1334 1.3618 4780.279741 4 0.0028 86 | 1/8 5 h-lim-p 0.0015 0.1518 2.4923 4780.213505 0 0.0031 99 | 1/8 6 h-lim-p 0.0028 0.0967 2.7632 4778.244896 0 0.0166 113 | 1/8 7 h-lim-p 0.0012 0.0109 38.0980 4776.763838 6 0.0012 138 | 1/8 8 h-lim-p 0.0067 0.0537 5.1002 4776.754037 3 0.0008 158 | 0/8 9 h-lim-p 0.0003 0.0921 12.3925 4776.710122 0 0.0006 171 | 0/8 10 h-lim-p 1.4569 20.0000 0.0053 4776.677900 4 1.1425 191 | 0/8 11 h-lim-p 2.5000 20.0000 0.0005 4776.677565 2 1.1719 215 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4776.677563 0 1.0938 235 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 4776.677563 0 1.0938 255 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 4776.677563 0 1.0938 275 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 4776.677563 0 0.3125 297 | 0/8 16 h-lim-p 0.0262 20.0000 0.0000 4776.677563 0 0.0033 319 Out... lnL = -4776.677563 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4776.677563 Node 7: lnL = -4776.677563 Node 8: lnL = -4776.677563 Node 9: lnL = -4776.677563 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 159 Sequential format.. Reading seq # 1: YJL047C_Sbay Reading seq # 2: YJL047C_Scer Reading seq # 3: YJL047C_Skud Reading seq # 4: YJL047C_Smik Reading seq # 5: YJL047C_Spar Sequences read.. Counting patterns.. # site patterns = 97 Counting frequencies.. 120 bytes for distance 15520 bytes for lkl0 12416 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.356325 0.122492 0.062262 0.154359 0.091728 0.233218 0.118869 0.066923 lnL0 = -713.084042 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 713.084042 x= 0.35633 0.12249 0.06226 0.15436 0.09173 0.23322 0.11887 0.06692 1 h-lim-p 0.0005 0.0037 31.5677 712.385863 0 0.0014 23 | 0/8 2 h-lim-p 0.0020 0.0161 13.2923 712.241849 2 0.0019 39 | 0/8 3 h-lim-p 0.0023 0.0182 8.1340 712.200420 7 0.0017 68 | 0/8 4 h-lim-p 0.0031 0.0756 4.4187 712.189685 4 0.0015 88 | 0/8 5 h-lim-p 0.0177 0.8294 0.3839 712.189473 4 0.0029 110 | 0/8 6 h-lim-p 0.0098 1.6366 0.1145 712.189462 2 0.0019 135 | 0/8 7 h-lim-p 0.0098 17.2870 0.0221 712.189461 0 0.0049 155 | 0/8 8 h-lim-p 0.1378 20.0000 0.0008 712.189347 0 0.5512 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 712.189346 1 0.9961 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 712.189346 0 1.0938 219 | 0/8 11 h-lim-p 1.3571 20.0000 0.0000 712.189346 0 2.0357 239 | 0/8 12 h-lim-p 0.6740 20.0000 0.0000 712.189346 0 0.3370 259 | 0/8 13 h-lim-p 0.0072 20.0000 0.0004 712.189346 0 0.0000 290 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 712.189346 0 0.0001 310 Out... lnL = -712.189346 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -712.189346 Node 7: lnL = -712.189346 Node 8: lnL = -712.189346 Node 9: lnL = -712.189346 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 474 Sequential format.. Reading seq # 1: YJL048C_Sbay Reading seq # 2: YJL048C_Scer Reading seq # 3: YJL048C_Skud Reading seq # 4: YJL048C_Smik Reading seq # 5: YJL048C_Spar Sequences read.. Counting patterns.. # site patterns = 187 Counting frequencies.. 120 bytes for distance 29920 bytes for lkl0 23936 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.264983 0.017337 0.111827 0.084898 0.072704 0.184176 0.167150 0.034849 lnL0 = -1940.173992 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1940.173992 x= 0.26498 0.01734 0.11183 0.08490 0.07270 0.18418 0.16715 0.03485 1 h-lim-p 0.0015 0.0502 159.9040 1937.393235 9 0.0003 45 | 0/8 2 h-lim-p 0.0007 0.0058 36.6703 1936.908267 4 0.0007 65 | 0/8 3 h-lim-p 0.0023 0.0300 11.6908 1936.892545 4 0.0003 86 | 0/8 4 h-lim-p 0.0011 0.0833 2.8173 1936.889711 5 0.0008 110 | 0/8 5 h-lim-p 0.0029 0.1826 0.7407 1936.889598 4 0.0004 135 | 0/8 6 h-lim-p 0.0020 1.0461 0.1652 1936.889588 2 0.0006 160 | 0/8 7 h-lim-p 0.0103 11.5116 0.0103 1936.889588 0 0.0023 181 | 0/8 8 h-lim-p 0.0596 20.0000 0.0004 1936.889534 0 0.7156 204 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1936.889531 0 1.0938 224 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1936.889531 0 2.1875 244 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1936.889531 0 1.0938 264 | 0/8 12 h-lim-p 0.0740 20.0000 0.0000 1936.889531 0 0.0000 300 | 0/8 13 h-lim-p 0.0004 20.0000 0.0000 1936.889531 0 0.0000 336 Out... lnL = -1936.889531 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1936.889531 Node 7: lnL = -1936.889531 Node 8: lnL = -1936.889531 Node 9: lnL = -1936.889531 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 270 Sequential format.. Reading seq # 1: YJL049W_Sbay Reading seq # 2: YJL049W_Scer Reading seq # 3: YJL049W_Skud Reading seq # 4: YJL049W_Smik Reading seq # 5: YJL049W_Spar Sequences read.. Counting patterns.. # site patterns = 146 Counting frequencies.. 120 bytes for distance 23360 bytes for lkl0 18688 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.305689 0.011864 0.060383 0.201405 0.224996 0.217038 0.315591 0.000060 lnL0 = -1223.087709 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1223.087709 x= 0.30569 0.01186 0.06038 0.20140 0.22500 0.21704 0.31559 0.00006 1 h-lim-p 0.0057 0.0455 32.6536 1222.758589 2 0.0007 28 | 0/8 2 h-lim-p 0.0001 0.0005 15.0465 1222.679953 m 0.0005 40 | 1/8 3 h-lim-p 0.0016 0.0357 4.4854 1222.668169 3 0.0013 58 | 1/8 4 h-lim-p 0.0046 0.2310 1.2744 1222.666174 4 0.0024 79 | 1/8 5 h-lim-p 0.0269 1.1211 0.1137 1222.662910 4 0.0296 101 | 1/8 6 h-lim-p 0.0094 0.1969 0.3570 1222.613651 0 0.0377 122 | 1/8 7 h-lim-p 0.0078 0.1951 1.7180 1222.606129 2 0.0037 145 | 1/8 8 h-lim-p 0.0230 1.2295 0.2740 1222.583007 0 0.0346 157 | 1/8 9 h-lim-p 0.0060 0.3890 1.5864 1222.578105 5 0.0030 189 | 1/8 10 h-lim-p 1.7720 20.0000 0.0027 1222.575728 5 0.9624 212 | 1/8 11 h-lim-p 2.5000 20.0000 0.0001 1222.575727 0 1.0938 231 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 1222.575727 0 1.0938 250 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 1222.575727 0 1.0938 269 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 1222.575727 0 3.7500 288 | 1/8 15 h-lim-p 1.3630 20.0000 0.0000 1222.575727 0 0.2982 308 | 1/8 16 h-lim-p 0.4249 20.0000 0.0000 1222.575727 0 0.1062 328 | 1/8 17 h-lim-p 0.1188 20.0000 0.0000 1222.575727 0 0.1188 347 | 1/8 18 h-lim-p 0.1348 20.0000 0.0000 1222.575727 0 0.0021 371 Out... lnL = -1222.575727 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1222.575727 Node 7: lnL = -1222.575727 Node 8: lnL = -1222.575727 Node 9: lnL = -1222.575727 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 421 Sequential format.. Reading seq # 1: YJL052W_Sbay Reading seq # 2: YJL052W_Scer Reading seq # 3: YJL052W_Skud Reading seq # 4: YJL052W_Smik Reading seq # 5: YJL052W_Spar Sequences read.. Counting patterns.. # site patterns = 122 Counting frequencies.. 120 bytes for distance 19520 bytes for lkl0 15616 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.188514 0.053759 0.043980 0.097553 0.097505 0.156613 0.134223 0.000060 lnL0 = -1333.560592 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1333.560592 x= 0.18851 0.05376 0.04398 0.09755 0.09750 0.15661 0.13422 0.00006 1 h-lim-p 0.0000 0.0000 80.1617 1333.384979 m 0.0000 22 | 1/8 2 h-lim-p 0.0002 0.0099 13.8484 1333.323513 0 0.0007 36 | 1/8 3 h-lim-p 0.0016 0.0177 5.7082 1333.314793 6 0.0006 63 | 1/8 4 h-lim-p 0.0038 0.2785 0.8843 1333.312503 6 0.0021 89 | 0/8 5 h-lim-p 0.0006 0.1324 2.9728 1333.290646 0 0.0051 111 | 0/8 6 h-lim-p 0.0025 0.0425 6.0686 1333.274950 7 0.0015 139 | 0/8 7 h-lim-p 0.0086 0.3183 1.0322 1333.247971 6 0.0062 165 | 0/8 8 h-lim-p 0.0032 0.0255 1.3902 1332.725676 m 0.0255 177 | 0/8 9 h-lim-p -0.0000 -0.0000 21.7243 h-lim-p: -1.81640646e-20 -1.45312517e-19 2.17243206e+01 1332.725676 .. | 0/8 10 h-lim-p 0.0000 0.0219 29.6656 1332.548602 0 0.0005 202 | 0/8 11 h-lim-p 0.0036 0.0288 2.8878 1332.546308 5 0.0006 229 | 0/8 12 h-lim-p 0.0016 0.2781 1.0187 1332.545956 2 0.0007 245 | 0/8 13 h-lim-p 0.0013 0.0102 0.2857 1332.545932 0 0.0006 257 | 0/8 14 h-lim-p 0.0033 3.8078 0.0489 1332.545921 1 0.0029 279 | 0/8 15 h-lim-p 0.0049 0.0995 0.0288 1332.545709 0 0.0194 301 | 0/8 16 h-lim-p 0.0029 0.5533 0.1918 1332.543806 0 0.0088 322 | 0/8 17 h-lim-p 0.0015 0.0133 1.1107 1332.542949 5 0.0009 355 | 0/8 18 h-lim-p 2.5000 20.0000 0.0003 1332.542880 2 0.9961 371 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1332.542880 0 1.0938 391 | 0/8 20 h-lim-p 1.0369 20.0000 0.0000 1332.542880 0 3.1106 412 | 0/8 21 h-lim-p 0.4807 9.4807 0.0001 1332.542880 0 0.0300 435 | 0/8 22 h-lim-p 0.0020 0.6399 0.0022 1332.542880 0 0.0008 456 | 0/8 23 h-lim-p 0.0004 0.3350 0.0042 1332.542880 0 0.0000 487 | 0/8 24 h-lim-p 0.0001 20.0000 0.0000 1332.542880 0 0.0000 521 Out... lnL = -1332.542880 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1332.542880 Node 7: lnL = -1332.542880 Node 8: lnL = -1332.542880 Node 9: lnL = -1332.542880 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 206 Sequential format.. Reading seq # 1: YJL053W_Sbay Reading seq # 2: YJL053W_Scer Reading seq # 3: YJL053W_Skud Reading seq # 4: YJL053W_Smik Reading seq # 5: YJL053W_Spar Sequences read.. Counting patterns.. # site patterns = 73 Counting frequencies.. 120 bytes for distance 11680 bytes for lkl0 9344 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.203188 0.048024 0.052788 0.078081 0.041489 0.119414 0.082235 0.039114 lnL0 = -769.285318 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 769.285318 x= 0.20319 0.04802 0.05279 0.07808 0.04149 0.11941 0.08223 0.03911 1 h-lim-p 0.0005 0.0041 47.2310 768.772926 2 0.0005 26 | 0/8 2 h-lim-p 0.0007 0.0052 17.7363 768.709462 7 0.0004 55 | 0/8 3 h-lim-p 0.0016 0.0378 4.9369 768.705524 5 0.0004 77 | 0/8 4 h-lim-p 0.0012 0.0971 1.3985 768.704997 2 0.0006 93 | 0/8 5 h-lim-p 0.0072 1.1924 0.1144 768.704993 2 0.0006 112 | 0/8 6 h-lim-p 0.0050 5.7271 0.0132 768.704992 0 0.0022 132 | 0/8 7 h-lim-p 0.0083 19.9833 0.0035 768.704839 0 0.1320 156 | 0/8 8 h-lim-p 0.0018 0.5364 0.2606 768.704699 2 0.0016 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 768.704698 0 1.0938 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 768.704698 0 1.0938 220 | 0/8 11 h-lim-p 0.4957 20.0000 0.0000 768.704698 0 0.0019 247 | 0/8 12 h-lim-p 0.0008 20.0000 0.0000 768.704698 0 0.0000 278 | 0/8 13 h-lim-p 0.0000 20.0000 0.0014 768.704698 0 0.0000 310 | 0/8 14 h-lim-p 0.0000 20.0000 0.0014 | 0/8 15 h-lim-p 0.0000 20.0000 0.0014 Out... lnL = -768.704698 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -768.704698 Node 7: lnL = -768.704698 Node 8: lnL = -768.704698 Node 9: lnL = -768.704698 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 295 Sequential format.. Reading seq # 1: YJL058C_Sbay Reading seq # 2: YJL058C_Scer Reading seq # 3: YJL058C_Skud Reading seq # 4: YJL058C_Smik Reading seq # 5: YJL058C_Spar Sequences read.. Counting patterns.. # site patterns = 110 Counting frequencies.. 120 bytes for distance 17600 bytes for lkl0 14080 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.201876 0.098975 0.071652 0.029072 0.075276 0.101228 0.238162 0.000060 lnL0 = -1012.150415 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1012.150415 x= 0.20188 0.09898 0.07165 0.02907 0.07528 0.10123 0.23816 0.00006 1 h-lim-p 0.0001 0.0007 35.2446 1011.894081 0 0.0003 24 | 0/8 2 h-lim-p 0.0000 0.0000 24.6392 1011.884072 m 0.0000 36 | 1/8 3 h-lim-p 0.0000 0.0190 16.2417 1011.817413 0 0.0011 53 | 1/8 4 h-lim-p 0.0023 0.0334 7.8203 1011.797497 4 0.0009 73 | 1/8 5 h-lim-p 0.0022 0.0558 3.2612 1011.795171 2 0.0005 90 | 1/8 6 h-lim-p 0.0036 0.3354 0.4935 1011.794796 4 0.0018 111 | 1/8 7 h-lim-p 0.0032 1.8868 0.2831 1011.793540 0 0.0064 131 | 1/8 8 h-lim-p 0.0184 0.9748 0.0978 1011.740386 0 0.0736 152 | 1/8 9 h-lim-p 0.7538 6.0301 0.0063 1011.723417 5 0.4279 184 | 0/8 10 h-lim-p 0.0793 20.0000 0.0342 1011.723415 1 0.0020 209 | 0/8 11 h-lim-p 0.1509 1.2068 0.0002 1011.723368 0 0.9051 231 | 0/8 12 h-lim-p 0.0365 0.2916 0.0001 1011.723368 m 0.2916 251 | 1/8 13 h-lim-p 0.0115 20.0000 0.0012 1011.723368 0 0.0230 272 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 1011.723368 0 1.0938 291 | 1/8 15 h-lim-p 1.8512 20.0000 0.0000 1011.723368 0 0.0000 330 Out... lnL = -1011.723368 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1011.723368 Node 7: lnL = -1011.723368 Node 8: lnL = -1011.723368 Node 9: lnL = -1011.723368 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 323 Sequential format.. Reading seq # 1: YJL062W-A_Sbay Reading seq # 2: YJL062W-A_Scer Reading seq # 3: YJL062W-A_Skud Reading seq # 4: YJL062W-A_Smik Reading seq # 5: YJL062W-A_Spar Sequences read.. Counting patterns.. # site patterns = 135 Counting frequencies.. 120 bytes for distance 21600 bytes for lkl0 17280 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.262987 0.150836 0.184610 0.086881 0.111209 0.182022 0.190541 0.000060 lnL0 = -1290.338391 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1290.338391 x= 0.26299 0.15084 0.18461 0.08688 0.11121 0.18202 0.19054 0.00006 1 h-lim-p 0.0000 0.0000 101.1895 1290.308692 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0053 47.5054 1289.560347 0 0.0010 40 | 1/8 3 h-lim-p 0.0049 0.0392 7.4469 1289.507940 7 0.0016 69 | 1/8 4 h-lim-p 0.0058 0.1525 2.1194 1289.453268 1 0.0072 83 | 1/8 5 h-lim-p 0.0098 0.2094 1.5557 1288.728748 0 0.0295 96 | 1/8 6 h-lim-p 0.0014 0.0110 10.4161 1286.183138 0 0.0055 110 | 1/8 7 h-lim-p 0.0025 0.0204 13.9645 1285.996865 6 0.0019 136 | 1/8 8 h-lim-p 0.0199 0.2033 1.3130 1285.992752 6 0.0030 167 | 1/8 9 h-lim-p 0.0686 4.1614 0.0580 1285.674410 0 0.4118 181 | 0/8 10 h-lim-p 0.0258 4.3245 0.9268 1285.673808 3 0.0014 210 | 0/8 11 h-lim-p 0.2676 3.8494 0.0047 1285.666113 0 0.8028 231 | 0/8 12 h-lim-p 2.5000 20.0000 0.0007 1285.665855 4 0.9422 259 | 0/8 13 h-lim-p 2.5000 20.0000 0.0001 1285.665852 1 0.6152 282 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1285.665852 0 1.0938 302 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1285.665852 0 1.0938 322 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1285.665852 0 2.1875 342 | 0/8 17 h-lim-p 1.8119 20.0000 0.0000 1285.665852 0 0.7927 362 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1285.665852 0 0.0012 392 Out... lnL = -1285.665852 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1285.665852 Node 7: lnL = -1285.665852 Node 8: lnL = -1285.665852 Node 9: lnL = -1285.665852 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 278 Sequential format.. Reading seq # 1: YJL063C_Sbay Reading seq # 2: YJL063C_Scer Reading seq # 3: YJL063C_Skud Reading seq # 4: YJL063C_Smik Reading seq # 5: YJL063C_Spar Sequences read.. Counting patterns.. # site patterns = 125 Counting frequencies.. 120 bytes for distance 20000 bytes for lkl0 16000 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.264045 0.116726 0.164492 0.084648 0.086586 0.182486 0.215279 0.000060 lnL0 = -1195.561816 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1195.561816 x= 0.26404 0.11673 0.16449 0.08465 0.08659 0.18249 0.21528 0.00006 1 h-lim-p 0.0000 0.0000 69.3834 1195.500891 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0145 29.2220 1195.249185 0 0.0007 38 | 1/8 3 h-lim-p 0.0024 0.0426 8.6328 1195.194997 6 0.0015 66 | 1/8 4 h-lim-p 0.0087 0.1876 1.5011 1195.181905 2 0.0041 82 | 1/8 5 h-lim-p 0.0086 0.3773 0.7101 1194.922942 0 0.0345 96 | 1/8 6 h-lim-p 0.0018 0.0147 8.8862 1194.208022 0 0.0037 116 | 1/8 7 h-lim-p 0.0017 0.0140 12.9948 1193.736458 0 0.0035 129 | 1/8 8 h-lim-p 0.0114 0.0915 3.2888 1193.727524 6 0.0016 159 | 1/8 9 h-lim-p 0.5099 20.0000 0.0106 1193.667990 0 1.0197 172 | 0/8 10 h-lim-p 0.0106 1.2755 1.0168 1193.666982 4 0.0019 202 | 0/8 11 h-lim-p 0.7636 6.1085 0.0023 1193.660447 0 1.1453 214 | 0/8 12 h-lim-p 2.5000 20.0000 0.0003 1193.660387 3 0.9482 240 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1193.660387 0 1.0938 260 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1193.660387 0 1.0938 280 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1193.660387 0 1.0938 300 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1193.660387 0 2.5000 320 | 0/8 17 h-lim-p 1.2490 20.0000 0.0000 1193.660387 0 1.0928 340 | 0/8 18 h-lim-p 0.0198 20.0000 0.0000 1193.660387 0 0.0025 362 | 0/8 19 h-lim-p 0.0009 20.0000 0.0000 1193.660387 0 0.0001 384 | 0/8 20 h-lim-p 0.0001 20.0000 0.0000 1193.660387 0 0.0000 415 | 0/8 21 h-lim-p 0.0000 20.0000 0.0000 1193.660387 0 0.0000 444 | 0/8 22 h-lim-p 0.0000 20.0000 0.0000 1193.660387 0 0.0000 471 | 0/8 23 h-lim-p 0.0000 20.0000 0.0000 | 0/8 24 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1193.660387 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1193.660387 Node 7: lnL = -1193.660387 Node 8: lnL = -1193.660387 Node 9: lnL = -1193.660387 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 212 Sequential format.. Reading seq # 1: YJL065C_Sbay Reading seq # 2: YJL065C_Scer Reading seq # 3: YJL065C_Skud Reading seq # 4: YJL065C_Smik Reading seq # 5: YJL065C_Spar Sequences read.. Counting patterns.. # site patterns = 103 Counting frequencies.. 120 bytes for distance 16480 bytes for lkl0 13184 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.247093 0.182205 0.064013 0.104931 0.080161 0.153186 0.097395 0.004535 lnL0 = -897.825707 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 897.825707 x= 0.24709 0.18220 0.06401 0.10493 0.08016 0.15319 0.09740 0.00453 1 h-lim-p 0.0002 0.0019 81.2304 895.057506 0 0.0009 24 | 0/8 2 h-lim-p 0.0011 0.0090 24.3570 894.672424 1 0.0014 38 | 0/8 3 h-lim-p 0.0010 0.0083 12.3484 894.628943 6 0.0007 64 | 0/8 4 h-lim-p 0.0011 0.0422 8.1611 894.606347 2 0.0010 80 | 0/8 5 h-lim-p 0.0060 0.1393 1.3467 894.604933 5 0.0016 103 | 0/8 6 h-lim-p 0.0136 0.5778 0.1623 894.604890 4 0.0021 127 | 0/8 7 h-lim-p 0.0040 6.2578 0.0844 894.604809 0 0.0060 147 | 0/8 8 h-lim-p 0.0176 3.3247 0.0288 894.596235 0 0.1410 170 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 894.596153 2 0.9961 194 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 894.596153 0 1.0938 214 | 0/8 11 h-lim-p 1.4198 20.0000 0.0000 894.596153 0 1.4198 234 | 0/8 12 h-lim-p 1.7120 20.0000 0.0000 894.596153 0 0.0007 264 | 0/8 13 h-lim-p 0.0002 20.0000 0.0000 894.596153 0 0.0000 293 | 0/8 14 h-lim-p 0.0000 20.0000 0.0006 894.596153 0 0.0000 319 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 894.596153 0 0.0026 347 | 0/8 16 h-lim-p 0.0128 20.0000 0.0000 894.596153 0 0.0002 372 | 0/8 17 h-lim-p 0.0003 20.0000 0.0000 894.596153 0 0.0016 394 | 0/8 18 h-lim-p 0.0015 20.0000 0.0000 894.596153 0 0.0004 415 | 0/8 19 h-lim-p 0.0001 20.0000 0.0002 894.596153 0 0.0000 443 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 21 h-lim-p 0.0000 20.0000 0.0008 | 0/8 22 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -894.596153 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -894.596153 Node 7: lnL = -894.596153 Node 8: lnL = -894.596153 Node 9: lnL = -894.596153 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 202 Sequential format.. Reading seq # 1: YJL066C_Sbay Reading seq # 2: YJL066C_Scer Reading seq # 3: YJL066C_Skud Reading seq # 4: YJL066C_Smik Reading seq # 5: YJL066C_Spar Sequences read.. Counting patterns.. # site patterns = 85 Counting frequencies.. 120 bytes for distance 13600 bytes for lkl0 10880 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.860846 0.200274 0.473801 0.114440 0.555086 3.286988 0.507643 0.000060 lnL0 = -816.591399 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 816.591399 x= 0.86085 0.20027 0.47380 0.11444 0.55509 3.28699 0.50764 0.00006 1 h-lim-p 0.0000 0.0000 163.1655 816.530276 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0000 380144.1904 785.016231 m 0.0000 34 | 2/8 3 h-lim-p 0.0002 0.0012 230.8021 755.568724 m 0.0012 46 | 3/8 4 h-lim-p 0.0012 0.0093 71.8381 742.119397 0 0.0046 60 | 3/8 5 h-lim-p 0.0316 0.2525 1.6401 739.519463 0 0.0947 73 | 2/8 6 h-lim-p 0.0001 0.0008 323.6699 737.122969 0 0.0004 87 | 2/8 7 h-lim-p 0.0032 0.0259 12.7651 727.035160 0 0.0194 101 | 1/8 8 h-lim-p 0.0004 0.0035 58.1284 726.185325 0 0.0009 114 | 1/8 9 h-lim-p 0.0615 0.4922 0.6409 722.179882 0 0.2461 128 | 0/8 10 h-lim-p 0.0096 0.4542 16.3713 721.814117 8 0.0028 168 | 0/8 11 h-lim-p 0.1481 1.1845 0.1219 721.118999 0 0.4442 181 | 0/8 12 h-lim-p 0.1858 1.4864 0.0409 720.732528 m 1.4864 201 | 0/8 13 h-lim-p 2.5000 20.0000 0.0038 720.723688 6 1.2966 235 | 0/8 14 h-lim-p 2.2369 17.8954 0.0011 720.723204 5 1.4043 269 | 0/8 15 h-lim-p 2.5000 20.0000 0.0004 720.723177 3 1.4879 297 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 720.723177 0 1.0938 317 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 720.723177 0 1.2500 337 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 720.723177 0 0.5469 358 | 0/8 19 h-lim-p 0.4621 20.0000 0.0000 720.723177 0 0.0253 381 Out... lnL = -720.723177 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -720.723177 Node 7: lnL = -720.723177 Node 8: lnL = -720.723177 Node 9: lnL = -720.723177 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 184 Sequential format.. Reading seq # 1: YJL068C_Sbay Reading seq # 2: YJL068C_Scer Reading seq # 3: YJL068C_Skud Reading seq # 4: YJL068C_Smik Reading seq # 5: YJL068C_Spar Sequences read.. Counting patterns.. # site patterns = 79 Counting frequencies.. 120 bytes for distance 12640 bytes for lkl0 10112 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.173475 0.018988 0.063663 0.028854 0.056019 0.141094 0.162216 0.013079 lnL0 = -665.307076 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 665.307076 x= 0.17348 0.01899 0.06366 0.02885 0.05602 0.14109 0.16222 0.01308 1 h-lim-p 0.0001 0.0006 83.9344 664.161327 0 0.0003 24 | 0/8 2 h-lim-p 0.0010 6.5910 23.8036 664.079945 6 0.0003 50 | 0/8 3 h-lim-p 0.0006 0.0071 13.8388 664.022871 0 0.0008 62 | 0/8 4 h-lim-p 0.0022 0.0211 5.3543 664.015552 7 0.0006 92 | 0/8 5 h-lim-p 0.0046 0.1190 0.7149 664.015302 3 0.0009 111 | 0/8 6 h-lim-p 0.0036 1.0750 0.1833 664.015163 2 0.0031 135 | 0/8 7 h-lim-p 0.0035 0.2411 0.1626 664.014396 0 0.0070 156 | 0/8 8 h-lim-p 0.0110 0.4819 0.1034 663.988061 0 0.0442 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 663.987909 2 1.0889 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 663.987908 0 1.0938 222 | 0/8 11 h-lim-p 1.8892 20.0000 0.0000 663.987908 0 0.2066 244 | 0/8 12 h-lim-p 0.1071 20.0000 0.0000 663.987908 0 0.0000 279 | 0/8 13 h-lim-p 0.0000 20.0000 0.0099 | 0/8 14 h-lim-p 0.0000 20.0000 0.0099 Out... lnL = -663.987908 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -663.987908 Node 7: lnL = -663.987908 Node 8: lnL = -663.987908 Node 9: lnL = -663.987908 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 340 Sequential format.. Reading seq # 1: YJL069C_Sbay Reading seq # 2: YJL069C_Scer Reading seq # 3: YJL069C_Skud Reading seq # 4: YJL069C_Smik Reading seq # 5: YJL069C_Spar Sequences read.. Counting patterns.. # site patterns = 166 Counting frequencies.. 120 bytes for distance 26560 bytes for lkl0 21248 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.318473 0.033863 0.098595 0.113542 0.107651 0.159741 0.273353 0.040305 lnL0 = -1422.974341 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1422.974341 x= 0.31847 0.03386 0.09859 0.11354 0.10765 0.15974 0.27335 0.04031 1 h-lim-p 0.0006 0.0049 50.3217 1422.191349 5 0.0006 32 | 0/8 2 h-lim-p 0.0008 0.0061 10.9984 1422.125098 0 0.0011 44 | 0/8 3 h-lim-p 0.0011 0.0090 5.9288 1422.112382 6 0.0009 67 | 0/8 4 h-lim-p 0.0029 0.0468 1.8349 1422.111323 3 0.0007 87 | 0/8 5 h-lim-p 0.0012 0.1466 1.1191 1422.110887 3 0.0009 105 | 0/8 6 h-lim-p 0.0035 1.1003 0.2939 1422.110833 2 0.0014 121 | 0/8 7 h-lim-p 0.0029 2.3303 0.1430 1422.110823 1 0.0013 143 | 0/8 8 h-lim-p 0.6242 20.0000 0.0003 1422.110781 0 1.2483 164 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1422.110778 1 0.9961 186 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1422.110778 0 1.0938 206 | 0/8 11 h-lim-p 1.1201 20.0000 0.0000 1422.110778 0 0.0038 233 | 0/8 12 h-lim-p 0.0002 20.0000 0.0001 1422.110778 0 0.0002 253 | 0/8 13 h-lim-p 0.0002 20.0000 0.0001 1422.110778 0 0.0000 282 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 1422.110778 0 0.0000 302 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 1422.110778 0 0.0000 367 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1422.110778 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1422.110778 Node 7: lnL = -1422.110778 Node 8: lnL = -1422.110778 Node 9: lnL = -1422.110778 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 288 Sequential format.. Reading seq # 1: YJL072C_Sbay Reading seq # 2: YJL072C_Scer Reading seq # 3: YJL072C_Skud Reading seq # 4: YJL072C_Smik Reading seq # 5: YJL072C_Spar Sequences read.. Counting patterns.. # site patterns = 145 Counting frequencies.. 120 bytes for distance 23200 bytes for lkl0 18560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.385838 0.103149 0.240354 0.101799 0.225959 0.693883 0.216723 0.000060 lnL0 = -1186.524375 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1186.524375 x= 0.38584 0.10315 0.24035 0.10180 0.22596 0.69388 0.21672 0.00006 1 h-lim-p 0.0000 0.0000 172.5617 1186.478995 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0021 184.1961 1171.949519 5 0.0013 50 | 1/8 3 h-lim-p 0.0007 0.0054 33.3884 1171.141135 0 0.0014 63 | 1/8 4 h-lim-p 0.0023 0.0184 18.8010 1170.841925 3 0.0020 81 | 1/8 5 h-lim-p 0.0043 0.0678 8.8113 1170.418679 0 0.0129 94 | 1/8 6 h-lim-p 0.0036 0.0290 26.8110 1169.914004 1 0.0045 108 | 1/8 7 h-lim-p 0.0061 0.0486 1.8493 1168.627360 m 0.0486 120 | 2/8 8 h-lim-p 0.0020 0.0159 15.8058 1168.261256 1 0.0025 134 | 2/8 9 h-lim-p 0.1114 0.8914 0.2655 1162.168581 0 0.4457 148 | 1/8 10 h-lim-p 0.0278 0.4246 4.2510 1162.154435 3 0.0015 175 | 1/8 11 h-lim-p 0.0667 1.5807 0.0927 1161.300705 8 0.8270 210 | 0/8 12 h-lim-p 0.0178 0.1420 0.8720 1161.299789 2 0.0039 234 | 0/8 13 h-lim-p 0.0604 17.0765 0.0561 1161.261441 0 0.4832 257 | 0/8 14 h-lim-p 0.6925 5.5402 0.0156 1161.244522 0 2.0776 278 | 0/8 15 h-lim-p 0.1251 1.0006 0.0092 1161.234264 m 1.0006 298 | 1/8 16 h-lim-p 0.9062 20.0000 0.0101 1161.231704 4 0.6364 328 | 1/8 17 h-lim-p 1.4590 20.0000 0.0044 1161.231166 3 0.3306 354 | 1/8 18 h-lim-p 1.0641 20.0000 0.0014 1161.231038 4 0.7218 384 | 1/8 19 h-lim-p 2.5000 20.0000 0.0003 1161.231028 2 1.3159 408 | 1/8 20 h-lim-p 2.5000 20.0000 0.0001 1161.231027 0 1.0938 427 | 1/8 21 h-lim-p 2.5000 20.0000 0.0000 1161.231027 0 1.0938 446 | 1/8 22 h-lim-p 2.5000 20.0000 0.0000 1161.231027 0 0.6250 466 | 1/8 23 h-lim-p 1.6663 20.0000 0.0000 1161.231027 0 0.0065 492 Out... lnL = -1161.231027 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1161.231027 Node 7: lnL = -1161.231027 Node 8: lnL = -1161.231027 Node 9: lnL = -1161.231027 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 351 Sequential format.. Reading seq # 1: YJL073W_Sbay Reading seq # 2: YJL073W_Scer Reading seq # 3: YJL073W_Skud Reading seq # 4: YJL073W_Smik Reading seq # 5: YJL073W_Spar Sequences read.. Counting patterns.. # site patterns = 137 Counting frequencies.. 120 bytes for distance 21920 bytes for lkl0 17536 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.238565 0.063190 0.051647 0.139537 0.064698 0.161204 0.186094 0.014354 lnL0 = -1516.018556 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1516.018556 x= 0.23857 0.06319 0.05165 0.13954 0.06470 0.16120 0.18609 0.01435 1 h-lim-p 0.0061 0.0491 41.1004 1515.712393 6 0.0004 36 | 0/8 2 h-lim-p 0.0011 0.0085 12.5241 1515.680358 3 0.0004 54 | 0/8 3 h-lim-p 0.0010 0.0350 5.8096 1515.671999 6 0.0006 82 | 0/8 4 h-lim-p 0.0015 0.0574 2.2536 1515.671185 2 0.0004 99 | 0/8 5 h-lim-p 0.0056 1.7653 0.1550 1515.671176 0 0.0007 113 | 0/8 6 h-lim-p 0.0133 20.0000 0.0081 1515.671176 0 0.0029 134 | 0/8 7 h-lim-p 0.0100 20.0000 0.0024 1515.671166 0 0.0602 156 | 0/8 8 h-lim-p 0.0032 20.0000 0.0448 1515.671105 0 0.0063 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1515.671100 1 0.9961 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1515.671100 0 2.1875 219 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1515.671100 0 1.0938 239 | 0/8 12 h-lim-p 0.1686 20.0000 0.0000 1515.671100 0 0.0316 261 | 0/8 13 h-lim-p 0.0031 20.0000 0.0004 1515.671100 0 0.0000 301 | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 1515.671100 0 0.0000 327 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1515.671100 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1515.671100 Node 7: lnL = -1515.671100 Node 8: lnL = -1515.671100 Node 9: lnL = -1515.671100 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 230 Sequential format.. Reading seq # 1: YJL076W_Sbay Reading seq # 2: YJL076W_Scer Reading seq # 3: YJL076W_Skud Reading seq # 4: YJL076W_Smik Reading seq # 5: YJL076W_Spar Sequences read.. Counting patterns.. # site patterns = 94 Counting frequencies.. 120 bytes for distance 15040 bytes for lkl0 12032 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.258810 0.100959 0.056918 0.127826 0.060659 0.138254 0.137888 0.031211 lnL0 = -883.511824 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 883.511824 x= 0.25881 0.10096 0.05692 0.12783 0.06066 0.13825 0.13789 0.03121 1 h-lim-p 0.0023 0.0185 23.4375 883.323236 8 0.0007 43 | 0/8 2 h-lim-p 0.0015 0.0141 11.1617 883.279752 7 0.0008 72 | 0/8 3 h-lim-p 0.0030 0.0699 3.0968 883.276019 6 0.0009 100 | 0/8 4 h-lim-p 0.0020 0.0909 1.3041 883.275417 3 0.0009 118 | 0/8 5 h-lim-p 0.0039 0.9468 0.2872 883.275368 3 0.0012 138 | 0/8 6 h-lim-p 0.0148 2.8688 0.0243 883.275368 0 0.0016 160 | 0/8 7 h-lim-p 0.0253 20.0000 0.0015 883.275366 0 0.0379 180 | 0/8 8 h-lim-p 0.0060 8.5114 0.0098 883.275325 0 0.0241 202 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 883.275325 0 1.0938 222 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 883.275325 0 2.1875 242 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 883.275325 0 1.0938 262 | 0/8 12 h-lim-p 0.1844 20.0000 0.0000 883.275325 0 5.8995 287 | 0/8 13 h-lim-p 0.2959 20.0000 0.0002 883.275325 0 0.1295 307 | 0/8 14 h-lim-p 0.0188 20.0000 0.0012 883.275325 0 0.0024 329 | 0/8 15 h-lim-p 0.0013 20.0000 0.0021 883.275325 0 0.0001 352 | 0/8 16 h-lim-p 0.0000 10.7244 0.0050 883.275325 0 0.0000 372 | 0/8 17 h-lim-p 0.0001 20.0000 0.0022 883.275325 0 0.0001 392 | 0/8 18 h-lim-p 0.0001 20.0000 0.0028 883.275325 0 0.0000 412 | 0/8 19 h-lim-p 0.0001 20.0000 0.0010 883.275325 0 0.0000 434 | 0/8 20 h-lim-p 0.0000 20.0000 0.0005 883.275325 0 0.0000 457 | 0/8 21 h-lim-p 0.0001 20.0000 0.0000 883.275325 0 0.0000 489 Out... lnL = -883.275325 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -883.275325 Node 7: lnL = -883.275325 Node 8: lnL = -883.275325 Node 9: lnL = -883.275325 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 335 Sequential format.. Reading seq # 1: YJL081C_Sbay Reading seq # 2: YJL081C_Scer Reading seq # 3: YJL081C_Skud Reading seq # 4: YJL081C_Smik Reading seq # 5: YJL081C_Spar Sequences read.. Counting patterns.. # site patterns = 128 Counting frequencies.. 120 bytes for distance 20480 bytes for lkl0 16384 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.243460 0.068791 0.056050 0.076319 0.049136 0.169340 0.163229 0.032078 lnL0 = -1313.933848 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1313.933848 x= 0.24346 0.06879 0.05605 0.07632 0.04914 0.16934 0.16323 0.03208 1 h-lim-p 0.0006 0.0052 54.8357 1313.156939 6 0.0006 33 | 0/8 2 h-lim-p 0.0005 0.0039 22.3415 1313.080175 6 0.0003 58 | 0/8 3 h-lim-p 0.0009 0.0157 8.9727 1313.060135 7 0.0006 88 | 0/8 4 h-lim-p 0.0014 0.0731 3.7462 1313.057487 5 0.0005 112 | 0/8 5 h-lim-p 0.0034 0.5717 0.4989 1313.057393 2 0.0008 129 | 0/8 6 h-lim-p 0.0019 0.9013 0.2082 1313.057384 0 0.0005 150 | 0/8 7 h-lim-p 0.0029 3.2133 0.0344 1313.057384 0 0.0013 170 | 0/8 8 h-lim-p 0.1234 20.0000 0.0004 1313.057286 0 0.9871 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1313.057284 0 1.0938 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1313.057284 0 1.0938 233 | 0/8 11 h-lim-p 1.0993 20.0000 0.0000 1313.057284 0 0.0000 284 | 0/8 12 h-lim-p 0.0000 20.0000 0.0007 | 0/8 13 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -1313.057284 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1313.057284 Node 7: lnL = -1313.057284 Node 8: lnL = -1313.057284 Node 9: lnL = -1313.057284 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 558 Sequential format.. Reading seq # 1: YJL082W_Sbay Reading seq # 2: YJL082W_Scer Reading seq # 3: YJL082W_Skud Reading seq # 4: YJL082W_Smik Reading seq # 5: YJL082W_Spar Sequences read.. Counting patterns.. # site patterns = 183 Counting frequencies.. 120 bytes for distance 29280 bytes for lkl0 23424 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.221627 0.032343 0.051211 0.069400 0.064474 0.135996 0.136735 0.039559 lnL0 = -2167.277978 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2167.277978 x= 0.22163 0.03234 0.05121 0.06940 0.06447 0.13600 0.13673 0.03956 1 h-lim-p 0.0062 1.6149 83.5791 2166.753408 8 0.0002 42 | 0/8 2 h-lim-p 0.0008 0.0071 16.5977 2166.704616 2 0.0004 58 | 0/8 3 h-lim-p 0.0008 0.0111 8.0339 2166.699743 2 0.0002 75 | 0/8 4 h-lim-p 0.0014 0.1813 1.0050 2166.699564 2 0.0004 92 | 0/8 5 h-lim-p 0.0009 0.3494 0.4061 2166.699545 2 0.0003 110 | 0/8 6 h-lim-p 0.0076 8.8573 0.0153 2166.699545 0 0.0004 133 | 0/8 7 h-lim-p 0.0011 14.7271 0.0057 2166.699545 0 0.0010 153 | 0/8 8 h-lim-p 0.0224 20.0000 0.0003 2166.699523 0 0.3582 177 | 0/8 9 h-lim-p 2.1195 20.0000 0.0000 2166.699523 0 1.8545 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2166.699523 0 1.0938 217 | 0/8 11 h-lim-p 0.5765 20.0000 0.0000 2166.699523 0 1.1530 238 | 0/8 12 h-lim-p 0.5176 20.0000 0.0001 2166.699523 0 0.5176 258 | 0/8 13 h-lim-p 0.0658 20.0000 0.0004 2166.699523 0 0.0021 282 | 0/8 14 h-lim-p 0.0008 20.0000 0.0011 2166.699523 0 0.0000 307 | 0/8 15 h-lim-p 0.0001 20.0000 0.0001 2166.699523 0 0.0000 337 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 2166.699523 0 0.0000 370 Out... lnL = -2166.699523 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2166.699523 Node 7: lnL = -2166.699523 Node 8: lnL = -2166.699523 Node 9: lnL = -2166.699523 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 846 Sequential format.. Reading seq # 1: YJL083W_Sbay Reading seq # 2: YJL083W_Scer Reading seq # 3: YJL083W_Skud Reading seq # 4: YJL083W_Smik Reading seq # 5: YJL083W_Spar Sequences read.. Counting patterns.. # site patterns = 329 Counting frequencies.. 120 bytes for distance 52640 bytes for lkl0 42112 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.283756 0.066865 0.047776 0.161540 0.108059 0.213385 0.225659 0.013392 lnL0 = -3889.762527 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3889.762527 x= 0.28376 0.06686 0.04778 0.16154 0.10806 0.21339 0.22566 0.01339 1 h-lim-p 0.0024 0.0227 180.6362 3887.033706 8 0.0002 45 | 0/8 2 h-lim-p 0.0004 0.0033 38.4217 3886.833302 8 0.0003 78 | 0/8 3 h-lim-p 0.0008 0.0163 13.0499 3886.803965 2 0.0004 94 | 0/8 4 h-lim-p 0.0007 0.0205 6.7476 3886.796896 4 0.0004 115 | 0/8 5 h-lim-p 0.0033 0.4087 0.7996 3886.796760 3 0.0004 135 | 0/8 6 h-lim-p 0.0020 1.7284 0.1777 3886.796753 0 0.0004 156 | 0/8 7 h-lim-p 0.0060 3.3031 0.0127 3886.796753 0 0.0026 176 | 0/8 8 h-lim-p 0.0332 20.0000 0.0010 3886.796509 0 0.3989 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3886.796502 0 1.0938 219 | 0/8 10 h-lim-p 2.3948 20.0000 0.0000 3886.796502 0 1.0477 239 | 0/8 11 h-lim-p 1.0439 20.0000 0.0000 3886.796502 0 2.0877 260 | 0/8 12 h-lim-p 0.2262 20.0000 0.0003 3886.796502 0 0.0990 280 | 0/8 13 h-lim-p 0.0202 20.0000 0.0013 3886.796502 0 0.0000 317 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 3886.796502 0 0.0001 337 Out... lnL = -3886.796502 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3886.796502 Node 7: lnL = -3886.796502 Node 8: lnL = -3886.796502 Node 9: lnL = -3886.796502 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 372 Sequential format.. Reading seq # 1: YJL085W_Sbay Reading seq # 2: YJL085W_Scer Reading seq # 3: YJL085W_Skud Reading seq # 4: YJL085W_Smik Reading seq # 5: YJL085W_Spar Sequences read.. Counting patterns.. # site patterns = 167 Counting frequencies.. 120 bytes for distance 26720 bytes for lkl0 21376 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.312262 0.111081 0.024798 0.146713 0.085903 0.268419 0.207572 0.018545 lnL0 = -1711.016290 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1711.016290 x= 0.31226 0.11108 0.02480 0.14671 0.08590 0.26842 0.20757 0.01855 1 h-lim-p 0.0030 0.4160 107.0213 1709.555878 4 0.0003 32 | 0/8 2 h-lim-p 0.0015 0.0117 18.0640 1709.398545 8 0.0010 65 | 0/8 3 h-lim-p 0.0017 0.0254 10.7951 1709.373359 6 0.0006 92 | 0/8 4 h-lim-p 0.0029 0.0688 2.0791 1709.371560 5 0.0009 118 | 0/8 5 h-lim-p 0.0074 1.4822 0.2473 1709.371529 3 0.0010 138 | 0/8 6 h-lim-p 0.0083 8.1026 0.0299 1709.371528 0 0.0009 160 | 0/8 7 h-lim-p 0.0105 20.0000 0.0026 1709.371527 0 0.0211 181 | 0/8 8 h-lim-p 0.0158 20.0000 0.0034 1709.371465 0 0.0947 203 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1709.371462 0 1.0938 223 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1709.371462 0 1.0938 243 | 0/8 11 h-lim-p 1.2822 20.0000 0.0000 1709.371462 0 1.2822 263 | 0/8 12 h-lim-p 0.6902 20.0000 0.0000 1709.371462 0 0.6039 283 | 0/8 13 h-lim-p 0.0191 20.0000 0.0007 1709.371462 0 0.0191 303 | 0/8 14 h-lim-p 0.0067 14.1314 0.0020 1709.371462 0 0.0000 335 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 1709.371462 0 0.0000 360 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 1709.371462 0 0.0000 395 Out... lnL = -1709.371462 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1709.371462 Node 7: lnL = -1709.371462 Node 8: lnL = -1709.371462 Node 9: lnL = -1709.371462 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 854 Sequential format.. Reading seq # 1: YJL089W_Sbay Reading seq # 2: YJL089W_Scer Reading seq # 3: YJL089W_Skud Reading seq # 4: YJL089W_Smik Reading seq # 5: YJL089W_Spar Sequences read.. Counting patterns.. # site patterns = 334 Counting frequencies.. 120 bytes for distance 53440 bytes for lkl0 42752 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.379399 0.062414 0.080907 0.119350 0.108984 0.286502 0.231531 0.050673 lnL0 = -3930.603683 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3930.603683 x= 0.37940 0.06241 0.08091 0.11935 0.10898 0.28650 0.23153 0.05067 1 h-lim-p 0.0023 0.0182 99.3492 3929.468210 7 0.0002 40 | 0/8 2 h-lim-p 0.0013 0.0142 17.9323 3929.403769 6 0.0004 68 | 0/8 3 h-lim-p 0.0005 0.0236 14.1220 3929.380901 5 0.0003 92 | 0/8 4 h-lim-p 0.0011 0.0650 4.2429 3929.377435 3 0.0004 110 | 0/8 5 h-lim-p 0.0020 0.1531 0.9374 3929.377258 2 0.0004 127 | 0/8 6 h-lim-p 0.0012 0.3262 0.3413 3929.377227 1 0.0006 149 | 0/8 7 h-lim-p 0.0950 20.0000 0.0022 3929.377223 0 0.0416 169 | 0/8 8 h-lim-p 0.0073 20.0000 0.0123 3929.377098 0 0.0292 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3929.377091 1 0.9961 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3929.377091 0 2.1875 233 | 0/8 11 h-lim-p 2.2876 20.0000 0.0000 3929.377091 0 1.1438 253 | 0/8 12 h-lim-p 0.1435 20.0000 0.0001 3929.377091 0 0.0078 276 | 0/8 13 h-lim-p 0.0022 20.0000 0.0005 3929.377091 0 0.0000 319 | 0/8 14 h-lim-p 0.0000 20.0000 0.0006 | 0/8 15 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -3929.377091 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3929.377091 Node 7: lnL = -3929.377091 Node 8: lnL = -3929.377091 Node 9: lnL = -3929.377091 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 859 Sequential format.. Reading seq # 1: YJL090C_Sbay Reading seq # 2: YJL090C_Scer Reading seq # 3: YJL090C_Skud Reading seq # 4: YJL090C_Smik Reading seq # 5: YJL090C_Spar Sequences read.. Counting patterns.. # site patterns = 336 Counting frequencies.. 120 bytes for distance 53760 bytes for lkl0 43008 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.319019 0.136945 0.057164 0.121445 0.105266 0.292435 0.216619 0.000838 lnL0 = -4001.676041 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4001.676041 x= 0.31902 0.13695 0.05716 0.12144 0.10527 0.29243 0.21662 0.00084 1 h-lim-p 0.0060 0.9917 115.0651 4000.375942 8 0.0002 44 | 0/8 2 h-lim-p 0.0015 0.0148 16.5542 4000.336938 5 0.0003 67 | 0/8 3 h-lim-p 0.0005 0.0412 9.1849 4000.324989 5 0.0004 92 | 0/8 4 h-lim-p 0.0008 0.0060 2.3596 4000.323668 5 0.0005 117 | 0/8 5 h-lim-p 0.0042 1.2963 0.2897 4000.323643 2 0.0006 135 | 0/8 6 h-lim-p 0.0037 4.1850 0.0439 4000.323643 0 0.0004 157 | 0/8 7 h-lim-p 0.0035 20.0000 0.0051 4000.323643 0 0.0015 177 | 0/8 8 h-lim-p 0.0794 20.0000 0.0001 4000.323642 0 1.2709 201 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4000.323642 0 1.0938 221 | 0/8 10 h-lim-p 0.2279 20.0000 0.0000 4000.323642 0 0.4558 242 | 0/8 11 h-lim-p 0.0781 20.0000 0.0002 4000.323642 0 0.0146 264 | 0/8 12 h-lim-p 0.0058 15.8466 0.0004 4000.323642 0 0.0001 289 | 0/8 13 h-lim-p 0.0007 20.0000 0.0001 4000.323642 0 0.0000 320 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 4000.323642 0 0.0000 345 Out... lnL = -4000.323642 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4000.323642 Node 7: lnL = -4000.323642 Node 8: lnL = -4000.323642 Node 9: lnL = -4000.323642 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 192 Sequential format.. Reading seq # 1: YJL091C_Sbay Reading seq # 2: YJL091C_Scer Reading seq # 3: YJL091C_Skud Reading seq # 4: YJL091C_Smik Reading seq # 5: YJL091C_Spar Sequences read.. Counting patterns.. # site patterns = 90 Counting frequencies.. 120 bytes for distance 14400 bytes for lkl0 11520 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.353798 0.000060 0.077064 0.121041 0.056361 0.261065 0.188694 0.089647 lnL0 = -858.199937 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 858.199937 x= 0.35380 0.00006 0.07706 0.12104 0.05636 0.26107 0.18869 0.08965 1 h-lim-p 0.0014 0.0112 54.8195 856.791813 9 0.0008 43 | 0/8 2 h-lim-p 0.0006 0.0046 43.9441 855.837803 0 0.0012 56 | 0/8 3 h-lim-p 0.0016 0.0130 16.4185 855.767505 7 0.0007 81 | 0/8 4 h-lim-p 0.0029 0.0325 3.7073 855.761735 5 0.0009 107 | 0/8 5 h-lim-p 0.0028 0.1033 1.1694 855.760307 5 0.0021 130 | 0/8 6 h-lim-p 0.0117 0.5069 0.2058 855.759837 3 0.0049 148 | 0/8 7 h-lim-p 0.0179 2.9340 0.0564 855.693272 0 0.2147 171 | 0/8 8 h-lim-p 0.0162 0.6443 0.7492 855.692614 5 0.0022 204 | 0/8 9 h-lim-p 0.3302 20.0000 0.0051 855.686008 0 0.9906 225 | 0/8 10 h-lim-p 2.5000 20.0000 0.0007 855.685849 2 0.9961 249 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 855.685849 0 1.0938 269 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 855.685849 0 1.0938 289 | 0/8 13 h-lim-p 1.7813 20.0000 0.0000 855.685849 0 1.7813 309 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 855.685849 0 0.1367 332 | 0/8 15 h-lim-p 0.0351 20.0000 0.0000 855.685849 0 0.0351 352 | 0/8 16 h-lim-p 0.0180 20.0000 0.0000 855.685849 0 0.0090 372 | 0/8 17 h-lim-p 0.0058 20.0000 0.0000 855.685849 0 0.0004 395 | 0/8 18 h-lim-p 0.0002 20.0000 0.0000 855.685849 0 0.0001 415 | 0/8 19 h-lim-p 0.0001 20.0000 0.0000 855.685849 0 0.0000 449 | 0/8 20 h-lim-p 0.0000 20.0000 0.0005 | 0/8 21 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -855.685849 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -855.685849 Node 7: lnL = -855.685849 Node 8: lnL = -855.685849 Node 9: lnL = -855.685849 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 673 Sequential format.. Reading seq # 1: YJL093C_Sbay Reading seq # 2: YJL093C_Scer Reading seq # 3: YJL093C_Skud Reading seq # 4: YJL093C_Smik Reading seq # 5: YJL093C_Spar Sequences read.. Counting patterns.. # site patterns = 177 Counting frequencies.. 120 bytes for distance 28320 bytes for lkl0 22656 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.885947 0.040651 0.001447 0.338991 3.091029 0.465463 0.507978 0.000060 lnL0 = -2826.550127 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2826.550127 x= 0.88595 0.04065 0.00145 0.33899 3.09103 0.46546 0.50798 0.00006 1 h-lim-p 0.0000 0.0000 517.1035 2826.394515 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0029 295.4087 2701.638244 3 0.0024 47 | 1/8 3 h-lim-p 0.0000 0.0003 313.0610 2688.238238 m 0.0003 59 | 2/8 4 h-lim-p 0.0007 0.0058 75.8182 2653.866480 0 0.0029 73 | 2/8 5 h-lim-p 0.0003 0.0021 87.9573 2650.453780 0 0.0008 86 | 2/8 6 h-lim-p 0.0020 0.0157 22.4999 2650.139538 2 0.0009 102 | 2/8 7 h-lim-p 0.0187 0.2660 1.1071 2640.396652 0 0.0748 116 | 1/8 8 h-lim-p 0.0012 0.0113 67.2788 2639.506360 8 0.0004 148 | 1/8 9 h-lim-p 0.4108 5.1084 0.0733 2636.060751 0 0.8217 161 | 0/8 10 h-lim-p 0.0111 0.6156 5.4405 2636.048159 6 0.0008 199 | 0/8 11 h-lim-p 0.2227 7.7530 0.0203 2635.344579 0 1.3361 213 | 0/8 12 h-lim-p 2.5000 20.0000 0.0051 2635.330208 3 1.0004 239 | 0/8 13 h-lim-p 2.5000 20.0000 0.0011 2635.329133 3 0.9961 265 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 2635.329115 0 1.0938 285 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2635.329115 0 1.0938 305 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 2635.329115 0 1.0938 325 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 2635.329115 0 0.1562 348 Out... lnL = -2635.329115 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2635.329115 Node 7: lnL = -2635.329115 Node 8: lnL = -2635.329115 Node 9: lnL = -2635.329115 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 297 Sequential format.. Reading seq # 1: YJL095W_Sbay Reading seq # 2: YJL095W_Scer Reading seq # 3: YJL095W_Skud Reading seq # 4: YJL095W_Smik Reading seq # 5: YJL095W_Spar Sequences read.. Counting patterns.. # site patterns = 151 Counting frequencies.. 120 bytes for distance 24160 bytes for lkl0 19328 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.299501 0.096821 0.082662 0.143433 0.073304 0.234281 0.310714 0.000060 lnL0 = -1365.401353 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1365.401353 x= 0.29950 0.09682 0.08266 0.14343 0.07330 0.23428 0.31071 0.00006 1 h-lim-p 0.0000 0.0000 57.3672 1365.391792 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0058 53.2658 1364.552185 0 0.0013 41 | 1/8 3 h-lim-p 0.0007 0.0052 27.8377 1364.394687 2 0.0006 57 | 1/8 4 h-lim-p 0.0049 0.0605 3.4663 1364.387295 3 0.0010 76 | 1/8 5 h-lim-p 0.0024 0.2396 1.4692 1364.375121 0 0.0048 89 | 1/8 6 h-lim-p 0.0087 0.4699 0.8148 1364.232503 0 0.0262 102 | 1/8 7 h-lim-p 0.0060 0.1995 3.5680 1363.450472 0 0.0120 122 | 1/8 8 h-lim-p 0.0027 0.0229 15.7798 1362.981335 6 0.0023 145 | 1/8 9 h-lim-p 2.5000 20.0000 0.0092 1362.954216 6 1.0560 172 | 1/8 10 h-lim-p 2.5000 20.0000 0.0023 1362.951737 3 1.1023 197 | 0/8 11 h-lim-p 0.0194 4.6374 0.1336 1362.951719 3 0.0026 224 | 0/8 12 h-lim-p 0.7889 20.0000 0.0004 1362.951636 0 1.1833 244 | 0/8 13 h-lim-p 2.5000 20.0000 0.0001 1362.951635 0 1.0938 264 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1362.951635 0 2.1875 284 | 0/8 15 h-lim-p 2.1073 20.0000 0.0000 1362.951635 0 0.9219 304 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1362.951635 0 0.3125 326 | 0/8 17 h-lim-p 0.4063 20.0000 0.0000 1362.951635 0 0.0444 348 | 0/8 18 h-lim-p 0.0394 20.0000 0.0000 1362.951635 0 0.0011 372 Out... lnL = -1362.951635 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1362.951635 Node 7: lnL = -1362.951635 Node 8: lnL = -1362.951635 Node 9: lnL = -1362.951635 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 354 Sequential format.. Reading seq # 1: YJL097W_Sbay Reading seq # 2: YJL097W_Scer Reading seq # 3: YJL097W_Skud Reading seq # 4: YJL097W_Smik Reading seq # 5: YJL097W_Spar Sequences read.. Counting patterns.. # site patterns = 187 Counting frequencies.. 120 bytes for distance 29920 bytes for lkl0 23936 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.529628 0.000060 0.057767 0.206770 0.035710 0.337670 0.405316 0.185437 lnL0 = -1578.195190 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1578.195190 x= 0.52963 0.00006 0.05777 0.20677 0.03571 0.33767 0.40532 0.18544 1 h-lim-p 0.0000 0.0000 467.9940 1577.696863 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0025 137.1307 1566.428277 6 0.0012 51 | 1/8 3 h-lim-p 0.0001 0.0008 178.2105 1558.443975 m 0.0008 63 | 2/8 4 h-lim-p 0.0035 0.0279 11.2207 1558.176277 8 0.0025 95 | 2/8 5 h-lim-p 0.0026 0.0321 10.9137 1557.750845 0 0.0052 108 | 2/8 6 h-lim-p 0.0070 0.0558 5.9282 1555.821120 0 0.0139 121 | 2/8 7 h-lim-p 0.0037 0.0297 14.3928 1555.064271 1 0.0046 135 | 2/8 8 h-lim-p 0.5072 4.9931 0.1317 1541.347063 0 1.5217 148 | 1/8 9 h-lim-p 0.0141 0.2063 14.2446 1541.129529 8 0.0022 185 | 1/8 10 h-lim-p 0.5966 5.6760 0.0534 1538.376471 0 2.3865 199 | 1/8 11 h-lim-p 2.5000 20.0000 0.0361 1537.218807 8 1.2237 233 | 1/8 12 h-lim-p 1.8369 14.6949 0.0182 1536.791538 4 1.8106 260 | 1/8 13 h-lim-p 2.5000 20.0000 0.0100 1536.742757 7 1.6870 296 | 1/8 14 h-lim-p 2.5000 20.0000 0.0026 1536.740313 4 1.2732 324 | 1/8 15 h-lim-p 2.5000 20.0000 0.0002 1536.740296 0 1.2500 343 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 1536.740296 0 1.2500 362 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 1536.740296 0 1.0938 381 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 1536.740296 0 2.1875 400 | 1/8 19 h-lim-p 1.9136 20.0000 0.0000 1536.740296 0 0.4186 420 | 1/8 20 h-lim-p 0.5982 20.0000 0.0000 1536.740296 0 0.0006 448 Out... lnL = -1536.740296 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1536.740296 Node 7: lnL = -1536.740296 Node 8: lnL = -1536.740296 Node 9: lnL = -1536.740296 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 346 Sequential format.. Reading seq # 1: YJL099W_Sbay Reading seq # 2: YJL099W_Scer Reading seq # 3: YJL099W_Skud Reading seq # 4: YJL099W_Smik Reading seq # 5: YJL099W_Spar Sequences read.. Counting patterns.. # site patterns = 152 Counting frequencies.. 120 bytes for distance 24320 bytes for lkl0 19456 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.271286 0.067006 0.078876 0.157949 0.042766 0.192520 0.217771 0.009015 lnL0 = -1508.236333 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1508.236333 x= 0.27129 0.06701 0.07888 0.15795 0.04277 0.19252 0.21777 0.00901 1 h-lim-p 0.0002 0.0017 38.6350 1507.983103 0 0.0004 23 | 0/8 2 h-lim-p 0.0003 0.0025 28.0063 1507.857570 0 0.0005 35 | 0/8 3 h-lim-p 0.0003 0.0028 7.1692 1507.840130 0 0.0007 48 | 0/8 4 h-lim-p 0.0023 0.1658 2.1141 1507.838930 3 0.0006 67 | 0/8 5 h-lim-p 0.0018 0.4133 0.6860 1507.838746 2 0.0008 83 | 0/8 6 h-lim-p 0.0041 0.2287 0.1394 1507.838712 2 0.0018 107 | 0/8 7 h-lim-p 0.0068 0.4431 0.0369 1507.838230 0 0.0272 129 | 0/8 8 h-lim-p 0.0052 0.5151 0.1925 1507.830334 0 0.0209 151 | 0/8 9 h-lim-p 2.5000 20.0000 0.0010 1507.829375 3 0.9961 177 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1507.829375 0 1.0938 197 | 0/8 11 h-lim-p 1.3048 20.0000 0.0000 1507.829375 0 0.5709 217 | 0/8 12 h-lim-p 0.3263 20.0000 0.0000 1507.829375 0 0.0816 238 | 0/8 13 h-lim-p 0.0345 20.0000 0.0001 1507.829375 0 0.0086 259 | 0/8 14 h-lim-p 0.0045 20.0000 0.0001 1507.829375 0 0.0000 297 | 0/8 15 h-lim-p 0.0000 20.0000 0.0008 | 0/8 16 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -1507.829375 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1507.829375 Node 7: lnL = -1507.829375 Node 8: lnL = -1507.829375 Node 9: lnL = -1507.829375 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 429 Sequential format.. Reading seq # 1: YJL103C_Sbay Reading seq # 2: YJL103C_Scer Reading seq # 3: YJL103C_Skud Reading seq # 4: YJL103C_Smik Reading seq # 5: YJL103C_Spar Sequences read.. Counting patterns.. # site patterns = 163 Counting frequencies.. 120 bytes for distance 26080 bytes for lkl0 20864 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.178180 0.066577 0.059047 0.123027 0.011095 0.138248 0.168251 0.000060 lnL0 = -1644.441368 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1644.441368 x= 0.17818 0.06658 0.05905 0.12303 0.01110 0.13825 0.16825 0.00006 1 h-lim-p 0.0000 0.0000 734.8596 1643.777361 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0014 174.7775 1637.983556 0 0.0005 39 | 1/8 3 h-lim-p 0.0003 0.0024 75.8207 1636.929988 0 0.0004 51 | 1/8 4 h-lim-p 0.0011 0.0087 20.3986 1636.853611 7 0.0004 81 | 1/8 5 h-lim-p 0.0027 0.0495 2.9508 1636.845007 6 0.0010 107 | 0/8 6 h-lim-p 0.0004 0.1489 7.2534 1636.821295 0 0.0008 120 | 0/8 7 h-lim-p 0.0018 0.0920 3.1601 1636.770042 0 0.0037 133 | 0/8 8 h-lim-p 0.0049 0.0591 2.3618 1636.431426 0 0.0098 146 | 0/8 9 h-lim-p 0.0009 0.0070 4.4034 1630.679194 m 0.0070 158 | 1/8 10 h-lim-p 2.5000 20.0000 0.0072 1628.672753 0 3.7500 170 | 1/8 11 h-lim-p 1.5445 12.3563 0.0103 1628.597786 7 0.8495 205 | 0/8 12 h-lim-p 0.0087 0.1739 1.0083 1628.596283 5 0.0051 236 | 0/8 13 h-lim-p 0.4658 3.7264 0.0048 1628.582504 0 0.9316 249 | 0/8 14 h-lim-p 2.5000 20.0000 0.0003 1628.582378 3 1.2347 276 | 0/8 15 h-lim-p 2.5000 20.0000 0.0001 1628.582375 0 1.2500 296 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1628.582375 0 1.0938 316 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1628.582375 0 2.1875 336 | 0/8 18 h-lim-p 1.7701 20.0000 0.0000 1628.582375 0 0.7744 356 | 0/8 19 h-lim-p 2.1036 20.0000 0.0000 1628.582375 0 0.2301 378 | 0/8 20 h-lim-p 0.1662 20.0000 0.0000 1628.582375 0 0.0831 398 | 0/8 21 h-lim-p 0.0557 20.0000 0.0000 1628.582375 0 0.0030 421 | 0/8 22 h-lim-p 0.0021 20.0000 0.0000 1628.582375 0 0.0000 458 Out... lnL = -1628.582375 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1628.582375 Node 7: lnL = -1628.582375 Node 8: lnL = -1628.582375 Node 9: lnL = -1628.582375 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 651 Sequential format.. Reading seq # 1: YJL104W_Sbay Reading seq # 2: YJL104W_Scer Reading seq # 3: YJL104W_Skud Reading seq # 4: YJL104W_Smik Reading seq # 5: YJL104W_Spar Sequences read.. Counting patterns.. # site patterns = 263 Counting frequencies.. 120 bytes for distance 42080 bytes for lkl0 33664 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.349139 0.070233 0.077315 0.128921 0.119457 0.197412 0.229026 0.044440 lnL0 = -3012.735250 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3012.735250 x= 0.34914 0.07023 0.07731 0.12892 0.11946 0.19741 0.22903 0.04444 1 h-lim-p 0.0077 1.3088 88.1961 3011.703373 9 0.0003 48 | 0/8 2 h-lim-p 0.0016 0.0142 15.5156 3011.645982 7 0.0005 79 | 0/8 3 h-lim-p 0.0009 0.0430 7.9957 3011.634758 2 0.0004 95 | 0/8 4 h-lim-p 0.0029 0.1787 1.2192 3011.634375 4 0.0005 118 | 0/8 5 h-lim-p 0.0021 0.9578 0.3098 3011.634340 2 0.0008 134 | 0/8 6 h-lim-p 0.0031 2.3050 0.0808 3011.634338 0 0.0008 155 | 0/8 7 h-lim-p 0.0043 9.4246 0.0145 3011.634338 0 0.0009 176 | 0/8 8 h-lim-p 0.0488 20.0000 0.0003 3011.634275 0 0.7814 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3011.634275 0 1.0938 220 | 0/8 10 h-lim-p 1.7167 20.0000 0.0000 3011.634275 0 1.5021 240 | 0/8 11 h-lim-p 2.1658 20.0000 0.0000 3011.634275 0 1.0829 260 | 0/8 12 h-lim-p 0.4842 20.0000 0.0000 3011.634275 0 0.0605 282 | 0/8 13 h-lim-p 0.0029 20.0000 0.0005 3011.634275 0 0.0000 315 | 0/8 14 h-lim-p 0.0005 20.0000 0.0000 3011.634275 0 0.0005 335 Out... lnL = -3011.634275 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3011.634275 Node 7: lnL = -3011.634275 Node 8: lnL = -3011.634275 Node 9: lnL = -3011.634275 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 846 Sequential format.. Reading seq # 1: YJL105W_Sbay Reading seq # 2: YJL105W_Scer Reading seq # 3: YJL105W_Skud Reading seq # 4: YJL105W_Smik Reading seq # 5: YJL105W_Spar Sequences read.. Counting patterns.. # site patterns = 200 Counting frequencies.. 120 bytes for distance 32000 bytes for lkl0 25600 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.166929 0.055697 0.038816 0.060540 0.038475 0.130899 0.091051 0.014698 lnL0 = -3079.220342 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3079.220342 x= 0.16693 0.05570 0.03882 0.06054 0.03847 0.13090 0.09105 0.01470 1 h-lim-p 0.0026 0.9644 154.1931 3078.253855 7 0.0001 42 | 0/8 2 h-lim-p 0.0003 0.0027 30.6950 3078.205518 6 0.0001 70 | 0/8 3 h-lim-p 0.0003 0.0078 11.9587 3078.200482 4 0.0001 93 | 0/8 4 h-lim-p 0.0004 0.0379 2.5996 3078.199910 2 0.0002 109 | 0/8 5 h-lim-p 0.0066 0.5454 0.0691 3078.199910 0 0.0002 125 | 0/8 6 h-lim-p 0.0010 5.0535 0.0128 3078.199910 0 0.0002 146 | 0/8 7 h-lim-p 0.0007 20.0000 0.0037 3078.199910 0 0.0002 167 | 0/8 8 h-lim-p 0.0033 20.0000 0.0002 3078.199907 0 0.8483 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3078.199907 0 1.0938 215 | 0/8 10 h-lim-p 0.8690 20.0000 0.0000 3078.199907 0 0.8690 235 | 0/8 11 h-lim-p 0.3209 20.0000 0.0001 3078.199907 0 0.0003 264 | 0/8 12 h-lim-p 0.0000 20.0000 0.0004 3078.199907 0 0.0000 288 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 3078.199907 0 0.0000 314 | 0/8 14 h-lim-p 0.0000 20.0000 0.0055 | 0/8 15 h-lim-p 0.0000 20.0000 0.0055 Out... lnL = -3078.199907 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3078.199907 Node 7: lnL = -3078.199907 Node 8: lnL = -3078.199907 Node 9: lnL = -3078.199907 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 881 Sequential format.. Reading seq # 1: YJL106W_Sbay Reading seq # 2: YJL106W_Scer Reading seq # 3: YJL106W_Skud Reading seq # 4: YJL106W_Smik Reading seq # 5: YJL106W_Spar Sequences read.. Counting patterns.. # site patterns = 271 Counting frequencies.. 120 bytes for distance 43360 bytes for lkl0 34688 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.291794 0.058994 0.048326 0.109914 0.062756 0.157331 0.213327 0.045672 lnL0 = -3765.870919 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3765.870919 x= 0.29179 0.05899 0.04833 0.10991 0.06276 0.15733 0.21333 0.04567 1 h-lim-p 0.0002 0.0013 182.2215 3763.501726 2 0.0002 26 | 0/8 2 h-lim-p 0.0003 0.0028 44.3916 3763.320228 7 0.0002 54 | 0/8 3 h-lim-p 0.0004 0.0158 20.5651 3763.292631 5 0.0002 76 | 0/8 4 h-lim-p 0.0003 0.0242 9.6792 3763.278193 1 0.0004 90 | 0/8 5 h-lim-p 0.0028 0.1827 1.4712 3763.277915 2 0.0003 108 | 0/8 6 h-lim-p 0.0017 0.7273 0.2337 3763.277906 1 0.0003 123 | 0/8 7 h-lim-p 0.0159 20.0000 0.0049 3763.277905 0 0.0070 143 | 0/8 8 h-lim-p 0.0064 20.0000 0.0053 3763.277728 0 0.0770 166 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3763.277724 0 1.0938 186 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3763.277724 0 1.0938 206 | 0/8 11 h-lim-p 1.3308 20.0000 0.0000 3763.277724 0 2.6616 227 | 0/8 12 h-lim-p 0.1389 20.0000 0.0005 3763.277724 0 0.0304 248 | 0/8 13 h-lim-p 0.0079 20.0000 0.0019 3763.277724 0 0.0020 269 | 0/8 14 h-lim-p 0.0005 9.4826 0.0074 3763.277724 0 0.0000 296 | 0/8 15 h-lim-p 0.0002 20.0000 0.0001 3763.277724 0 0.0001 316 | 0/8 16 h-lim-p 0.0002 20.0000 0.0000 3763.277724 0 0.0000 349 | 0/8 17 h-lim-p 0.0000 20.0000 0.0011 3763.277724 0 0.0000 380 | 0/8 18 h-lim-p 0.0000 20.0000 0.0157 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0011 | 0/8 20 h-lim-p 0.0000 20.0000 0.0011 Out... lnL = -3763.277724 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3763.277724 Node 7: lnL = -3763.277724 Node 8: lnL = -3763.277724 Node 9: lnL = -3763.277724 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 458 Sequential format.. Reading seq # 1: YJL110C_Sbay Reading seq # 2: YJL110C_Scer Reading seq # 3: YJL110C_Skud Reading seq # 4: YJL110C_Smik Reading seq # 5: YJL110C_Spar Sequences read.. Counting patterns.. # site patterns = 180 Counting frequencies.. 120 bytes for distance 28800 bytes for lkl0 23040 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.046269 0.049215 0.051840 0.145497 0.063303 0.159478 0.237377 0.204595 lnL0 = -2007.103155 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2007.103155 x= 0.04627 0.04921 0.05184 0.14550 0.06330 0.15948 0.23738 0.20459 1 h-lim-p 0.0029 0.9655 117.7517 2005.398377 8 0.0003 41 | 0/8 2 h-lim-p 0.0005 0.0038 26.1122 2005.270374 3 0.0004 59 | 0/8 3 h-lim-p 0.0010 0.0141 10.5695 2005.248797 2 0.0005 75 | 0/8 4 h-lim-p 0.0013 0.0576 3.8706 2005.246012 5 0.0004 101 | 0/8 5 h-lim-p 0.0016 0.2668 1.0756 2005.245606 2 0.0008 117 | 0/8 6 h-lim-p 0.0044 0.7425 0.1900 2005.245593 2 0.0007 136 | 0/8 7 h-lim-p 0.0125 20.0000 0.0110 2005.245584 2 0.0080 161 | 0/8 8 h-lim-p 0.0070 20.0000 0.0125 2005.244463 0 0.0562 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 2005.244402 2 0.9961 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2005.244402 0 1.0938 228 | 0/8 11 h-lim-p 1.4743 20.0000 0.0000 2005.244402 0 2.2115 248 | 0/8 12 h-lim-p 1.2231 20.0000 0.0000 2005.244402 0 1.2231 268 | 0/8 13 h-lim-p 0.0282 20.0000 0.0012 2005.244402 0 0.0053 290 | 0/8 14 h-lim-p 0.0016 17.1341 0.0039 2005.244402 0 0.0000 329 | 0/8 15 h-lim-p 0.0000 20.0000 0.0006 | 0/8 16 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -2005.244402 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2005.244402 Node 7: lnL = -2005.244402 Node 8: lnL = -2005.244402 Node 9: lnL = -2005.244402 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 888 Sequential format.. Reading seq # 1: YJL115W_Sbay Reading seq # 2: YJL115W_Scer Reading seq # 3: YJL115W_Skud Reading seq # 4: YJL115W_Smik Reading seq # 5: YJL115W_Spar Sequences read.. Counting patterns.. # site patterns = 329 Counting frequencies.. 120 bytes for distance 52640 bytes for lkl0 42112 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.028595 0.090176 0.115924 0.080791 0.071044 0.199218 0.525104 0.260091 lnL0 = -3887.159491 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3887.159491 x= 0.02859 0.09018 0.11592 0.08079 0.07104 0.19922 0.52510 0.26009 1 h-lim-p 0.0003 0.0026 82.7221 3886.296356 8 0.0003 39 | 0/8 2 h-lim-p 0.0008 0.0062 21.7753 3886.202712 5 0.0004 62 | 0/8 3 h-lim-p 0.0004 0.0034 25.2185 3886.167737 6 0.0002 90 | 0/8 4 h-lim-p 0.0004 0.0057 11.9538 3886.154013 5 0.0003 115 | 0/8 5 h-lim-p 0.0008 0.0268 4.2401 3886.148688 3 0.0007 133 | 0/8 6 h-lim-p 0.0033 0.1014 0.9339 3886.148332 3 0.0009 152 | 0/8 7 h-lim-p 0.0007 0.4908 1.1245 3886.148043 1 0.0009 174 | 0/8 8 h-lim-p 1.8488 20.0000 0.0006 3886.147851 3 1.0841 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3886.147850 0 1.0938 215 | 0/8 10 h-lim-p 1.3021 20.0000 0.0000 3886.147850 0 1.3021 235 | 0/8 11 h-lim-p 1.4048 20.0000 0.0000 3886.147850 0 0.1317 258 | 0/8 12 h-lim-p 0.0268 20.0000 0.0001 3886.147850 0 0.0134 278 | 0/8 13 h-lim-p 0.0052 20.0000 0.0003 3886.147850 0 0.0026 298 | 0/8 14 h-lim-p 0.0013 20.0000 0.0005 3886.147850 0 0.0000 340 | 0/8 15 h-lim-p 0.0000 20.0000 0.0015 | 0/8 16 h-lim-p 0.0000 20.0000 0.0015 Out... lnL = -3886.147850 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3886.147850 Node 7: lnL = -3886.147850 Node 8: lnL = -3886.147850 Node 9: lnL = -3886.147850 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 250 Sequential format.. Reading seq # 1: YJL117W_Sbay Reading seq # 2: YJL117W_Scer Reading seq # 3: YJL117W_Skud Reading seq # 4: YJL117W_Smik Reading seq # 5: YJL117W_Spar Sequences read.. Counting patterns.. # site patterns = 81 Counting frequencies.. 120 bytes for distance 12960 bytes for lkl0 10368 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.051220 0.037016 0.023746 0.056856 0.064526 0.072172 0.089560 0.140036 lnL0 = -864.472565 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 864.472565 x= 0.05122 0.03702 0.02375 0.05686 0.06453 0.07217 0.08956 0.14004 1 h-lim-p 0.0003 0.0024 99.6124 863.555894 9 0.0002 44 | 0/8 2 h-lim-p 0.0004 0.0030 23.8035 863.473119 7 0.0003 73 | 0/8 3 h-lim-p 0.0036 0.0688 2.0157 863.472356 3 0.0004 94 | 0/8 4 h-lim-p 0.0012 0.2546 0.6401 863.472266 3 0.0005 112 | 0/8 5 h-lim-p 0.0028 1.2927 0.1073 863.472264 1 0.0003 136 | 0/8 6 h-lim-p 0.0041 9.5075 0.0092 863.472263 0 0.0035 156 | 0/8 7 h-lim-p 0.0058 16.8448 0.0056 863.472185 0 0.0466 179 | 0/8 8 h-lim-p 0.0015 0.4334 0.1787 863.471991 0 0.0029 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 863.471969 2 0.9961 224 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 863.471969 0 2.1875 244 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 863.471969 0 1.0938 264 | 0/8 12 h-lim-p 0.2477 20.0000 0.0000 863.471969 0 3.9633 288 | 0/8 13 h-lim-p 1.8590 20.0000 0.0000 863.471969 0 0.0000 336 | 0/8 14 h-lim-p 0.0000 20.0000 0.0012 | 0/8 15 h-lim-p 0.0000 20.0000 0.0012 Out... lnL = -863.471969 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -863.471969 Node 7: lnL = -863.471969 Node 8: lnL = -863.471969 Node 9: lnL = -863.471969 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 315 Sequential format.. Reading seq # 1: YJL118W_Sbay Reading seq # 2: YJL118W_Scer Reading seq # 3: YJL118W_Skud Reading seq # 4: YJL118W_Smik Reading seq # 5: YJL118W_Spar Sequences read.. Counting patterns.. # site patterns = 108 Counting frequencies.. 120 bytes for distance 17280 bytes for lkl0 13824 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.801385 0.507905 0.856134 0.172500 0.968005 1.759064 0.588952 lnL0 = -1303.101342 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1303.101342 x= 0.00006 0.80138 0.50791 0.85613 0.17250 0.96800 1.75906 0.58895 1 h-lim-p 0.0000 0.0000 193.3141 1303.014534 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0067 54.6512 1281.814170 m 0.0067 41 | 2/8 3 h-lim-p 0.0016 0.0130 59.9361 1220.364180 0 0.0097 55 | 2/8 4 h-lim-p 0.0034 0.0276 34.1529 1210.445361 0 0.0138 69 | 1/8 5 h-lim-p 0.0001 0.0006 811.7917 1207.846587 0 0.0001 82 | 1/8 6 h-lim-p 0.0379 0.3029 1.5201 .. | 1/8 7 h-lim-p 0.0000 0.0113 101.4149 1205.132548 0 0.0006 137 | 1/8 8 h-lim-p 0.0006 0.0046 105.5299 1187.003225 0 0.0035 151 | 1/8 9 h-lim-p 0.0000 0.0002 890.0260 1177.485730 m 0.0002 163 | 1/8 10 h-lim-p 0.0009 0.0075 24.8827 1175.864494 0 0.0038 177 | 1/8 11 h-lim-p 0.0007 0.0057 73.3035 1169.280941 0 0.0043 191 | 1/8 12 h-lim-p 0.0022 0.0174 5.4839 1162.462094 m 0.0174 203 | 1/8 13 h-lim-p 0.0222 0.1772 1.8697 1144.316511 m 0.1772 215 | 0/8 14 h-lim-p 0.0000 0.0000 8.6019 h-lim-p: 9.19364935e-23 7.35491948e-22 8.60188772e+00 1144.316511 .. | 0/8 15 h-lim-p 0.0000 0.0485 2056.9327 1107.567035 0 0.0001 238 | 0/8 16 h-lim-p 0.0002 0.0018 150.4805 1095.108941 0 0.0009 252 | 0/8 17 h-lim-p 0.0001 0.0009 71.9532 1093.831583 0 0.0005 266 | 0/8 18 h-lim-p 0.0006 0.0048 29.2316 1093.469417 0 0.0012 279 | 0/8 19 h-lim-p 0.0094 0.0752 1.1724 1093.464127 6 0.0030 307 | 0/8 20 h-lim-p 0.0230 2.1482 0.1519 1091.866175 0 0.7345 324 | 0/8 21 h-lim-p 2.5000 20.0000 0.0159 1091.593618 5 1.0980 353 | 0/8 22 h-lim-p 2.5000 20.0000 0.0040 1091.163967 0 7.5000 374 | 0/8 23 h-lim-p 2.4075 20.0000 0.0125 1091.069364 5 1.0615 403 | 0/8 24 h-lim-p 2.5000 20.0000 0.0051 1091.063085 2 1.1719 427 | 0/8 25 h-lim-p 2.5000 20.0000 0.0007 1091.062964 3 1.0004 453 | 0/8 26 h-lim-p 2.5000 20.0000 0.0001 1091.062960 1 0.9961 475 | 0/8 27 h-lim-p 2.5000 20.0000 0.0000 1091.062960 0 1.0938 495 | 0/8 28 h-lim-p 1.0302 20.0000 0.0000 1091.062960 0 0.0000 539 | 0/8 29 h-lim-p 0.0000 20.0000 0.0002 1091.062960 0 0.0000 563 | 0/8 30 h-lim-p 0.0000 20.0000 0.0001 1091.062960 0 0.0000 598 | 0/8 31 h-lim-p 0.0000 20.0000 0.0002 1091.062960 0 0.0000 632 | 0/8 32 h-lim-p 0.0000 20.0000 0.0002 1091.062960 0 0.0000 665 | 0/8 33 h-lim-p 0.0000 20.0000 0.0002 | 0/8 34 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1091.062960 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1091.062960 Node 7: lnL = -1091.062960 Node 8: lnL = -1091.062960 Node 9: lnL = -1091.062960 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 517 Sequential format.. Reading seq # 1: YJL121C_Sbay Reading seq # 2: YJL121C_Scer Reading seq # 3: YJL121C_Skud Reading seq # 4: YJL121C_Smik Reading seq # 5: YJL121C_Spar Sequences read.. Counting patterns.. # site patterns = 226 Counting frequencies.. 120 bytes for distance 36160 bytes for lkl0 28928 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.048556 0.102901 0.033211 0.142329 0.103554 0.247776 0.579547 0.304644 lnL0 = -2613.149843 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2613.149843 x= 0.04856 0.10290 0.03321 0.14233 0.10355 0.24778 0.57955 0.30464 1 h-lim-p 0.0022 0.0213 154.0627 2610.479908 4 0.0003 32 | 0/8 2 h-lim-p 0.0008 0.0066 39.6092 2609.797577 6 0.0009 57 | 0/8 3 h-lim-p 0.0010 0.0077 22.1929 2609.724649 5 0.0004 79 | 0/8 4 h-lim-p 0.0019 0.0222 4.3455 2609.711547 4 0.0015 99 | 0/8 5 h-lim-p 0.0056 0.2261 1.1364 2609.711226 3 0.0005 119 | 0/8 6 h-lim-p 0.0037 4.1077 0.1646 2609.711163 1 0.0038 133 | 0/8 7 h-lim-p 0.0042 0.8186 0.1480 2609.711152 0 0.0011 154 | 0/8 8 h-lim-p 0.0769 20.0000 0.0020 2609.706787 0 0.9224 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 2609.706711 3 0.9482 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2609.706711 0 1.0938 223 | 0/8 11 h-lim-p 1.7140 20.0000 0.0000 2609.706711 0 1.4997 243 | 0/8 12 h-lim-p 1.6790 20.0000 0.0000 2609.706711 0 1.4692 263 | 0/8 13 h-lim-p 0.3813 20.0000 0.0000 2609.706711 0 0.0001 294 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 2609.706711 0 0.0000 319 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 2609.706711 0 0.0000 349 Out... lnL = -2609.706711 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2609.706711 Node 7: lnL = -2609.706711 Node 8: lnL = -2609.706711 Node 9: lnL = -2609.706711 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 296 Sequential format.. Reading seq # 1: YJL122W_Sbay Reading seq # 2: YJL122W_Scer Reading seq # 3: YJL122W_Skud Reading seq # 4: YJL122W_Smik Reading seq # 5: YJL122W_Spar Sequences read.. Counting patterns.. # site patterns = 145 Counting frequencies.. 120 bytes for distance 23200 bytes for lkl0 18560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.053138 0.088983 0.042065 0.097579 0.056810 0.213503 0.143991 0.204935 lnL0 = -1188.644866 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1188.644866 x= 0.05314 0.08898 0.04206 0.09758 0.05681 0.21350 0.14399 0.20494 1 h-lim-p 0.0037 0.2894 79.8844 1187.615994 7 0.0004 37 | 0/8 2 h-lim-p 0.0019 0.0150 14.4636 1187.535282 6 0.0008 63 | 0/8 3 h-lim-p 0.0015 0.0300 7.5301 1187.517715 6 0.0008 91 | 0/8 4 h-lim-p 0.0031 0.0725 1.8480 1187.516587 2 0.0007 108 | 0/8 5 h-lim-p 0.0040 0.4862 0.3364 1187.516521 3 0.0012 129 | 0/8 6 h-lim-p 0.0047 3.1024 0.0853 1187.516519 1 0.0009 152 | 0/8 7 h-lim-p 0.0116 18.7419 0.0068 1187.516518 0 0.0051 172 | 0/8 8 h-lim-p 0.0376 20.0000 0.0009 1187.516436 0 0.3011 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1187.516434 0 1.0938 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1187.516434 0 1.0938 235 | 0/8 11 h-lim-p 1.2255 20.0000 0.0000 1187.516434 0 0.0010 264 | 0/8 12 h-lim-p 0.0003 20.0000 0.0000 1187.516434 0 0.0000 286 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 1187.516434 0 0.0001 306 Out... lnL = -1187.516434 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1187.516434 Node 7: lnL = -1187.516434 Node 8: lnL = -1187.516434 Node 9: lnL = -1187.516434 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 393 Sequential format.. Reading seq # 1: YJL124C_Sbay Reading seq # 2: YJL124C_Scer Reading seq # 3: YJL124C_Skud Reading seq # 4: YJL124C_Smik Reading seq # 5: YJL124C_Spar Sequences read.. Counting patterns.. # site patterns = 139 Counting frequencies.. 120 bytes for distance 22240 bytes for lkl0 17792 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.033618 0.063423 0.071054 0.116381 0.045064 0.122881 0.152183 0.165056 lnL0 = -1594.350808 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1594.350808 x= 0.03362 0.06342 0.07105 0.11638 0.04506 0.12288 0.15218 0.16506 1 h-lim-p 0.0001 0.0009 100.9051 1592.903536 0 0.0003 23 | 0/8 2 h-lim-p 0.0009 0.0093 38.0610 1592.774065 2 0.0002 40 | 0/8 3 h-lim-p 0.0006 0.0108 13.6482 1592.742534 6 0.0004 67 | 0/8 4 h-lim-p 0.0027 0.0681 1.9098 1592.741735 3 0.0005 88 | 0/8 5 h-lim-p 0.0040 0.9170 0.2156 1592.741715 2 0.0006 106 | 0/8 6 h-lim-p 0.0025 3.9552 0.0544 1592.741634 0 0.0076 127 | 0/8 7 h-lim-p 0.0133 3.3315 0.0312 1592.734009 0 0.1064 150 | 0/8 8 h-lim-p 0.0020 0.0459 1.6963 1592.733073 5 0.0005 183 | 0/8 9 h-lim-p 1.1012 20.0000 0.0008 1592.732302 3 0.9980 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1592.732302 0 1.0938 221 | 0/8 11 h-lim-p 0.5847 20.0000 0.0000 1592.732302 0 0.5847 241 | 0/8 12 h-lim-p 0.3215 20.0000 0.0000 1592.732302 0 0.0050 266 | 0/8 13 h-lim-p 0.0020 20.0000 0.0001 1592.732302 0 0.0000 299 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 1592.732302 0 0.0000 333 Out... lnL = -1592.732302 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1592.732302 Node 7: lnL = -1592.732302 Node 8: lnL = -1592.732302 Node 9: lnL = -1592.732302 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 468 Sequential format.. Reading seq # 1: YJL125C_Sbay Reading seq # 2: YJL125C_Scer Reading seq # 3: YJL125C_Skud Reading seq # 4: YJL125C_Smik Reading seq # 5: YJL125C_Spar Sequences read.. Counting patterns.. # site patterns = 162 Counting frequencies.. 120 bytes for distance 25920 bytes for lkl0 20736 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.030467 0.048483 0.040997 0.088202 0.081752 0.179882 0.157833 0.161413 lnL0 = -1710.809994 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1710.809994 x= 0.03047 0.04848 0.04100 0.08820 0.08175 0.17988 0.15783 0.16141 1 h-lim-p 0.0362 4.4763 30.7315 1710.703139 3 0.0002 34 | 0/8 2 h-lim-p 0.0005 0.0123 13.5038 1710.656095 1 0.0007 48 | 0/8 3 h-lim-p 0.0024 0.0197 3.8467 1710.651523 6 0.0007 76 | 0/8 4 h-lim-p 0.0007 0.0275 3.5675 1710.649762 5 0.0005 102 | 0/8 5 h-lim-p 0.0017 0.1482 0.9261 1710.649608 2 0.0004 119 | 0/8 6 h-lim-p 0.0008 0.1474 0.4735 1710.649552 2 0.0006 143 | 0/8 7 h-lim-p 0.0039 0.7628 0.0768 1710.649551 0 0.0004 165 | 0/8 8 h-lim-p 0.0315 20.0000 0.0010 1710.649047 0 1.0095 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1710.649031 1 0.9961 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1710.649031 0 2.1875 232 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1710.649031 0 0.5469 253 | 0/8 12 h-lim-p 0.0513 20.0000 0.0000 1710.649031 0 0.0128 274 | 0/8 13 h-lim-p 0.0052 20.0000 0.0000 1710.649031 0 0.0000 315 | 0/8 14 h-lim-p 0.0000 20.0000 0.0016 | 0/8 15 h-lim-p 0.0000 20.0000 0.0016 Out... lnL = -1710.649031 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1710.649031 Node 7: lnL = -1710.649031 Node 8: lnL = -1710.649031 Node 9: lnL = -1710.649031 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 872 Sequential format.. Reading seq # 1: YJL133W_Sbay Reading seq # 2: YJL133W_Scer Reading seq # 3: YJL133W_Skud Reading seq # 4: YJL133W_Smik Reading seq # 5: YJL133W_Spar Sequences read.. Counting patterns.. # site patterns = 267 Counting frequencies.. 120 bytes for distance 42720 bytes for lkl0 34176 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.059248 0.063392 0.067578 0.096680 0.072723 0.159090 0.173961 0.211543 lnL0 = -3674.338742 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3674.338742 x= 0.05925 0.06339 0.06758 0.09668 0.07272 0.15909 0.17396 0.21154 1 h-lim-p 0.0022 0.7144 181.8521 3671.852779 8 0.0002 44 | 0/8 2 h-lim-p 0.0006 0.0046 33.0389 3671.742450 6 0.0002 72 | 0/8 3 h-lim-p 0.0005 0.0091 15.0167 3671.719959 5 0.0002 96 | 0/8 4 h-lim-p 0.0007 0.0408 4.9004 3671.716784 3 0.0003 114 | 0/8 5 h-lim-p 0.0028 0.4150 0.5326 3671.716741 2 0.0003 132 | 0/8 6 h-lim-p 0.0009 0.9997 0.1855 3671.716737 1 0.0002 155 | 0/8 7 h-lim-p 0.0042 11.3530 0.0095 3671.716735 0 0.0037 175 | 0/8 8 h-lim-p 0.0094 20.0000 0.0037 3671.716294 0 0.1510 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3671.716260 1 0.9961 221 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3671.716260 0 1.0938 241 | 0/8 11 h-lim-p 0.9449 20.0000 0.0000 3671.716260 0 0.0037 268 | 0/8 12 h-lim-p 0.0002 20.0000 0.0005 3671.716260 0 0.0000 302 | 0/8 13 h-lim-p 0.0000 20.0000 0.0005 | 0/8 14 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -3671.716260 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3671.716260 Node 7: lnL = -3671.716260 Node 8: lnL = -3671.716260 Node 9: lnL = -3671.716260 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 852 Sequential format.. Reading seq # 1: YJL134W_Sbay Reading seq # 2: YJL134W_Scer Reading seq # 3: YJL134W_Skud Reading seq # 4: YJL134W_Smik Reading seq # 5: YJL134W_Spar Sequences read.. Counting patterns.. # site patterns = 338 Counting frequencies.. 120 bytes for distance 54080 bytes for lkl0 43264 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.122522 0.026097 0.065979 0.151358 0.128337 0.238994 0.274213 0.341640 lnL0 = -4098.766565 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4098.766565 x= 0.12252 0.02610 0.06598 0.15136 0.12834 0.23899 0.27421 0.34164 1 h-lim-p 0.0010 0.0084 151.1245 4096.710774 8 0.0002 41 | 0/8 2 h-lim-p 0.0009 0.0074 24.9013 4096.594754 3 0.0004 59 | 0/8 3 h-lim-p 0.0007 0.0283 13.4705 4096.562442 6 0.0004 88 | 0/8 4 h-lim-p 0.0012 0.0546 5.0206 4096.557637 4 0.0005 108 | 0/8 5 h-lim-p 0.0019 0.2502 1.2133 4096.557106 1 0.0007 122 | 0/8 6 h-lim-p 0.0030 0.8168 0.3049 4096.557088 2 0.0004 140 | 0/8 7 h-lim-p 0.0017 3.0868 0.0712 4096.557086 0 0.0007 160 | 0/8 8 h-lim-p 0.2641 20.0000 0.0002 4096.556987 0 1.0562 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4096.556986 0 1.0938 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4096.556986 0 1.0938 222 | 0/8 11 h-lim-p 1.5188 20.0000 0.0000 4096.556986 0 0.6645 242 | 0/8 12 h-lim-p 0.2553 20.0000 0.0000 4096.556986 0 0.0319 264 | 0/8 13 h-lim-p 0.0094 20.0000 0.0001 4096.556986 0 0.0000 301 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 4096.556986 0 0.0000 322 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 | 0/8 17 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -4096.556986 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4096.556986 Node 7: lnL = -4096.556986 Node 8: lnL = -4096.556986 Node 9: lnL = -4096.556986 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 41 Sequential format.. Reading seq # 1: YJL137C_Sbay Reading seq # 2: YJL137C_Scer Reading seq # 3: YJL137C_Skud Reading seq # 4: YJL137C_Smik Reading seq # 5: YJL137C_Spar Sequences read.. Counting patterns.. # site patterns = 34 Counting frequencies.. 120 bytes for distance 5440 bytes for lkl0 4352 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.044867 0.347551 0.000060 0.438297 0.119476 0.566071 0.828357 0.424042 lnL0 = -206.572875 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 206.572875 x= 0.04487 0.34755 0.00006 0.43830 0.11948 0.56607 0.82836 0.42404 1 h-lim-p 0.0000 0.0000 9.9836 206.571294 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0339 21.9208 205.473141 0 0.0102 44 | 1/8 3 h-lim-p 0.0106 0.0844 1.1932 205.377871 m 0.0844 56 | 1/8 4 h-lim-p 0.0000 0.0000 2.6654 h-lim-p: 4.52904686e-18 3.62323749e-17 2.66535238e+00 205.377871 .. | 1/8 5 h-lim-p 0.0000 0.0436 7.5673 205.007035 0 0.0102 86 | 1/8 6 h-lim-p 0.0442 0.3539 1.4229 204.985371 6 0.0217 111 | 1/8 7 h-lim-p 0.0608 0.6471 0.5082 204.972693 0 0.1216 124 | 0/8 8 h-lim-p 0.0136 0.1090 2.8289 204.965952 7 0.0098 160 | 0/8 9 h-lim-p 0.0073 0.0585 1.3329 204.960806 0 0.0220 173 | 0/8 10 h-lim-p 0.0451 0.3608 0.0960 204.959045 0 0.0902 186 | 0/8 11 h-lim-p 0.0425 0.8279 0.2038 204.951451 0 0.1699 208 | 0/8 12 h-lim-p 0.4776 13.6754 0.0725 204.950172 6 0.3297 244 | 0/8 13 h-lim-p 2.5000 20.0000 0.0024 204.950031 4 0.9131 273 | 0/8 14 h-lim-p 2.5000 20.0000 0.0003 204.950031 0 1.0938 293 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 204.950031 0 1.0938 313 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 204.950031 0 2.1875 333 | 0/8 17 h-lim-p 2.0251 20.0000 0.0000 204.950031 0 0.8860 353 | 0/8 18 h-lim-p 1.9893 20.0000 0.0000 204.950031 0 0.0932 377 | 0/8 19 h-lim-p 0.0346 20.0000 0.0000 204.950031 0 0.0087 398 | 0/8 20 h-lim-p 0.0043 20.0000 0.0000 204.950031 0 0.0043 418 | 0/8 21 h-lim-p 0.0027 20.0000 0.0000 204.950031 0 0.0000 447 Out... lnL = -204.950031 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -204.950031 Node 7: lnL = -204.950031 Node 8: lnL = -204.950031 Node 9: lnL = -204.950031 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 300 Sequential format.. Reading seq # 1: YJL138C_Sbay Reading seq # 2: YJL138C_Scer Reading seq # 3: YJL138C_Skud Reading seq # 4: YJL138C_Smik Reading seq # 5: YJL138C_Spar Sequences read.. Counting patterns.. # site patterns = 104 Counting frequencies.. 120 bytes for distance 16640 bytes for lkl0 13312 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.343049 0.092674 0.065260 0.051793 0.028186 0.095909 0.063986 0.548842 lnL0 = -1209.634394 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1209.634394 x= 0.34305 0.09267 0.06526 0.05179 0.02819 0.09591 0.06399 0.54884 1 h-lim-p 0.0001 0.0008 76.7791 1208.795259 0 0.0004 24 | 0/8 2 h-lim-p 0.0008 0.0075 40.3480 1208.705488 7 0.0001 54 | 0/8 3 h-lim-p 0.0004 0.0083 14.2748 1208.654940 0 0.0006 66 | 0/8 4 h-lim-p 0.0010 0.0123 8.5010 1208.596922 0 0.0020 79 | 0/8 5 h-lim-p 0.0013 0.0107 5.4189 1208.591868 5 0.0005 101 | 0/8 6 h-lim-p 0.0022 0.5063 1.2591 1208.588559 0 0.0044 114 | 0/8 7 h-lim-p 0.0014 0.0562 3.9261 1208.587678 5 0.0004 141 | 0/8 8 h-lim-p 0.2716 17.3728 0.0061 1208.539436 0 1.0864 155 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 1208.538849 0 1.2500 175 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1208.538842 1 0.9961 197 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1208.538842 0 1.0938 217 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1208.538842 0 0.0195 243 | 0/8 13 h-lim-p 0.0093 20.0000 0.0000 1208.538842 0 0.0000 285 Out... lnL = -1208.538842 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1208.538842 Node 7: lnL = -1208.538842 Node 8: lnL = -1208.538842 Node 9: lnL = -1208.538842 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 529 Sequential format.. Reading seq # 1: YJL139C_Sbay Reading seq # 2: YJL139C_Scer Reading seq # 3: YJL139C_Skud Reading seq # 4: YJL139C_Smik Reading seq # 5: YJL139C_Spar Sequences read.. Counting patterns.. # site patterns = 165 Counting frequencies.. 120 bytes for distance 26400 bytes for lkl0 21120 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.027114 0.081042 0.064809 0.066507 0.043367 0.171548 0.114183 0.145438 lnL0 = -2086.789745 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2086.789745 x= 0.02711 0.08104 0.06481 0.06651 0.04337 0.17155 0.11418 0.14544 1 h-lim-p 0.0049 1.3377 92.7524 2085.819518 4 0.0002 33 | 0/8 2 h-lim-p 0.0004 0.0032 27.9940 2085.743945 4 0.0002 54 | 0/8 3 h-lim-p 0.0003 0.0070 17.9163 2085.715296 5 0.0002 76 | 0/8 4 h-lim-p 0.0018 0.1051 2.3956 2085.714112 2 0.0004 93 | 0/8 5 h-lim-p 0.0010 0.1186 0.9880 2085.714000 3 0.0003 112 | 0/8 6 h-lim-p 0.0012 0.6797 0.2280 2085.713991 2 0.0004 138 | 0/8 7 h-lim-p 0.0034 1.9155 0.0258 2085.713991 0 0.0004 160 | 0/8 8 h-lim-p 0.0244 20.0000 0.0004 2085.713835 0 0.7795 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2085.713834 0 1.0938 205 | 0/8 10 h-lim-p 1.2688 20.0000 0.0000 2085.713834 0 1.2688 225 | 0/8 11 h-lim-p 1.2685 20.0000 0.0000 2085.713834 0 0.0003 256 | 0/8 12 h-lim-p 0.0000 20.0000 0.0005 2085.713834 0 0.0000 276 | 0/8 13 h-lim-p 0.0002 20.0000 0.0000 2085.713834 0 0.0000 297 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 2085.713834 0 0.0000 322 | 0/8 15 h-lim-p 0.0065 20.0000 0.0000 2085.713834 0 0.0000 351 Out... lnL = -2085.713834 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2085.713834 Node 7: lnL = -2085.713834 Node 8: lnL = -2085.713834 Node 9: lnL = -2085.713834 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 609 Sequential format.. Reading seq # 1: YJL140W_Sbay Reading seq # 2: YJL140W_Scer Reading seq # 3: YJL140W_Skud Reading seq # 4: YJL140W_Smik Reading seq # 5: YJL140W_Spar Sequences read.. Counting patterns.. # site patterns = 261 Counting frequencies.. 120 bytes for distance 41760 bytes for lkl0 33408 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.061586 0.079016 0.079873 0.127846 0.111280 0.210047 0.222404 0.244409 lnL0 = -2820.639884 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2820.639884 x= 0.06159 0.07902 0.07987 0.12785 0.11128 0.21005 0.22240 0.24441 1 h-lim-p 0.0056 1.4875 99.9464 2819.215722 7 0.0003 41 | 0/8 2 h-lim-p 0.0019 0.0153 15.1506 2819.168150 5 0.0004 63 | 0/8 3 h-lim-p 0.0011 0.0277 5.8250 2819.161452 3 0.0005 81 | 0/8 4 h-lim-p 0.0030 0.2807 0.8765 2819.161238 3 0.0006 100 | 0/8 5 h-lim-p 0.0028 2.7691 0.1824 2819.161227 1 0.0007 123 | 0/8 6 h-lim-p 0.0071 20.0000 0.0176 2819.161227 0 0.0015 144 | 0/8 7 h-lim-p 0.0037 20.0000 0.0074 2819.161227 0 0.0016 164 | 0/8 8 h-lim-p 0.0430 20.0000 0.0003 2819.161202 0 0.5166 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2819.161202 0 1.0938 207 | 0/8 10 h-lim-p 1.4548 20.0000 0.0000 2819.161202 0 1.2730 227 | 0/8 11 h-lim-p 1.2248 20.0000 0.0000 2819.161202 0 2.4495 248 | 0/8 12 h-lim-p 0.2284 20.0000 0.0002 2819.161202 0 0.0143 271 | 0/8 13 h-lim-p 0.0031 20.0000 0.0007 2819.161202 0 0.0031 291 | 0/8 14 h-lim-p 0.0002 8.7177 0.0101 2819.161202 0 0.0000 313 | 0/8 15 h-lim-p 0.0007 20.0000 0.0006 2819.161202 0 0.0000 344 | 0/8 16 h-lim-p 0.0006 20.0000 0.0000 2819.161202 0 0.0000 376 Out... lnL = -2819.161202 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2819.161202 Node 7: lnL = -2819.161202 Node 8: lnL = -2819.161202 Node 9: lnL = -2819.161202 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 454 Sequential format.. Reading seq # 1: YJL143W_Sbay Reading seq # 2: YJL143W_Scer Reading seq # 3: YJL143W_Skud Reading seq # 4: YJL143W_Smik Reading seq # 5: YJL143W_Spar Sequences read.. Counting patterns.. # site patterns = 190 Counting frequencies.. 120 bytes for distance 30400 bytes for lkl0 24320 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.098197 0.000060 0.059954 0.131048 0.072750 0.234381 0.283281 0.269359 lnL0 = -1824.245624 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1824.245624 x= 0.09820 0.00006 0.05995 0.13105 0.07275 0.23438 0.28328 0.26936 1 h-lim-p 0.0005 0.0040 72.4465 1822.569868 2 0.0005 26 | 0/8 2 h-lim-p 0.0005 0.0037 48.5199 1821.972987 0 0.0009 39 | 0/8 3 h-lim-p 0.0007 0.0052 40.2082 1821.664263 6 0.0006 64 | 0/8 4 h-lim-p 0.0008 0.0099 31.9582 1821.545821 7 0.0005 94 | 0/8 5 h-lim-p 0.0012 0.0223 11.7517 1821.486310 2 0.0012 110 | 0/8 6 h-lim-p 0.0073 0.1170 1.8772 1821.485406 5 0.0005 135 | 0/8 7 h-lim-p 0.0065 1.5075 0.1447 1821.483236 0 0.0129 148 | 0/8 8 h-lim-p 0.0093 0.3861 0.2017 1821.331955 0 0.0742 171 | 0/8 9 h-lim-p 2.5000 20.0000 0.0017 1821.329648 5 0.9273 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1821.329639 1 0.9961 224 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1821.329639 0 1.0938 244 | 0/8 12 h-lim-p 1.5615 20.0000 0.0000 1821.329639 0 0.6831 264 | 0/8 13 h-lim-p 0.4122 20.0000 0.0000 1821.329639 0 0.0064 289 | 0/8 14 h-lim-p 0.0021 20.0000 0.0000 1821.329639 0 0.0000 325 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1821.329639 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1821.329639 Node 7: lnL = -1821.329639 Node 8: lnL = -1821.329639 Node 9: lnL = -1821.329639 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 350 Sequential format.. Reading seq # 1: YJL144W_Sbay Reading seq # 2: YJL144W_Scer Reading seq # 3: YJL144W_Skud Reading seq # 4: YJL144W_Smik Reading seq # 5: YJL144W_Spar Sequences read.. Counting patterns.. # site patterns = 149 Counting frequencies.. 120 bytes for distance 23840 bytes for lkl0 19072 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.090472 0.038935 0.052833 0.126537 0.094837 0.112816 0.182809 0.238347 lnL0 = -1433.612062 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1433.612062 x= 0.09047 0.03893 0.05283 0.12654 0.09484 0.11282 0.18281 0.23835 1 h-lim-p 0.0016 0.0131 95.6363 1432.123905 5 0.0004 32 | 0/8 2 h-lim-p 0.0009 0.0072 29.1625 1431.778812 2 0.0008 48 | 0/8 3 h-lim-p 0.0027 0.0262 9.1811 1431.757193 5 0.0006 74 | 0/8 4 h-lim-p 0.0019 0.0722 2.7404 1431.754924 5 0.0007 98 | 0/8 5 h-lim-p 0.0046 0.4146 0.3998 1431.754859 3 0.0008 118 | 0/8 6 h-lim-p 0.0208 8.0302 0.0155 1431.754859 0 0.0011 141 | 0/8 7 h-lim-p 0.0043 20.0000 0.0041 1431.754859 0 0.0085 162 | 0/8 8 h-lim-p 0.0208 20.0000 0.0017 1431.754807 0 0.1248 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1431.754807 0 1.0938 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1431.754807 0 1.0938 224 | 0/8 11 h-lim-p 1.3953 20.0000 0.0000 1431.754807 0 1.2209 244 | 0/8 12 h-lim-p 0.9748 20.0000 0.0000 1431.754807 0 0.4874 264 | 0/8 13 h-lim-p 0.0017 20.0000 0.0021 1431.754807 0 0.0015 284 | 0/8 14 h-lim-p 0.0006 20.0000 0.0049 1431.754807 0 0.0000 321 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 1431.754807 0 0.0000 351 Out... lnL = -1431.754807 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1431.754807 Node 7: lnL = -1431.754807 Node 8: lnL = -1431.754807 Node 9: lnL = -1431.754807 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 483 Sequential format.. Reading seq # 1: YJL145W_Sbay Reading seq # 2: YJL145W_Scer Reading seq # 3: YJL145W_Skud Reading seq # 4: YJL145W_Smik Reading seq # 5: YJL145W_Spar Sequences read.. Counting patterns.. # site patterns = 207 Counting frequencies.. 120 bytes for distance 33120 bytes for lkl0 26496 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.013733 0.128856 0.091730 0.137348 0.074201 0.210500 0.166391 0.181284 lnL0 = -2117.378296 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2117.378296 x= 0.01373 0.12886 0.09173 0.13735 0.07420 0.21050 0.16639 0.18128 1 h-lim-p 0.0017 0.0140 70.2214 2116.248963 9 0.0005 43 | 0/8 2 h-lim-p 0.0003 0.0021 23.1577 2116.112980 0 0.0005 56 | 0/8 3 h-lim-p 0.0014 0.0212 8.9781 2116.102610 4 0.0003 76 | 0/8 4 h-lim-p 0.0012 0.1511 2.3333 2116.101221 2 0.0005 92 | 0/8 5 h-lim-p 0.0019 0.3050 0.6521 2116.101100 3 0.0006 112 | 0/8 6 h-lim-p 0.0093 7.4331 0.0435 2116.101098 0 0.0010 134 | 0/8 7 h-lim-p 0.0021 11.1500 0.0215 2116.101087 0 0.0083 156 | 0/8 8 h-lim-p 0.0124 14.5277 0.0143 2116.100204 0 0.0993 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 2116.100175 2 0.9961 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2116.100175 0 1.0938 223 | 0/8 11 h-lim-p 0.9398 20.0000 0.0000 2116.100175 0 0.0147 248 | 0/8 12 h-lim-p 0.0001 3.9745 0.0052 2116.100175 0 0.0000 270 | 0/8 13 h-lim-p 0.0001 20.0000 0.0005 2116.100175 0 0.0001 290 | 0/8 14 h-lim-p 0.0000 20.0000 0.0015 2116.100175 0 0.0000 315 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 2116.100175 0 0.0000 338 Out... lnL = -2116.100175 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2116.100175 Node 7: lnL = -2116.100175 Node 8: lnL = -2116.100175 Node 9: lnL = -2116.100175 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 755 Sequential format.. Reading seq # 1: YJL146W_Sbay Reading seq # 2: YJL146W_Scer Reading seq # 3: YJL146W_Skud Reading seq # 4: YJL146W_Smik Reading seq # 5: YJL146W_Spar Sequences read.. Counting patterns.. # site patterns = 294 Counting frequencies.. 120 bytes for distance 47040 bytes for lkl0 37632 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.049852 0.083658 0.072303 0.142413 0.099401 0.252709 0.296620 0.248905 lnL0 = -3700.059645 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3700.059645 x= 0.04985 0.08366 0.07230 0.14241 0.09940 0.25271 0.29662 0.24891 1 h-lim-p 0.0005 0.0036 101.9646 3698.624432 6 0.0003 36 | 0/8 2 h-lim-p 0.0006 0.0044 28.1921 3698.460740 4 0.0004 56 | 0/8 3 h-lim-p 0.0011 0.0160 11.0404 3698.445026 5 0.0003 79 | 0/8 4 h-lim-p 0.0007 0.0487 4.8730 3698.441716 4 0.0003 101 | 0/8 5 h-lim-p 0.0013 0.3728 1.2990 3698.441280 2 0.0006 117 | 0/8 6 h-lim-p 0.0048 2.4738 0.1506 3698.441270 2 0.0008 135 | 0/8 7 h-lim-p 0.0066 9.7026 0.0176 3698.441270 0 0.0015 156 | 0/8 8 h-lim-p 0.0298 20.0000 0.0009 3698.441050 0 0.4767 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3698.441049 0 1.0938 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3698.441048 0 1.0938 220 | 0/8 11 h-lim-p 1.5234 20.0000 0.0000 3698.441048 0 1.5234 240 | 0/8 12 h-lim-p 0.2006 20.0000 0.0002 3698.441048 0 0.0501 261 | 0/8 13 h-lim-p 0.0109 20.0000 0.0007 3698.441048 0 0.0000 288 | 0/8 14 h-lim-p 0.0007 20.0000 0.0000 3698.441048 0 0.0007 308 | 0/8 15 h-lim-p 0.0005 20.0000 0.0001 3698.441048 0 0.0003 328 | 0/8 16 h-lim-p 0.0004 20.0000 0.0000 3698.441048 0 0.0000 357 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 3698.441048 0 0.0000 386 Out... lnL = -3698.441048 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3698.441048 Node 7: lnL = -3698.441048 Node 8: lnL = -3698.441048 Node 9: lnL = -3698.441048 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 752 Sequential format.. Reading seq # 1: YJL147C_Sbay Reading seq # 2: YJL147C_Scer Reading seq # 3: YJL147C_Skud Reading seq # 4: YJL147C_Smik Reading seq # 5: YJL147C_Spar Sequences read.. Counting patterns.. # site patterns = 290 Counting frequencies.. 120 bytes for distance 46400 bytes for lkl0 37120 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.046664 0.114070 0.089387 0.137733 0.104081 0.230408 0.283854 0.250991 lnL0 = -3711.793922 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3711.793922 x= 0.04666 0.11407 0.08939 0.13773 0.10408 0.23041 0.28385 0.25099 1 h-lim-p 0.0013 0.0107 93.5767 3710.444580 8 0.0003 39 | 0/8 2 h-lim-p 0.0009 0.0069 23.8440 3710.318542 5 0.0005 62 | 0/8 3 h-lim-p 0.0011 0.0144 10.3607 3710.306990 2 0.0003 79 | 0/8 4 h-lim-p 0.0011 0.0789 2.4736 3710.305664 2 0.0005 95 | 0/8 5 h-lim-p 0.0011 0.3222 1.0084 3710.305380 4 0.0006 118 | 0/8 6 h-lim-p 0.0055 2.6119 0.1176 3710.305377 1 0.0003 135 | 0/8 7 h-lim-p 0.0032 20.0000 0.0123 3710.305375 0 0.0048 155 | 0/8 8 h-lim-p 0.0187 20.0000 0.0032 3710.304986 0 0.2243 178 | 0/8 9 h-lim-p 1.0891 20.0000 0.0007 3710.304967 0 0.9530 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3710.304967 0 1.0938 218 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3710.304967 0 1.0938 238 | 0/8 12 h-lim-p 0.5006 20.0000 0.0000 3710.304967 0 0.0156 262 | 0/8 13 h-lim-p 0.0008 20.0000 0.0004 3710.304967 0 0.0000 288 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 3710.304967 0 0.0001 308 | 0/8 15 h-lim-p 0.0004 20.0000 0.0000 3710.304967 0 0.0000 339 Out... lnL = -3710.304967 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3710.304967 Node 7: lnL = -3710.304967 Node 8: lnL = -3710.304967 Node 9: lnL = -3710.304967 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 847 Sequential format.. Reading seq # 1: YJL148W_Sbay Reading seq # 2: YJL148W_Scer Reading seq # 3: YJL148W_Skud Reading seq # 4: YJL148W_Smik Reading seq # 5: YJL148W_Spar Sequences read.. Counting patterns.. # site patterns = 209 Counting frequencies.. 120 bytes for distance 33440 bytes for lkl0 26752 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.032719 0.027654 0.040198 0.067377 0.056828 0.085245 0.136073 0.123458 lnL0 = -3083.886333 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3083.886333 x= 0.03272 0.02765 0.04020 0.06738 0.05683 0.08524 0.13607 0.12346 1 h-lim-p 0.0005 0.0059 338.6780 3080.135110 9 0.0001 42 | 0/8 2 h-lim-p 0.0004 0.0035 24.8797 3080.094515 7 0.0001 71 | 0/8 3 h-lim-p 0.0004 0.0286 8.4169 3080.090122 4 0.0001 92 | 0/8 4 h-lim-p 0.0004 0.0401 2.6232 3080.089689 4 0.0001 114 | 0/8 5 h-lim-p 0.0006 0.2624 0.5844 3080.089658 2 0.0002 132 | 0/8 6 h-lim-p 0.0013 1.4604 0.0921 3080.089657 0 0.0001 154 | 0/8 7 h-lim-p 0.0052 20.0000 0.0025 3080.089657 0 0.0006 176 | 0/8 8 h-lim-p 0.0096 20.0000 0.0002 3080.089646 0 0.3062 201 | 0/8 9 h-lim-p 0.5903 20.0000 0.0001 3080.089645 0 1.1807 222 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3080.089645 0 1.0938 242 | 0/8 11 h-lim-p 0.7223 20.0000 0.0001 3080.089645 0 0.0049 268 | 0/8 12 h-lim-p 0.0001 20.0000 0.0022 3080.089645 0 0.0001 288 | 0/8 13 h-lim-p 0.0001 10.0942 0.0051 3080.089645 0 0.0001 308 | 0/8 14 h-lim-p 0.0002 20.0000 0.0017 3080.089645 0 0.0000 342 | 0/8 15 h-lim-p 0.0000 20.0000 0.0009 3080.089645 0 0.0006 368 | 0/8 16 h-lim-p 0.0048 20.0000 0.0001 3080.089645 0 0.0000 396 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 3080.089645 0 0.0000 419 | 0/8 18 h-lim-p 0.0000 20.0000 0.0003 3080.089645 0 0.0000 443 | 0/8 19 h-lim-p 0.0000 20.0000 0.0009 .. | 0/8 20 h-lim-p 0.0000 20.0000 0.0046 3080.089645 0 0.0000 496 | 0/8 21 h-lim-p 0.0001 20.0000 0.0004 3080.089645 0 0.0009 520 | 0/8 22 h-lim-p 0.0029 20.0000 0.0001 3080.089645 0 0.0000 550 | 0/8 23 h-lim-p 0.0000 20.0000 0.0001 3080.089645 0 0.0000 570 | 0/8 24 h-lim-p 0.0000 20.0000 0.0003 3080.089645 0 0.0000 590 | 0/8 25 h-lim-p 0.0000 12.6330 0.0041 .. | 0/8 26 h-lim-p 0.0000 20.0000 0.0052 3080.089645 0 0.0000 652 | 0/8 27 h-lim-p 0.0000 20.0000 0.0004 3080.089645 0 0.0013 679 | 0/8 28 h-lim-p 0.0038 20.0000 0.0001 3080.089645 0 0.0000 714 | 0/8 29 h-lim-p 0.0000 5.3023 0.0181 .. | 0/8 30 h-lim-p 0.0000 20.0000 0.0069 3080.089645 0 0.0000 776 | 0/8 31 h-lim-p 0.0000 20.0000 0.0006 3080.089645 0 0.0002 800 | 0/8 32 h-lim-p 0.0005 20.0000 0.0002 3080.089645 0 0.0005 820 | 0/8 33 h-lim-p 0.0010 20.0000 0.0001 3080.089645 0 0.0004 841 | 0/8 34 h-lim-p 0.0002 20.0000 0.0002 3080.089645 0 0.0000 880 | 0/8 35 h-lim-p 0.0000 20.0000 0.0069 | 0/8 36 h-lim-p 0.0000 20.0000 0.0069 Out... lnL = -3080.089645 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3080.089645 Node 7: lnL = -3080.089645 Node 8: lnL = -3080.089645 Node 9: lnL = -3080.089645 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 448 Sequential format.. Reading seq # 1: YJL151C_Sbay Reading seq # 2: YJL151C_Scer Reading seq # 3: YJL151C_Skud Reading seq # 4: YJL151C_Smik Reading seq # 5: YJL151C_Spar Sequences read.. Counting patterns.. # site patterns = 140 Counting frequencies.. 120 bytes for distance 22400 bytes for lkl0 17920 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.297062 0.684581 0.879518 0.271303 2.818073 0.664462 0.563851 lnL0 = -1817.866966 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1817.866966 x= 0.00006 0.29706 0.68458 0.87952 0.27130 2.81807 0.66446 0.56385 1 h-lim-p 0.0000 0.0000 226.1823 1817.808448 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0101 65.1215 1779.469165 m 0.0101 41 | 2/8 3 h-lim-p 0.0000 0.0003 623.6017 1777.315065 m 0.0003 53 | 3/8 4 h-lim-p 0.0001 0.0009 1132.9482 1746.729737 10 0.0006 91 | 3/8 5 h-lim-p 0.0010 0.0078 103.4301 1711.167426 0 0.0039 105 | 3/8 6 h-lim-p 0.1413 1.1301 0.5388 1708.846722 0 0.2825 118 | 2/8 7 h-lim-p 0.0008 0.0062 129.4878 1705.204235 4 0.0008 143 | 2/8 8 h-lim-p 0.1213 0.9705 0.4680 1700.808474 0 0.4853 157 | 2/8 9 h-lim-p 0.5889 4.7111 0.0816 .. | 2/8 10 h-lim-p 0.0000 0.0061 90.5597 1678.456335 8 0.0045 248 | 1/8 11 h-lim-p 0.0000 0.0002 729.8078 1664.690752 m 0.0002 260 | 1/8 12 h-lim-p -0.0000 -0.0000 42346.2630 h-lim-p: -2.26004220e-23 -1.80803376e-22 4.23462630e+04 1664.690752 .. | 1/8 13 h-lim-p 0.0000 0.0040 247.8122 1647.674884 0 0.0006 286 | 1/8 14 h-lim-p 0.0000 0.0002 109.7421 1645.770371 m 0.0002 298 | 2/8 15 h-lim-p 0.0001 0.0020 203.7858 1637.051437 0 0.0012 313 | 2/8 16 h-lim-p 0.0066 0.0530 6.9823 1636.943330 2 0.0031 329 | 2/8 17 h-lim-p 0.0225 0.7976 0.9623 1636.462668 0 0.0451 342 | 2/8 18 h-lim-p 0.0116 0.0924 3.1732 1636.428837 6 0.0039 376 | 2/8 19 h-lim-p 0.0730 1.7754 0.1695 1634.319192 0 0.4380 390 | 1/8 20 h-lim-p -0.0000 -0.0000 1.8222 h-lim-p: -4.56422749e-21 -3.65138199e-20 1.82222290e+00 1634.319192 .. | 1/8 21 h-lim-p 0.0000 0.2683 19.9107 1634.194954 0 0.0006 422 | 1/8 22 h-lim-p 0.0001 0.0006 2.8891 1634.190737 m 0.0006 434 | 2/8 23 h-lim-p 0.0018 0.3918 0.9207 1634.190098 2 0.0017 450 | 2/8 24 h-lim-p 0.0068 3.0094 0.2315 1634.190062 2 0.0013 473 | 2/8 25 h-lim-p 0.0074 6.4905 0.0408 1634.190022 1 0.0093 493 | 2/8 26 h-lim-p 0.0164 20.0000 0.0230 1634.186299 0 0.1970 514 | 1/8 27 h-lim-p 0.3001 20.0000 0.0151 1634.186298 1 0.0046 539 | 0/8 28 h-lim-p 0.0013 20.0000 0.0540 1634.186294 0 0.0026 559 | 0/8 29 h-lim-p 0.0148 0.1180 0.0026 1634.186289 0 0.0295 580 | 0/8 30 h-lim-p 0.0806 0.6447 0.0004 1634.186276 m 0.6447 600 | 1/8 31 h-lim-p 0.0421 0.3371 0.0002 1634.186275 m 0.3371 620 | 2/8 32 h-lim-p 0.0771 20.0000 0.0006 1634.186275 0 0.0674 639 | 2/8 33 h-lim-p 2.5000 20.0000 0.0000 1634.186275 0 1.0938 657 | 1/8 34 h-lim-p -0.0000 -0.0000 0.0005 h-lim-p: -0.00000000e+00 -0.00000000e+00 5.16931026e-04 1634.186275 .. | 2/8 35 h-lim-p 0.0000 20.0000 0.0040 1634.186275 0 0.0010 696 | 2/8 36 h-lim-p 0.0039 20.0000 0.0010 1634.186275 0 0.0017 714 | 2/8 37 h-lim-p 0.0040 20.0000 0.0004 1634.186275 0 0.0018 732 | 2/8 38 h-lim-p 0.0077 20.0000 0.0001 1634.186275 0 0.0017 751 | 2/8 39 h-lim-p 0.0101 20.0000 0.0000 1634.186275 0 0.0088 769 | 2/8 40 h-lim-p 0.0490 20.0000 0.0000 1634.186275 0 0.2943 789 | 2/8 41 h-lim-p 2.5000 20.0000 0.0000 1634.186275 0 1.0938 807 Out... lnL = -1634.186275 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1634.186275 Node 7: lnL = -1634.186275 Node 8: lnL = -1634.186275 Node 9: lnL = -1634.186275 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 341 Sequential format.. Reading seq # 1: YJL156C_Sbay Reading seq # 2: YJL156C_Scer Reading seq # 3: YJL156C_Skud Reading seq # 4: YJL156C_Smik Reading seq # 5: YJL156C_Spar Sequences read.. Counting patterns.. # site patterns = 144 Counting frequencies.. 120 bytes for distance 23040 bytes for lkl0 18432 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.037963 0.050336 0.080859 0.157515 0.067446 0.207490 0.204016 0.198861 lnL0 = -1540.452662 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1540.452662 x= 0.03796 0.05034 0.08086 0.15751 0.06745 0.20749 0.20402 0.19886 1 h-lim-p 0.0026 0.0207 39.7019 1540.132075 6 0.0004 36 | 0/8 2 h-lim-p 0.0013 0.0134 13.3876 1540.080028 4 0.0006 57 | 0/8 3 h-lim-p 0.0014 0.0416 6.0178 1540.072452 6 0.0005 83 | 0/8 4 h-lim-p 0.0016 0.1416 1.8574 1540.071497 4 0.0006 103 | 0/8 5 h-lim-p 0.0061 0.3762 0.1898 1540.071486 1 0.0007 119 | 0/8 6 h-lim-p 0.0059 11.1145 0.0215 1540.071486 0 0.0013 140 | 0/8 7 h-lim-p 0.0097 20.0000 0.0029 1540.071486 0 0.0012 162 | 0/8 8 h-lim-p 0.0364 20.0000 0.0001 1540.071484 0 0.5827 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1540.071484 0 1.0938 206 | 0/8 10 h-lim-p 1.0866 20.0000 0.0000 1540.071484 0 1.6300 226 | 0/8 11 h-lim-p 0.8113 20.0000 0.0000 1540.071484 0 2.4340 247 | 0/8 12 h-lim-p 0.0259 20.0000 0.0026 1540.071484 0 0.0016 270 | 0/8 13 h-lim-p 0.0005 6.5583 0.0092 1540.071484 0 0.0000 310 | 0/8 14 h-lim-p 0.0000 20.0000 0.0006 1540.071484 0 0.0000 343 | 0/8 15 h-lim-p 0.0000 20.0000 0.0006 | 0/8 16 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -1540.071484 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1540.071484 Node 7: lnL = -1540.071484 Node 8: lnL = -1540.071484 Node 9: lnL = -1540.071484 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 848 Sequential format.. Reading seq # 1: YJL159W_Sbay Reading seq # 2: YJL159W_Scer Reading seq # 3: YJL159W_Skud Reading seq # 4: YJL159W_Smik Reading seq # 5: YJL159W_Spar Sequences read.. Counting patterns.. # site patterns = 221 Counting frequencies.. 120 bytes for distance 35360 bytes for lkl0 28288 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.057176 0.044591 0.052051 0.068124 0.058708 0.121428 0.173760 0.171483 lnL0 = -3351.615426 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3351.615426 x= 0.05718 0.04459 0.05205 0.06812 0.05871 0.12143 0.17376 0.17148 1 h-lim-p 0.0002 0.0013 181.5933 3349.813617 7 0.0001 37 | 0/8 2 h-lim-p 0.0004 0.0034 26.5958 3349.744249 2 0.0002 53 | 0/8 3 h-lim-p 0.0005 0.0176 11.4603 3349.731151 2 0.0002 69 | 0/8 4 h-lim-p 0.0009 0.0364 3.0395 3349.730433 2 0.0002 86 | 0/8 5 h-lim-p 0.0003 0.1221 1.4697 3349.730299 2 0.0002 102 | 0/8 6 h-lim-p 0.0004 0.1669 0.6124 3349.730280 2 0.0001 119 | 0/8 7 h-lim-p 0.0064 15.1449 0.0111 3349.730280 0 0.0007 141 | 0/8 8 h-lim-p 0.0160 20.0000 0.0005 3349.730155 0 0.5129 166 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3349.730145 1 0.9961 188 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3349.730145 0 0.5469 209 | 0/8 11 h-lim-p 0.2840 20.0000 0.0000 3349.730145 0 0.0000 246 | 0/8 12 h-lim-p 0.0001 20.0000 0.0000 3349.730145 0 0.0000 277 Out... lnL = -3349.730145 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3349.730145 Node 7: lnL = -3349.730145 Node 8: lnL = -3349.730145 Node 9: lnL = -3349.730145 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 852 Sequential format.. Reading seq # 1: YJL161W_Sbay Reading seq # 2: YJL161W_Scer Reading seq # 3: YJL161W_Skud Reading seq # 4: YJL161W_Smik Reading seq # 5: YJL161W_Spar Sequences read.. Counting patterns.. # site patterns = 453 Counting frequencies.. 120 bytes for distance 72480 bytes for lkl0 57984 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.235722 0.039790 0.303560 0.231307 0.133169 0.302603 0.550820 0.605547 lnL0 = -4761.207283 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4761.207283 x= 0.23572 0.03979 0.30356 0.23131 0.13317 0.30260 0.55082 0.60555 1 h-lim-p 0.0018 0.0146 47.4613 4760.401196 6 0.0007 35 | 0/8 2 h-lim-p 0.0011 0.0088 28.8529 4760.225492 5 0.0005 59 | 0/8 3 h-lim-p 0.0019 0.0485 8.1873 4760.182844 6 0.0014 83 | 0/8 4 h-lim-p 0.0025 0.1505 4.6324 4760.160378 5 0.0027 108 | 0/8 5 h-lim-p 0.0034 0.1602 3.7620 4760.152827 4 0.0018 129 | 0/8 6 h-lim-p 0.0044 0.3965 1.5233 4760.150589 4 0.0026 152 | 0/8 7 h-lim-p 0.0164 3.6764 0.2418 4760.150518 2 0.0027 171 | 0/8 8 h-lim-p 2.0228 20.0000 0.0003 4760.150496 1 0.9956 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4760.150495 0 1.0938 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4760.150495 0 2.1875 234 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4760.150495 0 1.0938 254 | 0/8 12 h-lim-p 0.1551 20.0000 0.0000 4760.150495 0 0.2326 274 | 0/8 13 h-lim-p 0.0069 20.0000 0.0001 4760.150495 0 0.0000 301 | 0/8 14 h-lim-p 0.0031 20.0000 0.0000 4760.150495 0 0.0001 325 Out... lnL = -4760.150495 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4760.150495 Node 7: lnL = -4760.150495 Node 8: lnL = -4760.150495 Node 9: lnL = -4760.150495 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 843 Sequential format.. Reading seq # 1: YJL163C_Sbay Reading seq # 2: YJL163C_Scer Reading seq # 3: YJL163C_Skud Reading seq # 4: YJL163C_Smik Reading seq # 5: YJL163C_Spar Sequences read.. Counting patterns.. # site patterns = 332 Counting frequencies.. 120 bytes for distance 53120 bytes for lkl0 42496 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.047659 0.026783 0.075897 0.154859 0.120228 0.316040 0.261273 0.232497 lnL0 = -3747.907280 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3747.907280 x= 0.04766 0.02678 0.07590 0.15486 0.12023 0.31604 0.26127 0.23250 1 h-lim-p 0.0015 0.0123 119.4126 3746.529906 7 0.0002 39 | 0/8 2 h-lim-p 0.0004 0.0033 40.6873 3746.180109 1 0.0005 53 | 0/8 3 h-lim-p 0.0011 0.0208 18.8506 3746.114807 3 0.0005 71 | 0/8 4 h-lim-p 0.0007 0.0183 12.2609 3746.092035 6 0.0004 99 | 0/8 5 h-lim-p 0.0014 0.0555 3.8039 3746.088593 3 0.0006 117 | 0/8 6 h-lim-p 0.0020 0.1848 1.0838 3746.088196 3 0.0007 135 | 0/8 7 h-lim-p 0.0227 2.9430 0.0356 3746.088187 1 0.0023 151 | 0/8 8 h-lim-p 0.0073 20.0000 0.0110 3746.085015 0 0.1749 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 3746.084961 1 0.9961 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3746.084961 0 1.0938 217 | 0/8 11 h-lim-p 0.7864 20.0000 0.0000 3746.084961 0 0.7864 237 | 0/8 12 h-lim-p 0.5146 20.0000 0.0000 3746.084961 0 0.1286 258 | 0/8 13 h-lim-p 0.0358 20.0000 0.0001 3746.084961 0 0.0000 295 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 3746.084961 0 0.0000 328 Out... lnL = -3746.084961 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3746.084961 Node 7: lnL = -3746.084961 Node 8: lnL = -3746.084961 Node 9: lnL = -3746.084961 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 620 Sequential format.. Reading seq # 1: YJL164C_Sbay Reading seq # 2: YJL164C_Scer Reading seq # 3: YJL164C_Skud Reading seq # 4: YJL164C_Smik Reading seq # 5: YJL164C_Spar Sequences read.. Counting patterns.. # site patterns = 208 Counting frequencies.. 120 bytes for distance 33280 bytes for lkl0 26624 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.065038 0.089676 0.085003 0.077067 0.049226 0.125572 0.163449 0.200496 lnL0 = -2388.963569 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2388.963569 x= 0.06504 0.08968 0.08500 0.07707 0.04923 0.12557 0.16345 0.20050 1 h-lim-p 0.0079 1.8285 77.6976 2388.189502 5 0.0003 36 | 0/8 2 h-lim-p 0.0004 0.0035 20.6333 2388.154493 3 0.0002 54 | 0/8 3 h-lim-p 0.0005 0.0253 7.5490 2388.145132 4 0.0004 74 | 0/8 4 h-lim-p 0.0018 0.1352 1.5892 2388.144627 2 0.0004 91 | 0/8 5 h-lim-p 0.0011 0.2344 0.5830 2388.144582 3 0.0003 110 | 0/8 6 h-lim-p 0.0013 1.5528 0.1374 2388.144577 1 0.0005 132 | 0/8 7 h-lim-p 0.0417 20.0000 0.0017 2388.144571 0 0.0417 152 | 0/8 8 h-lim-p 0.0028 20.0000 0.0252 2388.144430 0 0.0112 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2388.144429 0 1.0938 194 | 0/8 10 h-lim-p 1.9165 20.0000 0.0000 2388.144429 0 1.6769 214 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2388.144429 0 1.0938 234 | 0/8 12 h-lim-p 0.3989 20.0000 0.0000 2388.144429 0 3.1910 257 | 0/8 13 h-lim-p 0.2373 20.0000 0.0002 2388.144429 0 0.1187 277 | 0/8 14 h-lim-p 0.0218 20.0000 0.0011 2388.144429 0 0.0218 297 | 0/8 15 h-lim-p 0.0092 20.0000 0.0027 2388.144429 0 0.0001 322 | 0/8 16 h-lim-p 0.0001 20.0000 0.0027 2388.144429 0 0.0000 352 | 0/8 17 h-lim-p 0.0001 20.0000 0.0000 2388.144429 0 0.0000 387 Out... lnL = -2388.144429 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2388.144429 Node 7: lnL = -2388.144429 Node 8: lnL = -2388.144429 Node 9: lnL = -2388.144429 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 530 Sequential format.. Reading seq # 1: YJL165C_Sbay Reading seq # 2: YJL165C_Scer Reading seq # 3: YJL165C_Skud Reading seq # 4: YJL165C_Smik Reading seq # 5: YJL165C_Spar Sequences read.. Counting patterns.. # site patterns = 145 Counting frequencies.. 120 bytes for distance 23200 bytes for lkl0 18560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.052222 0.021714 0.048349 0.051828 0.044458 0.134205 0.152842 0.151688 lnL0 = -1973.283555 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1973.283555 x= 0.05222 0.02171 0.04835 0.05183 0.04446 0.13421 0.15284 0.15169 1 h-lim-p 0.0028 0.9089 117.9241 1972.530072 8 0.0001 44 | 0/8 2 h-lim-p 0.0010 0.0078 14.4580 1972.498077 6 0.0003 70 | 0/8 3 h-lim-p 0.0005 0.0213 8.3957 1972.494115 5 0.0001 93 | 0/8 4 h-lim-p 0.0006 0.0552 2.1461 1972.493737 4 0.0002 115 | 0/8 5 h-lim-p 0.0009 0.5033 0.4164 1972.493702 2 0.0004 131 | 0/8 6 h-lim-p 0.0018 0.9350 0.0930 1972.493701 0 0.0002 153 | 0/8 7 h-lim-p 0.0005 2.3530 0.0404 1972.493701 0 0.0004 173 | 0/8 8 h-lim-p 0.3658 20.0000 0.0000 1972.493698 0 1.0973 194 | 0/8 9 h-lim-p 2.0457 20.0000 0.0000 1972.493698 0 1.7900 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1972.493698 0 1.0938 234 | 0/8 11 h-lim-p 0.4047 20.0000 0.0000 1972.493698 0 0.4047 254 | 0/8 12 h-lim-p 0.0287 20.0000 0.0003 1972.493698 0 0.0143 274 | 0/8 13 h-lim-p 0.0047 20.0000 0.0009 1972.493698 0 0.0024 294 | 0/8 14 h-lim-p 0.0011 20.0000 0.0019 1972.493698 0 0.0000 335 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 1972.493698 0 0.0000 370 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1972.493698 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1972.493698 Node 7: lnL = -1972.493698 Node 8: lnL = -1972.493698 Node 9: lnL = -1972.493698 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 448 Sequential format.. Reading seq # 1: YJL166W_Sbay Reading seq # 2: YJL166W_Scer Reading seq # 3: YJL166W_Skud Reading seq # 4: YJL166W_Smik Reading seq # 5: YJL166W_Spar Sequences read.. Counting patterns.. # site patterns = 149 Counting frequencies.. 120 bytes for distance 23840 bytes for lkl0 19072 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.012122 0.057835 0.051697 0.130107 0.078453 0.180979 0.149638 0.134211 lnL0 = -1746.319951 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1746.319951 x= 0.01212 0.05784 0.05170 0.13011 0.07845 0.18098 0.14964 0.13421 1 h-lim-p 0.0010 0.0080 110.5029 1744.707124 7 0.0003 38 | 0/8 2 h-lim-p 0.0005 0.0036 30.1866 1744.527354 2 0.0004 54 | 0/8 3 h-lim-p 0.0024 0.0461 5.3092 1744.521408 5 0.0004 79 | 0/8 4 h-lim-p 0.0019 0.0754 1.2243 1744.521081 2 0.0004 96 | 0/8 5 h-lim-p 0.0031 0.4879 0.1764 1744.521071 1 0.0006 111 | 0/8 6 h-lim-p 0.0012 2.5998 0.0893 1744.521070 1 0.0003 134 | 0/8 7 h-lim-p 0.0024 16.1602 0.0110 1744.521068 0 0.0048 155 | 0/8 8 h-lim-p 0.0159 20.0000 0.0034 1744.520723 0 0.1268 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1744.520710 0 1.0938 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1744.520710 0 1.0938 218 | 0/8 11 h-lim-p 1.7562 20.0000 0.0000 1744.520710 0 1.5367 238 | 0/8 12 h-lim-p 0.5844 20.0000 0.0001 1744.520710 0 0.0011 266 | 0/8 13 h-lim-p 0.0001 20.0000 0.0011 1744.520710 0 0.0000 294 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 1744.520710 0 0.0000 314 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 1744.520710 0 0.0000 341 | 0/8 16 h-lim-p 0.0000 20.0000 0.0006 | 0/8 17 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -1744.520710 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1744.520710 Node 7: lnL = -1744.520710 Node 8: lnL = -1744.520710 Node 9: lnL = -1744.520710 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 612 Sequential format.. Reading seq # 1: YJL167W_Sbay Reading seq # 2: YJL167W_Scer Reading seq # 3: YJL167W_Skud Reading seq # 4: YJL167W_Smik Reading seq # 5: YJL167W_Spar Sequences read.. Counting patterns.. # site patterns = 193 Counting frequencies.. 120 bytes for distance 30880 bytes for lkl0 24704 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.029723 0.061021 0.051396 0.109486 0.074237 0.136909 0.156310 0.148003 lnL0 = -2557.337719 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2557.337719 x= 0.02972 0.06102 0.05140 0.10949 0.07424 0.13691 0.15631 0.14800 1 h-lim-p 0.0009 0.0072 193.3822 2554.474447 9 0.0002 44 | 0/8 2 h-lim-p 0.0006 0.0049 25.5348 2554.390641 6 0.0003 70 | 0/8 3 h-lim-p 0.0006 0.0198 10.7767 2554.377004 5 0.0003 91 | 0/8 4 h-lim-p 0.0010 0.0649 2.9295 2554.375786 4 0.0003 114 | 0/8 5 h-lim-p 0.0030 1.2307 0.3049 2554.375774 2 0.0003 132 | 0/8 6 h-lim-p 0.0027 7.9627 0.0324 2554.375773 0 0.0006 153 | 0/8 7 h-lim-p 0.0034 20.0000 0.0056 2554.375772 0 0.0050 173 | 0/8 8 h-lim-p 0.0069 20.0000 0.0041 2554.375573 0 0.0829 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2554.375570 0 1.0938 216 | 0/8 10 h-lim-p 1.7219 20.0000 0.0000 2554.375570 0 1.5067 236 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2554.375570 0 2.1875 256 | 0/8 12 h-lim-p 1.4444 20.0000 0.0000 2554.375570 0 1.2639 276 | 0/8 13 h-lim-p 0.7801 20.0000 0.0000 2554.375570 0 2.3403 297 | 0/8 14 h-lim-p 0.8471 20.0000 0.0001 2554.375570 0 0.0058 323 | 0/8 15 h-lim-p 0.0000 0.6293 0.0787 2554.375570 0 0.0000 344 | 0/8 16 h-lim-p 0.0002 20.0000 0.0011 2554.375570 0 0.0000 379 | 0/8 17 h-lim-p 0.0000 20.0000 0.0024 2554.375570 0 0.0000 400 | 0/8 18 h-lim-p 0.0000 20.0000 0.0004 2554.375570 0 0.0011 426 | 0/8 19 h-lim-p 0.0064 20.0000 0.0001 2554.375570 0 0.0001 451 | 0/8 20 h-lim-p 0.0001 20.0000 0.0001 2554.375570 0 0.0001 471 | 0/8 21 h-lim-p 0.0000 20.0000 0.0005 2554.375570 0 0.0000 495 | 0/8 22 h-lim-p 0.0000 4.1538 0.0120 2554.375570 0 0.0000 515 | 0/8 23 h-lim-p 0.0000 10.2920 0.0048 2554.375570 0 0.0000 541 | 0/8 24 h-lim-p 0.0000 20.0000 0.0001 2554.375570 0 0.0000 561 | 0/8 25 h-lim-p 0.0000 20.0000 0.0003 2554.375570 0 0.0000 591 | 0/8 26 h-lim-p 0.0000 20.0000 0.0030 2554.375570 0 0.0000 611 | 0/8 27 h-lim-p 0.0001 20.0000 0.0002 2554.375570 0 0.0000 633 | 0/8 28 h-lim-p 0.0000 20.0000 0.0000 2554.375570 0 0.0000 663 | 0/8 29 h-lim-p 0.0000 20.0000 0.0029 | 0/8 30 h-lim-p 0.0000 20.0000 0.0029 Out... lnL = -2554.375570 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2554.375570 Node 7: lnL = -2554.375570 Node 8: lnL = -2554.375570 Node 9: lnL = -2554.375570 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 453 Sequential format.. Reading seq # 1: YJL170C_Sbay Reading seq # 2: YJL170C_Scer Reading seq # 3: YJL170C_Skud Reading seq # 4: YJL170C_Smik Reading seq # 5: YJL170C_Spar Sequences read.. Counting patterns.. # site patterns = 166 Counting frequencies.. 120 bytes for distance 26560 bytes for lkl0 21248 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.042573 0.085717 0.042898 0.143295 0.000060 0.242152 0.214609 0.162642 lnL0 = -1611.657927 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1611.657927 x= 0.04257 0.08572 0.04290 0.14329 0.00006 0.24215 0.21461 0.16264 1 h-lim-p 0.0001 0.0012 757.9179 1604.684605 7 0.0000 37 | 0/8 2 h-lim-p 0.0001 0.0011 84.7948 1602.880432 0 0.0006 51 | 0/8 3 h-lim-p 0.0008 0.0064 27.1669 1602.648020 3 0.0007 69 | 0/8 4 h-lim-p 0.0018 0.0147 9.9627 1602.616801 4 0.0007 89 | 0/8 5 h-lim-p 0.0037 0.0299 1.7534 1602.615995 5 0.0005 113 | 0/8 6 h-lim-p 0.0022 0.6999 0.4146 1602.615581 3 0.0023 133 | 0/8 7 h-lim-p 0.0374 8.9623 0.0260 1602.555747 0 0.2990 156 | 0/8 8 h-lim-p 0.0028 0.0973 2.7898 1602.548241 5 0.0016 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 1602.548193 2 1.1719 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1602.548183 0 5.0000 225 | 0/8 11 h-lim-p 2.3162 20.0000 0.0001 1602.548179 1 1.1400 248 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1602.548179 0 1.2500 268 | 0/8 13 h-lim-p 1.8825 20.0000 0.0000 1602.548179 0 0.8236 288 | 0/8 14 h-lim-p 0.5619 20.0000 0.0000 1602.548179 0 0.0022 315 | 0/8 15 h-lim-p 0.0007 20.0000 0.0001 1602.548179 0 0.0001 337 | 0/8 16 h-lim-p 0.0001 20.0000 0.0001 1602.548179 0 0.0000 374 | 0/8 17 h-lim-p 0.0000 20.0000 0.0007 | 0/8 18 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -1602.548179 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1602.548179 Node 7: lnL = -1602.548179 Node 8: lnL = -1602.548179 Node 9: lnL = -1602.548179 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 268 Sequential format.. Reading seq # 1: YJL171C_Sbay Reading seq # 2: YJL171C_Scer Reading seq # 3: YJL171C_Skud Reading seq # 4: YJL171C_Smik Reading seq # 5: YJL171C_Spar Sequences read.. Counting patterns.. # site patterns = 108 Counting frequencies.. 120 bytes for distance 17280 bytes for lkl0 13824 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.076453 0.017931 0.045872 0.069315 0.050942 0.138022 0.139681 0.184928 lnL0 = -1025.244548 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1025.244548 x= 0.07645 0.01793 0.04587 0.06932 0.05094 0.13802 0.13968 0.18493 1 h-lim-p 0.0002 0.0013 78.2589 1024.302523 0 0.0003 23 | 0/8 2 h-lim-p 0.0006 0.0045 21.5092 1024.171359 7 0.0006 52 | 0/8 3 h-lim-p 0.0016 0.0188 7.9586 1024.156408 6 0.0005 80 | 0/8 4 h-lim-p 0.0044 0.0636 0.9604 1024.156289 2 0.0003 99 | 0/8 5 h-lim-p 0.0007 0.4769 0.3674 1024.156259 3 0.0005 125 | 0/8 6 h-lim-p 0.0013 0.7305 0.1458 1024.156254 0 0.0006 145 | 0/8 7 h-lim-p 0.1866 20.0000 0.0004 1024.156253 0 0.0408 166 | 0/8 8 h-lim-p 0.0093 20.0000 0.0020 1024.156249 0 0.0279 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1024.156249 0 1.0938 207 | 0/8 10 h-lim-p 1.4818 20.0000 0.0000 1024.156249 0 1.4818 227 | 0/8 11 h-lim-p 1.9229 20.0000 0.0000 1024.156249 0 0.0000 278 Out... lnL = -1024.156249 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1024.156249 Node 7: lnL = -1024.156249 Node 8: lnL = -1024.156249 Node 9: lnL = -1024.156249 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 940 Sequential format.. Reading seq # 1: YJL173C_Sbay Reading seq # 2: YJL173C_Scer Reading seq # 3: YJL173C_Skud Reading seq # 4: YJL173C_Smik Reading seq # 5: YJL173C_Spar Sequences read.. Counting patterns.. # site patterns = 425 Counting frequencies.. 120 bytes for distance 68000 bytes for lkl0 54400 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.205715 0.102838 0.149126 0.161519 0.141159 0.213699 0.399041 0.491727 lnL0 = -4883.482594 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4883.482594 x= 0.20572 0.10284 0.14913 0.16152 0.14116 0.21370 0.39904 0.49173 1 h-lim-p 0.0101 0.0808 56.6843 4882.702199 5 0.0005 35 | 0/8 2 h-lim-p 0.0015 0.0195 18.4937 4882.627503 7 0.0005 65 | 0/8 3 h-lim-p 0.0012 0.0544 7.5583 4882.618589 5 0.0004 90 | 0/8 4 h-lim-p 0.0008 0.1531 3.4412 4882.611338 0 0.0016 103 | 0/8 5 h-lim-p 0.0023 0.2473 2.4548 4882.609578 2 0.0009 119 | 0/8 6 h-lim-p 0.0018 0.2632 1.1899 4882.609219 2 0.0007 135 | 0/8 7 h-lim-p 0.0226 8.9731 0.0364 4882.609217 0 0.0025 149 | 0/8 8 h-lim-p 0.1126 20.0000 0.0008 4882.608925 0 0.9007 172 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 4882.608915 1 0.9961 194 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4882.608915 0 1.0938 214 | 0/8 11 h-lim-p 2.1325 20.0000 0.0000 4882.608915 0 1.8659 234 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4882.608915 0 1.0938 254 | 0/8 13 h-lim-p 0.4812 20.0000 0.0000 4882.608915 0 2.8874 276 | 0/8 14 h-lim-p 0.0082 20.0000 0.0021 4882.608915 0 0.0123 296 | 0/8 15 h-lim-p 0.0001 0.9275 0.3209 4882.608915 0 0.0000 319 | 0/8 16 h-lim-p 0.0044 20.0000 0.0004 4882.608915 0 0.0000 352 | 0/8 17 h-lim-p 0.0028 20.0000 0.0000 4882.608915 0 0.0007 373 Out... lnL = -4882.608915 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4882.608915 Node 7: lnL = -4882.608915 Node 8: lnL = -4882.608915 Node 9: lnL = -4882.608915 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 548 Sequential format.. Reading seq # 1: YJL174W_Sbay Reading seq # 2: YJL174W_Scer Reading seq # 3: YJL174W_Skud Reading seq # 4: YJL174W_Smik Reading seq # 5: YJL174W_Spar Sequences read.. Counting patterns.. # site patterns = 197 Counting frequencies.. 120 bytes for distance 31520 bytes for lkl0 25216 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.030207 0.106586 0.066331 0.108322 0.078536 0.207919 0.128263 0.163974 lnL0 = -2284.413327 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2284.413327 x= 0.03021 0.10659 0.06633 0.10832 0.07854 0.20792 0.12826 0.16397 1 h-lim-p 0.0008 0.0068 65.3158 2283.716829 6 0.0003 33 | 0/8 2 h-lim-p 0.0008 0.0065 26.4482 2283.590690 4 0.0004 53 | 0/8 3 h-lim-p 0.0012 0.0303 8.9856 2283.578104 5 0.0004 78 | 0/8 4 h-lim-p 0.0006 0.0531 4.9797 2283.574648 5 0.0004 103 | 0/8 5 h-lim-p 0.0013 0.1764 1.4414 2283.574098 2 0.0006 119 | 0/8 6 h-lim-p 0.0036 0.8089 0.2334 2283.574089 2 0.0003 137 | 0/8 7 h-lim-p 0.0084 12.2705 0.0098 2283.574089 0 0.0005 160 | 0/8 8 h-lim-p 0.1659 20.0000 0.0000 2283.574088 0 0.9956 182 | 0/8 9 h-lim-p 1.1341 20.0000 0.0000 2283.574088 0 0.9924 202 | 0/8 10 h-lim-p 0.6994 20.0000 0.0000 2283.574088 0 0.0055 228 | 0/8 11 h-lim-p 0.0006 20.0000 0.0003 2283.574088 0 0.0001 250 | 0/8 12 h-lim-p 0.0000 20.0000 0.0006 2283.574088 0 0.0000 275 | 0/8 13 h-lim-p 0.0000 20.0000 0.0005 | 0/8 14 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -2283.574088 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2283.574088 Node 7: lnL = -2283.574088 Node 8: lnL = -2283.574088 Node 9: lnL = -2283.574088 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 877 Sequential format.. Reading seq # 1: YJL177W_Sbay Reading seq # 2: YJL177W_Scer Reading seq # 3: YJL177W_Skud Reading seq # 4: YJL177W_Smik Reading seq # 5: YJL177W_Spar Sequences read.. Counting patterns.. # site patterns = 277 Counting frequencies.. 120 bytes for distance 44320 bytes for lkl0 35456 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.045985 0.125190 0.049440 0.094723 0.069853 0.186962 0.171537 0.185174 lnL0 = -3796.050388 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3796.050388 x= 0.04598 0.12519 0.04944 0.09472 0.06985 0.18696 0.17154 0.18517 1 h-lim-p 0.0039 0.9922 139.1533 3794.632963 7 0.0002 43 | 0/8 2 h-lim-p 0.0006 0.0053 34.5325 3794.490314 6 0.0003 70 | 0/8 3 h-lim-p 0.0004 0.0069 20.8999 3794.459784 3 0.0002 88 | 0/8 4 h-lim-p 0.0008 0.0288 4.5753 3794.457128 4 0.0003 110 | 0/8 5 h-lim-p 0.0012 0.2271 0.9975 3794.456963 3 0.0003 129 | 0/8 6 h-lim-p 0.0026 0.9134 0.1278 3794.456962 0 0.0003 151 | 0/8 7 h-lim-p 0.0108 20.0000 0.0034 3794.456962 0 0.0024 172 | 0/8 8 h-lim-p 0.0209 20.0000 0.0004 3794.456946 0 0.3350 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3794.456945 0 1.0938 216 | 0/8 10 h-lim-p 1.1492 20.0000 0.0000 3794.456945 0 1.1492 236 | 0/8 11 h-lim-p 1.1704 20.0000 0.0000 3794.456945 0 0.0023 264 | 0/8 12 h-lim-p 0.0005 20.0000 0.0001 3794.456945 0 0.0008 284 | 0/8 13 h-lim-p 0.0017 20.0000 0.0001 3794.456945 0 0.0000 311 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 3794.456945 0 0.0000 341 | 0/8 15 h-lim-p 0.0000 20.0000 0.0018 | 0/8 16 h-lim-p 0.0000 20.0000 0.0018 Out... lnL = -3794.456945 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3794.456945 Node 7: lnL = -3794.456945 Node 8: lnL = -3794.456945 Node 9: lnL = -3794.456945 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 892 Sequential format.. Reading seq # 1: YJL178C_Sbay Reading seq # 2: YJL178C_Scer Reading seq # 3: YJL178C_Skud Reading seq # 4: YJL178C_Smik Reading seq # 5: YJL178C_Spar Sequences read.. Counting patterns.. # site patterns = 257 Counting frequencies.. 120 bytes for distance 41120 bytes for lkl0 32896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.061254 0.084362 0.051211 0.115390 0.090908 0.214048 0.242912 0.218240 lnL0 = -3459.435577 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3459.435577 x= 0.06125 0.08436 0.05121 0.11539 0.09091 0.21405 0.24291 0.21824 1 h-lim-p 0.0009 0.0069 96.9137 3458.478117 7 0.0002 37 | 0/8 2 h-lim-p 0.0005 0.0042 29.4667 3458.338446 7 0.0003 67 | 0/8 3 h-lim-p 0.0007 0.0176 14.2159 3458.314272 3 0.0003 85 | 0/8 4 h-lim-p 0.0011 0.0869 3.8201 3458.311057 2 0.0005 101 | 0/8 5 h-lim-p 0.0011 0.1666 1.7069 3458.310515 3 0.0005 119 | 0/8 6 h-lim-p 0.0065 2.7854 0.1203 3458.310510 0 0.0007 133 | 0/8 7 h-lim-p 0.0035 7.6530 0.0244 3458.310510 0 0.0004 155 | 0/8 8 h-lim-p 0.0514 20.0000 0.0002 3458.310472 0 0.8228 179 | 0/8 9 h-lim-p 1.5184 20.0000 0.0001 3458.310471 0 1.3286 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3458.310471 0 1.0938 219 | 0/8 11 h-lim-p 0.6088 20.0000 0.0000 3458.310471 0 1.2176 240 | 0/8 12 h-lim-p 1.0199 20.0000 0.0000 3458.310471 012.2385 263 | 0/8 13 h-lim-p 0.0109 2.3598 0.0322 3458.310471 0 0.0007 286 | 0/8 14 h-lim-p 0.0000 0.0263 2.8932 3458.310471 0 0.0000 308 | 0/8 15 h-lim-p 0.5293 20.0000 0.0000 3458.310471 0 1.0586 321 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 3458.310471 0 0.6250 342 | 0/8 17 h-lim-p 0.6771 20.0000 0.0000 3458.310471 0 0.0212 366 | 0/8 18 h-lim-p 0.0049 20.0000 0.0000 3458.310471 0 0.0000 402 Out... lnL = -3458.310471 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3458.310471 Node 7: lnL = -3458.310471 Node 8: lnL = -3458.310471 Node 9: lnL = -3458.310471 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 264 Sequential format.. Reading seq # 1: YJL179W_Sbay Reading seq # 2: YJL179W_Scer Reading seq # 3: YJL179W_Skud Reading seq # 4: YJL179W_Smik Reading seq # 5: YJL179W_Spar Sequences read.. Counting patterns.. # site patterns = 132 Counting frequencies.. 120 bytes for distance 21120 bytes for lkl0 16896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.038864 0.170869 0.039416 0.175683 0.143705 0.235266 0.130181 0.209954 lnL0 = -1181.264912 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1181.264912 x= 0.03886 0.17087 0.03942 0.17568 0.14371 0.23527 0.13018 0.20995 1 h-lim-p 0.0019 0.0154 25.4079 1181.069061 7 0.0006 39 | 0/8 2 h-lim-p 0.0020 0.0305 8.2793 1181.025927 7 0.0014 70 | 0/8 3 h-lim-p 0.0067 0.2260 1.6822 1181.024279 5 0.0012 96 | 0/8 4 h-lim-p 0.0067 0.7347 0.3043 1181.024229 3 0.0011 116 | 0/8 5 h-lim-p 0.0039 3.7195 0.0846 1181.024225 1 0.0010 139 | 0/8 6 h-lim-p 0.0036 6.1025 0.0228 1181.024225 0 0.0016 159 | 0/8 7 h-lim-p 0.0072 20.0000 0.0050 1181.024225 0 0.0063 179 | 0/8 8 h-lim-p 0.0787 20.0000 0.0004 1181.024206 0 0.4722 201 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1181.024206 0 1.0938 221 | 0/8 10 h-lim-p 2.0554 20.0000 0.0000 1181.024206 0 1.7985 241 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1181.024206 0 1.0938 261 | 0/8 12 h-lim-p 0.3651 20.0000 0.0000 1181.024206 0 0.1825 281 | 0/8 13 h-lim-p 0.0005 9.8849 0.0052 1181.024206 0 0.0000 322 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 1181.024206 0 0.0000 355 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 1181.024206 0 0.0000 375 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 1181.024206 0 0.0000 409 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 1181.024206 0 0.0000 444 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1181.024206 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1181.024206 Node 7: lnL = -1181.024206 Node 8: lnL = -1181.024206 Node 9: lnL = -1181.024206 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 243 Sequential format.. Reading seq # 1: YJL180C_Sbay Reading seq # 2: YJL180C_Scer Reading seq # 3: YJL180C_Skud Reading seq # 4: YJL180C_Smik Reading seq # 5: YJL180C_Spar Sequences read.. Counting patterns.. # site patterns = 133 Counting frequencies.. 120 bytes for distance 21280 bytes for lkl0 17024 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.088882 0.062418 0.029524 0.179589 0.146696 0.241710 0.212227 0.262814 lnL0 = -1157.828763 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1157.828763 x= 0.08888 0.06242 0.02952 0.17959 0.14670 0.24171 0.21223 0.26281 1 h-lim-p 0.0082 0.6624 52.9866 1157.274012 5 0.0004 37 | 0/8 2 h-lim-p 0.0026 0.0431 9.0744 1157.212730 7 0.0015 68 | 0/8 3 h-lim-p 0.0045 0.0879 3.1088 1157.206977 5 0.0013 92 | 0/8 4 h-lim-p 0.0086 0.4679 0.4780 1157.206792 3 0.0017 111 | 0/8 5 h-lim-p 0.0090 1.9128 0.0882 1157.206788 2 0.0012 137 | 0/8 6 h-lim-p 0.0069 17.5792 0.0151 1157.206788 0 0.0015 158 | 0/8 7 h-lim-p 0.0129 20.0000 0.0018 1157.206788 0 0.0056 178 | 0/8 8 h-lim-p 0.0502 20.0000 0.0002 1157.206785 0 0.4015 201 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1157.206785 0 1.2500 221 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1157.206785 0 1.0938 241 | 0/8 11 h-lim-p 0.8754 20.0000 0.0000 1157.206785 0 0.1094 263 | 0/8 12 h-lim-p 0.0017 20.0000 0.0004 1157.206785 0 0.0015 283 | 0/8 13 h-lim-p 0.0010 20.0000 0.0006 1157.206785 0 0.0002 304 | 0/8 14 h-lim-p 0.0003 20.0000 0.0005 1157.206785 0 0.0001 324 | 0/8 15 h-lim-p 0.0000 20.0000 0.0014 1157.206785 0 0.0000 354 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 1157.206785 0 0.0000 379 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 1157.206785 0 0.0000 406 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1157.206785 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1157.206785 Node 7: lnL = -1157.206785 Node 8: lnL = -1157.206785 Node 9: lnL = -1157.206785 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 351 Sequential format.. Reading seq # 1: YJL181W_Sbay Reading seq # 2: YJL181W_Scer Reading seq # 3: YJL181W_Skud Reading seq # 4: YJL181W_Smik Reading seq # 5: YJL181W_Spar Sequences read.. Counting patterns.. # site patterns = 172 Counting frequencies.. 120 bytes for distance 27520 bytes for lkl0 22016 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.098469 0.100940 0.069061 0.129010 0.079598 0.206600 0.192360 0.266625 lnL0 = -1566.201627 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1566.201627 x= 0.09847 0.10094 0.06906 0.12901 0.07960 0.20660 0.19236 0.26662 1 h-lim-p 0.0003 0.0022 67.6861 1564.874357 0 0.0006 23 | 0/8 2 h-lim-p 0.0022 0.0261 16.6847 1564.782558 7 0.0007 53 | 0/8 3 h-lim-p 0.0010 0.0180 11.5070 1564.751886 7 0.0006 83 | 0/8 4 h-lim-p 0.0014 0.0489 5.4100 1564.742300 5 0.0009 107 | 0/8 5 h-lim-p 0.0048 0.2501 0.9741 1564.741904 4 0.0009 129 | 0/8 6 h-lim-p 0.0114 5.6184 0.0724 1564.741823 3 0.0061 156 | 0/8 7 h-lim-p 0.0246 7.6720 0.0181 1564.730740 0 0.1966 179 | 0/8 8 h-lim-p 0.0701 4.4842 0.0509 1564.730738 1 0.0017 205 | 0/8 9 h-lim-p 0.1728 20.0000 0.0005 1564.730617 0 1.0366 227 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1564.730616 0 1.0938 247 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1564.730616 0 1.0938 267 | 0/8 12 h-lim-p 1.5444 20.0000 0.0000 1564.730616 0 1.3514 287 | 0/8 13 h-lim-p 1.3656 20.0000 0.0000 1564.730616 0 1.3656 307 | 0/8 14 h-lim-p 0.2106 20.0000 0.0000 1564.730616 0 0.0526 328 | 0/8 15 h-lim-p 0.0108 20.0000 0.0002 1564.730616 0 0.0108 348 | 0/8 16 h-lim-p 0.0045 20.0000 0.0004 1564.730616 0 0.0022 368 | 0/8 17 h-lim-p 0.0014 20.0000 0.0006 1564.730616 0 0.0007 388 | 0/8 18 h-lim-p 0.0003 20.0000 0.0012 1564.730616 0 0.0000 419 | 0/8 19 h-lim-p 0.0004 20.0000 0.0000 1564.730616 0 0.0000 445 Out... lnL = -1564.730616 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1564.730616 Node 7: lnL = -1564.730616 Node 8: lnL = -1564.730616 Node 9: lnL = -1564.730616 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 271 Sequential format.. Reading seq # 1: YJL183W_Sbay Reading seq # 2: YJL183W_Scer Reading seq # 3: YJL183W_Skud Reading seq # 4: YJL183W_Smik Reading seq # 5: YJL183W_Spar Sequences read.. Counting patterns.. # site patterns = 106 Counting frequencies.. 120 bytes for distance 16960 bytes for lkl0 13568 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.046223 0.033729 0.066927 0.071622 0.051280 0.157603 0.173128 0.156855 lnL0 = -1077.452414 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1077.452414 x= 0.04622 0.03373 0.06693 0.07162 0.05128 0.15760 0.17313 0.15686 1 h-lim-p 0.0002 0.0016 84.6396 1076.275691 0 0.0004 23 | 0/8 2 h-lim-p 0.0028 0.0224 9.4796 1076.244161 6 0.0007 49 | 0/8 3 h-lim-p 0.0009 0.0115 7.6822 1076.236749 3 0.0004 67 | 0/8 4 h-lim-p 0.0009 0.0544 2.9858 1076.235138 2 0.0004 83 | 0/8 5 h-lim-p 0.0036 0.4626 0.3716 1076.235052 4 0.0011 107 | 0/8 6 h-lim-p 0.0044 2.7680 0.0937 1076.234981 2 0.0038 131 | 0/8 7 h-lim-p 0.0057 1.4298 0.0622 1076.233257 0 0.0229 153 | 0/8 8 h-lim-p 0.0023 0.1531 0.6266 1076.219152 0 0.0068 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 1076.218799 2 0.9644 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1076.218799 0 1.0938 218 | 0/8 11 h-lim-p 1.5114 20.0000 0.0000 1076.218799 0 0.6612 238 | 0/8 12 h-lim-p 0.4347 20.0000 0.0000 1076.218799 0 0.0272 261 | 0/8 13 h-lim-p 0.0116 20.0000 0.0000 1076.218799 0 0.0029 282 | 0/8 14 h-lim-p 0.0016 20.0000 0.0001 1076.218799 0 0.0001 305 | 0/8 15 h-lim-p 0.0001 20.0000 0.0001 1076.218799 0 0.0000 338 | 0/8 16 h-lim-p 0.0000 20.0000 0.0008 | 0/8 17 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -1076.218799 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1076.218799 Node 7: lnL = -1076.218799 Node 8: lnL = -1076.218799 Node 9: lnL = -1076.218799 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 516 Sequential format.. Reading seq # 1: YJL184W_Sbay Reading seq # 2: YJL184W_Scer Reading seq # 3: YJL184W_Skud Reading seq # 4: YJL184W_Smik Reading seq # 5: YJL184W_Spar Sequences read.. Counting patterns.. # site patterns = 252 Counting frequencies.. 120 bytes for distance 40320 bytes for lkl0 32256 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.073551 0.113287 0.120155 0.221777 0.130511 0.281608 0.257498 0.293949 lnL0 = -2644.128138 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2644.128138 x= 0.07355 0.11329 0.12016 0.22178 0.13051 0.28161 0.25750 0.29395 1 h-lim-p 0.0020 0.0163 49.4717 2643.349851 6 0.0007 35 | 0/8 2 h-lim-p 0.0019 0.0151 15.1545 2643.258555 3 0.0009 53 | 0/8 3 h-lim-p 0.0018 0.0575 7.3545 2643.244382 5 0.0006 77 | 0/8 4 h-lim-p 0.0036 0.2370 1.3036 2643.243537 4 0.0010 100 | 0/8 5 h-lim-p 0.0066 1.8465 0.2039 2643.243512 2 0.0013 117 | 0/8 6 h-lim-p 0.0067 4.5499 0.0384 2643.243511 0 0.0015 138 | 0/8 7 h-lim-p 0.0087 20.0000 0.0065 2643.243510 0 0.0043 158 | 0/8 8 h-lim-p 0.0225 20.0000 0.0013 2643.243441 0 0.2701 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2643.243440 0 1.0938 201 | 0/8 10 h-lim-p 2.0388 20.0000 0.0000 2643.243440 0 0.8920 221 | 0/8 11 h-lim-p 0.7820 20.0000 0.0000 2643.243440 0 0.1711 242 | 0/8 12 h-lim-p 0.0420 20.0000 0.0000 2643.243440 0 0.0007 267 | 0/8 13 h-lim-p 0.0009 20.0000 0.0000 2643.243440 0 0.0000 295 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 2643.243440 0 0.0000 321 Out... lnL = -2643.243440 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2643.243440 Node 7: lnL = -2643.243440 Node 8: lnL = -2643.243440 Node 9: lnL = -2643.243440 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 522 Sequential format.. Reading seq # 1: YJL185C_Sbay Reading seq # 2: YJL185C_Scer Reading seq # 3: YJL185C_Skud Reading seq # 4: YJL185C_Smik Reading seq # 5: YJL185C_Spar Sequences read.. Counting patterns.. # site patterns = 249 Counting frequencies.. 120 bytes for distance 39840 bytes for lkl0 31872 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.092523 0.078635 0.112435 0.214917 0.137371 0.277351 0.286178 0.312730 lnL0 = -2662.848995 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2662.848995 x= 0.09252 0.07864 0.11244 0.21492 0.13737 0.27735 0.28618 0.31273 1 h-lim-p 0.0059 0.0474 65.5623 2661.722527 6 0.0006 36 | 0/8 2 h-lim-p 0.0016 0.0130 18.6373 2661.574663 7 0.0009 66 | 0/8 3 h-lim-p 0.0021 0.0504 8.1217 2661.554543 5 0.0007 90 | 0/8 4 h-lim-p 0.0037 0.2576 1.5889 2661.553273 5 0.0011 116 | 0/8 5 h-lim-p 0.0046 0.9600 0.3702 2661.553187 3 0.0014 136 | 0/8 6 h-lim-p 0.0072 3.5914 0.0700 2661.553183 1 0.0014 159 | 0/8 7 h-lim-p 0.0087 20.0000 0.0115 2661.553181 1 0.0070 181 | 0/8 8 h-lim-p 0.0211 20.0000 0.0038 2661.552834 0 0.1686 204 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2661.552831 0 1.0938 224 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2661.552831 0 1.0938 244 | 0/8 11 h-lim-p 1.4635 20.0000 0.0000 2661.552831 0 1.2806 264 | 0/8 12 h-lim-p 1.0857 20.0000 0.0000 2661.552831 0 4.3429 286 | 0/8 13 h-lim-p 0.1216 20.0000 0.0003 2661.552831 0 0.1064 306 | 0/8 14 h-lim-p 0.0255 20.0000 0.0013 2661.552831 0 0.0000 342 | 0/8 15 h-lim-p 0.0008 20.0000 0.0000 2661.552831 0 0.0000 378 Out... lnL = -2661.552831 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2661.552831 Node 7: lnL = -2661.552831 Node 8: lnL = -2661.552831 Node 9: lnL = -2661.552831 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 859 Sequential format.. Reading seq # 1: YJL187C_Sbay Reading seq # 2: YJL187C_Scer Reading seq # 3: YJL187C_Skud Reading seq # 4: YJL187C_Smik Reading seq # 5: YJL187C_Spar Sequences read.. Counting patterns.. # site patterns = 307 Counting frequencies.. 120 bytes for distance 49120 bytes for lkl0 39296 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.149043 0.000060 0.092685 0.112985 0.105221 0.198078 0.251355 0.313189 lnL0 = -3907.573112 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3907.573112 x= 0.14904 0.00006 0.09268 0.11298 0.10522 0.19808 0.25135 0.31319 1 h-lim-p 0.0002 0.0012 132.9237 3905.528960 0 0.0002 22 | 0/8 2 h-lim-p 0.0005 0.0056 62.8383 3904.839149 5 0.0004 43 | 0/8 3 h-lim-p 0.0002 0.0013 27.4039 3904.780161 0 0.0002 55 | 0/8 4 h-lim-p 0.0007 0.0439 8.8697 3904.767496 6 0.0004 79 | 0/8 5 h-lim-p 0.0008 0.0848 4.0877 3904.764927 2 0.0004 95 | 0/8 6 h-lim-p 0.0014 0.2581 1.1041 3904.764690 4 0.0004 119 | 0/8 7 h-lim-p 0.0008 0.3526 0.5695 3904.764642 1 0.0003 133 | 0/8 8 h-lim-p 0.0759 20.0000 0.0025 3904.757317 0 0.9108 156 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3904.757296 1 0.9961 178 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3904.757296 0 1.0938 198 | 0/8 11 h-lim-p 1.0399 20.0000 0.0000 3904.757296 0 1.0399 218 | 0/8 12 h-lim-p 0.4381 20.0000 0.0000 3904.757296 0 0.6571 238 | 0/8 13 h-lim-p 0.1067 20.0000 0.0001 3904.757296 0 0.0029 262 | 0/8 14 h-lim-p 0.0010 20.0000 0.0003 3904.757296 0 0.0000 295 | 0/8 15 h-lim-p 0.0006 20.0000 0.0000 3904.757296 0 0.0000 326 Out... lnL = -3904.757296 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3904.757296 Node 7: lnL = -3904.757296 Node 8: lnL = -3904.757296 Node 9: lnL = -3904.757296 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 665 Sequential format.. Reading seq # 1: YJL190C_Sbay Reading seq # 2: YJL190C_Scer Reading seq # 3: YJL190C_Skud Reading seq # 4: YJL190C_Smik Reading seq # 5: YJL190C_Spar Sequences read.. Counting patterns.. # site patterns = 276 Counting frequencies.. 120 bytes for distance 44160 bytes for lkl0 35328 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.066496 0.036769 0.081992 0.177745 0.081521 0.224943 0.271383 0.235799 lnL0 = -3222.912197 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3222.912197 x= 0.06650 0.03677 0.08199 0.17774 0.08152 0.22494 0.27138 0.23580 1 h-lim-p 0.0010 0.0081 147.5946 3220.547173 3 0.0002 29 | 0/8 2 h-lim-p 0.0004 0.0028 35.0694 3220.338105 5 0.0004 51 | 0/8 3 h-lim-p 0.0009 0.0198 13.6751 3220.312518 5 0.0003 75 | 0/8 4 h-lim-p 0.0025 0.2311 1.7157 3220.311568 4 0.0007 96 | 0/8 5 h-lim-p 0.0019 0.5496 0.5837 3220.311482 3 0.0006 116 | 0/8 6 h-lim-p 0.0044 3.4489 0.0771 3220.311480 1 0.0005 140 | 0/8 7 h-lim-p 0.0067 20.0000 0.0062 3220.311479 0 0.0059 160 | 0/8 8 h-lim-p 0.0117 20.0000 0.0031 3220.311308 0 0.1410 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3220.311302 0 1.0938 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3220.311302 0 1.0938 223 | 0/8 11 h-lim-p 1.1215 20.0000 0.0000 3220.311302 0 0.9813 243 | 0/8 12 h-lim-p 0.4753 20.0000 0.0000 3220.311302 0 0.0000 287 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 3220.311302 0 0.0000 310 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 3220.311302 0 0.0000 345 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 3220.311302 0 0.0000 372 | 0/8 16 h-lim-p 0.0000 20.0000 0.0019 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 3220.311302 0 0.0000 439 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -3220.311302 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3220.311302 Node 7: lnL = -3220.311302 Node 8: lnL = -3220.311302 Node 9: lnL = -3220.311302 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 394 Sequential format.. Reading seq # 1: YJL192C_Sbay Reading seq # 2: YJL192C_Scer Reading seq # 3: YJL192C_Skud Reading seq # 4: YJL192C_Smik Reading seq # 5: YJL192C_Spar Sequences read.. Counting patterns.. # site patterns = 188 Counting frequencies.. 120 bytes for distance 30080 bytes for lkl0 24064 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000567 0.170892 0.094765 0.196593 0.099397 0.252496 0.182312 0.169897 lnL0 = -1910.476422 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1910.476422 x= 0.00057 0.17089 0.09476 0.19659 0.09940 0.25250 0.18231 0.16990 1 h-lim-p 0.0103 2.0343 60.8592 1909.508038 6 0.0006 36 | 0/8 2 h-lim-p 0.0002 0.0016 20.4529 1909.384030 0 0.0008 50 | 0/8 3 h-lim-p 0.0029 0.0524 5.6613 1909.369898 6 0.0010 77 | 0/8 4 h-lim-p 0.0027 0.0215 1.1149 1909.369376 3 0.0009 97 | 0/8 5 h-lim-p 0.0015 0.4701 0.6296 1909.369281 2 0.0006 113 | 0/8 6 h-lim-p 0.0265 15.2140 0.0140 1909.368922 0 0.0795 134 | 0/8 7 h-lim-p 0.0063 2.6889 0.1780 1909.365624 0 0.0125 155 | 0/8 8 h-lim-p 0.0021 0.3542 1.0726 1909.364274 4 0.0015 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 1909.364250 1 1.0938 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1909.364249 0 1.0938 218 | 0/8 11 h-lim-p 1.1959 20.0000 0.0000 1909.364249 0 1.0464 238 | 0/8 12 h-lim-p 0.4660 20.0000 0.0001 1909.364249 0 0.0018 265 | 0/8 13 h-lim-p 0.0003 20.0000 0.0003 1909.364249 0 0.0001 285 | 0/8 14 h-lim-p 0.0001 15.0631 0.0006 1909.364249 0 0.0000 307 | 0/8 15 h-lim-p 0.0001 20.0000 0.0001 1909.364249 0 0.0000 336 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 1909.364249 0 0.0000 369 Out... lnL = -1909.364249 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1909.364249 Node 7: lnL = -1909.364249 Node 8: lnL = -1909.364249 Node 9: lnL = -1909.364249 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 531 Sequential format.. Reading seq # 1: YJL193W_Sbay Reading seq # 2: YJL193W_Scer Reading seq # 3: YJL193W_Skud Reading seq # 4: YJL193W_Smik Reading seq # 5: YJL193W_Spar Sequences read.. Counting patterns.. # site patterns = 236 Counting frequencies.. 120 bytes for distance 37760 bytes for lkl0 30208 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.066069 0.048853 0.072830 0.132866 0.164249 0.240055 0.212145 0.225447 lnL0 = -2494.520378 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2494.520378 x= 0.06607 0.04885 0.07283 0.13287 0.16425 0.24006 0.21214 0.22545 1 h-lim-p 0.0018 0.0144 109.1603 2492.904166 7 0.0003 38 | 0/8 2 h-lim-p 0.0014 0.0110 22.9320 2492.746378 3 0.0006 56 | 0/8 3 h-lim-p 0.0018 0.0348 7.8518 2492.731868 6 0.0005 85 | 0/8 4 h-lim-p 0.0023 0.1182 1.7880 2492.730973 4 0.0006 106 | 0/8 5 h-lim-p 0.0122 2.1526 0.0886 2492.730971 0 0.0007 121 | 0/8 6 h-lim-p 0.0041 13.4124 0.0145 2492.730970 0 0.0018 141 | 0/8 7 h-lim-p 0.0056 20.0000 0.0046 2492.730938 0 0.0447 164 | 0/8 8 h-lim-p 0.0032 11.9678 0.0644 2492.730725 0 0.0064 185 | 0/8 9 h-lim-p 1.8981 20.0000 0.0002 2492.730719 1 0.9342 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2492.730719 0 1.0938 228 | 0/8 11 h-lim-p 1.0049 20.0000 0.0000 2492.730719 0 1.0049 248 | 0/8 12 h-lim-p 0.6891 20.0000 0.0000 2492.730719 0 0.6891 268 | 0/8 13 h-lim-p 0.0481 20.0000 0.0002 2492.730719 0 0.0105 289 | 0/8 14 h-lim-p 0.0034 20.0000 0.0007 2492.730719 0 0.0034 309 | 0/8 15 h-lim-p 0.0018 20.0000 0.0014 2492.730719 0 0.0000 337 | 0/8 16 h-lim-p 0.0002 20.0000 0.0000 2492.730719 0 0.0000 371 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -2492.730719 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2492.730719 Node 7: lnL = -2492.730719 Node 8: lnL = -2492.730719 Node 9: lnL = -2492.730719 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 585 Sequential format.. Reading seq # 1: YJL194W_Sbay Reading seq # 2: YJL194W_Scer Reading seq # 3: YJL194W_Skud Reading seq # 4: YJL194W_Smik Reading seq # 5: YJL194W_Spar Sequences read.. Counting patterns.. # site patterns = 187 Counting frequencies.. 120 bytes for distance 29920 bytes for lkl0 23936 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.114329 0.042457 0.081126 0.068681 0.065623 0.138044 0.129484 0.236540 lnL0 = -2425.196918 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2425.196918 x= 0.11433 0.04246 0.08113 0.06868 0.06562 0.13804 0.12948 0.23654 1 h-lim-p 0.0013 0.0104 106.7971 2424.136823 8 0.0002 42 | 0/8 2 h-lim-p 0.0007 0.0053 29.9019 2423.977047 7 0.0004 71 | 0/8 3 h-lim-p 0.0006 0.0097 18.4336 2423.953959 6 0.0002 98 | 0/8 4 h-lim-p 0.0015 0.0430 2.2709 2423.953355 3 0.0002 119 | 0/8 5 h-lim-p 0.0006 0.2828 0.8828 2423.953205 3 0.0004 138 | 0/8 6 h-lim-p 0.0036 1.7068 0.1060 2423.953203 0 0.0004 160 | 0/8 7 h-lim-p 0.0128 20.0000 0.0037 2423.953199 0 0.0112 180 | 0/8 8 h-lim-p 0.0029 20.0000 0.0143 2423.952872 0 0.0232 203 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2423.952862 1 0.9961 225 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2423.952862 0 0.5469 246 | 0/8 11 h-lim-p 0.3771 20.0000 0.0000 2423.952862 0 0.0022 273 | 0/8 12 h-lim-p 0.0012 20.0000 0.0000 2423.952862 0 0.0000 299 | 0/8 13 h-lim-p 0.0000 20.0000 0.0002 2423.952862 0 0.0000 331 | 0/8 14 h-lim-p 0.0000 20.0000 0.0015 | 0/8 15 h-lim-p 0.0000 20.0000 0.0015 Out... lnL = -2423.952862 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2423.952862 Node 7: lnL = -2423.952862 Node 8: lnL = -2423.952862 Node 9: lnL = -2423.952862 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 481 Sequential format.. Reading seq # 1: YJL196C_Sbay Reading seq # 2: YJL196C_Scer Reading seq # 3: YJL196C_Skud Reading seq # 4: YJL196C_Smik Reading seq # 5: YJL196C_Spar Sequences read.. Counting patterns.. # site patterns = 172 Counting frequencies.. 120 bytes for distance 27520 bytes for lkl0 22016 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.131543 0.026977 0.065462 0.073798 0.060316 0.134886 0.091049 0.245655 lnL0 = -1913.856860 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1913.856860 x= 0.13154 0.02698 0.06546 0.07380 0.06032 0.13489 0.09105 0.24566 1 h-lim-p 0.0014 0.0114 152.1988 1912.018959 8 0.0002 39 | 0/8 2 h-lim-p 0.0007 0.0054 25.1405 1911.891883 8 0.0004 71 | 0/8 3 h-lim-p 0.0008 0.0114 12.8537 1911.873739 6 0.0003 97 | 0/8 4 h-lim-p 0.0009 0.0261 3.7990 1911.871990 5 0.0003 122 | 0/8 5 h-lim-p 0.0007 0.2432 1.3924 1911.871542 4 0.0005 143 | 0/8 6 h-lim-p 0.0021 0.3805 0.3438 1911.871520 2 0.0004 160 | 0/8 7 h-lim-p 0.0016 1.9323 0.0863 1911.871518 1 0.0004 183 | 0/8 8 h-lim-p 0.0758 20.0000 0.0005 1911.870893 0 1.2127 207 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1911.870890 1 0.9961 229 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1911.870890 0 0.6250 250 | 0/8 11 h-lim-p 0.4984 20.0000 0.0000 1911.870890 0 0.0156 274 | 0/8 12 h-lim-p 0.0089 20.0000 0.0000 1911.870890 0 0.0000 306 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 1911.870890 0 0.0000 338 Out... lnL = -1911.870890 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1911.870890 Node 7: lnL = -1911.870890 Node 8: lnL = -1911.870890 Node 9: lnL = -1911.870890 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 855 Sequential format.. Reading seq # 1: YJL198W_Sbay Reading seq # 2: YJL198W_Scer Reading seq # 3: YJL198W_Skud Reading seq # 4: YJL198W_Smik Reading seq # 5: YJL198W_Spar Sequences read.. Counting patterns.. # site patterns = 428 Counting frequencies.. 120 bytes for distance 68480 bytes for lkl0 54784 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.161517 0.021034 0.163949 0.151098 0.148385 0.296550 0.383905 0.398259 lnL0 = -4320.029619 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4320.029619 x= 0.16152 0.02103 0.16395 0.15110 0.14839 0.29655 0.38391 0.39826 1 h-lim-p 0.0068 1.3701 112.9571 4317.657526 2 0.0004 29 | 0/8 2 h-lim-p 0.0007 0.0054 30.3840 4317.437895 6 0.0005 54 | 0/8 3 h-lim-p 0.0016 0.0380 9.4305 4317.407808 2 0.0008 70 | 0/8 4 h-lim-p 0.0014 0.0861 5.0514 4317.397043 3 0.0011 88 | 0/8 5 h-lim-p 0.0034 0.3268 1.5984 4317.395788 4 0.0011 109 | 0/8 6 h-lim-p 0.0052 0.7731 0.3384 4317.395732 2 0.0010 126 | 0/8 7 h-lim-p 0.0327 20.0000 0.0108 4317.395731 0 0.0036 148 | 0/8 8 h-lim-p 0.0472 20.0000 0.0008 4317.395613 0 0.3775 171 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4317.395611 0 1.0938 191 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4317.395611 0 1.0938 211 | 0/8 11 h-lim-p 1.3297 20.0000 0.0000 4317.395611 0 0.6649 231 | 0/8 12 h-lim-p 0.3631 20.0000 0.0000 4317.395611 0 0.0000 271 | 0/8 13 h-lim-p 0.0000 20.0000 0.0003 4317.395611 0 0.0000 306 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -4317.395611 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4317.395611 Node 7: lnL = -4317.395611 Node 8: lnL = -4317.395611 Node 9: lnL = -4317.395611 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 196 Sequential format.. Reading seq # 1: YJL203W_Sbay Reading seq # 2: YJL203W_Scer Reading seq # 3: YJL203W_Skud Reading seq # 4: YJL203W_Smik Reading seq # 5: YJL203W_Spar Sequences read.. Counting patterns.. # site patterns = 96 Counting frequencies.. 120 bytes for distance 15360 bytes for lkl0 12288 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.096045 0.000060 0.132107 0.159312 0.053026 0.170262 0.260615 0.224600 lnL0 = -850.616847 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 850.616847 x= 0.09605 0.00006 0.13211 0.15931 0.05303 0.17026 0.26062 0.22460 1 h-lim-p 0.0001 0.0011 74.8072 848.623815 0 0.0006 24 | 0/8 2 h-lim-p 0.0004 0.0031 47.8331 847.957725 0 0.0008 37 | 0/8 3 h-lim-p 0.0002 0.0018 12.5906 847.913581 0 0.0009 51 | 0/8 4 h-lim-p 0.0039 0.0847 2.8713 847.907111 5 0.0017 75 | 0/8 5 h-lim-p 0.0087 0.2386 0.5494 847.906828 3 0.0017 94 | 0/8 6 h-lim-p 0.0100 0.8087 0.0954 847.906474 0 0.0150 114 | 0/8 7 h-lim-p 0.0154 0.4490 0.0930 847.902509 0 0.0308 135 | 0/8 8 h-lim-p 0.0045 0.1077 0.6372 847.891108 0 0.0067 155 | 0/8 9 h-lim-p 2.5000 20.0000 0.0012 847.890664 5 0.7555 190 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 847.890656 2 0.9644 214 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 847.890656 0 1.0938 234 | 0/8 12 h-lim-p 2.3088 20.0000 0.0000 847.890656 0 2.3088 254 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 847.890656 0 0.0781 278 | 0/8 14 h-lim-p 0.0195 20.0000 0.0000 847.890656 0 0.0024 300 | 0/8 15 h-lim-p 0.0011 20.0000 0.0000 847.890656 0 0.0006 320 | 0/8 16 h-lim-p 0.0005 20.0000 0.0000 847.890656 0 0.0005 340 | 0/8 17 h-lim-p 0.0003 20.0000 0.0000 847.890656 0 0.0000 380 | 0/8 18 h-lim-p 0.0000 20.0000 0.0016 847.890656 0 0.0000 408 | 0/8 19 h-lim-p 0.0000 20.0000 0.0003 .. | 0/8 20 h-lim-p 0.0000 20.0000 0.0016 | 0/8 21 h-lim-p 0.0000 20.0000 0.0016 Out... lnL = -847.890656 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -847.890656 Node 7: lnL = -847.890656 Node 8: lnL = -847.890656 Node 9: lnL = -847.890656 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 249 Sequential format.. Reading seq # 1: YJL206C_Sbay Reading seq # 2: YJL206C_Scer Reading seq # 3: YJL206C_Skud Reading seq # 4: YJL206C_Smik Reading seq # 5: YJL206C_Spar Sequences read.. Counting patterns.. # site patterns = 115 Counting frequencies.. 120 bytes for distance 18400 bytes for lkl0 14720 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.112921 0.000060 0.148534 0.171909 0.110772 0.170450 0.271375 0.258204 lnL0 = -932.648097 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 932.648097 x= 0.11292 0.00006 0.14853 0.17191 0.11077 0.17045 0.27137 0.25820 1 h-lim-p 0.0000 0.0000 84.2150 932.628454 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0177 20.1839 932.231184 0 0.0027 42 | 1/8 3 h-lim-p 0.0055 0.0442 3.7248 932.199946 4 0.0028 63 | 1/8 4 h-lim-p 0.0099 0.3289 1.0496 931.896790 0 0.0395 77 | 1/8 5 h-lim-p 0.0108 0.0861 2.9493 929.232922 0 0.0323 90 | 1/8 6 h-lim-p 0.0017 0.0136 15.3889 928.990876 5 0.0017 112 | 1/8 7 h-lim-p 0.0071 0.0596 3.6877 928.980067 4 0.0015 132 | 1/8 8 h-lim-p 0.1317 6.7529 0.0425 928.753645 0 0.5267 146 | 1/8 9 h-lim-p 2.5000 20.0000 0.0086 928.742763 4 0.6366 174 | 1/8 10 h-lim-p 2.5000 20.0000 0.0010 928.742482 4 0.8779 203 | 1/8 11 h-lim-p 2.5000 20.0000 0.0001 928.742479 2 0.7996 227 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 928.742479 0 1.0938 246 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 928.742479 0 1.0938 265 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 928.742479 0 0.2734 286 | 1/8 15 h-lim-p 0.1507 20.0000 0.0000 928.742479 0 0.0000 319 Out... lnL = -928.742479 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -928.742479 Node 7: lnL = -928.742479 Node 8: lnL = -928.742479 Node 9: lnL = -928.742479 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 220 Sequential format.. Reading seq # 1: YJL208C_Sbay Reading seq # 2: YJL208C_Scer Reading seq # 3: YJL208C_Skud Reading seq # 4: YJL208C_Smik Reading seq # 5: YJL208C_Spar Sequences read.. Counting patterns.. # site patterns = 107 Counting frequencies.. 120 bytes for distance 17120 bytes for lkl0 13696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.036904 0.056018 0.002142 0.095506 0.106080 0.197391 0.400979 0.180857 lnL0 = -967.021596 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 967.021596 x= 0.03690 0.05602 0.00214 0.09551 0.10608 0.19739 0.40098 0.18086 1 h-lim-p 0.0012 0.0095 37.1752 966.533184 9 0.0008 45 | 0/8 2 h-lim-p 0.0000 0.0001 23.4679 966.490445 m 0.0001 57 | 1/8 3 h-lim-p 0.0000 0.0036 72.2189 966.469778 0 0.0001 71 | 1/8 4 h-lim-p 0.0016 0.0230 4.0951 966.447157 5 0.0016 94 | 1/8 5 h-lim-p 0.0059 0.1228 1.0890 966.446432 3 0.0012 114 | 1/8 6 h-lim-p 0.0057 1.4922 0.2346 966.446355 2 0.0027 130 | 1/8 7 h-lim-p 0.0019 1.4322 0.3278 966.446326 2 0.0010 154 | 1/8 8 h-lim-p 0.1793 20.0000 0.0018 966.442779 0 1.4344 176 | 1/8 9 h-lim-p 2.5000 20.0000 0.0009 966.442166 4 1.3437 204 | 1/8 10 h-lim-p 2.5000 20.0000 0.0001 966.442159 1 0.9961 225 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 966.442159 0 1.0938 244 | 1/8 12 h-lim-p 1.3290 20.0000 0.0000 966.442159 0 1.1629 263 | 1/8 13 h-lim-p 0.3238 20.0000 0.0000 966.442159 0 0.0002 292 | 1/8 14 h-lim-p 0.0000 20.0000 0.0001 .. | 1/8 15 h-lim-p 0.0000 20.0000 0.0000 966.442159 0 0.0000 357 | 1/8 16 h-lim-p 0.0000 20.0000 0.0000 966.442159 0 0.0000 377 | 1/8 17 h-lim-p 0.0000 20.0000 0.0000 966.442159 0 0.0000 399 | 1/8 18 h-lim-p 0.0000 20.0000 0.0000 966.442159 0 0.0000 433 | 1/8 19 h-lim-p 0.0000 20.0000 0.0000 966.442159 0 0.0000 467 | 1/8 20 h-lim-p 0.0000 20.0000 0.0000 | 1/8 21 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -966.442159 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -966.442159 Node 7: lnL = -966.442159 Node 8: lnL = -966.442159 Node 9: lnL = -966.442159 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 313 Sequential format.. Reading seq # 1: YJL209W_Sbay Reading seq # 2: YJL209W_Scer Reading seq # 3: YJL209W_Skud Reading seq # 4: YJL209W_Smik Reading seq # 5: YJL209W_Spar Sequences read.. Counting patterns.. # site patterns = 160 Counting frequencies.. 120 bytes for distance 25600 bytes for lkl0 20480 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.116735 0.000060 0.291197 0.288176 0.218230 0.250485 0.380271 0.296737 lnL0 = -1457.670012 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1457.670012 x= 0.11674 0.00006 0.29120 0.28818 0.21823 0.25049 0.38027 0.29674 1 h-lim-p 0.0000 0.0000 193.8582 1457.628854 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0040 93.8521 1446.493916 4 0.0026 50 | 1/8 3 h-lim-p 0.0022 0.0173 23.4615 1445.532765 0 0.0032 62 | 1/8 4 h-lim-p 0.0062 0.0533 12.2474 1445.126913 8 0.0039 94 | 1/8 5 h-lim-p 0.0354 0.2865 1.3377 1430.240303 0 0.1417 108 | 1/8 6 h-lim-p 0.0007 0.0055 62.3165 1425.367390 0 0.0027 122 | 1/8 7 h-lim-p 0.0012 0.0096 38.1530 1424.458347 1 0.0015 136 | 1/8 8 h-lim-p 0.4759 4.3186 0.1203 1423.482928 2 0.4462 152 | 1/8 9 h-lim-p 1.1778 9.4224 0.0355 1423.335886 2 0.5521 175 | 1/8 10 h-lim-p 2.2170 20.0000 0.0088 1423.324299 2 0.5196 199 | 1/8 11 h-lim-p 1.1747 20.0000 0.0039 1423.322539 4 0.5205 225 | 1/8 12 h-lim-p 2.2634 20.0000 0.0009 1423.322393 4 0.8266 253 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 1423.322393 0 1.0938 272 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 1423.322393 0 1.0938 291 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 1423.322393 0 0.0195 316 | 1/8 16 h-lim-p 0.0100 20.0000 0.0000 1423.322393 0 0.0100 335 | 1/8 17 h-lim-p 0.0064 20.0000 0.0000 1423.322393 0 0.0001 360 Out... lnL = -1423.322393 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1423.322393 Node 7: lnL = -1423.322393 Node 8: lnL = -1423.322393 Node 9: lnL = -1423.322393 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 742 Sequential format.. Reading seq # 1: YJL210W_Sbay Reading seq # 2: YJL210W_Scer Reading seq # 3: YJL210W_Skud Reading seq # 4: YJL210W_Smik Reading seq # 5: YJL210W_Spar Sequences read.. Counting patterns.. # site patterns = 269 Counting frequencies.. 120 bytes for distance 43040 bytes for lkl0 34432 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.193712 0.055068 0.091612 0.086649 0.074008 0.188325 0.263452 0.376442 lnL0 = -3364.550727 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3364.550727 x= 0.19371 0.05507 0.09161 0.08665 0.07401 0.18833 0.26345 0.37644 1 h-lim-p 0.0003 0.0023 72.2848 3363.816769 6 0.0003 36 | 0/8 2 h-lim-p 0.0009 0.0159 22.3996 3363.704687 5 0.0005 59 | 0/8 3 h-lim-p 0.0005 0.0099 20.4471 3363.668575 4 0.0003 80 | 0/8 4 h-lim-p 0.0004 0.0225 13.1233 3363.649314 5 0.0004 101 | 0/8 5 h-lim-p 0.0013 0.0669 3.5982 3363.647575 2 0.0003 118 | 0/8 6 h-lim-p 0.0011 0.3650 1.0601 3363.647117 2 0.0009 134 | 0/8 7 h-lim-p 0.0020 0.8234 0.5036 3363.647034 1 0.0008 148 | 0/8 8 h-lim-p 0.7616 20.0000 0.0005 3363.646548 0 1.1424 168 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3363.646545 0 1.0938 188 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3363.646545 0 1.0938 208 | 0/8 11 h-lim-p 1.4153 20.0000 0.0000 3363.646545 0 1.2384 228 | 0/8 12 h-lim-p 1.2435 20.0000 0.0000 3363.646545 0 2.4870 249 | 0/8 13 h-lim-p 0.5036 20.0000 0.0000 3363.646545 0 0.4407 269 | 0/8 14 h-lim-p 0.0216 20.0000 0.0004 3363.646545 0 0.0003 295 | 0/8 15 h-lim-p 0.0011 20.0000 0.0001 3363.646545 0 0.0000 328 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 3363.646545 0 0.0000 362 Out... lnL = -3363.646545 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3363.646545 Node 7: lnL = -3363.646545 Node 8: lnL = -3363.646545 Node 9: lnL = -3363.646545 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 583 Sequential format.. Reading seq # 1: YJL212C_Sbay Reading seq # 2: YJL212C_Scer Reading seq # 3: YJL212C_Skud Reading seq # 4: YJL212C_Smik Reading seq # 5: YJL212C_Spar Sequences read.. Counting patterns.. # site patterns = 215 Counting frequencies.. 120 bytes for distance 34400 bytes for lkl0 27520 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.178940 0.043505 0.069707 0.094754 0.068787 0.175791 0.292404 0.352616 lnL0 = -2525.016064 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2525.016064 x= 0.17894 0.04350 0.06971 0.09475 0.06879 0.17579 0.29240 0.35262 1 h-lim-p 0.0140 2.2776 60.0196 2524.460058 6 0.0003 39 | 0/8 2 h-lim-p 0.0011 0.0099 17.6380 2524.409211 5 0.0004 63 | 0/8 3 h-lim-p 0.0006 0.0166 9.7628 2524.396052 6 0.0004 90 | 0/8 4 h-lim-p 0.0007 0.0741 4.9310 2524.387031 0 0.0011 102 | 0/8 5 h-lim-p 0.0067 0.2163 0.7712 2524.386868 4 0.0006 126 | 0/8 6 h-lim-p 0.0006 0.5699 0.6978 2524.386708 0 0.0013 147 | 0/8 7 h-lim-p 0.0084 1.9135 0.1054 2524.386704 1 0.0008 171 | 0/8 8 h-lim-p 0.1873 20.0000 0.0005 2524.386508 0 1.1237 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2524.386506 0 1.0938 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2524.386506 0 1.0938 233 | 0/8 11 h-lim-p 1.7078 20.0000 0.0000 2524.386506 0 1.7078 253 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2524.386506 0 0.0195 279 | 0/8 13 h-lim-p 0.0051 20.0000 0.0000 2524.386506 0 0.0011 300 | 0/8 14 h-lim-p 0.0005 20.0000 0.0000 2524.386506 0 0.0000 339 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -2524.386506 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2524.386506 Node 7: lnL = -2524.386506 Node 8: lnL = -2524.386506 Node 9: lnL = -2524.386506 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 902 Sequential format.. Reading seq # 1: YJL213W_Sbay Reading seq # 2: YJL213W_Scer Reading seq # 3: YJL213W_Skud Reading seq # 4: YJL213W_Smik Reading seq # 5: YJL213W_Spar Sequences read.. Counting patterns.. # site patterns = 473 Counting frequencies.. 120 bytes for distance 75680 bytes for lkl0 60544 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.252373 0.468426 0.000060 0.423712 0.746874 0.484218 0.717380 0.599531 lnL0 = -5394.893788 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 5394.893788 x= 0.25237 0.46843 0.00006 0.42371 0.74687 0.48422 0.71738 0.59953 1 h-lim-p 0.0000 0.0000 248.2821 5394.743183 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0001 4399.9818 5278.362917 m 0.0001 35 | 2/8 3 h-lim-p 0.0022 0.0176 45.2995 5276.590568 8 0.0016 67 | 2/8 4 h-lim-p 0.0065 0.1399 11.2036 5274.905403 0 0.0130 80 | 2/8 5 h-lim-p 0.0086 0.0691 13.3394 5274.699186 7 0.0025 110 | 2/8 6 h-lim-p 0.0641 0.7358 0.5245 5274.641540 7 0.0401 142 | 2/8 7 h-lim-p 0.0136 0.4918 1.5401 5273.284171 0 0.0818 162 | 2/8 8 h-lim-p 2.5000 20.0000 0.0256 5273.104002 6 2.0397 187 | 2/8 9 h-lim-p 0.7167 5.7337 0.0568 5269.582200 m 5.7337 205 | 3/8 10 h-lim-p 0.0227 0.1819 2.1030 5269.579649 4 0.0011 234 | 3/8 11 h-lim-p 0.0175 10.0917 0.1318 .. | 3/8 12 h-lim-p 0.0000 0.0547 52.8785 5267.148501 0 0.0019 294 | 3/8 13 h-lim-p 0.0020 0.0202 49.9219 5259.324031 0 0.0081 308 | 3/8 14 h-lim-p 0.0032 0.0254 26.2952 5259.074032 6 0.0011 335 | 3/8 15 h-lim-p 0.0032 0.1493 8.8605 5258.942734 1 0.0040 349 | 2/8 16 h-lim-p 0.0009 0.0521 37.6347 5258.626998 5 0.0008 370 | 2/8 17 h-lim-p 0.0262 1.3170 1.1641 5258.584046 6 0.0177 397 | 2/8 18 h-lim-p 0.0272 0.2172 0.4359 5257.748159 0 0.1629 411 | 2/8 19 h-lim-p 1.5968 20.0000 0.0445 5257.588330 7 1.0715 446 | 2/8 20 h-lim-p 1.8827 15.0619 0.0036 5257.585425 4 1.2771 475 | 2/8 21 h-lim-p 2.5000 20.0000 0.0001 5257.585423 0 1.0938 493 | 2/8 22 h-lim-p 2.5000 20.0000 0.0000 5257.585423 0 1.0938 511 | 2/8 23 h-lim-p 2.5000 20.0000 0.0000 5257.585423 0 2.1875 529 | 2/8 24 h-lim-p 1.9281 20.0000 0.0000 5257.585423 0 0.9640 547 | 2/8 25 h-lim-p 2.5000 20.0000 0.0000 5257.585423 0 1.2500 565 | 2/8 26 h-lim-p 0.1245 20.0000 0.0000 5257.585423 0 0.0019 588 Out... lnL = -5257.585423 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -5257.585423 Node 7: lnL = -5257.585423 Node 8: lnL = -5257.585423 Node 9: lnL = -5257.585423 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 758 Sequential format.. Reading seq # 1: YJL217W_Sbay Reading seq # 2: YJL217W_Scer Reading seq # 3: YJL217W_Skud Reading seq # 4: YJL217W_Smik Reading seq # 5: YJL217W_Spar Sequences read.. Counting patterns.. # site patterns = 266 Counting frequencies.. 120 bytes for distance 42560 bytes for lkl0 34048 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.184736 0.483390 0.162429 0.086976 0.019128 0.413421 0.273255 0.485231 lnL0 = -3588.542140 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3588.542140 x= 0.18474 0.48339 0.16243 0.08698 0.01913 0.41342 0.27326 0.48523 1 h-lim-p 0.0003 0.0025 151.9850 3587.396429 8 0.0001 40 | 0/8 2 h-lim-p 0.0001 0.0010 83.0832 3586.773561 0 0.0003 53 | 0/8 3 h-lim-p 0.0048 0.0647 4.4292 3586.750673 2 0.0023 69 | 0/8 4 h-lim-p 0.0031 0.1653 3.2613 3586.740009 3 0.0028 87 | 0/8 5 h-lim-p 0.0075 1.2821 1.2126 3586.738546 4 0.0023 111 | 0/8 6 h-lim-p 0.0024 0.4178 1.1956 3586.737584 2 0.0022 127 | 0/8 7 h-lim-p 0.0084 1.1113 0.3150 3586.737089 3 0.0065 145 | 0/8 8 h-lim-p 0.2646 20.0000 0.0077 3586.714583 0 0.5292 166 | 0/8 9 h-lim-p 2.5000 20.0000 0.0010 3586.712572 2 1.0889 190 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 3586.712543 3 1.4879 218 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3586.712542 0 1.0938 238 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3586.712542 0 0.5469 259 | 0/8 13 h-lim-p 0.3547 20.0000 0.0000 3586.712542 0 0.0014 286 Out... lnL = -3586.712542 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3586.712542 Node 7: lnL = -3586.712542 Node 8: lnL = -3586.712542 Node 9: lnL = -3586.712542 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 808 Sequential format.. Reading seq # 1: YJL218W_Sbay Reading seq # 2: YJL218W_Scer Reading seq # 3: YJL218W_Skud Reading seq # 4: YJL218W_Smik Reading seq # 5: YJL218W_Spar Sequences read.. Counting patterns.. # site patterns = 299 Counting frequencies.. 120 bytes for distance 47840 bytes for lkl0 38272 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.207794 0.000060 0.612215 0.100046 0.307440 0.541165 1.055354 0.585859 lnL0 = -3858.580215 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3858.580215 x= 0.20779 0.00006 0.61221 0.10005 0.30744 0.54117 1.05535 0.58586 1 h-lim-p 0.0000 0.0000 586.8683 3858.053453 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0032 128.9376 3814.547079 m 0.0032 40 | 2/8 3 h-lim-p 0.0000 0.0003 1919.8309 3780.613540 0 0.0001 54 | 2/8 4 h-lim-p 0.0017 0.0137 43.2968 3765.649848 m 0.0137 66 | 2/8 5 h-lim-p 0.0000 0.0000 15.2075 h-lim-p: 3.88957880e-19 3.11166304e-18 1.52074936e+01 3765.649848 .. | 1/8 6 h-lim-p 0.0000 0.0017 92.0995 3762.820527 0 0.0006 92 | 1/8 7 h-lim-p 0.0000 0.0002 190.2564 3761.992871 0 0.0002 106 | 1/8 8 h-lim-p 0.0000 0.0000 23.9204 3761.977614 m 0.0000 118 | 2/8 9 h-lim-p 0.0000 0.0638 38.1466 3760.573759 0 0.0046 138 | 2/8 10 h-lim-p 0.0127 0.1078 13.9221 3758.815746 0 0.0254 151 | 2/8 11 h-lim-p 0.0695 0.5556 1.2845 3758.787678 2 0.0163 168 | 2/8 12 h-lim-p 0.0706 1.4817 0.2963 3758.351350 0 0.2823 182 | 2/8 13 h-lim-p 0.3460 2.7682 0.1504 3757.987088 5 0.3658 210 | 2/8 14 h-lim-p 1.2108 20.0000 0.0454 3757.944192 6 0.8173 244 | 1/8 15 h-lim-p 0.0462 3.1278 0.8033 3757.943335 4 0.0034 275 | 1/8 16 h-lim-p 0.6280 20.0000 0.0044 3757.942448 0 1.2559 295 | 1/8 17 h-lim-p 2.5000 20.0000 0.0005 3757.942421 2 0.9644 318 | 1/8 18 h-lim-p 2.5000 20.0000 0.0001 3757.942420 0 1.0938 337 | 1/8 19 h-lim-p 2.5000 20.0000 0.0000 3757.942420 0 1.0938 356 | 1/8 20 h-lim-p 2.5000 20.0000 0.0000 3757.942420 0 0.5469 376 | 1/8 21 h-lim-p 1.0981 20.0000 0.0000 3757.942420 0 0.1030 398 | 1/8 22 h-lim-p 0.1009 20.0000 0.0000 3757.942420 0 0.0504 417 | 1/8 23 h-lim-p 0.0459 20.0000 0.0000 3757.942420 0 0.0230 436 Out... lnL = -3757.942420 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3757.942420 Node 7: lnL = -3757.942420 Node 8: lnL = -3757.942420 Node 9: lnL = -3757.942420 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 847 Sequential format.. Reading seq # 1: YJR001W_Sbay Reading seq # 2: YJR001W_Scer Reading seq # 3: YJR001W_Skud Reading seq # 4: YJR001W_Smik Reading seq # 5: YJR001W_Spar Sequences read.. Counting patterns.. # site patterns = 432 Counting frequencies.. 120 bytes for distance 69120 bytes for lkl0 55296 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.014195 0.397390 0.048637 0.258348 0.234307 0.292057 0.346259 0.272022 lnL0 = -4506.396587 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4506.396587 x= 0.01420 0.39739 0.04864 0.25835 0.23431 0.29206 0.34626 0.27202 1 h-lim-p 0.0008 0.0067 92.6643 4503.747890 4 0.0007 30 | 0/8 2 h-lim-p 0.0003 0.0022 46.5138 4503.079259 0 0.0008 43 | 0/8 3 h-lim-p 0.0011 0.0091 17.5771 4502.937433 2 0.0011 59 | 0/8 4 h-lim-p 0.0013 0.0105 8.9901 4502.898895 2 0.0012 75 | 0/8 5 h-lim-p 0.0049 0.0393 1.7161 4502.896637 4 0.0016 96 | 0/8 6 h-lim-p 0.0017 0.0758 1.6062 4502.896056 3 0.0007 114 | 0/8 7 h-lim-p 0.0063 2.1565 0.1836 4502.895989 1 0.0028 128 | 0/8 8 h-lim-p 0.0965 20.0000 0.0053 4502.888912 0 0.7716 151 | 0/8 9 h-lim-p 2.5000 20.0000 0.0010 4502.888150 3 1.0004 177 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4502.888150 0 1.0938 197 | 0/8 11 h-lim-p 1.9254 20.0000 0.0000 4502.888150 0 1.6847 217 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4502.888150 0 2.1875 237 | 0/8 13 h-lim-p 1.3755 20.0000 0.0000 4502.888150 0 1.2036 257 | 0/8 14 h-lim-p 0.5889 20.0000 0.0000 4502.888150 0 0.2945 277 | 0/8 15 h-lim-p 0.0019 3.2849 0.0044 4502.888150 0 0.0000 302 | 0/8 16 h-lim-p 0.0006 20.0000 0.0002 4502.888150 0 0.0001 324 | 0/8 17 h-lim-p 0.0003 20.0000 0.0001 4502.888150 0 0.0000 358 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 4502.888150 0 0.0000 384 | 0/8 19 h-lim-p 0.0000 20.0000 0.0003 .. | 0/8 20 h-lim-p 0.0000 20.0000 0.0002 4502.888150 0 0.0000 451 | 0/8 21 h-lim-p 0.0000 20.0000 0.0002 4502.888150 0 0.0000 486 | 0/8 22 h-lim-p 0.0000 20.0000 0.0002 | 0/8 23 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -4502.888150 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4502.888150 Node 7: lnL = -4502.888150 Node 8: lnL = -4502.888150 Node 9: lnL = -4502.888150 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 407 Sequential format.. Reading seq # 1: YJR003C_Sbay Reading seq # 2: YJR003C_Scer Reading seq # 3: YJR003C_Skud Reading seq # 4: YJR003C_Smik Reading seq # 5: YJR003C_Spar Sequences read.. Counting patterns.. # site patterns = 226 Counting frequencies.. 120 bytes for distance 36160 bytes for lkl0 28928 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.016424 0.136707 0.171723 0.127535 0.171444 0.267199 0.261197 0.202964 lnL0 = -1916.768740 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1916.768740 x= 0.01642 0.13671 0.17172 0.12754 0.17144 0.26720 0.26120 0.20296 1 h-lim-p 0.0063 0.0504 45.7116 1915.869550 9 0.0009 47 | 0/8 2 h-lim-p 0.0004 0.0032 17.0585 1915.745688 0 0.0008 60 | 0/8 3 h-lim-p 0.0036 0.1092 3.8011 1915.739128 5 0.0010 83 | 0/8 4 h-lim-p 0.0019 0.0334 1.9413 1915.737391 5 0.0011 110 | 0/8 5 h-lim-p 0.0082 1.0611 0.2677 1915.737335 3 0.0015 131 | 0/8 6 h-lim-p 0.0075 8.2964 0.0523 1915.737280 1 0.0093 153 | 0/8 7 h-lim-p 0.0141 1.6423 0.0346 1915.735776 0 0.0564 175 | 0/8 8 h-lim-p 0.0038 0.1736 0.5169 1915.733132 0 0.0057 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 1915.733085 1 0.9961 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1915.733085 0 1.0938 237 | 0/8 11 h-lim-p 1.9788 20.0000 0.0000 1915.733085 0 1.7315 257 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1915.733085 0 2.1875 277 | 0/8 13 h-lim-p 0.9438 20.0000 0.0000 1915.733085 0 1.8876 298 | 0/8 14 h-lim-p 0.3435 20.0000 0.0001 1915.733085 0 0.0054 323 | 0/8 15 h-lim-p 0.0006 15.9285 0.0011 1915.733085 0 0.0003 343 | 0/8 16 h-lim-p 0.0001 2.9423 0.0061 1915.733085 0 0.0000 364 | 0/8 17 h-lim-p 0.0001 20.0000 0.0006 1915.733085 0 0.0000 397 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1915.733085 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1915.733085 Node 7: lnL = -1915.733085 Node 8: lnL = -1915.733085 Node 9: lnL = -1915.733085 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 900 Sequential format.. Reading seq # 1: YJR004C_Sbay Reading seq # 2: YJR004C_Scer Reading seq # 3: YJR004C_Skud Reading seq # 4: YJR004C_Smik Reading seq # 5: YJR004C_Spar Sequences read.. Counting patterns.. # site patterns = 272 Counting frequencies.. 120 bytes for distance 43520 bytes for lkl0 34816 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.059778 0.082097 0.067164 0.140860 0.084218 0.232539 0.276770 0.211766 lnL0 = -4017.133352 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4017.133352 x= 0.05978 0.08210 0.06716 0.14086 0.08422 0.23254 0.27677 0.21177 1 h-lim-p 0.0003 0.0025 136.4173 4015.178705 9 0.0002 45 | 0/8 2 h-lim-p 0.0005 0.0039 33.0597 4015.037491 7 0.0003 74 | 0/8 3 h-lim-p 0.0005 0.0178 17.0692 4015.008953 2 0.0002 90 | 0/8 4 h-lim-p 0.0008 0.0537 5.3252 4015.003708 5 0.0004 113 | 0/8 5 h-lim-p 0.0019 0.2791 1.1836 4015.003360 4 0.0005 135 | 0/8 6 h-lim-p 0.0031 0.9771 0.2072 4015.003349 2 0.0005 153 | 0/8 7 h-lim-p 0.0033 3.3016 0.0310 4015.003348 0 0.0004 175 | 0/8 8 h-lim-p 0.1272 20.0000 0.0001 4015.003341 0 1.0178 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4015.003341 0 1.0938 218 | 0/8 10 h-lim-p 1.1222 20.0000 0.0000 4015.003341 0 0.9819 238 | 0/8 11 h-lim-p 0.4239 20.0000 0.0000 4015.003341 0 0.0265 261 | 0/8 12 h-lim-p 0.0048 20.0000 0.0003 4015.003341 0 0.0000 300 | 0/8 13 h-lim-p 0.0000 20.0000 0.0002 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -4015.003341 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4015.003341 Node 7: lnL = -4015.003341 Node 8: lnL = -4015.003341 Node 9: lnL = -4015.003341 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 845 Sequential format.. Reading seq # 1: YJR006W_Sbay Reading seq # 2: YJR006W_Scer Reading seq # 3: YJR006W_Skud Reading seq # 4: YJR006W_Smik Reading seq # 5: YJR006W_Spar Sequences read.. Counting patterns.. # site patterns = 263 Counting frequencies.. 120 bytes for distance 42080 bytes for lkl0 33664 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.045161 0.117106 0.022865 0.113215 0.068287 0.249118 0.129051 0.166425 lnL0 = -3137.973830 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3137.973830 x= 0.04516 0.11711 0.02286 0.11321 0.06829 0.24912 0.12905 0.16642 1 h-lim-p 0.0015 0.0120 143.1966 3136.615632 8 0.0001 39 | 0/8 2 h-lim-p 0.0005 0.0054 39.1632 3136.304234 3 0.0004 57 | 0/8 3 h-lim-p 0.0003 0.0050 55.3252 3136.103534 3 0.0003 75 | 0/8 4 h-lim-p 0.0004 0.0068 35.7894 3135.923518 0 0.0006 87 | 0/8 5 h-lim-p 0.0026 0.0209 8.7254 3135.914206 5 0.0003 110 | 0/8 6 h-lim-p 0.0009 0.0413 2.6978 3135.912588 3 0.0005 129 | 0/8 7 h-lim-p 0.0029 0.2328 0.4609 3135.912559 2 0.0003 147 | 0/8 8 h-lim-p 0.0224 20.0000 0.0057 3135.903685 0 0.7167 172 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 3135.903510 3 1.0449 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3135.903510 0 1.0938 218 | 0/8 11 h-lim-p 0.9922 20.0000 0.0000 3135.903510 0 0.8682 238 | 0/8 12 h-lim-p 0.6823 20.0000 0.0000 3135.903510 0 0.0006 267 | 0/8 13 h-lim-p 0.0004 20.0000 0.0001 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0014 | 0/8 15 h-lim-p 0.0000 20.0000 0.0014 Out... lnL = -3135.903510 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3135.903510 Node 7: lnL = -3135.903510 Node 8: lnL = -3135.903510 Node 9: lnL = -3135.903510 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 407 Sequential format.. Reading seq # 1: YJR007W_Sbay Reading seq # 2: YJR007W_Scer Reading seq # 3: YJR007W_Skud Reading seq # 4: YJR007W_Smik Reading seq # 5: YJR007W_Spar Sequences read.. Counting patterns.. # site patterns = 152 Counting frequencies.. 120 bytes for distance 24320 bytes for lkl0 19456 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.065260 0.031606 0.050026 0.086545 0.091124 0.189565 0.213599 0.175625 lnL0 = -1698.402993 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1698.402993 x= 0.06526 0.03161 0.05003 0.08654 0.09112 0.18956 0.21360 0.17563 1 h-lim-p 0.0048 0.2954 84.0619 1697.598626 7 0.0002 42 | 0/8 2 h-lim-p 0.0020 0.0167 10.1611 1697.571020 5 0.0005 65 | 0/8 3 h-lim-p 0.0014 0.0432 3.7823 1697.567843 5 0.0005 90 | 0/8 4 h-lim-p 0.0017 0.1315 1.1308 1697.567590 3 0.0004 109 | 0/8 5 h-lim-p 0.0021 0.8855 0.2318 1697.567570 2 0.0008 125 | 0/8 6 h-lim-p 0.0027 3.6551 0.0707 1697.567569 0 0.0007 146 | 0/8 7 h-lim-p 0.0021 2.8441 0.0231 1697.567569 0 0.0005 167 | 0/8 8 h-lim-p 0.3519 20.0000 0.0000 1697.567568 0 1.0556 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1697.567568 0 1.0938 208 | 0/8 10 h-lim-p 1.2920 20.0000 0.0000 1697.567568 0 2.5839 229 | 0/8 11 h-lim-p 1.2320 20.0000 0.0000 1697.567568 0 0.1540 251 | 0/8 12 h-lim-p 0.0031 20.0000 0.0010 1697.567568 0 0.0000 277 | 0/8 13 h-lim-p 0.0002 20.0000 0.0001 1697.567568 0 0.0000 301 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 1697.567568 0 0.0000 332 Out... lnL = -1697.567568 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1697.567568 Node 7: lnL = -1697.567568 Node 8: lnL = -1697.567568 Node 9: lnL = -1697.567568 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 520 Sequential format.. Reading seq # 1: YJR008W_Sbay Reading seq # 2: YJR008W_Scer Reading seq # 3: YJR008W_Skud Reading seq # 4: YJR008W_Smik Reading seq # 5: YJR008W_Spar Sequences read.. Counting patterns.. # site patterns = 139 Counting frequencies.. 120 bytes for distance 22240 bytes for lkl0 17792 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.015387 0.051226 0.045674 0.065990 0.056912 0.103836 0.114450 0.083861 lnL0 = -1701.628156 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1701.628156 x= 0.01539 0.05123 0.04567 0.06599 0.05691 0.10384 0.11445 0.08386 1 h-lim-p 0.0004 0.0029 68.8444 1701.274492 4 0.0002 31 | 0/8 2 h-lim-p 0.0005 0.0048 23.3847 1701.181075 3 0.0004 49 | 0/8 3 h-lim-p 0.0008 0.0126 10.6790 1701.171802 2 0.0002 66 | 0/8 4 h-lim-p 0.0007 0.0487 3.0771 1701.170889 4 0.0002 88 | 0/8 5 h-lim-p 0.0006 0.1571 1.0669 1701.170789 4 0.0002 111 | 0/8 6 h-lim-p 0.0018 0.5203 0.1144 1701.170788 0 0.0002 125 | 0/8 7 h-lim-p 0.0017 6.0167 0.0131 1701.170787 0 0.0017 145 | 0/8 8 h-lim-p 0.0121 20.0000 0.0019 1701.170526 0 0.1929 169 | 0/8 9 h-lim-p 1.4640 20.0000 0.0002 1701.170520 2 0.9658 195 | 0/8 10 h-lim-p 1.8619 20.0000 0.0001 1701.170520 0 0.8146 215 | 0/8 11 h-lim-p 2.0606 20.0000 0.0001 1701.170520 0 0.9015 235 | 0/8 12 h-lim-p 0.1233 20.0000 0.0004 1701.170520 0 0.0135 257 | 0/8 13 h-lim-p 0.0038 20.0000 0.0013 1701.170520 0 0.0000 285 | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 1701.170520 0 0.0000 321 | 0/8 15 h-lim-p 0.0000 20.0000 0.0012 1701.170520 0 0.0001 344 | 0/8 16 h-lim-p 0.0010 20.0000 0.0001 1701.170520 0 0.0040 366 | 0/8 17 h-lim-p 0.0056 20.0000 0.0001 1701.170520 0 0.0000 403 | 0/8 18 h-lim-p 0.0000 20.0000 0.0025 | 0/8 19 h-lim-p 0.0000 20.0000 0.0025 Out... lnL = -1701.170520 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1701.170520 Node 7: lnL = -1701.170520 Node 8: lnL = -1701.170520 Node 9: lnL = -1701.170520 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 928 Sequential format.. Reading seq # 1: YJR009C_Sbay Reading seq # 2: YJR009C_Scer Reading seq # 3: YJR009C_Skud Reading seq # 4: YJR009C_Smik Reading seq # 5: YJR009C_Spar Sequences read.. Counting patterns.. # site patterns = 309 Counting frequencies.. 120 bytes for distance 49440 bytes for lkl0 39552 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.676695 0.074269 0.088544 0.113816 0.194493 0.095081 0.185215 lnL0 = -4170.793335 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4170.793335 x= 0.00006 0.67670 0.07427 0.08854 0.11382 0.19449 0.09508 0.18521 1 h-lim-p 0.0000 0.0000 58.7676 4170.777319 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0080 25.4033 4170.671886 0 0.0003 39 | 1/8 3 h-lim-p 0.0003 0.0119 27.7468 4170.586615 0 0.0005 51 | 1/8 4 h-lim-p 0.0023 0.0407 5.3751 4170.581663 4 0.0004 74 | 1/8 5 h-lim-p 0.0005 0.1084 4.3809 4170.569758 0 0.0018 88 | 1/8 6 h-lim-p 0.0131 0.3964 0.6094 4170.569134 3 0.0011 110 | 1/8 7 h-lim-p 0.0006 0.2126 1.1071 4170.563567 0 0.0036 131 | 1/8 8 h-lim-p 0.0219 1.6205 0.1809 4170.158844 0 0.0874 145 | 0/8 9 h-lim-p 0.0125 0.6528 1.2609 4170.158472 4 0.0005 177 | 0/8 10 h-lim-p 0.8912 20.0000 0.0008 4170.158140 1 1.1140 191 | 0/8 11 h-lim-p 2.5000 20.0000 0.0001 4170.158139 0 1.0938 211 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4170.158139 0 1.0938 231 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 4170.158139 0 2.1875 251 | 0/8 14 h-lim-p 1.9391 20.0000 0.0000 4170.158139 0 0.9695 271 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 4170.158139 0 0.0000 313 Out... lnL = -4170.158139 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4170.158139 Node 7: lnL = -4170.158139 Node 8: lnL = -4170.158139 Node 9: lnL = -4170.158139 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 323 Sequential format.. Reading seq # 1: YJR010C-A_Sbay Reading seq # 2: YJR010C-A_Scer Reading seq # 3: YJR010C-A_Skud Reading seq # 4: YJR010C-A_Smik Reading seq # 5: YJR010C-A_Spar Sequences read.. Counting patterns.. # site patterns = 155 Counting frequencies.. 120 bytes for distance 24800 bytes for lkl0 19840 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.159819 0.023623 0.075725 0.148666 0.109638 0.219912 0.211851 0.313193 lnL0 = -1437.062218 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1437.062218 x= 0.15982 0.02362 0.07573 0.14867 0.10964 0.21991 0.21185 0.31319 1 h-lim-p 0.0010 0.0081 63.5267 1436.127865 7 0.0005 36 | 0/8 2 h-lim-p 0.0014 0.0108 14.3681 1436.036756 7 0.0009 65 | 0/8 3 h-lim-p 0.0021 0.0579 6.1395 1436.022684 3 0.0009 83 | 0/8 4 h-lim-p 0.0024 0.1235 2.2498 1436.020271 2 0.0011 99 | 0/8 5 h-lim-p 0.0065 0.7301 0.3927 1436.020162 2 0.0014 116 | 0/8 6 h-lim-p 0.0065 1.6126 0.0860 1436.020159 1 0.0008 140 | 0/8 7 h-lim-p 0.0046 16.2367 0.0150 1436.020159 0 0.0023 160 | 0/8 8 h-lim-p 0.1945 20.0000 0.0002 1436.020141 0 1.1667 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1436.020140 0 1.0938 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1436.020140 0 1.0938 222 | 0/8 11 h-lim-p 1.6234 20.0000 0.0000 1436.020140 0 0.7102 242 | 0/8 12 h-lim-p 0.4305 20.0000 0.0000 1436.020140 0 0.0118 266 | 0/8 13 h-lim-p 0.0045 20.0000 0.0000 1436.020140 0 0.0091 287 | 0/8 14 h-lim-p 0.0024 20.0000 0.0000 1436.020140 0 0.0012 307 | 0/8 15 h-lim-p 0.0030 20.0000 0.0000 1436.020140 0 0.0000 337 | 0/8 16 h-lim-p 0.0006 20.0000 0.0000 1436.020140 0 0.0000 373 Out... lnL = -1436.020140 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1436.020140 Node 7: lnL = -1436.020140 Node 8: lnL = -1436.020140 Node 9: lnL = -1436.020140 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 910 Sequential format.. Reading seq # 1: YJR010W_Sbay Reading seq # 2: YJR010W_Scer Reading seq # 3: YJR010W_Skud Reading seq # 4: YJR010W_Smik Reading seq # 5: YJR010W_Spar Sequences read.. Counting patterns.. # site patterns = 391 Counting frequencies.. 120 bytes for distance 62560 bytes for lkl0 50048 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.165138 0.011958 0.091550 0.242457 0.166512 0.375650 0.259492 0.367608 lnL0 = -4678.143764 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4678.143764 x= 0.16514 0.01196 0.09155 0.24246 0.16651 0.37565 0.25949 0.36761 1 h-lim-p 0.0041 0.1027 150.3608 4675.505091 7 0.0003 39 | 0/8 2 h-lim-p 0.0007 0.0060 51.5285 4674.414097 1 0.0009 53 | 0/8 3 h-lim-p 0.0038 0.0342 12.4837 4674.372416 6 0.0006 81 | 0/8 4 h-lim-p 0.0017 0.0537 4.1815 4674.368226 5 0.0005 107 | 0/8 5 h-lim-p 0.0026 0.2594 0.8776 4674.367944 3 0.0008 127 | 0/8 6 h-lim-p 0.0031 1.0104 0.2146 4674.367918 2 0.0008 152 | 0/8 7 h-lim-p 0.0050 4.1601 0.0352 4674.367679 0 0.0200 174 | 0/8 8 h-lim-p 0.0116 15.3031 0.0604 4674.358876 0 0.0466 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0008 4674.358488 2 1.0938 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4674.358487 0 1.0938 240 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4674.358487 0 1.0938 260 | 0/8 12 h-lim-p 1.1453 20.0000 0.0000 4674.358487 0 0.0000 303 Out... lnL = -4674.358487 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4674.358487 Node 7: lnL = -4674.358487 Node 8: lnL = -4674.358487 Node 9: lnL = -4674.358487 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 376 Sequential format.. Reading seq # 1: YJR011C_Sbay Reading seq # 2: YJR011C_Scer Reading seq # 3: YJR011C_Skud Reading seq # 4: YJR011C_Smik Reading seq # 5: YJR011C_Spar Sequences read.. Counting patterns.. # site patterns = 177 Counting frequencies.. 120 bytes for distance 28320 bytes for lkl0 22656 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.049080 0.138485 0.112479 0.145474 0.084761 0.237529 0.232239 0.204555 lnL0 = -1725.228478 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1725.228478 x= 0.04908 0.13848 0.11248 0.14547 0.08476 0.23753 0.23224 0.20456 1 h-lim-p 0.0006 0.0048 38.4385 1724.693814 1 0.0007 24 | 0/8 2 h-lim-p 0.0033 0.0283 8.5453 1724.676292 7 0.0005 56 | 0/8 3 h-lim-p 0.0011 0.0615 3.8037 1724.671034 4 0.0009 76 | 0/8 4 h-lim-p 0.0027 0.3175 1.2205 1724.670449 4 0.0009 97 | 0/8 5 h-lim-p 0.0084 0.8896 0.1276 1724.670442 1 0.0008 113 | 0/8 6 h-lim-p 0.0033 13.5127 0.0321 1724.670441 0 0.0015 133 | 0/8 7 h-lim-p 0.0141 20.0000 0.0033 1724.670441 0 0.0141 153 | 0/8 8 h-lim-p 0.0199 20.0000 0.0024 1724.670400 0 0.1191 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1724.670399 0 1.0938 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1724.670399 0 1.0938 215 | 0/8 11 h-lim-p 0.9681 20.0000 0.0000 1724.670399 0 0.9681 235 | 0/8 12 h-lim-p 0.0283 20.0000 0.0004 1724.670399 0 0.0124 255 | 0/8 13 h-lim-p 0.0039 20.0000 0.0013 1724.670399 0 0.0039 275 | 0/8 14 h-lim-p 0.0017 20.0000 0.0029 1724.670399 0 0.0017 295 | 0/8 15 h-lim-p 0.0013 16.0171 0.0038 1724.670399 0 0.0000 326 | 0/8 16 h-lim-p 0.0002 20.0000 0.0000 1724.670399 0 0.0000 362 Out... lnL = -1724.670399 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1724.670399 Node 7: lnL = -1724.670399 Node 8: lnL = -1724.670399 Node 9: lnL = -1724.670399 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 300 Sequential format.. Reading seq # 1: YJR013W_Sbay Reading seq # 2: YJR013W_Scer Reading seq # 3: YJR013W_Skud Reading seq # 4: YJR013W_Smik Reading seq # 5: YJR013W_Spar Sequences read.. Counting patterns.. # site patterns = 17 Counting frequencies.. 120 bytes for distance 2720 bytes for lkl0 2176 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.580486 0.065942 0.000060 1.222218 2.296286 1.973958 2.224591 1.018829 lnL0 = -759.598005 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 759.598005 x= 0.58049 0.06594 0.00006 1.22222 2.29629 1.97396 2.22459 1.01883 1 h-lim-p 0.0000 0.0000 33.8627 759.590672 m 0.0000 22 | 1/8 2 h-lim-p 0.0005 20.0000 0.3611 .. | 1/8 3 h-lim-p 0.0000 0.0041 32.4225 754.545163 m 0.0041 78 | 2/8 4 h-lim-p 0.2765 20.0000 0.4124 .. | 2/8 5 h-lim-p 0.0000 0.0230 38.8124 666.471711 m 0.0230 145 | 3/8 6 h-lim-p 0.7838 20.0000 0.9284 .. | 3/8 7 h-lim-p 0.0000 0.0042 146.5767 571.412616 m 0.0042 209 | 4/8 8 h-lim-p 0.1416 1.1326 0.1796 570.957433 1 0.1770 223 | 3/8 9 h-lim-p 0.0000 0.0000 0.0071 h-lim-p: 4.85826038e-16 3.88660831e-15 7.05453616e-03 570.957433 .. | 2/8 10 h-lim-p 0.0000 20.0000 5.2795 570.952450 0 0.0003 257 | 2/8 11 h-lim-p 0.0421 0.3365 0.0164 570.952450 1 0.0042 273 | 2/8 12 h-lim-p 1.7666 20.0000 0.0000 570.952450 0 1.5458 291 | 1/8 13 h-lim-p -0.0000 -0.0000 0.0213 h-lim-p: -1.51456690e-15 -1.21165352e-14 2.13243281e-02 570.952450 .. | 2/8 14 h-lim-p 0.0000 20.0000 0.0092 570.952450 0 0.0003 329 | 2/8 15 h-lim-p 0.0764 20.0000 0.0000 570.952450 0 1.2227 351 | 2/8 16 h-lim-p 0.2540 7.4397 0.0002 570.952450 0 0.0000 382 | 2/8 17 h-lim-p 0.0000 0.3185 0.0045 570.952450 0 0.0000 408 | 2/8 18 h-lim-p 0.0000 20.0000 0.0004 570.952450 0 0.0000 429 | 2/8 19 h-lim-p 0.0000 20.0000 0.0000 570.952450 0 0.0000 447 | 2/8 20 h-lim-p 0.0000 20.0000 0.0004 570.952450 0 0.0000 466 | 2/8 21 h-lim-p 0.0000 20.0000 0.0000 570.952450 0 0.0000 487 | 2/8 22 h-lim-p 0.0000 20.0000 0.0000 570.952450 0 0.0000 505 | 2/8 23 h-lim-p 0.0000 20.0000 0.0001 570.952450 0 0.0000 528 | 2/8 24 h-lim-p 0.0000 20.0000 0.0004 570.952450 0 0.0000 547 | 2/8 25 h-lim-p 0.0000 20.0000 0.0000 570.952450 0 0.0000 569 | 2/8 26 h-lim-p 0.0000 20.0000 0.0004 570.952450 0 0.0000 598 | 2/8 27 h-lim-p 0.0000 20.0000 0.0004 | 2/8 28 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -570.952450 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -570.952450 Node 7: lnL = -570.952450 Node 8: lnL = -570.952450 Node 9: lnL = -570.952450 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 245 Sequential format.. Reading seq # 1: YJR014W_Sbay Reading seq # 2: YJR014W_Scer Reading seq # 3: YJR014W_Skud Reading seq # 4: YJR014W_Smik Reading seq # 5: YJR014W_Spar Sequences read.. Counting patterns.. # site patterns = 153 Counting frequencies.. 120 bytes for distance 24480 bytes for lkl0 19584 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.060447 0.259087 0.019212 0.258901 0.111060 0.249831 0.203739 0.240709 lnL0 = -1205.794162 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1205.794162 x= 0.06045 0.25909 0.01921 0.25890 0.11106 0.24983 0.20374 0.24071 1 h-lim-p 0.0114 0.1026 46.0243 1205.218118 7 0.0006 43 | 0/8 2 h-lim-p 0.0025 0.0203 8.1948 1205.158176 7 0.0018 72 | 0/8 3 h-lim-p 0.0034 0.0285 4.4130 1205.143409 6 0.0019 98 | 0/8 4 h-lim-p 0.0087 0.2778 0.9600 1205.142288 5 0.0026 123 | 0/8 5 h-lim-p 0.0071 0.4260 0.3502 1205.142207 2 0.0016 148 | 0/8 6 h-lim-p 0.0119 8.0508 0.0456 1205.142204 0 0.0026 169 | 0/8 7 h-lim-p 0.0341 20.0000 0.0035 1205.142202 0 0.0298 189 | 0/8 8 h-lim-p 0.0263 15.0663 0.0040 1205.142134 0 0.1054 211 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1205.142133 0 1.0938 231 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1205.142133 0 1.0938 251 | 0/8 11 h-lim-p 1.2534 20.0000 0.0000 1205.142133 0 0.0196 276 | 0/8 12 h-lim-p 0.0047 20.0000 0.0000 1205.142133 0 0.0047 296 | 0/8 13 h-lim-p 0.0018 20.0000 0.0001 1205.142133 0 0.0001 320 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 1205.142133 0 0.0000 341 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 1205.142133 0 0.0001 361 Out... lnL = -1205.142133 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1205.142133 Node 7: lnL = -1205.142133 Node 8: lnL = -1205.142133 Node 9: lnL = -1205.142133 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 150 Sequential format.. Reading seq # 1: YJR017C_Sbay Reading seq # 2: YJR017C_Scer Reading seq # 3: YJR017C_Skud Reading seq # 4: YJR017C_Smik Reading seq # 5: YJR017C_Spar Sequences read.. Counting patterns.. # site patterns = 73 Counting frequencies.. 120 bytes for distance 11680 bytes for lkl0 9344 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.097399 0.070414 0.011051 0.093612 0.147069 0.182824 0.246204 0.228002 lnL0 = -673.381751 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 673.381751 x= 0.09740 0.07041 0.01105 0.09361 0.14707 0.18282 0.24620 0.22800 1 h-lim-p 0.0063 0.0500 34.8988 673.038203 7 0.0006 37 | 0/8 2 h-lim-p 0.0005 0.0043 14.3604 672.934798 0 0.0011 50 | 0/8 3 h-lim-p 0.0036 0.0289 4.2682 672.918923 5 0.0019 73 | 0/8 4 h-lim-p 0.0032 0.1009 2.5912 672.914808 4 0.0016 94 | 0/8 5 h-lim-p 0.0102 1.0270 0.4105 672.914610 2 0.0024 111 | 0/8 6 h-lim-p 0.0235 9.0228 0.0419 672.914605 2 0.0031 137 | 0/8 7 h-lim-p 0.0357 11.8075 0.0036 672.914159 0 0.2855 160 | 0/8 8 h-lim-p 0.0036 0.7784 0.2836 672.913887 2 0.0034 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 672.913870 2 1.0889 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 672.913870 0 1.0938 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 672.913870 0 0.2734 250 | 0/8 12 h-lim-p 0.1689 20.0000 0.0000 672.913870 0 0.0007 277 Out... lnL = -672.913870 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -672.913870 Node 7: lnL = -672.913870 Node 8: lnL = -672.913870 Node 9: lnL = -672.913870 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 160 Sequential format.. Reading seq # 1: YJR021C_Sbay Reading seq # 2: YJR021C_Scer Reading seq # 3: YJR021C_Skud Reading seq # 4: YJR021C_Smik Reading seq # 5: YJR021C_Spar Sequences read.. Counting patterns.. # site patterns = 95 Counting frequencies.. 120 bytes for distance 15200 bytes for lkl0 12160 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.048462 0.198195 0.066305 0.064867 0.090863 0.200020 0.183057 0.185125 lnL0 = -633.343328 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 633.343328 x= 0.04846 0.19819 0.06631 0.06487 0.09086 0.20002 0.18306 0.18513 1 h-lim-p 0.0009 0.0073 25.0956 632.511178 0 0.0037 24 | 0/8 2 h-lim-p 0.0010 0.0077 7.6291 632.474862 0 0.0019 37 | 0/8 3 h-lim-p 0.0047 0.0960 3.1544 632.467289 6 0.0018 61 | 0/8 4 h-lim-p 0.0020 0.0599 2.7455 632.462873 2 0.0019 77 | 0/8 5 h-lim-p 0.0086 0.0776 0.6091 632.462346 5 0.0025 101 | 0/8 6 h-lim-p 0.0079 1.8261 0.1948 632.461648 1 0.0098 123 | 0/8 7 h-lim-p 0.0134 0.6908 0.1429 632.450484 0 0.0536 145 | 0/8 8 h-lim-p 0.0037 0.1510 2.0863 632.413396 0 0.0073 166 | 0/8 9 h-lim-p 2.5000 20.0000 0.0013 632.412921 3 1.0449 184 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 632.412921 0 1.0938 204 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 632.412921 0 1.0938 224 | 0/8 12 h-lim-p 1.6210 20.0000 0.0000 632.412921 0 1.4184 244 | 0/8 13 h-lim-p 1.0300 20.0000 0.0000 632.412921 014.8604 268 | 0/8 14 h-lim-p 0.0656 20.0000 0.0011 632.412921 0 0.0082 290 | 0/8 15 h-lim-p 0.0024 20.0000 0.0039 632.412921 0 0.0001 313 | 0/8 16 h-lim-p 0.0000 2.8186 0.0280 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 632.412921 0 0.0000 378 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 632.412921 0 0.0000 401 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 632.412921 0 0.0000 468 | 0/8 21 h-lim-p 0.0000 20.0000 0.0001 | 0/8 22 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -632.412921 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -632.412921 Node 7: lnL = -632.412921 Node 8: lnL = -632.412921 Node 9: lnL = -632.412921 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 168 Sequential format.. Reading seq # 1: YJR022W_Sbay Reading seq # 2: YJR022W_Scer Reading seq # 3: YJR022W_Skud Reading seq # 4: YJR022W_Smik Reading seq # 5: YJR022W_Spar Sequences read.. Counting patterns.. # site patterns = 83 Counting frequencies.. 120 bytes for distance 13280 bytes for lkl0 10624 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.034265 0.098397 0.120545 0.086896 0.054143 0.139676 0.116486 0.139381 lnL0 = -647.031899 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 647.031899 x= 0.03427 0.09840 0.12055 0.08690 0.05414 0.13968 0.11649 0.13938 1 h-lim-p 0.0018 0.0146 26.0714 646.705907 8 0.0010 39 | 0/8 2 h-lim-p 0.0024 0.0193 5.1280 646.688240 7 0.0014 69 | 0/8 3 h-lim-p 0.0111 0.3748 0.6397 646.688058 3 0.0009 91 | 0/8 4 h-lim-p 0.0016 0.2494 0.3600 646.688018 2 0.0007 115 | 0/8 5 h-lim-p 0.0035 2.1787 0.0764 646.688015 2 0.0012 141 | 0/8 6 h-lim-p 0.0417 20.0000 0.0021 646.688014 1 0.0332 163 | 0/8 7 h-lim-p 0.0071 19.3098 0.0100 646.688002 0 0.0212 184 | 0/8 8 h-lim-p 0.0038 7.6675 0.0552 646.687974 0 0.0058 204 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 646.687973 0 1.0938 224 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 646.687973 0 1.0938 244 | 0/8 11 h-lim-p 1.3263 20.0000 0.0000 646.687973 0 1.3263 264 | 0/8 12 h-lim-p 0.9112 20.0000 0.0000 646.687973 m20.0000 286 | 0/8 13 h-lim-p 0.0096 10.9596 0.0184 646.687973 0 0.0021 307 | 0/8 14 h-lim-p 0.0012 1.5792 0.0332 646.687973 0 0.0000 334 | 0/8 15 h-lim-p 0.0002 20.0000 0.0010 646.687973 0 0.0000 368 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 646.687973 0 0.0000 389 | 0/8 17 h-lim-p 0.0001 20.0000 0.0000 646.687973 0 0.0000 417 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0002 | 0/8 20 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -646.687973 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -646.687973 Node 7: lnL = -646.687973 Node 8: lnL = -646.687973 Node 9: lnL = -646.687973 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 512 Sequential format.. Reading seq # 1: YJR025C_Sbay Reading seq # 2: YJR025C_Scer Reading seq # 3: YJR025C_Skud Reading seq # 4: YJR025C_Smik Reading seq # 5: YJR025C_Spar Sequences read.. Counting patterns.. # site patterns = 167 Counting frequencies.. 120 bytes for distance 26720 bytes for lkl0 21376 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.043170 0.038363 0.046437 0.110390 0.103630 0.112987 0.141500 0.133448 lnL0 = -2033.539952 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2033.539952 x= 0.04317 0.03836 0.04644 0.11039 0.10363 0.11299 0.14150 0.13345 1 h-lim-p 0.0005 0.0037 144.3049 2031.942042 9 0.0002 44 | 0/8 2 h-lim-p 0.0005 0.0039 32.1645 2031.780133 7 0.0003 73 | 0/8 3 h-lim-p 0.0021 0.0334 4.9170 2031.776690 5 0.0003 98 | 0/8 4 h-lim-p 0.0022 0.1590 0.6601 2031.776634 0 0.0003 112 | 0/8 5 h-lim-p 0.0016 4.0025 0.1125 2031.776632 1 0.0004 135 | 0/8 6 h-lim-p 0.0041 20.0000 0.0108 2031.776632 0 0.0009 156 | 0/8 7 h-lim-p 0.0088 20.0000 0.0011 2031.776625 0 0.0703 179 | 0/8 8 h-lim-p 0.0015 1.4949 0.0527 2031.776559 0 0.0029 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2031.776558 0 1.0938 220 | 0/8 10 h-lim-p 2.4431 20.0000 0.0000 2031.776558 0 1.0688 240 | 0/8 11 h-lim-p 0.9188 20.0000 0.0000 2031.776558 0 1.8376 261 | 0/8 12 h-lim-p 0.0590 20.0000 0.0008 2031.776558 0 0.0037 284 | 0/8 13 h-lim-p 0.0010 20.0000 0.0029 2031.776558 0 0.0000 323 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -2031.776558 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2031.776558 Node 7: lnL = -2031.776558 Node 8: lnL = -2031.776558 Node 9: lnL = -2031.776558 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 412 Sequential format.. Reading seq # 1: YJR030C_Sbay Reading seq # 2: YJR030C_Scer Reading seq # 3: YJR030C_Skud Reading seq # 4: YJR030C_Smik Reading seq # 5: YJR030C_Spar Sequences read.. Counting patterns.. # site patterns = 181 Counting frequencies.. 120 bytes for distance 28960 bytes for lkl0 23168 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.067954 0.065384 0.090893 0.126702 0.070135 0.203852 0.147989 0.189596 lnL0 = -1737.318802 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1737.318802 x= 0.06795 0.06538 0.09089 0.12670 0.07014 0.20385 0.14799 0.18960 1 h-lim-p 0.0015 0.0120 63.5045 1736.357377 8 0.0005 40 | 0/8 2 h-lim-p 0.0009 0.0070 20.0736 1736.201052 6 0.0008 66 | 0/8 3 h-lim-p 0.0016 0.0131 10.8139 1736.186265 3 0.0003 85 | 0/8 4 h-lim-p 0.0013 0.0575 2.6677 1736.184020 4 0.0007 106 | 0/8 5 h-lim-p 0.0025 0.1678 0.7372 1736.183813 4 0.0008 128 | 0/8 6 h-lim-p 0.0077 1.4079 0.0801 1736.183811 1 0.0008 152 | 0/8 7 h-lim-p 0.0393 20.0000 0.0016 1736.183665 0 0.3141 175 | 0/8 8 h-lim-p 0.0023 3.4741 0.2146 1736.183348 0 0.0034 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1736.183344 1 0.9961 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1736.183344 0 1.2500 237 | 0/8 11 h-lim-p 1.4771 20.0000 0.0000 1736.183344 0 0.1846 259 | 0/8 12 h-lim-p 0.0327 20.0000 0.0000 1736.183344 0 0.0163 279 | 0/8 13 h-lim-p 0.0062 20.0000 0.0001 1736.183344 0 0.0008 301 | 0/8 14 h-lim-p 0.0001 20.0000 0.0009 1736.183344 0 0.0000 334 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 1736.183344 0 0.0000 364 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 1736.183344 0 0.0000 391 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0003 | 0/8 19 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -1736.183344 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1736.183344 Node 7: lnL = -1736.183344 Node 8: lnL = -1736.183344 Node 9: lnL = -1736.183344 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 245 Sequential format.. Reading seq # 1: YJR034W_Sbay Reading seq # 2: YJR034W_Scer Reading seq # 3: YJR034W_Skud Reading seq # 4: YJR034W_Smik Reading seq # 5: YJR034W_Spar Sequences read.. Counting patterns.. # site patterns = 100 Counting frequencies.. 120 bytes for distance 16000 bytes for lkl0 12800 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.064357 0.050995 0.000060 0.127483 0.096064 0.114961 0.200673 0.162663 lnL0 = -1005.475060 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1005.475060 x= 0.06436 0.05100 0.00006 0.12748 0.09606 0.11496 0.20067 0.16266 1 h-lim-p 0.0005 0.4819 208.2352 1003.411567 7 0.0001 38 | 0/8 2 h-lim-p 0.0014 0.0139 13.6744 1003.342949 6 0.0007 65 | 0/8 3 h-lim-p 0.0054 0.0737 1.8724 1003.341892 2 0.0006 83 | 0/8 4 h-lim-p 0.0060 0.3760 0.1967 1003.341877 2 0.0008 101 | 0/8 5 h-lim-p 0.0030 9.3578 0.0519 1003.341875 0 0.0013 121 | 0/8 6 h-lim-p 0.0050 8.8753 0.0135 1003.341875 0 0.0011 142 | 0/8 7 h-lim-p 0.0175 20.0000 0.0008 1003.341875 0 0.0153 162 | 0/8 8 h-lim-p 0.0179 20.0000 0.0007 1003.341869 0 0.1072 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1003.341869 1 1.2305 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1003.341869 0 2.1875 227 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1003.341869 0 1.0938 247 | 0/8 12 h-lim-p 0.6579 20.0000 0.0000 1003.341869 0 5.2631 270 | 0/8 13 h-lim-p 1.7156 20.0000 0.0000 1003.341869 0 0.3753 291 | 0/8 14 h-lim-p 1.3426 20.0000 0.0000 1003.341869 0 0.0002 323 Out... lnL = -1003.341869 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1003.341869 Node 7: lnL = -1003.341869 Node 8: lnL = -1003.341869 Node 9: lnL = -1003.341869 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 342 Sequential format.. Reading seq # 1: YJR036C_Sbay Reading seq # 2: YJR036C_Scer Reading seq # 3: YJR036C_Skud Reading seq # 4: YJR036C_Smik Reading seq # 5: YJR036C_Spar Sequences read.. Counting patterns.. # site patterns = 138 Counting frequencies.. 120 bytes for distance 22080 bytes for lkl0 17664 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.071107 0.090507 0.107878 0.105044 0.031218 0.165070 0.098634 0.182260 lnL0 = -1401.924564 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1401.924564 x= 0.07111 0.09051 0.10788 0.10504 0.03122 0.16507 0.09863 0.18226 1 h-lim-p 0.0003 0.0026 44.0623 1401.497791 0 0.0006 23 | 0/8 2 h-lim-p 0.0007 0.0081 39.6317 1401.409024 7 0.0002 52 | 0/8 3 h-lim-p 0.0005 0.0087 12.9010 1401.371612 5 0.0005 76 | 0/8 4 h-lim-p 0.0047 0.1438 1.4750 1401.370889 4 0.0007 100 | 0/8 5 h-lim-p 0.0020 0.4818 0.4821 1401.370790 3 0.0008 118 | 0/8 6 h-lim-p 0.0044 2.2081 0.0845 1401.370597 0 0.0066 138 | 0/8 7 h-lim-p 0.0047 1.3307 0.1189 1401.362523 0 0.0373 161 | 0/8 8 h-lim-p 0.0020 0.0592 2.2319 1401.342990 1 0.0025 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0011 1401.342144 3 0.9961 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1401.342143 0 1.0938 221 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1401.342143 0 1.0938 241 | 0/8 12 h-lim-p 1.1614 20.0000 0.0000 1401.342143 0 2.3228 262 | 0/8 13 h-lim-p 0.6676 20.0000 0.0000 1401.342143 0 0.0834 284 | 0/8 14 h-lim-p 0.0016 20.0000 0.0014 1401.342143 0 0.0008 304 | 0/8 15 h-lim-p 0.0003 20.0000 0.0036 1401.342143 0 0.0002 324 | 0/8 16 h-lim-p 0.0000 2.1623 0.0511 1401.342143 0 0.0000 347 | 0/8 17 h-lim-p 0.0002 20.0000 0.0002 1401.342143 0 0.0000 377 | 0/8 18 h-lim-p 0.0002 20.0000 0.0000 1401.342143 0 0.0000 410 Out... lnL = -1401.342143 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1401.342143 Node 7: lnL = -1401.342143 Node 8: lnL = -1401.342143 Node 9: lnL = -1401.342143 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 501 Sequential format.. Reading seq # 1: YJR039W_Sbay Reading seq # 2: YJR039W_Scer Reading seq # 3: YJR039W_Skud Reading seq # 4: YJR039W_Smik Reading seq # 5: YJR039W_Spar Sequences read.. Counting patterns.. # site patterns = 179 Counting frequencies.. 120 bytes for distance 28640 bytes for lkl0 22912 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.065237 0.044372 0.092865 0.110484 0.040893 0.151620 0.179654 0.166664 lnL0 = -2042.772392 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2042.772392 x= 0.06524 0.04437 0.09286 0.11048 0.04089 0.15162 0.17965 0.16666 1 h-lim-p 0.0027 0.0262 122.3633 2041.161289 8 0.0002 44 | 0/8 2 h-lim-p 0.0004 0.0032 22.1357 2041.098617 5 0.0003 68 | 0/8 3 h-lim-p 0.0003 0.0091 20.3675 2041.052445 0 0.0004 80 | 0/8 4 h-lim-p 0.0040 0.1194 2.1730 2041.051383 2 0.0005 98 | 0/8 5 h-lim-p 0.0038 1.0354 0.2695 2041.051366 0 0.0005 112 | 0/8 6 h-lim-p 0.0041 6.0519 0.0311 2041.051359 2 0.0031 136 | 0/8 7 h-lim-p 0.0072 13.6447 0.0135 2041.050916 0 0.0434 158 | 0/8 8 h-lim-p 0.0007 0.3017 0.8202 2041.049453 0 0.0014 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2041.049423 2 1.3159 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2041.049423 0 1.0938 224 | 0/8 11 h-lim-p 2.1582 20.0000 0.0000 2041.049423 0 1.8884 244 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2041.049423 0 0.5469 265 | 0/8 13 h-lim-p 0.1589 20.0000 0.0000 2041.049423 0 0.0012 291 | 0/8 14 h-lim-p 0.0005 20.0000 0.0000 2041.049423 0 0.0000 325 | 0/8 15 h-lim-p 0.0000 20.0000 0.0024 | 0/8 16 h-lim-p 0.0000 20.0000 0.0024 Out... lnL = -2041.049423 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2041.049423 Node 7: lnL = -2041.049423 Node 8: lnL = -2041.049423 Node 9: lnL = -2041.049423 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 299 Sequential format.. Reading seq # 1: YJR042W_Sbay Reading seq # 2: YJR042W_Scer Reading seq # 3: YJR042W_Skud Reading seq # 4: YJR042W_Smik Reading seq # 5: YJR042W_Spar Sequences read.. Counting patterns.. # site patterns = 137 Counting frequencies.. 120 bytes for distance 21920 bytes for lkl0 17536 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.039419 0.129236 0.037960 0.176728 0.097905 0.264067 0.198612 0.171555 lnL0 = -1432.430073 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1432.430073 x= 0.03942 0.12924 0.03796 0.17673 0.09790 0.26407 0.19861 0.17155 1 h-lim-p 0.0006 0.0045 70.6494 1431.374554 7 0.0005 40 | 0/8 2 h-lim-p 0.0007 0.0056 22.3560 1431.212602 5 0.0007 62 | 0/8 3 h-lim-p 0.0014 0.0327 10.7752 1431.176042 7 0.0008 89 | 0/8 4 h-lim-p 0.0040 0.1502 2.1120 1431.173459 5 0.0012 115 | 0/8 5 h-lim-p 0.0208 3.9897 0.1239 1431.173452 2 0.0009 136 | 0/8 6 h-lim-p 0.0035 5.5879 0.0305 1431.173450 1 0.0017 159 | 0/8 7 h-lim-p 0.0151 20.0000 0.0035 1431.173281 0 0.1808 182 | 0/8 8 h-lim-p 0.0036 0.5147 0.1723 1431.172904 0 0.0055 202 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1431.172887 2 0.9961 226 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1431.172887 0 1.0938 246 | 0/8 11 h-lim-p 0.9506 20.0000 0.0000 1431.172887 0 0.8318 266 | 0/8 12 h-lim-p 0.4196 20.0000 0.0000 1431.172887 0 0.0033 292 | 0/8 13 h-lim-p 0.0006 20.0000 0.0001 1431.172887 0 0.0003 312 | 0/8 14 h-lim-p 0.0003 20.0000 0.0001 1431.172887 0 0.0002 332 | 0/8 15 h-lim-p 0.0001 20.0000 0.0003 1431.172887 0 0.0000 365 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1431.172887 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1431.172887 Node 7: lnL = -1431.172887 Node 8: lnL = -1431.172887 Node 9: lnL = -1431.172887 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 461 Sequential format.. Reading seq # 1: YJR046W_Sbay Reading seq # 2: YJR046W_Scer Reading seq # 3: YJR046W_Skud Reading seq # 4: YJR046W_Smik Reading seq # 5: YJR046W_Spar Sequences read.. Counting patterns.. # site patterns = 151 Counting frequencies.. 120 bytes for distance 24160 bytes for lkl0 19328 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.069417 0.054733 0.069835 0.057103 0.140683 0.192204 0.075872 lnL0 = -1620.069149 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1620.069149 x= 0.00006 0.06942 0.05473 0.06983 0.05710 0.14068 0.19220 0.07587 1 h-lim-p 0.0001 0.0009 148.4630 1617.811706 0 0.0002 23 | 0/8 2 h-lim-p 0.0007 0.0054 31.2287 1617.662477 2 0.0003 39 | 0/8 3 h-lim-p 0.0003 0.0039 28.3599 1617.588507 3 0.0003 57 | 0/8 4 h-lim-p 0.0008 0.0065 8.7000 1617.577052 5 0.0004 78 | 0/8 5 h-lim-p 0.0005 0.0047 6.1443 1617.567682 0 0.0010 91 | 0/8 6 h-lim-p 0.0009 0.0072 2.3836 1617.565238 0 0.0013 103 | 0/8 7 h-lim-p 0.0002 0.0016 7.8159 1617.559248 0 0.0008 117 | 0/8 8 h-lim-p 0.0005 0.0041 2.0591 1617.558625 2 0.0005 133 | 0/8 9 h-lim-p 0.7433 20.0000 0.0015 1617.557441 0 1.1149 145 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 1617.557421 1 0.9961 167 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1617.557421 0 0.5469 188 | 0/8 12 h-lim-p 0.9999 20.0000 0.0000 1617.557421 0 0.0039 215 | 0/8 13 h-lim-p 0.0033 20.0000 0.0000 1617.557421 0 0.0008 236 Out... lnL = -1617.557421 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1617.557421 Node 7: lnL = -1617.557421 Node 8: lnL = -1617.557421 Node 9: lnL = -1617.557421 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 859 Sequential format.. Reading seq # 1: YJR048W_Sbay Reading seq # 2: YJR048W_Scer Reading seq # 3: YJR048W_Skud Reading seq # 4: YJR048W_Smik Reading seq # 5: YJR048W_Spar Sequences read.. Counting patterns.. # site patterns = 263 Counting frequencies.. 120 bytes for distance 42080 bytes for lkl0 33664 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.076579 0.000060 0.044057 0.115785 0.065440 0.145183 0.277569 0.171973 lnL0 = -3293.799650 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3293.799650 x= 0.07658 0.00006 0.04406 0.11578 0.06544 0.14518 0.27757 0.17197 1 h-lim-p 0.0002 0.0018 219.5107 3289.703254 8 0.0001 41 | 0/8 2 h-lim-p 0.0002 0.0016 72.2175 3289.129666 0 0.0003 53 | 0/8 3 h-lim-p 0.0003 0.0032 66.5029 3288.807745 6 0.0002 78 | 0/8 4 h-lim-p 0.0004 0.0050 35.3881 3288.676367 6 0.0003 104 | 0/8 5 h-lim-p 0.0005 0.0110 21.6172 3288.639649 2 0.0002 120 | 0/8 6 h-lim-p 0.0008 0.0180 6.0875 3288.636688 2 0.0002 137 | 0/8 7 h-lim-p 0.0085 1.3739 0.1325 3288.636484 3 0.0027 157 | 0/8 8 h-lim-p 0.0083 1.1675 0.0436 3288.564174 0 0.1332 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0009 3288.563010 3 1.0004 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 3288.563007 0 1.0938 227 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3288.563007 0 1.0938 247 | 0/8 12 h-lim-p 1.0833 20.0000 0.0000 3288.563007 0 2.1667 268 | 0/8 13 h-lim-p 1.1927 20.0000 0.0000 3288.563007 0 0.0373 292 | 0/8 14 h-lim-p 0.0005 20.0000 0.0024 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0016 | 0/8 16 h-lim-p 0.0000 20.0000 0.0016 Out... lnL = -3288.563007 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3288.563007 Node 7: lnL = -3288.563007 Node 8: lnL = -3288.563007 Node 9: lnL = -3288.563007 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 233 Sequential format.. Reading seq # 1: YJR050W_Sbay Reading seq # 2: YJR050W_Scer Reading seq # 3: YJR050W_Skud Reading seq # 4: YJR050W_Smik Reading seq # 5: YJR050W_Spar Sequences read.. Counting patterns.. # site patterns = 101 Counting frequencies.. 120 bytes for distance 16160 bytes for lkl0 12928 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.049153 0.048391 0.056131 0.127216 0.075032 0.186074 0.126329 0.144481 lnL0 = -980.329342 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 980.329342 x= 0.04915 0.04839 0.05613 0.12722 0.07503 0.18607 0.12633 0.14448 1 h-lim-p 0.0008 0.0061 58.7190 979.636068 9 0.0004 46 | 0/8 2 h-lim-p 0.0016 0.0127 11.2826 979.590254 2 0.0007 62 | 0/8 3 h-lim-p 0.0020 0.0801 4.2314 979.585729 6 0.0006 90 | 0/8 4 h-lim-p 0.0022 0.4148 1.1152 979.585161 2 0.0010 106 | 0/8 5 h-lim-p 0.0044 0.3944 0.2608 979.585135 2 0.0008 123 | 0/8 6 h-lim-p 0.0097 5.5258 0.0227 979.585134 0 0.0011 145 | 0/8 7 h-lim-p 0.0055 20.0000 0.0044 979.585134 0 0.0048 165 | 0/8 8 h-lim-p 0.0330 20.0000 0.0006 979.585104 0 0.2636 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 979.585104 0 1.0938 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 979.585104 0 1.0938 228 | 0/8 11 h-lim-p 1.0608 20.0000 0.0000 979.585104 0 2.1216 249 | 0/8 12 h-lim-p 0.9671 20.0000 0.0000 979.585104 0 0.2418 270 | 0/8 13 h-lim-p 0.0002 2.7540 0.0262 979.585104 0 0.0000 293 | 0/8 14 h-lim-p 0.0002 20.0000 0.0019 979.585104 0 0.0000 314 | 0/8 15 h-lim-p 0.0001 20.0000 0.0010 979.585104 0 0.0000 338 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 979.585104 0 0.0000 366 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 979.585104 0 0.0000 398 | 0/8 18 h-lim-p 0.0000 20.0000 0.0004 | 0/8 19 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -979.585104 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -979.585104 Node 7: lnL = -979.585104 Node 8: lnL = -979.585104 Node 9: lnL = -979.585104 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 735 Sequential format.. Reading seq # 1: YJR052W_Sbay Reading seq # 2: YJR052W_Scer Reading seq # 3: YJR052W_Skud Reading seq # 4: YJR052W_Smik Reading seq # 5: YJR052W_Spar Sequences read.. Counting patterns.. # site patterns = 384 Counting frequencies.. 120 bytes for distance 61440 bytes for lkl0 49152 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.183800 0.000060 0.407016 0.326920 0.365039 0.371429 0.566667 0.402923 lnL0 = -4029.295857 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4029.295857 x= 0.18380 0.00006 0.40702 0.32692 0.36504 0.37143 0.56667 0.40292 1 h-lim-p 0.0000 0.0000 328.9861 4029.168732 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0044 140.4780 4011.999920 0 0.0019 41 | 1/8 3 h-lim-p 0.0016 0.0131 39.6204 4007.627289 0 0.0066 55 | 1/8 4 h-lim-p 0.0033 0.0268 15.5634 4006.745377 0 0.0067 68 | 1/8 5 h-lim-p 0.0168 0.1347 3.0021 3998.695542 0 0.0673 82 | 1/8 6 h-lim-p 0.0034 0.0274 21.3429 3974.282642 0 0.0137 96 | 1/8 7 h-lim-p 0.0017 0.0134 50.6667 3971.527268 0 0.0034 109 | 1/8 8 h-lim-p 0.2643 2.1145 0.3836 3967.734252 0 0.3965 121 | 1/8 9 h-lim-p 1.1604 9.2836 0.0927 3967.313700 6 0.4057 154 | 1/8 10 h-lim-p 0.8263 11.1924 0.0455 3967.266449 6 0.2789 189 | 1/8 11 h-lim-p 2.4104 20.0000 0.0053 3967.256678 5 0.7075 220 | 1/8 12 h-lim-p 1.8390 20.0000 0.0020 3967.256284 2 0.4310 244 | 1/8 13 h-lim-p 2.0044 20.0000 0.0004 3967.256252 2 0.6611 269 | 1/8 14 h-lim-p 2.5000 20.0000 0.0001 3967.256251 0 1.0938 288 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 3967.256251 0 1.0938 307 | 1/8 16 h-lim-p 1.8194 20.0000 0.0000 3967.256251 0 1.5920 326 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 3967.256251 0 1.0938 345 | 1/8 18 h-lim-p 0.6995 20.0000 0.0000 3967.256251 0 0.6121 364 | 1/8 19 h-lim-p 0.1055 20.0000 0.0000 3967.256251 0 0.0528 383 | 1/8 20 h-lim-p 0.0211 20.0000 0.0001 3967.256251 0 0.0000 426 | 1/8 21 h-lim-p 0.0000 20.0000 0.0000 | 1/8 22 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -3967.256251 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3967.256251 Node 7: lnL = -3967.256251 Node 8: lnL = -3967.256251 Node 9: lnL = -3967.256251 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 850 Sequential format.. Reading seq # 1: YJR055W_Sbay Reading seq # 2: YJR055W_Scer Reading seq # 3: YJR055W_Skud Reading seq # 4: YJR055W_Smik Reading seq # 5: YJR055W_Spar Sequences read.. Counting patterns.. # site patterns = 284 Counting frequencies.. 120 bytes for distance 45440 bytes for lkl0 36352 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.256665 0.000060 0.390541 0.505031 0.506354 0.444909 0.438454 0.460020 lnL0 = -3883.541987 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3883.541987 x= 0.25667 0.00006 0.39054 0.50503 0.50635 0.44491 0.43845 0.46002 1 h-lim-p 0.0000 0.0000 302.7804 3883.487282 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0003 1585.0763 3807.275435 m 0.0003 36 | 1/8 3 h-lim-p 0.0006 0.0045 93.4694 3802.660761 0 0.0011 49 | 1/8 4 h-lim-p 0.0014 0.0112 5.2973 3802.633673 4 0.0014 69 | 1/8 5 h-lim-p 0.0027 0.1989 2.6805 3801.239853 0 0.0870 86 | 1/8 6 h-lim-p 0.1298 3.0121 1.7954 3800.505215 3 0.1319 104 | 1/8 7 h-lim-p 0.5701 4.5604 0.1451 3800.229998 0 1.1401 117 | 1/8 8 h-lim-p 0.1049 0.8393 0.6237 3800.187138 0 0.1574 136 | 1/8 9 h-lim-p 2.5000 20.0000 0.0143 3800.178559 4 1.0721 162 | 1/8 10 h-lim-p 2.5000 20.0000 0.0038 3800.178229 2 0.9961 185 | 1/8 11 h-lim-p 2.5000 20.0000 0.0004 3800.178215 1 1.0938 206 | 1/8 12 h-lim-p 2.5000 20.0000 0.0002 3800.178215 0 1.0938 225 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 3800.178215 0 1.0938 244 | 1/8 14 h-lim-p 2.2281 20.0000 0.0000 3800.178215 0 0.9748 263 | 1/8 15 h-lim-p 0.2263 20.0000 0.0001 3800.178215 0 0.0018 288 | 1/8 16 h-lim-p 0.0005 20.0000 0.0003 3800.178215 0 0.0002 307 | 1/8 17 h-lim-p 0.0007 20.0000 0.0001 3800.178215 0 0.0000 343 | 1/8 18 h-lim-p 0.0000 20.0000 0.0001 | 1/8 19 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -3800.178215 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3800.178215 Node 7: lnL = -3800.178215 Node 8: lnL = -3800.178215 Node 9: lnL = -3800.178215 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 860 Sequential format.. Reading seq # 1: YJR056C_Sbay Reading seq # 2: YJR056C_Scer Reading seq # 3: YJR056C_Skud Reading seq # 4: YJR056C_Smik Reading seq # 5: YJR056C_Spar Sequences read.. Counting patterns.. # site patterns = 358 Counting frequencies.. 120 bytes for distance 57280 bytes for lkl0 45824 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.107226 0.088460 0.000060 0.265953 0.204062 0.276850 0.408568 0.286205 lnL0 = -3864.649169 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3864.649169 x= 0.10723 0.08846 0.00006 0.26595 0.20406 0.27685 0.40857 0.28620 1 h-lim-p 0.0022 0.0246 186.9834 3859.063762 3 0.0003 30 | 0/8 2 h-lim-p 0.0006 0.0044 67.0252 3857.683101 1 0.0007 44 | 0/8 3 h-lim-p 0.0018 0.0146 21.3239 3857.557153 7 0.0006 74 | 0/8 4 h-lim-p 0.0044 0.1490 3.0022 3857.550108 5 0.0016 98 | 0/8 5 h-lim-p 0.0011 0.0344 4.4307 3857.544517 4 0.0012 120 | 0/8 6 h-lim-p 0.0079 0.4523 0.6612 3857.544279 3 0.0010 140 | 0/8 7 h-lim-p 0.0036 1.4923 0.1903 3857.544068 0 0.0054 160 | 0/8 8 h-lim-p 0.0746 5.7912 0.0138 3857.511452 0 0.4477 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0010 3857.510837 3 0.9482 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3857.510836 0 1.0938 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3857.510836 0 1.0938 248 | 0/8 12 h-lim-p 1.1033 20.0000 0.0000 3857.510836 0 0.5516 268 | 0/8 13 h-lim-p 0.2334 20.0000 0.0000 3857.510836 0 0.0109 292 | 0/8 14 h-lim-p 0.0036 20.0000 0.0001 3857.510836 0 0.0000 331 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -3857.510836 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3857.510836 Node 7: lnL = -3857.510836 Node 8: lnL = -3857.510836 Node 9: lnL = -3857.510836 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 858 Sequential format.. Reading seq # 1: YJR057W_Sbay Reading seq # 2: YJR057W_Scer Reading seq # 3: YJR057W_Skud Reading seq # 4: YJR057W_Smik Reading seq # 5: YJR057W_Spar Sequences read.. Counting patterns.. # site patterns = 317 Counting frequencies.. 120 bytes for distance 50720 bytes for lkl0 40576 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.277501 0.154570 0.000060 0.465804 0.107954 0.540033 0.857031 0.570585 lnL0 = -4378.188745 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4378.188745 x= 0.27750 0.15457 0.00006 0.46580 0.10795 0.54003 0.85703 0.57058 1 h-lim-p 0.0000 0.0000 99.6461 4378.174279 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0048 24.7576 4376.724719 0 0.0037 42 | 1/8 3 h-lim-p 0.0172 0.1380 3.2801 4376.491178 6 0.0192 69 | 1/8 4 h-lim-p 0.0116 0.0930 4.2798 4375.983660 0 0.0233 82 | 1/8 5 h-lim-p 0.0019 0.0151 8.1826 4375.210128 m 0.0151 94 | 2/8 6 h-lim-p 0.0005 0.0053 131.1607 4374.178750 0 0.0010 107 | 2/8 7 h-lim-p 0.0235 0.1878 3.0122 4371.037752 0 0.0470 120 | 1/8 8 h-lim-p 0.0079 0.2778 17.8643 4370.611985 6 0.0028 145 | 1/8 9 h-lim-p 0.5569 5.3856 0.0901 4370.367661 6 0.3937 170 | 1/8 10 h-lim-p 0.9728 7.7825 0.0112 4370.176698 0 2.9184 190 | 1/8 11 h-lim-p 0.5765 19.8123 0.0569 4370.053008 0 1.1529 210 | 1/8 12 h-lim-p 2.5000 20.0000 0.0231 4369.980414 3 1.1328 235 | 1/8 13 h-lim-p 2.5000 20.0000 0.0022 4369.979920 3 1.0449 260 | 1/8 14 h-lim-p 2.5000 20.0000 0.0004 4369.979909 1 0.9961 281 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 4369.979909 0 1.0938 300 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 4369.979909 0 1.0938 319 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 4369.979909 0 0.1172 342 | 1/8 18 h-lim-p 0.0581 20.0000 0.0000 4369.979909 0 0.0036 364 | 1/8 19 h-lim-p 0.0103 20.0000 0.0000 4369.979909 0 0.0000 404 Out... lnL = -4369.979909 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4369.979909 Node 7: lnL = -4369.979909 Node 8: lnL = -4369.979909 Node 9: lnL = -4369.979909 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 680 Sequential format.. Reading seq # 1: YJR058C_Sbay Reading seq # 2: YJR058C_Scer Reading seq # 3: YJR058C_Skud Reading seq # 4: YJR058C_Smik Reading seq # 5: YJR058C_Spar Sequences read.. Counting patterns.. # site patterns = 199 Counting frequencies.. 120 bytes for distance 31840 bytes for lkl0 25472 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.079761 0.032122 0.063018 0.074011 0.061003 0.141937 0.150089 0.163959 lnL0 = -2657.055278 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2657.055278 x= 0.07976 0.03212 0.06302 0.07401 0.06100 0.14194 0.15009 0.16396 1 h-lim-p 0.0001 0.0009 188.6702 2654.613329 0 0.0002 22 | 0/8 2 h-lim-p 0.0007 0.0057 34.5600 2654.448479 5 0.0003 44 | 0/8 3 h-lim-p 0.0005 0.0107 18.8996 2654.422891 6 0.0002 70 | 0/8 4 h-lim-p 0.0004 0.0147 7.9947 2654.418744 5 0.0002 93 | 0/8 5 h-lim-p 0.0013 0.1553 0.9749 2654.418562 4 0.0004 116 | 0/8 6 h-lim-p 0.0102 3.0881 0.0352 2654.418258 2 0.0107 140 | 0/8 7 h-lim-p 0.0012 0.3607 0.3150 2654.408771 0 0.0095 163 | 0/8 8 h-lim-p 0.0010 0.0307 3.0058 2654.385593 3 0.0011 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 2654.384959 4 0.9802 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2654.384958 0 1.0938 230 | 0/8 11 h-lim-p 1.6802 20.0000 0.0000 2654.384958 0 1.4702 250 | 0/8 12 h-lim-p 2.3065 20.0000 0.0000 2654.384958 0 1.0091 270 | 0/8 13 h-lim-p 0.5393 20.0000 0.0000 2654.384958 0 0.0337 293 | 0/8 14 h-lim-p 0.0007 20.0000 0.0007 2654.384958 0 0.0003 314 | 0/8 15 h-lim-p 0.0009 20.0000 0.0002 2654.384958 0 0.0000 349 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 2654.384958 0 0.0000 370 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -2654.384958 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2654.384958 Node 7: lnL = -2654.384958 Node 8: lnL = -2654.384958 Node 9: lnL = -2654.384958 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 641 Sequential format.. Reading seq # 1: YJR059W_Sbay Reading seq # 2: YJR059W_Scer Reading seq # 3: YJR059W_Skud Reading seq # 4: YJR059W_Smik Reading seq # 5: YJR059W_Spar Sequences read.. Counting patterns.. # site patterns = 196 Counting frequencies.. 120 bytes for distance 31360 bytes for lkl0 25088 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.084173 0.024110 0.060927 0.074162 0.060852 0.146612 0.152039 0.168404 lnL0 = -2596.146339 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2596.146339 x= 0.08417 0.02411 0.06093 0.07416 0.06085 0.14661 0.15204 0.16840 1 h-lim-p 0.0001 0.0008 200.6332 2593.589704 0 0.0002 22 | 0/8 2 h-lim-p 0.0004 0.0035 44.0589 2593.365127 6 0.0002 47 | 0/8 3 h-lim-p 0.0004 0.0073 26.5254 2593.318321 5 0.0002 68 | 0/8 4 h-lim-p 0.0004 0.0108 11.0686 2593.309563 4 0.0002 89 | 0/8 5 h-lim-p 0.0017 0.1454 1.1168 2593.309332 2 0.0004 106 | 0/8 6 h-lim-p 0.0041 1.3257 0.1046 2593.309314 1 0.0008 121 | 0/8 7 h-lim-p 0.0054 7.1990 0.0156 2593.300543 0 0.1738 146 | 0/8 8 h-lim-p 0.0009 0.0266 3.1294 2593.289429 3 0.0008 172 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 2593.288968 3 0.9961 190 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2593.288968 0 1.0938 210 | 0/8 11 h-lim-p 1.0481 20.0000 0.0000 2593.288968 0 0.5241 230 | 0/8 12 h-lim-p 0.3199 20.0000 0.0000 2593.288968 0 0.0400 252 | 0/8 13 h-lim-p 0.0203 20.0000 0.0000 2593.288968 0 0.0203 272 | 0/8 14 h-lim-p 0.0119 20.0000 0.0001 2593.288968 0 0.0000 310 | 0/8 15 h-lim-p 0.0000 20.0000 0.0017 | 0/8 16 h-lim-p 0.0000 20.0000 0.0017 Out... lnL = -2593.288968 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2593.288968 Node 7: lnL = -2593.288968 Node 8: lnL = -2593.288968 Node 9: lnL = -2593.288968 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 553 Sequential format.. Reading seq # 1: YJR060W_Sbay Reading seq # 2: YJR060W_Scer Reading seq # 3: YJR060W_Skud Reading seq # 4: YJR060W_Smik Reading seq # 5: YJR060W_Spar Sequences read.. Counting patterns.. # site patterns = 206 Counting frequencies.. 120 bytes for distance 32960 bytes for lkl0 26368 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.082259 0.022660 0.055692 0.115521 0.065070 0.185256 0.202071 0.180391 lnL0 = -2307.646257 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2307.646257 x= 0.08226 0.02266 0.05569 0.11552 0.06507 0.18526 0.20207 0.18039 1 h-lim-p 0.0004 0.0035 135.8783 2306.203922 6 0.0002 33 | 0/8 2 h-lim-p 0.0009 0.0068 13.6274 2306.180724 6 0.0003 59 | 0/8 3 h-lim-p 0.0006 0.0652 5.9346 2306.175847 6 0.0003 86 | 0/8 4 h-lim-p 0.0009 0.1286 2.1542 2306.175027 2 0.0004 102 | 0/8 5 h-lim-p 0.0017 0.2872 0.5212 2306.174971 2 0.0005 119 | 0/8 6 h-lim-p 0.0014 1.3330 0.1691 2306.174966 1 0.0003 142 | 0/8 7 h-lim-p 0.0028 11.3810 0.0204 2306.174966 0 0.0006 163 | 0/8 8 h-lim-p 0.4664 20.0000 0.0000 2306.174964 0 0.9328 184 | 0/8 9 h-lim-p 1.8071 20.0000 0.0000 2306.174964 0 1.5812 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2306.174964 0 1.0938 224 | 0/8 11 h-lim-p 0.5467 20.0000 0.0000 2306.174964 0 0.0011 252 | 0/8 12 h-lim-p 0.0004 20.0000 0.0000 2306.174964 0 0.0004 272 | 0/8 13 h-lim-p 0.0003 20.0000 0.0000 2306.174964 0 0.0000 305 | 0/8 14 h-lim-p 0.0000 20.0000 0.0011 | 0/8 15 h-lim-p 0.0000 20.0000 0.0011 Out... lnL = -2306.174964 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2306.174964 Node 7: lnL = -2306.174964 Node 8: lnL = -2306.174964 Node 9: lnL = -2306.174964 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 767 Sequential format.. Reading seq # 1: YJR061W_Sbay Reading seq # 2: YJR061W_Scer Reading seq # 3: YJR061W_Skud Reading seq # 4: YJR061W_Smik Reading seq # 5: YJR061W_Spar Sequences read.. Counting patterns.. # site patterns = 247 Counting frequencies.. 120 bytes for distance 39520 bytes for lkl0 31616 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.112894 0.063001 0.048078 0.100247 0.059826 0.177991 0.186671 0.218782 lnL0 = -3171.086570 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3171.086570 x= 0.11289 0.06300 0.04808 0.10025 0.05983 0.17799 0.18667 0.21878 1 h-lim-p 0.0081 1.4295 88.2194 3170.436166 8 0.0002 45 | 0/8 2 h-lim-p 0.0005 0.0039 26.2415 3170.371663 3 0.0002 63 | 0/8 3 h-lim-p 0.0007 0.0119 7.6068 3170.366287 5 0.0002 89 | 0/8 4 h-lim-p 0.0005 0.0827 3.1258 3170.364764 4 0.0004 110 | 0/8 5 h-lim-p 0.0028 0.5984 0.3997 3170.364732 3 0.0004 131 | 0/8 6 h-lim-p 0.0009 1.2775 0.1912 3170.364728 1 0.0004 153 | 0/8 7 h-lim-p 0.0090 20.0000 0.0074 3170.364728 0 0.0023 174 | 0/8 8 h-lim-p 0.0210 20.0000 0.0008 3170.364622 0 0.2519 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3170.364621 0 1.0938 217 | 0/8 10 h-lim-p 2.0396 20.0000 0.0000 3170.364621 0 0.8923 237 | 0/8 11 h-lim-p 0.8429 20.0000 0.0000 3170.364621 0 0.0016 265 | 0/8 12 h-lim-p 0.0011 20.0000 0.0000 3170.364621 0 0.0000 299 | 0/8 13 h-lim-p 0.0000 20.0000 0.0010 | 0/8 14 h-lim-p 0.0000 20.0000 0.0010 Out... lnL = -3170.364621 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3170.364621 Node 7: lnL = -3170.364621 Node 8: lnL = -3170.364621 Node 9: lnL = -3170.364621 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 400 Sequential format.. Reading seq # 1: YJR062C_Sbay Reading seq # 2: YJR062C_Scer Reading seq # 3: YJR062C_Skud Reading seq # 4: YJR062C_Smik Reading seq # 5: YJR062C_Spar Sequences read.. Counting patterns.. # site patterns = 194 Counting frequencies.. 120 bytes for distance 31040 bytes for lkl0 24832 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.025054 0.150115 0.105876 0.140745 0.138040 0.215119 0.278859 0.164390 lnL0 = -1845.883767 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1845.883767 x= 0.02505 0.15012 0.10588 0.14075 0.13804 0.21512 0.27886 0.16439 1 h-lim-p 0.0176 0.1407 27.4677 1845.654061 7 0.0006 42 | 0/8 2 h-lim-p 0.0011 0.0092 9.4348 1845.615740 3 0.0010 60 | 0/8 3 h-lim-p 0.0035 0.1002 2.6004 1845.613103 3 0.0008 80 | 0/8 4 h-lim-p 0.0085 0.5306 0.2569 1845.613080 2 0.0007 100 | 0/8 5 h-lim-p 0.0024 3.3971 0.0755 1845.613078 0 0.0010 120 | 0/8 6 h-lim-p 0.0038 17.8143 0.0209 1845.613077 0 0.0017 140 | 0/8 7 h-lim-p 0.0092 20.0000 0.0038 1845.613077 0 0.0092 160 | 0/8 8 h-lim-p 0.0200 20.0000 0.0017 1845.613042 0 0.1602 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1845.613038 1 0.9961 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1845.613038 0 2.1875 225 | 0/8 11 h-lim-p 1.1530 20.0000 0.0000 1845.613038 0 4.6118 247 | 0/8 12 h-lim-p 0.0177 4.9517 0.0077 1845.613038 0 0.0078 267 | 0/8 13 h-lim-p 0.0021 1.3256 0.0286 1845.613038 0 0.0000 294 | 0/8 14 h-lim-p 0.0001 13.3896 0.0028 1845.613038 0 0.0000 330 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -1845.613038 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1845.613038 Node 7: lnL = -1845.613038 Node 8: lnL = -1845.613038 Node 9: lnL = -1845.613038 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 372 Sequential format.. Reading seq # 1: YJR063W_Sbay Reading seq # 2: YJR063W_Scer Reading seq # 3: YJR063W_Skud Reading seq # 4: YJR063W_Smik Reading seq # 5: YJR063W_Spar Sequences read.. Counting patterns.. # site patterns = 175 Counting frequencies.. 120 bytes for distance 28000 bytes for lkl0 22400 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.014185 0.168885 0.100176 0.131992 0.146793 0.191865 0.296388 0.152615 lnL0 = -1738.232578 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1738.232578 x= 0.01419 0.16888 0.10018 0.13199 0.14679 0.19186 0.29639 0.15261 1 h-lim-p 0.0369 5.4141 30.6808 1737.970434 6 0.0006 38 | 0/8 2 h-lim-p 0.0007 0.0060 8.5567 1737.937516 0 0.0011 50 | 0/8 3 h-lim-p 0.0035 0.0766 2.7477 1737.934274 5 0.0010 73 | 0/8 4 h-lim-p 0.0056 0.1280 0.4660 1737.934201 2 0.0007 91 | 0/8 5 h-lim-p 0.0028 1.8765 0.1170 1737.934195 2 0.0009 116 | 0/8 6 h-lim-p 0.0036 6.6352 0.0289 1737.934191 0 0.0031 136 | 0/8 7 h-lim-p 0.0208 20.0000 0.0043 1737.933667 0 0.3335 160 | 0/8 8 h-lim-p 0.0053 3.3895 0.2723 1737.933562 1 0.0021 182 | 0/8 9 h-lim-p 1.7170 20.0000 0.0003 1737.933512 3 1.0219 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1737.933512 0 1.0938 230 | 0/8 11 h-lim-p 1.2848 20.0000 0.0000 1737.933512 0 1.2848 250 | 0/8 12 h-lim-p 0.4910 20.0000 0.0000 1737.933512 0 0.0614 272 | 0/8 13 h-lim-p 0.0059 20.0000 0.0004 1737.933512 0 0.0119 293 | 0/8 14 h-lim-p 0.0046 20.0000 0.0011 1737.933512 0 0.0023 313 | 0/8 15 h-lim-p 0.0010 10.0708 0.0023 1737.933512 0 0.0005 333 | 0/8 16 h-lim-p 0.0006 12.4678 0.0019 1737.933512 0 0.0000 360 | 0/8 17 h-lim-p 0.0001 20.0000 0.0001 1737.933512 0 0.0000 388 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 1737.933512 0 0.0000 421 Out... lnL = -1737.933512 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1737.933512 Node 7: lnL = -1737.933512 Node 8: lnL = -1737.933512 Node 9: lnL = -1737.933512 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 210 Sequential format.. Reading seq # 1: YJR067C_Sbay Reading seq # 2: YJR067C_Scer Reading seq # 3: YJR067C_Skud Reading seq # 4: YJR067C_Smik Reading seq # 5: YJR067C_Spar Sequences read.. Counting patterns.. # site patterns = 109 Counting frequencies.. 120 bytes for distance 17440 bytes for lkl0 13952 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.063074 0.098627 0.083277 0.134026 0.132752 0.150882 0.211673 0.181800 lnL0 = -971.448869 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 971.448869 x= 0.06307 0.09863 0.08328 0.13403 0.13275 0.15088 0.21167 0.18180 1 h-lim-p 0.0012 0.0094 34.5915 970.869120 5 0.0010 31 | 0/8 2 h-lim-p 0.0032 0.0258 9.6236 970.813966 4 0.0013 51 | 0/8 3 h-lim-p 0.0032 0.0751 3.8214 970.806629 6 0.0012 77 | 0/8 4 h-lim-p 0.0049 0.2412 0.9032 970.806178 2 0.0012 94 | 0/8 5 h-lim-p 0.0059 1.8442 0.1779 970.806156 1 0.0015 117 | 0/8 6 h-lim-p 0.0520 20.0000 0.0050 970.806156 0 0.0033 140 | 0/8 7 h-lim-p 0.0077 20.0000 0.0021 970.806154 0 0.0309 162 | 0/8 8 h-lim-p 0.0053 20.0000 0.0123 970.806134 0 0.0212 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 970.806133 0 1.0938 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 970.806133 0 1.0938 224 | 0/8 11 h-lim-p 1.7078 20.0000 0.0000 970.806133 0 1.4944 244 | 0/8 12 h-lim-p 1.8713 20.0000 0.0000 970.806133 0 0.1170 267 | 0/8 13 h-lim-p 0.0291 20.0000 0.0000 970.806133 0 0.0000 296 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 970.806133 0 0.0000 336 Out... lnL = -970.806133 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -970.806133 Node 7: lnL = -970.806133 Node 8: lnL = -970.806133 Node 9: lnL = -970.806133 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 207 Sequential format.. Reading seq # 1: YJR068W_Sbay Reading seq # 2: YJR068W_Scer Reading seq # 3: YJR068W_Skud Reading seq # 4: YJR068W_Smik Reading seq # 5: YJR068W_Spar Sequences read.. Counting patterns.. # site patterns = 102 Counting frequencies.. 120 bytes for distance 16320 bytes for lkl0 13056 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.051898 0.150568 0.075888 0.159388 0.107390 0.117163 0.227878 0.173736 lnL0 = -954.353707 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 954.353707 x= 0.05190 0.15057 0.07589 0.15939 0.10739 0.11716 0.22788 0.17374 1 h-lim-p 0.0007 0.0055 25.3234 954.069429 0 0.0010 22 | 0/8 2 h-lim-p 0.0040 0.0322 6.3372 954.047740 6 0.0012 51 | 0/8 3 h-lim-p 0.0046 0.1226 1.5945 954.046237 5 0.0012 74 | 0/8 4 h-lim-p 0.0024 0.5428 0.8302 954.045960 3 0.0010 92 | 0/8 5 h-lim-p 0.0058 1.9465 0.1372 954.045906 3 0.0035 120 | 0/8 6 h-lim-p 0.0074 3.5491 0.0638 954.045744 0 0.0148 141 | 0/8 7 h-lim-p 0.0138 3.5803 0.0688 954.041890 0 0.0413 162 | 0/8 8 h-lim-p 0.0022 0.0779 1.3091 954.039231 3 0.0018 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 954.039216 1 0.9961 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 954.039216 0 1.0938 222 | 0/8 11 h-lim-p 1.7236 20.0000 0.0000 954.039216 0 1.5082 242 | 0/8 12 h-lim-p 1.8566 20.0000 0.0000 954.039216 0 0.0004 273 Out... lnL = -954.039216 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -954.039216 Node 7: lnL = -954.039216 Node 8: lnL = -954.039216 Node 9: lnL = -954.039216 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 242 Sequential format.. Reading seq # 1: YJR069C_Sbay Reading seq # 2: YJR069C_Scer Reading seq # 3: YJR069C_Skud Reading seq # 4: YJR069C_Smik Reading seq # 5: YJR069C_Spar Sequences read.. Counting patterns.. # site patterns = 102 Counting frequencies.. 120 bytes for distance 16320 bytes for lkl0 13056 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.053050 0.069936 0.069984 0.115585 0.071914 0.143365 0.176636 0.148124 lnL0 = -1003.601802 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1003.601802 x= 0.05305 0.06994 0.06998 0.11558 0.07191 0.14336 0.17664 0.14812 1 h-lim-p 0.0009 0.0075 48.6540 1002.897603 8 0.0006 41 | 0/8 2 h-lim-p 0.0012 0.0096 14.1593 1002.830860 8 0.0007 71 | 0/8 3 h-lim-p 0.0020 0.0387 5.0617 1002.825180 4 0.0005 92 | 0/8 4 h-lim-p 0.0042 0.4223 0.6081 1002.824986 4 0.0011 113 | 0/8 5 h-lim-p 0.0040 1.3951 0.1636 1002.824973 2 0.0010 138 | 0/8 6 h-lim-p 0.0135 17.1671 0.0126 1002.824973 1 0.0017 162 | 0/8 7 h-lim-p 0.0058 20.0000 0.0036 1002.824968 0 0.0230 184 | 0/8 8 h-lim-p 0.0036 4.6722 0.0236 1002.824865 0 0.0142 206 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1002.824862 1 0.9961 228 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1002.824862 0 0.5469 249 | 0/8 11 h-lim-p 0.3075 20.0000 0.0000 1002.824862 0 0.0002 279 | 0/8 12 h-lim-p 0.0004 20.0000 0.0000 1002.824862 0 0.0000 302 Out... lnL = -1002.824862 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1002.824862 Node 7: lnL = -1002.824862 Node 8: lnL = -1002.824862 Node 9: lnL = -1002.824862 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 377 Sequential format.. Reading seq # 1: YJR070C_Sbay Reading seq # 2: YJR070C_Scer Reading seq # 3: YJR070C_Skud Reading seq # 4: YJR070C_Smik Reading seq # 5: YJR070C_Spar Sequences read.. Counting patterns.. # site patterns = 103 Counting frequencies.. 120 bytes for distance 16480 bytes for lkl0 13184 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.034374 0.050730 0.014176 0.081813 0.059130 0.079607 0.081310 0.088402 lnL0 = -1305.129847 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1305.129847 x= 0.03437 0.05073 0.01418 0.08181 0.05913 0.07961 0.08131 0.08840 1 h-lim-p 0.0004 0.3979 259.4439 1303.093141 6 0.0001 34 | 0/8 2 h-lim-p 0.0005 0.0048 39.2181 1302.904869 6 0.0003 58 | 0/8 3 h-lim-p 0.0015 0.0145 6.4905 1302.899767 5 0.0002 83 | 0/8 4 h-lim-p 0.0029 0.2369 0.5457 1302.899726 2 0.0003 101 | 0/8 5 h-lim-p 0.0012 1.2782 0.1288 1302.899724 0 0.0003 122 | 0/8 6 h-lim-p 0.0018 3.9826 0.0187 1302.899724 0 0.0008 142 | 0/8 7 h-lim-p 0.0149 20.0000 0.0010 1302.899471 0 0.3581 166 | 0/8 8 h-lim-p 0.0007 0.1127 0.5287 1302.899225 2 0.0007 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1302.899223 0 1.0938 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1302.899223 0 1.2500 230 | 0/8 11 h-lim-p 1.2516 20.0000 0.0000 1302.899223 0 0.2738 251 | 0/8 12 h-lim-p 0.0775 20.0000 0.0001 1302.899223 0 0.0000 296 | 0/8 13 h-lim-p 0.0000 20.0000 0.0018 | 0/8 14 h-lim-p 0.0000 20.0000 0.0018 Out... lnL = -1302.899223 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1302.899223 Node 7: lnL = -1302.899223 Node 8: lnL = -1302.899223 Node 9: lnL = -1302.899223 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 252 Sequential format.. Reading seq # 1: YJR072C_Sbay Reading seq # 2: YJR072C_Scer Reading seq # 3: YJR072C_Skud Reading seq # 4: YJR072C_Smik Reading seq # 5: YJR072C_Spar Sequences read.. Counting patterns.. # site patterns = 114 Counting frequencies.. 120 bytes for distance 18240 bytes for lkl0 14592 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.096487 0.063368 0.008515 0.070984 0.078915 0.225815 0.188094 0.196309 lnL0 = -985.963110 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 985.963110 x= 0.09649 0.06337 0.00851 0.07098 0.07892 0.22582 0.18809 0.19631 1 h-lim-p 0.0006 0.0076 178.8071 983.874441 9 0.0002 43 | 0/8 2 h-lim-p 0.0006 0.0047 25.8430 983.594086 0 0.0009 55 | 0/8 3 h-lim-p 0.0011 0.0089 14.6696 983.521858 4 0.0009 75 | 0/8 4 h-lim-p 0.0019 0.0150 6.3724 983.509075 3 0.0008 93 | 0/8 5 h-lim-p 0.0030 0.0693 1.6936 983.507274 2 0.0014 109 | 0/8 6 h-lim-p 0.0041 0.6030 0.5663 983.507125 3 0.0010 128 | 0/8 7 h-lim-p 0.0267 20.0000 0.0217 983.507123 2 0.0043 154 | 0/8 8 h-lim-p 0.1111 20.0000 0.0008 983.506507 0 0.8890 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 983.506462 1 1.0938 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 983.506462 0 1.0938 219 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 983.506462 0 2.1875 239 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 983.506462 0 0.6250 260 | 0/8 13 h-lim-p 0.2717 20.0000 0.0000 983.506462 0 0.0003 289 Out... lnL = -983.506462 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -983.506462 Node 7: lnL = -983.506462 Node 8: lnL = -983.506462 Node 9: lnL = -983.506462 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 171 Sequential format.. Reading seq # 1: YJR073C_Sbay Reading seq # 2: YJR073C_Scer Reading seq # 3: YJR073C_Skud Reading seq # 4: YJR073C_Smik Reading seq # 5: YJR073C_Spar Sequences read.. Counting patterns.. # site patterns = 72 Counting frequencies.. 120 bytes for distance 11520 bytes for lkl0 9216 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.058780 0.108895 0.000060 0.109332 0.085539 0.189733 0.030420 0.132546 lnL0 = -630.507548 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 630.507548 x= 0.05878 0.10889 0.00006 0.10933 0.08554 0.18973 0.03042 0.13255 1 h-lim-p 0.0000 0.0000 56.1124 630.499920 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0031 24.2447 630.378447 0 0.0006 40 | 1/8 3 h-lim-p 0.0030 0.0270 5.1972 630.361714 3 0.0012 58 | 1/8 4 h-lim-p 0.0034 1.6339 1.9264 630.358385 3 0.0014 76 | 1/8 5 h-lim-p 0.0062 0.2335 0.4356 630.348149 0 0.0093 88 | 1/8 6 h-lim-p 0.0065 0.4056 0.6246 629.675802 0 0.0521 110 | 1/8 7 h-lim-p 0.0046 0.0369 6.3102 629.641817 6 0.0016 142 | 1/8 8 h-lim-p 2.0091 20.0000 0.0051 629.611481 7 1.4786 170 | 1/8 9 h-lim-p 2.5000 20.0000 0.0015 629.609740 3 1.2103 196 | 1/8 10 h-lim-p 2.5000 20.0000 0.0003 629.609664 2 1.1719 219 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 629.609664 0 1.0938 238 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 629.609664 0 1.0938 257 | 1/8 13 h-lim-p 2.2351 20.0000 0.0000 629.609664 0 0.9778 276 | 1/8 14 h-lim-p 0.8086 20.0000 0.0000 629.609664 0 2.4259 296 | 1/8 15 h-lim-p 0.1656 20.0000 0.0001 629.609664 0 0.0026 320 | 1/8 16 h-lim-p 0.0006 20.0000 0.0003 629.609664 0 0.0002 340 | 1/8 17 h-lim-p 0.0000 20.0000 0.0008 629.609664 0 0.0000 361 | 1/8 18 h-lim-p 0.0001 20.0000 0.0000 629.609664 0 0.0001 380 | 1/8 19 h-lim-p 0.0002 20.0000 0.0000 629.609664 0 0.0000 411 | 1/8 20 h-lim-p 0.0000 20.0000 0.0001 629.609664 0 0.0000 439 | 1/8 21 h-lim-p 0.0000 20.0000 0.0001 | 1/8 22 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -629.609664 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -629.609664 Node 7: lnL = -629.609664 Node 8: lnL = -629.609664 Node 9: lnL = -629.609664 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 267 Sequential format.. Reading seq # 1: YJR074W_Sbay Reading seq # 2: YJR074W_Scer Reading seq # 3: YJR074W_Skud Reading seq # 4: YJR074W_Smik Reading seq # 5: YJR074W_Spar Sequences read.. Counting patterns.. # site patterns = 95 Counting frequencies.. 120 bytes for distance 15200 bytes for lkl0 12160 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.056478 0.079324 0.005311 0.151844 0.065491 0.150367 0.119125 0.140382 lnL0 = -934.785038 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 934.785038 x= 0.05648 0.07932 0.00531 0.15184 0.06549 0.15037 0.11913 0.14038 1 h-lim-p 0.0006 0.0049 59.3047 934.185030 9 0.0004 48 | 0/8 2 h-lim-p 0.0001 0.0006 36.3389 933.999047 0 0.0004 62 | 0/8 3 h-lim-p 0.0015 0.0169 10.2999 933.969886 6 0.0006 88 | 0/8 4 h-lim-p 0.0027 0.0706 2.3175 933.967675 6 0.0009 115 | 0/8 5 h-lim-p 0.0035 0.0358 0.5813 933.967564 3 0.0007 134 | 0/8 6 h-lim-p 0.0042 1.4311 0.0896 933.967528 3 0.0027 162 | 0/8 7 h-lim-p 0.0151 18.4482 0.0163 933.962499 0 0.1807 185 | 0/8 8 h-lim-p 0.0020 0.1597 1.5080 933.959529 5 0.0014 217 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 933.959371 3 1.0449 235 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 933.959370 0 1.0938 255 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 933.959370 0 2.1875 275 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 933.959370 0 0.2734 297 | 0/8 13 h-lim-p 0.0456 20.0000 0.0000 933.959370 0 0.0000 330 Out... lnL = -933.959370 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -933.959370 Node 7: lnL = -933.959370 Node 8: lnL = -933.959370 Node 9: lnL = -933.959370 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 288 Sequential format.. Reading seq # 1: YJR075W_Sbay Reading seq # 2: YJR075W_Scer Reading seq # 3: YJR075W_Skud Reading seq # 4: YJR075W_Smik Reading seq # 5: YJR075W_Spar Sequences read.. Counting patterns.. # site patterns = 128 Counting frequencies.. 120 bytes for distance 20480 bytes for lkl0 16384 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.121398 0.002492 0.056102 0.111199 0.078231 0.168458 0.168109 0.220306 lnL0 = -1057.549910 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1057.549910 x= 0.12140 0.00249 0.05610 0.11120 0.07823 0.16846 0.16811 0.22031 1 h-lim-p 0.0006 0.0098 194.1689 1054.063977 3 0.0003 29 | 0/8 2 h-lim-p 0.0006 0.0049 27.0602 1053.768505 0 0.0009 41 | 0/8 3 h-lim-p 0.0021 0.0174 11.7035 1053.721948 7 0.0008 67 | 0/8 4 h-lim-p 0.0016 0.0324 5.9655 1053.708207 6 0.0010 95 | 0/8 5 h-lim-p 0.0165 0.2241 0.3543 1053.708151 2 0.0008 114 | 0/8 6 h-lim-p 0.0053 4.8146 0.0548 1053.708095 0 0.0080 134 | 0/8 7 h-lim-p 0.0202 10.7497 0.0216 1053.703789 0 0.1617 157 | 0/8 8 h-lim-p 0.0037 0.2551 0.9423 1053.702466 5 0.0020 188 | 0/8 9 h-lim-p 2.4410 20.0000 0.0008 1053.701889 5 1.4526 221 | 0/8 10 h-lim-p 2.5000 20.0000 0.0003 1053.701772 3 1.6342 248 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1053.701772 0 1.0938 268 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1053.701772 0 2.1875 288 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1053.701772 0 1.0938 308 | 0/8 14 h-lim-p 0.5752 20.0000 0.0000 1053.701772 0 4.6015 331 | 0/8 15 h-lim-p 2.3136 20.0000 0.0000 1053.701772 0 0.2531 353 | 0/8 16 h-lim-p 2.1446 20.0000 0.0000 1053.701772 0 0.0293 378 | 0/8 17 h-lim-p 0.0055 20.0000 0.0000 1053.701772 0 0.0002 402 Out... lnL = -1053.701772 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1053.701772 Node 7: lnL = -1053.701772 Node 8: lnL = -1053.701772 Node 9: lnL = -1053.701772 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 726 Sequential format.. Reading seq # 1: YJR076C_Sbay Reading seq # 2: YJR076C_Scer Reading seq # 3: YJR076C_Skud Reading seq # 4: YJR076C_Smik Reading seq # 5: YJR076C_Spar Sequences read.. Counting patterns.. # site patterns = 279 Counting frequencies.. 120 bytes for distance 44640 bytes for lkl0 35712 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.040327 0.133519 0.054061 0.153558 0.104795 0.192758 0.223965 0.160064 lnL0 = -3141.802498 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3141.802498 x= 0.04033 0.13352 0.05406 0.15356 0.10480 0.19276 0.22396 0.16006 1 h-lim-p 0.0004 0.0029 182.5178 3137.334698 8 0.0003 42 | 0/8 2 h-lim-p 0.0002 0.0018 76.4083 3136.302098 0 0.0004 55 | 0/8 3 h-lim-p 0.0006 0.0051 33.5947 3136.166334 2 0.0003 71 | 0/8 4 h-lim-p 0.0013 0.0321 7.9144 3136.152891 5 0.0005 96 | 0/8 5 h-lim-p 0.0017 0.0327 2.1148 3136.151961 4 0.0004 117 | 0/8 6 h-lim-p 0.0012 0.5874 0.8005 3136.151802 0 0.0006 129 | 0/8 7 h-lim-p 0.0036 2.0171 0.1273 3136.151768 0 0.0016 149 | 0/8 8 h-lim-p 0.0230 20.0000 0.0088 3136.140756 0 0.3676 173 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3136.140723 1 0.9961 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3136.140723 0 1.2500 215 | 0/8 11 h-lim-p 1.4021 20.0000 0.0000 3136.140723 0 1.2268 235 | 0/8 12 h-lim-p 1.1938 20.0000 0.0000 3136.140723 0 4.7754 257 | 0/8 13 h-lim-p 0.1451 20.0000 0.0008 3136.140723 0 0.0045 281 | 0/8 14 h-lim-p 0.0010 11.3686 0.0036 3136.140723 0 0.0003 302 | 0/8 15 h-lim-p 0.0002 20.0000 0.0039 3136.140723 0 0.0000 340 | 0/8 16 h-lim-p 0.0000 20.0000 0.0012 | 0/8 17 h-lim-p 0.0000 20.0000 0.0012 Out... lnL = -3136.140723 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3136.140723 Node 7: lnL = -3136.140723 Node 8: lnL = -3136.140723 Node 9: lnL = -3136.140723 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 737 Sequential format.. Reading seq # 1: YJR078W_Sbay Reading seq # 2: YJR078W_Scer Reading seq # 3: YJR078W_Skud Reading seq # 4: YJR078W_Smik Reading seq # 5: YJR078W_Spar Sequences read.. Counting patterns.. # site patterns = 217 Counting frequencies.. 120 bytes for distance 34720 bytes for lkl0 27776 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.216752 0.000060 0.122083 0.157990 0.050950 0.142752 0.260656 0.323003 lnL0 = -2890.311277 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2890.311277 x= 0.21675 0.00006 0.12208 0.15799 0.05095 0.14275 0.26066 0.32300 1 h-lim-p 0.0001 0.0012 268.7645 2868.199471 0 0.0006 24 | 0/8 2 h-lim-p 0.0003 0.0023 148.6947 2863.323320 0 0.0006 37 | 0/8 3 h-lim-p 0.0003 0.0020 82.2043 2862.418253 0 0.0004 49 | 0/8 4 h-lim-p 0.0015 0.0164 21.2892 2862.339438 5 0.0004 72 | 0/8 5 h-lim-p 0.0015 0.0297 5.3697 2862.335239 3 0.0003 91 | 0/8 6 h-lim-p 0.0053 0.7035 0.3102 2862.334599 5 0.0030 115 | 0/8 7 h-lim-p 0.0008 0.2921 1.2155 2862.332686 0 0.0015 136 | 0/8 8 h-lim-p 0.0106 1.0628 0.1737 2862.192734 0 0.0848 151 | 0/8 9 h-lim-p 2.5000 20.0000 0.0022 2862.185503 4 1.0199 180 | 0/8 10 h-lim-p 2.5000 20.0000 0.0003 2862.185426 2 1.0938 204 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2862.185425 0 1.0938 224 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2862.185425 0 1.0938 244 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2862.185425 0 0.6250 265 | 0/8 14 h-lim-p 0.4267 20.0000 0.0000 2862.185425 0 0.0133 289 | 0/8 15 h-lim-p 0.0071 20.0000 0.0000 2862.185425 0 0.0000 327 Out... lnL = -2862.185425 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2862.185425 Node 7: lnL = -2862.185425 Node 8: lnL = -2862.185425 Node 9: lnL = -2862.185425 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 316 Sequential format.. Reading seq # 1: YJR080C_Sbay Reading seq # 2: YJR080C_Scer Reading seq # 3: YJR080C_Skud Reading seq # 4: YJR080C_Smik Reading seq # 5: YJR080C_Spar Sequences read.. Counting patterns.. # site patterns = 147 Counting frequencies.. 120 bytes for distance 23520 bytes for lkl0 18816 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.111645 0.000060 0.142197 0.134266 0.085548 0.217775 0.320389 0.231648 lnL0 = -1481.916322 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1481.916322 x= 0.11164 0.00006 0.14220 0.13427 0.08555 0.21777 0.32039 0.23165 1 h-lim-p 0.0012 0.0096 63.2934 1480.287364 9 0.0007 42 | 0/8 2 h-lim-p 0.0009 0.0073 34.7003 1479.660930 0 0.0014 54 | 0/8 3 h-lim-p 0.0028 0.0225 16.4355 1479.569069 7 0.0009 83 | 0/8 4 h-lim-p 0.0013 0.0238 11.3197 1479.531164 6 0.0009 109 | 0/8 5 h-lim-p 0.0054 0.1522 1.8594 1479.529602 5 0.0009 134 | 0/8 6 h-lim-p 0.0051 0.6448 0.3472 1479.529496 3 0.0013 153 | 0/8 7 h-lim-p 0.0074 3.1187 0.0621 1479.528801 0 0.0298 175 | 0/8 8 h-lim-p 0.0100 0.4563 0.1843 1479.507276 0 0.0402 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0009 1479.506800 3 0.9961 223 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1479.506799 0 1.0938 243 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1479.506799 0 1.0938 263 | 0/8 12 h-lim-p 1.4569 20.0000 0.0000 1479.506799 0 0.7285 283 | 0/8 13 h-lim-p 0.4655 20.0000 0.0000 1479.506799 0 0.0073 308 | 0/8 14 h-lim-p 0.0030 20.0000 0.0000 1479.506799 0 0.0030 328 | 0/8 15 h-lim-p 0.0009 20.0000 0.0000 1479.506799 0 0.0000 352 | 0/8 16 h-lim-p 0.0002 20.0000 0.0000 1479.506799 0 0.0000 381 Out... lnL = -1479.506799 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1479.506799 Node 7: lnL = -1479.506799 Node 8: lnL = -1479.506799 Node 9: lnL = -1479.506799 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 410 Sequential format.. Reading seq # 1: YJR082C_Sbay Reading seq # 2: YJR082C_Scer Reading seq # 3: YJR082C_Skud Reading seq # 4: YJR082C_Smik Reading seq # 5: YJR082C_Spar Sequences read.. Counting patterns.. # site patterns = 218 Counting frequencies.. 120 bytes for distance 34880 bytes for lkl0 27904 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.118447 0.024500 0.163274 0.155451 0.055937 0.285006 0.287742 0.258079 lnL0 = -1889.041533 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1889.041533 x= 0.11845 0.02450 0.16327 0.15545 0.05594 0.28501 0.28774 0.25808 1 h-lim-p 0.0015 0.0119 64.0737 1887.897187 7 0.0006 39 | 0/8 2 h-lim-p 0.0005 0.0038 17.5443 1887.799765 0 0.0007 51 | 0/8 3 h-lim-p 0.0012 0.0390 10.3446 1887.765197 7 0.0008 82 | 0/8 4 h-lim-p 0.0030 0.1321 2.9104 1887.759457 5 0.0015 107 | 0/8 5 h-lim-p 0.0143 0.7610 0.3066 1887.759395 3 0.0014 127 | 0/8 6 h-lim-p 0.0216 17.9951 0.0193 1887.759383 2 0.0106 152 | 0/8 7 h-lim-p 0.0266 20.0000 0.0077 1887.758732 0 0.1064 174 | 0/8 8 h-lim-p 0.0024 0.5707 0.3395 1887.758587 3 0.0018 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1887.758553 1 0.9961 222 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1887.758552 0 1.0938 242 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1887.758552 0 2.1875 262 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1887.758552 0 1.0938 282 | 0/8 13 h-lim-p 0.5725 20.0000 0.0000 1887.758552 0 3.4353 304 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1887.758552 0 0.3125 326 | 0/8 15 h-lim-p 0.1734 20.0000 0.0000 1887.758552 0 0.0001 356 Out... lnL = -1887.758552 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1887.758552 Node 7: lnL = -1887.758552 Node 8: lnL = -1887.758552 Node 9: lnL = -1887.758552 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 200 Sequential format.. Reading seq # 1: YJR083C_Sbay Reading seq # 2: YJR083C_Scer Reading seq # 3: YJR083C_Skud Reading seq # 4: YJR083C_Smik Reading seq # 5: YJR083C_Spar Sequences read.. Counting patterns.. # site patterns = 107 Counting frequencies.. 120 bytes for distance 17120 bytes for lkl0 13696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.063032 0.163965 0.077347 0.205399 0.054850 0.238630 0.236315 0.194146 lnL0 = -961.568858 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 961.568858 x= 0.06303 0.16397 0.07735 0.20540 0.05485 0.23863 0.23631 0.19415 1 h-lim-p 0.0003 0.0026 37.4840 960.811337 0 0.0013 24 | 0/8 2 h-lim-p 0.0031 0.0791 15.7256 960.728183 4 0.0008 45 | 0/8 3 h-lim-p 0.0013 0.0114 9.1720 960.687452 2 0.0013 61 | 0/8 4 h-lim-p 0.0082 0.3115 1.4043 960.684953 6 0.0026 87 | 0/8 5 h-lim-p 0.0131 0.7944 0.2811 960.684823 3 0.0027 106 | 0/8 6 h-lim-p 0.0062 3.7782 0.1245 960.684701 1 0.0062 128 | 0/8 7 h-lim-p 0.0327 9.5120 0.0235 960.677612 0 0.2619 151 | 0/8 8 h-lim-p 0.0054 0.1974 1.1322 960.674117 6 0.0033 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0013 960.673616 3 0.9961 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 960.673616 0 1.0938 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 960.673616 0 1.0938 246 | 0/8 12 h-lim-p 1.3092 20.0000 0.0000 960.673616 0 2.6183 267 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 960.673616 0 0.0098 294 | 0/8 14 h-lim-p 0.0013 20.0000 0.0000 960.673616 0 0.0000 318 | 0/8 15 h-lim-p 0.0004 20.0000 0.0000 960.673616 0 0.0000 351 Out... lnL = -960.673616 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -960.673616 Node 7: lnL = -960.673616 Node 8: lnL = -960.673616 Node 9: lnL = -960.673616 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 201 Sequential format.. Reading seq # 1: YJR084W_Sbay Reading seq # 2: YJR084W_Scer Reading seq # 3: YJR084W_Skud Reading seq # 4: YJR084W_Smik Reading seq # 5: YJR084W_Spar Sequences read.. Counting patterns.. # site patterns = 123 Counting frequencies.. 120 bytes for distance 19680 bytes for lkl0 15744 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.039506 0.231130 0.072043 0.224520 0.046240 0.226123 0.190642 0.170414 lnL0 = -920.624417 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 920.624417 x= 0.03951 0.23113 0.07204 0.22452 0.04624 0.22612 0.19064 0.17041 1 h-lim-p 0.0057 0.0453 31.3173 920.152039 9 0.0010 45 | 0/8 2 h-lim-p 0.0010 0.0082 10.1851 920.075884 0 0.0021 58 | 0/8 3 h-lim-p 0.0082 0.0818 2.5603 920.070102 2 0.0019 75 | 0/8 4 h-lim-p 0.0046 0.1597 1.0606 920.069331 5 0.0016 100 | 0/8 5 h-lim-p 0.0056 0.7108 0.2986 920.069218 2 0.0024 116 | 0/8 6 h-lim-p 0.0223 10.9011 0.0327 920.069024 0 0.0335 136 | 0/8 7 h-lim-p 0.0196 7.0241 0.0558 920.064988 0 0.0786 158 | 0/8 8 h-lim-p 0.0140 0.9077 0.3131 920.064786 4 0.0038 187 | 0/8 9 h-lim-p 2.0760 20.0000 0.0006 920.064678 2 1.0299 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 920.064677 0 1.0938 231 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 920.064677 0 2.1875 251 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 920.064677 0 1.0938 271 | 0/8 13 h-lim-p 0.1057 20.0000 0.0000 920.064677 0 0.0264 292 | 0/8 14 h-lim-p 0.0002 20.0000 0.0010 920.064677 0 0.0002 312 | 0/8 15 h-lim-p 0.0002 20.0000 0.0010 920.064677 0 0.0000 335 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 920.064677 0 0.0000 363 | 0/8 17 h-lim-p 0.0002 20.0000 0.0000 920.064677 0 0.0000 388 Out... lnL = -920.064677 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -920.064677 Node 7: lnL = -920.064677 Node 8: lnL = -920.064677 Node 9: lnL = -920.064677 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 730 Sequential format.. Reading seq # 1: YJR085C_Sbay Reading seq # 2: YJR085C_Scer Reading seq # 3: YJR085C_Skud Reading seq # 4: YJR085C_Smik Reading seq # 5: YJR085C_Spar Sequences read.. Counting patterns.. # site patterns = 316 Counting frequencies.. 120 bytes for distance 50560 bytes for lkl0 40448 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.037496 0.213058 0.125332 0.208899 0.105638 0.252186 0.275648 0.190232 lnL0 = -3482.550167 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3482.550167 x= 0.03750 0.21306 0.12533 0.20890 0.10564 0.25219 0.27565 0.19023 1 h-lim-p 0.0009 0.0073 56.5007 3481.754606 8 0.0005 41 | 0/8 2 h-lim-p 0.0011 0.0089 18.3489 3481.669962 5 0.0005 65 | 0/8 3 h-lim-p 0.0015 0.0673 6.9282 3481.658998 6 0.0005 93 | 0/8 4 h-lim-p 0.0010 0.1107 3.6474 3481.656084 5 0.0006 117 | 0/8 5 h-lim-p 0.0024 0.3814 0.8673 3481.655867 3 0.0006 136 | 0/8 6 h-lim-p 0.0146 8.1606 0.0370 3481.655867 0 0.0016 158 | 0/8 7 h-lim-p 0.0253 20.0000 0.0023 3481.655865 0 0.0253 178 | 0/8 8 h-lim-p 0.0096 20.0000 0.0062 3481.655803 0 0.0385 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3481.655802 0 1.0938 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3481.655802 0 1.0938 240 | 0/8 11 h-lim-p 1.0623 20.0000 0.0000 3481.655802 0 1.0623 260 | 0/8 12 h-lim-p 0.1322 20.0000 0.0001 3481.655802 0 0.0000 295 | 0/8 13 h-lim-p 0.0002 20.0000 0.0000 3481.655802 0 0.0000 322 Out... lnL = -3481.655802 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3481.655802 Node 7: lnL = -3481.655802 Node 8: lnL = -3481.655802 Node 9: lnL = -3481.655802 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 688 Sequential format.. Reading seq # 1: YJR086W_Sbay Reading seq # 2: YJR086W_Scer Reading seq # 3: YJR086W_Skud Reading seq # 4: YJR086W_Smik Reading seq # 5: YJR086W_Spar Sequences read.. Counting patterns.. # site patterns = 306 Counting frequencies.. 120 bytes for distance 48960 bytes for lkl0 39168 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.055595 0.177884 0.202428 0.197373 0.122127 0.232567 0.284477 0.218327 lnL0 = -3424.504162 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3424.504162 x= 0.05559 0.17788 0.20243 0.19737 0.12213 0.23257 0.28448 0.21833 1 h-lim-p 0.0015 0.0123 54.6158 3423.501265 2 0.0007 26 | 0/8 2 h-lim-p 0.0013 0.0106 24.7497 3423.268848 7 0.0009 55 | 0/8 3 h-lim-p 0.0038 0.0875 5.7920 3423.261268 4 0.0005 77 | 0/8 4 h-lim-p 0.0011 0.0945 2.5511 3423.259732 4 0.0006 98 | 0/8 5 h-lim-p 0.0090 3.3020 0.1568 3423.259718 0 0.0011 112 | 0/8 6 h-lim-p 0.0033 5.6622 0.0541 3423.259717 0 0.0008 133 | 0/8 7 h-lim-p 0.0100 20.0000 0.0044 3423.259717 0 0.0050 153 | 0/8 8 h-lim-p 0.0238 20.0000 0.0009 3423.259683 0 0.2853 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3423.259682 0 1.0938 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3423.259682 0 1.0938 216 | 0/8 11 h-lim-p 0.9676 20.0000 0.0000 3423.259682 0 0.9676 236 | 0/8 12 h-lim-p 0.0358 20.0000 0.0003 3423.259682 0 0.0000 267 | 0/8 13 h-lim-p 0.0002 20.0000 0.0000 3423.259682 0 0.0000 297 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -3423.259682 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3423.259682 Node 7: lnL = -3423.259682 Node 8: lnL = -3423.259682 Node 9: lnL = -3423.259682 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 408 Sequential format.. Reading seq # 1: YJR088C_Sbay Reading seq # 2: YJR088C_Scer Reading seq # 3: YJR088C_Skud Reading seq # 4: YJR088C_Smik Reading seq # 5: YJR088C_Spar Sequences read.. Counting patterns.. # site patterns = 170 Counting frequencies.. 120 bytes for distance 27200 bytes for lkl0 21760 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.106351 0.052830 0.103081 0.187849 0.085986 0.178420 0.239874 0.228405 lnL0 = -1640.993346 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1640.993346 x= 0.10635 0.05283 0.10308 0.18785 0.08599 0.17842 0.23987 0.22840 1 h-lim-p 0.0005 0.0041 53.6573 1640.022605 0 0.0008 22 | 0/8 2 h-lim-p 0.0022 0.0179 17.6176 1639.857990 7 0.0012 52 | 0/8 3 h-lim-p 0.0016 0.0151 12.5189 1639.814320 2 0.0008 68 | 0/8 4 h-lim-p 0.0010 0.0325 9.6481 1639.787563 4 0.0010 88 | 0/8 5 h-lim-p 0.0025 0.0622 3.7673 1639.780938 4 0.0012 108 | 0/8 6 h-lim-p 0.0034 0.1711 1.3886 1639.779836 3 0.0013 126 | 0/8 7 h-lim-p 0.0048 0.6846 0.3875 1639.779749 3 0.0013 145 | 0/8 8 h-lim-p 0.2608 20.0000 0.0019 1639.777927 0 1.0434 167 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1639.777900 2 0.9961 191 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1639.777900 0 1.0938 211 | 0/8 11 h-lim-p 1.6222 20.0000 0.0000 1639.777900 0 1.4194 231 | 0/8 12 h-lim-p 1.4930 20.0000 0.0000 1639.777900 0 0.0029 259 | 0/8 13 h-lim-p 0.0007 20.0000 0.0000 1639.777900 0 0.0000 300 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1639.777900 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1639.777900 Node 7: lnL = -1639.777900 Node 8: lnL = -1639.777900 Node 9: lnL = -1639.777900 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 371 Sequential format.. Reading seq # 1: YJR089W_Sbay Reading seq # 2: YJR089W_Scer Reading seq # 3: YJR089W_Skud Reading seq # 4: YJR089W_Smik Reading seq # 5: YJR089W_Spar Sequences read.. Counting patterns.. # site patterns = 163 Counting frequencies.. 120 bytes for distance 26080 bytes for lkl0 20864 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.082996 0.126141 0.084846 0.192166 0.077444 0.195979 0.153394 0.201058 lnL0 = -1749.769112 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1749.769112 x= 0.08300 0.12614 0.08485 0.19217 0.07744 0.19598 0.15339 0.20106 1 h-lim-p 0.0034 0.0274 50.1816 1748.970769 4 0.0007 31 | 0/8 2 h-lim-p 0.0011 0.0092 18.7889 1748.877317 4 0.0006 52 | 0/8 3 h-lim-p 0.0016 0.0339 6.7166 1748.867119 6 0.0005 79 | 0/8 4 h-lim-p 0.0036 0.3175 0.9667 1748.866739 0 0.0008 92 | 0/8 5 h-lim-p 0.0073 3.4607 0.1038 1748.866734 0 0.0009 114 | 0/8 6 h-lim-p 0.0037 5.1376 0.0253 1748.866733 0 0.0016 134 | 0/8 7 h-lim-p 0.0318 20.0000 0.0013 1748.866625 0 0.3813 157 | 0/8 8 h-lim-p 0.0020 1.3924 0.2516 1748.866502 2 0.0019 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1748.866500 0 1.0938 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1748.866500 0 1.0938 221 | 0/8 11 h-lim-p 1.4061 20.0000 0.0000 1748.866500 0 1.4061 241 | 0/8 12 h-lim-p 1.2335 20.0000 0.0000 1748.866500 0 0.6167 261 | 0/8 13 h-lim-p 0.0359 20.0000 0.0001 1748.866500 0 0.0006 286 | 0/8 14 h-lim-p 0.0004 20.0000 0.0002 1748.866500 0 0.0000 319 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 1748.866500 0 0.0000 350 Out... lnL = -1748.866500 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1748.866500 Node 7: lnL = -1748.866500 Node 8: lnL = -1748.866500 Node 9: lnL = -1748.866500 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 396 Sequential format.. Reading seq # 1: YJR093C_Sbay Reading seq # 2: YJR093C_Scer Reading seq # 3: YJR093C_Skud Reading seq # 4: YJR093C_Smik Reading seq # 5: YJR093C_Spar Sequences read.. Counting patterns.. # site patterns = 165 Counting frequencies.. 120 bytes for distance 26400 bytes for lkl0 21120 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.073494 0.055315 0.068895 0.064823 0.076317 0.218312 0.224728 0.171836 lnL0 = -1678.860094 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1678.860094 x= 0.07349 0.05531 0.06889 0.06482 0.07632 0.21831 0.22473 0.17184 1 h-lim-p 0.0004 0.0035 119.6429 1676.480225 8 0.0004 40 | 0/8 2 h-lim-p 0.0007 0.0060 21.8416 1676.370326 8 0.0005 74 | 0/8 3 h-lim-p 0.0006 0.0093 15.8915 1676.338445 7 0.0004 104 | 0/8 4 h-lim-p 0.0023 0.0547 2.4067 1676.336844 3 0.0006 123 | 0/8 5 h-lim-p 0.0013 0.2858 1.0516 1676.336393 4 0.0010 145 | 0/8 6 h-lim-p 0.0141 3.9489 0.0723 1676.336389 1 0.0014 161 | 0/8 7 h-lim-p 0.0227 20.0000 0.0045 1676.336368 0 0.0341 181 | 0/8 8 h-lim-p 0.0035 20.0000 0.0431 1676.335687 0 0.0213 203 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1676.335681 1 0.9961 225 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1676.335681 0 1.0938 245 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1676.335681 0 2.1875 265 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1676.335681 0 0.5469 286 | 0/8 13 h-lim-p 0.1090 20.0000 0.0000 1676.335681 0 0.0004 313 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 1676.335681 0 0.0000 339 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 1676.335681 0 0.0000 366 Out... lnL = -1676.335681 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1676.335681 Node 7: lnL = -1676.335681 Node 8: lnL = -1676.335681 Node 9: lnL = -1676.335681 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 921 Sequential format.. Reading seq # 1: YJR095W_Sbay Reading seq # 2: YJR095W_Scer Reading seq # 3: YJR095W_Skud Reading seq # 4: YJR095W_Smik Reading seq # 5: YJR095W_Spar Sequences read.. Counting patterns.. # site patterns = 244 Counting frequencies.. 120 bytes for distance 39040 bytes for lkl0 31232 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.057189 0.078242 0.044442 0.097729 0.049596 0.153743 0.128569 0.135226 lnL0 = -3562.026983 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3562.026983 x= 0.05719 0.07824 0.04444 0.09773 0.04960 0.15374 0.12857 0.13523 1 h-lim-p 0.0004 0.0033 198.7288 3560.178290 8 0.0001 41 | 0/8 2 h-lim-p 0.0003 0.0025 29.8884 3560.110243 4 0.0002 61 | 0/8 3 h-lim-p 0.0003 0.0181 17.6363 3560.092371 6 0.0001 88 | 0/8 4 h-lim-p 0.0007 0.0380 3.9967 3560.090772 4 0.0002 109 | 0/8 5 h-lim-p 0.0028 0.4297 0.3100 3560.090760 2 0.0002 128 | 0/8 6 h-lim-p 0.0009 11.0719 0.0735 3560.090760 0 0.0002 149 | 0/8 7 h-lim-p 0.0019 10.8806 0.0080 3560.090760 0 0.0008 169 | 0/8 8 h-lim-p 0.0138 20.0000 0.0005 3560.090674 0 0.4414 194 | 0/8 9 h-lim-p 1.7040 20.0000 0.0001 3560.090666 1 0.8387 217 | 0/8 10 h-lim-p 2.2161 20.0000 0.0000 3560.090666 0 0.9696 237 | 0/8 11 h-lim-p 1.4183 20.0000 0.0000 3560.090666 0 0.0003 268 | 0/8 12 h-lim-p 0.0000 2.7896 0.0295 .. | 0/8 13 h-lim-p 0.0000 20.0000 0.0018 3560.090666 0 0.0000 328 | 0/8 14 h-lim-p 0.0000 20.0000 0.0006 3560.090666 0 0.0006 354 | 0/8 15 h-lim-p 0.0016 20.0000 0.0002 3560.090666 0 0.0004 375 | 0/8 16 h-lim-p 0.0013 20.0000 0.0001 3560.090666 0 0.0000 399 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 3560.090666 0 0.0000 419 | 0/8 18 h-lim-p 0.0000 20.0000 0.0015 3560.090666 0 0.0000 445 | 0/8 19 h-lim-p 0.0000 20.0000 0.0025 3560.090666 0 0.0000 473 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 3560.090666 0 0.0000 508 | 0/8 21 h-lim-p 0.0000 20.0000 0.0029 3560.090666 0 0.0000 540 | 0/8 22 h-lim-p 0.0000 20.0000 0.0021 .. | 0/8 23 h-lim-p 0.0000 20.0000 0.0029 | 0/8 24 h-lim-p 0.0000 20.0000 0.0029 Out... lnL = -3560.090666 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3560.090666 Node 7: lnL = -3560.090666 Node 8: lnL = -3560.090666 Node 9: lnL = -3560.090666 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 474 Sequential format.. Reading seq # 1: YJR096W_Sbay Reading seq # 2: YJR096W_Scer Reading seq # 3: YJR096W_Skud Reading seq # 4: YJR096W_Smik Reading seq # 5: YJR096W_Spar Sequences read.. Counting patterns.. # site patterns = 160 Counting frequencies.. 120 bytes for distance 25600 bytes for lkl0 20480 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.091292 0.050087 0.055628 0.099161 0.045304 0.170849 0.212624 0.184448 lnL0 = -2043.413743 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2043.413743 x= 0.09129 0.05009 0.05563 0.09916 0.04530 0.17085 0.21262 0.18445 1 h-lim-p 0.0001 0.0007 104.0941 2042.139913 0 0.0003 23 | 0/8 2 h-lim-p 0.0007 0.0974 39.3117 2042.021881 6 0.0002 47 | 0/8 3 h-lim-p 0.0006 0.0073 11.4550 2042.004886 2 0.0003 63 | 0/8 4 h-lim-p 0.0008 0.0521 3.8381 2042.001408 5 0.0005 89 | 0/8 5 h-lim-p 0.0025 0.3390 0.8186 2042.001188 3 0.0007 108 | 0/8 6 h-lim-p 0.0017 0.7087 0.3245 2042.001155 2 0.0005 133 | 0/8 7 h-lim-p 0.0068 7.7269 0.0258 2042.000543 0 0.0406 155 | 0/8 8 h-lim-p 0.0051 0.4314 0.2067 2041.987030 0 0.0152 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 2041.986890 2 0.9961 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2041.986890 0 1.0938 220 | 0/8 11 h-lim-p 1.2233 20.0000 0.0000 2041.986890 0 0.5352 240 | 0/8 12 h-lim-p 0.3042 20.0000 0.0000 2041.986890 0 0.0024 266 | 0/8 13 h-lim-p 0.0010 20.0000 0.0000 2041.986890 0 0.0000 305 | 0/8 14 h-lim-p 0.0000 20.0000 0.0007 2041.986890 0 0.0000 333 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 2041.986890 0 0.0026 361 | 0/8 16 h-lim-p 0.0051 20.0000 0.0002 2041.986890 0 0.0000 390 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0048 2041.986890 0 0.0000 455 | 0/8 19 h-lim-p 0.0000 20.0000 0.0013 2041.986890 0 0.0003 480 | 0/8 20 h-lim-p 0.0009 20.0000 0.0004 2041.986890 0 0.0000 506 | 0/8 21 h-lim-p 0.0000 20.0000 0.0018 .. | 0/8 22 h-lim-p 0.0000 20.0000 0.0045 2041.986890 0 0.0000 572 | 0/8 23 h-lim-p 0.0000 20.0000 0.0025 .. | 0/8 24 h-lim-p 0.0000 20.0000 0.0045 | 0/8 25 h-lim-p 0.0000 20.0000 0.0045 Out... lnL = -2041.986890 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2041.986890 Node 7: lnL = -2041.986890 Node 8: lnL = -2041.986890 Node 9: lnL = -2041.986890 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 392 Sequential format.. Reading seq # 1: YJR097W_Sbay Reading seq # 2: YJR097W_Scer Reading seq # 3: YJR097W_Skud Reading seq # 4: YJR097W_Smik Reading seq # 5: YJR097W_Spar Sequences read.. Counting patterns.. # site patterns = 204 Counting frequencies.. 120 bytes for distance 32640 bytes for lkl0 26112 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.189365 0.008272 0.089815 0.216456 0.130027 0.300137 0.261525 0.331392 lnL0 = -1995.867765 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1995.867765 x= 0.18937 0.00827 0.08982 0.21646 0.13003 0.30014 0.26152 0.33139 1 h-lim-p 0.0039 0.0312 80.4073 1994.341382 7 0.0005 40 | 0/8 2 h-lim-p 0.0013 0.0108 31.5885 1993.693151 7 0.0014 67 | 0/8 3 h-lim-p 0.0032 0.0259 13.2422 1993.636750 2 0.0008 84 | 0/8 4 h-lim-p 0.0021 0.0830 4.7220 1993.625392 6 0.0012 111 | 0/8 5 h-lim-p 0.0077 0.5249 0.7173 1993.624953 2 0.0017 128 | 0/8 6 h-lim-p 0.0069 1.2151 0.1741 1993.624924 2 0.0016 153 | 0/8 7 h-lim-p 0.0076 15.3695 0.0375 1993.624862 0 0.0151 174 | 0/8 8 h-lim-p 0.0312 20.0000 0.0182 1993.620137 0 0.1247 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 1993.619988 2 0.9961 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1993.619988 0 1.0938 240 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1993.619988 0 1.0938 260 | 0/8 12 h-lim-p 1.7443 20.0000 0.0000 1993.619988 0 0.7631 280 | 0/8 13 h-lim-p 0.5052 20.0000 0.0000 1993.619988 0 0.2526 300 | 0/8 14 h-lim-p 0.0790 20.0000 0.0000 1993.619988 0 0.0006 326 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 1993.619988 0 0.0000 360 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1993.619988 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1993.619988 Node 7: lnL = -1993.619988 Node 8: lnL = -1993.619988 Node 9: lnL = -1993.619988 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 453 Sequential format.. Reading seq # 1: YJR099W_Sbay Reading seq # 2: YJR099W_Scer Reading seq # 3: YJR099W_Skud Reading seq # 4: YJR099W_Smik Reading seq # 5: YJR099W_Spar Sequences read.. Counting patterns.. # site patterns = 240 Counting frequencies.. 120 bytes for distance 38400 bytes for lkl0 30720 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.079811 0.151386 0.040685 0.193229 0.158056 0.271200 0.210959 0.206701 lnL0 = -2153.668373 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2153.668373 x= 0.07981 0.15139 0.04069 0.19323 0.15806 0.27120 0.21096 0.20670 1 h-lim-p 0.0027 0.0217 87.3238 2152.309037 8 0.0004 41 | 0/8 2 h-lim-p 0.0015 0.0116 21.8968 2152.094481 7 0.0009 69 | 0/8 3 h-lim-p 0.0025 0.0412 8.0800 2152.071476 6 0.0008 95 | 0/8 4 h-lim-p 0.0045 0.1961 1.4471 2152.070471 2 0.0010 112 | 0/8 5 h-lim-p 0.0061 1.0823 0.2336 2152.070450 2 0.0008 130 | 0/8 6 h-lim-p 0.0037 7.7055 0.0504 2152.070449 1 0.0009 153 | 0/8 7 h-lim-p 0.0277 20.0000 0.0017 2152.070447 0 0.0416 173 | 0/8 8 h-lim-p 0.0161 20.0000 0.0043 2152.070409 0 0.0644 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2152.070405 1 0.9961 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2152.070405 0 1.0938 237 | 0/8 11 h-lim-p 1.0610 20.0000 0.0000 2152.070405 0 1.0610 257 | 0/8 12 h-lim-p 0.0142 20.0000 0.0006 2152.070405 0 0.0018 279 | 0/8 13 h-lim-p 0.0001 11.6028 0.0092 2152.070405 0 0.0000 304 | 0/8 14 h-lim-p 0.0003 20.0000 0.0001 2152.070405 0 0.0000 341 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 2152.070405 0 0.0000 368 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 2152.070405 0 0.0000 398 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 2152.070405 0 0.0000 433 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -2152.070405 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2152.070405 Node 7: lnL = -2152.070405 Node 8: lnL = -2152.070405 Node 9: lnL = -2152.070405 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 840 Sequential format.. Reading seq # 1: YJR100C_Sbay Reading seq # 2: YJR100C_Scer Reading seq # 3: YJR100C_Skud Reading seq # 4: YJR100C_Smik Reading seq # 5: YJR100C_Spar Sequences read.. Counting patterns.. # site patterns = 214 Counting frequencies.. 120 bytes for distance 34240 bytes for lkl0 27392 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.282742 0.000060 0.002758 0.729973 1.079272 0.156102 0.703903 0.572352 lnL0 = -3641.298793 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3641.298793 x= 0.28274 0.00006 0.00276 0.72997 1.07927 0.15610 0.70390 0.57235 1 h-lim-p 0.0000 0.0001 46.7867 3641.167970 m 0.0001 22 | 1/8 2 h-lim-p 0.0000 0.0003 17.0134 3641.088605 m 0.0003 34 | 2/8 3 h-lim-p 0.0003 0.0529 15.4629 3638.058710 0 0.0106 51 | 1/8 4 h-lim-p 0.0036 0.0291 35.6327 3635.901441 0 0.0073 64 | 1/8 5 h-lim-p 0.0169 0.1353 5.8748 3635.796899 7 0.0063 94 | 1/8 6 h-lim-p 0.0153 0.5500 2.4054 3635.758639 4 0.0148 115 | 0/8 7 h-lim-p 0.0032 0.2092 11.1959 3635.678774 5 0.0034 140 | 0/8 8 h-lim-p 0.0076 0.0605 1.2909 3635.665192 0 0.0302 154 | 0/8 9 h-lim-p 0.0292 0.2338 0.0839 3635.569353 m 0.2338 166 | 0/8 10 h-lim-p -0.0000 -0.0000 0.0697 h-lim-p: -1.59118417e-18 -1.27294734e-17 6.97268177e-02 3635.569353 .. | 0/8 11 h-lim-p 0.0000 7.7546 7.1700 3635.523014 0 0.0026 210 | 0/8 12 h-lim-p 0.0000 0.0000 4.4754 3635.522785 m 0.0000 222 | 1/8 13 h-lim-p 0.0000 0.1023 2.4701 3635.519177 0 0.0016 240 | 1/8 14 h-lim-p 0.0021 0.1467 1.9334 3635.515012 0 0.0041 253 | 1/8 15 h-lim-p 0.0105 0.3306 0.7625 3635.513250 4 0.0079 273 | 1/8 16 h-lim-p 0.0287 7.7312 0.2101 3635.512875 4 0.0177 304 | 1/8 17 h-lim-p 0.0108 3.9421 0.3446 3635.511974 0 0.0325 324 | 1/8 18 h-lim-p 2.5000 20.0000 0.0030 3635.507785 2 2.3438 347 | 1/8 19 h-lim-p 2.5000 20.0000 0.0013 3635.507645 1 1.0938 368 | 1/8 20 h-lim-p 2.5000 20.0000 0.0001 3635.507645 0 1.0938 387 | 1/8 21 h-lim-p 2.5000 20.0000 0.0000 3635.507645 0 1.0938 406 | 1/8 22 h-lim-p 2.5000 20.0000 0.0000 3635.507645 0 1.0938 425 | 1/8 23 h-lim-p 0.8412 20.0000 0.0000 3635.507645 0 0.0000 467 Out... lnL = -3635.507645 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3635.507645 Node 7: lnL = -3635.507645 Node 8: lnL = -3635.507645 Node 9: lnL = -3635.507645 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 838 Sequential format.. Reading seq # 1: YJR101W_Sbay Reading seq # 2: YJR101W_Scer Reading seq # 3: YJR101W_Skud Reading seq # 4: YJR101W_Smik Reading seq # 5: YJR101W_Spar Sequences read.. Counting patterns.. # site patterns = 475 Counting frequencies.. 120 bytes for distance 76000 bytes for lkl0 60800 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.122792 0.020654 0.139774 0.264519 0.180379 0.331377 0.430585 0.290478 lnL0 = -4409.427366 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4409.427366 x= 0.12279 0.02065 0.13977 0.26452 0.18038 0.33138 0.43058 0.29048 1 h-lim-p 0.0028 0.7455 176.8259 4404.344256 4 0.0004 32 | 0/8 2 h-lim-p 0.0042 0.0335 15.0225 4404.179926 7 0.0014 62 | 0/8 3 h-lim-p 0.0032 0.0819 6.8002 4404.161469 5 0.0009 87 | 0/8 4 h-lim-p 0.0030 0.1770 2.1243 4404.159903 4 0.0008 108 | 0/8 5 h-lim-p 0.0078 1.8553 0.2155 4404.159870 2 0.0012 126 | 0/8 6 h-lim-p 0.0130 14.8031 0.0205 4404.159845 0 0.0130 146 | 0/8 7 h-lim-p 0.0138 20.0000 0.0193 4404.158511 0 0.0830 168 | 0/8 8 h-lim-p 0.0026 1.0386 0.6231 4404.157538 3 0.0022 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4404.157529 1 0.9961 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4404.157529 0 1.0938 236 | 0/8 11 h-lim-p 1.6052 20.0000 0.0000 4404.157529 0 1.4045 256 | 0/8 12 h-lim-p 1.1048 20.0000 0.0000 4404.157529 0 3.3144 277 | 0/8 13 h-lim-p 0.1032 20.0000 0.0003 4404.157529 0 0.0008 303 | 0/8 14 h-lim-p 0.0012 20.0000 0.0002 4404.157529 0 0.0000 339 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -4404.157529 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4404.157529 Node 7: lnL = -4404.157529 Node 8: lnL = -4404.157529 Node 9: lnL = -4404.157529 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 886 Sequential format.. Reading seq # 1: YJR102C_Sbay Reading seq # 2: YJR102C_Scer Reading seq # 3: YJR102C_Skud Reading seq # 4: YJR102C_Smik Reading seq # 5: YJR102C_Spar Sequences read.. Counting patterns.. # site patterns = 360 Counting frequencies.. 120 bytes for distance 57600 bytes for lkl0 46080 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.090096 0.188981 0.050879 0.170432 0.160662 0.255055 0.294598 0.230807 lnL0 = -4401.554246 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4401.554246 x= 0.09010 0.18898 0.05088 0.17043 0.16066 0.25505 0.29460 0.23081 1 h-lim-p 0.0044 0.7658 140.9893 4399.488115 6 0.0002 38 | 0/8 2 h-lim-p 0.0022 0.0180 14.6731 4399.434329 2 0.0005 55 | 0/8 3 h-lim-p 0.0009 0.0489 7.8732 4399.419615 6 0.0006 82 | 0/8 4 h-lim-p 0.0035 0.3231 1.3091 4399.419038 3 0.0007 101 | 0/8 5 h-lim-p 0.0023 0.9635 0.4015 4399.418991 3 0.0006 120 | 0/8 6 h-lim-p 0.0039 5.7029 0.0634 4399.418991 0 0.0009 141 | 0/8 7 h-lim-p 0.0146 20.0000 0.0037 4399.418985 0 0.0293 162 | 0/8 8 h-lim-p 0.0099 20.0000 0.0109 4399.418741 0 0.0397 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4399.418736 0 1.0938 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4399.418736 0 1.0938 224 | 0/8 11 h-lim-p 1.4236 20.0000 0.0000 4399.418736 0 1.4236 244 | 0/8 12 h-lim-p 1.2464 20.0000 0.0000 4399.418736 0 0.0779 267 | 0/8 13 h-lim-p 0.0056 20.0000 0.0002 4399.418736 0 0.0000 293 | 0/8 14 h-lim-p 0.0005 20.0000 0.0000 4399.418736 0 0.0000 323 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 4399.418736 0 0.0001 343 Out... lnL = -4399.418736 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4399.418736 Node 7: lnL = -4399.418736 Node 8: lnL = -4399.418736 Node 9: lnL = -4399.418736 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 885 Sequential format.. Reading seq # 1: YJR103W_Sbay Reading seq # 2: YJR103W_Scer Reading seq # 3: YJR103W_Skud Reading seq # 4: YJR103W_Smik Reading seq # 5: YJR103W_Spar Sequences read.. Counting patterns.. # site patterns = 363 Counting frequencies.. 120 bytes for distance 58080 bytes for lkl0 46464 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.050910 0.181702 0.007173 0.210029 1.001873 0.260493 0.232197 0.257881 lnL0 = -3954.774825 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3954.774825 x= 0.05091 0.18170 0.00717 0.21003 1.00187 0.26049 0.23220 0.25788 1 h-lim-p 0.0002 0.0013 98.9883 3951.584439 0 0.0007 24 | 0/8 2 h-lim-p 0.0002 0.0017 30.1165 3951.443328 0 0.0004 37 | 0/8 3 h-lim-p 0.0013 0.0469 9.4341 3951.402036 4 0.0010 57 | 0/8 4 h-lim-p 0.0006 0.0173 17.1289 3951.318676 0 0.0017 70 | 0/8 5 h-lim-p 0.0022 0.0180 13.2059 3951.283693 2 0.0010 86 | 0/8 6 h-lim-p 0.0104 0.3256 1.3216 3951.282851 3 0.0010 106 | 0/8 7 h-lim-p 0.0026 1.9223 0.5205 3951.280008 0 0.0204 121 | 0/8 8 h-lim-p 1.8679 20.0000 0.0057 3951.267554 2 0.8756 145 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 3951.267483 2 1.0938 169 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3951.267483 0 1.0938 189 | 0/8 11 h-lim-p 1.3371 20.0000 0.0000 3951.267483 0 1.1699 209 | 0/8 12 h-lim-p 0.5987 20.0000 0.0000 3951.267483 0 0.0748 231 | 0/8 13 h-lim-p 0.0059 20.0000 0.0006 3951.267483 0 0.0000 273 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -3951.267483 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3951.267483 Node 7: lnL = -3951.267483 Node 8: lnL = -3951.267483 Node 9: lnL = -3951.267483 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 614 Sequential format.. Reading seq # 1: YJR104C_Sbay Reading seq # 2: YJR104C_Scer Reading seq # 3: YJR104C_Skud Reading seq # 4: YJR104C_Smik Reading seq # 5: YJR104C_Spar Sequences read.. Counting patterns.. # site patterns = 195 Counting frequencies.. 120 bytes for distance 31200 bytes for lkl0 24960 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.078168 0.019591 0.055988 0.085752 0.068331 0.123625 0.207588 0.152944 lnL0 = -2504.125838 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2504.125838 x= 0.07817 0.01959 0.05599 0.08575 0.06833 0.12362 0.20759 0.15294 1 h-lim-p 0.0005 0.0043 225.1515 2501.176980 9 0.0001 42 | 0/8 2 h-lim-p 0.0006 0.0048 23.7941 2501.102335 4 0.0003 61 | 0/8 3 h-lim-p 0.0010 0.0332 6.5707 2501.098102 3 0.0002 80 | 0/8 4 h-lim-p 0.0006 0.0722 2.2038 2501.097483 2 0.0003 96 | 0/8 5 h-lim-p 0.0013 0.4572 0.4919 2501.097423 2 0.0005 112 | 0/8 6 h-lim-p 0.0030 2.3389 0.0878 2501.097422 0 0.0003 134 | 0/8 7 h-lim-p 0.0035 17.6756 0.0081 2501.097422 0 0.0008 155 | 0/8 8 h-lim-p 0.0267 20.0000 0.0002 2501.097369 0 0.6408 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2501.097369 0 1.0938 199 | 0/8 10 h-lim-p 2.3381 20.0000 0.0000 2501.097369 0 2.0459 219 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2501.097369 0 1.0938 239 | 0/8 12 h-lim-p 0.1693 20.0000 0.0000 2501.097369 0 4.0627 263 | 0/8 13 h-lim-p 0.3449 20.0000 0.0002 2501.097369 0 0.0755 284 | 0/8 14 h-lim-p 0.0086 20.0000 0.0013 2501.097369 0 0.0000 328 | 0/8 15 h-lim-p 0.0000 20.0000 0.0010 | 0/8 16 h-lim-p 0.0000 20.0000 0.0010 Out... lnL = -2501.097369 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2501.097369 Node 7: lnL = -2501.097369 Node 8: lnL = -2501.097369 Node 9: lnL = -2501.097369 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 342 Sequential format.. Reading seq # 1: YJR107W_Sbay Reading seq # 2: YJR107W_Scer Reading seq # 3: YJR107W_Skud Reading seq # 4: YJR107W_Smik Reading seq # 5: YJR107W_Spar Sequences read.. Counting patterns.. # site patterns = 152 Counting frequencies.. 120 bytes for distance 24320 bytes for lkl0 19456 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.087489 0.006371 0.186798 0.115743 0.065862 0.243855 0.183292 0.193809 lnL0 = -1402.019085 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1402.019085 x= 0.08749 0.00637 0.18680 0.11574 0.06586 0.24386 0.18329 0.19381 1 h-lim-p 0.0021 0.0166 99.5460 1400.335337 4 0.0004 31 | 0/8 2 h-lim-p 0.0015 0.0121 14.7128 1400.213892 8 0.0011 62 | 0/8 3 h-lim-p 0.0014 0.0280 11.9139 1400.188742 6 0.0005 86 | 0/8 4 h-lim-p 0.0014 0.0528 4.5286 1400.180368 6 0.0010 112 | 0/8 5 h-lim-p 0.0038 0.2093 1.2084 1400.179627 5 0.0011 136 | 0/8 6 h-lim-p 0.0057 0.8840 0.2357 1400.179594 2 0.0013 153 | 0/8 7 h-lim-p 0.0423 20.0000 0.0070 1400.179594 0 0.0046 175 | 0/8 8 h-lim-p 0.0922 20.0000 0.0003 1400.179559 0 0.7379 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1400.179557 0 1.0938 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1400.179557 0 1.0938 238 | 0/8 11 h-lim-p 1.1760 20.0000 0.0000 1400.179557 0 4.7041 260 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1400.179557 0 0.0098 287 | 0/8 13 h-lim-p 0.0010 20.0000 0.0000 1400.179557 0 0.0003 308 | 0/8 14 h-lim-p 0.0001 20.0000 0.0001 1400.179557 0 0.0000 332 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 1400.179557 0 0.0000 356 Out... lnL = -1400.179557 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1400.179557 Node 7: lnL = -1400.179557 Node 8: lnL = -1400.179557 Node 9: lnL = -1400.179557 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 354 Sequential format.. Reading seq # 1: YJR111C_Sbay Reading seq # 2: YJR111C_Scer Reading seq # 3: YJR111C_Skud Reading seq # 4: YJR111C_Smik Reading seq # 5: YJR111C_Spar Sequences read.. Counting patterns.. # site patterns = 140 Counting frequencies.. 120 bytes for distance 22400 bytes for lkl0 17920 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.086836 0.027141 0.014468 0.142820 0.107968 0.172081 0.198676 0.171778 lnL0 = -1494.362286 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1494.362286 x= 0.08684 0.02714 0.01447 0.14282 0.10797 0.17208 0.19868 0.17178 1 h-lim-p 0.0009 0.7002 182.7320 1492.242172 9 0.0002 48 | 0/8 2 h-lim-p 0.0003 0.0027 28.7202 1492.079129 1 0.0004 62 | 0/8 3 h-lim-p 0.0018 0.0193 6.6324 1492.064933 6 0.0007 87 | 0/8 4 h-lim-p 0.0066 0.3613 0.6731 1492.064720 4 0.0009 111 | 0/8 5 h-lim-p 0.0023 1.1936 0.2768 1492.064700 2 0.0006 136 | 0/8 6 h-lim-p 0.0054 6.7668 0.0307 1492.064699 0 0.0014 157 | 0/8 7 h-lim-p 0.0087 20.0000 0.0048 1492.064680 0 0.0347 179 | 0/8 8 h-lim-p 0.0045 1.6059 0.0367 1492.064254 0 0.0181 201 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1492.064230 0 1.2500 221 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1492.064230 0 1.0938 241 | 0/8 11 h-lim-p 2.3630 20.0000 0.0000 1492.064230 0 1.0338 261 | 0/8 12 h-lim-p 0.9512 20.0000 0.0000 1492.064230 0 0.4756 281 | 0/8 13 h-lim-p 0.0021 20.0000 0.0016 1492.064230 0 0.0011 301 | 0/8 14 h-lim-p 0.0006 20.0000 0.0028 1492.064230 0 0.0000 341 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1492.064230 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1492.064230 Node 7: lnL = -1492.064230 Node 8: lnL = -1492.064230 Node 9: lnL = -1492.064230 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 861 Sequential format.. Reading seq # 1: YJR113C_Sbay Reading seq # 2: YJR113C_Scer Reading seq # 3: YJR113C_Skud Reading seq # 4: YJR113C_Smik Reading seq # 5: YJR113C_Spar Sequences read.. Counting patterns.. # site patterns = 407 Counting frequencies.. 120 bytes for distance 65120 bytes for lkl0 52096 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.248850 0.478429 0.088757 0.179528 0.033685 0.298694 0.321986 0.447481 lnL0 = -4504.741345 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4504.741345 x= 0.24885 0.47843 0.08876 0.17953 0.03369 0.29869 0.32199 0.44748 1 h-lim-p 0.0071 1.1379 112.6860 4503.499301 3 0.0002 32 | 0/8 2 h-lim-p 0.0005 0.0072 45.7629 4503.035115 5 0.0005 55 | 0/8 3 h-lim-p 0.0012 0.0191 18.5680 4502.805824 0 0.0019 67 | 0/8 4 h-lim-p 0.0023 0.0182 9.4293 4502.780724 5 0.0007 91 | 0/8 5 h-lim-p 0.0017 0.0878 3.9343 4502.764035 0 0.0035 104 | 0/8 6 h-lim-p 0.0047 0.2733 2.8984 4502.758147 2 0.0022 120 | 0/8 7 h-lim-p 0.0132 1.2425 0.4870 4502.757796 2 0.0029 137 | 0/8 8 h-lim-p 0.2120 20.0000 0.0066 4502.745165 0 0.8481 159 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 4502.744868 2 1.0938 183 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 4502.744866 0 1.0938 203 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4502.744866 0 2.1875 223 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4502.744866 0 1.0938 243 | 0/8 13 h-lim-p 0.6023 20.0000 0.0000 4502.744866 0 4.8182 266 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 4502.744866 0 0.0049 294 | 0/8 15 h-lim-p 0.0071 20.0000 0.0000 4502.744866 0 0.0000 334 Out... lnL = -4502.744866 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4502.744866 Node 7: lnL = -4502.744866 Node 8: lnL = -4502.744866 Node 9: lnL = -4502.744866 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 435 Sequential format.. Reading seq # 1: YJR116W_Sbay Reading seq # 2: YJR116W_Scer Reading seq # 3: YJR116W_Skud Reading seq # 4: YJR116W_Smik Reading seq # 5: YJR116W_Spar Sequences read.. Counting patterns.. # site patterns = 99 Counting frequencies.. 120 bytes for distance 15840 bytes for lkl0 12672 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.153837 0.061814 0.137453 0.070241 0.115187 4.587557 0.312837 lnL0 = -1317.838463 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1317.838463 x= 0.00006 0.15384 0.06181 0.13745 0.07024 0.11519 4.58756 0.31284 1 h-lim-p 0.0000 0.0000 250.4242 1317.738280 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0024 108.1918 1314.653919 0 0.0006 40 | 1/8 3 h-lim-p 0.0007 0.0053 42.6876 1313.964120 0 0.0010 52 | 1/8 4 h-lim-p 0.0057 0.0457 5.0091 1313.901578 7 0.0021 82 | 1/8 5 h-lim-p 0.0215 0.2320 0.4855 1304.611198 5 0.1575 106 | 1/8 6 h-lim-p 0.0005 0.0039 46.5572 1303.182269 0 0.0010 126 | 1/8 7 h-lim-p 0.2201 1.7612 0.0652 1302.248815 0 0.4403 139 | 0/8 8 h-lim-p 0.0067 0.1741 4.2820 1302.233885 2 0.0016 163 | 0/8 9 h-lim-p 0.3148 4.9309 0.0214 1302.014208 0 0.6297 176 | 0/8 10 h-lim-p 1.7669 20.0000 0.0076 1301.994060 5 0.5766 209 | 0/8 11 h-lim-p 2.4537 20.0000 0.0018 1301.992396 3 0.5559 236 | 0/8 12 h-lim-p 2.5000 20.0000 0.0003 1301.992329 3 0.8855 264 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1301.992329 0 1.0938 284 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1301.992329 0 1.0938 304 | 0/8 15 h-lim-p 1.0959 20.0000 0.0000 1301.992329 0 8.7671 327 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1301.992329 0 0.2734 349 | 0/8 17 h-lim-p 0.8546 20.0000 0.0000 1301.992329 0 0.0100 375 | 0/8 18 h-lim-p 0.0018 20.0000 0.0000 1301.992329 0 0.0001 398 | 0/8 19 h-lim-p 0.0001 20.0000 0.0001 1301.992329 0 0.0000 424 | 0/8 20 h-lim-p 0.0000 20.0000 0.0000 1301.992329 0 0.0000 456 Out... lnL = -1301.992329 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1301.992329 Node 7: lnL = -1301.992329 Node 8: lnL = -1301.992329 Node 9: lnL = -1301.992329 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 370 Sequential format.. Reading seq # 1: YJR117W_Sbay Reading seq # 2: YJR117W_Scer Reading seq # 3: YJR117W_Skud Reading seq # 4: YJR117W_Smik Reading seq # 5: YJR117W_Spar Sequences read.. Counting patterns.. # site patterns = 149 Counting frequencies.. 120 bytes for distance 23840 bytes for lkl0 19072 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.121295 0.176399 0.032347 0.145734 0.039616 0.267932 0.280921 0.238697 lnL0 = -1525.232800 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1525.232800 x= 0.12129 0.17640 0.03235 0.14573 0.03962 0.26793 0.28092 0.23870 1 h-lim-p 0.0003 0.0020 44.2070 1524.762467 0 0.0005 23 | 0/8 2 h-lim-p 0.0016 0.0581 14.2901 1524.732780 3 0.0003 42 | 0/8 3 h-lim-p 0.0006 0.0132 8.4651 1524.714733 1 0.0007 56 | 0/8 4 h-lim-p 0.0016 0.0850 3.7250 1524.706877 3 0.0014 74 | 0/8 5 h-lim-p 0.0064 0.2934 0.8414 1524.706250 5 0.0019 99 | 0/8 6 h-lim-p 0.0137 8.6919 0.1164 1524.706239 0 0.0017 121 | 0/8 7 h-lim-p 0.0076 13.1612 0.0262 1524.706237 0 0.0038 141 | 0/8 8 h-lim-p 0.1837 20.0000 0.0005 1524.706128 0 0.7349 163 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1524.706127 0 1.0938 183 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1524.706127 0 1.0938 203 | 0/8 11 h-lim-p 1.4199 20.0000 0.0000 1524.706127 0 2.8398 224 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1524.706127 0 0.0781 248 | 0/8 13 h-lim-p 0.0094 20.0000 0.0000 1524.706127 0 0.0000 286 Out... lnL = -1524.706127 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1524.706127 Node 7: lnL = -1524.706127 Node 8: lnL = -1524.706127 Node 9: lnL = -1524.706127 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 225 Sequential format.. Reading seq # 1: YJR118C_Sbay Reading seq # 2: YJR118C_Scer Reading seq # 3: YJR118C_Skud Reading seq # 4: YJR118C_Smik Reading seq # 5: YJR118C_Spar Sequences read.. Counting patterns.. # site patterns = 112 Counting frequencies.. 120 bytes for distance 17920 bytes for lkl0 14336 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.117324 0.094950 0.064623 0.070025 0.085801 0.136559 0.416109 0.224950 lnL0 = -1003.096234 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1003.096234 x= 0.11732 0.09495 0.06462 0.07002 0.08580 0.13656 0.41611 0.22495 1 h-lim-p 0.0005 0.0036 32.2848 1002.715429 0 0.0009 23 | 0/8 2 h-lim-p 0.0012 0.0165 24.6446 1002.503579 5 0.0010 44 | 0/8 3 h-lim-p 0.0015 0.0124 15.2543 1002.434189 7 0.0009 74 | 0/8 4 h-lim-p 0.0026 0.0300 5.1077 1002.421511 5 0.0012 95 | 0/8 5 h-lim-p 0.0097 0.2876 0.6180 1002.421237 5 0.0014 121 | 0/8 6 h-lim-p 0.0012 0.5620 0.7338 1002.420955 0 0.0023 142 | 0/8 7 h-lim-p 0.0049 0.6798 0.3506 1002.420819 4 0.0025 171 | 0/8 8 h-lim-p 0.1492 20.0000 0.0059 1002.411422 0 0.8951 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0009 1002.411029 3 1.0004 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1002.411029 0 1.0938 239 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1002.411029 0 1.0938 259 | 0/8 12 h-lim-p 1.4348 20.0000 0.0000 1002.411029 0 5.7391 281 | 0/8 13 h-lim-p 1.9657 20.0000 0.0000 1002.411029 0 0.2150 303 | 0/8 14 h-lim-p 0.7099 20.0000 0.0000 1002.411029 0 0.0111 328 | 0/8 15 h-lim-p 0.0139 20.0000 0.0000 1002.411029 0 0.0000 373 Out... lnL = -1002.411029 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1002.411029 Node 7: lnL = -1002.411029 Node 8: lnL = -1002.411029 Node 9: lnL = -1002.411029 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 664 Sequential format.. Reading seq # 1: YJR119C_Sbay Reading seq # 2: YJR119C_Scer Reading seq # 3: YJR119C_Skud Reading seq # 4: YJR119C_Smik Reading seq # 5: YJR119C_Spar Sequences read.. Counting patterns.. # site patterns = 326 Counting frequencies.. 120 bytes for distance 52160 bytes for lkl0 41728 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.155874 0.092095 0.104324 0.177263 0.146191 0.262401 0.180888 0.280849 lnL0 = -3246.917418 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3246.917418 x= 0.15587 0.09209 0.10432 0.17726 0.14619 0.26240 0.18089 0.28085 1 h-lim-p 0.0014 0.0113 122.3193 3243.886934 9 0.0004 45 | 0/8 2 h-lim-p 0.0014 0.0110 20.9967 3243.764876 3 0.0006 63 | 0/8 3 h-lim-p 0.0013 0.0537 8.9485 3243.746707 4 0.0005 83 | 0/8 4 h-lim-p 0.0017 0.1076 2.8330 3243.743445 5 0.0009 106 | 0/8 5 h-lim-p 0.0051 0.4432 0.5060 3243.743289 1 0.0013 121 | 0/8 6 h-lim-p 0.0128 5.1623 0.0506 3243.743287 0 0.0014 143 | 0/8 7 h-lim-p 0.0042 16.1860 0.0166 3243.743286 0 0.0037 163 | 0/8 8 h-lim-p 0.0430 20.0000 0.0014 3243.743033 0 0.3437 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3243.743030 0 1.0938 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3243.743030 0 1.0938 226 | 0/8 11 h-lim-p 1.5192 20.0000 0.0000 3243.743030 0 1.3293 246 | 0/8 12 h-lim-p 1.2593 20.0000 0.0000 3243.743030 0 0.6297 266 | 0/8 13 h-lim-p 0.0585 20.0000 0.0000 3243.743030 0 0.0000 300 | 0/8 14 h-lim-p 0.0012 20.0000 0.0000 3243.743030 0 0.0000 327 Out... lnL = -3243.743030 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3243.743030 Node 7: lnL = -3243.743030 Node 8: lnL = -3243.743030 Node 9: lnL = -3243.743030 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 135 Sequential format.. Reading seq # 1: YJR121W_Sbay Reading seq # 2: YJR121W_Scer Reading seq # 3: YJR121W_Skud Reading seq # 4: YJR121W_Smik Reading seq # 5: YJR121W_Spar Sequences read.. Counting patterns.. # site patterns = 34 Counting frequencies.. 120 bytes for distance 5440 bytes for lkl0 4352 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.030223 0.007447 0.023932 0.004439 0.019000 0.016612 0.090825 0.051920 lnL0 = -342.910044 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 342.910044 x= 0.03022 0.00745 0.02393 0.00444 0.01900 0.01661 0.09083 0.05192 1 h-lim-p 0.0000 0.0000 143.1312 342.201631 m 0.0000 22 | 1/8 2 h-lim-p 0.0001 0.0005 34.2450 342.124509 0 0.0001 35 | 1/8 3 h-lim-p 0.0005 0.0037 9.1612 342.118071 6 0.0002 62 | 1/8 4 h-lim-p 0.0003 0.0055 4.4987 342.116326 6 0.0002 91 | 1/8 5 h-lim-p 0.0011 0.0925 0.8350 342.115568 4 0.0012 112 | 1/8 6 h-lim-p 0.0006 0.0356 1.6214 342.115074 4 0.0004 142 | 1/8 7 h-lim-p 0.0146 0.9255 0.0397 341.832496 0 0.3505 158 | 1/8 8 h-lim-p 2.5000 20.0000 0.0027 341.817157 7 0.7017 195 | 1/8 9 h-lim-p 2.5000 20.0000 0.0007 341.816193 2 1.0889 218 | 1/8 10 h-lim-p 2.5000 20.0000 0.0000 341.816187 3 1.3437 244 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 341.816187 0 1.0938 263 | 1/8 12 h-lim-p 1.2674 20.0000 0.0000 341.816187 0 0.0000 296 Out... lnL = -341.816187 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -341.816187 Node 7: lnL = -341.816187 Node 8: lnL = -341.816187 Node 9: lnL = -341.816187 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 673 Sequential format.. Reading seq # 1: YJR122W_Sbay Reading seq # 2: YJR122W_Scer Reading seq # 3: YJR122W_Skud Reading seq # 4: YJR122W_Smik Reading seq # 5: YJR122W_Spar Sequences read.. Counting patterns.. # site patterns = 229 Counting frequencies.. 120 bytes for distance 36640 bytes for lkl0 29312 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.025586 0.128527 0.034668 0.116329 0.080805 0.145191 0.152456 0.097556 lnL0 = -2726.206499 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2726.206499 x= 0.02559 0.12853 0.03467 0.11633 0.08081 0.14519 0.15246 0.09756 1 h-lim-p 0.0011 0.0104 220.3352 2723.261439 6 0.0001 35 | 0/8 2 h-lim-p 0.0004 0.0034 60.4446 2722.691003 4 0.0003 55 | 0/8 3 h-lim-p 0.0006 0.0045 21.0302 2722.651159 6 0.0002 83 | 0/8 4 h-lim-p 0.0013 0.0564 3.2446 2722.649392 4 0.0003 104 | 0/8 5 h-lim-p 0.0018 0.4089 0.6405 2722.649316 2 0.0004 121 | 0/8 6 h-lim-p 0.0015 0.4278 0.1657 2722.649313 1 0.0002 145 | 0/8 7 h-lim-p 0.0007 5.6334 0.0414 2722.649313 0 0.0004 165 | 0/8 8 h-lim-p 0.1146 20.0000 0.0001 2722.649289 0 0.9172 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2722.649288 0 1.0938 208 | 0/8 10 h-lim-p 1.4249 20.0000 0.0000 2722.649288 0 1.2468 228 | 0/8 11 h-lim-p 1.4399 20.0000 0.0000 2722.649288 0 2.8798 249 | 0/8 12 h-lim-p 0.8120 20.0000 0.0001 2722.649288 0 0.0127 274 | 0/8 13 h-lim-p 0.0004 11.5207 0.0034 2722.649288 0 0.0004 294 | 0/8 14 h-lim-p 0.0000 0.8705 0.0447 2722.649288 0 0.0000 316 | 0/8 15 h-lim-p 0.0001 20.0000 0.0015 2722.649288 0 0.0000 355 | 0/8 16 h-lim-p 0.0000 20.0000 0.0031 2722.649288 0 0.0000 376 | 0/8 17 h-lim-p 0.0003 20.0000 0.0004 2722.649288 0 0.0010 398 | 0/8 18 h-lim-p 0.0026 20.0000 0.0001 2722.649288 0 0.0000 423 | 0/8 19 h-lim-p 0.0001 20.0000 0.0001 2722.649288 0 0.0001 443 | 0/8 20 h-lim-p 0.0000 20.0000 0.0002 2722.649288 0 0.0000 467 | 0/8 21 h-lim-p 0.0000 20.0000 0.0016 2722.649288 0 0.0000 490 | 0/8 22 h-lim-p 0.0000 2.7308 0.0142 2722.649288 0 0.0000 518 | 0/8 23 h-lim-p 0.0000 20.0000 0.0003 2722.649288 0 0.0000 543 | 0/8 24 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 25 h-lim-p 0.0000 20.0000 0.0030 | 0/8 26 h-lim-p 0.0000 20.0000 0.0030 Out... lnL = -2722.649288 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2722.649288 Node 7: lnL = -2722.649288 Node 8: lnL = -2722.649288 Node 9: lnL = -2722.649288 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 683 Sequential format.. Reading seq # 1: YJR123W_Sbay Reading seq # 2: YJR123W_Scer Reading seq # 3: YJR123W_Skud Reading seq # 4: YJR123W_Smik Reading seq # 5: YJR123W_Spar Sequences read.. Counting patterns.. # site patterns = 245 Counting frequencies.. 120 bytes for distance 39200 bytes for lkl0 31360 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.049292 0.054714 0.093283 0.089683 0.093310 0.198077 0.187477 0.130217 lnL0 = -2893.252481 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2893.252481 x= 0.04929 0.05471 0.09328 0.08968 0.09331 0.19808 0.18748 0.13022 1 h-lim-p 0.0028 0.8005 142.9819 2891.378022 8 0.0002 42 | 0/8 2 h-lim-p 0.0006 0.0049 21.3646 2891.307450 4 0.0003 63 | 0/8 3 h-lim-p 0.0008 0.0311 8.3017 2891.296030 2 0.0004 79 | 0/8 4 h-lim-p 0.0008 0.0515 3.7247 2891.294673 4 0.0002 102 | 0/8 5 h-lim-p 0.0017 0.4671 0.5087 2891.294628 1 0.0003 117 | 0/8 6 h-lim-p 0.0013 1.4873 0.1348 2891.294625 1 0.0003 140 | 0/8 7 h-lim-p 0.0015 6.9570 0.0295 2891.294625 0 0.0006 160 | 0/8 8 h-lim-p 0.1291 20.0000 0.0001 2891.294597 0 1.0331 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2891.294597 0 1.0938 203 | 0/8 10 h-lim-p 1.1127 20.0000 0.0000 2891.294597 0 0.9736 223 | 0/8 11 h-lim-p 0.8056 20.0000 0.0000 2891.294597 0 0.0000 256 | 0/8 12 h-lim-p 0.0007 20.0000 0.0000 2891.294597 0 0.0003 276 Out... lnL = -2891.294597 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2891.294597 Node 7: lnL = -2891.294597 Node 8: lnL = -2891.294597 Node 9: lnL = -2891.294597 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 528 Sequential format.. Reading seq # 1: YJR124C_Sbay Reading seq # 2: YJR124C_Scer Reading seq # 3: YJR124C_Skud Reading seq # 4: YJR124C_Smik Reading seq # 5: YJR124C_Spar Sequences read.. Counting patterns.. # site patterns = 258 Counting frequencies.. 120 bytes for distance 41280 bytes for lkl0 33024 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.102506 0.046286 0.101441 0.158516 0.102167 0.286305 0.255833 0.214404 lnL0 = -2451.419044 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2451.419044 x= 0.10251 0.04629 0.10144 0.15852 0.10217 0.28631 0.25583 0.21440 1 h-lim-p 0.0008 0.0060 48.4840 2450.880591 8 0.0005 42 | 0/8 2 h-lim-p 0.0012 0.0096 14.2241 2450.815345 7 0.0007 73 | 0/8 3 h-lim-p 0.0015 0.0582 6.6943 2450.803360 5 0.0007 94 | 0/8 4 h-lim-p 0.0009 0.0714 4.7680 2450.799470 6 0.0005 121 | 0/8 5 h-lim-p 0.0053 0.1723 0.4641 2450.799366 3 0.0010 140 | 0/8 6 h-lim-p 0.0069 5.0578 0.0674 2450.799364 1 0.0008 164 | 0/8 7 h-lim-p 0.0025 17.9766 0.0224 2450.799364 0 0.0011 184 | 0/8 8 h-lim-p 0.3798 20.0000 0.0001 2450.799360 0 1.1393 205 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2450.799360 0 1.0938 225 | 0/8 10 h-lim-p 2.0201 20.0000 0.0000 2450.799360 0 1.7676 245 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2450.799360 0 1.0938 265 | 0/8 12 h-lim-p 0.3757 20.0000 0.0000 2450.799360 0 1.1270 286 | 0/8 13 h-lim-p 0.0000 0.4888 0.2906 2450.799360 0 0.0011 311 | 0/8 14 h-lim-p 0.0651 20.0000 0.0047 2450.799360 0 0.0041 334 | 0/8 15 h-lim-p 0.0026 19.4777 0.0073 2450.799360 0 0.0007 355 | 0/8 16 h-lim-p 0.0014 20.0000 0.0035 2450.799360 0 0.0000 397 | 0/8 17 h-lim-p 0.0000 20.0000 0.0006 | 0/8 18 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -2450.799360 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2450.799360 Node 7: lnL = -2450.799360 Node 8: lnL = -2450.799360 Node 9: lnL = -2450.799360 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 346 Sequential format.. Reading seq # 1: YJR125C_Sbay Reading seq # 2: YJR125C_Scer Reading seq # 3: YJR125C_Skud Reading seq # 4: YJR125C_Smik Reading seq # 5: YJR125C_Spar Sequences read.. Counting patterns.. # site patterns = 154 Counting frequencies.. 120 bytes for distance 24640 bytes for lkl0 19712 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.102161 0.024127 0.067048 0.209752 0.085128 0.257039 0.253720 0.206531 lnL0 = -1532.767590 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1532.767590 x= 0.10216 0.02413 0.06705 0.20975 0.08513 0.25704 0.25372 0.20653 1 h-lim-p 0.0003 0.0027 124.2545 1529.880788 0 0.0005 22 | 0/8 2 h-lim-p 0.0004 0.0028 31.1036 1529.570298 0 0.0007 35 | 0/8 3 h-lim-p 0.0013 0.0378 17.6286 1529.468244 7 0.0009 63 | 0/8 4 h-lim-p 0.0069 0.1442 2.1911 1529.464226 3 0.0017 82 | 0/8 5 h-lim-p 0.0093 0.5836 0.3974 1529.464051 4 0.0017 104 | 0/8 6 h-lim-p 0.0122 5.4642 0.0558 1529.463252 0 0.0243 125 | 0/8 7 h-lim-p 0.0042 0.5155 0.3222 1529.450542 0 0.0168 147 | 0/8 8 h-lim-p 0.0032 0.0665 1.6982 1529.427337 0 0.0048 167 | 0/8 9 h-lim-p 2.5000 20.0000 0.0013 1529.426474 2 0.9644 183 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1529.426474 0 1.0938 203 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1529.426474 0 1.0938 223 | 0/8 12 h-lim-p 1.3354 20.0000 0.0000 1529.426474 0 1.1684 243 | 0/8 13 h-lim-p 0.9213 20.0000 0.0000 1529.426474 m20.0000 265 | 0/8 14 h-lim-p 0.0034 4.7884 0.0308 1529.426474 0 0.0545 289 | 0/8 15 h-lim-p 0.0066 0.5718 0.2551 1529.426474 0 0.0004 312 | 0/8 16 h-lim-p 0.0001 0.1240 1.1756 1529.426474 0 0.0000 349 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 1529.426474 0 0.0000 369 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 1529.426474 0 0.0000 401 | 0/8 19 h-lim-p 0.0000 20.0000 0.0009 | 0/8 20 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -1529.426474 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1529.426474 Node 7: lnL = -1529.426474 Node 8: lnL = -1529.426474 Node 9: lnL = -1529.426474 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 206 Sequential format.. Reading seq # 1: YJR129C_Sbay Reading seq # 2: YJR129C_Scer Reading seq # 3: YJR129C_Skud Reading seq # 4: YJR129C_Smik Reading seq # 5: YJR129C_Spar Sequences read.. Counting patterns.. # site patterns = 92 Counting frequencies.. 120 bytes for distance 14720 bytes for lkl0 11776 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.039442 0.107753 0.042148 0.080646 0.147743 0.191864 0.152463 0.119213 lnL0 = -850.791641 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 850.791641 x= 0.03944 0.10775 0.04215 0.08065 0.14774 0.19186 0.15246 0.11921 1 h-lim-p 0.0021 0.0168 43.1940 850.358416 7 0.0005 38 | 0/8 2 h-lim-p 0.0015 0.0121 8.4848 850.328254 7 0.0009 67 | 0/8 3 h-lim-p 0.0024 0.0618 3.0816 850.324656 6 0.0009 95 | 0/8 4 h-lim-p 0.0146 1.0375 0.1800 850.324635 3 0.0013 117 | 0/8 5 h-lim-p 0.0055 2.4012 0.0422 850.324634 0 0.0012 138 | 0/8 6 h-lim-p 0.0034 20.0000 0.0149 850.324634 0 0.0015 158 | 0/8 7 h-lim-p 0.4905 20.0000 0.0000 850.324633 0 0.9811 179 | 0/8 8 h-lim-p 0.0063 20.0000 0.0070 850.324633 0 0.0014 200 | 0/8 9 h-lim-p 1.0314 20.0000 0.0000 850.324633 0 1.5470 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 850.324633 0 1.0938 240 | 0/8 11 h-lim-p 0.8037 20.0000 0.0000 850.324633 0 3.2148 262 | 0/8 12 h-lim-p 0.1774 20.0000 0.0001 850.324633 0 0.0111 285 | 0/8 13 h-lim-p 0.0024 20.0000 0.0006 850.324633 0 0.0002 308 | 0/8 14 h-lim-p 0.0001 20.0000 0.0007 850.324633 0 0.0000 338 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 850.324633 0 0.0000 371 Out... lnL = -850.324633 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -850.324633 Node 7: lnL = -850.324633 Node 8: lnL = -850.324633 Node 9: lnL = -850.324633 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 385 Sequential format.. Reading seq # 1: YJR133W_Sbay Reading seq # 2: YJR133W_Scer Reading seq # 3: YJR133W_Skud Reading seq # 4: YJR133W_Smik Reading seq # 5: YJR133W_Spar Sequences read.. Counting patterns.. # site patterns = 166 Counting frequencies.. 120 bytes for distance 26560 bytes for lkl0 21248 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.119779 0.134809 0.055111 0.090750 0.091752 0.240990 0.190152 0.223363 lnL0 = -1738.430985 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1738.430985 x= 0.11978 0.13481 0.05511 0.09075 0.09175 0.24099 0.19015 0.22336 1 h-lim-p 0.0021 0.0166 78.8102 1737.234720 8 0.0004 43 | 0/8 2 h-lim-p 0.0006 0.0047 20.0221 1737.140354 3 0.0005 61 | 0/8 3 h-lim-p 0.0023 0.0535 4.2579 1737.134429 5 0.0007 86 | 0/8 4 h-lim-p 0.0018 0.1668 1.5967 1737.133301 5 0.0010 110 | 0/8 5 h-lim-p 0.0074 1.5127 0.2177 1737.133274 3 0.0011 132 | 0/8 6 h-lim-p 0.0069 6.9700 0.0342 1737.133273 0 0.0015 153 | 0/8 7 h-lim-p 0.0085 20.0000 0.0061 1737.133273 0 0.0075 173 | 0/8 8 h-lim-p 0.0342 20.0000 0.0013 1737.133190 0 0.2050 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1737.133189 0 1.0938 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1737.133189 0 1.0938 235 | 0/8 11 h-lim-p 1.7501 20.0000 0.0000 1737.133189 0 1.5314 255 | 0/8 12 h-lim-p 2.1294 20.0000 0.0000 1737.133189 0 0.1331 278 | 0/8 13 h-lim-p 0.0390 20.0000 0.0000 1737.133189 0 0.0012 302 | 0/8 14 h-lim-p 0.0003 20.0000 0.0000 1737.133189 0 0.0000 334 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -1737.133189 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1737.133189 Node 7: lnL = -1737.133189 Node 8: lnL = -1737.133189 Node 9: lnL = -1737.133189 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 218 Sequential format.. Reading seq # 1: YJR134C_Sbay Reading seq # 2: YJR134C_Scer Reading seq # 3: YJR134C_Skud Reading seq # 4: YJR134C_Smik Reading seq # 5: YJR134C_Spar Sequences read.. Counting patterns.. # site patterns = 97 Counting frequencies.. 120 bytes for distance 15520 bytes for lkl0 12416 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.091222 0.054819 0.061045 0.100332 0.070420 0.182983 0.201948 0.174221 lnL0 = -961.385400 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 961.385400 x= 0.09122 0.05482 0.06105 0.10033 0.07042 0.18298 0.20195 0.17422 1 h-lim-p 0.0005 0.0037 53.0748 960.619608 0 0.0007 22 | 0/8 2 h-lim-p 0.0036 0.0294 10.2372 960.561996 7 0.0011 51 | 0/8 3 h-lim-p 0.0025 0.0530 4.6448 960.552356 5 0.0011 75 | 0/8 4 h-lim-p 0.0025 0.0492 1.9330 960.551564 3 0.0005 94 | 0/8 5 h-lim-p 0.0018 0.5621 0.5342 960.551348 3 0.0015 112 | 0/8 6 h-lim-p 0.0436 12.7740 0.0180 960.548876 0 0.1742 134 | 0/8 7 h-lim-p 0.0054 0.1759 0.5832 960.534824 0 0.0108 155 | 0/8 8 h-lim-p 0.0035 0.0846 1.7940 960.532940 5 0.0010 187 | 0/8 9 h-lim-p 1.3331 20.0000 0.0014 960.531777 5 0.9743 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 960.531777 0 1.0938 231 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 960.531777 0 1.0938 251 | 0/8 12 h-lim-p 1.3688 20.0000 0.0000 960.531777 0 2.7376 272 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 960.531777 0 0.1562 295 | 0/8 14 h-lim-p 0.0134 20.0000 0.0000 960.531777 0 0.0050 316 | 0/8 15 h-lim-p 0.0019 20.0000 0.0000 960.531777 0 0.0000 344 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 960.531777 0 0.0000 374 Out... lnL = -960.531777 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -960.531777 Node 7: lnL = -960.531777 Node 8: lnL = -960.531777 Node 9: lnL = -960.531777 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 205 Sequential format.. Reading seq # 1: YJR135C_Sbay Reading seq # 2: YJR135C_Scer Reading seq # 3: YJR135C_Skud Reading seq # 4: YJR135C_Smik Reading seq # 5: YJR135C_Spar Sequences read.. Counting patterns.. # site patterns = 100 Counting frequencies.. 120 bytes for distance 16000 bytes for lkl0 12800 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.065803 0.123193 0.098003 0.122350 0.097391 0.161781 0.149099 0.148412 lnL0 = -900.160247 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 900.160247 x= 0.06580 0.12319 0.09800 0.12235 0.09739 0.16178 0.14910 0.14841 1 h-lim-p 0.0011 0.0085 13.4521 900.077574 3 0.0009 28 | 0/8 2 h-lim-p 0.0045 0.4466 2.6830 900.074671 5 0.0008 51 | 0/8 3 h-lim-p 0.0045 0.5924 0.4995 900.074506 4 0.0014 75 | 0/8 4 h-lim-p 0.0063 5.5072 0.1115 900.074500 2 0.0010 101 | 0/8 5 h-lim-p 0.0045 7.8156 0.0250 900.074500 1 0.0011 124 | 0/8 6 h-lim-p 0.0134 20.0000 0.0021 900.074500 0 0.0059 144 | 0/8 7 h-lim-p 0.0067 20.0000 0.0018 900.074499 0 0.0200 165 | 0/8 8 h-lim-p 0.0057 18.5753 0.0063 900.074494 0 0.0172 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 900.074494 0 1.0938 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 900.074494 0 1.0938 226 | 0/8 11 h-lim-p 1.0850 20.0000 0.0000 900.074494 0 0.0003 257 Out... lnL = -900.074494 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -900.074494 Node 7: lnL = -900.074494 Node 8: lnL = -900.074494 Node 9: lnL = -900.074494 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 205 Sequential format.. Reading seq # 1: YJR135W-A_Sbay Reading seq # 2: YJR135W-A_Scer Reading seq # 3: YJR135W-A_Skud Reading seq # 4: YJR135W-A_Smik Reading seq # 5: YJR135W-A_Spar Sequences read.. Counting patterns.. # site patterns = 100 Counting frequencies.. 120 bytes for distance 16000 bytes for lkl0 12800 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.071682 0.101703 0.106193 0.109747 0.109994 0.163324 0.138753 0.152878 lnL0 = -897.355592 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 897.355592 x= 0.07168 0.10170 0.10619 0.10975 0.10999 0.16332 0.13875 0.15288 1 h-lim-p 0.0025 0.0204 12.6474 897.275460 5 0.0010 32 | 0/8 2 h-lim-p 0.0072 0.1303 1.7773 897.273877 5 0.0010 58 | 0/8 3 h-lim-p 0.0031 0.9267 0.5819 897.273727 4 0.0010 81 | 0/8 4 h-lim-p 0.0081 3.7879 0.0684 897.273724 0 0.0010 103 | 0/8 5 h-lim-p 0.0051 8.1263 0.0138 897.273724 0 0.0011 124 | 0/8 6 h-lim-p 0.0077 20.0000 0.0020 897.273724 0 0.0017 145 | 0/8 7 h-lim-p 0.0206 20.0000 0.0002 897.273724 0 0.0824 167 | 0/8 8 h-lim-p 0.0049 20.0000 0.0027 897.273724 0 0.0148 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 897.273724 0 1.0938 208 | 0/8 10 h-lim-p 1.8008 20.0000 0.0000 897.273724 0 1.5757 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 897.273724 0 1.0938 248 | 0/8 12 h-lim-p 0.4523 20.0000 0.0000 897.273724 0 0.0141 272 | 0/8 13 h-lim-p 0.0003 20.0000 0.0003 897.273724 0 0.0000 297 | 0/8 14 h-lim-p 0.0000 20.0000 0.0010 897.273724 0 0.0000 317 | 0/8 15 h-lim-p 0.0000 20.0000 0.0026 897.273724 0 0.0000 337 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 897.273724 0 0.0000 357 | 0/8 17 h-lim-p 0.0001 20.0000 0.0002 897.273724 0 0.0000 387 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -897.273724 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -897.273724 Node 7: lnL = -897.273724 Node 8: lnL = -897.273724 Node 9: lnL = -897.273724 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 264 Sequential format.. Reading seq # 1: YJR136C_Sbay Reading seq # 2: YJR136C_Scer Reading seq # 3: YJR136C_Skud Reading seq # 4: YJR136C_Smik Reading seq # 5: YJR136C_Spar Sequences read.. Counting patterns.. # site patterns = 131 Counting frequencies.. 120 bytes for distance 20960 bytes for lkl0 16768 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.123832 0.086422 0.045717 0.089000 0.087486 0.183455 0.075822 0.197102 lnL0 = -1101.371039 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1101.371039 x= 0.12383 0.08642 0.04572 0.08900 0.08749 0.18345 0.07582 0.19710 1 h-lim-p 0.0036 2.1240 78.3894 1100.010290 8 0.0005 41 | 0/8 2 h-lim-p 0.0014 0.0109 15.7179 1099.920119 7 0.0008 70 | 0/8 3 h-lim-p 0.0021 0.0554 5.6874 1099.910953 6 0.0006 98 | 0/8 4 h-lim-p 0.0015 0.0606 2.3602 1099.908494 5 0.0010 122 | 0/8 5 h-lim-p 0.0113 0.9171 0.2177 1099.908456 3 0.0017 143 | 0/8 6 h-lim-p 0.0040 1.7643 0.0928 1099.908453 1 0.0008 166 | 0/8 7 h-lim-p 0.0073 20.0000 0.0100 1099.908453 0 0.0016 187 | 0/8 8 h-lim-p 0.5660 20.0000 0.0000 1099.908452 0 1.1320 208 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1099.908452 0 1.0938 228 | 0/8 10 h-lim-p 2.3764 20.0000 0.0000 1099.908452 0 4.7528 249 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1099.908452 0 0.0586 274 | 0/8 12 h-lim-p 0.3123 20.0000 0.0000 1099.908452 0 0.0000 323 Out... lnL = -1099.908452 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1099.908452 Node 7: lnL = -1099.908452 Node 8: lnL = -1099.908452 Node 9: lnL = -1099.908452 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 863 Sequential format.. Reading seq # 1: YJR137C_Sbay Reading seq # 2: YJR137C_Scer Reading seq # 3: YJR137C_Skud Reading seq # 4: YJR137C_Smik Reading seq # 5: YJR137C_Spar Sequences read.. Counting patterns.. # site patterns = 315 Counting frequencies.. 120 bytes for distance 50400 bytes for lkl0 40320 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.090692 0.079159 0.071431 0.134210 0.121188 0.206237 0.217033 0.180940 lnL0 = -4046.913883 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4046.913883 x= 0.09069 0.07916 0.07143 0.13421 0.12119 0.20624 0.21703 0.18094 1 h-lim-p 0.0032 1.0232 159.1024 4044.564861 7 0.0002 39 | 0/8 2 h-lim-p 0.0011 0.0089 21.2822 4044.500095 7 0.0003 65 | 0/8 3 h-lim-p 0.0009 0.0370 7.0198 4044.492071 4 0.0004 86 | 0/8 4 h-lim-p 0.0011 0.1312 2.2933 4044.491243 4 0.0004 108 | 0/8 5 h-lim-p 0.0026 0.9507 0.3128 4044.491219 1 0.0005 123 | 0/8 6 h-lim-p 0.0022 3.2017 0.0724 4044.491218 0 0.0005 144 | 0/8 7 h-lim-p 0.0047 20.0000 0.0075 4044.491218 0 0.0005 166 | 0/8 8 h-lim-p 0.1150 20.0000 0.0000 4044.491216 0 0.9200 189 | 0/8 9 h-lim-p 2.3792 20.0000 0.0000 4044.491216 0 1.0409 209 | 0/8 10 h-lim-p 1.1612 20.0000 0.0000 4044.491216 0 2.3223 230 | 0/8 11 h-lim-p 1.6814 20.0000 0.0000 4044.491216 0 0.7356 250 | 0/8 12 h-lim-p 0.0486 20.0000 0.0002 4044.491216 0 0.0122 271 | 0/8 13 h-lim-p 0.0043 20.0000 0.0007 4044.491216 0 0.0000 308 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 4044.491216 0 0.0000 340 Out... lnL = -4044.491216 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4044.491216 Node 7: lnL = -4044.491216 Node 8: lnL = -4044.491216 Node 9: lnL = -4044.491216 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 864 Sequential format.. Reading seq # 1: YJR138W_Sbay Reading seq # 2: YJR138W_Scer Reading seq # 3: YJR138W_Skud Reading seq # 4: YJR138W_Smik Reading seq # 5: YJR138W_Spar Sequences read.. Counting patterns.. # site patterns = 358 Counting frequencies.. 120 bytes for distance 57280 bytes for lkl0 45824 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.137272 0.038492 0.136630 0.174290 0.152487 0.265573 0.330600 0.258622 lnL0 = -4386.658402 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4386.658402 x= 0.13727 0.03849 0.13663 0.17429 0.15249 0.26557 0.33060 0.25862 1 h-lim-p 0.0052 0.9287 130.3755 4384.433514 5 0.0003 34 | 0/8 2 h-lim-p 0.0028 0.0323 13.2617 4384.377890 2 0.0006 51 | 0/8 3 h-lim-p 0.0007 0.0339 11.8142 4384.352724 4 0.0005 71 | 0/8 4 h-lim-p 0.0053 0.4900 1.2228 4384.352160 4 0.0008 94 | 0/8 5 h-lim-p 0.0043 1.3947 0.2246 4384.352145 2 0.0006 112 | 0/8 6 h-lim-p 0.0041 10.2491 0.0310 4384.352144 0 0.0018 132 | 0/8 7 h-lim-p 0.0239 20.0000 0.0023 4384.352024 0 0.1909 155 | 0/8 8 h-lim-p 0.0018 20.0000 0.2415 4384.351639 1 0.0023 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4384.351627 1 0.9961 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4384.351627 0 1.0938 219 | 0/8 11 h-lim-p 1.4369 20.0000 0.0000 4384.351627 0 0.2694 241 | 0/8 12 h-lim-p 0.0341 20.0000 0.0001 4384.351627 0 0.0000 279 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 4384.351627 0 0.0000 312 Out... lnL = -4384.351627 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4384.351627 Node 7: lnL = -4384.351627 Node 8: lnL = -4384.351627 Node 9: lnL = -4384.351627 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 235 Sequential format.. Reading seq # 1: YJR139C_Sbay Reading seq # 2: YJR139C_Scer Reading seq # 3: YJR139C_Skud Reading seq # 4: YJR139C_Smik Reading seq # 5: YJR139C_Spar Sequences read.. Counting patterns.. # site patterns = 104 Counting frequencies.. 120 bytes for distance 16640 bytes for lkl0 13312 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.092624 0.000060 0.097012 0.103422 0.097638 0.200744 0.182582 0.163483 lnL0 = -1014.537931 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1014.537931 x= 0.09262 0.00006 0.09701 0.10342 0.09764 0.20074 0.18258 0.16348 1 h-lim-p 0.0010 0.0077 56.9908 1013.608752 4 0.0005 31 | 0/8 2 h-lim-p 0.0009 0.0074 29.2448 1013.287191 5 0.0009 53 | 0/8 3 h-lim-p 0.0032 0.0269 8.1826 1013.263614 3 0.0008 72 | 0/8 4 h-lim-p 0.0030 0.0708 2.1129 1013.262142 2 0.0007 89 | 0/8 5 h-lim-p 0.0068 0.3287 0.2211 1013.262110 3 0.0011 109 | 0/8 6 h-lim-p 0.0081 5.6282 0.0303 1013.262003 0 0.0161 130 | 0/8 7 h-lim-p 0.0126 1.2412 0.0387 1013.258221 0 0.0506 152 | 0/8 8 h-lim-p 0.0017 0.0575 1.1828 1013.257127 5 0.0011 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1013.257094 2 0.9644 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1013.257094 0 1.0938 221 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1013.257094 0 1.0938 241 | 0/8 12 h-lim-p 1.1516 20.0000 0.0000 1013.257094 0 0.5038 261 | 0/8 13 h-lim-p 0.2035 20.0000 0.0000 1013.257094 0 0.0127 284 | 0/8 14 h-lim-p 0.0046 20.0000 0.0000 1013.257094 0 0.0023 304 | 0/8 15 h-lim-p 0.0010 20.0000 0.0001 1013.257094 0 0.0000 342 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1013.257094 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1013.257094 Node 7: lnL = -1013.257094 Node 8: lnL = -1013.257094 Node 9: lnL = -1013.257094 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 501 Sequential format.. Reading seq # 1: YJR148W_Sbay Reading seq # 2: YJR148W_Scer Reading seq # 3: YJR148W_Skud Reading seq # 4: YJR148W_Smik Reading seq # 5: YJR148W_Spar Sequences read.. Counting patterns.. # site patterns = 166 Counting frequencies.. 120 bytes for distance 26560 bytes for lkl0 21248 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.078278 0.047650 0.035517 0.091756 0.062307 0.117943 0.112786 0.133635 lnL0 = -1881.218063 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1881.218063 x= 0.07828 0.04765 0.03552 0.09176 0.06231 0.11794 0.11279 0.13364 1 h-lim-p 0.0015 0.8507 159.4344 1879.387137 7 0.0002 38 | 0/8 2 h-lim-p 0.0010 0.0080 24.7568 1879.289404 5 0.0003 62 | 0/8 3 h-lim-p 0.0016 0.0290 4.9317 1879.285916 5 0.0003 88 | 0/8 4 h-lim-p 0.0017 0.1072 0.8355 1879.285838 3 0.0002 108 | 0/8 5 h-lim-p 0.0014 1.1836 0.1409 1879.285834 1 0.0003 131 | 0/8 6 h-lim-p 0.0030 13.0470 0.0163 1879.285834 0 0.0006 152 | 0/8 7 h-lim-p 0.0160 20.0000 0.0007 1879.285833 0 0.0481 173 | 0/8 8 h-lim-p 0.0021 20.0000 0.0149 1879.285804 0 0.0085 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1879.285803 0 1.0938 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1879.285803 0 1.0938 235 | 0/8 11 h-lim-p 1.1290 20.0000 0.0000 1879.285803 0 4.5162 257 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1879.285803 0 0.0391 282 | 0/8 13 h-lim-p 0.0044 20.0000 0.0001 1879.285803 0 0.0008 304 | 0/8 14 h-lim-p 0.0003 20.0000 0.0003 1879.285803 0 0.0001 324 | 0/8 15 h-lim-p 0.0001 20.0000 0.0004 1879.285803 0 0.0000 360 | 0/8 16 h-lim-p 0.0000 20.0000 0.0018 | 0/8 17 h-lim-p 0.0000 20.0000 0.0018 Out... lnL = -1879.285803 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1879.285803 Node 7: lnL = -1879.285803 Node 8: lnL = -1879.285803 Node 9: lnL = -1879.285803 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 531 Sequential format.. Reading seq # 1: YJR149W_Sbay Reading seq # 2: YJR149W_Scer Reading seq # 3: YJR149W_Skud Reading seq # 4: YJR149W_Smik Reading seq # 5: YJR149W_Spar Sequences read.. Counting patterns.. # site patterns = 279 Counting frequencies.. 120 bytes for distance 44640 bytes for lkl0 35712 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.136835 0.171328 0.246408 0.116354 0.128347 0.220730 0.167490 0.264253 lnL0 = -2326.138066 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2326.138066 x= 0.13684 0.17133 0.24641 0.11635 0.12835 0.22073 0.16749 0.26425 1 h-lim-p 0.0118 2.5824 62.8290 2324.848523 2 0.0007 29 | 0/8 2 h-lim-p 0.0019 0.0151 11.7328 2324.779928 5 0.0010 52 | 0/8 3 h-lim-p 0.0034 0.1063 3.4676 2324.774734 6 0.0009 77 | 0/8 4 h-lim-p 0.0024 0.2333 1.3582 2324.773320 5 0.0018 101 | 0/8 5 h-lim-p 0.0064 1.0550 0.3746 2324.773243 3 0.0012 120 | 0/8 6 h-lim-p 0.0106 8.1057 0.0431 2324.773241 0 0.0023 141 | 0/8 7 h-lim-p 0.0124 20.0000 0.0081 2324.773241 0 0.0031 162 | 0/8 8 h-lim-p 0.1850 20.0000 0.0001 2324.773233 0 1.1100 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2324.773233 0 1.0938 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2324.773233 0 1.0938 224 | 0/8 11 h-lim-p 1.2364 20.0000 0.0000 2324.773233 0 1.8546 244 | 0/8 12 h-lim-p 1.5083 20.0000 0.0000 2324.773233 0 0.3771 265 | 0/8 13 h-lim-p 0.0284 20.0000 0.0001 2324.773233 0 0.0106 286 | 0/8 14 h-lim-p 0.0022 20.0000 0.0003 2324.773233 0 0.0005 307 | 0/8 15 h-lim-p 0.0015 20.0000 0.0001 2324.773233 0 0.0015 327 | 0/8 16 h-lim-p 0.0006 20.0000 0.0003 2324.773233 0 0.0000 351 | 0/8 17 h-lim-p 0.0012 20.0000 0.0000 2324.773233 0 0.0000 391 Out... lnL = -2324.773233 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2324.773233 Node 7: lnL = -2324.773233 Node 8: lnL = -2324.773233 Node 9: lnL = -2324.773233 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 936 Sequential format.. Reading seq # 1: YJR150C_Sbay Reading seq # 2: YJR150C_Scer Reading seq # 3: YJR150C_Skud Reading seq # 4: YJR150C_Smik Reading seq # 5: YJR150C_Spar Sequences read.. Counting patterns.. # site patterns = 315 Counting frequencies.. 120 bytes for distance 50400 bytes for lkl0 40320 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.290320 0.003702 0.067567 0.133761 0.117332 0.198702 0.288428 0.408810 lnL0 = -4396.683796 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4396.683796 x= 0.29032 0.00370 0.06757 0.13376 0.11733 0.19870 0.28843 0.40881 1 h-lim-p 0.0042 0.8256 145.4144 4394.759884 8 0.0002 42 | 0/8 2 h-lim-p 0.0007 0.0059 32.7004 4394.491389 6 0.0005 67 | 0/8 3 h-lim-p 0.0005 0.0098 31.3628 4394.334532 2 0.0005 83 | 0/8 4 h-lim-p 0.0015 0.0218 10.6484 4394.320212 3 0.0003 102 | 0/8 5 h-lim-p 0.0009 0.1270 3.7530 4394.313644 0 0.0013 114 | 0/8 6 h-lim-p 0.0025 0.1362 2.0080 4394.313071 3 0.0004 136 | 0/8 7 h-lim-p 0.0025 0.6191 0.2906 4394.313048 1 0.0005 151 | 0/8 8 h-lim-p 0.0990 20.0000 0.0015 4394.308731 0 1.1878 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 4394.308679 1 0.9961 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4394.308679 0 1.0938 216 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4394.308679 0 1.0938 236 | 0/8 12 h-lim-p 1.1112 20.0000 0.0000 4394.308679 0 0.9723 256 | 0/8 13 h-lim-p 0.2966 20.0000 0.0000 4394.308679 0 0.4449 276 | 0/8 14 h-lim-p 0.0983 20.0000 0.0000 4394.308679 0 0.0031 300 | 0/8 15 h-lim-p 0.0027 20.0000 0.0000 4394.308679 0 0.0000 330 | 0/8 16 h-lim-p 0.0004 20.0000 0.0000 4394.308679 0 0.0002 350 Out... lnL = -4394.308679 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4394.308679 Node 7: lnL = -4394.308679 Node 8: lnL = -4394.308679 Node 9: lnL = -4394.308679 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 850 Sequential format.. Reading seq # 1: YJR152W_Sbay Reading seq # 2: YJR152W_Scer Reading seq # 3: YJR152W_Skud Reading seq # 4: YJR152W_Smik Reading seq # 5: YJR152W_Spar Sequences read.. Counting patterns.. # site patterns = 276 Counting frequencies.. 120 bytes for distance 44160 bytes for lkl0 35328 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.120584 0.047457 0.045384 0.088450 0.095182 0.199679 0.227112 0.202929 lnL0 = -3714.739681 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3714.739681 x= 0.12058 0.04746 0.04538 0.08845 0.09518 0.19968 0.22711 0.20293 1 h-lim-p 0.0028 0.0316 164.3048 3712.971915 3 0.0001 31 | 0/8 2 h-lim-p 0.0005 0.0043 27.7887 3712.888059 3 0.0002 49 | 0/8 3 h-lim-p 0.0009 0.0269 7.3382 3712.883349 2 0.0002 66 | 0/8 4 h-lim-p 0.0005 0.0958 2.7975 3712.881602 2 0.0005 82 | 0/8 5 h-lim-p 0.0028 0.3909 0.5182 3712.881567 2 0.0003 100 | 0/8 6 h-lim-p 0.0007 1.0593 0.2127 3712.881560 1 0.0003 123 | 0/8 7 h-lim-p 0.0061 16.7099 0.0113 3712.881560 0 0.0027 143 | 0/8 8 h-lim-p 0.0200 20.0000 0.0015 3712.881285 0 0.3197 167 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3712.881256 1 0.9961 189 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3712.881256 0 2.1875 209 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3712.881256 0 1.0938 229 | 0/8 12 h-lim-p 0.1917 20.0000 0.0000 3712.881256 0 6.1348 254 | 0/8 13 h-lim-p 0.4098 20.0000 0.0001 3712.881256 0 0.0256 277 | 0/8 14 h-lim-p 0.0007 20.0000 0.0051 3712.881256 0 0.0000 305 | 0/8 15 h-lim-p 0.0016 20.0000 0.0000 3712.881256 0 0.0000 337 Out... lnL = -3712.881256 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3712.881256 Node 7: lnL = -3712.881256 Node 8: lnL = -3712.881256 Node 9: lnL = -3712.881256 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 843 Sequential format.. Reading seq # 1: YJR153W_Sbay Reading seq # 2: YJR153W_Scer Reading seq # 3: YJR153W_Skud Reading seq # 4: YJR153W_Smik Reading seq # 5: YJR153W_Spar Sequences read.. Counting patterns.. # site patterns = 360 Counting frequencies.. 120 bytes for distance 57600 bytes for lkl0 46080 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.221646 0.013126 0.184463 0.107420 0.120682 0.340046 0.220046 0.348621 lnL0 = -4277.891186 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4277.891186 x= 0.22165 0.01313 0.18446 0.10742 0.12068 0.34005 0.22005 0.34862 1 h-lim-p 0.0008 0.0065 181.8123 4273.884514 7 0.0003 39 | 0/8 2 h-lim-p 0.0006 0.0048 63.2662 4272.488561 0 0.0009 51 | 0/8 3 h-lim-p 0.0009 0.0074 48.1585 4272.311216 5 0.0002 73 | 0/8 4 h-lim-p 0.0008 0.0230 13.6534 4272.271529 7 0.0005 105 | 0/8 5 h-lim-p 0.0020 0.0672 3.3066 4272.269245 2 0.0004 122 | 0/8 6 h-lim-p 0.0078 0.9628 0.1871 4272.268709 4 0.0057 143 | 0/8 7 h-lim-p 0.0221 19.3693 0.0482 4272.200212 0 0.1771 166 | 0/8 8 h-lim-p 0.0101 0.6074 0.8460 4272.199812 2 0.0011 192 | 0/8 9 h-lim-p 0.6591 20.0000 0.0014 4272.197695 0 1.3181 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 4272.197666 1 0.9961 235 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4272.197666 0 1.0938 255 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4272.197666 0 1.0938 275 | 0/8 13 h-lim-p 1.0815 20.0000 0.0000 4272.197666 0 1.6222 295 | 0/8 14 h-lim-p 0.2189 20.0000 0.0000 4272.197666 0 0.0000 337 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -4272.197666 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4272.197666 Node 7: lnL = -4272.197666 Node 8: lnL = -4272.197666 Node 9: lnL = -4272.197666 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 957 Sequential format.. Reading seq # 1: YJR154W_Sbay Reading seq # 2: YJR154W_Scer Reading seq # 3: YJR154W_Skud Reading seq # 4: YJR154W_Smik Reading seq # 5: YJR154W_Spar Sequences read.. Counting patterns.. # site patterns = 512 Counting frequencies.. 120 bytes for distance 81920 bytes for lkl0 65536 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.241083 0.006896 0.000060 0.736423 0.479492 0.464070 0.556437 0.417388 lnL0 = -5009.630780 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 5009.630780 x= 0.24108 0.00690 0.00006 0.73642 0.47949 0.46407 0.55644 0.41739 1 h-lim-p 0.0000 0.0000 151.5743 5009.609053 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0028 315.7777 4980.914599 0 0.0013 41 | 1/8 3 h-lim-p 0.0017 0.0133 52.5062 4978.226035 0 0.0033 54 | 1/8 4 h-lim-p 0.0028 0.0227 16.1233 4978.062856 5 0.0014 77 | 1/8 5 h-lim-p 0.0075 0.1385 2.9695 4978.051511 5 0.0022 102 | 1/8 6 h-lim-p 0.0027 0.2403 2.3539 4978.042646 3 0.0028 120 | 1/8 7 h-lim-p 0.0413 2.5662 0.1572 4977.529907 0 0.3306 135 | 1/8 8 h-lim-p 1.9945 20.0000 0.0261 4977.438585 6 1.1869 169 | 1/8 9 h-lim-p 2.5000 20.0000 0.0047 4977.433751 2 1.1719 192 | 1/8 10 h-lim-p 2.5000 20.0000 0.0003 4977.433723 1 1.0938 213 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 4977.433722 0 1.0938 232 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 4977.433722 0 1.0938 251 | 1/8 13 h-lim-p 1.1331 20.0000 0.0000 4977.433722 0 0.8498 270 | 1/8 14 h-lim-p 0.0717 20.0000 0.0001 4977.433722 0 0.0717 289 | 1/8 15 h-lim-p 0.0220 20.0000 0.0002 4977.433722 0 0.0000 334 | 1/8 16 h-lim-p 0.0000 20.0000 0.0000 | 1/8 17 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -4977.433722 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4977.433722 Node 7: lnL = -4977.433722 Node 8: lnL = -4977.433722 Node 9: lnL = -4977.433722 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 310 Sequential format.. Reading seq # 1: YKL003C_Sbay Reading seq # 2: YKL003C_Scer Reading seq # 3: YKL003C_Skud Reading seq # 4: YKL003C_Smik Reading seq # 5: YKL003C_Spar Sequences read.. Counting patterns.. # site patterns = 136 Counting frequencies.. 120 bytes for distance 21760 bytes for lkl0 17408 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.072359 0.100456 0.096157 0.091632 0.075058 0.203198 0.234145 0.150958 lnL0 = -1384.008477 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1384.008477 x= 0.07236 0.10046 0.09616 0.09163 0.07506 0.20320 0.23414 0.15096 1 h-lim-p 0.0020 0.0161 22.8228 1383.825881 6 0.0007 37 | 0/8 2 h-lim-p 0.0027 0.0278 6.0324 1383.812612 5 0.0008 62 | 0/8 3 h-lim-p 0.0041 0.0795 1.1376 1383.812392 4 0.0004 86 | 0/8 4 h-lim-p 0.0023 2.2946 0.1773 1383.812375 0 0.0010 98 | 0/8 5 h-lim-p 0.0017 1.9015 0.1025 1383.812372 0 0.0008 118 | 0/8 6 h-lim-p 0.0067 17.0273 0.0117 1383.812372 0 0.0015 139 | 0/8 7 h-lim-p 0.0031 20.0000 0.0056 1383.812372 0 0.0027 159 | 0/8 8 h-lim-p 0.0283 20.0000 0.0005 1383.812353 0 0.3391 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1383.812353 0 1.0938 202 | 0/8 10 h-lim-p 1.1592 20.0000 0.0000 1383.812353 0 0.5071 222 | 0/8 11 h-lim-p 0.2933 20.0000 0.0000 1383.812353 0 0.0001 253 | 0/8 12 h-lim-p 0.0001 20.0000 0.0000 1383.812353 0 0.0000 277 Out... lnL = -1383.812353 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1383.812353 Node 7: lnL = -1383.812353 Node 8: lnL = -1383.812353 Node 9: lnL = -1383.812353 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 765 Sequential format.. Reading seq # 1: YKL004W_Sbay Reading seq # 2: YKL004W_Scer Reading seq # 3: YKL004W_Skud Reading seq # 4: YKL004W_Smik Reading seq # 5: YKL004W_Spar Sequences read.. Counting patterns.. # site patterns = 194 Counting frequencies.. 120 bytes for distance 31040 bytes for lkl0 24832 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.060609 0.045498 0.066644 0.068175 0.029773 0.111881 0.122452 0.107430 lnL0 = -2804.205325 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2804.205325 x= 0.06061 0.04550 0.06664 0.06818 0.02977 0.11188 0.12245 0.10743 1 h-lim-p 0.0001 0.0010 163.3924 2802.801537 2 0.0001 26 | 0/8 2 h-lim-p 0.0007 0.0074 28.4892 2802.757165 6 0.0001 53 | 0/8 3 h-lim-p 0.0001 0.0031 24.9240 2802.735379 3 0.0001 71 | 0/8 4 h-lim-p 0.0008 0.0280 3.4884 2802.734500 4 0.0002 92 | 0/8 5 h-lim-p 0.0008 0.3142 0.6732 2802.734456 2 0.0002 109 | 0/8 6 h-lim-p 0.0016 1.3779 0.0794 2802.734455 1 0.0002 133 | 0/8 7 h-lim-p 0.0026 18.9530 0.0063 2802.734453 0 0.0051 154 | 0/8 8 h-lim-p 0.0028 6.2273 0.0115 2802.733886 0 0.0446 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2802.733867 1 0.9961 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2802.733867 0 2.5000 220 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2802.733867 0 0.0012 250 | 0/8 12 h-lim-p 0.0001 20.0000 0.0000 2802.733867 0 0.0000 273 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0084 | 0/8 15 h-lim-p 0.0000 20.0000 0.0084 Out... lnL = -2802.733867 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2802.733867 Node 7: lnL = -2802.733867 Node 8: lnL = -2802.733867 Node 9: lnL = -2802.733867 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 765 Sequential format.. Reading seq # 1: YKL005C_Sbay Reading seq # 2: YKL005C_Scer Reading seq # 3: YKL005C_Skud Reading seq # 4: YKL005C_Smik Reading seq # 5: YKL005C_Spar Sequences read.. Counting patterns.. # site patterns = 195 Counting frequencies.. 120 bytes for distance 31200 bytes for lkl0 24960 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.062984 0.031423 0.062991 0.086514 0.031314 0.112077 0.136244 0.110711 lnL0 = -2846.425608 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2846.425608 x= 0.06298 0.03142 0.06299 0.08651 0.03131 0.11208 0.13624 0.11071 1 h-lim-p 0.0001 0.0007 209.5294 2844.607946 7 0.0001 39 | 0/8 2 h-lim-p 0.0005 0.0047 37.5025 2844.485140 6 0.0002 64 | 0/8 3 h-lim-p 0.0002 0.0017 29.0422 2844.461850 5 0.0001 86 | 0/8 4 h-lim-p 0.0003 0.0220 6.7007 2844.458375 2 0.0002 102 | 0/8 5 h-lim-p 0.0021 0.4656 0.5534 2844.458345 2 0.0002 120 | 0/8 6 h-lim-p 0.0012 1.6098 0.0953 2844.458345 0 0.0003 141 | 0/8 7 h-lim-p 0.0138 20.0000 0.0017 2844.458345 0 0.0060 161 | 0/8 8 h-lim-p 0.0045 20.0000 0.0023 2844.458314 0 0.0539 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2844.458313 0 1.0938 204 | 0/8 10 h-lim-p 1.8819 20.0000 0.0000 2844.458313 0 1.6466 224 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2844.458313 0 0.1367 247 | 0/8 12 h-lim-p 0.0487 20.0000 0.0000 2844.458313 0 0.0000 292 | 0/8 13 h-lim-p 0.0000 20.0000 0.0064 2844.458313 0 0.0000 325 | 0/8 14 h-lim-p 0.0000 17.6844 0.0052 2844.458313 0 0.0001 348 | 0/8 15 h-lim-p 0.0005 20.0000 0.0013 2844.458313 0 0.0004 368 | 0/8 16 h-lim-p 0.0005 20.0000 0.0012 2844.458313 0 0.0000 396 | 0/8 17 h-lim-p 0.0000 20.0000 0.0042 2844.458313 0 0.0000 423 | 0/8 18 h-lim-p 0.0000 20.0000 0.0025 2844.458313 0 0.0000 449 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 20 h-lim-p 0.0000 20.0000 0.0060 | 0/8 21 h-lim-p 0.0000 20.0000 0.0060 Out... lnL = -2844.458313 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2844.458313 Node 7: lnL = -2844.458313 Node 8: lnL = -2844.458313 Node 9: lnL = -2844.458313 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 815 Sequential format.. Reading seq # 1: YKL007W_Sbay Reading seq # 2: YKL007W_Scer Reading seq # 3: YKL007W_Skud Reading seq # 4: YKL007W_Smik Reading seq # 5: YKL007W_Spar Sequences read.. Counting patterns.. # site patterns = 221 Counting frequencies.. 120 bytes for distance 35360 bytes for lkl0 28288 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.129735 0.012204 0.054919 0.068731 0.037345 0.094854 0.138854 0.182447 lnL0 = -3042.952152 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3042.952152 x= 0.12973 0.01220 0.05492 0.06873 0.03734 0.09485 0.13885 0.18245 1 h-lim-p 0.0005 0.0038 365.4656 3038.875349 6 0.0001 37 | 0/8 2 h-lim-p 0.0003 0.0021 74.8008 3038.151710 6 0.0003 62 | 0/8 3 h-lim-p 0.0004 0.0040 44.8689 3038.075957 3 0.0001 81 | 0/8 4 h-lim-p 0.0003 0.0063 12.6657 3038.067929 5 0.0001 105 | 0/8 5 h-lim-p 0.0009 0.0588 1.6476 3038.067721 3 0.0002 125 | 0/8 6 h-lim-p 0.0005 0.4092 0.4588 3038.067698 1 0.0002 139 | 0/8 7 h-lim-p 0.0006 1.2802 0.1532 3038.067695 0 0.0003 159 | 0/8 8 h-lim-p 0.0895 20.0000 0.0005 3038.066037 0 1.4324 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 3038.065907 3 1.0449 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3038.065907 0 1.0938 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3038.065907 0 2.1875 249 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3038.065907 0 0.0781 273 | 0/8 13 h-lim-p 0.0111 20.0000 0.0000 3038.065907 0 0.0000 312 Out... lnL = -3038.065907 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3038.065907 Node 7: lnL = -3038.065907 Node 8: lnL = -3038.065907 Node 9: lnL = -3038.065907 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 387 Sequential format.. Reading seq # 1: YKL009W_Sbay Reading seq # 2: YKL009W_Scer Reading seq # 3: YKL009W_Skud Reading seq # 4: YKL009W_Smik Reading seq # 5: YKL009W_Spar Sequences read.. Counting patterns.. # site patterns = 95 Counting frequencies.. 120 bytes for distance 15200 bytes for lkl0 12160 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.088446 0.055867 0.111130 0.113703 0.126231 4.702107 0.262634 lnL0 = -1330.163901 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1330.163901 x= 0.00006 0.08845 0.05587 0.11113 0.11370 0.12623 4.70211 0.26263 1 h-lim-p 0.0000 0.0000 108.5358 1330.123173 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0053 48.1206 1329.527158 0 0.0006 40 | 1/8 3 h-lim-p 0.0022 0.0175 8.0515 1329.507789 5 0.0006 63 | 1/8 4 h-lim-p 0.0028 0.1992 1.6241 1329.498203 4 0.0024 82 | 1/8 5 h-lim-p 0.0087 0.3410 0.4547 1329.110149 0 0.0525 96 | 1/8 6 h-lim-p 0.0020 0.0193 12.1990 1327.343794 0 0.0039 116 | 1/8 7 h-lim-p 2.5000 20.0000 0.0106 1327.279335 6 0.7368 144 | 0/8 8 h-lim-p 0.0086 1.0376 0.9018 1327.278761 4 0.0014 173 | 0/8 9 h-lim-p 1.2096 20.0000 0.0011 1327.277951 4 0.7093 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1327.277946 1 0.6152 227 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1327.277946 0 1.0938 247 | 0/8 12 h-lim-p 1.4371 20.0000 0.0000 1327.277946 0 1.2575 267 | 0/8 13 h-lim-p 1.0294 20.0000 0.0000 1327.277946 0 2.0588 288 | 0/8 14 h-lim-p 0.2445 20.0000 0.0001 1327.277946 0 0.0000 321 | 0/8 15 h-lim-p 0.0004 20.0000 0.0000 1327.277946 0 0.0000 357 Out... lnL = -1327.277946 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1327.277946 Node 7: lnL = -1327.277946 Node 8: lnL = -1327.277946 Node 9: lnL = -1327.277946 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 220 Sequential format.. Reading seq # 1: YKL011C_Sbay Reading seq # 2: YKL011C_Scer Reading seq # 3: YKL011C_Skud Reading seq # 4: YKL011C_Smik Reading seq # 5: YKL011C_Spar Sequences read.. Counting patterns.. # site patterns = 124 Counting frequencies.. 120 bytes for distance 19840 bytes for lkl0 15872 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.146737 0.175623 0.098827 0.165815 0.066801 0.191724 0.174762 0.244960 lnL0 = -1030.937776 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1030.937776 x= 0.14674 0.17562 0.09883 0.16581 0.06680 0.19172 0.17476 0.24496 1 h-lim-p 0.0079 0.0633 18.5548 1030.759319 5 0.0011 34 | 0/8 2 h-lim-p 0.0020 0.0159 9.3872 1030.725725 2 0.0009 50 | 0/8 3 h-lim-p 0.0023 0.0574 3.8364 1030.717426 6 0.0014 77 | 0/8 4 h-lim-p 0.0045 0.2026 1.1614 1030.716255 2 0.0019 93 | 0/8 5 h-lim-p 0.0116 1.2733 0.1954 1030.716207 2 0.0025 110 | 0/8 6 h-lim-p 0.0049 3.4312 0.1011 1030.716200 2 0.0016 135 | 0/8 7 h-lim-p 0.0217 20.0000 0.0073 1030.716199 1 0.0053 158 | 0/8 8 h-lim-p 0.0692 20.0000 0.0006 1030.716165 0 0.5532 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1030.716162 1 0.9961 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1030.716162 0 2.1875 223 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1030.716162 0 0.5469 244 | 0/8 12 h-lim-p 0.2456 20.0000 0.0000 1030.716162 0 0.0134 267 | 0/8 13 h-lim-p 0.0062 20.0000 0.0000 1030.716162 0 0.0000 310 Out... lnL = -1030.716162 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1030.716162 Node 7: lnL = -1030.716162 Node 8: lnL = -1030.716162 Node 9: lnL = -1030.716162 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 614 Sequential format.. Reading seq # 1: YKL016C_Sbay Reading seq # 2: YKL016C_Scer Reading seq # 3: YKL016C_Skud Reading seq # 4: YKL016C_Smik Reading seq # 5: YKL016C_Spar Sequences read.. Counting patterns.. # site patterns = 238 Counting frequencies.. 120 bytes for distance 38080 bytes for lkl0 30464 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.100055 0.104847 0.073261 0.129350 0.079768 0.143723 0.168687 0.174521 lnL0 = -2600.875081 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2600.875081 x= 0.10005 0.10485 0.07326 0.12935 0.07977 0.14372 0.16869 0.17452 1 h-lim-p 0.0049 1.3663 103.3890 2599.372868 9 0.0003 45 | 0/8 2 h-lim-p 0.0009 0.0076 24.3877 2599.260851 3 0.0004 63 | 0/8 3 h-lim-p 0.0008 0.0181 12.7106 2599.237119 2 0.0004 79 | 0/8 4 h-lim-p 0.0011 0.0476 4.0828 2599.233686 4 0.0005 100 | 0/8 5 h-lim-p 0.0051 0.6196 0.3774 2599.233652 2 0.0005 118 | 0/8 6 h-lim-p 0.0024 2.7523 0.0757 2599.233650 0 0.0005 139 | 0/8 7 h-lim-p 0.0154 20.0000 0.0026 2599.233614 0 0.0926 161 | 0/8 8 h-lim-p 0.0031 20.0000 0.0791 2599.233192 0 0.0061 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2599.233173 1 0.9961 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2599.233173 0 1.0938 224 | 0/8 11 h-lim-p 1.2771 20.0000 0.0000 2599.233173 0 5.1085 246 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2599.233173 0 0.6250 267 | 0/8 13 h-lim-p 0.0736 20.0000 0.0001 2599.233173 0 0.0161 288 | 0/8 14 h-lim-p 0.0046 20.0000 0.0002 2599.233173 0 0.0006 310 | 0/8 15 h-lim-p 0.0019 20.0000 0.0001 2599.233173 0 0.0019 330 | 0/8 16 h-lim-p 0.0143 20.0000 0.0000 2599.233173 0 0.0036 351 | 0/8 17 h-lim-p 0.0008 20.0000 0.0000 2599.233173 0 0.0000 384 | 0/8 18 h-lim-p 0.0000 20.0000 0.0006 | 0/8 19 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -2599.233173 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2599.233173 Node 7: lnL = -2599.233173 Node 8: lnL = -2599.233173 Node 9: lnL = -2599.233173 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 256 Sequential format.. Reading seq # 1: YKL017C_Sbay Reading seq # 2: YKL017C_Scer Reading seq # 3: YKL017C_Skud Reading seq # 4: YKL017C_Smik Reading seq # 5: YKL017C_Spar Sequences read.. Counting patterns.. # site patterns = 111 Counting frequencies.. 120 bytes for distance 17760 bytes for lkl0 14208 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.069453 0.137877 0.106385 0.082633 0.083877 0.099121 0.232029 0.144986 lnL0 = -1048.080631 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1048.080631 x= 0.06945 0.13788 0.10638 0.08263 0.08388 0.09912 0.23203 0.14499 1 h-lim-p 0.0006 0.0047 27.7218 1047.824955 1 0.0007 24 | 0/8 2 h-lim-p 0.0036 0.1016 5.5968 1047.809868 6 0.0010 52 | 0/8 3 h-lim-p 0.0012 0.0512 4.5284 1047.804680 6 0.0007 80 | 0/8 4 h-lim-p 0.0034 0.2093 0.9990 1047.804193 5 0.0011 105 | 0/8 5 h-lim-p 0.0041 1.3638 0.2574 1047.804147 3 0.0015 133 | 0/8 6 h-lim-p 0.0089 3.4353 0.0423 1047.804140 2 0.0029 159 | 0/8 7 h-lim-p 0.0034 7.4030 0.0370 1047.804087 0 0.0101 180 | 0/8 8 h-lim-p 0.0081 3.8909 0.0460 1047.802460 0 0.0324 202 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1047.802458 0 1.0938 222 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1047.802458 0 1.0938 242 | 0/8 11 h-lim-p 1.8358 20.0000 0.0000 1047.802458 0 1.6063 262 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1047.802458 0 1.2500 282 | 0/8 13 h-lim-p 0.5285 20.0000 0.0000 1047.802458 0 0.0165 306 | 0/8 14 h-lim-p 0.0000 20.0000 0.0022 1047.802458 0 0.0000 343 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 1047.802458 0 0.0000 363 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 1047.802458 0 0.0000 383 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 1047.802458 0 0.0000 420 Out... lnL = -1047.802458 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1047.802458 Node 7: lnL = -1047.802458 Node 8: lnL = -1047.802458 Node 9: lnL = -1047.802458 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 288 Sequential format.. Reading seq # 1: YKL018C-A_Sbay Reading seq # 2: YKL018C-A_Scer Reading seq # 3: YKL018C-A_Skud Reading seq # 4: YKL018C-A_Smik Reading seq # 5: YKL018C-A_Spar Sequences read.. Counting patterns.. # site patterns = 142 Counting frequencies.. 120 bytes for distance 22720 bytes for lkl0 18176 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.032044 0.175449 0.086428 0.229793 0.059153 0.201875 0.170917 0.116289 lnL0 = -1180.745404 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1180.745404 x= 0.03204 0.17545 0.08643 0.22979 0.05915 0.20187 0.17092 0.11629 1 h-lim-p 0.0005 0.0037 32.5503 1180.177704 0 0.0009 23 | 0/8 2 h-lim-p 0.0019 0.0154 10.0091 1180.132093 4 0.0010 44 | 0/8 3 h-lim-p 0.0015 0.0199 6.5284 1180.119980 4 0.0008 65 | 0/8 4 h-lim-p 0.0060 1.2287 0.8379 1180.119516 2 0.0013 82 | 0/8 5 h-lim-p 0.0024 0.1394 0.4612 1180.119427 3 0.0008 109 | 0/8 6 h-lim-p 0.0038 2.3872 0.1001 1180.119228 0 0.0077 130 | 0/8 7 h-lim-p 0.0168 2.1921 0.0456 1180.100554 0 0.1344 153 | 0/8 8 h-lim-p 0.0112 0.5308 0.5491 1180.100257 4 0.0019 185 | 0/8 9 h-lim-p 1.0477 20.0000 0.0010 1180.099874 2 1.0395 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1180.099874 0 1.0938 229 | 0/8 11 h-lim-p 1.9100 20.0000 0.0000 1180.099874 0 1.6712 249 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1180.099874 0 0.6250 270 | 0/8 13 h-lim-p 0.2216 20.0000 0.0000 1180.099874 0 0.0554 291 | 0/8 14 h-lim-p 0.0197 20.0000 0.0001 1180.099874 0 0.0049 312 | 0/8 15 h-lim-p 0.0025 20.0000 0.0001 1180.099874 0 0.0000 346 | 0/8 16 h-lim-p 0.0000 20.0000 0.0007 | 0/8 17 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -1180.099874 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1180.099874 Node 7: lnL = -1180.099874 Node 8: lnL = -1180.099874 Node 9: lnL = -1180.099874 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 245 Sequential format.. Reading seq # 1: YKL018W_Sbay Reading seq # 2: YKL018W_Scer Reading seq # 3: YKL018W_Skud Reading seq # 4: YKL018W_Smik Reading seq # 5: YKL018W_Spar Sequences read.. Counting patterns.. # site patterns = 132 Counting frequencies.. 120 bytes for distance 21120 bytes for lkl0 16896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.089898 0.035537 0.115115 0.194246 0.125318 0.195110 0.217484 0.175595 lnL0 = -1122.331826 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1122.331826 x= 0.08990 0.03554 0.11511 0.19425 0.12532 0.19511 0.21748 0.17560 1 h-lim-p 0.0064 0.1374 59.3671 1121.403466 9 0.0006 44 | 0/8 2 h-lim-p 0.0030 0.0242 9.5013 1121.318463 8 0.0019 76 | 0/8 3 h-lim-p 0.0093 0.2222 1.9619 1121.316265 4 0.0012 98 | 0/8 4 h-lim-p 0.0052 0.7740 0.4473 1121.316128 4 0.0015 120 | 0/8 5 h-lim-p 0.0062 3.0716 0.1059 1121.316120 0 0.0016 141 | 0/8 6 h-lim-p 0.0206 20.0000 0.0080 1121.316118 0 0.0090 161 | 0/8 7 h-lim-p 0.0151 20.0000 0.0048 1121.316052 0 0.0904 183 | 0/8 8 h-lim-p 0.0037 11.6767 0.1153 1121.315926 1 0.0047 205 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1121.315926 0 1.0938 225 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1121.315926 0 1.0938 245 | 0/8 11 h-lim-p 1.4260 20.0000 0.0000 1121.315926 0 2.1390 265 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1121.315926 0 0.0391 290 | 0/8 13 h-lim-p 0.0068 20.0000 0.0000 1121.315926 0 0.0001 316 Out... lnL = -1121.315926 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1121.315926 Node 7: lnL = -1121.315926 Node 8: lnL = -1121.315926 Node 9: lnL = -1121.315926 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 507 Sequential format.. Reading seq # 1: YKL020C_Sbay Reading seq # 2: YKL020C_Scer Reading seq # 3: YKL020C_Skud Reading seq # 4: YKL020C_Smik Reading seq # 5: YKL020C_Spar Sequences read.. Counting patterns.. # site patterns = 170 Counting frequencies.. 120 bytes for distance 27200 bytes for lkl0 21760 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.066061 0.080893 0.072414 0.102439 0.053850 0.148400 0.144822 0.127182 lnL0 = -2089.014267 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2089.014267 x= 0.06606 0.08089 0.07241 0.10244 0.05385 0.14840 0.14482 0.12718 1 h-lim-p 0.0002 0.0018 72.5558 2088.269385 0 0.0003 22 | 0/8 2 h-lim-p 0.0010 0.0099 25.9195 2088.198333 5 0.0002 47 | 0/8 3 h-lim-p 0.0005 0.0106 13.5413 2088.181977 3 0.0002 65 | 0/8 4 h-lim-p 0.0019 0.0968 1.5906 2088.181545 4 0.0003 87 | 0/8 5 h-lim-p 0.0021 0.8869 0.2579 2088.181512 2 0.0007 105 | 0/8 6 h-lim-p 0.0061 4.4340 0.0291 2088.180876 0 0.0246 127 | 0/8 7 h-lim-p 0.0020 0.4584 0.3603 2088.165942 0 0.0079 149 | 0/8 8 h-lim-p 0.0007 0.0460 3.8447 2088.162672 4 0.0004 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 2088.162546 2 0.9961 194 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2088.162546 0 1.0938 214 | 0/8 11 h-lim-p 1.3101 20.0000 0.0000 2088.162546 0 1.9651 234 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2088.162546 0 0.2734 256 | 0/8 13 h-lim-p 0.0508 20.0000 0.0000 2088.162546 0 0.0032 279 | 0/8 14 h-lim-p 0.0015 20.0000 0.0000 2088.162546 0 0.0000 316 | 0/8 15 h-lim-p 0.0000 20.0000 0.0030 2088.162546 0 0.0000 348 | 0/8 16 h-lim-p 0.0000 20.0000 0.0013 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0030 | 0/8 18 h-lim-p 0.0000 20.0000 0.0030 Out... lnL = -2088.162546 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2088.162546 Node 7: lnL = -2088.162546 Node 8: lnL = -2088.162546 Node 9: lnL = -2088.162546 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 219 Sequential format.. Reading seq # 1: YKL022C_Sbay Reading seq # 2: YKL022C_Scer Reading seq # 3: YKL022C_Skud Reading seq # 4: YKL022C_Smik Reading seq # 5: YKL022C_Spar Sequences read.. Counting patterns.. # site patterns = 116 Counting frequencies.. 120 bytes for distance 18560 bytes for lkl0 14848 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.113434 0.087901 0.056758 0.156367 0.120597 0.190806 0.190897 0.187992 lnL0 = -950.662592 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 950.662592 x= 0.11343 0.08790 0.05676 0.15637 0.12060 0.19081 0.19090 0.18799 1 h-lim-p 0.0007 0.0060 59.0738 948.455169 0 0.0015 23 | 0/8 2 h-lim-p 0.0006 0.0048 30.4055 948.133402 0 0.0012 36 | 0/8 3 h-lim-p 0.0043 0.0340 6.5968 948.107411 7 0.0013 68 | 0/8 4 h-lim-p 0.0028 0.1656 3.0597 948.100304 5 0.0018 92 | 0/8 5 h-lim-p 0.0056 0.2122 0.9765 948.099282 4 0.0021 114 | 0/8 6 h-lim-p 0.0162 2.1386 0.1252 948.097837 3 0.0167 140 | 0/8 7 h-lim-p 0.0097 1.5259 0.2159 948.047525 0 0.0580 162 | 0/8 8 h-lim-p 0.0040 0.0624 3.1204 948.034547 6 0.0021 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0017 948.033028 3 1.0483 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 948.033026 0 1.0938 234 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 948.033026 0 1.0938 254 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 948.033026 0 2.1875 274 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 948.033026 0 0.6250 295 | 0/8 14 h-lim-p 0.1108 20.0000 0.0000 948.033026 0 0.0277 316 | 0/8 15 h-lim-p 0.0106 20.0000 0.0000 948.033026 0 0.0027 337 | 0/8 16 h-lim-p 0.0013 20.0000 0.0000 948.033026 0 0.0001 360 | 0/8 17 h-lim-p 0.0014 20.0000 0.0000 948.033026 0 0.0000 397 Out... lnL = -948.033026 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -948.033026 Node 7: lnL = -948.033026 Node 8: lnL = -948.033026 Node 9: lnL = -948.033026 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 610 Sequential format.. Reading seq # 1: YKL023W_Sbay Reading seq # 2: YKL023W_Scer Reading seq # 3: YKL023W_Skud Reading seq # 4: YKL023W_Smik Reading seq # 5: YKL023W_Spar Sequences read.. Counting patterns.. # site patterns = 190 Counting frequencies.. 120 bytes for distance 30400 bytes for lkl0 24320 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.089856 0.031879 0.060585 0.088796 0.071219 0.140407 0.160294 0.142545 lnL0 = -2484.349979 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2484.349979 x= 0.08986 0.03188 0.06059 0.08880 0.07122 0.14041 0.16029 0.14255 1 h-lim-p 0.0013 0.0263 194.7823 2481.966529 7 0.0001 38 | 0/8 2 h-lim-p 0.0008 0.0065 26.7448 2481.829897 2 0.0004 54 | 0/8 3 h-lim-p 0.0011 0.0263 9.2310 2481.821337 5 0.0002 76 | 0/8 4 h-lim-p 0.0009 0.0434 2.2602 2481.820810 2 0.0002 93 | 0/8 5 h-lim-p 0.0009 0.3824 0.5478 2481.820759 2 0.0004 109 | 0/8 6 h-lim-p 0.0061 4.9554 0.0325 2481.820759 0 0.0007 131 | 0/8 7 h-lim-p 0.0037 20.0000 0.0058 2481.820758 0 0.0019 151 | 0/8 8 h-lim-p 0.0068 20.0000 0.0016 2481.820629 0 0.1638 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2481.820628 0 1.0938 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2481.820628 0 1.0938 215 | 0/8 11 h-lim-p 1.1499 20.0000 0.0000 2481.820628 0 0.5031 235 | 0/8 12 h-lim-p 0.1541 20.0000 0.0000 2481.820628 0 0.0770 255 | 0/8 13 h-lim-p 0.0269 20.0000 0.0001 2481.820628 0 0.0017 278 | 0/8 14 h-lim-p 0.0001 20.0000 0.0023 2481.820628 0 0.0000 307 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 2481.820628 0 0.0000 331 Out... lnL = -2481.820628 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2481.820628 Node 7: lnL = -2481.820628 Node 8: lnL = -2481.820628 Node 9: lnL = -2481.820628 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 609 Sequential format.. Reading seq # 1: YKL024C_Sbay Reading seq # 2: YKL024C_Scer Reading seq # 3: YKL024C_Skud Reading seq # 4: YKL024C_Smik Reading seq # 5: YKL024C_Spar Sequences read.. Counting patterns.. # site patterns = 187 Counting frequencies.. 120 bytes for distance 29920 bytes for lkl0 23936 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.092462 0.044946 0.056617 0.089434 0.070581 0.140838 0.157109 0.146239 lnL0 = -2492.338201 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2492.338201 x= 0.09246 0.04495 0.05662 0.08943 0.07058 0.14084 0.15711 0.14624 1 h-lim-p 0.0022 0.0288 150.6119 2490.613790 7 0.0002 42 | 0/8 2 h-lim-p 0.0008 0.0065 27.6709 2490.476077 2 0.0004 58 | 0/8 3 h-lim-p 0.0009 0.0180 11.3695 2490.464031 2 0.0002 75 | 0/8 4 h-lim-p 0.0010 0.0467 2.5168 2490.463311 2 0.0002 92 | 0/8 5 h-lim-p 0.0015 0.4367 0.4177 2490.463279 2 0.0004 109 | 0/8 6 h-lim-p 0.0033 2.8849 0.0491 2490.463278 0 0.0004 131 | 0/8 7 h-lim-p 0.0046 20.0000 0.0039 2490.463271 0 0.0182 153 | 0/8 8 h-lim-p 0.0026 20.0000 0.0269 2490.462964 0 0.0157 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2490.462958 0 1.2500 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2490.462958 0 1.0938 215 | 0/8 11 h-lim-p 1.7311 20.0000 0.0000 2490.462958 0 1.5147 235 | 0/8 12 h-lim-p 1.6895 20.0000 0.0000 2490.462958 0 0.4224 256 | 0/8 13 h-lim-p 0.0892 20.0000 0.0000 2490.462958 0 0.0014 281 | 0/8 14 h-lim-p 0.0002 20.0000 0.0003 2490.462958 0 0.0000 306 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 2490.462958 0 0.0001 326 | 0/8 16 h-lim-p 0.0002 20.0000 0.0000 2490.462958 0 0.0000 358 Out... lnL = -2490.462958 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2490.462958 Node 7: lnL = -2490.462958 Node 8: lnL = -2490.462958 Node 9: lnL = -2490.462958 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 278 Sequential format.. Reading seq # 1: YKL025C_Sbay Reading seq # 2: YKL025C_Scer Reading seq # 3: YKL025C_Skud Reading seq # 4: YKL025C_Smik Reading seq # 5: YKL025C_Spar Sequences read.. Counting patterns.. # site patterns = 121 Counting frequencies.. 120 bytes for distance 19360 bytes for lkl0 15488 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.083005 0.087190 0.009074 0.097604 0.040976 0.133357 0.265363 0.140331 lnL0 = -1055.099514 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1055.099514 x= 0.08300 0.08719 0.00907 0.09760 0.04098 0.13336 0.26536 0.14033 1 h-lim-p 0.0002 0.0014 121.0175 1053.861602 0 0.0003 22 | 0/8 2 h-lim-p 0.0002 0.0015 30.9378 1053.688707 0 0.0004 35 | 0/8 3 h-lim-p 0.0006 0.0146 19.6099 1053.635054 6 0.0004 62 | 0/8 4 h-lim-p 0.0023 0.0907 3.2561 1053.629875 3 0.0010 80 | 0/8 5 h-lim-p 0.0043 0.2220 0.7935 1053.629450 5 0.0013 106 | 0/8 6 h-lim-p 0.0030 0.8567 0.3446 1053.629197 2 0.0028 130 | 0/8 7 h-lim-p 0.0169 2.5279 0.0567 1053.626042 0 0.0507 151 | 0/8 8 h-lim-p 0.0078 0.1041 0.3674 1053.571479 0 0.0157 172 | 0/8 9 h-lim-p 2.5000 20.0000 0.0019 1053.568897 5 0.9007 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1053.568894 1 0.9961 227 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1053.568894 0 1.2500 247 | 0/8 12 h-lim-p 2.3099 20.0000 0.0000 1053.568894 0 0.2526 269 | 0/8 13 h-lim-p 0.1285 20.0000 0.0000 1053.568894 0 0.0018 294 | 0/8 14 h-lim-p 0.0012 20.0000 0.0000 1053.568894 0 0.0000 319 Out... lnL = -1053.568894 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1053.568894 Node 7: lnL = -1053.568894 Node 8: lnL = -1053.568894 Node 9: lnL = -1053.568894 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 378 Sequential format.. Reading seq # 1: YKL026C_Sbay Reading seq # 2: YKL026C_Scer Reading seq # 3: YKL026C_Skud Reading seq # 4: YKL026C_Smik Reading seq # 5: YKL026C_Spar Sequences read.. Counting patterns.. # site patterns = 175 Counting frequencies.. 120 bytes for distance 28000 bytes for lkl0 22400 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.163179 0.023550 0.125508 0.075464 0.134132 0.193889 0.204146 0.241461 lnL0 = -1695.463092 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1695.463092 x= 0.16318 0.02355 0.12551 0.07546 0.13413 0.19389 0.20415 0.24146 1 h-lim-p 0.0013 0.0104 33.4136 1695.234432 7 0.0004 37 | 0/8 2 h-lim-p 0.0018 0.0368 7.9169 1695.208113 5 0.0009 60 | 0/8 3 h-lim-p 0.0036 0.0954 1.9509 1695.206838 3 0.0007 79 | 0/8 4 h-lim-p 0.0050 0.9159 0.2765 1695.206795 2 0.0012 96 | 0/8 5 h-lim-p 0.0031 5.5730 0.1040 1695.206793 0 0.0003 118 | 0/8 6 h-lim-p 0.0024 20.0000 0.0147 1695.206793 0 0.0021 138 | 0/8 7 h-lim-p 0.0099 20.0000 0.0032 1695.206793 0 0.0011 160 | 0/8 8 h-lim-p 0.1163 20.0000 0.0000 1695.206793 0 0.9307 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1695.206793 0 1.0938 203 | 0/8 10 h-lim-p 1.4727 20.0000 0.0000 1695.206793 0 2.9454 224 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1695.206793 0 0.0000 268 Out... lnL = -1695.206793 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1695.206793 Node 7: lnL = -1695.206793 Node 8: lnL = -1695.206793 Node 9: lnL = -1695.206793 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 851 Sequential format.. Reading seq # 1: YKL028W_Sbay Reading seq # 2: YKL028W_Scer Reading seq # 3: YKL028W_Skud Reading seq # 4: YKL028W_Smik Reading seq # 5: YKL028W_Spar Sequences read.. Counting patterns.. # site patterns = 279 Counting frequencies.. 120 bytes for distance 44640 bytes for lkl0 35712 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.130253 0.096186 0.053450 0.093649 0.078776 0.168363 0.240632 0.202368 lnL0 = -3870.483037 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3870.483037 x= 0.13025 0.09619 0.05345 0.09365 0.07878 0.16836 0.24063 0.20237 1 h-lim-p 0.0021 0.7147 192.1705 3867.611499 6 0.0002 38 | 0/8 2 h-lim-p 0.0005 0.0042 45.0003 3867.360669 4 0.0003 58 | 0/8 3 h-lim-p 0.0005 0.0070 25.3431 3867.308009 2 0.0002 74 | 0/8 4 h-lim-p 0.0006 0.0311 8.6681 3867.291215 3 0.0005 92 | 0/8 5 h-lim-p 0.0020 0.0746 2.2889 3867.290608 3 0.0002 112 | 0/8 6 h-lim-p 0.0011 0.5725 0.5029 3867.290553 1 0.0004 126 | 0/8 7 h-lim-p 0.0079 13.9554 0.0287 3867.290553 0 0.0009 148 | 0/8 8 h-lim-p 0.0679 20.0000 0.0004 3867.290373 0 0.8143 171 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3867.290371 0 1.0938 191 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3867.290371 0 1.0938 211 | 0/8 11 h-lim-p 1.1212 20.0000 0.0000 3867.290371 0 4.4848 233 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3867.290371 0 0.1367 256 | 0/8 13 h-lim-p 0.0617 20.0000 0.0000 3867.290371 0 0.0039 279 | 0/8 14 h-lim-p 0.0010 20.0000 0.0000 3867.290371 0 0.0010 299 | 0/8 15 h-lim-p 0.0007 20.0000 0.0001 3867.290371 0 0.0000 328 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 3867.290371 0 0.0000 362 Out... lnL = -3867.290371 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3867.290371 Node 7: lnL = -3867.290371 Node 8: lnL = -3867.290371 Node 9: lnL = -3867.290371 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 875 Sequential format.. Reading seq # 1: YKL029C_Sbay Reading seq # 2: YKL029C_Scer Reading seq # 3: YKL029C_Skud Reading seq # 4: YKL029C_Smik Reading seq # 5: YKL029C_Spar Sequences read.. Counting patterns.. # site patterns = 252 Counting frequencies.. 120 bytes for distance 40320 bytes for lkl0 32256 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.076977 0.113011 0.035882 0.083546 0.061332 0.151106 0.154439 0.132952 lnL0 = -3570.163355 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3570.163355 x= 0.07698 0.11301 0.03588 0.08355 0.06133 0.15111 0.15444 0.13295 1 h-lim-p 0.0010 0.0079 219.6561 3567.737870 3 0.0001 30 | 0/8 2 h-lim-p 0.0003 0.0023 53.7117 3567.475315 8 0.0002 62 | 0/8 3 h-lim-p 0.0004 0.0085 27.5360 3567.422135 2 0.0002 78 | 0/8 4 h-lim-p 0.0004 0.0172 11.3451 3567.410764 5 0.0002 103 | 0/8 5 h-lim-p 0.0016 0.1514 1.5267 3567.410545 2 0.0002 121 | 0/8 6 h-lim-p 0.0024 1.8953 0.1243 3567.410542 1 0.0003 137 | 0/8 7 h-lim-p 0.0157 20.0000 0.0024 3567.410391 0 0.1256 160 | 0/8 8 h-lim-p 0.0014 0.3156 0.2179 3567.409300 0 0.0027 181 | 0/8 9 h-lim-p 0.6657 20.0000 0.0009 3567.409258 0 1.3313 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 3567.409253 0 1.0938 222 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3567.409253 0 1.0938 242 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3567.409253 0 2.1875 262 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 3567.409253 0 0.5469 283 | 0/8 14 h-lim-p 0.1323 20.0000 0.0000 3567.409253 0 0.1323 303 | 0/8 15 h-lim-p 0.0430 20.0000 0.0001 3567.409253 0 0.0013 327 | 0/8 16 h-lim-p 0.0008 20.0000 0.0002 3567.409253 0 0.0001 349 | 0/8 17 h-lim-p 0.0007 20.0000 0.0000 3567.409253 0 0.0000 381 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 3567.409253 0 0.0000 401 Out... lnL = -3567.409253 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3567.409253 Node 7: lnL = -3567.409253 Node 8: lnL = -3567.409253 Node 9: lnL = -3567.409253 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 638 Sequential format.. Reading seq # 1: YKL041W_Sbay Reading seq # 2: YKL041W_Scer Reading seq # 3: YKL041W_Skud Reading seq # 4: YKL041W_Smik Reading seq # 5: YKL041W_Spar Sequences read.. Counting patterns.. # site patterns = 255 Counting frequencies.. 120 bytes for distance 40800 bytes for lkl0 32640 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.110399 0.092279 0.079923 0.141489 0.083389 0.233715 0.329563 0.196098 lnL0 = -3012.949372 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3012.949372 x= 0.11040 0.09228 0.07992 0.14149 0.08339 0.23371 0.32956 0.19610 1 h-lim-p 0.0012 0.0092 73.6199 3012.027406 8 0.0004 41 | 0/8 2 h-lim-p 0.0013 0.0101 17.4501 3011.948871 6 0.0005 67 | 0/8 3 h-lim-p 0.0007 0.0166 13.4953 3011.928172 2 0.0003 83 | 0/8 4 h-lim-p 0.0018 0.0807 2.4023 3011.926810 4 0.0005 104 | 0/8 5 h-lim-p 0.0018 0.3673 0.6680 3011.926603 4 0.0010 126 | 0/8 6 h-lim-p 0.0044 2.8253 0.1530 3011.926592 0 0.0010 147 | 0/8 7 h-lim-p 0.0067 10.8867 0.0223 3011.926592 0 0.0007 169 | 0/8 8 h-lim-p 0.1183 20.0000 0.0001 3011.926577 0 0.9462 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3011.926577 0 1.0938 212 | 0/8 10 h-lim-p 2.2896 20.0000 0.0000 3011.926577 0 2.0034 232 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3011.926577 0 1.0938 252 | 0/8 12 h-lim-p 0.1962 20.0000 0.0000 3011.926577 0 6.2782 277 | 0/8 13 h-lim-p 0.6618 20.0000 0.0001 3011.926577 0 0.3309 297 | 0/8 14 h-lim-p 0.0075 20.0000 0.0031 3011.926577 0 0.0019 318 | 0/8 15 h-lim-p 0.0015 20.0000 0.0038 3011.926577 0 0.0007 338 | 0/8 16 h-lim-p 0.0009 20.0000 0.0032 3011.926577 0 0.0000 371 | 0/8 17 h-lim-p 0.0015 20.0000 0.0000 3011.926577 0 0.0000 407 Out... lnL = -3011.926577 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3011.926577 Node 7: lnL = -3011.926577 Node 8: lnL = -3011.926577 Node 9: lnL = -3011.926577 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 653 Sequential format.. Reading seq # 1: YKL042W_Sbay Reading seq # 2: YKL042W_Scer Reading seq # 3: YKL042W_Skud Reading seq # 4: YKL042W_Smik Reading seq # 5: YKL042W_Spar Sequences read.. Counting patterns.. # site patterns = 227 Counting frequencies.. 120 bytes for distance 36320 bytes for lkl0 29056 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.097341 0.071475 0.055848 0.095294 0.064062 0.176193 0.156514 0.156698 lnL0 = -2734.966006 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2734.966006 x= 0.09734 0.07147 0.05585 0.09529 0.06406 0.17619 0.15651 0.15670 1 h-lim-p 0.0028 0.0224 138.5110 2733.114072 6 0.0002 39 | 0/8 2 h-lim-p 0.0005 0.0038 37.6951 2732.906968 7 0.0003 70 | 0/8 3 h-lim-p 0.0005 0.0076 24.7064 2732.858475 2 0.0002 86 | 0/8 4 h-lim-p 0.0012 0.0468 4.4775 2732.855694 3 0.0003 106 | 0/8 5 h-lim-p 0.0022 0.4312 0.5879 2732.855632 2 0.0004 124 | 0/8 6 h-lim-p 0.0010 1.0502 0.2073 2732.855624 1 0.0004 146 | 0/8 7 h-lim-p 0.0087 18.2662 0.0096 2732.855623 0 0.0038 166 | 0/8 8 h-lim-p 0.0102 20.0000 0.0036 2732.855207 0 0.1628 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2732.855169 2 0.9961 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2732.855169 0 1.0938 234 | 0/8 11 h-lim-p 1.1992 20.0000 0.0000 2732.855169 0 1.1992 254 | 0/8 12 h-lim-p 0.3292 20.0000 0.0000 2732.855169 0 0.0206 277 | 0/8 13 h-lim-p 0.0033 20.0000 0.0002 2732.855169 0 0.0016 297 | 0/8 14 h-lim-p 0.0016 20.0000 0.0002 2732.855169 0 0.0000 325 | 0/8 15 h-lim-p 0.0011 20.0000 0.0000 2732.855169 0 0.0000 356 Out... lnL = -2732.855169 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2732.855169 Node 7: lnL = -2732.855169 Node 8: lnL = -2732.855169 Node 9: lnL = -2732.855169 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 123 Sequential format.. Reading seq # 1: YKL043W_Sbay Reading seq # 2: YKL043W_Scer Reading seq # 3: YKL043W_Skud Reading seq # 4: YKL043W_Smik Reading seq # 5: YKL043W_Spar Sequences read.. Counting patterns.. # site patterns = 41 Counting frequencies.. 120 bytes for distance 6560 bytes for lkl0 5248 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.165473 0.000060 0.037519 0.052232 0.032854 0.043806 0.053417 0.199718 lnL0 = -368.981733 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 368.981733 x= 0.16547 0.00006 0.03752 0.05223 0.03285 0.04381 0.05342 0.19972 1 h-lim-p 0.0000 0.0000 108.0930 368.964898 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0010 49.7382 368.649758 0 0.0003 39 | 1/8 3 h-lim-p 0.0003 0.0023 13.5510 368.603599 0 0.0006 52 | 1/8 4 h-lim-p 0.0043 0.0638 1.8534 368.574944 1 0.0054 66 | 1/8 5 h-lim-p 0.0022 0.0365 4.6013 368.521517 0 0.0032 78 | 1/8 6 h-lim-p 0.0027 0.0218 3.5852 368.387175 0 0.0041 90 | 1/8 7 h-lim-p 0.0016 0.0125 4.6234 366.944747 0 0.0062 104 | 1/8 8 h-lim-p 0.2189 1.7514 0.0295 366.660975 0 0.4378 117 | 1/8 9 h-lim-p 0.4355 3.4836 0.0129 366.552516 0 0.8709 137 | 1/8 10 h-lim-p 0.7134 5.7075 0.0080 366.532955 6 0.3696 170 | 1/8 11 h-lim-p 0.7149 13.8340 0.0042 366.527078 4 0.7438 198 | 1/8 12 h-lim-p 2.5000 20.0000 0.0009 366.526675 5 0.7438 230 | 1/8 13 h-lim-p 2.5000 20.0000 0.0001 366.526660 2 1.0938 253 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 366.526659 0 2.1875 272 | 1/8 15 h-lim-p 1.8024 20.0000 0.0000 366.526659 0 0.3943 292 | 1/8 16 h-lim-p 0.6435 20.0000 0.0000 366.526659 0 0.0000 325 Out... lnL = -366.526659 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -366.526659 Node 7: lnL = -366.526659 Node 8: lnL = -366.526659 Node 9: lnL = -366.526659 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 857 Sequential format.. Reading seq # 1: YKL045W_Sbay Reading seq # 2: YKL045W_Scer Reading seq # 3: YKL045W_Skud Reading seq # 4: YKL045W_Smik Reading seq # 5: YKL045W_Spar Sequences read.. Counting patterns.. # site patterns = 336 Counting frequencies.. 120 bytes for distance 53760 bytes for lkl0 43008 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.082398 0.164991 0.102488 0.153740 0.144174 0.212643 0.218236 0.169960 lnL0 = -4158.305014 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4158.305014 x= 0.08240 0.16499 0.10249 0.15374 0.14417 0.21264 0.21824 0.16996 1 h-lim-p 0.0020 0.0158 95.0000 4157.044105 9 0.0003 47 | 0/8 2 h-lim-p 0.0014 0.0128 19.5280 4156.961608 7 0.0004 79 | 0/8 3 h-lim-p 0.0009 0.0334 9.6678 4156.947100 3 0.0004 98 | 0/8 4 h-lim-p 0.0024 0.1904 1.5322 4156.946646 4 0.0004 121 | 0/8 5 h-lim-p 0.0014 0.6959 0.4597 4156.946601 2 0.0004 138 | 0/8 6 h-lim-p 0.0019 3.3615 0.1046 4156.946599 1 0.0005 161 | 0/8 7 h-lim-p 0.0351 20.0000 0.0014 4156.946596 0 0.0351 181 | 0/8 8 h-lim-p 0.0035 20.0000 0.0142 4156.946522 0 0.0139 203 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4156.946520 0 1.0938 223 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4156.946520 0 1.0938 243 | 0/8 11 h-lim-p 1.1687 20.0000 0.0000 4156.946520 0 0.5113 263 | 0/8 12 h-lim-p 0.1738 20.0000 0.0000 4156.946520 0 0.0001 293 | 0/8 13 h-lim-p 0.0009 20.0000 0.0000 4156.946520 0 0.0009 313 Out... lnL = -4156.946520 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4156.946520 Node 7: lnL = -4156.946520 Node 8: lnL = -4156.946520 Node 9: lnL = -4156.946520 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 861 Sequential format.. Reading seq # 1: YKL046C_Sbay Reading seq # 2: YKL046C_Scer Reading seq # 3: YKL046C_Skud Reading seq # 4: YKL046C_Smik Reading seq # 5: YKL046C_Spar Sequences read.. Counting patterns.. # site patterns = 308 Counting frequencies.. 120 bytes for distance 49280 bytes for lkl0 39424 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.114136 0.059839 0.107286 0.150163 0.140661 0.214926 0.244388 0.197254 lnL0 = -4155.399678 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4155.399678 x= 0.11414 0.05984 0.10729 0.15016 0.14066 0.21493 0.24439 0.19725 1 h-lim-p 0.0041 0.0491 142.5943 4153.229788 3 0.0002 31 | 0/8 2 h-lim-p 0.0016 0.0126 20.9297 4153.129395 6 0.0005 58 | 0/8 3 h-lim-p 0.0009 0.0326 10.2186 4153.114321 6 0.0003 83 | 0/8 4 h-lim-p 0.0016 0.1022 2.2465 4153.113356 4 0.0004 104 | 0/8 5 h-lim-p 0.0029 1.7041 0.3157 4153.113330 2 0.0006 121 | 0/8 6 h-lim-p 0.0048 10.5955 0.0363 4153.113330 0 0.0005 143 | 0/8 7 h-lim-p 0.0097 20.0000 0.0020 4153.113329 0 0.0085 163 | 0/8 8 h-lim-p 0.0094 20.0000 0.0018 4153.113297 0 0.0755 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4153.113297 0 1.0938 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4153.113297 0 1.0938 226 | 0/8 11 h-lim-p 0.9049 20.0000 0.0000 4153.113297 0 3.6196 248 | 0/8 12 h-lim-p 0.0626 20.0000 0.0006 4153.113297 0 0.0626 268 | 0/8 13 h-lim-p 0.0171 20.0000 0.0020 4153.113297 0 0.0000 310 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -4153.113297 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4153.113297 Node 7: lnL = -4153.113297 Node 8: lnL = -4153.113297 Node 9: lnL = -4153.113297 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 336 Sequential format.. Reading seq # 1: YKL047W_Sbay Reading seq # 2: YKL047W_Scer Reading seq # 3: YKL047W_Skud Reading seq # 4: YKL047W_Smik Reading seq # 5: YKL047W_Spar Sequences read.. Counting patterns.. # site patterns = 170 Counting frequencies.. 120 bytes for distance 27200 bytes for lkl0 21760 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.088258 0.068907 0.068380 0.125980 0.080750 0.280509 0.403144 0.164691 lnL0 = -1613.103086 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1613.103086 x= 0.08826 0.06891 0.06838 0.12598 0.08075 0.28051 0.40314 0.16469 1 h-lim-p 0.0032 0.0257 46.0886 1612.511917 7 0.0006 39 | 0/8 2 h-lim-p 0.0008 0.0064 16.4251 1612.418563 2 0.0008 55 | 0/8 3 h-lim-p 0.0014 0.0169 8.9694 1612.398099 2 0.0006 71 | 0/8 4 h-lim-p 0.0016 0.0920 3.6590 1612.393285 6 0.0009 98 | 0/8 5 h-lim-p 0.0029 0.2844 1.1027 1612.392385 4 0.0017 121 | 0/8 6 h-lim-p 0.0030 0.4860 0.5983 1612.392249 3 0.0010 141 | 0/8 7 h-lim-p 0.0027 1.9571 0.2139 1612.392212 3 0.0018 168 | 0/8 8 h-lim-p 0.4081 20.0000 0.0009 1612.391541 0 1.2243 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1612.391540 0 1.0938 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1612.391540 0 1.0938 229 | 0/8 11 h-lim-p 1.4586 20.0000 0.0000 1612.391540 0 2.9171 250 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1612.391540 0 0.5469 271 | 0/8 13 h-lim-p 0.3214 20.0000 0.0000 1612.391540 0 0.0044 296 | 0/8 14 h-lim-p 0.0014 20.0000 0.0000 1612.391540 0 0.0014 316 | 0/8 15 h-lim-p 0.0010 20.0000 0.0000 1612.391540 0 0.0001 339 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 1612.391540 0 0.0000 371 Out... lnL = -1612.391540 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1612.391540 Node 7: lnL = -1612.391540 Node 8: lnL = -1612.391540 Node 9: lnL = -1612.391540 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 336 Sequential format.. Reading seq # 1: YKL048C_Sbay Reading seq # 2: YKL048C_Scer Reading seq # 3: YKL048C_Skud Reading seq # 4: YKL048C_Smik Reading seq # 5: YKL048C_Spar Sequences read.. Counting patterns.. # site patterns = 165 Counting frequencies.. 120 bytes for distance 26400 bytes for lkl0 21120 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.097993 0.054734 0.068224 0.123558 0.083172 0.302176 0.398290 0.175314 lnL0 = -1611.058842 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1611.058842 x= 0.09799 0.05473 0.06822 0.12356 0.08317 0.30218 0.39829 0.17531 1 h-lim-p 0.0081 0.0651 31.1235 1610.795328 8 0.0006 43 | 0/8 2 h-lim-p 0.0014 0.0115 7.5504 1610.776428 2 0.0007 59 | 0/8 3 h-lim-p 0.0018 0.0668 2.8357 1610.774436 5 0.0006 84 | 0/8 4 h-lim-p 0.0011 0.1965 1.4717 1610.773462 3 0.0011 102 | 0/8 5 h-lim-p 0.0041 0.4116 0.4162 1610.773343 3 0.0015 120 | 0/8 6 h-lim-p 0.0020 0.5869 0.3132 1610.773307 2 0.0011 145 | 0/8 7 h-lim-p 0.0066 7.0808 0.0510 1610.773305 1 0.0016 168 | 0/8 8 h-lim-p 0.3668 20.0000 0.0002 1610.773274 0 1.1005 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1610.773274 0 1.0938 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1610.773274 0 1.2500 229 | 0/8 11 h-lim-p 1.6248 20.0000 0.0000 1610.773274 0 0.2031 251 | 0/8 12 h-lim-p 0.0915 20.0000 0.0000 1610.773274 0 0.0114 273 | 0/8 13 h-lim-p 0.0063 20.0000 0.0000 1610.773274 0 0.0000 311 | 0/8 14 h-lim-p 0.0000 20.0000 0.0005 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -1610.773274 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1610.773274 Node 7: lnL = -1610.773274 Node 8: lnL = -1610.773274 Node 9: lnL = -1610.773274 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 668 Sequential format.. Reading seq # 1: YKL050C_Sbay Reading seq # 2: YKL050C_Scer Reading seq # 3: YKL050C_Skud Reading seq # 4: YKL050C_Smik Reading seq # 5: YKL050C_Spar Sequences read.. Counting patterns.. # site patterns = 267 Counting frequencies.. 120 bytes for distance 42720 bytes for lkl0 34176 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.070773 0.039984 0.140902 0.075225 0.128725 0.206195 0.280149 0.137018 lnL0 = -2805.034330 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2805.034330 x= 0.07077 0.03998 0.14090 0.07522 0.12873 0.20619 0.28015 0.13702 1 h-lim-p 0.0015 0.8041 191.6349 2800.432467 9 0.0003 42 | 0/8 2 h-lim-p 0.0004 0.0033 51.2858 2799.802979 1 0.0005 56 | 0/8 3 h-lim-p 0.0017 0.0165 15.4906 2799.738973 7 0.0006 86 | 0/8 4 h-lim-p 0.0015 0.0247 5.9858 2799.733008 5 0.0004 110 | 0/8 5 h-lim-p 0.0019 0.1575 1.2320 2799.732551 4 0.0006 132 | 0/8 6 h-lim-p 0.0025 1.2331 0.3156 2799.732512 2 0.0008 150 | 0/8 7 h-lim-p 0.0066 6.2516 0.0391 2799.732499 2 0.0035 175 | 0/8 8 h-lim-p 0.0270 20.0000 0.0051 2799.729681 0 0.2161 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 2799.729475 1 1.0938 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2799.729474 0 1.0938 240 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2799.729474 0 1.0938 260 | 0/8 12 h-lim-p 1.0558 20.0000 0.0000 2799.729474 0 4.2232 282 | 0/8 13 h-lim-p 0.5520 20.0000 0.0001 2799.729474 0 0.2760 302 | 0/8 14 h-lim-p 0.0114 20.0000 0.0021 2799.729474 0 0.0001 328 | 0/8 15 h-lim-p 0.0006 20.0000 0.0003 2799.729474 0 0.0000 361 | 0/8 16 h-lim-p 0.0000 20.0000 0.0011 | 0/8 17 h-lim-p 0.0000 20.0000 0.0011 Out... lnL = -2799.729474 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2799.729474 Node 7: lnL = -2799.729474 Node 8: lnL = -2799.729474 Node 9: lnL = -2799.729474 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 859 Sequential format.. Reading seq # 1: YKL051W_Sbay Reading seq # 2: YKL051W_Scer Reading seq # 3: YKL051W_Skud Reading seq # 4: YKL051W_Smik Reading seq # 5: YKL051W_Spar Sequences read.. Counting patterns.. # site patterns = 212 Counting frequencies.. 120 bytes for distance 33920 bytes for lkl0 27136 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.099800 0.021714 0.050913 0.078196 0.033759 0.132451 0.149840 0.142002 lnL0 = -3103.713106 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3103.713106 x= 0.09980 0.02171 0.05091 0.07820 0.03376 0.13245 0.14984 0.14200 1 h-lim-p 0.0001 0.0009 227.5066 3101.718598 6 0.0001 33 | 0/8 2 h-lim-p 0.0007 0.0071 28.6575 3101.627936 6 0.0002 58 | 0/8 3 h-lim-p 0.0005 0.0141 14.2331 3101.615138 6 0.0002 84 | 0/8 4 h-lim-p 0.0002 0.0068 9.1942 3101.612930 5 0.0001 109 | 0/8 5 h-lim-p 0.0009 0.2104 0.8024 3101.612848 3 0.0002 130 | 0/8 6 h-lim-p 0.0010 0.7432 0.1985 3101.612846 1 0.0001 154 | 0/8 7 h-lim-p 0.0111 20.0000 0.0022 3101.612846 0 0.0024 175 | 0/8 8 h-lim-p 0.0122 20.0000 0.0004 3101.612831 0 0.1957 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3101.612830 0 1.0938 219 | 0/8 10 h-lim-p 2.0690 20.0000 0.0000 3101.612830 0 0.9052 239 | 0/8 11 h-lim-p 0.7596 20.0000 0.0000 3101.612830 0 0.0030 266 | 0/8 12 h-lim-p 0.0014 20.0000 0.0000 3101.612830 0 0.0001 289 | 0/8 13 h-lim-p 0.0000 20.0000 0.0002 3101.612830 0 0.0000 321 | 0/8 14 h-lim-p 0.0000 20.0000 0.0020 | 0/8 15 h-lim-p 0.0000 20.0000 0.0020 Out... lnL = -3101.612830 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3101.612830 Node 7: lnL = -3101.612830 Node 8: lnL = -3101.612830 Node 9: lnL = -3101.612830 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 857 Sequential format.. Reading seq # 1: YKL052C_Sbay Reading seq # 2: YKL052C_Scer Reading seq # 3: YKL052C_Skud Reading seq # 4: YKL052C_Smik Reading seq # 5: YKL052C_Spar Sequences read.. Counting patterns.. # site patterns = 212 Counting frequencies.. 120 bytes for distance 33920 bytes for lkl0 27136 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.103185 0.016871 0.049205 0.079932 0.030477 0.132200 0.152769 0.145272 lnL0 = -3093.414891 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3093.414891 x= 0.10319 0.01687 0.04921 0.07993 0.03048 0.13220 0.15277 0.14527 1 h-lim-p 0.0001 0.0009 274.2470 3090.972377 7 0.0001 39 | 0/8 2 h-lim-p 0.0007 0.0063 30.9749 3090.852039 6 0.0003 64 | 0/8 3 h-lim-p 0.0005 0.0109 15.1004 3090.837016 6 0.0002 94 | 0/8 4 h-lim-p 0.0004 0.0068 5.8045 3090.836145 4 0.0001 118 | 0/8 5 h-lim-p 0.0003 0.0952 1.4042 3090.835975 3 0.0002 136 | 0/8 6 h-lim-p 0.0005 0.4609 0.5671 3090.835950 2 0.0002 152 | 0/8 7 h-lim-p 0.0146 20.0000 0.0071 3090.835950 0 0.0016 174 | 0/8 8 h-lim-p 0.0211 20.0000 0.0005 3090.835833 0 0.3372 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3090.835830 0 1.0938 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3090.835830 0 0.5469 239 | 0/8 11 h-lim-p 0.3721 20.0000 0.0000 3090.835830 0 0.0000 283 | 0/8 12 h-lim-p 0.0000 20.0000 0.0045 | 0/8 13 h-lim-p 0.0000 20.0000 0.0045 Out... lnL = -3090.835830 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3090.835830 Node 7: lnL = -3090.835830 Node 8: lnL = -3090.835830 Node 9: lnL = -3090.835830 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 143 Sequential format.. Reading seq # 1: YKL053C-A_Sbay Reading seq # 2: YKL053C-A_Scer Reading seq # 3: YKL053C-A_Skud Reading seq # 4: YKL053C-A_Smik Reading seq # 5: YKL053C-A_Spar Sequences read.. Counting patterns.. # site patterns = 76 Counting frequencies.. 120 bytes for distance 12160 bytes for lkl0 9728 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.124851 0.105696 0.070641 0.099855 0.064119 0.253840 0.186037 0.191990 lnL0 = -627.815695 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 627.815695 x= 0.12485 0.10570 0.07064 0.09986 0.06412 0.25384 0.18604 0.19199 1 h-lim-p 0.0006 0.0047 32.2325 627.080476 0 0.0012 23 | 0/8 2 h-lim-p 0.0008 0.0064 18.5243 626.926424 0 0.0016 36 | 0/8 3 h-lim-p 0.0022 0.0177 8.0968 626.894129 7 0.0012 63 | 0/8 4 h-lim-p 0.0028 0.1155 3.5377 626.886667 5 0.0015 86 | 0/8 5 h-lim-p 0.0093 0.2553 0.5585 626.886305 3 0.0020 106 | 0/8 6 h-lim-p 0.0220 4.7567 0.0497 626.883198 0 0.0880 128 | 0/8 7 h-lim-p 0.0101 0.2900 0.4325 626.859385 0 0.0202 149 | 0/8 8 h-lim-p 0.0053 0.1591 1.6552 626.853082 7 0.0033 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0015 626.852291 4 0.9422 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 626.852290 0 1.0938 227 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 626.852290 0 1.0938 247 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 626.852290 0 2.1875 267 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 626.852290 0 0.5469 288 | 0/8 14 h-lim-p 0.2288 20.0000 0.0000 626.852290 0 0.0215 311 | 0/8 15 h-lim-p 0.0103 20.0000 0.0000 626.852290 0 0.0000 340 Out... lnL = -626.852290 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -626.852290 Node 7: lnL = -626.852290 Node 8: lnL = -626.852290 Node 9: lnL = -626.852290 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 459 Sequential format.. Reading seq # 1: YKL054C_Sbay Reading seq # 2: YKL054C_Scer Reading seq # 3: YKL054C_Skud Reading seq # 4: YKL054C_Smik Reading seq # 5: YKL054C_Spar Sequences read.. Counting patterns.. # site patterns = 115 Counting frequencies.. 120 bytes for distance 18400 bytes for lkl0 14720 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.033618 0.002504 0.043517 0.082173 0.007710 1.077131 0.103193 0.118076 lnL0 = -1417.300518 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1417.300518 x= 0.03362 0.00250 0.04352 0.08217 0.00771 1.07713 0.10319 0.11808 1 h-lim-p 0.0002 0.0033 376.4928 1415.260907 7 0.0000 39 | 0/8 2 h-lim-p 0.0002 0.0018 82.2288 1414.808850 3 0.0001 57 | 0/8 3 h-lim-p 0.0001 0.0010 43.5317 1414.676200 0 0.0002 70 | 0/8 4 h-lim-p 0.0017 0.0185 6.2300 1414.671293 5 0.0003 97 | 0/8 5 h-lim-p 0.0009 0.0106 1.8190 1414.668058 0 0.0018 110 | 0/8 6 h-lim-p 0.0001 0.0010 14.3196 1414.647937 m 0.0010 122 | 0/8 7 h-lim-p 0.0119 0.3781 1.1889 1414.618941 0 0.0475 136 | 0/8 8 h-lim-p 0.0379 0.3031 0.0494 1414.598360 m 0.3031 148 | 0/8 9 h-lim-p 0.0000 0.0000 0.3189 h-lim-p: 7.81118350e-20 6.24894680e-19 3.18937644e-01 1414.598360 .. | 0/8 10 h-lim-p 0.0000 0.0512 6.8741 1414.593397 0 0.0002 188 | 0/8 11 h-lim-p 0.0000 0.0000 4.4152 1414.593097 m 0.0000 200 | 1/8 12 h-lim-p 0.0001 0.1249 0.8896 1414.592998 0 0.0002 213 | 1/8 13 h-lim-p 0.0008 0.5430 0.2380 1414.592932 0 0.0016 233 | 1/8 14 h-lim-p 0.0004 0.2619 0.9622 1414.592851 1 0.0005 254 | 1/8 15 h-lim-p 0.0012 0.6140 0.3953 1414.592801 2 0.0013 278 | 1/8 16 h-lim-p 0.0003 0.6400 1.5582 1414.591710 0 0.0080 301 | 1/8 17 h-lim-p 2.5000 20.0000 0.0009 1414.591426 2 1.0938 317 | 1/8 18 h-lim-p 2.5000 20.0000 0.0001 1414.591426 0 1.0938 336 | 1/8 19 h-lim-p 2.5000 20.0000 0.0000 1414.591426 0 2.1875 355 | 1/8 20 h-lim-p 2.5000 20.0000 0.0000 1414.591426 0 0.5469 375 | 1/8 21 h-lim-p 0.1210 20.0000 0.0001 1414.591426 0 0.0019 399 | 1/8 22 h-lim-p 0.0006 20.0000 0.0002 1414.591426 0 0.0000 427 | 1/8 23 h-lim-p 0.0000 20.0000 0.0000 1414.591426 0 0.0000 458 Out... lnL = -1414.591426 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1414.591426 Node 7: lnL = -1414.591426 Node 8: lnL = -1414.591426 Node 9: lnL = -1414.591426 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 432 Sequential format.. Reading seq # 1: YKL056C_Sbay Reading seq # 2: YKL056C_Scer Reading seq # 3: YKL056C_Skud Reading seq # 4: YKL056C_Smik Reading seq # 5: YKL056C_Spar Sequences read.. Counting patterns.. # site patterns = 111 Counting frequencies.. 120 bytes for distance 17760 bytes for lkl0 14208 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.041542 0.112458 0.087358 0.111080 4.703214 0.188689 0.212431 lnL0 = -1419.387289 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1419.387289 x= 0.00006 0.04154 0.11246 0.08736 0.11108 4.70321 0.18869 0.21243 1 h-lim-p 0.0000 0.0000 200.9391 1419.350503 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0031 97.4563 1416.671743 0 0.0006 40 | 1/8 3 h-lim-p 0.0011 0.0088 26.7270 1416.357129 6 0.0009 66 | 1/8 4 h-lim-p 0.0037 0.0293 5.6654 1416.320672 4 0.0014 86 | 1/8 5 h-lim-p 0.0034 0.0565 2.3902 1416.241229 1 0.0043 100 | 1/8 6 h-lim-p 0.0057 0.1008 1.7894 1409.290625 0 0.0455 115 | 1/8 7 h-lim-p 0.2535 2.0284 0.0495 1408.491560 0 0.7606 128 | 1/8 8 h-lim-p 2.0549 16.4396 0.0076 1408.452738 6 0.7006 162 | 1/8 9 h-lim-p 2.3180 20.0000 0.0023 1408.450719 4 0.6101 190 | 0/8 10 h-lim-p 0.0045 5.4703 0.3111 1408.450694 2 0.0005 215 | 0/8 11 h-lim-p 0.2576 2.0611 0.0002 1408.450686 0 0.5153 236 | 0/8 12 h-lim-p 0.0760 0.6082 0.0003 1408.450686 0 0.1521 257 | 0/8 13 h-lim-p 0.0035 0.0283 0.0041 1408.450686 0 0.0031 277 | 0/8 14 h-lim-p 0.1180 20.0000 0.0001 1408.450686 0 0.0258 298 | 0/8 15 h-lim-p 0.0506 2.2181 0.0001 1408.450686 0 0.0000 331 | 0/8 16 h-lim-p 0.0000 0.0221 0.0167 .. | 0/8 17 h-lim-p 0.0000 0.0007 0.1184 | 0/8 18 h-lim-p 0.0000 0.0007 0.1184 Out... lnL = -1408.450686 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1408.450686 Node 7: lnL = -1408.450686 Node 8: lnL = -1408.450686 Node 9: lnL = -1408.450686 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 470 Sequential format.. Reading seq # 1: YKL057C_Sbay Reading seq # 2: YKL057C_Scer Reading seq # 3: YKL057C_Skud Reading seq # 4: YKL057C_Smik Reading seq # 5: YKL057C_Spar Sequences read.. Counting patterns.. # site patterns = 141 Counting frequencies.. 120 bytes for distance 22560 bytes for lkl0 18048 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.056907 0.084699 0.058781 0.060451 0.047667 0.101202 0.099310 0.095199 lnL0 = -1729.982879 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1729.982879 x= 0.05691 0.08470 0.05878 0.06045 0.04767 0.10120 0.09931 0.09520 1 h-lim-p 0.0002 0.0013 113.3681 1728.629763 0 0.0002 22 | 0/8 2 h-lim-p 0.0017 0.0139 13.6426 1728.597083 3 0.0004 41 | 0/8 3 h-lim-p 0.0011 0.0115 4.3919 1728.595888 2 0.0001 59 | 0/8 4 h-lim-p 0.0009 0.1797 0.6412 1728.595832 3 0.0003 80 | 0/8 5 h-lim-p 0.0012 1.2757 0.1446 1728.595822 2 0.0006 105 | 0/8 6 h-lim-p 0.0018 2.2706 0.0508 1728.595799 0 0.0027 125 | 0/8 7 h-lim-p 0.0020 1.7733 0.0685 1728.594817 0 0.0157 148 | 0/8 8 h-lim-p 0.0016 0.1930 0.6702 1728.589769 0 0.0032 169 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 1728.589458 3 0.9961 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1728.589458 0 1.2500 215 | 0/8 11 h-lim-p 1.6560 20.0000 0.0000 1728.589458 0 0.1811 237 | 0/8 12 h-lim-p 0.0823 20.0000 0.0000 1728.589458 0 0.0039 261 | 0/8 13 h-lim-p 0.0022 20.0000 0.0000 1728.589458 0 0.0001 284 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 1728.589458 0 0.0002 304 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 1728.589458 0 0.0000 325 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 1728.589458 0 0.0000 351 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 1728.589458 0 0.0000 382 Out... lnL = -1728.589458 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1728.589458 Node 7: lnL = -1728.589458 Node 8: lnL = -1728.589458 Node 9: lnL = -1728.589458 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 762 Sequential format.. Reading seq # 1: YKL058W_Sbay Reading seq # 2: YKL058W_Scer Reading seq # 3: YKL058W_Skud Reading seq # 4: YKL058W_Smik Reading seq # 5: YKL058W_Spar Sequences read.. Counting patterns.. # site patterns = 334 Counting frequencies.. 120 bytes for distance 53440 bytes for lkl0 42752 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.090521 0.213480 0.117690 0.175070 0.158106 0.312474 0.308602 0.188525 lnL0 = -3962.355361 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3962.355361 x= 0.09052 0.21348 0.11769 0.17507 0.15811 0.31247 0.30860 0.18853 1 h-lim-p 0.0039 0.0311 49.4131 3961.739913 5 0.0005 34 | 0/8 2 h-lim-p 0.0016 0.0155 16.0566 3961.661346 3 0.0007 52 | 0/8 3 h-lim-p 0.0011 0.0507 9.7014 3961.642051 4 0.0005 72 | 0/8 4 h-lim-p 0.0024 0.2031 2.2461 3961.640996 3 0.0005 91 | 0/8 5 h-lim-p 0.0041 0.9980 0.2521 3961.640960 3 0.0012 111 | 0/8 6 h-lim-p 0.0046 4.3039 0.0669 3961.640959 0 0.0010 132 | 0/8 7 h-lim-p 0.0207 20.0000 0.0032 3961.640957 0 0.0207 152 | 0/8 8 h-lim-p 0.0146 20.0000 0.0046 3961.640873 0 0.0583 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3961.640872 0 1.0938 194 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3961.640872 0 1.0938 214 | 0/8 11 h-lim-p 1.2373 20.0000 0.0000 3961.640872 0 0.9280 234 | 0/8 12 h-lim-p 0.3554 20.0000 0.0000 3961.640872 0 0.0014 261 | 0/8 13 h-lim-p 0.0001 20.0000 0.0002 3961.640872 0 0.0000 282 | 0/8 14 h-lim-p 0.0001 20.0000 0.0001 3961.640872 0 0.0000 304 | 0/8 15 h-lim-p 0.0006 20.0000 0.0000 3961.640872 0 0.0000 329 Out... lnL = -3961.640872 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3961.640872 Node 7: lnL = -3961.640872 Node 8: lnL = -3961.640872 Node 9: lnL = -3961.640872 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 770 Sequential format.. Reading seq # 1: YKL059C_Sbay Reading seq # 2: YKL059C_Scer Reading seq # 3: YKL059C_Skud Reading seq # 4: YKL059C_Smik Reading seq # 5: YKL059C_Spar Sequences read.. Counting patterns.. # site patterns = 347 Counting frequencies.. 120 bytes for distance 55520 bytes for lkl0 44416 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.140067 0.105312 0.053984 0.172915 0.233913 0.316365 0.376080 0.237248 lnL0 = -4019.363441 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4019.363441 x= 0.14007 0.10531 0.05398 0.17292 0.23391 0.31636 0.37608 0.23725 1 h-lim-p 0.0071 0.0570 87.0998 4018.276121 7 0.0003 42 | 0/8 2 h-lim-p 0.0017 0.0136 13.7306 4018.229737 6 0.0005 68 | 0/8 3 h-lim-p 0.0017 0.1819 3.9327 4018.223694 3 0.0008 87 | 0/8 4 h-lim-p 0.0024 0.3635 1.3915 4018.222799 2 0.0010 103 | 0/8 5 h-lim-p 0.0058 0.8226 0.2504 4018.222767 2 0.0011 120 | 0/8 6 h-lim-p 0.0044 5.8180 0.0630 4018.222766 0 0.0010 141 | 0/8 7 h-lim-p 0.0188 20.0000 0.0033 4018.222766 0 0.0041 162 | 0/8 8 h-lim-p 0.0585 20.0000 0.0002 4018.222755 0 0.4683 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4018.222755 0 1.0938 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4018.222755 0 1.0938 225 | 0/8 11 h-lim-p 1.0555 20.0000 0.0000 4018.222755 0 3.1666 246 | 0/8 12 h-lim-p 0.9579 20.0000 0.0000 4018.222755 0 0.0000 283 | 0/8 13 h-lim-p 0.0003 20.0000 0.0000 4018.222755 0 0.0000 317 Out... lnL = -4018.222755 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4018.222755 Node 7: lnL = -4018.222755 Node 8: lnL = -4018.222755 Node 9: lnL = -4018.222755 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 701 Sequential format.. Reading seq # 1: YKL061W_Sbay Reading seq # 2: YKL061W_Scer Reading seq # 3: YKL061W_Skud Reading seq # 4: YKL061W_Smik Reading seq # 5: YKL061W_Spar Sequences read.. Counting patterns.. # site patterns = 286 Counting frequencies.. 120 bytes for distance 45760 bytes for lkl0 36608 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.184087 0.025194 0.139155 0.101054 0.070509 0.198519 0.295742 0.260983 lnL0 = -3193.737143 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3193.737143 x= 0.18409 0.02519 0.13916 0.10105 0.07051 0.19852 0.29574 0.26098 1 h-lim-p 0.0004 0.0028 122.9704 3191.674434 7 0.0003 37 | 0/8 2 h-lim-p 0.0010 0.0083 18.3861 3191.591027 2 0.0005 53 | 0/8 3 h-lim-p 0.0003 0.0130 29.4672 3191.529420 5 0.0003 74 | 0/8 4 h-lim-p 0.0015 0.0471 6.1911 3191.520749 6 0.0005 100 | 0/8 5 h-lim-p 0.0011 0.1381 2.8951 3191.519069 2 0.0005 116 | 0/8 6 h-lim-p 0.0018 0.2399 0.7820 3191.518921 3 0.0005 136 | 0/8 7 h-lim-p 0.0055 3.6354 0.0786 3191.518918 1 0.0011 159 | 0/8 8 h-lim-p 0.1674 20.0000 0.0005 3191.518507 0 1.3393 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3191.518498 1 0.9961 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3191.518498 0 1.0938 224 | 0/8 11 h-lim-p 1.2105 20.0000 0.0000 3191.518498 0 1.2105 244 | 0/8 12 h-lim-p 0.5710 20.0000 0.0000 3191.518498 0 0.0000 285 Out... lnL = -3191.518498 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3191.518498 Node 7: lnL = -3191.518498 Node 8: lnL = -3191.518498 Node 9: lnL = -3191.518498 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 846 Sequential format.. Reading seq # 1: YKL062W_Sbay Reading seq # 2: YKL062W_Scer Reading seq # 3: YKL062W_Skud Reading seq # 4: YKL062W_Smik Reading seq # 5: YKL062W_Spar Sequences read.. Counting patterns.. # site patterns = 183 Counting frequencies.. 120 bytes for distance 29280 bytes for lkl0 23424 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.050797 0.040534 0.042665 0.057069 0.040763 0.087155 0.105392 0.081829 lnL0 = -2888.809174 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2888.809174 x= 0.05080 0.04053 0.04267 0.05707 0.04076 0.08716 0.10539 0.08183 1 h-lim-p 0.0002 0.0017 155.9953 2887.942642 7 0.0001 38 | 0/8 2 h-lim-p 0.0004 0.0035 20.9069 2887.924270 4 0.0001 59 | 0/8 3 h-lim-p 0.0003 0.0328 6.1050 2887.922122 4 0.0001 81 | 0/8 4 h-lim-p 0.0004 0.0491 2.0740 2887.921905 4 0.0001 105 | 0/8 5 h-lim-p 0.0006 0.2135 0.3665 2887.921898 2 0.0001 123 | 0/8 6 h-lim-p 0.0003 1.4685 0.1099 2887.921898 0 0.0002 143 | 0/8 7 h-lim-p 0.1609 20.0000 0.0001 2887.921895 0 0.3217 164 | 0/8 8 h-lim-p 0.0003 0.9316 0.1053 2887.921886 0 0.0006 185 | 0/8 9 h-lim-p 1.0892 20.0000 0.0001 2887.921886 0 0.9530 205 | 0/8 10 h-lim-p 1.9344 20.0000 0.0000 2887.921886 0 1.6926 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2887.921886 0 1.0938 245 | 0/8 12 h-lim-p 0.3092 20.0000 0.0000 2887.921886 0 0.0145 269 | 0/8 13 h-lim-p 0.0003 20.0000 0.0014 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -2887.921886 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2887.921886 Node 7: lnL = -2887.921886 Node 8: lnL = -2887.921886 Node 9: lnL = -2887.921886 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 887 Sequential format.. Reading seq # 1: YKL063C_Sbay Reading seq # 2: YKL063C_Scer Reading seq # 3: YKL063C_Skud Reading seq # 4: YKL063C_Smik Reading seq # 5: YKL063C_Spar Sequences read.. Counting patterns.. # site patterns = 292 Counting frequencies.. 120 bytes for distance 46720 bytes for lkl0 37376 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.366689 0.344171 0.294081 0.180995 0.347128 0.318916 0.291172 0.000060 lnL0 = -3982.558388 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3982.558388 x= 0.36669 0.34417 0.29408 0.18099 0.34713 0.31892 0.29117 0.00006 1 h-lim-p 0.0000 0.0000 787.9186 3982.173380 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0005 814.1809 3817.284183 m 0.0005 37 | 1/8 3 h-lim-p 0.0001 0.0007 280.3847 3808.995564 0 0.0003 50 | 1/8 4 h-lim-p 0.0002 0.0015 90.7861 3807.413136 0 0.0004 63 | 1/8 5 h-lim-p 0.0026 0.0393 13.5009 3806.581871 0 0.0039 75 | 1/8 6 h-lim-p 0.0026 0.0238 20.0325 3804.626013 0 0.0053 88 | 1/8 7 h-lim-p 0.0078 0.0621 8.2393 3758.993535 0 0.0311 102 | 1/8 8 h-lim-p 0.0004 0.0034 134.8760 3750.234952 0 0.0009 115 | 1/8 9 h-lim-p 0.0503 0.4024 0.5858 3734.294311 0 0.2012 129 | 0/8 10 h-lim-p 0.0000 0.0000 5.1178 h-lim-p: 8.30509811e-23 6.64407849e-22 5.11776316e+00 3734.294311 .. | 0/8 11 h-lim-p 0.0000 0.0032 264.5566 3730.780692 0 0.0002 160 | 0/8 12 h-lim-p 0.0002 0.0014 85.1984 3730.014103 0 0.0003 172 | 0/8 13 h-lim-p 0.0007 0.0087 32.1404 3729.854427 4 0.0004 193 | 0/8 14 h-lim-p 0.0004 0.0032 5.4069 3729.850488 5 0.0003 219 | 0/8 15 h-lim-p 0.0009 0.0074 1.3944 3729.849991 2 0.0004 235 | 0/8 16 h-lim-p 0.0039 0.0313 0.1260 3729.845514 0 0.0156 249 | 0/8 17 h-lim-p 0.0020 0.2292 0.9655 3729.656647 0 0.0122 271 | 0/8 18 h-lim-p 0.0010 0.0215 11.6912 3729.504726 3 0.0009 297 | 0/8 19 h-lim-p 2.5000 20.0000 0.0017 3729.501319 5 0.9027 321 | 0/8 20 h-lim-p 2.5000 20.0000 0.0001 3729.501311 1 0.9961 343 | 0/8 21 h-lim-p 1.6134 20.0000 0.0000 3729.501311 0 1.4117 363 | 0/8 22 h-lim-p 2.1809 20.0000 0.0000 3729.501311 0 0.9541 383 | 0/8 23 h-lim-p 0.4315 20.0000 0.0001 3729.501311 0 0.0013 411 | 0/8 24 h-lim-p 0.0002 12.6379 0.0004 3729.501311 0 0.0000 443 | 0/8 25 h-lim-p 0.0001 20.0000 0.0000 3729.501311 0 0.0000 475 Out... lnL = -3729.501311 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3729.501311 Node 7: lnL = -3729.501311 Node 8: lnL = -3729.501311 Node 9: lnL = -3729.501311 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 794 Sequential format.. Reading seq # 1: YKL065C_Sbay Reading seq # 2: YKL065C_Scer Reading seq # 3: YKL065C_Skud Reading seq # 4: YKL065C_Smik Reading seq # 5: YKL065C_Spar Sequences read.. Counting patterns.. # site patterns = 232 Counting frequencies.. 120 bytes for distance 37120 bytes for lkl0 29696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.350965 0.318848 0.274541 0.170006 0.323336 0.298542 0.280753 0.000060 lnL0 = -3550.432812 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3550.432812 x= 0.35097 0.31885 0.27454 0.17001 0.32334 0.29854 0.28075 0.00006 1 h-lim-p 0.0000 0.0000 737.9732 3550.002538 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0005 880.1299 3393.721824 m 0.0005 37 | 1/8 3 h-lim-p 0.0001 0.0006 293.7264 3386.673002 0 0.0003 51 | 1/8 4 h-lim-p 0.0001 0.0011 104.0274 3385.052880 0 0.0004 64 | 1/8 5 h-lim-p 0.0018 0.0171 23.0098 3384.523386 4 0.0014 84 | 1/8 6 h-lim-p 0.0019 0.0197 17.3800 3383.582420 0 0.0037 97 | 1/8 7 h-lim-p 0.0116 0.0925 4.0050 3364.781240 0 0.0462 111 | 1/8 8 h-lim-p 0.0007 0.0057 88.8032 3342.648534 0 0.0029 125 | 1/8 9 h-lim-p 0.0454 0.3634 0.5085 3331.392094 0 0.1817 139 | 0/8 10 h-lim-p 0.0046 1.0359 20.0133 3331.239235 7 0.0007 179 | 0/8 11 h-lim-p 0.0841 1.6725 0.1715 3324.369842 0 0.3366 193 | 0/8 12 h-lim-p 0.4855 3.8839 0.0306 3323.974317 0 0.7282 213 | 0/8 13 h-lim-p 2.3612 20.0000 0.0094 3323.886537 4 1.0271 240 | 0/8 14 h-lim-p 2.5000 20.0000 0.0011 3323.882542 4 1.3159 269 | 0/8 15 h-lim-p 2.1338 20.0000 0.0007 3323.881631 2 0.9335 293 | 0/8 16 h-lim-p 2.5000 20.0000 0.0001 3323.881627 1 0.9961 315 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 3323.881627 0 1.0938 335 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 3323.881627 0 2.1875 355 | 0/8 19 h-lim-p 1.8846 20.0000 0.0000 3323.881627 0 0.8245 375 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 3323.881627 0 0.0098 402 Out... lnL = -3323.881627 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3323.881627 Node 7: lnL = -3323.881627 Node 8: lnL = -3323.881627 Node 9: lnL = -3323.881627 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 857 Sequential format.. Reading seq # 1: YKL067W_Sbay Reading seq # 2: YKL067W_Scer Reading seq # 3: YKL067W_Skud Reading seq # 4: YKL067W_Smik Reading seq # 5: YKL067W_Spar Sequences read.. Counting patterns.. # site patterns = 447 Counting frequencies.. 120 bytes for distance 71520 bytes for lkl0 57216 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.715907 0.674499 0.606943 0.373521 0.731341 0.634232 0.592946 0.000060 lnL0 = -5099.661493 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 5099.661493 x= 0.71591 0.67450 0.60694 0.37352 0.73134 0.63423 0.59295 0.00006 1 h-lim-p 0.0000 0.0000 352.9540 5099.556524 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0001 7038.9776 4957.770160 2 0.0001 41 | 1/8 3 h-lim-p 0.0004 0.0031 164.3750 4945.303078 0 0.0012 54 | 1/8 4 h-lim-p 0.0015 0.0119 54.9355 4940.989418 0 0.0030 67 | 1/8 5 h-lim-p 0.0036 0.0290 14.4031 4940.896340 5 0.0016 88 | 1/8 6 h-lim-p 0.0032 0.0738 7.1578 .. | 1/8 7 h-lim-p 0.0000 0.0035 240.4177 4859.500474 1 0.0028 143 | 1/8 8 h-lim-p 0.0001 0.0004 359.6936 4841.613566 m 0.0004 155 | 2/8 9 h-lim-p 0.0004 0.0125 204.9849 4837.195617 0 0.0005 167 | 2/8 10 h-lim-p 0.0019 0.0153 48.6054 4832.791230 0 0.0038 180 | 2/8 11 h-lim-p 0.0018 0.0142 61.3227 4829.460721 2 0.0017 196 | 2/8 12 h-lim-p 0.0030 0.0236 23.3587 4820.562268 0 0.0059 209 | 2/8 13 h-lim-p 0.0012 0.0095 50.2427 4818.299686 0 0.0018 221 | 2/8 14 h-lim-p 0.3194 2.5552 0.2745 4813.253839 0 0.6388 234 | 2/8 15 h-lim-p 2.1991 17.5926 0.0755 4812.118842 5 0.8553 262 | 2/8 16 h-lim-p 2.5000 20.0000 0.0125 4812.048544 6 1.0092 291 | 2/8 17 h-lim-p 2.5000 20.0000 0.0024 4812.045958 4 1.0660 319 | 1/8 18 h-lim-p 0.0764 20.0000 0.0333 4812.045957 0 0.0012 342 | 1/8 19 h-lim-p 0.1212 0.9696 0.0002 4812.045936 m 0.9696 361 | 2/8 20 h-lim-p 2.5000 20.0000 0.0000 4812.045936 0 1.0938 380 | 2/8 21 h-lim-p 2.5000 20.0000 0.0000 4812.045936 0 1.0938 398 | 2/8 22 h-lim-p 2.5000 20.0000 0.0000 4812.045936 0 1.0938 416 | 2/8 23 h-lim-p 2.5000 20.0000 0.0000 4812.045936 0 2.1875 434 | 2/8 24 h-lim-p 2.2847 20.0000 0.0000 4812.045936 0 1.1424 452 | 2/8 25 h-lim-p 2.5000 20.0000 0.0000 4812.045936 0 1.2500 470 | 2/8 26 h-lim-p 2.5000 20.0000 0.0000 4812.045936 0 0.3125 490 Out... lnL = -4812.045936 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4812.045936 Node 7: lnL = -4812.045936 Node 8: lnL = -4812.045936 Node 9: lnL = -4812.045936 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 882 Sequential format.. Reading seq # 1: YKL068W_Sbay Reading seq # 2: YKL068W_Scer Reading seq # 3: YKL068W_Skud Reading seq # 4: YKL068W_Smik Reading seq # 5: YKL068W_Spar Sequences read.. Counting patterns.. # site patterns = 299 Counting frequencies.. 120 bytes for distance 47840 bytes for lkl0 38272 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.381857 0.341994 0.292052 0.188871 0.353410 0.320309 0.302120 0.000060 lnL0 = -4099.755205 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4099.755205 x= 0.38186 0.34199 0.29205 0.18887 0.35341 0.32031 0.30212 0.00006 1 h-lim-p 0.0000 0.0000 761.5717 4099.325723 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0006 849.9603 3944.272584 m 0.0006 37 | 1/8 3 h-lim-p 0.0001 0.0004 284.1222 3939.955785 0 0.0002 50 | 1/8 4 h-lim-p 0.0001 0.0004 153.3386 3938.573490 0 0.0002 64 | 1/8 5 h-lim-p 0.0009 0.0100 36.0087 3937.900135 2 0.0008 80 | 1/8 6 h-lim-p 0.0002 0.0020 48.9557 3936.446838 m 0.0020 92 | 1/8 7 h-lim-p 0.0087 0.0693 9.0381 3933.562054 1 0.0108 106 | 1/8 8 h-lim-p 0.0090 0.0723 9.9736 3874.629119 0 0.0361 120 | 1/8 9 h-lim-p 0.0844 0.6753 0.2875 3865.784701 0 0.2532 133 | 1/8 10 h-lim-p 0.2134 1.7074 0.2256 3860.087841 0 0.3201 152 | 0/8 11 h-lim-p 0.0016 0.0240 43.9902 3859.459708 6 0.0007 182 | 0/8 12 h-lim-p 0.1679 1.3432 0.1032 3857.716027 0 0.5037 195 | 0/8 13 h-lim-p 2.5000 20.0000 0.0107 3857.338556 5 1.2130 226 | 0/8 14 h-lim-p 1.8515 20.0000 0.0070 3857.176150 6 1.4884 257 | 0/8 15 h-lim-p 2.5000 20.0000 0.0022 3857.163817 6 1.4551 293 | 0/8 16 h-lim-p 2.5000 20.0000 0.0005 3857.163571 2 1.1719 317 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 3857.163568 0 1.2500 337 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 3857.163568 0 1.0938 357 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 3857.163568 0 0.0586 382 | 0/8 20 h-lim-p 0.0403 20.0000 0.0000 3857.163568 0 0.0000 418 Out... lnL = -3857.163568 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3857.163568 Node 7: lnL = -3857.163568 Node 8: lnL = -3857.163568 Node 9: lnL = -3857.163568 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 654 Sequential format.. Reading seq # 1: YKL069W_Sbay Reading seq # 2: YKL069W_Scer Reading seq # 3: YKL069W_Skud Reading seq # 4: YKL069W_Smik Reading seq # 5: YKL069W_Spar Sequences read.. Counting patterns.. # site patterns = 379 Counting frequencies.. 120 bytes for distance 60640 bytes for lkl0 48512 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.894136 0.846072 0.745451 0.459397 0.855890 0.795081 0.672780 0.000060 lnL0 = -3636.951370 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3636.951370 x= 0.89414 0.84607 0.74545 0.45940 0.85589 0.79508 0.67278 0.00006 1 h-lim-p 0.0000 0.0000 191.2396 3636.876825 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0148 52.1503 3608.731013 m 0.0148 42 | 2/8 3 h-lim-p 0.0003 0.0025 755.7282 3574.222414 0 0.0012 56 | 2/8 4 h-lim-p 0.0026 0.0212 52.6223 3512.676333 0 0.0159 70 | 2/8 5 h-lim-p 0.0008 0.0066 53.0579 3508.757654 0 0.0033 84 | 2/8 6 h-lim-p 0.0041 0.0327 22.6394 3507.136983 0 0.0082 97 | 2/8 7 h-lim-p 0.0830 0.6641 1.0738 3500.392195 0 0.1660 110 | 1/8 8 h-lim-p 0.0004 0.0032 201.3740 3484.425931 0 0.0024 124 | 1/8 9 h-lim-p 0.0010 0.0076 35.8116 3481.892638 0 0.0038 138 | 1/8 10 h-lim-p 0.1899 1.5194 0.3074 3465.740281 0 1.1395 152 | 1/8 11 h-lim-p 0.3814 3.0512 0.2875 3455.991888 0 1.5256 173 | 0/8 12 h-lim-p 0.0084 0.0672 14.8013 3455.607347 6 0.0041 204 | 0/8 13 h-lim-p 0.0514 0.4110 0.3097 3452.339219 m 0.4110 216 | 0/8 14 h-lim-p -0.0000 -0.0000 0.6037 h-lim-p: -1.30373841e-18 -1.04299073e-17 6.03690587e-01 3452.339219 .. | 0/8 15 h-lim-p 0.0000 0.0045 56.1927 3450.716465 0 0.0013 259 | 0/8 16 h-lim-p 0.0017 0.0137 43.3761 3449.425441 1 0.0021 273 | 0/8 17 h-lim-p 0.0038 0.0308 11.7974 3449.275999 6 0.0024 300 | 0/8 18 h-lim-p 0.0035 0.0771 7.9342 3449.218185 6 0.0026 326 | 0/8 19 h-lim-p 0.0008 0.0062 3.2426 3449.209062 0 0.0031 340 | 0/8 20 h-lim-p 0.0033 0.0265 0.4598 3449.196940 m 0.0265 352 | 1/8 21 h-lim-p 0.0088 0.8767 1.2556 3449.179570 5 0.0075 383 | 1/8 22 h-lim-p 0.0581 13.3777 0.1611 3449.039803 0 0.1742 396 | 1/8 23 h-lim-p 0.0104 0.3847 2.7060 3449.018314 2 0.0049 419 | 1/8 24 h-lim-p 1.4674 20.0000 0.0090 3449.009615 5 0.9659 442 | 1/8 25 h-lim-p 2.5000 20.0000 0.0009 3449.009515 3 0.8800 468 | 1/8 26 h-lim-p 2.5000 20.0000 0.0001 3449.009514 0 1.0938 487 | 1/8 27 h-lim-p 2.5000 20.0000 0.0000 3449.009514 0 1.0938 506 | 1/8 28 h-lim-p 2.5000 20.0000 0.0000 3449.009514 0 1.2500 525 | 1/8 29 h-lim-p 2.5000 20.0000 0.0000 3449.009514 0 0.3125 546 | 1/8 30 h-lim-p 0.4550 20.0000 0.0000 3449.009514 0 0.0000 582 Out... lnL = -3449.009514 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3449.009514 Node 7: lnL = -3449.009514 Node 8: lnL = -3449.009514 Node 9: lnL = -3449.009514 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 874 Sequential format.. Reading seq # 1: YKL071W_Sbay Reading seq # 2: YKL071W_Scer Reading seq # 3: YKL071W_Skud Reading seq # 4: YKL071W_Smik Reading seq # 5: YKL071W_Spar Sequences read.. Counting patterns.. # site patterns = 496 Counting frequencies.. 120 bytes for distance 79360 bytes for lkl0 63488 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 1.059207 0.879698 0.716986 0.541734 1.069772 0.883030 0.767127 0.000060 lnL0 = -5555.491029 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 5555.491029 x= 1.05921 0.87970 0.71699 0.54173 1.06977 0.88303 0.76713 0.00006 1 h-lim-p 0.0000 0.0000 150.3076 5555.422562 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0123 87.8695 5533.677627 0 0.0051 43 | 1/8 3 h-lim-p 0.0026 0.0206 57.8893 5522.281987 0 0.0103 57 | 1/8 4 h-lim-p 0.0008 0.0063 87.7573 5508.992505 m 0.0063 69 | 2/8 5 h-lim-p 0.0002 0.0013 1314.1046 5475.439171 0 0.0007 83 | 2/8 6 h-lim-p 0.0015 0.0120 93.2147 5468.920292 0 0.0030 96 | 2/8 7 h-lim-p 0.0038 0.0305 35.3901 5454.298016 0 0.0152 110 | 1/8 8 h-lim-p 0.0004 0.0036 189.7053 5444.074956 0 0.0018 124 | 1/8 9 h-lim-p 0.0257 0.2055 0.7887 5436.435033 m 0.2055 136 | 1/8 10 h-lim-p -0.0000 -0.0000 7.0600 h-lim-p: -2.77614137e-23 -2.22091310e-22 7.06000334e+00 5436.435033 .. | 1/8 11 h-lim-p 0.0000 0.0061 103.6770 5369.443691 m 0.0061 170 | 1/8 12 h-lim-p 0.0000 0.0000 3646.9577 h-lim-p: 4.40307315e-22 3.52245852e-21 3.64695766e+03 5369.443691 .. | 1/8 13 h-lim-p 0.0000 0.0093 197.9446 5336.398189 0 0.0026 198 | 1/8 14 h-lim-p 0.0000 0.0001 168.6422 5335.032472 m 0.0001 210 | 2/8 15 h-lim-p 0.0003 0.0345 41.9784 5331.495563 0 0.0042 226 | 2/8 16 h-lim-p 0.0132 0.1054 9.5073 5330.272024 4 0.0103 246 | 2/8 17 h-lim-p 0.0089 0.0928 11.0872 5329.437898 4 0.0069 266 | 2/8 18 h-lim-p 0.0139 0.1109 0.5588 5328.340174 m 0.1109 278 | 2/8 19 h-lim-p -0.0000 -0.0000 9.4751 h-lim-p: -1.07131019e-19 -8.57048153e-19 9.47511708e+00 5328.340174 .. | 2/8 20 h-lim-p 0.0000 0.0064 82.4446 5323.622126 0 0.0013 311 | 2/8 21 h-lim-p 0.0068 0.0969 15.5883 5323.291988 6 0.0029 339 | 1/8 22 h-lim-p 0.0008 0.0087 54.0044 5322.222244 6 0.0008 367 | 1/8 23 h-lim-p 0.0004 0.0030 20.0172 5321.528021 m 0.0030 379 | 2/8 24 h-lim-p 0.0067 0.2018 7.8248 5321.340258 3 0.0061 397 | 2/8 25 h-lim-p 0.0555 0.7362 0.8561 5321.198494 7 0.0369 426 | 2/8 26 h-lim-p 0.0548 1.1865 0.5769 5319.702573 0 0.3288 446 | 1/8 27 h-lim-p 0.0026 0.0211 16.7828 5318.367542 0 0.0079 465 | 1/8 28 h-lim-p 0.0088 0.0706 6.9059 5318.203830 6 0.0086 492 | 1/8 29 h-lim-p 0.6266 5.8182 0.0950 5317.336318 0 0.9399 504 | 1/8 30 h-lim-p 2.0950 16.7603 0.0223 5317.270959 3 0.9493 529 | 1/8 31 h-lim-p 2.5000 20.0000 0.0037 5317.269515 3 0.9644 554 | 1/8 32 h-lim-p 2.5000 20.0000 0.0002 5317.269509 0 1.0938 573 | 1/8 33 h-lim-p 2.5000 20.0000 0.0000 5317.269508 0 1.0938 592 | 1/8 34 h-lim-p 2.5000 20.0000 0.0000 5317.269508 0 1.0938 611 | 1/8 35 h-lim-p 2.5000 20.0000 0.0000 5317.269508 0 1.0938 630 | 1/8 36 h-lim-p 2.5000 20.0000 0.0000 5317.269508 0 5.0000 650 | 1/8 37 h-lim-p 0.2559 20.0000 0.0000 5317.269508 0 0.0640 670 | 1/8 38 h-lim-p 0.0096 20.0000 0.0000 5317.269508 0 0.0000 705 | 1/8 39 h-lim-p 0.0000 20.0000 0.0000 5317.269508 0 0.0000 737 | 1/8 40 h-lim-p 0.0000 20.0000 0.0000 | 1/8 41 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -5317.269508 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -5317.269508 Node 7: lnL = -5317.269508 Node 8: lnL = -5317.269508 Node 9: lnL = -5317.269508 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 273 Sequential format.. Reading seq # 1: YKL073W_Sbay Reading seq # 2: YKL073W_Scer Reading seq # 3: YKL073W_Skud Reading seq # 4: YKL073W_Smik Reading seq # 5: YKL073W_Spar Sequences read.. Counting patterns.. # site patterns = 93 Counting frequencies.. 120 bytes for distance 14880 bytes for lkl0 11904 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 1.337772 0.743953 0.197926 1.001180 0.110155 1.910661 0.984234 0.000060 lnL0 = -1216.536398 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1216.536398 x= 1.33777 0.74395 0.19793 1.00118 0.11015 1.91066 0.98423 0.00006 1 h-lim-p 0.0000 0.0000 159.7608 1216.466431 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0057 44.7227 1204.856116 m 0.0057 41 | 2/8 3 h-lim-p 0.0026 0.0206 47.1903 1129.462775 0 0.0154 55 | 2/8 4 h-lim-p 0.0064 0.0509 28.4877 1096.721529 m 0.0509 67 | 1/8 5 h-lim-p -0.0000 -0.0000 44.3233 h-lim-p: -1.32684671e-19 -1.06147737e-18 4.43232755e+01 1096.721529 .. | 0/8 6 h-lim-p 0.0000 0.0248 230.2029 1086.692607 0 0.0005 92 | 0/8 7 h-lim-p 0.0005 0.0039 52.8386 1081.236237 m 0.0039 104 | 0/8 8 h-lim-p 0.0000 0.0000 274.8305 h-lim-p: 1.79291719e-20 1.43433375e-19 2.74830532e+02 1081.236237 .. | 0/8 9 h-lim-p 0.0000 0.0017 105.7479 1074.800827 6 0.0012 143 | 0/8 10 h-lim-p 0.0001 0.0006 103.9821 1071.096030 m 0.0006 155 | 0/8 11 h-lim-p 0.0000 0.0000 629.9199 h-lim-p: 1.41432205e-21 1.13145764e-20 6.29919937e+02 1071.096030 .. | 0/8 12 h-lim-p 0.0000 0.0009 84.7061 1066.138441 m 0.0009 179 | 0/8 13 h-lim-p -0.0000 -0.0000 191.7212 h-lim-p: -1.27389564e-21 -1.01911651e-20 1.91721232e+02 1066.138441 .. | 0/8 14 h-lim-p 0.0000 0.0021 69.3141 1055.505954 m 0.0021 204 | 0/8 15 h-lim-p 0.0000 0.0000 2077.0700 h-lim-p: 2.96586989e-22 2.37269591e-21 2.07707001e+03 1055.505954 .. | 0/8 16 h-lim-p 0.0000 0.0000 79.9694 1055.342454 m 0.0000 224 | 1/8 17 h-lim-p 0.0000 0.0001 6603.9694 1016.681592 m 0.0001 237 | 2/8 18 h-lim-p 0.0014 0.0110 65.6859 1011.465454 0 0.0055 251 | 1/8 19 h-lim-p 0.0000 0.0003 1454.5595 1002.357691 0 0.0001 265 | 1/8 20 h-lim-p 0.0002 0.0017 111.3648 998.598693 0 0.0008 279 | 1/8 21 h-lim-p 0.0410 0.3280 0.5191 995.533988 0 0.2460 293 | 1/8 22 h-lim-p 0.0006 0.0048 14.1226 989.713766 m 0.0048 312 | 2/8 23 h-lim-p 0.0013 0.0106 41.1431 984.214921 0 0.0053 326 | 2/8 24 h-lim-p 0.2697 2.1573 0.1751 978.677000 0 1.0786 340 | 1/8 25 h-lim-p 0.0034 0.0270 11.0282 978.240942 0 0.0135 360 | 1/8 26 h-lim-p 0.0749 0.5995 0.2782 976.583895 0 0.4496 374 | 0/8 27 h-lim-p 0.0005 0.0038 27.0140 976.283110 0 0.0010 394 | 0/8 28 h-lim-p 0.0420 0.3358 0.0713 976.237627 m 0.3358 406 | 0/8 29 h-lim-p -0.0000 -0.0000 0.2262 h-lim-p: -5.31780732e-19 -4.25424586e-18 2.26226736e-01 976.237627 .. | 0/8 30 h-lim-p 0.0000 0.0754 19.4161 976.123558 0 0.0006 448 | 0/8 31 h-lim-p 0.0000 0.0001 4.8612 976.121857 m 0.0001 460 | 1/8 32 h-lim-p 0.0003 0.1412 1.4576 976.121174 0 0.0008 473 | 1/8 33 h-lim-p 0.0110 1.5109 0.1052 976.121121 3 0.0039 493 | 1/8 34 h-lim-p 0.0108 6.0892 0.0376 976.120086 0 0.0434 514 | 0/8 35 h-lim-p 0.0038 0.3310 0.4315 976.113671 0 0.0151 535 | 0/8 36 h-lim-p 0.0079 0.0632 0.0891 976.113508 m 0.0632 555 | 1/8 37 h-lim-p 0.0000 0.0003 824.5907 976.113473 3 0.0000 586 | 1/8 38 h-lim-p 0.2276 20.0000 0.0016 976.113181 0 0.4552 599 | 1/8 39 h-lim-p 0.9549 20.0000 0.0008 976.113063 4 0.6512 628 | 0/8 40 h-lim-p 0.1494 20.0000 0.0033 976.113063 0 0.0041 651 | 0/8 41 h-lim-p 0.1660 1.3277 0.0001 976.113061 0 0.6639 673 | 0/8 42 h-lim-p 0.0555 0.4437 0.0000 976.113061 0 0.0000 704 | 0/8 43 h-lim-p 0.0000 0.0543 0.0007 976.113061 0 0.0000 731 | 0/8 44 h-lim-p 0.0000 0.0103 0.0018 976.113061 0 0.0000 763 | 0/8 45 h-lim-p 0.0000 0.0002 0.0788 976.113060 m 0.0002 785 | 1/8 46 h-lim-p 0.0004 3.1765 0.0334 976.113060 0 0.0014 807 | 1/8 47 h-lim-p 0.0107 20.0000 0.0045 976.113060 0 0.0012 828 | 1/8 48 h-lim-p 0.0029 20.0000 0.0018 976.113060 0 0.0025 847 | 1/8 49 h-lim-p 0.0168 20.0000 0.0003 976.113060 0 0.0672 868 | 1/8 50 h-lim-p 0.0049 20.0000 0.0037 976.113059 0 0.0148 888 | 1/8 51 h-lim-p 2.5000 20.0000 0.0000 976.113059 0 1.0938 907 | 1/8 52 h-lim-p 1.1202 20.0000 0.0000 976.113059 0 1.6803 926 | 1/8 53 h-lim-p 0.3344 20.0000 0.0001 976.113059 0 0.0026 951 | 1/8 54 h-lim-p 0.0003 20.0000 0.0005 976.113059 0 0.0000 986 | 1/8 55 h-lim-p 0.0000 20.0000 0.0002 | 1/8 56 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -976.113059 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -976.113059 Node 7: lnL = -976.113059 Node 8: lnL = -976.113059 Node 9: lnL = -976.113059 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 409 Sequential format.. Reading seq # 1: YKL077W_Sbay Reading seq # 2: YKL077W_Scer Reading seq # 3: YKL077W_Skud Reading seq # 4: YKL077W_Smik Reading seq # 5: YKL077W_Spar Sequences read.. Counting patterns.. # site patterns = 206 Counting frequencies.. 120 bytes for distance 32960 bytes for lkl0 26368 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.452212 0.250592 0.074977 0.325624 0.059397 0.416522 0.329021 0.000060 lnL0 = -1991.730132 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1991.730132 x= 0.45221 0.25059 0.07498 0.32562 0.05940 0.41652 0.32902 0.00006 1 h-lim-p 0.0000 0.0000 221.1155 1991.668752 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0004 572.7912 1976.927440 0 0.0002 38 | 1/8 3 h-lim-p 0.0005 0.0036 143.9757 1971.823623 0 0.0009 51 | 1/8 4 h-lim-p 0.0009 0.0068 58.0607 1969.675930 0 0.0017 64 | 1/8 5 h-lim-p 0.0088 0.0704 9.1500 1969.260907 7 0.0049 92 | 1/8 6 h-lim-p 0.0060 0.0546 7.4808 1968.314142 0 0.0089 104 | 1/8 7 h-lim-p 0.0093 0.0742 4.9372 1951.983604 0 0.0371 118 | 0/8 8 h-lim-p 0.0009 0.0072 35.9997 1951.217667 1 0.0011 132 | 0/8 9 h-lim-p 0.0004 0.0033 8.4614 1951.126176 m 0.0033 144 | 0/8 10 h-lim-p 0.2924 10.5770 0.0947 1947.972171 0 0.5848 157 | 0/8 11 h-lim-p 0.1553 1.2427 0.0303 1947.381273 m 1.2427 177 | 0/8 12 h-lim-p 1.5069 13.4243 0.0250 1946.980778 8 1.0507 216 | 0/8 13 h-lim-p 2.5000 20.0000 0.0067 1946.952707 4 1.0889 243 | 0/8 14 h-lim-p 2.5000 20.0000 0.0026 1946.950663 5 0.7695 277 | 0/8 15 h-lim-p 2.5000 20.0000 0.0003 1946.950615 1 1.0938 299 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1946.950614 0 1.0938 319 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1946.950614 0 1.0938 339 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1946.950614 0 1.0938 359 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1946.950614 0 2.1875 379 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 1946.950614 0 0.1562 402 | 0/8 21 h-lim-p 0.0633 20.0000 0.0000 1946.950614 0 0.0633 422 | 0/8 22 h-lim-p 0.0297 20.0000 0.0000 1946.950614 0 0.0000 465 Out... lnL = -1946.950614 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1946.950614 Node 7: lnL = -1946.950614 Node 8: lnL = -1946.950614 Node 9: lnL = -1946.950614 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 293 Sequential format.. Reading seq # 1: YKL078W_Sbay Reading seq # 2: YKL078W_Scer Reading seq # 3: YKL078W_Skud Reading seq # 4: YKL078W_Smik Reading seq # 5: YKL078W_Spar Sequences read.. Counting patterns.. # site patterns = 118 Counting frequencies.. 120 bytes for distance 18880 bytes for lkl0 15104 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.263796 0.114445 0.036402 0.172715 0.043968 0.224126 0.195426 0.000060 lnL0 = -1137.873190 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1137.873190 x= 0.26380 0.11445 0.03640 0.17272 0.04397 0.22413 0.19543 0.00006 1 h-lim-p 0.0000 0.0000 209.0562 1137.785810 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0005 384.7124 1127.860021 8 0.0003 57 | 1/8 3 h-lim-p 0.0001 0.0007 167.3724 1126.248101 0 0.0002 70 | 1/8 4 h-lim-p 0.0009 0.0071 25.6578 1125.954244 3 0.0009 88 | 1/8 5 h-lim-p 0.0030 0.0242 2.7874 1125.928221 6 0.0019 116 | 1/8 6 h-lim-p 0.0015 0.1205 3.4237 1125.609177 0 0.0091 130 | 1/8 7 h-lim-p 0.0074 0.0593 4.0529 1121.794175 0 0.0148 143 | 0/8 8 h-lim-p 0.0007 0.0057 37.7040 1121.120430 7 0.0007 169 | 0/8 9 h-lim-p 0.0011 0.0087 3.1743 1121.091771 0 0.0044 183 | 0/8 10 h-lim-p 0.0689 0.5515 0.0370 1120.307663 m 0.5515 195 | 1/8 11 h-lim-p 0.6006 8.2196 0.0295 1120.024397 1 0.7508 217 | 0/8 12 h-lim-p 0.0018 0.0401 12.0747 1119.889011 0 0.0028 236 | 0/8 13 h-lim-p 0.2493 1.9942 0.0199 1119.828531 0 0.9971 250 | 0/8 14 h-lim-p 1.2139 9.7110 0.0024 1119.827353 3 1.0180 277 | 0/8 15 h-lim-p 2.5000 20.0000 0.0002 1119.827341 2 0.9644 301 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1119.827341 0 1.0938 321 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1119.827341 0 1.0938 341 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1119.827341 0 2.1875 361 | 0/8 19 h-lim-p 2.2526 20.0000 0.0000 1119.827341 0 0.2464 383 | 0/8 20 h-lim-p 0.3789 20.0000 0.0000 1119.827341 0 0.0000 426 Out... lnL = -1119.827341 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1119.827341 Node 7: lnL = -1119.827341 Node 8: lnL = -1119.827341 Node 9: lnL = -1119.827341 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 609 Sequential format.. Reading seq # 1: YKL080W_Sbay Reading seq # 2: YKL080W_Scer Reading seq # 3: YKL080W_Skud Reading seq # 4: YKL080W_Smik Reading seq # 5: YKL080W_Spar Sequences read.. Counting patterns.. # site patterns = 174 Counting frequencies.. 120 bytes for distance 27840 bytes for lkl0 22272 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.217792 0.102681 0.038938 0.137143 0.028129 0.184134 0.160613 0.000060 lnL0 = -2178.306363 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2178.306363 x= 0.21779 0.10268 0.03894 0.13714 0.02813 0.18413 0.16061 0.00006 1 h-lim-p 0.0000 0.0000 415.0176 2178.118498 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0001 1129.1557 2163.850788 0 0.0001 36 | 1/8 3 h-lim-p 0.0001 0.0011 177.8524 2161.950939 1 0.0002 50 | 1/8 4 h-lim-p 0.0004 0.0030 51.5024 2161.471171 4 0.0004 70 | 1/8 5 h-lim-p 0.0033 0.0324 5.8669 2161.382664 5 0.0018 93 | 1/8 6 h-lim-p 0.0036 0.0581 2.9113 2160.559731 0 0.0072 106 | 1/8 7 h-lim-p 0.0008 0.0065 24.2903 2156.709317 0 0.0016 119 | 1/8 8 h-lim-p 0.0003 0.0026 63.4352 2149.670421 0 0.0013 133 | 1/8 9 h-lim-p 0.9792 7.8339 0.0283 2147.649772 6 1.0081 156 | 1/8 10 h-lim-p 1.1674 9.3394 0.0133 2147.037923 6 1.1748 189 | 1/8 11 h-lim-p 1.5851 20.0000 0.0099 2146.839604 8 1.0505 226 | 0/8 12 h-lim-p 0.0022 0.1032 4.7056 2146.832361 5 0.0008 257 | 0/8 13 h-lim-p 1.7035 20.0000 0.0022 2146.827097 4 0.7168 278 | 0/8 14 h-lim-p 2.5000 20.0000 0.0005 2146.826640 4 0.8479 309 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2146.826639 0 1.0938 329 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 2146.826639 0 1.0938 349 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 2146.826639 0 1.0938 369 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 2146.826639 0 0.5469 390 | 0/8 19 h-lim-p 1.4443 20.0000 0.0000 2146.826639 0 0.0004 421 Out... lnL = -2146.826639 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2146.826639 Node 7: lnL = -2146.826639 Node 8: lnL = -2146.826639 Node 9: lnL = -2146.826639 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 645 Sequential format.. Reading seq # 1: YKL081W_Sbay Reading seq # 2: YKL081W_Scer Reading seq # 3: YKL081W_Skud Reading seq # 4: YKL081W_Smik Reading seq # 5: YKL081W_Spar Sequences read.. Counting patterns.. # site patterns = 207 Counting frequencies.. 120 bytes for distance 33120 bytes for lkl0 26496 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.688709 0.496295 0.103471 0.518149 0.058371 0.642583 0.517988 0.000060 lnL0 = -3084.189517 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3084.189517 x= 0.68871 0.49630 0.10347 0.51815 0.05837 0.64258 0.51799 0.00006 1 h-lim-p 0.0000 0.0000 506.1236 3084.003700 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0010 866.2255 2863.014890 m 0.0010 38 | 1/8 3 h-lim-p 0.0001 0.0009 441.9451 2839.008120 0 0.0004 52 | 1/8 4 h-lim-p 0.0001 0.0004 718.4094 2831.627006 0 0.0001 65 | 1/8 5 h-lim-p 0.0012 0.0093 42.6440 2829.776153 0 0.0023 78 | 1/8 6 h-lim-p 0.0007 0.0053 17.5394 2829.527973 0 0.0013 91 | 0/8 7 h-lim-p 0.0003 0.0022 59.5669 2827.385587 0 0.0017 105 | 0/8 8 h-lim-p 0.0014 0.0109 17.8135 2824.486713 m 0.0109 117 | 0/8 9 h-lim-p 0.0045 0.0356 5.8935 2807.117616 m 0.0356 129 | 1/8 10 h-lim-p 2.2931 20.0000 0.0752 2806.048020 4 0.8991 149 | 1/8 11 h-lim-p 0.5942 4.7533 0.0516 2805.231098 7 0.6541 185 | 0/8 12 h-lim-p 0.0047 0.0545 7.1150 2805.199380 6 0.0018 216 | 0/8 13 h-lim-p 0.0743 0.5946 0.0411 2805.076750 m 0.5946 228 | 1/8 14 h-lim-p 1.8435 19.2482 0.0119 2805.015958 7 1.0732 265 | 1/8 15 h-lim-p 0.4180 7.6364 0.0307 2804.987006 6 0.2765 297 | 1/8 16 h-lim-p 2.5000 20.0000 0.0031 2804.981353 5 1.7248 329 | 1/8 17 h-lim-p 2.5000 20.0000 0.0014 2804.979880 4 1.8338 358 | 0/8 18 h-lim-p 0.0783 20.0000 0.0329 2804.979880 0 0.0011 382 | 0/8 19 h-lim-p 0.1084 1.4051 0.0003 2804.979828 m 1.4051 403 | 1/8 20 h-lim-p 2.5000 20.0000 0.0001 2804.979825 1 1.2305 426 | 1/8 21 h-lim-p 2.5000 20.0000 0.0000 2804.979825 0 2.1875 445 | 1/8 22 h-lim-p 2.1780 20.0000 0.0000 2804.979825 0 1.0890 464 | 1/8 23 h-lim-p 2.5000 20.0000 0.0000 2804.979825 0 0.5469 484 | 1/8 24 h-lim-p 1.2452 20.0000 0.0000 2804.979825 0 0.0049 510 Out... lnL = -2804.979825 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2804.979825 Node 7: lnL = -2804.979825 Node 8: lnL = -2804.979825 Node 9: lnL = -2804.979825 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 912 Sequential format.. Reading seq # 1: YKL090W_Sbay Reading seq # 2: YKL090W_Scer Reading seq # 3: YKL090W_Skud Reading seq # 4: YKL090W_Smik Reading seq # 5: YKL090W_Spar Sequences read.. Counting patterns.. # site patterns = 382 Counting frequencies.. 120 bytes for distance 61120 bytes for lkl0 48896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.603843 0.165039 0.095732 0.314611 0.093762 0.388956 0.429735 0.000060 lnL0 = -4455.173202 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4455.173202 x= 0.60384 0.16504 0.09573 0.31461 0.09376 0.38896 0.42973 0.00006 1 h-lim-p 0.0000 0.0000 267.5826 4454.956522 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0011 366.6621 4434.879406 5 0.0006 49 | 1/8 3 h-lim-p 0.0010 0.0078 59.6361 4433.158991 6 0.0011 75 | 1/8 4 h-lim-p 0.0038 0.0307 12.7862 4433.080257 2 0.0009 92 | 1/8 5 h-lim-p 0.0018 0.1342 6.2696 4433.001184 0 0.0037 105 | 1/8 6 h-lim-p 0.0022 0.0172 6.8212 4432.897285 1 0.0027 119 | 1/8 7 h-lim-p 0.0115 0.0919 1.3403 4428.258906 m 0.0919 131 | 0/8 8 h-lim-p 0.0028 0.0225 24.9112 4422.591364 0 0.0056 144 | 0/8 9 h-lim-p 0.0003 0.0026 12.3235 4422.426970 m 0.0026 156 | 0/8 10 h-lim-p 0.0000 0.0000 0.0508 h-lim-p: 4.34157961e-18 3.47326369e-17 5.07846095e-02 4422.426970 .. | 0/8 11 h-lim-p 0.0000 2.2043 84.3530 4421.359402 0 0.0003 189 | 0/8 12 h-lim-p 0.0007 0.0058 23.2057 4421.253112 7 0.0004 221 | 0/8 13 h-lim-p 0.0001 0.0007 7.2268 4421.241478 m 0.0007 233 | 1/8 14 h-lim-p 0.0016 0.0620 2.8981 4421.238422 4 0.0008 254 | 1/8 15 h-lim-p 0.0018 0.1071 1.3164 4421.237721 3 0.0010 273 | 1/8 16 h-lim-p 0.0057 2.3618 0.2275 4421.237694 2 0.0009 292 | 1/8 17 h-lim-p 0.0014 1.1034 0.1565 4421.237658 0 0.0028 312 | 1/8 18 h-lim-p 0.0488 20.0000 0.0088 4421.236856 0 0.0975 332 | 0/8 19 h-lim-p 0.0054 14.2148 0.1586 4421.236824 1 0.0024 353 | 0/8 20 h-lim-p 0.3121 2.4964 0.0012 4421.235955 0 0.6241 374 | 0/8 21 h-lim-p 2.5000 20.0000 0.0001 4421.235948 0 1.0938 394 | 0/8 22 h-lim-p 2.5000 20.0000 0.0000 4421.235948 0 1.0938 414 | 0/8 23 h-lim-p 0.5787 13.0680 0.0000 4421.235948 0 0.0001 446 | 0/8 24 h-lim-p 0.0001 20.0000 0.0000 4421.235948 0 0.0000 476 | 0/8 25 h-lim-p 0.0000 0.1190 0.0038 4421.235948 0 0.0005 501 | 0/8 26 h-lim-p 0.0001 0.0244 0.0150 4421.235948 0 0.0000 526 | 0/8 27 h-lim-p 0.0000 0.0004 0.9169 .. | 0/8 28 h-lim-p 0.0000 0.1022 0.0036 4421.235948 0 0.0000 584 | 0/8 29 h-lim-p 0.0000 0.0086 0.0399 .. | 0/8 30 h-lim-p 0.0000 0.1022 0.0036 | 0/8 31 h-lim-p 0.0000 0.1022 0.0036 Out... lnL = -4421.235948 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4421.235948 Node 7: lnL = -4421.235948 Node 8: lnL = -4421.235948 Node 9: lnL = -4421.235948 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 855 Sequential format.. Reading seq # 1: YKL091C_Sbay Reading seq # 2: YKL091C_Scer Reading seq # 3: YKL091C_Skud Reading seq # 4: YKL091C_Smik Reading seq # 5: YKL091C_Spar Sequences read.. Counting patterns.. # site patterns = 334 Counting frequencies.. 120 bytes for distance 53440 bytes for lkl0 42752 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.442472 0.192882 0.059043 0.297061 0.034100 0.376646 0.334381 0.000060 lnL0 = -3963.174996 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3963.174996 x= 0.44247 0.19288 0.05904 0.29706 0.03410 0.37665 0.33438 0.00006 1 h-lim-p 0.0000 0.0000 388.4618 3963.000085 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0002 824.6589 3947.805530 0 0.0001 37 | 1/8 3 h-lim-p 0.0002 0.0017 235.9028 3939.868792 0 0.0004 50 | 1/8 4 h-lim-p 0.0007 0.0058 59.1582 3938.644588 3 0.0007 68 | 1/8 5 h-lim-p 0.0049 0.0419 8.9033 3938.351255 7 0.0029 97 | 1/8 6 h-lim-p 0.0022 0.0177 7.1538 3937.598289 0 0.0044 110 | 1/8 7 h-lim-p 0.0033 0.0387 9.6582 3924.539996 0 0.0131 124 | 1/8 8 h-lim-p 0.0008 0.0067 72.4290 3918.400019 0 0.0017 137 | 1/8 9 h-lim-p 0.8105 6.4840 0.0578 3914.621648 0 1.6210 150 | 1/8 10 h-lim-p 1.9520 15.6156 0.0333 3912.313449 3 1.6317 175 | 0/8 11 h-lim-p 0.0075 0.1582 7.2767 3912.281364 4 0.0014 203 | 0/8 12 h-lim-p 0.4956 20.0000 0.0212 3911.871985 0 1.4868 216 | 0/8 13 h-lim-p 1.8493 14.7941 0.0119 3911.748384 6 1.0452 251 | 0/8 14 h-lim-p 2.5000 20.0000 0.0036 3911.743402 4 0.6351 281 | 0/8 15 h-lim-p 2.0783 20.0000 0.0011 3911.742882 2 0.9093 305 | 0/8 16 h-lim-p 2.5000 20.0000 0.0002 3911.742869 1 0.9961 327 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 3911.742869 0 1.0938 347 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 3911.742869 0 1.0938 367 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 3911.742869 0 0.5469 388 | 0/8 20 h-lim-p 0.8808 20.0000 0.0000 3911.742869 0 0.4404 408 | 0/8 21 h-lim-p 0.4114 20.0000 0.0000 3911.742869 0 0.0000 444 Out... lnL = -3911.742869 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3911.742869 Node 7: lnL = -3911.742869 Node 8: lnL = -3911.742869 Node 9: lnL = -3911.742869 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 248 Sequential format.. Reading seq # 1: YKL094W_Sbay Reading seq # 2: YKL094W_Scer Reading seq # 3: YKL094W_Skud Reading seq # 4: YKL094W_Smik Reading seq # 5: YKL094W_Spar Sequences read.. Counting patterns.. # site patterns = 134 Counting frequencies.. 120 bytes for distance 21440 bytes for lkl0 17152 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.040382 0.253974 0.155300 0.087015 0.059793 0.595935 0.309480 0.106685 lnL0 = -970.173985 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 970.173985 x= 0.04038 0.25397 0.15530 0.08702 0.05979 0.59593 0.30948 0.10669 1 h-lim-p 0.0010 0.0077 69.1873 967.924286 1 0.0012 24 | 0/8 2 h-lim-p 0.0014 0.0114 28.1900 966.740193 0 0.0029 37 | 0/8 3 h-lim-p 0.0007 0.0053 25.8831 966.638021 8 0.0005 67 | 0/8 4 h-lim-p 0.0011 0.0198 11.1534 966.345114 0 0.0069 81 | 0/8 5 h-lim-p 0.0005 0.0044 29.5968 966.105257 0 0.0022 95 | 0/8 6 h-lim-p 0.0079 0.0631 0.9798 966.101963 4 0.0067 117 | 0/8 7 h-lim-p 0.0033 0.0865 2.0126 966.088220 0 0.0197 139 | 0/8 8 h-lim-p 2.5000 20.0000 0.0097 966.074747 6 0.9225 165 | 0/8 9 h-lim-p 2.1105 20.0000 0.0042 966.073568 5 1.1344 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0004 966.073534 1 0.9961 218 | 0/8 11 h-lim-p 2.5000 20.0000 0.0001 966.073534 0 1.0938 238 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 966.073534 0 1.0938 258 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 966.073534 0 2.1875 278 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 966.073534 0 0.0171 304 | 0/8 15 h-lim-p 0.0074 20.0000 0.0000 966.073534 0 0.0005 327 Out... lnL = -966.073534 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -966.073534 Node 7: lnL = -966.073534 Node 8: lnL = -966.073534 Node 9: lnL = -966.073534 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 374 Sequential format.. Reading seq # 1: YKL096W-A_Sbay Reading seq # 2: YKL096W-A_Scer Reading seq # 3: YKL096W-A_Skud Reading seq # 4: YKL096W-A_Smik Reading seq # 5: YKL096W-A_Spar Sequences read.. Counting patterns.. # site patterns = 128 Counting frequencies.. 120 bytes for distance 20480 bytes for lkl0 16384 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.095023 0.039993 0.032384 0.047801 0.043315 0.145871 0.131049 0.120326 lnL0 = -1369.440549 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1369.440549 x= 0.09502 0.03999 0.03238 0.04780 0.04331 0.14587 0.13105 0.12033 1 h-lim-p 0.0002 0.0013 121.2503 1367.898988 0 0.0003 22 | 0/8 2 h-lim-p 0.0002 0.0017 29.5395 1367.750871 0 0.0004 35 | 0/8 3 h-lim-p 0.0008 0.0130 15.5697 1367.713673 2 0.0004 51 | 0/8 4 h-lim-p 0.0008 0.0461 7.4326 1367.709645 2 0.0002 68 | 0/8 5 h-lim-p 0.0008 0.0346 1.7954 1367.709352 2 0.0002 85 | 0/8 6 h-lim-p 0.0020 1.5674 0.1823 1367.709332 1 0.0008 99 | 0/8 7 h-lim-p 0.0073 11.8640 0.0201 1367.708879 0 0.0437 121 | 0/8 8 h-lim-p 0.0038 0.5113 0.2318 1367.701107 0 0.0151 143 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 1367.700286 4 1.0660 173 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1367.700280 0 1.0938 193 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1367.700280 0 1.0938 213 | 0/8 12 h-lim-p 1.5519 20.0000 0.0000 1367.700280 0 3.1038 234 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1367.700280 0 0.2734 256 | 0/8 14 h-lim-p 0.2401 20.0000 0.0000 1367.700280 0 0.0300 278 | 0/8 15 h-lim-p 0.0110 20.0000 0.0000 1367.700280 0 0.0000 311 Out... lnL = -1367.700280 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1367.700280 Node 7: lnL = -1367.700280 Node 8: lnL = -1367.700280 Node 9: lnL = -1367.700280 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 943 Sequential format.. Reading seq # 1: YKL096W_Sbay Reading seq # 2: YKL096W_Scer Reading seq # 3: YKL096W_Skud Reading seq # 4: YKL096W_Smik Reading seq # 5: YKL096W_Spar Sequences read.. Counting patterns.. # site patterns = 349 Counting frequencies.. 120 bytes for distance 55840 bytes for lkl0 44672 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.222007 0.066391 0.076515 0.131852 0.102868 0.219047 0.441727 0.280984 lnL0 = -4468.486554 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4468.486554 x= 0.22201 0.06639 0.07652 0.13185 0.10287 0.21905 0.44173 0.28098 1 h-lim-p 0.0007 0.0056 77.9329 4467.408065 5 0.0004 33 | 0/8 2 h-lim-p 0.0007 0.0053 24.4310 4467.304820 6 0.0004 60 | 0/8 3 h-lim-p 0.0010 0.0484 9.1357 4467.288794 4 0.0004 79 | 0/8 4 h-lim-p 0.0005 0.0352 8.4853 4467.281530 5 0.0003 102 | 0/8 5 h-lim-p 0.0016 0.2692 1.7949 4467.281080 2 0.0003 119 | 0/8 6 h-lim-p 0.0025 1.2822 0.2219 4467.281061 2 0.0008 137 | 0/8 7 h-lim-p 0.0026 3.1007 0.0698 4467.281056 0 0.0023 157 | 0/8 8 h-lim-p 0.4326 20.0000 0.0004 4467.280901 0 0.8651 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4467.280895 0 1.0938 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4467.280895 0 1.0938 218 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4467.280895 0 1.0938 238 | 0/8 12 h-lim-p 1.1140 20.0000 0.0000 4467.280895 0 3.3421 259 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 4467.280895 0 0.0781 283 | 0/8 14 h-lim-p 0.0107 20.0000 0.0000 4467.280895 0 0.0000 317 Out... lnL = -4467.280895 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4467.280895 Node 7: lnL = -4467.280895 Node 8: lnL = -4467.280895 Node 9: lnL = -4467.280895 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 324 Sequential format.. Reading seq # 1: YKL098W_Sbay Reading seq # 2: YKL098W_Scer Reading seq # 3: YKL098W_Skud Reading seq # 4: YKL098W_Smik Reading seq # 5: YKL098W_Spar Sequences read.. Counting patterns.. # site patterns = 163 Counting frequencies.. 120 bytes for distance 26080 bytes for lkl0 20864 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.120411 0.116946 0.061409 0.121687 0.124926 0.181707 0.183299 0.162920 lnL0 = -1420.220127 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1420.220127 x= 0.12041 0.11695 0.06141 0.12169 0.12493 0.18171 0.18330 0.16292 1 h-lim-p 0.0048 0.0388 38.1887 1419.804324 7 0.0006 38 | 0/8 2 h-lim-p 0.0020 0.0178 11.5175 1419.755522 6 0.0008 61 | 0/8 3 h-lim-p 0.0026 0.0988 3.4737 1419.750611 5 0.0009 85 | 0/8 4 h-lim-p 0.0022 0.1784 1.3968 1419.749934 4 0.0008 107 | 0/8 5 h-lim-p 0.0053 1.0158 0.2138 1419.749906 0 0.0013 120 | 0/8 6 h-lim-p 0.0042 3.8487 0.0687 1419.749904 0 0.0010 141 | 0/8 7 h-lim-p 0.0036 9.4018 0.0198 1419.749904 0 0.0016 161 | 0/8 8 h-lim-p 0.2639 20.0000 0.0001 1419.749894 0 1.0554 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1419.749894 0 1.0938 203 | 0/8 10 h-lim-p 2.4726 20.0000 0.0000 1419.749894 0 2.1635 223 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1419.749894 0 0.0098 250 Out... lnL = -1419.749894 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1419.749894 Node 7: lnL = -1419.749894 Node 8: lnL = -1419.749894 Node 9: lnL = -1419.749894 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 258 Sequential format.. Reading seq # 1: YKL100C_Sbay Reading seq # 2: YKL100C_Scer Reading seq # 3: YKL100C_Skud Reading seq # 4: YKL100C_Smik Reading seq # 5: YKL100C_Spar Sequences read.. Counting patterns.. # site patterns = 101 Counting frequencies.. 120 bytes for distance 16160 bytes for lkl0 12928 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.085932 0.091050 0.022479 0.105896 0.054842 0.230733 0.215509 0.121956 lnL0 = -1091.330709 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1091.330709 x= 0.08593 0.09105 0.02248 0.10590 0.05484 0.23073 0.21551 0.12196 1 h-lim-p 0.0007 0.0057 61.2348 1090.873359 6 0.0003 33 | 0/8 2 h-lim-p 0.0005 0.0040 22.4939 1090.698437 0 0.0008 45 | 0/8 3 h-lim-p 0.0033 0.0429 5.1960 1090.691857 6 0.0005 72 | 0/8 4 h-lim-p 0.0014 0.0716 1.9655 1090.690889 3 0.0006 90 | 0/8 5 h-lim-p 0.0020 0.8730 0.5727 1090.690723 4 0.0011 112 | 0/8 6 h-lim-p 0.0044 0.8745 0.1458 1090.690716 2 0.0007 139 | 0/8 7 h-lim-p 0.0874 20.0000 0.0012 1090.690424 0 0.6993 162 | 0/8 8 h-lim-p 0.0032 0.6960 0.2677 1090.690226 3 0.0025 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1090.690201 1 0.9961 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1090.690201 0 1.0938 230 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1090.690201 0 0.0781 254 | 0/8 12 h-lim-p 0.0380 20.0000 0.0000 1090.690201 0 0.0024 277 | 0/8 13 h-lim-p 0.0016 20.0000 0.0000 1090.690201 0 0.0008 297 | 0/8 14 h-lim-p 0.0007 20.0000 0.0000 1090.690201 0 0.0010 317 | 0/8 15 h-lim-p 0.0006 20.0000 0.0000 1090.690201 0 0.0000 351 | 0/8 16 h-lim-p 0.0000 20.0000 0.0011 | 0/8 17 h-lim-p 0.0000 20.0000 0.0011 Out... lnL = -1090.690201 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1090.690201 Node 7: lnL = -1090.690201 Node 8: lnL = -1090.690201 Node 9: lnL = -1090.690201 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 584 Sequential format.. Reading seq # 1: YKL101W_Sbay Reading seq # 2: YKL101W_Scer Reading seq # 3: YKL101W_Skud Reading seq # 4: YKL101W_Smik Reading seq # 5: YKL101W_Spar Sequences read.. Counting patterns.. # site patterns = 179 Counting frequencies.. 120 bytes for distance 28640 bytes for lkl0 22912 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.136893 0.026214 0.049092 0.079472 0.065556 0.121888 0.155690 0.167612 lnL0 = -2302.377662 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2302.377662 x= 0.13689 0.02621 0.04909 0.07947 0.06556 0.12189 0.15569 0.16761 1 h-lim-p 0.0002 0.0014 119.5766 2301.299837 2 0.0002 26 | 0/8 2 h-lim-p 0.0007 0.0053 24.6719 2301.232781 7 0.0002 57 | 0/8 3 h-lim-p 0.0005 0.0227 11.5915 2301.219830 2 0.0002 73 | 0/8 4 h-lim-p 0.0005 0.0297 4.8021 2301.217774 2 0.0002 89 | 0/8 5 h-lim-p 0.0013 0.2440 0.8220 2301.217667 2 0.0003 106 | 0/8 6 h-lim-p 0.0060 1.3238 0.0462 2301.217666 0 0.0003 129 | 0/8 7 h-lim-p 0.0006 14.8839 0.0248 2301.217666 0 0.0005 149 | 0/8 8 h-lim-p 0.3076 20.0000 0.0000 2301.217662 0 1.2303 171 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2301.217662 0 1.0938 191 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2301.217662 0 0.2734 213 | 0/8 11 h-lim-p 0.1558 20.0000 0.0000 2301.217662 0 0.0390 234 | 0/8 12 h-lim-p 0.0254 20.0000 0.0000 2301.217662 0 0.0032 256 | 0/8 13 h-lim-p 0.0023 20.0000 0.0000 2301.217662 0 0.0023 276 | 0/8 14 h-lim-p 0.0019 20.0000 0.0000 2301.217662 0 0.0009 296 | 0/8 15 h-lim-p 0.0006 20.0000 0.0000 2301.217662 0 0.0001 318 | 0/8 16 h-lim-p 0.0003 20.0000 0.0000 2301.217662 0 0.0000 340 Out... lnL = -2301.217662 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2301.217662 Node 7: lnL = -2301.217662 Node 8: lnL = -2301.217662 Node 9: lnL = -2301.217662 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 412 Sequential format.. Reading seq # 1: YKL103C_Sbay Reading seq # 2: YKL103C_Scer Reading seq # 3: YKL103C_Skud Reading seq # 4: YKL103C_Smik Reading seq # 5: YKL103C_Spar Sequences read.. Counting patterns.. # site patterns = 199 Counting frequencies.. 120 bytes for distance 31840 bytes for lkl0 25472 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.079433 0.156944 0.095230 0.190518 0.107652 0.162081 0.264688 0.127335 lnL0 = -1917.082528 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1917.082528 x= 0.07943 0.15694 0.09523 0.19052 0.10765 0.16208 0.26469 0.12734 1 h-lim-p 0.0059 0.0472 31.2368 1916.777264 6 0.0006 35 | 0/8 2 h-lim-p 0.0016 0.0184 12.4516 1916.720754 6 0.0008 61 | 0/8 3 h-lim-p 0.0019 0.0551 5.4576 1916.712372 5 0.0007 86 | 0/8 4 h-lim-p 0.0020 0.1890 1.8198 1916.710999 2 0.0010 102 | 0/8 5 h-lim-p 0.0039 0.4179 0.4430 1916.710937 3 0.0007 123 | 0/8 6 h-lim-p 0.0074 6.2948 0.0412 1916.710936 1 0.0009 147 | 0/8 7 h-lim-p 0.0082 20.0000 0.0046 1916.710936 0 0.0072 167 | 0/8 8 h-lim-p 0.0152 20.0000 0.0022 1916.710871 0 0.1218 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1916.710869 0 1.0938 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1916.710869 0 1.0938 230 | 0/8 11 h-lim-p 1.8279 20.0000 0.0000 1916.710869 0 0.7997 250 | 0/8 12 h-lim-p 0.5648 20.0000 0.0000 1916.710869 0 0.0353 273 | 0/8 13 h-lim-p 0.0100 20.0000 0.0000 1916.710869 0 0.0002 298 | 0/8 14 h-lim-p 0.0004 20.0000 0.0000 1916.710869 0 0.0000 331 Out... lnL = -1916.710869 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1916.710869 Node 7: lnL = -1916.710869 Node 8: lnL = -1916.710869 Node 9: lnL = -1916.710869 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 812 Sequential format.. Reading seq # 1: YKL104C_Sbay Reading seq # 2: YKL104C_Scer Reading seq # 3: YKL104C_Skud Reading seq # 4: YKL104C_Smik Reading seq # 5: YKL104C_Spar Sequences read.. Counting patterns.. # site patterns = 204 Counting frequencies.. 120 bytes for distance 32640 bytes for lkl0 26112 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.096607 0.034277 0.065964 0.052140 0.061283 0.108792 0.081902 0.121190 lnL0 = -2941.680389 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2941.680389 x= 0.09661 0.03428 0.06596 0.05214 0.06128 0.10879 0.08190 0.12119 1 h-lim-p 0.0011 0.5584 232.0623 2939.201304 8 0.0001 42 | 0/8 2 h-lim-p 0.0006 0.0046 34.5691 2939.086804 7 0.0002 72 | 0/8 3 h-lim-p 0.0004 0.0088 17.2107 2939.073005 6 0.0001 101 | 0/8 4 h-lim-p 0.0011 0.0590 1.7273 2939.072786 3 0.0002 121 | 0/8 5 h-lim-p 0.0008 0.4252 0.3454 2939.072776 0 0.0002 134 | 0/8 6 h-lim-p 0.0013 2.4464 0.0453 2939.072776 0 0.0003 155 | 0/8 7 h-lim-p 0.0063 20.0000 0.0020 2939.072757 0 0.0506 178 | 0/8 8 h-lim-p 0.0015 0.9025 0.0660 2939.072435 0 0.0061 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2939.072395 2 0.9961 224 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2939.072395 0 1.2500 244 | 0/8 11 h-lim-p 2.1176 20.0000 0.0000 2939.072395 0 0.4632 265 | 0/8 12 h-lim-p 0.2574 20.0000 0.0000 2939.072395 0 0.0040 290 | 0/8 13 h-lim-p 0.0020 20.0000 0.0000 2939.072395 0 0.0000 326 | 0/8 14 h-lim-p 0.0000 20.0000 0.0021 2939.072395 0 0.0000 356 | 0/8 15 h-lim-p 0.0000 20.0000 0.0009 2939.072395 0 0.0006 382 | 0/8 16 h-lim-p 0.0015 20.0000 0.0004 2939.072395 0 0.0000 412 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 2939.072395 0 0.0000 439 | 0/8 18 h-lim-p 0.0000 20.0000 0.0006 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0033 | 0/8 20 h-lim-p 0.0000 20.0000 0.0033 Out... lnL = -2939.072395 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2939.072395 Node 7: lnL = -2939.072395 Node 8: lnL = -2939.072395 Node 9: lnL = -2939.072395 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 663 Sequential format.. Reading seq # 1: YKL105C_Sbay Reading seq # 2: YKL105C_Scer Reading seq # 3: YKL105C_Skud Reading seq # 4: YKL105C_Smik Reading seq # 5: YKL105C_Spar Sequences read.. Counting patterns.. # site patterns = 229 Counting frequencies.. 120 bytes for distance 36640 bytes for lkl0 29312 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.112627 0.064681 0.031758 0.127419 0.084247 0.204572 0.187636 0.149587 lnL0 = -2914.309643 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2914.309643 x= 0.11263 0.06468 0.03176 0.12742 0.08425 0.20457 0.18764 0.14959 1 h-lim-p 0.0003 0.0026 114.4939 2913.372152 2 0.0002 26 | 0/8 2 h-lim-p 0.0004 0.0030 37.6588 2913.205938 7 0.0003 55 | 0/8 3 h-lim-p 0.0006 0.0166 16.0339 2913.174722 2 0.0003 71 | 0/8 4 h-lim-p 0.0008 0.0507 5.6305 2913.170112 3 0.0003 90 | 0/8 5 h-lim-p 0.0039 0.3401 0.4838 2913.170071 2 0.0004 108 | 0/8 6 h-lim-p 0.0025 3.2817 0.0719 2913.170070 0 0.0006 129 | 0/8 7 h-lim-p 0.0026 14.9546 0.0155 2913.170068 0 0.0026 149 | 0/8 8 h-lim-p 0.0171 20.0000 0.0023 2913.169615 0 0.2054 172 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2913.169594 1 0.9961 194 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2913.169594 0 1.2500 214 | 0/8 11 h-lim-p 1.7483 20.0000 0.0000 2913.169594 0 0.1639 237 | 0/8 12 h-lim-p 0.0727 20.0000 0.0000 2913.169594 0 0.0727 257 | 0/8 13 h-lim-p 0.0427 20.0000 0.0000 2913.169594 0 0.0000 299 | 0/8 14 h-lim-p 0.0000 20.0000 0.0008 | 0/8 15 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -2913.169594 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2913.169594 Node 7: lnL = -2913.169594 Node 8: lnL = -2913.169594 Node 9: lnL = -2913.169594 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 276 Sequential format.. Reading seq # 1: YKL106W_Sbay Reading seq # 2: YKL106W_Scer Reading seq # 3: YKL106W_Skud Reading seq # 4: YKL106W_Smik Reading seq # 5: YKL106W_Spar Sequences read.. Counting patterns.. # site patterns = 99 Counting frequencies.. 120 bytes for distance 15840 bytes for lkl0 12672 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.065595 0.052385 0.037412 0.107037 0.063668 0.134977 0.144259 0.092764 lnL0 = -1089.963260 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1089.963260 x= 0.06559 0.05239 0.03741 0.10704 0.06367 0.13498 0.14426 0.09276 1 h-lim-p 0.0017 0.0138 52.7550 1089.507830 6 0.0003 35 | 0/8 2 h-lim-p 0.0005 0.0039 13.6109 1089.478662 6 0.0003 61 | 0/8 3 h-lim-p 0.0034 0.1004 1.3367 1089.478190 4 0.0005 84 | 0/8 4 h-lim-p 0.0024 0.2758 0.2976 1089.478174 2 0.0004 103 | 0/8 5 h-lim-p 0.0021 6.4146 0.0556 1089.478173 1 0.0008 125 | 0/8 6 h-lim-p 0.0026 9.4747 0.0183 1089.478173 0 0.0011 145 | 0/8 7 h-lim-p 0.0114 20.0000 0.0018 1089.478173 0 0.0170 165 | 0/8 8 h-lim-p 0.0092 20.0000 0.0034 1089.478144 0 0.0554 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1089.478143 0 1.0938 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1089.478143 0 1.0938 227 | 0/8 11 h-lim-p 1.3427 20.0000 0.0000 1089.478143 0 4.0280 248 | 0/8 12 h-lim-p 2.3731 20.0000 0.0000 1089.478143 0 0.1298 271 | 0/8 13 h-lim-p 0.7447 20.0000 0.0000 1089.478143 0 0.0233 295 | 0/8 14 h-lim-p 0.0067 20.0000 0.0000 1089.478143 0 0.0000 339 Out... lnL = -1089.478143 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1089.478143 Node 7: lnL = -1089.478143 Node 8: lnL = -1089.478143 Node 9: lnL = -1089.478143 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 396 Sequential format.. Reading seq # 1: YKL107W_Sbay Reading seq # 2: YKL107W_Scer Reading seq # 3: YKL107W_Skud Reading seq # 4: YKL107W_Smik Reading seq # 5: YKL107W_Spar Sequences read.. Counting patterns.. # site patterns = 198 Counting frequencies.. 120 bytes for distance 31680 bytes for lkl0 25344 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.115150 0.247133 0.138639 0.189046 0.109574 0.236173 0.311689 0.177982 lnL0 = -1837.130672 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1837.130672 x= 0.11515 0.24713 0.13864 0.18905 0.10957 0.23617 0.31169 0.17798 1 h-lim-p 0.0278 3.4679 36.3750 1836.624150 2 0.0008 30 | 0/8 2 h-lim-p 0.0020 0.0261 15.1523 1836.495012 5 0.0013 53 | 0/8 3 h-lim-p 0.0021 0.0293 9.4005 1836.442351 4 0.0016 73 | 0/8 4 h-lim-p 0.0202 0.7034 0.7564 1836.441830 4 0.0019 97 | 0/8 5 h-lim-p 0.0038 1.0670 0.3673 1836.441714 3 0.0020 124 | 0/8 6 h-lim-p 0.0144 4.7493 0.0522 1836.441712 0 0.0016 146 | 0/8 7 h-lim-p 0.0190 20.0000 0.0043 1836.441687 0 0.0760 168 | 0/8 8 h-lim-p 0.0120 20.0000 0.0274 1836.441434 0 0.0361 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1836.441430 0 1.0938 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1836.441430 0 1.0938 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1836.441430 0 1.2500 249 | 0/8 12 h-lim-p 1.5630 20.0000 0.0000 1836.441430 0 0.0977 272 | 0/8 13 h-lim-p 0.0377 20.0000 0.0000 1836.441430 0 0.0188 292 | 0/8 14 h-lim-p 0.0110 20.0000 0.0000 1836.441430 0 0.0055 312 | 0/8 15 h-lim-p 0.0029 20.0000 0.0000 1836.441430 0 0.0000 348 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1836.441430 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1836.441430 Node 7: lnL = -1836.441430 Node 8: lnL = -1836.441430 Node 9: lnL = -1836.441430 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 581 Sequential format.. Reading seq # 1: YKL108W_Sbay Reading seq # 2: YKL108W_Scer Reading seq # 3: YKL108W_Skud Reading seq # 4: YKL108W_Smik Reading seq # 5: YKL108W_Spar Sequences read.. Counting patterns.. # site patterns = 199 Counting frequencies.. 120 bytes for distance 31840 bytes for lkl0 25472 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.081956 0.048997 0.032627 0.081683 0.066230 0.066957 0.164131 0.107210 lnL0 = -2115.137624 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2115.137624 x= 0.08196 0.04900 0.03263 0.08168 0.06623 0.06696 0.16413 0.10721 1 h-lim-p 0.0003 0.0028 163.2998 2113.272542 6 0.0002 33 | 0/8 2 h-lim-p 0.0002 0.0019 38.1893 2113.129049 5 0.0002 57 | 0/8 3 h-lim-p 0.0011 0.0211 7.2465 2113.123524 3 0.0002 76 | 0/8 4 h-lim-p 0.0005 0.0561 3.0484 2113.122033 4 0.0004 98 | 0/8 5 h-lim-p 0.0022 0.2282 0.5102 2113.121996 2 0.0003 116 | 0/8 6 h-lim-p 0.0017 1.7404 0.0882 2113.121995 0 0.0004 137 | 0/8 7 h-lim-p 0.0147 20.0000 0.0022 2113.121995 0 0.0016 159 | 0/8 8 h-lim-p 0.0084 20.0000 0.0004 2113.121981 0 0.2022 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2113.121980 0 1.0938 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2113.121980 0 2.1875 223 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2113.121980 0 0.5469 244 | 0/8 12 h-lim-p 0.1466 20.0000 0.0000 2113.121980 0 0.0006 271 | 0/8 13 h-lim-p 0.0002 20.0000 0.0000 2113.121980 0 0.0000 304 | 0/8 14 h-lim-p 0.0000 20.0000 0.0039 2113.121980 0 0.0000 335 | 0/8 15 h-lim-p 0.0000 20.0000 0.0006 2113.121980 0 0.0005 360 | 0/8 16 h-lim-p 0.0008 20.0000 0.0004 2113.121980 0 0.0000 388 | 0/8 17 h-lim-p 0.0000 20.0000 0.0006 2113.121980 0 0.0000 409 | 0/8 18 h-lim-p 0.0000 15.1767 0.0107 2113.121980 0 0.0000 437 | 0/8 19 h-lim-p 0.0000 20.0000 0.0025 2113.121980 0 0.0000 472 | 0/8 20 h-lim-p 0.0000 20.0000 0.0038 | 0/8 21 h-lim-p 0.0000 20.0000 0.0038 Out... lnL = -2113.121980 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2113.121980 Node 7: lnL = -2113.121980 Node 8: lnL = -2113.121980 Node 9: lnL = -2113.121980 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 890 Sequential format.. Reading seq # 1: YKL110C_Sbay Reading seq # 2: YKL110C_Scer Reading seq # 3: YKL110C_Skud Reading seq # 4: YKL110C_Smik Reading seq # 5: YKL110C_Spar Sequences read.. Counting patterns.. # site patterns = 301 Counting frequencies.. 120 bytes for distance 48160 bytes for lkl0 38528 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.175900 0.054862 0.052897 0.113145 0.071544 0.161751 0.205364 0.216331 lnL0 = -3827.412458 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3827.412458 x= 0.17590 0.05486 0.05290 0.11314 0.07154 0.16175 0.20536 0.21633 1 h-lim-p 0.0001 0.0010 160.6344 3825.247869 0 0.0002 22 | 0/8 2 h-lim-p 0.0004 0.0031 38.7972 3825.051811 6 0.0003 48 | 0/8 3 h-lim-p 0.0006 0.0119 18.6002 3824.992380 6 0.0004 76 | 0/8 4 h-lim-p 0.0029 0.0344 2.6768 3824.991774 2 0.0002 95 | 0/8 5 h-lim-p 0.0003 0.1867 1.7908 3824.991475 2 0.0003 111 | 0/8 6 h-lim-p 0.0010 0.6540 0.4429 3824.991437 2 0.0004 127 | 0/8 7 h-lim-p 0.0014 3.3386 0.1220 3824.991411 1 0.0011 149 | 0/8 8 h-lim-p 0.0163 12.6287 0.0085 3824.976592 0 0.2604 173 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 3824.976275 2 0.9961 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3824.976275 0 1.0938 217 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3824.976275 0 2.1875 237 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3824.976275 0 1.0938 257 | 0/8 13 h-lim-p 0.2871 20.0000 0.0000 3824.976275 0 4.5937 281 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 3824.976275 0 0.5469 302 | 0/8 15 h-lim-p 0.2203 20.0000 0.0000 3824.976275 0 0.0000 337 Out... lnL = -3824.976275 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3824.976275 Node 7: lnL = -3824.976275 Node 8: lnL = -3824.976275 Node 9: lnL = -3824.976275 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 716 Sequential format.. Reading seq # 1: YKL112W_Sbay Reading seq # 2: YKL112W_Scer Reading seq # 3: YKL112W_Skud Reading seq # 4: YKL112W_Smik Reading seq # 5: YKL112W_Spar Sequences read.. Counting patterns.. # site patterns = 229 Counting frequencies.. 120 bytes for distance 36640 bytes for lkl0 29312 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.107109 0.072757 0.062668 0.112177 0.101972 0.122768 0.165095 0.135420 lnL0 = -3067.748841 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3067.748841 x= 0.10711 0.07276 0.06267 0.11218 0.10197 0.12277 0.16510 0.13542 1 h-lim-p 0.0008 0.0060 189.5855 3064.246707 9 0.0002 45 | 0/8 2 h-lim-p 0.0005 0.0036 46.4138 3063.913075 6 0.0003 70 | 0/8 3 h-lim-p 0.0007 0.0085 20.5148 3063.854242 3 0.0003 88 | 0/8 4 h-lim-p 0.0013 0.0375 5.3660 3063.851055 3 0.0002 107 | 0/8 5 h-lim-p 0.0024 0.2660 0.5299 3063.851011 2 0.0003 125 | 0/8 6 h-lim-p 0.0019 2.6995 0.0913 3063.851008 1 0.0005 148 | 0/8 7 h-lim-p 0.0111 20.0000 0.0037 3063.850479 0 0.1779 172 | 0/8 8 h-lim-p 0.0012 19.6877 0.5695 3063.848447 0 0.0023 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3063.848357 2 0.9961 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3063.848357 0 1.0938 237 | 0/8 11 h-lim-p 2.1636 20.0000 0.0000 3063.848357 0 1.8931 257 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3063.848357 0 1.0938 277 | 0/8 13 h-lim-p 0.3334 20.0000 0.0000 3063.848357 0 4.0003 300 | 0/8 14 h-lim-p 0.6637 20.0000 0.0000 3063.848357 0 0.0000 344 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 3063.848357 0 0.0000 370 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 3063.848357 0 0.0000 391 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 3063.848357 0 0.0000 425 | 0/8 18 h-lim-p 0.0000 20.0000 0.0003 | 0/8 19 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -3063.848357 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3063.848357 Node 7: lnL = -3063.848357 Node 8: lnL = -3063.848357 Node 9: lnL = -3063.848357 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 717 Sequential format.. Reading seq # 1: YKL113C_Sbay Reading seq # 2: YKL113C_Scer Reading seq # 3: YKL113C_Skud Reading seq # 4: YKL113C_Smik Reading seq # 5: YKL113C_Spar Sequences read.. Counting patterns.. # site patterns = 231 Counting frequencies.. 120 bytes for distance 36960 bytes for lkl0 29568 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.116177 0.049348 0.043610 0.124963 0.109281 0.129750 0.174808 0.144217 lnL0 = -3081.219914 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3081.219914 x= 0.11618 0.04935 0.04361 0.12496 0.10928 0.12975 0.17481 0.14422 1 h-lim-p 0.0011 0.5049 238.4666 3076.923560 9 0.0002 48 | 0/8 2 h-lim-p 0.0003 0.0020 55.1344 3076.474346 1 0.0003 62 | 0/8 3 h-lim-p 0.0007 0.0070 25.5460 3076.379995 4 0.0003 82 | 0/8 4 h-lim-p 0.0024 0.0575 3.5821 3076.377936 4 0.0003 104 | 0/8 5 h-lim-p 0.0012 0.1957 0.9713 3076.377803 2 0.0003 121 | 0/8 6 h-lim-p 0.0019 1.0513 0.1565 3076.377796 0 0.0004 142 | 0/8 7 h-lim-p 0.0107 20.0000 0.0060 3076.377100 0 0.1279 165 | 0/8 8 h-lim-p 0.0016 12.1779 0.4972 3076.372409 0 0.0031 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 3076.372146 2 1.0889 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3076.372145 0 1.0938 230 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3076.372145 0 1.2500 250 | 0/8 12 h-lim-p 1.5913 20.0000 0.0000 3076.372145 0 0.3978 271 | 0/8 13 h-lim-p 0.2006 20.0000 0.0000 3076.372145 0 0.1003 291 | 0/8 14 h-lim-p 0.0579 20.0000 0.0000 3076.372145 0 0.0000 333 Out... lnL = -3076.372145 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3076.372145 Node 7: lnL = -3076.372145 Node 8: lnL = -3076.372145 Node 9: lnL = -3076.372145 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 294 Sequential format.. Reading seq # 1: YKL114C_Sbay Reading seq # 2: YKL114C_Scer Reading seq # 3: YKL114C_Skud Reading seq # 4: YKL114C_Smik Reading seq # 5: YKL114C_Spar Sequences read.. Counting patterns.. # site patterns = 133 Counting frequencies.. 120 bytes for distance 21280 bytes for lkl0 17024 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.127964 0.092136 0.070423 0.131572 0.056913 0.193197 0.197413 0.161186 lnL0 = -1291.190853 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1291.190853 x= 0.12796 0.09214 0.07042 0.13157 0.05691 0.19320 0.19741 0.16119 1 h-lim-p 0.0011 0.0088 29.1495 1290.855016 8 0.0008 39 | 0/8 2 h-lim-p 0.0008 0.0063 19.4995 1290.789607 7 0.0005 68 | 0/8 3 h-lim-p 0.0024 0.1330 3.6155 1290.784941 6 0.0008 96 | 0/8 4 h-lim-p 0.0030 0.1409 0.9214 1290.784623 4 0.0008 117 | 0/8 5 h-lim-p 0.0022 1.0416 0.3378 1290.784589 3 0.0006 146 | 0/8 6 h-lim-p 0.0050 4.2863 0.0430 1290.784588 0 0.0011 167 | 0/8 7 h-lim-p 0.0040 19.9860 0.0120 1290.784588 0 0.0035 187 | 0/8 8 h-lim-p 0.0413 20.0000 0.0010 1290.784500 0 0.3300 210 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1290.784499 0 1.0938 230 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1290.784499 0 1.0938 250 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1290.784499 0 1.0938 270 | 0/8 12 h-lim-p 1.0954 20.0000 0.0000 1290.784499 0 0.0000 309 Out... lnL = -1290.784499 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1290.784499 Node 7: lnL = -1290.784499 Node 8: lnL = -1290.784499 Node 9: lnL = -1290.784499 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 848 Sequential format.. Reading seq # 1: YKL117W_Sbay Reading seq # 2: YKL117W_Scer Reading seq # 3: YKL117W_Skud Reading seq # 4: YKL117W_Smik Reading seq # 5: YKL117W_Spar Sequences read.. Counting patterns.. # site patterns = 386 Counting frequencies.. 120 bytes for distance 61760 bytes for lkl0 49408 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.104204 0.096933 0.019725 0.268629 0.216698 0.488008 0.190992 0.151863 lnL0 = -4333.573630 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4333.573630 x= 0.10420 0.09693 0.01972 0.26863 0.21670 0.48801 0.19099 0.15186 1 h-lim-p 0.0012 0.4193 267.5408 4327.536775 8 0.0002 42 | 0/8 2 h-lim-p 0.0004 0.0033 68.1591 4325.517719 0 0.0008 55 | 0/8 3 h-lim-p 0.0014 0.0115 28.8145 4325.249526 5 0.0008 78 | 0/8 4 h-lim-p 0.0014 0.0244 15.5573 4325.189299 2 0.0007 94 | 0/8 5 h-lim-p 0.0010 0.0460 10.5594 4325.165933 3 0.0006 114 | 0/8 6 h-lim-p 0.0045 0.1868 1.4743 4325.165317 3 0.0006 134 | 0/8 7 h-lim-p 0.0044 1.0689 0.1884 4325.165150 3 0.0028 154 | 0/8 8 h-lim-p 0.0176 6.7491 0.0300 4325.114751 0 0.4236 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0027 4325.107696 4 1.1078 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 4325.107648 1 1.0938 227 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4325.107648 0 1.0938 247 | 0/8 12 h-lim-p 1.4439 20.0000 0.0000 4325.107648 0 1.4439 267 | 0/8 13 h-lim-p 1.1390 20.0000 0.0000 4325.107648 0 0.0044 294 | 0/8 14 h-lim-p 0.0015 20.0000 0.0000 4325.107648 0 0.0000 322 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 4325.107648 0 0.0001 343 Out... lnL = -4325.107648 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4325.107648 Node 7: lnL = -4325.107648 Node 8: lnL = -4325.107648 Node 9: lnL = -4325.107648 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 845 Sequential format.. Reading seq # 1: YKL119C_Sbay Reading seq # 2: YKL119C_Scer Reading seq # 3: YKL119C_Skud Reading seq # 4: YKL119C_Smik Reading seq # 5: YKL119C_Spar Sequences read.. Counting patterns.. # site patterns = 401 Counting frequencies.. 120 bytes for distance 64160 bytes for lkl0 51328 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.085883 0.390442 0.000060 0.633908 0.278974 0.603563 0.281313 0.153920 lnL0 = -4743.415260 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4743.415260 x= 0.08588 0.39044 0.00006 0.63391 0.27897 0.60356 0.28131 0.15392 1 h-lim-p 0.0000 0.0000 303.2125 4743.362377 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0007 783.0246 4695.229759 0 0.0003 39 | 1/8 3 h-lim-p 0.0003 0.0027 138.7558 4685.437105 0 0.0014 53 | 1/8 4 h-lim-p 0.0021 0.0165 53.1892 4683.180012 7 0.0020 83 | 1/8 5 h-lim-p 0.0031 0.0245 11.1306 4683.120173 6 0.0009 110 | 1/8 6 h-lim-p 0.0092 1.2132 1.1075 4682.790191 0 0.0368 124 | 1/8 7 h-lim-p 0.0166 0.2413 2.4583 4680.593923 0 0.0331 137 | 1/8 8 h-lim-p 0.3545 2.8359 0.0674 4679.990936 0 0.7090 150 | 1/8 9 h-lim-p 2.5000 20.0000 0.0130 4679.957808 4 0.9802 177 | 1/8 10 h-lim-p 2.5000 20.0000 0.0013 4679.957447 3 0.8059 204 | 1/8 11 h-lim-p 2.5000 20.0000 0.0001 4679.957442 1 0.9961 225 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 4679.957442 0 1.0938 244 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 4679.957442 0 1.0938 263 | 1/8 14 h-lim-p 1.6698 20.0000 0.0000 4679.957442 0 1.4611 282 | 1/8 15 h-lim-p 1.6466 20.0000 0.0000 4679.957442 0 1.6466 301 | 1/8 16 h-lim-p 0.5575 20.0000 0.0000 4679.957442 0 0.0000 343 | 1/8 17 h-lim-p 0.0000 20.0000 0.0000 4679.957442 0 0.0000 375 | 1/8 18 h-lim-p 0.0000 20.0000 0.0000 4679.957442 0 0.0000 408 | 1/8 19 h-lim-p 0.0000 20.0000 0.0000 | 1/8 20 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -4679.957442 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4679.957442 Node 7: lnL = -4679.957442 Node 8: lnL = -4679.957442 Node 9: lnL = -4679.957442 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 673 Sequential format.. Reading seq # 1: YKL120W_Sbay Reading seq # 2: YKL120W_Scer Reading seq # 3: YKL120W_Skud Reading seq # 4: YKL120W_Smik Reading seq # 5: YKL120W_Spar Sequences read.. Counting patterns.. # site patterns = 224 Counting frequencies.. 120 bytes for distance 35840 bytes for lkl0 28672 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.131752 0.043276 0.062394 0.104470 0.079284 0.194194 0.184455 0.162065 lnL0 = -2956.831414 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2956.831414 x= 0.13175 0.04328 0.06239 0.10447 0.07928 0.19419 0.18446 0.16207 1 h-lim-p 0.0006 0.0051 189.8555 2953.821101 9 0.0002 44 | 0/8 2 h-lim-p 0.0006 0.0047 41.4722 2953.483665 8 0.0004 76 | 0/8 3 h-lim-p 0.0006 0.0079 26.9878 2953.423848 7 0.0002 105 | 0/8 4 h-lim-p 0.0010 0.0239 5.7689 2953.419684 5 0.0003 129 | 0/8 5 h-lim-p 0.0041 0.7995 0.3809 2953.419651 2 0.0004 147 | 0/8 6 h-lim-p 0.0018 2.4644 0.0939 2953.419649 0 0.0004 168 | 0/8 7 h-lim-p 0.0020 12.1400 0.0185 2953.419648 0 0.0020 188 | 0/8 8 h-lim-p 0.0190 20.0000 0.0020 2953.419038 0 0.3034 212 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2953.419017 1 0.9961 234 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2953.419017 0 1.2500 254 | 0/8 11 h-lim-p 1.9737 20.0000 0.0000 2953.419017 0 0.2159 276 | 0/8 12 h-lim-p 0.1019 20.0000 0.0000 2953.419017 0 0.0064 299 | 0/8 13 h-lim-p 0.0055 20.0000 0.0000 2953.419017 0 0.0014 320 | 0/8 14 h-lim-p 0.0003 20.0000 0.0000 2953.419017 0 0.0000 352 | 0/8 15 h-lim-p 0.0000 20.0000 0.0012 | 0/8 16 h-lim-p 0.0000 20.0000 0.0012 Out... lnL = -2953.419017 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2953.419017 Node 7: lnL = -2953.419017 Node 8: lnL = -2953.419017 Node 9: lnL = -2953.419017 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 850 Sequential format.. Reading seq # 1: YKL121W_Sbay Reading seq # 2: YKL121W_Scer Reading seq # 3: YKL121W_Skud Reading seq # 4: YKL121W_Smik Reading seq # 5: YKL121W_Spar Sequences read.. Counting patterns.. # site patterns = 391 Counting frequencies.. 120 bytes for distance 62560 bytes for lkl0 50048 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.227722 0.077531 0.057769 0.217701 0.151482 0.244774 0.451966 0.280820 lnL0 = -4525.542790 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4525.542790 x= 0.22772 0.07753 0.05777 0.21770 0.15148 0.24477 0.45197 0.28082 1 h-lim-p 0.0003 0.0025 160.7724 4521.566736 8 0.0003 42 | 0/8 2 h-lim-p 0.0003 0.0027 63.3373 4520.836278 1 0.0004 56 | 0/8 3 h-lim-p 0.0010 0.0194 26.0289 4520.706214 6 0.0005 79 | 0/8 4 h-lim-p 0.0016 0.0653 7.5564 4520.675287 6 0.0012 103 | 0/8 5 h-lim-p 0.0028 0.1280 3.2625 4520.669902 2 0.0012 119 | 0/8 6 h-lim-p 0.0040 0.5933 0.9771 4520.669472 2 0.0010 136 | 0/8 7 h-lim-p 0.0069 1.2396 0.1421 4520.669461 0 0.0009 158 | 0/8 8 h-lim-p 0.0512 20.0000 0.0024 4520.666704 0 0.8185 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 4520.666603 1 1.0938 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4520.666602 0 1.0938 224 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4520.666602 0 1.0938 244 | 0/8 12 h-lim-p 2.0220 20.0000 0.0000 4520.666602 0 0.2212 266 | 0/8 13 h-lim-p 0.1156 20.0000 0.0000 4520.666602 0 0.0009 292 Out... lnL = -4520.666602 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4520.666602 Node 7: lnL = -4520.666602 Node 8: lnL = -4520.666602 Node 9: lnL = -4520.666602 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 901 Sequential format.. Reading seq # 1: YKL122C_Sbay Reading seq # 2: YKL122C_Scer Reading seq # 3: YKL122C_Skud Reading seq # 4: YKL122C_Smik Reading seq # 5: YKL122C_Spar Sequences read.. Counting patterns.. # site patterns = 446 Counting frequencies.. 120 bytes for distance 71360 bytes for lkl0 57088 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.155445 0.335459 0.000060 0.472697 0.410500 0.428209 0.624678 0.229171 lnL0 = -5202.412976 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 5202.412976 x= 0.15544 0.33546 0.00006 0.47270 0.41050 0.42821 0.62468 0.22917 1 h-lim-p 0.0000 0.0000 195.8469 5202.387026 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0021 303.9051 5173.905755 9 0.0012 63 | 1/8 3 h-lim-p 0.0015 0.0118 60.8845 5170.954336 0 0.0022 75 | 1/8 4 h-lim-p 0.0028 0.0228 26.0688 5170.598349 6 0.0013 98 | 1/8 5 h-lim-p 0.0252 0.4159 1.3031 5170.581167 4 0.0064 120 | 1/8 6 h-lim-p 0.0069 0.5747 1.2171 5170.415176 0 0.0274 134 | 1/8 7 h-lim-p 0.0099 0.1367 3.3630 5168.528657 0 0.0397 148 | 1/8 8 h-lim-p 1.2099 9.6793 0.0534 5168.311151 4 0.6162 169 | 1/8 9 h-lim-p 2.5000 20.0000 0.0072 5168.303715 5 0.9136 200 | 1/8 10 h-lim-p 2.5000 20.0000 0.0008 5168.303564 2 0.9644 223 | 1/8 11 h-lim-p 2.5000 20.0000 0.0001 5168.303563 0 1.0938 242 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 5168.303563 0 1.0938 261 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 5168.303563 0 1.0938 280 | 1/8 14 h-lim-p 1.8894 20.0000 0.0000 5168.303563 0 0.9447 299 | 1/8 15 h-lim-p 0.7188 20.0000 0.0000 5168.303563 0 0.7188 318 | 1/8 16 h-lim-p 0.0656 20.0000 0.0000 5168.303563 0 0.0000 356 | 1/8 17 h-lim-p 0.0000 20.0000 0.0000 | 1/8 18 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -5168.303563 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -5168.303563 Node 7: lnL = -5168.303563 Node 8: lnL = -5168.303563 Node 9: lnL = -5168.303563 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 491 Sequential format.. Reading seq # 1: YKL126W_Sbay Reading seq # 2: YKL126W_Scer Reading seq # 3: YKL126W_Skud Reading seq # 4: YKL126W_Smik Reading seq # 5: YKL126W_Spar Sequences read.. Counting patterns.. # site patterns = 172 Counting frequencies.. 120 bytes for distance 27520 bytes for lkl0 22016 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.094184 0.116354 0.028223 0.126168 0.052769 0.185204 0.163313 0.116316 lnL0 = -2078.354862 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2078.354862 x= 0.09418 0.11635 0.02822 0.12617 0.05277 0.18520 0.16331 0.11632 1 h-lim-p 0.0039 0.0901 103.3769 2077.508036 8 0.0002 43 | 0/8 2 h-lim-p 0.0008 0.0063 21.9150 2077.422555 2 0.0004 59 | 0/8 3 h-lim-p 0.0005 0.0101 15.4289 2077.399691 4 0.0003 80 | 0/8 4 h-lim-p 0.0011 0.0547 3.8590 2077.396720 3 0.0004 98 | 0/8 5 h-lim-p 0.0030 0.3979 0.5743 2077.396632 3 0.0005 118 | 0/8 6 h-lim-p 0.0089 4.1322 0.0342 2077.396632 0 0.0006 141 | 0/8 7 h-lim-p 0.0041 20.0000 0.0046 2077.396627 0 0.0164 163 | 0/8 8 h-lim-p 0.0071 4.4369 0.0107 2077.396397 0 0.0282 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2077.396393 0 1.0938 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2077.396393 0 1.0938 225 | 0/8 11 h-lim-p 1.6235 20.0000 0.0000 2077.396393 0 3.2471 246 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2077.396393 0 0.0024 275 | 0/8 13 h-lim-p 0.0060 20.0000 0.0000 2077.396393 0 0.0060 295 | 0/8 14 h-lim-p 0.0032 20.0000 0.0000 2077.396393 0 0.0000 323 Out... lnL = -2077.396393 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2077.396393 Node 7: lnL = -2077.396393 Node 8: lnL = -2077.396393 Node 9: lnL = -2077.396393 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 914 Sequential format.. Reading seq # 1: YKL127W_Sbay Reading seq # 2: YKL127W_Scer Reading seq # 3: YKL127W_Skud Reading seq # 4: YKL127W_Smik Reading seq # 5: YKL127W_Spar Sequences read.. Counting patterns.. # site patterns = 443 Counting frequencies.. 120 bytes for distance 70880 bytes for lkl0 56704 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.266511 0.043622 0.117370 0.249444 0.216490 0.273756 0.284551 0.309195 lnL0 = -4697.958781 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4697.958781 x= 0.26651 0.04362 0.11737 0.24944 0.21649 0.27376 0.28455 0.30919 1 h-lim-p 0.0035 0.8808 164.6670 4693.543870 3 0.0004 30 | 0/8 2 h-lim-p 0.0013 0.0106 44.7519 4692.612966 5 0.0010 54 | 0/8 3 h-lim-p 0.0047 0.0402 9.2362 4692.566321 5 0.0011 80 | 0/8 4 h-lim-p 0.0031 0.1082 3.3629 4692.563170 3 0.0006 99 | 0/8 5 h-lim-p 0.0029 0.7680 0.7410 4692.562969 3 0.0008 118 | 0/8 6 h-lim-p 0.0037 3.1787 0.1552 4692.562948 2 0.0014 142 | 0/8 7 h-lim-p 0.0139 20.0000 0.0158 4692.562724 0 0.0555 164 | 0/8 8 h-lim-p 0.0078 20.0000 0.1124 4692.557291 0 0.0234 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 4692.557204 2 0.9961 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4692.557204 0 1.0938 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4692.557204 0 1.0938 249 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4692.557204 0 1.2500 269 | 0/8 13 h-lim-p 1.4076 20.0000 0.0000 4692.557204 0 2.1115 289 | 0/8 14 h-lim-p 1.2151 20.0000 0.0000 4692.557204 0 0.6075 309 | 0/8 15 h-lim-p 0.0168 20.0000 0.0001 4692.557204 0 0.0021 331 | 0/8 16 h-lim-p 0.0247 20.0000 0.0000 4692.557204 0 0.0002 357 Out... lnL = -4692.557204 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4692.557204 Node 7: lnL = -4692.557204 Node 8: lnL = -4692.557204 Node 9: lnL = -4692.557204 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 859 Sequential format.. Reading seq # 1: YKL128C_Sbay Reading seq # 2: YKL128C_Scer Reading seq # 3: YKL128C_Skud Reading seq # 4: YKL128C_Smik Reading seq # 5: YKL128C_Spar Sequences read.. Counting patterns.. # site patterns = 466 Counting frequencies.. 120 bytes for distance 74560 bytes for lkl0 59648 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.302324 0.156978 0.023403 0.281760 0.209178 0.578001 0.628053 0.363362 lnL0 = -4968.506733 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4968.506733 x= 0.30232 0.15698 0.02340 0.28176 0.20918 0.57800 0.62805 0.36336 1 h-lim-p 0.0469 3.4314 46.0170 4967.833809 3 0.0007 33 | 0/8 2 h-lim-p 0.0006 0.0051 18.4806 4967.637545 0 0.0013 46 | 0/8 3 h-lim-p 0.0003 0.0026 20.1339 4967.486043 0 0.0013 60 | 0/8 4 h-lim-p 0.0012 0.0097 10.3110 4967.416319 0 0.0024 73 | 0/8 5 h-lim-p 0.0069 0.1897 3.6156 4967.405646 6 0.0020 100 | 0/8 6 h-lim-p 0.0053 0.1094 1.3690 4967.403881 1 0.0021 114 | 0/8 7 h-lim-p 0.0101 2.4804 0.2876 4967.403727 3 0.0036 133 | 0/8 8 h-lim-p 0.2915 20.0000 0.0035 4967.400249 0 1.1661 155 | 0/8 9 h-lim-p 2.5000 20.0000 0.0009 4967.400028 2 0.9961 179 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4967.400028 0 1.0938 199 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4967.400028 0 1.0938 219 | 0/8 12 h-lim-p 2.2240 20.0000 0.0000 4967.400028 0 2.2240 239 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 4967.400028 0 0.2734 261 | 0/8 14 h-lim-p 0.0394 20.0000 0.0000 4967.400028 0 0.0394 281 | 0/8 15 h-lim-p 0.0154 20.0000 0.0000 4967.400028 0 0.0019 303 Out... lnL = -4967.400028 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4967.400028 Node 7: lnL = -4967.400028 Node 8: lnL = -4967.400028 Node 9: lnL = -4967.400028 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 341 Sequential format.. Reading seq # 1: YKL130C_Sbay Reading seq # 2: YKL130C_Scer Reading seq # 3: YKL130C_Skud Reading seq # 4: YKL130C_Smik Reading seq # 5: YKL130C_Spar Sequences read.. Counting patterns.. # site patterns = 145 Counting frequencies.. 120 bytes for distance 23200 bytes for lkl0 18560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.123968 0.066873 0.043934 0.136034 0.083707 0.167058 0.213900 0.148050 lnL0 = -1488.252947 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1488.252947 x= 0.12397 0.06687 0.04393 0.13603 0.08371 0.16706 0.21390 0.14805 1 h-lim-p 0.0012 0.0094 67.0833 1487.410240 9 0.0004 47 | 0/8 2 h-lim-p 0.0009 0.0070 21.4441 1487.290746 7 0.0006 75 | 0/8 3 h-lim-p 0.0012 0.0293 9.6859 1487.267250 5 0.0006 100 | 0/8 4 h-lim-p 0.0016 0.0657 3.7192 1487.263213 2 0.0007 116 | 0/8 5 h-lim-p 0.0042 0.2634 0.6019 1487.263072 3 0.0008 135 | 0/8 6 h-lim-p 0.0050 2.9825 0.0975 1487.263068 1 0.0006 159 | 0/8 7 h-lim-p 0.0137 20.0000 0.0044 1487.263068 0 0.0060 179 | 0/8 8 h-lim-p 0.0178 20.0000 0.0015 1487.263003 0 0.1426 202 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1487.263001 0 1.0938 222 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1487.263001 0 1.0938 242 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1487.263001 0 0.5469 263 | 0/8 12 h-lim-p 0.3702 20.0000 0.0000 1487.263001 0 0.0694 285 | 0/8 13 h-lim-p 0.0413 20.0000 0.0000 1487.263001 0 0.0026 308 | 0/8 14 h-lim-p 0.0020 20.0000 0.0000 1487.263001 0 0.0005 329 Out... lnL = -1487.263001 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1487.263001 Node 7: lnL = -1487.263001 Node 8: lnL = -1487.263001 Node 9: lnL = -1487.263001 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 518 Sequential format.. Reading seq # 1: YKL132C_Sbay Reading seq # 2: YKL132C_Scer Reading seq # 3: YKL132C_Skud Reading seq # 4: YKL132C_Smik Reading seq # 5: YKL132C_Spar Sequences read.. Counting patterns.. # site patterns = 176 Counting frequencies.. 120 bytes for distance 28160 bytes for lkl0 22528 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.144626 0.028819 0.049114 0.143777 0.094090 0.215499 0.190633 0.169546 lnL0 = -2107.738351 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2107.738351 x= 0.14463 0.02882 0.04911 0.14378 0.09409 0.21550 0.19063 0.16955 1 h-lim-p 0.0011 0.0090 57.1952 2107.343539 3 0.0003 29 | 0/8 2 h-lim-p 0.0009 0.0085 15.8020 2107.295593 5 0.0004 50 | 0/8 3 h-lim-p 0.0011 0.0426 6.0232 2107.288420 5 0.0005 74 | 0/8 4 h-lim-p 0.0016 0.1460 1.6910 2107.287650 4 0.0006 96 | 0/8 5 h-lim-p 0.0043 0.4534 0.2339 2107.287637 1 0.0005 112 | 0/8 6 h-lim-p 0.0014 3.1323 0.0783 2107.287636 0 0.0006 132 | 0/8 7 h-lim-p 0.0199 20.0000 0.0024 2107.287636 0 0.0022 154 | 0/8 8 h-lim-p 0.0651 20.0000 0.0001 2107.287633 0 0.5211 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2107.287633 0 1.0938 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2107.287633 0 2.1875 217 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2107.287633 0 0.5469 238 | 0/8 12 h-lim-p 0.2032 20.0000 0.0000 2107.287633 0 0.0095 262 | 0/8 13 h-lim-p 0.0051 20.0000 0.0000 2107.287633 0 0.0000 305 Out... lnL = -2107.287633 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2107.287633 Node 7: lnL = -2107.287633 Node 8: lnL = -2107.287633 Node 9: lnL = -2107.287633 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 536 Sequential format.. Reading seq # 1: YKL133C_Sbay Reading seq # 2: YKL133C_Scer Reading seq # 3: YKL133C_Skud Reading seq # 4: YKL133C_Smik Reading seq # 5: YKL133C_Spar Sequences read.. Counting patterns.. # site patterns = 277 Counting frequencies.. 120 bytes for distance 44320 bytes for lkl0 35456 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.306193 0.042661 0.066632 0.201740 0.140829 0.291949 0.349589 0.347968 lnL0 = -2755.979626 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2755.979626 x= 0.30619 0.04266 0.06663 0.20174 0.14083 0.29195 0.34959 0.34797 1 h-lim-p 0.0145 2.1996 61.7107 2755.197942 2 0.0004 30 | 0/8 2 h-lim-p 0.0028 0.0450 9.2314 2755.160814 7 0.0009 59 | 0/8 3 h-lim-p 0.0016 0.1126 5.2042 2755.148178 6 0.0012 85 | 0/8 4 h-lim-p 0.0024 0.1540 2.5317 2755.145132 4 0.0012 107 | 0/8 5 h-lim-p 0.0047 0.6060 0.6699 2755.144610 4 0.0025 128 | 0/8 6 h-lim-p 0.0060 1.3770 0.2809 2755.144566 1 0.0013 151 | 0/8 7 h-lim-p 0.0042 4.7321 0.0883 2755.144561 2 0.0013 176 | 0/8 8 h-lim-p 0.1540 20.0000 0.0008 2755.144032 0 1.2320 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 2755.144006 1 0.9961 221 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2755.144006 0 1.0938 241 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2755.144006 0 0.1172 265 | 0/8 12 h-lim-p 0.0624 20.0000 0.0000 2755.144006 0 0.0000 304 Out... lnL = -2755.144006 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2755.144006 Node 7: lnL = -2755.144006 Node 8: lnL = -2755.144006 Node 9: lnL = -2755.144006 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 539 Sequential format.. Reading seq # 1: YKL135C_Sbay Reading seq # 2: YKL135C_Scer Reading seq # 3: YKL135C_Skud Reading seq # 4: YKL135C_Smik Reading seq # 5: YKL135C_Spar Sequences read.. Counting patterns.. # site patterns = 223 Counting frequencies.. 120 bytes for distance 35680 bytes for lkl0 28544 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.174139 0.000060 0.100789 0.132085 0.089977 0.232884 0.274016 0.203024 lnL0 = -2460.531158 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2460.531158 x= 0.17414 0.00006 0.10079 0.13208 0.08998 0.23288 0.27402 0.20302 1 h-lim-p 0.0016 0.0124 97.7190 2458.517176 4 0.0003 30 | 0/8 2 h-lim-p 0.0017 0.0135 19.1760 2458.365589 7 0.0009 60 | 0/8 3 h-lim-p 0.0010 0.0208 16.4268 2458.329680 3 0.0004 78 | 0/8 4 h-lim-p 0.0012 0.0647 5.7491 2458.322219 2 0.0006 94 | 0/8 5 h-lim-p 0.0064 0.5722 0.4972 2458.322098 3 0.0010 115 | 0/8 6 h-lim-p 0.0031 1.1847 0.1520 2458.322082 2 0.0008 140 | 0/8 7 h-lim-p 0.0042 2.6466 0.0301 2458.321790 0 0.0249 162 | 0/8 8 h-lim-p 0.0068 0.7711 0.1098 2458.314469 0 0.0273 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 2458.314286 2 0.9961 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2458.314286 0 1.0938 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2458.314286 0 1.0938 248 | 0/8 12 h-lim-p 1.2360 20.0000 0.0000 2458.314286 0 4.9442 270 | 0/8 13 h-lim-p 2.4836 20.0000 0.0000 2458.314286 0 0.3105 292 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 2458.314286 0 0.0781 316 | 0/8 15 h-lim-p 0.0078 20.0000 0.0000 2458.314286 0 0.0019 337 Out... lnL = -2458.314286 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2458.314286 Node 7: lnL = -2458.314286 Node 8: lnL = -2458.314286 Node 9: lnL = -2458.314286 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 326 Sequential format.. Reading seq # 1: YKL137W_Sbay Reading seq # 2: YKL137W_Scer Reading seq # 3: YKL137W_Skud Reading seq # 4: YKL137W_Smik Reading seq # 5: YKL137W_Spar Sequences read.. Counting patterns.. # site patterns = 160 Counting frequencies.. 120 bytes for distance 25600 bytes for lkl0 20480 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.150849 0.062490 0.093205 0.094921 0.131681 0.235623 0.204885 0.179381 lnL0 = -1452.966578 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1452.966578 x= 0.15085 0.06249 0.09321 0.09492 0.13168 0.23562 0.20489 0.17938 1 h-lim-p 0.0021 0.0165 29.4741 1452.576679 2 0.0010 26 | 0/8 2 h-lim-p 0.0013 0.0107 18.0027 1452.466136 6 0.0009 52 | 0/8 3 h-lim-p 0.0040 0.0911 3.8278 1452.461832 6 0.0006 82 | 0/8 4 h-lim-p 0.0018 0.1784 1.3708 1452.460955 5 0.0011 108 | 0/8 5 h-lim-p 0.0040 0.6342 0.3659 1452.460880 3 0.0012 129 | 0/8 6 h-lim-p 0.0215 7.9096 0.0199 1452.460878 1 0.0026 153 | 0/8 7 h-lim-p 0.0044 15.1182 0.0121 1452.460853 0 0.0174 175 | 0/8 8 h-lim-p 0.0041 2.4951 0.0510 1452.460419 0 0.0165 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1452.460415 1 0.9961 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1452.460415 0 2.1875 239 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1452.460415 0 1.0938 259 | 0/8 12 h-lim-p 1.1975 20.0000 0.0000 1452.460415 0 4.7900 281 | 0/8 13 h-lim-p 1.8220 20.0000 0.0000 1452.460415 0 0.2278 303 | 0/8 14 h-lim-p 0.5974 20.0000 0.0000 1452.460415 0 0.0373 326 | 0/8 15 h-lim-p 0.1296 20.0000 0.0000 1452.460415 0 0.0000 370 Out... lnL = -1452.460415 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1452.460415 Node 7: lnL = -1452.460415 Node 8: lnL = -1452.460415 Node 9: lnL = -1452.460415 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 328 Sequential format.. Reading seq # 1: YKL138C_Sbay Reading seq # 2: YKL138C_Scer Reading seq # 3: YKL138C_Skud Reading seq # 4: YKL138C_Smik Reading seq # 5: YKL138C_Spar Sequences read.. Counting patterns.. # site patterns = 165 Counting frequencies.. 120 bytes for distance 26400 bytes for lkl0 21120 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.113886 0.191638 0.061439 0.090414 0.128462 0.233782 0.227548 0.144440 lnL0 = -1510.026284 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1510.026284 x= 0.11389 0.19164 0.06144 0.09041 0.12846 0.23378 0.22755 0.14444 1 h-lim-p 0.0067 0.0539 20.9062 1509.847178 6 0.0008 35 | 0/8 2 h-lim-p 0.0012 0.0122 14.3216 1509.774129 4 0.0010 55 | 0/8 3 h-lim-p 0.0026 0.0248 5.2991 1509.765682 6 0.0007 83 | 0/8 4 h-lim-p 0.0051 0.3692 0.7537 1509.765488 4 0.0007 105 | 0/8 5 h-lim-p 0.0130 8.7506 0.0403 1509.765487 0 0.0014 127 | 0/8 6 h-lim-p 0.0034 17.7467 0.0166 1509.765486 0 0.0030 147 | 0/8 7 h-lim-p 0.0379 20.0000 0.0013 1509.765454 0 0.3031 170 | 0/8 8 h-lim-p 0.0048 4.0163 0.0838 1509.765405 2 0.0042 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1509.765403 0 1.0938 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1509.765403 0 1.0938 234 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1509.765403 0 2.1875 254 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1509.765403 0 0.5469 275 | 0/8 13 h-lim-p 0.2729 20.0000 0.0000 1509.765403 0 0.0021 301 Out... lnL = -1509.765403 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1509.765403 Node 7: lnL = -1509.765403 Node 8: lnL = -1509.765403 Node 9: lnL = -1509.765403 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 554 Sequential format.. Reading seq # 1: YKL139W_Sbay Reading seq # 2: YKL139W_Scer Reading seq # 3: YKL139W_Skud Reading seq # 4: YKL139W_Smik Reading seq # 5: YKL139W_Spar Sequences read.. Counting patterns.. # site patterns = 184 Counting frequencies.. 120 bytes for distance 29440 bytes for lkl0 23552 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.101802 0.066863 0.070778 0.099383 0.067501 0.183606 0.146527 0.123327 lnL0 = -2374.774521 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2374.774521 x= 0.10180 0.06686 0.07078 0.09938 0.06750 0.18361 0.14653 0.12333 1 h-lim-p 0.0037 0.0386 113.0214 2373.445552 3 0.0002 31 | 0/8 2 h-lim-p 0.0012 0.0097 13.4292 2373.419147 4 0.0003 54 | 0/8 3 h-lim-p 0.0005 0.0246 7.9959 2373.411337 6 0.0003 82 | 0/8 4 h-lim-p 0.0030 0.2247 0.8464 2373.411197 3 0.0004 102 | 0/8 5 h-lim-p 0.0029 2.8571 0.1151 2373.411194 1 0.0004 126 | 0/8 6 h-lim-p 0.0017 8.8934 0.0248 2373.411189 0 0.0034 147 | 0/8 7 h-lim-p 0.0036 7.3248 0.0230 2373.411104 0 0.0108 168 | 0/8 8 h-lim-p 0.0016 3.1071 0.1560 2373.409775 0 0.0064 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2373.409742 1 0.9961 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2373.409742 0 1.2500 232 | 0/8 11 h-lim-p 1.7707 20.0000 0.0000 2373.409742 0 0.1937 254 | 0/8 12 h-lim-p 0.0885 20.0000 0.0000 2373.409742 0 0.0007 280 | 0/8 13 h-lim-p 0.0004 20.0000 0.0000 2373.409742 0 0.0000 303 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 2373.409742 0 0.0000 325 Out... lnL = -2373.409742 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2373.409742 Node 7: lnL = -2373.409742 Node 8: lnL = -2373.409742 Node 9: lnL = -2373.409742 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 562 Sequential format.. Reading seq # 1: YKL140W_Sbay Reading seq # 2: YKL140W_Scer Reading seq # 3: YKL140W_Skud Reading seq # 4: YKL140W_Smik Reading seq # 5: YKL140W_Spar Sequences read.. Counting patterns.. # site patterns = 202 Counting frequencies.. 120 bytes for distance 32320 bytes for lkl0 25856 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.122239 0.092640 0.058733 0.142283 0.116524 0.161419 0.196282 0.148058 lnL0 = -2498.223757 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2498.223757 x= 0.12224 0.09264 0.05873 0.14228 0.11652 0.16142 0.19628 0.14806 1 h-lim-p 0.0112 1.9073 66.8182 2497.672267 8 0.0003 45 | 0/8 2 h-lim-p 0.0016 0.0259 10.9517 2497.643872 5 0.0005 71 | 0/8 3 h-lim-p 0.0013 0.0687 4.0506 2497.640349 5 0.0005 94 | 0/8 4 h-lim-p 0.0023 0.2825 0.8349 2497.640184 2 0.0005 111 | 0/8 5 h-lim-p 0.0028 2.7709 0.1503 2497.640179 1 0.0006 134 | 0/8 6 h-lim-p 0.0121 20.0000 0.0070 2497.640179 0 0.0007 157 | 0/8 7 h-lim-p 0.0050 20.0000 0.0009 2497.640179 0 0.0044 177 | 0/8 8 h-lim-p 0.0116 20.0000 0.0003 2497.640176 0 0.1398 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2497.640176 0 1.0938 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2497.640176 0 0.5469 241 | 0/8 11 h-lim-p 0.3574 20.0000 0.0000 2497.640176 0 0.0056 266 | 0/8 12 h-lim-p 0.0038 20.0000 0.0000 2497.640176 0 0.0000 303 Out... lnL = -2497.640176 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2497.640176 Node 7: lnL = -2497.640176 Node 8: lnL = -2497.640176 Node 9: lnL = -2497.640176 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 525 Sequential format.. Reading seq # 1: YKL141W_Sbay Reading seq # 2: YKL141W_Scer Reading seq # 3: YKL141W_Skud Reading seq # 4: YKL141W_Smik Reading seq # 5: YKL141W_Spar Sequences read.. Counting patterns.. # site patterns = 235 Counting frequencies.. 120 bytes for distance 37600 bytes for lkl0 30080 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.160737 0.084632 0.057241 0.142904 0.092558 0.306079 0.232088 0.182660 lnL0 = -2475.689909 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2475.689909 x= 0.16074 0.08463 0.05724 0.14290 0.09256 0.30608 0.23209 0.18266 1 h-lim-p 0.0006 0.0048 84.1806 2474.541450 8 0.0003 43 | 0/8 2 h-lim-p 0.0007 0.0055 22.3061 2474.427883 7 0.0005 73 | 0/8 3 h-lim-p 0.0009 0.0295 11.3775 2474.403278 6 0.0005 101 | 0/8 4 h-lim-p 0.0012 0.0667 4.3069 2474.397315 6 0.0008 131 | 0/8 5 h-lim-p 0.0065 0.6172 0.5083 2474.397203 3 0.0009 151 | 0/8 6 h-lim-p 0.0089 10.4533 0.0493 2474.397202 1 0.0011 175 | 0/8 7 h-lim-p 0.0371 20.0000 0.0015 2474.397201 0 0.0324 195 | 0/8 8 h-lim-p 0.0076 13.6830 0.0062 2474.397156 0 0.0305 217 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2474.397156 0 1.0938 237 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2474.397156 0 1.2500 257 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2474.397156 0 0.3125 279 | 0/8 12 h-lim-p 0.1765 20.0000 0.0000 2474.397156 0 0.0000 325 Out... lnL = -2474.397156 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2474.397156 Node 7: lnL = -2474.397156 Node 8: lnL = -2474.397156 Node 9: lnL = -2474.397156 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 410 Sequential format.. Reading seq # 1: YKL142W_Sbay Reading seq # 2: YKL142W_Scer Reading seq # 3: YKL142W_Skud Reading seq # 4: YKL142W_Smik Reading seq # 5: YKL142W_Spar Sequences read.. Counting patterns.. # site patterns = 195 Counting frequencies.. 120 bytes for distance 31200 bytes for lkl0 24960 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.199434 0.089565 0.050283 0.159516 0.096660 0.210561 0.268956 0.221968 lnL0 = -1897.619293 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1897.619293 x= 0.19943 0.08957 0.05028 0.15952 0.09666 0.21056 0.26896 0.22197 1 h-lim-p 0.0031 0.0247 103.6937 1895.441795 6 0.0005 38 | 0/8 2 h-lim-p 0.0006 0.0050 27.2710 1895.193921 7 0.0007 68 | 0/8 3 h-lim-p 0.0017 0.0327 10.9246 1895.154655 5 0.0008 89 | 0/8 4 h-lim-p 0.0021 0.0884 3.9737 1895.144396 5 0.0015 112 | 0/8 5 h-lim-p 0.0070 0.4887 0.8489 1895.143899 3 0.0015 131 | 0/8 6 h-lim-p 0.0119 4.1023 0.1038 1895.143891 1 0.0013 155 | 0/8 7 h-lim-p 0.0062 12.0026 0.0218 1895.143890 0 0.0031 175 | 0/8 8 h-lim-p 0.0423 20.0000 0.0016 1895.143503 0 0.6776 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1895.143460 2 0.9961 223 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1895.143460 0 1.0938 243 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1895.143460 0 0.3125 265 | 0/8 12 h-lim-p 0.1949 20.0000 0.0000 1895.143460 0 0.0030 290 Out... lnL = -1895.143460 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1895.143460 Node 7: lnL = -1895.143460 Node 8: lnL = -1895.143460 Node 9: lnL = -1895.143460 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 323 Sequential format.. Reading seq # 1: YKL144C_Sbay Reading seq # 2: YKL144C_Scer Reading seq # 3: YKL144C_Skud Reading seq # 4: YKL144C_Smik Reading seq # 5: YKL144C_Spar Sequences read.. Counting patterns.. # site patterns = 166 Counting frequencies.. 120 bytes for distance 26560 bytes for lkl0 21248 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.136309 0.116760 0.108809 0.134440 0.104721 0.165280 0.181659 0.156374 lnL0 = -1504.219219 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1504.219219 x= 0.13631 0.11676 0.10881 0.13444 0.10472 0.16528 0.18166 0.15637 1 h-lim-p 0.0072 0.0579 40.8389 1503.634043 6 0.0007 37 | 0/8 2 h-lim-p 0.0029 0.0270 10.4291 1503.587940 6 0.0009 65 | 0/8 3 h-lim-p 0.0026 0.0888 3.5696 1503.584452 2 0.0006 82 | 0/8 4 h-lim-p 0.0033 0.3725 0.6568 1503.584198 4 0.0012 103 | 0/8 5 h-lim-p 0.0148 6.1022 0.0541 1503.584196 1 0.0009 128 | 0/8 6 h-lim-p 0.0032 12.6832 0.0152 1503.584195 0 0.0028 148 | 0/8 7 h-lim-p 0.0240 20.0000 0.0018 1503.584149 0 0.1924 171 | 0/8 8 h-lim-p 0.0021 3.5742 0.1668 1503.584050 1 0.0026 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1503.584048 0 1.0938 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1503.584048 0 1.0938 233 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1503.584048 0 2.1875 253 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1503.584048 0 0.6250 274 | 0/8 13 h-lim-p 0.3608 20.0000 0.0000 1503.584048 0 0.0014 301 Out... lnL = -1503.584048 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1503.584048 Node 7: lnL = -1503.584048 Node 8: lnL = -1503.584048 Node 9: lnL = -1503.584048 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 389 Sequential format.. Reading seq # 1: YKL149C_Sbay Reading seq # 2: YKL149C_Scer Reading seq # 3: YKL149C_Skud Reading seq # 4: YKL149C_Smik Reading seq # 5: YKL149C_Spar Sequences read.. Counting patterns.. # site patterns = 152 Counting frequencies.. 120 bytes for distance 24320 bytes for lkl0 19456 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.072474 0.090943 0.016087 0.147862 0.067588 0.067609 0.102237 0.084054 lnL0 = -1409.935836 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1409.935836 x= 0.07247 0.09094 0.01609 0.14786 0.06759 0.06761 0.10224 0.08405 1 h-lim-p 0.0005 0.5592 247.9004 1404.385365 6 0.0002 34 | 0/8 2 h-lim-p 0.0004 0.0029 46.2272 1403.644905 0 0.0007 47 | 0/8 3 h-lim-p 0.0025 0.0228 13.4063 1403.582425 7 0.0008 77 | 0/8 4 h-lim-p 0.0014 0.0256 7.3644 1403.572489 6 0.0005 105 | 0/8 5 h-lim-p 0.0183 1.1027 0.1879 1403.572469 2 0.0009 124 | 0/8 6 h-lim-p 0.0071 5.6669 0.0233 1403.572373 0 0.0142 145 | 0/8 7 h-lim-p 0.0045 1.8218 0.0729 1403.569350 0 0.0273 167 | 0/8 8 h-lim-p 0.0014 0.0389 1.3807 1403.565130 5 0.0016 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 1403.564933 3 1.0004 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1403.564933 0 1.0938 237 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1403.564933 0 1.0938 257 | 0/8 12 h-lim-p 1.2585 20.0000 0.0000 1403.564933 0 0.0000 293 Out... lnL = -1403.564933 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1403.564933 Node 7: lnL = -1403.564933 Node 8: lnL = -1403.564933 Node 9: lnL = -1403.564933 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 649 Sequential format.. Reading seq # 1: YKL151C_Sbay Reading seq # 2: YKL151C_Scer Reading seq # 3: YKL151C_Skud Reading seq # 4: YKL151C_Smik Reading seq # 5: YKL151C_Spar Sequences read.. Counting patterns.. # site patterns = 213 Counting frequencies.. 120 bytes for distance 34080 bytes for lkl0 27264 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.126076 0.050245 0.046122 0.093563 0.063179 0.186516 0.201130 0.141851 lnL0 = -2781.932580 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2781.932580 x= 0.12608 0.05025 0.04612 0.09356 0.06318 0.18652 0.20113 0.14185 1 h-lim-p 0.0007 0.0060 150.3606 2780.193679 6 0.0002 34 | 0/8 2 h-lim-p 0.0004 0.0033 29.0387 2780.098849 7 0.0002 62 | 0/8 3 h-lim-p 0.0005 0.0110 14.4357 2780.075951 7 0.0003 92 | 0/8 4 h-lim-p 0.0006 0.0367 6.4763 2780.069943 5 0.0004 117 | 0/8 5 h-lim-p 0.0026 0.3046 0.9001 2780.069805 3 0.0003 137 | 0/8 6 h-lim-p 0.0014 1.4516 0.2216 2780.069796 2 0.0004 162 | 0/8 7 h-lim-p 0.0033 10.3404 0.0249 2780.069796 0 0.0007 183 | 0/8 8 h-lim-p 0.4695 20.0000 0.0000 2780.069792 0 0.9390 204 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2780.069792 0 1.0938 224 | 0/8 10 h-lim-p 2.1104 20.0000 0.0000 2780.069792 0 0.0021 253 | 0/8 11 h-lim-p 0.0008 20.0000 0.0000 2780.069792 0 0.0002 274 Out... lnL = -2780.069792 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2780.069792 Node 7: lnL = -2780.069792 Node 8: lnL = -2780.069792 Node 9: lnL = -2780.069792 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 544 Sequential format.. Reading seq # 1: YKL152C_Sbay Reading seq # 2: YKL152C_Scer Reading seq # 3: YKL152C_Skud Reading seq # 4: YKL152C_Smik Reading seq # 5: YKL152C_Spar Sequences read.. Counting patterns.. # site patterns = 179 Counting frequencies.. 120 bytes for distance 28640 bytes for lkl0 22912 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.085018 0.023021 0.045062 0.080223 0.069651 0.162315 0.150899 0.097343 lnL0 = -2160.964511 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2160.964511 x= 0.08502 0.02302 0.04506 0.08022 0.06965 0.16231 0.15090 0.09734 1 h-lim-p 0.0007 0.0057 242.6580 2158.077194 7 0.0001 37 | 0/8 2 h-lim-p 0.0006 0.0048 30.5375 2157.928666 5 0.0003 60 | 0/8 3 h-lim-p 0.0006 0.0111 15.0806 2157.903197 3 0.0003 79 | 0/8 4 h-lim-p 0.0008 0.0220 4.9255 2157.900932 4 0.0002 100 | 0/8 5 h-lim-p 0.0023 0.2993 0.4453 2157.900904 0 0.0003 114 | 0/8 6 h-lim-p 0.0015 3.0796 0.0873 2157.900903 0 0.0003 135 | 0/8 7 h-lim-p 0.0010 5.4227 0.0288 2157.900903 0 0.0009 155 | 0/8 8 h-lim-p 0.1096 20.0000 0.0002 2157.900736 0 1.3150 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2157.900727 1 0.9961 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2157.900727 0 1.0938 220 | 0/8 11 h-lim-p 1.3776 20.0000 0.0000 2157.900727 0 0.0861 243 | 0/8 12 h-lim-p 0.0385 20.0000 0.0000 2157.900727 0 0.0000 286 Out... lnL = -2157.900727 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2157.900727 Node 7: lnL = -2157.900727 Node 8: lnL = -2157.900727 Node 9: lnL = -2157.900727 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 282 Sequential format.. Reading seq # 1: YKL154W_Sbay Reading seq # 2: YKL154W_Scer Reading seq # 3: YKL154W_Skud Reading seq # 4: YKL154W_Smik Reading seq # 5: YKL154W_Spar Sequences read.. Counting patterns.. # site patterns = 147 Counting frequencies.. 120 bytes for distance 23520 bytes for lkl0 18816 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.189608 0.006386 0.077186 0.132920 0.087068 0.201105 0.322917 0.210537 lnL0 = -1322.980560 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1322.980560 x= 0.18961 0.00639 0.07719 0.13292 0.08707 0.20110 0.32292 0.21054 1 h-lim-p 0.0010 0.0080 61.2521 1322.152616 7 0.0005 37 | 0/8 2 h-lim-p 0.0024 0.0192 7.3894 1322.132191 7 0.0008 66 | 0/8 3 h-lim-p 0.0018 0.1537 3.0929 1322.128734 2 0.0008 82 | 0/8 4 h-lim-p 0.0013 0.2147 1.9500 1322.126871 3 0.0014 100 | 0/8 5 h-lim-p 0.0049 0.6736 0.5393 1322.126673 4 0.0015 123 | 0/8 6 h-lim-p 0.0029 1.6788 0.2821 1322.126638 2 0.0011 147 | 0/8 7 h-lim-p 0.0068 6.5719 0.0475 1322.126636 1 0.0017 170 | 0/8 8 h-lim-p 1.7341 20.0000 0.0000 1322.126634 1 1.3819 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1322.126634 0 1.0938 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1322.126634 0 1.0938 232 | 0/8 11 h-lim-p 2.4391 20.0000 0.0000 1322.126634 0 0.0024 261 Out... lnL = -1322.126634 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1322.126634 Node 7: lnL = -1322.126634 Node 8: lnL = -1322.126634 Node 9: lnL = -1322.126634 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 282 Sequential format.. Reading seq # 1: YKL155C_Sbay Reading seq # 2: YKL155C_Scer Reading seq # 3: YKL155C_Skud Reading seq # 4: YKL155C_Smik Reading seq # 5: YKL155C_Spar Sequences read.. Counting patterns.. # site patterns = 139 Counting frequencies.. 120 bytes for distance 22240 bytes for lkl0 17792 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.143210 0.049393 0.041175 0.129403 0.090585 0.185948 0.261445 0.161475 lnL0 = -1168.447294 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1168.447294 x= 0.14321 0.04939 0.04118 0.12940 0.09059 0.18595 0.26145 0.16148 1 h-lim-p 0.0012 0.0099 50.4125 1167.962621 8 0.0004 42 | 0/8 2 h-lim-p 0.0011 0.0084 12.8674 1167.895969 5 0.0008 64 | 0/8 3 h-lim-p 0.0014 0.0123 7.6262 1167.872411 6 0.0011 89 | 0/8 4 h-lim-p 0.0016 0.0273 5.0726 1167.861906 4 0.0012 109 | 0/8 5 h-lim-p 0.0056 0.1070 1.1204 1167.861161 2 0.0013 126 | 0/8 6 h-lim-p 0.0085 1.6687 0.1717 1167.861137 2 0.0016 143 | 0/8 7 h-lim-p 0.0109 2.0047 0.0259 1167.861137 0 0.0012 165 | 0/8 8 h-lim-p 0.1710 20.0000 0.0002 1167.861115 0 1.3682 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1167.861112 1 0.9961 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1167.861112 0 1.0938 230 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1167.861112 0 5.0000 251 | 0/8 12 h-lim-p 1.6593 20.0000 0.0000 1167.861112 0 0.1815 273 | 0/8 13 h-lim-p 0.3488 20.0000 0.0000 1167.861112 0 0.0095 297 | 0/8 14 h-lim-p 0.0164 20.0000 0.0000 1167.861112 0 0.0000 342 Out... lnL = -1167.861112 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1167.861112 Node 7: lnL = -1167.861112 Node 8: lnL = -1167.861112 Node 9: lnL = -1167.861112 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 880 Sequential format.. Reading seq # 1: YKL160W_Sbay Reading seq # 2: YKL160W_Scer Reading seq # 3: YKL160W_Skud Reading seq # 4: YKL160W_Smik Reading seq # 5: YKL160W_Spar Sequences read.. Counting patterns.. # site patterns = 410 Counting frequencies.. 120 bytes for distance 65600 bytes for lkl0 52480 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.163130 0.152000 0.188978 0.134093 0.146285 0.526460 0.337665 0.196357 lnL0 = -4591.583904 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4591.583904 x= 0.16313 0.15200 0.18898 0.13409 0.14628 0.52646 0.33767 0.19636 1 h-lim-p 0.0074 0.0590 60.2931 4590.644265 8 0.0005 44 | 0/8 2 h-lim-p 0.0009 0.0072 33.6300 4590.478398 7 0.0004 70 | 0/8 3 h-lim-p 0.0015 0.0372 8.3198 4590.453202 5 0.0008 93 | 0/8 4 h-lim-p 0.0015 0.0728 4.3794 4590.443800 3 0.0013 111 | 0/8 5 h-lim-p 0.0078 0.9388 0.7027 4590.443374 2 0.0018 128 | 0/8 6 h-lim-p 0.0118 3.1516 0.1091 4590.443361 2 0.0023 153 | 0/8 7 h-lim-p 0.0253 20.0000 0.0098 4590.443360 0 0.0055 174 | 0/8 8 h-lim-p 0.0162 20.0000 0.0034 4590.443101 0 0.1938 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4590.443098 0 1.0938 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4590.443098 0 1.0938 237 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4590.443098 0 2.1875 257 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4590.443098 0 1.0938 277 | 0/8 13 h-lim-p 0.3182 20.0000 0.0000 4590.443098 0 0.0003 306 Out... lnL = -4590.443098 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4590.443098 Node 7: lnL = -4590.443098 Node 8: lnL = -4590.443098 Node 9: lnL = -4590.443098 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 101 Sequential format.. Reading seq # 1: YKL166C_Sbay Reading seq # 2: YKL166C_Scer Reading seq # 3: YKL166C_Skud Reading seq # 4: YKL166C_Smik Reading seq # 5: YKL166C_Spar Sequences read.. Counting patterns.. # site patterns = 28 Counting frequencies.. 120 bytes for distance 4480 bytes for lkl0 3584 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.028442 0.000374 0.014821 0.083978 0.005489 0.058758 0.087644 0.033731 lnL0 = -265.589694 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 265.589694 x= 0.02844 0.00037 0.01482 0.08398 0.00549 0.05876 0.08764 0.03373 1 h-lim-p 0.0000 0.0003 355.8103 264.290039 0 0.0001 22 | 0/8 2 h-lim-p 0.0000 0.0001 51.2900 264.021030 m 0.0001 34 | 1/8 3 h-lim-p 0.0001 0.0023 25.2057 263.885580 0 0.0006 48 | 1/8 4 h-lim-p 0.0024 0.0188 4.3613 263.876814 7 0.0009 78 | 1/8 5 h-lim-p 0.0026 0.0232 1.4175 263.872508 5 0.0020 100 | 1/8 6 h-lim-p 0.0040 0.0322 0.4324 263.784130 m 0.0322 112 | 2/8 7 h-lim-p 0.0074 0.3203 1.5368 263.782452 6 0.0013 148 | 2/8 8 h-lim-p 0.1360 2.3288 0.0145 263.689006 0 0.5440 162 | 2/8 9 h-lim-p 2.5000 20.0000 0.0027 263.684790 6 0.8644 196 | 2/8 10 h-lim-p 2.5000 20.0000 0.0002 263.684760 3 0.9482 220 | 2/8 11 h-lim-p 2.5000 20.0000 0.0000 263.684760 0 1.0938 238 | 2/8 12 h-lim-p 2.5000 20.0000 0.0000 263.684760 0 1.0938 256 | 2/8 13 h-lim-p 2.1604 20.0000 0.0000 263.684760 0 3.2406 274 | 2/8 14 h-lim-p 2.5000 20.0000 0.0000 263.684760 0 0.1367 295 | 2/8 15 h-lim-p 0.4590 20.0000 0.0000 263.684760 0 0.0000 343 Out... lnL = -263.684760 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -263.684760 Node 7: lnL = -263.684760 Node 8: lnL = -263.684760 Node 9: lnL = -263.684760 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 524 Sequential format.. Reading seq # 1: YKL167C_Sbay Reading seq # 2: YKL167C_Scer Reading seq # 3: YKL167C_Skud Reading seq # 4: YKL167C_Smik Reading seq # 5: YKL167C_Spar Sequences read.. Counting patterns.. # site patterns = 194 Counting frequencies.. 120 bytes for distance 31040 bytes for lkl0 24832 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.094905 0.155507 0.000060 0.257131 0.113495 0.254532 0.256518 0.115326 lnL0 = -2113.766078 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2113.766078 x= 0.09491 0.15551 0.00006 0.25713 0.11350 0.25453 0.25652 0.11533 1 h-lim-p 0.0009 0.0070 67.7004 2112.500317 9 0.0005 45 | 0/8 2 h-lim-p 0.0002 0.0016 65.8495 2111.874738 0 0.0004 58 | 0/8 3 h-lim-p 0.0053 0.0421 4.4229 2111.869532 4 0.0005 81 | 0/8 4 h-lim-p 0.0046 0.5452 0.5176 2111.869360 2 0.0011 98 | 0/8 5 h-lim-p 0.0040 0.3246 0.1485 2111.869300 0 0.0020 118 | 0/8 6 h-lim-p 0.0027 0.6826 0.1103 2111.868387 0 0.0107 140 | 0/8 7 h-lim-p 0.0063 0.2617 0.1878 2111.854485 0 0.0251 162 | 0/8 8 h-lim-p 0.0045 0.0918 1.0563 2111.853624 4 0.0014 192 | 0/8 9 h-lim-p 1.4779 20.0000 0.0010 2111.852687 4 0.9728 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2111.852687 0 1.0938 233 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2111.852687 0 1.0938 253 | 0/8 12 h-lim-p 2.1438 20.0000 0.0000 2111.852687 0 3.2157 273 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2111.852687 0 0.2734 295 | 0/8 14 h-lim-p 0.6690 20.0000 0.0000 2111.852687 0 0.0007 324 Out... lnL = -2111.852687 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2111.852687 Node 7: lnL = -2111.852687 Node 8: lnL = -2111.852687 Node 9: lnL = -2111.852687 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 287 Sequential format.. Reading seq # 1: YKL168C_Sbay Reading seq # 2: YKL168C_Scer Reading seq # 3: YKL168C_Skud Reading seq # 4: YKL168C_Smik Reading seq # 5: YKL168C_Spar Sequences read.. Counting patterns.. # site patterns = 130 Counting frequencies.. 120 bytes for distance 20800 bytes for lkl0 16640 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.100015 0.072332 0.051091 0.163831 0.071181 0.161570 0.212690 0.116684 lnL0 = -1201.029589 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1201.029589 x= 0.10002 0.07233 0.05109 0.16383 0.07118 0.16157 0.21269 0.11668 1 h-lim-p 0.0019 0.0152 31.5155 1200.779442 8 0.0005 40 | 0/8 2 h-lim-p 0.0012 0.0121 13.9658 1200.713247 7 0.0008 69 | 0/8 3 h-lim-p 0.0026 0.0436 4.1528 1200.709077 4 0.0005 91 | 0/8 4 h-lim-p 0.0018 0.2243 1.2116 1200.708384 5 0.0010 115 | 0/8 5 h-lim-p 0.0083 1.8863 0.1513 1200.708373 0 0.0010 129 | 0/8 6 h-lim-p 0.0059 7.7576 0.0270 1200.708372 0 0.0013 150 | 0/8 7 h-lim-p 0.0079 20.0000 0.0044 1200.708372 0 0.0035 170 | 0/8 8 h-lim-p 0.0285 20.0000 0.0005 1200.708351 0 0.3420 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1200.708351 0 1.0938 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1200.708351 0 1.2500 233 | 0/8 11 h-lim-p 2.4891 20.0000 0.0000 1200.708351 0 0.2722 255 | 0/8 12 h-lim-p 0.1489 20.0000 0.0000 1200.708351 0 0.0047 279 | 0/8 13 h-lim-p 0.0032 20.0000 0.0000 1200.708351 0 0.0000 307 Out... lnL = -1200.708351 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1200.708351 Node 7: lnL = -1200.708351 Node 8: lnL = -1200.708351 Node 9: lnL = -1200.708351 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 424 Sequential format.. Reading seq # 1: YKL170W_Sbay Reading seq # 2: YKL170W_Scer Reading seq # 3: YKL170W_Skud Reading seq # 4: YKL170W_Smik Reading seq # 5: YKL170W_Spar Sequences read.. Counting patterns.. # site patterns = 201 Counting frequencies.. 120 bytes for distance 32160 bytes for lkl0 25728 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.138054 0.165740 0.056279 0.142660 0.094404 0.223680 0.159535 0.158662 lnL0 = -1957.337157 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1957.337157 x= 0.13805 0.16574 0.05628 0.14266 0.09440 0.22368 0.15953 0.15866 1 h-lim-p 0.0021 0.0170 72.5622 1956.415905 7 0.0004 40 | 0/8 2 h-lim-p 0.0011 0.0090 18.3926 1956.297606 6 0.0007 67 | 0/8 3 h-lim-p 0.0012 0.0190 11.4410 1956.267985 4 0.0006 88 | 0/8 4 h-lim-p 0.0036 0.1549 1.8919 1956.266323 5 0.0010 111 | 0/8 5 h-lim-p 0.0067 1.1364 0.2772 1956.266291 2 0.0009 129 | 0/8 6 h-lim-p 0.0127 20.0000 0.0191 1956.266291 0 0.0008 152 | 0/8 7 h-lim-p 0.0037 20.0000 0.0041 1956.266291 0 0.0033 172 | 0/8 8 h-lim-p 0.0276 20.0000 0.0005 1956.266273 0 0.3306 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1956.266273 0 1.0938 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1956.266273 0 2.1875 235 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1956.266273 0 1.0938 255 | 0/8 12 h-lim-p 1.1752 20.0000 0.0000 1956.266273 0 4.7007 277 | 0/8 13 h-lim-p 1.7824 20.0000 0.0000 1956.266273 0 0.3899 298 | 0/8 14 h-lim-p 1.6806 20.0000 0.0000 1956.266273 0 0.0004 329 Out... lnL = -1956.266273 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1956.266273 Node 7: lnL = -1956.266273 Node 8: lnL = -1956.266273 Node 9: lnL = -1956.266273 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 309 Sequential format.. Reading seq # 1: YKL173W_Sbay Reading seq # 2: YKL173W_Scer Reading seq # 3: YKL173W_Skud Reading seq # 4: YKL173W_Smik Reading seq # 5: YKL173W_Spar Sequences read.. Counting patterns.. # site patterns = 107 Counting frequencies.. 120 bytes for distance 17120 bytes for lkl0 13696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.079699 0.079611 0.068509 0.086786 0.046725 0.138025 0.122481 0.092700 lnL0 = -1200.052342 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1200.052342 x= 0.07970 0.07961 0.06851 0.08679 0.04672 0.13803 0.12248 0.09270 1 h-lim-p 0.0003 0.0023 70.6402 1199.128681 0 0.0004 22 | 0/8 2 h-lim-p 0.0018 0.0264 17.0364 1199.091117 7 0.0003 53 | 0/8 3 h-lim-p 0.0006 0.0252 8.3744 1199.077652 3 0.0005 71 | 0/8 4 h-lim-p 0.0053 0.2896 0.7528 1199.077477 2 0.0006 89 | 0/8 5 h-lim-p 0.0021 0.8813 0.2181 1199.077457 3 0.0008 117 | 0/8 6 h-lim-p 0.0137 12.8327 0.0120 1199.077216 0 0.0412 138 | 0/8 7 h-lim-p 0.0018 0.4360 0.2739 1199.073663 0 0.0072 160 | 0/8 8 h-lim-p 0.0014 0.1024 1.4163 1199.071626 2 0.0012 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1199.071623 1 0.9961 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1199.071623 0 1.0938 218 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1199.071623 0 2.1875 238 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1199.071623 0 1.0938 258 | 0/8 13 h-lim-p 0.8010 20.0000 0.0000 1199.071623 0 6.4076 281 | 0/8 14 h-lim-p 1.5068 20.0000 0.0000 1199.071623 0 0.3296 302 | 0/8 15 h-lim-p 0.7794 20.0000 0.0000 1199.071623 0 0.0030 329 | 0/8 16 h-lim-p 0.0114 20.0000 0.0000 1199.071623 0 0.0014 351 Out... lnL = -1199.071623 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1199.071623 Node 7: lnL = -1199.071623 Node 8: lnL = -1199.071623 Node 9: lnL = -1199.071623 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 845 Sequential format.. Reading seq # 1: YKL175W_Sbay Reading seq # 2: YKL175W_Scer Reading seq # 3: YKL175W_Skud Reading seq # 4: YKL175W_Smik Reading seq # 5: YKL175W_Spar Sequences read.. Counting patterns.. # site patterns = 262 Counting frequencies.. 120 bytes for distance 41920 bytes for lkl0 33536 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.114444 0.075983 0.043302 0.097342 0.051844 0.141180 0.124946 0.128242 lnL0 = -3357.279073 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3357.279073 x= 0.11444 0.07598 0.04330 0.09734 0.05184 0.14118 0.12495 0.12824 1 h-lim-p 0.0016 0.7792 206.8004 3354.968311 6 0.0001 39 | 0/8 2 h-lim-p 0.0004 0.0044 55.8288 3354.698655 5 0.0002 60 | 0/8 3 h-lim-p 0.0010 0.0101 9.9421 3354.687808 3 0.0002 79 | 0/8 4 h-lim-p 0.0004 0.0297 5.1131 3354.685395 4 0.0002 100 | 0/8 5 h-lim-p 0.0013 0.1656 0.8591 3354.685313 3 0.0002 121 | 0/8 6 h-lim-p 0.0011 1.0842 0.1911 3354.685308 1 0.0003 144 | 0/8 7 h-lim-p 0.0383 20.0000 0.0013 3354.685306 0 0.0335 164 | 0/8 8 h-lim-p 0.0040 7.7752 0.0110 3354.685226 0 0.0159 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3354.685222 0 1.0938 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3354.685221 0 1.2500 226 | 0/8 11 h-lim-p 2.2160 20.0000 0.0000 3354.685221 0 0.4848 247 | 0/8 12 h-lim-p 0.2869 20.0000 0.0000 3354.685221 0 0.0045 272 | 0/8 13 h-lim-p 0.0028 20.0000 0.0000 3354.685221 0 0.0000 310 Out... lnL = -3354.685221 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3354.685221 Node 7: lnL = -3354.685221 Node 8: lnL = -3354.685221 Node 9: lnL = -3354.685221 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 844 Sequential format.. Reading seq # 1: YKL176C_Sbay Reading seq # 2: YKL176C_Scer Reading seq # 3: YKL176C_Skud Reading seq # 4: YKL176C_Smik Reading seq # 5: YKL176C_Spar Sequences read.. Counting patterns.. # site patterns = 241 Counting frequencies.. 120 bytes for distance 38560 bytes for lkl0 30848 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.106331 0.073289 0.046504 0.101389 0.071888 0.138841 0.156872 0.120769 lnL0 = -3501.947358 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3501.947358 x= 0.10633 0.07329 0.04650 0.10139 0.07189 0.13884 0.15687 0.12077 1 h-lim-p 0.0004 0.0036 134.3854 3500.745318 8 0.0001 44 | 0/8 2 h-lim-p 0.0003 0.0024 33.2634 3500.657060 7 0.0002 72 | 0/8 3 h-lim-p 0.0007 0.0262 8.5669 3500.650299 5 0.0002 99 | 0/8 4 h-lim-p 0.0004 0.0400 4.5589 3500.648700 4 0.0002 120 | 0/8 5 h-lim-p 0.0015 0.6163 0.5814 3500.648658 2 0.0002 138 | 0/8 6 h-lim-p 0.0022 2.0678 0.0642 3500.648658 0 0.0002 160 | 0/8 7 h-lim-p 0.0307 20.0000 0.0005 3500.648610 0 0.3682 183 | 0/8 8 h-lim-p 0.0008 1.2201 0.2320 3500.648485 1 0.0010 205 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3500.648483 0 1.0938 225 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3500.648483 0 1.0938 245 | 0/8 11 h-lim-p 1.6966 20.0000 0.0000 3500.648483 0 3.3933 266 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3500.648483 0 0.5469 287 | 0/8 13 h-lim-p 1.1382 20.0000 0.0000 3500.648483 0 0.0001 319 Out... lnL = -3500.648483 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3500.648483 Node 7: lnL = -3500.648483 Node 8: lnL = -3500.648483 Node 9: lnL = -3500.648483 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 865 Sequential format.. Reading seq # 1: YKL178C_Sbay Reading seq # 2: YKL178C_Scer Reading seq # 3: YKL178C_Skud Reading seq # 4: YKL178C_Smik Reading seq # 5: YKL178C_Spar Sequences read.. Counting patterns.. # site patterns = 339 Counting frequencies.. 120 bytes for distance 54240 bytes for lkl0 43392 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.169723 0.057470 0.088509 0.160148 0.102402 0.207575 0.217591 0.182046 lnL0 = -4081.942395 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4081.942395 x= 0.16972 0.05747 0.08851 0.16015 0.10240 0.20757 0.21759 0.18205 1 h-lim-p 0.0045 0.8575 134.2114 4080.168501 8 0.0002 42 | 0/8 2 h-lim-p 0.0010 0.0078 24.0379 4080.069002 6 0.0004 69 | 0/8 3 h-lim-p 0.0006 0.0203 13.2897 4080.045379 5 0.0003 92 | 0/8 4 h-lim-p 0.0013 0.0722 3.3449 4080.043556 3 0.0004 111 | 0/8 5 h-lim-p 0.0029 0.6136 0.4184 4080.043519 2 0.0005 130 | 0/8 6 h-lim-p 0.0022 3.4147 0.0898 4080.043517 0 0.0005 151 | 0/8 7 h-lim-p 0.0154 20.0000 0.0028 4080.043506 0 0.0308 172 | 0/8 8 h-lim-p 0.0029 20.0000 0.0294 4080.043176 0 0.0118 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4080.043163 1 0.9961 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4080.043163 0 0.5469 237 | 0/8 11 h-lim-p 0.4379 20.0000 0.0000 4080.043163 0 0.0274 260 | 0/8 12 h-lim-p 0.0147 20.0000 0.0000 4080.043163 0 0.0002 285 Out... lnL = -4080.043163 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4080.043163 Node 7: lnL = -4080.043163 Node 8: lnL = -4080.043163 Node 9: lnL = -4080.043163 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 755 Sequential format.. Reading seq # 1: YKL179C_Sbay Reading seq # 2: YKL179C_Scer Reading seq # 3: YKL179C_Skud Reading seq # 4: YKL179C_Smik Reading seq # 5: YKL179C_Spar Sequences read.. Counting patterns.. # site patterns = 342 Counting frequencies.. 120 bytes for distance 54720 bytes for lkl0 43776 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.158894 0.029404 0.087559 0.226400 0.141629 0.262096 0.544086 0.175384 lnL0 = -3964.508675 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3964.508675 x= 0.15889 0.02940 0.08756 0.22640 0.14163 0.26210 0.54409 0.17538 1 h-lim-p 0.0028 0.8417 167.4866 3960.682220 8 0.0003 45 | 0/8 2 h-lim-p 0.0009 0.0076 38.6479 3960.129906 7 0.0008 71 | 0/8 3 h-lim-p 0.0020 0.0337 14.4808 3960.072490 6 0.0006 99 | 0/8 4 h-lim-p 0.0017 0.0598 5.3865 3960.065703 4 0.0005 121 | 0/8 5 h-lim-p 0.0016 0.1259 1.8408 3960.063440 2 0.0015 137 | 0/8 6 h-lim-p 0.0028 0.2991 0.9730 3960.063085 4 0.0010 159 | 0/8 7 h-lim-p 0.3061 20.0000 0.0030 3960.061108 0 0.6121 180 | 0/8 8 h-lim-p 0.0021 0.5225 0.8691 3960.058243 4 0.0024 211 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3960.058220 1 0.9961 233 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3960.058220 0 1.0938 253 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3960.058220 0 1.0938 273 | 0/8 12 h-lim-p 1.1019 20.0000 0.0000 3960.058220 0 1.1019 293 | 0/8 13 h-lim-p 0.4422 20.0000 0.0000 3960.058220 0 0.0000 334 Out... lnL = -3960.058220 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3960.058220 Node 7: lnL = -3960.058220 Node 8: lnL = -3960.058220 Node 9: lnL = -3960.058220 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 610 Sequential format.. Reading seq # 1: YKL183W_Sbay Reading seq # 2: YKL183W_Scer Reading seq # 3: YKL183W_Skud Reading seq # 4: YKL183W_Smik Reading seq # 5: YKL183W_Spar Sequences read.. Counting patterns.. # site patterns = 263 Counting frequencies.. 120 bytes for distance 42080 bytes for lkl0 33664 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.155947 0.045631 0.082025 0.164545 0.111461 0.285768 0.311951 0.169566 lnL0 = -2869.618102 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2869.618102 x= 0.15595 0.04563 0.08202 0.16454 0.11146 0.28577 0.31195 0.16957 1 h-lim-p 0.0026 0.0206 83.0761 2868.541798 4 0.0003 32 | 0/8 2 h-lim-p 0.0011 0.0087 17.3509 2868.454078 7 0.0006 61 | 0/8 3 h-lim-p 0.0013 0.0420 7.9531 2868.437192 4 0.0006 82 | 0/8 4 h-lim-p 0.0012 0.0617 4.2363 2868.432911 4 0.0006 103 | 0/8 5 h-lim-p 0.0054 0.9613 0.4946 2868.432789 3 0.0010 122 | 0/8 6 h-lim-p 0.0049 3.3359 0.1036 2868.432783 0 0.0011 143 | 0/8 7 h-lim-p 0.0057 9.7517 0.0195 2868.432780 1 0.0028 166 | 0/8 8 h-lim-p 0.0113 20.0000 0.0048 2868.431858 0 0.1810 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2868.431857 0 1.0938 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2868.431857 0 1.0938 230 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2868.431857 0 2.1875 250 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2868.431857 0 1.0938 270 | 0/8 13 h-lim-p 0.6353 20.0000 0.0000 2868.431857 0 0.4765 290 | 0/8 14 h-lim-p 0.2326 20.0000 0.0000 2868.431857 0 3.7217 314 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2868.431857 0 0.0002 347 Out... lnL = -2868.431857 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2868.431857 Node 7: lnL = -2868.431857 Node 8: lnL = -2868.431857 Node 9: lnL = -2868.431857 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 883 Sequential format.. Reading seq # 1: YKL185W_Sbay Reading seq # 2: YKL185W_Scer Reading seq # 3: YKL185W_Skud Reading seq # 4: YKL185W_Smik Reading seq # 5: YKL185W_Spar Sequences read.. Counting patterns.. # site patterns = 229 Counting frequencies.. 120 bytes for distance 36640 bytes for lkl0 29312 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.074259 0.055078 0.044418 0.089608 0.066414 0.130893 0.105058 0.081080 lnL0 = -3297.844436 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3297.844436 x= 0.07426 0.05508 0.04442 0.08961 0.06641 0.13089 0.10506 0.08108 1 h-lim-p 0.0002 0.0012 176.5193 3296.234648 8 0.0001 41 | 0/8 2 h-lim-p 0.0003 0.0024 43.3116 3296.120437 3 0.0001 59 | 0/8 3 h-lim-p 0.0004 0.0133 13.9914 3296.108320 5 0.0001 84 | 0/8 4 h-lim-p 0.0006 0.0554 3.2630 3296.107513 5 0.0002 108 | 0/8 5 h-lim-p 0.0017 0.4574 0.3126 3296.107506 1 0.0002 124 | 0/8 6 h-lim-p 0.0011 2.5515 0.0501 3296.107506 0 0.0002 145 | 0/8 7 h-lim-p 0.0056 20.0000 0.0021 3296.107504 0 0.0112 166 | 0/8 8 h-lim-p 0.0023 9.9675 0.0100 3296.107378 0 0.0185 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3296.107377 0 1.0938 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3296.107377 0 1.2500 229 | 0/8 11 h-lim-p 1.2017 20.0000 0.0000 3296.107377 0 0.2629 250 | 0/8 12 h-lim-p 0.1426 20.0000 0.0000 3296.107377 0 0.0356 271 | 0/8 13 h-lim-p 0.0233 20.0000 0.0000 3296.107377 0 0.0000 304 Out... lnL = -3296.107377 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3296.107377 Node 7: lnL = -3296.107377 Node 8: lnL = -3296.107377 Node 9: lnL = -3296.107377 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 985 Sequential format.. Reading seq # 1: YKL186C_Sbay Reading seq # 2: YKL186C_Scer Reading seq # 3: YKL186C_Skud Reading seq # 4: YKL186C_Smik Reading seq # 5: YKL186C_Spar Sequences read.. Counting patterns.. # site patterns = 344 Counting frequencies.. 120 bytes for distance 55040 bytes for lkl0 44032 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.133959 0.156472 0.075028 0.090020 0.081547 0.177937 0.201743 0.145494 lnL0 = -4323.065345 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4323.065345 x= 0.13396 0.15647 0.07503 0.09002 0.08155 0.17794 0.20174 0.14549 1 h-lim-p 0.0023 0.5945 193.4861 4319.731425 9 0.0002 49 | 0/8 2 h-lim-p 0.0004 0.0033 51.6571 4319.414593 7 0.0002 80 | 0/8 3 h-lim-p 0.0004 0.0062 36.6425 4319.296457 6 0.0002 106 | 0/8 4 h-lim-p 0.0015 0.0536 6.0548 4319.289565 4 0.0004 127 | 0/8 5 h-lim-p 0.0011 0.1529 2.0882 4319.288820 4 0.0004 148 | 0/8 6 h-lim-p 0.0013 0.2665 0.5970 4319.288780 2 0.0003 165 | 0/8 7 h-lim-p 0.0015 2.8042 0.1006 4319.288777 1 0.0006 187 | 0/8 8 h-lim-p 0.0873 20.0000 0.0007 4319.287790 0 1.3966 211 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 4319.287727 2 0.9961 235 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4319.287727 0 1.0938 255 | 0/8 11 h-lim-p 1.8994 20.0000 0.0000 4319.287727 0 0.9497 275 | 0/8 12 h-lim-p 0.7875 20.0000 0.0000 4319.287727 0 0.3937 295 | 0/8 13 h-lim-p 0.0360 20.0000 0.0000 4319.287727 0 0.0006 320 | 0/8 14 h-lim-p 0.0066 20.0000 0.0000 4319.287727 0 0.0000 350 Out... lnL = -4319.287727 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4319.287727 Node 7: lnL = -4319.287727 Node 8: lnL = -4319.287727 Node 9: lnL = -4319.287727 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 850 Sequential format.. Reading seq # 1: YKL187C_Sbay Reading seq # 2: YKL187C_Scer Reading seq # 3: YKL187C_Skud Reading seq # 4: YKL187C_Smik Reading seq # 5: YKL187C_Spar Sequences read.. Counting patterns.. # site patterns = 296 Counting frequencies.. 120 bytes for distance 47360 bytes for lkl0 37888 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.240020 0.019709 0.067952 0.105453 0.077487 0.170132 0.220507 0.251740 lnL0 = -3710.098814 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3710.098814 x= 0.24002 0.01971 0.06795 0.10545 0.07749 0.17013 0.22051 0.25174 1 h-lim-p 0.0018 0.0147 194.5502 3707.373294 9 0.0002 46 | 0/8 2 h-lim-p 0.0007 0.0056 42.3054 3707.063995 6 0.0004 72 | 0/8 3 h-lim-p 0.0005 0.0111 30.0562 3706.995920 5 0.0002 95 | 0/8 4 h-lim-p 0.0007 0.0389 9.6085 3706.977578 4 0.0005 117 | 0/8 5 h-lim-p 0.0016 0.0563 2.8563 3706.976686 4 0.0002 141 | 0/8 6 h-lim-p 0.0065 1.4141 0.1056 3706.976684 0 0.0004 156 | 0/8 7 h-lim-p 0.0141 20.0000 0.0027 3706.976475 0 0.2259 180 | 0/8 8 h-lim-p 0.0038 17.5601 0.1585 3706.975605 1 0.0047 202 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3706.975591 1 0.9961 224 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3706.975591 0 1.0938 244 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3706.975591 0 2.1875 264 | 0/8 12 h-lim-p 2.1167 20.0000 0.0000 3706.975591 0 0.9261 284 | 0/8 13 h-lim-p 1.8112 20.0000 0.0000 3706.975591 0 0.0141 310 | 0/8 14 h-lim-p 0.0063 20.0000 0.0000 3706.975591 0 0.0126 331 | 0/8 15 h-lim-p 0.0168 20.0000 0.0000 3706.975591 0 0.0000 366 Out... lnL = -3706.975591 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3706.975591 Node 7: lnL = -3706.975591 Node 8: lnL = -3706.975591 Node 9: lnL = -3706.975591 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 534 Sequential format.. Reading seq # 1: YKL188C_Sbay Reading seq # 2: YKL188C_Scer Reading seq # 3: YKL188C_Skud Reading seq # 4: YKL188C_Smik Reading seq # 5: YKL188C_Spar Sequences read.. Counting patterns.. # site patterns = 222 Counting frequencies.. 120 bytes for distance 35520 bytes for lkl0 28416 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.139939 0.038486 0.056842 0.136536 0.093875 0.184625 0.239052 0.150589 lnL0 = -2406.134403 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2406.134403 x= 0.13994 0.03849 0.05684 0.13654 0.09387 0.18462 0.23905 0.15059 1 h-lim-p 0.0009 0.0076 148.6787 2403.659353 9 0.0002 42 | 0/8 2 h-lim-p 0.0006 0.0051 28.1737 2403.481977 7 0.0005 70 | 0/8 3 h-lim-p 0.0009 0.0208 13.9337 2403.444082 6 0.0005 96 | 0/8 4 h-lim-p 0.0012 0.0463 5.5234 2403.436831 2 0.0006 112 | 0/8 5 h-lim-p 0.0054 0.4478 0.5722 2403.436728 0 0.0007 126 | 0/8 6 h-lim-p 0.0027 2.3737 0.1453 2403.436723 0 0.0006 147 | 0/8 7 h-lim-p 0.0062 18.2231 0.0138 2403.436722 0 0.0013 168 | 0/8 8 h-lim-p 0.0631 20.0000 0.0003 2403.436651 0 1.0089 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2403.436645 1 0.9961 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2403.436645 0 1.0938 234 | 0/8 11 h-lim-p 1.3753 20.0000 0.0000 2403.436645 0 0.3008 255 | 0/8 12 h-lim-p 0.1425 20.0000 0.0000 2403.436645 0 0.0000 296 Out... lnL = -2403.436645 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2403.436645 Node 7: lnL = -2403.436645 Node 8: lnL = -2403.436645 Node 9: lnL = -2403.436645 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 524 Sequential format.. Reading seq # 1: YKL190W_Sbay Reading seq # 2: YKL190W_Scer Reading seq # 3: YKL190W_Skud Reading seq # 4: YKL190W_Smik Reading seq # 5: YKL190W_Spar Sequences read.. Counting patterns.. # site patterns = 200 Counting frequencies.. 120 bytes for distance 32000 bytes for lkl0 25600 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.120516 0.035276 0.068099 0.199554 0.044895 0.178216 0.167746 0.130272 lnL0 = -2139.463001 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2139.463001 x= 0.12052 0.03528 0.06810 0.19955 0.04490 0.17822 0.16775 0.13027 1 h-lim-p 0.0013 0.0104 121.9135 2137.947000 8 0.0002 41 | 0/8 2 h-lim-p 0.0003 0.0021 55.4459 2137.274298 0 0.0005 54 | 0/8 3 h-lim-p 0.0024 0.0193 11.0396 2137.238974 6 0.0006 81 | 0/8 4 h-lim-p 0.0022 0.0866 3.0424 2137.236299 5 0.0006 106 | 0/8 5 h-lim-p 0.0040 0.2513 0.4680 2137.236263 2 0.0003 125 | 0/8 6 h-lim-p 0.0012 2.4276 0.1283 2137.236258 0 0.0006 145 | 0/8 7 h-lim-p 0.0037 11.3119 0.0207 2137.236246 0 0.0073 166 | 0/8 8 h-lim-p 0.0088 20.0000 0.0171 2137.234650 0 0.0708 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2137.234636 0 1.0938 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2137.234636 0 1.0938 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2137.234636 0 2.1875 249 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2137.234636 0 0.5469 270 | 0/8 13 h-lim-p 0.2619 20.0000 0.0000 2137.234636 0 0.0143 293 | 0/8 14 h-lim-p 0.0073 20.0000 0.0000 2137.234636 0 0.0036 313 | 0/8 15 h-lim-p 0.0024 20.0000 0.0000 2137.234636 0 0.0000 351 Out... lnL = -2137.234636 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2137.234636 Node 7: lnL = -2137.234636 Node 8: lnL = -2137.234636 Node 9: lnL = -2137.234636 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 525 Sequential format.. Reading seq # 1: YKL191W_Sbay Reading seq # 2: YKL191W_Scer Reading seq # 3: YKL191W_Skud Reading seq # 4: YKL191W_Smik Reading seq # 5: YKL191W_Spar Sequences read.. Counting patterns.. # site patterns = 231 Counting frequencies.. 120 bytes for distance 36960 bytes for lkl0 29568 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.127860 0.140696 0.058665 0.103364 0.151463 0.246924 0.236542 0.140648 lnL0 = -2498.446074 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2498.446074 x= 0.12786 0.14070 0.05866 0.10336 0.15146 0.24692 0.23654 0.14065 1 h-lim-p 0.0029 0.0233 77.1128 2497.506532 2 0.0003 28 | 0/8 2 h-lim-p 0.0014 0.0187 18.3267 2497.388216 4 0.0007 49 | 0/8 3 h-lim-p 0.0011 0.0280 12.2461 2497.362769 5 0.0005 74 | 0/8 4 h-lim-p 0.0025 0.1073 2.2307 2497.361446 2 0.0006 91 | 0/8 5 h-lim-p 0.0048 1.2825 0.2580 2497.361418 2 0.0009 108 | 0/8 6 h-lim-p 0.0105 10.5266 0.0227 2497.361417 0 0.0023 129 | 0/8 7 h-lim-p 0.0089 20.0000 0.0059 2497.361415 0 0.0089 149 | 0/8 8 h-lim-p 0.0058 9.6221 0.0090 2497.361235 0 0.0467 172 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2497.361229 1 0.9961 194 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2497.361229 0 1.0938 214 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2497.361229 0 3.7500 234 | 0/8 12 h-lim-p 2.3448 20.0000 0.0000 2497.361229 0 0.2565 256 | 0/8 13 h-lim-p 1.5775 20.0000 0.0000 2497.361229 0 0.0986 279 | 0/8 14 h-lim-p 0.0245 20.0000 0.0000 2497.361229 0 0.0015 302 Out... lnL = -2497.361229 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2497.361229 Node 7: lnL = -2497.361229 Node 8: lnL = -2497.361229 Node 9: lnL = -2497.361229 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 556 Sequential format.. Reading seq # 1: YKL192C_Sbay Reading seq # 2: YKL192C_Scer Reading seq # 3: YKL192C_Skud Reading seq # 4: YKL192C_Smik Reading seq # 5: YKL192C_Spar Sequences read.. Counting patterns.. # site patterns = 227 Counting frequencies.. 120 bytes for distance 36320 bytes for lkl0 29056 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.162984 0.077103 0.070134 0.108066 0.146761 0.253365 0.282894 0.167143 lnL0 = -2579.510551 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2579.510551 x= 0.16298 0.07710 0.07013 0.10807 0.14676 0.25336 0.28289 0.16714 1 h-lim-p 0.0069 0.1146 86.7517 2578.260732 3 0.0004 31 | 0/8 2 h-lim-p 0.0015 0.0118 16.5262 2578.171430 2 0.0007 47 | 0/8 3 h-lim-p 0.0011 0.0296 10.6813 2578.146490 6 0.0006 73 | 0/8 4 h-lim-p 0.0014 0.0707 4.4759 2578.141033 3 0.0007 92 | 0/8 5 h-lim-p 0.0108 1.0234 0.2809 2578.140999 2 0.0009 111 | 0/8 6 h-lim-p 0.0767 20.0000 0.0032 2578.140998 0 0.0084 133 | 0/8 7 h-lim-p 0.0099 20.0000 0.0027 2578.140955 0 0.0789 156 | 0/8 8 h-lim-p 0.0035 4.6203 0.0603 2578.140953 1 0.0009 179 | 0/8 9 h-lim-p 1.5487 20.0000 0.0000 2578.140952 0 1.3551 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2578.140951 0 1.0938 219 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2578.140951 0 1.0938 239 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2578.140951 0 5.0000 260 | 0/8 13 h-lim-p 1.5961 20.0000 0.0000 2578.140951 0 0.1995 282 | 0/8 14 h-lim-p 0.3525 20.0000 0.0000 2578.140951 0 0.0000 328 Out... lnL = -2578.140951 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2578.140951 Node 7: lnL = -2578.140951 Node 8: lnL = -2578.140951 Node 9: lnL = -2578.140951 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 311 Sequential format.. Reading seq # 1: YKL193C_Sbay Reading seq # 2: YKL193C_Scer Reading seq # 3: YKL193C_Skud Reading seq # 4: YKL193C_Smik Reading seq # 5: YKL193C_Spar Sequences read.. Counting patterns.. # site patterns = 103 Counting frequencies.. 120 bytes for distance 16480 bytes for lkl0 13184 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.090365 0.045734 0.016533 0.056556 0.019943 0.113417 0.136119 0.092230 lnL0 = -1066.863929 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1066.863929 x= 0.09036 0.04573 0.01653 0.05656 0.01994 0.11342 0.13612 0.09223 1 h-lim-p 0.0000 0.0002 112.6391 1066.020108 0 0.0001 24 | 0/8 2 h-lim-p 0.0002 1.8962 62.1750 1065.763208 7 0.0002 51 | 0/8 3 h-lim-p 0.0001 0.0011 20.0598 1065.738242 4 0.0001 71 | 0/8 4 h-lim-p 0.0005 0.0274 5.5744 1065.732225 5 0.0004 92 | 0/8 5 h-lim-p 0.0014 0.1288 1.7343 1065.731745 4 0.0003 113 | 0/8 6 h-lim-p 0.0017 0.4868 0.3517 1065.731697 1 0.0007 127 | 0/8 7 h-lim-p 0.0060 4.8913 0.0398 1065.731613 0 0.0090 147 | 0/8 8 h-lim-p 0.0118 0.8510 0.0305 1065.723347 0 0.0472 169 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1065.723163 2 0.9961 193 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1065.723163 0 1.0938 213 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1065.723163 0 3.7500 233 | 0/8 12 h-lim-p 1.4080 20.0000 0.0000 1065.723163 0 0.1540 255 | 0/8 13 h-lim-p 0.1832 20.0000 0.0000 1065.723163 0 0.0001 285 Out... lnL = -1065.723163 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1065.723163 Node 7: lnL = -1065.723163 Node 8: lnL = -1065.723163 Node 9: lnL = -1065.723163 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 220 Sequential format.. Reading seq # 1: YKL195W_Sbay Reading seq # 2: YKL195W_Scer Reading seq # 3: YKL195W_Skud Reading seq # 4: YKL195W_Smik Reading seq # 5: YKL195W_Spar Sequences read.. Counting patterns.. # site patterns = 101 Counting frequencies.. 120 bytes for distance 16160 bytes for lkl0 12928 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.147765 0.003325 0.034186 0.083307 0.091160 0.142878 0.264297 0.150667 lnL0 = -949.553813 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 949.553813 x= 0.14777 0.00332 0.03419 0.08331 0.09116 0.14288 0.26430 0.15067 1 h-lim-p 0.0017 1.0977 104.5759 948.142560 7 0.0003 38 | 0/8 2 h-lim-p 0.0021 0.0166 10.3908 948.096699 3 0.0009 56 | 0/8 3 h-lim-p 0.0020 0.0313 4.4065 948.088597 2 0.0010 72 | 0/8 4 h-lim-p 0.0028 0.0694 1.5260 948.087820 5 0.0008 95 | 0/8 5 h-lim-p 0.0016 0.4399 0.7235 948.087555 2 0.0012 111 | 0/8 6 h-lim-p 0.0026 0.4835 0.3393 948.087514 3 0.0009 139 | 0/8 7 h-lim-p 0.0023 1.5660 0.1366 948.087506 1 0.0010 161 | 0/8 8 h-lim-p 1.0162 20.0000 0.0001 948.087485 0 1.5243 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 948.087483 0 1.0938 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 948.087483 0 1.2500 221 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 948.087483 0 0.5469 242 | 0/8 12 h-lim-p 1.1402 20.0000 0.0000 948.087483 0 0.0033 270 Out... lnL = -948.087483 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -948.087483 Node 7: lnL = -948.087483 Node 8: lnL = -948.087483 Node 9: lnL = -948.087483 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 245 Sequential format.. Reading seq # 1: YKL205W_Sbay Reading seq # 2: YKL205W_Scer Reading seq # 3: YKL205W_Skud Reading seq # 4: YKL205W_Smik Reading seq # 5: YKL205W_Spar Sequences read.. Counting patterns.. # site patterns = 65 Counting frequencies.. 120 bytes for distance 10400 bytes for lkl0 8320 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.094715 0.125467 0.002032 0.069602 0.063511 0.165105 0.000060 0.096706 lnL0 = -736.082464 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 736.082464 x= 0.09472 0.12547 0.00203 0.06960 0.06351 0.16511 0.00006 0.09671 1 h-lim-p 0.0000 0.0000 336.4648 734.468285 m 0.0000 22 | 1/8 2 h-lim-p 0.0001 0.0013 57.5884 733.732112 0 0.0005 36 | 1/8 3 h-lim-p 0.0013 0.0103 15.5856 733.681271 7 0.0004 66 | 1/8 4 h-lim-p 0.0015 0.0300 4.7926 733.673805 2 0.0007 82 | 0/8 5 h-lim-p 0.0002 0.0258 13.5242 733.623661 0 0.0007 95 | 0/8 6 h-lim-p 0.0015 0.0320 6.5734 733.601838 3 0.0013 113 | 0/8 7 h-lim-p 0.0127 0.1972 0.6469 733.589160 0 0.0191 125 | 0/8 8 h-lim-p 0.2920 4.8249 0.0423 732.564058 0 0.5840 146 | 0/8 9 h-lim-p 2.5000 20.0000 0.0080 732.485396 7 1.5021 185 | 0/8 10 h-lim-p 1.2829 10.2628 0.0033 732.466049 0 2.5657 206 | 0/8 11 h-lim-p 0.4788 3.8305 0.0063 732.428348 m 3.8305 226 | 0/8 12 h-lim-p 0.0000 0.0000 0.0731 h-lim-p: 2.67482516e-19 2.13986013e-18 7.31302441e-02 732.428348 .. | 0/8 13 h-lim-p 0.0000 0.0366 8.4806 732.416795 0 0.0003 267 | 0/8 14 h-lim-p 0.0000 0.0001 3.3454 732.415998 m 0.0001 279 | 1/8 15 h-lim-p 0.0002 0.1062 1.6290 732.415635 0 0.0003 292 | 1/8 16 h-lim-p 0.0009 0.0986 0.5935 732.415571 2 0.0004 308 | 1/8 17 h-lim-p 0.0020 1.0116 0.1249 732.415527 0 0.0060 328 | 1/8 18 h-lim-p 0.0102 2.6123 0.0737 732.415524 1 0.0013 351 | 1/8 19 h-lim-p 0.0268 20.0000 0.0035 732.415449 0 0.1071 372 | 1/8 20 h-lim-p 0.0189 4.9837 0.0196 732.415011 0 0.0377 392 | 1/8 21 h-lim-p 2.5000 20.0000 0.0000 732.415011 0 1.0938 411 | 1/8 22 h-lim-p 2.5000 20.0000 0.0000 732.415011 0 1.0938 430 | 1/8 23 h-lim-p 2.5000 20.0000 0.0000 732.415011 0 0.0006 460 Out... lnL = -732.415011 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -732.415011 Node 7: lnL = -732.415011 Node 8: lnL = -732.415011 Node 9: lnL = -732.415011 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 244 Sequential format.. Reading seq # 1: YKL206C_Sbay Reading seq # 2: YKL206C_Scer Reading seq # 3: YKL206C_Skud Reading seq # 4: YKL206C_Smik Reading seq # 5: YKL206C_Spar Sequences read.. Counting patterns.. # site patterns = 91 Counting frequencies.. 120 bytes for distance 14560 bytes for lkl0 11648 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.062826 0.048369 0.101838 0.120106 0.000060 0.153353 0.121519 0.064774 lnL0 = -901.677153 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 901.677153 x= 0.06283 0.04837 0.10184 0.12011 0.00006 0.15335 0.12152 0.06477 1 h-lim-p 0.0001 0.0037 431.8276 897.424867 6 0.0001 35 | 0/8 2 h-lim-p 0.0004 0.0035 50.6105 896.232405 0 0.0009 48 | 0/8 3 h-lim-p 0.0006 0.0045 49.9286 895.461333 0 0.0011 61 | 0/8 4 h-lim-p 0.0002 0.0018 61.0535 894.690045 0 0.0009 75 | 0/8 5 h-lim-p 0.0081 0.0648 3.9453 894.685149 6 0.0006 104 | 0/8 6 h-lim-p 0.0025 0.0580 0.9951 894.684744 5 0.0008 129 | 0/8 7 h-lim-p 0.0033 0.7990 0.2295 894.684337 1 0.0041 151 | 0/8 8 h-lim-p 0.0286 2.5053 0.0328 894.608075 0 0.2292 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0012 894.591546 1 3.1250 196 | 0/8 10 h-lim-p 1.6061 20.0000 0.0024 894.590363 4 0.8161 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0005 894.590302 3 0.8800 253 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 894.590302 0 1.0938 273 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 894.590302 0 2.1875 293 | 0/8 14 h-lim-p 1.9265 20.0000 0.0000 894.590302 0 0.8428 313 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 894.590302 0 0.0011 343 Out... lnL = -894.590302 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -894.590302 Node 7: lnL = -894.590302 Node 8: lnL = -894.590302 Node 9: lnL = -894.590302 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 229 Sequential format.. Reading seq # 1: YKL207W_Sbay Reading seq # 2: YKL207W_Scer Reading seq # 3: YKL207W_Skud Reading seq # 4: YKL207W_Smik Reading seq # 5: YKL207W_Spar Sequences read.. Counting patterns.. # site patterns = 103 Counting frequencies.. 120 bytes for distance 16480 bytes for lkl0 13184 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.118707 0.109890 0.062008 0.084734 0.064516 0.286568 0.126461 0.121994 lnL0 = -925.431636 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 925.431636 x= 0.11871 0.10989 0.06201 0.08473 0.06452 0.28657 0.12646 0.12199 1 h-lim-p 0.0019 0.0153 56.8483 924.095747 7 0.0010 36 | 0/8 2 h-lim-p 0.0012 0.0094 11.0689 924.037632 6 0.0010 61 | 0/8 3 h-lim-p 0.0026 0.0434 4.0605 924.030361 5 0.0010 83 | 0/8 4 h-lim-p 0.0032 0.2779 1.2660 924.029537 5 0.0012 107 | 0/8 5 h-lim-p 0.0026 0.8392 0.5668 924.029265 3 0.0020 125 | 0/8 6 h-lim-p 0.0082 1.9694 0.1414 924.029246 2 0.0020 150 | 0/8 7 h-lim-p 0.0059 3.8224 0.0483 924.029244 0 0.0015 171 | 0/8 8 h-lim-p 0.7362 20.0000 0.0001 924.029238 0 1.4724 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 924.029237 0 1.0938 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 924.029237 0 1.0938 232 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 924.029237 0 5.0000 253 | 0/8 12 h-lim-p 1.4446 20.0000 0.0000 924.029237 0 0.1806 275 | 0/8 13 h-lim-p 0.2569 20.0000 0.0000 924.029237 0 0.0040 300 Out... lnL = -924.029237 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -924.029237 Node 7: lnL = -924.029237 Node 8: lnL = -924.029237 Node 9: lnL = -924.029237 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 845 Sequential format.. Reading seq # 1: YKL208W_Sbay Reading seq # 2: YKL208W_Scer Reading seq # 3: YKL208W_Skud Reading seq # 4: YKL208W_Smik Reading seq # 5: YKL208W_Spar Sequences read.. Counting patterns.. # site patterns = 368 Counting frequencies.. 120 bytes for distance 58880 bytes for lkl0 47104 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.158824 0.123471 0.034346 0.140472 0.129865 0.810441 0.253784 0.164695 lnL0 = -4394.220522 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4394.220522 x= 0.15882 0.12347 0.03435 0.14047 0.12987 0.81044 0.25378 0.16470 1 h-lim-p 0.0049 0.0553 133.6687 4392.270671 5 0.0002 35 | 0/8 2 h-lim-p 0.0010 0.0080 22.7329 4392.169760 5 0.0004 57 | 0/8 3 h-lim-p 0.0009 0.0438 10.0039 4392.153407 4 0.0004 79 | 0/8 4 h-lim-p 0.0012 0.1078 3.1577 4392.150156 5 0.0007 105 | 0/8 5 h-lim-p 0.0028 0.2726 0.8397 4392.149807 2 0.0011 121 | 0/8 6 h-lim-p 0.0016 0.4870 0.5551 4392.149731 1 0.0007 143 | 0/8 7 h-lim-p 0.0040 2.4109 0.0988 4392.149715 0 0.0035 163 | 0/8 8 h-lim-p 2.5000 20.0000 0.0001 4392.149699 0 1.2500 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4392.149699 0 1.0938 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4392.149699 0 1.2500 223 | 0/8 11 h-lim-p 2.1075 20.0000 0.0000 4392.149699 0 0.5269 244 | 0/8 12 h-lim-p 0.3097 20.0000 0.0000 4392.149699 0 0.1549 264 | 0/8 13 h-lim-p 0.0931 20.0000 0.0000 4392.149699 0 0.0000 296 Out... lnL = -4392.149699 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4392.149699 Node 7: lnL = -4392.149699 Node 8: lnL = -4392.149699 Node 9: lnL = -4392.149699 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 846 Sequential format.. Reading seq # 1: YKL209C_Sbay Reading seq # 2: YKL209C_Scer Reading seq # 3: YKL209C_Skud Reading seq # 4: YKL209C_Smik Reading seq # 5: YKL209C_Spar Sequences read.. Counting patterns.. # site patterns = 398 Counting frequencies.. 120 bytes for distance 63680 bytes for lkl0 50944 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.150106 0.072665 0.091395 0.130273 0.152197 0.417656 0.261560 0.154793 lnL0 = -4151.931574 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4151.931574 x= 0.15011 0.07266 0.09140 0.13027 0.15220 0.41766 0.26156 0.15479 1 h-lim-p 0.0026 0.0297 179.9037 4147.623595 3 0.0003 30 | 0/8 2 h-lim-p 0.0006 0.0051 48.7998 4146.835054 6 0.0007 55 | 0/8 3 h-lim-p 0.0006 0.0046 51.2877 4146.464369 6 0.0005 78 | 0/8 4 h-lim-p 0.0014 0.0168 17.9487 4146.389798 5 0.0006 101 | 0/8 5 h-lim-p 0.0058 0.1722 1.8333 4146.388395 5 0.0009 126 | 0/8 6 h-lim-p 0.0018 0.2449 0.8484 4146.388198 3 0.0007 146 | 0/8 7 h-lim-p 0.0063 3.9720 0.0883 4146.388184 2 0.0016 171 | 0/8 8 h-lim-p 0.0288 20.0000 0.0051 4146.383376 0 0.6903 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 4146.383243 2 0.9961 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4146.383242 0 1.0938 239 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4146.383242 0 1.2500 259 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4146.383242 0 0.3125 281 | 0/8 13 h-lim-p 0.2015 20.0000 0.0000 4146.383242 0 0.0063 305 Out... lnL = -4146.383242 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4146.383242 Node 7: lnL = -4146.383242 Node 8: lnL = -4146.383242 Node 9: lnL = -4146.383242 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 849 Sequential format.. Reading seq # 1: YKL211C_Sbay Reading seq # 2: YKL211C_Scer Reading seq # 3: YKL211C_Skud Reading seq # 4: YKL211C_Smik Reading seq # 5: YKL211C_Spar Sequences read.. Counting patterns.. # site patterns = 277 Counting frequencies.. 120 bytes for distance 44320 bytes for lkl0 35456 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.145580 0.041491 0.058496 0.139436 0.081960 0.171921 0.183713 0.148745 lnL0 = -3698.121741 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3698.121741 x= 0.14558 0.04149 0.05850 0.13944 0.08196 0.17192 0.18371 0.14874 1 h-lim-p 0.0004 0.0033 267.9673 3693.445320 9 0.0001 44 | 0/8 2 h-lim-p 0.0004 0.0036 34.8883 3693.296061 7 0.0002 73 | 0/8 3 h-lim-p 0.0005 0.0194 16.8711 3693.268198 2 0.0002 89 | 0/8 4 h-lim-p 0.0009 0.0594 4.4144 3693.265178 5 0.0003 112 | 0/8 5 h-lim-p 0.0022 0.2222 0.6931 3693.265104 3 0.0003 134 | 0/8 6 h-lim-p 0.0019 2.6957 0.1138 3693.265101 0 0.0004 155 | 0/8 7 h-lim-p 0.0045 20.0000 0.0105 3693.265101 0 0.0010 176 | 0/8 8 h-lim-p 0.0286 20.0000 0.0004 3693.265006 0 0.4574 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3693.265001 0 1.0938 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3693.265001 0 1.0938 240 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3693.265001 0 0.1367 263 | 0/8 12 h-lim-p 0.0922 20.0000 0.0000 3693.265001 0 0.0461 283 | 0/8 13 h-lim-p 0.0255 20.0000 0.0000 3693.265001 0 0.0128 303 | 0/8 14 h-lim-p 0.0647 20.0000 0.0000 3693.265001 0 0.0000 344 Out... lnL = -3693.265001 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3693.265001 Node 7: lnL = -3693.265001 Node 8: lnL = -3693.265001 Node 9: lnL = -3693.265001 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 280 Sequential format.. Reading seq # 1: YKL214C_Sbay Reading seq # 2: YKL214C_Scer Reading seq # 3: YKL214C_Skud Reading seq # 4: YKL214C_Smik Reading seq # 5: YKL214C_Spar Sequences read.. Counting patterns.. # site patterns = 131 Counting frequencies.. 120 bytes for distance 20960 bytes for lkl0 16768 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.136260 0.081782 0.102813 0.094793 0.077388 0.211078 0.185823 0.139737 lnL0 = -1270.116436 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1270.116436 x= 0.13626 0.08178 0.10281 0.09479 0.07739 0.21108 0.18582 0.13974 1 h-lim-p 0.0029 0.0232 50.8257 1269.309345 2 0.0007 27 | 0/8 2 h-lim-p 0.0023 0.0183 12.1266 1269.254592 7 0.0008 55 | 0/8 3 h-lim-p 0.0010 0.0223 9.2212 1269.232759 7 0.0007 86 | 0/8 4 h-lim-p 0.0139 0.5350 0.4884 1269.232618 4 0.0012 111 | 0/8 5 h-lim-p 0.0022 0.8275 0.2585 1269.232592 1 0.0010 133 | 0/8 6 h-lim-p 0.0073 7.7320 0.0345 1269.232592 0 0.0016 154 | 0/8 7 h-lim-p 0.0106 20.0000 0.0052 1269.232592 0 0.0023 175 | 0/8 8 h-lim-p 0.0405 20.0000 0.0003 1269.232577 0 0.6477 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1269.232577 0 1.0938 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1269.232577 0 1.0938 239 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1269.232577 0 2.5000 259 | 0/8 12 h-lim-p 2.0430 20.0000 0.0000 1269.232577 0 0.0319 284 | 0/8 13 h-lim-p 0.0297 20.0000 0.0000 1269.232577 0 0.0297 304 | 0/8 14 h-lim-p 0.0251 20.0000 0.0000 1269.232577 0 0.0001 331 Out... lnL = -1269.232577 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1269.232577 Node 7: lnL = -1269.232577 Node 8: lnL = -1269.232577 Node 9: lnL = -1269.232577 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 430 Sequential format.. Reading seq # 1: YKL215C_Sbay Reading seq # 2: YKL215C_Scer Reading seq # 3: YKL215C_Skud Reading seq # 4: YKL215C_Smik Reading seq # 5: YKL215C_Spar Sequences read.. Counting patterns.. # site patterns = 197 Counting frequencies.. 120 bytes for distance 31520 bytes for lkl0 25216 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.208458 0.095162 0.137734 0.129470 0.115775 0.146917 0.232180 0.212780 lnL0 = -2052.834785 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2052.834785 x= 0.20846 0.09516 0.13773 0.12947 0.11578 0.14692 0.23218 0.21278 1 h-lim-p 0.0006 0.0046 45.2514 2052.216987 7 0.0006 35 | 0/8 2 h-lim-p 0.0036 0.0307 7.5802 2052.188777 7 0.0010 64 | 0/8 3 h-lim-p 0.0017 0.0655 4.5426 2052.183517 2 0.0006 80 | 0/8 4 h-lim-p 0.0016 0.1670 1.8830 2052.182559 3 0.0007 99 | 0/8 5 h-lim-p 0.0027 0.4293 0.4608 2052.182492 2 0.0007 116 | 0/8 6 h-lim-p 0.0034 4.6530 0.0951 2052.182489 0 0.0007 137 | 0/8 7 h-lim-p 0.0059 20.0000 0.0120 2052.182489 0 0.0026 157 | 0/8 8 h-lim-p 0.1057 20.0000 0.0003 2052.182457 0 0.8455 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2052.182455 0 1.0938 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2052.182455 0 1.0938 220 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2052.182455 0 1.0938 240 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2052.182455 0 1.8750 260 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2052.182455 0 0.6250 281 | 0/8 14 h-lim-p 0.1757 20.0000 0.0000 2052.182455 0 0.0110 304 Out... lnL = -2052.182455 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2052.182455 Node 7: lnL = -2052.182455 Node 8: lnL = -2052.182455 Node 9: lnL = -2052.182455 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 875 Sequential format.. Reading seq # 1: YKL216W_Sbay Reading seq # 2: YKL216W_Scer Reading seq # 3: YKL216W_Skud Reading seq # 4: YKL216W_Smik Reading seq # 5: YKL216W_Spar Sequences read.. Counting patterns.. # site patterns = 428 Counting frequencies.. 120 bytes for distance 68480 bytes for lkl0 54784 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.206599 0.089803 0.305604 0.176522 0.152483 0.356144 0.916782 0.214706 lnL0 = -4964.560506 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4964.560506 x= 0.20660 0.08980 0.30560 0.17652 0.15248 0.35614 0.91678 0.21471 1 h-lim-p 0.0008 0.0062 66.3819 4962.875739 5 0.0008 31 | 0/8 2 h-lim-p 0.0019 0.0153 21.2785 4962.652393 7 0.0011 59 | 0/8 3 h-lim-p 0.0009 0.0208 24.3091 4962.561172 7 0.0006 89 | 0/8 4 h-lim-p 0.0009 0.0299 16.3007 4962.484654 0 0.0013 101 | 0/8 5 h-lim-p 0.0053 0.1266 3.9497 4962.464971 6 0.0029 128 | 0/8 6 h-lim-p 0.0098 0.5053 1.1815 4962.464105 4 0.0014 151 | 0/8 7 h-lim-p 0.0048 2.6881 0.3406 4962.463746 0 0.0073 163 | 0/8 8 h-lim-p 0.6951 20.0000 0.0036 4962.460645 0 1.0426 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 4962.460593 1 0.9961 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4962.460593 0 1.0938 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4962.460593 0 1.0938 245 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4962.460593 0 0.0000 290 Out... lnL = -4962.460593 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4962.460593 Node 7: lnL = -4962.460593 Node 8: lnL = -4962.460593 Node 9: lnL = -4962.460593 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 909 Sequential format.. Reading seq # 1: YKL217W_Sbay Reading seq # 2: YKL217W_Scer Reading seq # 3: YKL217W_Skud Reading seq # 4: YKL217W_Smik Reading seq # 5: YKL217W_Spar Sequences read.. Counting patterns.. # site patterns = 292 Counting frequencies.. 120 bytes for distance 46720 bytes for lkl0 37376 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.157625 0.052091 0.046635 0.105094 0.083672 0.166949 0.158221 0.160662 lnL0 = -3649.029585 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3649.029585 x= 0.15762 0.05209 0.04663 0.10509 0.08367 0.16695 0.15822 0.16066 1 h-lim-p 0.0005 0.0037 267.1628 3644.703373 8 0.0001 42 | 0/8 2 h-lim-p 0.0003 0.0022 62.4102 3644.203116 6 0.0003 69 | 0/8 3 h-lim-p 0.0005 0.0072 30.5317 3644.114942 6 0.0002 92 | 0/8 4 h-lim-p 0.0007 0.0186 9.9694 3644.103584 5 0.0003 115 | 0/8 5 h-lim-p 0.0031 0.2144 0.8386 3644.103462 2 0.0004 133 | 0/8 6 h-lim-p 0.0017 1.5512 0.1812 3644.103457 1 0.0003 156 | 0/8 7 h-lim-p 0.0037 17.2955 0.0163 3644.103455 0 0.0032 176 | 0/8 8 h-lim-p 0.0181 20.0000 0.0029 3644.102668 0 0.2895 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3644.102573 2 0.9961 224 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3644.102573 0 1.0938 244 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3644.102573 0 0.0001 278 Out... lnL = -3644.102573 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3644.102573 Node 7: lnL = -3644.102573 Node 8: lnL = -3644.102573 Node 9: lnL = -3644.102573 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 556 Sequential format.. Reading seq # 1: YKL222C_Sbay Reading seq # 2: YKL222C_Scer Reading seq # 3: YKL222C_Skud Reading seq # 4: YKL222C_Smik Reading seq # 5: YKL222C_Spar Sequences read.. Counting patterns.. # site patterns = 222 Counting frequencies.. 120 bytes for distance 35520 bytes for lkl0 28416 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.090607 0.124719 0.105878 0.110407 0.082133 0.284514 0.189743 0.094318 lnL0 = -2418.529727 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2418.529727 x= 0.09061 0.12472 0.10588 0.11041 0.08213 0.28451 0.18974 0.09432 1 h-lim-p 0.0021 0.0169 56.2423 2417.907689 4 0.0004 31 | 0/8 2 h-lim-p 0.0010 0.0083 13.2299 2417.883478 6 0.0003 58 | 0/8 3 h-lim-p 0.0012 0.1005 3.1442 2417.879519 5 0.0009 82 | 0/8 4 h-lim-p 0.0018 0.2798 1.4713 2417.879151 2 0.0004 99 | 0/8 5 h-lim-p 0.0017 1.1710 0.3539 2417.879112 1 0.0007 113 | 0/8 6 h-lim-p 0.0020 1.7116 0.1167 2417.879109 1 0.0005 136 | 0/8 7 h-lim-p 0.0156 20.0000 0.0037 2417.879109 0 0.0034 157 | 0/8 8 h-lim-p 0.0391 20.0000 0.0003 2417.879094 0 0.3129 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2417.879093 0 1.0938 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2417.879093 0 1.0938 220 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2417.879093 0 0.0391 245 | 0/8 12 h-lim-p 0.0191 20.0000 0.0000 2417.879093 0 0.0003 270 Out... lnL = -2417.879093 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2417.879093 Node 7: lnL = -2417.879093 Node 8: lnL = -2417.879093 Node 9: lnL = -2417.879093 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 531 Sequential format.. Reading seq # 1: YKR001C_Sbay Reading seq # 2: YKR001C_Scer Reading seq # 3: YKR001C_Skud Reading seq # 4: YKR001C_Smik Reading seq # 5: YKR001C_Spar Sequences read.. Counting patterns.. # site patterns = 213 Counting frequencies.. 120 bytes for distance 34080 bytes for lkl0 27264 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.148834 0.087123 0.037724 0.119206 0.090933 0.175816 0.194724 0.145017 lnL0 = -2413.469922 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2413.469922 x= 0.14883 0.08712 0.03772 0.11921 0.09093 0.17582 0.19472 0.14502 1 h-lim-p 0.0004 0.0028 138.3389 2411.135485 6 0.0003 34 | 0/8 2 h-lim-p 0.0003 0.0024 42.3672 2410.866690 5 0.0003 56 | 0/8 3 h-lim-p 0.0011 0.0152 11.9956 2410.847172 4 0.0003 77 | 0/8 4 h-lim-p 0.0011 0.0754 3.2601 2410.844727 2 0.0005 93 | 0/8 5 h-lim-p 0.0065 1.3361 0.2575 2410.844712 2 0.0004 112 | 0/8 6 h-lim-p 0.0030 6.1008 0.0367 2410.844711 0 0.0007 133 | 0/8 7 h-lim-p 0.0035 20.0000 0.0069 2410.844711 0 0.0015 153 | 0/8 8 h-lim-p 0.1118 20.0000 0.0001 2410.844705 0 0.8947 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2410.844704 0 1.0938 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2410.844704 0 1.0938 216 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2410.844704 0 0.0171 242 | 0/8 12 h-lim-p 0.0103 20.0000 0.0000 2410.844704 0 0.0026 263 Out... lnL = -2410.844704 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2410.844704 Node 7: lnL = -2410.844704 Node 8: lnL = -2410.844704 Node 9: lnL = -2410.844704 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 534 Sequential format.. Reading seq # 1: YKR002W_Sbay Reading seq # 2: YKR002W_Scer Reading seq # 3: YKR002W_Skud Reading seq # 4: YKR002W_Smik Reading seq # 5: YKR002W_Spar Sequences read.. Counting patterns.. # site patterns = 209 Counting frequencies.. 120 bytes for distance 33440 bytes for lkl0 26752 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.137868 0.077242 0.035854 0.121199 0.091581 0.190122 0.205256 0.134094 lnL0 = -2424.482883 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2424.482883 x= 0.13787 0.07724 0.03585 0.12120 0.09158 0.19012 0.20526 0.13409 1 h-lim-p 0.0007 0.0052 162.6414 2421.454017 4 0.0003 30 | 0/8 2 h-lim-p 0.0003 0.0023 48.2204 2421.070045 0 0.0004 42 | 0/8 3 h-lim-p 0.0013 0.0100 13.8778 2421.041923 4 0.0003 63 | 0/8 4 h-lim-p 0.0013 0.0745 3.3590 2421.039510 5 0.0005 89 | 0/8 5 h-lim-p 0.0056 0.6974 0.2736 2421.039463 2 0.0009 108 | 0/8 6 h-lim-p 0.0028 2.3598 0.0893 2421.039370 0 0.0042 128 | 0/8 7 h-lim-p 0.0051 3.9831 0.0741 2421.033843 0 0.0408 151 | 0/8 8 h-lim-p 0.0022 0.1984 1.3608 2421.025010 4 0.0024 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 2421.024932 2 1.0889 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2421.024930 0 1.2500 216 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2421.024930 0 1.0938 236 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2421.024930 0 0.5469 257 | 0/8 13 h-lim-p 0.4124 20.0000 0.0000 2421.024930 0 0.1031 278 | 0/8 14 h-lim-p 0.0683 20.0000 0.0000 2421.024930 0 0.0342 298 | 0/8 15 h-lim-p 0.0198 20.0000 0.0000 2421.024930 0 0.0006 322 Out... lnL = -2421.024930 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2421.024930 Node 7: lnL = -2421.024930 Node 8: lnL = -2421.024930 Node 9: lnL = -2421.024930 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 478 Sequential format.. Reading seq # 1: YKR003W_Sbay Reading seq # 2: YKR003W_Scer Reading seq # 3: YKR003W_Skud Reading seq # 4: YKR003W_Smik Reading seq # 5: YKR003W_Spar Sequences read.. Counting patterns.. # site patterns = 173 Counting frequencies.. 120 bytes for distance 27680 bytes for lkl0 22144 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.106693 0.074533 0.061968 0.091529 0.065343 0.210512 0.177241 0.103244 lnL0 = -2059.651979 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2059.651979 x= 0.10669 0.07453 0.06197 0.09153 0.06534 0.21051 0.17724 0.10324 1 h-lim-p 0.0004 0.0036 71.2008 2058.997650 8 0.0003 43 | 0/8 2 h-lim-p 0.0012 0.0096 7.4588 2058.991206 4 0.0002 64 | 0/8 3 h-lim-p 0.0008 0.0738 2.2427 2058.990429 2 0.0003 80 | 0/8 4 h-lim-p 0.0009 0.3718 0.8098 2058.990270 3 0.0005 101 | 0/8 5 h-lim-p 0.0030 0.7108 0.1494 2058.990264 2 0.0005 128 | 0/8 6 h-lim-p 0.0035 20.0000 0.0207 2058.990264 0 0.0004 150 | 0/8 7 h-lim-p 0.0137 20.0000 0.0007 2058.990263 0 0.0547 172 | 0/8 8 h-lim-p 0.0048 14.3378 0.0075 2058.990246 0 0.0145 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2058.990246 0 1.0938 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2058.990246 0 2.1875 233 | 0/8 11 h-lim-p 2.4897 20.0000 0.0000 2058.990246 0 0.2723 255 | 0/8 12 h-lim-p 0.2505 20.0000 0.0000 2058.990246 0 0.0039 280 Out... lnL = -2058.990246 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2058.990246 Node 7: lnL = -2058.990246 Node 8: lnL = -2058.990246 Node 9: lnL = -2058.990246 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 577 Sequential format.. Reading seq # 1: YKR005C_Sbay Reading seq # 2: YKR005C_Scer Reading seq # 3: YKR005C_Skud Reading seq # 4: YKR005C_Smik Reading seq # 5: YKR005C_Spar Sequences read.. Counting patterns.. # site patterns = 170 Counting frequencies.. 120 bytes for distance 27200 bytes for lkl0 21760 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.092351 0.048773 0.045151 0.093523 0.055848 0.135905 0.108878 0.089773 lnL0 = -2026.913746 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2026.913746 x= 0.09235 0.04877 0.04515 0.09352 0.05585 0.13591 0.10888 0.08977 1 h-lim-p 0.0008 0.0066 82.2457 2026.350936 7 0.0002 36 | 0/8 2 h-lim-p 0.0010 0.0077 13.6847 2026.329464 5 0.0002 61 | 0/8 3 h-lim-p 0.0005 0.0323 6.2723 2026.326170 4 0.0002 81 | 0/8 4 h-lim-p 0.0008 0.0715 1.6147 2026.325841 4 0.0003 102 | 0/8 5 h-lim-p 0.0044 1.9681 0.1000 2026.325839 1 0.0004 118 | 0/8 6 h-lim-p 0.0048 15.3426 0.0091 2026.325839 0 0.0003 141 | 0/8 7 h-lim-p 0.0032 20.0000 0.0008 2026.325839 0 0.0127 163 | 0/8 8 h-lim-p 0.0070 20.0000 0.0014 2026.325833 0 0.0417 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2026.325832 0 1.0938 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2026.325832 0 2.1875 225 | 0/8 11 h-lim-p 1.9056 20.0000 0.0000 2026.325832 0 0.8337 245 | 0/8 12 h-lim-p 2.1326 20.0000 0.0000 2026.325832 0 0.0010 275 Out... lnL = -2026.325832 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2026.325832 Node 7: lnL = -2026.325832 Node 8: lnL = -2026.325832 Node 9: lnL = -2026.325832 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 185 Sequential format.. Reading seq # 1: YKR006C_Sbay Reading seq # 2: YKR006C_Scer Reading seq # 3: YKR006C_Skud Reading seq # 4: YKR006C_Smik Reading seq # 5: YKR006C_Spar Sequences read.. Counting patterns.. # site patterns = 87 Counting frequencies.. 120 bytes for distance 13920 bytes for lkl0 11136 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.062161 0.107285 0.095124 0.191543 0.056380 0.149760 0.207709 0.058460 lnL0 = -823.562800 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 823.562800 x= 0.06216 0.10728 0.09512 0.19154 0.05638 0.14976 0.20771 0.05846 1 h-lim-p 0.0005 0.0041 23.1496 823.358070 0 0.0010 23 | 0/8 2 h-lim-p 0.0016 0.0300 15.2706 823.295806 2 0.0007 39 | 0/8 3 h-lim-p 0.0043 0.1544 2.6004 823.292702 5 0.0010 61 | 0/8 4 h-lim-p 0.0016 0.1086 1.5846 823.291808 5 0.0009 85 | 0/8 5 h-lim-p 0.0034 1.0664 0.4343 823.291693 3 0.0012 105 | 0/8 6 h-lim-p 0.0071 2.9267 0.0733 823.291537 0 0.0106 125 | 0/8 7 h-lim-p 0.0204 5.8327 0.0381 823.281363 0 0.1226 147 | 0/8 8 h-lim-p 0.0034 0.2581 1.3598 823.279494 2 0.0016 171 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 823.279471 2 1.0889 187 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 823.279471 0 1.0938 207 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 823.279471 0 2.1875 227 | 0/8 12 h-lim-p 2.1458 20.0000 0.0000 823.279471 0 0.9388 247 | 0/8 13 h-lim-p 1.7022 20.0000 0.0000 823.279471 0 0.0066 274 | 0/8 14 h-lim-p 0.0029 20.0000 0.0000 823.279471 0 0.0007 295 Out... lnL = -823.279471 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -823.279471 Node 7: lnL = -823.279471 Node 8: lnL = -823.279471 Node 9: lnL = -823.279471 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 187 Sequential format.. Reading seq # 1: YKR007W_Sbay Reading seq # 2: YKR007W_Scer Reading seq # 3: YKR007W_Skud Reading seq # 4: YKR007W_Smik Reading seq # 5: YKR007W_Spar Sequences read.. Counting patterns.. # site patterns = 91 Counting frequencies.. 120 bytes for distance 14560 bytes for lkl0 11648 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.068512 0.070095 0.112462 0.192505 0.087002 0.186544 0.195147 0.064671 lnL0 = -851.768607 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 851.768607 x= 0.06851 0.07009 0.11246 0.19250 0.08700 0.18654 0.19515 0.06467 1 h-lim-p 0.0013 0.0103 27.1862 851.439277 7 0.0009 38 | 0/8 2 h-lim-p 0.0018 0.0146 8.4710 851.409215 5 0.0009 60 | 0/8 3 h-lim-p 0.0023 0.1062 3.3084 851.403419 5 0.0012 83 | 0/8 4 h-lim-p 0.0052 0.1434 0.7749 851.403166 4 0.0009 107 | 0/8 5 h-lim-p 0.0028 2.3397 0.2454 851.403136 2 0.0011 131 | 0/8 6 h-lim-p 0.0126 10.9784 0.0211 851.403136 1 0.0016 155 | 0/8 7 h-lim-p 0.0243 20.0000 0.0013 851.403135 0 0.0243 175 | 0/8 8 h-lim-p 0.0151 20.0000 0.0022 851.403124 0 0.0908 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 851.403123 0 1.0938 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 851.403123 0 1.0938 237 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 851.403123 0 0.5469 258 | 0/8 12 h-lim-p 0.3596 20.0000 0.0000 851.403123 0 0.3596 278 | 0/8 13 h-lim-p 0.2461 20.0000 0.0000 851.403123 0 0.0308 300 | 0/8 14 h-lim-p 0.0173 20.0000 0.0000 851.403123 0 0.0000 337 Out... lnL = -851.403123 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -851.403123 Node 7: lnL = -851.403123 Node 8: lnL = -851.403123 Node 9: lnL = -851.403123 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 227 Sequential format.. Reading seq # 1: YKR008W_Sbay Reading seq # 2: YKR008W_Scer Reading seq # 3: YKR008W_Skud Reading seq # 4: YKR008W_Smik Reading seq # 5: YKR008W_Spar Sequences read.. Counting patterns.. # site patterns = 126 Counting frequencies.. 120 bytes for distance 20160 bytes for lkl0 16128 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.094980 0.031942 0.157993 0.148454 0.076260 0.178344 0.242366 0.090967 lnL0 = -984.612418 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 984.612418 x= 0.09498 0.03194 0.15799 0.14845 0.07626 0.17834 0.24237 0.09097 1 h-lim-p 0.0012 0.0094 74.6022 983.229286 8 0.0006 38 | 0/8 2 h-lim-p 0.0011 0.0086 16.4677 983.117995 4 0.0008 58 | 0/8 3 h-lim-p 0.0042 0.1297 3.3117 983.111124 6 0.0013 86 | 0/8 4 h-lim-p 0.0018 0.0578 2.4379 983.109324 2 0.0008 102 | 0/8 5 h-lim-p 0.0047 0.4791 0.4311 983.109206 4 0.0013 124 | 0/8 6 h-lim-p 0.0124 3.7871 0.0465 983.109204 1 0.0015 148 | 0/8 7 h-lim-p 0.0979 20.0000 0.0007 983.109166 0 0.5873 170 | 0/8 8 h-lim-p 0.0066 1.7134 0.0649 983.109099 2 0.0069 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 983.109099 0 1.0938 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 983.109099 0 1.0938 234 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 983.109099 0 0.0684 258 | 0/8 12 h-lim-p 0.0490 20.0000 0.0000 983.109099 0 0.0122 279 | 0/8 13 h-lim-p 0.0081 20.0000 0.0000 983.109099 0 0.0000 320 Out... lnL = -983.109099 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -983.109099 Node 7: lnL = -983.109099 Node 8: lnL = -983.109099 Node 9: lnL = -983.109099 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 884 Sequential format.. Reading seq # 1: YKR009C_Sbay Reading seq # 2: YKR009C_Scer Reading seq # 3: YKR009C_Skud Reading seq # 4: YKR009C_Smik Reading seq # 5: YKR009C_Spar Sequences read.. Counting patterns.. # site patterns = 406 Counting frequencies.. 120 bytes for distance 64960 bytes for lkl0 51968 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.237792 0.013098 0.100541 0.166804 0.141211 0.319365 0.369928 0.231905 lnL0 = -4500.723417 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4500.723417 x= 0.23779 0.01310 0.10054 0.16680 0.14121 0.31937 0.36993 0.23191 1 h-lim-p 0.0032 0.7847 167.7539 4497.415615 7 0.0003 41 | 0/8 2 h-lim-p 0.0011 0.0090 24.1417 4497.259462 2 0.0005 57 | 0/8 3 h-lim-p 0.0007 0.0244 18.5094 4497.188245 5 0.0006 78 | 0/8 4 h-lim-p 0.0016 0.0475 6.9300 4497.175265 4 0.0007 99 | 0/8 5 h-lim-p 0.0028 0.1822 1.6741 4497.174085 4 0.0009 120 | 0/8 6 h-lim-p 0.0143 1.3565 0.1062 4497.174080 0 0.0008 135 | 0/8 7 h-lim-p 0.0042 20.0000 0.0198 4497.174071 0 0.0084 156 | 0/8 8 h-lim-p 0.0203 20.0000 0.0082 4497.172659 0 0.1622 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 4497.172608 1 0.9961 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4497.172608 0 1.0938 221 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4497.172608 0 1.0938 241 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4497.172608 0 3.7500 261 | 0/8 13 h-lim-p 2.1907 20.0000 0.0000 4497.172608 0 0.0003 293 Out... lnL = -4497.172608 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4497.172608 Node 7: lnL = -4497.172608 Node 8: lnL = -4497.172608 Node 9: lnL = -4497.172608 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 838 Sequential format.. Reading seq # 1: YKR011C_Sbay Reading seq # 2: YKR011C_Scer Reading seq # 3: YKR011C_Skud Reading seq # 4: YKR011C_Smik Reading seq # 5: YKR011C_Spar Sequences read.. Counting patterns.. # site patterns = 324 Counting frequencies.. 120 bytes for distance 51840 bytes for lkl0 41472 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.199298 0.100652 0.036327 0.151953 0.107256 0.214688 0.242723 0.194566 lnL0 = -3818.459162 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3818.459162 x= 0.19930 0.10065 0.03633 0.15195 0.10726 0.21469 0.24272 0.19457 1 h-lim-p 0.0007 0.0055 143.7757 3816.963222 2 0.0002 27 | 0/8 2 h-lim-p 0.0006 0.0047 31.8358 3816.818878 5 0.0003 51 | 0/8 3 h-lim-p 0.0008 0.0373 12.2737 3816.797149 5 0.0003 72 | 0/8 4 h-lim-p 0.0009 0.0717 4.7737 3816.791999 5 0.0005 97 | 0/8 5 h-lim-p 0.0019 0.2236 1.3351 3816.791498 3 0.0006 117 | 0/8 6 h-lim-p 0.0019 0.9016 0.4280 3816.791449 3 0.0006 138 | 0/8 7 h-lim-p 0.0024 3.5804 0.0994 3816.791446 1 0.0006 161 | 0/8 8 h-lim-p 0.1298 20.0000 0.0005 3816.790750 0 1.0380 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3816.790744 0 1.0938 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3816.790744 0 1.0938 224 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3816.790744 0 2.1875 244 | 0/8 12 h-lim-p 2.0146 20.0000 0.0000 3816.790744 0 0.8814 264 | 0/8 13 h-lim-p 2.1932 20.0000 0.0000 3816.790744 0 0.0086 291 Out... lnL = -3816.790744 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3816.790744 Node 7: lnL = -3816.790744 Node 8: lnL = -3816.790744 Node 9: lnL = -3816.790744 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 879 Sequential format.. Reading seq # 1: YKR014C_Sbay Reading seq # 2: YKR014C_Scer Reading seq # 3: YKR014C_Skud Reading seq # 4: YKR014C_Smik Reading seq # 5: YKR014C_Spar Sequences read.. Counting patterns.. # site patterns = 361 Counting frequencies.. 120 bytes for distance 57760 bytes for lkl0 46208 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.209119 0.042970 0.081479 0.195254 0.134139 0.221930 0.285595 0.203954 lnL0 = -4249.776197 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4249.776197 x= 0.20912 0.04297 0.08148 0.19525 0.13414 0.22193 0.28560 0.20395 1 h-lim-p 0.0004 0.0033 149.3222 4246.895020 7 0.0003 39 | 0/8 2 h-lim-p 0.0005 0.0039 56.8266 4246.316000 7 0.0004 69 | 0/8 3 h-lim-p 0.0008 0.0136 27.2936 4246.202473 2 0.0004 85 | 0/8 4 h-lim-p 0.0012 0.0384 9.0965 4246.181662 2 0.0006 101 | 0/8 5 h-lim-p 0.0031 0.1059 1.6634 4246.180986 3 0.0005 122 | 0/8 6 h-lim-p 0.0028 1.3202 0.2961 4246.180968 2 0.0005 141 | 0/8 7 h-lim-p 0.0033 9.4031 0.0424 4246.180967 0 0.0007 162 | 0/8 8 h-lim-p 0.0833 20.0000 0.0004 4246.180841 0 0.9991 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4246.180837 0 1.0938 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4246.180837 0 1.0938 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4246.180837 0 1.0938 245 | 0/8 12 h-lim-p 1.5577 20.0000 0.0000 4246.180837 0 1.5577 265 | 0/8 13 h-lim-p 2.3030 20.0000 0.0000 4246.180837 0 2.3030 285 | 0/8 14 h-lim-p 2.0919 20.0000 0.0000 4246.180837 0 0.2615 307 | 0/8 15 h-lim-p 0.0750 20.0000 0.0000 4246.180837 0 0.0012 332 Out... lnL = -4246.180837 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4246.180837 Node 7: lnL = -4246.180837 Node 8: lnL = -4246.180837 Node 9: lnL = -4246.180837 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 869 Sequential format.. Reading seq # 1: YKR015C_Sbay Reading seq # 2: YKR015C_Scer Reading seq # 3: YKR015C_Skud Reading seq # 4: YKR015C_Smik Reading seq # 5: YKR015C_Spar Sequences read.. Counting patterns.. # site patterns = 428 Counting frequencies.. 120 bytes for distance 68480 bytes for lkl0 54784 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.277969 0.125965 0.128798 0.203475 0.155601 0.264856 0.496384 0.270595 lnL0 = -4594.261017 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4594.261017 x= 0.27797 0.12596 0.12880 0.20347 0.15560 0.26486 0.49638 0.27059 1 h-lim-p 0.1058 4.3343 29.4699 4594.015688 7 0.0006 46 | 0/8 2 h-lim-p 0.0014 0.0289 11.9185 4593.978574 3 0.0006 64 | 0/8 3 h-lim-p 0.0011 0.0693 6.4503 4593.968095 5 0.0007 89 | 0/8 4 h-lim-p 0.0014 0.1659 3.0436 4593.963776 2 0.0012 105 | 0/8 5 h-lim-p 0.0037 0.5761 1.0039 4593.963068 2 0.0016 121 | 0/8 6 h-lim-p 0.0026 0.6933 0.6140 4593.962955 3 0.0008 141 | 0/8 7 h-lim-p 0.0091 6.4120 0.0568 4593.962953 1 0.0011 165 | 0/8 8 h-lim-p 0.2492 20.0000 0.0003 4593.962897 0 0.9969 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4593.962897 0 1.0938 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4593.962897 0 1.0938 227 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4593.962897 0 0.6250 248 | 0/8 12 h-lim-p 0.5037 20.0000 0.0000 4593.962897 0 0.5037 268 | 0/8 13 h-lim-p 0.3918 20.0000 0.0000 4593.962897 0 0.3918 288 | 0/8 14 h-lim-p 0.3517 20.0000 0.0000 4593.962897 0 0.0000 328 Out... lnL = -4593.962897 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4593.962897 Node 7: lnL = -4593.962897 Node 8: lnL = -4593.962897 Node 9: lnL = -4593.962897 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 849 Sequential format.. Reading seq # 1: YKR016W_Sbay Reading seq # 2: YKR016W_Scer Reading seq # 3: YKR016W_Skud Reading seq # 4: YKR016W_Smik Reading seq # 5: YKR016W_Spar Sequences read.. Counting patterns.. # site patterns = 395 Counting frequencies.. 120 bytes for distance 63200 bytes for lkl0 50560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.262919 0.000060 0.377961 0.457527 0.462138 0.536039 0.509123 0.255943 lnL0 = -4669.642451 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4669.642451 x= 0.26292 0.00006 0.37796 0.45753 0.46214 0.53604 0.50912 0.25594 1 h-lim-p 0.0000 0.0000 454.5506 4669.501552 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0002 3167.1097 4519.315528 3 0.0001 44 | 1/8 3 h-lim-p 0.0013 0.0104 54.9050 4516.463711 0 0.0026 57 | 1/8 4 h-lim-p 0.0032 0.0254 27.7760 4515.352173 3 0.0032 75 | 1/8 5 h-lim-p 0.0046 0.0367 9.9547 4515.278247 6 0.0015 101 | 1/8 6 h-lim-p 0.0044 0.1486 3.3289 4515.224455 3 0.0040 119 | 1/8 7 h-lim-p 0.0282 1.2145 0.4698 4506.569082 0 0.3386 134 | 1/8 8 h-lim-p 1.0817 8.6537 0.0326 4506.476841 7 0.2812 170 | 1/8 9 h-lim-p 0.6204 20.0000 0.0148 4506.454879 4 0.4987 197 | 1/8 10 h-lim-p 2.5000 20.0000 0.0025 4506.454423 2 0.5444 221 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 4506.454423 0 1.0938 240 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 4506.454422 0 1.0938 259 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 4506.454422 0 1.0938 278 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 4506.454422 0 1.0938 297 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 4506.454422 0 1.0938 316 | 1/8 16 h-lim-p 2.0895 20.0000 0.0000 4506.454422 0 2.0895 335 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 4506.454422 0 0.6250 355 | 1/8 18 h-lim-p 0.2341 20.0000 0.0000 4506.454422 0 0.0000 396 Out... lnL = -4506.454422 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4506.454422 Node 7: lnL = -4506.454422 Node 8: lnL = -4506.454422 Node 9: lnL = -4506.454422 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 371 Sequential format.. Reading seq # 1: YKR018C_Sbay Reading seq # 2: YKR018C_Scer Reading seq # 3: YKR018C_Skud Reading seq # 4: YKR018C_Smik Reading seq # 5: YKR018C_Spar Sequences read.. Counting patterns.. # site patterns = 171 Counting frequencies.. 120 bytes for distance 27360 bytes for lkl0 21888 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.120476 0.030787 0.101208 0.124032 0.098167 0.235364 0.278159 0.108513 lnL0 = -1636.842370 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1636.842370 x= 0.12048 0.03079 0.10121 0.12403 0.09817 0.23536 0.27816 0.10851 1 h-lim-p 0.0017 0.0135 88.2426 1635.653738 3 0.0004 29 | 0/8 2 h-lim-p 0.0022 0.0227 13.9077 1635.564945 3 0.0009 47 | 0/8 3 h-lim-p 0.0022 0.0672 6.0088 1635.552439 6 0.0008 71 | 0/8 4 h-lim-p 0.0018 0.0627 2.7436 1635.550585 5 0.0006 96 | 0/8 5 h-lim-p 0.0033 0.7681 0.5081 1635.550464 3 0.0010 117 | 0/8 6 h-lim-p 0.0025 1.1009 0.1983 1635.550448 2 0.0009 141 | 0/8 7 h-lim-p 0.0132 9.9048 0.0142 1635.550447 0 0.0014 163 | 0/8 8 h-lim-p 0.1073 20.0000 0.0002 1635.550426 0 0.8584 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1635.550424 0 1.0938 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1635.550424 0 1.0938 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1635.550424 0 2.5000 246 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1635.550424 0 0.1562 269 | 0/8 13 h-lim-p 0.0831 20.0000 0.0000 1635.550424 0 0.0006 295 Out... lnL = -1635.550424 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1635.550424 Node 7: lnL = -1635.550424 Node 8: lnL = -1635.550424 Node 9: lnL = -1635.550424 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 286 Sequential format.. Reading seq # 1: YKR019C_Sbay Reading seq # 2: YKR019C_Scer Reading seq # 3: YKR019C_Skud Reading seq # 4: YKR019C_Smik Reading seq # 5: YKR019C_Spar Sequences read.. Counting patterns.. # site patterns = 90 Counting frequencies.. 120 bytes for distance 14400 bytes for lkl0 11520 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.099762 0.030483 0.064086 0.092861 0.034598 0.135750 0.106321 0.092522 lnL0 = -1092.335734 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1092.335734 x= 0.09976 0.03048 0.06409 0.09286 0.03460 0.13575 0.10632 0.09252 1 h-lim-p 0.0032 0.0256 59.0059 1091.950470 7 0.0002 41 | 0/8 2 h-lim-p 0.0014 0.0134 10.0339 1091.924066 4 0.0005 61 | 0/8 3 h-lim-p 0.0007 0.0299 7.4740 1091.919749 6 0.0002 89 | 0/8 4 h-lim-p 0.0012 0.1632 1.3601 1091.919363 4 0.0004 110 | 0/8 5 h-lim-p 0.0032 1.0110 0.1871 1091.919354 2 0.0005 129 | 0/8 6 h-lim-p 0.0082 19.7154 0.0120 1091.919354 0 0.0009 151 | 0/8 7 h-lim-p 0.0278 20.0000 0.0004 1091.919354 0 0.0243 171 | 0/8 8 h-lim-p 0.0045 20.0000 0.0021 1091.919352 0 0.0272 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1091.919352 0 1.0938 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1091.919352 0 0.0012 243 Out... lnL = -1091.919352 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1091.919352 Node 7: lnL = -1091.919352 Node 8: lnL = -1091.919352 Node 9: lnL = -1091.919352 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 286 Sequential format.. Reading seq # 1: YKR020W_Sbay Reading seq # 2: YKR020W_Scer Reading seq # 3: YKR020W_Skud Reading seq # 4: YKR020W_Smik Reading seq # 5: YKR020W_Spar Sequences read.. Counting patterns.. # site patterns = 90 Counting frequencies.. 120 bytes for distance 14400 bytes for lkl0 11520 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.100268 0.033940 0.059374 0.094540 0.032918 0.137938 0.105311 0.093025 lnL0 = -1092.269308 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1092.269308 x= 0.10027 0.03394 0.05937 0.09454 0.03292 0.13794 0.10531 0.09303 1 h-lim-p 0.0036 0.0285 56.9657 1091.915172 6 0.0002 36 | 0/8 2 h-lim-p 0.0007 0.0056 10.9187 1091.896718 3 0.0003 54 | 0/8 3 h-lim-p 0.0004 0.0220 8.3164 1091.886911 2 0.0004 70 | 0/8 4 h-lim-p 0.0041 0.3368 0.7921 1091.886772 2 0.0005 88 | 0/8 5 h-lim-p 0.0050 1.7056 0.0716 1091.886771 0 0.0005 110 | 0/8 6 h-lim-p 0.0050 20.0000 0.0078 1091.886771 0 0.0011 131 | 0/8 7 h-lim-p 0.0481 20.0000 0.0002 1091.886753 0 0.7694 155 | 0/8 8 h-lim-p 0.0333 20.0000 0.0041 1091.886753 0 0.0009 179 | 0/8 9 h-lim-p 0.1919 20.0000 0.0000 1091.886753 0 1.1511 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1091.886753 0 1.0938 221 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1091.886753 0 2.5000 241 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1091.886753 0 0.0000 290 Out... lnL = -1091.886753 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1091.886753 Node 7: lnL = -1091.886753 Node 8: lnL = -1091.886753 Node 9: lnL = -1091.886753 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 295 Sequential format.. Reading seq # 1: YKR022C_Sbay Reading seq # 2: YKR022C_Scer Reading seq # 3: YKR022C_Skud Reading seq # 4: YKR022C_Smik Reading seq # 5: YKR022C_Spar Sequences read.. Counting patterns.. # site patterns = 150 Counting frequencies.. 120 bytes for distance 24000 bytes for lkl0 19200 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.199203 0.101787 0.000060 0.175222 0.126648 0.316789 0.351082 0.184339 lnL0 = -1314.727197 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1314.727197 x= 0.19920 0.10179 0.00006 0.17522 0.12665 0.31679 0.35108 0.18434 1 h-lim-p 0.0008 0.0062 35.5802 1314.162483 4 0.0008 30 | 0/8 2 h-lim-p 0.0004 0.0034 26.3219 1313.998155 0 0.0006 42 | 0/8 3 h-lim-p 0.0015 0.0423 11.4707 1313.930065 3 0.0013 60 | 0/8 4 h-lim-p 0.0016 0.0391 9.3302 1313.845156 0 0.0033 73 | 0/8 5 h-lim-p 0.0065 0.0522 2.0280 1313.841740 5 0.0019 98 | 0/8 6 h-lim-p 0.0066 0.4026 0.5706 1313.841552 3 0.0012 117 | 0/8 7 h-lim-p 0.0194 4.3000 0.0367 1313.841519 2 0.0128 143 | 0/8 8 h-lim-p 0.0446 4.1574 0.0105 1313.839889 0 0.2676 165 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 1313.839848 2 0.9961 189 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1313.839847 0 1.0938 209 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1313.839847 0 0.0098 236 | 0/8 12 h-lim-p 0.0097 20.0000 0.0000 1313.839847 0 0.0000 272 Out... lnL = -1313.839847 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1313.839847 Node 7: lnL = -1313.839847 Node 8: lnL = -1313.839847 Node 9: lnL = -1313.839847 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 847 Sequential format.. Reading seq # 1: YKR027W_Sbay Reading seq # 2: YKR027W_Scer Reading seq # 3: YKR027W_Skud Reading seq # 4: YKR027W_Smik Reading seq # 5: YKR027W_Spar Sequences read.. Counting patterns.. # site patterns = 425 Counting frequencies.. 120 bytes for distance 68000 bytes for lkl0 54400 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.187525 0.154010 0.000060 0.253217 0.327820 0.345116 0.343306 0.170882 lnL0 = -4400.231614 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4400.231614 x= 0.18753 0.15401 0.00006 0.25322 0.32782 0.34512 0.34331 0.17088 1 h-lim-p 0.0000 0.0000 94.4294 4400.208524 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0107 71.5736 4398.959746 0 0.0006 40 | 1/8 3 h-lim-p 0.0029 0.0458 15.5822 4398.839248 6 0.0010 65 | 1/8 4 h-lim-p 0.0048 0.1270 3.4289 4398.827531 6 0.0013 91 | 1/8 5 h-lim-p 0.0026 0.2412 1.8039 4398.803733 0 0.0051 104 | 1/8 6 h-lim-p 0.0187 0.9638 0.4924 4395.742839 0 0.1495 119 | 0/8 7 h-lim-p 0.0064 0.0511 7.0023 4395.728573 4 0.0006 148 | 0/8 8 h-lim-p 0.0001 0.0007 4.3889 4395.726635 0 0.0003 162 | 0/8 9 h-lim-p 0.1249 20.0000 0.0116 4395.680424 0 0.9994 177 | 0/8 10 h-lim-p 2.5000 20.0000 0.0025 4395.677170 3 1.0004 203 | 0/8 11 h-lim-p 2.5000 20.0000 0.0002 4395.677145 2 0.7996 228 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4395.677144 0 1.0938 248 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 4395.677144 0 1.0938 268 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 4395.677144 0 1.0938 288 | 0/8 15 h-lim-p 2.1905 20.0000 0.0000 4395.677144 0 1.0952 308 | 0/8 16 h-lim-p 0.9986 20.0000 0.0000 4395.677144 0 0.0001 340 Out... lnL = -4395.677144 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4395.677144 Node 7: lnL = -4395.677144 Node 8: lnL = -4395.677144 Node 9: lnL = -4395.677144 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 69 Sequential format.. Reading seq # 1: YKR034W_Sbay Reading seq # 2: YKR034W_Scer Reading seq # 3: YKR034W_Skud Reading seq # 4: YKR034W_Smik Reading seq # 5: YKR034W_Spar Sequences read.. Counting patterns.. # site patterns = 32 Counting frequencies.. 120 bytes for distance 5120 bytes for lkl0 4096 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.028415 0.017066 0.058317 0.031615 0.035846 0.134135 0.057221 0.024048 lnL0 = -200.174387 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 200.174387 x= 0.02841 0.01707 0.05832 0.03161 0.03585 0.13414 0.05722 0.02405 1 h-lim-p 0.0001 0.0006 33.0983 199.646026 m 0.0006 22 | 1/8 2 h-lim-p 0.0007 0.0167 12.0754 199.609406 3 0.0007 40 | 1/8 3 h-lim-p 0.0052 0.0807 1.7378 199.607041 6 0.0016 68 | 1/8 4 h-lim-p 0.0021 0.0478 1.3525 199.606517 4 0.0008 88 | 1/8 5 h-lim-p 0.0057 2.6988 0.1965 199.606496 3 0.0010 109 | 1/8 6 h-lim-p 0.0063 1.2788 0.0314 199.606479 3 0.0048 134 | 1/8 7 h-lim-p 0.0110 3.8418 0.0137 199.602331 0 0.1765 157 | 1/8 8 h-lim-p 2.5000 20.0000 0.0002 199.602302 2 1.0889 180 | 1/8 9 h-lim-p 2.5000 20.0000 0.0000 199.602302 0 1.0938 199 | 1/8 10 h-lim-p 2.5000 20.0000 0.0000 199.602302 0 1.0938 218 | 1/8 11 h-lim-p 1.3440 20.0000 0.0000 199.602302 0 2.6881 238 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 199.602302 0 0.5469 258 | 1/8 13 h-lim-p 0.0672 20.0000 0.0000 199.602302 0 0.0168 278 | 1/8 14 h-lim-p 0.0058 20.0000 0.0000 199.602302 0 0.0000 304 Out... lnL = -199.602302 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -199.602302 Node 7: lnL = -199.602302 Node 8: lnL = -199.602302 Node 9: lnL = -199.602302 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 307 Sequential format.. Reading seq # 1: YKR036C_Sbay Reading seq # 2: YKR036C_Scer Reading seq # 3: YKR036C_Skud Reading seq # 4: YKR036C_Smik Reading seq # 5: YKR036C_Spar Sequences read.. Counting patterns.. # site patterns = 143 Counting frequencies.. 120 bytes for distance 22880 bytes for lkl0 18304 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.190917 0.035653 0.099290 0.166871 0.100164 0.128534 0.177227 0.179134 lnL0 = -1286.664451 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1286.664451 x= 0.19092 0.03565 0.09929 0.16687 0.10016 0.12853 0.17723 0.17913 1 h-lim-p 0.0016 0.0130 57.4387 1285.774589 7 0.0006 38 | 0/8 2 h-lim-p 0.0010 0.0081 18.5916 1285.601861 6 0.0011 62 | 0/8 3 h-lim-p 0.0026 0.0444 7.5612 1285.585116 5 0.0007 85 | 0/8 4 h-lim-p 0.0032 0.1525 1.6471 1285.583679 4 0.0011 106 | 0/8 5 h-lim-p 0.0057 0.5073 0.3251 1285.583631 3 0.0009 126 | 0/8 6 h-lim-p 0.0114 10.8022 0.0264 1285.583630 1 0.0023 149 | 0/8 7 h-lim-p 0.0103 20.0000 0.0058 1285.583626 0 0.0206 170 | 0/8 8 h-lim-p 0.0125 20.0000 0.0096 1285.583427 0 0.0500 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1285.583421 1 0.9961 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1285.583421 0 1.0938 234 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1285.583421 0 2.1875 254 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1285.583421 0 0.0098 281 Out... lnL = -1285.583421 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1285.583421 Node 7: lnL = -1285.583421 Node 8: lnL = -1285.583421 Node 9: lnL = -1285.583421 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 232 Sequential format.. Reading seq # 1: YKR037C_Sbay Reading seq # 2: YKR037C_Scer Reading seq # 3: YKR037C_Skud Reading seq # 4: YKR037C_Smik Reading seq # 5: YKR037C_Spar Sequences read.. Counting patterns.. # site patterns = 139 Counting frequencies.. 120 bytes for distance 22240 bytes for lkl0 17792 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.218454 0.042757 0.113350 0.215718 0.138068 0.237230 0.277438 0.202776 lnL0 = -1058.867572 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1058.867572 x= 0.21845 0.04276 0.11335 0.21572 0.13807 0.23723 0.27744 0.20278 1 h-lim-p 0.0024 0.0191 26.5696 1058.378100 8 0.0015 42 | 0/8 2 h-lim-p 0.0027 0.0212 10.7651 1058.285810 7 0.0018 72 | 0/8 3 h-lim-p 0.0047 0.0999 4.1144 1058.274154 7 0.0016 104 | 0/8 4 h-lim-p 0.0049 0.3000 1.3554 1058.271795 5 0.0029 129 | 0/8 5 h-lim-p 0.0124 1.3046 0.3177 1058.271670 2 0.0027 146 | 0/8 6 h-lim-p 0.0504 14.6622 0.0170 1058.271670 0 0.0028 169 | 0/8 7 h-lim-p 0.0195 20.0000 0.0024 1058.271670 0 0.0171 189 | 0/8 8 h-lim-p 0.0727 20.0000 0.0006 1058.271661 0 0.2909 211 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1058.271661 0 1.0938 231 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1058.271661 0 1.0938 251 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1058.271661 0 2.1875 271 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1058.271661 0 0.0000 315 Out... lnL = -1058.271661 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1058.271661 Node 7: lnL = -1058.271661 Node 8: lnL = -1058.271661 Node 9: lnL = -1058.271661 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 895 Sequential format.. Reading seq # 1: YKR038C_Sbay Reading seq # 2: YKR038C_Scer Reading seq # 3: YKR038C_Skud Reading seq # 4: YKR038C_Smik Reading seq # 5: YKR038C_Spar Sequences read.. Counting patterns.. # site patterns = 478 Counting frequencies.. 120 bytes for distance 76480 bytes for lkl0 61184 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.381170 0.000060 0.170736 0.347214 0.570015 0.371734 0.448021 0.357712 lnL0 = -4977.520677 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4977.520677 x= 0.38117 0.00006 0.17074 0.34721 0.57001 0.37173 0.44802 0.35771 1 h-lim-p 0.0000 0.0000 237.2876 4977.474411 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0021 303.7872 4948.779084 8 0.0010 60 | 1/8 3 h-lim-p 0.0021 0.0166 37.3957 4947.039161 1 0.0026 74 | 1/8 4 h-lim-p 0.0192 0.1539 4.2229 4946.897309 4 0.0074 94 | 1/8 5 h-lim-p 0.0331 0.4928 0.9477 4943.507295 0 0.1323 108 | 1/8 6 h-lim-p 0.0040 0.0317 17.3354 4938.991443 0 0.0079 128 | 0/8 7 h-lim-p 0.0012 0.0099 71.4861 4938.001433 7 0.0008 157 | 0/8 8 h-lim-p 0.0024 0.0194 4.1663 4937.990290 3 0.0012 175 | 0/8 9 h-lim-p 0.0399 3.0848 0.1250 4936.916379 0 0.4787 190 | 0/8 10 h-lim-p 2.5000 20.0000 0.0147 4936.846401 7 0.6966 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0039 4936.844519 4 0.6561 258 | 0/8 12 h-lim-p 2.5000 20.0000 0.0009 4936.844387 3 0.8855 286 | 0/8 13 h-lim-p 2.5000 20.0000 0.0001 4936.844384 0 1.0938 306 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 4936.844384 0 1.0938 326 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 4936.844384 0 1.0938 346 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 4936.844384 0 1.2500 366 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 4936.844384 0 2.5000 386 | 0/8 18 h-lim-p 1.6766 20.0000 0.0000 4936.844384 0 0.3668 407 | 0/8 19 h-lim-p 0.5790 20.0000 0.0000 4936.844384 0 0.2895 427 | 0/8 20 h-lim-p 0.3586 20.0000 0.0000 4936.844384 0 0.3586 447 | 0/8 21 h-lim-p 0.4639 20.0000 0.0000 4936.844384 0 0.1160 468 Out... lnL = -4936.844384 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4936.844384 Node 7: lnL = -4936.844384 Node 8: lnL = -4936.844384 Node 9: lnL = -4936.844384 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 843 Sequential format.. Reading seq # 1: YKR039W_Sbay Reading seq # 2: YKR039W_Scer Reading seq # 3: YKR039W_Skud Reading seq # 4: YKR039W_Smik Reading seq # 5: YKR039W_Spar Sequences read.. Counting patterns.. # site patterns = 319 Counting frequencies.. 120 bytes for distance 51040 bytes for lkl0 40832 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.217008 0.037669 0.046002 0.109719 0.083117 0.214630 1.047975 0.196487 lnL0 = -4138.513996 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4138.513996 x= 0.21701 0.03767 0.04600 0.10972 0.08312 0.21463 1.04798 0.19649 1 h-lim-p 0.0182 1.8894 67.4887 4138.099742 8 0.0002 46 | 0/8 2 h-lim-p 0.0007 0.0090 18.3162 4138.030433 6 0.0004 73 | 0/8 3 h-lim-p 0.0003 0.0094 25.8885 4137.932731 0 0.0006 86 | 0/8 4 h-lim-p 0.0007 0.0160 24.0093 4137.866374 6 0.0006 109 | 0/8 5 h-lim-p 0.0016 0.0414 8.8087 4137.855706 5 0.0004 132 | 0/8 6 h-lim-p 0.0017 0.1170 2.2107 4137.854553 4 0.0005 154 | 0/8 7 h-lim-p 0.3142 20.0000 0.0038 4137.854456 1 0.3142 168 | 0/8 8 h-lim-p 0.0313 15.0117 0.0382 4137.854214 1 0.0323 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4137.854213 0 1.0938 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4137.854213 0 1.0938 230 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4137.854213 0 0.0781 254 | 0/8 12 h-lim-p 0.0380 20.0000 0.0000 4137.854213 0 0.0000 284 Out... lnL = -4137.854213 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4137.854213 Node 7: lnL = -4137.854213 Node 8: lnL = -4137.854213 Node 9: lnL = -4137.854213 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 969 Sequential format.. Reading seq # 1: YKR041W_Sbay Reading seq # 2: YKR041W_Scer Reading seq # 3: YKR041W_Skud Reading seq # 4: YKR041W_Smik Reading seq # 5: YKR041W_Spar Sequences read.. Counting patterns.. # site patterns = 494 Counting frequencies.. 120 bytes for distance 79040 bytes for lkl0 63232 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.201186 0.322658 0.000060 0.491517 0.474873 0.610248 0.405164 0.179024 lnL0 = -4950.702187 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4950.702187 x= 0.20119 0.32266 0.00006 0.49152 0.47487 0.61025 0.40516 0.17902 1 h-lim-p 0.0000 0.0000 286.1253 4950.662596 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0024 187.9302 4916.640101 m 0.0024 39 | 1/8 3 h-lim-p -0.0000 -0.0000 58.5304 h-lim-p: -1.79868241e-19 -1.43894593e-18 5.85304227e+01 4916.640101 .. | 1/8 4 h-lim-p 0.0000 0.0024 179.9785 4902.012529 0 0.0010 65 | 1/8 5 h-lim-p 0.0008 0.0061 49.9869 4901.481624 8 0.0004 97 | 1/8 6 h-lim-p 0.0011 0.0262 20.7672 4901.310561 5 0.0009 119 | 1/8 7 h-lim-p 0.0041 0.0865 4.6504 4901.293894 4 0.0016 139 | 1/8 8 h-lim-p 0.0036 0.2631 2.0073 4901.287843 5 0.0027 163 | 1/8 9 h-lim-p 0.0065 0.9197 0.8357 4901.279710 0 0.0097 175 | 1/8 10 h-lim-p 0.0621 1.1707 0.1303 4900.888898 0 0.2483 196 | 1/8 11 h-lim-p 2.5000 20.0000 0.0087 4900.843038 6 0.9338 229 | 1/8 12 h-lim-p 2.5000 20.0000 0.0007 4900.842822 3 0.9482 254 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 4900.842822 0 1.0938 273 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 4900.842822 0 1.0938 292 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 4900.842822 0 2.1875 311 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 4900.842822 0 0.6250 331 | 1/8 17 h-lim-p 0.1487 20.0000 0.0000 4900.842822 0 0.0000 362 Out... lnL = -4900.842822 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4900.842822 Node 7: lnL = -4900.842822 Node 8: lnL = -4900.842822 Node 9: lnL = -4900.842822 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 315 Sequential format.. Reading seq # 1: YKR043C_Sbay Reading seq # 2: YKR043C_Scer Reading seq # 3: YKR043C_Skud Reading seq # 4: YKR043C_Smik Reading seq # 5: YKR043C_Spar Sequences read.. Counting patterns.. # site patterns = 135 Counting frequencies.. 120 bytes for distance 21600 bytes for lkl0 17280 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.196547 0.049522 0.119775 0.092712 0.076542 0.189780 0.154311 0.177170 lnL0 = -1419.376804 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1419.376804 x= 0.19655 0.04952 0.11978 0.09271 0.07654 0.18978 0.15431 0.17717 1 h-lim-p 0.0088 0.0702 36.4340 1419.065596 3 0.0005 31 | 0/8 2 h-lim-p 0.0020 0.0224 9.2632 1419.033970 4 0.0008 51 | 0/8 3 h-lim-p 0.0012 0.0522 5.9240 1419.027686 5 0.0005 74 | 0/8 4 h-lim-p 0.0037 0.2674 0.7748 1419.027445 2 0.0008 91 | 0/8 5 h-lim-p 0.0026 0.8639 0.2371 1419.027425 3 0.0008 120 | 0/8 6 h-lim-p 0.0027 3.5574 0.0670 1419.027423 1 0.0007 143 | 0/8 7 h-lim-p 0.0594 20.0000 0.0008 1419.027420 0 0.1188 164 | 0/8 8 h-lim-p 0.0059 5.0534 0.0152 1419.027393 0 0.0118 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1419.027392 0 1.0938 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1419.027392 0 1.0938 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1419.027392 0 3.7500 245 | 0/8 12 h-lim-p 2.2153 20.0000 0.0000 1419.027392 0 0.1211 268 | 0/8 13 h-lim-p 0.3394 20.0000 0.0000 1419.027392 0 0.0002 298 Out... lnL = -1419.027392 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1419.027392 Node 7: lnL = -1419.027392 Node 8: lnL = -1419.027392 Node 9: lnL = -1419.027392 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 321 Sequential format.. Reading seq # 1: YKR044W_Sbay Reading seq # 2: YKR044W_Scer Reading seq # 3: YKR044W_Skud Reading seq # 4: YKR044W_Smik Reading seq # 5: YKR044W_Spar Sequences read.. Counting patterns.. # site patterns = 136 Counting frequencies.. 120 bytes for distance 21760 bytes for lkl0 17408 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.137399 0.043244 0.111566 0.088519 0.080735 0.192344 0.159327 0.120234 lnL0 = -1383.568812 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1383.568812 x= 0.13740 0.04324 0.11157 0.08852 0.08073 0.19234 0.15933 0.12023 1 h-lim-p 0.0030 0.0243 63.3572 1382.793146 9 0.0004 45 | 0/8 2 h-lim-p 0.0017 0.0158 15.5453 1382.693384 4 0.0009 67 | 0/8 3 h-lim-p 0.0021 0.0497 6.4622 1382.685844 5 0.0004 91 | 0/8 4 h-lim-p 0.0019 0.1827 1.4195 1382.685086 3 0.0008 109 | 0/8 5 h-lim-p 0.0086 1.3154 0.1334 1382.685080 2 0.0006 128 | 0/8 6 h-lim-p 0.0028 9.3078 0.0272 1382.685080 0 0.0012 148 | 0/8 7 h-lim-p 0.0097 20.0000 0.0034 1382.685080 0 0.0085 168 | 0/8 8 h-lim-p 0.0262 20.0000 0.0011 1382.685047 0 0.2096 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1382.685044 0 1.0938 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1382.685044 0 1.0938 231 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1382.685044 0 2.1875 251 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1382.685044 0 0.3125 273 | 0/8 13 h-lim-p 0.1530 20.0000 0.0000 1382.685044 0 0.0383 294 | 0/8 14 h-lim-p 0.0203 20.0000 0.0000 1382.685044 0 0.0002 320 Out... lnL = -1382.685044 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1382.685044 Node 7: lnL = -1382.685044 Node 8: lnL = -1382.685044 Node 9: lnL = -1382.685044 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 237 Sequential format.. Reading seq # 1: YKR045C_Sbay Reading seq # 2: YKR045C_Scer Reading seq # 3: YKR045C_Skud Reading seq # 4: YKR045C_Smik Reading seq # 5: YKR045C_Spar Sequences read.. Counting patterns.. # site patterns = 99 Counting frequencies.. 120 bytes for distance 15840 bytes for lkl0 12672 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.167767 0.056210 0.063925 0.071831 0.063483 0.146448 0.172214 0.151574 lnL0 = -980.703997 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 980.703997 x= 0.16777 0.05621 0.06392 0.07183 0.06348 0.14645 0.17221 0.15157 1 h-lim-p 0.0006 0.0049 44.5863 980.203767 6 0.0005 33 | 0/8 2 h-lim-p 0.0014 0.0112 9.7075 980.177388 3 0.0006 51 | 0/8 3 h-lim-p 0.0009 0.0553 6.0214 980.166433 5 0.0008 76 | 0/8 4 h-lim-p 0.0031 0.1293 1.5429 980.165462 5 0.0009 101 | 0/8 5 h-lim-p 0.0037 0.6731 0.3703 980.165395 4 0.0011 123 | 0/8 6 h-lim-p 0.0024 0.8516 0.1643 980.165387 3 0.0007 151 | 0/8 7 h-lim-p 0.0089 13.9992 0.0131 980.165387 0 0.0019 172 | 0/8 8 h-lim-p 0.7032 20.0000 0.0000 980.165386 0 1.0547 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 980.165386 0 2.1875 212 | 0/8 10 h-lim-p 2.0528 20.0000 0.0000 980.165386 0 0.8981 232 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 980.165386 0 0.0021 261 Out... lnL = -980.165386 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -980.165386 Node 7: lnL = -980.165386 Node 8: lnL = -980.165386 Node 9: lnL = -980.165386 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 187 Sequential format.. Reading seq # 1: YKR046C_Sbay Reading seq # 2: YKR046C_Scer Reading seq # 3: YKR046C_Skud Reading seq # 4: YKR046C_Smik Reading seq # 5: YKR046C_Spar Sequences read.. Counting patterns.. # site patterns = 82 Counting frequencies.. 120 bytes for distance 13120 bytes for lkl0 10496 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.089378 0.075033 0.057739 0.073269 0.062625 0.116228 0.100216 0.077184 lnL0 = -696.941302 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 696.941302 x= 0.08938 0.07503 0.05774 0.07327 0.06263 0.11623 0.10022 0.07718 1 h-lim-p 0.0007 0.0057 70.4260 695.326223 5 0.0007 31 | 0/8 2 h-lim-p 0.0006 0.0047 26.1535 695.089531 0 0.0009 43 | 0/8 3 h-lim-p 0.0017 0.0136 11.7619 695.060071 7 0.0005 74 | 0/8 4 h-lim-p 0.0020 0.0988 3.0343 695.056506 4 0.0008 95 | 0/8 5 h-lim-p 0.0051 0.2775 0.4997 695.056395 4 0.0009 118 | 0/8 6 h-lim-p 0.0251 14.8733 0.0174 695.056009 0 0.0503 139 | 0/8 7 h-lim-p 0.0038 1.3270 0.2331 695.049786 0 0.0150 161 | 0/8 8 h-lim-p 0.0036 0.2228 0.9733 695.049271 5 0.0010 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 695.049150 2 1.1719 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 695.049149 0 1.0938 238 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 695.049149 0 1.2500 258 | 0/8 12 h-lim-p 2.3161 20.0000 0.0000 695.049149 0 0.5066 279 | 0/8 13 h-lim-p 0.2986 20.0000 0.0000 695.049149 0 0.0093 303 | 0/8 14 h-lim-p 0.0053 20.0000 0.0000 695.049149 0 0.0053 323 | 0/8 15 h-lim-p 0.0034 20.0000 0.0000 695.049149 0 0.0034 343 | 0/8 16 h-lim-p 0.0030 20.0000 0.0000 695.049149 0 0.0000 369 Out... lnL = -695.049149 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -695.049149 Node 7: lnL = -695.049149 Node 8: lnL = -695.049149 Node 9: lnL = -695.049149 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 225 Sequential format.. Reading seq # 1: YKR048C_Sbay Reading seq # 2: YKR048C_Scer Reading seq # 3: YKR048C_Skud Reading seq # 4: YKR048C_Smik Reading seq # 5: YKR048C_Spar Sequences read.. Counting patterns.. # site patterns = 124 Counting frequencies.. 120 bytes for distance 19840 bytes for lkl0 15872 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.379346 0.012799 0.090312 0.083248 0.086832 0.159971 0.294433 0.353666 lnL0 = -1036.862404 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1036.862404 x= 0.37935 0.01280 0.09031 0.08325 0.08683 0.15997 0.29443 0.35367 1 h-lim-p 0.0018 0.0142 45.5086 1036.017934 8 0.0009 41 | 0/8 2 h-lim-p 0.0017 0.0138 11.5188 1035.950107 6 0.0011 68 | 0/8 3 h-lim-p 0.0012 0.0327 9.8450 1035.901897 1 0.0016 82 | 0/8 4 h-lim-p 0.0026 0.0585 5.9790 1035.875711 5 0.0023 103 | 0/8 5 h-lim-p 0.0078 0.1018 1.7485 1035.873529 4 0.0017 123 | 0/8 6 h-lim-p 0.0049 0.3763 0.5937 1035.873219 3 0.0020 141 | 0/8 7 h-lim-p 0.0018 0.8898 0.6506 1035.872829 0 0.0036 162 | 0/8 8 h-lim-p 1.8393 20.0000 0.0013 1035.871744 5 1.2526 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1035.871739 1 0.9961 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1035.871739 0 1.0938 237 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1035.871739 0 2.1875 257 | 0/8 12 h-lim-p 1.8760 20.0000 0.0000 1035.871739 0 0.4690 278 | 0/8 13 h-lim-p 0.8420 20.0000 0.0000 1035.871739 0 0.0002 309 Out... lnL = -1035.871739 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1035.871739 Node 7: lnL = -1035.871739 Node 8: lnL = -1035.871739 Node 9: lnL = -1035.871739 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 549 Sequential format.. Reading seq # 1: YKR051W_Sbay Reading seq # 2: YKR051W_Scer Reading seq # 3: YKR051W_Skud Reading seq # 4: YKR051W_Smik Reading seq # 5: YKR051W_Spar Sequences read.. Counting patterns.. # site patterns = 262 Counting frequencies.. 120 bytes for distance 41920 bytes for lkl0 33536 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.270269 0.100464 0.000060 0.232740 0.174040 0.210755 0.323165 0.243640 lnL0 = -2671.573236 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2671.573236 x= 0.27027 0.10046 0.00006 0.23274 0.17404 0.21076 0.32316 0.24364 1 h-lim-p 0.0043 0.0345 60.4707 2670.918564 7 0.0003 41 | 0/8 2 h-lim-p 0.0002 0.0014 22.8104 2670.727774 0 0.0007 55 | 0/8 3 h-lim-p 0.0020 0.0470 7.7344 2670.692625 5 0.0013 80 | 0/8 4 h-lim-p 0.0019 0.0149 3.0211 2670.688728 3 0.0010 99 | 0/8 5 h-lim-p 0.0027 0.4471 1.1321 2670.688066 2 0.0012 115 | 0/8 6 h-lim-p 0.0053 1.1256 0.2487 2670.688013 1 0.0013 130 | 0/8 7 h-lim-p 0.0073 0.7777 0.0454 2670.687726 0 0.0146 151 | 0/8 8 h-lim-p 0.0049 0.4521 0.1346 2670.675797 0 0.0395 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 2670.675758 2 0.9961 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2670.675758 0 1.0938 218 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2670.675758 0 0.5469 239 | 0/8 12 h-lim-p 0.5610 20.0000 0.0000 2670.675758 0 0.0011 267 Out... lnL = -2670.675758 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2670.675758 Node 7: lnL = -2670.675758 Node 8: lnL = -2670.675758 Node 9: lnL = -2670.675758 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 293 Sequential format.. Reading seq # 1: YKR055W_Sbay Reading seq # 2: YKR055W_Scer Reading seq # 3: YKR055W_Skud Reading seq # 4: YKR055W_Smik Reading seq # 5: YKR055W_Spar Sequences read.. Counting patterns.. # site patterns = 144 Counting frequencies.. 120 bytes for distance 23040 bytes for lkl0 18432 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.101292 0.060890 0.101691 0.118848 0.110831 0.101083 0.246027 0.084205 lnL0 = -1268.176146 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1268.176146 x= 0.10129 0.06089 0.10169 0.11885 0.11083 0.10108 0.24603 0.08420 1 h-lim-p 0.0026 0.7344 98.5886 1265.899825 4 0.0005 31 | 0/8 2 h-lim-p 0.0017 0.0140 13.0150 1265.842087 4 0.0007 51 | 0/8 3 h-lim-p 0.0045 0.0837 1.9929 1265.840278 3 0.0009 70 | 0/8 4 h-lim-p 0.0021 0.2436 0.8851 1265.840024 4 0.0008 92 | 0/8 5 h-lim-p 0.0054 2.5523 0.1263 1265.840013 2 0.0013 117 | 0/8 6 h-lim-p 0.0038 6.0648 0.0441 1265.840011 0 0.0017 137 | 0/8 7 h-lim-p 0.0267 20.0000 0.0028 1265.839942 0 0.2136 160 | 0/8 8 h-lim-p 0.0064 9.5990 0.0916 1265.839603 0 0.0096 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1265.839590 1 0.9961 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1265.839590 0 1.2500 222 | 0/8 11 h-lim-p 1.9982 20.0000 0.0000 1265.839590 0 0.4995 243 | 0/8 12 h-lim-p 0.2697 20.0000 0.0000 1265.839590 0 0.0000 287 Out... lnL = -1265.839590 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1265.839590 Node 7: lnL = -1265.839590 Node 8: lnL = -1265.839590 Node 9: lnL = -1265.839590 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 490 Sequential format.. Reading seq # 1: YKR056W_Sbay Reading seq # 2: YKR056W_Scer Reading seq # 3: YKR056W_Skud Reading seq # 4: YKR056W_Smik Reading seq # 5: YKR056W_Spar Sequences read.. Counting patterns.. # site patterns = 241 Counting frequencies.. 120 bytes for distance 38560 bytes for lkl0 30848 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.133874 0.083976 0.140851 0.280254 0.097237 0.293563 0.239506 0.108566 lnL0 = -2295.026483 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2295.026483 x= 0.13387 0.08398 0.14085 0.28025 0.09724 0.29356 0.23951 0.10857 1 h-lim-p 0.0009 0.0069 60.6302 2293.626132 2 0.0008 26 | 0/8 2 h-lim-p 0.0004 0.0035 47.1930 2293.079415 0 0.0009 39 | 0/8 3 h-lim-p 0.0072 0.0666 5.8172 2293.063309 6 0.0010 65 | 0/8 4 h-lim-p 0.0042 0.2216 1.3638 2293.062579 4 0.0008 86 | 0/8 5 h-lim-p 0.0025 0.6877 0.4243 2293.062382 3 0.0015 106 | 0/8 6 h-lim-p 0.0040 1.5756 0.1588 2293.061859 0 0.0080 127 | 0/8 7 h-lim-p 0.0046 1.2876 0.2766 2293.050480 0 0.0184 149 | 0/8 8 h-lim-p 0.0026 0.2146 1.9438 2293.022112 0 0.0052 170 | 0/8 9 h-lim-p 2.5000 20.0000 0.0017 2293.020667 3 1.0449 188 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2293.020666 0 1.0938 208 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2293.020666 0 1.0938 228 | 0/8 12 h-lim-p 2.0309 20.0000 0.0000 2293.020666 0 0.8885 248 | 0/8 13 h-lim-p 0.6615 20.0000 0.0000 2293.020666 0 0.0413 271 | 0/8 14 h-lim-p 0.0077 20.0000 0.0000 2293.020666 0 0.0034 291 | 0/8 15 h-lim-p 0.0042 20.0000 0.0000 2293.020666 0 0.0021 311 | 0/8 16 h-lim-p 0.0003 20.0000 0.0001 2293.020666 0 0.0000 335 | 0/8 17 h-lim-p 0.0037 20.0000 0.0000 2293.020666 0 0.0001 360 Out... lnL = -2293.020666 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2293.020666 Node 7: lnL = -2293.020666 Node 8: lnL = -2293.020666 Node 9: lnL = -2293.020666 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 831 Sequential format.. Reading seq # 1: YKR058W_Sbay Reading seq # 2: YKR058W_Scer Reading seq # 3: YKR058W_Skud Reading seq # 4: YKR058W_Smik Reading seq # 5: YKR058W_Spar Sequences read.. Counting patterns.. # site patterns = 156 Counting frequencies.. 120 bytes for distance 24960 bytes for lkl0 19968 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.089213 0.044166 0.056595 0.080663 0.068846 0.135319 0.099839 0.077286 lnL0 = -2197.197305 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2197.197305 x= 0.08921 0.04417 0.05659 0.08066 0.06885 0.13532 0.09984 0.07729 1 h-lim-p 0.0007 0.0054 112.2515 2195.846132 8 0.0002 44 | 0/8 2 h-lim-p 0.0006 0.0045 29.1244 2195.725667 5 0.0003 67 | 0/8 3 h-lim-p 0.0023 0.0478 3.8458 2195.723684 3 0.0003 88 | 0/8 4 h-lim-p 0.0011 0.1648 0.9133 2195.723557 4 0.0003 110 | 0/8 5 h-lim-p 0.0013 0.7270 0.2235 2195.723546 2 0.0004 135 | 0/8 6 h-lim-p 0.0019 5.2110 0.0498 2195.723546 0 0.0004 156 | 0/8 7 h-lim-p 0.0377 20.0000 0.0006 2195.723546 0 0.0330 176 | 0/8 8 h-lim-p 0.0038 20.0000 0.0048 2195.723536 0 0.0153 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2195.723535 0 1.0938 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2195.723535 0 1.0938 238 | 0/8 11 h-lim-p 1.2445 20.0000 0.0000 2195.723535 0 3.7334 259 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2195.723535 0 0.3125 281 | 0/8 13 h-lim-p 1.1375 20.0000 0.0000 2195.723535 0 0.0178 306 | 0/8 14 h-lim-p 0.0037 20.0000 0.0000 2195.723535 0 0.0001 330 Out... lnL = -2195.723535 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2195.723535 Node 7: lnL = -2195.723535 Node 8: lnL = -2195.723535 Node 9: lnL = -2195.723535 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 428 Sequential format.. Reading seq # 1: YKR060W_Sbay Reading seq # 2: YKR060W_Scer Reading seq # 3: YKR060W_Skud Reading seq # 4: YKR060W_Smik Reading seq # 5: YKR060W_Spar Sequences read.. Counting patterns.. # site patterns = 191 Counting frequencies.. 120 bytes for distance 30560 bytes for lkl0 24448 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.121888 0.137214 0.040931 0.090730 0.101592 0.207241 0.137616 0.104384 lnL0 = -1833.626066 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1833.626066 x= 0.12189 0.13721 0.04093 0.09073 0.10159 0.20724 0.13762 0.10438 1 h-lim-p 0.0003 0.0025 123.0427 1831.036327 0 0.0005 22 | 0/8 2 h-lim-p 0.0003 0.0025 37.7450 1830.802207 7 0.0003 51 | 0/8 3 h-lim-p 0.0016 0.0274 8.1367 1830.776306 4 0.0008 72 | 0/8 4 h-lim-p 0.0037 0.1307 1.7820 1830.775414 5 0.0006 100 | 0/8 5 h-lim-p 0.0039 0.8120 0.2544 1830.775173 4 0.0023 122 | 0/8 6 h-lim-p 0.0041 0.9446 0.1441 1830.770838 0 0.0163 144 | 0/8 7 h-lim-p 0.0017 0.1789 1.3718 1830.743328 0 0.0051 165 | 0/8 8 h-lim-p 0.0018 0.0437 3.8438 1830.681923 1 0.0023 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0013 1830.680672 3 0.9644 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1830.680670 0 1.0938 217 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1830.680670 0 1.0938 237 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1830.680670 0 1.0938 257 | 0/8 13 h-lim-p 1.1135 20.0000 0.0000 1830.680670 0 8.9081 280 | 0/8 14 h-lim-p 1.9007 20.0000 0.0000 1830.680670 0 0.4158 301 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1830.680670 0 0.0024 330 Out... lnL = -1830.680670 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1830.680670 Node 7: lnL = -1830.680670 Node 8: lnL = -1830.680670 Node 9: lnL = -1830.680670 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 348 Sequential format.. Reading seq # 1: YKR061W_Sbay Reading seq # 2: YKR061W_Scer Reading seq # 3: YKR061W_Skud Reading seq # 4: YKR061W_Smik Reading seq # 5: YKR061W_Spar Sequences read.. Counting patterns.. # site patterns = 141 Counting frequencies.. 120 bytes for distance 22560 bytes for lkl0 18048 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.100603 0.094181 0.052758 0.060762 0.076878 0.185418 0.222255 0.084457 lnL0 = -1487.258757 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1487.258757 x= 0.10060 0.09418 0.05276 0.06076 0.07688 0.18542 0.22225 0.08446 1 h-lim-p 0.0009 0.0071 71.5007 1486.479022 8 0.0003 42 | 0/8 2 h-lim-p 0.0014 0.0114 13.3858 1486.440924 7 0.0004 74 | 0/8 3 h-lim-p 0.0006 0.0199 10.0954 1486.421839 2 0.0005 90 | 0/8 4 h-lim-p 0.0021 0.1394 2.6099 1486.420022 5 0.0006 115 | 0/8 5 h-lim-p 0.0018 0.2226 0.8526 1486.419825 4 0.0006 137 | 0/8 6 h-lim-p 0.0018 0.5087 0.2930 1486.419808 1 0.0005 160 | 0/8 7 h-lim-p 0.0053 8.8593 0.0252 1486.419807 0 0.0011 181 | 0/8 8 h-lim-p 0.1240 20.0000 0.0002 1486.419739 0 0.9918 204 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1486.419739 0 1.0938 224 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1486.419739 0 2.1875 244 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1486.419739 0 1.0938 264 | 0/8 12 h-lim-p 0.5061 20.0000 0.0000 1486.419739 0 4.0490 287 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1486.419739 0 0.0391 312 | 0/8 14 h-lim-p 0.1858 20.0000 0.0000 1486.419739 0 0.0000 356 Out... lnL = -1486.419739 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1486.419739 Node 7: lnL = -1486.419739 Node 8: lnL = -1486.419739 Node 9: lnL = -1486.419739 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 744 Sequential format.. Reading seq # 1: YKR062W_Sbay Reading seq # 2: YKR062W_Scer Reading seq # 3: YKR062W_Skud Reading seq # 4: YKR062W_Smik Reading seq # 5: YKR062W_Spar Sequences read.. Counting patterns.. # site patterns = 214 Counting frequencies.. 120 bytes for distance 34240 bytes for lkl0 27392 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.061971 0.059062 0.055667 0.114778 0.082922 0.159345 0.134342 0.048821 lnL0 = -3002.329038 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3002.329038 x= 0.06197 0.05906 0.05567 0.11478 0.08292 0.15935 0.13434 0.04882 1 h-lim-p 0.0018 0.7024 182.2332 3000.370702 9 0.0001 45 | 0/8 2 h-lim-p 0.0006 0.0045 21.8210 3000.334052 7 0.0002 72 | 0/8 3 h-lim-p 0.0006 0.0260 6.0508 3000.330458 4 0.0002 92 | 0/8 4 h-lim-p 0.0007 0.1945 1.7349 3000.330173 4 0.0002 114 | 0/8 5 h-lim-p 0.0010 0.5609 0.3620 3000.330155 2 0.0003 132 | 0/8 6 h-lim-p 0.0068 10.5515 0.0175 3000.330155 0 0.0004 155 | 0/8 7 h-lim-p 0.0032 20.0000 0.0020 3000.330155 0 0.0014 175 | 0/8 8 h-lim-p 0.0092 20.0000 0.0003 3000.330144 0 0.2211 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3000.330144 0 1.0938 219 | 0/8 10 h-lim-p 1.3075 20.0000 0.0000 3000.330144 0 1.1441 239 | 0/8 11 h-lim-p 1.0323 20.0000 0.0000 3000.330144 0 4.1293 261 | 0/8 12 h-lim-p 0.1608 20.0000 0.0003 3000.330144 0 0.0000 306 | 0/8 13 h-lim-p 0.0000 20.0000 0.0005 | 0/8 14 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -3000.330144 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3000.330144 Node 7: lnL = -3000.330144 Node 8: lnL = -3000.330144 Node 9: lnL = -3000.330144 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 238 Sequential format.. Reading seq # 1: YKR065C_Sbay Reading seq # 2: YKR065C_Scer Reading seq # 3: YKR065C_Skud Reading seq # 4: YKR065C_Smik Reading seq # 5: YKR065C_Spar Sequences read.. Counting patterns.. # site patterns = 137 Counting frequencies.. 120 bytes for distance 21920 bytes for lkl0 17536 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.179681 0.150400 0.045452 0.165561 0.083574 0.323642 0.201521 0.155844 lnL0 = -1068.777314 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1068.777314 x= 0.17968 0.15040 0.04545 0.16556 0.08357 0.32364 0.20152 0.15584 1 h-lim-p 0.0006 0.0049 24.1083 1068.478599 0 0.0012 23 | 0/8 2 h-lim-p 0.0020 0.0167 15.1165 1068.382914 7 0.0011 53 | 0/8 3 h-lim-p 0.0027 0.0234 6.1347 1068.364765 4 0.0012 72 | 0/8 4 h-lim-p 0.0028 0.1105 2.5334 1068.360568 6 0.0016 100 | 0/8 5 h-lim-p 0.0042 0.4904 0.9621 1068.359649 5 0.0023 123 | 0/8 6 h-lim-p 0.0080 1.3076 0.2714 1068.359485 2 0.0038 147 | 0/8 7 h-lim-p 0.0149 4.2882 0.0689 1068.359347 4 0.0101 177 | 0/8 8 h-lim-p 0.0194 3.5653 0.0360 1068.351441 0 0.1549 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0012 1068.350908 3 1.0004 226 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1068.350908 0 1.0938 246 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1068.350908 0 1.0938 266 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1068.350908 0 5.0000 287 | 0/8 13 h-lim-p 1.6839 20.0000 0.0000 1068.350908 0 0.3683 308 | 0/8 14 h-lim-p 1.1475 20.0000 0.0000 1068.350908 0 0.0269 333 | 0/8 15 h-lim-p 0.0349 20.0000 0.0000 1068.350908 0 0.0000 378 Out... lnL = -1068.350908 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1068.350908 Node 7: lnL = -1068.350908 Node 8: lnL = -1068.350908 Node 9: lnL = -1068.350908 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 822 Sequential format.. Reading seq # 1: YKR066C_Sbay Reading seq # 2: YKR066C_Scer Reading seq # 3: YKR066C_Skud Reading seq # 4: YKR066C_Smik Reading seq # 5: YKR066C_Spar Sequences read.. Counting patterns.. # site patterns = 323 Counting frequencies.. 120 bytes for distance 51680 bytes for lkl0 41344 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.248637 0.036764 0.130091 0.152368 0.120498 0.194820 0.244030 0.224268 lnL0 = -3831.011826 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3831.011826 x= 0.24864 0.03676 0.13009 0.15237 0.12050 0.19482 0.24403 0.22427 1 h-lim-p 0.0003 0.0023 127.2155 3828.343899 1 0.0004 24 | 0/8 2 h-lim-p 0.0006 0.0044 39.1687 3828.070031 7 0.0004 53 | 0/8 3 h-lim-p 0.0009 0.0239 16.1896 3828.027747 3 0.0004 71 | 0/8 4 h-lim-p 0.0009 0.0488 7.2701 3828.015244 6 0.0006 99 | 0/8 5 h-lim-p 0.0024 0.1947 1.7471 3828.014257 5 0.0007 124 | 0/8 6 h-lim-p 0.0070 2.2988 0.1729 3828.014244 0 0.0008 138 | 0/8 7 h-lim-p 0.0025 5.2303 0.0538 3828.014241 0 0.0011 158 | 0/8 8 h-lim-p 0.0228 20.0000 0.0026 3828.012559 0 0.5464 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3828.012533 1 0.9961 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3828.012533 0 1.0938 224 | 0/8 11 h-lim-p 2.1792 20.0000 0.0000 3828.012533 0 0.2724 246 | 0/8 12 h-lim-p 0.1546 20.0000 0.0000 3828.012533 0 0.0000 277 Out... lnL = -3828.012533 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3828.012533 Node 7: lnL = -3828.012533 Node 8: lnL = -3828.012533 Node 9: lnL = -3828.012533 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 799 Sequential format.. Reading seq # 1: YKR067W_Sbay Reading seq # 2: YKR067W_Scer Reading seq # 3: YKR067W_Skud Reading seq # 4: YKR067W_Smik Reading seq # 5: YKR067W_Spar Sequences read.. Counting patterns.. # site patterns = 308 Counting frequencies.. 120 bytes for distance 49280 bytes for lkl0 39424 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.258307 0.000254 0.098971 0.132732 0.096719 0.192860 0.328755 0.234652 lnL0 = -3722.073583 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3722.073583 x= 0.25831 0.00025 0.09897 0.13273 0.09672 0.19286 0.32875 0.23465 1 h-lim-p 0.0002 0.0016 131.9789 3719.821932 0 0.0003 22 | 0/8 2 h-lim-p 0.0011 0.0084 24.1578 3719.715551 7 0.0004 49 | 0/8 3 h-lim-p 0.0009 0.0458 10.4204 3719.697137 2 0.0004 65 | 0/8 4 h-lim-p 0.0005 0.0399 8.7486 3719.688443 5 0.0004 87 | 0/8 5 h-lim-p 0.0011 0.1094 2.8346 3719.685813 4 0.0008 109 | 0/8 6 h-lim-p 0.0030 0.5174 0.7415 3719.685592 3 0.0008 128 | 0/8 7 h-lim-p 0.0016 0.9840 0.3751 3719.685532 2 0.0007 152 | 0/8 8 h-lim-p 0.0409 6.0216 0.0063 3719.656166 0 0.6536 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 3719.656067 2 0.9961 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3719.656067 0 1.0938 220 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3719.656067 0 2.1875 240 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3719.656067 0 0.5469 261 | 0/8 13 h-lim-p 0.4014 20.0000 0.0000 3719.656067 0 0.0502 283 | 0/8 14 h-lim-p 0.0277 20.0000 0.0000 3719.656067 0 0.0139 303 | 0/8 15 h-lim-p 0.0091 20.0000 0.0000 3719.656067 0 0.0011 325 Out... lnL = -3719.656067 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3719.656067 Node 7: lnL = -3719.656067 Node 8: lnL = -3719.656067 Node 9: lnL = -3719.656067 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 792 Sequential format.. Reading seq # 1: YKR068C_Sbay Reading seq # 2: YKR068C_Scer Reading seq # 3: YKR068C_Skud Reading seq # 4: YKR068C_Smik Reading seq # 5: YKR068C_Spar Sequences read.. Counting patterns.. # site patterns = 199 Counting frequencies.. 120 bytes for distance 31840 bytes for lkl0 25472 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.174755 0.067433 0.179022 0.148811 0.134534 4.679306 0.245800 0.085969 lnL0 = -3133.155534 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3133.155534 x= 0.17476 0.06743 0.17902 0.14881 0.13453 4.67931 0.24580 0.08597 1 h-lim-p 0.0015 0.0118 40.4406 3132.839245 5 0.0004 33 | 0/8 2 h-lim-p 0.0014 0.0140 11.0796 3132.813588 5 0.0004 59 | 0/8 3 h-lim-p 0.0015 0.1560 3.2260 3132.811985 2 0.0003 76 | 0/8 4 h-lim-p 0.0024 0.6260 0.4570 3132.811922 3 0.0006 95 | 0/8 5 h-lim-p 0.0022 2.3550 0.1287 3132.811917 1 0.0005 118 | 0/8 6 h-lim-p 1.0855 20.0000 0.0001 3132.811913 0 1.0855 138 | 0/8 7 h-lim-p 2.5000 20.0000 0.0000 3132.811913 0 1.0938 158 | 0/8 8 h-lim-p 1.0634 20.0000 0.0000 3132.811913 0 2.1267 179 | 0/8 9 h-lim-p 0.1915 20.0000 0.0002 .. | 0/8 10 h-lim-p 0.0000 20.0000 0.0002 | 0/8 11 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -3132.811913 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3132.811913 Node 7: lnL = -3132.811913 Node 8: lnL = -3132.811913 Node 9: lnL = -3132.811913 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 183 Sequential format.. Reading seq # 1: YKR070W_Sbay Reading seq # 2: YKR070W_Scer Reading seq # 3: YKR070W_Skud Reading seq # 4: YKR070W_Smik Reading seq # 5: YKR070W_Spar Sequences read.. Counting patterns.. # site patterns = 107 Counting frequencies.. 120 bytes for distance 17120 bytes for lkl0 13696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.180621 0.342965 0.128304 0.157244 0.058517 0.172368 0.147303 0.143532 lnL0 = -806.181357 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 806.181357 x= 0.18062 0.34297 0.12830 0.15724 0.05852 0.17237 0.14730 0.14353 1 h-lim-p 0.0025 0.0199 13.9184 805.930577 7 0.0027 38 | 0/8 2 h-lim-p 0.0033 0.0492 11.0647 805.883460 7 0.0011 66 | 0/8 3 h-lim-p 0.0012 0.0352 10.2399 805.824033 0 0.0025 79 | 0/8 4 h-lim-p 0.0045 0.0708 5.5320 805.796908 6 0.0029 105 | 0/8 5 h-lim-p 0.0123 0.2172 1.3083 805.795348 5 0.0021 131 | 0/8 6 h-lim-p 0.0043 0.3407 0.6263 805.794748 2 0.0038 147 | 0/8 7 h-lim-p 0.0705 5.0125 0.0334 805.794681 3 0.0295 173 | 0/8 8 h-lim-p 0.0899 20.0000 0.0109 805.792941 0 0.2698 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 805.792908 1 0.9961 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 805.792908 0 1.0938 236 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 805.792908 0 1.0938 256 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 805.792908 0 3.7500 276 | 0/8 13 h-lim-p 2.0768 20.0000 0.0000 805.792908 0 0.2271 298 | 0/8 14 h-lim-p 0.5071 20.0000 0.0000 805.792908 0 0.0079 323 Out... lnL = -805.792908 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -805.792908 Node 7: lnL = -805.792908 Node 8: lnL = -805.792908 Node 9: lnL = -805.792908 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 489 Sequential format.. Reading seq # 1: YKR071C_Sbay Reading seq # 2: YKR071C_Scer Reading seq # 3: YKR071C_Skud Reading seq # 4: YKR071C_Smik Reading seq # 5: YKR071C_Spar Sequences read.. Counting patterns.. # site patterns = 159 Counting frequencies.. 120 bytes for distance 25440 bytes for lkl0 20352 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.109330 0.049779 0.038922 0.086206 0.053968 0.121180 0.110267 0.092600 lnL0 = -1822.870103 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1822.870103 x= 0.10933 0.04978 0.03892 0.08621 0.05397 0.12118 0.11027 0.09260 1 h-lim-p 0.0003 0.0023 118.4780 1821.695115 9 0.0002 44 | 0/8 2 h-lim-p 0.0003 0.0025 29.0929 1821.609086 6 0.0002 70 | 0/8 3 h-lim-p 0.0007 0.0254 8.3066 1821.602349 6 0.0002 99 | 0/8 4 h-lim-p 0.0013 0.0585 1.3517 1821.602012 4 0.0004 121 | 0/8 5 h-lim-p 0.0019 0.8521 0.2747 1821.602000 2 0.0003 139 | 0/8 6 h-lim-p 0.0033 6.0038 0.0251 1821.602000 0 0.0007 160 | 0/8 7 h-lim-p 0.0269 20.0000 0.0007 1821.601791 0 0.4299 184 | 0/8 8 h-lim-p 0.0007 0.2668 0.4278 1821.601712 3 0.0006 210 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1821.601708 1 0.9961 232 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1821.601708 0 2.1875 252 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1821.601708 0 1.0938 272 | 0/8 12 h-lim-p 0.6160 20.0000 0.0000 1821.601708 0 4.9280 295 | 0/8 13 h-lim-p 1.7717 20.0000 0.0000 1821.601708 0 0.2215 317 | 0/8 14 h-lim-p 0.5589 20.0000 0.0000 1821.601708 0 0.0000 356 Out... lnL = -1821.601708 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1821.601708 Node 7: lnL = -1821.601708 Node 8: lnL = -1821.601708 Node 9: lnL = -1821.601708 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 66 Sequential format.. Reading seq # 1: YKR072C_Sbay Reading seq # 2: YKR072C_Scer Reading seq # 3: YKR072C_Skud Reading seq # 4: YKR072C_Smik Reading seq # 5: YKR072C_Spar Sequences read.. Counting patterns.. # site patterns = 32 Counting frequencies.. 120 bytes for distance 5120 bytes for lkl0 4096 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.069674 0.008559 0.015443 0.013970 0.052371 0.156517 0.164955 0.056649 lnL0 = -226.437325 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 226.437325 x= 0.06967 0.00856 0.01544 0.01397 0.05237 0.15652 0.16496 0.05665 1 h-lim-p 0.0002 0.0013 46.4610 225.968629 0 0.0006 24 | 0/8 2 h-lim-p 0.0000 0.0004 23.8513 225.803663 m 0.0004 36 | 1/8 3 h-lim-p 0.0005 0.0339 8.6977 225.775831 0 0.0011 49 | 1/8 4 h-lim-p 0.0042 0.0636 2.1523 225.750442 1 0.0053 63 | 1/8 5 h-lim-p 0.0040 0.0316 1.2127 225.731105 0 0.0079 76 | 1/8 6 h-lim-p 0.0098 0.1331 0.9769 225.730286 5 0.0016 101 | 1/8 7 h-lim-p 0.0787 14.0971 0.0204 225.729609 1 0.0984 122 | 1/8 8 h-lim-p 0.0154 1.1449 0.1301 225.725700 0 0.0309 142 | 1/8 9 h-lim-p 2.5000 20.0000 0.0009 225.725368 5 0.7967 173 | 1/8 10 h-lim-p 2.5000 20.0000 0.0002 225.725356 3 0.9482 198 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 225.725356 0 1.0938 217 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 225.725356 0 2.1875 236 | 1/8 13 h-lim-p 2.3491 20.0000 0.0000 225.725356 0 0.0010 265 Out... lnL = -225.725356 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -225.725356 Node 7: lnL = -225.725356 Node 8: lnL = -225.725356 Node 9: lnL = -225.725356 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 780 Sequential format.. Reading seq # 1: YKR074W_Sbay Reading seq # 2: YKR074W_Scer Reading seq # 3: YKR074W_Skud Reading seq # 4: YKR074W_Smik Reading seq # 5: YKR074W_Spar Sequences read.. Counting patterns.. # site patterns = 445 Counting frequencies.. 120 bytes for distance 71200 bytes for lkl0 56960 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.216121 0.060017 0.208585 0.197318 0.168604 0.434233 0.350036 0.170203 lnL0 = -4129.988216 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4129.988216 x= 0.21612 0.06002 0.20858 0.19732 0.16860 0.43423 0.35004 0.17020 1 h-lim-p 0.0039 0.9662 146.2547 4125.073100 8 0.0005 41 | 0/8 2 h-lim-p 0.0013 0.0107 27.9910 4124.765787 8 0.0008 75 | 0/8 3 h-lim-p 0.0021 0.0424 10.5574 4124.728213 6 0.0008 102 | 0/8 4 h-lim-p 0.0036 0.1597 2.2313 4124.725346 5 0.0012 127 | 0/8 5 h-lim-p 0.0095 1.3275 0.2856 4124.725278 2 0.0015 145 | 0/8 6 h-lim-p 0.0163 15.6002 0.0264 4124.725246 1 0.0143 167 | 0/8 7 h-lim-p 0.0310 20.0000 0.0122 4124.723107 0 0.1858 189 | 0/8 8 h-lim-p 0.0055 1.0212 0.4116 4124.722824 2 0.0026 213 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 4124.722810 1 0.9961 235 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4124.722810 0 1.0938 255 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4124.722810 0 1.0938 275 | 0/8 12 h-lim-p 1.0405 20.0000 0.0000 4124.722810 0 1.0405 295 | 0/8 13 h-lim-p 0.1279 20.0000 0.0000 4124.722810 0 0.0000 336 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 4124.722810 0 0.0000 368 Out... lnL = -4124.722810 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4124.722810 Node 7: lnL = -4124.722810 Node 8: lnL = -4124.722810 Node 9: lnL = -4124.722810 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 877 Sequential format.. Reading seq # 1: YKR075C_Sbay Reading seq # 2: YKR075C_Scer Reading seq # 3: YKR075C_Skud Reading seq # 4: YKR075C_Smik Reading seq # 5: YKR075C_Spar Sequences read.. Counting patterns.. # site patterns = 334 Counting frequencies.. 120 bytes for distance 53440 bytes for lkl0 42752 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.163022 0.141846 0.062313 0.142117 0.114598 0.210661 0.234638 0.132161 lnL0 = -4107.754308 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4107.754308 x= 0.16302 0.14185 0.06231 0.14212 0.11460 0.21066 0.23464 0.13216 1 h-lim-p 0.0031 0.7424 163.5996 4105.142751 9 0.0002 45 | 0/8 2 h-lim-p 0.0011 0.0091 31.5285 4104.947340 7 0.0004 72 | 0/8 3 h-lim-p 0.0008 0.0180 15.8444 4104.914324 4 0.0003 92 | 0/8 4 h-lim-p 0.0052 0.2228 0.9770 4104.914145 3 0.0004 114 | 0/8 5 h-lim-p 0.0035 3.7547 0.1089 4104.914142 1 0.0007 137 | 0/8 6 h-lim-p 0.0018 7.3312 0.0427 4104.914141 0 0.0008 157 | 0/8 7 h-lim-p 0.0154 20.0000 0.0021 4104.914141 0 0.0135 177 | 0/8 8 h-lim-p 0.0066 20.0000 0.0044 4104.914089 0 0.0531 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4104.914088 0 1.0938 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4104.914088 0 1.0938 240 | 0/8 11 h-lim-p 1.2034 20.0000 0.0000 4104.914088 0 2.4069 261 | 0/8 12 h-lim-p 2.1863 20.0000 0.0000 4104.914088 0 0.9565 281 | 0/8 13 h-lim-p 0.1181 20.0000 0.0000 4104.914088 0 0.0001 310 | 0/8 14 h-lim-p 0.0016 20.0000 0.0000 4104.914088 0 0.0016 330 Out... lnL = -4104.914088 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4104.914088 Node 7: lnL = -4104.914088 Node 8: lnL = -4104.914088 Node 9: lnL = -4104.914088 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 878 Sequential format.. Reading seq # 1: YKR076W_Sbay Reading seq # 2: YKR076W_Scer Reading seq # 3: YKR076W_Skud Reading seq # 4: YKR076W_Smik Reading seq # 5: YKR076W_Spar Sequences read.. Counting patterns.. # site patterns = 463 Counting frequencies.. 120 bytes for distance 74080 bytes for lkl0 59264 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.206466 0.208390 0.226330 0.195534 0.250121 0.514948 0.260187 0.153598 lnL0 = -4742.658953 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4742.658953 x= 0.20647 0.20839 0.22633 0.19553 0.25012 0.51495 0.26019 0.15360 1 h-lim-p 0.0342 3.1601 52.6676 4741.766405 8 0.0007 46 | 0/8 2 h-lim-p 0.0019 0.0192 18.1161 4741.640724 4 0.0008 65 | 0/8 3 h-lim-p 0.0030 0.1645 5.0744 4741.630049 6 0.0009 94 | 0/8 4 h-lim-p 0.0013 0.1365 3.4285 4741.625555 3 0.0011 112 | 0/8 5 h-lim-p 0.0035 0.5733 1.0522 4741.624795 2 0.0016 128 | 0/8 6 h-lim-p 0.0259 5.0149 0.0660 4741.624788 0 0.0028 142 | 0/8 7 h-lim-p 0.0253 20.0000 0.0074 4741.624771 1 0.0316 164 | 0/8 8 h-lim-p 0.0131 20.0000 0.0179 4741.624314 0 0.0524 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4741.624310 0 1.0938 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4741.624310 0 1.0938 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4741.624310 0 1.0938 246 | 0/8 12 h-lim-p 1.0180 20.0000 0.0000 4741.624310 0 0.0318 270 | 0/8 13 h-lim-p 0.0067 20.0000 0.0000 4741.624310 0 0.0050 290 | 0/8 14 h-lim-p 0.0026 20.0000 0.0000 4741.624310 0 0.0000 316 | 0/8 15 h-lim-p 0.0027 20.0000 0.0000 4741.624310 0 0.0000 351 Out... lnL = -4741.624310 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4741.624310 Node 7: lnL = -4741.624310 Node 8: lnL = -4741.624310 Node 9: lnL = -4741.624310 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 287 Sequential format.. Reading seq # 1: YKR077W_Sbay Reading seq # 2: YKR077W_Scer Reading seq # 3: YKR077W_Skud Reading seq # 4: YKR077W_Smik Reading seq # 5: YKR077W_Spar Sequences read.. Counting patterns.. # site patterns = 105 Counting frequencies.. 120 bytes for distance 16800 bytes for lkl0 13440 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.111378 0.014785 0.036993 0.114942 0.086256 0.099932 0.113862 0.094832 lnL0 = -1034.291701 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1034.291701 x= 0.11138 0.01479 0.03699 0.11494 0.08626 0.09993 0.11386 0.09483 1 h-lim-p 0.0007 0.0059 97.2660 1033.164401 8 0.0003 40 | 0/8 2 h-lim-p 0.0004 0.0035 47.8012 1032.560147 0 0.0007 52 | 0/8 3 h-lim-p 0.0030 0.0238 9.1925 1032.530322 7 0.0008 82 | 0/8 4 h-lim-p 0.0042 0.0579 1.6576 1032.529587 3 0.0005 102 | 0/8 5 h-lim-p 0.0049 0.8996 0.1865 1032.529578 1 0.0005 118 | 0/8 6 h-lim-p 0.0065 9.4924 0.0152 1032.529574 2 0.0042 143 | 0/8 7 h-lim-p 0.0065 14.6491 0.0097 1032.529281 0 0.0524 166 | 0/8 8 h-lim-p 0.0013 0.5024 0.3881 1032.528780 0 0.0020 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1032.528742 2 1.0889 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1032.528742 0 1.0938 230 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1032.528742 0 2.1875 250 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1032.528742 0 0.2734 272 | 0/8 13 h-lim-p 0.1111 20.0000 0.0000 1032.528742 0 0.0069 295 | 0/8 14 h-lim-p 0.0035 20.0000 0.0000 1032.528742 0 0.0000 321 Out... lnL = -1032.528742 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1032.528742 Node 7: lnL = -1032.528742 Node 8: lnL = -1032.528742 Node 9: lnL = -1032.528742 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 250 Sequential format.. Reading seq # 1: YKR078W_Sbay Reading seq # 2: YKR078W_Scer Reading seq # 3: YKR078W_Skud Reading seq # 4: YKR078W_Smik Reading seq # 5: YKR078W_Spar Sequences read.. Counting patterns.. # site patterns = 119 Counting frequencies.. 120 bytes for distance 19040 bytes for lkl0 15232 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.132459 0.135376 0.049676 0.105408 0.040210 0.131703 0.251772 0.107675 lnL0 = -980.284696 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 980.284696 x= 0.13246 0.13538 0.04968 0.10541 0.04021 0.13170 0.25177 0.10767 1 h-lim-p 0.0015 0.0121 57.2560 979.708830 7 0.0004 40 | 0/8 2 h-lim-p 0.0008 0.0066 17.4233 979.629568 7 0.0006 70 | 0/8 3 h-lim-p 0.0013 0.0291 7.7159 979.598873 5 0.0012 93 | 0/8 4 h-lim-p 0.0028 0.0878 3.4155 979.593877 5 0.0011 115 | 0/8 5 h-lim-p 0.0024 0.1652 1.5152 979.592886 3 0.0011 133 | 0/8 6 h-lim-p 0.0087 2.0981 0.1860 979.592862 2 0.0014 152 | 0/8 7 h-lim-p 0.0027 2.6280 0.1007 979.592853 2 0.0021 176 | 0/8 8 h-lim-p 0.5586 20.0000 0.0004 979.592747 0 1.1171 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 979.592746 0 1.0938 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 979.592746 0 2.1875 237 | 0/8 11 h-lim-p 2.0322 20.0000 0.0000 979.592746 0 0.8891 257 | 0/8 12 h-lim-p 1.9909 20.0000 0.0000 979.592746 0 0.0005 288 Out... lnL = -979.592746 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -979.592746 Node 7: lnL = -979.592746 Node 8: lnL = -979.592746 Node 9: lnL = -979.592746 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 908 Sequential format.. Reading seq # 1: YKR079C_Sbay Reading seq # 2: YKR079C_Scer Reading seq # 3: YKR079C_Skud Reading seq # 4: YKR079C_Smik Reading seq # 5: YKR079C_Spar Sequences read.. Counting patterns.. # site patterns = 280 Counting frequencies.. 120 bytes for distance 44800 bytes for lkl0 35840 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.136459 0.073300 0.056427 0.163169 0.098192 0.217523 0.203775 0.109858 lnL0 = -4020.257529 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4020.257529 x= 0.13646 0.07330 0.05643 0.16317 0.09819 0.21752 0.20378 0.10986 1 h-lim-p 0.0043 0.0341 120.8852 4019.085172 8 0.0002 45 | 0/8 2 h-lim-p 0.0008 0.0082 26.8318 4018.963147 2 0.0004 61 | 0/8 3 h-lim-p 0.0007 0.0260 13.1970 4018.946209 4 0.0002 83 | 0/8 4 h-lim-p 0.0032 0.1185 0.9868 4018.946045 2 0.0003 101 | 0/8 5 h-lim-p 0.0013 1.0141 0.2653 4018.946033 1 0.0003 124 | 0/8 6 h-lim-p 0.0012 3.0608 0.0682 4018.946033 0 0.0005 144 | 0/8 7 h-lim-p 0.0140 20.0000 0.0026 4018.946033 0 0.0061 164 | 0/8 8 h-lim-p 0.0113 20.0000 0.0014 4018.945989 0 0.0904 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4018.945989 0 1.0938 207 | 0/8 10 h-lim-p 2.4493 20.0000 0.0000 4018.945989 0 2.1431 227 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4018.945989 0 1.0938 247 | 0/8 12 h-lim-p 0.1687 20.0000 0.0000 4018.945989 0 5.3986 272 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 4018.945989 0 0.2734 294 | 0/8 14 h-lim-p 0.0091 20.0000 0.0000 4018.945989 0 0.0000 334 | 0/8 15 h-lim-p 0.0000 20.0000 0.0010 4018.945989 0 0.0000 361 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0010 | 0/8 18 h-lim-p 0.0000 20.0000 0.0010 Out... lnL = -4018.945989 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4018.945989 Node 7: lnL = -4018.945989 Node 8: lnL = -4018.945989 Node 9: lnL = -4018.945989 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 243 Sequential format.. Reading seq # 1: YKR083C_Sbay Reading seq # 2: YKR083C_Scer Reading seq # 3: YKR083C_Skud Reading seq # 4: YKR083C_Smik Reading seq # 5: YKR083C_Spar Sequences read.. Counting patterns.. # site patterns = 127 Counting frequencies.. 120 bytes for distance 20320 bytes for lkl0 16256 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.139753 0.124195 0.070496 0.169263 0.080067 0.234984 0.172554 0.111341 lnL0 = -1131.027471 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1131.027471 x= 0.13975 0.12420 0.07050 0.16926 0.08007 0.23498 0.17255 0.11134 1 h-lim-p 0.0004 0.0032 67.1079 1129.051045 0 0.0012 23 | 0/8 2 h-lim-p 0.0007 0.0055 23.6512 1128.777845 0 0.0014 36 | 0/8 3 h-lim-p 0.0020 0.0177 16.4872 1128.729632 7 0.0005 62 | 0/8 4 h-lim-p 0.0041 0.1696 2.0806 1128.725795 3 0.0018 80 | 0/8 5 h-lim-p 0.0101 0.8875 0.3652 1128.725254 4 0.0037 101 | 0/8 6 h-lim-p 0.0076 1.5170 0.1778 1128.722201 0 0.0151 122 | 0/8 7 h-lim-p 0.0063 0.5710 0.4294 1128.635760 0 0.0500 145 | 0/8 8 h-lim-p 0.1221 1.5989 0.1760 1128.635705 3 0.0025 177 | 0/8 9 h-lim-p 0.0585 20.0000 0.0074 1128.628279 0 0.7014 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0003 1128.628238 2 0.9961 224 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1128.628238 0 1.0938 244 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1128.628238 0 1.0938 264 | 0/8 13 h-lim-p 1.8446 20.0000 0.0000 1128.628238 0 0.9223 284 | 0/8 14 h-lim-p 0.6755 20.0000 0.0000 1128.628238 0 0.1689 305 | 0/8 15 h-lim-p 0.0185 20.0000 0.0000 1128.628238 0 0.0000 344 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 1128.628238 0 0.0000 379 Out... lnL = -1128.628238 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1128.628238 Node 7: lnL = -1128.628238 Node 8: lnL = -1128.628238 Node 9: lnL = -1128.628238 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 184 Sequential format.. Reading seq # 1: YKR085C_Sbay Reading seq # 2: YKR085C_Scer Reading seq # 3: YKR085C_Skud Reading seq # 4: YKR085C_Smik Reading seq # 5: YKR085C_Spar Sequences read.. Counting patterns.. # site patterns = 88 Counting frequencies.. 120 bytes for distance 14080 bytes for lkl0 11264 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.111164 0.104287 0.010135 0.143425 0.082948 0.124692 0.115348 0.091265 lnL0 = -759.619320 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 759.619320 x= 0.11116 0.10429 0.01014 0.14343 0.08295 0.12469 0.11535 0.09126 1 h-lim-p 0.0007 0.0486 148.0381 757.802659 8 0.0002 38 | 0/8 2 h-lim-p 0.0008 0.0062 21.0761 757.596009 1 0.0010 52 | 0/8 3 h-lim-p 0.0031 0.0265 6.7179 757.575816 5 0.0010 76 | 0/8 4 h-lim-p 0.0046 0.1889 1.4270 757.574619 5 0.0012 99 | 0/8 5 h-lim-p 0.0048 0.8541 0.3646 757.574550 2 0.0011 116 | 0/8 6 h-lim-p 0.0071 4.2849 0.0543 757.574548 2 0.0011 142 | 0/8 7 h-lim-p 0.0634 20.0000 0.0010 757.574497 0 0.3803 164 | 0/8 8 h-lim-p 0.0026 1.6129 0.1439 757.574412 1 0.0032 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 757.574410 0 1.0938 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 757.574410 0 2.1875 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 757.574410 0 1.0938 246 | 0/8 12 h-lim-p 2.1022 20.0000 0.0000 757.574410 0 1.8394 266 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 757.574410 0 0.6250 287 | 0/8 14 h-lim-p 0.1652 20.0000 0.0000 757.574410 0 0.0826 307 | 0/8 15 h-lim-p 0.0295 20.0000 0.0000 757.574410 0 0.0074 328 | 0/8 16 h-lim-p 0.0042 20.0000 0.0000 757.574410 0 0.0000 365 Out... lnL = -757.574410 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -757.574410 Node 7: lnL = -757.574410 Node 8: lnL = -757.574410 Node 9: lnL = -757.574410 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 639 Sequential format.. Reading seq # 1: YKR089C_Sbay Reading seq # 2: YKR089C_Scer Reading seq # 3: YKR089C_Skud Reading seq # 4: YKR089C_Smik Reading seq # 5: YKR089C_Spar Sequences read.. Counting patterns.. # site patterns = 224 Counting frequencies.. 120 bytes for distance 35840 bytes for lkl0 28672 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.156064 0.033677 0.095262 0.091319 0.079519 0.228949 0.205978 0.130361 lnL0 = -2882.571704 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2882.571704 x= 0.15606 0.03368 0.09526 0.09132 0.07952 0.22895 0.20598 0.13036 1 h-lim-p 0.0002 0.0019 140.7102 2880.613055 2 0.0002 26 | 0/8 2 h-lim-p 0.0005 0.0043 24.8570 2880.528205 6 0.0003 50 | 0/8 3 h-lim-p 0.0005 0.0181 13.1487 2880.506858 6 0.0003 78 | 0/8 4 h-lim-p 0.0007 0.0336 5.7829 2880.502287 3 0.0003 97 | 0/8 5 h-lim-p 0.0025 0.1772 0.7907 2880.502154 3 0.0004 118 | 0/8 6 h-lim-p 0.0036 3.5460 0.0963 2880.502149 1 0.0007 141 | 0/8 7 h-lim-p 0.0026 10.6791 0.0270 2880.502129 0 0.0051 162 | 0/8 8 h-lim-p 0.0095 4.9105 0.0146 2880.499482 0 0.0758 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2880.499461 1 0.9961 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2880.499461 0 1.0938 227 | 0/8 11 h-lim-p 1.2270 20.0000 0.0000 2880.499461 0 3.6809 248 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2880.499461 0 0.4688 270 | 0/8 13 h-lim-p 0.0164 20.0000 0.0000 2880.499461 0 0.0000 305 Out... lnL = -2880.499461 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2880.499461 Node 7: lnL = -2880.499461 Node 8: lnL = -2880.499461 Node 9: lnL = -2880.499461 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 769 Sequential format.. Reading seq # 1: YKR091W_Sbay Reading seq # 2: YKR091W_Scer Reading seq # 3: YKR091W_Skud Reading seq # 4: YKR091W_Smik Reading seq # 5: YKR091W_Spar Sequences read.. Counting patterns.. # site patterns = 186 Counting frequencies.. 120 bytes for distance 29760 bytes for lkl0 23808 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.155920 0.025392 0.047336 0.134701 0.067360 0.158129 0.187511 0.127370 lnL0 = -2723.935894 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2723.935894 x= 0.15592 0.02539 0.04734 0.13470 0.06736 0.15813 0.18751 0.12737 1 h-lim-p 0.0003 0.0025 76.9546 2723.450276 8 0.0002 40 | 0/8 2 h-lim-p 0.0006 0.0047 18.7049 2723.407772 5 0.0003 61 | 0/8 3 h-lim-p 0.0005 0.0221 10.3472 2723.389258 2 0.0004 77 | 0/8 4 h-lim-p 0.0023 0.1152 1.9260 2723.388355 2 0.0005 94 | 0/8 5 h-lim-p 0.0016 0.1672 0.5925 2723.388307 2 0.0003 111 | 0/8 6 h-lim-p 0.0020 1.9945 0.0935 2723.388305 0 0.0004 132 | 0/8 7 h-lim-p 0.0025 9.5525 0.0163 2723.388305 0 0.0005 153 | 0/8 8 h-lim-p 0.0691 20.0000 0.0001 2723.388282 0 1.1049 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2723.388281 0 1.0938 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2723.388281 0 1.0938 217 | 0/8 11 h-lim-p 1.4682 20.0000 0.0000 2723.388281 0 0.0459 241 | 0/8 12 h-lim-p 0.0212 20.0000 0.0000 2723.388281 0 0.0159 261 | 0/8 13 h-lim-p 0.0103 20.0000 0.0000 2723.388281 0 0.0002 286 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 2723.388281 0 0.0000 320 | 0/8 15 h-lim-p 0.0000 20.0000 0.0008 | 0/8 16 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -2723.388281 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2723.388281 Node 7: lnL = -2723.388281 Node 8: lnL = -2723.388281 Node 9: lnL = -2723.388281 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 881 Sequential format.. Reading seq # 1: YKR095W_Sbay Reading seq # 2: YKR095W_Scer Reading seq # 3: YKR095W_Skud Reading seq # 4: YKR095W_Smik Reading seq # 5: YKR095W_Spar Sequences read.. Counting patterns.. # site patterns = 327 Counting frequencies.. 120 bytes for distance 52320 bytes for lkl0 41856 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.217101 0.094735 0.049003 0.166855 0.104919 0.242222 0.261805 0.175081 lnL0 = -4238.479323 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4238.479323 x= 0.21710 0.09473 0.04900 0.16686 0.10492 0.24222 0.26181 0.17508 1 h-lim-p 0.0029 0.6458 170.8857 4236.070282 8 0.0002 44 | 0/8 2 h-lim-p 0.0006 0.0050 39.4487 4235.761513 6 0.0004 72 | 0/8 3 h-lim-p 0.0007 0.0176 24.3935 4235.687474 3 0.0003 90 | 0/8 4 h-lim-p 0.0013 0.0479 5.9968 4235.678650 3 0.0005 108 | 0/8 5 h-lim-p 0.0021 0.1707 1.5603 4235.678034 3 0.0005 127 | 0/8 6 h-lim-p 0.0122 4.8206 0.0692 4235.678033 0 0.0007 142 | 0/8 7 h-lim-p 0.0033 20.0000 0.0142 4235.678032 0 0.0029 162 | 0/8 8 h-lim-p 0.0246 20.0000 0.0017 4235.677650 0 0.2948 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4235.677646 0 1.0938 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4235.677646 0 1.0938 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4235.677646 0 2.1875 245 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4235.677646 0 1.0938 265 | 0/8 13 h-lim-p 0.3881 20.0000 0.0000 4235.677646 0 3.1052 288 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 4235.677646 0 0.0012 318 Out... lnL = -4235.677646 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4235.677646 Node 7: lnL = -4235.677646 Node 8: lnL = -4235.677646 Node 9: lnL = -4235.677646 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 835 Sequential format.. Reading seq # 1: YKR096W_Sbay Reading seq # 2: YKR096W_Scer Reading seq # 3: YKR096W_Skud Reading seq # 4: YKR096W_Smik Reading seq # 5: YKR096W_Spar Sequences read.. Counting patterns.. # site patterns = 219 Counting frequencies.. 120 bytes for distance 35040 bytes for lkl0 28032 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.107455 0.060739 0.047688 0.087017 0.072137 0.183208 0.113762 0.082882 lnL0 = -3372.429220 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3372.429220 x= 0.10745 0.06074 0.04769 0.08702 0.07214 0.18321 0.11376 0.08288 1 h-lim-p 0.0005 0.0037 163.1061 3370.758004 8 0.0001 43 | 0/8 2 h-lim-p 0.0003 0.0022 47.8140 3370.544293 7 0.0002 72 | 0/8 3 h-lim-p 0.0006 0.0117 15.0776 3370.527696 4 0.0002 93 | 0/8 4 h-lim-p 0.0005 0.0416 4.8652 3370.525667 4 0.0002 113 | 0/8 5 h-lim-p 0.0005 0.1187 1.8722 3370.525312 0 0.0002 125 | 0/8 6 h-lim-p 0.0058 2.4464 0.0708 3370.525312 0 0.0002 141 | 0/8 7 h-lim-p 0.0152 20.0000 0.0008 3370.525309 0 0.0304 162 | 0/8 8 h-lim-p 0.0010 17.3124 0.0255 3370.525251 0 0.0060 184 | 0/8 9 h-lim-p 0.2971 20.0000 0.0005 3370.525241 0 0.8914 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 3370.525240 0 1.2500 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3370.525240 0 1.0938 245 | 0/8 12 h-lim-p 0.4755 20.0000 0.0000 3370.525240 0 5.7062 268 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 3370.525240 0 0.2734 290 | 0/8 14 h-lim-p 1.8570 20.0000 0.0000 3370.525240 0 0.0073 317 | 0/8 15 h-lim-p 0.0009 20.0000 0.0000 3370.525240 0 0.0001 339 | 0/8 16 h-lim-p 0.0002 20.0000 0.0000 3370.525240 0 0.0001 360 Out... lnL = -3370.525240 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3370.525240 Node 7: lnL = -3370.525240 Node 8: lnL = -3370.525240 Node 9: lnL = -3370.525240 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 834 Sequential format.. Reading seq # 1: YKR097W_Sbay Reading seq # 2: YKR097W_Scer Reading seq # 3: YKR097W_Skud Reading seq # 4: YKR097W_Smik Reading seq # 5: YKR097W_Spar Sequences read.. Counting patterns.. # site patterns = 251 Counting frequencies.. 120 bytes for distance 40160 bytes for lkl0 32128 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.129445 0.071624 0.040724 0.074302 0.069198 0.159155 0.156373 0.103318 lnL0 = -3398.896958 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3398.896958 x= 0.12945 0.07162 0.04072 0.07430 0.06920 0.15915 0.15637 0.10332 1 h-lim-p 0.0009 0.0448 270.1536 3395.053352 8 0.0001 43 | 0/8 2 h-lim-p 0.0004 0.0032 56.4531 3394.678398 8 0.0002 78 | 0/8 3 h-lim-p 0.0005 0.0081 27.7993 3394.627487 5 0.0002 102 | 0/8 4 h-lim-p 0.0005 0.0170 9.6068 3394.618322 4 0.0002 123 | 0/8 5 h-lim-p 0.0024 0.2545 0.9273 3394.618208 2 0.0003 141 | 0/8 6 h-lim-p 0.0007 0.4642 0.3486 3394.618196 2 0.0002 167 | 0/8 7 h-lim-p 0.0040 10.0198 0.0211 3394.618196 0 0.0004 189 | 0/8 8 h-lim-p 0.0625 20.0000 0.0001 3394.618121 0 1.0000 213 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3394.618121 0 1.0938 233 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3394.618121 0 2.1875 253 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3394.618121 0 1.0938 273 | 0/8 12 h-lim-p 0.3631 20.0000 0.0000 3394.618121 0 4.3573 296 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 3394.618121 0 0.3125 318 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 3394.618121 0 0.0006 349 Out... lnL = -3394.618121 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3394.618121 Node 7: lnL = -3394.618121 Node 8: lnL = -3394.618121 Node 9: lnL = -3394.618121 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 693 Sequential format.. Reading seq # 1: YKR098C_Sbay Reading seq # 2: YKR098C_Scer Reading seq # 3: YKR098C_Skud Reading seq # 4: YKR098C_Smik Reading seq # 5: YKR098C_Spar Sequences read.. Counting patterns.. # site patterns = 220 Counting frequencies.. 120 bytes for distance 35200 bytes for lkl0 28160 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.162265 0.044523 0.072030 0.087385 0.065486 0.135514 0.149565 0.134638 lnL0 = -2891.850402 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2891.850402 x= 0.16227 0.04452 0.07203 0.08738 0.06549 0.13551 0.14957 0.13464 1 h-lim-p 0.0023 0.8777 157.9318 2889.978393 9 0.0002 48 | 0/8 2 h-lim-p 0.0009 0.0068 26.8631 2889.867175 6 0.0003 73 | 0/8 3 h-lim-p 0.0005 0.0104 18.0338 2889.845575 4 0.0002 93 | 0/8 4 h-lim-p 0.0024 0.1053 1.3481 2889.845321 0 0.0003 107 | 0/8 5 h-lim-p 0.0022 1.4224 0.1878 2889.845316 1 0.0003 123 | 0/8 6 h-lim-p 0.0015 4.2391 0.0337 2889.845316 0 0.0003 144 | 0/8 7 h-lim-p 0.0040 20.0000 0.0027 2889.845315 0 0.0119 165 | 0/8 8 h-lim-p 0.0063 20.0000 0.0052 2889.845227 0 0.0506 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2889.845215 1 0.9961 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2889.845215 0 1.0938 230 | 0/8 11 h-lim-p 0.8838 20.0000 0.0000 2889.845215 0 0.0000 270 Out... lnL = -2889.845215 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2889.845215 Node 7: lnL = -2889.845215 Node 8: lnL = -2889.845215 Node 9: lnL = -2889.845215 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 697 Sequential format.. Reading seq # 1: YKR099W_Sbay Reading seq # 2: YKR099W_Scer Reading seq # 3: YKR099W_Skud Reading seq # 4: YKR099W_Smik Reading seq # 5: YKR099W_Spar Sequences read.. Counting patterns.. # site patterns = 215 Counting frequencies.. 120 bytes for distance 34400 bytes for lkl0 27520 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.156664 0.040247 0.078992 0.088554 0.064317 0.152415 0.144238 0.128908 lnL0 = -2912.530621 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2912.530621 x= 0.15666 0.04025 0.07899 0.08855 0.06432 0.15242 0.14424 0.12891 1 h-lim-p 0.0011 0.0086 175.9469 2910.276699 8 0.0002 42 | 0/8 2 h-lim-p 0.0006 0.0047 30.1362 2910.141678 4 0.0003 63 | 0/8 3 h-lim-p 0.0005 0.0104 17.8004 2910.120728 5 0.0002 88 | 0/8 4 h-lim-p 0.0011 0.0398 2.7193 2910.119911 3 0.0002 107 | 0/8 5 h-lim-p 0.0026 1.1097 0.2393 2910.119902 1 0.0003 123 | 0/8 6 h-lim-p 0.0016 5.1100 0.0475 2910.119901 0 0.0004 144 | 0/8 7 h-lim-p 0.0049 20.0000 0.0035 2910.119900 0 0.0074 164 | 0/8 8 h-lim-p 0.0062 20.0000 0.0041 2910.119787 0 0.0742 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2910.119781 1 0.9961 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2910.119781 0 1.0938 229 | 0/8 11 h-lim-p 0.8752 20.0000 0.0000 2910.119781 0 0.0273 253 | 0/8 12 h-lim-p 0.0126 20.0000 0.0000 2910.119781 0 0.0000 292 Out... lnL = -2910.119781 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2910.119781 Node 7: lnL = -2910.119781 Node 8: lnL = -2910.119781 Node 9: lnL = -2910.119781 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 294 Sequential format.. Reading seq # 1: YLL001W_Sbay Reading seq # 2: YLL001W_Scer Reading seq # 3: YLL001W_Skud Reading seq # 4: YLL001W_Smik Reading seq # 5: YLL001W_Spar Sequences read.. Counting patterns.. # site patterns = 107 Counting frequencies.. 120 bytes for distance 17120 bytes for lkl0 13696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.124188 0.044605 0.020021 0.121273 0.073231 0.112423 0.176835 0.099751 lnL0 = -1207.636572 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1207.636572 x= 0.12419 0.04461 0.02002 0.12127 0.07323 0.11242 0.17683 0.09975 1 h-lim-p 0.0035 0.0283 42.3802 1207.385138 8 0.0003 43 | 0/8 2 h-lim-p 0.0002 0.0017 16.2990 1207.359777 4 0.0002 64 | 0/8 3 h-lim-p 0.0022 0.1678 1.5791 1207.359145 2 0.0005 81 | 0/8 4 h-lim-p 0.0036 0.3739 0.2224 1207.359137 2 0.0003 99 | 0/8 5 h-lim-p 0.0026 7.1602 0.0302 1207.359137 0 0.0011 119 | 0/8 6 h-lim-p 0.0046 20.0000 0.0074 1207.359137 0 0.0023 139 | 0/8 7 h-lim-p 0.0044 20.0000 0.0039 1207.359136 0 0.0087 160 | 0/8 8 h-lim-p 0.0053 20.0000 0.0065 1207.359095 0 0.0315 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1207.359094 0 1.0938 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1207.359094 0 1.0938 222 | 0/8 11 h-lim-p 1.9788 20.0000 0.0000 1207.359094 0 3.9576 243 | 0/8 12 h-lim-p 2.1745 20.0000 0.0000 1207.359094 0 0.0037 271 | 0/8 13 h-lim-p 0.0099 20.0000 0.0000 1207.359094 0 0.0003 295 Out... lnL = -1207.359094 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1207.359094 Node 7: lnL = -1207.359094 Node 8: lnL = -1207.359094 Node 9: lnL = -1207.359094 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 287 Sequential format.. Reading seq # 1: YLL002W_Sbay Reading seq # 2: YLL002W_Scer Reading seq # 3: YLL002W_Skud Reading seq # 4: YLL002W_Smik Reading seq # 5: YLL002W_Spar Sequences read.. Counting patterns.. # site patterns = 146 Counting frequencies.. 120 bytes for distance 23360 bytes for lkl0 18688 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.175403 0.058346 0.130538 0.116784 0.054574 0.256083 0.358181 0.133556 lnL0 = -1266.232005 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1266.232005 x= 0.17540 0.05835 0.13054 0.11678 0.05457 0.25608 0.35818 0.13356 1 h-lim-p 0.0060 0.0477 35.9094 1265.693621 6 0.0009 38 | 0/8 2 h-lim-p 0.0009 0.0074 16.2511 1265.623377 7 0.0006 66 | 0/8 3 h-lim-p 0.0012 0.0238 8.2020 1265.576505 0 0.0018 78 | 0/8 4 h-lim-p 0.0117 0.1796 1.2793 1265.575103 5 0.0018 106 | 0/8 5 h-lim-p 0.0033 0.3549 0.6949 1265.574872 4 0.0012 128 | 0/8 6 h-lim-p 0.0039 1.9363 0.2130 1265.574831 2 0.0021 153 | 0/8 7 h-lim-p 0.0057 5.7587 0.0771 1265.574821 2 0.0030 178 | 0/8 8 h-lim-p 0.2076 20.0000 0.0011 1265.574296 0 0.8304 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1265.574285 1 0.9961 222 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1265.574285 0 1.0938 242 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1265.574285 0 2.1875 262 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1265.574285 0 0.0781 286 | 0/8 13 h-lim-p 0.0267 20.0000 0.0000 1265.574285 0 0.0033 308 Out... lnL = -1265.574285 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1265.574285 Node 7: lnL = -1265.574285 Node 8: lnL = -1265.574285 Node 9: lnL = -1265.574285 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 615 Sequential format.. Reading seq # 1: YLL004W_Sbay Reading seq # 2: YLL004W_Scer Reading seq # 3: YLL004W_Skud Reading seq # 4: YLL004W_Smik Reading seq # 5: YLL004W_Spar Sequences read.. Counting patterns.. # site patterns = 65 Counting frequencies.. 120 bytes for distance 10400 bytes for lkl0 8320 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.710147 0.000060 1.279641 0.097084 0.321311 1.984305 2.471938 0.596259 lnL0 = -1968.574243 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1968.574243 x= 0.71015 0.00006 1.27964 0.09708 0.32131 1.98431 2.47194 0.59626 1 h-lim-p 0.0000 0.0000 238.7924 1968.374175 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0170 60.8896 1834.151086 m 0.0170 42 | 2/8 3 h-lim-p 0.0002 0.0020 46.8752 1833.484013 0 0.0010 56 | 2/8 4 h-lim-p 0.0161 0.1289 0.8909 .. | 2/8 5 h-lim-p 0.0000 0.0012 179.9930 1816.724401 0 0.0009 116 | 2/8 6 h-lim-p 0.0000 0.0001 785.7866 1809.361377 m 0.0001 128 | 3/8 7 h-lim-p 0.0006 0.0073 79.1997 1804.843288 0 0.0017 141 | 3/8 8 h-lim-p 0.1196 20.0000 1.1058 1803.908013 9 0.0300 174 | 3/8 9 h-lim-p 0.0885 0.7443 0.3752 1795.942355 0 0.3539 188 | 2/8 10 h-lim-p 0.0027 0.0218 29.0295 1795.358054 9 0.0015 228 | 2/8 11 h-lim-p 1.1515 20.0000 0.0380 1794.253031 6 0.8141 253 | 2/8 12 h-lim-p 1.6606 20.0000 0.0186 1793.998006 6 1.4570 283 | 1/8 13 h-lim-p 0.0398 2.6276 0.6817 1793.997645 4 0.0016 313 | 1/8 14 h-lim-p 2.5000 20.0000 0.0001 1793.997634 0 1.2500 332 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 1793.997634 0 1.0938 351 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 1793.997634 0 0.3125 372 | 1/8 17 h-lim-p 0.4659 20.0000 0.0000 1793.997634 0 0.0032 397 Out... lnL = -1793.997634 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1793.997634 Node 7: lnL = -1793.997634 Node 8: lnL = -1793.997634 Node 9: lnL = -1793.997634 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 347 Sequential format.. Reading seq # 1: YLL006W_Sbay Reading seq # 2: YLL006W_Scer Reading seq # 3: YLL006W_Skud Reading seq # 4: YLL006W_Smik Reading seq # 5: YLL006W_Spar Sequences read.. Counting patterns.. # site patterns = 153 Counting frequencies.. 120 bytes for distance 24480 bytes for lkl0 19584 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.273522 0.000060 0.304007 0.165616 0.076386 1.119745 0.351254 0.204117 lnL0 = -1446.169710 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1446.169710 x= 0.27352 0.00006 0.30401 0.16562 0.07639 1.11975 0.35125 0.20412 1 h-lim-p 0.0000 0.0000 141.2990 1446.145222 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0021 191.6444 1435.200369 9 0.0011 63 | 1/8 3 h-lim-p 0.0008 0.0067 32.7466 1434.293652 0 0.0017 76 | 1/8 4 h-lim-p 0.0074 0.0590 5.8077 1434.113026 6 0.0076 99 | 1/8 5 h-lim-p 0.0038 0.2850 11.6833 1432.567089 0 0.0455 114 | 1/8 6 h-lim-p 0.0018 0.0142 28.3840 1432.314723 0 0.0027 126 | 1/8 7 h-lim-p 0.0962 0.7693 0.5855 1428.110253 0 0.3846 140 | 0/8 8 h-lim-p 0.0020 0.0161 21.9136 1427.984951 2 0.0009 163 | 0/8 9 h-lim-p 0.0507 3.7978 0.4085 1427.476184 0 0.6083 178 | 0/8 10 h-lim-p 1.0875 8.7002 0.0510 1427.387008 2 1.0196 202 | 0/8 11 h-lim-p 1.1636 9.6473 0.0446 1427.347942 1 1.4545 224 | 0/8 12 h-lim-p 0.5789 4.6315 0.0267 1427.299470 0 1.7368 245 | 0/8 13 h-lim-p 2.5000 20.0000 0.0100 1427.293959 5 0.9136 277 | 0/8 14 h-lim-p 2.0975 20.0000 0.0044 1427.293743 2 0.9832 301 | 0/8 15 h-lim-p 2.5000 20.0000 0.0006 1427.293729 2 0.6580 326 | 0/8 16 h-lim-p 2.5000 20.0000 0.0001 1427.293728 0 1.0938 346 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1427.293728 0 1.0938 366 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1427.293728 0 0.6250 387 | 0/8 19 h-lim-p 1.2014 20.0000 0.0000 1427.293728 0 0.1502 409 | 0/8 20 h-lim-p 0.1219 20.0000 0.0000 1427.293728 0 0.0038 433 Out... lnL = -1427.293728 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1427.293728 Node 7: lnL = -1427.293728 Node 8: lnL = -1427.293728 Node 9: lnL = -1427.293728 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 840 Sequential format.. Reading seq # 1: YLL012W_Sbay Reading seq # 2: YLL012W_Scer Reading seq # 3: YLL012W_Skud Reading seq # 4: YLL012W_Smik Reading seq # 5: YLL012W_Spar Sequences read.. Counting patterns.. # site patterns = 247 Counting frequencies.. 120 bytes for distance 39520 bytes for lkl0 31616 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.123436 0.033677 0.047732 0.073868 0.069353 0.113104 0.149920 0.100587 lnL0 = -3155.945748 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3155.945748 x= 0.12344 0.03368 0.04773 0.07387 0.06935 0.11310 0.14992 0.10059 1 h-lim-p 0.0006 0.0047 212.6702 3153.696499 7 0.0001 37 | 0/8 2 h-lim-p 0.0003 0.0023 31.9212 3153.606171 7 0.0002 66 | 0/8 3 h-lim-p 0.0004 0.0115 16.1084 3153.584370 6 0.0002 93 | 0/8 4 h-lim-p 0.0008 0.0351 4.0529 3153.583260 4 0.0001 116 | 0/8 5 h-lim-p 0.0005 0.1504 1.1930 3153.583111 2 0.0002 132 | 0/8 6 h-lim-p 0.0022 1.2169 0.1297 3153.583109 0 0.0002 146 | 0/8 7 h-lim-p 0.0009 6.0496 0.0331 3153.583109 0 0.0004 166 | 0/8 8 h-lim-p 0.0443 20.0000 0.0003 3153.582852 0 1.0637 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3153.582844 1 0.9961 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3153.582843 0 1.0938 232 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3153.582843 0 1.0938 252 | 0/8 12 h-lim-p 0.7208 20.0000 0.0000 3153.582843 0 0.0004 282 Out... lnL = -3153.582843 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3153.582843 Node 7: lnL = -3153.582843 Node 8: lnL = -3153.582843 Node 9: lnL = -3153.582843 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 329 Sequential format.. Reading seq # 1: YLL016W_Sbay Reading seq # 2: YLL016W_Scer Reading seq # 3: YLL016W_Skud Reading seq # 4: YLL016W_Smik Reading seq # 5: YLL016W_Spar Sequences read.. Counting patterns.. # site patterns = 213 Counting frequencies.. 120 bytes for distance 34080 bytes for lkl0 27264 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.208551 0.203016 0.000060 0.941640 0.318824 0.273613 0.273347 0.138985 lnL0 = -1744.785351 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1744.785351 x= 0.20855 0.20302 0.00006 0.94164 0.31882 0.27361 0.27335 0.13899 1 h-lim-p 0.0000 0.0000 68.6017 1744.770507 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0252 33.9072 1743.431686 0 0.0026 42 | 1/8 3 h-lim-p 0.0055 0.0488 15.9118 1742.721692 1 0.0068 56 | 1/8 4 h-lim-p 0.0080 0.0785 13.5653 1742.264888 2 0.0075 72 | 1/8 5 h-lim-p 0.0130 0.1043 2.9310 1742.221155 4 0.0050 92 | 1/8 6 h-lim-p 0.0237 0.5737 0.6212 1740.466720 0 0.1898 107 | 1/8 7 h-lim-p 0.0033 0.0268 13.5613 1738.794706 0 0.0067 127 | 1/8 8 h-lim-p 1.7895 14.3159 0.0448 1738.612892 3 0.8109 145 | 0/8 9 h-lim-p 0.0095 0.3262 3.8403 1738.602627 5 0.0015 177 | 0/8 10 h-lim-p 0.4941 20.0000 0.0120 1738.570855 0 1.9763 191 | 0/8 11 h-lim-p 2.2571 20.0000 0.0105 1738.564448 3 1.0228 217 | 0/8 12 h-lim-p 2.5000 20.0000 0.0021 1738.563998 4 0.8479 248 | 0/8 13 h-lim-p 2.5000 20.0000 0.0007 1738.563960 3 0.8855 276 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 1738.563960 0 1.0938 296 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1738.563960 0 1.0938 316 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1738.563960 0 1.0938 336 | 0/8 17 h-lim-p 1.0588 20.0000 0.0000 1738.563960 0 1.0588 356 | 0/8 18 h-lim-p 0.0018 20.0000 0.0010 1738.563960 0 0.0018 376 | 0/8 19 h-lim-p 0.0036 20.0000 0.0005 1738.563960 0 0.0000 409 | 0/8 20 h-lim-p 0.0000 20.0000 0.0000 1738.563960 0 0.0000 438 | 0/8 21 h-lim-p 0.0000 20.0000 0.0000 1738.563960 0 0.0000 458 Out... lnL = -1738.563960 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1738.563960 Node 7: lnL = -1738.563960 Node 8: lnL = -1738.563960 Node 9: lnL = -1738.563960 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 867 Sequential format.. Reading seq # 1: YLL018C-A_Sbay Reading seq # 2: YLL018C-A_Scer Reading seq # 3: YLL018C-A_Skud Reading seq # 4: YLL018C-A_Smik Reading seq # 5: YLL018C-A_Spar Sequences read.. Counting patterns.. # site patterns = 363 Counting frequencies.. 120 bytes for distance 58080 bytes for lkl0 46464 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.392584 0.206720 0.056960 0.510871 0.320761 0.553184 0.407439 0.304957 lnL0 = -4332.408388 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4332.408388 x= 0.39258 0.20672 0.05696 0.51087 0.32076 0.55318 0.40744 0.30496 1 h-lim-p 0.0044 0.0353 44.4778 4331.301831 5 0.0012 33 | 0/8 2 h-lim-p 0.0022 0.0269 23.6482 4330.645278 0 0.0033 45 | 0/8 3 h-lim-p 0.0042 0.0333 16.5154 4330.006982 0 0.0083 58 | 0/8 4 h-lim-p 0.0025 0.0197 20.4217 4329.562935 0 0.0049 71 | 0/8 5 h-lim-p 0.0088 0.0706 7.5388 4329.529270 4 0.0018 92 | 0/8 6 h-lim-p 0.0099 0.1812 1.3433 4329.517830 3 0.0102 110 | 0/8 7 h-lim-p 0.0487 2.3114 0.2821 4329.503940 5 0.0356 134 | 0/8 8 h-lim-p 0.0136 1.1298 0.7366 4329.314695 0 0.0545 156 | 0/8 9 h-lim-p 2.5000 20.0000 0.0056 4329.311799 4 0.9802 184 | 0/8 10 h-lim-p 2.5000 20.0000 0.0004 4329.311779 0 1.0938 204 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4329.311779 0 1.0938 224 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4329.311779 0 1.0938 244 | 0/8 13 h-lim-p 2.1273 20.0000 0.0000 4329.311779 0 1.8614 264 | 0/8 14 h-lim-p 1.5010 20.0000 0.0000 4329.311779 0 0.0000 302 Out... lnL = -4329.311779 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4329.311779 Node 7: lnL = -4329.311779 Node 8: lnL = -4329.311779 Node 9: lnL = -4329.311779 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 793 Sequential format.. Reading seq # 1: YLL021W_Sbay Reading seq # 2: YLL021W_Scer Reading seq # 3: YLL021W_Skud Reading seq # 4: YLL021W_Smik Reading seq # 5: YLL021W_Spar Sequences read.. Counting patterns.. # site patterns = 245 Counting frequencies.. 120 bytes for distance 39200 bytes for lkl0 31360 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.168016 0.091293 0.058231 0.088714 0.106773 0.181012 0.186547 0.127868 lnL0 = -3498.182009 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3498.182009 x= 0.16802 0.09129 0.05823 0.08871 0.10677 0.18101 0.18655 0.12787 1 h-lim-p 0.0013 0.0102 90.6428 3497.392425 8 0.0002 43 | 0/8 2 h-lim-p 0.0006 0.0046 25.0843 3497.301756 5 0.0003 66 | 0/8 3 h-lim-p 0.0008 0.0318 9.4269 3497.292667 6 0.0002 93 | 0/8 4 h-lim-p 0.0006 0.0660 3.5211 3497.291192 2 0.0003 109 | 0/8 5 h-lim-p 0.0016 0.4564 0.6026 3497.291132 1 0.0003 124 | 0/8 6 h-lim-p 0.0009 1.2166 0.2250 3497.291126 1 0.0002 147 | 0/8 7 h-lim-p 0.0024 11.2711 0.0216 3497.291126 0 0.0006 168 | 0/8 8 h-lim-p 0.0538 20.0000 0.0002 3497.291038 0 0.8612 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3497.291038 0 1.0938 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3497.291038 0 1.0938 232 | 0/8 11 h-lim-p 1.1827 20.0000 0.0000 3497.291038 0 4.7310 254 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3497.291038 0 0.0781 278 | 0/8 13 h-lim-p 0.5270 20.0000 0.0000 3497.291038 0 0.0165 302 | 0/8 14 h-lim-p 0.0022 20.0000 0.0000 3497.291038 0 0.0000 336 Out... lnL = -3497.291038 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3497.291038 Node 7: lnL = -3497.291038 Node 8: lnL = -3497.291038 Node 9: lnL = -3497.291038 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 252 Sequential format.. Reading seq # 1: YLL023C_Sbay Reading seq # 2: YLL023C_Scer Reading seq # 3: YLL023C_Skud Reading seq # 4: YLL023C_Smik Reading seq # 5: YLL023C_Spar Sequences read.. Counting patterns.. # site patterns = 97 Counting frequencies.. 120 bytes for distance 15520 bytes for lkl0 12416 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.105505 0.061449 0.031631 0.039742 0.072167 0.121532 0.149304 0.079295 lnL0 = -878.202256 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 878.202256 x= 0.10550 0.06145 0.03163 0.03974 0.07217 0.12153 0.14930 0.07929 1 h-lim-p 0.0003 0.0028 25.4310 878.080173 6 0.0004 35 | 0/8 2 h-lim-p 0.0008 0.0098 11.9810 878.051310 7 0.0005 65 | 0/8 3 h-lim-p 0.0018 0.1515 3.1886 878.049810 5 0.0003 90 | 0/8 4 h-lim-p 0.0008 0.0797 1.2757 878.049448 4 0.0005 112 | 0/8 5 h-lim-p 0.0047 1.1960 0.1415 878.049438 2 0.0010 129 | 0/8 6 h-lim-p 0.0134 13.2136 0.0108 878.049438 0 0.0007 152 | 0/8 7 h-lim-p 0.0029 20.0000 0.0027 878.049438 0 0.0013 172 | 0/8 8 h-lim-p 0.0586 20.0000 0.0001 878.049436 0 0.7030 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 878.049436 0 1.0938 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 878.049436 0 2.1875 235 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 878.049436 0 0.2734 257 | 0/8 12 h-lim-p 0.0811 20.0000 0.0000 878.049436 0 0.0000 305 Out... lnL = -878.049436 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -878.049436 Node 7: lnL = -878.049436 Node 8: lnL = -878.049436 Node 9: lnL = -878.049436 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 857 Sequential format.. Reading seq # 1: YLL027W_Sbay Reading seq # 2: YLL027W_Scer Reading seq # 3: YLL027W_Skud Reading seq # 4: YLL027W_Smik Reading seq # 5: YLL027W_Spar Sequences read.. Counting patterns.. # site patterns = 260 Counting frequencies.. 120 bytes for distance 41600 bytes for lkl0 33280 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.153005 0.033259 0.042945 0.088716 0.067953 0.164235 0.159949 0.120798 lnL0 = -3388.119966 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3388.119966 x= 0.15300 0.03326 0.04294 0.08872 0.06795 0.16423 0.15995 0.12080 1 h-lim-p 0.0015 0.0137 215.8693 3385.600779 6 0.0001 37 | 0/8 2 h-lim-p 0.0002 0.0019 33.4778 3385.509932 7 0.0002 67 | 0/8 3 h-lim-p 0.0006 0.0244 9.4893 3385.500804 4 0.0002 87 | 0/8 4 h-lim-p 0.0003 0.0266 6.3848 3385.497831 5 0.0002 112 | 0/8 5 h-lim-p 0.0017 0.3990 0.7630 3385.497725 2 0.0004 129 | 0/8 6 h-lim-p 0.0046 2.0611 0.0613 3385.497724 0 0.0002 152 | 0/8 7 h-lim-p 0.0007 9.8052 0.0213 3385.497724 0 0.0003 172 | 0/8 8 h-lim-p 0.0563 20.0000 0.0001 3385.497675 0 0.9000 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3385.497673 0 1.0938 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3385.497673 0 1.0938 236 | 0/8 11 h-lim-p 1.2498 20.0000 0.0000 3385.497673 0 0.0098 262 | 0/8 12 h-lim-p 0.0035 20.0000 0.0000 3385.497673 0 0.0035 282 | 0/8 13 h-lim-p 0.0028 20.0000 0.0000 3385.497673 0 0.0000 320 | 0/8 14 h-lim-p 0.0000 20.0000 0.0012 | 0/8 15 h-lim-p 0.0000 20.0000 0.0012 Out... lnL = -3385.497673 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3385.497673 Node 7: lnL = -3385.497673 Node 8: lnL = -3385.497673 Node 9: lnL = -3385.497673 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 849 Sequential format.. Reading seq # 1: YLL028W_Sbay Reading seq # 2: YLL028W_Scer Reading seq # 3: YLL028W_Skud Reading seq # 4: YLL028W_Smik Reading seq # 5: YLL028W_Spar Sequences read.. Counting patterns.. # site patterns = 279 Counting frequencies.. 120 bytes for distance 44640 bytes for lkl0 35712 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.199067 0.071665 0.048121 0.088260 0.072238 0.154419 0.156069 0.161584 lnL0 = -3573.267112 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3573.267112 x= 0.19907 0.07167 0.04812 0.08826 0.07224 0.15442 0.15607 0.16158 1 h-lim-p 0.0033 0.9944 146.7326 3571.662522 7 0.0002 40 | 0/8 2 h-lim-p 0.0004 0.0038 56.7740 3571.254222 6 0.0003 66 | 0/8 3 h-lim-p 0.0005 0.0066 30.9329 3571.181215 6 0.0002 90 | 0/8 4 h-lim-p 0.0005 0.0172 11.6267 3571.169553 4 0.0002 110 | 0/8 5 h-lim-p 0.0021 0.1656 1.1530 3571.169369 3 0.0003 130 | 0/8 6 h-lim-p 0.0009 0.4236 0.3801 3571.169354 2 0.0002 147 | 0/8 7 h-lim-p 0.0013 4.9748 0.0648 3571.169352 1 0.0006 170 | 0/8 8 h-lim-p 0.0514 20.0000 0.0008 3571.168275 0 0.8231 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3571.168266 1 0.9961 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3571.168266 0 1.0938 236 | 0/8 11 h-lim-p 1.2201 20.0000 0.0000 3571.168266 0 1.8301 256 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3571.168266 0 0.1562 279 | 0/8 13 h-lim-p 0.0377 20.0000 0.0000 3571.168266 0 0.0000 323 Out... lnL = -3571.168266 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3571.168266 Node 7: lnL = -3571.168266 Node 8: lnL = -3571.168266 Node 9: lnL = -3571.168266 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 780 Sequential format.. Reading seq # 1: YLL029W_Sbay Reading seq # 2: YLL029W_Scer Reading seq # 3: YLL029W_Skud Reading seq # 4: YLL029W_Smik Reading seq # 5: YLL029W_Spar Sequences read.. Counting patterns.. # site patterns = 231 Counting frequencies.. 120 bytes for distance 36960 bytes for lkl0 29568 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.233171 0.013695 0.133375 0.133703 0.108822 0.499001 0.252089 0.173109 lnL0 = -3274.297067 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3274.297067 x= 0.23317 0.01370 0.13338 0.13370 0.10882 0.49900 0.25209 0.17311 1 h-lim-p 0.0014 0.0108 83.8688 3273.151495 7 0.0003 38 | 0/8 2 h-lim-p 0.0008 0.0084 38.2192 3272.728062 3 0.0007 56 | 0/8 3 h-lim-p 0.0008 0.0169 30.9290 3272.598627 4 0.0004 77 | 0/8 4 h-lim-p 0.0004 0.0215 30.7707 3272.193096 0 0.0017 91 | 0/8 5 h-lim-p 0.0010 0.0091 51.3913 3271.869869 4 0.0010 111 | 0/8 6 h-lim-p 0.0032 0.0253 15.3599 3271.814632 6 0.0009 136 | 0/8 7 h-lim-p 0.0060 0.0479 2.1824 3271.795508 0 0.0090 148 | 0/8 8 h-lim-p 1.2692 20.0000 0.0154 3271.769104 3 1.3101 166 | 0/8 9 h-lim-p 2.5000 20.0000 0.0014 3271.768933 2 1.0938 190 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 3271.768933 0 1.0938 210 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3271.768933 0 2.1875 230 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3271.768933 0 1.0938 250 | 0/8 13 h-lim-p 1.0320 20.0000 0.0000 3271.768933 0 4.1281 272 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 3271.768933 0 0.1562 295 | 0/8 15 h-lim-p 0.3260 20.0000 0.0000 3271.768933 0 0.0051 320 | 0/8 16 h-lim-p 0.0017 20.0000 0.0000 3271.768933 0 0.0000 358 Out... lnL = -3271.768933 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3271.768933 Node 7: lnL = -3271.768933 Node 8: lnL = -3271.768933 Node 9: lnL = -3271.768933 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 273 Sequential format.. Reading seq # 1: YLL033W_Sbay Reading seq # 2: YLL033W_Scer Reading seq # 3: YLL033W_Skud Reading seq # 4: YLL033W_Smik Reading seq # 5: YLL033W_Spar Sequences read.. Counting patterns.. # site patterns = 85 Counting frequencies.. 120 bytes for distance 13600 bytes for lkl0 10880 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.162357 0.087466 0.110410 0.126389 0.070384 4.791204 0.056936 0.023368 lnL0 = -914.312280 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 914.312280 x= 0.16236 0.08747 0.11041 0.12639 0.07038 4.79120 0.05694 0.02337 1 h-lim-p 0.0045 2.9480 63.5903 913.339608 2 0.0005 28 | 0/8 2 h-lim-p 0.0018 0.0148 7.5238 913.315946 2 0.0009 44 | 0/8 3 h-lim-p 0.0013 0.0376 5.2093 913.309363 5 0.0007 67 | 0/8 4 h-lim-p 0.0083 0.4188 0.4140 913.309276 2 0.0010 85 | 0/8 5 h-lim-p 0.0085 4.1209 0.0503 913.309274 2 0.0014 112 | 0/8 6 h-lim-p 0.0744 20.0000 0.0009 913.308813 0 1.1899 136 | 0/8 7 h-lim-p 2.5000 20.0000 0.0003 913.308763 2 0.9961 160 | 0/8 8 h-lim-p 2.5000 20.0000 0.0000 913.308763 0 1.0938 180 | 0/8 9 h-lim-p 1.0437 20.0000 0.0000 913.308763 016.6986 204 | 0/8 10 h-lim-p 0.0759 20.0000 0.0018 913.308763 0 0.0018 229 | 0/8 11 h-lim-p 0.0006 13.1227 0.0049 913.308763 0 0.0006 249 | 0/8 12 h-lim-p 0.0002 4.4543 0.0144 913.308763 0 0.0000 271 | 0/8 13 h-lim-p 0.0007 20.0000 0.0005 913.308763 0 0.0000 295 | 0/8 14 h-lim-p 0.0001 20.0000 0.0001 913.308763 0 0.0000 316 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 913.308763 0 0.0000 338 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 913.308763 0 0.0000 361 Out... lnL = -913.308763 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -913.308763 Node 7: lnL = -913.308763 Node 8: lnL = -913.308763 Node 9: lnL = -913.308763 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 275 Sequential format.. Reading seq # 1: YLL034C_Sbay Reading seq # 2: YLL034C_Scer Reading seq # 3: YLL034C_Skud Reading seq # 4: YLL034C_Smik Reading seq # 5: YLL034C_Spar Sequences read.. Counting patterns.. # site patterns = 121 Counting frequencies.. 120 bytes for distance 19360 bytes for lkl0 15488 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.108797 0.086511 0.082609 0.128695 0.068078 0.242148 0.143854 0.071126 lnL0 = -1214.487071 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1214.487071 x= 0.10880 0.08651 0.08261 0.12869 0.06808 0.24215 0.14385 0.07113 1 h-lim-p 0.0029 0.0233 38.4186 1214.126448 6 0.0005 39 | 0/8 2 h-lim-p 0.0020 0.0221 9.5199 1214.097815 7 0.0007 66 | 0/8 3 h-lim-p 0.0015 0.0461 4.1032 1214.093003 4 0.0007 85 | 0/8 4 h-lim-p 0.0025 0.2745 1.1008 1214.092415 3 0.0011 104 | 0/8 5 h-lim-p 0.0038 0.8837 0.3027 1214.092381 1 0.0008 119 | 0/8 6 h-lim-p 0.0130 12.1377 0.0194 1214.092381 0 0.0014 141 | 0/8 7 h-lim-p 0.0051 20.0000 0.0054 1214.092381 0 0.0011 162 | 0/8 8 h-lim-p 0.0476 20.0000 0.0001 1214.092374 0 0.7622 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1214.092374 0 1.0938 206 | 0/8 10 h-lim-p 2.0299 20.0000 0.0000 1214.092374 0 0.5075 227 | 0/8 11 h-lim-p 0.3100 20.0000 0.0000 1214.092374 0 0.0002 257 Out... lnL = -1214.092374 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1214.092374 Node 7: lnL = -1214.092374 Node 8: lnL = -1214.092374 Node 9: lnL = -1214.092374 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 334 Sequential format.. Reading seq # 1: YLL035W_Sbay Reading seq # 2: YLL035W_Scer Reading seq # 3: YLL035W_Skud Reading seq # 4: YLL035W_Smik Reading seq # 5: YLL035W_Spar Sequences read.. Counting patterns.. # site patterns = 142 Counting frequencies.. 120 bytes for distance 22720 bytes for lkl0 18176 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.126581 0.052702 0.057651 0.143017 0.110604 0.216774 0.248056 0.085941 lnL0 = -1542.771502 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1542.771502 x= 0.12658 0.05270 0.05765 0.14302 0.11060 0.21677 0.24806 0.08594 1 h-lim-p 0.0013 0.0101 107.8973 1540.736458 9 0.0004 48 | 0/8 2 h-lim-p 0.0008 0.0066 19.5701 1540.600222 5 0.0007 69 | 0/8 3 h-lim-p 0.0024 0.0607 5.8310 1540.589417 6 0.0007 97 | 0/8 4 h-lim-p 0.0033 0.2409 1.2441 1540.588674 4 0.0010 120 | 0/8 5 h-lim-p 0.0029 0.6172 0.4354 1540.588609 3 0.0008 139 | 0/8 6 h-lim-p 0.0046 3.4272 0.0732 1540.588607 0 0.0010 160 | 0/8 7 h-lim-p 0.0045 18.4954 0.0162 1540.588606 0 0.0020 180 | 0/8 8 h-lim-p 0.0662 20.0000 0.0005 1540.588510 0 1.0588 204 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1540.588497 1 0.9961 226 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1540.588497 0 1.2500 246 | 0/8 11 h-lim-p 1.7049 20.0000 0.0000 1540.588497 0 0.3729 267 | 0/8 12 h-lim-p 0.1749 20.0000 0.0000 1540.588497 0 0.0437 288 | 0/8 13 h-lim-p 0.0230 20.0000 0.0000 1540.588497 0 0.0000 318 | 0/8 14 h-lim-p 0.0004 20.0000 0.0000 1540.588497 0 0.0000 352 Out... lnL = -1540.588497 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1540.588497 Node 7: lnL = -1540.588497 Node 8: lnL = -1540.588497 Node 9: lnL = -1540.588497 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 417 Sequential format.. Reading seq # 1: YLL046C_Sbay Reading seq # 2: YLL046C_Scer Reading seq # 3: YLL046C_Skud Reading seq # 4: YLL046C_Smik Reading seq # 5: YLL046C_Spar Sequences read.. Counting patterns.. # site patterns = 138 Counting frequencies.. 120 bytes for distance 22080 bytes for lkl0 17664 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.199391 0.000060 0.109984 0.124591 0.099831 4.775519 0.185900 0.060402 lnL0 = -1543.438809 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1543.438809 x= 0.19939 0.00006 0.10998 0.12459 0.09983 4.77552 0.18590 0.06040 1 h-lim-p 0.0029 0.0228 57.7511 1542.681425 7 0.0004 41 | 0/8 2 h-lim-p 0.0004 0.0032 20.0903 1542.555685 0 0.0008 54 | 0/8 3 h-lim-p 0.0025 0.0345 6.4644 1542.544980 2 0.0006 71 | 0/8 4 h-lim-p 0.0021 0.1304 1.8330 1542.544173 3 0.0005 90 | 0/8 5 h-lim-p 0.0041 0.8790 0.2293 1542.543639 0 0.0164 104 | 0/8 6 h-lim-p 0.0312 1.5218 0.1204 1542.543628 3 0.0012 135 | 0/8 7 h-lim-p 0.0304 20.0000 0.0046 1542.540214 0 0.4866 159 | 0/8 8 h-lim-p 2.5000 20.0000 0.0001 1542.540212 0 1.0938 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1542.540212 0 1.0938 199 | 0/8 10 h-lim-p 1.3025 20.0000 0.0000 1542.540212 0 0.5698 219 | 0/8 11 h-lim-p 0.2647 20.0000 0.0000 1542.540212 0 0.0165 242 | 0/8 12 h-lim-p 0.0063 20.0000 0.0001 1542.540212 0 0.0004 265 | 0/8 13 h-lim-p 0.0000 0.8903 0.1210 1542.540212 0 0.0000 287 | 0/8 14 h-lim-p 0.0021 20.0000 0.0001 1542.540212 0 0.0000 326 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1542.540212 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1542.540212 Node 7: lnL = -1542.540212 Node 8: lnL = -1542.540212 Node 9: lnL = -1542.540212 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 271 Sequential format.. Reading seq # 1: YLL049W_Sbay Reading seq # 2: YLL049W_Scer Reading seq # 3: YLL049W_Skud Reading seq # 4: YLL049W_Smik Reading seq # 5: YLL049W_Spar Sequences read.. Counting patterns.. # site patterns = 122 Counting frequencies.. 120 bytes for distance 19520 bytes for lkl0 15616 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.160733 0.041229 0.061731 0.114222 0.049319 0.238490 0.232090 0.121061 lnL0 = -1224.428949 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1224.428949 x= 0.16073 0.04123 0.06173 0.11422 0.04932 0.23849 0.23209 0.12106 1 h-lim-p 0.0002 0.0017 74.9609 1223.150049 0 0.0004 23 | 0/8 2 h-lim-p 0.0012 0.0093 20.1817 1222.993046 8 0.0008 54 | 0/8 3 h-lim-p 0.0007 0.0057 16.7795 1222.950707 7 0.0004 85 | 0/8 4 h-lim-p 0.0010 0.0331 7.2678 1222.934860 4 0.0008 105 | 0/8 5 h-lim-p 0.0114 0.2676 0.5110 1222.934699 4 0.0010 130 | 0/8 6 h-lim-p 0.0173 16.5287 0.0284 1222.930079 0 0.1388 153 | 0/8 7 h-lim-p 0.0050 0.1764 0.7890 1222.896012 0 0.0100 174 | 0/8 8 h-lim-p 0.0066 0.2691 1.2035 1222.894663 3 0.0017 201 | 0/8 9 h-lim-p 2.3460 20.0000 0.0009 1222.893927 4 1.0004 223 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1222.893925 0 1.0938 243 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1222.893925 0 1.0938 263 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1222.893925 0 2.5000 283 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1222.893925 0 0.0049 311 | 0/8 14 h-lim-p 0.0032 20.0000 0.0000 1222.893925 0 0.0000 348 Out... lnL = -1222.893925 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1222.893925 Node 7: lnL = -1222.893925 Node 8: lnL = -1222.893925 Node 9: lnL = -1222.893925 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 367 Sequential format.. Reading seq # 1: YLL051C_Sbay Reading seq # 2: YLL051C_Scer Reading seq # 3: YLL051C_Skud Reading seq # 4: YLL051C_Smik Reading seq # 5: YLL051C_Spar Sequences read.. Counting patterns.. # site patterns = 117 Counting frequencies.. 120 bytes for distance 18720 bytes for lkl0 14976 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.107999 0.000060 0.063225 0.080667 0.048328 0.111098 0.149964 0.083077 lnL0 = -1348.214294 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1348.214294 x= 0.10800 0.00006 0.06323 0.08067 0.04833 0.11110 0.14996 0.08308 1 h-lim-p 0.0004 0.4087 250.7683 1344.550050 8 0.0001 37 | 0/8 2 h-lim-p 0.0005 0.0042 28.0281 1344.378498 3 0.0004 55 | 0/8 3 h-lim-p 0.0007 0.0126 16.3210 1344.351131 6 0.0003 81 | 0/8 4 h-lim-p 0.0008 0.0246 5.0917 1344.347117 3 0.0004 99 | 0/8 5 h-lim-p 0.0018 0.2681 0.9908 1344.346893 3 0.0005 118 | 0/8 6 h-lim-p 0.0054 0.9600 0.0869 1344.346891 1 0.0003 143 | 0/8 7 h-lim-p 0.0023 12.0039 0.0128 1344.346890 0 0.0023 163 | 0/8 8 h-lim-p 0.0161 17.0716 0.0018 1344.346308 0 0.2574 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1344.346300 1 0.9961 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1344.346300 0 1.0938 229 | 0/8 11 h-lim-p 1.2896 20.0000 0.0000 1344.346300 0 1.1284 249 | 0/8 12 h-lim-p 0.6978 20.0000 0.0000 1344.346300 0 0.1745 270 | 0/8 13 h-lim-p 0.0071 20.0000 0.0001 1344.346300 0 0.0000 311 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1344.346300 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1344.346300 Node 7: lnL = -1344.346300 Node 8: lnL = -1344.346300 Node 9: lnL = -1344.346300 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 849 Sequential format.. Reading seq # 1: YLL055W_Sbay Reading seq # 2: YLL055W_Scer Reading seq # 3: YLL055W_Skud Reading seq # 4: YLL055W_Smik Reading seq # 5: YLL055W_Spar Sequences read.. Counting patterns.. # site patterns = 331 Counting frequencies.. 120 bytes for distance 52960 bytes for lkl0 42368 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.298374 0.074522 0.121561 0.087913 0.087774 0.201256 0.296033 0.242484 lnL0 = -3997.180701 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3997.180701 x= 0.29837 0.07452 0.12156 0.08791 0.08777 0.20126 0.29603 0.24248 1 h-lim-p 0.0077 1.3237 102.1842 3995.592192 8 0.0003 44 | 0/8 2 h-lim-p 0.0007 0.0053 36.3645 3995.449271 7 0.0002 71 | 0/8 3 h-lim-p 0.0004 0.0162 24.5851 3995.341914 0 0.0005 83 | 0/8 4 h-lim-p 0.0012 0.0291 10.6789 3995.309353 6 0.0007 112 | 0/8 5 h-lim-p 0.0027 0.0952 2.9172 3995.307086 2 0.0006 129 | 0/8 6 h-lim-p 0.0008 0.1483 2.1704 3995.306350 4 0.0005 151 | 0/8 7 h-lim-p 0.0020 0.8960 0.5011 3995.306249 2 0.0009 167 | 0/8 8 h-lim-p 0.3996 20.0000 0.0011 3995.304100 0 1.1988 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3995.304071 1 0.9961 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3995.304071 0 1.0938 230 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3995.304071 0 1.2500 250 | 0/8 12 h-lim-p 1.6524 20.0000 0.0000 3995.304071 0 0.4131 271 | 0/8 13 h-lim-p 0.2089 20.0000 0.0000 3995.304071 0 0.0000 313 Out... lnL = -3995.304071 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3995.304071 Node 7: lnL = -3995.304071 Node 8: lnL = -3995.304071 Node 9: lnL = -3995.304071 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 458 Sequential format.. Reading seq # 1: YLL057C_Sbay Reading seq # 2: YLL057C_Scer Reading seq # 3: YLL057C_Skud Reading seq # 4: YLL057C_Smik Reading seq # 5: YLL057C_Spar Sequences read.. Counting patterns.. # site patterns = 216 Counting frequencies.. 120 bytes for distance 34560 bytes for lkl0 27648 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.197394 0.111629 0.084296 0.139809 0.110348 0.232742 0.199500 0.148393 lnL0 = -2035.214728 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2035.214728 x= 0.19739 0.11163 0.08430 0.13981 0.11035 0.23274 0.19950 0.14839 1 h-lim-p 0.0183 2.7836 47.1407 2034.698189 7 0.0005 42 | 0/8 2 h-lim-p 0.0026 0.0212 5.9774 2034.689720 6 0.0005 71 | 0/8 3 h-lim-p 0.0014 0.0912 2.0968 2034.687592 4 0.0011 91 | 0/8 4 h-lim-p 0.0029 0.2941 0.7901 2034.687369 4 0.0008 114 | 0/8 5 h-lim-p 0.0151 5.9633 0.0422 2034.687368 1 0.0009 139 | 0/8 6 h-lim-p 0.0061 20.0000 0.0064 2034.687368 0 0.0013 160 | 0/8 7 h-lim-p 0.0046 20.0000 0.0018 2034.687368 0 0.0020 180 | 0/8 8 h-lim-p 0.1053 20.0000 0.0000 2034.687368 0 0.8420 203 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2034.687368 0 1.0938 223 | 0/8 10 h-lim-p 1.6304 20.0000 0.0000 2034.687368 0 0.0510 247 | 0/8 11 h-lim-p 0.0222 20.0000 0.0000 2034.687368 0 0.0222 267 | 0/8 12 h-lim-p 0.0123 20.0000 0.0000 2034.687368 0 0.0004 291 Out... lnL = -2034.687368 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2034.687368 Node 7: lnL = -2034.687368 Node 8: lnL = -2034.687368 Node 9: lnL = -2034.687368 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 632 Sequential format.. Reading seq # 1: YLL058W_Sbay Reading seq # 2: YLL058W_Scer Reading seq # 3: YLL058W_Skud Reading seq # 4: YLL058W_Smik Reading seq # 5: YLL058W_Spar Sequences read.. Counting patterns.. # site patterns = 311 Counting frequencies.. 120 bytes for distance 49760 bytes for lkl0 39808 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.354303 0.000060 0.125058 0.176693 0.130208 0.195112 0.392515 0.283718 lnL0 = -2954.284311 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2954.284311 x= 0.35430 0.00006 0.12506 0.17669 0.13021 0.19511 0.39252 0.28372 1 h-lim-p 0.0005 0.0036 71.5785 2952.535072 0 0.0007 22 | 0/8 2 h-lim-p 0.0009 0.0108 54.4585 2951.826114 5 0.0007 44 | 0/8 3 h-lim-p 0.0011 0.0087 17.9891 2951.733355 6 0.0007 72 | 0/8 4 h-lim-p 0.0012 0.0660 10.0805 2951.677532 0 0.0018 84 | 0/8 5 h-lim-p 0.0041 0.1053 4.4120 2951.665818 5 0.0015 107 | 0/8 6 h-lim-p 0.0111 0.5947 0.6020 2951.665570 3 0.0014 127 | 0/8 7 h-lim-p 0.0021 0.7253 0.3849 2951.665510 0 0.0011 147 | 0/8 8 h-lim-p 0.1301 15.0110 0.0032 2951.662993 0 1.0411 170 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 2951.662974 1 0.9961 192 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2951.662974 0 1.0938 212 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2951.662974 0 1.0938 232 | 0/8 12 h-lim-p 1.3712 20.0000 0.0000 2951.662974 0 0.6856 252 | 0/8 13 h-lim-p 0.2917 20.0000 0.0000 2951.662974 0 0.1458 272 | 0/8 14 h-lim-p 0.0352 20.0000 0.0000 2951.662974 0 0.0000 312 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 2951.662974 0 0.0000 335 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 2951.662974 0 0.0000 360 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 2951.662974 0 0.0000 382 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 2951.662974 0 0.0000 413 Out... lnL = -2951.662974 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2951.662974 Node 7: lnL = -2951.662974 Node 8: lnL = -2951.662974 Node 9: lnL = -2951.662974 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 392 Sequential format.. Reading seq # 1: YLR001C_Sbay Reading seq # 2: YLR001C_Scer Reading seq # 3: YLR001C_Skud Reading seq # 4: YLR001C_Smik Reading seq # 5: YLR001C_Spar Sequences read.. Counting patterns.. # site patterns = 173 Counting frequencies.. 120 bytes for distance 27680 bytes for lkl0 22144 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.203022 0.073786 0.030498 0.141478 0.104388 0.193576 0.239598 0.150974 lnL0 = -1802.065244 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1802.065244 x= 0.20302 0.07379 0.03050 0.14148 0.10439 0.19358 0.23960 0.15097 1 h-lim-p 0.0011 0.0092 140.1402 1800.121287 3 0.0002 29 | 0/8 2 h-lim-p 0.0007 0.0054 23.0572 1799.956946 2 0.0006 45 | 0/8 3 h-lim-p 0.0016 0.0445 9.1559 1799.933551 4 0.0006 65 | 0/8 4 h-lim-p 0.0024 0.1285 2.4107 1799.930773 4 0.0010 87 | 0/8 5 h-lim-p 0.0049 0.7336 0.5128 1799.930642 2 0.0011 104 | 0/8 6 h-lim-p 0.0106 2.5899 0.0515 1799.930640 0 0.0012 126 | 0/8 7 h-lim-p 0.0041 20.0000 0.0146 1799.930634 0 0.0082 147 | 0/8 8 h-lim-p 0.0175 11.5648 0.0068 1799.929834 0 0.1398 170 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1799.929815 2 0.9961 194 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1799.929815 0 1.0938 214 | 0/8 11 h-lim-p 1.6760 20.0000 0.0000 1799.929815 0 2.5140 234 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1799.929815 0 0.2344 257 | 0/8 13 h-lim-p 0.0330 20.0000 0.0000 1799.929815 0 0.0001 284 Out... lnL = -1799.929815 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1799.929815 Node 7: lnL = -1799.929815 Node 8: lnL = -1799.929815 Node 9: lnL = -1799.929815 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 693 Sequential format.. Reading seq # 1: YLR002C_Sbay Reading seq # 2: YLR002C_Scer Reading seq # 3: YLR002C_Skud Reading seq # 4: YLR002C_Smik Reading seq # 5: YLR002C_Spar Sequences read.. Counting patterns.. # site patterns = 324 Counting frequencies.. 120 bytes for distance 51840 bytes for lkl0 41472 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.199402 0.089212 0.000060 0.540992 0.279594 0.241384 0.264592 0.125607 lnL0 = -3405.428263 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3405.428263 x= 0.19940 0.08921 0.00006 0.54099 0.27959 0.24138 0.26459 0.12561 1 h-lim-p 0.0006 0.0047 50.2389 3404.633324 4 0.0006 30 | 0/8 2 h-lim-p 0.0009 0.0126 35.4464 3404.415235 6 0.0005 57 | 0/8 3 h-lim-p 0.0007 0.0058 18.0536 3404.348833 5 0.0005 79 | 0/8 4 h-lim-p 0.0029 0.1408 3.3887 3404.343609 5 0.0010 102 | 0/8 5 h-lim-p 0.0052 0.4016 0.6288 3404.343395 2 0.0011 119 | 0/8 6 h-lim-p 0.0015 0.1212 0.4749 3404.343278 2 0.0014 143 | 0/8 7 h-lim-p 0.0054 1.3144 0.1227 3404.343269 1 0.0011 166 | 0/8 8 h-lim-p 0.0839 20.0000 0.0016 3404.341997 0 0.6709 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3404.341986 1 0.9961 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3404.341986 0 1.0938 231 | 0/8 11 h-lim-p 1.2535 20.0000 0.0000 3404.341986 0 3.7605 252 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3404.341986 0 0.2344 275 | 0/8 13 h-lim-p 0.0085 20.0000 0.0000 3404.341986 0 0.0075 295 | 0/8 14 h-lim-p 0.0026 20.0000 0.0000 3404.341986 0 0.0002 318 | 0/8 15 h-lim-p 0.0001 20.0000 0.0001 3404.341986 0 0.0000 352 | 0/8 16 h-lim-p 0.0000 20.0000 0.0008 | 0/8 17 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -3404.341986 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3404.341986 Node 7: lnL = -3404.341986 Node 8: lnL = -3404.341986 Node 9: lnL = -3404.341986 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 222 Sequential format.. Reading seq # 1: YLR003C_Sbay Reading seq # 2: YLR003C_Scer Reading seq # 3: YLR003C_Skud Reading seq # 4: YLR003C_Smik Reading seq # 5: YLR003C_Spar Sequences read.. Counting patterns.. # site patterns = 109 Counting frequencies.. 120 bytes for distance 17440 bytes for lkl0 13952 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.116904 0.049453 0.057021 0.145362 0.076583 0.124003 0.153816 0.079455 lnL0 = -885.374377 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 885.374377 x= 0.11690 0.04945 0.05702 0.14536 0.07658 0.12400 0.15382 0.07945 1 h-lim-p 0.0023 0.0187 54.1977 884.713536 7 0.0005 40 | 0/8 2 h-lim-p 0.0007 0.0055 12.7065 884.646737 0 0.0010 52 | 0/8 3 h-lim-p 0.0069 0.1335 1.8888 884.645419 2 0.0008 70 | 0/8 4 h-lim-p 0.0039 0.6735 0.3636 884.645355 2 0.0010 87 | 0/8 5 h-lim-p 0.0026 0.6707 0.1346 884.645344 1 0.0012 109 | 0/8 6 h-lim-p 0.0130 20.0000 0.0119 884.645192 0 0.0519 131 | 0/8 7 h-lim-p 0.0048 2.5741 0.1293 884.643227 0 0.0144 152 | 0/8 8 h-lim-p 0.0038 0.6153 0.4860 884.643093 4 0.0011 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 884.643080 2 1.0938 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 884.643079 0 1.0938 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 884.643079 0 1.0938 246 | 0/8 12 h-lim-p 1.4683 20.0000 0.0000 884.643079 0 4.4048 267 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 884.643079 0 0.1367 290 | 0/8 14 h-lim-p 1.5097 20.0000 0.0000 884.643079 0 0.0000 324 Out... lnL = -884.643079 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -884.643079 Node 7: lnL = -884.643079 Node 8: lnL = -884.643079 Node 9: lnL = -884.643079 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 577 Sequential format.. Reading seq # 1: YLR004C_Sbay Reading seq # 2: YLR004C_Scer Reading seq # 3: YLR004C_Skud Reading seq # 4: YLR004C_Smik Reading seq # 5: YLR004C_Spar Sequences read.. Counting patterns.. # site patterns = 174 Counting frequencies.. 120 bytes for distance 27840 bytes for lkl0 22272 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.130769 0.029510 0.076014 0.063947 0.031992 0.155917 0.143916 0.096576 lnL0 = -2205.937210 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2205.937210 x= 0.13077 0.02951 0.07601 0.06395 0.03199 0.15592 0.14392 0.09658 1 h-lim-p 0.0001 0.0008 133.2023 2204.747802 0 0.0002 23 | 0/8 2 h-lim-p 0.0003 0.0028 65.1230 2204.578547 7 0.0001 53 | 0/8 3 h-lim-p 0.0002 0.0030 33.0376 2204.471316 0 0.0003 65 | 0/8 4 h-lim-p 0.0009 0.0297 10.5964 2204.456242 6 0.0003 92 | 0/8 5 h-lim-p 0.0043 0.1465 0.7654 2204.456144 3 0.0003 113 | 0/8 6 h-lim-p 0.0005 0.4267 0.4722 2204.456077 1 0.0005 135 | 0/8 7 h-lim-p 0.0031 3.2802 0.0701 2204.454767 0 0.0126 157 | 0/8 8 h-lim-p 0.0030 0.2239 0.2976 2204.402706 0 0.0237 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0019 2204.396928 4 0.9643 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2204.396922 1 0.9961 230 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2204.396922 0 1.0938 250 | 0/8 12 h-lim-p 1.3138 20.0000 0.0000 2204.396922 0 0.1642 272 | 0/8 13 h-lim-p 0.0729 20.0000 0.0000 2204.396922 0 0.0001 301 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 2204.396922 0 0.0000 324 Out... lnL = -2204.396922 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2204.396922 Node 7: lnL = -2204.396922 Node 8: lnL = -2204.396922 Node 9: lnL = -2204.396922 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 569 Sequential format.. Reading seq # 1: YLR005W_Sbay Reading seq # 2: YLR005W_Scer Reading seq # 3: YLR005W_Skud Reading seq # 4: YLR005W_Smik Reading seq # 5: YLR005W_Spar Sequences read.. Counting patterns.. # site patterns = 159 Counting frequencies.. 120 bytes for distance 25440 bytes for lkl0 20352 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.104601 0.041977 0.067489 0.066480 0.029459 0.164096 0.129114 0.072633 lnL0 = -2136.222125 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2136.222125 x= 0.10460 0.04198 0.06749 0.06648 0.02946 0.16410 0.12911 0.07263 1 h-lim-p 0.0002 0.0018 77.4220 2135.688728 3 0.0002 28 | 0/8 2 h-lim-p 0.0004 0.0044 35.0802 2135.627234 7 0.0001 58 | 0/8 3 h-lim-p 0.0002 0.0049 23.8953 2135.588519 6 0.0002 84 | 0/8 4 h-lim-p 0.0007 0.0458 7.1335 2135.582863 4 0.0003 104 | 0/8 5 h-lim-p 0.0027 0.2355 0.6765 2135.582793 2 0.0003 122 | 0/8 6 h-lim-p 0.0018 1.2535 0.1121 2135.582791 0 0.0004 143 | 0/8 7 h-lim-p 0.0018 5.5819 0.0244 2135.582791 0 0.0002 165 | 0/8 8 h-lim-p 0.0248 20.0000 0.0002 2135.582724 0 0.7946 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2135.582723 0 1.0938 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2135.582723 0 1.0938 230 | 0/8 11 h-lim-p 1.0249 20.0000 0.0000 2135.582723 0 0.8968 250 | 0/8 12 h-lim-p 0.4430 20.0000 0.0000 2135.582723 0 0.0002 280 | 0/8 13 h-lim-p 0.0004 20.0000 0.0000 2135.582723 0 0.0000 316 Out... lnL = -2135.582723 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2135.582723 Node 7: lnL = -2135.582723 Node 8: lnL = -2135.582723 Node 9: lnL = -2135.582723 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 527 Sequential format.. Reading seq # 1: YLR007W_Sbay Reading seq # 2: YLR007W_Scer Reading seq # 3: YLR007W_Skud Reading seq # 4: YLR007W_Smik Reading seq # 5: YLR007W_Spar Sequences read.. Counting patterns.. # site patterns = 186 Counting frequencies.. 120 bytes for distance 29760 bytes for lkl0 23808 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.164490 0.066357 0.058099 0.136017 0.060706 0.216294 0.595160 0.100607 lnL0 = -2102.629415 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2102.629415 x= 0.16449 0.06636 0.05810 0.13602 0.06071 0.21629 0.59516 0.10061 1 h-lim-p 0.0011 0.0085 70.2883 2101.954692 6 0.0003 35 | 0/8 2 h-lim-p 0.0016 0.0131 7.1816 2101.944818 2 0.0004 52 | 0/8 3 h-lim-p 0.0005 0.0598 5.9791 2101.939280 3 0.0005 70 | 0/8 4 h-lim-p 0.0006 0.1142 4.2764 2101.930530 0 0.0019 83 | 0/8 5 h-lim-p 0.0013 0.0997 6.2237 2101.912018 0 0.0026 96 | 0/8 6 h-lim-p 0.0040 0.0730 4.0990 2101.910052 4 0.0006 120 | 0/8 7 h-lim-p 0.0032 0.1752 0.7644 2101.908909 0 0.0047 132 | 0/8 8 h-lim-p 2.5000 20.0000 0.0009 2101.908432 3 0.9961 158 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2101.908431 0 1.0938 178 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2101.908431 0 1.0938 198 | 0/8 11 h-lim-p 1.6083 20.0000 0.0000 2101.908431 0 1.4073 218 | 0/8 12 h-lim-p 0.1710 20.0000 0.0000 2101.908431 0 0.1710 238 | 0/8 13 h-lim-p 0.0421 20.0000 0.0001 2101.908431 0 0.0000 270 | 0/8 14 h-lim-p 0.0009 20.0000 0.0000 2101.908431 0 0.0000 306 Out... lnL = -2101.908431 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2101.908431 Node 7: lnL = -2101.908431 Node 8: lnL = -2101.908431 Node 9: lnL = -2101.908431 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 481 Sequential format.. Reading seq # 1: YLR008C_Sbay Reading seq # 2: YLR008C_Scer Reading seq # 3: YLR008C_Skud Reading seq # 4: YLR008C_Smik Reading seq # 5: YLR008C_Spar Sequences read.. Counting patterns.. # site patterns = 146 Counting frequencies.. 120 bytes for distance 23360 bytes for lkl0 18688 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.099831 0.049343 0.048442 0.094253 0.095672 0.111005 0.117912 0.067753 lnL0 = -1847.595616 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1847.595616 x= 0.09983 0.04934 0.04844 0.09425 0.09567 0.11101 0.11791 0.06775 1 h-lim-p 0.0009 0.0070 63.4172 1847.204906 2 0.0002 27 | 0/8 2 h-lim-p 0.0010 0.0082 8.8844 1847.195735 2 0.0002 44 | 0/8 3 h-lim-p 0.0007 0.0488 3.0457 1847.194632 4 0.0003 64 | 0/8 4 h-lim-p 0.0014 0.2775 0.5737 1847.194583 2 0.0003 81 | 0/8 5 h-lim-p 0.0053 5.2020 0.0332 1847.194583 0 0.0003 104 | 0/8 6 h-lim-p 0.0022 20.0000 0.0043 1847.194583 0 0.0010 124 | 0/8 7 h-lim-p 0.0108 20.0000 0.0004 1847.194578 0 0.1720 148 | 0/8 8 h-lim-p 0.0008 1.2572 0.0860 1847.194568 1 0.0008 170 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1847.194567 0 1.0938 190 | 0/8 10 h-lim-p 2.4046 20.0000 0.0000 1847.194567 0 1.0520 210 | 0/8 11 h-lim-p 1.0152 20.0000 0.0000 1847.194567 0 4.0607 232 | 0/8 12 h-lim-p 0.4422 20.0000 0.0001 1847.194567 0 0.3869 252 | 0/8 13 h-lim-p 0.0317 20.0000 0.0010 1847.194567 0 0.0158 272 | 0/8 14 h-lim-p 0.0054 20.0000 0.0028 1847.194567 0 0.0013 293 | 0/8 15 h-lim-p 0.0008 20.0000 0.0049 1847.194567 0 0.0000 332 | 0/8 16 h-lim-p 0.0000 20.0000 0.0010 | 0/8 17 h-lim-p 0.0000 20.0000 0.0010 Out... lnL = -1847.194567 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1847.194567 Node 7: lnL = -1847.194567 Node 8: lnL = -1847.194567 Node 9: lnL = -1847.194567 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 478 Sequential format.. Reading seq # 1: YLR009W_Sbay Reading seq # 2: YLR009W_Scer Reading seq # 3: YLR009W_Skud Reading seq # 4: YLR009W_Smik Reading seq # 5: YLR009W_Spar Sequences read.. Counting patterns.. # site patterns = 152 Counting frequencies.. 120 bytes for distance 24320 bytes for lkl0 19456 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.109367 0.076071 0.053304 0.094467 0.095459 0.102945 0.105872 0.075345 lnL0 = -1871.683491 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1871.683491 x= 0.10937 0.07607 0.05330 0.09447 0.09546 0.10295 0.10587 0.07535 1 h-lim-p 0.0003 0.0021 49.1809 1871.362833 5 0.0003 31 | 0/8 2 h-lim-p 0.0021 0.0418 6.3550 1871.357843 3 0.0003 52 | 0/8 3 h-lim-p 0.0008 0.0493 2.1052 1871.357277 4 0.0003 72 | 0/8 4 h-lim-p 0.0017 0.6482 0.3445 1871.357258 2 0.0003 89 | 0/8 5 h-lim-p 0.0043 8.8784 0.0271 1871.357258 0 0.0005 111 | 0/8 6 h-lim-p 0.0076 20.0000 0.0017 1871.357258 0 0.0067 131 | 0/8 7 h-lim-p 0.0058 20.0000 0.0019 1871.357250 0 0.0464 154 | 0/8 8 h-lim-p 0.0008 1.1089 0.1047 1871.357242 1 0.0007 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1871.357242 0 1.0938 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1871.357242 0 1.0938 216 | 0/8 11 h-lim-p 1.1077 20.0000 0.0000 1871.357242 0 0.9692 236 | 0/8 12 h-lim-p 0.2623 20.0000 0.0000 1871.357242 0 0.0656 257 | 0/8 13 h-lim-p 0.0147 20.0000 0.0001 1871.357242 0 0.0000 298 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1871.357242 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1871.357242 Node 7: lnL = -1871.357242 Node 8: lnL = -1871.357242 Node 9: lnL = -1871.357242 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 870 Sequential format.. Reading seq # 1: YLR010C_Sbay Reading seq # 2: YLR010C_Scer Reading seq # 3: YLR010C_Skud Reading seq # 4: YLR010C_Smik Reading seq # 5: YLR010C_Spar Sequences read.. Counting patterns.. # site patterns = 448 Counting frequencies.. 120 bytes for distance 71680 bytes for lkl0 57344 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.279337 0.143379 0.140560 0.225544 0.172229 0.389957 0.539494 0.182420 lnL0 = -4853.246877 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4853.246877 x= 0.27934 0.14338 0.14056 0.22554 0.17223 0.38996 0.53949 0.18242 1 h-lim-p 0.0083 1.3828 108.2717 4850.146040 8 0.0006 41 | 0/8 2 h-lim-p 0.0014 0.0113 33.1001 4849.775286 4 0.0007 62 | 0/8 3 h-lim-p 0.0011 0.0236 21.6443 4849.582323 3 0.0011 80 | 0/8 4 h-lim-p 0.0059 0.0884 4.0821 4849.572455 4 0.0013 103 | 0/8 5 h-lim-p 0.0038 0.4525 1.3557 4849.570454 4 0.0024 125 | 0/8 6 h-lim-p 0.0101 1.5552 0.3270 4849.570389 0 0.0013 139 | 0/8 7 h-lim-p 0.0066 8.1947 0.0628 4849.570329 1 0.0082 161 | 0/8 8 h-lim-p 0.0451 20.0000 0.0114 4849.564064 0 0.3609 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 4849.563822 2 0.9961 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4849.563821 0 1.0938 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4849.563821 0 1.0938 248 | 0/8 12 h-lim-p 1.2110 20.0000 0.0000 4849.563821 0 1.8165 268 | 0/8 13 h-lim-p 0.9022 20.0000 0.0000 4849.563821 0 1.8045 289 | 0/8 14 h-lim-p 0.0024 20.0000 0.0041 4849.563821 0 0.0000 318 | 0/8 15 h-lim-p 0.0026 20.0000 0.0000 4849.563821 0 0.0001 343 Out... lnL = -4849.563821 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4849.563821 Node 7: lnL = -4849.563821 Node 8: lnL = -4849.563821 Node 9: lnL = -4849.563821 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 885 Sequential format.. Reading seq # 1: YLR012C_Sbay Reading seq # 2: YLR012C_Scer Reading seq # 3: YLR012C_Skud Reading seq # 4: YLR012C_Smik Reading seq # 5: YLR012C_Spar Sequences read.. Counting patterns.. # site patterns = 372 Counting frequencies.. 120 bytes for distance 59520 bytes for lkl0 47616 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.229991 0.090794 0.062666 0.183671 0.144754 0.227597 0.255934 0.167017 lnL0 = -4127.280423 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4127.280423 x= 0.22999 0.09079 0.06267 0.18367 0.14475 0.22760 0.25593 0.16702 1 h-lim-p 0.0072 1.1906 106.7366 4125.546012 8 0.0003 44 | 0/8 2 h-lim-p 0.0003 0.0025 35.2165 4125.325116 0 0.0005 56 | 0/8 3 h-lim-p 0.0015 0.0293 11.4261 4125.286492 2 0.0007 72 | 0/8 4 h-lim-p 0.0019 0.0611 4.1112 4125.283220 2 0.0004 89 | 0/8 5 h-lim-p 0.0013 0.2881 1.3887 4125.282582 4 0.0007 111 | 0/8 6 h-lim-p 0.0063 1.3222 0.1635 4125.282563 1 0.0008 127 | 0/8 7 h-lim-p 0.0149 20.0000 0.0086 4125.277724 0 0.2376 151 | 0/8 8 h-lim-p 0.0013 0.2091 1.5596 4125.272995 3 0.0015 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 4125.272913 2 1.0889 194 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4125.272913 0 1.0938 214 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4125.272913 0 1.0938 234 | 0/8 12 h-lim-p 1.2558 20.0000 0.0000 4125.272913 0 0.0392 258 | 0/8 13 h-lim-p 0.0100 20.0000 0.0000 4125.272913 0 0.0050 278 | 0/8 14 h-lim-p 0.0023 20.0000 0.0000 4125.272913 0 0.0004 300 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 4125.272913 0 0.0000 335 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 4125.272913 0 0.0000 362 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 | 0/8 19 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -4125.272913 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4125.272913 Node 7: lnL = -4125.272913 Node 8: lnL = -4125.272913 Node 9: lnL = -4125.272913 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 877 Sequential format.. Reading seq # 1: YLR013W_Sbay Reading seq # 2: YLR013W_Scer Reading seq # 3: YLR013W_Skud Reading seq # 4: YLR013W_Smik Reading seq # 5: YLR013W_Spar Sequences read.. Counting patterns.. # site patterns = 402 Counting frequencies.. 120 bytes for distance 64320 bytes for lkl0 51456 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.268406 0.000060 0.179336 0.205092 0.155810 0.775374 0.267938 0.172360 lnL0 = -4443.348482 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4443.348482 x= 0.26841 0.00006 0.17934 0.20509 0.15581 0.77537 0.26794 0.17236 1 h-lim-p 0.0000 0.0000 197.8568 4443.287009 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0092 35.6193 4442.701884 0 0.0010 40 | 1/8 3 h-lim-p 0.0016 0.0571 21.5711 4442.341791 1 0.0020 54 | 1/8 4 h-lim-p 0.0023 0.0259 18.2776 4442.220450 2 0.0011 70 | 1/8 5 h-lim-p 0.0138 0.2107 1.4485 4442.140162 7 0.0081 100 | 1/8 6 h-lim-p 0.0042 0.1157 2.7577 4440.463915 0 0.0170 114 | 1/8 7 h-lim-p 0.0016 0.0124 19.2897 4435.471920 0 0.0031 127 | 1/8 8 h-lim-p 1.7575 14.0597 0.0199 4435.224541 2 0.8238 143 | 0/8 9 h-lim-p 0.0004 0.0128 40.6194 4434.977056 4 0.0004 170 | 0/8 10 h-lim-p 0.8503 8.4797 0.0198 4434.781623 0 1.2754 182 | 0/8 11 h-lim-p 2.4469 19.5752 0.0054 4434.770808 5 0.8687 213 | 0/8 12 h-lim-p 2.5000 20.0000 0.0005 4434.770666 3 0.8855 241 | 0/8 13 h-lim-p 2.5000 20.0000 0.0001 4434.770663 1 0.6152 264 | 0/8 14 h-lim-p 1.7828 20.0000 0.0000 4434.770663 0 1.5600 284 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 4434.770663 0 1.0938 304 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 4434.770663 0 1.0938 324 | 0/8 17 h-lim-p 1.1473 20.0000 0.0000 4434.770663 0 0.8605 344 | 0/8 18 h-lim-p 0.3078 20.0000 0.0000 4434.770663 0 0.0000 390 Out... lnL = -4434.770663 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4434.770663 Node 7: lnL = -4434.770663 Node 8: lnL = -4434.770663 Node 9: lnL = -4434.770663 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 252 Sequential format.. Reading seq # 1: YLR014C_Sbay Reading seq # 2: YLR014C_Scer Reading seq # 3: YLR014C_Skud Reading seq # 4: YLR014C_Smik Reading seq # 5: YLR014C_Spar Sequences read.. Counting patterns.. # site patterns = 104 Counting frequencies.. 120 bytes for distance 16640 bytes for lkl0 13312 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.114794 0.150209 0.043423 0.103145 0.056060 0.126506 0.112159 0.070709 lnL0 = -1018.800691 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1018.800691 x= 0.11479 0.15021 0.04342 0.10315 0.05606 0.12651 0.11216 0.07071 1 h-lim-p 0.0025 0.0203 35.7692 1018.556115 6 0.0004 37 | 0/8 2 h-lim-p 0.0013 0.0105 10.2179 1018.524135 4 0.0007 57 | 0/8 3 h-lim-p 0.0011 0.0430 5.8151 1018.517801 5 0.0005 82 | 0/8 4 h-lim-p 0.0021 0.1228 1.3178 1018.517201 4 0.0007 104 | 0/8 5 h-lim-p 0.0033 0.7017 0.2971 1018.517164 3 0.0009 123 | 0/8 6 h-lim-p 0.0103 20.0000 0.0253 1018.517164 0 0.0006 146 | 0/8 7 h-lim-p 0.0096 20.0000 0.0015 1018.517164 0 0.0042 166 | 0/8 8 h-lim-p 0.0422 20.0000 0.0001 1018.517162 0 0.3378 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1018.517162 0 1.0938 209 | 0/8 10 h-lim-p 1.5361 20.0000 0.0000 1018.517162 0 1.3441 229 | 0/8 11 h-lim-p 1.1513 20.0000 0.0000 1018.517162 0 0.1079 252 | 0/8 12 h-lim-p 0.0007 20.0000 0.0009 1018.517162 0 0.0000 276 | 0/8 13 h-lim-p 0.0002 20.0000 0.0001 1018.517162 0 0.0000 316 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1018.517162 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1018.517162 Node 7: lnL = -1018.517162 Node 8: lnL = -1018.517162 Node 9: lnL = -1018.517162 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 212 Sequential format.. Reading seq # 1: YLR016C_Sbay Reading seq # 2: YLR016C_Scer Reading seq # 3: YLR016C_Skud Reading seq # 4: YLR016C_Smik Reading seq # 5: YLR016C_Spar Sequences read.. Counting patterns.. # site patterns = 100 Counting frequencies.. 120 bytes for distance 16000 bytes for lkl0 12800 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.145622 0.055861 0.040156 0.053643 0.079141 0.119669 0.211476 0.102435 lnL0 = -807.017926 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 807.017926 x= 0.14562 0.05586 0.04016 0.05364 0.07914 0.11967 0.21148 0.10243 1 h-lim-p 0.0030 0.0241 42.6916 806.426272 2 0.0007 27 | 0/8 2 h-lim-p 0.0004 0.0035 22.4247 806.242227 0 0.0009 40 | 0/8 3 h-lim-p 0.0022 0.0288 8.9240 806.216525 6 0.0008 66 | 0/8 4 h-lim-p 0.0017 0.0290 4.1814 806.212883 6 0.0005 94 | 0/8 5 h-lim-p 0.0032 0.4450 0.6891 806.212599 2 0.0013 110 | 0/8 6 h-lim-p 0.0040 0.7462 0.2177 806.212578 1 0.0010 133 | 0/8 7 h-lim-p 0.0034 3.5050 0.0646 806.212575 2 0.0011 158 | 0/8 8 h-lim-p 0.1948 20.0000 0.0004 806.212457 0 1.1689 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 806.212451 1 0.9961 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 806.212451 0 1.0938 222 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 806.212451 0 0.0098 249 | 0/8 12 h-lim-p 0.0046 20.0000 0.0000 806.212451 0 0.0000 287 Out... lnL = -806.212451 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -806.212451 Node 7: lnL = -806.212451 Node 8: lnL = -806.212451 Node 9: lnL = -806.212451 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 212 Sequential format.. Reading seq # 1: YLR017W_Sbay Reading seq # 2: YLR017W_Scer Reading seq # 3: YLR017W_Skud Reading seq # 4: YLR017W_Smik Reading seq # 5: YLR017W_Spar Sequences read.. Counting patterns.. # site patterns = 96 Counting frequencies.. 120 bytes for distance 15360 bytes for lkl0 12288 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.134057 0.050022 0.052663 0.082896 0.049888 0.165002 0.198603 0.089942 lnL0 = -866.477869 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 866.477869 x= 0.13406 0.05002 0.05266 0.08290 0.04989 0.16500 0.19860 0.08994 1 h-lim-p 0.0021 0.0164 67.7917 865.237905 7 0.0006 38 | 0/8 2 h-lim-p 0.0008 0.0062 15.3264 865.148235 4 0.0008 58 | 0/8 3 h-lim-p 0.0013 0.0131 8.8234 865.133276 7 0.0005 86 | 0/8 4 h-lim-p 0.0013 0.0674 3.4295 865.127368 2 0.0012 102 | 0/8 5 h-lim-p 0.0069 0.5160 0.5955 865.127117 2 0.0015 119 | 0/8 6 h-lim-p 0.0127 2.5899 0.0702 865.127113 1 0.0014 143 | 0/8 7 h-lim-p 0.0024 5.8164 0.0411 865.127109 1 0.0025 165 | 0/8 8 h-lim-p 0.0356 20.0000 0.0028 865.126145 0 0.5701 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 865.126104 2 0.9961 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 865.126104 0 1.0938 233 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 865.126104 0 2.1875 253 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 865.126104 0 0.5469 274 | 0/8 13 h-lim-p 0.3138 20.0000 0.0000 865.126104 0 0.0785 295 | 0/8 14 h-lim-p 0.0409 20.0000 0.0000 865.126104 0 0.0204 315 | 0/8 15 h-lim-p 0.0137 20.0000 0.0000 865.126104 0 0.0068 335 | 0/8 16 h-lim-p 0.0052 20.0000 0.0000 865.126104 0 0.0000 362 Out... lnL = -865.126104 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -865.126104 Node 7: lnL = -865.126104 Node 8: lnL = -865.126104 Node 9: lnL = -865.126104 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 735 Sequential format.. Reading seq # 1: YLR018C_Sbay Reading seq # 2: YLR018C_Scer Reading seq # 3: YLR018C_Skud Reading seq # 4: YLR018C_Smik Reading seq # 5: YLR018C_Spar Sequences read.. Counting patterns.. # site patterns = 254 Counting frequencies.. 120 bytes for distance 40640 bytes for lkl0 32512 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.181219 0.053960 0.073181 0.130205 0.096285 0.156015 0.148391 0.129154 lnL0 = -2804.316141 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2804.316141 x= 0.18122 0.05396 0.07318 0.13020 0.09628 0.15601 0.14839 0.12915 1 h-lim-p 0.0008 0.0066 103.0812 2803.022081 9 0.0003 46 | 0/8 2 h-lim-p 0.0005 0.0037 42.3533 2802.683390 2 0.0004 62 | 0/8 3 h-lim-p 0.0006 0.0066 29.2930 2802.567698 7 0.0004 93 | 0/8 4 h-lim-p 0.0012 0.0267 9.3355 2802.553270 5 0.0004 117 | 0/8 5 h-lim-p 0.0012 0.1094 2.9667 2802.552029 4 0.0003 138 | 0/8 6 h-lim-p 0.0011 0.1812 0.8355 2802.551892 2 0.0004 154 | 0/8 7 h-lim-p 0.0009 0.5488 0.3800 2802.551866 0 0.0004 174 | 0/8 8 h-lim-p 0.1809 20.0000 0.0009 2802.551268 0 1.0856 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2802.551248 1 0.9961 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2802.551248 0 1.2500 238 | 0/8 11 h-lim-p 2.2321 20.0000 0.0000 2802.551248 0 0.4883 259 | 0/8 12 h-lim-p 0.2937 20.0000 0.0000 2802.551248 0 0.0046 284 | 0/8 13 h-lim-p 0.0026 20.0000 0.0000 2802.551248 0 0.0013 304 | 0/8 14 h-lim-p 0.0005 20.0000 0.0000 2802.551248 0 0.0001 326 | 0/8 15 h-lim-p 0.0039 20.0000 0.0000 2802.551248 0 0.0000 365 Out... lnL = -2802.551248 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2802.551248 Node 7: lnL = -2802.551248 Node 8: lnL = -2802.551248 Node 9: lnL = -2802.551248 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 245 Sequential format.. Reading seq # 1: YLR020C_Sbay Reading seq # 2: YLR020C_Scer Reading seq # 3: YLR020C_Skud Reading seq # 4: YLR020C_Smik Reading seq # 5: YLR020C_Spar Sequences read.. Counting patterns.. # site patterns = 95 Counting frequencies.. 120 bytes for distance 15200 bytes for lkl0 12160 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.154102 0.072161 0.033461 0.075461 0.057086 0.157988 0.133748 0.111313 lnL0 = -944.314959 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 944.314959 x= 0.15410 0.07216 0.03346 0.07546 0.05709 0.15799 0.13375 0.11131 1 h-lim-p 0.0002 0.0019 51.9112 943.677534 0 0.0005 23 | 0/8 2 h-lim-p 0.0007 0.0057 20.5012 943.579835 6 0.0005 47 | 0/8 3 h-lim-p 0.0012 0.0166 8.9812 943.558913 6 0.0006 73 | 0/8 4 h-lim-p 0.0024 0.0926 2.2893 943.558048 4 0.0004 97 | 0/8 5 h-lim-p 0.0011 0.2137 0.7389 943.557929 2 0.0005 113 | 0/8 6 h-lim-p 0.0069 13.8571 0.0520 943.557927 1 0.0014 136 | 0/8 7 h-lim-p 0.0991 20.0000 0.0007 943.557556 0 0.7932 159 | 0/8 8 h-lim-p 0.0034 1.5404 0.1685 943.557539 2 0.0011 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 943.557539 0 1.0938 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 943.557539 0 1.0938 225 | 0/8 11 h-lim-p 1.6206 20.0000 0.0000 943.557539 0 1.6206 245 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 943.557539 0 0.0781 269 | 0/8 13 h-lim-p 0.0219 20.0000 0.0000 943.557539 0 0.0000 298 Out... lnL = -943.557539 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -943.557539 Node 7: lnL = -943.557539 Node 8: lnL = -943.557539 Node 9: lnL = -943.557539 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 245 Sequential format.. Reading seq # 1: YLR021W_Sbay Reading seq # 2: YLR021W_Scer Reading seq # 3: YLR021W_Skud Reading seq # 4: YLR021W_Smik Reading seq # 5: YLR021W_Spar Sequences read.. Counting patterns.. # site patterns = 98 Counting frequencies.. 120 bytes for distance 15680 bytes for lkl0 12544 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.160693 0.059762 0.040255 0.073236 0.059311 0.151194 0.142943 0.117559 lnL0 = -951.530929 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 951.530929 x= 0.16069 0.05976 0.04025 0.07324 0.05931 0.15119 0.14294 0.11756 1 h-lim-p 0.0002 0.0016 66.4615 950.511333 0 0.0004 23 | 0/8 2 h-lim-p 0.0006 0.0051 23.6661 950.339826 6 0.0007 49 | 0/8 3 h-lim-p 0.0013 0.0125 12.5119 950.302280 2 0.0006 65 | 0/8 4 h-lim-p 0.0027 0.0798 2.8548 950.300764 5 0.0004 91 | 0/8 5 h-lim-p 0.0014 0.1796 0.7981 950.300591 4 0.0005 111 | 0/8 6 h-lim-p 0.0024 1.2401 0.1791 950.300399 0 0.0048 132 | 0/8 7 h-lim-p 0.0357 4.5375 0.0239 950.261940 0 0.2854 155 | 0/8 8 h-lim-p 0.0096 0.3768 0.7077 950.261679 2 0.0010 181 | 0/8 9 h-lim-p 2.0090 20.0000 0.0004 950.261519 0 0.8789 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 950.261519 0 1.0938 221 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 950.261519 0 1.2500 241 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 950.261519 0 0.2734 263 | 0/8 13 h-lim-p 0.1487 20.0000 0.0000 950.261519 0 0.0003 291 Out... lnL = -950.261519 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -950.261519 Node 7: lnL = -950.261519 Node 8: lnL = -950.261519 Node 9: lnL = -950.261519 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 643 Sequential format.. Reading seq # 1: YLR022C_Sbay Reading seq # 2: YLR022C_Scer Reading seq # 3: YLR022C_Skud Reading seq # 4: YLR022C_Smik Reading seq # 5: YLR022C_Spar Sequences read.. Counting patterns.. # site patterns = 228 Counting frequencies.. 120 bytes for distance 36480 bytes for lkl0 29184 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.157757 0.037787 0.089286 0.124643 0.067326 0.178558 0.187591 0.106644 lnL0 = -2663.181495 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2663.181495 x= 0.15776 0.03779 0.08929 0.12464 0.06733 0.17856 0.18759 0.10664 1 h-lim-p 0.0075 0.0598 60.1228 2662.709756 8 0.0003 46 | 0/8 2 h-lim-p 0.0005 0.0038 23.3409 2662.627918 6 0.0003 71 | 0/8 3 h-lim-p 0.0011 0.0304 7.1327 2662.622178 3 0.0003 90 | 0/8 4 h-lim-p 0.0007 0.0601 2.5308 2662.621266 2 0.0003 106 | 0/8 5 h-lim-p 0.0051 0.9865 0.1656 2662.621260 2 0.0004 125 | 0/8 6 h-lim-p 0.0053 14.5085 0.0127 2662.621260 0 0.0012 146 | 0/8 7 h-lim-p 0.0030 20.0000 0.0048 2662.621260 0 0.0027 166 | 0/8 8 h-lim-p 0.0102 20.0000 0.0013 2662.621225 0 0.1625 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2662.621222 0 1.0938 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2662.621222 0 1.0938 230 | 0/8 11 h-lim-p 1.7676 20.0000 0.0000 2662.621222 0 2.6514 250 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2662.621222 0 0.3125 272 | 0/8 13 h-lim-p 0.0822 20.0000 0.0000 2662.621222 0 0.0206 293 | 0/8 14 h-lim-p 0.0088 20.0000 0.0000 2662.621222 0 0.0011 315 | 0/8 15 h-lim-p 0.0015 20.0000 0.0000 2662.621222 0 0.0000 350 | 0/8 16 h-lim-p 0.0000 20.0000 0.0015 | 0/8 17 h-lim-p 0.0000 20.0000 0.0015 Out... lnL = -2662.621222 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2662.621222 Node 7: lnL = -2662.621222 Node 8: lnL = -2662.621222 Node 9: lnL = -2662.621222 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 568 Sequential format.. Reading seq # 1: YLR023C_Sbay Reading seq # 2: YLR023C_Scer Reading seq # 3: YLR023C_Skud Reading seq # 4: YLR023C_Smik Reading seq # 5: YLR023C_Spar Sequences read.. Counting patterns.. # site patterns = 168 Counting frequencies.. 120 bytes for distance 26880 bytes for lkl0 21504 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.135175 0.036074 0.033207 0.059731 0.035603 0.174751 0.127309 0.098114 lnL0 = -2149.857271 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2149.857271 x= 0.13518 0.03607 0.03321 0.05973 0.03560 0.17475 0.12731 0.09811 1 h-lim-p 0.0003 0.0027 145.9449 2148.642810 8 0.0001 41 | 0/8 2 h-lim-p 0.0004 0.0035 23.0067 2148.597611 5 0.0002 63 | 0/8 3 h-lim-p 0.0004 0.0116 11.3632 2148.591498 4 0.0001 85 | 0/8 4 h-lim-p 0.0004 0.0466 3.4265 2148.590054 5 0.0003 109 | 0/8 5 h-lim-p 0.0009 0.0965 1.0335 2148.589958 2 0.0002 126 | 0/8 6 h-lim-p 0.0011 1.0251 0.1831 2148.589951 1 0.0005 140 | 0/8 7 h-lim-p 0.0347 20.0000 0.0024 2148.589951 0 0.0019 163 | 0/8 8 h-lim-p 0.0258 20.0000 0.0002 2148.589942 0 0.3093 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2148.589942 0 1.0938 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2148.589942 0 2.1875 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2148.589942 0 0.0098 253 | 0/8 12 h-lim-p 0.0013 20.0000 0.0000 2148.589942 0 0.0000 295 Out... lnL = -2148.589942 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2148.589942 Node 7: lnL = -2148.589942 Node 8: lnL = -2148.589942 Node 9: lnL = -2148.589942 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 397 Sequential format.. Reading seq # 1: YLR026C_Sbay Reading seq # 2: YLR026C_Scer Reading seq # 3: YLR026C_Skud Reading seq # 4: YLR026C_Smik Reading seq # 5: YLR026C_Spar Sequences read.. Counting patterns.. # site patterns = 116 Counting frequencies.. 120 bytes for distance 18560 bytes for lkl0 14848 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.204370 0.009332 0.118609 0.085501 0.074573 4.801354 0.159080 0.015178 lnL0 = -1339.956489 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1339.956489 x= 0.20437 0.00933 0.11861 0.08550 0.07457 4.80135 0.15908 0.01518 1 h-lim-p 0.0009 0.0074 66.2536 1339.081295 2 0.0004 26 | 0/8 2 h-lim-p 0.0008 0.0067 27.6358 1338.911635 7 0.0005 56 | 0/8 3 h-lim-p 0.0013 0.0171 10.8123 1338.888952 6 0.0005 81 | 0/8 4 h-lim-p 0.0031 0.0874 1.5779 1338.888455 4 0.0004 103 | 0/8 5 h-lim-p 0.0031 0.2504 0.2074 1338.888443 2 0.0006 120 | 0/8 6 h-lim-p 0.1717 20.0000 0.0007 1338.887859 0 1.3738 143 | 0/8 7 h-lim-p 2.5000 20.0000 0.0002 1338.887829 2 0.9961 167 | 0/8 8 h-lim-p 2.5000 20.0000 0.0000 1338.887829 0 1.0938 187 | 0/8 9 h-lim-p 0.6889 20.0000 0.0000 1338.887829 0 0.3014 207 | 0/8 10 h-lim-p 0.0266 20.0000 0.0005 1338.887829 0 0.0008 231 | 0/8 11 h-lim-p 0.0004 20.0000 0.0011 1338.887829 0 0.0008 252 | 0/8 12 h-lim-p 0.0003 12.2353 0.0030 1338.887829 0 0.0000 274 | 0/8 13 h-lim-p 0.0000 20.0000 0.0025 1338.887829 0 0.0000 308 | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 1338.887829 0 0.0005 333 | 0/8 15 h-lim-p 0.0029 20.0000 0.0001 1338.887829 0 0.0004 355 | 0/8 16 h-lim-p 0.0007 20.0000 0.0000 1338.887829 0 0.0223 380 | 0/8 17 h-lim-p 0.0039 20.0000 0.0002 1338.887829 0 0.0000 406 | 0/8 18 h-lim-p 0.0000 16.6888 0.0021 1338.887829 0 0.0000 427 | 0/8 19 h-lim-p 0.0000 0.0786 0.4589 .. | 0/8 20 h-lim-p 0.0000 20.0000 0.0004 | 0/8 21 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1338.887829 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1338.887829 Node 7: lnL = -1338.887829 Node 8: lnL = -1338.887829 Node 9: lnL = -1338.887829 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 838 Sequential format.. Reading seq # 1: YLR027C_Sbay Reading seq # 2: YLR027C_Scer Reading seq # 3: YLR027C_Skud Reading seq # 4: YLR027C_Smik Reading seq # 5: YLR027C_Spar Sequences read.. Counting patterns.. # site patterns = 247 Counting frequencies.. 120 bytes for distance 39520 bytes for lkl0 31616 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.420485 0.000060 0.194371 0.212913 0.183072 0.255755 0.284708 0.339198 lnL0 = -3582.245239 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3582.245239 x= 0.42048 0.00006 0.19437 0.21291 0.18307 0.25575 0.28471 0.33920 1 h-lim-p 0.0000 0.0000 343.9113 3582.171442 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0037 96.9129 3578.158177 0 0.0010 40 | 1/8 3 h-lim-p 0.0022 0.0174 23.2307 3577.721956 6 0.0015 65 | 1/8 4 h-lim-p 0.0042 0.0970 8.5251 3577.409616 1 0.0053 79 | 1/8 5 h-lim-p 0.0037 0.2067 12.1581 3574.856459 0 0.0295 94 | 1/8 6 h-lim-p 0.0114 0.0916 2.4410 3566.548932 0 0.0687 108 | 0/8 7 h-lim-p 0.0011 0.0089 70.5775 3555.852012 0 0.0033 121 | 0/8 8 h-lim-p 0.0002 0.0013 61.1960 3555.210497 0 0.0007 135 | 0/8 9 h-lim-p 0.2483 2.1260 0.1614 3554.505823 0 0.4967 148 | 0/8 10 h-lim-p 0.2742 2.1936 0.0402 3554.406302 0 0.5484 169 | 0/8 11 h-lim-p 0.3609 2.8874 0.0191 3554.391229 0 0.7218 190 | 0/8 12 h-lim-p 1.1765 9.4118 0.0020 3554.390547 4 0.5991 219 | 0/8 13 h-lim-p 1.1306 14.0773 0.0011 3554.390339 3 0.7960 246 | 0/8 14 h-lim-p 2.5000 20.0000 0.0002 3554.390325 2 0.7996 271 | 0/8 15 h-lim-p 2.0295 20.0000 0.0001 3554.390325 0 1.0148 291 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 3554.390325 0 1.0938 311 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 3554.390325 0 0.5469 332 | 0/8 18 h-lim-p 0.5329 20.0000 0.0000 3554.390325 0 0.0083 357 | 0/8 19 h-lim-p 0.0132 20.0000 0.0000 3554.390325 0 0.0008 380 Out... lnL = -3554.390325 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3554.390325 Node 7: lnL = -3554.390325 Node 8: lnL = -3554.390325 Node 9: lnL = -3554.390325 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 699 Sequential format.. Reading seq # 1: YLR028C_Sbay Reading seq # 2: YLR028C_Scer Reading seq # 3: YLR028C_Skud Reading seq # 4: YLR028C_Smik Reading seq # 5: YLR028C_Spar Sequences read.. Counting patterns.. # site patterns = 195 Counting frequencies.. 120 bytes for distance 31200 bytes for lkl0 24960 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.118929 0.070532 0.047737 0.070245 0.046446 0.140272 0.161882 0.078869 lnL0 = -2747.868171 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2747.868171 x= 0.11893 0.07053 0.04774 0.07025 0.04645 0.14027 0.16188 0.07887 1 h-lim-p 0.0014 0.0115 132.8836 2746.536307 8 0.0002 41 | 0/8 2 h-lim-p 0.0004 0.0032 38.8688 2746.374404 8 0.0002 75 | 0/8 3 h-lim-p 0.0004 0.0082 25.1078 2746.342504 4 0.0001 95 | 0/8 4 h-lim-p 0.0004 0.0202 8.8716 2746.335118 5 0.0002 121 | 0/8 5 h-lim-p 0.0022 0.3413 0.9014 2746.335008 1 0.0003 137 | 0/8 6 h-lim-p 0.0009 0.3706 0.2701 2746.335002 1 0.0002 160 | 0/8 7 h-lim-p 0.0011 3.7405 0.0464 2746.335002 0 0.0005 180 | 0/8 8 h-lim-p 0.0749 20.0000 0.0003 2746.334781 0 1.1990 204 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2746.334765 1 0.9961 226 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2746.334765 0 2.1875 246 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2746.334765 0 0.2734 268 | 0/8 12 h-lim-p 0.0384 20.0000 0.0000 2746.334765 0 0.0048 290 | 0/8 13 h-lim-p 0.0023 20.0000 0.0000 2746.334765 0 0.0000 316 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 2746.334765 0 0.0000 339 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 2746.334765 0 0.0000 359 Out... lnL = -2746.334765 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2746.334765 Node 7: lnL = -2746.334765 Node 8: lnL = -2746.334765 Node 9: lnL = -2746.334765 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 209 Sequential format.. Reading seq # 1: YLR031W_Sbay Reading seq # 2: YLR031W_Scer Reading seq # 3: YLR031W_Skud Reading seq # 4: YLR031W_Smik Reading seq # 5: YLR031W_Spar Sequences read.. Counting patterns.. # site patterns = 107 Counting frequencies.. 120 bytes for distance 17120 bytes for lkl0 13696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.316464 0.360853 0.000060 1.205142 0.456877 4.011695 0.469107 0.127272 lnL0 = -895.808275 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 895.808275 x= 0.31646 0.36085 0.00006 1.20514 0.45688 4.01169 0.46911 0.12727 1 h-lim-p 0.0000 0.0000 80.5100 895.790841 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0028 195.2404 874.699098 3 0.0022 47 | 1/8 3 h-lim-p 0.0040 0.0318 12.4487 874.183996 0 0.0080 60 | 1/8 4 h-lim-p 0.0068 0.0544 7.3387 872.976811 m 0.0544 72 | 1/8 5 h-lim-p 0.0787 0.6296 0.9551 872.649565 0 0.1574 85 | 1/8 6 h-lim-p 0.0342 0.2740 0.8663 872.475242 0 0.2055 106 | 1/8 7 h-lim-p 0.5542 4.4339 0.0828 872.421563 2 0.5196 129 | 1/8 8 h-lim-p 1.1182 12.3632 0.0385 872.406025 3 0.9347 154 | 0/8 9 h-lim-p 0.0641 1.0276 0.5610 872.405747 3 0.0042 182 | 0/8 10 h-lim-p 0.1172 20.0000 0.0202 872.403447 0 0.9378 205 | 0/8 11 h-lim-p 2.5000 20.0000 0.0021 872.403392 3 0.9482 231 | 0/8 12 h-lim-p 2.5000 20.0000 0.0003 872.403392 0 1.0938 251 | 0/8 13 h-lim-p 2.5000 20.0000 0.0001 872.403391 0 1.0938 271 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 872.403391 0 1.0938 291 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 872.403391 0 1.2500 311 | 0/8 16 h-lim-p 0.7620 20.0000 0.0000 872.403391 0 0.0357 335 | 0/8 17 h-lim-p 0.0010 20.0000 0.0002 872.403391 0 0.0001 357 | 0/8 18 h-lim-p 0.0004 20.0000 0.0001 872.403391 0 0.0000 391 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 872.403391 0 0.0000 411 | 0/8 20 h-lim-p 0.0000 20.0000 0.0000 872.403391 0 0.0000 431 | 0/8 21 h-lim-p 0.0000 20.0000 0.0000 872.403391 0 0.0000 453 | 0/8 22 h-lim-p 0.0000 20.0000 0.0001 872.403391 0 0.0000 488 | 0/8 23 h-lim-p 0.0000 20.0000 0.0000 | 0/8 24 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -872.403391 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -872.403391 Node 7: lnL = -872.403391 Node 8: lnL = -872.403391 Node 9: lnL = -872.403391 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 499 Sequential format.. Reading seq # 1: YLR034C_Sbay Reading seq # 2: YLR034C_Scer Reading seq # 3: YLR034C_Skud Reading seq # 4: YLR034C_Smik Reading seq # 5: YLR034C_Spar Sequences read.. Counting patterns.. # site patterns = 137 Counting frequencies.. 120 bytes for distance 21920 bytes for lkl0 17536 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.100585 0.040512 0.060913 0.075668 0.041148 0.113693 0.129279 0.066336 lnL0 = -1760.538246 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1760.538246 x= 0.10058 0.04051 0.06091 0.07567 0.04115 0.11369 0.12928 0.06634 1 h-lim-p 0.0001 0.0007 125.3377 1759.257114 0 0.0002 23 | 0/8 2 h-lim-p 0.0010 0.0161 21.5062 1759.219105 7 0.0002 55 | 0/8 3 h-lim-p 0.0004 0.0088 9.6009 1759.210373 6 0.0002 82 | 0/8 4 h-lim-p 0.0009 0.0655 2.4328 1759.209458 3 0.0003 100 | 0/8 5 h-lim-p 0.0031 0.5215 0.2617 1759.209446 0 0.0003 114 | 0/8 6 h-lim-p 0.0012 3.2458 0.0740 1759.209445 1 0.0003 137 | 0/8 7 h-lim-p 0.0048 20.0000 0.0046 1759.209445 0 0.0042 157 | 0/8 8 h-lim-p 0.0087 20.0000 0.0022 1759.209330 0 0.1048 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1759.209329 0 1.0938 200 | 0/8 10 h-lim-p 1.8906 20.0000 0.0000 1759.209329 0 0.8271 220 | 0/8 11 h-lim-p 0.6836 20.0000 0.0000 1759.209329 0 0.0427 243 | 0/8 12 h-lim-p 0.0187 20.0000 0.0000 1759.209329 0 0.0000 272 | 0/8 13 h-lim-p 0.0003 20.0000 0.0000 1759.209329 0 0.0000 310 Out... lnL = -1759.209329 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1759.209329 Node 7: lnL = -1759.209329 Node 8: lnL = -1759.209329 Node 9: lnL = -1759.209329 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 935 Sequential format.. Reading seq # 1: YLR035C_Sbay Reading seq # 2: YLR035C_Scer Reading seq # 3: YLR035C_Skud Reading seq # 4: YLR035C_Smik Reading seq # 5: YLR035C_Spar Sequences read.. Counting patterns.. # site patterns = 350 Counting frequencies.. 120 bytes for distance 56000 bytes for lkl0 44800 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.239308 0.000060 0.282695 0.105943 0.215397 0.887459 0.359052 0.127580 lnL0 = -4144.937882 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4144.937882 x= 0.23931 0.00006 0.28270 0.10594 0.21540 0.88746 0.35905 0.12758 1 h-lim-p 0.0000 0.0000 150.6917 4144.907521 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0019 168.0162 4141.932299 0 0.0003 39 | 1/8 3 h-lim-p 0.0019 0.0151 25.4002 4141.725569 6 0.0007 65 | 1/8 4 h-lim-p 0.0032 0.1148 5.2811 4141.692585 4 0.0016 85 | 1/8 5 h-lim-p 0.0009 0.1918 9.0263 4141.396467 0 0.0074 100 | 1/8 6 h-lim-p 0.0029 0.0456 23.1254 4141.164765 5 0.0025 121 | 1/8 7 h-lim-p 0.1096 1.3084 0.5252 4135.813735 0 0.3289 134 | 0/8 8 h-lim-p 0.0054 0.0433 20.5357 4135.692238 5 0.0009 166 | 0/8 9 h-lim-p 0.1292 1.0338 0.0518 4135.245915 m 1.0338 178 | 1/8 10 h-lim-p 2.5000 20.0000 0.0123 4135.188540 6 1.0689 209 | 1/8 11 h-lim-p 1.6595 20.0000 0.0079 4135.173753 2 0.7779 232 | 1/8 12 h-lim-p 2.5000 20.0000 0.0013 4135.173232 2 1.0889 255 | 1/8 13 h-lim-p 2.5000 20.0000 0.0001 4135.173230 0 1.0938 274 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 4135.173230 0 1.0938 293 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 4135.173230 0 1.0938 312 | 1/8 16 h-lim-p 1.1671 20.0000 0.0000 4135.173230 0 1.1671 331 | 1/8 17 h-lim-p 0.6497 20.0000 0.0000 4135.173230 0 0.0051 356 | 1/8 18 h-lim-p 0.0020 20.0000 0.0000 4135.173230 0 0.0000 387 Out... lnL = -4135.173230 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4135.173230 Node 7: lnL = -4135.173230 Node 8: lnL = -4135.173230 Node 9: lnL = -4135.173230 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 448 Sequential format.. Reading seq # 1: YLR039C_Sbay Reading seq # 2: YLR039C_Scer Reading seq # 3: YLR039C_Skud Reading seq # 4: YLR039C_Smik Reading seq # 5: YLR039C_Spar Sequences read.. Counting patterns.. # site patterns = 231 Counting frequencies.. 120 bytes for distance 36960 bytes for lkl0 29568 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.158616 0.133780 0.100200 0.159229 0.148519 0.242775 0.181730 0.082913 lnL0 = -2049.234818 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2049.234818 x= 0.15862 0.13378 0.10020 0.15923 0.14852 0.24277 0.18173 0.08291 1 h-lim-p 0.0042 0.0335 42.8603 2048.671635 8 0.0006 44 | 0/8 2 h-lim-p 0.0018 0.0160 15.2061 2048.584107 2 0.0008 60 | 0/8 3 h-lim-p 0.0072 0.1115 1.7592 2048.582977 3 0.0008 80 | 0/8 4 h-lim-p 0.0030 0.8589 0.4487 2048.582901 3 0.0008 99 | 0/8 5 h-lim-p 0.0037 3.3637 0.0969 2048.582897 1 0.0009 122 | 0/8 6 h-lim-p 0.0219 20.0000 0.0040 2048.582896 0 0.0096 142 | 0/8 7 h-lim-p 0.0087 20.0000 0.0044 2048.582889 0 0.0349 164 | 0/8 8 h-lim-p 0.0041 20.0000 0.0378 2048.582850 0 0.0061 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2048.582849 0 1.0938 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2048.582849 0 1.0938 224 | 0/8 11 h-lim-p 1.2822 20.0000 0.0000 2048.582849 0 1.9233 244 | 0/8 12 h-lim-p 1.9256 20.0000 0.0000 2048.582849 0 0.4212 265 | 0/8 13 h-lim-p 0.0587 20.0000 0.0000 2048.582849 0 0.0000 310 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 2048.582849 0 0.0000 339 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 2048.582849 0 0.0000 396 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 2048.582849 0 0.0000 416 | 0/8 18 h-lim-p 0.0001 20.0000 0.0000 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0002 2048.582849 0 0.0000 486 | 0/8 20 h-lim-p 0.0000 20.0000 0.0002 | 0/8 21 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -2048.582849 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2048.582849 Node 7: lnL = -2048.582849 Node 8: lnL = -2048.582849 Node 9: lnL = -2048.582849 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 414 Sequential format.. Reading seq # 1: YLR040C_Sbay Reading seq # 2: YLR040C_Scer Reading seq # 3: YLR040C_Skud Reading seq # 4: YLR040C_Smik Reading seq # 5: YLR040C_Spar Sequences read.. Counting patterns.. # site patterns = 168 Counting frequencies.. 120 bytes for distance 26880 bytes for lkl0 21504 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.142477 0.072959 0.071813 0.104809 0.077715 0.147600 0.157175 0.088993 lnL0 = -1692.908712 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1692.908712 x= 0.14248 0.07296 0.07181 0.10481 0.07772 0.14760 0.15718 0.08899 1 h-lim-p 0.0087 0.0757 62.4097 1692.272872 7 0.0003 43 | 0/8 2 h-lim-p 0.0013 0.0107 15.3286 1692.216749 6 0.0005 67 | 0/8 3 h-lim-p 0.0015 0.0170 5.1674 1692.210963 5 0.0005 91 | 0/8 4 h-lim-p 0.0025 0.2944 0.9772 1692.210654 3 0.0007 110 | 0/8 5 h-lim-p 0.0024 0.9042 0.2752 1692.210636 1 0.0005 133 | 0/8 6 h-lim-p 0.0036 5.2494 0.0361 1692.210636 0 0.0008 154 | 0/8 7 h-lim-p 0.0072 20.0000 0.0039 1692.210636 0 0.0016 175 | 0/8 8 h-lim-p 0.0516 20.0000 0.0001 1692.210630 0 0.8249 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1692.210630 0 1.0938 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1692.210630 0 1.0938 239 | 0/8 11 h-lim-p 1.2492 20.0000 0.0000 1692.210630 0 2.4985 260 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1692.210630 0 0.0006 291 Out... lnL = -1692.210630 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1692.210630 Node 7: lnL = -1692.210630 Node 8: lnL = -1692.210630 Node 9: lnL = -1692.210630 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 830 Sequential format.. Reading seq # 1: YLR042C_Sbay Reading seq # 2: YLR042C_Scer Reading seq # 3: YLR042C_Skud Reading seq # 4: YLR042C_Smik Reading seq # 5: YLR042C_Spar Sequences read.. Counting patterns.. # site patterns = 295 Counting frequencies.. 120 bytes for distance 47200 bytes for lkl0 37760 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.220514 0.008499 0.080279 0.103288 0.110577 0.289789 0.205539 0.151139 lnL0 = -3940.374775 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3940.374775 x= 0.22051 0.00850 0.08028 0.10329 0.11058 0.28979 0.20554 0.15114 1 h-lim-p 0.0023 0.6484 185.1218 3938.294025 3 0.0001 31 | 0/8 2 h-lim-p 0.0008 0.0170 30.6208 3938.037550 6 0.0006 57 | 0/8 3 h-lim-p 0.0020 0.0283 8.6084 3938.029079 4 0.0002 80 | 0/8 4 h-lim-p 0.0005 0.0849 4.2398 3938.026103 4 0.0004 101 | 0/8 5 h-lim-p 0.0025 0.3183 0.6792 3938.026033 1 0.0003 117 | 0/8 6 h-lim-p 0.0020 1.1860 0.1067 3938.026031 0 0.0005 138 | 0/8 7 h-lim-p 0.0014 1.5692 0.0374 3938.026031 0 0.0004 159 | 0/8 8 h-lim-p 0.1657 20.0000 0.0001 3938.026007 0 1.3253 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3938.026007 0 1.0938 202 | 0/8 10 h-lim-p 1.6748 20.0000 0.0000 3938.026007 0 0.1832 224 | 0/8 11 h-lim-p 0.0918 20.0000 0.0000 3938.026007 0 0.0115 246 | 0/8 12 h-lim-p 0.0069 20.0000 0.0000 3938.026007 0 0.0009 268 | 0/8 13 h-lim-p 0.0007 20.0000 0.0000 3938.026007 0 0.0003 288 | 0/8 14 h-lim-p 0.0006 20.0000 0.0000 3938.026007 0 0.0003 308 | 0/8 15 h-lim-p 0.0006 20.0000 0.0000 3938.026007 0 0.0000 344 Out... lnL = -3938.026007 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3938.026007 Node 7: lnL = -3938.026007 Node 8: lnL = -3938.026007 Node 9: lnL = -3938.026007 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 863 Sequential format.. Reading seq # 1: YLR047C_Sbay Reading seq # 2: YLR047C_Scer Reading seq # 3: YLR047C_Skud Reading seq # 4: YLR047C_Smik Reading seq # 5: YLR047C_Spar Sequences read.. Counting patterns.. # site patterns = 270 Counting frequencies.. 120 bytes for distance 43200 bytes for lkl0 34560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.160825 0.000060 0.072930 0.132112 0.104572 0.212361 0.145878 0.111868 lnL0 = -3426.031119 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3426.031119 x= 0.16083 0.00006 0.07293 0.13211 0.10457 0.21236 0.14588 0.11187 1 h-lim-p 0.0001 0.0007 225.6150 3419.455181 0 0.0002 23 | 0/8 2 h-lim-p 0.0001 0.0005 119.3501 3418.630949 0 0.0001 36 | 0/8 3 h-lim-p 0.0002 0.0033 75.4598 3418.351835 4 0.0001 56 | 0/8 4 h-lim-p 0.0004 0.0088 23.9771 3418.288066 7 0.0003 86 | 0/8 5 h-lim-p 0.0018 0.0179 3.4337 3418.286840 2 0.0002 104 | 0/8 6 h-lim-p 0.0028 0.6683 0.2652 3418.286741 3 0.0008 125 | 0/8 7 h-lim-p 0.0077 1.5759 0.0277 3418.249608 0 0.1237 149 | 0/8 8 h-lim-p 0.0005 0.0069 7.4333 3418.214958 5 0.0005 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 3418.214545 3 0.8855 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3418.214543 0 1.0938 220 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3418.214543 0 1.0938 240 | 0/8 12 h-lim-p 0.9338 20.0000 0.0000 3418.214543 0 0.0073 266 | 0/8 13 h-lim-p 0.0028 20.0000 0.0000 3418.214543 0 0.0000 304 | 0/8 14 h-lim-p 0.0000 20.0000 0.0017 | 0/8 15 h-lim-p 0.0000 20.0000 0.0017 Out... lnL = -3418.214543 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3418.214543 Node 7: lnL = -3418.214543 Node 8: lnL = -3418.214543 Node 9: lnL = -3418.214543 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 449 Sequential format.. Reading seq # 1: YLR049C_Sbay Reading seq # 2: YLR049C_Scer Reading seq # 3: YLR049C_Skud Reading seq # 4: YLR049C_Smik Reading seq # 5: YLR049C_Spar Sequences read.. Counting patterns.. # site patterns = 183 Counting frequencies.. 120 bytes for distance 29280 bytes for lkl0 23424 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.196198 0.022825 0.071333 0.084893 0.085119 0.132012 0.214763 0.139416 lnL0 = -1807.334089 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1807.334089 x= 0.19620 0.02282 0.07133 0.08489 0.08512 0.13201 0.21476 0.13942 1 h-lim-p 0.0004 0.0035 89.4711 1806.106796 5 0.0003 32 | 0/8 2 h-lim-p 0.0004 0.0030 37.5369 1805.770525 0 0.0006 44 | 0/8 3 h-lim-p 0.0006 0.0048 25.8563 1805.665601 4 0.0005 64 | 0/8 4 h-lim-p 0.0012 0.0128 9.6821 1805.651961 6 0.0004 92 | 0/8 5 h-lim-p 0.0035 0.2329 1.0023 1805.651554 2 0.0008 109 | 0/8 6 h-lim-p 0.0044 0.6210 0.1838 1805.651533 1 0.0011 124 | 0/8 7 h-lim-p 0.0116 12.8461 0.0175 1805.651459 0 0.0232 145 | 0/8 8 h-lim-p 0.0122 20.0000 0.0333 1805.648405 0 0.0489 167 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 1805.648258 1 0.9961 189 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1805.648258 0 1.0938 209 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1805.648258 0 1.0938 229 | 0/8 12 h-lim-p 1.3181 20.0000 0.0000 1805.648258 0 2.6362 250 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1805.648258 0 0.1367 273 | 0/8 14 h-lim-p 0.0067 20.0000 0.0000 1805.648258 0 0.0017 294 | 0/8 15 h-lim-p 0.0012 20.0000 0.0000 1805.648258 0 0.0000 332 Out... lnL = -1805.648258 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1805.648258 Node 7: lnL = -1805.648258 Node 8: lnL = -1805.648258 Node 9: lnL = -1805.648258 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 272 Sequential format.. Reading seq # 1: YLR050C_Sbay Reading seq # 2: YLR050C_Scer Reading seq # 3: YLR050C_Skud Reading seq # 4: YLR050C_Smik Reading seq # 5: YLR050C_Spar Sequences read.. Counting patterns.. # site patterns = 101 Counting frequencies.. 120 bytes for distance 16160 bytes for lkl0 12928 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.161159 0.029618 0.040131 0.094946 0.048560 0.084550 0.133424 0.118540 lnL0 = -1034.304906 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1034.304906 x= 0.16116 0.02962 0.04013 0.09495 0.04856 0.08455 0.13342 0.11854 1 h-lim-p 0.0002 0.0015 104.8949 1032.427081 0 0.0004 23 | 0/8 2 h-lim-p 0.0002 0.0019 22.9387 1032.344212 0 0.0004 35 | 0/8 3 h-lim-p 0.0005 0.0107 15.9584 1032.294942 4 0.0005 56 | 0/8 4 h-lim-p 0.0025 0.0417 3.3542 1032.291781 2 0.0006 73 | 0/8 5 h-lim-p 0.0026 0.0726 0.7771 1032.291700 2 0.0003 91 | 0/8 6 h-lim-p 0.0013 1.4253 0.1744 1032.291681 2 0.0010 115 | 0/8 7 h-lim-p 0.0024 1.7190 0.0728 1032.291668 2 0.0018 139 | 0/8 8 h-lim-p 0.0202 20.0000 0.0067 1032.286627 0 0.3229 163 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 1032.286406 2 1.0938 187 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1032.286406 0 1.0938 207 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1032.286406 0 0.6250 228 | 0/8 12 h-lim-p 0.5037 20.0000 0.0000 1032.286406 0 0.0001 259 Out... lnL = -1032.286406 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1032.286406 Node 7: lnL = -1032.286406 Node 8: lnL = -1032.286406 Node 9: lnL = -1032.286406 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 230 Sequential format.. Reading seq # 1: YLR051C_Sbay Reading seq # 2: YLR051C_Scer Reading seq # 3: YLR051C_Skud Reading seq # 4: YLR051C_Smik Reading seq # 5: YLR051C_Spar Sequences read.. Counting patterns.. # site patterns = 81 Counting frequencies.. 120 bytes for distance 12960 bytes for lkl0 10368 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.095150 0.048667 0.026626 0.079099 0.037074 0.197136 0.157315 0.053318 lnL0 = -904.146941 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 904.146941 x= 0.09515 0.04867 0.02663 0.07910 0.03707 0.19714 0.15731 0.05332 1 h-lim-p 0.0001 0.0011 51.1136 903.675291 0 0.0004 23 | 0/8 2 h-lim-p 0.0008 6.5462 25.5549 903.595465 6 0.0003 47 | 0/8 3 h-lim-p 0.0007 0.0269 11.2608 903.553095 0 0.0010 59 | 0/8 4 h-lim-p 0.0008 0.0060 4.8455 903.550372 5 0.0003 81 | 0/8 5 h-lim-p 0.0006 0.0865 2.1511 903.549548 5 0.0004 107 | 0/8 6 h-lim-p 0.0078 3.2862 0.1213 903.549533 2 0.0013 125 | 0/8 7 h-lim-p 0.0023 1.6978 0.0659 903.549520 1 0.0018 147 | 0/8 8 h-lim-p 0.0101 15.2481 0.0120 903.546034 0 0.2423 171 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 903.545940 3 1.0004 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 903.545940 0 0.6250 218 | 0/8 11 h-lim-p 0.4849 20.0000 0.0000 903.545940 0 0.0005 247 | 0/8 12 h-lim-p 0.0002 20.0000 0.0000 903.545940 0 0.0002 267 | 0/8 13 h-lim-p 0.0002 20.0000 0.0000 903.545940 0 0.0000 298 | 0/8 14 h-lim-p 0.0000 20.0000 0.0045 | 0/8 15 h-lim-p 0.0000 20.0000 0.0045 Out... lnL = -903.545940 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -903.545940 Node 7: lnL = -903.545940 Node 8: lnL = -903.545940 Node 9: lnL = -903.545940 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 230 Sequential format.. Reading seq # 1: YLR052W_Sbay Reading seq # 2: YLR052W_Scer Reading seq # 3: YLR052W_Skud Reading seq # 4: YLR052W_Smik Reading seq # 5: YLR052W_Spar Sequences read.. Counting patterns.. # site patterns = 81 Counting frequencies.. 120 bytes for distance 12960 bytes for lkl0 10368 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.096682 0.044701 0.027205 0.079099 0.037074 0.196557 0.161087 0.054786 lnL0 = -904.440677 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 904.440677 x= 0.09668 0.04470 0.02721 0.07910 0.03707 0.19656 0.16109 0.05479 1 h-lim-p 0.0002 0.0013 52.7489 903.947659 0 0.0003 23 | 0/8 2 h-lim-p 0.0008 0.0068 21.2808 903.884756 3 0.0003 41 | 0/8 3 h-lim-p 0.0006 0.0263 11.9343 903.840469 0 0.0009 53 | 0/8 4 h-lim-p 0.0039 0.0768 2.6777 903.838637 5 0.0006 78 | 0/8 5 h-lim-p 0.0056 0.1112 0.2652 903.838617 3 0.0004 100 | 0/8 6 h-lim-p 0.0005 1.4817 0.2471 903.838574 0 0.0010 121 | 0/8 7 h-lim-p 0.0018 0.8628 0.1349 903.838462 0 0.0035 142 | 0/8 8 h-lim-p 0.0115 1.4765 0.0413 903.823257 0 0.0921 165 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 903.823229 2 0.9961 189 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 903.823229 0 1.0938 209 | 0/8 11 h-lim-p 1.8644 20.0000 0.0000 903.823229 0 1.6314 229 | 0/8 12 h-lim-p 2.4713 20.0000 0.0000 903.823229 0 1.2356 249 | 0/8 13 h-lim-p 0.5577 20.0000 0.0000 903.823229 0 0.2788 269 | 0/8 14 h-lim-p 0.0003 10.4283 0.0077 903.823229 0 0.0002 289 | 0/8 15 h-lim-p 0.0000 1.6325 0.0489 903.823229 0 0.0000 321 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 903.823229 0 0.0000 355 Out... lnL = -903.823229 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -903.823229 Node 7: lnL = -903.823229 Node 8: lnL = -903.823229 Node 9: lnL = -903.823229 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 336 Sequential format.. Reading seq # 1: YLR053C_Sbay Reading seq # 2: YLR053C_Scer Reading seq # 3: YLR053C_Skud Reading seq # 4: YLR053C_Smik Reading seq # 5: YLR053C_Spar Sequences read.. Counting patterns.. # site patterns = 103 Counting frequencies.. 120 bytes for distance 16480 bytes for lkl0 13184 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.121190 0.037919 0.036078 0.070734 0.038208 0.134984 0.081499 0.084497 lnL0 = -1158.520290 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1158.520290 x= 0.12119 0.03792 0.03608 0.07073 0.03821 0.13498 0.08150 0.08450 1 h-lim-p 0.0002 0.0017 67.7121 1158.009482 1 0.0003 24 | 0/8 2 h-lim-p 0.0008 0.0061 21.1810 1157.915501 7 0.0005 54 | 0/8 3 h-lim-p 0.0013 0.0235 7.4876 1157.906475 6 0.0004 80 | 0/8 4 h-lim-p 0.0007 0.0156 3.8640 1157.905326 5 0.0002 104 | 0/8 5 h-lim-p 0.0017 0.4544 0.4553 1157.905283 1 0.0004 119 | 0/8 6 h-lim-p 0.0021 0.8434 0.0887 1157.905277 2 0.0007 144 | 0/8 7 h-lim-p 0.0033 6.9614 0.0187 1157.905068 0 0.0260 167 | 0/8 8 h-lim-p 0.0033 0.4761 0.1465 1157.901228 0 0.0133 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 1157.900842 2 0.9961 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1157.900842 0 1.0938 233 | 0/8 11 h-lim-p 1.8781 20.0000 0.0000 1157.900842 0 0.0000 269 Out... lnL = -1157.900842 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1157.900842 Node 7: lnL = -1157.900842 Node 8: lnL = -1157.900842 Node 9: lnL = -1157.900842 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 1212 Sequential format.. Reading seq # 1: YLR054C_Sbay Reading seq # 2: YLR054C_Scer Reading seq # 3: YLR054C_Skud Reading seq # 4: YLR054C_Smik Reading seq # 5: YLR054C_Spar Sequences read.. Counting patterns.. # site patterns = 325 Counting frequencies.. 120 bytes for distance 52000 bytes for lkl0 41600 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.541355 0.274310 0.000060 0.307448 0.739811 0.741401 0.547148 0.414575 lnL0 = -5553.042708 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 5553.042708 x= 0.54136 0.27431 0.00006 0.30745 0.73981 0.74140 0.54715 0.41458 1 h-lim-p 0.0000 0.0000 598.6318 5552.919529 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0011 399.6923 5463.687813 m 0.0011 38 | 1/8 3 h-lim-p 0.0006 0.0051 154.2072 5269.225202 m 0.0051 50 | 1/8 4 h-lim-p 0.0000 0.0000 286.9082 h-lim-p: 4.63337077e-20 3.70669661e-19 2.86908216e+02 5269.225202 .. | 1/8 5 h-lim-p 0.0000 0.0010 2266.0453 5205.306863 0 0.0001 73 | 1/8 6 h-lim-p 0.0001 0.0008 684.3894 4957.244625 m 0.0008 85 | 1/8 7 h-lim-p 0.0000 0.0000 361.0483 h-lim-p: 9.46278588e-21 7.57022870e-20 3.61048270e+02 4957.244625 .. | 1/8 8 h-lim-p 0.0000 0.0009 686.7452 4938.569283 0 0.0001 108 | 1/8 9 h-lim-p 0.0001 0.0004 285.8300 4920.772535 m 0.0004 120 | 1/8 10 h-lim-p 0.0008 0.0130 156.9914 4912.531682 0 0.0012 132 | 1/8 11 h-lim-p 0.0002 0.0016 291.2325 4903.909894 0 0.0006 145 | 1/8 12 h-lim-p 0.0011 0.0087 18.1796 4903.652729 0 0.0016 157 | 1/8 13 h-lim-p 0.0022 0.0173 12.9674 4903.433660 0 0.0043 170 | 1/8 14 h-lim-p 0.5557 4.4452 0.0547 4901.125861 0 2.2226 184 | 1/8 15 h-lim-p 2.1039 16.8314 0.0240 4900.857057 5 1.0187 214 | 1/8 16 h-lim-p 2.5000 20.0000 0.0042 4900.848764 5 0.8513 246 | 1/8 17 h-lim-p 2.5000 20.0000 0.0002 4900.848729 0 1.2500 265 | 1/8 18 h-lim-p 2.5000 20.0000 0.0001 4900.848728 0 2.1875 284 | 1/8 19 h-lim-p 2.5000 20.0000 0.0000 4900.848728 0 1.0938 303 | 1/8 20 h-lim-p 0.9474 20.0000 0.0001 4900.848728 0 0.9474 322 | 1/8 21 h-lim-p 0.4839 20.0000 0.0001 4900.848728 0 0.4234 341 | 1/8 22 h-lim-p 0.1424 20.0000 0.0003 4900.848728 0 0.0712 360 | 1/8 23 h-lim-p 0.0289 20.0000 0.0007 4900.848728 0 0.0005 384 | 1/8 24 h-lim-p 0.0001 3.9353 0.0039 4900.848728 0 0.0001 403 | 1/8 25 h-lim-p 0.0002 8.1386 0.0019 4900.848728 0 0.0000 430 | 1/8 26 h-lim-p 0.0001 20.0000 0.0000 4900.848728 0 0.0000 457 | 1/8 27 h-lim-p 0.0000 20.0000 0.0005 4900.848728 0 0.0006 482 | 1/8 28 h-lim-p 0.0008 20.0000 0.0004 4900.848728 0 0.0008 501 | 1/8 29 h-lim-p 0.0012 20.0000 0.0003 4900.848728 0 0.0000 525 | 1/8 30 h-lim-p 0.0000 20.0000 0.0001 4900.848728 0 0.0000 555 | 1/8 31 h-lim-p 0.0000 20.0000 0.0000 4900.848728 0 0.0000 589 | 1/8 32 h-lim-p 0.0000 20.0000 0.0013 | 1/8 33 h-lim-p 0.0000 20.0000 0.0013 Out... lnL = -4900.848728 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4900.848728 Node 7: lnL = -4900.848728 Node 8: lnL = -4900.848728 Node 9: lnL = -4900.848728 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 805 Sequential format.. Reading seq # 1: YLR055C_Sbay Reading seq # 2: YLR055C_Scer Reading seq # 3: YLR055C_Skud Reading seq # 4: YLR055C_Smik Reading seq # 5: YLR055C_Spar Sequences read.. Counting patterns.. # site patterns = 241 Counting frequencies.. 120 bytes for distance 38560 bytes for lkl0 30848 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.138583 0.043516 0.043439 0.081158 0.046069 0.171551 0.111430 0.094376 lnL0 = -2965.388308 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2965.388308 x= 0.13858 0.04352 0.04344 0.08116 0.04607 0.17155 0.11143 0.09438 1 h-lim-p 0.0001 0.0010 232.5750 2962.579521 3 0.0001 28 | 0/8 2 h-lim-p 0.0002 0.0015 61.1186 2962.211697 7 0.0002 55 | 0/8 3 h-lim-p 0.0002 0.0039 56.0551 2962.081148 7 0.0001 84 | 0/8 4 h-lim-p 0.0003 0.0070 24.4649 2962.034094 6 0.0002 112 | 0/8 5 h-lim-p 0.0009 0.0405 6.0276 2962.029473 3 0.0003 132 | 0/8 6 h-lim-p 0.0023 0.2116 0.7232 2962.029417 2 0.0002 150 | 0/8 7 h-lim-p 0.0018 1.0654 0.0873 2962.029416 0 0.0004 171 | 0/8 8 h-lim-p 0.1401 20.0000 0.0003 2962.029321 0 1.1208 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2962.029317 0 1.0938 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2962.029317 0 1.0938 234 | 0/8 11 h-lim-p 1.0812 20.0000 0.0000 2962.029317 0 0.9461 254 | 0/8 12 h-lim-p 0.7330 20.0000 0.0000 2962.029317 0 0.0458 277 | 0/8 13 h-lim-p 0.0113 20.0000 0.0000 2962.029317 0 0.0007 300 | 0/8 14 h-lim-p 0.0010 20.0000 0.0000 2962.029317 0 0.0019 321 | 0/8 15 h-lim-p 0.0006 20.0000 0.0001 2962.029317 0 0.0000 358 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 | 0/8 17 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -2962.029317 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2962.029317 Node 7: lnL = -2962.029317 Node 8: lnL = -2962.029317 Node 9: lnL = -2962.029317 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 808 Sequential format.. Reading seq # 1: YLR056W_Sbay Reading seq # 2: YLR056W_Scer Reading seq # 3: YLR056W_Skud Reading seq # 4: YLR056W_Smik Reading seq # 5: YLR056W_Spar Sequences read.. Counting patterns.. # site patterns = 173 Counting frequencies.. 120 bytes for distance 27680 bytes for lkl0 22144 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.238876 0.289104 0.000060 0.129272 0.210728 0.485217 0.169085 0.157601 lnL0 = -2749.361138 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2749.361138 x= 0.23888 0.28910 0.00006 0.12927 0.21073 0.48522 0.16908 0.15760 1 h-lim-p 0.0000 0.0000 757.3264 2749.164192 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0009 422.0586 2687.608237 1 0.0007 42 | 1/8 3 h-lim-p 0.0006 0.0046 51.8688 2686.864667 2 0.0005 58 | 1/8 4 h-lim-p 0.0008 0.0070 34.5959 2686.642941 4 0.0004 79 | 1/8 5 h-lim-p 0.0010 0.0423 14.3333 2685.700485 0 0.0060 93 | 1/8 6 h-lim-p 0.0006 0.0416 146.5843 2634.607823 0 0.0281 110 | 1/8 7 h-lim-p 0.0717 0.5740 2.1662 2627.294906 0 0.2152 123 | 1/8 8 h-lim-p 0.1367 1.2438 3.4119 2621.020477 0 0.2733 136 | 0/8 9 h-lim-p 0.0040 0.0317 106.2629 2620.968605 7 0.0003 169 | 0/8 10 h-lim-p 0.2153 1.7227 0.1447 2620.750697 0 0.4307 182 | 0/8 11 h-lim-p 0.4437 20.0000 0.1404 2620.665768 0 1.7749 204 | 0/8 12 h-lim-p 0.7927 9.4325 0.3144 2618.630814 0 7.8872 227 | 0/8 13 h-lim-p 0.9881 7.9047 0.0176 2617.377562 0 1.9762 248 | 0/8 14 h-lim-p 0.0147 0.2026 2.3647 2617.365528 1 0.0184 270 | 0/8 15 h-lim-p 1.1129 8.9031 0.0182 2617.161822 7 0.7832 299 | 0/8 16 h-lim-p 2.3473 18.7788 0.0054 2617.132148 3 1.9622 325 | 0/8 17 h-lim-p 2.5000 20.0000 0.0039 2617.123934 4 1.6473 355 | 0/8 18 h-lim-p 2.5000 20.0000 0.0006 2617.123761 3 1.3437 382 | 0/8 19 h-lim-p 2.5000 20.0000 0.0003 2617.123746 0 1.0938 402 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 2617.123746 0 1.0938 422 | 0/8 21 h-lim-p 2.5000 20.0000 0.0000 2617.123746 0 1.0938 442 | 0/8 22 h-lim-p 2.5000 20.0000 0.0000 2617.123746 0 2.1875 462 | 0/8 23 h-lim-p 2.5000 20.0000 0.0000 2617.123746 0 0.5469 483 | 0/8 24 h-lim-p 0.4487 20.0000 0.0000 2617.123746 0 0.0491 505 | 0/8 25 h-lim-p 0.0240 20.0000 0.0000 2617.123746 0 0.0000 540 Out... lnL = -2617.123746 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2617.123746 Node 7: lnL = -2617.123746 Node 8: lnL = -2617.123746 Node 9: lnL = -2617.123746 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 389 Sequential format.. Reading seq # 1: YLR057W_Sbay Reading seq # 2: YLR057W_Scer Reading seq # 3: YLR057W_Skud Reading seq # 4: YLR057W_Smik Reading seq # 5: YLR057W_Spar Sequences read.. Counting patterns.. # site patterns = 144 Counting frequencies.. 120 bytes for distance 23040 bytes for lkl0 18432 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.166063 0.037366 0.050547 0.091334 0.070232 0.164399 0.261111 0.102991 lnL0 = -1625.848275 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1625.848275 x= 0.16606 0.03737 0.05055 0.09133 0.07023 0.16440 0.26111 0.10299 1 h-lim-p 0.0026 0.0204 41.8907 1625.598079 2 0.0003 28 | 0/8 2 h-lim-p 0.0010 0.0147 12.3969 1625.556772 7 0.0006 60 | 0/8 3 h-lim-p 0.0012 0.0148 6.0681 1625.548907 4 0.0005 79 | 0/8 4 h-lim-p 0.0013 0.0589 2.4118 1625.547388 2 0.0006 95 | 0/8 5 h-lim-p 0.0010 0.2271 1.4774 1625.546914 4 0.0006 118 | 0/8 6 h-lim-p 0.0054 1.4157 0.1636 1625.546908 2 0.0004 137 | 0/8 7 h-lim-p 0.0048 5.4865 0.0149 1625.546908 0 0.0021 157 | 0/8 8 h-lim-p 0.0633 20.0000 0.0005 1625.546794 0 0.5065 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1625.546793 0 1.0938 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1625.546793 0 1.0938 220 | 0/8 11 h-lim-p 0.7970 20.0000 0.0000 1625.546793 0 1.1955 240 | 0/8 12 h-lim-p 1.2067 20.0000 0.0000 1625.546793 0 1.2067 260 | 0/8 13 h-lim-p 0.0576 20.0000 0.0001 1625.546793 0 0.0864 280 | 0/8 14 h-lim-p 0.0269 20.0000 0.0003 1625.546793 0 0.0000 309 | 0/8 15 h-lim-p 0.0001 20.0000 0.0001 1625.546793 0 0.0000 338 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1625.546793 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1625.546793 Node 7: lnL = -1625.546793 Node 8: lnL = -1625.546793 Node 9: lnL = -1625.546793 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 444 Sequential format.. Reading seq # 1: YLR059C_Sbay Reading seq # 2: YLR059C_Scer Reading seq # 3: YLR059C_Skud Reading seq # 4: YLR059C_Smik Reading seq # 5: YLR059C_Spar Sequences read.. Counting patterns.. # site patterns = 153 Counting frequencies.. 120 bytes for distance 24480 bytes for lkl0 19584 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.105188 0.066179 0.039883 0.085927 0.049413 0.229328 0.147507 0.052282 lnL0 = -1735.321288 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1735.321288 x= 0.10519 0.06618 0.03988 0.08593 0.04941 0.22933 0.14751 0.05228 1 h-lim-p 0.0016 0.0124 98.3661 1734.489940 4 0.0002 32 | 0/8 2 h-lim-p 0.0005 0.0042 21.9186 1734.385002 6 0.0004 59 | 0/8 3 h-lim-p 0.0004 0.0109 24.4316 1734.334725 6 0.0003 84 | 0/8 4 h-lim-p 0.0008 0.0249 9.1311 1734.319237 6 0.0005 112 | 0/8 5 h-lim-p 0.0020 0.0836 2.3011 1734.318269 3 0.0004 131 | 0/8 6 h-lim-p 0.0025 0.4726 0.3779 1734.318238 2 0.0005 148 | 0/8 7 h-lim-p 0.0071 9.0848 0.0255 1734.318238 0 0.0004 171 | 0/8 8 h-lim-p 0.0351 20.0000 0.0003 1734.318124 0 1.1217 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1734.318115 1 0.9961 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1734.318115 0 1.0938 238 | 0/8 11 h-lim-p 0.9244 20.0000 0.0000 1734.318115 0 0.9244 258 | 0/8 12 h-lim-p 0.0078 20.0000 0.0021 1734.318115 0 0.0078 278 | 0/8 13 h-lim-p 0.0024 11.3587 0.0067 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 1734.318115 0 0.0000 345 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 1734.318115 0 0.0000 371 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0003 | 0/8 18 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -1734.318115 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1734.318115 Node 7: lnL = -1734.318115 Node 8: lnL = -1734.318115 Node 9: lnL = -1734.318115 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 443 Sequential format.. Reading seq # 1: YLR060W_Sbay Reading seq # 2: YLR060W_Scer Reading seq # 3: YLR060W_Skud Reading seq # 4: YLR060W_Smik Reading seq # 5: YLR060W_Spar Sequences read.. Counting patterns.. # site patterns = 120 Counting frequencies.. 120 bytes for distance 19200 bytes for lkl0 15360 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.096897 0.007026 0.082624 0.074922 0.094776 0.070642 0.154580 0.053500 lnL0 = -1546.307661 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1546.307661 x= 0.09690 0.00703 0.08262 0.07492 0.09478 0.07064 0.15458 0.05350 1 h-lim-p 0.0006 0.0047 76.5330 1545.703108 7 0.0002 38 | 0/8 2 h-lim-p 0.0001 0.0010 29.8762 1545.491579 0 0.0005 52 | 0/8 3 h-lim-p 0.0001 0.0006 26.6404 1545.301706 m 0.0006 64 | 1/8 4 h-lim-p 0.0020 0.0182 7.5023 1545.295136 6 0.0003 90 | 1/8 5 h-lim-p 0.0015 0.1850 1.3581 1545.294377 3 0.0006 108 | 1/8 6 h-lim-p 0.0016 0.8140 0.4795 1545.294307 2 0.0004 125 | 1/8 7 h-lim-p 0.0012 1.0595 0.1700 1545.294268 1 0.0012 146 | 1/8 8 h-lim-p 0.0106 20.0000 0.0193 1545.278329 0 0.5095 170 | 1/8 9 h-lim-p 2.5000 20.0000 0.0013 1545.277792 2 1.0889 193 | 1/8 10 h-lim-p 2.5000 20.0000 0.0000 1545.277791 0 1.0938 212 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 1545.277791 0 1.2500 231 | 1/8 12 h-lim-p 1.3767 20.0000 0.0000 1545.277791 0 0.0215 255 | 1/8 13 h-lim-p 0.0069 20.0000 0.0000 1545.277791 0 0.0000 296 | 1/8 14 h-lim-p 0.0000 20.0000 0.0011 1545.277791 0 0.0000 326 | 1/8 15 h-lim-p 0.0000 20.0000 0.0012 1545.277791 0 0.0001 348 | 1/8 16 h-lim-p 0.0002 20.0000 0.0005 1545.277791 0 0.0000 369 | 1/8 17 h-lim-p 0.0000 20.0000 0.0005 1545.277791 0 0.0000 397 | 1/8 18 h-lim-p 0.0000 20.0000 0.0001 .. | 1/8 19 h-lim-p 0.0000 20.0000 0.0009 | 1/8 20 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -1545.277791 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1545.277791 Node 7: lnL = -1545.277791 Node 8: lnL = -1545.277791 Node 9: lnL = -1545.277791 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 301 Sequential format.. Reading seq # 1: YLR068W_Sbay Reading seq # 2: YLR068W_Scer Reading seq # 3: YLR068W_Skud Reading seq # 4: YLR068W_Smik Reading seq # 5: YLR068W_Spar Sequences read.. Counting patterns.. # site patterns = 79 Counting frequencies.. 120 bytes for distance 12640 bytes for lkl0 10112 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.239395 0.045425 0.127856 0.096265 0.089754 4.708319 0.161565 0.000060 lnL0 = -1032.003409 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1032.003409 x= 0.23939 0.04543 0.12786 0.09627 0.08975 4.70832 0.16156 0.00006 1 h-lim-p 0.0000 0.0000 133.4298 1031.937105 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0067 33.1000 1031.480853 0 0.0009 40 | 1/8 3 h-lim-p 0.0043 0.0411 7.2411 1031.453331 6 0.0009 64 | 1/8 4 h-lim-p 0.0041 0.1264 1.6307 1031.409735 0 0.0062 76 | 1/8 5 h-lim-p 0.0049 0.1045 2.0343 1030.690306 0 0.0198 90 | 1/8 6 h-lim-p 0.0034 0.0272 8.7691 1027.529215 0 0.0068 103 | 1/8 7 h-lim-p 0.9269 7.4150 0.0226 1027.417103 8 0.5343 135 | 1/8 8 h-lim-p 2.5000 20.0000 0.0044 1027.411502 4 0.6366 163 | 0/8 9 h-lim-p 0.0162 1.4767 0.1728 1027.411479 0 0.0018 184 | 0/8 10 h-lim-p 0.9660 19.9176 0.0003 1027.411432 2 0.7452 208 | 0/8 11 h-lim-p 1.7746 14.1965 0.0000 1027.411432 0 0.7764 228 | 0/8 12 h-lim-p 0.0009 0.0149 0.0231 1027.411432 0 0.0000 261 | 0/8 13 h-lim-p 0.0000 2.8788 0.0001 1027.411432 0 0.0000 283 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 1027.411432 0 0.0000 303 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 1027.411432 0 0.0000 328 Out... lnL = -1027.411432 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1027.411432 Node 7: lnL = -1027.411432 Node 8: lnL = -1027.411432 Node 9: lnL = -1027.411432 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 545 Sequential format.. Reading seq # 1: YLR074C_Sbay Reading seq # 2: YLR074C_Scer Reading seq # 3: YLR074C_Skud Reading seq # 4: YLR074C_Smik Reading seq # 5: YLR074C_Spar Sequences read.. Counting patterns.. # site patterns = 214 Counting frequencies.. 120 bytes for distance 34240 bytes for lkl0 27392 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.137203 0.037410 0.049079 0.127090 0.089966 0.192016 0.181325 0.077523 lnL0 = -2206.945801 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2206.945801 x= 0.13720 0.03741 0.04908 0.12709 0.08997 0.19202 0.18132 0.07752 1 h-lim-p 0.0035 1.3542 111.6276 2205.798242 3 0.0002 31 | 0/8 2 h-lim-p 0.0013 0.0105 16.5365 2205.737077 7 0.0005 61 | 0/8 3 h-lim-p 0.0015 0.0372 5.1000 2205.732070 6 0.0004 88 | 0/8 4 h-lim-p 0.0012 0.1401 1.7550 2205.731473 4 0.0004 109 | 0/8 5 h-lim-p 0.0043 0.6768 0.1779 2205.731468 2 0.0003 128 | 0/8 6 h-lim-p 0.0059 20.0000 0.0103 2205.731467 0 0.0026 148 | 0/8 7 h-lim-p 0.0020 10.6951 0.0131 2205.731455 0 0.0081 170 | 0/8 8 h-lim-p 0.0040 3.1237 0.0266 2205.731195 0 0.0160 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2205.731187 1 0.9961 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2205.731187 0 1.0938 234 | 0/8 11 h-lim-p 1.3564 20.0000 0.0000 2205.731187 0 1.1869 254 | 0/8 12 h-lim-p 0.2853 20.0000 0.0000 2205.731187 0 0.0001 284 | 0/8 13 h-lim-p 0.0001 20.0000 0.0001 2205.731187 0 0.0000 310 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 2205.731187 0 0.0000 343 Out... lnL = -2205.731187 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2205.731187 Node 7: lnL = -2205.731187 Node 8: lnL = -2205.731187 Node 9: lnL = -2205.731187 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 350 Sequential format.. Reading seq # 1: YLR079W_Sbay Reading seq # 2: YLR079W_Scer Reading seq # 3: YLR079W_Skud Reading seq # 4: YLR079W_Smik Reading seq # 5: YLR079W_Spar Sequences read.. Counting patterns.. # site patterns = 77 Counting frequencies.. 120 bytes for distance 12320 bytes for lkl0 9856 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.079490 0.007881 0.034499 0.053898 0.022989 0.099082 0.114463 0.048708 lnL0 = -994.356648 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 994.356648 x= 0.07949 0.00788 0.03450 0.05390 0.02299 0.09908 0.11446 0.04871 1 h-lim-p 0.0002 0.0018 172.0883 993.303791 6 0.0001 33 | 0/8 2 h-lim-p 0.0003 0.0020 26.6594 993.213350 3 0.0003 51 | 0/8 3 h-lim-p 0.0003 0.0062 24.4262 993.182775 7 0.0002 80 | 0/8 4 h-lim-p 0.0006 0.0178 6.9151 993.176446 5 0.0003 103 | 0/8 5 h-lim-p 0.0016 0.0444 1.3317 993.176191 4 0.0003 124 | 0/8 6 h-lim-p 0.0014 0.5015 0.2931 993.176176 2 0.0004 141 | 0/8 7 h-lim-p 0.0011 1.4983 0.0996 993.176174 1 0.0004 163 | 0/8 8 h-lim-p 0.1991 20.0000 0.0002 993.176100 0 1.1948 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 993.176097 1 0.9961 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 993.176097 0 2.1875 227 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 993.176097 0 1.0938 247 | 0/8 12 h-lim-p 0.5804 20.0000 0.0000 993.176097 0 3.4825 269 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 993.176097 0 0.2734 291 | 0/8 14 h-lim-p 0.4494 20.0000 0.0000 993.176097 0 0.0001 323 Out... lnL = -993.176097 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -993.176097 Node 7: lnL = -993.176097 Node 8: lnL = -993.176097 Node 9: lnL = -993.176097 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 520 Sequential format.. Reading seq # 1: YLR083C_Sbay Reading seq # 2: YLR083C_Scer Reading seq # 3: YLR083C_Skud Reading seq # 4: YLR083C_Smik Reading seq # 5: YLR083C_Spar Sequences read.. Counting patterns.. # site patterns = 129 Counting frequencies.. 120 bytes for distance 20640 bytes for lkl0 16512 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.252812 0.000060 0.119655 0.121054 0.106568 4.686939 0.257124 0.013418 lnL0 = -1853.532081 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1853.532081 x= 0.25281 0.00006 0.11966 0.12105 0.10657 4.68694 0.25712 0.01342 1 h-lim-p 0.0000 0.0000 196.2466 1853.483687 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0007 45.1779 1852.806123 m 0.0007 38 | 2/8 3 h-lim-p 0.0008 0.0062 18.7102 1848.104430 0 0.0031 52 | 2/8 4 h-lim-p 0.0003 0.0021 77.9082 1847.012996 0 0.0005 65 | 2/8 5 h-lim-p 0.0031 0.0245 10.5706 1846.984331 5 0.0005 91 | 1/8 6 h-lim-p 0.0002 0.0270 27.0641 1846.745324 0 0.0008 105 | 1/8 7 h-lim-p 0.0029 0.0716 7.4574 1846.721238 6 0.0009 131 | 1/8 8 h-lim-p 1.0353 12.0067 0.0068 1846.661710 6 0.7804 155 | 1/8 9 h-lim-p 2.5000 20.0000 0.0012 1846.660454 4 0.8875 183 | 0/8 10 h-lim-p 0.0111 1.9225 0.0963 1846.660452 1 0.0006 207 | 0/8 11 h-lim-p 0.1454 1.1629 0.0001 1846.660450 m 1.1629 227 | 1/8 12 h-lim-p 0.5799 20.0000 0.0001 1846.660450 0 0.1450 248 | 0/8 13 h-lim-p 0.0008 16.5471 0.0178 1846.660450 0 0.0000 270 | 1/8 14 h-lim-p 0.1033 20.0000 0.0000 1846.660450 0 1.6534 294 | 0/8 15 h-lim-p 0.0001 1.0735 0.1807 1846.660450 0 0.0000 315 | 1/8 16 h-lim-p 0.3687 20.0000 0.0000 1846.660450 0 1.4747 337 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 1846.660450 0 1.0938 356 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 1846.660450 0 0.2734 377 Out... lnL = -1846.660450 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1846.660450 Node 7: lnL = -1846.660450 Node 8: lnL = -1846.660450 Node 9: lnL = -1846.660450 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 459 Sequential format.. Reading seq # 1: YLR084C_Sbay Reading seq # 2: YLR084C_Scer Reading seq # 3: YLR084C_Skud Reading seq # 4: YLR084C_Smik Reading seq # 5: YLR084C_Spar Sequences read.. Counting patterns.. # site patterns = 107 Counting frequencies.. 120 bytes for distance 17120 bytes for lkl0 13696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.298340 0.000060 0.166003 0.090963 0.083879 4.646996 0.220214 0.058945 lnL0 = -1581.806571 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1581.806571 x= 0.29834 0.00006 0.16600 0.09096 0.08388 4.64700 0.22021 0.05895 1 h-lim-p 0.0000 0.0000 263.3656 1581.724823 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0011 129.4810 1576.562104 9 0.0007 59 | 1/8 3 h-lim-p 0.0025 0.0200 11.6298 1576.458194 5 0.0013 82 | 1/8 4 h-lim-p 0.0125 0.0998 1.2134 1576.254682 1 0.0156 96 | 1/8 5 h-lim-p 0.0033 0.0447 5.7156 1573.921090 0 0.0099 109 | 1/8 6 h-lim-p 0.0003 0.0028 48.9030 1568.193097 0 0.0014 123 | 1/8 7 h-lim-p 0.3008 2.4062 0.0495 1567.755928 1 0.3760 137 | 0/8 8 h-lim-p 0.0057 0.1265 3.2543 1567.753025 4 0.0006 166 | 0/8 9 h-lim-p 0.1369 4.0041 0.0131 1567.667762 0 0.8214 180 | 0/8 10 h-lim-p 0.9681 7.7447 0.0024 1567.664906 3 0.8119 207 | 0/8 11 h-lim-p 2.5000 20.0000 0.0003 1567.664857 2 0.6152 232 | 0/8 12 h-lim-p 2.5000 20.0000 0.0001 1567.664854 1 0.9961 254 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1567.664854 0 1.0938 274 | 0/8 14 h-lim-p 1.4865 20.0000 0.0000 1567.664854 0 2.2297 294 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1567.664854 0 0.5469 315 | 0/8 16 h-lim-p 0.0966 20.0000 0.0000 1567.664854 0 0.0002 343 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 1567.664854 0 0.0000 364 | 0/8 18 h-lim-p 0.0001 20.0000 0.0000 1567.664854 0 0.0000 388 Out... lnL = -1567.664854 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1567.664854 Node 7: lnL = -1567.664854 Node 8: lnL = -1567.664854 Node 9: lnL = -1567.664854 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 280 Sequential format.. Reading seq # 1: YLR085C_Sbay Reading seq # 2: YLR085C_Scer Reading seq # 3: YLR085C_Skud Reading seq # 4: YLR085C_Smik Reading seq # 5: YLR085C_Spar Sequences read.. Counting patterns.. # site patterns = 128 Counting frequencies.. 120 bytes for distance 20480 bytes for lkl0 16384 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.171805 0.121560 0.019414 0.129278 0.085162 0.163940 0.140010 0.107389 lnL0 = -1183.735722 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1183.735722 x= 0.17181 0.12156 0.01941 0.12928 0.08516 0.16394 0.14001 0.10739 1 h-lim-p 0.0008 0.0063 82.3392 1182.964558 7 0.0003 40 | 0/8 2 h-lim-p 0.0007 0.0056 22.8929 1182.783338 4 0.0007 60 | 0/8 3 h-lim-p 0.0016 0.0323 10.1008 1182.753336 6 0.0007 83 | 0/8 4 h-lim-p 0.0023 0.0584 3.0675 1182.749225 4 0.0010 104 | 0/8 5 h-lim-p 0.0100 0.6421 0.2971 1182.749179 1 0.0011 120 | 0/8 6 h-lim-p 0.0235 17.4571 0.0139 1182.749177 1 0.0029 144 | 0/8 7 h-lim-p 0.0129 20.0000 0.0031 1182.748991 0 0.2062 168 | 0/8 8 h-lim-p 0.0026 0.4994 0.2462 1182.748856 4 0.0019 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1182.748837 2 1.0938 222 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1182.748837 0 1.0938 242 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1182.748837 0 0.3125 264 | 0/8 12 h-lim-p 0.1722 20.0000 0.0000 1182.748837 0 0.0215 286 | 0/8 13 h-lim-p 0.0124 20.0000 0.0000 1182.748837 0 0.0004 310 Out... lnL = -1182.748837 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1182.748837 Node 7: lnL = -1182.748837 Node 8: lnL = -1182.748837 Node 9: lnL = -1182.748837 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 280 Sequential format.. Reading seq # 1: YLR086W_Sbay Reading seq # 2: YLR086W_Scer Reading seq # 3: YLR086W_Skud Reading seq # 4: YLR086W_Smik Reading seq # 5: YLR086W_Spar Sequences read.. Counting patterns.. # site patterns = 133 Counting frequencies.. 120 bytes for distance 21280 bytes for lkl0 17024 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.140169 0.156013 0.011007 0.135758 0.078682 0.178624 0.182083 0.073799 lnL0 = -1195.501254 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1195.501254 x= 0.14017 0.15601 0.01101 0.13576 0.07868 0.17862 0.18208 0.07380 1 h-lim-p 0.0004 0.0034 93.7304 1194.555158 9 0.0003 48 | 0/8 2 h-lim-p 0.0005 0.0037 30.3041 1194.290369 0 0.0007 60 | 0/8 3 h-lim-p 0.0012 0.0143 17.4585 1194.208412 7 0.0007 91 | 0/8 4 h-lim-p 0.0031 0.0438 4.0340 1194.201331 6 0.0009 121 | 0/8 5 h-lim-p 0.0060 0.2900 0.6285 1194.201145 4 0.0010 144 | 0/8 6 h-lim-p 0.0033 1.3880 0.1818 1194.201122 2 0.0013 168 | 0/8 7 h-lim-p 0.0072 8.3507 0.0324 1194.201087 0 0.0108 188 | 0/8 8 h-lim-p 0.0252 6.2400 0.0140 1194.197993 0 0.1510 210 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1194.197880 0 1.0938 230 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1194.197879 0 1.0938 250 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1194.197879 0 1.0938 270 | 0/8 12 h-lim-p 1.1507 20.0000 0.0000 1194.197879 0 4.6027 292 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1194.197879 0 0.0043 320 | 0/8 14 h-lim-p 0.0204 20.0000 0.0000 1194.197879 0 0.0000 348 Out... lnL = -1194.197879 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1194.197879 Node 7: lnL = -1194.197879 Node 8: lnL = -1194.197879 Node 9: lnL = -1194.197879 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 390 Sequential format.. Reading seq # 1: YLR088W_Sbay Reading seq # 2: YLR088W_Scer Reading seq # 3: YLR088W_Skud Reading seq # 4: YLR088W_Smik Reading seq # 5: YLR088W_Spar Sequences read.. Counting patterns.. # site patterns = 137 Counting frequencies.. 120 bytes for distance 21920 bytes for lkl0 17536 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.145888 0.046730 0.030591 0.101609 0.081108 0.153350 0.164607 0.091375 lnL0 = -1625.959591 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1625.959591 x= 0.14589 0.04673 0.03059 0.10161 0.08111 0.15335 0.16461 0.09137 1 h-lim-p 0.0005 0.0042 122.4279 1624.769829 8 0.0002 43 | 0/8 2 h-lim-p 0.0005 0.0043 26.5282 1624.644019 7 0.0004 72 | 0/8 3 h-lim-p 0.0014 0.0346 7.1990 1624.635051 6 0.0004 98 | 0/8 4 h-lim-p 0.0016 0.1275 1.6983 1624.634435 5 0.0005 124 | 0/8 5 h-lim-p 0.0029 1.0011 0.2657 1624.634418 2 0.0005 142 | 0/8 6 h-lim-p 0.0016 2.5676 0.0796 1624.634416 1 0.0004 165 | 0/8 7 h-lim-p 0.0027 17.0084 0.0113 1624.634416 0 0.0012 185 | 0/8 8 h-lim-p 0.0323 20.0000 0.0004 1624.634305 0 0.5174 209 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1624.634304 0 1.0938 229 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1624.634304 0 1.0938 249 | 0/8 11 h-lim-p 0.9654 20.0000 0.0000 1624.634304 0 1.4481 269 | 0/8 12 h-lim-p 1.4521 20.0000 0.0000 1624.634304 0 1.2706 289 | 0/8 13 h-lim-p 0.1553 20.0000 0.0001 1624.634304 0 0.0388 310 | 0/8 14 h-lim-p 0.0098 20.0000 0.0002 1624.634304 0 0.0003 334 | 0/8 15 h-lim-p 0.0003 20.0000 0.0002 1624.634304 0 0.0003 354 | 0/8 16 h-lim-p 0.0003 20.0000 0.0003 1624.634304 0 0.0000 384 | 0/8 17 h-lim-p 0.0002 20.0000 0.0000 1624.634304 0 0.0000 412 Out... lnL = -1624.634304 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1624.634304 Node 7: lnL = -1624.634304 Node 8: lnL = -1624.634304 Node 9: lnL = -1624.634304 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 273 Sequential format.. Reading seq # 1: YLR098C_Sbay Reading seq # 2: YLR098C_Scer Reading seq # 3: YLR098C_Skud Reading seq # 4: YLR098C_Smik Reading seq # 5: YLR098C_Spar Sequences read.. Counting patterns.. # site patterns = 85 Counting frequencies.. 120 bytes for distance 13600 bytes for lkl0 10880 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.239395 0.244389 0.188164 0.203100 0.205241 4.381582 0.216585 0.000060 lnL0 = -909.256328 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 909.256328 x= 0.23939 0.24439 0.18816 0.20310 0.20524 4.38158 0.21659 0.00006 1 h-lim-p 0.0000 0.0000 122.5854 909.211362 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0118 38.0317 906.748122 0 0.0038 42 | 1/8 3 h-lim-p 0.0022 0.0172 14.7958 906.301592 0 0.0043 55 | 1/8 4 h-lim-p 0.0186 0.1489 1.7966 905.449726 0 0.0744 69 | 1/8 5 h-lim-p 0.0014 0.0115 9.5584 904.124723 m 0.0115 81 | 1/8 6 h-lim-p 0.0043 0.0344 12.4218 897.352442 0 0.0172 95 | 0/8 7 h-lim-p 0.0086 0.0689 14.8423 897.152127 2 0.0020 112 | 0/8 8 h-lim-p 0.2170 1.8426 0.1380 896.335903 0 0.4340 125 | 0/8 9 h-lim-p 0.6252 5.0017 0.0379 896.197316 5 0.5243 156 | 0/8 10 h-lim-p 0.6871 5.4965 0.0220 896.165141 0 1.0306 176 | 0/8 11 h-lim-p 2.5000 20.0000 0.0024 896.163667 2 1.1719 200 | 0/8 12 h-lim-p 2.5000 20.0000 0.0011 896.163622 3 0.4029 229 | 0/8 13 h-lim-p 2.5000 20.0000 0.0001 896.163621 0 1.0938 249 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 896.163621 0 1.0938 269 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 896.163621 0 2.1875 289 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 896.163621 0 1.0938 309 | 0/8 17 h-lim-p 1.0440 20.0000 0.0000 896.163621 0 4.1761 331 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 896.163621 0 0.0002 364 Out... lnL = -896.163621 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -896.163621 Node 7: lnL = -896.163621 Node 8: lnL = -896.163621 Node 9: lnL = -896.163621 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 424 Sequential format.. Reading seq # 1: YLR099C_Sbay Reading seq # 2: YLR099C_Scer Reading seq # 3: YLR099C_Skud Reading seq # 4: YLR099C_Smik Reading seq # 5: YLR099C_Spar Sequences read.. Counting patterns.. # site patterns = 101 Counting frequencies.. 120 bytes for distance 16160 bytes for lkl0 12928 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.061851 0.003459 0.049742 0.078573 0.054741 0.099268 0.161487 0.025992 lnL0 = -1338.629399 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1338.629399 x= 0.06185 0.00346 0.04974 0.07857 0.05474 0.09927 0.16149 0.02599 1 h-lim-p 0.0004 0.0033 140.1977 1336.844763 9 0.0002 44 | 0/8 2 h-lim-p 0.0005 0.0041 43.6425 1336.384953 4 0.0005 64 | 0/8 3 h-lim-p 0.0006 0.0048 28.7467 1336.297388 6 0.0003 88 | 0/8 4 h-lim-p 0.0008 0.0122 10.8493 1336.283110 6 0.0003 112 | 0/8 5 h-lim-p 0.0009 0.0449 3.4722 1336.281100 3 0.0004 130 | 0/8 6 h-lim-p 0.0009 0.0327 1.5655 1336.280337 2 0.0007 146 | 0/8 7 h-lim-p 0.0008 0.0362 1.5180 1336.279864 2 0.0007 162 | 0/8 8 h-lim-p 0.4489 20.0000 0.0024 1336.271330 0 1.7956 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 1336.270899 4 1.3578 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1336.270897 0 1.0938 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1336.270897 0 2.1875 245 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1336.270897 0 0.6250 266 | 0/8 13 h-lim-p 0.3965 20.0000 0.0000 1336.270897 0 0.0124 290 | 0/8 14 h-lim-p 0.0061 20.0000 0.0000 1336.270897 0 0.0000 328 Out... lnL = -1336.270897 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1336.270897 Node 7: lnL = -1336.270897 Node 8: lnL = -1336.270897 Node 9: lnL = -1336.270897 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 436 Sequential format.. Reading seq # 1: YLR099W-A_Sbay Reading seq # 2: YLR099W-A_Scer Reading seq # 3: YLR099W-A_Skud Reading seq # 4: YLR099W-A_Smik Reading seq # 5: YLR099W-A_Spar Sequences read.. Counting patterns.. # site patterns = 166 Counting frequencies.. 120 bytes for distance 26560 bytes for lkl0 21248 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.157269 0.087987 0.040103 0.064571 0.109764 0.116402 0.126611 0.101821 lnL0 = -1672.789254 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1672.789254 x= 0.15727 0.08799 0.04010 0.06457 0.10976 0.11640 0.12661 0.10182 1 h-lim-p 0.0002 0.0019 111.0816 1670.232668 0 0.0005 23 | 0/8 2 h-lim-p 0.0001 0.0012 58.4611 1669.861426 0 0.0003 36 | 0/8 3 h-lim-p 0.0007 0.0058 17.6693 1669.825678 7 0.0003 65 | 0/8 4 h-lim-p 0.0013 0.0482 3.4813 1669.822471 3 0.0005 84 | 0/8 5 h-lim-p 0.0022 0.2744 0.8881 1669.822206 4 0.0006 106 | 0/8 6 h-lim-p 0.0056 1.9919 0.1005 1669.821839 1 0.0070 128 | 0/8 7 h-lim-p 0.0050 1.6834 0.1401 1669.800358 0 0.0402 151 | 0/8 8 h-lim-p 0.0014 0.0508 4.0552 1669.774585 2 0.0013 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0008 1669.773619 3 0.9961 193 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1669.773616 0 1.0938 213 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1669.773616 0 1.0938 233 | 0/8 12 h-lim-p 1.7823 20.0000 0.0000 1669.773616 0 1.5595 253 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1669.773616 0 2.1875 273 | 0/8 14 h-lim-p 2.0669 20.0000 0.0000 1669.773616 0 1.0335 293 | 0/8 15 h-lim-p 0.4344 20.0000 0.0000 1669.773616 0 0.0000 334 Out... lnL = -1669.773616 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1669.773616 Node 7: lnL = -1669.773616 Node 8: lnL = -1669.773616 Node 9: lnL = -1669.773616 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 223 Sequential format.. Reading seq # 1: YLR100W_Sbay Reading seq # 2: YLR100W_Scer Reading seq # 3: YLR100W_Skud Reading seq # 4: YLR100W_Smik Reading seq # 5: YLR100W_Spar Sequences read.. Counting patterns.. # site patterns = 68 Counting frequencies.. 120 bytes for distance 10880 bytes for lkl0 8704 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.139140 0.000060 0.124215 0.073478 0.024123 0.143831 0.180872 0.092439 lnL0 = -725.959480 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 725.959480 x= 0.13914 0.00006 0.12422 0.07348 0.02412 0.14383 0.18087 0.09244 1 h-lim-p 0.0000 0.0000 135.0098 725.753481 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0017 63.5295 724.774942 0 0.0006 38 | 1/8 3 h-lim-p 0.0012 0.0100 16.2644 724.660161 6 0.0009 64 | 1/8 4 h-lim-p 0.0013 0.0143 11.0725 724.555271 0 0.0027 77 | 0/8 5 h-lim-p 0.0014 0.0180 21.4338 724.465967 8 0.0004 112 | 0/8 6 h-lim-p 0.0008 0.0098 11.7108 724.383231 0 0.0023 125 | 0/8 7 h-lim-p 0.0049 0.0388 1.5510 724.363592 5 0.0051 147 | 0/8 8 h-lim-p 0.0237 0.1895 0.2356 722.338040 0 0.1421 161 | 0/8 9 h-lim-p 0.9195 7.3564 0.0187 722.164518 5 0.3966 190 | 0/8 10 h-lim-p 0.9929 13.6681 0.0075 722.140541 4 0.9890 218 | 0/8 11 h-lim-p 2.2525 20.0000 0.0033 722.136470 4 0.8832 246 | 0/8 12 h-lim-p 2.5000 20.0000 0.0008 722.135708 3 1.0449 272 | 0/8 13 h-lim-p 2.5000 20.0000 0.0003 722.135693 2 0.7996 297 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 722.135693 0 1.0938 317 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 722.135693 0 1.0938 337 | 0/8 16 h-lim-p 2.2361 20.0000 0.0000 722.135693 0 0.0003 369 Out... lnL = -722.135693 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -722.135693 Node 7: lnL = -722.135693 Node 8: lnL = -722.135693 Node 9: lnL = -722.135693 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 233 Sequential format.. Reading seq # 1: YLR102C_Sbay Reading seq # 2: YLR102C_Scer Reading seq # 3: YLR102C_Skud Reading seq # 4: YLR102C_Smik Reading seq # 5: YLR102C_Spar Sequences read.. Counting patterns.. # site patterns = 131 Counting frequencies.. 120 bytes for distance 20960 bytes for lkl0 16768 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.186048 0.104431 0.132643 0.171191 0.093828 0.268406 0.273630 0.093950 lnL0 = -1131.684750 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1131.684750 x= 0.18605 0.10443 0.13264 0.17119 0.09383 0.26841 0.27363 0.09395 1 h-lim-p 0.0135 0.1908 40.8874 1130.683593 5 0.0013 34 | 0/8 2 h-lim-p 0.0024 0.0189 14.7944 1130.526659 6 0.0016 61 | 0/8 3 h-lim-p 0.0024 0.0210 9.6076 1130.481125 8 0.0014 94 | 0/8 4 h-lim-p 0.0051 0.0833 2.5782 1130.475692 6 0.0018 122 | 0/8 5 h-lim-p 0.0080 0.8125 0.5934 1130.475218 4 0.0028 143 | 0/8 6 h-lim-p 0.0146 1.8652 0.1154 1130.475201 3 0.0021 173 | 0/8 7 h-lim-p 0.0525 20.0000 0.0047 1130.474448 0 0.4202 196 | 0/8 8 h-lim-p 0.0072 20.0000 0.2742 1130.473452 3 0.0079 223 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1130.473444 1 0.9961 245 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1130.473444 0 1.0938 265 | 0/8 11 h-lim-p 1.6801 20.0000 0.0000 1130.473444 0 1.4701 285 | 0/8 12 h-lim-p 1.1280 20.0000 0.0000 1130.473444 0 1.1280 305 | 0/8 13 h-lim-p 0.0254 20.0000 0.0002 1130.473444 0 0.0016 328 | 0/8 14 h-lim-p 0.0003 20.0000 0.0007 1130.473444 0 0.0000 363 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1130.473444 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1130.473444 Node 7: lnL = -1130.473444 Node 8: lnL = -1130.473444 Node 9: lnL = -1130.473444 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 406 Sequential format.. Reading seq # 1: YLR107W_Sbay Reading seq # 2: YLR107W_Scer Reading seq # 3: YLR107W_Skud Reading seq # 4: YLR107W_Smik Reading seq # 5: YLR107W_Spar Sequences read.. Counting patterns.. # site patterns = 155 Counting frequencies.. 120 bytes for distance 24800 bytes for lkl0 19840 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.136961 0.028293 0.095456 0.127911 0.106908 0.187102 0.204538 0.065409 lnL0 = -1661.819178 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1661.819178 x= 0.13696 0.02829 0.09546 0.12791 0.10691 0.18710 0.20454 0.06541 1 h-lim-p 0.0031 1.0310 103.1109 1660.125570 3 0.0004 30 | 0/8 2 h-lim-p 0.0003 0.0027 45.7270 1659.334855 0 0.0010 43 | 0/8 3 h-lim-p 0.0008 0.0066 18.9709 1659.251162 5 0.0006 68 | 0/8 4 h-lim-p 0.0019 0.0660 5.7189 1659.235119 4 0.0011 91 | 0/8 5 h-lim-p 0.0057 0.2651 1.0968 1659.234708 2 0.0007 109 | 0/8 6 h-lim-p 0.0012 0.4256 0.6189 1659.234492 2 0.0010 125 | 0/8 7 h-lim-p 0.0554 20.0000 0.0116 1659.199648 0 0.4431 148 | 0/8 8 h-lim-p 0.0011 0.0547 4.7628 1659.187301 6 0.0008 182 | 0/8 9 h-lim-p 1.8918 20.0000 0.0020 1659.183299 5 1.3469 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0003 1659.183214 2 1.1719 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1659.183214 0 1.0938 249 | 0/8 12 h-lim-p 1.6768 20.0000 0.0000 1659.183214 0 1.4672 269 | 0/8 13 h-lim-p 1.8257 20.0000 0.0000 1659.183214 0 0.4564 290 | 0/8 14 h-lim-p 0.1291 20.0000 0.0000 1659.183214 0 0.0323 311 | 0/8 15 h-lim-p 0.0112 20.0000 0.0001 1659.183214 0 0.0049 331 | 0/8 16 h-lim-p 0.0026 20.0000 0.0001 1659.183214 0 0.0000 367 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 | 0/8 18 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1659.183214 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1659.183214 Node 7: lnL = -1659.183214 Node 8: lnL = -1659.183214 Node 9: lnL = -1659.183214 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 714 Sequential format.. Reading seq # 1: YLR108C_Sbay Reading seq # 2: YLR108C_Scer Reading seq # 3: YLR108C_Skud Reading seq # 4: YLR108C_Smik Reading seq # 5: YLR108C_Spar Sequences read.. Counting patterns.. # site patterns = 154 Counting frequencies.. 120 bytes for distance 24640 bytes for lkl0 19712 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.133056 0.000060 0.128892 0.117929 0.070968 0.527778 0.175491 0.050502 lnL0 = -2348.870382 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2348.870382 x= 0.13306 0.00006 0.12889 0.11793 0.07097 0.52778 0.17549 0.05050 1 h-lim-p 0.0000 0.0000 149.8375 2348.824802 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0027 70.3244 2348.002657 0 0.0005 39 | 1/8 3 h-lim-p 0.0009 0.0074 21.4328 2347.941941 6 0.0003 66 | 1/8 4 h-lim-p 0.0013 0.0630 4.8155 2347.917858 0 0.0019 78 | 1/8 5 h-lim-p 0.0005 0.3242 17.4940 2347.325188 0 0.0171 95 | 1/8 6 h-lim-p 0.0013 0.0104 50.2555 2347.268576 6 0.0005 123 | 1/8 7 h-lim-p 0.2142 2.8532 0.1062 2345.285426 0 0.8568 137 | 0/8 8 h-lim-p 0.0349 0.2789 1.0556 2345.285178 3 0.0006 169 | 0/8 9 h-lim-p 0.0173 0.6648 0.0390 2345.167359 1 0.5811 188 | 0/8 10 h-lim-p 0.0200 0.1598 0.0183 2345.166513 m 0.1598 208 | 1/8 11 h-lim-p 0.1328 20.0000 0.0221 2345.164342 0 1.0626 231 | 1/8 12 h-lim-p 2.5000 20.0000 0.0014 2345.164020 2 0.4822 255 | 1/8 13 h-lim-p 0.1726 20.0000 0.0039 2345.163961 0 0.6906 276 | 1/8 14 h-lim-p 2.5000 20.0000 0.0003 2345.163960 0 1.0938 295 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 2345.163960 0 1.0938 314 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 2345.163960 0 1.0938 333 | 1/8 17 h-lim-p 1.3450 20.0000 0.0000 2345.163960 0 0.0210 357 | 1/8 18 h-lim-p 0.0052 20.0000 0.0000 2345.163960 0 0.0000 398 | 1/8 19 h-lim-p 0.0000 20.0000 0.0006 | 1/8 20 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -2345.163960 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2345.163960 Node 7: lnL = -2345.163960 Node 8: lnL = -2345.163960 Node 9: lnL = -2345.163960 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 716 Sequential format.. Reading seq # 1: YLR109W_Sbay Reading seq # 2: YLR109W_Scer Reading seq # 3: YLR109W_Skud Reading seq # 4: YLR109W_Smik Reading seq # 5: YLR109W_Spar Sequences read.. Counting patterns.. # site patterns = 224 Counting frequencies.. 120 bytes for distance 35840 bytes for lkl0 28672 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.114676 0.048469 0.040387 0.073257 0.062292 0.079323 0.158102 0.066210 lnL0 = -2625.724609 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2625.724609 x= 0.11468 0.04847 0.04039 0.07326 0.06229 0.07932 0.15810 0.06621 1 h-lim-p 0.0002 0.0014 328.2972 2619.128936 7 0.0001 35 | 0/8 2 h-lim-p 0.0001 0.0011 64.3042 2618.700970 0 0.0003 48 | 0/8 3 h-lim-p 0.0008 0.0064 20.8057 2618.674366 6 0.0001 76 | 0/8 4 h-lim-p 0.0005 0.0284 6.1481 2618.669807 6 0.0003 104 | 0/8 5 h-lim-p 0.0007 0.0914 2.1743 2618.669208 4 0.0003 124 | 0/8 6 h-lim-p 0.0017 0.4437 0.3530 2618.669164 1 0.0004 139 | 0/8 7 h-lim-p 0.0019 1.5639 0.0797 2618.668677 0 0.0077 161 | 0/8 8 h-lim-p 0.0037 1.8271 0.1671 2618.632751 0 0.0220 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 2618.632457 2 1.1719 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2618.632449 0 1.2500 227 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2618.632449 0 1.0938 247 | 0/8 12 h-lim-p 1.0465 20.0000 0.0000 2618.632449 0 0.5233 267 | 0/8 13 h-lim-p 0.1237 20.0000 0.0001 2618.632449 0 0.0541 287 | 0/8 14 h-lim-p 0.0186 20.0000 0.0002 2618.632449 0 0.0023 309 | 0/8 15 h-lim-p 0.0013 20.0000 0.0003 2618.632449 0 0.0000 341 | 0/8 16 h-lim-p 0.0003 20.0000 0.0000 2618.632449 0 0.0000 373 Out... lnL = -2618.632449 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2618.632449 Node 7: lnL = -2618.632449 Node 8: lnL = -2618.632449 Node 9: lnL = -2618.632449 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 306 Sequential format.. Reading seq # 1: YLR110C_Sbay Reading seq # 2: YLR110C_Scer Reading seq # 3: YLR110C_Skud Reading seq # 4: YLR110C_Smik Reading seq # 5: YLR110C_Spar Sequences read.. Counting patterns.. # site patterns = 65 Counting frequencies.. 120 bytes for distance 10400 bytes for lkl0 8320 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.264496 0.025502 0.124513 0.120982 0.043930 4.656506 0.151064 0.000060 lnL0 = -930.011559 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 930.011559 x= 0.26450 0.02550 0.12451 0.12098 0.04393 4.65651 0.15106 0.00006 1 h-lim-p 0.0000 0.0000 270.4798 929.922545 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0003 198.9814 923.242690 m 0.0003 37 | 2/8 3 h-lim-p 0.0005 0.0036 44.1663 913.003858 0 0.0018 51 | 2/8 4 h-lim-p 0.0002 0.0013 103.3862 910.269100 0 0.0006 65 | 2/8 5 h-lim-p 0.0006 0.0047 27.4854 910.134104 8 0.0004 96 | 2/8 6 h-lim-p 0.0017 0.0312 5.8934 910.123761 6 0.0006 123 | 1/8 7 h-lim-p 0.0001 0.0090 26.9936 910.043387 0 0.0004 136 | 1/8 8 h-lim-p 0.3603 4.3851 0.0295 909.636910 0 0.7206 149 | 1/8 9 h-lim-p 0.4212 3.3696 0.0139 909.541353 0 0.6318 168 | 1/8 10 h-lim-p 1.2625 10.0997 0.0041 909.526493 4 0.8253 196 | 0/8 11 h-lim-p 0.0208 8.4497 0.1622 909.526482 2 0.0009 224 | 0/8 12 h-lim-p 0.2717 2.1737 0.0003 909.526378 0 1.0868 246 | 0/8 13 h-lim-p 0.1157 0.9254 0.0001 909.526376 m 0.9254 266 | 1/8 14 h-lim-p 0.0979 20.0000 0.0006 909.526375 0 0.0856 286 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 909.526375 0 1.2500 305 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 909.526375 0 2.1875 324 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 909.526375 010.0000 345 | 1/8 18 h-lim-p 1.1765 20.0000 0.0000 909.526375 0 0.1287 366 | 1/8 19 h-lim-p 0.1551 20.0000 0.0000 909.526375 0 0.0021 390 Out... lnL = -909.526375 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -909.526375 Node 7: lnL = -909.526375 Node 8: lnL = -909.526375 Node 9: lnL = -909.526375 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 451 Sequential format.. Reading seq # 1: YLR113W_Sbay Reading seq # 2: YLR113W_Scer Reading seq # 3: YLR113W_Skud Reading seq # 4: YLR113W_Smik Reading seq # 5: YLR113W_Spar Sequences read.. Counting patterns.. # site patterns = 160 Counting frequencies.. 120 bytes for distance 25600 bytes for lkl0 20480 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.162982 0.015329 0.100540 0.092687 0.079015 0.813368 0.171482 0.053855 lnL0 = -1716.054921 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1716.054921 x= 0.16298 0.01533 0.10054 0.09269 0.07902 0.81337 0.17148 0.05385 1 h-lim-p 0.0007 0.0056 66.9255 1714.971477 7 0.0005 37 | 0/8 2 h-lim-p 0.0002 0.0019 32.2740 1714.806145 0 0.0005 50 | 0/8 3 h-lim-p 0.0013 0.0208 11.5150 1714.769701 2 0.0006 66 | 0/8 4 h-lim-p 0.0006 0.0235 11.3788 1714.737045 0 0.0013 79 | 0/8 5 h-lim-p 0.0005 0.0082 27.4879 1714.466632 7 0.0036 113 | 0/8 6 h-lim-p 0.0013 0.0105 11.0178 1714.455856 6 0.0004 140 | 0/8 7 h-lim-p 0.7864 20.0000 0.0061 1714.446427 1 0.9830 154 | 0/8 8 h-lim-p 0.0121 0.0966 0.2250 1714.445894 0 0.0242 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 1714.445755 3 1.0004 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1714.445755 0 1.0938 221 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1714.445755 0 1.0938 241 | 0/8 12 h-lim-p 1.1122 20.0000 0.0000 1714.445755 0 0.0000 285 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 1714.445755 0 0.0000 317 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 1714.445755 0 0.0000 347 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 1714.445755 0 0.0000 367 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1714.445755 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1714.445755 Node 7: lnL = -1714.445755 Node 8: lnL = -1714.445755 Node 9: lnL = -1714.445755 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 785 Sequential format.. Reading seq # 1: YLR114C_Sbay Reading seq # 2: YLR114C_Scer Reading seq # 3: YLR114C_Skud Reading seq # 4: YLR114C_Smik Reading seq # 5: YLR114C_Spar Sequences read.. Counting patterns.. # site patterns = 244 Counting frequencies.. 120 bytes for distance 39040 bytes for lkl0 31232 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.172332 0.125723 0.093593 0.105966 0.132744 0.764850 0.232218 0.046529 lnL0 = -3205.967178 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3205.967178 x= 0.17233 0.12572 0.09359 0.10597 0.13274 0.76485 0.23222 0.04653 1 h-lim-p 0.0004 0.0032 130.1942 3202.819423 5 0.0004 32 | 0/8 2 h-lim-p 0.0006 0.0045 52.1662 3202.392150 7 0.0004 64 | 0/8 3 h-lim-p 0.0008 0.0124 21.8071 3202.325659 5 0.0003 86 | 0/8 4 h-lim-p 0.0010 0.0317 7.5384 3202.313495 4 0.0005 108 | 0/8 5 h-lim-p 0.0005 0.0267 6.7540 3202.227670 0 0.0066 123 | 0/8 6 h-lim-p 0.0005 0.0038 47.4837 3202.167564 0 0.0009 136 | 0/8 7 h-lim-p 0.1857 1.4858 0.2160 3202.166865 2 0.0218 154 | 0/8 8 h-lim-p 0.3711 20.0000 0.0127 3202.156991 0 0.7421 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 3202.156962 1 0.9961 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3202.156962 0 1.0938 217 | 0/8 11 h-lim-p 1.8558 20.0000 0.0000 3202.156962 0 1.6239 237 | 0/8 12 h-lim-p 2.3225 20.0000 0.0000 3202.156962 0 1.0161 257 | 0/8 13 h-lim-p 0.3690 20.0000 0.0000 3202.156962 0 0.1845 277 | 0/8 14 h-lim-p 0.0206 20.0000 0.0003 3202.156962 0 0.0003 302 | 0/8 15 h-lim-p 0.0004 20.0000 0.0002 3202.156962 0 0.0002 322 | 0/8 16 h-lim-p 0.0005 20.0000 0.0001 3202.156962 0 0.0000 353 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -3202.156962 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3202.156962 Node 7: lnL = -3202.156962 Node 8: lnL = -3202.156962 Node 9: lnL = -3202.156962 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 785 Sequential format.. Reading seq # 1: YLR115W_Sbay Reading seq # 2: YLR115W_Scer Reading seq # 3: YLR115W_Skud Reading seq # 4: YLR115W_Smik Reading seq # 5: YLR115W_Spar Sequences read.. Counting patterns.. # site patterns = 255 Counting frequencies.. 120 bytes for distance 40800 bytes for lkl0 32640 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.236535 0.000060 0.222348 0.142182 0.110073 0.802833 0.189833 0.106315 lnL0 = -3223.106591 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3223.106591 x= 0.23653 0.00006 0.22235 0.14218 0.11007 0.80283 0.18983 0.10631 1 h-lim-p 0.0000 0.0000 95.1678 3223.077827 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0064 35.4698 3222.888424 0 0.0003 39 | 1/8 3 h-lim-p 0.0011 0.0576 10.7331 3222.843386 5 0.0008 60 | 1/8 4 h-lim-p 0.0013 0.1023 7.0366 3222.780826 0 0.0039 73 | 1/8 5 h-lim-p 0.0010 0.0582 26.3088 3222.617694 0 0.0021 86 | 1/8 6 h-lim-p 0.0022 0.0304 25.2321 3222.574830 6 0.0007 113 | 1/8 7 h-lim-p 0.3519 5.8858 0.0506 3221.147786 0 0.7038 126 | 0/8 8 h-lim-p 0.0048 0.0766 7.4581 3221.132896 6 0.0007 161 | 0/8 9 h-lim-p 0.3793 20.0000 0.0133 3221.077116 0 1.5171 175 | 0/8 10 h-lim-p 2.5000 20.0000 0.0060 3221.034903 3 2.5806 201 | 0/8 11 h-lim-p 1.8505 20.0000 0.0084 3221.025936 5 1.2959 233 | 0/8 12 h-lim-p 2.5000 20.0000 0.0017 3221.025842 2 0.9961 257 | 0/8 13 h-lim-p 2.5000 20.0000 0.0001 3221.025840 0 1.0938 277 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 3221.025840 0 1.0938 297 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 3221.025840 0 1.0938 317 | 0/8 16 h-lim-p 1.0295 20.0000 0.0000 3221.025840 0 4.1178 339 | 0/8 17 h-lim-p 0.0456 20.0000 0.0009 3221.025840 0 0.0000 379 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 3221.025840 0 0.0000 409 | 0/8 19 h-lim-p 0.0000 20.0000 0.0002 | 0/8 20 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -3221.025840 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3221.025840 Node 7: lnL = -3221.025840 Node 8: lnL = -3221.025840 Node 9: lnL = -3221.025840 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 213 Sequential format.. Reading seq # 1: YLR127C_Sbay Reading seq # 2: YLR127C_Scer Reading seq # 3: YLR127C_Skud Reading seq # 4: YLR127C_Smik Reading seq # 5: YLR127C_Spar Sequences read.. Counting patterns.. # site patterns = 93 Counting frequencies.. 120 bytes for distance 14880 bytes for lkl0 11904 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.185534 0.087184 0.038414 0.119772 0.083277 0.179349 0.209084 0.109704 lnL0 = -981.640034 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 981.640034 x= 0.18553 0.08718 0.03841 0.11977 0.08328 0.17935 0.20908 0.10970 1 h-lim-p 0.0009 0.0071 58.1470 980.954029 4 0.0005 31 | 0/8 2 h-lim-p 0.0010 0.0084 13.6260 980.875308 5 0.0009 54 | 0/8 3 h-lim-p 0.0023 0.0571 5.2734 980.866028 6 0.0008 80 | 0/8 4 h-lim-p 0.0024 0.1416 1.6605 980.863903 5 0.0017 104 | 0/8 5 h-lim-p 0.0199 1.7920 0.1432 980.863887 2 0.0016 124 | 0/8 6 h-lim-p 0.0113 12.2827 0.0208 980.863886 0 0.0025 145 | 0/8 7 h-lim-p 0.0081 20.0000 0.0063 980.863870 0 0.0324 167 | 0/8 8 h-lim-p 0.0095 2.9267 0.0217 980.863619 0 0.0284 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 980.863610 1 0.9961 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 980.863610 0 1.0938 230 | 0/8 11 h-lim-p 1.6811 20.0000 0.0000 980.863610 0 1.6811 250 | 0/8 12 h-lim-p 2.3028 20.0000 0.0000 980.863610 0 0.2878 272 | 0/8 13 h-lim-p 0.0690 20.0000 0.0000 980.863610 0 0.0032 296 | 0/8 14 h-lim-p 0.0016 20.0000 0.0000 980.863610 0 0.0001 319 | 0/8 15 h-lim-p 0.0004 20.0000 0.0000 980.863610 0 0.0000 354 Out... lnL = -980.863610 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -980.863610 Node 7: lnL = -980.863610 Node 8: lnL = -980.863610 Node 9: lnL = -980.863610 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 316 Sequential format.. Reading seq # 1: YLR132C_Sbay Reading seq # 2: YLR132C_Scer Reading seq # 3: YLR132C_Skud Reading seq # 4: YLR132C_Smik Reading seq # 5: YLR132C_Spar Sequences read.. Counting patterns.. # site patterns = 145 Counting frequencies.. 120 bytes for distance 23200 bytes for lkl0 18560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.164105 0.151362 0.087791 0.110003 0.093114 0.085889 0.148575 0.090016 lnL0 = -1300.310078 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1300.310078 x= 0.16411 0.15136 0.08779 0.11000 0.09311 0.08589 0.14858 0.09002 1 h-lim-p 0.0010 0.0082 45.6154 1299.757875 7 0.0006 37 | 0/8 2 h-lim-p 0.0030 0.0238 6.3946 1299.741296 7 0.0008 66 | 0/8 3 h-lim-p 0.0024 0.3026 2.1705 1299.740008 5 0.0006 88 | 0/8 4 h-lim-p 0.0016 0.2633 0.7993 1299.739794 2 0.0008 104 | 0/8 5 h-lim-p 0.0033 1.1403 0.1848 1299.739774 2 0.0013 128 | 0/8 6 h-lim-p 0.0068 5.6307 0.0348 1299.739774 0 0.0009 150 | 0/8 7 h-lim-p 0.0109 20.0000 0.0027 1299.739774 0 0.0024 171 | 0/8 8 h-lim-p 0.0409 20.0000 0.0002 1299.739769 0 0.6548 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1299.739768 0 1.0938 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1299.739768 0 1.0938 235 | 0/8 11 h-lim-p 1.2139 20.0000 0.0000 1299.739768 0 0.0000 276 Out... lnL = -1299.739768 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1299.739768 Node 7: lnL = -1299.739768 Node 8: lnL = -1299.739768 Node 9: lnL = -1299.739768 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 316 Sequential format.. Reading seq # 1: YLR133W_Sbay Reading seq # 2: YLR133W_Scer Reading seq # 3: YLR133W_Skud Reading seq # 4: YLR133W_Smik Reading seq # 5: YLR133W_Spar Sequences read.. Counting patterns.. # site patterns = 141 Counting frequencies.. 120 bytes for distance 22560 bytes for lkl0 18048 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.195767 0.128761 0.068373 0.117944 0.085172 0.184183 0.159525 0.114461 lnL0 = -1392.805084 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1392.805084 x= 0.19577 0.12876 0.06837 0.11794 0.08517 0.18418 0.15953 0.11446 1 h-lim-p 0.0010 0.0083 48.6376 1392.215742 8 0.0005 41 | 0/8 2 h-lim-p 0.0017 0.0133 11.5857 1392.167067 2 0.0008 57 | 0/8 3 h-lim-p 0.0017 0.0444 5.4605 1392.160342 5 0.0005 80 | 0/8 4 h-lim-p 0.0026 0.1412 1.1576 1392.159843 4 0.0008 104 | 0/8 5 h-lim-p 0.0036 0.9608 0.2526 1392.159802 3 0.0014 122 | 0/8 6 h-lim-p 0.0467 20.0000 0.0075 1392.159802 0 0.0051 144 | 0/8 7 h-lim-p 0.0202 20.0000 0.0019 1392.159756 0 0.1616 167 | 0/8 8 h-lim-p 0.0023 1.5932 0.1355 1392.159724 1 0.0018 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1392.159723 0 1.0938 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1392.159723 0 1.0938 229 | 0/8 11 h-lim-p 1.6175 20.0000 0.0000 1392.159723 0 0.0000 269 Out... lnL = -1392.159723 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1392.159723 Node 7: lnL = -1392.159723 Node 8: lnL = -1392.159723 Node 9: lnL = -1392.159723 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 894 Sequential format.. Reading seq # 1: YLR135W_Sbay Reading seq # 2: YLR135W_Scer Reading seq # 3: YLR135W_Skud Reading seq # 4: YLR135W_Smik Reading seq # 5: YLR135W_Spar Sequences read.. Counting patterns.. # site patterns = 250 Counting frequencies.. 120 bytes for distance 40000 bytes for lkl0 32000 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.355599 0.000060 0.293827 0.205663 0.137906 4.380036 0.544443 0.091103 lnL0 = -3638.590886 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3638.590886 x= 0.35560 0.00006 0.29383 0.20566 0.13791 4.38004 0.54444 0.09110 1 h-lim-p 0.0000 0.0000 219.6071 3638.536759 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0011 177.5941 3631.325813 7 0.0007 54 | 1/8 3 h-lim-p 0.0011 0.0089 36.2322 3630.292262 0 0.0017 66 | 1/8 4 h-lim-p 0.0017 0.0135 11.1790 3630.123843 0 0.0025 78 | 1/8 5 h-lim-p 0.0354 0.3444 0.7986 3628.834154 0 0.0708 91 | 1/8 6 h-lim-p 0.0060 0.0479 8.2074 3621.225724 0 0.0120 111 | 1/8 7 h-lim-p 0.4526 3.6210 0.0686 3620.305401 1 0.5658 125 | 1/8 8 h-lim-p 2.5000 20.0000 0.0093 3620.289591 2 0.6152 149 | 1/8 9 h-lim-p 2.5000 20.0000 0.0012 3620.288908 4 0.7063 179 | 0/8 10 h-lim-p 0.0823 20.0000 0.0105 3620.288908 0 0.0023 202 | 0/8 11 h-lim-p 0.0787 0.8809 0.0003 3620.288895 0 0.5824 225 | 0/8 12 h-lim-p 0.0363 0.2905 0.0000 3620.288895 m 0.2905 245 | 1/8 13 h-lim-p 0.6353 20.0000 0.0000 3620.288895 0 1.2706 266 | 1/8 14 h-lim-p 1.3511 20.0000 0.0000 3620.288895 0 1.1822 285 | 1/8 15 h-lim-p 0.9635 20.0000 0.0000 3620.288895 0 0.2409 305 | 1/8 16 h-lim-p 0.3943 20.0000 0.0000 3620.288895 0 0.7885 325 | 1/8 17 h-lim-p 0.2412 20.0000 0.0000 3620.288895 0 0.0151 347 | 1/8 18 h-lim-p 0.0033 20.0000 0.0002 3620.288895 0 0.0000 384 | 1/8 19 h-lim-p 0.0000 20.0000 0.0002 3620.288895 0 0.0000 411 | 1/8 20 h-lim-p 0.0000 20.0000 0.0002 | 1/8 21 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -3620.288895 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3620.288895 Node 7: lnL = -3620.288895 Node 8: lnL = -3620.288895 Node 9: lnL = -3620.288895 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 359 Sequential format.. Reading seq # 1: YLR136C_Sbay Reading seq # 2: YLR136C_Scer Reading seq # 3: YLR136C_Skud Reading seq # 4: YLR136C_Smik Reading seq # 5: YLR136C_Spar Sequences read.. Counting patterns.. # site patterns = 121 Counting frequencies.. 120 bytes for distance 19360 bytes for lkl0 15488 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.120445 0.096594 0.000060 0.070721 0.040694 0.181304 0.092092 0.074325 lnL0 = -1195.467521 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1195.467521 x= 0.12045 0.09659 0.00006 0.07072 0.04069 0.18130 0.09209 0.07433 1 h-lim-p 0.0002 0.0013 161.2371 1193.961561 9 0.0001 44 | 0/8 2 h-lim-p 0.0001 0.0010 125.0568 1192.713235 0 0.0002 57 | 0/8 3 h-lim-p 0.0003 0.0026 34.8515 1192.568168 3 0.0003 75 | 0/8 4 h-lim-p 0.0005 0.0066 19.9306 1192.515405 7 0.0003 104 | 0/8 5 h-lim-p 0.0006 0.0173 11.5540 1192.498194 7 0.0004 135 | 0/8 6 h-lim-p 0.0006 0.0248 7.5133 1192.488842 3 0.0005 153 | 0/8 7 h-lim-p 0.1806 7.1416 0.0211 1192.469544 5 0.1767 176 | 0/8 8 h-lim-p 0.0012 0.0151 3.1713 1192.380536 0 0.0024 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0018 1192.372835 3 1.0449 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1192.372800 3 0.8800 242 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1192.372799 0 1.0938 262 | 0/8 12 h-lim-p 1.8588 20.0000 0.0000 1192.372799 0 1.8588 282 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1192.372799 0 0.1367 305 | 0/8 14 h-lim-p 0.0311 20.0000 0.0000 1192.372799 0 0.0001 332 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 1192.372799 0 0.0002 352 Out... lnL = -1192.372799 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1192.372799 Node 7: lnL = -1192.372799 Node 8: lnL = -1192.372799 Node 9: lnL = -1192.372799 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 474 Sequential format.. Reading seq # 1: YLR142W_Sbay Reading seq # 2: YLR142W_Scer Reading seq # 3: YLR142W_Skud Reading seq # 4: YLR142W_Smik Reading seq # 5: YLR142W_Spar Sequences read.. Counting patterns.. # site patterns = 130 Counting frequencies.. 120 bytes for distance 20800 bytes for lkl0 16640 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.306636 0.000060 0.186027 0.126336 0.057548 4.631630 0.242102 0.042140 lnL0 = -1662.247748 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1662.247748 x= 0.30664 0.00006 0.18603 0.12634 0.05755 4.63163 0.24210 0.04214 1 h-lim-p 0.0000 0.0000 141.5627 1662.215170 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0020 74.2613 1660.933840 0 0.0006 40 | 1/8 3 h-lim-p 0.0045 0.0363 8.6365 1660.887769 6 0.0011 66 | 1/8 4 h-lim-p 0.0044 0.1148 2.2308 1660.870041 5 0.0027 92 | 1/8 5 h-lim-p 0.0044 0.1525 1.4001 1660.731226 0 0.0131 105 | 1/8 6 h-lim-p 0.0055 0.0616 3.3624 1657.143682 0 0.0219 119 | 1/8 7 h-lim-p 1.3721 10.9771 0.0128 1657.093160 5 0.6885 141 | 1/8 8 h-lim-p 2.5000 20.0000 0.0017 1657.092305 2 0.5444 165 | 0/8 9 h-lim-p 0.0406 19.0705 0.0235 1657.092305 0 0.0011 188 | 0/8 10 h-lim-p 0.1063 0.8508 0.0001 1657.092303 m 0.8508 208 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 1657.092303 0 1.0938 228 | 0/8 12 h-lim-p -0.0000 -0.0000 0.1393 h-lim-p: -2.02667294e-21 -1.62133835e-20 1.39257145e-01 1657.092303 .. | 1/8 13 h-lim-p 0.0000 12.3645 0.0146 1657.092303 0 0.0006 269 | 1/8 14 h-lim-p 0.0010 20.0000 0.0098 1657.092303 0 0.0002 289 | 1/8 15 h-lim-p 0.0009 20.0000 0.0023 1657.092303 0 0.0008 308 | 1/8 16 h-lim-p 0.0024 20.0000 0.0008 1657.092303 0 0.0006 328 | 1/8 17 h-lim-p 0.0026 20.0000 0.0002 1657.092303 0 0.0011 347 | 1/8 18 h-lim-p 0.0101 20.0000 0.0000 1657.092303 0 0.6445 372 | 1/8 19 h-lim-p 1.0745 20.0000 0.0000 1657.092303 0 8.5961 394 | 1/8 20 h-lim-p 0.4542 20.0000 0.0002 1657.092303 0 0.0142 417 | 1/8 21 h-lim-p 0.0013 20.0000 0.0025 1657.092303 0 0.0000 446 | 1/8 22 h-lim-p 0.0002 20.0000 0.0000 1657.092303 0 0.0001 465 Out... lnL = -1657.092303 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1657.092303 Node 7: lnL = -1657.092303 Node 8: lnL = -1657.092303 Node 9: lnL = -1657.092303 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 163 Sequential format.. Reading seq # 1: YLR144C_Sbay Reading seq # 2: YLR144C_Scer Reading seq # 3: YLR144C_Skud Reading seq # 4: YLR144C_Smik Reading seq # 5: YLR144C_Spar Sequences read.. Counting patterns.. # site patterns = 90 Counting frequencies.. 120 bytes for distance 14400 bytes for lkl0 11520 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.509544 0.000060 0.175965 0.184686 0.241236 3.956560 0.542299 0.219947 lnL0 = -708.548527 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 708.548527 x= 0.50954 0.00006 0.17597 0.18469 0.24124 3.95656 0.54230 0.21995 1 h-lim-p 0.0000 0.0000 50.8717 708.538013 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0105 33.9998 705.893303 0 0.0051 43 | 1/8 3 h-lim-p 0.0009 0.0070 26.6162 704.704095 0 0.0052 57 | 1/8 4 h-lim-p 0.0878 0.7025 0.6820 703.541445 0 0.3513 71 | 1/8 5 h-lim-p 0.0081 0.0648 5.3749 701.710895 0 0.0324 92 | 1/8 6 h-lim-p 0.0035 0.0278 9.4062 701.429525 0 0.0052 104 | 1/8 7 h-lim-p 0.2833 2.2661 0.1600 700.911955 0 0.5665 117 | 0/8 8 h-lim-p 0.0242 0.4954 3.7514 700.890351 6 0.0033 150 | 0/8 9 h-lim-p 0.2062 1.6496 0.0209 700.860984 0 0.8248 164 | 0/8 10 h-lim-p 1.9282 15.4255 0.0019 700.860722 3 0.7683 190 | 0/8 11 h-lim-p 2.2848 20.0000 0.0006 700.860697 3 0.8093 218 | 0/8 12 h-lim-p 2.5000 20.0000 0.0001 700.860697 0 1.0938 238 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 700.860697 0 1.0938 258 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 700.860697 0 1.0938 278 | 0/8 15 h-lim-p 2.2015 20.0000 0.0000 700.860697 0 0.9632 298 | 0/8 16 h-lim-p 0.6923 20.0000 0.0000 700.860697 0 0.0000 342 Out... lnL = -700.860697 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -700.860697 Node 7: lnL = -700.860697 Node 8: lnL = -700.860697 Node 9: lnL = -700.860697 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 161 Sequential format.. Reading seq # 1: YLR145W_Sbay Reading seq # 2: YLR145W_Scer Reading seq # 3: YLR145W_Skud Reading seq # 4: YLR145W_Smik Reading seq # 5: YLR145W_Spar Sequences read.. Counting patterns.. # site patterns = 89 Counting frequencies.. 120 bytes for distance 14240 bytes for lkl0 11392 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 1.268004 0.000060 0.356296 0.180332 0.207144 1.474911 1.105953 0.978407 lnL0 = -736.033395 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 736.033395 x= 1.26800 0.00006 0.35630 0.18033 0.20714 1.47491 1.10595 0.97841 1 h-lim-p 0.0000 0.0000 46.1789 736.022650 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0056 82.4031 720.113115 m 0.0056 41 | 1/8 3 h-lim-p 0.0002 0.0013 57.2920 718.371429 m 0.0013 53 | 2/8 4 h-lim-p 0.0090 0.1197 5.6212 717.248081 0 0.0362 67 | 2/8 5 h-lim-p 0.0236 0.1884 6.2515 715.658740 0 0.0707 80 | 2/8 6 h-lim-p 0.2944 2.3551 0.3196 714.592259 0 0.4416 92 | 2/8 7 h-lim-p 0.3551 2.8407 0.0622 714.415163 0 0.7102 111 | 2/8 8 h-lim-p 1.0515 8.4124 0.0404 714.389483 7 0.7270 146 | 2/8 9 h-lim-p 1.3044 20.0000 0.0225 714.383600 2 0.6114 168 | 2/8 10 h-lim-p 2.5000 20.0000 0.0021 714.383230 5 0.9273 197 | 2/8 11 h-lim-p 2.5000 20.0000 0.0001 714.383229 0 1.0938 215 | 2/8 12 h-lim-p 2.5000 20.0000 0.0000 714.383229 0 1.0938 233 | 2/8 13 h-lim-p 2.5000 20.0000 0.0000 714.383229 0 2.1875 251 | 2/8 14 h-lim-p 1.9026 20.0000 0.0000 714.383229 0 0.8324 269 | 2/8 15 h-lim-p 2.5000 20.0000 0.0000 714.383229 0 0.0085 294 Out... lnL = -714.383229 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -714.383229 Node 7: lnL = -714.383229 Node 8: lnL = -714.383229 Node 9: lnL = -714.383229 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 454 Sequential format.. Reading seq # 1: YLR146C_Sbay Reading seq # 2: YLR146C_Scer Reading seq # 3: YLR146C_Skud Reading seq # 4: YLR146C_Smik Reading seq # 5: YLR146C_Spar Sequences read.. Counting patterns.. # site patterns = 136 Counting frequencies.. 120 bytes for distance 21760 bytes for lkl0 17408 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.111541 0.100475 0.052527 0.096031 0.038620 0.161198 0.095871 0.051013 lnL0 = -1802.586360 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1802.586360 x= 0.11154 0.10047 0.05253 0.09603 0.03862 0.16120 0.09587 0.05101 1 h-lim-p 0.0006 0.0046 45.5231 1802.315467 2 0.0003 26 | 0/8 2 h-lim-p 0.0008 0.0082 15.0660 1802.280522 3 0.0003 44 | 0/8 3 h-lim-p 0.0019 0.0341 2.6866 1802.279790 2 0.0002 62 | 0/8 4 h-lim-p 0.0004 0.1207 1.3803 1802.279645 2 0.0002 78 | 0/8 5 h-lim-p 0.0015 1.3739 0.1760 1802.279639 0 0.0003 91 | 0/8 6 h-lim-p 0.0012 4.0356 0.0458 1802.279639 0 0.0005 111 | 0/8 7 h-lim-p 0.0038 20.0000 0.0067 1802.279639 0 0.0004 133 | 0/8 8 h-lim-p 0.0433 20.0000 0.0001 1802.279635 0 0.6934 157 | 0/8 9 h-lim-p 2.3513 20.0000 0.0000 1802.279635 0 1.0287 177 | 0/8 10 h-lim-p 1.1605 20.0000 0.0000 1802.279635 0 0.0006 207 | 0/8 11 h-lim-p 0.0001 20.0000 0.0001 1802.279635 0 0.0000 229 | 0/8 12 h-lim-p 0.0001 20.0000 0.0000 1802.279635 0 0.0000 250 Out... lnL = -1802.279635 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1802.279635 Node 7: lnL = -1802.279635 Node 8: lnL = -1802.279635 Node 9: lnL = -1802.279635 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 187 Sequential format.. Reading seq # 1: YLR147C_Sbay Reading seq # 2: YLR147C_Scer Reading seq # 3: YLR147C_Skud Reading seq # 4: YLR147C_Smik Reading seq # 5: YLR147C_Spar Sequences read.. Counting patterns.. # site patterns = 84 Counting frequencies.. 120 bytes for distance 13440 bytes for lkl0 10752 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.162236 0.101577 0.000060 0.101722 0.092356 0.141423 0.143253 0.095111 lnL0 = -781.480689 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 781.480689 x= 0.16224 0.10158 0.00006 0.10172 0.09236 0.14142 0.14325 0.09511 1 h-lim-p 0.0007 0.0157 153.8848 779.522842 9 0.0002 45 | 0/8 2 h-lim-p 0.0008 0.0068 30.0388 779.070826 1 0.0011 59 | 0/8 3 h-lim-p 0.0050 0.0397 5.4524 779.056025 3 0.0010 78 | 0/8 4 h-lim-p 0.0040 0.1243 1.4223 779.055114 2 0.0009 95 | 0/8 5 h-lim-p 0.0031 0.4338 0.4334 779.055035 3 0.0009 116 | 0/8 6 h-lim-p 0.0139 14.0027 0.0280 779.055033 2 0.0022 142 | 0/8 7 h-lim-p 0.0188 20.0000 0.0033 779.054871 0 0.1507 165 | 0/8 8 h-lim-p 0.0017 0.9913 0.2880 779.054610 0 0.0026 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 779.054603 2 1.0938 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 779.054603 0 2.1875 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 779.054603 0 1.0938 249 | 0/8 12 h-lim-p 1.8662 20.0000 0.0000 779.054603 0 2.7993 269 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 779.054603 0 0.2734 291 | 0/8 14 h-lim-p 0.3795 20.0000 0.0000 779.054603 0 0.0007 319 Out... lnL = -779.054603 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -779.054603 Node 7: lnL = -779.054603 Node 8: lnL = -779.054603 Node 9: lnL = -779.054603 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 182 Sequential format.. Reading seq # 1: YLR148W_Sbay Reading seq # 2: YLR148W_Scer Reading seq # 3: YLR148W_Skud Reading seq # 4: YLR148W_Smik Reading seq # 5: YLR148W_Spar Sequences read.. Counting patterns.. # site patterns = 88 Counting frequencies.. 120 bytes for distance 14080 bytes for lkl0 11264 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.179758 0.050768 0.008873 0.115347 0.069515 0.571525 0.126356 0.084287 lnL0 = -713.695680 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 713.695680 x= 0.17976 0.05077 0.00887 0.11535 0.06952 0.57152 0.12636 0.08429 1 h-lim-p 0.0011 0.0089 74.9492 712.833346 9 0.0004 44 | 0/8 2 h-lim-p 0.0008 0.0067 18.5316 712.599045 0 0.0017 57 | 0/8 3 h-lim-p 0.0008 0.0061 10.0229 712.462517 0 0.0030 71 | 0/8 4 h-lim-p 0.0015 0.0118 6.0721 712.452852 4 0.0007 91 | 0/8 5 h-lim-p 0.0036 0.3082 1.2493 712.448087 0 0.0071 104 | 0/8 6 h-lim-p 0.0025 0.1298 3.5821 712.441881 0 0.0037 116 | 0/8 7 h-lim-p 0.0484 0.5153 0.2767 712.441736 2 0.0024 135 | 0/8 8 h-lim-p 0.0494 9.5802 0.0135 712.418813 0 0.7903 159 | 0/8 9 h-lim-p 2.5000 20.0000 0.0032 712.414360 2 1.1719 183 | 0/8 10 h-lim-p 2.5000 20.0000 0.0004 712.414223 2 1.2305 208 | 0/8 11 h-lim-p 2.5000 20.0000 0.0001 712.414222 1 0.9961 230 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 712.414222 0 1.0938 250 | 0/8 13 h-lim-p 2.1693 20.0000 0.0000 712.414222 0 1.8981 270 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 712.414222 0 0.6250 291 | 0/8 15 h-lim-p 0.1545 20.0000 0.0000 712.414222 0 0.0772 311 | 0/8 16 h-lim-p 0.0223 20.0000 0.0000 712.414222 0 0.0000 351 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -712.414222 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -712.414222 Node 7: lnL = -712.414222 Node 8: lnL = -712.414222 Node 9: lnL = -712.414222 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 458 Sequential format.. Reading seq # 1: YLR153C_Sbay Reading seq # 2: YLR153C_Scer Reading seq # 3: YLR153C_Skud Reading seq # 4: YLR153C_Smik Reading seq # 5: YLR153C_Spar Sequences read.. Counting patterns.. # site patterns = 117 Counting frequencies.. 120 bytes for distance 18720 bytes for lkl0 14976 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.095321 0.052799 0.013119 0.026056 0.038039 0.895840 0.098393 0.000060 lnL0 = -1446.758669 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1446.758669 x= 0.09532 0.05280 0.01312 0.02606 0.03804 0.89584 0.09839 0.00006 1 h-lim-p 0.0000 0.0000 115.0653 1446.717810 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0004 91.1226 1446.308314 0 0.0002 38 | 1/8 3 h-lim-p 0.0001 0.0009 41.9707 1446.226090 1 0.0001 52 | 1/8 4 h-lim-p 0.0003 0.0032 21.5202 1446.201608 6 0.0001 77 | 1/8 5 h-lim-p 0.0001 0.0006 16.5525 1446.175450 0 0.0003 91 | 1/8 6 h-lim-p 0.0001 0.0006 8.5869 1446.156999 m 0.0006 103 | 1/8 7 h-lim-p -0.0000 -0.0000 2.8821 h-lim-p: -7.66260117e-19 -6.13008093e-18 2.88213046e+00 1446.156999 .. | 1/8 8 h-lim-p 0.0000 0.0007 139.3862 1445.086371 0 0.0001 126 | 1/8 9 h-lim-p 0.0001 0.0008 55.4134 1444.906804 0 0.0002 138 | 1/8 10 h-lim-p 0.0001 0.0010 27.4982 1444.868786 3 0.0001 156 | 1/8 11 h-lim-p 0.0005 0.0049 6.5804 1444.863583 4 0.0003 178 | 1/8 12 h-lim-p 0.0001 0.0009 9.0247 1444.851108 0 0.0007 192 | 1/8 13 h-lim-p 0.0000 0.0003 8.3633 1444.844982 m 0.0003 204 | 2/8 14 h-lim-p 0.0009 1.3011 2.9878 1444.819269 0 0.0104 219 | 1/8 15 h-lim-p 0.0060 3.1197 5.1369 1444.815893 5 0.0003 245 | 1/8 16 h-lim-p 0.2068 20.0000 0.0067 1444.810728 0 0.6205 258 | 0/8 17 h-lim-p 0.0007 0.0513 6.1232 1444.809477 3 0.0003 284 | 0/8 18 h-lim-p 0.0824 0.6594 0.0023 1444.808263 m 0.6594 296 | 1/8 19 h-lim-p 2.5000 20.0000 0.0004 1444.808234 1 0.2734 320 | 1/8 20 h-lim-p 0.4707 20.0000 0.0003 1444.808225 0 0.9414 340 | 1/8 21 h-lim-p 2.5000 20.0000 0.0000 1444.808225 0 1.0938 359 | 1/8 22 h-lim-p 2.5000 20.0000 0.0000 1444.808225 0 0.5469 379 | 1/8 23 h-lim-p 1.1539 20.0000 0.0000 1444.808225 0 0.0008 408 Out... lnL = -1444.808225 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1444.808225 Node 7: lnL = -1444.808225 Node 8: lnL = -1444.808225 Node 9: lnL = -1444.808225 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 672 Sequential format.. Reading seq # 1: YLR163C_Sbay Reading seq # 2: YLR163C_Scer Reading seq # 3: YLR163C_Skud Reading seq # 4: YLR163C_Smik Reading seq # 5: YLR163C_Spar Sequences read.. Counting patterns.. # site patterns = 216 Counting frequencies.. 120 bytes for distance 34560 bytes for lkl0 27648 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.340247 0.014419 0.220667 0.185175 0.141073 4.616209 0.347848 0.050650 lnL0 = -2857.400723 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2857.400723 x= 0.34025 0.01442 0.22067 0.18518 0.14107 4.61621 0.34785 0.05065 1 h-lim-p 0.0124 0.0993 19.0512 2857.294872 5 0.0006 35 | 0/8 2 h-lim-p 0.0014 0.0447 8.1037 2857.270944 6 0.0008 64 | 0/8 3 h-lim-p 0.0014 0.0316 4.8122 2857.264581 4 0.0007 85 | 0/8 4 h-lim-p 0.0034 0.2520 1.0593 2857.264092 4 0.0010 107 | 0/8 5 h-lim-p 0.0271 3.3557 0.0373 2857.264092 0 0.0015 122 | 0/8 6 h-lim-p 0.3452 20.0000 0.0002 2857.264089 0 1.3809 144 | 0/8 7 h-lim-p 2.5000 20.0000 0.0000 2857.264088 0 1.0938 164 | 0/8 8 h-lim-p 2.2664 20.0000 0.0000 2857.264088 0 0.9915 184 | 0/8 9 h-lim-p 0.8591 20.0000 0.0000 2857.264088 0 0.0470 207 | 0/8 10 h-lim-p 0.0020 20.0000 0.0005 2857.264088 0 0.0000 234 | 0/8 11 h-lim-p 0.0000 20.0000 0.0009 2857.264088 0 0.0000 268 | 0/8 12 h-lim-p 0.0000 20.0000 0.0002 2857.264088 0 0.0000 299 | 0/8 13 h-lim-p 0.0000 20.0000 0.0002 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -2857.264088 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2857.264088 Node 7: lnL = -2857.264088 Node 8: lnL = -2857.264088 Node 9: lnL = -2857.264088 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 1012 Sequential format.. Reading seq # 1: YLR166C_Sbay Reading seq # 2: YLR166C_Scer Reading seq # 3: YLR166C_Skud Reading seq # 4: YLR166C_Smik Reading seq # 5: YLR166C_Spar Sequences read.. Counting patterns.. # site patterns = 334 Counting frequencies.. 120 bytes for distance 53440 bytes for lkl0 42752 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.283401 0.112024 0.205846 0.215327 0.118416 0.890580 0.272280 0.101294 lnL0 = -4250.011190 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4250.011190 x= 0.28340 0.11202 0.20585 0.21533 0.11842 0.89058 0.27228 0.10129 1 h-lim-p 0.0008 0.0064 62.4472 4248.743119 6 0.0007 33 | 0/8 2 h-lim-p 0.0009 0.0072 26.0474 4248.575044 7 0.0006 62 | 0/8 3 h-lim-p 0.0008 0.0201 17.6472 4248.505436 4 0.0006 82 | 0/8 4 h-lim-p 0.0010 0.0467 11.8786 4248.452575 0 0.0014 94 | 0/8 5 h-lim-p 0.0013 0.0564 13.3028 4248.212475 0 0.0076 108 | 0/8 6 h-lim-p 0.0033 0.0264 17.8388 4248.165892 6 0.0011 136 | 0/8 7 h-lim-p 0.2235 3.2829 0.0864 4248.165683 3 0.0360 157 | 0/8 8 h-lim-p 0.2674 20.0000 0.0116 4248.163277 0 0.8023 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 4248.163258 1 1.0938 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 4248.163258 0 1.0938 220 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4248.163258 0 1.0938 240 | 0/8 12 h-lim-p 0.8925 20.0000 0.0000 4248.163258 0 0.8925 260 | 0/8 13 h-lim-p 0.0205 20.0000 0.0007 4248.163258 0 0.0010 284 | 0/8 14 h-lim-p 0.0002 20.0000 0.0027 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -4248.163258 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4248.163258 Node 7: lnL = -4248.163258 Node 8: lnL = -4248.163258 Node 9: lnL = -4248.163258 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 868 Sequential format.. Reading seq # 1: YLR167W_Sbay Reading seq # 2: YLR167W_Scer Reading seq # 3: YLR167W_Skud Reading seq # 4: YLR167W_Smik Reading seq # 5: YLR167W_Spar Sequences read.. Counting patterns.. # site patterns = 284 Counting frequencies.. 120 bytes for distance 45440 bytes for lkl0 36352 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.257011 0.054383 0.073459 0.222880 0.299867 0.472458 0.336215 0.110965 lnL0 = -3956.256885 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3956.256885 x= 0.25701 0.05438 0.07346 0.22288 0.29987 0.47246 0.33621 0.11096 1 h-lim-p 0.0036 0.0285 89.6850 3954.882283 7 0.0004 42 | 0/8 2 h-lim-p 0.0009 0.0130 37.6687 3954.283763 6 0.0010 70 | 0/8 3 h-lim-p 0.0016 0.0357 22.8592 3953.890397 0 0.0023 82 | 0/8 4 h-lim-p 0.0012 0.0141 43.8052 3953.052489 0 0.0025 95 | 0/8 5 h-lim-p 0.0044 0.0354 7.5588 3953.029668 3 0.0010 114 | 0/8 6 h-lim-p 0.0034 0.1479 2.2376 3953.027629 3 0.0009 133 | 0/8 7 h-lim-p 0.0224 1.0683 0.0910 3953.020736 0 0.1789 148 | 0/8 8 h-lim-p 0.0586 2.6896 0.2778 3952.979695 0 0.1173 169 | 0/8 9 h-lim-p 2.5000 20.0000 0.0059 3952.978250 2 1.0938 193 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 3952.978244 0 1.0938 213 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3952.978244 0 1.0938 233 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3952.978244 0 2.1875 253 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 3952.978244 0 1.0938 273 | 0/8 14 h-lim-p 0.2499 20.0000 0.0000 3952.978244 0 0.1249 293 | 0/8 15 h-lim-p 0.0122 20.0000 0.0002 3952.978244 0 0.0000 334 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -3952.978244 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3952.978244 Node 7: lnL = -3952.978244 Node 8: lnL = -3952.978244 Node 9: lnL = -3952.978244 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 73 Sequential format.. Reading seq # 1: YLR168C_Sbay Reading seq # 2: YLR168C_Scer Reading seq # 3: YLR168C_Skud Reading seq # 4: YLR168C_Smik Reading seq # 5: YLR168C_Spar Sequences read.. Counting patterns.. # site patterns = 52 Counting frequencies.. 120 bytes for distance 8320 bytes for lkl0 6656 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.272353 0.000060 0.142943 0.167389 0.125891 0.185945 0.364532 0.160801 lnL0 = -353.394804 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 353.394804 x= 0.27235 0.00006 0.14294 0.16739 0.12589 0.18595 0.36453 0.16080 1 h-lim-p 0.0152 0.1214 13.1489 353.075637 2 0.0036 27 | 0/8 2 h-lim-p 0.0078 0.0627 4.6035 353.005630 2 0.0073 43 | 0/8 3 h-lim-p 0.0202 0.1616 1.6523 352.998369 7 0.0060 72 | 0/8 4 h-lim-p 0.0126 0.7086 0.7927 352.996693 4 0.0066 93 | 0/8 5 h-lim-p 0.0152 1.1745 0.3436 352.996276 4 0.0083 122 | 0/8 6 h-lim-p 0.2183 17.7342 0.0130 352.995495 1 0.2729 144 | 0/8 7 h-lim-p 0.0214 0.6453 0.1655 352.993621 1 0.0268 166 | 0/8 8 h-lim-p 0.0129 0.5004 0.3428 352.993104 5 0.0077 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 352.993099 2 0.9644 223 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 352.993099 0 1.0938 243 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 352.993099 0 1.0938 263 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 352.993099 0 0.0000 310 Out... lnL = -352.993099 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -352.993099 Node 7: lnL = -352.993099 Node 8: lnL = -352.993099 Node 9: lnL = -352.993099 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 247 Sequential format.. Reading seq # 1: YLR170C_Sbay Reading seq # 2: YLR170C_Scer Reading seq # 3: YLR170C_Skud Reading seq # 4: YLR170C_Smik Reading seq # 5: YLR170C_Spar Sequences read.. Counting patterns.. # site patterns = 154 Counting frequencies.. 120 bytes for distance 24640 bytes for lkl0 19712 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.144497 0.005335 0.265987 0.187404 0.158208 0.411940 0.272582 0.020753 lnL0 = -1107.620034 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1107.620034 x= 0.14450 0.00533 0.26599 0.18740 0.15821 0.41194 0.27258 0.02075 1 h-lim-p 0.0078 2.6618 53.1642 1106.303725 7 0.0010 37 | 0/8 2 h-lim-p 0.0004 0.0033 18.7979 1105.986542 0 0.0017 51 | 0/8 3 h-lim-p 0.0020 0.0164 10.9517 1105.869184 1 0.0026 65 | 0/8 4 h-lim-p 0.0026 0.0209 4.5833 1105.852813 6 0.0019 90 | 0/8 5 h-lim-p 0.0060 0.3596 1.4745 1105.849040 5 0.0039 114 | 0/8 6 h-lim-p 0.0250 1.7151 0.2322 1105.848548 3 0.0123 133 | 0/8 7 h-lim-p 0.0952 8.7748 0.0300 1105.846217 0 0.1429 153 | 0/8 8 h-lim-p 0.0099 0.0975 0.4353 1105.836355 0 0.0197 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0013 1105.835588 2 1.0889 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 1105.835580 0 1.0938 218 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1105.835580 0 1.0938 238 | 0/8 12 h-lim-p 1.4098 20.0000 0.0000 1105.835580 0 1.4098 258 | 0/8 13 h-lim-p 0.7092 20.0000 0.0000 1105.835580 0 0.0000 301 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 1105.835580 0 0.0000 336 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1105.835580 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1105.835580 Node 7: lnL = -1105.835580 Node 8: lnL = -1105.835580 Node 9: lnL = -1105.835580 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 270 Sequential format.. Reading seq # 1: YLR172C_Sbay Reading seq # 2: YLR172C_Scer Reading seq # 3: YLR172C_Skud Reading seq # 4: YLR172C_Smik Reading seq # 5: YLR172C_Spar Sequences read.. Counting patterns.. # site patterns = 141 Counting frequencies.. 120 bytes for distance 22560 bytes for lkl0 18048 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.162543 0.181946 0.062677 0.108807 0.106955 0.270584 0.204903 0.063377 lnL0 = -1163.034079 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1163.034079 x= 0.16254 0.18195 0.06268 0.10881 0.10695 0.27058 0.20490 0.06338 1 h-lim-p 0.0030 0.0240 12.6866 1162.940876 4 0.0012 30 | 0/8 2 h-lim-p 0.0014 0.0276 10.7969 1162.888141 5 0.0013 52 | 0/8 3 h-lim-p 0.0021 0.0314 7.0168 1162.874226 5 0.0009 73 | 0/8 4 h-lim-p 0.0035 0.2401 1.8030 1162.871944 2 0.0016 89 | 0/8 5 h-lim-p 0.0031 0.2702 0.9561 1162.871501 3 0.0012 107 | 0/8 6 h-lim-p 0.0067 1.4649 0.1758 1162.871477 1 0.0017 130 | 0/8 7 h-lim-p 0.0068 4.1470 0.0433 1162.871476 1 0.0008 154 | 0/8 8 h-lim-p 0.0680 20.0000 0.0005 1162.871430 0 1.0879 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1162.871428 0 1.0938 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1162.871428 0 1.0938 218 | 0/8 11 h-lim-p 2.1411 20.0000 0.0000 1162.871428 0 0.9367 238 | 0/8 12 h-lim-p 0.6740 20.0000 0.0000 1162.871428 0 0.0000 282 Out... lnL = -1162.871428 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1162.871428 Node 7: lnL = -1162.871428 Node 8: lnL = -1162.871428 Node 9: lnL = -1162.871428 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 298 Sequential format.. Reading seq # 1: YLR173W_Sbay Reading seq # 2: YLR173W_Scer Reading seq # 3: YLR173W_Skud Reading seq # 4: YLR173W_Smik Reading seq # 5: YLR173W_Spar Sequences read.. Counting patterns.. # site patterns = 135 Counting frequencies.. 120 bytes for distance 21600 bytes for lkl0 17280 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.152309 0.167890 0.075106 0.117940 0.097821 0.226533 0.192666 0.058820 lnL0 = -1282.480500 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1282.480500 x= 0.15231 0.16789 0.07511 0.11794 0.09782 0.22653 0.19267 0.05882 1 h-lim-p 0.0046 0.0367 15.7342 1282.390097 7 0.0007 41 | 0/8 2 h-lim-p 0.0028 0.0479 4.1252 1282.381753 6 0.0010 67 | 0/8 3 h-lim-p 0.0017 0.0734 2.4908 1282.379942 4 0.0008 86 | 0/8 4 h-lim-p 0.0063 0.9470 0.3034 1282.379885 2 0.0013 103 | 0/8 5 h-lim-p 0.0030 1.6981 0.1272 1282.379878 2 0.0010 129 | 0/8 6 h-lim-p 0.0138 20.0000 0.0091 1282.379878 0 0.0030 150 | 0/8 7 h-lim-p 0.0161 20.0000 0.0017 1282.379878 0 0.0009 173 | 0/8 8 h-lim-p 0.0713 20.0000 0.0000 1282.379878 0 1.1416 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1282.379878 0 1.0938 217 | 0/8 10 h-lim-p 1.0578 20.0000 0.0000 1282.379878 0 1.0578 237 | 0/8 11 h-lim-p 0.4519 20.0000 0.0000 1282.379878 0 0.4519 257 | 0/8 12 h-lim-p 0.0674 20.0000 0.0001 1282.379878 0 0.0253 278 | 0/8 13 h-lim-p 0.0090 20.0000 0.0003 1282.379878 0 0.0045 298 | 0/8 14 h-lim-p 0.0019 20.0000 0.0007 1282.379878 0 0.0001 322 | 0/8 15 h-lim-p 0.0004 20.0000 0.0001 1282.379878 0 0.0000 357 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 1282.379878 0 0.0000 381 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 1282.379878 0 0.0000 416 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 1282.379878 0 0.0000 451 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1282.379878 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1282.379878 Node 7: lnL = -1282.379878 Node 8: lnL = -1282.379878 Node 9: lnL = -1282.379878 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 665 Sequential format.. Reading seq # 1: YLR179C_Sbay Reading seq # 2: YLR179C_Scer Reading seq # 3: YLR179C_Skud Reading seq # 4: YLR179C_Smik Reading seq # 5: YLR179C_Spar Sequences read.. Counting patterns.. # site patterns = 285 Counting frequencies.. 120 bytes for distance 45600 bytes for lkl0 36480 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.251133 0.036650 0.089392 0.096004 0.106232 0.154452 0.189860 0.162390 lnL0 = -2661.132409 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2661.132409 x= 0.25113 0.03665 0.08939 0.09600 0.10623 0.15445 0.18986 0.16239 1 h-lim-p 0.0014 0.1660 197.3124 2656.100739 6 0.0003 37 | 0/8 2 h-lim-p 0.0005 0.0038 50.4697 2655.375584 1 0.0006 51 | 0/8 3 h-lim-p 0.0008 0.0069 39.0838 2655.143692 7 0.0004 82 | 0/8 4 h-lim-p 0.0021 0.0253 8.1358 2655.128465 2 0.0005 99 | 0/8 5 h-lim-p 0.0036 0.2096 1.1205 2655.127974 2 0.0008 116 | 0/8 6 h-lim-p 0.0020 0.5626 0.4451 2655.127893 2 0.0009 132 | 0/8 7 h-lim-p 0.0076 3.6568 0.0509 2655.127866 2 0.0038 157 | 0/8 8 h-lim-p 0.0162 20.0000 0.0118 2655.120307 0 0.2591 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 2655.120253 2 0.9961 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2655.120253 0 1.0938 225 | 0/8 11 h-lim-p 2.4245 20.0000 0.0000 2655.120253 0 1.0607 245 | 0/8 12 h-lim-p 0.9930 20.0000 0.0000 2655.120253 0 1.9860 266 | 0/8 13 h-lim-p 0.0736 20.0000 0.0001 2655.120253 0 0.0368 286 | 0/8 14 h-lim-p 0.0116 20.0000 0.0002 2655.120253 0 0.0000 313 | 0/8 15 h-lim-p 0.0027 20.0000 0.0000 2655.120253 0 0.0000 346 Out... lnL = -2655.120253 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2655.120253 Node 7: lnL = -2655.120253 Node 8: lnL = -2655.120253 Node 9: lnL = -2655.120253 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 284 Sequential format.. Reading seq # 1: YLR182W_Sbay Reading seq # 2: YLR182W_Scer Reading seq # 3: YLR182W_Skud Reading seq # 4: YLR182W_Smik Reading seq # 5: YLR182W_Spar Sequences read.. Counting patterns.. # site patterns = 124 Counting frequencies.. 120 bytes for distance 19840 bytes for lkl0 15872 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.178190 0.078832 0.050114 0.129401 0.084778 0.160621 0.216138 0.096411 lnL0 = -1264.006800 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1264.006800 x= 0.17819 0.07883 0.05011 0.12940 0.08478 0.16062 0.21614 0.09641 1 h-lim-p 0.0034 0.0274 47.6558 1263.544247 4 0.0004 32 | 0/8 2 h-lim-p 0.0018 0.0161 11.4749 1263.495601 6 0.0008 55 | 0/8 3 h-lim-p 0.0021 0.0649 4.3157 1263.490885 6 0.0006 82 | 0/8 4 h-lim-p 0.0035 0.3817 0.7191 1263.490635 4 0.0010 104 | 0/8 5 h-lim-p 0.0030 1.1727 0.2437 1263.490606 2 0.0012 128 | 0/8 6 h-lim-p 0.0133 13.0835 0.0212 1263.490606 0 0.0015 150 | 0/8 7 h-lim-p 0.0084 20.0000 0.0037 1263.490606 0 0.0018 171 | 0/8 8 h-lim-p 0.1014 20.0000 0.0001 1263.490603 0 0.8114 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1263.490603 0 1.0938 214 | 0/8 10 h-lim-p 1.9134 20.0000 0.0000 1263.490603 0 1.6743 234 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1263.490603 0 0.0006 265 Out... lnL = -1263.490603 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1263.490603 Node 7: lnL = -1263.490603 Node 8: lnL = -1263.490603 Node 9: lnL = -1263.490603 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 112 Sequential format.. Reading seq # 1: YLR183C_Sbay Reading seq # 2: YLR183C_Scer Reading seq # 3: YLR183C_Skud Reading seq # 4: YLR183C_Smik Reading seq # 5: YLR183C_Spar Sequences read.. Counting patterns.. # site patterns = 68 Counting frequencies.. 120 bytes for distance 10880 bytes for lkl0 8704 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.243201 0.108712 0.051209 0.067149 0.162477 0.183432 0.237762 0.144477 lnL0 = -492.789972 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 492.789972 x= 0.24320 0.10871 0.05121 0.06715 0.16248 0.18343 0.23776 0.14448 1 h-lim-p 0.0040 0.0318 18.2597 492.506031 2 0.0019 26 | 0/8 2 h-lim-p 0.0017 0.0138 9.7336 492.413374 0 0.0026 38 | 0/8 3 h-lim-p 0.0051 0.0406 2.6027 492.405471 6 0.0026 65 | 0/8 4 h-lim-p 0.0058 0.2063 1.1553 492.404151 3 0.0024 83 | 0/8 5 h-lim-p 0.0072 0.6808 0.3880 492.403924 2 0.0034 99 | 0/8 6 h-lim-p 0.0130 7.5999 0.1002 492.403901 3 0.0043 126 | 0/8 7 h-lim-p 0.1584 20.0000 0.0027 492.403338 0 0.6338 148 | 0/8 8 h-lim-p 0.0099 1.3213 0.1717 492.403252 3 0.0049 175 | 0/8 9 h-lim-p 1.8932 20.0000 0.0004 492.403224 3 1.0175 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 492.403224 0 1.0938 222 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 492.403224 0 0.5469 243 | 0/8 12 h-lim-p 0.4105 20.0000 0.0000 492.403224 0 0.0032 269 | 0/8 13 h-lim-p 0.0018 20.0000 0.0000 492.403224 0 0.0009 289 Out... lnL = -492.403224 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -492.403224 Node 7: lnL = -492.403224 Node 8: lnL = -492.403224 Node 9: lnL = -492.403224 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 365 Sequential format.. Reading seq # 1: YLR186W_Sbay Reading seq # 2: YLR186W_Scer Reading seq # 3: YLR186W_Skud Reading seq # 4: YLR186W_Smik Reading seq # 5: YLR186W_Spar Sequences read.. Counting patterns.. # site patterns = 119 Counting frequencies.. 120 bytes for distance 19040 bytes for lkl0 15232 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.335882 0.000060 0.147609 0.093862 0.084351 4.680916 0.210825 0.021183 lnL0 = -1293.967177 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1293.967177 x= 0.33588 0.00006 0.14761 0.09386 0.08435 4.68092 0.21082 0.02118 1 h-lim-p 0.0000 0.0000 106.6236 1293.946954 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0060 48.4514 1293.316600 0 0.0006 40 | 1/8 3 h-lim-p 0.0030 0.0252 10.2154 1293.241242 2 0.0014 56 | 1/8 4 h-lim-p 0.0034 0.0275 1.9403 1293.224736 2 0.0034 72 | 1/8 5 h-lim-p 0.0126 0.3022 0.5293 1292.826529 0 0.0503 86 | 1/8 6 h-lim-p 0.0014 0.0160 18.6055 1290.732794 0 0.0057 107 | 1/8 7 h-lim-p 0.6129 4.9033 0.0304 1290.494418 1 0.7661 121 | 1/8 8 h-lim-p 2.5000 20.0000 0.0026 1290.491632 6 0.6876 155 | 1/8 9 h-lim-p 2.5000 20.0000 0.0005 1290.491537 2 0.9644 178 | 1/8 10 h-lim-p 2.5000 20.0000 0.0001 1290.491535 1 0.6152 200 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 1290.491535 0 1.0938 219 | 1/8 12 h-lim-p 1.9167 20.0000 0.0000 1290.491535 0 1.6771 238 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 1290.491535 0 1.0938 257 | 1/8 14 h-lim-p 0.7184 20.0000 0.0000 1290.491535 0 1.4368 277 | 1/8 15 h-lim-p 0.6986 20.0000 0.0000 1290.491535 0 0.0027 303 | 1/8 16 h-lim-p 0.0004 20.0000 0.0001 1290.491535 0 0.0002 322 | 1/8 17 h-lim-p 0.0004 20.0000 0.0001 1290.491535 0 0.0011 342 | 1/8 18 h-lim-p 0.0002 20.0000 0.0004 1290.491535 0 0.0000 374 | 1/8 19 h-lim-p 0.0000 20.0000 0.0002 | 1/8 20 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1290.491535 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1290.491535 Node 7: lnL = -1290.491535 Node 8: lnL = -1290.491535 Node 9: lnL = -1290.491535 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 488 Sequential format.. Reading seq # 1: YLR187W_Sbay Reading seq # 2: YLR187W_Scer Reading seq # 3: YLR187W_Skud Reading seq # 4: YLR187W_Smik Reading seq # 5: YLR187W_Spar Sequences read.. Counting patterns.. # site patterns = 201 Counting frequencies.. 120 bytes for distance 32160 bytes for lkl0 25728 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.195245 0.000060 0.009621 0.163013 0.979053 0.175979 0.171179 0.054848 lnL0 = -2238.599482 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2238.599482 x= 0.19524 0.00006 0.00962 0.16301 0.97905 0.17598 0.17118 0.05485 1 h-lim-p 0.0000 0.0002 162.2981 2234.614439 m 0.0002 22 | 1/8 2 h-lim-p 0.0002 0.0017 135.5252 2232.713249 0 0.0004 35 | 1/8 3 h-lim-p 0.0015 0.0124 17.5160 2232.642664 6 0.0005 63 | 1/8 4 h-lim-p 0.0008 0.3454 10.5873 2232.364356 0 0.0063 78 | 0/8 5 h-lim-p 0.0008 0.0061 28.3795 2232.255881 5 0.0004 102 | 0/8 6 h-lim-p 0.0007 0.0053 14.4020 2232.243961 5 0.0004 126 | 0/8 7 h-lim-p 0.0044 0.3612 1.2059 2232.243188 2 0.0010 143 | 0/8 8 h-lim-p 0.0385 16.5968 0.0326 2231.897666 0 0.4621 158 | 0/8 9 h-lim-p 2.5000 20.0000 0.0028 2231.887174 6 1.3994 194 | 0/8 10 h-lim-p 2.3260 20.0000 0.0017 2231.883591 4 2.4214 222 | 0/8 11 h-lim-p 2.5000 20.0000 0.0002 2231.883549 1 1.0938 244 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2231.883549 0 1.0938 264 | 0/8 13 h-lim-p 1.2890 20.0000 0.0000 2231.883549 0 1.1278 284 | 0/8 14 h-lim-p 0.7091 20.0000 0.0000 2231.883549 0 0.0166 309 | 0/8 15 h-lim-p 0.0014 20.0000 0.0004 2231.883549 0 0.0007 329 | 0/8 16 h-lim-p 0.0002 20.0000 0.0013 2231.883549 0 0.0000 350 | 0/8 17 h-lim-p 0.0000 20.0000 0.0018 2231.883549 0 0.0000 384 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -2231.883549 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2231.883549 Node 7: lnL = -2231.883549 Node 8: lnL = -2231.883549 Node 9: lnL = -2231.883549 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 833 Sequential format.. Reading seq # 1: YLR189C_Sbay Reading seq # 2: YLR189C_Scer Reading seq # 3: YLR189C_Skud Reading seq # 4: YLR189C_Smik Reading seq # 5: YLR189C_Spar Sequences read.. Counting patterns.. # site patterns = 257 Counting frequencies.. 120 bytes for distance 41120 bytes for lkl0 32896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.178849 0.042892 0.086259 0.098888 0.075127 0.187787 0.227882 0.090501 lnL0 = -3689.085575 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3689.085575 x= 0.17885 0.04289 0.08626 0.09889 0.07513 0.18779 0.22788 0.09050 1 h-lim-p 0.0003 0.0022 113.5036 3688.035840 8 0.0002 41 | 0/8 2 h-lim-p 0.0009 0.0115 21.9362 3687.943456 3 0.0004 59 | 0/8 3 h-lim-p 0.0007 0.0236 12.5657 3687.929768 6 0.0002 86 | 0/8 4 h-lim-p 0.0007 0.0383 3.9615 3687.928745 2 0.0002 103 | 0/8 5 h-lim-p 0.0006 0.1840 0.9603 3687.928610 1 0.0003 117 | 0/8 6 h-lim-p 0.0037 2.1025 0.0818 3687.928610 0 0.0004 139 | 0/8 7 h-lim-p 0.0016 8.1051 0.0204 3687.928610 0 0.0004 160 | 0/8 8 h-lim-p 0.0332 20.0000 0.0002 3687.928561 0 0.7960 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3687.928561 0 1.0938 204 | 0/8 10 h-lim-p 1.2993 20.0000 0.0000 3687.928561 0 0.6496 224 | 0/8 11 h-lim-p 0.3936 20.0000 0.0000 3687.928561 0 0.0246 247 | 0/8 12 h-lim-p 0.0104 20.0000 0.0001 3687.928561 0 0.0003 271 | 0/8 13 h-lim-p 0.0015 20.0000 0.0000 3687.928561 0 0.0001 294 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 3687.928561 0 0.0000 327 | 0/8 15 h-lim-p 0.0000 20.0000 0.0011 | 0/8 16 h-lim-p 0.0000 20.0000 0.0011 Out... lnL = -3687.928561 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3687.928561 Node 7: lnL = -3687.928561 Node 8: lnL = -3687.928561 Node 9: lnL = -3687.928561 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 833 Sequential format.. Reading seq # 1: YLR190W_Sbay Reading seq # 2: YLR190W_Scer Reading seq # 3: YLR190W_Skud Reading seq # 4: YLR190W_Smik Reading seq # 5: YLR190W_Spar Sequences read.. Counting patterns.. # site patterns = 319 Counting frequencies.. 120 bytes for distance 51040 bytes for lkl0 40832 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.214591 0.013511 0.096855 0.110328 0.061853 1.032513 0.241342 0.056590 lnL0 = -3870.345471 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3870.345471 x= 0.21459 0.01351 0.09685 0.11033 0.06185 1.03251 0.24134 0.05659 1 h-lim-p 0.0003 0.0024 129.6756 3869.001833 8 0.0002 41 | 0/8 2 h-lim-p 0.0004 0.0030 51.9503 3868.724109 7 0.0002 71 | 0/8 3 h-lim-p 0.0003 0.0044 34.3416 3868.551809 1 0.0004 85 | 0/8 4 h-lim-p 0.0004 0.0061 35.2994 3868.439872 3 0.0004 103 | 0/8 5 h-lim-p 0.0008 0.0074 16.1840 3868.379653 5 0.0007 124 | 0/8 6 h-lim-p 0.0026 0.0388 4.5150 3868.375649 5 0.0005 148 | 0/8 7 h-lim-p 0.0012 0.8246 1.7743 3868.366893 0 0.0069 162 | 0/8 8 h-lim-p 2.5000 20.0000 0.0012 3868.364870 3 1.0449 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3868.364843 1 1.0938 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3868.364843 0 1.0938 222 | 0/8 11 h-lim-p 1.2281 20.0000 0.0000 3868.364843 0 2.4562 243 | 0/8 12 h-lim-p 1.3908 20.0000 0.0000 3868.364843 0 0.6954 263 | 0/8 13 h-lim-p 0.0254 20.0000 0.0010 3868.364843 0 0.0003 289 | 0/8 14 h-lim-p 0.0000 4.4335 0.0208 3868.364843 0 0.0000 310 | 0/8 15 h-lim-p 0.0006 20.0000 0.0001 3868.364843 0 0.0006 330 | 0/8 16 h-lim-p 0.0002 20.0000 0.0003 3868.364843 0 0.0000 366 | 0/8 17 h-lim-p 0.0000 20.0000 0.0019 | 0/8 18 h-lim-p 0.0000 20.0000 0.0019 Out... lnL = -3868.364843 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3868.364843 Node 7: lnL = -3868.364843 Node 8: lnL = -3868.364843 Node 9: lnL = -3868.364843 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 292 Sequential format.. Reading seq # 1: YLR193C_Sbay Reading seq # 2: YLR193C_Scer Reading seq # 3: YLR193C_Skud Reading seq # 4: YLR193C_Smik Reading seq # 5: YLR193C_Spar Sequences read.. Counting patterns.. # site patterns = 114 Counting frequencies.. 120 bytes for distance 18240 bytes for lkl0 14592 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.154201 0.041971 0.069879 0.079247 0.070627 0.173731 0.170547 0.079076 lnL0 = -1193.724017 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1193.724017 x= 0.15420 0.04197 0.06988 0.07925 0.07063 0.17373 0.17055 0.07908 1 h-lim-p 0.0006 0.0046 34.1949 1193.382982 3 0.0006 28 | 0/8 2 h-lim-p 0.0005 0.0042 16.2661 1193.317086 1 0.0007 42 | 0/8 3 h-lim-p 0.0021 0.0305 5.0472 1193.311327 2 0.0005 59 | 0/8 4 h-lim-p 0.0017 0.4953 1.4675 1193.310923 2 0.0004 76 | 0/8 5 h-lim-p 0.0020 0.8599 0.2877 1193.310892 2 0.0008 92 | 0/8 6 h-lim-p 0.0020 1.5470 0.1139 1193.310887 1 0.0008 114 | 0/8 7 h-lim-p 0.0032 4.4897 0.0278 1193.310884 1 0.0026 136 | 0/8 8 h-lim-p 0.0218 20.0000 0.0033 1193.310110 0 0.2616 159 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1193.310105 1 0.9961 181 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1193.310105 0 1.0938 201 | 0/8 11 h-lim-p 1.1702 20.0000 0.0000 1193.310105 0 0.0080 227 | 0/8 12 h-lim-p 0.0008 20.0000 0.0001 1193.310105 0 0.0000 264 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 1193.310105 0 0.0000 290 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 1193.310105 0 0.0000 351 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1193.310105 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1193.310105 Node 7: lnL = -1193.310105 Node 8: lnL = -1193.310105 Node 9: lnL = -1193.310105 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 714 Sequential format.. Reading seq # 1: YLR196W_Sbay Reading seq # 2: YLR196W_Scer Reading seq # 3: YLR196W_Skud Reading seq # 4: YLR196W_Smik Reading seq # 5: YLR196W_Spar Sequences read.. Counting patterns.. # site patterns = 239 Counting frequencies.. 120 bytes for distance 38240 bytes for lkl0 30592 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.252322 0.000060 0.215056 0.163055 0.094756 0.858302 0.258260 0.095170 lnL0 = -2972.805017 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2972.805017 x= 0.25232 0.00006 0.21506 0.16306 0.09476 0.85830 0.25826 0.09517 1 h-lim-p 0.0000 0.0000 167.7587 2972.765190 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0162 44.7547 2972.451091 0 0.0003 39 | 1/8 3 h-lim-p 0.0007 0.0112 20.1841 2972.308322 6 0.0008 64 | 1/8 4 h-lim-p 0.0011 0.0553 14.1091 2971.944124 0 0.0045 78 | 1/8 5 h-lim-p 0.0016 0.0373 38.7782 2971.260176 0 0.0033 91 | 1/8 6 h-lim-p 0.0038 0.0304 12.0991 2971.192792 6 0.0014 117 | 1/8 7 h-lim-p 0.0910 1.7451 0.1840 2965.627791 0 0.7283 132 | 0/8 8 h-lim-p 0.0071 0.0566 5.6544 2965.617735 4 0.0009 161 | 0/8 9 h-lim-p 0.0986 1.0459 0.0500 2964.881236 3 0.6980 182 | 0/8 10 h-lim-p 2.5000 20.0000 0.0024 2964.878390 5 0.7847 216 | 0/8 11 h-lim-p 2.3017 20.0000 0.0008 2964.878272 3 1.3698 244 | 0/8 12 h-lim-p 0.9063 7.2500 0.0003 2964.878210 0 3.6250 266 | 0/8 13 h-lim-p 0.4567 3.6539 0.0004 2964.878203 0 1.3702 287 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 2964.878203 0 1.0938 307 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2964.878203 0 1.0938 327 | 0/8 16 h-lim-p 1.6605 20.0000 0.0000 2964.878203 0 1.4530 347 | 0/8 17 h-lim-p 2.1649 20.0000 0.0000 2964.878203 0 1.8943 367 | 0/8 18 h-lim-p 1.9674 20.0000 0.0000 2964.878203 0 0.8607 387 | 0/8 19 h-lim-p 0.4417 20.0000 0.0000 2964.878203 0 0.0000 432 Out... lnL = -2964.878203 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2964.878203 Node 7: lnL = -2964.878203 Node 8: lnL = -2964.878203 Node 9: lnL = -2964.878203 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 457 Sequential format.. Reading seq # 1: YLR197W_Sbay Reading seq # 2: YLR197W_Scer Reading seq # 3: YLR197W_Skud Reading seq # 4: YLR197W_Smik Reading seq # 5: YLR197W_Spar Sequences read.. Counting patterns.. # site patterns = 141 Counting frequencies.. 120 bytes for distance 22560 bytes for lkl0 18048 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.089937 0.052331 0.047298 0.069995 0.073561 0.113770 0.131540 0.034334 lnL0 = -1662.648024 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1662.648024 x= 0.08994 0.05233 0.04730 0.06999 0.07356 0.11377 0.13154 0.03433 1 h-lim-p 0.0015 0.0122 114.9519 1661.414092 6 0.0002 36 | 0/8 2 h-lim-p 0.0005 0.0042 19.0722 1661.370610 2 0.0002 52 | 0/8 3 h-lim-p 0.0025 0.0931 1.8596 1661.370187 3 0.0002 72 | 0/8 4 h-lim-p 0.0009 0.4875 0.4943 1661.370146 2 0.0004 88 | 0/8 5 h-lim-p 0.0019 0.8662 0.0980 1661.370145 1 0.0002 112 | 0/8 6 h-lim-p 0.0021 10.7970 0.0105 1661.370145 0 0.0019 132 | 0/8 7 h-lim-p 0.0017 15.4059 0.0114 1661.370140 0 0.0069 154 | 0/8 8 h-lim-p 0.0053 20.0000 0.0147 1661.369928 0 0.0214 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1661.369924 1 0.9961 198 | 0/8 10 h-lim-p 1.7782 20.0000 0.0000 1661.369924 0 1.5559 218 | 0/8 11 h-lim-p 2.3042 20.0000 0.0000 1661.369924 0 1.0081 238 | 0/8 12 h-lim-p 0.2502 20.0000 0.0001 1661.369924 0 0.0000 276 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 1661.369924 0 0.0001 296 Out... lnL = -1661.369924 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1661.369924 Node 7: lnL = -1661.369924 Node 8: lnL = -1661.369924 Node 9: lnL = -1661.369924 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 795 Sequential format.. Reading seq # 1: YLR199C_Sbay Reading seq # 2: YLR199C_Scer Reading seq # 3: YLR199C_Skud Reading seq # 4: YLR199C_Smik Reading seq # 5: YLR199C_Spar Sequences read.. Counting patterns.. # site patterns = 223 Counting frequencies.. 120 bytes for distance 35680 bytes for lkl0 28544 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.084406 0.036763 0.048783 0.132407 0.066396 0.213734 0.109951 0.020949 lnL0 = -2702.924111 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2702.924111 x= 0.08441 0.03676 0.04878 0.13241 0.06640 0.21373 0.10995 0.02095 1 h-lim-p 0.0001 0.0011 292.2746 2698.419375 9 0.0001 42 | 0/8 2 h-lim-p 0.0001 0.0005 126.5418 2696.501608 0 0.0003 56 | 0/8 3 h-lim-p 0.0001 0.0010 66.1252 2696.309803 2 0.0001 72 | 0/8 4 h-lim-p 0.0004 0.0093 20.6897 2696.254302 3 0.0003 90 | 0/8 5 h-lim-p 0.0007 0.0264 8.3260 2696.240321 6 0.0005 116 | 0/8 6 h-lim-p 0.0012 0.0821 3.3214 2696.239061 3 0.0003 135 | 0/8 7 h-lim-p 0.0014 0.1092 0.6429 2696.238994 2 0.0003 152 | 0/8 8 h-lim-p 0.0664 20.0000 0.0030 2696.221907 0 0.7967 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 2696.220710 4 1.3159 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 2696.220705 0 1.0938 224 | 0/8 11 h-lim-p 2.4676 20.0000 0.0001 2696.220705 0 1.0796 244 | 0/8 12 h-lim-p 0.5179 20.0000 0.0001 2696.220705 0 0.0003 274 | 0/8 13 h-lim-p 0.0001 20.0000 0.0007 2696.220705 0 0.0000 303 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -2696.220705 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2696.220705 Node 7: lnL = -2696.220705 Node 8: lnL = -2696.220705 Node 9: lnL = -2696.220705 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 532 Sequential format.. Reading seq # 1: YLR200W_Sbay Reading seq # 2: YLR200W_Scer Reading seq # 3: YLR200W_Skud Reading seq # 4: YLR200W_Smik Reading seq # 5: YLR200W_Spar Sequences read.. Counting patterns.. # site patterns = 135 Counting frequencies.. 120 bytes for distance 21600 bytes for lkl0 17280 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.098269 0.109437 0.013939 0.105342 0.054988 0.512717 0.163649 0.003946 lnL0 = -1782.697519 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1782.697519 x= 0.09827 0.10944 0.01394 0.10534 0.05499 0.51272 0.16365 0.00395 1 h-lim-p 0.0003 0.0026 231.7417 1778.357545 10 0.0002 47 | 0/8 2 h-lim-p 0.0003 0.0022 78.6441 1777.118433 0 0.0004 59 | 0/8 3 h-lim-p 0.0011 0.0090 24.6484 1776.978785 2 0.0005 75 | 0/8 4 h-lim-p 0.0004 0.0043 33.5983 1776.686663 0 0.0015 89 | 0/8 5 h-lim-p 0.0002 0.0012 73.9057 1776.336893 0 0.0006 103 | 0/8 6 h-lim-p 0.0013 0.0105 9.3119 1776.328665 5 0.0003 126 | 0/8 7 h-lim-p 0.0183 4.0418 0.1273 1776.322537 0 0.1464 141 | 0/8 8 h-lim-p 0.3254 10.7132 0.0573 1776.289894 6 0.2150 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0022 1776.289174 2 1.2402 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 1776.289149 2 0.9961 222 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1776.289149 0 1.0938 242 | 0/8 12 h-lim-p 1.4483 20.0000 0.0000 1776.289149 0 1.2673 262 | 0/8 13 h-lim-p 1.1037 20.0000 0.0000 1776.289149 0 2.2074 283 | 0/8 14 h-lim-p 0.1860 20.0000 0.0004 1776.289149 0 0.0058 307 | 0/8 15 h-lim-p 0.0014 20.0000 0.0017 1776.289149 0 0.0000 347 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1776.289149 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1776.289149 Node 7: lnL = -1776.289149 Node 8: lnL = -1776.289149 Node 9: lnL = -1776.289149 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 384 Sequential format.. Reading seq # 1: YLR201C_Sbay Reading seq # 2: YLR201C_Scer Reading seq # 3: YLR201C_Skud Reading seq # 4: YLR201C_Smik Reading seq # 5: YLR201C_Spar Sequences read.. Counting patterns.. # site patterns = 147 Counting frequencies.. 120 bytes for distance 23520 bytes for lkl0 18816 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.124299 0.035240 0.041458 0.120928 0.110912 0.172256 0.119584 0.055600 lnL0 = -1525.250820 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1525.250820 x= 0.12430 0.03524 0.04146 0.12093 0.11091 0.17226 0.11958 0.05560 1 h-lim-p 0.0017 0.0136 106.3898 1524.170630 8 0.0002 39 | 0/8 2 h-lim-p 0.0007 0.0054 19.0701 1524.101084 8 0.0004 72 | 0/8 3 h-lim-p 0.0014 0.0415 5.4595 1524.095989 5 0.0004 95 | 0/8 4 h-lim-p 0.0018 0.1688 1.1385 1524.095704 4 0.0005 116 | 0/8 5 h-lim-p 0.0028 1.0017 0.1908 1524.095693 0 0.0006 129 | 0/8 6 h-lim-p 0.0089 20.0000 0.0130 1524.095693 0 0.0005 152 | 0/8 7 h-lim-p 0.0034 20.0000 0.0019 1524.095693 0 0.0007 173 | 0/8 8 h-lim-p 0.0509 20.0000 0.0000 1524.095693 0 1.2226 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1524.095693 0 1.0938 217 | 0/8 10 h-lim-p 0.6213 20.0000 0.0000 1524.095693 0 0.0049 243 | 0/8 11 h-lim-p 0.0011 20.0000 0.0001 1524.095693 0 0.0003 264 | 0/8 12 h-lim-p 0.0004 20.0000 0.0000 1524.095693 0 0.0000 287 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 1524.095693 0 0.0000 312 Out... lnL = -1524.095693 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1524.095693 Node 7: lnL = -1524.095693 Node 8: lnL = -1524.095693 Node 9: lnL = -1524.095693 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 320 Sequential format.. Reading seq # 1: YLR204W_Sbay Reading seq # 2: YLR204W_Scer Reading seq # 3: YLR204W_Skud Reading seq # 4: YLR204W_Smik Reading seq # 5: YLR204W_Spar Sequences read.. Counting patterns.. # site patterns = 80 Counting frequencies.. 120 bytes for distance 12800 bytes for lkl0 10240 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.314699 0.049394 0.005382 0.163115 4.654922 0.195006 0.204194 0.000060 lnL0 = -1134.424213 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1134.424213 x= 0.31470 0.04939 0.00538 0.16311 4.65492 0.19501 0.20419 0.00006 1 h-lim-p 0.0000 0.0000 224.1252 1134.351720 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0071 45.6717 1132.917958 0 0.0013 41 | 1/8 3 h-lim-p 0.0006 0.0046 12.4333 1132.766586 0 0.0017 54 | 1/8 4 h-lim-p 0.0075 0.0765 2.8465 1132.466521 0 0.0113 66 | 1/8 5 h-lim-p 0.0067 0.0534 2.0182 1123.391853 m 0.0534 78 | 0/8 6 h-lim-p -0.0000 -0.0000 56.3162 h-lim-p: -6.80893538e-23 -5.44714831e-22 5.63161853e+01 1123.391853 .. | 0/8 7 h-lim-p 0.0000 0.0052 145.7926 1122.108389 0 0.0002 102 | 0/8 8 h-lim-p 0.0001 0.0004 76.4385 1120.731521 m 0.0004 114 | 1/8 9 h-lim-p 0.0006 0.0048 56.3795 1120.417690 8 0.0003 147 | 1/8 10 h-lim-p 0.0025 0.0373 6.9056 1120.396485 7 0.0009 176 | 1/8 11 h-lim-p 0.0154 0.1550 0.3921 1120.382900 6 0.0114 202 | 1/8 12 h-lim-p 0.0027 0.0300 1.6371 1120.361679 5 0.0029 231 | 1/8 13 h-lim-p 0.2443 2.3822 0.0195 1120.216006 0 0.7329 244 | 1/8 14 h-lim-p 2.5000 20.0000 0.0017 1120.214381 4 0.9422 271 | 0/8 15 h-lim-p 0.1476 20.0000 0.0106 1120.214381 0 0.0020 295 | 0/8 16 h-lim-p 0.1242 0.9933 0.0001 1120.214381 m 0.9933 315 | 1/8 17 h-lim-p 1.0072 20.0000 0.0000 1120.214381 0 0.8813 335 | 1/8 18 h-lim-p 0.3087 20.0000 0.0001 1120.214381 0 0.6174 355 | 1/8 19 h-lim-p 0.6253 20.0000 0.0001 1120.214381 0 0.0012 382 | 1/8 20 h-lim-p 0.0004 20.0000 0.0004 1120.214381 0 0.0000 404 | 1/8 21 h-lim-p 0.0000 20.0000 0.0005 1120.214381 0 0.0000 430 | 1/8 22 h-lim-p 0.0000 20.0000 0.0000 1120.214381 0 0.0000 458 Out... lnL = -1120.214381 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1120.214381 Node 7: lnL = -1120.214381 Node 8: lnL = -1120.214381 Node 9: lnL = -1120.214381 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 826 Sequential format.. Reading seq # 1: YLR205C_Sbay Reading seq # 2: YLR205C_Scer Reading seq # 3: YLR205C_Skud Reading seq # 4: YLR205C_Smik Reading seq # 5: YLR205C_Spar Sequences read.. Counting patterns.. # site patterns = 249 Counting frequencies.. 120 bytes for distance 39840 bytes for lkl0 31872 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 1.013092 0.072351 0.000060 0.626216 0.451880 0.514553 0.813869 0.771559 lnL0 = -3924.194456 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3924.194456 x= 1.01309 0.07235 0.00006 0.62622 0.45188 0.51455 0.81387 0.77156 1 h-lim-p 0.0000 0.0000 551.3805 3924.076705 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0038 171.1938 3859.841200 m 0.0038 40 | 1/8 3 h-lim-p 0.0039 0.0315 26.8938 3859.670973 5 0.0010 63 | 0/8 4 h-lim-p 0.0007 0.1118 40.3000 3859.436193 7 0.0004 89 | 0/8 5 h-lim-p 0.0001 0.0007 7.0269 .. | 0/8 6 h-lim-p 0.0000 0.0015 294.1342 3713.831842 m 0.0015 134 | 1/8 7 h-lim-p 0.0001 0.0007 1126.5476 3635.558191 0 0.0005 148 | 1/8 8 h-lim-p 0.0000 0.0000 4665.5130 3599.749761 m 0.0000 160 | 1/8 9 h-lim-p -0.0000 -0.0000 279.2781 h-lim-p: -2.04667875e-21 -1.63734300e-20 2.79278132e+02 3599.749761 .. | 1/8 10 h-lim-p 0.0000 0.0070 823.5417 3571.658311 0 0.0002 184 | 1/8 11 h-lim-p 0.0000 0.0002 152.5789 3568.779160 m 0.0002 196 | 2/8 12 h-lim-p 0.0005 0.0064 42.7194 3568.215136 7 0.0006 225 | 2/8 13 h-lim-p 0.0018 0.0597 14.4257 3566.146876 0 0.0141 240 | 2/8 14 h-lim-p 0.0290 3.4479 7.0166 3565.544220 3 0.0263 258 | 2/8 15 h-lim-p 0.1298 2.0623 1.4203 3565.344666 3 0.1176 276 | 2/8 16 h-lim-p 0.8962 7.1694 0.1652 3564.581914 8 0.6676 307 | 1/8 17 h-lim-p 0.0019 0.0190 58.4692 3564.473876 5 0.0009 337 | 1/8 18 h-lim-p 0.8125 10.6040 0.0666 3564.006093 0 3.2500 351 | 1/8 19 h-lim-p 0.3667 2.9332 0.0712 3563.486265 0 2.1999 372 | 1/8 20 h-lim-p 1.8984 20.0000 0.0825 3563.341378 6 1.0018 404 | 1/8 21 h-lim-p 1.2156 9.7249 0.0177 3563.336553 5 0.7845 435 | 1/8 22 h-lim-p 1.8721 20.0000 0.0074 3563.336128 3 0.6631 462 | 1/8 23 h-lim-p 2.5000 20.0000 0.0008 3563.336108 1 1.0938 483 | 1/8 24 h-lim-p 2.5000 20.0000 0.0001 3563.336107 0 2.1875 502 | 1/8 25 h-lim-p 2.5000 20.0000 0.0001 3563.336107 0 1.0938 521 | 1/8 26 h-lim-p 2.5000 20.0000 0.0000 3563.336107 0 1.0938 540 | 1/8 27 h-lim-p 2.5000 20.0000 0.0000 3563.336107 0 2.1875 559 | 1/8 28 h-lim-p 1.8999 20.0000 0.0000 3563.336107 0 0.9500 578 | 1/8 29 h-lim-p 2.5000 20.0000 0.0000 3563.336107 0 2.5000 597 | 1/8 30 h-lim-p 2.5000 20.0000 0.0000 3563.336107 010.0000 618 | 1/8 31 h-lim-p 2.5000 20.0000 0.0000 3563.336107 0 0.0000 663 Out... lnL = -3563.336107 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3563.336107 Node 7: lnL = -3563.336107 Node 8: lnL = -3563.336107 Node 9: lnL = -3563.336107 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 916 Sequential format.. Reading seq # 1: YLR206W_Sbay Reading seq # 2: YLR206W_Scer Reading seq # 3: YLR206W_Skud Reading seq # 4: YLR206W_Smik Reading seq # 5: YLR206W_Spar Sequences read.. Counting patterns.. # site patterns = 286 Counting frequencies.. 120 bytes for distance 45760 bytes for lkl0 36608 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.194800 0.548668 0.421173 0.222684 0.561997 0.470081 0.566495 lnL0 = -3885.519507 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3885.519507 x= 0.00006 0.19480 0.54867 0.42117 0.22268 0.56200 0.47008 0.56650 1 h-lim-p 0.0000 0.0000 769.8217 3885.182044 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0001 5734.1806 3676.502415 m 0.0001 34 | 1/8 3 h-lim-p 0.0002 0.0016 372.9622 3622.017677 0 0.0008 48 | 1/8 4 h-lim-p 0.0005 0.0039 49.6448 3621.073724 0 0.0010 61 | 0/8 5 h-lim-p 0.0004 0.0039 126.1564 3616.205812 0 0.0008 74 | 0/8 6 h-lim-p 0.0030 0.0242 22.2804 3616.076532 5 0.0013 95 | 0/8 7 h-lim-p 0.0102 0.2466 2.9243 .. | 0/8 8 h-lim-p 0.0000 0.0005 483.7527 3549.758204 m 0.0005 145 | 1/8 9 h-lim-p 0.0000 0.0002 1335.0871 3517.969337 0 0.0001 159 | 1/8 10 h-lim-p 0.0000 0.0004 568.2813 3507.652508 0 0.0001 172 | 1/8 11 h-lim-p 0.0001 0.0005 430.6361 3501.148289 0 0.0001 185 | 1/8 12 h-lim-p 0.0005 0.0044 69.2353 3499.361178 0 0.0011 198 | 1/8 13 h-lim-p 0.0007 0.0273 102.6160 3494.928073 0 0.0022 211 | 1/8 14 h-lim-p 1.3442 20.0000 0.1693 3469.312902 5 0.7150 234 | 1/8 15 h-lim-p 0.5505 4.4039 0.0522 3467.080228 0 1.1010 254 | 0/8 16 h-lim-p 0.0000 0.0000 10.1320 h-lim-p: 9.07056711e-20 7.25645369e-19 1.01319618e+01 3467.080228 .. | 0/8 17 h-lim-p 0.0000 0.0050 87.9225 3466.491691 0 0.0002 285 | 0/8 18 h-lim-p 0.0000 0.0000 39.6477 3466.451441 m 0.0000 297 | 1/8 19 h-lim-p 0.0001 0.0192 13.1442 3466.434666 0 0.0002 310 | 1/8 20 h-lim-p 0.0009 0.0547 3.3899 3466.432468 4 0.0004 332 | 1/8 21 h-lim-p 0.0011 0.3992 1.1935 3466.429043 0 0.0046 346 | 1/8 22 h-lim-p 0.0014 0.1665 4.0372 3466.426008 3 0.0014 364 | 1/8 23 h-lim-p 0.0009 0.3192 5.9389 3466.421837 0 0.0019 377 | 1/8 24 h-lim-p 1.5375 20.0000 0.0073 3466.369393 5 1.0157 400 | 1/8 25 h-lim-p 2.5000 20.0000 0.0002 3466.369378 1 0.9961 421 | 1/8 26 h-lim-p 2.5000 20.0000 0.0000 3466.369378 0 1.0938 440 | 1/8 27 h-lim-p 1.2473 20.0000 0.0000 3466.369378 0 1.2473 459 | 1/8 28 h-lim-p 0.6148 20.0000 0.0000 3466.369378 0 0.0002 489 | 1/8 29 h-lim-p 0.0006 20.0000 0.0000 3466.369378 0 0.0001 509 Out... lnL = -3466.369378 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3466.369378 Node 7: lnL = -3466.369378 Node 8: lnL = -3466.369378 Node 9: lnL = -3466.369378 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 264 Sequential format.. Reading seq # 1: YLR208W_Sbay Reading seq # 2: YLR208W_Scer Reading seq # 3: YLR208W_Skud Reading seq # 4: YLR208W_Smik Reading seq # 5: YLR208W_Spar Sequences read.. Counting patterns.. # site patterns = 78 Counting frequencies.. 120 bytes for distance 12480 bytes for lkl0 9984 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.071700 0.147627 0.141716 0.066513 0.115467 0.146233 0.176170 lnL0 = -962.077489 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 962.077489 x= 0.00006 0.07170 0.14763 0.14172 0.06651 0.11547 0.14623 0.17617 1 h-lim-p 0.0000 0.0000 245.9777 961.953692 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0016 103.9161 956.557922 0 0.0010 40 | 1/8 3 h-lim-p 0.0056 0.0446 6.2459 956.476267 5 0.0021 62 | 1/8 4 h-lim-p 0.0071 0.1038 1.8802 955.384526 0 0.0283 76 | 1/8 5 h-lim-p 0.0020 0.0160 11.7037 950.100796 0 0.0060 89 | 1/8 6 h-lim-p 0.0002 0.0013 75.3633 945.861821 0 0.0007 103 | 1/8 7 h-lim-p 0.0002 0.0018 79.0652 943.595943 0 0.0007 116 | 1/8 8 h-lim-p 0.0019 0.0149 7.6772 943.583341 5 0.0004 138 | 1/8 9 h-lim-p 0.0327 1.9206 0.0950 942.784667 0 0.3928 153 | 0/8 10 h-lim-p 0.0052 0.0416 5.9320 942.758120 5 0.0023 181 | 0/8 11 h-lim-p 0.3878 3.1022 0.0153 942.727359 5 0.3252 204 | 0/8 12 h-lim-p 0.8980 11.1229 0.0055 942.713865 7 0.5497 243 | 0/8 13 h-lim-p 1.4070 19.5711 0.0022 942.713000 4 0.4636 273 | 0/8 14 h-lim-p 2.5000 20.0000 0.0003 942.712922 4 0.7683 304 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 942.712922 0 1.0938 324 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 942.712922 0 1.0938 344 | 0/8 17 h-lim-p 2.3078 20.0000 0.0000 942.712922 0 1.0096 364 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 942.712922 0 0.0001 397 Out... lnL = -942.712922 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -942.712922 Node 7: lnL = -942.712922 Node 8: lnL = -942.712922 Node 9: lnL = -942.712922 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 299 Sequential format.. Reading seq # 1: YLR209C_Sbay Reading seq # 2: YLR209C_Scer Reading seq # 3: YLR209C_Skud Reading seq # 4: YLR209C_Smik Reading seq # 5: YLR209C_Spar Sequences read.. Counting patterns.. # site patterns = 132 Counting frequencies.. 120 bytes for distance 21120 bytes for lkl0 16896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.115822 0.236100 0.236017 0.139846 0.193292 0.264606 0.315188 lnL0 = -1319.506668 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1319.506668 x= 0.00006 0.11582 0.23610 0.23602 0.13985 0.19329 0.26461 0.31519 1 h-lim-p 0.0000 0.0000 183.3050 1319.415805 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0030 87.2077 1311.437165 9 0.0020 58 | 1/8 3 h-lim-p 0.0025 0.0200 15.8050 1311.128392 2 0.0023 74 | 1/8 4 h-lim-p 0.0226 0.1807 1.4885 1310.425632 0 0.0339 86 | 1/8 5 h-lim-p 0.0063 0.0503 7.0635 1303.150257 0 0.0188 99 | 1/8 6 h-lim-p 0.0006 0.0048 46.0750 1298.448029 0 0.0024 113 | 1/8 7 h-lim-p 0.0004 0.0031 38.5993 1297.916205 0 0.0008 126 | 1/8 8 h-lim-p 0.0147 0.2076 2.0149 1297.909930 6 0.0021 155 | 0/8 9 h-lim-p 0.0007 0.0716 5.8786 1297.836538 0 0.0058 170 | 0/8 10 h-lim-p 0.3770 4.6389 0.0908 1297.548732 8 0.2045 198 | 0/8 11 h-lim-p 0.5713 4.5703 0.0235 1297.473764 2 0.5356 222 | 0/8 12 h-lim-p 2.5000 20.0000 0.0033 1297.471568 5 0.7338 254 | 0/8 13 h-lim-p 1.7105 20.0000 0.0014 1297.471314 4 0.5832 284 | 0/8 14 h-lim-p 2.5000 20.0000 0.0002 1297.471306 2 0.6580 309 | 0/8 15 h-lim-p 1.5201 20.0000 0.0001 1297.471306 0 1.3301 329 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1297.471306 0 1.0938 349 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1297.471306 0 1.0938 369 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1297.471306 0 2.1875 389 | 0/8 19 h-lim-p 0.4994 20.0000 0.0000 1297.471306 0 0.9987 410 | 0/8 20 h-lim-p 0.1111 20.0000 0.0000 1297.471306 0 0.0833 430 | 0/8 21 h-lim-p 0.0237 20.0000 0.0000 1297.471306 0 0.0000 458 | 0/8 22 h-lim-p 0.0002 20.0000 0.0000 1297.471306 0 0.0000 489 Out... lnL = -1297.471306 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1297.471306 Node 7: lnL = -1297.471306 Node 8: lnL = -1297.471306 Node 9: lnL = -1297.471306 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 302 Sequential format.. Reading seq # 1: YLR210W_Sbay Reading seq # 2: YLR210W_Scer Reading seq # 3: YLR210W_Skud Reading seq # 4: YLR210W_Smik Reading seq # 5: YLR210W_Spar Sequences read.. Counting patterns.. # site patterns = 141 Counting frequencies.. 120 bytes for distance 22560 bytes for lkl0 18048 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.106503 0.203781 0.226362 0.135410 0.190029 0.247201 0.325342 lnL0 = -1336.202670 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1336.202670 x= 0.00006 0.10650 0.20378 0.22636 0.13541 0.19003 0.24720 0.32534 1 h-lim-p 0.0000 0.0000 165.4453 1336.091360 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0025 89.4203 1329.243231 0 0.0019 41 | 1/8 3 h-lim-p 0.0027 0.0212 14.4276 1328.995695 3 0.0022 59 | 1/8 4 h-lim-p 0.0144 0.1806 2.2273 1328.800143 3 0.0130 77 | 1/8 5 h-lim-p 0.0104 0.1069 2.7854 1326.461137 0 0.0312 90 | 1/8 6 h-lim-p 0.0012 0.0095 24.1560 1319.775182 0 0.0048 104 | 1/8 7 h-lim-p 0.0018 0.0146 21.6704 1319.497713 7 0.0012 135 | 1/8 8 h-lim-p 0.0033 0.0444 7.8049 1319.461380 4 0.0013 155 | 1/8 9 h-lim-p 0.3259 20.0000 0.0312 1319.262364 0 0.6518 168 | 1/8 10 h-lim-p 1.5909 13.4244 0.0128 1319.230376 6 0.5497 202 | 1/8 11 h-lim-p 2.1670 20.0000 0.0032 1319.227145 6 0.7206 236 | 1/8 12 h-lim-p 2.0630 20.0000 0.0011 1319.226882 3 0.6049 264 | 0/8 13 h-lim-p 0.0837 20.0000 0.0082 1319.226882 0 0.0046 286 | 0/8 14 h-lim-p 0.1195 1.3338 0.0003 1319.226871 0 0.4780 308 | 0/8 15 h-lim-p 0.0564 0.4512 0.0001 1319.226870 m 0.4512 328 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 1319.226870 0 1.0938 348 | 0/8 17 h-lim-p -0.0000 -0.0000 0.0080 h-lim-p: -2.51799005e-20 -2.01439204e-19 7.99199076e-03 1319.226870 .. | 1/8 18 h-lim-p 0.0000 20.0000 0.0027 1319.226870 0 0.0010 389 | 1/8 19 h-lim-p 0.0013 20.0000 0.0021 1319.226870 0 0.0011 408 | 1/8 20 h-lim-p 0.0044 20.0000 0.0005 1319.226870 0 0.0010 428 | 1/8 21 h-lim-p 0.0032 20.0000 0.0002 1319.226870 0 0.0014 447 | 1/8 22 h-lim-p 0.0058 20.0000 0.0000 1319.226870 0 0.0000 474 | 1/8 23 h-lim-p 0.0001 20.0000 0.0000 1319.226870 0 0.0000 498 Out... lnL = -1319.226870 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1319.226870 Node 7: lnL = -1319.226870 Node 8: lnL = -1319.226870 Node 9: lnL = -1319.226870 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 252 Sequential format.. Reading seq # 1: YLR215C_Sbay Reading seq # 2: YLR215C_Scer Reading seq # 3: YLR215C_Skud Reading seq # 4: YLR215C_Smik Reading seq # 5: YLR215C_Spar Sequences read.. Counting patterns.. # site patterns = 125 Counting frequencies.. 120 bytes for distance 20000 bytes for lkl0 16000 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.163942 0.314112 0.270334 0.139046 0.198828 0.297305 0.342156 lnL0 = -1147.187788 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1147.187788 x= 0.00006 0.16394 0.31411 0.27033 0.13905 0.19883 0.29730 0.34216 1 h-lim-p 0.0000 0.0000 185.8860 1147.106667 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0068 62.4988 1139.604239 0 0.0038 42 | 1/8 3 h-lim-p 0.0022 0.0178 25.4139 1138.644482 0 0.0033 54 | 1/8 4 h-lim-p 0.0079 0.0632 6.9116 1138.042789 0 0.0119 66 | 1/8 5 h-lim-p 0.0048 0.0380 7.2561 1137.305426 0 0.0095 79 | 1/8 6 h-lim-p 0.0101 0.0811 5.1948 1123.514894 0 0.0406 93 | 1/8 7 h-lim-p 0.0006 0.0051 64.9721 1118.893164 0 0.0026 107 | 1/8 8 h-lim-p 0.0017 0.0136 21.3225 1118.452390 7 0.0019 137 | 1/8 9 h-lim-p 0.3392 2.7134 0.1152 1117.799642 6 0.2840 162 | 0/8 10 h-lim-p 0.0045 0.2373 7.2595 1117.744430 2 0.0021 185 | 0/8 11 h-lim-p 0.0748 0.5980 0.0881 1117.441153 0 0.2990 199 | 0/8 12 h-lim-p 1.9060 15.2482 0.0094 1117.422839 6 0.6433 235 | 0/8 13 h-lim-p 1.0330 8.7221 0.0058 1117.420126 5 0.4585 264 | 0/8 14 h-lim-p 1.8107 20.0000 0.0015 1117.419529 4 0.7100 292 | 0/8 15 h-lim-p 2.5000 20.0000 0.0004 1117.419512 0 0.5469 313 | 0/8 16 h-lim-p 1.6492 20.0000 0.0001 1117.419510 1 0.6571 335 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1117.419509 0 1.0938 355 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1117.419509 0 1.0938 375 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1117.419509 0 2.1875 395 | 0/8 20 h-lim-p 1.7015 20.0000 0.0000 1117.419509 0 0.3722 416 | 0/8 21 h-lim-p 0.4549 20.0000 0.0000 1117.419509 0 0.0569 438 | 0/8 22 h-lim-p 0.0447 20.0000 0.0000 1117.419509 0 0.0112 459 Out... lnL = -1117.419509 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1117.419509 Node 7: lnL = -1117.419509 Node 8: lnL = -1117.419509 Node 9: lnL = -1117.419509 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 246 Sequential format.. Reading seq # 1: YLR219W_Sbay Reading seq # 2: YLR219W_Scer Reading seq # 3: YLR219W_Skud Reading seq # 4: YLR219W_Smik Reading seq # 5: YLR219W_Spar Sequences read.. Counting patterns.. # site patterns = 106 Counting frequencies.. 120 bytes for distance 16960 bytes for lkl0 13568 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.135165 0.282750 0.229023 0.121082 0.193740 0.273122 0.293240 lnL0 = -1070.767166 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1070.767166 x= 0.00006 0.13517 0.28275 0.22902 0.12108 0.19374 0.27312 0.29324 1 h-lim-p 0.0000 0.0000 204.0474 1070.699001 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0041 78.6748 1061.317132 7 0.0027 56 | 1/8 3 h-lim-p 0.0018 0.0145 22.0505 1060.786946 1 0.0023 70 | 1/8 4 h-lim-p 0.0064 0.0512 5.0708 1060.417382 0 0.0096 82 | 1/8 5 h-lim-p 0.0102 0.0817 2.7158 1052.949355 0 0.0613 96 | 1/8 6 h-lim-p 0.0008 0.0064 35.6869 1045.235322 0 0.0032 110 | 1/8 7 h-lim-p 0.0005 0.0037 76.2409 1041.212468 0 0.0014 123 | 1/8 8 h-lim-p 0.0083 0.0661 4.8623 1041.169340 6 0.0027 149 | 1/8 9 h-lim-p 0.0491 1.3437 0.2630 1039.950549 0 0.1963 163 | 0/8 10 h-lim-p 0.0146 0.2345 3.5281 1039.940068 6 0.0018 195 | 0/8 11 h-lim-p 0.1309 1.0470 0.0464 1039.836535 0 0.2617 208 | 0/8 12 h-lim-p 0.9409 20.0000 0.0129 1039.816604 2 0.4410 232 | 0/8 13 h-lim-p 0.7665 6.1319 0.0037 1039.813946 4 0.6613 259 | 0/8 14 h-lim-p 2.1099 20.0000 0.0012 1039.813698 4 0.7490 288 | 0/8 15 h-lim-p 2.5000 20.0000 0.0001 1039.813695 1 0.9961 310 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1039.813695 0 1.0938 330 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1039.813695 0 1.0938 350 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1039.813695 0 0.0037 379 Out... lnL = -1039.813695 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1039.813695 Node 7: lnL = -1039.813695 Node 8: lnL = -1039.813695 Node 9: lnL = -1039.813695 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 504 Sequential format.. Reading seq # 1: YLR220W_Sbay Reading seq # 2: YLR220W_Scer Reading seq # 3: YLR220W_Skud Reading seq # 4: YLR220W_Smik Reading seq # 5: YLR220W_Spar Sequences read.. Counting patterns.. # site patterns = 149 Counting frequencies.. 120 bytes for distance 23840 bytes for lkl0 19072 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.051500 0.110292 0.118154 0.065157 0.076282 0.133010 0.158293 lnL0 = -1687.457830 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1687.457830 x= 0.00006 0.05150 0.11029 0.11815 0.06516 0.07628 0.13301 0.15829 1 h-lim-p 0.0000 0.0000 297.3647 1687.196761 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0009 148.7972 1682.742551 0 0.0005 39 | 1/8 3 h-lim-p 0.0003 0.0024 46.3238 1682.333434 0 0.0004 51 | 1/8 4 h-lim-p 0.0024 0.0195 7.1272 1682.306889 6 0.0007 77 | 1/8 5 h-lim-p 0.0030 0.1041 1.6696 1682.132804 0 0.0091 90 | 1/8 6 h-lim-p 0.0037 0.0295 3.2748 1677.680359 0 0.0147 104 | 1/8 7 h-lim-p 0.0003 0.0025 63.9899 1674.292890 0 0.0006 117 | 1/8 8 h-lim-p 0.0003 0.0028 54.9622 1673.768857 6 0.0004 140 | 1/8 9 h-lim-p 0.3835 3.0680 0.0460 1673.186165 2 0.3595 156 | 1/8 10 h-lim-p 0.9806 7.8449 0.0074 1673.160644 6 0.5147 187 | 1/8 11 h-lim-p 2.4681 20.0000 0.0015 1673.158661 5 0.7135 220 | 0/8 12 h-lim-p 0.0027 0.9877 0.4135 1673.158619 2 0.0005 244 | 0/8 13 h-lim-p 0.3065 2.4521 0.0003 1673.158535 0 0.9195 265 | 0/8 14 h-lim-p 0.1765 1.4118 0.0001 1673.158531 0 0.7059 287 | 0/8 15 h-lim-p 0.0066 0.0526 0.0015 1673.158531 0 0.0000 326 | 0/8 16 h-lim-p 0.0000 0.0007 0.1681 1673.158531 0 0.0002 350 | 0/8 17 h-lim-p 0.0000 0.0002 0.3554 1673.158531 0 0.0000 371 | 0/8 18 h-lim-p 0.0000 0.0000 14.0095 .. | 0/8 19 h-lim-p 0.0000 0.8827 0.1206 1673.158529 0 0.0002 416 | 0/8 20 h-lim-p 0.0004 0.0033 0.0666 1673.158529 0 0.0002 436 | 0/8 21 h-lim-p 0.0002 0.0025 0.0542 1673.158529 0 0.0000 473 | 0/8 22 h-lim-p 0.0000 0.0343 0.0281 1673.158529 0 0.0002 497 | 0/8 23 h-lim-p 0.0009 0.0526 0.0048 1673.158529 0 0.0000 536 | 0/8 24 h-lim-p 0.0000 3.7276 0.0029 1673.158529 0 0.0003 561 | 0/8 25 h-lim-p 0.0012 0.3638 0.0008 1673.158529 0 0.0000 594 | 0/8 26 h-lim-p 0.0000 0.0104 0.0095 .. | 0/8 27 h-lim-p 0.0000 0.0004 0.1640 1673.158529 0 0.0001 650 | 0/8 28 h-lim-p 0.0000 0.0001 0.3602 .. | 0/8 29 h-lim-p 0.0000 0.0004 0.1410 1673.158529 0 0.0000 717 | 0/8 30 h-lim-p 0.0000 0.0001 0.9677 .. | 0/8 31 h-lim-p 0.0000 0.0004 0.1410 | 0/8 32 h-lim-p 0.0000 0.0004 0.1410 Out... lnL = -1673.158529 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1673.158529 Node 7: lnL = -1673.158529 Node 8: lnL = -1673.158529 Node 9: lnL = -1673.158529 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 319 Sequential format.. Reading seq # 1: YLR221C_Sbay Reading seq # 2: YLR221C_Scer Reading seq # 3: YLR221C_Skud Reading seq # 4: YLR221C_Smik Reading seq # 5: YLR221C_Spar Sequences read.. Counting patterns.. # site patterns = 149 Counting frequencies.. 120 bytes for distance 23840 bytes for lkl0 19072 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.100702 0.204606 0.194818 0.077768 0.162161 0.210933 0.252837 lnL0 = -1235.456109 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1235.456109 x= 0.00006 0.10070 0.20461 0.19482 0.07777 0.16216 0.21093 0.25284 1 h-lim-p 0.0000 0.0000 199.3661 1235.358696 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0045 62.7725 1231.796264 0 0.0019 41 | 1/8 3 h-lim-p 0.0036 0.0284 7.1805 1231.653866 2 0.0033 57 | 1/8 4 h-lim-p 0.0247 0.2226 0.9693 1228.831301 0 0.0986 71 | 1/8 5 h-lim-p 0.0006 0.0051 25.0329 1223.990392 0 0.0026 92 | 1/8 6 h-lim-p 0.0003 0.0025 74.8976 1218.723346 0 0.0012 106 | 1/8 7 h-lim-p 0.0007 0.0052 37.7855 1218.222646 1 0.0008 120 | 1/8 8 h-lim-p 0.0037 0.0293 8.2785 1218.194006 2 0.0009 137 | 1/8 9 h-lim-p 0.1051 2.7969 0.0676 1217.777581 0 0.4202 151 | 0/8 10 h-lim-p 0.0201 0.3945 1.4121 1217.776022 5 0.0015 184 | 0/8 11 h-lim-p 0.0893 10.7873 0.0233 1217.715099 0 0.3572 198 | 0/8 12 h-lim-p 0.5377 4.3014 0.0042 1217.710032 0 0.8065 218 | 0/8 13 h-lim-p 2.5000 20.0000 0.0012 1217.709519 4 0.6789 247 | 0/8 14 h-lim-p 2.5000 20.0000 0.0002 1217.709490 2 0.8246 273 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1217.709490 0 1.0938 293 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1217.709490 0 1.0938 313 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1217.709490 0 0.5469 334 | 0/8 18 h-lim-p 1.1355 20.0000 0.0000 1217.709490 0 0.0000 383 Out... lnL = -1217.709490 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1217.709490 Node 7: lnL = -1217.709490 Node 8: lnL = -1217.709490 Node 9: lnL = -1217.709490 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 505 Sequential format.. Reading seq # 1: YLR222C_Sbay Reading seq # 2: YLR222C_Scer Reading seq # 3: YLR222C_Skud Reading seq # 4: YLR222C_Smik Reading seq # 5: YLR222C_Spar Sequences read.. Counting patterns.. # site patterns = 194 Counting frequencies.. 120 bytes for distance 31040 bytes for lkl0 24832 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.159610 0.286319 0.256294 0.144785 0.237648 0.307996 0.345936 lnL0 = -2320.478494 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2320.478494 x= 0.00006 0.15961 0.28632 0.25629 0.14479 0.23765 0.30800 0.34594 1 h-lim-p 0.0000 0.0000 361.7743 2320.304843 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0011 316.8559 2279.591813 m 0.0011 38 | 1/8 3 h-lim-p 0.0004 0.0029 57.8969 2278.885059 1 0.0004 52 | 1/8 4 h-lim-p 0.0004 0.0031 30.6868 2278.438515 0 0.0011 65 | 1/8 5 h-lim-p 0.0003 0.0027 12.8907 2278.169875 m 0.0027 77 | 1/8 6 h-lim-p -0.0000 -0.0000 3.3228 h-lim-p: -1.75578579e-18 -1.40462863e-17 3.32278497e+00 2278.169875 .. | 1/8 7 h-lim-p 0.0000 0.0014 283.2659 2262.944667 0 0.0006 103 | 1/8 8 h-lim-p 0.0001 0.0009 217.1628 2257.524969 0 0.0004 117 | 1/8 9 h-lim-p 0.0004 0.0028 93.0212 2256.199643 1 0.0004 131 | 1/8 10 h-lim-p 0.0012 0.0099 27.2281 2255.996563 5 0.0006 156 | 1/8 11 h-lim-p 0.0026 0.0473 6.3022 2255.981480 4 0.0006 178 | 0/8 12 h-lim-p 0.0002 0.0907 16.3026 2255.795103 0 0.0015 192 | 0/8 13 h-lim-p 0.0007 0.0108 33.4793 2255.105180 0 0.0029 206 | 0/8 14 h-lim-p 0.0061 0.0484 6.1278 2255.078322 3 0.0013 225 | 0/8 15 h-lim-p 0.0731 1.3037 0.1061 2249.669218 0 0.5848 240 | 0/8 16 h-lim-p 0.6649 5.3190 0.0154 2249.539551 4 0.6597 268 | 0/8 17 h-lim-p 0.9839 10.1742 0.0104 2249.522021 2 0.9839 292 | 0/8 18 h-lim-p 2.5000 20.0000 0.0010 2249.521665 2 1.1719 316 | 0/8 19 h-lim-p 2.5000 20.0000 0.0001 2249.521663 0 1.0938 336 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 2249.521663 0 1.0938 356 | 0/8 21 h-lim-p 2.5000 20.0000 0.0000 2249.521663 0 1.0938 376 | 0/8 22 h-lim-p 2.5000 20.0000 0.0000 2249.521663 0 2.1875 396 | 0/8 23 h-lim-p 1.0145 20.0000 0.0000 2249.521663 0 0.8877 416 | 0/8 24 h-lim-p 0.5835 20.0000 0.0000 2249.521663 0 0.2918 436 | 0/8 25 h-lim-p 0.0500 20.0000 0.0000 2249.521663 0 0.0500 456 | 0/8 26 h-lim-p 0.0193 20.0000 0.0000 2249.521663 0 0.0000 497 Out... lnL = -2249.521663 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2249.521663 Node 7: lnL = -2249.521663 Node 8: lnL = -2249.521663 Node 9: lnL = -2249.521663 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 849 Sequential format.. Reading seq # 1: YLR224W_Sbay Reading seq # 2: YLR224W_Scer Reading seq # 3: YLR224W_Skud Reading seq # 4: YLR224W_Smik Reading seq # 5: YLR224W_Spar Sequences read.. Counting patterns.. # site patterns = 216 Counting frequencies.. 120 bytes for distance 34560 bytes for lkl0 27648 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.087988 0.183268 0.170157 0.095921 0.160990 0.215433 0.242720 lnL0 = -3440.298270 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3440.298270 x= 0.00006 0.08799 0.18327 0.17016 0.09592 0.16099 0.21543 0.24272 1 h-lim-p 0.0000 0.0000 622.9114 3439.955992 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0006 391.4674 3412.056104 0 0.0005 39 | 1/8 3 h-lim-p 0.0008 0.0063 28.1839 3411.897715 2 0.0004 55 | 1/8 4 h-lim-p 0.0008 0.0128 13.4960 3411.815519 5 0.0007 76 | 1/8 5 h-lim-p 0.0031 0.0396 2.9456 3411.312257 0 0.0062 89 | 1/8 6 h-lim-p 0.0012 0.0134 14.8821 3405.261768 0 0.0049 103 | 1/8 7 h-lim-p 0.0004 0.0036 60.5162 3379.021244 0 0.0018 117 | 1/8 8 h-lim-p 0.0006 0.0046 51.5357 3378.671492 2 0.0003 133 | 1/8 9 h-lim-p 0.1788 2.1519 0.0779 3377.176632 0 0.3577 146 | 0/8 10 h-lim-p 0.0059 0.6955 4.7339 3377.171773 6 0.0004 183 | 0/8 11 h-lim-p 0.0795 0.6489 0.0245 3376.802037 0 0.4772 197 | 0/8 12 h-lim-p 2.5000 20.0000 0.0038 3376.781253 6 0.6929 231 | 0/8 13 h-lim-p 2.5000 20.0000 0.0003 3376.781172 3 0.6718 258 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 3376.781167 1 0.9961 280 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 3376.781167 0 0.6250 301 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 3376.781167 0 1.0938 321 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 3376.781167 0 1.2500 341 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 3376.781167 0 0.0000 390 Out... lnL = -3376.781167 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3376.781167 Node 7: lnL = -3376.781167 Node 8: lnL = -3376.781167 Node 9: lnL = -3376.781167 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 455 Sequential format.. Reading seq # 1: YLR225C_Sbay Reading seq # 2: YLR225C_Scer Reading seq # 3: YLR225C_Skud Reading seq # 4: YLR225C_Smik Reading seq # 5: YLR225C_Spar Sequences read.. Counting patterns.. # site patterns = 207 Counting frequencies.. 120 bytes for distance 33120 bytes for lkl0 26496 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.159532 0.333195 0.280180 0.153614 0.246059 0.335832 0.360731 lnL0 = -2156.354710 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2156.354710 x= 0.00006 0.15953 0.33320 0.28018 0.15361 0.24606 0.33583 0.36073 1 h-lim-p 0.0000 0.0000 320.4099 2156.238978 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0024 199.1784 2125.324738 0 0.0019 41 | 1/8 3 h-lim-p 0.0018 0.0145 20.7407 2125.031158 6 0.0012 66 | 1/8 4 h-lim-p 0.0013 0.0210 18.8213 2124.772429 1 0.0016 80 | 1/8 5 h-lim-p 0.0103 0.0824 2.7314 2123.552322 0 0.0206 93 | 1/8 6 h-lim-p 0.0034 0.0275 12.2085 2105.134973 0 0.0138 107 | 1/8 7 h-lim-p 0.0007 0.0057 63.7343 2098.358353 0 0.0021 120 | 1/8 8 h-lim-p 0.0038 0.0304 13.6287 2098.209854 5 0.0015 142 | 1/8 9 h-lim-p 0.1301 1.3340 0.1581 2095.413608 0 0.3902 155 | 0/8 10 h-lim-p -0.0000 -0.0000 0.8451 h-lim-p: -3.03210485e-22 -2.42568388e-21 8.45086128e-01 2095.413608 .. | 0/8 11 h-lim-p 0.0000 0.0167 31.1526 2095.226622 0 0.0005 195 | 0/8 12 h-lim-p 0.0013 0.0157 11.4711 2095.191771 2 0.0006 211 | 0/8 13 h-lim-p 0.0025 0.0680 2.8265 2095.188937 6 0.0008 240 | 0/8 14 h-lim-p 0.0045 0.0616 0.4792 2095.188841 3 0.0008 259 | 0/8 15 h-lim-p 0.0012 0.0093 0.1777 2095.188825 2 0.0007 284 | 0/8 16 h-lim-p 0.0024 0.0654 0.0562 2095.188739 0 0.0094 306 | 0/8 17 h-lim-p 0.0004 0.0032 0.3590 2095.188286 m 0.0032 326 | 1/8 18 h-lim-p 0.0003 0.4891 2.4218 2095.188004 2 0.0003 350 | 1/8 19 h-lim-p 0.0111 2.9947 0.0664 2095.183232 0 0.0445 364 | 1/8 20 h-lim-p 2.5000 20.0000 0.0007 2095.182800 2 1.0889 387 | 1/8 21 h-lim-p 2.5000 20.0000 0.0001 2095.182795 0 1.2500 406 | 1/8 22 h-lim-p 2.5000 20.0000 0.0000 2095.182795 0 1.0938 425 | 1/8 23 h-lim-p 2.5000 20.0000 0.0000 2095.182795 0 2.1875 444 | 1/8 24 h-lim-p 1.8424 20.0000 0.0000 2095.182795 0 0.4606 464 | 1/8 25 h-lim-p 0.8539 20.0000 0.0000 2095.182795 0 0.0534 486 | 1/8 26 h-lim-p 0.0564 20.0000 0.0000 2095.182795 0 0.0062 507 Out... lnL = -2095.182795 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2095.182795 Node 7: lnL = -2095.182795 Node 8: lnL = -2095.182795 Node 9: lnL = -2095.182795 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 456 Sequential format.. Reading seq # 1: YLR226W_Sbay Reading seq # 2: YLR226W_Scer Reading seq # 3: YLR226W_Skud Reading seq # 4: YLR226W_Smik Reading seq # 5: YLR226W_Spar Sequences read.. Counting patterns.. # site patterns = 207 Counting frequencies.. 120 bytes for distance 33120 bytes for lkl0 26496 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.082650 0.104167 0.060754 0.183143 0.303615 0.311624 0.385165 lnL0 = -2154.879497 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2154.879497 x= 0.00006 0.08265 0.10417 0.06075 0.18314 0.30361 0.31162 0.38516 1 h-lim-p 0.0000 0.0000 165.5297 2154.831893 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0012 253.5962 2147.946916 0 0.0005 39 | 1/8 3 h-lim-p 0.0004 0.0032 112.7145 2145.376524 0 0.0006 51 | 1/8 4 h-lim-p 0.0006 0.0049 43.8102 2145.026760 4 0.0005 71 | 1/8 5 h-lim-p 0.0031 0.0515 6.6824 2144.983400 5 0.0015 94 | 1/8 6 h-lim-p 0.0046 0.0921 2.2321 2144.938452 5 0.0038 117 | 1/8 7 h-lim-p 0.0119 0.5084 0.7159 2140.694334 0 0.0955 132 | 0/8 8 h-lim-p 0.0016 0.0126 35.8030 2139.167202 2 0.0015 155 | 0/8 9 h-lim-p 0.0002 0.0018 10.8910 2139.076178 m 0.0018 167 | 0/8 10 h-lim-p -0.0000 -0.0000 0.0148 h-lim-p: -1.86194237e-17 -1.48955389e-16 1.47549571e-02 2139.076178 .. | 0/8 11 h-lim-p 0.0000 0.0290 44.1592 2138.766948 0 0.0003 200 | 0/8 12 h-lim-p 0.0011 0.0155 12.4776 2138.711578 6 0.0008 226 | 0/8 13 h-lim-p 0.0001 0.0006 4.0276 2138.705564 m 0.0006 238 | 1/8 14 h-lim-p 0.0098 4.5160 0.2502 2138.705541 3 0.0007 259 | 1/8 15 h-lim-p 0.0020 3.0005 0.0812 2138.705535 1 0.0016 280 | 1/8 16 h-lim-p 0.0182 20.0000 0.0072 2138.705429 0 0.0726 301 | 1/8 17 h-lim-p 0.0033 2.3748 0.1601 2138.704694 0 0.0066 321 | 1/8 18 h-lim-p 0.0021 0.6296 0.5016 2138.704361 2 0.0018 344 | 1/8 19 h-lim-p 2.5000 20.0000 0.0001 2138.704346 1 0.9961 365 | 1/8 20 h-lim-p 2.5000 20.0000 0.0000 2138.704346 0 1.0938 384 | 1/8 21 h-lim-p 2.5000 20.0000 0.0000 2138.704346 0 1.0938 403 | 1/8 22 h-lim-p 2.5000 20.0000 0.0000 2138.704346 0 2.1875 422 | 1/8 23 h-lim-p 1.8384 20.0000 0.0000 2138.704346 0 0.8043 441 | 1/8 24 h-lim-p 2.5000 20.0000 0.0000 2138.704346 0 0.0781 464 | 1/8 25 h-lim-p 0.0849 20.0000 0.0000 2138.704346 0 0.0000 509 Out... lnL = -2138.704346 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2138.704346 Node 7: lnL = -2138.704346 Node 8: lnL = -2138.704346 Node 9: lnL = -2138.704346 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 917 Sequential format.. Reading seq # 1: YLR227C_Sbay Reading seq # 2: YLR227C_Scer Reading seq # 3: YLR227C_Skud Reading seq # 4: YLR227C_Smik Reading seq # 5: YLR227C_Spar Sequences read.. Counting patterns.. # site patterns = 392 Counting frequencies.. 120 bytes for distance 62720 bytes for lkl0 50176 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.062746 0.109536 0.105036 0.122129 0.208441 0.248223 0.268377 0.624682 lnL0 = -4638.840337 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4638.840337 x= 0.06275 0.10954 0.10504 0.12213 0.20844 0.24822 0.26838 0.62468 1 h-lim-p 0.0162 1.9579 75.7928 4637.943119 8 0.0003 45 | 0/8 2 h-lim-p 0.0010 0.0111 23.8526 4637.797060 7 0.0006 74 | 0/8 3 h-lim-p 0.0011 0.0166 12.3327 4637.762301 5 0.0006 97 | 0/8 4 h-lim-p 0.0016 0.0833 4.5103 4637.751766 4 0.0012 117 | 0/8 5 h-lim-p 0.0033 0.2369 1.6504 4637.751014 3 0.0006 136 | 0/8 6 h-lim-p 0.0319 6.1697 0.0331 4637.751013 0 0.0009 152 | 0/8 7 h-lim-p 0.0113 20.0000 0.0026 4637.751000 0 0.0904 175 | 0/8 8 h-lim-p 0.0096 20.0000 0.0240 4637.750871 0 0.0192 196 | 0/8 9 h-lim-p 0.5352 20.0000 0.0009 4637.750859 0 1.0703 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 4637.750859 0 1.0938 237 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4637.750859 0 1.0938 257 | 0/8 12 h-lim-p 0.2668 20.0000 0.0000 4637.750859 0 0.2335 277 | 0/8 13 h-lim-p 0.0091 20.0000 0.0003 4637.750859 0 0.0045 297 | 0/8 14 h-lim-p 0.0015 20.0000 0.0009 4637.750859 0 0.0006 318 | 0/8 15 h-lim-p 0.0006 20.0000 0.0008 4637.750859 0 0.0000 351 | 0/8 16 h-lim-p 0.0002 20.0000 0.0000 4637.750859 0 0.0000 378 Out... lnL = -4637.750859 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4637.750859 Node 7: lnL = -4637.750859 Node 8: lnL = -4637.750859 Node 9: lnL = -4637.750859 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 831 Sequential format.. Reading seq # 1: YLR229C_Sbay Reading seq # 2: YLR229C_Scer Reading seq # 3: YLR229C_Skud Reading seq # 4: YLR229C_Smik Reading seq # 5: YLR229C_Spar Sequences read.. Counting patterns.. # site patterns = 253 Counting frequencies.. 120 bytes for distance 40480 bytes for lkl0 32384 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.062343 0.000060 0.076519 0.064072 0.101368 0.167916 0.231327 0.364085 lnL0 = -3415.146971 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3415.146971 x= 0.06234 0.00006 0.07652 0.06407 0.10137 0.16792 0.23133 0.36409 1 h-lim-p 0.0001 0.0005 314.6830 3401.651450 0 0.0002 24 | 0/8 2 h-lim-p 0.0003 0.0022 130.0183 3399.237406 0 0.0004 36 | 0/8 3 h-lim-p 0.0003 0.0021 95.4822 3398.712854 7 0.0002 63 | 0/8 4 h-lim-p 0.0011 0.0187 13.9842 3398.693785 6 0.0002 90 | 0/8 5 h-lim-p 0.0005 0.0270 5.7020 3398.686781 4 0.0005 110 | 0/8 6 h-lim-p 0.0044 0.2315 0.6343 3398.686702 2 0.0002 129 | 0/8 7 h-lim-p 0.0004 0.5622 0.3547 3398.686247 0 0.0017 151 | 0/8 8 h-lim-p 0.0087 1.2676 0.0703 3398.558079 0 0.1396 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0010 3398.556433 4 0.9131 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 3398.556424 2 0.7996 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3398.556424 0 1.0938 249 | 0/8 12 h-lim-p 1.3675 20.0000 0.0000 3398.556424 0 1.1966 269 | 0/8 13 h-lim-p 0.9959 20.0000 0.0000 3398.556424 0 5.9756 291 | 0/8 14 h-lim-p 0.1293 20.0000 0.0009 3398.556424 0 0.0141 313 | 0/8 15 h-lim-p 0.0028 20.0000 0.0043 3398.556424 0 0.0000 342 | 0/8 16 h-lim-p 0.0002 20.0000 0.0001 3398.556424 0 0.0000 374 | 0/8 17 h-lim-p 0.0000 20.0000 0.0011 3398.556424 0 0.0000 405 | 0/8 18 h-lim-p 0.0000 20.0000 0.0028 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0011 3398.556424 0 0.0000 465 | 0/8 20 h-lim-p 0.0000 20.0000 0.0003 3398.556424 0 0.0026 493 | 0/8 21 h-lim-p 0.0038 20.0000 0.0002 3398.556424 0 0.0000 522 | 0/8 22 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 23 h-lim-p 0.0000 20.0000 0.0054 3398.556424 0 0.0000 582 | 0/8 24 h-lim-p 0.0000 20.0000 0.0010 3398.556424 0 0.0005 607 | 0/8 25 h-lim-p 0.0008 20.0000 0.0007 3398.556424 0 0.0000 635 | 0/8 26 h-lim-p 0.0000 20.0000 0.0003 3398.556424 0 0.0000 655 | 0/8 27 h-lim-p 0.0002 20.0000 0.0000 3398.556424 0 0.0000 676 | 0/8 28 h-lim-p 0.0000 20.0000 0.0005 3398.556424 0 0.0000 696 | 0/8 29 h-lim-p 0.0000 20.0000 0.0024 .. | 0/8 30 h-lim-p 0.0000 20.0000 0.0057 3398.556424 0 0.0000 764 | 0/8 31 h-lim-p 0.0000 19.8427 0.0075 3398.556424 0 0.0000 796 | 0/8 32 h-lim-p 0.0000 20.0000 0.0020 3398.556424 0 0.0001 819 | 0/8 33 h-lim-p 0.0001 20.0000 0.0024 3398.556424 0 0.0000 842 | 0/8 34 h-lim-p 0.0000 20.0000 0.0006 3398.556424 0 0.0000 869 | 0/8 35 h-lim-p 0.0000 20.0000 0.0005 3398.556424 0 0.0000 890 | 0/8 36 h-lim-p 0.0002 20.0000 0.0001 .. | 0/8 37 h-lim-p 0.0000 20.0000 0.0053 | 0/8 38 h-lim-p 0.0000 20.0000 0.0053 Out... lnL = -3398.556424 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3398.556424 Node 7: lnL = -3398.556424 Node 8: lnL = -3398.556424 Node 9: lnL = -3398.556424 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 342 Sequential format.. Reading seq # 1: YLR231C_Sbay Reading seq # 2: YLR231C_Scer Reading seq # 3: YLR231C_Skud Reading seq # 4: YLR231C_Smik Reading seq # 5: YLR231C_Spar Sequences read.. Counting patterns.. # site patterns = 157 Counting frequencies.. 120 bytes for distance 25120 bytes for lkl0 20096 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.043965 0.030455 0.059955 0.056524 0.065516 0.163872 0.195844 0.350127 lnL0 = -1419.487235 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1419.487235 x= 0.04396 0.03045 0.05996 0.05652 0.06552 0.16387 0.19584 0.35013 1 h-lim-p 0.0007 0.0055 71.9268 1418.692910 3 0.0003 29 | 0/8 2 h-lim-p 0.0006 0.0048 17.2279 1418.643030 7 0.0003 58 | 0/8 3 h-lim-p 0.0007 0.0162 9.1780 1418.610732 0 0.0010 70 | 0/8 4 h-lim-p 0.0053 0.0739 1.7096 1418.610078 4 0.0005 93 | 0/8 5 h-lim-p 0.0014 0.2824 0.5687 1418.609962 4 0.0008 115 | 0/8 6 h-lim-p 0.0019 0.2418 0.2331 1418.609943 1 0.0008 137 | 0/8 7 h-lim-p 0.0023 2.9778 0.0773 1418.609940 0 0.0012 157 | 0/8 8 h-lim-p 0.1545 20.0000 0.0006 1418.609528 0 1.2364 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1418.609508 2 0.9961 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1418.609508 0 2.1875 224 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1418.609508 0 1.0938 244 | 0/8 12 h-lim-p 0.2148 20.0000 0.0000 1418.609508 0 5.1548 268 | 0/8 13 h-lim-p 1.2397 20.0000 0.0000 1418.609508 0 1.2397 288 | 0/8 14 h-lim-p 0.0077 13.0052 0.0061 1418.609508 0 0.0010 310 | 0/8 15 h-lim-p 0.0002 2.4990 0.0316 1418.609508 0 0.0000 344 | 0/8 16 h-lim-p 0.0002 20.0000 0.0000 1418.609508 0 0.0000 372 Out... lnL = -1418.609508 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1418.609508 Node 7: lnL = -1418.609508 Node 8: lnL = -1418.609508 Node 9: lnL = -1418.609508 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 273 Sequential format.. Reading seq # 1: YLR237W_Sbay Reading seq # 2: YLR237W_Scer Reading seq # 3: YLR237W_Skud Reading seq # 4: YLR237W_Smik Reading seq # 5: YLR237W_Spar Sequences read.. Counting patterns.. # site patterns = 135 Counting frequencies.. 120 bytes for distance 21600 bytes for lkl0 17280 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.024174 0.000060 0.172710 0.070040 0.301250 0.814053 0.563042 0.686782 lnL0 = -1057.133423 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1057.133423 x= 0.02417 0.00006 0.17271 0.07004 0.30125 0.81405 0.56304 0.68678 1 h-lim-p 0.0000 0.0000 136.2259 1057.101275 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0001 392.5851 1050.631914 m 0.0001 35 | 2/8 3 h-lim-p 0.0001 0.0007 263.3759 1035.958022 m 0.0007 47 | 3/8 4 h-lim-p 0.0003 0.0026 162.0104 1027.361984 0 0.0020 61 | 3/8 5 h-lim-p 0.0134 0.1075 17.2121 1022.259211 0 0.0269 74 | 3/8 6 h-lim-p 0.0132 0.1057 2.9040 1022.012604 0 0.0198 86 | 3/8 7 h-lim-p 0.0456 0.3647 0.5454 1020.835170 0 0.0912 99 | 3/8 8 h-lim-p 0.6175 19.1634 0.0805 1020.675968 0 1.2349 117 | 3/8 9 h-lim-p 1.5757 20.0000 0.0631 1020.632700 6 0.9741 149 | 3/8 10 h-lim-p 2.5000 20.0000 0.0119 1020.628074 5 0.8067 178 | 3/8 11 h-lim-p 2.2084 20.0000 0.0044 1020.627248 3 0.9260 202 | 2/8 12 h-lim-p 0.1315 20.0000 0.0307 1020.627246 0 0.0036 223 | 2/8 13 h-lim-p 0.1602 1.3805 0.0007 1020.627241 0 0.9613 243 | 2/8 14 h-lim-p 0.0426 0.3404 0.0001 1020.627241 0 0.0000 274 | 2/8 15 h-lim-p 0.0000 20.0000 0.0004 1020.627241 0 0.0819 305 | 2/8 16 h-lim-p 0.0472 0.3778 0.0002 .. | 2/8 17 h-lim-p 0.0000 0.0022 0.0242 1020.627241 0 0.0003 371 | 2/8 18 h-lim-p 0.0001 0.0006 0.0701 1020.627241 0 0.0000 402 | 2/8 19 h-lim-p 0.0000 0.0000 6.4841 .. | 2/8 20 h-lim-p 0.0000 20.0000 0.0115 1020.627241 0 0.0013 448 | 2/8 21 h-lim-p 0.0015 0.0332 0.0095 1020.627241 0 0.0013 466 | 2/8 22 h-lim-p 0.0011 0.0135 0.0119 1020.627241 0 0.0000 503 | 2/8 23 h-lim-p 0.0000 20.0000 0.0025 1020.627241 0 0.0051 530 | 2/8 24 h-lim-p 0.0019 0.1024 0.0068 1020.627241 0 0.0028 548 | 2/8 25 h-lim-p 0.0075 1.0618 0.0026 1020.627241 0 0.0075 566 | 2/8 26 h-lim-p 0.2930 2.3442 0.0001 1020.627241 0 0.2930 584 | 2/8 27 h-lim-p 0.0192 0.1533 0.0005 1020.627241 0 0.0383 603 | 2/8 28 h-lim-p 0.0041 0.0331 0.0016 1020.627241 0 0.0000 627 | 2/8 29 h-lim-p 0.0000 0.0131 0.0038 1020.627241 0 0.0000 645 | 2/8 30 h-lim-p 0.0000 0.0050 0.0096 1020.627241 0 0.0002 667 | 2/8 31 h-lim-p 0.0001 0.0017 0.0266 1020.627241 0 0.0000 691 | 2/8 32 h-lim-p 0.0000 0.0007 0.0653 1020.627241 0 0.0000 713 | 2/8 33 h-lim-p 0.0000 0.0002 0.2486 1020.627241 0 0.0000 736 | 2/8 34 h-lim-p 0.0000 0.0013 0.0347 .. | 2/8 35 h-lim-p 0.0000 0.0011 0.0253 1020.627241 0 0.0003 790 | 2/8 36 h-lim-p 0.0000 0.0003 0.0757 1020.627241 0 0.0000 820 | 2/8 37 h-lim-p 0.0000 0.0000 0.4894 1020.627241 0 0.0000 852 | 2/8 38 h-lim-p 0.0000 0.0005 0.0519 1020.627241 0 0.0000 871 | 2/8 39 h-lim-p 0.0001 0.0017 0.0195 1020.627241 0 0.0000 899 | 2/8 40 h-lim-p 0.0000 0.0011 0.0331 .. | 2/8 41 h-lim-p 0.0000 0.0007 0.0232 | 2/8 42 h-lim-p 0.0000 0.0007 0.0232 Out... lnL = -1020.627241 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1020.627241 Node 7: lnL = -1020.627241 Node 8: lnL = -1020.627241 Node 9: lnL = -1020.627241 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 224 Sequential format.. Reading seq # 1: YLR239C_Sbay Reading seq # 2: YLR239C_Scer Reading seq # 3: YLR239C_Skud Reading seq # 4: YLR239C_Smik Reading seq # 5: YLR239C_Spar Sequences read.. Counting patterns.. # site patterns = 85 Counting frequencies.. 120 bytes for distance 13600 bytes for lkl0 10880 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.073380 0.309887 0.072139 0.541309 2.032848 0.931091 1.135099 lnL0 = -967.385812 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 967.385812 x= 0.00006 0.07338 0.30989 0.07214 0.54131 2.03285 0.93109 1.13510 1 h-lim-p 0.0000 0.0000 174.2854 967.306436 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0006 335.2751 941.516496 m 0.0006 37 | 2/8 3 h-lim-p 0.0030 0.0240 10.6398 927.269452 m 0.0240 49 | 3/8 4 h-lim-p 0.0023 0.0185 25.0609 907.962043 0 0.0139 63 | 3/8 5 h-lim-p 0.0014 0.0110 25.6538 896.504720 0 0.0083 77 | 3/8 6 h-lim-p 0.0325 0.2596 3.6341 881.789357 0 0.1298 91 | 2/8 7 h-lim-p 0.0006 0.0051 109.1398 875.498586 0 0.0026 105 | 2/8 8 h-lim-p 0.0023 0.0183 39.3396 856.881101 0 0.0091 119 | 1/8 9 h-lim-p 0.0006 0.0046 119.0953 850.094819 0 0.0023 133 | 1/8 10 h-lim-p 0.5294 4.2349 0.0752 848.860327 0 1.0587 146 | 0/8 11 h-lim-p 0.0066 0.0525 7.8043 848.759106 6 0.0043 178 | 0/8 12 h-lim-p 0.0783 0.6608 0.4312 847.655338 0 0.2348 191 | 0/8 13 h-lim-p 2.5000 20.0000 0.0276 847.442620 2 1.1719 215 | 0/8 14 h-lim-p 2.5000 20.0000 0.0046 847.434003 4 0.9644 243 | 0/8 15 h-lim-p 1.5821 20.0000 0.0028 847.433538 5 0.9589 277 | 0/8 16 h-lim-p 2.5000 20.0000 0.0003 847.433520 2 1.1719 301 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 847.433520 0 1.2500 321 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 847.433520 0 2.1875 341 | 0/8 19 h-lim-p 1.9010 20.0000 0.0000 847.433520 0 0.8317 361 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 847.433520 0 0.0006 392 Out... lnL = -847.433520 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -847.433520 Node 7: lnL = -847.433520 Node 8: lnL = -847.433520 Node 9: lnL = -847.433520 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 225 Sequential format.. Reading seq # 1: YLR240W_Sbay Reading seq # 2: YLR240W_Scer Reading seq # 3: YLR240W_Skud Reading seq # 4: YLR240W_Smik Reading seq # 5: YLR240W_Spar Sequences read.. Counting patterns.. # site patterns = 116 Counting frequencies.. 120 bytes for distance 18560 bytes for lkl0 14848 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.076722 0.130163 0.058009 0.160993 0.290244 0.291688 0.390196 lnL0 = -1059.119471 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1059.119471 x= 0.00006 0.07672 0.13016 0.05801 0.16099 0.29024 0.29169 0.39020 1 h-lim-p 0.0000 0.0000 86.9712 1059.081532 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0014 146.7224 1056.818688 0 0.0006 40 | 1/8 3 h-lim-p 0.0011 0.0090 36.5958 1055.756291 0 0.0022 53 | 1/8 4 h-lim-p 0.0049 0.0395 14.4637 1055.660973 6 0.0011 77 | 1/8 5 h-lim-p 0.0061 0.1155 2.5117 1055.612279 5 0.0059 101 | 1/8 6 h-lim-p 0.0097 0.1345 1.5406 1055.313681 0 0.0194 114 | 0/8 7 h-lim-p 0.0031 0.0781 9.6929 1053.306316 0 0.0123 128 | 0/8 8 h-lim-p 0.0019 0.0153 7.2833 1053.036627 0 0.0077 142 | 0/8 9 h-lim-p 0.0008 0.0062 13.7970 1052.780473 0 0.0047 156 | 0/8 10 h-lim-p 0.1044 0.8349 0.0363 1052.448670 m 0.8349 168 | 1/8 11 h-lim-p 1.9433 19.5319 0.0143 1052.402981 2 0.8464 192 | 0/8 12 h-lim-p 0.0032 0.1631 3.7921 1052.376362 0 0.0048 211 | 0/8 13 h-lim-p 0.5128 4.1023 0.0059 1052.370615 0 1.0256 224 | 0/8 14 h-lim-p 2.5000 20.0000 0.0008 1052.370342 2 1.0889 248 | 0/8 15 h-lim-p 2.5000 20.0000 0.0002 1052.370339 1 0.9961 270 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1052.370339 0 1.0938 290 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1052.370339 0 0.5469 311 | 0/8 18 h-lim-p 0.8982 20.0000 0.0000 1052.370339 0 0.0140 336 | 0/8 19 h-lim-p 0.0111 20.0000 0.0000 1052.370339 0 0.0000 363 Out... lnL = -1052.370339 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1052.370339 Node 7: lnL = -1052.370339 Node 8: lnL = -1052.370339 Node 9: lnL = -1052.370339 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 335 Sequential format.. Reading seq # 1: YLR241W_Sbay Reading seq # 2: YLR241W_Scer Reading seq # 3: YLR241W_Skud Reading seq # 4: YLR241W_Smik Reading seq # 5: YLR241W_Spar Sequences read.. Counting patterns.. # site patterns = 95 Counting frequencies.. 120 bytes for distance 15200 bytes for lkl0 12160 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.070901 0.298608 0.066798 0.556091 1.968230 0.952719 1.135099 lnL0 = -1419.286427 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1419.286427 x= 0.00006 0.07090 0.29861 0.06680 0.55609 1.96823 0.95272 1.13510 1 h-lim-p 0.0000 0.0000 291.7657 1419.178480 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0001 2693.4210 1374.633728 m 0.0001 34 | 2/8 3 h-lim-p 0.0003 0.0026 203.2330 1318.342403 m 0.0026 46 | 2/8 4 h-lim-p 0.0002 0.0016 120.6178 1291.784841 m 0.0016 58 | 3/8 5 h-lim-p 0.0030 0.0244 23.6588 1282.374510 0 0.0091 71 | 3/8 6 h-lim-p 0.0041 0.0332 26.1419 1250.209083 0 0.0166 85 | 2/8 7 h-lim-p 0.0000 0.0002 2683.1530 1235.303121 0 0.0001 99 | 2/8 8 h-lim-p 0.0112 0.0894 2.5691 1219.310101 0 0.0335 112 | 1/8 9 h-lim-p 0.0001 0.0008 467.8031 1201.534203 0 0.0004 126 | 1/8 10 h-lim-p 0.0257 0.2052 0.5108 1194.929028 m 0.2052 138 | 2/8 11 h-lim-p 0.1897 1.5175 0.2488 1185.601243 0 0.7587 159 | 2/8 12 h-lim-p 2.5000 20.0000 0.0323 1184.674273 4 1.3122 186 | 2/8 13 h-lim-p 2.5000 20.0000 0.0133 1182.747224 0 3.7500 204 | 1/8 14 h-lim-p -0.0000 -0.0000 1.9270 h-lim-p: -6.79974902e-20 -5.43979921e-19 1.92696169e+00 1182.747224 .. | 1/8 15 h-lim-p 0.0000 0.0109 20.8420 1182.493571 0 0.0013 237 | 1/8 16 h-lim-p 0.0051 0.1822 5.2268 1182.488426 5 0.0004 264 | 1/8 17 h-lim-p 0.0014 0.0116 1.4900 1182.487866 4 0.0005 284 | 0/8 18 h-lim-p 0.0003 0.0054 2.3612 1182.485680 0 0.0007 297 | 0/8 19 h-lim-p 0.0003 0.0020 1.4350 1182.484939 0 0.0010 311 | 0/8 20 h-lim-p 0.0018 0.4258 0.8279 1182.484816 4 0.0006 333 | 0/8 21 h-lim-p 1.5242 20.0000 0.0003 1182.484743 3 0.9963 360 | 0/8 22 h-lim-p 2.5000 20.0000 0.0000 1182.484743 0 1.0938 380 | 0/8 23 h-lim-p 1.0994 20.0000 0.0000 1182.484743 0 2.1988 401 | 0/8 24 h-lim-p 0.6875 7.3278 0.0001 1182.484743 0 0.0007 430 | 0/8 25 h-lim-p 0.0000 0.4763 0.0012 .. | 0/8 26 h-lim-p 0.0000 1.6362 0.0010 1182.484743 0 0.0001 488 | 0/8 27 h-lim-p 0.0002 2.8664 0.0003 1182.484743 0 0.0015 510 | 0/8 28 h-lim-p 0.0046 20.0000 0.0001 1182.484743 0 0.0000 538 | 0/8 29 h-lim-p 0.0000 15.7302 0.0000 .. | 0/8 30 h-lim-p 0.0000 20.0000 0.0013 1182.484743 0 0.0000 593 | 0/8 31 h-lim-p 0.0007 15.0128 0.0000 1182.484743 0 0.0000 616 | 0/8 32 h-lim-p 0.0000 2.7788 0.0003 1182.484743 0 0.0000 636 | 0/8 33 h-lim-p 0.0000 0.0317 0.0248 1182.484743 0 0.0000 657 | 0/8 34 h-lim-p 0.0001 0.8655 0.0009 1182.484743 0 0.0000 691 | 0/8 35 h-lim-p 0.0000 20.0000 0.0012 1182.484743 0 0.0000 713 | 0/8 36 h-lim-p 0.0000 14.9518 0.0000 1182.484743 0 0.0000 734 | 0/8 37 h-lim-p 0.0000 2.5561 0.0003 .. | 0/8 38 h-lim-p 0.0000 20.0000 0.0012 | 0/8 39 h-lim-p 0.0000 20.0000 0.0012 Out... lnL = -1182.484743 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1182.484743 Node 7: lnL = -1182.484743 Node 8: lnL = -1182.484743 Node 9: lnL = -1182.484743 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 351 Sequential format.. Reading seq # 1: YLR242C_Sbay Reading seq # 2: YLR242C_Scer Reading seq # 3: YLR242C_Skud Reading seq # 4: YLR242C_Smik Reading seq # 5: YLR242C_Spar Sequences read.. Counting patterns.. # site patterns = 146 Counting frequencies.. 120 bytes for distance 23360 bytes for lkl0 18688 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.037321 0.074537 0.099051 0.123622 0.229923 0.282942 0.321661 lnL0 = -1525.332876 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1525.332876 x= 0.00006 0.03732 0.07454 0.09905 0.12362 0.22992 0.28294 0.32166 1 h-lim-p 0.0000 0.0000 166.9385 1525.236862 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0011 127.9851 1522.778856 0 0.0003 39 | 1/8 3 h-lim-p 0.0018 0.0224 22.5537 1522.490697 5 0.0012 64 | 1/8 4 h-lim-p 0.0012 0.0151 22.9703 1522.370431 5 0.0007 90 | 1/8 5 h-lim-p 0.0041 0.0374 4.0378 1522.344660 3 0.0017 108 | 1/8 6 h-lim-p 0.0032 0.1150 2.1619 1522.190658 0 0.0127 122 | 1/8 7 h-lim-p 0.0131 0.1049 1.7622 1517.600446 0 0.0525 136 | 0/8 8 h-lim-p 0.0021 0.0169 18.7726 1517.427126 5 0.0009 158 | 0/8 9 h-lim-p 0.0019 0.0151 1.0117 1517.382170 m 0.0151 170 | 0/8 10 h-lim-p 0.0513 2.6658 0.2989 1516.034249 0 0.1025 183 | 0/8 11 h-lim-p 1.7982 14.3854 0.0163 1515.939168 5 0.8800 215 | 0/8 12 h-lim-p 0.8421 6.7367 0.0033 1515.927001 0 1.6842 236 | 0/8 13 h-lim-p 2.5000 20.0000 0.0013 1515.925798 3 1.0449 262 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 1515.925792 0 1.0938 282 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1515.925792 0 1.0938 302 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1515.925792 0 1.0938 322 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1515.925792 0 2.1875 342 | 0/8 18 h-lim-p 2.1406 20.0000 0.0000 1515.925792 0 0.4683 363 | 0/8 19 h-lim-p 0.8784 20.0000 0.0000 1515.925792 0 0.0137 388 Out... lnL = -1515.925792 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1515.925792 Node 7: lnL = -1515.925792 Node 8: lnL = -1515.925792 Node 9: lnL = -1515.925792 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 351 Sequential format.. Reading seq # 1: YLR243W_Sbay Reading seq # 2: YLR243W_Scer Reading seq # 3: YLR243W_Skud Reading seq # 4: YLR243W_Smik Reading seq # 5: YLR243W_Spar Sequences read.. Counting patterns.. # site patterns = 146 Counting frequencies.. 120 bytes for distance 23360 bytes for lkl0 18688 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.044779 0.059477 0.110749 0.112992 0.229096 0.246366 0.323614 lnL0 = -1523.163151 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1523.163151 x= 0.00006 0.04478 0.05948 0.11075 0.11299 0.22910 0.24637 0.32361 1 h-lim-p 0.0000 0.0000 115.0011 1523.060706 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0029 49.9712 1522.570082 0 0.0006 39 | 1/8 3 h-lim-p 0.0018 0.0190 16.0050 1522.438797 8 0.0011 73 | 1/8 4 h-lim-p 0.0016 0.0125 11.2597 1522.407852 6 0.0006 96 | 1/8 5 h-lim-p 0.0041 0.1169 1.7079 1522.377493 0 0.0062 108 | 1/8 6 h-lim-p 0.0034 0.0516 3.0971 1522.246907 0 0.0068 121 | 0/8 7 h-lim-p 0.0036 0.0582 5.8633 1520.268306 0 0.0144 135 | 0/8 8 h-lim-p 0.0010 0.0078 12.0049 1519.374516 m 0.0078 147 | 0/8 9 h-lim-p -0.0000 -0.0000 14.5362 h-lim-p: -6.71092035e-20 -5.36873628e-19 1.45361597e+01 1519.374516 .. | 0/8 10 h-lim-p 0.0000 0.0186 47.1845 1518.947243 0 0.0005 172 | 0/8 11 h-lim-p 0.0000 0.0004 20.1421 1518.860573 m 0.0004 184 | 1/8 12 h-lim-p 0.0013 0.0492 5.7959 1518.848443 6 0.0008 212 | 1/8 13 h-lim-p 0.0015 0.0523 3.0630 1518.846590 4 0.0005 233 | 1/8 14 h-lim-p 0.0095 1.9895 0.1609 1518.846352 2 0.0044 249 | 1/8 15 h-lim-p 0.0033 0.3255 0.2187 1518.845255 0 0.0065 269 | 1/8 16 h-lim-p 0.0059 0.4438 0.2431 1518.826988 0 0.0176 289 | 1/8 17 h-lim-p 0.0054 0.3870 0.7926 1518.826376 4 0.0018 318 | 1/8 18 h-lim-p 0.5648 20.0000 0.0026 1518.823590 0 0.8472 337 | 1/8 19 h-lim-p 2.5000 20.0000 0.0002 1518.823569 2 0.9644 360 | 1/8 20 h-lim-p 2.5000 20.0000 0.0000 1518.823569 0 1.0938 379 | 1/8 21 h-lim-p 2.5000 20.0000 0.0000 1518.823569 0 1.0938 398 | 1/8 22 h-lim-p 2.5000 20.0000 0.0000 1518.823569 0 5.0000 418 | 1/8 23 h-lim-p 1.2502 20.0000 0.0000 1518.823569 0 0.2735 438 | 1/8 24 h-lim-p 0.3764 20.0000 0.0000 1518.823569 0 0.0000 473 Out... lnL = -1518.823569 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1518.823569 Node 7: lnL = -1518.823569 Node 8: lnL = -1518.823569 Node 9: lnL = -1518.823569 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 201 Sequential format.. Reading seq # 1: YLR244C_Sbay Reading seq # 2: YLR244C_Scer Reading seq # 3: YLR244C_Skud Reading seq # 4: YLR244C_Smik Reading seq # 5: YLR244C_Spar Sequences read.. Counting patterns.. # site patterns = 81 Counting frequencies.. 120 bytes for distance 12960 bytes for lkl0 10368 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.163877 0.101268 0.078038 0.132535 0.190365 0.201726 0.223056 lnL0 = -726.213762 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 726.213762 x= 0.00006 0.16388 0.10127 0.07804 0.13253 0.19036 0.20173 0.22306 1 h-lim-p 0.0000 0.0000 139.3489 726.179835 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0023 69.3142 722.599075 0 0.0018 41 | 1/8 3 h-lim-p 0.0011 0.0089 20.4441 722.279489 0 0.0022 54 | 1/8 4 h-lim-p 0.0013 0.0102 6.7480 722.192847 0 0.0026 67 | 1/8 5 h-lim-p 0.0136 0.1939 1.2681 721.459571 0 0.0544 81 | 1/8 6 h-lim-p 0.0048 0.0382 5.7198 714.411802 0 0.0191 95 | 0/8 7 h-lim-p 0.0010 0.0082 20.1363 714.175357 1 0.0013 109 | 0/8 8 h-lim-p 0.0009 0.0069 5.3334 714.154766 0 0.0017 122 | 0/8 9 h-lim-p 0.0144 0.3305 0.6393 714.139640 7 0.0097 153 | 0/8 10 h-lim-p 0.0078 0.2381 0.7970 713.810181 0 0.0311 175 | 0/8 11 h-lim-p 0.4387 3.5096 0.0237 713.743930 3 0.3667 201 | 0/8 12 h-lim-p 1.3537 20.0000 0.0064 713.737356 3 0.5658 227 | 0/8 13 h-lim-p 1.3280 20.0000 0.0027 713.735816 5 0.6731 259 | 0/8 14 h-lim-p 2.5000 20.0000 0.0004 713.735750 4 0.7412 290 | 0/8 15 h-lim-p 2.5000 20.0000 0.0001 713.735746 2 0.7996 315 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 713.735746 0 1.0938 335 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 713.735746 0 2.1875 355 | 0/8 18 h-lim-p 1.8987 20.0000 0.0000 713.735746 0 0.4153 376 | 0/8 19 h-lim-p 0.7264 20.0000 0.0000 713.735746 0 0.0014 404 Out... lnL = -713.735746 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -713.735746 Node 7: lnL = -713.735746 Node 8: lnL = -713.735746 Node 9: lnL = -713.735746 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 208 Sequential format.. Reading seq # 1: YLR245C_Sbay Reading seq # 2: YLR245C_Scer Reading seq # 3: YLR245C_Skud Reading seq # 4: YLR245C_Smik Reading seq # 5: YLR245C_Spar Sequences read.. Counting patterns.. # site patterns = 95 Counting frequencies.. 120 bytes for distance 15200 bytes for lkl0 12160 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.134663 0.108164 0.120349 0.106713 0.209560 0.219779 0.250441 lnL0 = -842.762234 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 842.762234 x= 0.00006 0.13466 0.10816 0.12035 0.10671 0.20956 0.21978 0.25044 1 h-lim-p 0.0000 0.0000 116.6110 842.729007 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0062 47.4890 841.135224 0 0.0019 41 | 1/8 3 h-lim-p 0.0019 0.0155 7.5456 841.046221 1 0.0024 55 | 1/8 4 h-lim-p 0.0047 0.0501 3.9100 840.908549 0 0.0070 67 | 1/8 5 h-lim-p 0.0140 0.1390 1.9618 838.889444 0 0.0561 81 | 0/8 6 h-lim-p 0.0016 0.0130 15.4504 835.643674 0 0.0065 95 | 0/8 7 h-lim-p 0.0002 0.0018 33.1932 834.997270 m 0.0018 107 | 0/8 8 h-lim-p 0.0000 0.0000 2.1548 h-lim-p: 1.47344397e-19 1.17875517e-18 2.15483464e+00 834.997270 .. | 0/8 9 h-lim-p 0.0000 0.0110 83.0011 834.069142 0 0.0003 132 | 0/8 10 h-lim-p 0.0011 0.0085 24.8929 833.820813 7 0.0009 159 | 0/8 11 h-lim-p 0.0005 0.0041 10.1092 833.781331 0 0.0010 172 | 0/8 12 h-lim-p 0.0090 0.1270 1.1364 833.780765 3 0.0009 192 | 0/8 13 h-lim-p 0.0113 1.6021 0.0904 833.780759 2 0.0011 210 | 0/8 14 h-lim-p 0.0136 20.0000 0.0072 833.780596 0 0.1091 233 | 0/8 15 h-lim-p 0.0056 1.4538 0.1414 833.779432 0 0.0112 254 | 0/8 16 h-lim-p 0.0597 8.8129 0.0265 833.779431 0 0.0019 278 | 0/8 17 h-lim-p 0.1912 20.0000 0.0003 833.779366 0 1.1473 300 | 0/8 18 h-lim-p 2.5000 20.0000 0.0001 833.779365 0 1.0938 320 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 833.779365 0 2.1875 340 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 833.779365 0 1.0938 360 | 0/8 21 h-lim-p 0.1359 20.0000 0.0000 833.779365 0 8.6969 386 | 0/8 22 h-lim-p 0.1317 9.1892 0.0012 833.779365 0 0.0005 413 | 0/8 23 h-lim-p 0.0001 1.0295 0.0103 833.779365 0 0.0001 433 | 0/8 24 h-lim-p 0.0002 2.7716 0.0038 833.779365 0 0.0000 455 | 0/8 25 h-lim-p 0.0001 20.0000 0.0009 833.779365 0 0.0000 485 | 0/8 26 h-lim-p 0.0001 20.0000 0.0000 833.779365 0 0.0000 508 Out... lnL = -833.779365 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -833.779365 Node 7: lnL = -833.779365 Node 8: lnL = -833.779365 Node 9: lnL = -833.779365 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 207 Sequential format.. Reading seq # 1: YLR246W_Sbay Reading seq # 2: YLR246W_Scer Reading seq # 3: YLR246W_Skud Reading seq # 4: YLR246W_Smik Reading seq # 5: YLR246W_Spar Sequences read.. Counting patterns.. # site patterns = 62 Counting frequencies.. 120 bytes for distance 9920 bytes for lkl0 7936 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.687681 0.597418 0.373332 0.605452 2.460858 0.855730 1.109997 lnL0 = -934.491387 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 934.491387 x= 0.00006 0.68768 0.59742 0.37333 0.60545 2.46086 0.85573 1.11000 1 h-lim-p 0.0000 0.0000 139.8681 934.437744 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0193 36.7361 904.994159 m 0.0193 42 | 2/8 3 h-lim-p 0.0011 0.0086 51.2790 899.469802 0 0.0043 56 | 2/8 4 h-lim-p 0.0083 0.0664 24.5916 840.257119 m 0.0664 68 | 2/8 5 h-lim-p 0.7489 5.9916 0.9914 838.622660 8 0.0759 102 | 1/8 6 h-lim-p 0.0024 0.0191 30.2959 838.188087 6 0.0010 131 | 1/8 7 h-lim-p 0.0289 0.2315 0.2245 .. | 1/8 8 h-lim-p 0.0000 0.0134 6.2682 838.065656 0 0.0051 196 | 1/8 9 h-lim-p 0.0005 0.0038 32.7258 837.563054 m 0.0038 208 | 1/8 10 h-lim-p 0.0000 0.0000 407.2227 h-lim-p: 6.05112685e-22 4.84090148e-21 4.07222693e+02 837.563054 .. | 1/8 11 h-lim-p 0.0000 0.0046 26.9000 837.210207 0 0.0010 234 | 1/8 12 h-lim-p 0.0019 0.2577 13.6799 837.081746 3 0.0017 252 | 1/8 13 h-lim-p 0.0017 0.0257 13.6524 833.357764 m 0.0257 265 | 2/8 14 h-lim-p 0.0336 0.2691 1.0788 .. | 2/8 15 h-lim-p 0.0000 0.0148 16.9750 832.931344 0 0.0026 322 | 2/8 16 h-lim-p 0.0006 0.0090 77.3886 822.817540 m 0.0090 335 | 1/8 17 h-lim-p 0.0000 0.0000 14418.4517 h-lim-p: 1.37129014e-22 1.09703211e-21 1.44184517e+04 822.817540 .. | 1/8 18 h-lim-p 0.0000 0.0274 188.3548 812.683219 0 0.0006 361 | 1/8 19 h-lim-p 0.0001 0.0006 51.3629 811.140725 m 0.0006 373 | 2/8 20 h-lim-p 0.0003 0.0028 122.3856 808.486018 0 0.0010 387 | 2/8 21 h-lim-p 0.0050 0.0399 3.3227 .. | 1/8 22 h-lim-p 0.0000 0.0187 142.1440 804.712870 0 0.0006 439 | 1/8 23 h-lim-p 0.0010 0.0083 71.6234 757.164642 m 0.0083 451 | 2/8 24 h-lim-p 0.0002 0.0013 73.2640 756.092830 0 0.0006 465 | 2/8 25 h-lim-p 0.0008 0.0063 24.0771 755.401486 0 0.0032 479 | 2/8 26 h-lim-p 0.0042 0.0339 1.8292 .. | 1/8 27 h-lim-p 0.0000 0.0048 116.9520 724.708436 m 0.0048 531 | 2/8 28 h-lim-p 0.0001 0.0010 114.8195 721.681566 0 0.0007 545 | 2/8 29 h-lim-p 0.0013 0.0106 24.6745 720.969312 0 0.0026 558 | 2/8 30 h-lim-p 0.0039 0.0310 10.4090 720.837881 7 0.0025 586 | 2/8 31 h-lim-p 0.0061 0.0488 3.2532 720.807115 3 0.0025 604 | 1/8 32 h-lim-p 0.0004 0.0183 18.7466 720.653680 0 0.0009 617 | 1/8 33 h-lim-p 0.0238 0.4096 0.6963 709.436861 7 0.3714 647 | 0/8 34 h-lim-p 0.0009 0.0068 9.2397 709.378050 0 0.0017 667 | 0/8 35 h-lim-p 0.0109 0.0871 0.0401 709.286314 m 0.0871 679 | 1/8 36 h-lim-p 0.1601 4.2811 0.0209 709.072680 0 0.6402 701 | 1/8 37 h-lim-p 0.5875 4.7001 0.0168 709.039733 2 0.5508 724 | 1/8 38 h-lim-p 2.5000 20.0000 0.0033 709.035816 4 0.8237 753 | 0/8 39 h-lim-p 0.0273 3.5880 0.0987 709.035811 2 0.0011 781 | 0/8 40 h-lim-p 0.0636 0.5089 0.0011 709.035557 m 0.5089 801 | 1/8 41 h-lim-p 2.3018 20.0000 0.0002 709.035526 3 0.9621 827 | 1/8 42 h-lim-p 2.5000 20.0000 0.0000 709.035526 0 1.0938 846 | 1/8 43 h-lim-p 2.5000 20.0000 0.0000 709.035526 0 1.0938 865 | 0/8 44 h-lim-p -0.0000 -0.0000 0.0035 h-lim-p: -1.54934472e-19 -1.23947577e-18 3.45706711e-03 709.035526 .. | 1/8 45 h-lim-p 0.0000 20.0000 0.0038 709.035526 0 0.0006 906 | 1/8 46 h-lim-p 0.0026 20.0000 0.0009 709.035526 0 0.0012 925 | 1/8 47 h-lim-p 0.0061 20.0000 0.0002 709.035526 0 0.0001 949 | 1/8 48 h-lim-p 0.0004 20.0000 0.0000 709.035526 0 0.0008 969 | 1/8 49 h-lim-p 0.0013 20.0000 0.0000 709.035526 0 0.0013 988 | 1/8 50 h-lim-p 0.0000 20.0000 0.0006 709.035526 0 0.0008 1011 | 1/8 51 h-lim-p 0.0101 20.0000 0.0000 709.035526 0 0.0806 1033 | 1/8 52 h-lim-p 0.0443 20.0000 0.0001 709.035526 0 0.0002 1059 | 1/8 53 h-lim-p 0.0001 20.0000 0.0002 709.035526 0 0.0000 1093 | 1/8 54 h-lim-p 0.0000 20.0000 0.0007 | 1/8 55 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -709.035526 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -709.035526 Node 7: lnL = -709.035526 Node 8: lnL = -709.035526 Node 9: lnL = -709.035526 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 859 Sequential format.. Reading seq # 1: YLR248W_Sbay Reading seq # 2: YLR248W_Scer Reading seq # 3: YLR248W_Skud Reading seq # 4: YLR248W_Smik Reading seq # 5: YLR248W_Spar Sequences read.. Counting patterns.. # site patterns = 253 Counting frequencies.. 120 bytes for distance 40480 bytes for lkl0 32384 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.022259 0.089524 0.038440 0.097853 0.063328 0.157703 0.122846 0.307408 lnL0 = -3599.458389 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3599.458389 x= 0.02226 0.08952 0.03844 0.09785 0.06333 0.15770 0.12285 0.30741 1 h-lim-p 0.0012 0.0100 187.7858 3597.687515 6 0.0001 38 | 0/8 2 h-lim-p 0.0005 0.0045 39.8125 3597.479661 6 0.0003 63 | 0/8 3 h-lim-p 0.0004 0.0079 25.3780 3597.444774 6 0.0001 89 | 0/8 4 h-lim-p 0.0011 0.0483 3.4585 3597.443334 0 0.0003 102 | 0/8 5 h-lim-p 0.0012 0.4888 0.7906 3597.443244 2 0.0003 119 | 0/8 6 h-lim-p 0.0016 1.0086 0.1564 3597.443241 1 0.0002 143 | 0/8 7 h-lim-p 0.0018 20.0000 0.0170 3597.443241 0 0.0004 164 | 0/8 8 h-lim-p 0.0698 20.0000 0.0001 3597.443222 0 1.1168 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3597.443221 0 1.0938 208 | 0/8 10 h-lim-p 1.0091 20.0000 0.0000 3597.443221 0 0.8830 228 | 0/8 11 h-lim-p 0.5067 20.0000 0.0001 3597.443221 0 0.0010 256 | 0/8 12 h-lim-p 0.0006 20.0000 0.0001 3597.443221 0 0.0000 295 | 0/8 13 h-lim-p 0.0000 20.0000 0.0010 | 0/8 14 h-lim-p 0.0000 20.0000 0.0010 Out... lnL = -3597.443221 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3597.443221 Node 7: lnL = -3597.443221 Node 8: lnL = -3597.443221 Node 9: lnL = -3597.443221 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 731 Sequential format.. Reading seq # 1: YLR249W_Sbay Reading seq # 2: YLR249W_Scer Reading seq # 3: YLR249W_Skud Reading seq # 4: YLR249W_Smik Reading seq # 5: YLR249W_Spar Sequences read.. Counting patterns.. # site patterns = 222 Counting frequencies.. 120 bytes for distance 35520 bytes for lkl0 28416 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.085000 0.075552 0.090282 0.095247 0.184782 0.175502 0.223447 lnL0 = -2884.959205 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2884.959205 x= 0.00006 0.08500 0.07555 0.09028 0.09525 0.18478 0.17550 0.22345 1 h-lim-p 0.0000 0.0000 335.2946 2884.713331 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0028 76.8916 2884.093206 0 0.0003 39 | 1/8 3 h-lim-p 0.0024 0.0278 10.4179 2884.053250 6 0.0006 66 | 1/8 4 h-lim-p 0.0019 0.0517 3.2990 2884.015287 3 0.0017 84 | 1/8 5 h-lim-p 0.0027 0.1657 2.0741 2882.463947 0 0.0217 99 | 1/8 6 h-lim-p 0.0007 0.0053 19.2464 2876.224820 0 0.0026 113 | 1/8 7 h-lim-p 0.0001 0.0008 108.3247 2874.038258 0 0.0003 126 | 1/8 8 h-lim-p 0.0006 0.0046 46.6249 2873.688802 7 0.0003 157 | 1/8 9 h-lim-p 0.7956 8.5957 0.0203 2873.349859 4 0.6138 177 | 0/8 10 h-lim-p 0.0179 1.1422 0.6954 2873.349718 3 0.0006 206 | 0/8 11 h-lim-p 0.1560 1.7054 0.0026 2873.344108 0 0.6239 228 | 0/8 12 h-lim-p 1.0908 8.7260 0.0006 2873.343552 3 0.8274 254 | 0/8 13 h-lim-p 0.4760 3.8077 0.0001 2873.343534 0 0.9519 275 | 0/8 14 h-lim-p 0.2032 1.6260 0.0001 2873.343534 0 0.0000 311 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 2873.343533 0 0.6554 347 | 0/8 16 h-lim-p 2.1683 20.0000 0.0000 2873.343533 0 0.2372 369 | 0/8 17 h-lim-p 0.4144 20.0000 0.0000 2873.343533 0 1.6575 391 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 2873.343533 0 1.0938 411 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 2873.343533 0 1.0938 431 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 2873.343533 0 0.3125 453 | 0/8 21 h-lim-p 0.2960 20.0000 0.0000 2873.343533 0 0.0093 477 Out... lnL = -2873.343533 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2873.343533 Node 7: lnL = -2873.343533 Node 8: lnL = -2873.343533 Node 9: lnL = -2873.343533 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 412 Sequential format.. Reading seq # 1: YLR250W_Sbay Reading seq # 2: YLR250W_Scer Reading seq # 3: YLR250W_Skud Reading seq # 4: YLR250W_Smik Reading seq # 5: YLR250W_Spar Sequences read.. Counting patterns.. # site patterns = 138 Counting frequencies.. 120 bytes for distance 22080 bytes for lkl0 17664 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.109341 0.060924 0.100768 0.079739 0.349396 0.206041 0.313440 lnL0 = -1503.408933 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1503.408933 x= 0.00006 0.10934 0.06092 0.10077 0.07974 0.34940 0.20604 0.31344 1 h-lim-p 0.0000 0.0000 199.8970 1503.318377 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0029 53.8388 1502.385091 0 0.0006 40 | 1/8 3 h-lim-p 0.0007 0.0059 31.1111 1501.687836 0 0.0022 53 | 1/8 4 h-lim-p 0.0006 0.0049 18.3222 1501.426229 0 0.0025 67 | 1/8 5 h-lim-p 0.0016 0.0132 12.9434 1501.303250 1 0.0021 81 | 1/8 6 h-lim-p 0.0023 0.0244 11.6694 1501.068889 0 0.0046 94 | 1/8 7 h-lim-p 0.0142 0.1134 2.2826 1500.967818 6 0.0070 120 | 1/8 8 h-lim-p 0.0169 0.1754 0.9400 1495.020392 0 0.0676 134 | 1/8 9 h-lim-p 0.7168 5.7346 0.0280 1494.858739 8 0.5269 171 | 1/8 10 h-lim-p 1.3500 16.4164 0.0109 1494.841223 5 0.5851 200 | 1/8 11 h-lim-p 2.5000 20.0000 0.0017 1494.840974 3 0.7330 228 | 0/8 12 h-lim-p 0.1195 20.0000 0.0105 1494.840974 0 0.0033 251 | 0/8 13 h-lim-p 0.1082 0.8658 0.0003 1494.840968 0 0.6494 273 | 0/8 14 h-lim-p 0.0291 0.2326 0.0000 1494.840968 m 0.2326 293 | 1/8 15 h-lim-p 0.2238 20.0000 0.0000 1494.840968 0 0.4476 314 | 1/8 16 h-lim-p 0.2633 20.0000 0.0000 1494.840968 0 0.2633 333 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 1494.840968 0 1.0938 352 | 1/8 18 h-lim-p 1.7867 20.0000 0.0000 1494.840968 0 1.5634 371 | 1/8 19 h-lim-p 2.4455 20.0000 0.0000 1494.840968 0 0.5349 391 | 1/8 20 h-lim-p 1.1405 20.0000 0.0000 1494.840968 0 0.0003 421 Out... lnL = -1494.840968 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1494.840968 Node 7: lnL = -1494.840968 Node 8: lnL = -1494.840968 Node 9: lnL = -1494.840968 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 457 Sequential format.. Reading seq # 1: YLR251W_Sbay Reading seq # 2: YLR251W_Scer Reading seq # 3: YLR251W_Skud Reading seq # 4: YLR251W_Smik Reading seq # 5: YLR251W_Spar Sequences read.. Counting patterns.. # site patterns = 177 Counting frequencies.. 120 bytes for distance 28320 bytes for lkl0 22656 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.123929 0.071256 0.114281 0.108811 0.227954 0.237620 0.283035 lnL0 = -1973.988559 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1973.988559 x= 0.00006 0.12393 0.07126 0.11428 0.10881 0.22795 0.23762 0.28303 1 h-lim-p 0.0000 0.0000 245.7129 1973.832332 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0013 94.9603 1971.446674 3 0.0006 45 | 1/8 3 h-lim-p 0.0011 0.0087 25.3064 1971.100567 6 0.0011 71 | 1/8 4 h-lim-p 0.0013 0.0101 7.6445 1971.055593 3 0.0011 89 | 1/8 5 h-lim-p 0.0064 0.2909 1.2652 1970.131597 0 0.0384 103 | 1/8 6 h-lim-p 0.0006 0.0050 15.1499 1967.121095 0 0.0038 117 | 1/8 7 h-lim-p 0.0007 0.0058 39.2779 1963.339594 0 0.0015 130 | 1/8 8 h-lim-p 0.0004 0.0029 36.9996 1962.672723 0 0.0011 143 | 1/8 9 h-lim-p 0.3647 2.9177 0.0906 1961.186030 1 0.4559 157 | 0/8 10 h-lim-p 0.0154 0.3162 2.6876 1961.181515 5 0.0013 189 | 0/8 11 h-lim-p 0.1849 3.6965 0.0185 1961.096981 0 0.3697 202 | 0/8 12 h-lim-p 0.7406 5.9245 0.0064 1961.076146 5 0.7862 232 | 0/8 13 h-lim-p 2.5000 20.0000 0.0009 1961.075255 5 0.8754 264 | 0/8 14 h-lim-p 2.5000 20.0000 0.0003 1961.075224 3 0.6718 291 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1961.075222 0 1.0938 311 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1961.075222 0 1.0938 331 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1961.075222 0 0.5469 352 | 0/8 18 h-lim-p 1.5414 20.0000 0.0000 1961.075222 0 0.0241 377 | 0/8 19 h-lim-p 0.0257 20.0000 0.0000 1961.075222 0 0.0000 419 Out... lnL = -1961.075222 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1961.075222 Node 7: lnL = -1961.075222 Node 8: lnL = -1961.075222 Node 9: lnL = -1961.075222 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 395 Sequential format.. Reading seq # 1: YLR253W_Sbay Reading seq # 2: YLR253W_Scer Reading seq # 3: YLR253W_Skud Reading seq # 4: YLR253W_Smik Reading seq # 5: YLR253W_Spar Sequences read.. Counting patterns.. # site patterns = 170 Counting frequencies.. 120 bytes for distance 27200 bytes for lkl0 21760 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.185265 0.133514 0.134598 0.178876 0.271856 0.316586 0.345686 lnL0 = -1809.365747 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1809.365747 x= 0.00006 0.18527 0.13351 0.13460 0.17888 0.27186 0.31659 0.34569 1 h-lim-p 0.0000 0.0000 216.0820 1809.285945 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0043 102.6710 1804.730956 0 0.0013 41 | 1/8 3 h-lim-p 0.0017 0.0134 15.1195 1804.487234 6 0.0018 67 | 1/8 4 h-lim-p 0.0094 0.1200 2.9013 1804.071320 0 0.0140 79 | 1/8 5 h-lim-p 0.0107 0.0949 3.8211 1797.165656 0 0.0320 92 | 0/8 6 h-lim-p 0.0004 0.0030 70.4554 1790.517621 0 0.0015 106 | 0/8 7 h-lim-p 0.0007 0.0052 69.3722 1788.798623 1 0.0008 120 | 0/8 8 h-lim-p 0.0016 0.0125 29.8624 1788.435861 8 0.0009 151 | 0/8 9 h-lim-p 0.0024 0.0192 5.9666 1788.322358 0 0.0096 165 | 0/8 10 h-lim-p 0.3697 2.9580 0.0800 1787.609839 7 0.4046 195 | 0/8 11 h-lim-p 2.5000 20.0000 0.0097 1787.565752 7 0.6882 232 | 0/8 12 h-lim-p 2.2937 20.0000 0.0029 1787.563139 2 1.0752 256 | 0/8 13 h-lim-p 2.5000 20.0000 0.0003 1787.563092 2 0.9961 280 | 0/8 14 h-lim-p 1.5653 20.0000 0.0002 1787.563091 1 0.3852 303 | 0/8 15 h-lim-p 2.4933 20.0000 0.0000 1787.563091 0 1.0908 323 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1787.563091 0 1.0938 343 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1787.563091 0 5.0000 364 | 0/8 18 h-lim-p 1.6104 20.0000 0.0000 1787.563091 0 0.3523 385 | 0/8 19 h-lim-p 0.7646 20.0000 0.0000 1787.563091 0 0.0060 411 Out... lnL = -1787.563091 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1787.563091 Node 7: lnL = -1787.563091 Node 8: lnL = -1787.563091 Node 9: lnL = -1787.563091 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 899 Sequential format.. Reading seq # 1: YLR257W_Sbay Reading seq # 2: YLR257W_Scer Reading seq # 3: YLR257W_Skud Reading seq # 4: YLR257W_Smik Reading seq # 5: YLR257W_Spar Sequences read.. Counting patterns.. # site patterns = 296 Counting frequencies.. 120 bytes for distance 47360 bytes for lkl0 37888 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.144958 0.149883 0.108896 0.138816 0.233918 0.224402 0.272153 lnL0 = -3782.208794 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3782.208794 x= 0.00006 0.14496 0.14988 0.10890 0.13882 0.23392 0.22440 0.27215 1 h-lim-p 0.0000 0.0000 539.6261 3782.066964 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0012 232.1617 3773.324008 0 0.0005 39 | 1/8 3 h-lim-p 0.0005 0.0042 43.4308 3772.766205 7 0.0006 70 | 1/8 4 h-lim-p 0.0027 0.0212 7.4866 3772.637357 7 0.0016 101 | 1/8 5 h-lim-p 0.0073 0.2084 1.6557 3762.212044 0 0.0581 116 | 1/8 6 h-lim-p 0.0004 0.0033 62.6459 3738.076428 0 0.0016 130 | 1/8 7 h-lim-p 0.0005 0.0040 91.8317 3736.489968 8 0.0004 160 | 1/8 8 h-lim-p 0.0032 0.0257 10.0413 3736.467371 4 0.0004 182 | 0/8 9 h-lim-p 0.0003 0.0687 15.9038 3736.424653 0 0.0005 195 | 0/8 10 h-lim-p 0.0689 1.5288 0.1156 3733.603051 0 0.2756 209 | 0/8 11 h-lim-p 2.0037 16.0294 0.0152 3733.471543 2 0.4696 234 | 0/8 12 h-lim-p 1.0053 8.0425 0.0040 3733.449161 4 0.7883 262 | 0/8 13 h-lim-p 2.5000 20.0000 0.0008 3733.448918 3 0.4741 289 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 3733.448903 0 0.6250 310 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 3733.448903 0 1.0938 330 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 3733.448902 0 1.0938 350 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 3733.448902 0 1.0938 370 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 3733.448902 0 1.2500 390 | 0/8 19 h-lim-p 0.6466 20.0000 0.0000 3733.448902 0 0.3233 410 | 0/8 20 h-lim-p 0.0383 20.0000 0.0000 3733.448902 0 0.0000 446 Out... lnL = -3733.448902 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3733.448902 Node 7: lnL = -3733.448902 Node 8: lnL = -3733.448902 Node 9: lnL = -3733.448902 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 833 Sequential format.. Reading seq # 1: YLR258W_Sbay Reading seq # 2: YLR258W_Scer Reading seq # 3: YLR258W_Skud Reading seq # 4: YLR258W_Smik Reading seq # 5: YLR258W_Spar Sequences read.. Counting patterns.. # site patterns = 290 Counting frequencies.. 120 bytes for distance 46400 bytes for lkl0 37120 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.277930 0.242350 0.157482 0.241710 0.695873 0.372973 0.475173 lnL0 = -3999.553356 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3999.553356 x= 0.00006 0.27793 0.24235 0.15748 0.24171 0.69587 0.37297 0.47517 1 h-lim-p 0.0000 0.0000 843.2116 3999.275979 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0004 1141.8579 3806.872001 0 0.0004 39 | 1/8 3 h-lim-p 0.0001 0.0008 269.3740 3790.352259 0 0.0006 53 | 1/8 4 h-lim-p 0.0001 0.0009 213.2104 3785.950504 0 0.0004 67 | 1/8 5 h-lim-p 0.0010 0.0112 91.3306 3777.914957 0 0.0041 81 | 1/8 6 h-lim-p 0.0006 0.0047 172.0286 3773.720366 0 0.0009 93 | 1/8 7 h-lim-p 0.0023 0.0188 2.1304 3769.908353 m 0.0188 105 | 1/8 8 h-lim-p 0.0010 0.0078 31.8421 3737.972303 0 0.0039 119 | 1/8 9 h-lim-p 0.2095 1.6760 0.3529 3731.507121 0 0.4190 132 | 0/8 10 h-lim-p 0.0018 0.0145 47.7528 3731.196879 5 0.0005 162 | 0/8 11 h-lim-p 0.0418 2.1247 0.5524 3727.740276 0 0.3343 177 | 0/8 12 h-lim-p 0.5644 4.5150 0.0665 3727.253291 2 0.5291 201 | 0/8 13 h-lim-p 0.5578 4.4624 0.0228 3727.179599 5 0.4951 230 | 0/8 14 h-lim-p 1.9191 20.0000 0.0059 3727.173723 5 0.7033 261 | 0/8 15 h-lim-p 2.5000 20.0000 0.0013 3727.173514 2 0.8246 287 | 0/8 16 h-lim-p 2.5000 20.0000 0.0001 3727.173510 1 0.6152 310 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 3727.173510 0 1.0938 330 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 3727.173510 0 1.0938 350 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 3727.173510 0 3.7500 370 | 0/8 20 h-lim-p 1.4212 20.0000 0.0000 3727.173510 0 0.0444 394 | 0/8 21 h-lim-p 0.0460 20.0000 0.0000 3727.173510 0 0.0000 427 Out... lnL = -3727.173510 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3727.173510 Node 7: lnL = -3727.173510 Node 8: lnL = -3727.173510 Node 9: lnL = -3727.173510 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 830 Sequential format.. Reading seq # 1: YLR259C_Sbay Reading seq # 2: YLR259C_Scer Reading seq # 3: YLR259C_Skud Reading seq # 4: YLR259C_Smik Reading seq # 5: YLR259C_Spar Sequences read.. Counting patterns.. # site patterns = 228 Counting frequencies.. 120 bytes for distance 36480 bytes for lkl0 29184 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.013189 0.000060 0.152445 0.111631 0.114583 0.087824 0.293409 0.286977 lnL0 = -3277.097483 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3277.097483 x= 0.01319 0.00006 0.15244 0.11163 0.11458 0.08782 0.29341 0.28698 1 h-lim-p 0.0000 0.0000 204.5043 3277.025987 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0076 41.6310 3276.538222 0 0.0006 40 | 1/8 3 h-lim-p 0.0037 0.0608 7.2130 3276.520898 5 0.0006 67 | 1/8 4 h-lim-p 0.0016 0.0129 2.6054 3276.509234 4 0.0013 88 | 1/8 5 h-lim-p 0.0053 0.2649 0.6434 3275.719338 0 0.0424 103 | 1/8 6 h-lim-p 0.0008 0.0077 34.0544 3272.873564 0 0.0024 123 | 1/8 7 h-lim-p 0.0015 0.0118 40.1025 3272.270568 7 0.0007 151 | 1/8 8 h-lim-p 1.0102 8.0817 0.0177 3272.078693 7 0.7352 180 | 0/8 9 h-lim-p 0.0018 0.1675 7.2086 3272.070600 5 0.0003 212 | 0/8 10 h-lim-p 0.7626 20.0000 0.0030 3272.061538 0 1.5253 225 | 0/8 11 h-lim-p 1.7161 20.0000 0.0027 3272.058684 5 1.2018 257 | 0/8 12 h-lim-p 2.5000 20.0000 0.0005 3272.058539 3 1.3159 284 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 3272.058537 0 1.0938 304 | 0/8 14 h-lim-p 2.3913 20.0000 0.0000 3272.058537 0 1.0462 324 | 0/8 15 h-lim-p 1.0553 20.0000 0.0000 3272.058537 0 2.1106 345 | 0/8 16 h-lim-p 0.1177 20.0000 0.0003 3272.058537 0 0.1030 365 | 0/8 17 h-lim-p 0.0272 20.0000 0.0013 3272.058537 0 0.0034 387 | 0/8 18 h-lim-p 0.0020 20.0000 0.0022 3272.058537 0 0.0000 421 | 0/8 19 h-lim-p 0.0010 20.0000 0.0000 3272.058537 0 0.0010 441 Out... lnL = -3272.058537 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3272.058537 Node 7: lnL = -3272.058537 Node 8: lnL = -3272.058537 Node 9: lnL = -3272.058537 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 843 Sequential format.. Reading seq # 1: YLR260W_Sbay Reading seq # 2: YLR260W_Scer Reading seq # 3: YLR260W_Skud Reading seq # 4: YLR260W_Smik Reading seq # 5: YLR260W_Spar Sequences read.. Counting patterns.. # site patterns = 204 Counting frequencies.. 120 bytes for distance 32640 bytes for lkl0 26112 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.050555 0.246270 0.176012 0.183374 0.432956 0.329156 0.364695 lnL0 = -3264.953536 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3264.953536 x= 0.00006 0.05056 0.24627 0.17601 0.18337 0.43296 0.32916 0.36469 1 h-lim-p 0.0000 0.0000 613.9791 3264.722914 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0009 120.3308 3256.836696 m 0.0009 38 | 2/8 3 h-lim-p 0.0005 0.0040 65.8219 3193.633572 0 0.0030 52 | 2/8 4 h-lim-p 0.0001 0.0008 222.3861 3189.255623 0 0.0002 65 | 2/8 5 h-lim-p 0.0007 0.0061 67.7240 3187.988384 8 0.0006 95 | 2/8 6 h-lim-p 0.0076 0.1978 5.3391 3187.911539 7 0.0048 123 | 1/8 7 h-lim-p 0.0009 0.0372 30.0027 3187.727225 7 0.0004 149 | 1/8 8 h-lim-p 0.0004 0.0327 33.5794 3187.468501 0 0.0031 164 | 1/8 9 h-lim-p 0.5865 4.6923 0.0992 3186.657293 8 0.3430 196 | 1/8 10 h-lim-p 2.5000 20.0000 0.0107 3186.440035 7 1.6151 230 | 0/8 11 h-lim-p 0.0149 0.7007 1.1644 3186.439589 3 0.0007 259 | 0/8 12 h-lim-p 0.0550 10.3008 0.0139 3186.164670 5 7.4304 289 | 0/8 13 h-lim-p 0.2338 1.8706 0.0339 3186.041924 m 1.8706 309 | 1/8 14 h-lim-p 0.6783 5.4267 0.0046 3186.039049 4 0.5535 338 | 1/8 15 h-lim-p 0.1536 1.2290 0.0134 3186.037973 4 0.0834 366 | 1/8 16 h-lim-p 0.5358 20.0000 0.0021 3186.037878 0 1.0716 386 | 1/8 17 h-lim-p 2.5000 20.0000 0.0001 3186.037877 0 1.0938 405 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 3186.037877 0 1.0938 424 | 1/8 19 h-lim-p 2.5000 20.0000 0.0000 3186.037877 0 0.0195 449 | 1/8 20 h-lim-p 0.0192 20.0000 0.0000 3186.037877 0 0.0012 471 Out... lnL = -3186.037877 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3186.037877 Node 7: lnL = -3186.037877 Node 8: lnL = -3186.037877 Node 9: lnL = -3186.037877 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 750 Sequential format.. Reading seq # 1: YLR262C-A_Sbay Reading seq # 2: YLR262C-A_Scer Reading seq # 3: YLR262C-A_Skud Reading seq # 4: YLR262C-A_Smik Reading seq # 5: YLR262C-A_Spar Sequences read.. Counting patterns.. # site patterns = 270 Counting frequencies.. 120 bytes for distance 43200 bytes for lkl0 34560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.166591 0.184582 0.210231 0.161125 0.274573 0.224039 0.348809 lnL0 = -3238.538738 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3238.538738 x= 0.00006 0.16659 0.18458 0.21023 0.16113 0.27457 0.22404 0.34881 1 h-lim-p 0.0000 0.0000 406.5622 3238.388668 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0021 125.1265 3230.107533 8 0.0010 63 | 1/8 3 h-lim-p 0.0041 0.0330 25.9119 3229.503997 6 0.0017 86 | 1/8 4 h-lim-p 0.0036 0.0289 6.6799 3229.213056 3 0.0037 104 | 1/8 5 h-lim-p 0.0070 0.0911 3.4979 3223.137183 0 0.0280 118 | 1/8 6 h-lim-p 0.0012 0.0099 47.1959 3203.108407 0 0.0037 131 | 0/8 7 h-lim-p 0.0003 0.0022 128.3192 3196.592365 0 0.0005 144 | 0/8 8 h-lim-p 0.0007 0.0054 22.5927 3196.469114 7 0.0005 174 | 0/8 9 h-lim-p 0.0031 0.0883 3.5787 3196.373578 0 0.0123 188 | 0/8 10 h-lim-p 0.0723 0.5783 0.2764 3194.603550 0 0.1446 201 | 0/8 11 h-lim-p 0.9032 7.2254 0.0368 3194.145395 6 0.6847 233 | 0/8 12 h-lim-p 2.5000 20.0000 0.0085 3194.112430 6 0.7683 269 | 0/8 13 h-lim-p 1.9223 20.0000 0.0034 3194.109295 3 0.4745 296 | 0/8 14 h-lim-p 1.7553 20.0000 0.0009 3194.109127 3 1.1317 324 | 0/8 15 h-lim-p 2.5000 20.0000 0.0001 3194.109125 0 0.5469 345 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 3194.109124 0 1.0938 365 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 3194.109124 0 1.0938 385 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 3194.109124 0 2.5000 405 | 0/8 19 h-lim-p 2.1702 20.0000 0.0000 3194.109124 0 0.0000 449 Out... lnL = -3194.109124 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3194.109124 Node 7: lnL = -3194.109124 Node 8: lnL = -3194.109124 Node 9: lnL = -3194.109124 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 610 Sequential format.. Reading seq # 1: YLR262C_Sbay Reading seq # 2: YLR262C_Scer Reading seq # 3: YLR262C_Skud Reading seq # 4: YLR262C_Smik Reading seq # 5: YLR262C_Spar Sequences read.. Counting patterns.. # site patterns = 267 Counting frequencies.. 120 bytes for distance 42720 bytes for lkl0 34176 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.097935 0.135016 0.249334 0.134544 0.267526 0.266072 0.396456 lnL0 = -3000.639786 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3000.639786 x= 0.00006 0.09794 0.13502 0.24933 0.13454 0.26753 0.26607 0.39646 1 h-lim-p 0.0000 0.0000 197.2870 3000.523866 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0129 33.7640 2999.923537 0 0.0011 40 | 1/8 3 h-lim-p 0.0054 0.0610 6.9463 2999.862964 6 0.0018 65 | 1/8 4 h-lim-p 0.0036 0.1407 3.3666 2999.784229 3 0.0037 83 | 1/8 5 h-lim-p 0.0038 0.0881 3.2595 2998.865629 0 0.0152 97 | 1/8 6 h-lim-p 0.0018 0.0141 12.8586 2994.134018 0 0.0070 111 | 0/8 7 h-lim-p 0.0007 0.0054 44.1689 2992.791563 0 0.0010 123 | 0/8 8 h-lim-p 0.0002 0.0019 14.5088 2992.571006 m 0.0019 135 | 0/8 9 h-lim-p 0.0000 0.0000 8.5248 h-lim-p: 1.20861127e-21 9.66889015e-21 8.52484109e+00 2992.571006 .. | 0/8 10 h-lim-p 0.0000 0.0254 84.9662 2991.813486 0 0.0002 159 | 0/8 11 h-lim-p 0.0011 0.0155 19.1175 2991.685576 6 0.0007 186 | 0/8 12 h-lim-p 0.0015 0.0118 2.3858 2991.683732 3 0.0007 204 | 0/8 13 h-lim-p 0.0012 0.0848 1.3394 2991.683320 2 0.0006 220 | 0/8 14 h-lim-p 0.0210 8.2422 0.0355 2991.683306 1 0.0042 235 | 0/8 15 h-lim-p 0.0192 1.7959 0.0077 2991.681308 0 0.1539 258 | 0/8 16 h-lim-p 0.0011 0.2161 1.0728 2991.680405 3 0.0009 284 | 0/8 17 h-lim-p 0.0033 0.4739 0.3036 2991.680376 2 0.0006 301 | 0/8 18 h-lim-p 0.5181 16.5641 0.0004 2991.680359 0 1.0361 322 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 2991.680359 0 1.0938 342 | 0/8 20 h-lim-p 0.5878 20.0000 0.0000 2991.680359 0 1.1756 363 | 0/8 21 h-lim-p 0.6258 20.0000 0.0000 2991.680359 0 0.1564 384 | 0/8 22 h-lim-p 0.0115 11.6134 0.0006 2991.680359 0 0.0100 404 | 0/8 23 h-lim-p 0.0034 3.9674 0.0016 2991.680359 0 0.0001 428 | 0/8 24 h-lim-p 0.0002 8.6527 0.0007 2991.680359 0 0.0000 454 | 0/8 25 h-lim-p 0.0003 20.0000 0.0000 2991.680359 0 0.0000 487 Out... lnL = -2991.680359 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2991.680359 Node 7: lnL = -2991.680359 Node 8: lnL = -2991.680359 Node 9: lnL = -2991.680359 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 187 Sequential format.. Reading seq # 1: YLR265C_Sbay Reading seq # 2: YLR265C_Scer Reading seq # 3: YLR265C_Skud Reading seq # 4: YLR265C_Smik Reading seq # 5: YLR265C_Spar Sequences read.. Counting patterns.. # site patterns = 91 Counting frequencies.. 120 bytes for distance 14560 bytes for lkl0 11648 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.109918 0.092040 0.183519 0.080029 0.201371 0.231076 0.286374 lnL0 = -743.237401 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 743.237401 x= 0.00006 0.10992 0.09204 0.18352 0.08003 0.20137 0.23108 0.28637 1 h-lim-p 0.0000 0.0000 38.1670 743.231002 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0081 25.7377 742.905772 0 0.0013 41 | 1/8 3 h-lim-p 0.0024 0.0195 8.4532 742.867734 5 0.0012 63 | 1/8 4 h-lim-p 0.0022 0.0392 4.6303 742.802366 0 0.0066 76 | 1/8 5 h-lim-p 0.0013 0.0101 10.5730 742.533007 m 0.0101 88 | 1/8 6 h-lim-p -0.0000 -0.0000 8.6275 h-lim-p: -1.16301933e-19 -9.30415462e-19 8.62754498e+00 742.533007 .. | 1/8 7 h-lim-p 0.0000 0.0176 44.1101 741.265298 0 0.0013 115 | 1/8 8 h-lim-p 0.0007 0.0055 24.7408 740.794993 0 0.0027 129 | 1/8 9 h-lim-p 0.0003 0.0022 12.0105 740.736273 0 0.0011 143 | 1/8 10 h-lim-p 0.0008 0.0066 1.7860 740.728780 0 0.0049 157 | 0/8 11 h-lim-p 0.0019 0.1249 4.5364 740.696306 0 0.0039 170 | 0/8 12 h-lim-p 0.0003 0.0023 4.2179 740.677265 m 0.0023 182 | 0/8 13 h-lim-p 0.0000 0.0000 2.6083 h-lim-p: 4.67306821e-21 3.73845457e-20 2.60828675e+00 740.677265 .. | 0/8 14 h-lim-p 0.0000 0.0162 9.7771 740.633467 0 0.0010 208 | 0/8 15 h-lim-p 0.0020 0.0161 2.1837 740.629316 3 0.0018 226 | 0/8 16 h-lim-p 0.0004 0.0031 1.3277 740.626491 m 0.0031 238 | 1/8 17 h-lim-p 0.0072 0.7261 0.5005 740.626115 3 0.0039 257 | 1/8 18 h-lim-p 0.0045 2.3742 0.4308 740.625718 0 0.0090 277 | 1/8 19 h-lim-p 0.0325 2.5650 0.1200 740.625688 2 0.0040 302 | 1/8 20 h-lim-p 0.0276 9.3816 0.0174 740.625681 2 0.0088 326 | 1/8 21 h-lim-p 0.1398 20.0000 0.0011 740.625633 0 0.8390 347 | 1/8 22 h-lim-p 2.5000 20.0000 0.0001 740.625631 1 0.9961 368 | 1/8 23 h-lim-p 2.5000 20.0000 0.0000 740.625631 0 1.0938 387 | 1/8 24 h-lim-p 1.4831 20.0000 0.0000 740.625631 0 1.2977 406 | 1/8 25 h-lim-p 0.3565 20.0000 0.0000 740.625631 0 0.0111 429 | 1/8 26 h-lim-p 0.0018 20.0000 0.0002 740.625631 0 0.0005 449 | 1/8 27 h-lim-p 0.0000 7.3577 0.0032 740.625631 0 0.0000 468 | 1/8 28 h-lim-p 0.0001 20.0000 0.0006 740.625631 0 0.0000 490 | 1/8 29 h-lim-p 0.0001 20.0000 0.0000 740.625631 0 0.0000 510 | 1/8 30 h-lim-p 0.0002 20.0000 0.0000 740.625631 0 0.0000 539 Out... lnL = -740.625631 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -740.625631 Node 7: lnL = -740.625631 Node 8: lnL = -740.625631 Node 9: lnL = -740.625631 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 521 Sequential format.. Reading seq # 1: YLR267W_Sbay Reading seq # 2: YLR267W_Scer Reading seq # 3: YLR267W_Skud Reading seq # 4: YLR267W_Smik Reading seq # 5: YLR267W_Spar Sequences read.. Counting patterns.. # site patterns = 186 Counting frequencies.. 120 bytes for distance 29760 bytes for lkl0 23808 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.030030 0.059025 0.066268 0.127989 0.063596 0.157351 0.156797 0.336856 lnL0 = -2275.461701 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2275.461701 x= 0.03003 0.05903 0.06627 0.12799 0.06360 0.15735 0.15680 0.33686 1 h-lim-p 0.0004 0.0035 109.7436 2273.800819 7 0.0003 39 | 0/8 2 h-lim-p 0.0005 0.0043 39.6130 2273.482223 3 0.0004 57 | 0/8 3 h-lim-p 0.0012 0.0169 14.9270 2273.459072 4 0.0002 79 | 0/8 4 h-lim-p 0.0005 0.0257 7.3002 2273.449425 2 0.0005 95 | 0/8 5 h-lim-p 0.0026 0.1664 1.3056 2273.449095 4 0.0004 119 | 0/8 6 h-lim-p 0.0070 1.9633 0.0743 2273.449093 0 0.0008 133 | 0/8 7 h-lim-p 0.0020 9.4031 0.0288 2273.449092 0 0.0009 153 | 0/8 8 h-lim-p 0.0306 20.0000 0.0008 2273.448899 0 0.4895 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2273.448887 1 0.9961 199 | 0/8 10 h-lim-p 1.9881 20.0000 0.0001 2273.448887 0 1.7396 219 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2273.448886 0 1.0938 239 | 0/8 12 h-lim-p 2.0645 20.0000 0.0000 2273.448886 0 0.9032 259 | 0/8 13 h-lim-p 0.6054 20.0000 0.0000 2273.448886 0 0.0004 289 | 0/8 14 h-lim-p 0.0002 20.0000 0.0001 2273.448886 0 0.0001 309 | 0/8 15 h-lim-p 0.0001 20.0000 0.0001 2273.448886 0 0.0000 329 | 0/8 16 h-lim-p 0.0003 20.0000 0.0000 2273.448886 0 0.0000 360 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -2273.448886 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2273.448886 Node 7: lnL = -2273.448886 Node 8: lnL = -2273.448886 Node 9: lnL = -2273.448886 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 291 Sequential format.. Reading seq # 1: YLR268W_Sbay Reading seq # 2: YLR268W_Scer Reading seq # 3: YLR268W_Skud Reading seq # 4: YLR268W_Smik Reading seq # 5: YLR268W_Spar Sequences read.. Counting patterns.. # site patterns = 121 Counting frequencies.. 120 bytes for distance 19360 bytes for lkl0 15488 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.045241 0.116597 0.111892 0.102437 0.234317 0.243694 0.292087 lnL0 = -1255.815818 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1255.815818 x= 0.00006 0.04524 0.11660 0.11189 0.10244 0.23432 0.24369 0.29209 1 h-lim-p 0.0000 0.0000 113.7474 1255.732795 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0062 30.6436 1255.248327 0 0.0011 39 | 1/8 3 h-lim-p 0.0042 0.0370 8.4100 1255.190337 6 0.0015 65 | 1/8 4 h-lim-p 0.0022 0.0582 6.0082 1255.165213 7 0.0014 95 | 1/8 5 h-lim-p 0.0069 0.1724 1.1860 1255.021519 0 0.0277 109 | 1/8 6 h-lim-p 0.0078 0.0627 2.7808 1253.762761 0 0.0157 122 | 1/8 7 h-lim-p 0.0006 0.0049 25.2055 1252.242442 0 0.0018 135 | 1/8 8 h-lim-p 0.0019 0.0152 19.8550 1251.808896 2 0.0018 151 | 1/8 9 h-lim-p 1.4489 11.5912 0.0238 1251.670885 3 0.6565 169 | 0/8 10 h-lim-p 0.1633 20.0000 0.0959 1251.670869 0 0.0026 193 | 0/8 11 h-lim-p 0.0801 1.2347 0.0031 1251.669263 4 0.5657 223 | 0/8 12 h-lim-p 0.1336 1.0686 0.0003 1251.669247 0 0.8014 245 | 0/8 13 h-lim-p 0.0249 0.1990 0.0002 1251.669247 0 0.1493 267 | 0/8 14 h-lim-p 0.0001 0.0009 0.0119 1251.669247 0 0.0000 297 | 0/8 15 h-lim-p 0.0000 0.0170 0.0006 1251.669247 m 0.0170 325 | 1/8 16 h-lim-p 0.0653 20.0000 0.0001 1251.669247 0 0.0000 365 | 0/8 17 h-lim-p 0.0000 2.5193 0.0611 1251.669246 0 0.0006 390 | 0/8 18 h-lim-p 0.0002 0.0013 0.0299 1251.669246 0 0.0002 410 | 0/8 19 h-lim-p 0.0001 0.0017 0.0363 1251.669246 0 0.0003 431 | 0/8 20 h-lim-p 0.0003 0.0024 0.0268 1251.669246 0 0.0003 451 | 0/8 21 h-lim-p 0.0004 0.0029 0.0154 1251.669246 0 0.0000 485 | 0/8 22 h-lim-p 0.0000 0.0133 0.0032 1251.669246 0 0.0000 516 | 0/8 23 h-lim-p 0.0000 0.1731 0.0002 1251.669246 0 0.0819 549 | 0/8 24 h-lim-p 0.0000 0.0003 0.0441 1251.669246 0 0.0001 570 | 0/8 25 h-lim-p 0.0009 0.0072 0.0033 1251.669246 0 0.0000 604 | 0/8 26 h-lim-p 0.0000 0.0274 0.0002 .. | 0/8 27 h-lim-p 0.0000 0.0001 0.0429 1251.669246 m 0.0001 658 | 1/8 28 h-lim-p 0.0001 20.0000 0.0168 1251.669246 0 0.0002 680 | 1/8 29 h-lim-p 0.0016 20.0000 0.0022 1251.669246 0 0.0014 699 | 1/8 30 h-lim-p 0.0026 20.0000 0.0012 1251.669246 0 0.0011 718 | 1/8 31 h-lim-p 0.0023 20.0000 0.0006 1251.669246 0 0.0000 746 | 1/8 32 h-lim-p 0.0000 20.0000 0.0001 1251.669246 0 0.0000 772 | 1/8 33 h-lim-p 0.0000 20.0000 0.0001 1251.669246 0 0.0000 795 | 1/8 34 h-lim-p 0.0000 20.0000 0.0000 1251.669246 0 0.0000 824 Out... lnL = -1251.669246 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1251.669246 Node 7: lnL = -1251.669246 Node 8: lnL = -1251.669246 Node 9: lnL = -1251.669246 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 565 Sequential format.. Reading seq # 1: YLR273C_Sbay Reading seq # 2: YLR273C_Scer Reading seq # 3: YLR273C_Skud Reading seq # 4: YLR273C_Smik Reading seq # 5: YLR273C_Spar Sequences read.. Counting patterns.. # site patterns = 210 Counting frequencies.. 120 bytes for distance 33600 bytes for lkl0 26880 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.122665 0.437524 0.310588 0.321259 0.946534 0.424252 0.553730 lnL0 = -2975.255256 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2975.255256 x= 0.00006 0.12267 0.43752 0.31059 0.32126 0.94653 0.42425 0.55373 1 h-lim-p 0.0000 0.0000 557.9674 2975.089481 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0000 52591.4105 2786.797608 m 0.0000 34 | 2/8 3 h-lim-p 0.0002 0.0017 246.4095 2750.153058 0 0.0008 48 | 2/8 4 h-lim-p 0.0004 0.0036 109.1796 2730.726422 0 0.0018 62 | 2/8 5 h-lim-p 0.0003 0.0023 91.0403 2724.849860 0 0.0011 76 | 1/8 6 h-lim-p 0.0001 0.0008 185.4422 2721.523405 0 0.0006 90 | 1/8 7 h-lim-p 0.0024 0.0190 41.7517 2717.933533 0 0.0048 103 | 1/8 8 h-lim-p 0.0007 0.0058 114.7437 2717.186876 8 0.0005 135 | 1/8 9 h-lim-p 0.1878 1.5021 0.1563 2715.493050 0 0.3755 148 | 0/8 10 h-lim-p 0.0113 3.5972 5.2064 2715.484633 4 0.0006 177 | 0/8 11 h-lim-p 0.0639 0.5110 0.0241 2715.227351 m 0.5110 189 | 1/8 12 h-lim-p 2.3884 20.0000 0.0050 2715.212514 5 1.0353 218 | 1/8 13 h-lim-p 2.5000 20.0000 0.0016 2715.212033 4 0.7412 248 | 1/8 14 h-lim-p 2.1735 20.0000 0.0005 2715.211985 2 0.8384 271 | 0/8 15 h-lim-p 0.0064 10.8601 0.0701 2715.211984 0 0.0014 291 | 0/8 16 h-lim-p 0.1248 0.9981 0.0001 2715.211982 m 0.9981 311 | 1/8 17 h-lim-p 0.2759 20.0000 0.0003 2715.211981 0 0.0604 332 | 1/8 18 h-lim-p 0.3999 20.0000 0.0000 2715.211981 0 1.5995 353 | 1/8 19 h-lim-p 2.5000 20.0000 0.0000 2715.211980 0 1.2500 372 | 1/8 20 h-lim-p 2.5000 20.0000 0.0000 2715.211980 0 2.5000 391 | 1/8 21 h-lim-p 2.5000 20.0000 0.0000 2715.211980 0 1.2500 410 | 1/8 22 h-lim-p 2.5000 20.0000 0.0000 2715.211980 0 0.0684 433 | 1/8 23 h-lim-p 0.0630 20.0000 0.0000 2715.211980 0 0.0079 454 Out... lnL = -2715.211980 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2715.211980 Node 7: lnL = -2715.211980 Node 8: lnL = -2715.211980 Node 9: lnL = -2715.211980 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 567 Sequential format.. Reading seq # 1: YLR274W_Sbay Reading seq # 2: YLR274W_Scer Reading seq # 3: YLR274W_Skud Reading seq # 4: YLR274W_Smik Reading seq # 5: YLR274W_Spar Sequences read.. Counting patterns.. # site patterns = 211 Counting frequencies.. 120 bytes for distance 33760 bytes for lkl0 27008 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.106184 0.422122 0.293014 0.297245 0.886209 0.384913 0.528484 lnL0 = -2938.855738 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2938.855738 x= 0.00006 0.10618 0.42212 0.29301 0.29724 0.88621 0.38491 0.52848 1 h-lim-p 0.0000 0.0000 549.8623 2938.692671 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0001 2237.9082 2842.820390 m 0.0001 35 | 2/8 3 h-lim-p 0.0005 0.0036 161.5486 2798.157761 0 0.0027 49 | 2/8 4 h-lim-p 0.0005 0.0040 87.7936 2793.220808 0 0.0015 62 | 2/8 5 h-lim-p 0.0007 0.0058 115.3838 2780.692999 0 0.0029 76 | 2/8 6 h-lim-p 0.0009 0.0073 154.1855 2754.535569 0 0.0036 90 | 2/8 7 h-lim-p 0.0274 0.2195 2.0493 2744.919165 0 0.1098 104 | 1/8 8 h-lim-p 0.0001 0.0007 364.2063 2733.742578 m 0.0007 116 | 1/8 9 h-lim-p 0.0012 0.0096 21.8045 2728.570935 0 0.0048 130 | 1/8 10 h-lim-p 0.0588 0.4703 0.8114 2720.914849 m 0.4703 142 | 0/8 11 h-lim-p -0.0000 -0.0000 100.1812 h-lim-p: -4.29584047e-21 -3.43667237e-20 1.00181180e+02 2720.914849 .. | 0/8 12 h-lim-p 0.0000 0.0900 110.3021 2719.854744 0 0.0002 173 | 0/8 13 h-lim-p 0.0002 0.0015 20.6217 2719.769266 0 0.0004 186 | 0/8 14 h-lim-p 0.0003 0.0021 12.0300 2719.728174 0 0.0011 200 | 0/8 15 h-lim-p 0.0001 0.0012 20.3641 2719.665039 0 0.0009 214 | 0/8 16 h-lim-p 0.0000 0.0001 34.0402 2719.646722 m 0.0001 226 | 0/8 17 h-lim-p 0.0002 0.0038 14.5567 2719.624518 0 0.0006 239 | 0/8 18 h-lim-p 0.0009 0.0359 9.7786 2719.562083 0 0.0035 253 | 0/8 19 h-lim-p 0.2196 1.7565 0.0210 2719.455737 0 0.8782 267 | 0/8 20 h-lim-p 1.5751 12.6005 0.0014 2719.453688 4 1.0368 296 | 0/8 21 h-lim-p 2.5000 20.0000 0.0001 2719.453685 0 1.0938 316 | 0/8 22 h-lim-p 2.1890 20.0000 0.0000 2719.453685 0 0.9577 336 | 0/8 23 h-lim-p 1.0051 20.0000 0.0000 2719.453685 0 0.0079 362 | 0/8 24 h-lim-p 0.0003 14.9235 0.0010 2719.453685 0 0.0001 383 | 0/8 25 h-lim-p 0.0002 20.0000 0.0003 2719.453685 0 0.0000 409 | 0/8 26 h-lim-p 0.0001 20.0000 0.0000 2719.453685 0 0.0001 429 Out... lnL = -2719.453685 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2719.453685 Node 7: lnL = -2719.453685 Node 8: lnL = -2719.453685 Node 9: lnL = -2719.453685 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 364 Sequential format.. Reading seq # 1: YLR276C_Sbay Reading seq # 2: YLR276C_Scer Reading seq # 3: YLR276C_Skud Reading seq # 4: YLR276C_Smik Reading seq # 5: YLR276C_Spar Sequences read.. Counting patterns.. # site patterns = 137 Counting frequencies.. 120 bytes for distance 21920 bytes for lkl0 17536 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.093565 0.218719 0.190172 0.171410 0.278948 0.279229 0.302868 lnL0 = -1514.015804 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1514.015804 x= 0.00006 0.09356 0.21872 0.19017 0.17141 0.27895 0.27923 0.30287 1 h-lim-p 0.0000 0.0000 231.0171 1513.944903 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0040 75.5983 1507.214688 6 0.0022 56 | 1/8 3 h-lim-p 0.0023 0.0186 17.4628 1506.648012 0 0.0047 69 | 1/8 4 h-lim-p 0.0105 0.0844 3.9569 1506.093969 1 0.0132 83 | 1/8 5 h-lim-p 0.0088 0.0703 2.8548 1496.346779 0 0.0352 97 | 1/8 6 h-lim-p 0.0003 0.0022 96.9520 1490.057106 0 0.0011 111 | 1/8 7 h-lim-p 0.0008 0.0064 53.0291 1486.705956 0 0.0016 124 | 1/8 8 h-lim-p 0.0025 0.0199 12.2050 1486.622150 5 0.0011 145 | 1/8 9 h-lim-p 0.0683 0.8411 0.1954 1485.422122 0 0.2730 159 | 0/8 10 h-lim-p 0.0241 0.9880 2.2140 1485.418279 3 0.0013 187 | 0/8 11 h-lim-p 0.0514 4.4772 0.0560 1485.208847 0 0.4112 202 | 0/8 12 h-lim-p 1.2915 10.3323 0.0161 1485.168187 6 0.4466 238 | 0/8 13 h-lim-p 1.4178 13.5355 0.0051 1485.160134 4 0.7221 267 | 0/8 14 h-lim-p 2.5000 20.0000 0.0013 1485.159828 2 0.5859 292 | 0/8 15 h-lim-p 2.5000 20.0000 0.0002 1485.159818 2 0.8246 318 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1485.159818 0 1.0938 338 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1485.159818 0 1.2500 358 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1485.159818 0 0.3125 380 | 0/8 19 h-lim-p 0.4216 20.0000 0.0000 1485.159818 0 0.0058 405 Out... lnL = -1485.159818 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1485.159818 Node 7: lnL = -1485.159818 Node 8: lnL = -1485.159818 Node 9: lnL = -1485.159818 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 559 Sequential format.. Reading seq # 1: YLR277C_Sbay Reading seq # 2: YLR277C_Scer Reading seq # 3: YLR277C_Skud Reading seq # 4: YLR277C_Smik Reading seq # 5: YLR277C_Spar Sequences read.. Counting patterns.. # site patterns = 257 Counting frequencies.. 120 bytes for distance 41120 bytes for lkl0 32896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.026631 0.064248 0.130903 0.128590 0.125258 0.265715 0.292497 0.498043 lnL0 = -2615.398666 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2615.398666 x= 0.02663 0.06425 0.13090 0.12859 0.12526 0.26571 0.29250 0.49804 1 h-lim-p 0.0032 0.0253 39.8633 2614.945337 7 0.0006 37 | 0/8 2 h-lim-p 0.0017 0.0230 14.0313 2614.880269 5 0.0007 58 | 0/8 3 h-lim-p 0.0011 0.0324 9.5494 2614.859804 6 0.0006 85 | 0/8 4 h-lim-p 0.0029 0.0811 2.0934 2614.857410 3 0.0012 103 | 0/8 5 h-lim-p 0.0026 0.2769 0.9588 2614.856978 2 0.0011 119 | 0/8 6 h-lim-p 0.0029 0.8391 0.3717 2614.856934 2 0.0008 144 | 0/8 7 h-lim-p 0.0498 7.1345 0.0058 2614.856934 0 0.0031 167 | 0/8 8 h-lim-p 0.0698 20.0000 0.0003 2614.856916 0 0.5584 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2614.856916 0 1.0938 210 | 0/8 10 h-lim-p 1.6740 20.0000 0.0000 2614.856916 0 0.8370 230 | 0/8 11 h-lim-p 0.5508 20.0000 0.0000 2614.856916 0 0.0043 256 | 0/8 12 h-lim-p 0.0002 20.0000 0.0002 2614.856916 0 0.0000 294 | 0/8 13 h-lim-p 0.0000 20.0000 0.0002 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -2614.856916 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2614.856916 Node 7: lnL = -2614.856916 Node 8: lnL = -2614.856916 Node 9: lnL = -2614.856916 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 267 Sequential format.. Reading seq # 1: YLR283W_Sbay Reading seq # 2: YLR283W_Scer Reading seq # 3: YLR283W_Skud Reading seq # 4: YLR283W_Smik Reading seq # 5: YLR283W_Spar Sequences read.. Counting patterns.. # site patterns = 125 Counting frequencies.. 120 bytes for distance 20000 bytes for lkl0 16000 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.640272 0.378541 0.651897 0.596208 2.710639 0.735383 1.059795 lnL0 = -1287.894779 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1287.894779 x= 0.00006 0.64027 0.37854 0.65190 0.59621 2.71064 0.73538 1.05979 1 h-lim-p 0.0000 0.0000 105.8433 1287.839924 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0630 16.3012 1283.878666 5 0.0319 53 | 1/8 3 h-lim-p 0.0090 0.0722 9.4116 .. | 1/8 4 h-lim-p 0.0000 0.0109 94.7465 1203.749775 9 0.0090 126 | 1/8 5 h-lim-p 0.0011 0.0089 36.5893 1202.566549 0 0.0022 139 | 1/8 6 h-lim-p 0.0020 0.0158 20.1328 1201.715722 0 0.0059 152 | 1/8 7 h-lim-p 0.0067 0.0538 8.4739 1201.432246 1 0.0084 166 | 1/8 8 h-lim-p 0.0124 0.0991 4.4264 1201.340583 6 0.0076 194 | 0/8 9 h-lim-p 0.0045 0.1234 7.4238 1200.996487 0 0.0136 207 | 0/8 10 h-lim-p 0.0273 0.2180 0.5510 1200.627191 m 0.2180 219 | 1/8 11 h-lim-p 2.3004 18.4029 0.0314 1200.620128 6 0.3166 254 | 0/8 12 h-lim-p 0.0143 1.6036 0.6940 1200.614983 0 0.0286 274 | 0/8 13 h-lim-p 1.4717 11.7732 0.0034 1200.613570 5 1.0478 305 | 0/8 14 h-lim-p 2.5000 20.0000 0.0007 1200.613535 2 1.1719 329 | 0/8 15 h-lim-p 2.5000 20.0000 0.0001 1200.613534 0 1.0938 349 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1200.613534 0 1.2500 369 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1200.613534 0 2.1875 389 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1200.613534 0 1.0938 409 | 0/8 19 h-lim-p 0.2973 20.0000 0.0000 1200.613534 0 0.2973 429 | 0/8 20 h-lim-p 0.0024 20.0000 0.0003 1200.613534 0 0.0024 449 | 0/8 21 h-lim-p 0.0014 20.0000 0.0005 1200.613534 0 0.0000 474 | 0/8 22 h-lim-p 0.0004 20.0000 0.0000 1200.613534 0 0.0000 502 | 0/8 23 h-lim-p 0.0000 20.0000 0.0000 1200.613534 0 0.0000 527 | 0/8 24 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 25 h-lim-p 0.0000 20.0000 0.0000 1200.613534 0 0.0000 594 | 0/8 26 h-lim-p 0.0000 20.0000 0.0000 1200.613534 0 0.0000 626 | 0/8 27 h-lim-p 0.0000 20.0000 0.0000 1200.613534 0 0.0000 651 | 0/8 28 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 29 h-lim-p 0.0000 20.0000 0.0000 | 0/8 30 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1200.613534 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1200.613534 Node 7: lnL = -1200.613534 Node 8: lnL = -1200.613534 Node 9: lnL = -1200.613534 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 334 Sequential format.. Reading seq # 1: YLR284C_Sbay Reading seq # 2: YLR284C_Scer Reading seq # 3: YLR284C_Skud Reading seq # 4: YLR284C_Smik Reading seq # 5: YLR284C_Spar Sequences read.. Counting patterns.. # site patterns = 117 Counting frequencies.. 120 bytes for distance 18720 bytes for lkl0 14976 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.776563 0.241734 0.798194 0.684674 2.384846 0.710394 1.059795 lnL0 = -1594.894728 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1594.894728 x= 0.00006 0.77656 0.24173 0.79819 0.68467 2.38485 0.71039 1.05979 1 h-lim-p 0.0000 0.0000 192.0141 1594.835921 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0525 33.3053 1499.614119 m 0.0525 44 | 1/8 3 h-lim-p 0.0000 0.0000 90.6894 h-lim-p: 1.31089993e-19 1.04871995e-18 9.06894133e+01 1499.614119 .. | 1/8 4 h-lim-p 0.0000 0.0069 174.6667 1490.064754 0 0.0010 70 | 1/8 5 h-lim-p 0.0005 0.0036 166.4047 1439.787862 m 0.0036 82 | 1/8 6 h-lim-p -0.0000 -0.0000 15.4629 h-lim-p: -6.83033584e-19 -5.46426867e-18 1.54629020e+01 1439.787862 .. | 0/8 7 h-lim-p 0.0000 0.0016 121.3713 1432.946835 0 0.0010 108 | 0/8 8 h-lim-p 0.0003 0.0022 28.5742 1432.515723 0 0.0011 122 | 0/8 9 h-lim-p 0.0003 0.0025 32.1108 1430.971600 m 0.0025 134 | 1/8 10 h-lim-p 0.0015 0.0116 4.1467 1430.929425 0 0.0029 147 | 1/8 11 h-lim-p 0.0060 0.0481 1.1616 .. | 1/8 12 h-lim-p 0.0000 0.0771 43.2900 1430.290652 0 0.0006 199 | 1/8 13 h-lim-p 0.0010 0.0559 29.1276 1335.060744 m 0.0559 214 | 2/8 14 h-lim-p 0.0001 0.0005 1226.9873 1334.513409 2 0.0001 230 | 2/8 15 h-lim-p 0.0026 0.0208 16.8142 1334.431699 3 0.0011 248 | 2/8 16 h-lim-p 0.1497 10.1753 0.1220 .. | 2/8 17 h-lim-p 0.0000 0.0035 131.0432 1310.086456 8 0.0026 332 | 1/8 18 h-lim-p 0.0000 0.0002 573.6135 1299.197030 m 0.0002 344 | 2/8 19 h-lim-p 0.0001 0.0011 334.7636 1286.353328 0 0.0006 358 | 2/8 20 h-lim-p 0.0028 0.0224 11.7692 1281.254516 0 0.0084 371 | 1/8 21 h-lim-p 0.0006 0.0048 48.0594 1279.063755 0 0.0012 384 | 1/8 22 h-lim-p 0.0005 0.0037 26.7090 1278.574327 0 0.0014 397 | 1/8 23 h-lim-p 0.0026 0.0207 1.7990 1278.565018 5 0.0028 421 | 1/8 24 h-lim-p 0.0327 2.2159 0.1516 1276.724770 0 0.5237 437 | 0/8 25 h-lim-p 0.0062 0.0494 8.6633 1276.656964 2 0.0029 460 | 0/8 26 h-lim-p 1.9654 20.0000 0.0128 1276.623448 6 1.0810 487 | 0/8 27 h-lim-p 2.5000 20.0000 0.0008 1276.623324 3 0.8800 514 | 0/8 28 h-lim-p 2.5000 20.0000 0.0001 1276.623323 0 1.0938 534 | 0/8 29 h-lim-p 2.5000 20.0000 0.0000 1276.623323 0 1.0938 554 | 0/8 30 h-lim-p 2.5000 20.0000 0.0000 1276.623323 0 0.6250 575 | 0/8 31 h-lim-p 1.8228 20.0000 0.0000 1276.623323 0 0.0142 601 Out... lnL = -1276.623323 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1276.623323 Node 7: lnL = -1276.623323 Node 8: lnL = -1276.623323 Node 9: lnL = -1276.623323 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 342 Sequential format.. Reading seq # 1: YLR285W_Sbay Reading seq # 2: YLR285W_Scer Reading seq # 3: YLR285W_Skud Reading seq # 4: YLR285W_Smik Reading seq # 5: YLR285W_Spar Sequences read.. Counting patterns.. # site patterns = 179 Counting frequencies.. 120 bytes for distance 28640 bytes for lkl0 22912 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.239432 0.080732 0.260075 0.223789 0.086197 0.272371 0.309691 lnL0 = -1514.881233 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1514.881233 x= 0.00006 0.23943 0.08073 0.26008 0.22379 0.08620 0.27237 0.30969 1 h-lim-p 0.0000 0.0000 168.5972 1514.841722 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0023 54.4332 1513.808887 0 0.0006 40 | 1/8 3 h-lim-p 0.0007 0.0101 46.8896 1513.092172 0 0.0011 52 | 1/8 4 h-lim-p 0.0059 0.0599 8.8222 1512.822454 4 0.0046 72 | 1/8 5 h-lim-p 0.0102 0.0821 3.9430 1512.292632 5 0.0114 95 | 1/8 6 h-lim-p 0.0113 0.0937 3.9776 1500.733915 0 0.0454 109 | 0/8 7 h-lim-p 0.0009 0.0070 52.7697 1496.695747 0 0.0017 122 | 0/8 8 h-lim-p 0.0006 0.0046 25.5811 1496.520826 6 0.0006 147 | 0/8 9 h-lim-p 0.0056 0.0451 1.1543 1496.499028 0 0.0226 161 | 0/8 10 h-lim-p 0.1824 1.9334 0.1428 1496.023899 0 0.3649 174 | 0/8 11 h-lim-p 2.2315 17.8520 0.0175 1495.883597 7 0.9463 213 | 0/8 12 h-lim-p 1.7931 20.0000 0.0093 1495.864185 6 0.7612 248 | 0/8 13 h-lim-p 2.2133 20.0000 0.0032 1495.862842 4 0.7081 278 | 0/8 14 h-lim-p 2.5000 20.0000 0.0007 1495.862647 4 0.7412 309 | 0/8 15 h-lim-p 2.5000 20.0000 0.0002 1495.862637 2 0.9644 333 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1495.862637 0 1.0938 353 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1495.862637 0 1.0938 373 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1495.862637 0 1.2500 393 | 0/8 19 h-lim-p 1.4143 20.0000 0.0000 1495.862637 0 2.8285 414 | 0/8 20 h-lim-p 0.2886 20.0000 0.0000 1495.862637 0 0.8657 435 | 0/8 21 h-lim-p 0.1492 20.0000 0.0000 1495.862637 0 0.0006 462 | 0/8 22 h-lim-p 0.0001 20.0000 0.0000 1495.862637 0 0.0001 482 | 0/8 23 h-lim-p 0.0002 20.0000 0.0000 1495.862637 0 0.0002 502 | 0/8 24 h-lim-p 0.0006 20.0000 0.0000 1495.862637 0 0.0000 536 Out... lnL = -1495.862637 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1495.862637 Node 7: lnL = -1495.862637 Node 8: lnL = -1495.862637 Node 9: lnL = -1495.862637 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 866 Sequential format.. Reading seq # 1: YLR286C_Sbay Reading seq # 2: YLR286C_Scer Reading seq # 3: YLR286C_Skud Reading seq # 4: YLR286C_Smik Reading seq # 5: YLR286C_Spar Sequences read.. Counting patterns.. # site patterns = 266 Counting frequencies.. 120 bytes for distance 42560 bytes for lkl0 34048 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.094328 0.035785 0.126273 0.104007 0.152238 0.212848 0.262016 lnL0 = -3659.394549 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3659.394549 x= 0.00006 0.09433 0.03578 0.12627 0.10401 0.15224 0.21285 0.26202 1 h-lim-p 0.0000 0.0000 220.7064 3659.246092 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0177 25.4383 3659.202773 0 0.0002 36 | 1/8 3 h-lim-p 0.0003 0.0190 12.3820 3659.180106 2 0.0003 52 | 1/8 4 h-lim-p 0.0010 0.1005 4.0308 3659.170988 5 0.0007 77 | 1/8 5 h-lim-p 0.0062 0.6341 0.4382 3658.459419 0 0.0497 92 | 0/8 6 h-lim-p 0.0007 0.0098 29.2671 3655.250847 0 0.0030 113 | 0/8 7 h-lim-p 0.0007 0.0059 17.3331 3655.183932 7 0.0005 142 | 0/8 8 h-lim-p 0.0002 0.0020 40.1465 3654.850211 6 0.0014 168 | 0/8 9 h-lim-p 0.0001 0.0006 42.8040 3654.777197 0 0.0003 182 | 0/8 10 h-lim-p 0.0593 0.4741 0.0257 3654.513891 m 0.4741 194 | 1/8 11 h-lim-p 0.4082 12.5895 0.0203 3654.505761 4 0.1449 223 | 0/8 12 h-lim-p 0.0157 2.8645 0.1874 3654.504206 2 0.0147 246 | 0/8 13 h-lim-p 0.0061 0.0489 0.0750 3654.466832 m 0.0489 266 | 1/8 14 h-lim-p 0.8687 20.0000 0.0032 3654.465509 4 0.3186 296 | 1/8 15 h-lim-p 0.5621 20.0000 0.0018 3654.463309 1 0.7026 317 | 0/8 16 h-lim-p -0.0000 -0.0000 0.0204 h-lim-p: -7.54345218e-19 -6.03476175e-18 2.03502581e-02 3654.463309 .. | 1/8 17 h-lim-p 0.0000 0.1014 0.9998 3654.463226 0 0.0002 356 | 1/8 18 h-lim-p 0.0003 0.4133 0.5526 3654.463192 0 0.0003 375 | 1/8 19 h-lim-p 0.0006 0.2155 0.2680 3654.463188 0 0.0001 395 | 1/8 20 h-lim-p 0.0008 6.4939 0.0465 3654.463188 0 0.0003 414 | 1/8 21 h-lim-p 0.0012 15.0109 0.0127 3654.463188 0 0.0005 433 | 1/8 22 h-lim-p 0.0014 20.0000 0.0047 3654.463188 0 0.0003 453 | 1/8 23 h-lim-p 0.0011 20.0000 0.0014 3654.463188 0 0.0005 472 | 1/8 24 h-lim-p 0.0647 20.0000 0.0000 3654.463187 0 1.0357 495 | 1/8 25 h-lim-p 2.5000 20.0000 0.0000 3654.463187 0 1.0938 514 | 1/8 26 h-lim-p 2.5000 20.0000 0.0000 3654.463187 0 3.7500 533 | 1/8 27 h-lim-p 1.3636 20.0000 0.0000 3654.463187 0 0.0000 577 Out... lnL = -3654.463187 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3654.463187 Node 7: lnL = -3654.463187 Node 8: lnL = -3654.463187 Node 9: lnL = -3654.463187 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 505 Sequential format.. Reading seq # 1: YLR287C_Sbay Reading seq # 2: YLR287C_Scer Reading seq # 3: YLR287C_Skud Reading seq # 4: YLR287C_Smik Reading seq # 5: YLR287C_Spar Sequences read.. Counting patterns.. # site patterns = 213 Counting frequencies.. 120 bytes for distance 34080 bytes for lkl0 27264 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.220272 0.030231 0.210200 0.177561 0.215618 0.265893 0.320268 lnL0 = -1989.524786 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1989.524786 x= 0.00006 0.22027 0.03023 0.21020 0.17756 0.21562 0.26589 0.32027 1 h-lim-p 0.0000 0.0000 280.2346 1989.428012 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0042 117.6482 1981.503871 0 0.0013 41 | 1/8 3 h-lim-p 0.0005 0.0037 47.8083 1980.043651 0 0.0019 55 | 1/8 4 h-lim-p 0.0015 0.0122 14.7801 1979.798367 0 0.0023 67 | 1/8 5 h-lim-p 0.0068 0.0699 4.9526 1979.428881 1 0.0085 81 | 1/8 6 h-lim-p 0.0065 0.0516 4.0450 1977.016465 0 0.0194 94 | 1/8 7 h-lim-p 0.0020 0.0159 16.9457 1962.324956 0 0.0080 108 | 1/8 8 h-lim-p 0.0015 0.0119 26.9640 1961.905759 8 0.0011 140 | 1/8 9 h-lim-p 0.1222 0.9775 0.1070 1960.578580 0 0.4888 154 | 1/8 10 h-lim-p 2.5000 20.0000 0.0123 1960.548354 3 0.5664 180 | 1/8 11 h-lim-p 2.5000 20.0000 0.0021 1960.547259 2 0.5859 204 | 1/8 12 h-lim-p 1.0449 20.0000 0.0012 1960.547084 2 0.4571 227 | 1/8 13 h-lim-p 2.5000 20.0000 0.0002 1960.547076 0 0.5469 247 | 1/8 14 h-lim-p 2.3167 20.0000 0.0000 1960.547075 0 1.0136 266 | 0/8 15 h-lim-p -0.0000 -0.0000 0.0004 h-lim-p: -3.73192899e-19 -2.98554319e-18 4.48379704e-04 1960.547075 .. | 1/8 16 h-lim-p 0.0000 14.5865 0.0142 1960.547075 0 0.0006 307 | 1/8 17 h-lim-p 0.0014 20.0000 0.0064 1960.547075 0 0.0006 326 | 1/8 18 h-lim-p 0.0016 20.0000 0.0024 1960.547075 0 0.0004 346 | 1/8 19 h-lim-p 0.0007 20.0000 0.0012 1960.547075 0 0.0007 365 | 1/8 20 h-lim-p 0.0018 20.0000 0.0005 1960.547075 0 0.0008 384 | 1/8 21 h-lim-p 0.0026 20.0000 0.0001 1960.547075 0 0.0038 403 | 1/8 22 h-lim-p 0.0106 20.0000 0.0001 1960.547075 0 0.0093 422 | 1/8 23 h-lim-p 0.0270 20.0000 0.0000 1960.547075 0 0.1082 443 | 1/8 24 h-lim-p 2.5000 20.0000 0.0000 1960.547075 0 0.0391 467 | 1/8 25 h-lim-p 0.0407 20.0000 0.0000 1960.547075 0 0.0000 495 Out... lnL = -1960.547075 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1960.547075 Node 7: lnL = -1960.547075 Node 8: lnL = -1960.547075 Node 9: lnL = -1960.547075 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 192 Sequential format.. Reading seq # 1: YLR288C_Sbay Reading seq # 2: YLR288C_Scer Reading seq # 3: YLR288C_Skud Reading seq # 4: YLR288C_Smik Reading seq # 5: YLR288C_Spar Sequences read.. Counting patterns.. # site patterns = 84 Counting frequencies.. 120 bytes for distance 13440 bytes for lkl0 10752 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.371725 0.111815 0.270231 0.213417 0.272796 0.324823 0.408022 lnL0 = -794.261710 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 794.261710 x= 0.00006 0.37172 0.11182 0.27023 0.21342 0.27280 0.32482 0.40802 1 h-lim-p 0.0000 0.0000 177.3937 794.199303 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0010 278.4176 766.338796 m 0.0010 38 | 1/8 3 h-lim-p 0.0024 0.0190 36.3210 761.884112 0 0.0071 51 | 1/8 4 h-lim-p 0.0006 0.0048 37.3919 760.375197 0 0.0036 65 | 1/8 5 h-lim-p 0.0010 0.0081 27.6786 758.811225 0 0.0061 79 | 1/8 6 h-lim-p 0.0065 0.0521 6.0705 757.341346 m 0.0521 91 | 2/8 7 h-lim-p 0.0060 0.0482 16.4353 756.711526 0 0.0090 103 | 2/8 8 h-lim-p 0.0581 0.4650 1.9020 753.163412 0 0.1744 116 | 1/8 9 h-lim-p 0.0006 0.0047 125.3051 751.340284 0 0.0024 130 | 1/8 10 h-lim-p 0.0750 0.5999 0.5376 750.466830 0 0.1500 143 | 0/8 11 h-lim-p 0.0045 0.0753 17.8150 750.181539 7 0.0019 175 | 0/8 12 h-lim-p 0.0615 1.2504 0.5601 749.204428 0 0.2461 189 | 0/8 13 h-lim-p 0.1084 0.8673 0.1492 748.795498 0 0.3252 210 | 0/8 14 h-lim-p 1.7266 13.8131 0.0217 748.743648 2 0.8094 234 | 0/8 15 h-lim-p 2.5000 20.0000 0.0068 748.734651 4 0.9644 262 | 0/8 16 h-lim-p 1.3585 20.0000 0.0048 748.733847 3 0.5990 288 | 0/8 17 h-lim-p 2.5000 20.0000 0.0009 748.733674 2 1.1719 312 | 0/8 18 h-lim-p 2.5000 20.0000 0.0003 748.733669 0 1.2500 332 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 748.733669 0 1.2500 352 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 748.733669 0 1.0938 372 | 0/8 21 h-lim-p 2.5000 20.0000 0.0000 748.733669 0 0.1562 395 | 0/8 22 h-lim-p 0.1534 20.0000 0.0000 748.733669 0 0.1534 415 | 0/8 23 h-lim-p 0.1505 20.0000 0.0000 748.733669 0 0.0000 453 Out... lnL = -748.733669 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -748.733669 Node 7: lnL = -748.733669 Node 8: lnL = -748.733669 Node 9: lnL = -748.733669 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 192 Sequential format.. Reading seq # 1: YLR289W_Sbay Reading seq # 2: YLR289W_Scer Reading seq # 3: YLR289W_Skud Reading seq # 4: YLR289W_Smik Reading seq # 5: YLR289W_Spar Sequences read.. Counting patterns.. # site patterns = 64 Counting frequencies.. 120 bytes for distance 10240 bytes for lkl0 8192 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.796278 0.309188 0.745971 0.649370 2.361875 0.717977 1.059795 lnL0 = -918.014497 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 918.014497 x= 0.00006 0.79628 0.30919 0.74597 0.64937 2.36187 0.71798 1.05979 1 h-lim-p 0.0000 0.0000 125.3550 917.970646 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0760 13.1069 900.255131 m 0.0760 43 | 2/8 3 h-lim-p 0.0050 0.0402 23.7281 893.797664 m 0.0402 55 | 3/8 4 h-lim-p 0.0177 0.1415 4.7567 881.238177 0 0.1061 69 | 2/8 5 h-lim-p 0.0007 0.0059 167.6266 789.032516 m 0.0059 81 | 2/8 6 h-lim-p -0.0000 -0.0000 73.1239 h-lim-p: -4.92337024e-18 -3.93869619e-17 7.31238542e+01 789.032516 .. | 1/8 7 h-lim-p 0.0000 0.0030 514.0509 777.496855 0 0.0002 105 | 1/8 8 h-lim-p 0.0002 0.0013 166.9735 766.004655 0 0.0009 119 | 1/8 9 h-lim-p 0.0013 0.0107 35.1534 751.906911 m 0.0107 131 | 2/8 10 h-lim-p 0.0001 0.0011 510.3598 740.517727 m 0.0011 143 | 3/8 11 h-lim-p 0.0105 0.0839 8.3083 738.660239 0 0.0210 156 | 2/8 12 h-lim-p 0.0021 0.0166 36.8758 737.710643 0 0.0041 169 | 2/8 13 h-lim-p 0.0246 0.1968 1.1558 .. | 2/8 14 h-lim-p 0.0000 0.0028 110.6057 721.325722 0 0.0019 224 | 1/8 15 h-lim-p 0.0000 0.0001 784.2558 717.774848 0 0.0001 238 | 1/8 16 h-lim-p 0.0010 0.0083 59.4047 709.493539 0 0.0041 252 | 1/8 17 h-lim-p 0.0042 0.0333 25.3968 709.008590 2 0.0020 268 | 1/8 18 h-lim-p 0.0140 0.1119 2.3044 708.945472 4 0.0071 289 | 1/8 19 h-lim-p 0.0400 0.8285 0.4107 706.418728 0 0.1599 303 | 1/8 20 h-lim-p 1.6953 14.5338 0.0387 706.061706 5 0.9018 333 | 0/8 21 h-lim-p 0.0329 3.1013 1.0613 706.060271 5 0.0025 368 | 0/8 22 h-lim-p 0.4306 20.0000 0.0061 706.017282 0 1.7225 382 | 0/8 23 h-lim-p 0.8274 6.6194 0.0045 706.012652 0 1.2411 402 | 0/8 24 h-lim-p 2.5000 20.0000 0.0008 706.012535 3 1.0004 428 | 0/8 25 h-lim-p 2.5000 20.0000 0.0000 706.012535 0 1.0938 448 | 0/8 26 h-lim-p 2.5000 20.0000 0.0000 706.012535 0 1.0938 468 | 0/8 27 h-lim-p 1.5032 20.0000 0.0000 706.012535 0 0.0029 496 Out... lnL = -706.012535 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -706.012535 Node 7: lnL = -706.012535 Node 8: lnL = -706.012535 Node 9: lnL = -706.012535 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 357 Sequential format.. Reading seq # 1: YLR290C_Sbay Reading seq # 2: YLR290C_Scer Reading seq # 3: YLR290C_Skud Reading seq # 4: YLR290C_Smik Reading seq # 5: YLR290C_Spar Sequences read.. Counting patterns.. # site patterns = 145 Counting frequencies.. 120 bytes for distance 23200 bytes for lkl0 18560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.127176 0.111006 0.175057 0.117173 0.154120 0.219184 0.292667 lnL0 = -1588.017907 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1588.017907 x= 0.00006 0.12718 0.11101 0.17506 0.11717 0.15412 0.21918 0.29267 1 h-lim-p 0.0000 0.0000 178.2247 1587.949373 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0056 38.3909 1587.317804 0 0.0013 41 | 1/8 3 h-lim-p 0.0012 0.0094 14.3502 1587.203368 3 0.0011 59 | 1/8 4 h-lim-p 0.0022 0.0364 6.9589 1587.113229 6 0.0023 84 | 1/8 5 h-lim-p 0.0130 0.1623 1.2591 1585.589221 0 0.0519 98 | 1/8 6 h-lim-p 0.0016 0.0126 16.8855 1578.161365 0 0.0063 112 | 1/8 7 h-lim-p 0.0006 0.0048 41.7678 1577.409579 0 0.0009 124 | 1/8 8 h-lim-p 0.0011 0.0086 31.3177 1577.079858 7 0.0009 153 | 1/8 9 h-lim-p 0.4265 6.2510 0.0639 1576.252792 7 0.4474 178 | 0/8 10 h-lim-p 0.0052 0.3216 5.5348 1576.233448 4 0.0013 206 | 0/8 11 h-lim-p 0.5888 5.8264 0.0124 1576.198097 3 0.5336 224 | 0/8 12 h-lim-p 2.4802 20.0000 0.0027 1576.195973 5 0.7904 256 | 0/8 13 h-lim-p 2.5000 20.0000 0.0004 1576.195876 2 1.0889 280 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1576.195875 0 1.0938 300 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1576.195875 0 1.0938 320 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1576.195875 0 1.0938 340 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1576.195875 0 5.0000 361 | 0/8 18 h-lim-p 1.4857 20.0000 0.0000 1576.195875 0 0.0232 386 | 0/8 19 h-lim-p 0.0257 20.0000 0.0000 1576.195875 0 0.0113 406 Out... lnL = -1576.195875 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1576.195875 Node 7: lnL = -1576.195875 Node 8: lnL = -1576.195875 Node 9: lnL = -1576.195875 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 343 Sequential format.. Reading seq # 1: YLR291C_Sbay Reading seq # 2: YLR291C_Scer Reading seq # 3: YLR291C_Skud Reading seq # 4: YLR291C_Smik Reading seq # 5: YLR291C_Spar Sequences read.. Counting patterns.. # site patterns = 141 Counting frequencies.. 120 bytes for distance 22560 bytes for lkl0 18048 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.089751 0.074148 0.132791 0.112265 0.157219 0.218391 0.294895 lnL0 = -1525.438347 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1525.438347 x= 0.00006 0.08975 0.07415 0.13279 0.11226 0.15722 0.21839 0.29490 1 h-lim-p 0.0000 0.0000 88.3280 1525.388134 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0194 12.4464 1525.348966 0 0.0007 38 | 1/8 3 h-lim-p 0.0024 0.0519 3.7442 1525.338888 2 0.0011 54 | 1/8 4 h-lim-p 0.0018 0.1469 2.3377 1525.321887 0 0.0036 67 | 1/8 5 h-lim-p 0.0209 0.5888 0.4045 1524.516682 0 0.0837 81 | 0/8 6 h-lim-p 0.0008 0.0062 20.2526 1523.454462 0 0.0016 101 | 0/8 7 h-lim-p 0.0009 0.0076 17.1258 1523.283174 6 0.0010 128 | 0/8 8 h-lim-p 0.0004 0.0034 3.8553 1523.276052 0 0.0008 141 | 0/8 9 h-lim-p 0.0003 0.0022 1.5544 1523.274664 0 0.0016 155 | 0/8 10 h-lim-p 0.9902 20.0000 0.0026 1523.271032 3 0.7924 173 | 0/8 11 h-lim-p 2.5000 20.0000 0.0003 1523.270978 3 0.8171 200 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1523.270978 0 1.0938 220 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1523.270978 0 1.0938 240 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1523.270978 0 0.5469 261 | 0/8 15 h-lim-p 1.1214 20.0000 0.0000 1523.270978 0 0.1402 283 | 0/8 16 h-lim-p 0.1419 20.0000 0.0000 1523.270978 0 0.0355 304 | 0/8 17 h-lim-p 0.0309 20.0000 0.0000 1523.270978 0 0.0000 338 Out... lnL = -1523.270978 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1523.270978 Node 7: lnL = -1523.270978 Node 8: lnL = -1523.270978 Node 9: lnL = -1523.270978 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 414 Sequential format.. Reading seq # 1: YLR292C_Sbay Reading seq # 2: YLR292C_Scer Reading seq # 3: YLR292C_Skud Reading seq # 4: YLR292C_Smik Reading seq # 5: YLR292C_Spar Sequences read.. Counting patterns.. # site patterns = 147 Counting frequencies.. 120 bytes for distance 23520 bytes for lkl0 18816 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.024450 0.027994 0.014997 0.117899 0.109115 0.151628 0.110494 0.261811 lnL0 = -1705.983072 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1705.983072 x= 0.02445 0.02799 0.01500 0.11790 0.10911 0.15163 0.11049 0.26181 1 h-lim-p 0.0010 0.0305 180.5275 1704.613505 5 0.0001 34 | 0/8 2 h-lim-p 0.0010 0.0101 17.7947 1704.563012 6 0.0003 60 | 0/8 3 h-lim-p 0.0009 0.0092 6.5715 1704.556287 3 0.0003 78 | 0/8 4 h-lim-p 0.0017 0.2256 1.3472 1704.555903 4 0.0004 99 | 0/8 5 h-lim-p 0.0032 0.7018 0.1880 1704.555896 2 0.0004 117 | 0/8 6 h-lim-p 0.0120 20.0000 0.0066 1704.555895 0 0.0052 137 | 0/8 7 h-lim-p 0.0180 20.0000 0.0019 1704.555746 0 0.1444 160 | 0/8 8 h-lim-p 0.0009 0.2120 0.2971 1704.555681 2 0.0009 184 | 0/8 9 h-lim-p 1.4870 20.0000 0.0002 1704.555679 1 1.1850 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1704.555679 0 1.0938 226 | 0/8 11 h-lim-p 0.8149 20.0000 0.0000 1704.555679 0 1.2223 246 | 0/8 12 h-lim-p 0.9663 20.0000 0.0000 1704.555679 0 0.0151 271 | 0/8 13 h-lim-p 0.0001 7.4910 0.0053 1704.555679 0 0.0001 291 | 0/8 14 h-lim-p 0.0001 20.0000 0.0030 1704.555679 0 0.0000 321 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 1704.555679 0 0.0000 351 Out... lnL = -1704.555679 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1704.555679 Node 7: lnL = -1704.555679 Node 8: lnL = -1704.555679 Node 9: lnL = -1704.555679 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 284 Sequential format.. Reading seq # 1: YLR293C_Sbay Reading seq # 2: YLR293C_Scer Reading seq # 3: YLR293C_Skud Reading seq # 4: YLR293C_Smik Reading seq # 5: YLR293C_Spar Sequences read.. Counting patterns.. # site patterns = 86 Counting frequencies.. 120 bytes for distance 13760 bytes for lkl0 11008 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.065842 0.026121 0.090381 0.074782 0.060005 0.110693 0.133934 lnL0 = -936.347361 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 936.347361 x= 0.00006 0.06584 0.02612 0.09038 0.07478 0.06001 0.11069 0.13393 1 h-lim-p 0.0000 0.0000 119.3308 936.307445 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0010 55.3676 936.071361 0 0.0002 38 | 1/8 3 h-lim-p 0.0006 0.0060 13.6540 936.050604 7 0.0002 68 | 1/8 4 h-lim-p 0.0019 0.0948 1.6565 936.042673 2 0.0018 84 | 1/8 5 h-lim-p 0.0023 0.1172 1.2747 935.958595 0 0.0094 98 | 1/8 6 h-lim-p 0.0025 0.0279 4.7251 935.083912 0 0.0051 111 | 1/8 7 h-lim-p 0.0006 0.0045 24.2026 933.679636 0 0.0011 124 | 1/8 8 h-lim-p 0.0060 0.0479 2.7587 933.677426 5 0.0006 148 | 1/8 9 h-lim-p 0.1764 20.0000 0.0088 933.525794 0 1.4108 163 | 1/8 10 h-lim-p 2.5000 20.0000 0.0036 933.509634 6 0.9136 196 | 0/8 11 h-lim-p 0.0319 20.0000 0.1038 933.509630 2 0.0007 225 | 0/8 12 h-lim-p 0.1380 1.1039 0.0004 933.509391 m 1.1039 245 | 1/8 13 h-lim-p 2.5000 20.0000 0.0002 933.509363 3 0.8171 272 | 0/8 14 h-lim-p 0.0062 11.5174 0.0205 933.509363 0 0.0007 293 | 0/8 15 h-lim-p 0.1260 1.0083 0.0000 933.509361 m 1.0083 313 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 933.509361 0 1.0938 333 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 933.509361 0 1.0938 352 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 933.509361 0 1.0938 371 | 1/8 19 h-lim-p 2.5000 20.0000 0.0000 933.509361 0 0.0012 400 Out... lnL = -933.509361 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -933.509361 Node 7: lnL = -933.509361 Node 8: lnL = -933.509361 Node 9: lnL = -933.509361 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 676 Sequential format.. Reading seq # 1: YLR295C_Sbay Reading seq # 2: YLR295C_Scer Reading seq # 3: YLR295C_Skud Reading seq # 4: YLR295C_Smik Reading seq # 5: YLR295C_Spar Sequences read.. Counting patterns.. # site patterns = 303 Counting frequencies.. 120 bytes for distance 48480 bytes for lkl0 38784 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.058391 0.111096 0.091483 0.153419 0.087124 0.213251 0.315223 0.527055 lnL0 = -3277.249450 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3277.249450 x= 0.05839 0.11110 0.09148 0.15342 0.08712 0.21325 0.31522 0.52705 1 h-lim-p 0.0005 0.0037 81.0152 3275.678915 7 0.0005 37 | 0/8 2 h-lim-p 0.0011 0.0089 22.6655 3275.511908 8 0.0007 71 | 0/8 3 h-lim-p 0.0016 0.0579 9.6288 3275.483411 3 0.0007 89 | 0/8 4 h-lim-p 0.0006 0.0291 12.0705 3275.466609 4 0.0005 109 | 0/8 5 h-lim-p 0.0010 0.0616 5.6930 3275.459221 5 0.0007 134 | 0/8 6 h-lim-p 0.0044 0.1316 0.9453 3275.458504 2 0.0017 150 | 0/8 7 h-lim-p 0.0192 3.1764 0.0828 3275.458499 1 0.0012 175 | 0/8 8 h-lim-p 0.1138 20.0000 0.0009 3275.457939 0 0.9105 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3275.457934 0 1.0938 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3275.457934 0 1.0938 238 | 0/8 11 h-lim-p 1.5658 20.0000 0.0000 3275.457934 0 1.3700 258 | 0/8 12 h-lim-p 1.4204 20.0000 0.0000 3275.457934 0 2.1306 278 | 0/8 13 h-lim-p 0.4421 20.0000 0.0000 3275.457934 0 0.0069 303 | 0/8 14 h-lim-p 0.0007 20.0000 0.0004 3275.457934 0 0.0000 335 | 0/8 15 h-lim-p 0.0004 20.0000 0.0000 3275.457934 0 0.0000 365 Out... lnL = -3275.457934 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3275.457934 Node 7: lnL = -3275.457934 Node 8: lnL = -3275.457934 Node 9: lnL = -3275.457934 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 811 Sequential format.. Reading seq # 1: YLR297W_Sbay Reading seq # 2: YLR297W_Scer Reading seq # 3: YLR297W_Skud Reading seq # 4: YLR297W_Smik Reading seq # 5: YLR297W_Spar Sequences read.. Counting patterns.. # site patterns = 220 Counting frequencies.. 120 bytes for distance 35200 bytes for lkl0 28160 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.209743 0.035717 0.036382 0.061308 0.050774 0.124210 0.123795 0.111752 lnL0 = -3054.966882 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3054.966882 x= 0.20974 0.03572 0.03638 0.06131 0.05077 0.12421 0.12380 0.11175 1 h-lim-p 0.0015 0.6266 200.4590 3053.072261 8 0.0001 40 | 0/8 2 h-lim-p 0.0002 0.0018 42.4224 3052.909934 3 0.0002 58 | 0/8 3 h-lim-p 0.0004 0.0100 19.2201 3052.885243 4 0.0002 78 | 0/8 4 h-lim-p 0.0003 0.0136 9.9076 3052.880058 4 0.0001 97 | 0/8 5 h-lim-p 0.0008 0.1079 1.7634 3052.879594 3 0.0003 115 | 0/8 6 h-lim-p 0.0033 0.6208 0.1705 3052.879591 0 0.0002 130 | 0/8 7 h-lim-p 0.0003 1.5649 0.1084 3052.879590 0 0.0003 150 | 0/8 8 h-lim-p 0.1090 20.0000 0.0003 3052.879213 0 1.3079 173 | 0/8 9 h-lim-p 1.0583 20.0000 0.0003 3052.879195 0 0.9260 193 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3052.879195 0 1.0938 213 | 0/8 11 h-lim-p 1.8405 20.0000 0.0000 3052.879195 0 1.6104 233 | 0/8 12 h-lim-p 1.6294 20.0000 0.0000 3052.879195 0 1.4258 253 | 0/8 13 h-lim-p 1.1530 20.0000 0.0000 3052.879195 0 1.0088 273 | 0/8 14 h-lim-p 0.5483 20.0000 0.0000 3052.879195 0 0.0685 295 | 0/8 15 h-lim-p 0.0054 20.0000 0.0002 3052.879195 0 0.0003 318 | 0/8 16 h-lim-p 0.0003 20.0000 0.0002 3052.879195 0 0.0000 356 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -3052.879195 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3052.879195 Node 7: lnL = -3052.879195 Node 8: lnL = -3052.879195 Node 9: lnL = -3052.879195 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 709 Sequential format.. Reading seq # 1: YLR298C_Sbay Reading seq # 2: YLR298C_Scer Reading seq # 3: YLR298C_Skud Reading seq # 4: YLR298C_Smik Reading seq # 5: YLR298C_Spar Sequences read.. Counting patterns.. # site patterns = 265 Counting frequencies.. 120 bytes for distance 42400 bytes for lkl0 33920 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.263038 0.073041 0.046193 0.150270 0.093797 0.209822 0.221617 0.110659 lnL0 = -3242.427120 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3242.427120 x= 0.26304 0.07304 0.04619 0.15027 0.09380 0.20982 0.22162 0.11066 1 h-lim-p 0.0022 0.0176 116.6784 3241.140049 8 0.0002 42 | 0/8 2 h-lim-p 0.0008 0.0061 26.6035 3241.025468 6 0.0003 65 | 0/8 3 h-lim-p 0.0007 0.0170 12.0545 3241.000637 7 0.0004 93 | 0/8 4 h-lim-p 0.0009 0.0444 5.6951 3240.994590 4 0.0005 114 | 0/8 5 h-lim-p 0.0050 0.5353 0.5286 3240.994502 2 0.0007 132 | 0/8 6 h-lim-p 0.0171 10.7153 0.0203 3240.994502 0 0.0009 155 | 0/8 7 h-lim-p 0.0055 20.0000 0.0034 3240.994502 0 0.0024 175 | 0/8 8 h-lim-p 0.0280 20.0000 0.0003 3240.994489 0 0.3360 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3240.994489 0 1.0938 218 | 0/8 10 h-lim-p 2.3781 20.0000 0.0000 3240.994489 0 2.0809 238 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3240.994489 0 1.0938 258 | 0/8 12 h-lim-p 0.1952 20.0000 0.0000 3240.994489 0 3.1231 282 | 0/8 13 h-lim-p 2.0195 20.0000 0.0000 3240.994489 0 0.0158 308 | 0/8 14 h-lim-p 0.0014 20.0000 0.0002 3240.994489 0 0.0000 345 | 0/8 15 h-lim-p 0.0000 20.0000 0.0012 | 0/8 16 h-lim-p 0.0000 20.0000 0.0012 Out... lnL = -3240.994489 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3240.994489 Node 7: lnL = -3240.994489 Node 8: lnL = -3240.994489 Node 9: lnL = -3240.994489 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 712 Sequential format.. Reading seq # 1: YLR299W_Sbay Reading seq # 2: YLR299W_Scer Reading seq # 3: YLR299W_Skud Reading seq # 4: YLR299W_Smik Reading seq # 5: YLR299W_Spar Sequences read.. Counting patterns.. # site patterns = 267 Counting frequencies.. 120 bytes for distance 42720 bytes for lkl0 34176 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.252688 0.072598 0.036853 0.146961 0.097106 0.213957 0.233753 0.102418 lnL0 = -3236.581998 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3236.581998 x= 0.25269 0.07260 0.03685 0.14696 0.09711 0.21396 0.23375 0.10242 1 h-lim-p 0.0036 0.9387 133.6647 3235.139849 8 0.0002 40 | 0/8 2 h-lim-p 0.0007 0.0060 28.5329 3235.005277 2 0.0003 56 | 0/8 3 h-lim-p 0.0010 0.0170 9.6164 3234.989694 6 0.0004 84 | 0/8 4 h-lim-p 0.0008 0.0600 4.6060 3234.984991 5 0.0005 109 | 0/8 5 h-lim-p 0.0045 0.4789 0.5511 3234.984896 3 0.0007 130 | 0/8 6 h-lim-p 0.0246 10.7848 0.0151 3234.984896 0 0.0013 153 | 0/8 7 h-lim-p 0.0046 20.0000 0.0044 3234.984895 0 0.0046 173 | 0/8 8 h-lim-p 0.0065 20.0000 0.0031 3234.984817 0 0.0782 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3234.984815 0 1.0938 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3234.984815 0 1.0938 236 | 0/8 11 h-lim-p 1.0973 20.0000 0.0000 3234.984815 0 0.0150 261 | 0/8 12 h-lim-p 0.0054 20.0000 0.0000 3234.984815 0 0.0003 284 | 0/8 13 h-lim-p 0.0012 20.0000 0.0000 3234.984815 0 0.0000 317 Out... lnL = -3234.984815 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3234.984815 Node 7: lnL = -3234.984815 Node 8: lnL = -3234.984815 Node 9: lnL = -3234.984815 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 857 Sequential format.. Reading seq # 1: YLR300W_Sbay Reading seq # 2: YLR300W_Scer Reading seq # 3: YLR300W_Skud Reading seq # 4: YLR300W_Smik Reading seq # 5: YLR300W_Spar Sequences read.. Counting patterns.. # site patterns = 280 Counting frequencies.. 120 bytes for distance 44800 bytes for lkl0 35840 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.214086 0.036111 0.078695 0.072005 0.052074 0.168889 0.204756 0.092871 lnL0 = -3447.676066 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3447.676066 x= 0.21409 0.03611 0.07870 0.07200 0.05207 0.16889 0.20476 0.09287 1 h-lim-p 0.0020 0.0162 176.4406 3445.706005 7 0.0001 39 | 0/8 2 h-lim-p 0.0005 0.0038 28.1327 3445.646866 5 0.0002 63 | 0/8 3 h-lim-p 0.0002 0.0077 20.5638 3445.613533 4 0.0002 83 | 0/8 4 h-lim-p 0.0009 0.0464 5.0453 3445.609538 4 0.0003 103 | 0/8 5 h-lim-p 0.0021 0.3082 0.8295 3445.609424 2 0.0003 122 | 0/8 6 h-lim-p 0.0008 0.3868 0.3490 3445.609414 0 0.0002 143 | 0/8 7 h-lim-p 0.0013 8.1976 0.0491 3445.609413 1 0.0006 166 | 0/8 8 h-lim-p 0.0538 20.0000 0.0006 3445.608714 0 0.8616 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3445.608712 0 1.0938 210 | 0/8 10 h-lim-p 1.9273 20.0000 0.0000 3445.608712 0 1.6864 230 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3445.608712 0 1.0938 250 | 0/8 12 h-lim-p 0.3870 20.0000 0.0000 3445.608712 0 1.1610 271 | 0/8 13 h-lim-p 0.1618 20.0000 0.0001 3445.608712 0 0.0000 304 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 3445.608712 0 0.0000 332 Out... lnL = -3445.608712 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3445.608712 Node 7: lnL = -3445.608712 Node 8: lnL = -3445.608712 Node 9: lnL = -3445.608712 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 840 Sequential format.. Reading seq # 1: YLR303W_Sbay Reading seq # 2: YLR303W_Scer Reading seq # 3: YLR303W_Skud Reading seq # 4: YLR303W_Smik Reading seq # 5: YLR303W_Spar Sequences read.. Counting patterns.. # site patterns = 337 Counting frequencies.. 120 bytes for distance 53920 bytes for lkl0 43136 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.208159 0.047527 0.034609 0.173870 0.139957 0.233807 0.269171 0.058441 lnL0 = -4123.527898 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4123.527898 x= 0.20816 0.04753 0.03461 0.17387 0.13996 0.23381 0.26917 0.05844 1 h-lim-p 0.0004 0.3310 436.6992 4111.983564 9 0.0001 45 | 0/8 2 h-lim-p 0.0006 0.0044 41.4932 4111.608302 5 0.0004 67 | 0/8 3 h-lim-p 0.0024 0.0214 7.5885 4111.599282 5 0.0003 91 | 0/8 4 h-lim-p 0.0018 0.2917 1.3971 4111.598646 3 0.0007 109 | 0/8 5 h-lim-p 0.0036 0.6050 0.2572 4111.598633 0 0.0005 123 | 0/8 6 h-lim-p 0.0017 6.2829 0.0669 4111.598631 0 0.0008 143 | 0/8 7 h-lim-p 0.0048 20.0000 0.0106 4111.598628 0 0.0072 163 | 0/8 8 h-lim-p 0.0178 20.0000 0.0043 4111.597956 0 0.1426 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4111.597950 0 1.0938 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4111.597950 0 1.0938 226 | 0/8 11 h-lim-p 1.7676 20.0000 0.0000 4111.597950 0 1.5466 246 | 0/8 12 h-lim-p 0.8680 20.0000 0.0000 4111.597950 0 1.7360 267 | 0/8 13 h-lim-p 0.0015 7.5656 0.0387 4111.597950 0 0.0000 295 | 0/8 14 h-lim-p 0.0005 20.0000 0.0003 4111.597950 0 0.0000 330 | 0/8 15 h-lim-p 0.0000 20.0000 0.0008 | 0/8 16 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -4111.597950 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4111.597950 Node 7: lnL = -4111.597950 Node 8: lnL = -4111.597950 Node 9: lnL = -4111.597950 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 315 Sequential format.. Reading seq # 1: YLR305C_Sbay Reading seq # 2: YLR305C_Scer Reading seq # 3: YLR305C_Skud Reading seq # 4: YLR305C_Smik Reading seq # 5: YLR305C_Spar Sequences read.. Counting patterns.. # site patterns = 139 Counting frequencies.. 120 bytes for distance 22240 bytes for lkl0 17792 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.174822 0.000060 0.088630 0.162144 0.066132 0.184377 0.205205 0.053947 lnL0 = -1235.071731 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1235.071731 x= 0.17482 0.00006 0.08863 0.16214 0.06613 0.18438 0.20521 0.05395 1 h-lim-p 0.0037 1.6885 81.9307 1233.667544 3 0.0004 30 | 0/8 2 h-lim-p 0.0004 0.0033 21.0780 1233.542718 0 0.0006 42 | 0/8 3 h-lim-p 0.0020 0.0196 6.5263 1233.526767 3 0.0008 60 | 0/8 4 h-lim-p 0.0032 0.1817 1.6880 1233.525345 5 0.0011 85 | 0/8 5 h-lim-p 0.0098 0.9273 0.1836 1233.525320 3 0.0014 107 | 0/8 6 h-lim-p 0.0066 2.2030 0.0400 1233.525318 1 0.0013 130 | 0/8 7 h-lim-p 0.0129 20.0000 0.0041 1233.525275 0 0.0776 152 | 0/8 8 h-lim-p 0.0058 11.4872 0.0545 1233.524907 0 0.0116 173 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1233.524899 1 1.0938 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1233.524899 0 1.0938 215 | 0/8 11 h-lim-p 1.4833 20.0000 0.0000 1233.524899 0 2.9666 236 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1233.524899 0 0.5469 257 | 0/8 13 h-lim-p 0.0796 20.0000 0.0001 1233.524899 0 0.0174 278 | 0/8 14 h-lim-p 0.0052 20.0000 0.0002 1233.524899 0 0.0000 310 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 1233.524899 0 0.0000 345 Out... lnL = -1233.524899 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1233.524899 Node 7: lnL = -1233.524899 Node 8: lnL = -1233.524899 Node 9: lnL = -1233.524899 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 811 Sequential format.. Reading seq # 1: YLR307W_Sbay Reading seq # 2: YLR307W_Scer Reading seq # 3: YLR307W_Skud Reading seq # 4: YLR307W_Smik Reading seq # 5: YLR307W_Spar Sequences read.. Counting patterns.. # site patterns = 375 Counting frequencies.. 120 bytes for distance 60000 bytes for lkl0 48000 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.345136 0.038345 0.080867 0.238868 0.154571 0.286313 0.257106 0.145786 lnL0 = -4125.217040 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4125.217040 x= 0.34514 0.03834 0.08087 0.23887 0.15457 0.28631 0.25711 0.14579 1 h-lim-p 0.0053 0.0424 101.4106 4123.790442 7 0.0003 37 | 0/8 2 h-lim-p 0.0011 0.0108 26.3183 4123.568750 7 0.0007 68 | 0/8 3 h-lim-p 0.0016 0.0173 11.3002 4123.544201 6 0.0005 96 | 0/8 4 h-lim-p 0.0034 0.1102 1.5132 4123.543513 4 0.0006 119 | 0/8 5 h-lim-p 0.0042 0.7894 0.2236 4123.543498 2 0.0006 137 | 0/8 6 h-lim-p 0.0526 20.0000 0.0024 4123.543498 0 0.0057 159 | 0/8 7 h-lim-p 0.0071 20.0000 0.0019 4123.543496 0 0.0286 181 | 0/8 8 h-lim-p 0.0026 5.2191 0.0208 4123.543487 0 0.0052 202 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4123.543487 0 1.0938 222 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4123.543487 0 1.0938 242 | 0/8 11 h-lim-p 0.9774 20.0000 0.0000 4123.543487 0 2.9321 263 | 0/8 12 h-lim-p 0.6042 20.0000 0.0000 4123.543487 0 0.0378 286 | 0/8 13 h-lim-p 0.0014 20.0000 0.0009 4123.543487 0 0.0000 311 | 0/8 14 h-lim-p 0.0029 20.0000 0.0000 4123.543487 0 0.0000 350 Out... lnL = -4123.543487 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4123.543487 Node 7: lnL = -4123.543487 Node 8: lnL = -4123.543487 Node 9: lnL = -4123.543487 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 846 Sequential format.. Reading seq # 1: YLR308W_Sbay Reading seq # 2: YLR308W_Scer Reading seq # 3: YLR308W_Skud Reading seq # 4: YLR308W_Smik Reading seq # 5: YLR308W_Spar Sequences read.. Counting patterns.. # site patterns = 264 Counting frequencies.. 120 bytes for distance 42240 bytes for lkl0 33792 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.242023 0.202807 0.263358 0.174241 0.298916 0.689641 0.373325 0.000060 lnL0 = -3535.144500 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3535.144500 x= 0.24202 0.20281 0.26336 0.17424 0.29892 0.68964 0.37332 0.00006 1 h-lim-p 0.0000 0.0000 555.9709 3534.636138 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0010 513.0347 3446.439056 1 0.0007 42 | 1/8 3 h-lim-p 0.0005 0.0040 74.3677 3443.943699 0 0.0010 55 | 1/8 4 h-lim-p 0.0023 0.0185 29.9738 3443.445330 7 0.0012 84 | 1/8 5 h-lim-p 0.0006 0.0169 56.1630 3442.328694 0 0.0019 97 | 1/8 6 h-lim-p 0.0020 0.0215 51.5310 3439.473727 0 0.0082 111 | 1/8 7 h-lim-p 0.0121 0.0964 2.2044 3431.968398 m 0.0964 123 | 2/8 8 h-lim-p 0.0015 0.0123 19.5033 3431.810266 5 0.0008 145 | 2/8 9 h-lim-p 0.0555 1.4110 0.2676 3414.977276 0 0.6658 160 | 1/8 10 h-lim-p 0.0096 0.0793 18.5478 3414.891776 6 0.0005 197 | 1/8 11 h-lim-p 0.0848 4.0459 0.1115 3414.157890 0 0.3393 211 | 1/8 12 h-lim-p 0.3191 7.3778 0.1185 3413.811807 0 0.6382 231 | 0/8 13 h-lim-p 0.0254 0.4505 2.9763 3413.809694 2 0.0007 258 | 0/8 14 h-lim-p 0.0258 12.6964 0.0859 3413.657204 0 1.2387 275 | 0/8 15 h-lim-p 1.9801 15.8410 0.0177 3413.329913 0 3.9603 296 | 0/8 16 h-lim-p 0.9701 7.7610 0.0240 3413.293350 4 0.7608 324 | 0/8 17 h-lim-p 2.5000 20.0000 0.0030 3413.292644 2 1.0889 348 | 0/8 18 h-lim-p 2.5000 20.0000 0.0006 3413.292616 2 0.9644 372 | 0/8 19 h-lim-p 2.5000 20.0000 0.0001 3413.292615 0 1.0938 392 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 3413.292615 0 1.0938 412 | 0/8 21 h-lim-p 2.5000 20.0000 0.0000 3413.292615 0 1.0938 432 | 0/8 22 h-lim-p 2.5000 20.0000 0.0000 3413.292615 0 0.2734 454 | 0/8 23 h-lim-p 0.3506 20.0000 0.0000 3413.292615 0 0.0877 475 | 0/8 24 h-lim-p 0.0870 20.0000 0.0000 3413.292615 0 0.0000 517 Out... lnL = -3413.292615 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3413.292615 Node 7: lnL = -3413.292615 Node 8: lnL = -3413.292615 Node 9: lnL = -3413.292615 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 284 Sequential format.. Reading seq # 1: YLR310C_Sbay Reading seq # 2: YLR310C_Scer Reading seq # 3: YLR310C_Skud Reading seq # 4: YLR310C_Smik Reading seq # 5: YLR310C_Spar Sequences read.. Counting patterns.. # site patterns = 99 Counting frequencies.. 120 bytes for distance 15840 bytes for lkl0 12672 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.176627 0.028841 0.065816 0.041884 0.065442 0.106546 0.189010 0.077488 lnL0 = -1116.911452 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1116.911452 x= 0.17663 0.02884 0.06582 0.04188 0.06544 0.10655 0.18901 0.07749 1 h-lim-p 0.0020 0.0161 70.2552 1116.294844 8 0.0003 41 | 0/8 2 h-lim-p 0.0011 0.0089 13.7377 1116.237284 8 0.0006 73 | 0/8 3 h-lim-p 0.0014 0.0282 6.0463 1116.232661 4 0.0003 95 | 0/8 4 h-lim-p 0.0008 0.0400 2.1929 1116.231911 2 0.0004 111 | 0/8 5 h-lim-p 0.0009 0.2417 0.8595 1116.231665 2 0.0008 127 | 0/8 6 h-lim-p 0.0023 0.4644 0.2952 1116.231649 2 0.0004 152 | 0/8 7 h-lim-p 0.0015 3.8693 0.0899 1116.231647 1 0.0006 174 | 0/8 8 h-lim-p 0.5820 20.0000 0.0001 1116.231634 0 1.1641 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1116.231634 0 1.0938 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1116.231634 0 0.6250 236 | 0/8 11 h-lim-p 0.4205 20.0000 0.0000 1116.231634 0 0.0014 263 | 0/8 12 h-lim-p 0.0007 20.0000 0.0000 1116.231634 0 0.0003 283 | 0/8 13 h-lim-p 0.0003 20.0000 0.0000 1116.231634 0 0.0003 303 | 0/8 14 h-lim-p 0.0003 20.0000 0.0000 1116.231634 0 0.0001 323 | 0/8 15 h-lim-p 0.0001 20.0000 0.0001 1116.231634 0 0.0001 343 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 1116.231634 0 0.0000 363 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 1116.231634 0 0.0000 392 | 0/8 18 h-lim-p 0.0000 20.0000 0.0013 | 0/8 19 h-lim-p 0.0000 20.0000 0.0013 Out... lnL = -1116.231634 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1116.231634 Node 7: lnL = -1116.231634 Node 8: lnL = -1116.231634 Node 9: lnL = -1116.231634 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 668 Sequential format.. Reading seq # 1: YLR312C_Sbay Reading seq # 2: YLR312C_Scer Reading seq # 3: YLR312C_Skud Reading seq # 4: YLR312C_Smik Reading seq # 5: YLR312C_Spar Sequences read.. Counting patterns.. # site patterns = 188 Counting frequencies.. 120 bytes for distance 30080 bytes for lkl0 24064 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.143141 0.046941 0.040441 0.110412 0.054132 0.161199 0.131488 0.046600 lnL0 = -2697.959313 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2697.959313 x= 0.14314 0.04694 0.04044 0.11041 0.05413 0.16120 0.13149 0.04660 1 h-lim-p 0.0003 0.0020 133.0325 2696.823621 5 0.0001 33 | 0/8 2 h-lim-p 0.0003 0.0025 32.2028 2696.728294 7 0.0002 64 | 0/8 3 h-lim-p 0.0004 0.0173 15.0505 2696.712808 5 0.0002 85 | 0/8 4 h-lim-p 0.0005 0.0389 5.1470 2696.710360 2 0.0002 101 | 0/8 5 h-lim-p 0.0011 0.1243 1.0077 2696.710243 2 0.0002 118 | 0/8 6 h-lim-p 0.0018 1.5180 0.1318 2696.710240 0 0.0004 131 | 0/8 7 h-lim-p 0.0151 20.0000 0.0034 2696.710240 0 0.0008 154 | 0/8 8 h-lim-p 0.0125 20.0000 0.0002 2696.710226 0 0.4000 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2696.710226 0 1.0938 199 | 0/8 10 h-lim-p 0.3773 20.0000 0.0000 2696.710226 0 1.1319 220 | 0/8 11 h-lim-p 0.5391 20.0000 0.0001 2696.710226 0 0.0042 246 | 0/8 12 h-lim-p 0.0004 20.0000 0.0006 2696.710226 0 0.0000 269 | 0/8 13 h-lim-p 0.0002 20.0000 0.0001 2696.710226 0 0.0001 289 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 2696.710226 0 0.0000 327 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -2696.710226 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2696.710226 Node 7: lnL = -2696.710226 Node 8: lnL = -2696.710226 Node 9: lnL = -2696.710226 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 804 Sequential format.. Reading seq # 1: YLR312W-A_Sbay Reading seq # 2: YLR312W-A_Scer Reading seq # 3: YLR312W-A_Skud Reading seq # 4: YLR312W-A_Smik Reading seq # 5: YLR312W-A_Spar Sequences read.. Counting patterns.. # site patterns = 209 Counting frequencies.. 120 bytes for distance 33440 bytes for lkl0 26752 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.121571 0.061989 0.027916 0.104712 0.053493 0.151535 0.115222 0.028707 lnL0 = -2960.710027 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2960.710027 x= 0.12157 0.06199 0.02792 0.10471 0.05349 0.15153 0.11522 0.02871 1 h-lim-p 0.0011 0.0085 165.6246 2959.485858 7 0.0001 40 | 0/8 2 h-lim-p 0.0004 0.0029 33.8850 2959.388526 2 0.0002 56 | 0/8 3 h-lim-p 0.0005 0.0121 12.7547 2959.377313 5 0.0002 82 | 0/8 4 h-lim-p 0.0009 0.0662 2.1638 2959.376775 4 0.0002 103 | 0/8 5 h-lim-p 0.0008 0.3318 0.6148 2959.376738 2 0.0002 120 | 0/8 6 h-lim-p 0.0009 0.4699 0.1381 2959.376736 0 0.0002 141 | 0/8 7 h-lim-p 0.0020 11.2117 0.0137 2959.376736 0 0.0009 161 | 0/8 8 h-lim-p 0.0120 20.0000 0.0010 2959.376444 0 0.2878 185 | 0/8 9 h-lim-p 2.2535 20.0000 0.0001 2959.376439 0 0.9859 205 | 0/8 10 h-lim-p 2.2331 20.0000 0.0001 2959.376439 0 0.9770 225 | 0/8 11 h-lim-p 0.9791 20.0000 0.0001 2959.376439 0 0.8567 245 | 0/8 12 h-lim-p 0.0458 20.0000 0.0011 .. | 0/8 13 h-lim-p 0.0000 20.0000 0.0007 2959.376439 0 0.0003 315 | 0/8 14 h-lim-p 0.0009 20.0000 0.0002 2959.376439 0 0.0000 339 | 0/8 15 h-lim-p 0.0001 20.0000 0.0001 2959.376439 0 0.0212 366 | 0/8 16 h-lim-p 0.0048 20.0000 0.0003 2959.376439 0 0.0000 393 | 0/8 17 h-lim-p 0.0000 16.9445 0.0025 2959.376439 0 0.0000 415 | 0/8 18 h-lim-p 0.0000 2.4060 0.0184 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0046 | 0/8 20 h-lim-p 0.0000 20.0000 0.0046 Out... lnL = -2959.376439 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2959.376439 Node 7: lnL = -2959.376439 Node 8: lnL = -2959.376439 Node 9: lnL = -2959.376439 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 279 Sequential format.. Reading seq # 1: YLR313C_Sbay Reading seq # 2: YLR313C_Scer Reading seq # 3: YLR313C_Skud Reading seq # 4: YLR313C_Smik Reading seq # 5: YLR313C_Spar Sequences read.. Counting patterns.. # site patterns = 107 Counting frequencies.. 120 bytes for distance 17120 bytes for lkl0 13696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.128546 0.081604 0.033565 0.057367 0.065162 0.182166 0.162276 0.024828 lnL0 = -1041.829452 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1041.829452 x= 0.12855 0.08160 0.03356 0.05737 0.06516 0.18217 0.16228 0.02483 1 h-lim-p 0.0008 0.0067 65.1245 1041.282711 9 0.0003 45 | 0/8 2 h-lim-p 0.0007 0.0054 19.6103 1041.171223 2 0.0006 61 | 0/8 3 h-lim-p 0.0013 0.0163 9.7152 1041.152688 5 0.0005 83 | 0/8 4 h-lim-p 0.0013 0.0412 3.7441 1041.149646 4 0.0005 104 | 0/8 5 h-lim-p 0.0020 0.0823 0.9646 1041.149400 4 0.0006 127 | 0/8 6 h-lim-p 0.0082 0.7175 0.0667 1041.149399 1 0.0005 152 | 0/8 7 h-lim-p 0.0015 8.3953 0.0229 1041.149398 0 0.0022 172 | 0/8 8 h-lim-p 0.0465 20.0000 0.0011 1041.149119 0 0.5580 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1041.149112 1 1.0938 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1041.149112 0 1.0938 237 | 0/8 11 h-lim-p 1.2054 20.0000 0.0000 1041.149112 0 2.4108 258 | 0/8 12 h-lim-p 1.5521 20.0000 0.0000 1041.149112 0 1.3581 278 | 0/8 13 h-lim-p 0.0839 20.0000 0.0004 1041.149112 0 0.0013 303 | 0/8 14 h-lim-p 0.0003 16.9638 0.0021 1041.149112 0 0.0000 325 | 0/8 15 h-lim-p 0.0001 20.0000 0.0010 1041.149112 0 0.0000 345 | 0/8 16 h-lim-p 0.0000 20.0000 0.0016 1041.149112 0 0.0000 372 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 1041.149112 0 0.0000 399 Out... lnL = -1041.149112 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1041.149112 Node 7: lnL = -1041.149112 Node 8: lnL = -1041.149112 Node 9: lnL = -1041.149112 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 712 Sequential format.. Reading seq # 1: YLR314C_Sbay Reading seq # 2: YLR314C_Scer Reading seq # 3: YLR314C_Skud Reading seq # 4: YLR314C_Smik Reading seq # 5: YLR314C_Spar Sequences read.. Counting patterns.. # site patterns = 284 Counting frequencies.. 120 bytes for distance 45440 bytes for lkl0 36352 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.350815 0.118860 0.075017 0.174044 0.083980 0.191900 0.214179 0.159233 lnL0 = -3233.884312 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3233.884312 x= 0.35082 0.11886 0.07502 0.17404 0.08398 0.19190 0.21418 0.15923 1 h-lim-p 0.0012 0.0093 65.0949 3233.265552 7 0.0003 39 | 0/8 2 h-lim-p 0.0005 0.0081 36.0574 3232.988832 2 0.0005 55 | 0/8 3 h-lim-p 0.0008 0.0096 23.2370 3232.876667 6 0.0006 79 | 0/8 4 h-lim-p 0.0015 0.0262 9.5373 3232.863897 3 0.0004 98 | 0/8 5 h-lim-p 0.0032 0.2597 1.0815 3232.863633 3 0.0005 119 | 0/8 6 h-lim-p 0.0038 1.6464 0.1355 3232.863628 1 0.0005 135 | 0/8 7 h-lim-p 0.0108 20.0000 0.0058 3232.863622 0 0.0217 156 | 0/8 8 h-lim-p 0.0187 20.0000 0.0067 3232.863370 0 0.0747 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3232.863350 1 0.9961 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3232.863350 0 1.0938 220 | 0/8 11 h-lim-p 1.3864 20.0000 0.0000 3232.863350 0 1.2131 240 | 0/8 12 h-lim-p 1.3227 20.0000 0.0000 3232.863350 0 2.6454 261 | 0/8 13 h-lim-p 0.5778 20.0000 0.0000 3232.863350 0 0.2889 281 | 0/8 14 h-lim-p 0.0108 20.0000 0.0006 3232.863350 0 0.0013 303 | 0/8 15 h-lim-p 0.0001 20.0000 0.0059 3232.863350 0 0.0001 323 | 0/8 16 h-lim-p 0.0514 20.0000 0.0000 3232.863350 0 0.0000 360 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -3232.863350 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3232.863350 Node 7: lnL = -3232.863350 Node 8: lnL = -3232.863350 Node 9: lnL = -3232.863350 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 716 Sequential format.. Reading seq # 1: YLR315W_Sbay Reading seq # 2: YLR315W_Scer Reading seq # 3: YLR315W_Skud Reading seq # 4: YLR315W_Smik Reading seq # 5: YLR315W_Spar Sequences read.. Counting patterns.. # site patterns = 280 Counting frequencies.. 120 bytes for distance 44800 bytes for lkl0 35840 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.274961 0.092590 0.064589 0.163098 0.094927 0.201971 0.234882 0.103731 lnL0 = -3398.188908 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3398.188908 x= 0.27496 0.09259 0.06459 0.16310 0.09493 0.20197 0.23488 0.10373 1 h-lim-p 0.0071 0.1579 97.6786 3396.838266 8 0.0003 44 | 0/8 2 h-lim-p 0.0006 0.0045 29.1420 3396.679487 6 0.0004 69 | 0/8 3 h-lim-p 0.0008 0.0197 15.1622 3396.641512 4 0.0004 90 | 0/8 4 h-lim-p 0.0008 0.0320 8.1280 3396.630691 5 0.0004 115 | 0/8 5 h-lim-p 0.0121 0.8114 0.2951 3396.630662 1 0.0007 132 | 0/8 6 h-lim-p 0.0055 5.4247 0.0351 3396.630661 0 0.0012 153 | 0/8 7 h-lim-p 0.0093 20.0000 0.0046 3396.630375 0 0.1493 177 | 0/8 8 h-lim-p 0.0020 14.5944 0.3386 3396.629610 1 0.0025 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3396.629602 1 0.9961 221 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3396.629602 0 1.0938 241 | 0/8 11 h-lim-p 1.2581 20.0000 0.0000 3396.629602 0 2.5162 262 | 0/8 12 h-lim-p 0.5964 20.0000 0.0000 3396.629602 0 0.8946 282 | 0/8 13 h-lim-p 0.0312 20.0000 0.0011 3396.629602 0 0.0156 302 | 0/8 14 h-lim-p 0.0034 20.0000 0.0052 3396.629602 0 0.0034 322 | 0/8 15 h-lim-p 0.0032 20.0000 0.0055 3396.629602 0 0.0000 360 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 3396.629602 0 0.0000 387 Out... lnL = -3396.629602 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3396.629602 Node 7: lnL = -3396.629602 Node 8: lnL = -3396.629602 Node 9: lnL = -3396.629602 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 488 Sequential format.. Reading seq # 1: YLR318W_Sbay Reading seq # 2: YLR318W_Scer Reading seq # 3: YLR318W_Skud Reading seq # 4: YLR318W_Smik Reading seq # 5: YLR318W_Spar Sequences read.. Counting patterns.. # site patterns = 138 Counting frequencies.. 120 bytes for distance 22080 bytes for lkl0 17664 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.243305 0.089505 0.444127 0.290903 0.032513 0.669902 0.412698 0.000060 lnL0 = -1823.848422 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1823.848422 x= 0.24330 0.08951 0.44413 0.29090 0.03251 0.66990 0.41270 0.00006 1 h-lim-p 0.0000 0.0000 371.3853 1823.747897 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0003 596.6750 1781.178220 m 0.0003 36 | 2/8 3 h-lim-p 0.0002 0.0017 302.8978 1753.197891 0 0.0008 50 | 2/8 4 h-lim-p 0.0008 0.0064 42.8371 1751.486063 0 0.0016 63 | 2/8 5 h-lim-p 0.0046 0.0391 14.9633 1740.837605 0 0.0183 77 | 2/8 6 h-lim-p 0.0007 0.0056 126.2520 1734.883030 0 0.0021 90 | 2/8 7 h-lim-p 0.0913 0.7306 2.5839 1731.958844 0 0.1827 103 | 1/8 8 h-lim-p 0.0062 0.0500 34.4426 1731.803404 7 0.0006 133 | 1/8 9 h-lim-p 0.0082 0.7118 2.3754 1729.813567 0 0.2612 150 | 0/8 10 h-lim-p 0.0008 0.0066 165.8825 1729.512111 8 0.0006 183 | 0/8 11 h-lim-p 0.1106 0.8844 0.3669 1728.874754 0 0.4422 197 | 0/8 12 h-lim-p 0.1137 0.9094 0.0636 1728.823082 m 0.9094 217 | 1/8 13 h-lim-p 2.5000 20.0000 0.0185 1728.817266 6 0.4666 251 | 1/8 14 h-lim-p 0.5814 20.0000 0.0149 1728.813539 1 0.7268 272 | 1/8 15 h-lim-p 2.5000 20.0000 0.0022 1728.813360 4 0.8524 301 | 1/8 16 h-lim-p 1.0536 20.0000 0.0018 1728.813335 0 0.9219 320 | 1/8 17 h-lim-p 2.5000 20.0000 0.0003 1728.813334 0 1.2500 339 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 1728.813334 0 1.0938 358 | 1/8 19 h-lim-p 2.5000 20.0000 0.0000 1728.813334 0 1.0938 377 | 1/8 20 h-lim-p 2.5000 20.0000 0.0000 1728.813334 0 5.0000 397 | 1/8 21 h-lim-p 2.5000 20.0000 0.0000 1728.813334 0 0.0098 423 Out... lnL = -1728.813334 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1728.813334 Node 7: lnL = -1728.813334 Node 8: lnL = -1728.813334 Node 9: lnL = -1728.813334 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 282 Sequential format.. Reading seq # 1: YLR323C_Sbay Reading seq # 2: YLR323C_Scer Reading seq # 3: YLR323C_Skud Reading seq # 4: YLR323C_Smik Reading seq # 5: YLR323C_Spar Sequences read.. Counting patterns.. # site patterns = 120 Counting frequencies.. 120 bytes for distance 19200 bytes for lkl0 15360 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.182023 0.009615 0.101344 0.132601 0.043669 0.155870 0.189112 0.060388 lnL0 = -1143.387819 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1143.387819 x= 0.18202 0.00961 0.10134 0.13260 0.04367 0.15587 0.18911 0.06039 1 h-lim-p 0.0017 0.0135 111.4877 1142.180859 8 0.0002 44 | 0/8 2 h-lim-p 0.0013 0.0103 8.5822 1142.153791 7 0.0007 73 | 0/8 3 h-lim-p 0.0010 0.0398 6.2540 1142.148126 4 0.0004 93 | 0/8 4 h-lim-p 0.0014 0.1376 1.8053 1142.146565 4 0.0011 113 | 0/8 5 h-lim-p 0.0115 2.2654 0.1714 1142.146546 2 0.0014 131 | 0/8 6 h-lim-p 0.0081 6.5008 0.0284 1142.146545 0 0.0009 153 | 0/8 7 h-lim-p 0.0114 20.0000 0.0022 1142.146545 0 0.0025 174 | 0/8 8 h-lim-p 0.0283 20.0000 0.0002 1142.146541 0 0.4526 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1142.146541 0 1.2500 218 | 0/8 10 h-lim-p 2.0614 20.0000 0.0000 1142.146541 0 1.8037 238 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1142.146541 0 0.5469 259 | 0/8 12 h-lim-p 0.2270 20.0000 0.0000 1142.146541 0 0.0003 288 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 1142.146541 0 0.0000 312 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 1142.146541 0 0.0000 336 Out... lnL = -1142.146541 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1142.146541 Node 7: lnL = -1142.146541 Node 8: lnL = -1142.146541 Node 9: lnL = -1142.146541 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 847 Sequential format.. Reading seq # 1: YLR326W_Sbay Reading seq # 2: YLR326W_Scer Reading seq # 3: YLR326W_Skud Reading seq # 4: YLR326W_Smik Reading seq # 5: YLR326W_Spar Sequences read.. Counting patterns.. # site patterns = 272 Counting frequencies.. 120 bytes for distance 43520 bytes for lkl0 34816 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.259933 0.055800 0.086883 0.107721 0.081038 0.236848 0.189855 0.103879 lnL0 = -3918.354179 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3918.354179 x= 0.25993 0.05580 0.08688 0.10772 0.08104 0.23685 0.18985 0.10388 1 h-lim-p 0.0006 0.0049 176.4050 3915.415824 8 0.0002 41 | 0/8 2 h-lim-p 0.0006 0.0048 40.2146 3915.069859 8 0.0004 72 | 0/8 3 h-lim-p 0.0008 0.0129 21.5112 3915.036561 3 0.0002 91 | 0/8 4 h-lim-p 0.0006 0.0315 6.8747 3915.031265 3 0.0003 109 | 0/8 5 h-lim-p 0.0013 0.2039 1.3924 3915.031011 2 0.0003 126 | 0/8 6 h-lim-p 0.0015 0.9677 0.2501 3915.030996 2 0.0005 144 | 0/8 7 h-lim-p 0.0065 16.2307 0.0195 3915.030983 0 0.0065 164 | 0/8 8 h-lim-p 0.0131 20.0000 0.0097 3915.028733 0 0.1048 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3915.028695 2 0.9961 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3915.028695 0 1.0938 231 | 0/8 11 h-lim-p 1.5646 20.0000 0.0000 3915.028695 0 1.5646 251 | 0/8 12 h-lim-p 1.3813 20.0000 0.0000 3915.028695 0 0.0040 279 | 0/8 13 h-lim-p 0.0001 20.0000 0.0008 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0009 3915.028695 0 0.0000 338 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 3915.028695 0 0.0000 367 | 0/8 16 h-lim-p 0.0000 20.0000 0.0007 3915.028695 0 0.0003 392 | 0/8 17 h-lim-p 0.0015 20.0000 0.0002 3915.028695 0 0.0011 412 | 0/8 18 h-lim-p 0.0077 20.0000 0.0000 3915.028695 0 0.0019 433 | 0/8 19 h-lim-p 0.0012 20.0000 0.0000 3915.028695 0 0.0000 460 | 0/8 20 h-lim-p 0.0000 20.0000 0.0002 3915.028695 0 0.0000 483 | 0/8 21 h-lim-p 0.0000 20.0000 0.0000 3915.028695 0 0.0000 516 Out... lnL = -3915.028695 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3915.028695 Node 7: lnL = -3915.028695 Node 8: lnL = -3915.028695 Node 9: lnL = -3915.028695 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 945 Sequential format.. Reading seq # 1: YLR327C_Sbay Reading seq # 2: YLR327C_Scer Reading seq # 3: YLR327C_Skud Reading seq # 4: YLR327C_Smik Reading seq # 5: YLR327C_Spar Sequences read.. Counting patterns.. # site patterns = 402 Counting frequencies.. 120 bytes for distance 64320 bytes for lkl0 51456 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.317601 0.054094 0.133521 0.081990 0.140997 0.313897 0.269139 0.118375 lnL0 = -4578.663479 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4578.663479 x= 0.31760 0.05409 0.13352 0.08199 0.14100 0.31390 0.26914 0.11837 1 h-lim-p 0.0024 0.0191 179.8256 4574.919103 6 0.0003 37 | 0/8 2 h-lim-p 0.0006 0.0044 61.4240 4574.330821 8 0.0003 70 | 0/8 3 h-lim-p 0.0005 0.0078 41.8101 4573.970206 1 0.0006 84 | 0/8 4 h-lim-p 0.0054 0.0563 4.7855 4573.965035 4 0.0005 109 | 0/8 5 h-lim-p 0.0017 0.1763 1.3263 4573.964613 4 0.0005 133 | 0/8 6 h-lim-p 0.0028 1.0004 0.2469 4573.964584 2 0.0007 150 | 0/8 7 h-lim-p 0.0059 14.8979 0.0304 4573.964373 0 0.0236 172 | 0/8 8 h-lim-p 0.0111 12.9686 0.0649 4573.955995 0 0.0443 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0008 4573.955616 2 1.0889 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4573.955615 0 1.0938 238 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4573.955615 0 1.0938 258 | 0/8 12 h-lim-p 1.0727 20.0000 0.0000 4573.955615 0 0.0000 294 Out... lnL = -4573.955615 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4573.955615 Node 7: lnL = -4573.955615 Node 8: lnL = -4573.955615 Node 9: lnL = -4573.955615 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 918 Sequential format.. Reading seq # 1: YLR328W_Sbay Reading seq # 2: YLR328W_Scer Reading seq # 3: YLR328W_Skud Reading seq # 4: YLR328W_Smik Reading seq # 5: YLR328W_Spar Sequences read.. Counting patterns.. # site patterns = 330 Counting frequencies.. 120 bytes for distance 52800 bytes for lkl0 42240 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.224711 0.033553 0.013484 0.151538 0.122707 0.112349 0.190248 0.097862 lnL0 = -3739.465330 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3739.465330 x= 0.22471 0.03355 0.01348 0.15154 0.12271 0.11235 0.19025 0.09786 1 h-lim-p 0.0003 0.2504 502.4457 3729.939531 8 0.0001 40 | 0/8 2 h-lim-p 0.0003 0.0026 117.5772 3727.544549 1 0.0004 54 | 0/8 3 h-lim-p 0.0007 0.0054 18.2111 3727.495500 2 0.0003 70 | 0/8 4 h-lim-p 0.0011 0.0198 5.3389 3727.491137 5 0.0003 95 | 0/8 5 h-lim-p 0.0015 0.2164 1.1787 3727.490863 4 0.0004 116 | 0/8 6 h-lim-p 0.0038 2.1451 0.1263 3727.490855 1 0.0008 131 | 0/8 7 h-lim-p 0.0161 20.0000 0.0059 3727.489817 0 0.1936 154 | 0/8 8 h-lim-p 0.0011 0.1971 1.0830 3727.485720 0 0.0021 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 3727.485515 2 1.1719 191 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 3727.485503 2 1.3159 216 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3727.485503 0 1.0938 236 | 0/8 12 h-lim-p 1.6220 20.0000 0.0000 3727.485503 0 0.2027 258 | 0/8 13 h-lim-p 0.0872 20.0000 0.0000 3727.485503 0 0.0027 282 | 0/8 14 h-lim-p 0.0010 20.0000 0.0001 3727.485503 0 0.0007 302 | 0/8 15 h-lim-p 0.0012 20.0000 0.0001 3727.485503 0 0.0000 343 | 0/8 16 h-lim-p 0.0000 20.0000 0.0019 3727.485503 0 0.0000 377 | 0/8 17 h-lim-p 0.0000 20.0000 0.0019 3727.485503 0 0.0000 406 | 0/8 18 h-lim-p 0.0000 20.0000 0.0004 3727.485503 0 0.0000 426 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 20 h-lim-p 0.0000 20.0000 0.0019 | 0/8 21 h-lim-p 0.0000 20.0000 0.0019 Out... lnL = -3727.485503 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3727.485503 Node 7: lnL = -3727.485503 Node 8: lnL = -3727.485503 Node 9: lnL = -3727.485503 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 657 Sequential format.. Reading seq # 1: YLR329W_Sbay Reading seq # 2: YLR329W_Scer Reading seq # 3: YLR329W_Skud Reading seq # 4: YLR329W_Smik Reading seq # 5: YLR329W_Spar Sequences read.. Counting patterns.. # site patterns = 295 Counting frequencies.. 120 bytes for distance 47200 bytes for lkl0 37760 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.241083 0.125346 0.256964 0.212064 0.071165 0.753702 0.341545 0.000060 lnL0 = -3248.317223 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3248.317223 x= 0.24108 0.12535 0.25696 0.21206 0.07116 0.75370 0.34155 0.00006 1 h-lim-p 0.0000 0.0000 328.8969 3248.197607 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0007 512.6292 3214.233864 0 0.0005 39 | 1/8 3 h-lim-p 0.0003 0.0026 121.4315 3209.041355 0 0.0010 52 | 1/8 4 h-lim-p 0.0002 0.0019 89.1643 3206.505916 0 0.0010 66 | 1/8 5 h-lim-p 0.0004 0.0029 55.2382 3205.038401 0 0.0014 80 | 1/8 6 h-lim-p 0.0022 0.0229 36.1239 3204.630915 2 0.0010 96 | 1/8 7 h-lim-p 0.0015 0.0119 19.2126 3204.383059 0 0.0022 108 | 1/8 8 h-lim-p 0.1960 1.5684 0.1334 3193.880015 0 0.7842 122 | 1/8 9 h-lim-p 0.8084 6.4675 0.0452 3193.443803 8 0.4915 163 | 1/8 10 h-lim-p 1.2788 20.0000 0.0174 3193.400866 6 0.8984 196 | 0/8 11 h-lim-p 0.0234 3.7704 0.6689 3193.400737 2 0.0007 223 | 0/8 12 h-lim-p 0.0994 20.0000 0.0046 3193.397416 0 1.1932 246 | 0/8 13 h-lim-p 1.3232 10.5856 0.0003 3193.397344 3 0.7112 273 | 0/8 14 h-lim-p 1.6844 20.0000 0.0001 3193.397342 1 0.8291 296 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 3193.397342 0 1.0938 316 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 3193.397342 0 1.0938 336 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 3193.397342 0 0.1562 359 | 0/8 18 h-lim-p 0.1081 20.0000 0.0000 3193.397342 0 0.0000 394 Out... lnL = -3193.397342 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3193.397342 Node 7: lnL = -3193.397342 Node 8: lnL = -3193.397342 Node 9: lnL = -3193.397342 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 363 Sequential format.. Reading seq # 1: YLR330W_Sbay Reading seq # 2: YLR330W_Scer Reading seq # 3: YLR330W_Skud Reading seq # 4: YLR330W_Smik Reading seq # 5: YLR330W_Spar Sequences read.. Counting patterns.. # site patterns = 205 Counting frequencies.. 120 bytes for distance 32800 bytes for lkl0 26240 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.232063 0.129825 0.111648 0.172166 0.140053 0.175037 0.230539 0.045447 lnL0 = -1759.425217 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1759.425217 x= 0.23206 0.12982 0.11165 0.17217 0.14005 0.17504 0.23054 0.04545 1 h-lim-p 0.0320 4.3578 33.1353 1759.054723 8 0.0007 47 | 0/8 2 h-lim-p 0.0032 0.0258 7.1553 1759.029417 6 0.0010 73 | 0/8 3 h-lim-p 0.0038 0.1012 1.9378 1759.027983 2 0.0008 90 | 0/8 4 h-lim-p 0.0057 1.5103 0.2795 1759.027938 2 0.0011 107 | 0/8 5 h-lim-p 0.0032 2.0326 0.1011 1759.027933 2 0.0010 132 | 0/8 6 h-lim-p 0.0274 20.0000 0.0037 1759.027933 0 0.0120 152 | 0/8 7 h-lim-p 0.0142 20.0000 0.0032 1759.027919 0 0.0568 174 | 0/8 8 h-lim-p 0.0029 17.2641 0.0623 1759.027892 0 0.0043 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1759.027891 0 1.0938 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1759.027891 0 1.0938 234 | 0/8 11 h-lim-p 1.2243 20.0000 0.0000 1759.027891 0 1.8365 254 | 0/8 12 h-lim-p 1.0479 20.0000 0.0000 .. | 0/8 13 h-lim-p 0.0000 20.0000 0.0004 | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1759.027891 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1759.027891 Node 7: lnL = -1759.027891 Node 8: lnL = -1759.027891 Node 9: lnL = -1759.027891 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 839 Sequential format.. Reading seq # 1: YLR332W_Sbay Reading seq # 2: YLR332W_Scer Reading seq # 3: YLR332W_Skud Reading seq # 4: YLR332W_Smik Reading seq # 5: YLR332W_Spar Sequences read.. Counting patterns.. # site patterns = 272 Counting frequencies.. 120 bytes for distance 43520 bytes for lkl0 34816 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.225857 0.012650 0.089105 0.070042 0.067461 0.953510 0.144962 0.003444 lnL0 = -3686.207634 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3686.207634 x= 0.22586 0.01265 0.08910 0.07004 0.06746 0.95351 0.14496 0.00344 1 h-lim-p 0.0001 0.0009 174.4041 3684.289703 1 0.0001 24 | 0/8 2 h-lim-p 0.0002 0.0019 52.1457 3684.039735 5 0.0002 45 | 0/8 3 h-lim-p 0.0003 0.0044 35.5857 3683.930337 6 0.0002 73 | 0/8 4 h-lim-p 0.0002 0.0043 35.3912 3683.829789 0 0.0004 85 | 0/8 5 h-lim-p 0.0003 0.0023 19.9068 3683.783427 0 0.0004 97 | 0/8 6 h-lim-p 0.0020 0.1411 4.3481 3683.777130 5 0.0007 120 | 0/8 7 h-lim-p 0.0004 0.0354 8.6130 3683.753969 0 0.0015 134 | 0/8 8 h-lim-p 2.5000 20.0000 0.0031 3683.746645 2 1.1719 150 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 3683.746603 1 1.0938 172 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3683.746603 0 1.0938 192 | 0/8 11 h-lim-p 1.1241 20.0000 0.0000 3683.746603 0 2.2481 213 | 0/8 12 h-lim-p 0.3602 20.0000 0.0003 3683.746603 0 0.0788 234 | 0/8 13 h-lim-p 0.0097 6.1516 0.0024 3683.746603 0 0.0097 254 | 0/8 14 h-lim-p 0.0038 2.3981 0.0060 3683.746603 0 0.0001 278 | 0/8 15 h-lim-p 0.0002 20.0000 0.0031 3683.746603 0 0.0001 298 | 0/8 16 h-lim-p 0.0004 20.0000 0.0009 3683.746603 0 0.0004 318 | 0/8 17 h-lim-p 0.0001 20.0000 0.0071 3683.746603 0 0.0001 338 | 0/8 18 h-lim-p 0.0001 3.2466 0.0045 3683.746603 0 0.0000 371 | 0/8 19 h-lim-p 0.0001 20.0000 0.0000 3683.746603 0 0.0000 405 Out... lnL = -3683.746603 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3683.746603 Node 7: lnL = -3683.746603 Node 8: lnL = -3683.746603 Node 9: lnL = -3683.746603 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 363 Sequential format.. Reading seq # 1: YLR335W_Sbay Reading seq # 2: YLR335W_Scer Reading seq # 3: YLR335W_Skud Reading seq # 4: YLR335W_Smik Reading seq # 5: YLR335W_Spar Sequences read.. Counting patterns.. # site patterns = 162 Counting frequencies.. 120 bytes for distance 25920 bytes for lkl0 20736 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.272339 0.480707 0.000060 0.498863 0.471670 0.345116 0.377694 0.008569 lnL0 = -1635.802145 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1635.802145 x= 0.27234 0.48071 0.00006 0.49886 0.47167 0.34512 0.37769 0.00857 1 h-lim-p 0.0000 0.0000 230.8456 1635.732950 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0032 257.1400 1562.532861 4 0.0023 50 | 1/8 3 h-lim-p 0.0025 0.0204 48.5121 1557.232909 0 0.0051 63 | 1/8 4 h-lim-p 0.0005 0.0040 22.6469 1556.739504 0 0.0020 77 | 1/8 5 h-lim-p 0.0029 0.0279 15.7041 1555.719221 0 0.0116 91 | 1/8 6 h-lim-p 0.0026 0.0211 13.4843 1554.049959 m 0.0211 103 | 2/8 7 h-lim-p 0.0014 0.0115 39.5726 1552.433802 0 0.0029 116 | 2/8 8 h-lim-p 0.6135 4.9083 0.0896 1552.203481 6 0.5326 140 | 1/8 9 h-lim-p 0.0602 6.5618 0.7924 1552.202356 3 0.0019 168 | 1/8 10 h-lim-p 0.0076 0.4548 0.1947 1552.060871 4 0.2582 199 | 1/8 11 h-lim-p 1.0585 8.4682 0.0187 1552.038182 5 0.9014 230 | 0/8 12 h-lim-p 0.0264 0.4208 0.6397 1552.037940 2 0.0015 256 | 0/8 13 h-lim-p 0.1621 2.2426 0.0061 1552.036040 1 1.5334 281 | 0/8 14 h-lim-p 0.0728 0.5824 0.0021 1552.035888 m 0.5824 301 | 1/8 15 h-lim-p 0.2612 20.0000 0.0046 1552.035790 3 0.2015 327 | 1/8 16 h-lim-p 2.5000 20.0000 0.0003 1552.035779 1 0.9961 348 | 1/8 17 h-lim-p 2.5000 20.0000 0.0001 1552.035779 0 2.1875 367 | 1/8 18 h-lim-p 2.5000 20.0000 0.0001 1552.035779 0 1.0938 386 | 1/8 19 h-lim-p 2.5000 20.0000 0.0000 1552.035779 0 1.0938 405 | 1/8 20 h-lim-p 2.5000 20.0000 0.0000 1552.035779 0 2.1875 424 | 1/8 21 h-lim-p 2.1904 20.0000 0.0000 1552.035779 0 0.9583 443 | 1/8 22 h-lim-p 2.5000 20.0000 0.0000 1552.035779 0 0.6250 463 | 1/8 23 h-lim-p 0.1049 20.0000 0.0000 1552.035779 0 0.0066 485 Out... lnL = -1552.035779 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1552.035779 Node 7: lnL = -1552.035779 Node 8: lnL = -1552.035779 Node 9: lnL = -1552.035779 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 702 Sequential format.. Reading seq # 1: YLR340W_Sbay Reading seq # 2: YLR340W_Scer Reading seq # 3: YLR340W_Skud Reading seq # 4: YLR340W_Smik Reading seq # 5: YLR340W_Spar Sequences read.. Counting patterns.. # site patterns = 266 Counting frequencies.. 120 bytes for distance 42560 bytes for lkl0 34048 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.237642 0.292223 0.197872 0.157441 0.109352 0.000060 0.271226 0.034734 lnL0 = -3189.431617 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3189.431617 x= 0.23764 0.29222 0.19787 0.15744 0.10935 0.00006 0.27123 0.03473 1 h-lim-p 0.0003 0.0025 339.5195 3172.719398 5 0.0003 32 | 0/8 2 h-lim-p 0.0004 0.0031 45.1983 3171.609474 0 0.0012 45 | 0/8 3 h-lim-p 0.0005 0.0040 52.9053 3170.813767 0 0.0010 58 | 0/8 4 h-lim-p 0.0012 0.0092 33.1090 3170.618525 6 0.0006 83 | 0/8 5 h-lim-p 0.0005 0.0047 38.2734 3170.435749 1 0.0007 97 | 0/8 6 h-lim-p 0.0028 0.0245 9.3763 3170.408584 6 0.0008 124 | 0/8 7 h-lim-p 0.0074 0.3022 1.0225 3170.407668 2 0.0016 141 | 0/8 8 h-lim-p 0.1762 20.0000 0.0094 3170.347182 0 1.0574 155 | 0/8 9 h-lim-p 2.0171 20.0000 0.0049 3170.327816 3 2.0821 181 | 0/8 10 h-lim-p 2.5000 20.0000 0.0012 3170.327095 2 1.0889 205 | 0/8 11 h-lim-p 2.5000 20.0000 0.0001 3170.327093 0 1.0938 225 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3170.327093 0 1.0938 245 | 0/8 13 h-lim-p 1.1338 20.0000 0.0000 3170.327093 0 0.9921 265 | 0/8 14 h-lim-p 0.2241 20.0000 0.0001 3170.327093 0 0.0009 292 | 0/8 15 h-lim-p 0.0002 20.0000 0.0003 3170.327093 0 0.0001 313 | 0/8 16 h-lim-p 0.0004 20.0000 0.0000 3170.327093 0 0.0000 345 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 3170.327093 0 0.0000 380 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -3170.327093 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3170.327093 Node 7: lnL = -3170.327093 Node 8: lnL = -3170.327093 Node 9: lnL = -3170.327093 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 651 Sequential format.. Reading seq # 1: YLR341W_Sbay Reading seq # 2: YLR341W_Scer Reading seq # 3: YLR341W_Skud Reading seq # 4: YLR341W_Smik Reading seq # 5: YLR341W_Spar Sequences read.. Counting patterns.. # site patterns = 303 Counting frequencies.. 120 bytes for distance 48480 bytes for lkl0 38784 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.343230 0.110958 0.046691 0.199436 0.124664 0.228166 0.313227 0.127089 lnL0 = -3260.355285 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3260.355285 x= 0.34323 0.11096 0.04669 0.19944 0.12466 0.22817 0.31323 0.12709 1 h-lim-p 0.0009 0.0069 82.3519 3259.171612 6 0.0004 33 | 0/8 2 h-lim-p 0.0008 0.0064 31.4784 3258.975899 8 0.0004 64 | 0/8 3 h-lim-p 0.0012 0.0309 11.2030 3258.946492 4 0.0005 83 | 0/8 4 h-lim-p 0.0013 0.0731 4.6284 3258.934463 3 0.0013 101 | 0/8 5 h-lim-p 0.0071 0.2499 0.8566 3258.934087 4 0.0011 125 | 0/8 6 h-lim-p 0.0072 2.5887 0.1267 3258.934080 1 0.0009 149 | 0/8 7 h-lim-p 0.0050 16.1609 0.0221 3258.934080 0 0.0011 170 | 0/8 8 h-lim-p 0.1189 20.0000 0.0002 3258.934050 0 0.9510 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3258.934049 0 1.0938 213 | 0/8 10 h-lim-p 2.3225 20.0000 0.0000 3258.934049 0 2.0322 233 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3258.934049 0 1.0938 253 | 0/8 12 h-lim-p 0.1477 20.0000 0.0000 3258.934049 0 0.0000 294 Out... lnL = -3258.934049 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3258.934049 Node 7: lnL = -3258.934049 Node 8: lnL = -3258.934049 Node 9: lnL = -3258.934049 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 516 Sequential format.. Reading seq # 1: YLR343W_Sbay Reading seq # 2: YLR343W_Scer Reading seq # 3: YLR343W_Skud Reading seq # 4: YLR343W_Smik Reading seq # 5: YLR343W_Spar Sequences read.. Counting patterns.. # site patterns = 208 Counting frequencies.. 120 bytes for distance 33280 bytes for lkl0 26624 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.245689 0.081398 0.092385 0.095681 0.060508 0.273848 0.214070 0.076956 lnL0 = -2355.303048 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2355.303048 x= 0.24569 0.08140 0.09238 0.09568 0.06051 0.27385 0.21407 0.07696 1 h-lim-p 0.0003 0.0027 59.9759 2354.567561 1 0.0004 24 | 0/8 2 h-lim-p 0.0011 0.0096 23.0991 2354.496228 7 0.0003 54 | 0/8 3 h-lim-p 0.0004 0.0083 16.1996 2354.454333 4 0.0005 75 | 0/8 4 h-lim-p 0.0015 0.0839 5.0914 2354.446877 2 0.0007 91 | 0/8 5 h-lim-p 0.0045 0.2139 0.7786 2354.446758 3 0.0004 112 | 0/8 6 h-lim-p 0.0015 0.8361 0.2078 2354.446742 2 0.0008 137 | 0/8 7 h-lim-p 0.0043 5.9034 0.0376 2354.446741 1 0.0010 160 | 0/8 8 h-lim-p 0.1007 20.0000 0.0004 2354.446599 0 0.8054 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2354.446596 0 1.0938 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2354.446596 0 1.0938 223 | 0/8 11 h-lim-p 1.1923 20.0000 0.0000 2354.446596 0 1.1923 243 | 0/8 12 h-lim-p 0.8054 20.0000 0.0000 2354.446596 0 1.2080 263 | 0/8 13 h-lim-p 0.0134 20.0000 0.0013 2354.446596 0 0.0134 283 | 0/8 14 h-lim-p 0.0042 20.0000 0.0042 2354.446596 0 0.0063 303 | 0/8 15 h-lim-p 0.0032 14.1262 0.0084 2354.446596 0 0.0000 344 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -2354.446596 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2354.446596 Node 7: lnL = -2354.446596 Node 8: lnL = -2354.446596 Node 9: lnL = -2354.446596 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 878 Sequential format.. Reading seq # 1: YLR348C_Sbay Reading seq # 2: YLR348C_Scer Reading seq # 3: YLR348C_Skud Reading seq # 4: YLR348C_Smik Reading seq # 5: YLR348C_Spar Sequences read.. Counting patterns.. # site patterns = 268 Counting frequencies.. 120 bytes for distance 42880 bytes for lkl0 34304 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.219198 0.000060 0.073087 0.100361 0.042163 0.158176 0.057768 0.109722 lnL0 = -3204.490635 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3204.490635 x= 0.21920 0.00006 0.07309 0.10036 0.04216 0.15818 0.05777 0.10972 1 h-lim-p 0.0001 0.0010 323.6029 3199.524817 9 0.0001 44 | 0/8 2 h-lim-p 0.0003 0.0023 44.6695 3199.310496 7 0.0002 71 | 0/8 3 h-lim-p 0.0003 0.0055 29.4937 3199.277327 6 0.0001 100 | 0/8 4 h-lim-p 0.0003 0.0143 11.8529 3199.265918 4 0.0002 120 | 0/8 5 h-lim-p 0.0026 0.1413 0.9237 3199.265776 3 0.0003 140 | 0/8 6 h-lim-p 0.0010 0.4186 0.3194 3199.265764 1 0.0002 163 | 0/8 7 h-lim-p 0.0013 3.3141 0.0611 3199.265763 0 0.0006 183 | 0/8 8 h-lim-p 0.1332 20.0000 0.0003 3199.265375 0 1.5988 206 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3199.265363 1 0.9961 228 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3199.265363 0 2.5000 248 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3199.265363 0 0.0684 272 | 0/8 12 h-lim-p 0.0291 20.0000 0.0000 3199.265363 0 0.0291 292 | 0/8 13 h-lim-p 0.0114 20.0000 0.0000 3199.265363 0 0.0029 313 | 0/8 14 h-lim-p 0.0019 20.0000 0.0000 3199.265363 0 0.0019 333 | 0/8 15 h-lim-p 0.0011 20.0000 0.0001 3199.265363 0 0.0000 357 | 0/8 16 h-lim-p 0.0015 20.0000 0.0000 3199.265363 0 0.0004 378 Out... lnL = -3199.265363 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3199.265363 Node 7: lnL = -3199.265363 Node 8: lnL = -3199.265363 Node 9: lnL = -3199.265363 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 837 Sequential format.. Reading seq # 1: YLR353W_Sbay Reading seq # 2: YLR353W_Scer Reading seq # 3: YLR353W_Skud Reading seq # 4: YLR353W_Smik Reading seq # 5: YLR353W_Spar Sequences read.. Counting patterns.. # site patterns = 164 Counting frequencies.. 120 bytes for distance 26240 bytes for lkl0 20992 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.206484 0.128509 0.156532 0.190742 0.071196 0.766953 0.236045 0.000060 lnL0 = -2814.066796 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2814.066796 x= 0.20648 0.12851 0.15653 0.19074 0.07120 0.76695 0.23604 0.00006 1 h-lim-p 0.0000 0.0000 857.0781 2813.713416 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0004 617.1181 2753.675058 2 0.0003 43 | 1/8 3 h-lim-p 0.0001 0.0009 141.5858 2751.304283 0 0.0002 56 | 1/8 4 h-lim-p 0.0002 0.0018 34.4415 2750.717985 0 0.0009 70 | 1/8 5 h-lim-p 0.0000 0.0003 63.6362 2750.101205 m 0.0003 82 | 2/8 6 h-lim-p 0.0000 0.0002 748.0186 2749.382476 0 0.0000 95 | 2/8 7 h-lim-p 0.0058 0.0487 5.6462 2748.835855 3 0.0053 113 | 2/8 8 h-lim-p 0.0103 0.0828 2.2224 2695.335232 0 0.0621 127 | 2/8 9 h-lim-p 0.3069 2.4550 0.1024 2693.386896 0 0.4603 139 | 2/8 10 h-lim-p 0.3690 5.6050 0.1278 .. | 2/8 11 h-lim-p 0.0000 0.0017 103.0513 2692.422736 0 0.0002 207 | 2/8 12 h-lim-p 0.0004 0.0064 44.2130 2692.334509 6 0.0001 234 | 2/8 13 h-lim-p 0.0002 0.0044 23.1834 2692.292300 4 0.0002 254 | 2/8 14 h-lim-p 0.0002 0.0235 30.1797 2692.023144 0 0.0012 269 | 2/8 15 h-lim-p 0.0002 0.0299 160.7131 2691.024051 0 0.0009 283 | 2/8 16 h-lim-p 0.0004 0.0035 191.3615 2690.684103 7 0.0003 312 | 2/8 17 h-lim-p 1.0888 20.0000 0.0499 2690.548927 0 1.6332 324 | 1/8 18 h-lim-p 0.0132 0.4062 6.1585 2690.548511 3 0.0003 352 | 1/8 19 h-lim-p 0.5096 20.0000 0.0040 2690.540834 0 1.0192 365 | 1/8 20 h-lim-p 1.1271 20.0000 0.0036 2690.540497 2 1.0567 388 | 1/8 21 h-lim-p 2.5000 20.0000 0.0005 2690.540493 0 1.0938 407 | 1/8 22 h-lim-p 2.5000 20.0000 0.0000 2690.540493 0 1.0938 426 | 1/8 23 h-lim-p 2.5000 20.0000 0.0000 2690.540493 0 0.1562 448 | 1/8 24 h-lim-p 0.1750 20.0000 0.0000 2690.540493 0 0.0438 468 | 1/8 25 h-lim-p 0.0428 20.0000 0.0000 2690.540493 0 0.0107 488 Out... lnL = -2690.540493 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2690.540493 Node 7: lnL = -2690.540493 Node 8: lnL = -2690.540493 Node 9: lnL = -2690.540493 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 741 Sequential format.. Reading seq # 1: YLR354C_Sbay Reading seq # 2: YLR354C_Scer Reading seq # 3: YLR354C_Skud Reading seq # 4: YLR354C_Smik Reading seq # 5: YLR354C_Spar Sequences read.. Counting patterns.. # site patterns = 170 Counting frequencies.. 120 bytes for distance 27200 bytes for lkl0 21760 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.147074 0.137327 0.061363 0.166628 0.055550 0.512427 0.174880 0.000060 lnL0 = -2317.700380 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2317.700380 x= 0.14707 0.13733 0.06136 0.16663 0.05555 0.51243 0.17488 0.00006 1 h-lim-p 0.0000 0.0000 643.8686 2317.331590 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0002 698.5687 2279.225399 m 0.0002 36 | 2/8 3 h-lim-p 0.0001 0.0011 109.1720 2271.131914 0 0.0006 50 | 2/8 4 h-lim-p 0.0002 0.0013 122.0302 2259.676165 0 0.0007 64 | 2/8 5 h-lim-p 0.0001 0.0009 153.3959 2257.126312 0 0.0002 77 | 1/8 6 h-lim-p 0.0001 0.0007 321.4644 2254.361367 1 0.0001 91 | 1/8 7 h-lim-p 0.0016 0.0124 15.9499 2254.270458 2 0.0007 107 | 0/8 8 h-lim-p 0.0001 0.0039 89.8457 2253.508431 0 0.0010 122 | 0/8 9 h-lim-p 0.0011 0.0088 15.5367 2253.122505 m 0.0088 134 | 1/8 10 h-lim-p 0.1934 1.5472 0.0949 2251.581472 0 0.5802 147 | 1/8 11 h-lim-p 0.5027 4.0219 0.0533 2251.567166 5 0.0804 179 | 0/8 12 h-lim-p 0.0011 0.0668 3.8036 2251.559554 0 0.0045 200 | 0/8 13 h-lim-p 0.3144 2.5151 0.0085 2251.456378 m 2.5151 212 | 0/8 14 h-lim-p -0.0000 -0.0000 0.0132 h-lim-p: -1.35614921e-17 -1.08491937e-16 1.31608003e-02 2251.456378 .. | 0/8 15 h-lim-p 0.0000 0.0280 11.3576 2251.449654 0 0.0001 251 | 0/8 16 h-lim-p 0.0003 0.0052 4.9550 2251.446992 2 0.0003 267 | 0/8 17 h-lim-p 0.0002 0.0047 6.9154 2251.443459 0 0.0004 280 | 0/8 18 h-lim-p 0.0000 0.0003 12.5041 2251.437239 m 0.0003 292 | 1/8 19 h-lim-p 0.0009 0.0070 3.3833 2251.436730 4 0.0002 315 | 1/8 20 h-lim-p 0.0060 1.0597 0.0914 2251.436710 1 0.0013 330 | 1/8 21 h-lim-p 0.0005 0.3350 0.2405 2251.436654 0 0.0015 350 | 1/8 22 h-lim-p 0.0161 5.2543 0.0222 2251.436446 0 0.1292 372 | 1/8 23 h-lim-p 0.1476 1.4803 0.0194 2251.435437 1 0.1522 393 | 1/8 24 h-lim-p 2.5000 20.0000 0.0001 2251.435436 0 1.0938 412 | 1/8 25 h-lim-p 2.5000 20.0000 0.0000 2251.435436 0 1.2500 431 | 1/8 26 h-lim-p 2.5000 20.0000 0.0000 2251.435436 0 0.2734 452 | 1/8 27 h-lim-p 0.3748 20.0000 0.0000 2251.435436 0 0.0051 476 Out... lnL = -2251.435436 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2251.435436 Node 7: lnL = -2251.435436 Node 8: lnL = -2251.435436 Node 9: lnL = -2251.435436 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 871 Sequential format.. Reading seq # 1: YLR356W_Sbay Reading seq # 2: YLR356W_Scer Reading seq # 3: YLR356W_Skud Reading seq # 4: YLR356W_Smik Reading seq # 5: YLR356W_Spar Sequences read.. Counting patterns.. # site patterns = 254 Counting frequencies.. 120 bytes for distance 40640 bytes for lkl0 32512 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.369404 0.796369 0.065031 0.132798 0.239649 0.778698 0.934899 0.000060 lnL0 = -3584.324288 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3584.324288 x= 0.36940 0.79637 0.06503 0.13280 0.23965 0.77870 0.93490 0.00006 1 h-lim-p 0.0000 0.0000 308.8011 3584.210980 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0003 390.9629 3563.416877 m 0.0003 36 | 2/8 3 h-lim-p 0.0000 0.0005 1550.7384 3501.607899 3 0.0004 57 | 2/8 4 h-lim-p 0.0009 0.0072 68.9042 3497.260667 0 0.0018 70 | 1/8 5 h-lim-p 0.0007 0.0080 174.3986 3483.647480 0 0.0014 83 | 1/8 6 h-lim-p 0.0029 0.0232 26.3173 3482.926534 5 0.0024 106 | 1/8 7 h-lim-p 0.0039 0.0390 16.5146 3474.155103 m 0.0390 119 | 1/8 8 h-lim-p 0.0496 0.3972 1.1218 3466.714050 0 0.1489 132 | 0/8 9 h-lim-p 0.0175 0.2073 9.5427 3466.682922 6 0.0007 164 | 0/8 10 h-lim-p 0.0494 0.9602 0.1269 3465.152405 0 0.3952 179 | 0/8 11 h-lim-p 0.1698 1.3588 0.1376 3464.533001 0 0.5095 200 | 0/8 12 h-lim-p 0.0909 0.7270 0.0945 3464.263755 m 0.7270 220 | 0/8 13 h-lim-p 2.5000 20.0000 0.0167 3464.190575 4 1.2347 249 | 0/8 14 h-lim-p 0.3913 3.1305 0.0089 3464.183506 0 0.7826 270 | 0/8 15 h-lim-p 1.8830 20.0000 0.0037 3464.181258 2 0.8827 294 | 0/8 16 h-lim-p 2.5000 20.0000 0.0012 3464.181118 2 1.1719 318 | 0/8 17 h-lim-p 2.5000 20.0000 0.0003 3464.181100 2 0.9644 342 | 0/8 18 h-lim-p 2.5000 20.0000 0.0001 3464.181099 0 1.0938 362 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 3464.181099 0 1.0938 382 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 3464.181099 0 1.2500 402 | 0/8 21 h-lim-p 2.5000 20.0000 0.0000 3464.181099 0 3.7500 422 | 0/8 22 h-lim-p 1.3769 20.0000 0.0000 3464.181099 0 0.6024 442 | 0/8 23 h-lim-p 1.5335 20.0000 0.0000 3464.181099 0 0.0958 465 | 0/8 24 h-lim-p 0.1053 20.0000 0.0000 3464.181099 0 0.0000 497 Out... lnL = -3464.181099 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3464.181099 Node 7: lnL = -3464.181099 Node 8: lnL = -3464.181099 Node 9: lnL = -3464.181099 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 456 Sequential format.. Reading seq # 1: YLR357W_Sbay Reading seq # 2: YLR357W_Scer Reading seq # 3: YLR357W_Skud Reading seq # 4: YLR357W_Smik Reading seq # 5: YLR357W_Spar Sequences read.. Counting patterns.. # site patterns = 161 Counting frequencies.. 120 bytes for distance 25760 bytes for lkl0 20608 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.189141 0.014962 0.044909 0.085231 0.052235 0.151914 0.235558 0.064021 lnL0 = -1864.449993 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1864.449993 x= 0.18914 0.01496 0.04491 0.08523 0.05224 0.15191 0.23556 0.06402 1 h-lim-p 0.0012 0.0096 154.7618 1862.597828 8 0.0002 44 | 0/8 2 h-lim-p 0.0009 0.0072 18.4613 1862.515774 5 0.0005 67 | 0/8 3 h-lim-p 0.0006 0.0216 15.0964 1862.495890 4 0.0003 86 | 0/8 4 h-lim-p 0.0007 0.0412 5.5897 1862.491366 4 0.0004 107 | 0/8 5 h-lim-p 0.0007 0.0880 2.6874 1862.489786 4 0.0006 127 | 0/8 6 h-lim-p 0.0285 4.0906 0.0527 1862.489785 0 0.0008 143 | 0/8 7 h-lim-p 0.0053 13.7243 0.0078 1862.489785 0 0.0006 165 | 0/8 8 h-lim-p 0.0317 20.0000 0.0001 1862.489763 0 1.0142 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1862.489762 0 1.0938 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1862.489762 0 1.0938 230 | 0/8 11 h-lim-p 0.2692 20.0000 0.0000 1862.489762 0 0.0042 255 | 0/8 12 h-lim-p 0.0009 20.0000 0.0001 1862.489762 0 0.0000 291 | 0/8 13 h-lim-p 0.0000 20.0000 0.0008 1862.489762 0 0.0000 317 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0008 | 0/8 16 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -1862.489762 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1862.489762 Node 7: lnL = -1862.489762 Node 8: lnL = -1862.489762 Node 9: lnL = -1862.489762 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 390 Sequential format.. Reading seq # 1: YLR360W_Sbay Reading seq # 2: YLR360W_Scer Reading seq # 3: YLR360W_Skud Reading seq # 4: YLR360W_Smik Reading seq # 5: YLR360W_Spar Sequences read.. Counting patterns.. # site patterns = 164 Counting frequencies.. 120 bytes for distance 26240 bytes for lkl0 20992 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.150345 0.100201 0.030457 0.125359 0.081510 0.217293 0.172853 0.012542 lnL0 = -1674.671585 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1674.671585 x= 0.15035 0.10020 0.03046 0.12536 0.08151 0.21729 0.17285 0.01254 1 h-lim-p 0.0038 0.0303 83.3750 1674.016696 6 0.0002 36 | 0/8 2 h-lim-p 0.0014 0.0113 9.5814 1673.999041 6 0.0004 62 | 0/8 3 h-lim-p 0.0012 0.0253 3.2304 1673.996234 4 0.0006 83 | 0/8 4 h-lim-p 0.0031 0.0907 0.6081 1673.996127 2 0.0006 100 | 0/8 5 h-lim-p 0.0013 1.1532 0.2742 1673.996111 2 0.0005 124 | 0/8 6 h-lim-p 0.0036 5.6433 0.0395 1673.996111 0 0.0008 145 | 0/8 7 h-lim-p 0.0058 20.0000 0.0053 1673.996111 0 0.0050 165 | 0/8 8 h-lim-p 0.0502 20.0000 0.0005 1673.996065 0 0.4015 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1673.996062 1 0.9961 210 | 0/8 10 h-lim-p 1.7806 20.0000 0.0000 1673.996062 0 1.5580 230 | 0/8 11 h-lim-p 0.0875 20.0000 0.0005 1673.996062 0 0.0007 256 | 0/8 12 h-lim-p 0.0004 20.0000 0.0008 1673.996062 0 0.0000 292 | 0/8 13 h-lim-p 0.0000 20.0000 0.0002 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1673.996062 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1673.996062 Node 7: lnL = -1673.996062 Node 8: lnL = -1673.996062 Node 9: lnL = -1673.996062 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 703 Sequential format.. Reading seq # 1: YLR361C_Sbay Reading seq # 2: YLR361C_Scer Reading seq # 3: YLR361C_Skud Reading seq # 4: YLR361C_Smik Reading seq # 5: YLR361C_Spar Sequences read.. Counting patterns.. # site patterns = 206 Counting frequencies.. 120 bytes for distance 32960 bytes for lkl0 26368 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.183814 0.054534 0.027485 0.140310 0.074580 0.142332 0.173148 0.055166 lnL0 = -3003.103300 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3003.103300 x= 0.18381 0.05453 0.02748 0.14031 0.07458 0.14233 0.17315 0.05517 1 h-lim-p 0.0001 0.0008 315.4352 2998.715821 3 0.0001 28 | 0/8 2 h-lim-p 0.0001 0.0008 103.1205 2997.833466 0 0.0002 41 | 0/8 3 h-lim-p 0.0005 0.0069 40.8558 2997.682639 7 0.0002 66 | 0/8 4 h-lim-p 0.0015 0.0287 5.8884 2997.678301 5 0.0003 91 | 0/8 5 h-lim-p 0.0015 0.1986 1.0133 2997.678062 4 0.0005 115 | 0/8 6 h-lim-p 0.0055 2.0156 0.0854 2997.677965 3 0.0029 134 | 0/8 7 h-lim-p 0.0071 4.8779 0.0346 2997.651759 0 0.1140 158 | 0/8 8 h-lim-p 0.0125 0.5446 0.3170 2997.651742 1 0.0003 184 | 0/8 9 h-lim-p 0.1353 20.0000 0.0007 2997.649847 0 1.0821 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2997.649798 1 1.2500 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2997.649798 0 1.0938 249 | 0/8 12 h-lim-p 1.1839 20.0000 0.0000 2997.649798 0 2.3678 270 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2997.649798 0 0.5469 291 | 0/8 14 h-lim-p 0.0309 20.0000 0.0000 2997.649798 0 0.0019 314 | 0/8 15 h-lim-p 0.0008 20.0000 0.0001 2997.649798 0 0.0000 338 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 2997.649798 0 0.0000 370 | 0/8 17 h-lim-p 0.0000 20.0000 0.0038 | 0/8 18 h-lim-p 0.0000 20.0000 0.0038 Out... lnL = -2997.649798 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2997.649798 Node 7: lnL = -2997.649798 Node 8: lnL = -2997.649798 Node 9: lnL = -2997.649798 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 326 Sequential format.. Reading seq # 1: YLR363C_Sbay Reading seq # 2: YLR363C_Scer Reading seq # 3: YLR363C_Skud Reading seq # 4: YLR363C_Smik Reading seq # 5: YLR363C_Spar Sequences read.. Counting patterns.. # site patterns = 124 Counting frequencies.. 120 bytes for distance 19840 bytes for lkl0 15872 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.270807 0.312909 0.152288 0.116008 0.143731 0.716728 0.470437 0.000060 lnL0 = -1347.448246 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1347.448246 x= 0.27081 0.31291 0.15229 0.11601 0.14373 0.71673 0.47044 0.00006 1 h-lim-p 0.0000 0.0000 173.7660 1347.395551 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0007 376.9387 1324.380432 m 0.0007 38 | 1/8 3 h-lim-p 0.0009 0.0074 63.7241 1321.181328 0 0.0018 51 | 1/8 4 h-lim-p 0.0023 0.0186 20.3225 1320.896374 6 0.0015 77 | 1/8 5 h-lim-p 0.0023 0.0181 8.5013 1320.542522 0 0.0091 91 | 1/8 6 h-lim-p 0.0170 0.1359 1.2954 1320.311545 1 0.0212 105 | 1/8 7 h-lim-p 0.0030 0.0751 9.1058 1314.867505 0 0.0242 120 | 1/8 8 h-lim-p 0.0297 0.2376 6.3064 1313.678351 0 0.0446 132 | 1/8 9 h-lim-p 0.5070 4.0560 0.1035 1313.319890 3 0.4595 150 | 0/8 10 h-lim-p 0.0499 0.5026 0.9531 1313.315805 3 0.0209 175 | 0/8 11 h-lim-p 0.2437 9.3851 0.0816 1313.273204 0 0.7311 196 | 0/8 12 h-lim-p 0.9357 7.4854 0.0073 1313.270713 4 0.7337 224 | 0/8 13 h-lim-p 2.2067 20.0000 0.0024 1313.270623 2 0.8792 248 | 0/8 14 h-lim-p 2.5000 20.0000 0.0002 1313.270622 1 0.9961 270 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1313.270622 0 1.0938 290 | 0/8 16 h-lim-p 1.3294 20.0000 0.0000 1313.270622 0 1.1632 310 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1313.270622 0 2.1875 330 | 0/8 18 h-lim-p 1.7664 20.0000 0.0000 1313.270622 0 0.7728 350 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1313.270622 0 0.0391 375 | 0/8 20 h-lim-p 0.0284 20.0000 0.0000 1313.270622 0 0.0000 406 Out... lnL = -1313.270622 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1313.270622 Node 7: lnL = -1313.270622 Node 8: lnL = -1313.270622 Node 9: lnL = -1313.270622 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 237 Sequential format.. Reading seq # 1: YLR368W_Sbay Reading seq # 2: YLR368W_Scer Reading seq # 3: YLR368W_Skud Reading seq # 4: YLR368W_Smik Reading seq # 5: YLR368W_Spar Sequences read.. Counting patterns.. # site patterns = 106 Counting frequencies.. 120 bytes for distance 16960 bytes for lkl0 13568 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.214274 0.027760 0.056264 0.087915 0.092748 0.181581 0.264787 0.065392 lnL0 = -1033.777701 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1033.777701 x= 0.21427 0.02776 0.05626 0.08791 0.09275 0.18158 0.26479 0.06539 1 h-lim-p 0.0016 0.0130 78.5861 1032.463749 9 0.0005 44 | 0/8 2 h-lim-p 0.0014 0.0112 13.0786 1032.396599 7 0.0008 72 | 0/8 3 h-lim-p 0.0022 0.0650 4.7196 1032.386253 2 0.0010 88 | 0/8 4 h-lim-p 0.0017 0.0826 2.8708 1032.383343 6 0.0010 114 | 0/8 5 h-lim-p 0.0037 0.4362 0.7433 1032.382985 2 0.0014 130 | 0/8 6 h-lim-p 0.0049 0.5149 0.2140 1032.382967 2 0.0008 156 | 0/8 7 h-lim-p 0.0053 4.3076 0.0317 1032.382966 0 0.0023 176 | 0/8 8 h-lim-p 0.0952 20.0000 0.0008 1032.382615 0 1.1429 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1032.382606 1 0.9961 221 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1032.382606 0 2.1875 241 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1032.382606 0 1.0938 261 | 0/8 12 h-lim-p 0.2986 20.0000 0.0000 1032.382606 0 4.7781 285 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1032.382606 0 0.5469 306 | 0/8 14 h-lim-p 0.0523 20.0000 0.0001 1032.382606 0 0.0033 329 | 0/8 15 h-lim-p 0.0009 20.0000 0.0003 1032.382606 0 0.0000 355 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 1032.382606 0 0.0000 380 | 0/8 17 h-lim-p 0.0002 20.0000 0.0000 1032.382606 0 0.0002 400 Out... lnL = -1032.382606 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1032.382606 Node 7: lnL = -1032.382606 Node 8: lnL = -1032.382606 Node 9: lnL = -1032.382606 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 250 Sequential format.. Reading seq # 1: YLR369W_Sbay Reading seq # 2: YLR369W_Scer Reading seq # 3: YLR369W_Skud Reading seq # 4: YLR369W_Smik Reading seq # 5: YLR369W_Spar Sequences read.. Counting patterns.. # site patterns = 121 Counting frequencies.. 120 bytes for distance 19360 bytes for lkl0 15488 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.249066 0.082528 0.027972 0.172547 0.051118 0.226296 0.244640 0.077899 lnL0 = -1111.864179 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1111.864179 x= 0.24907 0.08253 0.02797 0.17255 0.05112 0.22630 0.24464 0.07790 1 h-lim-p 0.0004 0.0030 41.7511 1111.451427 0 0.0006 22 | 0/8 2 h-lim-p 0.0010 0.0077 12.9258 1111.390471 6 0.0008 47 | 0/8 3 h-lim-p 0.0007 0.0280 13.9410 1111.363477 6 0.0005 76 | 0/8 4 h-lim-p 0.0029 0.0547 2.4271 1111.358802 6 0.0017 105 | 0/8 5 h-lim-p 0.0066 0.3850 0.6350 1111.358499 2 0.0015 122 | 0/8 6 h-lim-p 0.0076 1.3823 0.1276 1111.358475 1 0.0019 145 | 0/8 7 h-lim-p 0.0374 13.2516 0.0065 1111.355842 0 0.4482 168 | 0/8 8 h-lim-p 0.0038 0.1533 0.7648 1111.353257 3 0.0032 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 1111.353131 2 0.9644 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1111.353131 0 1.0938 238 | 0/8 11 h-lim-p 2.3142 20.0000 0.0000 1111.353131 0 2.0249 258 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1111.353131 0 0.5469 279 | 0/8 13 h-lim-p 0.1035 20.0000 0.0000 1111.353131 0 0.0776 299 | 0/8 14 h-lim-p 0.0344 20.0000 0.0000 1111.353131 0 0.0086 320 | 0/8 15 h-lim-p 0.0047 20.0000 0.0000 1111.353131 0 0.0006 342 | 0/8 16 h-lim-p 0.0004 20.0000 0.0000 1111.353131 0 0.0000 376 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 1111.353131 0 0.0000 406 | 0/8 18 h-lim-p 0.0000 20.0000 0.0004 1111.353131 0 0.0000 437 | 0/8 19 h-lim-p 0.0000 20.0000 0.0004 | 0/8 20 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1111.353131 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1111.353131 Node 7: lnL = -1111.353131 Node 8: lnL = -1111.353131 Node 9: lnL = -1111.353131 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 552 Sequential format.. Reading seq # 1: YLR370C_Sbay Reading seq # 2: YLR370C_Scer Reading seq # 3: YLR370C_Skud Reading seq # 4: YLR370C_Smik Reading seq # 5: YLR370C_Spar Sequences read.. Counting patterns.. # site patterns = 157 Counting frequencies.. 120 bytes for distance 25120 bytes for lkl0 20096 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.157057 0.063414 0.055968 0.079424 0.058982 0.163511 0.070284 0.048019 lnL0 = -2031.475736 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2031.475736 x= 0.15706 0.06341 0.05597 0.07942 0.05898 0.16351 0.07028 0.04802 1 h-lim-p 0.0011 0.0090 67.6880 2031.087671 8 0.0002 43 | 0/8 2 h-lim-p 0.0013 0.0120 8.9328 2031.078117 5 0.0002 68 | 0/8 3 h-lim-p 0.0010 0.0691 2.2165 2031.077432 5 0.0003 94 | 0/8 4 h-lim-p 0.0008 0.2583 0.8514 2031.077331 3 0.0003 112 | 0/8 5 h-lim-p 0.0013 0.5119 0.2102 2031.077325 1 0.0003 135 | 0/8 6 h-lim-p 0.0028 4.6128 0.0230 2031.077325 0 0.0003 157 | 0/8 7 h-lim-p 0.0035 20.0000 0.0020 2031.077325 0 0.0004 179 | 0/8 8 h-lim-p 0.0204 20.0000 0.0000 2031.077324 0 1.3071 205 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2031.077324 0 1.0938 225 | 0/8 10 h-lim-p 0.6262 20.0000 0.0000 2031.077324 0 3.7572 247 | 0/8 11 h-lim-p 1.9936 20.0000 0.0000 2031.077324 0 0.8722 267 | 0/8 12 h-lim-p 0.0622 20.0000 0.0007 2031.077324 0 0.0039 290 | 0/8 13 h-lim-p 0.0011 20.0000 0.0024 2031.077324 0 0.0000 314 | 0/8 14 h-lim-p 0.0001 20.0000 0.0009 2031.077324 0 0.0000 348 | 0/8 15 h-lim-p 0.0000 20.0000 0.0025 | 0/8 16 h-lim-p 0.0000 20.0000 0.0025 Out... lnL = -2031.077324 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2031.077324 Node 7: lnL = -2031.077324 Node 8: lnL = -2031.077324 Node 9: lnL = -2031.077324 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 502 Sequential format.. Reading seq # 1: YLR371W_Sbay Reading seq # 2: YLR371W_Scer Reading seq # 3: YLR371W_Skud Reading seq # 4: YLR371W_Smik Reading seq # 5: YLR371W_Spar Sequences read.. Counting patterns.. # site patterns = 153 Counting frequencies.. 120 bytes for distance 24480 bytes for lkl0 19584 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.173180 0.052716 0.053871 0.077898 0.060508 0.162385 0.081945 0.061170 lnL0 = -1950.897512 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1950.897512 x= 0.17318 0.05272 0.05387 0.07790 0.06051 0.16239 0.08194 0.06117 1 h-lim-p 0.0051 1.5715 87.3726 1950.271945 7 0.0002 41 | 0/8 2 h-lim-p 0.0011 0.0085 11.9963 1950.251296 6 0.0003 66 | 0/8 3 h-lim-p 0.0012 0.0536 2.9623 1950.250357 4 0.0002 87 | 0/8 4 h-lim-p 0.0010 0.2790 0.7006 1950.250278 3 0.0003 106 | 0/8 5 h-lim-p 0.0012 0.6940 0.1983 1950.250271 2 0.0003 131 | 0/8 6 h-lim-p 0.0017 3.5478 0.0362 1950.250271 0 0.0004 152 | 0/8 7 h-lim-p 0.0020 20.0000 0.0068 1950.250271 0 0.0004 173 | 0/8 8 h-lim-p 0.0244 20.0000 0.0001 1950.250255 0 0.7804 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1950.250255 0 1.0938 218 | 0/8 10 h-lim-p 1.0122 20.0000 0.0000 1950.250255 0 0.4428 238 | 0/8 11 h-lim-p 0.2530 20.0000 0.0000 1950.250255 0 0.0069 262 | 0/8 12 h-lim-p 0.0035 20.0000 0.0001 1950.250255 0 0.0009 283 | 0/8 13 h-lim-p 0.0005 20.0000 0.0001 1950.250255 0 0.0000 307 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 1950.250255 0 0.0000 327 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 1950.250255 0 0.0000 364 | 0/8 16 h-lim-p 0.0000 20.0000 0.0027 1950.250255 0 0.0000 389 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 1950.250255 0 0.0013 416 | 0/8 18 h-lim-p 0.0026 20.0000 0.0002 1950.250255 0 0.0000 444 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 1950.250255 0 0.0000 464 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 1950.250255 0 0.0000 487 | 0/8 21 h-lim-p 0.0000 20.0000 0.0009 1950.250255 0 0.0000 521 | 0/8 22 h-lim-p 0.0000 20.0000 0.0032 1950.250255 0 0.0000 550 | 0/8 23 h-lim-p 0.0000 20.0000 0.0004 1950.250255 0 0.0000 570 | 0/8 24 h-lim-p 0.0000 20.0000 0.0002 .. | 0/8 25 h-lim-p 0.0000 20.0000 0.0032 1950.250255 0 0.0000 634 | 0/8 26 h-lim-p 0.0000 20.0000 0.0003 1950.250255 0 0.0000 665 | 0/8 27 h-lim-p 0.0000 20.0000 0.0032 | 0/8 28 h-lim-p 0.0000 20.0000 0.0032 Out... lnL = -1950.250255 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1950.250255 Node 7: lnL = -1950.250255 Node 8: lnL = -1950.250255 Node 9: lnL = -1950.250255 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 618 Sequential format.. Reading seq # 1: YLR372W_Sbay Reading seq # 2: YLR372W_Scer Reading seq # 3: YLR372W_Skud Reading seq # 4: YLR372W_Smik Reading seq # 5: YLR372W_Spar Sequences read.. Counting patterns.. # site patterns = 175 Counting frequencies.. 120 bytes for distance 28000 bytes for lkl0 22400 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.127935 0.029346 0.043885 0.049900 0.058241 0.133987 0.138855 0.033852 lnL0 = -2263.105349 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2263.105349 x= 0.12793 0.02935 0.04389 0.04990 0.05824 0.13399 0.13885 0.03385 1 h-lim-p 0.0003 0.0028 197.2448 2261.094164 7 0.0001 36 | 0/8 2 h-lim-p 0.0003 0.0023 26.2718 2261.044801 4 0.0001 56 | 0/8 3 h-lim-p 0.0006 0.0327 6.5104 2261.040754 5 0.0002 80 | 0/8 4 h-lim-p 0.0004 0.0413 3.0177 2261.039928 2 0.0002 96 | 0/8 5 h-lim-p 0.0025 0.2585 0.2648 2261.039921 2 0.0002 114 | 0/8 6 h-lim-p 0.0011 2.8220 0.0554 2261.039920 0 0.0003 135 | 0/8 7 h-lim-p 0.0011 10.0302 0.0139 2261.039920 0 0.0005 155 | 0/8 8 h-lim-p 0.1164 20.0000 0.0001 2261.039906 0 0.9309 178 | 0/8 9 h-lim-p 0.6199 20.0000 0.0001 2261.039905 0 1.2398 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2261.039905 0 1.0938 219 | 0/8 11 h-lim-p 0.4330 20.0000 0.0000 2261.039905 0 3.4639 242 | 0/8 12 h-lim-p 0.8977 20.0000 0.0001 2261.039905 0 0.0140 267 | 0/8 13 h-lim-p 0.0000 0.9132 0.0581 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0038 2261.039905 0 0.0000 324 | 0/8 15 h-lim-p 0.0003 20.0000 0.0005 2261.039905 0 0.0012 346 | 0/8 16 h-lim-p 0.0039 20.0000 0.0002 2261.039905 0 0.0000 376 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 2261.039905 0 0.0000 396 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 2261.039905 0 0.0000 430 | 0/8 19 h-lim-p 0.0000 20.0000 0.0044 | 0/8 20 h-lim-p 0.0000 20.0000 0.0044 Out... lnL = -2261.039905 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2261.039905 Node 7: lnL = -2261.039905 Node 8: lnL = -2261.039905 Node 9: lnL = -2261.039905 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 95 Sequential format.. Reading seq # 1: YLR373C_Sbay Reading seq # 2: YLR373C_Scer Reading seq # 3: YLR373C_Skud Reading seq # 4: YLR373C_Smik Reading seq # 5: YLR373C_Spar Sequences read.. Counting patterns.. # site patterns = 46 Counting frequencies.. 120 bytes for distance 7360 bytes for lkl0 5888 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.143795 0.159855 0.139686 0.052862 0.129043 0.219794 0.216169 0.000060 lnL0 = -386.167282 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 386.167282 x= 0.14379 0.15986 0.13969 0.05286 0.12904 0.21979 0.21617 0.00006 1 h-lim-p 0.0000 0.0000 35.4983 386.159687 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0049 19.6831 385.961499 0 0.0013 41 | 1/8 3 h-lim-p 0.0017 0.0142 14.6122 385.781272 0 0.0034 54 | 1/8 4 h-lim-p 0.0102 0.0818 3.5734 385.757626 6 0.0033 81 | 1/8 5 h-lim-p 0.0074 0.1587 1.6168 385.738115 2 0.0069 97 | 1/8 6 h-lim-p 0.0347 0.7581 0.3224 384.572340 0 0.2776 112 | 1/8 7 h-lim-p 0.0028 0.0222 8.7790 384.461908 2 0.0026 135 | 1/8 8 h-lim-p 0.0640 0.7143 0.3565 384.460136 5 0.0102 160 | 0/8 9 h-lim-p 0.0006 0.1476 5.8993 384.430158 0 0.0025 181 | 0/8 10 h-lim-p 0.0825 0.6600 0.0383 384.380219 m 0.6600 193 | 1/8 11 h-lim-p 2.5000 20.0000 0.0058 384.375781 6 0.7213 229 | 0/8 12 h-lim-p 0.0039 0.3864 1.0801 384.374394 4 0.0030 256 | 0/8 13 h-lim-p 2.5000 20.0000 0.0013 384.374216 4 0.8479 279 | 0/8 14 h-lim-p 2.5000 20.0000 0.0003 384.374195 3 1.0004 305 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 384.374195 0 1.0938 325 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 384.374195 0 1.0938 345 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 384.374195 0 1.0938 365 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 384.374195 0 0.0098 392 Out... lnL = -384.374195 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -384.374195 Node 7: lnL = -384.374195 Node 8: lnL = -384.374195 Node 9: lnL = -384.374195 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 842 Sequential format.. Reading seq # 1: YLR374C_Sbay Reading seq # 2: YLR374C_Scer Reading seq # 3: YLR374C_Skud Reading seq # 4: YLR374C_Smik Reading seq # 5: YLR374C_Spar Sequences read.. Counting patterns.. # site patterns = 105 Counting frequencies.. 120 bytes for distance 16800 bytes for lkl0 13440 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.076105 0.033108 0.027742 0.041635 0.040169 0.083019 0.066542 0.016275 lnL0 = -2612.633262 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2612.633262 x= 0.07610 0.03311 0.02774 0.04163 0.04017 0.08302 0.06654 0.01627 1 h-lim-p 0.0004 0.0032 199.3977 2611.645527 6 0.0001 35 | 0/8 2 h-lim-p 0.0002 0.0020 30.9584 2611.609148 7 0.0001 65 | 0/8 3 h-lim-p 0.0004 0.0127 6.6062 2611.607403 2 0.0001 82 | 0/8 4 h-lim-p 0.0004 0.0385 1.5617 2611.607326 2 0.0001 99 | 0/8 5 h-lim-p 0.0003 0.4340 0.3484 2611.607319 1 0.0001 113 | 0/8 6 h-lim-p 0.0004 0.4337 0.0962 2611.607319 0 0.0001 134 | 0/8 7 h-lim-p 0.0009 3.4611 0.0100 2611.607319 0 0.0001 156 | 0/8 8 h-lim-p 0.0119 20.0000 0.0001 2611.607312 0 1.1395 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2611.607312 0 1.0938 202 | 0/8 10 h-lim-p 0.1589 20.0000 0.0001 2611.607312 0 0.3177 223 | 0/8 11 h-lim-p 0.1242 20.0000 0.0003 2611.607312 0 0.0005 250 | 0/8 12 h-lim-p 0.0002 20.0000 0.0007 2611.607312 0 0.0000 289 | 0/8 13 h-lim-p 0.0000 20.0000 0.0115 | 0/8 14 h-lim-p 0.0000 20.0000 0.0115 Out... lnL = -2611.607312 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2611.607312 Node 7: lnL = -2611.607312 Node 8: lnL = -2611.607312 Node 9: lnL = -2611.607312 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 357 Sequential format.. Reading seq # 1: YLR375W_Sbay Reading seq # 2: YLR375W_Scer Reading seq # 3: YLR375W_Skud Reading seq # 4: YLR375W_Smik Reading seq # 5: YLR375W_Spar Sequences read.. Counting patterns.. # site patterns = 90 Counting frequencies.. 120 bytes for distance 14400 bytes for lkl0 11520 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.084530 0.044680 0.057432 0.046237 0.055114 0.119883 0.092993 0.004337 lnL0 = -1206.464198 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1206.464198 x= 0.08453 0.04468 0.05743 0.04624 0.05511 0.11988 0.09299 0.00434 1 h-lim-p 0.0004 0.0033 70.7391 1205.994429 2 0.0002 26 | 0/8 2 h-lim-p 0.0002 0.0018 10.5708 1205.981059 5 0.0002 50 | 0/8 3 h-lim-p 0.0013 0.0346 2.0008 1205.980624 4 0.0002 73 | 0/8 4 h-lim-p 0.0009 0.2835 0.5182 1205.980582 2 0.0003 89 | 0/8 5 h-lim-p 0.0007 0.2620 0.2330 1205.980576 2 0.0002 114 | 0/8 6 h-lim-p 0.0017 1.7219 0.0331 1205.980576 0 0.0004 135 | 0/8 7 h-lim-p 0.0014 12.7098 0.0087 1205.980576 0 0.0021 155 | 0/8 8 h-lim-p 0.0139 20.0000 0.0013 1205.980445 0 0.2218 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1205.980442 1 0.9961 201 | 0/8 10 h-lim-p 0.9273 20.0000 0.0000 1205.980442 0 0.8114 221 | 0/8 11 h-lim-p 0.0694 18.4701 0.0006 1205.980442 0 0.0000 252 | 0/8 12 h-lim-p 0.0001 20.0000 0.0001 1205.980442 0 0.0000 283 | 0/8 13 h-lim-p 0.0000 20.0000 0.0003 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -1205.980442 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1205.980442 Node 7: lnL = -1205.980442 Node 8: lnL = -1205.980442 Node 9: lnL = -1205.980442 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 262 Sequential format.. Reading seq # 1: YLR381W_Sbay Reading seq # 2: YLR381W_Scer Reading seq # 3: YLR381W_Skud Reading seq # 4: YLR381W_Smik Reading seq # 5: YLR381W_Spar Sequences read.. Counting patterns.. # site patterns = 119 Counting frequencies.. 120 bytes for distance 19040 bytes for lkl0 15232 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.202561 0.041797 0.091217 0.120338 0.129605 0.196803 0.317477 0.030086 lnL0 = -974.067942 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 974.067942 x= 0.20256 0.04180 0.09122 0.12034 0.12961 0.19680 0.31748 0.03009 1 h-lim-p 0.0009 0.0074 52.7769 972.645172 1 0.0012 24 | 0/8 2 h-lim-p 0.0004 0.0029 26.9663 972.249695 0 0.0015 38 | 0/8 3 h-lim-p 0.0004 0.0036 20.4505 971.970603 0 0.0018 52 | 0/8 4 h-lim-p 0.0016 0.0126 21.7597 971.750563 0 0.0024 64 | 0/8 5 h-lim-p 0.0018 0.0142 16.3913 971.658173 6 0.0015 87 | 0/8 6 h-lim-p 0.0157 0.1259 1.5113 971.656536 5 0.0014 114 | 0/8 7 h-lim-p 0.0031 0.2307 0.6810 971.656045 5 0.0019 141 | 0/8 8 h-lim-p 0.0539 12.7749 0.0240 971.610732 0 0.6468 164 | 0/8 9 h-lim-p 2.5000 20.0000 0.0023 971.609690 3 1.0449 190 | 0/8 10 h-lim-p 2.5000 20.0000 0.0003 971.609670 1 1.0938 212 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 971.609670 0 1.0938 232 | 0/8 12 h-lim-p 2.1254 20.0000 0.0000 971.609670 0 1.0627 252 | 0/8 13 h-lim-p 0.9655 20.0000 0.0000 971.609670 0 3.8620 274 | 0/8 14 h-lim-p 0.0410 20.0000 0.0009 971.609670 0 0.0001 301 | 0/8 15 h-lim-p 0.0000 0.3424 0.0680 971.609670 0 0.0000 330 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 971.609670 0 0.0000 355 | 0/8 17 h-lim-p 0.0001 20.0000 0.0000 971.609670 0 0.0000 386 Out... lnL = -971.609670 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -971.609670 Node 7: lnL = -971.609670 Node 8: lnL = -971.609670 Node 9: lnL = -971.609670 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 180 Sequential format.. Reading seq # 1: YLR384C_Sbay Reading seq # 2: YLR384C_Scer Reading seq # 3: YLR384C_Skud Reading seq # 4: YLR384C_Smik Reading seq # 5: YLR384C_Spar Sequences read.. Counting patterns.. # site patterns = 101 Counting frequencies.. 120 bytes for distance 16160 bytes for lkl0 12928 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.156047 0.015929 0.037604 0.080521 0.092813 0.175507 0.189994 0.033979 lnL0 = -689.542022 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 689.542022 x= 0.15605 0.01593 0.03760 0.08052 0.09281 0.17551 0.18999 0.03398 1 h-lim-p 0.0007 0.0058 125.1192 686.371202 9 0.0005 44 | 0/8 2 h-lim-p 0.0004 0.0029 42.1078 685.443387 0 0.0015 58 | 0/8 3 h-lim-p 0.0012 0.0098 21.5722 685.274458 8 0.0009 89 | 0/8 4 h-lim-p 0.0041 0.0498 4.8411 685.262391 6 0.0011 114 | 0/8 5 h-lim-p 0.0082 0.5736 0.6527 685.261817 2 0.0019 131 | 0/8 6 h-lim-p 0.0049 0.3752 0.2533 685.260962 1 0.0062 153 | 0/8 7 h-lim-p 0.0106 1.6449 0.1478 685.224502 0 0.0848 176 | 0/8 8 h-lim-p 0.0049 0.0973 2.5833 685.196024 3 0.0041 202 | 0/8 9 h-lim-p 2.5000 20.0000 0.0020 685.195016 4 1.0199 223 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 685.194983 3 1.4660 252 | 0/8 11 h-lim-p 2.5000 20.0000 0.0001 685.194981 2 1.3159 277 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 685.194981 0 1.0938 297 | 0/8 13 h-lim-p 1.5007 20.0000 0.0000 685.194981 0 1.3131 317 | 0/8 14 h-lim-p 0.7555 20.0000 0.0000 685.194981 0 0.0472 340 | 0/8 15 h-lim-p 0.0013 20.0000 0.0005 685.194981 0 0.0000 374 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 685.194981 0 0.0001 394 Out... lnL = -685.194981 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -685.194981 Node 7: lnL = -685.194981 Node 8: lnL = -685.194981 Node 9: lnL = -685.194981 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 247 Sequential format.. Reading seq # 1: YLR385C_Sbay Reading seq # 2: YLR385C_Scer Reading seq # 3: YLR385C_Skud Reading seq # 4: YLR385C_Smik Reading seq # 5: YLR385C_Spar Sequences read.. Counting patterns.. # site patterns = 101 Counting frequencies.. 120 bytes for distance 16160 bytes for lkl0 12928 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.185719 0.120597 0.050361 0.148102 0.099625 0.093069 0.156357 0.038248 lnL0 = -1095.373773 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1095.373773 x= 0.18572 0.12060 0.05036 0.14810 0.09962 0.09307 0.15636 0.03825 1 h-lim-p 0.0039 0.0315 68.8515 1094.473861 8 0.0004 42 | 0/8 2 h-lim-p 0.0014 0.0109 14.9904 1094.370648 8 0.0009 75 | 0/8 3 h-lim-p 0.0058 0.0554 2.4425 1094.368491 4 0.0007 97 | 0/8 4 h-lim-p 0.0086 0.4686 0.2100 1094.368471 1 0.0009 113 | 0/8 5 h-lim-p 0.0053 5.9022 0.0342 1094.368471 0 0.0012 134 | 0/8 6 h-lim-p 0.0185 20.0000 0.0021 1094.368471 0 0.0081 154 | 0/8 7 h-lim-p 0.0053 20.0000 0.0033 1094.368470 0 0.0106 175 | 0/8 8 h-lim-p 0.0053 20.0000 0.0065 1094.368459 0 0.0211 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1094.368459 0 1.0938 217 | 0/8 10 h-lim-p 1.7689 20.0000 0.0000 1094.368459 0 1.5478 237 | 0/8 11 h-lim-p 2.3209 20.0000 0.0000 1094.368459 0 0.5077 258 | 0/8 12 h-lim-p 0.1676 20.0000 0.0000 1094.368459 0 0.0092 281 | 0/8 13 h-lim-p 0.0033 20.0000 0.0001 1094.368459 0 0.0000 322 | 0/8 14 h-lim-p 0.0000 20.0000 0.0006 | 0/8 15 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -1094.368459 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1094.368459 Node 7: lnL = -1094.368459 Node 8: lnL = -1094.368459 Node 9: lnL = -1094.368459 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 850 Sequential format.. Reading seq # 1: YLR387C_Sbay Reading seq # 2: YLR387C_Scer Reading seq # 3: YLR387C_Skud Reading seq # 4: YLR387C_Smik Reading seq # 5: YLR387C_Spar Sequences read.. Counting patterns.. # site patterns = 318 Counting frequencies.. 120 bytes for distance 50880 bytes for lkl0 40704 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.249071 0.045008 0.089119 0.136492 0.077061 0.178798 0.227071 0.076206 lnL0 = -3677.306125 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3677.306125 x= 0.24907 0.04501 0.08912 0.13649 0.07706 0.17880 0.22707 0.07621 1 h-lim-p 0.0004 0.0032 161.7991 3674.710564 8 0.0002 38 | 0/8 2 h-lim-p 0.0006 0.0048 43.5246 3674.342129 6 0.0004 65 | 0/8 3 h-lim-p 0.0006 0.0139 28.7602 3674.284094 6 0.0002 94 | 0/8 4 h-lim-p 0.0007 0.0231 8.1686 3674.274429 2 0.0003 110 | 0/8 5 h-lim-p 0.0018 0.1346 1.4372 3674.273922 4 0.0005 132 | 0/8 6 h-lim-p 0.0072 1.5451 0.1023 3674.273919 1 0.0004 149 | 0/8 7 h-lim-p 0.0031 13.4006 0.0145 3674.273919 0 0.0014 169 | 0/8 8 h-lim-p 0.0573 20.0000 0.0003 3674.273854 0 0.9171 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3674.273848 0 1.0938 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3674.273848 0 1.0938 233 | 0/8 11 h-lim-p 1.0388 20.0000 0.0000 3674.273848 0 0.9089 253 | 0/8 12 h-lim-p 0.4123 20.0000 0.0000 3674.273848 0 0.1031 274 | 0/8 13 h-lim-p 0.0207 20.0000 0.0002 3674.273848 0 0.0000 304 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 3674.273848 0 0.0000 364 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -3674.273848 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3674.273848 Node 7: lnL = -3674.273848 Node 8: lnL = -3674.273848 Node 9: lnL = -3674.273848 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 421 Sequential format.. Reading seq # 1: YLR389C_Sbay Reading seq # 2: YLR389C_Scer Reading seq # 3: YLR389C_Skud Reading seq # 4: YLR389C_Smik Reading seq # 5: YLR389C_Spar Sequences read.. Counting patterns.. # site patterns = 169 Counting frequencies.. 120 bytes for distance 27040 bytes for lkl0 21632 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.279620 0.000060 0.164353 0.134819 0.039048 0.948056 0.147993 0.011364 lnL0 = -1682.299279 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1682.299279 x= 0.27962 0.00006 0.16435 0.13482 0.03905 0.94806 0.14799 0.01136 1 h-lim-p 0.0001 0.0009 43.4519 1681.873789 0 0.0004 24 | 0/8 2 h-lim-p 0.0001 0.0006 30.6074 1681.771926 0 0.0003 38 | 0/8 3 h-lim-p 0.0001 0.0012 11.6737 1681.693512 m 0.0012 50 | 0/8 4 h-lim-p 0.0009 0.0149 16.3396 1681.622447 0 0.0013 62 | 0/8 5 h-lim-p 0.0015 0.0118 14.2571 1681.599562 4 0.0006 82 | 0/8 6 h-lim-p 0.0003 0.0028 2.3980 1681.597441 0 0.0010 95 | 0/8 7 h-lim-p 0.0015 0.5793 1.6295 1681.575692 0 0.0243 111 | 0/8 8 h-lim-p 2.5000 20.0000 0.0036 1681.569591 4 1.0049 131 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1681.569583 1 0.9961 153 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1681.569583 0 1.0938 173 | 0/8 11 h-lim-p 1.4665 20.0000 0.0000 1681.569583 0 1.2832 193 | 0/8 12 h-lim-p 0.5147 20.0000 0.0001 1681.569583 0 0.0020 220 | 0/8 13 h-lim-p 0.0003 7.7892 0.0004 1681.569583 0 0.0000 254 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 1681.569583 0 0.0026 282 | 0/8 15 h-lim-p 0.0042 20.0000 0.0001 1681.569583 0 0.0001 307 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 1681.569583 0 0.0001 328 | 0/8 17 h-lim-p 0.0001 20.0000 0.0002 1681.569583 0 0.0000 356 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0017 | 0/8 20 h-lim-p 0.0000 20.0000 0.0017 Out... lnL = -1681.569583 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1681.569583 Node 7: lnL = -1681.569583 Node 8: lnL = -1681.569583 Node 9: lnL = -1681.569583 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 334 Sequential format.. Reading seq # 1: YLR390W-A_Sbay Reading seq # 2: YLR390W-A_Scer Reading seq # 3: YLR390W-A_Skud Reading seq # 4: YLR390W-A_Smik Reading seq # 5: YLR390W-A_Spar Sequences read.. Counting patterns.. # site patterns = 111 Counting frequencies.. 120 bytes for distance 17760 bytes for lkl0 14208 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.174661 0.072786 0.037136 0.072821 0.027663 0.126154 0.098792 0.064600 lnL0 = -1270.800712 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1270.800712 x= 0.17466 0.07279 0.03714 0.07282 0.02766 0.12615 0.09879 0.06460 1 h-lim-p 0.0011 0.0085 53.5828 1270.444656 7 0.0003 36 | 0/8 2 h-lim-p 0.0003 0.0020 40.6477 1270.287195 4 0.0003 56 | 0/8 3 h-lim-p 0.0005 0.0040 16.8704 1270.259714 5 0.0002 80 | 0/8 4 h-lim-p 0.0013 0.0346 3.0815 1270.258140 4 0.0003 101 | 0/8 5 h-lim-p 0.0033 0.4334 0.3284 1270.258117 2 0.0004 119 | 0/8 6 h-lim-p 0.0011 1.4068 0.1332 1270.258115 2 0.0003 144 | 0/8 7 h-lim-p 0.0191 20.0000 0.0024 1270.258112 0 0.0191 164 | 0/8 8 h-lim-p 0.0041 20.0000 0.0111 1270.258001 0 0.0326 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1270.257997 1 0.9961 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1270.257997 0 0.0684 233 | 0/8 11 h-lim-p 0.0348 20.0000 0.0000 1270.257997 0 0.0043 255 | 0/8 12 h-lim-p 0.0027 20.0000 0.0000 1270.257997 0 0.0000 294 | 0/8 13 h-lim-p 0.0000 20.0000 0.0025 | 0/8 14 h-lim-p 0.0000 20.0000 0.0025 Out... lnL = -1270.257997 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1270.257997 Node 7: lnL = -1270.257997 Node 8: lnL = -1270.257997 Node 9: lnL = -1270.257997 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 539 Sequential format.. Reading seq # 1: YLR390W_Sbay Reading seq # 2: YLR390W_Scer Reading seq # 3: YLR390W_Skud Reading seq # 4: YLR390W_Smik Reading seq # 5: YLR390W_Spar Sequences read.. Counting patterns.. # site patterns = 223 Counting frequencies.. 120 bytes for distance 35680 bytes for lkl0 28544 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.248144 0.051669 0.052284 0.098737 0.070801 0.155197 0.228989 0.090067 lnL0 = -2288.027393 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2288.027393 x= 0.24814 0.05167 0.05228 0.09874 0.07080 0.15520 0.22899 0.09007 1 h-lim-p 0.0004 0.0036 164.1655 2284.385942 8 0.0003 42 | 0/8 2 h-lim-p 0.0002 0.0020 45.4154 2284.107111 1 0.0003 56 | 0/8 3 h-lim-p 0.0008 0.0149 18.5658 2284.018680 4 0.0006 76 | 0/8 4 h-lim-p 0.0011 0.0254 10.1825 2283.999053 2 0.0005 92 | 0/8 5 h-lim-p 0.0031 0.0707 1.6887 2283.998194 3 0.0006 111 | 0/8 6 h-lim-p 0.0038 0.6662 0.2881 2283.998166 2 0.0006 129 | 0/8 7 h-lim-p 0.0028 3.7759 0.0616 2283.998156 2 0.0019 155 | 0/8 8 h-lim-p 0.0287 20.0000 0.0040 2283.995047 0 0.3447 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 2283.994939 2 1.2402 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2283.994937 0 1.0938 222 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2283.994937 0 1.0938 242 | 0/8 12 h-lim-p 1.0962 20.0000 0.0000 2283.994937 0 4.3850 264 | 0/8 13 h-lim-p 0.1186 20.0000 0.0003 2283.994937 0 0.0009 290 | 0/8 14 h-lim-p 0.0007 20.0000 0.0004 2283.994937 0 0.0000 325 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -2283.994937 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2283.994937 Node 7: lnL = -2283.994937 Node 8: lnL = -2283.994937 Node 9: lnL = -2283.994937 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 823 Sequential format.. Reading seq # 1: YLR392C_Sbay Reading seq # 2: YLR392C_Scer Reading seq # 3: YLR392C_Skud Reading seq # 4: YLR392C_Smik Reading seq # 5: YLR392C_Spar Sequences read.. Counting patterns.. # site patterns = 296 Counting frequencies.. 120 bytes for distance 47360 bytes for lkl0 37888 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.217898 0.147897 0.065666 0.129472 0.085086 0.240904 0.204815 0.032231 lnL0 = -3818.734449 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3818.734449 x= 0.21790 0.14790 0.06567 0.12947 0.08509 0.24090 0.20482 0.03223 1 h-lim-p 0.0060 1.2794 112.7960 3817.430611 8 0.0002 45 | 0/8 2 h-lim-p 0.0008 0.0065 29.9760 3817.305407 7 0.0003 73 | 0/8 3 h-lim-p 0.0005 0.0143 16.5320 3817.263831 6 0.0004 100 | 0/8 4 h-lim-p 0.0024 0.0453 2.6866 3817.262582 5 0.0004 128 | 0/8 5 h-lim-p 0.0016 0.4867 0.6018 3817.262500 3 0.0005 149 | 0/8 6 h-lim-p 0.0067 5.0576 0.0423 3817.262500 0 0.0004 172 | 0/8 7 h-lim-p 0.0016 20.0000 0.0098 3817.262499 0 0.0032 193 | 0/8 8 h-lim-p 0.0162 20.0000 0.0019 3817.262307 0 0.1948 216 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3817.262307 0 1.0938 236 | 0/8 10 h-lim-p 0.9879 20.0000 0.0000 3817.262307 0 0.8644 256 | 0/8 11 h-lim-p 0.6556 20.0000 0.0000 3817.262307 0 0.3278 276 | 0/8 12 h-lim-p 0.0685 20.0000 0.0002 3817.262307 0 0.0171 297 | 0/8 13 h-lim-p 0.0061 20.0000 0.0005 3817.262307 0 0.0000 324 | 0/8 14 h-lim-p 0.0000 11.6153 0.0047 3817.262307 0 0.0000 351 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 3817.262307 0 0.0000 384 Out... lnL = -3817.262307 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3817.262307 Node 7: lnL = -3817.262307 Node 8: lnL = -3817.262307 Node 9: lnL = -3817.262307 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 868 Sequential format.. Reading seq # 1: YLR393W_Sbay Reading seq # 2: YLR393W_Scer Reading seq # 3: YLR393W_Skud Reading seq # 4: YLR393W_Smik Reading seq # 5: YLR393W_Spar Sequences read.. Counting patterns.. # site patterns = 292 Counting frequencies.. 120 bytes for distance 46720 bytes for lkl0 37376 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.240251 0.054538 0.066990 0.135448 0.082617 0.238161 0.254203 0.060246 lnL0 = -3866.355778 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3866.355778 x= 0.24025 0.05454 0.06699 0.13545 0.08262 0.23816 0.25420 0.06025 1 h-lim-p 0.0040 0.7993 138.7454 3864.607392 4 0.0002 33 | 0/8 2 h-lim-p 0.0006 0.0049 30.6504 3864.477547 2 0.0003 49 | 0/8 3 h-lim-p 0.0005 0.0176 17.3420 3864.439185 5 0.0003 73 | 0/8 4 h-lim-p 0.0007 0.0373 8.2822 3864.430409 2 0.0003 89 | 0/8 5 h-lim-p 0.0032 0.3867 0.8226 3864.430261 3 0.0004 109 | 0/8 6 h-lim-p 0.0039 2.9203 0.0913 3864.430259 0 0.0004 131 | 0/8 7 h-lim-p 0.0014 9.0409 0.0280 3864.430259 0 0.0012 151 | 0/8 8 h-lim-p 0.0523 20.0000 0.0007 3864.429899 0 0.6280 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3864.429896 0 1.0938 194 | 0/8 10 h-lim-p 2.3916 20.0000 0.0000 3864.429896 0 1.0463 214 | 0/8 11 h-lim-p 1.0699 20.0000 0.0000 3864.429896 0 3.2097 235 | 0/8 12 h-lim-p 0.2068 20.0000 0.0003 3864.429896 0 0.0129 258 | 0/8 13 h-lim-p 0.0028 20.0000 0.0014 3864.429896 0 0.0001 282 | 0/8 14 h-lim-p 0.0001 20.0000 0.0016 3864.429896 0 0.0000 312 | 0/8 15 h-lim-p 0.0000 20.0000 0.0008 | 0/8 16 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -3864.429896 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3864.429896 Node 7: lnL = -3864.429896 Node 8: lnL = -3864.429896 Node 9: lnL = -3864.429896 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 331 Sequential format.. Reading seq # 1: YLR395C_Sbay Reading seq # 2: YLR395C_Scer Reading seq # 3: YLR395C_Skud Reading seq # 4: YLR395C_Smik Reading seq # 5: YLR395C_Spar Sequences read.. Counting patterns.. # site patterns = 111 Counting frequencies.. 120 bytes for distance 17760 bytes for lkl0 14208 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.116711 0.107016 0.070579 0.055926 0.046054 0.163478 0.166551 0.000060 lnL0 = -1185.030524 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1185.030524 x= 0.11671 0.10702 0.07058 0.05593 0.04605 0.16348 0.16655 0.00006 1 h-lim-p 0.0000 0.0000 61.9427 1185.009281 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0028 31.1562 1184.864819 0 0.0003 39 | 1/8 3 h-lim-p 0.0013 0.0204 8.1718 1184.844462 6 0.0007 63 | 1/8 4 h-lim-p 0.0014 0.0329 3.7888 1184.841016 6 0.0005 89 | 1/8 5 h-lim-p 0.0042 0.3227 0.4695 1184.837253 2 0.0044 105 | 1/8 6 h-lim-p 0.0042 0.3033 0.4941 1184.647799 0 0.0335 127 | 1/8 7 h-lim-p 0.0020 0.0183 8.1791 1184.261213 1 0.0025 148 | 1/8 8 h-lim-p 0.0610 1.0891 0.3396 1184.261133 3 0.0010 171 | 1/8 9 h-lim-p 0.0550 20.0000 0.0063 1184.245808 0 0.6602 193 | 0/8 10 h-lim-p 0.0145 13.0306 0.2886 1184.245784 3 0.0005 224 | 0/8 11 h-lim-p 0.2071 2.1626 0.0007 1184.245027 0 0.8283 246 | 0/8 12 h-lim-p 0.1206 0.9647 0.0002 1184.245005 m 0.9647 266 | 1/8 13 h-lim-p 2.5000 20.0000 0.0001 1184.245003 1 0.6152 289 | 0/8 14 h-lim-p 0.0005 17.5474 0.0655 1184.245003 0 0.0001 309 | 0/8 15 h-lim-p 0.1295 1.0361 0.0000 1184.245002 m 1.0361 329 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 1184.245002 0 2.1875 349 | 1/8 17 h-lim-p 2.0162 20.0000 0.0000 1184.245002 0 0.8821 368 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 1184.245002 0 0.0000 414 Out... lnL = -1184.245002 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1184.245002 Node 7: lnL = -1184.245002 Node 8: lnL = -1184.245002 Node 9: lnL = -1184.245002 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 249 Sequential format.. Reading seq # 1: YLR396C_Sbay Reading seq # 2: YLR396C_Scer Reading seq # 3: YLR396C_Skud Reading seq # 4: YLR396C_Smik Reading seq # 5: YLR396C_Spar Sequences read.. Counting patterns.. # site patterns = 143 Counting frequencies.. 120 bytes for distance 22880 bytes for lkl0 18304 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.190393 0.177538 0.090977 0.205298 0.068869 0.238429 0.208528 0.000060 lnL0 = -1126.256995 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1126.256995 x= 0.19039 0.17754 0.09098 0.20530 0.06887 0.23843 0.20853 0.00006 1 h-lim-p 0.0000 0.0001 21.0419 1126.227748 m 0.0001 22 | 1/8 2 h-lim-p 0.0001 0.0141 13.2178 1126.159571 0 0.0009 37 | 1/8 3 h-lim-p 0.0082 0.2348 1.3931 1126.157689 4 0.0016 58 | 1/8 4 h-lim-p 0.0056 0.6196 0.3940 1126.154533 0 0.0084 70 | 1/8 5 h-lim-p 0.0088 1.4570 0.3734 1126.092715 0 0.0354 91 | 1/8 6 h-lim-p 0.0035 0.0846 3.7505 1125.958970 0 0.0070 111 | 1/8 7 h-lim-p 0.0049 0.0607 5.3961 1125.919681 2 0.0023 127 | 1/8 8 h-lim-p 0.0274 0.7529 0.4528 1125.919419 3 0.0023 149 | 0/8 9 h-lim-p 0.0003 0.2701 3.8278 1125.909281 0 0.0021 171 | 0/8 10 h-lim-p 0.4616 3.6931 0.0041 1125.905036 0 0.9233 184 | 0/8 11 h-lim-p 2.5000 20.0000 0.0004 1125.905001 2 0.9961 208 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1125.905001 0 1.2500 228 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1125.905001 0 1.0938 248 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1125.905001 0 5.0000 269 | 0/8 15 h-lim-p 1.4029 20.0000 0.0000 1125.905001 0 0.1754 291 | 0/8 16 h-lim-p 0.2242 20.0000 0.0000 1125.905001 0 0.0001 322 Out... lnL = -1125.905001 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1125.905001 Node 7: lnL = -1125.905001 Node 8: lnL = -1125.905001 Node 9: lnL = -1125.905001 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 307 Sequential format.. Reading seq # 1: YLR397C_Sbay Reading seq # 2: YLR397C_Scer Reading seq # 3: YLR397C_Skud Reading seq # 4: YLR397C_Smik Reading seq # 5: YLR397C_Spar Sequences read.. Counting patterns.. # site patterns = 175 Counting frequencies.. 120 bytes for distance 28000 bytes for lkl0 22400 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.366548 0.098646 0.088942 0.156987 0.108422 0.267599 0.389565 0.112636 lnL0 = -1557.952362 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1557.952362 x= 0.36655 0.09865 0.08894 0.15699 0.10842 0.26760 0.38956 0.11264 1 h-lim-p 0.0069 0.0549 18.0070 1557.789184 7 0.0010 43 | 0/8 2 h-lim-p 0.0030 0.0364 6.1531 1557.761480 5 0.0016 66 | 0/8 3 h-lim-p 0.0017 0.0611 5.9317 1557.748455 6 0.0012 92 | 0/8 4 h-lim-p 0.0026 0.1526 2.8568 1557.743617 6 0.0017 117 | 0/8 5 h-lim-p 0.0076 0.4196 0.6478 1557.743326 3 0.0015 136 | 0/8 6 h-lim-p 0.0044 1.4340 0.2222 1557.743280 0 0.0022 156 | 0/8 7 h-lim-p 0.0628 20.0000 0.0078 1557.743280 0 0.0069 178 | 0/8 8 h-lim-p 0.1407 20.0000 0.0004 1557.743255 0 0.5628 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1557.743255 0 1.0938 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1557.743255 0 1.0938 240 | 0/8 11 h-lim-p 1.2713 20.0000 0.0000 1557.743255 0 0.5562 260 | 0/8 12 h-lim-p 0.1804 20.0000 0.0000 1557.743255 0 0.0001 290 | 0/8 13 h-lim-p 0.0008 20.0000 0.0000 1557.743255 0 0.0000 323 Out... lnL = -1557.743255 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1557.743255 Node 7: lnL = -1557.743255 Node 8: lnL = -1557.743255 Node 9: lnL = -1557.743255 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 553 Sequential format.. Reading seq # 1: YLR398C_Sbay Reading seq # 2: YLR398C_Scer Reading seq # 3: YLR398C_Skud Reading seq # 4: YLR398C_Smik Reading seq # 5: YLR398C_Spar Sequences read.. Counting patterns.. # site patterns = 200 Counting frequencies.. 120 bytes for distance 32000 bytes for lkl0 25600 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.157195 0.072823 0.096969 0.101966 0.087804 0.165235 0.172651 0.013433 lnL0 = -2334.527281 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2334.527281 x= 0.15719 0.07282 0.09697 0.10197 0.08780 0.16524 0.17265 0.01343 1 h-lim-p 0.0084 1.8911 74.6118 2333.820681 8 0.0003 45 | 0/8 2 h-lim-p 0.0006 0.0045 12.2588 2333.798082 6 0.0003 70 | 0/8 3 h-lim-p 0.0016 0.1191 2.3656 2333.796974 4 0.0004 91 | 0/8 4 h-lim-p 0.0014 0.3221 0.6961 2333.796904 2 0.0003 108 | 0/8 5 h-lim-p 0.0016 0.3527 0.1438 2333.796900 1 0.0004 131 | 0/8 6 h-lim-p 0.0033 10.1097 0.0166 2333.796900 0 0.0007 152 | 0/8 7 h-lim-p 0.0131 20.0000 0.0009 2333.796899 0 0.0525 174 | 0/8 8 h-lim-p 0.0048 20.0000 0.0101 2333.796871 0 0.0144 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2333.796871 0 1.0938 215 | 0/8 10 h-lim-p 1.0468 20.0000 0.0000 2333.796871 0 0.9160 235 | 0/8 11 h-lim-p 0.4381 20.0000 0.0001 2333.796871 0 0.0009 263 | 0/8 12 h-lim-p 0.0003 20.0000 0.0002 2333.796871 0 0.0003 283 | 0/8 13 h-lim-p 0.0002 20.0000 0.0004 2333.796871 0 0.0000 314 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 2333.796871 0 0.0000 335 Out... lnL = -2333.796871 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2333.796871 Node 7: lnL = -2333.796871 Node 8: lnL = -2333.796871 Node 9: lnL = -2333.796871 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 494 Sequential format.. Reading seq # 1: YLR399C_Sbay Reading seq # 2: YLR399C_Scer Reading seq # 3: YLR399C_Skud Reading seq # 4: YLR399C_Smik Reading seq # 5: YLR399C_Spar Sequences read.. Counting patterns.. # site patterns = 126 Counting frequencies.. 120 bytes for distance 20160 bytes for lkl0 16128 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.111509 0.049419 0.030487 0.078951 0.052636 0.091732 0.115488 0.022152 lnL0 = -1763.042618 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1763.042618 x= 0.11151 0.04942 0.03049 0.07895 0.05264 0.09173 0.11549 0.02215 1 h-lim-p 0.0065 0.0658 73.9106 1762.606543 3 0.0002 32 | 0/8 2 h-lim-p 0.0002 0.0018 26.4462 1762.548961 3 0.0002 50 | 0/8 3 h-lim-p 0.0009 0.0182 5.1695 1762.546155 2 0.0002 67 | 0/8 4 h-lim-p 0.0017 0.1900 0.6745 1762.546113 2 0.0002 85 | 0/8 5 h-lim-p 0.0012 1.4485 0.1109 1762.546112 1 0.0001 109 | 0/8 6 h-lim-p 0.0007 6.2400 0.0220 1762.546111 0 0.0003 129 | 0/8 7 h-lim-p 0.0016 20.0000 0.0045 1762.546111 0 0.0007 149 | 0/8 8 h-lim-p 0.0125 20.0000 0.0002 1762.546093 0 0.4003 174 | 0/8 9 h-lim-p 1.7930 20.0000 0.0001 1762.546093 1 0.8825 197 | 0/8 10 h-lim-p 0.9484 20.0000 0.0001 1762.546093 0 0.8298 217 | 0/8 11 h-lim-p 0.6518 20.0000 0.0001 1762.546093 0 0.0001 249 | 0/8 12 h-lim-p 0.0001 20.0000 0.0001 1762.546093 0 0.0000 269 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 1762.546093 0 0.0000 300 | 0/8 14 h-lim-p 0.0000 20.0000 0.0017 1762.546093 0 0.0000 326 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 1762.546093 0 0.0013 353 | 0/8 16 h-lim-p 0.0069 20.0000 0.0001 1762.546093 0 0.0000 383 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0031 1762.546093 0 0.0000 443 | 0/8 19 h-lim-p 0.0000 20.0000 0.0005 1762.546093 0 0.0013 470 | 0/8 20 h-lim-p 0.0098 20.0000 0.0001 1762.546093 0 0.0000 498 | 0/8 21 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 22 h-lim-p 0.0000 20.0000 0.0046 | 0/8 23 h-lim-p 0.0000 20.0000 0.0046 Out... lnL = -1762.546093 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1762.546093 Node 7: lnL = -1762.546093 Node 8: lnL = -1762.546093 Node 9: lnL = -1762.546093 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 118 Sequential format.. Reading seq # 1: YLR401C_Sbay Reading seq # 2: YLR401C_Scer Reading seq # 3: YLR401C_Skud Reading seq # 4: YLR401C_Smik Reading seq # 5: YLR401C_Spar Sequences read.. Counting patterns.. # site patterns = 78 Counting frequencies.. 120 bytes for distance 12480 bytes for lkl0 9984 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.447907 0.013299 0.160888 0.155424 0.079589 0.208850 0.222226 0.199759 lnL0 = -592.909540 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 592.909540 x= 0.44791 0.01330 0.16089 0.15542 0.07959 0.20885 0.22223 0.19976 1 h-lim-p 0.0135 0.1082 29.5559 592.333073 6 0.0015 35 | 0/8 2 h-lim-p 0.0052 0.0416 5.6581 592.261557 5 0.0045 56 | 0/8 3 h-lim-p 0.0049 0.0661 5.2636 592.244403 6 0.0020 82 | 0/8 4 h-lim-p 0.0039 0.1300 2.6529 592.236344 3 0.0033 101 | 0/8 5 h-lim-p 0.0143 0.4538 0.6106 592.235699 3 0.0038 120 | 0/8 6 h-lim-p 0.0360 5.3685 0.0639 592.235684 2 0.0069 145 | 0/8 7 h-lim-p 0.0129 10.8103 0.0343 592.235680 1 0.0057 167 | 0/8 8 h-lim-p 0.1460 20.0000 0.0013 592.235431 0 0.8759 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 592.235422 1 0.9961 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 592.235422 0 1.0938 231 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 592.235422 0 1.0938 251 | 0/8 12 h-lim-p 2.0161 20.0000 0.0000 592.235422 0 1.7641 271 | 0/8 13 h-lim-p 1.9219 20.0000 0.0000 592.235422 0 0.4805 292 | 0/8 14 h-lim-p 0.0788 20.0000 0.0000 592.235422 0 0.0099 314 | 0/8 15 h-lim-p 0.0028 20.0000 0.0000 592.235422 0 0.0028 334 | 0/8 16 h-lim-p 0.0025 20.0000 0.0000 592.235422 0 0.0021 354 | 0/8 17 h-lim-p 0.0001 20.0000 0.0004 592.235422 0 0.0000 392 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 592.235422 0 0.0000 424 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 592.235422 0 0.0000 459 | 0/8 20 h-lim-p 0.0000 20.0000 0.0000 | 0/8 21 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -592.235422 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -592.235422 Node 7: lnL = -592.235422 Node 8: lnL = -592.235422 Node 9: lnL = -592.235422 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 528 Sequential format.. Reading seq # 1: YLR403W_Sbay Reading seq # 2: YLR403W_Scer Reading seq # 3: YLR403W_Skud Reading seq # 4: YLR403W_Smik Reading seq # 5: YLR403W_Spar Sequences read.. Counting patterns.. # site patterns = 180 Counting frequencies.. 120 bytes for distance 28800 bytes for lkl0 23040 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.139317 0.098074 0.070594 0.097970 0.075020 0.130226 0.143254 0.006190 lnL0 = -2105.445234 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2105.445234 x= 0.13932 0.09807 0.07059 0.09797 0.07502 0.13023 0.14325 0.00619 1 h-lim-p 0.0014 0.0115 70.4346 2104.824049 8 0.0003 45 | 0/8 2 h-lim-p 0.0003 0.0020 12.4899 2104.801472 1 0.0003 59 | 0/8 3 h-lim-p 0.0009 0.0285 4.3620 2104.798515 4 0.0003 79 | 0/8 4 h-lim-p 0.0026 0.1961 0.5724 2104.798467 2 0.0003 97 | 0/8 5 h-lim-p 0.0015 0.1420 0.1187 2104.798465 0 0.0003 118 | 0/8 6 h-lim-p 0.0009 3.5609 0.0427 2104.798464 0 0.0004 138 | 0/8 7 h-lim-p 0.0085 20.0000 0.0020 2104.798463 0 0.0170 159 | 0/8 8 h-lim-p 0.0044 20.0000 0.0076 2104.798409 0 0.0356 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2104.798402 1 0.9961 204 | 0/8 10 h-lim-p 1.4659 20.0000 0.0000 2104.798402 0 2.1988 224 | 0/8 11 h-lim-p 0.4809 20.0000 0.0002 2104.798402 0 0.0150 248 | 0/8 12 h-lim-p 0.0017 3.8902 0.0020 2104.798402 0 0.0000 277 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 2104.798402 0 0.0000 306 | 0/8 14 h-lim-p 0.0000 20.0000 0.0024 2104.798402 0 0.0000 327 | 0/8 15 h-lim-p 0.0002 20.0000 0.0004 2104.798402 0 0.0007 349 | 0/8 16 h-lim-p 0.0024 20.0000 0.0001 2104.798402 0 0.0021 369 | 0/8 17 h-lim-p 0.0036 20.0000 0.0001 2104.798402 0 0.0000 396 | 0/8 18 h-lim-p 0.0000 8.3471 0.0009 2104.798402 0 0.0000 419 | 0/8 19 h-lim-p 0.0000 0.5275 0.0151 2104.798402 0 0.0000 440 | 0/8 20 h-lim-p 0.0000 0.1090 0.0727 .. | 0/8 21 h-lim-p 0.0000 20.0000 0.0022 | 0/8 22 h-lim-p 0.0000 20.0000 0.0022 Out... lnL = -2104.798402 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2104.798402 Node 7: lnL = -2104.798402 Node 8: lnL = -2104.798402 Node 9: lnL = -2104.798402 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 962 Sequential format.. Reading seq # 1: YLR404W_Sbay Reading seq # 2: YLR404W_Scer Reading seq # 3: YLR404W_Skud Reading seq # 4: YLR404W_Smik Reading seq # 5: YLR404W_Spar Sequences read.. Counting patterns.. # site patterns = 391 Counting frequencies.. 120 bytes for distance 62560 bytes for lkl0 50048 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.267948 0.089734 0.053224 0.192212 0.136400 0.245165 0.287959 0.048535 lnL0 = -4504.142565 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4504.142565 x= 0.26795 0.08973 0.05322 0.19221 0.13640 0.24516 0.28796 0.04853 1 h-lim-p 0.0035 0.7750 159.8813 4501.868901 6 0.0002 36 | 0/8 2 h-lim-p 0.0009 0.0075 27.0934 4501.727358 5 0.0004 59 | 0/8 3 h-lim-p 0.0013 0.0491 8.3337 4501.711309 4 0.0005 79 | 0/8 4 h-lim-p 0.0014 0.1222 2.9862 4501.709105 3 0.0006 97 | 0/8 5 h-lim-p 0.0029 0.2869 0.5798 4501.709034 3 0.0004 119 | 0/8 6 h-lim-p 0.0024 5.1728 0.1005 4501.709032 0 0.0006 140 | 0/8 7 h-lim-p 0.0941 20.0000 0.0007 4501.709019 0 0.1881 161 | 0/8 8 h-lim-p 0.0022 20.0000 0.0559 4501.708945 0 0.0044 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4501.708944 0 1.0938 202 | 0/8 10 h-lim-p 1.3776 20.0000 0.0000 4501.708944 0 1.2054 222 | 0/8 11 h-lim-p 1.4431 20.0000 0.0000 4501.708944 0 1.4431 242 | 0/8 12 h-lim-p 0.6490 20.0000 0.0000 4501.708944 0 1.2981 263 | 0/8 13 h-lim-p 0.0277 20.0000 0.0019 4501.708944 0 0.0139 283 | 0/8 14 h-lim-p 0.0041 12.7327 0.0063 4501.708944 0 0.0041 303 | 0/8 15 h-lim-p 0.0022 6.7608 0.0118 4501.708944 0 0.0000 337 | 0/8 16 h-lim-p 0.0011 20.0000 0.0000 4501.708944 0 0.0000 370 Out... lnL = -4501.708944 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4501.708944 Node 7: lnL = -4501.708944 Node 8: lnL = -4501.708944 Node 9: lnL = -4501.708944 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 206 Sequential format.. Reading seq # 1: YLR405W_Sbay Reading seq # 2: YLR405W_Scer Reading seq # 3: YLR405W_Skud Reading seq # 4: YLR405W_Smik Reading seq # 5: YLR405W_Spar Sequences read.. Counting patterns.. # site patterns = 100 Counting frequencies.. 120 bytes for distance 16000 bytes for lkl0 12800 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.197937 0.200117 0.092018 0.092313 0.037935 0.186156 0.094984 0.028421 lnL0 = -807.168185 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 807.168185 x= 0.19794 0.20012 0.09202 0.09231 0.03793 0.18616 0.09498 0.02842 1 h-lim-p 0.0012 0.0094 34.0037 806.332929 0 0.0018 22 | 0/8 2 h-lim-p 0.0003 0.0027 29.2959 806.189201 0 0.0007 35 | 0/8 3 h-lim-p 0.0007 0.0055 9.2267 806.148727 0 0.0014 48 | 0/8 4 h-lim-p 0.0011 0.0088 4.6335 806.137999 1 0.0014 62 | 0/8 5 h-lim-p 0.0025 0.0798 2.5743 806.130936 1 0.0031 76 | 0/8 6 h-lim-p 0.0295 0.3295 0.2691 806.130856 3 0.0014 97 | 0/8 7 h-lim-p 0.0048 2.0101 0.0783 806.129808 0 0.0385 120 | 0/8 8 h-lim-p 0.0182 1.3029 0.1653 806.112072 0 0.0547 141 | 0/8 9 h-lim-p 2.5000 20.0000 0.0010 806.110845 3 1.1328 167 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 806.110831 2 1.0938 191 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 806.110831 0 1.0938 211 | 0/8 12 h-lim-p 2.3103 20.0000 0.0000 806.110831 0 1.0107 231 | 0/8 13 h-lim-p 0.7802 20.0000 0.0000 806.110831 0 0.1463 253 | 0/8 14 h-lim-p 0.0054 20.0000 0.0002 806.110831 0 0.0013 274 | 0/8 15 h-lim-p 0.0006 20.0000 0.0004 806.110831 0 0.0000 312 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 806.110831 0 0.0000 335 Out... lnL = -806.110831 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -806.110831 Node 7: lnL = -806.110831 Node 8: lnL = -806.110831 Node 9: lnL = -806.110831 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 829 Sequential format.. Reading seq # 1: YLR407W_Sbay Reading seq # 2: YLR407W_Scer Reading seq # 3: YLR407W_Skud Reading seq # 4: YLR407W_Smik Reading seq # 5: YLR407W_Spar Sequences read.. Counting patterns.. # site patterns = 340 Counting frequencies.. 120 bytes for distance 54400 bytes for lkl0 43520 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.266849 0.078436 0.156724 0.128199 0.119408 0.322714 0.224681 0.037994 lnL0 = -3980.189901 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3980.189901 x= 0.26685 0.07844 0.15672 0.12820 0.11941 0.32271 0.22468 0.03799 1 h-lim-p 0.0020 0.0160 110.1342 3978.356938 6 0.0003 37 | 0/8 2 h-lim-p 0.0006 0.0052 16.9135 3978.308741 5 0.0003 60 | 0/8 3 h-lim-p 0.0008 0.0121 7.1521 3978.301721 4 0.0003 80 | 0/8 4 h-lim-p 0.0013 0.2546 1.7088 3978.300625 5 0.0008 106 | 0/8 5 h-lim-p 0.0060 1.9267 0.2304 3978.300606 0 0.0008 120 | 0/8 6 h-lim-p 0.0025 3.5615 0.0690 3978.300605 0 0.0005 141 | 0/8 7 h-lim-p 0.0064 20.0000 0.0059 3978.300604 0 0.0056 161 | 0/8 8 h-lim-p 0.0253 20.0000 0.0013 3978.300510 0 0.2025 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3978.300510 0 1.0938 204 | 0/8 10 h-lim-p 0.9502 20.0000 0.0000 3978.300510 0 0.9502 224 | 0/8 11 h-lim-p 0.8581 20.0000 0.0000 3978.300510 0 0.2145 245 | 0/8 12 h-lim-p 0.0183 20.0000 0.0003 3978.300510 0 0.0000 284 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -3978.300510 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3978.300510 Node 7: lnL = -3978.300510 Node 8: lnL = -3978.300510 Node 9: lnL = -3978.300510 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 208 Sequential format.. Reading seq # 1: YLR408C_Sbay Reading seq # 2: YLR408C_Scer Reading seq # 3: YLR408C_Skud Reading seq # 4: YLR408C_Smik Reading seq # 5: YLR408C_Spar Sequences read.. Counting patterns.. # site patterns = 121 Counting frequencies.. 120 bytes for distance 19360 bytes for lkl0 15488 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.192597 0.234684 0.015821 0.113390 0.089449 0.242542 0.257188 0.000060 lnL0 = -871.206490 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 871.206490 x= 0.19260 0.23468 0.01582 0.11339 0.08945 0.24254 0.25719 0.00006 1 h-lim-p 0.0000 0.0000 27.9013 871.197258 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0260 12.8904 871.068496 0 0.0016 40 | 1/8 3 h-lim-p 0.0010 0.0081 7.5140 871.037227 0 0.0020 53 | 1/8 4 h-lim-p 0.0129 0.1196 1.1731 871.035414 6 0.0018 80 | 1/8 5 h-lim-p 0.0025 0.0477 0.8553 871.031101 0 0.0050 93 | 1/8 6 h-lim-p 0.0099 0.4673 0.4327 870.989468 0 0.0396 114 | 0/8 7 h-lim-p 0.0019 0.0153 2.3107 870.791819 0 0.0115 135 | 0/8 8 h-lim-p 0.0004 0.0028 4.1623 870.754397 m 0.0028 147 | 0/8 9 h-lim-p 0.0000 0.0000 1.2610 h-lim-p: 2.10411724e-18 1.68329379e-17 1.26097395e+00 870.754397 .. | 0/8 10 h-lim-p 0.0000 0.1604 6.6310 870.744448 0 0.0005 172 | 0/8 11 h-lim-p 0.0007 0.0059 3.0351 870.735556 0 0.0029 186 | 0/8 12 h-lim-p 0.0025 0.0203 1.4159 870.734684 4 0.0011 208 | 0/8 13 h-lim-p 0.0060 0.0477 0.1883 870.734643 2 0.0023 224 | 0/8 14 h-lim-p 0.0028 0.0267 0.1526 870.734635 2 0.0009 250 | 0/8 15 h-lim-p 0.0055 0.6925 0.0260 870.734629 1 0.0069 272 | 0/8 16 h-lim-p 0.0039 0.5428 0.0462 870.734623 2 0.0030 296 | 0/8 17 h-lim-p 0.0109 6.2779 0.0126 870.734205 0 0.1751 320 | 0/8 18 h-lim-p 2.5000 20.0000 0.0005 870.734155 2 0.9961 344 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 870.734155 0 2.1875 364 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 870.734155 0 0.5469 385 | 0/8 21 h-lim-p 0.1037 20.0000 0.0000 870.734155 0 0.1037 405 | 0/8 22 h-lim-p 0.0449 20.0000 0.0000 870.734155 0 0.0028 428 | 0/8 23 h-lim-p 0.0016 20.0000 0.0000 870.734155 0 0.0000 470 | 0/8 24 h-lim-p 0.0000 20.0000 0.0008 | 0/8 25 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -870.734155 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -870.734155 Node 7: lnL = -870.734155 Node 8: lnL = -870.734155 Node 9: lnL = -870.734155 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 314 Sequential format.. Reading seq # 1: YLR409C_Sbay Reading seq # 2: YLR409C_Scer Reading seq # 3: YLR409C_Skud Reading seq # 4: YLR409C_Smik Reading seq # 5: YLR409C_Spar Sequences read.. Counting patterns.. # site patterns = 154 Counting frequencies.. 120 bytes for distance 24640 bytes for lkl0 19712 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.233763 0.075143 0.019119 0.137528 0.087922 0.609916 0.163422 0.014943 lnL0 = -1349.072798 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1349.072798 x= 0.23376 0.07514 0.01912 0.13753 0.08792 0.60992 0.16342 0.01494 1 h-lim-p 0.0001 0.0008 79.6372 1347.499799 0 0.0006 24 | 0/8 2 h-lim-p 0.0000 0.0002 49.6535 1347.123564 m 0.0002 36 | 1/8 3 h-lim-p 0.0006 0.0053 18.3759 1346.999977 0 0.0009 48 | 1/8 4 h-lim-p 0.0012 0.0093 11.7960 1346.955843 5 0.0009 70 | 1/8 5 h-lim-p 0.0032 0.0583 3.2742 1346.947837 2 0.0016 86 | 1/8 6 h-lim-p 0.0017 0.2007 3.0909 1346.934824 0 0.0034 99 | 1/8 7 h-lim-p 0.0029 0.0844 3.6194 1346.929866 6 0.0016 125 | 1/8 8 h-lim-p 0.1193 1.4021 0.0485 1346.883395 0 0.1790 137 | 1/8 9 h-lim-p 0.1320 1.7984 0.0657 1346.741248 0 0.2640 157 | 1/8 10 h-lim-p 2.5000 20.0000 0.0023 1346.738731 5 0.8754 188 | 0/8 11 h-lim-p 2.5000 20.0000 0.0004 1346.738722 2 0.4123 214 | 0/8 12 h-lim-p 0.0004 0.0036 0.0657 1346.738710 m 0.0036 234 | 1/8 13 h-lim-p 2.2304 20.0000 0.0001 1346.738709 0 0.4879 255 | 0/8 14 h-lim-p 0.0010 2.6438 0.0432 1346.738709 0 0.0004 274 | 0/8 15 h-lim-p 0.1347 1.0773 0.0000 1346.738709 m 1.0773 294 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 1346.738709 0 2.1875 314 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 1346.738709 0 1.0938 333 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 1346.738709 0 0.2734 354 | 1/8 19 h-lim-p 0.3944 20.0000 0.0000 1346.738709 0 0.0246 376 Out... lnL = -1346.738709 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1346.738709 Node 7: lnL = -1346.738709 Node 8: lnL = -1346.738709 Node 9: lnL = -1346.738709 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 478 Sequential format.. Reading seq # 1: YLR411W_Sbay Reading seq # 2: YLR411W_Scer Reading seq # 3: YLR411W_Skud Reading seq # 4: YLR411W_Smik Reading seq # 5: YLR411W_Spar Sequences read.. Counting patterns.. # site patterns = 196 Counting frequencies.. 120 bytes for distance 31360 bytes for lkl0 25088 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.272608 0.218538 0.000060 0.843472 0.151506 0.244893 0.222764 0.034903 lnL0 = -2153.863104 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2153.863104 x= 0.27261 0.21854 0.00006 0.84347 0.15151 0.24489 0.22276 0.03490 1 h-lim-p 0.0000 0.0000 421.9334 2153.768410 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0020 174.7616 2133.043303 5 0.0013 51 | 1/8 3 h-lim-p 0.0013 0.0102 26.1542 2132.049255 0 0.0025 64 | 1/8 4 h-lim-p 0.0024 0.0320 27.9076 2130.693328 0 0.0048 77 | 1/8 5 h-lim-p 0.0020 0.0158 44.8773 2129.648748 7 0.0021 106 | 1/8 6 h-lim-p 0.0038 0.0306 4.2378 2126.847096 0 0.0153 120 | 1/8 7 h-lim-p 0.0023 0.0182 20.5827 2093.577449 m 0.0182 132 | 1/8 8 h-lim-p 0.3452 2.7620 0.2527 2086.826147 1 0.4316 146 | 1/8 9 h-lim-p 0.3319 2.6554 0.2228 2085.803997 2 0.1556 169 | 1/8 10 h-lim-p 0.5218 12.9305 0.0664 2085.549088 8 0.3298 208 | 1/8 11 h-lim-p 0.5132 9.4474 0.0427 2085.471552 1 0.6415 229 | 1/8 12 h-lim-p 2.5000 20.0000 0.0102 2085.461113 5 0.4781 259 | 1/8 13 h-lim-p 0.8502 20.0000 0.0058 2085.456712 4 0.9131 287 | 1/8 14 h-lim-p 2.5000 20.0000 0.0005 2085.456594 4 0.7683 317 | 1/8 15 h-lim-p 1.9862 20.0000 0.0002 2085.456589 0 0.8690 336 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 2085.456589 0 1.0938 355 | 1/8 17 h-lim-p 1.2441 20.0000 0.0000 2085.456589 0 2.4882 375 | 1/8 18 h-lim-p 0.4720 20.0000 0.0001 2085.456589 0 0.1032 395 | 1/8 19 h-lim-p 0.0090 20.0000 0.0010 2085.456589 0 0.0000 437 | 1/8 20 h-lim-p 0.0000 20.0000 0.0007 2085.456589 0 0.0000 471 | 1/8 21 h-lim-p 0.0000 20.0000 0.0007 | 1/8 22 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -2085.456589 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2085.456589 Node 7: lnL = -2085.456589 Node 8: lnL = -2085.456589 Node 9: lnL = -2085.456589 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 445 Sequential format.. Reading seq # 1: YLR412W_Sbay Reading seq # 2: YLR412W_Scer Reading seq # 3: YLR412W_Skud Reading seq # 4: YLR412W_Smik Reading seq # 5: YLR412W_Spar Sequences read.. Counting patterns.. # site patterns = 225 Counting frequencies.. 120 bytes for distance 36000 bytes for lkl0 28800 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.318166 0.069391 0.088054 0.166940 0.085938 0.203057 0.265251 0.101254 lnL0 = -1997.172598 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1997.172598 x= 0.31817 0.06939 0.08805 0.16694 0.08594 0.20306 0.26525 0.10125 1 h-lim-p 0.0064 0.0516 71.7279 1995.702915 5 0.0006 34 | 0/8 2 h-lim-p 0.0008 0.0063 19.2332 1995.564959 4 0.0008 54 | 0/8 3 h-lim-p 0.0014 0.0140 11.0907 1995.540372 4 0.0005 74 | 0/8 4 h-lim-p 0.0017 0.1287 3.4315 1995.534943 6 0.0010 103 | 0/8 5 h-lim-p 0.0032 0.2989 1.1088 1995.534070 3 0.0016 121 | 0/8 6 h-lim-p 0.0039 0.6290 0.4605 1995.533984 1 0.0010 136 | 0/8 7 h-lim-p 0.0439 17.1884 0.0101 1995.533966 2 0.0231 161 | 0/8 8 h-lim-p 0.0163 20.0000 0.0143 1995.533110 0 0.0981 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1995.533072 2 0.9961 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1995.533072 0 1.0938 227 | 0/8 11 h-lim-p 1.7248 20.0000 0.0000 1995.533072 0 1.5092 247 | 0/8 12 h-lim-p 1.8621 20.0000 0.0000 1995.533072 0 0.8147 267 | 0/8 13 h-lim-p 0.2823 20.0000 0.0000 1995.533072 0 0.0176 290 | 0/8 14 h-lim-p 0.0039 20.0000 0.0001 1995.533072 0 0.0000 318 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 1995.533072 0 0.0000 346 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 1995.533072 0 0.0000 381 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1995.533072 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1995.533072 Node 7: lnL = -1995.533072 Node 8: lnL = -1995.533072 Node 9: lnL = -1995.533072 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 858 Sequential format.. Reading seq # 1: YLR413W_Sbay Reading seq # 2: YLR413W_Scer Reading seq # 3: YLR413W_Skud Reading seq # 4: YLR413W_Smik Reading seq # 5: YLR413W_Spar Sequences read.. Counting patterns.. # site patterns = 271 Counting frequencies.. 120 bytes for distance 43360 bytes for lkl0 34688 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.208612 0.036632 0.081267 0.069848 0.047093 0.180726 0.191045 0.061238 lnL0 = -3580.737230 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3580.737230 x= 0.20861 0.03663 0.08127 0.06985 0.04709 0.18073 0.19104 0.06124 1 h-lim-p 0.0005 0.0039 169.1944 3578.912879 8 0.0001 40 | 0/8 2 h-lim-p 0.0019 0.0188 12.2562 3578.888839 5 0.0003 66 | 0/8 3 h-lim-p 0.0006 0.0405 6.8532 3578.886610 3 0.0001 85 | 0/8 4 h-lim-p 0.0003 0.0264 2.8074 3578.886146 2 0.0001 101 | 0/8 5 h-lim-p 0.0004 0.1015 1.1388 3578.886008 3 0.0003 120 | 0/8 6 h-lim-p 0.0011 0.8509 0.2528 3578.886000 0 0.0003 133 | 0/8 7 h-lim-p 0.0017 3.4017 0.0436 3578.885999 0 0.0004 154 | 0/8 8 h-lim-p 0.3070 20.0000 0.0001 3578.885990 0 1.2280 176 | 0/8 9 h-lim-p 0.9448 20.0000 0.0001 3578.885989 0 0.9448 196 | 0/8 10 h-lim-p 2.3122 20.0000 0.0000 3578.885989 0 2.0232 216 | 0/8 11 h-lim-p 1.8151 20.0000 0.0000 3578.885989 0 0.7941 236 | 0/8 12 h-lim-p 0.0491 20.0000 0.0005 3578.885989 0 0.0015 260 | 0/8 13 h-lim-p 0.0003 20.0000 0.0024 3578.885989 0 0.0000 299 | 0/8 14 h-lim-p 0.0000 20.0000 0.0022 | 0/8 15 h-lim-p 0.0000 20.0000 0.0022 Out... lnL = -3578.885989 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3578.885989 Node 7: lnL = -3578.885989 Node 8: lnL = -3578.885989 Node 9: lnL = -3578.885989 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 115 Sequential format.. Reading seq # 1: YLR414C_Sbay Reading seq # 2: YLR414C_Scer Reading seq # 3: YLR414C_Skud Reading seq # 4: YLR414C_Smik Reading seq # 5: YLR414C_Spar Sequences read.. Counting patterns.. # site patterns = 63 Counting frequencies.. 120 bytes for distance 10080 bytes for lkl0 8064 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.448841 0.000060 0.129745 0.080315 0.117189 0.195178 0.285664 0.221592 lnL0 = -550.318074 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 550.318074 x= 0.44884 0.00006 0.12975 0.08031 0.11719 0.19518 0.28566 0.22159 1 h-lim-p 0.0000 0.0000 39.7425 550.302798 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0075 15.3539 550.203999 0 0.0008 39 | 1/8 3 h-lim-p 0.0033 0.1800 3.6844 550.144489 0 0.0065 52 | 1/8 4 h-lim-p 0.0080 0.0945 2.9993 550.113234 7 0.0053 81 | 1/8 5 h-lim-p 0.0182 0.1790 0.8737 549.912843 0 0.0364 94 | 1/8 6 h-lim-p 0.0084 0.0671 2.7196 548.738652 0 0.0252 114 | 1/8 7 h-lim-p 0.0052 0.0414 6.8235 548.643510 7 0.0039 140 | 1/8 8 h-lim-p 1.8904 20.0000 0.0141 548.585128 5 0.8252 161 | 0/8 9 h-lim-p 0.0026 1.7109 4.3863 548.572425 4 0.0013 189 | 0/8 10 h-lim-p 0.6524 20.0000 0.0091 548.553596 0 1.3048 202 | 0/8 11 h-lim-p 2.5000 20.0000 0.0026 548.552530 4 1.0519 231 | 0/8 12 h-lim-p 2.5000 20.0000 0.0008 548.552438 3 0.8800 258 | 0/8 13 h-lim-p 2.5000 20.0000 0.0002 548.552435 1 0.9961 280 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 548.552435 0 1.0938 300 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 548.552435 0 1.0938 320 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 548.552435 0 2.5000 340 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 548.552435 0 0.0195 366 | 0/8 18 h-lim-p 0.0124 20.0000 0.0000 548.552435 0 0.0002 391 Out... lnL = -548.552435 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -548.552435 Node 7: lnL = -548.552435 Node 8: lnL = -548.552435 Node 9: lnL = -548.552435 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 127 Sequential format.. Reading seq # 1: YLR417W_Sbay Reading seq # 2: YLR417W_Scer Reading seq # 3: YLR417W_Skud Reading seq # 4: YLR417W_Smik Reading seq # 5: YLR417W_Spar Sequences read.. Counting patterns.. # site patterns = 60 Counting frequencies.. 120 bytes for distance 9600 bytes for lkl0 7680 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.615916 0.169175 0.371019 0.064998 0.262945 3.984360 0.389205 0.000060 lnL0 = -476.542291 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 476.542291 x= 0.61592 0.16918 0.37102 0.06500 0.26294 3.98436 0.38920 0.00006 1 h-lim-p 0.0000 0.0000 100.6319 476.482972 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0023 168.0439 450.632568 m 0.0023 39 | 2/8 3 h-lim-p 0.0013 0.0107 18.2048 449.925881 0 0.0054 53 | 2/8 4 h-lim-p 0.0029 0.0234 8.6201 449.681400 0 0.0058 66 | 2/8 5 h-lim-p 0.0487 0.3894 0.7615 448.415530 0 0.1460 79 | 1/8 6 h-lim-p 0.0115 0.0920 6.4946 446.655367 0 0.0230 98 | 1/8 7 h-lim-p 0.0005 0.0040 8.8724 446.559481 m 0.0040 110 | 1/8 8 h-lim-p -0.0000 -0.0000 0.0870 h-lim-p: -4.41933033e-17 -3.53546426e-16 8.70359791e-02 446.559481 .. | 1/8 9 h-lim-p 0.0000 0.0097 20.4150 446.378376 0 0.0010 143 | 1/8 10 h-lim-p 0.0018 0.0140 8.0224 446.355465 2 0.0008 159 | 1/8 11 h-lim-p 0.0017 0.0134 1.9326 446.349850 0 0.0034 172 | 1/8 12 h-lim-p 0.0004 0.0029 2.3219 446.346293 m 0.0029 184 | 1/8 13 h-lim-p 0.0061 0.3207 1.1103 446.344799 6 0.0037 213 | 1/8 14 h-lim-p 0.0011 0.0087 0.1090 446.344688 m 0.0087 225 | 2/8 15 h-lim-p 0.0003 0.2232 2.3625 446.344661 4 0.0002 255 | 2/8 16 h-lim-p 0.3993 20.0000 0.0010 446.344627 0 0.5990 267 | 1/8 17 h-lim-p 0.0111 14.1814 0.0557 446.344609 0 0.0222 286 | 1/8 18 h-lim-p 1.3485 20.0000 0.0009 446.344608 1 0.3319 308 | 1/8 19 h-lim-p 0.7194 20.0000 0.0004 446.344608 0 0.0000 348 | 1/8 20 h-lim-p 0.0000 2.9433 0.0006 446.344597 m 2.9433 383 | 2/8 21 h-lim-p 1.1590 20.0000 0.0010 446.344597 0 0.0000 424 | 1/8 22 h-lim-p 0.0000 0.0000 563863257.3521 h-lim-p: 1.21087402e-23 9.68699219e-23 5.63863257e+08 446.344597 .. | 1/8 23 h-lim-p 0.0000 0.0616 1.1159 446.344034 0 0.0010 456 | 1/8 24 h-lim-p 0.0027 0.3651 0.4021 446.343962 4 0.0010 477 | 1/8 25 h-lim-p 0.0030 0.8726 0.1313 446.343949 3 0.0018 504 | 1/8 26 h-lim-p 0.0041 7.1594 0.0562 446.343944 0 0.0036 523 | 1/8 27 h-lim-p 0.0048 0.0381 0.0120 446.343943 0 0.0095 543 | 1/8 28 h-lim-p 0.0006 0.0047 0.0113 446.343943 m 0.0047 562 | 2/8 29 h-lim-p 0.3571 20.0000 0.0001 446.343941 0 0.7141 582 | 1/8 30 h-lim-p 0.0075 20.0000 0.0073 446.343941 0 0.0075 600 | 1/8 31 h-lim-p 0.4840 3.8721 0.0000 446.343941 0 0.1059 620 | 0/8 32 h-lim-p 0.0136 20.0000 0.0003 446.343941 0 0.0136 639 | 0/8 33 h-lim-p 0.1247 0.9973 0.0000 446.343941 0 0.1870 659 | 0/8 34 h-lim-p 0.0009 0.0074 0.0006 446.343941 0 0.0005 679 | 0/8 35 h-lim-p 0.0001 0.0020 0.0020 446.343941 0 0.0000 707 | 0/8 36 h-lim-p 0.0000 0.0008 0.0050 .. | 0/8 37 h-lim-p 0.0000 0.0002 0.0241 446.343941 0 0.0001 763 | 0/8 38 h-lim-p 0.0000 0.0000 0.1370 446.343941 0 0.0000 794 | 0/8 39 h-lim-p 0.0000 0.0000 0.5954 446.343941 0 0.0000 815 | 0/8 40 h-lim-p 0.0000 0.0000 0.9076 446.343941 0 0.0000 842 | 0/8 41 h-lim-p 0.0000 0.0000 4.0626 .. | 0/8 42 h-lim-p 0.0000 8.8906 0.0096 446.343941 0 0.0003 884 | 0/8 43 h-lim-p 0.0000 0.0001 0.0494 446.343941 0 0.0000 917 | 0/8 44 h-lim-p 0.0000 0.0204 0.0016 446.343941 0 0.0026 945 | 0/8 45 h-lim-p 0.0011 0.0089 0.0008 446.343941 0 0.0044 967 | 1/8 46 h-lim-p 0.0004 0.0068 0.0084 446.343941 0 0.0000 999 | 1/8 47 h-lim-p 0.0000 0.0026 0.0235 446.343941 0 0.0000 1024 | 1/8 48 h-lim-p 0.0000 0.0000 11.6884 446.343941 0 0.0000 1053 | 1/8 49 h-lim-p 0.0004 17.3523 0.0000 446.343941 0 0.0909 1073 | 1/8 50 h-lim-p 0.1146 16.3820 0.0000 446.343941 0 0.0000 1105 Out... lnL = -446.343941 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -446.343941 Node 7: lnL = -446.343941 Node 8: lnL = -446.343941 Node 9: lnL = -446.343941 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 357 Sequential format.. Reading seq # 1: YLR418C_Sbay Reading seq # 2: YLR418C_Scer Reading seq # 3: YLR418C_Skud Reading seq # 4: YLR418C_Smik Reading seq # 5: YLR418C_Spar Sequences read.. Counting patterns.. # site patterns = 162 Counting frequencies.. 120 bytes for distance 25920 bytes for lkl0 20736 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.253917 0.000060 0.090278 0.135967 0.130579 0.550753 0.180740 0.023590 lnL0 = -1474.402492 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1474.402492 x= 0.25392 0.00006 0.09028 0.13597 0.13058 0.55075 0.18074 0.02359 1 h-lim-p 0.0005 0.0039 69.7094 1473.012726 7 0.0005 38 | 0/8 2 h-lim-p 0.0003 0.0020 39.4594 1472.524744 0 0.0008 51 | 0/8 3 h-lim-p 0.0009 0.0070 19.6938 1472.176018 0 0.0026 64 | 0/8 4 h-lim-p 0.0040 0.0322 12.7908 1472.095253 7 0.0015 94 | 0/8 5 h-lim-p 0.0012 0.0188 15.5119 1471.936390 0 0.0036 107 | 0/8 6 h-lim-p 0.0017 0.0135 20.9213 1471.868323 7 0.0012 137 | 0/8 7 h-lim-p 0.0011 0.0090 4.4521 1471.862386 5 0.0008 159 | 0/8 8 h-lim-p 0.2202 6.6435 0.0172 1471.796687 0 0.8808 173 | 0/8 9 h-lim-p 2.5000 20.0000 0.0026 1471.792929 5 0.9136 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 1471.792916 2 0.7996 230 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1471.792916 0 1.0938 250 | 0/8 12 h-lim-p 2.3617 20.0000 0.0000 1471.792916 0 1.0332 270 | 0/8 13 h-lim-p 0.8869 20.0000 0.0000 1471.792916 0 0.1109 292 | 0/8 14 h-lim-p 0.0009 8.2759 0.0025 1471.792916 0 0.0002 313 | 0/8 15 h-lim-p 0.0000 0.5858 0.0352 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1471.792916 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1471.792916 Node 7: lnL = -1471.792916 Node 8: lnL = -1471.792916 Node 9: lnL = -1471.792916 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 355 Sequential format.. Reading seq # 1: YLR419W_Sbay Reading seq # 2: YLR419W_Scer Reading seq # 3: YLR419W_Skud Reading seq # 4: YLR419W_Smik Reading seq # 5: YLR419W_Spar Sequences read.. Counting patterns.. # site patterns = 158 Counting frequencies.. 120 bytes for distance 25280 bytes for lkl0 20224 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.224729 0.064692 0.069295 0.141961 0.085653 0.264097 0.202419 0.035046 lnL0 = -1474.376144 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1474.376144 x= 0.22473 0.06469 0.06929 0.14196 0.08565 0.26410 0.20242 0.03505 1 h-lim-p 0.0021 0.0171 48.6794 1473.662999 6 0.0006 37 | 0/8 2 h-lim-p 0.0005 0.0043 26.7300 1473.461001 0 0.0008 49 | 0/8 3 h-lim-p 0.0019 0.0168 11.3182 1473.412183 5 0.0009 72 | 0/8 4 h-lim-p 0.0017 0.0414 6.3870 1473.399248 5 0.0009 96 | 0/8 5 h-lim-p 0.0014 0.0690 3.8979 1473.391752 3 0.0014 114 | 0/8 6 h-lim-p 0.0047 0.1830 1.1950 1473.391037 2 0.0012 131 | 0/8 7 h-lim-p 0.0411 5.1746 0.0340 1473.390967 0 0.0090 144 | 0/8 8 h-lim-p 0.0069 8.6512 0.0440 1473.385134 0 0.0834 167 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 1473.384914 3 1.0004 193 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1473.384914 0 1.0938 213 | 0/8 11 h-lim-p 1.5964 20.0000 0.0000 1473.384914 0 0.6984 233 | 0/8 12 h-lim-p 0.4024 20.0000 0.0000 1473.384914 0 0.0031 259 | 0/8 13 h-lim-p 0.0010 20.0000 0.0001 1473.384914 0 0.0000 291 | 0/8 14 h-lim-p 0.0000 20.0000 0.0006 | 0/8 15 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -1473.384914 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1473.384914 Node 7: lnL = -1473.384914 Node 8: lnL = -1473.384914 Node 9: lnL = -1473.384914 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 890 Sequential format.. Reading seq # 1: YLR420W_Sbay Reading seq # 2: YLR420W_Scer Reading seq # 3: YLR420W_Skud Reading seq # 4: YLR420W_Smik Reading seq # 5: YLR420W_Spar Sequences read.. Counting patterns.. # site patterns = 484 Counting frequencies.. 120 bytes for distance 77440 bytes for lkl0 61952 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.469433 0.169688 0.000060 0.326573 0.474955 0.409318 0.471647 0.089624 lnL0 = -4817.112447 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4817.112447 x= 0.46943 0.16969 0.00006 0.32657 0.47495 0.40932 0.47165 0.08962 1 h-lim-p 0.0000 0.0000 72.4581 4817.077147 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0333 44.7777 4816.237532 0 0.0014 41 | 1/8 3 h-lim-p 0.0038 0.0307 10.4451 4816.106804 6 0.0024 69 | 1/8 4 h-lim-p 0.0055 0.1767 4.4641 4816.068191 4 0.0029 90 | 1/8 5 h-lim-p 0.0123 0.6940 1.0492 4815.871542 0 0.0247 103 | 1/8 6 h-lim-p 0.0077 0.1840 3.3525 4812.280365 0 0.0309 117 | 0/8 7 h-lim-p 0.0031 0.0247 31.3592 4812.046696 8 0.0009 150 | 0/8 8 h-lim-p 0.0030 0.0239 6.5349 4812.013662 6 0.0016 175 | 0/8 9 h-lim-p 0.8077 20.0000 0.0132 4811.952867 1 1.0096 189 | 0/8 10 h-lim-p 2.5000 20.0000 0.0031 4811.950528 3 1.0449 215 | 0/8 11 h-lim-p 2.5000 20.0000 0.0005 4811.950473 2 0.8246 241 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4811.950473 0 1.0938 261 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 4811.950473 0 1.0938 281 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 4811.950473 0 1.0938 301 | 0/8 15 h-lim-p 1.0037 20.0000 0.0000 4811.950473 0 1.0037 321 | 0/8 16 h-lim-p 0.0577 20.0000 0.0001 4811.950473 0 0.0000 360 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 4811.950473 0 0.0000 382 Out... lnL = -4811.950473 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4811.950473 Node 7: lnL = -4811.950473 Node 8: lnL = -4811.950473 Node 9: lnL = -4811.950473 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 360 Sequential format.. Reading seq # 1: YLR421C_Sbay Reading seq # 2: YLR421C_Scer Reading seq # 3: YLR421C_Skud Reading seq # 4: YLR421C_Smik Reading seq # 5: YLR421C_Spar Sequences read.. Counting patterns.. # site patterns = 157 Counting frequencies.. 120 bytes for distance 25120 bytes for lkl0 20096 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.226276 0.087396 0.089851 0.126979 0.094292 0.185545 0.204888 0.038630 lnL0 = -1663.046786 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1663.046786 x= 0.22628 0.08740 0.08985 0.12698 0.09429 0.18555 0.20489 0.03863 1 h-lim-p 0.0200 0.1598 37.8636 1662.677504 6 0.0005 37 | 0/8 2 h-lim-p 0.0024 0.0194 7.1298 1662.663162 2 0.0006 54 | 0/8 3 h-lim-p 0.0019 0.0426 2.1587 1662.662103 4 0.0005 75 | 0/8 4 h-lim-p 0.0036 0.2654 0.2948 1662.662076 3 0.0006 95 | 0/8 5 h-lim-p 0.0070 10.1379 0.0267 1662.662076 0 0.0015 116 | 0/8 6 h-lim-p 0.0067 20.0000 0.0061 1662.662076 0 0.0029 136 | 0/8 7 h-lim-p 0.0046 20.0000 0.0039 1662.662075 0 0.0092 157 | 0/8 8 h-lim-p 0.0064 20.0000 0.0056 1662.662047 0 0.0382 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1662.662047 0 1.0938 199 | 0/8 10 h-lim-p 1.5432 20.0000 0.0000 1662.662047 0 1.3503 219 | 0/8 11 h-lim-p 1.4260 20.0000 0.0000 1662.662047 0 0.3565 240 | 0/8 12 h-lim-p 0.0626 20.0000 0.0001 1662.662047 0 0.0156 261 | 0/8 13 h-lim-p 0.0052 20.0000 0.0002 1662.662047 0 0.0045 281 | 0/8 14 h-lim-p 0.0021 20.0000 0.0004 1662.662047 0 0.0000 306 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 1662.662047 0 0.0000 339 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1662.662047 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1662.662047 Node 7: lnL = -1662.662047 Node 8: lnL = -1662.662047 Node 9: lnL = -1662.662047 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 230 Sequential format.. Reading seq # 1: YLR423C_Sbay Reading seq # 2: YLR423C_Scer Reading seq # 3: YLR423C_Skud Reading seq # 4: YLR423C_Smik Reading seq # 5: YLR423C_Spar Sequences read.. Counting patterns.. # site patterns = 112 Counting frequencies.. 120 bytes for distance 17920 bytes for lkl0 14336 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.202383 0.112454 0.088383 0.139107 0.104699 0.162482 0.157489 0.023248 lnL0 = -1053.114742 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1053.114742 x= 0.20238 0.11245 0.08838 0.13911 0.10470 0.16248 0.15749 0.02325 1 h-lim-p 0.0051 0.0411 13.5903 1053.043127 8 0.0008 44 | 0/8 2 h-lim-p 0.0031 0.0620 3.4928 1053.037628 6 0.0010 72 | 0/8 3 h-lim-p 0.0038 0.3636 0.8771 1053.037325 2 0.0008 89 | 0/8 4 h-lim-p 0.0058 3.0858 0.1250 1053.037317 2 0.0011 114 | 0/8 5 h-lim-p 0.0055 1.9581 0.0257 1053.037316 0 0.0012 135 | 0/8 6 h-lim-p 0.0158 20.0000 0.0020 1053.037316 0 0.0017 157 | 0/8 7 h-lim-p 0.0987 20.0000 0.0000 1053.037316 0 0.3950 179 | 0/8 8 h-lim-p 0.0022 16.0217 0.0060 1053.037316 0 0.0033 199 | 0/8 9 h-lim-p 1.9778 20.0000 0.0000 1053.037316 0 1.7306 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1053.037316 0 1.0938 239 | 0/8 11 h-lim-p 0.5438 20.0000 0.0000 1053.037316 0 1.6315 260 | 0/8 12 h-lim-p 0.1320 20.0000 0.0002 1053.037316 0 0.0072 283 | 0/8 13 h-lim-p 0.0018 20.0000 0.0006 1053.037316 0 0.0001 306 | 0/8 14 h-lim-p 0.0001 20.0000 0.0012 1053.037316 0 0.0000 331 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 1053.037316 0 0.0000 364 Out... lnL = -1053.037316 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1053.037316 Node 7: lnL = -1053.037316 Node 8: lnL = -1053.037316 Node 9: lnL = -1053.037316 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 337 Sequential format.. Reading seq # 1: YLR427W_Sbay Reading seq # 2: YLR427W_Scer Reading seq # 3: YLR427W_Skud Reading seq # 4: YLR427W_Smik Reading seq # 5: YLR427W_Spar Sequences read.. Counting patterns.. # site patterns = 106 Counting frequencies.. 120 bytes for distance 16960 bytes for lkl0 13568 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.130204 0.047713 0.027001 0.066428 0.052148 0.111785 0.118955 0.028378 lnL0 = -1232.722402 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1232.722402 x= 0.13020 0.04771 0.02700 0.06643 0.05215 0.11178 0.11896 0.02838 1 h-lim-p 0.0004 0.0032 137.8252 1231.584737 9 0.0001 47 | 0/8 2 h-lim-p 0.0006 0.0045 14.4728 1231.561317 5 0.0002 69 | 0/8 3 h-lim-p 0.0013 0.0507 2.5203 1231.560533 3 0.0003 88 | 0/8 4 h-lim-p 0.0013 0.1638 0.4843 1231.560490 3 0.0004 108 | 0/8 5 h-lim-p 0.0017 1.7619 0.1119 1231.560487 0 0.0004 129 | 0/8 6 h-lim-p 0.0044 7.8157 0.0109 1231.560487 0 0.0010 150 | 0/8 7 h-lim-p 0.0052 20.0000 0.0020 1231.560478 0 0.0418 173 | 0/8 8 h-lim-p 0.0025 1.4900 0.0337 1231.560371 0 0.0075 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1231.560369 0 1.0938 214 | 0/8 10 h-lim-p 2.4993 20.0000 0.0000 1231.560369 0 1.2496 234 | 0/8 11 h-lim-p 1.3254 20.0000 0.0000 1231.560369 0 0.2899 255 | 0/8 12 h-lim-p 0.1102 20.0000 0.0001 1231.560369 0 0.0009 281 | 0/8 13 h-lim-p 0.0004 20.0000 0.0001 1231.560369 0 0.0000 308 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0023 1231.560369 0 0.0000 375 | 0/8 16 h-lim-p 0.0000 20.0000 0.0023 | 0/8 17 h-lim-p 0.0000 20.0000 0.0023 Out... lnL = -1231.560369 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1231.560369 Node 7: lnL = -1231.560369 Node 8: lnL = -1231.560369 Node 9: lnL = -1231.560369 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 384 Sequential format.. Reading seq # 1: YLR429W_Sbay Reading seq # 2: YLR429W_Scer Reading seq # 3: YLR429W_Skud Reading seq # 4: YLR429W_Smik Reading seq # 5: YLR429W_Spar Sequences read.. Counting patterns.. # site patterns = 158 Counting frequencies.. 120 bytes for distance 25280 bytes for lkl0 20224 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.241356 0.000060 0.098088 0.073597 0.082424 0.196495 0.233863 0.072816 lnL0 = -1599.187345 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1599.187345 x= 0.24136 0.00006 0.09809 0.07360 0.08242 0.19650 0.23386 0.07282 1 h-lim-p 0.0008 0.0060 51.4072 1598.552141 3 0.0004 29 | 0/8 2 h-lim-p 0.0010 0.0080 15.0236 1598.493393 7 0.0006 58 | 0/8 3 h-lim-p 0.0019 0.0495 4.3180 1598.487085 4 0.0007 78 | 0/8 4 h-lim-p 0.0013 0.0551 2.4518 1598.486012 4 0.0005 99 | 0/8 5 h-lim-p 0.0013 0.4034 0.8750 1598.485860 3 0.0005 118 | 0/8 6 h-lim-p 0.0010 0.6419 0.4091 1598.485813 3 0.0006 145 | 0/8 7 h-lim-p 0.0192 9.7541 0.0136 1598.485675 0 0.0384 166 | 0/8 8 h-lim-p 0.0078 0.4519 0.0672 1598.482461 0 0.0233 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1598.482460 0 1.0938 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1598.482460 0 1.0938 227 | 0/8 11 h-lim-p 1.0785 20.0000 0.0000 1598.482460 0 0.0001 260 Out... lnL = -1598.482460 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1598.482460 Node 7: lnL = -1598.482460 Node 8: lnL = -1598.482460 Node 9: lnL = -1598.482460 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 324 Sequential format.. Reading seq # 1: YLR438C-A_Sbay Reading seq # 2: YLR438C-A_Scer Reading seq # 3: YLR438C-A_Skud Reading seq # 4: YLR438C-A_Smik Reading seq # 5: YLR438C-A_Spar Sequences read.. Counting patterns.. # site patterns = 170 Counting frequencies.. 120 bytes for distance 27200 bytes for lkl0 21760 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.284704 0.389954 0.202829 0.117234 0.164564 0.018500 0.363393 0.000060 lnL0 = -1353.987322 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1353.987322 x= 0.28470 0.38995 0.20283 0.11723 0.16456 0.01850 0.36339 0.00006 1 h-lim-p 0.0003 0.0025 34.8031 1353.197177 0 0.0012 24 | 0/8 2 h-lim-p 0.0018 0.0144 19.0165 1352.889960 1 0.0023 38 | 0/8 3 h-lim-p 0.0010 0.0084 24.2097 1352.695370 0 0.0016 50 | 0/8 4 h-lim-p 0.0032 0.0264 11.7705 1352.592969 4 0.0025 70 | 0/8 5 h-lim-p 0.0016 0.0128 4.2676 1352.561850 0 0.0048 83 | 0/8 6 h-lim-p 0.0108 0.1579 1.9105 1352.558804 5 0.0021 106 | 0/8 7 h-lim-p 0.0069 0.0549 0.5181 1352.557882 3 0.0058 125 | 0/8 8 h-lim-p 0.2060 20.0000 0.0145 1352.518755 0 0.8238 147 | 0/8 9 h-lim-p 2.5000 20.0000 0.0044 1352.516373 2 1.1719 171 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 1352.516362 1 1.0938 193 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1352.516362 0 1.0938 213 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1352.516362 0 1.0938 233 | 0/8 13 h-lim-p 0.9453 20.0000 0.0000 1352.516362 011.3434 256 | 0/8 14 h-lim-p 0.0874 15.3673 0.0009 1352.516362 0 0.0109 278 | 0/8 15 h-lim-p 0.0027 3.8200 0.0035 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1352.516362 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1352.516362 Node 7: lnL = -1352.516362 Node 8: lnL = -1352.516362 Node 9: lnL = -1352.516362 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 460 Sequential format.. Reading seq # 1: YLR440C_Sbay Reading seq # 2: YLR440C_Scer Reading seq # 3: YLR440C_Skud Reading seq # 4: YLR440C_Smik Reading seq # 5: YLR440C_Spar Sequences read.. Counting patterns.. # site patterns = 129 Counting frequencies.. 120 bytes for distance 20640 bytes for lkl0 16512 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.107758 0.018094 0.056175 0.064737 0.034521 0.118101 0.096606 0.017346 lnL0 = -1605.782679 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1605.782679 x= 0.10776 0.01809 0.05617 0.06474 0.03452 0.11810 0.09661 0.01735 1 h-lim-p 0.0001 0.0006 294.8483 1602.498900 0 0.0001 22 | 0/8 2 h-lim-p 0.0001 0.0010 48.6841 1602.323751 0 0.0002 34 | 0/8 3 h-lim-p 0.0003 0.0051 29.5232 1602.281540 5 0.0001 55 | 0/8 4 h-lim-p 0.0006 0.0178 6.0618 1602.276825 3 0.0003 73 | 0/8 5 h-lim-p 0.0048 0.3841 0.3422 1602.276753 3 0.0007 94 | 0/8 6 h-lim-p 0.0016 0.5172 0.1507 1602.276575 0 0.0025 114 | 0/8 7 h-lim-p 0.0068 1.0672 0.0545 1602.207427 0 0.1085 138 | 0/8 8 h-lim-p 0.0007 0.0052 7.5522 1602.198889 5 0.0002 168 | 0/8 9 h-lim-p 1.7804 20.0000 0.0011 1602.196037 5 1.0451 192 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1602.196023 1 1.0938 214 | 0/8 11 h-lim-p 2.4149 20.0000 0.0000 1602.196023 0 1.0565 234 | 0/8 12 h-lim-p 1.0418 20.0000 0.0000 1602.196023 0 8.3347 257 | 0/8 13 h-lim-p 0.0745 7.0009 0.0044 1602.196023 0 0.0186 278 | 0/8 14 h-lim-p 0.0045 1.6905 0.0183 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0023 | 0/8 16 h-lim-p 0.0000 20.0000 0.0023 Out... lnL = -1602.196023 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1602.196023 Node 7: lnL = -1602.196023 Node 8: lnL = -1602.196023 Node 9: lnL = -1602.196023 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 450 Sequential format.. Reading seq # 1: YLR441C_Sbay Reading seq # 2: YLR441C_Scer Reading seq # 3: YLR441C_Skud Reading seq # 4: YLR441C_Smik Reading seq # 5: YLR441C_Spar Sequences read.. Counting patterns.. # site patterns = 189 Counting frequencies.. 120 bytes for distance 30240 bytes for lkl0 24192 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.221903 0.067088 0.024116 0.110698 0.092656 0.154245 0.337132 0.041985 lnL0 = -1876.129688 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1876.129688 x= 0.22190 0.06709 0.02412 0.11070 0.09266 0.15425 0.33713 0.04199 1 h-lim-p 0.0013 0.0275 169.4959 1873.961878 8 0.0002 41 | 0/8 2 h-lim-p 0.0010 0.0102 30.7717 1873.582450 7 0.0008 71 | 0/8 3 h-lim-p 0.0009 0.0074 24.2731 1873.411926 2 0.0009 87 | 0/8 4 h-lim-p 0.0014 0.0207 15.1113 1873.371242 4 0.0005 107 | 0/8 5 h-lim-p 0.0014 0.0561 5.7569 1873.360708 5 0.0008 131 | 0/8 6 h-lim-p 0.0105 0.4036 0.4399 1873.360644 2 0.0006 150 | 0/8 7 h-lim-p 0.0073 5.3568 0.0390 1873.360642 1 0.0015 173 | 0/8 8 h-lim-p 0.0140 20.0000 0.0041 1873.359619 0 0.4472 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1873.359578 3 1.3437 225 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1873.359578 0 1.0938 245 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1873.359578 0 0.5469 266 | 0/8 12 h-lim-p 0.2513 20.0000 0.0000 1873.359578 0 0.0628 287 | 0/8 13 h-lim-p 0.0236 20.0000 0.0001 1873.359578 0 0.0118 307 | 0/8 14 h-lim-p 0.0056 20.0000 0.0002 1873.359578 0 0.0000 351 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 1873.359578 0 0.0000 381 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0005 | 0/8 18 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -1873.359578 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1873.359578 Node 7: lnL = -1873.359578 Node 8: lnL = -1873.359578 Node 9: lnL = -1873.359578 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 386 Sequential format.. Reading seq # 1: YLR442C_Sbay Reading seq # 2: YLR442C_Scer Reading seq # 3: YLR442C_Skud Reading seq # 4: YLR442C_Smik Reading seq # 5: YLR442C_Spar Sequences read.. Counting patterns.. # site patterns = 153 Counting frequencies.. 120 bytes for distance 24480 bytes for lkl0 19584 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.222668 0.055872 0.061769 0.092393 0.066566 0.171331 0.130654 0.069922 lnL0 = -1634.801401 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1634.801401 x= 0.22267 0.05587 0.06177 0.09239 0.06657 0.17133 0.13065 0.06992 1 h-lim-p 0.0003 0.0021 83.4025 1633.713808 0 0.0004 22 | 0/8 2 h-lim-p 0.0011 0.0086 19.9191 1633.609367 4 0.0005 43 | 0/8 3 h-lim-p 0.0015 0.0264 7.4051 1633.600011 5 0.0004 66 | 0/8 4 h-lim-p 0.0008 0.0374 3.5566 1633.598536 5 0.0003 89 | 0/8 5 h-lim-p 0.0065 0.9491 0.1559 1633.598465 3 0.0018 108 | 0/8 6 h-lim-p 0.0022 0.9973 0.1241 1633.597649 0 0.0088 130 | 0/8 7 h-lim-p 0.0051 0.6518 0.2167 1633.570070 0 0.0203 152 | 0/8 8 h-lim-p 0.0016 0.0820 2.6705 1633.566609 2 0.0008 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 1633.566187 2 0.9644 192 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1633.566187 0 1.0938 212 | 0/8 11 h-lim-p 1.8386 20.0000 0.0000 1633.566187 0 1.6088 232 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1633.566187 0 0.5469 253 | 0/8 13 h-lim-p 0.1997 20.0000 0.0000 1633.566187 0 0.0023 279 | 0/8 14 h-lim-p 0.0009 20.0000 0.0000 1633.566187 0 0.0005 299 | 0/8 15 h-lim-p 0.0004 20.0000 0.0000 1633.566187 0 0.0002 319 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 1633.566187 0 0.0000 339 | 0/8 17 h-lim-p 0.0004 20.0000 0.0000 1633.566187 0 0.0000 371 | 0/8 18 h-lim-p 0.0000 20.0000 0.0012 | 0/8 19 h-lim-p 0.0000 20.0000 0.0012 Out... lnL = -1633.566187 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1633.566187 Node 7: lnL = -1633.566187 Node 8: lnL = -1633.566187 Node 9: lnL = -1633.566187 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 392 Sequential format.. Reading seq # 1: YLR443W_Sbay Reading seq # 2: YLR443W_Scer Reading seq # 3: YLR443W_Skud Reading seq # 4: YLR443W_Smik Reading seq # 5: YLR443W_Spar Sequences read.. Counting patterns.. # site patterns = 153 Counting frequencies.. 120 bytes for distance 24480 bytes for lkl0 19584 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.221351 0.059049 0.066708 0.089933 0.069026 0.164391 0.126169 0.068871 lnL0 = -1644.266370 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1644.266370 x= 0.22135 0.05905 0.06671 0.08993 0.06903 0.16439 0.12617 0.06887 1 h-lim-p 0.0003 0.0021 91.0601 1642.976824 0 0.0004 22 | 0/8 2 h-lim-p 0.0010 0.0077 16.8980 1642.910401 5 0.0005 44 | 0/8 3 h-lim-p 0.0010 0.0234 8.3284 1642.901134 6 0.0003 72 | 0/8 4 h-lim-p 0.0008 0.0473 3.2646 1642.899153 4 0.0004 93 | 0/8 5 h-lim-p 0.0102 1.5693 0.1401 1642.899042 3 0.0027 112 | 0/8 6 h-lim-p 0.0056 1.9124 0.0688 1642.895969 0 0.0223 134 | 0/8 7 h-lim-p 0.0016 0.1248 0.9506 1642.864419 0 0.0065 156 | 0/8 8 h-lim-p 0.0114 0.2655 0.5402 1642.864310 3 0.0007 185 | 0/8 9 h-lim-p 0.4235 20.0000 0.0010 1642.863288 0 0.8471 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1642.863274 1 0.9961 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1642.863274 0 1.0938 248 | 0/8 12 h-lim-p 1.1725 20.0000 0.0000 1642.863274 0 1.7587 268 | 0/8 13 h-lim-p 0.4882 20.0000 0.0000 1642.863274 0 0.0610 290 | 0/8 14 h-lim-p 0.0044 20.0000 0.0005 1642.863274 0 0.0000 316 | 0/8 15 h-lim-p 0.0009 20.0000 0.0000 1642.863274 0 0.0002 337 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 1642.863274 0 0.0001 357 | 0/8 17 h-lim-p 0.0001 20.0000 0.0000 1642.863274 0 0.0001 377 | 0/8 18 h-lim-p 0.0002 20.0000 0.0000 1642.863274 0 0.0001 397 Out... lnL = -1642.863274 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1642.863274 Node 7: lnL = -1642.863274 Node 8: lnL = -1642.863274 Node 9: lnL = -1642.863274 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 644 Sequential format.. Reading seq # 1: YLR446W_Sbay Reading seq # 2: YLR446W_Scer Reading seq # 3: YLR446W_Skud Reading seq # 4: YLR446W_Smik Reading seq # 5: YLR446W_Spar Sequences read.. Counting patterns.. # site patterns = 204 Counting frequencies.. 120 bytes for distance 32640 bytes for lkl0 26112 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.197732 0.047174 0.053546 0.079398 0.083956 0.164551 0.130430 0.051036 lnL0 = -2566.497997 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2566.497997 x= 0.19773 0.04717 0.05355 0.07940 0.08396 0.16455 0.13043 0.05104 1 h-lim-p 0.0013 0.0266 201.6298 2563.457492 5 0.0002 34 | 0/8 2 h-lim-p 0.0006 0.0052 21.5257 2563.399614 4 0.0003 54 | 0/8 3 h-lim-p 0.0008 0.0285 6.7947 2563.393792 6 0.0003 81 | 0/8 4 h-lim-p 0.0008 0.0648 2.4438 2563.392996 3 0.0003 99 | 0/8 5 h-lim-p 0.0030 2.4081 0.2509 2563.392984 2 0.0004 117 | 0/8 6 h-lim-p 0.0044 8.9813 0.0224 2563.392983 0 0.0010 138 | 0/8 7 h-lim-p 0.0015 12.2873 0.0144 2563.392981 0 0.0030 159 | 0/8 8 h-lim-p 0.0087 20.0000 0.0049 2563.392597 0 0.1045 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2563.392586 1 0.9961 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2563.392586 0 1.0938 224 | 0/8 11 h-lim-p 1.4607 20.0000 0.0000 2563.392586 0 2.1910 244 | 0/8 12 h-lim-p 0.4949 20.0000 0.0001 2563.392586 0 0.0309 267 | 0/8 13 h-lim-p 0.0019 20.0000 0.0014 2563.392586 0 0.0005 288 | 0/8 14 h-lim-p 0.0002 20.0000 0.0029 2563.392586 0 0.0002 308 | 0/8 15 h-lim-p 0.0002 20.0000 0.0034 2563.392586 0 0.0002 328 | 0/8 16 h-lim-p 0.0001 20.0000 0.0097 2563.392586 0 0.0000 349 | 0/8 17 h-lim-p 0.0002 20.0000 0.0010 2563.392586 0 0.0000 373 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 2563.392586 0 0.0000 409 | 0/8 19 h-lim-p 0.0000 20.0000 0.0009 | 0/8 20 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -2563.392586 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2563.392586 Node 7: lnL = -2563.392586 Node 8: lnL = -2563.392586 Node 9: lnL = -2563.392586 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 873 Sequential format.. Reading seq # 1: YLR449W_Sbay Reading seq # 2: YLR449W_Scer Reading seq # 3: YLR449W_Skud Reading seq # 4: YLR449W_Smik Reading seq # 5: YLR449W_Spar Sequences read.. Counting patterns.. # site patterns = 410 Counting frequencies.. 120 bytes for distance 65600 bytes for lkl0 52480 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.411929 0.098675 0.116406 0.276740 0.176246 0.261576 0.320750 0.093423 lnL0 = -4459.360407 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4459.360407 x= 0.41193 0.09867 0.11641 0.27674 0.17625 0.26158 0.32075 0.09342 1 h-lim-p 0.0056 0.0448 76.9998 4458.112435 8 0.0004 46 | 0/8 2 h-lim-p 0.0015 0.0120 20.6638 4457.973841 2 0.0007 62 | 0/8 3 h-lim-p 0.0019 0.0466 7.5388 4457.958225 5 0.0006 86 | 0/8 4 h-lim-p 0.0058 0.4498 0.8121 4457.957937 4 0.0009 111 | 0/8 5 h-lim-p 0.0058 3.4464 0.1242 4457.957928 1 0.0012 134 | 0/8 6 h-lim-p 0.0026 7.0499 0.0550 4457.957926 1 0.0013 157 | 0/8 7 h-lim-p 0.0242 20.0000 0.0029 4457.957845 0 0.1449 179 | 0/8 8 h-lim-p 0.0042 20.0000 0.1015 4457.957471 0 0.0063 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4457.957466 0 1.0938 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4457.957466 0 1.0938 239 | 0/8 11 h-lim-p 1.2794 20.0000 0.0000 4457.957466 0 1.2794 259 | 0/8 12 h-lim-p 0.6574 20.0000 0.0000 4457.957466 0 0.1438 280 | 0/8 13 h-lim-p 0.0065 20.0000 0.0004 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -4457.957466 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4457.957466 Node 7: lnL = -4457.957466 Node 8: lnL = -4457.957466 Node 9: lnL = -4457.957466 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 649 Sequential format.. Reading seq # 1: YLR450W_Sbay Reading seq # 2: YLR450W_Scer Reading seq # 3: YLR450W_Skud Reading seq # 4: YLR450W_Smik Reading seq # 5: YLR450W_Spar Sequences read.. Counting patterns.. # site patterns = 214 Counting frequencies.. 120 bytes for distance 34240 bytes for lkl0 27392 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.206612 0.050638 0.071697 0.119539 0.094440 0.174867 0.214165 0.031470 lnL0 = -2863.334060 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2863.334060 x= 0.20661 0.05064 0.07170 0.11954 0.09444 0.17487 0.21417 0.03147 1 h-lim-p 0.0031 0.0733 135.6898 2861.645687 4 0.0002 33 | 0/8 2 h-lim-p 0.0011 0.0089 22.9273 2861.533480 4 0.0004 53 | 0/8 3 h-lim-p 0.0009 0.0211 11.3690 2861.515479 4 0.0003 73 | 0/8 4 h-lim-p 0.0012 0.0671 3.2877 2861.513986 3 0.0003 92 | 0/8 5 h-lim-p 0.0020 0.3431 0.5044 2861.513945 2 0.0003 111 | 0/8 6 h-lim-p 0.0037 4.8827 0.0442 2861.513944 0 0.0008 132 | 0/8 7 h-lim-p 0.0023 11.5248 0.0155 2861.513933 0 0.0070 153 | 0/8 8 h-lim-p 0.0070 20.0000 0.0155 2861.512864 0 0.0559 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2861.512849 1 0.9961 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2861.512849 0 1.0938 218 | 0/8 11 h-lim-p 0.9377 20.0000 0.0000 2861.512849 0 1.4065 238 | 0/8 12 h-lim-p 0.0106 10.9435 0.0044 2861.512849 0 0.0005 262 | 0/8 13 h-lim-p 0.0000 0.4770 0.1015 2861.512849 0 0.0000 282 | 0/8 14 h-lim-p 0.0000 0.3978 0.1217 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0007 2861.512849 0 0.0000 336 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 2861.512849 0 0.0000 366 | 0/8 17 h-lim-p 0.0000 20.0000 0.0003 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0007 2861.512849 0 0.0000 419 | 0/8 19 h-lim-p 0.0001 20.0000 0.0002 2861.512849 0 0.0000 439 | 0/8 20 h-lim-p 0.0001 20.0000 0.0001 .. | 0/8 21 h-lim-p 0.0000 20.0000 0.0007 2861.512849 0 0.0000 497 | 0/8 22 h-lim-p 0.0000 20.0000 0.0002 .. | 0/8 23 h-lim-p 0.0000 20.0000 0.0007 | 0/8 24 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -2861.512849 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2861.512849 Node 7: lnL = -2861.512849 Node 8: lnL = -2861.512849 Node 9: lnL = -2861.512849 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 468 Sequential format.. Reading seq # 1: YLR452C_Sbay Reading seq # 2: YLR452C_Scer Reading seq # 3: YLR452C_Skud Reading seq # 4: YLR452C_Smik Reading seq # 5: YLR452C_Spar Sequences read.. Counting patterns.. # site patterns = 191 Counting frequencies.. 120 bytes for distance 30560 bytes for lkl0 24448 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.291987 0.055998 0.099762 0.185101 0.147848 0.151969 0.233202 0.067795 lnL0 = -2217.338990 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2217.338990 x= 0.29199 0.05600 0.09976 0.18510 0.14785 0.15197 0.23320 0.06779 1 h-lim-p 0.0016 0.0132 68.4193 2216.352626 8 0.0005 41 | 0/8 2 h-lim-p 0.0017 0.0144 18.2760 2216.238885 3 0.0007 60 | 0/8 3 h-lim-p 0.0014 0.0280 9.6832 2216.215192 2 0.0006 76 | 0/8 4 h-lim-p 0.0035 0.1636 1.7711 2216.214136 3 0.0007 95 | 0/8 5 h-lim-p 0.0041 0.7471 0.3020 2216.214109 3 0.0006 117 | 0/8 6 h-lim-p 0.0059 5.0921 0.0307 2216.214109 0 0.0013 138 | 0/8 7 h-lim-p 0.0135 20.0000 0.0029 2216.214108 0 0.0118 158 | 0/8 8 h-lim-p 0.0209 20.0000 0.0016 2216.214075 0 0.1257 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2216.214074 0 1.0938 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2216.214074 0 1.0938 220 | 0/8 11 h-lim-p 1.1977 20.0000 0.0000 2216.214074 0 4.7907 242 | 0/8 12 h-lim-p 0.3331 20.0000 0.0001 2216.214074 0 0.0026 268 | 0/8 13 h-lim-p 0.0000 0.7994 0.1340 2216.214074 0 0.0000 296 | 0/8 14 h-lim-p 0.0006 20.0000 0.0000 2216.214074 0 0.0003 316 Out... lnL = -2216.214074 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2216.214074 Node 7: lnL = -2216.214074 Node 8: lnL = -2216.214074 Node 9: lnL = -2216.214074 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 903 Sequential format.. Reading seq # 1: YLR453C_Sbay Reading seq # 2: YLR453C_Scer Reading seq # 3: YLR453C_Skud Reading seq # 4: YLR453C_Smik Reading seq # 5: YLR453C_Spar Sequences read.. Counting patterns.. # site patterns = 374 Counting frequencies.. 120 bytes for distance 59840 bytes for lkl0 47872 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.305617 0.094150 0.069250 0.191999 0.125544 0.280953 0.363587 0.040158 lnL0 = -4411.986072 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4411.986072 x= 0.30562 0.09415 0.06925 0.19200 0.12554 0.28095 0.36359 0.04016 1 h-lim-p 0.0005 0.0040 121.5842 4410.000054 7 0.0003 39 | 0/8 2 h-lim-p 0.0007 0.0059 30.0520 4409.823924 7 0.0004 67 | 0/8 3 h-lim-p 0.0007 0.0096 17.2428 4409.776870 6 0.0004 95 | 0/8 4 h-lim-p 0.0013 0.0431 5.2335 4409.769074 2 0.0006 111 | 0/8 5 h-lim-p 0.0022 0.1341 1.5112 4409.768027 2 0.0010 127 | 0/8 6 h-lim-p 0.0130 0.7358 0.1196 4409.768024 1 0.0004 145 | 0/8 7 h-lim-p 0.0053 20.0000 0.0090 4409.768024 0 0.0023 165 | 0/8 8 h-lim-p 0.0494 20.0000 0.0004 4409.767985 0 0.5927 188 | 0/8 9 h-lim-p 1.3752 20.0000 0.0002 4409.767984 0 1.2033 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4409.767984 0 1.0938 228 | 0/8 11 h-lim-p 0.8164 20.0000 0.0000 4409.767984 0 0.7143 248 | 0/8 12 h-lim-p 0.3934 20.0000 0.0000 4409.767984 0 0.0983 269 | 0/8 13 h-lim-p 0.0301 20.0000 0.0001 4409.767984 0 0.0005 294 | 0/8 14 h-lim-p 0.0006 20.0000 0.0001 4409.767984 0 0.0003 314 | 0/8 15 h-lim-p 0.0006 20.0000 0.0001 4409.767984 0 0.0002 335 | 0/8 16 h-lim-p 0.0008 20.0000 0.0000 4409.767984 0 0.0000 363 Out... lnL = -4409.767984 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4409.767984 Node 7: lnL = -4409.767984 Node 8: lnL = -4409.767984 Node 9: lnL = -4409.767984 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 853 Sequential format.. Reading seq # 1: YLR455W_Sbay Reading seq # 2: YLR455W_Scer Reading seq # 3: YLR455W_Skud Reading seq # 4: YLR455W_Smik Reading seq # 5: YLR455W_Spar Sequences read.. Counting patterns.. # site patterns = 333 Counting frequencies.. 120 bytes for distance 53280 bytes for lkl0 42624 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.230244 0.137140 0.064660 0.198479 0.142238 0.205482 0.233262 0.005042 lnL0 = -4091.421138 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4091.421138 x= 0.23024 0.13714 0.06466 0.19848 0.14224 0.20548 0.23326 0.00504 1 h-lim-p 0.0036 0.8096 150.3259 4089.009910 4 0.0002 33 | 0/8 2 h-lim-p 0.0010 0.0094 34.3045 4088.730477 5 0.0005 57 | 0/8 3 h-lim-p 0.0006 0.0050 10.6313 4088.711145 6 0.0004 86 | 0/8 4 h-lim-p 0.0017 0.1350 2.3707 4088.709842 5 0.0005 110 | 0/8 5 h-lim-p 0.0024 0.0926 0.4830 4088.709804 3 0.0004 131 | 0/8 6 h-lim-p 0.0098 20.0000 0.0177 4088.709802 1 0.0024 154 | 0/8 7 h-lim-p 0.0145 20.0000 0.0029 4088.709128 0 0.2322 178 | 0/8 8 h-lim-p 0.0013 0.5487 0.5218 4088.709027 0 0.0007 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4088.709025 0 1.0938 218 | 0/8 10 h-lim-p 1.2200 20.0000 0.0000 4088.709025 0 1.0675 238 | 0/8 11 h-lim-p 1.1455 20.0000 0.0000 4088.709025 0 4.5821 260 | 0/8 12 h-lim-p 0.0612 6.3370 0.0028 4088.709025 0 0.0005 286 | 0/8 13 h-lim-p 0.0005 5.9865 0.0029 4088.709025 0 0.0000 321 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 4088.709025 0 0.0000 348 | 0/8 15 h-lim-p 0.0000 20.0000 0.0008 | 0/8 16 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -4088.709025 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4088.709025 Node 7: lnL = -4088.709025 Node 8: lnL = -4088.709025 Node 9: lnL = -4088.709025 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 550 Sequential format.. Reading seq # 1: YLR456W_Sbay Reading seq # 2: YLR456W_Scer Reading seq # 3: YLR456W_Skud Reading seq # 4: YLR456W_Smik Reading seq # 5: YLR456W_Spar Sequences read.. Counting patterns.. # site patterns = 189 Counting frequencies.. 120 bytes for distance 30240 bytes for lkl0 24192 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.199741 0.119777 0.057981 0.134970 0.041682 0.198767 0.143435 0.026754 lnL0 = -2332.745449 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2332.745449 x= 0.19974 0.11978 0.05798 0.13497 0.04168 0.19877 0.14343 0.02675 1 h-lim-p 0.0030 0.0239 76.0235 2332.144015 6 0.0002 38 | 0/8 2 h-lim-p 0.0003 0.0027 21.0136 2332.103943 7 0.0002 67 | 0/8 3 h-lim-p 0.0005 0.0231 8.3549 2332.090202 2 0.0005 83 | 0/8 4 h-lim-p 0.0024 0.0556 1.5814 2332.089637 3 0.0005 102 | 0/8 5 h-lim-p 0.0024 0.8098 0.3147 2332.089616 2 0.0005 119 | 0/8 6 h-lim-p 0.0103 18.0211 0.0140 2332.089616 0 0.0011 141 | 0/8 7 h-lim-p 0.0117 20.0000 0.0014 2332.089616 0 0.0026 162 | 0/8 8 h-lim-p 0.0145 20.0000 0.0002 2332.089612 0 0.2328 186 | 0/8 9 h-lim-p 2.1455 20.0000 0.0000 2332.089612 0 0.9387 206 | 0/8 10 h-lim-p 0.8886 20.0000 0.0000 2332.089612 0 0.0052 233 | 0/8 11 h-lim-p 0.0017 20.0000 0.0001 2332.089612 0 0.0000 270 | 0/8 12 h-lim-p 0.0000 20.0000 0.0025 2332.089612 0 0.0000 305 | 0/8 13 h-lim-p 0.0000 20.0000 0.0025 | 0/8 14 h-lim-p 0.0000 20.0000 0.0025 Out... lnL = -2332.089612 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2332.089612 Node 7: lnL = -2332.089612 Node 8: lnL = -2332.089612 Node 9: lnL = -2332.089612 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 595 Sequential format.. Reading seq # 1: YLR457C_Sbay Reading seq # 2: YLR457C_Scer Reading seq # 3: YLR457C_Skud Reading seq # 4: YLR457C_Smik Reading seq # 5: YLR457C_Spar Sequences read.. Counting patterns.. # site patterns = 268 Counting frequencies.. 120 bytes for distance 42880 bytes for lkl0 34304 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.329750 0.051792 0.115879 0.156755 0.103137 0.278915 0.281603 0.076992 lnL0 = -2893.840206 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2893.840206 x= 0.32975 0.05179 0.11588 0.15675 0.10314 0.27891 0.28160 0.07699 1 h-lim-p 0.0011 0.0085 59.7864 2893.132173 5 0.0004 32 | 0/8 2 h-lim-p 0.0018 0.0171 13.9540 2893.058401 5 0.0008 53 | 0/8 3 h-lim-p 0.0010 0.0286 11.5546 2893.039302 2 0.0004 69 | 0/8 4 h-lim-p 0.0014 0.0564 3.6876 2893.036358 5 0.0005 93 | 0/8 5 h-lim-p 0.0067 1.6616 0.2856 2893.036319 3 0.0009 113 | 0/8 6 h-lim-p 0.0056 5.6613 0.0462 2893.036318 0 0.0012 134 | 0/8 7 h-lim-p 0.0046 17.2691 0.0122 2893.036318 0 0.0020 154 | 0/8 8 h-lim-p 0.0598 20.0000 0.0004 2893.036277 0 0.7176 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2893.036275 0 1.0938 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2893.036275 0 1.0938 217 | 0/8 11 h-lim-p 1.2067 20.0000 0.0000 2893.036275 0 1.0559 237 | 0/8 12 h-lim-p 0.3579 20.0000 0.0000 2893.036275 0 0.0671 259 | 0/8 13 h-lim-p 0.0126 20.0000 0.0002 2893.036275 0 0.0047 280 | 0/8 14 h-lim-p 0.0020 20.0000 0.0004 2893.036275 0 0.0000 314 | 0/8 15 h-lim-p 0.0004 20.0000 0.0000 2893.036275 0 0.0000 341 Out... lnL = -2893.036275 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2893.036275 Node 7: lnL = -2893.036275 Node 8: lnL = -2893.036275 Node 9: lnL = -2893.036275 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 524 Sequential format.. Reading seq # 1: YLR459W_Sbay Reading seq # 2: YLR459W_Scer Reading seq # 3: YLR459W_Skud Reading seq # 4: YLR459W_Smik Reading seq # 5: YLR459W_Spar Sequences read.. Counting patterns.. # site patterns = 232 Counting frequencies.. 120 bytes for distance 37120 bytes for lkl0 29696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.364326 0.000060 0.245221 0.159022 0.176815 0.174375 0.360895 0.120115 lnL0 = -2648.279209 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2648.279209 x= 0.36433 0.00006 0.24522 0.15902 0.17681 0.17437 0.36089 0.12011 1 h-lim-p 0.0001 0.0012 177.7149 2638.113898 0 0.0006 24 | 0/8 2 h-lim-p 0.0005 0.0042 75.1364 2636.705395 7 0.0006 54 | 0/8 3 h-lim-p 0.0015 0.0118 26.0822 2636.466596 5 0.0008 77 | 0/8 4 h-lim-p 0.0027 0.0578 7.6967 2636.435570 5 0.0011 101 | 0/8 5 h-lim-p 0.0018 0.0407 5.0120 2636.429962 5 0.0006 126 | 0/8 6 h-lim-p 0.0016 0.1655 1.8363 2636.428867 3 0.0007 144 | 0/8 7 h-lim-p 0.0369 3.4589 0.0340 2636.364250 0 0.2949 159 | 0/8 8 h-lim-p 0.0023 0.0505 4.3815 2636.309345 2 0.0021 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0012 2636.308621 3 1.0449 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2636.308619 0 1.0938 221 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2636.308619 0 1.0938 241 | 0/8 12 h-lim-p 1.3525 20.0000 0.0000 2636.308619 0 1.3525 261 | 0/8 13 h-lim-p 0.9058 20.0000 0.0000 2636.308619 0 1.3587 281 | 0/8 14 h-lim-p 0.0010 11.5981 0.0146 2636.308619 0 0.0001 303 | 0/8 15 h-lim-p 0.0010 20.0000 0.0019 2636.308619 0 0.0000 335 | 0/8 16 h-lim-p 0.0003 20.0000 0.0000 2636.308619 0 0.0000 369 Out... lnL = -2636.308619 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2636.308619 Node 7: lnL = -2636.308619 Node 8: lnL = -2636.308619 Node 9: lnL = -2636.308619 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 456 Sequential format.. Reading seq # 1: YML001W_Sbay Reading seq # 2: YML001W_Scer Reading seq # 3: YML001W_Skud Reading seq # 4: YML001W_Smik Reading seq # 5: YML001W_Spar Sequences read.. Counting patterns.. # site patterns = 187 Counting frequencies.. 120 bytes for distance 29920 bytes for lkl0 23936 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.244595 0.155716 0.032063 0.149005 0.098282 0.227896 0.186279 0.028547 lnL0 = -2101.353326 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2101.353326 x= 0.24460 0.15572 0.03206 0.14900 0.09828 0.22790 0.18628 0.02855 1 h-lim-p 0.0043 0.0344 44.1343 2101.094470 7 0.0003 42 | 0/8 2 h-lim-p 0.0013 0.0144 9.6525 2101.071622 3 0.0005 60 | 0/8 3 h-lim-p 0.0020 0.0548 2.5262 2101.070114 4 0.0005 81 | 0/8 4 h-lim-p 0.0016 0.4946 0.7763 2101.069907 0 0.0007 93 | 0/8 5 h-lim-p 0.0094 3.5067 0.0583 2101.069906 0 0.0010 115 | 0/8 6 h-lim-p 0.0066 20.0000 0.0091 2101.069906 0 0.0007 137 | 0/8 7 h-lim-p 0.0049 20.0000 0.0013 2101.069906 0 0.0074 157 | 0/8 8 h-lim-p 0.0171 20.0000 0.0006 2101.069901 0 0.1371 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2101.069901 0 1.0938 200 | 0/8 10 h-lim-p 1.4114 20.0000 0.0000 2101.069901 0 0.3087 221 | 0/8 11 h-lim-p 0.1046 20.0000 0.0001 2101.069901 0 0.0065 244 | 0/8 12 h-lim-p 0.0027 20.0000 0.0001 2101.069901 0 0.0013 264 | 0/8 13 h-lim-p 0.0007 20.0000 0.0003 2101.069901 0 0.0000 287 | 0/8 14 h-lim-p 0.0001 20.0000 0.0001 2101.069901 0 0.0000 317 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 2101.069901 0 0.0000 345 Out... lnL = -2101.069901 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2101.069901 Node 7: lnL = -2101.069901 Node 8: lnL = -2101.069901 Node 9: lnL = -2101.069901 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 202 Sequential format.. Reading seq # 1: YML002W_Sbay Reading seq # 2: YML002W_Scer Reading seq # 3: YML002W_Skud Reading seq # 4: YML002W_Smik Reading seq # 5: YML002W_Spar Sequences read.. Counting patterns.. # site patterns = 117 Counting frequencies.. 120 bytes for distance 18720 bytes for lkl0 14976 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.345298 0.217570 0.103628 0.898657 0.267525 0.219212 0.313434 0.000060 lnL0 = -1030.303587 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1030.303587 x= 0.34530 0.21757 0.10363 0.89866 0.26752 0.21921 0.31343 0.00006 1 h-lim-p 0.0000 0.0000 143.8039 1030.267645 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0109 60.5255 1022.235410 0 0.0051 43 | 1/8 3 h-lim-p 0.0029 0.0233 15.8008 1021.240238 0 0.0088 56 | 1/8 4 h-lim-p 0.0086 0.0690 13.9273 1020.178704 0 0.0129 68 | 1/8 5 h-lim-p 0.0006 0.0045 46.7714 1018.320084 m 0.0045 80 | 2/8 6 h-lim-p 0.0012 0.0099 35.4012 1016.954178 0 0.0025 93 | 2/8 7 h-lim-p 0.0042 0.0334 10.8238 1016.431837 0 0.0084 106 | 2/8 8 h-lim-p 0.0414 0.3312 1.3392 1006.292689 0 0.1656 120 | 1/8 9 h-lim-p 0.0071 0.0566 18.6706 1006.112296 6 0.0011 147 | 1/8 10 h-lim-p 0.0950 2.7118 0.2225 1005.359115 0 0.3800 161 | 1/8 11 h-lim-p 0.3729 3.4793 0.2267 1004.973697 0 0.7457 181 | 0/8 12 h-lim-p 0.0134 0.1072 7.3439 1004.954430 2 0.0016 206 | 0/8 13 h-lim-p 0.1492 2.0276 0.0773 1004.504888 8 0.9746 243 | 0/8 14 h-lim-p 1.9479 19.8529 0.0387 1004.468440 6 0.7855 274 | 0/8 15 h-lim-p 2.1048 16.8387 0.0094 1004.465773 5 0.6928 305 | 0/8 16 h-lim-p 1.5260 20.0000 0.0043 1004.465298 3 0.6106 331 | 0/8 17 h-lim-p 2.5000 20.0000 0.0005 1004.465241 3 0.8800 358 | 0/8 18 h-lim-p 2.1084 20.0000 0.0002 1004.465239 1 0.5189 381 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1004.465239 0 1.0938 401 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 1004.465239 0 1.0938 421 | 0/8 21 h-lim-p 2.5000 20.0000 0.0000 1004.465239 0 1.0938 441 | 0/8 22 h-lim-p 2.5000 20.0000 0.0000 1004.465239 0 0.2734 463 | 0/8 23 h-lim-p 0.0516 20.0000 0.0000 1004.465239 0 0.0516 483 | 0/8 24 h-lim-p 0.0197 20.0000 0.0000 1004.465239 0 0.0000 520 Out... lnL = -1004.465239 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1004.465239 Node 7: lnL = -1004.465239 Node 8: lnL = -1004.465239 Node 9: lnL = -1004.465239 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 861 Sequential format.. Reading seq # 1: YML004C_Sbay Reading seq # 2: YML004C_Scer Reading seq # 3: YML004C_Skud Reading seq # 4: YML004C_Smik Reading seq # 5: YML004C_Spar Sequences read.. Counting patterns.. # site patterns = 365 Counting frequencies.. 120 bytes for distance 58400 bytes for lkl0 46720 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.278499 0.117612 0.066686 0.153205 0.113878 0.214667 0.220116 0.046915 lnL0 = -3988.770283 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3988.770283 x= 0.27850 0.11761 0.06669 0.15321 0.11388 0.21467 0.22012 0.04692 1 h-lim-p 0.0041 0.7416 139.7625 3986.787632 7 0.0002 37 | 0/8 2 h-lim-p 0.0010 0.0082 32.1977 3986.558249 2 0.0004 53 | 0/8 3 h-lim-p 0.0009 0.0183 15.6372 3986.525505 6 0.0003 79 | 0/8 4 h-lim-p 0.0019 0.1979 2.6292 3986.523995 2 0.0005 96 | 0/8 5 h-lim-p 0.0016 0.2249 0.7432 3986.523857 3 0.0005 115 | 0/8 6 h-lim-p 0.0074 8.6588 0.0530 3986.523856 0 0.0008 137 | 0/8 7 h-lim-p 0.0036 20.0000 0.0119 3986.523846 0 0.0072 158 | 0/8 8 h-lim-p 0.0046 20.0000 0.0184 3986.522928 0 0.0557 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3986.522887 1 0.9961 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3986.522887 0 1.0938 223 | 0/8 11 h-lim-p 1.0602 20.0000 0.0000 3986.522887 0 0.4639 243 | 0/8 12 h-lim-p 0.0453 20.0000 0.0002 3986.522887 0 0.0028 266 | 0/8 13 h-lim-p 0.0010 20.0000 0.0007 3986.522887 0 0.0000 304 | 0/8 14 h-lim-p 0.0000 20.0000 0.0005 3986.522887 0 0.0000 325 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0005 | 0/8 17 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -3986.522887 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3986.522887 Node 7: lnL = -3986.522887 Node 8: lnL = -3986.522887 Node 9: lnL = -3986.522887 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 892 Sequential format.. Reading seq # 1: YML005W_Sbay Reading seq # 2: YML005W_Scer Reading seq # 3: YML005W_Skud Reading seq # 4: YML005W_Smik Reading seq # 5: YML005W_Spar Sequences read.. Counting patterns.. # site patterns = 446 Counting frequencies.. 120 bytes for distance 71360 bytes for lkl0 57088 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.607046 0.334637 0.299141 0.215288 0.170582 0.411459 0.308200 0.113762 lnL0 = -5102.290584 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 5102.290584 x= 0.60705 0.33464 0.29914 0.21529 0.17058 0.41146 0.30820 0.11376 1 h-lim-p 0.0016 0.0126 22.5952 5101.947538 6 0.0013 35 | 0/8 2 h-lim-p 0.0014 0.0261 21.3143 5101.867540 5 0.0006 57 | 0/8 3 h-lim-p 0.0014 0.0521 8.7467 5101.818726 0 0.0020 69 | 0/8 4 h-lim-p 0.0128 0.3105 1.3874 5101.815586 4 0.0034 90 | 0/8 5 h-lim-p 0.0076 2.5094 0.6150 5101.815131 4 0.0028 111 | 0/8 6 h-lim-p 0.0055 0.9757 0.3130 5101.815058 2 0.0017 136 | 0/8 7 h-lim-p 0.0084 9.5224 0.0654 5101.815050 1 0.0021 159 | 0/8 8 h-lim-p 0.0260 20.0000 0.0052 5101.813336 0 0.4161 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 5101.813304 1 0.9961 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 5101.813304 0 1.0938 225 | 0/8 11 h-lim-p 1.2326 20.0000 0.0000 5101.813304 0 1.8488 245 | 0/8 12 h-lim-p 0.3011 20.0000 0.0000 5101.813304 0 0.0018 272 | 0/8 13 h-lim-p 0.0037 20.0000 0.0000 5101.813304 0 0.0018 292 | 0/8 14 h-lim-p 0.0034 20.0000 0.0000 5101.813304 0 0.0000 326 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 5101.813304 0 0.0000 349 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -5101.813304 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -5101.813304 Node 7: lnL = -5101.813304 Node 8: lnL = -5101.813304 Node 9: lnL = -5101.813304 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 843 Sequential format.. Reading seq # 1: YML006C_Sbay Reading seq # 2: YML006C_Scer Reading seq # 3: YML006C_Skud Reading seq # 4: YML006C_Smik Reading seq # 5: YML006C_Spar Sequences read.. Counting patterns.. # site patterns = 208 Counting frequencies.. 120 bytes for distance 33280 bytes for lkl0 26624 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.134376 0.037419 0.044708 0.076455 0.065436 0.123498 0.093620 0.021104 lnL0 = -3104.464762 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3104.464762 x= 0.13438 0.03742 0.04471 0.07646 0.06544 0.12350 0.09362 0.02110 1 h-lim-p 0.0002 0.0015 193.5525 3102.905834 2 0.0001 26 | 0/8 2 h-lim-p 0.0004 0.0031 32.6624 3102.839616 6 0.0001 53 | 0/8 3 h-lim-p 0.0004 0.0421 9.2411 3102.833618 6 0.0002 80 | 0/8 4 h-lim-p 0.0005 0.0400 2.9709 3102.833045 4 0.0001 104 | 0/8 5 h-lim-p 0.0020 0.4663 0.2122 3102.833042 1 0.0001 121 | 0/8 6 h-lim-p 0.0004 1.5666 0.0648 3102.833042 0 0.0002 141 | 0/8 7 h-lim-p 0.0052 13.5139 0.0022 3102.833032 0 0.0207 163 | 0/8 8 h-lim-p 0.0008 0.8406 0.0601 3102.832658 0 0.0062 186 | 0/8 9 h-lim-p 0.1850 16.1976 0.0020 3102.832644 0 0.7399 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0003 3102.832644 0 1.0938 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3102.832644 0 1.2500 248 | 0/8 12 h-lim-p 0.2938 20.0000 0.0002 3102.832644 0 0.0161 271 | 0/8 13 h-lim-p 0.0023 20.0000 0.0012 3102.832644 0 0.0000 313 | 0/8 14 h-lim-p 0.0000 20.0000 0.0013 | 0/8 15 h-lim-p 0.0000 20.0000 0.0013 Out... lnL = -3102.832644 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3102.832644 Node 7: lnL = -3102.832644 Node 8: lnL = -3102.832644 Node 9: lnL = -3102.832644 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 633 Sequential format.. Reading seq # 1: YML007W_Sbay Reading seq # 2: YML007W_Scer Reading seq # 3: YML007W_Skud Reading seq # 4: YML007W_Smik Reading seq # 5: YML007W_Spar Sequences read.. Counting patterns.. # site patterns = 217 Counting frequencies.. 120 bytes for distance 34720 bytes for lkl0 27776 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.201875 0.006968 0.071363 0.111147 0.104907 0.148439 0.186028 0.040211 lnL0 = -2642.180546 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2642.180546 x= 0.20187 0.00697 0.07136 0.11115 0.10491 0.14844 0.18603 0.04021 1 h-lim-p 0.0004 0.3057 343.4979 2637.976804 8 0.0001 42 | 0/8 2 h-lim-p 0.0008 0.0128 37.4965 2637.745205 3 0.0003 60 | 0/8 3 h-lim-p 0.0009 0.0178 13.9104 2637.712183 3 0.0004 78 | 0/8 4 h-lim-p 0.0015 0.0802 3.5285 2637.710391 3 0.0003 97 | 0/8 5 h-lim-p 0.0016 0.4163 0.6927 2637.710303 1 0.0004 112 | 0/8 6 h-lim-p 0.0057 3.4973 0.0478 2637.710302 0 0.0006 134 | 0/8 7 h-lim-p 0.0089 20.0000 0.0034 2637.710297 0 0.0177 155 | 0/8 8 h-lim-p 0.0022 5.1497 0.0273 2637.710056 0 0.0175 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2637.710053 1 1.2305 201 | 0/8 10 h-lim-p 1.3616 20.0000 0.0000 2637.710053 0 1.3616 221 | 0/8 11 h-lim-p 2.2994 20.0000 0.0000 2637.710053 0 1.0060 241 | 0/8 12 h-lim-p 0.7266 20.0000 0.0000 2637.710053 0 0.0000 282 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 2637.710053 0 0.0000 305 Out... lnL = -2637.710053 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2637.710053 Node 7: lnL = -2637.710053 Node 8: lnL = -2637.710053 Node 9: lnL = -2637.710053 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 344 Sequential format.. Reading seq # 1: YML009C_Sbay Reading seq # 2: YML009C_Scer Reading seq # 3: YML009C_Skud Reading seq # 4: YML009C_Smik Reading seq # 5: YML009C_Spar Sequences read.. Counting patterns.. # site patterns = 146 Counting frequencies.. 120 bytes for distance 23360 bytes for lkl0 18688 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.218714 0.018322 0.076237 0.149968 0.071581 0.214684 0.195986 0.035976 lnL0 = -1511.871252 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1511.871252 x= 0.21871 0.01832 0.07624 0.14997 0.07158 0.21468 0.19599 0.03598 1 h-lim-p 0.0019 0.0266 126.8836 1510.212297 6 0.0002 35 | 0/8 2 h-lim-p 0.0006 0.0048 21.9482 1510.062007 4 0.0006 55 | 0/8 3 h-lim-p 0.0015 0.0242 9.2929 1510.039206 4 0.0006 76 | 0/8 4 h-lim-p 0.0014 0.0282 4.0154 1510.036255 6 0.0004 104 | 0/8 5 h-lim-p 0.0038 1.2142 0.4684 1510.036179 3 0.0007 123 | 0/8 6 h-lim-p 0.0034 2.5011 0.0992 1510.036173 2 0.0011 149 | 0/8 7 h-lim-p 0.0131 7.6749 0.0085 1510.036173 0 0.0057 169 | 0/8 8 h-lim-p 0.0273 20.0000 0.0018 1510.035917 0 0.3273 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1510.035907 1 0.9961 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1510.035907 0 1.0938 234 | 0/8 11 h-lim-p 1.2354 20.0000 0.0000 1510.035907 0 0.2702 255 | 0/8 12 h-lim-p 0.0889 20.0000 0.0000 1510.035907 0 0.0056 278 | 0/8 13 h-lim-p 0.0024 20.0000 0.0001 1510.035907 0 0.0000 304 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 1510.035907 0 0.0000 336 | 0/8 15 h-lim-p 0.0000 20.0000 0.0007 | 0/8 16 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -1510.035907 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1510.035907 Node 7: lnL = -1510.035907 Node 8: lnL = -1510.035907 Node 9: lnL = -1510.035907 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 242 Sequential format.. Reading seq # 1: YML012W_Sbay Reading seq # 2: YML012W_Scer Reading seq # 3: YML012W_Skud Reading seq # 4: YML012W_Smik Reading seq # 5: YML012W_Spar Sequences read.. Counting patterns.. # site patterns = 61 Counting frequencies.. 120 bytes for distance 9760 bytes for lkl0 7808 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.089884 0.028170 0.029827 0.031751 0.021087 0.098151 0.118136 0.009051 lnL0 = -699.538259 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 699.538259 x= 0.08988 0.02817 0.02983 0.03175 0.02109 0.09815 0.11814 0.00905 1 h-lim-p 0.0001 0.0009 70.9992 699.102614 0 0.0002 23 | 0/8 2 h-lim-p 0.0009 0.0090 19.0710 699.081992 5 0.0001 49 | 0/8 3 h-lim-p 0.0004 0.0083 6.1432 699.075972 3 0.0004 67 | 0/8 4 h-lim-p 0.0005 0.0296 4.1335 699.073499 4 0.0004 87 | 0/8 5 h-lim-p 0.0018 0.0739 0.9065 699.073363 3 0.0003 106 | 0/8 6 h-lim-p 0.0014 0.2636 0.2212 699.073351 2 0.0004 131 | 0/8 7 h-lim-p 0.0011 1.8754 0.0734 699.073285 0 0.0042 153 | 0/8 8 h-lim-p 0.0144 2.1922 0.0215 699.060059 0 0.1155 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 699.059859 2 0.9961 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 699.059858 0 1.0938 220 | 0/8 11 h-lim-p 1.1785 20.0000 0.0000 699.059858 0 0.0000 254 | 0/8 12 h-lim-p 0.0000 20.0000 0.0002 699.059858 0 0.0000 287 | 0/8 13 h-lim-p 0.0000 20.0000 0.0031 | 0/8 14 h-lim-p 0.0000 20.0000 0.0031 Out... lnL = -699.059858 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -699.059858 Node 7: lnL = -699.059858 Node 8: lnL = -699.059858 Node 9: lnL = -699.059858 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 209 Sequential format.. Reading seq # 1: YML014W_Sbay Reading seq # 2: YML014W_Scer Reading seq # 3: YML014W_Skud Reading seq # 4: YML014W_Smik Reading seq # 5: YML014W_Spar Sequences read.. Counting patterns.. # site patterns = 101 Counting frequencies.. 120 bytes for distance 16160 bytes for lkl0 12928 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.252971 0.132706 0.124391 0.126452 0.040261 0.186941 0.193193 0.036000 lnL0 = -961.127651 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 961.127651 x= 0.25297 0.13271 0.12439 0.12645 0.04026 0.18694 0.19319 0.03600 1 h-lim-p 0.0009 0.0068 25.9523 960.935759 7 0.0006 38 | 0/8 2 h-lim-p 0.0009 0.0068 14.1410 960.860303 6 0.0009 64 | 0/8 3 h-lim-p 0.0049 0.0401 2.7003 960.855809 5 0.0013 87 | 0/8 4 h-lim-p 0.0072 0.4119 0.4900 960.855625 2 0.0016 104 | 0/8 5 h-lim-p 0.0058 1.9761 0.1315 960.855608 3 0.0021 131 | 0/8 6 h-lim-p 0.0321 20.0000 0.0084 960.855608 1 0.0040 155 | 0/8 7 h-lim-p 0.0746 20.0000 0.0004 960.855575 0 0.5970 178 | 0/8 8 h-lim-p 0.0035 1.4547 0.0753 960.855570 2 0.0014 202 | 0/8 9 h-lim-p 1.7488 20.0000 0.0001 960.855567 2 0.9205 227 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 960.855567 0 1.0938 247 | 0/8 11 h-lim-p 1.4198 20.0000 0.0000 960.855567 0 2.1296 267 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 960.855567 0 0.1562 290 | 0/8 13 h-lim-p 0.0295 20.0000 0.0000 960.855567 0 0.0000 320 | 0/8 14 h-lim-p 0.0004 20.0000 0.0000 960.855567 0 0.0000 355 Out... lnL = -960.855567 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -960.855567 Node 7: lnL = -960.855567 Node 8: lnL = -960.855567 Node 9: lnL = -960.855567 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 209 Sequential format.. Reading seq # 1: YML015C_Sbay Reading seq # 2: YML015C_Scer Reading seq # 3: YML015C_Skud Reading seq # 4: YML015C_Smik Reading seq # 5: YML015C_Spar Sequences read.. Counting patterns.. # site patterns = 105 Counting frequencies.. 120 bytes for distance 16800 bytes for lkl0 13440 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.252149 0.174338 0.124983 0.129775 0.036939 0.186349 0.183600 0.027409 lnL0 = -967.716169 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 967.716169 x= 0.25215 0.17434 0.12498 0.12977 0.03694 0.18635 0.18360 0.02741 1 h-lim-p 0.0015 0.0118 27.3803 967.512118 4 0.0006 30 | 0/8 2 h-lim-p 0.0011 0.0094 14.8275 967.417832 4 0.0011 50 | 0/8 3 h-lim-p 0.0020 0.0162 3.7886 967.408139 6 0.0015 77 | 0/8 4 h-lim-p 0.0071 0.3293 0.7877 967.407538 5 0.0020 103 | 0/8 5 h-lim-p 0.0056 0.8896 0.2880 967.407474 4 0.0017 135 | 0/8 6 h-lim-p 0.0132 1.1493 0.0378 967.407473 0 0.0016 157 | 0/8 7 h-lim-p 0.0052 20.0000 0.0121 967.407473 0 0.0045 177 | 0/8 8 h-lim-p 0.1917 20.0000 0.0003 967.407438 0 0.7668 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 967.407437 0 1.0938 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 967.407437 0 1.0938 239 | 0/8 11 h-lim-p 1.1794 20.0000 0.0000 967.407437 0 0.0092 265 | 0/8 12 h-lim-p 0.0029 20.0000 0.0000 967.407437 0 0.0015 285 | 0/8 13 h-lim-p 0.0008 20.0000 0.0000 967.407437 0 0.0004 305 | 0/8 14 h-lim-p 0.0002 20.0000 0.0001 967.407437 0 0.0000 331 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 967.407437 0 0.0000 357 Out... lnL = -967.407437 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -967.407437 Node 7: lnL = -967.407437 Node 8: lnL = -967.407437 Node 9: lnL = -967.407437 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 1229 Sequential format.. Reading seq # 1: YML017W_Sbay Reading seq # 2: YML017W_Scer Reading seq # 3: YML017W_Skud Reading seq # 4: YML017W_Smik Reading seq # 5: YML017W_Spar Sequences read.. Counting patterns.. # site patterns = 274 Counting frequencies.. 120 bytes for distance 43840 bytes for lkl0 35072 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.122217 0.045138 0.029593 0.111399 0.047083 0.114138 0.100178 0.012207 lnL0 = -3889.101982 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3889.101982 x= 0.12222 0.04514 0.02959 0.11140 0.04708 0.11414 0.10018 0.01221 1 h-lim-p 0.0001 0.0008 320.3760 3885.345428 7 0.0001 36 | 0/8 2 h-lim-p 0.0001 0.0007 178.3182 3883.702920 0 0.0001 48 | 0/8 3 h-lim-p 0.0002 0.0013 46.4450 3883.595603 7 0.0001 79 | 0/8 4 h-lim-p 0.0006 0.0218 7.9552 3883.591425 4 0.0001 99 | 0/8 5 h-lim-p 0.0008 0.0636 1.3388 3883.591316 3 0.0001 121 | 0/8 6 h-lim-p 0.0010 0.5133 0.1654 3883.591309 0 0.0002 134 | 0/8 7 h-lim-p 0.0006 1.9005 0.0594 3883.591172 0 0.0047 157 | 0/8 8 h-lim-p 0.0024 0.7997 0.1168 3883.572754 0 0.0191 180 | 0/8 9 h-lim-p 0.5743 8.4236 0.0039 3883.572321 0 1.1486 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 3883.572312 1 0.9961 223 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3883.572312 0 1.0938 243 | 0/8 12 h-lim-p 0.3294 20.0000 0.0001 3883.572312 0 0.6588 264 | 0/8 13 h-lim-p 0.3176 20.0000 0.0002 3883.572312 0 0.1389 284 | 0/8 14 h-lim-p 0.0435 20.0000 0.0006 3883.572312 0 0.0054 306 | 0/8 15 h-lim-p 0.0023 18.3307 0.0015 3883.572312 0 0.0023 326 | 0/8 16 h-lim-p 0.0013 10.4342 0.0026 3883.572312 0 0.0000 365 | 0/8 17 h-lim-p 0.0000 20.0000 0.0031 | 0/8 18 h-lim-p 0.0000 20.0000 0.0031 Out... lnL = -3883.572312 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3883.572312 Node 7: lnL = -3883.572312 Node 8: lnL = -3883.572312 Node 9: lnL = -3883.572312 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 820 Sequential format.. Reading seq # 1: YML018C_Sbay Reading seq # 2: YML018C_Scer Reading seq # 3: YML018C_Skud Reading seq # 4: YML018C_Smik Reading seq # 5: YML018C_Spar Sequences read.. Counting patterns.. # site patterns = 200 Counting frequencies.. 120 bytes for distance 32000 bytes for lkl0 25600 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.139101 0.036046 0.047712 0.051812 0.058893 0.109638 0.091453 0.027722 lnL0 = -2950.438997 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2950.438997 x= 0.13910 0.03605 0.04771 0.05181 0.05889 0.10964 0.09145 0.02772 1 h-lim-p 0.0014 0.0121 206.9089 2948.771770 4 0.0001 33 | 0/8 2 h-lim-p 0.0006 0.0050 25.1998 2948.722413 4 0.0002 54 | 0/8 3 h-lim-p 0.0005 0.0232 7.8799 2948.719789 4 0.0001 76 | 0/8 4 h-lim-p 0.0005 0.0689 1.4910 2948.719637 3 0.0001 97 | 0/8 5 h-lim-p 0.0009 0.3280 0.2404 2948.719633 1 0.0001 113 | 0/8 6 h-lim-p 0.0006 2.9866 0.0448 2948.719633 0 0.0003 133 | 0/8 7 h-lim-p 0.0011 15.5984 0.0106 2948.719633 0 0.0009 153 | 0/8 8 h-lim-p 0.0075 20.0000 0.0013 2948.719445 0 0.2393 178 | 0/8 9 h-lim-p 0.2984 20.0000 0.0011 2948.719436 0 1.1938 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0003 2948.719436 0 1.0938 220 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2948.719436 0 1.2500 240 | 0/8 12 h-lim-p 0.3512 20.0000 0.0001 2948.719436 0 0.0014 267 | 0/8 13 h-lim-p 0.0001 20.0000 0.0013 2948.719436 0 0.0000 295 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 2948.719436 0 0.0000 316 Out... lnL = -2948.719436 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2948.719436 Node 7: lnL = -2948.719436 Node 8: lnL = -2948.719436 Node 9: lnL = -2948.719436 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 351 Sequential format.. Reading seq # 1: YML019W_Sbay Reading seq # 2: YML019W_Scer Reading seq # 3: YML019W_Skud Reading seq # 4: YML019W_Smik Reading seq # 5: YML019W_Spar Sequences read.. Counting patterns.. # site patterns = 161 Counting frequencies.. 120 bytes for distance 25760 bytes for lkl0 20608 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.273728 0.070381 0.084055 0.137192 0.056327 0.192079 0.124312 0.073108 lnL0 = -1535.826297 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1535.826297 x= 0.27373 0.07038 0.08405 0.13719 0.05633 0.19208 0.12431 0.07311 1 h-lim-p 0.0114 2.5428 51.8885 1535.259494 8 0.0004 44 | 0/8 2 h-lim-p 0.0007 0.0054 16.5044 1535.196938 7 0.0005 72 | 0/8 3 h-lim-p 0.0010 0.0188 8.4316 1535.179855 6 0.0006 100 | 0/8 4 h-lim-p 0.0033 0.1262 1.5458 1535.178942 3 0.0008 119 | 0/8 5 h-lim-p 0.0088 1.2652 0.1416 1535.178933 1 0.0010 135 | 0/8 6 h-lim-p 0.0095 10.4944 0.0144 1535.178932 0 0.0021 156 | 0/8 7 h-lim-p 0.0085 20.0000 0.0035 1535.178890 0 0.0681 179 | 0/8 8 h-lim-p 0.0025 5.3419 0.0950 1535.178716 0 0.0050 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1535.178715 0 1.0938 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1535.178715 0 1.0938 240 | 0/8 11 h-lim-p 1.8479 20.0000 0.0000 1535.178715 0 1.6169 260 | 0/8 12 h-lim-p 1.4136 20.0000 0.0000 1535.178715 0 2.1204 280 | 0/8 13 h-lim-p 0.2690 20.0000 0.0001 1535.178715 0 0.0672 301 | 0/8 14 h-lim-p 0.0103 20.0000 0.0004 1535.178715 0 0.0000 335 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 1535.178715 0 0.0000 363 Out... lnL = -1535.178715 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1535.178715 Node 7: lnL = -1535.178715 Node 8: lnL = -1535.178715 Node 9: lnL = -1535.178715 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 352 Sequential format.. Reading seq # 1: YML020W_Sbay Reading seq # 2: YML020W_Scer Reading seq # 3: YML020W_Skud Reading seq # 4: YML020W_Smik Reading seq # 5: YML020W_Spar Sequences read.. Counting patterns.. # site patterns = 118 Counting frequencies.. 120 bytes for distance 18880 bytes for lkl0 15104 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.182163 0.073608 0.063103 0.131237 0.065082 0.113289 0.118196 0.026962 lnL0 = -1436.466918 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1436.466918 x= 0.18216 0.07361 0.06310 0.13124 0.06508 0.11329 0.11820 0.02696 1 h-lim-p 0.0010 0.0081 45.4768 1436.087443 8 0.0004 39 | 0/8 2 h-lim-p 0.0011 0.0110 15.9632 1436.043180 6 0.0004 64 | 0/8 3 h-lim-p 0.0022 0.0473 2.8145 1436.041348 3 0.0005 83 | 0/8 4 h-lim-p 0.0024 0.3073 0.5602 1436.041287 3 0.0004 103 | 0/8 5 h-lim-p 0.0038 2.1254 0.0576 1436.041287 0 0.0004 125 | 0/8 6 h-lim-p 0.0029 11.9429 0.0083 1436.041287 0 0.0006 146 | 0/8 7 h-lim-p 0.0195 20.0000 0.0003 1436.041284 0 0.1564 169 | 0/8 8 h-lim-p 0.0011 1.4941 0.0369 1436.041276 0 0.0023 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1436.041276 0 1.0938 210 | 0/8 10 h-lim-p 1.5188 20.0000 0.0000 1436.041276 0 0.6645 230 | 0/8 11 h-lim-p 0.2958 20.0000 0.0000 1436.041276 0 0.0277 253 | 0/8 12 h-lim-p 0.0082 20.0000 0.0001 1436.041276 0 0.0001 278 | 0/8 13 h-lim-p 0.0000 17.0772 0.0029 1436.041276 0 0.0000 303 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 1436.041276 0 0.0000 338 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 | 0/8 16 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -1436.041276 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1436.041276 Node 7: lnL = -1436.041276 Node 8: lnL = -1436.041276 Node 9: lnL = -1436.041276 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 389 Sequential format.. Reading seq # 1: YML021C_Sbay Reading seq # 2: YML021C_Scer Reading seq # 3: YML021C_Skud Reading seq # 4: YML021C_Smik Reading seq # 5: YML021C_Spar Sequences read.. Counting patterns.. # site patterns = 127 Counting frequencies.. 120 bytes for distance 20320 bytes for lkl0 16256 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.163227 0.064202 0.070278 0.131751 0.054657 0.108605 0.120929 0.016287 lnL0 = -1446.336621 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1446.336621 x= 0.16323 0.06420 0.07028 0.13175 0.05466 0.10860 0.12093 0.01629 1 h-lim-p 0.0020 0.0156 57.9024 1445.822903 7 0.0003 39 | 0/8 2 h-lim-p 0.0012 0.0112 15.9709 1445.774670 7 0.0004 68 | 0/8 3 h-lim-p 0.0016 0.0323 4.0104 1445.771443 5 0.0004 91 | 0/8 4 h-lim-p 0.0023 0.1739 0.7581 1445.771317 3 0.0005 110 | 0/8 5 h-lim-p 0.0028 0.7977 0.1238 1445.771314 1 0.0003 134 | 0/8 6 h-lim-p 0.0029 20.0000 0.0148 1445.771314 0 0.0006 155 | 0/8 7 h-lim-p 0.1052 20.0000 0.0001 1445.771314 0 0.2104 176 | 0/8 8 h-lim-p 0.0013 1.9451 0.0147 1445.771313 0 0.0025 197 | 0/8 9 h-lim-p 1.5674 20.0000 0.0000 1445.771312 0 1.3714 217 | 0/8 10 h-lim-p 2.2877 20.0000 0.0000 1445.771312 0 1.0009 237 | 0/8 11 h-lim-p 0.5281 20.0000 0.0000 1445.771312 0 0.0010 265 | 0/8 12 h-lim-p 0.0000 5.3759 0.0069 1445.771312 0 0.0000 285 | 0/8 13 h-lim-p 0.0002 20.0000 0.0002 1445.771312 0 0.0002 305 | 0/8 14 h-lim-p 0.0000 16.4789 0.0022 1445.771312 0 0.0000 339 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1445.771312 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1445.771312 Node 7: lnL = -1445.771312 Node 8: lnL = -1445.771312 Node 9: lnL = -1445.771312 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 290 Sequential format.. Reading seq # 1: YML022W_Sbay Reading seq # 2: YML022W_Scer Reading seq # 3: YML022W_Skud Reading seq # 4: YML022W_Smik Reading seq # 5: YML022W_Spar Sequences read.. Counting patterns.. # site patterns = 119 Counting frequencies.. 120 bytes for distance 19040 bytes for lkl0 15232 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.167305 0.106466 0.053866 0.165336 0.117488 0.178473 0.176711 0.000060 lnL0 = -1223.472241 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1223.472241 x= 0.16730 0.10647 0.05387 0.16534 0.11749 0.17847 0.17671 0.00006 1 h-lim-p 0.0000 0.0000 78.6054 1223.454741 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0267 6.5835 1223.424024 0 0.0015 39 | 1/8 3 h-lim-p 0.0043 0.1378 2.2541 1223.416020 5 0.0016 63 | 1/8 4 h-lim-p 0.0016 0.0541 2.1718 1223.399218 0 0.0025 75 | 1/8 5 h-lim-p 0.0038 0.2050 1.3997 1222.797288 0 0.0306 90 | 1/8 6 h-lim-p 0.0016 0.0126 13.8565 1221.221522 0 0.0032 103 | 1/8 7 h-lim-p 0.0028 0.0225 9.0671 1221.179459 7 0.0010 132 | 1/8 8 h-lim-p 0.0063 0.1821 1.4680 1221.178077 4 0.0012 153 | 1/8 9 h-lim-p 0.1243 20.0000 0.0144 1221.109821 0 0.9944 168 | 0/8 10 h-lim-p 0.0134 2.4835 1.0638 1221.109356 2 0.0008 194 | 0/8 11 h-lim-p 0.3136 3.4302 0.0028 1221.106524 0 0.9409 207 | 0/8 12 h-lim-p 2.5000 20.0000 0.0006 1221.106347 3 0.8800 234 | 0/8 13 h-lim-p 2.5000 20.0000 0.0001 1221.106346 1 0.9961 256 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1221.106346 0 1.0938 276 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1221.106346 0 2.1875 296 | 0/8 16 h-lim-p 1.8206 20.0000 0.0000 1221.106346 0 0.7965 316 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1221.106346 0 0.0391 341 | 0/8 18 h-lim-p 0.0333 20.0000 0.0000 1221.106346 0 0.0042 363 Out... lnL = -1221.106346 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1221.106346 Node 7: lnL = -1221.106346 Node 8: lnL = -1221.106346 Node 9: lnL = -1221.106346 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 290 Sequential format.. Reading seq # 1: YML023C_Sbay Reading seq # 2: YML023C_Scer Reading seq # 3: YML023C_Skud Reading seq # 4: YML023C_Smik Reading seq # 5: YML023C_Spar Sequences read.. Counting patterns.. # site patterns = 119 Counting frequencies.. 120 bytes for distance 19040 bytes for lkl0 15232 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.166460 0.099613 0.055517 0.160622 0.114558 0.176771 0.170169 0.000060 lnL0 = -1221.916800 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1221.916800 x= 0.16646 0.09961 0.05552 0.16062 0.11456 0.17677 0.17017 0.00006 1 h-lim-p 0.0000 0.0000 68.0683 1221.901790 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0116 5.9658 1221.890409 0 0.0005 38 | 1/8 3 h-lim-p 0.0011 0.0970 3.0314 1221.881582 0 0.0016 50 | 1/8 4 h-lim-p 0.0102 0.2917 0.4760 1221.825955 0 0.0203 63 | 1/8 5 h-lim-p 0.0033 0.0753 2.8975 1220.801073 0 0.0133 84 | 1/8 6 h-lim-p 0.0011 0.0089 23.2170 1220.218068 0 0.0017 96 | 1/8 7 h-lim-p 0.0035 0.0282 5.0674 1220.208158 5 0.0008 118 | 1/8 8 h-lim-p 0.0052 0.3307 0.7396 1220.207752 4 0.0013 139 | 0/8 9 h-lim-p 0.0001 0.2022 6.4859 1220.191108 0 0.0009 160 | 0/8 10 h-lim-p 0.9754 7.8032 0.0052 1220.174646 2 0.9144 176 | 0/8 11 h-lim-p 2.5000 20.0000 0.0008 1220.174336 4 0.9422 204 | 0/8 12 h-lim-p 2.5000 20.0000 0.0001 1220.174334 0 1.0938 224 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1220.174334 0 1.0938 244 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1220.174334 0 1.0938 264 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1220.174334 0 2.1875 284 | 0/8 16 h-lim-p 1.7246 20.0000 0.0000 1220.174334 0 5.1737 305 | 0/8 17 h-lim-p 0.0911 20.0000 0.0000 1220.174334 0 0.1366 325 | 0/8 18 h-lim-p 0.0369 20.0000 0.0000 1220.174334 0 0.0012 349 | 0/8 19 h-lim-p 0.0005 20.0000 0.0000 1220.174334 0 0.0000 372 | 0/8 20 h-lim-p 0.0001 20.0000 0.0000 1220.174334 0 0.0000 406 | 0/8 21 h-lim-p 0.0000 20.0000 0.0001 1220.174334 0 0.0000 435 | 0/8 22 h-lim-p 0.0000 20.0000 0.0001 1220.174334 0 0.0000 459 | 0/8 23 h-lim-p 0.0000 20.0000 0.0000 1220.174334 0 0.0000 482 | 0/8 24 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 25 h-lim-p 0.0000 20.0000 0.0001 1220.174334 0 0.0000 550 | 0/8 26 h-lim-p 0.0000 20.0000 0.0001 | 0/8 27 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1220.174334 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1220.174334 Node 7: lnL = -1220.174334 Node 8: lnL = -1220.174334 Node 9: lnL = -1220.174334 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 341 Sequential format.. Reading seq # 1: YML030W_Sbay Reading seq # 2: YML030W_Scer Reading seq # 3: YML030W_Skud Reading seq # 4: YML030W_Smik Reading seq # 5: YML030W_Spar Sequences read.. Counting patterns.. # site patterns = 137 Counting frequencies.. 120 bytes for distance 21920 bytes for lkl0 17536 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.167560 0.079943 0.074140 0.109908 0.094263 0.247336 0.145053 0.000060 lnL0 = -1307.231973 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1307.231973 x= 0.16756 0.07994 0.07414 0.10991 0.09426 0.24734 0.14505 0.00006 1 h-lim-p 0.0000 0.0000 68.2380 1307.213744 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0408 8.8736 1307.189755 0 0.0007 38 | 1/8 3 h-lim-p 0.0026 0.0368 2.3261 1307.185180 2 0.0012 54 | 1/8 4 h-lim-p 0.0040 0.3460 0.7082 1307.169849 0 0.0080 67 | 1/8 5 h-lim-p 0.0032 0.1993 1.7833 1306.931865 0 0.0127 88 | 1/8 6 h-lim-p 0.0035 0.0281 6.4699 1306.185656 0 0.0053 100 | 1/8 7 h-lim-p 0.0015 0.0118 15.3219 1306.038934 8 0.0010 131 | 1/8 8 h-lim-p 0.0027 0.0234 5.7389 1306.028659 5 0.0007 156 | 1/8 9 h-lim-p 0.9625 20.0000 0.0039 1306.019049 3 0.8046 174 | 0/8 10 h-lim-p 0.0128 3.4186 0.2441 1306.019026 1 0.0008 198 | 0/8 11 h-lim-p 0.3523 2.8188 0.0002 1306.019010 0 0.7047 219 | 0/8 12 h-lim-p 0.1530 1.2239 0.0002 1306.019010 0 0.2295 239 | 0/8 13 h-lim-p 0.0011 0.0091 0.0166 1306.019010 0 0.0000 272 | 0/8 14 h-lim-p 0.0000 1.6256 0.0002 1306.019010 0 0.0410 304 | 0/8 15 h-lim-p 0.1098 20.0000 0.0001 1306.019010 0 0.2197 325 | 0/8 16 h-lim-p 0.0146 0.2159 0.0009 1306.019010 0 0.0000 365 | 0/8 17 h-lim-p 0.0000 0.7304 0.0002 .. | 0/8 18 h-lim-p 0.0000 0.0024 0.0635 1306.019010 0 0.0000 431 | 0/8 19 h-lim-p 0.0000 0.0000 6.1643 .. | 0/8 20 h-lim-p 0.0000 4.9040 0.0503 1306.019009 0 0.0003 479 | 0/8 21 h-lim-p 0.0004 0.0112 0.0361 1306.019009 0 0.0001 500 | 0/8 22 h-lim-p 0.0002 0.1451 0.0178 1306.019009 0 0.0004 521 | 0/8 23 h-lim-p 0.0013 0.1919 0.0055 1306.019009 0 0.0000 558 | 0/8 24 h-lim-p 0.0000 3.3124 0.0013 1306.019009 0 0.0002 582 | 0/8 25 h-lim-p 0.0002 1.1719 0.0012 1306.019009 0 0.0000 615 | 0/8 26 h-lim-p 0.0000 0.3440 0.0019 1306.019009 0 0.0000 639 | 0/8 27 h-lim-p 0.0000 0.0448 0.0053 1306.019009 0 0.0000 673 | 0/8 28 h-lim-p 0.0000 0.0018 0.0738 1306.019009 0 0.0000 694 | 0/8 29 h-lim-p 0.0000 0.0004 0.3209 1306.019009 0 0.0000 714 | 0/8 30 h-lim-p 0.0000 0.0008 0.2216 1306.019009 0 0.0000 734 | 0/8 31 h-lim-p 0.0001 0.0202 0.0231 1306.019009 0 0.0000 755 | 0/8 32 h-lim-p 0.0002 1.5214 0.0028 1306.019009 0 0.0006 777 | 0/8 33 h-lim-p 0.0008 1.2661 0.0020 1306.019009 0 0.0001 800 | 0/8 34 h-lim-p 0.0001 1.7111 0.0012 1306.019009 0 0.0004 822 | 0/8 35 h-lim-p 0.0002 0.2402 0.0018 1306.019009 0 0.0000 853 | 0/8 36 h-lim-p 0.0000 0.1964 0.0062 1306.019009 0 0.0000 880 | 0/8 37 h-lim-p 0.0000 20.0000 0.0000 1306.019009 0 0.0000 905 | 0/8 38 h-lim-p 0.0000 0.0017 0.0722 | 0/8 39 h-lim-p 0.0000 0.0017 0.0722 Out... lnL = -1306.019009 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1306.019009 Node 7: lnL = -1306.019009 Node 8: lnL = -1306.019009 Node 9: lnL = -1306.019009 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 699 Sequential format.. Reading seq # 1: YML034W_Sbay Reading seq # 2: YML034W_Scer Reading seq # 3: YML034W_Skud Reading seq # 4: YML034W_Smik Reading seq # 5: YML034W_Spar Sequences read.. Counting patterns.. # site patterns = 231 Counting frequencies.. 120 bytes for distance 36960 bytes for lkl0 29568 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.190017 0.029877 0.046890 0.115253 0.054237 0.152598 0.174292 0.035692 lnL0 = -2851.701492 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2851.701492 x= 0.19002 0.02988 0.04689 0.11525 0.05424 0.15260 0.17429 0.03569 1 h-lim-p 0.0001 0.0010 266.4042 2847.707500 3 0.0001 28 | 0/8 2 h-lim-p 0.0002 0.0016 41.6722 2847.553041 7 0.0002 53 | 0/8 3 h-lim-p 0.0003 0.0177 21.5102 2847.519080 4 0.0002 74 | 0/8 4 h-lim-p 0.0008 0.0415 4.5996 2847.515521 4 0.0004 95 | 0/8 5 h-lim-p 0.0010 0.0650 1.5653 2847.515247 2 0.0002 112 | 0/8 6 h-lim-p 0.0030 0.5295 0.1265 2847.515245 0 0.0003 126 | 0/8 7 h-lim-p 0.0071 20.0000 0.0059 2847.515244 0 0.0036 146 | 0/8 8 h-lim-p 0.0126 20.0000 0.0017 2847.515096 0 0.1508 169 | 0/8 9 h-lim-p 0.4801 20.0000 0.0005 2847.515084 0 0.9602 190 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2847.515084 0 1.0938 210 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2847.515084 0 2.1875 230 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2847.515084 0 1.0938 250 | 0/8 13 h-lim-p 0.2636 20.0000 0.0000 2847.515084 0 0.0005 278 | 0/8 14 h-lim-p 0.0000 16.9246 0.0035 2847.515084 0 0.0000 311 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 | 0/8 16 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -2847.515084 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2847.515084 Node 7: lnL = -2847.515084 Node 8: lnL = -2847.515084 Node 9: lnL = -2847.515084 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 596 Sequential format.. Reading seq # 1: YML035C_Sbay Reading seq # 2: YML035C_Scer Reading seq # 3: YML035C_Skud Reading seq # 4: YML035C_Smik Reading seq # 5: YML035C_Spar Sequences read.. Counting patterns.. # site patterns = 197 Counting frequencies.. 120 bytes for distance 31520 bytes for lkl0 25216 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.195152 0.017786 0.052106 0.111081 0.048041 0.158735 0.175890 0.041244 lnL0 = -2422.421582 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2422.421582 x= 0.19515 0.01779 0.05211 0.11108 0.04804 0.15874 0.17589 0.04124 1 h-lim-p 0.0001 0.0007 257.8547 2418.617860 0 0.0001 22 | 0/8 2 h-lim-p 0.0003 0.0020 40.7582 2418.393076 4 0.0003 44 | 0/8 3 h-lim-p 0.0004 0.0152 28.2063 2418.350190 5 0.0001 66 | 0/8 4 h-lim-p 0.0006 0.0376 6.9936 2418.341575 5 0.0004 90 | 0/8 5 h-lim-p 0.0020 0.0671 1.3421 2418.341279 4 0.0003 113 | 0/8 6 h-lim-p 0.0017 0.3634 0.2762 2418.341261 2 0.0004 130 | 0/8 7 h-lim-p 0.0034 6.3324 0.0360 2418.341231 0 0.0067 151 | 0/8 8 h-lim-p 0.0167 3.3055 0.0145 2418.333591 0 0.1335 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 2418.333480 2 0.9961 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2418.333480 0 1.0938 218 | 0/8 11 h-lim-p 0.8434 20.0000 0.0000 2418.333480 0 0.1845 239 | 0/8 12 h-lim-p 0.0527 20.0000 0.0001 2418.333480 0 0.0016 263 | 0/8 13 h-lim-p 0.0005 20.0000 0.0002 2418.333480 0 0.0005 283 | 0/8 14 h-lim-p 0.0006 20.0000 0.0002 2418.333480 0 0.0001 305 | 0/8 15 h-lim-p 0.0000 20.0000 0.0006 2418.333480 0 0.0000 329 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 2418.333480 0 0.0000 358 | 0/8 17 h-lim-p 0.0000 20.0000 0.0014 | 0/8 18 h-lim-p 0.0000 20.0000 0.0014 Out... lnL = -2418.333480 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2418.333480 Node 7: lnL = -2418.333480 Node 8: lnL = -2418.333480 Node 9: lnL = -2418.333480 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 236 Sequential format.. Reading seq # 1: YML037C_Sbay Reading seq # 2: YML037C_Scer Reading seq # 3: YML037C_Skud Reading seq # 4: YML037C_Smik Reading seq # 5: YML037C_Spar Sequences read.. Counting patterns.. # site patterns = 101 Counting frequencies.. 120 bytes for distance 16160 bytes for lkl0 12928 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.187278 0.138270 0.002353 0.143573 0.059336 0.207777 0.179649 0.004275 lnL0 = -1028.892425 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1028.892425 x= 0.18728 0.13827 0.00235 0.14357 0.05934 0.20778 0.17965 0.00428 1 h-lim-p 0.0002 0.0020 204.7925 1026.836966 9 0.0001 45 | 0/8 2 h-lim-p 0.0002 0.0015 41.9972 1026.441681 0 0.0004 58 | 0/8 3 h-lim-p 0.0008 0.0061 15.1173 1026.363236 5 0.0008 79 | 0/8 4 h-lim-p 0.0056 0.1066 2.1144 1026.360332 2 0.0013 96 | 0/8 5 h-lim-p 0.0041 0.0325 0.2590 1026.360267 3 0.0012 117 | 0/8 6 h-lim-p 0.0042 3.4318 0.0744 1026.359733 0 0.0166 139 | 0/8 7 h-lim-p 0.0112 0.5072 0.1105 1026.344909 0 0.0447 161 | 0/8 8 h-lim-p 0.0052 0.2228 0.9488 1026.344200 5 0.0014 194 | 0/8 9 h-lim-p 1.2015 20.0000 0.0011 1026.342825 3 0.9575 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1026.342797 2 2.3438 244 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1026.342796 0 1.0938 264 | 0/8 12 h-lim-p 1.8089 20.0000 0.0000 1026.342796 0 1.5828 284 | 0/8 13 h-lim-p 1.9361 20.0000 0.0000 1026.342796 0 0.4235 305 | 0/8 14 h-lim-p 0.0750 20.0000 0.0001 1026.342796 0 0.0094 327 | 0/8 15 h-lim-p 0.0030 20.0000 0.0002 1026.342796 0 0.0030 347 | 0/8 16 h-lim-p 0.0015 12.0056 0.0005 1026.342796 0 0.0001 371 | 0/8 17 h-lim-p 0.0001 15.5661 0.0004 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0005 | 0/8 19 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -1026.342796 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1026.342796 Node 7: lnL = -1026.342796 Node 8: lnL = -1026.342796 Node 9: lnL = -1026.342796 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 306 Sequential format.. Reading seq # 1: YML038C_Sbay Reading seq # 2: YML038C_Scer Reading seq # 3: YML038C_Skud Reading seq # 4: YML038C_Smik Reading seq # 5: YML038C_Spar Sequences read.. Counting patterns.. # site patterns = 112 Counting frequencies.. 120 bytes for distance 17920 bytes for lkl0 14336 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.190141 0.022284 0.068334 0.109299 0.048555 0.186927 0.105423 0.039731 lnL0 = -1202.564377 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1202.564377 x= 0.19014 0.02228 0.06833 0.10930 0.04856 0.18693 0.10542 0.03973 1 h-lim-p 0.0009 0.0075 71.4268 1202.064272 3 0.0002 29 | 0/8 2 h-lim-p 0.0007 0.0054 20.6410 1201.978367 7 0.0004 60 | 0/8 3 h-lim-p 0.0013 0.0329 6.6373 1201.969879 5 0.0004 84 | 0/8 4 h-lim-p 0.0009 0.0393 3.2123 1201.967950 4 0.0005 105 | 0/8 5 h-lim-p 0.0011 0.1087 1.3203 1201.967579 2 0.0005 121 | 0/8 6 h-lim-p 0.0102 1.4881 0.0685 1201.967578 0 0.0006 136 | 0/8 7 h-lim-p 0.0052 8.6956 0.0074 1201.967578 0 0.0011 157 | 0/8 8 h-lim-p 0.1399 20.0000 0.0001 1201.967574 0 1.1190 180 | 0/8 9 h-lim-p 0.8666 20.0000 0.0001 1201.967574 0 0.8666 200 | 0/8 10 h-lim-p 2.1968 20.0000 0.0000 1201.967574 0 1.0984 220 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1201.967574 0 2.5000 240 | 0/8 12 h-lim-p 1.6780 20.0000 0.0000 1201.967574 0 0.7341 260 | 0/8 13 h-lim-p 0.0629 20.0000 0.0002 1201.967574 0 0.0236 281 | 0/8 14 h-lim-p 0.0069 20.0000 0.0008 1201.967574 0 0.0004 304 | 0/8 15 h-lim-p 0.0002 20.0000 0.0014 1201.967574 0 0.0000 344 | 0/8 16 h-lim-p 0.0000 20.0000 0.0007 | 0/8 17 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -1201.967574 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1201.967574 Node 7: lnL = -1201.967574 Node 8: lnL = -1201.967574 Node 9: lnL = -1201.967574 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 877 Sequential format.. Reading seq # 1: YML041C_Sbay Reading seq # 2: YML041C_Scer Reading seq # 3: YML041C_Skud Reading seq # 4: YML041C_Smik Reading seq # 5: YML041C_Spar Sequences read.. Counting patterns.. # site patterns = 406 Counting frequencies.. 120 bytes for distance 64960 bytes for lkl0 51968 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.411426 0.043523 0.032973 0.301485 0.227929 0.173168 0.372350 0.098202 lnL0 = -4450.908581 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4450.908581 x= 0.41143 0.04352 0.03297 0.30149 0.22793 0.17317 0.37235 0.09820 1 h-lim-p 0.0011 0.5493 279.0855 4441.677487 3 0.0003 29 | 0/8 2 h-lim-p 0.0005 0.0040 50.0290 4440.590383 0 0.0010 42 | 0/8 3 h-lim-p 0.0016 0.0124 14.4737 4440.513668 4 0.0008 63 | 0/8 4 h-lim-p 0.0027 0.1234 4.2253 4440.503116 2 0.0013 79 | 0/8 5 h-lim-p 0.0037 0.2293 1.4530 4440.502226 3 0.0009 98 | 0/8 6 h-lim-p 0.0046 0.5104 0.2874 4440.502147 2 0.0015 116 | 0/8 7 h-lim-p 0.0399 20.0000 0.0110 4440.495434 0 0.3196 139 | 0/8 8 h-lim-p 0.0024 0.5523 1.4533 4440.486187 4 0.0026 168 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 4440.485891 3 1.3437 187 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4440.485890 0 1.0938 207 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4440.485890 0 1.0938 227 | 0/8 12 h-lim-p 1.1017 20.0000 0.0000 4440.485890 0 0.2754 248 | 0/8 13 h-lim-p 0.0627 20.0000 0.0000 4440.485890 0 0.0078 270 | 0/8 14 h-lim-p 0.0027 20.0000 0.0001 4440.485890 0 0.0000 300 | 0/8 15 h-lim-p 0.0014 20.0000 0.0000 4440.485890 0 0.0001 324 Out... lnL = -4440.485890 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4440.485890 Node 7: lnL = -4440.485890 Node 8: lnL = -4440.485890 Node 9: lnL = -4440.485890 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 903 Sequential format.. Reading seq # 1: YML042W_Sbay Reading seq # 2: YML042W_Scer Reading seq # 3: YML042W_Skud Reading seq # 4: YML042W_Smik Reading seq # 5: YML042W_Spar Sequences read.. Counting patterns.. # site patterns = 363 Counting frequencies.. 120 bytes for distance 58080 bytes for lkl0 46464 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.244661 0.198111 0.081751 0.214330 0.145596 0.197926 0.289576 0.000060 lnL0 = -4069.228028 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4069.228028 x= 0.24466 0.19811 0.08175 0.21433 0.14560 0.19793 0.28958 0.00006 1 h-lim-p 0.0000 0.0000 188.3832 4069.107112 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0168 56.3923 4068.603055 0 0.0004 39 | 1/8 3 h-lim-p 0.0011 0.0215 18.2981 4068.475663 7 0.0008 67 | 1/8 4 h-lim-p 0.0042 0.0722 3.5097 4068.454512 4 0.0016 87 | 1/8 5 h-lim-p 0.0052 0.3025 1.0944 4068.074564 0 0.0208 101 | 1/8 6 h-lim-p 0.0035 0.0515 6.5322 4064.435894 0 0.0070 114 | 1/8 7 h-lim-p 0.0008 0.0068 43.1791 4062.861352 1 0.0011 128 | 1/8 8 h-lim-p 0.0094 0.0748 3.8700 4062.857663 3 0.0005 149 | 1/8 9 h-lim-p 0.1519 20.0000 0.0125 4062.738805 0 0.9114 163 | 1/8 10 h-lim-p 2.5000 20.0000 0.0010 4062.737787 3 0.9644 188 | 0/8 11 h-lim-p 0.3377 20.0000 0.0029 4062.737787 0 0.0023 213 | 0/8 12 h-lim-p 0.1144 0.9422 0.0001 4062.737786 0 0.6863 235 | 0/8 13 h-lim-p 0.0254 0.2031 0.0000 4062.737786 m 0.2031 255 | 1/8 14 h-lim-p 0.4171 20.0000 0.0000 4062.737786 0 0.8342 276 | 1/8 15 h-lim-p 0.8246 20.0000 0.0000 4062.737786 0 0.7215 295 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 4062.737786 0 1.0938 314 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 4062.737786 0 2.1875 333 | 1/8 18 h-lim-p 1.8395 20.0000 0.0000 4062.737786 0 0.0287 357 | 1/8 19 h-lim-p 0.0295 20.0000 0.0000 4062.737786 0 0.0000 399 Out... lnL = -4062.737786 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4062.737786 Node 7: lnL = -4062.737786 Node 8: lnL = -4062.737786 Node 9: lnL = -4062.737786 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 900 Sequential format.. Reading seq # 1: YML043C_Sbay Reading seq # 2: YML043C_Scer Reading seq # 3: YML043C_Skud Reading seq # 4: YML043C_Smik Reading seq # 5: YML043C_Spar Sequences read.. Counting patterns.. # site patterns = 374 Counting frequencies.. 120 bytes for distance 59840 bytes for lkl0 47872 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.259106 0.064383 0.058808 0.174791 0.130749 0.202615 0.271036 0.021388 lnL0 = -4073.624516 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4073.624516 x= 0.25911 0.06438 0.05881 0.17479 0.13075 0.20262 0.27104 0.02139 1 h-lim-p 0.0020 0.6296 201.7751 4070.071164 7 0.0002 39 | 0/8 2 h-lim-p 0.0007 0.0055 41.0595 4069.765846 5 0.0004 62 | 0/8 3 h-lim-p 0.0013 0.0113 11.3450 4069.744769 4 0.0004 83 | 0/8 4 h-lim-p 0.0022 0.0383 1.8292 4069.744166 4 0.0004 107 | 0/8 5 h-lim-p 0.0023 1.3809 0.2889 4069.744146 1 0.0005 122 | 0/8 6 h-lim-p 0.0017 2.4923 0.0875 4069.744142 0 0.0007 142 | 0/8 7 h-lim-p 0.0032 7.7767 0.0200 4069.744141 0 0.0028 162 | 0/8 8 h-lim-p 0.0307 20.0000 0.0018 4069.743552 0 0.3686 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4069.743531 1 0.9961 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4069.743531 0 1.0938 227 | 0/8 11 h-lim-p 1.0826 20.0000 0.0000 4069.743531 0 8.6611 250 | 0/8 12 h-lim-p 0.0477 7.8525 0.0053 4069.743531 0 0.0030 273 | 0/8 13 h-lim-p 0.0012 3.1376 0.0132 4069.743531 0 0.0000 313 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 4069.743531 0 0.0000 333 Out... lnL = -4069.743531 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4069.743531 Node 7: lnL = -4069.743531 Node 8: lnL = -4069.743531 Node 9: lnL = -4069.743531 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 432 Sequential format.. Reading seq # 1: YML046W_Sbay Reading seq # 2: YML046W_Scer Reading seq # 3: YML046W_Skud Reading seq # 4: YML046W_Smik Reading seq # 5: YML046W_Spar Sequences read.. Counting patterns.. # site patterns = 177 Counting frequencies.. 120 bytes for distance 28320 bytes for lkl0 22656 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.277858 0.128778 0.028524 0.144921 0.076756 0.223388 0.201124 0.047251 lnL0 = -1985.128345 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1985.128345 x= 0.27786 0.12878 0.02852 0.14492 0.07676 0.22339 0.20112 0.04725 1 h-lim-p 0.0005 0.0037 127.7483 1983.211162 9 0.0003 44 | 0/8 2 h-lim-p 0.0004 0.0032 32.5943 1982.964208 1 0.0005 58 | 0/8 3 h-lim-p 0.0009 0.0076 18.0958 1982.907574 4 0.0004 78 | 0/8 4 h-lim-p 0.0023 0.0400 3.5371 1982.903032 5 0.0008 102 | 0/8 5 h-lim-p 0.0048 0.4439 0.5650 1982.902858 2 0.0011 119 | 0/8 6 h-lim-p 0.0056 0.8228 0.1135 1982.902853 2 0.0007 145 | 0/8 7 h-lim-p 0.0196 20.0000 0.0043 1982.902811 0 0.0784 167 | 0/8 8 h-lim-p 0.0067 2.8427 0.0504 1982.902190 0 0.0200 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1982.902138 1 1.0938 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1982.902138 0 1.0938 230 | 0/8 11 h-lim-p 1.7500 20.0000 0.0000 1982.902138 0 1.5312 250 | 0/8 12 h-lim-p 1.8207 20.0000 0.0000 1982.902138 0 1.5931 270 | 0/8 13 h-lim-p 0.3947 20.0000 0.0000 1982.902138 0 0.0031 296 | 0/8 14 h-lim-p 0.0002 20.0000 0.0007 1982.902138 0 0.0000 332 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1982.902138 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1982.902138 Node 7: lnL = -1982.902138 Node 8: lnL = -1982.902138 Node 9: lnL = -1982.902138 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 475 Sequential format.. Reading seq # 1: YML047C_Sbay Reading seq # 2: YML047C_Scer Reading seq # 3: YML047C_Skud Reading seq # 4: YML047C_Smik Reading seq # 5: YML047C_Spar Sequences read.. Counting patterns.. # site patterns = 173 Counting frequencies.. 120 bytes for distance 27680 bytes for lkl0 22144 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.217313 0.061787 0.038402 0.132442 0.089235 0.216589 0.212251 0.019171 lnL0 = -1973.502817 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1973.502817 x= 0.21731 0.06179 0.03840 0.13244 0.08923 0.21659 0.21225 0.01917 1 h-lim-p 0.0005 0.0040 122.4997 1971.631854 9 0.0003 42 | 0/8 2 h-lim-p 0.0002 0.0019 33.7064 1971.379051 0 0.0005 55 | 0/8 3 h-lim-p 0.0004 0.0033 12.7151 1971.351579 2 0.0004 71 | 0/8 4 h-lim-p 0.0018 0.1158 2.7217 1971.348709 2 0.0008 87 | 0/8 5 h-lim-p 0.0034 0.2410 0.6748 1971.348564 2 0.0007 104 | 0/8 6 h-lim-p 0.0098 0.5515 0.0465 1971.348564 0 0.0005 127 | 0/8 7 h-lim-p 0.0027 20.0000 0.0093 1971.348563 0 0.0040 147 | 0/8 8 h-lim-p 0.0353 20.0000 0.0011 1971.348424 0 0.2824 170 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1971.348423 0 1.0938 190 | 0/8 10 h-lim-p 2.3477 20.0000 0.0000 1971.348423 0 1.0271 210 | 0/8 11 h-lim-p 0.9171 20.0000 0.0000 1971.348423 0 0.0143 235 | 0/8 12 h-lim-p 0.0002 20.0000 0.0016 1971.348423 0 0.0002 255 | 0/8 13 h-lim-p 0.0006 20.0000 0.0005 1971.348423 0 0.0354 281 | 0/8 14 h-lim-p 0.0465 20.0000 0.0004 1971.348423 0 0.1860 303 | 0/8 15 h-lim-p 0.0005 0.1255 0.1376 1971.348423 0 0.0000 334 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 1971.348423 0 0.0000 370 | 0/8 17 h-lim-p 0.0000 20.0000 0.0009 1971.348423 0 0.0000 393 | 0/8 18 h-lim-p 0.0000 20.0000 0.0003 1971.348423 0 0.0013 420 | 0/8 19 h-lim-p 0.0049 20.0000 0.0001 1971.348423 0 0.0002 444 | 0/8 20 h-lim-p 0.0002 20.0000 0.0000 .. | 0/8 21 h-lim-p 0.0000 20.0000 0.0011 1971.348423 0 0.0000 515 | 0/8 22 h-lim-p 0.0000 20.0000 0.0011 | 0/8 23 h-lim-p 0.0000 20.0000 0.0011 Out... lnL = -1971.348423 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1971.348423 Node 7: lnL = -1971.348423 Node 8: lnL = -1971.348423 Node 9: lnL = -1971.348423 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 122 Sequential format.. Reading seq # 1: YML048W_Sbay Reading seq # 2: YML048W_Scer Reading seq # 3: YML048W_Skud Reading seq # 4: YML048W_Smik Reading seq # 5: YML048W_Spar Sequences read.. Counting patterns.. # site patterns = 41 Counting frequencies.. 120 bytes for distance 6560 bytes for lkl0 5248 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.126043 0.035369 0.034928 0.002219 0.041021 0.080841 0.110362 0.031101 lnL0 = -401.917507 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 401.917507 x= 0.12604 0.03537 0.03493 0.00222 0.04102 0.08084 0.11036 0.03110 1 h-lim-p 0.0002 0.0125 182.2961 401.534016 9 0.0000 47 | 0/8 2 h-lim-p 0.0003 0.0039 20.7952 401.433715 0 0.0006 60 | 0/8 3 h-lim-p 0.0017 0.0162 7.2278 401.414606 2 0.0008 76 | 0/8 4 h-lim-p 0.0022 0.0297 2.6606 401.412998 2 0.0005 93 | 0/8 5 h-lim-p 0.0018 0.1523 0.7716 401.412763 2 0.0008 109 | 0/8 6 h-lim-p 0.0020 0.1989 0.3268 401.412735 4 0.0006 139 | 0/8 7 h-lim-p 0.0053 5.6379 0.0347 401.412689 0 0.0106 160 | 0/8 8 h-lim-p 0.0146 2.4120 0.0251 401.408126 0 0.1171 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 401.407772 2 0.9644 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 401.407771 0 1.0938 227 | 0/8 11 h-lim-p 2.0530 20.0000 0.0000 401.407771 0 0.8982 247 | 0/8 12 h-lim-p 0.3830 20.0000 0.0000 401.407771 0 0.0000 282 | 0/8 13 h-lim-p 0.0000 20.0000 0.0002 401.407771 0 0.0000 306 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 401.407771 0 0.0000 338 | 0/8 15 h-lim-p 0.0000 20.0000 0.0241 | 0/8 16 h-lim-p 0.0000 20.0000 0.0241 Out... lnL = -401.407771 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -401.407771 Node 7: lnL = -401.407771 Node 8: lnL = -401.407771 Node 9: lnL = -401.407771 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 259 Sequential format.. Reading seq # 1: YML050W_Sbay Reading seq # 2: YML050W_Scer Reading seq # 3: YML050W_Skud Reading seq # 4: YML050W_Smik Reading seq # 5: YML050W_Spar Sequences read.. Counting patterns.. # site patterns = 119 Counting frequencies.. 120 bytes for distance 19040 bytes for lkl0 15232 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.309184 0.074107 0.119250 0.114348 0.037348 0.175676 0.252939 0.070420 lnL0 = -1145.286000 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1145.286000 x= 0.30918 0.07411 0.11925 0.11435 0.03735 0.17568 0.25294 0.07042 1 h-lim-p 0.0010 0.0080 21.0904 1145.104360 3 0.0008 28 | 0/8 2 h-lim-p 0.0012 0.0168 14.4079 1145.079504 5 0.0003 51 | 0/8 3 h-lim-p 0.0009 0.0217 5.4413 1145.066192 0 0.0013 63 | 0/8 4 h-lim-p 0.0067 0.1239 1.0498 1145.065674 4 0.0010 86 | 0/8 5 h-lim-p 0.0032 0.6326 0.3217 1145.065628 3 0.0009 107 | 0/8 6 h-lim-p 0.0047 4.7859 0.0645 1145.065623 0 0.0024 127 | 0/8 7 h-lim-p 0.0072 16.7145 0.0212 1145.065618 0 0.0072 147 | 0/8 8 h-lim-p 0.0361 20.0000 0.0042 1145.065232 0 0.2888 170 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1145.065210 2 0.9961 194 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1145.065210 0 1.2500 214 | 0/8 11 h-lim-p 1.7856 20.0000 0.0000 1145.065210 0 0.4464 235 | 0/8 12 h-lim-p 0.2291 20.0000 0.0000 1145.065210 0 0.0286 257 | 0/8 13 h-lim-p 0.0140 20.0000 0.0000 1145.065210 0 0.0001 284 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 1145.065210 0 0.0000 307 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 1145.065210 0 0.0000 333 Out... lnL = -1145.065210 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1145.065210 Node 7: lnL = -1145.065210 Node 8: lnL = -1145.065210 Node 9: lnL = -1145.065210 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 705 Sequential format.. Reading seq # 1: YML052W_Sbay Reading seq # 2: YML052W_Scer Reading seq # 3: YML052W_Skud Reading seq # 4: YML052W_Smik Reading seq # 5: YML052W_Spar Sequences read.. Counting patterns.. # site patterns = 236 Counting frequencies.. 120 bytes for distance 37760 bytes for lkl0 30208 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.202578 0.105089 0.066781 0.095103 0.068993 0.147222 0.209224 0.012765 lnL0 = -2955.002298 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2955.002298 x= 0.20258 0.10509 0.06678 0.09510 0.06899 0.14722 0.20922 0.01276 1 h-lim-p 0.0087 1.9563 82.2156 2954.367160 7 0.0002 42 | 0/8 2 h-lim-p 0.0007 0.0058 22.9314 2954.305765 7 0.0003 70 | 0/8 3 h-lim-p 0.0006 0.0050 8.7105 2954.296104 2 0.0003 86 | 0/8 4 h-lim-p 0.0029 0.0403 0.8783 2954.295964 2 0.0004 104 | 0/8 5 h-lim-p 0.0008 0.8564 0.3905 2954.295937 2 0.0004 129 | 0/8 6 h-lim-p 0.0035 3.6978 0.0476 2954.295937 0 0.0004 151 | 0/8 7 h-lim-p 0.0045 20.0000 0.0041 2954.295937 0 0.0019 171 | 0/8 8 h-lim-p 0.0221 20.0000 0.0004 2954.295917 0 0.3541 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2954.295917 0 1.0938 215 | 0/8 10 h-lim-p 0.8995 20.0000 0.0000 2954.295917 0 0.7870 235 | 0/8 11 h-lim-p 0.2464 20.0000 0.0001 2954.295917 0 0.0000 270 | 0/8 12 h-lim-p 0.0001 20.0000 0.0000 2954.295917 0 0.0001 290 Out... lnL = -2954.295917 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2954.295917 Node 7: lnL = -2954.295917 Node 8: lnL = -2954.295917 Node 9: lnL = -2954.295917 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 705 Sequential format.. Reading seq # 1: YML053C_Sbay Reading seq # 2: YML053C_Scer Reading seq # 3: YML053C_Skud Reading seq # 4: YML053C_Smik Reading seq # 5: YML053C_Spar Sequences read.. Counting patterns.. # site patterns = 235 Counting frequencies.. 120 bytes for distance 37600 bytes for lkl0 30080 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.224448 0.056611 0.050488 0.094934 0.069162 0.160816 0.158354 0.049180 lnL0 = -2893.721349 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2893.721349 x= 0.22445 0.05661 0.05049 0.09493 0.06916 0.16082 0.15835 0.04918 1 h-lim-p 0.0040 1.1972 119.9031 2892.631165 9 0.0002 48 | 0/8 2 h-lim-p 0.0007 0.0057 23.8621 2892.557596 6 0.0003 72 | 0/8 3 h-lim-p 0.0006 0.0158 10.1280 2892.546439 4 0.0003 92 | 0/8 4 h-lim-p 0.0009 0.0774 2.9889 2892.545370 4 0.0003 116 | 0/8 5 h-lim-p 0.0028 0.8752 0.2833 2892.545352 2 0.0005 135 | 0/8 6 h-lim-p 0.0066 12.0259 0.0199 2892.545352 0 0.0004 158 | 0/8 7 h-lim-p 0.0012 20.0000 0.0060 2892.545352 0 0.0010 178 | 0/8 8 h-lim-p 0.0203 20.0000 0.0003 2892.545321 0 0.3243 202 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2892.545321 0 1.0938 222 | 0/8 10 h-lim-p 0.6571 20.0000 0.0000 2892.545321 0 1.3142 243 | 0/8 11 h-lim-p 1.5180 20.0000 0.0000 2892.545321 0 0.0949 266 | 0/8 12 h-lim-p 0.0137 20.0000 0.0001 2892.545321 0 0.0137 286 | 0/8 13 h-lim-p 0.0043 20.0000 0.0005 2892.545321 0 0.0000 321 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 2892.545321 0 0.0000 355 Out... lnL = -2892.545321 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2892.545321 Node 7: lnL = -2892.545321 Node 8: lnL = -2892.545321 Node 9: lnL = -2892.545321 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 661 Sequential format.. Reading seq # 1: YML055W_Sbay Reading seq # 2: YML055W_Scer Reading seq # 3: YML055W_Skud Reading seq # 4: YML055W_Smik Reading seq # 5: YML055W_Spar Sequences read.. Counting patterns.. # site patterns = 196 Counting frequencies.. 120 bytes for distance 31360 bytes for lkl0 25088 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.147420 0.036989 0.034075 0.090740 0.070363 0.195712 0.152896 0.001288 lnL0 = -2589.098187 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2589.098187 x= 0.14742 0.03699 0.03408 0.09074 0.07036 0.19571 0.15290 0.00129 1 h-lim-p 0.0026 0.9118 140.9100 2588.242855 8 0.0001 45 | 0/8 2 h-lim-p 0.0000 0.0003 11.7618 2588.231037 0 0.0001 59 | 0/8 3 h-lim-p 0.0003 0.0020 1.2337 2588.230911 3 0.0002 79 | 0/8 4 h-lim-p 0.0011 2.3490 0.1890 2588.230904 2 0.0003 96 | 0/8 5 h-lim-p 0.0015 0.0619 0.0419 2588.230904 0 0.0003 117 | 0/8 6 h-lim-p 0.0008 9.0294 0.0173 2588.230903 0 0.0016 138 | 0/8 7 h-lim-p 0.0009 0.1270 0.0321 2588.230899 0 0.0018 159 | 0/8 8 h-lim-p 0.0033 0.0644 0.0169 2588.230565 0 0.0266 182 | 0/8 9 h-lim-p 0.2179 1.7432 0.0004 2588.230550 0 0.8716 204 | 0/8 10 h-lim-p 0.0000 0.0001 4.1196 2588.230550 0 0.0000 224 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2588.230550 0 0.5469 237 | 0/8 12 h-lim-p 0.0228 2.3932 0.0002 2588.230550 0 0.0000 272 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 2588.230550 0 0.0000 295 | 0/8 14 h-lim-p 0.0000 18.8558 0.0000 2588.230550 0 0.0000 318 | 0/8 15 h-lim-p 0.0000 13.0055 0.0000 .. | 0/8 16 h-lim-p 0.0000 0.0016 0.1171 | 0/8 17 h-lim-p 0.0000 0.0016 0.1171 Out... lnL = -2588.230550 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2588.230550 Node 7: lnL = -2588.230550 Node 8: lnL = -2588.230550 Node 9: lnL = -2588.230550 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 533 Sequential format.. Reading seq # 1: YML057W_Sbay Reading seq # 2: YML057W_Scer Reading seq # 3: YML057W_Skud Reading seq # 4: YML057W_Smik Reading seq # 5: YML057W_Spar Sequences read.. Counting patterns.. # site patterns = 225 Counting frequencies.. 120 bytes for distance 36000 bytes for lkl0 28800 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.730313 0.079965 0.005148 0.099406 0.085929 0.220304 0.139935 0.388077 lnL0 = -2237.096410 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2237.096410 x= 0.73031 0.07997 0.00515 0.09941 0.08593 0.22030 0.13994 0.38808 1 h-lim-p 0.0002 0.0012 535.9979 2227.670028 6 0.0001 35 | 0/8 2 h-lim-p 0.0001 0.0010 105.0234 2225.763765 0 0.0004 48 | 0/8 3 h-lim-p 0.0007 0.0057 49.0901 2225.437939 2 0.0003 64 | 0/8 4 h-lim-p 0.0010 0.0132 16.9343 2225.368643 7 0.0005 92 | 0/8 5 h-lim-p 0.0031 0.1186 2.9651 2225.339364 0 0.0063 105 | 0/8 6 h-lim-p 0.0119 0.2457 1.5646 2225.338949 4 0.0004 129 | 0/8 7 h-lim-p 0.0029 0.6619 0.2163 2225.338068 0 0.0175 143 | 0/8 8 h-lim-p 0.2875 20.0000 0.0132 2225.316549 0 0.4313 163 | 0/8 9 h-lim-p 2.5000 20.0000 0.0010 2225.315573 3 1.0449 189 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2225.315556 0 2.5000 209 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2225.315554 0 1.2500 229 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2225.315554 0 1.0938 249 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2225.315554 0 0.5469 270 | 0/8 14 h-lim-p 0.3605 20.0000 0.0000 2225.315554 0 0.0000 314 Out... lnL = -2225.315554 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2225.315554 Node 7: lnL = -2225.315554 Node 8: lnL = -2225.315554 Node 9: lnL = -2225.315554 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 540 Sequential format.. Reading seq # 1: YML058W-A_Sbay Reading seq # 2: YML058W-A_Scer Reading seq # 3: YML058W-A_Skud Reading seq # 4: YML058W-A_Smik Reading seq # 5: YML058W-A_Spar Sequences read.. Counting patterns.. # site patterns = 199 Counting frequencies.. 120 bytes for distance 31840 bytes for lkl0 25472 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.255042 0.058202 0.040151 0.084906 0.067777 0.156933 0.154849 0.075080 lnL0 = -2238.700407 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2238.700407 x= 0.25504 0.05820 0.04015 0.08491 0.06778 0.15693 0.15485 0.07508 1 h-lim-p 0.0013 0.0106 133.9227 2237.390745 8 0.0002 40 | 0/8 2 h-lim-p 0.0006 0.0052 20.3770 2237.324899 4 0.0003 60 | 0/8 3 h-lim-p 0.0006 0.0362 11.4247 2237.309103 5 0.0003 83 | 0/8 4 h-lim-p 0.0011 0.0385 3.1375 2237.307707 5 0.0003 107 | 0/8 5 h-lim-p 0.0024 0.3628 0.4199 2237.307668 2 0.0005 124 | 0/8 6 h-lim-p 0.0022 2.7502 0.0867 2237.307667 0 0.0005 145 | 0/8 7 h-lim-p 0.0026 6.4435 0.0163 2237.307667 0 0.0011 165 | 0/8 8 h-lim-p 0.1358 20.0000 0.0001 2237.307639 0 1.0864 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2237.307637 0 1.0938 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2237.307637 0 2.1875 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2237.307637 0 1.0938 248 | 0/8 12 h-lim-p 0.2154 20.0000 0.0000 2237.307637 0 3.4456 272 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2237.307637 0 0.1562 295 | 0/8 14 h-lim-p 0.0070 20.0000 0.0000 2237.307637 0 0.0052 315 | 0/8 15 h-lim-p 0.0020 20.0000 0.0001 2237.307637 0 0.0005 336 | 0/8 16 h-lim-p 0.0002 20.0000 0.0002 2237.307637 0 0.0000 365 | 0/8 17 h-lim-p 0.0001 20.0000 0.0000 2237.307637 0 0.0000 394 Out... lnL = -2237.307637 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2237.307637 Node 7: lnL = -2237.307637 Node 8: lnL = -2237.307637 Node 9: lnL = -2237.307637 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 444 Sequential format.. Reading seq # 1: YML058W_Sbay Reading seq # 2: YML058W_Scer Reading seq # 3: YML058W_Skud Reading seq # 4: YML058W_Smik Reading seq # 5: YML058W_Spar Sequences read.. Counting patterns.. # site patterns = 116 Counting frequencies.. 120 bytes for distance 18560 bytes for lkl0 14848 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.716322 0.032772 0.509481 0.167342 0.083020 3.637634 0.468196 0.000060 lnL0 = -1731.417906 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1731.417906 x= 0.71632 0.03277 0.50948 0.16734 0.08302 3.63763 0.46820 0.00006 1 h-lim-p 0.0000 0.0000 344.3656 1731.321282 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0000 1672.7283 1711.490929 m 0.0000 34 | 2/8 3 h-lim-p 0.0000 0.0002 741.6315 1675.343889 m 0.0002 46 | 2/8 4 h-lim-p -0.0000 -0.0000 49.9640 h-lim-p: -3.80407673e-19 -3.04326138e-18 4.99640086e+01 1675.343889 .. | 2/8 5 h-lim-p 0.0000 0.0022 252.8874 1603.007855 0 0.0018 73 | 2/8 6 h-lim-p 0.0005 0.0040 107.1199 1596.469407 0 0.0010 86 | 2/8 7 h-lim-p 0.0003 0.0024 74.3285 1595.813870 1 0.0004 100 | 2/8 8 h-lim-p 0.0015 0.0332 18.6986 1595.749152 7 0.0004 127 | 1/8 9 h-lim-p 0.0002 0.0059 38.5996 1595.313863 0 0.0008 141 | 1/8 10 h-lim-p 0.0009 0.0071 32.3810 1595.030848 1 0.0011 155 | 1/8 11 h-lim-p 0.1266 1.0129 0.0875 1593.534669 0 0.7597 169 | 1/8 12 h-lim-p 2.5000 20.0000 0.0114 1593.465834 6 1.0724 199 | 0/8 13 h-lim-p 0.0171 1.4560 0.7168 1593.465550 3 0.0011 227 | 0/8 14 h-lim-p 0.2855 20.0000 0.0029 1593.463381 0 1.1420 249 | 0/8 15 h-lim-p 2.5000 20.0000 0.0006 1593.463281 2 0.9961 273 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1593.463281 0 1.0938 293 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1593.463281 0 1.0938 313 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1593.463281 0 0.6250 334 | 0/8 19 h-lim-p 0.4315 20.0000 0.0000 1593.463281 0 0.0000 371 Out... lnL = -1593.463281 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1593.463281 Node 7: lnL = -1593.463281 Node 8: lnL = -1593.463281 Node 9: lnL = -1593.463281 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 359 Sequential format.. Reading seq # 1: YML060W_Sbay Reading seq # 2: YML060W_Scer Reading seq # 3: YML060W_Skud Reading seq # 4: YML060W_Smik Reading seq # 5: YML060W_Spar Sequences read.. Counting patterns.. # site patterns = 143 Counting frequencies.. 120 bytes for distance 22880 bytes for lkl0 18304 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.189722 0.102336 0.062278 0.099970 0.071304 0.167863 0.163104 0.003417 lnL0 = -1520.348822 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1520.348822 x= 0.18972 0.10234 0.06228 0.09997 0.07130 0.16786 0.16310 0.00342 1 h-lim-p 0.0059 0.0493 71.5231 1519.546246 3 0.0003 31 | 0/8 2 h-lim-p 0.0014 0.0116 11.8425 1519.511216 6 0.0005 57 | 0/8 3 h-lim-p 0.0012 0.0469 5.2074 1519.504004 5 0.0006 80 | 0/8 4 h-lim-p 0.0085 1.4009 0.3804 1519.503969 2 0.0005 99 | 0/8 5 h-lim-p 0.0039 0.8957 0.0482 1519.503968 0 0.0009 120 | 0/8 6 h-lim-p 0.0053 19.6351 0.0078 1519.503968 0 0.0012 141 | 0/8 7 h-lim-p 0.0043 12.0418 0.0021 1519.503967 0 0.0172 163 | 0/8 8 h-lim-p 0.0061 20.0000 0.0060 1519.503937 0 0.0244 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1519.503937 0 1.0938 205 | 0/8 10 h-lim-p 1.3916 20.0000 0.0000 1519.503937 0 1.2177 225 | 0/8 11 h-lim-p 1.1880 20.0000 0.0000 1519.503937 0 0.2599 246 | 0/8 12 h-lim-p 0.0231 20.0000 0.0003 1519.503937 0 0.0051 267 | 0/8 13 h-lim-p 0.0016 8.1538 0.0009 1519.503937 0 0.0001 290 | 0/8 14 h-lim-p 0.0001 5.2279 0.0013 1519.503937 0 0.0000 324 | 0/8 15 h-lim-p 0.0000 20.0000 0.0008 | 0/8 16 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -1519.503937 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1519.503937 Node 7: lnL = -1519.503937 Node 8: lnL = -1519.503937 Node 9: lnL = -1519.503937 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 631 Sequential format.. Reading seq # 1: YML064C_Sbay Reading seq # 2: YML064C_Scer Reading seq # 3: YML064C_Skud Reading seq # 4: YML064C_Smik Reading seq # 5: YML064C_Spar Sequences read.. Counting patterns.. # site patterns = 227 Counting frequencies.. 120 bytes for distance 36320 bytes for lkl0 29056 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.212646 0.068453 0.057825 0.100728 0.078624 0.190522 0.197545 0.017506 lnL0 = -2734.918163 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2734.918163 x= 0.21265 0.06845 0.05783 0.10073 0.07862 0.19052 0.19755 0.01751 1 h-lim-p 0.0046 1.5904 109.4851 2733.702195 8 0.0002 43 | 0/8 2 h-lim-p 0.0008 0.0064 21.8438 2733.636493 6 0.0003 68 | 0/8 3 h-lim-p 0.0007 0.0160 8.6129 2733.626277 3 0.0003 86 | 0/8 4 h-lim-p 0.0009 0.0437 3.0793 2733.624640 3 0.0004 104 | 0/8 5 h-lim-p 0.0038 0.3833 0.3218 2733.624613 2 0.0005 122 | 0/8 6 h-lim-p 0.0013 1.6772 0.1272 2733.624610 1 0.0003 145 | 0/8 7 h-lim-p 0.0016 2.2377 0.0249 2733.624610 0 0.0007 165 | 0/8 8 h-lim-p 0.1313 20.0000 0.0001 2733.624578 0 1.0508 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2733.624577 0 1.0938 208 | 0/8 10 h-lim-p 2.2455 20.0000 0.0000 2733.624577 0 1.9648 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2733.624577 0 1.0938 248 | 0/8 12 h-lim-p 0.3272 20.0000 0.0001 2733.624577 0 0.0102 272 | 0/8 13 h-lim-p 0.0009 20.0000 0.0006 2733.624577 0 0.0000 307 | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -2733.624577 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2733.624577 Node 7: lnL = -2733.624577 Node 8: lnL = -2733.624577 Node 9: lnL = -2733.624577 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 728 Sequential format.. Reading seq # 1: YML065W_Sbay Reading seq # 2: YML065W_Scer Reading seq # 3: YML065W_Skud Reading seq # 4: YML065W_Smik Reading seq # 5: YML065W_Spar Sequences read.. Counting patterns.. # site patterns = 306 Counting frequencies.. 120 bytes for distance 48960 bytes for lkl0 39168 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.349123 0.095040 0.074466 0.150451 0.136212 0.248609 0.287882 0.056005 lnL0 = -3623.173434 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3623.173434 x= 0.34912 0.09504 0.07447 0.15045 0.13621 0.24861 0.28788 0.05601 1 h-lim-p 0.0039 0.0310 74.8743 3622.287409 8 0.0003 43 | 0/8 2 h-lim-p 0.0013 0.0105 19.4582 3622.204565 7 0.0005 72 | 0/8 3 h-lim-p 0.0011 0.0525 8.2173 3622.188357 4 0.0006 93 | 0/8 4 h-lim-p 0.0010 0.0717 4.6740 3622.183425 5 0.0006 119 | 0/8 5 h-lim-p 0.0045 0.5976 0.6275 3622.183312 3 0.0006 139 | 0/8 6 h-lim-p 0.0021 1.3356 0.1768 3622.183303 2 0.0007 165 | 0/8 7 h-lim-p 0.1046 20.0000 0.0012 3622.183266 0 0.2092 186 | 0/8 8 h-lim-p 0.0028 13.2494 0.0880 3622.183102 0 0.0056 207 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3622.183095 1 0.9961 229 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3622.183095 0 2.1875 249 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3622.183095 0 1.0938 269 | 0/8 12 h-lim-p 0.1959 20.0000 0.0001 3622.183095 0 0.1959 289 | 0/8 13 h-lim-p 0.0354 20.0000 0.0003 3622.183095 0 0.0044 311 | 0/8 14 h-lim-p 0.0012 20.0000 0.0012 3622.183095 0 0.0003 332 | 0/8 15 h-lim-p 0.0002 20.0000 0.0024 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -3622.183095 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3622.183095 Node 7: lnL = -3622.183095 Node 8: lnL = -3622.183095 Node 9: lnL = -3622.183095 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 711 Sequential format.. Reading seq # 1: YML066C_Sbay Reading seq # 2: YML066C_Scer Reading seq # 3: YML066C_Skud Reading seq # 4: YML066C_Smik Reading seq # 5: YML066C_Spar Sequences read.. Counting patterns.. # site patterns = 316 Counting frequencies.. 120 bytes for distance 50560 bytes for lkl0 40448 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.357924 0.083790 0.087538 0.168354 0.147383 0.220508 0.312528 0.057221 lnL0 = -3610.467150 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3610.467150 x= 0.35792 0.08379 0.08754 0.16835 0.14738 0.22051 0.31253 0.05722 1 h-lim-p 0.0014 0.0110 70.7492 3609.526035 8 0.0004 42 | 0/8 2 h-lim-p 0.0014 0.0115 19.3810 3609.437820 7 0.0005 73 | 0/8 3 h-lim-p 0.0010 0.0366 9.6227 3609.409171 5 0.0008 95 | 0/8 4 h-lim-p 0.0017 0.0739 4.4033 3609.405271 5 0.0005 122 | 0/8 5 h-lim-p 0.0067 0.4976 0.3282 3609.405229 0 0.0007 136 | 0/8 6 h-lim-p 0.0064 4.3207 0.0376 3609.405229 0 0.0007 158 | 0/8 7 h-lim-p 0.0047 20.0000 0.0056 3609.405226 0 0.0095 179 | 0/8 8 h-lim-p 0.0080 20.0000 0.0066 3609.405035 0 0.0641 202 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3609.405034 0 1.0938 222 | 0/8 10 h-lim-p 1.6969 20.0000 0.0000 3609.405034 0 1.4848 242 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3609.405034 0 1.2500 262 | 0/8 12 h-lim-p 0.6328 20.0000 0.0000 3609.405034 0 0.6328 282 | 0/8 13 h-lim-p 0.0248 20.0000 0.0004 3609.405034 0 0.0062 303 | 0/8 14 h-lim-p 0.0025 20.0000 0.0010 3609.405034 0 0.0022 323 | 0/8 15 h-lim-p 0.0002 8.5839 0.0105 3609.405034 0 0.0000 354 | 0/8 16 h-lim-p 0.0006 20.0000 0.0000 3609.405034 0 0.0000 387 Out... lnL = -3609.405034 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3609.405034 Node 7: lnL = -3609.405034 Node 8: lnL = -3609.405034 Node 9: lnL = -3609.405034 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 298 Sequential format.. Reading seq # 1: YML069W_Sbay Reading seq # 2: YML069W_Scer Reading seq # 3: YML069W_Skud Reading seq # 4: YML069W_Smik Reading seq # 5: YML069W_Spar Sequences read.. Counting patterns.. # site patterns = 109 Counting frequencies.. 120 bytes for distance 17440 bytes for lkl0 13952 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.741423 0.347943 0.136073 0.392518 3.386008 0.464007 0.539392 0.000060 lnL0 = -1239.233258 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1239.233258 x= 0.74142 0.34794 0.13607 0.39252 3.38601 0.46401 0.53939 0.00006 1 h-lim-p 0.0000 0.0000 224.3312 1239.177356 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0004 847.1240 1188.393111 m 0.0004 37 | 2/8 3 h-lim-p 0.0008 0.0063 74.1856 1176.783442 0 0.0047 51 | 2/8 4 h-lim-p 0.0015 0.0117 16.9228 1176.461775 0 0.0044 64 | 2/8 5 h-lim-p 0.0186 0.1855 3.9906 .. | 2/8 6 h-lim-p 0.0000 0.0055 119.3390 1137.894513 0 0.0038 120 | 2/8 7 h-lim-p 0.0001 0.0007 345.9687 1128.990532 0 0.0005 134 | 2/8 8 h-lim-p 0.0003 0.0024 112.3674 1125.663419 0 0.0009 147 | 1/8 9 h-lim-p 0.0003 0.0026 245.2042 1114.292023 0 0.0007 160 | 1/8 10 h-lim-p 0.0003 0.0025 68.2665 1112.835101 0 0.0009 173 | 1/8 11 h-lim-p 0.0080 0.0638 3.7408 1112.818039 2 0.0019 190 | 1/8 12 h-lim-p 0.0696 2.1911 0.1005 1110.746150 0 0.8347 205 | 1/8 13 h-lim-p 2.5000 20.0000 0.0070 1110.722263 5 1.2177 237 | 0/8 14 h-lim-p 0.0072 0.5567 1.1874 1110.721530 3 0.0014 263 | 0/8 15 h-lim-p 0.8096 20.0000 0.0020 1110.718139 0 1.6191 276 | 0/8 16 h-lim-p 2.5000 20.0000 0.0007 1110.717786 2 1.0938 300 | 0/8 17 h-lim-p 2.5000 20.0000 0.0002 1110.717769 3 1.4879 328 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1110.717769 0 1.0938 348 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1110.717769 0 1.0938 368 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 1110.717769 0 3.7500 388 | 0/8 21 h-lim-p 1.7663 20.0000 0.0000 1110.717769 0 0.0552 412 Out... lnL = -1110.717769 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1110.717769 Node 7: lnL = -1110.717769 Node 8: lnL = -1110.717769 Node 9: lnL = -1110.717769 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 851 Sequential format.. Reading seq # 1: YML070W_Sbay Reading seq # 2: YML070W_Scer Reading seq # 3: YML070W_Skud Reading seq # 4: YML070W_Smik Reading seq # 5: YML070W_Spar Sequences read.. Counting patterns.. # site patterns = 393 Counting frequencies.. 120 bytes for distance 62880 bytes for lkl0 50304 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.402800 0.064086 0.130332 0.169059 0.137463 0.359185 0.304563 0.061508 lnL0 = -4497.814306 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4497.814306 x= 0.40280 0.06409 0.13033 0.16906 0.13746 0.35918 0.30456 0.06151 1 h-lim-p 0.0056 1.0480 126.5838 4495.250702 8 0.0003 40 | 0/8 2 h-lim-p 0.0016 0.0128 23.5100 4495.110401 6 0.0005 67 | 0/8 3 h-lim-p 0.0006 0.0194 19.5762 4495.018057 1 0.0008 81 | 0/8 4 h-lim-p 0.0137 0.1769 1.1183 4495.017476 4 0.0009 104 | 0/8 5 h-lim-p 0.0028 0.8492 0.3736 4495.017426 3 0.0007 123 | 0/8 6 h-lim-p 0.0036 8.6539 0.0785 4495.017420 0 0.0016 143 | 0/8 7 h-lim-p 0.0163 20.0000 0.0075 4495.017317 0 0.0650 165 | 0/8 8 h-lim-p 0.0035 10.3165 0.1381 4495.015952 0 0.0106 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 4495.015914 1 1.0938 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4495.015913 0 1.0938 228 | 0/8 11 h-lim-p 1.4316 20.0000 0.0000 4495.015913 0 1.2526 248 | 0/8 12 h-lim-p 0.9159 20.0000 0.0000 4495.015913 0 0.4007 268 | 0/8 13 h-lim-p 0.0004 5.0198 0.0199 4495.015913 0 0.0004 288 | 0/8 14 h-lim-p 0.0001 0.7344 0.1359 4495.015913 0 0.0000 311 | 0/8 15 h-lim-p 0.0004 20.0000 0.0013 4495.015913 0 0.0000 336 | 0/8 16 h-lim-p 0.0011 20.0000 0.0000 4495.015913 0 0.0000 367 Out... lnL = -4495.015913 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4495.015913 Node 7: lnL = -4495.015913 Node 8: lnL = -4495.015913 Node 9: lnL = -4495.015913 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 831 Sequential format.. Reading seq # 1: YML071C_Sbay Reading seq # 2: YML071C_Scer Reading seq # 3: YML071C_Skud Reading seq # 4: YML071C_Smik Reading seq # 5: YML071C_Spar Sequences read.. Counting patterns.. # site patterns = 415 Counting frequencies.. 120 bytes for distance 66400 bytes for lkl0 53120 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.439958 0.000060 0.082917 0.361329 0.292752 0.314502 0.478267 0.055797 lnL0 = -4605.585728 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4605.585728 x= 0.43996 0.00006 0.08292 0.36133 0.29275 0.31450 0.47827 0.05580 1 h-lim-p 0.0005 0.0037 72.8398 4604.192339 0 0.0007 22 | 0/8 2 h-lim-p 0.0001 0.0012 32.1000 4603.915900 0 0.0006 36 | 0/8 3 h-lim-p 0.0012 0.0105 15.5725 4603.843011 6 0.0008 62 | 0/8 4 h-lim-p 0.0049 0.2288 2.3895 4603.839448 4 0.0013 83 | 0/8 5 h-lim-p 0.0043 0.1635 0.7011 4603.839002 3 0.0016 101 | 0/8 6 h-lim-p 0.0062 3.6434 0.1838 4603.838377 0 0.0093 121 | 0/8 7 h-lim-p 0.0303 2.4549 0.0564 4603.796341 0 0.1214 143 | 0/8 8 h-lim-p 0.0019 0.0151 3.4887 4603.781528 4 0.0015 171 | 0/8 9 h-lim-p 2.5000 20.0000 0.0019 4603.779770 3 0.9482 189 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4603.779770 0 1.0938 209 | 0/8 11 h-lim-p 1.9198 20.0000 0.0000 4603.779770 0 1.6798 229 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4603.779770 0 1.0938 249 | 0/8 13 h-lim-p 0.4515 20.0000 0.0000 4603.779770 0 0.9029 270 | 0/8 14 h-lim-p 0.0014 3.4943 0.0135 4603.779770 0 0.0014 290 | 0/8 15 h-lim-p 0.0006 1.5454 0.0304 4603.779770 0 0.0000 316 | 0/8 16 h-lim-p 0.0005 20.0000 0.0003 4603.779770 0 0.0000 339 | 0/8 17 h-lim-p 0.0004 20.0000 0.0000 4603.779770 0 0.0000 367 | 0/8 18 h-lim-p 0.0001 20.0000 0.0000 4603.779770 0 0.0000 399 Out... lnL = -4603.779770 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4603.779770 Node 7: lnL = -4603.779770 Node 8: lnL = -4603.779770 Node 9: lnL = -4603.779770 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 397 Sequential format.. Reading seq # 1: YML072C_Sbay Reading seq # 2: YML072C_Scer Reading seq # 3: YML072C_Skud Reading seq # 4: YML072C_Smik Reading seq # 5: YML072C_Spar Sequences read.. Counting patterns.. # site patterns = 120 Counting frequencies.. 120 bytes for distance 19200 bytes for lkl0 15360 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.154552 0.008133 0.055515 0.079684 0.038437 0.122408 0.181896 0.018035 lnL0 = -1466.285117 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1466.285117 x= 0.15455 0.00813 0.05552 0.07968 0.03844 0.12241 0.18190 0.01803 1 h-lim-p 0.0015 0.0116 92.0401 1465.879880 7 0.0001 43 | 0/8 2 h-lim-p 0.0005 0.0068 18.6047 1465.808559 3 0.0004 61 | 0/8 3 h-lim-p 0.0017 0.0411 4.7582 1465.806338 2 0.0002 79 | 0/8 4 h-lim-p 0.0005 0.0364 2.0490 1465.805893 3 0.0003 98 | 0/8 5 h-lim-p 0.0006 0.2358 0.8382 1465.805748 3 0.0005 116 | 0/8 6 h-lim-p 0.0024 0.2087 0.1716 1465.805744 0 0.0003 138 | 0/8 7 h-lim-p 0.0015 1.0825 0.0335 1465.805744 0 0.0003 159 | 0/8 8 h-lim-p 0.0610 20.0000 0.0002 1465.805693 0 0.9759 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1465.805692 0 1.2500 203 | 0/8 10 h-lim-p 1.7224 20.0000 0.0000 1465.805692 0 0.8612 223 | 0/8 11 h-lim-p 0.6424 20.0000 0.0000 1465.805692 0 0.1405 244 | 0/8 12 h-lim-p 0.0448 20.0000 0.0001 1465.805692 0 0.0056 266 | 0/8 13 h-lim-p 0.0025 20.0000 0.0003 1465.805692 0 0.0002 289 | 0/8 14 h-lim-p 0.0000 20.0000 0.0011 1465.805692 0 0.0000 324 | 0/8 15 h-lim-p 0.0000 20.0000 0.0017 | 0/8 16 h-lim-p 0.0000 20.0000 0.0017 Out... lnL = -1465.805692 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1465.805692 Node 7: lnL = -1465.805692 Node 8: lnL = -1465.805692 Node 9: lnL = -1465.805692 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 933 Sequential format.. Reading seq # 1: YML074C_Sbay Reading seq # 2: YML074C_Scer Reading seq # 3: YML074C_Skud Reading seq # 4: YML074C_Smik Reading seq # 5: YML074C_Spar Sequences read.. Counting patterns.. # site patterns = 431 Counting frequencies.. 120 bytes for distance 68960 bytes for lkl0 55168 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.388186 0.164513 0.134086 0.169798 0.151162 0.334070 0.498973 0.000060 lnL0 = -4915.901816 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4915.901816 x= 0.38819 0.16451 0.13409 0.16980 0.15116 0.33407 0.49897 0.00006 1 h-lim-p 0.0000 0.0001 62.4553 4915.678817 m 0.0001 22 | 1/8 2 h-lim-p 0.0002 0.0086 24.2580 4915.562635 0 0.0005 35 | 1/8 3 h-lim-p 0.0008 0.0389 14.2835 4915.487033 1 0.0010 49 | 1/8 4 h-lim-p 0.0022 0.0544 6.4050 4915.476021 5 0.0007 73 | 1/8 5 h-lim-p 0.0026 0.3222 1.6371 4915.472787 5 0.0016 97 | 0/8 6 h-lim-p 0.0003 0.0985 8.6256 4915.416628 0 0.0025 112 | 0/8 7 h-lim-p 0.0027 0.0513 7.7880 4915.385012 6 0.0017 140 | 0/8 8 h-lim-p 0.0113 0.5344 1.1366 4915.375057 5 0.0057 165 | 0/8 9 h-lim-p 0.0421 0.4719 0.1532 4914.702594 0 0.2529 179 | 0/8 10 h-lim-p 2.5000 20.0000 0.0036 4914.693918 3 1.1023 205 | 0/8 11 h-lim-p 2.5000 20.0000 0.0001 4914.693910 0 1.0938 225 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4914.693910 0 1.0938 245 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 4914.693910 0 1.0938 265 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 4914.693910 0 5.0000 286 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 4914.693910 0 0.2734 308 | 0/8 16 h-lim-p 0.1500 20.0000 0.0000 4914.693910 0 0.0001 337 Out... lnL = -4914.693910 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4914.693910 Node 7: lnL = -4914.693910 Node 8: lnL = -4914.693910 Node 9: lnL = -4914.693910 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 336 Sequential format.. Reading seq # 1: YML077W_Sbay Reading seq # 2: YML077W_Scer Reading seq # 3: YML077W_Skud Reading seq # 4: YML077W_Smik Reading seq # 5: YML077W_Spar Sequences read.. Counting patterns.. # site patterns = 148 Counting frequencies.. 120 bytes for distance 23680 bytes for lkl0 18944 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.231035 0.146882 0.056912 0.093969 0.097365 0.229061 0.176565 0.000060 lnL0 = -1336.754937 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1336.754937 x= 0.23104 0.14688 0.05691 0.09397 0.09736 0.22906 0.17656 0.00006 1 h-lim-p 0.0000 0.0000 45.3806 1336.670527 m 0.0000 22 | 1/8 2 h-lim-p 0.0002 0.0146 11.7161 1336.631769 0 0.0007 36 | 1/8 3 h-lim-p 0.0009 0.0610 9.0358 1336.596998 0 0.0017 49 | 1/8 4 h-lim-p 0.0042 0.0700 3.6939 1336.589638 5 0.0012 74 | 1/8 5 h-lim-p 0.0019 0.0438 2.4299 1336.587591 3 0.0008 92 | 1/8 6 h-lim-p 0.0118 1.4339 0.1559 1336.514923 0 0.0941 107 | 1/8 7 h-lim-p 0.0062 0.0643 2.3652 1336.098304 0 0.0124 127 | 1/8 8 h-lim-p 0.0085 0.2648 3.4344 1336.083226 6 0.0025 155 | 1/8 9 h-lim-p 1.5902 20.0000 0.0053 1336.059989 7 0.8670 182 | 0/8 10 h-lim-p 0.1655 20.0000 0.0279 1336.059988 0 0.0023 206 | 0/8 11 h-lim-p 0.1240 1.0495 0.0005 1336.059911 1 0.8096 230 | 0/8 12 h-lim-p 0.0305 0.2438 0.0001 1336.059911 m 0.2438 250 | 1/8 13 h-lim-p 0.0616 20.0000 0.0002 1336.059911 0 0.0925 270 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 1336.059911 0 2.1875 289 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 1336.059911 0 2.1875 308 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 1336.059911 0 1.0938 327 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 1336.059911 0 2.1875 346 | 1/8 18 h-lim-p 1.8392 20.0000 0.0000 1336.059911 0 0.2012 367 | 1/8 19 h-lim-p 0.2516 20.0000 0.0000 1336.059911 0 0.0629 387 | 1/8 20 h-lim-p 0.0671 20.0000 0.0000 1336.059911 0 0.0042 409 Out... lnL = -1336.059911 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1336.059911 Node 7: lnL = -1336.059911 Node 8: lnL = -1336.059911 Node 9: lnL = -1336.059911 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 171 Sequential format.. Reading seq # 1: YML078W_Sbay Reading seq # 2: YML078W_Scer Reading seq # 3: YML078W_Skud Reading seq # 4: YML078W_Smik Reading seq # 5: YML078W_Spar Sequences read.. Counting patterns.. # site patterns = 78 Counting frequencies.. 120 bytes for distance 12480 bytes for lkl0 9984 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.143960 0.077170 0.119125 0.044663 0.079073 0.122376 0.046829 0.000060 lnL0 = -589.834064 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 589.834064 x= 0.14396 0.07717 0.11912 0.04466 0.07907 0.12238 0.04683 0.00006 1 h-lim-p 0.0000 0.0000 70.8673 589.784883 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0123 19.7501 589.476981 0 0.0017 39 | 1/8 3 h-lim-p 0.0024 0.0190 10.1999 589.449815 6 0.0006 64 | 1/8 4 h-lim-p 0.0009 0.0234 7.0882 589.429746 1 0.0012 78 | 1/8 5 h-lim-p 0.0026 0.0451 3.1482 589.423614 2 0.0012 94 | 1/8 6 h-lim-p 0.0082 1.4011 0.4697 589.393331 0 0.0163 107 | 1/8 7 h-lim-p 0.0086 0.3698 0.8923 587.793608 0 0.0688 129 | 0/8 8 h-lim-p 0.0025 0.0197 11.5974 587.737636 8 0.0008 168 | 0/8 9 h-lim-p 0.1004 2.9482 0.0964 587.736596 6 0.0283 194 | 0/8 10 h-lim-p 0.0457 0.7937 0.0596 587.698976 0 0.1829 216 | 0/8 11 h-lim-p 2.5000 20.0000 0.0023 587.695417 5 1.2951 248 | 0/8 12 h-lim-p 2.5000 20.0000 0.0008 587.694921 5 1.6759 280 | 0/8 13 h-lim-p 2.5000 20.0000 0.0001 587.694915 1 1.0938 302 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 587.694915 0 1.0938 322 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 587.694915 0 1.0938 342 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 587.694915 010.0000 364 | 0/8 17 h-lim-p 1.2049 20.0000 0.0000 587.694915 0 0.1506 386 | 0/8 18 h-lim-p 0.1872 20.0000 0.0000 587.694915 0 0.0117 409 | 0/8 19 h-lim-p 0.0124 20.0000 0.0000 587.694915 0 0.0124 429 | 0/8 20 h-lim-p 0.0131 20.0000 0.0000 587.694915 0 0.0033 450 Out... lnL = -587.694915 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -587.694915 Node 7: lnL = -587.694915 Node 8: lnL = -587.694915 Node 9: lnL = -587.694915 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 336 Sequential format.. Reading seq # 1: YML080W_Sbay Reading seq # 2: YML080W_Scer Reading seq # 3: YML080W_Skud Reading seq # 4: YML080W_Smik Reading seq # 5: YML080W_Spar Sequences read.. Counting patterns.. # site patterns = 117 Counting frequencies.. 120 bytes for distance 18720 bytes for lkl0 14976 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.194217 0.099207 0.095060 0.150349 0.068232 0.145370 0.183839 0.000060 lnL0 = -1321.844026 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1321.844026 x= 0.19422 0.09921 0.09506 0.15035 0.06823 0.14537 0.18384 0.00006 1 h-lim-p 0.0000 0.0000 42.9531 1321.835928 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0290 11.9482 1321.793464 0 0.0009 40 | 1/8 3 h-lim-p 0.0046 0.1730 2.3054 1321.790779 4 0.0009 61 | 1/8 4 h-lim-p 0.0040 0.3583 0.5152 1321.787290 1 0.0050 75 | 1/8 5 h-lim-p 0.0030 0.3124 0.8464 1321.754111 0 0.0121 96 | 1/8 6 h-lim-p 0.0052 0.1098 1.9620 1321.385882 0 0.0104 116 | 1/8 7 h-lim-p 0.0018 0.0201 11.2956 1321.276020 7 0.0012 146 | 1/8 8 h-lim-p 0.0135 0.1571 1.0368 1321.275532 3 0.0009 167 | 0/8 9 h-lim-p 0.0005 1.4365 1.7171 1321.274174 0 0.0011 180 | 0/8 10 h-lim-p 0.8700 6.9894 0.0022 1321.271732 4 0.8515 202 | 0/8 11 h-lim-p 2.5000 20.0000 0.0001 1321.271722 2 0.7996 227 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1321.271722 0 1.0938 247 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1321.271722 0 0.6250 268 | 0/8 14 h-lim-p 1.8600 20.0000 0.0000 1321.271722 0 0.0109 295 Out... lnL = -1321.271722 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1321.271722 Node 7: lnL = -1321.271722 Node 8: lnL = -1321.271722 Node 9: lnL = -1321.271722 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 640 Sequential format.. Reading seq # 1: YML081C-A_Sbay Reading seq # 2: YML081C-A_Scer Reading seq # 3: YML081C-A_Skud Reading seq # 4: YML081C-A_Smik Reading seq # 5: YML081C-A_Spar Sequences read.. Counting patterns.. # site patterns = 209 Counting frequencies.. 120 bytes for distance 33440 bytes for lkl0 26752 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.201264 0.052336 0.066025 0.097323 0.081061 0.214036 0.138931 0.012639 lnL0 = -2769.284151 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2769.284151 x= 0.20126 0.05234 0.06603 0.09732 0.08106 0.21404 0.13893 0.01264 1 h-lim-p 0.0012 0.0100 129.3972 2767.936062 9 0.0002 45 | 0/8 2 h-lim-p 0.0011 0.0090 20.4349 2767.869350 7 0.0003 74 | 0/8 3 h-lim-p 0.0007 0.0266 8.9253 2767.861521 6 0.0002 101 | 0/8 4 h-lim-p 0.0009 0.0679 2.1900 2767.860809 4 0.0003 124 | 0/8 5 h-lim-p 0.0009 0.4004 0.7752 2767.860703 2 0.0004 140 | 0/8 6 h-lim-p 0.0163 1.8735 0.0186 2767.860703 0 0.0004 164 | 0/8 7 h-lim-p 0.0594 20.0000 0.0001 2767.860702 0 0.2374 186 | 0/8 8 h-lim-p 0.0008 0.8090 0.0401 2767.860696 0 0.0017 207 | 0/8 9 h-lim-p 1.8789 20.0000 0.0000 2767.860696 0 1.6441 227 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2767.860696 0 1.0938 247 | 0/8 11 h-lim-p 0.5342 20.0000 0.0000 2767.860696 0 1.6027 268 | 0/8 12 h-lim-p 0.2659 20.0000 0.0002 2767.860696 0 0.0249 291 | 0/8 13 h-lim-p 0.0047 18.4452 0.0013 2767.860696 0 0.0012 312 | 0/8 14 h-lim-p 0.0004 6.9789 0.0034 2767.860696 0 0.0000 337 | 0/8 15 h-lim-p 0.0004 20.0000 0.0001 2767.860696 0 0.0000 366 | 0/8 16 h-lim-p 0.0003 20.0000 0.0000 2767.860696 0 0.0000 397 Out... lnL = -2767.860696 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2767.860696 Node 7: lnL = -2767.860696 Node 8: lnL = -2767.860696 Node 9: lnL = -2767.860696 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 637 Sequential format.. Reading seq # 1: YML081W_Sbay Reading seq # 2: YML081W_Scer Reading seq # 3: YML081W_Skud Reading seq # 4: YML081W_Smik Reading seq # 5: YML081W_Spar Sequences read.. Counting patterns.. # site patterns = 203 Counting frequencies.. 120 bytes for distance 32480 bytes for lkl0 25984 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.196000 0.076038 0.070923 0.098509 0.082355 0.209046 0.164310 0.000060 lnL0 = -2796.551923 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2796.551923 x= 0.19600 0.07604 0.07092 0.09851 0.08235 0.20905 0.16431 0.00006 1 h-lim-p 0.0005 0.0043 83.3719 2795.837365 5 0.0002 32 | 0/8 2 h-lim-p 0.0001 0.0009 14.2274 2795.806623 0 0.0004 46 | 0/8 3 h-lim-p 0.0010 0.0391 6.3681 2795.802761 2 0.0002 63 | 0/8 4 h-lim-p 0.0010 0.0923 1.4042 2795.802528 2 0.0003 80 | 0/8 5 h-lim-p 0.0020 1.0484 0.1768 2795.802520 0 0.0004 93 | 0/8 6 h-lim-p 0.0016 5.1152 0.0495 2795.802513 0 0.0016 113 | 0/8 7 h-lim-p 0.0018 0.0628 0.0437 2795.802454 0 0.0036 134 | 0/8 8 h-lim-p 0.0007 1.6958 0.2152 2795.799843 0 0.0117 158 | 0/8 9 h-lim-p 0.0397 0.3179 0.0115 2795.799812 m 0.3179 178 | 1/8 10 h-lim-p 0.0105 7.0250 0.2469 2795.799811 0 0.0001 203 | 1/8 11 h-lim-p 0.2458 20.0000 0.0001 2795.799787 0 0.9831 224 | 0/8 12 h-lim-p 0.0865 20.0000 0.0016 2795.799787 0 0.0024 247 | 0/8 13 h-lim-p 0.1289 1.0313 0.0000 2795.799787 0 0.1289 267 | 0/8 14 h-lim-p 0.0754 0.6033 0.0000 2795.799787 0 0.0000 301 | 0/8 15 h-lim-p 0.0000 0.7910 0.0000 2795.799787 0 0.0000 326 Out... lnL = -2795.799787 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2795.799787 Node 7: lnL = -2795.799787 Node 8: lnL = -2795.799787 Node 9: lnL = -2795.799787 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 492 Sequential format.. Reading seq # 1: YML087C_Sbay Reading seq # 2: YML087C_Scer Reading seq # 3: YML087C_Skud Reading seq # 4: YML087C_Smik Reading seq # 5: YML087C_Spar Sequences read.. Counting patterns.. # site patterns = 195 Counting frequencies.. 120 bytes for distance 31200 bytes for lkl0 24960 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.221055 0.044254 0.086069 0.093879 0.051117 0.158797 0.241358 0.020325 lnL0 = -2021.316581 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2021.316581 x= 0.22105 0.04425 0.08607 0.09388 0.05112 0.15880 0.24136 0.02032 1 h-lim-p 0.0033 1.0125 110.3756 2019.646106 9 0.0003 48 | 0/8 2 h-lim-p 0.0006 0.0044 22.7133 2019.562789 7 0.0003 79 | 0/8 3 h-lim-p 0.0005 0.0048 14.7289 2019.532579 6 0.0004 105 | 0/8 4 h-lim-p 0.0017 0.0413 3.1616 2019.529908 5 0.0006 128 | 0/8 5 h-lim-p 0.0018 0.2214 1.0335 2019.529541 2 0.0008 144 | 0/8 6 h-lim-p 0.0033 0.3231 0.2395 2019.529521 0 0.0007 157 | 0/8 7 h-lim-p 0.0081 7.0629 0.0214 2019.529520 0 0.0009 179 | 0/8 8 h-lim-p 0.0195 20.0000 0.0010 2019.529147 0 0.6247 204 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2019.529146 0 1.0938 224 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2019.529146 0 1.0938 244 | 0/8 11 h-lim-p 1.4900 20.0000 0.0000 2019.529146 0 2.9799 265 | 0/8 12 h-lim-p 1.1719 20.0000 0.0000 2019.529146 0 1.1719 285 | 0/8 13 h-lim-p 0.0171 9.5513 0.0033 2019.529146 0 0.0001 311 | 0/8 14 h-lim-p 0.0004 20.0000 0.0013 2019.529146 0 0.0000 335 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 2019.529146 0 0.0000 362 | 0/8 16 h-lim-p 0.0002 20.0000 0.0000 2019.529146 0 0.0000 388 Out... lnL = -2019.529146 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2019.529146 Node 7: lnL = -2019.529146 Node 8: lnL = -2019.529146 Node 9: lnL = -2019.529146 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 854 Sequential format.. Reading seq # 1: YML088W_Sbay Reading seq # 2: YML088W_Scer Reading seq # 3: YML088W_Skud Reading seq # 4: YML088W_Smik Reading seq # 5: YML088W_Spar Sequences read.. Counting patterns.. # site patterns = 372 Counting frequencies.. 120 bytes for distance 59520 bytes for lkl0 47616 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.374649 0.020312 0.117494 0.137877 0.127871 0.553291 0.248538 0.031215 lnL0 = -4358.505709 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4358.505709 x= 0.37465 0.02031 0.11749 0.13788 0.12787 0.55329 0.24854 0.03122 1 h-lim-p 0.0018 0.0142 161.2097 4355.672774 8 0.0002 42 | 0/8 2 h-lim-p 0.0006 0.0048 51.9397 4354.706594 0 0.0009 54 | 0/8 3 h-lim-p 0.0014 0.0115 33.6418 4354.578864 3 0.0003 73 | 0/8 4 h-lim-p 0.0007 0.0129 16.1914 4354.498301 0 0.0010 85 | 0/8 5 h-lim-p 0.0014 0.0368 11.0839 4354.473388 3 0.0006 103 | 0/8 6 h-lim-p 0.0026 0.0863 2.6308 4354.471375 3 0.0006 123 | 0/8 7 h-lim-p 0.0061 0.7762 0.2748 4354.471266 1 0.0015 138 | 0/8 8 h-lim-p 0.0310 20.0000 0.0136 4354.435954 0 0.4959 162 | 0/8 9 h-lim-p 2.5000 20.0000 0.0009 4354.435031 4 1.3578 191 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 4354.435027 0 1.0938 211 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4354.435027 0 1.0938 231 | 0/8 12 h-lim-p 1.1085 20.0000 0.0000 4354.435027 0 1.6627 251 | 0/8 13 h-lim-p 0.2870 20.0000 0.0001 4354.435027 0 0.0078 275 | 0/8 14 h-lim-p 0.0017 20.0000 0.0005 4354.435027 0 0.0004 296 | 0/8 15 h-lim-p 0.0007 20.0000 0.0003 4354.435027 0 0.0000 331 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 4354.435027 0 0.0000 360 Out... lnL = -4354.435027 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4354.435027 Node 7: lnL = -4354.435027 Node 8: lnL = -4354.435027 Node 9: lnL = -4354.435027 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 388 Sequential format.. Reading seq # 1: YML092C_Sbay Reading seq # 2: YML092C_Scer Reading seq # 3: YML092C_Skud Reading seq # 4: YML092C_Smik Reading seq # 5: YML092C_Spar Sequences read.. Counting patterns.. # site patterns = 144 Counting frequencies.. 120 bytes for distance 23040 bytes for lkl0 18432 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.211687 0.039774 0.036870 0.170098 0.077771 0.185516 0.122873 0.025916 lnL0 = -1577.414670 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1577.414670 x= 0.21169 0.03977 0.03687 0.17010 0.07777 0.18552 0.12287 0.02592 1 h-lim-p 0.0012 0.9123 163.4053 1574.347065 7 0.0003 35 | 0/8 2 h-lim-p 0.0016 0.0129 16.2853 1574.257163 5 0.0007 56 | 0/8 3 h-lim-p 0.0050 0.0640 2.2654 1574.255549 4 0.0006 78 | 0/8 4 h-lim-p 0.0030 0.4765 0.4791 1574.255452 3 0.0009 99 | 0/8 5 h-lim-p 0.0045 1.8451 0.0935 1574.255449 1 0.0006 123 | 0/8 6 h-lim-p 0.0035 20.0000 0.0146 1574.255448 0 0.0031 143 | 0/8 7 h-lim-p 0.0219 20.0000 0.0021 1574.255361 0 0.1748 166 | 0/8 8 h-lim-p 0.0021 0.4856 0.1765 1574.255195 1 0.0026 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1574.255194 0 1.0938 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1574.255194 0 1.0938 228 | 0/8 11 h-lim-p 1.0732 20.0000 0.0000 1574.255194 0 0.0037 255 | 0/8 12 h-lim-p 0.0011 20.0000 0.0000 1574.255194 0 0.0000 282 | 0/8 13 h-lim-p 0.0003 20.0000 0.0000 1574.255194 0 0.0000 321 Out... lnL = -1574.255194 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1574.255194 Node 7: lnL = -1574.255194 Node 8: lnL = -1574.255194 Node 9: lnL = -1574.255194 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 121 Sequential format.. Reading seq # 1: YML095C_Sbay Reading seq # 2: YML095C_Scer Reading seq # 3: YML095C_Skud Reading seq # 4: YML095C_Smik Reading seq # 5: YML095C_Spar Sequences read.. Counting patterns.. # site patterns = 68 Counting frequencies.. 120 bytes for distance 10880 bytes for lkl0 8704 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.330122 0.159805 0.056057 0.087065 0.083275 0.207301 0.114554 0.079583 lnL0 = -543.717817 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 543.717817 x= 0.33012 0.15981 0.05606 0.08707 0.08327 0.20730 0.11455 0.07958 1 h-lim-p 0.0080 0.6164 36.8893 543.059341 8 0.0011 42 | 0/8 2 h-lim-p 0.0028 0.0224 5.5719 543.035918 6 0.0015 67 | 0/8 3 h-lim-p 0.0041 0.1356 2.0476 543.031456 6 0.0024 95 | 0/8 4 h-lim-p 0.0066 0.3864 0.7442 543.030956 5 0.0021 120 | 0/8 5 h-lim-p 0.0115 2.1102 0.1330 543.030930 3 0.0030 147 | 0/8 6 h-lim-p 0.0073 3.9069 0.0549 543.030924 1 0.0037 169 | 0/8 7 h-lim-p 0.0221 20.0000 0.0091 543.030917 1 0.0276 191 | 0/8 8 h-lim-p 0.0459 20.0000 0.0055 543.030624 0 0.1837 213 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 543.030624 0 1.0938 233 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 543.030624 0 1.0938 253 | 0/8 11 h-lim-p 1.8890 20.0000 0.0000 543.030624 0 1.6529 273 | 0/8 12 h-lim-p 2.1815 20.0000 0.0000 543.030624 0 0.0085 300 | 0/8 13 h-lim-p 0.0019 20.0000 0.0000 543.030624 0 0.0002 322 Out... lnL = -543.030624 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -543.030624 Node 7: lnL = -543.030624 Node 8: lnL = -543.030624 Node 9: lnL = -543.030624 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 226 Sequential format.. Reading seq # 1: YML096W_Sbay Reading seq # 2: YML096W_Scer Reading seq # 3: YML096W_Skud Reading seq # 4: YML096W_Smik Reading seq # 5: YML096W_Spar Sequences read.. Counting patterns.. # site patterns = 96 Counting frequencies.. 120 bytes for distance 15360 bytes for lkl0 12288 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.232198 0.110680 0.064937 0.136418 0.056122 0.170463 0.114962 0.027557 lnL0 = -981.708662 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 981.708662 x= 0.23220 0.11068 0.06494 0.13642 0.05612 0.17046 0.11496 0.02756 1 h-lim-p 0.0007 0.0055 33.3301 981.353439 2 0.0006 26 | 0/8 2 h-lim-p 0.0012 0.0096 16.7855 981.275762 7 0.0007 55 | 0/8 3 h-lim-p 0.0019 0.0768 5.7335 981.267949 6 0.0006 83 | 0/8 4 h-lim-p 0.0045 0.3953 0.7040 981.267745 4 0.0008 104 | 0/8 5 h-lim-p 0.0066 1.7503 0.0901 981.267740 2 0.0011 131 | 0/8 6 h-lim-p 0.0145 20.0000 0.0068 981.267739 1 0.0072 154 | 0/8 7 h-lim-p 0.0076 10.7067 0.0063 981.267592 0 0.0611 177 | 0/8 8 h-lim-p 0.0018 1.0813 0.2161 981.267549 3 0.0013 204 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 981.267545 1 0.9961 226 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 981.267545 0 0.6250 247 | 0/8 11 h-lim-p 0.2368 20.0000 0.0000 981.267545 0 0.0001 277 | 0/8 12 h-lim-p 0.0002 20.0000 0.0000 981.267545 0 0.0000 299 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 981.267545 0 0.0000 328 Out... lnL = -981.267545 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -981.267545 Node 7: lnL = -981.267545 Node 8: lnL = -981.267545 Node 9: lnL = -981.267545 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 226 Sequential format.. Reading seq # 1: YML097C_Sbay Reading seq # 2: YML097C_Scer Reading seq # 3: YML097C_Skud Reading seq # 4: YML097C_Smik Reading seq # 5: YML097C_Spar Sequences read.. Counting patterns.. # site patterns = 91 Counting frequencies.. 120 bytes for distance 14560 bytes for lkl0 11648 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.234280 0.102820 0.061155 0.140967 0.039476 0.183290 0.107378 0.033059 lnL0 = -972.765265 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 972.765265 x= 0.23428 0.10282 0.06116 0.14097 0.03948 0.18329 0.10738 0.03306 1 h-lim-p 0.0008 0.0062 59.8825 972.260376 7 0.0003 35 | 0/8 2 h-lim-p 0.0008 0.0062 22.9598 972.107696 3 0.0006 53 | 0/8 3 h-lim-p 0.0018 0.0442 8.0785 972.090126 6 0.0006 79 | 0/8 4 h-lim-p 0.0028 0.1362 1.8161 972.088773 5 0.0009 104 | 0/8 5 h-lim-p 0.0077 0.7667 0.2047 972.088750 3 0.0010 124 | 0/8 6 h-lim-p 0.0174 14.6156 0.0122 972.088736 2 0.0111 149 | 0/8 7 h-lim-p 0.0036 1.5411 0.0373 972.088375 0 0.0217 171 | 0/8 8 h-lim-p 0.0027 0.2744 0.3041 972.087444 1 0.0033 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 972.087439 1 0.9961 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 972.087439 0 2.1875 235 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 972.087439 0 0.6250 256 | 0/8 12 h-lim-p 0.0933 20.0000 0.0000 972.087439 0 0.0117 278 | 0/8 13 h-lim-p 0.0042 20.0000 0.0000 972.087439 0 0.0021 298 | 0/8 14 h-lim-p 0.0011 20.0000 0.0001 972.087439 0 0.0000 324 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0008 | 0/8 17 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -972.087439 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -972.087439 Node 7: lnL = -972.087439 Node 8: lnL = -972.087439 Node 9: lnL = -972.087439 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 238 Sequential format.. Reading seq # 1: YML098W_Sbay Reading seq # 2: YML098W_Scer Reading seq # 3: YML098W_Skud Reading seq # 4: YML098W_Smik Reading seq # 5: YML098W_Spar Sequences read.. Counting patterns.. # site patterns = 77 Counting frequencies.. 120 bytes for distance 12320 bytes for lkl0 9856 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.137170 0.060413 0.027047 0.066111 0.048397 0.112111 0.134640 0.007034 lnL0 = -861.204249 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 861.204249 x= 0.13717 0.06041 0.02705 0.06611 0.04840 0.11211 0.13464 0.00703 1 h-lim-p 0.0004 0.0033 103.3750 860.268765 7 0.0002 37 | 0/8 2 h-lim-p 0.0004 0.0031 25.0478 860.143312 4 0.0004 57 | 0/8 3 h-lim-p 0.0019 0.0433 5.2660 860.138869 5 0.0003 83 | 0/8 4 h-lim-p 0.0010 0.1180 1.6970 860.138224 2 0.0005 99 | 0/8 5 h-lim-p 0.0021 0.0493 0.4025 860.138186 1 0.0005 114 | 0/8 6 h-lim-p 0.0028 2.9060 0.0738 860.138184 0 0.0007 135 | 0/8 7 h-lim-p 0.0033 6.7542 0.0156 860.138182 1 0.0026 157 | 0/8 8 h-lim-p 0.0136 15.6680 0.0030 860.137455 0 0.2176 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 860.137454 0 1.0938 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 860.137454 0 1.0938 221 | 0/8 11 h-lim-p 0.8695 20.0000 0.0000 860.137454 0 0.0015 249 | 0/8 12 h-lim-p 0.0003 20.0000 0.0001 860.137454 0 0.0000 273 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 860.137454 0 0.0000 294 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 860.137454 0 0.0000 316 | 0/8 15 h-lim-p 0.0000 20.0000 0.0011 860.137454 0 0.0000 348 | 0/8 16 h-lim-p 0.0000 20.0000 0.0011 | 0/8 17 h-lim-p 0.0000 20.0000 0.0011 Out... lnL = -860.137454 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -860.137454 Node 7: lnL = -860.137454 Node 8: lnL = -860.137454 Node 9: lnL = -860.137454 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 238 Sequential format.. Reading seq # 1: YML099C_Sbay Reading seq # 2: YML099C_Scer Reading seq # 3: YML099C_Skud Reading seq # 4: YML099C_Smik Reading seq # 5: YML099C_Spar Sequences read.. Counting patterns.. # site patterns = 74 Counting frequencies.. 120 bytes for distance 11840 bytes for lkl0 9472 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.137784 0.049852 0.032658 0.065922 0.048586 0.103604 0.130155 0.010905 lnL0 = -854.260114 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 854.260114 x= 0.13778 0.04985 0.03266 0.06592 0.04859 0.10360 0.13016 0.01090 1 h-lim-p 0.0008 0.0062 73.5343 853.691143 8 0.0002 44 | 0/8 2 h-lim-p 0.0006 0.0049 16.4499 853.642147 7 0.0004 74 | 0/8 3 h-lim-p 0.0015 0.0419 4.0601 853.638908 6 0.0004 100 | 0/8 4 h-lim-p 0.0010 0.0893 1.7784 853.638298 2 0.0004 116 | 0/8 5 h-lim-p 0.0024 0.0710 0.3353 853.638276 3 0.0004 137 | 0/8 6 h-lim-p 0.0045 1.8751 0.0317 853.638276 1 0.0005 161 | 0/8 7 h-lim-p 0.0031 20.0000 0.0056 853.638275 0 0.0062 182 | 0/8 8 h-lim-p 0.0113 16.3158 0.0031 853.638116 0 0.0902 205 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 853.638113 1 0.9961 227 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 853.638113 0 2.1875 247 | 0/8 11 h-lim-p 2.2034 20.0000 0.0000 853.638113 0 0.4820 268 | 0/8 12 h-lim-p 0.0584 20.0000 0.0002 853.638113 0 0.0009 293 | 0/8 13 h-lim-p 0.0002 20.0000 0.0008 853.638113 0 0.0001 313 | 0/8 14 h-lim-p 0.0001 19.7695 0.0009 853.638113 0 0.0002 334 | 0/8 15 h-lim-p 0.0001 7.4534 0.0024 853.638113 0 0.0000 356 | 0/8 16 h-lim-p 0.0000 20.0000 0.0008 853.638113 0 0.0000 390 | 0/8 17 h-lim-p 0.0000 20.0000 0.0016 | 0/8 18 h-lim-p 0.0000 20.0000 0.0016 Out... lnL = -853.638113 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -853.638113 Node 7: lnL = -853.638113 Node 8: lnL = -853.638113 Node 9: lnL = -853.638113 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 574 Sequential format.. Reading seq # 1: YML101C_Sbay Reading seq # 2: YML101C_Scer Reading seq # 3: YML101C_Skud Reading seq # 4: YML101C_Smik Reading seq # 5: YML101C_Spar Sequences read.. Counting patterns.. # site patterns = 165 Counting frequencies.. 120 bytes for distance 26400 bytes for lkl0 21120 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.392527 0.170267 0.000060 0.080313 0.069968 0.114065 0.011600 0.181117 lnL0 = -1998.555330 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1998.555330 x= 0.39253 0.17027 0.00006 0.08031 0.06997 0.11407 0.01160 0.18112 1 h-lim-p 0.0002 0.0013 175.2185 1995.960643 1 0.0002 24 | 0/8 2 h-lim-p 0.0000 0.0002 103.4767 1995.311103 m 0.0002 36 | 0/8 3 h-lim-p 0.0004 0.0051 55.3760 1994.796904 0 0.0006 48 | 0/8 4 h-lim-p 0.0003 0.0023 87.2114 1994.152611 0 0.0006 61 | 0/8 5 h-lim-p 0.0002 0.0012 10.4086 1994.137802 0 0.0003 74 | 0/8 6 h-lim-p 0.0008 0.0486 3.9671 1994.127682 0 0.0016 87 | 0/8 7 h-lim-p 0.0099 0.1924 0.6408 1994.127464 2 0.0006 106 | 0/8 8 h-lim-p 0.0141 14.9043 0.0276 1994.006090 0 0.4518 131 | 0/8 9 h-lim-p 2.5000 20.0000 0.0015 1994.002221 2 1.1719 155 | 0/8 10 h-lim-p 2.4891 20.0000 0.0007 1994.001918 4 1.3519 184 | 0/8 11 h-lim-p 2.5000 20.0000 0.0001 1994.001914 0 1.0938 204 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1994.001914 0 2.1875 224 | 0/8 13 h-lim-p 2.4171 20.0000 0.0000 1994.001914 0 0.5287 245 | 0/8 14 h-lim-p 0.5670 20.0000 0.0000 1994.001914 0 0.0005 274 Out... lnL = -1994.001914 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1994.001914 Node 7: lnL = -1994.001914 Node 8: lnL = -1994.001914 Node 9: lnL = -1994.001914 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 315 Sequential format.. Reading seq # 1: YML105C_Sbay Reading seq # 2: YML105C_Scer Reading seq # 3: YML105C_Skud Reading seq # 4: YML105C_Smik Reading seq # 5: YML105C_Spar Sequences read.. Counting patterns.. # site patterns = 122 Counting frequencies.. 120 bytes for distance 19520 bytes for lkl0 15616 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.192050 0.128184 0.049528 0.106209 0.102204 0.151397 0.143242 0.000060 lnL0 = -1183.308850 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1183.308850 x= 0.19205 0.12818 0.04953 0.10621 0.10220 0.15140 0.14324 0.00006 1 h-lim-p 0.0000 0.0001 32.2225 1183.190276 m 0.0001 22 | 1/8 2 h-lim-p 0.0003 0.0085 15.5964 1183.134719 0 0.0005 35 | 1/8 3 h-lim-p 0.0022 0.0712 3.8108 1183.129526 5 0.0008 61 | 1/8 4 h-lim-p 0.0058 0.3561 0.4975 1183.129002 5 0.0017 88 | 1/8 5 h-lim-p 0.0023 0.7545 0.3834 1183.126213 0 0.0068 108 | 0/8 6 h-lim-p 0.0026 0.8527 1.0004 1183.084438 0 0.0104 129 | 0/8 7 h-lim-p 0.0010 0.0226 10.8958 1182.972385 0 0.0029 142 | 0/8 8 h-lim-p 0.0057 0.0457 0.7646 1182.958828 m 0.0457 154 | 0/8 9 h-lim-p 0.0000 0.0000 66.8909 h-lim-p: 4.27342368e-21 3.41873895e-20 6.68909146e+01 1182.958828 .. | 0/8 10 h-lim-p 0.0000 0.1088 4.3534 1182.952664 0 0.0006 188 | 0/8 11 h-lim-p 0.0025 0.1715 1.1328 1182.952270 3 0.0007 207 | 0/8 12 h-lim-p 0.0023 0.0228 0.3323 1182.952243 2 0.0005 224 | 0/8 13 h-lim-p 0.0064 0.3563 0.0275 1182.952243 0 0.0007 246 | 0/8 14 h-lim-p 0.0037 20.0000 0.0051 1182.952243 0 0.0016 266 | 0/8 15 h-lim-p 0.0051 9.4017 0.0016 1182.952243 0 0.0026 286 | 0/8 16 h-lim-p 0.0083 20.0000 0.0005 1182.952243 0 0.0661 309 | 0/8 17 h-lim-p 0.0029 20.0000 0.0115 1182.952241 0 0.0058 330 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1182.952241 0 1.0938 350 | 0/8 19 h-lim-p 1.2109 20.0000 0.0000 1182.952241 0 1.0595 370 | 0/8 20 h-lim-p 0.8210 20.0000 0.0000 1182.952241 0 0.0128 395 | 0/8 21 h-lim-p 0.0002 1.2234 0.0019 1182.952241 0 0.0000 426 | 0/8 22 h-lim-p 0.0001 20.0000 0.0000 1182.952241 0 0.0000 451 Out... lnL = -1182.952241 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1182.952241 Node 7: lnL = -1182.952241 Node 8: lnL = -1182.952241 Node 9: lnL = -1182.952241 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 356 Sequential format.. Reading seq # 1: YML106W_Sbay Reading seq # 2: YML106W_Scer Reading seq # 3: YML106W_Skud Reading seq # 4: YML106W_Smik Reading seq # 5: YML106W_Spar Sequences read.. Counting patterns.. # site patterns = 93 Counting frequencies.. 120 bytes for distance 14880 bytes for lkl0 11904 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.182134 0.006791 0.030695 0.037043 0.055382 0.127669 0.081972 0.059504 lnL0 = -1263.257363 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1263.257363 x= 0.18213 0.00679 0.03070 0.03704 0.05538 0.12767 0.08197 0.05950 1 h-lim-p 0.0001 0.0011 130.2323 1262.725721 7 0.0001 38 | 0/8 2 h-lim-p 0.0003 0.0023 22.7774 1262.679891 6 0.0002 65 | 0/8 3 h-lim-p 0.0003 0.0199 12.3217 1262.665494 6 0.0002 92 | 0/8 4 h-lim-p 0.0006 0.0183 5.2722 1262.662926 3 0.0002 110 | 0/8 5 h-lim-p 0.0011 0.0707 1.1182 1262.662815 4 0.0002 134 | 0/8 6 h-lim-p 0.0005 0.2994 0.4025 1262.662795 3 0.0003 153 | 0/8 7 h-lim-p 0.0176 20.0000 0.0063 1262.662794 1 0.0043 176 | 0/8 8 h-lim-p 0.0180 10.8551 0.0015 1262.662563 0 0.1441 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1262.662559 1 0.9961 221 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1262.662559 0 2.1875 241 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1262.662559 0 1.0938 261 | 0/8 12 h-lim-p 0.2953 20.0000 0.0000 1262.662559 0 4.7244 285 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1262.662559 0 0.0098 312 | 0/8 14 h-lim-p 0.0015 20.0000 0.0000 1262.662559 0 0.0002 334 | 0/8 15 h-lim-p 0.0001 20.0000 0.0001 1262.662559 0 0.0000 373 | 0/8 16 h-lim-p 0.0000 20.0000 0.0036 | 0/8 17 h-lim-p 0.0000 20.0000 0.0036 Out... lnL = -1262.662559 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1262.662559 Node 7: lnL = -1262.662559 Node 8: lnL = -1262.662559 Node 9: lnL = -1262.662559 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 351 Sequential format.. Reading seq # 1: YML108W_Sbay Reading seq # 2: YML108W_Scer Reading seq # 3: YML108W_Skud Reading seq # 4: YML108W_Smik Reading seq # 5: YML108W_Spar Sequences read.. Counting patterns.. # site patterns = 139 Counting frequencies.. 120 bytes for distance 22240 bytes for lkl0 17792 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.294594 0.243049 0.083218 0.128397 0.315847 0.283898 0.209318 lnL0 = -1470.475362 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1470.475362 x= 0.00006 0.29459 0.24305 0.08322 0.12840 0.31585 0.28390 0.20932 1 h-lim-p 0.0000 0.0000 191.2071 1470.405009 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0012 244.0543 1452.578053 0 0.0009 40 | 1/8 3 h-lim-p 0.0002 0.0015 70.7400 1451.064252 0 0.0007 54 | 1/8 4 h-lim-p 0.0013 0.0105 28.7850 1450.408141 0 0.0020 66 | 1/8 5 h-lim-p 0.0101 0.0806 4.7265 1450.302221 3 0.0042 84 | 1/8 6 h-lim-p 0.0082 0.0764 2.4296 1449.777503 0 0.0164 97 | 1/8 7 h-lim-p 0.0040 0.0327 9.8446 1445.108473 0 0.0162 111 | 1/8 8 h-lim-p 0.0009 0.0074 41.8088 1439.832587 0 0.0028 124 | 1/8 9 h-lim-p 0.4280 3.4238 0.1083 1438.365015 1 0.5350 138 | 1/8 10 h-lim-p 2.2999 20.0000 0.0252 1438.237499 3 0.5211 164 | 1/8 11 h-lim-p 1.4743 20.0000 0.0089 1438.222873 6 0.5440 197 | 1/8 12 h-lim-p 0.9672 20.0000 0.0050 1438.219488 5 0.5011 228 | 1/8 13 h-lim-p 2.5000 20.0000 0.0010 1438.219296 0 0.5469 248 | 0/8 14 h-lim-p 0.0091 9.1576 0.0596 1438.219294 1 0.0011 271 | 0/8 15 h-lim-p 0.1715 1.3723 0.0001 1438.219289 0 1.0292 293 | 0/8 16 h-lim-p 0.0194 0.1554 0.0001 1438.219289 0 0.0000 329 | 0/8 17 h-lim-p 0.0000 0.0003 0.0627 | 0/8 18 h-lim-p 0.0000 0.0003 0.0627 Out... lnL = -1438.219289 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1438.219289 Node 7: lnL = -1438.219289 Node 8: lnL = -1438.219289 Node 9: lnL = -1438.219289 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 710 Sequential format.. Reading seq # 1: YML109W_Sbay Reading seq # 2: YML109W_Scer Reading seq # 3: YML109W_Skud Reading seq # 4: YML109W_Smik Reading seq # 5: YML109W_Spar Sequences read.. Counting patterns.. # site patterns = 238 Counting frequencies.. 120 bytes for distance 38080 bytes for lkl0 30464 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.079078 0.072372 0.041088 0.109207 0.091422 0.168046 0.193237 0.286414 lnL0 = -3222.549858 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3222.549858 x= 0.07908 0.07237 0.04109 0.10921 0.09142 0.16805 0.19324 0.28641 1 h-lim-p 0.0002 0.0017 164.9039 3220.272513 6 0.0002 33 | 0/8 2 h-lim-p 0.0003 0.0026 57.2944 3219.911039 7 0.0002 61 | 0/8 3 h-lim-p 0.0006 0.0119 24.1918 3219.835441 6 0.0003 86 | 0/8 4 h-lim-p 0.0006 0.0181 12.3890 3219.816291 5 0.0003 109 | 0/8 5 h-lim-p 0.0023 0.2127 1.7308 3219.815753 3 0.0004 130 | 0/8 6 h-lim-p 0.0022 0.6637 0.2860 3219.815739 2 0.0004 149 | 0/8 7 h-lim-p 0.0025 2.9970 0.0416 3219.815738 0 0.0006 170 | 0/8 8 h-lim-p 0.0819 20.0000 0.0003 3219.815545 0 0.9832 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3219.815542 0 1.0938 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3219.815542 0 1.0938 233 | 0/8 11 h-lim-p 0.4262 20.0000 0.0000 3219.815542 0 0.1066 254 | 0/8 12 h-lim-p 0.0342 20.0000 0.0000 3219.815542 0 0.0005 279 | 0/8 13 h-lim-p 0.0005 20.0000 0.0001 3219.815542 0 0.0003 299 | 0/8 14 h-lim-p 0.0002 20.0000 0.0001 3219.815542 0 0.0000 336 | 0/8 15 h-lim-p 0.0000 20.0000 0.0012 3219.815542 0 0.0000 364 | 0/8 16 h-lim-p 0.0000 20.0000 0.0005 3219.815542 0 0.0010 390 | 0/8 17 h-lim-p 0.0034 20.0000 0.0002 3219.815542 0 0.0002 414 | 0/8 18 h-lim-p 0.0004 20.0000 0.0001 3219.815542 0 0.0034 437 | 0/8 19 h-lim-p 0.0074 20.0000 0.0000 3219.815542 0 0.0000 469 | 0/8 20 h-lim-p 0.0000 20.0000 0.0000 3219.815542 0 0.0000 504 | 0/8 21 h-lim-p 0.0000 20.0000 0.0021 | 0/8 22 h-lim-p 0.0000 20.0000 0.0021 Out... lnL = -3219.815542 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3219.815542 Node 7: lnL = -3219.815542 Node 8: lnL = -3219.815542 Node 9: lnL = -3219.815542 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 710 Sequential format.. Reading seq # 1: YML110C_Sbay Reading seq # 2: YML110C_Scer Reading seq # 3: YML110C_Skud Reading seq # 4: YML110C_Smik Reading seq # 5: YML110C_Spar Sequences read.. Counting patterns.. # site patterns = 240 Counting frequencies.. 120 bytes for distance 38400 bytes for lkl0 30720 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.082460 0.065377 0.043273 0.110380 0.094125 0.162711 0.205431 0.292191 lnL0 = -3242.292564 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3242.292564 x= 0.08246 0.06538 0.04327 0.11038 0.09413 0.16271 0.20543 0.29219 1 h-lim-p 0.0003 0.0022 170.7465 3239.842475 8 0.0002 39 | 0/8 2 h-lim-p 0.0004 0.0031 54.3238 3239.487381 5 0.0003 62 | 0/8 3 h-lim-p 0.0006 0.0133 21.9205 3239.418559 4 0.0003 83 | 0/8 4 h-lim-p 0.0006 0.0190 12.2190 3239.400021 5 0.0003 106 | 0/8 5 h-lim-p 0.0021 0.1502 1.9430 3239.399303 3 0.0004 125 | 0/8 6 h-lim-p 0.0020 0.5797 0.3889 3239.399273 1 0.0004 140 | 0/8 7 h-lim-p 0.0015 1.4817 0.1002 3239.399271 1 0.0004 163 | 0/8 8 h-lim-p 0.2646 20.0000 0.0001 3239.399228 0 1.0584 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3239.399227 0 1.0938 205 | 0/8 10 h-lim-p 1.9686 20.0000 0.0000 3239.399227 0 0.8613 225 | 0/8 11 h-lim-p 0.6522 20.0000 0.0000 3239.399227 0 0.0178 249 | 0/8 12 h-lim-p 0.0047 20.0000 0.0001 3239.399227 0 0.0001 274 | 0/8 13 h-lim-p 0.0005 20.0000 0.0000 3239.399227 0 0.0000 309 Out... lnL = -3239.399227 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3239.399227 Node 7: lnL = -3239.399227 Node 8: lnL = -3239.399227 Node 9: lnL = -3239.399227 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 958 Sequential format.. Reading seq # 1: YML111W_Sbay Reading seq # 2: YML111W_Scer Reading seq # 3: YML111W_Skud Reading seq # 4: YML111W_Smik Reading seq # 5: YML111W_Spar Sequences read.. Counting patterns.. # site patterns = 339 Counting frequencies.. 120 bytes for distance 54240 bytes for lkl0 43392 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.039010 0.219675 0.033867 0.110980 0.101640 0.252496 0.258551 0.314289 lnL0 = -4473.115943 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4473.115943 x= 0.03901 0.21967 0.03387 0.11098 0.10164 0.25250 0.25855 0.31429 1 h-lim-p 0.0004 0.0032 162.6111 4470.881676 3 0.0002 29 | 0/8 2 h-lim-p 0.0006 0.0045 37.0431 4470.633583 6 0.0004 54 | 0/8 3 h-lim-p 0.0004 0.0113 32.0404 4470.529588 7 0.0003 85 | 0/8 4 h-lim-p 0.0008 0.0158 12.4897 4470.509112 3 0.0003 104 | 0/8 5 h-lim-p 0.0012 0.0650 3.6320 4470.505942 2 0.0005 120 | 0/8 6 h-lim-p 0.0018 0.2249 1.0896 4470.505633 3 0.0006 140 | 0/8 7 h-lim-p 0.0047 0.9053 0.1336 4470.505625 1 0.0009 155 | 0/8 8 h-lim-p 0.1834 20.0000 0.0007 4470.504483 0 1.4668 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 4470.504434 1 0.9961 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4470.504434 0 1.0938 220 | 0/8 11 h-lim-p 1.3719 20.0000 0.0000 4470.504434 0 1.3719 240 | 0/8 12 h-lim-p 0.3114 20.0000 0.0001 4470.504434 0 0.1557 260 | 0/8 13 h-lim-p 0.0252 20.0000 0.0005 4470.504434 0 0.0126 280 | 0/8 14 h-lim-p 0.0048 20.0000 0.0014 4470.504434 0 0.0000 306 | 0/8 15 h-lim-p 0.0006 20.0000 0.0001 4470.504434 0 0.0000 338 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 4470.504434 0 0.0000 363 Out... lnL = -4470.504434 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4470.504434 Node 7: lnL = -4470.504434 Node 8: lnL = -4470.504434 Node 9: lnL = -4470.504434 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 299 Sequential format.. Reading seq # 1: YML112W_Sbay Reading seq # 2: YML112W_Scer Reading seq # 3: YML112W_Skud Reading seq # 4: YML112W_Smik Reading seq # 5: YML112W_Spar Sequences read.. Counting patterns.. # site patterns = 115 Counting frequencies.. 120 bytes for distance 18400 bytes for lkl0 14720 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.012155 0.065306 0.077899 0.061396 0.082684 0.101315 0.189438 0.169113 lnL0 = -1150.591342 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1150.591342 x= 0.01215 0.06531 0.07790 0.06140 0.08268 0.10132 0.18944 0.16911 1 h-lim-p 0.0011 0.0091 45.9771 1150.142370 5 0.0004 32 | 0/8 2 h-lim-p 0.0024 0.0188 6.1415 1150.129545 7 0.0007 62 | 0/8 3 h-lim-p 0.0030 0.0349 1.3955 1150.129144 4 0.0004 86 | 0/8 4 h-lim-p 0.0011 0.0857 0.5288 1150.129094 3 0.0004 104 | 0/8 5 h-lim-p 0.0020 1.9522 0.1156 1150.129088 0 0.0009 124 | 0/8 6 h-lim-p 0.0017 2.9222 0.0576 1150.129087 0 0.0008 144 | 0/8 7 h-lim-p 0.0174 17.7598 0.0025 1150.129087 0 0.0038 165 | 0/8 8 h-lim-p 0.0252 20.0000 0.0004 1150.129077 0 0.3024 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1150.129077 0 1.0938 208 | 0/8 10 h-lim-p 1.1775 20.0000 0.0000 1150.129077 0 0.5152 228 | 0/8 11 h-lim-p 0.2354 20.0000 0.0000 1150.129077 0 0.0018 254 | 0/8 12 h-lim-p 0.0007 20.0000 0.0001 1150.129077 0 0.0007 274 | 0/8 13 h-lim-p 0.0004 20.0000 0.0002 1150.129077 0 0.0000 297 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 1150.129077 0 0.0000 317 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 1150.129077 0 0.0000 340 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 1150.129077 0 0.0000 370 | 0/8 17 h-lim-p 0.0000 20.0000 0.0008 1150.129077 0 0.0000 396 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 1150.129077 0 0.0000 416 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 1150.129077 0 0.0000 437 | 0/8 20 h-lim-p 0.0000 20.0000 0.0000 1150.129077 0 0.0000 472 | 0/8 21 h-lim-p 0.0000 20.0000 0.0008 | 0/8 22 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -1150.129077 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1150.129077 Node 7: lnL = -1150.129077 Node 8: lnL = -1150.129077 Node 9: lnL = -1150.129077 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 520 Sequential format.. Reading seq # 1: YML113W_Sbay Reading seq # 2: YML113W_Scer Reading seq # 3: YML113W_Skud Reading seq # 4: YML113W_Smik Reading seq # 5: YML113W_Spar Sequences read.. Counting patterns.. # site patterns = 165 Counting frequencies.. 120 bytes for distance 26400 bytes for lkl0 21120 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.026587 0.053060 0.047508 0.092538 0.057478 0.162210 0.161853 0.184514 lnL0 = -2050.624386 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2050.624386 x= 0.02659 0.05306 0.04751 0.09254 0.05748 0.16221 0.16185 0.18451 1 h-lim-p 0.0002 0.0017 108.1735 2049.284670 1 0.0003 24 | 0/8 2 h-lim-p 0.0004 0.0036 26.1117 2049.177339 7 0.0003 52 | 0/8 3 h-lim-p 0.0008 0.0148 11.2817 2049.157899 2 0.0004 68 | 0/8 4 h-lim-p 0.0010 0.0189 3.9567 2049.156733 4 0.0002 91 | 0/8 5 h-lim-p 0.0010 0.2163 0.7090 2049.156664 3 0.0003 111 | 0/8 6 h-lim-p 0.0041 1.1393 0.0499 2049.156660 1 0.0010 134 | 0/8 7 h-lim-p 0.0040 14.1404 0.0127 2049.156333 0 0.0475 157 | 0/8 8 h-lim-p 0.0021 0.3596 0.2871 2049.153750 0 0.0042 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2049.153727 2 0.9961 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2049.153727 0 2.1875 222 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2049.153727 0 1.0938 242 | 0/8 12 h-lim-p 0.2188 20.0000 0.0001 2049.153727 0 0.0068 266 | 0/8 13 h-lim-p 0.0008 20.0000 0.0006 2049.153727 0 0.0008 286 | 0/8 14 h-lim-p 0.0003 20.0000 0.0013 2049.153727 0 0.0000 322 | 0/8 15 h-lim-p 0.0000 20.0000 0.0006 2049.153727 0 0.0000 351 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 2049.153727 0 0.0010 377 | 0/8 17 h-lim-p 0.0024 20.0000 0.0002 2049.153727 0 0.0021 397 | 0/8 18 h-lim-p 0.0008 20.0000 0.0004 2049.153727 0 0.0000 426 | 0/8 19 h-lim-p 0.0000 20.0000 0.0013 2049.153727 0 0.0006 452 | 0/8 20 h-lim-p 0.0073 20.0000 0.0001 2049.153727 0 0.0000 485 | 0/8 21 h-lim-p 0.0000 20.0000 0.0000 2049.153727 0 0.0000 505 | 0/8 22 h-lim-p 0.0000 20.0000 0.0000 2049.153727 0 0.0000 540 Out... lnL = -2049.153727 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2049.153727 Node 7: lnL = -2049.153727 Node 8: lnL = -2049.153727 Node 9: lnL = -2049.153727 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 519 Sequential format.. Reading seq # 1: YML114C_Sbay Reading seq # 2: YML114C_Scer Reading seq # 3: YML114C_Skud Reading seq # 4: YML114C_Smik Reading seq # 5: YML114C_Spar Sequences read.. Counting patterns.. # site patterns = 171 Counting frequencies.. 120 bytes for distance 27360 bytes for lkl0 21888 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.035943 0.057415 0.052088 0.094321 0.058378 0.156477 0.147063 0.197194 lnL0 = -2057.934471 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2057.934471 x= 0.03594 0.05741 0.05209 0.09432 0.05838 0.15648 0.14706 0.19719 1 h-lim-p 0.0003 0.0025 82.4772 2057.038342 7 0.0003 34 | 0/8 2 h-lim-p 0.0007 0.0054 19.3734 2056.978623 5 0.0003 56 | 0/8 3 h-lim-p 0.0007 0.0188 8.6849 2056.969211 4 0.0003 76 | 0/8 4 h-lim-p 0.0009 0.0320 2.8690 2056.968495 2 0.0002 93 | 0/8 5 h-lim-p 0.0010 0.2618 0.5732 2056.968453 3 0.0003 112 | 0/8 6 h-lim-p 0.0026 1.2062 0.0589 2056.968452 0 0.0006 133 | 0/8 7 h-lim-p 0.0084 20.0000 0.0039 2056.968452 0 0.0011 155 | 0/8 8 h-lim-p 0.0285 20.0000 0.0001 2056.968444 0 0.4566 179 | 0/8 9 h-lim-p 2.4294 20.0000 0.0000 2056.968443 0 1.0629 199 | 0/8 10 h-lim-p 1.4318 20.0000 0.0000 2056.968443 0 1.2529 219 | 0/8 11 h-lim-p 0.9347 20.0000 0.0000 2056.968443 0 0.9347 239 | 0/8 12 h-lim-p 0.0001 0.2850 0.2110 2056.968443 0 0.0000 263 | 0/8 13 h-lim-p 0.0001 20.0000 0.0084 2056.968443 0 0.0000 285 | 0/8 14 h-lim-p 0.0001 20.0000 0.0011 2056.968443 0 0.0000 317 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 2056.968443 0 0.0000 352 Out... lnL = -2056.968443 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2056.968443 Node 7: lnL = -2056.968443 Node 8: lnL = -2056.968443 Node 9: lnL = -2056.968443 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 832 Sequential format.. Reading seq # 1: YML119W_Sbay Reading seq # 2: YML119W_Scer Reading seq # 3: YML119W_Skud Reading seq # 4: YML119W_Smik Reading seq # 5: YML119W_Spar Sequences read.. Counting patterns.. # site patterns = 262 Counting frequencies.. 120 bytes for distance 41920 bytes for lkl0 33536 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.031222 0.042133 0.073247 0.131006 0.090930 0.183153 0.191527 0.225020 lnL0 = -3767.451733 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3767.451733 x= 0.03122 0.04213 0.07325 0.13101 0.09093 0.18315 0.19153 0.22502 1 h-lim-p 0.0012 0.0269 253.4959 3763.262636 8 0.0001 41 | 0/8 2 h-lim-p 0.0008 0.0066 40.0966 3762.976529 4 0.0004 60 | 0/8 3 h-lim-p 0.0009 0.0183 16.8406 3762.952001 2 0.0002 77 | 0/8 4 h-lim-p 0.0013 0.0649 2.5976 3762.950898 4 0.0003 98 | 0/8 5 h-lim-p 0.0016 0.3133 0.5502 3762.950852 2 0.0003 115 | 0/8 6 h-lim-p 0.0035 3.2536 0.0500 3762.950852 0 0.0008 136 | 0/8 7 h-lim-p 0.0049 20.0000 0.0079 3762.950844 0 0.0098 157 | 0/8 8 h-lim-p 0.0041 20.0000 0.0190 3762.950019 0 0.0325 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3762.950013 0 1.0938 200 | 0/8 10 h-lim-p 1.9007 20.0000 0.0000 3762.950013 0 0.9503 220 | 0/8 11 h-lim-p 1.0830 20.0000 0.0000 3762.950013 0 0.0169 245 | 0/8 12 h-lim-p 0.0028 20.0000 0.0002 3762.950013 0 0.0002 268 | 0/8 13 h-lim-p 0.0003 20.0000 0.0001 3762.950013 0 0.0000 294 | 0/8 14 h-lim-p 0.0003 20.0000 0.0000 3762.950013 0 0.0000 331 Out... lnL = -3762.950013 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3762.950013 Node 7: lnL = -3762.950013 Node 8: lnL = -3762.950013 Node 9: lnL = -3762.950013 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 832 Sequential format.. Reading seq # 1: YML120C_Sbay Reading seq # 2: YML120C_Scer Reading seq # 3: YML120C_Skud Reading seq # 4: YML120C_Smik Reading seq # 5: YML120C_Spar Sequences read.. Counting patterns.. # site patterns = 259 Counting frequencies.. 120 bytes for distance 41440 bytes for lkl0 33152 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.031679 0.038731 0.064713 0.134602 0.090763 0.191128 0.195616 0.225128 lnL0 = -3766.362659 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3766.362659 x= 0.03168 0.03873 0.06471 0.13460 0.09076 0.19113 0.19562 0.22513 1 h-lim-p 0.0012 0.0175 253.6550 3762.346033 3 0.0001 30 | 0/8 2 h-lim-p 0.0006 0.0049 46.3364 3761.984810 8 0.0003 62 | 0/8 3 h-lim-p 0.0008 0.0153 19.9168 3761.949391 4 0.0002 83 | 0/8 4 h-lim-p 0.0011 0.0413 3.9026 3761.947227 5 0.0003 108 | 0/8 5 h-lim-p 0.0018 0.2799 0.6256 3761.947159 2 0.0004 125 | 0/8 6 h-lim-p 0.0024 1.9245 0.0919 3761.947156 0 0.0005 146 | 0/8 7 h-lim-p 0.0025 18.4611 0.0197 3761.947110 0 0.0099 168 | 0/8 8 h-lim-p 0.0042 20.0000 0.0470 3761.943211 0 0.0332 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 3761.942985 3 1.0004 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3761.942985 0 1.0938 237 | 0/8 11 h-lim-p 1.3100 20.0000 0.0000 3761.942985 0 1.1462 257 | 0/8 12 h-lim-p 0.3660 20.0000 0.0001 3761.942985 0 0.0114 281 | 0/8 13 h-lim-p 0.0014 20.0000 0.0007 3761.942985 0 0.0000 306 | 0/8 14 h-lim-p 0.0004 20.0000 0.0000 3761.942985 0 0.0000 335 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 3761.942985 0 0.0000 355 Out... lnL = -3761.942985 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3761.942985 Node 7: lnL = -3761.942985 Node 8: lnL = -3761.942985 Node 9: lnL = -3761.942985 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 526 Sequential format.. Reading seq # 1: YML121W_Sbay Reading seq # 2: YML121W_Scer Reading seq # 3: YML121W_Skud Reading seq # 4: YML121W_Smik Reading seq # 5: YML121W_Spar Sequences read.. Counting patterns.. # site patterns = 252 Counting frequencies.. 120 bytes for distance 40320 bytes for lkl0 32256 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.170955 0.000060 0.078260 0.165230 0.169968 0.281421 0.379058 0.494847 lnL0 = -2611.531165 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2611.531165 x= 0.17095 0.00006 0.07826 0.16523 0.16997 0.28142 0.37906 0.49485 1 h-lim-p 0.0000 0.0000 41.0709 2611.515376 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0158 25.7072 2611.306274 0 0.0009 40 | 1/8 3 h-lim-p 0.0033 0.0594 7.3060 2611.282717 5 0.0010 65 | 1/8 4 h-lim-p 0.0045 0.4882 1.5799 2611.278941 2 0.0021 81 | 1/8 5 h-lim-p 0.0100 2.8825 0.3325 2611.253015 0 0.0299 94 | 1/8 6 h-lim-p 0.0043 0.1766 2.2934 2611.185646 2 0.0041 117 | 1/8 7 h-lim-p 0.0018 0.1285 5.2236 2610.708718 0 0.0071 131 | 1/8 8 h-lim-p 2.5000 20.0000 0.0068 2610.689280 5 1.0181 154 | 1/8 9 h-lim-p 2.5000 20.0000 0.0006 2610.689115 3 1.0004 179 | 1/8 10 h-lim-p 2.5000 20.0000 0.0000 2610.689114 0 1.0938 198 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 2610.689114 0 1.0938 217 | 1/8 12 h-lim-p 1.2515 20.0000 0.0000 2610.689114 0 1.0951 236 | 1/8 13 h-lim-p 0.5636 20.0000 0.0000 2610.689114 0 0.2466 255 | 1/8 14 h-lim-p 0.0293 20.0000 0.0001 2610.689114 0 0.0009 278 | 1/8 15 h-lim-p 0.0012 20.0000 0.0001 2610.689114 0 0.0000 310 | 1/8 16 h-lim-p 0.0002 20.0000 0.0000 2610.689114 0 0.0000 334 Out... lnL = -2610.689114 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2610.689114 Node 7: lnL = -2610.689114 Node 8: lnL = -2610.689114 Node 9: lnL = -2610.689114 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 246 Sequential format.. Reading seq # 1: YML123C_Sbay Reading seq # 2: YML123C_Scer Reading seq # 3: YML123C_Skud Reading seq # 4: YML123C_Smik Reading seq # 5: YML123C_Spar Sequences read.. Counting patterns.. # site patterns = 109 Counting frequencies.. 120 bytes for distance 17440 bytes for lkl0 13952 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.058212 0.000060 0.098260 0.042166 0.040938 0.317360 0.267562 0.260134 lnL0 = -1053.392390 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1053.392390 x= 0.05821 0.00006 0.09826 0.04217 0.04094 0.31736 0.26756 0.26013 1 h-lim-p 0.0001 0.0008 64.4620 1052.686559 0 0.0004 24 | 0/8 2 h-lim-p 0.0003 0.0022 48.7175 1052.370069 0 0.0006 37 | 0/8 3 h-lim-p 0.0005 0.0043 21.1354 1052.298985 7 0.0004 65 | 0/8 4 h-lim-p 0.0018 0.0323 4.5987 1052.281756 2 0.0017 81 | 0/8 5 h-lim-p 0.0026 0.0205 2.0606 1052.280399 3 0.0007 100 | 0/8 6 h-lim-p 0.0012 1.0498 1.1887 1052.279103 0 0.0017 112 | 0/8 7 h-lim-p 0.0523 1.3231 0.0398 1052.184543 0 0.4181 127 | 0/8 8 h-lim-p 0.0044 0.0801 3.8208 1052.139599 6 0.0035 160 | 0/8 9 h-lim-p 2.5000 20.0000 0.0029 1052.133291 5 1.0583 185 | 0/8 10 h-lim-p 2.5000 20.0000 0.0003 1052.133180 2 0.9961 209 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1052.133179 0 1.0938 229 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1052.133179 0 1.0938 249 | 0/8 13 h-lim-p 1.3013 20.0000 0.0000 1052.133179 0 1.1386 269 | 0/8 14 h-lim-p 0.9422 20.0000 0.0000 1052.133179 0 0.0018 297 | 0/8 15 h-lim-p 0.0000 8.2905 0.0094 1052.133179 0 0.0000 324 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 1052.133179 0 0.0000 353 Out... lnL = -1052.133179 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1052.133179 Node 7: lnL = -1052.133179 Node 8: lnL = -1052.133179 Node 9: lnL = -1052.133179 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 406 Sequential format.. Reading seq # 1: YML125C_Sbay Reading seq # 2: YML125C_Scer Reading seq # 3: YML125C_Skud Reading seq # 4: YML125C_Smik Reading seq # 5: YML125C_Spar Sequences read.. Counting patterns.. # site patterns = 162 Counting frequencies.. 120 bytes for distance 25920 bytes for lkl0 20736 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.063983 0.066811 0.062262 0.131165 0.079593 0.174541 0.126924 0.258169 lnL0 = -1615.840009 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1615.840009 x= 0.06398 0.06681 0.06226 0.13117 0.07959 0.17454 0.12692 0.25817 1 h-lim-p 0.0034 0.0354 97.4193 1613.839373 7 0.0005 39 | 0/8 2 h-lim-p 0.0008 0.0061 31.0138 1613.498922 4 0.0008 59 | 0/8 3 h-lim-p 0.0013 0.0103 15.8709 1613.454480 7 0.0004 91 | 0/8 4 h-lim-p 0.0027 0.0681 2.5914 1613.452029 5 0.0008 116 | 0/8 5 h-lim-p 0.0053 0.5487 0.3688 1613.451962 3 0.0010 135 | 0/8 6 h-lim-p 0.0073 3.6242 0.0505 1613.451959 1 0.0015 158 | 0/8 7 h-lim-p 0.0198 20.0000 0.0037 1613.451354 0 0.3170 182 | 0/8 8 h-lim-p 0.0025 0.7878 0.4660 1613.450505 3 0.0025 208 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1613.450481 2 0.9961 232 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1613.450481 0 1.0938 252 | 0/8 11 h-lim-p 1.6527 20.0000 0.0000 1613.450481 0 1.4461 272 | 0/8 12 h-lim-p 1.5568 20.0000 0.0000 1613.450481 0 1.3622 292 | 0/8 13 h-lim-p 0.3444 20.0000 0.0000 1613.450481 0 0.0054 317 | 0/8 14 h-lim-p 0.0011 20.0000 0.0001 1613.450481 0 0.0008 337 | 0/8 15 h-lim-p 0.0004 20.0000 0.0002 1613.450481 0 0.0000 371 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1613.450481 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1613.450481 Node 7: lnL = -1613.450481 Node 8: lnL = -1613.450481 Node 9: lnL = -1613.450481 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 398 Sequential format.. Reading seq # 1: YML127W_Sbay Reading seq # 2: YML127W_Scer Reading seq # 3: YML127W_Skud Reading seq # 4: YML127W_Smik Reading seq # 5: YML127W_Spar Sequences read.. Counting patterns.. # site patterns = 109 Counting frequencies.. 120 bytes for distance 17440 bytes for lkl0 13952 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.001141 0.583661 0.000060 0.286445 0.361031 0.265644 0.811102 0.377311 lnL0 = -1509.621121 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1509.621121 x= 0.00114 0.58366 0.00006 0.28645 0.36103 0.26564 0.81110 0.37731 1 h-lim-p 0.0000 0.0000 419.2687 1509.482283 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0000 78330.9709 1507.217335 m 0.0000 34 | 2/8 3 h-lim-p 0.0000 0.0028 194.7262 1385.971519 m 0.0028 50 | 1/8 4 h-lim-p 0.0000 0.0000 444.6955 h-lim-p: 3.76126317e-21 3.00901054e-20 4.44695485e+02 1385.971519 .. | 1/8 5 h-lim-p 0.0000 0.0006 542.4390 1352.775527 1 0.0004 77 | 1/8 6 h-lim-p 0.0001 0.0006 258.8611 1337.545838 0 0.0004 91 | 1/8 7 h-lim-p 0.0001 0.0009 197.8841 1334.719435 0 0.0002 104 | 1/8 8 h-lim-p 0.0002 0.0013 226.5436 1321.837797 0 0.0010 118 | 1/8 9 h-lim-p 0.0000 0.0003 484.3433 1310.161621 m 0.0003 130 | 2/8 10 h-lim-p 0.0000 0.0000 69699.9634 1309.134880 8 0.0000 162 | 2/8 11 h-lim-p 0.0026 0.0205 5.7611 1308.729562 0 0.0051 175 | 2/8 12 h-lim-p 0.0556 1.2629 0.5300 1291.425200 10 0.7435 216 | 1/8 13 h-lim-p 0.0022 0.0177 26.1962 1291.074845 8 0.0016 251 | 1/8 14 h-lim-p 0.1360 1.0881 0.2515 1286.866169 0 0.5440 265 | 1/8 15 h-lim-p 0.6350 5.0803 0.0569 1286.557354 6 0.5335 297 | 1/8 16 h-lim-p 0.6894 5.5150 0.0189 1286.514203 6 0.4088 331 | 1/8 17 h-lim-p 1.0128 20.0000 0.0076 1286.504748 0 1.5191 350 | 1/8 18 h-lim-p 2.0768 20.0000 0.0056 1286.473518 217.0379 376 | 1/8 19 h-lim-p 0.4823 3.8587 0.0703 1286.383699 m 3.8587 395 | 1/8 20 h-lim-p 0.0000 0.0000 0.5658 h-lim-p: 1.12616321e-18 9.00930570e-18 5.65839335e-01 1286.383699 .. | 1/8 21 h-lim-p 0.0000 0.0142 3.9971 1286.382023 0 0.0002 433 | 1/8 22 h-lim-p 0.0004 0.0586 2.6701 1286.381426 4 0.0002 456 | 1/8 23 h-lim-p 0.0005 0.0712 1.1712 1286.381267 3 0.0003 477 | 1/8 24 h-lim-p 0.0006 0.4886 0.5591 1286.381206 2 0.0005 493 | 1/8 25 h-lim-p 0.0012 0.0096 0.2053 1286.381165 0 0.0024 513 | 1/8 26 h-lim-p 0.0009 0.0075 0.0614 1286.381162 0 0.0019 533 | 1/8 27 h-lim-p 0.0004 0.0032 0.1179 1286.381148 m 0.0032 552 | 2/8 28 h-lim-p 0.0718 20.0000 0.0037 1286.381145 1 0.0286 573 | 2/8 29 h-lim-p 0.7690 20.0000 0.0001 1286.381123 0 1.5380 592 | 2/8 30 h-lim-p 2.5000 20.0000 0.0001 1286.381117 1 1.2305 613 | 2/8 31 h-lim-p 2.5000 20.0000 0.0000 1286.381117 0 1.0938 631 | 2/8 32 h-lim-p 2.5000 20.0000 0.0000 1286.381117 0 0.5469 650 | 2/8 33 h-lim-p 1.2002 20.0000 0.0000 1286.381117 0 0.0006 678 Out... lnL = -1286.381117 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1286.381117 Node 7: lnL = -1286.381117 Node 8: lnL = -1286.381117 Node 9: lnL = -1286.381117 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 474 Sequential format.. Reading seq # 1: YML129C_Sbay Reading seq # 2: YML129C_Scer Reading seq # 3: YML129C_Skud Reading seq # 4: YML129C_Smik Reading seq # 5: YML129C_Spar Sequences read.. Counting patterns.. # site patterns = 227 Counting frequencies.. 120 bytes for distance 36320 bytes for lkl0 29056 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.016195 0.070247 0.070959 0.145491 0.094740 0.269148 0.277943 0.246020 lnL0 = -2085.212572 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2085.212572 x= 0.01620 0.07025 0.07096 0.14549 0.09474 0.26915 0.27794 0.24602 1 h-lim-p 0.0031 0.9905 115.4914 2082.846242 8 0.0004 42 | 0/8 2 h-lim-p 0.0008 0.0060 14.9057 2082.773811 5 0.0007 63 | 0/8 3 h-lim-p 0.0013 0.0107 7.7151 2082.753487 5 0.0008 86 | 0/8 4 h-lim-p 0.0020 0.1280 3.1532 2082.750049 3 0.0009 104 | 0/8 5 h-lim-p 0.0080 0.2108 0.3351 2082.749991 2 0.0011 122 | 0/8 6 h-lim-p 0.0050 3.5821 0.0709 2082.749986 2 0.0016 148 | 0/8 7 h-lim-p 0.0054 5.6697 0.0217 2082.749978 1 0.0067 170 | 0/8 8 h-lim-p 0.0224 20.0000 0.0065 2082.748847 0 0.1795 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2082.748846 0 1.0938 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2082.748846 0 1.0938 233 | 0/8 11 h-lim-p 1.2662 20.0000 0.0000 2082.748846 0 1.8993 253 | 0/8 12 h-lim-p 0.7361 20.0000 0.0000 2082.748846 0 0.0403 276 | 0/8 13 h-lim-p 0.0005 8.5323 0.0033 2082.748846 0 0.0000 309 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 2082.748846 0 0.0000 336 Out... lnL = -2082.748846 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2082.748846 Node 7: lnL = -2082.748846 Node 8: lnL = -2082.748846 Node 9: lnL = -2082.748846 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 911 Sequential format.. Reading seq # 1: YML130C_Sbay Reading seq # 2: YML130C_Scer Reading seq # 3: YML130C_Skud Reading seq # 4: YML130C_Smik Reading seq # 5: YML130C_Spar Sequences read.. Counting patterns.. # site patterns = 422 Counting frequencies.. 120 bytes for distance 67520 bytes for lkl0 54016 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.027051 0.145466 0.245441 0.115121 0.870458 0.276540 0.381630 lnL0 = -4672.949847 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4672.949847 x= 0.00006 0.02705 0.14547 0.24544 0.11512 0.87046 0.27654 0.38163 1 h-lim-p 0.0007 0.0058 69.9282 4671.785995 7 0.0005 39 | 0/8 2 h-lim-p 0.0000 0.0001 46.4426 4671.683463 m 0.0001 51 | 1/8 3 h-lim-p 0.0001 0.0076 33.7001 4671.502052 0 0.0005 65 | 1/8 4 h-lim-p 0.0008 0.0091 23.6302 4671.398292 3 0.0006 83 | 1/8 5 h-lim-p 0.0056 0.1927 2.7266 4671.391344 5 0.0017 109 | 1/8 6 h-lim-p 0.0020 0.6923 2.4046 4671.383364 0 0.0039 122 | 1/8 7 h-lim-p 0.0072 0.3215 1.3119 4671.379718 4 0.0027 142 | 1/8 8 h-lim-p 0.0262 1.8711 0.1351 4671.131296 0 0.2099 157 | 1/8 9 h-lim-p 0.1493 1.1946 0.1376 4670.941446 7 0.0835 194 | 0/8 10 h-lim-p 0.0414 2.7611 0.2775 4670.941382 3 0.0014 223 | 0/8 11 h-lim-p 0.0688 15.8376 0.0056 4670.934558 0 0.8251 246 | 0/8 12 h-lim-p 2.5000 20.0000 0.0004 4670.934519 1 0.9961 268 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 4670.934519 0 1.0938 288 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 4670.934519 0 1.0938 308 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 4670.934519 0 1.2500 328 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 4670.934519 0 0.0000 369 Out... lnL = -4670.934519 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4670.934519 Node 7: lnL = -4670.934519 Node 8: lnL = -4670.934519 Node 9: lnL = -4670.934519 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 852 Sequential format.. Reading seq # 1: YML131W_Sbay Reading seq # 2: YML131W_Scer Reading seq # 3: YML131W_Skud Reading seq # 4: YML131W_Smik Reading seq # 5: YML131W_Spar Sequences read.. Counting patterns.. # site patterns = 408 Counting frequencies.. 120 bytes for distance 65280 bytes for lkl0 52224 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.143548 0.000060 0.306170 0.207517 0.206885 0.234359 0.428331 0.518105 lnL0 = -4512.841159 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4512.841159 x= 0.14355 0.00006 0.30617 0.20752 0.20688 0.23436 0.42833 0.51811 1 h-lim-p 0.0000 0.0000 123.8451 4512.816893 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0084 71.1352 4510.989940 0 0.0010 40 | 1/8 3 h-lim-p 0.0065 0.0521 9.8258 4510.932213 7 0.0011 72 | 1/8 4 h-lim-p 0.0031 0.1773 3.4393 4510.905607 5 0.0023 96 | 1/8 5 h-lim-p 0.0111 0.5981 0.7068 4509.638007 0 0.0890 111 | 1/8 6 h-lim-p 0.0024 0.0209 26.5833 4505.692940 0 0.0047 131 | 1/8 7 h-lim-p 0.0050 0.0397 10.2390 4505.630609 2 0.0012 148 | 1/8 8 h-lim-p 1.2018 20.0000 0.0099 4505.600223 5 0.8057 172 | 1/8 9 h-lim-p 2.5000 20.0000 0.0008 4505.599962 4 0.7731 203 | 1/8 10 h-lim-p 2.5000 20.0000 0.0001 4505.599959 1 0.9961 224 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 4505.599959 0 1.0938 243 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 4505.599959 0 1.0938 262 | 1/8 13 h-lim-p 0.8134 20.0000 0.0000 4505.599959 0 0.2033 282 | 1/8 14 h-lim-p 0.0878 20.0000 0.0000 4505.599959 0 0.0048 304 | 1/8 15 h-lim-p 0.0019 20.0000 0.0000 4505.599959 0 0.0000 330 | 1/8 16 h-lim-p 0.0003 20.0000 0.0000 4505.599959 0 0.0000 354 Out... lnL = -4505.599959 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4505.599959 Node 7: lnL = -4505.599959 Node 8: lnL = -4505.599959 Node 9: lnL = -4505.599959 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 841 Sequential format.. Reading seq # 1: YMR001C_Sbay Reading seq # 2: YMR001C_Scer Reading seq # 3: YMR001C_Skud Reading seq # 4: YMR001C_Smik Reading seq # 5: YMR001C_Spar Sequences read.. Counting patterns.. # site patterns = 263 Counting frequencies.. 120 bytes for distance 42080 bytes for lkl0 33664 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.025100 0.084535 0.039326 0.120581 0.061915 0.136990 0.168965 0.186507 lnL0 = -3551.063705 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3551.063705 x= 0.02510 0.08454 0.03933 0.12058 0.06192 0.13699 0.16897 0.18651 1 h-lim-p 0.0002 0.0019 250.5063 3547.264157 8 0.0001 41 | 0/8 2 h-lim-p 0.0002 0.0017 67.0540 3546.859776 5 0.0002 63 | 0/8 3 h-lim-p 0.0004 0.0067 29.0642 3546.810765 6 0.0001 90 | 0/8 4 h-lim-p 0.0004 0.0098 9.0633 3546.800912 5 0.0003 117 | 0/8 5 h-lim-p 0.0014 0.1351 1.6917 3546.800476 2 0.0003 134 | 0/8 6 h-lim-p 0.0034 1.7169 0.1569 3546.800473 1 0.0002 151 | 0/8 7 h-lim-p 0.0254 20.0000 0.0013 3546.800465 0 0.0508 172 | 0/8 8 h-lim-p 0.0013 3.1948 0.0492 3546.800285 0 0.0080 194 | 0/8 9 h-lim-p 0.7171 20.0000 0.0005 3546.800277 0 1.0756 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 3546.800277 0 1.0938 234 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3546.800277 0 2.1875 254 | 0/8 12 h-lim-p 0.7493 20.0000 0.0000 3546.800277 0 0.7493 274 | 0/8 13 h-lim-p 0.3846 20.0000 0.0001 3546.800277 0 0.1923 294 | 0/8 14 h-lim-p 0.0563 20.0000 0.0002 3546.800277 0 0.0035 317 | 0/8 15 h-lim-p 0.0013 20.0000 0.0005 3546.800277 0 0.0001 340 | 0/8 16 h-lim-p 0.0005 20.0000 0.0001 3546.800277 0 0.0000 369 | 0/8 17 h-lim-p 0.0001 20.0000 0.0000 3546.800277 0 0.0000 399 Out... lnL = -3546.800277 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3546.800277 Node 7: lnL = -3546.800277 Node 8: lnL = -3546.800277 Node 9: lnL = -3546.800277 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 868 Sequential format.. Reading seq # 1: YMR002W_Sbay Reading seq # 2: YMR002W_Scer Reading seq # 3: YMR002W_Skud Reading seq # 4: YMR002W_Smik Reading seq # 5: YMR002W_Spar Sequences read.. Counting patterns.. # site patterns = 326 Counting frequencies.. 120 bytes for distance 52160 bytes for lkl0 41728 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.179395 0.119434 0.063194 0.124782 0.096427 0.192109 0.180522 0.452678 lnL0 = -4136.189191 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4136.189191 x= 0.17940 0.11943 0.06319 0.12478 0.09643 0.19211 0.18052 0.45268 1 h-lim-p 0.0002 0.0016 113.2889 4134.700402 1 0.0002 24 | 0/8 2 h-lim-p 0.0007 0.0055 20.0041 4134.641584 4 0.0003 43 | 0/8 3 h-lim-p 0.0007 0.0688 8.2503 4134.627798 5 0.0005 67 | 0/8 4 h-lim-p 0.0004 0.0304 9.2980 4134.620640 5 0.0003 89 | 0/8 5 h-lim-p 0.0008 0.0537 3.6977 4134.618861 2 0.0004 105 | 0/8 6 h-lim-p 0.0085 1.3152 0.1611 4134.618853 1 0.0005 122 | 0/8 7 h-lim-p 0.0063 20.0000 0.0133 4134.618797 0 0.0253 144 | 0/8 8 h-lim-p 0.0126 5.6143 0.0267 4134.617138 0 0.0504 166 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 4134.616928 2 0.9961 190 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4134.616928 0 1.0938 210 | 0/8 11 h-lim-p 0.9870 20.0000 0.0000 4134.616928 0 0.4318 230 | 0/8 12 h-lim-p 0.2723 20.0000 0.0000 4134.616928 0 0.0170 253 | 0/8 13 h-lim-p 0.0094 20.0000 0.0000 4134.616928 0 0.0047 273 | 0/8 14 h-lim-p 0.0035 20.0000 0.0000 4134.616928 0 0.0000 316 | 0/8 15 h-lim-p 0.0000 20.0000 0.0014 4134.616928 0 0.0000 343 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 4134.616928 0 0.0000 363 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 4134.616928 0 0.0000 387 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0014 | 0/8 20 h-lim-p 0.0000 20.0000 0.0014 Out... lnL = -4134.616928 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4134.616928 Node 7: lnL = -4134.616928 Node 8: lnL = -4134.616928 Node 9: lnL = -4134.616928 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 475 Sequential format.. Reading seq # 1: YMR003W_Sbay Reading seq # 2: YMR003W_Scer Reading seq # 3: YMR003W_Skud Reading seq # 4: YMR003W_Smik Reading seq # 5: YMR003W_Spar Sequences read.. Counting patterns.. # site patterns = 195 Counting frequencies.. 120 bytes for distance 31200 bytes for lkl0 24960 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.027401 0.085108 0.046079 0.109320 0.092402 0.187943 0.204715 0.215884 lnL0 = -2096.653416 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2096.653416 x= 0.02740 0.08511 0.04608 0.10932 0.09240 0.18794 0.20472 0.21588 1 h-lim-p 0.0045 0.0359 72.3832 2095.817601 6 0.0003 39 | 0/8 2 h-lim-p 0.0004 0.0031 28.2418 2095.640265 0 0.0006 51 | 0/8 3 h-lim-p 0.0018 0.0193 8.8958 2095.625170 2 0.0004 68 | 0/8 4 h-lim-p 0.0011 0.0439 3.3280 2095.623182 5 0.0004 93 | 0/8 5 h-lim-p 0.0027 0.4740 0.5165 2095.623083 4 0.0008 115 | 0/8 6 h-lim-p 0.0032 2.0368 0.1222 2095.623074 1 0.0008 138 | 0/8 7 h-lim-p 0.0019 1.5894 0.0504 2095.623052 0 0.0038 159 | 0/8 8 h-lim-p 0.0112 20.0000 0.0171 2095.619660 0 0.0896 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 2095.619619 2 0.9961 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2095.619619 0 1.0938 226 | 0/8 11 h-lim-p 1.1877 20.0000 0.0000 2095.619619 0 2.3755 247 | 0/8 12 h-lim-p 0.5397 20.0000 0.0001 2095.619619 0 0.5397 267 | 0/8 13 h-lim-p 0.0352 20.0000 0.0012 2095.619619 0 0.0308 287 | 0/8 14 h-lim-p 0.0104 13.5649 0.0037 2095.619619 0 0.0013 309 | 0/8 15 h-lim-p 0.0004 3.8112 0.0130 2095.619619 0 0.0001 330 | 0/8 16 h-lim-p 0.0002 9.9849 0.0050 2095.619619 0 0.0001 350 | 0/8 17 h-lim-p 0.0002 13.5850 0.0037 2095.619619 0 0.0000 383 | 0/8 18 h-lim-p 0.0001 20.0000 0.0000 2095.619619 0 0.0000 416 Out... lnL = -2095.619619 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2095.619619 Node 7: lnL = -2095.619619 Node 8: lnL = -2095.619619 Node 9: lnL = -2095.619619 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 338 Sequential format.. Reading seq # 1: YMR004W_Sbay Reading seq # 2: YMR004W_Scer Reading seq # 3: YMR004W_Skud Reading seq # 4: YMR004W_Smik Reading seq # 5: YMR004W_Spar Sequences read.. Counting patterns.. # site patterns = 123 Counting frequencies.. 120 bytes for distance 19680 bytes for lkl0 15744 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.009618 0.081965 0.046405 0.052406 0.059580 0.205600 0.156443 0.162420 lnL0 = -1302.991757 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1302.991757 x= 0.00962 0.08196 0.04640 0.05241 0.05958 0.20560 0.15644 0.16242 1 h-lim-p 0.0196 3.2250 36.4274 1302.817701 6 0.0003 38 | 0/8 2 h-lim-p 0.0012 0.0151 8.2450 1302.805561 6 0.0004 65 | 0/8 3 h-lim-p 0.0006 0.0445 4.9901 1302.799969 2 0.0006 81 | 0/8 4 h-lim-p 0.0051 0.0596 0.5648 1302.799865 3 0.0007 101 | 0/8 5 h-lim-p 0.0011 0.5035 0.3398 1302.799843 2 0.0005 125 | 0/8 6 h-lim-p 0.0025 3.3281 0.0649 1302.799842 0 0.0006 146 | 0/8 7 h-lim-p 0.0029 7.6157 0.0123 1302.799842 0 0.0006 167 | 0/8 8 h-lim-p 0.0865 20.0000 0.0001 1302.799838 0 1.0385 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1302.799838 0 1.0938 210 | 0/8 10 h-lim-p 1.1215 20.0000 0.0000 1302.799838 0 1.1215 230 | 0/8 11 h-lim-p 0.2785 20.0000 0.0001 1302.799838 0 0.0087 254 | 0/8 12 h-lim-p 0.0018 20.0000 0.0005 1302.799838 0 0.0000 280 | 0/8 13 h-lim-p 0.0000 1.9738 0.0070 1302.799838 0 0.0000 300 | 0/8 14 h-lim-p 0.0000 4.7708 0.0029 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1302.799838 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1302.799838 Node 7: lnL = -1302.799838 Node 8: lnL = -1302.799838 Node 9: lnL = -1302.799838 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 722 Sequential format.. Reading seq # 1: YMR005W_Sbay Reading seq # 2: YMR005W_Scer Reading seq # 3: YMR005W_Skud Reading seq # 4: YMR005W_Smik Reading seq # 5: YMR005W_Spar Sequences read.. Counting patterns.. # site patterns = 270 Counting frequencies.. 120 bytes for distance 43200 bytes for lkl0 34560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.045824 0.063738 0.099211 0.153827 0.139458 0.247807 0.252874 0.297598 lnL0 = -3028.203567 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3028.203567 x= 0.04582 0.06374 0.09921 0.15383 0.13946 0.24781 0.25287 0.29760 1 h-lim-p 0.0032 0.0311 137.1510 3025.157954 3 0.0004 30 | 0/8 2 h-lim-p 0.0009 0.0073 20.3062 3025.018765 7 0.0007 58 | 0/8 3 h-lim-p 0.0018 0.0242 7.5108 3025.005637 6 0.0005 85 | 0/8 4 h-lim-p 0.0021 0.1516 1.8983 3025.004035 2 0.0010 101 | 0/8 5 h-lim-p 0.0045 0.5179 0.4066 3025.003982 3 0.0007 123 | 0/8 6 h-lim-p 0.0100 19.1730 0.0270 3025.003979 1 0.0025 146 | 0/8 7 h-lim-p 0.0054 20.0000 0.0124 3025.003954 0 0.0161 167 | 0/8 8 h-lim-p 0.0048 20.0000 0.0414 3025.003127 0 0.0193 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3025.003104 1 0.9961 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3025.003104 0 1.0938 231 | 0/8 11 h-lim-p 1.2398 20.0000 0.0000 3025.003104 0 2.4796 252 | 0/8 12 h-lim-p 0.2602 20.0000 0.0001 3025.003104 0 0.2277 272 | 0/8 13 h-lim-p 0.0406 20.0000 0.0008 3025.003104 0 0.0051 294 | 0/8 14 h-lim-p 0.0012 20.0000 0.0031 3025.003104 0 0.0006 314 | 0/8 15 h-lim-p 0.0011 20.0000 0.0018 3025.003104 0 0.0000 349 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 3025.003104 0 0.0000 376 Out... lnL = -3025.003104 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3025.003104 Node 7: lnL = -3025.003104 Node 8: lnL = -3025.003104 Node 9: lnL = -3025.003104 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 294 Sequential format.. Reading seq # 1: YMR006C_Sbay Reading seq # 2: YMR006C_Scer Reading seq # 3: YMR006C_Skud Reading seq # 4: YMR006C_Smik Reading seq # 5: YMR006C_Spar Sequences read.. Counting patterns.. # site patterns = 134 Counting frequencies.. 120 bytes for distance 21440 bytes for lkl0 17152 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.060307 0.121006 0.029740 0.123569 0.110044 0.198607 0.197886 0.268251 lnL0 = -1379.191557 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1379.191557 x= 0.06031 0.12101 0.02974 0.12357 0.11004 0.19861 0.19789 0.26825 1 h-lim-p 0.0013 0.0101 81.2179 1378.029591 9 0.0004 45 | 0/8 2 h-lim-p 0.0010 0.0080 21.7386 1377.830414 5 0.0009 66 | 0/8 3 h-lim-p 0.0033 0.0655 5.8769 1377.814836 7 0.0010 97 | 0/8 4 h-lim-p 0.0022 0.1026 2.5504 1377.812271 3 0.0009 115 | 0/8 5 h-lim-p 0.0044 0.4185 0.5466 1377.812124 2 0.0010 132 | 0/8 6 h-lim-p 0.0050 2.4024 0.1129 1377.812115 2 0.0013 157 | 0/8 7 h-lim-p 0.0682 20.0000 0.0022 1377.812110 1 0.0544 179 | 0/8 8 h-lim-p 0.0090 5.1360 0.0130 1377.812003 0 0.0271 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1377.812000 0 1.0938 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1377.812000 0 1.0938 240 | 0/8 11 h-lim-p 1.2894 20.0000 0.0000 1377.812000 0 0.0025 268 | 0/8 12 h-lim-p 0.0008 20.0000 0.0000 1377.812000 0 0.0004 288 | 0/8 13 h-lim-p 0.0001 20.0000 0.0001 1377.812000 0 0.0000 323 | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 1377.812000 0 0.0000 349 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 1377.812000 0 0.0000 370 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 1377.812000 0 0.0000 403 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 | 0/8 18 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1377.812000 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1377.812000 Node 7: lnL = -1377.812000 Node 8: lnL = -1377.812000 Node 9: lnL = -1377.812000 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 853 Sequential format.. Reading seq # 1: YMR009W_Sbay Reading seq # 2: YMR009W_Scer Reading seq # 3: YMR009W_Skud Reading seq # 4: YMR009W_Smik Reading seq # 5: YMR009W_Spar Sequences read.. Counting patterns.. # site patterns = 381 Counting frequencies.. 120 bytes for distance 60960 bytes for lkl0 48768 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.052349 0.218269 0.072717 0.120181 0.145206 0.224424 0.405527 0.358147 lnL0 = -4249.371390 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4249.371390 x= 0.05235 0.21827 0.07272 0.12018 0.14521 0.22442 0.40553 0.35815 1 h-lim-p 0.0005 0.0037 107.4819 4247.484933 8 0.0003 39 | 0/8 2 h-lim-p 0.0007 0.0052 42.2031 4247.160627 6 0.0004 67 | 0/8 3 h-lim-p 0.0007 0.0101 24.2870 4247.077862 5 0.0004 90 | 0/8 4 h-lim-p 0.0014 0.0353 6.4708 4247.069349 5 0.0005 114 | 0/8 5 h-lim-p 0.0016 0.0709 1.7848 4247.067883 5 0.0010 141 | 0/8 6 h-lim-p 0.0021 0.5660 0.8592 4247.067527 4 0.0012 164 | 0/8 7 h-lim-p 0.0116 5.9728 0.0862 4247.067523 0 0.0013 186 | 0/8 8 h-lim-p 0.4993 20.0000 0.0002 4247.067479 0 0.9986 207 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4247.067479 0 1.0938 227 | 0/8 10 h-lim-p 1.6360 20.0000 0.0000 4247.067479 0 1.4315 247 | 0/8 11 h-lim-p 1.8207 20.0000 0.0000 4247.067479 0 1.5932 267 | 0/8 12 h-lim-p 0.8279 20.0000 0.0000 4247.067479 0 0.8279 287 | 0/8 13 h-lim-p 0.0061 20.0000 0.0027 4247.067479 0 0.0031 307 | 0/8 14 h-lim-p 0.0009 8.7816 0.0096 4247.067479 0 0.0000 339 | 0/8 15 h-lim-p 0.0005 20.0000 0.0000 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 4247.067479 0 0.0000 399 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 4247.067479 0 0.0000 425 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 4247.067479 0 0.0000 450 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 4247.067479 0 0.0000 478 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 4247.067479 0 0.0000 502 | 0/8 21 h-lim-p 0.0000 20.0000 0.0004 4247.067479 0 0.0000 527 | 0/8 22 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 23 h-lim-p 0.0000 20.0000 0.0003 | 0/8 24 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -4247.067479 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4247.067479 Node 7: lnL = -4247.067479 Node 8: lnL = -4247.067479 Node 9: lnL = -4247.067479 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 499 Sequential format.. Reading seq # 1: YMR010W_Sbay Reading seq # 2: YMR010W_Scer Reading seq # 3: YMR010W_Skud Reading seq # 4: YMR010W_Smik Reading seq # 5: YMR010W_Spar Sequences read.. Counting patterns.. # site patterns = 133 Counting frequencies.. 120 bytes for distance 21280 bytes for lkl0 17024 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.029370 0.029201 0.043704 0.066261 0.022282 0.113876 0.103255 0.130224 lnL0 = -1710.026247 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1710.026247 x= 0.02937 0.02920 0.04370 0.06626 0.02228 0.11388 0.10325 0.13022 1 h-lim-p 0.0001 0.0006 163.5020 1708.773132 0 0.0002 23 | 0/8 2 h-lim-p 0.0005 0.0039 55.9145 1708.690840 5 0.0001 47 | 0/8 3 h-lim-p 0.0001 0.0029 23.2942 1708.643407 0 0.0002 59 | 0/8 4 h-lim-p 0.0007 0.0219 7.4793 1708.637440 4 0.0002 80 | 0/8 5 h-lim-p 0.0035 0.4753 0.5114 1708.637343 3 0.0005 100 | 0/8 6 h-lim-p 0.0018 0.6094 0.1371 1708.636912 0 0.0035 121 | 0/8 7 h-lim-p 0.0011 0.1694 0.4229 1708.631277 0 0.0046 143 | 0/8 8 h-lim-p 0.0012 0.0348 1.6711 1708.540066 0 0.0046 165 | 0/8 9 h-lim-p 2.5000 20.0000 0.0019 1708.532231 6 0.9225 191 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1708.532228 0 1.0938 211 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1708.532228 0 1.0938 231 | 0/8 12 h-lim-p 0.8884 20.0000 0.0000 1708.532228 0 0.0004 261 | 0/8 13 h-lim-p 0.0002 20.0000 0.0001 1708.532228 0 0.0000 295 | 0/8 14 h-lim-p 0.0000 20.0000 0.0008 1708.532228 0 0.0006 321 | 0/8 15 h-lim-p 0.0010 20.0000 0.0005 1708.532228 0 0.0000 352 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 1708.532228 0 0.0051 381 | 0/8 17 h-lim-p 0.0183 20.0000 0.0001 1708.532228 0 0.0000 411 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 1708.532228 0 0.0000 438 | 0/8 19 h-lim-p 0.0000 20.0000 0.0018 1708.532228 0 0.0001 461 | 0/8 20 h-lim-p 0.0021 20.0000 0.0001 1708.532228 0 0.0019 481 | 0/8 21 h-lim-p 0.0026 20.0000 0.0001 1708.532228 0 0.0000 508 | 0/8 22 h-lim-p 0.0000 20.0000 0.0021 1708.532228 0 0.0001 531 | 0/8 23 h-lim-p 0.1296 20.0000 0.0000 1708.532228 0 0.0041 555 | 0/8 24 h-lim-p 0.0041 20.0000 0.0000 1708.532228 0 0.0000 581 Out... lnL = -1708.532228 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1708.532228 Node 7: lnL = -1708.532228 Node 8: lnL = -1708.532228 Node 9: lnL = -1708.532228 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 841 Sequential format.. Reading seq # 1: YMR011W_Sbay Reading seq # 2: YMR011W_Scer Reading seq # 3: YMR011W_Skud Reading seq # 4: YMR011W_Smik Reading seq # 5: YMR011W_Spar Sequences read.. Counting patterns.. # site patterns = 236 Counting frequencies.. 120 bytes for distance 37760 bytes for lkl0 30208 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.050693 0.041269 0.047982 0.068038 0.069849 0.133248 0.168212 0.194300 lnL0 = -3378.309587 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3378.309587 x= 0.05069 0.04127 0.04798 0.06804 0.06985 0.13325 0.16821 0.19430 1 h-lim-p 0.0017 0.0136 192.5861 3376.529437 4 0.0001 33 | 0/8 2 h-lim-p 0.0007 0.0055 24.4900 3376.479290 5 0.0002 56 | 0/8 3 h-lim-p 0.0005 0.0465 8.0044 3376.474866 5 0.0002 80 | 0/8 4 h-lim-p 0.0004 0.0508 3.3328 3376.474031 3 0.0002 99 | 0/8 5 h-lim-p 0.0010 0.3495 0.6001 3376.473973 2 0.0003 116 | 0/8 6 h-lim-p 0.0027 1.7643 0.0708 3376.473973 0 0.0003 138 | 0/8 7 h-lim-p 0.0008 5.9762 0.0262 3376.473973 0 0.0007 158 | 0/8 8 h-lim-p 0.0341 20.0000 0.0005 3376.473645 0 0.5460 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3376.473644 0 1.0938 202 | 0/8 10 h-lim-p 1.0286 20.0000 0.0000 3376.473644 0 1.0286 222 | 0/8 11 h-lim-p 1.0410 20.0000 0.0000 3376.473644 0 4.1641 244 | 0/8 12 h-lim-p 0.0091 5.6650 0.0141 3376.473644 0 0.0046 264 | 0/8 13 h-lim-p 0.0018 2.2811 0.0350 3376.473644 0 0.0002 286 | 0/8 14 h-lim-p 0.0005 18.2903 0.0155 3376.473644 0 0.0000 327 | 0/8 15 h-lim-p 0.0000 20.0000 0.0012 3376.473644 0 0.0000 347 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 3376.473644 0 0.0000 381 | 0/8 17 h-lim-p 0.0000 20.0000 0.0011 3376.473644 0 0.0001 404 | 0/8 18 h-lim-p 0.0003 20.0000 0.0004 3376.473644 0 0.0000 430 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 3376.473644 0 0.0051 459 | 0/8 20 h-lim-p 0.0110 20.0000 0.0001 3376.473644 0 0.0000 488 | 0/8 21 h-lim-p 0.0000 20.0000 0.0001 3376.473644 0 0.0000 508 | 0/8 22 h-lim-p 0.0000 20.0000 0.0005 .. | 0/8 23 h-lim-p 0.0000 20.0000 0.0045 3376.473644 0 0.0000 571 | 0/8 24 h-lim-p 0.0000 20.0000 0.0012 3376.473644 0 0.0003 596 | 0/8 25 h-lim-p 0.0007 20.0000 0.0005 3376.473644 0 0.0006 616 | 0/8 26 h-lim-p 0.0017 20.0000 0.0002 3376.473644 0 0.0000 642 | 0/8 27 h-lim-p 0.0000 20.0000 0.0001 3376.473644 0 0.0000 662 | 0/8 28 h-lim-p 0.0000 20.0000 0.0005 3376.473644 0 0.0000 684 | 0/8 29 h-lim-p 0.0000 6.7272 0.0118 3376.473644 0 0.0002 708 | 0/8 30 h-lim-p 0.0005 20.0000 0.0035 3376.473644 0 0.0000 732 | 0/8 31 h-lim-p 0.0076 20.0000 0.0000 3376.473644 0 0.0002 757 Out... lnL = -3376.473644 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3376.473644 Node 7: lnL = -3376.473644 Node 8: lnL = -3376.473644 Node 9: lnL = -3376.473644 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 859 Sequential format.. Reading seq # 1: YMR012W_Sbay Reading seq # 2: YMR012W_Scer Reading seq # 3: YMR012W_Skud Reading seq # 4: YMR012W_Smik Reading seq # 5: YMR012W_Spar Sequences read.. Counting patterns.. # site patterns = 295 Counting frequencies.. 120 bytes for distance 47200 bytes for lkl0 37760 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.075016 0.045568 0.000060 0.342390 0.278878 0.145946 0.418596 0.325768 lnL0 = -3824.187735 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3824.187735 x= 0.07502 0.04557 0.00006 0.34239 0.27888 0.14595 0.41860 0.32577 1 h-lim-p 0.0000 0.0000 202.9785 3824.158985 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0071 73.0751 3821.075775 0 0.0013 41 | 1/8 3 h-lim-p 0.0031 0.0245 26.3443 3820.702790 5 0.0012 63 | 1/8 4 h-lim-p 0.0039 0.0543 8.2718 3820.635513 2 0.0018 79 | 1/8 5 h-lim-p 0.0062 0.0500 2.0897 3820.593258 5 0.0049 102 | 1/8 6 h-lim-p 0.0041 0.1067 2.5010 3820.256252 0 0.0165 116 | 1/8 7 h-lim-p 0.0017 0.0138 12.9255 3815.516702 m 0.0138 128 | 1/8 8 h-lim-p 1.5831 12.6651 0.0373 3815.216565 2 0.7421 144 | 1/8 9 h-lim-p 0.8661 6.9284 0.0054 3815.212188 3 0.7849 169 | 1/8 10 h-lim-p 2.5000 20.0000 0.0008 3815.212048 3 0.8855 196 | 1/8 11 h-lim-p 2.5000 20.0000 0.0002 3815.212039 0 1.0938 215 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 3815.212038 0 1.0938 234 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 3815.212038 0 1.0938 253 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 3815.212038 0 1.0938 272 | 1/8 15 h-lim-p 0.7808 20.0000 0.0000 3815.212038 0 1.5616 292 | 1/8 16 h-lim-p 2.3261 20.0000 0.0000 3815.212038 0 0.0000 328 Out... lnL = -3815.212038 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3815.212038 Node 7: lnL = -3815.212038 Node 8: lnL = -3815.212038 Node 9: lnL = -3815.212038 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 857 Sequential format.. Reading seq # 1: YMR013C_Sbay Reading seq # 2: YMR013C_Scer Reading seq # 3: YMR013C_Skud Reading seq # 4: YMR013C_Smik Reading seq # 5: YMR013C_Spar Sequences read.. Counting patterns.. # site patterns = 180 Counting frequencies.. 120 bytes for distance 28800 bytes for lkl0 23040 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.053550 0.000060 0.500875 0.377649 0.391071 0.474282 0.468217 0.380760 lnL0 = -3369.814712 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3369.814712 x= 0.05355 0.00006 0.50088 0.37765 0.39107 0.47428 0.46822 0.38076 1 h-lim-p 0.0000 0.0000 957.3800 3369.550441 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0001 1555.4102 3262.715923 m 0.0001 35 | 2/8 3 h-lim-p 0.0006 0.0044 150.7432 3208.705052 0 0.0022 49 | 2/8 4 h-lim-p 0.0002 0.0019 223.5517 3146.141316 m 0.0019 61 | 3/8 5 h-lim-p 0.0000 0.0002 4442.8036 3096.829929 0 0.0001 75 | 3/8 6 h-lim-p 0.0209 0.1673 8.5671 3095.363976 0 0.0418 88 | 2/8 7 h-lim-p 0.0033 0.0268 56.0689 3095.022476 8 0.0002 119 | 2/8 8 h-lim-p 0.0002 0.0096 61.4425 3094.394104 0 0.0025 134 | 2/8 9 h-lim-p 0.0703 0.5627 0.5655 3094.092177 1 0.0879 148 | 2/8 10 h-lim-p 0.9752 7.8014 0.0167 .. | 2/8 11 h-lim-p 0.0000 0.0004 486.0273 3042.278934 1 0.0004 221 | 2/8 12 h-lim-p 0.0000 0.0002 1276.8522 2974.096412 0 0.0002 235 | 2/8 13 h-lim-p 0.0000 0.0003 1285.6056 2919.776429 0 0.0002 249 | 2/8 14 h-lim-p 0.0001 0.0008 308.6883 2915.681581 0 0.0002 262 | 2/8 15 h-lim-p 0.0005 0.0042 54.9450 2915.347157 7 0.0002 290 | 2/8 16 h-lim-p 0.0320 0.7626 0.3823 2894.065695 0 0.2558 305 | 1/8 17 h-lim-p 0.0003 0.0021 201.6827 2889.890413 7 0.0003 340 | 1/8 18 h-lim-p 0.0603 3.3391 0.9645 2885.164035 0 1.4475 356 | 1/8 19 h-lim-p 0.6153 4.9224 0.4963 2884.220144 0 2.4612 377 | 1/8 20 h-lim-p 1.1891 9.5129 0.0978 2883.682749 3 1.0776 402 | 0/8 21 h-lim-p 0.0141 0.1132 7.1089 2883.681391 4 0.0013 433 | 0/8 22 h-lim-p 0.0246 3.3711 0.3747 2883.637872 0 0.3937 449 | 0/8 23 h-lim-p 0.0810 0.6480 0.0871 2883.472695 m 0.6480 469 | 1/8 24 h-lim-p 0.0000 0.0002 238.8923 2883.360241 m 0.0002 489 | 1/8 25 h-lim-p -0.0000 -0.0000 1.1943 h-lim-p: -1.51076141e-19 -1.20860913e-18 1.19434210e+00 2883.360241 .. | 1/8 26 h-lim-p 0.0000 0.0099 28.7127 2883.285470 0 0.0002 513 | 1/8 27 h-lim-p 0.0000 0.0000 18.5598 2883.276257 m 0.0000 525 | 2/8 28 h-lim-p 0.0000 0.0137 22.6287 2883.270388 0 0.0001 539 | 2/8 29 h-lim-p 0.0034 0.3253 0.5887 2883.270325 1 0.0004 555 | 2/8 30 h-lim-p 0.0006 3.3409 0.3593 2883.270179 0 0.0024 575 | 2/8 31 h-lim-p 0.0003 0.3306 3.4926 2883.263951 0 0.0160 599 | 2/8 32 h-lim-p 0.0013 0.0258 42.6747 2883.262094 3 0.0003 619 | 2/8 33 h-lim-p 1.0999 20.0000 0.0123 2883.261146 3 1.1628 637 | 2/8 34 h-lim-p 2.5000 20.0000 0.0014 2883.261004 3 1.4660 664 | 2/8 35 h-lim-p 2.5000 20.0000 0.0001 2883.261003 0 1.0938 682 | 2/8 36 h-lim-p 2.5000 20.0000 0.0000 2883.261003 0 1.0938 700 | 2/8 37 h-lim-p 2.5000 20.0000 0.0000 2883.261003 0 2.1875 718 | 2/8 38 h-lim-p 1.8424 20.0000 0.0000 2883.261003 0 0.4606 737 | 2/8 39 h-lim-p 0.8546 20.0000 0.0000 2883.261003 0 0.0000 770 Out... lnL = -2883.261003 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2883.261003 Node 7: lnL = -2883.261003 Node 8: lnL = -2883.261003 Node 9: lnL = -2883.261003 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 519 Sequential format.. Reading seq # 1: YMR014W_Sbay Reading seq # 2: YMR014W_Scer Reading seq # 3: YMR014W_Skud Reading seq # 4: YMR014W_Smik Reading seq # 5: YMR014W_Spar Sequences read.. Counting patterns.. # site patterns = 165 Counting frequencies.. 120 bytes for distance 26400 bytes for lkl0 21120 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.017611 0.040495 0.052319 0.077280 0.058829 0.121255 0.145229 0.140447 lnL0 = -1974.093454 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1974.093454 x= 0.01761 0.04050 0.05232 0.07728 0.05883 0.12126 0.14523 0.14045 1 h-lim-p 0.0015 0.8716 160.6012 1972.184593 7 0.0002 39 | 0/8 2 h-lim-p 0.0010 0.0081 10.7969 1972.170338 2 0.0002 56 | 0/8 3 h-lim-p 0.0005 0.0293 5.5721 1972.165912 4 0.0003 76 | 0/8 4 h-lim-p 0.0034 0.1948 0.5766 1972.165864 3 0.0003 98 | 0/8 5 h-lim-p 0.0021 1.2614 0.0808 1972.165863 1 0.0003 122 | 0/8 6 h-lim-p 0.0025 12.5385 0.0084 1972.165863 0 0.0011 142 | 0/8 7 h-lim-p 0.0020 20.0000 0.0045 1972.165863 0 0.0041 163 | 0/8 8 h-lim-p 0.0033 20.0000 0.0055 1972.165802 0 0.0266 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1972.165799 0 1.0938 206 | 0/8 10 h-lim-p 1.8274 20.0000 0.0000 1972.165799 0 1.5990 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1972.165799 0 1.0938 246 | 0/8 12 h-lim-p 0.5252 20.0000 0.0000 1972.165799 0 0.0985 268 | 0/8 13 h-lim-p 0.0000 0.3708 0.0884 1972.165799 0 0.0000 302 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 1972.165799 0 0.0000 333 Out... lnL = -1972.165799 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1972.165799 Node 7: lnL = -1972.165799 Node 8: lnL = -1972.165799 Node 9: lnL = -1972.165799 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 776 Sequential format.. Reading seq # 1: YMR015C_Sbay Reading seq # 2: YMR015C_Scer Reading seq # 3: YMR015C_Skud Reading seq # 4: YMR015C_Smik Reading seq # 5: YMR015C_Spar Sequences read.. Counting patterns.. # site patterns = 213 Counting frequencies.. 120 bytes for distance 34080 bytes for lkl0 27264 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.041090 0.047446 0.050304 0.062652 0.048878 0.097916 0.134476 0.163009 lnL0 = -2880.382295 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2880.382295 x= 0.04109 0.04745 0.05030 0.06265 0.04888 0.09792 0.13448 0.16301 1 h-lim-p 0.0005 0.0041 164.8644 2878.887678 3 0.0001 29 | 0/8 2 h-lim-p 0.0006 0.0050 23.4208 2878.845634 4 0.0002 50 | 0/8 3 h-lim-p 0.0004 0.0211 8.5708 2878.840811 5 0.0001 74 | 0/8 4 h-lim-p 0.0002 0.0286 5.3035 2878.839368 5 0.0001 98 | 0/8 5 h-lim-p 0.0008 0.1668 0.9832 2878.839276 3 0.0002 117 | 0/8 6 h-lim-p 0.0009 0.3937 0.2114 2878.839273 1 0.0001 141 | 0/8 7 h-lim-p 0.0020 5.7395 0.0122 2878.839273 0 0.0009 161 | 0/8 8 h-lim-p 0.0137 20.0000 0.0008 2878.839054 0 0.4371 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2878.839040 1 0.9961 208 | 0/8 10 h-lim-p 1.9409 20.0000 0.0000 2878.839040 0 0.8491 228 | 0/8 11 h-lim-p 0.3410 20.0000 0.0001 2878.839040 0 0.0000 273 | 0/8 12 h-lim-p 0.0000 20.0000 0.0005 | 0/8 13 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -2878.839040 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2878.839040 Node 7: lnL = -2878.839040 Node 8: lnL = -2878.839040 Node 9: lnL = -2878.839040 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 874 Sequential format.. Reading seq # 1: YMR016C_Sbay Reading seq # 2: YMR016C_Scer Reading seq # 3: YMR016C_Skud Reading seq # 4: YMR016C_Smik Reading seq # 5: YMR016C_Spar Sequences read.. Counting patterns.. # site patterns = 207 Counting frequencies.. 120 bytes for distance 33120 bytes for lkl0 26496 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.039914 0.034359 0.047906 0.061106 0.039852 0.092155 0.124338 0.145668 lnL0 = -3100.039135 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3100.039135 x= 0.03991 0.03436 0.04791 0.06111 0.03985 0.09215 0.12434 0.14567 1 h-lim-p 0.0001 0.0009 185.4503 3098.650914 7 0.0001 36 | 0/8 2 h-lim-p 0.0009 0.0073 14.7034 3098.637173 6 0.0001 64 | 0/8 3 h-lim-p 0.0004 0.0327 5.1549 3098.634976 4 0.0002 86 | 0/8 4 h-lim-p 0.0006 0.2569 1.5669 3098.634895 2 0.0001 104 | 0/8 5 h-lim-p 0.0003 0.2457 0.3797 3098.634885 1 0.0001 119 | 0/8 6 h-lim-p 0.0012 1.9959 0.0470 3098.634885 0 0.0001 141 | 0/8 7 h-lim-p 0.0022 20.0000 0.0028 3098.634885 0 0.0011 161 | 0/8 8 h-lim-p 0.0054 20.0000 0.0006 3098.634862 0 0.1716 186 | 0/8 9 h-lim-p 0.7982 20.0000 0.0001 3098.634862 0 1.1973 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3098.634862 0 1.0938 226 | 0/8 11 h-lim-p 0.5103 20.0000 0.0000 3098.634862 0 2.0412 248 | 0/8 12 h-lim-p 0.0309 19.9570 0.0030 3098.634862 0 0.0270 268 | 0/8 13 h-lim-p 0.0080 5.8818 0.0101 3098.634862 0 0.0000 311 | 0/8 14 h-lim-p 0.0000 20.0000 0.0015 | 0/8 15 h-lim-p 0.0000 20.0000 0.0015 Out... lnL = -3098.634862 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3098.634862 Node 7: lnL = -3098.634862 Node 8: lnL = -3098.634862 Node 9: lnL = -3098.634862 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 918 Sequential format.. Reading seq # 1: YMR017W_Sbay Reading seq # 2: YMR017W_Scer Reading seq # 3: YMR017W_Skud Reading seq # 4: YMR017W_Smik Reading seq # 5: YMR017W_Spar Sequences read.. Counting patterns.. # site patterns = 327 Counting frequencies.. 120 bytes for distance 52320 bytes for lkl0 41856 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.018688 0.155066 0.095251 0.146083 0.096962 0.235261 0.232710 0.246954 lnL0 = -4259.145286 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4259.145286 x= 0.01869 0.15507 0.09525 0.14608 0.09696 0.23526 0.23271 0.24695 1 h-lim-p 0.0003 0.0022 113.6959 4257.069119 1 0.0003 24 | 0/8 2 h-lim-p 0.0004 0.0029 28.4426 4256.898249 0 0.0006 36 | 0/8 3 h-lim-p 0.0014 0.0411 11.3172 4256.883123 5 0.0003 60 | 0/8 4 h-lim-p 0.0006 0.0415 5.1124 4256.880318 2 0.0003 76 | 0/8 5 h-lim-p 0.0020 0.3634 0.6678 4256.880188 3 0.0006 96 | 0/8 6 h-lim-p 0.0019 1.6035 0.2144 4256.880174 1 0.0005 119 | 0/8 7 h-lim-p 0.0035 8.1632 0.0280 4256.879998 0 0.0141 141 | 0/8 8 h-lim-p 0.0039 3.2252 0.1001 4256.873542 0 0.0315 164 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 4256.873139 3 1.0004 190 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4256.873139 0 1.0938 210 | 0/8 11 h-lim-p 1.0779 20.0000 0.0000 4256.873139 0 0.9432 230 | 0/8 12 h-lim-p 0.1327 20.0000 0.0002 4256.873139 0 0.0083 253 | 0/8 13 h-lim-p 0.0024 20.0000 0.0009 4256.873139 0 0.0000 281 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 4256.873139 0 0.0000 303 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 4256.873139 0 0.0000 332 Out... lnL = -4256.873139 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4256.873139 Node 7: lnL = -4256.873139 Node 8: lnL = -4256.873139 Node 9: lnL = -4256.873139 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 869 Sequential format.. Reading seq # 1: YMR018W_Sbay Reading seq # 2: YMR018W_Scer Reading seq # 3: YMR018W_Skud Reading seq # 4: YMR018W_Smik Reading seq # 5: YMR018W_Spar Sequences read.. Counting patterns.. # site patterns = 393 Counting frequencies.. 120 bytes for distance 62880 bytes for lkl0 50304 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.094490 0.063514 0.091388 0.167846 0.181417 0.248266 0.300193 0.362400 lnL0 = -4441.749641 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4441.749641 x= 0.09449 0.06351 0.09139 0.16785 0.18142 0.24827 0.30019 0.36240 1 h-lim-p 0.0057 1.1009 125.0493 4439.680913 4 0.0003 33 | 0/8 2 h-lim-p 0.0017 0.0133 19.9599 4439.581106 7 0.0005 64 | 0/8 3 h-lim-p 0.0010 0.0385 10.1087 4439.552603 6 0.0007 91 | 0/8 4 h-lim-p 0.0017 0.0917 3.9272 4439.548825 5 0.0006 115 | 0/8 5 h-lim-p 0.0048 0.4580 0.4813 4439.548760 0 0.0006 129 | 0/8 6 h-lim-p 0.0037 4.5537 0.0787 4439.548756 1 0.0009 152 | 0/8 7 h-lim-p 0.0312 20.0000 0.0023 4439.548504 0 0.2493 175 | 0/8 8 h-lim-p 0.0020 1.7855 0.2896 4439.547797 0 0.0029 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4439.547792 0 1.0938 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4439.547792 0 1.0938 235 | 0/8 11 h-lim-p 1.3896 20.0000 0.0000 4439.547792 0 1.3896 255 | 0/8 12 h-lim-p 1.1240 20.0000 0.0000 4439.547792 0 0.1229 277 | 0/8 13 h-lim-p 0.0036 20.0000 0.0005 4439.547792 0 0.0008 298 | 0/8 14 h-lim-p 0.0004 20.0000 0.0011 4439.547792 0 0.0000 334 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 | 0/8 16 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -4439.547792 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4439.547792 Node 7: lnL = -4439.547792 Node 8: lnL = -4439.547792 Node 9: lnL = -4439.547792 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 597 Sequential format.. Reading seq # 1: YMR019W_Sbay Reading seq # 2: YMR019W_Scer Reading seq # 3: YMR019W_Skud Reading seq # 4: YMR019W_Smik Reading seq # 5: YMR019W_Spar Sequences read.. Counting patterns.. # site patterns = 302 Counting frequencies.. 120 bytes for distance 48320 bytes for lkl0 38656 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.218540 0.000060 0.242445 0.223517 0.244363 0.326835 0.545650 0.586215 lnL0 = -2960.520876 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2960.520876 x= 0.21854 0.00006 0.24244 0.22352 0.24436 0.32684 0.54565 0.58622 1 h-lim-p 0.0000 0.0000 123.8393 2960.493155 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0181 62.8917 2956.645474 0 0.0026 42 | 1/8 3 h-lim-p 0.0023 0.0186 30.0296 2955.612060 1 0.0029 56 | 1/8 4 h-lim-p 0.0060 0.0482 11.0422 2955.393442 7 0.0035 85 | 1/8 5 h-lim-p 0.0080 0.1620 4.8771 2955.226284 4 0.0079 105 | 1/8 6 h-lim-p 0.0334 0.4794 1.1555 2953.064254 0 0.1001 118 | 1/8 7 h-lim-p 0.0033 0.0262 13.7963 2948.569194 0 0.0098 131 | 1/8 8 h-lim-p 0.9662 7.7295 0.0758 2947.918036 8 0.7145 163 | 0/8 9 h-lim-p 0.0393 1.7180 1.3792 2947.916877 3 0.0012 193 | 0/8 10 h-lim-p 0.0684 0.5471 0.0120 2947.897737 m 0.5471 205 | 1/8 11 h-lim-p 1.7052 20.0000 0.0037 2947.896268 4 0.6467 233 | 1/8 12 h-lim-p 2.5000 20.0000 0.0005 2947.896220 2 0.8246 258 | 1/8 13 h-lim-p 2.5000 20.0000 0.0001 2947.896217 1 0.6152 280 | 1/8 14 h-lim-p 2.1707 20.0000 0.0000 2947.896217 0 0.9497 299 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 2947.896217 0 1.0938 318 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 2947.896217 0 1.0938 337 | 1/8 17 h-lim-p 1.9334 20.0000 0.0000 2947.896217 0 0.3625 358 | 1/8 18 h-lim-p 0.1939 20.0000 0.0000 2947.896217 0 0.0242 379 | 1/8 19 h-lim-p 0.0122 20.0000 0.0000 2947.896217 0 0.0002 403 Out... lnL = -2947.896217 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2947.896217 Node 7: lnL = -2947.896217 Node 8: lnL = -2947.896217 Node 9: lnL = -2947.896217 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 355 Sequential format.. Reading seq # 1: YMR021C_Sbay Reading seq # 2: YMR021C_Scer Reading seq # 3: YMR021C_Skud Reading seq # 4: YMR021C_Smik Reading seq # 5: YMR021C_Spar Sequences read.. Counting patterns.. # site patterns = 85 Counting frequencies.. 120 bytes for distance 13600 bytes for lkl0 10880 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.578051 0.630630 0.107105 3.258569 0.284953 0.650697 0.633071 lnL0 = -1312.391381 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1312.391381 x= 0.00006 0.57805 0.63063 0.10711 3.25857 0.28495 0.65070 0.63307 1 h-lim-p 0.0000 0.0000 248.7965 1312.324345 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0018 170.9092 1276.709261 m 0.0018 39 | 2/8 3 h-lim-p 0.0005 0.0044 161.7734 1250.355987 m 0.0044 51 | 3/8 4 h-lim-p 0.0020 0.0163 33.3636 1243.311943 0 0.0061 64 | 3/8 5 h-lim-p 0.0034 0.0270 8.1820 .. | 2/8 6 h-lim-p 0.0000 0.0024 118.2999 1223.353080 m 0.0024 115 | 2/8 7 h-lim-p 0.0007 0.0054 186.4581 1149.934849 0 0.0041 129 | 2/8 8 h-lim-p 0.0000 0.0002 1345.8225 1142.785354 0 0.0001 143 | 2/8 9 h-lim-p 0.0010 0.0078 40.6010 1141.900899 0 0.0015 155 | 1/8 10 h-lim-p 0.0002 0.0013 362.2846 1131.995423 0 0.0005 168 | 1/8 11 h-lim-p 0.0002 0.0018 87.7628 1129.565754 0 0.0009 182 | 1/8 12 h-lim-p 0.1082 0.8659 0.1904 1121.455032 0 0.6495 196 | 0/8 13 h-lim-p 0.0050 1.3599 24.7471 1121.212022 6 0.0008 229 | 0/8 14 h-lim-p 0.1505 1.2937 0.1352 1120.706482 0 0.2258 241 | 0/8 15 h-lim-p 0.8189 6.5514 0.0203 1120.253037 0 1.6379 262 | 0/8 16 h-lim-p 2.5000 20.0000 0.0065 1120.223111 2 1.1719 286 | 0/8 17 h-lim-p 2.5000 20.0000 0.0018 1120.221574 4 0.8779 316 | 0/8 18 h-lim-p 2.5000 20.0000 0.0001 1120.221566 1 1.0938 338 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1120.221566 0 1.0938 358 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 1120.221566 0 1.0938 378 | 0/8 21 h-lim-p 2.5000 20.0000 0.0000 1120.221566 0 5.0000 399 | 0/8 22 h-lim-p 2.3867 20.0000 0.0000 1120.221566 0 0.5967 420 | 0/8 23 h-lim-p 0.7734 20.0000 0.0000 1120.221566 0 0.0000 464 Out... lnL = -1120.221566 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1120.221566 Node 7: lnL = -1120.221566 Node 8: lnL = -1120.221566 Node 9: lnL = -1120.221566 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 269 Sequential format.. Reading seq # 1: YMR022W_Sbay Reading seq # 2: YMR022W_Scer Reading seq # 3: YMR022W_Skud Reading seq # 4: YMR022W_Smik Reading seq # 5: YMR022W_Spar Sequences read.. Counting patterns.. # site patterns = 130 Counting frequencies.. 120 bytes for distance 20800 bytes for lkl0 16640 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.040552 0.053057 0.109327 0.862430 0.149201 0.126795 0.228611 lnL0 = -1162.514083 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1162.514083 x= 0.00006 0.04055 0.05306 0.10933 0.86243 0.14920 0.12680 0.22861 1 h-lim-p 0.0000 0.0000 89.9014 1162.480723 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0041 32.2973 1162.090712 0 0.0007 40 | 1/8 3 h-lim-p 0.0015 0.0170 15.6106 1161.998628 6 0.0009 67 | 1/8 4 h-lim-p 0.0022 0.0235 6.5850 1161.981815 5 0.0009 89 | 1/8 5 h-lim-p 0.0012 0.0419 4.5677 1161.915346 0 0.0100 104 | 1/8 6 h-lim-p 0.0147 0.1536 3.1115 1161.901976 6 0.0025 132 | 1/8 7 h-lim-p 0.0016 0.0972 4.8920 1161.776550 0 0.0130 147 | 1/8 8 h-lim-p 0.3297 5.0941 0.1925 1160.281230 0 0.4945 159 | 0/8 9 h-lim-p 0.0495 2.8081 1.9235 1160.279048 3 0.0012 188 | 0/8 10 h-lim-p 0.0640 14.4304 0.0353 1160.235134 0 1.0232 204 | 0/8 11 h-lim-p 2.5000 20.0000 0.0040 1160.233884 2 1.1719 228 | 0/8 12 h-lim-p 2.5000 20.0000 0.0002 1160.233856 3 1.3437 255 | 0/8 13 h-lim-p 2.5000 20.0000 0.0001 1160.233855 0 1.2500 275 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1160.233855 0 1.0938 295 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1160.233855 0 1.0938 315 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1160.233855 0 5.0000 336 | 0/8 17 h-lim-p 1.6765 20.0000 0.0000 1160.233855 0 0.1834 358 | 0/8 18 h-lim-p 0.1974 20.0000 0.0000 1160.233855 0 0.0247 380 | 0/8 19 h-lim-p 0.0209 20.0000 0.0000 1160.233855 0 0.0052 401 Out... lnL = -1160.233855 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1160.233855 Node 7: lnL = -1160.233855 Node 8: lnL = -1160.233855 Node 9: lnL = -1160.233855 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 468 Sequential format.. Reading seq # 1: YMR026C_Sbay Reading seq # 2: YMR026C_Scer Reading seq # 3: YMR026C_Skud Reading seq # 4: YMR026C_Smik Reading seq # 5: YMR026C_Spar Sequences read.. Counting patterns.. # site patterns = 223 Counting frequencies.. 120 bytes for distance 35680 bytes for lkl0 28544 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.058971 0.067916 0.065921 0.162484 0.122495 0.243374 0.264905 0.284817 lnL0 = -2228.694368 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2228.694368 x= 0.05897 0.06792 0.06592 0.16248 0.12249 0.24337 0.26490 0.28482 1 h-lim-p 0.0016 0.0128 51.6870 2228.135995 6 0.0004 35 | 0/8 2 h-lim-p 0.0015 0.0135 15.2619 2228.071218 6 0.0006 58 | 0/8 3 h-lim-p 0.0030 0.1139 2.9902 2228.068234 2 0.0007 75 | 0/8 4 h-lim-p 0.0017 0.2332 1.2324 2228.067768 3 0.0007 93 | 0/8 5 h-lim-p 0.0102 2.1946 0.0875 2228.067764 1 0.0010 109 | 0/8 6 h-lim-p 0.0019 8.4440 0.0465 2228.067763 1 0.0009 132 | 0/8 7 h-lim-p 0.0057 20.0000 0.0077 2228.067763 0 0.0012 153 | 0/8 8 h-lim-p 0.1301 20.0000 0.0001 2228.067759 0 1.0407 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2228.067759 0 1.0938 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2228.067759 0 2.1875 216 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2228.067759 0 1.0938 236 | 0/8 12 h-lim-p 0.1455 20.0000 0.0000 2228.067759 0 9.3092 262 | 0/8 13 h-lim-p 0.2154 20.0000 0.0005 2228.067759 0 0.0404 284 | 0/8 14 h-lim-p 0.0078 20.0000 0.0024 2228.067759 0 0.0000 312 | 0/8 15 h-lim-p 0.0001 20.0000 0.0003 2228.067759 0 0.0000 350 | 0/8 16 h-lim-p 0.0000 20.0000 0.0009 | 0/8 17 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -2228.067759 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2228.067759 Node 7: lnL = -2228.067759 Node 8: lnL = -2228.067759 Node 9: lnL = -2228.067759 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 468 Sequential format.. Reading seq # 1: YMR027W_Sbay Reading seq # 2: YMR027W_Scer Reading seq # 3: YMR027W_Skud Reading seq # 4: YMR027W_Smik Reading seq # 5: YMR027W_Spar Sequences read.. Counting patterns.. # site patterns = 211 Counting frequencies.. 120 bytes for distance 33760 bytes for lkl0 27008 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.115592 0.019289 0.088347 0.173694 0.111285 0.223154 0.286915 0.356819 lnL0 = -2270.712258 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2270.712258 x= 0.11559 0.01929 0.08835 0.17369 0.11128 0.22315 0.28692 0.35682 1 h-lim-p 0.0008 0.0064 47.5977 2270.136670 6 0.0005 35 | 0/8 2 h-lim-p 0.0014 0.0111 17.2997 2270.069774 7 0.0005 62 | 0/8 3 h-lim-p 0.0023 0.1325 3.7047 2270.063195 3 0.0010 80 | 0/8 4 h-lim-p 0.0023 0.1580 1.6476 2270.062393 4 0.0007 104 | 0/8 5 h-lim-p 0.0022 0.6538 0.5406 2270.062282 2 0.0009 120 | 0/8 6 h-lim-p 0.0014 0.9683 0.3254 2270.062248 3 0.0008 149 | 0/8 7 h-lim-p 0.0047 5.0303 0.0579 2270.062246 1 0.0012 172 | 0/8 8 h-lim-p 0.1403 20.0000 0.0005 2270.062062 0 1.1223 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2270.062056 1 0.9961 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2270.062056 0 1.0938 237 | 0/8 11 h-lim-p 0.6449 20.0000 0.0000 2270.062056 0 0.0050 263 | 0/8 12 h-lim-p 0.0014 20.0000 0.0000 2270.062056 0 0.0000 303 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -2270.062056 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2270.062056 Node 7: lnL = -2270.062056 Node 8: lnL = -2270.062056 Node 9: lnL = -2270.062056 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 218 Sequential format.. Reading seq # 1: YMR028W_Sbay Reading seq # 2: YMR028W_Scer Reading seq # 3: YMR028W_Skud Reading seq # 4: YMR028W_Smik Reading seq # 5: YMR028W_Spar Sequences read.. Counting patterns.. # site patterns = 115 Counting frequencies.. 120 bytes for distance 18400 bytes for lkl0 14720 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.080750 0.065968 0.056071 0.181301 0.101057 0.213987 0.253505 0.303032 lnL0 = -1009.017202 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1009.017202 x= 0.08075 0.06597 0.05607 0.18130 0.10106 0.21399 0.25350 0.30303 1 h-lim-p 0.0008 0.0065 37.6142 1008.340366 0 0.0012 22 | 0/8 2 h-lim-p 0.0020 0.0161 12.5769 1008.256194 8 0.0011 54 | 0/8 3 h-lim-p 0.0031 0.0714 4.6107 1008.248996 3 0.0008 73 | 0/8 4 h-lim-p 0.0031 0.1307 1.1400 1008.248102 2 0.0015 89 | 0/8 5 h-lim-p 0.0172 3.0889 0.0973 1008.247784 4 0.0126 111 | 0/8 6 h-lim-p 0.0086 1.0097 0.1431 1008.244750 0 0.0257 132 | 0/8 7 h-lim-p 0.0062 0.3516 0.5913 1008.230406 0 0.0125 153 | 0/8 8 h-lim-p 0.0056 0.2137 1.3124 1008.225067 6 0.0040 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 1008.224931 2 0.9644 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1008.224931 0 1.0938 224 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1008.224931 0 1.0938 244 | 0/8 12 h-lim-p 1.2113 20.0000 0.0000 1008.224931 0 1.0598 264 | 0/8 13 h-lim-p 0.4462 20.0000 0.0000 1008.224931 0 0.0976 285 | 0/8 14 h-lim-p 0.0138 20.0000 0.0001 1008.224931 0 0.0035 306 | 0/8 15 h-lim-p 0.0014 20.0000 0.0002 1008.224931 0 0.0002 328 | 0/8 16 h-lim-p 0.0002 20.0000 0.0001 1008.224931 0 0.0000 357 | 0/8 17 h-lim-p 0.0005 20.0000 0.0000 1008.224931 0 0.0000 385 Out... lnL = -1008.224931 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1008.224931 Node 7: lnL = -1008.224931 Node 8: lnL = -1008.224931 Node 9: lnL = -1008.224931 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 577 Sequential format.. Reading seq # 1: YMR029C_Sbay Reading seq # 2: YMR029C_Scer Reading seq # 3: YMR029C_Skud Reading seq # 4: YMR029C_Smik Reading seq # 5: YMR029C_Spar Sequences read.. Counting patterns.. # site patterns = 127 Counting frequencies.. 120 bytes for distance 20320 bytes for lkl0 16256 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.535294 0.666917 0.068176 0.502783 3.048635 0.626468 0.633071 lnL0 = -2468.369304 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2468.369304 x= 0.00006 0.53529 0.66692 0.06818 0.50278 3.04864 0.62647 0.63307 1 h-lim-p 0.0000 0.0000 494.0056 2468.211422 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0000 12116.6705 2397.566017 m 0.0000 34 | 2/8 3 h-lim-p 0.0000 0.0000 16969.8109 2233.429161 0 0.0000 48 | 2/8 4 h-lim-p 0.0009 0.0075 68.0051 2228.144938 0 0.0019 61 | 1/8 5 h-lim-p 0.0001 0.0006 1774.7836 2218.979412 0 0.0001 74 | 1/8 6 h-lim-p 0.0111 0.0892 8.8936 2215.955623 0 0.0446 88 | 1/8 7 h-lim-p 0.0353 0.2822 0.5443 2215.882692 3 0.0295 106 | 1/8 8 h-lim-p 0.5399 20.0000 0.0297 .. | 1/8 9 h-lim-p 0.0000 0.0010 367.7307 2134.160387 m 0.0010 177 | 1/8 10 h-lim-p 0.0000 0.0000 385.2480 h-lim-p: 5.34656161e-21 4.27724929e-20 3.85247998e+02 2134.160387 .. | 1/8 11 h-lim-p 0.0000 0.0013 541.4302 2104.353173 0 0.0003 202 | 1/8 12 h-lim-p 0.0000 0.0003 318.2065 2083.383822 m 0.0003 214 | 2/8 13 h-lim-p 0.0001 0.0006 728.0381 2062.958199 0 0.0003 228 | 2/8 14 h-lim-p 0.0002 0.0017 151.7541 2059.384316 0 0.0004 241 | 2/8 15 h-lim-p 0.0019 0.0155 21.7212 2058.254939 2 0.0018 257 | 1/8 16 h-lim-p 0.0007 0.0063 55.6614 2056.759708 1 0.0009 271 | 1/8 17 h-lim-p 0.0003 0.0022 32.2867 2056.498351 0 0.0006 284 | 1/8 18 h-lim-p 0.2680 2.1437 0.0466 2055.078162 0 0.8039 297 | 0/8 19 h-lim-p 0.0132 0.8857 2.8458 2055.075186 4 0.0007 326 | 0/8 20 h-lim-p 0.2915 4.0525 0.0071 2055.031974 0 0.8746 339 | 0/8 21 h-lim-p 2.5000 20.0000 0.0014 2055.029753 4 0.8228 368 | 0/8 22 h-lim-p 2.5000 20.0000 0.0003 2055.029691 3 0.7439 396 | 0/8 23 h-lim-p 2.5000 20.0000 0.0000 2055.029690 0 1.0938 416 | 0/8 24 h-lim-p 2.5000 20.0000 0.0000 2055.029690 0 2.1875 436 | 0/8 25 h-lim-p 1.8737 20.0000 0.0000 2055.029690 0 0.8198 456 | 0/8 26 h-lim-p 2.5000 20.0000 0.0000 2055.029690 0 0.0391 481 Out... lnL = -2055.029690 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2055.029690 Node 7: lnL = -2055.029690 Node 8: lnL = -2055.029690 Node 9: lnL = -2055.029690 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 600 Sequential format.. Reading seq # 1: YMR030W_Sbay Reading seq # 2: YMR030W_Scer Reading seq # 3: YMR030W_Skud Reading seq # 4: YMR030W_Smik Reading seq # 5: YMR030W_Spar Sequences read.. Counting patterns.. # site patterns = 206 Counting frequencies.. 120 bytes for distance 32960 bytes for lkl0 26368 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.026327 0.091379 0.057635 0.104212 0.065320 0.181521 0.164637 0.187160 lnL0 = -2437.323940 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2437.323940 x= 0.02633 0.09138 0.05763 0.10421 0.06532 0.18152 0.16464 0.18716 1 h-lim-p 0.0046 0.0370 89.8127 2436.453892 7 0.0002 42 | 0/8 2 h-lim-p 0.0008 0.0067 23.0901 2436.356455 2 0.0004 58 | 0/8 3 h-lim-p 0.0006 0.0105 15.5759 2436.334887 5 0.0002 83 | 0/8 4 h-lim-p 0.0018 0.0825 2.1373 2436.333743 5 0.0005 108 | 0/8 5 h-lim-p 0.0027 0.2427 0.4011 2436.333718 1 0.0003 124 | 0/8 6 h-lim-p 0.0014 3.1443 0.0970 2436.333715 0 0.0006 144 | 0/8 7 h-lim-p 0.0131 20.0000 0.0046 2436.333715 0 0.0007 167 | 0/8 8 h-lim-p 0.0164 20.0000 0.0002 2436.333699 0 0.5264 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2436.333699 0 1.0938 212 | 0/8 10 h-lim-p 0.8598 20.0000 0.0000 2436.333699 0 0.7523 232 | 0/8 11 h-lim-p 0.4853 20.0000 0.0000 2436.333699 0 0.0009 260 | 0/8 12 h-lim-p 0.0005 20.0000 0.0001 2436.333699 0 0.0000 283 | 0/8 13 h-lim-p 0.0003 20.0000 0.0000 2436.333699 0 0.0000 314 | 0/8 14 h-lim-p 0.0000 20.0000 0.0014 | 0/8 15 h-lim-p 0.0000 20.0000 0.0014 Out... lnL = -2436.333699 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2436.333699 Node 7: lnL = -2436.333699 Node 8: lnL = -2436.333699 Node 9: lnL = -2436.333699 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 433 Sequential format.. Reading seq # 1: YMR035W_Sbay Reading seq # 2: YMR035W_Scer Reading seq # 3: YMR035W_Skud Reading seq # 4: YMR035W_Smik Reading seq # 5: YMR035W_Spar Sequences read.. Counting patterns.. # site patterns = 158 Counting frequencies.. 120 bytes for distance 25280 bytes for lkl0 20224 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.036348 0.038953 0.072209 0.078731 0.094857 0.165298 0.133617 0.174105 lnL0 = -1802.186137 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1802.186137 x= 0.03635 0.03895 0.07221 0.07873 0.09486 0.16530 0.13362 0.17411 1 h-lim-p 0.0049 1.3258 85.9687 1801.451609 7 0.0002 41 | 0/8 2 h-lim-p 0.0022 0.0225 8.4023 1801.435013 5 0.0005 63 | 0/8 3 h-lim-p 0.0013 0.0909 3.0712 1801.433325 4 0.0004 87 | 0/8 4 h-lim-p 0.0013 0.1281 0.9684 1801.433189 2 0.0003 104 | 0/8 5 h-lim-p 0.0023 1.2223 0.1345 1801.433184 0 0.0006 125 | 0/8 6 h-lim-p 0.0040 6.3288 0.0188 1801.433184 0 0.0004 147 | 0/8 7 h-lim-p 0.0051 20.0000 0.0016 1801.433184 0 0.0011 168 | 0/8 8 h-lim-p 0.0208 20.0000 0.0001 1801.433183 0 0.6664 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1801.433183 0 1.0938 213 | 0/8 10 h-lim-p 0.7707 20.0000 0.0000 1801.433183 0 2.3120 234 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1801.433183 0 0.5469 255 | 0/8 12 h-lim-p 0.0996 20.0000 0.0001 1801.433183 0 0.0016 280 | 0/8 13 h-lim-p 0.0003 20.0000 0.0003 1801.433183 0 0.0000 302 | 0/8 14 h-lim-p 0.0001 20.0000 0.0001 1801.433183 0 0.0000 339 | 0/8 15 h-lim-p 0.0000 20.0000 0.0016 | 0/8 16 h-lim-p 0.0000 20.0000 0.0016 Out... lnL = -1801.433183 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1801.433183 Node 7: lnL = -1801.433183 Node 8: lnL = -1801.433183 Node 9: lnL = -1801.433183 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 427 Sequential format.. Reading seq # 1: YMR038C_Sbay Reading seq # 2: YMR038C_Scer Reading seq # 3: YMR038C_Skud Reading seq # 4: YMR038C_Smik Reading seq # 5: YMR038C_Spar Sequences read.. Counting patterns.. # site patterns = 158 Counting frequencies.. 120 bytes for distance 25280 bytes for lkl0 20224 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.087101 0.058822 0.024473 0.081021 0.064259 0.174771 0.151755 0.236276 lnL0 = -1689.206136 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1689.206136 x= 0.08710 0.05882 0.02447 0.08102 0.06426 0.17477 0.15176 0.23628 1 h-lim-p 0.0013 0.0102 61.1982 1688.758055 4 0.0003 31 | 0/8 2 h-lim-p 0.0002 0.0018 31.5220 1688.611867 0 0.0004 44 | 0/8 3 h-lim-p 0.0015 0.0278 9.5594 1688.591093 6 0.0005 71 | 0/8 4 h-lim-p 0.0026 0.0540 1.8757 1688.590570 2 0.0003 89 | 0/8 5 h-lim-p 0.0013 0.5841 0.4402 1688.590539 0 0.0003 102 | 0/8 6 h-lim-p 0.0015 1.5041 0.0927 1688.590516 1 0.0019 124 | 0/8 7 h-lim-p 0.0247 20.0000 0.0072 1688.584241 0 0.2958 147 | 0/8 8 h-lim-p 0.0029 0.3288 0.7486 1688.584001 4 0.0008 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1688.583985 1 0.9961 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1688.583985 0 1.0938 220 | 0/8 11 h-lim-p 1.6346 20.0000 0.0000 1688.583985 0 0.3576 241 | 0/8 12 h-lim-p 0.1555 20.0000 0.0000 1688.583985 0 0.0085 264 | 0/8 13 h-lim-p 0.0039 20.0000 0.0000 1688.583985 0 0.0000 290 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 1688.583985 0 0.0000 310 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 1688.583985 0 0.0002 330 Out... lnL = -1688.583985 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1688.583985 Node 7: lnL = -1688.583985 Node 8: lnL = -1688.583985 Node 9: lnL = -1688.583985 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 821 Sequential format.. Reading seq # 1: YMR039C_Sbay Reading seq # 2: YMR039C_Scer Reading seq # 3: YMR039C_Skud Reading seq # 4: YMR039C_Smik Reading seq # 5: YMR039C_Spar Sequences read.. Counting patterns.. # site patterns = 158 Counting frequencies.. 120 bytes for distance 25280 bytes for lkl0 20224 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.305600 0.245840 0.239904 0.498582 3.348608 0.532170 0.607969 lnL0 = -3368.810403 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3368.810403 x= 0.00006 0.30560 0.24584 0.23990 0.49858 3.34861 0.53217 0.60797 1 h-lim-p 0.0000 0.0000 824.9296 3368.551062 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0001 4689.1571 3173.255736 m 0.0001 34 | 1/8 3 h-lim-p -0.0000 -0.0000 182.1344 h-lim-p: -3.89607539e-20 -3.11686031e-19 1.82134409e+02 3173.255736 .. | 1/8 4 h-lim-p 0.0000 0.0009 603.4633 2897.559946 m 0.0009 58 | 1/8 5 h-lim-p 0.0000 0.0002 780.9915 2877.400168 0 0.0001 72 | 1/8 6 h-lim-p 0.0002 0.0013 195.8875 2873.606187 0 0.0003 85 | 1/8 7 h-lim-p 0.0005 0.0036 70.4260 2872.963303 8 0.0003 114 | 1/8 8 h-lim-p 0.0017 0.0343 12.3478 2872.938973 6 0.0003 142 | 0/8 9 h-lim-p 0.0001 0.0363 45.7409 2872.517650 0 0.0006 157 | 0/8 10 h-lim-p 0.0536 0.4289 0.1136 2869.063793 m 0.4289 169 | 1/8 11 h-lim-p 0.2529 2.0234 0.0474 2867.431220 0 0.5059 190 | 0/8 12 h-lim-p 0.0011 0.0166 21.6638 2867.321442 6 0.0005 221 | 0/8 13 h-lim-p 2.4665 20.0000 0.0043 2867.279656 5 1.0878 242 | 0/8 14 h-lim-p 2.5000 20.0000 0.0006 2867.278837 2 1.1719 266 | 0/8 15 h-lim-p 2.5000 20.0000 0.0001 2867.278820 2 0.8246 292 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 2867.278820 0 1.0938 312 | 0/8 17 h-lim-p 1.1558 20.0000 0.0000 2867.278820 0 0.2528 333 | 0/8 18 h-lim-p 0.0993 20.0000 0.0001 2867.278820 0 0.0000 364 | 0/8 19 h-lim-p 0.0005 20.0000 0.0000 2867.278820 0 0.0000 403 Out... lnL = -2867.278820 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2867.278820 Node 7: lnL = -2867.278820 Node 8: lnL = -2867.278820 Node 9: lnL = -2867.278820 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 871 Sequential format.. Reading seq # 1: YMR040W_Sbay Reading seq # 2: YMR040W_Scer Reading seq # 3: YMR040W_Skud Reading seq # 4: YMR040W_Smik Reading seq # 5: YMR040W_Spar Sequences read.. Counting patterns.. # site patterns = 264 Counting frequencies.. 120 bytes for distance 42240 bytes for lkl0 33792 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.049125 0.049505 0.053703 0.117913 0.061855 0.151921 0.120830 0.185652 lnL0 = -3412.647482 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3412.647482 x= 0.04913 0.04951 0.05370 0.11791 0.06185 0.15192 0.12083 0.18565 1 h-lim-p 0.0040 0.9815 131.1929 3411.536268 9 0.0001 46 | 0/8 2 h-lim-p 0.0003 0.0027 44.2413 3411.321376 7 0.0002 75 | 0/8 3 h-lim-p 0.0007 0.0161 16.2942 3411.304149 2 0.0002 92 | 0/8 4 h-lim-p 0.0006 0.0472 3.9737 3411.302667 4 0.0002 114 | 0/8 5 h-lim-p 0.0011 0.4078 0.7367 3411.302590 3 0.0003 133 | 0/8 6 h-lim-p 0.0032 2.0176 0.0676 3411.302590 0 0.0003 155 | 0/8 7 h-lim-p 0.0040 20.0000 0.0058 3411.302589 0 0.0035 175 | 0/8 8 h-lim-p 0.0051 20.0000 0.0040 3411.302353 0 0.0816 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3411.302349 0 1.0938 219 | 0/8 10 h-lim-p 1.3781 20.0000 0.0000 3411.302349 0 1.2059 239 | 0/8 11 h-lim-p 1.4060 20.0000 0.0000 3411.302349 0 1.4060 259 | 0/8 12 h-lim-p 0.8430 20.0000 0.0000 3411.302349 0 0.0527 282 | 0/8 13 h-lim-p 0.0002 5.5333 0.0141 3411.302349 0 0.0000 316 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 3411.302349 0 0.0000 353 Out... lnL = -3411.302349 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3411.302349 Node 7: lnL = -3411.302349 Node 8: lnL = -3411.302349 Node 9: lnL = -3411.302349 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 665 Sequential format.. Reading seq # 1: YMR041C_Sbay Reading seq # 2: YMR041C_Scer Reading seq # 3: YMR041C_Skud Reading seq # 4: YMR041C_Smik Reading seq # 5: YMR041C_Spar Sequences read.. Counting patterns.. # site patterns = 265 Counting frequencies.. 120 bytes for distance 42400 bytes for lkl0 33920 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.028340 0.145904 0.080750 0.126510 0.108019 0.177798 0.182914 0.220269 lnL0 = -2968.985560 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2968.985560 x= 0.02834 0.14590 0.08075 0.12651 0.10802 0.17780 0.18291 0.22027 1 h-lim-p 0.0043 0.2792 117.1006 2966.872010 9 0.0003 49 | 0/8 2 h-lim-p 0.0011 0.0099 35.3504 2966.568889 2 0.0005 65 | 0/8 3 h-lim-p 0.0011 0.0217 16.2152 2966.531500 6 0.0003 93 | 0/8 4 h-lim-p 0.0032 0.1286 1.7478 2966.530465 2 0.0007 110 | 0/8 5 h-lim-p 0.0044 0.6838 0.2755 2966.530445 0 0.0005 124 | 0/8 6 h-lim-p 0.0019 1.2204 0.0717 2966.530442 0 0.0008 144 | 0/8 7 h-lim-p 0.0087 20.0000 0.0066 2966.530371 0 0.0349 166 | 0/8 8 h-lim-p 0.0016 5.6433 0.1456 2966.528939 0 0.0096 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 2966.528926 1 0.9961 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2966.528926 0 1.0938 230 | 0/8 11 h-lim-p 0.8287 20.0000 0.0000 2966.528926 0 0.7251 250 | 0/8 12 h-lim-p 0.0178 20.0000 0.0009 2966.528926 0 0.0000 279 | 0/8 13 h-lim-p 0.0001 20.0000 0.0002 2966.528926 0 0.0000 309 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 2966.528926 0 0.0000 339 Out... lnL = -2966.528926 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2966.528926 Node 7: lnL = -2966.528926 Node 8: lnL = -2966.528926 Node 9: lnL = -2966.528926 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 783 Sequential format.. Reading seq # 1: YMR043W_Sbay Reading seq # 2: YMR043W_Scer Reading seq # 3: YMR043W_Skud Reading seq # 4: YMR043W_Smik Reading seq # 5: YMR043W_Spar Sequences read.. Counting patterns.. # site patterns = 193 Counting frequencies.. 120 bytes for distance 30880 bytes for lkl0 24704 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.045212 0.074322 0.031550 0.044578 0.063065 0.117057 0.129306 0.161936 lnL0 = -2655.950735 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2655.950735 x= 0.04521 0.07432 0.03155 0.04458 0.06306 0.11706 0.12931 0.16194 1 h-lim-p 0.0004 0.0031 270.5116 2652.603459 8 0.0001 41 | 0/8 2 h-lim-p 0.0002 0.0020 102.5413 2651.189207 1 0.0003 55 | 0/8 3 h-lim-p 0.0004 0.0042 88.7336 2650.797301 2 0.0002 71 | 0/8 4 h-lim-p 0.0002 0.0026 74.7081 2650.382502 0 0.0003 83 | 0/8 5 h-lim-p 0.0013 0.0101 11.7242 2650.372399 5 0.0002 109 | 0/8 6 h-lim-p 0.0005 0.0563 4.1032 2650.370778 2 0.0002 125 | 0/8 7 h-lim-p 0.0005 0.0642 1.7032 2650.369410 0 0.0010 138 | 0/8 8 h-lim-p 0.4563 20.0000 0.0038 2650.352385 0 1.3689 151 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 2650.351666 2 1.0889 175 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2650.351655 1 1.2305 198 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2650.351655 0 1.0938 218 | 0/8 12 h-lim-p 1.2169 20.0000 0.0000 2650.351655 0 2.4338 239 | 0/8 13 h-lim-p 2.1465 20.0000 0.0000 2650.351655 0 0.0021 268 | 0/8 14 h-lim-p 0.0002 20.0000 0.0002 2650.351655 0 0.0001 288 | 0/8 15 h-lim-p 0.0003 20.0000 0.0001 2650.351655 0 0.0003 308 | 0/8 16 h-lim-p 0.0015 20.0000 0.0000 2650.351655 0 0.0000 335 | 0/8 17 h-lim-p 0.0002 20.0000 0.0000 2650.351655 0 0.0000 369 Out... lnL = -2650.351655 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2650.351655 Node 7: lnL = -2650.351655 Node 8: lnL = -2650.351655 Node 9: lnL = -2650.351655 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 310 Sequential format.. Reading seq # 1: YMR047C_Sbay Reading seq # 2: YMR047C_Scer Reading seq # 3: YMR047C_Skud Reading seq # 4: YMR047C_Smik Reading seq # 5: YMR047C_Spar Sequences read.. Counting patterns.. # site patterns = 129 Counting frequencies.. 120 bytes for distance 20640 bytes for lkl0 16512 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.039477 0.030819 0.067642 0.131949 0.087792 0.158651 0.158677 0.187252 lnL0 = -1306.373925 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1306.373925 x= 0.03948 0.03082 0.06764 0.13195 0.08779 0.15865 0.15868 0.18725 1 h-lim-p 0.0014 0.0109 42.5549 1306.083575 6 0.0003 35 | 0/8 2 h-lim-p 0.0012 0.0135 11.5799 1306.041980 5 0.0007 58 | 0/8 3 h-lim-p 0.0031 0.1873 2.4905 1306.040475 5 0.0005 82 | 0/8 4 h-lim-p 0.0019 0.1724 0.6625 1306.040354 4 0.0006 105 | 0/8 5 h-lim-p 0.0030 1.6836 0.1285 1306.040349 1 0.0006 128 | 0/8 6 h-lim-p 0.0130 20.0000 0.0059 1306.040349 0 0.0029 149 | 0/8 7 h-lim-p 0.0275 20.0000 0.0006 1306.040325 0 0.2197 172 | 0/8 8 h-lim-p 0.0011 0.5065 0.1220 1306.040311 0 0.0010 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1306.040311 0 1.0938 212 | 0/8 10 h-lim-p 1.9453 20.0000 0.0000 1306.040311 0 0.8511 232 | 0/8 11 h-lim-p 0.6170 20.0000 0.0000 1306.040311 0 0.0042 258 | 0/8 12 h-lim-p 0.0009 20.0000 0.0001 1306.040311 0 0.0000 285 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 1306.040311 0 0.0000 320 Out... lnL = -1306.040311 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1306.040311 Node 7: lnL = -1306.040311 Node 8: lnL = -1306.040311 Node 9: lnL = -1306.040311 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 314 Sequential format.. Reading seq # 1: YMR048W_Sbay Reading seq # 2: YMR048W_Scer Reading seq # 3: YMR048W_Skud Reading seq # 4: YMR048W_Smik Reading seq # 5: YMR048W_Spar Sequences read.. Counting patterns.. # site patterns = 144 Counting frequencies.. 120 bytes for distance 23040 bytes for lkl0 18432 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.033665 0.049304 0.086470 0.125487 0.094253 0.121960 0.143637 0.180011 lnL0 = -1279.094998 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1279.094998 x= 0.03366 0.04930 0.08647 0.12549 0.09425 0.12196 0.14364 0.18001 1 h-lim-p 0.0025 0.0199 50.8635 1278.532654 7 0.0005 38 | 0/8 2 h-lim-p 0.0019 0.0162 11.9863 1278.485183 7 0.0007 66 | 0/8 3 h-lim-p 0.0045 0.1297 1.8426 1278.484360 2 0.0005 84 | 0/8 4 h-lim-p 0.0040 0.9673 0.2275 1278.484343 2 0.0006 102 | 0/8 5 h-lim-p 0.0062 5.3231 0.0233 1278.484343 0 0.0014 123 | 0/8 6 h-lim-p 0.0077 20.0000 0.0041 1278.484343 0 0.0034 143 | 0/8 7 h-lim-p 0.0163 20.0000 0.0009 1278.484335 0 0.1308 166 | 0/8 8 h-lim-p 0.0018 5.6204 0.0622 1278.484322 1 0.0018 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1278.484322 0 1.0938 208 | 0/8 10 h-lim-p 1.1905 20.0000 0.0000 1278.484322 0 1.0417 228 | 0/8 11 h-lim-p 0.9046 20.0000 0.0000 1278.484322 0 0.0141 253 | 0/8 12 h-lim-p 0.0003 20.0000 0.0008 1278.484322 0 0.0000 277 | 0/8 13 h-lim-p 0.0001 20.0000 0.0001 1278.484322 0 0.0000 303 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 1278.484322 0 0.0001 323 Out... lnL = -1278.484322 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1278.484322 Node 7: lnL = -1278.484322 Node 8: lnL = -1278.484322 Node 9: lnL = -1278.484322 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 851 Sequential format.. Reading seq # 1: YMR049C_Sbay Reading seq # 2: YMR049C_Scer Reading seq # 3: YMR049C_Skud Reading seq # 4: YMR049C_Smik Reading seq # 5: YMR049C_Spar Sequences read.. Counting patterns.. # site patterns = 416 Counting frequencies.. 120 bytes for distance 66560 bytes for lkl0 53248 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.078326 0.109975 0.028753 0.233559 0.267266 0.269679 0.339242 0.363633 lnL0 = -4551.601021 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4551.601021 x= 0.07833 0.10998 0.02875 0.23356 0.26727 0.26968 0.33924 0.36363 1 h-lim-p 0.0020 0.5259 213.8781 4546.928688 3 0.0002 30 | 0/8 2 h-lim-p 0.0014 0.0111 33.5794 4546.561357 2 0.0007 46 | 0/8 3 h-lim-p 0.0029 0.0518 7.6476 4546.538336 6 0.0008 74 | 0/8 4 h-lim-p 0.0031 0.1818 2.0670 4546.536044 4 0.0012 94 | 0/8 5 h-lim-p 0.0031 0.2562 0.7687 4546.535833 3 0.0008 113 | 0/8 6 h-lim-p 0.0077 5.7847 0.0813 4546.535826 1 0.0015 136 | 0/8 7 h-lim-p 0.0133 20.0000 0.0094 4546.535693 0 0.0533 158 | 0/8 8 h-lim-p 0.0058 10.4150 0.0869 4546.533372 0 0.0173 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4546.533361 1 0.9961 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4546.533361 0 1.0938 221 | 0/8 11 h-lim-p 1.0573 20.0000 0.0000 4546.533361 0 0.3965 242 | 0/8 12 h-lim-p 0.0120 20.0000 0.0004 4546.533361 0 0.0015 264 | 0/8 13 h-lim-p 0.0003 20.0000 0.0023 4546.533361 0 0.0000 288 | 0/8 14 h-lim-p 0.0003 20.0000 0.0001 4546.533361 0 0.0001 308 | 0/8 15 h-lim-p 0.0010 20.0000 0.0000 4546.533361 0 0.0000 337 Out... lnL = -4546.533361 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4546.533361 Node 7: lnL = -4546.533361 Node 8: lnL = -4546.533361 Node 9: lnL = -4546.533361 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 1032 Sequential format.. Reading seq # 1: YMR052W_Sbay Reading seq # 2: YMR052W_Scer Reading seq # 3: YMR052W_Skud Reading seq # 4: YMR052W_Smik Reading seq # 5: YMR052W_Spar Sequences read.. Counting patterns.. # site patterns = 416 Counting frequencies.. 120 bytes for distance 66560 bytes for lkl0 53248 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.087465 0.067435 0.000060 0.368123 0.269068 0.290886 0.425411 0.399322 lnL0 = -4961.437962 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4961.437962 x= 0.08746 0.06744 0.00006 0.36812 0.26907 0.29089 0.42541 0.39932 1 h-lim-p 0.0021 0.1025 215.9155 4952.657727 9 0.0004 49 | 0/8 2 h-lim-p 0.0007 0.0055 60.2275 4950.998155 0 0.0010 61 | 0/8 3 h-lim-p 0.0015 0.0116 20.5500 4950.833586 7 0.0009 92 | 0/8 4 h-lim-p 0.0035 0.0557 5.1433 4950.818059 5 0.0013 117 | 0/8 5 h-lim-p 0.0032 0.2586 2.0279 4950.815715 3 0.0013 135 | 0/8 6 h-lim-p 0.0095 0.6814 0.2725 4950.815571 2 0.0022 152 | 0/8 7 h-lim-p 0.0226 5.0346 0.0268 4950.808866 0 0.1811 175 | 0/8 8 h-lim-p 0.0045 0.9654 1.0679 4950.789586 4 0.0048 203 | 0/8 9 h-lim-p 2.5000 20.0000 0.0017 4950.787824 2 1.1719 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 4950.787812 0 1.0938 239 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4950.787812 0 1.0938 259 | 0/8 12 h-lim-p 1.4392 20.0000 0.0000 4950.787812 0 1.2593 279 | 0/8 13 h-lim-p 0.8327 20.0000 0.0000 4950.787812 0 0.8327 299 | 0/8 14 h-lim-p 0.0017 16.4885 0.0075 4950.787812 0 0.0000 341 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 4950.787812 0 0.0000 362 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 4950.787812 0 0.0000 389 | 0/8 17 h-lim-p 0.0000 20.0000 0.0009 4950.787812 0 0.0000 424 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 | 0/8 19 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -4950.787812 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4950.787812 Node 7: lnL = -4950.787812 Node 8: lnL = -4950.787812 Node 9: lnL = -4950.787812 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 449 Sequential format.. Reading seq # 1: YMR053C_Sbay Reading seq # 2: YMR053C_Scer Reading seq # 3: YMR053C_Skud Reading seq # 4: YMR053C_Smik Reading seq # 5: YMR053C_Spar Sequences read.. Counting patterns.. # site patterns = 154 Counting frequencies.. 120 bytes for distance 24640 bytes for lkl0 19712 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.065545 0.048309 0.023048 0.094625 0.078037 0.140915 0.132339 0.191434 lnL0 = -1764.009010 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1764.009010 x= 0.06555 0.04831 0.02305 0.09463 0.07804 0.14092 0.13234 0.19143 1 h-lim-p 0.0024 1.0320 122.1778 1763.032546 7 0.0001 38 | 0/8 2 h-lim-p 0.0005 0.0040 24.6042 1762.930044 6 0.0004 64 | 0/8 3 h-lim-p 0.0017 0.0330 5.2071 1762.924929 2 0.0004 81 | 0/8 4 h-lim-p 0.0015 0.1177 1.3509 1762.924653 2 0.0003 98 | 0/8 5 h-lim-p 0.0018 1.0761 0.2439 1762.924642 1 0.0004 113 | 0/8 6 h-lim-p 0.0016 4.2304 0.0568 1762.924641 0 0.0007 133 | 0/8 7 h-lim-p 0.0086 20.0000 0.0045 1762.924641 0 0.0038 153 | 0/8 8 h-lim-p 0.0414 20.0000 0.0004 1762.924602 0 0.3316 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1762.924602 0 1.0938 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1762.924602 0 2.1875 216 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1762.924602 0 1.0938 236 | 0/8 12 h-lim-p 0.2279 20.0000 0.0000 1762.924602 0 7.2940 261 | 0/8 13 h-lim-p 0.5514 20.0000 0.0002 1762.924602 0 0.0172 285 | 0/8 14 h-lim-p 0.0006 14.6396 0.0062 1762.924602 0 0.0000 310 | 0/8 15 h-lim-p 0.0002 20.0000 0.0002 1762.924602 0 0.0001 331 | 0/8 16 h-lim-p 0.0001 20.0000 0.0001 1762.924602 0 0.0000 367 | 0/8 17 h-lim-p 0.0000 20.0000 0.0019 1762.924602 0 0.0000 392 | 0/8 18 h-lim-p 0.0000 20.0000 0.0007 1762.924602 0 0.0010 418 | 0/8 19 h-lim-p 0.0030 20.0000 0.0002 1762.924602 0 0.0001 442 | 0/8 20 h-lim-p 0.0005 20.0000 0.0000 1762.924602 0 0.0000 465 | 0/8 21 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 22 h-lim-p 0.0000 20.0000 0.0028 1762.924602 0 0.0000 533 | 0/8 23 h-lim-p 0.0000 20.0000 0.0015 .. | 0/8 24 h-lim-p 0.0000 20.0000 0.0028 | 0/8 25 h-lim-p 0.0000 20.0000 0.0028 Out... lnL = -1762.924602 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1762.924602 Node 7: lnL = -1762.924602 Node 8: lnL = -1762.924602 Node 9: lnL = -1762.924602 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 449 Sequential format.. Reading seq # 1: YMR054W_Sbay Reading seq # 2: YMR054W_Scer Reading seq # 3: YMR054W_Skud Reading seq # 4: YMR054W_Smik Reading seq # 5: YMR054W_Spar Sequences read.. Counting patterns.. # site patterns = 152 Counting frequencies.. 120 bytes for distance 24320 bytes for lkl0 19456 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.053428 0.048522 0.027612 0.094608 0.078055 0.132956 0.136011 0.175387 lnL0 = -1747.133793 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1747.133793 x= 0.05343 0.04852 0.02761 0.09461 0.07805 0.13296 0.13601 0.17539 1 h-lim-p 0.0028 1.1912 111.4346 1746.153216 7 0.0002 38 | 0/8 2 h-lim-p 0.0004 0.0031 25.7378 1746.046837 5 0.0003 59 | 0/8 3 h-lim-p 0.0016 0.0319 5.3609 1746.041429 4 0.0004 81 | 0/8 4 h-lim-p 0.0015 0.1229 1.3970 1746.041115 2 0.0004 98 | 0/8 5 h-lim-p 0.0016 0.7489 0.3119 1746.041098 0 0.0003 111 | 0/8 6 h-lim-p 0.0021 3.5665 0.0518 1746.041097 0 0.0005 132 | 0/8 7 h-lim-p 0.0055 20.0000 0.0043 1746.041097 0 0.0055 152 | 0/8 8 h-lim-p 0.0090 20.0000 0.0026 1746.040979 0 0.1085 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1746.040973 1 0.9961 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1746.040973 0 1.0938 217 | 0/8 11 h-lim-p 1.0116 20.0000 0.0000 1746.040973 0 0.0020 245 | 0/8 12 h-lim-p 0.0001 20.0000 0.0005 .. | 0/8 13 h-lim-p 0.0000 20.0000 0.0004 | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1746.040973 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1746.040973 Node 7: lnL = -1746.040973 Node 8: lnL = -1746.040973 Node 9: lnL = -1746.040973 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 318 Sequential format.. Reading seq # 1: YMR055C_Sbay Reading seq # 2: YMR055C_Scer Reading seq # 3: YMR055C_Skud Reading seq # 4: YMR055C_Smik Reading seq # 5: YMR055C_Spar Sequences read.. Counting patterns.. # site patterns = 151 Counting frequencies.. 120 bytes for distance 24160 bytes for lkl0 19328 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.269735 0.000060 0.094120 0.102773 0.097252 0.233592 0.146783 0.498858 lnL0 = -1349.983934 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1349.983934 x= 0.26974 0.00006 0.09412 0.10277 0.09725 0.23359 0.14678 0.49886 1 h-lim-p 0.0010 0.0078 51.4361 1348.778316 8 0.0008 40 | 0/8 2 h-lim-p 0.0007 0.0059 36.6751 1348.219851 0 0.0011 52 | 0/8 3 h-lim-p 0.0011 0.0086 22.1571 1348.080756 4 0.0008 72 | 0/8 4 h-lim-p 0.0021 0.0273 8.7263 1348.052839 5 0.0009 93 | 0/8 5 h-lim-p 0.0014 0.0376 5.7038 1348.040166 5 0.0011 114 | 0/8 6 h-lim-p 0.0081 0.6306 0.8034 1348.038869 4 0.0041 136 | 0/8 7 h-lim-p 0.0057 0.2178 0.5809 1348.038730 3 0.0011 163 | 0/8 8 h-lim-p 0.1399 20.0000 0.0045 1348.030170 0 1.1189 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1348.030146 2 0.9961 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1348.030146 0 1.0938 230 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1348.030146 0 1.0938 250 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1348.030146 0 2.1875 270 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1348.030146 0 0.5469 291 | 0/8 14 h-lim-p 0.1854 20.0000 0.0000 1348.030146 0 0.0116 314 | 0/8 15 h-lim-p 0.0051 20.0000 0.0000 1348.030146 0 0.0006 336 Out... lnL = -1348.030146 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1348.030146 Node 7: lnL = -1348.030146 Node 8: lnL = -1348.030146 Node 9: lnL = -1348.030146 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 411 Sequential format.. Reading seq # 1: YMR059W_Sbay Reading seq # 2: YMR059W_Scer Reading seq # 3: YMR059W_Skud Reading seq # 4: YMR059W_Smik Reading seq # 5: YMR059W_Spar Sequences read.. Counting patterns.. # site patterns = 223 Counting frequencies.. 120 bytes for distance 35680 bytes for lkl0 28544 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.093749 0.083543 0.068890 0.087809 0.185370 0.192177 0.379522 0.325824 lnL0 = -1887.871576 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1887.871576 x= 0.09375 0.08354 0.06889 0.08781 0.18537 0.19218 0.37952 0.32582 1 h-lim-p 0.0159 3.2015 48.7501 1887.221418 9 0.0006 48 | 0/8 2 h-lim-p 0.0020 0.0254 14.2050 1887.120444 7 0.0011 77 | 0/8 3 h-lim-p 0.0021 0.0300 7.4252 1887.100962 5 0.0009 98 | 0/8 4 h-lim-p 0.0031 0.0767 2.1114 1887.098699 5 0.0011 123 | 0/8 5 h-lim-p 0.0110 1.8782 0.2152 1887.098661 3 0.0016 145 | 0/8 6 h-lim-p 0.0029 2.0660 0.1214 1887.098647 2 0.0022 169 | 0/8 7 h-lim-p 0.0328 20.0000 0.0082 1887.098644 1 0.0131 191 | 0/8 8 h-lim-p 0.0209 20.0000 0.0051 1887.098386 0 0.1669 214 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1887.098361 2 0.9961 238 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1887.098361 0 1.2500 258 | 0/8 11 h-lim-p 1.6879 20.0000 0.0000 1887.098361 0 0.2110 280 | 0/8 12 h-lim-p 0.0776 20.0000 0.0000 1887.098361 0 0.0024 304 | 0/8 13 h-lim-p 0.0014 20.0000 0.0000 1887.098361 0 0.0007 324 | 0/8 14 h-lim-p 0.0004 20.0000 0.0000 1887.098361 0 0.0000 358 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1887.098361 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1887.098361 Node 7: lnL = -1887.098361 Node 8: lnL = -1887.098361 Node 9: lnL = -1887.098361 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 249 Sequential format.. Reading seq # 1: YMR060C_Sbay Reading seq # 2: YMR060C_Scer Reading seq # 3: YMR060C_Skud Reading seq # 4: YMR060C_Smik Reading seq # 5: YMR060C_Spar Sequences read.. Counting patterns.. # site patterns = 109 Counting frequencies.. 120 bytes for distance 17440 bytes for lkl0 13952 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.078552 0.039138 0.047957 0.144139 0.062027 0.145691 0.159762 0.225664 lnL0 = -1070.205265 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1070.205265 x= 0.07855 0.03914 0.04796 0.14414 0.06203 0.14569 0.15976 0.22566 1 h-lim-p 0.0002 0.0015 69.9709 1069.171930 0 0.0004 23 | 0/8 2 h-lim-p 0.0017 0.0177 15.4293 1069.077916 5 0.0008 46 | 0/8 3 h-lim-p 0.0029 0.0534 4.5049 1069.073471 6 0.0005 73 | 0/8 4 h-lim-p 0.0011 0.0625 2.0486 1069.072440 5 0.0006 98 | 0/8 5 h-lim-p 0.0013 0.1595 0.9192 1069.072207 2 0.0006 114 | 0/8 6 h-lim-p 0.0137 3.5996 0.0431 1069.071579 0 0.0274 135 | 0/8 7 h-lim-p 0.0067 0.8908 0.1755 1069.056950 0 0.0270 157 | 0/8 8 h-lim-p 0.0019 0.0921 2.4542 1069.048339 5 0.0015 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1069.048249 2 0.9644 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1069.048249 0 1.0938 223 | 0/8 11 h-lim-p 2.4893 20.0000 0.0000 1069.048249 0 1.0891 243 | 0/8 12 h-lim-p 1.0445 20.0000 0.0000 1069.048249 0 4.1779 265 | 0/8 13 h-lim-p 0.2015 20.0000 0.0001 1069.048249 0 0.1763 285 | 0/8 14 h-lim-p 0.0357 20.0000 0.0006 1069.048249 0 0.0089 306 | 0/8 15 h-lim-p 0.0039 20.0000 0.0014 1069.048249 0 0.0005 328 | 0/8 16 h-lim-p 0.0002 20.0000 0.0035 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0003 1069.048249 0 0.0000 392 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 1069.048249 0 0.0051 421 | 0/8 19 h-lim-p 0.0122 20.0000 0.0001 1069.048249 0 0.0000 451 | 0/8 20 h-lim-p 0.0000 20.0000 0.0000 1069.048249 0 0.0000 471 | 0/8 21 h-lim-p 0.0000 20.0000 0.0001 1069.048249 0 0.0000 491 | 0/8 22 h-lim-p 0.0000 20.0000 0.0005 1069.048249 0 0.0000 515 | 0/8 23 h-lim-p 0.0000 20.0000 0.0006 .. | 0/8 24 h-lim-p 0.0000 20.0000 0.0019 1069.048249 0 0.0000 582 | 0/8 25 h-lim-p 0.0000 20.0000 0.0019 | 0/8 26 h-lim-p 0.0000 20.0000 0.0019 Out... lnL = -1069.048249 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1069.048249 Node 7: lnL = -1069.048249 Node 8: lnL = -1069.048249 Node 9: lnL = -1069.048249 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 249 Sequential format.. Reading seq # 1: YMR061W_Sbay Reading seq # 2: YMR061W_Scer Reading seq # 3: YMR061W_Skud Reading seq # 4: YMR061W_Smik Reading seq # 5: YMR061W_Spar Sequences read.. Counting patterns.. # site patterns = 108 Counting frequencies.. 120 bytes for distance 17280 bytes for lkl0 13824 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.078132 0.029715 0.051520 0.145815 0.060351 0.139793 0.169535 0.224185 lnL0 = -1067.235261 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1067.235261 x= 0.07813 0.02972 0.05152 0.14582 0.06035 0.13979 0.16954 0.22419 1 h-lim-p 0.0002 0.0016 69.8464 1066.252391 0 0.0004 23 | 0/8 2 h-lim-p 0.0016 0.0201 17.5016 1066.132209 5 0.0008 46 | 0/8 3 h-lim-p 0.0039 0.0736 3.7813 1066.129258 3 0.0004 66 | 0/8 4 h-lim-p 0.0008 0.0875 2.1298 1066.127953 2 0.0007 82 | 0/8 5 h-lim-p 0.0026 0.1412 0.6103 1066.127867 3 0.0005 101 | 0/8 6 h-lim-p 0.0047 2.3824 0.0663 1066.127857 0 0.0021 121 | 0/8 7 h-lim-p 0.0060 8.0148 0.0229 1066.127738 0 0.0239 143 | 0/8 8 h-lim-p 0.0076 1.6679 0.0720 1066.125220 0 0.0303 165 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 1066.124965 3 1.0004 191 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1066.124965 0 1.0938 211 | 0/8 11 h-lim-p 1.7787 20.0000 0.0000 1066.124965 0 0.3891 232 | 0/8 12 h-lim-p 0.2261 20.0000 0.0000 1066.124965 0 0.0106 256 | 0/8 13 h-lim-p 0.0061 20.0000 0.0000 1066.124965 0 0.0002 280 | 0/8 14 h-lim-p 0.0003 20.0000 0.0000 1066.124965 0 0.0000 308 | 0/8 15 h-lim-p 0.0000 20.0000 0.0013 | 0/8 16 h-lim-p 0.0000 20.0000 0.0013 Out... lnL = -1066.124965 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1066.124965 Node 7: lnL = -1066.124965 Node 8: lnL = -1066.124965 Node 9: lnL = -1066.124965 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 755 Sequential format.. Reading seq # 1: YMR063W_Sbay Reading seq # 2: YMR063W_Scer Reading seq # 3: YMR063W_Skud Reading seq # 4: YMR063W_Smik Reading seq # 5: YMR063W_Spar Sequences read.. Counting patterns.. # site patterns = 305 Counting frequencies.. 120 bytes for distance 48800 bytes for lkl0 39040 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.048738 0.096516 0.085222 0.162947 0.090853 0.245876 0.262237 0.257067 lnL0 = -3544.834721 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3544.834721 x= 0.04874 0.09652 0.08522 0.16295 0.09085 0.24588 0.26224 0.25707 1 h-lim-p 0.0044 0.0349 71.5937 3544.094169 8 0.0003 42 | 0/8 2 h-lim-p 0.0009 0.0069 21.2142 3544.004885 4 0.0004 62 | 0/8 3 h-lim-p 0.0007 0.0128 12.7572 3543.984882 2 0.0003 78 | 0/8 4 h-lim-p 0.0018 0.1647 2.3168 3543.983210 5 0.0007 101 | 0/8 5 h-lim-p 0.0025 0.3306 0.6092 3543.983121 1 0.0005 116 | 0/8 6 h-lim-p 0.0025 2.9849 0.1211 3543.983116 1 0.0006 139 | 0/8 7 h-lim-p 0.0022 6.2252 0.0339 3543.983116 0 0.0005 160 | 0/8 8 h-lim-p 0.1256 20.0000 0.0001 3543.983093 0 1.0052 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3543.983093 0 1.0938 203 | 0/8 10 h-lim-p 1.0831 20.0000 0.0000 3543.983093 0 0.4739 223 | 0/8 11 h-lim-p 0.0729 20.0000 0.0001 3543.983093 0 0.0000 264 | 0/8 12 h-lim-p 0.0000 20.0000 0.0004 | 0/8 13 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -3543.983093 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3543.983093 Node 7: lnL = -3543.983093 Node 8: lnL = -3543.983093 Node 9: lnL = -3543.983093 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 265 Sequential format.. Reading seq # 1: YMR065W_Sbay Reading seq # 2: YMR065W_Scer Reading seq # 3: YMR065W_Skud Reading seq # 4: YMR065W_Smik Reading seq # 5: YMR065W_Spar Sequences read.. Counting patterns.. # site patterns = 145 Counting frequencies.. 120 bytes for distance 23200 bytes for lkl0 18560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.114916 0.126681 0.144468 0.071958 0.269273 0.152794 0.178415 lnL0 = -1150.237995 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1150.237995 x= 0.00006 0.11492 0.12668 0.14447 0.07196 0.26927 0.15279 0.17842 1 h-lim-p 0.0000 0.0000 25.8591 1150.229538 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0206 11.9156 1150.154548 0 0.0013 39 | 1/8 3 h-lim-p 0.0044 0.1713 3.4661 1150.149316 3 0.0009 58 | 1/8 4 h-lim-p 0.0045 0.3377 0.6990 1150.147284 4 0.0034 78 | 1/8 5 h-lim-p 0.0041 0.5585 0.5901 1150.138679 0 0.0082 98 | 1/8 6 h-lim-p 0.0057 0.2961 0.8474 1149.996107 0 0.0227 119 | 1/8 7 h-lim-p 0.0029 0.0364 6.5416 1149.763128 1 0.0037 140 | 1/8 8 h-lim-p 0.0150 0.1367 1.6035 1149.761498 5 0.0013 167 | 1/8 9 h-lim-p 0.6352 20.0000 0.0032 1149.757436 0 1.2704 180 | 1/8 10 h-lim-p 2.5000 20.0000 0.0007 1149.757207 3 1.0004 205 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 1149.757207 0 1.0938 224 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 1149.757207 0 1.0938 243 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 1149.757207 0 1.0938 262 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 1149.757207 0 0.0006 292 Out... lnL = -1149.757207 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1149.757207 Node 7: lnL = -1149.757207 Node 8: lnL = -1149.757207 Node 9: lnL = -1149.757207 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 783 Sequential format.. Reading seq # 1: YMR067C_Sbay Reading seq # 2: YMR067C_Scer Reading seq # 3: YMR067C_Skud Reading seq # 4: YMR067C_Smik Reading seq # 5: YMR067C_Spar Sequences read.. Counting patterns.. # site patterns = 319 Counting frequencies.. 120 bytes for distance 51040 bytes for lkl0 40832 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000543 0.227694 0.037596 0.185599 0.113084 0.348659 0.229675 0.235381 lnL0 = -3216.021634 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3216.021634 x= 0.00054 0.22769 0.03760 0.18560 0.11308 0.34866 0.22967 0.23538 1 h-lim-p 0.0031 0.0246 100.9649 3214.295631 4 0.0004 32 | 0/8 2 h-lim-p 0.0008 0.0061 37.6021 3213.795952 3 0.0008 50 | 0/8 3 h-lim-p 0.0007 0.0083 42.4908 3213.443663 5 0.0007 72 | 0/8 4 h-lim-p 0.0018 0.0235 16.4899 3213.373043 4 0.0007 92 | 0/8 5 h-lim-p 0.0004 0.0028 7.2439 3213.357865 0 0.0007 105 | 0/8 6 h-lim-p 0.0025 0.1711 2.0565 3213.356084 4 0.0009 125 | 0/8 7 h-lim-p 0.0047 0.7552 0.4153 3213.355994 2 0.0011 142 | 0/8 8 h-lim-p 0.2333 20.0000 0.0019 3213.351684 0 0.9333 164 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 3213.351420 1 0.9961 186 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3213.351419 0 1.0938 206 | 0/8 11 h-lim-p 2.1646 20.0000 0.0000 3213.351419 0 1.0823 226 | 0/8 12 h-lim-p 0.9916 20.0000 0.0000 3213.351419 0 2.9748 247 | 0/8 13 h-lim-p 0.0319 3.8859 0.0024 3213.351419 0 0.0001 275 | 0/8 14 h-lim-p 0.0002 20.0000 0.0014 3213.351419 0 0.0000 302 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 3213.351419 0 0.0000 334 Out... lnL = -3213.351419 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3213.351419 Node 7: lnL = -3213.351419 Node 8: lnL = -3213.351419 Node 9: lnL = -3213.351419 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 779 Sequential format.. Reading seq # 1: YMR068W_Sbay Reading seq # 2: YMR068W_Scer Reading seq # 3: YMR068W_Skud Reading seq # 4: YMR068W_Smik Reading seq # 5: YMR068W_Spar Sequences read.. Counting patterns.. # site patterns = 321 Counting frequencies.. 120 bytes for distance 51360 bytes for lkl0 41088 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.016094 0.142084 0.061109 0.171102 0.129743 0.271445 0.230542 0.225860 lnL0 = -3153.216100 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3153.216100 x= 0.01609 0.14208 0.06111 0.17110 0.12974 0.27144 0.23054 0.22586 1 h-lim-p 0.0029 0.0234 106.8497 3151.332496 4 0.0003 32 | 0/8 2 h-lim-p 0.0010 0.0084 29.2282 3151.067032 7 0.0007 64 | 0/8 3 h-lim-p 0.0009 0.0087 21.1684 3150.981058 7 0.0005 95 | 0/8 4 h-lim-p 0.0017 0.0182 6.8113 3150.966282 5 0.0008 116 | 0/8 5 h-lim-p 0.0017 0.0271 3.0966 3150.962824 4 0.0009 137 | 0/8 6 h-lim-p 0.0027 0.4252 1.0008 3150.962420 4 0.0009 158 | 0/8 7 h-lim-p 0.0034 1.5665 0.2653 3150.962387 3 0.0010 178 | 0/8 8 h-lim-p 0.3380 20.0000 0.0008 3150.961471 0 1.3519 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3150.961453 1 0.9961 222 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3150.961453 0 1.0938 242 | 0/8 11 h-lim-p 1.0102 20.0000 0.0000 3150.961453 0 8.0819 265 | 0/8 12 h-lim-p 0.0171 3.3374 0.0114 3150.961453 0 0.0032 287 | 0/8 13 h-lim-p 0.0006 0.5839 0.0649 3150.961453 0 0.0000 314 | 0/8 14 h-lim-p 0.0003 20.0000 0.0008 3150.961453 0 0.0000 343 | 0/8 15 h-lim-p 0.0005 20.0000 0.0000 3150.961453 0 0.0005 363 Out... lnL = -3150.961453 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3150.961453 Node 7: lnL = -3150.961453 Node 8: lnL = -3150.961453 Node 9: lnL = -3150.961453 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 374 Sequential format.. Reading seq # 1: YMR071C_Sbay Reading seq # 2: YMR071C_Scer Reading seq # 3: YMR071C_Skud Reading seq # 4: YMR071C_Smik Reading seq # 5: YMR071C_Spar Sequences read.. Counting patterns.. # site patterns = 128 Counting frequencies.. 120 bytes for distance 20480 bytes for lkl0 16384 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.026446 0.048543 0.062904 0.069027 0.053925 0.152377 0.122464 0.140154 lnL0 = -1322.849202 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1322.849202 x= 0.02645 0.04854 0.06290 0.06903 0.05392 0.15238 0.12246 0.14015 1 h-lim-p 0.0009 0.0070 55.5377 1322.398675 6 0.0003 35 | 0/8 2 h-lim-p 0.0012 0.0096 9.2840 1322.385084 5 0.0003 58 | 0/8 3 h-lim-p 0.0010 0.0279 2.8933 1322.383444 3 0.0004 76 | 0/8 4 h-lim-p 0.0010 0.3103 1.2137 1322.383149 2 0.0005 92 | 0/8 5 h-lim-p 0.0024 0.2283 0.2456 1322.383136 2 0.0005 109 | 0/8 6 h-lim-p 0.0021 2.8719 0.0540 1322.383136 1 0.0005 132 | 0/8 7 h-lim-p 0.0121 20.0000 0.0023 1322.383136 0 0.0013 154 | 0/8 8 h-lim-p 0.0136 20.0000 0.0002 1322.383129 0 0.4360 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1322.383128 0 1.0938 199 | 0/8 10 h-lim-p 1.1306 20.0000 0.0000 1322.383128 0 0.9893 219 | 0/8 11 h-lim-p 0.8112 20.0000 0.0000 1322.383128 0 0.0000 261 | 0/8 12 h-lim-p 0.0000 20.0000 0.0001 1322.383128 0 0.0000 291 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 1322.383128 0 0.0000 315 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1322.383128 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1322.383128 Node 7: lnL = -1322.383128 Node 8: lnL = -1322.383128 Node 9: lnL = -1322.383128 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 335 Sequential format.. Reading seq # 1: YMR072W_Sbay Reading seq # 2: YMR072W_Scer Reading seq # 3: YMR072W_Skud Reading seq # 4: YMR072W_Smik Reading seq # 5: YMR072W_Spar Sequences read.. Counting patterns.. # site patterns = 132 Counting frequencies.. 120 bytes for distance 21120 bytes for lkl0 16896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.009808 0.038783 0.084717 0.070820 0.104867 0.189736 0.112700 0.135502 lnL0 = -1222.805380 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1222.805380 x= 0.00981 0.03878 0.08472 0.07082 0.10487 0.18974 0.11270 0.13550 1 h-lim-p 0.0006 0.0047 81.9235 1221.840827 5 0.0003 33 | 0/8 2 h-lim-p 0.0007 0.0057 20.8269 1221.679514 7 0.0008 62 | 0/8 3 h-lim-p 0.0027 0.0300 5.9528 1221.671339 5 0.0005 85 | 0/8 4 h-lim-p 0.0042 0.3360 0.7043 1221.671211 2 0.0005 103 | 0/8 5 h-lim-p 0.0023 0.1774 0.1642 1221.671205 1 0.0005 126 | 0/8 6 h-lim-p 0.0101 13.6169 0.0080 1221.671204 0 0.0044 146 | 0/8 7 h-lim-p 0.0217 20.0000 0.0016 1221.671033 0 0.2600 169 | 0/8 8 h-lim-p 0.2825 20.0000 0.0015 1221.671033 0 0.0039 194 | 0/8 9 h-lim-p 0.0447 20.0000 0.0001 1221.671032 0 0.3575 217 | 0/8 10 h-lim-p 1.5449 20.0000 0.0000 1221.671032 0 1.3518 237 | 0/8 11 h-lim-p 2.4511 20.0000 0.0000 1221.671032 0 1.0724 257 | 0/8 12 h-lim-p 0.5780 20.0000 0.0000 1221.671032 0 1.1561 278 | 0/8 13 h-lim-p 0.0104 6.3186 0.0034 1221.671032 0 0.0002 303 | 0/8 14 h-lim-p 0.0000 1.9274 0.0113 1221.671032 0 0.0000 324 | 0/8 15 h-lim-p 0.0000 5.4328 0.0040 1221.671032 0 0.0000 345 | 0/8 16 h-lim-p 0.0001 20.0000 0.0004 1221.671032 0 0.0001 365 | 0/8 17 h-lim-p 0.0000 20.0000 0.0010 1221.671032 0 0.0000 393 | 0/8 18 h-lim-p 0.0001 20.0000 0.0000 1221.671032 0 0.0000 425 Out... lnL = -1221.671032 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1221.671032 Node 7: lnL = -1221.671032 Node 8: lnL = -1221.671032 Node 9: lnL = -1221.671032 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 172 Sequential format.. Reading seq # 1: YMR073C_Sbay Reading seq # 2: YMR073C_Scer Reading seq # 3: YMR073C_Skud Reading seq # 4: YMR073C_Smik Reading seq # 5: YMR073C_Spar Sequences read.. Counting patterns.. # site patterns = 100 Counting frequencies.. 120 bytes for distance 16000 bytes for lkl0 12800 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.126394 0.036080 0.085459 0.153927 0.047271 0.195345 0.258798 0.327074 lnL0 = -782.474742 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 782.474742 x= 0.12639 0.03608 0.08546 0.15393 0.04727 0.19535 0.25880 0.32707 1 h-lim-p 0.0005 0.0040 25.4478 782.127217 0 0.0010 23 | 0/8 2 h-lim-p 0.0035 20.0000 7.4314 782.107633 3 0.0008 42 | 0/8 3 h-lim-p 0.0015 0.0476 3.8406 782.097718 6 0.0017 69 | 0/8 4 h-lim-p 0.0037 0.0696 1.7345 782.094730 5 0.0025 94 | 0/8 5 h-lim-p 0.0129 0.3459 0.3337 782.094475 4 0.0046 115 | 0/8 6 h-lim-p 0.0184 2.8825 0.0834 782.094447 2 0.0048 140 | 0/8 7 h-lim-p 0.0317 8.7644 0.0127 782.093989 0 0.1266 162 | 0/8 8 h-lim-p 0.0065 0.5958 0.2476 782.091927 0 0.0130 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 782.091703 3 1.0004 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 782.091703 0 1.0938 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 782.091703 0 0.5469 250 | 0/8 12 h-lim-p 0.4008 20.0000 0.0000 782.091703 0 0.0063 275 | 0/8 13 h-lim-p 0.0037 20.0000 0.0000 782.091703 0 0.0000 306 Out... lnL = -782.091703 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -782.091703 Node 7: lnL = -782.091703 Node 8: lnL = -782.091703 Node 9: lnL = -782.091703 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 548 Sequential format.. Reading seq # 1: YMR074C_Sbay Reading seq # 2: YMR074C_Scer Reading seq # 3: YMR074C_Skud Reading seq # 4: YMR074C_Smik Reading seq # 5: YMR074C_Spar Sequences read.. Counting patterns.. # site patterns = 178 Counting frequencies.. 120 bytes for distance 28480 bytes for lkl0 22784 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.034890 0.105809 0.013527 0.059869 0.049297 0.222929 0.124505 0.164706 lnL0 = -2151.609141 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2151.609141 x= 0.03489 0.10581 0.01353 0.05987 0.04930 0.22293 0.12450 0.16471 1 h-lim-p 0.0007 0.0052 124.6714 2150.991351 6 0.0001 36 | 0/8 2 h-lim-p 0.0004 0.0050 29.3979 2150.876719 7 0.0003 64 | 0/8 3 h-lim-p 0.0005 0.0140 16.1355 2150.858792 6 0.0002 93 | 0/8 4 h-lim-p 0.0005 0.0227 5.7273 2150.855512 2 0.0002 109 | 0/8 5 h-lim-p 0.0005 0.0416 2.5435 2150.854939 3 0.0002 127 | 0/8 6 h-lim-p 0.0015 0.4610 0.3585 2150.854915 1 0.0004 142 | 0/8 7 h-lim-p 0.0039 8.4608 0.0351 2150.854914 0 0.0009 163 | 0/8 8 h-lim-p 0.1363 20.0000 0.0002 2150.854694 0 1.0902 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2150.854690 1 0.9961 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2150.854690 0 1.2500 228 | 0/8 11 h-lim-p 1.1354 20.0000 0.0000 2150.854690 0 1.1354 248 | 0/8 12 h-lim-p 0.0506 20.0000 0.0006 2150.854690 0 0.0221 268 | 0/8 13 h-lim-p 0.0066 20.0000 0.0020 2150.854690 0 0.0001 293 | 0/8 14 h-lim-p 0.0000 10.2639 0.0057 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 2150.854690 0 0.0000 363 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -2150.854690 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2150.854690 Node 7: lnL = -2150.854690 Node 8: lnL = -2150.854690 Node 9: lnL = -2150.854690 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 551 Sequential format.. Reading seq # 1: YMR075W_Sbay Reading seq # 2: YMR075W_Scer Reading seq # 3: YMR075W_Skud Reading seq # 4: YMR075W_Smik Reading seq # 5: YMR075W_Spar Sequences read.. Counting patterns.. # site patterns = 178 Counting frequencies.. 120 bytes for distance 28480 bytes for lkl0 22784 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.019154 0.090324 0.021576 0.058232 0.050935 0.202322 0.151460 0.136064 lnL0 = -2060.035089 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2060.035089 x= 0.01915 0.09032 0.02158 0.05823 0.05093 0.20232 0.15146 0.13606 1 h-lim-p 0.0003 0.0022 102.8448 2059.245817 7 0.0002 38 | 0/8 2 h-lim-p 0.0002 0.0016 34.1398 2059.119360 0 0.0003 50 | 0/8 3 h-lim-p 0.0007 0.0170 13.3959 2059.102851 7 0.0002 82 | 0/8 4 h-lim-p 0.0003 0.0083 8.2857 2059.096810 6 0.0002 110 | 0/8 5 h-lim-p 0.0007 0.0315 2.9232 2059.096083 4 0.0002 133 | 0/8 6 h-lim-p 0.0008 0.4474 0.7153 2059.095961 3 0.0005 154 | 0/8 7 h-lim-p 0.0118 9.4752 0.0295 2059.095924 3 0.0069 183 | 0/8 8 h-lim-p 0.0100 4.4025 0.0204 2059.091276 0 0.0801 206 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2059.091248 2 1.0938 230 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2059.091248 0 1.0938 250 | 0/8 11 h-lim-p 1.4604 20.0000 0.0000 2059.091248 0 1.4604 270 | 0/8 12 h-lim-p 0.3314 20.0000 0.0001 2059.091248 0 0.2900 290 | 0/8 13 h-lim-p 0.0463 20.0000 0.0008 2059.091248 0 0.0007 315 | 0/8 14 h-lim-p 0.0003 20.0000 0.0017 2059.091248 0 0.0002 335 | 0/8 15 h-lim-p 0.0001 10.4858 0.0035 2059.091248 0 0.0000 358 | 0/8 16 h-lim-p 0.0001 20.0000 0.0002 2059.091248 0 0.0000 390 | 0/8 17 h-lim-p 0.0000 20.0000 0.0009 | 0/8 18 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -2059.091248 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2059.091248 Node 7: lnL = -2059.091248 Node 8: lnL = -2059.091248 Node 9: lnL = -2059.091248 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 375 Sequential format.. Reading seq # 1: YMR077C_Sbay Reading seq # 2: YMR077C_Scer Reading seq # 3: YMR077C_Skud Reading seq # 4: YMR077C_Smik Reading seq # 5: YMR077C_Spar Sequences read.. Counting patterns.. # site patterns = 174 Counting frequencies.. 120 bytes for distance 27840 bytes for lkl0 22272 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.104609 0.076624 0.052988 0.107864 0.100360 0.265635 0.219977 0.296366 lnL0 = -1791.423457 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1791.423457 x= 0.10461 0.07662 0.05299 0.10786 0.10036 0.26563 0.21998 0.29637 1 h-lim-p 0.0010 0.0079 70.5707 1790.468619 7 0.0004 38 | 0/8 2 h-lim-p 0.0011 0.0087 20.0683 1790.325618 7 0.0007 70 | 0/8 3 h-lim-p 0.0010 0.0198 15.0776 1790.275633 6 0.0006 96 | 0/8 4 h-lim-p 0.0023 0.0404 4.1631 1790.271003 4 0.0006 117 | 0/8 5 h-lim-p 0.0023 0.2267 1.1076 1790.270431 2 0.0010 133 | 0/8 6 h-lim-p 0.0031 0.7075 0.3618 1790.270379 3 0.0009 153 | 0/8 7 h-lim-p 0.0099 5.4097 0.0331 1790.270378 1 0.0012 177 | 0/8 8 h-lim-p 0.1959 20.0000 0.0002 1790.270326 0 1.1753 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1790.270324 0 1.0938 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1790.270324 0 1.0938 239 | 0/8 11 h-lim-p 1.4137 20.0000 0.0000 1790.270324 0 2.1206 259 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1790.270324 0 0.3125 281 | 0/8 13 h-lim-p 0.0630 20.0000 0.0000 1790.270324 0 0.0020 305 | 0/8 14 h-lim-p 0.0012 20.0000 0.0000 1790.270324 0 0.0002 327 | 0/8 15 h-lim-p 0.0009 20.0000 0.0000 1790.270324 0 0.0000 365 Out... lnL = -1790.270324 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1790.270324 Node 7: lnL = -1790.270324 Node 8: lnL = -1790.270324 Node 9: lnL = -1790.270324 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 263 Sequential format.. Reading seq # 1: YMR078C_Sbay Reading seq # 2: YMR078C_Scer Reading seq # 3: YMR078C_Skud Reading seq # 4: YMR078C_Smik Reading seq # 5: YMR078C_Spar Sequences read.. Counting patterns.. # site patterns = 100 Counting frequencies.. 120 bytes for distance 16000 bytes for lkl0 12800 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.052682 0.048627 0.073537 0.075099 0.087466 0.007002 0.119935 0.153694 lnL0 = -1020.828830 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1020.828830 x= 0.05268 0.04863 0.07354 0.07510 0.08747 0.00700 0.11994 0.15369 1 h-lim-p 0.0000 0.0079 972.0957 1007.765145 0 0.0001 24 | 0/8 2 h-lim-p 0.0005 0.0041 45.0583 1007.045044 0 0.0010 37 | 0/8 3 h-lim-p 0.0005 0.0038 19.2321 1006.962084 6 0.0005 61 | 0/8 4 h-lim-p 0.0024 0.0427 4.0237 1006.957395 6 0.0006 85 | 0/8 5 h-lim-p 0.0030 0.1371 0.8037 1006.957194 4 0.0005 109 | 0/8 6 h-lim-p 0.0057 2.4282 0.0723 1006.954706 0 0.0228 131 | 0/8 7 h-lim-p 0.0031 0.2995 0.5246 1006.847982 0 0.0252 154 | 0/8 8 h-lim-p 0.0018 0.0181 7.4205 1006.806244 7 0.0011 193 | 0/8 9 h-lim-p 2.4349 20.0000 0.0034 1006.641491 0 4.8698 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0038 1006.631628 6 0.9225 240 | 0/8 11 h-lim-p 2.5000 20.0000 0.0003 1006.631518 2 0.9644 264 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1006.631518 0 1.0938 284 | 0/8 13 h-lim-p 1.9931 20.0000 0.0000 1006.631518 0 0.8720 304 | 0/8 14 h-lim-p 0.6681 20.0000 0.0000 1006.631518 0 0.0026 331 | 0/8 15 h-lim-p 0.0005 20.0000 0.0001 1006.631518 0 0.0003 351 | 0/8 16 h-lim-p 0.0000 20.0000 0.0005 1006.631518 0 0.0000 378 | 0/8 17 h-lim-p 0.0001 20.0000 0.0000 1006.631518 0 0.0000 402 Out... lnL = -1006.631518 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1006.631518 Node 7: lnL = -1006.631518 Node 8: lnL = -1006.631518 Node 9: lnL = -1006.631518 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 700 Sequential format.. Reading seq # 1: YMR081C_Sbay Reading seq # 2: YMR081C_Scer Reading seq # 3: YMR081C_Skud Reading seq # 4: YMR081C_Smik Reading seq # 5: YMR081C_Spar Sequences read.. Counting patterns.. # site patterns = 209 Counting frequencies.. 120 bytes for distance 33440 bytes for lkl0 26752 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.063045 0.029645 0.052812 0.070484 0.046016 0.154737 0.174099 0.184499 lnL0 = -2820.454334 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2820.454334 x= 0.06304 0.02965 0.05281 0.07048 0.04602 0.15474 0.17410 0.18450 1 h-lim-p 0.0002 0.0014 159.3856 2818.933158 8 0.0001 40 | 0/8 2 h-lim-p 0.0006 0.0045 24.4367 2818.879151 6 0.0002 67 | 0/8 3 h-lim-p 0.0003 0.0206 13.1525 2818.868251 2 0.0002 83 | 0/8 4 h-lim-p 0.0003 0.0191 7.8980 2818.864414 5 0.0002 107 | 0/8 5 h-lim-p 0.0011 0.1417 1.2680 2818.864206 2 0.0003 124 | 0/8 6 h-lim-p 0.0006 0.2735 0.5491 2818.864177 2 0.0002 140 | 0/8 7 h-lim-p 0.0031 4.8358 0.0419 2818.864176 0 0.0004 162 | 0/8 8 h-lim-p 0.3271 20.0000 0.0000 2818.864169 0 1.3083 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2818.864169 0 1.0938 204 | 0/8 10 h-lim-p 1.4298 20.0000 0.0000 2818.864169 0 1.2511 224 | 0/8 11 h-lim-p 1.2284 20.0000 0.0000 2818.864169 0 0.0000 261 | 0/8 12 h-lim-p 0.0002 20.0000 0.0000 2818.864169 0 0.0000 284 Out... lnL = -2818.864169 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2818.864169 Node 7: lnL = -2818.864169 Node 8: lnL = -2818.864169 Node 9: lnL = -2818.864169 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 897 Sequential format.. Reading seq # 1: YMR083W_Sbay Reading seq # 2: YMR083W_Scer Reading seq # 3: YMR083W_Skud Reading seq # 4: YMR083W_Smik Reading seq # 5: YMR083W_Spar Sequences read.. Counting patterns.. # site patterns = 250 Counting frequencies.. 120 bytes for distance 40000 bytes for lkl0 32000 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.071370 0.011595 0.044052 0.111353 0.070667 0.073364 0.156995 0.182948 lnL0 = -3223.708959 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3223.708959 x= 0.07137 0.01160 0.04405 0.11135 0.07067 0.07336 0.15699 0.18295 1 h-lim-p 0.0003 0.0021 326.3848 3219.852242 8 0.0001 40 | 0/8 2 h-lim-p 0.0002 0.0014 94.3077 3218.930794 0 0.0003 52 | 0/8 3 h-lim-p 0.0004 0.0031 46.0992 3218.793990 3 0.0002 70 | 0/8 4 h-lim-p 0.0006 0.0137 12.7548 3218.775241 5 0.0003 91 | 0/8 5 h-lim-p 0.0030 0.1389 1.0861 3218.775037 2 0.0003 109 | 0/8 6 h-lim-p 0.0019 1.0572 0.1819 3218.775015 2 0.0006 127 | 0/8 7 h-lim-p 0.0033 2.4410 0.0357 3218.774346 0 0.0196 149 | 0/8 8 h-lim-p 0.0021 0.4591 0.3416 3218.756115 0 0.0082 171 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 3218.755639 4 1.3578 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 3218.755631 0 1.0938 220 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3218.755631 0 2.1875 240 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3218.755630 0 1.0938 260 | 0/8 13 h-lim-p 0.1350 20.0000 0.0000 3218.755630 0 4.3190 285 | 0/8 14 h-lim-p 0.9169 20.0000 0.0001 3218.755630 0 0.4584 305 | 0/8 15 h-lim-p 0.0004 0.9331 0.1188 3218.755630 0 0.0000 329 | 0/8 16 h-lim-p 0.0004 20.0000 0.0043 3218.755630 0 0.0000 365 | 0/8 17 h-lim-p 0.0000 20.0000 0.0033 | 0/8 18 h-lim-p 0.0000 20.0000 0.0033 Out... lnL = -3218.755630 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3218.755630 Node 7: lnL = -3218.755630 Node 8: lnL = -3218.755630 Node 9: lnL = -3218.755630 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 165 Sequential format.. Reading seq # 1: YMR087W_Sbay Reading seq # 2: YMR087W_Scer Reading seq # 3: YMR087W_Skud Reading seq # 4: YMR087W_Smik Reading seq # 5: YMR087W_Spar Sequences read.. Counting patterns.. # site patterns = 90 Counting frequencies.. 120 bytes for distance 14400 bytes for lkl0 11520 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.399298 0.000060 0.074442 0.075668 0.083313 0.153109 0.276487 0.657526 lnL0 = -736.217201 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 736.217201 x= 0.39930 0.00006 0.07444 0.07567 0.08331 0.15311 0.27649 0.65753 1 h-lim-p 0.0003 0.0022 53.5034 734.876141 0 0.0011 24 | 0/8 2 h-lim-p 0.0015 0.0122 11.6177 734.802872 5 0.0012 46 | 0/8 3 h-lim-p 0.0014 0.0154 9.5109 734.770854 7 0.0011 73 | 0/8 4 h-lim-p 0.0049 0.1804 2.0346 734.764326 6 0.0033 100 | 0/8 5 h-lim-p 0.0015 0.0686 4.5643 734.753298 0 0.0030 113 | 0/8 6 h-lim-p 0.0045 0.2046 3.0335 734.749227 2 0.0021 129 | 0/8 7 h-lim-p 0.0132 1.2355 0.4842 734.744079 0 0.0264 142 | 0/8 8 h-lim-p 0.5792 6.8388 0.0220 734.690995 3 0.4842 168 | 0/8 9 h-lim-p 2.5000 20.0000 0.0012 734.690608 3 0.9961 194 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 734.690606 1 1.0938 216 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 734.690606 0 1.0938 236 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 734.690606 0 1.0938 256 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 734.690606 0 5.0000 277 | 0/8 14 h-lim-p 1.8793 20.0000 0.0000 734.690606 0 0.4698 298 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 734.690606 0 0.1562 321 | 0/8 16 h-lim-p 0.0606 20.0000 0.0000 734.690606 0 0.0001 349 Out... lnL = -734.690606 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -734.690606 Node 7: lnL = -734.690606 Node 8: lnL = -734.690606 Node 9: lnL = -734.690606 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 519 Sequential format.. Reading seq # 1: YMR088C_Sbay Reading seq # 2: YMR088C_Scer Reading seq # 3: YMR088C_Skud Reading seq # 4: YMR088C_Smik Reading seq # 5: YMR088C_Spar Sequences read.. Counting patterns.. # site patterns = 113 Counting frequencies.. 120 bytes for distance 18080 bytes for lkl0 14464 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.327991 0.013304 0.050390 0.069434 0.012408 0.086830 0.128103 0.511156 lnL0 = -1649.025414 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1649.025414 x= 0.32799 0.01330 0.05039 0.06943 0.01241 0.08683 0.12810 0.51116 1 h-lim-p 0.0001 0.0007 80.5638 1648.373567 0 0.0002 23 | 0/8 2 h-lim-p 0.0001 0.0010 39.4489 1648.340327 5 0.0001 46 | 0/8 3 h-lim-p 0.0001 0.0011 20.7515 1648.309241 0 0.0002 59 | 0/8 4 h-lim-p 0.0001 0.0006 19.8024 1648.189029 m 0.0006 71 | 1/8 5 h-lim-p 0.0003 0.0072 26.5281 1648.183211 2 0.0001 88 | 1/8 6 h-lim-p 0.0009 0.1069 2.3998 1648.155029 0 0.0052 102 | 1/8 7 h-lim-p 0.0092 1.1115 1.3577 1648.151863 4 0.0040 121 | 1/8 8 h-lim-p 0.2544 16.9916 0.0211 1648.140079 0 0.3817 133 | 1/8 9 h-lim-p 2.5000 20.0000 0.0020 1648.139223 3 0.9961 158 | 1/8 10 h-lim-p 2.5000 20.0000 0.0000 1648.139222 0 1.0938 177 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 1648.139222 0 1.0938 196 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 1648.139222 0 0.0391 220 | 1/8 13 h-lim-p 0.0191 20.0000 0.0000 1648.139222 0 0.0095 239 | 1/8 14 h-lim-p 0.0065 20.0000 0.0000 1648.139222 0 0.0016 259 Out... lnL = -1648.139222 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1648.139222 Node 7: lnL = -1648.139222 Node 8: lnL = -1648.139222 Node 9: lnL = -1648.139222 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 893 Sequential format.. Reading seq # 1: YMR090W_Sbay Reading seq # 2: YMR090W_Scer Reading seq # 3: YMR090W_Skud Reading seq # 4: YMR090W_Smik Reading seq # 5: YMR090W_Spar Sequences read.. Counting patterns.. # site patterns = 376 Counting frequencies.. 120 bytes for distance 60160 bytes for lkl0 48128 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.037942 0.088809 0.253081 0.226670 0.117545 0.341662 0.255384 0.305269 lnL0 = -4563.168080 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4563.168080 x= 0.03794 0.08881 0.25308 0.22667 0.11755 0.34166 0.25538 0.30527 1 h-lim-p 0.0917 4.1715 31.5448 4562.925582 7 0.0005 46 | 0/8 2 h-lim-p 0.0012 0.0184 13.2388 4562.875338 6 0.0007 73 | 0/8 3 h-lim-p 0.0014 0.0235 6.2082 4562.868928 5 0.0004 97 | 0/8 4 h-lim-p 0.0015 0.1014 1.6897 4562.868045 2 0.0007 113 | 0/8 5 h-lim-p 0.0031 0.3115 0.3606 4562.867995 2 0.0008 130 | 0/8 6 h-lim-p 0.0036 2.9051 0.0815 4562.867992 0 0.0008 151 | 0/8 7 h-lim-p 0.0051 20.0000 0.0127 4562.867992 0 0.0022 171 | 0/8 8 h-lim-p 0.1004 20.0000 0.0003 4562.867959 0 0.8035 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4562.867959 0 1.0938 214 | 0/8 10 h-lim-p 1.2200 20.0000 0.0000 4562.867959 0 1.0675 234 | 0/8 11 h-lim-p 0.8796 20.0000 0.0000 4562.867959 0 0.0137 259 | 0/8 12 h-lim-p 0.0005 20.0000 0.0007 4562.867959 0 0.0000 290 | 0/8 13 h-lim-p 0.0006 20.0000 0.0000 4562.867959 0 0.0001 312 Out... lnL = -4562.867959 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4562.867959 Node 7: lnL = -4562.867959 Node 8: lnL = -4562.867959 Node 9: lnL = -4562.867959 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 296 Sequential format.. Reading seq # 1: YMR091C_Sbay Reading seq # 2: YMR091C_Scer Reading seq # 3: YMR091C_Skud Reading seq # 4: YMR091C_Smik Reading seq # 5: YMR091C_Spar Sequences read.. Counting patterns.. # site patterns = 149 Counting frequencies.. 120 bytes for distance 23840 bytes for lkl0 19072 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.025076 0.104773 0.053942 0.146542 0.076281 0.232438 0.208791 0.191463 lnL0 = -1308.574196 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1308.574196 x= 0.02508 0.10477 0.05394 0.14654 0.07628 0.23244 0.20879 0.19146 1 h-lim-p 0.0036 0.0285 69.4740 1307.431524 8 0.0005 41 | 0/8 2 h-lim-p 0.0009 0.0070 16.1479 1307.330974 2 0.0008 57 | 0/8 3 h-lim-p 0.0018 0.0161 7.3546 1307.315551 5 0.0007 79 | 0/8 4 h-lim-p 0.0049 0.2625 1.0322 1307.314994 2 0.0011 96 | 0/8 5 h-lim-p 0.0037 0.2443 0.3015 1307.314951 3 0.0011 116 | 0/8 6 h-lim-p 0.0044 4.2238 0.0746 1307.314948 0 0.0011 137 | 0/8 7 h-lim-p 0.0123 20.0000 0.0067 1307.314948 0 0.0061 157 | 0/8 8 h-lim-p 0.0569 20.0000 0.0007 1307.314897 0 0.3416 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1307.314896 0 1.2500 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1307.314896 0 1.0938 219 | 0/8 11 h-lim-p 1.1622 20.0000 0.0000 1307.314896 0 1.1622 239 | 0/8 12 h-lim-p 0.0879 20.0000 0.0002 1307.314896 0 0.0769 259 | 0/8 13 h-lim-p 0.0225 20.0000 0.0005 1307.314896 0 0.0056 280 | 0/8 14 h-lim-p 0.0025 20.0000 0.0012 1307.314896 0 0.0000 319 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 1307.314896 0 0.0000 349 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1307.314896 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1307.314896 Node 7: lnL = -1307.314896 Node 8: lnL = -1307.314896 Node 9: lnL = -1307.314896 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 588 Sequential format.. Reading seq # 1: YMR093W_Sbay Reading seq # 2: YMR093W_Scer Reading seq # 3: YMR093W_Skud Reading seq # 4: YMR093W_Smik Reading seq # 5: YMR093W_Spar Sequences read.. Counting patterns.. # site patterns = 243 Counting frequencies.. 120 bytes for distance 38880 bytes for lkl0 31104 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.060876 0.066141 0.093572 0.145564 0.094811 0.234695 0.246012 0.249999 lnL0 = -2748.194630 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2748.194630 x= 0.06088 0.06614 0.09357 0.14556 0.09481 0.23470 0.24601 0.25000 1 h-lim-p 0.0015 0.0123 98.7442 2746.664801 6 0.0003 35 | 0/8 2 h-lim-p 0.0010 0.0077 16.7126 2746.601300 2 0.0004 51 | 0/8 3 h-lim-p 0.0008 0.0369 9.4291 2746.584586 6 0.0005 79 | 0/8 4 h-lim-p 0.0015 0.0839 2.9873 2746.582051 4 0.0006 98 | 0/8 5 h-lim-p 0.0049 1.4208 0.3901 2746.581996 3 0.0007 119 | 0/8 6 h-lim-p 0.0045 5.0695 0.0636 2746.581995 0 0.0010 140 | 0/8 7 h-lim-p 0.0043 11.4665 0.0146 2746.581994 0 0.0022 160 | 0/8 8 h-lim-p 0.0235 20.0000 0.0013 2746.581785 0 0.3758 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2746.581781 0 1.0938 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2746.581781 0 1.0938 224 | 0/8 11 h-lim-p 1.0581 20.0000 0.0000 2746.581781 0 0.4629 244 | 0/8 12 h-lim-p 0.1242 20.0000 0.0000 2746.581781 0 0.0155 266 | 0/8 13 h-lim-p 0.0058 20.0000 0.0001 2746.581781 0 0.0007 288 | 0/8 14 h-lim-p 0.0010 20.0000 0.0001 2746.581781 0 0.0000 321 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 2746.581781 0 0.0000 350 Out... lnL = -2746.581781 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2746.581781 Node 7: lnL = -2746.581781 Node 8: lnL = -2746.581781 Node 9: lnL = -2746.581781 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 509 Sequential format.. Reading seq # 1: YMR095C_Sbay Reading seq # 2: YMR095C_Scer Reading seq # 3: YMR095C_Skud Reading seq # 4: YMR095C_Smik Reading seq # 5: YMR095C_Spar Sequences read.. Counting patterns.. # site patterns = 208 Counting frequencies.. 120 bytes for distance 33280 bytes for lkl0 26624 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.068487 0.030719 0.070345 0.142983 0.090254 0.206695 0.263293 0.241780 lnL0 = -2281.567965 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2281.567965 x= 0.06849 0.03072 0.07035 0.14298 0.09025 0.20669 0.26329 0.24178 1 h-lim-p 0.0018 0.0143 131.1831 2279.466728 8 0.0003 44 | 0/8 2 h-lim-p 0.0008 0.0066 16.9442 2279.401006 7 0.0005 74 | 0/8 3 h-lim-p 0.0010 0.0354 7.6407 2279.388183 4 0.0005 95 | 0/8 4 h-lim-p 0.0015 0.1240 2.6064 2279.385717 5 0.0008 118 | 0/8 5 h-lim-p 0.0043 0.9046 0.4998 2279.385620 3 0.0008 137 | 0/8 6 h-lim-p 0.0083 4.3956 0.0495 2279.385620 0 0.0009 159 | 0/8 7 h-lim-p 0.0044 16.9751 0.0101 2279.385619 0 0.0039 179 | 0/8 8 h-lim-p 0.0427 20.0000 0.0009 2279.385474 0 0.3415 202 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2279.385473 0 1.0938 222 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2279.385473 0 1.0938 242 | 0/8 11 h-lim-p 1.1070 20.0000 0.0000 2279.385473 0 0.0086 268 | 0/8 12 h-lim-p 0.0019 20.0000 0.0000 2279.385473 0 0.0000 299 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 2279.385473 0 0.0000 330 Out... lnL = -2279.385473 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2279.385473 Node 7: lnL = -2279.385473 Node 8: lnL = -2279.385473 Node 9: lnL = -2279.385473 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 492 Sequential format.. Reading seq # 1: YMR096W_Sbay Reading seq # 2: YMR096W_Scer Reading seq # 3: YMR096W_Skud Reading seq # 4: YMR096W_Smik Reading seq # 5: YMR096W_Spar Sequences read.. Counting patterns.. # site patterns = 208 Counting frequencies.. 120 bytes for distance 33280 bytes for lkl0 26624 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.087658 0.025573 0.088986 0.137517 0.098836 0.197762 0.215243 0.261775 lnL0 = -2240.485542 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2240.485542 x= 0.08766 0.02557 0.08899 0.13752 0.09884 0.19776 0.21524 0.26178 1 h-lim-p 0.0032 0.0489 118.1643 2238.672203 8 0.0003 43 | 0/8 2 h-lim-p 0.0013 0.0101 21.8229 2238.500537 7 0.0007 73 | 0/8 3 h-lim-p 0.0015 0.0255 10.5032 2238.479166 6 0.0005 101 | 0/8 4 h-lim-p 0.0014 0.0580 3.5361 2238.476077 4 0.0006 122 | 0/8 5 h-lim-p 0.0039 0.3541 0.5099 2238.475977 2 0.0008 139 | 0/8 6 h-lim-p 0.0065 4.3854 0.0620 2238.475976 0 0.0007 161 | 0/8 7 h-lim-p 0.0146 20.0000 0.0030 2238.475967 0 0.0439 182 | 0/8 8 h-lim-p 0.0070 20.0000 0.0187 2238.475716 0 0.0281 204 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2238.475706 1 0.9961 226 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2238.475706 0 2.1875 246 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2238.475706 0 1.0938 266 | 0/8 12 h-lim-p 0.1511 20.0000 0.0000 2238.475706 0 9.6720 292 | 0/8 13 h-lim-p 0.3429 20.0000 0.0003 2238.475706 0 0.0027 318 | 0/8 14 h-lim-p 0.0004 20.0000 0.0018 2238.475706 0 0.0000 353 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 2238.475706 0 0.0000 390 Out... lnL = -2238.475706 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2238.475706 Node 7: lnL = -2238.475706 Node 8: lnL = -2238.475706 Node 9: lnL = -2238.475706 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 259 Sequential format.. Reading seq # 1: YMR097C_Sbay Reading seq # 2: YMR097C_Scer Reading seq # 3: YMR097C_Skud Reading seq # 4: YMR097C_Smik Reading seq # 5: YMR097C_Spar Sequences read.. Counting patterns.. # site patterns = 117 Counting frequencies.. 120 bytes for distance 18720 bytes for lkl0 14976 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.052146 0.123194 0.034134 0.135938 0.067219 0.243943 0.189330 0.222803 lnL0 = -1154.199333 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1154.199333 x= 0.05215 0.12319 0.03413 0.13594 0.06722 0.24394 0.18933 0.22280 1 h-lim-p 0.0040 0.0317 26.9189 1154.004611 8 0.0006 43 | 0/8 2 h-lim-p 0.0010 0.0127 15.3639 1153.914950 2 0.0009 59 | 0/8 3 h-lim-p 0.0024 0.0263 5.8684 1153.906734 2 0.0006 76 | 0/8 4 h-lim-p 0.0023 0.1597 1.4610 1153.905742 2 0.0010 92 | 0/8 5 h-lim-p 0.0049 0.7119 0.2984 1153.905695 2 0.0011 109 | 0/8 6 h-lim-p 0.0063 8.7305 0.0511 1153.905693 0 0.0016 130 | 0/8 7 h-lim-p 0.0240 20.0000 0.0033 1153.905693 0 0.0060 151 | 0/8 8 h-lim-p 0.0174 20.0000 0.0011 1153.905666 0 0.1393 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1153.905665 0 1.0938 194 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1153.905665 0 1.0938 214 | 0/8 11 h-lim-p 1.0480 20.0000 0.0000 1153.905665 0 4.1920 236 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1153.905665 0 0.0391 261 | 0/8 13 h-lim-p 0.0045 20.0000 0.0001 1153.905665 0 0.0000 300 | 0/8 14 h-lim-p 0.0000 20.0000 0.0011 1153.905665 0 0.0000 333 | 0/8 15 h-lim-p 0.0000 20.0000 0.0011 1153.905665 0 0.0000 361 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 1153.905665 0 0.0000 381 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 1153.905665 0 0.0000 403 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 1153.905665 0 0.0000 427 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 1153.905665 0 0.0000 455 | 0/8 20 h-lim-p 0.0000 20.0000 0.0011 1153.905665 0 0.0000 481 | 0/8 21 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 22 h-lim-p 0.0000 20.0000 0.0011 | 0/8 23 h-lim-p 0.0000 20.0000 0.0011 Out... lnL = -1153.905665 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1153.905665 Node 7: lnL = -1153.905665 Node 8: lnL = -1153.905665 Node 9: lnL = -1153.905665 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 877 Sequential format.. Reading seq # 1: YMR098C_Sbay Reading seq # 2: YMR098C_Scer Reading seq # 3: YMR098C_Skud Reading seq # 4: YMR098C_Smik Reading seq # 5: YMR098C_Spar Sequences read.. Counting patterns.. # site patterns = 488 Counting frequencies.. 120 bytes for distance 78080 bytes for lkl0 62464 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.169634 0.249408 0.000060 0.426657 0.377348 0.550274 0.689992 0.537721 lnL0 = -5203.964145 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 5203.964145 x= 0.16963 0.24941 0.00006 0.42666 0.37735 0.55027 0.68999 0.53772 1 h-lim-p 0.0000 0.0000 172.0891 5203.936840 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0394 29.0932 5200.506089 0 0.0102 44 | 1/8 3 h-lim-p 0.0035 0.0280 21.2305 5200.155442 5 0.0019 67 | 1/8 4 h-lim-p 0.0027 0.0255 14.7037 5199.852021 1 0.0034 81 | 1/8 5 h-lim-p 0.0043 0.0454 11.5919 5199.561962 2 0.0040 97 | 1/8 6 h-lim-p 0.0061 0.1169 7.6458 5198.616679 0 0.0182 110 | 1/8 7 h-lim-p 0.0270 0.2164 2.6818 5182.434768 0 0.1623 124 | 1/8 8 h-lim-p 0.3508 2.8061 0.2253 5180.688802 1 0.4385 138 | 1/8 9 h-lim-p 1.0222 8.4942 0.0966 5180.535981 7 0.3058 176 | 1/8 10 h-lim-p 2.4862 20.0000 0.0119 5180.514625 6 0.8268 210 | 1/8 11 h-lim-p 2.5000 20.0000 0.0029 5180.513251 3 0.8246 237 | 1/8 12 h-lim-p 2.5000 20.0000 0.0002 5180.513246 0 1.0938 256 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 5180.513246 0 1.0938 275 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 5180.513245 0 1.0938 294 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 5180.513245 0 1.0938 313 | 1/8 16 h-lim-p 1.2252 20.0000 0.0000 5180.513245 0 1.8377 332 | 1/8 17 h-lim-p 0.8264 20.0000 0.0000 5180.513245 0 0.2066 352 | 1/8 18 h-lim-p 0.0109 20.0000 0.0001 5180.513245 0 0.0109 371 | 1/8 19 h-lim-p 0.0131 20.0000 0.0001 5180.513245 0 0.0008 393 | 1/8 20 h-lim-p 0.0010 20.0000 0.0001 5180.513245 0 0.0000 424 | 1/8 21 h-lim-p 0.0001 20.0000 0.0000 5180.513245 0 0.0000 456 Out... lnL = -5180.513245 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -5180.513245 Node 7: lnL = -5180.513245 Node 8: lnL = -5180.513245 Node 9: lnL = -5180.513245 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 853 Sequential format.. Reading seq # 1: YMR099C_Sbay Reading seq # 2: YMR099C_Scer Reading seq # 3: YMR099C_Skud Reading seq # 4: YMR099C_Smik Reading seq # 5: YMR099C_Spar Sequences read.. Counting patterns.. # site patterns = 387 Counting frequencies.. 120 bytes for distance 61920 bytes for lkl0 49536 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.050009 0.223524 0.203610 0.189503 0.099744 0.348424 0.251019 0.319775 lnL0 = -4482.180820 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4482.180820 x= 0.05001 0.22352 0.20361 0.18950 0.09974 0.34842 0.25102 0.31977 1 h-lim-p 0.0022 0.0175 55.4103 4481.573095 7 0.0004 37 | 0/8 2 h-lim-p 0.0008 0.0083 28.8909 4481.448828 2 0.0004 53 | 0/8 3 h-lim-p 0.0031 0.0254 3.4639 4481.444170 4 0.0008 74 | 0/8 4 h-lim-p 0.0017 0.3060 1.5663 4481.443258 3 0.0009 93 | 0/8 5 h-lim-p 0.0034 1.0632 0.3934 4481.443198 1 0.0009 108 | 0/8 6 h-lim-p 0.0040 6.1097 0.0849 4481.443195 1 0.0010 131 | 0/8 7 h-lim-p 0.0133 20.0000 0.0062 4481.443194 0 0.0116 151 | 0/8 8 h-lim-p 0.0696 20.0000 0.0010 4481.443126 0 0.2089 172 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4481.443125 0 1.0938 192 | 0/8 10 h-lim-p 1.7253 20.0000 0.0000 4481.443125 0 1.5096 212 | 0/8 11 h-lim-p 2.1270 20.0000 0.0000 4481.443125 0 1.8611 232 | 0/8 12 h-lim-p 0.9837 20.0000 0.0000 4481.443125 0 0.9837 252 | 0/8 13 h-lim-p 0.0970 20.0000 0.0002 4481.443125 0 0.0243 273 | 0/8 14 h-lim-p 0.0070 20.0000 0.0008 4481.443125 0 0.0062 293 | 0/8 15 h-lim-p 0.0028 20.0000 0.0017 4481.443125 0 0.0000 333 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 4481.443125 0 0.0000 355 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0003 | 0/8 19 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -4481.443125 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4481.443125 Node 7: lnL = -4481.443125 Node 8: lnL = -4481.443125 Node 9: lnL = -4481.443125 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 394 Sequential format.. Reading seq # 1: YMR101C_Sbay Reading seq # 2: YMR101C_Scer Reading seq # 3: YMR101C_Skud Reading seq # 4: YMR101C_Smik Reading seq # 5: YMR101C_Spar Sequences read.. Counting patterns.. # site patterns = 159 Counting frequencies.. 120 bytes for distance 25440 bytes for lkl0 20352 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.056184 0.064645 0.058542 0.128771 0.052722 0.213074 0.224314 0.207843 lnL0 = -1769.270775 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1769.270775 x= 0.05618 0.06464 0.05854 0.12877 0.05272 0.21307 0.22431 0.20784 1 h-lim-p 0.0004 0.0030 70.2663 1768.385404 3 0.0004 28 | 0/8 2 h-lim-p 0.0009 0.0072 15.5914 1768.328693 5 0.0005 51 | 0/8 3 h-lim-p 0.0011 0.0410 6.7388 1768.323820 3 0.0003 70 | 0/8 4 h-lim-p 0.0012 0.1302 1.3916 1768.323037 5 0.0009 94 | 0/8 5 h-lim-p 0.0043 1.2199 0.2774 1768.323004 1 0.0009 109 | 0/8 6 h-lim-p 0.0042 4.7032 0.0617 1768.323003 1 0.0005 133 | 0/8 7 h-lim-p 0.0021 20.0000 0.0150 1768.323002 0 0.0019 153 | 0/8 8 h-lim-p 0.1446 20.0000 0.0002 1768.322968 0 0.8674 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1768.322968 0 1.0938 195 | 0/8 10 h-lim-p 2.4718 20.0000 0.0000 1768.322968 0 2.1628 215 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1768.322968 0 1.0938 235 | 0/8 12 h-lim-p 0.1281 20.0000 0.0000 1768.322968 0 8.1966 261 | 0/8 13 h-lim-p 0.3716 20.0000 0.0003 1768.322968 0 0.0174 285 | 0/8 14 h-lim-p 0.0017 20.0000 0.0027 1768.322968 0 0.0004 306 | 0/8 15 h-lim-p 0.0001 13.0004 0.0068 1768.322968 0 0.0000 335 | 0/8 16 h-lim-p 0.0004 20.0000 0.0000 1768.322968 0 0.0000 370 Out... lnL = -1768.322968 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1768.322968 Node 7: lnL = -1768.322968 Node 8: lnL = -1768.322968 Node 9: lnL = -1768.322968 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 459 Sequential format.. Reading seq # 1: YMR104C_Sbay Reading seq # 2: YMR104C_Scer Reading seq # 3: YMR104C_Skud Reading seq # 4: YMR104C_Smik Reading seq # 5: YMR104C_Spar Sequences read.. Counting patterns.. # site patterns = 160 Counting frequencies.. 120 bytes for distance 25600 bytes for lkl0 20480 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.070749 0.063860 0.021825 0.100550 0.061199 0.143055 0.110772 0.184257 lnL0 = -1828.816285 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1828.816285 x= 0.07075 0.06386 0.02182 0.10055 0.06120 0.14306 0.11077 0.18426 1 h-lim-p 0.0020 0.0157 116.2039 1827.935896 8 0.0001 42 | 0/8 2 h-lim-p 0.0004 0.0034 35.9366 1827.770733 8 0.0003 74 | 0/8 3 h-lim-p 0.0012 0.0330 8.1825 1827.762737 3 0.0003 93 | 0/8 4 h-lim-p 0.0006 0.0305 3.4904 1827.760887 5 0.0004 118 | 0/8 5 h-lim-p 0.0035 0.7631 0.3528 1827.760858 2 0.0005 136 | 0/8 6 h-lim-p 0.0022 2.4863 0.0750 1827.760857 0 0.0005 157 | 0/8 7 h-lim-p 0.0854 20.0000 0.0004 1827.760678 0 0.6834 180 | 0/8 8 h-lim-p 0.0008 0.2273 0.3437 1827.760590 2 0.0008 204 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1827.760587 0 1.0938 224 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1827.760587 0 1.0938 244 | 0/8 11 h-lim-p 0.8583 20.0000 0.0000 1827.760587 0 1.7166 265 | 0/8 12 h-lim-p 1.6658 20.0000 0.0000 1827.760587 0 0.0000 312 | 0/8 13 h-lim-p 0.0000 20.0000 0.0009 1827.760587 0 0.0000 340 | 0/8 14 h-lim-p 0.0000 20.0000 0.0005 1827.760587 0 0.0013 367 | 0/8 15 h-lim-p 0.0033 20.0000 0.0002 1827.760587 0 0.0000 400 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 1827.760587 0 0.0000 420 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0020 | 0/8 19 h-lim-p 0.0000 20.0000 0.0020 Out... lnL = -1827.760587 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1827.760587 Node 7: lnL = -1827.760587 Node 8: lnL = -1827.760587 Node 9: lnL = -1827.760587 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 862 Sequential format.. Reading seq # 1: YMR106C_Sbay Reading seq # 2: YMR106C_Scer Reading seq # 3: YMR106C_Skud Reading seq # 4: YMR106C_Smik Reading seq # 5: YMR106C_Spar Sequences read.. Counting patterns.. # site patterns = 400 Counting frequencies.. 120 bytes for distance 64000 bytes for lkl0 51200 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.219724 0.103465 0.082373 0.217645 0.142630 0.223073 0.374878 0.497276 lnL0 = -4505.916102 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4505.916102 x= 0.21972 0.10347 0.08237 0.21765 0.14263 0.22307 0.37488 0.49728 1 h-lim-p 0.0006 0.0052 152.2093 4502.262965 7 0.0003 39 | 0/8 2 h-lim-p 0.0004 0.0035 46.0107 4501.729567 1 0.0006 53 | 0/8 3 h-lim-p 0.0011 0.0157 23.3939 4501.620919 2 0.0005 69 | 0/8 4 h-lim-p 0.0022 0.1136 5.3442 4501.600355 6 0.0015 96 | 0/8 5 h-lim-p 0.0019 0.1030 4.3375 4501.592667 5 0.0012 120 | 0/8 6 h-lim-p 0.0088 0.8695 0.6016 4501.592470 2 0.0011 138 | 0/8 7 h-lim-p 0.0027 1.4087 0.2390 4501.592432 2 0.0014 163 | 0/8 8 h-lim-p 0.2298 20.0000 0.0015 4501.589961 0 0.9193 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 4501.589860 1 1.2500 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4501.589860 0 1.0938 227 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4501.589860 0 1.0938 247 | 0/8 12 h-lim-p 1.1279 20.0000 0.0000 4501.589860 0 1.1279 267 | 0/8 13 h-lim-p 0.5084 20.0000 0.0000 4501.589860 0 0.0000 307 Out... lnL = -4501.589860 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4501.589860 Node 7: lnL = -4501.589860 Node 8: lnL = -4501.589860 Node 9: lnL = -4501.589860 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 863 Sequential format.. Reading seq # 1: YMR107W_Sbay Reading seq # 2: YMR107W_Scer Reading seq # 3: YMR107W_Skud Reading seq # 4: YMR107W_Smik Reading seq # 5: YMR107W_Spar Sequences read.. Counting patterns.. # site patterns = 339 Counting frequencies.. 120 bytes for distance 54240 bytes for lkl0 43392 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.037820 0.152838 0.124167 0.103189 0.090183 0.307174 0.439211 0.274721 lnL0 = -4301.553991 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4301.553991 x= 0.03782 0.15284 0.12417 0.10319 0.09018 0.30717 0.43921 0.27472 1 h-lim-p 0.0004 0.0031 78.9487 4300.342633 6 0.0004 33 | 0/8 2 h-lim-p 0.0006 0.0045 28.1586 4300.127732 6 0.0006 60 | 0/8 3 h-lim-p 0.0003 0.0027 37.1037 4300.055724 5 0.0002 84 | 0/8 4 h-lim-p 0.0013 0.0151 6.2815 4300.049336 6 0.0004 111 | 0/8 5 h-lim-p 0.0022 0.6219 1.0201 4300.048696 4 0.0012 134 | 0/8 6 h-lim-p 0.0027 0.1688 0.4741 4300.048636 0 0.0007 147 | 0/8 7 h-lim-p 0.0033 4.0277 0.0949 4300.048630 1 0.0013 169 | 0/8 8 h-lim-p 0.1792 20.0000 0.0007 4300.048158 0 1.0754 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4300.048156 0 1.0938 211 | 0/8 10 h-lim-p 2.3583 20.0000 0.0000 4300.048156 0 1.0317 231 | 0/8 11 h-lim-p 1.0052 20.0000 0.0000 4300.048156 0 4.0208 253 | 0/8 12 h-lim-p 0.0716 20.0000 0.0010 4300.048156 0 0.0000 293 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 4300.048156 0 0.0000 326 Out... lnL = -4300.048156 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4300.048156 Node 7: lnL = -4300.048156 Node 8: lnL = -4300.048156 Node 9: lnL = -4300.048156 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 801 Sequential format.. Reading seq # 1: YMR108W_Sbay Reading seq # 2: YMR108W_Scer Reading seq # 3: YMR108W_Skud Reading seq # 4: YMR108W_Smik Reading seq # 5: YMR108W_Spar Sequences read.. Counting patterns.. # site patterns = 233 Counting frequencies.. 120 bytes for distance 37280 bytes for lkl0 29824 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.037732 0.051510 0.063861 0.094876 0.054541 0.136194 0.174258 0.155013 lnL0 = -3100.706307 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3100.706307 x= 0.03773 0.05151 0.06386 0.09488 0.05454 0.13619 0.17426 0.15501 1 h-lim-p 0.0003 0.0022 146.4796 3099.233210 5 0.0001 33 | 0/8 2 h-lim-p 0.0011 0.0093 19.4612 3099.175558 6 0.0003 59 | 0/8 3 h-lim-p 0.0008 0.0286 7.7580 3099.169814 5 0.0002 83 | 0/8 4 h-lim-p 0.0006 0.0285 2.6165 3099.169473 3 0.0001 104 | 0/8 5 h-lim-p 0.0006 0.3286 0.5041 3099.169437 1 0.0003 118 | 0/8 6 h-lim-p 0.0024 2.4500 0.0615 3099.169436 0 0.0003 140 | 0/8 7 h-lim-p 0.0215 20.0000 0.0008 3099.169436 0 0.0215 160 | 0/8 8 h-lim-p 0.0018 20.0000 0.0090 3099.169406 0 0.0145 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3099.169405 0 1.0938 203 | 0/8 10 h-lim-p 0.9163 20.0000 0.0000 3099.169405 0 0.8018 223 | 0/8 11 h-lim-p 0.6169 20.0000 0.0000 3099.169405 0 0.1542 244 | 0/8 12 h-lim-p 0.0527 20.0000 0.0001 3099.169405 0 0.0033 267 | 0/8 13 h-lim-p 0.0014 20.0000 0.0003 3099.169405 0 0.0014 287 | 0/8 14 h-lim-p 0.0011 20.0000 0.0004 3099.169405 0 0.0000 329 | 0/8 15 h-lim-p 0.0000 20.0000 0.0022 | 0/8 16 h-lim-p 0.0000 20.0000 0.0022 Out... lnL = -3099.169405 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3099.169405 Node 7: lnL = -3099.169405 Node 8: lnL = -3099.169405 Node 9: lnL = -3099.169405 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 492 Sequential format.. Reading seq # 1: YMR110C_Sbay Reading seq # 2: YMR110C_Scer Reading seq # 3: YMR110C_Skud Reading seq # 4: YMR110C_Smik Reading seq # 5: YMR110C_Spar Sequences read.. Counting patterns.. # site patterns = 236 Counting frequencies.. 120 bytes for distance 37760 bytes for lkl0 30208 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.020030 0.200950 0.049834 0.237649 0.179910 0.199627 0.288899 0.238954 lnL0 = -2351.988793 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2351.988793 x= 0.02003 0.20095 0.04983 0.23765 0.17991 0.19963 0.28890 0.23895 1 h-lim-p 0.0031 0.0248 51.3092 2351.339459 8 0.0005 43 | 0/8 2 h-lim-p 0.0012 0.0113 21.9760 2351.161736 7 0.0008 71 | 0/8 3 h-lim-p 0.0013 0.0106 4.4242 2351.153312 5 0.0009 96 | 0/8 4 h-lim-p 0.0030 0.1883 1.3243 2351.152501 4 0.0010 117 | 0/8 5 h-lim-p 0.0069 0.2993 0.1921 2351.152487 0 0.0007 131 | 0/8 6 h-lim-p 0.0041 10.4132 0.0351 2351.152486 0 0.0018 151 | 0/8 7 h-lim-p 0.0067 20.0000 0.0094 2351.152486 0 0.0059 171 | 0/8 8 h-lim-p 0.0581 20.0000 0.0009 2351.152406 0 0.4651 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2351.152402 0 1.0938 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2351.152402 0 1.0938 234 | 0/8 11 h-lim-p 1.3898 20.0000 0.0000 2351.152402 0 1.3898 254 | 0/8 12 h-lim-p 0.8269 20.0000 0.0000 2351.152402 0 0.8269 274 | 0/8 13 h-lim-p 0.0027 3.8454 0.0073 2351.152402 0 0.0002 297 | 0/8 14 h-lim-p 0.0004 10.0754 0.0028 2351.152402 0 0.0000 326 | 0/8 15 h-lim-p 0.0006 20.0000 0.0000 2351.152402 0 0.0000 359 Out... lnL = -2351.152402 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2351.152402 Node 7: lnL = -2351.152402 Node 8: lnL = -2351.152402 Node 9: lnL = -2351.152402 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 581 Sequential format.. Reading seq # 1: YMR112C_Sbay Reading seq # 2: YMR112C_Scer Reading seq # 3: YMR112C_Skud Reading seq # 4: YMR112C_Smik Reading seq # 5: YMR112C_Spar Sequences read.. Counting patterns.. # site patterns = 261 Counting frequencies.. 120 bytes for distance 41760 bytes for lkl0 33408 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.112329 0.170700 0.043459 0.102085 0.106636 0.323254 0.216086 0.314882 lnL0 = -2740.539689 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2740.539689 x= 0.11233 0.17070 0.04346 0.10208 0.10664 0.32325 0.21609 0.31488 1 h-lim-p 0.0055 0.0441 89.4885 2739.396920 3 0.0003 31 | 0/8 2 h-lim-p 0.0009 0.0073 18.3347 2739.322472 4 0.0005 51 | 0/8 3 h-lim-p 0.0009 0.0199 9.5386 2739.298532 6 0.0006 76 | 0/8 4 h-lim-p 0.0013 0.0520 4.5807 2739.292476 5 0.0007 99 | 0/8 5 h-lim-p 0.0028 0.6034 1.1872 2739.291825 4 0.0010 120 | 0/8 6 h-lim-p 0.0051 0.7660 0.2339 2739.291802 2 0.0008 138 | 0/8 7 h-lim-p 0.0142 20.0000 0.0135 2739.291802 0 0.0016 160 | 0/8 8 h-lim-p 0.2341 20.0000 0.0001 2739.291791 0 0.9365 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2739.291790 0 1.0938 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2739.291790 0 1.0938 222 | 0/8 11 h-lim-p 1.1249 20.0000 0.0000 2739.291790 0 0.0088 248 | 0/8 12 h-lim-p 0.0018 20.0000 0.0000 2739.291790 0 0.0009 268 | 0/8 13 h-lim-p 0.0001 20.0000 0.0005 2739.291790 0 0.0001 289 | 0/8 14 h-lim-p 0.0011 20.0000 0.0001 2739.291790 0 0.0001 311 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 2739.291790 0 0.0001 332 | 0/8 16 h-lim-p 0.0002 20.0000 0.0000 2739.291790 0 0.0000 367 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 2739.291790 0 0.0000 402 | 0/8 18 h-lim-p 0.0000 20.0000 0.0004 2739.291790 0 0.0000 423 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 2739.291790 0 0.0000 451 | 0/8 20 h-lim-p 0.0000 20.0000 0.0004 2739.291790 0 0.0000 479 | 0/8 21 h-lim-p 0.0000 20.0000 0.0003 .. | 0/8 22 h-lim-p 0.0000 20.0000 0.0004 2739.291790 0 0.0000 534 | 0/8 23 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 24 h-lim-p 0.0000 20.0000 0.0004 | 0/8 25 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -2739.291790 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2739.291790 Node 7: lnL = -2739.291790 Node 8: lnL = -2739.291790 Node 9: lnL = -2739.291790 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 314 Sequential format.. Reading seq # 1: YMR117C_Sbay Reading seq # 2: YMR117C_Scer Reading seq # 3: YMR117C_Skud Reading seq # 4: YMR117C_Smik Reading seq # 5: YMR117C_Spar Sequences read.. Counting patterns.. # site patterns = 179 Counting frequencies.. 120 bytes for distance 28640 bytes for lkl0 22912 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.075648 0.151433 0.055190 0.218515 0.093091 0.275800 0.246116 0.278325 lnL0 = -1444.663203 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1444.663203 x= 0.07565 0.15143 0.05519 0.21852 0.09309 0.27580 0.24612 0.27833 1 h-lim-p 0.0010 0.0079 31.7693 1444.143756 6 0.0011 37 | 0/8 2 h-lim-p 0.0017 0.0134 9.1512 1444.096854 6 0.0012 62 | 0/8 3 h-lim-p 0.0023 0.0555 4.7288 1444.090280 5 0.0007 86 | 0/8 4 h-lim-p 0.0022 0.0995 1.5880 1444.088456 4 0.0017 106 | 0/8 5 h-lim-p 0.0084 0.6512 0.3160 1444.088352 3 0.0022 125 | 0/8 6 h-lim-p 0.0096 4.3275 0.0723 1444.088347 1 0.0019 148 | 0/8 7 h-lim-p 0.0106 20.0000 0.0130 1444.088347 0 0.0027 169 | 0/8 8 h-lim-p 0.2127 20.0000 0.0002 1444.088338 0 0.8510 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1444.088338 0 1.0938 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1444.088338 0 1.0938 231 | 0/8 11 h-lim-p 1.1887 20.0000 0.0000 1444.088338 0 1.1887 251 | 0/8 12 h-lim-p 0.4575 20.0000 0.0000 1444.088338 0 0.0007 280 | 0/8 13 h-lim-p 0.0002 20.0000 0.0000 1444.088338 0 0.0000 304 | 0/8 14 h-lim-p 0.0006 20.0000 0.0000 1444.088338 0 0.0000 334 Out... lnL = -1444.088338 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1444.088338 Node 7: lnL = -1444.088338 Node 8: lnL = -1444.088338 Node 9: lnL = -1444.088338 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 937 Sequential format.. Reading seq # 1: YMR118C_Sbay Reading seq # 2: YMR118C_Scer Reading seq # 3: YMR118C_Skud Reading seq # 4: YMR118C_Smik Reading seq # 5: YMR118C_Spar Sequences read.. Counting patterns.. # site patterns = 336 Counting frequencies.. 120 bytes for distance 53760 bytes for lkl0 43008 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.411362 0.000060 0.608216 0.451376 0.283846 0.752764 0.817609 0.750354 lnL0 = -4586.873643 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4586.873643 x= 0.41136 0.00006 0.60822 0.45138 0.28385 0.75276 0.81761 0.75035 1 h-lim-p 0.0000 0.0000 261.8646 4586.791630 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0056 147.6903 4542.045628 0 0.0038 42 | 1/8 3 h-lim-p 0.0014 0.0109 32.4017 4539.671086 0 0.0055 56 | 1/8 4 h-lim-p 0.0054 0.0429 15.0420 4538.101107 0 0.0107 69 | 0/8 5 h-lim-p 0.0016 0.0126 54.5423 4536.354453 6 0.0017 95 | 0/8 6 h-lim-p 0.0041 0.0325 7.1980 4534.821783 0 0.0162 109 | 0/8 7 h-lim-p 0.0015 0.0121 9.7859 4527.349456 m 0.0121 121 | 0/8 8 h-lim-p 0.0019 0.0155 33.4322 4518.515299 0 0.0078 135 | 0/8 9 h-lim-p 0.0043 0.0345 0.1562 4518.274724 m 0.0345 147 | 0/8 10 h-lim-p 0.0000 0.0000 0.4174 h-lim-p: 7.86679587e-20 6.29343670e-19 4.17415650e-01 4518.274724 .. | 0/8 11 h-lim-p 0.0000 0.0722 67.4614 4517.109255 0 0.0006 189 | 0/8 12 h-lim-p 0.0000 0.0001 33.0614 4517.062975 m 0.0001 201 | 1/8 13 h-lim-p 0.0001 0.0670 13.5823 4516.663087 0 0.0057 218 | 1/8 14 h-lim-p 0.0133 0.1066 3.9854 4516.622078 6 0.0045 245 | 1/8 15 h-lim-p 0.0065 0.1736 2.7314 4516.588877 4 0.0069 265 | 1/8 16 h-lim-p 0.0048 0.1184 3.9345 4516.567499 5 0.0035 289 | 1/8 17 h-lim-p 0.0480 3.7795 0.2832 4516.422884 0 0.1441 302 | 1/8 18 h-lim-p 0.0598 0.6832 0.6817 4515.932899 1 0.0748 323 | 1/8 19 h-lim-p 2.5000 20.0000 0.0071 4515.920718 6 0.9225 356 | 1/8 20 h-lim-p 2.5000 20.0000 0.0004 4515.920698 1 0.9961 377 | 1/8 21 h-lim-p 2.5000 20.0000 0.0001 4515.920698 0 1.0938 396 | 1/8 22 h-lim-p 2.5000 20.0000 0.0000 4515.920698 0 1.0938 415 | 1/8 23 h-lim-p 2.4153 20.0000 0.0000 4515.920698 0 1.0567 434 | 1/8 24 h-lim-p 0.7907 20.0000 0.0000 4515.920698 0 0.0000 477 Out... lnL = -4515.920698 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4515.920698 Node 7: lnL = -4515.920698 Node 8: lnL = -4515.920698 Node 9: lnL = -4515.920698 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 825 Sequential format.. Reading seq # 1: YMR119W_Sbay Reading seq # 2: YMR119W_Scer Reading seq # 3: YMR119W_Skud Reading seq # 4: YMR119W_Smik Reading seq # 5: YMR119W_Spar Sequences read.. Counting patterns.. # site patterns = 222 Counting frequencies.. 120 bytes for distance 35520 bytes for lkl0 28416 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.093963 0.033648 0.126241 0.132360 0.088832 0.163316 0.268512 0.263146 lnL0 = -3373.604194 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3373.604194 x= 0.09396 0.03365 0.12624 0.13236 0.08883 0.16332 0.26851 0.26315 1 h-lim-p 0.0011 0.5023 245.5729 3365.720172 5 0.0003 33 | 0/8 2 h-lim-p 0.0004 0.0033 77.6725 3363.286119 0 0.0008 46 | 0/8 3 h-lim-p 0.0015 0.0121 17.2388 3363.170775 5 0.0008 69 | 0/8 4 h-lim-p 0.0024 0.0391 5.9307 3363.160323 6 0.0007 96 | 0/8 5 h-lim-p 0.0095 0.6088 0.4099 3363.159995 2 0.0019 113 | 0/8 6 h-lim-p 0.0023 0.9714 0.3327 3363.158979 0 0.0047 134 | 0/8 7 h-lim-p 0.0141 3.8510 0.1105 3363.011203 0 0.1688 157 | 0/8 8 h-lim-p 0.0055 0.0946 3.4103 3363.005273 4 0.0010 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0012 3363.004653 3 0.9961 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3363.004651 0 1.0938 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3363.004651 0 1.0938 246 | 0/8 12 h-lim-p 1.1198 20.0000 0.0000 3363.004651 0 1.6798 266 | 0/8 13 h-lim-p 1.8149 20.0000 0.0000 3363.004651 0 0.7940 286 | 0/8 14 h-lim-p 0.1361 20.0000 0.0001 3363.004651 0 0.0005 313 | 0/8 15 h-lim-p 0.0005 20.0000 0.0001 3363.004651 0 0.0000 352 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -3363.004651 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3363.004651 Node 7: lnL = -3363.004651 Node 8: lnL = -3363.004651 Node 9: lnL = -3363.004651 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 472 Sequential format.. Reading seq # 1: YMR120C_Sbay Reading seq # 2: YMR120C_Scer Reading seq # 3: YMR120C_Skud Reading seq # 4: YMR120C_Smik Reading seq # 5: YMR120C_Spar Sequences read.. Counting patterns.. # site patterns = 195 Counting frequencies.. 120 bytes for distance 31200 bytes for lkl0 24960 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.049084 0.060191 0.074141 0.072788 0.065331 0.154193 0.206123 0.174016 lnL0 = -1973.010311 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1973.010311 x= 0.04908 0.06019 0.07414 0.07279 0.06533 0.15419 0.20612 0.17402 1 h-lim-p 0.0007 0.0053 136.4401 1970.515699 7 0.0003 37 | 0/8 2 h-lim-p 0.0010 0.0080 18.8370 1970.440243 6 0.0004 60 | 0/8 3 h-lim-p 0.0005 0.0113 14.9037 1970.420746 2 0.0003 76 | 0/8 4 h-lim-p 0.0020 0.0627 1.9204 1970.419852 3 0.0005 95 | 0/8 5 h-lim-p 0.0018 0.5105 0.5278 1970.419779 3 0.0006 115 | 0/8 6 h-lim-p 0.0012 0.6933 0.2587 1970.419767 2 0.0005 139 | 0/8 7 h-lim-p 0.0029 6.9260 0.0396 1970.419765 0 0.0013 159 | 0/8 8 h-lim-p 0.0567 20.0000 0.0009 1970.419153 0 0.9064 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1970.419140 1 0.9961 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1970.419140 0 1.0938 225 | 0/8 11 h-lim-p 1.0710 20.0000 0.0000 1970.419140 017.1365 249 | 0/8 12 h-lim-p 0.0473 13.4857 0.0055 1970.419140 0 0.0059 271 | 0/8 13 h-lim-p 0.0016 3.6434 0.0204 1970.419140 0 0.0000 300 | 0/8 14 h-lim-p 0.0003 20.0000 0.0001 1970.419140 0 0.0000 340 | 0/8 15 h-lim-p 0.0000 20.0000 0.0009 | 0/8 16 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -1970.419140 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1970.419140 Node 7: lnL = -1970.419140 Node 8: lnL = -1970.419140 Node 9: lnL = -1970.419140 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 251 Sequential format.. Reading seq # 1: YMR122W-A_Sbay Reading seq # 2: YMR122W-A_Scer Reading seq # 3: YMR122W-A_Skud Reading seq # 4: YMR122W-A_Smik Reading seq # 5: YMR122W-A_Spar Sequences read.. Counting patterns.. # site patterns = 115 Counting frequencies.. 120 bytes for distance 18400 bytes for lkl0 14720 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.064496 0.105037 0.048731 0.128262 0.088547 0.153811 0.173028 0.205895 lnL0 = -1127.693382 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1127.693382 x= 0.06450 0.10504 0.04873 0.12826 0.08855 0.15381 0.17303 0.20590 1 h-lim-p 0.0040 1.6158 74.9337 1126.430838 8 0.0005 40 | 0/8 2 h-lim-p 0.0018 0.0144 15.8253 1126.318675 4 0.0009 61 | 0/8 3 h-lim-p 0.0029 0.0564 4.9432 1126.309465 6 0.0008 87 | 0/8 4 h-lim-p 0.0026 0.1276 1.6016 1126.308087 2 0.0012 103 | 0/8 5 h-lim-p 0.0052 0.8585 0.3728 1126.308010 2 0.0012 120 | 0/8 6 h-lim-p 0.1240 20.0000 0.0036 1126.308006 1 0.0247 143 | 0/8 7 h-lim-p 0.0067 17.5321 0.0135 1126.307917 0 0.0267 165 | 0/8 8 h-lim-p 0.0018 1.7645 0.1995 1126.307834 1 0.0022 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1126.307829 1 0.9961 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1126.307829 0 1.0938 229 | 0/8 11 h-lim-p 1.1686 20.0000 0.0000 1126.307829 0 4.6745 251 | 0/8 12 h-lim-p 1.2729 20.0000 0.0000 1126.307829 0 1.2729 271 | 0/8 13 h-lim-p 0.0199 20.0000 0.0014 1126.307829 0 0.0002 297 | 0/8 14 h-lim-p 0.0003 20.0000 0.0010 1126.307829 0 0.0000 321 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 1126.307829 0 0.0000 354 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 1126.307829 0 0.0000 388 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 1126.307829 0 0.0000 418 | 0/8 18 h-lim-p 0.0000 20.0000 0.0004 | 0/8 19 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1126.307829 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1126.307829 Node 7: lnL = -1126.307829 Node 8: lnL = -1126.307829 Node 9: lnL = -1126.307829 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 543 Sequential format.. Reading seq # 1: YMR124W_Sbay Reading seq # 2: YMR124W_Scer Reading seq # 3: YMR124W_Skud Reading seq # 4: YMR124W_Smik Reading seq # 5: YMR124W_Spar Sequences read.. Counting patterns.. # site patterns = 195 Counting frequencies.. 120 bytes for distance 31200 bytes for lkl0 24960 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.069662 0.033390 0.070008 0.126687 0.065753 0.238755 0.199658 0.214501 lnL0 = -2369.375917 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2369.375917 x= 0.06966 0.03339 0.07001 0.12669 0.06575 0.23876 0.19966 0.21450 1 h-lim-p 0.0003 0.0020 150.8206 2367.060210 3 0.0002 28 | 0/8 2 h-lim-p 0.0006 0.0045 27.6605 2366.906741 6 0.0004 53 | 0/8 3 h-lim-p 0.0006 0.0139 17.7924 2366.873888 2 0.0003 69 | 0/8 4 h-lim-p 0.0008 0.0361 6.5751 2366.865408 5 0.0005 95 | 0/8 5 h-lim-p 0.0063 0.3085 0.4922 2366.865345 2 0.0005 114 | 0/8 6 h-lim-p 0.0019 2.1680 0.1317 2366.865339 1 0.0007 136 | 0/8 7 h-lim-p 0.0115 20.0000 0.0086 2366.865339 0 0.0014 158 | 0/8 8 h-lim-p 0.0295 20.0000 0.0004 2366.865272 0 0.4714 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2366.865270 0 1.0938 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2366.865270 0 1.0938 222 | 0/8 11 h-lim-p 1.0717 20.0000 0.0000 2366.865270 0 2.1433 243 | 0/8 12 h-lim-p 2.2459 20.0000 0.0000 2366.865270 0 0.9826 263 | 0/8 13 h-lim-p 0.1582 20.0000 0.0001 2366.865270 0 0.0198 285 | 0/8 14 h-lim-p 0.0048 20.0000 0.0003 2366.865270 0 0.0000 326 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 2366.865270 0 0.0000 359 | 0/8 16 h-lim-p 0.0000 20.0000 0.0005 | 0/8 17 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -2366.865270 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2366.865270 Node 7: lnL = -2366.865270 Node 8: lnL = -2366.865270 Node 9: lnL = -2366.865270 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 617 Sequential format.. Reading seq # 1: YMR125W_Sbay Reading seq # 2: YMR125W_Scer Reading seq # 3: YMR125W_Skud Reading seq # 4: YMR125W_Smik Reading seq # 5: YMR125W_Spar Sequences read.. Counting patterns.. # site patterns = 204 Counting frequencies.. 120 bytes for distance 32640 bytes for lkl0 26112 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.021408 0.074669 0.058898 0.146579 0.070858 0.152184 0.164502 0.143082 lnL0 = -2394.109381 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2394.109381 x= 0.02141 0.07467 0.05890 0.14658 0.07086 0.15218 0.16450 0.14308 1 h-lim-p 0.0002 0.0017 72.3504 2393.492254 1 0.0003 24 | 0/8 2 h-lim-p 0.0003 0.0028 34.3720 2393.316471 5 0.0003 46 | 0/8 3 h-lim-p 0.0013 0.0215 9.4402 2393.302705 5 0.0003 69 | 0/8 4 h-lim-p 0.0006 0.0173 5.7704 2393.297662 5 0.0004 94 | 0/8 5 h-lim-p 0.0015 0.1551 1.5612 2393.297308 2 0.0003 111 | 0/8 6 h-lim-p 0.0026 0.8072 0.1940 2393.297297 1 0.0005 126 | 0/8 7 h-lim-p 0.0105 20.0000 0.0096 2393.297267 0 0.0210 147 | 0/8 8 h-lim-p 0.0051 3.7434 0.0392 2393.295615 0 0.0308 169 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 2393.295553 2 0.9961 193 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2393.295553 0 1.0938 213 | 0/8 11 h-lim-p 0.9173 20.0000 0.0000 2393.295553 0 0.8026 233 | 0/8 12 h-lim-p 0.0769 20.0000 0.0005 2393.295553 0 0.0036 257 | 0/8 13 h-lim-p 0.0013 19.6263 0.0013 2393.295553 0 0.0000 295 | 0/8 14 h-lim-p 0.0000 20.0000 0.0008 | 0/8 15 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -2393.295553 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2393.295553 Node 7: lnL = -2393.295553 Node 8: lnL = -2393.295553 Node 9: lnL = -2393.295553 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 586 Sequential format.. Reading seq # 1: YMR126C_Sbay Reading seq # 2: YMR126C_Scer Reading seq # 3: YMR126C_Skud Reading seq # 4: YMR126C_Smik Reading seq # 5: YMR126C_Spar Sequences read.. Counting patterns.. # site patterns = 217 Counting frequencies.. 120 bytes for distance 34720 bytes for lkl0 27776 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.038833 0.124520 0.071081 0.131309 0.071764 0.196964 0.189810 0.189251 lnL0 = -2587.839445 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2587.839445 x= 0.03883 0.12452 0.07108 0.13131 0.07176 0.19696 0.18981 0.18925 1 h-lim-p 0.0039 0.0311 73.2510 2587.090537 7 0.0003 42 | 0/8 2 h-lim-p 0.0008 0.0065 23.6195 2586.998389 6 0.0004 65 | 0/8 3 h-lim-p 0.0008 0.0180 10.6067 2586.983392 4 0.0003 85 | 0/8 4 h-lim-p 0.0041 0.3532 0.8198 2586.983221 3 0.0005 105 | 0/8 5 h-lim-p 0.0015 1.2042 0.2730 2586.983205 2 0.0005 131 | 0/8 6 h-lim-p 0.0044 5.6251 0.0315 2586.983204 0 0.0010 152 | 0/8 7 h-lim-p 0.0032 20.0000 0.0093 2586.983204 0 0.0014 172 | 0/8 8 h-lim-p 0.0320 20.0000 0.0004 2586.983153 0 0.5123 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2586.983153 0 1.0938 216 | 0/8 10 h-lim-p 1.1278 20.0000 0.0000 2586.983153 0 0.9868 236 | 0/8 11 h-lim-p 0.7049 20.0000 0.0000 2586.983153 0 0.0193 260 | 0/8 12 h-lim-p 0.0014 20.0000 0.0004 2586.983153 0 0.0002 282 | 0/8 13 h-lim-p 0.0002 20.0000 0.0003 2586.983153 0 0.0000 316 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 2586.983153 0 0.0000 343 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 2586.983153 0 0.0000 371 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 2586.983153 0 0.0000 392 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 2586.983153 0 0.0000 424 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -2586.983153 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2586.983153 Node 7: lnL = -2586.983153 Node 8: lnL = -2586.983153 Node 9: lnL = -2586.983153 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 417 Sequential format.. Reading seq # 1: YMR127C_Sbay Reading seq # 2: YMR127C_Scer Reading seq # 3: YMR127C_Skud Reading seq # 4: YMR127C_Smik Reading seq # 5: YMR127C_Spar Sequences read.. Counting patterns.. # site patterns = 165 Counting frequencies.. 120 bytes for distance 26400 bytes for lkl0 21120 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.032597 0.119333 0.090243 0.147411 0.085205 0.196726 0.196112 0.189919 lnL0 = -1781.655700 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1781.655700 x= 0.03260 0.11933 0.09024 0.14741 0.08521 0.19673 0.19611 0.18992 1 h-lim-p 0.0037 0.0299 43.4329 1781.137047 8 0.0006 43 | 0/8 2 h-lim-p 0.0012 0.0093 11.0723 1781.093549 4 0.0008 65 | 0/8 3 h-lim-p 0.0027 0.1048 3.0920 1781.091744 5 0.0004 93 | 0/8 4 h-lim-p 0.0021 0.4814 0.6060 1781.091585 2 0.0009 109 | 0/8 5 h-lim-p 0.0037 0.8792 0.1493 1781.091578 2 0.0007 134 | 0/8 6 h-lim-p 0.0053 10.6156 0.0201 1781.091577 0 0.0023 154 | 0/8 7 h-lim-p 0.0059 20.0000 0.0078 1781.091576 0 0.0052 174 | 0/8 8 h-lim-p 0.0121 20.0000 0.0034 1781.091462 0 0.0966 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1781.091459 0 1.0938 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1781.091459 0 1.0938 237 | 0/8 11 h-lim-p 1.1889 20.0000 0.0000 1781.091459 0 1.0403 257 | 0/8 12 h-lim-p 0.4891 20.0000 0.0000 1781.091459 0 0.0134 281 | 0/8 13 h-lim-p 0.0016 20.0000 0.0002 1781.091459 0 0.0000 316 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1781.091459 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1781.091459 Node 7: lnL = -1781.091459 Node 8: lnL = -1781.091459 Node 9: lnL = -1781.091459 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 317 Sequential format.. Reading seq # 1: YMR129W_Sbay Reading seq # 2: YMR129W_Scer Reading seq # 3: YMR129W_Skud Reading seq # 4: YMR129W_Smik Reading seq # 5: YMR129W_Spar Sequences read.. Counting patterns.. # site patterns = 162 Counting frequencies.. 120 bytes for distance 25920 bytes for lkl0 20736 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.074451 0.079214 0.108988 0.150358 0.133470 0.250521 0.251682 0.254180 lnL0 = -1590.421943 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1590.421943 x= 0.07445 0.07921 0.10899 0.15036 0.13347 0.25052 0.25168 0.25418 1 h-lim-p 0.0113 0.1189 52.9972 1589.498325 8 0.0007 42 | 0/8 2 h-lim-p 0.0022 0.0179 8.6629 1589.457961 5 0.0011 66 | 0/8 3 h-lim-p 0.0029 0.0659 3.2891 1589.453887 5 0.0009 91 | 0/8 4 h-lim-p 0.0039 0.4715 0.7287 1589.453532 4 0.0014 112 | 0/8 5 h-lim-p 0.0067 2.3574 0.1536 1589.453516 1 0.0013 135 | 0/8 6 h-lim-p 0.0141 20.0000 0.0145 1589.453515 0 0.0031 156 | 0/8 7 h-lim-p 0.0079 20.0000 0.0056 1589.453513 0 0.0158 177 | 0/8 8 h-lim-p 0.0143 20.0000 0.0063 1589.453417 0 0.0572 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1589.453415 0 1.0938 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1589.453415 0 1.0938 239 | 0/8 11 h-lim-p 1.5288 20.0000 0.0000 1589.453415 0 0.6688 259 | 0/8 12 h-lim-p 0.3927 20.0000 0.0000 1589.453415 0 0.0000 297 | 0/8 13 h-lim-p 0.0000 20.0000 0.0002 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1589.453415 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1589.453415 Node 7: lnL = -1589.453415 Node 8: lnL = -1589.453415 Node 9: lnL = -1589.453415 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 312 Sequential format.. Reading seq # 1: YMR130W_Sbay Reading seq # 2: YMR130W_Scer Reading seq # 3: YMR130W_Skud Reading seq # 4: YMR130W_Smik Reading seq # 5: YMR130W_Spar Sequences read.. Counting patterns.. # site patterns = 167 Counting frequencies.. 120 bytes for distance 26720 bytes for lkl0 21376 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.116863 0.007150 0.070588 0.166898 0.121946 0.202313 0.268849 0.280808 lnL0 = -1489.238446 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1489.238446 x= 0.11686 0.00715 0.07059 0.16690 0.12195 0.20231 0.26885 0.28081 1 h-lim-p 0.0024 0.0191 80.7482 1488.096538 6 0.0004 36 | 0/8 2 h-lim-p 0.0025 0.0202 12.2823 1488.012565 7 0.0011 63 | 0/8 3 h-lim-p 0.0034 0.0837 4.0515 1488.002914 5 0.0013 85 | 0/8 4 h-lim-p 0.0030 0.1153 1.7534 1488.001758 5 0.0009 110 | 0/8 5 h-lim-p 0.0030 0.5983 0.5281 1488.001592 2 0.0013 126 | 0/8 6 h-lim-p 0.1167 20.0000 0.0058 1488.001592 0 0.0032 150 | 0/8 7 h-lim-p 0.0129 20.0000 0.0014 1488.001591 0 0.0259 171 | 0/8 8 h-lim-p 0.0074 20.0000 0.0050 1488.001574 0 0.0296 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1488.001574 0 1.0938 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1488.001574 0 1.2500 233 | 0/8 11 h-lim-p 1.5456 20.0000 0.0000 1488.001574 0 0.1932 255 | 0/8 12 h-lim-p 0.0795 20.0000 0.0000 1488.001574 0 0.0199 276 | 0/8 13 h-lim-p 0.0104 20.0000 0.0000 1488.001574 0 0.0104 296 | 0/8 14 h-lim-p 0.0070 20.0000 0.0000 1488.001574 0 0.0002 320 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 1488.001574 0 0.0000 352 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1488.001574 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1488.001574 Node 7: lnL = -1488.001574 Node 8: lnL = -1488.001574 Node 9: lnL = -1488.001574 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 260 Sequential format.. Reading seq # 1: YMR131C_Sbay Reading seq # 2: YMR131C_Scer Reading seq # 3: YMR131C_Skud Reading seq # 4: YMR131C_Smik Reading seq # 5: YMR131C_Spar Sequences read.. Counting patterns.. # site patterns = 81 Counting frequencies.. 120 bytes for distance 12960 bytes for lkl0 10368 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.153811 0.131666 0.214604 0.141436 4.153636 0.333139 0.482462 lnL0 = -969.497361 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 969.497361 x= 0.00006 0.15381 0.13167 0.21460 0.14144 4.15364 0.33314 0.48246 1 h-lim-p 0.0000 0.0000 254.5749 969.404534 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0038 80.7161 956.233493 m 0.0038 40 | 2/8 3 h-lim-p 0.0001 0.0009 503.9909 948.951705 0 0.0004 54 | 2/8 4 h-lim-p 0.0003 0.0022 97.4696 939.858894 0 0.0011 68 | 1/8 5 h-lim-p 0.0000 0.0001 1375.3276 933.734293 0 0.0000 82 | 1/8 6 h-lim-p 0.0021 0.0169 28.4763 932.439047 0 0.0042 95 | 1/8 7 h-lim-p 0.2507 2.0052 0.2492 925.382069 0 0.7520 108 | 0/8 8 h-lim-p 0.0075 0.0600 14.5621 925.174882 7 0.0022 143 | 0/8 9 h-lim-p 0.1663 1.3306 0.1001 921.185720 0 0.9979 157 | 0/8 10 h-lim-p 0.0522 0.4178 0.0840 920.587873 m 0.4178 177 | 0/8 11 h-lim-p 2.5000 20.0000 0.0117 920.370132 2 1.1719 201 | 0/8 12 h-lim-p 1.5750 14.0811 0.0087 920.139130 0 2.3626 221 | 0/8 13 h-lim-p 0.0597 0.4779 0.0090 920.120455 m 0.4779 241 | 1/8 14 h-lim-p 0.5748 20.0000 0.0047 920.115496 0 1.1495 262 | 0/8 15 h-lim-p 0.0115 1.1276 0.4646 920.114758 5 0.0079 294 | 0/8 16 h-lim-p 0.0577 0.4613 0.0105 920.111371 m 0.4613 314 | 0/8 17 h-lim-p -0.0000 -0.0000 0.0044 h-lim-p: -3.40267068e-18 -2.72213655e-17 4.36761822e-03 920.111371 .. | 0/8 18 h-lim-p 0.0000 0.0365 1.6613 920.110957 0 0.0003 355 | 0/8 19 h-lim-p 0.0009 0.2713 0.5819 920.110856 4 0.0007 377 | 0/8 20 h-lim-p 0.0024 0.7894 0.1617 920.110847 2 0.0008 403 | 0/8 21 h-lim-p 0.0021 0.0169 0.0358 920.110845 0 0.0019 423 | 0/8 22 h-lim-p 0.0011 0.0088 0.0441 920.110843 0 0.0044 445 | 0/8 23 h-lim-p 0.0000 0.0000 115.8399 920.110843 0 0.0000 466 | 0/8 24 h-lim-p 0.4377 20.0000 0.0001 920.110839 0 0.8755 479 | 0/8 25 h-lim-p 0.5688 4.5501 0.0000 920.110838 0 1.1375 500 | 0/8 26 h-lim-p 0.1588 1.2703 0.0001 920.110838 0 0.0000 536 | 0/8 27 h-lim-p 0.0000 0.0154 0.0204 .. | 0/8 28 h-lim-p 0.0000 0.0026 0.0362 920.110838 0 0.0001 592 | 0/8 29 h-lim-p 0.0000 0.0006 0.1652 920.110838 0 0.0000 626 | 0/8 30 h-lim-p 0.0000 0.0000 8.0131 .. | 0/8 31 h-lim-p 0.0000 4.5392 0.0185 920.110838 0 0.0002 672 | 0/8 32 h-lim-p 0.0001 0.0040 0.0460 920.110838 0 0.0000 704 | 0/8 33 h-lim-p 0.0000 20.0000 0.0059 920.110838 0 0.0010 730 | 0/8 34 h-lim-p 0.0018 1.4129 0.0031 920.110838 0 0.0008 750 | 0/8 35 h-lim-p 0.0038 2.8645 0.0007 920.110838 0 0.0000 780 | 0/8 36 h-lim-p 0.0000 2.4427 0.0004 920.110838 0 0.0000 808 | 0/8 37 h-lim-p 0.0000 4.3643 0.0000 920.110838 0 0.0000 828 | 0/8 38 h-lim-p 0.0000 6.5968 0.0001 .. | 0/8 39 h-lim-p 0.0000 0.0024 0.0362 920.110838 0 0.0000 882 | 0/8 40 h-lim-p 0.0000 0.0005 0.1813 920.110838 0 0.0000 912 | 0/8 41 h-lim-p 0.0000 0.0000 2.8248 920.110838 0 0.0000 944 | 0/8 42 h-lim-p 0.0000 0.1330 0.0042 920.110838 0 0.0000 967 | 0/8 43 h-lim-p 0.0000 0.0000 50.1068 .. | 0/8 44 h-lim-p 0.0000 0.0766 0.0101 920.110838 0 0.0000 1024 | 0/8 45 h-lim-p 0.0000 0.0015 0.1575 .. | 0/8 46 h-lim-p 0.0000 0.0024 0.0360 | 0/8 47 h-lim-p 0.0000 0.0024 0.0360 Out... lnL = -920.110838 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -920.110838 Node 7: lnL = -920.110838 Node 8: lnL = -920.110838 Node 9: lnL = -920.110838 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 654 Sequential format.. Reading seq # 1: YMR132C_Sbay Reading seq # 2: YMR132C_Scer Reading seq # 3: YMR132C_Skud Reading seq # 4: YMR132C_Smik Reading seq # 5: YMR132C_Spar Sequences read.. Counting patterns.. # site patterns = 182 Counting frequencies.. 120 bytes for distance 29120 bytes for lkl0 23296 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.119140 0.214671 0.225741 0.195545 4.311441 0.377154 0.482462 lnL0 = -2608.787448 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2608.787448 x= 0.00006 0.11914 0.21467 0.22574 0.19555 4.31144 0.37715 0.48246 1 h-lim-p 0.0000 0.0000 186.3848 2608.716664 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0117 50.9862 2606.649445 0 0.0019 41 | 1/8 3 h-lim-p 0.0031 0.0252 22.3085 2606.291132 4 0.0016 62 | 1/8 4 h-lim-p 0.0157 0.2784 2.2834 2606.016422 6 0.0169 89 | 1/8 5 h-lim-p 0.0209 0.1738 1.8408 2600.426230 0 0.0838 103 | 0/8 6 h-lim-p 0.0014 0.0111 38.4228 2597.357252 0 0.0021 115 | 0/8 7 h-lim-p 0.0004 0.0034 22.4812 2596.545338 m 0.0034 127 | 0/8 8 h-lim-p 1.4789 11.8315 0.0485 2595.551954 2 0.6933 143 | 0/8 9 h-lim-p 0.2407 1.9258 0.0092 2595.532400 0 0.9629 165 | 0/8 10 h-lim-p 0.4658 3.7267 0.0028 2595.530284 0 0.9317 186 | 0/8 11 h-lim-p 2.5000 20.0000 0.0004 2595.530245 2 0.9644 210 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2595.530245 0 1.0938 230 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2595.530245 0 1.0938 250 | 0/8 14 h-lim-p 1.4556 20.0000 0.0000 2595.530245 0 1.2737 270 | 0/8 15 h-lim-p 1.4251 20.0000 0.0000 2595.530245 0 0.7125 290 | 0/8 16 h-lim-p 0.2268 20.0000 0.0000 2595.530245 0 0.0992 310 | 0/8 17 h-lim-p 0.0280 20.0000 0.0000 2595.530245 0 0.0140 330 | 0/8 18 h-lim-p 0.0056 20.0000 0.0001 2595.530245 0 0.0000 372 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -2595.530245 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2595.530245 Node 7: lnL = -2595.530245 Node 8: lnL = -2595.530245 Node 9: lnL = -2595.530245 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 669 Sequential format.. Reading seq # 1: YMR133W_Sbay Reading seq # 2: YMR133W_Scer Reading seq # 3: YMR133W_Skud Reading seq # 4: YMR133W_Smik Reading seq # 5: YMR133W_Spar Sequences read.. Counting patterns.. # site patterns = 326 Counting frequencies.. 120 bytes for distance 52160 bytes for lkl0 41728 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.079179 0.168928 0.227932 0.154604 0.159933 0.290238 0.278945 0.320942 lnL0 = -3247.856940 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3247.856940 x= 0.07918 0.16893 0.22793 0.15460 0.15993 0.29024 0.27894 0.32094 1 h-lim-p 0.0071 0.0571 24.8172 3247.554077 6 0.0010 38 | 0/8 2 h-lim-p 0.0022 0.0393 11.1830 3247.514191 6 0.0007 65 | 0/8 3 h-lim-p 0.0010 0.0335 8.6632 3247.497732 5 0.0007 89 | 0/8 4 h-lim-p 0.0039 0.2455 1.4943 3247.496267 4 0.0014 110 | 0/8 5 h-lim-p 0.0050 1.2597 0.4139 3247.496183 1 0.0011 125 | 0/8 6 h-lim-p 0.0078 5.2369 0.0578 3247.496181 0 0.0010 147 | 0/8 7 h-lim-p 0.0062 20.0000 0.0091 3247.496181 0 0.0055 167 | 0/8 8 h-lim-p 0.0741 20.0000 0.0007 3247.496133 0 0.5925 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3247.496130 0 1.0938 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3247.496130 0 1.0938 230 | 0/8 11 h-lim-p 1.3995 20.0000 0.0000 3247.496130 0 1.3995 250 | 0/8 12 h-lim-p 1.2420 20.0000 0.0000 3247.496130 0 0.5434 270 | 0/8 13 h-lim-p 0.0333 20.0000 0.0001 3247.496130 0 0.0083 291 | 0/8 14 h-lim-p 0.0028 20.0000 0.0004 3247.496130 0 0.0014 311 | 0/8 15 h-lim-p 0.0004 20.0000 0.0017 3247.496130 0 0.0000 348 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -3247.496130 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3247.496130 Node 7: lnL = -3247.496130 Node 8: lnL = -3247.496130 Node 9: lnL = -3247.496130 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 881 Sequential format.. Reading seq # 1: YMR135C_Sbay Reading seq # 2: YMR135C_Scer Reading seq # 3: YMR135C_Skud Reading seq # 4: YMR135C_Smik Reading seq # 5: YMR135C_Spar Sequences read.. Counting patterns.. # site patterns = 233 Counting frequencies.. 120 bytes for distance 37280 bytes for lkl0 29824 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.103696 0.024807 0.046341 0.034245 0.059197 0.140057 0.105366 0.200111 lnL0 = -3225.721428 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3225.721428 x= 0.10370 0.02481 0.04634 0.03424 0.05920 0.14006 0.10537 0.20011 1 h-lim-p 0.0001 0.0006 260.3010 3223.057466 0 0.0001 22 | 0/8 2 h-lim-p 0.0002 0.0015 56.5138 3222.864203 6 0.0001 50 | 0/8 3 h-lim-p 0.0002 0.0016 46.0652 3222.798232 5 0.0001 75 | 0/8 4 h-lim-p 0.0002 0.0097 23.3738 3222.775290 6 0.0001 100 | 0/8 5 h-lim-p 0.0011 0.0743 2.5158 3222.774436 2 0.0003 117 | 0/8 6 h-lim-p 0.0006 0.0837 1.2247 3222.774348 0 0.0001 130 | 0/8 7 h-lim-p 0.0067 7.1343 0.0256 3222.772429 0 0.0402 144 | 0/8 8 h-lim-p 0.0021 0.1090 0.4920 3222.709446 0 0.0084 166 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 3222.709159 3 0.9644 192 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3222.709158 0 1.0938 212 | 0/8 11 h-lim-p 1.3881 20.0000 0.0000 3222.709158 0 2.7763 233 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3222.709158 0 0.5469 254 | 0/8 13 h-lim-p 0.3682 20.0000 0.0000 3222.709158 0 0.0014 281 | 0/8 14 h-lim-p 0.0005 20.0000 0.0000 3222.709158 0 0.0000 311 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 3222.709158 0 0.0000 331 Out... lnL = -3222.709158 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3222.709158 Node 7: lnL = -3222.709158 Node 8: lnL = -3222.709158 Node 9: lnL = -3222.709158 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 826 Sequential format.. Reading seq # 1: YMR136W_Sbay Reading seq # 2: YMR136W_Scer Reading seq # 3: YMR136W_Skud Reading seq # 4: YMR136W_Smik Reading seq # 5: YMR136W_Spar Sequences read.. Counting patterns.. # site patterns = 228 Counting frequencies.. 120 bytes for distance 36480 bytes for lkl0 29184 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.110756 0.035573 0.063869 0.034782 0.040065 0.142806 0.137254 0.217890 lnL0 = -3140.496294 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3140.496294 x= 0.11076 0.03557 0.06387 0.03478 0.04006 0.14281 0.13725 0.21789 1 h-lim-p 0.0001 0.0010 178.4232 3138.827917 2 0.0001 26 | 0/8 2 h-lim-p 0.0002 0.0019 48.6696 3138.704057 2 0.0001 42 | 0/8 3 h-lim-p 0.0002 0.0039 24.1440 3138.671925 6 0.0001 72 | 0/8 4 h-lim-p 0.0002 0.0099 20.2079 3138.660283 6 0.0001 100 | 0/8 5 h-lim-p 0.0003 0.0432 5.5727 3138.657995 4 0.0002 122 | 0/8 6 h-lim-p 0.0013 0.2924 0.7529 3138.657907 2 0.0003 139 | 0/8 7 h-lim-p 0.0055 4.2847 0.0430 3138.657906 0 0.0006 161 | 0/8 8 h-lim-p 0.0480 20.0000 0.0005 3138.657343 0 0.7686 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3138.657336 1 0.9961 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3138.657336 0 0.0024 236 | 0/8 11 h-lim-p 0.0012 20.0000 0.0000 3138.657336 0 0.0017 256 | 0/8 12 h-lim-p 0.0011 20.0000 0.0000 3138.657336 0 0.0000 293 | 0/8 13 h-lim-p 0.0000 20.0000 0.0076 | 0/8 14 h-lim-p 0.0000 20.0000 0.0076 Out... lnL = -3138.657336 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3138.657336 Node 7: lnL = -3138.657336 Node 8: lnL = -3138.657336 Node 9: lnL = -3138.657336 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 216 Sequential format.. Reading seq # 1: YMR138W_Sbay Reading seq # 2: YMR138W_Scer Reading seq # 3: YMR138W_Skud Reading seq # 4: YMR138W_Smik Reading seq # 5: YMR138W_Spar Sequences read.. Counting patterns.. # site patterns = 131 Counting frequencies.. 120 bytes for distance 20960 bytes for lkl0 16768 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.035138 0.044205 0.038488 0.191635 0.218273 0.261176 0.255452 0.200636 lnL0 = -958.118898 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 958.118898 x= 0.03514 0.04421 0.03849 0.19164 0.21827 0.26118 0.25545 0.20064 1 h-lim-p 0.0133 0.1950 38.0087 957.614763 2 0.0008 29 | 0/8 2 h-lim-p 0.0015 0.0119 9.3811 957.545303 1 0.0019 43 | 0/8 3 h-lim-p 0.0055 0.0652 3.1914 957.536059 6 0.0020 69 | 0/8 4 h-lim-p 0.0206 0.5092 0.3155 957.535931 2 0.0026 87 | 0/8 5 h-lim-p 0.0096 0.8278 0.0843 957.535925 2 0.0016 114 | 0/8 6 h-lim-p 0.0065 20.0000 0.0206 957.535901 0 0.0194 135 | 0/8 7 h-lim-p 0.0263 19.1255 0.0152 957.535229 0 0.1051 157 | 0/8 8 h-lim-p 0.0060 1.0143 0.2675 957.535083 4 0.0032 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 957.535074 0 1.2500 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 957.535074 0 1.0938 226 | 0/8 11 h-lim-p 2.4696 20.0000 0.0000 957.535074 0 1.2348 246 | 0/8 12 h-lim-p 1.2100 20.0000 0.0000 957.535074 0 0.5294 266 | 0/8 13 h-lim-p 0.0444 20.0000 0.0001 957.535074 0 0.0056 288 | 0/8 14 h-lim-p 0.0017 20.0000 0.0003 957.535074 0 0.0001 311 | 0/8 15 h-lim-p 0.0001 20.0000 0.0003 957.535074 0 0.0001 331 | 0/8 16 h-lim-p 0.0021 20.0000 0.0000 957.535074 0 0.0000 359 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 957.535074 0 0.0000 381 | 0/8 18 h-lim-p 0.0001 20.0000 0.0000 957.535074 0 0.0000 410 Out... lnL = -957.535074 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -957.535074 Node 7: lnL = -957.535074 Node 8: lnL = -957.535074 Node 9: lnL = -957.535074 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 588 Sequential format.. Reading seq # 1: YMR140W_Sbay Reading seq # 2: YMR140W_Scer Reading seq # 3: YMR140W_Skud Reading seq # 4: YMR140W_Smik Reading seq # 5: YMR140W_Spar Sequences read.. Counting patterns.. # site patterns = 247 Counting frequencies.. 120 bytes for distance 39520 bytes for lkl0 31616 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.031663 0.121930 0.090937 0.138486 0.102281 0.255021 0.186881 0.188957 lnL0 = -2690.884365 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2690.884365 x= 0.03166 0.12193 0.09094 0.13849 0.10228 0.25502 0.18688 0.18896 1 h-lim-p 0.0003 0.0028 129.6645 2687.110628 0 0.0005 22 | 0/8 2 h-lim-p 0.0002 0.0018 48.9233 2686.768400 0 0.0004 35 | 0/8 3 h-lim-p 0.0032 0.0399 6.9293 2686.749736 3 0.0008 54 | 0/8 4 h-lim-p 0.0017 0.1272 3.1364 2686.747907 2 0.0004 71 | 0/8 5 h-lim-p 0.0024 0.1605 0.5571 2686.747752 3 0.0008 91 | 0/8 6 h-lim-p 0.0042 4.1223 0.1051 2686.747078 0 0.0084 112 | 0/8 7 h-lim-p 0.0047 1.2386 0.1857 2686.720984 0 0.0378 135 | 0/8 8 h-lim-p 0.0019 0.0634 3.7809 2686.704457 6 0.0013 171 | 0/8 9 h-lim-p 2.5000 20.0000 0.0014 2686.702099 2 1.0889 187 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2686.702078 0 1.2500 207 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2686.702078 0 1.0938 227 | 0/8 12 h-lim-p 1.0974 20.0000 0.0000 2686.702078 0 1.0974 247 | 0/8 13 h-lim-p 0.5272 20.0000 0.0000 2686.702078 0 0.0988 269 | 0/8 14 h-lim-p 0.0103 20.0000 0.0005 2686.702078 0 0.0000 299 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 2686.702078 0 0.0000 330 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 2686.702078 0 0.0000 354 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 | 0/8 19 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -2686.702078 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2686.702078 Node 7: lnL = -2686.702078 Node 8: lnL = -2686.702078 Node 9: lnL = -2686.702078 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 490 Sequential format.. Reading seq # 1: YMR144W_Sbay Reading seq # 2: YMR144W_Scer Reading seq # 3: YMR144W_Skud Reading seq # 4: YMR144W_Smik Reading seq # 5: YMR144W_Spar Sequences read.. Counting patterns.. # site patterns = 161 Counting frequencies.. 120 bytes for distance 25760 bytes for lkl0 20608 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.031899 0.030547 0.032998 0.096116 0.076065 0.132496 0.160146 0.124026 lnL0 = -1893.134714 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1893.134714 x= 0.03190 0.03055 0.03300 0.09612 0.07606 0.13250 0.16015 0.12403 1 h-lim-p 0.0024 1.0809 124.7823 1892.163222 6 0.0001 36 | 0/8 2 h-lim-p 0.0006 0.0044 17.5818 1892.124674 2 0.0003 52 | 0/8 3 h-lim-p 0.0008 0.0223 5.5229 1892.120809 5 0.0003 77 | 0/8 4 h-lim-p 0.0013 0.1706 1.1873 1892.120578 3 0.0003 96 | 0/8 5 h-lim-p 0.0017 0.9473 0.2379 1892.120569 1 0.0003 111 | 0/8 6 h-lim-p 0.0011 2.0922 0.0732 1892.120568 0 0.0005 131 | 0/8 7 h-lim-p 0.0075 14.6489 0.0047 1892.120568 0 0.0009 153 | 0/8 8 h-lim-p 0.0140 20.0000 0.0003 1892.120542 0 0.4471 178 | 0/8 9 h-lim-p 2.3027 20.0000 0.0001 1892.120540 0 1.0074 198 | 0/8 10 h-lim-p 2.1149 20.0000 0.0000 1892.120540 0 1.8506 218 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1892.120540 0 0.0684 242 | 0/8 12 h-lim-p 0.0132 20.0000 0.0001 1892.120540 0 0.0029 263 | 0/8 13 h-lim-p 0.0011 20.0000 0.0002 1892.120540 0 0.0000 289 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 1892.120540 0 0.0000 323 | 0/8 15 h-lim-p 0.0000 20.0000 0.0036 | 0/8 16 h-lim-p 0.0000 20.0000 0.0036 Out... lnL = -1892.120540 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1892.120540 Node 7: lnL = -1892.120540 Node 8: lnL = -1892.120540 Node 9: lnL = -1892.120540 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 737 Sequential format.. Reading seq # 1: YMR146C_Sbay Reading seq # 2: YMR146C_Scer Reading seq # 3: YMR146C_Skud Reading seq # 4: YMR146C_Smik Reading seq # 5: YMR146C_Spar Sequences read.. Counting patterns.. # site patterns = 284 Counting frequencies.. 120 bytes for distance 45440 bytes for lkl0 36352 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.085211 0.000060 0.123485 0.131204 0.103460 0.190105 0.279140 0.237524 lnL0 = -3315.943674 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3315.943674 x= 0.08521 0.00006 0.12349 0.13120 0.10346 0.19011 0.27914 0.23752 1 h-lim-p 0.0007 0.0055 117.6033 3313.948003 8 0.0002 40 | 0/8 2 h-lim-p 0.0007 0.0055 27.7771 3313.790651 7 0.0004 72 | 0/8 3 h-lim-p 0.0014 0.0207 8.6275 3313.780246 3 0.0003 91 | 0/8 4 h-lim-p 0.0010 0.0673 2.6686 3313.779074 4 0.0004 113 | 0/8 5 h-lim-p 0.0012 0.3715 0.8224 3313.778845 4 0.0007 136 | 0/8 6 h-lim-p 0.0047 0.6151 0.1290 3313.778839 0 0.0006 158 | 0/8 7 h-lim-p 0.0029 7.3648 0.0260 3313.778819 0 0.0058 179 | 0/8 8 h-lim-p 0.0107 3.3021 0.0141 3313.776438 0 0.0856 202 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3313.776428 1 0.9961 224 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3313.776428 0 2.1875 244 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3313.776428 0 1.0938 264 | 0/8 12 h-lim-p 0.0885 20.0000 0.0000 3313.776428 0 0.0664 284 | 0/8 13 h-lim-p 0.0001 11.4479 0.0098 3313.776428 0 0.0000 320 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 3313.776428 0 0.0000 349 Out... lnL = -3313.776428 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3313.776428 Node 7: lnL = -3313.776428 Node 8: lnL = -3313.776428 Node 9: lnL = -3313.776428 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 734 Sequential format.. Reading seq # 1: YMR147W_Sbay Reading seq # 2: YMR147W_Scer Reading seq # 3: YMR147W_Skud Reading seq # 4: YMR147W_Smik Reading seq # 5: YMR147W_Spar Sequences read.. Counting patterns.. # site patterns = 273 Counting frequencies.. 120 bytes for distance 43680 bytes for lkl0 34944 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.094916 0.040424 0.091470 0.132087 0.094669 0.214224 0.230502 0.242037 lnL0 = -3313.234697 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3313.234697 x= 0.09492 0.04042 0.09147 0.13209 0.09467 0.21422 0.23050 0.24204 1 h-lim-p 0.0104 1.5994 79.7726 3312.538521 8 0.0002 44 | 0/8 2 h-lim-p 0.0014 0.0119 12.5619 3312.513469 3 0.0003 63 | 0/8 3 h-lim-p 0.0011 0.0338 3.7419 3312.511374 4 0.0003 86 | 0/8 4 h-lim-p 0.0010 0.1941 1.2615 3312.511020 4 0.0005 107 | 0/8 5 h-lim-p 0.0046 1.9995 0.1363 3312.511014 1 0.0006 123 | 0/8 6 h-lim-p 0.0060 14.6608 0.0126 3312.511014 0 0.0007 145 | 0/8 7 h-lim-p 0.0034 20.0000 0.0025 3312.511014 0 0.0015 165 | 0/8 8 h-lim-p 0.0099 20.0000 0.0004 3312.511008 0 0.3177 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3312.511007 0 1.0938 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3312.511007 0 0.6250 231 | 0/8 11 h-lim-p 0.4482 20.0000 0.0000 3312.511007 0 0.0140 255 | 0/8 12 h-lim-p 0.0069 20.0000 0.0000 3312.511007 0 0.0035 275 | 0/8 13 h-lim-p 0.0016 20.0000 0.0001 3312.511007 0 0.0002 297 | 0/8 14 h-lim-p 0.0003 20.0000 0.0001 3312.511007 0 0.0003 317 | 0/8 15 h-lim-p 0.0003 20.0000 0.0001 3312.511007 0 0.0000 352 | 0/8 16 h-lim-p 0.0000 20.0000 0.0014 | 0/8 17 h-lim-p 0.0000 20.0000 0.0014 Out... lnL = -3312.511007 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3312.511007 Node 7: lnL = -3312.511007 Node 8: lnL = -3312.511007 Node 9: lnL = -3312.511007 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 514 Sequential format.. Reading seq # 1: YMR148W_Sbay Reading seq # 2: YMR148W_Scer Reading seq # 3: YMR148W_Skud Reading seq # 4: YMR148W_Smik Reading seq # 5: YMR148W_Spar Sequences read.. Counting patterns.. # site patterns = 147 Counting frequencies.. 120 bytes for distance 23520 bytes for lkl0 18816 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.049022 0.069271 0.017888 0.063794 0.070829 0.167419 0.125106 0.140133 lnL0 = -2033.652606 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2033.652606 x= 0.04902 0.06927 0.01789 0.06379 0.07083 0.16742 0.12511 0.14013 1 h-lim-p 0.0006 0.3864 261.0309 2031.429957 5 0.0001 34 | 0/8 2 h-lim-p 0.0012 0.0094 12.4686 2031.410521 5 0.0003 56 | 0/8 3 h-lim-p 0.0006 0.0474 5.5568 2031.407383 4 0.0002 77 | 0/8 4 h-lim-p 0.0009 0.0872 1.4545 2031.407086 4 0.0003 99 | 0/8 5 h-lim-p 0.0027 2.6483 0.1654 2031.407079 2 0.0004 117 | 0/8 6 h-lim-p 0.0017 2.7602 0.0432 2031.407079 0 0.0004 138 | 0/8 7 h-lim-p 0.0516 20.0000 0.0003 2031.407079 0 0.0113 159 | 0/8 8 h-lim-p 0.0021 20.0000 0.0017 2031.407078 0 0.0331 183 | 0/8 9 h-lim-p 1.7450 20.0000 0.0000 2031.407078 0 1.5269 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2031.407078 0 1.0938 223 | 0/8 11 h-lim-p 0.7412 20.0000 0.0000 2031.407078 0 5.9297 246 | 0/8 12 h-lim-p 1.3966 20.0000 0.0001 2031.407078 0 1.2220 266 | 0/8 13 h-lim-p 0.0100 6.1245 0.0117 2031.407078 0 0.0005 290 | 0/8 14 h-lim-p 0.0001 1.1905 0.0602 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0034 | 0/8 16 h-lim-p 0.0000 20.0000 0.0034 Out... lnL = -2031.407078 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2031.407078 Node 7: lnL = -2031.407078 Node 8: lnL = -2031.407078 Node 9: lnL = -2031.407078 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 601 Sequential format.. Reading seq # 1: YMR150C_Sbay Reading seq # 2: YMR150C_Scer Reading seq # 3: YMR150C_Skud Reading seq # 4: YMR150C_Smik Reading seq # 5: YMR150C_Spar Sequences read.. Counting patterns.. # site patterns = 276 Counting frequencies.. 120 bytes for distance 44160 bytes for lkl0 35328 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.121457 0.063367 0.143219 0.145454 0.118095 0.229542 0.355587 0.316127 lnL0 = -3009.681721 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3009.681721 x= 0.12146 0.06337 0.14322 0.14545 0.11809 0.22954 0.35559 0.31613 1 h-lim-p 0.0019 0.0150 62.1840 3008.686223 8 0.0005 43 | 0/8 2 h-lim-p 0.0024 0.0196 10.9915 3008.654481 3 0.0005 62 | 0/8 3 h-lim-p 0.0012 0.0684 5.1423 3008.649383 3 0.0005 80 | 0/8 4 h-lim-p 0.0013 0.2605 1.8514 3008.647642 2 0.0012 96 | 0/8 5 h-lim-p 0.0029 0.6097 0.7646 3008.647404 4 0.0010 117 | 0/8 6 h-lim-p 0.0021 0.7837 0.3476 3008.647359 2 0.0009 141 | 0/8 7 h-lim-p 0.1037 20.0000 0.0031 3008.647358 0 0.0227 162 | 0/8 8 h-lim-p 0.0318 20.0000 0.0022 3008.647308 0 0.1273 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3008.647307 0 1.0938 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3008.647307 0 1.0938 224 | 0/8 11 h-lim-p 1.3222 20.0000 0.0000 3008.647307 0 1.9833 244 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3008.647307 0 0.2734 266 | 0/8 13 h-lim-p 0.0589 20.0000 0.0000 3008.647307 0 0.0000 308 | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -3008.647307 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3008.647307 Node 7: lnL = -3008.647307 Node 8: lnL = -3008.647307 Node 9: lnL = -3008.647307 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 162 Sequential format.. Reading seq # 1: YMR152W_Sbay Reading seq # 2: YMR152W_Scer Reading seq # 3: YMR152W_Skud Reading seq # 4: YMR152W_Smik Reading seq # 5: YMR152W_Spar Sequences read.. Counting patterns.. # site patterns = 110 Counting frequencies.. 120 bytes for distance 17600 bytes for lkl0 14080 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.038200 0.218511 0.166488 0.060587 0.275431 0.252910 0.383154 0.264055 lnL0 = -764.051770 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 764.051770 x= 0.03820 0.21851 0.16649 0.06059 0.27543 0.25291 0.38315 0.26405 1 h-lim-p 0.0094 0.0749 33.9381 763.191840 6 0.0017 36 | 0/8 2 h-lim-p 0.0030 0.0246 18.8813 762.655922 0 0.0045 48 | 0/8 3 h-lim-p 0.0030 0.0240 8.5260 762.550908 1 0.0037 62 | 0/8 4 h-lim-p 0.0109 0.1162 2.9227 762.532950 6 0.0049 85 | 0/8 5 h-lim-p 0.0090 0.1795 1.5768 762.527637 6 0.0054 112 | 0/8 6 h-lim-p 0.0185 1.4020 0.4574 762.526944 4 0.0060 134 | 0/8 7 h-lim-p 0.0537 4.9429 0.0508 762.520371 0 0.2149 156 | 0/8 8 h-lim-p 0.0313 1.4942 0.3484 762.506677 0 0.0470 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0026 762.506222 3 1.0449 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 762.506220 0 1.2500 222 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 762.506220 0 1.0938 242 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 762.506220 0 1.0938 262 | 0/8 13 h-lim-p 1.1851 20.0000 0.0000 762.506220 0 2.3702 283 | 0/8 14 h-lim-p 0.1526 20.0000 0.0000 762.506220 0 0.0095 306 | 0/8 15 h-lim-p 0.0025 20.0000 0.0001 762.506220 0 0.0025 326 | 0/8 16 h-lim-p 0.0008 20.0000 0.0004 762.506220 0 0.0000 364 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -762.506220 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -762.506220 Node 7: lnL = -762.506220 Node 8: lnL = -762.506220 Node 9: lnL = -762.506220 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 265 Sequential format.. Reading seq # 1: YMR153W_Sbay Reading seq # 2: YMR153W_Scer Reading seq # 3: YMR153W_Skud Reading seq # 4: YMR153W_Smik Reading seq # 5: YMR153W_Spar Sequences read.. Counting patterns.. # site patterns = 140 Counting frequencies.. 120 bytes for distance 22400 bytes for lkl0 17920 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.071253 0.063010 0.167809 0.069937 0.301086 0.301751 0.138709 0.251858 lnL0 = -1151.601234 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1151.601234 x= 0.07125 0.06301 0.16781 0.06994 0.30109 0.30175 0.13871 0.25186 1 h-lim-p 0.0028 0.0226 36.6026 1150.999966 8 0.0010 41 | 0/8 2 h-lim-p 0.0019 0.0154 15.6882 1150.820276 6 0.0017 64 | 0/8 3 h-lim-p 0.0025 0.0308 10.2595 1150.722401 4 0.0026 84 | 0/8 4 h-lim-p 0.0048 0.0477 5.6732 1150.696008 5 0.0023 107 | 0/8 5 h-lim-p 0.0038 0.0703 3.4735 1150.688501 4 0.0019 127 | 0/8 6 h-lim-p 0.0054 0.2183 1.2010 1150.687173 3 0.0023 145 | 0/8 7 h-lim-p 0.0060 0.6714 0.4505 1150.686986 3 0.0021 164 | 0/8 8 h-lim-p 0.5125 20.0000 0.0019 1150.686446 0 1.0250 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1150.686434 1 0.9961 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1150.686434 0 1.0938 227 | 0/8 11 h-lim-p 1.4375 20.0000 0.0000 1150.686434 0 0.6289 247 | 0/8 12 h-lim-p 0.3457 20.0000 0.0000 1150.686434 0 0.0216 270 | 0/8 13 h-lim-p 0.0078 20.0000 0.0000 1150.686434 0 0.0000 309 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1150.686434 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1150.686434 Node 7: lnL = -1150.686434 Node 8: lnL = -1150.686434 Node 9: lnL = -1150.686434 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 375 Sequential format.. Reading seq # 1: YMR154C_Sbay Reading seq # 2: YMR154C_Scer Reading seq # 3: YMR154C_Skud Reading seq # 4: YMR154C_Smik Reading seq # 5: YMR154C_Spar Sequences read.. Counting patterns.. # site patterns = 142 Counting frequencies.. 120 bytes for distance 22720 bytes for lkl0 18176 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.080293 0.055837 0.064273 0.126685 0.087665 0.135943 0.151654 0.197348 lnL0 = -1661.912553 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1661.912553 x= 0.08029 0.05584 0.06427 0.12669 0.08767 0.13594 0.15165 0.19735 1 h-lim-p 0.0006 0.0048 72.3252 1661.091414 7 0.0003 39 | 0/8 2 h-lim-p 0.0012 0.0095 13.3419 1661.053502 6 0.0004 64 | 0/8 3 h-lim-p 0.0014 0.0734 4.0980 1661.050217 5 0.0004 90 | 0/8 4 h-lim-p 0.0022 0.2275 0.8117 1661.050014 4 0.0006 113 | 0/8 5 h-lim-p 0.0036 0.8056 0.1454 1661.050009 2 0.0006 140 | 0/8 6 h-lim-p 0.0036 15.0493 0.0242 1661.050009 0 0.0008 161 | 0/8 7 h-lim-p 0.0256 20.0000 0.0007 1661.050009 0 0.0028 183 | 0/8 8 h-lim-p 0.0175 20.0000 0.0001 1661.050008 0 0.2801 207 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1661.050008 0 1.0938 227 | 0/8 10 h-lim-p 1.1649 20.0000 0.0000 1661.050008 0 2.3298 248 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1661.050008 0 0.5469 269 | 0/8 12 h-lim-p 0.0342 20.0000 0.0000 1661.050008 0 0.0043 291 | 0/8 13 h-lim-p 0.0018 20.0000 0.0000 1661.050008 0 0.0018 311 | 0/8 14 h-lim-p 0.0006 20.0000 0.0001 1661.050008 0 0.0000 348 | 0/8 15 h-lim-p 0.0000 20.0000 0.0010 | 0/8 16 h-lim-p 0.0000 20.0000 0.0010 Out... lnL = -1661.050008 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1661.050008 Node 7: lnL = -1661.050008 Node 8: lnL = -1661.050008 Node 9: lnL = -1661.050008 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 410 Sequential format.. Reading seq # 1: YMR155W_Sbay Reading seq # 2: YMR155W_Scer Reading seq # 3: YMR155W_Skud Reading seq # 4: YMR155W_Smik Reading seq # 5: YMR155W_Spar Sequences read.. Counting patterns.. # site patterns = 162 Counting frequencies.. 120 bytes for distance 25920 bytes for lkl0 20736 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.083853 0.036487 0.059002 0.136970 0.087494 0.139086 0.149812 0.198351 lnL0 = -1725.585360 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1725.585360 x= 0.08385 0.03649 0.05900 0.13697 0.08749 0.13909 0.14981 0.19835 1 h-lim-p 0.0006 0.0049 96.6249 1724.443581 5 0.0003 31 | 0/8 2 h-lim-p 0.0008 0.0064 20.1203 1724.356710 8 0.0004 64 | 0/8 3 h-lim-p 0.0010 0.0221 9.0132 1724.342097 5 0.0004 85 | 0/8 4 h-lim-p 0.0030 0.1631 1.2817 1724.341614 3 0.0006 104 | 0/8 5 h-lim-p 0.0089 3.0031 0.0860 1724.341612 0 0.0005 119 | 0/8 6 h-lim-p 0.0021 5.8226 0.0200 1724.341612 0 0.0009 139 | 0/8 7 h-lim-p 0.0590 20.0000 0.0003 1724.341510 0 0.9442 163 | 0/8 8 h-lim-p 0.0232 10.3713 0.0127 1724.341510 0 0.0007 187 | 0/8 9 h-lim-p 0.1234 20.0000 0.0001 1724.341509 0 0.9873 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1724.341509 0 1.0938 230 | 0/8 11 h-lim-p 0.7830 20.0000 0.0000 1724.341509 0 2.3491 251 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1724.341509 0 0.2734 273 | 0/8 13 h-lim-p 0.0269 20.0000 0.0000 1724.341509 0 0.0059 294 | 0/8 14 h-lim-p 0.0024 20.0000 0.0000 1724.341509 0 0.0000 321 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 1724.341509 0 0.0001 341 Out... lnL = -1724.341509 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1724.341509 Node 7: lnL = -1724.341509 Node 8: lnL = -1724.341509 Node 9: lnL = -1724.341509 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 316 Sequential format.. Reading seq # 1: YMR156C_Sbay Reading seq # 2: YMR156C_Scer Reading seq # 3: YMR156C_Skud Reading seq # 4: YMR156C_Smik Reading seq # 5: YMR156C_Spar Sequences read.. Counting patterns.. # site patterns = 161 Counting frequencies.. 120 bytes for distance 25760 bytes for lkl0 20608 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.108221 0.121649 0.119901 0.131023 0.108472 0.268548 0.275057 0.297389 lnL0 = -1377.187210 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1377.187210 x= 0.10822 0.12165 0.11990 0.13102 0.10847 0.26855 0.27506 0.29739 1 h-lim-p 0.0076 0.0606 18.5936 1377.044169 3 0.0009 30 | 0/8 2 h-lim-p 0.0027 0.0398 5.9663 1377.027422 4 0.0010 50 | 0/8 3 h-lim-p 0.0054 0.1443 1.1336 1377.026436 4 0.0016 73 | 0/8 4 h-lim-p 0.0073 1.2692 0.2467 1377.026371 3 0.0021 94 | 0/8 5 h-lim-p 0.0108 5.0065 0.0491 1377.026369 1 0.0013 118 | 0/8 6 h-lim-p 0.0039 20.0000 0.0169 1377.026369 0 0.0034 138 | 0/8 7 h-lim-p 0.0508 20.0000 0.0011 1377.026369 0 0.0444 158 | 0/8 8 h-lim-p 0.0266 20.0000 0.0019 1377.026361 0 0.0799 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1377.026361 0 1.0938 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1377.026361 0 2.1875 219 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1377.026361 0 1.0938 239 | 0/8 12 h-lim-p 0.3571 20.0000 0.0000 1377.026361 0 2.8569 262 | 0/8 13 h-lim-p 1.1063 20.0000 0.0000 1377.026361 0 0.8297 282 | 0/8 14 h-lim-p 0.0010 18.2251 0.0081 1377.026361 0 0.0001 304 | 0/8 15 h-lim-p 0.0002 20.0000 0.0044 1377.026361 0 0.0000 341 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1377.026361 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1377.026361 Node 7: lnL = -1377.026361 Node 8: lnL = -1377.026361 Node 9: lnL = -1377.026361 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 236 Sequential format.. Reading seq # 1: YMR157C_Sbay Reading seq # 2: YMR157C_Scer Reading seq # 3: YMR157C_Skud Reading seq # 4: YMR157C_Smik Reading seq # 5: YMR157C_Spar Sequences read.. Counting patterns.. # site patterns = 111 Counting frequencies.. 120 bytes for distance 17760 bytes for lkl0 14208 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.031280 0.135807 0.086200 0.128360 0.093317 0.199239 0.185460 0.170455 lnL0 = -1032.986738 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1032.986738 x= 0.03128 0.13581 0.08620 0.12836 0.09332 0.19924 0.18546 0.17045 1 h-lim-p 0.0052 0.0412 41.8996 1032.305258 6 0.0008 37 | 0/8 2 h-lim-p 0.0032 0.0253 9.3245 1032.247522 5 0.0014 58 | 0/8 3 h-lim-p 0.0025 0.0437 5.1207 1032.237962 5 0.0009 82 | 0/8 4 h-lim-p 0.0080 0.4291 0.5905 1032.237779 3 0.0011 102 | 0/8 5 h-lim-p 0.0049 1.5664 0.1299 1032.237765 2 0.0019 126 | 0/8 6 h-lim-p 0.0142 20.0000 0.0173 1032.237764 0 0.0031 147 | 0/8 7 h-lim-p 0.0066 20.0000 0.0081 1032.237761 0 0.0132 168 | 0/8 8 h-lim-p 0.0156 20.0000 0.0069 1032.237622 0 0.0934 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1032.237618 1 0.9961 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1032.237618 0 2.1875 232 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1032.237618 0 1.0938 252 | 0/8 12 h-lim-p 0.1340 20.0000 0.0000 1032.237618 0 0.0335 273 | 0/8 13 h-lim-p 0.0008 20.0000 0.0005 1032.237618 0 0.0008 293 | 0/8 14 h-lim-p 0.0001 20.0000 0.0026 1032.237618 0 0.0000 325 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 1032.237618 0 0.0000 350 Out... lnL = -1032.237618 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1032.237618 Node 7: lnL = -1032.237618 Node 8: lnL = -1032.237618 Node 9: lnL = -1032.237618 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 236 Sequential format.. Reading seq # 1: YMR158W_Sbay Reading seq # 2: YMR158W_Scer Reading seq # 3: YMR158W_Skud Reading seq # 4: YMR158W_Smik Reading seq # 5: YMR158W_Spar Sequences read.. Counting patterns.. # site patterns = 106 Counting frequencies.. 120 bytes for distance 16960 bytes for lkl0 13568 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.022842 0.138257 0.080261 0.133680 0.087997 0.205179 0.181064 0.159159 lnL0 = -1021.536631 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1021.536631 x= 0.02284 0.13826 0.08026 0.13368 0.08800 0.20518 0.18106 0.15916 1 h-lim-p 0.0024 0.0195 35.7392 1021.065620 7 0.0008 38 | 0/8 2 h-lim-p 0.0020 0.0158 8.2307 1021.030586 7 0.0011 65 | 0/8 3 h-lim-p 0.0025 0.0931 3.6159 1021.024162 2 0.0011 81 | 0/8 4 h-lim-p 0.0050 0.2927 0.8379 1021.023879 4 0.0009 104 | 0/8 5 h-lim-p 0.0052 1.5279 0.1403 1021.023866 2 0.0013 129 | 0/8 6 h-lim-p 0.0066 8.0491 0.0272 1021.023866 0 0.0014 150 | 0/8 7 h-lim-p 0.0599 20.0000 0.0007 1021.023864 0 0.1198 171 | 0/8 8 h-lim-p 0.0072 20.0000 0.0109 1021.023850 0 0.0144 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1021.023850 0 1.0938 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1021.023850 0 1.0938 232 | 0/8 11 h-lim-p 1.0959 20.0000 0.0000 1021.023850 0 0.1199 254 | 0/8 12 h-lim-p 0.0208 20.0000 0.0001 1021.023850 0 0.0000 286 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 1021.023850 0 0.0000 307 Out... lnL = -1021.023850 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1021.023850 Node 7: lnL = -1021.023850 Node 8: lnL = -1021.023850 Node 9: lnL = -1021.023850 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 215 Sequential format.. Reading seq # 1: YMR159C_Sbay Reading seq # 2: YMR159C_Scer Reading seq # 3: YMR159C_Skud Reading seq # 4: YMR159C_Smik Reading seq # 5: YMR159C_Spar Sequences read.. Counting patterns.. # site patterns = 120 Counting frequencies.. 120 bytes for distance 19200 bytes for lkl0 15360 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.062329 0.180972 0.000060 0.160479 0.154824 0.227480 0.230102 0.224371 lnL0 = -981.218220 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 981.218220 x= 0.06233 0.18097 0.00006 0.16048 0.15482 0.22748 0.23010 0.22437 1 h-lim-p 0.0031 0.0508 79.9764 978.634189 8 0.0008 38 | 0/8 2 h-lim-p 0.0010 0.0082 24.3206 978.002750 0 0.0020 51 | 0/8 3 h-lim-p 0.0045 0.0363 7.5618 977.942195 4 0.0023 72 | 0/8 4 h-lim-p 0.0081 0.1060 2.1696 977.936226 6 0.0028 100 | 0/8 5 h-lim-p 0.0108 0.6504 0.5565 977.935913 3 0.0021 119 | 0/8 6 h-lim-p 0.0069 0.6592 0.1682 977.935819 3 0.0044 147 | 0/8 7 h-lim-p 0.0351 13.9894 0.0213 977.933637 0 0.1404 169 | 0/8 8 h-lim-p 0.0056 0.4612 0.5366 977.927815 0 0.0111 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0012 977.927110 2 1.1719 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 977.927107 1 0.9961 236 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 977.927107 0 1.0938 256 | 0/8 12 h-lim-p 1.7410 20.0000 0.0000 977.927107 0 1.5234 276 | 0/8 13 h-lim-p 1.2811 20.0000 0.0000 977.927107 0 0.6405 296 | 0/8 14 h-lim-p 0.0377 20.0000 0.0001 977.927107 0 0.0001 324 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 977.927107 0 0.0002 344 | 0/8 16 h-lim-p 0.0002 20.0000 0.0000 977.927107 0 0.0000 367 | 0/8 17 h-lim-p 0.0004 20.0000 0.0000 977.927107 0 0.0000 397 Out... lnL = -977.927107 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -977.927107 Node 7: lnL = -977.927107 Node 8: lnL = -977.927107 Node 9: lnL = -977.927107 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 149 Sequential format.. Reading seq # 1: YMR160W_Sbay Reading seq # 2: YMR160W_Scer Reading seq # 3: YMR160W_Skud Reading seq # 4: YMR160W_Smik Reading seq # 5: YMR160W_Spar Sequences read.. Counting patterns.. # site patterns = 78 Counting frequencies.. 120 bytes for distance 12480 bytes for lkl0 9984 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.100477 0.095481 0.011424 0.164972 0.106747 0.242507 0.115400 0.238122 lnL0 = -677.746105 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 677.746105 x= 0.10048 0.09548 0.01142 0.16497 0.10675 0.24251 0.11540 0.23812 1 h-lim-p 0.0030 0.2369 67.4286 676.995999 9 0.0004 43 | 0/8 2 h-lim-p 0.0032 0.0276 8.7079 676.909645 8 0.0023 76 | 0/8 3 h-lim-p 0.0070 0.0799 2.8956 676.904457 4 0.0014 97 | 0/8 4 h-lim-p 0.0117 0.7751 0.3411 676.904321 3 0.0023 116 | 0/8 5 h-lim-p 0.0075 2.7357 0.1069 676.904310 3 0.0020 143 | 0/8 6 h-lim-p 0.0058 7.6605 0.0370 676.904308 1 0.0023 165 | 0/8 7 h-lim-p 0.0682 20.0000 0.0013 676.904096 0 0.5454 188 | 0/8 8 h-lim-p 0.0039 0.5124 0.1754 676.903922 3 0.0041 214 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 676.903916 1 0.9961 236 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 676.903916 0 1.0938 256 | 0/8 11 h-lim-p 2.2302 20.0000 0.0000 676.903916 0 2.2302 276 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 676.903916 0 0.0000 320 Out... lnL = -676.903916 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -676.903916 Node 7: lnL = -676.903916 Node 8: lnL = -676.903916 Node 9: lnL = -676.903916 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 246 Sequential format.. Reading seq # 1: YMR161W_Sbay Reading seq # 2: YMR161W_Scer Reading seq # 3: YMR161W_Skud Reading seq # 4: YMR161W_Smik Reading seq # 5: YMR161W_Spar Sequences read.. Counting patterns.. # site patterns = 93 Counting frequencies.. 120 bytes for distance 14880 bytes for lkl0 11904 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.056930 0.036470 0.015342 0.034007 0.039866 0.122343 0.104532 0.125316 lnL0 = -840.328414 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 840.328414 x= 0.05693 0.03647 0.01534 0.03401 0.03987 0.12234 0.10453 0.12532 1 h-lim-p 0.0001 0.0149 373.8617 835.136957 6 0.0001 34 | 0/8 2 h-lim-p 0.0007 0.0060 21.8972 835.007098 6 0.0005 59 | 0/8 3 h-lim-p 0.0009 0.0180 13.3043 834.988369 7 0.0003 91 | 0/8 4 h-lim-p 0.0010 0.0227 3.7445 834.985617 3 0.0004 109 | 0/8 5 h-lim-p 0.0016 0.0823 1.0617 834.985393 5 0.0004 134 | 0/8 6 h-lim-p 0.0012 0.5335 0.3778 834.985359 2 0.0005 150 | 0/8 7 h-lim-p 0.0158 14.2220 0.0127 834.985358 0 0.0017 172 | 0/8 8 h-lim-p 0.1035 20.0000 0.0002 834.985260 0 1.6556 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 834.985231 3 1.4879 224 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 834.985230 0 1.0938 244 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 834.985230 0 1.0938 264 | 0/8 12 h-lim-p 1.0973 20.0000 0.0000 834.985230 0 0.1372 286 | 0/8 13 h-lim-p 0.0024 20.0000 0.0004 834.985230 0 0.0000 312 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 834.985230 0 0.0000 343 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 834.985230 0 0.0026 371 | 0/8 16 h-lim-p 0.0067 20.0000 0.0001 834.985230 0 0.0000 402 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 834.985230 0 0.0000 422 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0011 | 0/8 20 h-lim-p 0.0000 20.0000 0.0011 Out... lnL = -834.985230 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -834.985230 Node 7: lnL = -834.985230 Node 8: lnL = -834.985230 Node 9: lnL = -834.985230 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 847 Sequential format.. Reading seq # 1: YMR163C_Sbay Reading seq # 2: YMR163C_Scer Reading seq # 3: YMR163C_Skud Reading seq # 4: YMR163C_Smik Reading seq # 5: YMR163C_Spar Sequences read.. Counting patterns.. # site patterns = 280 Counting frequencies.. 120 bytes for distance 44800 bytes for lkl0 35840 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.183711 0.000060 0.011233 0.359532 0.488501 0.452167 0.523591 0.432073 lnL0 = -4003.658924 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4003.658924 x= 0.18371 0.00006 0.01123 0.35953 0.48850 0.45217 0.52359 0.43207 1 h-lim-p 0.0000 0.0000 223.8704 4003.617479 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0018 202.0110 3988.265616 3 0.0012 47 | 1/8 3 h-lim-p 0.0002 0.0015 70.3815 3984.123265 m 0.0015 59 | 2/8 4 h-lim-p 0.0014 0.0120 66.6733 3975.500435 0 0.0027 72 | 2/8 5 h-lim-p 0.0094 0.0751 14.1162 3975.332888 7 0.0016 103 | 2/8 6 h-lim-p 0.0819 1.9313 0.2792 3971.913182 0 0.4916 117 | 2/8 7 h-lim-p 0.0412 1.2554 3.3304 3971.771199 6 0.0243 151 | 2/8 8 h-lim-p 2.5000 20.0000 0.0293 3971.623270 7 0.7629 182 | 2/8 9 h-lim-p 2.5000 20.0000 0.0056 3971.617971 5 0.7967 212 | 2/8 10 h-lim-p 2.5000 20.0000 0.0012 3971.617650 3 0.8855 238 | 2/8 11 h-lim-p 2.5000 20.0000 0.0001 3971.617645 1 0.6152 259 | 2/8 12 h-lim-p 2.3936 20.0000 0.0000 3971.617644 0 1.0472 277 | 2/8 13 h-lim-p 2.2321 20.0000 0.0000 3971.617644 0 1.9531 295 | 2/8 14 h-lim-p 2.5000 20.0000 0.0000 3971.617644 0 1.0938 313 | 2/8 15 h-lim-p 0.2970 20.0000 0.0000 3971.617644 0 0.2970 331 | 2/8 16 h-lim-p 0.0238 20.0000 0.0004 3971.617644 0 0.0059 350 | 2/8 17 h-lim-p 0.0018 20.0000 0.0012 3971.617644 0 0.0018 368 | 2/8 18 h-lim-p 0.0013 20.0000 0.0018 3971.617644 0 0.0026 387 | 2/8 19 h-lim-p 0.0012 20.0000 0.0038 3971.617644 0 0.0000 423 | 2/8 20 h-lim-p 0.0000 20.0000 0.0000 3971.617644 0 0.0000 448 Out... lnL = -3971.617644 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3971.617644 Node 7: lnL = -3971.617644 Node 8: lnL = -3971.617644 Node 9: lnL = -3971.617644 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 863 Sequential format.. Reading seq # 1: YMR170C_Sbay Reading seq # 2: YMR170C_Scer Reading seq # 3: YMR170C_Skud Reading seq # 4: YMR170C_Smik Reading seq # 5: YMR170C_Spar Sequences read.. Counting patterns.. # site patterns = 303 Counting frequencies.. 120 bytes for distance 48480 bytes for lkl0 38784 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.085923 0.081879 0.076344 0.120199 0.092673 0.267566 0.155913 0.222142 lnL0 = -3850.136022 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3850.136022 x= 0.08592 0.08188 0.07634 0.12020 0.09267 0.26757 0.15591 0.22214 1 h-lim-p 0.0006 0.0049 86.1637 3849.391067 8 0.0002 44 | 0/8 2 h-lim-p 0.0010 0.0101 17.7476 3849.355431 2 0.0002 61 | 0/8 3 h-lim-p 0.0007 0.0495 5.8435 3849.351273 4 0.0003 81 | 0/8 4 h-lim-p 0.0009 0.1327 1.6570 3849.350866 4 0.0003 104 | 0/8 5 h-lim-p 0.0012 0.6036 0.4373 3849.350833 2 0.0004 122 | 0/8 6 h-lim-p 0.0013 2.5318 0.1347 3849.350830 1 0.0003 145 | 0/8 7 h-lim-p 0.0120 20.0000 0.0036 3849.350830 0 0.0026 166 | 0/8 8 h-lim-p 0.0450 20.0000 0.0002 3849.350816 0 0.3600 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3849.350816 0 1.0938 209 | 0/8 10 h-lim-p 1.8862 20.0000 0.0000 3849.350816 0 1.6504 229 | 0/8 11 h-lim-p 1.1576 20.0000 0.0000 3849.350816 0 1.1576 249 | 0/8 12 h-lim-p 0.0370 20.0000 0.0006 3849.350816 0 0.0003 275 | 0/8 13 h-lim-p 0.0011 20.0000 0.0002 3849.350816 0 0.0000 309 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 3849.350816 0 0.0000 341 Out... lnL = -3849.350816 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3849.350816 Node 7: lnL = -3849.350816 Node 8: lnL = -3849.350816 Node 9: lnL = -3849.350816 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 474 Sequential format.. Reading seq # 1: YMR171C_Sbay Reading seq # 2: YMR171C_Scer Reading seq # 3: YMR171C_Skud Reading seq # 4: YMR171C_Smik Reading seq # 5: YMR171C_Spar Sequences read.. Counting patterns.. # site patterns = 172 Counting frequencies.. 120 bytes for distance 27520 bytes for lkl0 22016 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.066456 0.155680 0.056846 0.079111 0.081696 0.239873 0.142661 0.196097 lnL0 = -2144.003277 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2144.003277 x= 0.06646 0.15568 0.05685 0.07911 0.08170 0.23987 0.14266 0.19610 1 h-lim-p 0.0007 0.0057 77.0301 2143.200949 3 0.0003 28 | 0/8 2 h-lim-p 0.0013 0.0102 10.5388 2143.182474 5 0.0003 51 | 0/8 3 h-lim-p 0.0005 0.0352 7.4082 2143.171489 1 0.0006 65 | 0/8 4 h-lim-p 0.0023 0.0758 1.8985 2143.170837 4 0.0004 89 | 0/8 5 h-lim-p 0.0026 0.7040 0.2933 2143.170818 2 0.0004 107 | 0/8 6 h-lim-p 0.0028 5.0555 0.0435 2143.170817 0 0.0012 127 | 0/8 7 h-lim-p 0.0058 20.0000 0.0091 2143.170810 0 0.0116 148 | 0/8 8 h-lim-p 0.0087 9.7934 0.0121 2143.170399 0 0.0699 171 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 2143.170370 2 0.9961 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2143.170370 0 1.0938 215 | 0/8 11 h-lim-p 1.3643 20.0000 0.0000 2143.170370 0 1.1937 235 | 0/8 12 h-lim-p 0.1732 20.0000 0.0001 2143.170370 0 0.0054 259 | 0/8 13 h-lim-p 0.0013 20.0000 0.0003 2143.170370 0 0.0002 281 | 0/8 14 h-lim-p 0.0000 20.0000 0.0016 2143.170370 0 0.0000 315 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 2143.170370 0 0.0000 344 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -2143.170370 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2143.170370 Node 7: lnL = -2143.170370 Node 8: lnL = -2143.170370 Node 9: lnL = -2143.170370 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 700 Sequential format.. Reading seq # 1: YMR174C_Sbay Reading seq # 2: YMR174C_Scer Reading seq # 3: YMR174C_Skud Reading seq # 4: YMR174C_Smik Reading seq # 5: YMR174C_Spar Sequences read.. Counting patterns.. # site patterns = 246 Counting frequencies.. 120 bytes for distance 39360 bytes for lkl0 31488 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.059781 0.048827 0.060320 0.118549 0.089107 0.194202 0.225593 0.178438 lnL0 = -3049.075203 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3049.075203 x= 0.05978 0.04883 0.06032 0.11855 0.08911 0.19420 0.22559 0.17844 1 h-lim-p 0.0006 0.0049 99.0045 3048.216514 8 0.0002 42 | 0/8 2 h-lim-p 0.0007 0.0064 25.8246 3048.118517 5 0.0003 63 | 0/8 3 h-lim-p 0.0007 0.0223 10.7831 3048.106192 5 0.0002 87 | 0/8 4 h-lim-p 0.0012 0.0709 2.2282 3048.105481 3 0.0003 106 | 0/8 5 h-lim-p 0.0016 0.8199 0.4142 3048.105433 2 0.0006 122 | 0/8 6 h-lim-p 0.0032 3.4591 0.0803 3048.105432 0 0.0003 144 | 0/8 7 h-lim-p 0.0016 3.8182 0.0179 3048.105432 0 0.0003 165 | 0/8 8 h-lim-p 0.0414 20.0000 0.0001 3048.105395 0 0.9947 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3048.105395 0 1.0938 209 | 0/8 10 h-lim-p 2.0437 20.0000 0.0000 3048.105395 0 1.7882 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3048.105395 0 1.0938 249 | 0/8 12 h-lim-p 0.3903 20.0000 0.0000 3048.105395 0 0.0061 274 | 0/8 13 h-lim-p 0.0003 20.0000 0.0005 3048.105395 0 0.0000 298 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 3048.105395 0 0.0000 322 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 3048.105395 0 0.0000 354 Out... lnL = -3048.105395 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3048.105395 Node 7: lnL = -3048.105395 Node 8: lnL = -3048.105395 Node 9: lnL = -3048.105395 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 711 Sequential format.. Reading seq # 1: YMR175W_Sbay Reading seq # 2: YMR175W_Scer Reading seq # 3: YMR175W_Skud Reading seq # 4: YMR175W_Smik Reading seq # 5: YMR175W_Spar Sequences read.. Counting patterns.. # site patterns = 241 Counting frequencies.. 120 bytes for distance 38560 bytes for lkl0 30848 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.049424 0.049204 0.071812 0.119649 0.085930 0.176965 0.233020 0.166153 lnL0 = -3063.335742 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3063.335742 x= 0.04942 0.04920 0.07181 0.11965 0.08593 0.17696 0.23302 0.16615 1 h-lim-p 0.0007 0.0056 99.9790 3062.412254 8 0.0002 42 | 0/8 2 h-lim-p 0.0008 0.0066 22.5592 3062.341306 6 0.0003 68 | 0/8 3 h-lim-p 0.0008 0.0279 7.9731 3062.333994 5 0.0003 93 | 0/8 4 h-lim-p 0.0009 0.0849 2.3298 3062.333249 4 0.0003 116 | 0/8 5 h-lim-p 0.0015 0.3729 0.4595 3062.333199 2 0.0005 134 | 0/8 6 h-lim-p 0.0012 0.9141 0.1920 3062.333194 1 0.0003 157 | 0/8 7 h-lim-p 0.0245 20.0000 0.0023 3062.333194 0 0.0007 181 | 0/8 8 h-lim-p 0.0424 20.0000 0.0000 3062.333193 0 0.6784 205 | 0/8 9 h-lim-p 0.8610 20.0000 0.0000 3062.333193 0 0.8610 225 | 0/8 10 h-lim-p 0.8402 20.0000 0.0000 3062.333193 0 1.6804 246 | 0/8 11 h-lim-p 1.7406 20.0000 0.0000 3062.333193 0 1.5230 266 | 0/8 12 h-lim-p 0.0609 20.0000 0.0007 3062.333193 0 0.0002 293 | 0/8 13 h-lim-p 0.0000 1.2313 0.0612 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0010 | 0/8 15 h-lim-p 0.0000 20.0000 0.0010 Out... lnL = -3062.333193 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3062.333193 Node 7: lnL = -3062.333193 Node 8: lnL = -3062.333193 Node 9: lnL = -3062.333193 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 539 Sequential format.. Reading seq # 1: YMR176W_Sbay Reading seq # 2: YMR176W_Scer Reading seq # 3: YMR176W_Skud Reading seq # 4: YMR176W_Smik Reading seq # 5: YMR176W_Spar Sequences read.. Counting patterns.. # site patterns = 254 Counting frequencies.. 120 bytes for distance 40640 bytes for lkl0 32512 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.123397 0.108187 0.076198 0.145670 0.116561 0.382513 0.182625 0.299382 lnL0 = -2557.030974 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2557.030974 x= 0.12340 0.10819 0.07620 0.14567 0.11656 0.38251 0.18263 0.29938 1 h-lim-p 0.0039 0.0310 52.1501 2556.482668 5 0.0004 33 | 0/8 2 h-lim-p 0.0010 0.0081 18.2250 2556.379085 7 0.0007 63 | 0/8 3 h-lim-p 0.0018 0.0180 7.0925 2556.362084 3 0.0008 81 | 0/8 4 h-lim-p 0.0014 0.0983 3.9798 2556.357927 4 0.0007 102 | 0/8 5 h-lim-p 0.0090 0.7161 0.3069 2556.357892 2 0.0007 121 | 0/8 6 h-lim-p 0.0048 19.5306 0.0461 2556.357890 0 0.0021 141 | 0/8 7 h-lim-p 0.0135 20.0000 0.0072 2556.357890 0 0.0059 161 | 0/8 8 h-lim-p 0.0288 20.0000 0.0015 2556.357790 0 0.2307 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2556.357787 0 1.0938 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2556.357787 0 1.0938 224 | 0/8 11 h-lim-p 1.6082 20.0000 0.0000 2556.357787 0 1.4072 244 | 0/8 12 h-lim-p 1.5635 20.0000 0.0000 2556.357787 0 0.0000 292 Out... lnL = -2556.357787 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2556.357787 Node 7: lnL = -2556.357787 Node 8: lnL = -2556.357787 Node 9: lnL = -2556.357787 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 616 Sequential format.. Reading seq # 1: YMR177W_Sbay Reading seq # 2: YMR177W_Scer Reading seq # 3: YMR177W_Skud Reading seq # 4: YMR177W_Smik Reading seq # 5: YMR177W_Spar Sequences read.. Counting patterns.. # site patterns = 170 Counting frequencies.. 120 bytes for distance 27200 bytes for lkl0 21760 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.017939 0.093429 0.067190 0.078103 0.033144 0.178077 0.166962 0.113451 lnL0 = -2480.369820 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2480.369820 x= 0.01794 0.09343 0.06719 0.07810 0.03314 0.17808 0.16696 0.11345 1 h-lim-p 0.0003 0.0021 69.1405 2479.863798 6 0.0002 35 | 0/8 2 h-lim-p 0.0004 0.0033 29.0755 2479.822735 6 0.0001 60 | 0/8 3 h-lim-p 0.0002 0.0033 15.5002 2479.806861 3 0.0002 78 | 0/8 4 h-lim-p 0.0012 0.0664 2.2913 2479.806304 3 0.0002 97 | 0/8 5 h-lim-p 0.0007 0.2792 0.6785 2479.806228 1 0.0004 111 | 0/8 6 h-lim-p 0.0022 0.8536 0.1119 2479.806227 0 0.0002 133 | 0/8 7 h-lim-p 0.0112 20.0000 0.0024 2479.806221 0 0.0337 154 | 0/8 8 h-lim-p 0.0045 6.4298 0.0183 2479.806018 0 0.0179 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2479.806017 0 1.0938 196 | 0/8 10 h-lim-p 1.1084 20.0000 0.0000 2479.806017 0 1.1084 216 | 0/8 11 h-lim-p 0.6904 20.0000 0.0001 2479.806017 0 1.0356 236 | 0/8 12 h-lim-p 0.0488 16.4044 0.0015 2479.806017 0 0.0008 261 | 0/8 13 h-lim-p 0.0003 5.6932 0.0045 2479.806017 0 0.0000 284 | 0/8 14 h-lim-p 0.0000 20.0000 0.0023 2479.806017 0 0.0000 307 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 2479.806017 0 0.0000 327 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 2479.806017 0 0.0000 355 | 0/8 17 h-lim-p 0.0000 20.0000 0.0021 | 0/8 18 h-lim-p 0.0000 20.0000 0.0021 Out... lnL = -2479.806017 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2479.806017 Node 7: lnL = -2479.806017 Node 8: lnL = -2479.806017 Node 9: lnL = -2479.806017 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 397 Sequential format.. Reading seq # 1: YMR178W_Sbay Reading seq # 2: YMR178W_Scer Reading seq # 3: YMR178W_Skud Reading seq # 4: YMR178W_Smik Reading seq # 5: YMR178W_Spar Sequences read.. Counting patterns.. # site patterns = 146 Counting frequencies.. 120 bytes for distance 23360 bytes for lkl0 18688 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.036002 0.122421 0.041889 0.098985 0.077403 0.153289 0.180976 0.144026 lnL0 = -1652.972264 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1652.972264 x= 0.03600 0.12242 0.04189 0.09899 0.07740 0.15329 0.18098 0.14403 1 h-lim-p 0.0013 0.0106 41.4560 1652.605017 8 0.0004 41 | 0/8 2 h-lim-p 0.0005 0.0040 16.6742 1652.549138 3 0.0005 59 | 0/8 3 h-lim-p 0.0008 0.0205 8.9498 1652.536124 4 0.0004 79 | 0/8 4 h-lim-p 0.0020 0.0575 1.9007 1652.535547 4 0.0003 102 | 0/8 5 h-lim-p 0.0009 0.2934 0.7310 1652.535408 3 0.0006 121 | 0/8 6 h-lim-p 0.0092 4.4737 0.0468 1652.535408 0 0.0006 144 | 0/8 7 h-lim-p 0.0019 13.8761 0.0139 1652.535408 0 0.0005 165 | 0/8 8 h-lim-p 0.0950 20.0000 0.0001 1652.535402 0 1.1394 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1652.535402 0 1.0938 208 | 0/8 10 h-lim-p 1.1473 20.0000 0.0000 1652.535402 0 0.5019 228 | 0/8 11 h-lim-p 0.2711 20.0000 0.0000 1652.535402 0 0.0339 250 | 0/8 12 h-lim-p 0.0151 20.0000 0.0001 1652.535402 0 0.0019 272 | 0/8 13 h-lim-p 0.0011 20.0000 0.0001 1652.535402 0 0.0001 294 | 0/8 14 h-lim-p 0.0000 20.0000 0.0016 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0012 | 0/8 16 h-lim-p 0.0000 20.0000 0.0012 Out... lnL = -1652.535402 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1652.535402 Node 7: lnL = -1652.535402 Node 8: lnL = -1652.535402 Node 9: lnL = -1652.535402 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 635 Sequential format.. Reading seq # 1: YMR179W_Sbay Reading seq # 2: YMR179W_Scer Reading seq # 3: YMR179W_Skud Reading seq # 4: YMR179W_Smik Reading seq # 5: YMR179W_Spar Sequences read.. Counting patterns.. # site patterns = 257 Counting frequencies.. 120 bytes for distance 41120 bytes for lkl0 32896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.060805 0.047478 0.084512 0.135245 0.123955 0.177430 0.268484 0.194312 lnL0 = -2807.988480 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2807.988480 x= 0.06081 0.04748 0.08451 0.13524 0.12395 0.17743 0.26848 0.19431 1 h-lim-p 0.0078 1.3338 84.9956 2807.109208 5 0.0003 36 | 0/8 2 h-lim-p 0.0010 0.0081 14.9498 2807.053211 6 0.0005 63 | 0/8 3 h-lim-p 0.0031 0.0825 2.4526 2807.050855 4 0.0008 84 | 0/8 4 h-lim-p 0.0016 0.1766 1.2177 2807.050631 2 0.0004 101 | 0/8 5 h-lim-p 0.0046 1.9676 0.0998 2807.050628 1 0.0006 117 | 0/8 6 h-lim-p 0.0025 8.9197 0.0221 2807.050628 0 0.0006 138 | 0/8 7 h-lim-p 0.0289 20.0000 0.0005 2807.050585 0 0.4617 162 | 0/8 8 h-lim-p 0.0011 2.2284 0.2122 2807.050530 0 0.0009 182 | 0/8 9 h-lim-p 1.0803 20.0000 0.0002 2807.050527 0 0.9453 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2807.050527 0 1.0938 222 | 0/8 11 h-lim-p 0.6703 20.0000 0.0000 2807.050527 0 1.3406 243 | 0/8 12 h-lim-p 0.4482 20.0000 0.0000 2807.050527 0 0.0000 286 | 0/8 13 h-lim-p 0.0000 20.0000 0.0002 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -2807.050527 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2807.050527 Node 7: lnL = -2807.050527 Node 8: lnL = -2807.050527 Node 9: lnL = -2807.050527 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 428 Sequential format.. Reading seq # 1: YMR180C_Sbay Reading seq # 2: YMR180C_Scer Reading seq # 3: YMR180C_Skud Reading seq # 4: YMR180C_Smik Reading seq # 5: YMR180C_Spar Sequences read.. Counting patterns.. # site patterns = 142 Counting frequencies.. 120 bytes for distance 22720 bytes for lkl0 18176 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.072067 0.022378 0.020089 0.066160 0.065685 0.129266 0.212927 0.160906 lnL0 = -1657.731292 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1657.731292 x= 0.07207 0.02238 0.02009 0.06616 0.06568 0.12927 0.21293 0.16091 1 h-lim-p 0.0006 0.0051 140.7787 1656.670779 6 0.0001 35 | 0/8 2 h-lim-p 0.0004 0.0032 26.4476 1656.585726 7 0.0003 67 | 0/8 3 h-lim-p 0.0014 0.0445 4.6552 1656.581682 5 0.0004 90 | 0/8 4 h-lim-p 0.0006 0.0414 2.8964 1656.580720 3 0.0003 109 | 0/8 5 h-lim-p 0.0012 0.7407 0.7506 1656.580536 4 0.0007 132 | 0/8 6 h-lim-p 0.0015 0.2047 0.3509 1656.580521 2 0.0003 157 | 0/8 7 h-lim-p 0.0091 9.4857 0.0114 1656.580519 0 0.0040 177 | 0/8 8 h-lim-p 0.0200 16.2482 0.0023 1656.579998 0 0.1602 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1656.579990 1 0.9961 222 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1656.579990 0 0.0684 246 | 0/8 11 h-lim-p 0.0304 20.0000 0.0000 1656.579990 0 0.0000 275 | 0/8 12 h-lim-p 0.0001 20.0000 0.0000 1656.579990 0 0.0000 296 | 0/8 13 h-lim-p 0.0000 20.0000 0.0002 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0016 | 0/8 15 h-lim-p 0.0000 20.0000 0.0016 Out... lnL = -1656.579990 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1656.579990 Node 7: lnL = -1656.579990 Node 8: lnL = -1656.579990 Node 9: lnL = -1656.579990 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 418 Sequential format.. Reading seq # 1: YMR183C_Sbay Reading seq # 2: YMR183C_Scer Reading seq # 3: YMR183C_Skud Reading seq # 4: YMR183C_Smik Reading seq # 5: YMR183C_Spar Sequences read.. Counting patterns.. # site patterns = 162 Counting frequencies.. 120 bytes for distance 25920 bytes for lkl0 20736 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.064733 0.066706 0.050364 0.119796 0.089381 0.087594 0.113467 0.157928 lnL0 = -1537.785378 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1537.785378 x= 0.06473 0.06671 0.05036 0.11980 0.08938 0.08759 0.11347 0.15793 1 h-lim-p 0.0029 0.1447 103.4545 1536.183632 3 0.0003 30 | 0/8 2 h-lim-p 0.0006 0.0046 21.7252 1536.054216 2 0.0005 46 | 0/8 3 h-lim-p 0.0017 0.0229 6.9411 1536.045279 2 0.0004 63 | 0/8 4 h-lim-p 0.0020 0.1019 1.3720 1536.044830 2 0.0005 80 | 0/8 5 h-lim-p 0.0053 1.6825 0.1305 1536.044825 1 0.0005 96 | 0/8 6 h-lim-p 0.0060 18.7043 0.0113 1536.044823 1 0.0048 118 | 0/8 7 h-lim-p 0.0057 18.9714 0.0095 1536.044707 0 0.0459 141 | 0/8 8 h-lim-p 0.0017 1.2509 0.2574 1536.044409 0 0.0034 162 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1536.044374 2 0.9961 186 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1536.044374 0 1.0938 206 | 0/8 11 h-lim-p 1.2630 20.0000 0.0000 1536.044374 0 1.1052 226 | 0/8 12 h-lim-p 1.1747 20.0000 0.0000 1536.044374 0 9.3975 249 | 0/8 13 h-lim-p 0.2796 20.0000 0.0003 1536.044374 0 0.1223 269 | 0/8 14 h-lim-p 0.0183 20.0000 0.0019 1536.044374 0 0.0046 290 | 0/8 15 h-lim-p 0.0013 15.6310 0.0068 1536.044374 0 0.0013 310 | 0/8 16 h-lim-p 0.0015 18.1239 0.0058 1536.044374 0 0.0000 349 | 0/8 17 h-lim-p 0.0001 20.0000 0.0000 1536.044374 0 0.0000 381 Out... lnL = -1536.044374 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1536.044374 Node 7: lnL = -1536.044374 Node 8: lnL = -1536.044374 Node 9: lnL = -1536.044374 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 420 Sequential format.. Reading seq # 1: YMR184W_Sbay Reading seq # 2: YMR184W_Scer Reading seq # 3: YMR184W_Skud Reading seq # 4: YMR184W_Smik Reading seq # 5: YMR184W_Spar Sequences read.. Counting patterns.. # site patterns = 145 Counting frequencies.. 120 bytes for distance 23200 bytes for lkl0 18560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.057704 0.059109 0.036702 0.125411 0.083766 0.127983 0.122751 0.151385 lnL0 = -1652.530108 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1652.530108 x= 0.05770 0.05911 0.03670 0.12541 0.08377 0.12798 0.12275 0.15138 1 h-lim-p 0.0015 0.0121 100.3330 1651.470932 9 0.0002 46 | 0/8 2 h-lim-p 0.0005 0.0041 29.5319 1651.316409 8 0.0004 76 | 0/8 3 h-lim-p 0.0015 0.0204 7.3305 1651.307393 2 0.0004 93 | 0/8 4 h-lim-p 0.0041 0.2193 0.6350 1651.307320 3 0.0004 114 | 0/8 5 h-lim-p 0.0018 1.1464 0.1316 1651.307317 0 0.0004 135 | 0/8 6 h-lim-p 0.0052 20.0000 0.0097 1651.307316 0 0.0023 155 | 0/8 7 h-lim-p 0.0201 20.0000 0.0011 1651.307233 0 0.2413 178 | 0/8 8 h-lim-p 0.0010 1.4835 0.2678 1651.307179 2 0.0008 202 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1651.307177 0 1.0938 222 | 0/8 10 h-lim-p 2.4382 20.0000 0.0000 1651.307177 0 1.0667 242 | 0/8 11 h-lim-p 1.1045 20.0000 0.0000 1651.307177 0 3.3136 263 | 0/8 12 h-lim-p 1.4891 20.0000 0.0000 1651.307177 0 0.0931 286 | 0/8 13 h-lim-p 0.0032 20.0000 0.0008 1651.307177 0 0.0000 319 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0013 1651.307177 0 0.0000 380 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 1651.307177 0 0.0013 407 | 0/8 17 h-lim-p 0.0121 20.0000 0.0000 1651.307177 0 0.0000 438 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 1651.307177 0 0.0000 472 | 0/8 19 h-lim-p 0.0000 20.0000 0.0018 1651.307177 0 0.0000 505 | 0/8 20 h-lim-p 0.0000 20.0000 0.0018 1651.307177 0 0.0000 531 | 0/8 21 h-lim-p 0.0000 20.0000 0.0002 .. | 0/8 22 h-lim-p 0.0000 20.0000 0.0018 | 0/8 23 h-lim-p 0.0000 20.0000 0.0018 Out... lnL = -1651.307177 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1651.307177 Node 7: lnL = -1651.307177 Node 8: lnL = -1651.307177 Node 9: lnL = -1651.307177 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 406 Sequential format.. Reading seq # 1: YMR186W_Sbay Reading seq # 2: YMR186W_Scer Reading seq # 3: YMR186W_Skud Reading seq # 4: YMR186W_Smik Reading seq # 5: YMR186W_Spar Sequences read.. Counting patterns.. # site patterns = 177 Counting frequencies.. 120 bytes for distance 28320 bytes for lkl0 22656 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.418044 0.097148 0.054311 0.102292 0.064387 0.240866 0.127568 0.626293 lnL0 = -1888.385474 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1888.385474 x= 0.41804 0.09715 0.05431 0.10229 0.06439 0.24087 0.12757 0.62629 1 h-lim-p 0.0014 0.0108 62.1289 1887.767297 8 0.0003 43 | 0/8 2 h-lim-p 0.0009 0.0074 24.6826 1887.522435 4 0.0009 63 | 0/8 3 h-lim-p 0.0004 0.0030 46.1983 1887.113004 0 0.0011 76 | 0/8 4 h-lim-p 0.0012 0.0095 26.4182 1886.995043 6 0.0007 104 | 0/8 5 h-lim-p 0.0020 0.0206 9.8038 1886.970425 6 0.0007 130 | 0/8 6 h-lim-p 0.0017 0.0446 4.1866 1886.964673 4 0.0008 150 | 0/8 7 h-lim-p 0.0019 1.1168 1.9064 1886.958103 0 0.0056 163 | 0/8 8 h-lim-p 2.5000 20.0000 0.0030 1886.954105 3 1.0483 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1886.954085 0 1.2500 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1886.954084 0 1.0938 222 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1886.954084 0 1.0938 242 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1886.954084 0 5.0000 263 | 0/8 13 h-lim-p 1.7320 20.0000 0.0000 1886.954084 0 0.2165 285 | 0/8 14 h-lim-p 0.4897 20.0000 0.0000 1886.954084 0 0.1224 306 | 0/8 15 h-lim-p 0.2113 20.0000 0.0000 1886.954084 0 0.0000 338 Out... lnL = -1886.954084 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1886.954084 Node 7: lnL = -1886.954084 Node 8: lnL = -1886.954084 Node 9: lnL = -1886.954084 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 331 Sequential format.. Reading seq # 1: YMR187C_Sbay Reading seq # 2: YMR187C_Scer Reading seq # 3: YMR187C_Skud Reading seq # 4: YMR187C_Smik Reading seq # 5: YMR187C_Spar Sequences read.. Counting patterns.. # site patterns = 151 Counting frequencies.. 120 bytes for distance 24160 bytes for lkl0 19328 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.095308 0.094943 0.064998 0.141319 0.092195 0.214026 0.188410 0.225205 lnL0 = -1536.525056 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1536.525056 x= 0.09531 0.09494 0.06500 0.14132 0.09219 0.21403 0.18841 0.22521 1 h-lim-p 0.0014 0.0114 70.5132 1535.064135 3 0.0006 28 | 0/8 2 h-lim-p 0.0011 0.0089 23.9149 1534.804568 5 0.0010 50 | 0/8 3 h-lim-p 0.0019 0.0178 12.2435 1534.768897 6 0.0006 78 | 0/8 4 h-lim-p 0.0017 0.0532 4.4324 1534.763082 4 0.0007 99 | 0/8 5 h-lim-p 0.0094 1.0397 0.3267 1534.763012 3 0.0013 119 | 0/8 6 h-lim-p 0.0178 11.1623 0.0232 1534.763003 2 0.0069 143 | 0/8 7 h-lim-p 0.0103 12.2942 0.0156 1534.762804 0 0.0410 165 | 0/8 8 h-lim-p 0.0025 1.9331 0.2533 1534.761619 0 0.0050 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1534.761602 2 0.9644 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1534.761602 0 1.0938 230 | 0/8 11 h-lim-p 1.6614 20.0000 0.0000 1534.761602 0 1.4537 250 | 0/8 12 h-lim-p 1.7347 20.0000 0.0000 1534.761602 0 0.1084 273 | 0/8 13 h-lim-p 0.0276 20.0000 0.0000 1534.761602 0 0.0069 294 | 0/8 14 h-lim-p 0.0026 20.0000 0.0000 1534.761602 0 0.0013 314 | 0/8 15 h-lim-p 0.0015 20.0000 0.0000 1534.761602 0 0.0000 344 | 0/8 16 h-lim-p 0.0003 20.0000 0.0000 1534.761602 0 0.0000 379 Out... lnL = -1534.761602 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1534.761602 Node 7: lnL = -1534.761602 Node 8: lnL = -1534.761602 Node 9: lnL = -1534.761602 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 571 Sequential format.. Reading seq # 1: YMR188C_Sbay Reading seq # 2: YMR188C_Scer Reading seq # 3: YMR188C_Skud Reading seq # 4: YMR188C_Smik Reading seq # 5: YMR188C_Spar Sequences read.. Counting patterns.. # site patterns = 224 Counting frequencies.. 120 bytes for distance 35840 bytes for lkl0 28672 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.057219 0.110993 0.081678 0.192613 0.101501 0.168356 0.204959 0.187652 lnL0 = -2516.057909 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2516.057909 x= 0.05722 0.11099 0.08168 0.19261 0.10150 0.16836 0.20496 0.18765 1 h-lim-p 0.0097 1.6669 71.8982 2515.076113 7 0.0004 40 | 0/8 2 h-lim-p 0.0012 0.0097 17.4275 2514.996398 2 0.0006 56 | 0/8 3 h-lim-p 0.0014 0.0380 7.2129 2514.986664 6 0.0004 82 | 0/8 4 h-lim-p 0.0021 0.1556 1.5356 2514.985898 4 0.0007 104 | 0/8 5 h-lim-p 0.0036 0.9635 0.3024 2514.985875 3 0.0005 125 | 0/8 6 h-lim-p 0.0062 14.2998 0.0256 2514.985874 1 0.0015 148 | 0/8 7 h-lim-p 0.0078 20.0000 0.0050 2514.985808 0 0.0626 171 | 0/8 8 h-lim-p 0.0030 20.0000 0.1049 2514.985382 0 0.0060 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2514.985375 1 0.9961 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2514.985375 0 1.0938 234 | 0/8 11 h-lim-p 1.2977 20.0000 0.0000 2514.985375 0 0.5677 254 | 0/8 12 h-lim-p 0.1167 20.0000 0.0001 2514.985375 0 0.0002 282 | 0/8 13 h-lim-p 0.0004 20.0000 0.0000 2514.985375 0 0.0000 311 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 2514.985375 0 0.0000 337 Out... lnL = -2514.985375 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2514.985375 Node 7: lnL = -2514.985375 Node 8: lnL = -2514.985375 Node 9: lnL = -2514.985375 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 348 Sequential format.. Reading seq # 1: YMR192W_Sbay Reading seq # 2: YMR192W_Scer Reading seq # 3: YMR192W_Skud Reading seq # 4: YMR192W_Smik Reading seq # 5: YMR192W_Spar Sequences read.. Counting patterns.. # site patterns = 142 Counting frequencies.. 120 bytes for distance 22720 bytes for lkl0 18176 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.023413 0.095510 0.119857 0.142103 0.087945 0.168498 0.135133 0.133466 lnL0 = -1413.660273 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1413.660273 x= 0.02341 0.09551 0.11986 0.14210 0.08794 0.16850 0.13513 0.13347 1 h-lim-p 0.0011 0.0089 45.1612 1412.991051 9 0.0007 46 | 0/8 2 h-lim-p 0.0006 0.0048 10.8745 1412.956486 3 0.0006 64 | 0/8 3 h-lim-p 0.0015 0.0353 4.4525 1412.950435 2 0.0007 80 | 0/8 4 h-lim-p 0.0125 0.7800 0.2494 1412.950404 3 0.0010 102 | 0/8 5 h-lim-p 0.0079 8.2772 0.0317 1412.950404 1 0.0010 126 | 0/8 6 h-lim-p 0.0046 14.1513 0.0068 1412.950404 0 0.0010 147 | 0/8 7 h-lim-p 0.0030 20.0000 0.0023 1412.950404 0 0.0044 167 | 0/8 8 h-lim-p 0.0138 20.0000 0.0007 1412.950396 0 0.1652 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1412.950396 0 1.0938 210 | 0/8 10 h-lim-p 1.0868 20.0000 0.0000 1412.950396 0 0.9509 230 | 0/8 11 h-lim-p 0.2735 20.0000 0.0001 1412.950396 0 0.0085 254 | 0/8 12 h-lim-p 0.0020 20.0000 0.0003 1412.950396 0 0.0000 295 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 1412.950396 0 0.0000 318 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1412.950396 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1412.950396 Node 7: lnL = -1412.950396 Node 8: lnL = -1412.950396 Node 9: lnL = -1412.950396 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 852 Sequential format.. Reading seq # 1: YMR193W_Sbay Reading seq # 2: YMR193W_Scer Reading seq # 3: YMR193W_Skud Reading seq # 4: YMR193W_Smik Reading seq # 5: YMR193W_Spar Sequences read.. Counting patterns.. # site patterns = 384 Counting frequencies.. 120 bytes for distance 61440 bytes for lkl0 49152 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.055984 0.107650 0.148467 0.170696 0.155097 0.491816 0.289345 0.251241 lnL0 = -4444.082654 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4444.082654 x= 0.05598 0.10765 0.14847 0.17070 0.15510 0.49182 0.28935 0.25124 1 h-lim-p 0.0287 2.2564 55.6463 4443.485382 7 0.0004 40 | 0/8 2 h-lim-p 0.0014 0.0108 14.5755 4443.436790 6 0.0005 67 | 0/8 3 h-lim-p 0.0015 0.0493 4.7532 4443.429495 2 0.0007 83 | 0/8 4 h-lim-p 0.0013 0.1038 2.5470 4443.428121 3 0.0005 101 | 0/8 5 h-lim-p 0.0044 1.0255 0.3174 4443.428083 2 0.0008 118 | 0/8 6 h-lim-p 0.0021 5.8988 0.1255 4443.428074 1 0.0010 141 | 0/8 7 h-lim-p 0.0432 20.0000 0.0030 4443.428073 0 0.0189 161 | 0/8 8 h-lim-p 0.0158 20.0000 0.0036 4443.428007 0 0.0631 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4443.428005 0 1.0938 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4443.428005 0 1.0938 223 | 0/8 11 h-lim-p 1.1457 20.0000 0.0000 4443.428005 0 1.0025 243 | 0/8 12 h-lim-p 0.2349 20.0000 0.0001 4443.428005 0 0.0294 265 | 0/8 13 h-lim-p 0.0067 20.0000 0.0003 4443.428005 0 0.0000 302 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 4443.428005 0 0.0000 332 Out... lnL = -4443.428005 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4443.428005 Node 7: lnL = -4443.428005 Node 8: lnL = -4443.428005 Node 9: lnL = -4443.428005 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 913 Sequential format.. Reading seq # 1: YMR194W_Sbay Reading seq # 2: YMR194W_Scer Reading seq # 3: YMR194W_Skud Reading seq # 4: YMR194W_Smik Reading seq # 5: YMR194W_Spar Sequences read.. Counting patterns.. # site patterns = 356 Counting frequencies.. 120 bytes for distance 56960 bytes for lkl0 45568 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.029837 0.093175 0.170440 0.051545 0.164217 0.285668 0.246750 0.176396 lnL0 = -3881.364225 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3881.364225 x= 0.02984 0.09318 0.17044 0.05154 0.16422 0.28567 0.24675 0.17640 1 h-lim-p 0.0014 0.0155 236.7663 3874.997026 4 0.0003 31 | 0/8 2 h-lim-p 0.0005 0.0039 41.5658 3874.540518 7 0.0005 61 | 0/8 3 h-lim-p 0.0009 0.0087 24.2781 3874.443247 2 0.0004 77 | 0/8 4 h-lim-p 0.0014 0.0510 7.3780 3874.411573 2 0.0013 93 | 0/8 5 h-lim-p 0.0077 0.2067 1.2637 3874.411134 3 0.0006 116 | 0/8 6 h-lim-p 0.0038 1.1314 0.1866 3874.411118 1 0.0008 131 | 0/8 7 h-lim-p 0.0031 5.6281 0.0455 3874.411077 0 0.0062 152 | 0/8 8 h-lim-p 0.0205 20.0000 0.0139 3874.403524 0 0.1639 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0008 3874.403171 3 1.0004 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 3874.403171 0 1.0938 221 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3874.403171 0 1.0938 241 | 0/8 12 h-lim-p 0.7718 20.0000 0.0000 3874.403171 0 0.7718 261 | 0/8 13 h-lim-p 0.0000 0.0081 6.9251 3874.403171 0 0.0000 284 | 0/8 14 h-lim-p 1.4456 20.0000 0.0000 3874.403171 0 0.0000 322 Out... lnL = -3874.403171 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3874.403171 Node 7: lnL = -3874.403171 Node 8: lnL = -3874.403171 Node 9: lnL = -3874.403171 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 574 Sequential format.. Reading seq # 1: YMR197C_Sbay Reading seq # 2: YMR197C_Scer Reading seq # 3: YMR197C_Skud Reading seq # 4: YMR197C_Smik Reading seq # 5: YMR197C_Spar Sequences read.. Counting patterns.. # site patterns = 243 Counting frequencies.. 120 bytes for distance 38880 bytes for lkl0 31104 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.074307 0.045373 0.061289 0.137252 0.110409 0.186821 0.220576 0.191681 lnL0 = -2639.406490 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2639.406490 x= 0.07431 0.04537 0.06129 0.13725 0.11041 0.18682 0.22058 0.19168 1 h-lim-p 0.0030 0.0284 133.6821 2637.597887 7 0.0002 41 | 0/8 2 h-lim-p 0.0011 0.0085 17.8000 2637.534417 5 0.0004 63 | 0/8 3 h-lim-p 0.0011 0.0441 6.4165 2637.525688 4 0.0005 85 | 0/8 4 h-lim-p 0.0015 0.1223 2.0587 2637.524672 4 0.0005 107 | 0/8 5 h-lim-p 0.0033 0.3640 0.3442 2637.524647 2 0.0004 125 | 0/8 6 h-lim-p 0.0025 2.6651 0.0589 2637.524646 0 0.0005 146 | 0/8 7 h-lim-p 0.0061 20.0000 0.0053 2637.524646 0 0.0027 166 | 0/8 8 h-lim-p 0.0260 20.0000 0.0005 2637.524602 0 0.4165 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2637.524598 0 1.0938 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2637.524598 0 1.0938 230 | 0/8 11 h-lim-p 1.2456 20.0000 0.0000 2637.524598 0 1.8684 250 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2637.524598 0 0.5469 271 | 0/8 13 h-lim-p 0.1226 20.0000 0.0000 2637.524598 0 0.0001 300 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0007 2637.524598 0 0.0000 362 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 2637.524598 0 0.0000 387 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0007 | 0/8 19 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -2637.524598 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2637.524598 Node 7: lnL = -2637.524598 Node 8: lnL = -2637.524598 Node 9: lnL = -2637.524598 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 574 Sequential format.. Reading seq # 1: YMR198W_Sbay Reading seq # 2: YMR198W_Scer Reading seq # 3: YMR198W_Skud Reading seq # 4: YMR198W_Smik Reading seq # 5: YMR198W_Spar Sequences read.. Counting patterns.. # site patterns = 233 Counting frequencies.. 120 bytes for distance 37280 bytes for lkl0 29824 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.068425 0.045513 0.069079 0.135725 0.101528 0.191967 0.207687 0.183605 lnL0 = -2609.279378 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2609.279378 x= 0.06843 0.04551 0.06908 0.13573 0.10153 0.19197 0.20769 0.18360 1 h-lim-p 0.0043 1.1509 109.7239 2608.082057 4 0.0002 33 | 0/8 2 h-lim-p 0.0028 0.0280 8.3768 2608.067676 6 0.0004 61 | 0/8 3 h-lim-p 0.0008 0.0583 4.2296 2608.064193 5 0.0005 87 | 0/8 4 h-lim-p 0.0031 0.3626 0.6424 2608.064101 3 0.0005 109 | 0/8 5 h-lim-p 0.0032 1.6004 0.0929 2608.064099 1 0.0004 133 | 0/8 6 h-lim-p 0.0023 20.0000 0.0155 2608.064099 0 0.0010 153 | 0/8 7 h-lim-p 0.0042 20.0000 0.0038 2608.064097 0 0.0083 174 | 0/8 8 h-lim-p 0.0044 20.0000 0.0072 2608.063997 0 0.0352 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2608.063996 0 1.0938 217 | 0/8 10 h-lim-p 1.7877 20.0000 0.0000 2608.063996 0 0.7821 237 | 0/8 11 h-lim-p 0.6098 20.0000 0.0000 2608.063996 0 0.2668 257 | 0/8 12 h-lim-p 0.1311 20.0000 0.0000 2608.063996 0 0.0123 280 | 0/8 13 h-lim-p 0.0059 20.0000 0.0001 2608.063996 0 0.0000 320 | 0/8 14 h-lim-p 0.0000 20.0000 0.0011 2608.063996 0 0.0000 344 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0011 | 0/8 17 h-lim-p 0.0000 20.0000 0.0011 Out... lnL = -2608.063996 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2608.063996 Node 7: lnL = -2608.063996 Node 8: lnL = -2608.063996 Node 9: lnL = -2608.063996 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 834 Sequential format.. Reading seq # 1: YMR199W_Sbay Reading seq # 2: YMR199W_Scer Reading seq # 3: YMR199W_Skud Reading seq # 4: YMR199W_Smik Reading seq # 5: YMR199W_Spar Sequences read.. Counting patterns.. # site patterns = 183 Counting frequencies.. 120 bytes for distance 29280 bytes for lkl0 23424 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.051306 0.037227 0.037914 0.049489 0.059574 0.090560 0.084339 0.112119 lnL0 = -2916.353884 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2916.353884 x= 0.05131 0.03723 0.03791 0.04949 0.05957 0.09056 0.08434 0.11212 1 h-lim-p 0.0004 0.0033 124.0623 2915.771779 4 0.0001 31 | 0/8 2 h-lim-p 0.0004 0.0031 25.1557 2915.736289 7 0.0001 62 | 0/8 3 h-lim-p 0.0004 0.0184 7.8407 2915.733642 4 0.0001 84 | 0/8 4 h-lim-p 0.0007 0.0742 1.0314 2915.733600 0 0.0001 98 | 0/8 5 h-lim-p 0.0003 0.4663 0.2563 2915.733596 0 0.0001 110 | 0/8 6 h-lim-p 0.0009 3.6510 0.0389 2915.733596 0 0.0001 132 | 0/8 7 h-lim-p 0.0084 20.0000 0.0005 2915.733596 0 0.0037 152 | 0/8 8 h-lim-p 0.0032 20.0000 0.0005 2915.733594 0 0.0507 176 | 0/8 9 h-lim-p 0.3095 20.0000 0.0001 2915.733593 0 0.9284 197 | 0/8 10 h-lim-p 1.9514 20.0000 0.0000 2915.733593 0 0.8537 217 | 0/8 11 h-lim-p 0.6832 20.0000 0.0001 2915.733593 0 0.6832 237 | 0/8 12 h-lim-p 0.1816 20.0000 0.0002 2915.733593 0 0.0397 258 | 0/8 13 h-lim-p 0.0123 20.0000 0.0006 2915.733593 0 0.0000 297 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 2915.733593 0 0.0000 330 Out... lnL = -2915.733593 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2915.733593 Node 7: lnL = -2915.733593 Node 8: lnL = -2915.733593 Node 9: lnL = -2915.733593 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 535 Sequential format.. Reading seq # 1: YMR202W_Sbay Reading seq # 2: YMR202W_Scer Reading seq # 3: YMR202W_Skud Reading seq # 4: YMR202W_Smik Reading seq # 5: YMR202W_Spar Sequences read.. Counting patterns.. # site patterns = 213 Counting frequencies.. 120 bytes for distance 34080 bytes for lkl0 27264 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.054515 0.143992 0.059343 0.105368 0.073024 0.206078 0.243309 0.181407 lnL0 = -2444.468686 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2444.468686 x= 0.05451 0.14399 0.05934 0.10537 0.07302 0.20608 0.24331 0.18141 1 h-lim-p 0.0005 0.0043 120.4109 2442.204197 9 0.0003 46 | 0/8 2 h-lim-p 0.0004 0.0033 32.4454 2442.007690 2 0.0004 62 | 0/8 3 h-lim-p 0.0005 0.0104 23.2706 2441.928969 4 0.0004 82 | 0/8 4 h-lim-p 0.0021 0.0349 4.5805 2441.924373 5 0.0005 104 | 0/8 5 h-lim-p 0.0046 0.7316 0.4672 2441.924266 2 0.0010 121 | 0/8 6 h-lim-p 0.0128 8.8129 0.0363 2441.924265 0 0.0014 143 | 0/8 7 h-lim-p 0.0024 6.0080 0.0216 2441.924265 0 0.0021 163 | 0/8 8 h-lim-p 0.0274 20.0000 0.0016 2441.924037 0 0.3286 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2441.924030 1 0.9961 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2441.924030 0 1.0938 228 | 0/8 11 h-lim-p 0.9789 20.0000 0.0000 2441.924030 0 0.8566 248 | 0/8 12 h-lim-p 0.5048 20.0000 0.0000 2441.924030 0 0.0158 272 | 0/8 13 h-lim-p 0.0034 20.0000 0.0001 2441.924030 0 0.0069 293 | 0/8 14 h-lim-p 0.0029 20.0000 0.0003 2441.924030 0 0.0002 316 | 0/8 15 h-lim-p 0.0003 20.0000 0.0002 2441.924030 0 0.0000 353 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -2441.924030 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2441.924030 Node 7: lnL = -2441.924030 Node 8: lnL = -2441.924030 Node 9: lnL = -2441.924030 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 302 Sequential format.. Reading seq # 1: YMR203W_Sbay Reading seq # 2: YMR203W_Scer Reading seq # 3: YMR203W_Skud Reading seq # 4: YMR203W_Smik Reading seq # 5: YMR203W_Spar Sequences read.. Counting patterns.. # site patterns = 112 Counting frequencies.. 120 bytes for distance 17920 bytes for lkl0 14336 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.228838 0.096714 0.110834 0.004632 0.268491 0.180961 0.265229 0.000060 lnL0 = -1180.568643 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1180.568643 x= 0.22884 0.09671 0.11083 0.00463 0.26849 0.18096 0.26523 0.00006 1 h-lim-p 0.0000 0.0000 381.4998 1180.186552 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0008 274.8989 1155.012148 2 0.0007 44 | 1/8 3 h-lim-p 0.0001 0.0006 260.4231 1148.677174 0 0.0003 58 | 1/8 4 h-lim-p 0.0004 0.0034 36.0023 1148.362372 1 0.0005 72 | 1/8 5 h-lim-p 0.0014 0.0122 13.7218 1148.312838 3 0.0006 90 | 1/8 6 h-lim-p 0.0068 0.1662 1.1812 1148.305046 3 0.0028 108 | 0/8 7 h-lim-p 0.0008 0.0706 4.3644 1148.275794 0 0.0015 121 | 0/8 8 h-lim-p 0.0009 0.0359 7.6382 1147.910622 0 0.0140 137 | 0/8 9 h-lim-p 0.0079 0.0630 1.7751 1146.436673 m 0.0630 149 | 1/8 10 h-lim-p 0.4013 8.5875 0.1968 1146.316524 5 0.0842 173 | 1/8 11 h-lim-p 0.2842 3.1062 0.0583 1144.349992 0 0.5684 193 | 0/8 12 h-lim-p 0.0116 0.3296 2.8602 1144.344389 3 0.0013 220 | 0/8 13 h-lim-p 0.3208 14.0847 0.0117 1143.804926 0 1.9247 234 | 0/8 14 h-lim-p 2.1340 17.0723 0.0068 1143.739535 8 1.2162 275 | 0/8 15 h-lim-p 2.5000 20.0000 0.0006 1143.739278 2 1.1719 299 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1143.739275 1 1.2305 322 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1143.739275 0 1.0938 342 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1143.739275 0 2.1875 362 | 0/8 19 h-lim-p 2.0579 20.0000 0.0000 1143.739275 0 0.9003 382 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 1143.739275 0 0.0037 411 Out... lnL = -1143.739275 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1143.739275 Node 7: lnL = -1143.739275 Node 8: lnL = -1143.739275 Node 9: lnL = -1143.739275 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 610 Sequential format.. Reading seq # 1: YMR204C_Sbay Reading seq # 2: YMR204C_Scer Reading seq # 3: YMR204C_Skud Reading seq # 4: YMR204C_Smik Reading seq # 5: YMR204C_Spar Sequences read.. Counting patterns.. # site patterns = 178 Counting frequencies.. 120 bytes for distance 28480 bytes for lkl0 22784 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.165850 0.067127 0.075433 0.011477 0.170009 0.131764 0.180548 0.000060 lnL0 = -2125.100235 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2125.100235 x= 0.16585 0.06713 0.07543 0.01148 0.17001 0.13176 0.18055 0.00006 1 h-lim-p 0.0000 0.0000 589.0467 2122.620363 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0003 661.3651 2076.709202 0 0.0002 38 | 1/8 3 h-lim-p 0.0001 0.0007 129.2296 2075.503376 0 0.0002 51 | 1/8 4 h-lim-p 0.0004 0.0033 41.0583 2075.314365 7 0.0002 81 | 1/8 5 h-lim-p 0.0011 0.0289 9.6438 2075.298338 6 0.0003 108 | 1/8 6 h-lim-p 0.0007 0.0400 4.4192 2075.291753 5 0.0005 131 | 1/8 7 h-lim-p 0.0084 0.5465 0.2507 2074.634090 0 0.0672 146 | 1/8 8 h-lim-p 0.0004 0.0033 24.9021 2073.311536 0 0.0008 166 | 1/8 9 h-lim-p 1.0559 20.0000 0.0193 2070.407414 1 1.3199 180 | 0/8 10 h-lim-p 0.0030 1.5594 8.4782 2070.391709 6 0.0004 215 | 0/8 11 h-lim-p 0.4473 6.9851 0.0083 2070.041243 0 1.3420 228 | 0/8 12 h-lim-p 2.5000 20.0000 0.0014 2070.026294 6 1.4675 262 | 0/8 13 h-lim-p 2.5000 20.0000 0.0007 2070.025259 4 0.9169 292 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 2070.025238 2 0.9961 316 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2070.025238 0 1.0938 336 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 2070.025238 0 2.5000 356 | 0/8 17 h-lim-p 1.6879 20.0000 0.0000 2070.025238 0 0.0004 387 Out... lnL = -2070.025238 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2070.025238 Node 7: lnL = -2070.025238 Node 8: lnL = -2070.025238 Node 9: lnL = -2070.025238 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 864 Sequential format.. Reading seq # 1: YMR205C_Sbay Reading seq # 2: YMR205C_Scer Reading seq # 3: YMR205C_Skud Reading seq # 4: YMR205C_Smik Reading seq # 5: YMR205C_Spar Sequences read.. Counting patterns.. # site patterns = 185 Counting frequencies.. 120 bytes for distance 29600 bytes for lkl0 23680 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.170248 0.018680 0.029179 0.044768 0.035094 0.096821 0.075147 0.017731 lnL0 = -2829.827008 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2829.827008 x= 0.17025 0.01868 0.02918 0.04477 0.03509 0.09682 0.07515 0.01773 1 h-lim-p 0.0004 0.2740 397.5831 2826.624665 5 0.0000 34 | 0/8 2 h-lim-p 0.0002 0.0020 36.6627 2826.548941 2 0.0001 50 | 0/8 3 h-lim-p 0.0002 0.0062 22.0004 2826.533322 3 0.0001 68 | 0/8 4 h-lim-p 0.0003 0.0098 5.8400 2826.532124 2 0.0001 85 | 0/8 5 h-lim-p 0.0008 0.2631 0.5497 2826.532101 2 0.0002 102 | 0/8 6 h-lim-p 0.0010 0.5243 0.0855 2826.532100 0 0.0001 124 | 0/8 7 h-lim-p 0.0018 20.0000 0.0052 2826.532100 0 0.0008 144 | 0/8 8 h-lim-p 0.0103 20.0000 0.0004 2826.532030 0 0.3307 169 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2826.532024 0 1.0938 189 | 0/8 10 h-lim-p 0.7690 20.0000 0.0001 2826.532024 0 0.6729 209 | 0/8 11 h-lim-p 0.5007 20.0000 0.0001 2826.532024 0 0.0078 234 | 0/8 12 h-lim-p 0.0035 20.0000 0.0002 2826.532024 0 0.0000 267 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 2826.532024 0 0.0000 287 Out... lnL = -2826.532024 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2826.532024 Node 7: lnL = -2826.532024 Node 8: lnL = -2826.532024 Node 9: lnL = -2826.532024 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 1137 Sequential format.. Reading seq # 1: YMR206W_Sbay Reading seq # 2: YMR206W_Scer Reading seq # 3: YMR206W_Skud Reading seq # 4: YMR206W_Smik Reading seq # 5: YMR206W_Spar Sequences read.. Counting patterns.. # site patterns = 232 Counting frequencies.. 120 bytes for distance 37120 bytes for lkl0 29696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.240854 0.020796 0.049454 0.060562 0.056219 0.139505 0.161817 0.010009 lnL0 = -3605.527342 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3605.527342 x= 0.24085 0.02080 0.04945 0.06056 0.05622 0.13950 0.16182 0.01001 1 h-lim-p 0.0007 0.0197 331.3332 3601.547448 9 0.0001 47 | 0/8 2 h-lim-p 0.0005 0.0037 37.2829 3601.378289 7 0.0002 73 | 0/8 3 h-lim-p 0.0003 0.0059 30.7759 3601.333808 2 0.0001 89 | 0/8 4 h-lim-p 0.0004 0.0091 10.1384 3601.328267 5 0.0001 115 | 0/8 5 h-lim-p 0.0013 0.1867 1.0022 3601.328146 3 0.0002 134 | 0/8 6 h-lim-p 0.0006 0.3502 0.4266 3601.328134 2 0.0002 151 | 0/8 7 h-lim-p 0.0149 20.0000 0.0044 3601.328123 1 0.0186 173 | 0/8 8 h-lim-p 0.0038 3.0024 0.0212 3601.327263 0 0.0308 196 | 0/8 9 h-lim-p 1.1605 20.0000 0.0006 3601.327186 2 1.0109 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 3601.327186 0 1.0938 240 | 0/8 11 h-lim-p 1.9749 20.0000 0.0000 3601.327186 0 1.7280 260 | 0/8 12 h-lim-p 0.3250 20.0000 0.0002 3601.327186 0 0.0203 283 | 0/8 13 h-lim-p 0.0028 11.9932 0.0015 3601.327186 0 0.0000 321 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 3601.327186 0 0.0000 342 Out... lnL = -3601.327186 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3601.327186 Node 7: lnL = -3601.327186 Node 8: lnL = -3601.327186 Node 9: lnL = -3601.327186 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 832 Sequential format.. Reading seq # 1: YMR208W_Sbay Reading seq # 2: YMR208W_Scer Reading seq # 3: YMR208W_Skud Reading seq # 4: YMR208W_Smik Reading seq # 5: YMR208W_Spar Sequences read.. Counting patterns.. # site patterns = 220 Counting frequencies.. 120 bytes for distance 35200 bytes for lkl0 28160 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.253996 0.099768 0.111107 0.017940 0.262726 0.189651 0.271817 0.000060 lnL0 = -3561.289779 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3561.289779 x= 0.25400 0.09977 0.11111 0.01794 0.26273 0.18965 0.27182 0.00006 1 h-lim-p 0.0000 0.0000 889.2203 3559.435723 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0003 924.4727 3488.110893 0 0.0002 38 | 1/8 3 h-lim-p 0.0000 0.0002 620.1312 3479.775557 0 0.0001 52 | 1/8 4 h-lim-p 0.0002 0.0019 112.3361 3478.509485 2 0.0002 68 | 1/8 5 h-lim-p 0.0004 0.0033 52.1150 3478.344544 6 0.0001 94 | 1/8 6 h-lim-p 0.0015 0.0448 5.0866 3478.331332 6 0.0004 123 | 0/8 7 h-lim-p 0.0001 0.0899 20.4929 3478.206943 0 0.0004 137 | 0/8 8 h-lim-p 0.0003 0.0121 27.9609 3475.575140 2 0.0108 157 | 0/8 9 h-lim-p 0.0340 0.2719 1.1488 3467.236898 m 0.2719 169 | 0/8 10 h-lim-p 0.0000 0.0000 0.0695 h-lim-p: 3.04567853e-17 2.43654282e-16 6.94716767e-02 3467.236898 .. | 0/8 11 h-lim-p 0.0000 0.0077 399.7393 3461.317369 0 0.0001 200 | 0/8 12 h-lim-p 0.0002 0.0015 57.6574 3461.060710 7 0.0002 225 | 0/8 13 h-lim-p 0.0006 0.0150 16.0372 3461.026782 4 0.0003 246 | 0/8 14 h-lim-p 0.0003 0.0021 3.5625 3461.025796 5 0.0002 271 | 0/8 15 h-lim-p 0.0004 0.1764 1.3946 3461.025598 3 0.0002 290 | 0/8 16 h-lim-p 0.0017 0.8542 0.1889 3461.025562 1 0.0007 304 | 0/8 17 h-lim-p 0.0008 2.3375 0.1590 3460.998743 0 0.2004 332 | 0/8 18 h-lim-p 0.0005 0.0043 69.0405 3460.974092 5 0.0005 366 | 0/8 19 h-lim-p 2.5000 20.0000 0.0094 3460.972776 3 1.0449 384 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 3460.972776 0 1.0938 404 | 0/8 21 h-lim-p 0.8288 20.0000 0.0000 3460.972776 0 1.2432 424 | 0/8 22 h-lim-p 1.1811 20.0000 0.0000 3460.972776 0 0.0000 462 | 0/8 23 h-lim-p 0.0000 20.0000 0.0000 3460.972776 0 0.0000 489 Out... lnL = -3460.972776 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3460.972776 Node 7: lnL = -3460.972776 Node 8: lnL = -3460.972776 Node 9: lnL = -3460.972776 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 242 Sequential format.. Reading seq # 1: YMR210W_Sbay Reading seq # 2: YMR210W_Scer Reading seq # 3: YMR210W_Skud Reading seq # 4: YMR210W_Smik Reading seq # 5: YMR210W_Spar Sequences read.. Counting patterns.. # site patterns = 102 Counting frequencies.. 120 bytes for distance 16320 bytes for lkl0 13056 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.292654 0.116592 0.124857 0.018465 0.317875 0.226814 0.319383 0.000060 lnL0 = -1094.577663 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1094.577663 x= 0.29265 0.11659 0.12486 0.01846 0.31788 0.22681 0.31938 0.00006 1 h-lim-p 0.0000 0.0000 228.1733 1094.111868 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0008 282.6214 1070.844323 m 0.0008 38 | 1/8 3 h-lim-p 0.0002 0.0014 163.3660 1065.472428 0 0.0007 52 | 1/8 4 h-lim-p 0.0002 0.0014 34.4786 1065.150421 0 0.0007 66 | 1/8 5 h-lim-p 0.0018 0.0146 11.5825 1065.103966 6 0.0007 91 | 1/8 6 h-lim-p 0.0180 0.7319 0.4635 1064.819254 0 0.0720 105 | 0/8 7 h-lim-p 0.0019 0.0373 17.9347 1063.715577 0 0.0056 125 | 0/8 8 h-lim-p 0.0026 0.0207 14.1015 1063.480501 7 0.0019 155 | 0/8 9 h-lim-p 0.0053 0.0425 2.8936 1062.964003 m 0.0425 167 | 1/8 10 h-lim-p 0.1166 0.9331 0.3145 1062.892960 2 0.0547 183 | 0/8 11 h-lim-p 0.0033 0.0754 5.2668 1062.138004 1 0.0580 208 | 0/8 12 h-lim-p 0.0369 0.2951 1.0533 1061.122435 m 0.2951 220 | 1/8 13 h-lim-p 2.3707 18.9656 0.0646 1061.079564 7 0.1978 252 | 1/8 14 h-lim-p 0.0697 0.9517 0.1832 1060.774704 0 0.1394 272 | 0/8 15 h-lim-p 0.0622 1.4917 0.4109 1060.774400 3 0.0031 300 | 0/8 16 h-lim-p 0.0961 0.7684 0.0052 1060.746050 m 0.7684 320 | 1/8 17 h-lim-p 0.6802 20.0000 0.0055 1060.728079 0 1.3604 341 | 1/8 18 h-lim-p 2.3361 20.0000 0.0032 1060.725888 5 0.8562 371 | 0/8 19 h-lim-p 0.0235 2.0386 0.1172 1060.725856 3 0.0070 398 | 0/8 20 h-lim-p 0.1642 1.3135 0.0009 1060.725657 m 1.3135 418 | 1/8 21 h-lim-p 2.5000 20.0000 0.0002 1060.725645 2 0.8246 444 | 0/8 22 h-lim-p 0.0025 14.9021 0.0612 1060.725641 0 0.0022 463 | 0/8 23 h-lim-p 0.0860 0.6881 0.0003 1060.725641 0 0.3440 485 | 0/8 24 h-lim-p 0.0234 0.1873 0.0005 1060.725641 0 0.0468 506 | 0/8 25 h-lim-p 0.0024 0.0191 0.0035 1060.725641 0 0.0000 542 | 0/8 26 h-lim-p 0.0000 0.0287 0.0023 .. | 0/8 27 h-lim-p 0.0000 0.0013 0.0588 1060.725641 0 0.0003 600 | 0/8 28 h-lim-p 0.0001 0.0007 0.0522 1060.725641 0 0.0000 621 | 0/8 29 h-lim-p 0.0000 0.0002 0.1761 1060.725641 0 0.0000 651 | 0/8 30 h-lim-p 0.0000 0.0000 1.1225 .. | 0/8 31 h-lim-p 0.0000 2.1763 0.0155 1060.725641 0 0.0003 700 | 0/8 32 h-lim-p 0.0001 0.0031 0.0388 1060.725641 0 0.0001 720 | 0/8 33 h-lim-p 0.0006 20.0000 0.0073 1060.725641 0 0.0012 741 | 0/8 34 h-lim-p 0.0023 0.1249 0.0038 1060.725641 0 0.0003 763 | 0/8 35 h-lim-p 0.0007 0.2712 0.0014 1060.725641 0 0.0000 796 | 0/8 36 h-lim-p 0.0000 12.6538 0.0004 1060.725641 0 0.0026 824 | 0/8 37 h-lim-p 0.0144 2.4381 0.0001 1060.725641 0 0.0144 844 | 0/8 38 h-lim-p 0.0005 0.0238 0.0024 1060.725641 0 0.0000 877 | 0/8 39 h-lim-p 0.0000 0.0306 0.0052 1060.725641 0 0.0000 909 | 0/8 40 h-lim-p 0.0000 1.6041 0.0000 .. | 0/8 41 h-lim-p 0.0000 0.0010 0.0351 1060.725641 0 0.0000 964 | 0/8 42 h-lim-p 0.0000 0.0002 0.1708 1060.725641 0 0.0000 996 | 0/8 43 h-lim-p 0.0000 0.0000 0.9567 .. | 0/8 44 h-lim-p 0.0000 0.0010 0.0347 1060.725641 0 0.0000 1048 | 0/8 45 h-lim-p 0.0000 0.0002 0.1833 1060.725641 0 0.0000 1083 | 0/8 46 h-lim-p 0.0000 0.0001 0.6094 1060.725641 0 0.0000 1113 | 0/8 47 h-lim-p 0.0000 0.0000 1.4882 .. | 0/8 48 h-lim-p 0.0000 0.0387 0.0086 1060.725641 0 0.0000 1167 | 0/8 49 h-lim-p 0.0000 0.0008 0.1136 .. | 0/8 50 h-lim-p 0.0000 0.0010 0.0346 1060.725641 0 0.0000 1226 | 0/8 51 h-lim-p 0.0000 0.0002 0.1841 1060.725641 0 0.0000 1260 | 0/8 52 h-lim-p 0.0000 0.0000 0.8776 .. | 0/8 53 h-lim-p 0.0000 0.0010 0.0346 1060.725641 0 0.0000 1316 | 0/8 54 h-lim-p 0.0000 0.0002 0.1849 .. | 0/8 55 h-lim-p 0.0000 0.0010 0.0346 | 0/8 56 h-lim-p 0.0000 0.0010 0.0346 Out... lnL = -1060.725641 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1060.725641 Node 7: lnL = -1060.725641 Node 8: lnL = -1060.725641 Node 9: lnL = -1060.725641 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 242 Sequential format.. Reading seq # 1: YMR211W_Sbay Reading seq # 2: YMR211W_Scer Reading seq # 3: YMR211W_Skud Reading seq # 4: YMR211W_Smik Reading seq # 5: YMR211W_Spar Sequences read.. Counting patterns.. # site patterns = 123 Counting frequencies.. 120 bytes for distance 19680 bytes for lkl0 15744 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.365439 0.153118 0.176539 0.009200 0.424791 0.287690 0.423501 0.000060 lnL0 = -1131.992609 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1131.992609 x= 0.36544 0.15312 0.17654 0.00920 0.42479 0.28769 0.42350 0.00006 1 h-lim-p 0.0000 0.0000 193.9477 1131.849638 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0016 269.1412 1094.948292 1 0.0014 43 | 1/8 3 h-lim-p 0.0001 0.0010 162.5004 1090.916643 0 0.0005 57 | 1/8 4 h-lim-p 0.0006 0.0048 24.1087 1090.439700 0 0.0018 70 | 1/8 5 h-lim-p 0.0016 0.0126 22.6537 1090.294958 8 0.0009 103 | 1/8 6 h-lim-p 0.0091 0.1300 2.1780 1090.273318 6 0.0033 128 | 0/8 7 h-lim-p 0.0006 0.3993 11.3770 1090.021396 0 0.0038 142 | 0/8 8 h-lim-p 0.0025 0.0227 17.7906 1089.305707 0 0.0098 156 | 0/8 9 h-lim-p 0.0576 0.4608 0.4709 1087.989851 m 0.4608 168 | 1/8 10 h-lim-p 1.0966 8.9208 0.1403 1087.841178 6 0.2073 201 | 1/8 11 h-lim-p 0.2272 1.8290 0.1280 1087.102695 0 0.3408 220 | 1/8 12 h-lim-p 2.5000 20.0000 0.0112 1086.882887 5 1.6305 251 | 1/8 13 h-lim-p 2.5000 20.0000 0.0060 1086.859257 5 1.3438 281 | 1/8 14 h-lim-p 2.5000 20.0000 0.0005 1086.859049 3 1.6118 308 | 0/8 15 h-lim-p 0.0106 7.8221 0.0762 1086.859039 2 0.0041 331 | 0/8 16 h-lim-p 2.5000 20.0000 0.0001 1086.859029 2 1.9287 355 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1086.859028 0 1.0938 375 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1086.859028 0 1.0938 395 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1086.859028 0 5.0000 416 | 0/8 20 h-lim-p 1.5722 20.0000 0.0000 1086.859028 0 0.0860 439 | 0/8 21 h-lim-p 0.1085 20.0000 0.0000 1086.859028 0 0.0542 459 | 0/8 22 h-lim-p 0.0627 20.0000 0.0000 1086.859028 0 0.0000 499 Out... lnL = -1086.859028 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1086.859028 Node 7: lnL = -1086.859028 Node 8: lnL = -1086.859028 Node 9: lnL = -1086.859028 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 362 Sequential format.. Reading seq # 1: YMR212C_Sbay Reading seq # 2: YMR212C_Scer Reading seq # 3: YMR212C_Skud Reading seq # 4: YMR212C_Smik Reading seq # 5: YMR212C_Spar Sequences read.. Counting patterns.. # site patterns = 132 Counting frequencies.. 120 bytes for distance 21120 bytes for lkl0 16896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.244393 0.103703 0.122140 0.003504 0.292191 0.193878 0.286668 0.000060 lnL0 = -1516.434475 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1516.434475 x= 0.24439 0.10370 0.12214 0.00350 0.29219 0.19388 0.28667 0.00006 1 h-lim-p 0.0000 0.0000 859.9450 1515.756065 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0012 314.8063 1466.458974 0 0.0009 40 | 1/8 3 h-lim-p 0.0000 0.0003 448.5241 1461.282907 0 0.0001 54 | 1/8 4 h-lim-p 0.0006 0.0046 47.1894 1460.952680 6 0.0003 79 | 0/8 5 h-lim-p 0.0002 0.0044 79.6354 1459.770632 0 0.0005 92 | 0/8 6 h-lim-p 0.0003 0.0025 64.7439 1456.819683 m 0.0025 104 | 1/8 7 h-lim-p 0.0010 0.0081 20.5026 1456.732255 2 0.0005 120 | 1/8 8 h-lim-p 0.0075 0.1171 1.2989 1456.721017 6 0.0021 146 | 1/8 9 h-lim-p 0.0067 0.4131 0.4130 1453.603636 0 0.1069 162 | 0/8 10 h-lim-p 0.0003 0.0026 88.6169 1450.087000 0 0.0013 183 | 0/8 11 h-lim-p 0.2243 1.7940 0.1141 1445.678036 0 0.8970 197 | 0/8 12 h-lim-p 0.4780 3.8238 0.0396 1443.911969 0 1.9119 219 | 0/8 13 h-lim-p 0.8492 6.7934 0.0136 1443.419901 0 3.3967 241 | 0/8 14 h-lim-p 2.0862 16.6897 0.0113 1443.347733 7 1.2535 280 | 0/8 15 h-lim-p 2.5000 20.0000 0.0017 1443.338123 6 1.7048 315 | 0/8 16 h-lim-p 2.5000 20.0000 0.0003 1443.337963 2 1.2305 340 | 0/8 17 h-lim-p 2.5000 20.0000 0.0001 1443.337957 2 1.3159 365 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1443.337956 0 2.1875 385 | 0/8 19 h-lim-p 2.4800 20.0000 0.0000 1443.337956 0 1.0850 405 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 1443.337956 0 1.0938 425 | 0/8 21 h-lim-p 2.5000 20.0000 0.0000 1443.337956 0 0.1367 448 | 0/8 22 h-lim-p 0.1495 20.0000 0.0000 1443.337956 0 0.0000 483 Out... lnL = -1443.337956 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1443.337956 Node 7: lnL = -1443.337956 Node 8: lnL = -1443.337956 Node 9: lnL = -1443.337956 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 129 Sequential format.. Reading seq # 1: YMR214W_Sbay Reading seq # 2: YMR214W_Scer Reading seq # 3: YMR214W_Skud Reading seq # 4: YMR214W_Smik Reading seq # 5: YMR214W_Spar Sequences read.. Counting patterns.. # site patterns = 57 Counting frequencies.. 120 bytes for distance 9120 bytes for lkl0 7296 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.236527 0.097657 0.110968 0.012574 0.268488 0.182641 0.265756 0.000060 lnL0 = -522.385626 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 522.385626 x= 0.23653 0.09766 0.11097 0.01257 0.26849 0.18264 0.26576 0.00006 1 h-lim-p 0.0000 0.0000 202.3611 521.972594 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0022 115.8432 510.545608 0 0.0017 40 | 1/8 3 h-lim-p 0.0003 0.0023 93.9079 508.247898 0 0.0009 53 | 1/8 4 h-lim-p 0.0008 0.0066 28.3281 507.920845 1 0.0010 67 | 1/8 5 h-lim-p 0.0029 0.0235 6.3649 507.893920 6 0.0013 90 | 1/8 6 h-lim-p 0.0062 0.1824 1.3345 507.883752 6 0.0038 117 | 1/8 7 h-lim-p 0.0046 0.3398 1.1128 507.720274 0 0.0276 131 | 1/8 8 h-lim-p 0.0168 0.2909 1.8282 506.371820 0 0.0336 144 | 1/8 9 h-lim-p 0.9425 7.5396 0.0310 504.976412 0 1.8849 157 | 0/8 10 h-lim-p 0.0282 2.0747 2.0722 504.969492 6 0.0030 189 | 0/8 11 h-lim-p 0.3512 20.0000 0.0178 504.731421 0 1.4047 203 | 0/8 12 h-lim-p 2.5000 20.0000 0.0067 504.678154 7 1.7799 238 | 0/8 13 h-lim-p 2.5000 20.0000 0.0015 504.676621 4 1.2321 266 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 504.676608 1 1.2500 288 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 504.676608 1 1.2305 311 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 504.676608 0 1.0938 331 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 504.676608 0 1.0938 351 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 504.676608 0 0.0049 379 Out... lnL = -504.676608 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -504.676608 Node 7: lnL = -504.676608 Node 8: lnL = -504.676608 Node 9: lnL = -504.676608 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 333 Sequential format.. Reading seq # 1: YMR215W_Sbay Reading seq # 2: YMR215W_Scer Reading seq # 3: YMR215W_Skud Reading seq # 4: YMR215W_Smik Reading seq # 5: YMR215W_Spar Sequences read.. Counting patterns.. # site patterns = 152 Counting frequencies.. 120 bytes for distance 24320 bytes for lkl0 19456 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.343713 0.147602 0.171690 0.003647 0.410290 0.271966 0.403026 0.000060 lnL0 = -1534.309618 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1534.309618 x= 0.34371 0.14760 0.17169 0.00365 0.41029 0.27197 0.40303 0.00006 1 h-lim-p 0.0000 0.0000 224.9568 1534.228598 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0002 2026.2215 1471.555447 0 0.0002 38 | 1/8 3 h-lim-p 0.0003 0.0021 77.2039 1470.140173 0 0.0005 51 | 1/8 4 h-lim-p 0.0008 0.0074 51.3600 1469.430293 2 0.0007 67 | 1/8 5 h-lim-p 0.0017 0.0138 16.2911 1469.358516 6 0.0006 92 | 1/8 6 h-lim-p 0.0066 0.2378 1.5119 1469.326215 3 0.0067 110 | 1/8 7 h-lim-p 0.0142 0.5749 0.7172 1468.580441 0 0.0567 124 | 1/8 8 h-lim-p 0.0026 0.0744 15.5046 1467.552017 7 0.0026 161 | 1/8 9 h-lim-p 0.7862 6.2899 0.0434 1466.515866 1 0.9828 175 | 0/8 10 h-lim-p 0.0069 0.1160 6.1875 1466.487326 4 0.0017 204 | 0/8 11 h-lim-p 1.2138 20.0000 0.0085 1466.441429 2 1.1379 220 | 0/8 12 h-lim-p 2.5000 20.0000 0.0015 1466.438587 5 1.4456 254 | 0/8 13 h-lim-p 2.5000 20.0000 0.0002 1466.438571 1 1.2500 276 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1466.438571 0 1.2500 296 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1466.438571 0 2.1875 316 | 0/8 16 h-lim-p 2.0026 20.0000 0.0000 1466.438571 0 0.8761 336 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1466.438571 0 0.0391 361 | 0/8 18 h-lim-p 0.0396 20.0000 0.0000 1466.438571 0 0.0000 394 Out... lnL = -1466.438571 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1466.438571 Node 7: lnL = -1466.438571 Node 8: lnL = -1466.438571 Node 9: lnL = -1466.438571 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 265 Sequential format.. Reading seq # 1: YMR218C_Sbay Reading seq # 2: YMR218C_Scer Reading seq # 3: YMR218C_Skud Reading seq # 4: YMR218C_Smik Reading seq # 5: YMR218C_Spar Sequences read.. Counting patterns.. # site patterns = 129 Counting frequencies.. 120 bytes for distance 20640 bytes for lkl0 16512 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.327295 0.135068 0.161278 0.007802 0.385179 0.261030 0.379458 0.000060 lnL0 = -1275.349606 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1275.349606 x= 0.32729 0.13507 0.16128 0.00780 0.38518 0.26103 0.37946 0.00006 1 h-lim-p 0.0000 0.0000 355.7096 1275.091020 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0013 227.7106 1239.044193 m 0.0013 38 | 1/8 3 h-lim-p 0.0001 0.0010 228.9487 1230.506806 0 0.0005 52 | 1/8 4 h-lim-p 0.0006 0.0048 36.2957 1230.178397 2 0.0006 68 | 1/8 5 h-lim-p 0.0014 0.0182 14.4369 1230.079006 7 0.0010 96 | 1/8 6 h-lim-p 0.0095 0.0762 1.0997 1230.027513 5 0.0104 120 | 0/8 7 h-lim-p 0.0015 0.1216 7.8674 1229.747396 0 0.0058 134 | 0/8 8 h-lim-p 0.0031 0.0260 14.6260 1229.113873 0 0.0062 147 | 0/8 9 h-lim-p 0.0034 0.0273 4.5465 1226.010987 m 0.0273 159 | 1/8 10 h-lim-p 0.7114 5.6910 0.0977 1224.061937 8 0.7778 191 | 1/8 11 h-lim-p 0.1314 1.0508 0.3751 1222.231256 0 0.1970 210 | 1/8 12 h-lim-p 1.3541 10.8332 0.0330 1220.863429 1 1.6927 231 | 0/8 13 h-lim-p 0.0111 0.3158 5.0384 1220.841303 5 0.0018 263 | 0/8 14 h-lim-p 0.5487 8.3678 0.0164 1220.448575 0 1.6461 276 | 0/8 15 h-lim-p 2.5000 20.0000 0.0043 1220.433136 2 1.1719 300 | 0/8 16 h-lim-p 2.5000 20.0000 0.0012 1220.432246 3 1.1328 326 | 0/8 17 h-lim-p 2.5000 20.0000 0.0001 1220.432236 2 1.3159 351 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1220.432236 1 1.2305 374 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1220.432236 0 1.2500 394 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 1220.432236 0 2.1875 414 | 0/8 21 h-lim-p 2.4696 20.0000 0.0000 1220.432236 0 1.0805 434 | 0/8 22 h-lim-p 2.5000 20.0000 0.0000 1220.432236 0 5.0000 455 | 0/8 23 h-lim-p 1.4472 20.0000 0.0000 1220.432236 0 0.3166 476 | 0/8 24 h-lim-p 0.5230 20.0000 0.0000 1220.432236 0 0.0082 501 Out... lnL = -1220.432236 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1220.432236 Node 7: lnL = -1220.432236 Node 8: lnL = -1220.432236 Node 9: lnL = -1220.432236 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 264 Sequential format.. Reading seq # 1: YMR219W_Sbay Reading seq # 2: YMR219W_Scer Reading seq # 3: YMR219W_Skud Reading seq # 4: YMR219W_Smik Reading seq # 5: YMR219W_Spar Sequences read.. Counting patterns.. # site patterns = 128 Counting frequencies.. 120 bytes for distance 20480 bytes for lkl0 16384 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.332172 0.136790 0.162428 0.008982 0.389240 0.264190 0.386829 0.000060 lnL0 = -1282.279283 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1282.279283 x= 0.33217 0.13679 0.16243 0.00898 0.38924 0.26419 0.38683 0.00006 1 h-lim-p 0.0000 0.0000 341.2191 1282.010708 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0013 234.7572 1242.648052 0 0.0013 41 | 1/8 3 h-lim-p 0.0001 0.0008 244.3128 1234.751837 0 0.0004 55 | 1/8 4 h-lim-p 0.0001 0.0012 57.6931 1234.287173 0 0.0003 68 | 1/8 5 h-lim-p 0.0009 0.0176 18.8868 1234.084911 0 0.0013 80 | 1/8 6 h-lim-p 0.0076 0.1037 3.3573 1234.061463 6 0.0021 107 | 0/8 7 h-lim-p 0.0004 3.1206 16.9251 1233.809191 0 0.0017 121 | 0/8 8 h-lim-p 0.0015 0.0190 18.3330 1233.199098 0 0.0062 135 | 0/8 9 h-lim-p 0.0665 0.5320 0.2674 1228.689090 m 0.5320 147 | 0/8 10 h-lim-p -0.0000 -0.0000 0.1971 h-lim-p: -4.06132415e-18 -3.24905932e-17 1.97089872e-01 1228.689090 .. | 0/8 11 h-lim-p 0.0000 0.0964 150.1624 1224.404326 0 0.0005 188 | 0/8 12 h-lim-p 0.0000 0.0000 27.5757 1224.372726 m 0.0000 200 | 1/8 13 h-lim-p 0.0003 0.0395 4.8714 1224.364107 0 0.0008 213 | 1/8 14 h-lim-p 0.0018 0.0609 2.0061 1224.361632 5 0.0013 238 | 1/8 15 h-lim-p 0.0032 0.1593 0.8035 1224.360833 2 0.0017 255 | 1/8 16 h-lim-p 0.0151 2.6625 0.0883 1224.308947 0 0.1211 277 | 1/8 17 h-lim-p 0.0041 0.0544 2.5873 1224.191983 0 0.0062 296 | 1/8 18 h-lim-p 0.0107 0.2424 1.5001 1224.189873 5 0.0018 322 | 1/8 19 h-lim-p 1.2889 20.0000 0.0021 1224.187814 5 0.9288 347 | 0/8 20 h-lim-p 0.0627 16.3076 0.0318 1224.187813 1 0.0019 372 | 0/8 21 h-lim-p 0.1411 1.1285 0.0001 1224.187809 m 1.1285 392 | 1/8 22 h-lim-p 2.5000 20.0000 0.0000 1224.187809 0 1.2500 412 | 0/8 23 h-lim-p 0.0189 20.0000 0.0015 1224.187809 0 0.0010 434 | 1/8 24 h-lim-p 0.1027 20.0000 0.0000 1224.187809 0 0.4109 456 | 1/8 25 h-lim-p 2.5000 20.0000 0.0000 1224.187809 0 1.0938 475 | 1/8 26 h-lim-p 2.5000 20.0000 0.0000 1224.187809 0 2.1875 494 | 1/8 27 h-lim-p 2.2312 20.0000 0.0000 1224.187809 0 0.0087 520 Out... lnL = -1224.187809 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1224.187809 Node 7: lnL = -1224.187809 Node 8: lnL = -1224.187809 Node 9: lnL = -1224.187809 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 489 Sequential format.. Reading seq # 1: YMR222C_Sbay Reading seq # 2: YMR222C_Scer Reading seq # 3: YMR222C_Skud Reading seq # 4: YMR222C_Smik Reading seq # 5: YMR222C_Spar Sequences read.. Counting patterns.. # site patterns = 160 Counting frequencies.. 120 bytes for distance 25600 bytes for lkl0 20480 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.256413 0.106206 0.125741 0.007238 0.301256 0.203720 0.295913 0.000060 lnL0 = -1952.168817 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1952.168817 x= 0.25641 0.10621 0.12574 0.00724 0.30126 0.20372 0.29591 0.00006 1 h-lim-p 0.0000 0.0000 963.8613 1950.920425 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0008 337.7093 1905.764543 6 0.0006 49 | 1/8 3 h-lim-p 0.0001 0.0005 423.3614 1894.546725 0 0.0002 63 | 1/8 4 h-lim-p 0.0004 0.0035 73.0457 1894.054289 2 0.0002 79 | 1/8 5 h-lim-p 0.0005 0.0058 31.3012 1893.882385 6 0.0004 105 | 1/8 6 h-lim-p 0.0041 0.0636 3.1124 1893.863120 6 0.0015 133 | 0/8 7 h-lim-p 0.0002 0.0213 22.6189 1893.622666 0 0.0016 148 | 0/8 8 h-lim-p 0.0008 0.0060 43.0627 1892.941389 0 0.0023 161 | 0/8 9 h-lim-p 0.0361 0.2886 0.4755 1884.792650 m 0.2886 173 | 1/8 10 h-lim-p 0.8608 14.2670 0.1127 1881.853317 9 0.5937 215 | 1/8 11 h-lim-p 0.0925 0.7403 0.4017 1873.875940 0 0.2776 235 | 0/8 12 h-lim-p 0.0013 0.0103 34.6978 1873.109104 0 0.0026 255 | 0/8 13 h-lim-p 0.5584 4.4675 0.0273 1871.085099 0 2.2337 269 | 0/8 14 h-lim-p 1.1484 9.1869 0.0297 1870.595176 0 1.7225 289 | 0/8 15 h-lim-p 2.5000 20.0000 0.0081 1870.582910 6 0.7851 324 | 0/8 16 h-lim-p 2.5000 20.0000 0.0007 1870.582305 2 1.0889 348 | 0/8 17 h-lim-p 2.5000 20.0000 0.0001 1870.582295 2 1.3159 373 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1870.582295 0 2.1875 393 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1870.582294 0 1.0938 413 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 1870.582294 0 2.1875 433 | 0/8 21 h-lim-p 2.5000 20.0000 0.0000 1870.582294 0 1.0938 453 | 0/8 22 h-lim-p 2.5000 20.0000 0.0000 1870.582294 0 1.2500 473 | 0/8 23 h-lim-p 2.5000 20.0000 0.0000 1870.582294 0 0.0000 518 Out... lnL = -1870.582294 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1870.582294 Node 7: lnL = -1870.582294 Node 8: lnL = -1870.582294 Node 9: lnL = -1870.582294 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 445 Sequential format.. Reading seq # 1: YMR223W_Sbay Reading seq # 2: YMR223W_Scer Reading seq # 3: YMR223W_Skud Reading seq # 4: YMR223W_Smik Reading seq # 5: YMR223W_Spar Sequences read.. Counting patterns.. # site patterns = 175 Counting frequencies.. 120 bytes for distance 28000 bytes for lkl0 22400 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.338257 0.330988 0.266244 0.135600 0.020206 0.345987 0.342156 0.000060 lnL0 = -2076.048913 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2076.048913 x= 0.33826 0.33099 0.26624 0.13560 0.02021 0.34599 0.34216 0.00006 1 h-lim-p 0.0000 0.0000 346.4152 2075.956060 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0004 1413.0578 1989.648304 9 0.0003 55 | 1/8 3 h-lim-p 0.0000 0.0003 402.8358 1982.524426 0 0.0002 69 | 1/8 4 h-lim-p 0.0002 0.0017 63.4809 1981.561233 0 0.0006 82 | 1/8 5 h-lim-p 0.0010 0.0079 40.3438 1981.128191 8 0.0007 114 | 0/8 6 h-lim-p 0.0004 0.0081 69.5521 1979.496191 0 0.0008 127 | 0/8 7 h-lim-p 0.0006 0.0052 56.7259 1978.794171 1 0.0008 141 | 0/8 8 h-lim-p 0.0016 0.0131 16.5094 1978.734303 5 0.0006 163 | 0/8 9 h-lim-p 0.1169 1.3333 0.0880 1973.517271 m 1.3333 176 | 1/8 10 h-lim-p 0.5869 4.6954 0.0326 1972.478820 0 1.1739 197 | 0/8 11 h-lim-p 0.0039 0.0607 9.8195 1972.438792 3 0.0009 223 | 0/8 12 h-lim-p 0.6855 5.4841 0.0067 1972.329049 0 1.3710 236 | 0/8 13 h-lim-p 0.1817 1.4536 0.0068 1972.303893 m 1.4536 256 | 1/8 14 h-lim-p 2.5000 20.0000 0.0011 1972.303185 4 0.9644 284 | 1/8 15 h-lim-p 0.7476 20.0000 0.0015 1972.303077 2 0.3504 307 | 1/8 16 h-lim-p 2.5000 20.0000 0.0001 1972.303067 2 1.6492 332 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 1972.303066 0 2.1875 351 | 0/8 18 h-lim-p -0.0000 -0.0000 0.0026 h-lim-p: -1.11359454e-17 -8.90875634e-17 2.57673972e-03 1972.303066 .. | 1/8 19 h-lim-p 0.0000 20.0000 0.0338 1972.303066 0 0.0002 390 | 1/8 20 h-lim-p 0.0007 9.1369 0.0122 1972.303066 0 0.0006 409 | 1/8 21 h-lim-p 0.0018 20.0000 0.0039 1972.303066 0 0.0005 429 | 1/8 22 h-lim-p 0.0006 20.0000 0.0031 1972.303066 0 0.0006 448 | 1/8 23 h-lim-p 0.0018 20.0000 0.0010 1972.303066 0 0.0016 467 | 1/8 24 h-lim-p 0.0121 20.0000 0.0001 1972.303066 0 0.0026 487 | 1/8 25 h-lim-p 0.0160 20.0000 0.0000 1972.303066 0 0.0040 507 | 1/8 26 h-lim-p 0.0122 20.0000 0.0000 1972.303066 0 0.0978 529 | 1/8 27 h-lim-p 1.8843 20.0000 0.0000 1972.303066 0 0.0589 552 | 1/8 28 h-lim-p 0.0626 20.0000 0.0000 1972.303066 0 0.0039 574 Out... lnL = -1972.303066 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1972.303066 Node 7: lnL = -1972.303066 Node 8: lnL = -1972.303066 Node 9: lnL = -1972.303066 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 379 Sequential format.. Reading seq # 1: YMR225C_Sbay Reading seq # 2: YMR225C_Scer Reading seq # 3: YMR225C_Skud Reading seq # 4: YMR225C_Smik Reading seq # 5: YMR225C_Spar Sequences read.. Counting patterns.. # site patterns = 134 Counting frequencies.. 120 bytes for distance 21440 bytes for lkl0 17152 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 1.143046 1.269803 0.938682 0.415495 0.044425 0.975626 1.761252 0.000060 lnL0 = -1601.456787 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1601.456787 x= 1.14305 1.26980 0.93868 0.41549 0.04442 0.97563 1.76125 0.00006 1 h-lim-p 0.0000 0.0000 127.1096 1601.333571 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0001 1045.7804 1591.184467 m 0.0001 35 | 2/8 3 h-lim-p 0.0006 0.0049 117.5051 1568.185435 0 0.0036 49 | 1/8 4 h-lim-p 0.0001 0.0010 169.7713 1565.030369 0 0.0008 63 | 1/8 5 h-lim-p 0.0278 0.3562 4.7443 1512.773475 m 0.3562 76 | 2/8 6 h-lim-p 0.0018 0.0142 139.6287 1509.951882 1 0.0022 90 | 2/8 7 h-lim-p 0.0057 0.0456 24.5331 1474.960903 m 0.0456 102 | 2/8 8 h-lim-p 0.0019 0.0152 13.1381 1471.823648 0 0.0076 116 | 1/8 9 h-lim-p 0.0011 0.0091 27.3966 1468.985932 m 0.0091 128 | 2/8 10 h-lim-p 0.0104 0.0835 3.8056 1434.648988 m 0.0835 140 | 1/8 11 h-lim-p -0.0000 -0.0000 196.5114 h-lim-p: -9.82792421e-21 -7.86233937e-20 1.96511380e+02 1434.648988 .. | 1/8 12 h-lim-p 0.0000 0.0064 1020.3906 1399.727038 0 0.0002 164 | 1/8 13 h-lim-p 0.0001 0.0011 119.1461 1385.744969 m 0.0011 176 | 1/8 14 h-lim-p 0.0003 0.0022 251.6105 1370.276862 0 0.0011 190 | 1/8 15 h-lim-p 0.0003 0.0024 26.1971 1369.874439 0 0.0012 204 | 0/8 16 h-lim-p 0.0000 0.0003 161.0440 1367.864293 m 0.0003 216 | 2/8 17 h-lim-p 0.0076 0.0996 4.7833 1367.714328 7 0.0056 245 | 2/8 18 h-lim-p 0.0888 1.0767 0.3038 1363.793334 0 0.3554 259 | 1/8 19 h-lim-p 0.0251 1.3594 4.2979 1363.763927 3 0.0028 285 | 1/8 20 h-lim-p 0.1591 1.6172 0.0769 1362.922545 0 0.6364 299 | 0/8 21 h-lim-p 0.3331 20.0000 0.1469 1362.918332 6 0.0311 333 | 0/8 22 h-lim-p 0.0154 0.1232 0.1827 1362.680652 m 0.1232 353 | 1/8 23 h-lim-p 2.2060 20.0000 0.0100 1362.581017 3 1.8441 379 | 1/8 24 h-lim-p 0.6621 5.2968 0.0064 1362.540780 0 2.6484 400 | 0/8 25 h-lim-p 0.0052 0.0419 1.3781 1362.538324 5 0.0028 430 | 0/8 26 h-lim-p 0.8971 20.0000 0.0043 1362.531456 1 1.1214 444 | 0/8 27 h-lim-p 2.5000 20.0000 0.0006 1362.531308 2 1.1719 468 | 0/8 28 h-lim-p 2.5000 20.0000 0.0000 1362.531308 0 1.0938 488 | 0/8 29 h-lim-p 2.5000 20.0000 0.0000 1362.531308 0 1.0938 508 | 0/8 30 h-lim-p 2.5000 20.0000 0.0000 1362.531308 0 1.2500 528 | 0/8 31 h-lim-p 2.5000 20.0000 0.0000 1362.531308 0 0.3125 550 | 0/8 32 h-lim-p 0.2810 20.0000 0.0000 1362.531308 0 0.1229 570 Out... lnL = -1362.531308 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1362.531308 Node 7: lnL = -1362.531308 Node 8: lnL = -1362.531308 Node 9: lnL = -1362.531308 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 320 Sequential format.. Reading seq # 1: YMR232W_Sbay Reading seq # 2: YMR232W_Scer Reading seq # 3: YMR232W_Skud Reading seq # 4: YMR232W_Smik Reading seq # 5: YMR232W_Spar Sequences read.. Counting patterns.. # site patterns = 143 Counting frequencies.. 120 bytes for distance 22880 bytes for lkl0 18304 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.311723 0.320965 0.238097 0.109068 0.026730 0.264982 0.299063 0.000060 lnL0 = -1411.706340 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1411.706340 x= 0.31172 0.32097 0.23810 0.10907 0.02673 0.26498 0.29906 0.00006 1 h-lim-p 0.0000 0.0000 218.3718 1411.632172 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0006 847.3260 1383.552707 4 0.0003 46 | 1/8 3 h-lim-p 0.0003 0.0020 67.5421 1382.291553 0 0.0008 59 | 1/8 4 h-lim-p 0.0004 0.0031 85.4772 1381.475920 1 0.0005 73 | 1/8 5 h-lim-p 0.0027 0.0215 13.4656 1381.359607 6 0.0012 96 | 1/8 6 h-lim-p 0.0071 0.1127 2.2676 1381.198904 0 0.0106 108 | 1/8 7 h-lim-p 0.0107 0.1016 2.2445 1378.721550 0 0.0214 121 | 1/8 8 h-lim-p 0.0014 0.0110 31.0795 1376.930263 0 0.0021 133 | 1/8 9 h-lim-p 1.7855 20.0000 0.0358 1375.867648 9 0.9939 168 | 1/8 10 h-lim-p 1.7851 14.2807 0.0173 1374.834100 7 1.9113 203 | 0/8 11 h-lim-p 0.0520 2.7960 0.6340 1374.833519 5 0.0020 239 | 0/8 12 h-lim-p 0.0971 20.0000 0.0133 1374.727711 0 0.7766 262 | 0/8 13 h-lim-p 2.5000 20.0000 0.0026 1374.719048 5 1.2494 292 | 0/8 14 h-lim-p 2.5000 20.0000 0.0005 1374.718821 2 1.0889 316 | 0/8 15 h-lim-p 2.5000 20.0000 0.0001 1374.718813 1 1.2305 339 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1374.718813 0 1.0938 359 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1374.718813 0 1.0938 379 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1374.718813 0 0.1562 402 | 0/8 19 h-lim-p 0.0389 20.0000 0.0000 1374.718813 0 0.0389 422 | 0/8 20 h-lim-p 0.0164 20.0000 0.0000 1374.718813 0 0.0164 442 | 0/8 21 h-lim-p 0.0086 20.0000 0.0000 1374.718813 0 0.0000 478 Out... lnL = -1374.718813 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1374.718813 Node 7: lnL = -1374.718813 Node 8: lnL = -1374.718813 Node 9: lnL = -1374.718813 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 432 Sequential format.. Reading seq # 1: YMR234W_Sbay Reading seq # 2: YMR234W_Scer Reading seq # 3: YMR234W_Skud Reading seq # 4: YMR234W_Smik Reading seq # 5: YMR234W_Spar Sequences read.. Counting patterns.. # site patterns = 182 Counting frequencies.. 120 bytes for distance 29120 bytes for lkl0 23296 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.386945 0.299337 0.241343 0.149861 0.045882 0.316943 0.364700 0.000060 lnL0 = -2055.746955 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2055.746955 x= 0.38694 0.29934 0.24134 0.14986 0.04588 0.31694 0.36470 0.00006 1 h-lim-p 0.0000 0.0000 238.7335 2055.639572 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0004 801.9450 2028.679429 4 0.0003 46 | 1/8 3 h-lim-p 0.0001 0.0009 289.1346 2023.129655 0 0.0002 59 | 1/8 4 h-lim-p 0.0002 0.0018 83.6860 2020.925837 0 0.0009 73 | 1/8 5 h-lim-p 0.0030 0.0239 11.6293 2020.786459 7 0.0018 102 | 1/8 6 h-lim-p 0.0050 0.0982 4.0975 2020.710262 6 0.0034 128 | 1/8 7 h-lim-p 0.0262 1.0626 0.5342 2014.167452 0 0.2097 143 | 0/8 8 h-lim-p 0.0014 0.0108 35.5231 2012.681080 0 0.0020 162 | 0/8 9 h-lim-p 0.0192 0.2430 3.7459 2012.666724 3 0.0019 182 | 0/8 10 h-lim-p 0.1414 3.8588 0.0509 2011.916206 0 0.8484 196 | 0/8 11 h-lim-p 1.7932 14.3454 0.0180 2011.535584 7 1.3106 232 | 0/8 12 h-lim-p 1.9990 20.0000 0.0118 2011.406792 8 1.1457 273 | 0/8 13 h-lim-p 2.5000 20.0000 0.0032 2011.393364 6 1.4329 309 | 0/8 14 h-lim-p 2.5000 20.0000 0.0010 2011.392507 3 1.0483 336 | 0/8 15 h-lim-p 2.5000 20.0000 0.0001 2011.392495 1 1.0938 358 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 2011.392495 0 1.0938 378 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 2011.392495 0 1.2500 398 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 2011.392495 0 0.4688 420 | 0/8 19 h-lim-p 0.5307 20.0000 0.0000 2011.392495 0 0.0000 459 Out... lnL = -2011.392495 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2011.392495 Node 7: lnL = -2011.392495 Node 8: lnL = -2011.392495 Node 9: lnL = -2011.392495 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 263 Sequential format.. Reading seq # 1: YMR235C_Sbay Reading seq # 2: YMR235C_Scer Reading seq # 3: YMR235C_Skud Reading seq # 4: YMR235C_Smik Reading seq # 5: YMR235C_Spar Sequences read.. Counting patterns.. # site patterns = 120 Counting frequencies.. 120 bytes for distance 19200 bytes for lkl0 15360 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.411034 0.376447 0.284906 0.161152 0.042885 0.372004 0.420808 0.000060 lnL0 = -1287.154247 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1287.154247 x= 0.41103 0.37645 0.28491 0.16115 0.04289 0.37200 0.42081 0.00006 1 h-lim-p 0.0000 0.0000 179.1071 1287.079548 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0012 358.9390 1249.014870 m 0.0012 38 | 1/8 3 h-lim-p 0.0003 0.0022 84.3992 1246.939688 0 0.0008 51 | 1/8 4 h-lim-p 0.0021 0.0171 9.5063 1246.871538 7 0.0012 80 | 0/8 5 h-lim-p 0.0005 0.0080 21.8340 1246.403749 0 0.0021 94 | 0/8 6 h-lim-p 0.0016 0.0156 28.2340 1245.958931 1 0.0020 108 | 0/8 7 h-lim-p 0.0005 0.0043 50.7858 1245.115953 0 0.0021 122 | 0/8 8 h-lim-p 0.0590 0.4722 0.4692 1241.707620 m 0.4722 134 | 1/8 9 h-lim-p 0.0035 0.0283 13.4558 1241.455530 7 0.0025 169 | 1/8 10 h-lim-p 0.1868 1.8908 0.1810 1241.211126 6 0.1925 192 | 0/8 11 h-lim-p 0.0070 0.0922 4.9973 1241.112956 0 0.0139 212 | 0/8 12 h-lim-p 0.2269 1.8155 0.0554 1240.681359 0 0.9078 226 | 0/8 13 h-lim-p 0.5302 4.2412 0.0109 1240.565807 0 2.1206 248 | 0/8 14 h-lim-p 2.5000 20.0000 0.0076 1240.561853 3 1.0938 274 | 0/8 15 h-lim-p 2.5000 20.0000 0.0011 1240.561582 3 1.6492 302 | 0/8 16 h-lim-p 2.5000 20.0000 0.0005 1240.561546 3 1.6342 329 | 0/8 17 h-lim-p 2.5000 20.0000 0.0001 1240.561544 1 1.2305 352 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1240.561544 0 1.0938 372 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1240.561544 0 1.0938 392 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 1240.561544 0 5.0000 413 | 0/8 21 h-lim-p 1.5478 20.0000 0.0000 1240.561544 0 0.3386 434 | 0/8 22 h-lim-p 0.6651 20.0000 0.0000 1240.561544 0 0.0208 458 | 0/8 23 h-lim-p 0.0273 20.0000 0.0000 1240.561544 0 0.0017 481 Out... lnL = -1240.561544 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1240.561544 Node 7: lnL = -1240.561544 Node 8: lnL = -1240.561544 Node 9: lnL = -1240.561544 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 288 Sequential format.. Reading seq # 1: YMR236W_Sbay Reading seq # 2: YMR236W_Scer Reading seq # 3: YMR236W_Skud Reading seq # 4: YMR236W_Smik Reading seq # 5: YMR236W_Spar Sequences read.. Counting patterns.. # site patterns = 125 Counting frequencies.. 120 bytes for distance 20000 bytes for lkl0 16000 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.391382 0.340594 0.260011 0.154453 0.046815 0.359419 0.389530 0.000060 lnL0 = -1301.544709 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1301.544709 x= 0.39138 0.34059 0.26001 0.15445 0.04682 0.35942 0.38953 0.00006 1 h-lim-p 0.0000 0.0000 183.9377 1301.462546 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0010 407.9129 1265.166461 m 0.0010 38 | 1/8 3 h-lim-p 0.0002 0.0015 95.7609 1263.304160 0 0.0008 52 | 1/8 4 h-lim-p 0.0007 0.0055 12.5438 1263.233422 6 0.0008 79 | 0/8 5 h-lim-p 0.0004 0.0443 25.3059 1262.609434 0 0.0022 93 | 0/8 6 h-lim-p 0.0017 0.0135 28.8043 1260.944113 0 0.0068 107 | 0/8 7 h-lim-p 0.0020 0.0156 12.0340 1260.866628 6 0.0014 133 | 0/8 8 h-lim-p 0.0250 0.4763 0.6635 1260.473956 0 0.0751 146 | 0/8 9 h-lim-p 0.0019 0.0150 15.7190 1256.904781 m 0.0150 166 | 1/8 10 h-lim-p 2.5000 20.0000 0.0184 1256.475628 8 1.4663 196 | 0/8 11 h-lim-p 0.0055 0.9202 4.8967 1256.447233 5 0.0024 224 | 0/8 12 h-lim-p 0.0753 0.6025 0.0285 1256.410017 m 0.6025 236 | 1/8 13 h-lim-p 0.6465 20.0000 0.0197 1256.402559 4 0.2851 263 | 1/8 14 h-lim-p 0.3234 19.8011 0.0173 1256.382168 0 0.4852 282 | 0/8 15 h-lim-p 0.0000 0.0000 0.0228 h-lim-p: 2.88560826e-18 2.30848661e-17 2.27762089e-02 1256.382168 .. | 0/8 16 h-lim-p 0.0000 0.0497 1.1362 1256.381791 0 0.0006 323 | 0/8 17 h-lim-p 0.0013 0.8212 0.5783 1256.381670 3 0.0009 343 | 0/8 18 h-lim-p 0.0050 1.4033 0.1025 1256.381664 1 0.0012 366 | 0/8 19 h-lim-p 0.0022 0.0301 0.0570 1256.381662 0 0.0010 386 | 0/8 20 h-lim-p 0.0016 0.0126 0.0268 1256.381662 0 0.0024 406 | 0/8 21 h-lim-p 0.0004 0.0031 0.0866 1256.381661 0 0.0016 428 | 0/8 22 h-lim-p 0.0019 0.0155 0.0224 1256.381661 0 0.0004 449 | 0/8 23 h-lim-p 0.0012 0.0486 0.0079 1256.381661 0 0.0000 484 | 0/8 24 h-lim-p 0.0000 20.0000 0.0002 1256.381657 0 0.6554 520 | 0/8 25 h-lim-p 1.1818 20.0000 0.0001 1256.381656 0 1.1818 540 | 0/8 26 h-lim-p 0.0042 0.0338 0.0105 1256.381656 0 0.0002 563 | 0/8 27 h-lim-p 0.0327 20.0000 0.0001 1256.381656 0 0.1963 585 | 0/8 28 h-lim-p 2.2730 20.0000 0.0000 1256.381656 0 0.0000 623 Out... lnL = -1256.381656 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1256.381656 Node 7: lnL = -1256.381656 Node 8: lnL = -1256.381656 Node 9: lnL = -1256.381656 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 329 Sequential format.. Reading seq # 1: YMR237W_Sbay Reading seq # 2: YMR237W_Scer Reading seq # 3: YMR237W_Skud Reading seq # 4: YMR237W_Smik Reading seq # 5: YMR237W_Spar Sequences read.. Counting patterns.. # site patterns = 127 Counting frequencies.. 120 bytes for distance 20320 bytes for lkl0 16256 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.246295 0.100951 0.067749 0.167125 0.041891 0.172180 0.130639 0.000060 lnL0 = -1378.969012 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1378.969012 x= 0.24630 0.10095 0.06775 0.16712 0.04189 0.17218 0.13064 0.00006 1 h-lim-p 0.0000 0.0000 67.0052 1378.946492 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0036 37.6284 1378.604151 0 0.0006 40 | 1/8 3 h-lim-p 0.0017 0.0212 13.9977 1378.551937 6 0.0006 65 | 1/8 4 h-lim-p 0.0016 0.0505 5.3922 1378.541365 3 0.0008 83 | 1/8 5 h-lim-p 0.0029 0.4677 1.5250 1378.539611 4 0.0011 103 | 1/8 6 h-lim-p 0.0059 0.7567 0.2845 1378.527593 0 0.0177 116 | 1/8 7 h-lim-p 0.0067 0.3397 0.7474 1378.138555 0 0.0269 137 | 1/8 8 h-lim-p 0.0017 0.0182 11.5325 1377.988042 6 0.0014 170 | 1/8 9 h-lim-p 2.5000 20.0000 0.0021 1377.985903 4 1.0049 190 | 1/8 10 h-lim-p 2.5000 20.0000 0.0002 1377.985869 2 1.1719 213 | 0/8 11 h-lim-p 0.0542 20.0000 0.0040 1377.985869 0 0.0030 235 | 0/8 12 h-lim-p 0.1230 0.9838 0.0000 1377.985868 m 0.9838 255 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 1377.985868 0 0.5469 276 | 1/8 14 h-lim-p 2.3174 20.0000 0.0000 1377.985868 0 0.1267 298 | 1/8 15 h-lim-p 0.1594 20.0000 0.0000 1377.985868 0 0.0000 329 Out... lnL = -1377.985868 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1377.985868 Node 7: lnL = -1377.985868 Node 8: lnL = -1377.985868 Node 9: lnL = -1377.985868 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 494 Sequential format.. Reading seq # 1: YMR238W_Sbay Reading seq # 2: YMR238W_Scer Reading seq # 3: YMR238W_Skud Reading seq # 4: YMR238W_Smik Reading seq # 5: YMR238W_Spar Sequences read.. Counting patterns.. # site patterns = 178 Counting frequencies.. 120 bytes for distance 28480 bytes for lkl0 22784 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.286375 0.208834 0.156005 0.109644 0.037893 0.236839 0.266279 0.000060 lnL0 = -2068.054378 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2068.054378 x= 0.28638 0.20883 0.15600 0.10964 0.03789 0.23684 0.26628 0.00006 1 h-lim-p 0.0000 0.0000 349.4569 2067.793422 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0003 815.8299 2032.931439 0 0.0002 38 | 1/8 3 h-lim-p 0.0002 0.0014 89.5512 2030.920114 0 0.0005 51 | 1/8 4 h-lim-p 0.0008 0.0063 22.2536 2030.820773 6 0.0004 76 | 1/8 5 h-lim-p 0.0006 0.0094 15.4960 2030.779041 6 0.0004 102 | 1/8 6 h-lim-p 0.0019 0.0970 3.5688 2030.754209 3 0.0019 120 | 1/8 7 h-lim-p 0.0342 1.2717 0.1982 2027.021024 0 0.2737 135 | 0/8 8 h-lim-p 0.0005 0.0041 42.0952 2025.566569 0 0.0010 155 | 0/8 9 h-lim-p 0.0030 0.0916 14.4225 2025.460168 7 0.0011 185 | 0/8 10 h-lim-p 0.4796 3.8370 0.0280 2025.200175 4 0.4759 205 | 0/8 11 h-lim-p 2.1201 20.0000 0.0063 2025.082575 6 1.5723 239 | 0/8 12 h-lim-p 2.5000 20.0000 0.0020 2025.078037 2 1.1719 263 | 0/8 13 h-lim-p 2.5000 20.0000 0.0004 2025.077822 2 1.2402 287 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 2025.077820 0 1.0938 307 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2025.077820 0 1.0938 327 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 2025.077820 0 1.0938 347 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 2025.077820 0 0.0684 371 | 0/8 18 h-lim-p 0.0456 20.0000 0.0000 2025.077820 0 0.0000 401 Out... lnL = -2025.077820 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2025.077820 Node 7: lnL = -2025.077820 Node 8: lnL = -2025.077820 Node 9: lnL = -2025.077820 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 272 Sequential format.. Reading seq # 1: YMR239C_Sbay Reading seq # 2: YMR239C_Scer Reading seq # 3: YMR239C_Skud Reading seq # 4: YMR239C_Smik Reading seq # 5: YMR239C_Spar Sequences read.. Counting patterns.. # site patterns = 123 Counting frequencies.. 120 bytes for distance 19680 bytes for lkl0 15744 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.268339 0.270171 0.190094 0.107806 0.026761 0.227674 0.277051 0.000060 lnL0 = -1134.015481 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1134.015481 x= 0.26834 0.27017 0.19009 0.10781 0.02676 0.22767 0.27705 0.00006 1 h-lim-p 0.0000 0.0000 328.8012 1133.831562 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0010 284.7061 1104.653706 m 0.0010 38 | 1/8 3 h-lim-p 0.0002 0.0018 114.3242 1103.106791 0 0.0004 51 | 1/8 4 h-lim-p 0.0005 0.0044 40.9082 1102.777618 5 0.0005 74 | 1/8 5 h-lim-p 0.0016 0.0126 10.2091 1102.749100 7 0.0005 106 | 0/8 6 h-lim-p 0.0002 0.1310 25.5227 1102.420987 0 0.0011 120 | 0/8 7 h-lim-p 0.0012 0.0103 23.7430 1101.609930 0 0.0047 134 | 0/8 8 h-lim-p 0.0288 0.2303 1.1161 1101.370740 5 0.0250 155 | 0/8 9 h-lim-p 0.0023 0.0187 7.0907 1097.309600 m 0.0187 167 | 1/8 10 h-lim-p 2.2934 20.0000 0.0416 1095.043893 8 1.3248 199 | 1/8 11 h-lim-p 0.0975 0.7800 0.3154 1093.915767 0 0.1950 219 | 0/8 12 h-lim-p 0.0113 0.0901 3.1524 1093.891897 6 0.0080 251 | 0/8 13 h-lim-p 0.4742 3.7936 0.0181 1093.729299 0 1.8968 265 | 0/8 14 h-lim-p 2.4031 19.2252 0.0138 1093.672673 4 1.2239 294 | 0/8 15 h-lim-p 0.7811 6.2489 0.0040 1093.664849 0 1.5622 315 | 0/8 16 h-lim-p 2.1082 16.8657 0.0013 1093.662910 2 1.9764 339 | 0/8 17 h-lim-p 2.5000 20.0000 0.0004 1093.662733 4 1.3578 368 | 0/8 18 h-lim-p 2.5000 20.0000 0.0001 1093.662725 2 1.3159 393 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1093.662724 0 2.1875 413 | 0/8 20 h-lim-p 2.3912 20.0000 0.0000 1093.662724 0 1.0462 433 | 0/8 21 h-lim-p 2.5000 20.0000 0.0000 1093.662724 0 2.1875 453 | 0/8 22 h-lim-p 2.5000 20.0000 0.0000 1093.662724 0 1.0938 473 | 0/8 23 h-lim-p 2.5000 20.0000 0.0000 1093.662724 0 3.7500 493 | 0/8 24 h-lim-p 2.1252 20.0000 0.0000 1093.662724 0 0.0000 531 Out... lnL = -1093.662724 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1093.662724 Node 7: lnL = -1093.662724 Node 8: lnL = -1093.662724 Node 9: lnL = -1093.662724 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 760 Sequential format.. Reading seq # 1: YMR241W_Sbay Reading seq # 2: YMR241W_Scer Reading seq # 3: YMR241W_Skud Reading seq # 4: YMR241W_Smik Reading seq # 5: YMR241W_Spar Sequences read.. Counting patterns.. # site patterns = 233 Counting frequencies.. 120 bytes for distance 37280 bytes for lkl0 29824 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.292766 0.176118 0.134274 0.106889 0.049909 0.216108 0.242037 0.000060 lnL0 = -3312.485192 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3312.485192 x= 0.29277 0.17612 0.13427 0.10689 0.04991 0.21611 0.24204 0.00006 1 h-lim-p 0.0000 0.0000 442.1221 3312.110714 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0002 843.6280 3298.031051 0 0.0001 37 | 1/8 3 h-lim-p 0.0001 0.0011 165.7526 3295.405020 0 0.0003 50 | 1/8 4 h-lim-p 0.0001 0.0009 155.9834 3293.693459 0 0.0002 63 | 1/8 5 h-lim-p 0.0015 0.0119 17.6684 3293.545880 5 0.0008 86 | 1/8 6 h-lim-p 0.0030 0.0762 4.5332 3293.291482 0 0.0046 98 | 1/8 7 h-lim-p 0.0062 0.0688 3.3599 3287.025312 0 0.0246 112 | 1/8 8 h-lim-p 0.0006 0.0045 58.0730 3275.191451 0 0.0017 125 | 1/8 9 h-lim-p 2.1755 18.0402 0.0450 3272.664991 9 0.6312 162 | 0/8 10 h-lim-p 0.0019 0.7442 15.2656 3272.591724 7 0.0006 199 | 0/8 11 h-lim-p 0.4937 8.2725 0.0197 3272.142608 0 0.9873 212 | 0/8 12 h-lim-p 2.0459 20.0000 0.0095 3272.009036 2 0.9590 236 | 0/8 13 h-lim-p 2.5000 20.0000 0.0010 3272.003885 5 1.5934 268 | 0/8 14 h-lim-p 1.4125 20.0000 0.0011 3272.002584 3 0.6976 295 | 0/8 15 h-lim-p 2.5000 20.0000 0.0002 3272.002505 2 0.9961 319 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 3272.002505 0 1.2500 339 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 3272.002505 0 1.0938 359 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 3272.002505 0 5.0000 380 | 0/8 19 h-lim-p 1.3714 20.0000 0.0000 3272.002505 0 0.3428 401 | 0/8 20 h-lim-p 0.5693 20.0000 0.0000 3272.002505 0 0.0001 432 Out... lnL = -3272.002505 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3272.002505 Node 7: lnL = -3272.002505 Node 8: lnL = -3272.002505 Node 9: lnL = -3272.002505 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 860 Sequential format.. Reading seq # 1: YMR242C_Sbay Reading seq # 2: YMR242C_Scer Reading seq # 3: YMR242C_Skud Reading seq # 4: YMR242C_Smik Reading seq # 5: YMR242C_Spar Sequences read.. Counting patterns.. # site patterns = 411 Counting frequencies.. 120 bytes for distance 65760 bytes for lkl0 52608 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.850158 0.176274 0.000060 0.900985 0.245543 0.266965 0.341960 0.049620 lnL0 = -4387.959828 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4387.959828 x= 0.85016 0.17627 0.00006 0.90099 0.24554 0.26696 0.34196 0.04962 1 h-lim-p 0.0000 0.0000 211.8666 4387.911872 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0031 113.4221 4381.519616 0 0.0013 41 | 1/8 3 h-lim-p 0.0035 0.0282 35.7275 4379.329155 1 0.0044 55 | 1/8 4 h-lim-p 0.0078 0.0620 10.2389 4379.116243 2 0.0036 71 | 1/8 5 h-lim-p 0.0051 0.0406 6.4748 4378.881998 0 0.0076 83 | 1/8 6 h-lim-p 0.0151 0.1206 2.0763 4376.739815 0 0.0603 97 | 1/8 7 h-lim-p 0.0107 0.0856 7.1803 4368.154470 0 0.0214 110 | 1/8 8 h-lim-p 1.8224 14.5788 0.0776 4367.649269 6 0.7817 133 | 0/8 9 h-lim-p 0.0224 0.4602 2.7102 4367.648591 3 0.0007 162 | 0/8 10 h-lim-p 0.0814 0.6514 0.0143 4367.628437 m 0.6514 174 | 1/8 11 h-lim-p 2.0887 20.0000 0.0044 4367.626838 5 0.6022 207 | 1/8 12 h-lim-p 1.1823 20.0000 0.0023 4367.626681 3 0.3864 233 | 1/8 13 h-lim-p 2.3204 20.0000 0.0004 4367.626663 2 0.8951 256 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 4367.626663 0 1.0938 275 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 4367.626663 0 1.0938 294 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 4367.626663 0 1.0938 313 | 1/8 17 h-lim-p 1.6063 20.0000 0.0000 4367.626663 0 1.4056 332 | 1/8 18 h-lim-p 1.3763 20.0000 0.0000 4367.626663 0 1.3763 351 | 1/8 19 h-lim-p 0.3032 20.0000 0.0000 4367.626663 0 0.0000 393 | 1/8 20 h-lim-p 0.0000 20.0000 0.0000 4367.626663 0 0.0000 427 Out... lnL = -4367.626663 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4367.626663 Node 7: lnL = -4367.626663 Node 8: lnL = -4367.626663 Node 9: lnL = -4367.626663 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 862 Sequential format.. Reading seq # 1: YMR243C_Sbay Reading seq # 2: YMR243C_Scer Reading seq # 3: YMR243C_Skud Reading seq # 4: YMR243C_Smik Reading seq # 5: YMR243C_Spar Sequences read.. Counting patterns.. # site patterns = 333 Counting frequencies.. 120 bytes for distance 53280 bytes for lkl0 42624 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.427783 0.022206 0.060261 0.134469 0.080732 0.207764 0.216745 0.043248 lnL0 = -3855.120392 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3855.120392 x= 0.42778 0.02221 0.06026 0.13447 0.08073 0.20776 0.21674 0.04325 1 h-lim-p 0.0034 0.8001 150.4030 3853.338880 5 0.0002 35 | 0/8 2 h-lim-p 0.0004 0.0029 41.3576 3853.057813 2 0.0003 51 | 0/8 3 h-lim-p 0.0006 0.0125 23.9126 3852.985514 7 0.0003 80 | 0/8 4 h-lim-p 0.0010 0.0191 7.9222 3852.979158 2 0.0002 97 | 0/8 5 h-lim-p 0.0010 0.1433 1.9204 3852.978320 4 0.0005 118 | 0/8 6 h-lim-p 0.0039 0.4267 0.2419 3852.978295 1 0.0008 133 | 0/8 7 h-lim-p 0.0034 4.4109 0.0604 3852.978294 0 0.0007 154 | 0/8 8 h-lim-p 0.0268 20.0000 0.0017 3852.976688 0 0.8573 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 3852.976503 2 0.9961 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3852.976503 0 1.0938 223 | 0/8 11 h-lim-p 0.6910 20.0000 0.0000 3852.976503 0 0.6910 243 | 0/8 12 h-lim-p 0.2805 20.0000 0.0000 3852.976503 0 0.0000 276 | 0/8 13 h-lim-p 0.0007 20.0000 0.0000 3852.976503 0 0.0000 313 Out... lnL = -3852.976503 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3852.976503 Node 7: lnL = -3852.976503 Node 8: lnL = -3852.976503 Node 9: lnL = -3852.976503 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 865 Sequential format.. Reading seq # 1: YMR244W_Sbay Reading seq # 2: YMR244W_Scer Reading seq # 3: YMR244W_Skud Reading seq # 4: YMR244W_Smik Reading seq # 5: YMR244W_Spar Sequences read.. Counting patterns.. # site patterns = 363 Counting frequencies.. 120 bytes for distance 58080 bytes for lkl0 46464 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.674698 0.036428 0.074297 0.151601 0.095018 0.266786 0.190880 0.147464 lnL0 = -4214.043222 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4214.043222 x= 0.67470 0.03643 0.07430 0.15160 0.09502 0.26679 0.19088 0.14746 1 h-lim-p 0.0012 0.0099 121.6504 4212.496669 6 0.0002 37 | 0/8 2 h-lim-p 0.0007 0.0059 38.3593 4212.134709 4 0.0005 57 | 0/8 3 h-lim-p 0.0006 0.0084 32.8128 4211.993953 5 0.0004 82 | 0/8 4 h-lim-p 0.0008 0.0171 15.9457 4211.946396 7 0.0005 112 | 0/8 5 h-lim-p 0.0010 0.0441 8.5169 4211.929694 4 0.0007 134 | 0/8 6 h-lim-p 0.0118 0.3246 0.4683 4211.929651 2 0.0004 154 | 0/8 7 h-lim-p 0.0017 2.3843 0.1045 4211.929631 0 0.0035 175 | 0/8 8 h-lim-p 0.2148 20.0000 0.0017 4211.926780 0 0.8592 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 4211.926735 1 0.9961 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4211.926735 0 1.0938 239 | 0/8 11 h-lim-p 1.3776 20.0000 0.0000 4211.926735 0 0.0646 263 | 0/8 12 h-lim-p 0.0180 20.0000 0.0000 4211.926735 0 0.0000 300 | 0/8 13 h-lim-p 0.0000 20.0000 0.0006 | 0/8 14 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -4211.926735 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4211.926735 Node 7: lnL = -4211.926735 Node 8: lnL = -4211.926735 Node 9: lnL = -4211.926735 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 691 Sequential format.. Reading seq # 1: YMR246W_Sbay Reading seq # 2: YMR246W_Scer Reading seq # 3: YMR246W_Skud Reading seq # 4: YMR246W_Smik Reading seq # 5: YMR246W_Spar Sequences read.. Counting patterns.. # site patterns = 208 Counting frequencies.. 120 bytes for distance 33280 bytes for lkl0 26624 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.352520 0.038120 0.044414 0.076730 0.053497 0.087938 0.142781 0.069925 lnL0 = -2751.537440 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2751.537440 x= 0.35252 0.03812 0.04441 0.07673 0.05350 0.08794 0.14278 0.06992 1 h-lim-p 0.0030 0.9764 135.2109 2750.367123 9 0.0001 46 | 0/8 2 h-lim-p 0.0003 0.0025 33.2188 2750.280209 5 0.0002 69 | 0/8 3 h-lim-p 0.0004 0.0145 12.7241 2750.253841 4 0.0004 88 | 0/8 4 h-lim-p 0.0007 0.0263 6.8948 2750.250362 5 0.0002 112 | 0/8 5 h-lim-p 0.0008 0.0735 1.7010 2750.250079 4 0.0002 133 | 0/8 6 h-lim-p 0.0009 0.4498 0.3973 2750.250056 2 0.0003 150 | 0/8 7 h-lim-p 0.0005 0.6629 0.2449 2750.250047 0 0.0004 170 | 0/8 8 h-lim-p 0.2802 20.0000 0.0004 2750.249558 0 1.1208 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2750.249555 0 1.0938 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2750.249555 0 1.0938 232 | 0/8 11 h-lim-p 2.4307 20.0000 0.0000 2750.249555 0 2.1268 252 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2750.249555 0 0.5469 273 | 0/8 13 h-lim-p 0.1232 20.0000 0.0000 2750.249555 0 0.0077 296 | 0/8 14 h-lim-p 0.0023 20.0000 0.0002 2750.249555 0 0.0000 328 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 2750.249555 0 0.0000 362 Out... lnL = -2750.249555 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2750.249555 Node 7: lnL = -2750.249555 Node 8: lnL = -2750.249555 Node 9: lnL = -2750.249555 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 867 Sequential format.. Reading seq # 1: YMR250W_Sbay Reading seq # 2: YMR250W_Scer Reading seq # 3: YMR250W_Skud Reading seq # 4: YMR250W_Smik Reading seq # 5: YMR250W_Spar Sequences read.. Counting patterns.. # site patterns = 428 Counting frequencies.. 120 bytes for distance 68480 bytes for lkl0 54784 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.685592 0.210478 0.164600 0.269139 0.146463 0.411429 0.477065 0.000060 lnL0 = -4733.310714 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4733.310714 x= 0.68559 0.21048 0.16460 0.26914 0.14646 0.41143 0.47706 0.00006 1 h-lim-p 0.0000 0.0000 141.7523 4733.179080 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0051 126.8809 4728.622547 0 0.0010 40 | 1/8 3 h-lim-p 0.0025 0.0203 33.2661 4727.793345 7 0.0017 69 | 1/8 4 h-lim-p 0.0085 0.0836 6.6634 4727.732589 4 0.0022 90 | 1/8 5 h-lim-p 0.0038 0.1696 3.8352 4727.664657 1 0.0047 104 | 1/8 6 h-lim-p 0.0034 0.0895 5.3004 4727.559276 5 0.0035 125 | 1/8 7 h-lim-p 0.0188 0.3420 0.9943 4722.920058 0 0.0751 139 | 1/8 8 h-lim-p 0.0046 0.0478 16.2797 4722.220495 3 0.0042 164 | 1/8 9 h-lim-p 1.5709 12.5670 0.0261 4722.065261 4 0.6878 183 | 1/8 10 h-lim-p 2.5000 20.0000 0.0031 4722.062964 4 0.7088 212 | 1/8 11 h-lim-p 2.5000 20.0000 0.0002 4722.062957 1 0.9961 233 | 0/8 12 h-lim-p -0.0000 -0.0000 0.0023 h-lim-p: -2.03815457e-19 -1.63052366e-18 2.25131793e-03 4722.062957 .. | 1/8 13 h-lim-p 0.0000 20.0000 0.0203 4722.062956 0 0.0006 274 | 1/8 14 h-lim-p 0.0008 20.0000 0.0166 4722.062956 0 0.0012 293 | 1/8 15 h-lim-p 0.0024 20.0000 0.0080 4722.062956 0 0.0011 312 | 1/8 16 h-lim-p 0.0030 20.0000 0.0029 4722.062956 0 0.0026 331 | 1/8 17 h-lim-p 0.0095 20.0000 0.0008 4722.062956 0 0.0010 352 | 1/8 18 h-lim-p 0.0039 20.0000 0.0002 4722.062956 0 0.0020 371 | 1/8 19 h-lim-p 0.0028 20.0000 0.0001 4722.062956 0 0.0028 390 | 1/8 20 h-lim-p 0.0359 20.0000 0.0000 4722.062956 0 0.5741 413 | 1/8 21 h-lim-p 2.5000 20.0000 0.0000 4722.062956 0 1.0938 432 | 1/8 22 h-lim-p 2.5000 20.0000 0.0000 4722.062956 0 1.0938 451 | 1/8 23 h-lim-p 2.5000 20.0000 0.0000 4722.062956 0 2.5000 470 | 1/8 24 h-lim-p 1.6656 20.0000 0.0000 4722.062956 0 1.6656 489 | 1/8 25 h-lim-p 2.5000 20.0000 0.0000 4722.062956 0 0.0000 537 Out... lnL = -4722.062956 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4722.062956 Node 7: lnL = -4722.062956 Node 8: lnL = -4722.062956 Node 9: lnL = -4722.062956 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 792 Sequential format.. Reading seq # 1: YMR251W-A_Sbay Reading seq # 2: YMR251W-A_Scer Reading seq # 3: YMR251W-A_Skud Reading seq # 4: YMR251W-A_Smik Reading seq # 5: YMR251W-A_Spar Sequences read.. Counting patterns.. # site patterns = 231 Counting frequencies.. 120 bytes for distance 36960 bytes for lkl0 29568 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.245543 0.032959 0.056643 0.072911 0.055549 0.172889 0.148867 0.000060 lnL0 = -3009.981549 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3009.981549 x= 0.24554 0.03296 0.05664 0.07291 0.05555 0.17289 0.14887 0.00006 1 h-lim-p 0.0002 0.0016 164.2058 3008.260534 9 0.0001 46 | 0/8 2 h-lim-p 0.0005 0.0038 49.1619 3007.911603 8 0.0003 77 | 0/8 3 h-lim-p 0.0006 0.0047 19.6457 3007.891106 3 0.0001 96 | 0/8 4 h-lim-p 0.0004 0.0062 6.0834 3007.888197 2 0.0002 112 | 0/8 5 h-lim-p 0.0008 0.0131 1.3045 3007.887970 3 0.0003 132 | 0/8 6 h-lim-p 0.0014 0.3461 0.2666 3007.887965 0 0.0002 146 | 0/8 7 h-lim-p 0.0008 7.7527 0.0537 3007.887965 0 0.0004 166 | 0/8 8 h-lim-p 0.0019 20.0000 0.0107 3007.887959 0 0.0611 191 | 0/8 9 h-lim-p 1.0023 16.7957 0.0007 3007.887923 2 0.5276 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3007.887923 0 1.0938 236 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3007.887923 0 1.0938 256 | 0/8 12 h-lim-p 2.1276 20.0000 0.0000 3007.887923 0 0.0665 280 | 0/8 13 h-lim-p 0.0015 20.0000 0.0001 3007.887923 0 0.0000 318 | 0/8 14 h-lim-p 0.0000 20.0000 0.0005 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -3007.887923 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3007.887923 Node 7: lnL = -3007.887923 Node 8: lnL = -3007.887923 Node 9: lnL = -3007.887923 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 253 Sequential format.. Reading seq # 1: YMR252C_Sbay Reading seq # 2: YMR252C_Scer Reading seq # 3: YMR252C_Skud Reading seq # 4: YMR252C_Smik Reading seq # 5: YMR252C_Spar Sequences read.. Counting patterns.. # site patterns = 112 Counting frequencies.. 120 bytes for distance 17920 bytes for lkl0 14336 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.321041 0.027550 0.062358 0.125774 0.053957 0.117628 0.265171 0.002892 lnL0 = -1053.505369 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1053.505369 x= 0.32104 0.02755 0.06236 0.12577 0.05396 0.11763 0.26517 0.00289 1 h-lim-p 0.0002 0.0017 62.0043 1052.540593 0 0.0006 23 | 0/8 2 h-lim-p 0.0016 0.0128 17.6227 1052.463649 8 0.0005 55 | 0/8 3 h-lim-p 0.0009 0.0097 10.3299 1052.443319 5 0.0005 78 | 0/8 4 h-lim-p 0.0028 0.0683 1.8351 1052.441474 3 0.0012 96 | 0/8 5 h-lim-p 0.0038 0.4763 0.5613 1052.441206 2 0.0016 112 | 0/8 6 h-lim-p 0.0053 0.1909 0.1762 1052.441057 2 0.0041 136 | 0/8 7 h-lim-p 0.0038 0.2157 0.1867 1052.440730 1 0.0048 158 | 0/8 8 h-lim-p 0.0139 1.1320 0.0644 1052.421173 0 0.1108 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0017 1052.419446 4 0.9644 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1052.419445 0 1.0938 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1052.419445 0 1.0938 249 | 0/8 12 h-lim-p 1.1719 20.0000 0.0000 1052.419445 0 4.6875 271 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1052.419445 0 0.5469 292 | 0/8 14 h-lim-p 0.0333 20.0000 0.0000 1052.419445 0 0.0083 313 | 0/8 15 h-lim-p 0.0023 20.0000 0.0001 1052.419445 0 0.0006 334 | 0/8 16 h-lim-p 0.0003 20.0000 0.0002 1052.419445 0 0.0000 369 | 0/8 17 h-lim-p 0.0000 20.0000 0.0009 | 0/8 18 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -1052.419445 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1052.419445 Node 7: lnL = -1052.419445 Node 8: lnL = -1052.419445 Node 9: lnL = -1052.419445 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 89 Sequential format.. Reading seq # 1: YMR255W_Sbay Reading seq # 2: YMR255W_Scer Reading seq # 3: YMR255W_Skud Reading seq # 4: YMR255W_Smik Reading seq # 5: YMR255W_Spar Sequences read.. Counting patterns.. # site patterns = 62 Counting frequencies.. 120 bytes for distance 9920 bytes for lkl0 7936 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.436937 0.103250 0.112583 0.127414 0.095522 0.252925 0.369986 0.000060 lnL0 = -422.439119 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 422.439119 x= 0.43694 0.10325 0.11258 0.12741 0.09552 0.25292 0.36999 0.00006 1 h-lim-p 0.0000 0.0000 34.2970 422.412072 m 0.0000 22 | 1/8 2 h-lim-p 0.0001 0.0456 8.7165 422.149131 0 0.0086 40 | 1/8 3 h-lim-p 0.0046 0.0365 5.4680 422.100179 7 0.0032 70 | 1/8 4 h-lim-p 0.0067 0.0995 2.6504 422.029252 0 0.0133 83 | 1/8 5 h-lim-p 0.0084 0.0669 3.8281 421.807550 0 0.0167 96 | 1/8 6 h-lim-p 0.0126 0.1008 2.1619 420.825948 0 0.0504 110 | 1/8 7 h-lim-p 0.0020 0.0158 9.3884 420.333099 0 0.0079 124 | 1/8 8 h-lim-p 0.0427 0.3416 1.2467 420.318706 7 0.0136 152 | 1/8 9 h-lim-p 0.2458 7.1435 0.0690 420.176234 0 0.4917 165 | 0/8 10 h-lim-p 0.1249 3.1630 0.2718 420.175139 6 0.0171 198 | 0/8 11 h-lim-p 0.0298 0.2382 0.0361 420.164160 m 0.2382 218 | 1/8 12 h-lim-p 2.5000 20.0000 0.0020 420.162979 4 1.0660 248 | 1/8 13 h-lim-p 2.5000 20.0000 0.0004 420.162964 3 0.9482 273 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 420.162964 0 1.0938 292 | 1/8 15 h-lim-p 1.4723 20.0000 0.0000 420.162964 0 1.2882 311 | 0/8 16 h-lim-p 0.0000 0.0000 0.0004 h-lim-p: 6.21138089e-17 4.96910471e-16 4.09590335e-04 420.162964 .. | 1/8 17 h-lim-p 0.0000 20.0000 0.0016 420.162964 0 0.0051 355 | 1/8 18 h-lim-p 0.0125 20.0000 0.0007 420.162964 0 0.0055 374 | 1/8 19 h-lim-p 0.0118 20.0000 0.0003 420.162964 0 0.0052 393 | 1/8 20 h-lim-p 0.0108 20.0000 0.0001 420.162964 0 0.0000 422 | 1/8 21 h-lim-p 0.0000 20.0000 0.0001 420.162964 0 0.0051 450 | 1/8 22 h-lim-p 0.0343 20.0000 0.0000 420.162964 0 0.0150 469 | 1/8 23 h-lim-p 0.0203 20.0000 0.0000 420.162964 0 0.0003 493 | 1/8 24 h-lim-p 0.0005 20.0000 0.0000 420.162964 0 0.0670 519 | 1/8 25 h-lim-p 0.9256 20.0000 0.0000 420.162964 0 0.1157 540 | 1/8 26 h-lim-p 0.1308 20.0000 0.0000 420.162964 0 0.0327 560 | 1/8 27 h-lim-p 0.0338 20.0000 0.0000 420.162964 0 0.0032 582 Out... lnL = -420.162964 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -420.162964 Node 7: lnL = -420.162964 Node 8: lnL = -420.162964 Node 9: lnL = -420.162964 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 610 Sequential format.. Reading seq # 1: YMR257C_Sbay Reading seq # 2: YMR257C_Scer Reading seq # 3: YMR257C_Skud Reading seq # 4: YMR257C_Smik Reading seq # 5: YMR257C_Spar Sequences read.. Counting patterns.. # site patterns = 206 Counting frequencies.. 120 bytes for distance 32960 bytes for lkl0 26368 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.283713 0.167524 0.035632 0.172803 0.054268 0.260080 0.262769 0.000060 lnL0 = -2599.720560 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2599.720560 x= 0.28371 0.16752 0.03563 0.17280 0.05427 0.26008 0.26277 0.00006 1 h-lim-p 0.0000 0.0000 334.4241 2599.631845 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0002 370.2696 2594.160355 0 0.0001 37 | 1/8 3 h-lim-p 0.0003 0.0029 128.5397 2591.858265 8 0.0004 67 | 1/8 4 h-lim-p 0.0003 0.0021 84.4836 2591.035691 0 0.0004 79 | 1/8 5 h-lim-p 0.0036 0.0285 9.1460 2590.927553 6 0.0013 103 | 1/8 6 h-lim-p 0.0018 0.0538 6.9423 2590.538922 0 0.0035 116 | 1/8 7 h-lim-p 0.0082 0.0701 2.9720 2576.850417 0 0.0330 130 | 1/8 8 h-lim-p 0.0004 0.0035 103.1453 2566.744201 0 0.0009 143 | 1/8 9 h-lim-p 0.8506 6.8051 0.0384 2565.204570 6 0.8568 168 | 0/8 10 h-lim-p 0.0012 0.0188 26.6761 2564.937893 4 0.0010 195 | 0/8 11 h-lim-p 0.9980 7.9841 0.0253 2564.593560 6 0.6386 221 | 0/8 12 h-lim-p 1.0030 17.6278 0.0161 2564.500883 6 0.6634 254 | 0/8 13 h-lim-p 2.5000 20.0000 0.0031 2564.492822 5 0.9487 284 | 0/8 14 h-lim-p 2.5000 20.0000 0.0008 2564.492529 3 0.8855 312 | 0/8 15 h-lim-p 2.5000 20.0000 0.0002 2564.492515 2 0.6580 337 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 2564.492515 0 1.0938 357 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 2564.492515 0 1.0938 377 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 2564.492515 0 2.1875 397 | 0/8 19 h-lim-p 1.7254 20.0000 0.0000 2564.492515 0 0.8627 417 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 2564.492515 0 0.0000 466 Out... lnL = -2564.492515 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2564.492515 Node 7: lnL = -2564.492515 Node 8: lnL = -2564.492515 Node 9: lnL = -2564.492515 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 358 Sequential format.. Reading seq # 1: YMR258C_Sbay Reading seq # 2: YMR258C_Scer Reading seq # 3: YMR258C_Skud Reading seq # 4: YMR258C_Smik Reading seq # 5: YMR258C_Spar Sequences read.. Counting patterns.. # site patterns = 148 Counting frequencies.. 120 bytes for distance 23680 bytes for lkl0 18944 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.374091 0.214981 0.064263 0.230223 0.074646 0.324362 0.334286 0.000060 lnL0 = -1693.606487 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1693.606487 x= 0.37409 0.21498 0.06426 0.23022 0.07465 0.32436 0.33429 0.00006 1 h-lim-p 0.0000 0.0000 184.1594 1693.546317 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0009 214.2078 1686.684313 0 0.0005 39 | 1/8 3 h-lim-p 0.0004 0.0029 140.3742 1682.737117 0 0.0007 52 | 1/8 4 h-lim-p 0.0005 0.0042 36.2465 1682.308347 0 0.0010 65 | 1/8 5 h-lim-p 0.0055 0.0440 6.8975 1682.190454 3 0.0023 83 | 1/8 6 h-lim-p 0.0036 0.0711 4.3752 1681.172325 0 0.0145 97 | 1/8 7 h-lim-p 0.0049 0.0394 7.6476 1671.810177 0 0.0197 111 | 1/8 8 h-lim-p 0.0011 0.0088 47.1857 1666.547024 0 0.0033 124 | 1/8 9 h-lim-p 1.8069 14.4556 0.0601 1664.553642 6 0.8867 148 | 1/8 10 h-lim-p 1.6992 13.5939 0.0201 1663.897212 7 1.4531 180 | 1/8 11 h-lim-p 1.6882 20.0000 0.0173 1663.837256 7 0.6289 215 | 0/8 12 h-lim-p 0.0129 1.1422 0.8423 1663.836565 4 0.0022 245 | 0/8 13 h-lim-p 0.2674 20.0000 0.0070 1663.824334 0 0.5347 266 | 0/8 14 h-lim-p 2.3378 20.0000 0.0016 1663.823465 4 0.8574 296 | 0/8 15 h-lim-p 2.5000 20.0000 0.0002 1663.823451 2 0.7996 321 | 0/8 16 h-lim-p 2.5000 20.0000 0.0001 1663.823450 0 1.0938 341 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1663.823450 0 1.0938 361 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1663.823450 0 1.0938 381 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1663.823450 0 1.2500 401 | 0/8 20 h-lim-p 2.0799 20.0000 0.0000 1663.823450 0 0.1300 424 | 0/8 21 h-lim-p 0.0096 20.0000 0.0000 1663.823450 0 0.0024 445 Out... lnL = -1663.823450 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1663.823450 Node 7: lnL = -1663.823450 Node 8: lnL = -1663.823450 Node 9: lnL = -1663.823450 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 544 Sequential format.. Reading seq # 1: YMR259C_Sbay Reading seq # 2: YMR259C_Scer Reading seq # 3: YMR259C_Skud Reading seq # 4: YMR259C_Smik Reading seq # 5: YMR259C_Spar Sequences read.. Counting patterns.. # site patterns = 235 Counting frequencies.. 120 bytes for distance 37600 bytes for lkl0 30080 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.366624 0.131778 0.056278 0.144922 0.106648 0.227971 0.305092 0.000060 lnL0 = -2458.683545 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2458.683545 x= 0.36662 0.13178 0.05628 0.14492 0.10665 0.22797 0.30509 0.00006 1 h-lim-p 0.0000 0.0000 136.7096 2458.534371 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0065 71.1110 2457.484834 0 0.0005 39 | 1/8 3 h-lim-p 0.0014 0.0114 23.8551 2457.266940 8 0.0009 73 | 1/8 4 h-lim-p 0.0029 0.0310 7.0297 2457.243798 7 0.0008 102 | 1/8 5 h-lim-p 0.0016 0.1495 3.7035 2457.220777 1 0.0020 116 | 1/8 6 h-lim-p 0.0040 0.1717 1.8379 2457.102317 0 0.0081 129 | 1/8 7 h-lim-p 0.0093 0.1194 1.6027 2453.247313 0 0.0370 143 | 1/8 8 h-lim-p 0.0072 0.0574 6.8185 2453.209425 6 0.0016 168 | 1/8 9 h-lim-p 0.9465 20.0000 0.0115 2453.128539 6 0.6874 196 | 0/8 10 h-lim-p 0.0558 18.2886 0.1419 2453.128514 2 0.0018 223 | 0/8 11 h-lim-p 0.1071 3.5332 0.0024 2453.126177 0 0.6427 245 | 0/8 12 h-lim-p 0.3748 2.9983 0.0003 2453.126129 0 0.7496 266 | 0/8 13 h-lim-p 0.2149 1.7193 0.0001 2453.126128 0 0.6447 287 | 0/8 14 h-lim-p 0.0195 0.1559 0.0008 2453.126128 0 0.0000 321 | 0/8 15 h-lim-p 0.0000 0.1437 0.0009 2453.126128 0 0.0000 348 | 0/8 16 h-lim-p 0.0000 3.6735 0.0001 2453.126128 0 0.1638 382 | 0/8 17 h-lim-p 0.3830 20.0000 0.0000 2453.126128 0 0.0000 417 | 0/8 18 h-lim-p 0.0000 0.5267 0.0003 2453.126128 0 0.0000 438 | 0/8 19 h-lim-p 0.0000 0.0342 0.0039 2453.126128 0 0.0000 463 | 0/8 20 h-lim-p 0.0000 0.5079 0.0004 2453.126128 0 0.0410 495 | 0/8 21 h-lim-p 0.1876 20.0000 0.0001 2453.126128 0 0.3751 516 | 0/8 22 h-lim-p 0.0157 0.1255 0.0011 2453.126128 0 0.0000 550 | 0/8 23 h-lim-p 0.0000 0.0152 0.0089 2453.126128 0 0.0000 585 | 0/8 24 h-lim-p 0.0000 0.0043 0.0456 2453.126128 0 0.0003 610 | 0/8 25 h-lim-p 0.0001 0.0013 0.1036 2453.126128 0 0.0000 639 | 0/8 26 h-lim-p 0.0000 0.0000 10.4269 .. | 0/8 27 h-lim-p 0.0000 7.0218 0.0370 2453.126128 0 0.0003 687 | 0/8 28 h-lim-p 0.0005 0.0201 0.0257 2453.126128 0 0.0007 707 | 0/8 29 h-lim-p 0.0012 0.0236 0.0153 2453.126128 0 0.0000 743 | 0/8 30 h-lim-p 0.0000 20.0000 0.0056 2453.126128 0 0.0019 770 | 0/8 31 h-lim-p 0.0107 0.4411 0.0010 2453.126128 0 0.0000 806 | 0/8 32 h-lim-p 0.0000 0.9992 0.0005 .. | 0/8 33 h-lim-p 0.0000 0.0026 0.0455 2453.126128 0 0.0002 863 | 0/8 34 h-lim-p 0.0001 0.0007 0.1435 2453.126128 0 0.0000 898 | 0/8 35 h-lim-p 0.0000 0.0002 0.4822 2453.126128 0 0.0000 933 | 0/8 36 h-lim-p 0.0000 0.0022 0.0702 .. | 0/8 37 h-lim-p 0.0000 0.0025 0.0411 | 0/8 38 h-lim-p 0.0000 0.0025 0.0411 Out... lnL = -2453.126128 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2453.126128 Node 7: lnL = -2453.126128 Node 8: lnL = -2453.126128 Node 9: lnL = -2453.126128 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 390 Sequential format.. Reading seq # 1: YMR260C_Sbay Reading seq # 2: YMR260C_Scer Reading seq # 3: YMR260C_Skud Reading seq # 4: YMR260C_Smik Reading seq # 5: YMR260C_Spar Sequences read.. Counting patterns.. # site patterns = 137 Counting frequencies.. 120 bytes for distance 21920 bytes for lkl0 17536 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.235179 0.074203 0.079490 0.177930 0.075669 0.206349 0.197132 0.000060 lnL0 = -1544.641206 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1544.641206 x= 0.23518 0.07420 0.07949 0.17793 0.07567 0.20635 0.19713 0.00006 1 h-lim-p 0.0000 0.0000 234.2751 1544.563430 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0014 219.4063 1534.985589 0 0.0006 40 | 1/8 3 h-lim-p 0.0016 0.0130 18.1670 1534.797093 7 0.0011 71 | 1/8 4 h-lim-p 0.0050 0.0512 3.8761 1534.752909 4 0.0019 91 | 1/8 5 h-lim-p 0.0069 0.1744 1.0839 1531.504747 0 0.0550 106 | 1/8 6 h-lim-p 0.0009 0.0074 31.2503 1526.414901 0 0.0019 119 | 1/8 7 h-lim-p 0.0004 0.0031 84.4849 1524.408057 0 0.0008 132 | 1/8 8 h-lim-p 0.0028 0.0224 10.8491 1524.371523 2 0.0006 149 | 0/8 9 h-lim-p 0.0003 0.0218 22.1886 1524.197230 0 0.0012 163 | 0/8 10 h-lim-p 0.3277 2.6216 0.0688 1523.074543 0 0.6554 176 | 0/8 11 h-lim-p 2.3745 18.9959 0.0134 1522.925980 6 0.8055 211 | 0/8 12 h-lim-p 2.4529 20.0000 0.0044 1522.919898 5 0.5291 241 | 0/8 13 h-lim-p 2.1798 20.0000 0.0011 1522.919424 4 0.6699 272 | 0/8 14 h-lim-p 2.2335 20.0000 0.0003 1522.919392 3 0.7200 300 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1522.919391 1 0.9961 322 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1522.919391 0 1.0938 342 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1522.919391 0 1.0938 362 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1522.919391 0 2.1875 382 | 0/8 19 h-lim-p 1.6262 20.0000 0.0000 1522.919391 0 0.4065 403 | 0/8 20 h-lim-p 0.5865 20.0000 0.0000 1522.919391 0 0.0023 430 Out... lnL = -1522.919391 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1522.919391 Node 7: lnL = -1522.919391 Node 8: lnL = -1522.919391 Node 9: lnL = -1522.919391 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 374 Sequential format.. Reading seq # 1: YMR261C_Sbay Reading seq # 2: YMR261C_Scer Reading seq # 3: YMR261C_Skud Reading seq # 4: YMR261C_Smik Reading seq # 5: YMR261C_Spar Sequences read.. Counting patterns.. # site patterns = 130 Counting frequencies.. 120 bytes for distance 20800 bytes for lkl0 16640 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.259242 0.049404 0.062942 0.142057 0.063011 0.203522 0.187093 0.000060 lnL0 = -1510.666960 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1510.666960 x= 0.25924 0.04940 0.06294 0.14206 0.06301 0.20352 0.18709 0.00006 1 h-lim-p 0.0000 0.0000 153.9912 1510.575796 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0040 64.8618 1509.399624 0 0.0006 40 | 1/8 3 h-lim-p 0.0017 0.0138 14.9019 1509.326328 4 0.0007 60 | 1/8 4 h-lim-p 0.0023 0.0334 4.3811 1509.313725 5 0.0010 83 | 1/8 5 h-lim-p 0.0070 0.3608 0.5954 1509.097530 0 0.0280 97 | 1/8 6 h-lim-p 0.0023 0.0239 7.1102 1507.338904 0 0.0070 117 | 0/8 7 h-lim-p 0.0005 0.0041 36.7395 1505.887343 0 0.0010 130 | 0/8 8 h-lim-p 0.0003 0.0024 14.9125 1505.661000 m 0.0024 142 | 0/8 9 h-lim-p 0.0699 0.5591 0.3978 1505.660117 4 0.0027 169 | 0/8 10 h-lim-p 0.0002 0.0018 0.0611 1505.656571 m 0.0018 189 | 0/8 11 h-lim-p 0.0000 0.0000 0.0395 h-lim-p: 1.05577628e-21 8.44621023e-21 3.94669594e-02 1505.656571 .. | 0/8 12 h-lim-p 0.0000 0.0564 40.6386 1505.515107 0 0.0002 229 | 0/8 13 h-lim-p 0.0007 0.0134 9.2501 1505.498473 6 0.0004 256 | 0/8 14 h-lim-p 0.0023 0.1697 1.6368 1505.497971 4 0.0004 278 | 0/8 15 h-lim-p 0.0011 0.1390 0.5485 1505.497921 2 0.0004 296 | 0/8 16 h-lim-p 0.0010 1.4928 0.1962 1505.497883 0 0.0021 317 | 0/8 17 h-lim-p 0.0006 0.5029 0.6606 1505.497637 0 0.0050 340 | 0/8 18 h-lim-p 0.0006 0.0645 5.0845 1505.497084 0 0.0013 361 | 0/8 19 h-lim-p 0.1205 3.5140 0.0545 1505.497083 0 0.0008 379 | 0/8 20 h-lim-p 0.1320 20.0000 0.0003 1505.497079 0 1.0556 402 | 0/8 21 h-lim-p 2.5000 20.0000 0.0000 1505.497079 0 1.0938 422 | 0/8 22 h-lim-p 2.5000 20.0000 0.0000 1505.497079 0 0.0049 450 | 0/8 23 h-lim-p 0.0100 20.0000 0.0000 1505.497079 0 0.0025 471 Out... lnL = -1505.497079 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1505.497079 Node 7: lnL = -1505.497079 Node 8: lnL = -1505.497079 Node 9: lnL = -1505.497079 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 374 Sequential format.. Reading seq # 1: YMR262W_Sbay Reading seq # 2: YMR262W_Scer Reading seq # 3: YMR262W_Skud Reading seq # 4: YMR262W_Smik Reading seq # 5: YMR262W_Spar Sequences read.. Counting patterns.. # site patterns = 131 Counting frequencies.. 120 bytes for distance 20960 bytes for lkl0 16768 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.258215 0.045313 0.060024 0.139092 0.062595 0.202792 0.187959 0.000060 lnL0 = -1508.868105 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1508.868105 x= 0.25822 0.04531 0.06002 0.13909 0.06259 0.20279 0.18796 0.00006 1 h-lim-p 0.0000 0.0000 148.8834 1508.778445 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0041 58.6984 1507.805296 0 0.0007 40 | 1/8 3 h-lim-p 0.0019 0.0153 14.1423 1507.741656 7 0.0007 70 | 1/8 4 h-lim-p 0.0022 0.0323 4.2147 1507.730813 3 0.0009 88 | 1/8 5 h-lim-p 0.0059 0.3319 0.6496 1507.574825 0 0.0238 102 | 1/8 6 h-lim-p 0.0026 0.0211 6.0408 1506.533957 0 0.0051 122 | 0/8 7 h-lim-p 0.0007 0.0056 24.6094 1504.664049 0 0.0014 135 | 0/8 8 h-lim-p 0.0002 0.0014 19.1377 1504.359805 m 0.0014 147 | 0/8 9 h-lim-p -0.0000 -0.0000 2.2497 h-lim-p: -5.61617407e-19 -4.49293925e-18 2.24966732e+00 1504.359805 .. | 0/8 10 h-lim-p 0.0000 0.0040 15.0637 1504.331076 0 0.0003 172 | 0/8 11 h-lim-p 0.0014 0.0856 3.5440 1504.329012 4 0.0003 194 | 0/8 12 h-lim-p 0.0006 0.0450 2.0066 1504.328570 2 0.0003 210 | 0/8 13 h-lim-p 0.0021 0.0360 0.2799 1504.328547 3 0.0006 229 | 0/8 14 h-lim-p 0.0025 0.0516 0.0618 1504.328545 2 0.0008 254 | 0/8 15 h-lim-p 0.0033 5.6879 0.0150 1504.328516 0 0.0132 276 | 0/8 16 h-lim-p 0.0025 0.8853 0.0799 1504.327657 0 0.0099 298 | 0/8 17 h-lim-p 0.0012 0.0137 0.6819 1504.327093 2 0.0011 322 | 0/8 18 h-lim-p 2.5000 20.0000 0.0001 1504.327086 1 0.9961 344 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1504.327086 0 1.0938 364 | 0/8 20 h-lim-p 0.9949 20.0000 0.0000 1504.327086 014.4394 388 | 0/8 21 h-lim-p 0.0315 0.2523 0.0057 1504.327086 0 0.0000 417 | 0/8 22 h-lim-p 0.0002 1.5209 0.0009 1504.327086 0 0.0000 445 | 0/8 23 h-lim-p 0.0000 14.4750 0.0001 1504.327086 0 0.0000 479 | 0/8 24 h-lim-p 0.0000 5.1582 0.0018 1504.327086 0 0.0000 506 | 0/8 25 h-lim-p 0.0000 5.3137 0.0009 1504.327086 0 0.0010 532 | 0/8 26 h-lim-p 0.0041 14.4982 0.0002 1504.327086 0 0.0004 554 | 0/8 27 h-lim-p 0.0012 20.0000 0.0001 1504.327086 0 0.0023 575 | 0/8 28 h-lim-p 0.0005 3.6950 0.0004 1504.327086 0 0.0000 607 | 0/8 29 h-lim-p 0.0000 0.0546 0.0272 1504.327086 0 0.0000 636 | 0/8 30 h-lim-p 0.0000 0.6035 0.0025 1504.327086 0 0.0000 667 | 0/8 31 h-lim-p 0.0000 20.0000 0.0033 | 0/8 32 h-lim-p 0.0000 20.0000 0.0033 Out... lnL = -1504.327086 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1504.327086 Node 7: lnL = -1504.327086 Node 8: lnL = -1504.327086 Node 9: lnL = -1504.327086 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 290 Sequential format.. Reading seq # 1: YMR263W_Sbay Reading seq # 2: YMR263W_Scer Reading seq # 3: YMR263W_Skud Reading seq # 4: YMR263W_Smik Reading seq # 5: YMR263W_Spar Sequences read.. Counting patterns.. # site patterns = 128 Counting frequencies.. 120 bytes for distance 20480 bytes for lkl0 16384 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.318828 0.070423 0.048043 0.134242 0.080483 0.137887 0.150434 0.000580 lnL0 = -1142.687429 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1142.687429 x= 0.31883 0.07042 0.04804 0.13424 0.08048 0.13789 0.15043 0.00058 1 h-lim-p 0.0014 0.0113 69.0488 1141.634620 9 0.0005 46 | 0/8 2 h-lim-p 0.0012 0.0093 20.3614 1141.475413 8 0.0008 79 | 0/8 3 h-lim-p 0.0025 0.0333 6.6927 1141.460711 5 0.0007 104 | 0/8 4 h-lim-p 0.0020 0.0727 2.4974 1141.458062 3 0.0010 122 | 0/8 5 h-lim-p 0.0067 0.4303 0.3660 1141.458002 3 0.0009 142 | 0/8 6 h-lim-p 0.0059 0.3361 0.0559 1141.458000 0 0.0013 163 | 0/8 7 h-lim-p 0.0142 13.5150 0.0050 1141.458000 0 0.0031 184 | 0/8 8 h-lim-p 0.0513 20.0000 0.0003 1141.457979 0 0.4106 207 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1141.457978 0 1.0938 227 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1141.457978 0 1.0938 247 | 0/8 11 h-lim-p 1.0469 20.0000 0.0000 1141.457978 0 3.1406 268 | 0/8 12 h-lim-p 1.3783 20.0000 0.0000 1141.457978 0 1.2060 288 | 0/8 13 h-lim-p 0.0337 19.6915 0.0008 1141.457978 0 0.0001 316 | 0/8 14 h-lim-p 0.0000 0.0670 0.2408 1141.457978 0 0.0000 336 | 0/8 15 h-lim-p 0.0006 7.6886 0.0021 1141.457978 0 0.0000 374 | 0/8 16 h-lim-p 0.0000 20.0000 0.0005 1141.457978 0 0.0000 400 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 1141.457978 0 0.0000 435 | 0/8 18 h-lim-p 0.0000 20.0000 0.0005 | 0/8 19 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -1141.457978 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1141.457978 Node 7: lnL = -1141.457978 Node 8: lnL = -1141.457978 Node 9: lnL = -1141.457978 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 299 Sequential format.. Reading seq # 1: YMR264W_Sbay Reading seq # 2: YMR264W_Scer Reading seq # 3: YMR264W_Skud Reading seq # 4: YMR264W_Smik Reading seq # 5: YMR264W_Spar Sequences read.. Counting patterns.. # site patterns = 108 Counting frequencies.. 120 bytes for distance 17280 bytes for lkl0 13824 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.305827 0.035258 0.014678 0.086656 0.065459 0.166541 0.228370 0.008053 lnL0 = -1258.078260 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1258.078260 x= 0.30583 0.03526 0.01468 0.08666 0.06546 0.16654 0.22837 0.00805 1 h-lim-p 0.0019 0.0155 100.3960 1257.334876 7 0.0002 39 | 0/8 2 h-lim-p 0.0006 0.0048 23.0662 1257.197408 2 0.0006 55 | 0/8 3 h-lim-p 0.0017 0.0468 7.5506 1257.179911 4 0.0007 75 | 0/8 4 h-lim-p 0.0011 0.0320 4.8449 1257.175990 4 0.0005 94 | 0/8 5 h-lim-p 0.0023 0.1006 0.9585 1257.175431 4 0.0013 116 | 0/8 6 h-lim-p 0.0147 0.3439 0.0850 1257.175426 2 0.0010 143 | 0/8 7 h-lim-p 0.0023 0.7723 0.0365 1257.175424 1 0.0018 165 | 0/8 8 h-lim-p 0.0387 20.0000 0.0017 1257.174382 0 0.4639 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1257.174380 0 1.0938 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1257.174380 0 1.2500 228 | 0/8 11 h-lim-p 1.4662 20.0000 0.0000 1257.174380 0 0.1833 250 | 0/8 12 h-lim-p 0.0780 20.0000 0.0000 1257.174380 0 0.0043 273 | 0/8 13 h-lim-p 0.0024 20.0000 0.0000 1257.174380 0 0.0000 305 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 1257.174380 0 0.0000 337 Out... lnL = -1257.174380 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1257.174380 Node 7: lnL = -1257.174380 Node 8: lnL = -1257.174380 Node 9: lnL = -1257.174380 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 635 Sequential format.. Reading seq # 1: YMR265C_Sbay Reading seq # 2: YMR265C_Scer Reading seq # 3: YMR265C_Skud Reading seq # 4: YMR265C_Smik Reading seq # 5: YMR265C_Spar Sequences read.. Counting patterns.. # site patterns = 187 Counting frequencies.. 120 bytes for distance 29920 bytes for lkl0 23936 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.247479 0.024765 0.065076 0.060074 0.050690 0.137666 0.165899 0.000060 lnL0 = -2493.616009 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2493.616009 x= 0.24748 0.02477 0.06508 0.06007 0.05069 0.13767 0.16590 0.00006 1 h-lim-p 0.0003 0.0021 186.9114 2491.333100 9 0.0001 43 | 0/8 2 h-lim-p 0.0006 0.0051 29.0775 2491.202722 3 0.0003 61 | 0/8 3 h-lim-p 0.0005 0.0210 17.6591 2491.186794 4 0.0001 82 | 0/8 4 h-lim-p 0.0006 0.0207 4.0420 2491.185407 4 0.0002 104 | 0/8 5 h-lim-p 0.0005 0.0175 1.5980 2491.185042 3 0.0003 123 | 0/8 6 h-lim-p 0.0012 0.0419 0.4326 2491.185008 2 0.0004 141 | 0/8 7 h-lim-p 0.0006 0.0461 0.2993 2491.184519 0 0.0185 166 | 0/8 8 h-lim-p 0.0002 0.0016 5.4420 2491.184128 0 0.0008 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0015 2491.184090 2 0.9961 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2491.184090 0 1.0938 224 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2491.184090 0 2.5000 244 | 0/8 12 h-lim-p 2.0965 20.0000 0.0000 2491.184090 0 0.1310 267 | 0/8 13 h-lim-p 0.1919 20.0000 0.0000 2491.184090 0 0.0007 294 Out... lnL = -2491.184090 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2491.184090 Node 7: lnL = -2491.184090 Node 8: lnL = -2491.184090 Node 9: lnL = -2491.184090 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 620 Sequential format.. Reading seq # 1: YMR266W_Sbay Reading seq # 2: YMR266W_Scer Reading seq # 3: YMR266W_Skud Reading seq # 4: YMR266W_Smik Reading seq # 5: YMR266W_Spar Sequences read.. Counting patterns.. # site patterns = 171 Counting frequencies.. 120 bytes for distance 27360 bytes for lkl0 21888 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.242942 0.021114 0.061013 0.075577 0.049293 0.152734 0.182165 0.000060 lnL0 = -2430.647843 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2430.647843 x= 0.24294 0.02111 0.06101 0.07558 0.04929 0.15273 0.18216 0.00006 1 h-lim-p 0.0001 0.0008 173.7231 2428.633495 0 0.0001 22 | 0/8 2 h-lim-p 0.0005 0.0044 46.6530 2428.415977 4 0.0002 42 | 0/8 3 h-lim-p 0.0003 0.0043 31.3101 2428.342062 4 0.0002 64 | 0/8 4 h-lim-p 0.0007 0.0126 9.0874 2428.336184 2 0.0002 81 | 0/8 5 h-lim-p 0.0005 0.0039 2.7294 2428.334958 4 0.0004 101 | 0/8 6 h-lim-p 0.0010 0.0102 1.0016 2428.334843 3 0.0003 120 | 0/8 7 h-lim-p 0.0009 0.0091 0.3071 2428.334167 m 0.0091 133 | 1/8 8 h-lim-p 0.0141 0.5135 0.1582 2428.332600 3 0.0059 159 | 1/8 9 h-lim-p 0.4417 20.0000 0.0021 2428.327712 0 0.8834 179 | 0/8 10 h-lim-p 0.0015 0.3341 1.2634 2428.327083 4 0.0008 209 | 0/8 11 h-lim-p 0.2611 2.0887 0.0010 2428.326819 0 0.7833 222 | 0/8 12 h-lim-p 2.5000 20.0000 0.0001 2428.326807 2 0.9644 246 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2428.326807 0 1.0938 266 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 2428.326807 0 1.0938 286 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2428.326807 0 0.1562 309 | 0/8 16 h-lim-p 0.0486 20.0000 0.0000 2428.326807 0 0.0008 334 Out... lnL = -2428.326807 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2428.326807 Node 7: lnL = -2428.326807 Node 8: lnL = -2428.326807 Node 9: lnL = -2428.326807 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 450 Sequential format.. Reading seq # 1: YMR267W_Sbay Reading seq # 2: YMR267W_Scer Reading seq # 3: YMR267W_Skud Reading seq # 4: YMR267W_Smik Reading seq # 5: YMR267W_Spar Sequences read.. Counting patterns.. # site patterns = 209 Counting frequencies.. 120 bytes for distance 33440 bytes for lkl0 26752 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.436363 0.064721 0.066404 0.149070 0.108737 0.257955 0.438786 0.000060 lnL0 = -2009.772960 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2009.772960 x= 0.43636 0.06472 0.06640 0.14907 0.10874 0.25796 0.43879 0.00006 1 h-lim-p 0.0000 0.0000 146.7824 2009.273314 m 0.0000 22 | 1/8 2 h-lim-p 0.0001 0.0064 42.5593 2008.517008 0 0.0013 38 | 1/8 3 h-lim-p 0.0030 0.0237 11.1008 2008.444277 4 0.0012 58 | 1/8 4 h-lim-p 0.0024 0.0453 5.3306 2008.418615 7 0.0015 91 | 1/8 5 h-lim-p 0.0028 0.1778 2.7509 2008.297720 0 0.0114 105 | 1/8 6 h-lim-p 0.0142 0.1140 1.4386 2007.407366 0 0.0285 118 | 0/8 7 h-lim-p 0.0017 0.0135 16.1673 2005.112990 0 0.0034 131 | 0/8 8 h-lim-p 0.0002 0.0017 23.1498 2004.232735 m 0.0017 143 | 1/8 9 h-lim-p 0.1546 1.2367 0.1071 2004.228077 4 0.0303 164 | 1/8 10 h-lim-p 0.0219 1.4373 0.1482 2004.124451 0 0.1751 186 | 1/8 11 h-lim-p 2.5000 20.0000 0.0049 2004.117427 6 0.8692 221 | 1/8 12 h-lim-p 1.4240 20.0000 0.0030 2004.116371 3 0.7654 247 | 1/8 13 h-lim-p 2.5000 20.0000 0.0005 2004.116312 2 0.6580 271 | 1/8 14 h-lim-p 2.2077 20.0000 0.0001 2004.116307 1 0.8796 292 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 2004.116307 0 1.0938 311 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 2004.116307 0 1.0938 330 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 2004.116307 0 0.5469 350 | 1/8 18 h-lim-p 1.2042 20.0000 0.0000 2004.116307 0 0.0165 374 Out... lnL = -2004.116307 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2004.116307 Node 7: lnL = -2004.116307 Node 8: lnL = -2004.116307 Node 9: lnL = -2004.116307 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 460 Sequential format.. Reading seq # 1: YMR268C_Sbay Reading seq # 2: YMR268C_Scer Reading seq # 3: YMR268C_Skud Reading seq # 4: YMR268C_Smik Reading seq # 5: YMR268C_Spar Sequences read.. Counting patterns.. # site patterns = 144 Counting frequencies.. 120 bytes for distance 23040 bytes for lkl0 18432 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.228305 0.037422 0.024238 0.131224 0.078312 0.176732 0.152758 0.000060 lnL0 = -1832.986995 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1832.986995 x= 0.22830 0.03742 0.02424 0.13122 0.07831 0.17673 0.15276 0.00006 1 h-lim-p 0.0000 0.0000 117.0238 1832.857667 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0027 89.0924 1832.102453 0 0.0003 38 | 1/8 3 h-lim-p 0.0003 0.0026 29.2691 1832.014999 7 0.0002 67 | 1/8 4 h-lim-p 0.0008 0.0379 8.2957 1832.002916 5 0.0004 88 | 1/8 5 h-lim-p 0.0011 0.0386 2.7445 1832.000298 2 0.0005 104 | 1/8 6 h-lim-p 0.0079 1.3874 0.1821 1831.809182 0 0.0947 119 | 0/8 7 h-lim-p 0.0011 0.0089 9.7517 1830.591113 0 0.0044 140 | 0/8 8 h-lim-p 0.0004 0.0032 13.2610 1830.552433 4 0.0004 160 | 0/8 9 h-lim-p 0.0020 0.0161 2.1975 1830.520482 m 0.0161 172 | 1/8 10 h-lim-p 0.5609 5.0790 0.0451 1830.485195 4 0.1428 193 | 0/8 11 h-lim-p 0.0007 0.0372 9.6748 1830.398140 0 0.0027 214 | 0/8 12 h-lim-p 0.1100 0.8796 0.0338 1830.380695 0 0.6597 228 | 0/8 13 h-lim-p 2.5000 20.0000 0.0054 1830.380076 4 0.8228 257 | 0/8 14 h-lim-p 2.5000 20.0000 0.0004 1830.380045 2 0.7996 282 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1830.380045 0 1.0938 302 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1830.380045 0 2.1875 322 | 0/8 17 h-lim-p 2.0793 20.0000 0.0000 1830.380045 0 0.9097 342 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1830.380045 0 0.0000 387 Out... lnL = -1830.380045 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1830.380045 Node 7: lnL = -1830.380045 Node 8: lnL = -1830.380045 Node 9: lnL = -1830.380045 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 481 Sequential format.. Reading seq # 1: YMR270C_Sbay Reading seq # 2: YMR270C_Scer Reading seq # 3: YMR270C_Skud Reading seq # 4: YMR270C_Smik Reading seq # 5: YMR270C_Spar Sequences read.. Counting patterns.. # site patterns = 190 Counting frequencies.. 120 bytes for distance 30400 bytes for lkl0 24320 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.411747 0.034636 0.081149 0.156936 0.082016 0.246352 0.360777 0.000060 lnL0 = -2235.687363 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2235.687363 x= 0.41175 0.03464 0.08115 0.15694 0.08202 0.24635 0.36078 0.00006 1 h-lim-p 0.0001 0.0009 129.3978 2232.688448 0 0.0003 23 | 0/8 2 h-lim-p 0.0000 0.0000 44.9904 2232.624777 m 0.0000 35 | 1/8 3 h-lim-p 0.0001 0.0248 17.0912 2232.491089 0 0.0015 51 | 1/8 4 h-lim-p 0.0029 0.0415 9.0650 2232.460163 6 0.0010 78 | 1/8 5 h-lim-p 0.0016 0.1252 5.5475 2232.450264 6 0.0009 105 | 1/8 6 h-lim-p 0.0048 0.0890 1.0215 2232.449656 5 0.0007 131 | 0/8 7 h-lim-p 0.0002 0.1801 3.7553 2232.431929 0 0.0030 147 | 0/8 8 h-lim-p 0.0029 0.1700 3.9474 2232.413600 1 0.0036 161 | 0/8 9 h-lim-p 0.1292 1.0333 0.0415 2232.100049 0 0.5166 175 | 0/8 10 h-lim-p 0.1585 1.2682 0.0194 2232.085831 0 0.2378 195 | 0/8 11 h-lim-p 1.5455 20.0000 0.0030 2232.079540 6 0.9554 230 | 0/8 12 h-lim-p 2.5000 20.0000 0.0002 2232.079517 2 0.9961 254 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2232.079517 0 1.0938 274 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 2232.079517 0 1.0938 294 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2232.079517 0 3.7500 314 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 2232.079517 0 0.1367 337 | 0/8 17 h-lim-p 0.0264 20.0000 0.0000 2232.079517 0 0.0132 357 Out... lnL = -2232.079517 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2232.079517 Node 7: lnL = -2232.079517 Node 8: lnL = -2232.079517 Node 9: lnL = -2232.079517 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 495 Sequential format.. Reading seq # 1: YMR272C_Sbay Reading seq # 2: YMR272C_Scer Reading seq # 3: YMR272C_Skud Reading seq # 4: YMR272C_Smik Reading seq # 5: YMR272C_Spar Sequences read.. Counting patterns.. # site patterns = 147 Counting frequencies.. 120 bytes for distance 23520 bytes for lkl0 18816 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.241711 0.060744 0.013375 0.060345 0.038913 0.116094 0.131715 0.014403 lnL0 = -1817.007872 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1817.007872 x= 0.24171 0.06074 0.01338 0.06034 0.03891 0.11609 0.13171 0.01440 1 h-lim-p 0.0009 0.5692 195.7622 1815.423225 3 0.0001 30 | 0/8 2 h-lim-p 0.0004 0.0034 49.6146 1815.101116 8 0.0003 63 | 0/8 3 h-lim-p 0.0006 0.0131 22.5117 1815.065952 6 0.0002 88 | 0/8 4 h-lim-p 0.0004 0.0185 9.7826 1815.052289 3 0.0004 106 | 0/8 5 h-lim-p 0.0009 0.0513 4.0033 1815.050801 4 0.0002 127 | 0/8 6 h-lim-p 0.0019 0.3198 0.4771 1815.050750 1 0.0005 142 | 0/8 7 h-lim-p 0.0025 0.5250 0.0912 1815.050748 1 0.0005 165 | 0/8 8 h-lim-p 0.3695 20.0000 0.0001 1815.050700 0 1.4779 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1815.050694 0 1.0938 207 | 0/8 10 h-lim-p 2.4993 20.0000 0.0000 1815.050694 0 2.1869 227 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1815.050694 0 1.0938 247 | 0/8 12 h-lim-p 0.2259 20.0000 0.0000 1815.050694 0 3.6151 271 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1815.050694 0 0.5469 292 | 0/8 14 h-lim-p 0.1244 20.0000 0.0000 1815.050694 0 0.0000 329 | 0/8 15 h-lim-p 0.0000 20.0000 0.0038 1815.050694 0 0.0000 355 | 0/8 16 h-lim-p 0.0000 20.0000 0.0007 1815.050694 0 0.0010 381 | 0/8 17 h-lim-p 0.0014 20.0000 0.0005 1815.050694 0 0.0000 410 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 1815.050694 0 0.0000 430 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 1815.050694 0 0.0000 450 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 1815.050694 0 0.0000 473 | 0/8 21 h-lim-p 0.0000 10.3746 0.0031 1815.050694 0 0.0000 504 | 0/8 22 h-lim-p 0.0000 20.0000 0.0001 1815.050694 0 0.0000 526 | 0/8 23 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 24 h-lim-p 0.0000 20.0000 0.0055 | 0/8 25 h-lim-p 0.0000 20.0000 0.0055 Out... lnL = -1815.050694 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1815.050694 Node 7: lnL = -1815.050694 Node 8: lnL = -1815.050694 Node 9: lnL = -1815.050694 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 402 Sequential format.. Reading seq # 1: YMR273C_Sbay Reading seq # 2: YMR273C_Scer Reading seq # 3: YMR273C_Skud Reading seq # 4: YMR273C_Smik Reading seq # 5: YMR273C_Spar Sequences read.. Counting patterns.. # site patterns = 109 Counting frequencies.. 120 bytes for distance 17440 bytes for lkl0 13952 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.202175 0.056730 0.051238 0.082126 0.050304 0.087301 0.114132 0.000060 lnL0 = -1455.695240 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1455.695240 x= 0.20217 0.05673 0.05124 0.08213 0.05030 0.08730 0.11413 0.00006 1 h-lim-p 0.0000 0.0000 127.0799 1455.491528 m 0.0000 22 | 1/8 2 h-lim-p 0.0001 0.0102 26.5988 1455.416511 0 0.0002 36 | 1/8 3 h-lim-p 0.0009 0.0192 6.8928 1455.408848 6 0.0003 61 | 1/8 4 h-lim-p 0.0011 0.1474 1.8833 1455.402949 0 0.0017 73 | 1/8 5 h-lim-p 0.0025 0.0668 1.3166 1455.381474 0 0.0037 85 | 1/8 6 h-lim-p 0.0013 0.0452 3.7900 1455.223675 0 0.0026 98 | 1/8 7 h-lim-p 0.0009 0.0070 7.5097 1454.369839 0 0.0026 111 | 1/8 8 h-lim-p 0.0003 0.0023 42.5142 1453.833972 0 0.0004 123 | 1/8 9 h-lim-p 2.5000 20.0000 0.0056 1453.788499 6 0.6876 150 | 1/8 10 h-lim-p 2.5000 20.0000 0.0007 1453.787839 3 0.8059 177 | 1/8 11 h-lim-p 2.5000 20.0000 0.0001 1453.787831 2 0.7996 201 | 0/8 12 h-lim-p 0.1231 20.0000 0.0006 1453.787831 0 0.0067 223 | 0/8 13 h-lim-p 0.1145 0.9163 0.0000 1453.787831 0 0.4581 245 | 0/8 14 h-lim-p 0.0328 0.2626 0.0000 1453.787831 0 0.1313 267 | 1/8 15 h-lim-p 0.1246 20.0000 0.0000 1453.787831 0 0.2492 288 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 1453.787831 0 2.1875 307 | 1/8 17 h-lim-p 1.9972 20.0000 0.0000 1453.787831 0 0.2184 328 | 1/8 18 h-lim-p 0.2736 20.0000 0.0000 1453.787831 0 0.0005 355 Out... lnL = -1453.787831 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1453.787831 Node 7: lnL = -1453.787831 Node 8: lnL = -1453.787831 Node 9: lnL = -1453.787831 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 365 Sequential format.. Reading seq # 1: YMR274C_Sbay Reading seq # 2: YMR274C_Scer Reading seq # 3: YMR274C_Skud Reading seq # 4: YMR274C_Smik Reading seq # 5: YMR274C_Spar Sequences read.. Counting patterns.. # site patterns = 141 Counting frequencies.. 120 bytes for distance 22560 bytes for lkl0 18048 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.298688 0.084594 0.081634 0.073930 0.066101 0.157959 0.202402 0.000060 lnL0 = -1488.573659 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1488.573659 x= 0.29869 0.08459 0.08163 0.07393 0.06610 0.15796 0.20240 0.00006 1 h-lim-p 0.0000 0.0000 86.1736 1488.352496 m 0.0000 22 | 1/8 2 h-lim-p 0.0001 0.0050 42.8238 1488.095633 0 0.0005 37 | 1/8 3 h-lim-p 0.0020 0.0160 10.4710 1488.063448 7 0.0006 68 | 1/8 4 h-lim-p 0.0022 0.0782 2.8979 1488.057430 2 0.0010 84 | 1/8 5 h-lim-p 0.0018 0.1078 1.6935 1488.047552 0 0.0036 97 | 1/8 6 h-lim-p 0.0046 0.0706 1.3005 1487.966745 0 0.0093 110 | 1/8 7 h-lim-p 0.0049 0.0457 2.4636 1486.597427 0 0.0147 123 | 0/8 8 h-lim-p 0.0050 0.0465 7.2789 1486.575131 6 0.0008 150 | 0/8 9 h-lim-p 0.0023 0.0184 0.3274 1486.573111 m 0.0184 162 | 0/8 10 h-lim-p -0.0000 -0.0000 0.0122 h-lim-p: -7.89370643e-18 -6.31496514e-17 1.22138732e-02 1486.573111 .. | 0/8 11 h-lim-p 0.0000 0.0122 11.8975 1486.548977 0 0.0003 203 | 0/8 12 h-lim-p 0.0015 0.0999 2.4737 1486.546069 4 0.0010 225 | 0/8 13 h-lim-p 0.0010 0.0076 0.8814 1486.545934 3 0.0004 243 | 0/8 14 h-lim-p 0.0008 0.0063 0.2580 1486.545924 0 0.0003 263 | 0/8 15 h-lim-p 0.0007 0.0097 0.1191 1486.545921 1 0.0004 286 | 0/8 16 h-lim-p 0.0011 0.0167 0.0389 1486.545921 0 0.0010 306 | 0/8 17 h-lim-p 0.0011 0.0088 0.0190 1486.545921 0 0.0000 348 | 0/8 18 h-lim-p 0.0000 0.0155 0.8709 1486.545795 0 0.0003 373 | 0/8 19 h-lim-p 0.0008 0.0062 0.0703 1486.545793 0 0.0007 393 | 0/8 20 h-lim-p 0.0004 0.0028 0.0959 1486.545793 0 0.0003 413 | 0/8 21 h-lim-p 0.0004 0.0029 0.0558 1486.545793 0 0.0000 448 | 0/8 22 h-lim-p 0.0000 0.0000 314.6325 .. | 0/8 23 h-lim-p 0.0000 3.4353 0.0429 1486.545793 0 0.0005 491 | 0/8 24 h-lim-p 0.0007 0.0152 0.0286 1486.545793 0 0.0003 511 | 0/8 25 h-lim-p 0.0003 0.0093 0.0314 1486.545793 0 0.0000 546 | 0/8 26 h-lim-p 0.0000 0.0887 0.0212 1486.545793 0 0.0003 571 | 0/8 27 h-lim-p 0.0011 20.0000 0.0060 1486.545793 0 0.0010 591 | 0/8 28 h-lim-p 0.0021 0.1732 0.0028 1486.545793 0 0.0000 626 | 0/8 29 h-lim-p 0.0000 1.3880 0.0004 1486.545793 0 0.0000 654 | 0/8 30 h-lim-p 0.0000 0.1854 0.0015 1486.545793 0 0.0102 684 | 0/8 31 h-lim-p 0.0002 0.0025 0.0704 1486.545793 0 0.0000 720 | 0/8 32 h-lim-p 0.0000 0.1359 0.0013 1486.545793 0 0.0000 750 | 0/8 33 h-lim-p 0.0000 0.0030 0.0421 1486.545793 0 0.0002 774 | 0/8 34 h-lim-p 0.0001 0.0010 0.1207 1486.545793 0 0.0000 810 | 0/8 35 h-lim-p 0.0000 0.0001 2.0394 .. | 0/8 36 h-lim-p 0.0000 3.6244 0.0216 1486.545793 0 0.0001 858 | 0/8 37 h-lim-p 0.0000 0.0039 0.0571 1486.545793 0 0.0000 885 | 0/8 38 h-lim-p 0.0000 20.0000 0.0044 1486.545793 0 0.0010 911 | 0/8 39 h-lim-p 0.0012 0.5348 0.0035 1486.545793 0 0.0001 933 | 0/8 40 h-lim-p 0.0003 1.8037 0.0014 1486.545793 0 0.0000 962 | 0/8 41 h-lim-p 0.0000 2.6144 0.0005 1486.545793 0 0.0000 986 | 0/8 42 h-lim-p 0.0000 20.0000 0.0007 1486.545793 0 0.0051 1015 | 0/8 43 h-lim-p 0.0192 3.5096 0.0002 1486.545793 0 0.0000 1047 | 0/8 44 h-lim-p 0.0000 0.1793 0.0011 1486.545793 0 0.0003 1072 | 0/8 45 h-lim-p 0.0310 13.8661 0.0000 1486.545793 0 0.0001 1100 | 0/8 46 h-lim-p 0.0000 9.0881 0.0000 1486.545793 0 0.0000 1136 | 0/8 47 h-lim-p 0.0000 0.0028 0.0396 1486.545793 0 0.0001 1158 | 0/8 48 h-lim-p 0.0000 0.0007 0.1792 1486.545793 0 0.0000 1189 | 0/8 49 h-lim-p 0.0000 0.0001 1.9062 1486.545793 0 0.0000 1220 | 0/8 50 h-lim-p 0.0000 0.0708 0.0071 1486.545793 0 0.0000 1241 | 0/8 51 h-lim-p 0.0000 0.0000 171053.9892 .. | 0/8 52 h-lim-p 0.0000 0.0938 0.0158 | 0/8 53 h-lim-p 0.0000 0.0028 0.0387 Out... lnL = -1486.545793 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1486.545793 Node 7: lnL = -1486.545793 Node 8: lnL = -1486.545793 Node 9: lnL = -1486.545793 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 254 Sequential format.. Reading seq # 1: YMR275C_Sbay Reading seq # 2: YMR275C_Scer Reading seq # 3: YMR275C_Skud Reading seq # 4: YMR275C_Smik Reading seq # 5: YMR275C_Spar Sequences read.. Counting patterns.. # site patterns = 103 Counting frequencies.. 120 bytes for distance 16480 bytes for lkl0 13184 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.294120 0.163096 0.141819 0.090665 0.102822 0.133523 0.251082 0.000060 lnL0 = -1120.610936 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1120.610936 x= 0.29412 0.16310 0.14182 0.09066 0.10282 0.13352 0.25108 0.00006 1 h-lim-p 0.0000 0.0000 159.8858 1120.559107 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0014 156.9697 1114.840127 0 0.0006 40 | 1/8 3 h-lim-p 0.0002 0.0019 79.2495 1113.658556 0 0.0005 53 | 1/8 4 h-lim-p 0.0005 0.0036 37.5183 1113.356545 0 0.0007 65 | 1/8 5 h-lim-p 0.0026 0.0208 6.4356 1113.236738 1 0.0033 79 | 1/8 6 h-lim-p 0.0023 0.0184 5.8066 1113.124178 5 0.0024 101 | 1/8 7 h-lim-p 0.0046 0.0973 3.0607 1108.708215 0 0.0367 116 | 0/8 8 h-lim-p 0.0011 0.0088 37.1529 1103.927714 0 0.0044 130 | 0/8 9 h-lim-p 0.0049 0.0390 4.7301 1103.563186 m 0.0390 142 | 1/8 10 h-lim-p 0.1386 1.1086 0.2097 1102.454220 0 0.2079 154 | 0/8 11 h-lim-p 0.0016 0.0152 27.1907 1101.775104 0 0.0032 174 | 0/8 12 h-lim-p 0.1593 1.2744 0.0834 1101.503818 0 0.6372 188 | 0/8 13 h-lim-p 0.3702 2.9616 0.0184 1101.447412 0 0.7404 209 | 0/8 14 h-lim-p 0.2727 2.1817 0.0183 1101.438449 0 1.0908 231 | 0/8 15 h-lim-p 2.5000 20.0000 0.0037 1101.435972 4 0.9932 259 | 0/8 16 h-lim-p 2.5000 20.0000 0.0006 1101.435823 2 1.1719 283 | 0/8 17 h-lim-p 2.5000 20.0000 0.0003 1101.435811 2 1.3159 308 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1101.435810 1 1.2305 331 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1101.435810 0 1.0938 351 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 1101.435810 0 0.6250 372 | 0/8 21 h-lim-p 0.6843 20.0000 0.0000 1101.435810 0 0.0027 399 | 0/8 22 h-lim-p 0.0018 20.0000 0.0000 1101.435810 0 0.0000 440 Out... lnL = -1101.435810 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1101.435810 Node 7: lnL = -1101.435810 Node 8: lnL = -1101.435810 Node 9: lnL = -1101.435810 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 254 Sequential format.. Reading seq # 1: YMR276W_Sbay Reading seq # 2: YMR276W_Scer Reading seq # 3: YMR276W_Skud Reading seq # 4: YMR276W_Smik Reading seq # 5: YMR276W_Spar Sequences read.. Counting patterns.. # site patterns = 104 Counting frequencies.. 120 bytes for distance 16640 bytes for lkl0 13312 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.295742 0.161285 0.142256 0.091852 0.101950 0.135083 0.248117 0.000060 lnL0 = -1120.951151 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1120.951151 x= 0.29574 0.16128 0.14226 0.09185 0.10195 0.13508 0.24812 0.00006 1 h-lim-p 0.0000 0.0000 158.9816 1120.898741 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0016 142.3711 1115.556206 0 0.0006 40 | 1/8 3 h-lim-p 0.0003 0.0023 71.9899 1114.367922 0 0.0006 53 | 1/8 4 h-lim-p 0.0006 0.0046 31.5576 1114.109878 7 0.0006 83 | 1/8 5 h-lim-p 0.0019 0.0149 8.4357 1113.990892 0 0.0028 95 | 1/8 6 h-lim-p 0.0023 0.0182 6.6085 1113.880877 4 0.0023 115 | 1/8 7 h-lim-p 0.0086 0.1777 1.7894 1107.832031 0 0.0690 130 | 0/8 8 h-lim-p 0.0010 0.0078 45.3204 1104.111202 0 0.0019 143 | 0/8 9 h-lim-p 0.0126 0.1007 0.6293 1103.620383 m 0.1007 155 | 1/8 10 h-lim-p 0.0079 0.0634 3.4095 1103.586481 7 0.0028 193 | 0/8 11 h-lim-p 0.0011 0.0360 8.4779 1103.261442 0 0.0177 209 | 0/8 12 h-lim-p 0.0679 0.5435 0.2815 1102.189224 m 0.5435 221 | 0/8 13 h-lim-p 1.5979 12.7829 0.0345 1102.045490 7 0.5925 257 | 0/8 14 h-lim-p 0.2511 2.0092 0.0098 1102.024521 0 1.0046 279 | 0/8 15 h-lim-p 1.6440 20.0000 0.0060 1102.021283 6 0.9564 314 | 0/8 16 h-lim-p 2.5000 20.0000 0.0018 1102.021132 2 1.2402 338 | 0/8 17 h-lim-p 2.5000 20.0000 0.0005 1102.021114 2 0.7996 363 | 0/8 18 h-lim-p 1.9835 20.0000 0.0002 1102.021113 0 0.9917 383 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1102.021113 0 1.0938 403 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 1102.021113 0 0.0000 438 Out... lnL = -1102.021113 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1102.021113 Node 7: lnL = -1102.021113 Node 8: lnL = -1102.021113 Node 9: lnL = -1102.021113 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 322 Sequential format.. Reading seq # 1: YMR278W_Sbay Reading seq # 2: YMR278W_Scer Reading seq # 3: YMR278W_Skud Reading seq # 4: YMR278W_Smik Reading seq # 5: YMR278W_Spar Sequences read.. Counting patterns.. # site patterns = 138 Counting frequencies.. 120 bytes for distance 22080 bytes for lkl0 17664 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.348049 0.265312 0.168119 0.111373 0.115882 0.152991 0.237358 0.000060 lnL0 = -1325.356930 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1325.356930 x= 0.34805 0.26531 0.16812 0.11137 0.11588 0.15299 0.23736 0.00006 1 h-lim-p 0.0000 0.0000 184.8384 1325.307083 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0016 165.8810 1318.539663 0 0.0006 40 | 1/8 3 h-lim-p 0.0002 0.0017 126.3203 1315.831166 0 0.0007 53 | 1/8 4 h-lim-p 0.0009 0.0069 43.2464 1315.209964 6 0.0008 77 | 1/8 5 h-lim-p 0.0034 0.0274 7.9487 1315.081391 7 0.0021 107 | 1/8 6 h-lim-p 0.0050 0.0907 3.4183 1313.934117 0 0.0200 121 | 1/8 7 h-lim-p 0.0042 0.0339 8.3086 1300.938764 0 0.0170 135 | 1/8 8 h-lim-p 0.0019 0.0154 20.0351 1300.647998 8 0.0013 166 | 1/8 9 h-lim-p 0.3107 2.8354 0.0831 1298.159643 0 0.6214 179 | 1/8 10 h-lim-p 1.5002 20.0000 0.0344 1297.601770 9 0.8622 222 | 1/8 11 h-lim-p 0.9091 7.2727 0.0248 1297.522433 6 0.4422 256 | 1/8 12 h-lim-p 1.2350 10.8290 0.0089 1297.500851 2 0.5789 279 | 0/8 13 h-lim-p 0.0043 0.3883 1.1832 1297.499859 4 0.0015 308 | 0/8 14 h-lim-p 1.0482 12.4247 0.0017 1297.497292 1 1.3102 322 | 0/8 15 h-lim-p 2.5000 20.0000 0.0006 1297.497025 2 1.2402 346 | 0/8 16 h-lim-p 2.5000 20.0000 0.0001 1297.497018 0 1.0938 366 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1297.497018 0 1.0938 386 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1297.497018 0 1.0938 406 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1297.497018 0 2.1875 426 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 1297.497018 0 0.2344 449 | 0/8 21 h-lim-p 0.1621 20.0000 0.0000 1297.497018 0 0.0006 476 Out... lnL = -1297.497018 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1297.497018 Node 7: lnL = -1297.497018 Node 8: lnL = -1297.497018 Node 9: lnL = -1297.497018 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 745 Sequential format.. Reading seq # 1: YMR279C_Sbay Reading seq # 2: YMR279C_Scer Reading seq # 3: YMR279C_Skud Reading seq # 4: YMR279C_Smik Reading seq # 5: YMR279C_Spar Sequences read.. Counting patterns.. # site patterns = 252 Counting frequencies.. 120 bytes for distance 40320 bytes for lkl0 32256 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.361304 0.141396 0.169630 0.094689 0.100014 0.150845 0.291607 0.000060 lnL0 = -3263.766290 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3263.766290 x= 0.36130 0.14140 0.16963 0.09469 0.10001 0.15085 0.29161 0.00006 1 h-lim-p 0.0000 0.0000 297.5938 3263.652697 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0007 292.4691 3254.633682 0 0.0003 39 | 1/8 3 h-lim-p 0.0006 0.0050 48.1681 3254.094430 4 0.0005 59 | 1/8 4 h-lim-p 0.0024 0.0300 9.6372 3254.023134 2 0.0011 75 | 1/8 5 h-lim-p 0.0024 0.0246 4.5524 3253.966890 6 0.0018 100 | 1/8 6 h-lim-p 0.0035 0.0703 2.3687 3253.041511 0 0.0139 114 | 1/8 7 h-lim-p 0.0012 0.0096 25.8134 3247.599299 0 0.0024 127 | 1/8 8 h-lim-p 0.0009 0.0069 52.1386 3241.890715 0 0.0017 140 | 1/8 9 h-lim-p 0.6552 5.2419 0.0392 3241.130287 8 0.4840 173 | 1/8 10 h-lim-p 2.2499 20.0000 0.0084 3241.102438 5 0.4537 202 | 0/8 11 h-lim-p 0.0032 2.2433 1.1962 3241.101829 3 0.0009 228 | 0/8 12 h-lim-p 0.8231 20.0000 0.0012 3241.101120 2 0.7170 244 | 0/8 13 h-lim-p 2.5000 20.0000 0.0001 3241.101104 2 0.8246 270 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 3241.101104 0 1.0938 290 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 3241.101104 0 1.0938 310 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 3241.101104 0 2.1875 330 | 0/8 17 h-lim-p 1.7668 20.0000 0.0000 3241.101104 0 0.7730 350 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 3241.101104 0 0.0049 378 Out... lnL = -3241.101104 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3241.101104 Node 7: lnL = -3241.101104 Node 8: lnL = -3241.101104 Node 9: lnL = -3241.101104 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 861 Sequential format.. Reading seq # 1: YMR280C_Sbay Reading seq # 2: YMR280C_Scer Reading seq # 3: YMR280C_Skud Reading seq # 4: YMR280C_Smik Reading seq # 5: YMR280C_Spar Sequences read.. Counting patterns.. # site patterns = 372 Counting frequencies.. 120 bytes for distance 59520 bytes for lkl0 47616 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.500004 0.198898 0.208550 0.158047 0.159032 0.185179 0.340333 0.000060 lnL0 = -4320.529064 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4320.529064 x= 0.50000 0.19890 0.20855 0.15805 0.15903 0.18518 0.34033 0.00006 1 h-lim-p 0.0000 0.0000 198.0045 4320.457411 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0027 137.5907 4316.168218 0 0.0006 40 | 1/8 3 h-lim-p 0.0006 0.0048 65.6052 4315.164030 6 0.0006 64 | 1/8 4 h-lim-p 0.0024 0.0189 16.1100 4314.986586 7 0.0013 94 | 1/8 5 h-lim-p 0.0027 0.0438 7.9023 4314.917532 6 0.0017 121 | 1/8 6 h-lim-p 0.0036 0.0886 3.8377 4314.832441 5 0.0031 142 | 1/8 7 h-lim-p 0.0080 0.2615 1.5028 4308.974989 0 0.0643 157 | 1/8 8 h-lim-p 0.0008 0.0063 38.3248 4305.687489 0 0.0023 170 | 1/8 9 h-lim-p 0.9743 7.7947 0.0429 4305.155492 8 0.6564 204 | 0/8 10 h-lim-p 0.0240 2.9314 1.1747 4305.154485 2 0.0014 230 | 0/8 11 h-lim-p 0.3693 20.0000 0.0045 4305.141891 0 0.7386 243 | 0/8 12 h-lim-p 2.1027 16.8215 0.0008 4305.141559 3 0.6778 271 | 0/8 13 h-lim-p 2.5000 20.0000 0.0001 4305.141546 2 0.9644 295 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 4305.141546 0 1.0938 315 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 4305.141546 0 1.0938 335 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 4305.141546 0 1.0938 355 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 4305.141546 0 0.6250 376 | 0/8 18 h-lim-p 1.1066 20.0000 0.0000 4305.141546 0 0.0692 399 | 0/8 19 h-lim-p 0.0393 20.0000 0.0000 4305.141546 0 0.0197 419 Out... lnL = -4305.141546 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4305.141546 Node 7: lnL = -4305.141546 Node 8: lnL = -4305.141546 Node 9: lnL = -4305.141546 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 883 Sequential format.. Reading seq # 1: YMR281W_Sbay Reading seq # 2: YMR281W_Scer Reading seq # 3: YMR281W_Skud Reading seq # 4: YMR281W_Smik Reading seq # 5: YMR281W_Spar Sequences read.. Counting patterns.. # site patterns = 403 Counting frequencies.. 120 bytes for distance 64480 bytes for lkl0 51584 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.562021 0.250337 0.209703 0.192384 0.157181 0.208483 0.334321 0.000060 lnL0 = -4467.671439 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4467.671439 x= 0.56202 0.25034 0.20970 0.19238 0.15718 0.20848 0.33432 0.00006 1 h-lim-p 0.0000 0.0000 172.4621 4467.593468 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0037 152.2952 4462.418570 0 0.0006 40 | 1/8 3 h-lim-p 0.0011 0.0090 56.3093 4461.395823 6 0.0008 65 | 1/8 4 h-lim-p 0.0020 0.0158 17.1594 4461.194565 7 0.0014 93 | 1/8 5 h-lim-p 0.0034 0.0704 7.2206 4461.105248 6 0.0027 116 | 1/8 6 h-lim-p 0.0119 0.2459 1.6549 4460.958635 5 0.0091 138 | 1/8 7 h-lim-p 0.0052 0.1466 2.9222 4455.144893 0 0.0413 153 | 0/8 8 h-lim-p 0.0012 0.0096 26.4852 4454.386905 0 0.0018 165 | 0/8 9 h-lim-p 0.0001 0.0012 3.5098 4454.374986 m 0.0012 177 | 0/8 10 h-lim-p 0.0734 7.9786 0.0561 4453.647458 0 0.5874 192 | 0/8 11 h-lim-p 0.0659 0.5272 0.0083 4453.632355 m 0.5272 212 | 1/8 12 h-lim-p 2.2734 20.0000 0.0017 4453.630461 0 1.1367 232 | 1/8 13 h-lim-p 2.0140 20.0000 0.0010 4453.630377 3 0.5412 258 | 0/8 14 h-lim-p 0.0153 20.0000 0.0343 4453.630372 0 0.0153 277 | 0/8 15 h-lim-p 2.1712 17.3695 0.0001 4453.630364 1 0.8651 299 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 4453.630364 0 1.0938 319 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 4453.630364 0 1.0938 339 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 4453.630364 0 1.0938 359 | 0/8 19 h-lim-p 1.7942 20.0000 0.0000 4453.630364 0 1.5699 379 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 4453.630364 0 1.2500 399 | 0/8 21 h-lim-p 0.3051 20.0000 0.0000 4453.630364 0 0.2289 419 | 0/8 22 h-lim-p 0.0280 20.0000 0.0000 4453.630364 0 0.0280 439 | 0/8 23 h-lim-p 0.0101 11.1698 0.0000 4453.630364 0 0.0000 480 | 0/8 24 h-lim-p 0.0000 20.0000 0.0001 4453.630364 0 0.0000 501 | 0/8 25 h-lim-p 0.0000 20.0000 0.0000 4453.630364 0 0.0000 521 | 0/8 26 h-lim-p 0.0000 20.0000 0.0000 4453.630364 0 0.0000 541 | 0/8 27 h-lim-p 0.0000 11.4862 0.0000 4453.630364 0 0.0000 575 | 0/8 28 h-lim-p 0.0000 20.0000 0.0001 | 0/8 29 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -4453.630364 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4453.630364 Node 7: lnL = -4453.630364 Node 8: lnL = -4453.630364 Node 9: lnL = -4453.630364 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 878 Sequential format.. Reading seq # 1: YMR283C_Sbay Reading seq # 2: YMR283C_Scer Reading seq # 3: YMR283C_Skud Reading seq # 4: YMR283C_Smik Reading seq # 5: YMR283C_Spar Sequences read.. Counting patterns.. # site patterns = 337 Counting frequencies.. 120 bytes for distance 53920 bytes for lkl0 43136 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.986775 0.698894 0.580076 0.268919 0.393523 0.000060 0.832354 0.104905 lnL0 = -4509.146750 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4509.146750 x= 0.98678 0.69889 0.58008 0.26892 0.39352 0.00006 0.83235 0.10491 1 h-lim-p 0.0000 0.0000 80.8293 4509.118176 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0017 222.9310 4486.087318 m 0.0017 39 | 2/8 3 h-lim-p 0.0012 0.0098 63.3968 4479.306649 0 0.0049 53 | 2/8 4 h-lim-p 0.0078 0.0621 10.5128 4478.929257 7 0.0069 79 | 1/8 5 h-lim-p 0.0014 0.0179 51.5439 4477.075988 0 0.0028 92 | 1/8 6 h-lim-p 0.0220 0.1763 3.1798 4476.999762 6 0.0110 116 | 1/8 7 h-lim-p 0.0167 0.3322 2.0921 4476.717362 0 0.0667 130 | 1/8 8 h-lim-p 0.1166 0.9327 0.6662 4475.127932 0 0.2332 143 | 0/8 9 h-lim-p 0.0349 0.2795 3.1337 4475.038254 6 0.0236 178 | 0/8 10 h-lim-p 2.5000 20.0000 0.0214 4475.018526 5 0.9422 200 | 0/8 11 h-lim-p 2.0097 16.2692 0.0100 4475.015985 4 1.0212 230 | 0/8 12 h-lim-p 2.5000 20.0000 0.0012 4475.015921 2 0.9644 254 | 0/8 13 h-lim-p 2.5000 20.0000 0.0003 4475.015908 0 1.2500 274 | 0/8 14 h-lim-p 1.6241 20.0000 0.0002 4475.015905 0 1.4211 294 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 4475.015905 0 1.0938 314 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 4475.015905 0 1.0938 334 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 4475.015905 0 2.5000 354 | 0/8 18 h-lim-p 2.2501 20.0000 0.0000 4475.015905 0 3.3751 374 | 0/8 19 h-lim-p 0.1617 20.0000 0.0000 4475.015905 0 0.0101 397 | 0/8 20 h-lim-p 0.0000 5.2952 0.0173 4475.015905 0 0.0000 432 | 0/8 21 h-lim-p 0.0000 20.0000 0.0000 4475.015905 0 0.0000 458 Out... lnL = -4475.015905 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4475.015905 Node 7: lnL = -4475.015905 Node 8: lnL = -4475.015905 Node 9: lnL = -4475.015905 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 837 Sequential format.. Reading seq # 1: YMR284W_Sbay Reading seq # 2: YMR284W_Scer Reading seq # 3: YMR284W_Skud Reading seq # 4: YMR284W_Smik Reading seq # 5: YMR284W_Spar Sequences read.. Counting patterns.. # site patterns = 392 Counting frequencies.. 120 bytes for distance 62720 bytes for lkl0 50176 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.168454 0.095488 0.035334 0.310464 0.396633 0.121772 0.414323 0.298903 lnL0 = -4324.816821 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4324.816821 x= 0.16845 0.09549 0.03533 0.31046 0.39663 0.12177 0.41432 0.29890 1 h-lim-p 0.0013 0.4942 259.3987 4312.285797 9 0.0004 46 | 0/8 2 h-lim-p 0.0003 0.0026 54.9214 4310.771117 0 0.0013 60 | 0/8 3 h-lim-p 0.0007 0.0053 14.9090 4310.599911 0 0.0020 73 | 0/8 4 h-lim-p 0.0068 0.1620 4.3552 4310.586328 3 0.0015 92 | 0/8 5 h-lim-p 0.0102 0.9833 0.6568 4310.585360 2 0.0025 109 | 0/8 6 h-lim-p 0.0047 1.4535 0.3502 4310.582922 0 0.0095 130 | 0/8 7 h-lim-p 0.0133 3.4771 0.2492 4310.461688 0 0.0532 152 | 0/8 8 h-lim-p 0.0029 0.1632 4.5236 4310.426757 4 0.0023 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0037 4310.412737 5 1.4823 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0011 4310.412144 2 1.2402 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4310.412143 0 1.0938 249 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4310.412143 0 1.0938 269 | 0/8 13 h-lim-p 1.2507 20.0000 0.0000 4310.412143 0 0.4690 290 | 0/8 14 h-lim-p 0.1158 20.0000 0.0000 4310.412143 0 0.1158 310 | 0/8 15 h-lim-p 0.0395 20.0000 0.0000 4310.412143 0 0.0099 331 | 0/8 16 h-lim-p 0.0078 20.0000 0.0001 4310.412143 0 0.0039 351 | 0/8 17 h-lim-p 0.0000 19.6640 0.0129 4310.412143 0 0.0000 371 | 0/8 18 h-lim-p 0.0037 20.0000 0.0000 4310.412143 0 0.0000 404 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 4310.412143 0 0.0000 432 Out... lnL = -4310.412143 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4310.412143 Node 7: lnL = -4310.412143 Node 8: lnL = -4310.412143 Node 9: lnL = -4310.412143 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 276 Sequential format.. Reading seq # 1: YMR285C_Sbay Reading seq # 2: YMR285C_Scer Reading seq # 3: YMR285C_Skud Reading seq # 4: YMR285C_Smik Reading seq # 5: YMR285C_Spar Sequences read.. Counting patterns.. # site patterns = 131 Counting frequencies.. 120 bytes for distance 20960 bytes for lkl0 16768 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.113046 0.085645 0.069832 0.149393 0.097717 0.183581 0.191925 0.192500 lnL0 = -1253.057763 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1253.057763 x= 0.11305 0.08565 0.06983 0.14939 0.09772 0.18358 0.19192 0.19250 1 h-lim-p 0.0020 0.0160 28.0628 1252.758523 6 0.0008 35 | 0/8 2 h-lim-p 0.0019 0.0152 9.0175 1252.731187 4 0.0007 55 | 0/8 3 h-lim-p 0.0028 0.1073 2.3750 1252.728297 4 0.0011 75 | 0/8 4 h-lim-p 0.0044 0.3296 0.5918 1252.728147 3 0.0009 94 | 0/8 5 h-lim-p 0.0030 0.9430 0.1845 1252.728132 2 0.0010 120 | 0/8 6 h-lim-p 0.0057 6.5808 0.0319 1252.728132 0 0.0012 141 | 0/8 7 h-lim-p 0.0124 20.0000 0.0032 1252.728132 0 0.0014 163 | 0/8 8 h-lim-p 0.0802 20.0000 0.0001 1252.728131 0 0.6418 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1252.728131 0 1.0938 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1252.728131 0 2.1875 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1252.728131 0 0.5469 247 | 0/8 12 h-lim-p 0.1586 20.0000 0.0000 1252.728131 0 0.1388 267 | 0/8 13 h-lim-p 0.0704 20.0000 0.0000 1252.728131 0 0.0006 293 Out... lnL = -1252.728131 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1252.728131 Node 7: lnL = -1252.728131 Node 8: lnL = -1252.728131 Node 9: lnL = -1252.728131 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 316 Sequential format.. Reading seq # 1: YMR286W_Sbay Reading seq # 2: YMR286W_Scer Reading seq # 3: YMR286W_Skud Reading seq # 4: YMR286W_Smik Reading seq # 5: YMR286W_Spar Sequences read.. Counting patterns.. # site patterns = 138 Counting frequencies.. 120 bytes for distance 22080 bytes for lkl0 17664 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.089168 0.143175 0.057613 0.156870 0.083484 0.197664 0.174235 0.169345 lnL0 = -1349.164816 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1349.164816 x= 0.08917 0.14317 0.05761 0.15687 0.08348 0.19766 0.17423 0.16934 1 h-lim-p 0.0029 0.0236 34.0513 1348.860131 7 0.0006 37 | 0/8 2 h-lim-p 0.0018 0.0293 10.6304 1348.804462 7 0.0011 68 | 0/8 3 h-lim-p 0.0035 0.0944 3.1846 1348.800982 4 0.0008 91 | 0/8 4 h-lim-p 0.0050 0.4110 0.4778 1348.800880 3 0.0009 111 | 0/8 5 h-lim-p 0.0034 1.4994 0.1242 1348.800873 2 0.0009 136 | 0/8 6 h-lim-p 0.0038 11.1792 0.0293 1348.800873 0 0.0017 156 | 0/8 7 h-lim-p 0.0168 20.0000 0.0029 1348.800873 0 0.0018 178 | 0/8 8 h-lim-p 0.1501 20.0000 0.0000 1348.800872 0 1.2012 201 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1348.800872 0 1.0938 221 | 0/8 10 h-lim-p 2.0244 20.0000 0.0000 1348.800872 0 1.7714 241 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1348.800872 0 0.5469 262 | 0/8 12 h-lim-p 0.1497 20.0000 0.0000 1348.800872 0 0.0561 283 | 0/8 13 h-lim-p 0.0249 20.0000 0.0000 1348.800872 0 0.0000 326 | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 1348.800872 0 0.0000 357 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1348.800872 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1348.800872 Node 7: lnL = -1348.800872 Node 8: lnL = -1348.800872 Node 9: lnL = -1348.800872 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 853 Sequential format.. Reading seq # 1: YMR290C_Sbay Reading seq # 2: YMR290C_Scer Reading seq # 3: YMR290C_Skud Reading seq # 4: YMR290C_Smik Reading seq # 5: YMR290C_Spar Sequences read.. Counting patterns.. # site patterns = 308 Counting frequencies.. 120 bytes for distance 49280 bytes for lkl0 39424 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.111575 0.049969 0.063349 0.142540 0.124830 0.239539 0.217799 0.193666 lnL0 = -3933.113589 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3933.113589 x= 0.11158 0.04997 0.06335 0.14254 0.12483 0.23954 0.21780 0.19367 1 h-lim-p 0.0024 0.0487 182.4751 3930.421794 8 0.0002 43 | 0/8 2 h-lim-p 0.0013 0.0112 25.2852 3930.296487 7 0.0004 72 | 0/8 3 h-lim-p 0.0008 0.0231 11.8658 3930.275795 3 0.0004 90 | 0/8 4 h-lim-p 0.0013 0.0688 3.1576 3930.274211 4 0.0003 111 | 0/8 5 h-lim-p 0.0026 0.4441 0.4167 3930.274173 2 0.0004 129 | 0/8 6 h-lim-p 0.0038 11.5128 0.0464 3930.274172 0 0.0008 150 | 0/8 7 h-lim-p 0.0042 20.0000 0.0091 3930.274170 0 0.0042 170 | 0/8 8 h-lim-p 0.0065 20.0000 0.0059 3930.273727 0 0.0785 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3930.273725 0 1.0938 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3930.273725 0 1.0938 233 | 0/8 11 h-lim-p 1.5104 20.0000 0.0000 3930.273725 0 1.5104 253 | 0/8 12 h-lim-p 1.2769 20.0000 0.0000 3930.273725 0 0.0399 277 | 0/8 13 h-lim-p 0.0028 20.0000 0.0001 3930.273725 0 0.0000 318 | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 3930.273725 0 0.0000 344 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 3930.273725 0 0.0000 379 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -3930.273725 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3930.273725 Node 7: lnL = -3930.273725 Node 8: lnL = -3930.273725 Node 9: lnL = -3930.273725 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 860 Sequential format.. Reading seq # 1: YMR291W_Sbay Reading seq # 2: YMR291W_Scer Reading seq # 3: YMR291W_Skud Reading seq # 4: YMR291W_Smik Reading seq # 5: YMR291W_Spar Sequences read.. Counting patterns.. # site patterns = 288 Counting frequencies.. 120 bytes for distance 46080 bytes for lkl0 36864 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.122128 0.052928 0.052879 0.141289 0.104080 0.235762 0.170499 0.199575 lnL0 = -3854.522656 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3854.522656 x= 0.12213 0.05293 0.05288 0.14129 0.10408 0.23576 0.17050 0.19958 1 h-lim-p 0.0013 0.0106 161.5786 3852.661362 2 0.0002 28 | 0/8 2 h-lim-p 0.0008 0.0065 25.3713 3852.572700 6 0.0003 56 | 0/8 3 h-lim-p 0.0007 0.0588 9.7824 3852.561029 5 0.0003 78 | 0/8 4 h-lim-p 0.0012 0.1069 2.3677 3852.560163 4 0.0003 101 | 0/8 5 h-lim-p 0.0020 0.4742 0.3907 3852.560127 0 0.0005 114 | 0/8 6 h-lim-p 0.0033 4.3783 0.0592 3852.560126 0 0.0007 135 | 0/8 7 h-lim-p 0.0116 20.0000 0.0036 3852.559983 0 0.0932 158 | 0/8 8 h-lim-p 0.0021 0.5534 0.1637 3852.559064 0 0.0041 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3852.559061 0 1.0938 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3852.559061 0 1.0938 219 | 0/8 11 h-lim-p 0.9861 20.0000 0.0000 3852.559061 0 0.9861 239 | 0/8 12 h-lim-p 0.7943 20.0000 0.0000 3852.559061 0 0.7943 259 | 0/8 13 h-lim-p 0.0428 20.0000 0.0002 3852.559061 0 0.0107 280 | 0/8 14 h-lim-p 0.0031 20.0000 0.0006 3852.559061 0 0.0000 316 | 0/8 15 h-lim-p 0.0005 20.0000 0.0000 3852.559061 0 0.0000 347 Out... lnL = -3852.559061 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3852.559061 Node 7: lnL = -3852.559061 Node 8: lnL = -3852.559061 Node 9: lnL = -3852.559061 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 182 Sequential format.. Reading seq # 1: YMR293C_Sbay Reading seq # 2: YMR293C_Scer Reading seq # 3: YMR293C_Skud Reading seq # 4: YMR293C_Smik Reading seq # 5: YMR293C_Spar Sequences read.. Counting patterns.. # site patterns = 113 Counting frequencies.. 120 bytes for distance 18080 bytes for lkl0 14464 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.081701 0.234014 0.110687 0.165814 0.040965 0.192816 0.365886 0.187886 lnL0 = -854.281632 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 854.281632 x= 0.08170 0.23401 0.11069 0.16581 0.04097 0.19282 0.36589 0.18789 1 h-lim-p 0.0019 0.0152 40.9029 853.821999 7 0.0006 37 | 0/8 2 h-lim-p 0.0013 0.0103 16.8155 853.655808 3 0.0013 55 | 0/8 3 h-lim-p 0.0051 0.0673 4.2980 853.623674 7 0.0038 83 | 0/8 4 h-lim-p 0.0057 0.2026 2.8208 853.617965 6 0.0020 112 | 0/8 5 h-lim-p 0.0127 0.5343 0.4371 853.617504 3 0.0051 130 | 0/8 6 h-lim-p 0.0188 1.5914 0.1173 853.617483 3 0.0033 159 | 0/8 7 h-lim-p 0.0059 9.3183 0.0661 853.617477 2 0.0031 184 | 0/8 8 h-lim-p 0.5011 20.0000 0.0004 853.617366 0 1.0022 205 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 853.617362 1 0.9961 227 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 853.617362 0 1.0938 247 | 0/8 11 h-lim-p 2.2994 20.0000 0.0000 853.617362 0 0.0003 279 Out... lnL = -853.617362 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -853.617362 Node 7: lnL = -853.617362 Node 8: lnL = -853.617362 Node 9: lnL = -853.617362 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 177 Sequential format.. Reading seq # 1: YMR294W_Sbay Reading seq # 2: YMR294W_Scer Reading seq # 3: YMR294W_Skud Reading seq # 4: YMR294W_Smik Reading seq # 5: YMR294W_Spar Sequences read.. Counting patterns.. # site patterns = 114 Counting frequencies.. 120 bytes for distance 18240 bytes for lkl0 14592 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.084813 0.312709 0.086333 0.169789 0.036990 0.226101 0.321694 0.196641 lnL0 = -826.595480 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 826.595480 x= 0.08481 0.31271 0.08633 0.16979 0.03699 0.22610 0.32169 0.19664 1 h-lim-p 0.0024 0.0195 63.5233 825.667311 7 0.0005 37 | 0/8 2 h-lim-p 0.0012 0.0094 20.0499 825.354004 0 0.0018 49 | 0/8 3 h-lim-p 0.0050 0.0730 7.0515 825.250969 2 0.0047 65 | 0/8 4 h-lim-p 0.0052 0.0420 5.8842 825.219450 7 0.0029 94 | 0/8 5 h-lim-p 0.0067 0.0560 2.5544 825.211947 2 0.0031 110 | 0/8 6 h-lim-p 0.0084 0.2321 0.9534 825.210360 5 0.0042 134 | 0/8 7 h-lim-p 0.0268 3.6565 0.1507 825.210248 4 0.0091 165 | 0/8 8 h-lim-p 0.6946 20.0000 0.0020 825.209234 1 0.8682 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 825.209221 0 1.2500 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 825.209220 1 1.2305 230 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 825.209220 0 1.0938 250 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 825.209220 0 2.5000 270 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 825.209220 0 0.0024 299 Out... lnL = -825.209220 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -825.209220 Node 7: lnL = -825.209220 Node 8: lnL = -825.209220 Node 9: lnL = -825.209220 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 354 Sequential format.. Reading seq # 1: YMR295C_Sbay Reading seq # 2: YMR295C_Scer Reading seq # 3: YMR295C_Skud Reading seq # 4: YMR295C_Smik Reading seq # 5: YMR295C_Spar Sequences read.. Counting patterns.. # site patterns = 104 Counting frequencies.. 120 bytes for distance 16640 bytes for lkl0 13312 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.091789 0.024257 0.050047 0.053947 0.018398 0.096416 0.172290 0.138501 lnL0 = -1281.395221 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1281.395221 x= 0.09179 0.02426 0.05005 0.05395 0.01840 0.09642 0.17229 0.13850 1 h-lim-p 0.0032 0.0675 89.3615 1280.681294 7 0.0002 40 | 0/8 2 h-lim-p 0.0002 0.0018 13.2275 1280.672141 2 0.0001 56 | 0/8 3 h-lim-p 0.0002 0.0372 6.3662 1280.664790 0 0.0004 69 | 0/8 4 h-lim-p 0.0025 0.0980 1.1249 1280.664607 2 0.0003 87 | 0/8 5 h-lim-p 0.0013 0.5494 0.2712 1280.664595 3 0.0004 107 | 0/8 6 h-lim-p 0.0012 0.9737 0.0837 1280.664594 0 0.0003 128 | 0/8 7 h-lim-p 0.0019 15.0456 0.0120 1280.664594 0 0.0009 148 | 0/8 8 h-lim-p 0.2075 20.0000 0.0001 1280.664588 0 0.8302 170 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1280.664588 0 2.1875 190 | 0/8 10 h-lim-p 2.4895 20.0000 0.0000 1280.664588 0 1.0892 210 | 0/8 11 h-lim-p 1.9785 20.0000 0.0000 1280.664588 0 3.9571 231 | 0/8 12 h-lim-p 1.9499 20.0000 0.0000 1280.664588 0 0.4265 252 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1280.664588 0 0.0005 284 Out... lnL = -1280.664588 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1280.664588 Node 7: lnL = -1280.664588 Node 8: lnL = -1280.664588 Node 9: lnL = -1280.664588 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 351 Sequential format.. Reading seq # 1: YMR298W_Sbay Reading seq # 2: YMR298W_Scer Reading seq # 3: YMR298W_Skud Reading seq # 4: YMR298W_Smik Reading seq # 5: YMR298W_Spar Sequences read.. Counting patterns.. # site patterns = 164 Counting frequencies.. 120 bytes for distance 26240 bytes for lkl0 20992 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.110664 0.131883 0.054042 0.130320 0.104129 0.176884 0.180426 0.190856 lnL0 = -1553.518928 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1553.518928 x= 0.11066 0.13188 0.05404 0.13032 0.10413 0.17688 0.18043 0.19086 1 h-lim-p 0.0129 0.9188 49.0124 1553.000818 9 0.0005 47 | 0/8 2 h-lim-p 0.0016 0.0189 14.0144 1552.921212 5 0.0009 70 | 0/8 3 h-lim-p 0.0023 0.0741 5.2276 1552.912483 6 0.0007 97 | 0/8 4 h-lim-p 0.0028 0.1408 1.3588 1552.911821 5 0.0008 121 | 0/8 5 h-lim-p 0.0031 0.8154 0.3395 1552.911769 3 0.0009 142 | 0/8 6 h-lim-p 0.0399 20.0000 0.0078 1552.911769 0 0.0011 166 | 0/8 7 h-lim-p 0.0085 20.0000 0.0010 1552.911768 0 0.0339 188 | 0/8 8 h-lim-p 0.0074 20.0000 0.0046 1552.911758 0 0.0295 210 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1552.911757 0 1.0938 230 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1552.911757 0 2.1875 250 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1552.911757 0 1.0938 270 | 0/8 12 h-lim-p 0.2771 20.0000 0.0000 1552.911757 0 4.4332 294 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1552.911757 0 0.6250 315 | 0/8 14 h-lim-p 0.0668 20.0000 0.0000 1552.911757 0 0.0000 356 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 1552.911757 0 0.0000 377 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0003 | 0/8 18 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -1552.911757 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1552.911757 Node 7: lnL = -1552.911757 Node 8: lnL = -1552.911757 Node 9: lnL = -1552.911757 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 767 Sequential format.. Reading seq # 1: YMR302C_Sbay Reading seq # 2: YMR302C_Scer Reading seq # 3: YMR302C_Skud Reading seq # 4: YMR302C_Smik Reading seq # 5: YMR302C_Spar Sequences read.. Counting patterns.. # site patterns = 358 Counting frequencies.. 120 bytes for distance 57280 bytes for lkl0 45824 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.225487 0.138556 0.066881 0.200357 0.111862 0.294928 0.313678 0.348858 lnL0 = -3932.344127 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3932.344127 x= 0.22549 0.13856 0.06688 0.20036 0.11186 0.29493 0.31368 0.34886 1 h-lim-p 0.0025 0.0202 94.3672 3930.901590 9 0.0003 44 | 0/8 2 h-lim-p 0.0009 0.0098 37.8783 3930.396438 2 0.0008 60 | 0/8 3 h-lim-p 0.0013 0.0174 22.8275 3930.302187 7 0.0005 90 | 0/8 4 h-lim-p 0.0017 0.0543 6.4661 3930.278108 5 0.0013 112 | 0/8 5 h-lim-p 0.0033 0.1351 2.5187 3930.275884 3 0.0008 131 | 0/8 6 h-lim-p 0.0033 0.8004 0.6266 3930.275698 3 0.0010 152 | 0/8 7 h-lim-p 0.0030 1.9601 0.2014 3930.275679 2 0.0010 178 | 0/8 8 h-lim-p 0.1708 20.0000 0.0012 3930.273839 0 1.0249 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 3930.273799 1 1.0938 222 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3930.273799 0 1.0938 242 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3930.273799 0 2.1875 262 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3930.273799 0 1.0938 282 | 0/8 13 h-lim-p 0.2832 20.0000 0.0000 3930.273799 0 4.5308 306 | 0/8 14 h-lim-p 1.4722 20.0000 0.0000 3930.273799 0 0.7361 326 | 0/8 15 h-lim-p 0.0162 20.0000 0.0004 3930.273799 0 0.0162 346 | 0/8 16 h-lim-p 0.0022 20.0000 0.0032 3930.273799 0 0.0022 366 | 0/8 17 h-lim-p 0.0042 20.0000 0.0017 3930.273799 0 0.0000 393 | 0/8 18 h-lim-p 0.0006 20.0000 0.0000 3930.273799 0 0.0000 424 | 0/8 19 h-lim-p 0.0000 20.0000 0.0002 | 0/8 20 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -3930.273799 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3930.273799 Node 7: lnL = -3930.273799 Node 8: lnL = -3930.273799 Node 9: lnL = -3930.273799 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 689 Sequential format.. Reading seq # 1: YMR303C_Sbay Reading seq # 2: YMR303C_Scer Reading seq # 3: YMR303C_Skud Reading seq # 4: YMR303C_Smik Reading seq # 5: YMR303C_Spar Sequences read.. Counting patterns.. # site patterns = 201 Counting frequencies.. 120 bytes for distance 32160 bytes for lkl0 25728 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.098038 0.023911 0.051645 0.096330 0.068862 0.115636 0.142475 0.151846 lnL0 = -2720.485650 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2720.485650 x= 0.09804 0.02391 0.05164 0.09633 0.06886 0.11564 0.14247 0.15185 1 h-lim-p 0.0015 0.7684 191.1778 2718.531080 8 0.0001 43 | 0/8 2 h-lim-p 0.0007 0.0052 17.9218 2718.490118 4 0.0003 63 | 0/8 3 h-lim-p 0.0007 0.0313 6.8609 2718.485972 5 0.0002 88 | 0/8 4 h-lim-p 0.0009 0.0788 1.5753 2718.485732 2 0.0002 105 | 0/8 5 h-lim-p 0.0008 0.2199 0.4167 2718.485707 1 0.0003 119 | 0/8 6 h-lim-p 0.0017 3.1520 0.0755 2718.485706 0 0.0004 140 | 0/8 7 h-lim-p 0.0023 13.9178 0.0123 2718.485706 0 0.0005 161 | 0/8 8 h-lim-p 0.0529 20.0000 0.0001 2718.485676 0 0.8460 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2718.485676 0 1.0938 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2718.485676 0 0.5469 226 | 0/8 11 h-lim-p 0.3309 20.0000 0.0000 2718.485676 0 0.0090 250 | 0/8 12 h-lim-p 0.0051 20.0000 0.0000 2718.485676 0 0.0000 280 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 2718.485676 0 0.0000 302 Out... lnL = -2718.485676 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2718.485676 Node 7: lnL = -2718.485676 Node 8: lnL = -2718.485676 Node 9: lnL = -2718.485676 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 859 Sequential format.. Reading seq # 1: YMR305C_Sbay Reading seq # 2: YMR305C_Scer Reading seq # 3: YMR305C_Skud Reading seq # 4: YMR305C_Smik Reading seq # 5: YMR305C_Spar Sequences read.. Counting patterns.. # site patterns = 245 Counting frequencies.. 120 bytes for distance 39200 bytes for lkl0 31360 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.078735 0.040859 0.052781 0.080013 0.057316 0.152803 0.150154 0.127294 lnL0 = -3415.293951 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3415.293951 x= 0.07873 0.04086 0.05278 0.08001 0.05732 0.15280 0.15015 0.12729 1 h-lim-p 0.0011 0.5576 252.3979 3412.340010 8 0.0001 39 | 0/8 2 h-lim-p 0.0006 0.0050 24.9230 3412.288510 6 0.0002 65 | 0/8 3 h-lim-p 0.0003 0.0149 14.1719 3412.274731 4 0.0002 88 | 0/8 4 h-lim-p 0.0010 0.0758 2.5229 3412.274102 2 0.0002 105 | 0/8 5 h-lim-p 0.0010 0.2563 0.5278 3412.274079 2 0.0002 123 | 0/8 6 h-lim-p 0.0014 1.9426 0.0623 3412.274079 0 0.0003 144 | 0/8 7 h-lim-p 0.0012 19.1505 0.0151 3412.274079 0 0.0005 164 | 0/8 8 h-lim-p 0.0422 20.0000 0.0002 3412.273998 0 0.6745 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3412.273997 0 1.0938 208 | 0/8 10 h-lim-p 1.8662 20.0000 0.0000 3412.273997 0 1.6330 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3412.273997 0 1.0938 248 | 0/8 12 h-lim-p 0.4138 20.0000 0.0000 3412.273997 0 3.3103 271 | 0/8 13 h-lim-p 0.8337 20.0000 0.0001 3412.273997 0 3.3346 293 | 0/8 14 h-lim-p 0.0109 6.9363 0.0172 3412.273997 0 0.0007 316 | 0/8 15 h-lim-p 0.0000 0.1262 0.9474 3412.273997 0 0.0000 342 | 0/8 16 h-lim-p 0.0002 20.0000 0.0004 3412.273997 0 0.0000 376 | 0/8 17 h-lim-p 0.0001 20.0000 0.0000 3412.273997 0 0.0000 406 Out... lnL = -3412.273997 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3412.273997 Node 7: lnL = -3412.273997 Node 8: lnL = -3412.273997 Node 9: lnL = -3412.273997 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 439 Sequential format.. Reading seq # 1: YMR307W_Sbay Reading seq # 2: YMR307W_Scer Reading seq # 3: YMR307W_Skud Reading seq # 4: YMR307W_Smik Reading seq # 5: YMR307W_Spar Sequences read.. Counting patterns.. # site patterns = 103 Counting frequencies.. 120 bytes for distance 16480 bytes for lkl0 13184 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.052506 0.017006 0.026462 0.048543 0.033221 0.090095 0.101669 0.081695 lnL0 = -1459.503670 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1459.503670 x= 0.05251 0.01701 0.02646 0.04854 0.03322 0.09009 0.10167 0.08170 1 h-lim-p 0.0006 0.0077 215.2615 1457.959694 4 0.0001 32 | 0/8 2 h-lim-p 0.0006 0.0046 25.6958 1457.881719 3 0.0002 50 | 0/8 3 h-lim-p 0.0006 0.0075 11.1577 1457.873409 5 0.0002 74 | 0/8 4 h-lim-p 0.0006 0.0576 2.8323 1457.872936 3 0.0001 93 | 0/8 5 h-lim-p 0.0004 0.1102 0.8392 1457.872881 2 0.0002 109 | 0/8 6 h-lim-p 0.0062 4.0882 0.0232 1457.872881 0 0.0003 132 | 0/8 7 h-lim-p 0.0013 10.0061 0.0060 1457.872881 0 0.0011 152 | 0/8 8 h-lim-p 0.0097 20.0000 0.0007 1457.872817 0 0.2327 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1457.872812 0 1.0938 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1457.872812 0 0.6250 217 | 0/8 11 h-lim-p 0.4345 20.0000 0.0000 1457.872812 0 0.0017 244 | 0/8 12 h-lim-p 0.0011 20.0000 0.0000 1457.872812 0 0.0000 285 | 0/8 13 h-lim-p 0.0000 20.0000 0.0089 | 0/8 14 h-lim-p 0.0000 20.0000 0.0089 Out... lnL = -1457.872812 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1457.872812 Node 7: lnL = -1457.872812 Node 8: lnL = -1457.872812 Node 9: lnL = -1457.872812 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 319 Sequential format.. Reading seq # 1: YMR309C_Sbay Reading seq # 2: YMR309C_Scer Reading seq # 3: YMR309C_Skud Reading seq # 4: YMR309C_Smik Reading seq # 5: YMR309C_Spar Sequences read.. Counting patterns.. # site patterns = 70 Counting frequencies.. 120 bytes for distance 11200 bytes for lkl0 8960 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.040451 0.034950 0.000060 0.044070 0.023610 0.079205 0.079016 0.063861 lnL0 = -930.611135 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 930.611135 x= 0.04045 0.03495 0.00006 0.04407 0.02361 0.07921 0.07902 0.06386 1 h-lim-p 0.0000 0.0003 315.1208 929.749013 4 0.0000 31 | 0/8 2 h-lim-p 0.0000 0.0002 119.8002 928.928815 0 0.0001 45 | 0/8 3 h-lim-p 0.0002 0.0013 43.0925 928.826498 4 0.0001 65 | 0/8 4 h-lim-p 0.0009 0.0125 6.2626 928.820969 5 0.0003 89 | 0/8 5 h-lim-p 0.0020 0.0831 0.9267 928.820875 2 0.0002 107 | 0/8 6 h-lim-p 0.0134 7.1497 0.0159 928.820872 1 0.0027 130 | 0/8 7 h-lim-p 0.0144 1.9788 0.0029 928.818399 0 0.1733 153 | 0/8 8 h-lim-p 0.0020 0.3227 0.2551 928.818388 2 0.0003 179 | 0/8 9 h-lim-p 0.7188 20.0000 0.0001 928.818357 0 1.0782 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 928.818356 0 1.2500 219 | 0/8 11 h-lim-p 2.0760 20.0000 0.0000 928.818356 0 1.0380 239 | 0/8 12 h-lim-p 0.8761 20.0000 0.0000 928.818356 0 0.0001 272 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 928.818356 0 0.0000 292 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 928.818356 0 0.0000 315 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 928.818356 0 0.0000 335 | 0/8 16 h-lim-p 0.0000 20.0000 0.0018 928.818356 0 0.0000 370 | 0/8 17 h-lim-p 0.0000 20.0000 0.0018 | 0/8 18 h-lim-p 0.0000 20.0000 0.0018 Out... lnL = -928.818356 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -928.818356 Node 7: lnL = -928.818356 Node 8: lnL = -928.818356 Node 9: lnL = -928.818356 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 268 Sequential format.. Reading seq # 1: YMR310C_Sbay Reading seq # 2: YMR310C_Scer Reading seq # 3: YMR310C_Skud Reading seq # 4: YMR310C_Smik Reading seq # 5: YMR310C_Spar Sequences read.. Counting patterns.. # site patterns = 108 Counting frequencies.. 120 bytes for distance 17280 bytes for lkl0 13824 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.052209 0.048404 0.044000 0.085535 0.053108 0.136414 0.169991 0.097470 lnL0 = -993.760822 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 993.760822 x= 0.05221 0.04840 0.04400 0.08553 0.05311 0.13641 0.16999 0.09747 1 h-lim-p 0.0001 0.0009 110.3225 991.767976 0 0.0005 24 | 0/8 2 h-lim-p 0.0019 0.0189 26.5472 991.671372 7 0.0003 54 | 0/8 3 h-lim-p 0.0006 0.0074 14.2946 991.629909 2 0.0005 70 | 0/8 4 h-lim-p 0.0012 0.0291 6.0496 991.618364 6 0.0008 99 | 0/8 5 h-lim-p 0.0047 0.1374 0.9754 991.617941 5 0.0007 126 | 0/8 6 h-lim-p 0.0102 3.6951 0.0710 991.611508 0 0.0409 148 | 0/8 7 h-lim-p 0.0044 0.2187 0.6638 991.493762 0 0.0175 170 | 0/8 8 h-lim-p 0.0037 0.0328 3.1631 991.490347 5 0.0007 203 | 0/8 9 h-lim-p 2.0495 20.0000 0.0011 991.489289 3 0.9922 222 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 991.489279 2 1.0938 246 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 991.489279 0 1.0938 266 | 0/8 12 h-lim-p 2.0194 20.0000 0.0000 991.489279 0 1.7669 286 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 991.489279 0 0.5469 307 | 0/8 14 h-lim-p 0.1729 20.0000 0.0000 991.489279 0 0.0024 332 | 0/8 15 h-lim-p 0.0011 20.0000 0.0000 991.489279 0 0.0000 360 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 991.489279 0 0.0000 397 Out... lnL = -991.489279 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -991.489279 Node 7: lnL = -991.489279 Node 8: lnL = -991.489279 Node 9: lnL = -991.489279 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 849 Sequential format.. Reading seq # 1: YMR311C_Sbay Reading seq # 2: YMR311C_Scer Reading seq # 3: YMR311C_Skud Reading seq # 4: YMR311C_Smik Reading seq # 5: YMR311C_Spar Sequences read.. Counting patterns.. # site patterns = 351 Counting frequencies.. 120 bytes for distance 56160 bytes for lkl0 44928 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.087829 0.165719 0.114596 0.181329 0.134279 0.298622 0.242423 0.183392 lnL0 = -4320.137423 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4320.137423 x= 0.08783 0.16572 0.11460 0.18133 0.13428 0.29862 0.24242 0.18339 1 h-lim-p 0.0030 0.0242 85.8920 4318.837262 4 0.0004 32 | 0/8 2 h-lim-p 0.0011 0.0085 22.9721 4318.715972 2 0.0005 48 | 0/8 3 h-lim-p 0.0010 0.0378 11.7181 4318.691638 3 0.0004 66 | 0/8 4 h-lim-p 0.0016 0.1351 3.2340 4318.689165 3 0.0005 86 | 0/8 5 h-lim-p 0.0022 0.4347 0.7637 4318.689003 3 0.0006 105 | 0/8 6 h-lim-p 0.0024 2.3366 0.1868 4318.688993 1 0.0006 128 | 0/8 7 h-lim-p 0.0345 20.0000 0.0032 4318.688822 0 0.1378 150 | 0/8 8 h-lim-p 0.0028 10.6421 0.1568 4318.687911 0 0.0057 171 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4318.687901 1 0.9961 193 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4318.687901 0 1.0938 213 | 0/8 11 h-lim-p 0.9991 20.0000 0.0000 4318.687901 0 0.9991 233 | 0/8 12 h-lim-p 0.0016 17.5099 0.0075 4318.687901 0 0.0000 265 | 0/8 13 h-lim-p 0.0011 20.0000 0.0000 4318.687901 0 0.0000 300 Out... lnL = -4318.687901 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4318.687901 Node 7: lnL = -4318.687901 Node 8: lnL = -4318.687901 Node 9: lnL = -4318.687901 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 426 Sequential format.. Reading seq # 1: YMR313C_Sbay Reading seq # 2: YMR313C_Scer Reading seq # 3: YMR313C_Skud Reading seq # 4: YMR313C_Smik Reading seq # 5: YMR313C_Spar Sequences read.. Counting patterns.. # site patterns = 190 Counting frequencies.. 120 bytes for distance 30400 bytes for lkl0 24320 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.108533 0.078228 0.075936 0.067467 0.107645 0.232497 0.210796 0.178700 lnL0 = -1871.548928 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1871.548928 x= 0.10853 0.07823 0.07594 0.06747 0.10765 0.23250 0.21080 0.17870 1 h-lim-p 0.0005 0.0038 57.8168 1870.858345 2 0.0004 26 | 0/8 2 h-lim-p 0.0021 0.0169 9.5507 1870.823256 7 0.0008 54 | 0/8 3 h-lim-p 0.0015 0.0452 5.1675 1870.816594 4 0.0006 76 | 0/8 4 h-lim-p 0.0010 0.0978 3.1680 1870.815470 5 0.0003 102 | 0/8 5 h-lim-p 0.0012 0.2554 0.8301 1870.815291 2 0.0006 118 | 0/8 6 h-lim-p 0.0061 3.2238 0.0780 1870.815287 0 0.0013 139 | 0/8 7 h-lim-p 0.1025 20.0000 0.0010 1870.814953 0 0.8198 162 | 0/8 8 h-lim-p 0.0022 0.4612 0.3797 1870.814787 4 0.0013 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1870.814768 2 0.9961 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1870.814768 0 2.1875 238 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1870.814768 0 0.5469 259 | 0/8 12 h-lim-p 0.0487 20.0000 0.0000 1870.814768 0 0.0061 281 | 0/8 13 h-lim-p 0.0023 20.0000 0.0000 1870.814768 0 0.0000 317 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -1870.814768 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1870.814768 Node 7: lnL = -1870.814768 Node 8: lnL = -1870.814768 Node 9: lnL = -1870.814768 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 428 Sequential format.. Reading seq # 1: YMR314W_Sbay Reading seq # 2: YMR314W_Scer Reading seq # 3: YMR314W_Skud Reading seq # 4: YMR314W_Smik Reading seq # 5: YMR314W_Spar Sequences read.. Counting patterns.. # site patterns = 184 Counting frequencies.. 120 bytes for distance 29440 bytes for lkl0 23552 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.119939 0.055179 0.079756 0.073575 0.104725 0.241527 0.236879 0.192229 lnL0 = -1967.365923 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1967.365923 x= 0.11994 0.05518 0.07976 0.07358 0.10472 0.24153 0.23688 0.19223 1 h-lim-p 0.0003 0.0022 74.6400 1966.332639 0 0.0004 22 | 0/8 2 h-lim-p 0.0017 0.0132 13.3394 1966.295130 6 0.0004 47 | 0/8 3 h-lim-p 0.0007 0.0175 7.9244 1966.285451 5 0.0004 70 | 0/8 4 h-lim-p 0.0011 0.0942 2.8920 1966.283433 4 0.0006 91 | 0/8 5 h-lim-p 0.0020 0.3484 0.8217 1966.283200 3 0.0008 109 | 0/8 6 h-lim-p 0.0026 1.0471 0.2374 1966.283180 2 0.0007 134 | 0/8 7 h-lim-p 0.0094 15.8606 0.0176 1966.283156 0 0.0141 154 | 0/8 8 h-lim-p 0.0167 6.5691 0.0148 1966.281351 0 0.1002 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1966.281331 2 0.9961 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1966.281331 0 2.1875 220 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1966.281331 0 0.5469 241 | 0/8 12 h-lim-p 0.1346 20.0000 0.0000 1966.281331 0 0.0011 267 | 0/8 13 h-lim-p 0.0006 20.0000 0.0000 1966.281331 0 0.0000 301 Out... lnL = -1966.281331 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1966.281331 Node 7: lnL = -1966.281331 Node 8: lnL = -1966.281331 Node 9: lnL = -1966.281331 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 434 Sequential format.. Reading seq # 1: YMR315W_Sbay Reading seq # 2: YMR315W_Scer Reading seq # 3: YMR315W_Skud Reading seq # 4: YMR315W_Smik Reading seq # 5: YMR315W_Spar Sequences read.. Counting patterns.. # site patterns = 185 Counting frequencies.. 120 bytes for distance 29600 bytes for lkl0 23680 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.077821 0.133828 0.065383 0.108976 0.050428 0.197217 0.189206 0.143619 lnL0 = -1847.490389 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1847.490389 x= 0.07782 0.13383 0.06538 0.10898 0.05043 0.19722 0.18921 0.14362 1 h-lim-p 0.0002 0.0013 64.7497 1846.757304 0 0.0003 23 | 0/8 2 h-lim-p 0.0006 0.0311 35.5612 1846.620138 2 0.0003 39 | 0/8 3 h-lim-p 0.0008 0.0124 11.6333 1846.588587 6 0.0005 65 | 0/8 4 h-lim-p 0.0017 0.0528 3.6127 1846.585580 6 0.0005 93 | 0/8 5 h-lim-p 0.0049 0.7464 0.3799 1846.585514 3 0.0008 113 | 0/8 6 h-lim-p 0.0016 1.5560 0.1863 1846.585479 2 0.0013 137 | 0/8 7 h-lim-p 0.0088 9.2004 0.0273 1846.584289 0 0.0706 160 | 0/8 8 h-lim-p 0.0053 0.2717 0.3666 1846.575264 0 0.0105 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0008 1846.574479 3 0.9961 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1846.574478 0 1.0938 227 | 0/8 11 h-lim-p 2.2643 20.0000 0.0000 1846.574478 0 0.2477 249 | 0/8 12 h-lim-p 0.1343 20.0000 0.0000 1846.574478 0 0.0005 276 | 0/8 13 h-lim-p 0.0009 20.0000 0.0000 1846.574478 0 0.0005 296 Out... lnL = -1846.574478 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1846.574478 Node 7: lnL = -1846.574478 Node 8: lnL = -1846.574478 Node 9: lnL = -1846.574478 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 907 Sequential format.. Reading seq # 1: YMR316W_Sbay Reading seq # 2: YMR316W_Scer Reading seq # 3: YMR316W_Skud Reading seq # 4: YMR316W_Smik Reading seq # 5: YMR316W_Spar Sequences read.. Counting patterns.. # site patterns = 408 Counting frequencies.. 120 bytes for distance 65280 bytes for lkl0 52224 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.274244 0.002682 0.101418 0.219040 0.139113 0.365904 0.281525 0.386741 lnL0 = -4555.346941 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4555.346941 x= 0.27424 0.00268 0.10142 0.21904 0.13911 0.36590 0.28152 0.38674 1 h-lim-p 0.0044 0.9853 144.2598 4552.809507 4 0.0003 33 | 0/8 2 h-lim-p 0.0010 0.0088 39.1926 4552.160462 2 0.0009 49 | 0/8 3 h-lim-p 0.0013 0.0149 26.4513 4552.027576 4 0.0005 69 | 0/8 4 h-lim-p 0.0012 0.0289 11.3437 4551.996018 4 0.0006 90 | 0/8 5 h-lim-p 0.0038 0.2414 1.8751 4551.993729 5 0.0013 113 | 0/8 6 h-lim-p 0.0066 1.3828 0.3821 4551.993632 2 0.0013 130 | 0/8 7 h-lim-p 0.0197 16.1717 0.0246 4551.993466 0 0.0197 150 | 0/8 8 h-lim-p 0.0077 20.0000 0.0632 4551.984172 0 0.0461 172 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 4551.983660 3 1.0004 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4551.983660 0 1.0938 218 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4551.983660 0 0.5469 239 | 0/8 12 h-lim-p 0.3571 20.0000 0.0000 4551.983660 0 0.0446 261 | 0/8 13 h-lim-p 0.0265 20.0000 0.0000 4551.983660 0 0.0000 300 Out... lnL = -4551.983660 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4551.983660 Node 7: lnL = -4551.983660 Node 8: lnL = -4551.983660 Node 9: lnL = -4551.983660 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 368 Sequential format.. Reading seq # 1: YNL001W_Sbay Reading seq # 2: YNL001W_Scer Reading seq # 3: YNL001W_Skud Reading seq # 4: YNL001W_Smik Reading seq # 5: YNL001W_Spar Sequences read.. Counting patterns.. # site patterns = 172 Counting frequencies.. 120 bytes for distance 27520 bytes for lkl0 22016 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.113619 0.151027 0.053559 0.194582 0.091645 0.233262 0.204499 0.196377 lnL0 = -1728.103207 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1728.103207 x= 0.11362 0.15103 0.05356 0.19458 0.09165 0.23326 0.20450 0.19638 1 h-lim-p 0.0004 0.0031 58.1318 1726.769855 0 0.0008 23 | 0/8 2 h-lim-p 0.0014 0.0108 14.4022 1726.684430 6 0.0009 49 | 0/8 3 h-lim-p 0.0073 0.1509 1.7077 1726.683307 4 0.0008 73 | 0/8 4 h-lim-p 0.0011 0.1367 1.1961 1726.683001 4 0.0006 94 | 0/8 5 h-lim-p 0.0032 0.6759 0.2218 1726.682972 3 0.0011 113 | 0/8 6 h-lim-p 0.0043 7.7680 0.0569 1726.682959 2 0.0033 137 | 0/8 7 h-lim-p 0.0194 20.0000 0.0098 1726.681717 0 0.1553 160 | 0/8 8 h-lim-p 0.0028 0.5265 0.5371 1726.680463 1 0.0035 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 1726.680421 2 0.9961 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1726.680421 0 1.0938 226 | 0/8 11 h-lim-p 1.6082 20.0000 0.0000 1726.680421 0 1.6082 246 | 0/8 12 h-lim-p 1.9110 20.0000 0.0000 1726.680421 0 0.0448 271 | 0/8 13 h-lim-p 0.0095 20.0000 0.0000 1726.680421 0 0.0000 301 | 0/8 14 h-lim-p 0.0003 20.0000 0.0000 1726.680421 0 0.0000 336 Out... lnL = -1726.680421 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1726.680421 Node 7: lnL = -1726.680421 Node 8: lnL = -1726.680421 Node 9: lnL = -1726.680421 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 385 Sequential format.. Reading seq # 1: YNL003C_Sbay Reading seq # 2: YNL003C_Scer Reading seq # 3: YNL003C_Skud Reading seq # 4: YNL003C_Smik Reading seq # 5: YNL003C_Spar Sequences read.. Counting patterns.. # site patterns = 160 Counting frequencies.. 120 bytes for distance 25600 bytes for lkl0 20480 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.068865 0.095968 0.055967 0.144045 0.086954 0.182438 0.250300 0.136576 lnL0 = -1738.636134 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1738.636134 x= 0.06886 0.09597 0.05597 0.14405 0.08695 0.18244 0.25030 0.13658 1 h-lim-p 0.0011 0.0087 72.3963 1737.612122 7 0.0004 39 | 0/8 2 h-lim-p 0.0011 0.0088 18.0215 1737.523861 7 0.0006 69 | 0/8 3 h-lim-p 0.0014 0.0351 7.5632 1737.511379 4 0.0005 89 | 0/8 4 h-lim-p 0.0018 0.1385 2.1633 1737.509692 3 0.0008 107 | 0/8 5 h-lim-p 0.0024 0.4310 0.7236 1737.509527 3 0.0007 127 | 0/8 6 h-lim-p 0.0031 1.7374 0.1707 1737.509518 0 0.0007 148 | 0/8 7 h-lim-p 0.0241 20.0000 0.0047 1737.509517 0 0.0105 168 | 0/8 8 h-lim-p 0.0150 20.0000 0.0033 1737.509388 0 0.1201 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1737.509388 0 1.0938 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1737.509388 0 1.0938 231 | 0/8 11 h-lim-p 1.1521 20.0000 0.0000 1737.509388 0 2.3041 252 | 0/8 12 h-lim-p 2.3859 20.0000 0.0000 1737.509388 0 0.0746 276 | 0/8 13 h-lim-p 0.0105 20.0000 0.0000 1737.509388 0 0.0052 296 | 0/8 14 h-lim-p 0.0016 20.0000 0.0002 1737.509388 0 0.0000 334 | 0/8 15 h-lim-p 0.0000 20.0000 0.0006 1737.509388 0 0.0000 356 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0006 | 0/8 18 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -1737.509388 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1737.509388 Node 7: lnL = -1737.509388 Node 8: lnL = -1737.509388 Node 9: lnL = -1737.509388 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 866 Sequential format.. Reading seq # 1: YNL005C_Sbay Reading seq # 2: YNL005C_Scer Reading seq # 3: YNL005C_Skud Reading seq # 4: YNL005C_Smik Reading seq # 5: YNL005C_Spar Sequences read.. Counting patterns.. # site patterns = 277 Counting frequencies.. 120 bytes for distance 44320 bytes for lkl0 35456 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.096750 0.067607 0.064297 0.137880 0.085168 0.184931 0.194913 0.162151 lnL0 = -3854.494615 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3854.494615 x= 0.09675 0.06761 0.06430 0.13788 0.08517 0.18493 0.19491 0.16215 1 h-lim-p 0.0005 0.0042 146.3690 3852.838458 9 0.0002 45 | 0/8 2 h-lim-p 0.0005 0.0042 24.3427 3852.777755 4 0.0002 65 | 0/8 3 h-lim-p 0.0006 0.0462 8.7313 3852.769702 3 0.0002 83 | 0/8 4 h-lim-p 0.0010 0.1172 2.1135 3852.768898 3 0.0004 101 | 0/8 5 h-lim-p 0.0036 1.1799 0.2293 3852.768889 1 0.0004 117 | 0/8 6 h-lim-p 0.0048 10.8503 0.0168 3852.768889 0 0.0003 140 | 0/8 7 h-lim-p 0.0020 20.0000 0.0025 3852.768889 0 0.0018 160 | 0/8 8 h-lim-p 0.0252 20.0000 0.0002 3852.768881 0 0.3019 183 | 0/8 9 h-lim-p 2.0947 20.0000 0.0000 3852.768881 0 0.9164 203 | 0/8 10 h-lim-p 1.6004 20.0000 0.0000 3852.768881 0 1.4003 223 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3852.768881 0 2.1875 243 | 0/8 12 h-lim-p 1.6050 20.0000 0.0000 3852.768881 0 0.7022 263 | 0/8 13 h-lim-p 0.1879 20.0000 0.0000 3852.768881 0 0.0000 295 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 3852.768881 0 0.0000 315 | 0/8 15 h-lim-p 0.0005 20.0000 0.0000 3852.768881 0 0.0000 348 Out... lnL = -3852.768881 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3852.768881 Node 7: lnL = -3852.768881 Node 8: lnL = -3852.768881 Node 9: lnL = -3852.768881 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 517 Sequential format.. Reading seq # 1: YNL006W_Sbay Reading seq # 2: YNL006W_Scer Reading seq # 3: YNL006W_Skud Reading seq # 4: YNL006W_Smik Reading seq # 5: YNL006W_Spar Sequences read.. Counting patterns.. # site patterns = 178 Counting frequencies.. 120 bytes for distance 28480 bytes for lkl0 22784 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.076623 0.067256 0.059370 0.067626 0.056643 0.162423 0.183641 0.130136 lnL0 = -2121.548273 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2121.548273 x= 0.07662 0.06726 0.05937 0.06763 0.05664 0.16242 0.18364 0.13014 1 h-lim-p 0.0003 0.0024 98.7841 2120.437842 4 0.0002 30 | 0/8 2 h-lim-p 0.0005 0.0042 28.3442 2120.337931 4 0.0003 51 | 0/8 3 h-lim-p 0.0006 0.0126 11.8893 2120.323155 4 0.0002 71 | 0/8 4 h-lim-p 0.0005 0.0304 5.7714 2120.318802 5 0.0003 95 | 0/8 5 h-lim-p 0.0018 0.2692 1.0460 2120.318669 4 0.0003 118 | 0/8 6 h-lim-p 0.0008 0.6556 0.3464 2120.318641 2 0.0005 135 | 0/8 7 h-lim-p 0.0030 3.3484 0.0566 2120.318641 0 0.0007 156 | 0/8 8 h-lim-p 0.0978 20.0000 0.0004 2120.318397 0 1.1737 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2120.318391 1 0.9961 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2120.318391 0 0.1562 224 | 0/8 11 h-lim-p 0.0791 20.0000 0.0000 2120.318391 0 0.0002 252 | 0/8 12 h-lim-p 0.0027 20.0000 0.0000 2120.318391 0 0.0000 292 Out... lnL = -2120.318391 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2120.318391 Node 7: lnL = -2120.318391 Node 8: lnL = -2120.318391 Node 9: lnL = -2120.318391 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 544 Sequential format.. Reading seq # 1: YNL007C_Sbay Reading seq # 2: YNL007C_Scer Reading seq # 3: YNL007C_Skud Reading seq # 4: YNL007C_Smik Reading seq # 5: YNL007C_Spar Sequences read.. Counting patterns.. # site patterns = 168 Counting frequencies.. 120 bytes for distance 26880 bytes for lkl0 21504 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.085306 0.457141 0.000060 0.493246 0.964392 0.325919 0.540072 0.193398 lnL0 = -2175.355484 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2175.355484 x= 0.08531 0.45714 0.00006 0.49325 0.96439 0.32592 0.54007 0.19340 1 h-lim-p 0.0000 0.0000 467.9482 2175.251484 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0007 1059.6255 1998.526586 9 0.0006 55 | 1/8 3 h-lim-p 0.0001 0.0006 310.0336 1986.164412 0 0.0003 69 | 1/8 4 h-lim-p 0.0005 0.0040 74.0551 1984.350779 0 0.0010 82 | 1/8 5 h-lim-p 0.0007 0.0056 48.8006 1983.828803 3 0.0006 100 | 1/8 6 h-lim-p 0.0033 0.4796 8.7377 1966.419174 0 0.2099 118 | 1/8 7 h-lim-p 0.6233 4.9866 0.0824 1966.115829 7 0.3718 147 | 1/8 8 h-lim-p 0.3787 13.2310 0.0809 1966.028970 0 0.7573 167 | 1/8 9 h-lim-p 1.5720 20.0000 0.0390 1966.019352 4 1.2127 194 | 0/8 10 h-lim-p 0.0317 3.0246 1.4928 1966.019294 2 0.0004 222 | 0/8 11 h-lim-p 0.0065 20.0000 0.0900 1966.009159 0 3.3507 243 | 0/8 12 h-lim-p 1.6000 20.0000 0.1884 1965.989175 5 1.7732 275 | 0/8 13 h-lim-p 1.4340 20.0000 0.2329 1965.979893 1 1.7925 297 | 0/8 14 h-lim-p 1.8828 20.0000 0.2218 1965.973961 1 2.3535 319 | 0/8 15 h-lim-p 2.3572 20.0000 0.2214 1965.971319 3 2.4769 345 | 0/8 16 h-lim-p 2.2419 20.0000 0.2446 1965.970169 0 3.3628 365 | 0/8 17 h-lim-p 2.5000 20.0000 0.1604 1965.969750 4 1.6456 394 | 0/8 18 h-lim-p 1.1715 20.0000 0.2252 1965.969490 0 7.0290 416 | 0/8 19 h-lim-p 2.5000 20.0000 0.1245 1965.969452 1 1.2500 438 | 0/8 20 h-lim-p 1.2688 20.0000 0.1227 1965.969439 010.1128 461 | 0/8 21 h-lim-p 2.5000 20.0000 0.1295 1965.969434 1 1.2305 484 | 0/8 22 h-lim-p 0.9185 20.0000 0.1734 1965.969432 0 7.3482 507 | 0/8 23 h-lim-p 0.9857 7.8858 0.3150 1965.969432 0 1.4786 527 | 0/8 24 h-lim-p 0.4434 3.5470 0.5691 1965.969432 0 0.4434 547 | 0/8 25 h-lim-p 0.0243 0.1942 9.0941 1965.969432 0 0.0243 567 | 0/8 26 h-lim-p 1.1206 20.0000 0.1970 1965.969432 0 0.9806 579 | 0/8 27 h-lim-p 2.5000 20.0000 0.0196 1965.969432 0 2.5000 599 | 0/8 28 h-lim-p 0.1701 5.8695 0.2879 1965.969432 0 0.0851 619 | 0/8 29 h-lim-p 0.0369 2.5110 0.6633 1965.969432 0 0.0323 639 | 0/8 30 h-lim-p 0.0171 1.3083 1.2566 1965.969432 0 0.0149 659 | 0/8 31 h-lim-p 1.1188 20.0000 0.0168 1965.969432 0 1.6781 671 | 0/8 32 h-lim-p 2.5000 20.0000 0.0030 1965.969432 m20.0000 691 | 0/8 33 h-lim-p 0.0784 2.0911 0.7620 1965.969432 0 0.0343 711 | 0/8 34 h-lim-p 0.0222 1.3317 1.1770 1965.969432 0 0.0024 733 | 0/8 35 h-lim-p 1.1869 20.0000 0.0024 1965.969432 0 3.5608 746 | 0/8 36 h-lim-p 2.5000 20.0000 0.0016 1965.969432 0 1.0938 766 | 0/8 37 h-lim-p 0.3047 20.0000 0.0059 1965.969432 0 0.0095 790 | 0/8 38 h-lim-p 0.0025 20.0000 0.0225 1965.969432 0 0.0000 819 | 0/8 39 h-lim-p 0.0002 20.0000 0.0002 1965.969432 0 0.0002 839 | 0/8 40 h-lim-p 0.0001 20.0000 0.0004 1965.969432 0 0.0000 873 | 0/8 41 h-lim-p 0.0000 20.0000 0.0020 1965.969432 0 0.0001 896 | 0/8 42 h-lim-p 0.0004 20.0000 0.0004 1965.969432 0 0.0004 916 | 0/8 43 h-lim-p 0.0024 20.0000 0.0001 1965.969432 0 0.0000 943 | 0/8 44 h-lim-p 0.0000 20.0000 0.0001 1965.969432 0 0.0000 963 | 0/8 45 h-lim-p 0.0000 11.5172 0.0024 1965.969432 0 0.0000 983 | 0/8 46 h-lim-p 0.0000 0.9929 0.0279 1965.969432 0 0.0000 1009 | 0/8 47 h-lim-p 0.0000 14.7811 0.0018 1965.969432 0 0.0000 1038 | 0/8 48 h-lim-p 0.0000 20.0000 0.0004 1965.969432 0 0.0000 1069 | 0/8 49 h-lim-p 0.0000 20.0000 0.0012 1965.969432 0 0.0000 1090 | 0/8 50 h-lim-p 0.0001 20.0000 0.0002 .. | 0/8 51 h-lim-p 0.0000 20.0000 0.0011 | 0/8 52 h-lim-p 0.0000 20.0000 0.0011 Out... lnL = -1965.969432 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1965.969432 Node 7: lnL = -1965.969432 Node 8: lnL = -1965.969432 Node 9: lnL = -1965.969432 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 594 Sequential format.. Reading seq # 1: YNL009W_Sbay Reading seq # 2: YNL009W_Scer Reading seq # 3: YNL009W_Skud Reading seq # 4: YNL009W_Smik Reading seq # 5: YNL009W_Spar Sequences read.. Counting patterns.. # site patterns = 199 Counting frequencies.. 120 bytes for distance 31840 bytes for lkl0 25472 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.143006 0.135398 0.080367 0.160554 0.100161 0.229434 0.252815 0.221769 lnL0 = -2514.581461 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2514.581461 x= 0.14301 0.13540 0.08037 0.16055 0.10016 0.22943 0.25281 0.22177 1 h-lim-p 0.0007 0.0058 24.8590 2514.423969 8 0.0005 42 | 0/8 2 h-lim-p 0.0016 0.3176 7.9620 2514.412006 5 0.0004 65 | 0/8 3 h-lim-p 0.0022 0.2472 1.5037 2514.410879 2 0.0010 81 | 0/8 4 h-lim-p 0.0041 0.8476 0.3757 2514.410823 1 0.0008 96 | 0/8 5 h-lim-p 0.0017 2.0666 0.1848 2514.410814 1 0.0007 118 | 0/8 6 h-lim-p 0.0032 9.9057 0.0384 2514.410814 0 0.0008 139 | 0/8 7 h-lim-p 0.0064 20.0000 0.0048 2514.410814 0 0.0056 159 | 0/8 8 h-lim-p 0.0444 20.0000 0.0006 2514.410790 0 0.3549 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2514.410787 0 1.0938 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2514.410787 0 1.0938 222 | 0/8 11 h-lim-p 1.8406 20.0000 0.0000 2514.410787 0 0.8053 242 | 0/8 12 h-lim-p 0.5923 20.0000 0.0000 2514.410787 0 0.0006 271 Out... lnL = -2514.410787 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2514.410787 Node 7: lnL = -2514.410787 Node 8: lnL = -2514.410787 Node 9: lnL = -2514.410787 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 521 Sequential format.. Reading seq # 1: YNL010W_Sbay Reading seq # 2: YNL010W_Scer Reading seq # 3: YNL010W_Skud Reading seq # 4: YNL010W_Smik Reading seq # 5: YNL010W_Spar Sequences read.. Counting patterns.. # site patterns = 188 Counting frequencies.. 120 bytes for distance 30080 bytes for lkl0 24064 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.082596 0.123138 0.045691 0.148396 0.074814 0.181428 0.184306 0.141256 lnL0 = -2264.540902 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2264.540902 x= 0.08260 0.12314 0.04569 0.14840 0.07481 0.18143 0.18431 0.14126 1 h-lim-p 0.0053 0.0424 83.9189 2263.801501 8 0.0002 47 | 0/8 2 h-lim-p 0.0008 0.0068 14.3420 2263.764819 6 0.0004 70 | 0/8 3 h-lim-p 0.0008 0.0459 6.2658 2263.757187 6 0.0005 96 | 0/8 4 h-lim-p 0.0022 0.1807 1.3022 2263.756738 2 0.0006 113 | 0/8 5 h-lim-p 0.0054 2.1500 0.1391 2263.756734 1 0.0003 130 | 0/8 6 h-lim-p 0.0024 16.9316 0.0195 2263.756734 0 0.0010 150 | 0/8 7 h-lim-p 0.0234 20.0000 0.0009 2263.756734 0 0.0103 170 | 0/8 8 h-lim-p 0.0137 20.0000 0.0006 2263.756731 0 0.1097 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2263.756731 0 1.0938 213 | 0/8 10 h-lim-p 2.0817 20.0000 0.0000 2263.756731 0 1.8215 233 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2263.756731 0 0.2734 255 | 0/8 12 h-lim-p 0.0599 20.0000 0.0000 2263.756731 0 0.0150 276 | 0/8 13 h-lim-p 0.0067 20.0000 0.0000 2263.756731 0 0.0004 299 | 0/8 14 h-lim-p 0.0002 20.0000 0.0001 2263.756731 0 0.0000 329 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 2263.756731 0 0.0000 359 Out... lnL = -2263.756731 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2263.756731 Node 7: lnL = -2263.756731 Node 8: lnL = -2263.756731 Node 9: lnL = -2263.756731 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 515 Sequential format.. Reading seq # 1: YNL011C_Sbay Reading seq # 2: YNL011C_Scer Reading seq # 3: YNL011C_Skud Reading seq # 4: YNL011C_Smik Reading seq # 5: YNL011C_Spar Sequences read.. Counting patterns.. # site patterns = 156 Counting frequencies.. 120 bytes for distance 24960 bytes for lkl0 19968 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.013417 0.119289 0.000060 0.232464 4.641294 0.269470 0.225374 0.219763 lnL0 = -2038.954091 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2038.954091 x= 0.01342 0.11929 0.00006 0.23246 4.64129 0.26947 0.22537 0.21976 1 h-lim-p 0.0000 0.0000 98.7533 2038.931685 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0088 37.6901 2038.464874 0 0.0006 40 | 1/8 3 h-lim-p 0.0010 0.0083 10.6639 2038.417844 3 0.0009 58 | 1/8 4 h-lim-p 0.0073 0.2251 1.2721 2038.397760 5 0.0055 80 | 1/8 5 h-lim-p 0.0101 0.3847 0.6937 2037.080219 0 0.0811 95 | 1/8 6 h-lim-p 0.0011 0.0086 38.1848 2035.850459 0 0.0022 115 | 1/8 7 h-lim-p 1.4428 11.5421 0.0158 2035.738430 7 0.8481 143 | 1/8 8 h-lim-p 2.5000 20.0000 0.0008 2035.738186 4 0.7998 172 | 1/8 9 h-lim-p 2.5000 20.0000 0.0001 2035.738185 1 0.6152 194 | 1/8 10 h-lim-p 2.5000 20.0000 0.0000 2035.738184 0 1.0938 213 | 1/8 11 h-lim-p 1.4405 20.0000 0.0000 2035.738184 0 1.2605 232 | 1/8 12 h-lim-p 1.8864 20.0000 0.0000 2035.738184 0 1.6506 251 | 1/8 13 h-lim-p 1.1942 20.0000 0.0000 2035.738184 0 0.1493 272 | 1/8 14 h-lim-p 0.0245 20.0000 0.0000 2035.738184 0 0.0490 292 | 1/8 15 h-lim-p 0.0178 20.0000 0.0001 2035.738184 0 0.0011 314 | 1/8 16 h-lim-p 0.0011 20.0000 0.0001 2035.738184 0 0.0000 352 | 1/8 17 h-lim-p 0.0000 20.0000 0.0002 | 1/8 18 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -2035.738184 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2035.738184 Node 7: lnL = -2035.738184 Node 8: lnL = -2035.738184 Node 9: lnL = -2035.738184 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 973 Sequential format.. Reading seq # 1: YNL015W_Sbay Reading seq # 2: YNL015W_Scer Reading seq # 3: YNL015W_Skud Reading seq # 4: YNL015W_Smik Reading seq # 5: YNL015W_Spar Sequences read.. Counting patterns.. # site patterns = 301 Counting frequencies.. 120 bytes for distance 48160 bytes for lkl0 38528 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.114957 0.088317 0.077648 0.090757 0.081800 0.163234 0.226210 0.175567 lnL0 = -4005.447528 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4005.447528 x= 0.11496 0.08832 0.07765 0.09076 0.08180 0.16323 0.22621 0.17557 1 h-lim-p 0.0032 0.0257 121.2915 4004.029386 7 0.0002 40 | 0/8 2 h-lim-p 0.0009 0.0096 25.9859 4003.937590 7 0.0003 69 | 0/8 3 h-lim-p 0.0006 0.0328 11.9731 4003.925845 5 0.0002 93 | 0/8 4 h-lim-p 0.0004 0.0474 5.4761 4003.921992 5 0.0003 116 | 0/8 5 h-lim-p 0.0014 0.2333 1.2139 4003.921708 4 0.0004 139 | 0/8 6 h-lim-p 0.0059 1.4414 0.0836 4003.921708 0 0.0003 154 | 0/8 7 h-lim-p 0.0020 19.2388 0.0134 4003.921707 0 0.0018 174 | 0/8 8 h-lim-p 0.0259 20.0000 0.0009 4003.921504 0 0.4149 198 | 0/8 9 h-lim-p 1.6776 20.0000 0.0002 4003.921495 1 0.8257 221 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4003.921495 0 1.0938 241 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4003.921495 0 1.0938 261 | 0/8 12 h-lim-p 0.8449 20.0000 0.0000 4003.921495 0 0.0462 284 | 0/8 13 h-lim-p 0.0158 20.0000 0.0000 4003.921495 0 0.0000 322 | 0/8 14 h-lim-p 0.0000 20.0000 0.0009 4003.921495 0 0.0000 350 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0009 | 0/8 17 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -4003.921495 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4003.921495 Node 7: lnL = -4003.921495 Node 8: lnL = -4003.921495 Node 9: lnL = -4003.921495 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 481 Sequential format.. Reading seq # 1: YNL016W_Sbay Reading seq # 2: YNL016W_Scer Reading seq # 3: YNL016W_Skud Reading seq # 4: YNL016W_Smik Reading seq # 5: YNL016W_Spar Sequences read.. Counting patterns.. # site patterns = 158 Counting frequencies.. 120 bytes for distance 25280 bytes for lkl0 20224 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.072180 0.052334 0.052850 0.089621 0.080523 0.131758 0.156671 0.116476 lnL0 = -1922.951874 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1922.951874 x= 0.07218 0.05233 0.05285 0.08962 0.08052 0.13176 0.15667 0.11648 1 h-lim-p 0.0009 0.0070 142.9144 1921.010352 4 0.0002 31 | 0/8 2 h-lim-p 0.0006 0.0046 25.0648 1920.893860 6 0.0004 58 | 0/8 3 h-lim-p 0.0011 0.0218 8.9498 1920.882046 6 0.0003 85 | 0/8 4 h-lim-p 0.0014 0.0623 2.1302 1920.881208 4 0.0004 108 | 0/8 5 h-lim-p 0.0094 2.2765 0.0884 1920.881207 1 0.0005 125 | 0/8 6 h-lim-p 0.0053 20.0000 0.0078 1920.881207 0 0.0006 147 | 0/8 7 h-lim-p 0.0020 20.0000 0.0023 1920.881206 0 0.0040 168 | 0/8 8 h-lim-p 0.0076 20.0000 0.0012 1920.881188 0 0.0910 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1920.881188 0 1.0938 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1920.881188 0 0.5469 232 | 0/8 11 h-lim-p 0.4086 20.0000 0.0000 1920.881188 0 0.0128 256 | 0/8 12 h-lim-p 0.0064 20.0000 0.0000 1920.881188 0 0.0016 277 | 0/8 13 h-lim-p 0.0010 20.0000 0.0000 1920.881188 0 0.0003 298 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 1920.881188 0 0.0001 319 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 1920.881188 0 0.0000 347 | 0/8 16 h-lim-p 0.0000 20.0000 0.0012 1920.881188 0 0.0000 379 | 0/8 17 h-lim-p 0.0000 20.0000 0.0012 1920.881188 0 0.0000 403 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 1920.881188 0 0.0000 426 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 20 h-lim-p 0.0000 20.0000 0.0012 | 0/8 21 h-lim-p 0.0000 20.0000 0.0012 Out... lnL = -1920.881188 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1920.881188 Node 7: lnL = -1920.881188 Node 8: lnL = -1920.881188 Node 9: lnL = -1920.881188 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 803 Sequential format.. Reading seq # 1: YNL019C_Sbay Reading seq # 2: YNL019C_Scer Reading seq # 3: YNL019C_Skud Reading seq # 4: YNL019C_Smik Reading seq # 5: YNL019C_Spar Sequences read.. Counting patterns.. # site patterns = 394 Counting frequencies.. 120 bytes for distance 63040 bytes for lkl0 50432 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.242407 0.065304 0.058767 0.219253 0.086514 0.207177 0.272332 0.327201 lnL0 = -3664.753083 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3664.753083 x= 0.24241 0.06530 0.05877 0.21925 0.08651 0.20718 0.27233 0.32720 1 h-lim-p 0.0008 0.0065 224.6715 3657.797439 8 0.0003 41 | 0/8 2 h-lim-p 0.0005 0.0037 76.6049 3656.260236 0 0.0007 53 | 0/8 3 h-lim-p 0.0023 0.0180 22.6158 3656.088071 6 0.0007 78 | 0/8 4 h-lim-p 0.0023 0.0299 7.4426 3656.069604 4 0.0007 100 | 0/8 5 h-lim-p 0.0022 0.1025 2.5137 3656.067389 5 0.0008 124 | 0/8 6 h-lim-p 0.0048 0.4063 0.4068 3656.066868 4 0.0035 145 | 0/8 7 h-lim-p 0.0055 0.4622 0.2577 3656.066406 4 0.0031 175 | 0/8 8 h-lim-p 0.0097 8.5318 0.0833 3656.010753 0 0.1159 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0018 3656.008101 4 1.0660 228 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 3656.008051 3 1.4660 257 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3656.008051 0 1.0938 277 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3656.008051 0 1.0938 297 | 0/8 13 h-lim-p 1.5611 20.0000 0.0000 3656.008051 0 0.0122 323 | 0/8 14 h-lim-p 0.0036 20.0000 0.0000 3656.008051 0 0.0000 362 Out... lnL = -3656.008051 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3656.008051 Node 7: lnL = -3656.008051 Node 8: lnL = -3656.008051 Node 9: lnL = -3656.008051 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 339 Sequential format.. Reading seq # 1: YNL021W_Sbay Reading seq # 2: YNL021W_Scer Reading seq # 3: YNL021W_Skud Reading seq # 4: YNL021W_Smik Reading seq # 5: YNL021W_Spar Sequences read.. Counting patterns.. # site patterns = 118 Counting frequencies.. 120 bytes for distance 18880 bytes for lkl0 15104 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.071745 0.022203 0.076518 0.083717 0.062341 0.097564 0.107567 0.109173 lnL0 = -1292.014452 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1292.014452 x= 0.07175 0.02220 0.07652 0.08372 0.06234 0.09756 0.10757 0.10917 1 h-lim-p 0.0006 0.0047 126.6929 1290.821611 8 0.0002 40 | 0/8 2 h-lim-p 0.0006 0.0050 17.7220 1290.765272 7 0.0004 70 | 0/8 3 h-lim-p 0.0015 0.0380 4.3607 1290.762406 3 0.0003 89 | 0/8 4 h-lim-p 0.0010 0.1006 1.3999 1290.762011 2 0.0004 105 | 0/8 5 h-lim-p 0.0028 1.4722 0.2190 1290.762000 2 0.0004 123 | 0/8 6 h-lim-p 0.0040 5.8971 0.0240 1290.762000 0 0.0004 145 | 0/8 7 h-lim-p 0.0079 20.0000 0.0013 1290.761999 0 0.0069 165 | 0/8 8 h-lim-p 0.0076 20.0000 0.0012 1290.761980 0 0.0913 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1290.761979 0 1.0938 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1290.761979 0 2.1875 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1290.761979 0 1.0938 248 | 0/8 12 h-lim-p 0.3268 20.0000 0.0000 1290.761979 0 5.2287 272 | 0/8 13 h-lim-p 2.3000 20.0000 0.0000 1290.761979 0 0.1258 295 | 0/8 14 h-lim-p 0.5167 20.0000 0.0000 1290.761979 0 0.0161 319 | 0/8 15 h-lim-p 0.0077 20.0000 0.0000 1290.761979 0 0.0010 341 | 0/8 16 h-lim-p 0.0007 20.0000 0.0000 1290.761979 0 0.0000 367 Out... lnL = -1290.761979 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1290.761979 Node 7: lnL = -1290.761979 Node 8: lnL = -1290.761979 Node 9: lnL = -1290.761979 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 339 Sequential format.. Reading seq # 1: YNL022C_Sbay Reading seq # 2: YNL022C_Scer Reading seq # 3: YNL022C_Skud Reading seq # 4: YNL022C_Smik Reading seq # 5: YNL022C_Spar Sequences read.. Counting patterns.. # site patterns = 119 Counting frequencies.. 120 bytes for distance 19040 bytes for lkl0 15232 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.081547 0.013707 0.076197 0.089148 0.060670 0.102563 0.096139 0.119190 lnL0 = -1293.073433 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1293.073433 x= 0.08155 0.01371 0.07620 0.08915 0.06067 0.10256 0.09614 0.11919 1 h-lim-p 0.0007 0.0060 162.6863 1291.669858 9 0.0001 44 | 0/8 2 h-lim-p 0.0006 0.0047 26.0571 1291.530083 7 0.0004 72 | 0/8 3 h-lim-p 0.0013 0.0209 8.2042 1291.521288 5 0.0003 94 | 0/8 4 h-lim-p 0.0014 0.0750 1.6847 1291.520727 4 0.0004 117 | 0/8 5 h-lim-p 0.0043 1.5901 0.1612 1291.520721 1 0.0004 133 | 0/8 6 h-lim-p 0.0090 13.2971 0.0078 1291.520721 0 0.0005 156 | 0/8 7 h-lim-p 0.0033 20.0000 0.0012 1291.520721 0 0.0029 176 | 0/8 8 h-lim-p 0.0126 20.0000 0.0003 1291.520717 0 0.2013 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1291.520717 0 2.1875 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1291.520717 0 1.0938 240 | 0/8 11 h-lim-p 1.6618 20.0000 0.0000 1291.520717 0 0.0909 263 | 0/8 12 h-lim-p 0.0463 20.0000 0.0000 1291.520717 0 0.0029 286 | 0/8 13 h-lim-p 0.0021 20.0000 0.0000 1291.520717 0 0.0021 306 | 0/8 14 h-lim-p 0.0014 20.0000 0.0000 1291.520717 0 0.0000 332 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 1291.520717 0 0.0000 353 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 1291.520717 0 0.0000 386 | 0/8 17 h-lim-p 0.0000 20.0000 0.0025 | 0/8 18 h-lim-p 0.0000 20.0000 0.0025 Out... lnL = -1291.520717 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1291.520717 Node 7: lnL = -1291.520717 Node 8: lnL = -1291.520717 Node 9: lnL = -1291.520717 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 275 Sequential format.. Reading seq # 1: YNL023C_Sbay Reading seq # 2: YNL023C_Scer Reading seq # 3: YNL023C_Skud Reading seq # 4: YNL023C_Smik Reading seq # 5: YNL023C_Spar Sequences read.. Counting patterns.. # site patterns = 138 Counting frequencies.. 120 bytes for distance 22080 bytes for lkl0 17664 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.089225 0.137586 0.063618 0.159126 0.083853 0.263940 0.168317 0.156509 lnL0 = -1281.314763 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1281.314763 x= 0.08922 0.13759 0.06362 0.15913 0.08385 0.26394 0.16832 0.15651 1 h-lim-p 0.0011 0.0086 38.1148 1280.867069 8 0.0007 45 | 0/8 2 h-lim-p 0.0022 0.0174 6.8737 1280.849119 6 0.0008 70 | 0/8 3 h-lim-p 0.0017 0.1184 3.1492 1280.846226 3 0.0007 88 | 0/8 4 h-lim-p 0.0027 0.4576 0.8388 1280.845788 4 0.0014 109 | 0/8 5 h-lim-p 0.0084 1.0786 0.1356 1280.845780 0 0.0009 131 | 0/8 6 h-lim-p 0.0054 20.0000 0.0232 1280.845780 0 0.0012 152 | 0/8 7 h-lim-p 0.0093 20.0000 0.0029 1280.845779 0 0.0082 172 | 0/8 8 h-lim-p 0.0471 20.0000 0.0005 1280.845767 0 0.3768 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1280.845766 0 1.0938 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1280.845766 0 1.0938 235 | 0/8 11 h-lim-p 1.6896 20.0000 0.0000 1280.845766 0 0.1848 257 | 0/8 12 h-lim-p 0.0898 20.0000 0.0000 1280.845766 0 0.0006 283 | 0/8 13 h-lim-p 0.0003 20.0000 0.0000 1280.845766 0 0.0000 318 | 0/8 14 h-lim-p 0.0000 20.0000 0.0005 1280.845766 0 0.0000 343 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 1280.845766 0 0.0000 364 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 1280.845766 0 0.0017 388 | 0/8 17 h-lim-p 0.0041 20.0000 0.0000 1280.845766 0 0.0021 408 | 0/8 18 h-lim-p 0.0017 20.0000 0.0000 1280.845766 0 0.0002 430 | 0/8 19 h-lim-p 0.0000 20.0000 0.0004 1280.845766 0 0.0000 450 | 0/8 20 h-lim-p 0.0000 20.0000 0.0014 1280.845766 0 0.0000 475 | 0/8 21 h-lim-p 0.0000 20.0000 0.0002 1280.845766 0 0.0000 508 | 0/8 22 h-lim-p 0.0000 20.0000 0.0005 1280.845766 0 0.0000 535 | 0/8 23 h-lim-p 0.0000 20.0000 0.0002 1280.845766 0 0.0000 559 | 0/8 24 h-lim-p 0.0000 20.0000 0.0000 1280.845766 0 0.0000 584 | 0/8 25 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 26 h-lim-p 0.0000 20.0000 0.0005 | 0/8 27 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -1280.845766 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1280.845766 Node 7: lnL = -1280.845766 Node 8: lnL = -1280.845766 Node 9: lnL = -1280.845766 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 461 Sequential format.. Reading seq # 1: YNL024C_Sbay Reading seq # 2: YNL024C_Scer Reading seq # 3: YNL024C_Skud Reading seq # 4: YNL024C_Smik Reading seq # 5: YNL024C_Spar Sequences read.. Counting patterns.. # site patterns = 197 Counting frequencies.. 120 bytes for distance 31520 bytes for lkl0 25216 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.097512 0.068297 0.058670 0.117370 0.098798 0.229147 0.183657 0.149033 lnL0 = -1960.518225 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1960.518225 x= 0.09751 0.06830 0.05867 0.11737 0.09880 0.22915 0.18366 0.14903 1 h-lim-p 0.0027 0.0217 86.2563 1959.200013 7 0.0004 40 | 0/8 2 h-lim-p 0.0005 0.0037 21.5808 1959.093128 4 0.0005 60 | 0/8 3 h-lim-p 0.0016 0.0304 6.3104 1959.083358 4 0.0005 82 | 0/8 4 h-lim-p 0.0017 0.1054 1.9812 1959.082460 4 0.0005 105 | 0/8 5 h-lim-p 0.0015 0.2775 0.6471 1959.082312 2 0.0008 122 | 0/8 6 h-lim-p 0.0295 13.9400 0.0167 1959.082309 0 0.0032 144 | 0/8 7 h-lim-p 0.0016 12.8625 0.0331 1959.082281 0 0.0065 166 | 0/8 8 h-lim-p 0.0062 20.0000 0.0348 1959.081467 0 0.0248 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1959.081455 1 0.9961 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1959.081455 0 1.0938 230 | 0/8 11 h-lim-p 1.3246 20.0000 0.0000 1959.081455 0 2.6492 251 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1959.081455 0 0.0049 279 Out... lnL = -1959.081455 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1959.081455 Node 7: lnL = -1959.081455 Node 8: lnL = -1959.081455 Node 9: lnL = -1959.081455 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 845 Sequential format.. Reading seq # 1: YNL025C_Sbay Reading seq # 2: YNL025C_Scer Reading seq # 3: YNL025C_Skud Reading seq # 4: YNL025C_Smik Reading seq # 5: YNL025C_Spar Sequences read.. Counting patterns.. # site patterns = 184 Counting frequencies.. 120 bytes for distance 29440 bytes for lkl0 23552 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.048190 0.018648 0.019115 0.058879 0.056004 0.121693 0.104637 0.073291 lnL0 = -2941.861410 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2941.861410 x= 0.04819 0.01865 0.01911 0.05888 0.05600 0.12169 0.10464 0.07329 1 h-lim-p 0.0004 0.3173 385.9581 2939.075891 5 0.0000 33 | 0/8 2 h-lim-p 0.0001 0.0008 62.3694 2938.874527 4 0.0001 53 | 0/8 3 h-lim-p 0.0002 0.0034 34.5339 2938.817658 7 0.0001 81 | 0/8 4 h-lim-p 0.0007 0.0150 6.2568 2938.815556 5 0.0001 106 | 0/8 5 h-lim-p 0.0011 0.1624 0.6365 2938.815529 1 0.0001 122 | 0/8 6 h-lim-p 0.0003 1.1364 0.2839 2938.815525 1 0.0001 144 | 0/8 7 h-lim-p 0.0008 1.6570 0.0419 2938.815525 0 0.0002 165 | 0/8 8 h-lim-p 0.0444 20.0000 0.0002 2938.815370 0 1.0646 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2938.815363 0 1.0938 209 | 0/8 10 h-lim-p 2.4670 20.0000 0.0000 2938.815363 0 2.1587 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2938.815363 0 1.0938 249 | 0/8 12 h-lim-p 0.3418 20.0000 0.0000 2938.815363 0 2.7342 272 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2938.815363 0 0.0003 304 Out... lnL = -2938.815363 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2938.815363 Node 7: lnL = -2938.815363 Node 8: lnL = -2938.815363 Node 9: lnL = -2938.815363 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 694 Sequential format.. Reading seq # 1: YNL032W_Sbay Reading seq # 2: YNL032W_Scer Reading seq # 3: YNL032W_Skud Reading seq # 4: YNL032W_Smik Reading seq # 5: YNL032W_Spar Sequences read.. Counting patterns.. # site patterns = 232 Counting frequencies.. 120 bytes for distance 37120 bytes for lkl0 29696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.082778 0.119595 0.114614 0.134455 0.088143 0.116456 0.148981 0.133814 lnL0 = -3035.292762 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3035.292762 x= 0.08278 0.11960 0.11461 0.13445 0.08814 0.11646 0.14898 0.13381 1 h-lim-p 0.0003 0.0023 67.5784 3034.573290 7 0.0003 40 | 0/8 2 h-lim-p 0.0009 0.0119 23.9734 3034.502584 7 0.0003 71 | 0/8 3 h-lim-p 0.0010 0.0330 6.8463 3034.496833 6 0.0003 99 | 0/8 4 h-lim-p 0.0012 0.1671 1.5005 3034.496494 4 0.0003 120 | 0/8 5 h-lim-p 0.0024 0.7364 0.1954 3034.496488 1 0.0003 136 | 0/8 6 h-lim-p 0.0020 7.8728 0.0287 3034.496487 0 0.0005 157 | 0/8 7 h-lim-p 0.0192 20.0000 0.0008 3034.496248 0 0.6139 182 | 0/8 8 h-lim-p 0.0012 0.9143 0.3779 3034.496213 2 0.0004 207 | 0/8 9 h-lim-p 2.2828 20.0000 0.0001 3034.496207 0 0.9987 227 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3034.496207 0 0.2734 249 | 0/8 11 h-lim-p 0.1637 20.0000 0.0000 3034.496207 0 0.0358 270 | 0/8 12 h-lim-p 0.0202 20.0000 0.0000 3034.496207 0 0.0025 292 | 0/8 13 h-lim-p 0.0018 20.0000 0.0000 3034.496207 0 0.0005 313 | 0/8 14 h-lim-p 0.0005 20.0000 0.0000 3034.496207 0 0.0001 335 | 0/8 15 h-lim-p 0.0007 20.0000 0.0000 3034.496207 0 0.0000 366 Out... lnL = -3034.496207 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3034.496207 Node 7: lnL = -3034.496207 Node 8: lnL = -3034.496207 Node 9: lnL = -3034.496207 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 858 Sequential format.. Reading seq # 1: YNL035C_Sbay Reading seq # 2: YNL035C_Scer Reading seq # 3: YNL035C_Skud Reading seq # 4: YNL035C_Smik Reading seq # 5: YNL035C_Spar Sequences read.. Counting patterns.. # site patterns = 390 Counting frequencies.. 120 bytes for distance 62400 bytes for lkl0 49920 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.216401 0.024369 0.119493 0.153416 0.139763 0.793929 0.308641 0.320226 lnL0 = -3933.780310 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3933.780310 x= 0.21640 0.02437 0.11949 0.15342 0.13976 0.79393 0.30864 0.32023 1 h-lim-p 0.0011 0.0089 69.9099 3932.085740 9 0.0007 43 | 0/8 2 h-lim-p 0.0007 0.0054 58.9256 3931.479093 7 0.0005 71 | 0/8 3 h-lim-p 0.0020 0.0319 14.7038 3931.439591 3 0.0004 90 | 0/8 4 h-lim-p 0.0007 0.0382 8.7945 3931.415929 1 0.0009 104 | 0/8 5 h-lim-p 0.0013 0.0429 5.8812 3931.401649 2 0.0012 120 | 0/8 6 h-lim-p 0.0023 0.0536 3.1208 3931.396340 5 0.0016 145 | 0/8 7 h-lim-p 0.0453 4.1871 0.1088 3931.396286 2 0.0087 162 | 0/8 8 h-lim-p 1.2505 20.0000 0.0008 3931.396060 3 0.9486 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3931.396059 0 1.0938 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3931.396059 0 1.0938 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3931.396059 0 2.1875 248 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3931.396059 0 0.5469 269 | 0/8 13 h-lim-p 0.0478 20.0000 0.0000 3931.396059 0 0.0060 291 | 0/8 14 h-lim-p 0.0030 20.0000 0.0000 3931.396059 0 0.0000 328 Out... lnL = -3931.396059 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3931.396059 Node 7: lnL = -3931.396059 Node 8: lnL = -3931.396059 Node 9: lnL = -3931.396059 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 853 Sequential format.. Reading seq # 1: YNL036W_Sbay Reading seq # 2: YNL036W_Scer Reading seq # 3: YNL036W_Skud Reading seq # 4: YNL036W_Smik Reading seq # 5: YNL036W_Spar Sequences read.. Counting patterns.. # site patterns = 302 Counting frequencies.. 120 bytes for distance 48320 bytes for lkl0 38656 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.057790 0.065662 0.065274 0.126008 0.019753 0.171272 0.123202 0.095992 lnL0 = -3361.360919 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3361.360919 x= 0.05779 0.06566 0.06527 0.12601 0.01975 0.17127 0.12320 0.09599 1 h-lim-p 0.0002 0.1954 562.0514 3353.508318 7 0.0001 40 | 0/8 2 h-lim-p 0.0003 0.0023 95.7536 3352.734270 7 0.0002 70 | 0/8 3 h-lim-p 0.0008 0.0066 17.9564 3352.703127 2 0.0002 87 | 0/8 4 h-lim-p 0.0006 0.0281 6.1866 3352.698856 4 0.0002 106 | 0/8 5 h-lim-p 0.0012 0.2525 1.2322 3352.698651 2 0.0003 123 | 0/8 6 h-lim-p 0.0023 1.4909 0.1457 3352.698644 1 0.0005 138 | 0/8 7 h-lim-p 0.0135 20.0000 0.0050 3352.697500 0 0.1616 161 | 0/8 8 h-lim-p 0.0012 0.0903 0.6605 3352.689394 0 0.0024 182 | 0/8 9 h-lim-p 1.9215 20.0000 0.0008 3352.689253 3 1.0114 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3352.689252 0 1.0938 229 | 0/8 11 h-lim-p 1.4804 20.0000 0.0000 3352.689252 0 1.2953 249 | 0/8 12 h-lim-p 1.5104 20.0000 0.0000 3352.689252 0 0.3776 270 | 0/8 13 h-lim-p 0.0624 20.0000 0.0001 3352.689252 0 0.0312 290 | 0/8 14 h-lim-p 0.0109 20.0000 0.0003 3352.689252 0 0.0007 313 | 0/8 15 h-lim-p 0.0006 20.0000 0.0004 3352.689252 0 0.0006 333 | 0/8 16 h-lim-p 0.0008 20.0000 0.0003 3352.689252 0 0.0000 362 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 3352.689252 0 0.0000 384 | 0/8 18 h-lim-p 0.0002 20.0000 0.0000 3352.689252 0 0.0000 416 Out... lnL = -3352.689252 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3352.689252 Node 7: lnL = -3352.689252 Node 8: lnL = -3352.689252 Node 9: lnL = -3352.689252 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 483 Sequential format.. Reading seq # 1: YNL044W_Sbay Reading seq # 2: YNL044W_Scer Reading seq # 3: YNL044W_Skud Reading seq # 4: YNL044W_Smik Reading seq # 5: YNL044W_Spar Sequences read.. Counting patterns.. # site patterns = 199 Counting frequencies.. 120 bytes for distance 31840 bytes for lkl0 25472 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.078984 0.044796 0.037995 0.166243 0.105662 0.220961 0.149356 0.125930 lnL0 = -1944.059041 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1944.059041 x= 0.07898 0.04480 0.03799 0.16624 0.10566 0.22096 0.14936 0.12593 1 h-lim-p 0.0007 0.0057 110.4238 1942.749810 9 0.0002 43 | 0/8 2 h-lim-p 0.0005 0.0037 30.8100 1942.524499 7 0.0005 74 | 0/8 3 h-lim-p 0.0010 0.0127 14.7872 1942.482330 2 0.0005 90 | 0/8 4 h-lim-p 0.0027 0.1120 2.6688 1942.480969 5 0.0004 116 | 0/8 5 h-lim-p 0.0074 3.2993 0.1438 1942.480962 1 0.0007 132 | 0/8 6 h-lim-p 0.0042 6.2718 0.0255 1942.480962 0 0.0009 153 | 0/8 7 h-lim-p 0.0028 20.0000 0.0082 1942.480961 0 0.0042 173 | 0/8 8 h-lim-p 0.0072 20.0000 0.0048 1942.480834 0 0.1160 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1942.480819 1 0.9961 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1942.480819 0 1.2500 239 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1942.480819 0 1.0938 259 | 0/8 12 h-lim-p 0.9518 20.0000 0.0000 1942.480819 0 5.7110 281 | 0/8 13 h-lim-p 0.5698 20.0000 0.0001 1942.480819 0 0.1425 302 | 0/8 14 h-lim-p 0.0055 20.0000 0.0020 1942.480819 0 0.0000 328 | 0/8 15 h-lim-p 0.0005 20.0000 0.0002 1942.480819 0 0.0000 352 | 0/8 16 h-lim-p 0.0003 20.0000 0.0000 1942.480819 0 0.0000 374 Out... lnL = -1942.480819 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1942.480819 Node 7: lnL = -1942.480819 Node 8: lnL = -1942.480819 Node 9: lnL = -1942.480819 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 148 Sequential format.. Reading seq # 1: YNL045W_Sbay Reading seq # 2: YNL045W_Scer Reading seq # 3: YNL045W_Skud Reading seq # 4: YNL045W_Smik Reading seq # 5: YNL045W_Spar Sequences read.. Counting patterns.. # site patterns = 63 Counting frequencies.. 120 bytes for distance 10080 bytes for lkl0 8064 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.062477 0.031347 0.018063 0.097043 0.027920 0.071954 0.151348 0.090274 lnL0 = -513.987561 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 513.987561 x= 0.06248 0.03135 0.01806 0.09704 0.02792 0.07195 0.15135 0.09027 1 h-lim-p 0.0003 0.0020 78.2287 513.399635 2 0.0002 26 | 0/8 2 h-lim-p 0.0002 0.0016 27.3512 513.213548 0 0.0008 40 | 0/8 3 h-lim-p 0.0001 0.0012 28.4575 513.147763 0 0.0003 53 | 0/8 4 h-lim-p 0.0005 0.0252 15.3249 513.101423 1 0.0007 67 | 0/8 5 h-lim-p 0.0020 0.0160 3.8113 513.096827 6 0.0007 93 | 0/8 6 h-lim-p 0.0020 0.0972 1.3837 513.096211 5 0.0007 117 | 0/8 7 h-lim-p 0.0195 5.3186 0.0510 513.095828 3 0.0156 135 | 0/8 8 h-lim-p 0.0068 2.0506 0.1176 513.074670 0 0.0543 158 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 513.074265 4 1.2732 187 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 513.074253 0 1.0938 207 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 513.074253 0 1.0938 227 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 513.074253 0 2.1875 247 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 513.074253 0 0.5469 268 | 0/8 14 h-lim-p 0.1936 20.0000 0.0000 513.074253 0 0.0242 290 | 0/8 15 h-lim-p 0.0120 20.0000 0.0000 513.074253 0 0.0000 324 Out... lnL = -513.074253 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -513.074253 Node 7: lnL = -513.074253 Node 8: lnL = -513.074253 Node 9: lnL = -513.074253 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 460 Sequential format.. Reading seq # 1: YNL046W_Sbay Reading seq # 2: YNL046W_Scer Reading seq # 3: YNL046W_Skud Reading seq # 4: YNL046W_Smik Reading seq # 5: YNL046W_Spar Sequences read.. Counting patterns.. # site patterns = 153 Counting frequencies.. 120 bytes for distance 24480 bytes for lkl0 19584 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.079673 0.073943 0.048977 0.101488 0.077870 0.173252 0.165899 0.123463 lnL0 = -1914.129324 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1914.129324 x= 0.07967 0.07394 0.04898 0.10149 0.07787 0.17325 0.16590 0.12346 1 h-lim-p 0.0047 1.1824 90.3056 1913.345939 7 0.0002 40 | 0/8 2 h-lim-p 0.0028 0.0225 6.7505 1913.337949 5 0.0004 65 | 0/8 3 h-lim-p 0.0009 0.1624 2.7555 1913.336469 4 0.0004 86 | 0/8 4 h-lim-p 0.0028 0.2211 0.4327 1913.336426 3 0.0005 106 | 0/8 5 h-lim-p 0.0023 4.1519 0.0849 1913.336425 1 0.0003 130 | 0/8 6 h-lim-p 0.0021 20.0000 0.0117 1913.336425 0 0.0009 150 | 0/8 7 h-lim-p 0.0065 20.0000 0.0017 1913.336425 0 0.0007 172 | 0/8 8 h-lim-p 0.0262 20.0000 0.0000 1913.336424 0 0.8388 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1913.336424 0 1.0938 217 | 0/8 10 h-lim-p 1.3163 20.0000 0.0000 1913.336424 0 1.9745 237 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1913.336424 0 0.5469 258 | 0/8 12 h-lim-p 0.1108 20.0000 0.0000 1913.336424 0 0.0277 279 | 0/8 13 h-lim-p 0.0107 20.0000 0.0000 1913.336424 0 0.0054 299 | 0/8 14 h-lim-p 0.0026 20.0000 0.0001 1913.336424 0 0.0000 331 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 1913.336424 0 0.0000 356 Out... lnL = -1913.336424 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1913.336424 Node 7: lnL = -1913.336424 Node 8: lnL = -1913.336424 Node 9: lnL = -1913.336424 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 566 Sequential format.. Reading seq # 1: YNL051W_Sbay Reading seq # 2: YNL051W_Scer Reading seq # 3: YNL051W_Skud Reading seq # 4: YNL051W_Smik Reading seq # 5: YNL051W_Spar Sequences read.. Counting patterns.. # site patterns = 167 Counting frequencies.. 120 bytes for distance 26720 bytes for lkl0 21376 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.009354 0.077735 0.044721 0.092202 0.061861 1.085326 0.272597 0.096421 lnL0 = -1980.405557 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1980.405557 x= 0.00935 0.07773 0.04472 0.09220 0.06186 1.08533 0.27260 0.09642 1 h-lim-p 0.0002 0.0031 422.0064 1966.864891 9 0.0002 42 | 0/8 2 h-lim-p 0.0003 0.0023 116.0193 1962.011815 0 0.0006 55 | 0/8 3 h-lim-p 0.0004 0.0031 80.6350 1961.358481 8 0.0003 88 | 0/8 4 h-lim-p 0.0013 0.0106 15.8427 1961.318820 2 0.0003 105 | 0/8 5 h-lim-p 0.0058 0.2060 0.8930 1961.317906 4 0.0015 126 | 0/8 6 h-lim-p 0.0006 0.0697 2.2332 1961.264604 2 0.0380 155 | 0/8 7 h-lim-p 0.1029 0.8234 0.3978 1961.175118 0 0.3088 168 | 0/8 8 h-lim-p 0.3495 2.7960 0.3051 1961.150468 5 0.2944 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0170 1961.145291 5 1.0082 228 | 0/8 10 h-lim-p 2.5000 20.0000 0.0047 1961.144798 4 1.4725 258 | 0/8 11 h-lim-p 2.5000 20.0000 0.0023 1961.144775 2 0.9644 282 | 0/8 12 h-lim-p 2.5000 20.0000 0.0001 1961.144775 0 1.0938 302 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1961.144775 0 1.0938 322 | 0/8 14 h-lim-p 1.3476 20.0000 0.0000 1961.144775 0 8.0854 344 | 0/8 15 h-lim-p 0.3108 20.0000 0.0004 1961.144775 0 0.0002 374 | 0/8 16 h-lim-p 0.0003 20.0000 0.0002 1961.144775 0 0.0000 398 | 0/8 17 h-lim-p 0.0003 20.0000 0.0000 1961.144775 0 0.0000 434 Out... lnL = -1961.144775 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1961.144775 Node 7: lnL = -1961.144775 Node 8: lnL = -1961.144775 Node 9: lnL = -1961.144775 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 331 Sequential format.. Reading seq # 1: YNL052W_Sbay Reading seq # 2: YNL052W_Scer Reading seq # 3: YNL052W_Skud Reading seq # 4: YNL052W_Smik Reading seq # 5: YNL052W_Spar Sequences read.. Counting patterns.. # site patterns = 127 Counting frequencies.. 120 bytes for distance 20320 bytes for lkl0 16256 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.055502 0.078455 0.015676 0.099688 0.003925 0.119060 0.178347 0.088677 lnL0 = -1249.155847 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1249.155847 x= 0.05550 0.07845 0.01568 0.09969 0.00392 0.11906 0.17835 0.08868 1 h-lim-p 0.0000 0.1089 947.1819 1241.640944 0 0.0000 22 | 0/8 2 h-lim-p 0.0004 0.0028 84.9694 1240.697640 7 0.0003 48 | 0/8 3 h-lim-p 0.0007 0.0055 24.2225 1240.567757 8 0.0005 81 | 0/8 4 h-lim-p 0.0030 0.0437 3.7964 1240.563719 4 0.0006 102 | 0/8 5 h-lim-p 0.0027 0.1261 0.8000 1240.563587 3 0.0004 124 | 0/8 6 h-lim-p 0.0035 1.7940 0.0904 1240.563496 1 0.0037 146 | 0/8 7 h-lim-p 0.0077 4.3085 0.0429 1240.547807 0 0.1232 170 | 0/8 8 h-lim-p 0.0043 0.0381 1.2400 1240.450518 0 0.0064 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0010 1240.448955 5 0.9284 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1240.448933 2 1.1719 238 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1240.448933 0 1.0938 258 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1240.448933 0 2.1875 278 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1240.448933 0 1.0938 298 | 0/8 14 h-lim-p 0.2705 20.0000 0.0000 1240.448933 0 4.3279 322 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1240.448933 0 0.5469 343 | 0/8 16 h-lim-p 0.0217 20.0000 0.0000 1240.448933 0 0.0001 370 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 1240.448933 0 0.0000 391 | 0/8 18 h-lim-p 0.0001 20.0000 0.0000 1240.448933 0 0.0000 423 | 0/8 19 h-lim-p 0.0000 20.0000 0.0008 1240.448933 0 0.0000 450 | 0/8 20 h-lim-p 0.0000 20.0000 0.0005 1240.448933 0 0.0026 478 | 0/8 21 h-lim-p 0.0073 20.0000 0.0002 1240.448933 0 0.0000 516 | 0/8 22 h-lim-p 0.0000 20.0000 0.0035 | 0/8 23 h-lim-p 0.0000 20.0000 0.0035 Out... lnL = -1240.448933 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1240.448933 Node 7: lnL = -1240.448933 Node 8: lnL = -1240.448933 Node 9: lnL = -1240.448933 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 379 Sequential format.. Reading seq # 1: YNL053W_Sbay Reading seq # 2: YNL053W_Scer Reading seq # 3: YNL053W_Skud Reading seq # 4: YNL053W_Smik Reading seq # 5: YNL053W_Spar Sequences read.. Counting patterns.. # site patterns = 99 Counting frequencies.. 120 bytes for distance 15840 bytes for lkl0 12672 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.048349 0.026827 0.030936 0.020618 0.028723 0.059680 0.059528 0.066220 lnL0 = -1100.367842 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1100.367842 x= 0.04835 0.02683 0.03094 0.02062 0.02872 0.05968 0.05953 0.06622 1 h-lim-p 0.0001 0.0009 94.7466 1099.954831 7 0.0001 37 | 0/8 2 h-lim-p 0.0002 0.0019 26.0763 1099.918929 2 0.0001 53 | 0/8 3 h-lim-p 0.0003 0.0123 10.6878 1099.912406 4 0.0001 73 | 0/8 4 h-lim-p 0.0004 0.0188 3.3558 1099.911790 5 0.0001 98 | 0/8 5 h-lim-p 0.0007 0.1595 0.5977 1099.911763 2 0.0002 115 | 0/8 6 h-lim-p 0.0011 1.1877 0.0820 1099.911762 0 0.0002 136 | 0/8 7 h-lim-p 0.0090 20.0000 0.0022 1099.911762 0 0.0078 156 | 0/8 8 h-lim-p 0.0070 11.3551 0.0025 1099.911708 0 0.0559 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1099.911701 2 0.9644 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1099.911701 0 0.5469 224 | 0/8 11 h-lim-p 0.3895 20.0000 0.0000 1099.911701 0 0.0000 271 | 0/8 12 h-lim-p 0.0000 20.0000 0.0071 | 0/8 13 h-lim-p 0.0000 20.0000 0.0071 Out... lnL = -1099.911701 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1099.911701 Node 7: lnL = -1099.911701 Node 8: lnL = -1099.911701 Node 9: lnL = -1099.911701 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 642 Sequential format.. Reading seq # 1: YNL055C_Sbay Reading seq # 2: YNL055C_Scer Reading seq # 3: YNL055C_Skud Reading seq # 4: YNL055C_Smik Reading seq # 5: YNL055C_Spar Sequences read.. Counting patterns.. # site patterns = 317 Counting frequencies.. 120 bytes for distance 50720 bytes for lkl0 40576 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.103558 0.000060 0.066274 0.245133 0.248268 0.254518 0.323696 0.170623 lnL0 = -3232.501726 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3232.501726 x= 0.10356 0.00006 0.06627 0.24513 0.24827 0.25452 0.32370 0.17062 1 h-lim-p 0.0021 0.7900 176.8922 3227.866731 5 0.0003 34 | 0/8 2 h-lim-p 0.0006 0.0050 39.4281 3227.375634 4 0.0006 54 | 0/8 3 h-lim-p 0.0019 0.0284 13.0859 3227.318873 5 0.0007 76 | 0/8 4 h-lim-p 0.0028 0.0222 2.1758 3227.317447 2 0.0006 93 | 0/8 5 h-lim-p 0.0030 0.8086 0.4362 3227.317343 3 0.0012 111 | 0/8 6 h-lim-p 0.0479 20.0000 0.0105 3227.317322 1 0.0191 133 | 0/8 7 h-lim-p 0.0056 10.1706 0.0357 3227.316790 0 0.0224 155 | 0/8 8 h-lim-p 0.0019 1.8034 0.4160 3227.316013 0 0.0029 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 3227.315972 1 0.9961 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3227.315972 0 1.0938 217 | 0/8 11 h-lim-p 1.3270 20.0000 0.0000 3227.315972 0 1.1612 237 | 0/8 12 h-lim-p 0.6388 20.0000 0.0000 3227.315972 0 0.2396 258 | 0/8 13 h-lim-p 0.0109 20.0000 0.0003 3227.315972 0 0.0002 283 | 0/8 14 h-lim-p 0.0008 20.0000 0.0001 3227.315972 0 0.0000 315 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -3227.315972 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3227.315972 Node 7: lnL = -3227.315972 Node 8: lnL = -3227.315972 Node 9: lnL = -3227.315972 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 546 Sequential format.. Reading seq # 1: YNL056W_Sbay Reading seq # 2: YNL056W_Scer Reading seq # 3: YNL056W_Skud Reading seq # 4: YNL056W_Smik Reading seq # 5: YNL056W_Spar Sequences read.. Counting patterns.. # site patterns = 223 Counting frequencies.. 120 bytes for distance 35680 bytes for lkl0 28544 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.103516 0.109165 0.095998 0.156691 0.051533 0.181866 0.188718 0.151029 lnL0 = -2453.114474 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2453.114474 x= 0.10352 0.10917 0.09600 0.15669 0.05153 0.18187 0.18872 0.15103 1 h-lim-p 0.0062 1.7813 88.6446 2452.199898 8 0.0002 45 | 0/8 2 h-lim-p 0.0005 0.0041 31.0062 2452.047261 6 0.0004 72 | 0/8 3 h-lim-p 0.0013 0.0278 8.4546 2452.026766 2 0.0006 88 | 0/8 4 h-lim-p 0.0060 0.3654 0.8464 2452.026515 2 0.0007 106 | 0/8 5 h-lim-p 0.0038 1.3077 0.1589 2452.026508 1 0.0005 130 | 0/8 6 h-lim-p 0.0089 20.0000 0.0082 2452.026508 0 0.0020 151 | 0/8 7 h-lim-p 0.0059 20.0000 0.0027 2452.026500 0 0.0470 174 | 0/8 8 h-lim-p 0.0027 7.9853 0.0482 2452.026426 0 0.0053 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2452.026425 0 1.0938 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2452.026425 0 1.0938 235 | 0/8 11 h-lim-p 1.2970 20.0000 0.0000 2452.026425 0 0.6485 255 | 0/8 12 h-lim-p 0.3495 20.0000 0.0000 2452.026425 0 0.0764 276 | 0/8 13 h-lim-p 0.0267 20.0000 0.0000 2452.026425 0 0.0001 303 | 0/8 14 h-lim-p 0.0003 20.0000 0.0000 2452.026425 0 0.0001 324 Out... lnL = -2452.026425 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2452.026425 Node 7: lnL = -2452.026425 Node 8: lnL = -2452.026425 Node 9: lnL = -2452.026425 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 335 Sequential format.. Reading seq # 1: YNL061W_Sbay Reading seq # 2: YNL061W_Scer Reading seq # 3: YNL061W_Skud Reading seq # 4: YNL061W_Smik Reading seq # 5: YNL061W_Spar Sequences read.. Counting patterns.. # site patterns = 123 Counting frequencies.. 120 bytes for distance 19680 bytes for lkl0 15744 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.074312 0.014257 0.058380 0.127376 0.050974 0.184191 0.180811 0.109110 lnL0 = -1370.179578 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1370.179578 x= 0.07431 0.01426 0.05838 0.12738 0.05097 0.18419 0.18081 0.10911 1 h-lim-p 0.0003 0.0022 111.2584 1369.268592 7 0.0002 41 | 0/8 2 h-lim-p 0.0006 0.0045 22.1013 1369.167869 7 0.0004 69 | 0/8 3 h-lim-p 0.0007 0.0293 12.9431 1369.147992 6 0.0003 93 | 0/8 4 h-lim-p 0.0011 0.0914 3.5372 1369.144365 6 0.0006 122 | 0/8 5 h-lim-p 0.0036 0.2775 0.6266 1369.144265 3 0.0005 143 | 0/8 6 h-lim-p 0.0037 0.8277 0.0918 1369.144263 1 0.0005 167 | 0/8 7 h-lim-p 0.0013 6.2160 0.0309 1369.144263 0 0.0012 187 | 0/8 8 h-lim-p 0.1244 20.0000 0.0003 1369.144102 0 0.9952 210 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1369.144098 0 1.0938 230 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1369.144098 0 0.0098 257 | 0/8 11 h-lim-p 0.0047 20.0000 0.0000 1369.144098 0 0.0001 281 | 0/8 12 h-lim-p 0.0001 20.0000 0.0000 1369.144098 0 0.0000 315 | 0/8 13 h-lim-p 0.0000 20.0000 0.0013 | 0/8 14 h-lim-p 0.0000 20.0000 0.0013 Out... lnL = -1369.144098 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1369.144098 Node 7: lnL = -1369.144098 Node 8: lnL = -1369.144098 Node 9: lnL = -1369.144098 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 335 Sequential format.. Reading seq # 1: YNL062C_Sbay Reading seq # 2: YNL062C_Scer Reading seq # 3: YNL062C_Skud Reading seq # 4: YNL062C_Smik Reading seq # 5: YNL062C_Spar Sequences read.. Counting patterns.. # site patterns = 121 Counting frequencies.. 120 bytes for distance 19360 bytes for lkl0 15488 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.074071 0.007602 0.058099 0.128974 0.049376 0.182661 0.181791 0.108372 lnL0 = -1366.397323 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1366.397323 x= 0.07407 0.00760 0.05810 0.12897 0.04938 0.18266 0.18179 0.10837 1 h-lim-p 0.0003 0.0022 151.7010 1365.093944 6 0.0001 36 | 0/8 2 h-lim-p 0.0004 0.0032 26.7638 1364.951106 4 0.0004 56 | 0/8 3 h-lim-p 0.0007 0.0195 16.2972 1364.919435 2 0.0003 72 | 0/8 4 h-lim-p 0.0011 0.0466 4.4559 1364.914116 4 0.0006 93 | 0/8 5 h-lim-p 0.0025 0.1990 1.0689 1364.913844 3 0.0005 112 | 0/8 6 h-lim-p 0.0029 0.4782 0.1891 1364.913836 2 0.0005 131 | 0/8 7 h-lim-p 0.0028 6.8011 0.0326 1364.913835 0 0.0012 151 | 0/8 8 h-lim-p 0.0791 20.0000 0.0005 1364.913507 0 0.9495 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1364.913486 0 1.2500 194 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1364.913486 0 1.0938 214 | 0/8 11 h-lim-p 1.5246 20.0000 0.0000 1364.913486 0 0.3335 235 | 0/8 12 h-lim-p 0.1897 20.0000 0.0000 1364.913486 0 0.0015 261 | 0/8 13 h-lim-p 0.0010 20.0000 0.0000 1364.913486 0 0.0002 282 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 1364.913486 0 0.0000 302 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 1364.913486 0 0.0000 337 | 0/8 16 h-lim-p 0.0000 20.0000 0.0013 1364.913486 0 0.0000 361 | 0/8 17 h-lim-p 0.0000 20.0000 0.0005 1364.913486 0 0.0013 388 | 0/8 18 h-lim-p 0.0054 20.0000 0.0001 1364.913486 0 0.0000 418 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 1364.913486 0 0.0000 438 | 0/8 20 h-lim-p 0.0000 20.0000 0.0000 1364.913486 0 0.0000 468 | 0/8 21 h-lim-p 0.0000 20.0000 0.0022 1364.913486 0 0.0000 496 | 0/8 22 h-lim-p 0.0000 20.0000 0.0003 1364.913486 0 0.0013 523 | 0/8 23 h-lim-p 0.0036 20.0000 0.0001 1364.913486 0 0.0000 553 | 0/8 24 h-lim-p 0.0000 20.0000 0.0001 1364.913486 0 0.0000 574 | 0/8 25 h-lim-p 0.0000 20.0000 0.0002 .. | 0/8 26 h-lim-p 0.0000 20.0000 0.0023 | 0/8 27 h-lim-p 0.0000 20.0000 0.0023 Out... lnL = -1364.913486 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1364.913486 Node 7: lnL = -1364.913486 Node 8: lnL = -1364.913486 Node 9: lnL = -1364.913486 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 695 Sequential format.. Reading seq # 1: YNL063W_Sbay Reading seq # 2: YNL063W_Scer Reading seq # 3: YNL063W_Skud Reading seq # 4: YNL063W_Smik Reading seq # 5: YNL063W_Spar Sequences read.. Counting patterns.. # site patterns = 219 Counting frequencies.. 120 bytes for distance 35040 bytes for lkl0 28032 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.101557 0.022000 0.048768 0.093131 0.082389 0.157393 0.174430 0.137037 lnL0 = -2862.339872 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2862.339872 x= 0.10156 0.02200 0.04877 0.09313 0.08239 0.15739 0.17443 0.13704 1 h-lim-p 0.0006 0.0044 285.8494 2858.397831 8 0.0001 43 | 0/8 2 h-lim-p 0.0007 0.0053 28.8340 2858.267531 2 0.0003 59 | 0/8 3 h-lim-p 0.0007 0.0176 12.0239 2858.250862 6 0.0003 84 | 0/8 4 h-lim-p 0.0007 0.0336 4.3134 2858.249121 5 0.0002 109 | 0/8 5 h-lim-p 0.0025 0.5061 0.3717 2858.249098 2 0.0003 127 | 0/8 6 h-lim-p 0.0029 4.5582 0.0419 2858.249098 0 0.0003 149 | 0/8 7 h-lim-p 0.0011 15.2667 0.0126 2858.249098 0 0.0005 169 | 0/8 8 h-lim-p 0.1207 20.0000 0.0000 2858.249088 0 1.4483 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2858.249087 0 1.0938 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2858.249087 0 2.1875 232 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2858.249087 0 0.6250 253 | 0/8 12 h-lim-p 0.1407 20.0000 0.0000 2858.249087 0 0.0000 288 Out... lnL = -2858.249087 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2858.249087 Node 7: lnL = -2858.249087 Node 8: lnL = -2858.249087 Node 9: lnL = -2858.249087 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 933 Sequential format.. Reading seq # 1: YNL067W_Sbay Reading seq # 2: YNL067W_Scer Reading seq # 3: YNL067W_Skud Reading seq # 4: YNL067W_Smik Reading seq # 5: YNL067W_Spar Sequences read.. Counting patterns.. # site patterns = 423 Counting frequencies.. 120 bytes for distance 67680 bytes for lkl0 54144 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.173317 0.036924 0.104893 0.187368 0.145692 0.272380 0.652259 0.252264 lnL0 = -4810.830911 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4810.830911 x= 0.17332 0.03692 0.10489 0.18737 0.14569 0.27238 0.65226 0.25226 1 h-lim-p 0.0015 0.0122 100.8765 4808.957383 4 0.0004 31 | 0/8 2 h-lim-p 0.0008 0.0061 41.4616 4808.515935 6 0.0006 55 | 0/8 3 h-lim-p 0.0010 0.0158 24.3432 4808.405401 4 0.0005 77 | 0/8 4 h-lim-p 0.0013 0.0388 9.4979 4808.378324 6 0.0007 106 | 0/8 5 h-lim-p 0.0021 0.0893 3.3913 4808.373764 3 0.0009 124 | 0/8 6 h-lim-p 0.0027 0.1078 1.1834 4808.372685 4 0.0018 145 | 0/8 7 h-lim-p 0.0016 0.2068 1.3376 4808.372313 3 0.0008 164 | 0/8 8 h-lim-p 0.7950 20.0000 0.0013 4808.370490 0 1.5901 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 4808.370309 2 0.9961 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4808.370309 0 1.0938 221 | 0/8 11 h-lim-p 1.7410 20.0000 0.0000 4808.370309 0 0.7617 241 | 0/8 12 h-lim-p 0.5054 20.0000 0.0000 4808.370309 0 0.0079 266 | 0/8 13 h-lim-p 0.0020 20.0000 0.0000 4808.370309 0 0.0001 289 | 0/8 14 h-lim-p 0.0008 20.0000 0.0000 4808.370309 0 0.0008 309 Out... lnL = -4808.370309 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4808.370309 Node 7: lnL = -4808.370309 Node 8: lnL = -4808.370309 Node 9: lnL = -4808.370309 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 287 Sequential format.. Reading seq # 1: YNL071W_Sbay Reading seq # 2: YNL071W_Scer Reading seq # 3: YNL071W_Skud Reading seq # 4: YNL071W_Smik Reading seq # 5: YNL071W_Spar Sequences read.. Counting patterns.. # site patterns = 116 Counting frequencies.. 120 bytes for distance 18560 bytes for lkl0 14848 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.096030 0.132074 0.000060 0.143708 0.078571 0.129220 0.111188 0.132123 lnL0 = -1156.654250 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1156.654250 x= 0.09603 0.13207 0.00006 0.14371 0.07857 0.12922 0.11119 0.13212 1 h-lim-p 0.0006 0.0169 194.3801 1154.419716 8 0.0001 42 | 0/8 2 h-lim-p 0.0005 0.0041 26.0917 1154.251329 2 0.0005 58 | 0/8 3 h-lim-p 0.0019 0.0318 6.5175 1154.238903 6 0.0006 84 | 0/8 4 h-lim-p 0.0033 0.1821 1.2161 1154.238197 5 0.0010 109 | 0/8 5 h-lim-p 0.0046 0.7337 0.2615 1154.238173 3 0.0007 130 | 0/8 6 h-lim-p 0.0070 9.7697 0.0279 1154.238173 1 0.0009 154 | 0/8 7 h-lim-p 0.0277 20.0000 0.0009 1154.237927 0 0.6645 178 | 0/8 8 h-lim-p 0.0017 0.2647 0.3279 1154.237806 4 0.0012 208 | 0/8 9 h-lim-p 2.1695 20.0000 0.0002 1154.237767 2 1.1419 233 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1154.237767 0 1.0938 253 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1154.237767 0 0.2734 275 | 0/8 12 h-lim-p 0.1590 20.0000 0.0000 1154.237767 0 0.0003 303 Out... lnL = -1154.237767 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1154.237767 Node 7: lnL = -1154.237767 Node 8: lnL = -1154.237767 Node 9: lnL = -1154.237767 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 217 Sequential format.. Reading seq # 1: YNL072W_Sbay Reading seq # 2: YNL072W_Scer Reading seq # 3: YNL072W_Skud Reading seq # 4: YNL072W_Smik Reading seq # 5: YNL072W_Spar Sequences read.. Counting patterns.. # site patterns = 124 Counting frequencies.. 120 bytes for distance 19840 bytes for lkl0 15872 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.139568 0.055289 0.054789 0.105473 0.092969 0.267169 0.300170 0.192141 lnL0 = -1002.812519 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1002.812519 x= 0.13957 0.05529 0.05479 0.10547 0.09297 0.26717 0.30017 0.19214 1 h-lim-p 0.0056 0.0445 40.1160 1002.326252 3 0.0006 30 | 0/8 2 h-lim-p 0.0036 0.0291 5.2936 1002.311517 7 0.0011 60 | 0/8 3 h-lim-p 0.0017 0.1063 3.2180 1002.306514 6 0.0013 86 | 0/8 4 h-lim-p 0.0034 0.1514 1.1930 1002.305646 4 0.0015 105 | 0/8 5 h-lim-p 0.0057 1.0184 0.3063 1002.305550 2 0.0023 121 | 0/8 6 h-lim-p 0.0072 2.8815 0.0954 1002.305543 0 0.0018 142 | 0/8 7 h-lim-p 0.0065 11.3361 0.0264 1002.305542 0 0.0029 162 | 0/8 8 h-lim-p 0.6345 20.0000 0.0001 1002.305530 0 1.2691 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1002.305530 0 1.0938 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1002.305530 0 1.0938 223 | 0/8 11 h-lim-p 1.5527 20.0000 0.0000 1002.305530 0 1.3586 243 | 0/8 12 h-lim-p 1.3360 20.0000 0.0000 1002.305530 0 1.3360 263 | 0/8 13 h-lim-p 0.1682 20.0000 0.0000 1002.305530 0 0.1682 283 | 0/8 14 h-lim-p 0.0407 20.0000 0.0000 1002.305530 0 0.0000 322 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 1002.305530 0 0.0000 356 Out... lnL = -1002.305530 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1002.305530 Node 7: lnL = -1002.305530 Node 8: lnL = -1002.305530 Node 9: lnL = -1002.305530 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 271 Sequential format.. Reading seq # 1: YNL073W_Sbay Reading seq # 2: YNL073W_Scer Reading seq # 3: YNL073W_Skud Reading seq # 4: YNL073W_Smik Reading seq # 5: YNL073W_Spar Sequences read.. Counting patterns.. # site patterns = 107 Counting frequencies.. 120 bytes for distance 17120 bytes for lkl0 13696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.132366 0.027507 0.038191 0.086806 0.051661 0.134213 0.159781 0.166939 lnL0 = -1098.059232 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1098.059232 x= 0.13237 0.02751 0.03819 0.08681 0.05166 0.13421 0.15978 0.16694 1 h-lim-p 0.0010 0.0077 100.6265 1096.778866 9 0.0003 42 | 0/8 2 h-lim-p 0.0007 0.0058 22.6178 1096.618663 7 0.0006 67 | 0/8 3 h-lim-p 0.0011 0.0126 13.8835 1096.577103 5 0.0006 90 | 0/8 4 h-lim-p 0.0015 0.0214 5.2728 1096.572555 5 0.0004 113 | 0/8 5 h-lim-p 0.0035 0.3230 0.5903 1096.572431 3 0.0007 132 | 0/8 6 h-lim-p 0.0015 0.7750 0.2940 1096.572407 2 0.0007 156 | 0/8 7 h-lim-p 0.1143 20.0000 0.0018 1096.572288 0 0.2286 177 | 0/8 8 h-lim-p 0.0026 1.8691 0.1562 1096.571724 0 0.0052 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1096.571708 2 0.9961 222 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1096.571708 0 1.2500 242 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1096.571708 0 0.0781 266 | 0/8 12 h-lim-p 0.0368 20.0000 0.0000 1096.571708 0 0.0092 287 | 0/8 13 h-lim-p 0.0056 20.0000 0.0000 1096.571708 0 0.0003 311 Out... lnL = -1096.571708 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1096.571708 Node 7: lnL = -1096.571708 Node 8: lnL = -1096.571708 Node 9: lnL = -1096.571708 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 339 Sequential format.. Reading seq # 1: YNL075W_Sbay Reading seq # 2: YNL075W_Scer Reading seq # 3: YNL075W_Skud Reading seq # 4: YNL075W_Smik Reading seq # 5: YNL075W_Spar Sequences read.. Counting patterns.. # site patterns = 146 Counting frequencies.. 120 bytes for distance 23360 bytes for lkl0 18688 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.070602 0.081254 0.071428 0.183502 0.064105 0.141840 0.205555 0.112538 lnL0 = -1437.749372 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1437.749372 x= 0.07060 0.08125 0.07143 0.18350 0.06411 0.14184 0.20556 0.11254 1 h-lim-p 0.0047 0.0378 55.4039 1437.085456 7 0.0005 37 | 0/8 2 h-lim-p 0.0010 0.0082 12.8771 1437.043803 4 0.0005 58 | 0/8 3 h-lim-p 0.0012 0.0373 5.5999 1437.037416 4 0.0005 78 | 0/8 4 h-lim-p 0.0084 1.4509 0.3210 1437.037368 2 0.0009 96 | 0/8 5 h-lim-p 0.0069 5.9535 0.0428 1437.037367 1 0.0008 120 | 0/8 6 h-lim-p 0.0020 17.1698 0.0183 1437.037367 0 0.0009 140 | 0/8 7 h-lim-p 0.0061 20.0000 0.0026 1437.037366 0 0.0092 160 | 0/8 8 h-lim-p 0.0111 20.0000 0.0021 1437.037335 0 0.0886 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1437.037335 0 1.0938 203 | 0/8 10 h-lim-p 1.6612 20.0000 0.0000 1437.037335 0 1.4535 223 | 0/8 11 h-lim-p 1.9217 20.0000 0.0000 1437.037335 0 1.6815 243 | 0/8 12 h-lim-p 0.8024 20.0000 0.0000 1437.037335 0 3.2096 265 | 0/8 13 h-lim-p 0.0603 20.0000 0.0004 1437.037335 0 0.0000 298 | 0/8 14 h-lim-p 0.0005 20.0000 0.0000 1437.037335 0 0.0000 323 Out... lnL = -1437.037335 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1437.037335 Node 7: lnL = -1437.037335 Node 8: lnL = -1437.037335 Node 9: lnL = -1437.037335 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 450 Sequential format.. Reading seq # 1: YNL077W_Sbay Reading seq # 2: YNL077W_Scer Reading seq # 3: YNL077W_Skud Reading seq # 4: YNL077W_Smik Reading seq # 5: YNL077W_Spar Sequences read.. Counting patterns.. # site patterns = 171 Counting frequencies.. 120 bytes for distance 27360 bytes for lkl0 21888 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.088232 0.063395 0.082427 0.108025 0.041322 0.159683 0.179239 0.126616 lnL0 = -1826.274890 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1826.274890 x= 0.08823 0.06339 0.08243 0.10802 0.04132 0.15968 0.17924 0.12662 1 h-lim-p 0.0112 0.0895 41.3103 1826.028138 5 0.0003 38 | 0/8 2 h-lim-p 0.0007 0.0059 10.0285 1826.018211 6 0.0002 66 | 0/8 3 h-lim-p 0.0005 0.0419 4.1947 1826.014595 2 0.0005 82 | 0/8 4 h-lim-p 0.0016 0.1789 1.2292 1826.014261 4 0.0005 105 | 0/8 5 h-lim-p 0.0102 3.6399 0.0585 1826.014260 0 0.0006 120 | 0/8 6 h-lim-p 0.0044 20.0000 0.0074 1826.014260 0 0.0010 141 | 0/8 7 h-lim-p 0.0101 20.0000 0.0007 1826.014260 0 0.0303 162 | 0/8 8 h-lim-p 0.0021 20.0000 0.0103 1826.014248 0 0.0083 184 | 0/8 9 h-lim-p 2.3164 20.0000 0.0000 1826.014247 0 1.0134 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1826.014247 0 1.0938 224 | 0/8 11 h-lim-p 1.6677 20.0000 0.0000 1826.014247 0 1.6677 244 | 0/8 12 h-lim-p 1.9419 20.0000 0.0000 1826.014247 0 0.0000 279 Out... lnL = -1826.014247 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1826.014247 Node 7: lnL = -1826.014247 Node 8: lnL = -1826.014247 Node 9: lnL = -1826.014247 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 673 Sequential format.. Reading seq # 1: YNL078W_Sbay Reading seq # 2: YNL078W_Scer Reading seq # 3: YNL078W_Skud Reading seq # 4: YNL078W_Smik Reading seq # 5: YNL078W_Spar Sequences read.. Counting patterns.. # site patterns = 255 Counting frequencies.. 120 bytes for distance 40800 bytes for lkl0 32640 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.168422 0.045556 0.053623 0.089581 0.087254 0.193370 0.249867 0.216461 lnL0 = -2824.693538 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2824.693538 x= 0.16842 0.04556 0.05362 0.08958 0.08725 0.19337 0.24987 0.21646 1 h-lim-p 0.0009 0.0075 104.1628 2823.274712 7 0.0003 40 | 0/8 2 h-lim-p 0.0004 0.0032 25.4851 2823.189148 7 0.0003 69 | 0/8 3 h-lim-p 0.0009 0.0188 7.6078 2823.181464 6 0.0003 97 | 0/8 4 h-lim-p 0.0005 0.0517 4.4965 2823.176160 0 0.0007 109 | 0/8 5 h-lim-p 0.0022 0.1081 1.5033 2823.175740 2 0.0004 126 | 0/8 6 h-lim-p 0.0007 0.2752 0.9526 2823.175585 3 0.0005 146 | 0/8 7 h-lim-p 0.0043 2.6513 0.1048 2823.175581 1 0.0009 169 | 0/8 8 h-lim-p 0.2668 20.0000 0.0003 2823.175422 0 1.0670 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2823.175420 0 1.0938 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2823.175420 0 1.0938 231 | 0/8 11 h-lim-p 1.7537 20.0000 0.0000 2823.175420 0 0.7673 251 | 0/8 12 h-lim-p 0.5480 20.0000 0.0000 2823.175420 0 0.0342 274 | 0/8 13 h-lim-p 0.0128 20.0000 0.0000 2823.175420 0 0.0128 294 | 0/8 14 h-lim-p 0.0078 20.0000 0.0000 2823.175420 0 0.0000 329 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 2823.175420 0 0.0000 363 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -2823.175420 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2823.175420 Node 7: lnL = -2823.175420 Node 8: lnL = -2823.175420 Node 9: lnL = -2823.175420 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 666 Sequential format.. Reading seq # 1: YNL079C_Sbay Reading seq # 2: YNL079C_Scer Reading seq # 3: YNL079C_Skud Reading seq # 4: YNL079C_Smik Reading seq # 5: YNL079C_Spar Sequences read.. Counting patterns.. # site patterns = 253 Counting frequencies.. 120 bytes for distance 40480 bytes for lkl0 32384 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.155574 0.018541 0.055141 0.093434 0.083401 0.194180 0.263661 0.201469 lnL0 = -2824.368872 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2824.368872 x= 0.15557 0.01854 0.05514 0.09343 0.08340 0.19418 0.26366 0.20147 1 h-lim-p 0.0004 0.0033 179.7402 2821.639824 3 0.0002 29 | 0/8 2 h-lim-p 0.0005 0.0037 24.1321 2821.560445 6 0.0003 56 | 0/8 3 h-lim-p 0.0007 0.0200 9.0587 2821.548556 3 0.0003 74 | 0/8 4 h-lim-p 0.0005 0.0513 6.2690 2821.542338 2 0.0004 90 | 0/8 5 h-lim-p 0.0020 0.2373 1.3937 2821.541899 2 0.0005 107 | 0/8 6 h-lim-p 0.0008 0.4230 0.8309 2821.541776 3 0.0005 127 | 0/8 7 h-lim-p 0.0087 6.4943 0.0474 2821.541774 0 0.0010 149 | 0/8 8 h-lim-p 0.0742 20.0000 0.0006 2821.541121 0 1.1872 173 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2821.541099 1 0.9961 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2821.541099 0 1.0938 215 | 0/8 11 h-lim-p 1.3605 20.0000 0.0000 2821.541099 0 2.0407 235 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2821.541099 0 0.3125 257 | 0/8 13 h-lim-p 0.0646 20.0000 0.0000 2821.541099 0 0.0485 277 | 0/8 14 h-lim-p 0.0219 20.0000 0.0000 2821.541099 0 0.0219 297 | 0/8 15 h-lim-p 0.0098 20.0000 0.0000 2821.541099 0 0.0000 334 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 | 0/8 17 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -2821.541099 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2821.541099 Node 7: lnL = -2821.541099 Node 8: lnL = -2821.541099 Node 9: lnL = -2821.541099 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 578 Sequential format.. Reading seq # 1: YNL080C_Sbay Reading seq # 2: YNL080C_Scer Reading seq # 3: YNL080C_Skud Reading seq # 4: YNL080C_Smik Reading seq # 5: YNL080C_Spar Sequences read.. Counting patterns.. # site patterns = 166 Counting frequencies.. 120 bytes for distance 26560 bytes for lkl0 21248 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.113081 0.011813 0.045417 0.035781 0.035026 0.098099 0.123633 0.139346 lnL0 = -1982.704840 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1982.704840 x= 0.11308 0.01181 0.04542 0.03578 0.03503 0.09810 0.12363 0.13935 1 h-lim-p 0.0002 0.0013 260.8173 1980.337182 8 0.0001 39 | 0/8 2 h-lim-p 0.0004 0.0029 28.6858 1980.241391 6 0.0002 65 | 0/8 3 h-lim-p 0.0002 0.0057 35.4470 1980.200148 6 0.0001 92 | 0/8 4 h-lim-p 0.0008 0.0135 5.3251 1980.198429 4 0.0001 115 | 0/8 5 h-lim-p 0.0005 0.0479 1.3267 1980.198327 2 0.0001 132 | 0/8 6 h-lim-p 0.0010 1.8184 0.1575 1980.198323 1 0.0003 147 | 0/8 7 h-lim-p 0.0015 6.2188 0.0271 1980.198323 0 0.0006 167 | 0/8 8 h-lim-p 0.2160 20.0000 0.0001 1980.198296 0 1.2959 189 | 0/8 9 h-lim-p 2.2602 20.0000 0.0000 1980.198294 0 1.1301 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1980.198294 0 1.0938 229 | 0/8 11 h-lim-p 1.9454 20.0000 0.0000 1980.198294 0 0.4255 250 | 0/8 12 h-lim-p 0.2985 20.0000 0.0000 1980.198294 0 0.0023 276 | 0/8 13 h-lim-p 0.0014 20.0000 0.0000 1980.198294 0 0.0002 298 Out... lnL = -1980.198294 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1980.198294 Node 7: lnL = -1980.198294 Node 8: lnL = -1980.198294 Node 9: lnL = -1980.198294 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 327 Sequential format.. Reading seq # 1: YNL081C_Sbay Reading seq # 2: YNL081C_Scer Reading seq # 3: YNL081C_Skud Reading seq # 4: YNL081C_Smik Reading seq # 5: YNL081C_Spar Sequences read.. Counting patterns.. # site patterns = 150 Counting frequencies.. 120 bytes for distance 24000 bytes for lkl0 19200 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.121286 0.051300 0.089028 0.144084 0.071947 0.317577 0.217430 0.164886 lnL0 = -1541.916525 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1541.916525 x= 0.12129 0.05130 0.08903 0.14408 0.07195 0.31758 0.21743 0.16489 1 h-lim-p 0.0005 0.0038 42.5763 1541.444448 1 0.0006 24 | 0/8 2 h-lim-p 0.0032 0.0402 7.7322 1541.424474 4 0.0007 44 | 0/8 3 h-lim-p 0.0026 0.0378 2.0700 1541.423687 5 0.0004 72 | 0/8 4 h-lim-p 0.0013 0.9776 0.6360 1541.423418 1 0.0016 86 | 0/8 5 h-lim-p 0.0081 2.5643 0.1254 1541.423400 2 0.0018 111 | 0/8 6 h-lim-p 0.0039 6.5499 0.0576 1541.423379 1 0.0040 133 | 0/8 7 h-lim-p 0.0054 3.3696 0.0423 1541.423153 0 0.0217 155 | 0/8 8 h-lim-p 0.0069 0.6509 0.1325 1541.420412 0 0.0139 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1541.420393 2 0.9961 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1541.420393 0 1.0938 220 | 0/8 11 h-lim-p 1.8324 20.0000 0.0000 1541.420393 0 1.6033 240 | 0/8 12 h-lim-p 2.4014 20.0000 0.0000 1541.420393 0 0.6003 261 | 0/8 13 h-lim-p 0.1956 20.0000 0.0000 1541.420393 0 0.1956 281 | 0/8 14 h-lim-p 0.0641 20.0000 0.0000 1541.420393 0 0.0000 328 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 1541.420393 0 0.0000 352 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 1541.420393 0 0.0000 387 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 1541.420393 0 0.0000 422 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 1541.420393 0 0.0000 455 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1541.420393 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1541.420393 Node 7: lnL = -1541.420393 Node 8: lnL = -1541.420393 Node 9: lnL = -1541.420393 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 282 Sequential format.. Reading seq # 1: YNL084C_Sbay Reading seq # 2: YNL084C_Scer Reading seq # 3: YNL084C_Skud Reading seq # 4: YNL084C_Smik Reading seq # 5: YNL084C_Spar Sequences read.. Counting patterns.. # site patterns = 109 Counting frequencies.. 120 bytes for distance 17440 bytes for lkl0 13952 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.107274 0.101915 0.039426 0.076803 0.077796 0.153595 0.124464 0.138386 lnL0 = -1193.441933 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1193.441933 x= 0.10727 0.10192 0.03943 0.07680 0.07780 0.15360 0.12446 0.13839 1 h-lim-p 0.0007 0.0058 86.1584 1192.437990 6 0.0003 35 | 0/8 2 h-lim-p 0.0008 0.0067 20.1099 1192.309909 5 0.0007 57 | 0/8 3 h-lim-p 0.0014 0.0278 9.4357 1192.292569 6 0.0005 85 | 0/8 4 h-lim-p 0.0018 0.0493 2.4844 1192.291071 5 0.0005 110 | 0/8 5 h-lim-p 0.0037 0.4779 0.3553 1192.291027 2 0.0007 127 | 0/8 6 h-lim-p 0.0036 4.3037 0.0715 1192.291025 0 0.0008 148 | 0/8 7 h-lim-p 0.0228 20.0000 0.0024 1192.291023 0 0.0200 168 | 0/8 8 h-lim-p 0.0088 11.8161 0.0055 1192.290933 0 0.0529 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1192.290930 1 0.9961 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1192.290930 0 1.0938 232 | 0/8 11 h-lim-p 1.5654 20.0000 0.0000 1192.290930 0 3.1308 253 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1192.290930 0 0.3125 275 | 0/8 13 h-lim-p 0.3558 20.0000 0.0000 1192.290930 0 0.0389 297 | 0/8 14 h-lim-p 0.0133 20.0000 0.0000 1192.290930 0 0.0017 319 | 0/8 15 h-lim-p 0.0011 20.0000 0.0000 1192.290930 0 0.0000 349 Out... lnL = -1192.290930 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1192.290930 Node 7: lnL = -1192.290930 Node 8: lnL = -1192.290930 Node 9: lnL = -1192.290930 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 456 Sequential format.. Reading seq # 1: YNL086W_Sbay Reading seq # 2: YNL086W_Scer Reading seq # 3: YNL086W_Skud Reading seq # 4: YNL086W_Smik Reading seq # 5: YNL086W_Spar Sequences read.. Counting patterns.. # site patterns = 188 Counting frequencies.. 120 bytes for distance 30080 bytes for lkl0 24064 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.119854 0.148483 0.053847 0.179730 0.113563 0.252575 0.226145 0.167478 lnL0 = -2068.875165 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2068.875165 x= 0.11985 0.14848 0.05385 0.17973 0.11356 0.25258 0.22614 0.16748 1 h-lim-p 0.0094 0.0753 63.4283 2068.140211 8 0.0004 43 | 0/8 2 h-lim-p 0.0019 0.0160 13.1913 2068.067880 7 0.0009 69 | 0/8 3 h-lim-p 0.0015 0.0394 7.3262 2068.053662 4 0.0007 88 | 0/8 4 h-lim-p 0.0061 0.3979 0.8035 2068.053368 4 0.0009 113 | 0/8 5 h-lim-p 0.0034 1.0638 0.2243 2068.053345 3 0.0009 140 | 0/8 6 h-lim-p 0.0043 9.4999 0.0475 2068.053344 0 0.0009 161 | 0/8 7 h-lim-p 0.0071 20.0000 0.0063 2068.053344 0 0.0031 181 | 0/8 8 h-lim-p 0.0517 20.0000 0.0004 2068.053309 0 0.4136 204 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2068.053308 0 1.0938 224 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2068.053308 0 1.0938 244 | 0/8 11 h-lim-p 1.7187 20.0000 0.0000 2068.053308 0 0.3760 265 | 0/8 12 h-lim-p 0.2061 20.0000 0.0000 2068.053308 0 0.0004 293 Out... lnL = -2068.053308 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2068.053308 Node 7: lnL = -2068.053308 Node 8: lnL = -2068.053308 Node 9: lnL = -2068.053308 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 579 Sequential format.. Reading seq # 1: YNL088W_Sbay Reading seq # 2: YNL088W_Scer Reading seq # 3: YNL088W_Skud Reading seq # 4: YNL088W_Smik Reading seq # 5: YNL088W_Spar Sequences read.. Counting patterns.. # site patterns = 203 Counting frequencies.. 120 bytes for distance 32480 bytes for lkl0 25984 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.113156 0.021404 0.082008 0.156224 0.081164 0.240366 0.237937 0.152882 lnL0 = -2267.427845 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2267.427845 x= 0.11316 0.02140 0.08201 0.15622 0.08116 0.24037 0.23794 0.15288 1 h-lim-p 0.0041 0.0650 105.0438 2266.164637 8 0.0003 39 | 0/8 2 h-lim-p 0.0008 0.0063 35.2351 2265.839626 7 0.0006 68 | 0/8 3 h-lim-p 0.0016 0.0217 12.2446 2265.800675 6 0.0006 96 | 0/8 4 h-lim-p 0.0007 0.0236 10.7693 2265.782734 6 0.0005 121 | 0/8 5 h-lim-p 0.0185 1.3135 0.2897 2265.782707 3 0.0006 143 | 0/8 6 h-lim-p 0.0023 4.7566 0.0796 2265.782702 1 0.0011 166 | 0/8 7 h-lim-p 0.0048 8.8214 0.0184 2265.782698 1 0.0038 188 | 0/8 8 h-lim-p 0.0140 20.0000 0.0050 2265.781696 0 0.1683 211 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2265.781684 1 0.9961 233 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2265.781684 0 1.0938 253 | 0/8 11 h-lim-p 1.9225 20.0000 0.0000 2265.781684 0 1.6822 273 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2265.781684 0 0.5469 294 | 0/8 13 h-lim-p 0.1841 20.0000 0.0000 2265.781684 0 0.0460 315 | 0/8 14 h-lim-p 0.0189 20.0000 0.0000 2265.781684 0 0.0283 335 | 0/8 15 h-lim-p 0.0148 20.0000 0.0000 2265.781684 0 0.0074 355 | 0/8 16 h-lim-p 0.0053 20.0000 0.0000 2265.781684 0 0.0000 381 | 0/8 17 h-lim-p 0.0018 20.0000 0.0000 2265.781684 0 0.0000 418 Out... lnL = -2265.781684 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2265.781684 Node 7: lnL = -2265.781684 Node 8: lnL = -2265.781684 Node 9: lnL = -2265.781684 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 484 Sequential format.. Reading seq # 1: YNL090W_Sbay Reading seq # 2: YNL090W_Scer Reading seq # 3: YNL090W_Skud Reading seq # 4: YNL090W_Smik Reading seq # 5: YNL090W_Spar Sequences read.. Counting patterns.. # site patterns = 240 Counting frequencies.. 120 bytes for distance 38400 bytes for lkl0 30720 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.058435 0.068804 0.056794 0.110034 0.094616 1.046574 0.190516 0.121694 lnL0 = -2290.032121 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2290.032121 x= 0.05844 0.06880 0.05679 0.11003 0.09462 1.04657 0.19052 0.12169 1 h-lim-p 0.0009 0.0068 76.9582 2289.026336 6 0.0004 35 | 0/8 2 h-lim-p 0.0005 0.0037 30.8952 2288.764659 0 0.0009 48 | 0/8 3 h-lim-p 0.0004 0.0029 25.1956 2288.577678 0 0.0011 61 | 0/8 4 h-lim-p 0.0002 0.0019 24.0748 2288.472353 0 0.0010 75 | 0/8 5 h-lim-p 0.0005 0.0043 13.8890 2288.433296 0 0.0011 88 | 0/8 6 h-lim-p 0.0010 0.0080 5.1825 2288.422134 4 0.0011 111 | 0/8 7 h-lim-p 0.0007 0.2860 8.4063 2288.377589 0 0.0041 125 | 0/8 8 h-lim-p 2.1681 20.0000 0.0158 2288.329981 5 0.9623 146 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 2288.329844 3 1.0449 172 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2288.329842 0 1.0938 192 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2288.329842 0 1.2500 212 | 0/8 12 h-lim-p 1.4041 20.0000 0.0000 2288.329842 0 2.1062 232 | 0/8 13 h-lim-p 0.4871 20.0000 0.0001 2288.329842 0 0.0000 273 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 2288.329842 0 0.0000 301 Out... lnL = -2288.329842 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2288.329842 Node 7: lnL = -2288.329842 Node 8: lnL = -2288.329842 Node 9: lnL = -2288.329842 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 362 Sequential format.. Reading seq # 1: YNL091W_Sbay Reading seq # 2: YNL091W_Scer Reading seq # 3: YNL091W_Skud Reading seq # 4: YNL091W_Smik Reading seq # 5: YNL091W_Spar Sequences read.. Counting patterns.. # site patterns = 119 Counting frequencies.. 120 bytes for distance 19040 bytes for lkl0 15232 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.060521 0.075004 0.041648 0.097243 0.063909 0.082727 0.144512 0.085304 lnL0 = -1363.549068 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1363.549068 x= 0.06052 0.07500 0.04165 0.09724 0.06391 0.08273 0.14451 0.08530 1 h-lim-p 0.0063 0.1147 65.7854 1363.013277 6 0.0003 38 | 0/8 2 h-lim-p 0.0006 0.0048 17.9466 1362.958499 7 0.0004 68 | 0/8 3 h-lim-p 0.0013 0.0355 4.9311 1362.953245 4 0.0005 90 | 0/8 4 h-lim-p 0.0019 0.1529 1.2319 1362.952928 2 0.0004 107 | 0/8 5 h-lim-p 0.0021 0.5103 0.2539 1362.952918 2 0.0003 126 | 0/8 6 h-lim-p 0.0032 6.5003 0.0275 1362.952918 0 0.0007 147 | 0/8 7 h-lim-p 0.0689 20.0000 0.0003 1362.952824 0 1.1016 171 | 0/8 8 h-lim-p 0.0028 3.2195 0.1117 1362.952822 1 0.0003 195 | 0/8 9 h-lim-p 0.6494 20.0000 0.0001 1362.952816 0 1.2987 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1362.952816 0 1.0938 236 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1362.952816 0 2.1875 256 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1362.952816 0 1.0938 276 | 0/8 13 h-lim-p 0.3653 20.0000 0.0000 1362.952816 0 4.3830 299 | 0/8 14 h-lim-p 2.4369 20.0000 0.0000 1362.952816 0 0.0381 324 | 0/8 15 h-lim-p 0.1464 20.0000 0.0000 1362.952816 0 0.0001 353 Out... lnL = -1362.952816 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1362.952816 Node 7: lnL = -1362.952816 Node 8: lnL = -1362.952816 Node 9: lnL = -1362.952816 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 428 Sequential format.. Reading seq # 1: YNL092W_Sbay Reading seq # 2: YNL092W_Scer Reading seq # 3: YNL092W_Skud Reading seq # 4: YNL092W_Smik Reading seq # 5: YNL092W_Spar Sequences read.. Counting patterns.. # site patterns = 218 Counting frequencies.. 120 bytes for distance 34880 bytes for lkl0 27904 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.109446 0.324139 0.101611 0.145853 0.061502 0.208205 0.247298 0.164499 lnL0 = -1910.348403 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1910.348403 x= 0.10945 0.32414 0.10161 0.14585 0.06150 0.20820 0.24730 0.16450 1 h-lim-p 0.0045 0.0361 56.5747 1909.509498 6 0.0006 35 | 0/8 2 h-lim-p 0.0010 0.0077 27.8738 1909.141381 1 0.0012 49 | 0/8 3 h-lim-p 0.0021 0.0164 13.8017 1909.063131 3 0.0010 67 | 0/8 4 h-lim-p 0.0058 0.3602 2.4880 1909.056261 5 0.0023 88 | 0/8 5 h-lim-p 0.0059 0.2731 0.9907 1909.055849 3 0.0010 109 | 0/8 6 h-lim-p 0.0149 3.8588 0.0643 1909.055834 2 0.0029 134 | 0/8 7 h-lim-p 0.0035 5.5847 0.0533 1909.055718 0 0.0139 156 | 0/8 8 h-lim-p 0.0236 20.0000 0.0313 1909.052778 0 0.0472 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 1909.052636 3 1.0449 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1909.052635 0 1.0938 223 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1909.052635 0 1.0938 243 | 0/8 12 h-lim-p 1.4483 20.0000 0.0000 1909.052635 0 1.2673 263 | 0/8 13 h-lim-p 0.6000 20.0000 0.0000 1909.052635 0 0.3000 283 | 0/8 14 h-lim-p 0.0174 20.0000 0.0001 1909.052635 0 0.0174 303 | 0/8 15 h-lim-p 0.0080 20.0000 0.0002 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1909.052635 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1909.052635 Node 7: lnL = -1909.052635 Node 8: lnL = -1909.052635 Node 9: lnL = -1909.052635 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 595 Sequential format.. Reading seq # 1: YNL093W_Sbay Reading seq # 2: YNL093W_Scer Reading seq # 3: YNL093W_Skud Reading seq # 4: YNL093W_Smik Reading seq # 5: YNL093W_Spar Sequences read.. Counting patterns.. # site patterns = 272 Counting frequencies.. 120 bytes for distance 43520 bytes for lkl0 34816 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.168583 0.048176 0.120274 0.146596 0.127618 0.281049 0.364695 0.223253 lnL0 = -2864.988330 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2864.988330 x= 0.16858 0.04818 0.12027 0.14660 0.12762 0.28105 0.36470 0.22325 1 h-lim-p 0.0007 0.0057 67.3137 2863.809641 7 0.0005 35 | 0/8 2 h-lim-p 0.0013 0.0101 15.8565 2863.744621 6 0.0005 62 | 0/8 3 h-lim-p 0.0013 0.0661 6.6936 2863.732976 2 0.0006 78 | 0/8 4 h-lim-p 0.0015 0.1153 2.6071 2863.730883 2 0.0007 94 | 0/8 5 h-lim-p 0.0074 0.5889 0.2512 2863.730827 1 0.0019 109 | 0/8 6 h-lim-p 0.0087 5.8876 0.0540 2863.730825 1 0.0017 132 | 0/8 7 h-lim-p 0.0166 20.0000 0.0056 2863.730825 0 0.0018 154 | 0/8 8 h-lim-p 0.0590 20.0000 0.0002 2863.730816 0 0.7085 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2863.730815 0 1.0938 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2863.730815 0 1.2500 217 | 0/8 11 h-lim-p 1.5847 20.0000 0.0000 2863.730815 0 0.3962 238 | 0/8 12 h-lim-p 0.1864 20.0000 0.0000 2863.730815 0 0.0000 273 Out... lnL = -2863.730815 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2863.730815 Node 7: lnL = -2863.730815 Node 8: lnL = -2863.730815 Node 9: lnL = -2863.730815 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 788 Sequential format.. Reading seq # 1: YNL094W_Sbay Reading seq # 2: YNL094W_Scer Reading seq # 3: YNL094W_Skud Reading seq # 4: YNL094W_Smik Reading seq # 5: YNL094W_Spar Sequences read.. Counting patterns.. # site patterns = 198 Counting frequencies.. 120 bytes for distance 31680 bytes for lkl0 25344 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.075760 0.025987 0.046328 0.091944 0.066770 0.139176 0.127243 0.100568 lnL0 = -3088.002019 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3088.002019 x= 0.07576 0.02599 0.04633 0.09194 0.06677 0.13918 0.12724 0.10057 1 h-lim-p 0.0004 0.0033 316.7310 3084.496580 4 0.0001 31 | 0/8 2 h-lim-p 0.0004 0.0034 38.3635 3084.354459 3 0.0002 49 | 0/8 3 h-lim-p 0.0004 0.0143 16.9263 3084.335480 5 0.0002 73 | 0/8 4 h-lim-p 0.0007 0.0292 4.0253 3084.334215 4 0.0002 94 | 0/8 5 h-lim-p 0.0016 0.1648 0.4156 3084.334201 1 0.0002 110 | 0/8 6 h-lim-p 0.0005 2.4664 0.1294 3084.334200 0 0.0002 130 | 0/8 7 h-lim-p 0.0014 12.0789 0.0204 3084.334200 0 0.0003 151 | 0/8 8 h-lim-p 0.0853 20.0000 0.0001 3084.334171 0 1.3654 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3084.334170 0 1.0938 195 | 0/8 10 h-lim-p 2.4513 20.0000 0.0000 3084.334170 0 1.0724 215 | 0/8 11 h-lim-p 0.9035 20.0000 0.0000 3084.334170 0 0.0141 240 | 0/8 12 h-lim-p 0.0004 20.0000 0.0003 3084.334170 0 0.0001 261 | 0/8 13 h-lim-p 0.0014 20.0000 0.0000 3084.334170 0 0.0022 281 | 0/8 14 h-lim-p 0.0006 20.0000 0.0001 3084.334170 0 0.0000 311 | 0/8 15 h-lim-p 0.0004 20.0000 0.0000 3084.334170 0 0.0000 350 Out... lnL = -3084.334170 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3084.334170 Node 7: lnL = -3084.334170 Node 8: lnL = -3084.334170 Node 9: lnL = -3084.334170 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 884 Sequential format.. Reading seq # 1: YNL098C_Sbay Reading seq # 2: YNL098C_Scer Reading seq # 3: YNL098C_Skud Reading seq # 4: YNL098C_Smik Reading seq # 5: YNL098C_Spar Sequences read.. Counting patterns.. # site patterns = 283 Counting frequencies.. 120 bytes for distance 45280 bytes for lkl0 36224 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.122099 0.094831 0.041480 0.115360 0.063370 0.215502 0.162990 0.158522 lnL0 = -3572.404583 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3572.404583 x= 0.12210 0.09483 0.04148 0.11536 0.06337 0.21550 0.16299 0.15852 1 h-lim-p 0.0001 0.0009 159.1035 3570.221880 0 0.0002 23 | 0/8 2 h-lim-p 0.0004 0.0032 39.2406 3570.057580 7 0.0002 53 | 0/8 3 h-lim-p 0.0008 0.0078 10.7380 3570.050356 5 0.0001 78 | 0/8 4 h-lim-p 0.0003 0.0621 4.4150 3570.047792 2 0.0003 94 | 0/8 5 h-lim-p 0.0010 0.0953 1.3659 3570.047392 2 0.0004 110 | 0/8 6 h-lim-p 0.0035 2.0589 0.1707 3570.047167 3 0.0028 128 | 0/8 7 h-lim-p 0.0058 1.9895 0.0825 3570.030302 0 0.0462 151 | 0/8 8 h-lim-p 0.0014 0.0633 2.7239 3569.981920 0 0.0021 171 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 3569.981137 2 0.9961 187 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3569.981137 0 1.0938 207 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3569.981137 0 1.0938 227 | 0/8 12 h-lim-p 1.1356 20.0000 0.0000 3569.981137 0 2.2711 248 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 3569.981137 0 0.0009 279 Out... lnL = -3569.981137 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3569.981137 Node 7: lnL = -3569.981137 Node 8: lnL = -3569.981137 Node 9: lnL = -3569.981137 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 393 Sequential format.. Reading seq # 1: YNL099C_Sbay Reading seq # 2: YNL099C_Scer Reading seq # 3: YNL099C_Skud Reading seq # 4: YNL099C_Smik Reading seq # 5: YNL099C_Spar Sequences read.. Counting patterns.. # site patterns = 175 Counting frequencies.. 120 bytes for distance 28000 bytes for lkl0 22400 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.218643 0.000060 0.130052 0.139587 0.078105 0.172604 0.361647 0.266957 lnL0 = -1658.110000 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1658.110000 x= 0.21864 0.00006 0.13005 0.13959 0.07811 0.17260 0.36165 0.26696 1 h-lim-p 0.0010 0.0084 33.1293 1657.547745 4 0.0008 30 | 0/8 2 h-lim-p 0.0021 0.0246 12.8632 1657.427133 4 0.0017 50 | 0/8 3 h-lim-p 0.0020 0.0412 10.6291 1657.386537 7 0.0011 80 | 0/8 4 h-lim-p 0.0012 0.0270 9.7396 1657.370470 6 0.0007 106 | 0/8 5 h-lim-p 0.0044 0.1478 1.5191 1657.369007 5 0.0014 132 | 0/8 6 h-lim-p 0.0121 2.2403 0.1721 1657.368904 3 0.0032 151 | 0/8 7 h-lim-p 0.0027 0.3351 0.2030 1657.368739 2 0.0030 176 | 0/8 8 h-lim-p 0.0156 3.7336 0.0395 1657.351344 0 0.1247 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0009 1657.350930 2 0.9961 223 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1657.350930 0 1.0938 243 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1657.350930 0 1.0938 263 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1657.350930 0 0.3125 285 | 0/8 13 h-lim-p 0.2017 20.0000 0.0000 1657.350930 0 0.0126 308 | 0/8 14 h-lim-p 0.0076 20.0000 0.0000 1657.350930 0 0.0005 331 Out... lnL = -1657.350930 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1657.350930 Node 7: lnL = -1657.350930 Node 8: lnL = -1657.350930 Node 9: lnL = -1657.350930 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 491 Sequential format.. Reading seq # 1: YNL100W_Sbay Reading seq # 2: YNL100W_Scer Reading seq # 3: YNL100W_Skud Reading seq # 4: YNL100W_Smik Reading seq # 5: YNL100W_Spar Sequences read.. Counting patterns.. # site patterns = 212 Counting frequencies.. 120 bytes for distance 33920 bytes for lkl0 27136 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.105473 0.143877 0.099800 0.130440 0.091533 0.273823 0.192422 0.151267 lnL0 = -2338.844669 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2338.844669 x= 0.10547 0.14388 0.09980 0.13044 0.09153 0.27382 0.19242 0.15127 1 h-lim-p 0.0004 0.0030 72.5460 2337.547165 0 0.0008 23 | 0/8 2 h-lim-p 0.0013 0.0102 17.8853 2337.442454 5 0.0007 46 | 0/8 3 h-lim-p 0.0017 0.0234 7.0214 2337.433900 2 0.0004 63 | 0/8 4 h-lim-p 0.0008 0.1806 3.3958 2337.431176 5 0.0006 88 | 0/8 5 h-lim-p 0.0025 0.4825 0.7614 2337.430663 2 0.0012 104 | 0/8 6 h-lim-p 0.0170 4.6617 0.0533 2337.408867 0 0.1019 126 | 0/8 7 h-lim-p 0.0017 0.0619 3.1960 2337.284754 0 0.0034 147 | 0/8 8 h-lim-p 0.0030 0.0778 3.6335 2337.276226 5 0.0012 170 | 0/8 9 h-lim-p 2.2832 20.0000 0.0019 2337.273300 3 0.9574 189 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2337.273292 1 0.9961 211 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2337.273292 0 1.0938 231 | 0/8 12 h-lim-p 1.7634 20.0000 0.0000 2337.273292 0 1.7634 251 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2337.273292 0 0.0586 276 | 0/8 14 h-lim-p 0.0153 20.0000 0.0000 2337.273292 0 0.0077 296 | 0/8 15 h-lim-p 0.0042 20.0000 0.0000 2337.273292 0 0.0021 316 | 0/8 16 h-lim-p 0.0018 20.0000 0.0000 2337.273292 0 0.0018 336 | 0/8 17 h-lim-p 0.0009 20.0000 0.0000 2337.273292 0 0.0000 360 | 0/8 18 h-lim-p 0.0006 20.0000 0.0000 2337.273292 0 0.0000 395 Out... lnL = -2337.273292 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2337.273292 Node 7: lnL = -2337.273292 Node 8: lnL = -2337.273292 Node 9: lnL = -2337.273292 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 532 Sequential format.. Reading seq # 1: YNL101W_Sbay Reading seq # 2: YNL101W_Scer Reading seq # 3: YNL101W_Skud Reading seq # 4: YNL101W_Smik Reading seq # 5: YNL101W_Spar Sequences read.. Counting patterns.. # site patterns = 197 Counting frequencies.. 120 bytes for distance 31520 bytes for lkl0 25216 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.176324 0.041156 0.104687 0.083861 0.088514 0.213029 0.219477 0.218917 lnL0 = -2458.501908 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2458.501908 x= 0.17632 0.04116 0.10469 0.08386 0.08851 0.21303 0.21948 0.21892 1 h-lim-p 0.0032 0.0259 62.1760 2457.910263 7 0.0003 37 | 0/8 2 h-lim-p 0.0014 0.0111 14.8875 2457.840729 2 0.0006 53 | 0/8 3 h-lim-p 0.0015 0.0401 6.3424 2457.830703 4 0.0006 73 | 0/8 4 h-lim-p 0.0027 0.0742 1.3820 2457.830462 3 0.0003 93 | 0/8 5 h-lim-p 0.0007 0.7457 0.5571 2457.830397 3 0.0005 112 | 0/8 6 h-lim-p 0.0009 0.7088 0.2838 2457.830383 0 0.0004 132 | 0/8 7 h-lim-p 0.0171 20.0000 0.0067 2457.830382 0 0.0075 152 | 0/8 8 h-lim-p 0.0147 20.0000 0.0034 2457.830196 0 0.1173 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2457.830189 1 0.9961 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2457.830189 0 1.0938 217 | 0/8 11 h-lim-p 1.3265 20.0000 0.0000 2457.830189 0 2.6529 238 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2457.830189 0 0.6250 259 | 0/8 13 h-lim-p 0.1124 20.0000 0.0000 2457.830189 0 0.1124 279 | 0/8 14 h-lim-p 0.0380 20.0000 0.0000 2457.830189 0 0.0024 302 | 0/8 15 h-lim-p 0.0031 20.0000 0.0000 2457.830189 0 0.0008 323 Out... lnL = -2457.830189 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2457.830189 Node 7: lnL = -2457.830189 Node 8: lnL = -2457.830189 Node 9: lnL = -2457.830189 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 836 Sequential format.. Reading seq # 1: YNL103W_Sbay Reading seq # 2: YNL103W_Scer Reading seq # 3: YNL103W_Skud Reading seq # 4: YNL103W_Smik Reading seq # 5: YNL103W_Spar Sequences read.. Counting patterns.. # site patterns = 247 Counting frequencies.. 120 bytes for distance 39520 bytes for lkl0 31616 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.118770 0.056150 0.030500 0.080270 0.059176 0.165741 0.156466 0.142875 lnL0 = -3321.110372 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3321.110372 x= 0.11877 0.05615 0.03050 0.08027 0.05918 0.16574 0.15647 0.14288 1 h-lim-p 0.0003 0.0026 163.7594 3319.949704 7 0.0001 39 | 0/8 2 h-lim-p 0.0003 0.0025 42.1902 3319.794090 7 0.0002 69 | 0/8 3 h-lim-p 0.0005 0.0177 16.7966 3319.776450 6 0.0001 96 | 0/8 4 h-lim-p 0.0003 0.0217 8.3850 3319.770655 5 0.0002 119 | 0/8 5 h-lim-p 0.0014 0.1926 1.2420 3319.770512 3 0.0002 139 | 0/8 6 h-lim-p 0.0005 0.6572 0.4775 3319.770486 2 0.0003 156 | 0/8 7 h-lim-p 0.0053 9.7836 0.0231 3319.770486 0 0.0006 178 | 0/8 8 h-lim-p 0.0657 20.0000 0.0002 3319.770364 0 1.0512 202 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3319.770351 1 0.9961 224 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3319.770351 0 1.0938 244 | 0/8 11 h-lim-p 1.2037 20.0000 0.0000 3319.770351 0 1.0533 264 | 0/8 12 h-lim-p 0.2941 20.0000 0.0000 3319.770351 0 0.2941 284 | 0/8 13 h-lim-p 0.0646 20.0000 0.0001 3319.770351 0 0.0020 308 | 0/8 14 h-lim-p 0.0009 20.0000 0.0001 3319.770351 0 0.0000 332 | 0/8 15 h-lim-p 0.0012 20.0000 0.0000 3319.770351 0 0.0000 362 Out... lnL = -3319.770351 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3319.770351 Node 7: lnL = -3319.770351 Node 8: lnL = -3319.770351 Node 9: lnL = -3319.770351 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 849 Sequential format.. Reading seq # 1: YNL104C_Sbay Reading seq # 2: YNL104C_Scer Reading seq # 3: YNL104C_Skud Reading seq # 4: YNL104C_Smik Reading seq # 5: YNL104C_Spar Sequences read.. Counting patterns.. # site patterns = 243 Counting frequencies.. 120 bytes for distance 38880 bytes for lkl0 31104 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.105510 0.044599 0.035752 0.060487 0.057758 0.131170 0.149441 0.126745 lnL0 = -3180.342740 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3180.342740 x= 0.10551 0.04460 0.03575 0.06049 0.05776 0.13117 0.14944 0.12674 1 h-lim-p 0.0007 0.0052 166.4759 3178.574469 7 0.0001 40 | 0/8 2 h-lim-p 0.0001 0.0011 42.4992 3178.458613 5 0.0001 63 | 0/8 3 h-lim-p 0.0003 0.0140 21.3371 3178.423812 6 0.0002 89 | 0/8 4 h-lim-p 0.0013 0.0304 3.0498 3178.423327 3 0.0001 111 | 0/8 5 h-lim-p 0.0002 0.1189 1.4829 3178.423092 1 0.0003 125 | 0/8 6 h-lim-p 0.0020 0.3979 0.2060 3178.423089 0 0.0001 140 | 0/8 7 h-lim-p 0.0012 8.6277 0.0194 3178.423089 0 0.0005 160 | 0/8 8 h-lim-p 0.0605 20.0000 0.0002 3178.423030 0 0.9682 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3178.423029 0 1.0938 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3178.423029 0 1.0938 224 | 0/8 11 h-lim-p 0.7967 20.0000 0.0000 3178.423029 0 0.0012 253 | 0/8 12 h-lim-p 0.0003 20.0000 0.0000 3178.423029 0 0.0000 289 | 0/8 13 h-lim-p 0.0000 20.0000 0.0051 | 0/8 14 h-lim-p 0.0000 20.0000 0.0051 Out... lnL = -3178.423029 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3178.423029 Node 7: lnL = -3178.423029 Node 8: lnL = -3178.423029 Node 9: lnL = -3178.423029 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 317 Sequential format.. Reading seq # 1: YNL107W_Sbay Reading seq # 2: YNL107W_Scer Reading seq # 3: YNL107W_Skud Reading seq # 4: YNL107W_Smik Reading seq # 5: YNL107W_Spar Sequences read.. Counting patterns.. # site patterns = 147 Counting frequencies.. 120 bytes for distance 23520 bytes for lkl0 18816 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.116999 0.093237 0.101029 0.131788 0.094701 0.249819 0.250364 0.153400 lnL0 = -1441.888111 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1441.888111 x= 0.11700 0.09324 0.10103 0.13179 0.09470 0.24982 0.25036 0.15340 1 h-lim-p 0.0006 0.0047 49.0667 1440.973712 0 0.0009 22 | 0/8 2 h-lim-p 0.0041 0.0325 8.2679 1440.936350 7 0.0011 51 | 0/8 3 h-lim-p 0.0035 0.1238 2.6570 1440.931236 2 0.0016 67 | 0/8 4 h-lim-p 0.0035 0.1002 1.2408 1440.930904 4 0.0005 91 | 0/8 5 h-lim-p 0.0059 1.5942 0.1100 1440.930841 3 0.0041 110 | 0/8 6 h-lim-p 0.0076 3.1233 0.0594 1440.930329 0 0.0229 131 | 0/8 7 h-lim-p 0.0055 0.9129 0.2462 1440.926573 0 0.0110 152 | 0/8 8 h-lim-p 0.0024 0.1912 1.1213 1440.920871 0 0.0036 172 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 1440.920784 2 0.9961 188 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1440.920784 0 1.0938 208 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1440.920784 0 2.1875 228 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1440.920784 0 0.5469 249 | 0/8 13 h-lim-p 0.1626 20.0000 0.0000 1440.920784 0 0.0102 272 | 0/8 14 h-lim-p 0.0048 20.0000 0.0000 1440.920784 0 0.0000 301 Out... lnL = -1440.920784 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1440.920784 Node 7: lnL = -1440.920784 Node 8: lnL = -1440.920784 Node 9: lnL = -1440.920784 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 316 Sequential format.. Reading seq # 1: YNL108C_Sbay Reading seq # 2: YNL108C_Scer Reading seq # 3: YNL108C_Skud Reading seq # 4: YNL108C_Smik Reading seq # 5: YNL108C_Spar Sequences read.. Counting patterns.. # site patterns = 140 Counting frequencies.. 120 bytes for distance 22400 bytes for lkl0 17920 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.125050 0.055696 0.101466 0.144670 0.076752 0.275595 0.237901 0.160541 lnL0 = -1432.270746 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1432.270746 x= 0.12505 0.05570 0.10147 0.14467 0.07675 0.27559 0.23790 0.16054 1 h-lim-p 0.0005 0.0039 56.1103 1431.259707 0 0.0007 22 | 0/8 2 h-lim-p 0.0031 0.0244 12.2218 1431.172366 5 0.0012 43 | 0/8 3 h-lim-p 0.0025 0.0351 5.9315 1431.159843 5 0.0009 68 | 0/8 4 h-lim-p 0.0012 0.0866 4.2335 1431.156056 4 0.0006 89 | 0/8 5 h-lim-p 0.0109 0.8623 0.2476 1431.155995 3 0.0018 109 | 0/8 6 h-lim-p 0.0062 3.6641 0.0711 1431.155981 1 0.0027 131 | 0/8 7 h-lim-p 0.0129 9.3583 0.0148 1431.155591 0 0.0518 153 | 0/8 8 h-lim-p 0.0031 0.4061 0.2440 1431.152872 0 0.0094 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1431.152856 2 0.9961 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1431.152856 0 1.0938 218 | 0/8 11 h-lim-p 1.4215 20.0000 0.0000 1431.152856 0 4.2645 239 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1431.152856 0 0.0000 284 Out... lnL = -1431.152856 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1431.152856 Node 7: lnL = -1431.152856 Node 8: lnL = -1431.152856 Node 9: lnL = -1431.152856 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 510 Sequential format.. Reading seq # 1: YNL110C_Sbay Reading seq # 2: YNL110C_Scer Reading seq # 3: YNL110C_Skud Reading seq # 4: YNL110C_Smik Reading seq # 5: YNL110C_Spar Sequences read.. Counting patterns.. # site patterns = 200 Counting frequencies.. 120 bytes for distance 32000 bytes for lkl0 25600 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.127866 0.068079 0.074600 0.130718 0.081337 0.216116 0.186729 0.159399 lnL0 = -2283.867801 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2283.867801 x= 0.12787 0.06808 0.07460 0.13072 0.08134 0.21612 0.18673 0.15940 1 h-lim-p 0.0016 0.0129 71.9751 2282.946129 3 0.0004 29 | 0/8 2 h-lim-p 0.0007 0.0053 19.0482 2282.860080 6 0.0005 55 | 0/8 3 h-lim-p 0.0012 0.0301 8.1393 2282.846136 5 0.0005 76 | 0/8 4 h-lim-p 0.0020 0.0464 2.0191 2282.845656 2 0.0003 94 | 0/8 5 h-lim-p 0.0028 1.4658 0.1932 2282.845640 2 0.0009 112 | 0/8 6 h-lim-p 0.0116 20.0000 0.0151 2282.845637 1 0.0046 134 | 0/8 7 h-lim-p 0.0028 8.8134 0.0246 2282.845576 0 0.0114 156 | 0/8 8 h-lim-p 0.0023 4.5567 0.1240 2282.844767 0 0.0090 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 2282.844728 2 0.9961 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2282.844728 0 1.0938 222 | 0/8 11 h-lim-p 1.6282 20.0000 0.0000 2282.844728 0 1.4247 242 | 0/8 12 h-lim-p 1.7412 20.0000 0.0000 2282.844728 0 0.4353 263 | 0/8 13 h-lim-p 0.1302 20.0000 0.0000 2282.844728 0 0.0081 286 | 0/8 14 h-lim-p 0.0027 20.0000 0.0000 2282.844728 0 0.0000 319 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 2282.844728 0 0.0000 339 Out... lnL = -2282.844728 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2282.844728 Node 7: lnL = -2282.844728 Node 8: lnL = -2282.844728 Node 9: lnL = -2282.844728 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 550 Sequential format.. Reading seq # 1: YNL111C_Sbay Reading seq # 2: YNL111C_Scer Reading seq # 3: YNL111C_Skud Reading seq # 4: YNL111C_Smik Reading seq # 5: YNL111C_Spar Sequences read.. Counting patterns.. # site patterns = 169 Counting frequencies.. 120 bytes for distance 27040 bytes for lkl0 21632 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.074934 0.062910 0.020170 0.119847 0.085371 0.124288 0.109454 0.095675 lnL0 = -2180.462093 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2180.462093 x= 0.07493 0.06291 0.02017 0.11985 0.08537 0.12429 0.10945 0.09568 1 h-lim-p 0.0014 0.0111 125.6275 2179.151643 4 0.0002 32 | 0/8 2 h-lim-p 0.0001 0.0007 53.4539 2178.907338 0 0.0002 45 | 0/8 3 h-lim-p 0.0006 0.0089 14.6408 2178.882263 5 0.0003 66 | 0/8 4 h-lim-p 0.0028 0.1869 1.3446 2178.881991 2 0.0003 84 | 0/8 5 h-lim-p 0.0017 0.5176 0.2349 2178.881981 1 0.0003 99 | 0/8 6 h-lim-p 0.0052 11.3422 0.0156 2178.881934 0 0.0104 120 | 0/8 7 h-lim-p 0.0017 0.4844 0.0930 2178.880779 0 0.0070 142 | 0/8 8 h-lim-p 0.0004 0.0390 1.5374 2178.878582 0 0.0008 163 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 2178.878401 1 0.9961 177 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2178.878400 0 1.0938 197 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2178.878400 0 2.1875 217 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2178.878400 0 1.0938 237 | 0/8 13 h-lim-p 0.4087 20.0000 0.0000 2178.878400 0 6.5394 261 | 0/8 14 h-lim-p 1.5829 20.0000 0.0000 2178.878400 0 0.3463 282 | 0/8 15 h-lim-p 0.9341 20.0000 0.0000 2178.878400 0 0.0055 309 | 0/8 16 h-lim-p 0.0205 20.0000 0.0000 2178.878400 0 0.0000 350 Out... lnL = -2178.878400 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2178.878400 Node 7: lnL = -2178.878400 Node 8: lnL = -2178.878400 Node 9: lnL = -2178.878400 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 759 Sequential format.. Reading seq # 1: YNL113W_Sbay Reading seq # 2: YNL113W_Scer Reading seq # 3: YNL113W_Skud Reading seq # 4: YNL113W_Smik Reading seq # 5: YNL113W_Spar Sequences read.. Counting patterns.. # site patterns = 347 Counting frequencies.. 120 bytes for distance 55520 bytes for lkl0 44416 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.155978 0.039019 0.096975 0.184908 0.120807 0.296771 0.369464 0.199234 lnL0 = -3855.555603 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3855.555603 x= 0.15598 0.03902 0.09697 0.18491 0.12081 0.29677 0.36946 0.19923 1 h-lim-p 0.0012 0.0093 142.7734 3852.664744 8 0.0003 41 | 0/8 2 h-lim-p 0.0005 0.0042 32.8898 3852.423903 5 0.0005 62 | 0/8 3 h-lim-p 0.0011 0.0399 13.4947 3852.389736 4 0.0004 82 | 0/8 4 h-lim-p 0.0020 0.1110 3.0066 3852.386329 3 0.0008 100 | 0/8 5 h-lim-p 0.0050 0.7940 0.4905 3852.386217 2 0.0010 117 | 0/8 6 h-lim-p 0.0023 1.4638 0.2023 3852.386203 2 0.0007 142 | 0/8 7 h-lim-p 0.0028 5.7687 0.0534 3852.386201 0 0.0012 162 | 0/8 8 h-lim-p 0.0981 20.0000 0.0007 3852.385743 0 0.7850 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3852.385725 1 0.9961 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3852.385725 0 1.0938 227 | 0/8 11 h-lim-p 1.4852 20.0000 0.0000 3852.385725 0 0.3713 248 | 0/8 12 h-lim-p 0.1918 20.0000 0.0000 3852.385725 0 0.0480 269 | 0/8 13 h-lim-p 0.0235 20.0000 0.0000 3852.385725 0 0.0059 290 | 0/8 14 h-lim-p 0.0028 20.0000 0.0000 3852.385725 0 0.0007 311 | 0/8 15 h-lim-p 0.0018 20.0000 0.0000 3852.385725 0 0.0000 346 Out... lnL = -3852.385725 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3852.385725 Node 7: lnL = -3852.385725 Node 8: lnL = -3852.385725 Node 9: lnL = -3852.385725 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 344 Sequential format.. Reading seq # 1: YNL116W_Sbay Reading seq # 2: YNL116W_Scer Reading seq # 3: YNL116W_Skud Reading seq # 4: YNL116W_Smik Reading seq # 5: YNL116W_Spar Sequences read.. Counting patterns.. # site patterns = 146 Counting frequencies.. 120 bytes for distance 23360 bytes for lkl0 18688 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.110264 0.031111 0.071612 0.117801 0.072728 0.142306 0.224902 0.137369 lnL0 = -1336.862163 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1336.862163 x= 0.11026 0.03111 0.07161 0.11780 0.07273 0.14231 0.22490 0.13737 1 h-lim-p 0.0004 0.0036 68.8809 1335.589525 0 0.0007 22 | 0/8 2 h-lim-p 0.0007 0.0052 17.9246 1335.505112 3 0.0005 40 | 0/8 3 h-lim-p 0.0010 0.0320 10.1385 1335.480500 7 0.0006 68 | 0/8 4 h-lim-p 0.0021 0.0997 2.9357 1335.476181 4 0.0011 89 | 0/8 5 h-lim-p 0.0013 0.1015 2.5639 1335.475182 4 0.0005 109 | 0/8 6 h-lim-p 0.0041 0.5963 0.3019 1335.475085 2 0.0016 125 | 0/8 7 h-lim-p 0.0036 1.6363 0.1363 1335.475025 3 0.0022 153 | 0/8 8 h-lim-p 0.0141 4.0261 0.0209 1335.455940 0 0.2250 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0009 1335.455442 4 0.9644 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1335.455442 0 1.0938 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1335.455442 0 1.0938 245 | 0/8 12 h-lim-p 1.9379 20.0000 0.0000 1335.455442 0 0.4239 266 | 0/8 13 h-lim-p 0.2363 20.0000 0.0000 1335.455442 0 0.1034 286 | 0/8 14 h-lim-p 0.0567 20.0000 0.0000 1335.455442 0 0.0000 324 Out... lnL = -1335.455442 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1335.455442 Node 7: lnL = -1335.455442 Node 8: lnL = -1335.455442 Node 9: lnL = -1335.455442 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 847 Sequential format.. Reading seq # 1: YNL117W_Sbay Reading seq # 2: YNL117W_Scer Reading seq # 3: YNL117W_Skud Reading seq # 4: YNL117W_Smik Reading seq # 5: YNL117W_Spar Sequences read.. Counting patterns.. # site patterns = 248 Counting frequencies.. 120 bytes for distance 39680 bytes for lkl0 31744 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.128840 0.000060 0.123416 0.121983 0.095224 0.161804 0.256707 0.159857 lnL0 = -3352.872374 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3352.872374 x= 0.12884 0.00006 0.12342 0.12198 0.09522 0.16180 0.25671 0.15986 1 h-lim-p 0.0010 0.0080 79.4598 3351.906507 8 0.0003 43 | 0/8 2 h-lim-p 0.0005 0.0055 45.6385 3351.613033 6 0.0003 69 | 0/8 3 h-lim-p 0.0007 0.0159 24.3820 3351.525008 7 0.0004 101 | 0/8 4 h-lim-p 0.0010 0.0420 9.5462 3351.510995 5 0.0004 124 | 0/8 5 h-lim-p 0.0005 0.0343 7.3995 3351.501563 4 0.0005 145 | 0/8 6 h-lim-p 0.0021 0.0210 1.9515 3351.499986 2 0.0010 161 | 0/8 7 h-lim-p 0.0017 0.0621 1.1371 3351.499764 3 0.0004 180 | 0/8 8 h-lim-p 0.3415 20.0000 0.0015 3351.496329 0 1.3659 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 3351.495983 2 0.9961 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3351.495983 0 1.0938 238 | 0/8 11 h-lim-p 1.2130 20.0000 0.0000 3351.495983 0 1.0614 258 | 0/8 12 h-lim-p 0.3714 20.0000 0.0000 3351.495983 0 0.1857 278 | 0/8 13 h-lim-p 0.0306 20.0000 0.0001 3351.495983 0 0.0019 301 | 0/8 14 h-lim-p 0.0040 20.0000 0.0000 3351.495983 0 0.0000 332 | 0/8 15 h-lim-p 0.0041 20.0000 0.0000 3351.495983 0 0.0000 366 Out... lnL = -3351.495983 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3351.495983 Node 7: lnL = -3351.495983 Node 8: lnL = -3351.495983 Node 9: lnL = -3351.495983 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 516 Sequential format.. Reading seq # 1: YNL119W_Sbay Reading seq # 2: YNL119W_Scer Reading seq # 3: YNL119W_Skud Reading seq # 4: YNL119W_Smik Reading seq # 5: YNL119W_Spar Sequences read.. Counting patterns.. # site patterns = 228 Counting frequencies.. 120 bytes for distance 36480 bytes for lkl0 29184 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.113688 0.109218 0.052168 0.155119 0.133889 0.241735 0.234581 0.149586 lnL0 = -2491.168038 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2491.168038 x= 0.11369 0.10922 0.05217 0.15512 0.13389 0.24173 0.23458 0.14959 1 h-lim-p 0.0044 1.1810 106.7969 2489.507152 9 0.0003 47 | 0/8 2 h-lim-p 0.0022 0.0176 15.2327 2489.430135 7 0.0007 76 | 0/8 3 h-lim-p 0.0018 0.0301 5.7330 2489.422393 6 0.0005 103 | 0/8 4 h-lim-p 0.0043 0.6252 0.7186 2489.422160 2 0.0009 120 | 0/8 5 h-lim-p 0.0034 1.2649 0.1965 2489.422149 2 0.0005 146 | 0/8 6 h-lim-p 0.0073 20.0000 0.0146 2489.422149 0 0.0016 167 | 0/8 7 h-lim-p 0.0042 20.0000 0.0055 2489.422149 0 0.0037 187 | 0/8 8 h-lim-p 0.0210 20.0000 0.0010 2489.422103 0 0.1677 210 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2489.422102 0 1.0938 230 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2489.422102 0 1.0938 250 | 0/8 11 h-lim-p 1.3440 20.0000 0.0000 2489.422102 0 2.6880 271 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2489.422102 0 0.3125 293 | 0/8 13 h-lim-p 0.1331 20.0000 0.0000 2489.422102 0 0.0333 314 | 0/8 14 h-lim-p 0.0138 20.0000 0.0000 2489.422102 0 0.0000 353 Out... lnL = -2489.422102 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2489.422102 Node 7: lnL = -2489.422102 Node 8: lnL = -2489.422102 Node 9: lnL = -2489.422102 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 508 Sequential format.. Reading seq # 1: YNL121C_Sbay Reading seq # 2: YNL121C_Scer Reading seq # 3: YNL121C_Skud Reading seq # 4: YNL121C_Smik Reading seq # 5: YNL121C_Spar Sequences read.. Counting patterns.. # site patterns = 229 Counting frequencies.. 120 bytes for distance 36640 bytes for lkl0 29312 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.141529 0.060391 0.043680 0.160629 0.133485 0.244984 0.268700 0.177781 lnL0 = -2474.210446 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2474.210446 x= 0.14153 0.06039 0.04368 0.16063 0.13349 0.24498 0.26870 0.17778 1 h-lim-p 0.0024 0.9722 144.7887 2471.592106 3 0.0003 30 | 0/8 2 h-lim-p 0.0011 0.0090 18.3133 2471.494913 4 0.0006 51 | 0/8 3 h-lim-p 0.0016 0.0363 6.6018 2471.482994 6 0.0006 75 | 0/8 4 h-lim-p 0.0024 0.2174 1.6705 2471.481972 3 0.0008 95 | 0/8 5 h-lim-p 0.0022 0.6169 0.6006 2471.481841 3 0.0008 113 | 0/8 6 h-lim-p 0.0108 6.6940 0.0457 2471.481839 1 0.0013 137 | 0/8 7 h-lim-p 0.0113 20.0000 0.0054 2471.481812 0 0.0454 159 | 0/8 8 h-lim-p 0.0058 20.0000 0.0419 2471.481157 0 0.0175 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2471.481155 0 1.0938 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2471.481155 0 1.0938 220 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2471.481155 0 2.1875 240 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2471.481155 0 0.6250 261 | 0/8 13 h-lim-p 0.1516 20.0000 0.0000 2471.481155 0 0.0379 282 | 0/8 14 h-lim-p 0.0179 20.0000 0.0000 2471.481155 0 0.0003 307 Out... lnL = -2471.481155 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2471.481155 Node 7: lnL = -2471.481155 Node 8: lnL = -2471.481155 Node 9: lnL = -2471.481155 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 364 Sequential format.. Reading seq # 1: YNL122C_Sbay Reading seq # 2: YNL122C_Scer Reading seq # 3: YNL122C_Skud Reading seq # 4: YNL122C_Smik Reading seq # 5: YNL122C_Spar Sequences read.. Counting patterns.. # site patterns = 112 Counting frequencies.. 120 bytes for distance 17920 bytes for lkl0 14336 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.045933 0.018937 0.083699 0.076168 0.132453 4.811991 0.140336 0.151874 lnL0 = -1281.077146 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1281.077146 x= 0.04593 0.01894 0.08370 0.07617 0.13245 4.81199 0.14034 0.15187 1 h-lim-p 0.0006 0.0048 60.8844 1280.462507 9 0.0003 45 | 0/8 2 h-lim-p 0.0007 0.0052 20.5851 1280.371143 7 0.0005 74 | 0/8 3 h-lim-p 0.0020 0.0471 4.8672 1280.366161 2 0.0005 91 | 0/8 4 h-lim-p 0.0031 0.3348 0.7187 1280.365973 2 0.0007 108 | 0/8 5 h-lim-p 0.0065 0.9454 0.0812 1280.365971 1 0.0004 133 | 0/8 6 h-lim-p 0.2991 20.0000 0.0001 1280.365952 0 1.1962 155 | 0/8 7 h-lim-p 2.5000 20.0000 0.0000 1280.365952 0 1.0938 175 | 0/8 8 h-lim-p 1.4652 20.0000 0.0000 1280.365952 0 1.2820 195 | 0/8 9 h-lim-p 1.4205 20.0000 0.0000 1280.365952 0 0.3551 216 | 0/8 10 h-lim-p 0.0827 20.0000 0.0001 1280.365952 0 0.0000 257 | 0/8 11 h-lim-p 0.0000 20.0000 0.0011 | 0/8 12 h-lim-p 0.0000 20.0000 0.0011 Out... lnL = -1280.365952 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1280.365952 Node 7: lnL = -1280.365952 Node 8: lnL = -1280.365952 Node 9: lnL = -1280.365952 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 330 Sequential format.. Reading seq # 1: YNL123W_Sbay Reading seq # 2: YNL123W_Scer Reading seq # 3: YNL123W_Skud Reading seq # 4: YNL123W_Smik Reading seq # 5: YNL123W_Spar Sequences read.. Counting patterns.. # site patterns = 148 Counting frequencies.. 120 bytes for distance 23680 bytes for lkl0 18944 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.106315 0.044254 0.091836 0.149015 0.062712 0.242140 0.137230 0.135616 lnL0 = -1410.510878 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1410.510878 x= 0.10632 0.04425 0.09184 0.14901 0.06271 0.24214 0.13723 0.13562 1 h-lim-p 0.0035 0.0283 53.0618 1409.948270 4 0.0004 32 | 0/8 2 h-lim-p 0.0012 0.0098 15.5355 1409.870143 7 0.0007 61 | 0/8 3 h-lim-p 0.0012 0.0200 8.7590 1409.856597 6 0.0005 87 | 0/8 4 h-lim-p 0.0021 0.1658 1.9195 1409.854889 2 0.0010 103 | 0/8 5 h-lim-p 0.0033 0.5023 0.5744 1409.854756 3 0.0009 122 | 0/8 6 h-lim-p 0.0264 6.3933 0.0190 1409.854755 1 0.0016 147 | 0/8 7 h-lim-p 0.0306 20.0000 0.0010 1409.854514 0 0.4889 171 | 0/8 8 h-lim-p 0.0021 0.6966 0.2373 1409.854487 2 0.0008 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1409.854487 0 1.0938 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1409.854487 0 1.0938 235 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1409.854487 0 2.1875 255 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1409.854487 0 0.6250 276 | 0/8 13 h-lim-p 0.1487 20.0000 0.0000 1409.854487 0 0.0743 296 | 0/8 14 h-lim-p 0.0346 20.0000 0.0000 1409.854487 0 0.0011 320 | 0/8 15 h-lim-p 0.0018 20.0000 0.0000 1409.854487 0 0.0001 343 Out... lnL = -1409.854487 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1409.854487 Node 7: lnL = -1409.854487 Node 8: lnL = -1409.854487 Node 9: lnL = -1409.854487 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 913 Sequential format.. Reading seq # 1: YNL124W_Sbay Reading seq # 2: YNL124W_Scer Reading seq # 3: YNL124W_Skud Reading seq # 4: YNL124W_Smik Reading seq # 5: YNL124W_Spar Sequences read.. Counting patterns.. # site patterns = 311 Counting frequencies.. 120 bytes for distance 49760 bytes for lkl0 39808 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.128381 0.184908 0.085930 0.088061 0.086820 0.208427 0.167698 0.163675 lnL0 = -3932.509377 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3932.509377 x= 0.12838 0.18491 0.08593 0.08806 0.08682 0.20843 0.16770 0.16367 1 h-lim-p 0.0004 0.0031 127.5708 3930.560914 6 0.0003 35 | 0/8 2 h-lim-p 0.0010 0.0081 26.6889 3930.430295 7 0.0004 62 | 0/8 3 h-lim-p 0.0003 0.0111 30.7408 3930.362245 5 0.0003 85 | 0/8 4 h-lim-p 0.0026 0.1327 3.0976 3930.359782 3 0.0005 104 | 0/8 5 h-lim-p 0.0025 0.3639 0.6664 3930.359715 2 0.0003 122 | 0/8 6 h-lim-p 0.0014 1.5377 0.1482 3930.359711 1 0.0003 145 | 0/8 7 h-lim-p 0.0009 6.3297 0.0537 3930.359710 0 0.0004 165 | 0/8 8 h-lim-p 0.1084 20.0000 0.0002 3930.359638 0 1.3002 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3930.359637 0 1.0938 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3930.359637 0 1.0938 228 | 0/8 11 h-lim-p 1.4066 20.0000 0.0000 3930.359637 0 1.4066 248 | 0/8 12 h-lim-p 1.5380 20.0000 0.0000 3930.359637 0 0.0023 277 | 0/8 13 h-lim-p 0.0015 20.0000 0.0000 3930.359637 0 0.0000 309 Out... lnL = -3930.359637 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3930.359637 Node 7: lnL = -3930.359637 Node 8: lnL = -3930.359637 Node 9: lnL = -3930.359637 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 430 Sequential format.. Reading seq # 1: YNL126W_Sbay Reading seq # 2: YNL126W_Scer Reading seq # 3: YNL126W_Skud Reading seq # 4: YNL126W_Smik Reading seq # 5: YNL126W_Spar Sequences read.. Counting patterns.. # site patterns = 134 Counting frequencies.. 120 bytes for distance 21440 bytes for lkl0 17152 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.184434 0.184932 0.125015 0.130428 0.117660 0.296208 4.550293 0.265273 lnL0 = -1747.843334 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1747.843334 x= 0.18443 0.18493 0.12501 0.13043 0.11766 0.29621 4.55029 0.26527 1 h-lim-p 0.0056 0.0452 10.3162 1747.792177 7 0.0010 41 | 0/8 2 h-lim-p 0.0009 0.0221 11.0292 1747.751892 0 0.0014 53 | 0/8 3 h-lim-p 0.0031 0.0364 4.8344 1747.741096 3 0.0013 71 | 0/8 4 h-lim-p 0.0060 0.4209 1.0582 1747.740240 5 0.0016 96 | 0/8 5 h-lim-p 0.0310 7.2254 0.0563 1747.740235 0 0.0017 111 | 0/8 6 h-lim-p 0.0248 20.0000 0.0038 1747.738933 0 0.5959 135 | 0/8 7 h-lim-p 2.5000 20.0000 0.0001 1747.738926 1 0.9961 157 | 0/8 8 h-lim-p 2.5000 20.0000 0.0000 1747.738926 0 1.0938 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1747.738926 0 1.2500 197 | 0/8 10 h-lim-p 1.2973 20.0000 0.0000 1747.738926 0 0.6486 217 | 0/8 11 h-lim-p 0.2582 20.0000 0.0000 1747.738926 0 0.0000 259 Out... lnL = -1747.738926 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1747.738926 Node 7: lnL = -1747.738926 Node 8: lnL = -1747.738926 Node 9: lnL = -1747.738926 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 199 Sequential format.. Reading seq # 1: YNL128W_Sbay Reading seq # 2: YNL128W_Scer Reading seq # 3: YNL128W_Skud Reading seq # 4: YNL128W_Smik Reading seq # 5: YNL128W_Spar Sequences read.. Counting patterns.. # site patterns = 102 Counting frequencies.. 120 bytes for distance 16320 bytes for lkl0 13056 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.107622 0.026966 0.052387 0.152394 0.089072 0.343528 0.287582 0.134211 lnL0 = -854.880522 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 854.880522 x= 0.10762 0.02697 0.05239 0.15239 0.08907 0.34353 0.28758 0.13421 1 h-lim-p 0.0011 0.0092 72.5964 853.416839 8 0.0007 43 | 0/8 2 h-lim-p 0.0015 0.0122 11.6448 853.311514 3 0.0016 61 | 0/8 3 h-lim-p 0.0026 0.0405 6.9739 853.287489 4 0.0013 81 | 0/8 4 h-lim-p 0.0032 0.1292 2.8323 853.278575 5 0.0027 102 | 0/8 5 h-lim-p 0.0132 0.2383 0.5843 853.278308 3 0.0016 122 | 0/8 6 h-lim-p 0.0087 4.1496 0.1103 853.278297 2 0.0020 147 | 0/8 7 h-lim-p 0.0069 13.9372 0.0326 853.278295 1 0.0034 170 | 0/8 8 h-lim-p 0.9914 20.0000 0.0001 853.278286 0 1.9828 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 853.278285 0 1.0938 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 853.278285 0 1.0938 231 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 853.278285 0 1.0938 251 | 0/8 12 h-lim-p 1.2887 20.0000 0.0000 853.278285 0 1.2887 271 | 0/8 13 h-lim-p 0.6044 20.0000 0.0000 853.278285 0 0.6044 291 | 0/8 14 h-lim-p 0.0368 20.0000 0.0000 853.278285 0 0.0092 312 | 0/8 15 h-lim-p 0.0032 20.0000 0.0001 853.278285 0 0.0000 339 | 0/8 16 h-lim-p 0.0010 20.0000 0.0000 853.278285 0 0.0000 376 Out... lnL = -853.278285 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -853.278285 Node 7: lnL = -853.278285 Node 8: lnL = -853.278285 Node 9: lnL = -853.278285 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 335 Sequential format.. Reading seq # 1: YNL129W_Sbay Reading seq # 2: YNL129W_Scer Reading seq # 3: YNL129W_Skud Reading seq # 4: YNL129W_Smik Reading seq # 5: YNL129W_Spar Sequences read.. Counting patterns.. # site patterns = 163 Counting frequencies.. 120 bytes for distance 26080 bytes for lkl0 20864 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.153753 0.086554 0.041660 0.192522 0.092826 0.261050 0.237315 0.182032 lnL0 = -1592.308121 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1592.308121 x= 0.15375 0.08655 0.04166 0.19252 0.09283 0.26105 0.23731 0.18203 1 h-lim-p 0.0059 0.0471 67.0677 1591.487039 9 0.0004 48 | 0/8 2 h-lim-p 0.0011 0.0091 16.9453 1591.374594 7 0.0008 78 | 0/8 3 h-lim-p 0.0028 0.0531 4.9234 1591.366738 5 0.0007 103 | 0/8 4 h-lim-p 0.0034 0.3704 1.0124 1591.366243 4 0.0010 126 | 0/8 5 h-lim-p 0.0047 2.3574 0.2165 1591.366215 2 0.0013 143 | 0/8 6 h-lim-p 0.0098 13.2608 0.0275 1591.366215 1 0.0012 167 | 0/8 7 h-lim-p 0.1374 20.0000 0.0002 1591.366191 0 1.0990 190 | 0/8 8 h-lim-p 0.0039 4.0811 0.0676 1591.366182 2 0.0026 216 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1591.366181 0 1.0938 236 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1591.366181 0 1.0938 256 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1591.366181 0 2.1875 276 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1591.366181 0 1.0938 296 | 0/8 13 h-lim-p 0.5356 20.0000 0.0000 1591.366181 0 4.2848 319 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1591.366181 0 0.4688 341 | 0/8 15 h-lim-p 0.7309 20.0000 0.0000 1591.366181 0 0.1827 362 | 0/8 16 h-lim-p 0.0501 20.0000 0.0000 1591.366181 0 0.0000 397 Out... lnL = -1591.366181 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1591.366181 Node 7: lnL = -1591.366181 Node 8: lnL = -1591.366181 Node 9: lnL = -1591.366181 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 308 Sequential format.. Reading seq # 1: YNL131W_Sbay Reading seq # 2: YNL131W_Scer Reading seq # 3: YNL131W_Skud Reading seq # 4: YNL131W_Smik Reading seq # 5: YNL131W_Spar Sequences read.. Counting patterns.. # site patterns = 130 Counting frequencies.. 120 bytes for distance 20800 bytes for lkl0 16640 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.066522 0.118130 0.059780 0.105469 0.088613 0.188771 0.157005 0.087227 lnL0 = -1286.772842 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1286.772842 x= 0.06652 0.11813 0.05978 0.10547 0.08861 0.18877 0.15701 0.08723 1 h-lim-p 0.0005 0.0043 52.2907 1286.162317 6 0.0005 33 | 0/8 2 h-lim-p 0.0013 0.0107 10.0585 1286.137985 7 0.0005 61 | 0/8 3 h-lim-p 0.0022 0.1744 2.2161 1286.136732 2 0.0005 78 | 0/8 4 h-lim-p 0.0018 0.3360 0.6364 1286.136578 2 0.0008 94 | 0/8 5 h-lim-p 0.0028 1.0807 0.1828 1286.136569 1 0.0006 117 | 0/8 6 h-lim-p 0.0085 18.7722 0.0131 1286.136569 0 0.0019 138 | 0/8 7 h-lim-p 0.0079 20.0000 0.0031 1286.136567 0 0.0157 159 | 0/8 8 h-lim-p 0.0102 20.0000 0.0048 1286.136519 0 0.0407 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1286.136518 0 1.0938 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1286.136518 0 1.0938 221 | 0/8 11 h-lim-p 1.5558 20.0000 0.0000 1286.136518 0 1.5558 241 | 0/8 12 h-lim-p 2.3159 20.0000 0.0000 1286.136518 0 0.0633 265 | 0/8 13 h-lim-p 0.0183 20.0000 0.0000 1286.136518 0 0.0023 287 | 0/8 14 h-lim-p 0.0012 20.0000 0.0000 1286.136518 0 0.0001 310 | 0/8 15 h-lim-p 0.0009 20.0000 0.0000 1286.136518 0 0.0000 347 Out... lnL = -1286.136518 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1286.136518 Node 7: lnL = -1286.136518 Node 8: lnL = -1286.136518 Node 9: lnL = -1286.136518 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 336 Sequential format.. Reading seq # 1: YNL136W_Sbay Reading seq # 2: YNL136W_Scer Reading seq # 3: YNL136W_Skud Reading seq # 4: YNL136W_Smik Reading seq # 5: YNL136W_Spar Sequences read.. Counting patterns.. # site patterns = 163 Counting frequencies.. 120 bytes for distance 26080 bytes for lkl0 20864 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.177584 0.063254 0.044434 0.144348 0.082075 0.221484 0.244990 0.204234 lnL0 = -1592.582040 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1592.582040 x= 0.17758 0.06325 0.04443 0.14435 0.08207 0.22148 0.24499 0.20423 1 h-lim-p 0.0312 0.2494 29.2415 1592.314828 7 0.0006 41 | 0/8 2 h-lim-p 0.0006 0.0050 21.9771 1592.193321 5 0.0007 64 | 0/8 3 h-lim-p 0.0036 0.0377 4.2373 1592.189676 2 0.0004 82 | 0/8 4 h-lim-p 0.0025 0.1803 0.7268 1592.189469 3 0.0008 101 | 0/8 5 h-lim-p 0.0029 1.9752 0.2011 1592.189445 1 0.0013 123 | 0/8 6 h-lim-p 0.0046 4.7268 0.0564 1592.189444 1 0.0011 146 | 0/8 7 h-lim-p 0.0024 17.3600 0.0264 1592.189443 0 0.0021 166 | 0/8 8 h-lim-p 0.0797 20.0000 0.0007 1592.189296 0 0.6379 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1592.189295 0 1.0938 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1592.189295 0 1.0938 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1592.189295 0 2.5000 249 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1592.189295 0 0.0195 275 | 0/8 13 h-lim-p 0.0159 20.0000 0.0000 1592.189295 0 0.0002 300 Out... lnL = -1592.189295 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1592.189295 Node 7: lnL = -1592.189295 Node 8: lnL = -1592.189295 Node 9: lnL = -1592.189295 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 335 Sequential format.. Reading seq # 1: YNL137C_Sbay Reading seq # 2: YNL137C_Scer Reading seq # 3: YNL137C_Skud Reading seq # 4: YNL137C_Smik Reading seq # 5: YNL137C_Spar Sequences read.. Counting patterns.. # site patterns = 166 Counting frequencies.. 120 bytes for distance 26560 bytes for lkl0 21248 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.180976 0.058567 0.050758 0.163433 0.080822 0.218305 0.260305 0.208489 lnL0 = -1614.358524 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1614.358524 x= 0.18098 0.05857 0.05076 0.16343 0.08082 0.21831 0.26031 0.20849 1 h-lim-p 0.0393 5.5098 28.6570 1614.113673 7 0.0006 42 | 0/8 2 h-lim-p 0.0008 0.0064 16.8210 1614.033698 3 0.0007 60 | 0/8 3 h-lim-p 0.0021 0.0167 5.2774 1614.025057 6 0.0007 86 | 0/8 4 h-lim-p 0.0020 0.0567 1.8630 1614.023977 4 0.0007 107 | 0/8 5 h-lim-p 0.0021 0.2871 0.6442 1614.023697 4 0.0016 127 | 0/8 6 h-lim-p 0.0071 3.0370 0.1416 1614.023685 2 0.0014 152 | 0/8 7 h-lim-p 0.0057 7.3828 0.0336 1614.023684 0 0.0013 173 | 0/8 8 h-lim-p 0.1451 20.0000 0.0003 1614.023617 0 1.1609 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1614.023608 1 0.9961 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1614.023608 0 2.1875 238 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1614.023608 0 0.5469 259 | 0/8 12 h-lim-p 0.5140 20.0000 0.0000 1614.023608 0 0.0080 284 | 0/8 13 h-lim-p 0.0053 20.0000 0.0000 1614.023608 0 0.0003 307 Out... lnL = -1614.023608 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1614.023608 Node 7: lnL = -1614.023608 Node 8: lnL = -1614.023608 Node 9: lnL = -1614.023608 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 863 Sequential format.. Reading seq # 1: YNL138W_Sbay Reading seq # 2: YNL138W_Scer Reading seq # 3: YNL138W_Skud Reading seq # 4: YNL138W_Smik Reading seq # 5: YNL138W_Spar Sequences read.. Counting patterns.. # site patterns = 211 Counting frequencies.. 120 bytes for distance 33760 bytes for lkl0 27008 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.123063 0.036091 0.096107 0.116878 0.105516 0.743722 0.168057 0.157842 lnL0 = -3397.817637 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3397.817637 x= 0.12306 0.03609 0.09611 0.11688 0.10552 0.74372 0.16806 0.15784 1 h-lim-p 0.0003 0.0021 202.9701 3393.490772 6 0.0002 33 | 0/8 2 h-lim-p 0.0003 0.0022 79.5117 3392.711393 5 0.0003 56 | 0/8 3 h-lim-p 0.0009 0.0097 24.7825 3392.643091 6 0.0002 84 | 0/8 4 h-lim-p 0.0007 0.0266 9.4719 3392.629380 6 0.0004 109 | 0/8 5 h-lim-p 0.0014 0.0874 2.4573 3392.625371 3 0.0014 127 | 0/8 6 h-lim-p 0.0004 0.0200 8.3222 3392.605679 0 0.0025 141 | 0/8 7 h-lim-p 0.0417 0.7662 0.5070 3392.603202 3 0.0206 159 | 0/8 8 h-lim-p 2.5000 20.0000 0.0006 3392.603149 1 0.9961 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3392.603149 0 1.0938 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3392.603149 0 1.0938 221 | 0/8 11 h-lim-p 1.2847 20.0000 0.0000 3392.603149 0 0.0000 266 Out... lnL = -3392.603149 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3392.603149 Node 7: lnL = -3392.603149 Node 8: lnL = -3392.603149 Node 9: lnL = -3392.603149 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 851 Sequential format.. Reading seq # 1: YNL139C_Sbay Reading seq # 2: YNL139C_Scer Reading seq # 3: YNL139C_Skud Reading seq # 4: YNL139C_Smik Reading seq # 5: YNL139C_Spar Sequences read.. Counting patterns.. # site patterns = 246 Counting frequencies.. 120 bytes for distance 39360 bytes for lkl0 31488 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.086661 0.105991 0.035691 0.134800 0.104001 0.167758 0.169461 0.107853 lnL0 = -3772.964913 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3772.964913 x= 0.08666 0.10599 0.03569 0.13480 0.10400 0.16776 0.16946 0.10785 1 h-lim-p 0.0002 0.0020 261.7112 3768.831219 9 0.0001 45 | 0/8 2 h-lim-p 0.0002 0.0016 91.9574 3767.861748 1 0.0003 59 | 0/8 3 h-lim-p 0.0009 0.0121 25.8551 3767.796236 2 0.0002 76 | 0/8 4 h-lim-p 0.0015 0.0719 3.6973 3767.794140 3 0.0003 96 | 0/8 5 h-lim-p 0.0026 0.6981 0.4429 3767.794114 1 0.0003 112 | 0/8 6 h-lim-p 0.0007 1.3496 0.1561 3767.794110 0 0.0003 132 | 0/8 7 h-lim-p 0.0159 20.0000 0.0032 3767.794033 0 0.0636 154 | 0/8 8 h-lim-p 0.0012 1.0455 0.1731 3767.792973 0 0.0047 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3767.792930 2 1.0938 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3767.792929 0 1.0938 220 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3767.792929 0 0.5469 241 | 0/8 12 h-lim-p 0.3264 20.0000 0.0000 3767.792929 0 0.0000 286 Out... lnL = -3767.792929 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3767.792929 Node 7: lnL = -3767.792929 Node 8: lnL = -3767.792929 Node 9: lnL = -3767.792929 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 695 Sequential format.. Reading seq # 1: YNL141W_Sbay Reading seq # 2: YNL141W_Scer Reading seq # 3: YNL141W_Skud Reading seq # 4: YNL141W_Smik Reading seq # 5: YNL141W_Spar Sequences read.. Counting patterns.. # site patterns = 299 Counting frequencies.. 120 bytes for distance 47840 bytes for lkl0 38272 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.166937 0.087775 0.000060 0.192360 0.171541 0.215107 0.275338 0.195920 lnL0 = -3146.214545 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3146.214545 x= 0.16694 0.08778 0.00006 0.19236 0.17154 0.21511 0.27534 0.19592 1 h-lim-p 0.0009 0.4079 264.9372 3139.473785 6 0.0002 35 | 0/8 2 h-lim-p 0.0009 0.0072 29.6015 3139.209409 8 0.0006 67 | 0/8 3 h-lim-p 0.0021 0.0374 8.5762 3139.187965 6 0.0006 97 | 0/8 4 h-lim-p 0.0028 0.1634 1.9404 3139.186037 4 0.0011 117 | 0/8 5 h-lim-p 0.0074 0.7829 0.2831 3139.186008 1 0.0007 133 | 0/8 6 h-lim-p 0.0073 7.3300 0.0284 3139.186007 0 0.0008 155 | 0/8 7 h-lim-p 0.0042 20.0000 0.0054 3139.186007 0 0.0037 175 | 0/8 8 h-lim-p 0.0340 20.0000 0.0006 3139.185946 0 0.2716 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3139.185945 0 1.0938 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3139.185945 0 1.0938 238 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3139.185945 0 2.1875 258 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3139.185945 0 0.5469 279 | 0/8 13 h-lim-p 0.1467 20.0000 0.0000 3139.185945 0 0.0092 302 | 0/8 14 h-lim-p 0.0029 20.0000 0.0000 3139.185945 0 0.0000 332 Out... lnL = -3139.185945 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3139.185945 Node 7: lnL = -3139.185945 Node 8: lnL = -3139.185945 Node 9: lnL = -3139.185945 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 855 Sequential format.. Reading seq # 1: YNL144C_Sbay Reading seq # 2: YNL144C_Scer Reading seq # 3: YNL144C_Skud Reading seq # 4: YNL144C_Smik Reading seq # 5: YNL144C_Spar Sequences read.. Counting patterns.. # site patterns = 337 Counting frequencies.. 120 bytes for distance 53920 bytes for lkl0 43136 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.168548 0.107380 0.085317 0.143238 0.080859 0.230712 0.341884 0.199896 lnL0 = -3831.875682 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3831.875682 x= 0.16855 0.10738 0.08532 0.14324 0.08086 0.23071 0.34188 0.19990 1 h-lim-p 0.0072 1.3263 103.3244 3830.080759 4 0.0004 33 | 0/8 2 h-lim-p 0.0010 0.0082 30.8386 3829.851702 5 0.0005 55 | 0/8 3 h-lim-p 0.0011 0.0290 13.9727 3829.781467 6 0.0009 79 | 0/8 4 h-lim-p 0.0057 0.0678 2.0912 3829.779786 5 0.0008 104 | 0/8 5 h-lim-p 0.0075 1.3080 0.2214 3829.779765 0 0.0008 118 | 0/8 6 h-lim-p 0.0046 7.0351 0.0393 3829.779757 1 0.0037 140 | 0/8 7 h-lim-p 0.0059 13.6527 0.0248 3829.779663 0 0.0234 162 | 0/8 8 h-lim-p 0.0091 20.0000 0.0640 3829.777975 0 0.0181 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3829.777945 1 0.9961 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3829.777945 0 1.0938 225 | 0/8 11 h-lim-p 2.1476 20.0000 0.0000 3829.777945 0 1.8791 245 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3829.777945 0 0.5469 266 | 0/8 13 h-lim-p 0.1391 20.0000 0.0000 3829.777945 0 0.1391 286 | 0/8 14 h-lim-p 0.0685 20.0000 0.0000 3829.777945 0 0.0086 308 | 0/8 15 h-lim-p 0.0048 20.0000 0.0000 3829.777945 0 0.0000 335 Out... lnL = -3829.777945 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3829.777945 Node 7: lnL = -3829.777945 Node 8: lnL = -3829.777945 Node 9: lnL = -3829.777945 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 388 Sequential format.. Reading seq # 1: YNL146W_Sbay Reading seq # 2: YNL146W_Scer Reading seq # 3: YNL146W_Skud Reading seq # 4: YNL146W_Smik Reading seq # 5: YNL146W_Spar Sequences read.. Counting patterns.. # site patterns = 182 Counting frequencies.. 120 bytes for distance 29120 bytes for lkl0 23296 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.189993 0.030158 0.210360 0.148067 0.052419 0.198310 0.252923 0.220672 lnL0 = -1727.167555 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1727.167555 x= 0.18999 0.03016 0.21036 0.14807 0.05242 0.19831 0.25292 0.22067 1 h-lim-p 0.0001 0.0012 63.0400 1726.020178 0 0.0006 24 | 0/8 2 h-lim-p 0.0011 0.0396 34.6964 1725.816968 7 0.0004 53 | 0/8 3 h-lim-p 0.0014 0.0113 9.7353 1725.779387 7 0.0009 82 | 0/8 4 h-lim-p 0.0026 0.1142 3.3214 1725.773305 4 0.0012 103 | 0/8 5 h-lim-p 0.0082 0.3675 0.5058 1725.773105 2 0.0016 120 | 0/8 6 h-lim-p 0.0062 1.7178 0.1276 1725.773091 2 0.0016 145 | 0/8 7 h-lim-p 0.0077 3.7240 0.0272 1725.773088 0 0.0034 165 | 0/8 8 h-lim-p 0.0499 20.0000 0.0018 1725.772665 0 0.3992 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1725.772663 0 1.0938 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1725.772663 0 1.0938 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1725.772663 0 2.1875 248 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1725.772663 0 0.5469 269 | 0/8 13 h-lim-p 0.3469 20.0000 0.0000 1725.772663 0 0.0217 292 | 0/8 14 h-lim-p 0.0107 20.0000 0.0000 1725.772663 0 0.0027 313 Out... lnL = -1725.772663 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1725.772663 Node 7: lnL = -1725.772663 Node 8: lnL = -1725.772663 Node 9: lnL = -1725.772663 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 308 Sequential format.. Reading seq # 1: YNL148C_Sbay Reading seq # 2: YNL148C_Scer Reading seq # 3: YNL148C_Skud Reading seq # 4: YNL148C_Smik Reading seq # 5: YNL148C_Spar Sequences read.. Counting patterns.. # site patterns = 154 Counting frequencies.. 120 bytes for distance 24640 bytes for lkl0 19712 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.072953 0.136177 0.102607 0.117942 0.081211 0.303670 0.150210 0.098446 lnL0 = -1313.549522 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1313.549522 x= 0.07295 0.13618 0.10261 0.11794 0.08121 0.30367 0.15021 0.09845 1 h-lim-p 0.0026 0.0210 17.8163 1313.443883 4 0.0007 31 | 0/8 2 h-lim-p 0.0014 0.0413 8.3311 1313.409466 3 0.0012 49 | 0/8 3 h-lim-p 0.0020 0.0922 5.0875 1313.402101 5 0.0008 70 | 0/8 4 h-lim-p 0.0023 0.0961 1.7610 1313.401206 5 0.0007 96 | 0/8 5 h-lim-p 0.0024 0.6363 0.4957 1313.401105 4 0.0009 117 | 0/8 6 h-lim-p 0.0036 1.3850 0.1227 1313.401094 1 0.0016 139 | 0/8 7 h-lim-p 0.0084 20.0000 0.0231 1313.401094 0 0.0009 161 | 0/8 8 h-lim-p 0.1222 20.0000 0.0002 1313.401069 0 0.9777 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1313.401069 0 1.0938 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1313.401069 0 0.5469 225 | 0/8 11 h-lim-p 0.3614 20.0000 0.0000 1313.401069 0 0.0903 246 | 0/8 12 h-lim-p 0.0533 20.0000 0.0000 1313.401069 0 0.0116 267 | 0/8 13 h-lim-p 0.0077 20.0000 0.0000 1313.401069 0 0.0000 297 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 1313.401069 0 0.0000 330 Out... lnL = -1313.401069 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1313.401069 Node 7: lnL = -1313.401069 Node 8: lnL = -1313.401069 Node 9: lnL = -1313.401069 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 860 Sequential format.. Reading seq # 1: YNL151C_Sbay Reading seq # 2: YNL151C_Scer Reading seq # 3: YNL151C_Skud Reading seq # 4: YNL151C_Smik Reading seq # 5: YNL151C_Spar Sequences read.. Counting patterns.. # site patterns = 430 Counting frequencies.. 120 bytes for distance 68800 bytes for lkl0 55040 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.261730 0.154212 0.139657 0.140260 0.163310 0.267032 0.588316 0.308508 lnL0 = -4579.773716 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4579.773716 x= 0.26173 0.15421 0.13966 0.14026 0.16331 0.26703 0.58832 0.30851 1 h-lim-p 0.0258 2.4430 59.5938 4579.013255 8 0.0004 43 | 0/8 2 h-lim-p 0.0010 0.0114 26.1625 4578.853669 5 0.0005 66 | 0/8 3 h-lim-p 0.0013 0.0345 11.2491 4578.801444 5 0.0010 89 | 0/8 4 h-lim-p 0.0032 0.1356 3.4716 4578.795216 5 0.0012 114 | 0/8 5 h-lim-p 0.0027 0.2849 1.5153 4578.794246 3 0.0010 132 | 0/8 6 h-lim-p 0.0038 0.7246 0.4006 4578.794144 3 0.0013 151 | 0/8 7 h-lim-p 0.0121 6.8565 0.0443 4578.794136 0 0.0061 171 | 0/8 8 h-lim-p 0.2448 20.0000 0.0011 4578.793693 0 0.9793 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 4578.793656 1 0.9961 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4578.793656 0 1.0938 235 | 0/8 11 h-lim-p 2.2498 20.0000 0.0000 4578.793656 0 0.2812 257 | 0/8 12 h-lim-p 0.1518 20.0000 0.0000 4578.793656 0 0.0024 282 Out... lnL = -4578.793656 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4578.793656 Node 7: lnL = -4578.793656 Node 8: lnL = -4578.793656 Node 9: lnL = -4578.793656 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 268 Sequential format.. Reading seq # 1: YNL152W_Sbay Reading seq # 2: YNL152W_Scer Reading seq # 3: YNL152W_Skud Reading seq # 4: YNL152W_Smik Reading seq # 5: YNL152W_Spar Sequences read.. Counting patterns.. # site patterns = 118 Counting frequencies.. 120 bytes for distance 18880 bytes for lkl0 15104 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.092962 0.122147 0.052336 0.111773 0.080960 0.216883 0.149920 0.108158 lnL0 = -1176.321879 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1176.321879 x= 0.09296 0.12215 0.05234 0.11177 0.08096 0.21688 0.14992 0.10816 1 h-lim-p 0.0026 0.0209 22.8116 1176.177253 5 0.0006 33 | 0/8 2 h-lim-p 0.0017 0.0137 7.7538 1176.158259 3 0.0007 51 | 0/8 3 h-lim-p 0.0016 0.1346 3.4211 1176.153696 5 0.0009 76 | 0/8 4 h-lim-p 0.0164 1.1312 0.1961 1176.153683 2 0.0007 96 | 0/8 5 h-lim-p 0.0020 2.3726 0.0626 1176.153682 0 0.0009 116 | 0/8 6 h-lim-p 0.0038 12.7953 0.0147 1176.153682 0 0.0008 137 | 0/8 7 h-lim-p 0.0055 20.0000 0.0022 1176.153682 0 0.0014 158 | 0/8 8 h-lim-p 0.1415 20.0000 0.0000 1176.153682 0 1.1319 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1176.153682 0 1.0938 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1176.153682 0 2.1875 221 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1176.153682 0 0.2734 243 | 0/8 12 h-lim-p 0.1252 20.0000 0.0000 1176.153682 0 0.0001 273 Out... lnL = -1176.153682 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1176.153682 Node 7: lnL = -1176.153682 Node 8: lnL = -1176.153682 Node 9: lnL = -1176.153682 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 267 Sequential format.. Reading seq # 1: YNL153C_Sbay Reading seq # 2: YNL153C_Scer Reading seq # 3: YNL153C_Skud Reading seq # 4: YNL153C_Smik Reading seq # 5: YNL153C_Spar Sequences read.. Counting patterns.. # site patterns = 119 Counting frequencies.. 120 bytes for distance 19040 bytes for lkl0 15232 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.078034 0.133242 0.052430 0.114377 0.078355 0.229748 0.179335 0.093671 lnL0 = -1186.554990 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1186.554990 x= 0.07803 0.13324 0.05243 0.11438 0.07836 0.22975 0.17933 0.09367 1 h-lim-p 0.0015 0.0122 29.8445 1186.337177 6 0.0005 35 | 0/8 2 h-lim-p 0.0021 0.0172 7.0901 1186.321917 7 0.0006 67 | 0/8 3 h-lim-p 0.0017 0.0772 2.6485 1186.318816 6 0.0010 94 | 0/8 4 h-lim-p 0.0028 0.1587 0.9613 1186.318556 0 0.0006 107 | 0/8 5 h-lim-p 0.0029 0.9366 0.2014 1186.318533 1 0.0013 129 | 0/8 6 h-lim-p 0.0048 4.2961 0.0528 1186.318532 1 0.0006 153 | 0/8 7 h-lim-p 0.0047 20.0000 0.0066 1186.318532 0 0.0021 173 | 0/8 8 h-lim-p 0.1222 20.0000 0.0001 1186.318525 0 0.9775 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1186.318524 0 1.0938 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1186.318524 0 1.0938 236 | 0/8 11 h-lim-p 1.9086 20.0000 0.0000 1186.318524 0 0.0019 265 Out... lnL = -1186.318524 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1186.318524 Node 7: lnL = -1186.318524 Node 8: lnL = -1186.318524 Node 9: lnL = -1186.318524 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 601 Sequential format.. Reading seq # 1: YNL155W_Sbay Reading seq # 2: YNL155W_Scer Reading seq # 3: YNL155W_Skud Reading seq # 4: YNL155W_Smik Reading seq # 5: YNL155W_Spar Sequences read.. Counting patterns.. # site patterns = 168 Counting frequencies.. 120 bytes for distance 26880 bytes for lkl0 21504 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.086069 0.024748 0.040577 0.083236 0.069731 0.132726 0.150935 0.096732 lnL0 = -2294.053721 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2294.053721 x= 0.08607 0.02475 0.04058 0.08324 0.06973 0.13273 0.15094 0.09673 1 h-lim-p 0.0004 0.0030 251.0979 2291.049049 8 0.0001 42 | 0/8 2 h-lim-p 0.0004 0.0035 28.3741 2290.969601 2 0.0002 58 | 0/8 3 h-lim-p 0.0008 0.0644 7.4247 2290.963563 6 0.0002 87 | 0/8 4 h-lim-p 0.0007 0.0616 2.4929 2290.962814 4 0.0003 107 | 0/8 5 h-lim-p 0.0040 0.3468 0.1688 2290.962812 1 0.0002 124 | 0/8 6 h-lim-p 0.0020 14.0571 0.0168 2290.962811 0 0.0004 145 | 0/8 7 h-lim-p 0.0034 20.0000 0.0022 2290.962811 0 0.0134 167 | 0/8 8 h-lim-p 0.0057 20.0000 0.0051 2290.962764 0 0.0227 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2290.962762 0 1.0938 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2290.962762 0 1.0938 229 | 0/8 11 h-lim-p 1.9966 20.0000 0.0000 2290.962762 0 1.7470 249 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2290.962762 0 1.0938 269 | 0/8 13 h-lim-p 0.3584 20.0000 0.0000 2290.962762 0 5.7340 293 | 0/8 14 h-lim-p 1.8856 20.0000 0.0000 2290.962762 0 0.2062 315 | 0/8 15 h-lim-p 0.5665 20.0000 0.0000 2290.962762 0 0.0006 344 Out... lnL = -2290.962762 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2290.962762 Node 7: lnL = -2290.962762 Node 8: lnL = -2290.962762 Node 9: lnL = -2290.962762 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 572 Sequential format.. Reading seq # 1: YNL156C_Sbay Reading seq # 2: YNL156C_Scer Reading seq # 3: YNL156C_Skud Reading seq # 4: YNL156C_Smik Reading seq # 5: YNL156C_Spar Sequences read.. Counting patterns.. # site patterns = 165 Counting frequencies.. 120 bytes for distance 26400 bytes for lkl0 21120 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.080997 0.017127 0.037200 0.083851 0.069116 0.144401 0.161150 0.091589 lnL0 = -2249.758969 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2249.758969 x= 0.08100 0.01713 0.03720 0.08385 0.06912 0.14440 0.16115 0.09159 1 h-lim-p 0.0005 0.0037 295.2217 2246.483569 5 0.0001 32 | 0/8 2 h-lim-p 0.0003 0.0023 32.6150 2246.379055 7 0.0002 62 | 0/8 3 h-lim-p 0.0006 0.0510 10.9196 2246.365518 5 0.0003 83 | 0/8 4 h-lim-p 0.0007 0.0355 3.9060 2246.363799 4 0.0003 105 | 0/8 5 h-lim-p 0.0032 0.5348 0.3185 2246.363785 2 0.0003 124 | 0/8 6 h-lim-p 0.0004 0.6572 0.1890 2246.363781 1 0.0002 147 | 0/8 7 h-lim-p 0.0010 3.6486 0.0385 2246.363781 0 0.0005 167 | 0/8 8 h-lim-p 0.1568 20.0000 0.0001 2246.363718 0 1.2541 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2246.363714 0 1.0938 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2246.363714 0 1.0938 230 | 0/8 11 h-lim-p 1.1979 20.0000 0.0000 2246.363714 0 0.0094 256 | 0/8 12 h-lim-p 0.0039 20.0000 0.0000 2246.363714 0 0.0002 279 Out... lnL = -2246.363714 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2246.363714 Node 7: lnL = -2246.363714 Node 8: lnL = -2246.363714 Node 9: lnL = -2246.363714 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 301 Sequential format.. Reading seq # 1: YNL158W_Sbay Reading seq # 2: YNL158W_Scer Reading seq # 3: YNL158W_Skud Reading seq # 4: YNL158W_Smik Reading seq # 5: YNL158W_Spar Sequences read.. Counting patterns.. # site patterns = 161 Counting frequencies.. 120 bytes for distance 25760 bytes for lkl0 20608 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.174216 0.139698 0.094482 0.156790 0.121978 0.202894 0.231434 0.195532 lnL0 = -1440.821331 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1440.821331 x= 0.17422 0.13970 0.09448 0.15679 0.12198 0.20289 0.23143 0.19553 1 h-lim-p 0.0044 0.0349 27.3543 1440.505554 6 0.0009 37 | 0/8 2 h-lim-p 0.0030 0.0294 8.1550 1440.464682 6 0.0013 60 | 0/8 3 h-lim-p 0.0021 0.0648 5.0257 1440.454812 4 0.0010 82 | 0/8 4 h-lim-p 0.0050 0.2237 1.0539 1440.454200 2 0.0012 99 | 0/8 5 h-lim-p 0.0067 1.7123 0.1852 1440.454174 2 0.0016 116 | 0/8 6 h-lim-p 0.0130 14.7649 0.0221 1440.454174 0 0.0014 138 | 0/8 7 h-lim-p 0.0590 20.0000 0.0005 1440.454174 0 0.0258 158 | 0/8 8 h-lim-p 0.0149 20.0000 0.0009 1440.454172 0 0.0596 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1440.454172 0 1.0938 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1440.454172 0 1.0938 220 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1440.454172 0 0.0391 245 | 0/8 12 h-lim-p 0.0201 20.0000 0.0000 1440.454172 0 0.0000 275 Out... lnL = -1440.454172 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1440.454172 Node 7: lnL = -1440.454172 Node 8: lnL = -1440.454172 Node 9: lnL = -1440.454172 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 301 Sequential format.. Reading seq # 1: YNL159C_Sbay Reading seq # 2: YNL159C_Scer Reading seq # 3: YNL159C_Skud Reading seq # 4: YNL159C_Smik Reading seq # 5: YNL159C_Spar Sequences read.. Counting patterns.. # site patterns = 157 Counting frequencies.. 120 bytes for distance 25120 bytes for lkl0 20096 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.158533 0.151040 0.130490 0.140847 0.126932 0.192337 0.205699 0.179734 lnL0 = -1443.138590 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1443.138590 x= 0.15853 0.15104 0.13049 0.14085 0.12693 0.19234 0.20570 0.17973 1 h-lim-p 0.0011 0.0085 27.2892 1442.746717 5 0.0011 32 | 0/8 2 h-lim-p 0.0072 0.0724 4.0742 1442.732980 2 0.0017 49 | 0/8 3 h-lim-p 0.0051 0.6400 1.3482 1442.732214 4 0.0009 72 | 0/8 4 h-lim-p 0.0027 0.6090 0.4657 1442.732123 3 0.0010 92 | 0/8 5 h-lim-p 0.0052 3.6387 0.0847 1442.732119 0 0.0013 113 | 0/8 6 h-lim-p 0.0084 20.0000 0.0133 1442.732119 0 0.0018 134 | 0/8 7 h-lim-p 0.0148 20.0000 0.0016 1442.732119 0 0.0032 155 | 0/8 8 h-lim-p 0.0830 20.0000 0.0001 1442.732118 0 0.6640 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1442.732118 0 1.0938 198 | 0/8 10 h-lim-p 2.4654 20.0000 0.0000 1442.732118 0 2.1572 218 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1442.732118 0 0.0781 242 | 0/8 12 h-lim-p 0.0101 20.0000 0.0000 1442.732118 0 0.0050 262 | 0/8 13 h-lim-p 0.0016 20.0000 0.0000 1442.732118 0 0.0014 282 Out... lnL = -1442.732118 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1442.732118 Node 7: lnL = -1442.732118 Node 8: lnL = -1442.732118 Node 9: lnL = -1442.732118 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 505 Sequential format.. Reading seq # 1: YNL161W_Sbay Reading seq # 2: YNL161W_Scer Reading seq # 3: YNL161W_Skud Reading seq # 4: YNL161W_Smik Reading seq # 5: YNL161W_Spar Sequences read.. Counting patterns.. # site patterns = 159 Counting frequencies.. 120 bytes for distance 25440 bytes for lkl0 20352 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.108486 0.081372 0.074462 0.072061 0.067463 0.196570 0.124203 0.122231 lnL0 = -2005.758951 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2005.758951 x= 0.10849 0.08137 0.07446 0.07206 0.06746 0.19657 0.12420 0.12223 1 h-lim-p 0.0002 0.0019 82.7627 2004.712338 0 0.0004 22 | 0/8 2 h-lim-p 0.0013 0.0104 15.1159 2004.658922 6 0.0005 49 | 0/8 3 h-lim-p 0.0010 0.0617 6.9709 2004.654696 3 0.0002 68 | 0/8 4 h-lim-p 0.0010 0.2442 1.4460 2004.654112 4 0.0006 90 | 0/8 5 h-lim-p 0.0018 0.4086 0.4760 2004.654061 2 0.0005 107 | 0/8 6 h-lim-p 0.0015 1.8178 0.1470 2004.654043 3 0.0009 135 | 0/8 7 h-lim-p 0.0032 2.9189 0.0412 2004.653860 0 0.0130 157 | 0/8 8 h-lim-p 0.0040 1.1329 0.1346 2004.644418 0 0.0159 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 2004.644009 3 0.9961 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2004.644009 0 1.0938 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2004.644009 0 2.1875 245 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2004.644009 0 1.0938 265 | 0/8 13 h-lim-p 0.5228 20.0000 0.0000 2004.644009 0 4.1825 288 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 2004.644009 0 0.2734 310 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2004.644009 0 0.0781 334 | 0/8 16 h-lim-p 0.0061 20.0000 0.0000 2004.644009 0 0.0091 354 | 0/8 17 h-lim-p 0.0040 20.0000 0.0000 2004.644009 0 0.0000 385 Out... lnL = -2004.644009 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2004.644009 Node 7: lnL = -2004.644009 Node 8: lnL = -2004.644009 Node 9: lnL = -2004.644009 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 278 Sequential format.. Reading seq # 1: YNL162W-A_Sbay Reading seq # 2: YNL162W-A_Scer Reading seq # 3: YNL162W-A_Skud Reading seq # 4: YNL162W-A_Smik Reading seq # 5: YNL162W-A_Spar Sequences read.. Counting patterns.. # site patterns = 122 Counting frequencies.. 120 bytes for distance 19520 bytes for lkl0 15616 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.122806 0.055371 0.063607 0.096860 0.114665 0.159051 0.245512 0.138499 lnL0 = -1202.218681 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1202.218681 x= 0.12281 0.05537 0.06361 0.09686 0.11466 0.15905 0.24551 0.13850 1 h-lim-p 0.0053 0.0421 48.0603 1201.703316 7 0.0005 40 | 0/8 2 h-lim-p 0.0020 0.0197 11.2850 1201.644049 2 0.0010 56 | 0/8 3 h-lim-p 0.0025 0.0838 4.4001 1201.637932 6 0.0007 83 | 0/8 4 h-lim-p 0.0016 0.1416 1.9456 1201.636127 5 0.0012 107 | 0/8 5 h-lim-p 0.0067 0.5837 0.3351 1201.636084 2 0.0008 125 | 0/8 6 h-lim-p 0.0050 3.6390 0.0531 1201.636083 1 0.0010 148 | 0/8 7 h-lim-p 0.0060 20.0000 0.0087 1201.636083 0 0.0013 169 | 0/8 8 h-lim-p 0.1487 20.0000 0.0001 1201.636081 0 1.1893 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1201.636080 0 1.0938 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1201.636080 0 1.0938 232 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1201.636080 0 0.0049 260 | 0/8 12 h-lim-p 0.0025 20.0000 0.0000 1201.636080 0 0.0000 287 Out... lnL = -1201.636080 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1201.636080 Node 7: lnL = -1201.636080 Node 8: lnL = -1201.636080 Node 9: lnL = -1201.636080 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 469 Sequential format.. Reading seq # 1: YNL164C_Sbay Reading seq # 2: YNL164C_Scer Reading seq # 3: YNL164C_Skud Reading seq # 4: YNL164C_Smik Reading seq # 5: YNL164C_Spar Sequences read.. Counting patterns.. # site patterns = 179 Counting frequencies.. 120 bytes for distance 28640 bytes for lkl0 22912 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.163081 0.094794 0.056205 0.138615 0.104616 0.169427 0.116897 0.179410 lnL0 = -2005.036278 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2005.036278 x= 0.16308 0.09479 0.05621 0.13861 0.10462 0.16943 0.11690 0.17941 1 h-lim-p 0.0011 0.0085 54.3576 2004.394640 7 0.0005 39 | 0/8 2 h-lim-p 0.0007 0.0055 15.9731 2004.344535 7 0.0004 71 | 0/8 3 h-lim-p 0.0011 0.0231 6.2483 2004.336951 3 0.0004 89 | 0/8 4 h-lim-p 0.0021 0.1583 1.3222 2004.336467 4 0.0006 111 | 0/8 5 h-lim-p 0.0032 0.5795 0.2490 2004.336452 2 0.0005 130 | 0/8 6 h-lim-p 0.0019 3.4513 0.0688 2004.336450 1 0.0005 153 | 0/8 7 h-lim-p 0.0249 20.0000 0.0013 2004.336449 0 0.0373 173 | 0/8 8 h-lim-p 0.0059 20.0000 0.0081 2004.336409 0 0.0237 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2004.336409 0 1.0938 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2004.336409 0 1.0938 235 | 0/8 11 h-lim-p 2.4739 20.0000 0.0000 2004.336409 0 2.1646 255 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2004.336409 0 0.0098 282 Out... lnL = -2004.336409 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2004.336409 Node 7: lnL = -2004.336409 Node 8: lnL = -2004.336409 Node 9: lnL = -2004.336409 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 281 Sequential format.. Reading seq # 1: YNL165W_Sbay Reading seq # 2: YNL165W_Scer Reading seq # 3: YNL165W_Skud Reading seq # 4: YNL165W_Smik Reading seq # 5: YNL165W_Spar Sequences read.. Counting patterns.. # site patterns = 104 Counting frequencies.. 120 bytes for distance 16640 bytes for lkl0 13312 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.110446 0.100047 0.048093 0.111449 0.071398 0.142823 0.134585 0.124075 lnL0 = -1195.083554 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1195.083554 x= 0.11045 0.10005 0.04809 0.11145 0.07140 0.14282 0.13458 0.12408 1 h-lim-p 0.0003 0.0024 77.9125 1193.982198 0 0.0005 22 | 0/8 2 h-lim-p 0.0007 0.0053 18.7697 1193.892435 6 0.0005 45 | 0/8 3 h-lim-p 0.0011 0.0310 8.7425 1193.878314 4 0.0004 65 | 0/8 4 h-lim-p 0.0021 0.1322 1.8802 1193.876882 3 0.0009 83 | 0/8 5 h-lim-p 0.0113 2.0052 0.1441 1193.876828 3 0.0021 102 | 0/8 6 h-lim-p 0.0265 8.2858 0.0116 1193.864925 0 0.4232 126 | 0/8 7 h-lim-p 0.0017 0.0667 2.9039 1193.857952 6 0.0010 163 | 0/8 8 h-lim-p 0.2030 16.7378 0.0139 1193.857939 2 0.0098 182 | 0/8 9 h-lim-p 0.0094 20.0000 0.0145 1193.856864 0 0.0751 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1193.856864 0 1.0938 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1193.856864 0 1.0938 245 | 0/8 12 h-lim-p 2.3516 20.0000 0.0000 1193.856864 0 1.0288 265 | 0/8 13 h-lim-p 0.9411 20.0000 0.0000 1193.856864 0 0.1176 287 | 0/8 14 h-lim-p 0.0001 20.0000 0.0011 1193.856864 0 0.0000 321 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 1193.856864 0 0.0000 356 Out... lnL = -1193.856864 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1193.856864 Node 7: lnL = -1193.856864 Node 8: lnL = -1193.856864 Node 9: lnL = -1193.856864 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 281 Sequential format.. Reading seq # 1: YNL166C_Sbay Reading seq # 2: YNL166C_Scer Reading seq # 3: YNL166C_Skud Reading seq # 4: YNL166C_Smik Reading seq # 5: YNL166C_Spar Sequences read.. Counting patterns.. # site patterns = 104 Counting frequencies.. 120 bytes for distance 16640 bytes for lkl0 13312 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.108075 0.091375 0.053249 0.111377 0.071469 0.137668 0.139480 0.121550 lnL0 = -1192.863608 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1192.863608 x= 0.10808 0.09138 0.05325 0.11138 0.07147 0.13767 0.13948 0.12155 1 h-lim-p 0.0003 0.0024 73.0437 1191.852277 0 0.0006 23 | 0/8 2 h-lim-p 0.0014 0.0110 16.6419 1191.760264 5 0.0007 46 | 0/8 3 h-lim-p 0.0017 0.0505 6.6849 1191.752746 3 0.0004 65 | 0/8 4 h-lim-p 0.0011 0.0892 2.3056 1191.750884 5 0.0008 90 | 0/8 5 h-lim-p 0.0109 1.3783 0.1628 1191.750261 5 0.0062 115 | 0/8 6 h-lim-p 0.0073 1.5447 0.1381 1191.722197 0 0.0583 138 | 0/8 7 h-lim-p 0.0019 0.0266 4.2694 1191.649834 1 0.0024 160 | 0/8 8 h-lim-p 0.0163 0.2721 0.6159 1191.649681 3 0.0008 181 | 0/8 9 h-lim-p 0.2001 20.0000 0.0024 1191.645322 0 0.8002 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0003 1191.645244 3 1.0004 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1191.645244 0 1.0938 249 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1191.645244 0 1.0938 269 | 0/8 13 h-lim-p 1.4835 20.0000 0.0000 1191.645244 0 0.0464 293 | 0/8 14 h-lim-p 0.0204 20.0000 0.0000 1191.645244 0 0.0003 318 Out... lnL = -1191.645244 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1191.645244 Node 7: lnL = -1191.645244 Node 8: lnL = -1191.645244 Node 9: lnL = -1191.645244 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 841 Sequential format.. Reading seq # 1: YNL167C_Sbay Reading seq # 2: YNL167C_Scer Reading seq # 3: YNL167C_Skud Reading seq # 4: YNL167C_Smik Reading seq # 5: YNL167C_Spar Sequences read.. Counting patterns.. # site patterns = 252 Counting frequencies.. 120 bytes for distance 40320 bytes for lkl0 32256 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.138752 0.056514 0.072147 0.099922 0.076858 0.170708 0.183525 0.153863 lnL0 = -3690.358788 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3690.358788 x= 0.13875 0.05651 0.07215 0.09992 0.07686 0.17071 0.18353 0.15386 1 h-lim-p 0.0053 0.0654 118.3053 3689.335523 2 0.0002 30 | 0/8 2 h-lim-p 0.0008 0.0065 15.2421 3689.314252 2 0.0002 47 | 0/8 3 h-lim-p 0.0004 0.0193 6.8126 3689.308829 4 0.0003 69 | 0/8 4 h-lim-p 0.0008 0.0886 2.1957 3689.308276 4 0.0003 93 | 0/8 5 h-lim-p 0.0017 0.6478 0.3363 3689.308259 2 0.0003 110 | 0/8 6 h-lim-p 0.0030 2.5415 0.0376 3689.308258 0 0.0003 132 | 0/8 7 h-lim-p 0.0071 20.0000 0.0017 3689.308258 0 0.0143 153 | 0/8 8 h-lim-p 0.0044 20.0000 0.0055 3689.308210 0 0.0355 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3689.308204 0 1.0938 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3689.308204 0 1.0938 216 | 0/8 11 h-lim-p 2.4668 20.0000 0.0000 3689.308204 0 2.1584 236 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3689.308204 0 1.0938 256 | 0/8 13 h-lim-p 0.2090 20.0000 0.0000 3689.308204 0 0.0000 290 Out... lnL = -3689.308204 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3689.308204 Node 7: lnL = -3689.308204 Node 8: lnL = -3689.308204 Node 9: lnL = -3689.308204 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 664 Sequential format.. Reading seq # 1: YNL168C_Sbay Reading seq # 2: YNL168C_Scer Reading seq # 3: YNL168C_Skud Reading seq # 4: YNL168C_Smik Reading seq # 5: YNL168C_Spar Sequences read.. Counting patterns.. # site patterns = 260 Counting frequencies.. 120 bytes for distance 41600 bytes for lkl0 33280 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.172178 0.047164 0.093035 0.124247 0.144029 0.224179 0.251183 0.191767 lnL0 = -3158.006091 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3158.006091 x= 0.17218 0.04716 0.09303 0.12425 0.14403 0.22418 0.25118 0.19177 1 h-lim-p 0.0015 0.0117 166.5575 3154.430062 4 0.0003 31 | 0/8 2 h-lim-p 0.0009 0.0070 31.6104 3154.106603 5 0.0007 53 | 0/8 3 h-lim-p 0.0010 0.0169 19.7748 3154.037096 3 0.0005 71 | 0/8 4 h-lim-p 0.0016 0.0322 5.9410 3154.029411 5 0.0005 97 | 0/8 5 h-lim-p 0.0043 0.3620 0.6840 3154.029262 3 0.0006 119 | 0/8 6 h-lim-p 0.0033 1.5762 0.1309 3154.029253 0 0.0008 140 | 0/8 7 h-lim-p 0.0083 20.0000 0.0130 3154.029160 0 0.0332 162 | 0/8 8 h-lim-p 0.0076 19.3682 0.0571 3154.025927 0 0.0302 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3154.025917 1 0.9961 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3154.025917 0 1.0938 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3154.025917 0 2.1875 246 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3154.025917 0 1.0938 266 | 0/8 13 h-lim-p 0.5823 20.0000 0.0000 3154.025917 0 3.4941 288 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 3154.025917 0 0.1562 311 | 0/8 15 h-lim-p 0.1937 20.0000 0.0000 3154.025917 0 0.0011 338 Out... lnL = -3154.025917 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3154.025917 Node 7: lnL = -3154.025917 Node 8: lnL = -3154.025917 Node 9: lnL = -3154.025917 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 381 Sequential format.. Reading seq # 1: YNL169C_Sbay Reading seq # 2: YNL169C_Scer Reading seq # 3: YNL169C_Skud Reading seq # 4: YNL169C_Smik Reading seq # 5: YNL169C_Spar Sequences read.. Counting patterns.. # site patterns = 131 Counting frequencies.. 120 bytes for distance 20960 bytes for lkl0 16768 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.091101 0.015713 0.065368 0.131003 0.058701 0.159167 0.181325 0.103684 lnL0 = -1577.290778 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1577.290778 x= 0.09110 0.01571 0.06537 0.13100 0.05870 0.15917 0.18132 0.10368 1 h-lim-p 0.0019 0.0266 129.3585 1576.042306 9 0.0002 48 | 0/8 2 h-lim-p 0.0013 0.0102 13.9266 1576.005493 6 0.0004 77 | 0/8 3 h-lim-p 0.0019 0.1109 2.8470 1576.004332 5 0.0003 102 | 0/8 4 h-lim-p 0.0008 0.2377 1.0769 1576.004061 4 0.0005 124 | 0/8 5 h-lim-p 0.0029 0.6504 0.1979 1576.004050 2 0.0006 141 | 0/8 6 h-lim-p 0.0030 9.6428 0.0379 1576.004050 0 0.0006 162 | 0/8 7 h-lim-p 0.0053 20.0000 0.0047 1576.004050 0 0.0023 182 | 0/8 8 h-lim-p 0.0257 20.0000 0.0004 1576.004008 0 0.4116 206 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1576.004006 0 1.0938 226 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1576.004006 0 1.2500 246 | 0/8 11 h-lim-p 2.2765 20.0000 0.0000 1576.004006 0 0.2490 268 | 0/8 12 h-lim-p 0.1351 20.0000 0.0000 1576.004006 0 0.0021 293 | 0/8 13 h-lim-p 0.0018 20.0000 0.0000 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0020 | 0/8 15 h-lim-p 0.0000 20.0000 0.0020 Out... lnL = -1576.004006 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1576.004006 Node 7: lnL = -1576.004006 Node 8: lnL = -1576.004006 Node 9: lnL = -1576.004006 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 495 Sequential format.. Reading seq # 1: YNL177C_Sbay Reading seq # 2: YNL177C_Scer Reading seq # 3: YNL177C_Skud Reading seq # 4: YNL177C_Smik Reading seq # 5: YNL177C_Spar Sequences read.. Counting patterns.. # site patterns = 219 Counting frequencies.. 120 bytes for distance 35040 bytes for lkl0 28032 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.203492 0.088752 0.081735 0.109107 0.105345 0.272045 0.232303 0.224336 lnL0 = -2352.737373 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2352.737373 x= 0.20349 0.08875 0.08174 0.10911 0.10535 0.27204 0.23230 0.22434 1 h-lim-p 0.0006 0.0050 64.7356 2351.887098 8 0.0004 44 | 0/8 2 h-lim-p 0.0020 0.0158 11.1575 2351.845861 7 0.0007 75 | 0/8 3 h-lim-p 0.0008 0.0405 9.0684 2351.830715 4 0.0005 97 | 0/8 4 h-lim-p 0.0014 0.0480 3.6744 2351.827802 3 0.0006 115 | 0/8 5 h-lim-p 0.0035 0.7716 0.5852 2351.827593 3 0.0012 134 | 0/8 6 h-lim-p 0.0227 7.3131 0.0322 2351.827592 0 0.0012 157 | 0/8 7 h-lim-p 0.0063 20.0000 0.0064 2351.827592 0 0.0014 178 | 0/8 8 h-lim-p 0.1287 20.0000 0.0001 2351.827590 0 1.0296 201 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2351.827590 0 1.0938 221 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2351.827590 0 1.0938 241 | 0/8 11 h-lim-p 1.8126 20.0000 0.0000 2351.827590 0 0.1133 264 | 0/8 12 h-lim-p 0.0549 20.0000 0.0000 2351.827590 0 0.0549 284 | 0/8 13 h-lim-p 0.0339 20.0000 0.0000 2351.827590 0 0.0064 306 | 0/8 14 h-lim-p 0.0053 20.0000 0.0000 2351.827590 0 0.0000 341 Out... lnL = -2351.827590 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2351.827590 Node 7: lnL = -2351.827590 Node 8: lnL = -2351.827590 Node 9: lnL = -2351.827590 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 926 Sequential format.. Reading seq # 1: YNL178W_Sbay Reading seq # 2: YNL178W_Scer Reading seq # 3: YNL178W_Skud Reading seq # 4: YNL178W_Smik Reading seq # 5: YNL178W_Spar Sequences read.. Counting patterns.. # site patterns = 353 Counting frequencies.. 120 bytes for distance 56480 bytes for lkl0 45184 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.161472 0.064865 0.080947 0.130010 0.112629 0.253173 0.265594 0.181132 lnL0 = -4219.913070 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4219.913070 x= 0.16147 0.06487 0.08095 0.13001 0.11263 0.25317 0.26559 0.18113 1 h-lim-p 0.0058 1.3102 120.4800 4218.421230 6 0.0002 40 | 0/8 2 h-lim-p 0.0015 0.0122 16.0967 4218.385990 6 0.0003 68 | 0/8 3 h-lim-p 0.0009 0.0331 5.0304 4218.381436 3 0.0004 86 | 0/8 4 h-lim-p 0.0013 0.2246 1.5160 4218.380875 3 0.0005 104 | 0/8 5 h-lim-p 0.0021 0.7532 0.3883 4218.380845 1 0.0004 119 | 0/8 6 h-lim-p 0.0015 3.3106 0.1101 4218.380843 0 0.0006 139 | 0/8 7 h-lim-p 0.0058 20.0000 0.0122 4218.380843 0 0.0013 160 | 0/8 8 h-lim-p 0.1930 20.0000 0.0001 4218.380832 0 1.1579 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4218.380831 0 1.0938 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4218.380831 0 1.0938 222 | 0/8 11 h-lim-p 1.4859 20.0000 0.0000 4218.380831 0 2.2288 242 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4218.380831 0 0.3125 264 | 0/8 13 h-lim-p 0.0269 20.0000 0.0000 4218.380831 0 0.0269 284 | 0/8 14 h-lim-p 0.0119 20.0000 0.0000 4218.380831 0 0.0000 316 Out... lnL = -4218.380831 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4218.380831 Node 7: lnL = -4218.380831 Node 8: lnL = -4218.380831 Node 9: lnL = -4218.380831 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 748 Sequential format.. Reading seq # 1: YNL181W_Sbay Reading seq # 2: YNL181W_Scer Reading seq # 3: YNL181W_Skud Reading seq # 4: YNL181W_Smik Reading seq # 5: YNL181W_Spar Sequences read.. Counting patterns.. # site patterns = 286 Counting frequencies.. 120 bytes for distance 45760 bytes for lkl0 36608 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.161281 0.136024 0.105651 0.163929 0.141785 0.217519 0.229160 0.173121 lnL0 = -3353.129722 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3353.129722 x= 0.16128 0.13602 0.10565 0.16393 0.14179 0.21752 0.22916 0.17312 1 h-lim-p 0.0044 0.0352 60.6556 3352.313403 6 0.0005 38 | 0/8 2 h-lim-p 0.0011 0.0132 25.1938 3352.104315 7 0.0007 67 | 0/8 3 h-lim-p 0.0011 0.0172 17.5705 3352.048555 5 0.0005 92 | 0/8 4 h-lim-p 0.0012 0.0331 7.9318 3352.026720 5 0.0009 114 | 0/8 5 h-lim-p 0.0030 0.1304 2.4203 3352.024921 2 0.0007 131 | 0/8 6 h-lim-p 0.0051 0.8449 0.3384 3352.024883 2 0.0007 149 | 0/8 7 h-lim-p 0.0048 4.8621 0.0471 3352.024880 0 0.0021 169 | 0/8 8 h-lim-p 0.0990 20.0000 0.0010 3352.024528 0 0.7917 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3352.024525 0 1.0938 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3352.024525 0 1.0938 232 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3352.024525 0 1.0938 252 | 0/8 12 h-lim-p 1.3009 20.0000 0.0000 3352.024525 0 5.2035 274 | 0/8 13 h-lim-p 2.0228 20.0000 0.0000 3352.024525 0 0.2529 296 | 0/8 14 h-lim-p 1.0859 20.0000 0.0000 3352.024525 0 0.0000 335 Out... lnL = -3352.024525 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3352.024525 Node 7: lnL = -3352.024525 Node 8: lnL = -3352.024525 Node 9: lnL = -3352.024525 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 414 Sequential format.. Reading seq # 1: YNL187W_Sbay Reading seq # 2: YNL187W_Scer Reading seq # 3: YNL187W_Skud Reading seq # 4: YNL187W_Smik Reading seq # 5: YNL187W_Spar Sequences read.. Counting patterns.. # site patterns = 184 Counting frequencies.. 120 bytes for distance 29440 bytes for lkl0 23552 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.296315 0.164689 0.000060 0.223824 0.307423 0.308215 0.460382 0.311093 lnL0 = -1664.133482 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1664.133482 x= 0.29631 0.16469 0.00006 0.22382 0.30742 0.30821 0.46038 0.31109 1 h-lim-p 0.0000 0.0000 99.5099 1664.042416 m 0.0000 22 | 1/8 2 h-lim-p 0.0001 0.0195 17.3967 1663.629692 0 0.0025 39 | 1/8 3 h-lim-p 0.0022 0.0339 19.8033 1662.891669 0 0.0044 52 | 1/8 4 h-lim-p 0.0103 0.0822 6.2459 1662.489694 6 0.0113 79 | 1/8 5 h-lim-p 0.0092 0.0737 5.9955 1661.846560 0 0.0138 91 | 1/8 6 h-lim-p 0.0117 0.0936 3.3052 1655.683594 0 0.0468 105 | 0/8 7 h-lim-p 0.0005 0.0040 61.1416 1654.666367 0 0.0010 118 | 0/8 8 h-lim-p 0.0018 0.0154 33.0113 1652.431361 0 0.0037 131 | 0/8 9 h-lim-p 0.5487 4.3892 0.0947 1651.928430 6 0.5363 157 | 0/8 10 h-lim-p 0.7083 5.6667 0.0245 1651.845906 1 0.8854 179 | 0/8 11 h-lim-p 2.5000 20.0000 0.0068 1651.837742 5 0.8779 211 | 0/8 12 h-lim-p 2.5000 20.0000 0.0014 1651.837300 2 1.1719 235 | 0/8 13 h-lim-p 2.1564 20.0000 0.0007 1651.837282 1 0.4717 258 | 0/8 14 h-lim-p 2.1119 20.0000 0.0002 1651.837278 0 0.9240 278 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1651.837278 0 1.0938 298 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1651.837278 0 0.5469 319 | 0/8 17 h-lim-p 0.9519 20.0000 0.0000 1651.837278 0 0.0521 342 | 0/8 18 h-lim-p 0.0427 20.0000 0.0000 1651.837278 0 0.0214 362 | 0/8 19 h-lim-p 0.0149 20.0000 0.0000 1651.837278 0 0.0000 392 Out... lnL = -1651.837278 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1651.837278 Node 7: lnL = -1651.837278 Node 8: lnL = -1651.837278 Node 9: lnL = -1651.837278 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 469 Sequential format.. Reading seq # 1: YNL188W_Sbay Reading seq # 2: YNL188W_Scer Reading seq # 3: YNL188W_Skud Reading seq # 4: YNL188W_Smik Reading seq # 5: YNL188W_Spar Sequences read.. Counting patterns.. # site patterns = 157 Counting frequencies.. 120 bytes for distance 25120 bytes for lkl0 20096 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.091295 0.032206 0.097832 0.086800 0.071682 0.145038 0.185107 0.098430 lnL0 = -1882.025366 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1882.025366 x= 0.09129 0.03221 0.09783 0.08680 0.07168 0.14504 0.18511 0.09843 1 h-lim-p 0.0026 0.0385 119.7545 1880.619717 8 0.0002 43 | 0/8 2 h-lim-p 0.0011 0.0086 20.5247 1880.523761 5 0.0005 65 | 0/8 3 h-lim-p 0.0015 0.0346 6.2692 1880.515675 5 0.0004 89 | 0/8 4 h-lim-p 0.0010 0.0690 2.6800 1880.514762 5 0.0003 115 | 0/8 5 h-lim-p 0.0018 0.3923 0.4620 1880.514717 2 0.0004 132 | 0/8 6 h-lim-p 0.0182 20.0000 0.0110 1880.514717 0 0.0010 155 | 0/8 7 h-lim-p 0.0027 20.0000 0.0040 1880.514717 0 0.0055 176 | 0/8 8 h-lim-p 0.0085 20.0000 0.0026 1880.514662 0 0.0678 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1880.514661 0 1.0938 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1880.514661 0 1.0938 239 | 0/8 11 h-lim-p 2.0330 20.0000 0.0000 1880.514661 0 4.0660 260 | 0/8 12 h-lim-p 2.0577 20.0000 0.0000 1880.514661 0 0.2572 282 | 0/8 13 h-lim-p 1.0544 20.0000 0.0000 1880.514661 0 0.0021 310 Out... lnL = -1880.514661 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1880.514661 Node 7: lnL = -1880.514661 Node 8: lnL = -1880.514661 Node 9: lnL = -1880.514661 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 902 Sequential format.. Reading seq # 1: YNL189W_Sbay Reading seq # 2: YNL189W_Scer Reading seq # 3: YNL189W_Skud Reading seq # 4: YNL189W_Smik Reading seq # 5: YNL189W_Spar Sequences read.. Counting patterns.. # site patterns = 285 Counting frequencies.. 120 bytes for distance 45600 bytes for lkl0 36480 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.114803 0.123210 0.050637 0.099263 0.073536 0.208231 0.214164 0.123745 lnL0 = -3893.736951 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3893.736951 x= 0.11480 0.12321 0.05064 0.09926 0.07354 0.20823 0.21416 0.12375 1 h-lim-p 0.0030 0.7078 162.0512 3891.865039 3 0.0002 31 | 0/8 2 h-lim-p 0.0006 0.0048 26.4777 3891.785084 4 0.0002 51 | 0/8 3 h-lim-p 0.0003 0.0118 17.7658 3891.756417 5 0.0002 74 | 0/8 4 h-lim-p 0.0026 0.0953 1.6517 3891.756010 2 0.0003 92 | 0/8 5 h-lim-p 0.0009 0.4078 0.5885 3891.755945 1 0.0004 106 | 0/8 6 h-lim-p 0.0064 9.6531 0.0402 3891.755945 0 0.0003 129 | 0/8 7 h-lim-p 0.0131 20.0000 0.0011 3891.755942 0 0.0525 151 | 0/8 8 h-lim-p 0.0036 6.9482 0.0156 3891.755882 0 0.0108 172 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3891.755880 0 1.0938 192 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3891.755880 0 2.1875 212 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3891.755880 0 1.0938 232 | 0/8 12 h-lim-p 1.0496 20.0000 0.0000 3891.755880 0 4.1985 254 | 0/8 13 h-lim-p 1.9356 20.0000 0.0000 3891.755880 0 0.2117 276 | 0/8 14 h-lim-p 0.6351 20.0000 0.0000 3891.755880 0 0.0050 302 | 0/8 15 h-lim-p 0.0051 20.0000 0.0000 3891.755880 0 0.0013 323 Out... lnL = -3891.755880 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3891.755880 Node 7: lnL = -3891.755880 Node 8: lnL = -3891.755880 Node 9: lnL = -3891.755880 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 832 Sequential format.. Reading seq # 1: YNL190W_Sbay Reading seq # 2: YNL190W_Scer Reading seq # 3: YNL190W_Skud Reading seq # 4: YNL190W_Smik Reading seq # 5: YNL190W_Spar Sequences read.. Counting patterns.. # site patterns = 196 Counting frequencies.. 120 bytes for distance 31360 bytes for lkl0 25088 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.069247 0.017475 0.042625 0.042511 0.047490 0.041344 0.113671 0.073149 lnL0 = -2751.879575 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2751.879575 x= 0.06925 0.01747 0.04262 0.04251 0.04749 0.04134 0.11367 0.07315 1 h-lim-p 0.0001 0.2140 628.1940 2742.088487 4 0.0001 31 | 0/8 2 h-lim-p 0.0002 0.0012 77.3165 2741.736604 4 0.0001 51 | 0/8 3 h-lim-p 0.0005 0.0107 17.5888 2741.722697 6 0.0001 79 | 0/8 4 h-lim-p 0.0002 0.0154 8.3798 2741.719016 5 0.0001 103 | 0/8 5 h-lim-p 0.0005 0.0496 2.0862 2741.718767 2 0.0001 120 | 0/8 6 h-lim-p 0.0009 0.4161 0.2878 2741.718762 1 0.0001 136 | 0/8 7 h-lim-p 0.0065 18.5983 0.0050 2741.718751 0 0.0130 157 | 0/8 8 h-lim-p 0.0021 20.0000 0.0313 2741.717141 0 0.0166 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 2741.717051 2 0.9961 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2741.717050 0 1.0938 224 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2741.717050 0 1.2500 244 | 0/8 12 h-lim-p 1.3080 20.0000 0.0000 2741.717050 0 0.0409 268 | 0/8 13 h-lim-p 0.0199 20.0000 0.0000 2741.717050 0 0.0000 304 Out... lnL = -2741.717050 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2741.717050 Node 7: lnL = -2741.717050 Node 8: lnL = -2741.717050 Node 9: lnL = -2741.717050 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 864 Sequential format.. Reading seq # 1: YNL193W_Sbay Reading seq # 2: YNL193W_Scer Reading seq # 3: YNL193W_Skud Reading seq # 4: YNL193W_Smik Reading seq # 5: YNL193W_Spar Sequences read.. Counting patterns.. # site patterns = 325 Counting frequencies.. 120 bytes for distance 52000 bytes for lkl0 41600 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.197334 0.069889 0.067142 0.126080 0.102525 0.170727 0.253625 0.207656 lnL0 = -3925.808799 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3925.808799 x= 0.19733 0.06989 0.06714 0.12608 0.10253 0.17073 0.25363 0.20766 1 h-lim-p 0.0018 0.0146 169.0975 3922.882673 4 0.0002 32 | 0/8 2 h-lim-p 0.0006 0.0048 46.5818 3922.517272 8 0.0004 64 | 0/8 3 h-lim-p 0.0007 0.0129 23.0345 3922.429074 6 0.0004 90 | 0/8 4 h-lim-p 0.0007 0.0204 13.7773 3922.405969 4 0.0003 110 | 0/8 5 h-lim-p 0.0031 0.1289 1.5155 3922.405466 4 0.0005 133 | 0/8 6 h-lim-p 0.0020 0.7001 0.3468 3922.405441 1 0.0004 148 | 0/8 7 h-lim-p 0.0013 3.4720 0.1018 3922.405433 1 0.0011 170 | 0/8 8 h-lim-p 0.0375 20.0000 0.0029 3922.400044 0 0.6006 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3922.400012 2 0.9961 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3922.400012 0 1.0938 238 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3922.400012 0 2.1875 258 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3922.400012 0 0.5469 279 | 0/8 13 h-lim-p 0.4167 20.0000 0.0000 3922.400012 0 0.0521 301 | 0/8 14 h-lim-p 0.0225 20.0000 0.0000 3922.400012 0 0.0098 321 | 0/8 15 h-lim-p 0.0675 20.0000 0.0000 3922.400012 0 0.0001 349 Out... lnL = -3922.400012 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3922.400012 Node 7: lnL = -3922.400012 Node 8: lnL = -3922.400012 Node 9: lnL = -3922.400012 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 855 Sequential format.. Reading seq # 1: YNL194C_Sbay Reading seq # 2: YNL194C_Scer Reading seq # 3: YNL194C_Skud Reading seq # 4: YNL194C_Smik Reading seq # 5: YNL194C_Spar Sequences read.. Counting patterns.. # site patterns = 322 Counting frequencies.. 120 bytes for distance 51520 bytes for lkl0 41216 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.211371 0.103523 0.069417 0.122817 0.105788 0.175768 0.226786 0.222189 lnL0 = -3963.326839 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3963.326839 x= 0.21137 0.10352 0.06942 0.12282 0.10579 0.17577 0.22679 0.22219 1 h-lim-p 0.0019 0.0153 122.0807 3961.643116 9 0.0002 42 | 0/8 2 h-lim-p 0.0006 0.0081 47.0672 3961.156332 5 0.0005 63 | 0/8 3 h-lim-p 0.0008 0.0098 28.5292 3961.069862 5 0.0003 87 | 0/8 4 h-lim-p 0.0011 0.0361 7.5436 3961.060637 6 0.0004 113 | 0/8 5 h-lim-p 0.0018 0.2071 1.4863 3961.060201 2 0.0004 130 | 0/8 6 h-lim-p 0.0011 0.7987 0.5286 3961.060142 1 0.0005 144 | 0/8 7 h-lim-p 0.0033 3.1775 0.0724 3961.060140 0 0.0007 165 | 0/8 8 h-lim-p 0.0733 20.0000 0.0007 3961.059390 0 1.1723 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3961.059308 2 0.9961 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3961.059308 0 1.0938 233 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3961.059308 0 0.0049 261 Out... lnL = -3961.059308 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3961.059308 Node 7: lnL = -3961.059308 Node 8: lnL = -3961.059308 Node 9: lnL = -3961.059308 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 443 Sequential format.. Reading seq # 1: YNL196C_Sbay Reading seq # 2: YNL196C_Scer Reading seq # 3: YNL196C_Skud Reading seq # 4: YNL196C_Smik Reading seq # 5: YNL196C_Spar Sequences read.. Counting patterns.. # site patterns = 193 Counting frequencies.. 120 bytes for distance 30880 bytes for lkl0 24704 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.226266 0.057510 0.055539 0.135986 0.100047 0.205294 0.212548 0.236776 lnL0 = -2067.966968 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2067.966968 x= 0.22627 0.05751 0.05554 0.13599 0.10005 0.20529 0.21255 0.23678 1 h-lim-p 0.0003 0.0024 110.0915 2065.458956 0 0.0006 23 | 0/8 2 h-lim-p 0.0004 0.0035 29.3671 2065.208297 0 0.0006 35 | 0/8 3 h-lim-p 0.0012 0.0195 15.4510 2065.152981 2 0.0006 51 | 0/8 4 h-lim-p 0.0007 0.0202 12.0746 2065.124042 6 0.0006 78 | 0/8 5 h-lim-p 0.0069 0.2352 1.0917 2065.123101 3 0.0014 97 | 0/8 6 h-lim-p 0.0098 1.6274 0.1551 2065.122466 4 0.0061 121 | 0/8 7 h-lim-p 0.0082 1.2127 0.1141 2065.026011 0 0.1316 145 | 0/8 8 h-lim-p 0.0045 0.1016 3.3495 2065.015925 6 0.0015 181 | 0/8 9 h-lim-p 2.2035 20.0000 0.0024 2065.013140 5 0.9431 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2065.013138 0 1.0938 222 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2065.013138 0 1.0938 242 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2065.013138 0 1.0938 262 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2065.013138 0 5.0000 283 | 0/8 14 h-lim-p 1.6430 20.0000 0.0000 2065.013138 0 0.3594 304 | 0/8 15 h-lim-p 0.9680 20.0000 0.0000 2065.013138 0 0.0605 327 | 0/8 16 h-lim-p 0.0811 20.0000 0.0000 2065.013138 0 0.0000 367 Out... lnL = -2065.013138 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2065.013138 Node 7: lnL = -2065.013138 Node 8: lnL = -2065.013138 Node 9: lnL = -2065.013138 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 835 Sequential format.. Reading seq # 1: YNL199C_Sbay Reading seq # 2: YNL199C_Scer Reading seq # 3: YNL199C_Skud Reading seq # 4: YNL199C_Smik Reading seq # 5: YNL199C_Spar Sequences read.. Counting patterns.. # site patterns = 217 Counting frequencies.. 120 bytes for distance 34720 bytes for lkl0 27776 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.107482 0.041910 0.046916 0.071530 0.055202 0.114980 0.174958 0.113782 lnL0 = -3271.117777 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3271.117777 x= 0.10748 0.04191 0.04692 0.07153 0.05520 0.11498 0.17496 0.11378 1 h-lim-p 0.0001 0.0011 204.3543 3268.984317 3 0.0001 28 | 0/8 2 h-lim-p 0.0005 0.0038 37.1457 3268.876713 7 0.0002 57 | 0/8 3 h-lim-p 0.0005 0.0170 11.5611 3268.868656 4 0.0001 78 | 0/8 4 h-lim-p 0.0002 0.0237 6.1018 3268.866522 4 0.0001 101 | 0/8 5 h-lim-p 0.0004 0.0981 2.0696 3268.866062 4 0.0002 124 | 0/8 6 h-lim-p 0.0009 0.2276 0.5871 3268.866038 2 0.0002 141 | 0/8 7 h-lim-p 0.0016 2.7142 0.0612 3268.866037 0 0.0003 162 | 0/8 8 h-lim-p 0.0415 20.0000 0.0005 3268.865268 0 0.9959 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3268.865257 1 0.9961 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3268.865257 0 2.1875 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3268.865257 0 0.5469 249 | 0/8 12 h-lim-p 0.4986 20.0000 0.0000 3268.865257 0 0.0039 275 | 0/8 13 h-lim-p 0.0017 20.0000 0.0000 3268.865257 0 0.0000 300 Out... lnL = -3268.865257 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3268.865257 Node 7: lnL = -3268.865257 Node 8: lnL = -3268.865257 Node 9: lnL = -3268.865257 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 557 Sequential format.. Reading seq # 1: YNL200C_Sbay Reading seq # 2: YNL200C_Scer Reading seq # 3: YNL200C_Skud Reading seq # 4: YNL200C_Smik Reading seq # 5: YNL200C_Spar Sequences read.. Counting patterns.. # site patterns = 217 Counting frequencies.. 120 bytes for distance 34720 bytes for lkl0 27776 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.137460 0.087499 0.019551 0.134891 0.100695 0.215294 0.224277 0.146608 lnL0 = -2415.288992 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2415.288992 x= 0.13746 0.08750 0.01955 0.13489 0.10070 0.21529 0.22428 0.14661 1 h-lim-p 0.0003 0.0028 209.7555 2412.476772 7 0.0002 37 | 0/8 2 h-lim-p 0.0003 0.0024 56.9667 2411.876552 0 0.0004 49 | 0/8 3 h-lim-p 0.0012 0.0142 20.9539 2411.799116 7 0.0004 77 | 0/8 4 h-lim-p 0.0016 0.0519 5.2080 2411.791873 4 0.0006 99 | 0/8 5 h-lim-p 0.0077 0.8086 0.3853 2411.791808 2 0.0007 117 | 0/8 6 h-lim-p 0.0018 1.1209 0.1576 2411.791763 1 0.0018 139 | 0/8 7 h-lim-p 0.0182 18.7095 0.0157 2411.787134 0 0.1459 162 | 0/8 8 h-lim-p 0.0014 0.1041 1.6301 2411.780409 1 0.0018 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 2411.780242 3 1.3437 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2411.780235 0 1.0938 223 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2411.780235 0 1.0938 243 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2411.780235 0 0.3125 265 | 0/8 13 h-lim-p 0.2011 20.0000 0.0000 2411.780235 0 0.0063 289 | 0/8 14 h-lim-p 0.0033 20.0000 0.0000 2411.780235 0 0.0008 310 Out... lnL = -2411.780235 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2411.780235 Node 7: lnL = -2411.780235 Node 8: lnL = -2411.780235 Node 9: lnL = -2411.780235 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 552 Sequential format.. Reading seq # 1: YNL201C_Sbay Reading seq # 2: YNL201C_Scer Reading seq # 3: YNL201C_Skud Reading seq # 4: YNL201C_Smik Reading seq # 5: YNL201C_Spar Sequences read.. Counting patterns.. # site patterns = 160 Counting frequencies.. 120 bytes for distance 25600 bytes for lkl0 20480 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.092310 0.043224 0.035045 0.072359 0.051837 0.140769 0.073652 0.097587 lnL0 = -2010.840843 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2010.840843 x= 0.09231 0.04322 0.03504 0.07236 0.05184 0.14077 0.07365 0.09759 1 h-lim-p 0.0003 0.0023 154.8714 2009.328083 3 0.0001 29 | 0/8 2 h-lim-p 0.0003 0.0020 43.8134 2009.147664 4 0.0002 49 | 0/8 3 h-lim-p 0.0013 0.0396 6.5078 2009.143832 6 0.0002 78 | 0/8 4 h-lim-p 0.0006 0.0923 1.8718 2009.143513 4 0.0002 102 | 0/8 5 h-lim-p 0.0014 0.4916 0.2637 2009.143503 1 0.0003 117 | 0/8 6 h-lim-p 0.0008 1.0485 0.0893 2009.143502 0 0.0004 137 | 0/8 7 h-lim-p 0.0021 7.1141 0.0157 2009.143501 0 0.0009 157 | 0/8 8 h-lim-p 0.0181 20.0000 0.0008 2009.143235 0 0.4342 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2009.143230 1 0.9961 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2009.143230 0 1.0938 223 | 0/8 11 h-lim-p 2.1488 20.0000 0.0000 2009.143230 0 2.1488 243 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2009.143230 0 0.0098 270 | 0/8 13 h-lim-p 0.0018 20.0000 0.0000 2009.143230 0 0.0001 294 Out... lnL = -2009.143230 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2009.143230 Node 7: lnL = -2009.143230 Node 8: lnL = -2009.143230 Node 9: lnL = -2009.143230 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 608 Sequential format.. Reading seq # 1: YNL202W_Sbay Reading seq # 2: YNL202W_Scer Reading seq # 3: YNL202W_Skud Reading seq # 4: YNL202W_Smik Reading seq # 5: YNL202W_Spar Sequences read.. Counting patterns.. # site patterns = 180 Counting frequencies.. 120 bytes for distance 28800 bytes for lkl0 23040 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.132996 0.123946 0.093794 0.146436 0.113147 0.216040 0.216172 0.134894 lnL0 = -1958.712844 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1958.712844 x= 0.13300 0.12395 0.09379 0.14644 0.11315 0.21604 0.21617 0.13489 1 h-lim-p 0.0028 0.0227 56.7155 1957.649905 7 0.0007 37 | 0/8 2 h-lim-p 0.0011 0.0090 13.6706 1957.575612 5 0.0008 61 | 0/8 3 h-lim-p 0.0027 0.0757 4.2317 1957.567673 5 0.0010 84 | 0/8 4 h-lim-p 0.0046 0.3715 0.8898 1957.567169 5 0.0013 109 | 0/8 5 h-lim-p 0.0059 1.4088 0.2014 1957.567146 2 0.0012 134 | 0/8 6 h-lim-p 0.0044 5.7554 0.0543 1957.567145 1 0.0011 157 | 0/8 7 h-lim-p 0.0192 20.0000 0.0030 1957.567141 0 0.0384 178 | 0/8 8 h-lim-p 0.0121 20.0000 0.0096 1957.567025 0 0.0485 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1957.567025 0 1.0938 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1957.567025 0 1.0938 240 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1957.567025 0 2.1875 260 | 0/8 12 h-lim-p 2.4153 20.0000 0.0000 1957.567025 0 0.0094 287 Out... lnL = -1957.567025 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1957.567025 Node 7: lnL = -1957.567025 Node 8: lnL = -1957.567025 Node 9: lnL = -1957.567025 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 229 Sequential format.. Reading seq # 1: YNL204C_Sbay Reading seq # 2: YNL204C_Scer Reading seq # 3: YNL204C_Skud Reading seq # 4: YNL204C_Smik Reading seq # 5: YNL204C_Spar Sequences read.. Counting patterns.. # site patterns = 111 Counting frequencies.. 120 bytes for distance 17760 bytes for lkl0 14208 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.147784 0.103899 0.074767 0.176949 0.081682 0.152636 0.177860 0.149488 lnL0 = -934.575775 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 934.575775 x= 0.14778 0.10390 0.07477 0.17695 0.08168 0.15264 0.17786 0.14949 1 h-lim-p 0.0044 0.0352 50.0126 933.580884 6 0.0009 37 | 0/8 2 h-lim-p 0.0008 0.0062 15.3077 933.460057 0 0.0015 50 | 0/8 3 h-lim-p 0.0044 0.0505 5.3465 933.443333 7 0.0013 79 | 0/8 4 h-lim-p 0.0095 0.4688 0.7456 933.442873 4 0.0016 103 | 0/8 5 h-lim-p 0.0109 2.0794 0.1101 933.442758 2 0.0054 127 | 0/8 6 h-lim-p 0.0088 4.2658 0.0682 933.440419 0 0.0527 149 | 0/8 7 h-lim-p 0.0074 1.2430 0.4869 933.430852 0 0.0111 169 | 0/8 8 h-lim-p 0.0067 0.2093 0.8017 933.430191 5 0.0019 203 | 0/8 9 h-lim-p 2.0512 20.0000 0.0008 933.429988 4 1.0766 232 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 933.429985 1 1.2305 255 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 933.429985 0 1.0938 275 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 933.429985 0 2.1875 295 | 0/8 13 h-lim-p 1.8480 20.0000 0.0000 933.429985 0 0.8085 315 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 933.429985 0 0.0195 341 Out... lnL = -933.429985 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -933.429985 Node 7: lnL = -933.429985 Node 8: lnL = -933.429985 Node 9: lnL = -933.429985 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 367 Sequential format.. Reading seq # 1: YNL207W_Sbay Reading seq # 2: YNL207W_Scer Reading seq # 3: YNL207W_Skud Reading seq # 4: YNL207W_Smik Reading seq # 5: YNL207W_Spar Sequences read.. Counting patterns.. # site patterns = 192 Counting frequencies.. 120 bytes for distance 30720 bytes for lkl0 24576 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.212662 0.021692 0.123790 0.134499 0.163708 0.163057 0.293728 0.214730 lnL0 = -1740.452308 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1740.452308 x= 0.21266 0.02169 0.12379 0.13450 0.16371 0.16306 0.29373 0.21473 1 h-lim-p 0.0085 0.0681 57.8367 1739.406745 8 0.0007 45 | 0/8 2 h-lim-p 0.0014 0.0115 20.8267 1739.155392 5 0.0013 66 | 0/8 3 h-lim-p 0.0060 0.0836 4.3380 1739.142538 2 0.0014 83 | 0/8 4 h-lim-p 0.0039 0.2385 1.5763 1739.141373 4 0.0011 104 | 0/8 5 h-lim-p 0.0023 0.6678 0.7146 1739.141089 4 0.0013 127 | 0/8 6 h-lim-p 0.0030 1.3486 0.3131 1739.141046 3 0.0011 154 | 0/8 7 h-lim-p 0.1224 20.0000 0.0027 1739.140959 0 0.1836 174 | 0/8 8 h-lim-p 0.0038 5.4038 0.1312 1739.140358 0 0.0076 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1739.140352 1 0.9961 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1739.140352 0 1.0938 237 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1739.140352 0 2.1875 257 | 0/8 12 h-lim-p 1.8492 20.0000 0.0000 1739.140352 0 0.4045 278 | 0/8 13 h-lim-p 0.6721 20.0000 0.0000 1739.140352 0 0.1260 300 | 0/8 14 h-lim-p 0.1352 20.0000 0.0000 1739.140352 0 0.0005 327 Out... lnL = -1739.140352 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1739.140352 Node 7: lnL = -1739.140352 Node 8: lnL = -1739.140352 Node 9: lnL = -1739.140352 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 612 Sequential format.. Reading seq # 1: YNL208W_Sbay Reading seq # 2: YNL208W_Scer Reading seq # 3: YNL208W_Skud Reading seq # 4: YNL208W_Smik Reading seq # 5: YNL208W_Spar Sequences read.. Counting patterns.. # site patterns = 199 Counting frequencies.. 120 bytes for distance 31840 bytes for lkl0 25472 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.151297 0.020331 0.046823 0.103417 0.093892 0.162752 0.176834 0.152687 lnL0 = -2471.398661 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2471.398661 x= 0.15130 0.02033 0.04682 0.10342 0.09389 0.16275 0.17683 0.15269 1 h-lim-p 0.0007 0.4330 266.8863 2467.033691 6 0.0001 36 | 0/8 2 h-lim-p 0.0008 0.0066 25.6793 2466.873728 8 0.0005 69 | 0/8 3 h-lim-p 0.0011 0.0192 11.5481 2466.852967 6 0.0004 96 | 0/8 4 h-lim-p 0.0012 0.0388 3.3999 2466.851311 4 0.0003 117 | 0/8 5 h-lim-p 0.0039 0.9783 0.2752 2466.851291 2 0.0005 135 | 0/8 6 h-lim-p 0.0021 1.2428 0.0686 2466.851289 0 0.0005 156 | 0/8 7 h-lim-p 0.0094 20.0000 0.0033 2466.851119 0 0.1511 180 | 0/8 8 h-lim-p 0.0027 3.4301 0.1809 2466.849773 0 0.0055 201 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2466.849743 1 0.9961 223 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2466.849743 0 1.0938 243 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2466.849743 0 1.0938 263 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2466.849743 0 0.2344 286 | 0/8 13 h-lim-p 0.1463 20.0000 0.0000 2466.849743 0 0.0731 306 | 0/8 14 h-lim-p 0.0411 20.0000 0.0000 2466.849743 0 0.0000 337 Out... lnL = -2466.849743 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2466.849743 Node 7: lnL = -2466.849743 Node 8: lnL = -2466.849743 Node 9: lnL = -2466.849743 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 698 Sequential format.. Reading seq # 1: YNL210W_Sbay Reading seq # 2: YNL210W_Scer Reading seq # 3: YNL210W_Skud Reading seq # 4: YNL210W_Smik Reading seq # 5: YNL210W_Spar Sequences read.. Counting patterns.. # site patterns = 348 Counting frequencies.. 120 bytes for distance 55680 bytes for lkl0 44544 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.294589 0.015603 0.059900 0.236148 0.425821 0.315169 0.326027 0.297553 lnL0 = -3670.432200 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3670.432200 x= 0.29459 0.01560 0.05990 0.23615 0.42582 0.31517 0.32603 0.29755 1 h-lim-p 0.0051 0.9960 119.7333 3667.868064 8 0.0004 44 | 0/8 2 h-lim-p 0.0018 0.0149 26.6506 3667.353830 7 0.0015 74 | 0/8 3 h-lim-p 0.0026 0.0232 15.1195 3667.265006 7 0.0010 103 | 0/8 4 h-lim-p 0.0061 0.2096 2.4640 3667.260151 5 0.0016 126 | 0/8 5 h-lim-p 0.0242 0.7471 0.1681 3667.260109 2 0.0019 145 | 0/8 6 h-lim-p 0.0095 20.0000 0.0343 3667.259829 0 0.0285 166 | 0/8 7 h-lim-p 0.0140 20.0000 0.0697 3667.250522 0 0.0559 188 | 0/8 8 h-lim-p 0.0200 6.4197 0.1953 3667.250487 2 0.0019 214 | 0/8 9 h-lim-p 0.5138 20.0000 0.0007 3667.250084 0 1.0276 235 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3667.250083 0 1.0938 255 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3667.250083 0 1.0938 275 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3667.250083 0 0.5469 296 | 0/8 13 h-lim-p 1.1330 20.0000 0.0000 3667.250083 0 0.0354 320 Out... lnL = -3667.250083 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3667.250083 Node 7: lnL = -3667.250083 Node 8: lnL = -3667.250083 Node 9: lnL = -3667.250083 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 655 Sequential format.. Reading seq # 1: YNL211C_Sbay Reading seq # 2: YNL211C_Scer Reading seq # 3: YNL211C_Skud Reading seq # 4: YNL211C_Smik Reading seq # 5: YNL211C_Spar Sequences read.. Counting patterns.. # site patterns = 345 Counting frequencies.. 120 bytes for distance 55200 bytes for lkl0 44160 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.217937 0.177826 0.074687 0.194240 0.488823 0.346564 0.203828 0.220965 lnL0 = -3657.025651 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3657.025651 x= 0.21794 0.17783 0.07469 0.19424 0.48882 0.34656 0.20383 0.22096 1 h-lim-p 0.0118 0.0944 50.6065 3656.404004 8 0.0005 45 | 0/8 2 h-lim-p 0.0020 0.0370 12.7181 3656.308559 6 0.0012 72 | 0/8 3 h-lim-p 0.0051 0.1542 3.0645 3656.302571 4 0.0014 93 | 0/8 4 h-lim-p 0.0077 0.7308 0.5390 3656.302346 1 0.0015 108 | 0/8 5 h-lim-p 0.0057 3.1723 0.1459 3656.302334 0 0.0012 129 | 0/8 6 h-lim-p 0.0034 4.5601 0.0524 3656.302332 1 0.0008 152 | 0/8 7 h-lim-p 0.0157 20.0000 0.0028 3656.302330 0 0.0314 173 | 0/8 8 h-lim-p 0.0147 20.0000 0.0061 3656.302251 0 0.0587 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3656.302249 0 1.0938 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3656.302249 0 1.0938 235 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3656.302249 0 2.1875 255 | 0/8 12 h-lim-p 1.9287 20.0000 0.0000 3656.302249 0 0.8438 275 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 3656.302249 0 0.0391 300 Out... lnL = -3656.302249 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3656.302249 Node 7: lnL = -3656.302249 Node 8: lnL = -3656.302249 Node 9: lnL = -3656.302249 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 383 Sequential format.. Reading seq # 1: YNL213C_Sbay Reading seq # 2: YNL213C_Scer Reading seq # 3: YNL213C_Skud Reading seq # 4: YNL213C_Smik Reading seq # 5: YNL213C_Spar Sequences read.. Counting patterns.. # site patterns = 158 Counting frequencies.. 120 bytes for distance 25280 bytes for lkl0 20224 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.151192 0.099023 0.019773 0.154487 0.115515 0.231634 0.206516 0.152950 lnL0 = -1766.763142 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1766.763142 x= 0.15119 0.09902 0.01977 0.15449 0.11551 0.23163 0.20652 0.15295 1 h-lim-p 0.0003 0.0024 29.7194 1766.465187 0 0.0006 23 | 0/8 2 h-lim-p 0.0021 0.0401 8.4600 1766.448748 2 0.0005 40 | 0/8 3 h-lim-p 0.0005 0.0055 7.7181 1766.440343 3 0.0005 58 | 0/8 4 h-lim-p 0.0025 0.1351 1.3872 1766.439849 2 0.0006 75 | 0/8 5 h-lim-p 0.0034 1.6306 0.2280 1766.439820 3 0.0009 94 | 0/8 6 h-lim-p 0.0033 5.9798 0.0620 1766.439774 0 0.0050 114 | 0/8 7 h-lim-p 0.0052 5.5810 0.0596 1766.438766 0 0.0208 136 | 0/8 8 h-lim-p 0.0025 0.1164 0.4873 1766.432963 0 0.0076 157 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 1766.432721 3 1.0004 183 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1766.432721 0 1.0938 203 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1766.432721 0 0.5469 224 | 0/8 12 h-lim-p 1.1474 20.0000 0.0000 1766.432721 0 0.0067 251 Out... lnL = -1766.432721 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1766.432721 Node 7: lnL = -1766.432721 Node 8: lnL = -1766.432721 Node 9: lnL = -1766.432721 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 374 Sequential format.. Reading seq # 1: YNL215W_Sbay Reading seq # 2: YNL215W_Scer Reading seq # 3: YNL215W_Skud Reading seq # 4: YNL215W_Smik Reading seq # 5: YNL215W_Spar Sequences read.. Counting patterns.. # site patterns = 122 Counting frequencies.. 120 bytes for distance 19520 bytes for lkl0 15616 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.118999 0.028188 0.137125 0.119394 0.096668 4.754844 0.190403 0.124534 lnL0 = -1321.851476 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1321.851476 x= 0.11900 0.02819 0.13712 0.11939 0.09667 4.75484 0.19040 0.12453 1 h-lim-p 0.0033 0.0268 27.6522 1321.638375 8 0.0006 43 | 0/8 2 h-lim-p 0.0016 0.0212 9.8775 1321.594834 7 0.0010 73 | 0/8 3 h-lim-p 0.0049 0.1465 1.9673 1321.593681 4 0.0006 96 | 0/8 4 h-lim-p 0.0049 0.5526 0.2547 1321.593656 2 0.0008 115 | 0/8 5 h-lim-p 0.0091 3.5589 0.0225 1321.593656 0 0.0010 137 | 0/8 6 h-lim-p 0.3068 20.0000 0.0001 1321.593651 0 1.2273 159 | 0/8 7 h-lim-p 2.5000 20.0000 0.0000 1321.593651 0 1.0938 179 | 0/8 8 h-lim-p 1.6414 20.0000 0.0000 1321.593651 0 0.8207 199 | 0/8 9 h-lim-p 0.6118 20.0000 0.0000 1321.593651 0 0.0001 232 | 0/8 10 h-lim-p 0.0002 20.0000 0.0000 1321.593651 0 0.0001 253 Out... lnL = -1321.593651 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1321.593651 Node 7: lnL = -1321.593651 Node 8: lnL = -1321.593651 Node 9: lnL = -1321.593651 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 352 Sequential format.. Reading seq # 1: YNL217W_Sbay Reading seq # 2: YNL217W_Scer Reading seq # 3: YNL217W_Skud Reading seq # 4: YNL217W_Smik Reading seq # 5: YNL217W_Spar Sequences read.. Counting patterns.. # site patterns = 146 Counting frequencies.. 120 bytes for distance 23360 bytes for lkl0 18688 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.159781 0.043346 0.083940 0.085327 0.129924 0.165011 0.148047 0.161317 lnL0 = -1536.173494 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1536.173494 x= 0.15978 0.04335 0.08394 0.08533 0.12992 0.16501 0.14805 0.16132 1 h-lim-p 0.0008 0.0062 21.6769 1536.061363 7 0.0005 40 | 0/8 2 h-lim-p 0.0018 0.0144 5.8971 1536.053087 6 0.0005 67 | 0/8 3 h-lim-p 0.0020 0.1776 1.4957 1536.052456 5 0.0006 93 | 0/8 4 h-lim-p 0.0036 0.3465 0.2493 1536.052442 2 0.0005 111 | 0/8 5 h-lim-p 0.0014 5.5872 0.0876 1536.052441 1 0.0003 134 | 0/8 6 h-lim-p 0.0014 6.5301 0.0214 1536.052441 0 0.0012 154 | 0/8 7 h-lim-p 0.0255 20.0000 0.0010 1536.052441 0 0.0056 175 | 0/8 8 h-lim-p 0.0159 20.0000 0.0004 1536.052438 0 0.1273 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1536.052438 0 1.0938 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1536.052438 0 1.0938 238 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1536.052438 0 0.0586 263 | 0/8 12 h-lim-p 0.0374 20.0000 0.0000 1536.052438 0 0.0094 284 Out... lnL = -1536.052438 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1536.052438 Node 7: lnL = -1536.052438 Node 8: lnL = -1536.052438 Node 9: lnL = -1536.052438 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 762 Sequential format.. Reading seq # 1: YNL220W_Sbay Reading seq # 2: YNL220W_Scer Reading seq # 3: YNL220W_Skud Reading seq # 4: YNL220W_Smik Reading seq # 5: YNL220W_Spar Sequences read.. Counting patterns.. # site patterns = 218 Counting frequencies.. 120 bytes for distance 34880 bytes for lkl0 27904 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.103830 0.037495 0.058050 0.085089 0.064007 0.145922 0.171332 0.105039 lnL0 = -3074.224528 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3074.224528 x= 0.10383 0.03749 0.05805 0.08509 0.06401 0.14592 0.17133 0.10504 1 h-lim-p 0.0015 0.0119 176.3245 3072.462947 7 0.0001 39 | 0/8 2 h-lim-p 0.0006 0.0051 16.7064 3072.438895 6 0.0002 64 | 0/8 3 h-lim-p 0.0004 0.0482 6.7989 3072.434816 2 0.0002 80 | 0/8 4 h-lim-p 0.0006 0.0617 2.3459 3072.434282 3 0.0002 98 | 0/8 5 h-lim-p 0.0015 0.6618 0.3560 3072.434262 0 0.0003 111 | 0/8 6 h-lim-p 0.0020 5.2022 0.0569 3072.434262 0 0.0004 132 | 0/8 7 h-lim-p 0.0028 11.2196 0.0089 3072.434262 0 0.0003 154 | 0/8 8 h-lim-p 0.0662 20.0000 0.0000 3072.434259 0 1.0588 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3072.434258 0 1.0938 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3072.434258 0 2.5000 218 | 0/8 11 h-lim-p 2.2830 20.0000 0.0000 3072.434258 0 0.1427 241 | 0/8 12 h-lim-p 0.1577 20.0000 0.0000 3072.434258 0 0.0099 264 | 0/8 13 h-lim-p 0.0052 20.0000 0.0000 3072.434258 0 0.0000 306 Out... lnL = -3072.434258 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3072.434258 Node 7: lnL = -3072.434258 Node 8: lnL = -3072.434258 Node 9: lnL = -3072.434258 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 767 Sequential format.. Reading seq # 1: YNL221C_Sbay Reading seq # 2: YNL221C_Scer Reading seq # 3: YNL221C_Skud Reading seq # 4: YNL221C_Smik Reading seq # 5: YNL221C_Spar Sequences read.. Counting patterns.. # site patterns = 222 Counting frequencies.. 120 bytes for distance 35520 bytes for lkl0 28416 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.103115 0.034858 0.056210 0.086525 0.060854 0.149686 0.151941 0.104286 lnL0 = -3052.706160 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3052.706160 x= 0.10312 0.03486 0.05621 0.08653 0.06085 0.14969 0.15194 0.10429 1 h-lim-p 0.0012 0.5077 225.3537 3050.075968 8 0.0001 43 | 0/8 2 h-lim-p 0.0005 0.0043 28.0769 3049.990618 5 0.0002 64 | 0/8 3 h-lim-p 0.0004 0.0202 14.7100 3049.975437 3 0.0002 82 | 0/8 4 h-lim-p 0.0007 0.0326 3.9216 3049.974116 5 0.0002 107 | 0/8 5 h-lim-p 0.0037 1.1875 0.1997 3049.974111 1 0.0002 124 | 0/8 6 h-lim-p 0.0016 9.7802 0.0279 3049.974111 0 0.0004 145 | 0/8 7 h-lim-p 0.0066 20.0000 0.0015 3049.974111 0 0.0033 165 | 0/8 8 h-lim-p 0.0034 20.0000 0.0015 3049.974089 0 0.0540 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3049.974088 0 1.0938 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3049.974088 0 1.0938 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3049.974088 0 0.0000 273 Out... lnL = -3049.974088 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3049.974088 Node 7: lnL = -3049.974088 Node 8: lnL = -3049.974088 Node 9: lnL = -3049.974088 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 282 Sequential format.. Reading seq # 1: YNL222W_Sbay Reading seq # 2: YNL222W_Scer Reading seq # 3: YNL222W_Skud Reading seq # 4: YNL222W_Smik Reading seq # 5: YNL222W_Spar Sequences read.. Counting patterns.. # site patterns = 107 Counting frequencies.. 120 bytes for distance 17120 bytes for lkl0 13696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.172080 0.069669 0.048362 0.079307 0.082198 0.200858 0.160681 0.173623 lnL0 = -1160.520271 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1160.520271 x= 0.17208 0.06967 0.04836 0.07931 0.08220 0.20086 0.16068 0.17362 1 h-lim-p 0.0101 2.2784 47.8296 1160.083136 5 0.0004 37 | 0/8 2 h-lim-p 0.0033 0.0262 5.5859 1160.071316 2 0.0008 54 | 0/8 3 h-lim-p 0.0011 0.0558 3.8910 1160.067177 6 0.0007 80 | 0/8 4 h-lim-p 0.0060 0.2746 0.4873 1160.067091 1 0.0007 96 | 0/8 5 h-lim-p 0.0020 1.1241 0.1862 1160.067075 3 0.0010 123 | 0/8 6 h-lim-p 0.0233 20.0000 0.0084 1160.067075 0 0.0015 146 | 0/8 7 h-lim-p 0.0142 20.0000 0.0009 1160.067075 0 0.0125 166 | 0/8 8 h-lim-p 0.0215 20.0000 0.0005 1160.067072 0 0.1288 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1160.067072 0 1.0938 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1160.067072 0 0.5469 229 | 0/8 11 h-lim-p 1.1470 20.0000 0.0000 1160.067072 0 0.0011 258 Out... lnL = -1160.067072 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1160.067072 Node 7: lnL = -1160.067072 Node 8: lnL = -1160.067072 Node 9: lnL = -1160.067072 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 244 Sequential format.. Reading seq # 1: YNL224C_Sbay Reading seq # 2: YNL224C_Scer Reading seq # 3: YNL224C_Skud Reading seq # 4: YNL224C_Smik Reading seq # 5: YNL224C_Spar Sequences read.. Counting patterns.. # site patterns = 103 Counting frequencies.. 120 bytes for distance 16480 bytes for lkl0 13184 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.083391 0.073470 0.062538 0.104240 0.073051 0.159645 0.178074 0.084701 lnL0 = -1009.332934 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1009.332934 x= 0.08339 0.07347 0.06254 0.10424 0.07305 0.15964 0.17807 0.08470 1 h-lim-p 0.0010 0.0076 44.8695 1008.849489 6 0.0005 35 | 0/8 2 h-lim-p 0.0018 0.0142 7.3001 1008.832161 6 0.0007 60 | 0/8 3 h-lim-p 0.0014 0.0674 3.3735 1008.828908 2 0.0007 76 | 0/8 4 h-lim-p 0.0020 0.1609 1.1533 1008.828474 3 0.0007 94 | 0/8 5 h-lim-p 0.0112 1.9469 0.0763 1008.828472 0 0.0006 109 | 0/8 6 h-lim-p 0.0090 20.0000 0.0052 1008.828472 0 0.0020 130 | 0/8 7 h-lim-p 0.0165 20.0000 0.0006 1008.828472 0 0.0144 150 | 0/8 8 h-lim-p 0.0158 20.0000 0.0006 1008.828470 0 0.0948 172 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1008.828470 0 1.0938 192 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1008.828470 0 2.1875 212 | 0/8 11 h-lim-p 1.9957 20.0000 0.0000 1008.828470 0 0.2495 234 | 0/8 12 h-lim-p 0.3161 20.0000 0.0000 1008.828470 0 0.0025 260 Out... lnL = -1008.828470 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1008.828470 Node 7: lnL = -1008.828470 Node 8: lnL = -1008.828470 Node 9: lnL = -1008.828470 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 342 Sequential format.. Reading seq # 1: YNL225C_Sbay Reading seq # 2: YNL225C_Scer Reading seq # 3: YNL225C_Skud Reading seq # 4: YNL225C_Smik Reading seq # 5: YNL225C_Spar Sequences read.. Counting patterns.. # site patterns = 178 Counting frequencies.. 120 bytes for distance 28480 bytes for lkl0 22784 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.228378 0.435787 0.000060 0.490075 0.577899 0.239051 0.412661 0.231054 lnL0 = -1657.360763 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1657.360763 x= 0.22838 0.43579 0.00006 0.49008 0.57790 0.23905 0.41266 0.23105 1 h-lim-p 0.0000 0.0000 185.1432 1657.305075 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0048 124.5050 1624.182315 0 0.0037 42 | 1/8 3 h-lim-p 0.0006 0.0046 35.9872 1620.534276 m 0.0046 54 | 1/8 4 h-lim-p 0.0056 0.0598 29.3978 1618.628757 7 0.0059 79 | 1/8 5 h-lim-p 0.0135 0.1079 9.1312 1616.959169 0 0.0270 92 | 1/8 6 h-lim-p 0.0074 0.0591 8.9457 1613.843191 0 0.0296 106 | 1/8 7 h-lim-p 0.0150 0.1197 6.6503 1608.621478 0 0.0598 120 | 1/8 8 h-lim-p 0.0515 0.4120 0.9649 1607.507957 0 0.2060 134 | 1/8 9 h-lim-p 0.5822 4.6575 0.1493 1606.804611 4 0.5776 161 | 1/8 10 h-lim-p 1.2126 11.9843 0.0711 1606.751767 5 0.2986 191 | 1/8 11 h-lim-p 2.1645 17.3159 0.0058 1606.747697 5 0.6984 222 | 1/8 12 h-lim-p 1.8958 20.0000 0.0021 1606.747393 2 0.8257 245 | 1/8 13 h-lim-p 2.5000 20.0000 0.0003 1606.747388 0 0.6250 265 | 1/8 14 h-lim-p 2.5000 20.0000 0.0001 1606.747388 0 1.0938 284 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 1606.747388 0 1.0938 303 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 1606.747388 0 1.0938 322 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 1606.747388 0 2.1875 341 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 1606.747388 0 0.6250 361 | 1/8 19 h-lim-p 0.5040 20.0000 0.0000 1606.747388 0 0.5040 380 | 1/8 20 h-lim-p 0.3204 20.0000 0.0000 1606.747388 0 0.0801 400 | 1/8 21 h-lim-p 0.0484 20.0000 0.0000 1606.747388 0 0.0726 419 | 1/8 22 h-lim-p 0.0498 20.0000 0.0000 1606.747388 0 0.0000 454 Out... lnL = -1606.747388 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1606.747388 Node 7: lnL = -1606.747388 Node 8: lnL = -1606.747388 Node 9: lnL = -1606.747388 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 363 Sequential format.. Reading seq # 1: YNL227C_Sbay Reading seq # 2: YNL227C_Scer Reading seq # 3: YNL227C_Skud Reading seq # 4: YNL227C_Smik Reading seq # 5: YNL227C_Spar Sequences read.. Counting patterns.. # site patterns = 151 Counting frequencies.. 120 bytes for distance 24160 bytes for lkl0 19328 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.120291 0.057410 0.088663 0.078519 0.092988 0.209290 0.257976 0.121915 lnL0 = -1554.360691 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1554.360691 x= 0.12029 0.05741 0.08866 0.07852 0.09299 0.20929 0.25798 0.12191 1 h-lim-p 0.0053 1.9082 76.5356 1553.088757 6 0.0005 37 | 0/8 2 h-lim-p 0.0012 0.0098 15.7849 1553.008461 6 0.0007 62 | 0/8 3 h-lim-p 0.0011 0.0297 9.4256 1552.982729 6 0.0008 88 | 0/8 4 h-lim-p 0.0027 0.1150 2.6093 1552.980370 6 0.0008 115 | 0/8 5 h-lim-p 0.0064 1.0144 0.3157 1552.980308 2 0.0012 132 | 0/8 6 h-lim-p 0.0037 1.7942 0.1041 1552.980303 0 0.0009 153 | 0/8 7 h-lim-p 0.0781 20.0000 0.0012 1552.979917 0 0.6247 176 | 0/8 8 h-lim-p 0.0019 2.3762 0.4151 1552.979585 2 0.0018 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1552.979584 0 1.0938 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1552.979584 0 1.0938 240 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1552.979584 0 2.1875 260 | 0/8 12 h-lim-p 1.9009 20.0000 0.0000 1552.979584 0 0.8316 280 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1552.979584 0 0.1172 304 | 0/8 14 h-lim-p 0.0734 20.0000 0.0000 1552.979584 0 0.0000 347 Out... lnL = -1552.979584 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1552.979584 Node 7: lnL = -1552.979584 Node 8: lnL = -1552.979584 Node 9: lnL = -1552.979584 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 480 Sequential format.. Reading seq # 1: YNL229C_Sbay Reading seq # 2: YNL229C_Scer Reading seq # 3: YNL229C_Skud Reading seq # 4: YNL229C_Smik Reading seq # 5: YNL229C_Spar Sequences read.. Counting patterns.. # site patterns = 180 Counting frequencies.. 120 bytes for distance 28800 bytes for lkl0 23040 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.145917 0.013264 0.089709 0.098238 0.099106 0.136360 0.198543 0.140837 lnL0 = -2062.774027 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2062.774027 x= 0.14592 0.01326 0.08971 0.09824 0.09911 0.13636 0.19854 0.14084 1 h-lim-p 0.0007 0.0083 244.1516 2058.554348 4 0.0002 31 | 0/8 2 h-lim-p 0.0008 0.0066 21.5667 2058.444984 5 0.0005 55 | 0/8 3 h-lim-p 0.0016 0.0380 6.4841 2058.433340 4 0.0006 75 | 0/8 4 h-lim-p 0.0013 0.0539 2.9946 2058.431955 5 0.0004 101 | 0/8 5 h-lim-p 0.0015 0.4711 0.7711 2058.431779 2 0.0006 117 | 0/8 6 h-lim-p 0.0030 0.6493 0.1623 2058.431773 2 0.0005 144 | 0/8 7 h-lim-p 0.0117 20.0000 0.0069 2058.431763 0 0.0176 164 | 0/8 8 h-lim-p 0.0094 20.0000 0.0129 2058.430690 0 0.0754 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2058.430672 1 0.9961 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2058.430672 0 1.2500 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2058.430672 0 0.3125 251 | 0/8 12 h-lim-p 0.2131 20.0000 0.0000 2058.430672 0 0.0000 290 Out... lnL = -2058.430672 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2058.430672 Node 7: lnL = -2058.430672 Node 8: lnL = -2058.430672 Node 9: lnL = -2058.430672 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 557 Sequential format.. Reading seq # 1: YNL230C_Sbay Reading seq # 2: YNL230C_Scer Reading seq # 3: YNL230C_Skud Reading seq # 4: YNL230C_Smik Reading seq # 5: YNL230C_Spar Sequences read.. Counting patterns.. # site patterns = 198 Counting frequencies.. 120 bytes for distance 31680 bytes for lkl0 25344 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.160166 0.048583 0.057627 0.127425 0.074429 0.170237 0.189434 0.154762 lnL0 = -2329.137891 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2329.137891 x= 0.16017 0.04858 0.05763 0.12743 0.07443 0.17024 0.18943 0.15476 1 h-lim-p 0.0002 0.0016 138.1402 2326.952587 0 0.0003 22 | 0/8 2 h-lim-p 0.0012 0.0093 27.7080 2326.756040 2 0.0005 38 | 0/8 3 h-lim-p 0.0010 0.0153 15.2038 2326.728990 6 0.0003 65 | 0/8 4 h-lim-p 0.0006 0.0286 7.7816 2326.721019 5 0.0003 90 | 0/8 5 h-lim-p 0.0056 0.2978 0.4763 2326.720933 2 0.0006 108 | 0/8 6 h-lim-p 0.0024 1.9234 0.1120 2326.720659 0 0.0048 129 | 0/8 7 h-lim-p 0.0098 1.8708 0.0544 2326.674496 0 0.1176 152 | 0/8 8 h-lim-p 0.0099 0.2766 0.6479 2326.674360 3 0.0007 181 | 0/8 9 h-lim-p 0.7267 20.0000 0.0006 2326.674030 0 1.0901 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2326.674023 1 0.9961 223 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2326.674023 0 2.1875 243 | 0/8 12 h-lim-p 2.1496 20.0000 0.0000 2326.674023 0 0.9404 263 | 0/8 13 h-lim-p 1.8232 20.0000 0.0000 2326.674023 0 0.0036 291 Out... lnL = -2326.674023 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2326.674023 Node 7: lnL = -2326.674023 Node 8: lnL = -2326.674023 Node 9: lnL = -2326.674023 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 552 Sequential format.. Reading seq # 1: YNL231C_Sbay Reading seq # 2: YNL231C_Scer Reading seq # 3: YNL231C_Skud Reading seq # 4: YNL231C_Smik Reading seq # 5: YNL231C_Spar Sequences read.. Counting patterns.. # site patterns = 165 Counting frequencies.. 120 bytes for distance 26400 bytes for lkl0 21120 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.103083 0.041655 0.048226 0.039361 0.025146 0.117817 0.147027 0.099603 lnL0 = -1909.140280 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1909.140280 x= 0.10308 0.04166 0.04823 0.03936 0.02515 0.11782 0.14703 0.09960 1 h-lim-p 0.0001 0.0007 96.4051 1908.482811 0 0.0002 23 | 0/8 2 h-lim-p 0.0003 0.0144 51.7547 1908.384603 6 0.0001 50 | 0/8 3 h-lim-p 0.0002 0.0037 24.5566 1908.342031 3 0.0002 68 | 0/8 4 h-lim-p 0.0004 0.0113 10.7149 1908.332638 3 0.0002 86 | 0/8 5 h-lim-p 0.0006 0.0316 3.8513 1908.331021 3 0.0003 104 | 0/8 6 h-lim-p 0.0012 0.2908 0.8336 1908.330873 4 0.0004 125 | 0/8 7 h-lim-p 0.0161 6.8923 0.0225 1908.330751 2 0.0128 149 | 0/8 8 h-lim-p 0.0044 1.0260 0.0659 1908.321125 0 0.0351 172 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 1908.320711 3 0.9961 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1908.320711 0 1.0938 218 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1908.320711 0 0.0006 249 Out... lnL = -1908.320711 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1908.320711 Node 7: lnL = -1908.320711 Node 8: lnL = -1908.320711 Node 9: lnL = -1908.320711 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 420 Sequential format.. Reading seq # 1: YNL233W_Sbay Reading seq # 2: YNL233W_Scer Reading seq # 3: YNL233W_Skud Reading seq # 4: YNL233W_Smik Reading seq # 5: YNL233W_Spar Sequences read.. Counting patterns.. # site patterns = 145 Counting frequencies.. 120 bytes for distance 23200 bytes for lkl0 18560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.136478 0.026723 0.069740 0.078677 0.062149 0.148656 0.189220 0.131826 lnL0 = -1791.719718 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1791.719718 x= 0.13648 0.02672 0.06974 0.07868 0.06215 0.14866 0.18922 0.13183 1 h-lim-p 0.0015 0.7320 154.9755 1789.261276 9 0.0002 46 | 0/8 2 h-lim-p 0.0012 0.0100 24.3152 1789.077154 3 0.0006 64 | 0/8 3 h-lim-p 0.0009 0.0142 17.3703 1789.050548 6 0.0002 91 | 0/8 4 h-lim-p 0.0012 0.0680 3.5013 1789.047748 3 0.0005 109 | 0/8 5 h-lim-p 0.0014 0.2071 1.1925 1789.047444 4 0.0005 130 | 0/8 6 h-lim-p 0.0016 0.5148 0.3507 1789.047422 1 0.0004 145 | 0/8 7 h-lim-p 0.0029 4.9528 0.0493 1789.047420 1 0.0007 168 | 0/8 8 h-lim-p 0.0765 20.0000 0.0005 1789.047116 0 1.2239 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1789.047094 1 1.0938 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1789.047094 0 1.0938 234 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1789.047094 0 2.1875 254 | 0/8 12 h-lim-p 2.3615 20.0000 0.0000 1789.047094 0 0.0369 279 | 0/8 13 h-lim-p 0.0294 20.0000 0.0000 1789.047094 0 0.0000 326 Out... lnL = -1789.047094 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1789.047094 Node 7: lnL = -1789.047094 Node 8: lnL = -1789.047094 Node 9: lnL = -1789.047094 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 315 Sequential format.. Reading seq # 1: YNL234W_Sbay Reading seq # 2: YNL234W_Scer Reading seq # 3: YNL234W_Skud Reading seq # 4: YNL234W_Smik Reading seq # 5: YNL234W_Spar Sequences read.. Counting patterns.. # site patterns = 114 Counting frequencies.. 120 bytes for distance 18240 bytes for lkl0 14592 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.145943 0.033829 0.060897 0.052947 0.036140 0.149964 0.208740 0.141366 lnL0 = -1202.564765 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1202.564765 x= 0.14594 0.03383 0.06090 0.05295 0.03614 0.14996 0.20874 0.14137 1 h-lim-p 0.0006 0.0047 65.7878 1201.845414 9 0.0004 47 | 0/8 2 h-lim-p 0.0016 0.0125 8.7458 1201.827105 7 0.0005 78 | 0/8 3 h-lim-p 0.0008 0.0186 5.1529 1201.822206 6 0.0005 106 | 0/8 4 h-lim-p 0.0007 0.0827 3.5778 1201.821000 3 0.0003 125 | 0/8 5 h-lim-p 0.0007 0.1807 1.3901 1201.820501 3 0.0007 143 | 0/8 6 h-lim-p 0.0027 1.0724 0.3476 1201.820444 2 0.0010 159 | 0/8 7 h-lim-p 0.0102 9.3632 0.0350 1201.820443 0 0.0011 181 | 0/8 8 h-lim-p 0.2931 20.0000 0.0001 1201.820416 0 1.1724 203 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1201.820416 0 1.0938 223 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1201.820416 0 0.5469 244 | 0/8 11 h-lim-p 0.8405 20.0000 0.0000 1201.820416 0 0.0066 270 Out... lnL = -1201.820416 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1201.820416 Node 7: lnL = -1201.820416 Node 8: lnL = -1201.820416 Node 9: lnL = -1201.820416 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 389 Sequential format.. Reading seq # 1: YNL236W_Sbay Reading seq # 2: YNL236W_Scer Reading seq # 3: YNL236W_Skud Reading seq # 4: YNL236W_Smik Reading seq # 5: YNL236W_Spar Sequences read.. Counting patterns.. # site patterns = 162 Counting frequencies.. 120 bytes for distance 25920 bytes for lkl0 20736 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.129422 0.149174 0.060972 0.098810 0.063140 0.206503 0.187863 0.123555 lnL0 = -1705.928906 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1705.928906 x= 0.12942 0.14917 0.06097 0.09881 0.06314 0.20650 0.18786 0.12355 1 h-lim-p 0.0047 0.0379 43.5554 1705.603964 8 0.0004 47 | 0/8 2 h-lim-p 0.0038 0.0363 4.1644 1705.599321 6 0.0005 76 | 0/8 3 h-lim-p 0.0006 0.0747 3.4930 1705.597603 5 0.0004 100 | 0/8 4 h-lim-p 0.0022 0.3708 0.6585 1705.597469 4 0.0007 123 | 0/8 5 h-lim-p 0.0039 1.4629 0.1093 1705.597466 0 0.0005 145 | 0/8 6 h-lim-p 0.0043 20.0000 0.0124 1705.597466 0 0.0019 165 | 0/8 7 h-lim-p 0.0809 20.0000 0.0003 1705.597466 0 0.0177 186 | 0/8 8 h-lim-p 0.0109 20.0000 0.0005 1705.597465 0 0.0655 208 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1705.597465 0 1.0938 228 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1705.597465 0 0.0085 255 | 0/8 11 h-lim-p 0.0048 20.0000 0.0000 1705.597465 0 0.0000 287 Out... lnL = -1705.597465 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1705.597465 Node 7: lnL = -1705.597465 Node 8: lnL = -1705.597465 Node 9: lnL = -1705.597465 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 352 Sequential format.. Reading seq # 1: YNL237W_Sbay Reading seq # 2: YNL237W_Scer Reading seq # 3: YNL237W_Skud Reading seq # 4: YNL237W_Smik Reading seq # 5: YNL237W_Spar Sequences read.. Counting patterns.. # site patterns = 126 Counting frequencies.. 120 bytes for distance 20160 bytes for lkl0 16128 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.114148 0.046798 0.081296 0.077256 0.071641 0.649157 0.125648 0.107172 lnL0 = -1257.021055 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1257.021055 x= 0.11415 0.04680 0.08130 0.07726 0.07164 0.64916 0.12565 0.10717 1 h-lim-p 0.0001 0.0011 102.1506 1254.338216 0 0.0006 24 | 0/8 2 h-lim-p 0.0008 0.0063 20.8582 1254.227395 7 0.0005 51 | 0/8 3 h-lim-p 0.0007 0.0109 15.2111 1254.182861 4 0.0005 71 | 0/8 4 h-lim-p 0.0004 0.0074 18.5464 1254.097766 0 0.0013 84 | 0/8 5 h-lim-p 0.0008 0.0060 14.5618 1254.052618 0 0.0011 96 | 0/8 6 h-lim-p 0.0207 0.2794 0.7923 1254.052355 4 0.0008 122 | 0/8 7 h-lim-p 0.0013 1.3518 0.4774 1254.049880 0 0.0211 146 | 0/8 8 h-lim-p 1.0137 13.5391 0.0100 1254.029502 4 0.7949 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1254.029464 3 0.8800 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1254.029463 0 1.0938 221 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1254.029463 0 1.0938 241 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1254.029463 0 2.1875 261 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1254.029463 0 1.0938 281 | 0/8 14 h-lim-p 0.4211 20.0000 0.0000 1254.029463 0 0.2106 301 | 0/8 15 h-lim-p 0.0565 20.0000 0.0000 1254.029463 0 0.0565 321 | 0/8 16 h-lim-p 0.0237 20.0000 0.0000 1254.029463 0 0.0000 362 Out... lnL = -1254.029463 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1254.029463 Node 7: lnL = -1254.029463 Node 8: lnL = -1254.029463 Node 9: lnL = -1254.029463 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 613 Sequential format.. Reading seq # 1: YNL244C_Sbay Reading seq # 2: YNL244C_Scer Reading seq # 3: YNL244C_Skud Reading seq # 4: YNL244C_Smik Reading seq # 5: YNL244C_Spar Sequences read.. Counting patterns.. # site patterns = 212 Counting frequencies.. 120 bytes for distance 33920 bytes for lkl0 27136 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.151611 0.022630 0.075878 0.089230 0.073458 0.199777 0.233701 0.146176 lnL0 = -2623.872349 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2623.872349 x= 0.15161 0.02263 0.07588 0.08923 0.07346 0.19978 0.23370 0.14618 1 h-lim-p 0.0027 0.0260 139.5999 2622.148892 8 0.0002 46 | 0/8 2 h-lim-p 0.0014 0.0115 11.3398 2622.132171 6 0.0003 74 | 0/8 3 h-lim-p 0.0005 0.0222 5.5920 2622.128021 5 0.0003 101 | 0/8 4 h-lim-p 0.0010 0.2535 1.8490 2622.127273 4 0.0005 122 | 0/8 5 h-lim-p 0.0030 0.6536 0.3032 2622.127254 3 0.0004 143 | 0/8 6 h-lim-p 0.0008 1.6835 0.1739 2622.127247 2 0.0005 168 | 0/8 7 h-lim-p 0.0345 20.0000 0.0025 2622.127247 0 0.0151 188 | 0/8 8 h-lim-p 0.0130 20.0000 0.0029 2622.127173 0 0.0783 210 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2622.127172 0 1.0938 230 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2622.127172 0 1.0938 250 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2622.127172 0 2.5000 270 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2622.127172 0 0.0024 299 Out... lnL = -2622.127172 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2622.127172 Node 7: lnL = -2622.127172 Node 8: lnL = -2622.127172 Node 9: lnL = -2622.127172 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 354 Sequential format.. Reading seq # 1: YNL252C_Sbay Reading seq # 2: YNL252C_Scer Reading seq # 3: YNL252C_Skud Reading seq # 4: YNL252C_Smik Reading seq # 5: YNL252C_Spar Sequences read.. Counting patterns.. # site patterns = 139 Counting frequencies.. 120 bytes for distance 22240 bytes for lkl0 17792 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.142591 0.069030 0.055386 0.168550 0.074897 0.179589 0.171646 0.137056 lnL0 = -1451.634441 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1451.634441 x= 0.14259 0.06903 0.05539 0.16855 0.07490 0.17959 0.17165 0.13706 1 h-lim-p 0.0045 0.0361 18.2753 1451.538573 4 0.0006 32 | 0/8 2 h-lim-p 0.0012 0.0129 8.9696 1451.517747 5 0.0006 55 | 0/8 3 h-lim-p 0.0023 0.1538 2.3663 1451.516666 5 0.0004 80 | 0/8 4 h-lim-p 0.0021 0.4416 0.4817 1451.516584 3 0.0007 99 | 0/8 5 h-lim-p 0.0041 1.6035 0.0859 1451.516582 1 0.0005 123 | 0/8 6 h-lim-p 0.0033 17.7033 0.0132 1451.516581 0 0.0014 143 | 0/8 7 h-lim-p 0.0281 20.0000 0.0007 1451.516573 0 0.2251 166 | 0/8 8 h-lim-p 0.0027 8.7031 0.0572 1451.516546 0 0.0040 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1451.516545 0 1.0938 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1451.516545 0 1.0938 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1451.516545 0 2.1875 246 | 0/8 12 h-lim-p 2.4337 20.0000 0.0000 1451.516545 0 0.3042 268 | 0/8 13 h-lim-p 0.2979 20.0000 0.0000 1451.516545 0 0.0000 305 Out... lnL = -1451.516545 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1451.516545 Node 7: lnL = -1451.516545 Node 8: lnL = -1451.516545 Node 9: lnL = -1451.516545 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 891 Sequential format.. Reading seq # 1: YNL253W_Sbay Reading seq # 2: YNL253W_Scer Reading seq # 3: YNL253W_Skud Reading seq # 4: YNL253W_Smik Reading seq # 5: YNL253W_Spar Sequences read.. Counting patterns.. # site patterns = 375 Counting frequencies.. 120 bytes for distance 60000 bytes for lkl0 48000 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.128003 0.179885 0.052394 0.139867 0.131839 0.279981 0.285808 0.120519 lnL0 = -4280.546334 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4280.546334 x= 0.12800 0.17989 0.05239 0.13987 0.13184 0.27998 0.28581 0.12052 1 h-lim-p 0.0035 0.0278 145.4123 4278.170277 7 0.0002 41 | 0/8 2 h-lim-p 0.0008 0.0067 43.4290 4277.737623 8 0.0005 73 | 0/8 3 h-lim-p 0.0009 0.0169 23.1948 4277.663777 4 0.0004 93 | 0/8 4 h-lim-p 0.0016 0.0433 5.2297 4277.659022 2 0.0004 110 | 0/8 5 h-lim-p 0.0022 0.4298 0.8673 4277.658805 3 0.0006 129 | 0/8 6 h-lim-p 0.0011 0.9353 0.4499 4277.658763 2 0.0005 153 | 0/8 7 h-lim-p 0.0053 16.6594 0.0419 4277.658762 0 0.0012 174 | 0/8 8 h-lim-p 0.0684 20.0000 0.0007 4277.658349 0 1.0947 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 4277.658328 1 0.9961 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4277.658328 0 1.0938 240 | 0/8 11 h-lim-p 2.0545 20.0000 0.0000 4277.658328 0 2.0545 260 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4277.658328 0 0.0000 308 Out... lnL = -4277.658328 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4277.658328 Node 7: lnL = -4277.658328 Node 8: lnL = -4277.658328 Node 9: lnL = -4277.658328 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 891 Sequential format.. Reading seq # 1: YNL254C_Sbay Reading seq # 2: YNL254C_Scer Reading seq # 3: YNL254C_Skud Reading seq # 4: YNL254C_Smik Reading seq # 5: YNL254C_Spar Sequences read.. Counting patterns.. # site patterns = 365 Counting frequencies.. 120 bytes for distance 58400 bytes for lkl0 46720 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.133638 0.172967 0.076707 0.138104 0.133601 0.265659 0.277215 0.126079 lnL0 = -4288.256444 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4288.256444 x= 0.13364 0.17297 0.07671 0.13810 0.13360 0.26566 0.27722 0.12608 1 h-lim-p 0.0010 0.0084 135.6498 4285.609185 9 0.0003 44 | 0/8 2 h-lim-p 0.0008 0.0067 48.3527 4285.097268 6 0.0005 72 | 0/8 3 h-lim-p 0.0009 0.0180 26.0851 4285.009692 7 0.0003 100 | 0/8 4 h-lim-p 0.0016 0.0470 5.3646 4285.004945 2 0.0004 117 | 0/8 5 h-lim-p 0.0021 0.3416 0.8952 4285.004704 3 0.0006 138 | 0/8 6 h-lim-p 0.0013 0.8497 0.4352 4285.004666 2 0.0005 162 | 0/8 7 h-lim-p 0.0266 20.0000 0.0080 4285.004665 0 0.0058 183 | 0/8 8 h-lim-p 0.0194 20.0000 0.0024 4285.004455 0 0.2323 206 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4285.004449 0 1.0938 226 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4285.004449 0 1.0938 246 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4285.004449 0 1.0938 266 | 0/8 12 h-lim-p 1.3966 20.0000 0.0000 4285.004449 0 0.3055 287 | 0/8 13 h-lim-p 0.1428 20.0000 0.0000 4285.004449 0 0.0045 311 | 0/8 14 h-lim-p 0.0011 20.0000 0.0000 4285.004449 0 0.0000 345 Out... lnL = -4285.004449 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4285.004449 Node 7: lnL = -4285.004449 Node 8: lnL = -4285.004449 Node 9: lnL = -4285.004449 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 260 Sequential format.. Reading seq # 1: YNL255C_Sbay Reading seq # 2: YNL255C_Scer Reading seq # 3: YNL255C_Skud Reading seq # 4: YNL255C_Smik Reading seq # 5: YNL255C_Spar Sequences read.. Counting patterns.. # site patterns = 110 Counting frequencies.. 120 bytes for distance 17600 bytes for lkl0 14080 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.100578 0.057162 0.030591 0.124509 0.090576 0.206551 0.156495 0.095850 lnL0 = -1118.505736 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1118.505736 x= 0.10058 0.05716 0.03059 0.12451 0.09058 0.20655 0.15650 0.09585 1 h-lim-p 0.0016 0.0129 87.5774 1117.514786 9 0.0003 43 | 0/8 2 h-lim-p 0.0012 0.0094 13.1364 1117.453239 7 0.0007 76 | 0/8 3 h-lim-p 0.0023 0.0612 4.0961 1117.448352 6 0.0006 103 | 0/8 4 h-lim-p 0.0036 0.3210 0.7185 1117.448155 2 0.0008 120 | 0/8 5 h-lim-p 0.0026 0.8158 0.2221 1117.448136 2 0.0008 146 | 0/8 6 h-lim-p 0.0024 5.6457 0.0788 1117.448134 1 0.0009 168 | 0/8 7 h-lim-p 0.0060 19.6222 0.0125 1117.448133 0 0.0013 189 | 0/8 8 h-lim-p 0.2661 20.0000 0.0001 1117.448129 0 1.0643 211 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1117.448129 0 1.0938 231 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1117.448129 0 1.2500 251 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1117.448129 0 0.0000 294 Out... lnL = -1117.448129 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1117.448129 Node 7: lnL = -1117.448129 Node 8: lnL = -1117.448129 Node 9: lnL = -1117.448129 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 339 Sequential format.. Reading seq # 1: YNL259C_Sbay Reading seq # 2: YNL259C_Scer Reading seq # 3: YNL259C_Skud Reading seq # 4: YNL259C_Smik Reading seq # 5: YNL259C_Spar Sequences read.. Counting patterns.. # site patterns = 157 Counting frequencies.. 120 bytes for distance 25120 bytes for lkl0 20096 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.155161 0.101697 0.109595 0.085623 0.114610 0.176179 0.189991 0.148965 lnL0 = -1432.932294 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1432.932294 x= 0.15516 0.10170 0.10959 0.08562 0.11461 0.17618 0.18999 0.14896 1 h-lim-p 0.0011 0.0087 47.8181 1432.171916 7 0.0007 38 | 0/8 2 h-lim-p 0.0016 0.0127 17.3038 1432.067333 4 0.0008 59 | 0/8 3 h-lim-p 0.0025 0.0453 5.3745 1432.055685 6 0.0009 86 | 0/8 4 h-lim-p 0.0054 0.1503 0.8860 1432.055375 4 0.0008 110 | 0/8 5 h-lim-p 0.0098 4.2116 0.0727 1432.055369 2 0.0019 135 | 0/8 6 h-lim-p 0.0055 10.0035 0.0251 1432.055362 1 0.0044 157 | 0/8 7 h-lim-p 0.0065 13.2890 0.0168 1432.055109 0 0.0393 179 | 0/8 8 h-lim-p 0.0022 0.4853 0.2976 1432.054427 0 0.0044 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1432.054384 2 0.9961 224 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1432.054384 0 1.2500 244 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1432.054384 0 0.1367 267 | 0/8 12 h-lim-p 0.0871 20.0000 0.0000 1432.054384 0 0.0871 287 | 0/8 13 h-lim-p 0.0614 20.0000 0.0000 1432.054384 0 0.0001 315 Out... lnL = -1432.054384 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1432.054384 Node 7: lnL = -1432.054384 Node 8: lnL = -1432.054384 Node 9: lnL = -1432.054384 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 477 Sequential format.. Reading seq # 1: YNL265C_Sbay Reading seq # 2: YNL265C_Scer Reading seq # 3: YNL265C_Skud Reading seq # 4: YNL265C_Smik Reading seq # 5: YNL265C_Spar Sequences read.. Counting patterns.. # site patterns = 214 Counting frequencies.. 120 bytes for distance 34240 bytes for lkl0 27392 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.101553 0.079405 0.084836 0.174706 0.092399 0.204805 0.156933 0.095956 lnL0 = -2012.133787 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2012.133787 x= 0.10155 0.07940 0.08484 0.17471 0.09240 0.20480 0.15693 0.09596 1 h-lim-p 0.0014 0.0112 64.6601 2011.055793 5 0.0005 32 | 0/8 2 h-lim-p 0.0008 0.0060 34.0974 2010.797049 7 0.0005 59 | 0/8 3 h-lim-p 0.0023 0.0404 7.8456 2010.784464 6 0.0004 84 | 0/8 4 h-lim-p 0.0017 0.1103 1.9916 2010.783415 3 0.0006 104 | 0/8 5 h-lim-p 0.0017 0.4514 0.6680 2010.783297 3 0.0006 124 | 0/8 6 h-lim-p 0.0036 2.3175 0.1102 2010.783293 1 0.0007 147 | 0/8 7 h-lim-p 0.0081 17.6026 0.0098 2010.783293 0 0.0020 168 | 0/8 8 h-lim-p 0.0242 20.0000 0.0008 2010.783201 0 0.3871 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2010.783201 0 1.0938 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2010.783201 0 1.0938 232 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2010.783201 0 1.0938 252 | 0/8 12 h-lim-p 1.1474 20.0000 0.0000 2010.783201 0 0.8606 272 | 0/8 13 h-lim-p 0.2454 20.0000 0.0000 2010.783201 0 0.2454 292 | 0/8 14 h-lim-p 0.0653 20.0000 0.0000 2010.783201 0 0.0490 312 | 0/8 15 h-lim-p 0.0156 20.0000 0.0000 2010.783201 0 0.0000 349 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 2010.783201 0 0.0000 371 Out... lnL = -2010.783201 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2010.783201 Node 7: lnL = -2010.783201 Node 8: lnL = -2010.783201 Node 9: lnL = -2010.783201 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 537 Sequential format.. Reading seq # 1: YNL268W_Sbay Reading seq # 2: YNL268W_Scer Reading seq # 3: YNL268W_Skud Reading seq # 4: YNL268W_Smik Reading seq # 5: YNL268W_Spar Sequences read.. Counting patterns.. # site patterns = 260 Counting frequencies.. 120 bytes for distance 41600 bytes for lkl0 33280 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.172976 0.000060 0.070899 0.232310 0.171985 0.179236 0.439861 0.166348 lnL0 = -2470.170431 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2470.170431 x= 0.17298 0.00006 0.07090 0.23231 0.17198 0.17924 0.43986 0.16635 1 h-lim-p 0.0000 0.0000 112.5794 2470.074219 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0097 25.4706 2469.846183 0 0.0011 39 | 1/8 3 h-lim-p 0.0040 0.0756 6.8863 2469.804173 6 0.0017 63 | 1/8 4 h-lim-p 0.0039 0.0934 3.0099 2469.791438 2 0.0018 79 | 1/8 5 h-lim-p 0.0079 0.4345 0.6893 2469.692408 0 0.0159 92 | 1/8 6 h-lim-p 0.0032 0.0598 3.4113 2468.145457 0 0.0128 113 | 1/8 7 h-lim-p 0.0006 0.0047 28.2864 2467.433988 0 0.0012 126 | 1/8 8 h-lim-p 2.5000 20.0000 0.0115 2467.328222 7 0.7625 158 | 0/8 9 h-lim-p 0.0004 4.6580 21.2539 2467.254111 3 0.0003 183 | 0/8 10 h-lim-p 0.9451 20.0000 0.0078 2467.222524 0 1.4177 195 | 0/8 11 h-lim-p 2.5000 20.0000 0.0018 2467.220810 5 0.8152 227 | 0/8 12 h-lim-p 2.5000 20.0000 0.0004 2467.220768 3 0.8855 255 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2467.220767 0 1.0938 275 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 2467.220767 0 1.0938 295 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2467.220767 0 1.0938 315 | 0/8 16 h-lim-p 1.3079 20.0000 0.0000 2467.220767 0 1.3079 335 | 0/8 17 h-lim-p 1.3459 20.0000 0.0000 2467.220767 0 0.1682 357 | 0/8 18 h-lim-p 0.0313 20.0000 0.0000 2467.220767 0 0.0078 378 | 0/8 19 h-lim-p 0.0000 20.0000 0.0006 2467.220767 0 0.0000 410 | 0/8 20 h-lim-p 0.0000 20.0000 0.0000 2467.220767 0 0.0000 432 | 0/8 21 h-lim-p 0.0000 20.0000 0.0000 2467.220767 0 0.0000 466 Out... lnL = -2467.220767 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2467.220767 Node 7: lnL = -2467.220767 Node 8: lnL = -2467.220767 Node 9: lnL = -2467.220767 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 471 Sequential format.. Reading seq # 1: YNL275W_Sbay Reading seq # 2: YNL275W_Scer Reading seq # 3: YNL275W_Skud Reading seq # 4: YNL275W_Smik Reading seq # 5: YNL275W_Spar Sequences read.. Counting patterns.. # site patterns = 216 Counting frequencies.. 120 bytes for distance 34560 bytes for lkl0 27648 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.175461 0.135844 0.032134 0.135937 0.136688 0.224053 0.255556 0.159509 lnL0 = -2188.294883 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2188.294883 x= 0.17546 0.13584 0.03213 0.13594 0.13669 0.22405 0.25556 0.15951 1 h-lim-p 0.0018 0.0140 59.7491 2187.834244 8 0.0003 44 | 0/8 2 h-lim-p 0.0010 0.0150 17.2782 2187.729026 4 0.0007 64 | 0/8 3 h-lim-p 0.0014 0.0321 9.5754 2187.703995 4 0.0007 85 | 0/8 4 h-lim-p 0.0022 0.0830 3.0371 2187.700917 5 0.0008 109 | 0/8 5 h-lim-p 0.0025 0.5118 0.9415 2187.700582 4 0.0008 132 | 0/8 6 h-lim-p 0.0054 2.5896 0.1450 2187.700574 2 0.0007 158 | 0/8 7 h-lim-p 0.0124 20.0000 0.0083 2187.700573 0 0.0054 178 | 0/8 8 h-lim-p 0.0328 20.0000 0.0014 2187.700418 0 0.2622 201 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2187.700414 1 0.9961 223 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2187.700414 0 2.1875 243 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2187.700414 0 0.6250 264 | 0/8 12 h-lim-p 0.3695 20.0000 0.0000 2187.700414 0 0.0231 287 | 0/8 13 h-lim-p 0.0134 20.0000 0.0000 2187.700414 0 0.0033 308 Out... lnL = -2187.700414 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2187.700414 Node 7: lnL = -2187.700414 Node 8: lnL = -2187.700414 Node 9: lnL = -2187.700414 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 851 Sequential format.. Reading seq # 1: YNL282W_Sbay Reading seq # 2: YNL282W_Scer Reading seq # 3: YNL282W_Skud Reading seq # 4: YNL282W_Smik Reading seq # 5: YNL282W_Spar Sequences read.. Counting patterns.. # site patterns = 239 Counting frequencies.. 120 bytes for distance 38240 bytes for lkl0 30592 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.119507 0.048513 0.053653 0.107426 0.054242 0.142833 0.153905 0.109493 lnL0 = -3455.241159 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3455.241159 x= 0.11951 0.04851 0.05365 0.10743 0.05424 0.14283 0.15390 0.10949 1 h-lim-p 0.0021 0.7279 181.7029 3453.549010 5 0.0001 36 | 0/8 2 h-lim-p 0.0004 0.0028 22.8637 3453.515998 6 0.0001 63 | 0/8 3 h-lim-p 0.0004 0.0254 7.3450 3453.510157 5 0.0002 89 | 0/8 4 h-lim-p 0.0010 0.0923 1.7870 3453.509821 2 0.0002 106 | 0/8 5 h-lim-p 0.0027 1.0172 0.1535 3453.509818 0 0.0003 120 | 0/8 6 h-lim-p 0.0023 4.8769 0.0197 3453.509817 0 0.0003 142 | 0/8 7 h-lim-p 0.0036 20.0000 0.0014 3453.509817 0 0.0144 164 | 0/8 8 h-lim-p 0.0038 20.0000 0.0051 3453.509775 0 0.0231 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3453.509774 0 1.0938 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3453.509774 0 1.0938 226 | 0/8 11 h-lim-p 1.8427 20.0000 0.0000 3453.509774 0 2.7640 246 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3453.509774 0 0.1562 269 | 0/8 13 h-lim-p 0.1191 20.0000 0.0000 3453.509774 0 0.0261 290 | 0/8 14 h-lim-p 0.0111 20.0000 0.0000 3453.509774 0 0.0003 314 Out... lnL = -3453.509774 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3453.509774 Node 7: lnL = -3453.509774 Node 8: lnL = -3453.509774 Node 9: lnL = -3453.509774 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 853 Sequential format.. Reading seq # 1: YNL284C_Sbay Reading seq # 2: YNL284C_Scer Reading seq # 3: YNL284C_Skud Reading seq # 4: YNL284C_Smik Reading seq # 5: YNL284C_Spar Sequences read.. Counting patterns.. # site patterns = 436 Counting frequencies.. 120 bytes for distance 69760 bytes for lkl0 55808 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.344861 0.449734 0.282756 0.279871 0.280084 0.680296 0.468596 0.303694 lnL0 = -4524.889863 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4524.889863 x= 0.34486 0.44973 0.28276 0.27987 0.28008 0.68030 0.46860 0.30369 1 h-lim-p 0.0151 0.1206 13.2124 4524.581990 6 0.0037 34 | 0/8 2 h-lim-p 0.0073 0.0884 6.6259 4524.555929 4 0.0014 55 | 0/8 3 h-lim-p 0.0016 0.0920 6.0220 4524.532331 0 0.0024 67 | 0/8 4 h-lim-p 0.0035 0.1816 4.1155 4524.512325 0 0.0052 79 | 0/8 5 h-lim-p 0.0411 1.3135 0.5208 4524.510706 5 0.0125 105 | 0/8 6 h-lim-p 0.0226 2.1655 0.2865 4524.510394 3 0.0095 131 | 0/8 7 h-lim-p 0.0148 5.2981 0.1836 4524.510170 1 0.0185 153 | 0/8 8 h-lim-p 0.6756 20.0000 0.0050 4524.509229 0 1.0135 173 | 0/8 9 h-lim-p 2.5000 20.0000 0.0008 4524.509195 1 0.9961 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4524.509195 0 1.0938 215 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4524.509195 0 1.0938 235 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4524.509195 0 1.2500 255 | 0/8 13 h-lim-p 0.8326 20.0000 0.0000 4524.509195 0 0.8326 275 | 0/8 14 h-lim-p 0.0431 20.0000 0.0000 4524.509195 0 0.0647 295 | 0/8 15 h-lim-p 0.0030 20.0000 0.0003 4524.509195 0 0.0008 316 | 0/8 16 h-lim-p 0.0397 20.0000 0.0000 4524.509195 0 0.0000 349 Out... lnL = -4524.509195 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4524.509195 Node 7: lnL = -4524.509195 Node 8: lnL = -4524.509195 Node 9: lnL = -4524.509195 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 431 Sequential format.. Reading seq # 1: YNL286W_Sbay Reading seq # 2: YNL286W_Scer Reading seq # 3: YNL286W_Skud Reading seq # 4: YNL286W_Smik Reading seq # 5: YNL286W_Spar Sequences read.. Counting patterns.. # site patterns = 216 Counting frequencies.. 120 bytes for distance 34560 bytes for lkl0 27648 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.296313 0.181123 0.000060 0.206047 0.408655 0.374728 0.418225 0.278358 lnL0 = -2112.618215 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2112.618215 x= 0.29631 0.18112 0.00006 0.20605 0.40866 0.37473 0.41822 0.27836 1 h-lim-p 0.0000 0.0000 272.8208 2112.520233 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0008 688.3425 2055.712294 9 0.0005 59 | 1/8 3 h-lim-p 0.0005 0.0036 121.6527 2051.316961 0 0.0009 72 | 1/8 4 h-lim-p 0.0022 0.0177 18.2699 2051.092015 7 0.0012 100 | 1/8 5 h-lim-p 0.0028 0.0360 8.0743 2050.979704 3 0.0024 118 | 1/8 6 h-lim-p 0.0079 0.1428 2.4039 2050.648878 1 0.0099 132 | 0/8 7 h-lim-p 0.0013 0.0585 18.2317 2049.989350 1 0.0016 146 | 0/8 8 h-lim-p 0.0010 0.0077 13.2113 2037.046861 m 0.0077 158 | 1/8 9 h-lim-p 1.6167 20.0000 0.0610 2033.688421 8 1.7638 188 | 1/8 10 h-lim-p 2.5000 20.0000 0.0142 2033.581824 7 0.9199 223 | 1/8 11 h-lim-p 1.8677 20.0000 0.0070 2033.576986 2 0.4377 247 | 1/8 12 h-lim-p 2.1447 20.0000 0.0014 2033.575734 4 1.3827 276 | 1/8 13 h-lim-p 2.5000 20.0000 0.0001 2033.575729 0 1.0938 295 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 2033.575729 0 1.2500 314 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 2033.575729 0 1.0938 333 | 1/8 16 h-lim-p 1.8036 20.0000 0.0000 2033.575729 0 0.9018 352 | 1/8 17 h-lim-p 0.6320 20.0000 0.0000 2033.575729 0 0.0198 375 | 1/8 18 h-lim-p 0.0056 20.0000 0.0000 2033.575729 0 0.0056 394 | 1/8 19 h-lim-p 0.0012 20.0000 0.0000 2033.575729 0 0.0000 421 | 1/8 20 h-lim-p 0.0023 20.0000 0.0000 2033.575729 0 0.0000 455 Out... lnL = -2033.575729 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2033.575729 Node 7: lnL = -2033.575729 Node 8: lnL = -2033.575729 Node 9: lnL = -2033.575729 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 594 Sequential format.. Reading seq # 1: YNL287W_Sbay Reading seq # 2: YNL287W_Scer Reading seq # 3: YNL287W_Skud Reading seq # 4: YNL287W_Smik Reading seq # 5: YNL287W_Spar Sequences read.. Counting patterns.. # site patterns = 150 Counting frequencies.. 120 bytes for distance 24000 bytes for lkl0 19200 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.057164 0.046142 0.027886 0.072433 0.050132 0.102567 0.126651 0.050370 lnL0 = -2089.073315 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2089.073315 x= 0.05716 0.04614 0.02789 0.07243 0.05013 0.10257 0.12665 0.05037 1 h-lim-p 0.0002 0.0013 122.7428 2088.334624 8 0.0001 44 | 0/8 2 h-lim-p 0.0002 0.0019 31.1872 2088.274119 6 0.0001 69 | 0/8 3 h-lim-p 0.0005 0.0197 8.8852 2088.269093 6 0.0001 98 | 0/8 4 h-lim-p 0.0005 0.0689 2.4909 2088.268515 3 0.0002 116 | 0/8 5 h-lim-p 0.0005 0.2441 0.9360 2088.268445 3 0.0002 135 | 0/8 6 h-lim-p 0.0009 0.8518 0.1909 2088.268441 0 0.0002 156 | 0/8 7 h-lim-p 0.0012 4.9565 0.0362 2088.268441 0 0.0003 177 | 0/8 8 h-lim-p 0.1185 20.0000 0.0001 2088.268409 0 0.9481 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2088.268408 0 1.0938 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2088.268408 0 0.6250 241 | 0/8 11 h-lim-p 0.4166 20.0000 0.0000 2088.268408 0 0.0260 264 | 0/8 12 h-lim-p 0.0146 20.0000 0.0000 2088.268408 0 0.0073 284 | 0/8 13 h-lim-p 0.0050 20.0000 0.0000 2088.268408 0 0.0000 326 | 0/8 14 h-lim-p 0.0000 20.0000 0.0026 | 0/8 15 h-lim-p 0.0000 20.0000 0.0026 Out... lnL = -2088.268408 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2088.268408 Node 7: lnL = -2088.268408 Node 8: lnL = -2088.268408 Node 9: lnL = -2088.268408 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 416 Sequential format.. Reading seq # 1: YNL290W_Sbay Reading seq # 2: YNL290W_Scer Reading seq # 3: YNL290W_Skud Reading seq # 4: YNL290W_Smik Reading seq # 5: YNL290W_Spar Sequences read.. Counting patterns.. # site patterns = 195 Counting frequencies.. 120 bytes for distance 31200 bytes for lkl0 24960 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.160468 0.090353 0.057504 0.205063 0.091343 0.243824 0.224015 0.145083 lnL0 = -1941.204160 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1941.204160 x= 0.16047 0.09035 0.05750 0.20506 0.09134 0.24382 0.22402 0.14508 1 h-lim-p 0.0006 0.0049 55.0624 1940.553919 7 0.0005 37 | 0/8 2 h-lim-p 0.0012 0.0096 14.4120 1940.493440 4 0.0006 58 | 0/8 3 h-lim-p 0.0010 0.0435 8.4788 1940.478454 5 0.0005 81 | 0/8 4 h-lim-p 0.0031 0.2358 1.5072 1940.477426 5 0.0010 107 | 0/8 5 h-lim-p 0.0052 0.8638 0.2762 1940.477397 3 0.0008 129 | 0/8 6 h-lim-p 0.0047 6.3372 0.0451 1940.477395 1 0.0012 152 | 0/8 7 h-lim-p 0.0138 20.0000 0.0038 1940.477393 0 0.0138 172 | 0/8 8 h-lim-p 0.0089 15.1048 0.0059 1940.477278 0 0.0713 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1940.477273 1 0.9961 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1940.477273 0 2.1875 237 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1940.477273 0 1.0938 257 | 0/8 12 h-lim-p 0.6121 20.0000 0.0000 1940.477273 0 4.8965 280 | 0/8 13 h-lim-p 2.2091 20.0000 0.0000 1940.477273 0 0.5523 301 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1940.477273 0 0.1562 324 | 0/8 15 h-lim-p 0.0254 20.0000 0.0000 1940.477273 0 0.0001 351 Out... lnL = -1940.477273 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1940.477273 Node 7: lnL = -1940.477273 Node 8: lnL = -1940.477273 Node 9: lnL = -1940.477273 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 416 Sequential format.. Reading seq # 1: YNL291C_Sbay Reading seq # 2: YNL291C_Scer Reading seq # 3: YNL291C_Skud Reading seq # 4: YNL291C_Smik Reading seq # 5: YNL291C_Spar Sequences read.. Counting patterns.. # site patterns = 196 Counting frequencies.. 120 bytes for distance 31360 bytes for lkl0 25088 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.159664 0.094725 0.068698 0.200987 0.084027 0.238361 0.223400 0.144230 lnL0 = -1937.358865 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1937.358865 x= 0.15966 0.09473 0.06870 0.20099 0.08403 0.23836 0.22340 0.14423 1 h-lim-p 0.0007 0.0053 46.9336 1936.850487 8 0.0005 42 | 0/8 2 h-lim-p 0.0018 0.0144 10.0619 1936.819032 7 0.0006 71 | 0/8 3 h-lim-p 0.0012 0.0436 5.1816 1936.814477 5 0.0004 96 | 0/8 4 h-lim-p 0.0043 1.2560 0.5075 1936.814377 3 0.0008 115 | 0/8 5 h-lim-p 0.0070 4.1532 0.0589 1936.814376 0 0.0009 137 | 0/8 6 h-lim-p 0.0059 20.0000 0.0087 1936.814376 0 0.0013 158 | 0/8 7 h-lim-p 0.0177 20.0000 0.0006 1936.814376 0 0.0155 178 | 0/8 8 h-lim-p 0.0311 20.0000 0.0003 1936.814374 0 0.1245 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1936.814374 0 1.0938 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1936.814374 0 2.1875 240 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1936.814374 0 1.0938 260 | 0/8 12 h-lim-p 0.4643 20.0000 0.0000 1936.814374 0 0.3482 280 | 0/8 13 h-lim-p 0.1085 20.0000 0.0000 1936.814374 0 0.0271 301 | 0/8 14 h-lim-p 0.0062 20.0000 0.0000 1936.814374 0 0.0001 326 | 0/8 15 h-lim-p 0.0017 20.0000 0.0000 1936.814374 0 0.0000 362 Out... lnL = -1936.814374 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1936.814374 Node 7: lnL = -1936.814374 Node 8: lnL = -1936.814374 Node 9: lnL = -1936.814374 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 290 Sequential format.. Reading seq # 1: YNL292W_Sbay Reading seq # 2: YNL292W_Scer Reading seq # 3: YNL292W_Skud Reading seq # 4: YNL292W_Smik Reading seq # 5: YNL292W_Spar Sequences read.. Counting patterns.. # site patterns = 116 Counting frequencies.. 120 bytes for distance 18560 bytes for lkl0 14848 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.136944 0.014283 0.064103 0.106818 0.063158 0.147280 0.191470 0.126348 lnL0 = -1194.032750 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1194.032750 x= 0.13694 0.01428 0.06410 0.10682 0.06316 0.14728 0.19147 0.12635 1 h-lim-p 0.0005 0.0041 117.7380 1192.485780 7 0.0003 38 | 0/8 2 h-lim-p 0.0013 0.0102 18.6113 1192.338050 6 0.0009 65 | 0/8 3 h-lim-p 0.0016 0.0241 10.0746 1192.318632 7 0.0005 96 | 0/8 4 h-lim-p 0.0010 0.0294 4.8875 1192.313487 6 0.0006 124 | 0/8 5 h-lim-p 0.0043 0.3771 0.6368 1192.313314 3 0.0009 143 | 0/8 6 h-lim-p 0.0059 1.9543 0.0952 1192.313311 1 0.0006 167 | 0/8 7 h-lim-p 0.0324 20.0000 0.0017 1192.313305 0 0.0648 188 | 0/8 8 h-lim-p 0.0056 3.7662 0.0200 1192.313176 0 0.0225 210 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1192.313171 1 1.0938 232 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1192.313171 0 1.0938 252 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1192.313171 0 1.0938 272 | 0/8 12 h-lim-p 1.3035 20.0000 0.0000 1192.313171 0 1.1406 292 | 0/8 13 h-lim-p 0.7107 20.0000 0.0000 1192.313171 0 0.7107 312 | 0/8 14 h-lim-p 0.0235 20.0000 0.0000 1192.313171 0 0.0206 332 | 0/8 15 h-lim-p 0.0120 20.0000 0.0000 1192.313171 0 0.0000 364 | 0/8 16 h-lim-p 0.0029 20.0000 0.0000 1192.313171 0 0.0057 385 Out... lnL = -1192.313171 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1192.313171 Node 7: lnL = -1192.313171 Node 8: lnL = -1192.313171 Node 9: lnL = -1192.313171 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 432 Sequential format.. Reading seq # 1: YNL293W_Sbay Reading seq # 2: YNL293W_Scer Reading seq # 3: YNL293W_Skud Reading seq # 4: YNL293W_Smik Reading seq # 5: YNL293W_Spar Sequences read.. Counting patterns.. # site patterns = 143 Counting frequencies.. 120 bytes for distance 22880 bytes for lkl0 18304 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.121955 0.054541 0.055462 0.100857 0.064680 0.162655 0.213219 0.110768 lnL0 = -1737.825695 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1737.825695 x= 0.12195 0.05454 0.05546 0.10086 0.06468 0.16265 0.21322 0.11077 1 h-lim-p 0.0037 0.0298 77.9786 1737.027281 9 0.0003 48 | 0/8 2 h-lim-p 0.0010 0.0082 11.2617 1737.004881 6 0.0004 76 | 0/8 3 h-lim-p 0.0009 0.0508 4.3672 1737.001903 4 0.0004 96 | 0/8 4 h-lim-p 0.0017 0.2034 0.9395 1737.001694 4 0.0005 120 | 0/8 5 h-lim-p 0.0078 4.0779 0.0617 1737.001692 0 0.0009 142 | 0/8 6 h-lim-p 0.0022 11.7116 0.0238 1737.001692 0 0.0010 162 | 0/8 7 h-lim-p 0.0041 20.0000 0.0057 1737.001692 0 0.0018 182 | 0/8 8 h-lim-p 0.0963 20.0000 0.0001 1737.001683 0 0.7703 205 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1737.001683 0 1.0938 225 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1737.001683 0 2.5000 245 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1737.001683 0 0.0342 270 | 0/8 12 h-lim-p 0.0241 20.0000 0.0000 1737.001683 0 0.0002 296 Out... lnL = -1737.001683 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1737.001683 Node 7: lnL = -1737.001683 Node 8: lnL = -1737.001683 Node 9: lnL = -1737.001683 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 389 Sequential format.. Reading seq # 1: YNL294C_Sbay Reading seq # 2: YNL294C_Scer Reading seq # 3: YNL294C_Skud Reading seq # 4: YNL294C_Smik Reading seq # 5: YNL294C_Spar Sequences read.. Counting patterns.. # site patterns = 145 Counting frequencies.. 120 bytes for distance 23200 bytes for lkl0 18560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.118758 0.074325 0.050420 0.093312 0.064188 0.170778 0.193334 0.107620 lnL0 = -1641.161198 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1641.161198 x= 0.11876 0.07433 0.05042 0.09331 0.06419 0.17078 0.19333 0.10762 1 h-lim-p 0.0045 1.5543 85.1466 1640.244823 4 0.0003 33 | 0/8 2 h-lim-p 0.0012 0.0095 14.4150 1640.204750 6 0.0004 60 | 0/8 3 h-lim-p 0.0012 0.0274 4.9532 1640.200248 4 0.0004 81 | 0/8 4 h-lim-p 0.0022 0.1847 0.9198 1640.200033 2 0.0005 98 | 0/8 5 h-lim-p 0.0127 5.7296 0.0374 1640.200033 0 0.0007 121 | 0/8 6 h-lim-p 0.0028 20.0000 0.0092 1640.200033 0 0.0007 142 | 0/8 7 h-lim-p 0.0046 20.0000 0.0014 1640.200032 0 0.0183 164 | 0/8 8 h-lim-p 0.0096 20.0000 0.0027 1640.200016 0 0.0385 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1640.200016 0 1.0938 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1640.200016 0 2.1875 226 | 0/8 11 h-lim-p 2.3567 20.0000 0.0000 1640.200016 0 1.0310 246 | 0/8 12 h-lim-p 1.3778 20.0000 0.0000 1640.200016 010.7667 269 | 0/8 13 h-lim-p 1.2917 20.0000 0.0000 1640.200016 0 0.0404 293 | 0/8 14 h-lim-p 0.0496 20.0000 0.0000 1640.200016 0 0.0000 335 Out... lnL = -1640.200016 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1640.200016 Node 7: lnL = -1640.200016 Node 8: lnL = -1640.200016 Node 9: lnL = -1640.200016 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 503 Sequential format.. Reading seq # 1: YNL295W_Sbay Reading seq # 2: YNL295W_Scer Reading seq # 3: YNL295W_Skud Reading seq # 4: YNL295W_Smik Reading seq # 5: YNL295W_Spar Sequences read.. Counting patterns.. # site patterns = 79 Counting frequencies.. 120 bytes for distance 12640 bytes for lkl0 10112 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.182774 0.000060 0.144265 0.071569 0.108332 4.654826 0.235788 0.138106 lnL0 = -1515.107154 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1515.107154 x= 0.18277 0.00006 0.14426 0.07157 0.10833 4.65483 0.23579 0.13811 1 h-lim-p 0.0000 0.0000 152.6599 1515.040732 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0030 87.9598 1513.090757 0 0.0006 40 | 1/8 3 h-lim-p 0.0017 0.0132 20.6693 1512.847643 8 0.0012 71 | 1/8 4 h-lim-p 0.0179 0.1742 1.3804 1512.815883 7 0.0051 103 | 1/8 5 h-lim-p 0.0048 0.1436 1.4774 1511.984334 0 0.0192 117 | 1/8 6 h-lim-p 0.0011 0.0090 14.2094 1508.557790 0 0.0034 130 | 1/8 7 h-lim-p 0.7162 5.7297 0.0209 1508.421544 7 0.5184 161 | 1/8 8 h-lim-p 2.5000 20.0000 0.0040 1508.417033 2 0.6250 185 | 1/8 9 h-lim-p 2.5000 20.0000 0.0002 1508.417012 3 0.7439 212 | 0/8 10 h-lim-p 0.0000 0.0000 0.0024 h-lim-p: 1.67463770e-19 1.33971016e-18 2.43102916e-03 1508.417012 .. | 1/8 11 h-lim-p 0.0000 8.1425 0.0403 1508.417012 0 0.0003 252 | 1/8 12 h-lim-p 0.0006 9.4756 0.0200 1508.417012 0 0.0006 271 | 1/8 13 h-lim-p 0.0015 18.9155 0.0075 1508.417012 0 0.0007 290 | 1/8 14 h-lim-p 0.0034 20.0000 0.0015 1508.417012 0 0.0007 310 | 1/8 15 h-lim-p 0.0229 20.0000 0.0000 1508.417012 0 0.0100 329 | 1/8 16 h-lim-p 0.0149 20.0000 0.0000 1508.417012 0 0.1196 351 | 1/8 17 h-lim-p 1.2585 20.0000 0.0000 1508.417012 0 1.8878 370 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 1508.417012 0 0.2734 391 | 1/8 19 h-lim-p 0.0559 20.0000 0.0000 1508.417012 0 0.0280 410 | 1/8 20 h-lim-p 0.0116 20.0000 0.0000 1508.417012 0 0.0029 430 | 1/8 21 h-lim-p 0.0017 20.0000 0.0000 1508.417012 0 0.0004 450 | 1/8 22 h-lim-p 0.0007 20.0000 0.0000 1508.417012 0 0.0000 477 | 1/8 23 h-lim-p 0.0001 20.0000 0.0000 1508.417012 0 0.0000 498 Out... lnL = -1508.417012 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1508.417012 Node 7: lnL = -1508.417012 Node 8: lnL = -1508.417012 Node 9: lnL = -1508.417012 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 539 Sequential format.. Reading seq # 1: YNL298W_Sbay Reading seq # 2: YNL298W_Scer Reading seq # 3: YNL298W_Skud Reading seq # 4: YNL298W_Smik Reading seq # 5: YNL298W_Spar Sequences read.. Counting patterns.. # site patterns = 170 Counting frequencies.. 120 bytes for distance 27200 bytes for lkl0 21760 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.137164 0.070868 0.031891 0.057478 0.053216 0.139354 0.121292 0.127750 lnL0 = -2121.969651 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2121.969651 x= 0.13716 0.07087 0.03189 0.05748 0.05322 0.13935 0.12129 0.12775 1 h-lim-p 0.0011 0.0087 75.0306 2121.558645 8 0.0002 41 | 0/8 2 h-lim-p 0.0004 0.0044 26.7346 2121.474255 7 0.0003 71 | 0/8 3 h-lim-p 0.0006 0.0152 11.2827 2121.464258 6 0.0002 98 | 0/8 4 h-lim-p 0.0004 0.0161 5.3738 2121.461163 5 0.0003 123 | 0/8 5 h-lim-p 0.0015 0.1642 0.9877 2121.461087 2 0.0002 141 | 0/8 6 h-lim-p 0.0040 4.7308 0.0389 2121.461087 0 0.0004 163 | 0/8 7 h-lim-p 0.0100 20.0000 0.0017 2121.461087 0 0.0044 183 | 0/8 8 h-lim-p 0.0120 20.0000 0.0006 2121.461073 0 0.0959 206 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2121.461073 0 1.0938 226 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2121.461073 0 0.0011 256 Out... lnL = -2121.461073 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2121.461073 Node 7: lnL = -2121.461073 Node 8: lnL = -2121.461073 Node 9: lnL = -2121.461073 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 545 Sequential format.. Reading seq # 1: YNL299W_Sbay Reading seq # 2: YNL299W_Scer Reading seq # 3: YNL299W_Skud Reading seq # 4: YNL299W_Smik Reading seq # 5: YNL299W_Spar Sequences read.. Counting patterns.. # site patterns = 216 Counting frequencies.. 120 bytes for distance 34560 bytes for lkl0 27648 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.121537 0.061920 0.095600 0.136234 0.077867 0.192883 0.230141 0.108394 lnL0 = -2342.336110 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2342.336110 x= 0.12154 0.06192 0.09560 0.13623 0.07787 0.19288 0.23014 0.10839 1 h-lim-p 0.0014 0.0109 97.9626 2340.876409 8 0.0003 38 | 0/8 2 h-lim-p 0.0008 0.0064 20.1251 2340.793362 5 0.0004 61 | 0/8 3 h-lim-p 0.0011 0.0393 7.8335 2340.784862 6 0.0003 87 | 0/8 4 h-lim-p 0.0021 0.1934 1.1939 2340.784376 4 0.0007 109 | 0/8 5 h-lim-p 0.0027 1.2167 0.3177 2340.784348 1 0.0006 124 | 0/8 6 h-lim-p 0.0030 5.7775 0.0610 2340.784347 0 0.0007 145 | 0/8 7 h-lim-p 0.0023 18.8145 0.0175 2340.784346 0 0.0020 165 | 0/8 8 h-lim-p 0.0322 20.0000 0.0011 2340.784081 0 0.5147 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2340.784075 1 0.9961 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2340.784075 0 1.0938 231 | 0/8 11 h-lim-p 1.3231 20.0000 0.0000 2340.784075 0 2.6462 252 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2340.784075 0 0.4688 274 | 0/8 13 h-lim-p 0.0211 20.0000 0.0000 2340.784075 0 0.0211 294 | 0/8 14 h-lim-p 0.0079 20.0000 0.0000 2340.784075 0 0.0000 328 Out... lnL = -2340.784075 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2340.784075 Node 7: lnL = -2340.784075 Node 8: lnL = -2340.784075 Node 9: lnL = -2340.784075 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 856 Sequential format.. Reading seq # 1: YNL300W_Sbay Reading seq # 2: YNL300W_Scer Reading seq # 3: YNL300W_Skud Reading seq # 4: YNL300W_Smik Reading seq # 5: YNL300W_Spar Sequences read.. Counting patterns.. # site patterns = 335 Counting frequencies.. 120 bytes for distance 53600 bytes for lkl0 42880 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.131737 0.047659 0.069122 0.175079 0.101558 0.181649 0.240800 0.110956 lnL0 = -3853.572840 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3853.572840 x= 0.13174 0.04766 0.06912 0.17508 0.10156 0.18165 0.24080 0.11096 1 h-lim-p 0.0004 0.0031 187.9076 3850.668637 3 0.0002 29 | 0/8 2 h-lim-p 0.0004 0.0031 40.3697 3850.470327 6 0.0002 55 | 0/8 3 h-lim-p 0.0008 0.0346 12.5775 3850.451890 6 0.0003 81 | 0/8 4 h-lim-p 0.0043 0.4471 0.7407 3850.451768 2 0.0004 99 | 0/8 5 h-lim-p 0.0011 0.8155 0.3040 3850.451751 1 0.0004 121 | 0/8 6 h-lim-p 0.0024 2.8304 0.0523 3850.451751 0 0.0005 142 | 0/8 7 h-lim-p 0.0050 20.0000 0.0056 3850.451751 0 0.0044 162 | 0/8 8 h-lim-p 0.0188 20.0000 0.0013 3850.451661 0 0.1503 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3850.451658 0 1.0938 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3850.451657 0 1.0938 225 | 0/8 11 h-lim-p 1.5154 20.0000 0.0000 3850.451657 0 0.3315 246 | 0/8 12 h-lim-p 0.1803 20.0000 0.0000 3850.451657 0 0.0225 268 | 0/8 13 h-lim-p 0.0143 20.0000 0.0000 3850.451657 0 0.0000 306 | 0/8 14 h-lim-p 0.0000 20.0000 0.0009 | 0/8 15 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -3850.451657 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3850.451657 Node 7: lnL = -3850.451657 Node 8: lnL = -3850.451657 Node 9: lnL = -3850.451657 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 741 Sequential format.. Reading seq # 1: YNL304W_Sbay Reading seq # 2: YNL304W_Scer Reading seq # 3: YNL304W_Skud Reading seq # 4: YNL304W_Smik Reading seq # 5: YNL304W_Spar Sequences read.. Counting patterns.. # site patterns = 215 Counting frequencies.. 120 bytes for distance 34400 bytes for lkl0 27520 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.096984 0.074714 0.042536 0.101150 0.110448 0.191499 0.155817 0.080020 lnL0 = -2874.652435 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2874.652435 x= 0.09698 0.07471 0.04254 0.10115 0.11045 0.19150 0.15582 0.08002 1 h-lim-p 0.0002 0.0017 173.7409 2872.254833 8 0.0002 39 | 0/8 2 h-lim-p 0.0002 0.0019 67.1967 2871.778611 4 0.0002 59 | 0/8 3 h-lim-p 0.0011 0.0183 14.0642 2871.744040 6 0.0004 85 | 0/8 4 h-lim-p 0.0009 0.0386 5.6249 2871.739307 5 0.0003 108 | 0/8 5 h-lim-p 0.0009 0.1136 2.1563 2871.738763 4 0.0003 132 | 0/8 6 h-lim-p 0.0037 0.6465 0.1603 2871.738757 2 0.0003 151 | 0/8 7 h-lim-p 0.0026 17.2385 0.0183 2871.738695 0 0.0104 173 | 0/8 8 h-lim-p 0.0037 1.4671 0.0516 2871.733531 0 0.0295 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 2871.733512 1 1.0938 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2871.733512 0 1.0938 238 | 0/8 11 h-lim-p 1.2613 20.0000 0.0000 2871.733512 0 1.1036 258 | 0/8 12 h-lim-p 1.3420 20.0000 0.0000 2871.733512 0 5.3678 280 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2871.733512 0 0.2734 302 | 0/8 14 h-lim-p 2.4362 20.0000 0.0000 2871.733512 0 0.0095 329 | 0/8 15 h-lim-p 0.0010 20.0000 0.0000 2871.733512 0 0.0000 367 | 0/8 16 h-lim-p 0.0000 20.0000 0.0019 | 0/8 17 h-lim-p 0.0000 20.0000 0.0019 Out... lnL = -2871.733512 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2871.733512 Node 7: lnL = -2871.733512 Node 8: lnL = -2871.733512 Node 9: lnL = -2871.733512 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 603 Sequential format.. Reading seq # 1: YNL306W_Sbay Reading seq # 2: YNL306W_Scer Reading seq # 3: YNL306W_Skud Reading seq # 4: YNL306W_Smik Reading seq # 5: YNL306W_Spar Sequences read.. Counting patterns.. # site patterns = 185 Counting frequencies.. 120 bytes for distance 29600 bytes for lkl0 23680 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.117890 0.030235 0.048749 0.111470 0.071128 0.145553 0.171510 0.102293 lnL0 = -2540.073801 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2540.073801 x= 0.11789 0.03024 0.04875 0.11147 0.07113 0.14555 0.17151 0.10229 1 h-lim-p 0.0004 0.0033 253.3053 2536.448060 8 0.0001 41 | 0/8 2 h-lim-p 0.0004 0.0032 31.4361 2536.344673 6 0.0002 65 | 0/8 3 h-lim-p 0.0007 0.0385 9.7332 2536.334639 6 0.0002 92 | 0/8 4 h-lim-p 0.0011 0.1296 2.0033 2536.334017 4 0.0003 114 | 0/8 5 h-lim-p 0.0009 0.1808 0.6973 2536.333956 3 0.0003 135 | 0/8 6 h-lim-p 0.0010 1.2893 0.2021 2536.333949 1 0.0004 157 | 0/8 7 h-lim-p 0.0033 9.6197 0.0237 2536.333949 0 0.0007 178 | 0/8 8 h-lim-p 0.0438 20.0000 0.0004 2536.333674 0 1.0511 202 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2536.333668 1 0.9961 224 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2536.333668 0 1.0938 244 | 0/8 11 h-lim-p 1.1817 20.0000 0.0000 2536.333668 0 0.0003 275 Out... lnL = -2536.333668 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2536.333668 Node 7: lnL = -2536.333668 Node 8: lnL = -2536.333668 Node 9: lnL = -2536.333668 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 603 Sequential format.. Reading seq # 1: YNL307C_Sbay Reading seq # 2: YNL307C_Scer Reading seq # 3: YNL307C_Skud Reading seq # 4: YNL307C_Smik Reading seq # 5: YNL307C_Spar Sequences read.. Counting patterns.. # site patterns = 180 Counting frequencies.. 120 bytes for distance 28800 bytes for lkl0 23040 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.121120 0.027720 0.050256 0.112887 0.071913 0.141734 0.183066 0.105252 lnL0 = -2568.359714 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2568.359714 x= 0.12112 0.02772 0.05026 0.11289 0.07191 0.14173 0.18307 0.10525 1 h-lim-p 0.0006 0.0044 274.8336 2564.149535 4 0.0001 31 | 0/8 2 h-lim-p 0.0004 0.0031 34.3944 2564.019098 8 0.0002 61 | 0/8 3 h-lim-p 0.0007 0.0413 10.5353 2564.007246 5 0.0002 85 | 0/8 4 h-lim-p 0.0012 0.1249 2.1156 2564.006509 4 0.0003 108 | 0/8 5 h-lim-p 0.0009 0.1432 0.8166 2564.006427 3 0.0003 128 | 0/8 6 h-lim-p 0.0010 1.1793 0.2401 2564.006417 1 0.0004 150 | 0/8 7 h-lim-p 0.0065 13.9132 0.0143 2564.006417 0 0.0014 171 | 0/8 8 h-lim-p 0.0236 20.0000 0.0009 2564.006056 0 0.5662 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2564.006045 1 0.9961 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2564.006045 0 1.0938 237 | 0/8 11 h-lim-p 1.2118 20.0000 0.0000 2564.006045 0 0.0757 260 | 0/8 12 h-lim-p 0.0303 20.0000 0.0000 2564.006045 0 0.0000 300 Out... lnL = -2564.006045 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2564.006045 Node 7: lnL = -2564.006045 Node 8: lnL = -2564.006045 Node 9: lnL = -2564.006045 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 572 Sequential format.. Reading seq # 1: YNL308C_Sbay Reading seq # 2: YNL308C_Scer Reading seq # 3: YNL308C_Skud Reading seq # 4: YNL308C_Smik Reading seq # 5: YNL308C_Spar Sequences read.. Counting patterns.. # site patterns = 203 Counting frequencies.. 120 bytes for distance 32480 bytes for lkl0 25984 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.108378 0.031347 0.042170 0.106836 0.088647 0.157098 0.093577 0.094255 lnL0 = -2172.232010 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2172.232010 x= 0.10838 0.03135 0.04217 0.10684 0.08865 0.15710 0.09358 0.09426 1 h-lim-p 0.0007 0.0055 230.5816 2168.236610 7 0.0002 36 | 0/8 2 h-lim-p 0.0007 0.0056 52.3912 2167.759270 8 0.0004 65 | 0/8 3 h-lim-p 0.0008 0.0061 16.7056 2167.725320 6 0.0003 90 | 0/8 4 h-lim-p 0.0011 0.0201 4.0039 2167.722442 4 0.0004 113 | 0/8 5 h-lim-p 0.0013 0.1568 1.1821 2167.722230 2 0.0003 130 | 0/8 6 h-lim-p 0.0030 1.1297 0.1342 2167.722227 0 0.0003 144 | 0/8 7 h-lim-p 0.0016 7.9148 0.0272 2167.722226 0 0.0008 164 | 0/8 8 h-lim-p 0.0300 20.0000 0.0007 2167.721885 0 0.9589 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 2167.721840 2 0.9961 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2167.721840 0 1.0938 233 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2167.721840 0 0.1562 256 | 0/8 12 h-lim-p 0.0825 20.0000 0.0000 2167.721840 0 0.0001 284 Out... lnL = -2167.721840 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2167.721840 Node 7: lnL = -2167.721840 Node 8: lnL = -2167.721840 Node 9: lnL = -2167.721840 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 143 Sequential format.. Reading seq # 1: YNL310C_Sbay Reading seq # 2: YNL310C_Scer Reading seq # 3: YNL310C_Skud Reading seq # 4: YNL310C_Smik Reading seq # 5: YNL310C_Spar Sequences read.. Counting patterns.. # site patterns = 70 Counting frequencies.. 120 bytes for distance 11200 bytes for lkl0 8960 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.221957 0.218945 0.084405 0.000060 0.293745 0.292939 0.319099 0.205454 lnL0 = -544.034779 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 544.034779 x= 0.22196 0.21895 0.08441 0.00006 0.29374 0.29294 0.31910 0.20545 1 h-lim-p 0.0000 0.0000 75.9565 544.005596 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0106 22.4597 541.675167 0 0.0096 43 | 1/8 3 h-lim-p 0.0059 0.0472 8.2591 540.938241 0 0.0118 56 | 1/8 4 h-lim-p 0.0003 0.0022 3.7818 540.799626 m 0.0022 68 | 2/8 5 h-lim-p 0.0000 0.0012 318.8770 540.028136 0 0.0002 84 | 2/8 6 h-lim-p 0.0050 0.0400 7.9010 537.752551 0 0.0200 98 | 2/8 7 h-lim-p 0.0167 0.1333 4.6532 535.419333 0 0.0500 111 | 2/8 8 h-lim-p 0.1871 1.4972 0.3098 534.261136 0 0.3743 124 | 2/8 9 h-lim-p 0.3988 3.1907 0.1147 533.417224 0 0.7977 143 | 2/8 10 h-lim-p 0.4717 3.7735 0.0839 533.015933 0 0.9434 162 | 1/8 11 h-lim-p -0.0000 -0.0000 1.6135 h-lim-p: -1.86979709e-20 -1.49583767e-19 1.61349206e+00 533.015933 .. | 1/8 12 h-lim-p 0.0000 0.0301 8.6174 532.914010 0 0.0026 196 | 1/8 13 h-lim-p 0.0003 0.0028 3.2239 532.904684 0 0.0021 210 | 1/8 14 h-lim-p 0.0002 0.0019 2.1439 532.899942 m 0.0019 222 | 2/8 15 h-lim-p 0.0068 0.6784 0.5606 532.898300 5 0.0050 246 | 2/8 16 h-lim-p 0.0228 1.8120 0.1242 532.898271 3 0.0037 273 | 2/8 17 h-lim-p 0.0580 20.0000 0.0079 532.898222 0 0.1160 292 | 2/8 18 h-lim-p 0.0285 7.3909 0.0320 532.897901 0 0.0569 311 | 2/8 19 h-lim-p 2.5000 20.0000 0.0002 532.897894 2 0.9961 333 | 2/8 20 h-lim-p 2.5000 20.0000 0.0000 532.897894 0 1.0938 351 | 2/8 21 h-lim-p 2.5000 20.0000 0.0000 532.897894 0 2.1875 369 | 2/8 22 h-lim-p 2.3732 20.0000 0.0000 532.897894 0 0.5933 388 | 2/8 23 h-lim-p 0.6707 20.0000 0.0000 532.897894 0 0.1677 407 | 2/8 24 h-lim-p 0.0982 20.0000 0.0000 532.897894 0 0.0000 447 Out... lnL = -532.897894 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -532.897894 Node 7: lnL = -532.897894 Node 8: lnL = -532.897894 Node 9: lnL = -532.897894 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 168 Sequential format.. Reading seq # 1: YNL314W_Sbay Reading seq # 2: YNL314W_Scer Reading seq # 3: YNL314W_Skud Reading seq # 4: YNL314W_Smik Reading seq # 5: YNL314W_Spar Sequences read.. Counting patterns.. # site patterns = 58 Counting frequencies.. 120 bytes for distance 9280 bytes for lkl0 7424 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.090867 0.038645 0.036898 0.059704 0.044133 0.115513 0.163411 0.078487 lnL0 = -635.715732 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 635.715732 x= 0.09087 0.03864 0.03690 0.05970 0.04413 0.11551 0.16341 0.07849 1 h-lim-p 0.0011 0.0091 40.0663 635.406781 8 0.0004 41 | 0/8 2 h-lim-p 0.0010 0.0078 6.6275 635.394783 5 0.0006 65 | 0/8 3 h-lim-p 0.0016 0.0822 2.3145 635.392734 4 0.0008 86 | 0/8 4 h-lim-p 0.0012 0.0476 1.6644 635.392288 3 0.0005 104 | 0/8 5 h-lim-p 0.0017 0.6331 0.4631 635.392224 3 0.0007 122 | 0/8 6 h-lim-p 0.0034 0.9721 0.0916 635.392222 2 0.0005 148 | 0/8 7 h-lim-p 0.0066 20.0000 0.0076 635.392222 0 0.0029 168 | 0/8 8 h-lim-p 0.0488 20.0000 0.0004 635.392172 0 0.5861 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 635.392172 0 1.0938 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 635.392172 0 1.0938 231 | 0/8 11 h-lim-p 2.2248 20.0000 0.0000 635.392172 0 4.4497 252 | 0/8 12 h-lim-p 1.9018 20.0000 0.0000 635.392172 0 0.2080 274 | 0/8 13 h-lim-p 0.5868 20.0000 0.0000 635.392172 0 0.0092 299 | 0/8 14 h-lim-p 0.0119 20.0000 0.0000 635.392172 0 0.0000 336 Out... lnL = -635.392172 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -635.392172 Node 7: lnL = -635.392172 Node 8: lnL = -635.392172 Node 9: lnL = -635.392172 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 168 Sequential format.. Reading seq # 1: YNL315C_Sbay Reading seq # 2: YNL315C_Scer Reading seq # 3: YNL315C_Skud Reading seq # 4: YNL315C_Smik Reading seq # 5: YNL315C_Spar Sequences read.. Counting patterns.. # site patterns = 59 Counting frequencies.. 120 bytes for distance 9440 bytes for lkl0 7552 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.099922 0.035927 0.039226 0.059714 0.044123 0.113185 0.165353 0.087228 lnL0 = -641.196918 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 641.196918 x= 0.09992 0.03593 0.03923 0.05971 0.04412 0.11319 0.16535 0.08723 1 h-lim-p 0.0011 0.0085 43.4101 640.824517 6 0.0004 35 | 0/8 2 h-lim-p 0.0008 0.0065 7.6809 640.807130 7 0.0006 64 | 0/8 3 h-lim-p 0.0013 0.0578 3.4103 640.802441 4 0.0010 85 | 0/8 4 h-lim-p 0.0023 0.0456 1.3928 640.802071 2 0.0004 102 | 0/8 5 h-lim-p 0.0010 0.4363 0.6206 640.801968 3 0.0007 122 | 0/8 6 h-lim-p 0.0030 0.6012 0.1378 640.801963 2 0.0006 147 | 0/8 7 h-lim-p 0.0045 9.3442 0.0177 640.801962 1 0.0011 170 | 0/8 8 h-lim-p 0.0837 20.0000 0.0002 640.801915 0 1.3394 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 640.801911 1 0.9961 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 640.801911 0 2.1875 236 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 640.801911 0 0.0684 260 | 0/8 12 h-lim-p 0.0386 20.0000 0.0000 640.801911 0 0.0012 284 Out... lnL = -640.801911 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -640.801911 Node 7: lnL = -640.801911 Node 8: lnL = -640.801911 Node 9: lnL = -640.801911 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 321 Sequential format.. Reading seq # 1: YNL317W_Sbay Reading seq # 2: YNL317W_Scer Reading seq # 3: YNL317W_Skud Reading seq # 4: YNL317W_Smik Reading seq # 5: YNL317W_Spar Sequences read.. Counting patterns.. # site patterns = 139 Counting frequencies.. 120 bytes for distance 22240 bytes for lkl0 17792 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.113694 0.086162 0.065444 0.140398 0.071599 0.178584 0.166378 0.095214 lnL0 = -1345.255400 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1345.255400 x= 0.11369 0.08616 0.06544 0.14040 0.07160 0.17858 0.16638 0.09521 1 h-lim-p 0.0058 1.8649 68.0430 1344.310217 8 0.0004 45 | 0/8 2 h-lim-p 0.0015 0.0120 12.0224 1344.265554 6 0.0006 71 | 0/8 3 h-lim-p 0.0014 0.0571 5.3431 1344.255834 6 0.0008 97 | 0/8 4 h-lim-p 0.0100 0.4260 0.4281 1344.255758 3 0.0008 118 | 0/8 5 h-lim-p 0.0055 2.4605 0.0640 1344.255756 0 0.0012 139 | 0/8 6 h-lim-p 0.0080 18.7358 0.0096 1344.255756 0 0.0017 160 | 0/8 7 h-lim-p 0.0037 20.0000 0.0045 1344.255753 0 0.0148 182 | 0/8 8 h-lim-p 0.0059 20.0000 0.0114 1344.255677 0 0.0236 204 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1344.255675 0 1.0938 224 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1344.255675 0 1.0938 244 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1344.255675 0 0.3125 266 | 0/8 12 h-lim-p 0.1797 20.0000 0.0000 1344.255675 0 0.0000 310 Out... lnL = -1344.255675 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1344.255675 Node 7: lnL = -1344.255675 Node 8: lnL = -1344.255675 Node 9: lnL = -1344.255675 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 500 Sequential format.. Reading seq # 1: YNL322C_Sbay Reading seq # 2: YNL322C_Scer Reading seq # 3: YNL322C_Skud Reading seq # 4: YNL322C_Smik Reading seq # 5: YNL322C_Spar Sequences read.. Counting patterns.. # site patterns = 165 Counting frequencies.. 120 bytes for distance 26400 bytes for lkl0 21120 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.166050 0.062515 0.156581 0.012942 0.002465 0.185329 0.245575 0.145829 lnL0 = -2036.497744 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2036.497744 x= 0.16605 0.06251 0.15658 0.01294 0.00247 0.18533 0.24557 0.14583 1 h-lim-p 0.0000 0.0000 110.1425 2036.329709 0 0.0000 24 | 0/8 2 h-lim-p 0.0000 0.3149 327.0383 2035.159386 0 0.0001 39 | 0/8 3 h-lim-p 0.0000 0.0002 132.2678 2034.914000 0 0.0001 52 | 0/8 4 h-lim-p 0.0005 0.0179 14.5536 2034.844207 0 0.0010 65 | 0/8 5 h-lim-p 0.0033 0.0649 4.4418 2034.837283 2 0.0008 82 | 0/8 6 h-lim-p 0.0033 0.4485 1.0366 2034.836845 2 0.0008 99 | 0/8 7 h-lim-p 0.0143 4.0663 0.0565 2034.835775 0 0.0287 112 | 0/8 8 h-lim-p 0.0123 0.1813 0.1314 2034.793347 0 0.0493 134 | 0/8 9 h-lim-p 2.5000 20.0000 0.0018 2034.789181 3 1.0004 160 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 2034.789140 2 1.2305 185 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2034.789140 0 0.0781 209 | 0/8 12 h-lim-p 0.0847 20.0000 0.0000 2034.789140 0 0.0000 243 | 0/8 13 h-lim-p 0.0000 20.0000 0.0028 2034.789140 0 0.0000 271 | 0/8 14 h-lim-p 0.0000 20.0000 0.0008 2034.789140 0 0.0000 298 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 16 h-lim-p 0.0000 0.1709 0.3087 | 0/8 17 h-lim-p 0.0000 0.1709 0.3087 Out... lnL = -2034.789140 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2034.789140 Node 7: lnL = -2034.789140 Node 8: lnL = -2034.789140 Node 9: lnL = -2034.789140 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 418 Sequential format.. Reading seq # 1: YNL326C_Sbay Reading seq # 2: YNL326C_Scer Reading seq # 3: YNL326C_Skud Reading seq # 4: YNL326C_Smik Reading seq # 5: YNL326C_Spar Sequences read.. Counting patterns.. # site patterns = 178 Counting frequencies.. 120 bytes for distance 28480 bytes for lkl0 22784 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.142577 0.180190 0.267953 0.005225 0.007773 0.224533 0.267474 0.115866 lnL0 = -1800.272084 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1800.272084 x= 0.14258 0.18019 0.26795 0.00523 0.00777 0.22453 0.26747 0.11587 1 h-lim-p 0.0000 0.0003 36.6987 1800.202912 0 0.0001 24 | 0/8 2 h-lim-p 0.0001 1.8341 73.2081 1800.163985 6 0.0000 53 | 0/8 3 h-lim-p 0.0000 0.0016 68.6815 1799.927901 0 0.0003 68 | 0/8 4 h-lim-p 0.0028 0.0290 8.0704 1799.894491 6 0.0011 91 | 0/8 5 h-lim-p 0.0040 0.1320 2.2590 1799.891446 4 0.0013 113 | 0/8 6 h-lim-p 0.0126 1.3840 0.2307 1799.891382 3 0.0022 134 | 0/8 7 h-lim-p 0.0963 20.0000 0.0054 1799.890159 0 0.3853 156 | 0/8 8 h-lim-p 0.0056 1.0103 0.3662 1799.888070 3 0.0058 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1799.888013 3 0.9482 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1799.888012 0 1.0938 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1799.888012 0 0.0006 259 Out... lnL = -1799.888012 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1799.888012 Node 7: lnL = -1799.888012 Node 8: lnL = -1799.888012 Node 9: lnL = -1799.888012 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 846 Sequential format.. Reading seq # 1: YNL327W_Sbay Reading seq # 2: YNL327W_Scer Reading seq # 3: YNL327W_Skud Reading seq # 4: YNL327W_Smik Reading seq # 5: YNL327W_Spar Sequences read.. Counting patterns.. # site patterns = 197 Counting frequencies.. 120 bytes for distance 31520 bytes for lkl0 25216 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.169954 0.044874 0.154879 0.001473 0.001123 0.144576 0.181781 0.152264 lnL0 = -3146.569102 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3146.569102 x= 0.16995 0.04487 0.15488 0.00147 0.00112 0.14458 0.18178 0.15226 1 h-lim-p 0.0000 0.0000 419.1931 3146.001340 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0012 82.1994 3145.504955 0 0.0002 38 | 1/8 3 h-lim-p 0.0011 0.0141 13.8834 3145.472604 3 0.0003 58 | 1/8 4 h-lim-p 0.0020 0.0585 2.3936 3145.471560 4 0.0004 81 | 1/8 5 h-lim-p 0.0019 0.4956 0.4461 3145.471341 3 0.0010 100 | 1/8 6 h-lim-p 0.0067 4.8099 0.0684 3145.461517 0 0.0535 122 | 1/8 7 h-lim-p 0.0018 0.1099 1.9841 3145.429948 4 0.0016 148 | 1/8 8 h-lim-p 1.0993 20.0000 0.0029 3145.414136 1 1.3741 162 | 1/8 9 h-lim-p 2.5000 20.0000 0.0004 3145.413732 2 1.0938 185 | 1/8 10 h-lim-p 2.5000 20.0000 0.0000 3145.413732 0 0.0000 231 | 1/8 11 h-lim-p 0.0000 5.3681 2.6999 | 1/8 12 h-lim-p 0.0000 5.3681 2.6999 Out... lnL = -3145.413732 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3145.413732 Node 7: lnL = -3145.413732 Node 8: lnL = -3145.413732 Node 9: lnL = -3145.413732 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 884 Sequential format.. Reading seq # 1: YNL328C_Sbay Reading seq # 2: YNL328C_Scer Reading seq # 3: YNL328C_Skud Reading seq # 4: YNL328C_Smik Reading seq # 5: YNL328C_Spar Sequences read.. Counting patterns.. # site patterns = 202 Counting frequencies.. 120 bytes for distance 32320 bytes for lkl0 25856 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.156151 0.053242 0.162227 0.001935 0.000660 0.147310 0.160003 0.138882 lnL0 = -3206.470368 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3206.470368 x= 0.15615 0.05324 0.16223 0.00193 0.00066 0.14731 0.16000 0.13888 1 h-lim-p 0.0000 0.0000 392.5275 3206.193626 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0573 112.8655 3205.790383 0 0.0001 37 | 1/8 3 h-lim-p 0.0005 0.0149 18.6120 3205.732040 5 0.0004 61 | 1/8 4 h-lim-p 0.0045 0.1705 1.4859 3205.731674 4 0.0003 86 | 1/8 5 h-lim-p 0.0044 1.9597 0.1164 .. | 1/8 6 h-lim-p 0.0000 0.0000 65.7400 3205.722201 5 0.0000 151 | 1/8 7 h-lim-p 0.0000 5.3882 19.9033 3205.690422 0 0.0002 167 | 1/8 8 h-lim-p 0.0016 0.0746 2.6986 3205.689073 2 0.0004 184 | 1/8 9 h-lim-p 0.0026 0.5762 0.3891 3205.689046 2 0.0003 202 | 1/8 10 h-lim-p 0.0036 9.3003 0.0371 3205.689044 1 0.0009 224 | 1/8 11 h-lim-p 0.0061 20.0000 0.0054 3205.688826 0 0.0729 246 | 1/8 12 h-lim-p 0.0012 0.2044 0.3270 3205.687928 0 0.0024 266 | 1/8 13 h-lim-p 2.5000 20.0000 0.0001 3205.687895 1 1.0938 287 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 3205.687895 0 0.0000 328 | 1/8 15 h-lim-p 0.0000 9.4608 0.0317 .. | 1/8 16 h-lim-p 0.0000 1.4040 0.1810 | 1/8 17 h-lim-p 0.0000 1.4040 0.1810 Out... lnL = -3205.687895 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3205.687895 Node 7: lnL = -3205.687895 Node 8: lnL = -3205.687895 Node 9: lnL = -3205.687895 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 254 Sequential format.. Reading seq # 1: YNL330C_Sbay Reading seq # 2: YNL330C_Scer Reading seq # 3: YNL330C_Skud Reading seq # 4: YNL330C_Smik Reading seq # 5: YNL330C_Spar Sequences read.. Counting patterns.. # site patterns = 102 Counting frequencies.. 120 bytes for distance 16320 bytes for lkl0 13056 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.109944 0.109212 0.257278 0.003351 0.017958 0.172951 0.145774 0.089676 lnL0 = -1001.965292 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1001.965292 x= 0.10994 0.10921 0.25728 0.00335 0.01796 0.17295 0.14577 0.08968 1 h-lim-p 0.0000 0.0001 29.7357 1001.940096 0 0.0001 24 | 0/8 2 h-lim-p 0.0001 0.0004 24.8466 1001.909145 0 0.0002 38 | 0/8 3 h-lim-p 0.0003 0.0101 18.0228 1001.846358 0 0.0006 51 | 0/8 4 h-lim-p 0.0020 0.0527 5.2486 1001.834407 5 0.0010 74 | 0/8 5 h-lim-p 0.0038 0.1701 1.4440 1001.833249 4 0.0012 96 | 0/8 6 h-lim-p 0.0057 0.3086 0.3079 1001.833172 3 0.0015 115 | 0/8 7 h-lim-p 0.0071 1.9955 0.0664 1001.833144 3 0.0042 144 | 0/8 8 h-lim-p 0.0554 6.5150 0.0050 1001.829245 0 0.3324 166 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1001.829131 3 1.0004 192 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 .. | 0/8 11 h-lim-p 0.0000 20.0000 0.0627 | 0/8 12 h-lim-p 0.0000 20.0000 0.0627 Out... lnL = -1001.829131 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1001.829131 Node 7: lnL = -1001.829131 Node 8: lnL = -1001.829131 Node 9: lnL = -1001.829131 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 798 Sequential format.. Reading seq # 1: YNL331C_Sbay Reading seq # 2: YNL331C_Scer Reading seq # 3: YNL331C_Skud Reading seq # 4: YNL331C_Smik Reading seq # 5: YNL331C_Spar Sequences read.. Counting patterns.. # site patterns = 272 Counting frequencies.. 120 bytes for distance 43520 bytes for lkl0 34816 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.234374 0.215845 0.271358 0.000583 0.015612 0.194956 0.593669 0.197763 lnL0 = -3706.711415 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3706.711415 x= 0.23437 0.21585 0.27136 0.00058 0.01561 0.19496 0.59367 0.19776 1 h-lim-p 0.0001 0.0005 893.4627 3705.532735 7 0.0000 40 | 0/8 2 h-lim-p 0.0000 0.0001 174.4527 3705.112924 0 0.0000 53 | 0/8 3 h-lim-p 0.0002 0.0272 22.8499 3704.857363 0 0.0010 67 | 0/8 4 h-lim-p 0.0019 0.0234 12.2702 3704.807190 5 0.0008 92 | 0/8 5 h-lim-p 0.0030 0.1203 3.3929 3704.801217 4 0.0011 112 | 0/8 6 h-lim-p 0.0024 0.5109 1.6439 3704.798727 2 0.0022 128 | 0/8 7 h-lim-p 0.0161 1.9301 0.2260 3704.798570 2 0.0038 145 | 0/8 8 h-lim-p 0.4195 7.3656 0.0020 3704.786332 4 0.4435 173 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 3704.785597 2 2.1875 197 | 0/8 10 h-lim-p 1.7614 20.0000 0.0004 3704.785551 3 1.0329 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3704.785551 0 0.5469 247 | 0/8 12 h-lim-p 1.1953 20.0000 0.0000 3704.785551 0 0.0000 294 | 0/8 13 h-lim-p 0.0000 20.0000 0.0545 | 0/8 14 h-lim-p 0.0000 20.0000 0.0545 Out... lnL = -3704.785551 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3704.785551 Node 7: lnL = -3704.785551 Node 8: lnL = -3704.785551 Node 9: lnL = -3704.785551 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 213 Sequential format.. Reading seq # 1: YNR001C_Sbay Reading seq # 2: YNR001C_Scer Reading seq # 3: YNR001C_Skud Reading seq # 4: YNR001C_Smik Reading seq # 5: YNR001C_Spar Sequences read.. Counting patterns.. # site patterns = 84 Counting frequencies.. 120 bytes for distance 13440 bytes for lkl0 10752 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.163174 0.002708 0.055377 0.123853 0.050764 0.218628 0.183770 0.138734 lnL0 = -908.770070 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 908.770070 x= 0.16317 0.00271 0.05538 0.12385 0.05076 0.21863 0.18377 0.13873 1 h-lim-p 0.0009 0.0072 57.4410 908.321783 9 0.0003 46 | 0/8 2 h-lim-p 0.0005 0.0043 14.1361 908.263319 1 0.0007 60 | 0/8 3 h-lim-p 0.0015 0.0264 6.4512 908.253659 5 0.0006 82 | 0/8 4 h-lim-p 0.0013 0.0729 2.7290 908.250583 4 0.0010 102 | 0/8 5 h-lim-p 0.0056 0.3274 0.4865 908.250480 3 0.0009 123 | 0/8 6 h-lim-p 0.0128 6.2327 0.0343 908.250477 1 0.0026 146 | 0/8 7 h-lim-p 0.0094 20.0000 0.0094 908.250452 0 0.0374 168 | 0/8 8 h-lim-p 0.0117 4.1071 0.0299 908.250015 0 0.0235 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 908.250000 1 0.9961 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 908.250000 0 1.2500 231 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 908.250000 0 1.0938 251 | 0/8 12 h-lim-p 2.0979 20.0000 0.0000 908.250000 0 4.1959 272 | 0/8 13 h-lim-p 2.1185 20.0000 0.0000 908.250000 0 0.0662 296 | 0/8 14 h-lim-p 0.1782 20.0000 0.0000 908.250000 0 0.0028 321 Out... lnL = -908.250000 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -908.250000 Node 7: lnL = -908.250000 Node 8: lnL = -908.250000 Node 9: lnL = -908.250000 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 536 Sequential format.. Reading seq # 1: YNR002C_Sbay Reading seq # 2: YNR002C_Scer Reading seq # 3: YNR002C_Skud Reading seq # 4: YNR002C_Smik Reading seq # 5: YNR002C_Spar Sequences read.. Counting patterns.. # site patterns = 180 Counting frequencies.. 120 bytes for distance 28800 bytes for lkl0 23040 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.169169 0.056202 0.048842 0.103910 0.048773 0.190972 0.156670 0.144588 lnL0 = -2214.144184 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2214.144184 x= 0.16917 0.05620 0.04884 0.10391 0.04877 0.19097 0.15667 0.14459 1 h-lim-p 0.0009 0.0072 101.6685 2213.242718 3 0.0002 29 | 0/8 2 h-lim-p 0.0007 0.0058 19.1456 2213.201279 7 0.0002 57 | 0/8 3 h-lim-p 0.0005 0.0177 9.4028 2213.188767 6 0.0003 84 | 0/8 4 h-lim-p 0.0009 0.0542 3.4903 2213.186551 2 0.0004 100 | 0/8 5 h-lim-p 0.0032 0.3520 0.4765 2213.186515 1 0.0003 116 | 0/8 6 h-lim-p 0.0024 4.3033 0.0690 2213.186513 1 0.0006 139 | 0/8 7 h-lim-p 0.0338 20.0000 0.0012 2213.186513 0 0.0296 159 | 0/8 8 h-lim-p 0.0129 20.0000 0.0028 2213.186488 0 0.0387 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2213.186488 0 1.0938 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2213.186488 0 2.1875 220 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2213.186488 0 1.0938 240 | 0/8 12 h-lim-p 0.8671 20.0000 0.0000 2213.186488 0 3.4682 262 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2213.186488 0 0.0391 287 | 0/8 14 h-lim-p 0.1820 20.0000 0.0000 2213.186488 0 0.0000 323 Out... lnL = -2213.186488 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2213.186488 Node 7: lnL = -2213.186488 Node 8: lnL = -2213.186488 Node 9: lnL = -2213.186488 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 683 Sequential format.. Reading seq # 1: YNR003C_Sbay Reading seq # 2: YNR003C_Scer Reading seq # 3: YNR003C_Skud Reading seq # 4: YNR003C_Smik Reading seq # 5: YNR003C_Spar Sequences read.. Counting patterns.. # site patterns = 300 Counting frequencies.. 120 bytes for distance 48000 bytes for lkl0 38400 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.205261 0.000060 0.243307 0.123574 0.096915 0.356826 0.407588 0.163524 lnL0 = -3419.123907 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3419.123907 x= 0.20526 0.00006 0.24331 0.12357 0.09691 0.35683 0.40759 0.16352 1 h-lim-p 0.0005 0.0037 67.8941 3417.533224 0 0.0007 22 | 0/8 2 h-lim-p 0.0005 0.0037 78.8139 3416.985462 8 0.0003 56 | 0/8 3 h-lim-p 0.0014 0.0130 17.8416 3416.883799 6 0.0007 82 | 0/8 4 h-lim-p 0.0011 0.0383 11.7364 3416.839037 3 0.0009 100 | 0/8 5 h-lim-p 0.0012 0.0100 5.0231 3416.834543 5 0.0005 124 | 0/8 6 h-lim-p 0.0034 0.1210 0.6702 3416.834097 4 0.0018 145 | 0/8 7 h-lim-p 0.1428 20.0000 0.0084 3416.804325 0 0.8566 167 | 0/8 8 h-lim-p 0.0046 0.0419 1.5687 3416.802623 5 0.0012 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 3416.802445 2 0.9961 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3416.802445 0 1.0938 234 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3416.802445 0 1.0938 254 | 0/8 12 h-lim-p 1.1517 20.0000 0.0000 3416.802445 0 0.1440 276 | 0/8 13 h-lim-p 0.0329 20.0000 0.0000 3416.802445 0 0.0164 296 | 0/8 14 h-lim-p 0.0069 20.0000 0.0000 3416.802445 0 0.0000 322 | 0/8 15 h-lim-p 0.0026 20.0000 0.0000 3416.802445 0 0.0000 358 Out... lnL = -3416.802445 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3416.802445 Node 7: lnL = -3416.802445 Node 8: lnL = -3416.802445 Node 9: lnL = -3416.802445 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 866 Sequential format.. Reading seq # 1: YNR004W_Sbay Reading seq # 2: YNR004W_Scer Reading seq # 3: YNR004W_Skud Reading seq # 4: YNR004W_Smik Reading seq # 5: YNR004W_Spar Sequences read.. Counting patterns.. # site patterns = 315 Counting frequencies.. 120 bytes for distance 50400 bytes for lkl0 40320 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.159946 0.068540 0.146857 0.123168 0.087241 0.268763 0.438235 0.121444 lnL0 = -3760.178590 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3760.178590 x= 0.15995 0.06854 0.14686 0.12317 0.08724 0.26876 0.43824 0.12144 1 h-lim-p 0.0021 0.0164 111.2065 3757.921715 6 0.0004 35 | 0/8 2 h-lim-p 0.0005 0.0044 72.1105 3756.784130 5 0.0006 58 | 0/8 3 h-lim-p 0.0013 0.0100 29.6081 3756.625930 6 0.0004 83 | 0/8 4 h-lim-p 0.0009 0.0387 14.5751 3756.568914 4 0.0007 103 | 0/8 5 h-lim-p 0.0015 0.0449 6.8051 3756.553326 5 0.0009 129 | 0/8 6 h-lim-p 0.0018 0.1028 3.1931 3756.550847 5 0.0006 153 | 0/8 7 h-lim-p 0.6863 20.0000 0.0029 3756.540412 0 1.3726 166 | 0/8 8 h-lim-p 0.0174 0.9716 0.2297 3756.540387 1 0.0010 191 | 0/8 9 h-lim-p 0.8365 20.0000 0.0003 3756.540273 1 1.0456 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3756.540273 0 1.0938 233 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3756.540273 0 1.2500 253 | 0/8 12 h-lim-p 1.5518 20.0000 0.0000 3756.540273 0 0.3879 274 | 0/8 13 h-lim-p 0.1938 20.0000 0.0000 3756.540273 0 0.0061 298 | 0/8 14 h-lim-p 0.0037 20.0000 0.0000 3756.540273 0 0.0000 333 | 0/8 15 h-lim-p 0.0000 20.0000 0.0007 3756.540273 0 0.0000 365 | 0/8 16 h-lim-p 0.0000 20.0000 0.0030 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0007 | 0/8 18 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -3756.540273 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3756.540273 Node 7: lnL = -3756.540273 Node 8: lnL = -3756.540273 Node 9: lnL = -3756.540273 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 662 Sequential format.. Reading seq # 1: YNR006W_Sbay Reading seq # 2: YNR006W_Scer Reading seq # 3: YNR006W_Skud Reading seq # 4: YNR006W_Smik Reading seq # 5: YNR006W_Spar Sequences read.. Counting patterns.. # site patterns = 270 Counting frequencies.. 120 bytes for distance 43200 bytes for lkl0 34560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.217687 0.048957 0.059356 0.131865 0.109647 0.262851 0.255257 0.184192 lnL0 = -3101.761424 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3101.761424 x= 0.21769 0.04896 0.05936 0.13186 0.10965 0.26285 0.25526 0.18419 1 h-lim-p 0.0011 0.0090 86.7656 3100.875192 7 0.0002 35 | 0/8 2 h-lim-p 0.0012 0.0095 17.8849 3100.810593 5 0.0004 59 | 0/8 3 h-lim-p 0.0008 0.0368 8.9947 3100.794221 6 0.0005 86 | 0/8 4 h-lim-p 0.0010 0.0597 4.3324 3100.790569 2 0.0005 102 | 0/8 5 h-lim-p 0.0027 0.4367 0.7764 3100.790344 3 0.0008 122 | 0/8 6 h-lim-p 0.0047 1.3335 0.1331 3100.790340 1 0.0005 146 | 0/8 7 h-lim-p 0.0165 20.0000 0.0038 3100.790340 0 0.0018 168 | 0/8 8 h-lim-p 0.0433 20.0000 0.0002 3100.790333 0 0.6930 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3100.790333 0 1.0938 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3100.790333 0 1.0938 232 | 0/8 11 h-lim-p 1.9018 20.0000 0.0000 3100.790333 0 1.6640 252 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3100.790333 0 1.0938 272 | 0/8 13 h-lim-p 0.4499 20.0000 0.0000 3100.790333 0 0.0035 298 | 0/8 14 h-lim-p 0.0057 20.0000 0.0000 3100.790333 0 0.0004 321 Out... lnL = -3100.790333 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3100.790333 Node 7: lnL = -3100.790333 Node 8: lnL = -3100.790333 Node 9: lnL = -3100.790333 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 298 Sequential format.. Reading seq # 1: YNR007C_Sbay Reading seq # 2: YNR007C_Scer Reading seq # 3: YNR007C_Skud Reading seq # 4: YNR007C_Smik Reading seq # 5: YNR007C_Spar Sequences read.. Counting patterns.. # site patterns = 104 Counting frequencies.. 120 bytes for distance 16640 bytes for lkl0 13312 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.139476 0.019261 0.041484 0.063851 0.073428 0.134885 0.207616 0.118507 lnL0 = -1201.214835 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1201.214835 x= 0.13948 0.01926 0.04148 0.06385 0.07343 0.13489 0.20762 0.11851 1 h-lim-p 0.0017 0.0562 120.6311 1199.763258 9 0.0002 47 | 0/8 2 h-lim-p 0.0004 0.0035 22.2661 1199.611098 0 0.0007 59 | 0/8 3 h-lim-p 0.0008 0.0129 17.5514 1199.556656 7 0.0005 90 | 0/8 4 h-lim-p 0.0025 0.0309 3.6689 1199.553619 4 0.0005 111 | 0/8 5 h-lim-p 0.0009 0.0873 2.0621 1199.552774 5 0.0005 135 | 0/8 6 h-lim-p 0.0038 0.2934 0.2748 1199.552760 2 0.0004 153 | 0/8 7 h-lim-p 0.0029 8.3772 0.0354 1199.552757 2 0.0018 178 | 0/8 8 h-lim-p 0.0257 20.0000 0.0025 1199.551932 0 0.4108 202 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1199.551911 2 1.3159 227 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1199.551909 0 1.2500 247 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1199.551909 0 1.2500 267 | 0/8 12 h-lim-p 2.1401 20.0000 0.0000 1199.551909 0 0.9363 287 | 0/8 13 h-lim-p 0.6766 20.0000 0.0000 1199.551909 0 0.3383 307 | 0/8 14 h-lim-p 0.0465 20.0000 0.0000 1199.551909 0 0.0000 344 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1199.551909 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1199.551909 Node 7: lnL = -1199.551909 Node 8: lnL = -1199.551909 Node 9: lnL = -1199.551909 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 298 Sequential format.. Reading seq # 1: YNR008W_Sbay Reading seq # 2: YNR008W_Scer Reading seq # 3: YNR008W_Skud Reading seq # 4: YNR008W_Smik Reading seq # 5: YNR008W_Spar Sequences read.. Counting patterns.. # site patterns = 106 Counting frequencies.. 120 bytes for distance 16960 bytes for lkl0 13568 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.147195 0.006301 0.045007 0.062031 0.075248 0.133858 0.220478 0.125901 lnL0 = -1208.659924 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1208.659924 x= 0.14719 0.00630 0.04501 0.06203 0.07525 0.13386 0.22048 0.12590 1 h-lim-p 0.0010 0.6634 153.9013 1206.891400 8 0.0002 43 | 0/8 2 h-lim-p 0.0009 0.0070 18.7799 1206.732284 4 0.0009 63 | 0/8 3 h-lim-p 0.0012 0.0182 13.9875 1206.699910 4 0.0005 83 | 0/8 4 h-lim-p 0.0019 0.0526 3.3767 1206.696207 6 0.0007 109 | 0/8 5 h-lim-p 0.0019 0.2570 1.2546 1206.695982 4 0.0003 132 | 0/8 6 h-lim-p 0.0025 0.4669 0.1657 1206.695978 2 0.0003 150 | 0/8 7 h-lim-p 0.0134 20.0000 0.0041 1206.695975 0 0.0201 170 | 0/8 8 h-lim-p 0.0136 20.0000 0.0060 1206.695723 0 0.0814 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1206.695705 1 1.0938 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1206.695705 0 1.0938 234 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1206.695705 0 1.2500 254 | 0/8 12 h-lim-p 1.5676 20.0000 0.0000 1206.695705 0 0.0245 279 | 0/8 13 h-lim-p 0.0108 20.0000 0.0000 1206.695705 0 0.0054 299 | 0/8 14 h-lim-p 0.0033 20.0000 0.0000 1206.695705 0 0.0033 319 | 0/8 15 h-lim-p 0.0021 20.0000 0.0000 1206.695705 0 0.0011 339 | 0/8 16 h-lim-p 0.0008 20.0000 0.0000 1206.695705 0 0.0000 364 Out... lnL = -1206.695705 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1206.695705 Node 7: lnL = -1206.695705 Node 8: lnL = -1206.695705 Node 9: lnL = -1206.695705 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 328 Sequential format.. Reading seq # 1: YNR009W_Sbay Reading seq # 2: YNR009W_Scer Reading seq # 3: YNR009W_Skud Reading seq # 4: YNR009W_Smik Reading seq # 5: YNR009W_Spar Sequences read.. Counting patterns.. # site patterns = 87 Counting frequencies.. 120 bytes for distance 13920 bytes for lkl0 11136 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.079321 0.046315 0.000060 0.051200 0.044197 0.066094 0.067808 0.068098 lnL0 = -1038.229566 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1038.229566 x= 0.07932 0.04631 0.00006 0.05120 0.04420 0.06609 0.06781 0.06810 1 h-lim-p 0.0000 0.0193 914.8971 1033.170807 9 0.0000 44 | 0/8 2 h-lim-p 0.0004 0.0036 42.8930 1032.909320 6 0.0003 69 | 0/8 3 h-lim-p 0.0010 0.0080 11.8527 1032.895329 6 0.0002 93 | 0/8 4 h-lim-p 0.0010 0.0339 2.4372 1032.894743 3 0.0002 112 | 0/8 5 h-lim-p 0.0027 0.8651 0.1861 1032.894738 0 0.0003 126 | 0/8 6 h-lim-p 0.0035 6.9951 0.0158 1032.894738 0 0.0004 148 | 0/8 7 h-lim-p 0.0028 20.0000 0.0021 1032.894738 0 0.0028 168 | 0/8 8 h-lim-p 0.0118 20.0000 0.0005 1032.894645 0 0.2833 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1032.894637 1 1.0938 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1032.894637 0 1.2500 234 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1032.894637 0 0.2734 256 | 0/8 12 h-lim-p 0.1643 20.0000 0.0000 1032.894637 0 0.0013 282 | 0/8 13 h-lim-p 0.0007 20.0000 0.0000 1032.894637 0 0.0000 307 Out... lnL = -1032.894637 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1032.894637 Node 7: lnL = -1032.894637 Node 8: lnL = -1032.894637 Node 9: lnL = -1032.894637 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 347 Sequential format.. Reading seq # 1: YNR010W_Sbay Reading seq # 2: YNR010W_Scer Reading seq # 3: YNR010W_Skud Reading seq # 4: YNR010W_Smik Reading seq # 5: YNR010W_Spar Sequences read.. Counting patterns.. # site patterns = 155 Counting frequencies.. 120 bytes for distance 24800 bytes for lkl0 19840 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.104178 0.168303 0.130345 0.112405 0.037914 0.165084 0.158521 0.076290 lnL0 = -1478.482614 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1478.482614 x= 0.10418 0.16830 0.13035 0.11240 0.03791 0.16508 0.15852 0.07629 1 h-lim-p 0.0002 0.0017 40.9387 1478.090569 0 0.0004 23 | 0/8 2 h-lim-p 0.0005 0.0316 31.8454 1477.980799 7 0.0003 54 | 0/8 3 h-lim-p 0.0014 0.0314 7.1868 1477.964834 2 0.0007 70 | 0/8 4 h-lim-p 0.0016 0.0735 2.8881 1477.961711 5 0.0009 93 | 0/8 5 h-lim-p 0.0048 0.4431 0.5300 1477.961623 3 0.0006 113 | 0/8 6 h-lim-p 0.0035 4.4105 0.0961 1477.961595 3 0.0024 141 | 0/8 7 h-lim-p 0.0143 9.3751 0.0165 1477.959364 0 0.1143 164 | 0/8 8 h-lim-p 0.0025 0.1308 0.7465 1477.954656 0 0.0038 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1477.954623 2 0.9961 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1477.954623 0 1.0938 228 | 0/8 11 h-lim-p 1.8555 20.0000 0.0000 1477.954623 0 0.8118 248 | 0/8 12 h-lim-p 0.5462 20.0000 0.0000 1477.954623 0 0.0683 270 | 0/8 13 h-lim-p 0.0159 20.0000 0.0000 1477.954623 0 0.0159 290 | 0/8 14 h-lim-p 0.0084 20.0000 0.0000 1477.954623 0 0.0042 310 | 0/8 15 h-lim-p 0.0015 20.0000 0.0001 1477.954623 0 0.0015 330 | 0/8 16 h-lim-p 0.0026 20.0000 0.0001 1477.954623 0 0.0000 364 | 0/8 17 h-lim-p 0.0005 20.0000 0.0000 1477.954623 0 0.0000 396 Out... lnL = -1477.954623 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1477.954623 Node 7: lnL = -1477.954623 Node 8: lnL = -1477.954623 Node 9: lnL = -1477.954623 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 831 Sequential format.. Reading seq # 1: YNR014W_Sbay Reading seq # 2: YNR014W_Scer Reading seq # 3: YNR014W_Skud Reading seq # 4: YNR014W_Smik Reading seq # 5: YNR014W_Spar Sequences read.. Counting patterns.. # site patterns = 280 Counting frequencies.. 120 bytes for distance 44800 bytes for lkl0 35840 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.238513 0.000060 0.205944 0.096876 0.120335 1.002560 0.309891 0.185467 lnL0 = -3407.537438 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3407.537438 x= 0.23851 0.00006 0.20594 0.09688 0.12034 1.00256 0.30989 0.18547 1 h-lim-p 0.0000 0.0000 218.7504 3407.478535 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0045 153.2394 3404.857452 0 0.0003 39 | 1/8 3 h-lim-p 0.0012 0.0123 39.8913 3404.044620 2 0.0012 55 | 1/8 4 h-lim-p 0.0024 0.0306 18.8375 3403.652418 4 0.0024 75 | 1/8 5 h-lim-p 0.0014 0.0216 32.8366 3402.909870 0 0.0028 88 | 1/8 6 h-lim-p 0.0013 0.0183 68.4364 3401.599577 0 0.0027 101 | 1/8 7 h-lim-p 0.1323 1.0580 0.1444 3393.694527 0 0.5290 115 | 0/8 8 h-lim-p 0.0066 0.0531 3.6670 3393.689275 4 0.0008 144 | 0/8 9 h-lim-p 0.0865 9.2770 0.0358 3393.233486 0 0.6920 159 | 0/8 10 h-lim-p 1.4866 13.3629 0.0167 3393.144012 1 1.8583 181 | 0/8 11 h-lim-p 0.9259 7.4071 0.0273 3392.922387 0 3.7035 203 | 0/8 12 h-lim-p 0.9890 7.9122 0.0217 3392.899586 4 1.0296 231 | 0/8 13 h-lim-p 2.2466 20.0000 0.0099 3392.897301 4 1.1792 260 | 0/8 14 h-lim-p 2.5000 20.0000 0.0020 3392.897175 3 0.9482 286 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 3392.897174 0 1.0938 306 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 3392.897174 0 1.0938 326 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 3392.897174 0 1.0938 346 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 3392.897174 0 0.0342 371 | 0/8 19 h-lim-p 0.0355 20.0000 0.0000 3392.897174 0 0.0000 412 Out... lnL = -3392.897174 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3392.897174 Node 7: lnL = -3392.897174 Node 8: lnL = -3392.897174 Node 9: lnL = -3392.897174 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 368 Sequential format.. Reading seq # 1: YNR015W_Sbay Reading seq # 2: YNR015W_Scer Reading seq # 3: YNR015W_Skud Reading seq # 4: YNR015W_Smik Reading seq # 5: YNR015W_Spar Sequences read.. Counting patterns.. # site patterns = 150 Counting frequencies.. 120 bytes for distance 24000 bytes for lkl0 19200 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.095921 0.052921 0.095530 0.060276 0.092594 0.159509 0.307027 0.063869 lnL0 = -1384.366320 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1384.366320 x= 0.09592 0.05292 0.09553 0.06028 0.09259 0.15951 0.30703 0.06387 1 h-lim-p 0.0052 0.0967 73.2517 1383.331848 5 0.0004 36 | 0/8 2 h-lim-p 0.0007 0.0053 28.1877 1383.120543 3 0.0006 54 | 0/8 3 h-lim-p 0.0028 0.0448 5.9935 1383.099276 3 0.0013 72 | 0/8 4 h-lim-p 0.0028 0.0845 2.6799 1383.096184 5 0.0010 96 | 0/8 5 h-lim-p 0.0029 0.1659 0.9631 1383.095826 4 0.0009 119 | 0/8 6 h-lim-p 0.0030 1.0113 0.2828 1383.095809 2 0.0005 146 | 0/8 7 h-lim-p 0.0020 1.1290 0.0693 1383.095805 2 0.0013 172 | 0/8 8 h-lim-p 0.1624 20.0000 0.0006 1383.095454 0 1.2995 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1383.095442 1 0.9961 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1383.095442 0 1.0938 237 | 0/8 11 h-lim-p 1.2539 20.0000 0.0000 1383.095442 0 0.3135 258 | 0/8 12 h-lim-p 0.0805 20.0000 0.0000 1383.095442 0 0.0002 286 | 0/8 13 h-lim-p 0.0002 20.0000 0.0000 1383.095442 0 0.0000 317 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 1383.095442 0 0.0000 337 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 1383.095442 0 0.0000 358 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 1383.095442 0 0.0000 385 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 1383.095442 0 0.0000 410 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1383.095442 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1383.095442 Node 7: lnL = -1383.095442 Node 8: lnL = -1383.095442 Node 9: lnL = -1383.095442 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 851 Sequential format.. Reading seq # 1: YNR017W_Sbay Reading seq # 2: YNR017W_Scer Reading seq # 3: YNR017W_Skud Reading seq # 4: YNR017W_Smik Reading seq # 5: YNR017W_Spar Sequences read.. Counting patterns.. # site patterns = 217 Counting frequencies.. 120 bytes for distance 34720 bytes for lkl0 27776 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.284014 0.000060 0.043090 0.140985 0.055080 0.078889 0.188867 0.254907 lnL0 = -3151.643879 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3151.643879 x= 0.28401 0.00006 0.04309 0.14098 0.05508 0.07889 0.18887 0.25491 1 h-lim-p 0.0000 0.0000 372.2353 3151.541359 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0003 315.1428 3148.201089 0 0.0001 37 | 1/8 3 h-lim-p 0.0002 0.0018 135.1673 3147.279274 8 0.0001 67 | 1/8 4 h-lim-p 0.0011 0.0249 17.6259 3147.187494 7 0.0006 96 | 1/8 5 h-lim-p 0.0005 0.0089 18.7806 3147.149848 6 0.0003 123 | 1/8 6 h-lim-p 0.0009 0.0437 6.2824 3147.120523 3 0.0008 141 | 1/8 7 h-lim-p 0.0187 0.7221 0.2682 3136.144540 0 0.2249 156 | 0/8 8 h-lim-p 0.0011 0.0091 40.1618 3136.074620 7 0.0001 193 | 0/8 9 h-lim-p 0.2458 20.0000 0.0168 3135.357326 0 0.9831 207 | 0/8 10 h-lim-p 0.5045 4.0359 0.0062 3135.210355 0 1.0090 228 | 0/8 11 h-lim-p 0.8537 6.8298 0.0026 3135.200322 3 0.8471 254 | 0/8 12 h-lim-p 2.5000 20.0000 0.0007 3135.199723 4 0.9131 283 | 0/8 13 h-lim-p 2.5000 20.0000 0.0001 3135.199714 1 1.0938 305 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 3135.199714 0 1.0938 325 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 3135.199714 0 2.1875 345 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 3135.199714 0 0.2734 367 | 0/8 17 h-lim-p 0.1699 20.0000 0.0000 3135.199714 0 0.0027 392 Out... lnL = -3135.199714 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3135.199714 Node 7: lnL = -3135.199714 Node 8: lnL = -3135.199714 Node 9: lnL = -3135.199714 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 743 Sequential format.. Reading seq # 1: YNR018W_Sbay Reading seq # 2: YNR018W_Scer Reading seq # 3: YNR018W_Skud Reading seq # 4: YNR018W_Smik Reading seq # 5: YNR018W_Spar Sequences read.. Counting patterns.. # site patterns = 193 Counting frequencies.. 120 bytes for distance 30880 bytes for lkl0 24704 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.173907 0.040643 0.031877 0.048109 0.053168 0.121436 0.140817 0.148483 lnL0 = -2785.525199 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2785.525199 x= 0.17391 0.04064 0.03188 0.04811 0.05317 0.12144 0.14082 0.14848 1 h-lim-p 0.0009 0.5637 244.2239 2782.786404 5 0.0001 33 | 0/8 2 h-lim-p 0.0002 0.0018 56.5685 2782.491167 6 0.0002 56 | 0/8 3 h-lim-p 0.0003 0.0048 36.3077 2782.410928 7 0.0002 83 | 0/8 4 h-lim-p 0.0003 0.0097 17.7961 2782.380679 5 0.0003 105 | 0/8 5 h-lim-p 0.0019 0.0441 2.3220 2782.380275 4 0.0002 129 | 0/8 6 h-lim-p 0.0014 0.5210 0.2516 2782.380266 1 0.0003 144 | 0/8 7 h-lim-p 0.0026 10.1935 0.0270 2782.380265 0 0.0012 164 | 0/8 8 h-lim-p 0.0284 20.0000 0.0011 2782.379542 0 0.4544 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2782.379529 1 1.0938 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2782.379529 0 1.0938 230 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2782.379529 0 0.0003 262 Out... lnL = -2782.379529 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2782.379529 Node 7: lnL = -2782.379529 Node 8: lnL = -2782.379529 Node 9: lnL = -2782.379529 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 427 Sequential format.. Reading seq # 1: YNR019W_Sbay Reading seq # 2: YNR019W_Scer Reading seq # 3: YNR019W_Skud Reading seq # 4: YNR019W_Smik Reading seq # 5: YNR019W_Spar Sequences read.. Counting patterns.. # site patterns = 149 Counting frequencies.. 120 bytes for distance 23840 bytes for lkl0 19072 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.156098 0.013908 0.046276 0.084735 0.048508 0.120441 0.107111 0.132436 lnL0 = -1587.184901 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1587.184901 x= 0.15610 0.01391 0.04628 0.08473 0.04851 0.12044 0.10711 0.13244 1 h-lim-p 0.0020 1.1379 126.7332 1585.796315 5 0.0002 34 | 0/8 2 h-lim-p 0.0004 0.0035 43.7355 1585.370852 6 0.0005 60 | 0/8 3 h-lim-p 0.0013 0.0107 8.3822 1585.361256 5 0.0003 82 | 0/8 4 h-lim-p 0.0005 0.0287 5.0168 1585.357613 4 0.0004 102 | 0/8 5 h-lim-p 0.0011 0.0640 1.7002 1585.357232 4 0.0003 124 | 0/8 6 h-lim-p 0.0033 0.4480 0.1637 1585.357228 1 0.0003 140 | 0/8 7 h-lim-p 0.0010 1.3481 0.0524 1585.357227 1 0.0005 163 | 0/8 8 h-lim-p 0.1264 20.0000 0.0002 1585.357104 0 1.0113 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1585.357101 0 1.0938 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1585.357101 0 1.0938 226 | 0/8 11 h-lim-p 2.4801 20.0000 0.0000 1585.357101 0 1.0851 246 | 0/8 12 h-lim-p 1.2153 20.0000 0.0000 1585.357101 0 9.7226 269 | 0/8 13 h-lim-p 1.5631 20.0000 0.0000 1585.357101 0 0.3908 290 | 0/8 14 h-lim-p 1.1868 20.0000 0.0000 1585.357101 0 0.0000 341 Out... lnL = -1585.357101 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1585.357101 Node 7: lnL = -1585.357101 Node 8: lnL = -1585.357101 Node 9: lnL = -1585.357101 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 322 Sequential format.. Reading seq # 1: YNR020C_Sbay Reading seq # 2: YNR020C_Scer Reading seq # 3: YNR020C_Skud Reading seq # 4: YNR020C_Smik Reading seq # 5: YNR020C_Spar Sequences read.. Counting patterns.. # site patterns = 107 Counting frequencies.. 120 bytes for distance 17120 bytes for lkl0 13696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.228154 0.000060 0.124049 0.160369 0.130948 4.552490 0.306969 0.108182 lnL0 = -1010.350278 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1010.350278 x= 0.22815 0.00006 0.12405 0.16037 0.13095 4.55249 0.30697 0.10818 1 h-lim-p 0.0003 0.0025 75.7384 1005.650794 0 0.0013 24 | 0/8 2 h-lim-p 0.0022 0.0178 24.8923 1005.440150 7 0.0008 52 | 0/8 3 h-lim-p 0.0122 0.1753 1.5903 1005.435294 5 0.0035 78 | 0/8 4 h-lim-p 0.0043 0.1958 1.3076 1005.433605 5 0.0023 101 | 0/8 5 h-lim-p 0.0021 0.1513 1.4334 1005.391620 0 0.0672 118 | 0/8 6 h-lim-p 0.0007 0.0054 21.1604 1005.360235 0 0.0027 132 | 0/8 7 h-lim-p 2.5000 20.0000 0.0031 1005.358922 4 0.9644 152 | 0/8 8 h-lim-p 2.5000 20.0000 0.0001 1005.358921 1 0.9961 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1005.358921 0 1.0938 194 | 0/8 10 h-lim-p 1.7479 20.0000 0.0000 1005.358921 0 0.7647 214 | 0/8 11 h-lim-p 0.3845 20.0000 0.0000 1005.358921 0 0.0060 239 | 0/8 12 h-lim-p 0.0015 20.0000 0.0001 1005.358921 0 0.0008 259 | 0/8 13 h-lim-p 0.0004 20.0000 0.0001 1005.358921 0 0.0000 299 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 1005.358921 0 0.0000 326 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 1005.358921 0 0.0000 389 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1005.358921 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1005.358921 Node 7: lnL = -1005.358921 Node 8: lnL = -1005.358921 Node 9: lnL = -1005.358921 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 179 Sequential format.. Reading seq # 1: YNR032C-A_Sbay Reading seq # 2: YNR032C-A_Scer Reading seq # 3: YNR032C-A_Skud Reading seq # 4: YNR032C-A_Smik Reading seq # 5: YNR032C-A_Spar Sequences read.. Counting patterns.. # site patterns = 68 Counting frequencies.. 120 bytes for distance 10880 bytes for lkl0 8704 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.135744 0.051732 0.029236 0.068449 0.081726 0.130225 0.147569 0.110295 lnL0 = -712.344656 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 712.344656 x= 0.13574 0.05173 0.02924 0.06845 0.08173 0.13023 0.14757 0.11030 1 h-lim-p 0.0015 0.0124 84.5804 711.388547 3 0.0003 29 | 0/8 2 h-lim-p 0.0012 0.0093 16.8557 711.231727 2 0.0011 45 | 0/8 3 h-lim-p 0.0075 0.1144 2.4647 711.229383 4 0.0008 69 | 0/8 4 h-lim-p 0.0048 0.2434 0.4067 711.229324 4 0.0007 94 | 0/8 5 h-lim-p 0.0025 1.6936 0.1233 711.229317 1 0.0010 116 | 0/8 6 h-lim-p 0.0049 5.2861 0.0247 711.229316 1 0.0012 139 | 0/8 7 h-lim-p 0.0019 14.0450 0.0160 711.229312 0 0.0056 160 | 0/8 8 h-lim-p 0.0149 12.9652 0.0060 711.228953 0 0.1193 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 711.228927 2 1.0889 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 711.228927 0 1.0938 227 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 711.228927 0 0.0012 257 Out... lnL = -711.228927 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -711.228927 Node 7: lnL = -711.228927 Node 8: lnL = -711.228927 Node 9: lnL = -711.228927 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 836 Sequential format.. Reading seq # 1: YNR034W-A_Sbay Reading seq # 2: YNR034W-A_Scer Reading seq # 3: YNR034W-A_Skud Reading seq # 4: YNR034W-A_Smik Reading seq # 5: YNR034W-A_Spar Sequences read.. Counting patterns.. # site patterns = 209 Counting frequencies.. 120 bytes for distance 33440 bytes for lkl0 26752 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.242127 0.030898 0.060491 0.051137 0.040912 0.102795 0.153508 0.212066 lnL0 = -3343.567708 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3343.567708 x= 0.24213 0.03090 0.06049 0.05114 0.04091 0.10280 0.15351 0.21207 1 h-lim-p 0.0001 0.0005 181.9388 3341.860505 0 0.0001 23 | 0/8 2 h-lim-p 0.0005 0.0080 49.5261 3341.750502 4 0.0001 44 | 0/8 3 h-lim-p 0.0001 0.0044 39.3965 3341.654528 0 0.0002 56 | 0/8 4 h-lim-p 0.0004 0.0085 19.9595 3341.626754 5 0.0002 79 | 0/8 5 h-lim-p 0.0009 0.0328 4.3164 3341.625526 5 0.0001 105 | 0/8 6 h-lim-p 0.0005 0.1110 1.2162 3341.625355 0 0.0003 117 | 0/8 7 h-lim-p 0.0008 0.5239 0.3619 3341.625251 2 0.0010 134 | 0/8 8 h-lim-p 0.0521 10.1168 0.0066 3341.572005 0 0.6248 157 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3341.571939 2 0.9644 181 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3341.571939 0 1.0938 201 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3341.571939 0 3.7500 221 | 0/8 12 h-lim-p 2.1942 20.0000 0.0000 3341.571939 0 0.2400 243 | 0/8 13 h-lim-p 1.0726 20.0000 0.0000 3341.571939 0 0.0005 273 Out... lnL = -3341.571939 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3341.571939 Node 7: lnL = -3341.571939 Node 8: lnL = -3341.571939 Node 9: lnL = -3341.571939 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 344 Sequential format.. Reading seq # 1: YNR035C_Sbay Reading seq # 2: YNR035C_Scer Reading seq # 3: YNR035C_Skud Reading seq # 4: YNR035C_Smik Reading seq # 5: YNR035C_Spar Sequences read.. Counting patterns.. # site patterns = 148 Counting frequencies.. 120 bytes for distance 23680 bytes for lkl0 18944 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.123044 0.067464 0.074474 0.094562 0.080918 0.189463 0.154136 0.092723 lnL0 = -1360.685815 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1360.685815 x= 0.12304 0.06746 0.07447 0.09456 0.08092 0.18946 0.15414 0.09272 1 h-lim-p 0.0062 0.0539 66.1395 1359.810196 9 0.0004 47 | 0/8 2 h-lim-p 0.0024 0.0190 10.6825 1359.769030 7 0.0007 76 | 0/8 3 h-lim-p 0.0013 0.0322 6.0849 1359.762044 5 0.0005 99 | 0/8 4 h-lim-p 0.0024 0.2396 1.2204 1359.761410 4 0.0009 119 | 0/8 5 h-lim-p 0.0078 1.8324 0.1417 1359.761402 1 0.0008 135 | 0/8 6 h-lim-p 0.0043 9.6581 0.0254 1359.761402 0 0.0009 156 | 0/8 7 h-lim-p 0.0036 20.0000 0.0067 1359.761402 0 0.0031 176 | 0/8 8 h-lim-p 0.0332 20.0000 0.0006 1359.761355 0 0.3979 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1359.761354 0 1.0938 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1359.761354 0 1.0938 239 | 0/8 11 h-lim-p 2.3678 20.0000 0.0000 1359.761354 0 2.0719 259 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1359.761354 0 0.0000 299 Out... lnL = -1359.761354 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1359.761354 Node 7: lnL = -1359.761354 Node 8: lnL = -1359.761354 Node 9: lnL = -1359.761354 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 303 Sequential format.. Reading seq # 1: YNR036C_Sbay Reading seq # 2: YNR036C_Scer Reading seq # 3: YNR036C_Skud Reading seq # 4: YNR036C_Smik Reading seq # 5: YNR036C_Spar Sequences read.. Counting patterns.. # site patterns = 140 Counting frequencies.. 120 bytes for distance 22400 bytes for lkl0 17920 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.150857 0.099089 0.030363 0.135433 0.141332 0.191443 0.132632 0.116858 lnL0 = -1261.429282 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1261.429282 x= 0.15086 0.09909 0.03036 0.13543 0.14133 0.19144 0.13263 0.11686 1 h-lim-p 0.0213 0.1701 33.9986 1261.175723 8 0.0005 46 | 0/8 2 h-lim-p 0.0011 0.0086 8.8394 1261.146867 6 0.0008 74 | 0/8 3 h-lim-p 0.0054 0.1449 1.2798 1261.146201 4 0.0008 99 | 0/8 4 h-lim-p 0.0040 0.6898 0.2656 1261.146162 3 0.0011 118 | 0/8 5 h-lim-p 0.0164 16.8741 0.0176 1261.146162 0 0.0018 140 | 0/8 6 h-lim-p 0.0126 20.0000 0.0025 1261.146162 0 0.0110 160 | 0/8 7 h-lim-p 0.0085 20.0000 0.0032 1261.146153 0 0.0340 182 | 0/8 8 h-lim-p 0.0020 1.4251 0.0548 1261.146137 0 0.0030 202 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1261.146137 0 1.0938 222 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1261.146137 0 1.0938 242 | 0/8 11 h-lim-p 1.5401 20.0000 0.0000 1261.146137 0 0.0060 269 | 0/8 12 h-lim-p 0.0024 20.0000 0.0000 1261.146137 0 0.0000 294 Out... lnL = -1261.146137 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1261.146137 Node 7: lnL = -1261.146137 Node 8: lnL = -1261.146137 Node 9: lnL = -1261.146137 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 281 Sequential format.. Reading seq # 1: YNR037C_Sbay Reading seq # 2: YNR037C_Scer Reading seq # 3: YNR037C_Skud Reading seq # 4: YNR037C_Smik Reading seq # 5: YNR037C_Spar Sequences read.. Counting patterns.. # site patterns = 118 Counting frequencies.. 120 bytes for distance 18880 bytes for lkl0 15104 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.155517 0.012686 0.061845 0.123405 0.063472 0.159394 0.205190 0.125313 lnL0 = -1218.126110 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1218.126110 x= 0.15552 0.01269 0.06184 0.12340 0.06347 0.15939 0.20519 0.12531 1 h-lim-p 0.0002 0.0017 144.3287 1215.701164 0 0.0004 23 | 0/8 2 h-lim-p 0.0003 0.0024 34.8476 1215.431637 0 0.0006 36 | 0/8 3 h-lim-p 0.0007 0.0117 28.7514 1215.312418 7 0.0004 68 | 0/8 4 h-lim-p 0.0017 0.0319 7.4194 1215.291863 4 0.0008 88 | 0/8 5 h-lim-p 0.0023 0.0448 2.6905 1215.289374 5 0.0008 112 | 0/8 6 h-lim-p 0.0035 0.7812 0.5797 1215.288876 2 0.0016 128 | 0/8 7 h-lim-p 0.0287 5.2089 0.0331 1215.164162 0 0.4598 152 | 0/8 8 h-lim-p 0.0015 0.0117 7.7856 1215.050585 1 0.0018 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0034 1215.042651 3 1.0449 192 | 0/8 10 h-lim-p 2.5000 20.0000 0.0003 1215.042564 2 1.0938 216 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1215.042564 0 1.0938 236 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1215.042564 0 1.0938 256 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1215.042564 0 2.1875 276 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1215.042564 0 0.5469 297 | 0/8 15 h-lim-p 0.2066 20.0000 0.0000 1215.042564 0 0.0056 321 | 0/8 16 h-lim-p 0.0029 20.0000 0.0000 1215.042564 0 0.0029 341 | 0/8 17 h-lim-p 0.0016 20.0000 0.0000 1215.042564 0 0.0000 376 Out... lnL = -1215.042564 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1215.042564 Node 7: lnL = -1215.042564 Node 8: lnL = -1215.042564 Node 9: lnL = -1215.042564 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 281 Sequential format.. Reading seq # 1: YNR038W_Sbay Reading seq # 2: YNR038W_Scer Reading seq # 3: YNR038W_Skud Reading seq # 4: YNR038W_Smik Reading seq # 5: YNR038W_Spar Sequences read.. Counting patterns.. # site patterns = 116 Counting frequencies.. 120 bytes for distance 18560 bytes for lkl0 14848 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.164228 0.029021 0.062716 0.124658 0.062219 0.158524 0.188565 0.133227 lnL0 = -1219.450329 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1219.450329 x= 0.16423 0.02902 0.06272 0.12466 0.06222 0.15852 0.18856 0.13323 1 h-lim-p 0.0002 0.0015 89.9515 1217.853459 0 0.0004 23 | 0/8 2 h-lim-p 0.0008 0.0062 24.9812 1217.667022 3 0.0006 41 | 0/8 3 h-lim-p 0.0011 0.0241 14.4644 1217.638708 7 0.0004 70 | 0/8 4 h-lim-p 0.0011 0.0489 4.7611 1217.631259 6 0.0008 96 | 0/8 5 h-lim-p 0.0027 0.0774 1.3233 1217.630729 2 0.0006 113 | 0/8 6 h-lim-p 0.0023 0.9508 0.3699 1217.630661 2 0.0009 129 | 0/8 7 h-lim-p 0.0175 11.2504 0.0193 1217.629669 0 0.0699 151 | 0/8 8 h-lim-p 0.0050 0.6905 0.2679 1217.616184 0 0.0151 172 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1217.616151 2 0.9961 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1217.616151 0 1.0938 216 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1217.616151 0 0.5469 237 | 0/8 12 h-lim-p 0.3566 20.0000 0.0000 1217.616151 0 0.0446 259 | 0/8 13 h-lim-p 0.0244 20.0000 0.0000 1217.616151 0 0.0031 281 | 0/8 14 h-lim-p 0.0021 20.0000 0.0000 1217.616151 0 0.0009 301 | 0/8 15 h-lim-p 0.0008 20.0000 0.0000 1217.616151 0 0.0000 333 Out... lnL = -1217.616151 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1217.616151 Node 7: lnL = -1217.616151 Node 8: lnL = -1217.616151 Node 9: lnL = -1217.616151 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 265 Sequential format.. Reading seq # 1: YNR039C_Sbay Reading seq # 2: YNR039C_Scer Reading seq # 3: YNR039C_Skud Reading seq # 4: YNR039C_Smik Reading seq # 5: YNR039C_Spar Sequences read.. Counting patterns.. # site patterns = 110 Counting frequencies.. 120 bytes for distance 17600 bytes for lkl0 14080 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.112552 0.070827 0.030834 0.141635 0.094172 0.146251 0.187374 0.083194 lnL0 = -1161.834618 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1161.834618 x= 0.11255 0.07083 0.03083 0.14163 0.09417 0.14625 0.18737 0.08319 1 h-lim-p 0.0030 0.0239 78.1546 1160.903017 3 0.0003 30 | 0/8 2 h-lim-p 0.0010 0.0080 22.8651 1160.751872 8 0.0006 63 | 0/8 3 h-lim-p 0.0022 0.0406 6.3450 1160.737827 6 0.0008 91 | 0/8 4 h-lim-p 0.0027 0.1251 1.7680 1160.736639 5 0.0008 118 | 0/8 5 h-lim-p 0.0038 0.4046 0.3809 1160.736592 3 0.0007 139 | 0/8 6 h-lim-p 0.0049 3.9390 0.0525 1160.736591 1 0.0010 162 | 0/8 7 h-lim-p 0.0220 20.0000 0.0023 1160.736588 0 0.0330 182 | 0/8 8 h-lim-p 0.0075 7.8150 0.0101 1160.736474 0 0.0302 204 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1160.736472 0 1.0938 224 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1160.736472 0 1.0938 244 | 0/8 11 h-lim-p 2.0826 20.0000 0.0000 1160.736472 0 2.0826 264 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1160.736472 0 0.0684 288 | 0/8 13 h-lim-p 0.0101 20.0000 0.0000 1160.736472 0 0.0038 309 | 0/8 14 h-lim-p 0.0019 20.0000 0.0000 1160.736472 0 0.0014 329 | 0/8 15 h-lim-p 0.0009 20.0000 0.0000 1160.736472 0 0.0000 353 Out... lnL = -1160.736472 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1160.736472 Node 7: lnL = -1160.736472 Node 8: lnL = -1160.736472 Node 9: lnL = -1160.736472 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 273 Sequential format.. Reading seq # 1: YNR040W_Sbay Reading seq # 2: YNR040W_Scer Reading seq # 3: YNR040W_Skud Reading seq # 4: YNR040W_Smik Reading seq # 5: YNR040W_Spar Sequences read.. Counting patterns.. # site patterns = 122 Counting frequencies.. 120 bytes for distance 19520 bytes for lkl0 15616 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.120488 0.095050 0.023757 0.138496 0.088575 0.154011 0.134159 0.091520 lnL0 = -1147.568848 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1147.568848 x= 0.12049 0.09505 0.02376 0.13850 0.08857 0.15401 0.13416 0.09152 1 h-lim-p 0.0020 0.0161 88.0994 1146.369575 8 0.0004 43 | 0/8 2 h-lim-p 0.0006 0.0052 32.6803 1146.067133 7 0.0006 70 | 0/8 3 h-lim-p 0.0035 0.0365 5.8725 1146.054665 5 0.0008 95 | 0/8 4 h-lim-p 0.0033 0.1031 1.3460 1146.054096 3 0.0007 114 | 0/8 5 h-lim-p 0.0033 0.7472 0.2689 1146.054061 3 0.0010 135 | 0/8 6 h-lim-p 0.0078 5.6615 0.0333 1146.054060 0 0.0017 156 | 0/8 7 h-lim-p 0.0056 17.2728 0.0101 1146.054053 0 0.0112 177 | 0/8 8 h-lim-p 0.0132 6.0255 0.0085 1146.053641 0 0.0794 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1146.053634 1 0.9961 221 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1146.053634 0 2.1875 241 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1146.053634 0 0.2734 263 | 0/8 12 h-lim-p 0.0963 20.0000 0.0000 1146.053634 0 0.0181 285 | 0/8 13 h-lim-p 0.0085 20.0000 0.0000 1146.053634 0 0.0021 306 | 0/8 14 h-lim-p 0.0016 20.0000 0.0000 1146.053634 0 0.0000 332 Out... lnL = -1146.053634 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1146.053634 Node 7: lnL = -1146.053634 Node 8: lnL = -1146.053634 Node 9: lnL = -1146.053634 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 192 Sequential format.. Reading seq # 1: YNR046W_Sbay Reading seq # 2: YNR046W_Scer Reading seq # 3: YNR046W_Skud Reading seq # 4: YNR046W_Smik Reading seq # 5: YNR046W_Spar Sequences read.. Counting patterns.. # site patterns = 89 Counting frequencies.. 120 bytes for distance 14240 bytes for lkl0 11392 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.140044 0.034545 0.046867 0.105000 0.130687 0.161256 0.170035 0.109999 lnL0 = -833.026942 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 833.026942 x= 0.14004 0.03454 0.04687 0.10500 0.13069 0.16126 0.17003 0.11000 1 h-lim-p 0.0031 1.6576 73.2314 831.728772 8 0.0006 41 | 0/8 2 h-lim-p 0.0012 0.0097 12.5386 831.610743 0 0.0018 53 | 0/8 3 h-lim-p 0.0032 0.0260 4.6495 831.601405 7 0.0010 83 | 0/8 4 h-lim-p 0.0052 0.3232 0.8733 831.600806 5 0.0016 109 | 0/8 5 h-lim-p 0.0114 0.6977 0.1259 831.600786 3 0.0020 138 | 0/8 6 h-lim-p 0.0095 12.4250 0.0267 831.600743 0 0.0143 158 | 0/8 7 h-lim-p 0.0057 2.4691 0.0664 831.599961 0 0.0229 180 | 0/8 8 h-lim-p 0.0029 0.6702 0.5235 831.598477 0 0.0058 201 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 831.598296 3 1.0449 227 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 831.598295 1 1.2305 250 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 831.598295 0 1.0938 270 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 831.598295 0 0.0391 295 | 0/8 13 h-lim-p 0.0194 20.0000 0.0000 831.598295 0 0.0024 317 | 0/8 14 h-lim-p 0.0017 20.0000 0.0000 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -831.598295 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -831.598295 Node 7: lnL = -831.598295 Node 8: lnL = -831.598295 Node 9: lnL = -831.598295 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 450 Sequential format.. Reading seq # 1: YNR049C_Sbay Reading seq # 2: YNR049C_Scer Reading seq # 3: YNR049C_Skud Reading seq # 4: YNR049C_Smik Reading seq # 5: YNR049C_Spar Sequences read.. Counting patterns.. # site patterns = 196 Counting frequencies.. 120 bytes for distance 31360 bytes for lkl0 25088 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.136537 0.125884 0.055072 0.165605 0.153096 0.231647 0.146303 0.098060 lnL0 = -2019.905271 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2019.905271 x= 0.13654 0.12588 0.05507 0.16560 0.15310 0.23165 0.14630 0.09806 1 h-lim-p 0.0042 1.2577 97.9463 2018.178417 8 0.0004 41 | 0/8 2 h-lim-p 0.0029 0.0230 12.5975 2018.103226 7 0.0010 69 | 0/8 3 h-lim-p 0.0031 0.0904 3.9033 2018.097881 3 0.0008 88 | 0/8 4 h-lim-p 0.0063 0.6485 0.4723 2018.097775 3 0.0009 110 | 0/8 5 h-lim-p 0.0040 3.6677 0.1089 2018.097772 2 0.0006 136 | 0/8 6 h-lim-p 0.0022 7.2276 0.0321 2018.097771 0 0.0010 156 | 0/8 7 h-lim-p 0.0239 20.0000 0.0013 2018.097765 0 0.0956 178 | 0/8 8 h-lim-p 0.0052 20.0000 0.0238 2018.097689 0 0.0103 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2018.097686 0 1.0938 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2018.097686 0 1.0938 239 | 0/8 11 h-lim-p 2.0921 20.0000 0.0000 2018.097686 0 0.5230 260 | 0/8 12 h-lim-p 0.3227 20.0000 0.0000 2018.097686 0 0.0022 286 | 0/8 13 h-lim-p 0.0013 20.0000 0.0000 2018.097686 0 0.0007 306 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 2018.097686 0 0.0001 326 | 0/8 15 h-lim-p 0.0004 20.0000 0.0000 2018.097686 0 0.0000 352 Out... lnL = -2018.097686 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2018.097686 Node 7: lnL = -2018.097686 Node 8: lnL = -2018.097686 Node 9: lnL = -2018.097686 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 842 Sequential format.. Reading seq # 1: YNR051C_Sbay Reading seq # 2: YNR051C_Scer Reading seq # 3: YNR051C_Skud Reading seq # 4: YNR051C_Smik Reading seq # 5: YNR051C_Spar Sequences read.. Counting patterns.. # site patterns = 195 Counting frequencies.. 120 bytes for distance 31200 bytes for lkl0 24960 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.092705 0.035055 0.027453 0.064056 0.043710 0.133866 0.132216 0.072460 lnL0 = -3068.598551 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3068.598551 x= 0.09270 0.03505 0.02745 0.06406 0.04371 0.13387 0.13222 0.07246 1 h-lim-p 0.0014 0.4844 207.7678 3067.073319 5 0.0001 34 | 0/8 2 h-lim-p 0.0001 0.0009 39.6661 3067.008837 6 0.0001 58 | 0/8 3 h-lim-p 0.0002 0.0119 14.7430 3066.994777 4 0.0001 80 | 0/8 4 h-lim-p 0.0005 0.0192 4.2459 3066.993827 2 0.0001 97 | 0/8 5 h-lim-p 0.0002 0.0587 2.1201 3066.993619 2 0.0001 113 | 0/8 6 h-lim-p 0.0070 5.3484 0.0342 3066.993619 0 0.0002 129 | 0/8 7 h-lim-p 0.0019 20.0000 0.0034 3066.993619 0 0.0019 149 | 0/8 8 h-lim-p 0.0022 20.0000 0.0030 3066.993535 0 0.0690 174 | 0/8 9 h-lim-p 0.1413 20.0000 0.0015 3066.993513 0 0.5653 196 | 0/8 10 h-lim-p 2.0224 20.0000 0.0004 3066.993506 1 0.9954 219 | 0/8 11 h-lim-p 0.8454 20.0000 0.0005 3066.993504 0 1.6909 240 | 0/8 12 h-lim-p 2.5000 20.0000 0.0001 3066.993504 0 1.0938 260 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 3066.993504 0 2.1875 280 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 3066.993504 0 0.2734 302 | 0/8 15 h-lim-p 0.2623 20.0000 0.0000 3066.993504 0 0.0000 345 Out... lnL = -3066.993504 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3066.993504 Node 7: lnL = -3066.993504 Node 8: lnL = -3066.993504 Node 9: lnL = -3066.993504 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 559 Sequential format.. Reading seq # 1: YNR052C_Sbay Reading seq # 2: YNR052C_Scer Reading seq # 3: YNR052C_Skud Reading seq # 4: YNR052C_Smik Reading seq # 5: YNR052C_Spar Sequences read.. Counting patterns.. # site patterns = 165 Counting frequencies.. 120 bytes for distance 26400 bytes for lkl0 21120 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.076263 0.075163 0.084216 0.083284 0.059324 0.194401 0.096461 0.050685 lnL0 = -2076.257041 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2076.257041 x= 0.07626 0.07516 0.08422 0.08328 0.05932 0.19440 0.09646 0.05068 1 h-lim-p 0.0002 0.0020 75.2174 2075.550472 5 0.0003 32 | 0/8 2 h-lim-p 0.0011 0.0084 16.6219 2075.515661 4 0.0003 53 | 0/8 3 h-lim-p 0.0008 0.0187 5.5815 2075.511370 4 0.0003 73 | 0/8 4 h-lim-p 0.0008 0.6152 2.2043 2075.510722 3 0.0003 91 | 0/8 5 h-lim-p 0.0005 0.1456 1.2849 2075.510545 3 0.0003 110 | 0/8 6 h-lim-p 0.0020 0.6484 0.1809 2075.510540 2 0.0003 128 | 0/8 7 h-lim-p 0.0098 18.9761 0.0060 2075.510540 0 0.0021 149 | 0/8 8 h-lim-p 0.0086 20.0000 0.0015 2075.510435 0 0.1372 173 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2075.510431 1 0.9961 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2075.510431 0 0.5469 216 | 0/8 11 h-lim-p 0.3854 20.0000 0.0000 2075.510431 0 0.0030 242 | 0/8 12 h-lim-p 0.0018 20.0000 0.0000 2075.510431 0 0.0004 263 | 0/8 13 h-lim-p 0.0002 20.0000 0.0001 2075.510431 0 0.0000 297 | 0/8 14 h-lim-p 0.0000 20.0000 0.0032 2075.510431 0 0.0000 329 | 0/8 15 h-lim-p 0.0000 20.0000 0.0012 2075.510431 0 0.0000 354 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0032 | 0/8 18 h-lim-p 0.0000 20.0000 0.0032 Out... lnL = -2075.510431 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2075.510431 Node 7: lnL = -2075.510431 Node 8: lnL = -2075.510431 Node 9: lnL = -2075.510431 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 264 Sequential format.. Reading seq # 1: YNR053C_Sbay Reading seq # 2: YNR053C_Scer Reading seq # 3: YNR053C_Skud Reading seq # 4: YNR053C_Smik Reading seq # 5: YNR053C_Spar Sequences read.. Counting patterns.. # site patterns = 115 Counting frequencies.. 120 bytes for distance 18400 bytes for lkl0 14720 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.100150 0.051112 0.041741 0.075269 0.062734 0.955595 0.081841 0.043723 lnL0 = -1133.421099 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1133.421099 x= 0.10015 0.05111 0.04174 0.07527 0.06273 0.95560 0.08184 0.04372 1 h-lim-p 0.0005 0.0038 63.4827 1132.662440 7 0.0004 39 | 0/8 2 h-lim-p 0.0005 0.0043 20.3949 1132.581795 5 0.0004 61 | 0/8 3 h-lim-p 0.0014 0.0467 6.0271 1132.560647 2 0.0013 77 | 0/8 4 h-lim-p 0.0005 0.0462 16.1232 1132.464818 0 0.0030 91 | 0/8 5 h-lim-p 0.0017 0.0262 28.6397 1132.421502 6 0.0007 114 | 0/8 6 h-lim-p 0.0274 0.2194 0.5486 1132.421402 2 0.0007 134 | 0/8 7 h-lim-p 0.0008 0.1566 0.4399 1132.421236 0 0.0025 155 | 0/8 8 h-lim-p 0.3277 20.0000 0.0033 1132.420138 0 1.3109 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 1132.420059 3 1.0004 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1132.420059 0 1.0938 223 | 0/8 11 h-lim-p 1.9638 20.0000 0.0000 1132.420059 0 0.8592 243 | 0/8 12 h-lim-p 0.2700 20.0000 0.0000 1132.420059 0 0.0063 268 | 0/8 13 h-lim-p 0.0017 20.0000 0.0001 1132.420059 0 0.0017 288 | 0/8 14 h-lim-p 0.0005 20.0000 0.0004 1132.420059 0 0.0000 322 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 1132.420059 0 0.0000 346 Out... lnL = -1132.420059 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1132.420059 Node 7: lnL = -1132.420059 Node 8: lnL = -1132.420059 Node 9: lnL = -1132.420059 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 897 Sequential format.. Reading seq # 1: YNR054C_Sbay Reading seq # 2: YNR054C_Scer Reading seq # 3: YNR054C_Skud Reading seq # 4: YNR054C_Smik Reading seq # 5: YNR054C_Spar Sequences read.. Counting patterns.. # site patterns = 358 Counting frequencies.. 120 bytes for distance 57280 bytes for lkl0 45824 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.123063 0.121298 0.048128 0.463615 0.183670 0.211328 0.163303 0.066369 lnL0 = -4363.383725 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4363.383725 x= 0.12306 0.12130 0.04813 0.46362 0.18367 0.21133 0.16330 0.06637 1 h-lim-p 0.0013 0.0107 75.6975 4362.652590 5 0.0003 32 | 0/8 2 h-lim-p 0.0006 0.0065 34.3814 4362.433520 6 0.0004 58 | 0/8 3 h-lim-p 0.0011 0.0195 13.7038 4362.412112 5 0.0003 83 | 0/8 4 h-lim-p 0.0007 0.0450 5.4893 4362.407086 4 0.0004 106 | 0/8 5 h-lim-p 0.0010 0.2730 2.1442 4362.405416 3 0.0008 125 | 0/8 6 h-lim-p 0.0020 0.2078 0.9151 4362.405268 2 0.0004 142 | 0/8 7 h-lim-p 0.0114 8.5176 0.0348 4362.405267 0 0.0006 165 | 0/8 8 h-lim-p 0.0692 20.0000 0.0003 4362.405121 0 1.1077 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4362.405117 0 1.0938 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4362.405117 0 1.0938 229 | 0/8 11 h-lim-p 1.1520 20.0000 0.0000 4362.405117 0 2.3041 250 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4362.405117 0 1.0938 270 | 0/8 13 h-lim-p 0.2005 20.0000 0.0001 4362.405117 0 0.0251 292 | 0/8 14 h-lim-p 0.0044 20.0000 0.0005 4362.405117 0 0.0008 314 | 0/8 15 h-lim-p 0.0011 20.0000 0.0004 4362.405117 0 0.0000 349 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 4362.405117 0 0.0000 383 Out... lnL = -4362.405117 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4362.405117 Node 7: lnL = -4362.405117 Node 8: lnL = -4362.405117 Node 9: lnL = -4362.405117 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 228 Sequential format.. Reading seq # 1: YNR057C_Sbay Reading seq # 2: YNR057C_Scer Reading seq # 3: YNR057C_Skud Reading seq # 4: YNR057C_Smik Reading seq # 5: YNR057C_Spar Sequences read.. Counting patterns.. # site patterns = 86 Counting frequencies.. 120 bytes for distance 13760 bytes for lkl0 11008 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.125296 0.053634 0.046355 0.075538 0.047084 0.126390 0.157900 0.095221 lnL0 = -910.583034 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 910.583034 x= 0.12530 0.05363 0.04636 0.07554 0.04708 0.12639 0.15790 0.09522 1 h-lim-p 0.0002 0.0017 56.3208 910.009759 0 0.0004 23 | 0/8 2 h-lim-p 0.0026 0.0290 9.3274 909.990742 6 0.0005 52 | 0/8 3 h-lim-p 0.0011 0.0178 3.8909 909.988455 4 0.0003 74 | 0/8 4 h-lim-p 0.0010 0.1773 1.4186 909.987806 3 0.0007 92 | 0/8 5 h-lim-p 0.0034 0.4752 0.3075 909.987742 3 0.0012 112 | 0/8 6 h-lim-p 0.0065 2.9794 0.0576 909.987683 3 0.0049 138 | 0/8 7 h-lim-p 0.0056 3.0594 0.0501 909.984190 0 0.0450 161 | 0/8 8 h-lim-p 0.0019 0.1006 1.1990 909.978008 1 0.0024 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 909.977973 2 0.9961 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 909.977973 0 1.0938 219 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 909.977973 0 2.1875 239 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 909.977973 0 0.2734 261 | 0/8 13 h-lim-p 0.0806 20.0000 0.0000 909.977973 0 0.0001 290 Out... lnL = -909.977973 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -909.977973 Node 7: lnL = -909.977973 Node 8: lnL = -909.977973 Node 9: lnL = -909.977973 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 228 Sequential format.. Reading seq # 1: YNR058W_Sbay Reading seq # 2: YNR058W_Scer Reading seq # 3: YNR058W_Skud Reading seq # 4: YNR058W_Smik Reading seq # 5: YNR058W_Spar Sequences read.. Counting patterns.. # site patterns = 89 Counting frequencies.. 120 bytes for distance 14240 bytes for lkl0 11392 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.127344 0.043619 0.048290 0.075414 0.047207 0.124456 0.169662 0.097201 lnL0 = -912.909795 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 912.909795 x= 0.12734 0.04362 0.04829 0.07541 0.04721 0.12446 0.16966 0.09720 1 h-lim-p 0.0003 0.0023 61.2265 912.258637 0 0.0004 22 | 0/8 2 h-lim-p 0.0024 0.0191 8.7655 912.238918 4 0.0005 42 | 0/8 3 h-lim-p 0.0012 0.0187 3.8885 912.236670 4 0.0003 65 | 0/8 4 h-lim-p 0.0010 0.1327 1.3986 912.236188 5 0.0006 90 | 0/8 5 h-lim-p 0.0032 0.7480 0.2454 912.236136 2 0.0014 106 | 0/8 6 h-lim-p 0.0029 1.4577 0.1166 912.236095 3 0.0021 133 | 0/8 7 h-lim-p 0.0052 3.1972 0.0464 912.234850 0 0.0311 155 | 0/8 8 h-lim-p 0.0035 0.2042 0.4144 912.224782 0 0.0070 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 912.224601 2 0.9644 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 912.224601 0 1.0938 220 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 912.224601 0 2.1875 240 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 912.224601 0 1.0938 260 | 0/8 13 h-lim-p 0.5426 20.0000 0.0000 912.224601 0 4.3408 283 | 0/8 14 h-lim-p 2.4484 20.0000 0.0000 912.224601 0 0.2678 305 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 912.224601 0 0.0003 337 Out... lnL = -912.224601 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -912.224601 Node 7: lnL = -912.224601 Node 8: lnL = -912.224601 Node 9: lnL = -912.224601 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 900 Sequential format.. Reading seq # 1: YNR059W_Sbay Reading seq # 2: YNR059W_Scer Reading seq # 3: YNR059W_Skud Reading seq # 4: YNR059W_Smik Reading seq # 5: YNR059W_Spar Sequences read.. Counting patterns.. # site patterns = 420 Counting frequencies.. 120 bytes for distance 67200 bytes for lkl0 53760 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.387788 0.168806 0.094671 0.192288 0.101492 0.369992 0.338090 0.306867 lnL0 = -4563.306598 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4563.306598 x= 0.38779 0.16881 0.09467 0.19229 0.10149 0.36999 0.33809 0.30687 1 h-lim-p 0.0094 0.0754 87.9883 4561.755901 8 0.0004 44 | 0/8 2 h-lim-p 0.0007 0.0056 32.7701 4561.549661 6 0.0004 73 | 0/8 3 h-lim-p 0.0005 0.0172 25.4784 4561.376228 0 0.0008 85 | 0/8 4 h-lim-p 0.0049 0.0910 4.2569 4561.368550 5 0.0009 110 | 0/8 5 h-lim-p 0.0026 0.2752 1.4410 4561.367784 4 0.0008 133 | 0/8 6 h-lim-p 0.0032 0.7090 0.3703 4561.367675 3 0.0017 152 | 0/8 7 h-lim-p 0.0094 4.5595 0.0655 4561.367660 0 0.0041 172 | 0/8 8 h-lim-p 0.1355 20.0000 0.0020 4561.366008 0 0.5422 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 4561.365918 2 0.9961 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4561.365918 0 1.0938 238 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4561.365918 0 2.1875 258 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4561.365918 0 0.5469 279 | 0/8 13 h-lim-p 0.2249 20.0000 0.0000 4561.365918 0 0.0070 303 | 0/8 14 h-lim-p 0.0019 20.0000 0.0000 4561.365918 0 0.0000 336 Out... lnL = -4561.365918 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4561.365918 Node 7: lnL = -4561.365918 Node 8: lnL = -4561.365918 Node 9: lnL = -4561.365918 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 861 Sequential format.. Reading seq # 1: YNR060W_Sbay Reading seq # 2: YNR060W_Scer Reading seq # 3: YNR060W_Skud Reading seq # 4: YNR060W_Smik Reading seq # 5: YNR060W_Spar Sequences read.. Counting patterns.. # site patterns = 257 Counting frequencies.. 120 bytes for distance 41120 bytes for lkl0 32896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.144790 0.029621 0.067737 0.086432 0.069371 0.425977 0.131613 0.101994 lnL0 = -3741.653305 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3741.653305 x= 0.14479 0.02962 0.06774 0.08643 0.06937 0.42598 0.13161 0.10199 1 h-lim-p 0.0004 0.0029 96.7685 3741.090344 7 0.0001 40 | 0/8 2 h-lim-p 0.0005 0.0042 25.4239 3741.025756 3 0.0002 58 | 0/8 3 h-lim-p 0.0003 0.0202 15.9687 3740.992989 4 0.0003 79 | 0/8 4 h-lim-p 0.0003 0.0165 16.5573 3740.975878 6 0.0002 106 | 0/8 5 h-lim-p 0.0005 0.0321 7.4624 3740.971034 3 0.0003 125 | 0/8 6 h-lim-p 0.0062 0.3458 0.3170 3740.971017 1 0.0003 142 | 0/8 7 h-lim-p 0.0040 6.6193 0.0270 3740.971017 0 0.0004 164 | 0/8 8 h-lim-p 0.1378 20.0000 0.0001 3740.970998 0 1.1026 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3740.970998 0 1.0938 207 | 0/8 10 h-lim-p 1.9116 20.0000 0.0000 3740.970998 0 1.6726 227 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3740.970998 0 1.0938 247 | 0/8 12 h-lim-p 0.4417 20.0000 0.0000 3740.970998 0 0.4417 267 | 0/8 13 h-lim-p 0.0008 20.0000 0.0064 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 3740.970998 0 0.0000 330 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 3740.970998 0 0.0000 363 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -3740.970998 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3740.970998 Node 7: lnL = -3740.970998 Node 8: lnL = -3740.970998 Node 9: lnL = -3740.970998 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 915 Sequential format.. Reading seq # 1: YNR063W_Sbay Reading seq # 2: YNR063W_Scer Reading seq # 3: YNR063W_Skud Reading seq # 4: YNR063W_Smik Reading seq # 5: YNR063W_Spar Sequences read.. Counting patterns.. # site patterns = 346 Counting frequencies.. 120 bytes for distance 55360 bytes for lkl0 44288 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.443173 0.000060 0.494062 0.177995 0.153855 0.456054 0.445305 0.348316 lnL0 = -4227.726032 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4227.726032 x= 0.44317 0.00006 0.49406 0.17799 0.15386 0.45605 0.44530 0.34832 1 h-lim-p 0.0000 0.0000 103.9713 4227.700523 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0068 91.2742 4224.650379 0 0.0013 41 | 1/8 3 h-lim-p 0.0106 0.0846 10.9493 4224.278395 7 0.0063 70 | 1/8 4 h-lim-p 0.0082 0.0804 8.4039 4224.173470 2 0.0038 86 | 1/8 5 h-lim-p 0.0072 0.1646 4.5090 4224.125061 5 0.0046 110 | 1/8 6 h-lim-p 0.0082 0.2234 2.5340 4224.083627 4 0.0063 130 | 1/8 7 h-lim-p 0.0868 1.4425 0.1851 4221.647697 0 0.2605 143 | 1/8 8 h-lim-p 2.5000 20.0000 0.0074 4221.619407 6 0.8366 176 | 1/8 9 h-lim-p 2.5000 20.0000 0.0012 4221.619316 3 0.8800 202 | 1/8 10 h-lim-p 2.5000 20.0000 0.0003 4221.619312 1 0.9961 223 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 4221.619312 0 1.0938 242 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 4221.619312 0 1.0938 261 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 4221.619312 0 0.6250 281 | 1/8 14 h-lim-p 0.4424 20.0000 0.0000 4221.619312 0 0.0000 323 Out... lnL = -4221.619312 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4221.619312 Node 7: lnL = -4221.619312 Node 8: lnL = -4221.619312 Node 9: lnL = -4221.619312 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 390 Sequential format.. Reading seq # 1: YNR064C_Sbay Reading seq # 2: YNR064C_Scer Reading seq # 3: YNR064C_Skud Reading seq # 4: YNR064C_Smik Reading seq # 5: YNR064C_Spar Sequences read.. Counting patterns.. # site patterns = 175 Counting frequencies.. 120 bytes for distance 28000 bytes for lkl0 22400 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.167216 0.214420 0.106613 0.094066 0.059229 0.171453 0.436357 0.108477 lnL0 = -1621.890594 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1621.890594 x= 0.16722 0.21442 0.10661 0.09407 0.05923 0.17145 0.43636 0.10848 1 h-lim-p 0.0007 0.0055 39.6495 1621.243141 0 0.0010 22 | 0/8 2 h-lim-p 0.0033 0.0444 12.3819 1621.213405 6 0.0004 47 | 0/8 3 h-lim-p 0.0004 0.0301 11.8927 1621.149478 0 0.0018 61 | 0/8 4 h-lim-p 0.0030 0.0302 7.1448 1621.135961 7 0.0009 92 | 0/8 5 h-lim-p 0.0047 0.6233 1.3036 1621.133472 5 0.0031 116 | 0/8 6 h-lim-p 0.0049 0.1773 0.8407 1621.132834 2 0.0023 132 | 0/8 7 h-lim-p 0.0173 4.2539 0.1110 1621.132612 4 0.0114 161 | 0/8 8 h-lim-p 0.0599 15.3212 0.0211 1621.118731 0 0.3595 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0008 1621.118601 2 0.9961 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1621.118601 0 1.0938 227 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1621.118601 0 1.0938 247 | 0/8 12 h-lim-p 1.5932 20.0000 0.0000 1621.118601 0 1.3941 267 | 0/8 13 h-lim-p 0.7515 20.0000 0.0000 1621.118601 0 0.3757 287 | 0/8 14 h-lim-p 0.0064 20.0000 0.0002 1621.118601 0 0.0028 307 | 0/8 15 h-lim-p 0.0024 20.0000 0.0002 1621.118601 0 0.0011 327 | 0/8 16 h-lim-p 0.0012 20.0000 0.0002 1621.118601 0 0.0001 351 | 0/8 17 h-lim-p 0.0003 20.0000 0.0000 1621.118601 0 0.0000 386 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 1621.118601 0 0.0000 419 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 | 0/8 20 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1621.118601 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1621.118601 Node 7: lnL = -1621.118601 Node 8: lnL = -1621.118601 Node 9: lnL = -1621.118601 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 836 Sequential format.. Reading seq # 1: YOL001W_Sbay Reading seq # 2: YOL001W_Scer Reading seq # 3: YOL001W_Skud Reading seq # 4: YOL001W_Smik Reading seq # 5: YOL001W_Spar Sequences read.. Counting patterns.. # site patterns = 151 Counting frequencies.. 120 bytes for distance 24160 bytes for lkl0 19328 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.090824 0.047242 0.038452 0.029808 0.029045 0.088596 0.097374 0.070152 lnL0 = -2795.573290 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2795.573290 x= 0.09082 0.04724 0.03845 0.02981 0.02905 0.08860 0.09737 0.07015 1 h-lim-p 0.0003 0.0025 91.8947 2795.251408 6 0.0001 36 | 0/8 2 h-lim-p 0.0003 0.0037 23.8451 2795.223599 6 0.0001 64 | 0/8 3 h-lim-p 0.0002 0.0040 11.6756 2795.220456 3 0.0001 83 | 0/8 4 h-lim-p 0.0002 0.0288 3.8044 2795.219961 2 0.0001 99 | 0/8 5 h-lim-p 0.0002 0.0348 1.6556 2795.219887 2 0.0001 115 | 0/8 6 h-lim-p 0.0008 0.8392 0.1428 2795.219885 0 0.0002 128 | 0/8 7 h-lim-p 0.0032 20.0000 0.0075 2795.219885 0 0.0002 151 | 0/8 8 h-lim-p 0.0954 20.0000 0.0000 2795.219884 0 1.1452 174 | 0/8 9 h-lim-p 1.7502 20.0000 0.0000 2795.219884 0 0.8751 194 | 0/8 10 h-lim-p 0.6987 20.0000 0.0000 2795.219884 0 0.0007 223 | 0/8 11 h-lim-p 0.0002 20.0000 0.0000 2795.219884 0 0.0000 247 | 0/8 12 h-lim-p 0.0000 20.0000 0.0000 2795.219884 0 0.0000 279 Out... lnL = -2795.219884 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2795.219884 Node 7: lnL = -2795.219884 Node 8: lnL = -2795.219884 Node 9: lnL = -2795.219884 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 833 Sequential format.. Reading seq # 1: YOL002C_Sbay Reading seq # 2: YOL002C_Scer Reading seq # 3: YOL002C_Skud Reading seq # 4: YOL002C_Smik Reading seq # 5: YOL002C_Spar Sequences read.. Counting patterns.. # site patterns = 166 Counting frequencies.. 120 bytes for distance 26560 bytes for lkl0 21248 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.091047 0.041506 0.040552 0.034616 0.029485 0.089509 0.098033 0.070308 lnL0 = -2778.934175 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2778.934175 x= 0.09105 0.04151 0.04055 0.03462 0.02948 0.08951 0.09803 0.07031 1 h-lim-p 0.0005 0.0043 119.1839 2778.392564 7 0.0001 40 | 0/8 2 h-lim-p 0.0003 0.0022 24.1630 2778.371262 7 0.0001 70 | 0/8 3 h-lim-p 0.0001 0.0065 12.3234 2778.366528 4 0.0001 91 | 0/8 4 h-lim-p 0.0003 0.0205 3.6122 2778.365940 2 0.0001 107 | 0/8 5 h-lim-p 0.0003 0.0858 1.2594 2778.365884 3 0.0001 126 | 0/8 6 h-lim-p 0.0006 0.8317 0.1658 2778.365882 1 0.0001 141 | 0/8 7 h-lim-p 0.0043 20.0000 0.0055 2778.365882 0 0.0002 164 | 0/8 8 h-lim-p 0.0233 20.0000 0.0001 2778.365877 0 0.7444 189 | 0/8 9 h-lim-p 0.8618 20.0000 0.0000 2778.365876 0 0.8618 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2778.365876 0 1.0938 229 | 0/8 11 h-lim-p 0.4941 20.0000 0.0000 2778.365876 0 0.0005 258 | 0/8 12 h-lim-p 0.0001 20.0000 0.0000 2778.365876 0 0.0000 279 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 2778.365876 0 0.0000 307 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 2778.365876 0 0.0000 339 Out... lnL = -2778.365876 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2778.365876 Node 7: lnL = -2778.365876 Node 8: lnL = -2778.365876 Node 9: lnL = -2778.365876 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 469 Sequential format.. Reading seq # 1: YOL003C_Sbay Reading seq # 2: YOL003C_Scer Reading seq # 3: YOL003C_Skud Reading seq # 4: YOL003C_Smik Reading seq # 5: YOL003C_Spar Sequences read.. Counting patterns.. # site patterns = 219 Counting frequencies.. 120 bytes for distance 35040 bytes for lkl0 28032 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.222661 0.091999 0.071616 0.188167 0.092294 0.227743 0.194674 0.170755 lnL0 = -2135.018626 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2135.018626 x= 0.22266 0.09200 0.07162 0.18817 0.09229 0.22774 0.19467 0.17075 1 h-lim-p 0.0004 0.0031 47.6515 2134.208771 0 0.0008 23 | 0/8 2 h-lim-p 0.0014 0.0112 11.4636 2134.171171 5 0.0006 44 | 0/8 3 h-lim-p 0.0009 0.0396 8.0589 2134.155369 3 0.0007 62 | 0/8 4 h-lim-p 0.0031 0.0593 1.7388 2134.154461 3 0.0007 81 | 0/8 5 h-lim-p 0.0014 0.4891 0.8357 2134.154235 4 0.0008 103 | 0/8 6 h-lim-p 0.0040 1.4541 0.1673 2134.154222 1 0.0009 126 | 0/8 7 h-lim-p 0.0060 10.6664 0.0246 2134.154215 1 0.0048 148 | 0/8 8 h-lim-p 0.0186 20.0000 0.0063 2134.153091 0 0.2233 171 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2134.153089 0 1.0938 191 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2134.153089 0 1.0938 211 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2134.153089 0 0.5469 232 | 0/8 12 h-lim-p 0.3610 20.0000 0.0000 2134.153089 0 0.0677 254 | 0/8 13 h-lim-p 0.0385 20.0000 0.0000 2134.153089 0 0.0000 294 Out... lnL = -2134.153089 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2134.153089 Node 7: lnL = -2134.153089 Node 8: lnL = -2134.153089 Node 9: lnL = -2134.153089 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 784 Sequential format.. Reading seq # 1: YOL005C_Sbay Reading seq # 2: YOL005C_Scer Reading seq # 3: YOL005C_Skud Reading seq # 4: YOL005C_Smik Reading seq # 5: YOL005C_Spar Sequences read.. Counting patterns.. # site patterns = 297 Counting frequencies.. 120 bytes for distance 47520 bytes for lkl0 38016 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.200230 0.022632 0.063884 0.132454 0.122979 0.196221 0.188146 0.156652 lnL0 = -3586.247202 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3586.247202 x= 0.20023 0.02263 0.06388 0.13245 0.12298 0.19622 0.18815 0.15665 1 h-lim-p 0.0006 0.3335 341.2654 3579.477416 8 0.0001 40 | 0/8 2 h-lim-p 0.0007 0.0059 39.5685 3579.006366 6 0.0006 63 | 0/8 3 h-lim-p 0.0057 0.0464 4.1577 3579.003270 4 0.0004 87 | 0/8 4 h-lim-p 0.0025 0.3391 0.5910 3579.003198 2 0.0004 105 | 0/8 5 h-lim-p 0.0019 2.6747 0.1243 3579.003194 0 0.0005 126 | 0/8 6 h-lim-p 0.0017 4.0929 0.0353 3579.003190 0 0.0015 146 | 0/8 7 h-lim-p 0.0023 12.2303 0.0224 3579.002954 0 0.0188 169 | 0/8 8 h-lim-p 0.0022 3.1275 0.1947 3579.000175 0 0.0065 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3579.000151 1 0.9961 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3579.000151 0 1.0938 232 | 0/8 11 h-lim-p 2.2809 20.0000 0.0000 3579.000151 0 0.9979 252 | 0/8 12 h-lim-p 0.8752 20.0000 0.0000 3579.000151 0 0.6564 272 | 0/8 13 h-lim-p 0.0089 20.0000 0.0003 3579.000151 0 0.0044 292 | 0/8 14 h-lim-p 0.0044 20.0000 0.0003 3579.000151 0 0.0000 318 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 3579.000151 0 0.0000 347 | 0/8 16 h-lim-p 0.0005 20.0000 0.0000 3579.000151 0 0.0000 374 Out... lnL = -3579.000151 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3579.000151 Node 7: lnL = -3579.000151 Node 8: lnL = -3579.000151 Node 9: lnL = -3579.000151 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 181 Sequential format.. Reading seq # 1: YOL008W_Sbay Reading seq # 2: YOL008W_Scer Reading seq # 3: YOL008W_Skud Reading seq # 4: YOL008W_Smik Reading seq # 5: YOL008W_Spar Sequences read.. Counting patterns.. # site patterns = 85 Counting frequencies.. 120 bytes for distance 13600 bytes for lkl0 10880 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.122673 0.122625 0.066040 0.139759 0.078472 0.113984 0.250745 0.074431 lnL0 = -806.359562 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 806.359562 x= 0.12267 0.12263 0.06604 0.13976 0.07847 0.11398 0.25075 0.07443 1 h-lim-p 0.0029 0.0228 36.6293 805.929750 7 0.0007 37 | 0/8 2 h-lim-p 0.0025 0.0199 9.6529 805.882114 5 0.0011 58 | 0/8 3 h-lim-p 0.0037 0.1059 2.8225 805.876670 5 0.0015 82 | 0/8 4 h-lim-p 0.0041 0.1623 1.0228 805.876144 5 0.0011 107 | 0/8 5 h-lim-p 0.0035 0.7389 0.3288 805.876081 3 0.0013 125 | 0/8 6 h-lim-p 0.0072 5.5195 0.0611 805.876079 1 0.0009 149 | 0/8 7 h-lim-p 0.0065 20.0000 0.0084 805.876078 0 0.0032 169 | 0/8 8 h-lim-p 0.0342 20.0000 0.0008 805.876011 0 0.5472 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 805.876006 1 0.9961 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 805.876006 0 0.0024 244 | 0/8 11 h-lim-p 0.0007 20.0000 0.0000 805.876006 0 0.0007 264 | 0/8 12 h-lim-p 0.0002 20.0000 0.0000 805.876006 0 0.0002 284 | 0/8 13 h-lim-p 0.0002 20.0000 0.0000 805.876006 0 0.0000 322 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -805.876006 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -805.876006 Node 7: lnL = -805.876006 Node 8: lnL = -805.876006 Node 9: lnL = -805.876006 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 181 Sequential format.. Reading seq # 1: YOL009C_Sbay Reading seq # 2: YOL009C_Scer Reading seq # 3: YOL009C_Skud Reading seq # 4: YOL009C_Smik Reading seq # 5: YOL009C_Spar Sequences read.. Counting patterns.. # site patterns = 87 Counting frequencies.. 120 bytes for distance 13920 bytes for lkl0 11136 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.129126 0.123072 0.082972 0.139051 0.079181 0.109965 0.268633 0.078591 lnL0 = -817.850317 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 817.850317 x= 0.12913 0.12307 0.08297 0.13905 0.07918 0.10996 0.26863 0.07859 1 h-lim-p 0.0029 0.0233 22.7415 817.631654 9 0.0009 47 | 0/8 2 h-lim-p 0.0025 0.0333 7.9977 817.596818 2 0.0012 63 | 0/8 3 h-lim-p 0.0032 0.1069 2.9557 817.591645 5 0.0014 87 | 0/8 4 h-lim-p 0.0031 0.1597 1.2796 817.590784 3 0.0013 105 | 0/8 5 h-lim-p 0.0042 0.5760 0.3805 817.590682 4 0.0016 125 | 0/8 6 h-lim-p 0.0162 7.3098 0.0373 817.590681 1 0.0010 150 | 0/8 7 h-lim-p 0.0148 20.0000 0.0025 817.590680 0 0.0222 170 | 0/8 8 h-lim-p 0.0098 20.0000 0.0057 817.590623 0 0.0585 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 817.590622 0 1.0938 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 817.590622 0 1.0938 232 | 0/8 11 h-lim-p 1.8149 20.0000 0.0000 817.590622 0 0.0018 261 | 0/8 12 h-lim-p 0.0009 20.0000 0.0000 817.590622 0 0.0000 289 Out... lnL = -817.590622 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -817.590622 Node 7: lnL = -817.590622 Node 8: lnL = -817.590622 Node 9: lnL = -817.590622 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 734 Sequential format.. Reading seq # 1: YOL010W_Sbay Reading seq # 2: YOL010W_Scer Reading seq # 3: YOL010W_Skud Reading seq # 4: YOL010W_Smik Reading seq # 5: YOL010W_Spar Sequences read.. Counting patterns.. # site patterns = 192 Counting frequencies.. 120 bytes for distance 30720 bytes for lkl0 24576 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.199574 0.000060 0.145214 0.160137 0.087299 1.045251 0.262175 0.115559 lnL0 = -2389.106659 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2389.106659 x= 0.19957 0.00006 0.14521 0.16014 0.08730 1.04525 0.26218 0.11556 1 h-lim-p 0.0000 0.0000 245.3094 2389.052941 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0026 107.9392 2386.294131 0 0.0006 40 | 1/8 3 h-lim-p 0.0005 0.0038 49.6886 2385.763958 7 0.0005 70 | 1/8 4 h-lim-p 0.0014 0.0146 17.3858 2385.593899 4 0.0011 90 | 1/8 5 h-lim-p 0.0056 0.1992 3.5081 2385.089975 0 0.0225 104 | 1/8 6 h-lim-p 0.0020 0.0464 38.8314 2377.831878 0 0.0244 119 | 1/8 7 h-lim-p 0.0887 0.7094 2.9186 2372.964132 0 0.3547 133 | 0/8 8 h-lim-p 0.0025 0.0199 53.5983 2372.936907 6 0.0003 158 | 0/8 9 h-lim-p 0.0355 7.0481 0.4657 2371.795012 0 0.5684 174 | 0/8 10 h-lim-p 0.1810 1.4480 0.2881 2371.533574 0 0.3620 195 | 0/8 11 h-lim-p 2.1608 20.0000 0.0483 2371.506393 5 0.7651 227 | 0/8 12 h-lim-p 2.5000 20.0000 0.0098 2371.504559 5 0.8644 261 | 0/8 13 h-lim-p 2.5000 20.0000 0.0012 2371.503906 3 1.6492 289 | 0/8 14 h-lim-p 0.9750 20.0000 0.0021 2371.503572 1 1.2187 311 | 0/8 15 h-lim-p 1.7241 20.0000 0.0015 2371.503441 3 1.1116 339 | 0/8 16 h-lim-p 2.5000 20.0000 0.0002 2371.503440 0 1.0938 359 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 2371.503440 0 1.0938 379 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 2371.503440 0 2.1875 399 | 0/8 19 h-lim-p 1.7271 20.0000 0.0000 2371.503440 0 0.7556 419 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 2371.503440 0 0.2344 442 | 0/8 21 h-lim-p 0.1937 20.0000 0.0000 2371.503440 0 0.0023 468 Out... lnL = -2371.503440 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2371.503440 Node 7: lnL = -2371.503440 Node 8: lnL = -2371.503440 Node 9: lnL = -2371.503440 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 882 Sequential format.. Reading seq # 1: YOL011W_Sbay Reading seq # 2: YOL011W_Scer Reading seq # 3: YOL011W_Skud Reading seq # 4: YOL011W_Smik Reading seq # 5: YOL011W_Spar Sequences read.. Counting patterns.. # site patterns = 244 Counting frequencies.. 120 bytes for distance 39040 bytes for lkl0 31232 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.153292 0.068980 0.067981 0.076229 0.060512 0.158813 0.170630 0.110828 lnL0 = -3674.781839 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3674.781839 x= 0.15329 0.06898 0.06798 0.07623 0.06051 0.15881 0.17063 0.11083 1 h-lim-p 0.0021 0.7399 187.6245 3672.271469 9 0.0002 46 | 0/8 2 h-lim-p 0.0004 0.0030 36.8752 3672.171584 6 0.0002 72 | 0/8 3 h-lim-p 0.0003 0.0135 18.2629 3672.139520 4 0.0002 92 | 0/8 4 h-lim-p 0.0008 0.0339 5.6785 3672.135415 4 0.0003 112 | 0/8 5 h-lim-p 0.0031 0.2815 0.5297 3672.135385 3 0.0002 134 | 0/8 6 h-lim-p 0.0006 1.1792 0.1868 3672.135380 0 0.0003 154 | 0/8 7 h-lim-p 0.0141 20.0000 0.0038 3672.135372 0 0.0212 174 | 0/8 8 h-lim-p 0.0038 20.0000 0.0210 3672.134904 0 0.0227 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3672.134899 0 1.0938 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3672.134899 0 1.0938 236 | 0/8 11 h-lim-p 1.5390 20.0000 0.0000 3672.134899 0 2.3086 256 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3672.134899 0 0.3125 278 | 0/8 13 h-lim-p 0.0184 20.0000 0.0000 3672.134899 0 0.0184 298 | 0/8 14 h-lim-p 0.0083 20.0000 0.0000 3672.134899 0 0.0000 339 | 0/8 15 h-lim-p 0.0000 20.0000 0.0017 | 0/8 16 h-lim-p 0.0000 20.0000 0.0017 Out... lnL = -3672.134899 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3672.134899 Node 7: lnL = -3672.134899 Node 8: lnL = -3672.134899 Node 9: lnL = -3672.134899 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 853 Sequential format.. Reading seq # 1: YOL012C_Sbay Reading seq # 2: YOL012C_Scer Reading seq # 3: YOL012C_Skud Reading seq # 4: YOL012C_Smik Reading seq # 5: YOL012C_Spar Sequences read.. Counting patterns.. # site patterns = 302 Counting frequencies.. 120 bytes for distance 48320 bytes for lkl0 38656 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.198704 0.037596 0.031829 0.161156 0.023936 0.226348 0.249419 0.148244 lnL0 = -3597.007216 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3597.007216 x= 0.19870 0.03760 0.03183 0.16116 0.02394 0.22635 0.24942 0.14824 1 h-lim-p 0.0004 0.0188 424.2232 3585.105204 4 0.0002 31 | 0/8 2 h-lim-p 0.0002 0.0020 95.7832 3583.507887 0 0.0005 44 | 0/8 3 h-lim-p 0.0005 0.0041 56.2823 3582.749283 0 0.0008 56 | 0/8 4 h-lim-p 0.0031 0.0244 7.8815 3582.730555 5 0.0006 78 | 0/8 5 h-lim-p 0.0028 0.0488 1.7458 3582.729594 3 0.0005 97 | 0/8 6 h-lim-p 0.0011 0.4288 0.8271 3582.728670 1 0.0014 111 | 0/8 7 h-lim-p 0.0068 1.5995 0.1722 3582.693905 0 0.0407 133 | 0/8 8 h-lim-p 0.0021 0.1653 3.3211 3582.428173 0 0.0042 154 | 0/8 9 h-lim-p 2.5000 20.0000 0.0030 3582.384823 3 2.5806 172 | 0/8 10 h-lim-p 2.5000 20.0000 0.0020 3582.380584 2 1.2500 196 | 0/8 11 h-lim-p 2.5000 20.0000 0.0001 3582.380580 0 1.0938 216 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3582.380580 0 1.0938 236 | 0/8 13 h-lim-p 1.4114 20.0000 0.0000 3582.380580 0 0.6175 256 | 0/8 14 h-lim-p 0.3517 20.0000 0.0000 3582.380580 0 0.1758 276 | 0/8 15 h-lim-p 0.0856 20.0000 0.0000 3582.380580 0 0.0856 296 | 0/8 16 h-lim-p 0.0478 20.0000 0.0000 3582.380580 0 0.0000 325 | 0/8 17 h-lim-p 0.0003 20.0000 0.0000 3582.380580 0 0.0000 356 Out... lnL = -3582.380580 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3582.380580 Node 7: lnL = -3582.380580 Node 8: lnL = -3582.380580 Node 9: lnL = -3582.380580 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 594 Sequential format.. Reading seq # 1: YOL013C_Sbay Reading seq # 2: YOL013C_Scer Reading seq # 3: YOL013C_Skud Reading seq # 4: YOL013C_Smik Reading seq # 5: YOL013C_Spar Sequences read.. Counting patterns.. # site patterns = 204 Counting frequencies.. 120 bytes for distance 32640 bytes for lkl0 26112 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.161356 0.062570 0.063449 0.115083 0.063080 0.140156 0.171740 0.117868 lnL0 = -2495.065443 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2495.065443 x= 0.16136 0.06257 0.06345 0.11508 0.06308 0.14016 0.17174 0.11787 1 h-lim-p 0.0011 0.0090 98.9427 2494.050073 4 0.0002 31 | 0/8 2 h-lim-p 0.0009 0.0074 19.5966 2493.992537 7 0.0003 60 | 0/8 3 h-lim-p 0.0005 0.0200 11.0207 2493.979605 4 0.0003 80 | 0/8 4 h-lim-p 0.0008 0.0533 3.8987 2493.977528 3 0.0003 99 | 0/8 5 h-lim-p 0.0074 1.5907 0.1695 2493.977522 0 0.0005 114 | 0/8 6 h-lim-p 0.0048 13.0524 0.0164 2493.977521 0 0.0010 135 | 0/8 7 h-lim-p 0.0035 20.0000 0.0049 2493.977514 0 0.0138 157 | 0/8 8 h-lim-p 0.0025 20.0000 0.0273 2493.977304 0 0.0151 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2493.977296 1 0.9961 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2493.977296 0 1.0938 221 | 0/8 11 h-lim-p 1.8135 20.0000 0.0000 2493.977296 0 1.8135 241 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2493.977296 0 0.0391 266 | 0/8 13 h-lim-p 0.0109 20.0000 0.0000 2493.977296 0 0.0000 303 Out... lnL = -2493.977296 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2493.977296 Node 7: lnL = -2493.977296 Node 8: lnL = -2493.977296 Node 9: lnL = -2493.977296 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 900 Sequential format.. Reading seq # 1: YOL014W_Sbay Reading seq # 2: YOL014W_Scer Reading seq # 3: YOL014W_Skud Reading seq # 4: YOL014W_Smik Reading seq # 5: YOL014W_Spar Sequences read.. Counting patterns.. # site patterns = 424 Counting frequencies.. 120 bytes for distance 67840 bytes for lkl0 54272 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.366931 0.009489 0.377303 0.174202 0.119829 0.318563 0.395473 0.266128 lnL0 = -4246.940713 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4246.940713 x= 0.36693 0.00949 0.37730 0.17420 0.11983 0.31856 0.39547 0.26613 1 h-lim-p 0.0193 2.0449 66.3647 4245.317696 5 0.0008 37 | 0/8 2 h-lim-p 0.0010 0.0078 26.0359 4245.177294 2 0.0005 53 | 0/8 3 h-lim-p 0.0006 0.0305 21.0926 4244.991833 0 0.0011 66 | 0/8 4 h-lim-p 0.0055 0.0704 4.3067 4244.980499 2 0.0013 83 | 0/8 5 h-lim-p 0.0044 0.4649 1.2812 4244.977819 4 0.0036 104 | 0/8 6 h-lim-p 0.0488 6.5034 0.0934 4244.977765 0 0.0061 118 | 0/8 7 h-lim-p 0.0096 11.4027 0.0593 4244.977585 0 0.0192 139 | 0/8 8 h-lim-p 0.0154 14.4879 0.0739 4244.972507 0 0.0617 161 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 4244.972369 2 1.0889 185 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4244.972369 0 1.0938 205 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4244.972369 0 1.0938 225 | 0/8 12 h-lim-p 1.5172 20.0000 0.0000 4244.972369 0 1.3276 245 | 0/8 13 h-lim-p 0.9479 20.0000 0.0000 4244.972369 0 0.0009 274 Out... lnL = -4244.972369 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4244.972369 Node 7: lnL = -4244.972369 Node 8: lnL = -4244.972369 Node 9: lnL = -4244.972369 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 842 Sequential format.. Reading seq # 1: YOL015W_Sbay Reading seq # 2: YOL015W_Scer Reading seq # 3: YOL015W_Skud Reading seq # 4: YOL015W_Smik Reading seq # 5: YOL015W_Spar Sequences read.. Counting patterns.. # site patterns = 366 Counting frequencies.. 120 bytes for distance 58560 bytes for lkl0 46848 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.377403 0.124942 0.222106 0.149647 0.105768 0.173314 0.462814 0.283337 lnL0 = -4094.891781 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4094.891781 x= 0.37740 0.12494 0.22211 0.14965 0.10577 0.17331 0.46281 0.28334 1 h-lim-p 0.0046 0.0366 52.5027 4093.717394 4 0.0009 31 | 0/8 2 h-lim-p 0.0015 0.0117 22.7475 4093.366153 5 0.0015 53 | 0/8 3 h-lim-p 0.0009 0.0070 39.0537 4093.286194 7 0.0003 83 | 0/8 4 h-lim-p 0.0021 0.1313 5.0361 4093.258820 1 0.0026 97 | 0/8 5 h-lim-p 0.0041 0.1027 3.1965 4093.255266 2 0.0010 114 | 0/8 6 h-lim-p 0.0016 0.2241 1.9712 4093.253717 4 0.0012 134 | 0/8 7 h-lim-p 0.0093 2.8137 0.2502 4093.253641 0 0.0023 147 | 0/8 8 h-lim-p 0.1712 20.0000 0.0034 4093.248688 0 1.3699 170 | 0/8 9 h-lim-p 2.5000 20.0000 0.0012 4093.248050 3 1.0004 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4093.248050 0 1.0938 216 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4093.248050 0 1.0938 236 | 0/8 12 h-lim-p 1.8637 20.0000 0.0000 4093.248050 0 0.0073 263 | 0/8 13 h-lim-p 0.0023 20.0000 0.0000 4093.248050 0 0.0001 286 Out... lnL = -4093.248050 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4093.248050 Node 7: lnL = -4093.248050 Node 8: lnL = -4093.248050 Node 9: lnL = -4093.248050 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 501 Sequential format.. Reading seq # 1: YOL018C_Sbay Reading seq # 2: YOL018C_Scer Reading seq # 3: YOL018C_Skud Reading seq # 4: YOL018C_Smik Reading seq # 5: YOL018C_Spar Sequences read.. Counting patterns.. # site patterns = 183 Counting frequencies.. 120 bytes for distance 29280 bytes for lkl0 23424 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.221139 0.150621 0.070863 0.250404 0.067209 0.933385 0.094664 0.129103 lnL0 = -1909.099012 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1909.099012 x= 0.22114 0.15062 0.07086 0.25040 0.06721 0.93338 0.09466 0.12910 1 h-lim-p 0.0004 0.0032 169.8809 1901.851375 0 0.0008 23 | 0/8 2 h-lim-p 0.0003 0.0021 76.3738 1900.163964 0 0.0005 36 | 0/8 3 h-lim-p 0.0011 0.0087 19.6689 1899.983044 2 0.0010 52 | 0/8 4 h-lim-p 0.0042 0.1122 4.7939 1899.967584 5 0.0014 77 | 0/8 5 h-lim-p 0.0021 0.0518 3.2322 1899.949314 0 0.0041 90 | 0/8 6 h-lim-p 0.0016 0.0129 7.4467 1899.842119 m 0.0129 102 | 1/8 7 h-lim-p 0.0471 7.3060 1.4068 .. | 1/8 8 h-lim-p 0.0000 0.0083 34.6662 1899.395028 0 0.0006 157 | 1/8 9 h-lim-p 0.0014 0.0204 16.1525 1899.309230 7 0.0008 186 | 1/8 10 h-lim-p 0.0045 0.2436 2.7757 1899.304894 4 0.0012 207 | 1/8 11 h-lim-p 0.0026 0.1302 1.2160 1899.304052 2 0.0013 223 | 1/8 12 h-lim-p 0.0033 1.1272 0.4879 1899.303516 0 0.0066 236 | 1/8 13 h-lim-p 0.0025 3.4275 1.2859 1899.300301 0 0.0150 257 | 1/8 14 h-lim-p 2.5000 20.0000 0.0054 1899.295141 6 0.8320 283 | 0/8 15 h-lim-p 0.0073 1.6888 0.6140 1899.294876 2 0.0017 307 | 0/8 16 h-lim-p 0.6462 20.0000 0.0016 1899.292932 3 8.0402 338 | 0/8 17 h-lim-p 2.5000 20.0000 0.0039 1899.291987 4 1.5366 369 | 0/8 18 h-lim-p 2.5000 20.0000 0.0002 1899.291987 0 1.0938 389 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1899.291987 0 1.0938 409 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 1899.291987 0 1.0938 429 | 0/8 21 h-lim-p 0.3318 20.0000 0.0000 1899.291987 0 0.0726 450 | 0/8 22 h-lim-p 0.0136 20.0000 0.0002 1899.291987 0 0.0136 470 | 0/8 23 h-lim-p 0.0055 20.0000 0.0004 1899.291987 0 0.0000 510 | 0/8 24 h-lim-p 0.0000 20.0000 0.0000 1899.291987 0 0.0000 542 | 0/8 25 h-lim-p 0.0000 20.0000 0.0000 1899.291987 0 0.0000 576 | 0/8 26 h-lim-p 0.0000 20.0000 0.0000 | 0/8 27 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1899.291987 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1899.291987 Node 7: lnL = -1899.291987 Node 8: lnL = -1899.291987 Node 9: lnL = -1899.291987 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 861 Sequential format.. Reading seq # 1: YOL019W_Sbay Reading seq # 2: YOL019W_Scer Reading seq # 3: YOL019W_Skud Reading seq # 4: YOL019W_Smik Reading seq # 5: YOL019W_Spar Sequences read.. Counting patterns.. # site patterns = 261 Counting frequencies.. 120 bytes for distance 41760 bytes for lkl0 33408 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.160829 0.000060 0.088602 0.115861 0.090975 0.194592 0.197829 0.119934 lnL0 = -3686.607677 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3686.607677 x= 0.16083 0.00006 0.08860 0.11586 0.09097 0.19459 0.19783 0.11993 1 h-lim-p 0.0003 0.0025 203.7980 3683.070063 4 0.0001 31 | 0/8 2 h-lim-p 0.0003 0.0022 91.3611 3682.013820 7 0.0003 56 | 0/8 3 h-lim-p 0.0007 0.0083 37.6632 3681.910678 7 0.0002 82 | 0/8 4 h-lim-p 0.0008 0.0167 8.3386 3681.901295 6 0.0003 109 | 0/8 5 h-lim-p 0.0024 0.1157 1.0005 3681.901162 2 0.0003 127 | 0/8 6 h-lim-p 0.0043 2.0845 0.0607 3681.901038 1 0.0054 141 | 0/8 7 h-lim-p 0.0014 0.6717 0.2247 3681.900184 0 0.0029 162 | 0/8 8 h-lim-p 0.0018 0.1116 0.3695 3681.877644 0 0.0071 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3681.877574 2 0.9644 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3681.877574 0 1.0938 228 | 0/8 11 h-lim-p 1.5191 20.0000 0.0000 3681.877574 0 1.3292 248 | 0/8 12 h-lim-p 1.5699 20.0000 0.0000 3681.877574 0 1.5699 268 | 0/8 13 h-lim-p 1.2548 20.0000 0.0000 3681.877574 0 0.3137 289 | 0/8 14 h-lim-p 0.0558 20.0000 0.0000 3681.877574 0 0.0140 310 | 0/8 15 h-lim-p 0.0053 20.0000 0.0001 3681.877574 0 0.0000 349 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -3681.877574 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3681.877574 Node 7: lnL = -3681.877574 Node 8: lnL = -3681.877574 Node 9: lnL = -3681.877574 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 820 Sequential format.. Reading seq # 1: YOL020W_Sbay Reading seq # 2: YOL020W_Scer Reading seq # 3: YOL020W_Skud Reading seq # 4: YOL020W_Smik Reading seq # 5: YOL020W_Spar Sequences read.. Counting patterns.. # site patterns = 334 Counting frequencies.. 120 bytes for distance 53440 bytes for lkl0 42752 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.042451 0.075198 0.422893 0.262223 0.296029 0.462751 0.441147 lnL0 = -3955.541108 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3955.541108 x= 0.00006 0.04245 0.07520 0.42289 0.26222 0.29603 0.46275 0.44115 1 h-lim-p 0.0000 0.0000 458.8515 3955.285482 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0006 930.1211 3871.844014 1 0.0004 41 | 1/8 3 h-lim-p 0.0003 0.0020 169.8660 3865.188898 0 0.0005 54 | 1/8 4 h-lim-p 0.0006 0.0046 83.4587 3863.322888 1 0.0007 68 | 1/8 5 h-lim-p 0.0034 0.0273 15.7876 3863.169021 7 0.0012 97 | 1/8 6 h-lim-p 0.0109 0.4351 1.6938 3862.955325 5 0.0121 120 | 1/8 7 h-lim-p 0.0088 0.1319 2.3367 3848.971656 9 0.0565 155 | 0/8 8 h-lim-p 0.0004 0.0030 69.8731 3847.337560 0 0.0006 167 | 0/8 9 h-lim-p 0.0004 0.0035 9.4104 3847.137630 m 0.0035 179 | 0/8 10 h-lim-p 0.4598 4.2418 0.0709 3845.973730 4 0.4706 199 | 0/8 11 h-lim-p 0.1349 1.0789 0.0181 3845.927325 0 0.5394 221 | 0/8 12 h-lim-p 0.1876 1.5006 0.0052 3845.924129 0 0.7503 243 | 0/8 13 h-lim-p 2.5000 20.0000 0.0012 3845.923841 4 0.7088 273 | 0/8 14 h-lim-p 2.5000 20.0000 0.0002 3845.923826 2 0.7996 298 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 3845.923826 0 1.0938 318 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 3845.923826 0 1.0938 338 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 3845.923826 0 1.0938 358 | 0/8 18 h-lim-p 1.8342 20.0000 0.0000 3845.923826 0 0.1146 381 | 0/8 19 h-lim-p 0.0240 20.0000 0.0000 3845.923826 0 0.0000 424 Out... lnL = -3845.923826 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3845.923826 Node 7: lnL = -3845.923826 Node 8: lnL = -3845.923826 Node 9: lnL = -3845.923826 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 824 Sequential format.. Reading seq # 1: YOL021C_Sbay Reading seq # 2: YOL021C_Scer Reading seq # 3: YOL021C_Skud Reading seq # 4: YOL021C_Smik Reading seq # 5: YOL021C_Spar Sequences read.. Counting patterns.. # site patterns = 342 Counting frequencies.. 120 bytes for distance 54720 bytes for lkl0 43776 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.042364 0.072826 0.411813 0.255566 0.289035 0.448435 0.429961 lnL0 = -3837.199283 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3837.199283 x= 0.00006 0.04236 0.07283 0.41181 0.25557 0.28904 0.44843 0.42996 1 h-lim-p 0.0000 0.0000 463.9233 3836.927741 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0007 828.9018 3763.092708 0 0.0003 39 | 1/8 3 h-lim-p 0.0004 0.0031 154.6883 3754.065522 0 0.0008 52 | 1/8 4 h-lim-p 0.0010 0.0077 50.0475 3752.819423 1 0.0012 66 | 1/8 5 h-lim-p 0.0049 0.0394 7.2029 3752.699341 3 0.0021 84 | 1/8 6 h-lim-p 0.0065 0.1820 2.2774 3750.189628 0 0.0260 98 | 1/8 7 h-lim-p 0.0025 0.0198 17.6147 3737.219629 0 0.0050 111 | 1/8 8 h-lim-p 0.0011 0.0085 56.3051 3735.504523 7 0.0009 140 | 1/8 9 h-lim-p 0.1771 1.4168 0.1284 3729.874141 0 0.5313 153 | 1/8 10 h-lim-p 2.0902 16.7217 0.0256 3729.612287 7 0.6549 190 | 1/8 11 h-lim-p 2.1404 20.0000 0.0078 3729.597683 5 0.4742 219 | 1/8 12 h-lim-p 2.5000 20.0000 0.0005 3729.597495 3 0.7439 246 | 1/8 13 h-lim-p 2.5000 20.0000 0.0001 3729.597490 0 0.6250 266 | 1/8 14 h-lim-p 1.6557 20.0000 0.0000 3729.597490 0 0.7244 285 | 0/8 15 h-lim-p 0.0158 20.0000 0.0018 3729.597490 0 0.0034 305 | 0/8 16 h-lim-p 0.1192 0.9538 0.0000 3729.597490 m 0.9538 325 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 3729.597490 0 1.0938 345 | 1/8 18 h-lim-p 1.6298 20.0000 0.0000 3729.597490 0 0.7130 364 | 1/8 19 h-lim-p 2.5000 20.0000 0.0000 3729.597490 0 0.0000 398 Out... lnL = -3729.597490 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3729.597490 Node 7: lnL = -3729.597490 Node 8: lnL = -3729.597490 Node 9: lnL = -3729.597490 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 859 Sequential format.. Reading seq # 1: YOL022C_Sbay Reading seq # 2: YOL022C_Scer Reading seq # 3: YOL022C_Skud Reading seq # 4: YOL022C_Smik Reading seq # 5: YOL022C_Spar Sequences read.. Counting patterns.. # site patterns = 309 Counting frequencies.. 120 bytes for distance 49440 bytes for lkl0 39552 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.066757 0.121472 0.689279 0.431291 0.505669 0.751263 0.717151 lnL0 = -4071.689590 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4071.689590 x= 0.00006 0.06676 0.12147 0.68928 0.43129 0.50567 0.75126 0.71715 1 h-lim-p 0.0000 0.0000 502.7780 4071.411473 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0000 12905.5650 3946.143836 m 0.0000 34 | 2/8 3 h-lim-p 0.0001 0.0007 928.4322 3816.990436 0 0.0005 48 | 2/8 4 h-lim-p 0.0002 0.0013 248.5042 3801.302519 0 0.0006 62 | 2/8 5 h-lim-p 0.0002 0.0018 222.1878 3790.794626 0 0.0007 75 | 2/8 6 h-lim-p 0.0040 0.0324 27.8154 3789.569082 5 0.0031 98 | 1/8 7 h-lim-p 0.0009 0.0121 96.0151 3787.830074 5 0.0006 122 | 1/8 8 h-lim-p 0.0020 0.0374 27.7456 3786.377942 0 0.0061 135 | 1/8 9 h-lim-p 0.3286 2.6290 0.2331 3783.558135 2 0.3081 151 | 1/8 10 h-lim-p 1.3536 10.8288 0.0313 3783.127177 7 1.0288 183 | 1/8 11 h-lim-p 2.0041 16.0331 0.0112 3783.069941 7 1.4328 219 | 1/8 12 h-lim-p 2.5000 20.0000 0.0047 3783.058068 4 2.1038 247 | 1/8 13 h-lim-p 2.5000 20.0000 0.0009 3783.057661 2 1.2305 271 | 1/8 14 h-lim-p 2.5000 20.0000 0.0002 3783.057652 0 1.0938 290 | 0/8 15 h-lim-p 0.0334 20.0000 0.0052 3783.057652 0 0.0036 311 | 0/8 16 h-lim-p 0.1241 0.9931 0.0000 3783.057652 m 0.9931 331 | 1/8 17 h-lim-p 1.3555 20.0000 0.0000 3783.057652 0 0.2965 352 | 1/8 18 h-lim-p 2.1570 20.0000 0.0000 3783.057652 0 1.8874 371 | 1/8 19 h-lim-p 2.5000 20.0000 0.0000 3783.057652 0 1.0938 390 | 1/8 20 h-lim-p 2.5000 20.0000 0.0000 3783.057652 0 2.1875 409 | 1/8 21 h-lim-p 2.5000 20.0000 0.0000 3783.057652 0 0.0781 432 | 1/8 22 h-lim-p 0.0779 20.0000 0.0000 3783.057652 0 0.0195 452 Out... lnL = -3783.057652 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3783.057652 Node 7: lnL = -3783.057652 Node 8: lnL = -3783.057652 Node 9: lnL = -3783.057652 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 642 Sequential format.. Reading seq # 1: YOL025W_Sbay Reading seq # 2: YOL025W_Scer Reading seq # 3: YOL025W_Skud Reading seq # 4: YOL025W_Smik Reading seq # 5: YOL025W_Spar Sequences read.. Counting patterns.. # site patterns = 309 Counting frequencies.. 120 bytes for distance 49440 bytes for lkl0 39552 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.050903 0.091454 0.530565 0.326242 0.373579 0.578404 0.542603 lnL0 = -3303.300118 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3303.300118 x= 0.00006 0.05090 0.09145 0.53057 0.32624 0.37358 0.57840 0.54260 1 h-lim-p 0.0000 0.0000 376.6647 3303.167539 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0008 677.2079 3213.979424 8 0.0006 57 | 1/8 3 h-lim-p 0.0006 0.0051 101.6647 3206.980958 0 0.0013 70 | 1/8 4 h-lim-p 0.0016 0.0129 41.2627 3205.782183 6 0.0016 96 | 1/8 5 h-lim-p 0.0067 0.0536 8.1015 3205.310995 1 0.0084 110 | 1/8 6 h-lim-p 0.0092 0.0735 4.1715 3203.326452 0 0.0367 124 | 1/8 7 h-lim-p 0.0073 0.0582 3.8354 3189.555406 0 0.0291 138 | 1/8 8 h-lim-p 0.0024 0.0193 26.6433 3188.882299 6 0.0018 162 | 1/8 9 h-lim-p 0.1160 0.9278 0.2922 3186.456928 0 0.4639 176 | 1/8 10 h-lim-p 0.5300 4.2401 0.0453 3186.242596 2 0.4969 199 | 1/8 11 h-lim-p 0.9202 13.5615 0.0245 3186.216791 4 0.3549 226 | 1/8 12 h-lim-p 1.5076 20.0000 0.0058 3186.213315 5 0.5134 258 | 1/8 13 h-lim-p 2.5000 20.0000 0.0007 3186.213217 2 0.5859 282 | 1/8 14 h-lim-p 2.5000 20.0000 0.0001 3186.213214 1 0.6152 304 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 3186.213213 0 1.0938 323 | 0/8 16 h-lim-p 0.0000 0.0000 0.0009 h-lim-p: 2.55292416e-19 2.04233933e-18 9.10090044e-04 3186.213213 .. | 1/8 17 h-lim-p 0.0000 20.0000 0.0051 3186.213213 0 0.0006 364 | 1/8 18 h-lim-p 0.0011 20.0000 0.0030 3186.213213 0 0.0010 383 | 1/8 19 h-lim-p 0.0019 20.0000 0.0015 3186.213213 0 0.0008 402 | 1/8 20 h-lim-p 0.0015 20.0000 0.0009 3186.213213 0 0.0003 422 | 1/8 21 h-lim-p 0.0015 20.0000 0.0002 3186.213213 0 0.0022 441 | 1/8 22 h-lim-p 0.0053 20.0000 0.0001 3186.213213 0 0.0023 460 | 1/8 23 h-lim-p 0.0239 20.0000 0.0000 3186.213213 0 0.0477 480 | 1/8 24 h-lim-p 0.0189 20.0000 0.0000 3186.213213 0 0.0377 500 | 1/8 25 h-lim-p 2.5000 20.0000 0.0000 3186.213213 0 1.2500 519 | 1/8 26 h-lim-p 2.5000 20.0000 0.0000 3186.213213 0 0.6250 539 | 1/8 27 h-lim-p 1.6663 20.0000 0.0000 3186.213213 0 0.0000 579 Out... lnL = -3186.213213 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3186.213213 Node 7: lnL = -3186.213213 Node 8: lnL = -3186.213213 Node 9: lnL = -3186.213213 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 633 Sequential format.. Reading seq # 1: YOL026C_Sbay Reading seq # 2: YOL026C_Scer Reading seq # 3: YOL026C_Skud Reading seq # 4: YOL026C_Smik Reading seq # 5: YOL026C_Spar Sequences read.. Counting patterns.. # site patterns = 310 Counting frequencies.. 120 bytes for distance 49600 bytes for lkl0 39680 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.061498 0.120658 0.687206 0.426400 0.485784 0.762688 0.705557 lnL0 = -3599.846406 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3599.846406 x= 0.00006 0.06150 0.12066 0.68721 0.42640 0.48578 0.76269 0.70556 1 h-lim-p 0.0000 0.0000 368.9759 3599.734015 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0000 265004.7003 3540.949059 m 0.0000 34 | 2/8 3 h-lim-p 0.0002 0.0012 582.7128 3433.603755 0 0.0009 48 | 2/8 4 h-lim-p 0.0002 0.0015 193.1179 3423.115630 0 0.0008 62 | 2/8 5 h-lim-p 0.0005 0.0043 106.0913 3416.475514 0 0.0011 75 | 2/8 6 h-lim-p 0.0011 0.0088 29.1863 3415.330290 0 0.0022 88 | 1/8 7 h-lim-p 0.0011 0.0850 57.2428 3414.452880 4 0.0006 109 | 1/8 8 h-lim-p 0.0027 0.0251 11.9616 3414.247934 6 0.0023 134 | 1/8 9 h-lim-p 0.0896 0.7165 0.2881 3408.071638 0 0.3583 148 | 1/8 10 h-lim-p 0.1416 1.1329 0.1434 3403.706088 m 1.1329 167 | 0/8 11 h-lim-p 0.0000 0.0000 8.1850 h-lim-p: 3.25316009e-19 2.60252807e-18 8.18496212e+00 3403.706088 .. | 0/8 12 h-lim-p 0.0000 0.0095 22.2370 3403.570508 0 0.0006 200 | 0/8 13 h-lim-p 0.0001 0.0004 12.4682 3403.535510 m 0.0004 212 | 1/8 14 h-lim-p 0.0008 0.1972 5.4670 3403.523978 5 0.0009 238 | 1/8 15 h-lim-p 0.0007 0.0128 7.3680 3403.511391 0 0.0014 251 | 1/8 16 h-lim-p 0.0010 0.0079 3.2750 3403.507577 2 0.0010 267 | 1/8 17 h-lim-p 0.0052 0.2068 0.6228 3403.506972 4 0.0029 290 | 1/8 18 h-lim-p 0.0111 2.4427 0.1637 3403.506913 1 0.0028 312 | 1/8 19 h-lim-p 0.1474 20.0000 0.0031 3403.502639 0 1.1794 334 | 1/8 20 h-lim-p 2.5000 20.0000 0.0011 3403.502115 3 1.0004 359 | 1/8 21 h-lim-p 2.5000 20.0000 0.0000 3403.502115 0 1.0938 378 | 1/8 22 h-lim-p 1.9352 20.0000 0.0000 3403.502115 0 0.8467 397 | 1/8 23 h-lim-p 0.5104 20.0000 0.0000 3403.502115 0 0.0020 423 | 1/8 24 h-lim-p 0.0008 20.0000 0.0001 3403.502115 0 0.0008 442 | 1/8 25 h-lim-p 0.0008 20.0000 0.0001 3403.502115 0 0.0000 477 | 1/8 26 h-lim-p 0.0000 20.0000 0.0004 | 1/8 27 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -3403.502115 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3403.502115 Node 7: lnL = -3403.502115 Node 8: lnL = -3403.502115 Node 9: lnL = -3403.502115 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 297 Sequential format.. Reading seq # 1: YOL027C_Sbay Reading seq # 2: YOL027C_Scer Reading seq # 3: YOL027C_Skud Reading seq # 4: YOL027C_Smik Reading seq # 5: YOL027C_Spar Sequences read.. Counting patterns.. # site patterns = 97 Counting frequencies.. 120 bytes for distance 15520 bytes for lkl0 12416 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.021450 0.034841 0.207323 0.128314 0.144857 0.225477 0.212299 lnL0 = -1098.533381 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1098.533381 x= 0.00006 0.02145 0.03484 0.20732 0.12831 0.14486 0.22548 0.21230 1 h-lim-p 0.0000 0.0000 237.2610 1098.462918 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0009 357.5910 1082.487588 0 0.0005 39 | 1/8 3 h-lim-p 0.0002 0.0015 78.1900 1081.034836 0 0.0006 52 | 1/8 4 h-lim-p 0.0022 0.0173 13.5329 1080.974669 8 0.0006 85 | 1/8 5 h-lim-p 0.0059 0.0829 1.4469 1080.921219 2 0.0055 101 | 1/8 6 h-lim-p 0.0031 0.0745 2.5485 1079.441236 0 0.0188 115 | 1/8 7 h-lim-p 0.0005 0.0044 23.4485 1072.188096 0 0.0033 129 | 1/8 8 h-lim-p 0.0016 0.0129 12.3808 1072.137605 5 0.0006 150 | 1/8 9 h-lim-p 0.1812 4.7856 0.0441 1071.418613 0 0.5435 163 | 0/8 10 h-lim-p 0.0220 0.3734 1.0908 1071.417674 5 0.0010 197 | 0/8 11 h-lim-p 0.0192 0.1536 0.0384 1071.295241 m 0.1536 209 | 1/8 12 h-lim-p 1.1247 10.2696 0.0052 1071.269601 6 0.7047 245 | 1/8 13 h-lim-p 1.7115 20.0000 0.0021 1071.266365 4 0.6711 272 | 1/8 14 h-lim-p 2.5000 20.0000 0.0003 1071.266321 3 0.8171 298 | 1/8 15 h-lim-p 2.5000 20.0000 0.0001 1071.266318 1 0.9961 319 | 0/8 16 h-lim-p 0.0089 20.0000 0.0059 1071.266318 0 0.0039 338 | 0/8 17 h-lim-p 0.1193 0.9545 0.0000 1071.266318 m 0.9545 358 | 1/8 18 h-lim-p 0.3518 20.0000 0.0001 1071.266318 0 0.0385 380 | 1/8 19 h-lim-p 1.6319 20.0000 0.0000 1071.266318 0 1.4279 399 | 1/8 20 h-lim-p 2.5000 20.0000 0.0000 1071.266318 0 2.1875 418 | 1/8 21 h-lim-p 2.3907 20.0000 0.0000 1071.266318 0 2.0919 437 | 1/8 22 h-lim-p 2.4101 20.0000 0.0000 1071.266318 0 1.0544 456 | 1/8 23 h-lim-p 2.5000 20.0000 0.0000 1071.266318 0 7.5000 476 | 1/8 24 h-lim-p 1.2593 20.0000 0.0000 1071.266318 0 0.3148 496 | 1/8 25 h-lim-p 0.4595 20.0000 0.0000 1071.266318 0 0.0287 518 | 1/8 26 h-lim-p 0.0296 20.0000 0.0000 1071.266318 0 0.0000 559 Out... lnL = -1071.266318 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1071.266318 Node 7: lnL = -1071.266318 Node 8: lnL = -1071.266318 Node 9: lnL = -1071.266318 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 704 Sequential format.. Reading seq # 1: YOL028C_Sbay Reading seq # 2: YOL028C_Scer Reading seq # 3: YOL028C_Skud Reading seq # 4: YOL028C_Smik Reading seq # 5: YOL028C_Spar Sequences read.. Counting patterns.. # site patterns = 268 Counting frequencies.. 120 bytes for distance 42880 bytes for lkl0 34304 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.041546 0.065623 0.370600 0.230946 0.264418 0.410819 0.397601 lnL0 = -2955.278712 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2955.278712 x= 0.00006 0.04155 0.06562 0.37060 0.23095 0.26442 0.41082 0.39760 1 h-lim-p 0.0000 0.0000 440.4698 2954.949616 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0004 997.2596 2881.894205 2 0.0003 43 | 1/8 3 h-lim-p 0.0002 0.0016 148.2716 2876.337229 0 0.0006 56 | 1/8 4 h-lim-p 0.0007 0.0056 70.3227 2874.347451 0 0.0011 68 | 1/8 5 h-lim-p 0.0036 0.0288 8.4103 2874.265271 2 0.0017 84 | 1/8 6 h-lim-p 0.0369 0.3638 0.3854 2867.906213 4 0.2674 107 | 1/8 7 h-lim-p 0.0009 0.0069 37.0776 2859.616244 0 0.0034 128 | 1/8 8 h-lim-p 0.0013 0.0102 22.8206 2859.343626 4 0.0010 148 | 1/8 9 h-lim-p 0.8870 20.0000 0.0256 2858.990490 8 0.4930 179 | 0/8 10 h-lim-p 0.0047 0.9177 2.7046 2858.986605 3 0.0010 205 | 0/8 11 h-lim-p 0.0883 0.7065 0.0202 2858.938493 0 0.3532 219 | 0/8 12 h-lim-p 0.3337 2.6699 0.0038 2858.934974 0 0.6675 240 | 0/8 13 h-lim-p 2.5000 20.0000 0.0008 2858.934707 3 0.8855 268 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 2858.934703 1 0.9961 290 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2858.934703 0 1.0938 310 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 2858.934703 0 1.0938 330 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 2858.934703 0 1.0938 350 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 2858.934703 0 2.5000 370 | 0/8 19 h-lim-p 2.0798 20.0000 0.0000 2858.934703 0 0.0000 417 Out... lnL = -2858.934703 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2858.934703 Node 7: lnL = -2858.934703 Node 8: lnL = -2858.934703 Node 9: lnL = -2858.934703 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 685 Sequential format.. Reading seq # 1: YOL030W_Sbay Reading seq # 2: YOL030W_Scer Reading seq # 3: YOL030W_Skud Reading seq # 4: YOL030W_Smik Reading seq # 5: YOL030W_Spar Sequences read.. Counting patterns.. # site patterns = 200 Counting frequencies.. 120 bytes for distance 32000 bytes for lkl0 25600 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.031672 0.052703 0.292302 0.180253 0.204798 0.320870 0.305156 lnL0 = -2958.127939 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2958.127939 x= 0.00006 0.03167 0.05270 0.29230 0.18025 0.20480 0.32087 0.30516 1 h-lim-p 0.0000 0.0000 545.7071 2957.772202 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0002 1783.3595 2875.079564 2 0.0002 41 | 1/8 3 h-lim-p 0.0000 0.0003 482.5617 2868.979115 0 0.0001 54 | 1/8 4 h-lim-p 0.0002 0.0016 136.7663 2866.858581 0 0.0003 66 | 1/8 5 h-lim-p 0.0005 0.0040 69.5481 2866.242231 5 0.0003 90 | 1/8 6 h-lim-p 0.0020 0.0272 11.3731 2866.170685 3 0.0008 108 | 1/8 7 h-lim-p 0.0125 0.3642 0.7545 2863.355638 0 0.0749 122 | 1/8 8 h-lim-p 0.0009 0.0074 31.0158 2847.748763 0 0.0037 143 | 1/8 9 h-lim-p 1.2418 9.9341 0.0538 2845.243456 2 0.5821 159 | 1/8 10 h-lim-p 0.5666 7.4856 0.0552 2844.309098 7 0.3791 194 | 0/8 11 h-lim-p 0.0076 2.3136 2.7391 2844.306395 5 0.0006 226 | 0/8 12 h-lim-p 0.1045 11.8773 0.0165 2843.574828 0 1.2539 241 | 0/8 13 h-lim-p 2.2189 20.0000 0.0094 2843.496682 6 0.7529 275 | 0/8 14 h-lim-p 2.5000 20.0000 0.0016 2843.492589 5 0.8900 306 | 0/8 15 h-lim-p 2.5000 20.0000 0.0003 2843.492400 2 1.0889 330 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 2843.492397 0 1.0938 350 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 2843.492397 0 1.0938 370 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 2843.492397 0 0.5469 391 | 0/8 19 h-lim-p 1.1033 20.0000 0.0000 2843.492397 0 0.0005 421 Out... lnL = -2843.492397 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2843.492397 Node 7: lnL = -2843.492397 Node 8: lnL = -2843.492397 Node 9: lnL = -2843.492397 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 685 Sequential format.. Reading seq # 1: YOL031C_Sbay Reading seq # 2: YOL031C_Scer Reading seq # 3: YOL031C_Skud Reading seq # 4: YOL031C_Smik Reading seq # 5: YOL031C_Spar Sequences read.. Counting patterns.. # site patterns = 215 Counting frequencies.. 120 bytes for distance 34400 bytes for lkl0 27520 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.173016 0.134540 0.066638 0.160330 0.205089 0.268541 0.291244 lnL0 = -2824.631601 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2824.631601 x= 0.00006 0.17302 0.13454 0.06664 0.16033 0.20509 0.26854 0.29124 1 h-lim-p 0.0000 0.0000 513.9121 2824.423739 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0005 625.9183 2789.407197 3 0.0003 45 | 1/8 3 h-lim-p 0.0006 0.0046 46.1808 2788.854388 3 0.0005 63 | 1/8 4 h-lim-p 0.0015 0.0156 15.9913 2788.785000 7 0.0005 94 | 1/8 5 h-lim-p 0.0007 0.0287 10.6815 2788.695022 0 0.0011 106 | 1/8 6 h-lim-p 0.0054 0.0694 2.0812 2786.923438 0 0.0217 120 | 1/8 7 h-lim-p 0.0027 0.0234 16.5659 2765.841322 0 0.0082 133 | 1/8 8 h-lim-p 0.0002 0.0016 111.8543 2763.449501 0 0.0004 146 | 1/8 9 h-lim-p 0.1335 1.0684 0.1151 2760.263161 0 0.2671 159 | 0/8 10 h-lim-p 0.0045 0.2208 6.8291 2760.249617 5 0.0006 191 | 0/8 11 h-lim-p 0.1717 20.0000 0.0227 2759.696933 0 0.6866 205 | 0/8 12 h-lim-p 2.4178 19.3420 0.0051 2759.654725 6 0.8203 239 | 0/8 13 h-lim-p 2.5000 20.0000 0.0012 2759.653381 2 0.5859 264 | 0/8 14 h-lim-p 2.4603 20.0000 0.0003 2759.653313 3 0.6612 291 | 0/8 15 h-lim-p 2.1815 20.0000 0.0001 2759.653305 0 0.9544 311 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 2759.653305 0 1.0938 331 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 2759.653305 0 1.0938 351 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 2759.653305 0 2.1875 371 | 0/8 19 h-lim-p 1.9954 20.0000 0.0000 2759.653305 0 0.4989 392 | 0/8 20 h-lim-p 0.9561 20.0000 0.0000 2759.653305 0 0.0149 417 Out... lnL = -2759.653305 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2759.653305 Node 7: lnL = -2759.653305 Node 8: lnL = -2759.653305 Node 9: lnL = -2759.653305 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 355 Sequential format.. Reading seq # 1: YOL032W_Sbay Reading seq # 2: YOL032W_Scer Reading seq # 3: YOL032W_Skud Reading seq # 4: YOL032W_Smik Reading seq # 5: YOL032W_Spar Sequences read.. Counting patterns.. # site patterns = 110 Counting frequencies.. 120 bytes for distance 17600 bytes for lkl0 14080 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.905409 0.627616 0.239114 0.833432 1.688758 1.223905 1.279623 lnL0 = -1575.539922 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1575.539922 x= 0.00006 0.90541 0.62762 0.23911 0.83343 1.68876 1.22391 1.27962 1 h-lim-p 0.0000 0.0000 196.5011 1575.400837 m 0.0000 22 | 1/8 2 h-lim-p 0.0001 0.1960 10.4296 .. | 1/8 3 h-lim-p 0.0000 0.0018 195.8977 1501.866026 m 0.0018 67 | 2/8 4 h-lim-p 0.0039 0.0308 38.1394 1482.068187 0 0.0154 81 | 2/8 5 h-lim-p 0.0045 0.0357 64.6360 .. | 2/8 6 h-lim-p 0.0000 0.0033 96.6749 1474.914376 0 0.0013 134 | 2/8 7 h-lim-p 0.0029 0.0490 42.0110 1313.818710 2 0.0443 153 | 1/8 8 h-lim-p 0.0001 0.0004 539.6023 1313.318165 2 0.0000 169 | 1/8 9 h-lim-p 0.0001 0.0007 50.7702 1312.841696 m 0.0007 181 | 0/8 10 h-lim-p 0.0000 0.0000 199.6284 h-lim-p: 2.72145395e-21 2.17716316e-20 1.99628364e+02 1312.841696 .. | 0/8 11 h-lim-p 0.0000 0.0022 507.4045 1287.427437 0 0.0003 206 | 0/8 12 h-lim-p 0.0002 0.0013 221.7336 1246.203235 m 0.0013 218 | 1/8 13 h-lim-p 0.0002 0.0017 169.7979 1236.435572 0 0.0008 232 | 1/8 14 h-lim-p 0.0002 0.0017 100.6788 1234.426098 0 0.0007 245 | 1/8 15 h-lim-p 0.0021 0.0168 21.1615 1234.136040 8 0.0014 276 | 1/8 16 h-lim-p 0.2402 2.0514 0.1250 1233.240314 0 0.3603 288 | 0/8 17 h-lim-p 0.0050 0.5752 9.0498 1233.208337 7 0.0008 325 | 0/8 18 h-lim-p 0.1401 1.1208 0.0442 1232.928944 0 0.5604 339 | 0/8 19 h-lim-p 2.5000 20.0000 0.0052 1232.918884 6 0.8638 374 | 0/8 20 h-lim-p 2.5000 20.0000 0.0004 1232.918795 2 0.9961 398 | 0/8 21 h-lim-p 2.5000 20.0000 0.0000 1232.918794 0 1.0938 418 | 0/8 22 h-lim-p 2.5000 20.0000 0.0000 1232.918794 0 1.0938 438 | 0/8 23 h-lim-p 1.5427 20.0000 0.0000 1232.918794 0 1.3499 458 | 0/8 24 h-lim-p 1.3544 20.0000 0.0000 1232.918794 0 1.1851 478 | 0/8 25 h-lim-p 0.1391 20.0000 0.0001 1232.918794 0 0.0000 510 | 0/8 26 h-lim-p 0.0002 20.0000 0.0000 1232.918794 0 0.0000 542 Out... lnL = -1232.918794 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1232.918794 Node 7: lnL = -1232.918794 Node 8: lnL = -1232.918794 Node 9: lnL = -1232.918794 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 719 Sequential format.. Reading seq # 1: YOL036W_Sbay Reading seq # 2: YOL036W_Scer Reading seq # 3: YOL036W_Skud Reading seq # 4: YOL036W_Smik Reading seq # 5: YOL036W_Spar Sequences read.. Counting patterns.. # site patterns = 246 Counting frequencies.. 120 bytes for distance 39360 bytes for lkl0 31488 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.191425 0.132773 0.079785 0.185535 0.227178 0.287382 0.323315 lnL0 = -3079.986116 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3079.986116 x= 0.00006 0.19143 0.13277 0.07978 0.18554 0.22718 0.28738 0.32332 1 h-lim-p 0.0000 0.0000 457.7676 3079.788286 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0012 348.0361 3060.651349 9 0.0005 65 | 1/8 3 h-lim-p 0.0003 0.0026 82.4899 3058.467150 0 0.0007 78 | 1/8 4 h-lim-p 0.0006 0.0046 26.4472 3058.210547 1 0.0007 92 | 1/8 5 h-lim-p 0.0017 0.0313 11.1048 3058.002626 5 0.0019 116 | 1/8 6 h-lim-p 0.0079 0.1222 2.6873 3054.904850 0 0.0315 130 | 1/8 7 h-lim-p 0.0017 0.0133 18.5408 3028.385821 0 0.0066 144 | 1/8 8 h-lim-p 0.0004 0.0031 66.4794 3027.269187 1 0.0005 158 | 1/8 9 h-lim-p 0.1753 1.4027 0.1348 3021.702995 0 0.5260 171 | 0/8 10 h-lim-p 0.0516 0.4131 1.3567 3021.702053 4 0.0009 203 | 0/8 11 h-lim-p 0.0787 10.4262 0.0151 3021.596798 0 0.6296 218 | 0/8 12 h-lim-p 2.5000 20.0000 0.0033 3021.589423 3 0.5664 245 | 0/8 13 h-lim-p 1.0366 12.7454 0.0018 3021.587434 4 0.6146 276 | 0/8 14 h-lim-p 2.5000 20.0000 0.0003 3021.587377 1 0.6250 299 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 3021.587377 0 1.0938 319 | 0/8 16 h-lim-p 2.3154 20.0000 0.0000 3021.587377 0 1.0130 339 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 3021.587377 0 1.0938 359 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 3021.587377 0 1.0938 379 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 3021.587377 0 3.7500 399 | 0/8 20 h-lim-p 1.6099 20.0000 0.0000 3021.587377 0 0.3522 420 | 0/8 21 h-lim-p 0.6654 20.0000 0.0000 3021.587377 0 0.0023 447 Out... lnL = -3021.587377 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3021.587377 Node 7: lnL = -3021.587377 Node 8: lnL = -3021.587377 Node 9: lnL = -3021.587377 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 336 Sequential format.. Reading seq # 1: YOL038W_Sbay Reading seq # 2: YOL038W_Scer Reading seq # 3: YOL038W_Skud Reading seq # 4: YOL038W_Smik Reading seq # 5: YOL038W_Spar Sequences read.. Counting patterns.. # site patterns = 161 Counting frequencies.. 120 bytes for distance 25760 bytes for lkl0 20608 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.277441 0.197296 0.110795 0.262387 0.328735 0.420101 0.447783 lnL0 = -1690.592303 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1690.592303 x= 0.00006 0.27744 0.19730 0.11080 0.26239 0.32873 0.42010 0.44778 1 h-lim-p 0.0000 0.0000 196.1682 1690.521284 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0024 271.5825 1667.616713 4 0.0012 48 | 1/8 3 h-lim-p 0.0011 0.0089 22.6151 1667.195040 0 0.0017 60 | 1/8 4 h-lim-p 0.0098 0.0808 3.8696 1667.094998 2 0.0046 76 | 1/8 5 h-lim-p 0.0087 0.1743 2.0396 1664.508313 0 0.0694 91 | 1/8 6 h-lim-p 0.0023 0.0186 17.7260 1656.339146 0 0.0093 105 | 1/8 7 h-lim-p 0.0009 0.0073 38.6011 1654.941552 0 0.0018 118 | 1/8 8 h-lim-p 0.0060 0.0482 7.1041 1654.884762 6 0.0020 145 | 0/8 9 h-lim-p 0.0006 0.0221 24.0737 1653.893196 0 0.0070 160 | 0/8 10 h-lim-p 0.3039 2.4310 0.1172 1652.845783 0 0.4558 172 | 0/8 11 h-lim-p 0.8114 6.4915 0.0499 1652.610264 7 0.4596 209 | 0/8 12 h-lim-p 1.7617 14.0934 0.0123 1652.580535 7 1.0539 248 | 0/8 13 h-lim-p 2.5000 20.0000 0.0027 1652.578790 5 0.8754 280 | 0/8 14 h-lim-p 1.8764 20.0000 0.0012 1652.578673 3 0.5501 309 | 0/8 15 h-lim-p 1.8067 20.0000 0.0004 1652.578664 2 0.9510 334 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1652.578664 0 1.0938 354 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1652.578664 0 2.1875 374 | 0/8 18 h-lim-p 2.0085 20.0000 0.0000 1652.578664 0 0.8787 394 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1652.578664 0 0.0781 418 | 0/8 20 h-lim-p 0.0590 20.0000 0.0000 1652.578664 0 0.0005 444 Out... lnL = -1652.578664 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1652.578664 Node 7: lnL = -1652.578664 Node 8: lnL = -1652.578664 Node 9: lnL = -1652.578664 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 765 Sequential format.. Reading seq # 1: YOL039W_Sbay Reading seq # 2: YOL039W_Scer Reading seq # 3: YOL039W_Skud Reading seq # 4: YOL039W_Smik Reading seq # 5: YOL039W_Spar Sequences read.. Counting patterns.. # site patterns = 228 Counting frequencies.. 120 bytes for distance 36480 bytes for lkl0 29184 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.204250 0.143740 0.077528 0.196700 0.252832 0.308870 0.320786 lnL0 = -3383.655362 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3383.655362 x= 0.00006 0.20425 0.14374 0.07753 0.19670 0.25283 0.30887 0.32079 1 h-lim-p 0.0000 0.0000 575.7137 3383.463182 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0009 365.1388 3354.924446 2 0.0006 44 | 1/8 3 h-lim-p 0.0001 0.0006 204.4725 3348.099389 m 0.0006 56 | 2/8 4 h-lim-p 0.0006 0.0046 69.1922 3341.117917 0 0.0011 69 | 1/8 5 h-lim-p 0.0003 0.0021 225.9924 3338.890468 5 0.0002 90 | 1/8 6 h-lim-p 0.0009 0.0076 45.4535 3338.301004 8 0.0006 122 | 1/8 7 h-lim-p 0.0026 0.0266 11.0411 3338.083051 7 0.0018 153 | 1/8 8 h-lim-p 0.0016 0.0262 12.4443 3337.707902 1 0.0020 167 | 1/8 9 h-lim-p 0.0084 0.1424 2.9238 3298.572920 0 0.0672 182 | 1/8 10 h-lim-p 0.1448 1.1588 0.1796 3288.726824 0 0.5794 196 | 0/8 11 h-lim-p 0.0104 0.0894 10.0179 3288.700985 5 0.0005 228 | 0/8 12 h-lim-p 0.0941 3.9706 0.0525 3286.902136 0 0.7530 243 | 0/8 13 h-lim-p 0.3256 2.6048 0.0179 3286.703720 0 0.6512 264 | 0/8 14 h-lim-p 1.5308 12.2464 0.0053 3286.671841 6 0.7752 298 | 0/8 15 h-lim-p 2.5000 20.0000 0.0013 3286.670845 1 0.4980 321 | 0/8 16 h-lim-p 2.5000 20.0000 0.0002 3286.670801 3 0.7330 350 | 0/8 17 h-lim-p 2.5000 20.0000 0.0001 3286.670799 1 0.6152 373 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 3286.670799 0 1.0938 393 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 3286.670799 0 1.0938 413 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 3286.670799 0 2.1875 433 | 0/8 21 h-lim-p 1.8498 20.0000 0.0000 3286.670799 0 0.0578 457 | 0/8 22 h-lim-p 0.0584 20.0000 0.0000 3286.670799 0 0.0292 477 | 0/8 23 h-lim-p 0.0274 20.0000 0.0000 3286.670799 0 0.0068 498 Out... lnL = -3286.670799 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3286.670799 Node 7: lnL = -3286.670799 Node 8: lnL = -3286.670799 Node 9: lnL = -3286.670799 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 762 Sequential format.. Reading seq # 1: YOL040C_Sbay Reading seq # 2: YOL040C_Scer Reading seq # 3: YOL040C_Skud Reading seq # 4: YOL040C_Smik Reading seq # 5: YOL040C_Spar Sequences read.. Counting patterns.. # site patterns = 236 Counting frequencies.. 120 bytes for distance 37760 bytes for lkl0 30208 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.205632 0.146816 0.076520 0.199908 0.254133 0.309497 0.326071 lnL0 = -3391.671865 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3391.671865 x= 0.00006 0.20563 0.14682 0.07652 0.19991 0.25413 0.30950 0.32607 1 h-lim-p 0.0000 0.0000 561.7145 3391.483876 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0007 515.5225 3357.290654 0 0.0005 39 | 1/8 3 h-lim-p 0.0002 0.0014 94.5918 3354.638872 0 0.0007 53 | 1/8 4 h-lim-p 0.0020 0.0158 13.3061 3354.469882 5 0.0011 76 | 1/8 5 h-lim-p 0.0011 0.0176 13.2184 3354.238779 6 0.0012 103 | 1/8 6 h-lim-p 0.0024 0.0459 6.6593 3349.887923 0 0.0094 117 | 1/8 7 h-lim-p 0.0012 0.0095 35.6281 3315.376554 0 0.0048 131 | 0/8 8 h-lim-p 0.0002 0.0017 187.8791 3308.305535 0 0.0004 144 | 0/8 9 h-lim-p 0.0008 0.0064 10.9381 3308.099919 0 0.0032 158 | 0/8 10 h-lim-p 0.0784 0.6274 0.3481 3300.617877 0 0.2353 171 | 0/8 11 h-lim-p 0.5162 4.1295 0.0262 3300.161137 1 0.6452 193 | 0/8 12 h-lim-p 1.0795 8.6361 0.0112 3300.084768 6 0.6907 227 | 0/8 13 h-lim-p 0.8266 6.7705 0.0093 3300.068254 5 0.7132 256 | 0/8 14 h-lim-p 2.5000 20.0000 0.0015 3300.067680 4 0.9169 286 | 0/8 15 h-lim-p 2.5000 20.0000 0.0002 3300.067659 2 0.6580 311 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 3300.067658 0 1.0938 331 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 3300.067658 0 1.0938 351 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 3300.067658 0 1.0938 371 | 0/8 19 h-lim-p 2.2314 20.0000 0.0000 3300.067658 0 0.2789 393 | 0/8 20 h-lim-p 0.2376 20.0000 0.0000 3300.067658 0 0.2376 413 | 0/8 21 h-lim-p 0.1843 20.0000 0.0000 3300.067658 0 0.0058 437 | 0/8 22 h-lim-p 0.0036 20.0000 0.0000 3300.067658 0 0.0000 473 Out... lnL = -3300.067658 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3300.067658 Node 7: lnL = -3300.067658 Node 8: lnL = -3300.067658 Node 9: lnL = -3300.067658 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 589 Sequential format.. Reading seq # 1: YOL041C_Sbay Reading seq # 2: YOL041C_Scer Reading seq # 3: YOL041C_Skud Reading seq # 4: YOL041C_Smik Reading seq # 5: YOL041C_Spar Sequences read.. Counting patterns.. # site patterns = 224 Counting frequencies.. 120 bytes for distance 35840 bytes for lkl0 28672 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.210901 0.146115 0.079230 0.199166 0.252781 0.280311 0.330670 lnL0 = -2526.088648 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2526.088648 x= 0.00006 0.21090 0.14612 0.07923 0.19917 0.25278 0.28031 0.33067 1 h-lim-p 0.0000 0.0000 383.3364 2525.953540 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0028 160.0228 2509.820567 0 0.0013 41 | 1/8 3 h-lim-p 0.0002 0.0018 132.4934 2507.271327 0 0.0004 54 | 1/8 4 h-lim-p 0.0013 0.0105 34.2592 2506.649714 7 0.0011 82 | 1/8 5 h-lim-p 0.0016 0.0180 23.6068 2506.155642 1 0.0019 96 | 1/8 6 h-lim-p 0.0035 0.0278 10.5585 2505.556840 0 0.0052 108 | 1/8 7 h-lim-p 0.0217 0.1738 2.3651 2479.638930 0 0.0869 122 | 1/8 8 h-lim-p 0.0003 0.0020 122.5284 2468.377156 0 0.0010 136 | 1/8 9 h-lim-p 0.2186 1.7486 0.1858 2465.588278 0 0.4371 149 | 0/8 10 h-lim-p 0.0105 0.1151 7.7049 2465.565731 6 0.0008 187 | 0/8 11 h-lim-p 0.1278 1.0225 0.0320 2465.208338 0 0.7669 201 | 0/8 12 h-lim-p 1.2649 10.1193 0.0194 2465.144376 7 0.4614 237 | 0/8 13 h-lim-p 2.5000 20.0000 0.0031 2465.140440 5 0.7208 270 | 0/8 14 h-lim-p 0.7755 6.2044 0.0013 2465.139938 4 0.5105 299 | 0/8 15 h-lim-p 2.5000 20.0000 0.0001 2465.139936 1 0.6152 322 | 0/8 16 h-lim-p 1.4042 20.0000 0.0000 2465.139936 0 0.6143 342 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 2465.139936 0 1.0938 362 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 2465.139936 0 1.0938 382 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 2465.139936 0 1.2500 402 | 0/8 20 h-lim-p 0.0796 20.0000 0.0000 2465.139936 0 0.0000 436 Out... lnL = -2465.139936 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2465.139936 Node 7: lnL = -2465.139936 Node 8: lnL = -2465.139936 Node 9: lnL = -2465.139936 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 305 Sequential format.. Reading seq # 1: YOL042W_Sbay Reading seq # 2: YOL042W_Scer Reading seq # 3: YOL042W_Skud Reading seq # 4: YOL042W_Smik Reading seq # 5: YOL042W_Spar Sequences read.. Counting patterns.. # site patterns = 99 Counting frequencies.. 120 bytes for distance 15840 bytes for lkl0 12672 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.917977 0.629507 0.242695 0.842804 1.672219 1.223036 1.279623 lnL0 = -1481.892483 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1481.892483 x= 0.00006 0.91798 0.62951 0.24270 0.84280 1.67222 1.22304 1.27962 1 h-lim-p 0.0000 0.0000 157.9228 1481.806660 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.1045 15.7124 1443.365198 m 0.1045 43 | 2/8 3 h-lim-p 0.0012 0.0099 55.2310 1425.085331 0 0.0050 57 | 2/8 4 h-lim-p 0.0106 0.0850 25.4508 1343.108656 0 0.0637 71 | 2/8 5 h-lim-p 0.3650 2.9202 2.2486 .. | 1/8 6 h-lim-p 0.0000 0.0058 83.3693 1336.555023 0 0.0026 131 | 1/8 7 h-lim-p 0.0003 0.0023 62.1277 1335.431552 0 0.0009 144 | 1/8 8 h-lim-p 0.0653 0.6393 0.8339 1332.896680 m 0.6393 157 | 0/8 9 h-lim-p -0.0000 -0.0000 27.5582 h-lim-p: -2.05945978e-21 -1.64756783e-20 2.75581615e+01 1332.896680 .. | 0/8 10 h-lim-p 0.0000 1.2748 15.2124 1332.820249 0 0.0006 190 | 0/8 11 h-lim-p 0.0006 0.0048 3.9226 1332.811218 0 0.0012 203 | 0/8 12 h-lim-p 0.0012 0.1516 4.0287 1330.040519 m 0.1516 220 | 1/8 13 h-lim-p 0.0000 0.0000 0.8870 .. | 1/8 14 h-lim-p 0.0000 0.0448 7.9629 1329.797444 0 0.0077 270 | 1/8 15 h-lim-p 0.0002 0.0013 81.3650 1328.991297 m 0.0013 282 | 2/8 16 h-lim-p 0.0000 0.0001 2882.5193 1326.850478 m 0.0001 294 | 2/8 17 h-lim-p -0.0000 -0.0000 365.3252 h-lim-p: -4.79130708e-21 -3.83304566e-20 3.65325168e+02 1326.850478 .. | 2/8 18 h-lim-p 0.0000 0.0202 98.8384 1322.973826 0 0.0013 321 | 2/8 19 h-lim-p 0.0059 0.0818 21.5807 1275.574543 m 0.0818 334 | 1/8 20 h-lim-p 0.0000 0.0000 6967.9127 h-lim-p: 1.37950780e-21 1.10360624e-20 6.96791271e+03 1275.574543 .. | 1/8 21 h-lim-p 0.0000 0.0065 4984.8433 1196.801634 0 0.0000 356 | 1/8 22 h-lim-p 0.0008 0.0066 27.3801 1196.514616 2 0.0008 372 | 0/8 23 h-lim-p 0.0001 0.0035 247.7483 1188.103598 0 0.0003 386 | 0/8 24 h-lim-p 0.0000 0.0002 118.5225 1186.369095 m 0.0002 398 | 1/8 25 h-lim-p 0.0033 0.0266 4.8166 1186.280758 4 0.0035 418 | 1/8 26 h-lim-p 0.0231 0.2134 0.7222 1178.328051 m 0.2134 431 | 2/8 27 h-lim-p 0.0082 0.0657 6.0816 1178.136419 2 0.0039 454 | 2/8 28 h-lim-p 0.0240 0.4210 0.9778 1178.117450 7 0.0072 485 | 2/8 29 h-lim-p 0.1764 5.5174 0.0399 1177.928818 0 0.7057 505 | 1/8 30 h-lim-p 0.0066 0.0655 4.2405 1177.913417 5 0.0032 534 | 1/8 31 h-lim-p 1.0788 20.0000 0.0127 1177.360722 0 8.6305 549 | 1/8 32 h-lim-p 0.2320 1.8559 0.0554 1176.664037 m 1.8559 568 | 2/8 33 h-lim-p 2.5000 20.0000 0.0112 .. | 2/8 34 h-lim-p 0.0000 0.0214 8.0346 1176.640474 0 0.0006 642 | 2/8 35 h-lim-p 0.0019 0.1322 2.6375 1176.637811 5 0.0008 663 | 2/8 36 h-lim-p 0.0046 0.7375 0.4777 1176.637681 2 0.0011 680 | 2/8 37 h-lim-p 0.0073 3.4250 0.0752 1176.637677 2 0.0012 704 | 2/8 38 h-lim-p 0.0029 11.2760 0.0306 1176.637674 0 0.0029 722 | 2/8 39 h-lim-p 0.0474 20.0000 0.0018 1176.637291 0 0.3794 743 | 2/8 40 h-lim-p 2.5000 20.0000 0.0000 1176.637290 0 1.0938 761 | 2/8 41 h-lim-p 2.5000 20.0000 0.0000 1176.637290 0 1.0938 779 | 2/8 42 h-lim-p 2.5000 20.0000 0.0000 1176.637290 0 2.1875 797 | 2/8 43 h-lim-p 1.8421 20.0000 0.0000 1176.637290 0 0.4030 816 | 2/8 44 h-lim-p 0.6750 20.0000 0.0000 1176.637290 0 0.0844 836 | 2/8 45 h-lim-p 0.0921 20.0000 0.0000 1176.637290 0 0.0004 861 Out... lnL = -1176.637290 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1176.637290 Node 7: lnL = -1176.637290 Node 8: lnL = -1176.637290 Node 9: lnL = -1176.637290 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 862 Sequential format.. Reading seq # 1: YOL047C_Sbay Reading seq # 2: YOL047C_Scer Reading seq # 3: YOL047C_Skud Reading seq # 4: YOL047C_Smik Reading seq # 5: YOL047C_Spar Sequences read.. Counting patterns.. # site patterns = 265 Counting frequencies.. 120 bytes for distance 42400 bytes for lkl0 33920 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.231736 0.143057 0.087330 0.196610 0.193028 0.295325 0.335490 lnL0 = -3448.782503 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3448.782503 x= 0.00006 0.23174 0.14306 0.08733 0.19661 0.19303 0.29532 0.33549 1 h-lim-p 0.0000 0.0000 440.4614 3448.636600 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0008 495.2427 3422.959847 0 0.0003 39 | 1/8 3 h-lim-p 0.0004 0.0029 89.3566 3419.839736 0 0.0007 52 | 1/8 4 h-lim-p 0.0005 0.0039 42.5045 3418.976402 0 0.0010 65 | 1/8 5 h-lim-p 0.0011 0.0091 13.9597 3418.603446 0 0.0034 78 | 1/8 6 h-lim-p 0.0005 0.0042 11.0606 3418.447546 0 0.0021 92 | 1/8 7 h-lim-p 0.0054 0.0726 4.3117 3416.361109 0 0.0215 106 | 1/8 8 h-lim-p 0.0038 0.0306 12.6525 3393.151910 0 0.0115 119 | 1/8 9 h-lim-p 0.2597 2.0779 0.0954 3389.713192 0 0.5195 132 | 0/8 10 h-lim-p 0.0057 0.5754 8.6961 3389.690815 3 0.0006 159 | 0/8 11 h-lim-p 0.2631 13.1448 0.0197 3389.582606 0 0.5263 172 | 0/8 12 h-lim-p 2.5000 20.0000 0.0029 3389.577348 4 0.7998 202 | 0/8 13 h-lim-p 2.0038 20.0000 0.0012 3389.576904 4 0.5442 231 | 0/8 14 h-lim-p 2.5000 20.0000 0.0002 3389.576887 0 0.6250 252 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 3389.576887 0 1.0938 272 | 0/8 16 h-lim-p 2.2645 20.0000 0.0000 3389.576887 0 0.9907 292 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 3389.576887 0 1.0938 312 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 3389.576887 0 1.0938 332 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 3389.576887 0 2.1875 352 | 0/8 20 h-lim-p 2.1046 20.0000 0.0000 3389.576887 0 0.5262 373 | 0/8 21 h-lim-p 0.7606 20.0000 0.0000 3389.576887 0 0.0357 397 | 0/8 22 h-lim-p 0.0179 20.0000 0.0000 3389.576887 0 0.0000 436 Out... lnL = -3389.576887 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3389.576887 Node 7: lnL = -3389.576887 Node 8: lnL = -3389.576887 Node 9: lnL = -3389.576887 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 823 Sequential format.. Reading seq # 1: YOL048C_Sbay Reading seq # 2: YOL048C_Scer Reading seq # 3: YOL048C_Skud Reading seq # 4: YOL048C_Smik Reading seq # 5: YOL048C_Spar Sequences read.. Counting patterns.. # site patterns = 223 Counting frequencies.. 120 bytes for distance 35680 bytes for lkl0 28544 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.286672 0.557585 0.632356 0.595447 0.781686 0.708468 0.786778 lnL0 = -4281.025161 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4281.025161 x= 0.00006 0.28667 0.55758 0.63236 0.59545 0.78169 0.70847 0.78678 1 h-lim-p 0.0000 0.0000 501.6960 4280.925933 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0150 86.6733 4079.252229 m 0.0150 42 | 2/8 3 h-lim-p 0.0004 0.0030 129.8555 4066.890911 0 0.0011 55 | 2/8 4 h-lim-p 0.0011 0.0087 113.1757 4049.066333 0 0.0043 69 | 2/8 5 h-lim-p 0.0129 0.1028 13.2421 4048.396181 6 0.0129 94 | 1/8 6 h-lim-p 0.0012 0.0123 145.9146 4047.969865 7 0.0003 124 | 1/8 7 h-lim-p 0.0166 0.2217 2.8890 .. | 1/8 8 h-lim-p 0.0000 0.0061 112.6217 4019.850775 0 0.0038 180 | 0/8 9 h-lim-p 0.0000 0.0000 8822.1484 3989.700838 m 0.0000 192 | 0/8 10 h-lim-p -0.0000 -0.0000 2519.9346 h-lim-p: -1.34969549e-21 -1.07975639e-20 2.51993464e+03 3989.700838 .. | 0/8 11 h-lim-p 0.0000 0.0010 3136.0104 3902.096361 0 0.0000 214 | 0/8 12 h-lim-p 0.0001 0.0009 353.4619 3765.994398 m 0.0009 226 | 1/8 13 h-lim-p 0.0018 0.0141 35.4717 3764.834303 0 0.0026 238 | 1/8 14 h-lim-p 0.0012 0.0094 45.6547 3764.301024 0 0.0018 250 | 1/8 15 h-lim-p 0.0044 0.0355 9.7582 .. | 1/8 16 h-lim-p 0.0000 0.0006 497.2469 3690.930363 0 0.0004 301 | 1/8 17 h-lim-p 0.0000 0.0000 3138.3530 3629.111708 m 0.0000 313 | 2/8 18 h-lim-p 0.0000 0.0003 475.5452 3616.837629 0 0.0002 327 | 2/8 19 h-lim-p 0.0001 0.0014 654.6293 3551.617632 0 0.0009 341 | 2/8 20 h-lim-p 0.0036 0.0291 39.1705 3529.930067 0 0.0145 355 | 1/8 21 h-lim-p 0.0001 0.0005 1343.6310 3516.570151 0 0.0003 369 | 1/8 22 h-lim-p 0.0713 0.5706 0.7282 3506.700633 m 0.5706 381 | 0/8 23 h-lim-p -0.0000 -0.0000 1904.1259 h-lim-p: -1.43621389e-21 -1.14897111e-20 1.90412589e+03 3506.700633 .. | 0/8 24 h-lim-p 0.0000 0.1146 682.9918 3494.398926 0 0.0001 411 | 0/8 25 h-lim-p 0.0000 0.0001 94.5432 3493.643212 m 0.0001 423 | 1/8 26 h-lim-p 0.0000 0.0007 265.8624 3492.073198 0 0.0002 438 | 1/8 27 h-lim-p 0.0001 0.0011 106.1521 3491.049920 0 0.0004 451 | 1/8 28 h-lim-p 0.0012 0.0099 16.5453 3489.911162 0 0.0025 464 | 1/8 29 h-lim-p 0.0033 0.1034 12.2452 3488.880339 0 0.0133 478 | 1/8 30 h-lim-p 0.0142 0.1135 8.6463 3488.571537 5 0.0113 500 | 1/8 31 h-lim-p 2.5000 20.0000 0.0119 3488.307722 4 0.9482 520 | 1/8 32 h-lim-p 2.5000 20.0000 0.0045 3488.285842 6 1.7048 554 | 0/8 33 h-lim-p 0.0003 0.0126 23.0448 3488.255793 0 0.0007 574 | 0/8 34 h-lim-p 1.1792 9.4333 0.0082 3488.203504 0 2.3583 587 | 0/8 35 h-lim-p 2.5000 20.0000 0.0056 3488.200577 4 1.1078 614 | 0/8 36 h-lim-p 2.5000 20.0000 0.0011 3488.200458 2 0.9961 638 | 0/8 37 h-lim-p 2.5000 20.0000 0.0001 3488.200457 0 1.0938 658 | 0/8 38 h-lim-p 2.5000 20.0000 0.0000 3488.200457 0 1.0938 678 | 0/8 39 h-lim-p 2.2731 20.0000 0.0000 3488.200457 0 0.9945 698 | 0/8 40 h-lim-p 0.6266 20.0000 0.0000 3488.200457 0 0.0685 720 | 0/8 41 h-lim-p 0.0068 20.0000 0.0002 3488.200457 0 0.0000 763 | 0/8 42 h-lim-p 0.0000 20.0000 0.0000 | 0/8 43 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -3488.200457 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3488.200457 Node 7: lnL = -3488.200457 Node 8: lnL = -3488.200457 Node 9: lnL = -3488.200457 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 447 Sequential format.. Reading seq # 1: YOL049W_Sbay Reading seq # 2: YOL049W_Scer Reading seq # 3: YOL049W_Skud Reading seq # 4: YOL049W_Smik Reading seq # 5: YOL049W_Spar Sequences read.. Counting patterns.. # site patterns = 187 Counting frequencies.. 120 bytes for distance 29920 bytes for lkl0 23936 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.153450 0.256701 0.202968 0.243316 0.378364 0.343171 0.381714 lnL0 = -1860.905455 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1860.905455 x= 0.00006 0.15345 0.25670 0.20297 0.24332 0.37836 0.34317 0.38171 1 h-lim-p 0.0000 0.0000 363.0134 1860.790738 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0012 368.7631 1809.935556 m 0.0012 38 | 1/8 3 h-lim-p 0.0000 0.0002 162.1264 1808.728026 m 0.0002 50 | 1/8 4 h-lim-p 0.0002 0.0014 144.2252 1806.206207 0 0.0004 63 | 1/8 5 h-lim-p 0.0000 0.0003 46.9727 1805.780315 m 0.0003 75 | 1/8 6 h-lim-p 0.0006 0.0182 20.4448 1805.395123 0 0.0013 88 | 1/8 7 h-lim-p 0.0008 0.0064 7.0736 1803.599344 m 0.0064 100 | 1/8 8 h-lim-p 0.0052 0.0751 8.7581 1786.370649 0 0.0310 114 | 1/8 9 h-lim-p 0.0844 0.6749 0.4807 1776.836737 0 0.3375 128 | 1/8 10 h-lim-p 0.3162 2.5295 0.1510 1770.640460 0 0.6324 148 | 1/8 11 h-lim-p 1.1593 9.2741 0.0308 1769.738103 0 1.7389 167 | 0/8 12 h-lim-p 0.0030 0.0280 17.8758 1769.608510 7 0.0010 204 | 0/8 13 h-lim-p 0.8133 20.0000 0.0230 1769.130965 0 1.6266 217 | 0/8 14 h-lim-p 2.5000 20.0000 0.0115 1769.009496 6 1.6209 252 | 0/8 15 h-lim-p 2.5000 20.0000 0.0022 1769.000126 6 1.5455 287 | 0/8 16 h-lim-p 2.5000 20.0000 0.0007 1768.998468 2 2.1777 311 | 0/8 17 h-lim-p 2.5000 20.0000 0.0004 1768.998381 2 1.0889 335 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1768.998380 0 1.0938 355 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1768.998380 0 1.0938 375 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 1768.998380 0 5.0000 396 | 0/8 21 h-lim-p 1.3481 20.0000 0.0000 1768.998380 0 0.0737 419 | 0/8 22 h-lim-p 0.0820 20.0000 0.0000 1768.998380 0 0.0000 455 Out... lnL = -1768.998380 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1768.998380 Node 7: lnL = -1768.998380 Node 8: lnL = -1768.998380 Node 9: lnL = -1768.998380 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 907 Sequential format.. Reading seq # 1: YOL055C_Sbay Reading seq # 2: YOL055C_Scer Reading seq # 3: YOL055C_Skud Reading seq # 4: YOL055C_Smik Reading seq # 5: YOL055C_Spar Sequences read.. Counting patterns.. # site patterns = 349 Counting frequencies.. 120 bytes for distance 55840 bytes for lkl0 44672 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.182288 0.244671 0.191148 0.301440 0.350932 0.357448 0.425809 lnL0 = -4356.500105 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4356.500105 x= 0.00006 0.18229 0.24467 0.19115 0.30144 0.35093 0.35745 0.42581 1 h-lim-p 0.0000 0.0000 589.9983 4356.294580 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0007 423.8977 4285.426582 m 0.0007 38 | 2/8 3 h-lim-p 0.0009 0.0076 61.8720 4250.585903 0 0.0038 52 | 2/8 4 h-lim-p 0.0003 0.0020 170.8887 4239.931236 0 0.0005 65 | 2/8 5 h-lim-p 0.0003 0.0021 161.3484 4235.370376 0 0.0005 78 | 2/8 6 h-lim-p 0.0028 0.0222 17.5300 4235.280293 3 0.0006 97 | 1/8 7 h-lim-p 0.0002 0.0518 63.2112 4235.035185 6 0.0001 120 | 1/8 8 h-lim-p 0.0044 0.2254 1.8699 4234.994607 2 0.0038 136 | 1/8 9 h-lim-p 0.0071 0.3539 1.0035 4228.202110 0 0.1134 152 | 1/8 10 h-lim-p 2.5000 20.0000 0.0202 4227.897568 6 0.8029 178 | 0/8 11 h-lim-p 0.0291 2.0773 0.5579 4227.897433 2 0.0010 205 | 0/8 12 h-lim-p 0.1364 1.2028 0.0039 4227.890797 0 0.8181 227 | 0/8 13 h-lim-p 0.6788 5.4307 0.0006 4227.890509 0 1.0182 247 | 0/8 14 h-lim-p 0.1115 0.8922 0.0002 4227.890498 m 0.8922 267 | 1/8 15 h-lim-p 0.7693 20.0000 0.0002 4227.890495 0 0.3366 287 | 1/8 16 h-lim-p 1.5143 20.0000 0.0000 4227.890493 0 1.3250 306 | 0/8 17 h-lim-p 0.0087 20.0000 0.0067 4227.890493 0 0.0011 327 | 0/8 18 h-lim-p 0.1256 1.0045 0.0000 4227.890493 m 1.0045 347 | 1/8 19 h-lim-p 2.5000 20.0000 0.0000 4227.890493 0 1.0938 367 | 1/8 20 h-lim-p 2.5000 20.0000 0.0000 4227.890493 0 1.0938 386 | 1/8 21 h-lim-p 2.5000 20.0000 0.0000 4227.890493 0 0.6250 406 | 1/8 22 h-lim-p 1.4229 20.0000 0.0000 4227.890493 0 0.0445 429 | 1/8 23 h-lim-p 0.0456 20.0000 0.0000 4227.890493 0 0.0004 454 Out... lnL = -4227.890493 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4227.890493 Node 7: lnL = -4227.890493 Node 8: lnL = -4227.890493 Node 9: lnL = -4227.890493 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 856 Sequential format.. Reading seq # 1: YOL058W_Sbay Reading seq # 2: YOL058W_Scer Reading seq # 3: YOL058W_Skud Reading seq # 4: YOL058W_Smik Reading seq # 5: YOL058W_Spar Sequences read.. Counting patterns.. # site patterns = 231 Counting frequencies.. 120 bytes for distance 36960 bytes for lkl0 29568 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.047147 0.066191 0.108493 0.052367 0.109547 0.154500 0.272682 lnL0 = -3286.358788 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3286.358788 x= 0.00006 0.04715 0.06619 0.10849 0.05237 0.10955 0.15450 0.27268 1 h-lim-p 0.0000 0.0003 191.8633 3284.039022 0 0.0001 23 | 0/8 2 h-lim-p 0.0004 0.0087 49.9363 3283.835050 6 0.0002 46 | 0/8 3 h-lim-p 0.0001 0.0009 16.0050 3283.810368 0 0.0002 59 | 0/8 4 h-lim-p 0.0006 0.0361 5.9437 3283.807294 4 0.0002 80 | 0/8 5 h-lim-p 0.0012 0.0944 0.9864 3283.807209 3 0.0002 102 | 0/8 6 h-lim-p 0.0022 4.6631 0.0784 3283.807203 1 0.0011 125 | 0/8 7 h-lim-p 0.0003 1.0883 0.3375 3283.806753 0 0.0244 151 | 0/8 8 h-lim-p 0.0005 0.0223 17.4156 3283.805614 0 0.0009 172 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 3283.805553 2 0.9961 188 | 0/8 10 h-lim-p 1.1137 20.0000 0.0002 3283.805553 0 0.9744 208 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3283.805553 0 1.0938 228 | 0/8 12 h-lim-p 0.6676 20.0000 0.0000 3283.805553 0 0.0046 254 | 0/8 13 h-lim-p 0.0005 20.0000 0.0004 3283.805553 0 0.0000 294 | 0/8 14 h-lim-p 0.0000 15.9106 0.0023 3283.805553 0 0.0003 319 | 0/8 15 h-lim-p 0.0014 20.0000 0.0005 3283.805553 0 0.0000 360 | 0/8 16 h-lim-p 0.0000 20.0000 0.0074 | 0/8 17 h-lim-p 0.0000 20.0000 0.0074 Out... lnL = -3283.805553 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3283.805553 Node 7: lnL = -3283.805553 Node 8: lnL = -3283.805553 Node 9: lnL = -3283.805553 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 261 Sequential format.. Reading seq # 1: YOL061W_Sbay Reading seq # 2: YOL061W_Scer Reading seq # 3: YOL061W_Skud Reading seq # 4: YOL061W_Smik Reading seq # 5: YOL061W_Spar Sequences read.. Counting patterns.. # site patterns = 98 Counting frequencies.. 120 bytes for distance 15680 bytes for lkl0 12544 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.093859 0.164343 0.118804 0.165538 0.203236 0.228641 0.254304 lnL0 = -1048.979609 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1048.979609 x= 0.00006 0.09386 0.16434 0.11880 0.16554 0.20324 0.22864 0.25430 1 h-lim-p 0.0000 0.0000 226.1515 1048.894229 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0022 110.4193 1040.577223 9 0.0014 59 | 1/8 3 h-lim-p 0.0019 0.0153 16.2789 1040.247918 6 0.0021 87 | 1/8 4 h-lim-p 0.0068 0.0567 5.0166 1039.918707 1 0.0085 101 | 1/8 5 h-lim-p 0.0062 0.0493 3.3312 1038.109508 0 0.0185 114 | 1/8 6 h-lim-p 0.0012 0.0095 24.1657 1029.133656 0 0.0047 128 | 1/8 7 h-lim-p 0.0003 0.0022 88.1024 1022.294197 0 0.0011 142 | 1/8 8 h-lim-p 0.0027 0.0213 13.1303 1022.212821 8 0.0009 176 | 1/8 9 h-lim-p 0.1431 1.8329 0.0840 1021.783652 0 0.2862 189 | 0/8 10 h-lim-p 0.0048 0.6327 5.0448 1021.770678 5 0.0010 221 | 0/8 11 h-lim-p 0.2341 7.9074 0.0219 1021.675663 0 0.4681 234 | 0/8 12 h-lim-p 0.1779 1.4229 0.0146 1021.659855 0 0.3557 255 | 0/8 13 h-lim-p 1.2591 20.0000 0.0041 1021.653391 5 0.6640 286 | 0/8 14 h-lim-p 2.4495 20.0000 0.0011 1021.652994 4 0.6944 316 | 0/8 15 h-lim-p 2.5000 20.0000 0.0002 1021.652982 2 0.6580 341 | 0/8 16 h-lim-p 2.1448 20.0000 0.0001 1021.652980 1 0.8546 363 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1021.652980 0 1.0938 383 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1021.652980 0 0.6250 404 | 0/8 19 h-lim-p 1.5291 20.0000 0.0000 1021.652980 0 0.0030 432 Out... lnL = -1021.652980 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1021.652980 Node 7: lnL = -1021.652980 Node 8: lnL = -1021.652980 Node 9: lnL = -1021.652980 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 285 Sequential format.. Reading seq # 1: YOL063C_Sbay Reading seq # 2: YOL063C_Scer Reading seq # 3: YOL063C_Skud Reading seq # 4: YOL063C_Smik Reading seq # 5: YOL063C_Spar Sequences read.. Counting patterns.. # site patterns = 119 Counting frequencies.. 120 bytes for distance 19040 bytes for lkl0 15232 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.027506 0.069410 0.063281 0.056751 0.054723 0.204607 0.135527 0.382253 lnL0 = -1171.724539 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1171.724539 x= 0.02751 0.06941 0.06328 0.05675 0.05472 0.20461 0.13553 0.38225 1 h-lim-p 0.0009 0.0075 43.2974 1171.224647 9 0.0006 45 | 0/8 2 h-lim-p 0.0015 0.0141 16.7601 1171.087666 6 0.0011 69 | 0/8 3 h-lim-p 0.0013 0.0119 14.2760 1171.060302 7 0.0004 97 | 0/8 4 h-lim-p 0.0009 0.0199 6.9704 1171.051766 5 0.0005 122 | 0/8 5 h-lim-p 0.0022 0.0831 1.5595 1171.051254 3 0.0005 141 | 0/8 6 h-lim-p 0.0021 0.6151 0.3525 1171.051179 4 0.0013 165 | 0/8 7 h-lim-p 0.0190 12.8907 0.0236 1171.051169 2 0.0073 189 | 0/8 8 h-lim-p 0.0339 20.0000 0.0051 1171.049981 0 0.2711 212 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1171.049975 1 0.9961 234 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1171.049975 0 2.1875 254 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1171.049975 0 1.0938 274 | 0/8 12 h-lim-p 0.1369 20.0000 0.0000 1171.049975 0 8.7625 300 | 0/8 13 h-lim-p 0.3760 20.0000 0.0002 1171.049975 0 0.0235 323 | 0/8 14 h-lim-p 0.0025 20.0000 0.0017 1171.049975 0 0.0003 345 | 0/8 15 h-lim-p 0.0000 2.1913 0.0275 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0007 | 0/8 17 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -1171.049975 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1171.049975 Node 7: lnL = -1171.049975 Node 8: lnL = -1171.049975 Node 9: lnL = -1171.049975 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 225 Sequential format.. Reading seq # 1: YOL064C_Sbay Reading seq # 2: YOL064C_Scer Reading seq # 3: YOL064C_Skud Reading seq # 4: YOL064C_Smik Reading seq # 5: YOL064C_Spar Sequences read.. Counting patterns.. # site patterns = 103 Counting frequencies.. 120 bytes for distance 16480 bytes for lkl0 13184 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.141848 0.219988 0.171028 0.207897 0.274235 0.292823 0.332769 lnL0 = -996.017114 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 996.017114 x= 0.00006 0.14185 0.21999 0.17103 0.20790 0.27423 0.29282 0.33277 1 h-lim-p 0.0000 0.0000 189.4863 995.955387 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0011 272.3850 969.268352 m 0.0011 38 | 1/8 3 h-lim-p 0.0002 0.0012 98.9221 967.611339 0 0.0006 52 | 1/8 4 h-lim-p 0.0009 0.0068 51.3860 966.460464 0 0.0017 65 | 1/8 5 h-lim-p 0.0085 0.0677 5.5884 966.292179 8 0.0057 98 | 1/8 6 h-lim-p 0.0076 0.1276 4.1942 965.878542 0 0.0152 111 | 1/8 7 h-lim-p 0.0075 0.0598 6.3210 964.183475 0 0.0149 124 | 1/8 8 h-lim-p 0.0031 0.0252 16.3309 959.643215 0 0.0126 138 | 1/8 9 h-lim-p 0.2243 1.7940 0.1733 956.747078 0 0.4485 151 | 1/8 10 h-lim-p 0.3985 3.1879 0.0964 955.968171 4 0.4078 178 | 0/8 11 h-lim-p 0.0082 0.3225 4.7779 955.951024 6 0.0015 212 | 0/8 12 h-lim-p 0.1880 3.3324 0.0391 955.892130 0 0.3759 225 | 0/8 13 h-lim-p 2.5000 20.0000 0.0041 955.884281 5 0.9487 255 | 0/8 14 h-lim-p 2.5000 20.0000 0.0010 955.882068 4 1.7557 285 | 0/8 15 h-lim-p 2.5000 20.0000 0.0005 955.881931 2 1.0889 309 | 0/8 16 h-lim-p 2.5000 20.0000 0.0002 955.881926 2 0.6580 334 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 955.881926 0 1.0938 354 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 955.881926 0 2.1875 374 | 0/8 19 h-lim-p 1.8052 20.0000 0.0000 955.881926 0 0.7898 394 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 955.881926 0 0.0021 423 Out... lnL = -955.881926 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -955.881926 Node 7: lnL = -955.881926 Node 8: lnL = -955.881926 Node 9: lnL = -955.881926 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 233 Sequential format.. Reading seq # 1: YOL065C_Sbay Reading seq # 2: YOL065C_Scer Reading seq # 3: YOL065C_Skud Reading seq # 4: YOL065C_Smik Reading seq # 5: YOL065C_Spar Sequences read.. Counting patterns.. # site patterns = 79 Counting frequencies.. 120 bytes for distance 12640 bytes for lkl0 10112 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.423877 0.927241 0.552907 0.873836 1.020307 2.288447 1.254521 lnL0 = -1058.523205 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1058.523205 x= 0.00006 0.42388 0.92724 0.55291 0.87384 1.02031 2.28845 1.25452 1 h-lim-p 0.0000 0.0000 114.3962 1058.435498 m 0.0000 22 | 1/8 2 h-lim-p 0.0002 0.3209 4.3824 .. | 1/8 3 h-lim-p 0.0000 0.0073 114.1303 938.484726 m 0.0073 70 | 2/8 4 h-lim-p 0.0002 0.0015 222.7426 932.081352 0 0.0008 84 | 2/8 5 h-lim-p 0.0245 0.1964 5.4235 .. | 1/8 6 h-lim-p 0.0000 0.0131 92.5023 916.042040 m 0.0131 140 | 2/8 7 h-lim-p 0.0001 0.0005 281.5519 908.540883 m 0.0005 152 | 3/8 8 h-lim-p 0.0019 0.0193 46.3614 895.954562 0 0.0117 166 | 3/8 9 h-lim-p 0.0030 0.0241 8.6598 887.130564 0 0.0181 180 | 2/8 10 h-lim-p 0.0001 0.0005 159.0112 882.510382 m 0.0005 192 | 2/8 11 h-lim-p 0.0009 0.0082 82.5407 824.684031 m 0.0082 205 | 2/8 12 h-lim-p -0.0000 -0.0000 7.5383 h-lim-p: -4.32384195e-19 -3.45907356e-18 7.53827415e+00 824.684031 .. | 2/8 13 h-lim-p 0.0000 0.0057 521.0325 818.058669 0 0.0001 228 | 2/8 14 h-lim-p 0.0003 0.0020 74.5831 813.647039 m 0.0020 240 | 2/8 15 h-lim-p 0.0027 0.0217 24.1970 813.141054 6 0.0020 265 | 2/8 16 h-lim-p 0.0009 0.0072 55.4980 812.585709 0 0.0013 277 | 2/8 17 h-lim-p 0.1731 1.3850 0.1835 812.301991 7 0.1900 309 | 1/8 18 h-lim-p 0.0031 0.2793 11.0845 811.969484 7 0.0031 342 | 1/8 19 h-lim-p 0.0015 0.0117 3.5798 811.812641 m 0.0117 354 | 2/8 20 h-lim-p 1.7766 14.2129 0.0042 811.804412 6 1.1980 381 | 1/8 21 h-lim-p 0.0261 1.5879 0.1919 811.804339 4 0.0037 410 | 1/8 22 h-lim-p 0.0215 0.1724 0.0062 811.803936 m 0.1724 429 | 2/8 23 h-lim-p 0.4467 20.0000 0.0018 811.803503 0 0.8934 449 | 2/8 24 h-lim-p 0.9198 20.0000 0.0017 811.802833 1 1.1497 469 | 1/8 25 h-lim-p 0.0291 8.4212 0.0688 811.802818 3 0.0094 495 | 1/8 26 h-lim-p 0.9414 20.0000 0.0007 811.802693 0 1.4122 514 | 1/8 27 h-lim-p 2.5000 20.0000 0.0002 811.802686 2 1.6492 539 | 0/8 28 h-lim-p 0.0642 20.0000 0.0055 811.802686 0 0.0070 560 | 0/8 29 h-lim-p 0.1307 1.0458 0.0000 811.802686 m 1.0458 580 | 1/8 30 h-lim-p 2.5000 20.0000 0.0000 811.802686 0 0.5469 601 | 1/8 31 h-lim-p 1.0169 20.0000 0.0000 811.802686 0 1.0169 620 | 1/8 32 h-lim-p 2.5000 20.0000 0.0000 811.802686 0 1.0938 639 | 1/8 33 h-lim-p 2.5000 20.0000 0.0000 811.802686 0 0.3125 660 | 1/8 34 h-lim-p 0.4027 20.0000 0.0000 811.802686 0 0.0126 683 Out... lnL = -811.802686 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -811.802686 Node 7: lnL = -811.802686 Node 8: lnL = -811.802686 Node 9: lnL = -811.802686 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 215 Sequential format.. Reading seq # 1: YOL068C_Sbay Reading seq # 2: YOL068C_Scer Reading seq # 3: YOL068C_Skud Reading seq # 4: YOL068C_Smik Reading seq # 5: YOL068C_Spar Sequences read.. Counting patterns.. # site patterns = 97 Counting frequencies.. 120 bytes for distance 15520 bytes for lkl0 12416 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.105931 0.178684 0.145816 0.215023 0.277729 0.320731 0.296876 lnL0 = -806.662778 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 806.662778 x= 0.00006 0.10593 0.17868 0.14582 0.21502 0.27773 0.32073 0.29688 1 h-lim-p 0.0000 0.0000 132.2043 806.630140 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0018 112.3816 793.056958 m 0.0018 39 | 2/8 3 h-lim-p 0.0043 0.0347 11.7908 792.012724 0 0.0087 52 | 2/8 4 h-lim-p 0.0088 0.0701 4.7129 788.947876 0 0.0263 65 | 2/8 5 h-lim-p 0.0019 0.0148 19.5987 784.039825 0 0.0074 79 | 2/8 6 h-lim-p 0.0034 0.0270 10.8229 783.934209 7 0.0018 107 | 1/8 7 h-lim-p 0.0008 0.0442 24.0818 783.886373 6 0.0002 131 | 1/8 8 h-lim-p 0.0016 0.0501 2.8978 783.870013 0 0.0032 144 | 1/8 9 h-lim-p 0.0409 0.6957 0.2262 783.201404 0 0.1636 158 | 0/8 10 h-lim-p 0.0149 3.8128 2.4810 783.196869 4 0.0015 187 | 0/8 11 h-lim-p 0.2134 8.6988 0.0170 783.170281 0 0.6401 200 | 0/8 12 h-lim-p 0.4267 3.4138 0.0069 783.165211 0 0.8535 221 | 0/8 13 h-lim-p 2.5000 20.0000 0.0012 783.164893 4 0.8228 250 | 0/8 14 h-lim-p 2.5000 20.0000 0.0003 783.164876 3 0.7330 279 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 783.164876 0 1.0938 299 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 783.164876 0 0.5469 320 | 0/8 17 h-lim-p 1.4310 20.0000 0.0000 783.164876 0 0.0000 368 Out... lnL = -783.164876 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -783.164876 Node 7: lnL = -783.164876 Node 8: lnL = -783.164876 Node 9: lnL = -783.164876 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 219 Sequential format.. Reading seq # 1: YOL071W_Sbay Reading seq # 2: YOL071W_Scer Reading seq # 3: YOL071W_Skud Reading seq # 4: YOL071W_Smik Reading seq # 5: YOL071W_Spar Sequences read.. Counting patterns.. # site patterns = 124 Counting frequencies.. 120 bytes for distance 19840 bytes for lkl0 15872 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.220261 0.388498 0.231098 0.353757 0.449521 0.482949 0.506829 lnL0 = -973.570576 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 973.570576 x= 0.00006 0.22026 0.38850 0.23110 0.35376 0.44952 0.48295 0.50683 1 h-lim-p 0.0000 0.0000 137.3127 973.521996 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0066 87.8755 948.312598 0 0.0058 43 | 1/8 3 h-lim-p 0.0004 0.0035 58.1954 943.297251 m 0.0035 55 | 2/8 4 h-lim-p 0.0024 0.0195 28.9891 941.434129 0 0.0049 68 | 2/8 5 h-lim-p 0.0078 0.0621 8.8473 939.953560 0 0.0155 81 | 2/8 6 h-lim-p 0.0083 0.0661 3.4468 938.568458 0 0.0248 94 | 1/8 7 h-lim-p 0.0054 0.0431 12.4746 936.695585 0 0.0108 107 | 1/8 8 h-lim-p 0.0042 0.0339 19.2369 932.420537 0 0.0127 120 | 1/8 9 h-lim-p 0.0022 0.0173 11.8610 931.467023 0 0.0086 134 | 0/8 10 h-lim-p 0.0009 0.0074 32.8651 930.876105 0 0.0019 147 | 0/8 11 h-lim-p 0.1579 1.2632 0.3418 928.919099 0 0.3158 160 | 0/8 12 h-lim-p 0.1903 1.5224 0.3040 927.435484 0 0.3806 181 | 0/8 13 h-lim-p 0.1433 1.1462 0.0215 927.401181 0 0.8596 203 | 0/8 14 h-lim-p 0.0986 0.7884 0.0111 927.395844 m 0.7884 223 | 0/8 15 h-lim-p -0.0000 -0.0000 0.0048 h-lim-p: -6.82224780e-18 -5.45779824e-17 4.83054071e-03 927.395844 .. | 0/8 16 h-lim-p 0.0000 2.0521 1.2916 927.395080 0 0.0010 265 | 0/8 17 h-lim-p 0.0035 0.6730 0.3580 927.394991 2 0.0015 281 | 0/8 18 h-lim-p 0.0049 0.1122 0.1106 927.394970 2 0.0038 305 | 0/8 19 h-lim-p 0.0019 0.0149 0.0644 927.394967 1 0.0019 327 | 0/8 20 h-lim-p 0.0065 0.0524 0.0190 927.394966 1 0.0032 350 | 0/8 21 h-lim-p 0.0026 0.0207 0.0221 927.394965 0 0.0078 371 | 0/8 22 h-lim-p 0.0002 0.0013 0.2076 927.394965 0 0.0007 393 | 0/8 23 h-lim-p 0.0096 0.0766 0.0076 927.394965 0 0.0042 413 | 0/8 24 h-lim-p 0.1112 20.0000 0.0003 927.394962 0 0.4446 435 | 0/8 25 h-lim-p 0.7553 20.0000 0.0002 927.394961 0 1.5106 456 | 0/8 26 h-lim-p 2.5000 20.0000 0.0000 927.394961 0 1.0938 476 | 0/8 27 h-lim-p 2.5000 20.0000 0.0000 927.394961 0 1.0938 496 | 0/8 28 h-lim-p 2.5000 20.0000 0.0000 927.394961 0 2.1875 516 | 0/8 29 h-lim-p 2.1833 20.0000 0.0000 927.394961 0 0.1194 539 | 0/8 30 h-lim-p 0.1367 20.0000 0.0000 927.394961 0 0.0598 559 | 0/8 31 h-lim-p 0.0498 20.0000 0.0000 927.394961 0 0.0000 599 Out... lnL = -927.394961 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -927.394961 Node 7: lnL = -927.394961 Node 8: lnL = -927.394961 Node 9: lnL = -927.394961 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 306 Sequential format.. Reading seq # 1: YOL076W_Sbay Reading seq # 2: YOL076W_Scer Reading seq # 3: YOL076W_Skud Reading seq # 4: YOL076W_Smik Reading seq # 5: YOL076W_Spar Sequences read.. Counting patterns.. # site patterns = 144 Counting frequencies.. 120 bytes for distance 23040 bytes for lkl0 18432 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.126311 0.266405 0.200013 0.235897 0.325384 0.349991 0.376496 lnL0 = -1458.606326 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1458.606326 x= 0.00006 0.12631 0.26640 0.20001 0.23590 0.32538 0.34999 0.37650 1 h-lim-p 0.0000 0.0000 254.3211 1458.527184 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0015 238.8040 1425.982338 9 0.0013 60 | 1/8 3 h-lim-p 0.0009 0.0076 43.5493 1424.754435 0 0.0014 72 | 1/8 4 h-lim-p 0.0016 0.0127 25.5192 1424.215078 1 0.0020 86 | 1/8 5 h-lim-p 0.0050 0.0397 4.9887 1423.926607 0 0.0074 98 | 1/8 6 h-lim-p 0.0153 0.2030 2.4222 1417.387509 0 0.0613 112 | 1/8 7 h-lim-p 0.0019 0.0155 30.1298 1405.412561 0 0.0078 126 | 1/8 8 h-lim-p 0.0050 0.0403 6.0478 1405.372775 6 0.0017 151 | 0/8 9 h-lim-p 0.0007 0.0560 15.2974 1405.234593 0 0.0013 164 | 0/8 10 h-lim-p 0.0398 0.3188 0.3021 1404.493626 0 0.1195 177 | 0/8 11 h-lim-p 0.7096 9.6534 0.0509 1404.105433 5 0.4628 209 | 0/8 12 h-lim-p 2.5000 20.0000 0.0076 1404.097711 5 0.4450 241 | 0/8 13 h-lim-p 2.3236 20.0000 0.0015 1404.097128 4 0.7185 273 | 0/8 14 h-lim-p 2.5000 20.0000 0.0004 1404.097066 3 0.8171 300 | 0/8 15 h-lim-p 1.4032 20.0000 0.0002 1404.097061 1 0.5591 322 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1404.097060 0 1.0938 342 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1404.097060 0 2.1875 362 | 0/8 18 h-lim-p 2.0742 20.0000 0.0000 1404.097060 0 0.9075 382 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1404.097060 0 0.0098 409 Out... lnL = -1404.097060 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1404.097060 Node 7: lnL = -1404.097060 Node 8: lnL = -1404.097060 Node 9: lnL = -1404.097060 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 307 Sequential format.. Reading seq # 1: YOL077C_Sbay Reading seq # 2: YOL077C_Scer Reading seq # 3: YOL077C_Skud Reading seq # 4: YOL077C_Smik Reading seq # 5: YOL077C_Spar Sequences read.. Counting patterns.. # site patterns = 134 Counting frequencies.. 120 bytes for distance 21440 bytes for lkl0 17152 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.130046 0.270095 0.200326 0.237497 0.324238 0.347130 0.376719 lnL0 = -1479.882691 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1479.882691 x= 0.00006 0.13005 0.27010 0.20033 0.23750 0.32424 0.34713 0.37672 1 h-lim-p 0.0000 0.0000 255.1057 1479.804984 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0016 222.8238 1448.803230 1 0.0014 43 | 1/8 3 h-lim-p 0.0007 0.0054 52.7366 1447.080725 0 0.0013 56 | 1/8 4 h-lim-p 0.0016 0.0125 26.2773 1446.518119 1 0.0019 70 | 1/8 5 h-lim-p 0.0059 0.0474 5.2125 1446.164299 0 0.0118 83 | 1/8 6 h-lim-p 0.0248 0.1988 2.1066 1438.103361 0 0.0994 97 | 1/8 7 h-lim-p 0.0010 0.0080 38.3131 1427.773212 0 0.0040 111 | 1/8 8 h-lim-p 0.0009 0.0069 49.7238 1426.587647 0 0.0013 123 | 1/8 9 h-lim-p 0.3971 3.1766 0.0875 1424.910340 0 0.5956 135 | 1/8 10 h-lim-p 0.4628 3.7023 0.0602 1424.806588 7 0.2318 168 | 1/8 11 h-lim-p 0.3665 6.6649 0.0381 1424.748183 4 0.2580 196 | 0/8 12 h-lim-p 0.1287 18.3164 0.0764 1424.748131 3 0.0043 225 | 0/8 13 h-lim-p 0.0107 0.0852 0.0139 1424.743756 m 0.0852 245 | 1/8 14 h-lim-p 0.7375 20.0000 0.0015 1424.741336 1 0.9219 267 | 1/8 15 h-lim-p 1.5463 20.0000 0.0009 1424.741195 3 0.5865 292 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 1424.741194 0 1.0938 311 | 0/8 17 h-lim-p 0.0262 20.0000 0.0020 1424.741194 0 0.0057 331 | 0/8 18 h-lim-p 0.1162 0.9295 0.0000 1424.741194 0 0.6971 353 | 0/8 19 h-lim-p 0.0045 0.0364 0.0001 1424.741194 m 0.0364 373 | 1/8 20 h-lim-p 0.2799 20.0000 0.0000 1424.741194 0 0.2799 393 | 1/8 21 h-lim-p 0.6691 20.0000 0.0000 1424.741194 0 0.5854 412 | 1/8 22 h-lim-p 2.5000 20.0000 0.0000 1424.741194 0 0.2734 433 | 1/8 23 h-lim-p 0.3694 20.0000 0.0000 1424.741194 0 0.0462 454 | 1/8 24 h-lim-p 0.0481 20.0000 0.0000 1424.741194 0 0.0000 489 Out... lnL = -1424.741194 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1424.741194 Node 7: lnL = -1424.741194 Node 8: lnL = -1424.741194 Node 9: lnL = -1424.741194 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 283 Sequential format.. Reading seq # 1: YOL077W-A_Sbay Reading seq # 2: YOL077W-A_Scer Reading seq # 3: YOL077W-A_Skud Reading seq # 4: YOL077W-A_Smik Reading seq # 5: YOL077W-A_Spar Sequences read.. Counting patterns.. # site patterns = 112 Counting frequencies.. 120 bytes for distance 17920 bytes for lkl0 14336 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.043597 0.066644 0.191884 0.209208 0.274290 0.296490 0.327486 lnL0 = -1153.021023 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1153.021023 x= 0.00006 0.04360 0.06664 0.19188 0.20921 0.27429 0.29649 0.32749 1 h-lim-p 0.0000 0.0000 160.3365 1152.972247 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0024 175.4340 1144.663683 5 0.0010 52 | 1/8 3 h-lim-p 0.0025 0.0199 23.4169 1143.877887 7 0.0028 79 | 1/8 4 h-lim-p 0.0075 0.0604 4.1041 1143.604354 1 0.0094 93 | 1/8 5 h-lim-p 0.0163 0.1482 2.3738 1140.490508 0 0.0489 106 | 1/8 6 h-lim-p 0.0011 0.0086 27.2426 1133.899751 0 0.0043 120 | 1/8 7 h-lim-p 0.0009 0.0072 35.2897 1133.226282 1 0.0011 134 | 1/8 8 h-lim-p 0.0028 0.0225 12.3325 1133.135964 5 0.0012 157 | 1/8 9 h-lim-p 0.1127 1.1195 0.1289 1130.730970 0 0.4507 171 | 0/8 10 h-lim-p 0.0068 0.4724 8.5476 1130.681409 4 0.0013 199 | 0/8 11 h-lim-p 0.0832 0.6655 0.0849 1130.280968 0 0.3327 213 | 0/8 12 h-lim-p 0.5990 4.7916 0.0056 1130.270573 1 0.7487 235 | 0/8 13 h-lim-p 0.9699 20.0000 0.0043 1130.268482 3 0.4812 261 | 0/8 14 h-lim-p 2.5000 20.0000 0.0005 1130.268396 4 0.6789 290 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1130.268395 0 1.0938 310 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1130.268395 0 1.0938 330 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1130.268395 0 1.0938 350 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1130.268395 0 3.7500 370 | 0/8 19 h-lim-p 1.7812 20.0000 0.0000 1130.268395 0 0.0000 405 Out... lnL = -1130.268395 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1130.268395 Node 7: lnL = -1130.268395 Node 8: lnL = -1130.268395 Node 9: lnL = -1130.268395 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 265 Sequential format.. Reading seq # 1: YOL078W_Sbay Reading seq # 2: YOL078W_Scer Reading seq # 3: YOL078W_Skud Reading seq # 4: YOL078W_Smik Reading seq # 5: YOL078W_Spar Sequences read.. Counting patterns.. # site patterns = 135 Counting frequencies.. 120 bytes for distance 21600 bytes for lkl0 17280 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.074786 0.068857 0.263046 0.276179 0.338692 0.330066 0.384961 lnL0 = -1217.502713 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1217.502713 x= 0.00006 0.07479 0.06886 0.26305 0.27618 0.33869 0.33007 0.38496 1 h-lim-p 0.0000 0.0000 160.6837 1217.449595 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0028 192.2610 1199.097275 0 0.0019 41 | 1/8 3 h-lim-p 0.0009 0.0072 46.8496 1197.816442 0 0.0018 54 | 1/8 4 h-lim-p 0.0040 0.0321 9.1707 1197.689434 8 0.0023 86 | 1/8 5 h-lim-p 0.0130 0.1878 1.6204 1196.949834 0 0.0389 99 | 0/8 6 h-lim-p 0.0028 0.0223 19.5136 1191.381118 0 0.0112 113 | 0/8 7 h-lim-p 0.0003 0.0027 78.9773 1186.668550 m 0.0027 125 | 1/8 8 h-lim-p 0.0017 0.0138 23.4767 1185.441022 0 0.0026 137 | 1/8 9 h-lim-p 0.0038 0.0303 9.1789 1185.356647 5 0.0017 158 | 1/8 10 h-lim-p 0.1738 3.9542 0.0876 1183.666723 0 1.0425 172 | 0/8 11 h-lim-p 0.0057 0.1362 16.0593 1183.482102 6 0.0015 203 | 0/8 12 h-lim-p 0.2574 2.0589 0.0522 1183.009190 0 0.7721 216 | 0/8 13 h-lim-p 0.7936 6.3490 0.0231 1182.926010 4 0.6122 244 | 0/8 14 h-lim-p 0.9359 20.0000 0.0151 1182.916491 6 0.3301 278 | 0/8 15 h-lim-p 2.5000 20.0000 0.0011 1182.915966 3 1.0004 304 | 0/8 16 h-lim-p 2.5000 20.0000 0.0001 1182.915963 2 0.7996 329 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1182.915963 0 1.0938 349 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1182.915963 0 1.0938 369 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1182.915963 0 2.1875 389 | 0/8 20 h-lim-p 1.8574 20.0000 0.0000 1182.915963 0 0.8126 409 | 0/8 21 h-lim-p 2.5000 20.0000 0.0000 1182.915963 0 0.3125 431 | 0/8 22 h-lim-p 0.1898 20.0000 0.0000 1182.915963 0 0.0415 452 | 0/8 23 h-lim-p 0.0210 20.0000 0.0000 1182.915963 0 0.0000 489 Out... lnL = -1182.915963 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1182.915963 Node 7: lnL = -1182.915963 Node 8: lnL = -1182.915963 Node 9: lnL = -1182.915963 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 291 Sequential format.. Reading seq # 1: YOL080C_Sbay Reading seq # 2: YOL080C_Scer Reading seq # 3: YOL080C_Skud Reading seq # 4: YOL080C_Smik Reading seq # 5: YOL080C_Spar Sequences read.. Counting patterns.. # site patterns = 99 Counting frequencies.. 120 bytes for distance 15840 bytes for lkl0 12672 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.031371 0.202492 0.825467 0.921689 2.560323 1.022231 1.229420 lnL0 = -1350.762262 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1350.762262 x= 0.00006 0.03137 0.20249 0.82547 0.92169 2.56032 1.02223 1.22942 1 h-lim-p 0.0000 0.0000 160.8426 1350.711059 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0745 17.7774 1301.225596 m 0.0745 44 | 2/8 3 h-lim-p 0.0020 0.0163 46.2429 1261.524454 0 0.0122 58 | 1/8 4 h-lim-p 0.0004 0.0035 84.5000 1247.616256 m 0.0035 70 | 1/8 5 h-lim-p -0.0000 -0.0000 611.9165 h-lim-p: -4.07015971e-21 -3.25612777e-20 6.11916520e+02 1247.616256 .. | 1/8 6 h-lim-p 0.0000 0.0069 264.2441 1235.529591 0 0.0006 96 | 1/8 7 h-lim-p 0.0006 0.0049 140.6596 1145.880502 m 0.0049 108 | 2/8 8 h-lim-p 0.0000 0.0001 3615.4531 1133.727134 0 0.0001 122 | 2/8 9 h-lim-p 0.0009 0.0071 21.5100 1132.891825 0 0.0035 136 | 1/8 10 h-lim-p 0.0004 0.0030 76.8952 1130.635294 0 0.0011 149 | 1/8 11 h-lim-p 0.0308 0.2464 0.5689 .. | 1/8 12 h-lim-p 0.0000 0.0051 109.2639 1102.923422 0 0.0038 213 | 1/8 13 h-lim-p 0.0001 0.0007 336.3853 1096.753564 0 0.0003 227 | 1/8 14 h-lim-p 0.0001 0.0006 147.3623 1092.955128 m 0.0006 239 | 1/8 15 h-lim-p 0.0004 0.0032 58.1329 1092.369491 0 0.0006 251 | 1/8 16 h-lim-p 0.0092 0.0737 3.7427 1092.332965 5 0.0017 274 | 0/8 17 h-lim-p 0.0003 0.0519 24.3591 1091.875962 0 0.0021 289 | 0/8 18 h-lim-p 0.0178 0.1421 0.6207 1085.340881 m 0.1421 301 | 1/8 19 h-lim-p 2.4498 20.0000 0.0294 1084.383244 9 1.5204 344 | 1/8 20 h-lim-p 0.8853 7.0826 0.0295 1084.244958 4 0.6943 371 | 1/8 21 h-lim-p 2.5000 20.0000 0.0042 1084.225787 6 1.4543 405 | 0/8 22 h-lim-p 0.0915 20.0000 0.0661 1084.225784 1 0.0014 431 | 0/8 23 h-lim-p 0.2407 1.9255 0.0004 1084.225487 m 1.9255 451 | 1/8 24 h-lim-p 2.5000 20.0000 0.0002 1084.225463 2 0.9644 475 | 1/8 25 h-lim-p 2.5000 20.0000 0.0000 1084.225462 0 1.0938 494 | 0/8 26 h-lim-p 0.0952 20.0000 0.0005 1084.225462 0 0.0208 514 | 0/8 27 h-lim-p 0.1208 0.9668 0.0000 1084.225462 m 0.9668 534 | 1/8 28 h-lim-p 0.9985 20.0000 0.0000 1084.225462 0 0.1092 556 | 1/8 29 h-lim-p 0.0599 20.0000 0.0000 1084.225462 0 0.4796 578 | 1/8 30 h-lim-p 0.4935 20.0000 0.0000 1084.225462 0 0.0308 600 | 1/8 31 h-lim-p 0.0073 20.0000 0.0001 1084.225462 0 0.0000 638 | 1/8 32 h-lim-p 0.0000 20.0000 0.0001 | 1/8 33 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1084.225462 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1084.225462 Node 7: lnL = -1084.225462 Node 8: lnL = -1084.225462 Node 9: lnL = -1084.225462 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 410 Sequential format.. Reading seq # 1: YOL083W_Sbay Reading seq # 2: YOL083W_Scer Reading seq # 3: YOL083W_Skud Reading seq # 4: YOL083W_Smik Reading seq # 5: YOL083W_Spar Sequences read.. Counting patterns.. # site patterns = 209 Counting frequencies.. 120 bytes for distance 33440 bytes for lkl0 26752 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.062781 0.097106 0.258413 0.230539 0.357499 0.398388 0.491030 lnL0 = -1992.311187 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1992.311187 x= 0.00006 0.06278 0.09711 0.25841 0.23054 0.35750 0.39839 0.49103 1 h-lim-p 0.0000 0.0000 189.5732 1992.184208 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0030 144.3697 1982.788412 0 0.0013 41 | 1/8 3 h-lim-p 0.0016 0.0124 39.5178 1980.873202 0 0.0031 54 | 1/8 4 h-lim-p 0.0147 0.1176 6.7176 1980.684950 6 0.0050 81 | 1/8 5 h-lim-p 0.0140 0.1202 2.3927 1979.945737 0 0.0280 94 | 1/8 6 h-lim-p 0.0082 0.0657 4.9811 1972.614173 0 0.0329 108 | 1/8 7 h-lim-p 0.0009 0.0074 39.3499 1971.323767 0 0.0014 120 | 1/8 8 h-lim-p 0.0082 0.0817 6.6202 1971.235439 5 0.0033 142 | 1/8 9 h-lim-p 0.1381 1.6604 0.1566 1968.913667 0 0.5525 156 | 0/8 10 h-lim-p 0.0206 1.0130 4.2022 1968.886759 6 0.0028 189 | 0/8 11 h-lim-p 0.1165 0.9319 0.0627 1968.478774 0 0.4660 203 | 0/8 12 h-lim-p 1.7468 19.8117 0.0167 1968.400380 5 0.7741 232 | 0/8 13 h-lim-p 2.5000 20.0000 0.0049 1968.394079 4 0.7330 263 | 0/8 14 h-lim-p 2.5000 20.0000 0.0006 1968.394013 3 0.8800 290 | 0/8 15 h-lim-p 2.5000 20.0000 0.0001 1968.394010 1 0.9961 312 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1968.394010 0 1.0938 332 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1968.394010 0 0.5469 353 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1968.394010 0 1.0938 373 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1968.394010 0 0.4688 395 | 0/8 20 h-lim-p 0.3890 20.0000 0.0000 1968.394010 0 0.0486 417 | 0/8 21 h-lim-p 0.0246 20.0000 0.0000 1968.394010 0 0.0000 452 Out... lnL = -1968.394010 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1968.394010 Node 7: lnL = -1968.394010 Node 8: lnL = -1968.394010 Node 9: lnL = -1968.394010 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 556 Sequential format.. Reading seq # 1: YOL087C_Sbay Reading seq # 2: YOL087C_Scer Reading seq # 3: YOL087C_Skud Reading seq # 4: YOL087C_Smik Reading seq # 5: YOL087C_Spar Sequences read.. Counting patterns.. # site patterns = 192 Counting frequencies.. 120 bytes for distance 30720 bytes for lkl0 24576 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.009813 0.050896 0.064646 0.070591 0.085873 0.150128 0.142221 0.322829 lnL0 = -2308.533985 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2308.533985 x= 0.00981 0.05090 0.06465 0.07059 0.08587 0.15013 0.14222 0.32283 1 h-lim-p 0.0004 0.0030 116.5806 2306.898468 6 0.0003 38 | 0/8 2 h-lim-p 0.0005 0.0038 33.8978 2306.726235 7 0.0003 67 | 0/8 3 h-lim-p 0.0007 0.0151 15.5879 2306.698235 5 0.0003 88 | 0/8 4 h-lim-p 0.0008 0.0239 5.2398 2306.694793 5 0.0003 114 | 0/8 5 h-lim-p 0.0021 0.4435 0.7155 2306.694666 2 0.0005 131 | 0/8 6 h-lim-p 0.0020 1.1114 0.1792 2306.694661 2 0.0003 157 | 0/8 7 h-lim-p 0.0039 15.2899 0.0145 2306.694661 0 0.0017 177 | 0/8 8 h-lim-p 0.0608 20.0000 0.0004 2306.694560 0 0.7291 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2306.694558 0 1.0938 220 | 0/8 10 h-lim-p 1.7272 20.0000 0.0000 2306.694558 0 0.8636 240 | 0/8 11 h-lim-p 0.7268 20.0000 0.0000 2306.694558 0 0.0681 263 | 0/8 12 h-lim-p 0.0221 20.0000 0.0001 2306.694558 0 0.0000 291 | 0/8 13 h-lim-p 0.0002 20.0000 0.0000 2306.694558 0 0.0000 326 | 0/8 14 h-lim-p 0.0000 20.0000 0.0014 | 0/8 15 h-lim-p 0.0000 20.0000 0.0014 Out... lnL = -2306.694558 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2306.694558 Node 7: lnL = -2306.694558 Node 8: lnL = -2306.694558 Node 9: lnL = -2306.694558 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 578 Sequential format.. Reading seq # 1: YOL088C_Sbay Reading seq # 2: YOL088C_Scer Reading seq # 3: YOL088C_Skud Reading seq # 4: YOL088C_Smik Reading seq # 5: YOL088C_Spar Sequences read.. Counting patterns.. # site patterns = 264 Counting frequencies.. 120 bytes for distance 42240 bytes for lkl0 33792 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.045900 0.045530 0.220253 0.160781 0.234502 0.260693 0.446088 lnL0 = -2741.952061 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2741.952061 x= 0.00006 0.04590 0.04553 0.22025 0.16078 0.23450 0.26069 0.44609 1 h-lim-p 0.0003 0.0024 87.9511 2740.162235 0 0.0006 23 | 0/8 2 h-lim-p 0.0001 0.0008 29.4038 2740.002337 0 0.0004 37 | 0/8 3 h-lim-p 0.0000 0.0002 19.2492 2739.957549 m 0.0002 49 | 1/8 4 h-lim-p 0.0007 0.0655 5.3524 2739.943775 0 0.0011 61 | 1/8 5 h-lim-p 0.0080 0.4650 0.7221 2739.940402 2 0.0035 77 | 1/8 6 h-lim-p 0.0016 0.3038 1.5912 2739.926633 0 0.0048 97 | 1/8 7 h-lim-p 0.0088 0.1436 0.8603 2739.832108 0 0.0132 109 | 1/8 8 h-lim-p 0.0060 0.0850 1.8949 2739.831156 4 0.0005 140 | 1/8 9 h-lim-p 0.1021 20.0000 0.0095 2739.785023 0 0.8164 155 | 1/8 10 h-lim-p 2.5000 20.0000 0.0009 2739.784406 3 1.0004 180 | 0/8 11 h-lim-p 0.3639 20.0000 0.0025 2739.784406 0 0.0050 204 | 0/8 12 h-lim-p 0.1206 0.9650 0.0000 2739.784405 m 0.9650 224 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 2739.784405 0 1.0938 244 | 1/8 14 h-lim-p 1.8802 20.0000 0.0000 2739.784405 0 0.8226 263 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 2739.784405 0 0.0684 286 | 1/8 16 h-lim-p 0.0733 20.0000 0.0000 2739.784405 0 0.0006 311 Out... lnL = -2739.784405 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2739.784405 Node 7: lnL = -2739.784405 Node 8: lnL = -2739.784405 Node 9: lnL = -2739.784405 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 221 Sequential format.. Reading seq # 1: YOL090W_Sbay Reading seq # 2: YOL090W_Scer Reading seq # 3: YOL090W_Skud Reading seq # 4: YOL090W_Smik Reading seq # 5: YOL090W_Spar Sequences read.. Counting patterns.. # site patterns = 104 Counting frequencies.. 120 bytes for distance 16640 bytes for lkl0 13312 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.043797 0.033305 0.203217 0.091745 0.229129 0.227533 0.320469 lnL0 = -952.502007 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 952.502007 x= 0.00006 0.04380 0.03330 0.20322 0.09174 0.22913 0.22753 0.32047 1 h-lim-p 0.0000 0.0000 138.9801 952.369570 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0012 98.8259 948.495896 0 0.0009 40 | 1/8 3 h-lim-p 0.0003 0.0026 24.8065 948.303594 0 0.0007 53 | 1/8 4 h-lim-p 0.0019 0.0429 8.5123 948.222973 6 0.0021 79 | 1/8 5 h-lim-p 0.0127 0.2529 1.3890 948.022820 0 0.0253 92 | 0/8 6 h-lim-p 0.0045 0.0448 7.8937 945.230593 0 0.0267 106 | 0/8 7 h-lim-p 0.0020 0.0160 12.6450 944.984458 6 0.0022 133 | 0/8 8 h-lim-p 0.0036 0.0461 7.5159 944.879322 2 0.0034 149 | 0/8 9 h-lim-p 0.0017 0.0137 10.6118 944.717134 0 0.0052 162 | 0/8 10 h-lim-p 0.0416 0.3331 0.2412 944.193617 0 0.1665 176 | 0/8 11 h-lim-p 0.2238 1.7901 0.0578 944.086002 0 0.6713 197 | 0/8 12 h-lim-p 1.4031 11.2244 0.0096 944.072242 6 1.0295 230 | 0/8 13 h-lim-p 2.5000 20.0000 0.0013 944.071186 4 1.0785 257 | 0/8 14 h-lim-p 1.8679 20.0000 0.0008 944.071119 4 1.0555 288 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 944.071118 0 1.0938 308 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 944.071118 0 1.0938 328 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 944.071118 0 1.0938 348 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 944.071118 0 1.0938 368 | 0/8 19 h-lim-p 1.1166 20.0000 0.0000 944.071118 018.9330 392 | 0/8 20 h-lim-p 2.3681 20.0000 0.0000 944.071118 0 1.0360 412 | 0/8 21 h-lim-p 0.0389 20.0000 0.0001 944.071118 0 0.0000 457 | 0/8 22 h-lim-p 0.0000 20.0000 0.0002 | 0/8 23 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -944.071118 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -944.071118 Node 7: lnL = -944.071118 Node 8: lnL = -944.071118 Node 9: lnL = -944.071118 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 214 Sequential format.. Reading seq # 1: YOL091W_Sbay Reading seq # 2: YOL091W_Scer Reading seq # 3: YOL091W_Skud Reading seq # 4: YOL091W_Smik Reading seq # 5: YOL091W_Spar Sequences read.. Counting patterns.. # site patterns = 93 Counting frequencies.. 120 bytes for distance 14880 bytes for lkl0 11904 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.045351 0.028897 0.189983 0.215593 0.259552 0.263116 0.294124 lnL0 = -877.304724 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 877.304724 x= 0.00006 0.04535 0.02890 0.18998 0.21559 0.25955 0.26312 0.29412 1 h-lim-p 0.0000 0.0000 132.6071 877.263353 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0035 111.7942 871.314158 0 0.0013 41 | 1/8 3 h-lim-p 0.0009 0.0070 37.1206 870.476723 0 0.0018 54 | 1/8 4 h-lim-p 0.0052 0.0417 7.5837 870.412842 6 0.0019 79 | 1/8 5 h-lim-p 0.0162 0.3466 0.8942 870.055978 0 0.0486 92 | 0/8 6 h-lim-p 0.0040 0.0321 4.2543 864.379614 0 0.0240 113 | 0/8 7 h-lim-p 0.0003 0.0028 30.4885 863.778462 0 0.0014 127 | 0/8 8 h-lim-p 0.0003 0.0022 15.7011 863.592931 m 0.0022 139 | 0/8 9 h-lim-p -0.0000 -0.0000 1.6608 h-lim-p: -1.71138100e-19 -1.36910480e-18 1.66082362e+00 863.592931 .. | 0/8 10 h-lim-p 0.0000 0.0101 26.2780 863.466577 0 0.0005 164 | 0/8 11 h-lim-p 0.0006 0.0067 22.1493 863.351580 1 0.0007 178 | 0/8 12 h-lim-p 0.0014 0.0108 3.1932 863.346661 5 0.0010 202 | 0/8 13 h-lim-p 0.0029 0.1911 1.0904 863.346020 3 0.0012 220 | 0/8 14 h-lim-p 0.0088 0.2177 0.1457 863.345986 2 0.0019 237 | 0/8 15 h-lim-p 0.0045 3.4672 0.0620 863.345892 0 0.0090 258 | 0/8 16 h-lim-p 0.0049 0.3373 0.1133 863.344312 0 0.0197 280 | 0/8 17 h-lim-p 0.0044 0.0652 0.5069 863.338574 0 0.0066 300 | 0/8 18 h-lim-p 2.5000 20.0000 0.0006 863.338287 3 0.9644 326 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 863.338287 0 1.0938 346 | 0/8 20 h-lim-p 2.4850 20.0000 0.0000 863.338287 0 1.0872 366 | 0/8 21 h-lim-p 1.0078 20.0000 0.0000 863.338287 0 4.0313 388 | 0/8 22 h-lim-p 1.8434 20.0000 0.0000 863.338287 0 0.8065 408 | 0/8 23 h-lim-p 0.0505 16.7122 0.0005 863.338287 0 0.0110 429 | 0/8 24 h-lim-p 0.0032 4.7876 0.0018 863.338287 0 0.0004 451 | 0/8 25 h-lim-p 0.0002 2.6339 0.0033 863.338287 0 0.0002 471 | 0/8 26 h-lim-p 0.0001 0.8703 0.0099 863.338287 0 0.0000 492 | 0/8 27 h-lim-p 0.0000 2.7310 0.0032 863.338287 0 0.0000 513 | 0/8 28 h-lim-p 0.0001 11.3988 0.0008 863.338287 0 0.0000 545 | 0/8 29 h-lim-p 0.0000 20.0000 0.0009 863.338287 0 0.0000 574 | 0/8 30 h-lim-p 0.0000 20.0000 0.0005 863.338287 0 0.0026 602 | 0/8 31 h-lim-p 0.0138 20.0000 0.0001 863.338287 0 0.0015 624 | 0/8 32 h-lim-p 0.0027 20.0000 0.0001 863.338287 0 0.0000 651 | 0/8 33 h-lim-p 0.0000 20.0000 0.0001 863.338287 0 0.0000 671 | 0/8 34 h-lim-p 0.0000 2.3805 0.0036 .. | 0/8 35 h-lim-p 0.0000 20.0000 0.0023 | 0/8 36 h-lim-p 0.0000 20.0000 0.0023 Out... lnL = -863.338287 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -863.338287 Node 7: lnL = -863.338287 Node 8: lnL = -863.338287 Node 9: lnL = -863.338287 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 539 Sequential format.. Reading seq # 1: YOL092W_Sbay Reading seq # 2: YOL092W_Scer Reading seq # 3: YOL092W_Skud Reading seq # 4: YOL092W_Smik Reading seq # 5: YOL092W_Spar Sequences read.. Counting patterns.. # site patterns = 249 Counting frequencies.. 120 bytes for distance 39840 bytes for lkl0 31872 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.050167 0.089108 0.285051 0.260910 0.368793 0.341734 0.460659 lnL0 = -2699.823498 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2699.823498 x= 0.00006 0.05017 0.08911 0.28505 0.26091 0.36879 0.34173 0.46066 1 h-lim-p 0.0000 0.0000 255.2589 2699.681631 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0016 258.0234 2683.604691 0 0.0010 40 | 1/8 3 h-lim-p 0.0008 0.0063 71.4791 2680.563605 0 0.0016 53 | 1/8 4 h-lim-p 0.0140 0.1123 4.0538 2680.429706 7 0.0050 81 | 1/8 5 h-lim-p 0.0046 0.1206 4.4085 2679.697058 0 0.0092 94 | 1/8 6 h-lim-p 0.0052 0.0417 6.7729 2668.793355 0 0.0208 108 | 0/8 7 h-lim-p 0.0004 0.0031 76.0602 2665.265385 0 0.0008 121 | 0/8 8 h-lim-p 0.0004 0.0031 25.7911 2664.565499 0 0.0015 135 | 0/8 9 h-lim-p 0.0001 0.0005 39.0217 2664.209547 m 0.0005 147 | 1/8 10 h-lim-p 0.0464 1.0491 0.2884 2663.271810 0 0.1856 161 | 1/8 11 h-lim-p 0.1547 1.2377 0.2155 2662.530390 1 0.1934 182 | 1/8 12 h-lim-p 2.5000 20.0000 0.0150 2662.341644 6 1.0501 214 | 1/8 13 h-lim-p 1.8779 20.0000 0.0084 2662.262790 6 1.3462 248 | 1/8 14 h-lim-p 2.1496 20.0000 0.0053 2662.249274 4 0.8565 275 | 1/8 15 h-lim-p 2.5000 20.0000 0.0010 2662.248849 4 0.7998 304 | 1/8 16 h-lim-p 2.5000 20.0000 0.0002 2662.248816 2 0.9644 327 | 0/8 17 h-lim-p 0.0154 20.0000 0.0154 2662.248816 0 0.0034 347 | 0/8 18 h-lim-p 0.1313 1.0503 0.0001 2662.248815 m 1.0503 367 | 1/8 19 h-lim-p 2.5000 20.0000 0.0000 2662.248815 0 0.5469 388 | 1/8 20 h-lim-p 0.9085 20.0000 0.0000 2662.248815 0 0.7949 407 | 1/8 21 h-lim-p 2.3947 20.0000 0.0000 2662.248815 0 1.0477 426 | 1/8 22 h-lim-p 2.5000 20.0000 0.0000 2662.248815 0 1.0938 445 | 1/8 23 h-lim-p 2.5000 20.0000 0.0000 2662.248815 0 0.0049 472 Out... lnL = -2662.248815 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2662.248815 Node 7: lnL = -2662.248815 Node 8: lnL = -2662.248815 Node 9: lnL = -2662.248815 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 272 Sequential format.. Reading seq # 1: YOL093W_Sbay Reading seq # 2: YOL093W_Scer Reading seq # 3: YOL093W_Skud Reading seq # 4: YOL093W_Smik Reading seq # 5: YOL093W_Spar Sequences read.. Counting patterns.. # site patterns = 115 Counting frequencies.. 120 bytes for distance 18400 bytes for lkl0 14720 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.040777 0.059716 0.189440 0.182254 0.249396 0.254999 0.310967 lnL0 = -1199.670206 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1199.670206 x= 0.00006 0.04078 0.05972 0.18944 0.18225 0.24940 0.25500 0.31097 1 h-lim-p 0.0000 0.0000 163.9421 1199.606071 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0016 66.6976 1198.065751 0 0.0010 40 | 1/8 3 h-lim-p 0.0009 0.0075 40.6529 1197.665295 6 0.0007 65 | 1/8 4 h-lim-p 0.0010 0.0088 27.3024 1197.246326 0 0.0020 78 | 1/8 5 h-lim-p 0.0065 0.0524 5.8436 1196.961903 7 0.0058 102 | 1/8 6 h-lim-p 0.0115 0.1074 2.9410 1192.972484 0 0.0459 116 | 0/8 7 h-lim-p 0.0007 0.0058 61.3481 1185.467025 0 0.0029 130 | 0/8 8 h-lim-p 0.0012 0.0094 30.7525 1184.248963 0 0.0024 143 | 0/8 9 h-lim-p 0.0010 0.0084 14.8417 1183.395949 m 0.0084 155 | 0/8 10 h-lim-p 0.0000 0.0000 0.1440 h-lim-p: 3.08303975e-18 2.46643180e-17 1.44005897e-01 1183.395949 .. | 0/8 11 h-lim-p 0.0000 0.0032 114.6963 1181.055903 0 0.0005 188 | 0/8 12 h-lim-p 0.0004 0.0034 41.9695 1180.573505 0 0.0006 200 | 0/8 13 h-lim-p 0.0012 0.0095 7.6017 1180.544038 6 0.0011 223 | 0/8 14 h-lim-p 0.0006 0.0044 3.9791 1180.535320 0 0.0017 236 | 0/8 15 h-lim-p 0.0003 0.0023 5.7984 1180.506295 m 0.0023 248 | 1/8 16 h-lim-p 0.0010 0.0554 9.2545 1180.505405 4 0.0002 270 | 1/8 17 h-lim-p 0.0037 0.4034 0.4267 1180.504874 5 0.0023 295 | 1/8 18 h-lim-p 0.0061 1.7078 0.1618 1180.500790 0 0.0245 316 | 1/8 19 h-lim-p 0.0059 0.2249 0.6698 1180.443768 0 0.0178 336 | 1/8 20 h-lim-p 1.9816 20.0000 0.0060 1180.404495 7 1.2088 375 | 1/8 21 h-lim-p 2.5000 20.0000 0.0010 1180.403544 3 0.9961 400 | 1/8 22 h-lim-p 2.5000 20.0000 0.0001 1180.403541 1 0.9961 421 | 1/8 23 h-lim-p 2.5000 20.0000 0.0000 1180.403541 0 1.0938 440 | 1/8 24 h-lim-p 2.5000 20.0000 0.0000 1180.403541 0 2.1875 459 | 1/8 25 h-lim-p 1.8387 20.0000 0.0000 1180.403541 0 0.8045 478 | 1/8 26 h-lim-p 2.5000 20.0000 0.0000 1180.403541 0 0.0781 501 | 1/8 27 h-lim-p 0.0847 20.0000 0.0000 1180.403541 0 0.0013 525 Out... lnL = -1180.403541 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1180.403541 Node 7: lnL = -1180.403541 Node 8: lnL = -1180.403541 Node 9: lnL = -1180.403541 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 272 Sequential format.. Reading seq # 1: YOL094C_Sbay Reading seq # 2: YOL094C_Scer Reading seq # 3: YOL094C_Skud Reading seq # 4: YOL094C_Smik Reading seq # 5: YOL094C_Spar Sequences read.. Counting patterns.. # site patterns = 115 Counting frequencies.. 120 bytes for distance 18400 bytes for lkl0 14720 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.043533 0.060238 0.193386 0.189593 0.254674 0.260579 0.312514 lnL0 = -1202.953364 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1202.953364 x= 0.00006 0.04353 0.06024 0.19339 0.18959 0.25467 0.26058 0.31251 1 h-lim-p 0.0000 0.0000 169.0560 1202.891199 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0058 56.0424 1201.253392 0 0.0013 41 | 1/8 3 h-lim-p 0.0007 0.0054 40.9723 1200.410835 0 0.0013 54 | 1/8 4 h-lim-p 0.0008 0.0066 37.9602 1200.115815 4 0.0007 73 | 1/8 5 h-lim-p 0.0034 0.0384 8.0177 1199.802655 0 0.0051 85 | 1/8 6 h-lim-p 0.0103 0.0821 3.7270 1197.490514 0 0.0205 98 | 1/8 7 h-lim-p 0.0026 0.0205 14.5419 1182.888737 0 0.0103 112 | 1/8 8 h-lim-p 0.0023 0.0183 12.5152 1182.778451 7 0.0013 140 | 1/8 9 h-lim-p 0.1188 1.3151 0.1413 1181.532962 0 0.3564 153 | 1/8 10 h-lim-p 0.5553 4.4427 0.0470 1181.194497 2 0.5206 176 | 0/8 11 h-lim-p 0.0153 1.0592 1.5963 1181.192601 5 0.0014 209 | 0/8 12 h-lim-p 0.1304 11.0261 0.0172 1181.138905 0 0.5216 223 | 0/8 13 h-lim-p 2.5000 20.0000 0.0035 1181.133365 4 0.7998 253 | 0/8 14 h-lim-p 1.8155 20.0000 0.0015 1181.132408 2 0.8510 277 | 0/8 15 h-lim-p 2.5000 20.0000 0.0002 1181.132383 3 0.8855 305 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1181.132383 0 1.0938 325 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1181.132383 0 1.0938 345 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1181.132383 0 0.6250 366 | 0/8 19 h-lim-p 1.3751 20.0000 0.0000 1181.132383 0 0.0107 392 Out... lnL = -1181.132383 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1181.132383 Node 7: lnL = -1181.132383 Node 8: lnL = -1181.132383 Node 9: lnL = -1181.132383 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 179 Sequential format.. Reading seq # 1: YOL096C_Sbay Reading seq # 2: YOL096C_Scer Reading seq # 3: YOL096C_Skud Reading seq # 4: YOL096C_Smik Reading seq # 5: YOL096C_Spar Sequences read.. Counting patterns.. # site patterns = 96 Counting frequencies.. 120 bytes for distance 15360 bytes for lkl0 12288 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.036667 0.078100 0.233214 0.178904 0.340740 0.300021 0.403003 lnL0 = -852.192239 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 852.192239 x= 0.00006 0.03667 0.07810 0.23321 0.17890 0.34074 0.30002 0.40300 1 h-lim-p 0.0000 0.0000 101.1115 852.097157 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0015 81.5904 848.227943 6 0.0015 54 | 1/8 3 h-lim-p 0.0002 0.0018 88.8929 846.702133 0 0.0009 68 | 1/8 4 h-lim-p 0.0040 0.0320 11.2513 846.438125 2 0.0037 84 | 1/8 5 h-lim-p 0.0165 0.1320 1.7965 845.990232 0 0.0330 97 | 0/8 6 h-lim-p 0.0059 0.0475 8.0752 843.857133 0 0.0238 111 | 0/8 7 h-lim-p 0.0011 0.0087 42.5102 840.810913 0 0.0044 125 | 0/8 8 h-lim-p 0.0060 0.0477 7.7876 840.727095 2 0.0028 141 | 0/8 9 h-lim-p 0.0166 0.1456 1.3120 840.488152 0 0.0996 155 | 0/8 10 h-lim-p 0.0788 0.6305 0.7053 839.875612 0 0.2364 168 | 0/8 11 h-lim-p 0.1562 1.2500 0.1463 839.724186 0 0.3125 189 | 0/8 12 h-lim-p 0.4050 3.2403 0.0436 839.695793 0 0.8101 210 | 0/8 13 h-lim-p 0.5833 4.6664 0.0287 839.689146 1 0.7291 232 | 0/8 14 h-lim-p 2.5000 20.0000 0.0028 839.688641 3 1.0004 258 | 0/8 15 h-lim-p 2.5000 20.0000 0.0003 839.688625 3 0.8800 285 | 0/8 16 h-lim-p 2.5000 20.0000 0.0001 839.688624 0 1.0938 305 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 839.688623 0 2.1875 325 | 0/8 18 h-lim-p 2.4339 20.0000 0.0000 839.688623 0 1.0648 345 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 839.688623 0 2.1875 365 | 0/8 20 h-lim-p 1.6000 20.0000 0.0000 839.688623 0 0.7000 385 | 0/8 21 h-lim-p 1.5331 20.0000 0.0000 839.688623 0 0.0060 412 Out... lnL = -839.688623 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -839.688623 Node 7: lnL = -839.688623 Node 8: lnL = -839.688623 Node 9: lnL = -839.688623 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 861 Sequential format.. Reading seq # 1: YOL101C_Sbay Reading seq # 2: YOL101C_Scer Reading seq # 3: YOL101C_Skud Reading seq # 4: YOL101C_Smik Reading seq # 5: YOL101C_Spar Sequences read.. Counting patterns.. # site patterns = 295 Counting frequencies.. 120 bytes for distance 47200 bytes for lkl0 37760 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.029950 0.054207 0.197966 0.195745 0.296931 0.301897 0.339571 lnL0 = -3700.265493 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3700.265493 x= 0.00006 0.02995 0.05421 0.19797 0.19574 0.29693 0.30190 0.33957 1 h-lim-p 0.0000 0.0000 471.6248 3700.041263 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0007 478.6510 3679.064322 0 0.0003 39 | 1/8 3 h-lim-p 0.0002 0.0015 130.6633 3675.312104 0 0.0006 52 | 1/8 4 h-lim-p 0.0018 0.0141 29.3153 3675.028676 7 0.0006 80 | 1/8 5 h-lim-p 0.0053 0.0580 3.5623 3674.779848 2 0.0050 96 | 1/8 6 h-lim-p 0.0059 0.1035 3.0002 3661.333483 0 0.0471 111 | 0/8 7 h-lim-p 0.0003 0.0022 127.9246 3654.403026 0 0.0006 124 | 0/8 8 h-lim-p 0.0001 0.0010 87.5494 3652.463175 0 0.0005 138 | 0/8 9 h-lim-p 0.0001 0.0009 39.2708 3651.617222 m 0.0009 150 | 0/8 10 h-lim-p 0.0000 0.0000 0.1205 h-lim-p: 5.89453459e-18 4.71562767e-17 1.20503341e-01 3651.617222 .. | 0/8 11 h-lim-p 0.0000 0.0008 281.5647 3645.906645 0 0.0002 182 | 0/8 12 h-lim-p 0.0001 0.0010 117.6994 3644.814132 0 0.0003 195 | 0/8 13 h-lim-p 0.0009 0.0099 33.0006 3644.670679 6 0.0003 222 | 0/8 14 h-lim-p 0.0006 0.0049 7.3608 3644.661721 5 0.0003 247 | 0/8 15 h-lim-p 0.0011 0.0121 2.3495 3644.660630 4 0.0004 267 | 0/8 16 h-lim-p 0.0007 0.0127 1.4636 3644.645892 m 0.0127 281 | 1/8 17 h-lim-p 0.0006 0.0119 21.6150 3644.643224 4 0.0001 303 | 1/8 18 h-lim-p 0.0008 0.0600 2.1410 3644.642322 3 0.0003 321 | 1/8 19 h-lim-p 0.0410 20.0000 0.0165 3644.516392 0 0.6559 337 | 0/8 20 h-lim-p 0.0158 5.2876 0.6880 3644.516235 3 0.0006 367 | 0/8 21 h-lim-p 0.0779 1.2604 0.0056 3644.502727 0 0.6231 390 | 0/8 22 h-lim-p 0.2298 1.8386 0.0009 3644.501441 0 0.9193 412 | 0/8 23 h-lim-p 0.1089 0.8716 0.0002 3644.501399 m 0.8716 432 | 1/8 24 h-lim-p 1.0631 20.0000 0.0001 3644.501393 1 0.5233 455 | 1/8 25 h-lim-p 2.5000 20.0000 0.0000 3644.501392 0 1.0938 474 | 1/8 26 h-lim-p 2.5000 20.0000 0.0000 3644.501392 0 2.1875 493 | 1/8 27 h-lim-p 2.5000 20.0000 0.0000 3644.501392 0 1.0938 512 | 1/8 28 h-lim-p 2.5000 20.0000 0.0000 3644.501392 0 0.0342 536 | 1/8 29 h-lim-p 0.0354 20.0000 0.0000 3644.501392 0 0.0000 566 Out... lnL = -3644.501392 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3644.501392 Node 7: lnL = -3644.501392 Node 8: lnL = -3644.501392 Node 9: lnL = -3644.501392 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 324 Sequential format.. Reading seq # 1: YOL102C_Sbay Reading seq # 2: YOL102C_Scer Reading seq # 3: YOL102C_Skud Reading seq # 4: YOL102C_Smik Reading seq # 5: YOL102C_Spar Sequences read.. Counting patterns.. # site patterns = 163 Counting frequencies.. 120 bytes for distance 26080 bytes for lkl0 20864 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.274762 0.008990 0.089019 0.165078 0.091852 0.259331 0.302939 0.163983 lnL0 = -1548.537084 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1548.537084 x= 0.27476 0.00899 0.08902 0.16508 0.09185 0.25933 0.30294 0.16398 1 h-lim-p 0.0131 2.9469 48.6343 1547.922338 7 0.0006 43 | 0/8 2 h-lim-p 0.0019 0.0149 10.7419 1547.859498 6 0.0011 72 | 0/8 3 h-lim-p 0.0015 0.0136 7.8961 1547.839388 7 0.0009 101 | 0/8 4 h-lim-p 0.0034 0.1132 2.1023 1547.837134 5 0.0012 125 | 0/8 5 h-lim-p 0.0080 1.5744 0.3046 1547.837042 2 0.0021 142 | 0/8 6 h-lim-p 0.0044 1.5649 0.1439 1547.837029 2 0.0015 168 | 0/8 7 h-lim-p 0.0053 10.4984 0.0399 1547.837028 1 0.0021 190 | 0/8 8 h-lim-p 0.2531 20.0000 0.0003 1547.836959 0 1.0125 212 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1547.836958 0 1.0938 232 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1547.836958 0 1.0938 252 | 0/8 11 h-lim-p 1.9111 20.0000 0.0000 1547.836958 0 0.0149 278 | 0/8 12 h-lim-p 0.0069 20.0000 0.0000 1547.836958 0 0.0004 301 Out... lnL = -1547.836958 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1547.836958 Node 7: lnL = -1547.836958 Node 8: lnL = -1547.836958 Node 9: lnL = -1547.836958 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 764 Sequential format.. Reading seq # 1: YOL103W_Sbay Reading seq # 2: YOL103W_Scer Reading seq # 3: YOL103W_Skud Reading seq # 4: YOL103W_Smik Reading seq # 5: YOL103W_Spar Sequences read.. Counting patterns.. # site patterns = 294 Counting frequencies.. 120 bytes for distance 47040 bytes for lkl0 37632 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.172346 0.062276 0.042608 0.438135 0.132230 0.195974 0.223421 0.063318 lnL0 = -3754.812177 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3754.812177 x= 0.17235 0.06228 0.04261 0.43814 0.13223 0.19597 0.22342 0.06332 1 h-lim-p 0.0056 1.1483 115.2928 3753.601211 7 0.0002 40 | 0/8 2 h-lim-p 0.0009 0.0079 25.2339 3753.426147 5 0.0006 64 | 0/8 3 h-lim-p 0.0016 0.0341 9.1591 3753.401261 5 0.0007 88 | 0/8 4 h-lim-p 0.0008 0.0300 7.4948 3753.393294 5 0.0004 111 | 0/8 5 h-lim-p 0.0058 0.2416 0.5685 3753.393210 3 0.0005 132 | 0/8 6 h-lim-p 0.0021 0.9832 0.1390 3753.393206 0 0.0005 153 | 0/8 7 h-lim-p 0.0340 20.0000 0.0019 3753.393200 0 0.0510 173 | 0/8 8 h-lim-p 0.0044 20.0000 0.0215 3753.393051 0 0.0177 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3753.393044 0 1.0938 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3753.393044 0 1.0938 235 | 0/8 11 h-lim-p 1.2327 20.0000 0.0000 3753.393044 0 1.8491 255 | 0/8 12 h-lim-p 1.7180 20.0000 0.0000 3753.393044 0 0.7516 275 | 0/8 13 h-lim-p 0.0923 20.0000 0.0002 3753.393044 0 0.0115 297 | 0/8 14 h-lim-p 0.0034 20.0000 0.0005 3753.393044 0 0.0000 336 | 0/8 15 h-lim-p 0.0000 20.0000 0.0009 3753.393044 0 0.0000 370 | 0/8 16 h-lim-p 0.0000 20.0000 0.0009 | 0/8 17 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -3753.393044 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3753.393044 Node 7: lnL = -3753.393044 Node 8: lnL = -3753.393044 Node 9: lnL = -3753.393044 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 592 Sequential format.. Reading seq # 1: YOL104C_Sbay Reading seq # 2: YOL104C_Scer Reading seq # 3: YOL104C_Skud Reading seq # 4: YOL104C_Smik Reading seq # 5: YOL104C_Spar Sequences read.. Counting patterns.. # site patterns = 269 Counting frequencies.. 120 bytes for distance 43040 bytes for lkl0 34432 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.195790 0.084424 0.042453 0.597057 0.111694 0.224521 0.253373 0.066535 lnL0 = -3002.150409 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3002.150409 x= 0.19579 0.08442 0.04245 0.59706 0.11169 0.22452 0.25337 0.06653 1 h-lim-p 0.0012 0.0094 87.8586 3000.957712 7 0.0003 39 | 0/8 2 h-lim-p 0.0003 0.0024 49.9722 3000.378354 0 0.0006 52 | 0/8 3 h-lim-p 0.0023 0.0186 11.6775 3000.336770 6 0.0007 78 | 0/8 4 h-lim-p 0.0012 0.1517 6.5763 3000.309467 0 0.0017 90 | 0/8 5 h-lim-p 0.0033 0.0717 3.4709 3000.306264 4 0.0007 110 | 0/8 6 h-lim-p 0.0099 0.6409 0.2505 3000.306226 1 0.0011 126 | 0/8 7 h-lim-p 0.0066 7.5812 0.0408 3000.306171 1 0.0069 148 | 0/8 8 h-lim-p 0.0137 20.0000 0.0205 3000.300510 0 0.1092 171 | 0/8 9 h-lim-p 2.5000 20.0000 0.0008 3000.300040 2 1.0889 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3000.300038 0 1.0938 215 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3000.300038 0 2.1875 235 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3000.300038 0 1.0938 255 | 0/8 13 h-lim-p 0.0766 20.0000 0.0000 3000.300038 0 0.1532 276 | 0/8 14 h-lim-p 0.0004 14.5345 0.0069 3000.300038 0 0.0001 297 | 0/8 15 h-lim-p 0.0001 20.0000 0.0054 3000.300038 0 0.0000 331 | 0/8 16 h-lim-p 0.0006 20.0000 0.0000 3000.300038 0 0.0000 360 Out... lnL = -3000.300038 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3000.300038 Node 7: lnL = -3000.300038 Node 8: lnL = -3000.300038 Node 9: lnL = -3000.300038 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 425 Sequential format.. Reading seq # 1: YOL109W_Sbay Reading seq # 2: YOL109W_Scer Reading seq # 3: YOL109W_Skud Reading seq # 4: YOL109W_Smik Reading seq # 5: YOL109W_Spar Sequences read.. Counting patterns.. # site patterns = 146 Counting frequencies.. 120 bytes for distance 23360 bytes for lkl0 18688 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.158878 0.037906 0.040367 0.066364 0.069616 0.136449 0.153395 0.095952 lnL0 = -1698.367342 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1698.367342 x= 0.15888 0.03791 0.04037 0.06636 0.06962 0.13645 0.15340 0.09595 1 h-lim-p 0.0008 0.0060 191.5440 1695.018749 10 0.0002 47 | 0/8 2 h-lim-p 0.0003 0.0025 40.2942 1694.706930 1 0.0004 61 | 0/8 3 h-lim-p 0.0008 0.0102 20.1534 1694.651389 5 0.0003 82 | 0/8 4 h-lim-p 0.0010 0.0245 6.4633 1694.643819 4 0.0004 102 | 0/8 5 h-lim-p 0.0020 0.1429 1.3152 1694.643402 3 0.0005 121 | 0/8 6 h-lim-p 0.0014 0.3092 0.4577 1694.643362 3 0.0004 142 | 0/8 7 h-lim-p 0.0095 17.4013 0.0202 1694.643358 1 0.0038 164 | 0/8 8 h-lim-p 0.0202 20.0000 0.0038 1694.642092 0 0.3229 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1694.642026 2 0.9961 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1694.642026 0 1.0938 232 | 0/8 11 h-lim-p 1.4308 20.0000 0.0000 1694.642026 0 0.6260 252 | 0/8 12 h-lim-p 0.4123 20.0000 0.0000 1694.642026 0 0.0032 278 | 0/8 13 h-lim-p 0.0019 20.0000 0.0000 1694.642026 0 0.0019 298 | 0/8 14 h-lim-p 0.0010 20.0000 0.0000 1694.642026 0 0.0000 336 | 0/8 15 h-lim-p 0.0000 20.0000 0.0008 | 0/8 16 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -1694.642026 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1694.642026 Node 7: lnL = -1694.642026 Node 8: lnL = -1694.642026 Node 9: lnL = -1694.642026 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 319 Sequential format.. Reading seq # 1: YOL110W_Sbay Reading seq # 2: YOL110W_Scer Reading seq # 3: YOL110W_Skud Reading seq # 4: YOL110W_Smik Reading seq # 5: YOL110W_Spar Sequences read.. Counting patterns.. # site patterns = 168 Counting frequencies.. 120 bytes for distance 26880 bytes for lkl0 21504 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.251053 0.007662 0.121955 0.172661 0.135510 0.251197 0.304147 0.137035 lnL0 = -1501.336595 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1501.336595 x= 0.25105 0.00766 0.12195 0.17266 0.13551 0.25120 0.30415 0.13704 1 h-lim-p 0.0026 0.0204 72.5820 1499.995788 3 0.0006 29 | 0/8 2 h-lim-p 0.0026 0.0211 9.7015 1499.931392 7 0.0014 55 | 0/8 3 h-lim-p 0.0025 0.0807 5.2776 1499.917454 3 0.0012 73 | 0/8 4 h-lim-p 0.0030 0.1350 2.2135 1499.914494 2 0.0015 89 | 0/8 5 h-lim-p 0.0085 0.6061 0.3846 1499.914348 2 0.0020 106 | 0/8 6 h-lim-p 0.0136 4.8281 0.0564 1499.914346 0 0.0015 128 | 0/8 7 h-lim-p 0.0332 20.0000 0.0025 1499.914346 0 0.0145 148 | 0/8 8 h-lim-p 0.0604 20.0000 0.0006 1499.914329 0 0.3627 170 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1499.914328 0 1.0938 190 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1499.914328 0 1.0938 210 | 0/8 11 h-lim-p 2.1500 20.0000 0.0000 1499.914328 0 0.2687 232 | 0/8 12 h-lim-p 0.1393 20.0000 0.0000 1499.914328 0 0.0696 252 | 0/8 13 h-lim-p 0.0414 20.0000 0.0000 1499.914328 0 0.0002 279 Out... lnL = -1499.914328 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1499.914328 Node 7: lnL = -1499.914328 Node 8: lnL = -1499.914328 Node 9: lnL = -1499.914328 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 320 Sequential format.. Reading seq # 1: YOL111C_Sbay Reading seq # 2: YOL111C_Scer Reading seq # 3: YOL111C_Skud Reading seq # 4: YOL111C_Smik Reading seq # 5: YOL111C_Spar Sequences read.. Counting patterns.. # site patterns = 161 Counting frequencies.. 120 bytes for distance 25760 bytes for lkl0 20608 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.220828 0.015306 0.104129 0.179345 0.134290 0.255310 0.305803 0.111525 lnL0 = -1485.807020 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1485.807020 x= 0.22083 0.01531 0.10413 0.17935 0.13429 0.25531 0.30580 0.11152 1 h-lim-p 0.0065 0.4321 67.5590 1484.694459 7 0.0005 40 | 0/8 2 h-lim-p 0.0035 0.0282 10.0085 1484.613893 2 0.0017 56 | 0/8 3 h-lim-p 0.0035 0.0899 4.7243 1484.602241 6 0.0012 81 | 0/8 4 h-lim-p 0.0030 0.1845 1.9628 1484.600338 3 0.0012 99 | 0/8 5 h-lim-p 0.0065 1.3511 0.3592 1484.600230 3 0.0017 118 | 0/8 6 h-lim-p 0.0100 3.2777 0.0615 1484.600228 1 0.0012 142 | 0/8 7 h-lim-p 0.0200 20.0000 0.0038 1484.600219 0 0.0400 163 | 0/8 8 h-lim-p 0.0106 20.0000 0.0144 1484.599993 0 0.0422 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1484.599987 1 1.0938 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1484.599987 0 1.0938 227 | 0/8 11 h-lim-p 2.4305 20.0000 0.0000 1484.599987 0 1.0633 247 | 0/8 12 h-lim-p 0.9111 20.0000 0.0000 1484.599987 0 0.7972 267 | 0/8 13 h-lim-p 0.0001 6.0100 0.0269 1484.599987 0 0.0000 294 | 0/8 14 h-lim-p 0.0006 20.0000 0.0000 1484.599987 0 0.0006 314 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 1484.599987 0 0.0001 335 | 0/8 16 h-lim-p 0.0004 20.0000 0.0000 1484.599987 0 0.0000 360 Out... lnL = -1484.599987 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1484.599987 Node 7: lnL = -1484.599987 Node 8: lnL = -1484.599987 Node 9: lnL = -1484.599987 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 444 Sequential format.. Reading seq # 1: YOL112W_Sbay Reading seq # 2: YOL112W_Scer Reading seq # 3: YOL112W_Skud Reading seq # 4: YOL112W_Smik Reading seq # 5: YOL112W_Spar Sequences read.. Counting patterns.. # site patterns = 160 Counting frequencies.. 120 bytes for distance 25600 bytes for lkl0 20480 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.190518 0.061734 0.058644 0.073505 0.037810 0.167910 0.224520 0.112657 lnL0 = -1871.424400 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1871.424400 x= 0.19052 0.06173 0.05864 0.07351 0.03781 0.16791 0.22452 0.11266 1 h-lim-p 0.0001 0.0007 102.8934 1870.119870 0 0.0003 23 | 0/8 2 h-lim-p 0.0008 0.0249 33.4644 1870.050996 6 0.0001 51 | 0/8 3 h-lim-p 0.0005 0.0223 9.0789 1870.032138 4 0.0005 72 | 0/8 4 h-lim-p 0.0021 0.0778 2.1274 1870.031251 3 0.0004 91 | 0/8 5 h-lim-p 0.0012 0.1614 0.7467 1870.031146 3 0.0004 111 | 0/8 6 h-lim-p 0.0077 3.7623 0.0411 1870.031139 2 0.0030 135 | 0/8 7 h-lim-p 0.0044 13.3432 0.0274 1870.031041 0 0.0177 157 | 0/8 8 h-lim-p 0.0088 2.1477 0.0551 1870.029169 0 0.0177 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1870.029129 2 0.9961 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1870.029129 0 1.0938 222 | 0/8 11 h-lim-p 1.1471 20.0000 0.0000 1870.029129 0 9.1768 245 | 0/8 12 h-lim-p 1.5996 20.0000 0.0000 1870.029129 0 0.0008 275 | 0/8 13 h-lim-p 0.0008 20.0000 0.0000 1870.029129 0 0.0001 297 | 0/8 14 h-lim-p 0.0004 20.0000 0.0000 1870.029129 0 0.0000 336 Out... lnL = -1870.029129 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1870.029129 Node 7: lnL = -1870.029129 Node 8: lnL = -1870.029129 Node 9: lnL = -1870.029129 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 411 Sequential format.. Reading seq # 1: YOL113W_Sbay Reading seq # 2: YOL113W_Scer Reading seq # 3: YOL113W_Skud Reading seq # 4: YOL113W_Smik Reading seq # 5: YOL113W_Spar Sequences read.. Counting patterns.. # site patterns = 118 Counting frequencies.. 120 bytes for distance 18880 bytes for lkl0 15104 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.103407 0.006786 0.071271 0.107979 0.043371 0.143828 0.106543 0.050375 lnL0 = -1556.155901 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1556.155901 x= 0.10341 0.00679 0.07127 0.10798 0.04337 0.14383 0.10654 0.05037 1 h-lim-p 0.0002 0.0019 347.0551 1553.255675 8 0.0001 42 | 0/8 2 h-lim-p 0.0003 0.0025 29.1747 1553.167067 7 0.0002 71 | 0/8 3 h-lim-p 0.0004 0.0084 13.8334 1553.150829 2 0.0002 87 | 0/8 4 h-lim-p 0.0015 0.0726 1.8174 1553.150263 2 0.0004 104 | 0/8 5 h-lim-p 0.0042 1.6835 0.1552 1553.150260 1 0.0003 121 | 0/8 6 h-lim-p 0.0016 12.4432 0.0253 1553.150259 0 0.0007 141 | 0/8 7 h-lim-p 0.0134 20.0000 0.0013 1553.150257 0 0.0269 162 | 0/8 8 h-lim-p 0.0033 20.0000 0.0107 1553.150135 0 0.0263 185 | 0/8 9 h-lim-p 1.3286 20.0000 0.0002 1553.150123 2 1.0250 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1553.150123 0 1.0938 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1553.150123 0 1.2500 249 | 0/8 12 h-lim-p 0.9241 20.0000 0.0000 1553.150123 0 0.0001 282 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 1553.150123 0 0.0000 316 | 0/8 14 h-lim-p 0.0000 20.0000 0.0012 1553.150123 0 0.0000 342 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 1553.150123 0 0.0013 369 | 0/8 16 h-lim-p 0.0062 20.0000 0.0001 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0023 1553.150123 0 0.0000 443 | 0/8 18 h-lim-p 0.0000 20.0000 0.0006 1553.150123 0 0.0000 474 | 0/8 19 h-lim-p 0.0000 20.0000 0.0004 1553.150123 0 0.0026 502 | 0/8 20 h-lim-p 0.0036 20.0000 0.0003 1553.150123 0 0.0000 532 | 0/8 21 h-lim-p 0.0000 20.0000 0.0006 1553.150123 0 0.0026 560 | 0/8 22 h-lim-p 0.0038 20.0000 0.0004 1553.150123 0 0.0001 584 | 0/8 23 h-lim-p 0.0011 20.0000 0.0000 1553.150123 0 0.0017 604 | 0/8 24 h-lim-p 0.0046 20.0000 0.0000 1553.150123 0 0.0000 630 | 0/8 25 h-lim-p 0.0000 20.0000 0.0002 .. | 0/8 26 h-lim-p 0.0000 20.0000 0.0040 1553.150123 0 0.0000 691 | 0/8 27 h-lim-p 0.0000 20.0000 0.0009 1553.150123 0 0.0006 717 | 0/8 28 h-lim-p 0.0016 20.0000 0.0004 1553.150123 0 0.0000 745 | 0/8 29 h-lim-p 0.0000 20.0000 0.0001 1553.150123 0 0.0000 767 | 0/8 30 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 31 h-lim-p 0.0000 20.0000 0.0045 | 0/8 32 h-lim-p 0.0000 20.0000 0.0045 Out... lnL = -1553.150123 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1553.150123 Node 7: lnL = -1553.150123 Node 8: lnL = -1553.150123 Node 9: lnL = -1553.150123 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 456 Sequential format.. Reading seq # 1: YOL114C_Sbay Reading seq # 2: YOL114C_Scer Reading seq # 3: YOL114C_Skud Reading seq # 4: YOL114C_Smik Reading seq # 5: YOL114C_Spar Sequences read.. Counting patterns.. # site patterns = 127 Counting frequencies.. 120 bytes for distance 20320 bytes for lkl0 16256 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.107922 0.011503 0.063646 0.099543 0.051806 0.146369 0.110072 0.054105 lnL0 = -1686.026323 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1686.026323 x= 0.10792 0.01150 0.06365 0.09954 0.05181 0.14637 0.11007 0.05410 1 h-lim-p 0.0003 0.0026 290.7462 1683.419671 6 0.0001 34 | 0/8 2 h-lim-p 0.0005 0.0040 21.7762 1683.367072 4 0.0002 53 | 0/8 3 h-lim-p 0.0007 0.0186 7.2469 1683.361603 5 0.0002 77 | 0/8 4 h-lim-p 0.0010 0.1326 1.6133 1683.361164 4 0.0004 100 | 0/8 5 h-lim-p 0.0017 0.4743 0.3309 1683.361145 1 0.0004 115 | 0/8 6 h-lim-p 0.0020 3.8355 0.0606 1683.361145 0 0.0004 136 | 0/8 7 h-lim-p 0.0104 20.0000 0.0026 1683.361145 0 0.0011 158 | 0/8 8 h-lim-p 0.0239 20.0000 0.0001 1683.361132 0 0.5739 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1683.361132 0 1.0938 202 | 0/8 10 h-lim-p 1.8522 20.0000 0.0000 1683.361132 0 0.8103 222 | 0/8 11 h-lim-p 0.5795 20.0000 0.0000 1683.361132 0 0.0000 270 | 0/8 12 h-lim-p 0.0000 20.0000 0.0008 | 0/8 13 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -1683.361132 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1683.361132 Node 7: lnL = -1683.361132 Node 8: lnL = -1683.361132 Node 9: lnL = -1683.361132 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 556 Sequential format.. Reading seq # 1: YOL115W_Sbay Reading seq # 2: YOL115W_Scer Reading seq # 3: YOL115W_Skud Reading seq # 4: YOL115W_Smik Reading seq # 5: YOL115W_Spar Sequences read.. Counting patterns.. # site patterns = 206 Counting frequencies.. 120 bytes for distance 32960 bytes for lkl0 26368 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.163085 0.048723 0.047489 0.118897 0.070010 0.149678 0.145286 0.093335 lnL0 = -2234.322420 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2234.322420 x= 0.16308 0.04872 0.04749 0.11890 0.07001 0.14968 0.14529 0.09333 1 h-lim-p 0.0004 0.0030 104.2406 2233.364779 8 0.0002 40 | 0/8 2 h-lim-p 0.0006 0.0046 19.6630 2233.316941 5 0.0003 61 | 0/8 3 h-lim-p 0.0006 0.0339 7.6754 2233.310093 3 0.0003 79 | 0/8 4 h-lim-p 0.0015 0.1629 1.3920 2233.309706 4 0.0004 101 | 0/8 5 h-lim-p 0.0046 1.5314 0.1268 2233.309702 0 0.0005 115 | 0/8 6 h-lim-p 0.0039 5.9723 0.0167 2233.309702 0 0.0004 137 | 0/8 7 h-lim-p 0.0217 20.0000 0.0003 2233.309700 0 0.1305 159 | 0/8 8 h-lim-p 0.0017 4.1258 0.0242 2233.309686 0 0.0035 180 | 0/8 9 h-lim-p 1.8637 20.0000 0.0000 2233.309686 0 1.6308 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2233.309685 0 1.0938 220 | 0/8 11 h-lim-p 2.1051 20.0000 0.0000 2233.309685 0 0.9210 240 | 0/8 12 h-lim-p 0.9396 20.0000 0.0000 2233.309685 0 0.0110 266 | 0/8 13 h-lim-p 0.0009 20.0000 0.0001 2233.309685 0 0.0005 286 | 0/8 14 h-lim-p 0.0008 20.0000 0.0001 2233.309685 0 0.0000 319 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 2233.309685 0 0.0001 339 Out... lnL = -2233.309685 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2233.309685 Node 7: lnL = -2233.309685 Node 8: lnL = -2233.309685 Node 9: lnL = -2233.309685 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 361 Sequential format.. Reading seq # 1: YOL116W_Sbay Reading seq # 2: YOL116W_Scer Reading seq # 3: YOL116W_Skud Reading seq # 4: YOL116W_Smik Reading seq # 5: YOL116W_Spar Sequences read.. Counting patterns.. # site patterns = 107 Counting frequencies.. 120 bytes for distance 17120 bytes for lkl0 13696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.110433 0.019779 0.042620 0.098635 0.047151 0.126739 0.124529 0.058431 lnL0 = -1295.808738 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1295.808738 x= 0.11043 0.01978 0.04262 0.09863 0.04715 0.12674 0.12453 0.05843 1 h-lim-p 0.0001 0.0010 159.6346 1294.145025 1 0.0002 24 | 0/8 2 h-lim-p 0.0002 0.0015 36.6807 1293.983441 0 0.0003 36 | 0/8 3 h-lim-p 0.0006 0.0292 17.5750 1293.949088 2 0.0003 52 | 0/8 4 h-lim-p 0.0020 0.0319 2.3953 1293.948190 4 0.0003 75 | 0/8 5 h-lim-p 0.0010 0.2409 0.7873 1293.948070 2 0.0004 91 | 0/8 6 h-lim-p 0.0172 8.7409 0.0194 1293.948033 3 0.0101 120 | 0/8 7 h-lim-p 0.0037 1.9923 0.0531 1293.946902 0 0.0147 142 | 0/8 8 h-lim-p 0.0008 0.0852 0.9338 1293.943791 0 0.0017 163 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1293.943528 2 1.0938 187 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1293.943527 0 1.0938 207 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1293.943527 0 0.5469 228 | 0/8 12 h-lim-p 0.3553 20.0000 0.0000 1293.943527 0 0.0097 252 | 0/8 13 h-lim-p 0.0055 20.0000 0.0000 1293.943527 0 0.0003 275 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 1293.943527 0 0.0000 300 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 1293.943527 0 0.0000 336 Out... lnL = -1293.943527 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1293.943527 Node 7: lnL = -1293.943527 Node 8: lnL = -1293.943527 Node 9: lnL = -1293.943527 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 668 Sequential format.. Reading seq # 1: YOL117W_Sbay Reading seq # 2: YOL117W_Scer Reading seq # 3: YOL117W_Skud Reading seq # 4: YOL117W_Smik Reading seq # 5: YOL117W_Spar Sequences read.. Counting patterns.. # site patterns = 248 Counting frequencies.. 120 bytes for distance 39680 bytes for lkl0 31744 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.248912 0.065133 0.078702 0.123523 0.081630 0.210900 0.272744 0.146419 lnL0 = -3160.803788 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3160.803788 x= 0.24891 0.06513 0.07870 0.12352 0.08163 0.21090 0.27274 0.14642 1 h-lim-p 0.0199 2.1462 56.3578 3160.383076 5 0.0003 36 | 0/8 2 h-lim-p 0.0009 0.0091 16.6177 3160.338546 6 0.0003 61 | 0/8 3 h-lim-p 0.0005 0.0244 10.5893 3160.320295 5 0.0004 85 | 0/8 4 h-lim-p 0.0009 0.0627 5.0523 3160.315565 4 0.0005 106 | 0/8 5 h-lim-p 0.0041 0.9396 0.5988 3160.315457 3 0.0006 128 | 0/8 6 h-lim-p 0.0015 0.8684 0.2381 3160.315448 1 0.0004 151 | 0/8 7 h-lim-p 0.0107 20.0000 0.0082 3160.315447 0 0.0047 171 | 0/8 8 h-lim-p 0.0342 20.0000 0.0011 3160.315321 0 0.2738 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3160.315320 0 1.0938 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3160.315320 0 1.0938 234 | 0/8 11 h-lim-p 1.2479 20.0000 0.0000 3160.315320 0 2.4959 255 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3160.315320 0 0.0781 279 | 0/8 13 h-lim-p 0.0072 20.0000 0.0000 3160.315320 0 0.0031 299 | 0/8 14 h-lim-p 0.0017 20.0000 0.0000 3160.315320 0 0.0000 333 | 0/8 15 h-lim-p 0.0000 20.0000 0.0009 3160.315320 0 0.0000 366 | 0/8 16 h-lim-p 0.0000 20.0000 0.0009 | 0/8 17 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -3160.315320 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3160.315320 Node 7: lnL = -3160.315320 Node 8: lnL = -3160.315320 Node 9: lnL = -3160.315320 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 870 Sequential format.. Reading seq # 1: YOL124C_Sbay Reading seq # 2: YOL124C_Scer Reading seq # 3: YOL124C_Skud Reading seq # 4: YOL124C_Smik Reading seq # 5: YOL124C_Spar Sequences read.. Counting patterns.. # site patterns = 304 Counting frequencies.. 120 bytes for distance 48640 bytes for lkl0 38912 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.171632 0.052262 0.067248 0.123048 0.150095 0.286589 0.199529 0.070625 lnL0 = -3792.300973 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3792.300973 x= 0.17163 0.05226 0.06725 0.12305 0.15009 0.28659 0.19953 0.07063 1 h-lim-p 0.0009 0.0136 298.1878 3784.591695 4 0.0002 31 | 0/8 2 h-lim-p 0.0004 0.0029 45.3061 3784.132977 0 0.0005 43 | 0/8 3 h-lim-p 0.0010 0.0084 20.4229 3784.066964 6 0.0004 69 | 0/8 4 h-lim-p 0.0008 0.0406 9.5891 3784.048798 5 0.0005 95 | 0/8 5 h-lim-p 0.0027 0.1615 1.7635 3784.047987 3 0.0005 114 | 0/8 6 h-lim-p 0.0020 0.2488 0.4659 3784.047923 2 0.0005 131 | 0/8 7 h-lim-p 0.0026 1.8370 0.0964 3784.047826 1 0.0032 153 | 0/8 8 h-lim-p 0.0088 20.0000 0.0354 3784.026796 0 0.1406 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0014 3784.024215 2 1.1719 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 3784.024108 3 1.3437 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3784.024107 0 1.0938 248 | 0/8 12 h-lim-p 2.0548 20.0000 0.0000 3784.024107 0 1.0274 268 | 0/8 13 h-lim-p 0.9338 20.0000 0.0000 3784.024107 0 0.7003 288 | 0/8 14 h-lim-p 0.0000 0.1889 0.5457 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -3784.024107 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3784.024107 Node 7: lnL = -3784.024107 Node 8: lnL = -3784.024107 Node 9: lnL = -3784.024107 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 909 Sequential format.. Reading seq # 1: YOL128C_Sbay Reading seq # 2: YOL128C_Scer Reading seq # 3: YOL128C_Skud Reading seq # 4: YOL128C_Smik Reading seq # 5: YOL128C_Spar Sequences read.. Counting patterns.. # site patterns = 250 Counting frequencies.. 120 bytes for distance 40000 bytes for lkl0 32000 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.161232 0.030694 0.071228 0.093243 0.062780 0.170367 0.177583 0.084060 lnL0 = -3660.377584 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3660.377584 x= 0.16123 0.03069 0.07123 0.09324 0.06278 0.17037 0.17758 0.08406 1 h-lim-p 0.0051 1.0714 119.5761 3659.597669 7 0.0001 43 | 0/8 2 h-lim-p 0.0008 0.0070 16.2604 3659.572239 2 0.0002 60 | 0/8 3 h-lim-p 0.0005 0.0278 7.0293 3659.568897 5 0.0002 86 | 0/8 4 h-lim-p 0.0006 0.0691 1.9650 3659.568562 4 0.0002 108 | 0/8 5 h-lim-p 0.0011 0.5513 0.3513 3659.568545 2 0.0003 125 | 0/8 6 h-lim-p 0.0034 8.9392 0.0291 3659.568545 0 0.0004 147 | 0/8 7 h-lim-p 0.0011 16.5254 0.0098 3659.568545 0 0.0005 167 | 0/8 8 h-lim-p 0.0575 20.0000 0.0001 3659.568531 0 0.9196 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3659.568531 0 1.0938 211 | 0/8 10 h-lim-p 2.1427 20.0000 0.0000 3659.568531 0 1.8749 231 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3659.568531 0 0.3125 253 | 0/8 12 h-lim-p 0.0787 20.0000 0.0000 3659.568531 0 0.0148 275 | 0/8 13 h-lim-p 0.0059 20.0000 0.0001 3659.568531 0 0.0000 309 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 3659.568531 0 0.0000 340 Out... lnL = -3659.568531 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3659.568531 Node 7: lnL = -3659.568531 Node 8: lnL = -3659.568531 Node 9: lnL = -3659.568531 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 662 Sequential format.. Reading seq # 1: YOL129W_Sbay Reading seq # 2: YOL129W_Scer Reading seq # 3: YOL129W_Skud Reading seq # 4: YOL129W_Smik Reading seq # 5: YOL129W_Spar Sequences read.. Counting patterns.. # site patterns = 333 Counting frequencies.. 120 bytes for distance 53280 bytes for lkl0 42624 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.214297 0.351345 0.053112 0.208600 0.181408 0.308112 0.314091 0.052952 lnL0 = -3428.328404 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3428.328404 x= 0.21430 0.35135 0.05311 0.20860 0.18141 0.30811 0.31409 0.05295 1 h-lim-p 0.0169 1.7985 63.6947 3427.419318 3 0.0005 32 | 0/8 2 h-lim-p 0.0017 0.0222 17.4764 3427.260417 7 0.0011 61 | 0/8 3 h-lim-p 0.0020 0.0335 9.5870 3427.230860 5 0.0008 84 | 0/8 4 h-lim-p 0.0031 0.1522 2.5352 3427.227377 4 0.0012 104 | 0/8 5 h-lim-p 0.0034 0.5246 0.8799 3427.226947 4 0.0013 126 | 0/8 6 h-lim-p 0.0037 0.6056 0.3037 3427.226918 2 0.0007 151 | 0/8 7 h-lim-p 0.0039 3.9293 0.0556 3427.226913 1 0.0019 174 | 0/8 8 h-lim-p 0.1542 20.0000 0.0007 3427.226581 0 1.2335 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3427.226565 1 0.9961 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3427.226565 0 1.0938 239 | 0/8 11 h-lim-p 1.0743 20.0000 0.0000 3427.226565 0 0.1343 261 | 0/8 12 h-lim-p 0.0013 20.0000 0.0011 3427.226565 0 0.0000 294 | 0/8 13 h-lim-p 0.0010 20.0000 0.0000 3427.226565 0 0.0000 331 Out... lnL = -3427.226565 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3427.226565 Node 7: lnL = -3427.226565 Node 8: lnL = -3427.226565 Node 9: lnL = -3427.226565 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 822 Sequential format.. Reading seq # 1: YOL130W_Sbay Reading seq # 2: YOL130W_Scer Reading seq # 3: YOL130W_Skud Reading seq # 4: YOL130W_Smik Reading seq # 5: YOL130W_Spar Sequences read.. Counting patterns.. # site patterns = 280 Counting frequencies.. 120 bytes for distance 44800 bytes for lkl0 35840 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.219674 0.047744 0.070882 0.087312 0.085749 0.164638 0.216951 0.127324 lnL0 = -3663.883432 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3663.883432 x= 0.21967 0.04774 0.07088 0.08731 0.08575 0.16464 0.21695 0.12732 1 h-lim-p 0.0023 0.8136 178.3158 3661.527797 9 0.0002 46 | 0/8 2 h-lim-p 0.0007 0.0055 28.1674 3661.438261 6 0.0002 71 | 0/8 3 h-lim-p 0.0004 0.0153 14.8311 3661.415696 6 0.0003 99 | 0/8 4 h-lim-p 0.0009 0.0631 4.0320 3661.413071 3 0.0004 117 | 0/8 5 h-lim-p 0.0009 0.2013 1.5516 3661.412695 2 0.0004 133 | 0/8 6 h-lim-p 0.0016 0.6067 0.3340 3661.412681 2 0.0003 151 | 0/8 7 h-lim-p 0.0016 5.8639 0.0536 3661.412680 0 0.0007 171 | 0/8 8 h-lim-p 0.0820 20.0000 0.0005 3661.412184 0 0.9841 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3661.412182 0 1.0938 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3661.412182 0 1.0938 234 | 0/8 11 h-lim-p 2.3170 20.0000 0.0000 3661.412182 0 2.0274 254 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3661.412182 0 0.6250 275 | 0/8 13 h-lim-p 0.1551 20.0000 0.0000 3661.412182 0 0.0194 297 | 0/8 14 h-lim-p 0.0064 20.0000 0.0000 3661.412182 0 0.0000 327 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 3661.412182 0 0.0000 360 | 0/8 16 h-lim-p 0.0000 20.0000 0.0007 | 0/8 17 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -3661.412182 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3661.412182 Node 7: lnL = -3661.412182 Node 8: lnL = -3661.412182 Node 9: lnL = -3661.412182 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 360 Sequential format.. Reading seq # 1: YOL131W_Sbay Reading seq # 2: YOL131W_Scer Reading seq # 3: YOL131W_Skud Reading seq # 4: YOL131W_Smik Reading seq # 5: YOL131W_Spar Sequences read.. Counting patterns.. # site patterns = 210 Counting frequencies.. 120 bytes for distance 33600 bytes for lkl0 26880 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.287924 0.112823 0.023369 0.193267 0.289086 0.275765 0.313082 0.142037 lnL0 = -1858.244295 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1858.244295 x= 0.28792 0.11282 0.02337 0.19327 0.28909 0.27576 0.31308 0.14204 1 h-lim-p 0.0035 0.0795 103.3446 1856.125831 9 0.0005 41 | 0/8 2 h-lim-p 0.0020 0.0159 22.0492 1855.708079 5 0.0017 62 | 0/8 3 h-lim-p 0.0066 0.0802 5.7874 1855.683763 2 0.0015 79 | 0/8 4 h-lim-p 0.0047 0.2064 1.9060 1855.679908 5 0.0023 101 | 0/8 5 h-lim-p 0.0407 2.7356 0.1101 1855.679895 2 0.0016 121 | 0/8 6 h-lim-p 0.0083 17.2815 0.0216 1855.679861 0 0.0166 142 | 0/8 7 h-lim-p 0.0246 20.0000 0.0145 1855.677359 0 0.1479 164 | 0/8 8 h-lim-p 0.0532 7.2293 0.0404 1855.677358 1 0.0016 190 | 0/8 9 h-lim-p 0.5052 20.0000 0.0001 1855.677352 0 1.0105 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1855.677352 0 1.0938 231 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1855.677352 0 1.0938 251 | 0/8 12 h-lim-p 1.1725 20.0000 0.0000 1855.677352 0 0.2931 272 | 0/8 13 h-lim-p 0.0634 20.0000 0.0000 1855.677352 0 0.0317 292 | 0/8 14 h-lim-p 0.0120 20.0000 0.0000 1855.677352 0 0.0000 336 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1855.677352 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1855.677352 Node 7: lnL = -1855.677352 Node 8: lnL = -1855.677352 Node 9: lnL = -1855.677352 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 673 Sequential format.. Reading seq # 1: YOL132W_Sbay Reading seq # 2: YOL132W_Scer Reading seq # 3: YOL132W_Skud Reading seq # 4: YOL132W_Smik Reading seq # 5: YOL132W_Spar Sequences read.. Counting patterns.. # site patterns = 274 Counting frequencies.. 120 bytes for distance 43840 bytes for lkl0 35072 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.244815 0.098205 0.105518 0.130210 0.107853 0.251205 0.254398 0.123549 lnL0 = -3250.254323 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3250.254323 x= 0.24481 0.09820 0.10552 0.13021 0.10785 0.25120 0.25440 0.12355 1 h-lim-p 0.0145 2.2538 67.0155 3249.466406 6 0.0004 37 | 0/8 2 h-lim-p 0.0012 0.0093 17.8538 3249.400327 4 0.0004 57 | 0/8 3 h-lim-p 0.0007 0.0287 11.5390 3249.370495 3 0.0006 75 | 0/8 4 h-lim-p 0.0029 0.0896 2.4082 3249.369096 4 0.0005 98 | 0/8 5 h-lim-p 0.0028 1.1343 0.4476 3249.369032 0 0.0007 111 | 0/8 6 h-lim-p 0.0028 1.7251 0.1127 3249.369028 0 0.0007 132 | 0/8 7 h-lim-p 0.0293 20.0000 0.0027 3249.369022 0 0.0293 152 | 0/8 8 h-lim-p 0.0046 20.0000 0.0170 3249.368848 0 0.0276 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3249.368842 1 0.9961 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3249.368842 0 1.0938 216 | 0/8 11 h-lim-p 1.0070 20.0000 0.0000 3249.368842 0 0.4406 236 | 0/8 12 h-lim-p 0.0011 20.0000 0.0030 3249.368842 0 0.0000 264 | 0/8 13 h-lim-p 0.0015 20.0000 0.0000 3249.368842 0 0.0000 294 Out... lnL = -3249.368842 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3249.368842 Node 7: lnL = -3249.368842 Node 8: lnL = -3249.368842 Node 9: lnL = -3249.368842 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 317 Sequential format.. Reading seq # 1: YOL133W_Sbay Reading seq # 2: YOL133W_Scer Reading seq # 3: YOL133W_Skud Reading seq # 4: YOL133W_Smik Reading seq # 5: YOL133W_Spar Sequences read.. Counting patterns.. # site patterns = 146 Counting frequencies.. 120 bytes for distance 23360 bytes for lkl0 18688 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.204024 0.080655 0.150347 0.156689 0.156947 0.205087 0.259732 0.083221 lnL0 = -1524.301828 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1524.301828 x= 0.20402 0.08065 0.15035 0.15669 0.15695 0.20509 0.25973 0.08322 1 h-lim-p 0.0068 0.0546 26.3627 1524.012469 7 0.0009 42 | 0/8 2 h-lim-p 0.0036 0.0697 6.2645 1523.980306 2 0.0017 58 | 0/8 3 h-lim-p 0.0038 0.1219 2.8201 1523.976041 5 0.0013 82 | 0/8 4 h-lim-p 0.0045 0.3295 0.8071 1523.975745 2 0.0010 99 | 0/8 5 h-lim-p 0.0048 1.3435 0.1654 1523.975726 3 0.0014 128 | 0/8 6 h-lim-p 0.0095 15.6745 0.0243 1523.975725 0 0.0021 149 | 0/8 7 h-lim-p 0.0159 20.0000 0.0032 1523.975724 0 0.0238 169 | 0/8 8 h-lim-p 0.0112 20.0000 0.0067 1523.975661 0 0.0674 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1523.975660 0 1.0938 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1523.975660 0 1.0938 231 | 0/8 11 h-lim-p 1.4658 20.0000 0.0000 1523.975660 0 1.2826 251 | 0/8 12 h-lim-p 0.9177 20.0000 0.0000 1523.975660 0 0.0574 274 | 0/8 13 h-lim-p 0.0002 20.0000 0.0016 1523.975660 0 0.0000 302 | 0/8 14 h-lim-p 0.0005 20.0000 0.0000 1523.975660 0 0.0001 323 Out... lnL = -1523.975660 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1523.975660 Node 7: lnL = -1523.975660 Node 8: lnL = -1523.975660 Node 9: lnL = -1523.975660 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 111 Sequential format.. Reading seq # 1: YOL135C_Sbay Reading seq # 2: YOL135C_Scer Reading seq # 3: YOL135C_Skud Reading seq # 4: YOL135C_Smik Reading seq # 5: YOL135C_Spar Sequences read.. Counting patterns.. # site patterns = 62 Counting frequencies.. 120 bytes for distance 9920 bytes for lkl0 7936 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.185347 0.015428 0.202292 0.217104 0.069987 0.013238 0.244731 0.087450 lnL0 = -491.395162 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 491.395162 x= 0.18535 0.01543 0.20229 0.21710 0.06999 0.01324 0.24473 0.08745 1 h-lim-p 0.0008 0.6604 110.6214 488.422417 4 0.0008 30 | 0/8 2 h-lim-p 0.0032 0.0257 11.6238 488.124796 0 0.0048 42 | 0/8 3 h-lim-p 0.0045 0.0361 10.4632 488.060507 3 0.0019 60 | 0/8 4 h-lim-p 0.0046 0.0826 4.2709 488.033044 7 0.0040 85 | 0/8 5 h-lim-p 0.0152 0.1814 1.1116 488.030227 5 0.0050 110 | 0/8 6 h-lim-p 0.0272 1.6231 0.2029 488.030129 4 0.0038 133 | 0/8 7 h-lim-p 0.0302 12.7349 0.0259 488.029445 0 0.0905 154 | 0/8 8 h-lim-p 0.0109 2.1875 0.2150 488.024885 0 0.0327 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0014 488.024424 4 1.5996 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0005 488.024214 2 2.3438 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 488.024214 0 1.0938 249 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 488.024214 0 1.0938 269 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 488.024214 0 2.1875 289 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 488.024214 0 0.2734 311 | 0/8 15 h-lim-p 0.0489 20.0000 0.0000 488.024214 0 0.0000 357 Out... lnL = -488.024214 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -488.024214 Node 7: lnL = -488.024214 Node 8: lnL = -488.024214 Node 9: lnL = -488.024214 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 672 Sequential format.. Reading seq # 1: YOL136C_Sbay Reading seq # 2: YOL136C_Scer Reading seq # 3: YOL136C_Skud Reading seq # 4: YOL136C_Smik Reading seq # 5: YOL136C_Spar Sequences read.. Counting patterns.. # site patterns = 170 Counting frequencies.. 120 bytes for distance 27200 bytes for lkl0 21760 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.128020 0.028734 0.043019 0.070756 0.042766 0.133691 0.107721 0.071393 lnL0 = -2468.132284 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2468.132284 x= 0.12802 0.02873 0.04302 0.07076 0.04277 0.13369 0.10772 0.07139 1 h-lim-p 0.0003 0.0023 121.4319 2467.453240 8 0.0001 43 | 0/8 2 h-lim-p 0.0006 0.0053 21.2498 2467.414190 7 0.0002 74 | 0/8 3 h-lim-p 0.0004 0.0267 8.6997 2467.409761 6 0.0001 103 | 0/8 4 h-lim-p 0.0004 0.0279 3.0562 2467.409290 4 0.0001 126 | 0/8 5 h-lim-p 0.0006 0.1499 0.5966 2467.409260 3 0.0002 147 | 0/8 6 h-lim-p 0.0005 0.9372 0.2080 2467.409257 0 0.0002 167 | 0/8 7 h-lim-p 0.0024 9.1023 0.0190 2467.409257 0 0.0003 189 | 0/8 8 h-lim-p 0.1519 20.0000 0.0000 2467.409254 0 1.2151 212 | 0/8 9 h-lim-p 2.1418 20.0000 0.0000 2467.409254 0 0.9370 232 | 0/8 10 h-lim-p 0.9774 20.0000 0.0000 2467.409254 0 0.0076 258 | 0/8 11 h-lim-p 0.0020 20.0000 0.0001 2467.409254 0 0.0000 294 | 0/8 12 h-lim-p 0.0000 20.0000 0.0011 | 0/8 13 h-lim-p 0.0000 20.0000 0.0011 Out... lnL = -2467.409254 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2467.409254 Node 7: lnL = -2467.409254 Node 8: lnL = -2467.409254 Node 9: lnL = -2467.409254 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 325 Sequential format.. Reading seq # 1: YOL139C_Sbay Reading seq # 2: YOL139C_Scer Reading seq # 3: YOL139C_Skud Reading seq # 4: YOL139C_Smik Reading seq # 5: YOL139C_Spar Sequences read.. Counting patterns.. # site patterns = 83 Counting frequencies.. 120 bytes for distance 13280 bytes for lkl0 10624 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.084501 0.000060 0.024294 0.038220 0.028806 0.116804 0.127814 0.044273 lnL0 = -1051.777761 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1051.777761 x= 0.08450 0.00006 0.02429 0.03822 0.02881 0.11680 0.12781 0.04427 1 h-lim-p 0.0002 0.0014 112.4636 1051.256265 8 0.0001 37 | 0/8 2 h-lim-p 0.0002 0.0012 17.9638 1051.234168 3 0.0001 55 | 0/8 3 h-lim-p 0.0010 0.0397 2.6069 1051.233169 5 0.0003 81 | 0/8 4 h-lim-p 0.0004 0.0524 2.1449 1051.232904 2 0.0002 97 | 0/8 5 h-lim-p 0.0011 0.1840 0.3350 1051.232889 2 0.0003 114 | 0/8 6 h-lim-p 0.0035 2.3520 0.0259 1051.232889 0 0.0004 136 | 0/8 7 h-lim-p 0.0004 4.2478 0.0227 1051.232889 0 0.0002 156 | 0/8 8 h-lim-p 0.1686 20.0000 0.0000 1051.232888 0 1.0115 178 | 0/8 9 h-lim-p 1.7518 20.0000 0.0000 1051.232888 0 3.5037 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1051.232888 0 0.2734 221 | 0/8 11 h-lim-p 2.3804 20.0000 0.0000 1051.232888 0 0.0003 253 Out... lnL = -1051.232888 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1051.232888 Node 7: lnL = -1051.232888 Node 8: lnL = -1051.232888 Node 9: lnL = -1051.232888 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 485 Sequential format.. Reading seq # 1: YOL142W_Sbay Reading seq # 2: YOL142W_Scer Reading seq # 3: YOL142W_Skud Reading seq # 4: YOL142W_Smik Reading seq # 5: YOL142W_Spar Sequences read.. Counting patterns.. # site patterns = 213 Counting frequencies.. 120 bytes for distance 34080 bytes for lkl0 27264 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.201111 0.144506 0.139085 0.166641 0.081013 0.293648 0.214239 0.076357 lnL0 = -2289.478390 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2289.478390 x= 0.20111 0.14451 0.13908 0.16664 0.08101 0.29365 0.21424 0.07636 1 h-lim-p 0.0053 0.0425 22.3360 2289.322236 2 0.0006 28 | 0/8 2 h-lim-p 0.0023 0.0293 6.0512 2289.311561 4 0.0006 49 | 0/8 3 h-lim-p 0.0010 0.0658 3.9673 2289.307966 3 0.0006 69 | 0/8 4 h-lim-p 0.0029 0.3472 0.8689 2289.307698 3 0.0008 88 | 0/8 5 h-lim-p 0.0055 2.4377 0.1212 2289.307689 0 0.0012 109 | 0/8 6 h-lim-p 0.0096 20.0000 0.0152 2289.307689 0 0.0042 129 | 0/8 7 h-lim-p 0.0110 20.0000 0.0058 2289.307685 0 0.0165 149 | 0/8 8 h-lim-p 0.0065 20.0000 0.0148 2289.307556 0 0.0260 171 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2289.307555 0 1.0938 191 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2289.307555 0 1.0938 211 | 0/8 11 h-lim-p 1.1841 20.0000 0.0000 2289.307555 0 0.5180 231 | 0/8 12 h-lim-p 0.1782 20.0000 0.0000 2289.307555 0 0.0003 259 | 0/8 13 h-lim-p 0.0003 20.0000 0.0000 2289.307555 0 0.0003 279 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 2289.307555 0 0.0001 299 | 0/8 15 h-lim-p 0.0001 20.0000 0.0001 2289.307555 0 0.0000 323 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 2289.307555 0 0.0000 351 Out... lnL = -2289.307555 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2289.307555 Node 7: lnL = -2289.307555 Node 8: lnL = -2289.307555 Node 9: lnL = -2289.307555 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 485 Sequential format.. Reading seq # 1: YOL143C_Sbay Reading seq # 2: YOL143C_Scer Reading seq # 3: YOL143C_Skud Reading seq # 4: YOL143C_Smik Reading seq # 5: YOL143C_Spar Sequences read.. Counting patterns.. # site patterns = 211 Counting frequencies.. 120 bytes for distance 33760 bytes for lkl0 27008 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.202571 0.137961 0.145784 0.153636 0.090574 0.291318 0.215757 0.077904 lnL0 = -2286.598463 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2286.598463 x= 0.20257 0.13796 0.14578 0.15364 0.09057 0.29132 0.21576 0.07790 1 h-lim-p 0.0034 0.0275 22.4443 2286.441114 7 0.0006 40 | 0/8 2 h-lim-p 0.0025 0.0633 5.6633 2286.428815 5 0.0008 64 | 0/8 3 h-lim-p 0.0011 0.0460 4.2595 2286.425418 2 0.0005 80 | 0/8 4 h-lim-p 0.0026 0.4209 0.8850 2286.425136 4 0.0008 103 | 0/8 5 h-lim-p 0.0054 2.2520 0.1250 2286.425127 1 0.0012 126 | 0/8 6 h-lim-p 0.0075 12.7188 0.0198 2286.425127 0 0.0016 147 | 0/8 7 h-lim-p 0.0058 20.0000 0.0056 2286.425127 0 0.0025 167 | 0/8 8 h-lim-p 0.0573 20.0000 0.0002 2286.425114 0 0.4584 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2286.425114 0 1.0938 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2286.425114 0 1.0938 230 | 0/8 11 h-lim-p 1.0558 20.0000 0.0000 2286.425114 0 1.0558 250 | 0/8 12 h-lim-p 0.1426 20.0000 0.0001 2286.425114 0 0.0156 272 | 0/8 13 h-lim-p 0.0041 20.0000 0.0002 2286.425114 0 0.0001 297 | 0/8 14 h-lim-p 0.0001 20.0000 0.0001 2286.425114 0 0.0000 318 | 0/8 15 h-lim-p 0.0005 20.0000 0.0000 2286.425114 0 0.0000 345 Out... lnL = -2286.425114 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2286.425114 Node 7: lnL = -2286.425114 Node 8: lnL = -2286.425114 Node 9: lnL = -2286.425114 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 321 Sequential format.. Reading seq # 1: YOL144W_Sbay Reading seq # 2: YOL144W_Scer Reading seq # 3: YOL144W_Skud Reading seq # 4: YOL144W_Smik Reading seq # 5: YOL144W_Spar Sequences read.. Counting patterns.. # site patterns = 152 Counting frequencies.. 120 bytes for distance 24320 bytes for lkl0 19456 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.235573 0.045277 0.091382 0.153449 0.069267 0.200645 0.240616 0.122405 lnL0 = -1495.924403 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1495.924403 x= 0.23557 0.04528 0.09138 0.15345 0.06927 0.20065 0.24062 0.12241 1 h-lim-p 0.0004 0.0031 31.5044 1495.672983 0 0.0006 22 | 0/8 2 h-lim-p 0.0012 0.0506 15.0334 1495.619044 2 0.0006 38 | 0/8 3 h-lim-p 0.0019 0.0250 4.5004 1495.612746 5 0.0007 63 | 0/8 4 h-lim-p 0.0023 0.1919 1.3328 1495.612107 4 0.0008 85 | 0/8 5 h-lim-p 0.0118 3.3561 0.0893 1495.612086 2 0.0028 102 | 0/8 6 h-lim-p 0.0053 5.4083 0.0462 1495.611989 0 0.0107 123 | 0/8 7 h-lim-p 0.0035 1.7225 0.1406 1495.611414 0 0.0070 144 | 0/8 8 h-lim-p 0.0035 0.4223 0.2805 1495.608228 0 0.0070 165 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1495.608207 1 0.9961 187 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1495.608207 0 1.0938 207 | 0/8 11 h-lim-p 1.6179 20.0000 0.0000 1495.608207 0 3.2358 228 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1495.608207 0 0.5469 249 | 0/8 13 h-lim-p 0.8466 20.0000 0.0000 1495.608207 0 0.0017 277 Out... lnL = -1495.608207 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1495.608207 Node 7: lnL = -1495.608207 Node 8: lnL = -1495.608207 Node 9: lnL = -1495.608207 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 355 Sequential format.. Reading seq # 1: YOL145C_Sbay Reading seq # 2: YOL145C_Scer Reading seq # 3: YOL145C_Skud Reading seq # 4: YOL145C_Smik Reading seq # 5: YOL145C_Spar Sequences read.. Counting patterns.. # site patterns = 159 Counting frequencies.. 120 bytes for distance 25440 bytes for lkl0 20352 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.198211 0.065555 0.100785 0.148825 0.069433 0.199263 0.216567 0.090117 lnL0 = -1464.255224 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1464.255224 x= 0.19821 0.06556 0.10079 0.14882 0.06943 0.19926 0.21657 0.09012 1 h-lim-p 0.0006 0.0045 40.2030 1463.695726 0 0.0008 22 | 0/8 2 h-lim-p 0.0018 0.0211 18.7514 1463.630678 6 0.0004 47 | 0/8 3 h-lim-p 0.0011 0.0207 7.4074 1463.612865 6 0.0008 74 | 0/8 4 h-lim-p 0.0026 0.1577 2.2030 1463.610787 5 0.0010 98 | 0/8 5 h-lim-p 0.0048 0.6709 0.4378 1463.610574 2 0.0021 114 | 0/8 6 h-lim-p 0.0030 1.0489 0.3090 1463.610510 2 0.0014 138 | 0/8 7 h-lim-p 0.0629 20.0000 0.0068 1463.601319 0 0.5028 161 | 0/8 8 h-lim-p 0.0024 0.1667 1.3996 1463.599462 5 0.0015 196 | 0/8 9 h-lim-p 2.4735 20.0000 0.0008 1463.599082 3 0.9898 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1463.599081 0 1.0938 234 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1463.599081 0 2.1875 254 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1463.599081 0 0.5469 275 | 0/8 13 h-lim-p 0.2104 20.0000 0.0000 1463.599081 0 0.0921 295 | 0/8 14 h-lim-p 0.0457 20.0000 0.0000 1463.599081 0 0.0114 316 | 0/8 15 h-lim-p 0.0076 20.0000 0.0000 1463.599081 0 0.0076 336 | 0/8 16 h-lim-p 0.0052 20.0000 0.0000 1463.599081 0 0.0003 359 | 0/8 17 h-lim-p 0.0002 20.0000 0.0000 1463.599081 0 0.0000 395 | 0/8 18 h-lim-p 0.0000 20.0000 0.0008 | 0/8 19 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -1463.599081 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1463.599081 Node 7: lnL = -1463.599081 Node 8: lnL = -1463.599081 Node 9: lnL = -1463.599081 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 382 Sequential format.. Reading seq # 1: YOL148C_Sbay Reading seq # 2: YOL148C_Scer Reading seq # 3: YOL148C_Skud Reading seq # 4: YOL148C_Smik Reading seq # 5: YOL148C_Spar Sequences read.. Counting patterns.. # site patterns = 160 Counting frequencies.. 120 bytes for distance 25600 bytes for lkl0 20480 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.144589 0.081241 0.073443 0.134844 0.124168 0.182855 0.263843 0.040980 lnL0 = -1750.060808 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1750.060808 x= 0.14459 0.08124 0.07344 0.13484 0.12417 0.18285 0.26384 0.04098 1 h-lim-p 0.0076 0.1951 67.6624 1749.203631 3 0.0004 31 | 0/8 2 h-lim-p 0.0034 0.0291 7.9032 1749.174664 7 0.0009 59 | 0/8 3 h-lim-p 0.0022 0.0989 3.3095 1749.171009 5 0.0008 85 | 0/8 4 h-lim-p 0.0031 0.3209 0.8347 1749.170750 3 0.0008 104 | 0/8 5 h-lim-p 0.0030 0.7337 0.2264 1749.170737 2 0.0006 129 | 0/8 6 h-lim-p 0.0061 10.8058 0.0214 1749.170736 0 0.0013 150 | 0/8 7 h-lim-p 0.0083 20.0000 0.0034 1749.170736 0 0.0125 170 | 0/8 8 h-lim-p 0.0108 20.0000 0.0039 1749.170673 0 0.0867 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1749.170668 1 0.9961 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1749.170668 0 0.0037 244 | 0/8 11 h-lim-p 0.0004 20.0000 0.0001 1749.170668 0 0.0000 281 | 0/8 12 h-lim-p 0.0000 20.0000 0.0004 | 0/8 13 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1749.170668 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1749.170668 Node 7: lnL = -1749.170668 Node 8: lnL = -1749.170668 Node 9: lnL = -1749.170668 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 176 Sequential format.. Reading seq # 1: YOL149W_Sbay Reading seq # 2: YOL149W_Scer Reading seq # 3: YOL149W_Skud Reading seq # 4: YOL149W_Smik Reading seq # 5: YOL149W_Spar Sequences read.. Counting patterns.. # site patterns = 100 Counting frequencies.. 120 bytes for distance 16000 bytes for lkl0 12800 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.244380 0.090613 0.083790 0.139881 0.114437 0.121531 0.328054 0.121571 lnL0 = -795.197165 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 795.197165 x= 0.24438 0.09061 0.08379 0.13988 0.11444 0.12153 0.32805 0.12157 1 h-lim-p 0.0012 0.0096 19.9489 794.883367 0 0.0018 22 | 0/8 2 h-lim-p 0.0038 0.0307 8.7441 794.834290 4 0.0015 42 | 0/8 3 h-lim-p 0.0037 0.1059 3.5503 794.818115 5 0.0030 65 | 0/8 4 h-lim-p 0.0056 0.2319 1.9175 794.815863 6 0.0016 93 | 0/8 5 h-lim-p 0.0030 0.1182 1.0405 794.815268 3 0.0015 112 | 0/8 6 h-lim-p 0.0135 2.8777 0.1132 794.815243 1 0.0030 127 | 0/8 7 h-lim-p 0.0058 7.1646 0.0577 794.815210 1 0.0072 149 | 0/8 8 h-lim-p 0.0316 12.0850 0.0132 794.812695 0 0.2528 172 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 794.812686 2 0.9961 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 794.812686 0 2.1875 216 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 794.812686 0 1.0938 236 | 0/8 12 h-lim-p 0.7743 20.0000 0.0000 794.812686 0 3.0973 258 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 794.812686 0 0.0391 283 | 0/8 14 h-lim-p 0.0027 20.0000 0.0000 794.812686 0 0.0010 304 Out... lnL = -794.812686 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -794.812686 Node 7: lnL = -794.812686 Node 8: lnL = -794.812686 Node 9: lnL = -794.812686 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 875 Sequential format.. Reading seq # 1: YOL151W_Sbay Reading seq # 2: YOL151W_Scer Reading seq # 3: YOL151W_Skud Reading seq # 4: YOL151W_Smik Reading seq # 5: YOL151W_Spar Sequences read.. Counting patterns.. # site patterns = 441 Counting frequencies.. 120 bytes for distance 70560 bytes for lkl0 56448 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.461320 0.057852 0.227162 0.196912 0.098472 0.424947 0.500146 0.244238 lnL0 = -4702.337259 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4702.337259 x= 0.46132 0.05785 0.22716 0.19691 0.09847 0.42495 0.50015 0.24424 1 h-lim-p 0.0012 0.0093 49.1680 4701.436391 8 0.0008 42 | 0/8 2 h-lim-p 0.0049 0.0394 7.6230 4701.397274 6 0.0014 69 | 0/8 3 h-lim-p 0.0014 0.0995 7.4337 4701.371220 4 0.0015 91 | 0/8 4 h-lim-p 0.0007 0.0442 17.0557 4701.358157 5 0.0004 116 | 0/8 5 h-lim-p 0.0087 0.9957 0.7440 4701.357580 2 0.0022 133 | 0/8 6 h-lim-p 0.0127 2.9339 0.1272 4701.357568 0 0.0016 155 | 0/8 7 h-lim-p 0.0321 20.0000 0.0063 4701.357566 0 0.0160 175 | 0/8 8 h-lim-p 0.0380 20.0000 0.0026 4701.357453 0 0.1520 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4701.357451 0 1.0938 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4701.357451 0 1.0938 237 | 0/8 11 h-lim-p 2.3908 20.0000 0.0000 4701.357451 0 1.0460 257 | 0/8 12 h-lim-p 0.9415 20.0000 0.0000 4701.357451 0 0.9415 277 | 0/8 13 h-lim-p 0.0036 20.0000 0.0009 4701.357451 0 0.0000 306 | 0/8 14 h-lim-p 0.0038 20.0000 0.0000 4701.357451 0 0.0002 329 Out... lnL = -4701.357451 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4701.357451 Node 7: lnL = -4701.357451 Node 8: lnL = -4701.357451 Node 9: lnL = -4701.357451 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 949 Sequential format.. Reading seq # 1: YOL153C_Sbay Reading seq # 2: YOL153C_Scer Reading seq # 3: YOL153C_Skud Reading seq # 4: YOL153C_Smik Reading seq # 5: YOL153C_Spar Sequences read.. Counting patterns.. # site patterns = 420 Counting frequencies.. 120 bytes for distance 67200 bytes for lkl0 53760 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.459409 0.165775 0.269655 0.193133 0.065217 0.323229 0.434248 0.240878 lnL0 = -4989.847662 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4989.847662 x= 0.45941 0.16577 0.26965 0.19313 0.06522 0.32323 0.43425 0.24088 1 h-lim-p 0.0015 0.0118 64.4506 4989.064653 5 0.0004 33 | 0/8 2 h-lim-p 0.0004 0.0048 61.6940 4988.534622 5 0.0004 56 | 0/8 3 h-lim-p 0.0010 0.0138 25.5558 4988.285123 2 0.0010 72 | 0/8 4 h-lim-p 0.0115 0.1353 2.1837 4988.281185 5 0.0017 97 | 0/8 5 h-lim-p 0.0046 1.0543 0.7997 4988.280825 3 0.0012 116 | 0/8 6 h-lim-p 0.0035 1.3252 0.2812 4988.280789 2 0.0012 142 | 0/8 7 h-lim-p 0.0066 12.4118 0.0494 4988.280780 1 0.0052 164 | 0/8 8 h-lim-p 0.1705 20.0000 0.0015 4988.280262 0 0.6819 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4988.280261 0 1.0938 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4988.280261 0 1.0938 226 | 0/8 11 h-lim-p 1.7012 20.0000 0.0000 4988.280261 0 0.3190 248 | 0/8 12 h-lim-p 0.1605 20.0000 0.0000 4988.280261 0 0.0803 268 | 0/8 13 h-lim-p 0.0432 20.0000 0.0000 4988.280261 0 0.0040 291 | 0/8 14 h-lim-p 0.0037 20.0000 0.0000 4988.280261 0 0.0001 315 | 0/8 15 h-lim-p 0.0024 20.0000 0.0000 4988.280261 0 0.0048 336 Out... lnL = -4988.280261 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4988.280261 Node 7: lnL = -4988.280261 Node 8: lnL = -4988.280261 Node 9: lnL = -4988.280261 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 942 Sequential format.. Reading seq # 1: YOL154W_Sbay Reading seq # 2: YOL154W_Scer Reading seq # 3: YOL154W_Skud Reading seq # 4: YOL154W_Smik Reading seq # 5: YOL154W_Spar Sequences read.. Counting patterns.. # site patterns = 383 Counting frequencies.. 120 bytes for distance 61280 bytes for lkl0 49024 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.354364 0.060577 0.185617 0.105923 0.124913 0.240242 0.280848 0.199831 lnL0 = -4583.358860 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4583.358860 x= 0.35436 0.06058 0.18562 0.10592 0.12491 0.24024 0.28085 0.19983 1 h-lim-p 0.0005 0.0044 90.9462 4582.098678 7 0.0003 38 | 0/8 2 h-lim-p 0.0006 0.0044 29.2334 4582.009622 5 0.0002 61 | 0/8 3 h-lim-p 0.0020 0.0836 3.2693 4582.005713 5 0.0007 84 | 0/8 4 h-lim-p 0.0032 0.6323 0.7473 4582.005508 2 0.0008 101 | 0/8 5 h-lim-p 0.0022 1.5538 0.2530 4582.005482 1 0.0009 123 | 0/8 6 h-lim-p 0.0023 3.3469 0.0981 4582.005480 0 0.0005 144 | 0/8 7 h-lim-p 0.0035 20.0000 0.0140 4582.005480 0 0.0015 164 | 0/8 8 h-lim-p 0.0753 20.0000 0.0003 4582.005421 0 0.6021 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4582.005420 0 1.0938 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4582.005420 0 1.0938 227 | 0/8 11 h-lim-p 1.1988 20.0000 0.0000 4582.005420 0 1.7983 247 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4582.005420 0 0.0781 271 | 0/8 13 h-lim-p 0.0187 20.0000 0.0000 4582.005420 0 0.0047 292 | 0/8 14 h-lim-p 0.0014 20.0000 0.0000 4582.005420 0 0.0002 314 | 0/8 15 h-lim-p 0.0022 20.0000 0.0000 4582.005420 0 0.0006 335 Out... lnL = -4582.005420 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4582.005420 Node 7: lnL = -4582.005420 Node 8: lnL = -4582.005420 Node 9: lnL = -4582.005420 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 881 Sequential format.. Reading seq # 1: YOL157C_Sbay Reading seq # 2: YOL157C_Scer Reading seq # 3: YOL157C_Skud Reading seq # 4: YOL157C_Smik Reading seq # 5: YOL157C_Spar Sequences read.. Counting patterns.. # site patterns = 385 Counting frequencies.. 120 bytes for distance 61600 bytes for lkl0 49280 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.453392 0.232341 0.150926 0.109282 0.087303 0.268357 0.164019 0.275155 lnL0 = -4369.661343 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4369.661343 x= 0.45339 0.23234 0.15093 0.10928 0.08730 0.26836 0.16402 0.27516 1 h-lim-p 0.0003 0.0022 55.4198 4369.139011 1 0.0003 24 | 0/8 2 h-lim-p 0.0011 0.1245 17.3224 4369.106904 4 0.0002 46 | 0/8 3 h-lim-p 0.0003 0.0390 11.8861 4369.074320 0 0.0007 59 | 0/8 4 h-lim-p 0.0013 0.0361 6.3063 4369.063259 6 0.0008 88 | 0/8 5 h-lim-p 0.0013 0.0632 3.6933 4369.058552 5 0.0010 110 | 0/8 6 h-lim-p 0.0026 0.2655 1.4580 4369.057901 4 0.0008 134 | 0/8 7 h-lim-p 0.0384 20.0000 0.0300 4369.057899 1 0.0024 151 | 0/8 8 h-lim-p 0.0681 20.0000 0.0010 4369.057539 0 0.5450 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4369.057538 0 1.0938 194 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4369.057538 0 1.0938 214 | 0/8 11 h-lim-p 2.1270 20.0000 0.0000 4369.057538 0 1.8611 234 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4369.057538 0 0.0781 258 | 0/8 13 h-lim-p 0.0209 20.0000 0.0000 4369.057538 0 0.0052 279 | 0/8 14 h-lim-p 0.0026 20.0000 0.0000 4369.057538 0 0.0026 299 | 0/8 15 h-lim-p 0.0015 20.0000 0.0000 4369.057538 0 0.0000 334 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -4369.057538 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4369.057538 Node 7: lnL = -4369.057538 Node 8: lnL = -4369.057538 Node 9: lnL = -4369.057538 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 757 Sequential format.. Reading seq # 1: YOR001W_Sbay Reading seq # 2: YOR001W_Scer Reading seq # 3: YOR001W_Skud Reading seq # 4: YOR001W_Smik Reading seq # 5: YOR001W_Spar Sequences read.. Counting patterns.. # site patterns = 357 Counting frequencies.. 120 bytes for distance 57120 bytes for lkl0 45696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.368809 0.185833 0.166293 0.133105 0.179715 0.359332 0.750882 0.141745 lnL0 = -3765.451182 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3765.451182 x= 0.36881 0.18583 0.16629 0.13310 0.17972 0.35933 0.75088 0.14174 1 h-lim-p 0.0016 0.0124 34.8216 3765.064805 6 0.0007 37 | 0/8 2 h-lim-p 0.0011 0.0086 20.6718 3764.993426 4 0.0004 57 | 0/8 3 h-lim-p 0.0021 0.1045 4.1827 3764.968247 0 0.0031 69 | 0/8 4 h-lim-p 0.0045 0.0975 2.8889 3764.962418 5 0.0019 90 | 0/8 5 h-lim-p 0.0069 0.3695 0.8137 3764.962102 4 0.0011 113 | 0/8 6 h-lim-p 0.0035 2.4929 0.2564 3764.962003 2 0.0033 137 | 0/8 7 h-lim-p 0.0078 3.0396 0.1083 3764.961974 2 0.0060 161 | 0/8 8 h-lim-p 1.6293 20.0000 0.0004 3764.961876 2 1.0748 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3764.961876 0 1.0938 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3764.961876 0 1.0938 227 | 0/8 11 h-lim-p 1.1472 20.0000 0.0000 3764.961876 0 1.7208 247 | 0/8 12 h-lim-p 0.6481 20.0000 0.0000 3764.961876 0 0.3241 267 | 0/8 13 h-lim-p 0.0133 20.0000 0.0002 3764.961876 0 0.0017 289 | 0/8 14 h-lim-p 0.0000 0.1787 1.0902 3764.961876 0 0.0000 310 | 0/8 15 h-lim-p 0.3171 20.0000 0.0000 3764.961876 0 1.9024 324 | 0/8 16 h-lim-p 1.6866 20.0000 0.0000 3764.961876 0 0.4216 345 | 0/8 17 h-lim-p 0.6564 20.0000 0.0000 3764.961876 0 0.0205 369 | 0/8 18 h-lim-p 0.0212 20.0000 0.0000 3764.961876 0 0.0000 402 Out... lnL = -3764.961876 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3764.961876 Node 7: lnL = -3764.961876 Node 8: lnL = -3764.961876 Node 9: lnL = -3764.961876 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 408 Sequential format.. Reading seq # 1: YOR002W_Sbay Reading seq # 2: YOR002W_Scer Reading seq # 3: YOR002W_Skud Reading seq # 4: YOR002W_Smik Reading seq # 5: YOR002W_Spar Sequences read.. Counting patterns.. # site patterns = 173 Counting frequencies.. 120 bytes for distance 27680 bytes for lkl0 22144 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.188436 0.110789 0.068924 0.146032 0.088817 0.182164 0.211344 0.073674 lnL0 = -1865.569520 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1865.569520 x= 0.18844 0.11079 0.06892 0.14603 0.08882 0.18216 0.21134 0.07367 1 h-lim-p 0.0011 0.0090 43.3086 1865.188704 6 0.0004 34 | 0/8 2 h-lim-p 0.0021 0.0165 8.6747 1865.170591 2 0.0005 51 | 0/8 3 h-lim-p 0.0015 0.0795 2.8801 1865.168899 5 0.0004 76 | 0/8 4 h-lim-p 0.0028 0.5176 0.4654 1865.168824 3 0.0007 95 | 0/8 5 h-lim-p 0.0134 9.2141 0.0255 1865.168823 0 0.0015 117 | 0/8 6 h-lim-p 0.0109 20.0000 0.0034 1865.168823 0 0.0054 137 | 0/8 7 h-lim-p 0.0036 20.0000 0.0052 1865.168820 0 0.0144 159 | 0/8 8 h-lim-p 0.0031 6.3258 0.0237 1865.168791 0 0.0063 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1865.168790 0 1.0938 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1865.168790 0 1.0938 220 | 0/8 11 h-lim-p 1.0446 20.0000 0.0000 1865.168790 0 4.1783 242 | 0/8 12 h-lim-p 0.5266 20.0000 0.0001 1865.168790 0 0.2633 262 | 0/8 13 h-lim-p 0.0132 20.0000 0.0015 1865.168790 0 0.0016 284 | 0/8 14 h-lim-p 0.0010 20.0000 0.0025 1865.168790 0 0.0010 304 | 0/8 15 h-lim-p 0.0005 20.0000 0.0049 1865.168790 0 0.0005 324 | 0/8 16 h-lim-p 0.0000 0.4771 0.2104 1865.168790 0 0.0000 344 | 0/8 17 h-lim-p 0.0001 16.9997 0.0155 1865.168790 0 0.0000 382 | 0/8 18 h-lim-p 0.0000 20.0000 0.0007 | 0/8 19 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -1865.168790 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1865.168790 Node 7: lnL = -1865.168790 Node 8: lnL = -1865.168790 Node 9: lnL = -1865.168790 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 473 Sequential format.. Reading seq # 1: YOR014W_Sbay Reading seq # 2: YOR014W_Scer Reading seq # 3: YOR014W_Skud Reading seq # 4: YOR014W_Smik Reading seq # 5: YOR014W_Spar Sequences read.. Counting patterns.. # site patterns = 150 Counting frequencies.. 120 bytes for distance 24000 bytes for lkl0 19200 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.126904 0.071029 0.046452 0.087987 0.055771 0.128937 0.120979 0.052751 lnL0 = -1846.129346 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1846.129346 x= 0.12690 0.07103 0.04645 0.08799 0.05577 0.12894 0.12098 0.05275 1 h-lim-p 0.0003 0.0028 68.3310 1845.674593 8 0.0002 42 | 0/8 2 h-lim-p 0.0011 0.0098 12.3694 1845.655258 2 0.0003 59 | 0/8 3 h-lim-p 0.0014 0.1196 2.3758 1845.654776 4 0.0002 81 | 0/8 4 h-lim-p 0.0006 0.2003 0.6967 1845.654694 3 0.0004 101 | 0/8 5 h-lim-p 0.0031 3.0637 0.0863 1845.654693 0 0.0003 123 | 0/8 6 h-lim-p 0.0019 10.0130 0.0150 1845.654693 0 0.0009 143 | 0/8 7 h-lim-p 0.0204 20.0000 0.0006 1845.654691 0 0.0612 164 | 0/8 8 h-lim-p 0.0021 5.3149 0.0181 1845.654667 0 0.0063 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1845.654667 0 1.0938 205 | 0/8 10 h-lim-p 1.4393 20.0000 0.0000 1845.654667 0 1.2594 225 | 0/8 11 h-lim-p 1.0325 20.0000 0.0000 1845.654667 0 0.1291 247 | 0/8 12 h-lim-p 0.0019 20.0000 0.0012 .. | 0/8 13 h-lim-p 0.0000 20.0000 0.0006 | 0/8 14 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -1845.654667 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1845.654667 Node 7: lnL = -1845.654667 Node 8: lnL = -1845.654667 Node 9: lnL = -1845.654667 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 344 Sequential format.. Reading seq # 1: YOR016C_Sbay Reading seq # 2: YOR016C_Scer Reading seq # 3: YOR016C_Skud Reading seq # 4: YOR016C_Smik Reading seq # 5: YOR016C_Spar Sequences read.. Counting patterns.. # site patterns = 141 Counting frequencies.. 120 bytes for distance 22560 bytes for lkl0 18048 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.147822 0.092569 0.042529 0.142406 0.077533 0.161877 0.152080 0.054901 lnL0 = -1425.113669 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1425.113669 x= 0.14782 0.09257 0.04253 0.14241 0.07753 0.16188 0.15208 0.05490 1 h-lim-p 0.0018 0.0140 49.8268 1424.694783 7 0.0004 36 | 0/8 2 h-lim-p 0.0009 0.0078 19.1634 1424.591199 8 0.0006 69 | 0/8 3 h-lim-p 0.0024 0.0330 5.0577 1424.584073 3 0.0006 88 | 0/8 4 h-lim-p 0.0045 0.2018 0.6771 1424.583954 2 0.0005 106 | 0/8 5 h-lim-p 0.0023 0.7182 0.1532 1424.583948 1 0.0005 129 | 0/8 6 h-lim-p 0.0028 18.6508 0.0257 1424.583948 0 0.0012 149 | 0/8 7 h-lim-p 0.0927 20.0000 0.0003 1424.583948 0 0.0406 169 | 0/8 8 h-lim-p 0.0054 20.0000 0.0025 1424.583946 0 0.0215 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1424.583946 0 1.0938 211 | 0/8 10 h-lim-p 1.7036 20.0000 0.0000 1424.583946 0 0.7453 231 | 0/8 11 h-lim-p 0.4654 20.0000 0.0000 1424.583946 0 0.0036 257 | 0/8 12 h-lim-p 0.0011 20.0000 0.0001 1424.583946 0 0.0000 293 | 0/8 13 h-lim-p 0.0000 20.0000 0.0003 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -1424.583946 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1424.583946 Node 7: lnL = -1424.583946 Node 8: lnL = -1424.583946 Node 9: lnL = -1424.583946 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 831 Sequential format.. Reading seq # 1: YOR019W_Sbay Reading seq # 2: YOR019W_Scer Reading seq # 3: YOR019W_Skud Reading seq # 4: YOR019W_Smik Reading seq # 5: YOR019W_Spar Sequences read.. Counting patterns.. # site patterns = 217 Counting frequencies.. 120 bytes for distance 34720 bytes for lkl0 27776 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.434202 0.000060 0.284059 0.243247 0.181342 4.391033 0.517585 0.063216 lnL0 = -3795.120887 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3795.120887 x= 0.43420 0.00006 0.28406 0.24325 0.18134 4.39103 0.51758 0.06322 1 h-lim-p 0.0000 0.0000 143.9214 3795.071093 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0232 26.2552 3794.566468 0 0.0016 41 | 1/8 3 h-lim-p 0.0041 0.0781 10.4609 3794.489018 6 0.0015 68 | 1/8 4 h-lim-p 0.0056 0.1922 2.7527 3794.434324 3 0.0058 86 | 1/8 5 h-lim-p 0.0138 0.2970 1.1514 3793.782003 0 0.0413 99 | 1/8 6 h-lim-p 0.0066 0.0525 6.9192 3789.732714 0 0.0131 112 | 1/8 7 h-lim-p 2.5000 20.0000 0.0087 3789.707717 5 0.7334 137 | 0/8 8 h-lim-p 0.0121 2.0477 0.5251 3789.707530 2 0.0015 162 | 0/8 9 h-lim-p 1.0787 20.0000 0.0007 3789.707430 2 0.8596 186 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 3789.707429 0 1.0938 206 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3789.707429 0 1.0938 226 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3789.707429 0 1.0938 246 | 0/8 13 h-lim-p 1.1994 20.0000 0.0000 3789.707429 0 1.0495 266 | 0/8 14 h-lim-p 0.7439 20.0000 0.0000 3789.707429 0 0.0465 289 | 0/8 15 h-lim-p 0.0012 20.0000 0.0005 3789.707429 0 0.0000 325 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 3789.707429 0 0.0000 354 Out... lnL = -3789.707429 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3789.707429 Node 7: lnL = -3789.707429 Node 8: lnL = -3789.707429 Node 9: lnL = -3789.707429 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 916 Sequential format.. Reading seq # 1: YOR020C_Sbay Reading seq # 2: YOR020C_Scer Reading seq # 3: YOR020C_Skud Reading seq # 4: YOR020C_Smik Reading seq # 5: YOR020C_Spar Sequences read.. Counting patterns.. # site patterns = 415 Counting frequencies.. 120 bytes for distance 66400 bytes for lkl0 53120 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.229325 0.078093 0.138004 0.213289 0.228319 0.593078 0.265138 0.041840 lnL0 = -4817.433320 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4817.433320 x= 0.22933 0.07809 0.13800 0.21329 0.22832 0.59308 0.26514 0.04184 1 h-lim-p 0.0211 2.1178 67.5703 4816.678383 7 0.0003 43 | 0/8 2 h-lim-p 0.0009 0.0076 16.1068 4816.602397 6 0.0006 70 | 0/8 3 h-lim-p 0.0009 0.0578 11.0369 4816.554184 0 0.0013 82 | 0/8 4 h-lim-p 0.0025 0.0626 5.9130 4816.545847 4 0.0007 103 | 0/8 5 h-lim-p 0.0025 0.1650 1.5408 4816.545135 3 0.0007 122 | 0/8 6 h-lim-p 0.0186 3.9047 0.0551 4816.545127 1 0.0023 138 | 0/8 7 h-lim-p 0.0053 17.4552 0.0237 4816.545084 0 0.0107 159 | 0/8 8 h-lim-p 0.0045 4.4277 0.0559 4816.543515 0 0.0362 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 4816.543511 0 1.0938 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4816.543510 0 1.0938 222 | 0/8 11 h-lim-p 0.7200 20.0000 0.0000 4816.543510 0 1.0801 242 | 0/8 12 h-lim-p 0.3943 20.0000 0.0001 4816.543510 0 0.0370 265 | 0/8 13 h-lim-p 0.0059 20.0000 0.0004 4816.543510 0 0.0030 285 | 0/8 14 h-lim-p 0.0013 20.0000 0.0009 4816.543510 0 0.0000 322 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 4816.543510 0 0.0000 344 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 4816.543510 0 0.0000 411 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -4816.543510 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4816.543510 Node 7: lnL = -4816.543510 Node 8: lnL = -4816.543510 Node 9: lnL = -4816.543510 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 318 Sequential format.. Reading seq # 1: YOR021C_Sbay Reading seq # 2: YOR021C_Scer Reading seq # 3: YOR021C_Skud Reading seq # 4: YOR021C_Smik Reading seq # 5: YOR021C_Spar Sequences read.. Counting patterns.. # site patterns = 163 Counting frequencies.. 120 bytes for distance 26080 bytes for lkl0 20864 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.220313 0.078941 0.115964 0.176857 0.091455 0.230506 0.258206 0.086178 lnL0 = -1421.407801 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1421.407801 x= 0.22031 0.07894 0.11596 0.17686 0.09145 0.23051 0.25821 0.08618 1 h-lim-p 0.0037 0.0292 45.4677 1420.605554 2 0.0009 27 | 0/8 2 h-lim-p 0.0022 0.0173 12.8336 1420.500441 7 0.0014 58 | 0/8 3 h-lim-p 0.0018 0.0328 9.4056 1420.473911 2 0.0009 74 | 0/8 4 h-lim-p 0.0034 0.1170 2.3922 1420.470480 4 0.0013 94 | 0/8 5 h-lim-p 0.0071 0.6650 0.4501 1420.470344 2 0.0014 111 | 0/8 6 h-lim-p 0.0189 8.1782 0.0336 1420.470344 0 0.0012 134 | 0/8 7 h-lim-p 0.0135 20.0000 0.0029 1420.470343 0 0.0118 154 | 0/8 8 h-lim-p 0.0266 20.0000 0.0013 1420.470327 0 0.2128 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1420.470326 0 1.0938 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1420.470326 0 1.0938 217 | 0/8 11 h-lim-p 1.5866 20.0000 0.0000 1420.470326 0 1.3883 237 | 0/8 12 h-lim-p 1.3934 20.0000 0.0000 1420.470326 0 0.0435 261 | 0/8 13 h-lim-p 0.0029 20.0000 0.0001 1420.470326 0 0.0000 292 | 0/8 14 h-lim-p 0.0004 20.0000 0.0000 1420.470326 0 0.0001 313 Out... lnL = -1420.470326 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1420.470326 Node 7: lnL = -1420.470326 Node 8: lnL = -1420.470326 Node 9: lnL = -1420.470326 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 148 Sequential format.. Reading seq # 1: YOR023C_Sbay Reading seq # 2: YOR023C_Scer Reading seq # 3: YOR023C_Skud Reading seq # 4: YOR023C_Smik Reading seq # 5: YOR023C_Spar Sequences read.. Counting patterns.. # site patterns = 81 Counting frequencies.. 120 bytes for distance 12960 bytes for lkl0 10368 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.302489 0.114769 0.000060 0.193373 0.068003 0.217093 0.109073 0.181319 lnL0 = -669.419500 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 669.419500 x= 0.30249 0.11477 0.00006 0.19337 0.06800 0.21709 0.10907 0.18132 1 h-lim-p 0.0019 0.0213 84.0488 667.698544 3 0.0004 29 | 0/8 2 h-lim-p 0.0007 0.0060 27.0772 667.158221 0 0.0015 42 | 0/8 3 h-lim-p 0.0011 0.0087 17.8114 667.009814 1 0.0014 56 | 0/8 4 h-lim-p 0.0022 0.0341 10.8625 666.952220 5 0.0015 80 | 0/8 5 h-lim-p 0.0055 0.0507 2.8854 666.943401 3 0.0024 98 | 0/8 6 h-lim-p 0.0227 0.8664 0.3074 666.943246 4 0.0032 122 | 0/8 7 h-lim-p 0.0344 7.0991 0.0287 666.943228 3 0.0092 149 | 0/8 8 h-lim-p 0.0305 8.8048 0.0087 666.941256 0 0.2439 172 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 666.940992 2 1.0889 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 666.940988 1 0.9961 218 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 666.940988 0 1.0938 238 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 666.940988 0 1.0938 258 | 0/8 13 h-lim-p 1.4035 20.0000 0.0000 666.940988 0 0.1754 280 | 0/8 14 h-lim-p 0.0656 20.0000 0.0000 666.940988 0 0.0021 304 | 0/8 15 h-lim-p 0.0010 20.0000 0.0000 666.940988 0 0.0000 339 Out... lnL = -666.940988 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -666.940988 Node 7: lnL = -666.940988 Node 8: lnL = -666.940988 Node 9: lnL = -666.940988 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 51 Sequential format.. Reading seq # 1: YOR025W_Sbay Reading seq # 2: YOR025W_Scer Reading seq # 3: YOR025W_Skud Reading seq # 4: YOR025W_Smik Reading seq # 5: YOR025W_Spar Sequences read.. Counting patterns.. # site patterns = 35 Counting frequencies.. 120 bytes for distance 5600 bytes for lkl0 4480 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.491791 0.068063 0.065829 0.202024 0.019075 0.197867 0.058187 0.342210 lnL0 = -229.090008 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 229.090008 x= 0.49179 0.06806 0.06583 0.20202 0.01908 0.19787 0.05819 0.34221 1 h-lim-p 0.0002 0.0018 17.5072 228.663926 m 0.0018 22 | 1/8 2 h-lim-p 0.0032 15.9848 7.8098 228.615903 6 0.0021 48 | 1/8 3 h-lim-p 0.0065 0.1729 2.4768 228.600633 5 0.0057 70 | 1/8 4 h-lim-p 0.0169 0.5519 0.8303 228.592686 0 0.0254 82 | 1/8 5 h-lim-p 0.0540 0.4323 0.2298 228.591748 6 0.0180 116 | 1/8 6 h-lim-p 0.0234 0.4057 0.1761 228.589464 0 0.0469 136 | 1/8 7 h-lim-p 0.0565 0.4633 0.1462 228.575468 0 0.0847 155 | 1/8 8 h-lim-p 2.5000 20.0000 0.0014 228.575184 5 0.9394 184 | 1/8 9 h-lim-p 2.5000 20.0000 0.0001 228.575182 1 0.9961 205 | 1/8 10 h-lim-p 2.5000 20.0000 0.0000 228.575182 0 1.0938 224 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 228.575182 0 1.0938 243 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 228.575182 0 1.0938 262 | 1/8 13 h-lim-p 2.1888 20.0000 0.0000 228.575182 0 0.2736 283 | 1/8 14 h-lim-p 0.1063 20.0000 0.0000 228.575182 0 0.1063 302 | 1/8 15 h-lim-p 0.0498 20.0000 0.0000 228.575182 0 0.0249 321 | 1/8 16 h-lim-p 0.0129 20.0000 0.0000 228.575182 0 0.0000 359 Out... lnL = -228.575182 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -228.575182 Node 7: lnL = -228.575182 Node 8: lnL = -228.575182 Node 9: lnL = -228.575182 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 249 Sequential format.. Reading seq # 1: YOR026W_Sbay Reading seq # 2: YOR026W_Scer Reading seq # 3: YOR026W_Skud Reading seq # 4: YOR026W_Smik Reading seq # 5: YOR026W_Spar Sequences read.. Counting patterns.. # site patterns = 127 Counting frequencies.. 120 bytes for distance 20320 bytes for lkl0 16256 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.347163 0.016148 0.102177 0.115067 0.092598 0.193186 0.223395 0.212482 lnL0 = -1149.205786 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1149.205786 x= 0.34716 0.01615 0.10218 0.11507 0.09260 0.19319 0.22340 0.21248 1 h-lim-p 0.0035 0.0281 70.4001 1147.538071 7 0.0008 39 | 0/8 2 h-lim-p 0.0014 0.0108 28.1741 1146.855006 0 0.0020 51 | 0/8 3 h-lim-p 0.0025 0.0197 13.0902 1146.789243 4 0.0009 71 | 0/8 4 h-lim-p 0.0015 0.0398 8.0085 1146.760774 6 0.0012 94 | 0/8 5 h-lim-p 0.0160 0.4129 0.6234 1146.760552 4 0.0011 117 | 0/8 6 h-lim-p 0.0103 5.9699 0.0655 1146.760349 1 0.0129 139 | 0/8 7 h-lim-p 0.0029 1.2857 0.2954 1146.759227 0 0.0086 160 | 0/8 8 h-lim-p 0.0168 20.0000 0.1511 1146.747527 0 0.0336 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0018 1146.746386 4 1.3437 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1146.746385 0 1.0938 230 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1146.746385 0 1.0938 250 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1146.746385 0 1.0938 270 | 0/8 13 h-lim-p 1.0969 20.0000 0.0000 1146.746385 0 2.1939 291 | 0/8 14 h-lim-p 0.2058 20.0000 0.0000 1146.746385 0 0.0000 324 | 0/8 15 h-lim-p 0.0004 20.0000 0.0000 1146.746385 0 0.0000 353 Out... lnL = -1146.746385 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1146.746385 Node 7: lnL = -1146.746385 Node 8: lnL = -1146.746385 Node 9: lnL = -1146.746385 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 264 Sequential format.. Reading seq # 1: YOR027W_Sbay Reading seq # 2: YOR027W_Scer Reading seq # 3: YOR027W_Skud Reading seq # 4: YOR027W_Smik Reading seq # 5: YOR027W_Spar Sequences read.. Counting patterns.. # site patterns = 114 Counting frequencies.. 120 bytes for distance 18240 bytes for lkl0 14592 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.184265 0.043654 0.024088 0.081827 0.060584 0.112095 0.172307 0.103518 lnL0 = -1032.559872 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1032.559872 x= 0.18427 0.04365 0.02409 0.08183 0.06058 0.11210 0.17231 0.10352 1 h-lim-p 0.0024 1.4041 91.9869 1031.639655 8 0.0002 43 | 0/8 2 h-lim-p 0.0006 0.0045 27.2476 1031.440295 5 0.0006 65 | 0/8 3 h-lim-p 0.0020 0.0229 7.8914 1031.407723 7 0.0011 93 | 0/8 4 h-lim-p 0.0053 0.1160 1.6732 1031.406728 5 0.0007 118 | 0/8 5 h-lim-p 0.0020 0.2519 0.6197 1031.406610 4 0.0007 141 | 0/8 6 h-lim-p 0.0018 0.9035 0.2399 1031.406597 3 0.0005 170 | 0/8 7 h-lim-p 0.0014 1.6996 0.0890 1031.406595 1 0.0006 192 | 0/8 8 h-lim-p 0.5313 20.0000 0.0001 1031.406583 0 1.0627 213 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1031.406583 0 1.0938 233 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1031.406583 0 1.2500 253 | 0/8 11 h-lim-p 1.7897 20.0000 0.0000 1031.406583 0 0.0122 279 | 0/8 12 h-lim-p 0.0054 20.0000 0.0000 1031.406583 0 0.0000 316 Out... lnL = -1031.406583 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1031.406583 Node 7: lnL = -1031.406583 Node 8: lnL = -1031.406583 Node 9: lnL = -1031.406583 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 209 Sequential format.. Reading seq # 1: YOR028C_Sbay Reading seq # 2: YOR028C_Scer Reading seq # 3: YOR028C_Skud Reading seq # 4: YOR028C_Smik Reading seq # 5: YOR028C_Spar Sequences read.. Counting patterns.. # site patterns = 114 Counting frequencies.. 120 bytes for distance 18240 bytes for lkl0 14592 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.235381 0.073447 0.096074 0.095818 0.098816 0.149957 0.286825 0.113267 lnL0 = -941.012543 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 941.012543 x= 0.23538 0.07345 0.09607 0.09582 0.09882 0.14996 0.28683 0.11327 1 h-lim-p 0.0012 0.0099 33.9157 940.488850 4 0.0010 30 | 0/8 2 h-lim-p 0.0013 0.0101 10.5044 940.440447 7 0.0009 60 | 0/8 3 h-lim-p 0.0025 0.0609 3.8731 940.430054 6 0.0016 89 | 0/8 4 h-lim-p 0.0045 0.1016 1.3417 940.427909 5 0.0027 114 | 0/8 5 h-lim-p 0.0113 0.7610 0.3209 940.427830 4 0.0016 138 | 0/8 6 h-lim-p 0.0099 2.1918 0.0518 940.427827 1 0.0020 161 | 0/8 7 h-lim-p 0.0049 14.0384 0.0207 940.427827 0 0.0022 181 | 0/8 8 h-lim-p 0.2042 20.0000 0.0002 940.427803 0 0.8170 203 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 940.427802 0 1.0938 223 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 940.427802 0 1.0938 243 | 0/8 11 h-lim-p 2.1331 20.0000 0.0000 940.427802 0 1.8665 263 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 940.427802 0 0.2734 285 | 0/8 13 h-lim-p 0.0638 20.0000 0.0000 940.427802 0 0.0319 305 | 0/8 14 h-lim-p 0.0160 20.0000 0.0000 940.427802 0 0.0004 330 Out... lnL = -940.427802 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -940.427802 Node 7: lnL = -940.427802 Node 8: lnL = -940.427802 Node 9: lnL = -940.427802 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 631 Sequential format.. Reading seq # 1: YOR031W_Sbay Reading seq # 2: YOR031W_Scer Reading seq # 3: YOR031W_Skud Reading seq # 4: YOR031W_Smik Reading seq # 5: YOR031W_Spar Sequences read.. Counting patterns.. # site patterns = 308 Counting frequencies.. 120 bytes for distance 49280 bytes for lkl0 39424 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.238063 0.253162 0.057431 0.224906 0.147730 0.245094 0.232498 0.076718 lnL0 = -3023.978779 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3023.978779 x= 0.23806 0.25316 0.05743 0.22491 0.14773 0.24509 0.23250 0.07672 1 h-lim-p 0.0019 0.0148 93.4663 3022.483447 8 0.0004 38 | 0/8 2 h-lim-p 0.0017 0.0159 20.4672 3022.300518 6 0.0009 63 | 0/8 3 h-lim-p 0.0024 0.0402 7.6538 3022.283197 6 0.0007 90 | 0/8 4 h-lim-p 0.0109 0.5875 0.4679 3022.283121 2 0.0007 109 | 0/8 5 h-lim-p 0.0023 1.1625 0.1372 3022.283112 1 0.0009 131 | 0/8 6 h-lim-p 0.0051 16.6148 0.0244 3022.283110 1 0.0025 154 | 0/8 7 h-lim-p 0.0071 20.0000 0.0087 3022.283065 0 0.0568 177 | 0/8 8 h-lim-p 0.0116 20.0000 0.0425 3022.282623 0 0.0232 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3022.282564 2 0.9961 222 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3022.282564 0 1.0938 242 | 0/8 11 h-lim-p 1.3188 20.0000 0.0000 3022.282564 0 1.1540 262 | 0/8 12 h-lim-p 0.4588 20.0000 0.0000 3022.282564 0 0.0251 285 | 0/8 13 h-lim-p 0.0032 20.0000 0.0002 3022.282564 0 0.0000 319 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 3022.282564 0 0.0000 341 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 3022.282564 0 0.0000 363 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 3022.282564 0 0.0000 396 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 3022.282564 0 0.0000 430 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -3022.282564 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3022.282564 Node 7: lnL = -3022.282564 Node 8: lnL = -3022.282564 Node 9: lnL = -3022.282564 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 260 Sequential format.. Reading seq # 1: YOR035C_Sbay Reading seq # 2: YOR035C_Scer Reading seq # 3: YOR035C_Skud Reading seq # 4: YOR035C_Smik Reading seq # 5: YOR035C_Spar Sequences read.. Counting patterns.. # site patterns = 134 Counting frequencies.. 120 bytes for distance 21440 bytes for lkl0 17152 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.138488 0.060742 0.062766 0.151696 0.084309 0.204473 0.234302 0.036130 lnL0 = -1115.135259 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1115.135259 x= 0.13849 0.06074 0.06277 0.15170 0.08431 0.20447 0.23430 0.03613 1 h-lim-p 0.0006 0.0050 53.4210 1114.280685 4 0.0006 30 | 0/8 2 h-lim-p 0.0018 0.0144 13.5051 1114.200507 4 0.0009 51 | 0/8 3 h-lim-p 0.0015 0.0348 8.1589 1114.183010 2 0.0007 67 | 0/8 4 h-lim-p 0.0019 0.0974 2.9952 1114.178928 6 0.0011 95 | 0/8 5 h-lim-p 0.0075 0.2390 0.4309 1114.178849 0 0.0008 109 | 0/8 6 h-lim-p 0.0063 1.7761 0.0568 1114.178847 1 0.0012 132 | 0/8 7 h-lim-p 0.0076 20.0000 0.0093 1114.178847 0 0.0033 152 | 0/8 8 h-lim-p 0.0834 20.0000 0.0004 1114.178814 0 0.6674 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1114.178813 0 1.0938 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1114.178813 0 1.0938 215 | 0/8 11 h-lim-p 1.1602 20.0000 0.0000 1114.178813 0 0.0363 239 | 0/8 12 h-lim-p 0.0072 20.0000 0.0000 1114.178813 0 0.0000 271 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 1114.178813 0 0.0000 291 Out... lnL = -1114.178813 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1114.178813 Node 7: lnL = -1114.178813 Node 8: lnL = -1114.178813 Node 9: lnL = -1114.178813 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 260 Sequential format.. Reading seq # 1: YOR036W_Sbay Reading seq # 2: YOR036W_Scer Reading seq # 3: YOR036W_Skud Reading seq # 4: YOR036W_Smik Reading seq # 5: YOR036W_Spar Sequences read.. Counting patterns.. # site patterns = 138 Counting frequencies.. 120 bytes for distance 22080 bytes for lkl0 17664 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.168974 0.094069 0.105430 0.136822 0.018749 0.217306 0.256673 0.054937 lnL0 = -1141.020267 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1141.020267 x= 0.16897 0.09407 0.10543 0.13682 0.01875 0.21731 0.25667 0.05494 1 h-lim-p 0.0021 1.0821 104.0392 1139.409326 7 0.0004 39 | 0/8 2 h-lim-p 0.0015 0.0116 18.0716 1139.217855 5 0.0012 63 | 0/8 3 h-lim-p 0.0034 0.0268 6.6132 1139.189479 5 0.0015 84 | 0/8 4 h-lim-p 0.0043 0.1050 2.2547 1139.187070 5 0.0011 109 | 0/8 5 h-lim-p 0.0077 1.0645 0.3125 1139.186954 4 0.0024 133 | 0/8 6 h-lim-p 0.0183 5.7224 0.0408 1139.186946 1 0.0040 156 | 0/8 7 h-lim-p 0.0181 18.7450 0.0090 1139.186485 0 0.1448 179 | 0/8 8 h-lim-p 0.0069 0.3501 0.1901 1139.184723 0 0.0103 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1139.184694 2 1.0938 223 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1139.184694 0 1.0938 243 | 0/8 11 h-lim-p 2.1850 20.0000 0.0000 1139.184694 0 0.9559 263 | 0/8 12 h-lim-p 0.7509 20.0000 0.0000 1139.184694 0 0.0469 286 | 0/8 13 h-lim-p 0.0035 20.0000 0.0001 1139.184694 0 0.0000 330 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1139.184694 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1139.184694 Node 7: lnL = -1139.184694 Node 8: lnL = -1139.184694 Node 9: lnL = -1139.184694 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 236 Sequential format.. Reading seq # 1: YOR037W_Sbay Reading seq # 2: YOR037W_Scer Reading seq # 3: YOR037W_Skud Reading seq # 4: YOR037W_Smik Reading seq # 5: YOR037W_Spar Sequences read.. Counting patterns.. # site patterns = 139 Counting frequencies.. 120 bytes for distance 22240 bytes for lkl0 17792 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.257854 0.000060 0.132854 0.142701 0.202297 0.344193 0.317954 0.103018 lnL0 = -1196.638189 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1196.638189 x= 0.25785 0.00006 0.13285 0.14270 0.20230 0.34419 0.31795 0.10302 1 h-lim-p 0.0000 0.0000 27.6597 1196.634338 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0561 10.5270 1196.526958 0 0.0026 42 | 1/8 3 h-lim-p 0.0076 0.0612 3.2584 1196.519292 4 0.0015 63 | 1/8 4 h-lim-p 0.0052 0.2304 0.9164 1196.515724 3 0.0044 81 | 1/8 5 h-lim-p 0.0161 0.8041 0.2498 1196.455504 0 0.0643 102 | 1/8 6 h-lim-p 0.0056 0.0983 2.8456 1196.140981 0 0.0113 122 | 1/8 7 h-lim-p 0.0045 0.0544 7.1229 1196.070045 7 0.0026 151 | 1/8 8 h-lim-p 2.5000 20.0000 0.0069 1196.060428 6 0.9070 178 | 1/8 9 h-lim-p 2.5000 20.0000 0.0002 1196.060418 2 0.7996 202 | 1/8 10 h-lim-p 2.5000 20.0000 0.0000 1196.060418 0 1.0938 221 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 1196.060418 0 1.0938 240 | 1/8 12 h-lim-p 1.8747 20.0000 0.0000 1196.060418 0 0.8202 259 | 1/8 13 h-lim-p 0.6331 20.0000 0.0000 1196.060418 0 0.1583 279 | 1/8 14 h-lim-p 0.0412 20.0000 0.0000 1196.060418 0 0.0006 303 | 1/8 15 h-lim-p 0.0005 20.0000 0.0000 1196.060418 0 0.0005 322 | 1/8 16 h-lim-p 0.0001 20.0000 0.0001 1196.060418 0 0.0000 355 | 1/8 17 h-lim-p 0.0000 20.0000 0.0000 | 1/8 18 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1196.060418 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1196.060418 Node 7: lnL = -1196.060418 Node 8: lnL = -1196.060418 Node 9: lnL = -1196.060418 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 399 Sequential format.. Reading seq # 1: YOR038C_Sbay Reading seq # 2: YOR038C_Scer Reading seq # 3: YOR038C_Skud Reading seq # 4: YOR038C_Smik Reading seq # 5: YOR038C_Spar Sequences read.. Counting patterns.. # site patterns = 133 Counting frequencies.. 120 bytes for distance 21280 bytes for lkl0 17024 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.147793 0.000060 0.118084 0.088324 0.055083 0.169637 0.206618 0.057832 lnL0 = -1653.469246 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1653.469246 x= 0.14779 0.00006 0.11808 0.08832 0.05508 0.16964 0.20662 0.05783 1 h-lim-p 0.0002 0.0012 167.9656 1650.377841 1 0.0002 24 | 0/8 2 h-lim-p 0.0003 0.0026 41.5103 1650.067357 5 0.0004 47 | 0/8 3 h-lim-p 0.0006 0.0063 27.2133 1650.002545 5 0.0002 71 | 0/8 4 h-lim-p 0.0007 0.0259 8.8042 1649.981949 3 0.0006 89 | 0/8 5 h-lim-p 0.0015 0.0804 3.7560 1649.979220 4 0.0005 111 | 0/8 6 h-lim-p 0.0053 1.0253 0.3318 1649.979158 3 0.0009 131 | 0/8 7 h-lim-p 0.0034 1.4940 0.0836 1649.979065 2 0.0038 156 | 0/8 8 h-lim-p 0.0139 1.6734 0.0231 1649.957311 0 0.1669 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 1649.956701 3 0.9482 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1649.956701 0 1.0938 225 | 0/8 11 h-lim-p 1.9729 20.0000 0.0000 1649.956701 0 1.7263 245 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1649.956701 0 1.0938 265 | 0/8 13 h-lim-p 0.4486 20.0000 0.0000 1649.956701 m20.0000 288 | 0/8 14 h-lim-p 0.0297 8.6021 0.0096 1649.956701 0 0.0002 314 | 0/8 15 h-lim-p 0.0000 0.2928 0.2810 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0006 | 0/8 17 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -1649.956701 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1649.956701 Node 7: lnL = -1649.956701 Node 8: lnL = -1649.956701 Node 9: lnL = -1649.956701 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 398 Sequential format.. Reading seq # 1: YOR039W_Sbay Reading seq # 2: YOR039W_Scer Reading seq # 3: YOR039W_Skud Reading seq # 4: YOR039W_Smik Reading seq # 5: YOR039W_Spar Sequences read.. Counting patterns.. # site patterns = 131 Counting frequencies.. 120 bytes for distance 20960 bytes for lkl0 16768 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.131524 0.023377 0.101246 0.086335 0.049220 0.139098 0.171921 0.045873 lnL0 = -1615.517078 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1615.517078 x= 0.13152 0.02338 0.10125 0.08633 0.04922 0.13910 0.17192 0.04587 1 h-lim-p 0.0015 0.0330 149.2613 1613.837173 8 0.0002 40 | 0/8 2 h-lim-p 0.0010 0.0078 7.7535 1613.829934 4 0.0002 61 | 0/8 3 h-lim-p 0.0005 0.0689 3.7198 1613.827675 4 0.0004 81 | 0/8 4 h-lim-p 0.0009 0.1309 1.5424 1613.827214 3 0.0005 100 | 0/8 5 h-lim-p 0.0026 0.9998 0.2691 1613.827200 2 0.0004 119 | 0/8 6 h-lim-p 0.0061 8.4758 0.0194 1613.827200 0 0.0007 141 | 0/8 7 h-lim-p 0.0055 20.0000 0.0023 1613.827200 0 0.0055 161 | 0/8 8 h-lim-p 0.0154 20.0000 0.0008 1613.827171 0 0.1844 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1613.827170 0 1.0938 204 | 0/8 10 h-lim-p 2.2410 20.0000 0.0000 1613.827170 0 0.9804 224 | 0/8 11 h-lim-p 0.8437 20.0000 0.0000 1613.827170 0 0.0000 267 | 0/8 12 h-lim-p 0.0000 20.0000 0.0001 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1613.827170 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1613.827170 Node 7: lnL = -1613.827170 Node 8: lnL = -1613.827170 Node 9: lnL = -1613.827170 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 551 Sequential format.. Reading seq # 1: YOR042W_Sbay Reading seq # 2: YOR042W_Scer Reading seq # 3: YOR042W_Skud Reading seq # 4: YOR042W_Smik Reading seq # 5: YOR042W_Spar Sequences read.. Counting patterns.. # site patterns = 206 Counting frequencies.. 120 bytes for distance 32960 bytes for lkl0 26368 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.110811 0.058377 0.046493 0.110621 0.099036 0.174635 0.113725 0.027034 lnL0 = -2253.063191 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2253.063191 x= 0.11081 0.05838 0.04649 0.11062 0.09904 0.17463 0.11372 0.02703 1 h-lim-p 0.0014 0.0111 174.1330 2250.566259 4 0.0002 32 | 0/8 2 h-lim-p 0.0006 0.0049 31.6475 2250.389968 6 0.0004 59 | 0/8 3 h-lim-p 0.0013 0.0306 8.9089 2250.377363 5 0.0003 82 | 0/8 4 h-lim-p 0.0010 0.0304 3.1305 2250.375985 4 0.0003 104 | 0/8 5 h-lim-p 0.0011 0.2037 0.8864 2250.375881 3 0.0003 123 | 0/8 6 h-lim-p 0.0034 1.3959 0.0763 2250.375879 0 0.0004 145 | 0/8 7 h-lim-p 0.0093 20.0000 0.0031 2250.375877 0 0.0139 165 | 0/8 8 h-lim-p 0.0044 20.0000 0.0097 2250.375690 0 0.0352 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2250.375689 0 1.0938 208 | 0/8 10 h-lim-p 1.2937 20.0000 0.0000 2250.375689 0 1.1319 228 | 0/8 11 h-lim-p 1.0427 20.0000 0.0000 2250.375689 0 2.0854 249 | 0/8 12 h-lim-p 0.0546 20.0000 0.0013 2250.375689 0 0.0004 275 | 0/8 13 h-lim-p 0.0000 3.6123 0.0121 2250.375689 0 0.0000 298 | 0/8 14 h-lim-p 0.0001 20.0000 0.0008 2250.375689 0 0.0000 331 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -2250.375689 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2250.375689 Node 7: lnL = -2250.375689 Node 8: lnL = -2250.375689 Node 9: lnL = -2250.375689 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 867 Sequential format.. Reading seq # 1: YOR043W_Sbay Reading seq # 2: YOR043W_Scer Reading seq # 3: YOR043W_Skud Reading seq # 4: YOR043W_Smik Reading seq # 5: YOR043W_Spar Sequences read.. Counting patterns.. # site patterns = 226 Counting frequencies.. 120 bytes for distance 36160 bytes for lkl0 28928 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.133044 0.039486 0.055343 0.079184 0.055299 0.114476 0.122318 0.058566 lnL0 = -3271.332837 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3271.332837 x= 0.13304 0.03949 0.05534 0.07918 0.05530 0.11448 0.12232 0.05857 1 h-lim-p 0.0001 0.0011 236.5296 3268.743310 6 0.0001 34 | 0/8 2 h-lim-p 0.0004 0.0030 51.6993 3268.476706 8 0.0002 66 | 0/8 3 h-lim-p 0.0007 0.0138 14.9246 3268.465751 6 0.0001 96 | 0/8 4 h-lim-p 0.0003 0.0215 4.7875 3268.464496 4 0.0001 118 | 0/8 5 h-lim-p 0.0010 0.2071 0.6044 3268.464465 2 0.0002 135 | 0/8 6 h-lim-p 0.0015 2.6637 0.0760 3268.464464 0 0.0002 157 | 0/8 7 h-lim-p 0.0023 20.0000 0.0054 3268.464464 0 0.0005 178 | 0/8 8 h-lim-p 0.0166 20.0000 0.0002 3268.464448 0 0.5319 203 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3268.464447 0 1.2500 223 | 0/8 10 h-lim-p 1.4245 20.0000 0.0000 3268.464447 0 0.7123 243 | 0/8 11 h-lim-p 0.4852 20.0000 0.0000 3268.464447 0 0.1213 264 | 0/8 12 h-lim-p 0.0468 20.0000 0.0001 3268.464447 0 0.0205 284 | 0/8 13 h-lim-p 0.0101 20.0000 0.0002 3268.464447 0 0.0003 308 | 0/8 14 h-lim-p 0.0002 20.0000 0.0003 3268.464447 0 0.0000 330 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 3268.464447 0 0.0000 358 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 3268.464447 0 0.0000 379 Out... lnL = -3268.464447 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3268.464447 Node 7: lnL = -3268.464447 Node 8: lnL = -3268.464447 Node 9: lnL = -3268.464447 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 732 Sequential format.. Reading seq # 1: YOR044W_Sbay Reading seq # 2: YOR044W_Scer Reading seq # 3: YOR044W_Skud Reading seq # 4: YOR044W_Smik Reading seq # 5: YOR044W_Spar Sequences read.. Counting patterns.. # site patterns = 252 Counting frequencies.. 120 bytes for distance 40320 bytes for lkl0 32256 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.172029 0.143534 0.061230 0.104983 0.062468 0.142717 0.194317 0.061622 lnL0 = -3113.431283 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3113.431283 x= 0.17203 0.14353 0.06123 0.10498 0.06247 0.14272 0.19432 0.06162 1 h-lim-p 0.0002 0.0014 132.7514 3111.471899 0 0.0003 22 | 0/8 2 h-lim-p 0.0006 0.0051 35.1881 3111.246301 7 0.0004 53 | 0/8 3 h-lim-p 0.0012 0.0168 11.0785 3111.229041 4 0.0003 75 | 0/8 4 h-lim-p 0.0018 0.0539 1.9326 3111.228560 4 0.0003 99 | 0/8 5 h-lim-p 0.0003 0.1699 1.8810 3111.228291 2 0.0002 115 | 0/8 6 h-lim-p 0.0012 1.2460 0.3556 3111.228260 2 0.0004 132 | 0/8 7 h-lim-p 0.0028 5.0942 0.0501 3111.228143 0 0.0057 153 | 0/8 8 h-lim-p 0.0062 2.3813 0.0460 3111.212724 0 0.0741 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 3111.212442 2 0.9644 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3111.212442 0 1.0938 220 | 0/8 11 h-lim-p 1.4764 20.0000 0.0000 3111.212442 0 1.2918 240 | 0/8 12 h-lim-p 1.2274 20.0000 0.0000 3111.212442 0 2.4548 261 | 0/8 13 h-lim-p 0.2575 20.0000 0.0002 3111.212442 0 0.2575 281 | 0/8 14 h-lim-p 0.0429 20.0000 0.0010 3111.212442 0 0.0010 306 | 0/8 15 h-lim-p 0.0005 20.0000 0.0020 3111.212442 0 0.0000 341 | 0/8 16 h-lim-p 0.0002 20.0000 0.0000 3111.212442 0 0.0000 373 Out... lnL = -3111.212442 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3111.212442 Node 7: lnL = -3111.212442 Node 8: lnL = -3111.212442 Node 9: lnL = -3111.212442 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 518 Sequential format.. Reading seq # 1: YOR046C_Sbay Reading seq # 2: YOR046C_Scer Reading seq # 3: YOR046C_Skud Reading seq # 4: YOR046C_Smik Reading seq # 5: YOR046C_Spar Sequences read.. Counting patterns.. # site patterns = 202 Counting frequencies.. 120 bytes for distance 32320 bytes for lkl0 25856 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.396088 0.079051 0.122647 0.364369 0.346124 4.300512 0.341411 0.000060 lnL0 = -2070.669781 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2070.669781 x= 0.39609 0.07905 0.12265 0.36437 0.34612 4.30051 0.34141 0.00006 1 h-lim-p 0.0000 0.0000 127.5230 2070.626201 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0102 40.3363 2067.670440 0 0.0038 42 | 1/8 3 h-lim-p 0.0042 0.0340 13.8528 2067.354936 8 0.0032 69 | 1/8 4 h-lim-p 0.0218 0.1741 1.1464 2066.827349 0 0.0435 82 | 1/8 5 h-lim-p 0.0038 0.0307 3.4000 2062.098827 m 0.0307 94 | 1/8 6 h-lim-p 0.0019 0.0156 27.0454 2060.931153 0 0.0029 106 | 1/8 7 h-lim-p 1.1363 9.0902 0.0689 2060.605535 6 0.5773 132 | 0/8 8 h-lim-p 0.0187 0.6173 2.1271 2060.600478 5 0.0027 165 | 0/8 9 h-lim-p 0.7584 6.8295 0.0077 2060.590909 2 0.7110 181 | 0/8 10 h-lim-p 2.5000 20.0000 0.0004 2060.590880 2 0.7996 206 | 0/8 11 h-lim-p 2.5000 20.0000 0.0001 2060.590879 1 0.6152 229 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2060.590879 0 1.0938 249 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2060.590879 0 1.0938 269 | 0/8 14 h-lim-p 1.1947 20.0000 0.0000 2060.590879 0 1.0454 289 | 0/8 15 h-lim-p 0.5560 20.0000 0.0000 2060.590879 0 0.0087 314 | 0/8 16 h-lim-p 0.0001 20.0000 0.0003 2060.590879 0 0.0000 335 | 0/8 17 h-lim-p 0.0006 20.0000 0.0000 2060.590879 0 0.0000 362 | 0/8 18 h-lim-p 0.0003 20.0000 0.0000 2060.590879 0 0.0000 394 Out... lnL = -2060.590879 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2060.590879 Node 7: lnL = -2060.590879 Node 8: lnL = -2060.590879 Node 9: lnL = -2060.590879 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 834 Sequential format.. Reading seq # 1: YOR047C_Sbay Reading seq # 2: YOR047C_Scer Reading seq # 3: YOR047C_Skud Reading seq # 4: YOR047C_Smik Reading seq # 5: YOR047C_Spar Sequences read.. Counting patterns.. # site patterns = 262 Counting frequencies.. 120 bytes for distance 41920 bytes for lkl0 33536 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.181575 0.021451 0.056310 0.093497 0.070952 0.156771 0.187253 0.087164 lnL0 = -3476.666793 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3476.666793 x= 0.18158 0.02145 0.05631 0.09350 0.07095 0.15677 0.18725 0.08716 1 h-lim-p 0.0009 0.4139 282.9024 3473.088284 3 0.0001 30 | 0/8 2 h-lim-p 0.0015 0.0118 19.2513 3473.028951 5 0.0003 52 | 0/8 3 h-lim-p 0.0004 0.0163 13.9791 3473.016607 4 0.0002 72 | 0/8 4 h-lim-p 0.0012 0.1012 2.0355 3473.016102 2 0.0003 89 | 0/8 5 h-lim-p 0.0008 0.3606 0.6334 3473.016051 2 0.0003 106 | 0/8 6 h-lim-p 0.0101 6.5358 0.0169 3473.016051 0 0.0006 129 | 0/8 7 h-lim-p 0.0071 20.0000 0.0013 3473.016005 0 0.1143 153 | 0/8 8 h-lim-p 0.0009 20.0000 0.1588 3473.015819 0 0.0019 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3473.015811 1 0.9961 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3473.015811 0 2.1875 216 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3473.015811 0 1.0938 236 | 0/8 12 h-lim-p 0.2144 20.0000 0.0000 3473.015811 0 0.1072 256 | 0/8 13 h-lim-p 0.0122 20.0000 0.0003 3473.015811 0 0.0031 277 | 0/8 14 h-lim-p 0.0018 20.0000 0.0006 3473.015811 0 0.0000 316 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -3473.015811 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3473.015811 Node 7: lnL = -3473.015811 Node 8: lnL = -3473.015811 Node 9: lnL = -3473.015811 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 741 Sequential format.. Reading seq # 1: YOR051C_Sbay Reading seq # 2: YOR051C_Scer Reading seq # 3: YOR051C_Skud Reading seq # 4: YOR051C_Smik Reading seq # 5: YOR051C_Spar Sequences read.. Counting patterns.. # site patterns = 206 Counting frequencies.. 120 bytes for distance 32960 bytes for lkl0 26368 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.132494 0.021170 0.020627 0.094268 0.077621 0.134287 0.154602 0.057170 lnL0 = -2835.810833 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2835.810833 x= 0.13249 0.02117 0.02063 0.09427 0.07762 0.13429 0.15460 0.05717 1 h-lim-p 0.0006 0.3765 318.9448 2832.661420 4 0.0001 32 | 0/8 2 h-lim-p 0.0002 0.0013 36.6234 2832.564064 2 0.0001 48 | 0/8 3 h-lim-p 0.0006 0.0214 9.5051 2832.556150 5 0.0002 72 | 0/8 4 h-lim-p 0.0012 0.1068 1.5139 2832.555853 2 0.0003 89 | 0/8 5 h-lim-p 0.0024 0.6220 0.1765 2832.555850 1 0.0001 106 | 0/8 6 h-lim-p 0.0004 2.9516 0.0609 2832.555850 0 0.0004 126 | 0/8 7 h-lim-p 0.0014 9.0541 0.0159 2832.555848 0 0.0014 146 | 0/8 8 h-lim-p 0.0116 20.0000 0.0019 2832.555311 0 0.1848 170 | 0/8 9 h-lim-p 0.3827 20.0000 0.0009 2832.555271 0 1.5307 192 | 0/8 10 h-lim-p 2.5000 20.0000 0.0004 2832.555266 0 1.0938 212 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2832.555266 0 1.0938 232 | 0/8 12 h-lim-p 0.7503 20.0000 0.0000 2832.555266 0 0.7503 252 | 0/8 13 h-lim-p 0.2823 20.0000 0.0001 2832.555266 0 0.0706 273 | 0/8 14 h-lim-p 0.0192 20.0000 0.0002 2832.555266 0 0.0000 303 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 2832.555266 0 0.0000 334 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 2832.555266 0 0.0000 365 | 0/8 17 h-lim-p 0.0000 20.0000 0.0007 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0004 2832.555266 0 0.0000 425 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 2832.555266 0 0.0051 454 | 0/8 20 h-lim-p 0.0260 20.0000 0.0000 2832.555266 0 0.0000 484 | 0/8 21 h-lim-p 0.0000 20.0000 0.0001 2832.555266 0 0.0000 504 | 0/8 22 h-lim-p 0.0000 20.0000 0.0019 2832.555266 0 0.0000 536 | 0/8 23 h-lim-p 0.0000 20.0000 0.0057 | 0/8 24 h-lim-p 0.0000 20.0000 0.0057 Out... lnL = -2832.555266 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2832.555266 Node 7: lnL = -2832.555266 Node 8: lnL = -2832.555266 Node 9: lnL = -2832.555266 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 651 Sequential format.. Reading seq # 1: YOR052C_Sbay Reading seq # 2: YOR052C_Scer Reading seq # 3: YOR052C_Skud Reading seq # 4: YOR052C_Smik Reading seq # 5: YOR052C_Spar Sequences read.. Counting patterns.. # site patterns = 198 Counting frequencies.. 120 bytes for distance 31680 bytes for lkl0 25344 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.102368 0.032670 0.054460 0.054344 0.079093 0.119131 0.133999 0.033393 lnL0 = -2398.912900 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2398.912900 x= 0.10237 0.03267 0.05446 0.05434 0.07909 0.11913 0.13400 0.03339 1 h-lim-p 0.0011 0.0090 192.0160 2397.016272 8 0.0001 38 | 0/8 2 h-lim-p 0.0007 0.0059 25.5210 2396.934746 7 0.0003 70 | 0/8 3 h-lim-p 0.0006 0.0155 11.5255 2396.926469 4 0.0001 91 | 0/8 4 h-lim-p 0.0007 0.0387 2.5076 2396.925951 4 0.0002 112 | 0/8 5 h-lim-p 0.0032 1.0664 0.1381 2396.925949 1 0.0003 128 | 0/8 6 h-lim-p 0.0017 8.6815 0.0258 2396.925948 0 0.0002 150 | 0/8 7 h-lim-p 0.0032 20.0000 0.0017 2396.925948 0 0.0007 171 | 0/8 8 h-lim-p 0.0067 20.0000 0.0002 2396.925945 0 0.3225 196 | 0/8 9 h-lim-p 1.9633 20.0000 0.0000 2396.925945 0 1.7179 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2396.925945 0 1.0938 236 | 0/8 11 h-lim-p 0.6538 20.0000 0.0000 2396.925945 0 3.9227 258 | 0/8 12 h-lim-p 1.0090 20.0000 0.0001 2396.925945 0 4.0362 280 | 0/8 13 h-lim-p 0.0167 1.8005 0.0308 2396.925945 0 0.0000 326 | 0/8 14 h-lim-p 0.0000 20.0000 0.0053 2396.925945 0 0.0000 346 | 0/8 15 h-lim-p 0.0000 20.0000 0.0012 2396.925945 0 0.0005 369 | 0/8 16 h-lim-p 0.0011 20.0000 0.0005 2396.925945 0 0.0000 400 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 2396.925945 0 0.0000 428 | 0/8 18 h-lim-p 0.0000 20.0000 0.0058 2396.925945 0 0.0000 457 | 0/8 19 h-lim-p 0.0000 20.0000 0.0005 .. | 0/8 20 h-lim-p 0.0000 20.0000 0.0058 2396.925945 0 0.0000 520 | 0/8 21 h-lim-p 0.0000 20.0000 0.0006 2396.925945 0 0.0000 552 | 0/8 22 h-lim-p 0.0000 20.0000 0.0058 2396.925945 0 0.0000 583 | 0/8 23 h-lim-p 0.0000 20.0000 0.0008 2396.925945 0 0.0001 606 | 0/8 24 h-lim-p 0.0005 20.0000 0.0002 2396.925945 0 0.0010 627 | 0/8 25 h-lim-p 0.0005 20.0000 0.0004 2396.925945 0 0.0001 649 | 0/8 26 h-lim-p 0.0000 7.5970 0.0073 2396.925945 0 0.0000 674 | 0/8 27 h-lim-p 0.0000 1.4068 0.0397 2396.925945 0 0.0000 704 | 0/8 28 h-lim-p 0.0000 20.0000 0.0005 2396.925945 0 0.0000 736 | 0/8 29 h-lim-p 0.0000 20.0000 0.0057 | 0/8 30 h-lim-p 0.0000 20.0000 0.0057 Out... lnL = -2396.925945 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2396.925945 Node 7: lnL = -2396.925945 Node 8: lnL = -2396.925945 Node 9: lnL = -2396.925945 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 584 Sequential format.. Reading seq # 1: YOR057W_Sbay Reading seq # 2: YOR057W_Scer Reading seq # 3: YOR057W_Skud Reading seq # 4: YOR057W_Smik Reading seq # 5: YOR057W_Spar Sequences read.. Counting patterns.. # site patterns = 272 Counting frequencies.. 120 bytes for distance 43520 bytes for lkl0 34816 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.285116 0.032947 0.069332 0.201497 0.142434 0.233304 0.346186 0.127767 lnL0 = -2977.552571 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2977.552571 x= 0.28512 0.03295 0.06933 0.20150 0.14243 0.23330 0.34619 0.12777 1 h-lim-p 0.0042 1.1685 118.8078 2975.397117 8 0.0003 45 | 0/8 2 h-lim-p 0.0013 0.0105 25.0946 2975.176820 8 0.0007 75 | 0/8 3 h-lim-p 0.0016 0.0311 11.4576 2975.140902 3 0.0007 93 | 0/8 4 h-lim-p 0.0018 0.0954 4.1060 2975.133119 6 0.0011 120 | 0/8 5 h-lim-p 0.0028 0.1403 1.5563 2975.132207 4 0.0009 143 | 0/8 6 h-lim-p 0.0039 0.6798 0.3404 2975.132160 2 0.0009 160 | 0/8 7 h-lim-p 0.0044 4.9721 0.0671 2975.132156 1 0.0011 183 | 0/8 8 h-lim-p 0.0614 20.0000 0.0012 2975.130911 0 0.9821 207 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2975.130896 1 0.9961 229 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2975.130896 0 1.0938 249 | 0/8 11 h-lim-p 1.4573 20.0000 0.0000 2975.130896 0 1.2752 269 | 0/8 12 h-lim-p 1.0151 20.0000 0.0000 2975.130896 0 3.0454 290 | 0/8 13 h-lim-p 0.0666 20.0000 0.0003 2975.130896 0 0.0003 317 | 0/8 14 h-lim-p 0.0018 20.0000 0.0000 2975.130896 0 0.0018 337 | 0/8 15 h-lim-p 0.0011 20.0000 0.0001 2975.130896 0 0.0000 373 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -2975.130896 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2975.130896 Node 7: lnL = -2975.130896 Node 8: lnL = -2975.130896 Node 9: lnL = -2975.130896 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 832 Sequential format.. Reading seq # 1: YOR058C_Sbay Reading seq # 2: YOR058C_Scer Reading seq # 3: YOR058C_Skud Reading seq # 4: YOR058C_Smik Reading seq # 5: YOR058C_Spar Sequences read.. Counting patterns.. # site patterns = 248 Counting frequencies.. 120 bytes for distance 39680 bytes for lkl0 31744 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.340893 0.000060 0.174962 0.167681 0.181376 0.554672 0.324741 0.138052 lnL0 = -3517.959346 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3517.959346 x= 0.34089 0.00006 0.17496 0.16768 0.18138 0.55467 0.32474 0.13805 1 h-lim-p 0.0000 0.0000 125.4144 3517.928722 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0191 26.4868 3517.629199 0 0.0010 40 | 1/8 3 h-lim-p 0.0024 0.0769 10.4076 3517.554104 6 0.0015 67 | 1/8 4 h-lim-p 0.0015 0.0929 10.4457 3517.441785 0 0.0030 80 | 1/8 5 h-lim-p 0.0013 0.1421 24.3185 3516.784914 0 0.0103 95 | 1/8 6 h-lim-p 0.0027 0.0218 41.4743 3516.636481 3 0.0012 113 | 1/8 7 h-lim-p 0.6143 5.0135 0.0835 3514.218781 1 0.7679 127 | 0/8 8 h-lim-p 0.0638 0.7078 1.0045 3514.218391 2 0.0010 155 | 0/8 9 h-lim-p 0.0628 0.7929 0.0158 3514.200034 m 0.7929 168 | 1/8 10 h-lim-p 1.8977 20.0000 0.0066 3514.199302 4 0.6470 198 | 1/8 11 h-lim-p 0.9374 20.0000 0.0046 3514.199097 2 0.7470 221 | 1/8 12 h-lim-p 2.5000 20.0000 0.0008 3514.199078 1 0.9961 242 | 1/8 13 h-lim-p 2.5000 20.0000 0.0002 3514.199078 0 2.1875 261 | 1/8 14 h-lim-p 2.5000 20.0000 0.0002 3514.199077 0 1.0938 280 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 3514.199077 0 1.0938 299 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 3514.199077 0 2.1875 318 | 1/8 17 h-lim-p 1.0502 20.0000 0.0000 3514.199077 0 0.0003 348 | 1/8 18 h-lim-p 0.0017 20.0000 0.0000 3514.199077 0 0.0000 381 Out... lnL = -3514.199077 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3514.199077 Node 7: lnL = -3514.199077 Node 8: lnL = -3514.199077 Node 9: lnL = -3514.199077 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 863 Sequential format.. Reading seq # 1: YOR062C_Sbay Reading seq # 2: YOR062C_Scer Reading seq # 3: YOR062C_Skud Reading seq # 4: YOR062C_Smik Reading seq # 5: YOR062C_Spar Sequences read.. Counting patterns.. # site patterns = 306 Counting frequencies.. 120 bytes for distance 48960 bytes for lkl0 39168 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.293361 0.057900 0.061977 0.128898 0.094751 0.186347 0.250404 0.149275 lnL0 = -4029.063539 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4029.063539 x= 0.29336 0.05790 0.06198 0.12890 0.09475 0.18635 0.25040 0.14927 1 h-lim-p 0.0003 0.0025 110.1383 4027.742943 8 0.0002 41 | 0/8 2 h-lim-p 0.0004 0.0030 28.9201 4027.632367 6 0.0003 67 | 0/8 3 h-lim-p 0.0007 0.0282 11.2713 4027.608366 6 0.0004 96 | 0/8 4 h-lim-p 0.0005 0.0210 9.1069 4027.602214 4 0.0002 115 | 0/8 5 h-lim-p 0.0010 0.1413 2.0367 4027.601366 2 0.0005 131 | 0/8 6 h-lim-p 0.0018 0.4333 0.4966 4027.601329 2 0.0003 149 | 0/8 7 h-lim-p 0.0012 1.8276 0.1227 4027.601325 0 0.0006 169 | 0/8 8 h-lim-p 0.1586 20.0000 0.0005 4027.600893 0 1.2686 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4027.600880 1 0.9961 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4027.600880 0 1.0938 234 | 0/8 11 h-lim-p 1.1033 20.0000 0.0000 4027.600880 0 4.4132 256 | 0/8 12 h-lim-p 0.9288 20.0000 0.0000 4027.600880 0 0.2322 277 | 0/8 13 h-lim-p 0.0001 1.8287 0.1181 4027.600880 0 0.0000 309 | 0/8 14 h-lim-p 0.0016 20.0000 0.0000 4027.600880 0 0.0000 342 Out... lnL = -4027.600880 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4027.600880 Node 7: lnL = -4027.600880 Node 8: lnL = -4027.600880 Node 9: lnL = -4027.600880 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 722 Sequential format.. Reading seq # 1: YOR064C_Sbay Reading seq # 2: YOR064C_Scer Reading seq # 3: YOR064C_Skud Reading seq # 4: YOR064C_Smik Reading seq # 5: YOR064C_Spar Sequences read.. Counting patterns.. # site patterns = 158 Counting frequencies.. 120 bytes for distance 25280 bytes for lkl0 20224 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.100818 0.020510 0.009654 0.082699 0.048346 0.105755 0.121660 0.039693 lnL0 = -2531.628359 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2531.628359 x= 0.10082 0.02051 0.00965 0.08270 0.04835 0.10576 0.12166 0.03969 1 h-lim-p 0.0007 0.0357 266.5924 2530.572544 6 0.0000 37 | 0/8 2 h-lim-p 0.0001 0.0007 54.9967 2530.459361 6 0.0001 60 | 0/8 3 h-lim-p 0.0003 0.0081 13.5369 2530.446784 2 0.0001 76 | 0/8 4 h-lim-p 0.0008 0.0653 2.4899 2530.446248 2 0.0002 93 | 0/8 5 h-lim-p 0.0010 0.1456 0.4651 2530.446238 0 0.0001 107 | 0/8 6 h-lim-p 0.0003 0.9409 0.1749 2530.446236 1 0.0001 130 | 0/8 7 h-lim-p 0.0020 8.4564 0.0122 2530.446235 0 0.0009 150 | 0/8 8 h-lim-p 0.0181 20.0000 0.0006 2530.445947 0 0.2900 174 | 0/8 9 h-lim-p 0.4897 20.0000 0.0003 2530.445938 0 0.9795 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2530.445938 0 1.2500 215 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2530.445938 0 0.2734 237 | 0/8 12 h-lim-p 0.0867 20.0000 0.0001 2530.445938 0 0.0020 262 | 0/8 13 h-lim-p 0.0009 20.0000 0.0002 2530.445938 0 0.0000 294 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 2530.445938 0 0.0000 314 Out... lnL = -2530.445938 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2530.445938 Node 7: lnL = -2530.445938 Node 8: lnL = -2530.445938 Node 9: lnL = -2530.445938 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 723 Sequential format.. Reading seq # 1: YOR065W_Sbay Reading seq # 2: YOR065W_Scer Reading seq # 3: YOR065W_Skud Reading seq # 4: YOR065W_Smik Reading seq # 5: YOR065W_Spar Sequences read.. Counting patterns.. # site patterns = 165 Counting frequencies.. 120 bytes for distance 26400 bytes for lkl0 21120 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.102304 0.027831 0.009863 0.086138 0.053239 0.103197 0.123418 0.038978 lnL0 = -2573.625000 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2573.625000 x= 0.10230 0.02783 0.00986 0.08614 0.05324 0.10320 0.12342 0.03898 1 h-lim-p 0.0012 0.5867 202.9789 2572.884276 4 0.0000 34 | 0/8 2 h-lim-p 0.0001 0.0012 40.5827 2572.801972 7 0.0001 64 | 0/8 3 h-lim-p 0.0004 0.0066 10.5007 2572.795141 4 0.0001 86 | 0/8 4 h-lim-p 0.0008 0.0546 1.7551 2572.794939 3 0.0001 107 | 0/8 5 h-lim-p 0.0005 0.3138 0.5009 2572.794923 2 0.0001 124 | 0/8 6 h-lim-p 0.0014 4.0104 0.0458 2572.794922 0 0.0003 145 | 0/8 7 h-lim-p 0.0013 13.0273 0.0114 2572.794922 0 0.0013 165 | 0/8 8 h-lim-p 0.0123 17.5152 0.0012 2572.794617 0 0.1974 189 | 0/8 9 h-lim-p 0.8591 20.0000 0.0003 2572.794605 1 1.0738 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2572.794605 0 2.1875 231 | 0/8 11 h-lim-p 2.2483 20.0000 0.0000 2572.794605 0 0.9836 251 | 0/8 12 h-lim-p 0.4533 20.0000 0.0000 2572.794605 0 0.0013 279 | 0/8 13 h-lim-p 0.0003 20.0000 0.0002 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0013 | 0/8 15 h-lim-p 0.0000 20.0000 0.0013 Out... lnL = -2572.794605 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2572.794605 Node 7: lnL = -2572.794605 Node 8: lnL = -2572.794605 Node 9: lnL = -2572.794605 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 838 Sequential format.. Reading seq # 1: YOR066W_Sbay Reading seq # 2: YOR066W_Scer Reading seq # 3: YOR066W_Skud Reading seq # 4: YOR066W_Smik Reading seq # 5: YOR066W_Spar Sequences read.. Counting patterns.. # site patterns = 211 Counting frequencies.. 120 bytes for distance 33760 bytes for lkl0 27008 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.113727 0.030591 0.035622 0.062269 0.045783 0.162900 0.109130 0.042352 lnL0 = -3090.890938 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3090.890938 x= 0.11373 0.03059 0.03562 0.06227 0.04578 0.16290 0.10913 0.04235 1 h-lim-p 0.0004 0.0029 256.0381 3088.631446 3 0.0001 29 | 0/8 2 h-lim-p 0.0004 0.0037 42.8715 3088.502709 5 0.0001 53 | 0/8 3 h-lim-p 0.0004 0.0106 15.2944 3088.491860 4 0.0001 74 | 0/8 4 h-lim-p 0.0003 0.0253 6.2391 3088.489508 4 0.0001 96 | 0/8 5 h-lim-p 0.0004 0.0505 2.3311 3088.489107 2 0.0002 112 | 0/8 6 h-lim-p 0.0008 0.4172 0.4645 3088.489087 0 0.0002 125 | 0/8 7 h-lim-p 0.0007 0.6169 0.1300 3088.489086 0 0.0001 146 | 0/8 8 h-lim-p 0.1348 20.0000 0.0001 3088.488949 0 1.0786 169 | 0/8 9 h-lim-p 1.2527 20.0000 0.0001 3088.488946 0 1.0961 189 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3088.488946 0 1.0938 209 | 0/8 11 h-lim-p 0.7377 20.0000 0.0000 3088.488946 0 1.4755 230 | 0/8 12 h-lim-p 0.1758 20.0000 0.0003 3088.488946 0 0.1538 250 | 0/8 13 h-lim-p 0.0370 20.0000 0.0012 3088.488946 0 0.0023 273 | 0/8 14 h-lim-p 0.0013 20.0000 0.0021 3088.488946 0 0.0001 296 | 0/8 15 h-lim-p 0.0003 20.0000 0.0008 3088.488946 0 0.0000 334 | 0/8 16 h-lim-p 0.0000 20.0000 0.0013 3088.488946 0 0.0001 357 | 0/8 17 h-lim-p 0.0002 20.0000 0.0006 3088.488946 0 0.0000 385 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 3088.488946 0 0.0038 413 | 0/8 19 h-lim-p 0.0105 20.0000 0.0001 3088.488946 0 0.0000 452 | 0/8 20 h-lim-p 0.0000 20.0000 0.0078 3088.488946 0 0.0000 484 | 0/8 21 h-lim-p 0.0000 20.0000 0.0023 3088.488946 0 0.0003 509 | 0/8 22 h-lim-p 0.0008 20.0000 0.0009 3088.488946 0 0.0000 535 | 0/8 23 h-lim-p 0.0000 20.0000 0.0002 3088.488946 0 0.0006 559 | 0/8 24 h-lim-p 0.0010 20.0000 0.0001 3088.488946 0 0.0021 580 | 0/8 25 h-lim-p 0.0040 20.0000 0.0001 3088.488946 0 0.0000 610 | 0/8 26 h-lim-p 0.0000 20.0000 0.0005 3088.488946 0 0.0000 630 | 0/8 27 h-lim-p 0.0000 5.6302 0.0322 3088.488946 0 0.0000 656 | 0/8 28 h-lim-p 0.0003 20.0000 0.0000 3088.488946 0 0.0000 691 Out... lnL = -3088.488946 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3088.488946 Node 7: lnL = -3088.488946 Node 8: lnL = -3088.488946 Node 9: lnL = -3088.488946 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 317 Sequential format.. Reading seq # 1: YOR067C_Sbay Reading seq # 2: YOR067C_Scer Reading seq # 3: YOR067C_Skud Reading seq # 4: YOR067C_Smik Reading seq # 5: YOR067C_Spar Sequences read.. Counting patterns.. # site patterns = 143 Counting frequencies.. 120 bytes for distance 22880 bytes for lkl0 18304 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.192526 0.100778 0.079534 0.150490 0.133870 0.131889 0.118884 0.072299 lnL0 = -1429.384304 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1429.384304 x= 0.19253 0.10078 0.07953 0.15049 0.13387 0.13189 0.11888 0.07230 1 h-lim-p 0.0014 0.0109 48.7919 1428.644481 4 0.0007 31 | 0/8 2 h-lim-p 0.0011 0.0088 20.3766 1428.510658 8 0.0007 63 | 0/8 3 h-lim-p 0.0034 0.0579 4.4196 1428.503384 2 0.0008 80 | 0/8 4 h-lim-p 0.0060 0.3745 0.5842 1428.503264 2 0.0007 98 | 0/8 5 h-lim-p 0.0066 3.7330 0.0620 1428.503262 0 0.0007 120 | 0/8 6 h-lim-p 0.0051 20.0000 0.0087 1428.503262 0 0.0011 141 | 0/8 7 h-lim-p 0.0213 20.0000 0.0005 1428.503239 0 0.5101 165 | 0/8 8 h-lim-p 0.0021 2.3028 0.1102 1428.503228 3 0.0013 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1428.503228 0 1.0938 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1428.503228 0 1.0938 233 | 0/8 11 h-lim-p 1.2389 20.0000 0.0000 1428.503228 0 1.8583 253 | 0/8 12 h-lim-p 1.3001 20.0000 0.0000 1428.503228 0 1.1376 273 | 0/8 13 h-lim-p 0.0447 20.0000 0.0002 1428.503228 0 0.0112 294 | 0/8 14 h-lim-p 0.0033 20.0000 0.0008 1428.503228 0 0.0000 336 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 1428.503228 0 0.0000 359 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 1428.503228 0 0.0000 425 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 1428.503228 0 0.0000 454 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1428.503228 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1428.503228 Node 7: lnL = -1428.503228 Node 8: lnL = -1428.503228 Node 9: lnL = -1428.503228 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 339 Sequential format.. Reading seq # 1: YOR069W_Sbay Reading seq # 2: YOR069W_Scer Reading seq # 3: YOR069W_Skud Reading seq # 4: YOR069W_Smik Reading seq # 5: YOR069W_Spar Sequences read.. Counting patterns.. # site patterns = 136 Counting frequencies.. 120 bytes for distance 21760 bytes for lkl0 17408 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.552083 0.855905 0.000060 1.022857 0.687010 2.654429 0.882582 0.130894 lnL0 = -1695.249761 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1695.249761 x= 0.55208 0.85591 0.00006 1.02286 0.68701 2.65443 0.88258 0.13089 1 h-lim-p 0.0000 0.0000 154.5892 1695.198055 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.1422 9.0154 .. | 1/8 3 h-lim-p 0.0000 0.0017 152.0597 1652.488583 m 0.0017 66 | 2/8 4 h-lim-p 0.0083 0.0666 12.7391 1644.139964 m 0.0666 78 | 3/8 5 h-lim-p 0.0021 0.0172 66.8637 1626.299707 0 0.0086 92 | 3/8 6 h-lim-p 0.0181 0.1444 24.4364 1613.547000 m 0.1444 104 | 4/8 7 h-lim-p 0.0098 0.0786 28.4384 1607.781342 0 0.0295 117 | 4/8 8 h-lim-p 0.1388 1.1101 4.5479 1563.038174 0 0.8326 131 | 3/8 9 h-lim-p 0.0001 0.0007 1776.3343 1561.534198 0 0.0001 143 | 3/8 10 h-lim-p 0.1809 1.4472 0.5469 1512.959059 m 1.4472 155 | 2/8 11 h-lim-p -0.0000 -0.0000 2.2408 h-lim-p: -3.62296833e-23 -2.89837466e-22 2.24084844e+00 1512.959059 .. | 2/8 12 h-lim-p 0.0000 0.0093 125.2158 1507.861171 0 0.0013 187 | 2/8 13 h-lim-p 0.0000 0.0001 159.2937 1506.624108 m 0.0001 199 | 3/8 14 h-lim-p 0.0004 0.0154 38.7892 1503.360863 0 0.0044 214 | 3/8 15 h-lim-p 0.0028 0.0222 9.2517 1501.824555 0 0.0111 228 | 3/8 16 h-lim-p 0.0221 1.2656 4.6438 1499.884803 0 0.1770 243 | 3/8 17 h-lim-p 0.1039 0.8316 1.0182 1493.617798 0 0.3118 256 | 2/8 18 h-lim-p 0.0052 0.0414 15.1907 1493.463709 5 0.0052 278 | 2/8 19 h-lim-p 0.1382 3.3234 0.5704 1492.104478 0 0.8292 292 | 1/8 20 h-lim-p 0.0202 0.1614 7.5736 1492.080761 5 0.0014 325 | 1/8 21 h-lim-p 0.0749 1.1337 0.1441 1491.974944 5 0.4788 351 | 1/8 22 h-lim-p 0.6943 5.5543 0.0162 1491.970777 2 0.6509 374 | 1/8 23 h-lim-p 2.4153 20.0000 0.0044 1491.970553 4 0.7113 403 | 0/8 24 h-lim-p 0.0267 8.1467 0.1163 1491.970547 1 0.0015 427 | 0/8 25 h-lim-p 0.2381 1.9045 0.0006 1491.970537 0 0.9523 449 | 0/8 26 h-lim-p 0.0674 0.5391 0.0002 1491.970537 0 0.0147 470 | 0/8 27 h-lim-p 0.0000 0.0001 1.6182 .. | 0/8 28 h-lim-p 0.0000 1.2814 0.0317 1491.970537 0 0.0006 521 | 0/8 29 h-lim-p 0.0009 0.0078 0.0234 1491.970537 0 0.0000 558 | 0/8 30 h-lim-p 0.0000 0.1197 0.0061 1491.970537 0 0.0002 582 | 0/8 31 h-lim-p 0.0003 0.7912 0.0030 1491.970537 0 0.0010 603 | 0/8 32 h-lim-p 0.0005 0.8146 0.0054 1491.970536 0 0.0174 628 | 0/8 33 h-lim-p 0.0274 0.4005 0.0034 .. | 0/8 34 h-lim-p 0.0000 0.0015 0.0524 1491.970536 0 0.0001 696 | 0/8 35 h-lim-p 0.0000 0.0004 0.1965 1491.970536 0 0.0000 726 | 0/8 36 h-lim-p 0.0000 0.0001 1.0858 .. | 0/8 37 h-lim-p 0.0000 0.0650 0.0057 1491.970536 0 0.0000 772 | 0/8 38 h-lim-p 0.0000 0.0005 1.2647 1491.970536 0 0.0000 798 | 0/8 39 h-lim-p 0.0001 20.0000 0.0018 1491.970536 0 0.0034 816 | 0/8 40 h-lim-p 0.0016 3.1285 0.0039 1491.970536 0 0.0065 838 | 0/8 41 h-lim-p 0.0078 20.0000 0.0032 1491.970536 0 0.0017 859 | 0/8 42 h-lim-p 0.0120 20.0000 0.0005 1491.970536 0 0.0718 881 | 0/8 43 h-lim-p 0.0868 20.0000 0.0004 1491.970536 0 0.0000 917 | 0/8 44 h-lim-p 0.0000 20.0000 0.0000 1491.970536 0 0.0000 942 | 0/8 45 h-lim-p 0.0000 0.0014 0.0498 1491.970536 0 0.0000 963 | 0/8 46 h-lim-p 0.0000 0.0002 0.3677 1491.970536 0 0.0000 991 | 0/8 47 h-lim-p 0.0000 0.0001 0.5657 1491.970536 0 0.0000 1024 | 0/8 48 h-lim-p 0.0000 0.0023 0.0494 .. | 0/8 49 h-lim-p 0.0000 0.0014 0.0494 | 0/8 50 h-lim-p 0.0000 0.0014 0.0494 Out... lnL = -1491.970536 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1491.970536 Node 7: lnL = -1491.970536 Node 8: lnL = -1491.970536 Node 9: lnL = -1491.970536 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 874 Sequential format.. Reading seq # 1: YOR070C_Sbay Reading seq # 2: YOR070C_Scer Reading seq # 3: YOR070C_Skud Reading seq # 4: YOR070C_Smik Reading seq # 5: YOR070C_Spar Sequences read.. Counting patterns.. # site patterns = 331 Counting frequencies.. 120 bytes for distance 52960 bytes for lkl0 42368 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.248927 0.021137 0.027943 0.227406 0.000060 0.251331 0.287075 0.115662 lnL0 = -3842.990033 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3842.990033 x= 0.24893 0.02114 0.02794 0.22741 0.00006 0.25133 0.28708 0.11566 1 h-lim-p 0.0000 0.0647 1607.3312 3817.117713 0 0.0001 23 | 0/8 2 h-lim-p 0.0008 0.0068 94.1127 3815.794809 6 0.0003 47 | 0/8 3 h-lim-p 0.0007 0.0081 42.7330 3815.218164 4 0.0007 67 | 0/8 4 h-lim-p 0.0014 0.0203 22.4205 3815.099997 3 0.0006 85 | 0/8 5 h-lim-p 0.0016 0.0302 8.6603 3815.073754 5 0.0008 109 | 0/8 6 h-lim-p 0.0043 0.1314 1.7070 3815.072625 4 0.0008 131 | 0/8 7 h-lim-p 0.0309 5.0063 0.0417 3815.066416 0 0.0619 144 | 0/8 8 h-lim-p 0.0067 0.2234 0.3869 3814.388757 0 0.0534 167 | 0/8 9 h-lim-p 1.8843 15.0743 0.0073 3814.357258 2 0.8833 191 | 0/8 10 h-lim-p 2.5000 20.0000 0.0010 3814.356103 3 1.0004 217 | 0/8 11 h-lim-p 2.5000 20.0000 0.0002 3814.356087 2 0.9644 241 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3814.356087 0 1.0938 261 | 0/8 13 h-lim-p 2.1992 20.0000 0.0000 3814.356087 0 0.9622 281 | 0/8 14 h-lim-p 0.7840 20.0000 0.0000 3814.356087 0 1.1760 301 | 0/8 15 h-lim-p 0.0819 20.0000 0.0002 3814.356087 0 0.0410 321 | 0/8 16 h-lim-p 0.0131 20.0000 0.0005 3814.356087 0 0.0016 343 | 0/8 17 h-lim-p 0.0002 20.0000 0.0045 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -3814.356087 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3814.356087 Node 7: lnL = -3814.356087 Node 8: lnL = -3814.356087 Node 9: lnL = -3814.356087 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 853 Sequential format.. Reading seq # 1: YOR073W_Sbay Reading seq # 2: YOR073W_Scer Reading seq # 3: YOR073W_Skud Reading seq # 4: YOR073W_Smik Reading seq # 5: YOR073W_Spar Sequences read.. Counting patterns.. # site patterns = 410 Counting frequencies.. 120 bytes for distance 65600 bytes for lkl0 52480 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.309229 0.047806 0.080527 0.188916 0.205801 0.332889 0.399335 0.113548 lnL0 = -4636.396228 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4636.396228 x= 0.30923 0.04781 0.08053 0.18892 0.20580 0.33289 0.39933 0.11355 1 h-lim-p 0.0026 0.7097 190.5834 4631.500601 3 0.0003 30 | 0/8 2 h-lim-p 0.0014 0.0111 22.0948 4631.346079 2 0.0007 46 | 0/8 3 h-lim-p 0.0013 0.0228 11.2397 4631.309685 6 0.0007 72 | 0/8 4 h-lim-p 0.0029 0.1854 2.6993 4631.306467 3 0.0009 92 | 0/8 5 h-lim-p 0.0023 0.3957 1.0889 4631.305993 2 0.0009 108 | 0/8 6 h-lim-p 0.0096 3.7146 0.1053 4631.305984 1 0.0012 124 | 0/8 7 h-lim-p 0.1382 20.0000 0.0009 4631.304697 0 1.1057 147 | 0/8 8 h-lim-p 0.0706 20.0000 0.0142 4631.304697 0 0.0010 172 | 0/8 9 h-lim-p 0.0500 20.0000 0.0003 4631.304683 0 0.8006 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4631.304683 0 1.0938 216 | 0/8 11 h-lim-p 1.7906 20.0000 0.0000 4631.304683 0 1.5668 236 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4631.304683 0 1.0938 256 | 0/8 13 h-lim-p 0.4448 20.0000 0.0000 4631.304683 0 0.0002 286 | 0/8 14 h-lim-p 0.0007 20.0000 0.0000 4631.304683 0 0.0000 317 Out... lnL = -4631.304683 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4631.304683 Node 7: lnL = -4631.304683 Node 8: lnL = -4631.304683 Node 9: lnL = -4631.304683 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 685 Sequential format.. Reading seq # 1: YOR075W_Sbay Reading seq # 2: YOR075W_Scer Reading seq # 3: YOR075W_Skud Reading seq # 4: YOR075W_Smik Reading seq # 5: YOR075W_Spar Sequences read.. Counting patterns.. # site patterns = 347 Counting frequencies.. 120 bytes for distance 55520 bytes for lkl0 44416 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.277140 0.200639 0.104602 0.219899 0.172766 0.284489 0.287720 0.066878 lnL0 = -3427.733322 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3427.733322 x= 0.27714 0.20064 0.10460 0.21990 0.17277 0.28449 0.28772 0.06688 1 h-lim-p 0.0065 0.0517 54.4754 3426.931569 7 0.0006 40 | 0/8 2 h-lim-p 0.0018 0.0150 16.8959 3426.817554 2 0.0009 56 | 0/8 3 h-lim-p 0.0020 0.0566 7.3274 3426.798488 5 0.0008 77 | 0/8 4 h-lim-p 0.0034 0.2775 1.8430 3426.797154 3 0.0008 96 | 0/8 5 h-lim-p 0.0032 0.3173 0.4842 3426.797058 3 0.0008 115 | 0/8 6 h-lim-p 0.0063 5.6761 0.0651 3426.797055 0 0.0014 136 | 0/8 7 h-lim-p 0.0098 20.0000 0.0092 3426.797052 0 0.0098 156 | 0/8 8 h-lim-p 0.0296 20.0000 0.0030 3426.796856 0 0.2372 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3426.796842 1 0.9961 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3426.796842 0 1.0938 221 | 0/8 11 h-lim-p 0.9651 20.0000 0.0000 3426.796842 0 0.9651 241 | 0/8 12 h-lim-p 0.0013 10.2671 0.0100 3426.796842 0 0.0000 272 | 0/8 13 h-lim-p 0.0003 20.0000 0.0000 3426.796842 0 0.0000 311 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 3426.796842 0 0.0000 333 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -3426.796842 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3426.796842 Node 7: lnL = -3426.796842 Node 8: lnL = -3426.796842 Node 9: lnL = -3426.796842 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 301 Sequential format.. Reading seq # 1: YOR076C_Sbay Reading seq # 2: YOR076C_Scer Reading seq # 3: YOR076C_Skud Reading seq # 4: YOR076C_Smik Reading seq # 5: YOR076C_Spar Sequences read.. Counting patterns.. # site patterns = 167 Counting frequencies.. 120 bytes for distance 26720 bytes for lkl0 21376 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.228053 0.190773 0.061259 0.149329 0.124379 0.236464 0.223376 0.061322 lnL0 = -1397.449142 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1397.449142 x= 0.22805 0.19077 0.06126 0.14933 0.12438 0.23646 0.22338 0.06132 1 h-lim-p 0.0113 2.1218 49.7685 1396.687811 3 0.0007 31 | 0/8 2 h-lim-p 0.0049 0.0397 6.5970 1396.666352 5 0.0010 53 | 0/8 3 h-lim-p 0.0023 0.0756 2.8086 1396.661020 5 0.0016 77 | 0/8 4 h-lim-p 0.0050 0.4379 0.8756 1396.660581 3 0.0012 96 | 0/8 5 h-lim-p 0.0051 0.6861 0.2152 1396.660543 3 0.0017 123 | 0/8 6 h-lim-p 0.0090 5.8598 0.0397 1396.660538 2 0.0029 148 | 0/8 7 h-lim-p 0.0195 20.0000 0.0058 1396.660137 0 0.2336 171 | 0/8 8 h-lim-p 0.0070 10.7308 0.1953 1396.659463 3 0.0072 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1396.659462 0 1.0938 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1396.659462 0 1.0938 237 | 0/8 11 h-lim-p 1.4216 20.0000 0.0000 1396.659462 0 1.4216 257 | 0/8 12 h-lim-p 1.0710 20.0000 0.0000 1396.659462 0 0.0669 280 | 0/8 13 h-lim-p 0.0010 20.0000 0.0006 1396.659462 0 0.0000 304 | 0/8 14 h-lim-p 0.0001 20.0000 0.0002 1396.659462 0 0.0001 324 | 0/8 15 h-lim-p 0.0001 20.0000 0.0003 1396.659462 0 0.0000 344 | 0/8 16 h-lim-p 0.0003 20.0000 0.0000 1396.659462 0 0.0000 376 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1396.659462 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1396.659462 Node 7: lnL = -1396.659462 Node 8: lnL = -1396.659462 Node 9: lnL = -1396.659462 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 305 Sequential format.. Reading seq # 1: YOR077W_Sbay Reading seq # 2: YOR077W_Scer Reading seq # 3: YOR077W_Skud Reading seq # 4: YOR077W_Smik Reading seq # 5: YOR077W_Spar Sequences read.. Counting patterns.. # site patterns = 163 Counting frequencies.. 120 bytes for distance 26080 bytes for lkl0 20864 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.241838 0.188150 0.064268 0.147106 0.126602 0.291601 0.202437 0.068476 lnL0 = -1480.981657 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1480.981657 x= 0.24184 0.18815 0.06427 0.14711 0.12660 0.29160 0.20244 0.06848 1 h-lim-p 0.0175 1.7297 41.1429 1480.446810 8 0.0007 46 | 0/8 2 h-lim-p 0.0037 0.0300 5.5604 1480.433005 2 0.0009 63 | 0/8 3 h-lim-p 0.0029 0.2237 1.6685 1480.431304 2 0.0014 79 | 0/8 4 h-lim-p 0.0038 0.6946 0.5949 1480.431049 2 0.0017 95 | 0/8 5 h-lim-p 0.0121 2.8866 0.0825 1480.431045 1 0.0012 119 | 0/8 6 h-lim-p 0.0055 18.1741 0.0180 1480.431045 0 0.0024 139 | 0/8 7 h-lim-p 0.0187 20.0000 0.0023 1480.431044 0 0.0187 159 | 0/8 8 h-lim-p 0.0284 20.0000 0.0015 1480.431027 0 0.1135 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1480.431027 0 1.0938 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1480.431027 0 1.0938 221 | 0/8 11 h-lim-p 1.2145 20.0000 0.0000 1480.431027 0 4.8581 243 | 0/8 12 h-lim-p 0.4057 20.0000 0.0001 1480.431027 0 0.1775 263 | 0/8 13 h-lim-p 0.0166 20.0000 0.0008 1480.431027 0 0.0000 299 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 1480.431027 0 0.0000 323 Out... lnL = -1480.431027 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1480.431027 Node 7: lnL = -1480.431027 Node 8: lnL = -1480.431027 Node 9: lnL = -1480.431027 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 212 Sequential format.. Reading seq # 1: YOR078W_Sbay Reading seq # 2: YOR078W_Scer Reading seq # 3: YOR078W_Skud Reading seq # 4: YOR078W_Smik Reading seq # 5: YOR078W_Spar Sequences read.. Counting patterns.. # site patterns = 62 Counting frequencies.. 120 bytes for distance 9920 bytes for lkl0 7936 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.157201 0.083326 0.065846 0.158258 0.099606 0.184175 0.000060 0.076359 lnL0 = -600.689988 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 600.689988 x= 0.15720 0.08333 0.06585 0.15826 0.09961 0.18417 0.00006 0.07636 1 h-lim-p 0.0003 0.0021 71.9253 598.069336 0 0.0010 24 | 0/8 2 h-lim-p 0.0009 0.0075 15.2040 597.925417 0 0.0019 37 | 0/8 3 h-lim-p 0.0023 0.0187 9.8370 597.884438 5 0.0011 60 | 0/8 4 h-lim-p 0.0068 0.1208 1.6385 597.881708 6 0.0021 88 | 0/8 5 h-lim-p 0.0022 0.1066 1.5307 597.878052 0 0.0045 101 | 0/8 6 h-lim-p 0.0039 0.0746 1.7789 597.876861 2 0.0017 117 | 0/8 7 h-lim-p 0.0282 5.2083 0.1062 597.876460 3 0.0109 135 | 0/8 8 h-lim-p 0.0189 2.5806 0.0612 597.847551 0 0.1510 158 | 0/8 9 h-lim-p 2.5000 20.0000 0.0025 597.844455 6 1.4742 193 | 0/8 10 h-lim-p 2.5000 20.0000 0.0005 597.844420 2 1.0889 217 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 597.844420 0 1.0938 237 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 597.844420 0 2.1875 257 | 0/8 13 h-lim-p 2.3652 20.0000 0.0000 597.844420 0 1.0348 277 | 0/8 14 h-lim-p 1.4016 20.0000 0.0000 597.844420 010.9095 300 | 0/8 15 h-lim-p 1.6442 20.0000 0.0000 597.844420 0 0.3597 321 | 0/8 16 h-lim-p 1.0535 20.0000 0.0000 597.844420 0 0.0062 348 | 0/8 17 h-lim-p 0.0472 20.0000 0.0000 597.844420 0 0.0000 383 Out... lnL = -597.844420 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -597.844420 Node 7: lnL = -597.844420 Node 8: lnL = -597.844420 Node 9: lnL = -597.844420 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 137 Sequential format.. Reading seq # 1: YOR079C_Sbay Reading seq # 2: YOR079C_Scer Reading seq # 3: YOR079C_Skud Reading seq # 4: YOR079C_Smik Reading seq # 5: YOR079C_Spar Sequences read.. Counting patterns.. # site patterns = 73 Counting frequencies.. 120 bytes for distance 11680 bytes for lkl0 9344 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.159299 0.093827 0.064000 0.142857 0.099929 0.216538 0.180428 0.032197 lnL0 = -638.480219 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 638.480219 x= 0.15930 0.09383 0.06400 0.14286 0.09993 0.21654 0.18043 0.03220 1 h-lim-p 0.0007 0.0053 26.4687 638.038212 0 0.0013 23 | 0/8 2 h-lim-p 0.0042 0.0337 5.6857 638.013503 5 0.0016 45 | 0/8 3 h-lim-p 0.0079 0.2839 1.1564 638.012149 5 0.0021 68 | 0/8 4 h-lim-p 0.0043 0.3104 0.5685 638.012000 4 0.0011 89 | 0/8 5 h-lim-p 0.0060 2.9373 0.1063 638.011987 3 0.0019 117 | 0/8 6 h-lim-p 0.0054 3.8883 0.0383 638.011970 1 0.0067 139 | 0/8 7 h-lim-p 0.0125 11.1060 0.0207 638.011397 0 0.0748 161 | 0/8 8 h-lim-p 0.0052 0.9005 0.2986 638.010478 1 0.0065 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 638.010467 2 0.9961 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 638.010467 0 2.1875 227 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 638.010467 0 1.0938 247 | 0/8 12 h-lim-p 0.2501 20.0000 0.0000 638.010467 0 6.0014 271 | 0/8 13 h-lim-p 1.0854 20.0000 0.0000 638.010467 0 1.0854 291 | 0/8 14 h-lim-p 0.0005 0.5929 0.0836 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 638.010467 0 0.0000 351 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0005 | 0/8 18 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -638.010467 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -638.010467 Node 7: lnL = -638.010467 Node 8: lnL = -638.010467 Node 9: lnL = -638.010467 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 179 Sequential format.. Reading seq # 1: YOR080W_Sbay Reading seq # 2: YOR080W_Scer Reading seq # 3: YOR080W_Skud Reading seq # 4: YOR080W_Smik Reading seq # 5: YOR080W_Spar Sequences read.. Counting patterns.. # site patterns = 97 Counting frequencies.. 120 bytes for distance 15520 bytes for lkl0 12416 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.157377 0.120544 0.067879 0.149021 0.093765 0.197413 0.146293 0.031467 lnL0 = -776.399842 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 776.399842 x= 0.15738 0.12054 0.06788 0.14902 0.09377 0.19741 0.14629 0.03147 1 h-lim-p 0.0005 0.0043 34.1043 775.766142 0 0.0011 23 | 0/8 2 h-lim-p 0.0036 0.0284 9.4150 775.702365 5 0.0015 44 | 0/8 3 h-lim-p 0.0050 0.0545 2.8898 775.699313 5 0.0008 69 | 0/8 4 h-lim-p 0.0039 0.3595 0.5916 775.699029 2 0.0017 85 | 0/8 5 h-lim-p 0.0098 1.4291 0.1029 775.699023 1 0.0011 109 | 0/8 6 h-lim-p 0.0089 18.2886 0.0124 775.699023 0 0.0020 130 | 0/8 7 h-lim-p 0.0223 20.0000 0.0011 775.699023 0 0.0195 150 | 0/8 8 h-lim-p 0.0151 20.0000 0.0014 775.699018 0 0.0908 172 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 775.699017 0 1.0938 192 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 775.699017 0 1.0938 212 | 0/8 11 h-lim-p 1.0836 20.0000 0.0000 775.699017 0 0.0148 237 | 0/8 12 h-lim-p 0.0015 20.0000 0.0001 775.699017 0 0.0000 265 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 775.699017 0 0.0000 287 Out... lnL = -775.699017 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -775.699017 Node 7: lnL = -775.699017 Node 8: lnL = -775.699017 Node 9: lnL = -775.699017 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 125 Sequential format.. Reading seq # 1: YOR081C_Sbay Reading seq # 2: YOR081C_Scer Reading seq # 3: YOR081C_Skud Reading seq # 4: YOR081C_Smik Reading seq # 5: YOR081C_Spar Sequences read.. Counting patterns.. # site patterns = 62 Counting frequencies.. 120 bytes for distance 9920 bytes for lkl0 7936 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.292476 0.052663 0.000060 0.095243 0.055370 0.221631 0.263448 0.162189 lnL0 = -494.925326 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 494.925326 x= 0.29248 0.05266 0.00006 0.09524 0.05537 0.22163 0.26345 0.16219 1 h-lim-p 0.0000 0.0000 38.0783 494.920774 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0549 5.5451 494.870458 0 0.0035 42 | 1/8 3 h-lim-p 0.0058 0.0465 3.2846 494.861027 6 0.0020 68 | 1/8 4 h-lim-p 0.0256 0.3191 0.2628 494.851425 5 0.0214 91 | 1/8 5 h-lim-p 0.0121 0.1754 0.4657 494.537913 0 0.0484 112 | 1/8 6 h-lim-p 0.0146 0.2204 1.5446 494.530735 4 0.0056 139 | 1/8 7 h-lim-p 0.0168 0.4991 0.5160 494.530322 4 0.0032 160 | 1/8 8 h-lim-p 0.2816 14.7964 0.0058 494.523895 0 0.8449 180 | 1/8 9 h-lim-p 2.5000 20.0000 0.0004 494.523838 4 0.9422 207 | 1/8 10 h-lim-p 2.5000 20.0000 0.0001 494.523838 1 0.6152 229 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 494.523838 0 1.0938 248 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 494.523838 0 1.0938 267 | 1/8 13 h-lim-p 2.0956 20.0000 0.0000 494.523838 0 0.0082 293 | 1/8 14 h-lim-p 0.0038 20.0000 0.0000 494.523838 0 0.0000 325 Out... lnL = -494.523838 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -494.523838 Node 7: lnL = -494.523838 Node 8: lnL = -494.523838 Node 9: lnL = -494.523838 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 380 Sequential format.. Reading seq # 1: YOR093C_Sbay Reading seq # 2: YOR093C_Scer Reading seq # 3: YOR093C_Skud Reading seq # 4: YOR093C_Smik Reading seq # 5: YOR093C_Spar Sequences read.. Counting patterns.. # site patterns = 184 Counting frequencies.. 120 bytes for distance 29440 bytes for lkl0 23552 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.213768 0.049903 0.052933 0.145096 0.041576 0.247940 0.223468 0.081904 lnL0 = -1642.140933 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1642.140933 x= 0.21377 0.04990 0.05293 0.14510 0.04158 0.24794 0.22347 0.08190 1 h-lim-p 0.0029 1.4424 106.4718 1640.458088 3 0.0003 30 | 0/8 2 h-lim-p 0.0009 0.0073 24.1345 1640.289629 6 0.0006 55 | 0/8 3 h-lim-p 0.0020 0.0489 7.1067 1640.271601 4 0.0008 75 | 0/8 4 h-lim-p 0.0018 0.0873 3.0734 1640.268224 2 0.0008 91 | 0/8 5 h-lim-p 0.0038 0.8070 0.6835 1640.268021 2 0.0009 108 | 0/8 6 h-lim-p 0.0068 3.1451 0.0948 1640.268017 1 0.0008 132 | 0/8 7 h-lim-p 0.0044 10.3789 0.0178 1640.268017 0 0.0019 152 | 0/8 8 h-lim-p 0.4851 20.0000 0.0001 1640.268012 0 0.9703 173 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1640.268012 0 1.2500 193 | 0/8 10 h-lim-p 2.2421 20.0000 0.0000 1640.268012 0 1.9618 213 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1640.268012 0 1.0938 233 | 0/8 12 h-lim-p 0.2156 20.0000 0.0000 1640.268012 0 6.8987 258 | 0/8 13 h-lim-p 0.7278 20.0000 0.0001 1640.268012 0 0.0455 281 | 0/8 14 h-lim-p 0.0007 20.0000 0.0047 1640.268012 0 0.0000 320 | 0/8 15 h-lim-p 0.0000 20.0000 0.0007 1640.268012 0 0.0000 354 | 0/8 16 h-lim-p 0.0000 20.0000 0.0007 | 0/8 17 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -1640.268012 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1640.268012 Node 7: lnL = -1640.268012 Node 8: lnL = -1640.268012 Node 9: lnL = -1640.268012 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 420 Sequential format.. Reading seq # 1: YOR094W_Sbay Reading seq # 2: YOR094W_Scer Reading seq # 3: YOR094W_Skud Reading seq # 4: YOR094W_Smik Reading seq # 5: YOR094W_Spar Sequences read.. Counting patterns.. # site patterns = 120 Counting frequencies.. 120 bytes for distance 19200 bytes for lkl0 15360 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.446291 0.058809 0.228983 0.274490 0.205023 4.324816 0.409089 0.000060 lnL0 = -1564.082034 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1564.082034 x= 0.44629 0.05881 0.22898 0.27449 0.20502 4.32482 0.40909 0.00006 1 h-lim-p 0.0000 0.0000 258.7765 1563.942710 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0066 55.9709 1555.777732 9 0.0043 65 | 1/8 3 h-lim-p 0.0016 0.0124 23.7762 1554.576127 0 0.0031 78 | 1/8 4 h-lim-p 0.0044 0.0350 12.6310 1553.129375 0 0.0087 91 | 1/8 5 h-lim-p 0.0030 0.0241 4.9707 1546.400650 m 0.0241 103 | 2/8 6 h-lim-p 0.0012 0.0099 37.3547 1534.606985 0 0.0049 117 | 2/8 7 h-lim-p 0.0019 0.0149 33.3304 1521.085404 0 0.0075 131 | 2/8 8 h-lim-p 0.2781 2.2248 0.1594 1520.222210 2 0.2607 147 | 1/8 9 h-lim-p 0.0023 0.0994 18.1869 1520.084706 4 0.0009 173 | 1/8 10 h-lim-p 0.1812 4.8397 0.0884 1519.909472 0 0.3624 186 | 1/8 11 h-lim-p 1.0850 8.6803 0.0106 1519.880687 5 0.5364 215 | 1/8 12 h-lim-p 0.6390 6.5399 0.0089 1519.877606 2 0.2995 238 | 1/8 13 h-lim-p 0.5500 20.0000 0.0049 1519.875524 3 0.6151 264 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 1519.875524 0 1.2500 283 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 1519.875524 0 1.0938 302 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 1519.875524 0 1.0938 321 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 1519.875524 0 0.1562 343 Out... lnL = -1519.875524 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1519.875524 Node 7: lnL = -1519.875524 Node 8: lnL = -1519.875524 Node 9: lnL = -1519.875524 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 864 Sequential format.. Reading seq # 1: YOR095C_Sbay Reading seq # 2: YOR095C_Scer Reading seq # 3: YOR095C_Skud Reading seq # 4: YOR095C_Smik Reading seq # 5: YOR095C_Spar Sequences read.. Counting patterns.. # site patterns = 350 Counting frequencies.. 120 bytes for distance 56000 bytes for lkl0 44800 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.275043 0.099408 0.072337 0.149007 0.103737 0.202194 0.327525 0.105924 lnL0 = -4163.199005 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4163.199005 x= 0.27504 0.09941 0.07234 0.14901 0.10374 0.20219 0.32753 0.10592 1 h-lim-p 0.0043 0.9285 139.3258 4161.216528 8 0.0002 42 | 0/8 2 h-lim-p 0.0011 0.0100 27.6710 4161.091198 7 0.0003 72 | 0/8 3 h-lim-p 0.0009 0.0289 10.5146 4161.072467 4 0.0004 91 | 0/8 4 h-lim-p 0.0013 0.0962 3.1422 4161.069269 5 0.0007 116 | 0/8 5 h-lim-p 0.0019 0.3341 1.1890 4161.068849 3 0.0007 135 | 0/8 6 h-lim-p 0.0025 0.8845 0.3210 4161.068828 2 0.0005 152 | 0/8 7 h-lim-p 0.0041 7.3489 0.0373 4161.068827 0 0.0010 173 | 0/8 8 h-lim-p 0.0819 20.0000 0.0005 4161.068538 0 0.9829 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4161.068534 0 1.0938 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4161.068534 0 1.0938 236 | 0/8 11 h-lim-p 1.5536 20.0000 0.0000 4161.068534 0 1.5536 256 | 0/8 12 h-lim-p 1.4929 20.0000 0.0000 4161.068534 0 0.0700 280 | 0/8 13 h-lim-p 0.0096 20.0000 0.0001 4161.068534 0 0.0006 303 | 0/8 14 h-lim-p 0.0003 20.0000 0.0001 4161.068534 0 0.0000 338 | 0/8 15 h-lim-p 0.0000 20.0000 0.0007 | 0/8 16 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -4161.068534 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4161.068534 Node 7: lnL = -4161.068534 Node 8: lnL = -4161.068534 Node 9: lnL = -4161.068534 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 717 Sequential format.. Reading seq # 1: YOR099W_Sbay Reading seq # 2: YOR099W_Scer Reading seq # 3: YOR099W_Skud Reading seq # 4: YOR099W_Smik Reading seq # 5: YOR099W_Spar Sequences read.. Counting patterns.. # site patterns = 248 Counting frequencies.. 120 bytes for distance 39680 bytes for lkl0 31744 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.182767 0.055454 0.051439 0.099913 0.101794 0.219776 0.193712 0.061411 lnL0 = -3000.067604 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3000.067604 x= 0.18277 0.05545 0.05144 0.09991 0.10179 0.21978 0.19371 0.06141 1 h-lim-p 0.0037 1.1282 127.5060 2998.780160 5 0.0002 37 | 0/8 2 h-lim-p 0.0015 0.0117 13.1755 2998.754929 4 0.0003 58 | 0/8 3 h-lim-p 0.0010 0.0760 4.0348 2998.752183 3 0.0004 76 | 0/8 4 h-lim-p 0.0009 0.1426 1.6609 2998.751790 4 0.0003 96 | 0/8 5 h-lim-p 0.0044 1.3508 0.1284 2998.751787 1 0.0003 113 | 0/8 6 h-lim-p 0.0015 8.8460 0.0226 2998.751787 0 0.0007 133 | 0/8 7 h-lim-p 0.0025 20.0000 0.0060 2998.751787 0 0.0006 154 | 0/8 8 h-lim-p 0.0273 20.0000 0.0001 2998.751786 0 0.8736 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2998.751786 0 1.0938 199 | 0/8 10 h-lim-p 0.5588 20.0000 0.0000 2998.751786 0 0.4890 219 | 0/8 11 h-lim-p 0.2103 20.0000 0.0000 2998.751786 0 0.0033 244 | 0/8 12 h-lim-p 0.0009 20.0000 0.0001 2998.751786 0 0.0001 267 | 0/8 13 h-lim-p 0.0005 20.0000 0.0000 2998.751786 0 0.0001 289 | 0/8 14 h-lim-p 0.0007 20.0000 0.0000 2998.751786 0 0.0000 317 Out... lnL = -2998.751786 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2998.751786 Node 7: lnL = -2998.751786 Node 8: lnL = -2998.751786 Node 9: lnL = -2998.751786 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 878 Sequential format.. Reading seq # 1: YOR100C_Sbay Reading seq # 2: YOR100C_Scer Reading seq # 3: YOR100C_Skud Reading seq # 4: YOR100C_Smik Reading seq # 5: YOR100C_Spar Sequences read.. Counting patterns.. # site patterns = 299 Counting frequencies.. 120 bytes for distance 47840 bytes for lkl0 38272 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.290395 0.020051 0.051150 0.088259 0.079891 0.185284 0.267565 0.151222 lnL0 = -3767.849359 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3767.849359 x= 0.29040 0.02005 0.05115 0.08826 0.07989 0.18528 0.26757 0.15122 1 h-lim-p 0.0002 0.0020 197.0238 3765.086643 9 0.0002 46 | 0/8 2 h-lim-p 0.0005 0.0037 35.5230 3764.955252 2 0.0002 62 | 0/8 3 h-lim-p 0.0004 0.0140 18.4814 3764.923885 7 0.0002 90 | 0/8 4 h-lim-p 0.0004 0.0293 11.1544 3764.903981 1 0.0005 104 | 0/8 5 h-lim-p 0.0009 0.0603 6.0798 3764.900158 5 0.0003 128 | 0/8 6 h-lim-p 0.0010 0.1272 1.7887 3764.899485 2 0.0005 144 | 0/8 7 h-lim-p 0.0026 1.2145 0.3464 3764.899454 1 0.0006 159 | 0/8 8 h-lim-p 0.4609 20.0000 0.0004 3764.899057 0 1.3826 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3764.899034 1 0.9961 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3764.899034 0 1.0938 222 | 0/8 11 h-lim-p 1.5669 20.0000 0.0000 3764.899034 0 0.6855 242 | 0/8 12 h-lim-p 0.3714 20.0000 0.0000 3764.899034 0 0.0464 264 | 0/8 13 h-lim-p 0.0145 20.0000 0.0000 3764.899034 0 0.0001 290 | 0/8 14 h-lim-p 0.0012 20.0000 0.0000 3764.899034 0 0.0005 310 Out... lnL = -3764.899034 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3764.899034 Node 7: lnL = -3764.899034 Node 8: lnL = -3764.899034 Node 9: lnL = -3764.899034 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 882 Sequential format.. Reading seq # 1: YOR101W_Sbay Reading seq # 2: YOR101W_Scer Reading seq # 3: YOR101W_Skud Reading seq # 4: YOR101W_Smik Reading seq # 5: YOR101W_Spar Sequences read.. Counting patterns.. # site patterns = 309 Counting frequencies.. 120 bytes for distance 49440 bytes for lkl0 39552 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.581620 0.000060 0.161271 0.106642 0.164829 0.145040 0.343999 0.370320 lnL0 = -4086.654688 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4086.654688 x= 0.58162 0.00006 0.16127 0.10664 0.16483 0.14504 0.34400 0.37032 1 h-lim-p 0.0000 0.0000 483.0194 4086.443607 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0005 592.4549 4052.128612 3 0.0003 45 | 1/8 3 h-lim-p 0.0006 0.0051 76.9219 4050.371794 2 0.0006 61 | 1/8 4 h-lim-p 0.0011 0.0088 35.2231 4049.947023 7 0.0008 89 | 1/8 5 h-lim-p 0.0007 0.0086 41.4390 4049.599456 6 0.0007 117 | 1/8 6 h-lim-p 0.0011 0.0478 27.1995 4049.446022 7 0.0007 147 | 1/8 7 h-lim-p 0.1071 1.2570 0.1727 4035.201409 0 0.4284 161 | 0/8 8 h-lim-p 0.0051 0.0471 14.5122 4035.159213 6 0.0004 197 | 0/8 9 h-lim-p 0.0469 0.6631 0.1219 4032.432173 8 0.3047 234 | 0/8 10 h-lim-p 1.9881 15.9048 0.0183 4032.250588 3 0.8310 260 | 0/8 11 h-lim-p 2.2569 20.0000 0.0068 4032.223030 6 1.4441 294 | 0/8 12 h-lim-p 1.8032 20.0000 0.0054 4032.213895 4 0.9464 323 | 0/8 13 h-lim-p 2.5000 20.0000 0.0006 4032.213586 4 0.7063 354 | 0/8 14 h-lim-p 2.5000 20.0000 0.0002 4032.213577 1 0.9961 376 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 4032.213577 0 1.0938 396 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 4032.213577 0 2.1875 416 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 4032.213577 0 1.0938 436 | 0/8 18 h-lim-p 0.6177 20.0000 0.0000 4032.213577 0 4.9416 459 | 0/8 19 h-lim-p 2.0721 20.0000 0.0000 4032.213577 0 0.1943 482 | 0/8 20 h-lim-p 0.6565 20.0000 0.0000 4032.213577 0 0.0010 511 Out... lnL = -4032.213577 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4032.213577 Node 7: lnL = -4032.213577 Node 8: lnL = -4032.213577 Node 9: lnL = -4032.213577 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 901 Sequential format.. Reading seq # 1: YOR103C_Sbay Reading seq # 2: YOR103C_Scer Reading seq # 3: YOR103C_Skud Reading seq # 4: YOR103C_Smik Reading seq # 5: YOR103C_Spar Sequences read.. Counting patterns.. # site patterns = 291 Counting frequencies.. 120 bytes for distance 46560 bytes for lkl0 37248 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.223316 0.069068 0.080898 0.146194 0.101291 0.217991 0.197039 0.074341 lnL0 = -4021.744208 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4021.744208 x= 0.22332 0.06907 0.08090 0.14619 0.10129 0.21799 0.19704 0.07434 1 h-lim-p 0.0040 0.9466 142.1679 4019.899523 4 0.0002 33 | 0/8 2 h-lim-p 0.0012 0.0116 24.1033 4019.791879 6 0.0004 58 | 0/8 3 h-lim-p 0.0007 0.0218 13.4071 4019.772630 4 0.0003 78 | 0/8 4 h-lim-p 0.0025 0.2112 1.4225 4019.772310 2 0.0003 96 | 0/8 5 h-lim-p 0.0019 1.1674 0.2325 4019.772297 0 0.0005 109 | 0/8 6 h-lim-p 0.0089 12.3448 0.0125 4019.772296 0 0.0019 130 | 0/8 7 h-lim-p 0.0059 20.0000 0.0042 4019.772270 0 0.0352 152 | 0/8 8 h-lim-p 0.0014 20.0000 0.1056 4019.772034 0 0.0028 173 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4019.772027 0 1.0938 193 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4019.772027 0 1.0938 213 | 0/8 11 h-lim-p 2.0236 20.0000 0.0000 4019.772027 0 0.8853 233 | 0/8 12 h-lim-p 0.4629 20.0000 0.0000 4019.772027 0 0.0145 257 | 0/8 13 h-lim-p 0.0025 20.0000 0.0002 4019.772027 0 0.0000 299 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -4019.772027 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4019.772027 Node 7: lnL = -4019.772027 Node 8: lnL = -4019.772027 Node 9: lnL = -4019.772027 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 894 Sequential format.. Reading seq # 1: YOR104W_Sbay Reading seq # 2: YOR104W_Scer Reading seq # 3: YOR104W_Skud Reading seq # 4: YOR104W_Smik Reading seq # 5: YOR104W_Spar Sequences read.. Counting patterns.. # site patterns = 291 Counting frequencies.. 120 bytes for distance 46560 bytes for lkl0 37248 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.236023 0.061407 0.085332 0.141210 0.079596 0.229696 0.209691 0.085010 lnL0 = -4009.842822 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4009.842822 x= 0.23602 0.06141 0.08533 0.14121 0.07960 0.22970 0.20969 0.08501 1 h-lim-p 0.0009 0.0075 131.9779 4008.149600 8 0.0002 40 | 0/8 2 h-lim-p 0.0009 0.0074 25.8786 4008.035535 6 0.0003 65 | 0/8 3 h-lim-p 0.0005 0.0155 18.2354 4008.008195 2 0.0002 81 | 0/8 4 h-lim-p 0.0008 0.0503 5.2963 4008.004494 4 0.0003 101 | 0/8 5 h-lim-p 0.0043 0.7657 0.3693 4008.004460 0 0.0005 115 | 0/8 6 h-lim-p 0.0055 8.9239 0.0315 4008.004459 0 0.0006 137 | 0/8 7 h-lim-p 0.0023 20.0000 0.0085 4008.004458 0 0.0045 158 | 0/8 8 h-lim-p 0.0061 20.0000 0.0063 4008.004151 0 0.0732 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4008.004141 1 0.9961 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4008.004141 0 1.0938 223 | 0/8 11 h-lim-p 1.0139 20.0000 0.0000 4008.004141 0 2.0277 244 | 0/8 12 h-lim-p 0.0214 20.0000 0.0016 4008.004141 0 0.0000 290 | 0/8 13 h-lim-p 0.0000 20.0000 0.0003 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -4008.004141 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4008.004141 Node 7: lnL = -4008.004141 Node 8: lnL = -4008.004141 Node 9: lnL = -4008.004141 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 650 Sequential format.. Reading seq # 1: YOR106W_Sbay Reading seq # 2: YOR106W_Scer Reading seq # 3: YOR106W_Skud Reading seq # 4: YOR106W_Smik Reading seq # 5: YOR106W_Spar Sequences read.. Counting patterns.. # site patterns = 287 Counting frequencies.. 120 bytes for distance 45920 bytes for lkl0 36736 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.319654 0.041936 0.040255 0.164759 0.157167 0.262076 0.380459 0.126798 lnL0 = -3175.491304 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3175.491304 x= 0.31965 0.04194 0.04025 0.16476 0.15717 0.26208 0.38046 0.12680 1 h-lim-p 0.0016 0.0130 109.9135 3173.714312 4 0.0003 31 | 0/8 2 h-lim-p 0.0004 0.0029 34.2610 3173.424127 0 0.0005 43 | 0/8 3 h-lim-p 0.0014 0.0198 13.6317 3173.358090 6 0.0008 72 | 0/8 4 h-lim-p 0.0012 0.0324 9.5211 3173.336324 5 0.0007 97 | 0/8 5 h-lim-p 0.0022 0.1467 2.9621 3173.331718 5 0.0012 121 | 0/8 6 h-lim-p 0.0088 0.8769 0.4174 3173.331655 2 0.0007 140 | 0/8 7 h-lim-p 0.0022 1.0818 0.1352 3173.331644 1 0.0011 163 | 0/8 8 h-lim-p 0.1117 20.0000 0.0013 3173.329384 0 0.8933 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 3173.329335 1 0.9961 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3173.329335 0 1.0938 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3173.329335 0 1.0938 248 | 0/8 12 h-lim-p 1.0379 20.0000 0.0000 3173.329335 0 3.1138 269 | 0/8 13 h-lim-p 0.2716 20.0000 0.0001 3173.329335 0 0.0679 290 | 0/8 14 h-lim-p 0.0120 20.0000 0.0005 3173.329335 0 0.0060 310 | 0/8 15 h-lim-p 0.0014 20.0000 0.0020 3173.329335 0 0.0014 330 | 0/8 16 h-lim-p 0.0016 20.0000 0.0017 3173.329335 0 0.0000 371 | 0/8 17 h-lim-p 0.0000 20.0000 0.0003 | 0/8 18 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -3173.329335 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3173.329335 Node 7: lnL = -3173.329335 Node 8: lnL = -3173.329335 Node 9: lnL = -3173.329335 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 833 Sequential format.. Reading seq # 1: YOR108W_Sbay Reading seq # 2: YOR108W_Scer Reading seq # 3: YOR108W_Skud Reading seq # 4: YOR108W_Smik Reading seq # 5: YOR108W_Spar Sequences read.. Counting patterns.. # site patterns = 293 Counting frequencies.. 120 bytes for distance 46880 bytes for lkl0 37504 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.228939 0.086166 0.057819 0.125898 0.108576 0.204669 0.214423 0.080709 lnL0 = -3632.560085 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3632.560085 x= 0.22894 0.08617 0.05782 0.12590 0.10858 0.20467 0.21442 0.08071 1 h-lim-p 0.0007 0.0058 113.8261 3631.229632 8 0.0002 43 | 0/8 2 h-lim-p 0.0007 0.0054 30.5449 3631.088994 2 0.0003 59 | 0/8 3 h-lim-p 0.0007 0.0219 13.5838 3631.060109 6 0.0004 83 | 0/8 4 h-lim-p 0.0009 0.0416 5.8827 3631.055033 3 0.0004 101 | 0/8 5 h-lim-p 0.0039 0.6055 0.5408 3631.054969 2 0.0004 119 | 0/8 6 h-lim-p 0.0017 1.2274 0.1384 3631.054966 1 0.0004 142 | 0/8 7 h-lim-p 0.0131 20.0000 0.0043 3631.054966 0 0.0016 164 | 0/8 8 h-lim-p 0.0198 20.0000 0.0004 3631.054942 0 0.3173 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3631.054942 0 1.0938 208 | 0/8 10 h-lim-p 1.4949 20.0000 0.0000 3631.054942 0 1.3081 228 | 0/8 11 h-lim-p 1.4415 20.0000 0.0000 3631.054942 0 0.0901 251 | 0/8 12 h-lim-p 0.0212 20.0000 0.0001 3631.054942 0 0.0000 282 | 0/8 13 h-lim-p 0.0007 20.0000 0.0000 3631.054942 0 0.0000 313 Out... lnL = -3631.054942 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3631.054942 Node 7: lnL = -3631.054942 Node 8: lnL = -3631.054942 Node 9: lnL = -3631.054942 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 499 Sequential format.. Reading seq # 1: YOR109W_Sbay Reading seq # 2: YOR109W_Scer Reading seq # 3: YOR109W_Skud Reading seq # 4: YOR109W_Smik Reading seq # 5: YOR109W_Spar Sequences read.. Counting patterns.. # site patterns = 140 Counting frequencies.. 120 bytes for distance 22400 bytes for lkl0 17920 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.471392 0.049621 0.348391 0.133568 0.305320 3.880365 0.418565 0.000060 lnL0 = -1905.402119 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1905.402119 x= 0.47139 0.04962 0.34839 0.13357 0.30532 3.88036 0.41857 0.00006 1 h-lim-p 0.0000 0.0000 366.9198 1905.279290 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0003 459.0359 1874.735243 m 0.0003 36 | 2/8 3 h-lim-p 0.0003 0.0024 143.8644 1853.580084 0 0.0018 50 | 2/8 4 h-lim-p 0.0005 0.0040 68.7650 1845.264298 0 0.0020 64 | 2/8 5 h-lim-p 0.0026 0.0211 15.1777 1828.117467 0 0.0106 78 | 2/8 6 h-lim-p 0.0068 0.0543 11.9507 1827.249634 7 0.0057 107 | 2/8 7 h-lim-p 0.0234 0.1940 2.9274 1811.978735 0 0.0938 121 | 1/8 8 h-lim-p 0.0117 0.0935 5.2441 1811.919886 7 0.0042 151 | 0/8 9 h-lim-p 0.0006 0.0139 39.2772 1811.663745 0 0.0011 164 | 0/8 10 h-lim-p 0.0565 0.4517 0.2971 1809.786958 0 0.3388 178 | 0/8 11 h-lim-p 0.7723 6.1786 0.0797 1809.630439 4 0.3933 207 | 0/8 12 h-lim-p 1.6042 19.1168 0.0195 1809.594487 2 0.7520 231 | 0/8 13 h-lim-p 2.5000 20.0000 0.0024 1809.593573 3 1.0449 257 | 0/8 14 h-lim-p 2.5000 20.0000 0.0004 1809.593536 2 0.7996 282 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1809.593535 0 1.0938 302 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1809.593535 0 1.0938 322 | 0/8 17 h-lim-p 2.1906 20.0000 0.0000 1809.593535 0 0.9584 342 | 0/8 18 h-lim-p 0.1953 20.0000 0.0000 1809.593535 0 0.0015 368 Out... lnL = -1809.593535 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1809.593535 Node 7: lnL = -1809.593535 Node 8: lnL = -1809.593535 Node 9: lnL = -1809.593535 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 422 Sequential format.. Reading seq # 1: YOR110W_Sbay Reading seq # 2: YOR110W_Scer Reading seq # 3: YOR110W_Skud Reading seq # 4: YOR110W_Smik Reading seq # 5: YOR110W_Spar Sequences read.. Counting patterns.. # site patterns = 212 Counting frequencies.. 120 bytes for distance 33920 bytes for lkl0 27136 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.327693 0.044914 0.113208 0.209321 0.083499 0.262363 0.339629 0.128101 lnL0 = -1993.745767 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1993.745767 x= 0.32769 0.04491 0.11321 0.20932 0.08350 0.26236 0.33963 0.12810 1 h-lim-p 0.0194 1.1928 45.3701 1993.117319 5 0.0006 36 | 0/8 2 h-lim-p 0.0014 0.0109 13.6770 1993.033932 7 0.0009 65 | 0/8 3 h-lim-p 0.0011 0.0317 12.2473 1992.974439 1 0.0013 79 | 0/8 4 h-lim-p 0.0080 0.1328 2.0297 1992.972050 4 0.0012 104 | 0/8 5 h-lim-p 0.0073 1.0221 0.3454 1992.971943 2 0.0019 121 | 0/8 6 h-lim-p 0.0211 8.4211 0.0313 1992.971940 1 0.0026 145 | 0/8 7 h-lim-p 0.0067 20.0000 0.0121 1992.971922 0 0.0202 166 | 0/8 8 h-lim-p 0.0092 20.0000 0.0265 1992.971461 0 0.0367 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1992.971451 1 1.0938 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1992.971451 0 1.0938 230 | 0/8 11 h-lim-p 2.1593 20.0000 0.0000 1992.971451 0 0.9447 250 | 0/8 12 h-lim-p 0.7532 20.0000 0.0000 1992.971451 0 0.0941 272 | 0/8 13 h-lim-p 0.0088 20.0000 0.0001 1992.971451 0 0.0000 313 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 1992.971451 0 0.0000 336 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1992.971451 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1992.971451 Node 7: lnL = -1992.971451 Node 8: lnL = -1992.971451 Node 9: lnL = -1992.971451 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 194 Sequential format.. Reading seq # 1: YOR111W_Sbay Reading seq # 2: YOR111W_Scer Reading seq # 3: YOR111W_Skud Reading seq # 4: YOR111W_Smik Reading seq # 5: YOR111W_Spar Sequences read.. Counting patterns.. # site patterns = 124 Counting frequencies.. 120 bytes for distance 19840 bytes for lkl0 15872 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.248331 0.142975 0.108998 0.140238 0.042479 0.321125 0.541720 0.033909 lnL0 = -938.061004 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 938.061004 x= 0.24833 0.14298 0.10900 0.14024 0.04248 0.32112 0.54172 0.03391 1 h-lim-p 0.0041 0.0331 59.1278 937.147987 8 0.0006 43 | 0/8 2 h-lim-p 0.0012 0.0095 17.8223 936.889549 0 0.0018 55 | 0/8 3 h-lim-p 0.0019 0.0149 5.6839 936.837279 0 0.0037 68 | 0/8 4 h-lim-p 0.0108 0.0990 1.9634 936.833099 3 0.0024 87 | 0/8 5 h-lim-p 0.0100 1.1778 0.4819 936.832798 5 0.0028 112 | 0/8 6 h-lim-p 0.0051 0.2454 0.2620 936.832704 4 0.0034 143 | 0/8 7 h-lim-p 0.0527 20.0000 0.0171 936.832698 2 0.0203 167 | 0/8 8 h-lim-p 0.1440 20.0000 0.0024 936.832550 0 0.5760 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 936.832533 2 0.9961 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 936.832533 0 2.1875 233 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 936.832533 0 1.0938 253 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 936.832533 0 1.0938 273 | 0/8 13 h-lim-p 1.1152 20.0000 0.0000 936.832533 0 8.9217 296 | 0/8 14 h-lim-p 0.4925 20.0000 0.0001 936.832533 0 0.0077 321 | 0/8 15 h-lim-p 0.0004 20.0000 0.0015 936.832533 0 0.0000 355 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 936.832533 0 0.0000 375 Out... lnL = -936.832533 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -936.832533 Node 7: lnL = -936.832533 Node 8: lnL = -936.832533 Node 9: lnL = -936.832533 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 825 Sequential format.. Reading seq # 1: YOR114W_Sbay Reading seq # 2: YOR114W_Scer Reading seq # 3: YOR114W_Skud Reading seq # 4: YOR114W_Smik Reading seq # 5: YOR114W_Spar Sequences read.. Counting patterns.. # site patterns = 275 Counting frequencies.. 120 bytes for distance 44000 bytes for lkl0 35200 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.148452 0.156464 0.072961 0.108702 0.075865 0.139578 0.205627 0.017711 lnL0 = -3399.906539 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3399.906539 x= 0.14845 0.15646 0.07296 0.10870 0.07587 0.13958 0.20563 0.01771 1 h-lim-p 0.0046 1.1940 121.4117 3397.937548 4 0.0003 33 | 0/8 2 h-lim-p 0.0002 0.0020 59.5812 3397.469008 0 0.0004 45 | 0/8 3 h-lim-p 0.0004 0.0033 29.0186 3397.394859 6 0.0002 70 | 0/8 4 h-lim-p 0.0010 0.0449 6.2960 3397.388911 5 0.0003 96 | 0/8 5 h-lim-p 0.0007 0.0223 2.7925 3397.387873 2 0.0003 112 | 0/8 6 h-lim-p 0.0067 1.7248 0.1317 3397.387829 1 0.0017 127 | 0/8 7 h-lim-p 0.0170 16.8131 0.0131 3397.379714 0 0.1358 150 | 0/8 8 h-lim-p 0.0005 0.5674 3.7861 3397.370245 1 0.0006 172 | 0/8 9 h-lim-p 2.1714 20.0000 0.0010 3397.369988 2 1.0772 188 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 3397.369987 0 1.0938 208 | 0/8 11 h-lim-p 1.4452 20.0000 0.0000 3397.369987 0 1.4452 228 | 0/8 12 h-lim-p 0.8043 20.0000 0.0001 3397.369987 0 0.2011 249 | 0/8 13 h-lim-p 0.0043 7.6638 0.0036 3397.369987 0 0.0000 284 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 3397.369987 0 0.0000 310 Out... lnL = -3397.369987 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3397.369987 Node 7: lnL = -3397.369987 Node 8: lnL = -3397.369987 Node 9: lnL = -3397.369987 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 840 Sequential format.. Reading seq # 1: YOR117W_Sbay Reading seq # 2: YOR117W_Scer Reading seq # 3: YOR117W_Skud Reading seq # 4: YOR117W_Smik Reading seq # 5: YOR117W_Spar Sequences read.. Counting patterns.. # site patterns = 273 Counting frequencies.. 120 bytes for distance 43680 bytes for lkl0 34944 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.197447 0.108534 0.047275 0.154810 0.118133 0.246844 0.191951 0.040736 lnL0 = -3961.742052 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3961.742052 x= 0.19745 0.10853 0.04728 0.15481 0.11813 0.24684 0.19195 0.04074 1 h-lim-p 0.0008 0.0063 177.5050 3959.103457 3 0.0002 29 | 0/8 2 h-lim-p 0.0005 0.0041 41.7277 3958.832771 8 0.0003 61 | 0/8 3 h-lim-p 0.0011 0.0180 12.1388 3958.813588 4 0.0003 82 | 0/8 4 h-lim-p 0.0017 0.1501 2.0453 3958.812694 3 0.0004 101 | 0/8 5 h-lim-p 0.0031 0.7382 0.2920 3958.812680 0 0.0003 115 | 0/8 6 h-lim-p 0.0012 6.3380 0.0799 3958.812679 0 0.0005 135 | 0/8 7 h-lim-p 0.0033 18.1329 0.0132 3958.812679 0 0.0016 155 | 0/8 8 h-lim-p 0.0290 20.0000 0.0007 3958.812499 0 0.4636 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3958.812489 1 0.9961 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3958.812489 0 1.0938 221 | 0/8 11 h-lim-p 0.6504 20.0000 0.0001 3958.812489 0 0.0406 244 | 0/8 12 h-lim-p 0.0033 20.0000 0.0007 3958.812489 0 0.0000 272 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 3958.812489 0 0.0000 304 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -3958.812489 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3958.812489 Node 7: lnL = -3958.812489 Node 8: lnL = -3958.812489 Node 9: lnL = -3958.812489 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 546 Sequential format.. Reading seq # 1: YOR118W_Sbay Reading seq # 2: YOR118W_Scer Reading seq # 3: YOR118W_Skud Reading seq # 4: YOR118W_Smik Reading seq # 5: YOR118W_Spar Sequences read.. Counting patterns.. # site patterns = 209 Counting frequencies.. 120 bytes for distance 33440 bytes for lkl0 26752 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.174061 0.102516 0.086517 0.085422 0.073406 0.217769 0.147111 0.038976 lnL0 = -2326.216291 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2326.216291 x= 0.17406 0.10252 0.08652 0.08542 0.07341 0.21777 0.14711 0.03898 1 h-lim-p 0.0137 1.9193 58.2697 2325.739431 7 0.0003 43 | 0/8 2 h-lim-p 0.0012 0.0099 14.1507 2325.714743 4 0.0003 63 | 0/8 3 h-lim-p 0.0006 0.0242 5.6721 2325.708644 6 0.0004 91 | 0/8 4 h-lim-p 0.0020 0.3266 1.2565 2325.708286 2 0.0005 108 | 0/8 5 h-lim-p 0.0014 0.2353 0.4252 2325.708243 2 0.0006 124 | 0/8 6 h-lim-p 0.0038 3.9123 0.0630 2325.708242 1 0.0005 148 | 0/8 7 h-lim-p 0.0012 7.0312 0.0236 2325.708242 0 0.0005 168 | 0/8 8 h-lim-p 0.0724 20.0000 0.0002 2325.708201 0 1.1592 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2325.708200 0 1.0938 212 | 0/8 10 h-lim-p 1.8604 20.0000 0.0000 2325.708200 0 0.8139 232 | 0/8 11 h-lim-p 0.6333 20.0000 0.0000 2325.708200 0 0.3166 252 | 0/8 12 h-lim-p 0.1322 20.0000 0.0001 2325.708200 0 0.0018 277 | 0/8 13 h-lim-p 0.0007 20.0000 0.0002 2325.708200 0 0.0000 313 | 0/8 14 h-lim-p 0.0000 20.0000 0.0011 | 0/8 15 h-lim-p 0.0000 20.0000 0.0011 Out... lnL = -2325.708200 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2325.708200 Node 7: lnL = -2325.708200 Node 8: lnL = -2325.708200 Node 9: lnL = -2325.708200 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 878 Sequential format.. Reading seq # 1: YOR119C_Sbay Reading seq # 2: YOR119C_Scer Reading seq # 3: YOR119C_Skud Reading seq # 4: YOR119C_Smik Reading seq # 5: YOR119C_Spar Sequences read.. Counting patterns.. # site patterns = 315 Counting frequencies.. 120 bytes for distance 50400 bytes for lkl0 40320 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.220321 0.142387 0.095358 0.134673 0.092376 0.273121 0.198752 0.045390 lnL0 = -4102.408482 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4102.408482 x= 0.22032 0.14239 0.09536 0.13467 0.09238 0.27312 0.19875 0.04539 1 h-lim-p 0.0131 2.0082 79.1091 4101.635404 8 0.0003 48 | 0/8 2 h-lim-p 0.0009 0.0084 21.6304 4101.574607 5 0.0003 73 | 0/8 3 h-lim-p 0.0006 0.0191 10.1741 4101.555862 5 0.0004 96 | 0/8 4 h-lim-p 0.0018 0.1070 2.4474 4101.554615 2 0.0005 113 | 0/8 5 h-lim-p 0.0015 0.3746 0.7493 4101.554497 3 0.0005 133 | 0/8 6 h-lim-p 0.0052 4.7527 0.0687 4101.554495 1 0.0006 157 | 0/8 7 h-lim-p 0.0164 20.0000 0.0027 4101.554495 0 0.0018 179 | 0/8 8 h-lim-p 0.0088 20.0000 0.0005 4101.554479 0 0.2101 203 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4101.554479 0 1.0938 223 | 0/8 10 h-lim-p 1.0991 20.0000 0.0000 4101.554479 0 2.1982 244 | 0/8 11 h-lim-p 0.3003 20.0000 0.0002 4101.554479 0 0.0188 267 | 0/8 12 h-lim-p 0.0026 20.0000 0.0013 4101.554479 0 0.0000 310 | 0/8 13 h-lim-p 0.0000 20.0000 0.0009 | 0/8 14 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -4101.554479 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4101.554479 Node 7: lnL = -4101.554479 Node 8: lnL = -4101.554479 Node 9: lnL = -4101.554479 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 877 Sequential format.. Reading seq # 1: YOR120W_Sbay Reading seq # 2: YOR120W_Scer Reading seq # 3: YOR120W_Skud Reading seq # 4: YOR120W_Smik Reading seq # 5: YOR120W_Spar Sequences read.. Counting patterns.. # site patterns = 316 Counting frequencies.. 120 bytes for distance 50560 bytes for lkl0 40448 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.229450 0.166905 0.084343 0.128931 0.108558 0.275389 0.209678 0.047253 lnL0 = -4148.639446 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4148.639446 x= 0.22945 0.16690 0.08434 0.12893 0.10856 0.27539 0.20968 0.04725 1 h-lim-p 0.0046 0.0368 63.6022 4148.097223 2 0.0003 29 | 0/8 2 h-lim-p 0.0011 0.0119 15.4524 4148.060896 6 0.0003 57 | 0/8 3 h-lim-p 0.0006 0.0206 8.6507 4148.049948 4 0.0004 79 | 0/8 4 h-lim-p 0.0019 0.1648 1.7119 4148.049309 2 0.0005 96 | 0/8 5 h-lim-p 0.0012 0.4280 0.6653 4148.049210 1 0.0005 110 | 0/8 6 h-lim-p 0.0143 15.3281 0.0248 4148.049210 0 0.0016 132 | 0/8 7 h-lim-p 0.0021 7.2129 0.0184 4148.049208 0 0.0018 152 | 0/8 8 h-lim-p 0.0114 20.0000 0.0030 4148.048958 0 0.1820 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4148.048931 1 0.9961 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4148.048931 0 2.1875 218 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4148.048931 0 1.0938 238 | 0/8 12 h-lim-p 0.2168 20.0000 0.0001 4148.048931 0 0.0474 259 | 0/8 13 h-lim-p 0.0056 20.0000 0.0005 4148.048931 0 0.0014 280 | 0/8 14 h-lim-p 0.0000 2.0585 0.0323 4148.048931 0 0.0000 305 | 0/8 15 h-lim-p 0.0006 20.0000 0.0000 4148.048931 0 0.0000 334 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 4148.048931 0 0.0000 363 Out... lnL = -4148.048931 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4148.048931 Node 7: lnL = -4148.048931 Node 8: lnL = -4148.048931 Node 9: lnL = -4148.048931 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 415 Sequential format.. Reading seq # 1: YOR124C_Sbay Reading seq # 2: YOR124C_Scer Reading seq # 3: YOR124C_Skud Reading seq # 4: YOR124C_Smik Reading seq # 5: YOR124C_Spar Sequences read.. Counting patterns.. # site patterns = 149 Counting frequencies.. 120 bytes for distance 23840 bytes for lkl0 19072 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.154137 0.063851 0.087855 0.115143 0.050264 0.168203 0.153713 0.034511 lnL0 = -1724.468360 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1724.468360 x= 0.15414 0.06385 0.08786 0.11514 0.05026 0.16820 0.15371 0.03451 1 h-lim-p 0.0003 0.0022 48.8400 1724.146163 3 0.0003 28 | 0/8 2 h-lim-p 0.0010 0.0380 13.8219 1724.126790 2 0.0002 45 | 0/8 3 h-lim-p 0.0007 0.0256 4.2592 1724.122937 6 0.0005 72 | 0/8 4 h-lim-p 0.0019 0.2276 1.0317 1724.122693 2 0.0005 89 | 0/8 5 h-lim-p 0.0096 3.3240 0.0546 1724.122692 0 0.0005 104 | 0/8 6 h-lim-p 0.0082 20.0000 0.0035 1724.122691 0 0.0082 124 | 0/8 7 h-lim-p 0.0014 7.4757 0.0198 1724.122673 0 0.0058 146 | 0/8 8 h-lim-p 0.0018 1.2602 0.0641 1724.122573 0 0.0036 167 | 0/8 9 h-lim-p 0.8137 20.0000 0.0003 1724.122572 0 0.8137 187 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1724.122572 0 1.0938 207 | 0/8 11 h-lim-p 1.1394 20.0000 0.0000 1724.122572 0 0.5697 227 | 0/8 12 h-lim-p 0.3484 20.0000 0.0000 1724.122572 0 0.0871 248 | 0/8 13 h-lim-p 0.0399 20.0000 0.0001 1724.122572 0 0.0199 268 | 0/8 14 h-lim-p 0.0109 20.0000 0.0001 1724.122572 0 0.0000 296 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 1724.122572 0 0.0000 327 | 0/8 16 h-lim-p 0.0000 20.0000 0.0016 1724.122572 0 0.0000 362 | 0/8 17 h-lim-p 0.0000 20.0000 0.0016 | 0/8 18 h-lim-p 0.0000 20.0000 0.0016 Out... lnL = -1724.122572 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1724.122572 Node 7: lnL = -1724.122572 Node 8: lnL = -1724.122572 Node 9: lnL = -1724.122572 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 534 Sequential format.. Reading seq # 1: YOR126C_Sbay Reading seq # 2: YOR126C_Scer Reading seq # 3: YOR126C_Skud Reading seq # 4: YOR126C_Smik Reading seq # 5: YOR126C_Spar Sequences read.. Counting patterns.. # site patterns = 184 Counting frequencies.. 120 bytes for distance 29440 bytes for lkl0 23552 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.191813 0.044986 0.021540 0.118335 0.053647 0.809484 0.098664 0.009006 lnL0 = -2342.301598 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2342.301598 x= 0.19181 0.04499 0.02154 0.11834 0.05365 0.80948 0.09866 0.00901 1 h-lim-p 0.0012 0.0093 72.6123 2342.011419 6 0.0001 37 | 0/8 2 h-lim-p 0.0005 0.0048 18.5052 2341.949893 5 0.0004 60 | 0/8 3 h-lim-p 0.0008 0.0074 8.4763 2341.929097 3 0.0007 78 | 0/8 4 h-lim-p 0.0029 0.1553 2.0107 2341.928042 3 0.0006 97 | 0/8 5 h-lim-p 0.0003 0.0854 3.9042 2341.925897 0 0.0009 110 | 0/8 6 h-lim-p 0.0005 0.0377 6.6655 2341.923626 3 0.0005 128 | 0/8 7 h-lim-p 0.0182 1.6197 0.1903 2341.923620 1 0.0003 147 | 0/8 8 h-lim-p 0.1115 20.0000 0.0005 2341.923439 0 0.8919 170 | 0/8 9 h-lim-p 1.4147 20.0000 0.0003 2341.923430 2 0.9049 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2341.923430 0 1.0938 215 | 0/8 11 h-lim-p 1.0246 20.0000 0.0000 2341.923430 0 2.0492 236 | 0/8 12 h-lim-p 1.5638 20.0000 0.0000 2341.923430 0 0.3909 257 | 0/8 13 h-lim-p 0.0498 20.0000 0.0003 2341.923430 0 0.0000 286 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 2341.923430 0 0.0000 313 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 2341.923430 0 0.0000 340 Out... lnL = -2341.923430 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2341.923430 Node 7: lnL = -2341.923430 Node 8: lnL = -2341.923430 Node 9: lnL = -2341.923430 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 532 Sequential format.. Reading seq # 1: YOR127W_Sbay Reading seq # 2: YOR127W_Scer Reading seq # 3: YOR127W_Skud Reading seq # 4: YOR127W_Smik Reading seq # 5: YOR127W_Spar Sequences read.. Counting patterns.. # site patterns = 171 Counting frequencies.. 120 bytes for distance 27360 bytes for lkl0 21888 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.150030 0.029816 0.032357 0.115682 0.056301 0.306230 0.118202 0.034312 lnL0 = -2166.215906 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2166.215906 x= 0.15003 0.02982 0.03236 0.11568 0.05630 0.30623 0.11820 0.03431 1 h-lim-p 0.0006 0.0049 100.0657 2165.439978 7 0.0002 38 | 0/8 2 h-lim-p 0.0002 0.0012 49.7960 2165.214354 0 0.0002 50 | 0/8 3 h-lim-p 0.0006 0.0103 19.0028 2165.165006 5 0.0003 73 | 0/8 4 h-lim-p 0.0005 0.0116 13.5003 2165.142226 5 0.0004 97 | 0/8 5 h-lim-p 0.0006 0.0145 8.8662 2165.135095 4 0.0003 118 | 0/8 6 h-lim-p 0.0025 0.0792 1.0089 2165.134939 3 0.0003 138 | 0/8 7 h-lim-p 0.0633 20.0000 0.0049 2165.134872 3 0.0408 158 | 0/8 8 h-lim-p 0.0017 2.2875 0.1151 2165.133446 0 0.0070 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2165.133444 0 1.0938 200 | 0/8 10 h-lim-p 1.4680 20.0000 0.0000 2165.133444 0 1.2845 220 | 0/8 11 h-lim-p 1.8089 20.0000 0.0000 2165.133444 0 0.3957 241 | 0/8 12 h-lim-p 0.1365 20.0000 0.0001 2165.133444 0 0.0021 266 | 0/8 13 h-lim-p 0.0008 20.0000 0.0002 2165.133444 0 0.0001 288 | 0/8 14 h-lim-p 0.0001 20.0000 0.0001 2165.133444 0 0.0000 322 | 0/8 15 h-lim-p 0.0000 20.0000 0.0020 | 0/8 16 h-lim-p 0.0000 20.0000 0.0020 Out... lnL = -2165.133444 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2165.133444 Node 7: lnL = -2165.133444 Node 8: lnL = -2165.133444 Node 9: lnL = -2165.133444 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 726 Sequential format.. Reading seq # 1: YOR128C_Sbay Reading seq # 2: YOR128C_Scer Reading seq # 3: YOR128C_Skud Reading seq # 4: YOR128C_Smik Reading seq # 5: YOR128C_Spar Sequences read.. Counting patterns.. # site patterns = 336 Counting frequencies.. 120 bytes for distance 53760 bytes for lkl0 43008 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.285451 0.106575 0.074072 0.173854 0.167710 0.299193 0.616797 0.039989 lnL0 = -3852.554833 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3852.554833 x= 0.28545 0.10657 0.07407 0.17385 0.16771 0.29919 0.61680 0.03999 1 h-lim-p 0.0016 0.0128 80.3503 3851.315998 8 0.0004 41 | 0/8 2 h-lim-p 0.0008 0.0067 26.7730 3851.099622 4 0.0007 61 | 0/8 3 h-lim-p 0.0010 0.0081 13.9924 3851.026075 2 0.0009 77 | 0/8 4 h-lim-p 0.0016 0.0438 8.2390 3851.008915 2 0.0007 93 | 0/8 5 h-lim-p 0.0024 0.1439 2.4718 3851.003633 4 0.0020 115 | 0/8 6 h-lim-p 0.0046 0.4145 1.0839 3851.003189 3 0.0009 134 | 0/8 7 h-lim-p 0.0022 0.4445 0.4454 3851.003109 2 0.0010 150 | 0/8 8 h-lim-p 0.6641 20.0000 0.0007 3851.002760 0 1.3282 171 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3851.002751 1 0.9961 193 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3851.002751 0 2.1875 213 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3851.002751 0 1.0938 233 | 0/8 12 h-lim-p 0.1660 20.0000 0.0000 3851.002751 0 0.0052 257 | 0/8 13 h-lim-p 0.0005 20.0000 0.0002 3851.002751 0 0.0000 281 | 0/8 14 h-lim-p 0.0004 20.0000 0.0000 3851.002751 0 0.0000 307 Out... lnL = -3851.002751 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3851.002751 Node 7: lnL = -3851.002751 Node 8: lnL = -3851.002751 Node 9: lnL = -3851.002751 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 821 Sequential format.. Reading seq # 1: YOR130C_Sbay Reading seq # 2: YOR130C_Scer Reading seq # 3: YOR130C_Skud Reading seq # 4: YOR130C_Smik Reading seq # 5: YOR130C_Spar Sequences read.. Counting patterns.. # site patterns = 315 Counting frequencies.. 120 bytes for distance 50400 bytes for lkl0 40320 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.407420 0.088018 0.142174 0.253113 0.220032 0.010366 0.369418 0.172057 lnL0 = -4053.839453 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4053.839453 x= 0.40742 0.08802 0.14217 0.25311 0.22003 0.01037 0.36942 0.17206 1 h-lim-p 0.0001 0.1009 997.9770 4016.104035 0 0.0002 23 | 0/8 2 h-lim-p 0.0013 0.0107 17.2925 4015.918673 2 0.0013 39 | 0/8 3 h-lim-p 0.0010 0.0095 22.4864 4015.700753 0 0.0019 52 | 0/8 4 h-lim-p 0.0036 0.0497 12.0262 4015.663623 2 0.0008 69 | 0/8 5 h-lim-p 0.0043 0.2127 2.3607 4015.659145 4 0.0017 89 | 0/8 6 h-lim-p 0.0067 0.8651 0.5933 4015.658387 3 0.0028 107 | 0/8 7 h-lim-p 0.0933 20.0000 0.0179 4015.369071 0 1.4923 131 | 0/8 8 h-lim-p 0.0026 0.0445 10.0952 4015.121399 3 0.0027 157 | 0/8 9 h-lim-p 0.9765 7.8117 0.0258 4014.851407 0 1.9529 170 | 0/8 10 h-lim-p 2.5000 20.0000 0.0041 4014.844971 4 1.0199 199 | 0/8 11 h-lim-p 2.5000 20.0000 0.0004 4014.844931 0 1.0938 219 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4014.844931 0 1.0938 239 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 4014.844931 0 1.0938 259 | 0/8 14 h-lim-p 1.2351 20.0000 0.0000 4014.844931 0 1.2351 279 | 0/8 15 h-lim-p 0.3686 20.0000 0.0000 4014.844931 0 0.0115 303 | 0/8 16 h-lim-p 0.0006 20.0000 0.0003 4014.844931 0 0.0000 340 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -4014.844931 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4014.844931 Node 7: lnL = -4014.844931 Node 8: lnL = -4014.844931 Node 9: lnL = -4014.844931 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 660 Sequential format.. Reading seq # 1: YOR137C_Sbay Reading seq # 2: YOR137C_Scer Reading seq # 3: YOR137C_Skud Reading seq # 4: YOR137C_Smik Reading seq # 5: YOR137C_Spar Sequences read.. Counting patterns.. # site patterns = 180 Counting frequencies.. 120 bytes for distance 28800 bytes for lkl0 23040 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.184550 0.038111 0.051885 0.076871 0.050539 0.174097 0.164674 0.071107 lnL0 = -2688.067923 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2688.067923 x= 0.18455 0.03811 0.05188 0.07687 0.05054 0.17410 0.16467 0.07111 1 h-lim-p 0.0002 0.0015 129.9667 2686.965977 6 0.0001 36 | 0/8 2 h-lim-p 0.0008 0.0061 18.7022 2686.927414 7 0.0002 65 | 0/8 3 h-lim-p 0.0006 0.0284 7.3188 2686.920464 4 0.0003 86 | 0/8 4 h-lim-p 0.0010 0.2837 2.0489 2686.920239 2 0.0001 104 | 0/8 5 h-lim-p 0.0005 0.2204 0.5084 2686.920215 1 0.0002 118 | 0/8 6 h-lim-p 0.0006 1.5392 0.1686 2686.920211 1 0.0003 141 | 0/8 7 h-lim-p 0.0023 8.7610 0.0218 2686.920211 0 0.0005 162 | 0/8 8 h-lim-p 0.1132 20.0000 0.0001 2686.920182 0 0.9056 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2686.920181 0 1.0938 205 | 0/8 10 h-lim-p 1.4786 20.0000 0.0000 2686.920181 0 1.2938 225 | 0/8 11 h-lim-p 1.5296 20.0000 0.0000 2686.920181 0 0.6692 245 | 0/8 12 h-lim-p 0.2829 20.0000 0.0000 2686.920181 0 0.0265 268 | 0/8 13 h-lim-p 0.0078 20.0000 0.0001 2686.920181 0 0.0000 296 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 2686.920181 0 0.0000 332 Out... lnL = -2686.920181 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2686.920181 Node 7: lnL = -2686.920181 Node 8: lnL = -2686.920181 Node 9: lnL = -2686.920181 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 704 Sequential format.. Reading seq # 1: YOR140W_Sbay Reading seq # 2: YOR140W_Scer Reading seq # 3: YOR140W_Skud Reading seq # 4: YOR140W_Smik Reading seq # 5: YOR140W_Spar Sequences read.. Counting patterns.. # site patterns = 227 Counting frequencies.. 120 bytes for distance 36320 bytes for lkl0 29056 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.221830 0.099822 0.044716 0.072819 0.058542 0.141681 0.151728 0.089314 lnL0 = -2872.386447 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2872.386447 x= 0.22183 0.09982 0.04472 0.07282 0.05854 0.14168 0.15173 0.08931 1 h-lim-p 0.0005 0.0043 105.8277 2871.302416 8 0.0002 37 | 0/8 2 h-lim-p 0.0003 0.0025 40.2556 2871.111531 5 0.0003 58 | 0/8 3 h-lim-p 0.0011 0.0171 9.9675 2871.093578 6 0.0004 86 | 0/8 4 h-lim-p 0.0005 0.0117 8.1456 2871.090591 5 0.0001 112 | 0/8 5 h-lim-p 0.0031 0.6589 0.3556 2871.090575 2 0.0003 132 | 0/8 6 h-lim-p 0.0005 1.1250 0.1789 2871.090571 1 0.0003 155 | 0/8 7 h-lim-p 0.0028 20.0000 0.0165 2871.090569 0 0.0024 175 | 0/8 8 h-lim-p 0.0133 20.0000 0.0030 2871.089901 0 0.2121 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2871.089895 1 0.9961 221 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2871.089895 0 0.5469 242 | 0/8 11 h-lim-p 0.4137 20.0000 0.0000 2871.089895 0 0.0048 268 | 0/8 12 h-lim-p 0.0030 20.0000 0.0000 2871.089895 0 0.0015 288 | 0/8 13 h-lim-p 0.0008 20.0000 0.0001 2871.089895 0 0.0016 309 | 0/8 14 h-lim-p 0.0010 20.0000 0.0001 2871.089895 0 0.0005 329 | 0/8 15 h-lim-p 0.0008 20.0000 0.0001 2871.089895 0 0.0008 349 | 0/8 16 h-lim-p 0.0002 20.0000 0.0002 2871.089895 0 0.0001 369 | 0/8 17 h-lim-p 0.0002 20.0000 0.0001 2871.089895 0 0.0000 407 | 0/8 18 h-lim-p 0.0000 20.0000 0.0041 | 0/8 19 h-lim-p 0.0000 20.0000 0.0041 Out... lnL = -2871.089895 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2871.089895 Node 7: lnL = -2871.089895 Node 8: lnL = -2871.089895 Node 9: lnL = -2871.089895 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 479 Sequential format.. Reading seq # 1: YOR141C_Sbay Reading seq # 2: YOR141C_Scer Reading seq # 3: YOR141C_Skud Reading seq # 4: YOR141C_Smik Reading seq # 5: YOR141C_Spar Sequences read.. Counting patterns.. # site patterns = 162 Counting frequencies.. 120 bytes for distance 25920 bytes for lkl0 20736 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.166182 0.097827 0.082153 0.090194 0.053322 0.146402 0.209967 0.031593 lnL0 = -2076.911615 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2076.911615 x= 0.16618 0.09783 0.08215 0.09019 0.05332 0.14640 0.20997 0.03159 1 h-lim-p 0.0003 0.0023 51.3952 2076.543767 4 0.0003 30 | 0/8 2 h-lim-p 0.0010 0.0403 15.1261 2076.521354 3 0.0002 49 | 0/8 3 h-lim-p 0.0004 0.0371 7.4294 2076.510943 4 0.0005 69 | 0/8 4 h-lim-p 0.0021 0.1470 1.6480 2076.510300 3 0.0005 89 | 0/8 5 h-lim-p 0.0015 0.5021 0.5617 2076.510244 3 0.0004 108 | 0/8 6 h-lim-p 0.0027 2.3196 0.0826 2076.510243 1 0.0003 132 | 0/8 7 h-lim-p 0.0040 18.7315 0.0068 2076.510243 0 0.0035 152 | 0/8 8 h-lim-p 0.0276 20.0000 0.0009 2076.510162 0 0.2209 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2076.510162 0 1.0938 195 | 0/8 10 h-lim-p 1.4922 20.0000 0.0000 2076.510162 0 1.3057 215 | 0/8 11 h-lim-p 1.2534 20.0000 0.0000 2076.510162 0 2.5069 236 | 0/8 12 h-lim-p 0.3766 20.0000 0.0001 2076.510162 0 0.0000 275 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 2076.510162 0 0.0000 307 Out... lnL = -2076.510162 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2076.510162 Node 7: lnL = -2076.510162 Node 8: lnL = -2076.510162 Node 9: lnL = -2076.510162 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 481 Sequential format.. Reading seq # 1: YOR142W_Sbay Reading seq # 2: YOR142W_Scer Reading seq # 3: YOR142W_Skud Reading seq # 4: YOR142W_Smik Reading seq # 5: YOR142W_Spar Sequences read.. Counting patterns.. # site patterns = 160 Counting frequencies.. 120 bytes for distance 25600 bytes for lkl0 20480 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.164237 0.075136 0.086900 0.095616 0.047901 0.144631 0.234273 0.030657 lnL0 = -2072.974410 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2072.974410 x= 0.16424 0.07514 0.08690 0.09562 0.04790 0.14463 0.23427 0.03066 1 h-lim-p 0.0004 0.0033 45.2860 2072.689575 7 0.0003 40 | 0/8 2 h-lim-p 0.0009 0.0440 13.9991 2072.672757 3 0.0002 59 | 0/8 3 h-lim-p 0.0004 0.0187 6.3482 2072.665166 5 0.0005 83 | 0/8 4 h-lim-p 0.0013 0.1206 2.2698 2072.664085 4 0.0005 103 | 0/8 5 h-lim-p 0.0014 0.3567 0.7802 2072.663977 3 0.0004 123 | 0/8 6 h-lim-p 0.0042 1.8627 0.0786 2072.663976 0 0.0005 145 | 0/8 7 h-lim-p 0.0025 12.6711 0.0142 2072.663976 0 0.0011 165 | 0/8 8 h-lim-p 0.0496 20.0000 0.0003 2072.663906 0 0.7933 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2072.663899 1 0.9961 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2072.663899 0 0.0085 238 | 0/8 11 h-lim-p 0.0014 20.0000 0.0001 2072.663899 0 0.0000 272 | 0/8 12 h-lim-p 0.0000 20.0000 0.0011 2072.663899 0 0.0000 298 | 0/8 13 h-lim-p 0.0000 20.0000 0.0003 2072.663899 0 0.0019 325 | 0/8 14 h-lim-p 0.0109 20.0000 0.0001 2072.663899 0 0.0001 351 | 0/8 15 h-lim-p 0.0001 20.0000 0.0001 2072.663899 0 0.0000 373 | 0/8 16 h-lim-p 0.0000 20.0000 0.0009 2072.663899 0 0.0000 403 | 0/8 17 h-lim-p 0.0000 20.0000 0.0022 | 0/8 18 h-lim-p 0.0000 20.0000 0.0022 Out... lnL = -2072.663899 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2072.663899 Node 7: lnL = -2072.663899 Node 8: lnL = -2072.663899 Node 9: lnL = -2072.663899 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 402 Sequential format.. Reading seq # 1: YOR143C_Sbay Reading seq # 2: YOR143C_Scer Reading seq # 3: YOR143C_Skud Reading seq # 4: YOR143C_Smik Reading seq # 5: YOR143C_Spar Sequences read.. Counting patterns.. # site patterns = 182 Counting frequencies.. 120 bytes for distance 29120 bytes for lkl0 23296 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.214450 0.013861 0.058222 0.135950 0.088623 0.209884 0.212608 0.069864 lnL0 = -1773.027515 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1773.027515 x= 0.21445 0.01386 0.05822 0.13595 0.08862 0.20988 0.21261 0.06986 1 h-lim-p 0.0015 0.0609 152.5746 1770.445793 7 0.0003 40 | 0/8 2 h-lim-p 0.0012 0.0097 17.1494 1770.335729 7 0.0008 71 | 0/8 3 h-lim-p 0.0027 0.0874 4.7264 1770.329165 2 0.0006 88 | 0/8 4 h-lim-p 0.0014 0.0605 2.2084 1770.328108 3 0.0005 106 | 0/8 5 h-lim-p 0.0026 0.3827 0.4466 1770.328030 3 0.0008 126 | 0/8 6 h-lim-p 0.0034 0.9027 0.1078 1770.328026 1 0.0007 149 | 0/8 7 h-lim-p 0.0043 14.7718 0.0170 1770.328026 0 0.0019 169 | 0/8 8 h-lim-p 0.4937 20.0000 0.0001 1770.328022 0 0.9875 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1770.328022 0 2.1875 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1770.328022 0 1.0938 230 | 0/8 11 h-lim-p 0.7604 20.0000 0.0000 1770.328022 0 0.6654 250 | 0/8 12 h-lim-p 0.4151 20.0000 0.0000 1770.328022 0 0.0000 296 | 0/8 13 h-lim-p 0.0000 20.0000 0.0004 | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1770.328022 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1770.328022 Node 7: lnL = -1770.328022 Node 8: lnL = -1770.328022 Node 9: lnL = -1770.328022 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 270 Sequential format.. Reading seq # 1: YOR144C_Sbay Reading seq # 2: YOR144C_Scer Reading seq # 3: YOR144C_Skud Reading seq # 4: YOR144C_Smik Reading seq # 5: YOR144C_Spar Sequences read.. Counting patterns.. # site patterns = 123 Counting frequencies.. 120 bytes for distance 19680 bytes for lkl0 15744 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.204059 0.067997 0.053040 0.102547 0.070017 0.225689 0.191315 0.060065 lnL0 = -1193.318802 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1193.318802 x= 0.20406 0.06800 0.05304 0.10255 0.07002 0.22569 0.19131 0.06007 1 h-lim-p 0.0117 2.4409 45.2225 1192.911158 7 0.0004 41 | 0/8 2 h-lim-p 0.0020 0.0167 9.7381 1192.877031 4 0.0008 61 | 0/8 3 h-lim-p 0.0014 0.0225 5.0602 1192.871178 4 0.0006 81 | 0/8 4 h-lim-p 0.0059 0.2243 0.4875 1192.871066 3 0.0009 102 | 0/8 5 h-lim-p 0.0027 2.8197 0.1714 1192.871053 2 0.0010 126 | 0/8 6 h-lim-p 0.0055 5.8632 0.0326 1192.871053 1 0.0007 150 | 0/8 7 h-lim-p 0.0043 20.0000 0.0051 1192.871053 0 0.0019 170 | 0/8 8 h-lim-p 0.1155 20.0000 0.0001 1192.871048 0 0.9243 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1192.871048 0 1.0938 213 | 0/8 10 h-lim-p 1.2066 20.0000 0.0000 1192.871048 0 2.4133 234 | 0/8 11 h-lim-p 2.3679 20.0000 0.0000 1192.871048 0 0.0370 259 | 0/8 12 h-lim-p 0.0047 20.0000 0.0001 1192.871048 0 0.0012 280 | 0/8 13 h-lim-p 0.0004 20.0000 0.0002 1192.871048 0 0.0000 317 | 0/8 14 h-lim-p 0.0000 20.0000 0.0005 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -1192.871048 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1192.871048 Node 7: lnL = -1192.871048 Node 8: lnL = -1192.871048 Node 9: lnL = -1192.871048 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 382 Sequential format.. Reading seq # 1: YOR145C_Sbay Reading seq # 2: YOR145C_Scer Reading seq # 3: YOR145C_Skud Reading seq # 4: YOR145C_Smik Reading seq # 5: YOR145C_Spar Sequences read.. Counting patterns.. # site patterns = 122 Counting frequencies.. 120 bytes for distance 19520 bytes for lkl0 15616 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.521595 0.145179 0.266252 0.341902 0.085376 3.949298 0.434945 0.000060 lnL0 = -1530.707435 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1530.707435 x= 0.52159 0.14518 0.26625 0.34190 0.08538 3.94930 0.43494 0.00006 1 h-lim-p 0.0000 0.0000 248.2512 1530.633802 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0020 194.5956 1503.637543 m 0.0020 39 | 1/8 3 h-lim-p 0.0006 0.0047 66.5866 1501.858238 0 0.0012 52 | 1/8 4 h-lim-p 0.0028 0.0224 21.2982 1501.257909 2 0.0026 68 | 1/8 5 h-lim-p 0.0052 0.0413 9.1717 1500.958367 4 0.0040 88 | 1/8 6 h-lim-p 0.0411 0.3286 0.8817 1477.432754 0 0.2464 102 | 1/8 7 h-lim-p 0.2883 2.3068 0.0734 1476.826142 0 0.4325 121 | 1/8 8 h-lim-p 0.5012 4.0092 0.0461 1476.655745 7 0.3722 156 | 0/8 9 h-lim-p 0.0072 0.2346 2.3761 1476.650659 6 0.0020 188 | 0/8 10 h-lim-p 0.5113 20.0000 0.0091 1476.621493 0 1.0226 201 | 0/8 11 h-lim-p 2.5000 20.0000 0.0030 1476.620413 4 0.4822 230 | 0/8 12 h-lim-p 2.5000 20.0000 0.0005 1476.620307 3 0.8800 257 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1476.620307 0 1.0938 277 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1476.620307 0 1.0938 297 | 0/8 15 h-lim-p 1.1228 20.0000 0.0000 1476.620307 0 1.6843 317 | 0/8 16 h-lim-p 0.8765 20.0000 0.0000 1476.620307 0 0.0548 340 | 0/8 17 h-lim-p 0.0000 1.0115 0.0752 1476.620307 0 0.0000 361 | 0/8 18 h-lim-p 0.0001 20.0000 0.0018 1476.620307 0 0.0000 392 | 0/8 19 h-lim-p 0.0002 20.0000 0.0000 1476.620307 0 0.0000 426 Out... lnL = -1476.620307 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1476.620307 Node 7: lnL = -1476.620307 Node 8: lnL = -1476.620307 Node 9: lnL = -1476.620307 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 669 Sequential format.. Reading seq # 1: YOR148C_Sbay Reading seq # 2: YOR148C_Scer Reading seq # 3: YOR148C_Skud Reading seq # 4: YOR148C_Smik Reading seq # 5: YOR148C_Spar Sequences read.. Counting patterns.. # site patterns = 319 Counting frequencies.. 120 bytes for distance 51040 bytes for lkl0 40832 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.269623 0.258691 0.132505 0.198049 0.185406 0.384785 0.336391 0.000060 lnL0 = -3322.612936 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3322.612936 x= 0.26962 0.25869 0.13251 0.19805 0.18541 0.38479 0.33639 0.00006 1 h-lim-p 0.0014 0.0115 32.2329 3321.918046 2 0.0013 26 | 0/8 2 h-lim-p 0.0002 0.0013 18.7082 3321.748983 m 0.0013 38 | 0/8 3 h-lim-p 0.0000 0.0000 12.5179 h-lim-p: 1.43194986e-20 1.14555988e-19 1.25179113e+01 3321.748983 .. | 0/8 4 h-lim-p 0.0000 0.0237 10.9309 3321.714004 0 0.0006 64 | 0/8 5 h-lim-p 0.0017 0.1232 4.2283 3321.703811 4 0.0013 84 | 0/8 6 h-lim-p 0.0015 0.0123 2.7742 3321.699556 3 0.0015 102 | 0/8 7 h-lim-p 0.0042 0.5662 1.0054 3321.699194 3 0.0008 121 | 0/8 8 h-lim-p 0.0036 0.0287 0.2356 3321.699145 2 0.0019 138 | 0/8 9 h-lim-p 0.0166 5.8835 0.0268 3321.699144 0 0.0018 160 | 0/8 10 h-lim-p 0.0051 20.0000 0.0095 3321.699127 0 0.0306 182 | 0/8 11 h-lim-p 0.0188 0.7392 0.0155 3321.698850 0 0.0377 203 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3321.698850 0 1.0938 223 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 3321.698850 0 1.0938 243 | 0/8 14 h-lim-p 1.1620 20.0000 0.0000 3321.698850 0 1.0168 263 | 0/8 15 h-lim-p 0.0984 16.1214 0.0002 3321.698850 0 0.0061 286 | 0/8 16 h-lim-p 0.0017 4.4871 0.0005 3321.698850 0 0.0017 306 | 0/8 17 h-lim-p 0.0018 4.7035 0.0005 3321.698850 0 0.0000 348 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -3321.698850 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3321.698850 Node 7: lnL = -3321.698850 Node 8: lnL = -3321.698850 Node 9: lnL = -3321.698850 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 640 Sequential format.. Reading seq # 1: YOR150W_Sbay Reading seq # 2: YOR150W_Scer Reading seq # 3: YOR150W_Skud Reading seq # 4: YOR150W_Smik Reading seq # 5: YOR150W_Spar Sequences read.. Counting patterns.. # site patterns = 273 Counting frequencies.. 120 bytes for distance 43680 bytes for lkl0 34944 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.268845 0.274678 0.039992 0.157821 0.146278 0.275293 0.256396 0.043498 lnL0 = -3289.996551 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3289.996551 x= 0.26885 0.27468 0.03999 0.15782 0.14628 0.27529 0.25640 0.04350 1 h-lim-p 0.0013 0.0100 93.0462 3288.739002 8 0.0003 43 | 0/8 2 h-lim-p 0.0010 0.0080 21.9284 3288.580453 7 0.0007 74 | 0/8 3 h-lim-p 0.0011 0.0322 13.7933 3288.539483 5 0.0006 97 | 0/8 4 h-lim-p 0.0020 0.0695 3.9626 3288.535187 5 0.0006 122 | 0/8 5 h-lim-p 0.0029 0.3419 0.8294 3288.534793 3 0.0012 140 | 0/8 6 h-lim-p 0.0028 0.7172 0.3619 3288.534757 0 0.0006 161 | 0/8 7 h-lim-p 0.0691 20.0000 0.0032 3288.534754 1 0.0275 183 | 0/8 8 h-lim-p 0.0140 20.0000 0.0064 3288.534624 0 0.0560 205 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3288.534623 0 1.0938 225 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3288.534623 0 1.0938 245 | 0/8 11 h-lim-p 1.0602 20.0000 0.0000 3288.534623 0 0.1160 267 | 0/8 12 h-lim-p 0.0182 20.0000 0.0001 3288.534623 0 0.0000 306 | 0/8 13 h-lim-p 0.0000 20.0000 0.0006 | 0/8 14 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -3288.534623 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3288.534623 Node 7: lnL = -3288.534623 Node 8: lnL = -3288.534623 Node 9: lnL = -3288.534623 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 858 Sequential format.. Reading seq # 1: YOR152C_Sbay Reading seq # 2: YOR152C_Scer Reading seq # 3: YOR152C_Skud Reading seq # 4: YOR152C_Smik Reading seq # 5: YOR152C_Spar Sequences read.. Counting patterns.. # site patterns = 375 Counting frequencies.. 120 bytes for distance 60000 bytes for lkl0 48000 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.304685 0.097445 0.064118 0.215503 0.127828 0.258421 0.344829 0.085099 lnL0 = -4336.872550 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4336.872550 x= 0.30468 0.09744 0.06412 0.21550 0.12783 0.25842 0.34483 0.08510 1 h-lim-p 0.0031 0.9033 167.3611 4333.132312 8 0.0003 42 | 0/8 2 h-lim-p 0.0010 0.0078 36.9959 4332.746855 7 0.0006 73 | 0/8 3 h-lim-p 0.0015 0.0162 14.0711 4332.701462 6 0.0005 100 | 0/8 4 h-lim-p 0.0017 0.0466 4.2467 4332.695629 3 0.0007 118 | 0/8 5 h-lim-p 0.0022 0.3211 1.3654 4332.694829 2 0.0010 134 | 0/8 6 h-lim-p 0.0034 0.7905 0.3898 4332.694781 2 0.0007 151 | 0/8 7 h-lim-p 0.0042 4.7732 0.0636 4332.694772 1 0.0021 174 | 0/8 8 h-lim-p 0.0530 20.0000 0.0025 4332.692123 0 0.6359 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 4332.692088 1 0.9961 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4332.692088 0 1.0938 239 | 0/8 11 h-lim-p 1.1795 20.0000 0.0000 4332.692088 0 0.1106 262 | 0/8 12 h-lim-p 0.0102 20.0000 0.0001 4332.692088 0 0.0000 289 | 0/8 13 h-lim-p 0.0003 20.0000 0.0000 4332.692088 0 0.0000 319 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 4332.692088 0 0.0000 347 Out... lnL = -4332.692088 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4332.692088 Node 7: lnL = -4332.692088 Node 8: lnL = -4332.692088 Node 9: lnL = -4332.692088 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 368 Sequential format.. Reading seq # 1: YOR154W_Sbay Reading seq # 2: YOR154W_Scer Reading seq # 3: YOR154W_Skud Reading seq # 4: YOR154W_Smik Reading seq # 5: YOR154W_Spar Sequences read.. Counting patterns.. # site patterns = 119 Counting frequencies.. 120 bytes for distance 19040 bytes for lkl0 15232 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.521595 0.082359 0.243851 0.286658 0.076809 4.052137 0.427626 0.000060 lnL0 = -1382.532390 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1382.532390 x= 0.52159 0.08236 0.24385 0.28666 0.07681 4.05214 0.42763 0.00006 1 h-lim-p 0.0000 0.0000 254.3213 1382.442505 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0007 250.7710 1358.858197 m 0.0007 38 | 2/8 3 h-lim-p 0.0007 0.0053 62.2704 1350.484087 0 0.0026 52 | 2/8 4 h-lim-p 0.0012 0.0097 33.6179 1344.983097 0 0.0048 66 | 2/8 5 h-lim-p 0.0010 0.0077 22.2709 1337.973759 0 0.0038 80 | 2/8 6 h-lim-p 0.0107 0.0860 4.7333 1337.810899 8 0.0067 112 | 2/8 7 h-lim-p 0.0434 0.3647 0.7288 1332.256555 0 0.1737 126 | 1/8 8 h-lim-p 0.0065 0.0523 4.0312 1332.237657 6 0.0040 159 | 1/8 9 h-lim-p 0.3109 2.4873 0.0169 1332.204072 0 0.6218 172 | 1/8 10 h-lim-p 2.5000 20.0000 0.0039 1332.203068 2 0.5444 196 | 0/8 11 h-lim-p 0.0393 20.0000 0.0545 1332.203065 0 0.0022 218 | 0/8 12 h-lim-p 0.1721 1.3764 0.0005 1332.203032 0 0.6882 240 | 0/8 13 h-lim-p 0.0894 0.7152 0.0001 1332.203031 m 0.7152 260 | 1/8 14 h-lim-p 0.2818 20.0000 0.0002 1332.203030 0 0.2466 280 | 1/8 15 h-lim-p 1.5270 20.0000 0.0000 1332.203030 0 0.6681 299 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 1332.203030 0 1.0938 318 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 1332.203030 0 0.2734 339 | 1/8 18 h-lim-p 0.1134 20.0000 0.0000 1332.203030 0 0.0001 367 Out... lnL = -1332.203030 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1332.203030 Node 7: lnL = -1332.203030 Node 8: lnL = -1332.203030 Node 9: lnL = -1332.203030 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 442 Sequential format.. Reading seq # 1: YOR157C_Sbay Reading seq # 2: YOR157C_Scer Reading seq # 3: YOR157C_Skud Reading seq # 4: YOR157C_Smik Reading seq # 5: YOR157C_Spar Sequences read.. Counting patterns.. # site patterns = 201 Counting frequencies.. 120 bytes for distance 32160 bytes for lkl0 25728 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.309486 0.000060 0.168109 0.245826 0.078794 0.235182 0.331033 0.121122 lnL0 = -2165.982897 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2165.982897 x= 0.30949 0.00006 0.16811 0.24583 0.07879 0.23518 0.33103 0.12112 1 h-lim-p 0.0000 0.0000 85.7967 2165.968594 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0280 26.8180 2165.628166 0 0.0013 41 | 1/8 3 h-lim-p 0.0014 0.0108 22.2761 2165.505968 6 0.0007 66 | 1/8 4 h-lim-p 0.0019 0.0306 8.5342 2165.470438 7 0.0011 96 | 1/8 5 h-lim-p 0.0064 0.2476 1.4772 2165.443085 2 0.0060 112 | 1/8 6 h-lim-p 0.0106 0.5810 0.8374 2164.241159 0 0.0845 127 | 1/8 7 h-lim-p 0.0015 0.0120 30.1089 2162.138209 0 0.0030 147 | 1/8 8 h-lim-p 2.5000 20.0000 0.0216 2162.020625 7 0.8511 176 | 1/8 9 h-lim-p 2.5000 20.0000 0.0014 2162.020117 4 0.8779 205 | 1/8 10 h-lim-p 2.5000 20.0000 0.0004 2162.020077 3 0.7330 233 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 2162.020076 0 1.0938 252 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 2162.020076 0 1.0938 271 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 2162.020076 0 1.0938 290 | 1/8 14 h-lim-p 1.2307 20.0000 0.0000 2162.020076 0 0.5384 309 | 1/8 15 h-lim-p 0.2802 20.0000 0.0000 2162.020076 0 0.2802 328 | 1/8 16 h-lim-p 0.1182 20.0000 0.0000 2162.020076 0 0.0037 351 | 1/8 17 h-lim-p 0.0009 20.0000 0.0000 2162.020076 0 0.0001 372 | 1/8 18 h-lim-p 0.0020 20.0000 0.0000 2162.020076 0 0.0000 403 Out... lnL = -2162.020076 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2162.020076 Node 7: lnL = -2162.020076 Node 8: lnL = -2162.020076 Node 9: lnL = -2162.020076 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 435 Sequential format.. Reading seq # 1: YOR158W_Sbay Reading seq # 2: YOR158W_Scer Reading seq # 3: YOR158W_Skud Reading seq # 4: YOR158W_Smik Reading seq # 5: YOR158W_Spar Sequences read.. Counting patterns.. # site patterns = 200 Counting frequencies.. 120 bytes for distance 32000 bytes for lkl0 25600 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.226900 0.129107 0.085348 0.199441 0.100990 0.228281 0.249667 0.037161 lnL0 = -2152.716435 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2152.716435 x= 0.22690 0.12911 0.08535 0.19944 0.10099 0.22828 0.24967 0.03716 1 h-lim-p 0.0009 0.0069 59.8353 2151.628830 8 0.0006 41 | 0/8 2 h-lim-p 0.0008 0.0063 15.6918 2151.544750 2 0.0007 57 | 0/8 3 h-lim-p 0.0021 0.0466 5.4482 2151.538298 2 0.0005 74 | 0/8 4 h-lim-p 0.0016 0.0980 1.6986 2151.537076 5 0.0009 98 | 0/8 5 h-lim-p 0.0035 0.5180 0.4645 2151.536986 3 0.0009 117 | 0/8 6 h-lim-p 0.0036 4.0162 0.1159 2151.536980 1 0.0009 140 | 0/8 7 h-lim-p 0.0089 20.0000 0.0117 2151.536978 1 0.0044 163 | 0/8 8 h-lim-p 0.0301 20.0000 0.0017 2151.536800 0 0.2408 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2151.536797 0 1.0938 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2151.536797 0 1.0938 226 | 0/8 11 h-lim-p 1.1423 20.0000 0.0000 2151.536797 0 0.5712 246 | 0/8 12 h-lim-p 0.0970 20.0000 0.0001 2151.536797 0 0.0008 272 | 0/8 13 h-lim-p 0.0001 20.0000 0.0005 2151.536797 0 0.0001 292 | 0/8 14 h-lim-p 0.0003 20.0000 0.0002 2151.536797 0 0.0000 327 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -2151.536797 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2151.536797 Node 7: lnL = -2151.536797 Node 8: lnL = -2151.536797 Node 9: lnL = -2151.536797 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 308 Sequential format.. Reading seq # 1: YOR159C_Sbay Reading seq # 2: YOR159C_Scer Reading seq # 3: YOR159C_Skud Reading seq # 4: YOR159C_Smik Reading seq # 5: YOR159C_Spar Sequences read.. Counting patterns.. # site patterns = 109 Counting frequencies.. 120 bytes for distance 17440 bytes for lkl0 13952 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.546696 0.089055 0.398114 0.096592 0.143903 3.878164 0.420123 0.000060 lnL0 = -1189.384199 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1189.384199 x= 0.54670 0.08906 0.39811 0.09659 0.14390 3.87816 0.42012 0.00006 1 h-lim-p 0.0000 0.0000 177.8900 1189.346231 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0002 992.6791 1156.823518 m 0.0002 36 | 2/8 3 h-lim-p 0.0005 0.0041 87.4399 1145.499974 0 0.0020 50 | 2/8 4 h-lim-p 0.0015 0.0119 19.5690 1141.197302 0 0.0059 64 | 2/8 5 h-lim-p 0.0018 0.0148 27.7642 1138.062950 0 0.0037 77 | 2/8 6 h-lim-p 0.0036 0.0288 13.1566 1137.819698 8 0.0024 108 | 2/8 7 h-lim-p 0.2443 1.9540 0.1158 1136.904394 0 0.4885 121 | 1/8 8 h-lim-p 0.0617 0.6567 0.9169 1136.902911 5 0.0029 152 | 1/8 9 h-lim-p 0.0988 9.0390 0.0269 1136.808938 0 0.5929 173 | 0/8 10 h-lim-p 0.0079 1.0148 2.0081 1136.805817 4 0.0016 201 | 0/8 11 h-lim-p 1.5597 13.1174 0.0020 1136.805142 3 0.6241 219 | 0/8 12 h-lim-p 1.7956 20.0000 0.0007 1136.805049 2 0.8417 243 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1136.805049 0 1.0938 263 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1136.805049 0 1.0938 283 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1136.805049 0 1.0938 303 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1136.805049 0 1.0938 323 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1136.805049 0 0.0195 349 Out... lnL = -1136.805049 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1136.805049 Node 7: lnL = -1136.805049 Node 8: lnL = -1136.805049 Node 9: lnL = -1136.805049 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 287 Sequential format.. Reading seq # 1: YOR160W_Sbay Reading seq # 2: YOR160W_Scer Reading seq # 3: YOR160W_Skud Reading seq # 4: YOR160W_Smik Reading seq # 5: YOR160W_Spar Sequences read.. Counting patterns.. # site patterns = 133 Counting frequencies.. 120 bytes for distance 21280 bytes for lkl0 17024 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.246902 0.179049 0.057253 0.090133 0.107102 0.158591 0.066540 0.085233 lnL0 = -1162.183524 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1162.183524 x= 0.24690 0.17905 0.05725 0.09013 0.10710 0.15859 0.06654 0.08523 1 h-lim-p 0.0003 0.0026 43.7883 1160.888391 0 0.0013 24 | 0/8 2 h-lim-p 0.0007 0.0054 21.5648 1160.678326 0 0.0014 37 | 0/8 3 h-lim-p 0.0006 0.0045 17.1005 1160.614968 0 0.0008 49 | 0/8 4 h-lim-p 0.0027 0.0278 5.3678 1160.601004 4 0.0012 68 | 0/8 5 h-lim-p 0.0049 0.2812 1.2527 1160.600509 4 0.0006 90 | 0/8 6 h-lim-p 0.0023 0.1614 0.3545 1160.600413 2 0.0011 106 | 0/8 7 h-lim-p 0.0022 1.1409 0.1719 1160.599895 0 0.0089 128 | 0/8 8 h-lim-p 0.0302 1.4678 0.0504 1160.572741 0 0.1209 150 | 0/8 9 h-lim-p 2.5000 20.0000 0.0012 1160.572277 2 1.0889 174 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1160.572276 0 1.0938 194 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1160.572276 0 1.0938 214 | 0/8 12 h-lim-p 1.2437 20.0000 0.0000 1160.572276 0 0.0012 243 | 0/8 13 h-lim-p 0.0002 20.0000 0.0000 1160.572276 0 0.0000 265 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 1160.572276 0 0.0000 285 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 1160.572276 0 0.0000 318 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 1160.572276 0 0.0000 344 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 1160.572276 0 0.0000 368 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 1160.572276 0 0.0000 394 | 0/8 19 h-lim-p 0.0000 20.0000 0.0002 1160.572276 0 0.0000 420 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 1160.572276 0 0.0000 442 | 0/8 21 h-lim-p 0.0000 20.0000 0.0000 1160.572276 0 0.0000 462 | 0/8 22 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 23 h-lim-p 0.0000 20.0000 0.0002 | 0/8 24 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1160.572276 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1160.572276 Node 7: lnL = -1160.572276 Node 8: lnL = -1160.572276 Node 9: lnL = -1160.572276 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 801 Sequential format.. Reading seq # 1: YOR162C_Sbay Reading seq # 2: YOR162C_Scer Reading seq # 3: YOR162C_Skud Reading seq # 4: YOR162C_Smik Reading seq # 5: YOR162C_Spar Sequences read.. Counting patterns.. # site patterns = 302 Counting frequencies.. 120 bytes for distance 48320 bytes for lkl0 38656 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.231833 0.199570 0.134774 0.166575 0.070140 0.241394 0.213963 0.020970 lnL0 = -3478.048734 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3478.048734 x= 0.23183 0.19957 0.13477 0.16657 0.07014 0.24139 0.21396 0.02097 1 h-lim-p 0.0010 0.0079 63.0688 3477.607084 2 0.0002 27 | 0/8 2 h-lim-p 0.0005 0.0067 27.8692 3477.504229 7 0.0003 55 | 0/8 3 h-lim-p 0.0011 0.0101 7.9246 3477.467816 1 0.0013 69 | 0/8 4 h-lim-p 0.0013 0.0108 5.8977 3477.461383 3 0.0005 87 | 0/8 5 h-lim-p 0.0049 0.0636 0.6550 3477.461246 3 0.0007 107 | 0/8 6 h-lim-p 0.0011 1.3659 0.3876 3477.461195 2 0.0009 131 | 0/8 7 h-lim-p 0.0026 1.7955 0.1331 3477.461185 1 0.0013 154 | 0/8 8 h-lim-p 0.3440 20.0000 0.0005 3477.461041 0 1.0319 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3477.461041 0 1.0938 195 | 0/8 10 h-lim-p 1.8790 20.0000 0.0000 3477.461041 0 1.6441 215 | 0/8 11 h-lim-p 2.4996 20.0000 0.0000 3477.461041 0 1.0936 235 | 0/8 12 h-lim-p 0.3741 20.0000 0.0000 3477.461041 0 0.0234 258 | 0/8 13 h-lim-p 0.0025 20.0000 0.0003 3477.461041 0 0.0000 297 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 3477.461041 0 0.0000 317 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 3477.461041 0 0.0000 351 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 3477.461041 0 0.0000 378 | 0/8 17 h-lim-p 0.0000 20.0000 0.0006 3477.461041 0 0.0000 410 | 0/8 18 h-lim-p 0.0000 20.0000 0.0003 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -3477.461041 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3477.461041 Node 7: lnL = -3477.461041 Node 8: lnL = -3477.461041 Node 9: lnL = -3477.461041 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 811 Sequential format.. Reading seq # 1: YOR163W_Sbay Reading seq # 2: YOR163W_Scer Reading seq # 3: YOR163W_Skud Reading seq # 4: YOR163W_Smik Reading seq # 5: YOR163W_Spar Sequences read.. Counting patterns.. # site patterns = 333 Counting frequencies.. 120 bytes for distance 53280 bytes for lkl0 42624 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.275409 0.060762 0.128959 0.158320 0.078394 0.224382 0.289798 0.073574 lnL0 = -3915.337812 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3915.337812 x= 0.27541 0.06076 0.12896 0.15832 0.07839 0.22438 0.28980 0.07357 1 h-lim-p 0.0056 0.0449 94.1915 3914.135889 3 0.0003 31 | 0/8 2 h-lim-p 0.0012 0.0098 16.3803 3914.087958 5 0.0004 56 | 0/8 3 h-lim-p 0.0005 0.0180 11.5932 3914.074423 4 0.0003 77 | 0/8 4 h-lim-p 0.0010 0.1038 3.4233 3914.071655 5 0.0005 102 | 0/8 5 h-lim-p 0.0024 0.4650 0.7787 3914.071462 3 0.0007 122 | 0/8 6 h-lim-p 0.0025 0.9400 0.2237 3914.071452 2 0.0004 148 | 0/8 7 h-lim-p 0.0020 3.9286 0.0438 3914.071452 0 0.0009 168 | 0/8 8 h-lim-p 0.1785 20.0000 0.0002 3914.071385 0 1.4276 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3914.071380 0 1.0938 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3914.071380 0 1.0938 231 | 0/8 11 h-lim-p 1.1610 20.0000 0.0000 3914.071380 0 1.0159 251 | 0/8 12 h-lim-p 0.5657 20.0000 0.0000 3914.071380 0 0.0707 273 | 0/8 13 h-lim-p 0.0079 20.0000 0.0002 3914.071380 0 0.0000 302 | 0/8 14 h-lim-p 0.0007 20.0000 0.0000 3914.071380 0 0.0007 322 Out... lnL = -3914.071380 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3914.071380 Node 7: lnL = -3914.071380 Node 8: lnL = -3914.071380 Node 9: lnL = -3914.071380 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 250 Sequential format.. Reading seq # 1: YOR164C_Sbay Reading seq # 2: YOR164C_Scer Reading seq # 3: YOR164C_Skud Reading seq # 4: YOR164C_Smik Reading seq # 5: YOR164C_Spar Sequences read.. Counting patterns.. # site patterns = 97 Counting frequencies.. 120 bytes for distance 15520 bytes for lkl0 12416 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.178785 0.104385 0.014615 0.101595 0.047696 0.172235 0.120482 0.054338 lnL0 = -999.827572 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 999.827572 x= 0.17878 0.10438 0.01461 0.10159 0.04770 0.17223 0.12048 0.05434 1 h-lim-p 0.0012 0.0099 72.9796 999.419188 7 0.0002 39 | 0/8 2 h-lim-p 0.0007 0.0069 17.0430 999.315037 6 0.0007 64 | 0/8 3 h-lim-p 0.0021 0.0289 6.0979 999.308808 6 0.0004 92 | 0/8 4 h-lim-p 0.0009 0.0617 2.4352 999.307171 5 0.0006 117 | 0/8 5 h-lim-p 0.0035 0.3721 0.4519 999.307102 3 0.0007 136 | 0/8 6 h-lim-p 0.0045 1.6412 0.0696 999.307100 1 0.0009 159 | 0/8 7 h-lim-p 0.0059 20.0000 0.0107 999.307100 0 0.0015 180 | 0/8 8 h-lim-p 0.0722 20.0000 0.0002 999.307054 0 0.8669 203 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 999.307053 0 1.0938 223 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 999.307053 0 1.0938 243 | 0/8 11 h-lim-p 1.1799 20.0000 0.0000 999.307053 0 2.3597 264 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 999.307053 0 0.0000 312 Out... lnL = -999.307053 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -999.307053 Node 7: lnL = -999.307053 Node 8: lnL = -999.307053 Node 9: lnL = -999.307053 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 245 Sequential format.. Reading seq # 1: YOR165W_Sbay Reading seq # 2: YOR165W_Scer Reading seq # 3: YOR165W_Skud Reading seq # 4: YOR165W_Smik Reading seq # 5: YOR165W_Spar Sequences read.. Counting patterns.. # site patterns = 94 Counting frequencies.. 120 bytes for distance 15040 bytes for lkl0 12032 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.267660 0.052820 0.027224 0.117947 0.031344 0.166054 0.142286 0.126044 lnL0 = -848.283088 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 848.283088 x= 0.26766 0.05282 0.02722 0.11795 0.03134 0.16605 0.14229 0.12604 1 h-lim-p 0.0021 0.0172 90.4278 847.499731 3 0.0002 30 | 0/8 2 h-lim-p 0.0010 0.0115 20.5194 847.286959 7 0.0010 58 | 0/8 3 h-lim-p 0.0009 0.0096 23.7728 847.127392 1 0.0011 72 | 0/8 4 h-lim-p 0.0008 0.0064 29.9169 846.985722 5 0.0009 95 | 0/8 5 h-lim-p 0.0019 0.0153 10.0451 846.946854 7 0.0012 125 | 0/8 6 h-lim-p 0.0025 0.0293 4.9178 846.929018 3 0.0021 143 | 0/8 7 h-lim-p 0.0078 0.0895 1.3171 846.928500 4 0.0007 168 | 0/8 8 h-lim-p 0.1189 20.0000 0.0073 846.919830 0 0.9511 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0009 846.919679 3 1.0449 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 846.919678 1 1.2305 232 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 846.919678 0 1.2500 252 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 846.919678 0 0.5469 273 | 0/8 13 h-lim-p 0.3849 20.0000 0.0000 846.919678 0 0.0004 302 Out... lnL = -846.919678 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -846.919678 Node 7: lnL = -846.919678 Node 8: lnL = -846.919678 Node 9: lnL = -846.919678 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 338 Sequential format.. Reading seq # 1: YOR166C_Sbay Reading seq # 2: YOR166C_Scer Reading seq # 3: YOR166C_Skud Reading seq # 4: YOR166C_Smik Reading seq # 5: YOR166C_Spar Sequences read.. Counting patterns.. # site patterns = 176 Counting frequencies.. 120 bytes for distance 28160 bytes for lkl0 22528 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.246951 0.231767 0.000060 0.219278 0.562109 0.223169 0.214255 0.004567 lnL0 = -1585.833488 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1585.833488 x= 0.24695 0.23177 0.00006 0.21928 0.56211 0.22317 0.21425 0.00457 1 h-lim-p 0.0000 0.0001 152.2738 1584.369910 m 0.0001 22 | 1/8 2 h-lim-p 0.0000 0.0025 177.5180 1575.006930 7 0.0013 57 | 1/8 3 h-lim-p 0.0003 0.0021 75.1007 1572.442070 0 0.0011 71 | 1/8 4 h-lim-p 0.0016 0.0129 24.5439 1571.872387 0 0.0024 83 | 1/8 5 h-lim-p 0.0057 0.0681 10.4292 1571.709974 7 0.0036 113 | 1/8 6 h-lim-p 0.0142 0.1476 2.6192 1571.681246 5 0.0057 134 | 1/8 7 h-lim-p 0.0247 0.3267 0.6016 1571.600617 6 0.0272 160 | 1/8 8 h-lim-p 0.0098 0.1300 1.6733 1569.215997 0 0.0392 181 | 1/8 9 h-lim-p 0.2608 2.0867 0.0694 1568.740384 0 0.7825 194 | 0/8 10 h-lim-p 0.0073 0.0585 3.2598 1568.736105 5 0.0010 227 | 0/8 11 h-lim-p 0.5014 20.0000 0.0067 1568.725160 0 1.0029 240 | 0/8 12 h-lim-p 2.5000 20.0000 0.0017 1568.724235 4 0.8479 271 | 0/8 13 h-lim-p 2.5000 20.0000 0.0004 1568.724197 3 0.8059 299 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1568.724197 0 1.0938 319 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1568.724197 0 1.0938 339 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1568.724197 0 1.0938 359 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1568.724197 0 3.7500 379 | 0/8 18 h-lim-p 0.4264 20.0000 0.0000 1568.724197 0 0.6396 399 | 0/8 19 h-lim-p 0.0899 20.0000 0.0000 1568.724197 0 0.0000 433 Out... lnL = -1568.724197 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1568.724197 Node 7: lnL = -1568.724197 Node 8: lnL = -1568.724197 Node 9: lnL = -1568.724197 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 306 Sequential format.. Reading seq # 1: YOR167C_Sbay Reading seq # 2: YOR167C_Scer Reading seq # 3: YOR167C_Skud Reading seq # 4: YOR167C_Smik Reading seq # 5: YOR167C_Spar Sequences read.. Counting patterns.. # site patterns = 117 Counting frequencies.. 120 bytes for distance 18720 bytes for lkl0 14976 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.162928 0.000060 0.086485 0.082067 0.053183 0.152608 0.146620 0.054344 lnL0 = -1187.506819 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1187.506819 x= 0.16293 0.00006 0.08648 0.08207 0.05318 0.15261 0.14662 0.05434 1 h-lim-p 0.0009 0.0076 126.7887 1185.481768 8 0.0002 41 | 0/8 2 h-lim-p 0.0008 0.0065 26.5812 1185.303780 8 0.0005 73 | 0/8 3 h-lim-p 0.0012 0.0170 11.6466 1185.281850 5 0.0004 97 | 0/8 4 h-lim-p 0.0007 0.0276 6.7325 1185.273981 6 0.0005 123 | 0/8 5 h-lim-p 0.0020 0.1206 1.5606 1185.273372 4 0.0005 144 | 0/8 6 h-lim-p 0.0027 0.6858 0.3076 1185.273340 2 0.0007 161 | 0/8 7 h-lim-p 0.0067 5.0547 0.0312 1185.273337 2 0.0022 187 | 0/8 8 h-lim-p 0.0370 17.1693 0.0018 1185.272148 0 0.5925 211 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1185.272080 2 0.9961 235 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1185.272080 0 1.0938 255 | 0/8 11 h-lim-p 1.3788 20.0000 0.0000 1185.272080 0 0.0027 283 | 0/8 12 h-lim-p 0.0009 20.0000 0.0000 1185.272080 0 0.0004 303 | 0/8 13 h-lim-p 0.0001 20.0000 0.0001 1185.272080 0 0.0000 325 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 1185.272080 0 0.0000 352 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 1185.272080 0 0.0000 379 Out... lnL = -1185.272080 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1185.272080 Node 7: lnL = -1185.272080 Node 8: lnL = -1185.272080 Node 9: lnL = -1185.272080 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 306 Sequential format.. Reading seq # 1: YOR168W_Sbay Reading seq # 2: YOR168W_Scer Reading seq # 3: YOR168W_Skud Reading seq # 4: YOR168W_Smik Reading seq # 5: YOR168W_Spar Sequences read.. Counting patterns.. # site patterns = 118 Counting frequencies.. 120 bytes for distance 18880 bytes for lkl0 15104 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.150131 0.020440 0.052319 0.099568 0.041892 0.165513 0.160307 0.038585 lnL0 = -1196.279504 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1196.279504 x= 0.15013 0.02044 0.05232 0.09957 0.04189 0.16551 0.16031 0.03859 1 h-lim-p 0.0003 0.0028 135.6546 1194.439110 7 0.0002 38 | 0/8 2 h-lim-p 0.0004 0.0035 18.1461 1194.377714 5 0.0004 61 | 0/8 3 h-lim-p 0.0010 0.0207 7.0059 1194.372832 2 0.0002 78 | 0/8 4 h-lim-p 0.0006 0.0910 2.6517 1194.370591 1 0.0007 92 | 0/8 5 h-lim-p 0.0023 0.1578 0.8472 1194.370429 2 0.0005 109 | 0/8 6 h-lim-p 0.0046 1.9123 0.0943 1194.370426 2 0.0008 136 | 0/8 7 h-lim-p 0.0042 8.1859 0.0168 1194.370426 0 0.0009 157 | 0/8 8 h-lim-p 0.6233 20.0000 0.0000 1194.370425 0 1.2467 178 | 0/8 9 h-lim-p 1.8503 20.0000 0.0000 1194.370424 0 1.6190 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1194.370424 0 1.0938 218 | 0/8 11 h-lim-p 0.5912 20.0000 0.0000 1194.370424 0 2.3649 240 | 0/8 12 h-lim-p 1.4919 20.0000 0.0000 1194.370424 0 0.0233 265 | 0/8 13 h-lim-p 0.0008 20.0000 0.0006 1194.370424 0 0.0002 286 | 0/8 14 h-lim-p 0.0001 20.0000 0.0017 1194.370424 0 0.0000 306 | 0/8 15 h-lim-p 0.0002 20.0000 0.0003 1194.370424 0 0.0000 343 | 0/8 16 h-lim-p 0.0000 20.0000 0.0008 | 0/8 17 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -1194.370424 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1194.370424 Node 7: lnL = -1194.370424 Node 8: lnL = -1194.370424 Node 9: lnL = -1194.370424 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 341 Sequential format.. Reading seq # 1: YOR171C_Sbay Reading seq # 2: YOR171C_Scer Reading seq # 3: YOR171C_Skud Reading seq # 4: YOR171C_Smik Reading seq # 5: YOR171C_Spar Sequences read.. Counting patterns.. # site patterns = 158 Counting frequencies.. 120 bytes for distance 25280 bytes for lkl0 20224 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.261582 0.035753 0.086523 0.130711 0.124117 0.264708 0.161170 0.085069 lnL0 = -1627.235138 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1627.235138 x= 0.26158 0.03575 0.08652 0.13071 0.12412 0.26471 0.16117 0.08507 1 h-lim-p 0.0009 0.0074 105.7960 1624.999452 6 0.0005 36 | 0/8 2 h-lim-p 0.0004 0.0028 38.5755 1624.424065 0 0.0007 49 | 0/8 3 h-lim-p 0.0017 0.0138 15.8884 1624.335818 2 0.0008 65 | 0/8 4 h-lim-p 0.0033 0.0565 3.9112 1624.331014 3 0.0007 84 | 0/8 5 h-lim-p 0.0024 0.3555 1.0965 1624.330289 4 0.0012 105 | 0/8 6 h-lim-p 0.0126 1.6912 0.1076 1624.330181 4 0.0039 129 | 0/8 7 h-lim-p 0.0103 2.5140 0.0407 1624.315995 0 0.1651 153 | 0/8 8 h-lim-p 0.0032 0.1270 2.1194 1624.311830 3 0.0014 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0012 1624.310326 3 1.1328 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0003 1624.310247 3 1.3437 224 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1624.310247 0 1.0938 244 | 0/8 12 h-lim-p 2.2128 20.0000 0.0000 1624.310247 0 1.9362 264 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1624.310247 0 1.0938 284 | 0/8 14 h-lim-p 0.2794 20.0000 0.0000 1624.310247 0 4.4711 308 | 0/8 15 h-lim-p 0.1213 20.0000 0.0002 1624.310247 0 0.0000 355 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1624.310247 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1624.310247 Node 7: lnL = -1624.310247 Node 8: lnL = -1624.310247 Node 9: lnL = -1624.310247 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 341 Sequential format.. Reading seq # 1: YOR172W_Sbay Reading seq # 2: YOR172W_Scer Reading seq # 3: YOR172W_Skud Reading seq # 4: YOR172W_Smik Reading seq # 5: YOR172W_Spar Sequences read.. Counting patterns.. # site patterns = 158 Counting frequencies.. 120 bytes for distance 25280 bytes for lkl0 20224 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.257385 0.031066 0.088160 0.125602 0.124903 0.268174 0.164165 0.082250 lnL0 = -1626.972589 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1626.972589 x= 0.25738 0.03107 0.08816 0.12560 0.12490 0.26817 0.16416 0.08225 1 h-lim-p 0.0026 0.9436 112.9052 1624.779078 9 0.0004 44 | 0/8 2 h-lim-p 0.0005 0.0038 33.5481 1624.237044 0 0.0010 57 | 0/8 3 h-lim-p 0.0028 0.0221 11.3756 1624.186337 6 0.0009 83 | 0/8 4 h-lim-p 0.0031 0.0665 3.2632 1624.182686 4 0.0008 106 | 0/8 5 h-lim-p 0.0021 0.3060 1.1650 1624.182067 3 0.0010 125 | 0/8 6 h-lim-p 0.0126 2.2394 0.0945 1624.182054 0 0.0016 139 | 0/8 7 h-lim-p 0.0063 7.7842 0.0234 1624.181913 0 0.0254 161 | 0/8 8 h-lim-p 0.0060 1.7405 0.0986 1624.177549 0 0.0361 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 1624.177164 3 1.0449 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1624.177163 0 1.0938 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1624.177163 0 1.0938 249 | 0/8 12 h-lim-p 1.5709 20.0000 0.0000 1624.177163 0 1.5709 269 | 0/8 13 h-lim-p 0.6591 20.0000 0.0000 1624.177163 0 0.0000 306 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 1624.177163 0 0.0000 336 Out... lnL = -1624.177163 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1624.177163 Node 7: lnL = -1624.177163 Node 8: lnL = -1624.177163 Node 9: lnL = -1624.177163 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 523 Sequential format.. Reading seq # 1: YOR174W_Sbay Reading seq # 2: YOR174W_Scer Reading seq # 3: YOR174W_Skud Reading seq # 4: YOR174W_Smik Reading seq # 5: YOR174W_Spar Sequences read.. Counting patterns.. # site patterns = 236 Counting frequencies.. 120 bytes for distance 37760 bytes for lkl0 30208 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.318245 0.040617 0.111489 0.143579 0.112844 0.192317 0.220905 0.123027 lnL0 = -2338.231573 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2338.231573 x= 0.31825 0.04062 0.11149 0.14358 0.11284 0.19232 0.22091 0.12303 1 h-lim-p 0.0114 0.1423 64.1618 2337.461370 8 0.0004 44 | 0/8 2 h-lim-p 0.0019 0.0150 9.6023 2337.435540 7 0.0006 77 | 0/8 3 h-lim-p 0.0016 0.0767 3.3536 2337.432747 4 0.0006 100 | 0/8 4 h-lim-p 0.0019 0.2084 0.9841 2337.432402 1 0.0007 114 | 0/8 5 h-lim-p 0.0047 1.2706 0.1555 2337.432389 0 0.0010 135 | 0/8 6 h-lim-p 0.0025 3.4058 0.0654 2337.432388 1 0.0006 158 | 0/8 7 h-lim-p 0.0167 20.0000 0.0024 2337.432388 0 0.0146 178 | 0/8 8 h-lim-p 0.0368 20.0000 0.0009 2337.432366 0 0.1470 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2337.432366 0 1.0938 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2337.432366 0 1.0938 240 | 0/8 11 h-lim-p 1.1179 20.0000 0.0000 2337.432366 0 0.1397 262 | 0/8 12 h-lim-p 0.0275 20.0000 0.0000 2337.432366 0 0.0275 282 | 0/8 13 h-lim-p 0.0115 20.0000 0.0001 2337.432366 0 0.0086 302 | 0/8 14 h-lim-p 0.0042 20.0000 0.0002 2337.432366 0 0.0000 335 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 2337.432366 0 0.0000 362 Out... lnL = -2337.432366 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2337.432366 Node 7: lnL = -2337.432366 Node 8: lnL = -2337.432366 Node 9: lnL = -2337.432366 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 757 Sequential format.. Reading seq # 1: YOR175C_Sbay Reading seq # 2: YOR175C_Scer Reading seq # 3: YOR175C_Skud Reading seq # 4: YOR175C_Smik Reading seq # 5: YOR175C_Spar Sequences read.. Counting patterns.. # site patterns = 225 Counting frequencies.. 120 bytes for distance 36000 bytes for lkl0 28800 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.162141 0.042043 0.076242 0.101700 0.056293 0.164216 0.168372 0.035885 lnL0 = -3150.271885 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3150.271885 x= 0.16214 0.04204 0.07624 0.10170 0.05629 0.16422 0.16837 0.03589 1 h-lim-p 0.0003 0.0021 147.9674 3148.667037 7 0.0002 40 | 0/8 2 h-lim-p 0.0004 0.0035 26.1207 3148.598199 2 0.0002 56 | 0/8 3 h-lim-p 0.0004 0.0203 11.9335 3148.589135 6 0.0002 83 | 0/8 4 h-lim-p 0.0005 0.0499 3.8083 3148.587514 3 0.0003 102 | 0/8 5 h-lim-p 0.0037 0.2480 0.2597 3148.587506 1 0.0002 119 | 0/8 6 h-lim-p 0.0018 6.3609 0.0331 3148.587506 0 0.0004 140 | 0/8 7 h-lim-p 0.0015 20.0000 0.0086 3148.587506 0 0.0007 160 | 0/8 8 h-lim-p 0.0563 20.0000 0.0001 3148.587498 0 0.9003 184 | 0/8 9 h-lim-p 1.7965 20.0000 0.0001 3148.587498 0 1.5720 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3148.587498 0 1.0938 224 | 0/8 11 h-lim-p 0.2199 20.0000 0.0000 3148.587498 0 0.0069 248 | 0/8 12 h-lim-p 0.0012 20.0000 0.0002 3148.587498 0 0.0000 276 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 3148.587498 0 0.0000 310 Out... lnL = -3148.587498 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3148.587498 Node 7: lnL = -3148.587498 Node 8: lnL = -3148.587498 Node 9: lnL = -3148.587498 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 800 Sequential format.. Reading seq # 1: YOR176W_Sbay Reading seq # 2: YOR176W_Scer Reading seq # 3: YOR176W_Skud Reading seq # 4: YOR176W_Smik Reading seq # 5: YOR176W_Spar Sequences read.. Counting patterns.. # site patterns = 221 Counting frequencies.. 120 bytes for distance 35360 bytes for lkl0 28288 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.163632 0.036329 0.082613 0.102355 0.055639 0.159474 0.167897 0.032511 lnL0 = -3196.353369 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3196.353369 x= 0.16363 0.03633 0.08261 0.10236 0.05564 0.15947 0.16790 0.03251 1 h-lim-p 0.0002 0.0019 158.1398 3194.634052 8 0.0001 44 | 0/8 2 h-lim-p 0.0005 0.0040 33.1731 3194.503019 4 0.0002 64 | 0/8 3 h-lim-p 0.0006 0.0161 13.5702 3194.492098 2 0.0001 81 | 0/8 4 h-lim-p 0.0004 0.0371 4.5949 3194.490134 2 0.0002 98 | 0/8 5 h-lim-p 0.0044 0.3996 0.2118 3194.490128 0 0.0003 113 | 0/8 6 h-lim-p 0.0015 4.8044 0.0388 3194.490128 0 0.0007 133 | 0/8 7 h-lim-p 0.0297 20.0000 0.0009 3194.490126 0 0.0297 153 | 0/8 8 h-lim-p 0.0012 4.4992 0.0213 3194.490074 0 0.0097 176 | 0/8 9 h-lim-p 1.0410 20.0000 0.0002 3194.490067 0 1.0410 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3194.490067 0 1.2500 216 | 0/8 11 h-lim-p 0.9159 20.0000 0.0000 3194.490067 0 0.2003 237 | 0/8 12 h-lim-p 0.0556 20.0000 0.0001 3194.490067 0 0.0001 265 | 0/8 13 h-lim-p 0.0000 18.4261 0.0029 3194.490067 0 0.0000 285 | 0/8 14 h-lim-p 0.0001 20.0000 0.0003 3194.490067 0 0.0000 309 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 3194.490067 0 0.0000 340 | 0/8 16 h-lim-p 0.0000 20.0000 0.0031 | 0/8 17 h-lim-p 0.0000 20.0000 0.0031 Out... lnL = -3194.490067 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3194.490067 Node 7: lnL = -3194.490067 Node 8: lnL = -3194.490067 Node 9: lnL = -3194.490067 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 867 Sequential format.. Reading seq # 1: YOR179C_Sbay Reading seq # 2: YOR179C_Scer Reading seq # 3: YOR179C_Skud Reading seq # 4: YOR179C_Smik Reading seq # 5: YOR179C_Spar Sequences read.. Counting patterns.. # site patterns = 344 Counting frequencies.. 120 bytes for distance 55040 bytes for lkl0 44032 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.399349 0.131146 0.052104 0.207122 0.143221 0.150214 0.321537 0.148542 lnL0 = -3949.062531 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3949.062531 x= 0.39935 0.13115 0.05210 0.20712 0.14322 0.15021 0.32154 0.14854 1 h-lim-p 0.0053 0.0426 115.5512 3946.268512 9 0.0005 48 | 0/8 2 h-lim-p 0.0006 0.0046 51.8056 3945.460273 1 0.0007 62 | 0/8 3 h-lim-p 0.0005 0.0042 28.3245 3945.320290 6 0.0005 85 | 0/8 4 h-lim-p 0.0015 0.0128 8.8141 3945.284721 6 0.0011 110 | 0/8 5 h-lim-p 0.0036 0.0778 2.5555 3945.281253 4 0.0012 132 | 0/8 6 h-lim-p 0.0027 0.4338 1.1065 3945.280579 2 0.0013 148 | 0/8 7 h-lim-p 0.0069 2.9163 0.2017 3945.280498 2 0.0023 166 | 0/8 8 h-lim-p 0.0578 20.0000 0.0079 3945.259190 0 0.6937 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0011 3945.258464 2 1.0889 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3945.258464 0 1.0938 233 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3945.258464 0 1.0938 253 | 0/8 12 h-lim-p 1.0460 20.0000 0.0000 3945.258464 0 0.2615 274 | 0/8 13 h-lim-p 0.0405 20.0000 0.0000 3945.258464 0 0.0405 294 | 0/8 14 h-lim-p 0.0139 20.0000 0.0001 3945.258464 0 0.0001 321 | 0/8 15 h-lim-p 0.0007 20.0000 0.0000 3945.258464 0 0.0000 357 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 3945.258464 0 0.0000 382 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 3945.258464 0 0.0000 441 | 0/8 19 h-lim-p 0.0000 20.0000 0.0007 .. | 0/8 20 h-lim-p 0.0000 20.0000 0.0002 | 0/8 21 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -3945.258464 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3945.258464 Node 7: lnL = -3945.258464 Node 8: lnL = -3945.258464 Node 9: lnL = -3945.258464 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 826 Sequential format.. Reading seq # 1: YOR180C_Sbay Reading seq # 2: YOR180C_Scer Reading seq # 3: YOR180C_Skud Reading seq # 4: YOR180C_Smik Reading seq # 5: YOR180C_Spar Sequences read.. Counting patterns.. # site patterns = 359 Counting frequencies.. 120 bytes for distance 57440 bytes for lkl0 45952 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.236858 0.224077 0.087127 0.166480 0.104188 0.242115 0.300371 0.004837 lnL0 = -3881.252165 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3881.252165 x= 0.23686 0.22408 0.08713 0.16648 0.10419 0.24212 0.30037 0.00484 1 h-lim-p 0.0013 0.0101 86.1626 3879.793689 7 0.0004 36 | 0/8 2 h-lim-p 0.0002 0.0014 30.2304 3879.581153 0 0.0007 50 | 0/8 3 h-lim-p 0.0001 0.0011 24.6092 3879.505474 0 0.0004 63 | 0/8 4 h-lim-p 0.0014 0.0341 7.3195 3879.493925 5 0.0005 86 | 0/8 5 h-lim-p 0.0028 0.0569 1.3233 3879.493212 4 0.0008 109 | 0/8 6 h-lim-p 0.0014 0.2801 0.7622 3879.493053 2 0.0007 125 | 0/8 7 h-lim-p 0.0242 20.0000 0.0212 3879.491894 0 0.0726 146 | 0/8 8 h-lim-p 0.0046 1.1520 0.3379 3879.478395 0 0.0137 167 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 3879.478293 2 0.9961 191 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3879.478293 0 1.0938 211 | 0/8 11 h-lim-p 1.1281 20.0000 0.0000 3879.478293 0 0.9871 231 | 0/8 12 h-lim-p 0.3185 20.0000 0.0001 3879.478293 0 0.0199 254 | 0/8 13 h-lim-p 0.0045 20.0000 0.0004 3879.478293 0 0.0023 274 | 0/8 14 h-lim-p 0.0014 13.8733 0.0006 3879.478293 0 0.0000 298 | 0/8 15 h-lim-p 0.0001 20.0000 0.0003 3879.478293 0 0.0000 331 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 3879.478293 0 0.0000 356 Out... lnL = -3879.478293 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3879.478293 Node 7: lnL = -3879.478293 Node 8: lnL = -3879.478293 Node 9: lnL = -3879.478293 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 833 Sequential format.. Reading seq # 1: YOR181W_Sbay Reading seq # 2: YOR181W_Scer Reading seq # 3: YOR181W_Skud Reading seq # 4: YOR181W_Smik Reading seq # 5: YOR181W_Spar Sequences read.. Counting patterns.. # site patterns = 339 Counting frequencies.. 120 bytes for distance 54240 bytes for lkl0 43392 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.259674 0.199289 0.081125 0.175337 0.093322 0.259808 0.250087 0.032304 lnL0 = -3938.204420 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3938.204420 x= 0.25967 0.19929 0.08112 0.17534 0.09332 0.25981 0.25009 0.03230 1 h-lim-p 0.0005 0.0042 84.6245 3936.895677 8 0.0004 42 | 0/8 2 h-lim-p 0.0012 0.0096 23.0043 3936.764693 4 0.0005 61 | 0/8 3 h-lim-p 0.0007 0.0167 16.5563 3936.733381 3 0.0003 79 | 0/8 4 h-lim-p 0.0009 0.0444 6.1977 3936.725643 6 0.0005 106 | 0/8 5 h-lim-p 0.0030 0.2603 1.0323 3936.725242 3 0.0008 125 | 0/8 6 h-lim-p 0.0025 0.4464 0.3239 3936.725217 1 0.0005 140 | 0/8 7 h-lim-p 0.0069 10.1144 0.0254 3936.725217 0 0.0015 161 | 0/8 8 h-lim-p 0.1449 20.0000 0.0003 3936.725151 0 1.1591 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3936.725147 0 1.0938 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3936.725147 0 1.0938 224 | 0/8 11 h-lim-p 1.0822 20.0000 0.0000 3936.725147 0 0.9469 244 | 0/8 12 h-lim-p 0.3135 20.0000 0.0001 3936.725147 0 0.0049 269 | 0/8 13 h-lim-p 0.0012 20.0000 0.0002 3936.725147 0 0.0003 290 | 0/8 14 h-lim-p 0.0001 20.0000 0.0010 3936.725147 0 0.0000 322 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 3936.725147 0 0.0000 351 Out... lnL = -3936.725147 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3936.725147 Node 7: lnL = -3936.725147 Node 8: lnL = -3936.725147 Node 9: lnL = -3936.725147 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 138 Sequential format.. Reading seq # 1: YOR184W_Sbay Reading seq # 2: YOR184W_Scer Reading seq # 3: YOR184W_Skud Reading seq # 4: YOR184W_Smik Reading seq # 5: YOR184W_Spar Sequences read.. Counting patterns.. # site patterns = 67 Counting frequencies.. 120 bytes for distance 10720 bytes for lkl0 8576 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.317730 0.191620 0.000060 0.173439 0.111256 0.267801 0.285979 0.105679 lnL0 = -550.060782 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 550.060782 x= 0.31773 0.19162 0.00006 0.17344 0.11126 0.26780 0.28598 0.10568 1 h-lim-p 0.0000 0.0000 13.8866 550.058085 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0315 6.2235 550.012210 0 0.0035 41 | 1/8 3 h-lim-p 0.0118 0.1254 1.8663 550.002087 2 0.0055 57 | 1/8 4 h-lim-p 0.0178 0.7607 0.5827 549.996634 6 0.0130 83 | 1/8 5 h-lim-p 0.0143 0.6478 0.5299 549.971248 0 0.0285 103 | 1/8 6 h-lim-p 0.0175 0.2540 0.8630 549.824066 0 0.0350 123 | 1/8 7 h-lim-p 0.0082 0.0988 3.6934 549.742003 2 0.0077 146 | 1/8 8 h-lim-p 2.5000 20.0000 0.0026 549.741314 5 0.8380 170 | 0/8 9 h-lim-p 0.0031 1.2340 0.7205 549.741048 3 0.0013 195 | 0/8 10 h-lim-p 1.1479 20.0000 0.0008 549.740941 2 1.1837 219 | 0/8 11 h-lim-p 2.5000 20.0000 0.0001 549.740939 2 0.7996 244 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 549.740939 0 1.0938 264 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 549.740939 0 1.0938 284 | 0/8 14 h-lim-p 1.7805 20.0000 0.0000 549.740939 0 0.7790 304 | 0/8 15 h-lim-p 0.4645 20.0000 0.0000 549.740939 0 0.0036 330 | 0/8 16 h-lim-p 0.0011 20.0000 0.0000 549.740939 0 0.0011 350 | 0/8 17 h-lim-p 0.0003 20.0000 0.0000 549.740939 0 0.0001 370 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 549.740939 0 0.0000 390 | 0/8 19 h-lim-p 0.0001 20.0000 0.0001 549.740939 0 0.0000 415 | 0/8 20 h-lim-p 0.0000 20.0000 0.0000 549.740939 0 0.0000 441 | 0/8 21 h-lim-p 0.0000 20.0000 0.0000 549.740939 0 0.0000 461 | 0/8 22 h-lim-p 0.0000 20.0000 0.0000 549.740939 0 0.0000 489 Out... lnL = -549.740939 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -549.740939 Node 7: lnL = -549.740939 Node 8: lnL = -549.740939 Node 9: lnL = -549.740939 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 865 Sequential format.. Reading seq # 1: YOR185C_Sbay Reading seq # 2: YOR185C_Scer Reading seq # 3: YOR185C_Skud Reading seq # 4: YOR185C_Smik Reading seq # 5: YOR185C_Spar Sequences read.. Counting patterns.. # site patterns = 314 Counting frequencies.. 120 bytes for distance 50240 bytes for lkl0 40192 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.243943 0.030789 0.063687 0.134246 0.131936 0.195205 0.257738 0.065499 lnL0 = -3835.564883 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3835.564883 x= 0.24394 0.03079 0.06369 0.13425 0.13194 0.19521 0.25774 0.06550 1 h-lim-p 0.0024 0.0193 173.4023 3833.348611 6 0.0002 37 | 0/8 2 h-lim-p 0.0006 0.0051 29.5194 3833.216601 5 0.0003 60 | 0/8 3 h-lim-p 0.0006 0.0202 15.1427 3833.178190 6 0.0004 87 | 0/8 4 h-lim-p 0.0014 0.0537 4.3286 3833.175145 4 0.0004 109 | 0/8 5 h-lim-p 0.0011 0.1010 1.4758 3833.174808 3 0.0003 129 | 0/8 6 h-lim-p 0.0024 0.7915 0.2143 3833.174802 0 0.0003 143 | 0/8 7 h-lim-p 0.0047 20.0000 0.0135 3833.174799 0 0.0041 163 | 0/8 8 h-lim-p 0.0135 20.0000 0.0041 3833.173895 0 0.1619 186 | 0/8 9 h-lim-p 2.4477 20.0000 0.0003 3833.173891 0 1.0709 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3833.173891 0 1.0938 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3833.173891 0 2.1875 246 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3833.173891 0 1.0938 266 | 0/8 13 h-lim-p 0.3163 20.0000 0.0000 3833.173891 0 0.0198 289 | 0/8 14 h-lim-p 0.0011 20.0000 0.0006 3833.173891 0 0.0000 315 | 0/8 15 h-lim-p 0.0006 20.0000 0.0000 3833.173891 0 0.0000 345 Out... lnL = -3833.173891 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3833.173891 Node 7: lnL = -3833.173891 Node 8: lnL = -3833.173891 Node 9: lnL = -3833.173891 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 867 Sequential format.. Reading seq # 1: YOR186W_Sbay Reading seq # 2: YOR186W_Scer Reading seq # 3: YOR186W_Skud Reading seq # 4: YOR186W_Smik Reading seq # 5: YOR186W_Spar Sequences read.. Counting patterns.. # site patterns = 343 Counting frequencies.. 120 bytes for distance 54880 bytes for lkl0 43904 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.329523 0.058665 0.043559 0.153550 0.123532 0.208885 0.303459 0.117595 lnL0 = -4019.803138 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4019.803138 x= 0.32952 0.05867 0.04356 0.15355 0.12353 0.20888 0.30346 0.11760 1 h-lim-p 0.0022 0.0174 166.4198 4017.667096 8 0.0002 44 | 0/8 2 h-lim-p 0.0006 0.0061 46.2743 4017.219294 8 0.0004 77 | 0/8 3 h-lim-p 0.0008 0.0169 25.0311 4017.130070 5 0.0004 98 | 0/8 4 h-lim-p 0.0008 0.0287 11.1553 4017.101401 6 0.0006 123 | 0/8 5 h-lim-p 0.0015 0.0670 4.3620 4017.097720 5 0.0005 147 | 0/8 6 h-lim-p 0.0023 0.2254 0.8909 4017.097474 3 0.0007 167 | 0/8 7 h-lim-p 0.0032 0.9723 0.1871 4017.097467 0 0.0004 189 | 0/8 8 h-lim-p 0.2732 20.0000 0.0003 4017.097183 0 1.0929 211 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4017.097175 1 0.9961 233 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4017.097175 0 1.0938 253 | 0/8 11 h-lim-p 1.1707 20.0000 0.0000 4017.097175 0 7.0241 275 | 0/8 12 h-lim-p 1.5959 20.0000 0.0000 4017.097175 0 0.7980 295 | 0/8 13 h-lim-p 0.0303 20.0000 0.0012 4017.097175 0 0.0000 339 | 0/8 14 h-lim-p 0.0000 20.0000 0.0015 | 0/8 15 h-lim-p 0.0000 20.0000 0.0015 Out... lnL = -4017.097175 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4017.097175 Node 7: lnL = -4017.097175 Node 8: lnL = -4017.097175 Node 9: lnL = -4017.097175 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 529 Sequential format.. Reading seq # 1: YOR187W_Sbay Reading seq # 2: YOR187W_Scer Reading seq # 3: YOR187W_Skud Reading seq # 4: YOR187W_Smik Reading seq # 5: YOR187W_Spar Sequences read.. Counting patterns.. # site patterns = 228 Counting frequencies.. 120 bytes for distance 36480 bytes for lkl0 29184 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.256466 0.013707 0.076124 0.129208 0.070951 0.219776 0.241996 0.083198 lnL0 = -2365.627353 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2365.627353 x= 0.25647 0.01371 0.07612 0.12921 0.07095 0.21978 0.24200 0.08320 1 h-lim-p 0.0018 0.7222 163.4671 2362.872517 5 0.0002 34 | 0/8 2 h-lim-p 0.0008 0.0065 20.8405 2362.754431 7 0.0005 63 | 0/8 3 h-lim-p 0.0010 0.0251 11.7620 2362.731323 2 0.0004 79 | 0/8 4 h-lim-p 0.0014 0.0884 3.6401 2362.728129 3 0.0005 97 | 0/8 5 h-lim-p 0.0038 0.4654 0.5227 2362.728025 1 0.0008 112 | 0/8 6 h-lim-p 0.0022 1.2242 0.1836 2362.728015 2 0.0007 138 | 0/8 7 h-lim-p 0.0045 13.5305 0.0293 2362.728014 0 0.0011 159 | 0/8 8 h-lim-p 0.0981 20.0000 0.0003 2362.727843 0 1.1767 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2362.727842 0 1.0938 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2362.727842 0 1.0938 222 | 0/8 11 h-lim-p 1.1765 20.0000 0.0000 2362.727842 0 1.0294 242 | 0/8 12 h-lim-p 0.2386 20.0000 0.0000 2362.727842 0 0.0298 264 | 0/8 13 h-lim-p 0.0071 20.0000 0.0002 2362.727842 0 0.0000 291 | 0/8 14 h-lim-p 0.0003 20.0000 0.0000 2362.727842 0 0.0000 320 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 2362.727842 0 0.0000 353 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -2362.727842 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2362.727842 Node 7: lnL = -2362.727842 Node 8: lnL = -2362.727842 Node 9: lnL = -2362.727842 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 453 Sequential format.. Reading seq # 1: YOR188W_Sbay Reading seq # 2: YOR188W_Scer Reading seq # 3: YOR188W_Skud Reading seq # 4: YOR188W_Smik Reading seq # 5: YOR188W_Spar Sequences read.. Counting patterns.. # site patterns = 109 Counting frequencies.. 120 bytes for distance 17440 bytes for lkl0 13952 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.571798 0.256115 0.145388 0.194481 0.137271 3.919752 0.437472 0.000060 lnL0 = -1666.667405 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1666.667405 x= 0.57180 0.25611 0.14539 0.19448 0.13727 3.91975 0.43747 0.00006 1 h-lim-p 0.0000 0.0000 453.2959 1666.535201 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0003 975.5238 1573.092978 m 0.0003 36 | 2/8 3 h-lim-p 0.0003 0.0020 216.3355 1545.878937 0 0.0010 50 | 2/8 4 h-lim-p 0.0012 0.0094 37.5664 1544.560153 0 0.0018 62 | 2/8 5 h-lim-p 0.0058 0.0463 2.7140 1542.747370 0 0.0231 76 | 2/8 6 h-lim-p 0.0037 0.0298 10.1141 1519.014745 0 0.0149 90 | 2/8 7 h-lim-p 0.2590 2.0717 0.0866 1518.175035 0 0.3884 102 | 2/8 8 h-lim-p 0.5984 4.7869 0.0354 1518.030310 4 0.3047 129 | 1/8 9 h-lim-p 0.0013 0.0461 8.0664 1518.011750 6 0.0007 159 | 1/8 10 h-lim-p 1.3311 20.0000 0.0042 1518.008920 4 0.4386 181 | 1/8 11 h-lim-p 1.4546 20.0000 0.0013 1518.008732 2 0.3409 205 | 0/8 12 h-lim-p 0.0000 0.0000 0.0092 h-lim-p: 6.72223305e-20 5.37778644e-19 9.15090175e-03 1518.008732 .. | 1/8 13 h-lim-p 0.0000 0.1503 0.0804 1518.008731 0 0.0003 245 | 1/8 14 h-lim-p 0.0011 16.3346 0.0244 1518.008730 0 0.0005 264 | 1/8 15 h-lim-p 0.0010 10.0142 0.0107 1518.008730 0 0.0005 283 | 1/8 16 h-lim-p 0.0009 6.0105 0.0052 1518.008730 0 0.0004 302 | 1/8 17 h-lim-p 0.0052 20.0000 0.0004 1518.008730 0 0.0003 324 | 1/8 18 h-lim-p 0.0022 20.0000 0.0001 1518.008730 0 0.8436 351 | 1/8 19 h-lim-p 1.2145 20.0000 0.0000 1518.008730 0 1.0626 370 | 1/8 20 h-lim-p 0.1342 20.0000 0.0003 1518.008730 0 0.0042 393 | 1/8 21 h-lim-p 0.0011 6.3888 0.0011 1518.008730 0 0.0000 428 | 1/8 22 h-lim-p 0.0002 20.0000 0.0000 1518.008730 0 0.0000 457 Out... lnL = -1518.008730 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1518.008730 Node 7: lnL = -1518.008730 Node 8: lnL = -1518.008730 Node 9: lnL = -1518.008730 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 489 Sequential format.. Reading seq # 1: YOR189W_Sbay Reading seq # 2: YOR189W_Scer Reading seq # 3: YOR189W_Skud Reading seq # 4: YOR189W_Smik Reading seq # 5: YOR189W_Spar Sequences read.. Counting patterns.. # site patterns = 220 Counting frequencies.. 120 bytes for distance 35200 bytes for lkl0 28160 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.297083 0.089368 0.045126 0.206744 0.126088 0.191147 0.263633 0.079640 lnL0 = -2317.452895 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2317.452895 x= 0.29708 0.08937 0.04513 0.20674 0.12609 0.19115 0.26363 0.07964 1 h-lim-p 0.0006 0.0052 91.9948 2315.691779 8 0.0005 41 | 0/8 2 h-lim-p 0.0006 0.0050 37.9479 2315.359220 3 0.0005 59 | 0/8 3 h-lim-p 0.0015 0.0327 12.9699 2315.307155 2 0.0007 75 | 0/8 4 h-lim-p 0.0019 0.0581 4.8209 2315.296548 6 0.0010 100 | 0/8 5 h-lim-p 0.0039 0.1390 1.3079 2315.295886 2 0.0008 117 | 0/8 6 h-lim-p 0.0309 8.4122 0.0357 2315.295885 1 0.0009 135 | 0/8 7 h-lim-p 0.0197 20.0000 0.0017 2315.295883 0 0.0395 156 | 0/8 8 h-lim-p 0.0072 20.0000 0.0094 2315.295829 0 0.0289 178 | 0/8 9 h-lim-p 1.4252 20.0000 0.0002 2315.295827 0 1.2471 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2315.295827 0 1.0938 218 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2315.295827 0 1.0938 238 | 0/8 12 h-lim-p 0.5626 20.0000 0.0000 2315.295827 0 0.5626 258 | 0/8 13 h-lim-p 0.2219 20.0000 0.0000 2315.295827 0 0.0069 282 | 0/8 14 h-lim-p 0.0022 20.0000 0.0001 2315.295827 0 0.0000 318 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -2315.295827 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2315.295827 Node 7: lnL = -2315.295827 Node 8: lnL = -2315.295827 Node 9: lnL = -2315.295827 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 834 Sequential format.. Reading seq # 1: YOR190W_Sbay Reading seq # 2: YOR190W_Scer Reading seq # 3: YOR190W_Skud Reading seq # 4: YOR190W_Smik Reading seq # 5: YOR190W_Spar Sequences read.. Counting patterns.. # site patterns = 394 Counting frequencies.. 120 bytes for distance 63040 bytes for lkl0 50432 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.409932 0.062377 0.105191 0.238554 0.187121 0.240688 0.338388 0.124869 lnL0 = -4140.399145 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4140.399145 x= 0.40993 0.06238 0.10519 0.23855 0.18712 0.24069 0.33839 0.12487 1 h-lim-p 0.0022 0.0177 70.2395 4139.303702 7 0.0005 39 | 0/8 2 h-lim-p 0.0009 0.0070 27.0578 4139.063407 3 0.0007 58 | 0/8 3 h-lim-p 0.0016 0.0145 12.6877 4139.011436 4 0.0008 79 | 0/8 4 h-lim-p 0.0020 0.0793 4.9434 4139.002270 2 0.0009 95 | 0/8 5 h-lim-p 0.0067 0.6191 0.6573 4139.002023 3 0.0012 116 | 0/8 6 h-lim-p 0.0053 2.3182 0.1467 4139.002009 0 0.0012 137 | 0/8 7 h-lim-p 0.0057 7.1715 0.0299 4139.002004 1 0.0028 160 | 0/8 8 h-lim-p 0.0246 20.0000 0.0034 4139.000986 0 0.3929 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 4139.000946 1 0.9961 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4139.000945 0 1.0938 226 | 0/8 11 h-lim-p 1.3027 20.0000 0.0000 4139.000945 0 1.1399 246 | 0/8 12 h-lim-p 0.4385 20.0000 0.0000 4139.000945 0 0.0034 272 | 0/8 13 h-lim-p 0.0025 20.0000 0.0000 4139.000945 0 0.0001 296 | 0/8 14 h-lim-p 0.0026 20.0000 0.0000 4139.000945 0 0.0000 332 Out... lnL = -4139.000945 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4139.000945 Node 7: lnL = -4139.000945 Node 8: lnL = -4139.000945 Node 9: lnL = -4139.000945 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 352 Sequential format.. Reading seq # 1: YOR194C_Sbay Reading seq # 2: YOR194C_Scer Reading seq # 3: YOR194C_Skud Reading seq # 4: YOR194C_Smik Reading seq # 5: YOR194C_Spar Sequences read.. Counting patterns.. # site patterns = 148 Counting frequencies.. 120 bytes for distance 23680 bytes for lkl0 18944 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.188481 0.000060 0.124170 0.112538 0.060615 0.197315 0.221003 0.050947 lnL0 = -1340.709746 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1340.709746 x= 0.18848 0.00006 0.12417 0.11254 0.06061 0.19732 0.22100 0.05095 1 h-lim-p 0.0001 0.0011 116.1759 1337.334281 0 0.0004 23 | 0/8 2 h-lim-p 0.0001 0.0009 113.0248 1335.705745 0 0.0004 37 | 0/8 3 h-lim-p 0.0006 0.0046 28.0303 1335.551104 4 0.0005 57 | 0/8 4 h-lim-p 0.0011 0.5106 11.9484 1335.508857 7 0.0007 87 | 0/8 5 h-lim-p 0.0009 0.0077 9.4423 1335.493390 7 0.0005 117 | 0/8 6 h-lim-p 0.0037 0.0300 1.3708 1335.492981 2 0.0004 135 | 0/8 7 h-lim-p 0.0070 3.7080 0.0851 1335.492804 2 0.0079 152 | 0/8 8 h-lim-p 0.0196 2.1338 0.0346 1335.477080 0 0.1565 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0008 1335.476619 3 1.0004 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1335.476618 0 1.0938 221 | 0/8 11 h-lim-p 1.6738 20.0000 0.0000 1335.476618 0 0.7323 241 | 0/8 12 h-lim-p 0.4998 20.0000 0.0000 1335.476618 0 0.2187 261 | 0/8 13 h-lim-p 0.0956 20.0000 0.0001 1335.476618 0 0.0002 289 | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 1335.476618 0 0.0000 323 | 0/8 15 h-lim-p 0.0000 20.0000 0.0013 | 0/8 16 h-lim-p 0.0000 20.0000 0.0013 Out... lnL = -1335.476618 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1335.476618 Node 7: lnL = -1335.476618 Node 8: lnL = -1335.476618 Node 9: lnL = -1335.476618 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 351 Sequential format.. Reading seq # 1: YOR195W_Sbay Reading seq # 2: YOR195W_Scer Reading seq # 3: YOR195W_Skud Reading seq # 4: YOR195W_Smik Reading seq # 5: YOR195W_Spar Sequences read.. Counting patterns.. # site patterns = 161 Counting frequencies.. 120 bytes for distance 25760 bytes for lkl0 20608 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.187778 0.033998 0.093530 0.152992 0.000060 0.198839 0.233091 0.051485 lnL0 = -1382.625937 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1382.625937 x= 0.18778 0.03400 0.09353 0.15299 0.00006 0.19884 0.23309 0.05148 1 h-lim-p 0.0002 0.0013 419.0632 1376.816066 6 0.0001 34 | 0/8 2 h-lim-p 0.0001 0.0011 77.6978 1374.916929 0 0.0006 48 | 0/8 3 h-lim-p 0.0008 0.0067 28.4604 1374.768190 4 0.0004 69 | 0/8 4 h-lim-p 0.0026 0.0539 4.6220 1374.755303 2 0.0012 85 | 0/8 5 h-lim-p 0.0063 0.3305 0.9052 1374.754981 2 0.0008 103 | 0/8 6 h-lim-p 0.0022 0.3730 0.3253 1374.754880 3 0.0014 131 | 0/8 7 h-lim-p 0.0077 5.1760 0.0597 1374.754080 0 0.0307 153 | 0/8 8 h-lim-p 0.0116 0.2619 0.1576 1374.735924 0 0.0233 174 | 0/8 9 h-lim-p 2.5000 20.0000 0.0009 1374.730943 3 2.0898 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0008 1374.730018 4 1.3159 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1374.730018 0 1.0938 249 | 0/8 12 h-lim-p 1.6189 20.0000 0.0000 1374.730018 0 1.4165 269 | 0/8 13 h-lim-p 1.3760 20.0000 0.0000 1374.730018 0 2.7520 290 | 0/8 14 h-lim-p 0.1847 20.0000 0.0003 1374.730018 0 0.0029 315 | 0/8 15 h-lim-p 0.0006 19.5640 0.0015 1374.730018 0 0.0003 335 | 0/8 16 h-lim-p 0.0002 14.0034 0.0020 1374.730018 0 0.0000 358 | 0/8 17 h-lim-p 0.0000 20.0000 0.0011 1374.730018 0 0.0000 385 | 0/8 18 h-lim-p 0.0002 20.0000 0.0000 1374.730018 0 0.0000 410 Out... lnL = -1374.730018 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1374.730018 Node 7: lnL = -1374.730018 Node 8: lnL = -1374.730018 Node 9: lnL = -1374.730018 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 195 Sequential format.. Reading seq # 1: YOR196C_Sbay Reading seq # 2: YOR196C_Scer Reading seq # 3: YOR196C_Skud Reading seq # 4: YOR196C_Smik Reading seq # 5: YOR196C_Spar Sequences read.. Counting patterns.. # site patterns = 99 Counting frequencies.. 120 bytes for distance 15840 bytes for lkl0 12672 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.204614 0.016355 0.109116 0.167582 0.060576 0.212107 0.234783 0.029882 lnL0 = -878.593334 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 878.593334 x= 0.20461 0.01636 0.10912 0.16758 0.06058 0.21211 0.23478 0.02988 1 h-lim-p 0.0024 0.0195 15.7354 878.461479 3 0.0011 28 | 0/8 2 h-lim-p 0.0005 0.0036 6.5375 878.449831 0 0.0007 40 | 0/8 3 h-lim-p 0.0032 0.2532 1.4008 878.448606 3 0.0013 58 | 0/8 4 h-lim-p 0.0030 0.1342 0.6135 878.448494 2 0.0007 75 | 0/8 5 h-lim-p 0.0033 1.5472 0.1317 878.448480 2 0.0017 100 | 0/8 6 h-lim-p 0.0239 18.8341 0.0096 878.448479 0 0.0052 121 | 0/8 7 h-lim-p 0.0056 14.7020 0.0090 878.448471 0 0.0225 143 | 0/8 8 h-lim-p 0.0130 20.0000 0.0155 878.448373 0 0.0261 164 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 878.448373 0 1.0938 184 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 878.448373 0 1.0938 204 | 0/8 11 h-lim-p 1.0342 20.0000 0.0000 878.448373 0 8.2737 227 | 0/8 12 h-lim-p 0.2518 20.0000 0.0003 878.448373 0 0.0069 251 | 0/8 13 h-lim-p 0.0012 20.0000 0.0018 878.448373 0 0.0006 271 | 0/8 14 h-lim-p 0.0002 6.8532 0.0063 878.448373 0 0.0000 296 | 0/8 15 h-lim-p 0.0001 20.0000 0.0002 878.448373 0 0.0000 318 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 878.448373 0 0.0000 338 | 0/8 17 h-lim-p 0.0001 20.0000 0.0000 878.448373 0 0.0000 374 | 0/8 18 h-lim-p 0.0000 20.0000 0.0005 878.448373 0 0.0000 408 | 0/8 19 h-lim-p 0.0000 20.0000 0.0005 | 0/8 20 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -878.448373 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -878.448373 Node 7: lnL = -878.448373 Node 8: lnL = -878.448373 Node 9: lnL = -878.448373 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 322 Sequential format.. Reading seq # 1: YOR197W_Sbay Reading seq # 2: YOR197W_Scer Reading seq # 3: YOR197W_Skud Reading seq # 4: YOR197W_Smik Reading seq # 5: YOR197W_Spar Sequences read.. Counting patterns.. # site patterns = 124 Counting frequencies.. 120 bytes for distance 19840 bytes for lkl0 15872 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.216139 0.028009 0.076091 0.179858 0.052758 0.251045 0.233091 0.036917 lnL0 = -1189.017342 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1189.017342 x= 0.21614 0.02801 0.07609 0.17986 0.05276 0.25105 0.23309 0.03692 1 h-lim-p 0.0004 0.0030 44.1702 1188.244626 0 0.0007 23 | 0/8 2 h-lim-p 0.0005 0.0037 9.0782 1188.214978 0 0.0009 36 | 0/8 3 h-lim-p 0.0013 0.0519 6.6757 1188.198445 3 0.0011 54 | 0/8 4 h-lim-p 0.0062 0.0841 1.1357 1188.198006 2 0.0007 72 | 0/8 5 h-lim-p 0.0016 0.1258 0.5001 1188.197821 2 0.0015 88 | 0/8 6 h-lim-p 0.0256 3.5326 0.0300 1188.196935 0 0.0513 109 | 0/8 7 h-lim-p 0.0040 0.2274 0.3831 1188.191566 0 0.0080 130 | 0/8 8 h-lim-p 0.0023 0.0800 1.3280 1188.181392 0 0.0046 151 | 0/8 9 h-lim-p 2.5000 20.0000 0.0014 1188.180540 3 1.0004 169 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1188.180539 0 1.0938 189 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1188.180539 0 1.0938 209 | 0/8 12 h-lim-p 0.9967 20.0000 0.0000 1188.180539 0 3.9867 231 | 0/8 13 h-lim-p 0.1245 20.0000 0.0004 1188.180539 0 0.0039 255 | 0/8 14 h-lim-p 0.0010 20.0000 0.0015 1188.180539 0 0.0001 278 | 0/8 15 h-lim-p 0.0002 20.0000 0.0006 1188.180539 0 0.0000 299 | 0/8 16 h-lim-p 0.0001 20.0000 0.0004 1188.180539 0 0.0000 333 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1188.180539 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1188.180539 Node 7: lnL = -1188.180539 Node 8: lnL = -1188.180539 Node 9: lnL = -1188.180539 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 118 Sequential format.. Reading seq # 1: YOR198C_Sbay Reading seq # 2: YOR198C_Scer Reading seq # 3: YOR198C_Skud Reading seq # 4: YOR198C_Smik Reading seq # 5: YOR198C_Spar Sequences read.. Counting patterns.. # site patterns = 42 Counting frequencies.. 120 bytes for distance 6720 bytes for lkl0 5376 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.141024 0.024304 0.061942 0.060380 0.033787 0.067988 0.079540 0.051342 lnL0 = -410.162956 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 410.162956 x= 0.14102 0.02430 0.06194 0.06038 0.03379 0.06799 0.07954 0.05134 1 h-lim-p 0.0010 0.0082 26.6722 409.939844 6 0.0007 36 | 0/8 2 h-lim-p 0.0008 0.0060 10.7242 409.904656 3 0.0007 54 | 0/8 3 h-lim-p 0.0027 0.0431 2.6905 409.901916 6 0.0008 82 | 0/8 4 h-lim-p 0.0013 0.0396 1.6846 409.901342 3 0.0005 100 | 0/8 5 h-lim-p 0.0191 1.7343 0.0482 409.901340 1 0.0010 117 | 0/8 6 h-lim-p 0.0052 12.7356 0.0087 409.901340 0 0.0023 137 | 0/8 7 h-lim-p 0.0057 20.0000 0.0035 409.901339 0 0.0170 158 | 0/8 8 h-lim-p 0.0056 7.1176 0.0107 409.901291 0 0.0226 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 409.901290 1 0.9961 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 409.901290 0 1.0938 222 | 0/8 11 h-lim-p 1.1047 20.0000 0.0000 409.901290 0 0.0005 252 | 0/8 12 h-lim-p 0.0002 20.0000 0.0000 409.901290 0 0.0000 276 | 0/8 13 h-lim-p 0.0000 20.0000 0.0003 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0013 | 0/8 15 h-lim-p 0.0000 20.0000 0.0013 Out... lnL = -409.901290 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -409.901290 Node 7: lnL = -409.901290 Node 8: lnL = -409.901290 Node 9: lnL = -409.901290 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 307 Sequential format.. Reading seq # 1: YOR204W_Sbay Reading seq # 2: YOR204W_Scer Reading seq # 3: YOR204W_Skud Reading seq # 4: YOR204W_Smik Reading seq # 5: YOR204W_Spar Sequences read.. Counting patterns.. # site patterns = 137 Counting frequencies.. 120 bytes for distance 21920 bytes for lkl0 17536 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.163677 0.094568 0.043402 0.098201 0.065199 0.152984 0.106734 0.032207 lnL0 = -1215.594415 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1215.594415 x= 0.16368 0.09457 0.04340 0.09820 0.06520 0.15298 0.10673 0.03221 1 h-lim-p 0.0007 0.0059 112.4594 1213.685263 3 0.0003 29 | 0/8 2 h-lim-p 0.0006 0.0045 30.4126 1213.434348 5 0.0006 51 | 0/8 3 h-lim-p 0.0022 0.0189 7.6807 1213.418505 4 0.0006 72 | 0/8 4 h-lim-p 0.0027 0.0762 1.6272 1213.417775 2 0.0006 89 | 0/8 5 h-lim-p 0.0032 0.4877 0.3019 1213.417741 2 0.0007 106 | 0/8 6 h-lim-p 0.0104 8.4720 0.0215 1213.417741 0 0.0011 128 | 0/8 7 h-lim-p 0.1386 20.0000 0.0002 1213.417735 0 0.5546 150 | 0/8 8 h-lim-p 0.0013 0.9349 0.0780 1213.417730 1 0.0010 172 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1213.417730 0 1.0938 192 | 0/8 10 h-lim-p 1.5415 20.0000 0.0000 1213.417730 0 1.3488 212 | 0/8 11 h-lim-p 1.3143 20.0000 0.0000 1213.417730 0 1.1500 232 | 0/8 12 h-lim-p 0.1520 20.0000 0.0001 1213.417730 0 0.0048 256 | 0/8 13 h-lim-p 0.0013 20.0000 0.0004 1213.417730 0 0.0000 294 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1213.417730 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1213.417730 Node 7: lnL = -1213.417730 Node 8: lnL = -1213.417730 Node 9: lnL = -1213.417730 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 296 Sequential format.. Reading seq # 1: YOR205C_Sbay Reading seq # 2: YOR205C_Scer Reading seq # 3: YOR205C_Skud Reading seq # 4: YOR205C_Smik Reading seq # 5: YOR205C_Spar Sequences read.. Counting patterns.. # site patterns = 148 Counting frequencies.. 120 bytes for distance 23680 bytes for lkl0 18944 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.194919 0.086483 0.050910 0.163088 0.098746 0.185385 0.179242 0.027065 lnL0 = -1288.570579 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1288.570579 x= 0.19492 0.08648 0.05091 0.16309 0.09875 0.18539 0.17924 0.02707 1 h-lim-p 0.0010 0.0077 94.5484 1286.451172 8 0.0005 41 | 0/8 2 h-lim-p 0.0004 0.0032 37.8986 1285.797915 0 0.0012 54 | 0/8 3 h-lim-p 0.0004 0.0031 25.4943 1285.651400 0 0.0008 67 | 0/8 4 h-lim-p 0.0037 0.0549 5.3568 1285.635334 5 0.0012 91 | 0/8 5 h-lim-p 0.0045 0.0867 1.4344 1285.634230 4 0.0011 113 | 0/8 6 h-lim-p 0.0022 0.2670 0.7421 1285.633931 4 0.0013 136 | 0/8 7 h-lim-p 0.0107 2.9222 0.0868 1285.633827 4 0.0054 165 | 0/8 8 h-lim-p 0.0138 9.2776 0.0343 1285.620290 0 0.2205 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0014 1285.619682 3 1.0449 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1285.619677 2 1.3159 240 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1285.619677 0 1.0938 260 | 0/8 12 h-lim-p 2.0426 20.0000 0.0000 1285.619677 0 1.7873 280 | 0/8 13 h-lim-p 1.9131 20.0000 0.0000 1285.619677 0 1.6740 300 | 0/8 14 h-lim-p 0.3055 20.0000 0.0001 1285.619677 0 0.0048 325 | 0/8 15 h-lim-p 0.0005 20.0000 0.0005 1285.619677 0 0.0001 346 | 0/8 16 h-lim-p 0.0002 20.0000 0.0003 1285.619677 0 0.0001 366 | 0/8 17 h-lim-p 0.0001 20.0000 0.0006 1285.619677 0 0.0000 403 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 1285.619677 0 0.0000 435 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 1285.619677 0 0.0000 469 | 0/8 20 h-lim-p 0.0000 20.0000 0.0000 | 0/8 21 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1285.619677 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1285.619677 Node 7: lnL = -1285.619677 Node 8: lnL = -1285.619677 Node 9: lnL = -1285.619677 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 294 Sequential format.. Reading seq # 1: YOR206W_Sbay Reading seq # 2: YOR206W_Scer Reading seq # 3: YOR206W_Skud Reading seq # 4: YOR206W_Smik Reading seq # 5: YOR206W_Spar Sequences read.. Counting patterns.. # site patterns = 142 Counting frequencies.. 120 bytes for distance 22720 bytes for lkl0 18176 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.216754 0.009932 0.052985 0.170368 0.091466 0.200203 0.311498 0.038048 lnL0 = -1216.538579 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1216.538579 x= 0.21675 0.00993 0.05299 0.17037 0.09147 0.20020 0.31150 0.03805 1 h-lim-p 0.0019 1.0702 113.2793 1214.295408 6 0.0004 35 | 0/8 2 h-lim-p 0.0009 0.0070 20.3680 1214.028186 0 0.0013 47 | 0/8 3 h-lim-p 0.0012 0.0097 13.5508 1213.971201 7 0.0008 77 | 0/8 4 h-lim-p 0.0025 0.0414 4.5169 1213.955976 7 0.0017 109 | 0/8 5 h-lim-p 0.0094 0.2165 0.8347 1213.955481 5 0.0015 135 | 0/8 6 h-lim-p 0.0181 2.7872 0.0680 1213.955477 2 0.0015 163 | 0/8 7 h-lim-p 0.0084 10.5979 0.0121 1213.955472 0 0.0168 184 | 0/8 8 h-lim-p 0.0656 20.0000 0.0031 1213.955008 0 0.2623 206 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1213.955006 1 0.9961 228 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1213.955006 0 1.0938 248 | 0/8 11 h-lim-p 1.2241 20.0000 0.0000 1213.955006 0 1.8362 268 | 0/8 12 h-lim-p 0.5588 20.0000 0.0000 1213.955006 0 0.2794 288 | 0/8 13 h-lim-p 0.0150 20.0000 0.0004 1213.955006 0 0.0005 312 | 0/8 14 h-lim-p 0.0001 20.0000 0.0018 1213.955006 0 0.0000 346 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1213.955006 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1213.955006 Node 7: lnL = -1213.955006 Node 8: lnL = -1213.955006 Node 9: lnL = -1213.955006 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 648 Sequential format.. Reading seq # 1: YOR209C_Sbay Reading seq # 2: YOR209C_Scer Reading seq # 3: YOR209C_Skud Reading seq # 4: YOR209C_Smik Reading seq # 5: YOR209C_Spar Sequences read.. Counting patterns.. # site patterns = 216 Counting frequencies.. 120 bytes for distance 34560 bytes for lkl0 27648 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.189571 0.116704 0.079796 0.133484 0.080983 0.182470 0.139663 0.023351 lnL0 = -2827.503078 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2827.503078 x= 0.18957 0.11670 0.07980 0.13348 0.08098 0.18247 0.13966 0.02335 1 h-lim-p 0.0016 0.0131 43.9565 2827.223286 8 0.0003 43 | 0/8 2 h-lim-p 0.0007 0.0059 9.6879 2827.210111 4 0.0003 63 | 0/8 3 h-lim-p 0.0011 0.0522 2.6230 2827.209318 2 0.0003 80 | 0/8 4 h-lim-p 0.0014 0.5537 0.4759 2827.209278 2 0.0004 97 | 0/8 5 h-lim-p 0.0013 0.6222 0.1308 2827.209275 1 0.0003 120 | 0/8 6 h-lim-p 0.0020 15.4733 0.0215 2827.209275 0 0.0004 141 | 0/8 7 h-lim-p 0.0054 20.0000 0.0018 2827.209275 0 0.0012 162 | 0/8 8 h-lim-p 0.0207 20.0000 0.0001 2827.209273 0 0.6619 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2827.209273 0 1.0938 207 | 0/8 10 h-lim-p 0.7610 20.0000 0.0000 2827.209273 0 0.7610 227 | 0/8 11 h-lim-p 0.2795 20.0000 0.0001 2827.209273 0 0.2446 247 | 0/8 12 h-lim-p 0.0671 20.0000 0.0003 2827.209273 0 0.0010 272 | 0/8 13 h-lim-p 0.0005 20.0000 0.0008 2827.209273 0 0.0005 292 | 0/8 14 h-lim-p 0.0003 20.0000 0.0012 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 2827.209273 0 0.0000 356 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -2827.209273 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2827.209273 Node 7: lnL = -2827.209273 Node 8: lnL = -2827.209273 Node 9: lnL = -2827.209273 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 608 Sequential format.. Reading seq # 1: YOR210W_Sbay Reading seq # 2: YOR210W_Scer Reading seq # 3: YOR210W_Skud Reading seq # 4: YOR210W_Smik Reading seq # 5: YOR210W_Spar Sequences read.. Counting patterns.. # site patterns = 206 Counting frequencies.. 120 bytes for distance 32960 bytes for lkl0 26368 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.202634 0.087812 0.086301 0.128727 0.085741 0.178685 0.160602 0.035082 lnL0 = -2753.731497 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2753.731497 x= 0.20263 0.08781 0.08630 0.12873 0.08574 0.17868 0.16060 0.03508 1 h-lim-p 0.0008 0.0066 48.8221 2753.400757 8 0.0003 42 | 0/8 2 h-lim-p 0.0019 0.0148 7.3244 2753.391658 6 0.0003 68 | 0/8 3 h-lim-p 0.0019 0.0690 1.3576 2753.391336 2 0.0004 85 | 0/8 4 h-lim-p 0.0010 0.7474 0.5057 2753.391304 3 0.0003 105 | 0/8 5 h-lim-p 0.0010 1.3168 0.1454 2753.391300 1 0.0004 127 | 0/8 6 h-lim-p 0.0049 20.0000 0.0117 2753.391300 0 0.0005 149 | 0/8 7 h-lim-p 0.0022 20.0000 0.0029 2753.391300 0 0.0009 169 | 0/8 8 h-lim-p 0.0363 20.0000 0.0001 2753.391297 0 0.5815 193 | 0/8 9 h-lim-p 1.6694 20.0000 0.0000 2753.391297 0 1.4607 213 | 0/8 10 h-lim-p 2.2939 20.0000 0.0000 2753.391297 0 1.1469 233 | 0/8 11 h-lim-p 0.5610 20.0000 0.0000 2753.391297 0 0.4208 253 | 0/8 12 h-lim-p 0.0022 7.8235 0.0065 2753.391297 0 0.0000 280 | 0/8 13 h-lim-p 0.0003 20.0000 0.0002 2753.391297 0 0.0000 309 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 2753.391297 0 0.0000 333 Out... lnL = -2753.391297 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2753.391297 Node 7: lnL = -2753.391297 Node 8: lnL = -2753.391297 Node 9: lnL = -2753.391297 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 853 Sequential format.. Reading seq # 1: YOR211C_Sbay Reading seq # 2: YOR211C_Scer Reading seq # 3: YOR211C_Skud Reading seq # 4: YOR211C_Smik Reading seq # 5: YOR211C_Spar Sequences read.. Counting patterns.. # site patterns = 320 Counting frequencies.. 120 bytes for distance 51200 bytes for lkl0 40960 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.287805 0.103851 0.060440 0.175274 0.109836 0.224457 0.210724 0.076018 lnL0 = -4038.868670 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4038.868670 x= 0.28781 0.10385 0.06044 0.17527 0.10984 0.22446 0.21072 0.07602 1 h-lim-p 0.0008 0.0066 141.6605 4036.766235 9 0.0002 45 | 0/8 2 h-lim-p 0.0005 0.0043 45.2674 4036.364460 4 0.0004 65 | 0/8 3 h-lim-p 0.0007 0.0123 26.3038 4036.283526 6 0.0003 89 | 0/8 4 h-lim-p 0.0015 0.0541 5.3431 4036.276847 5 0.0005 112 | 0/8 5 h-lim-p 0.0024 0.3197 1.0942 4036.276540 2 0.0005 129 | 0/8 6 h-lim-p 0.0798 20.0000 0.0073 4036.276538 1 0.0049 146 | 0/8 7 h-lim-p 0.0051 20.0000 0.0070 4036.276269 0 0.0815 170 | 0/8 8 h-lim-p 0.0010 4.1600 0.5503 4036.276162 3 0.0006 197 | 0/8 9 h-lim-p 0.4561 20.0000 0.0007 4036.276157 0 0.9123 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4036.276157 0 1.0938 238 | 0/8 11 h-lim-p 1.5530 20.0000 0.0000 4036.276157 0 1.3589 258 | 0/8 12 h-lim-p 1.4668 20.0000 0.0000 4036.276157 0 1.2835 278 | 0/8 13 h-lim-p 0.4285 20.0000 0.0000 4036.276157 0 0.0000 319 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 4036.276157 0 0.0000 348 Out... lnL = -4036.276157 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4036.276157 Node 7: lnL = -4036.276157 Node 8: lnL = -4036.276157 Node 9: lnL = -4036.276157 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 858 Sequential format.. Reading seq # 1: YOR212W_Sbay Reading seq # 2: YOR212W_Scer Reading seq # 3: YOR212W_Skud Reading seq # 4: YOR212W_Smik Reading seq # 5: YOR212W_Spar Sequences read.. Counting patterns.. # site patterns = 309 Counting frequencies.. 120 bytes for distance 49440 bytes for lkl0 39552 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.194434 0.089473 0.061050 0.101280 0.090536 0.143095 0.172660 0.034776 lnL0 = -3424.664509 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3424.664509 x= 0.19443 0.08947 0.06105 0.10128 0.09054 0.14310 0.17266 0.03478 1 h-lim-p 0.0002 0.0019 148.7630 3422.510338 7 0.0002 39 | 0/8 2 h-lim-p 0.0005 0.0039 41.2434 3422.293026 7 0.0003 67 | 0/8 3 h-lim-p 0.0007 0.0151 16.4925 3422.271079 6 0.0002 94 | 0/8 4 h-lim-p 0.0007 0.0335 4.2984 3422.268927 4 0.0003 116 | 0/8 5 h-lim-p 0.0011 0.1391 0.9790 3422.268742 3 0.0004 135 | 0/8 6 h-lim-p 0.0027 1.0648 0.1408 3422.268740 0 0.0003 157 | 0/8 7 h-lim-p 0.0137 20.0000 0.0030 3422.268740 0 0.0015 179 | 0/8 8 h-lim-p 0.0346 20.0000 0.0001 3422.268735 0 0.5540 203 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3422.268735 0 1.0938 223 | 0/8 10 h-lim-p 1.0538 20.0000 0.0000 3422.268735 0 2.1076 244 | 0/8 11 h-lim-p 0.2995 20.0000 0.0002 3422.268735 0 0.1311 264 | 0/8 12 h-lim-p 0.0218 20.0000 0.0012 3422.268735 0 0.0095 284 | 0/8 13 h-lim-p 0.0034 18.9648 0.0034 3422.268735 0 0.0000 312 | 0/8 14 h-lim-p 0.0007 20.0000 0.0000 3422.268735 0 0.0000 348 | 0/8 15 h-lim-p 0.0000 20.0000 0.0015 | 0/8 16 h-lim-p 0.0000 20.0000 0.0015 Out... lnL = -3422.268735 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3422.268735 Node 7: lnL = -3422.268735 Node 8: lnL = -3422.268735 Node 9: lnL = -3422.268735 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 321 Sequential format.. Reading seq # 1: YOR213C_Sbay Reading seq # 2: YOR213C_Scer Reading seq # 3: YOR213C_Skud Reading seq # 4: YOR213C_Smik Reading seq # 5: YOR213C_Spar Sequences read.. Counting patterns.. # site patterns = 142 Counting frequencies.. 120 bytes for distance 22720 bytes for lkl0 18176 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.203746 0.033952 0.082400 0.134424 0.114626 0.189179 0.189211 0.031677 lnL0 = -1436.593634 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1436.593634 x= 0.20375 0.03395 0.08240 0.13442 0.11463 0.18918 0.18921 0.03168 1 h-lim-p 0.0021 0.0170 73.0404 1435.703836 8 0.0004 41 | 0/8 2 h-lim-p 0.0009 0.0071 14.4498 1435.629849 3 0.0007 59 | 0/8 3 h-lim-p 0.0019 0.0753 5.6336 1435.618208 5 0.0008 80 | 0/8 4 h-lim-p 0.0043 0.1440 1.1044 1435.617854 4 0.0006 104 | 0/8 5 h-lim-p 0.0037 1.3855 0.1786 1435.617839 2 0.0010 121 | 0/8 6 h-lim-p 0.0057 2.7572 0.0310 1435.617839 0 0.0012 142 | 0/8 7 h-lim-p 0.0545 20.0000 0.0007 1435.617837 0 0.0818 162 | 0/8 8 h-lim-p 0.0030 20.0000 0.0190 1435.617813 0 0.0091 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1435.617812 0 1.2500 203 | 0/8 10 h-lim-p 2.0774 20.0000 0.0000 1435.617812 0 0.9089 223 | 0/8 11 h-lim-p 0.8676 20.0000 0.0000 1435.617812 0 0.0271 247 | 0/8 12 h-lim-p 0.0077 20.0000 0.0001 1435.617812 0 0.0001 272 | 0/8 13 h-lim-p 0.0003 20.0000 0.0000 1435.617812 0 0.0000 305 | 0/8 14 h-lim-p 0.0000 20.0000 0.0005 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -1435.617812 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1435.617812 Node 7: lnL = -1435.617812 Node 8: lnL = -1435.617812 Node 9: lnL = -1435.617812 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 522 Sequential format.. Reading seq # 1: YOR214C_Sbay Reading seq # 2: YOR214C_Scer Reading seq # 3: YOR214C_Skud Reading seq # 4: YOR214C_Smik Reading seq # 5: YOR214C_Spar Sequences read.. Counting patterns.. # site patterns = 170 Counting frequencies.. 120 bytes for distance 27200 bytes for lkl0 21760 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.213623 0.047316 0.088540 0.107105 0.082421 0.158854 0.121342 0.057020 lnL0 = -2037.375618 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2037.375618 x= 0.21362 0.04732 0.08854 0.10711 0.08242 0.15885 0.12134 0.05702 1 h-lim-p 0.0011 0.0085 79.7681 2036.565978 4 0.0003 31 | 0/8 2 h-lim-p 0.0013 0.0102 13.6773 2036.532617 6 0.0004 59 | 0/8 3 h-lim-p 0.0014 0.0803 3.4450 2036.530791 3 0.0003 78 | 0/8 4 h-lim-p 0.0013 0.3109 0.8553 2036.530625 3 0.0005 97 | 0/8 5 h-lim-p 0.0073 2.0865 0.0547 2036.530624 0 0.0008 119 | 0/8 6 h-lim-p 0.0053 20.0000 0.0082 2036.530624 0 0.0006 141 | 0/8 7 h-lim-p 0.0369 20.0000 0.0001 2036.530618 0 0.5899 165 | 0/8 8 h-lim-p 0.0011 1.2527 0.0681 2036.530614 0 0.0010 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2036.530614 0 1.0938 205 | 0/8 10 h-lim-p 1.1049 20.0000 0.0000 2036.530614 0 2.2098 226 | 0/8 11 h-lim-p 2.0701 20.0000 0.0000 2036.530614 0 0.4528 247 | 0/8 12 h-lim-p 0.0565 20.0000 0.0001 2036.530614 0 0.0018 271 | 0/8 13 h-lim-p 0.0005 20.0000 0.0004 2036.530614 0 0.0001 293 | 0/8 14 h-lim-p 0.0003 20.0000 0.0001 2036.530614 0 0.0000 326 | 0/8 15 h-lim-p 0.0000 20.0000 0.0009 | 0/8 16 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -2036.530614 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2036.530614 Node 7: lnL = -2036.530614 Node 8: lnL = -2036.530614 Node 9: lnL = -2036.530614 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 252 Sequential format.. Reading seq # 1: YOR215C_Sbay Reading seq # 2: YOR215C_Scer Reading seq # 3: YOR215C_Skud Reading seq # 4: YOR215C_Smik Reading seq # 5: YOR215C_Spar Sequences read.. Counting patterns.. # site patterns = 124 Counting frequencies.. 120 bytes for distance 19840 bytes for lkl0 15872 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.174877 0.030539 0.000060 0.200805 0.111251 0.266554 0.159518 0.019068 lnL0 = -1092.575946 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1092.575946 x= 0.17488 0.03054 0.00006 0.20081 0.11125 0.26655 0.15952 0.01907 1 h-lim-p 0.0013 0.0100 74.2318 1091.647807 3 0.0003 29 | 0/8 2 h-lim-p 0.0006 0.0052 34.0315 1091.226019 0 0.0010 41 | 0/8 3 h-lim-p 0.0009 0.0073 9.6536 1091.179451 0 0.0014 53 | 0/8 4 h-lim-p 0.0041 0.0784 3.2674 1091.174257 5 0.0011 76 | 0/8 5 h-lim-p 0.0028 0.0430 1.2684 1091.173831 2 0.0006 93 | 0/8 6 h-lim-p 0.0019 0.2015 0.4129 1091.173739 4 0.0011 116 | 0/8 7 h-lim-p 0.0038 0.5249 0.1158 1091.173701 3 0.0022 145 | 0/8 8 h-lim-p 0.0175 20.0000 0.0147 1091.165281 0 0.2804 169 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 1091.165233 2 0.9961 193 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1091.165232 0 1.0938 213 | 0/8 11 h-lim-p 1.3198 20.0000 0.0000 1091.165232 0 2.6396 234 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1091.165232 0 0.6250 255 | 0/8 13 h-lim-p 0.1006 20.0000 0.0001 1091.165232 0 0.0251 276 | 0/8 14 h-lim-p 0.0068 20.0000 0.0002 1091.165232 0 0.0017 297 | 0/8 15 h-lim-p 0.0009 20.0000 0.0004 1091.165232 0 0.0000 323 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 1091.165232 0 0.0000 343 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 1091.165232 0 0.0000 363 | 0/8 18 h-lim-p 0.0001 20.0000 0.0000 1091.165232 0 0.0000 394 | 0/8 19 h-lim-p 0.0000 20.0000 0.0006 | 0/8 20 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -1091.165232 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1091.165232 Node 7: lnL = -1091.165232 Node 8: lnL = -1091.165232 Node 9: lnL = -1091.165232 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 353 Sequential format.. Reading seq # 1: YOR220W_Sbay Reading seq # 2: YOR220W_Scer Reading seq # 3: YOR220W_Skud Reading seq # 4: YOR220W_Smik Reading seq # 5: YOR220W_Spar Sequences read.. Counting patterns.. # site patterns = 133 Counting frequencies.. 120 bytes for distance 21280 bytes for lkl0 17024 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.161369 0.029243 0.063451 0.131993 0.023492 0.134425 0.143627 0.033993 lnL0 = -1310.585687 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1310.585687 x= 0.16137 0.02924 0.06345 0.13199 0.02349 0.13442 0.14363 0.03399 1 h-lim-p 0.0006 0.6750 203.6385 1306.786571 9 0.0002 42 | 0/8 2 h-lim-p 0.0003 0.0024 32.3483 1306.556998 0 0.0004 54 | 0/8 3 h-lim-p 0.0016 0.0131 8.3968 1306.534251 4 0.0007 75 | 0/8 4 h-lim-p 0.0029 0.1046 2.0170 1306.532995 2 0.0007 92 | 0/8 5 h-lim-p 0.0029 0.3875 0.4630 1306.532921 1 0.0007 107 | 0/8 6 h-lim-p 0.0075 3.3761 0.0450 1306.532920 1 0.0009 131 | 0/8 7 h-lim-p 0.0087 20.0000 0.0048 1306.532887 0 0.0524 153 | 0/8 8 h-lim-p 0.0059 20.0000 0.0425 1306.532171 0 0.0235 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1306.532147 2 0.9961 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1306.532147 0 1.2500 219 | 0/8 11 h-lim-p 1.5502 20.0000 0.0000 1306.532147 0 0.3391 240 | 0/8 12 h-lim-p 0.0828 20.0000 0.0001 1306.532147 0 0.0207 261 | 0/8 13 h-lim-p 0.0074 20.0000 0.0002 1306.532147 0 0.0000 296 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 1306.532147 0 0.0000 328 Out... lnL = -1306.532147 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1306.532147 Node 7: lnL = -1306.532147 Node 8: lnL = -1306.532147 Node 9: lnL = -1306.532147 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 515 Sequential format.. Reading seq # 1: YOR222W_Sbay Reading seq # 2: YOR222W_Scer Reading seq # 3: YOR222W_Skud Reading seq # 4: YOR222W_Smik Reading seq # 5: YOR222W_Spar Sequences read.. Counting patterns.. # site patterns = 177 Counting frequencies.. 120 bytes for distance 28320 bytes for lkl0 22656 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.208769 0.098863 0.068236 0.092715 0.056889 0.216253 0.177352 0.036425 lnL0 = -2286.278477 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2286.278477 x= 0.20877 0.09886 0.06824 0.09272 0.05689 0.21625 0.17735 0.03643 1 h-lim-p 0.0022 0.0179 47.1363 2285.980544 7 0.0003 38 | 0/8 2 h-lim-p 0.0014 0.0189 9.3160 2285.962456 6 0.0004 66 | 0/8 3 h-lim-p 0.0005 0.0286 8.6526 2285.956934 5 0.0002 91 | 0/8 4 h-lim-p 0.0029 0.2690 0.7064 2285.956815 3 0.0005 112 | 0/8 5 h-lim-p 0.0035 3.6298 0.1031 2285.956813 1 0.0004 136 | 0/8 6 h-lim-p 0.0022 12.7902 0.0200 2285.956813 0 0.0005 157 | 0/8 7 h-lim-p 0.0010 15.8541 0.0096 2285.956813 0 0.0004 177 | 0/8 8 h-lim-p 0.2405 20.0000 0.0000 2285.956813 0 0.9619 199 | 0/8 9 h-lim-p 0.7361 20.0000 0.0000 2285.956813 0 0.3221 219 | 0/8 10 h-lim-p 0.1451 20.0000 0.0001 2285.956813 0 0.0045 243 | 0/8 11 h-lim-p 0.0020 20.0000 0.0001 2285.956813 0 0.0010 263 | 0/8 12 h-lim-p 0.0006 20.0000 0.0002 2285.956813 0 0.0000 288 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 2285.956813 0 0.0000 321 | 0/8 14 h-lim-p 0.0000 20.0000 0.0019 | 0/8 15 h-lim-p 0.0000 20.0000 0.0019 Out... lnL = -2285.956813 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2285.956813 Node 7: lnL = -2285.956813 Node 8: lnL = -2285.956813 Node 9: lnL = -2285.956813 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 562 Sequential format.. Reading seq # 1: YOR223W_Sbay Reading seq # 2: YOR223W_Scer Reading seq # 3: YOR223W_Skud Reading seq # 4: YOR223W_Smik Reading seq # 5: YOR223W_Spar Sequences read.. Counting patterns.. # site patterns = 194 Counting frequencies.. 120 bytes for distance 31040 bytes for lkl0 24832 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.139571 0.032188 0.135371 0.069050 0.128512 0.136883 0.138894 0.000060 lnL0 = -2167.611867 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2167.611867 x= 0.13957 0.03219 0.13537 0.06905 0.12851 0.13688 0.13889 0.00006 1 h-lim-p 0.0006 0.0048 160.2392 2165.562376 9 0.0002 42 | 0/8 2 h-lim-p 0.0003 0.0027 39.8458 2165.141739 0 0.0007 55 | 0/8 3 h-lim-p 0.0013 0.0106 17.0854 2165.105292 6 0.0003 79 | 0/8 4 h-lim-p 0.0003 0.0021 5.4309 2165.100197 0 0.0004 91 | 0/8 5 h-lim-p 0.0019 0.2668 1.1304 2165.099936 2 0.0004 108 | 0/8 6 h-lim-p 0.0015 0.1033 0.3183 2165.099892 2 0.0007 124 | 0/8 7 h-lim-p 0.0025 0.0679 0.0818 2165.099402 0 0.0203 147 | 0/8 8 h-lim-p 0.0002 0.0016 2.2202 2165.096459 m 0.0016 167 | 0/8 9 h-lim-p 0.0215 1.3223 0.1620 2165.088931 0 0.1719 182 | 0/8 10 h-lim-p 0.1148 0.9180 0.0306 2165.081960 m 0.9180 202 | 1/8 11 h-lim-p 2.5000 20.0000 0.0035 2165.081960 0 0.0085 229 | 0/8 12 h-lim-p -0.0000 -0.0000 0.1084 h-lim-p: -3.95073589e-18 -3.16058871e-17 1.08449913e-01 2165.081960 .. | 1/8 13 h-lim-p 0.0000 1.6523 0.4524 2165.081926 0 0.0003 269 | 1/8 14 h-lim-p 0.0008 0.6687 0.1827 2165.081921 0 0.0004 288 | 1/8 15 h-lim-p 0.0012 2.9159 0.0620 2165.081920 0 0.0005 307 | 1/8 16 h-lim-p 0.0017 13.0948 0.0181 2165.081920 0 0.0008 326 | 1/8 17 h-lim-p 0.0093 20.0000 0.0015 2165.081920 0 0.0005 348 | 1/8 18 h-lim-p 0.0031 20.0000 0.0002 2165.081920 0 0.0027 367 | 1/8 19 h-lim-p 0.0063 20.0000 0.0001 2165.081920 0 0.0752 389 | 1/8 20 h-lim-p 0.0013 20.0000 0.0062 2165.081920 0 0.0013 408 | 1/8 21 h-lim-p 2.5000 20.0000 0.0000 2165.081920 0 1.0938 427 | 1/8 22 h-lim-p 2.5000 20.0000 0.0000 2165.081920 0 0.0342 451 | 1/8 23 h-lim-p 0.0354 20.0000 0.0000 2165.081920 0 0.0000 482 Out... lnL = -2165.081920 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2165.081920 Node 7: lnL = -2165.081920 Node 8: lnL = -2165.081920 Node 9: lnL = -2165.081920 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 128 Sequential format.. Reading seq # 1: YOR224C_Sbay Reading seq # 2: YOR224C_Scer Reading seq # 3: YOR224C_Skud Reading seq # 4: YOR224C_Smik Reading seq # 5: YOR224C_Spar Sequences read.. Counting patterns.. # site patterns = 58 Counting frequencies.. 120 bytes for distance 9280 bytes for lkl0 7424 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.158465 0.022945 0.023382 0.056526 0.047991 0.135304 0.131015 0.050731 lnL0 = -473.471116 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 473.471116 x= 0.15847 0.02294 0.02338 0.05653 0.04799 0.13530 0.13101 0.05073 1 h-lim-p 0.0001 0.0007 46.3133 472.924302 0 0.0005 24 | 0/8 2 h-lim-p 0.0006 0.0050 35.7693 472.705485 3 0.0005 42 | 0/8 3 h-lim-p 0.0013 0.0100 13.0427 472.657656 8 0.0007 74 | 0/8 4 h-lim-p 0.0009 0.0072 7.0939 472.645506 5 0.0006 98 | 0/8 5 h-lim-p 0.0054 0.1826 0.8355 472.645087 4 0.0012 118 | 0/8 6 h-lim-p 0.0025 0.2122 0.4070 472.645027 3 0.0008 146 | 0/8 7 h-lim-p 0.0206 4.8757 0.0157 472.644394 0 0.0824 168 | 0/8 8 h-lim-p 0.0070 0.8245 0.1856 472.640207 0 0.0139 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 472.640097 2 1.0938 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 472.640095 1 0.9961 235 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 472.640095 0 0.1367 258 | 0/8 12 h-lim-p 0.0870 20.0000 0.0000 472.640095 0 0.0095 280 | 0/8 13 h-lim-p 0.0065 20.0000 0.0000 472.640095 0 0.0001 306 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 472.640095 0 0.0000 330 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 472.640095 0 0.0000 364 | 0/8 16 h-lim-p 0.0000 20.0000 0.0094 | 0/8 17 h-lim-p 0.0000 20.0000 0.0094 Out... lnL = -472.640095 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -472.640095 Node 7: lnL = -472.640095 Node 8: lnL = -472.640095 Node 9: lnL = -472.640095 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 839 Sequential format.. Reading seq # 1: YOR226C_Sbay Reading seq # 2: YOR226C_Scer Reading seq # 3: YOR226C_Skud Reading seq # 4: YOR226C_Smik Reading seq # 5: YOR226C_Spar Sequences read.. Counting patterns.. # site patterns = 204 Counting frequencies.. 120 bytes for distance 32640 bytes for lkl0 26112 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.211851 0.041455 0.030635 0.082507 0.037039 0.127891 0.137701 0.081394 lnL0 = -3160.159672 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3160.159672 x= 0.21185 0.04145 0.03063 0.08251 0.03704 0.12789 0.13770 0.08139 1 h-lim-p 0.0012 0.0195 233.2779 3158.175869 9 0.0001 47 | 0/8 2 h-lim-p 0.0002 0.0019 54.3906 3157.941861 7 0.0002 76 | 0/8 3 h-lim-p 0.0002 0.0053 44.5739 3157.866821 5 0.0001 100 | 0/8 4 h-lim-p 0.0003 0.0099 15.0273 3157.850816 5 0.0002 124 | 0/8 5 h-lim-p 0.0014 0.1476 1.8228 3157.850435 4 0.0002 146 | 0/8 6 h-lim-p 0.0032 0.7010 0.1332 3157.850434 0 0.0002 161 | 0/8 7 h-lim-p 0.0007 5.1582 0.0320 3157.850434 0 0.0006 181 | 0/8 8 h-lim-p 0.1055 20.0000 0.0002 3157.850297 0 0.8444 204 | 0/8 9 h-lim-p 0.4060 20.0000 0.0004 3157.850289 0 1.2180 225 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 3157.850288 0 1.0938 245 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3157.850288 0 1.0938 265 | 0/8 12 h-lim-p 0.4144 20.0000 0.0000 3157.850288 0 0.0024 292 | 0/8 13 h-lim-p 0.0007 20.0000 0.0001 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0026 3157.850288 0 0.0000 365 | 0/8 15 h-lim-p 0.0000 20.0000 0.0026 | 0/8 16 h-lim-p 0.0000 20.0000 0.0026 Out... lnL = -3157.850288 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3157.850288 Node 7: lnL = -3157.850288 Node 8: lnL = -3157.850288 Node 9: lnL = -3157.850288 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 843 Sequential format.. Reading seq # 1: YOR227W_Sbay Reading seq # 2: YOR227W_Scer Reading seq # 3: YOR227W_Skud Reading seq # 4: YOR227W_Smik Reading seq # 5: YOR227W_Spar Sequences read.. Counting patterns.. # site patterns = 200 Counting frequencies.. 120 bytes for distance 32000 bytes for lkl0 25600 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.207994 0.041571 0.029089 0.080718 0.038827 0.119563 0.134210 0.080621 lnL0 = -3136.997843 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3136.997843 x= 0.20799 0.04157 0.02909 0.08072 0.03883 0.11956 0.13421 0.08062 1 h-lim-p 0.0013 0.5994 222.0865 3135.200099 8 0.0001 44 | 0/8 2 h-lim-p 0.0003 0.0025 54.0385 3134.972395 5 0.0002 67 | 0/8 3 h-lim-p 0.0003 0.0053 33.2320 3134.920392 2 0.0001 83 | 0/8 4 h-lim-p 0.0003 0.0096 15.8021 3134.906175 6 0.0001 110 | 0/8 5 h-lim-p 0.0046 0.5491 0.5125 3134.906144 1 0.0002 127 | 0/8 6 h-lim-p 0.0010 2.8454 0.1156 3134.906143 0 0.0002 148 | 0/8 7 h-lim-p 0.0006 5.8545 0.0391 3134.906143 0 0.0003 168 | 0/8 8 h-lim-p 0.0588 20.0000 0.0002 3134.905950 0 0.9410 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3134.905947 0 1.0938 212 | 0/8 10 h-lim-p 2.3974 20.0000 0.0000 3134.905947 0 0.2622 234 | 0/8 11 h-lim-p 0.1474 20.0000 0.0000 3134.905947 0 0.0092 257 | 0/8 12 h-lim-p 0.0050 20.0000 0.0001 3134.905947 0 0.0012 278 | 0/8 13 h-lim-p 0.0009 20.0000 0.0001 3134.905947 0 0.0001 300 | 0/8 14 h-lim-p 0.0000 20.0000 0.0006 3134.905947 0 0.0000 335 | 0/8 15 h-lim-p 0.0000 20.0000 0.0042 | 0/8 16 h-lim-p 0.0000 20.0000 0.0042 Out... lnL = -3134.905947 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3134.905947 Node 7: lnL = -3134.905947 Node 8: lnL = -3134.905947 Node 9: lnL = -3134.905947 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 686 Sequential format.. Reading seq # 1: YOR228C_Sbay Reading seq # 2: YOR228C_Scer Reading seq # 3: YOR228C_Skud Reading seq # 4: YOR228C_Smik Reading seq # 5: YOR228C_Spar Sequences read.. Counting patterns.. # site patterns = 263 Counting frequencies.. 120 bytes for distance 42080 bytes for lkl0 33664 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.219898 0.084597 0.062187 0.130725 0.100117 0.181906 0.146453 0.046448 lnL0 = -2970.966029 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2970.966029 x= 0.21990 0.08460 0.06219 0.13073 0.10012 0.18191 0.14645 0.04645 1 h-lim-p 0.0011 0.0092 105.4397 2969.722818 3 0.0002 29 | 0/8 2 h-lim-p 0.0008 0.0062 23.4737 2969.633615 5 0.0003 50 | 0/8 3 h-lim-p 0.0009 0.0233 8.4943 2969.623538 6 0.0003 76 | 0/8 4 h-lim-p 0.0012 0.0888 2.1870 2969.622793 4 0.0003 97 | 0/8 5 h-lim-p 0.0021 1.3074 0.3501 2969.622769 2 0.0004 114 | 0/8 6 h-lim-p 0.0049 9.0091 0.0284 2969.622769 0 0.0005 136 | 0/8 7 h-lim-p 0.0038 20.0000 0.0041 2969.622769 0 0.0033 156 | 0/8 8 h-lim-p 0.0267 20.0000 0.0005 2969.622741 0 0.2135 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2969.622739 0 1.0938 199 | 0/8 10 h-lim-p 1.5879 20.0000 0.0000 2969.622739 0 1.3894 219 | 0/8 11 h-lim-p 1.9666 20.0000 0.0000 2969.622739 0 0.8604 239 | 0/8 12 h-lim-p 0.4065 20.0000 0.0000 2969.622739 0 0.0127 263 | 0/8 13 h-lim-p 0.0021 20.0000 0.0002 2969.622739 0 0.0005 284 | 0/8 14 h-lim-p 0.0005 20.0000 0.0002 2969.622739 0 0.0000 322 | 0/8 15 h-lim-p 0.0000 20.0000 0.0006 2969.622739 0 0.0000 351 | 0/8 16 h-lim-p 0.0000 20.0000 0.0007 2969.622739 0 0.0000 383 | 0/8 17 h-lim-p 0.0000 20.0000 0.0008 2969.622739 0 0.0000 412 | 0/8 18 h-lim-p 0.0000 20.0000 0.0011 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0006 | 0/8 20 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -2969.622739 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2969.622739 Node 7: lnL = -2969.622739 Node 8: lnL = -2969.622739 Node 9: lnL = -2969.622739 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 933 Sequential format.. Reading seq # 1: YOR230W_Sbay Reading seq # 2: YOR230W_Scer Reading seq # 3: YOR230W_Skud Reading seq # 4: YOR230W_Smik Reading seq # 5: YOR230W_Spar Sequences read.. Counting patterns.. # site patterns = 279 Counting frequencies.. 120 bytes for distance 44640 bytes for lkl0 35712 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.238776 0.028406 0.063100 0.099812 0.070374 0.170096 0.154349 0.080937 lnL0 = -3716.378994 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3716.378994 x= 0.23878 0.02841 0.06310 0.09981 0.07037 0.17010 0.15435 0.08094 1 h-lim-p 0.0013 0.4463 241.6880 3713.050722 3 0.0001 30 | 0/8 2 h-lim-p 0.0002 0.0017 59.0870 3712.626399 1 0.0003 44 | 0/8 3 h-lim-p 0.0006 0.0084 27.2896 3712.564800 6 0.0002 73 | 0/8 4 h-lim-p 0.0009 0.0179 6.0419 3712.562248 5 0.0002 98 | 0/8 5 h-lim-p 0.0018 0.4593 0.5031 3712.562200 1 0.0004 113 | 0/8 6 h-lim-p 0.0023 2.1437 0.0859 3712.562199 0 0.0003 135 | 0/8 7 h-lim-p 0.0174 20.0000 0.0014 3712.560856 0 0.5578 160 | 0/8 8 h-lim-p 0.0011 0.1889 0.7179 3712.560735 2 0.0004 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3712.560721 0 1.0938 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3712.560721 0 2.1875 224 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3712.560721 0 1.0938 244 | 0/8 12 h-lim-p 0.4651 20.0000 0.0000 3712.560721 0 1.8602 266 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 3712.560721 0 0.5469 287 | 0/8 14 h-lim-p 0.1209 20.0000 0.0000 3712.560721 0 0.0001 316 | 0/8 15 h-lim-p 0.0012 20.0000 0.0000 3712.560721 0 0.0000 351 Out... lnL = -3712.560721 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3712.560721 Node 7: lnL = -3712.560721 Node 8: lnL = -3712.560721 Node 9: lnL = -3712.560721 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 477 Sequential format.. Reading seq # 1: YOR232W_Sbay Reading seq # 2: YOR232W_Scer Reading seq # 3: YOR232W_Skud Reading seq # 4: YOR232W_Smik Reading seq # 5: YOR232W_Spar Sequences read.. Counting patterns.. # site patterns = 192 Counting frequencies.. 120 bytes for distance 30720 bytes for lkl0 24576 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.193433 0.111162 0.064863 0.140025 0.096963 0.215817 0.191719 0.002791 lnL0 = -2123.317250 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2123.317250 x= 0.19343 0.11116 0.06486 0.14002 0.09696 0.21582 0.19172 0.00279 1 h-lim-p 0.0001 0.0004 45.9306 2122.961407 m 0.0004 22 | 1/8 2 h-lim-p 0.0019 0.0166 9.7544 2122.938782 4 0.0005 43 | 1/8 3 h-lim-p 0.0014 0.0420 3.3316 2122.936226 4 0.0005 64 | 1/8 4 h-lim-p 0.0025 0.3037 0.6924 2122.936084 2 0.0006 81 | 1/8 5 h-lim-p 0.0035 2.5773 0.1200 2122.936056 2 0.0017 105 | 0/8 6 h-lim-p 0.0003 2.4518 0.6583 2122.935876 0 0.0010 125 | 0/8 7 h-lim-p 0.0009 0.4728 0.7092 2122.935548 0 0.0018 146 | 0/8 8 h-lim-p 0.0063 1.9718 0.1986 2122.935477 3 0.0019 174 | 0/8 9 h-lim-p 0.0225 0.2993 0.0166 2122.926790 3 0.1764 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2122.926783 1 0.9961 224 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2122.926783 0 1.0938 244 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2122.926783 0 0.5469 265 | 0/8 13 h-lim-p 0.7966 20.0000 0.0000 2122.926783 0 0.0498 288 | 0/8 14 h-lim-p 0.0248 20.0000 0.0000 2122.926783 0 0.0248 308 | 0/8 15 h-lim-p 0.0142 20.0000 0.0000 2122.926783 0 0.0009 331 Out... lnL = -2122.926783 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2122.926783 Node 7: lnL = -2122.926783 Node 8: lnL = -2122.926783 Node 9: lnL = -2122.926783 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 627 Sequential format.. Reading seq # 1: YOR233W_Sbay Reading seq # 2: YOR233W_Scer Reading seq # 3: YOR233W_Skud Reading seq # 4: YOR233W_Smik Reading seq # 5: YOR233W_Spar Sequences read.. Counting patterns.. # site patterns = 205 Counting frequencies.. 120 bytes for distance 32800 bytes for lkl0 26240 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.176987 0.056291 0.048200 0.101288 0.064558 0.162746 0.183645 0.026444 lnL0 = -2550.180498 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2550.180498 x= 0.17699 0.05629 0.04820 0.10129 0.06456 0.16275 0.18365 0.02644 1 h-lim-p 0.0007 0.0056 116.8605 2549.143142 2 0.0002 27 | 0/8 2 h-lim-p 0.0008 0.0062 17.7938 2549.107963 7 0.0002 57 | 0/8 3 h-lim-p 0.0007 0.0240 6.0718 2549.104509 5 0.0002 83 | 0/8 4 h-lim-p 0.0007 0.0497 1.7442 2549.104004 3 0.0004 102 | 0/8 5 h-lim-p 0.0013 0.4939 0.4979 2549.103959 3 0.0004 122 | 0/8 6 h-lim-p 0.0051 5.2186 0.0397 2549.103959 0 0.0003 145 | 0/8 7 h-lim-p 0.0018 20.0000 0.0060 2549.103959 0 0.0016 165 | 0/8 8 h-lim-p 0.0184 20.0000 0.0005 2549.103901 0 0.2950 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2549.103901 0 1.0938 209 | 0/8 10 h-lim-p 2.1377 20.0000 0.0000 2549.103901 0 1.8705 229 | 0/8 11 h-lim-p 2.4288 20.0000 0.0000 2549.103901 0 1.0626 249 | 0/8 12 h-lim-p 0.3168 20.0000 0.0001 2549.103901 0 0.0025 275 | 0/8 13 h-lim-p 0.0004 20.0000 0.0004 2549.103901 0 0.0001 297 | 0/8 14 h-lim-p 0.0000 20.0000 0.0005 2549.103901 0 0.0000 325 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 2549.103901 0 0.0000 358 Out... lnL = -2549.103901 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2549.103901 Node 7: lnL = -2549.103901 Node 8: lnL = -2549.103901 Node 9: lnL = -2549.103901 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 785 Sequential format.. Reading seq # 1: YOR236W_Sbay Reading seq # 2: YOR236W_Scer Reading seq # 3: YOR236W_Skud Reading seq # 4: YOR236W_Smik Reading seq # 5: YOR236W_Spar Sequences read.. Counting patterns.. # site patterns = 229 Counting frequencies.. 120 bytes for distance 36640 bytes for lkl0 29312 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.119245 0.021369 0.060693 0.104725 0.045542 0.112143 0.122491 0.009388 lnL0 = -2919.099764 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2919.099764 x= 0.11924 0.02137 0.06069 0.10472 0.04554 0.11214 0.12249 0.00939 1 h-lim-p 0.0002 0.2269 485.1667 2911.938529 10 0.0001 48 | 0/8 2 h-lim-p 0.0001 0.0006 41.9399 2911.790808 0 0.0002 61 | 0/8 3 h-lim-p 0.0006 0.0125 10.4230 2911.781323 5 0.0002 86 | 0/8 4 h-lim-p 0.0006 0.0918 3.3292 2911.780635 2 0.0001 103 | 0/8 5 h-lim-p 0.0004 0.0238 1.1542 2911.780528 0 0.0002 115 | 0/8 6 h-lim-p 0.0017 1.6364 0.1171 2911.780526 1 0.0002 131 | 0/8 7 h-lim-p 0.0011 14.2995 0.0211 2911.780524 0 0.0017 151 | 0/8 8 h-lim-p 0.0085 3.8597 0.0043 2911.779287 0 0.1357 175 | 0/8 9 h-lim-p 0.2555 5.7107 0.0023 2911.779169 0 1.5330 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0009 2911.779161 1 0.9961 219 | 0/8 11 h-lim-p 2.5000 20.0000 0.0004 2911.779160 0 1.0938 239 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2911.779160 0 1.2500 259 | 0/8 13 h-lim-p 0.0686 20.0000 0.0001 2911.779160 0 0.2743 281 | 0/8 14 h-lim-p 0.0571 20.0000 0.0003 2911.779160 0 0.0250 301 | 0/8 15 h-lim-p 0.0093 11.7768 0.0009 2911.779160 0 0.0023 322 | 0/8 16 h-lim-p 0.0012 6.0145 0.0017 2911.779160 0 0.0012 342 | 0/8 17 h-lim-p 0.0006 3.2957 0.0030 2911.779160 0 0.0002 363 | 0/8 18 h-lim-p 0.0002 4.5375 0.0022 2911.779160 0 0.0001 384 | 0/8 19 h-lim-p 0.0000 3.8040 0.0026 .. | 0/8 20 h-lim-p 0.0000 20.0000 0.0044 | 0/8 21 h-lim-p 0.0000 20.0000 0.0044 Out... lnL = -2911.779160 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2911.779160 Node 7: lnL = -2911.779160 Node 8: lnL = -2911.779160 Node 9: lnL = -2911.779160 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 475 Sequential format.. Reading seq # 1: YOR237W_Sbay Reading seq # 2: YOR237W_Scer Reading seq # 3: YOR237W_Skud Reading seq # 4: YOR237W_Smik Reading seq # 5: YOR237W_Spar Sequences read.. Counting patterns.. # site patterns = 156 Counting frequencies.. 120 bytes for distance 24960 bytes for lkl0 19968 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.159449 0.013854 0.039757 0.068122 0.054305 0.138326 0.126912 0.043633 lnL0 = -1732.400147 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1732.400147 x= 0.15945 0.01385 0.03976 0.06812 0.05431 0.13833 0.12691 0.04363 1 h-lim-p 0.0004 0.0215 277.7190 1729.543494 3 0.0001 29 | 0/8 2 h-lim-p 0.0005 0.0040 40.9813 1729.147931 2 0.0005 45 | 0/8 3 h-lim-p 0.0011 0.0087 12.9420 1729.131345 4 0.0002 66 | 0/8 4 h-lim-p 0.0015 0.0971 1.8837 1729.130777 2 0.0003 83 | 0/8 5 h-lim-p 0.0026 0.4834 0.2311 1729.130768 0 0.0003 97 | 0/8 6 h-lim-p 0.0072 6.1169 0.0106 1729.130768 0 0.0016 118 | 0/8 7 h-lim-p 0.0079 20.0000 0.0021 1729.130642 0 0.1257 142 | 0/8 8 h-lim-p 0.0007 0.2260 0.4011 1729.130463 0 0.0010 162 | 0/8 9 h-lim-p 2.2624 20.0000 0.0002 1729.130436 0 1.1312 182 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1729.130436 0 1.0938 202 | 0/8 11 h-lim-p 1.6555 20.0000 0.0000 1729.130436 0 1.4486 222 | 0/8 12 h-lim-p 1.3666 20.0000 0.0000 1729.130436 0 2.7333 243 | 0/8 13 h-lim-p 0.2889 20.0000 0.0002 1729.130436 0 0.0135 267 | 0/8 14 h-lim-p 0.0017 20.0000 0.0016 1729.130436 0 0.0006 288 | 0/8 15 h-lim-p 0.0004 20.0000 0.0026 1729.130436 0 0.0000 315 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0006 | 0/8 18 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -1729.130436 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1729.130436 Node 7: lnL = -1729.130436 Node 8: lnL = -1729.130436 Node 9: lnL = -1729.130436 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 392 Sequential format.. Reading seq # 1: YOR238W_Sbay Reading seq # 2: YOR238W_Scer Reading seq # 3: YOR238W_Skud Reading seq # 4: YOR238W_Smik Reading seq # 5: YOR238W_Spar Sequences read.. Counting patterns.. # site patterns = 227 Counting frequencies.. 120 bytes for distance 36320 bytes for lkl0 29056 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.319527 0.245196 0.064722 0.242730 0.209902 0.308130 0.232428 0.010903 lnL0 = -2065.834226 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2065.834226 x= 0.31953 0.24520 0.06472 0.24273 0.20990 0.30813 0.23243 0.01090 1 h-lim-p 0.0234 2.6537 42.0438 2065.223630 6 0.0007 40 | 0/8 2 h-lim-p 0.0043 0.0353 7.2223 2065.188149 6 0.0014 67 | 0/8 3 h-lim-p 0.0038 0.0475 2.6163 2065.183251 4 0.0016 88 | 0/8 4 h-lim-p 0.0082 0.9668 0.5152 2065.183053 3 0.0015 107 | 0/8 5 h-lim-p 0.0054 0.2888 0.1472 2065.183040 0 0.0014 128 | 0/8 6 h-lim-p 0.0099 16.1746 0.0201 2065.183039 0 0.0043 148 | 0/8 7 h-lim-p 0.0287 20.0000 0.0030 2065.183038 0 0.0251 168 | 0/8 8 h-lim-p 0.0194 20.0000 0.0039 2065.182987 0 0.0777 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2065.182987 0 1.0938 210 | 0/8 10 h-lim-p 1.6070 20.0000 0.0000 2065.182987 0 1.4061 230 | 0/8 11 h-lim-p 1.3860 20.0000 0.0000 2065.182987 0 1.2128 250 | 0/8 12 h-lim-p 0.1607 20.0000 0.0001 2065.182987 0 0.0088 273 | 0/8 13 h-lim-p 0.0025 20.0000 0.0003 2065.182987 0 0.0002 296 | 0/8 14 h-lim-p 0.0002 20.0000 0.0002 2065.182987 0 0.0002 316 | 0/8 15 h-lim-p 0.0004 20.0000 0.0001 2065.182987 0 0.0000 351 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 2065.182987 0 0.0000 372 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 2065.182987 0 0.0000 407 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -2065.182987 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2065.182987 Node 7: lnL = -2065.182987 Node 8: lnL = -2065.182987 Node 9: lnL = -2065.182987 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 386 Sequential format.. Reading seq # 1: YOR242C_Sbay Reading seq # 2: YOR242C_Scer Reading seq # 3: YOR242C_Skud Reading seq # 4: YOR242C_Smik Reading seq # 5: YOR242C_Spar Sequences read.. Counting patterns.. # site patterns = 139 Counting frequencies.. 120 bytes for distance 22240 bytes for lkl0 17792 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.179557 0.092695 0.064804 0.127480 0.050581 0.120340 0.145944 0.026548 lnL0 = -1543.846965 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1543.846965 x= 0.17956 0.09269 0.06480 0.12748 0.05058 0.12034 0.14594 0.02655 1 h-lim-p 0.0004 0.0034 33.6756 1543.677257 6 0.0003 35 | 0/8 2 h-lim-p 0.0012 0.0422 8.3174 1543.666515 5 0.0003 58 | 0/8 3 h-lim-p 0.0006 0.0314 4.4496 1543.663870 5 0.0003 81 | 0/8 4 h-lim-p 0.0034 0.2077 0.4378 1543.663811 3 0.0006 101 | 0/8 5 h-lim-p 0.0026 3.8190 0.0991 1543.663809 0 0.0006 122 | 0/8 6 h-lim-p 0.0050 17.6376 0.0115 1543.663809 0 0.0005 144 | 0/8 7 h-lim-p 0.0162 20.0000 0.0004 1543.663809 0 0.0486 165 | 0/8 8 h-lim-p 0.0026 19.4998 0.0073 1543.663802 0 0.0103 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1543.663802 0 1.0938 207 | 0/8 10 h-lim-p 1.0328 20.0000 0.0000 1543.663802 0 0.9037 227 | 0/8 11 h-lim-p 0.2677 20.0000 0.0001 1543.663802 0 0.0010 254 | 0/8 12 h-lim-p 0.0003 20.0000 0.0003 1543.663802 0 0.0000 291 | 0/8 13 h-lim-p 0.0000 20.0000 0.0002 1543.663802 0 0.0000 311 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 1543.663802 0 0.0000 333 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 1543.663802 0 0.0000 386 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 | 0/8 19 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1543.663802 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1543.663802 Node 7: lnL = -1543.663802 Node 8: lnL = -1543.663802 Node 9: lnL = -1543.663802 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 306 Sequential format.. Reading seq # 1: YOR243C_Sbay Reading seq # 2: YOR243C_Scer Reading seq # 3: YOR243C_Skud Reading seq # 4: YOR243C_Smik Reading seq # 5: YOR243C_Spar Sequences read.. Counting patterns.. # site patterns = 144 Counting frequencies.. 120 bytes for distance 23040 bytes for lkl0 18432 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.259582 0.090127 0.127360 0.189639 0.084994 0.251415 0.266859 0.018481 lnL0 = -1506.334490 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1506.334490 x= 0.25958 0.09013 0.12736 0.18964 0.08499 0.25141 0.26686 0.01848 1 h-lim-p 0.0008 0.0061 26.8155 1506.030770 7 0.0008 38 | 0/8 2 h-lim-p 0.0015 0.0214 14.7624 1505.969562 2 0.0007 54 | 0/8 3 h-lim-p 0.0020 0.0158 3.7577 1505.961724 6 0.0012 83 | 0/8 4 h-lim-p 0.0035 0.3031 1.2995 1505.960942 5 0.0010 108 | 0/8 5 h-lim-p 0.0051 0.8138 0.2668 1505.960909 2 0.0010 125 | 0/8 6 h-lim-p 0.0102 20.0000 0.0255 1505.960908 0 0.0022 146 | 0/8 7 h-lim-p 0.0085 20.0000 0.0067 1505.960906 0 0.0127 166 | 0/8 8 h-lim-p 0.0140 20.0000 0.0061 1505.960781 0 0.0842 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1505.960779 0 1.0938 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1505.960779 0 1.0938 228 | 0/8 11 h-lim-p 1.1491 20.0000 0.0000 1505.960779 0 0.5027 248 | 0/8 12 h-lim-p 0.1583 20.0000 0.0000 1505.960779 0 0.0396 269 | 0/8 13 h-lim-p 0.0136 20.0000 0.0001 1505.960779 0 0.0009 292 | 0/8 14 h-lim-p 0.0004 20.0000 0.0002 1505.960779 0 0.0000 324 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 1505.960779 0 0.0000 358 Out... lnL = -1505.960779 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1505.960779 Node 7: lnL = -1505.960779 Node 8: lnL = -1505.960779 Node 9: lnL = -1505.960779 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 305 Sequential format.. Reading seq # 1: YOR244W_Sbay Reading seq # 2: YOR244W_Scer Reading seq # 3: YOR244W_Skud Reading seq # 4: YOR244W_Smik Reading seq # 5: YOR244W_Spar Sequences read.. Counting patterns.. # site patterns = 139 Counting frequencies.. 120 bytes for distance 22240 bytes for lkl0 17792 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.333693 0.042546 0.113430 0.189742 0.074908 0.270336 0.304774 0.077462 lnL0 = -1532.002037 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1532.002037 x= 0.33369 0.04255 0.11343 0.18974 0.07491 0.27034 0.30477 0.07746 1 h-lim-p 0.0009 0.0069 42.9675 1531.267391 7 0.0008 40 | 0/8 2 h-lim-p 0.0015 0.0121 18.2472 1531.137901 7 0.0009 71 | 0/8 3 h-lim-p 0.0012 0.0194 13.5547 1531.083774 6 0.0009 96 | 0/8 4 h-lim-p 0.0015 0.0463 7.7281 1531.065232 7 0.0009 129 | 0/8 5 h-lim-p 0.0130 0.2404 0.5503 1531.064976 4 0.0017 151 | 0/8 6 h-lim-p 0.0379 8.5081 0.0248 1531.064975 0 0.0021 174 | 0/8 7 h-lim-p 0.0154 20.0000 0.0033 1531.064909 0 0.1233 197 | 0/8 8 h-lim-p 0.0045 2.0969 0.0910 1531.064717 0 0.0090 218 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1531.064700 1 0.9961 240 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1531.064700 0 1.0938 260 | 0/8 11 h-lim-p 2.4338 20.0000 0.0000 1531.064700 0 2.1296 280 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1531.064700 0 1.0938 300 | 0/8 13 h-lim-p 0.1186 20.0000 0.0000 1531.064700 0 0.1186 320 | 0/8 14 h-lim-p 0.0007 20.0000 0.0012 1531.064700 0 0.0000 346 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 1531.064700 0 0.0000 381 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 1531.064700 0 0.0000 401 Out... lnL = -1531.064700 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1531.064700 Node 7: lnL = -1531.064700 Node 8: lnL = -1531.064700 Node 9: lnL = -1531.064700 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 535 Sequential format.. Reading seq # 1: YOR245C_Sbay Reading seq # 2: YOR245C_Scer Reading seq # 3: YOR245C_Skud Reading seq # 4: YOR245C_Smik Reading seq # 5: YOR245C_Spar Sequences read.. Counting patterns.. # site patterns = 193 Counting frequencies.. 120 bytes for distance 30880 bytes for lkl0 24704 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.242005 0.046311 0.073155 0.127334 0.092827 0.173246 0.167851 0.061806 lnL0 = -2265.582779 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2265.582779 x= 0.24201 0.04631 0.07316 0.12733 0.09283 0.17325 0.16785 0.06181 1 h-lim-p 0.0009 0.0069 92.2288 2264.599381 9 0.0003 44 | 0/8 2 h-lim-p 0.0016 0.0145 14.2004 2264.557034 5 0.0004 67 | 0/8 3 h-lim-p 0.0011 0.0460 5.4314 2264.552214 6 0.0004 93 | 0/8 4 h-lim-p 0.0015 0.1390 1.3303 2264.551868 4 0.0004 115 | 0/8 5 h-lim-p 0.0025 0.5170 0.2312 2264.551855 1 0.0005 130 | 0/8 6 h-lim-p 0.0015 4.3756 0.0764 2264.551854 0 0.0007 150 | 0/8 7 h-lim-p 0.1342 20.0000 0.0004 2264.551849 0 0.2013 170 | 0/8 8 h-lim-p 0.0020 5.3897 0.0379 2264.551823 0 0.0039 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2264.551822 0 1.0938 211 | 0/8 10 h-lim-p 0.9124 20.0000 0.0000 2264.551822 0 0.7983 231 | 0/8 11 h-lim-p 0.6318 20.0000 0.0000 2264.551822 0 0.0000 265 | 0/8 12 h-lim-p 0.0001 20.0000 0.0000 2264.551822 0 0.0000 294 Out... lnL = -2264.551822 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2264.551822 Node 7: lnL = -2264.551822 Node 8: lnL = -2264.551822 Node 9: lnL = -2264.551822 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 877 Sequential format.. Reading seq # 1: YOR246C_Sbay Reading seq # 2: YOR246C_Scer Reading seq # 3: YOR246C_Skud Reading seq # 4: YOR246C_Smik Reading seq # 5: YOR246C_Spar Sequences read.. Counting patterns.. # site patterns = 260 Counting frequencies.. 120 bytes for distance 41600 bytes for lkl0 33280 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.279960 0.066641 0.036475 0.095495 0.145274 0.906145 0.211399 0.000060 lnL0 = -3396.959208 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3396.959208 x= 0.27996 0.06664 0.03648 0.09550 0.14527 0.90615 0.21140 0.00006 1 h-lim-p 0.0000 0.0000 269.4166 3396.889977 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0022 145.3334 3393.892313 0 0.0003 39 | 1/8 3 h-lim-p 0.0020 0.0169 23.7862 3393.769985 3 0.0004 58 | 1/8 4 h-lim-p 0.0015 0.0218 7.1372 3393.749194 2 0.0007 74 | 1/8 5 h-lim-p 0.0004 0.0056 13.7942 3393.671277 0 0.0014 88 | 1/8 6 h-lim-p 0.0011 0.0084 10.5628 3393.608157 0 0.0021 101 | 1/8 7 h-lim-p 0.0028 0.1387 7.9812 3393.097993 0 0.0167 115 | 1/8 8 h-lim-p 0.0619 0.4954 0.4096 3387.282820 0 0.2477 129 | 0/8 9 h-lim-p 1.5597 13.9270 0.0650 3387.243534 4 0.1892 159 | 0/8 10 h-lim-p 0.0003 0.0027 10.2907 3387.132155 m 0.0027 179 | 0/8 11 h-lim-p 1.0367 8.2934 0.0041 3387.124265 3 0.8296 197 | 0/8 12 h-lim-p 1.9938 20.0000 0.0017 3387.123716 4 0.6762 228 | 0/8 13 h-lim-p 2.5000 20.0000 0.0003 3387.123706 0 0.6250 249 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 3387.123706 0 1.0938 269 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 3387.123706 0 1.0938 289 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 3387.123706 0 1.0938 309 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 3387.123706 0 2.5000 329 | 0/8 18 h-lim-p 1.7399 20.0000 0.0000 3387.123706 0 0.1087 352 | 0/8 19 h-lim-p 0.0877 20.0000 0.0000 3387.123706 0 0.0110 374 Out... lnL = -3387.123706 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3387.123706 Node 7: lnL = -3387.123706 Node 8: lnL = -3387.123706 Node 9: lnL = -3387.123706 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 250 Sequential format.. Reading seq # 1: YOR249C_Sbay Reading seq # 2: YOR249C_Scer Reading seq # 3: YOR249C_Skud Reading seq # 4: YOR249C_Smik Reading seq # 5: YOR249C_Spar Sequences read.. Counting patterns.. # site patterns = 134 Counting frequencies.. 120 bytes for distance 21440 bytes for lkl0 17152 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.205447 0.082738 0.057735 0.158975 0.086858 0.229672 0.165723 0.019602 lnL0 = -1084.114590 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1084.114590 x= 0.20545 0.08274 0.05774 0.15897 0.08686 0.22967 0.16572 0.01960 1 h-lim-p 0.0122 3.1564 42.1334 1083.617183 4 0.0006 33 | 0/8 2 h-lim-p 0.0024 0.0216 10.3210 1083.556252 6 0.0012 57 | 0/8 3 h-lim-p 0.0030 0.0457 4.1565 1083.549606 6 0.0009 84 | 0/8 4 h-lim-p 0.0040 0.3296 0.9303 1083.549056 4 0.0013 107 | 0/8 5 h-lim-p 0.0096 2.2564 0.1308 1083.549045 2 0.0013 133 | 0/8 6 h-lim-p 0.0037 1.2421 0.0442 1083.549044 1 0.0015 155 | 0/8 7 h-lim-p 0.0252 20.0000 0.0026 1083.549042 0 0.0252 175 | 0/8 8 h-lim-p 0.0089 20.0000 0.0074 1083.548960 0 0.0535 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1083.548958 0 1.0938 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1083.548958 0 1.0938 237 | 0/8 11 h-lim-p 1.1931 20.0000 0.0000 1083.548958 0 2.3862 258 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1083.548958 0 0.5469 279 | 0/8 13 h-lim-p 0.0965 20.0000 0.0000 1083.548958 0 0.0483 299 | 0/8 14 h-lim-p 0.0144 20.0000 0.0001 1083.548958 0 0.0001 325 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 1083.548958 0 0.0000 345 | 0/8 16 h-lim-p 0.0001 20.0000 0.0001 1083.548958 0 0.0000 368 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 1083.548958 0 0.0000 388 | 0/8 18 h-lim-p 0.0001 20.0000 0.0000 1083.548958 0 0.0000 418 Out... lnL = -1083.548958 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1083.548958 Node 7: lnL = -1083.548958 Node 8: lnL = -1083.548958 Node 9: lnL = -1083.548958 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 266 Sequential format.. Reading seq # 1: YOR250C_Sbay Reading seq # 2: YOR250C_Scer Reading seq # 3: YOR250C_Skud Reading seq # 4: YOR250C_Smik Reading seq # 5: YOR250C_Spar Sequences read.. Counting patterns.. # site patterns = 127 Counting frequencies.. 120 bytes for distance 20320 bytes for lkl0 16256 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.233129 0.102355 0.101982 0.167040 0.104000 0.143655 0.193331 0.029925 lnL0 = -1201.463349 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1201.463349 x= 0.23313 0.10235 0.10198 0.16704 0.10400 0.14365 0.19333 0.02992 1 h-lim-p 0.0029 0.0231 57.5053 1200.163149 8 0.0009 42 | 0/8 2 h-lim-p 0.0014 0.0109 18.4508 1199.968984 3 0.0012 60 | 0/8 3 h-lim-p 0.0040 0.0736 5.6302 1199.954344 6 0.0010 87 | 0/8 4 h-lim-p 0.0029 0.1537 2.0138 1199.952473 5 0.0010 110 | 0/8 5 h-lim-p 0.0202 0.6745 0.1043 1199.952467 1 0.0011 127 | 0/8 6 h-lim-p 0.1084 20.0000 0.0011 1199.952335 0 0.4335 149 | 0/8 7 h-lim-p 0.0023 1.8323 0.2013 1199.952185 0 0.0034 169 | 0/8 8 h-lim-p 0.0522 11.0104 0.0132 1199.952185 0 0.0016 193 | 0/8 9 h-lim-p 0.0771 20.0000 0.0003 1199.952166 0 0.9253 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1199.952166 0 1.0938 236 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1199.952166 0 1.0938 256 | 0/8 12 h-lim-p 0.9639 20.0000 0.0000 1199.952166 0 0.8434 276 | 0/8 13 h-lim-p 0.0161 20.0000 0.0005 1199.952166 0 0.0000 305 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 1199.952166 0 0.0000 342 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 1199.952166 0 0.0000 372 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 1199.952166 0 0.0000 393 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 1199.952166 0 0.0000 461 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1199.952166 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1199.952166 Node 7: lnL = -1199.952166 Node 8: lnL = -1199.952166 Node 9: lnL = -1199.952166 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 347 Sequential format.. Reading seq # 1: YOR251C_Sbay Reading seq # 2: YOR251C_Scer Reading seq # 3: YOR251C_Skud Reading seq # 4: YOR251C_Smik Reading seq # 5: YOR251C_Spar Sequences read.. Counting patterns.. # site patterns = 131 Counting frequencies.. 120 bytes for distance 20960 bytes for lkl0 16768 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.193845 0.018450 0.075454 0.057664 0.077612 0.170686 0.212924 0.039699 lnL0 = -1442.299084 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1442.299084 x= 0.19385 0.01845 0.07545 0.05766 0.07761 0.17069 0.21292 0.03970 1 h-lim-p 0.0063 1.9472 67.5945 1441.753362 5 0.0003 37 | 0/8 2 h-lim-p 0.0011 0.0085 8.8888 1441.735454 5 0.0005 58 | 0/8 3 h-lim-p 0.0011 0.0213 3.8782 1441.733223 4 0.0003 79 | 0/8 4 h-lim-p 0.0011 0.1455 1.2502 1441.732838 4 0.0005 100 | 0/8 5 h-lim-p 0.0015 0.5214 0.4673 1441.732789 3 0.0005 120 | 0/8 6 h-lim-p 0.0018 0.8070 0.1324 1441.732783 2 0.0007 144 | 0/8 7 h-lim-p 0.0033 9.9547 0.0282 1441.732783 0 0.0015 164 | 0/8 8 h-lim-p 0.1963 20.0000 0.0002 1441.732711 0 1.1780 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1441.732710 0 1.0938 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1441.732710 0 1.2500 226 | 0/8 11 h-lim-p 1.4114 20.0000 0.0000 1441.732710 0 0.3087 247 | 0/8 12 h-lim-p 0.1408 20.0000 0.0000 1441.732710 0 0.0176 269 | 0/8 13 h-lim-p 0.0092 20.0000 0.0000 1441.732710 0 0.0000 312 | 0/8 14 h-lim-p 0.0000 20.0000 0.0018 1441.732710 0 0.0000 338 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 1441.732710 0 0.0013 365 | 0/8 16 h-lim-p 0.0030 20.0000 0.0001 1441.732710 0 0.0000 392 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 1441.732710 0 0.0000 427 | 0/8 18 h-lim-p 0.0000 20.0000 0.0021 1441.732710 0 0.0000 462 | 0/8 19 h-lim-p 0.0000 20.0000 0.0021 | 0/8 20 h-lim-p 0.0000 20.0000 0.0021 Out... lnL = -1441.732710 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1441.732710 Node 7: lnL = -1441.732710 Node 8: lnL = -1441.732710 Node 9: lnL = -1441.732710 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 345 Sequential format.. Reading seq # 1: YOR252W_Sbay Reading seq # 2: YOR252W_Scer Reading seq # 3: YOR252W_Skud Reading seq # 4: YOR252W_Smik Reading seq # 5: YOR252W_Spar Sequences read.. Counting patterns.. # site patterns = 147 Counting frequencies.. 120 bytes for distance 23520 bytes for lkl0 18816 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.135221 0.137170 0.147857 0.220251 0.143578 0.311144 0.246187 lnL0 = -1393.198134 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1393.198134 x= 0.00006 0.13522 0.13717 0.14786 0.22025 0.14358 0.31114 0.24619 1 h-lim-p 0.0000 0.0000 203.5048 1393.107237 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0029 116.0956 1382.581795 0 0.0019 41 | 1/8 3 h-lim-p 0.0012 0.0099 29.4536 1381.932542 1 0.0016 55 | 1/8 4 h-lim-p 0.0035 0.0282 9.0160 1381.748267 5 0.0031 76 | 1/8 5 h-lim-p 0.0039 0.0311 3.8086 1381.524897 0 0.0058 88 | 1/8 6 h-lim-p 0.0031 0.0245 6.5384 1379.674854 0 0.0122 102 | 1/8 7 h-lim-p 0.0017 0.0139 20.7187 1369.567025 0 0.0069 116 | 1/8 8 h-lim-p 0.0009 0.0074 44.9531 1368.102212 0 0.0018 129 | 1/8 9 h-lim-p 0.4041 3.2325 0.1007 1367.315339 6 0.3548 153 | 0/8 10 h-lim-p 0.0024 0.0479 15.0942 1367.169019 6 0.0016 185 | 0/8 11 h-lim-p 0.9473 7.5785 0.0164 1367.111580 7 0.5833 215 | 0/8 12 h-lim-p 2.5000 20.0000 0.0030 1367.109721 4 0.6351 245 | 0/8 13 h-lim-p 1.3046 20.0000 0.0015 1367.109311 3 0.6443 272 | 0/8 14 h-lim-p 2.5000 20.0000 0.0003 1367.109273 3 0.8059 300 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1367.109272 1 0.6152 323 | 0/8 16 h-lim-p 2.1948 20.0000 0.0000 1367.109272 0 0.9602 343 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1367.109272 0 1.0938 363 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1367.109272 0 2.1875 383 | 0/8 19 h-lim-p 1.9277 20.0000 0.0000 1367.109272 0 0.4819 404 | 0/8 20 h-lim-p 0.8538 20.0000 0.0000 1367.109272 0 0.0233 428 | 0/8 21 h-lim-p 0.0190 20.0000 0.0000 1367.109272 0 0.0000 460 Out... lnL = -1367.109272 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1367.109272 Node 7: lnL = -1367.109272 Node 8: lnL = -1367.109272 Node 9: lnL = -1367.109272 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 254 Sequential format.. Reading seq # 1: YOR254C_Sbay Reading seq # 2: YOR254C_Scer Reading seq # 3: YOR254C_Skud Reading seq # 4: YOR254C_Smik Reading seq # 5: YOR254C_Spar Sequences read.. Counting patterns.. # site patterns = 85 Counting frequencies.. 120 bytes for distance 13600 bytes for lkl0 10880 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.075588 0.101604 0.132828 0.143831 0.072043 0.207877 0.151833 lnL0 = -1016.394915 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1016.394915 x= 0.00006 0.07559 0.10160 0.13283 0.14383 0.07204 0.20788 0.15183 1 h-lim-p 0.0000 0.0000 224.3781 1016.284731 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0007 264.1382 1007.725543 0 0.0003 39 | 1/8 3 h-lim-p 0.0006 0.0051 47.8937 1006.837518 0 0.0010 51 | 1/8 4 h-lim-p 0.0025 0.0196 9.9156 1006.783578 7 0.0009 77 | 1/8 5 h-lim-p 0.0042 0.1621 2.1718 1006.686332 0 0.0084 90 | 1/8 6 h-lim-p 0.0028 0.0227 4.7764 1006.087185 0 0.0057 103 | 1/8 7 h-lim-p 0.0010 0.0081 11.7506 1000.472012 0 0.0061 117 | 1/8 8 h-lim-p 0.0004 0.0030 69.0181 999.325328 0 0.0006 129 | 1/8 9 h-lim-p 0.7257 20.0000 0.0532 997.523599 7 0.7144 155 | 1/8 10 h-lim-p 2.0349 16.2788 0.0137 997.103967 7 1.7258 193 | 1/8 11 h-lim-p 2.5000 20.0000 0.0048 997.086291 6 0.9422 224 | 0/8 12 h-lim-p 0.0021 0.1088 2.1641 997.084490 4 0.0009 250 | 0/8 13 h-lim-p 1.4930 20.0000 0.0013 997.083584 5 0.7461 272 | 0/8 14 h-lim-p 2.5000 20.0000 0.0003 997.083514 3 0.9482 298 | 0/8 15 h-lim-p 2.5000 20.0000 0.0001 997.083510 1 0.9961 320 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 997.083510 0 1.0938 340 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 997.083510 0 1.0938 360 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 997.083510 0 0.0011 390 Out... lnL = -997.083510 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -997.083510 Node 7: lnL = -997.083510 Node 8: lnL = -997.083510 Node 9: lnL = -997.083510 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 254 Sequential format.. Reading seq # 1: YOR255W_Sbay Reading seq # 2: YOR255W_Scer Reading seq # 3: YOR255W_Skud Reading seq # 4: YOR255W_Smik Reading seq # 5: YOR255W_Spar Sequences read.. Counting patterns.. # site patterns = 89 Counting frequencies.. 120 bytes for distance 14240 bytes for lkl0 11392 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.076957 0.099159 0.131102 0.142347 0.074352 0.201480 0.151769 lnL0 = -1013.963997 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1013.963997 x= 0.00006 0.07696 0.09916 0.13110 0.14235 0.07435 0.20148 0.15177 1 h-lim-p 0.0000 0.0000 222.8166 1013.832584 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0007 263.9947 1005.384277 0 0.0003 39 | 1/8 3 h-lim-p 0.0006 0.0044 50.1400 1004.510011 0 0.0011 52 | 1/8 4 h-lim-p 0.0026 0.0210 7.8734 1004.469695 6 0.0010 77 | 1/8 5 h-lim-p 0.0051 0.1886 1.4990 1004.208841 0 0.0152 90 | 1/8 6 h-lim-p 0.0075 0.0713 3.0456 997.985976 0 0.0299 104 | 0/8 7 h-lim-p 0.0002 0.0012 57.5916 997.164061 0 0.0005 117 | 0/8 8 h-lim-p 0.0022 0.0173 11.5114 997.129648 7 0.0006 143 | 0/8 9 h-lim-p 0.0019 0.0657 3.4786 997.119294 5 0.0012 166 | 0/8 10 h-lim-p 0.0401 12.8131 0.1074 995.256873 0 0.3206 181 | 0/8 11 h-lim-p 1.5021 12.0166 0.0147 995.024928 7 1.6279 218 | 0/8 12 h-lim-p 2.5000 20.0000 0.0048 995.013818 6 0.8204 251 | 0/8 13 h-lim-p 2.5000 20.0000 0.0014 995.012402 4 0.9932 279 | 0/8 14 h-lim-p 2.5000 20.0000 0.0003 995.012354 3 0.8059 307 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 995.012352 1 1.2305 330 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 995.012352 0 1.0938 350 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 995.012352 0 1.0938 370 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 995.012352 0 0.0781 394 | 0/8 19 h-lim-p 0.0583 20.0000 0.0000 995.012352 0 0.0009 419 Out... lnL = -995.012352 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -995.012352 Node 7: lnL = -995.012352 Node 8: lnL = -995.012352 Node 9: lnL = -995.012352 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 338 Sequential format.. Reading seq # 1: YOR256C_Sbay Reading seq # 2: YOR256C_Scer Reading seq # 3: YOR256C_Skud Reading seq # 4: YOR256C_Smik Reading seq # 5: YOR256C_Spar Sequences read.. Counting patterns.. # site patterns = 137 Counting frequencies.. 120 bytes for distance 21920 bytes for lkl0 17536 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.018068 0.071985 0.034420 0.096852 0.076246 0.197403 0.182973 0.230305 lnL0 = -1451.231344 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1451.231344 x= 0.01807 0.07199 0.03442 0.09685 0.07625 0.19740 0.18297 0.23031 1 h-lim-p 0.0010 0.0081 50.9199 1450.917884 7 0.0003 38 | 0/8 2 h-lim-p 0.0007 0.0058 8.6465 1450.890777 3 0.0007 56 | 0/8 3 h-lim-p 0.0017 0.0757 3.8103 1450.887708 4 0.0005 79 | 0/8 4 h-lim-p 0.0015 0.1510 1.2332 1450.887360 4 0.0005 100 | 0/8 5 h-lim-p 0.0027 0.7514 0.2305 1450.887345 1 0.0006 115 | 0/8 6 h-lim-p 0.0047 2.9214 0.0293 1450.887345 0 0.0006 137 | 0/8 7 h-lim-p 0.0195 20.0000 0.0009 1450.887345 0 0.0085 157 | 0/8 8 h-lim-p 0.0202 20.0000 0.0004 1450.887343 0 0.1619 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1450.887343 0 1.0938 200 | 0/8 10 h-lim-p 1.1620 20.0000 0.0000 1450.887343 0 0.5084 220 | 0/8 11 h-lim-p 0.0381 20.0000 0.0003 1450.887343 0 0.0000 263 | 0/8 12 h-lim-p 0.0000 20.0000 0.0003 | 0/8 13 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -1450.887343 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1450.887343 Node 7: lnL = -1450.887343 Node 8: lnL = -1450.887343 Node 9: lnL = -1450.887343 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 192 Sequential format.. Reading seq # 1: YOR258W_Sbay Reading seq # 2: YOR258W_Scer Reading seq # 3: YOR258W_Skud Reading seq # 4: YOR258W_Smik Reading seq # 5: YOR258W_Spar Sequences read.. Counting patterns.. # site patterns = 98 Counting frequencies.. 120 bytes for distance 15680 bytes for lkl0 12544 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.159857 0.138667 0.154224 0.150752 0.145999 0.206371 0.232335 lnL0 = -814.310724 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 814.310724 x= 0.00006 0.15986 0.13867 0.15422 0.15075 0.14600 0.20637 0.23234 1 h-lim-p 0.0000 0.0000 121.2918 814.194990 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0036 79.8457 809.561277 0 0.0015 41 | 1/8 3 h-lim-p 0.0004 0.0034 56.4513 808.340945 0 0.0013 54 | 1/8 4 h-lim-p 0.0015 0.0120 10.2813 808.225244 0 0.0022 66 | 1/8 5 h-lim-p 0.0147 0.1174 1.5499 807.738522 0 0.0293 79 | 1/8 6 h-lim-p 0.0054 0.0431 4.9359 802.299204 0 0.0215 93 | 1/8 7 h-lim-p 0.0010 0.0081 24.1476 801.912995 0 0.0020 106 | 1/8 8 h-lim-p 0.0041 0.0325 6.3561 801.861998 7 0.0022 135 | 1/8 9 h-lim-p 0.0890 1.4664 0.1596 800.772944 0 0.3559 149 | 0/8 10 h-lim-p 0.0097 0.5073 5.8480 800.737683 3 0.0020 175 | 0/8 11 h-lim-p 0.2867 8.5300 0.0414 800.254888 0 1.1466 189 | 0/8 12 h-lim-p 1.1372 9.0980 0.0168 800.105072 6 0.9725 220 | 0/8 13 h-lim-p 2.5000 20.0000 0.0039 800.098915 5 1.0113 252 | 0/8 14 h-lim-p 2.5000 20.0000 0.0006 800.098766 2 1.0889 276 | 0/8 15 h-lim-p 2.5000 20.0000 0.0002 800.098755 1 0.9961 298 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 800.098755 0 1.0938 318 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 800.098755 0 1.0938 338 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 800.098755 0 2.5000 358 | 0/8 19 h-lim-p 1.9375 20.0000 0.0000 800.098755 0 0.0019 387 Out... lnL = -800.098755 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -800.098755 Node 7: lnL = -800.098755 Node 8: lnL = -800.098755 Node 9: lnL = -800.098755 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 371 Sequential format.. Reading seq # 1: YOR261C_Sbay Reading seq # 2: YOR261C_Scer Reading seq # 3: YOR261C_Skud Reading seq # 4: YOR261C_Smik Reading seq # 5: YOR261C_Spar Sequences read.. Counting patterns.. # site patterns = 165 Counting frequencies.. 120 bytes for distance 26400 bytes for lkl0 21120 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.139358 0.229229 0.231946 0.250145 0.092131 0.363979 0.275780 lnL0 = -1793.447782 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1793.447782 x= 0.00006 0.13936 0.22923 0.23195 0.25014 0.09213 0.36398 0.27578 1 h-lim-p 0.0000 0.0000 225.7795 1793.361714 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0012 346.1865 1778.444291 0 0.0005 39 | 1/8 3 h-lim-p 0.0006 0.0046 68.7762 1775.634948 0 0.0012 52 | 1/8 4 h-lim-p 0.0062 0.0495 7.4790 1775.522245 5 0.0020 76 | 1/8 5 h-lim-p 0.0034 0.0812 4.4388 1775.038345 0 0.0067 89 | 1/8 6 h-lim-p 0.0055 0.0439 5.4405 1768.362864 0 0.0164 102 | 1/8 7 h-lim-p 0.0008 0.0061 56.3396 1762.944767 0 0.0015 115 | 1/8 8 h-lim-p 0.0102 0.0816 4.1387 1762.926717 7 0.0015 147 | 1/8 9 h-lim-p 0.0681 20.0000 0.0898 1759.902091 0 0.5448 162 | 1/8 10 h-lim-p 1.7417 16.8782 0.0281 1758.913539 6 1.5014 192 | 0/8 11 h-lim-p 0.0051 0.2050 8.2388 1758.879154 6 0.0011 223 | 0/8 12 h-lim-p 0.7989 20.0000 0.0113 1758.814084 0 1.1983 235 | 0/8 13 h-lim-p 2.5000 20.0000 0.0035 1758.808360 5 0.9563 265 | 0/8 14 h-lim-p 2.5000 20.0000 0.0007 1758.808192 4 0.8479 296 | 0/8 15 h-lim-p 2.5000 20.0000 0.0001 1758.808188 1 0.9961 318 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1758.808188 0 1.0938 338 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1758.808188 0 1.0938 358 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1758.808188 0 0.0000 393 Out... lnL = -1758.808188 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1758.808188 Node 7: lnL = -1758.808188 Node 8: lnL = -1758.808188 Node 9: lnL = -1758.808188 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 371 Sequential format.. Reading seq # 1: YOR262W_Sbay Reading seq # 2: YOR262W_Scer Reading seq # 3: YOR262W_Skud Reading seq # 4: YOR262W_Smik Reading seq # 5: YOR262W_Spar Sequences read.. Counting patterns.. # site patterns = 166 Counting frequencies.. 120 bytes for distance 26560 bytes for lkl0 21248 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.131385 0.218159 0.228535 0.246787 0.095955 0.362626 0.267992 lnL0 = -1784.284971 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1784.284971 x= 0.00006 0.13138 0.21816 0.22853 0.24679 0.09595 0.36263 0.26799 1 h-lim-p 0.0000 0.0000 231.9108 1784.188271 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0011 351.1744 1768.098849 0 0.0005 39 | 1/8 3 h-lim-p 0.0005 0.0044 73.0476 1765.104097 0 0.0011 52 | 1/8 4 h-lim-p 0.0036 0.0290 11.3666 1764.995187 6 0.0012 79 | 1/8 5 h-lim-p 0.0026 0.0705 5.2435 1764.796784 0 0.0039 91 | 1/8 6 h-lim-p 0.0076 0.0748 2.7287 1760.641147 0 0.0303 105 | 1/8 7 h-lim-p 0.0010 0.0083 39.8589 1752.218761 0 0.0031 118 | 1/8 8 h-lim-p 0.0066 0.0527 6.6081 1752.194859 6 0.0009 146 | 0/8 9 h-lim-p 0.0003 0.0380 20.8968 1751.972331 0 0.0012 160 | 0/8 10 h-lim-p 0.2226 1.7809 0.0773 1749.411171 0 0.8905 174 | 0/8 11 h-lim-p 1.6116 12.8931 0.0247 1748.520619 2 1.5109 198 | 0/8 12 h-lim-p 2.5000 20.0000 0.0071 1748.469601 7 1.3890 235 | 0/8 13 h-lim-p 2.5000 20.0000 0.0020 1748.467286 4 1.0199 264 | 0/8 14 h-lim-p 2.5000 20.0000 0.0003 1748.467266 3 0.7330 293 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1748.467266 0 1.0938 313 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1748.467266 0 1.0938 333 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1748.467266 0 2.1875 353 | 0/8 18 h-lim-p 2.2629 20.0000 0.0000 1748.467266 0 0.9900 373 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1748.467266 0 0.6250 394 | 0/8 20 h-lim-p 0.0207 20.0000 0.0000 1748.467266 0 0.0006 418 Out... lnL = -1748.467266 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1748.467266 Node 7: lnL = -1748.467266 Node 8: lnL = -1748.467266 Node 9: lnL = -1748.467266 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 576 Sequential format.. Reading seq # 1: YOR264W_Sbay Reading seq # 2: YOR264W_Scer Reading seq # 3: YOR264W_Skud Reading seq # 4: YOR264W_Smik Reading seq # 5: YOR264W_Spar Sequences read.. Counting patterns.. # site patterns = 218 Counting frequencies.. 120 bytes for distance 34880 bytes for lkl0 27904 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.028335 0.096230 0.090971 0.157485 0.100638 0.184842 0.183125 0.301291 lnL0 = -2686.565733 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2686.565733 x= 0.02833 0.09623 0.09097 0.15749 0.10064 0.18484 0.18313 0.30129 1 h-lim-p 0.0017 0.0133 51.9707 2686.080815 7 0.0004 37 | 0/8 2 h-lim-p 0.0015 0.0174 12.5775 2686.034796 5 0.0006 58 | 0/8 3 h-lim-p 0.0017 0.0813 4.4804 2686.031995 4 0.0003 81 | 0/8 4 h-lim-p 0.0026 0.6364 0.5406 2686.031896 3 0.0007 100 | 0/8 5 h-lim-p 0.0048 1.1350 0.0776 2686.031894 0 0.0006 122 | 0/8 6 h-lim-p 0.0049 7.7675 0.0094 2686.031894 0 0.0011 143 | 0/8 7 h-lim-p 0.0176 20.0000 0.0006 2686.031894 0 0.0077 163 | 0/8 8 h-lim-p 0.0053 20.0000 0.0008 2686.031891 0 0.0632 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2686.031891 0 1.0938 206 | 0/8 10 h-lim-p 1.0235 20.0000 0.0000 2686.031891 0 0.4478 226 | 0/8 11 h-lim-p 0.1062 20.0000 0.0001 2686.031891 0 0.0029 250 | 0/8 12 h-lim-p 0.0004 20.0000 0.0005 2686.031891 0 0.0002 270 | 0/8 13 h-lim-p 0.0005 20.0000 0.0002 2686.031891 0 0.0005 290 | 0/8 14 h-lim-p 0.0001 20.0000 0.0019 2686.031891 0 0.0000 310 | 0/8 15 h-lim-p 0.0005 20.0000 0.0001 2686.031891 0 0.0000 346 | 0/8 16 h-lim-p 0.0000 20.0000 0.0006 | 0/8 17 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -2686.031891 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2686.031891 Node 7: lnL = -2686.031891 Node 8: lnL = -2686.031891 Node 9: lnL = -2686.031891 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 310 Sequential format.. Reading seq # 1: YOR265W_Sbay Reading seq # 2: YOR265W_Scer Reading seq # 3: YOR265W_Skud Reading seq # 4: YOR265W_Smik Reading seq # 5: YOR265W_Spar Sequences read.. Counting patterns.. # site patterns = 178 Counting frequencies.. 120 bytes for distance 28480 bytes for lkl0 22784 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.030379 0.222394 0.123531 0.173500 0.138737 0.222171 0.198118 0.402090 lnL0 = -1576.030258 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1576.030258 x= 0.03038 0.22239 0.12353 0.17350 0.13874 0.22217 0.19812 0.40209 1 h-lim-p 0.0036 0.0291 26.2580 1575.560774 4 0.0014 30 | 0/8 2 h-lim-p 0.0022 0.0176 15.4359 1575.425682 7 0.0014 60 | 0/8 3 h-lim-p 0.0027 0.0302 8.2592 1575.387292 7 0.0015 91 | 0/8 4 h-lim-p 0.0067 0.3106 1.8728 1575.384639 4 0.0016 112 | 0/8 5 h-lim-p 0.0048 0.2141 0.6463 1575.384325 3 0.0017 131 | 0/8 6 h-lim-p 0.0168 1.9079 0.0648 1575.384322 2 0.0013 158 | 0/8 7 h-lim-p 0.0270 20.0000 0.0032 1575.384322 0 0.0118 178 | 0/8 8 h-lim-p 0.0211 20.0000 0.0018 1575.384299 0 0.1688 201 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1575.384299 0 1.0938 221 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1575.384299 0 1.0938 241 | 0/8 11 h-lim-p 1.3979 20.0000 0.0000 1575.384299 0 1.2231 261 | 0/8 12 h-lim-p 0.6132 20.0000 0.0000 1575.384299 0 0.0575 284 | 0/8 13 h-lim-p 0.0033 20.0000 0.0002 1575.384299 0 0.0002 307 | 0/8 14 h-lim-p 0.0001 20.0000 0.0004 1575.384299 0 0.0000 329 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 1575.384299 0 0.0001 349 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 1575.384299 0 0.0000 381 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 1575.384299 0 0.0000 415 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 | 0/8 19 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1575.384299 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1575.384299 Node 7: lnL = -1575.384299 Node 8: lnL = -1575.384299 Node 9: lnL = -1575.384299 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 276 Sequential format.. Reading seq # 1: YOR266W_Sbay Reading seq # 2: YOR266W_Scer Reading seq # 3: YOR266W_Skud Reading seq # 4: YOR266W_Smik Reading seq # 5: YOR266W_Spar Sequences read.. Counting patterns.. # site patterns = 133 Counting frequencies.. 120 bytes for distance 21280 bytes for lkl0 17024 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.044486 0.095028 0.053936 0.103538 0.116732 0.205677 0.213103 0.314016 lnL0 = -1222.271467 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1222.271467 x= 0.04449 0.09503 0.05394 0.10354 0.11673 0.20568 0.21310 0.31402 1 h-lim-p 0.0011 0.0084 37.3138 1221.732661 6 0.0008 35 | 0/8 2 h-lim-p 0.0009 0.0070 14.7573 1221.626306 1 0.0011 49 | 0/8 3 h-lim-p 0.0019 0.0308 8.3533 1221.603233 2 0.0009 65 | 0/8 4 h-lim-p 0.0037 0.0968 2.0290 1221.601530 3 0.0009 85 | 0/8 5 h-lim-p 0.0027 0.2257 0.6829 1221.601291 2 0.0012 101 | 0/8 6 h-lim-p 0.0051 1.8686 0.1575 1221.601274 3 0.0015 129 | 0/8 7 h-lim-p 0.0181 20.0000 0.0131 1221.601274 0 0.0040 150 | 0/8 8 h-lim-p 0.0818 20.0000 0.0006 1221.601196 0 0.6547 173 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1221.601193 1 0.9961 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1221.601193 0 1.0938 215 | 0/8 11 h-lim-p 1.1026 20.0000 0.0000 1221.601193 0 8.8205 238 | 0/8 12 h-lim-p 0.3408 20.0000 0.0002 1221.601193 0 0.0213 261 | 0/8 13 h-lim-p 0.0029 20.0000 0.0014 1221.601193 0 0.0001 285 | 0/8 14 h-lim-p 0.0003 20.0000 0.0004 1221.601193 0 0.0000 323 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 1221.601193 0 0.0000 356 | 0/8 16 h-lim-p 0.0000 20.0000 0.0005 | 0/8 17 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -1221.601193 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1221.601193 Node 7: lnL = -1221.601193 Node 8: lnL = -1221.601193 Node 9: lnL = -1221.601193 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 698 Sequential format.. Reading seq # 1: YOR267C_Sbay Reading seq # 2: YOR267C_Scer Reading seq # 3: YOR267C_Skud Reading seq # 4: YOR267C_Smik Reading seq # 5: YOR267C_Spar Sequences read.. Counting patterns.. # site patterns = 204 Counting frequencies.. 120 bytes for distance 32640 bytes for lkl0 26112 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.149570 0.000060 0.456901 0.301675 0.393162 0.344147 0.654644 0.656759 lnL0 = -3332.224918 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3332.224918 x= 0.14957 0.00006 0.45690 0.30168 0.39316 0.34415 0.65464 0.65676 1 h-lim-p 0.0000 0.0000 617.0120 3332.026279 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0016 296.9226 3226.571174 m 0.0016 39 | 2/8 3 h-lim-p 0.0005 0.0038 330.3288 3045.402794 0 0.0029 53 | 2/8 4 h-lim-p 0.0003 0.0024 186.6695 3033.305584 0 0.0009 66 | 1/8 5 h-lim-p 0.0001 0.0008 489.4915 3028.829334 2 0.0001 82 | 1/8 6 h-lim-p 0.0009 0.0508 55.0177 3011.515025 0 0.0137 98 | 1/8 7 h-lim-p 0.0027 0.0216 13.8338 2995.962812 m 0.0216 110 | 2/8 8 h-lim-p 0.0038 0.0307 17.1736 2995.071812 5 0.0043 133 | 2/8 9 h-lim-p 0.0606 0.4848 1.0083 .. | 2/8 10 h-lim-p 0.0000 0.0005 333.8128 2973.872272 5 0.0003 197 | 2/8 11 h-lim-p 0.0000 0.0002 516.5965 2967.445805 0 0.0001 211 | 2/8 12 h-lim-p 0.0002 0.0012 274.6297 2958.585939 0 0.0003 224 | 2/8 13 h-lim-p 0.0088 0.1667 9.5685 2957.042597 0 0.0351 238 | 1/8 14 h-lim-p 0.0056 0.0448 53.8902 2956.595948 8 0.0004 272 | 1/8 15 h-lim-p 0.0008 0.0446 27.1445 2955.468481 0 0.0094 287 | 1/8 16 h-lim-p 0.6539 5.2316 0.1521 2951.500926 0 1.3079 300 | 1/8 17 h-lim-p 0.4819 3.8554 0.1311 2949.381332 0 0.9639 320 | 1/8 18 h-lim-p 1.0642 8.5134 0.0373 2949.200245 6 0.6995 352 | 1/8 19 h-lim-p 0.9589 19.5032 0.0272 2949.164862 4 0.7398 379 | 1/8 20 h-lim-p 2.5000 20.0000 0.0029 2949.160870 3 1.0483 405 | 1/8 21 h-lim-p 2.5000 20.0000 0.0007 2949.160851 2 0.9644 428 | 1/8 22 h-lim-p 2.5000 20.0000 0.0000 2949.160850 0 1.0938 447 | 1/8 23 h-lim-p 2.5000 20.0000 0.0000 2949.160850 0 1.2500 466 | 1/8 24 h-lim-p 2.5000 20.0000 0.0000 2949.160850 0 1.0938 485 | 1/8 25 h-lim-p 1.1815 20.0000 0.0000 2949.160850 0 0.2954 505 | 1/8 26 h-lim-p 0.0173 20.0000 0.0000 2949.160850 0 0.0000 545 | 1/8 27 h-lim-p 0.0000 20.0000 0.0000 2949.160850 0 0.0000 577 | 1/8 28 h-lim-p 0.0000 20.0000 0.0000 | 1/8 29 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -2949.160850 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2949.160850 Node 7: lnL = -2949.160850 Node 8: lnL = -2949.160850 Node 9: lnL = -2949.160850 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 842 Sequential format.. Reading seq # 1: YOR271C_Sbay Reading seq # 2: YOR271C_Scer Reading seq # 3: YOR271C_Skud Reading seq # 4: YOR271C_Smik Reading seq # 5: YOR271C_Spar Sequences read.. Counting patterns.. # site patterns = 267 Counting frequencies.. 120 bytes for distance 42720 bytes for lkl0 34176 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.003407 0.046104 0.042166 0.087417 0.086917 0.171740 0.152011 0.183941 lnL0 = -3482.575454 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3482.575454 x= 0.00341 0.04610 0.04217 0.08742 0.08692 0.17174 0.15201 0.18394 1 h-lim-p 0.0005 0.3958 361.5608 3476.766033 7 0.0001 36 | 0/8 2 h-lim-p 0.0007 0.0052 27.7392 3476.685053 6 0.0002 63 | 0/8 3 h-lim-p 0.0008 0.0064 7.3805 3476.680108 4 0.0002 85 | 0/8 4 h-lim-p 0.0007 0.0756 2.0433 3476.679598 3 0.0003 103 | 0/8 5 h-lim-p 0.0020 1.5184 0.2679 3476.679590 0 0.0002 117 | 0/8 6 h-lim-p 0.0023 6.1410 0.0254 3476.679590 0 0.0005 138 | 0/8 7 h-lim-p 0.0013 4.1346 0.0100 3476.679590 0 0.0013 158 | 0/8 8 h-lim-p 0.0115 20.0000 0.0011 3476.679406 0 0.1838 182 | 0/8 9 h-lim-p 0.7817 20.0000 0.0003 3476.679402 0 0.7817 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3476.679402 0 1.0938 222 | 0/8 11 h-lim-p 0.4659 20.0000 0.0001 3476.679402 0 1.8635 244 | 0/8 12 h-lim-p 0.7721 20.0000 0.0001 3476.679402 0 0.0483 267 | 0/8 13 h-lim-p 0.0003 0.6183 0.0185 3476.679402 0 0.0000 307 | 0/8 14 h-lim-p 0.0000 20.0000 0.0038 3476.679402 0 0.0000 328 | 0/8 15 h-lim-p 0.0002 20.0000 0.0007 3476.679402 0 0.0005 349 | 0/8 16 h-lim-p 0.0023 20.0000 0.0001 3476.679402 0 0.0000 374 | 0/8 17 h-lim-p 0.0001 20.0000 0.0001 3476.679402 0 0.0000 405 | 0/8 18 h-lim-p 0.0000 20.0000 0.0004 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0034 3476.679402 0 0.0000 464 | 0/8 20 h-lim-p 0.0000 20.0000 0.0002 3476.679402 0 0.0000 486 | 0/8 21 h-lim-p 0.0000 20.0000 0.0001 3476.679402 0 0.0000 520 | 0/8 22 h-lim-p 0.0000 20.0000 0.0034 | 0/8 23 h-lim-p 0.0000 20.0000 0.0034 Out... lnL = -3476.679402 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3476.679402 Node 7: lnL = -3476.679402 Node 8: lnL = -3476.679402 Node 9: lnL = -3476.679402 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 941 Sequential format.. Reading seq # 1: YOR274W_Sbay Reading seq # 2: YOR274W_Scer Reading seq # 3: YOR274W_Skud Reading seq # 4: YOR274W_Smik Reading seq # 5: YOR274W_Spar Sequences read.. Counting patterns.. # site patterns = 271 Counting frequencies.. 120 bytes for distance 43360 bytes for lkl0 34688 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.002509 0.200675 0.052370 0.101070 0.099447 0.249305 0.215248 0.299854 lnL0 = -3653.248002 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3653.248002 x= 0.00251 0.20068 0.05237 0.10107 0.09945 0.24931 0.21525 0.29985 1 h-lim-p 0.0001 0.0009 184.6505 3648.980810 0 0.0002 23 | 0/8 2 h-lim-p 0.0001 0.0007 43.0297 3648.739923 0 0.0004 37 | 0/8 3 h-lim-p 0.0000 0.0003 38.6540 3648.584821 m 0.0003 49 | 1/8 4 h-lim-p 0.0007 0.0157 19.9260 3648.537442 6 0.0003 75 | 1/8 5 h-lim-p 0.0009 0.0499 7.8184 3648.489258 0 0.0017 88 | 1/8 6 h-lim-p 0.0191 0.6285 0.7097 3648.467707 6 0.0109 115 | 0/8 7 h-lim-p 0.0012 0.6025 6.3081 3648.447274 5 0.0009 144 | 0/8 8 h-lim-p 0.0018 0.1073 3.3137 3648.425164 0 0.0027 156 | 0/8 9 h-lim-p 0.0024 0.0195 0.6514 3648.417817 m 0.0195 168 | 1/8 10 h-lim-p 2.5000 20.0000 0.0023 3648.409788 5 0.9563 198 | 1/8 11 h-lim-p 0.0950 13.1581 0.0229 3648.409500 3 0.0337 225 | 1/8 12 h-lim-p 2.5000 20.0000 0.0001 3648.409481 1 1.9922 246 | 1/8 13 h-lim-p 2.5000 20.0000 0.0001 3648.409478 1 1.2305 268 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 3648.409478 0 1.0938 287 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 3648.409478 0 1.0938 306 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 3648.409478 0 5.0000 326 | 1/8 17 h-lim-p 1.2497 20.0000 0.0000 3648.409478 0 0.3124 346 | 1/8 18 h-lim-p 0.4543 20.0000 0.0000 3648.409478 0 0.0497 367 | 1/8 19 h-lim-p 0.0524 20.0000 0.0000 3648.409478 0 0.0033 389 Out... lnL = -3648.409478 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3648.409478 Node 7: lnL = -3648.409478 Node 8: lnL = -3648.409478 Node 9: lnL = -3648.409478 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 275 Sequential format.. Reading seq # 1: YOR275C_Sbay Reading seq # 2: YOR275C_Scer Reading seq # 3: YOR275C_Skud Reading seq # 4: YOR275C_Smik Reading seq # 5: YOR275C_Spar Sequences read.. Counting patterns.. # site patterns = 130 Counting frequencies.. 120 bytes for distance 20800 bytes for lkl0 16640 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.003649 0.069416 0.035650 0.188354 0.137613 0.226070 0.158919 0.242187 lnL0 = -1248.091399 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1248.091399 x= 0.00365 0.06942 0.03565 0.18835 0.13761 0.22607 0.15892 0.24219 1 h-lim-p 0.0012 0.0098 52.5016 1247.590331 6 0.0004 36 | 0/8 2 h-lim-p 0.0001 0.0010 7.6152 1247.563017 m 0.0010 48 | 0/8 3 h-lim-p 0.0078 0.1697 1.0066 1247.562473 5 0.0011 74 | 0/8 4 h-lim-p 0.0052 1.2703 0.2111 1247.562455 2 0.0008 92 | 0/8 5 h-lim-p 0.0004 0.0031 0.0756 1247.562454 0 0.0008 113 | 0/8 6 h-lim-p 0.0001 0.0004 0.3897 1247.562454 0 0.0000 134 | 0/8 7 h-lim-p 0.0000 0.0001 1.5767 1247.562454 0 0.0000 154 | 0/8 8 h-lim-p 0.0014 4.4267 0.0048 1247.562452 0 0.0231 170 | 0/8 9 h-lim-p 0.0125 20.0000 0.0088 1247.562323 0 0.0749 192 | 0/8 10 h-lim-p 0.4534 20.0000 0.0015 1247.562321 0 0.0567 214 | 0/8 11 h-lim-p 0.9691 20.0000 0.0001 1247.562318 0 0.9691 234 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1247.562318 0 1.0938 254 | 0/8 13 h-lim-p 0.1140 5.4769 0.0000 1247.562318 0 0.0001 283 | 0/8 14 h-lim-p 0.0001 2.2789 0.0001 1247.562318 0 0.0000 312 | 0/8 15 h-lim-p 0.0000 0.0022 0.0385 | 0/8 16 h-lim-p 0.0000 0.0022 0.0385 Out... lnL = -1247.562318 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1247.562318 Node 7: lnL = -1247.562318 Node 8: lnL = -1247.562318 Node 9: lnL = -1247.562318 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 283 Sequential format.. Reading seq # 1: YOR276W_Sbay Reading seq # 2: YOR276W_Scer Reading seq # 3: YOR276W_Skud Reading seq # 4: YOR276W_Smik Reading seq # 5: YOR276W_Spar Sequences read.. Counting patterns.. # site patterns = 138 Counting frequencies.. 120 bytes for distance 22080 bytes for lkl0 17664 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.198999 0.161627 0.253351 0.214280 0.180355 0.270432 0.241893 lnL0 = -1296.311057 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1296.311057 x= 0.00006 0.19900 0.16163 0.25335 0.21428 0.18035 0.27043 0.24189 1 h-lim-p 0.0000 0.0000 158.7031 1296.254528 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0036 89.1264 1287.852224 5 0.0024 51 | 1/8 3 h-lim-p 0.0065 0.0524 8.0761 1287.692770 4 0.0033 72 | 1/8 4 h-lim-p 0.0146 0.1744 1.8473 1287.125563 0 0.0291 85 | 1/8 5 h-lim-p 0.0053 0.0425 8.1770 1283.893323 0 0.0106 98 | 1/8 6 h-lim-p 0.0016 0.0129 28.8705 1277.704984 0 0.0065 112 | 1/8 7 h-lim-p 0.0033 0.0265 5.1776 1277.689591 5 0.0010 137 | 0/8 8 h-lim-p 0.0002 0.0349 25.8080 1277.353851 0 0.0012 151 | 0/8 9 h-lim-p 0.0075 0.0599 3.5325 1277.344781 6 0.0011 181 | 0/8 10 h-lim-p 0.0217 1.6949 0.1826 1276.451365 0 0.3477 197 | 0/8 11 h-lim-p 2.5000 20.0000 0.0126 1276.412037 7 0.8295 233 | 0/8 12 h-lim-p 2.5000 20.0000 0.0038 1276.409332 4 0.6351 263 | 0/8 13 h-lim-p 2.5000 20.0000 0.0004 1276.409291 3 0.8171 290 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 1276.409288 2 0.7996 315 | 0/8 15 h-lim-p 2.1888 20.0000 0.0000 1276.409287 0 0.9576 335 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1276.409287 0 1.0938 355 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1276.409287 0 1.0938 375 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1276.409287 0 2.1875 395 | 0/8 19 h-lim-p 2.3345 20.0000 0.0000 1276.409287 0 0.0730 419 | 0/8 20 h-lim-p 0.0396 20.0000 0.0000 1276.409287 0 0.0099 440 Out... lnL = -1276.409287 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1276.409287 Node 7: lnL = -1276.409287 Node 8: lnL = -1276.409287 Node 9: lnL = -1276.409287 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 862 Sequential format.. Reading seq # 1: YOR278W_Sbay Reading seq # 2: YOR278W_Scer Reading seq # 3: YOR278W_Skud Reading seq # 4: YOR278W_Smik Reading seq # 5: YOR278W_Spar Sequences read.. Counting patterns.. # site patterns = 217 Counting frequencies.. 120 bytes for distance 34720 bytes for lkl0 27776 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.056170 0.076592 0.100691 0.082717 0.117352 0.147528 0.153956 lnL0 = -3360.887280 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3360.887280 x= 0.00006 0.05617 0.07659 0.10069 0.08272 0.11735 0.14753 0.15396 1 h-lim-p 0.0000 0.0000 158.0135 3360.234672 m 0.0000 22 | 1/8 2 h-lim-p 0.0001 0.0072 30.2242 3360.141981 0 0.0002 34 | 1/8 3 h-lim-p 0.0010 0.0293 6.4321 3360.137017 3 0.0002 53 | 1/8 4 h-lim-p 0.0009 0.0705 1.7422 3360.135718 2 0.0004 69 | 1/8 5 h-lim-p 0.0008 2.4466 0.8671 3360.129094 0 0.0016 82 | 1/8 6 h-lim-p 0.0005 0.0678 2.7109 3360.018181 0 0.0032 103 | 1/8 7 h-lim-p 0.0012 0.0137 6.9745 3358.876581 0 0.0025 116 | 1/8 8 h-lim-p 0.0017 0.0208 10.1745 3358.864381 6 0.0002 145 | 1/8 9 h-lim-p 0.6674 20.0000 0.0036 3358.840330 0 1.0011 157 | 0/8 10 h-lim-p -0.0000 -0.0000 0.0197 h-lim-p: -1.10651889e-20 -8.85215110e-20 1.96813620e-02 3358.840330 .. | 0/8 11 h-lim-p 0.0000 0.0431 2.4807 3358.839798 0 0.0002 196 | 0/8 12 h-lim-p 0.0007 0.4724 0.6004 3358.839775 1 0.0001 211 | 0/8 13 h-lim-p 0.0000 0.0004 0.2145 3358.839775 0 0.0000 231 | 0/8 14 h-lim-p 0.0000 0.0004 0.2211 3358.839775 0 0.0000 265 | 0/8 15 h-lim-p 0.0000 0.0005 0.1807 .. | 0/8 16 h-lim-p 0.0000 0.0002 0.2846 3358.839774 0 0.0001 321 | 0/8 17 h-lim-p 0.0000 0.0001 0.6216 .. | 0/8 18 h-lim-p 0.0000 0.0001 0.2316 | 0/8 19 h-lim-p 0.0000 0.0001 0.2316 Out... lnL = -3358.839774 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3358.839774 Node 7: lnL = -3358.839774 Node 8: lnL = -3358.839774 Node 9: lnL = -3358.839774 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 398 Sequential format.. Reading seq # 1: YOR279C_Sbay Reading seq # 2: YOR279C_Scer Reading seq # 3: YOR279C_Skud Reading seq # 4: YOR279C_Smik Reading seq # 5: YOR279C_Spar Sequences read.. Counting patterns.. # site patterns = 179 Counting frequencies.. 120 bytes for distance 28640 bytes for lkl0 22912 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.315048 0.133409 0.225110 0.181603 0.230657 0.287221 0.310319 lnL0 = -1860.694097 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1860.694097 x= 0.00006 0.31505 0.13341 0.22511 0.18160 0.23066 0.28722 0.31032 1 h-lim-p 0.0000 0.0000 181.2799 1860.592892 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0040 64.3984 1855.866239 7 0.0024 55 | 1/8 3 h-lim-p 0.0014 0.0111 10.4304 1855.721668 0 0.0028 68 | 1/8 4 h-lim-p 0.0097 0.0991 2.9972 1855.441783 3 0.0098 86 | 1/8 5 h-lim-p 0.0075 0.0876 3.9143 1849.640043 0 0.0301 100 | 1/8 6 h-lim-p 0.0008 0.0066 32.5905 1844.293849 0 0.0033 114 | 1/8 7 h-lim-p 0.0009 0.0075 28.3011 1843.898988 5 0.0010 135 | 1/8 8 h-lim-p 0.0041 0.0691 6.7277 1843.854482 2 0.0019 151 | 1/8 9 h-lim-p 0.1312 4.2067 0.0976 1843.058147 0 0.5249 165 | 0/8 10 h-lim-p 0.0272 0.5355 1.8860 1843.055100 5 0.0019 199 | 0/8 11 h-lim-p 0.4581 3.6651 0.0074 1843.045251 5 0.4950 224 | 0/8 12 h-lim-p 1.5073 16.2663 0.0024 1843.043943 4 0.8101 253 | 0/8 13 h-lim-p 2.5000 20.0000 0.0002 1843.043936 2 0.7996 278 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1843.043936 0 1.0938 298 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1843.043936 0 1.0938 318 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1843.043936 0 1.0938 338 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1843.043936 0 2.5000 358 | 0/8 18 h-lim-p 1.7031 20.0000 0.0000 1843.043936 0 0.0266 383 | 0/8 19 h-lim-p 0.0254 20.0000 0.0000 1843.043936 0 0.0000 411 Out... lnL = -1843.043936 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1843.043936 Node 7: lnL = -1843.043936 Node 8: lnL = -1843.043936 Node 9: lnL = -1843.043936 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 352 Sequential format.. Reading seq # 1: YOR281C_Sbay Reading seq # 2: YOR281C_Scer Reading seq # 3: YOR281C_Skud Reading seq # 4: YOR281C_Smik Reading seq # 5: YOR281C_Spar Sequences read.. Counting patterns.. # site patterns = 162 Counting frequencies.. 120 bytes for distance 25920 bytes for lkl0 20736 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.017073 0.072929 0.061838 0.107755 0.081407 0.206889 0.249459 0.257233 lnL0 = -1544.293507 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1544.293507 x= 0.01707 0.07293 0.06184 0.10775 0.08141 0.20689 0.24946 0.25723 1 h-lim-p 0.0082 0.0656 46.4459 1543.862624 3 0.0004 31 | 0/8 2 h-lim-p 0.0017 0.0233 11.7661 1543.802926 6 0.0009 56 | 0/8 3 h-lim-p 0.0014 0.0575 7.5461 1543.792898 6 0.0005 82 | 0/8 4 h-lim-p 0.0019 0.0282 1.8754 1543.791583 4 0.0008 101 | 0/8 5 h-lim-p 0.0035 0.5091 0.4414 1543.791498 3 0.0009 120 | 0/8 6 h-lim-p 0.0034 1.5936 0.1223 1543.791491 1 0.0008 143 | 0/8 7 h-lim-p 0.0031 5.6686 0.0331 1543.791490 0 0.0013 163 | 0/8 8 h-lim-p 0.0678 20.0000 0.0007 1543.791237 0 0.8138 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1543.791234 1 0.9961 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1543.791234 0 0.0195 234 | 0/8 11 h-lim-p 0.0011 20.0000 0.0003 1543.791234 0 0.0001 257 | 0/8 12 h-lim-p 0.0001 20.0000 0.0002 1543.791234 0 0.0000 289 | 0/8 13 h-lim-p 0.0000 20.0000 0.0003 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -1543.791234 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1543.791234 Node 7: lnL = -1543.791234 Node 8: lnL = -1543.791234 Node 9: lnL = -1543.791234 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 133 Sequential format.. Reading seq # 1: YOR283W_Sbay Reading seq # 2: YOR283W_Scer Reading seq # 3: YOR283W_Skud Reading seq # 4: YOR283W_Smik Reading seq # 5: YOR283W_Spar Sequences read.. Counting patterns.. # site patterns = 84 Counting frequencies.. 120 bytes for distance 13440 bytes for lkl0 10752 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.020118 0.090939 0.095571 0.152799 0.142761 0.323547 0.203794 0.331387 lnL0 = -650.215307 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 650.215307 x= 0.02012 0.09094 0.09557 0.15280 0.14276 0.32355 0.20379 0.33139 1 h-lim-p 0.0095 0.0764 20.2193 649.834059 5 0.0020 34 | 0/8 2 h-lim-p 0.0046 0.0416 8.7935 649.720660 6 0.0034 60 | 0/8 3 h-lim-p 0.0068 0.0675 4.3567 649.696295 2 0.0032 76 | 0/8 4 h-lim-p 0.0048 0.1059 2.9031 649.687245 6 0.0032 102 | 0/8 5 h-lim-p 0.0121 0.0972 0.4828 649.686885 4 0.0033 123 | 0/8 6 h-lim-p 0.0248 4.9551 0.0637 649.686877 3 0.0033 151 | 0/8 7 h-lim-p 0.0653 20.0000 0.0032 649.686780 0 0.3916 173 | 0/8 8 h-lim-p 0.0167 2.2142 0.0761 649.686596 0 0.0250 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 649.686588 1 0.9961 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 649.686588 0 1.0938 235 | 0/8 11 h-lim-p 1.9099 20.0000 0.0000 649.686588 0 1.6712 255 | 0/8 12 h-lim-p 1.1229 20.0000 0.0000 649.686588 0 2.2459 276 | 0/8 13 h-lim-p 0.0259 20.0000 0.0005 649.686588 0 0.0130 296 | 0/8 14 h-lim-p 0.0040 20.0000 0.0018 649.686588 0 0.0000 325 | 0/8 15 h-lim-p 0.0001 20.0000 0.0001 649.686588 0 0.0000 349 | 0/8 16 h-lim-p 0.0002 20.0000 0.0000 649.686588 0 0.0001 369 Out... lnL = -649.686588 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -649.686588 Node 7: lnL = -649.686588 Node 8: lnL = -649.686588 Node 9: lnL = -649.686588 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 410 Sequential format.. Reading seq # 1: YOR284W_Sbay Reading seq # 2: YOR284W_Scer Reading seq # 3: YOR284W_Skud Reading seq # 4: YOR284W_Smik Reading seq # 5: YOR284W_Spar Sequences read.. Counting patterns.. # site patterns = 185 Counting frequencies.. 120 bytes for distance 29600 bytes for lkl0 23680 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.196777 0.126714 0.155176 0.089930 0.232870 0.292987 0.233726 lnL0 = -1640.285304 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1640.285304 x= 0.00006 0.19678 0.12671 0.15518 0.08993 0.23287 0.29299 0.23373 1 h-lim-p 0.0000 0.0000 183.2140 1640.169107 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0019 111.1517 1633.269064 3 0.0013 47 | 1/8 3 h-lim-p 0.0019 0.0149 15.4777 1633.056662 2 0.0017 63 | 1/8 4 h-lim-p 0.0041 0.0330 4.1965 1632.981099 5 0.0036 84 | 1/8 5 h-lim-p 0.0120 0.3123 1.2666 1631.047669 0 0.0964 99 | 1/8 6 h-lim-p 0.0017 0.0134 13.9546 1626.241395 0 0.0067 113 | 1/8 7 h-lim-p 0.0011 0.0089 39.6964 1625.690888 7 0.0008 142 | 1/8 8 h-lim-p 0.0049 0.0477 6.5114 1625.655653 7 0.0015 172 | 1/8 9 h-lim-p 0.0897 2.8370 0.1103 1624.594662 0 0.3588 186 | 1/8 10 h-lim-p 0.7482 8.2849 0.0529 1624.373715 8 0.4096 223 | 1/8 11 h-lim-p 2.5000 20.0000 0.0074 1624.350067 6 0.8900 255 | 1/8 12 h-lim-p 2.3667 20.0000 0.0028 1624.348882 3 0.5842 281 | 0/8 13 h-lim-p 0.0500 10.3224 0.0327 1624.348881 0 0.0027 303 | 0/8 14 h-lim-p 0.1633 1.6760 0.0005 1624.348821 0 0.9796 325 | 0/8 15 h-lim-p 0.0478 0.3827 0.0002 1624.348820 m 0.3827 345 | 1/8 16 h-lim-p 0.3748 20.0000 0.0001 1624.348819 0 0.3748 365 | 1/8 17 h-lim-p 0.9932 20.0000 0.0001 1624.348818 0 0.8691 384 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 1624.348818 0 1.0938 403 | 1/8 19 h-lim-p 2.5000 20.0000 0.0000 1624.348818 0 1.0938 422 | 1/8 20 h-lim-p 2.5000 20.0000 0.0000 1624.348818 0 0.6250 442 | 1/8 21 h-lim-p 1.6986 20.0000 0.0000 1624.348818 0 0.0000 483 Out... lnL = -1624.348818 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1624.348818 Node 7: lnL = -1624.348818 Node 8: lnL = -1624.348818 Node 9: lnL = -1624.348818 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 533 Sequential format.. Reading seq # 1: YOR285W_Sbay Reading seq # 2: YOR285W_Scer Reading seq # 3: YOR285W_Skud Reading seq # 4: YOR285W_Smik Reading seq # 5: YOR285W_Spar Sequences read.. Counting patterns.. # site patterns = 232 Counting frequencies.. 120 bytes for distance 37120 bytes for lkl0 29696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.031094 0.052588 0.068460 0.195154 0.140085 0.330155 0.344109 0.372419 lnL0 = -2525.859562 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2525.859562 x= 0.03109 0.05259 0.06846 0.19515 0.14009 0.33016 0.34411 0.37242 1 h-lim-p 0.0026 0.0205 95.5101 2524.000314 8 0.0004 42 | 0/8 2 h-lim-p 0.0013 0.0105 14.5126 2523.922976 6 0.0007 68 | 0/8 3 h-lim-p 0.0019 0.0303 5.6933 2523.909658 6 0.0009 92 | 0/8 4 h-lim-p 0.0038 0.0933 1.4049 2523.908113 2 0.0017 108 | 0/8 5 h-lim-p 0.0061 0.9251 0.3870 2523.908024 2 0.0013 125 | 0/8 6 h-lim-p 0.0063 1.9092 0.0808 2523.908020 1 0.0013 148 | 0/8 7 h-lim-p 0.1261 20.0000 0.0008 2523.908019 0 0.1104 168 | 0/8 8 h-lim-p 0.0151 20.0000 0.0059 2523.908001 0 0.0303 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2523.908001 0 1.0938 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2523.908001 0 1.0938 229 | 0/8 11 h-lim-p 1.0701 20.0000 0.0000 2523.908001 0 0.9363 249 | 0/8 12 h-lim-p 0.1482 20.0000 0.0001 2523.908001 0 0.0000 292 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 2523.908001 0 0.0000 313 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 2523.908001 0 0.0000 342 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -2523.908001 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2523.908001 Node 7: lnL = -2523.908001 Node 8: lnL = -2523.908001 Node 9: lnL = -2523.908001 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 267 Sequential format.. Reading seq # 1: YOR286W_Sbay Reading seq # 2: YOR286W_Scer Reading seq # 3: YOR286W_Skud Reading seq # 4: YOR286W_Smik Reading seq # 5: YOR286W_Spar Sequences read.. Counting patterns.. # site patterns = 122 Counting frequencies.. 120 bytes for distance 19520 bytes for lkl0 15616 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.039578 0.088562 0.029251 0.061501 0.066468 0.154847 0.120061 0.218989 lnL0 = -1034.691271 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1034.691271 x= 0.03958 0.08856 0.02925 0.06150 0.06647 0.15485 0.12006 0.21899 1 h-lim-p 0.0093 3.7769 47.1840 1034.290476 7 0.0004 39 | 0/8 2 h-lim-p 0.0006 0.0047 18.5114 1034.200408 3 0.0006 57 | 0/8 3 h-lim-p 0.0017 0.0206 6.4174 1034.189380 6 0.0006 82 | 0/8 4 h-lim-p 0.0019 0.0847 2.0149 1034.188271 5 0.0006 108 | 0/8 5 h-lim-p 0.0021 0.2242 0.5870 1034.188200 2 0.0005 125 | 0/8 6 h-lim-p 0.0034 1.1760 0.0788 1034.188197 2 0.0011 151 | 0/8 7 h-lim-p 0.0273 20.0000 0.0032 1034.188197 0 0.0030 173 | 0/8 8 h-lim-p 0.0381 20.0000 0.0003 1034.188187 0 0.3045 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1034.188187 0 1.0938 216 | 0/8 10 h-lim-p 1.9213 20.0000 0.0000 1034.188187 0 0.4203 237 | 0/8 11 h-lim-p 0.2367 20.0000 0.0000 1034.188187 0 0.0148 260 | 0/8 12 h-lim-p 0.0082 20.0000 0.0000 1034.188187 0 0.0000 301 | 0/8 13 h-lim-p 0.0000 20.0000 0.0015 | 0/8 14 h-lim-p 0.0000 20.0000 0.0015 Out... lnL = -1034.188187 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1034.188187 Node 7: lnL = -1034.188187 Node 8: lnL = -1034.188187 Node 9: lnL = -1034.188187 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 283 Sequential format.. Reading seq # 1: YOR288C_Sbay Reading seq # 2: YOR288C_Scer Reading seq # 3: YOR288C_Skud Reading seq # 4: YOR288C_Smik Reading seq # 5: YOR288C_Spar Sequences read.. Counting patterns.. # site patterns = 109 Counting frequencies.. 120 bytes for distance 17440 bytes for lkl0 13952 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.801004 0.854653 0.805321 0.780647 2.127949 0.978756 0.802696 lnL0 = -1375.254058 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1375.254058 x= 0.00006 0.80100 0.85465 0.80532 0.78065 2.12795 0.97876 0.80270 1 h-lim-p 0.0000 0.0000 117.7126 1375.214601 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0827 16.6620 1362.143095 0 0.0595 45 | 1/8 3 h-lim-p 0.0809 0.6472 4.7268 1316.141363 m 0.6472 57 | 2/8 4 h-lim-p 0.2473 1.9781 2.7860 .. | 2/8 5 h-lim-p 0.0000 0.0059 130.4501 1243.309193 5 0.0046 126 | 2/8 6 h-lim-p 0.0835 0.6683 0.9139 1243.307056 4 0.0051 151 | 2/8 7 h-lim-p 0.0331 20.0000 0.1410 1229.404712 m20.0000 176 | 2/8 8 h-lim-p 0.3979 3.1832 2.8353 .. | 2/8 9 h-lim-p 0.0000 0.0063 29.6115 1228.520528 0 0.0026 242 | 2/8 10 h-lim-p 0.0008 0.0086 98.1009 1188.381842 m 0.0086 255 | 2/8 11 h-lim-p -0.0000 -0.0000 24.0752 h-lim-p: -1.15496671e-20 -9.23973364e-20 2.40752477e+01 1188.381842 .. | 2/8 12 h-lim-p 0.0000 0.0105 207.3090 1180.812428 0 0.0005 280 | 2/8 13 h-lim-p 0.0010 0.0078 100.0815 1136.856762 0 0.0059 294 | 1/8 14 h-lim-p 0.0000 0.0004 553.5025 1130.647930 0 0.0003 308 | 1/8 15 h-lim-p 0.0011 0.0091 20.5778 1129.535660 0 0.0046 322 | 1/8 16 h-lim-p 0.0033 0.0261 4.9792 1129.275473 0 0.0065 335 | 1/8 17 h-lim-p 0.0138 0.1100 2.2688 1117.669207 m 0.1100 347 | 0/8 18 h-lim-p 0.0000 0.0000 31.5606 h-lim-p: 8.07645708e-20 6.46116566e-19 3.15606157e+01 1117.669207 .. | 0/8 19 h-lim-p 0.0000 0.0044 175.1257 1113.013119 0 0.0003 372 | 0/8 20 h-lim-p 0.0005 0.0043 46.4449 1111.890757 0 0.0011 385 | 0/8 21 h-lim-p 0.0014 0.0114 16.2056 1111.799032 8 0.0008 417 | 0/8 22 h-lim-p 0.0074 0.1610 1.7673 1111.796846 4 0.0014 438 | 0/8 23 h-lim-p 0.0376 5.6965 0.0656 1111.795630 2 0.0329 454 | 0/8 24 h-lim-p 0.0248 8.9557 0.0869 1111.742301 0 0.0992 476 | 0/8 25 h-lim-p 2.5000 20.0000 0.0013 1111.741669 4 0.8779 506 | 0/8 26 h-lim-p 2.5000 20.0000 0.0000 1111.741668 0 1.0938 526 | 0/8 27 h-lim-p 2.5000 20.0000 0.0000 1111.741668 0 1.0938 546 | 0/8 28 h-lim-p 0.6977 20.0000 0.0000 1111.741668 0 0.0218 570 | 0/8 29 h-lim-p 0.0014 20.0000 0.0002 .. | 0/8 30 h-lim-p 0.0000 20.0000 0.0001 1111.741668 0 0.0000 630 | 0/8 31 h-lim-p 0.0000 20.0000 0.0000 1111.741668 0 0.0000 660 | 0/8 32 h-lim-p 0.0000 20.0000 0.0001 1111.741668 0 0.0000 690 | 0/8 33 h-lim-p 0.0000 20.0000 0.0001 | 0/8 34 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1111.741668 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1111.741668 Node 7: lnL = -1111.741668 Node 8: lnL = -1111.741668 Node 9: lnL = -1111.741668 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 341 Sequential format.. Reading seq # 1: YOR289W_Sbay Reading seq # 2: YOR289W_Scer Reading seq # 3: YOR289W_Skud Reading seq # 4: YOR289W_Smik Reading seq # 5: YOR289W_Spar Sequences read.. Counting patterns.. # site patterns = 133 Counting frequencies.. 120 bytes for distance 21280 bytes for lkl0 17024 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.821127 0.869356 0.823722 0.798339 2.062047 1.006377 0.802696 lnL0 = -1555.621960 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1555.621960 x= 0.00006 0.82113 0.86936 0.82372 0.79834 2.06205 1.00638 0.80270 1 h-lim-p 0.0000 0.0000 119.3874 1555.585732 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.1062 15.6686 1535.755273 8 0.0678 61 | 1/8 3 h-lim-p 0.0033 0.0261 34.0325 1535.424863 2 0.0031 77 | 1/8 4 h-lim-p 0.1713 10.3049 0.6066 .. | 1/8 5 h-lim-p 0.0000 0.0168 76.7601 1411.117580 0 0.0135 145 | 1/8 6 h-lim-p 0.0000 0.0003 1052.8898 1407.597328 0 0.0001 158 | 1/8 7 h-lim-p 0.0137 0.1566 7.2765 1407.493236 5 0.0141 179 | 0/8 8 h-lim-p 0.0001 0.0011 918.0917 1385.834279 m 0.0011 192 | 0/8 9 h-lim-p 0.0000 0.0000 1379.9774 h-lim-p: 1.11204264e-20 8.89634114e-20 1.37997739e+03 1385.834279 .. | 0/8 10 h-lim-p 0.0000 0.0024 762.1732 1331.572542 0 0.0003 217 | 0/8 11 h-lim-p 0.0003 0.0024 156.5736 1310.509771 0 0.0012 231 | 0/8 12 h-lim-p 0.0002 0.0013 370.8387 1274.272163 0 0.0010 245 | 0/8 13 h-lim-p 0.0001 0.0012 142.0442 1271.035471 0 0.0006 259 | 0/8 14 h-lim-p 0.0006 0.0052 43.6250 1270.305677 0 0.0013 272 | 0/8 15 h-lim-p 0.5085 13.8745 0.1106 1263.295781 0 0.7628 284 | 0/8 16 h-lim-p 1.8291 14.6325 0.0190 1263.262044 3 0.4144 311 | 0/8 17 h-lim-p 1.0522 20.0000 0.0075 1263.217024 0 1.5783 331 | 0/8 18 h-lim-p 2.5000 20.0000 0.0018 1263.213496 5 1.4668 364 | 0/8 19 h-lim-p 2.5000 20.0000 0.0010 1263.211714 3 2.4683 390 | 0/8 20 h-lim-p 2.5000 20.0000 0.0003 1263.211533 3 2.0898 416 | 0/8 21 h-lim-p 2.5000 20.0000 0.0001 1263.211527 1 0.9961 438 | 0/8 22 h-lim-p 2.5000 20.0000 0.0000 1263.211527 0 1.0938 458 | 0/8 23 h-lim-p 1.1437 20.0000 0.0000 1263.211527 0 4.5748 480 | 0/8 24 h-lim-p 0.3850 20.0000 0.0001 1263.211527 0 0.0008 508 | 0/8 25 h-lim-p 0.0003 20.0000 0.0002 1263.211527 0 0.0000 532 | 0/8 26 h-lim-p 0.0004 20.0000 0.0000 1263.211527 0 0.0000 566 Out... lnL = -1263.211527 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1263.211527 Node 7: lnL = -1263.211527 Node 8: lnL = -1263.211527 Node 9: lnL = -1263.211527 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 860 Sequential format.. Reading seq # 1: YOR291W_Sbay Reading seq # 2: YOR291W_Scer Reading seq # 3: YOR291W_Skud Reading seq # 4: YOR291W_Smik Reading seq # 5: YOR291W_Spar Sequences read.. Counting patterns.. # site patterns = 334 Counting frequencies.. 120 bytes for distance 53440 bytes for lkl0 42752 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.239053 0.221511 0.220760 0.213642 0.182112 0.325952 0.298470 lnL0 = -4154.773702 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4154.773702 x= 0.00006 0.23905 0.22151 0.22076 0.21364 0.18211 0.32595 0.29847 1 h-lim-p 0.0000 0.0000 370.1628 4154.589173 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0100 93.7569 4151.010517 0 0.0010 40 | 1/8 3 h-lim-p 0.0012 0.0094 37.9365 4150.322702 5 0.0010 61 | 1/8 4 h-lim-p 0.0047 0.0947 8.0603 4150.146751 6 0.0023 85 | 1/8 5 h-lim-p 0.0075 0.2211 2.5038 4145.880572 0 0.0453 99 | 1/8 6 h-lim-p 0.0019 0.0151 21.6962 4124.747119 0 0.0075 113 | 1/8 7 h-lim-p 0.0003 0.0023 89.4345 4123.056904 0 0.0006 126 | 1/8 8 h-lim-p 0.0018 0.0145 17.5523 4122.926096 2 0.0008 142 | 1/8 9 h-lim-p 0.1710 6.1222 0.0871 4120.614999 0 0.5130 155 | 0/8 10 h-lim-p 0.0034 0.1725 13.1525 4120.550838 2 0.0008 179 | 0/8 11 h-lim-p 0.2896 12.5615 0.0362 4120.326473 0 0.5791 192 | 0/8 12 h-lim-p 2.3881 19.1045 0.0048 4120.299499 2 1.1194 216 | 0/8 13 h-lim-p 2.5000 20.0000 0.0004 4120.299387 3 0.8855 244 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 4120.299383 1 0.9961 266 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 4120.299383 0 1.0938 286 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 4120.299383 0 1.0938 306 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 4120.299383 0 0.6250 327 | 0/8 18 h-lim-p 1.7995 20.0000 0.0000 4120.299383 0 0.2249 349 | 0/8 19 h-lim-p 0.2504 20.0000 0.0000 4120.299383 0 0.0156 372 Out... lnL = -4120.299383 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4120.299383 Node 7: lnL = -4120.299383 Node 8: lnL = -4120.299383 Node 9: lnL = -4120.299383 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 555 Sequential format.. Reading seq # 1: YOR292C_Sbay Reading seq # 2: YOR292C_Scer Reading seq # 3: YOR292C_Skud Reading seq # 4: YOR292C_Smik Reading seq # 5: YOR292C_Spar Sequences read.. Counting patterns.. # site patterns = 226 Counting frequencies.. 120 bytes for distance 36160 bytes for lkl0 28928 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.015910 0.083393 0.053599 0.167944 0.081051 0.319148 0.211403 0.281923 lnL0 = -2408.520855 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2408.520855 x= 0.01591 0.08339 0.05360 0.16794 0.08105 0.31915 0.21140 0.28192 1 h-lim-p 0.0038 0.0814 112.4601 2406.916702 9 0.0003 46 | 0/8 2 h-lim-p 0.0006 0.0045 28.7284 2406.647281 1 0.0007 60 | 0/8 3 h-lim-p 0.0006 0.0044 26.8780 2406.514943 6 0.0006 86 | 0/8 4 h-lim-p 0.0015 0.0160 10.8131 2406.481964 4 0.0007 108 | 0/8 5 h-lim-p 0.0027 0.0216 2.3478 2406.478974 4 0.0012 127 | 0/8 6 h-lim-p 0.0016 0.2304 1.6696 2406.478095 4 0.0009 148 | 0/8 7 h-lim-p 0.0073 1.2296 0.2025 2406.478070 3 0.0010 168 | 0/8 8 h-lim-p 0.0971 20.0000 0.0020 2406.472396 0 0.7767 191 | 0/8 9 h-lim-p 2.2025 20.0000 0.0007 2406.471996 2 1.0324 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2406.471995 0 1.0938 235 | 0/8 11 h-lim-p 2.0239 20.0000 0.0000 2406.471995 0 0.8854 255 | 0/8 12 h-lim-p 0.6145 20.0000 0.0000 2406.471995 0 0.1536 276 | 0/8 13 h-lim-p 0.0251 20.0000 0.0002 2406.471995 0 0.0251 296 | 0/8 14 h-lim-p 0.0096 20.0000 0.0005 2406.471995 0 0.0000 327 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 2406.471995 0 0.0000 359 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 2406.471995 0 0.0000 380 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 | 0/8 19 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -2406.471995 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2406.471995 Node 7: lnL = -2406.471995 Node 8: lnL = -2406.471995 Node 9: lnL = -2406.471995 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 773 Sequential format.. Reading seq # 1: YOR294W_Sbay Reading seq # 2: YOR294W_Scer Reading seq # 3: YOR294W_Skud Reading seq # 4: YOR294W_Smik Reading seq # 5: YOR294W_Spar Sequences read.. Counting patterns.. # site patterns = 210 Counting frequencies.. 120 bytes for distance 33600 bytes for lkl0 26880 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.009448 0.110456 0.045151 0.129522 0.068457 0.143275 0.102228 0.191469 lnL0 = -2470.561454 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2470.561454 x= 0.00945 0.11046 0.04515 0.12952 0.06846 0.14328 0.10223 0.19147 1 h-lim-p 0.0021 0.0192 151.7232 2468.044647 6 0.0002 35 | 0/8 2 h-lim-p 0.0006 0.0047 34.2655 2467.786360 4 0.0005 55 | 0/8 3 h-lim-p 0.0003 0.0025 18.0240 2467.745736 4 0.0003 75 | 0/8 4 h-lim-p 0.0009 0.0073 3.2464 2467.743912 3 0.0004 93 | 0/8 5 h-lim-p 0.0029 0.8343 0.4111 2467.743876 3 0.0004 115 | 0/8 6 h-lim-p 0.0026 2.1596 0.0667 2467.743875 1 0.0006 138 | 0/8 7 h-lim-p 0.0059 16.4435 0.0072 2467.743875 0 0.0026 158 | 0/8 8 h-lim-p 0.0290 20.0000 0.0006 2467.743819 0 0.4645 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2467.743816 0 1.0938 202 | 0/8 10 h-lim-p 2.3241 20.0000 0.0000 2467.743816 0 1.0168 222 | 0/8 11 h-lim-p 0.9098 20.0000 0.0000 2467.743816 0 0.0071 248 | 0/8 12 h-lim-p 0.0001 10.9486 0.0015 2467.743816 0 0.0000 269 | 0/8 13 h-lim-p 0.0002 20.0000 0.0003 2467.743816 0 0.0000 295 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 2467.743816 0 0.0000 316 Out... lnL = -2467.743816 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2467.743816 Node 7: lnL = -2467.743816 Node 8: lnL = -2467.743816 Node 9: lnL = -2467.743816 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 331 Sequential format.. Reading seq # 1: YOR297C_Sbay Reading seq # 2: YOR297C_Scer Reading seq # 3: YOR297C_Skud Reading seq # 4: YOR297C_Smik Reading seq # 5: YOR297C_Spar Sequences read.. Counting patterns.. # site patterns = 170 Counting frequencies.. 120 bytes for distance 27200 bytes for lkl0 21760 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.030180 0.039236 0.086253 0.159185 0.119442 0.210874 0.161478 0.265512 lnL0 = -1430.526324 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1430.526324 x= 0.03018 0.03924 0.08625 0.15919 0.11944 0.21087 0.16148 0.26551 1 h-lim-p 0.0061 2.1637 68.6231 1429.475773 7 0.0005 40 | 0/8 2 h-lim-p 0.0022 0.0175 9.3788 1429.424223 6 0.0012 65 | 0/8 3 h-lim-p 0.0045 0.1335 2.4921 1429.421445 4 0.0010 85 | 0/8 4 h-lim-p 0.0031 0.3445 0.7683 1429.421223 3 0.0008 104 | 0/8 5 h-lim-p 0.0063 0.8824 0.1021 1429.421217 2 0.0010 131 | 0/8 6 h-lim-p 0.0066 9.6722 0.0160 1429.421217 0 0.0029 151 | 0/8 7 h-lim-p 0.0229 20.0000 0.0020 1429.421213 0 0.0459 172 | 0/8 8 h-lim-p 0.0054 20.0000 0.0170 1429.421141 0 0.0217 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1429.421138 1 0.9961 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1429.421138 0 2.1875 236 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1429.421138 0 1.0938 256 | 0/8 12 h-lim-p 0.1942 20.0000 0.0000 1429.421138 0 0.0121 279 | 0/8 13 h-lim-p 0.0023 20.0000 0.0002 1429.421138 0 0.0020 299 | 0/8 14 h-lim-p 0.0007 20.0000 0.0008 1429.421138 0 0.0000 333 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 1429.421138 0 0.0000 355 Out... lnL = -1429.421138 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1429.421138 Node 7: lnL = -1429.421138 Node 8: lnL = -1429.421138 Node 9: lnL = -1429.421138 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 361 Sequential format.. Reading seq # 1: YOR298W_Sbay Reading seq # 2: YOR298W_Scer Reading seq # 3: YOR298W_Skud Reading seq # 4: YOR298W_Smik Reading seq # 5: YOR298W_Spar Sequences read.. Counting patterns.. # site patterns = 150 Counting frequencies.. 120 bytes for distance 24000 bytes for lkl0 19200 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.030832 0.026229 0.071212 0.159735 0.129512 0.208026 0.209103 0.269991 lnL0 = -1519.653446 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1519.653446 x= 0.03083 0.02623 0.07121 0.15973 0.12951 0.20803 0.20910 0.26999 1 h-lim-p 0.0046 1.7252 80.8716 1518.472814 9 0.0004 48 | 0/8 2 h-lim-p 0.0023 0.0185 9.5545 1518.428962 5 0.0010 71 | 0/8 3 h-lim-p 0.0052 0.1383 1.7664 1518.427454 4 0.0010 92 | 0/8 4 h-lim-p 0.0047 0.6514 0.3773 1518.427399 3 0.0008 112 | 0/8 5 h-lim-p 0.0040 1.3151 0.0768 1518.427396 0 0.0009 133 | 0/8 6 h-lim-p 0.0148 20.0000 0.0046 1518.427395 1 0.0073 156 | 0/8 7 h-lim-p 0.0061 20.0000 0.0054 1518.427386 0 0.0246 178 | 0/8 8 h-lim-p 0.0041 9.0240 0.0321 1518.427323 0 0.0083 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1518.427323 0 1.0938 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1518.427323 0 1.0938 239 | 0/8 11 h-lim-p 1.1238 20.0000 0.0000 1518.427323 0 0.0351 263 | 0/8 12 h-lim-p 0.0056 20.0000 0.0001 1518.427323 0 0.0000 300 | 0/8 13 h-lim-p 0.0000 20.0000 0.0003 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -1518.427323 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1518.427323 Node 7: lnL = -1518.427323 Node 8: lnL = -1518.427323 Node 9: lnL = -1518.427323 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 109 Sequential format.. Reading seq # 1: YOR301W_Sbay Reading seq # 2: YOR301W_Scer Reading seq # 3: YOR301W_Skud Reading seq # 4: YOR301W_Smik Reading seq # 5: YOR301W_Spar Sequences read.. Counting patterns.. # site patterns = 63 Counting frequencies.. 120 bytes for distance 10080 bytes for lkl0 8064 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.474040 0.246803 0.207887 0.684741 0.308401 2.461519 0.777595 lnL0 = -451.818432 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 451.818432 x= 0.00006 0.47404 0.24680 0.20789 0.68474 0.30840 2.46152 0.77759 1 h-lim-p 0.0000 0.0000 71.6945 451.787125 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0017 474.1702 416.520618 1 0.0014 43 | 1/8 3 h-lim-p 0.0005 0.0038 46.3959 415.260517 0 0.0014 56 | 1/8 4 h-lim-p 0.0020 0.0157 18.3335 414.066893 0 0.0079 70 | 1/8 5 h-lim-p 0.0028 0.0228 11.5906 413.616203 0 0.0057 83 | 1/8 6 h-lim-p 0.0120 0.0964 2.1222 410.242639 0 0.0723 97 | 0/8 7 h-lim-p 0.0018 0.0142 8.9820 409.719247 m 0.0142 109 | 1/8 8 h-lim-p 0.3688 20.0000 0.3366 407.979060 8 0.2349 139 | 1/8 9 h-lim-p 0.0118 0.0945 3.7942 407.395408 0 0.0709 160 | 1/8 10 h-lim-p 0.3741 2.9927 0.0584 407.091712 0 1.4963 174 | 1/8 11 h-lim-p 0.4412 3.5296 0.0179 407.067225 0 0.8824 194 | 1/8 12 h-lim-p 0.4222 3.3774 0.0109 407.065611 0 1.2665 214 | 0/8 13 h-lim-p 0.0493 0.3945 0.0906 407.065589 3 0.0087 241 | 0/8 14 h-lim-p 0.6488 20.0000 0.0012 407.065486 0 1.2975 262 | 0/8 15 h-lim-p 1.7783 20.0000 0.0009 407.065475 2 1.3719 286 | 0/8 16 h-lim-p 2.5000 20.0000 0.0001 407.065474 1 1.2305 309 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 407.065474 0 1.0938 329 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 407.065474 0 0.6250 350 | 0/8 19 h-lim-p 1.1190 20.0000 0.0000 407.065474 0 0.0000 398 Out... lnL = -407.065474 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -407.065474 Node 7: lnL = -407.065474 Node 8: lnL = -407.065474 Node 9: lnL = -407.065474 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 719 Sequential format.. Reading seq # 1: YOR310C_Sbay Reading seq # 2: YOR310C_Scer Reading seq # 3: YOR310C_Skud Reading seq # 4: YOR310C_Smik Reading seq # 5: YOR310C_Spar Sequences read.. Counting patterns.. # site patterns = 236 Counting frequencies.. 120 bytes for distance 37760 bytes for lkl0 30208 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.146034 0.000060 0.431582 0.113529 0.415109 0.378970 0.199846 0.597776 lnL0 = -2826.451486 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2826.451486 x= 0.14603 0.00006 0.43158 0.11353 0.41511 0.37897 0.19985 0.59778 1 h-lim-p 0.0000 0.0000 284.0356 2826.356767 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0025 197.3481 2788.377299 0 0.0019 41 | 1/8 3 h-lim-p 0.0007 0.0055 56.8897 2785.751513 0 0.0014 54 | 1/8 4 h-lim-p 0.0011 0.0091 56.9988 2783.720703 0 0.0023 67 | 1/8 5 h-lim-p 0.0028 0.0227 18.9348 2783.246534 6 0.0030 91 | 1/8 6 h-lim-p 0.0485 0.3880 1.0984 2781.569333 0 0.0970 104 | 1/8 7 h-lim-p 0.0042 0.0336 9.7203 2769.024346 0 0.0168 118 | 1/8 8 h-lim-p 0.3756 3.0045 0.1144 2767.923067 4 0.3741 138 | 1/8 9 h-lim-p 0.8544 10.9693 0.0501 2767.561690 2 0.8010 161 | 1/8 10 h-lim-p 2.5000 20.0000 0.0113 2767.531498 6 0.7156 197 | 1/8 11 h-lim-p 2.5000 20.0000 0.0022 2767.530945 3 0.8800 223 | 1/8 12 h-lim-p 2.5000 20.0000 0.0007 2767.530900 2 0.9644 246 | 1/8 13 h-lim-p 2.5000 20.0000 0.0001 2767.530899 0 1.0938 265 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 2767.530899 0 1.0938 284 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 2767.530899 0 1.0938 303 | 1/8 16 h-lim-p 1.0917 20.0000 0.0000 2767.530899 0 4.3669 324 | 1/8 17 h-lim-p 1.2704 20.0000 0.0000 2767.530899 0 1.2704 343 | 1/8 18 h-lim-p 0.0058 20.0000 0.0021 2767.530899 0 0.0004 365 | 1/8 19 h-lim-p 0.0013 20.0000 0.0006 2767.530899 0 0.0000 403 | 1/8 20 h-lim-p 0.0000 20.0000 0.0001 | 1/8 21 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -2767.530899 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2767.530899 Node 7: lnL = -2767.530899 Node 8: lnL = -2767.530899 Node 9: lnL = -2767.530899 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 344 Sequential format.. Reading seq # 1: YOR311C_Sbay Reading seq # 2: YOR311C_Scer Reading seq # 3: YOR311C_Skud Reading seq # 4: YOR311C_Smik Reading seq # 5: YOR311C_Spar Sequences read.. Counting patterns.. # site patterns = 121 Counting frequencies.. 120 bytes for distance 19360 bytes for lkl0 15488 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.024195 0.046096 0.066198 0.111167 0.053444 0.113582 0.118850 0.184787 lnL0 = -1361.789364 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1361.789364 x= 0.02419 0.04610 0.06620 0.11117 0.05344 0.11358 0.11885 0.18479 1 h-lim-p 0.0002 0.0019 83.1397 1360.780496 0 0.0004 22 | 0/8 2 h-lim-p 0.0014 0.0114 13.5116 1360.737952 7 0.0005 52 | 0/8 3 h-lim-p 0.0009 0.0093 7.1675 1360.732169 6 0.0003 82 | 0/8 4 h-lim-p 0.0017 0.1619 1.1480 1360.731797 3 0.0006 102 | 0/8 5 h-lim-p 0.0027 0.6294 0.2388 1360.731753 3 0.0009 121 | 0/8 6 h-lim-p 0.0022 0.8198 0.0994 1360.731553 0 0.0043 142 | 0/8 7 h-lim-p 0.0075 1.5159 0.0575 1360.710385 0 0.0597 165 | 0/8 8 h-lim-p 0.0024 0.0470 1.4436 1360.709703 4 0.0006 194 | 0/8 9 h-lim-p 1.4881 20.0000 0.0006 1360.709275 4 0.9795 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1360.709275 0 1.0938 235 | 0/8 11 h-lim-p 1.9350 20.0000 0.0000 1360.709275 0 1.6931 255 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1360.709275 0 0.5469 276 | 0/8 13 h-lim-p 0.1917 20.0000 0.0000 1360.709275 0 0.0002 305 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 1360.709275 0 0.0000 325 | 0/8 15 h-lim-p 0.0001 20.0000 0.0001 1360.709275 0 0.0001 345 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 1360.709275 0 0.0000 367 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 1360.709275 0 0.0000 400 | 0/8 18 h-lim-p 0.0000 20.0000 0.0012 | 0/8 19 h-lim-p 0.0000 20.0000 0.0012 Out... lnL = -1360.709275 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1360.709275 Node 7: lnL = -1360.709275 Node 8: lnL = -1360.709275 Node 9: lnL = -1360.709275 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 242 Sequential format.. Reading seq # 1: YOR313C_Sbay Reading seq # 2: YOR313C_Scer Reading seq # 3: YOR313C_Skud Reading seq # 4: YOR313C_Smik Reading seq # 5: YOR313C_Spar Sequences read.. Counting patterns.. # site patterns = 69 Counting frequencies.. 120 bytes for distance 11040 bytes for lkl0 8832 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.006698 0.019066 0.021823 0.079917 0.043471 0.178272 0.187629 0.154247 lnL0 = -772.776198 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 772.776198 x= 0.00670 0.01907 0.02182 0.07992 0.04347 0.17827 0.18763 0.15425 1 h-lim-p 0.0009 0.0071 89.4580 771.870119 9 0.0003 45 | 0/8 2 h-lim-p 0.0002 0.0012 18.1015 771.809877 0 0.0003 58 | 0/8 3 h-lim-p 0.0002 0.0014 7.0648 771.799531 0 0.0007 72 | 0/8 4 h-lim-p 0.0019 0.0150 1.3812 771.798532 5 0.0011 96 | 0/8 5 h-lim-p 0.0021 0.2223 0.7406 771.798379 4 0.0007 117 | 0/8 6 h-lim-p 0.0019 0.5616 0.2597 771.798360 3 0.0006 146 | 0/8 7 h-lim-p 0.0042 3.3281 0.0347 771.798296 0 0.0169 168 | 0/8 8 h-lim-p 0.0358 1.7138 0.0164 771.794570 0 0.1075 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 771.794478 3 1.0449 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 771.794475 2 1.6492 241 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 771.794475 0 1.0938 261 | 0/8 12 h-lim-p 1.1075 20.0000 0.0000 771.794475 0 2.2150 282 | 0/8 13 h-lim-p 2.0732 20.0000 0.0000 771.794475 0 0.9070 302 | 0/8 14 h-lim-p 0.1211 20.0000 0.0001 771.794475 0 0.0019 327 | 0/8 15 h-lim-p 0.0005 7.4605 0.0005 771.794475 0 0.0001 349 | 0/8 16 h-lim-p 0.0000 5.0902 0.0008 771.794475 0 0.0000 369 | 0/8 17 h-lim-p 0.0000 20.0000 0.0005 771.794475 0 0.0000 396 | 0/8 18 h-lim-p 0.0001 20.0000 0.0000 771.794475 0 0.0000 422 Out... lnL = -771.794475 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -771.794475 Node 7: lnL = -771.794475 Node 8: lnL = -771.794475 Node 9: lnL = -771.794475 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 201 Sequential format.. Reading seq # 1: YOR315W_Sbay Reading seq # 2: YOR315W_Scer Reading seq # 3: YOR315W_Skud Reading seq # 4: YOR315W_Smik Reading seq # 5: YOR315W_Spar Sequences read.. Counting patterns.. # site patterns = 74 Counting frequencies.. 120 bytes for distance 11840 bytes for lkl0 9472 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.019702 0.041760 0.026684 0.122239 0.029735 0.117582 0.106160 0.155158 lnL0 = -746.662531 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 746.662531 x= 0.01970 0.04176 0.02668 0.12224 0.02973 0.11758 0.10616 0.15516 1 h-lim-p 0.0001 0.0007 107.4755 745.278616 0 0.0004 24 | 0/8 2 h-lim-p 0.0001 0.0009 25.7448 745.170925 0 0.0004 37 | 0/8 3 h-lim-p 0.0003 0.0075 30.1283 745.079756 1 0.0004 51 | 0/8 4 h-lim-p 0.0047 0.0377 1.6519 745.078866 4 0.0006 73 | 0/8 5 h-lim-p 0.0049 0.9135 0.2140 745.078698 2 0.0023 89 | 0/8 6 h-lim-p 0.0091 4.0584 0.0539 745.066059 0 0.0728 112 | 0/8 7 h-lim-p 0.0021 0.0372 1.8716 745.007568 0 0.0042 133 | 0/8 8 h-lim-p 0.0029 0.0796 2.6604 745.004693 4 0.0008 154 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 745.004571 3 0.9482 172 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 745.004569 0 1.0938 192 | 0/8 11 h-lim-p 1.8467 20.0000 0.0000 745.004569 0 0.8079 212 | 0/8 12 h-lim-p 0.7193 20.0000 0.0000 745.004569 0 0.0003 242 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 745.004569 0 0.0000 270 | 0/8 14 h-lim-p 0.0000 20.0000 0.0007 | 0/8 15 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -745.004569 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -745.004569 Node 7: lnL = -745.004569 Node 8: lnL = -745.004569 Node 9: lnL = -745.004569 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 870 Sequential format.. Reading seq # 1: YOR316C_Sbay Reading seq # 2: YOR316C_Scer Reading seq # 3: YOR316C_Skud Reading seq # 4: YOR316C_Smik Reading seq # 5: YOR316C_Spar Sequences read.. Counting patterns.. # site patterns = 417 Counting frequencies.. 120 bytes for distance 66720 bytes for lkl0 53376 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.102659 0.085665 0.160701 0.155297 0.130977 0.173143 0.376055 0.471611 lnL0 = -4309.781799 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4309.781799 x= 0.10266 0.08567 0.16070 0.15530 0.13098 0.17314 0.37606 0.47161 1 h-lim-p 0.0010 0.0082 141.9954 4305.519010 6 0.0005 33 | 0/8 2 h-lim-p 0.0007 0.0058 31.5839 4305.303650 7 0.0004 63 | 0/8 3 h-lim-p 0.0006 0.0090 25.0287 4305.179045 4 0.0006 84 | 0/8 4 h-lim-p 0.0018 0.0411 8.0445 4305.156259 2 0.0008 100 | 0/8 5 h-lim-p 0.0021 0.1191 3.1961 4305.150032 5 0.0014 125 | 0/8 6 h-lim-p 0.0041 0.4034 1.1039 4305.149420 4 0.0012 147 | 0/8 7 h-lim-p 0.0079 3.8637 0.1641 4305.149399 2 0.0015 164 | 0/8 8 h-lim-p 0.1657 20.0000 0.0015 4305.147144 0 1.3254 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 4305.147035 2 0.9961 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4305.147035 0 1.0938 231 | 0/8 11 h-lim-p 1.7583 20.0000 0.0000 4305.147035 0 1.5385 251 | 0/8 12 h-lim-p 1.5848 20.0000 0.0000 4305.147035 0 1.3867 271 | 0/8 13 h-lim-p 0.3707 20.0000 0.0000 4305.147035 0 0.0463 293 | 0/8 14 h-lim-p 0.0055 20.0000 0.0002 4305.147035 0 0.0007 315 | 0/8 15 h-lim-p 0.0003 20.0000 0.0007 4305.147035 0 0.0000 350 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 4305.147035 0 0.0001 370 Out... lnL = -4305.147035 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4305.147035 Node 7: lnL = -4305.147035 Node 8: lnL = -4305.147035 Node 9: lnL = -4305.147035 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 419 Sequential format.. Reading seq # 1: YOR319W_Sbay Reading seq # 2: YOR319W_Scer Reading seq # 3: YOR319W_Skud Reading seq # 4: YOR319W_Smik Reading seq # 5: YOR319W_Spar Sequences read.. Counting patterns.. # site patterns = 190 Counting frequencies.. 120 bytes for distance 30400 bytes for lkl0 24320 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.023849 0.100920 0.054933 0.151854 0.090226 0.201916 0.229321 0.273628 lnL0 = -1907.526017 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1907.526017 x= 0.02385 0.10092 0.05493 0.15185 0.09023 0.20192 0.22932 0.27363 1 h-lim-p 0.0048 1.3409 89.1694 1906.160171 9 0.0004 48 | 0/8 2 h-lim-p 0.0012 0.0093 19.1153 1906.042283 8 0.0007 81 | 0/8 3 h-lim-p 0.0012 0.0319 10.2166 1906.017942 2 0.0006 97 | 0/8 4 h-lim-p 0.0023 0.0446 2.6404 1906.015202 5 0.0009 119 | 0/8 5 h-lim-p 0.0037 0.5557 0.6139 1906.015012 4 0.0011 141 | 0/8 6 h-lim-p 0.0192 2.5926 0.0347 1906.015011 0 0.0012 164 | 0/8 7 h-lim-p 0.0113 19.8775 0.0037 1906.015009 0 0.0169 184 | 0/8 8 h-lim-p 0.0088 20.0000 0.0071 1906.014876 0 0.0703 207 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1906.014867 1 0.9961 229 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1906.014867 0 2.1875 249 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1906.014867 0 1.0938 269 | 0/8 12 h-lim-p 0.1919 20.0000 0.0000 1906.014867 0 0.0030 294 | 0/8 13 h-lim-p 0.0001 20.0000 0.0012 1906.014867 0 0.0000 317 | 0/8 14 h-lim-p 0.0003 20.0000 0.0000 1906.014867 0 0.0000 351 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 1906.014867 0 0.0000 378 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 1906.014867 0 0.0000 435 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0002 | 0/8 20 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1906.014867 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1906.014867 Node 7: lnL = -1906.014867 Node 8: lnL = -1906.014867 Node 9: lnL = -1906.014867 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 828 Sequential format.. Reading seq # 1: YOR320C_Sbay Reading seq # 2: YOR320C_Scer Reading seq # 3: YOR320C_Skud Reading seq # 4: YOR320C_Smik Reading seq # 5: YOR320C_Spar Sequences read.. Counting patterns.. # site patterns = 295 Counting frequencies.. 120 bytes for distance 47200 bytes for lkl0 37760 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.007582 0.118516 0.093130 0.135496 0.098154 0.194559 0.153589 0.246801 lnL0 = -3819.766207 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3819.766207 x= 0.00758 0.11852 0.09313 0.13550 0.09815 0.19456 0.15359 0.24680 1 h-lim-p 0.0005 0.0036 105.9910 3818.466727 5 0.0002 33 | 0/8 2 h-lim-p 0.0014 0.0127 17.7779 3818.411825 4 0.0004 54 | 0/8 3 h-lim-p 0.0008 0.0397 8.2126 3818.405214 5 0.0002 81 | 0/8 4 h-lim-p 0.0009 0.0845 2.1568 3818.404595 4 0.0003 102 | 0/8 5 h-lim-p 0.0045 0.2881 0.1406 3818.404591 0 0.0005 116 | 0/8 6 h-lim-p 0.0019 6.3724 0.0357 3818.404591 0 0.0004 137 | 0/8 7 h-lim-p 0.0028 20.0000 0.0053 3818.404591 0 0.0025 157 | 0/8 8 h-lim-p 0.0199 20.0000 0.0007 3818.404549 0 0.3184 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3818.404548 0 1.0938 201 | 0/8 10 h-lim-p 1.5133 20.0000 0.0001 3818.404547 0 1.3242 221 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3818.404547 0 2.1875 241 | 0/8 12 h-lim-p 1.1998 20.0000 0.0000 3818.404547 0 1.0498 261 | 0/8 13 h-lim-p 0.2472 20.0000 0.0002 3818.404547 0 0.0019 287 | 0/8 14 h-lim-p 0.0003 15.3778 0.0011 3818.404547 0 0.0002 307 | 0/8 15 h-lim-p 0.0002 20.0000 0.0008 3818.404547 0 0.0001 328 | 0/8 16 h-lim-p 0.0000 10.6280 0.0016 3818.404547 0 0.0000 358 | 0/8 17 h-lim-p 0.0001 20.0000 0.0000 3818.404547 0 0.0000 390 Out... lnL = -3818.404547 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3818.404547 Node 7: lnL = -3818.404547 Node 8: lnL = -3818.404547 Node 9: lnL = -3818.404547 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 525 Sequential format.. Reading seq # 1: YOR322C_Sbay Reading seq # 2: YOR322C_Scer Reading seq # 3: YOR322C_Skud Reading seq # 4: YOR322C_Smik Reading seq # 5: YOR322C_Spar Sequences read.. Counting patterns.. # site patterns = 190 Counting frequencies.. 120 bytes for distance 30400 bytes for lkl0 24320 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.066625 0.039866 0.058037 0.120516 0.083135 0.175972 0.199080 0.282220 lnL0 = -2307.028821 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2307.028821 x= 0.06663 0.03987 0.05804 0.12052 0.08314 0.17597 0.19908 0.28222 1 h-lim-p 0.0010 0.0083 78.0004 2306.399829 5 0.0002 34 | 0/8 2 h-lim-p 0.0012 0.0101 13.9408 2306.361256 6 0.0004 61 | 0/8 3 h-lim-p 0.0015 0.0295 3.7826 2306.358349 5 0.0004 85 | 0/8 4 h-lim-p 0.0012 0.0997 1.3981 2306.358043 4 0.0004 108 | 0/8 5 h-lim-p 0.0030 0.4194 0.1629 2306.358038 0 0.0003 122 | 0/8 6 h-lim-p 0.0109 20.0000 0.0049 2306.358038 0 0.0014 144 | 0/8 7 h-lim-p 0.0093 20.0000 0.0007 2306.358035 0 0.0744 167 | 0/8 8 h-lim-p 0.0026 5.4909 0.0207 2306.358022 0 0.0052 188 | 0/8 9 h-lim-p 1.4481 20.0000 0.0001 2306.358021 0 1.2671 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2306.358021 0 1.0938 228 | 0/8 11 h-lim-p 0.4789 20.0000 0.0000 2306.358021 0 0.4190 248 | 0/8 12 h-lim-p 0.1651 20.0000 0.0000 2306.358021 0 0.1651 268 | 0/8 13 h-lim-p 0.0686 20.0000 0.0001 2306.358021 0 0.0003 295 | 0/8 14 h-lim-p 0.0004 20.0000 0.0001 2306.358021 0 0.0002 315 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 2306.358021 0 0.0000 335 | 0/8 16 h-lim-p 0.0002 20.0000 0.0001 2306.358021 0 0.0000 366 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 | 0/8 18 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -2306.358021 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2306.358021 Node 7: lnL = -2306.358021 Node 8: lnL = -2306.358021 Node 9: lnL = -2306.358021 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 362 Sequential format.. Reading seq # 1: YOR323C_Sbay Reading seq # 2: YOR323C_Scer Reading seq # 3: YOR323C_Skud Reading seq # 4: YOR323C_Smik Reading seq # 5: YOR323C_Spar Sequences read.. Counting patterns.. # site patterns = 185 Counting frequencies.. 120 bytes for distance 29600 bytes for lkl0 23680 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.096286 0.008276 0.156996 0.156082 0.076534 0.149384 0.230346 0.360587 lnL0 = -1692.336426 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1692.336426 x= 0.09629 0.00828 0.15700 0.15608 0.07653 0.14938 0.23035 0.36059 1 h-lim-p 0.0017 0.9954 139.4183 1689.039960 8 0.0004 42 | 0/8 2 h-lim-p 0.0019 0.0153 15.5093 1688.929861 2 0.0009 58 | 0/8 3 h-lim-p 0.0019 0.0256 7.1487 1688.907058 6 0.0011 83 | 0/8 4 h-lim-p 0.0042 0.0925 1.7891 1688.905541 3 0.0010 103 | 0/8 5 h-lim-p 0.0046 0.6654 0.3998 1688.905413 3 0.0017 121 | 0/8 6 h-lim-p 0.0214 4.4973 0.0323 1688.905412 1 0.0013 146 | 0/8 7 h-lim-p 0.0045 20.0000 0.0094 1688.905411 0 0.0090 167 | 0/8 8 h-lim-p 0.0391 20.0000 0.0022 1688.905253 0 0.3132 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1688.905234 1 0.9961 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1688.905234 0 1.0938 232 | 0/8 11 h-lim-p 1.2459 20.0000 0.0000 1688.905234 0 1.0902 252 | 0/8 12 h-lim-p 0.3607 20.0000 0.0000 1688.905234 0 0.0225 275 | 0/8 13 h-lim-p 0.0032 20.0000 0.0001 1688.905234 0 0.0000 318 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1688.905234 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1688.905234 Node 7: lnL = -1688.905234 Node 8: lnL = -1688.905234 Node 9: lnL = -1688.905234 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 712 Sequential format.. Reading seq # 1: YOR324C_Sbay Reading seq # 2: YOR324C_Scer Reading seq # 3: YOR324C_Skud Reading seq # 4: YOR324C_Smik Reading seq # 5: YOR324C_Spar Sequences read.. Counting patterns.. # site patterns = 232 Counting frequencies.. 120 bytes for distance 37120 bytes for lkl0 29696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.042543 0.040365 0.059748 0.087586 0.081724 0.159977 0.180797 0.229653 lnL0 = -3032.318703 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3032.318703 x= 0.04254 0.04036 0.05975 0.08759 0.08172 0.15998 0.18080 0.22965 1 h-lim-p 0.0012 0.0095 126.8456 3031.251753 3 0.0001 30 | 0/8 2 h-lim-p 0.0011 0.0085 15.6061 3031.217803 5 0.0003 53 | 0/8 3 h-lim-p 0.0006 0.0198 7.2843 3031.213484 5 0.0002 77 | 0/8 4 h-lim-p 0.0013 0.1052 1.0902 3031.213353 3 0.0002 98 | 0/8 5 h-lim-p 0.0008 0.4730 0.3220 3031.213332 2 0.0004 115 | 0/8 6 h-lim-p 0.0039 3.7209 0.0338 3031.213331 0 0.0009 136 | 0/8 7 h-lim-p 0.0019 4.7467 0.0153 3031.213324 0 0.0038 157 | 0/8 8 h-lim-p 0.0038 20.0000 0.0150 3031.212515 0 0.0306 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3031.212499 1 0.9961 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3031.212499 0 1.0938 222 | 0/8 11 h-lim-p 1.3673 20.0000 0.0000 3031.212499 0 4.1020 243 | 0/8 12 h-lim-p 0.4529 20.0000 0.0002 3031.212499 0 0.0566 265 | 0/8 13 h-lim-p 0.0038 15.7820 0.0037 3031.212499 0 0.0000 301 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 3031.212499 0 0.0000 336 | 0/8 15 h-lim-p 0.0000 20.0000 0.0024 | 0/8 16 h-lim-p 0.0000 20.0000 0.0024 Out... lnL = -3031.212499 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3031.212499 Node 7: lnL = -3031.212499 Node 8: lnL = -3031.212499 Node 9: lnL = -3031.212499 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 835 Sequential format.. Reading seq # 1: YOR327C_Sbay Reading seq # 2: YOR327C_Scer Reading seq # 3: YOR327C_Skud Reading seq # 4: YOR327C_Smik Reading seq # 5: YOR327C_Spar Sequences read.. Counting patterns.. # site patterns = 308 Counting frequencies.. 120 bytes for distance 49280 bytes for lkl0 39424 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.042998 0.053552 0.079820 0.112696 0.093470 0.209177 0.220889 0.274529 lnL0 = -3580.638307 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3580.638307 x= 0.04300 0.05355 0.07982 0.11270 0.09347 0.20918 0.22089 0.27453 1 h-lim-p 0.0019 0.0150 134.9534 3578.707889 4 0.0002 32 | 0/8 2 h-lim-p 0.0011 0.0088 21.4115 3578.638130 7 0.0003 61 | 0/8 3 h-lim-p 0.0006 0.0268 10.9990 3578.623779 2 0.0003 77 | 0/8 4 h-lim-p 0.0009 0.0742 3.6245 3578.621320 2 0.0004 93 | 0/8 5 h-lim-p 0.0018 0.2033 0.8847 3578.621138 3 0.0005 113 | 0/8 6 h-lim-p 0.0015 0.9115 0.2990 3578.621123 0 0.0004 134 | 0/8 7 h-lim-p 0.0099 20.0000 0.0117 3578.621123 0 0.0022 155 | 0/8 8 h-lim-p 0.0432 20.0000 0.0006 3578.621007 0 0.5182 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3578.621006 0 1.0938 198 | 0/8 10 h-lim-p 2.1484 20.0000 0.0000 3578.621006 0 0.9399 218 | 0/8 11 h-lim-p 0.7992 20.0000 0.0000 3578.621006 0 0.0008 247 | 0/8 12 h-lim-p 0.0002 20.0000 0.0001 3578.621006 0 0.0000 269 | 0/8 13 h-lim-p 0.0010 20.0000 0.0000 3578.621006 0 0.0010 289 Out... lnL = -3578.621006 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3578.621006 Node 7: lnL = -3578.621006 Node 8: lnL = -3578.621006 Node 9: lnL = -3578.621006 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 201 Sequential format.. Reading seq # 1: YOR332W_Sbay Reading seq # 2: YOR332W_Scer Reading seq # 3: YOR332W_Skud Reading seq # 4: YOR332W_Smik Reading seq # 5: YOR332W_Spar Sequences read.. Counting patterns.. # site patterns = 39 Counting frequencies.. 120 bytes for distance 6240 bytes for lkl0 4992 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.131334 0.445662 0.334795 0.052840 2.897440 0.033424 0.752493 lnL0 = -654.665124 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 654.665124 x= 0.00006 0.13133 0.44566 0.33480 0.05284 2.89744 0.03342 0.75249 1 h-lim-p 0.0000 0.0000 310.5470 654.540008 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0000 2406.1874 629.143833 m 0.0000 34 | 2/8 3 h-lim-p 0.0000 0.0001 1147.0081 595.299749 m 0.0001 46 | 3/8 4 h-lim-p 0.0001 0.0006 89.8733 590.697497 m 0.0006 58 | 4/8 5 h-lim-p 0.0005 0.0054 114.5002 552.015579 1 0.0042 75 | 3/8 6 h-lim-p 0.0000 0.0001 956.7300 550.583256 0 0.0000 88 | 3/8 7 h-lim-p 0.0001 0.0007 92.6505 546.392421 0 0.0005 102 | 3/8 8 h-lim-p 0.0126 0.1004 3.2118 519.909321 0 0.0753 116 | 2/8 9 h-lim-p 0.0000 0.0000 5894.1815 515.864399 0 0.0000 130 | 2/8 10 h-lim-p 0.4021 20.0000 0.1522 512.810003 9 0.3087 164 | 2/8 11 h-lim-p 0.5957 4.7653 0.0419 512.151551 0 1.1913 183 | 1/8 12 h-lim-p 0.0026 0.0212 12.5357 511.953357 0 0.0040 201 | 0/8 13 h-lim-p 0.0004 0.0033 71.3760 511.869042 7 0.0003 231 | 0/8 14 h-lim-p 0.2733 2.1866 0.0089 511.631469 m 2.1866 243 | 1/8 15 h-lim-p 1.2758 10.2064 0.0114 511.614839 7 0.6686 277 | 0/8 16 h-lim-p 0.0005 0.0081 15.2887 511.605219 7 0.0004 315 | 0/8 17 h-lim-p 2.5000 20.0000 0.0008 511.600825 4 1.9287 335 | 0/8 18 h-lim-p 0.9280 20.0000 0.0016 511.600484 0 1.8561 356 | 0/8 19 h-lim-p 2.5000 20.0000 0.0001 511.600479 0 1.0938 376 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 511.600479 0 1.0938 396 | 0/8 21 h-lim-p 2.5000 20.0000 0.0000 511.600479 0 2.1875 416 | 0/8 22 h-lim-p 1.7724 20.0000 0.0000 511.600479 0 0.3877 437 | 0/8 23 h-lim-p 0.5607 20.0000 0.0000 511.600479 0 0.0701 459 | 0/8 24 h-lim-p 0.0654 20.0000 0.0000 511.600479 0 0.0327 479 Out... lnL = -511.600479 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -511.600479 Node 7: lnL = -511.600479 Node 8: lnL = -511.600479 Node 9: lnL = -511.600479 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 255 Sequential format.. Reading seq # 1: YOR334W_Sbay Reading seq # 2: YOR334W_Scer Reading seq # 3: YOR334W_Skud Reading seq # 4: YOR334W_Smik Reading seq # 5: YOR334W_Spar Sequences read.. Counting patterns.. # site patterns = 97 Counting frequencies.. 120 bytes for distance 15520 bytes for lkl0 12416 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.012560 0.138821 0.000060 0.133824 0.039385 0.386159 0.076438 0.212137 lnL0 = -883.089242 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 883.089242 x= 0.01256 0.13882 0.00006 0.13382 0.03938 0.38616 0.07644 0.21214 1 h-lim-p 0.0000 0.0000 120.9167 883.063362 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0003 72.2646 882.231839 m 0.0003 37 | 2/8 3 h-lim-p 0.0017 0.0170 12.1620 877.726299 0 0.0067 51 | 2/8 4 h-lim-p 0.0007 0.0057 41.9224 877.385468 9 0.0004 87 | 2/8 5 h-lim-p 0.0010 0.0076 17.6511 877.310740 7 0.0006 117 | 2/8 6 h-lim-p 0.0038 0.1529 2.5835 877.280602 0 0.0075 130 | 1/8 7 h-lim-p 0.0014 0.0385 14.1105 877.220661 8 0.0008 164 | 1/8 8 h-lim-p 0.0092 0.3515 1.1832 877.219831 5 0.0017 188 | 1/8 9 h-lim-p 0.0616 13.6562 0.0327 876.838703 0 0.9853 204 | 1/8 10 h-lim-p 2.5000 20.0000 0.0060 876.808680 3 1.1328 229 | 1/8 11 h-lim-p 2.5000 20.0000 0.0008 876.808296 3 1.0004 254 | 1/8 12 h-lim-p 2.5000 20.0000 0.0001 876.808292 2 0.9644 277 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 876.808292 0 1.0938 296 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 876.808292 0 2.1875 315 | 1/8 15 h-lim-p 1.8288 20.0000 0.0000 876.808292 0 0.4572 335 | 1/8 16 h-lim-p 0.8291 20.0000 0.0000 876.808292 0 0.0130 359 | 1/8 17 h-lim-p 0.0127 20.0000 0.0000 876.808292 0 0.0032 379 Out... lnL = -876.808292 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -876.808292 Node 7: lnL = -876.808292 Node 8: lnL = -876.808292 Node 9: lnL = -876.808292 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 725 Sequential format.. Reading seq # 1: YOR335C_Sbay Reading seq # 2: YOR335C_Scer Reading seq # 3: YOR335C_Skud Reading seq # 4: YOR335C_Smik Reading seq # 5: YOR335C_Spar Sequences read.. Counting patterns.. # site patterns = 317 Counting frequencies.. 120 bytes for distance 50720 bytes for lkl0 40576 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.153861 0.000060 0.173410 0.200634 0.074383 0.241516 0.318312 0.472264 lnL0 = -3323.021100 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3323.021100 x= 0.15386 0.00006 0.17341 0.20063 0.07438 0.24152 0.31831 0.47226 1 h-lim-p 0.0002 0.0012 219.5682 3305.377532 0 0.0006 24 | 0/8 2 h-lim-p 0.0004 0.0030 60.4566 3304.535761 0 0.0006 36 | 0/8 3 h-lim-p 0.0002 0.0014 63.9274 3303.753213 0 0.0007 50 | 0/8 4 h-lim-p 0.0020 0.0157 15.0052 3303.695992 7 0.0006 80 | 0/8 5 h-lim-p 0.0008 0.0175 11.1142 3303.649628 0 0.0012 92 | 0/8 6 h-lim-p 0.0026 0.0525 5.1039 3303.641544 6 0.0008 120 | 0/8 7 h-lim-p 0.0025 0.1125 1.6313 3303.640521 5 0.0007 144 | 0/8 8 h-lim-p 0.0410 8.1177 0.0279 3303.371644 0 0.6557 160 | 0/8 9 h-lim-p 2.5000 20.0000 0.0019 3303.369319 3 1.0449 186 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 3303.369309 1 0.9961 208 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3303.369309 0 1.0938 228 | 0/8 12 h-lim-p 2.4863 20.0000 0.0000 3303.369309 0 1.0878 248 | 0/8 13 h-lim-p 1.0207 20.0000 0.0000 3303.369309 0 0.0159 273 | 0/8 14 h-lim-p 0.0001 20.0000 0.0018 3303.369309 0 0.0000 310 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 3303.369309 0 0.0000 345 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -3303.369309 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3303.369309 Node 7: lnL = -3303.369309 Node 8: lnL = -3303.369309 Node 9: lnL = -3303.369309 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 733 Sequential format.. Reading seq # 1: YOR336W_Sbay Reading seq # 2: YOR336W_Scer Reading seq # 3: YOR336W_Skud Reading seq # 4: YOR336W_Smik Reading seq # 5: YOR336W_Spar Sequences read.. Counting patterns.. # site patterns = 302 Counting frequencies.. 120 bytes for distance 48320 bytes for lkl0 38656 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.071120 0.137435 0.170764 0.097262 0.203701 0.628996 0.333747 lnL0 = -3552.262469 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3552.262469 x= 0.00006 0.07112 0.13743 0.17076 0.09726 0.20370 0.62900 0.33375 1 h-lim-p 0.0000 0.0000 181.0663 3552.214445 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0065 90.9948 3549.986957 0 0.0006 40 | 1/8 3 h-lim-p 0.0007 0.0064 78.5789 3548.427935 1 0.0009 54 | 1/8 4 h-lim-p 0.0021 0.0166 34.4997 3548.110057 7 0.0007 84 | 1/8 5 h-lim-p 0.0033 0.0265 7.4735 3548.064023 5 0.0013 105 | 1/8 6 h-lim-p 0.0016 0.0453 6.3247 3547.965981 0 0.0031 118 | 1/8 7 h-lim-p 0.0057 0.0542 3.4810 3547.796554 5 0.0061 141 | 1/8 8 h-lim-p 0.0154 0.2075 1.3781 3540.193116 0 0.0617 155 | 1/8 9 h-lim-p 2.5000 20.0000 0.0129 3540.145344 5 0.6088 181 | 0/8 10 h-lim-p 0.0214 7.7748 0.3666 3540.145275 3 0.0009 210 | 0/8 11 h-lim-p 0.0737 20.0000 0.0047 3540.141130 0 0.8845 233 | 0/8 12 h-lim-p 2.5000 20.0000 0.0010 3540.140664 3 1.0004 259 | 0/8 13 h-lim-p 2.5000 20.0000 0.0002 3540.140653 2 0.8246 285 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 3540.140652 0 1.0938 305 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 3540.140652 0 1.0938 325 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 3540.140652 0 1.0938 345 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 3540.140652 0 1.0938 365 | 0/8 18 h-lim-p 2.2406 20.0000 0.0000 3540.140652 0 4.4811 386 | 0/8 19 h-lim-p 0.9116 20.0000 0.0000 3540.140652 0 0.1994 407 | 0/8 20 h-lim-p 0.0018 13.5556 0.0000 3540.140652 0 0.0018 427 | 0/8 21 h-lim-p 0.0003 2.0489 0.0003 3540.140652 0 0.0001 447 | 0/8 22 h-lim-p 0.0003 4.2016 0.0001 3540.140652 0 0.0000 484 | 0/8 23 h-lim-p 0.0000 20.0000 0.0001 3540.140652 0 0.0000 505 | 0/8 24 h-lim-p 0.0000 8.0667 0.0001 3540.140652 0 0.0000 528 | 0/8 25 h-lim-p 0.0000 5.1172 0.0001 3540.140652 0 0.0000 553 | 0/8 26 h-lim-p 0.0000 5.1659 0.0001 .. | 0/8 27 h-lim-p 0.0000 20.0000 0.0001 | 0/8 28 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -3540.140652 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3540.140652 Node 7: lnL = -3540.140652 Node 8: lnL = -3540.140652 Node 9: lnL = -3540.140652 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 498 Sequential format.. Reading seq # 1: YOR337W_Sbay Reading seq # 2: YOR337W_Scer Reading seq # 3: YOR337W_Skud Reading seq # 4: YOR337W_Smik Reading seq # 5: YOR337W_Spar Sequences read.. Counting patterns.. # site patterns = 206 Counting frequencies.. 120 bytes for distance 32960 bytes for lkl0 26368 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.076658 0.065583 0.072623 0.136679 0.074709 0.190382 0.172968 0.311471 lnL0 = -2191.494739 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2191.494739 x= 0.07666 0.06558 0.07262 0.13668 0.07471 0.19038 0.17297 0.31147 1 h-lim-p 0.0002 0.0015 99.7142 2189.674870 0 0.0004 23 | 0/8 2 h-lim-p 0.0011 0.0086 29.2094 2189.463583 4 0.0005 43 | 0/8 3 h-lim-p 0.0021 0.0379 7.4948 2189.449412 6 0.0005 70 | 0/8 4 h-lim-p 0.0009 0.0830 4.3054 2189.447412 5 0.0003 95 | 0/8 5 h-lim-p 0.0011 0.2009 1.0792 2189.447039 4 0.0007 117 | 0/8 6 h-lim-p 0.0089 2.6386 0.0859 2189.447036 2 0.0007 136 | 0/8 7 h-lim-p 0.0024 4.4967 0.0259 2189.447022 0 0.0047 157 | 0/8 8 h-lim-p 0.0115 12.6311 0.0107 2189.445403 0 0.0922 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 2189.445365 2 0.9961 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2189.445365 0 1.0938 224 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2189.445365 0 2.1875 244 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2189.445365 0 1.0938 264 | 0/8 13 h-lim-p 0.4392 20.0000 0.0000 2189.445365 0 7.0278 288 | 0/8 14 h-lim-p 0.4832 20.0000 0.0002 2189.445365 0 0.2114 308 | 0/8 15 h-lim-p 0.0137 20.0000 0.0025 2189.445365 0 0.0034 329 | 0/8 16 h-lim-p 0.0017 20.0000 0.0050 2189.445365 0 0.0001 352 | 0/8 17 h-lim-p 0.0001 20.0000 0.0074 2189.445365 0 0.0000 373 | 0/8 18 h-lim-p 0.0000 20.0000 0.0036 2189.445365 0 0.0000 400 | 0/8 19 h-lim-p 0.0004 20.0000 0.0000 .. | 0/8 20 h-lim-p 0.0000 20.0000 0.0013 2189.445365 0 0.0000 461 | 0/8 21 h-lim-p 0.0000 20.0000 0.0005 2189.445365 0 0.0006 487 | 0/8 22 h-lim-p 0.0024 20.0000 0.0001 2189.445365 0 0.0012 507 | 0/8 23 h-lim-p 0.0032 20.0000 0.0001 2189.445365 0 0.0000 534 | 0/8 24 h-lim-p 0.0000 20.0000 0.0000 2189.445365 0 0.0000 567 | 0/8 25 h-lim-p 0.0000 20.0000 0.0016 | 0/8 26 h-lim-p 0.0000 20.0000 0.0016 Out... lnL = -2189.445365 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2189.445365 Node 7: lnL = -2189.445365 Node 8: lnL = -2189.445365 Node 9: lnL = -2189.445365 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 295 Sequential format.. Reading seq # 1: YOR338W_Sbay Reading seq # 2: YOR338W_Scer Reading seq # 3: YOR338W_Skud Reading seq # 4: YOR338W_Smik Reading seq # 5: YOR338W_Spar Sequences read.. Counting patterns.. # site patterns = 93 Counting frequencies.. 120 bytes for distance 14880 bytes for lkl0 11904 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.018213 0.030923 0.052099 0.054314 0.047537 0.126115 0.106253 0.142522 lnL0 = -1069.469577 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1069.469577 x= 0.01821 0.03092 0.05210 0.05431 0.04754 0.12612 0.10625 0.14252 1 h-lim-p 0.0004 0.0029 129.3671 1067.901146 9 0.0002 46 | 0/8 2 h-lim-p 0.0006 0.0047 20.8910 1067.775680 6 0.0006 70 | 0/8 3 h-lim-p 0.0015 0.0224 8.2197 1067.765816 2 0.0003 87 | 0/8 4 h-lim-p 0.0018 0.0381 1.5919 1067.765508 5 0.0003 113 | 0/8 5 h-lim-p 0.0007 0.1634 0.6089 1067.765428 4 0.0005 134 | 0/8 6 h-lim-p 0.0038 1.5041 0.0771 1067.765427 0 0.0004 156 | 0/8 7 h-lim-p 0.0017 9.1149 0.0185 1067.765427 0 0.0004 177 | 0/8 8 h-lim-p 0.0666 20.0000 0.0001 1067.765407 0 1.0653 201 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1067.765406 0 1.0938 221 | 0/8 10 h-lim-p 1.7343 20.0000 0.0000 1067.765406 0 0.7587 241 | 0/8 11 h-lim-p 0.6074 20.0000 0.0000 1067.765406 0 0.2657 261 | 0/8 12 h-lim-p 0.1399 20.0000 0.0000 1067.765406 0 0.0022 286 | 0/8 13 h-lim-p 0.0011 20.0000 0.0001 1067.765406 0 0.0001 308 | 0/8 14 h-lim-p 0.0002 20.0000 0.0001 1067.765406 0 0.0000 343 | 0/8 15 h-lim-p 0.0000 20.0000 0.0017 | 0/8 16 h-lim-p 0.0000 20.0000 0.0017 Out... lnL = -1067.765406 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1067.765406 Node 7: lnL = -1067.765406 Node 8: lnL = -1067.765406 Node 9: lnL = -1067.765406 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 434 Sequential format.. Reading seq # 1: YOR339C_Sbay Reading seq # 2: YOR339C_Scer Reading seq # 3: YOR339C_Skud Reading seq # 4: YOR339C_Smik Reading seq # 5: YOR339C_Spar Sequences read.. Counting patterns.. # site patterns = 184 Counting frequencies.. 120 bytes for distance 29440 bytes for lkl0 23552 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.042580 0.064831 0.084854 0.103054 0.116340 0.179947 0.146576 0.248482 lnL0 = -1869.921192 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1869.921192 x= 0.04258 0.06483 0.08485 0.10305 0.11634 0.17995 0.14658 0.24848 1 h-lim-p 0.0053 0.0711 83.9747 1868.676562 8 0.0004 43 | 0/8 2 h-lim-p 0.0013 0.0102 19.2661 1868.547822 7 0.0007 71 | 0/8 3 h-lim-p 0.0031 0.0722 4.4395 1868.542965 5 0.0005 96 | 0/8 4 h-lim-p 0.0021 0.2246 1.1128 1868.542661 3 0.0005 115 | 0/8 5 h-lim-p 0.0045 0.6522 0.1285 1868.542656 2 0.0007 134 | 0/8 6 h-lim-p 0.0542 20.0000 0.0017 1868.542634 0 0.1084 155 | 0/8 7 h-lim-p 0.0030 10.1272 0.0626 1868.542420 0 0.0060 176 | 0/8 8 h-lim-p 0.0017 1.3527 0.2291 1868.542396 2 0.0008 201 | 0/8 9 h-lim-p 1.4063 20.0000 0.0001 1868.542386 2 1.0849 225 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1868.542386 0 1.0938 245 | 0/8 11 h-lim-p 2.1518 20.0000 0.0000 1868.542386 0 0.9414 265 | 0/8 12 h-lim-p 0.6083 20.0000 0.0000 1868.542386 0 0.0006 294 | 0/8 13 h-lim-p 0.0005 20.0000 0.0000 1868.542386 0 0.0000 330 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1868.542386 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1868.542386 Node 7: lnL = -1868.542386 Node 8: lnL = -1868.542386 Node 9: lnL = -1868.542386 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 842 Sequential format.. Reading seq # 1: YOR340C_Sbay Reading seq # 2: YOR340C_Scer Reading seq # 3: YOR340C_Skud Reading seq # 4: YOR340C_Smik Reading seq # 5: YOR340C_Spar Sequences read.. Counting patterns.. # site patterns = 287 Counting frequencies.. 120 bytes for distance 45920 bytes for lkl0 36736 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.031768 0.069198 0.074233 0.126106 0.082725 0.209945 0.203234 0.248519 lnL0 = -3829.307488 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3829.307488 x= 0.03177 0.06920 0.07423 0.12611 0.08273 0.20994 0.20323 0.24852 1 h-lim-p 0.0041 0.0495 135.9350 3827.683443 8 0.0002 45 | 0/8 2 h-lim-p 0.0010 0.0078 14.1972 3827.664551 4 0.0002 66 | 0/8 3 h-lim-p 0.0006 0.0383 4.2966 3827.662430 3 0.0002 84 | 0/8 4 h-lim-p 0.0013 0.3634 0.8475 3827.662266 3 0.0005 102 | 0/8 5 h-lim-p 0.0015 0.6711 0.2734 3827.662255 0 0.0003 123 | 0/8 6 h-lim-p 0.0033 6.0962 0.0271 3827.662255 0 0.0007 144 | 0/8 7 h-lim-p 0.0193 20.0000 0.0010 3827.662255 0 0.0042 165 | 0/8 8 h-lim-p 0.0128 20.0000 0.0003 3827.662251 0 0.2052 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3827.662251 0 1.0938 209 | 0/8 10 h-lim-p 0.9802 20.0000 0.0000 3827.662251 0 1.4703 229 | 0/8 11 h-lim-p 1.7304 20.0000 0.0000 3827.662251 0 0.7571 249 | 0/8 12 h-lim-p 0.1752 20.0000 0.0001 3827.662251 0 0.0109 272 | 0/8 13 h-lim-p 0.0026 20.0000 0.0004 3827.662251 0 0.0013 292 | 0/8 14 h-lim-p 0.0008 20.0000 0.0007 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0012 | 0/8 16 h-lim-p 0.0000 20.0000 0.0012 Out... lnL = -3827.662251 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3827.662251 Node 7: lnL = -3827.662251 Node 8: lnL = -3827.662251 Node 9: lnL = -3827.662251 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 550 Sequential format.. Reading seq # 1: YOR342C_Sbay Reading seq # 2: YOR342C_Scer Reading seq # 3: YOR342C_Skud Reading seq # 4: YOR342C_Smik Reading seq # 5: YOR342C_Spar Sequences read.. Counting patterns.. # site patterns = 189 Counting frequencies.. 120 bytes for distance 30240 bytes for lkl0 24192 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.044662 0.019744 0.061818 0.087012 0.063821 0.138310 0.164058 0.204663 lnL0 = -2204.426425 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2204.426425 x= 0.04466 0.01974 0.06182 0.08701 0.06382 0.13831 0.16406 0.20466 1 h-lim-p 0.0009 0.4647 222.8379 2201.659909 9 0.0001 46 | 0/8 2 h-lim-p 0.0008 0.0065 19.5984 2201.573808 7 0.0004 74 | 0/8 3 h-lim-p 0.0011 0.0324 7.7607 2201.567210 4 0.0002 94 | 0/8 4 h-lim-p 0.0009 0.0673 2.1635 2201.566666 4 0.0003 117 | 0/8 5 h-lim-p 0.0007 0.2698 0.8037 2201.566556 3 0.0004 137 | 0/8 6 h-lim-p 0.0036 1.5216 0.0895 2201.566555 1 0.0002 162 | 0/8 7 h-lim-p 0.0026 9.2685 0.0077 2201.566555 0 0.0023 182 | 0/8 8 h-lim-p 0.0236 20.0000 0.0007 2201.566393 0 0.3774 206 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2201.566393 0 1.0938 226 | 0/8 10 h-lim-p 1.4222 20.0000 0.0000 2201.566393 0 0.6222 246 | 0/8 11 h-lim-p 0.3462 20.0000 0.0000 2201.566393 0 0.0216 269 | 0/8 12 h-lim-p 0.0079 20.0000 0.0001 2201.566393 0 0.0000 297 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 2201.566393 0 0.0000 328 | 0/8 14 h-lim-p 0.0000 20.0000 0.0014 | 0/8 15 h-lim-p 0.0000 20.0000 0.0014 Out... lnL = -2201.566393 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2201.566393 Node 7: lnL = -2201.566393 Node 8: lnL = -2201.566393 Node 9: lnL = -2201.566393 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 880 Sequential format.. Reading seq # 1: YOR344C_Sbay Reading seq # 2: YOR344C_Scer Reading seq # 3: YOR344C_Skud Reading seq # 4: YOR344C_Smik Reading seq # 5: YOR344C_Spar Sequences read.. Counting patterns.. # site patterns = 159 Counting frequencies.. 120 bytes for distance 25440 bytes for lkl0 20352 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.014468 0.014130 0.034622 0.038445 0.037722 0.061679 0.086261 0.092961 lnL0 = -2656.303265 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2656.303265 x= 0.01447 0.01413 0.03462 0.03844 0.03772 0.06168 0.08626 0.09296 1 h-lim-p 0.0004 0.2805 380.6616 2654.290602 8 0.0000 40 | 0/8 2 h-lim-p 0.0002 0.0013 49.4921 2654.213129 3 0.0001 58 | 0/8 3 h-lim-p 0.0007 0.0053 4.8854 2654.212270 2 0.0001 76 | 0/8 4 h-lim-p 0.0003 0.0389 1.1976 2654.212224 2 0.0001 93 | 0/8 5 h-lim-p 0.0003 0.4838 0.2468 2654.212221 1 0.0001 108 | 0/8 6 h-lim-p 0.0004 1.4709 0.0561 2654.212221 0 0.0002 128 | 0/8 7 h-lim-p 0.0005 6.3835 0.0171 2654.212221 0 0.0005 148 | 0/8 8 h-lim-p 0.0082 20.0000 0.0010 2654.211893 0 0.3959 173 | 0/8 9 h-lim-p 0.1269 6.4873 0.0030 2654.211861 0 1.0153 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2654.211859 0 1.0938 216 | 0/8 11 h-lim-p 0.6676 20.0000 0.0001 2654.211859 0 1.3352 237 | 0/8 12 h-lim-p 1.5113 20.0000 0.0001 2654.211859 0 1.3224 257 | 0/8 13 h-lim-p 0.0122 1.1755 0.0133 2654.211859 0 0.0004 281 | 0/8 14 h-lim-p 0.0001 0.4395 0.0355 2654.211859 0 0.0000 313 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 2654.211859 0 0.0000 340 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 2654.211859 0 0.0000 371 Out... lnL = -2654.211859 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2654.211859 Node 7: lnL = -2654.211859 Node 8: lnL = -2654.211859 Node 9: lnL = -2654.211859 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 908 Sequential format.. Reading seq # 1: YOR348C_Sbay Reading seq # 2: YOR348C_Scer Reading seq # 3: YOR348C_Skud Reading seq # 4: YOR348C_Smik Reading seq # 5: YOR348C_Spar Sequences read.. Counting patterns.. # site patterns = 370 Counting frequencies.. 120 bytes for distance 59200 bytes for lkl0 47360 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.070851 0.431354 0.127899 0.087630 0.088641 0.224848 0.808632 0.597955 lnL0 = -4707.583800 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4707.583800 x= 0.07085 0.43135 0.12790 0.08763 0.08864 0.22485 0.80863 0.59796 1 h-lim-p 0.0006 0.0048 73.8292 4706.899516 5 0.0003 31 | 0/8 2 h-lim-p 0.0004 0.0028 38.6458 4706.760633 7 0.0002 61 | 0/8 3 h-lim-p 0.0004 0.0190 20.7816 4706.516952 0 0.0017 75 | 0/8 4 h-lim-p 0.0011 0.0087 25.6192 4706.443482 3 0.0005 93 | 0/8 5 h-lim-p 0.0044 0.0379 2.8994 4706.428731 4 0.0037 114 | 0/8 6 h-lim-p 0.0063 0.2751 1.6848 4706.424378 5 0.0040 140 | 0/8 7 h-lim-p 2.5000 20.0000 0.0024 4706.422405 3 1.0004 158 | 0/8 8 h-lim-p 0.0247 5.7999 0.0981 4706.422354 1 0.0099 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4706.422351 0 1.0938 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4706.422351 0 1.0938 220 | 0/8 11 h-lim-p 2.0575 20.0000 0.0000 4706.422351 0 0.1125 243 | 0/8 12 h-lim-p 0.0536 20.0000 0.0000 4706.422351 0 0.0000 286 | 0/8 13 h-lim-p 0.0000 20.0000 0.0013 4706.422351 0 0.0000 309 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 4706.422351 0 0.0000 331 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0013 | 0/8 17 h-lim-p 0.0000 20.0000 0.0013 Out... lnL = -4706.422351 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4706.422351 Node 7: lnL = -4706.422351 Node 8: lnL = -4706.422351 Node 9: lnL = -4706.422351 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 752 Sequential format.. Reading seq # 1: YOR351C_Sbay Reading seq # 2: YOR351C_Scer Reading seq # 3: YOR351C_Skud Reading seq # 4: YOR351C_Smik Reading seq # 5: YOR351C_Spar Sequences read.. Counting patterns.. # site patterns = 303 Counting frequencies.. 120 bytes for distance 48480 bytes for lkl0 38784 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.045823 0.046557 0.088067 0.164346 0.099432 0.224240 0.229061 0.289038 lnL0 = -3446.192944 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3446.192944 x= 0.04582 0.04656 0.08807 0.16435 0.09943 0.22424 0.22906 0.28904 1 h-lim-p 0.0056 0.0653 110.9723 3444.821340 7 0.0002 42 | 0/8 2 h-lim-p 0.0013 0.0106 14.4610 3444.788564 2 0.0003 59 | 0/8 3 h-lim-p 0.0007 0.0338 6.3436 3444.781699 5 0.0004 84 | 0/8 4 h-lim-p 0.0011 0.0981 2.2757 3444.780570 3 0.0005 102 | 0/8 5 h-lim-p 0.0024 0.6255 0.4690 3444.780502 3 0.0007 121 | 0/8 6 h-lim-p 0.0039 3.8411 0.0782 3444.780500 0 0.0004 143 | 0/8 7 h-lim-p 0.0060 15.9155 0.0057 3444.780499 0 0.0060 163 | 0/8 8 h-lim-p 0.0124 20.0000 0.0027 3444.780351 0 0.0993 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3444.780345 0 1.0938 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3444.780345 0 1.0938 226 | 0/8 11 h-lim-p 1.0882 20.0000 0.0000 3444.780345 0 0.9522 246 | 0/8 12 h-lim-p 0.4645 20.0000 0.0000 3444.780345 0 0.0001 277 | 0/8 13 h-lim-p 0.0000 20.0000 0.0005 3444.780345 0 0.0000 298 | 0/8 14 h-lim-p 0.0005 20.0000 0.0000 3444.780345 0 0.0001 319 Out... lnL = -3444.780345 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3444.780345 Node 7: lnL = -3444.780345 Node 8: lnL = -3444.780345 Node 9: lnL = -3444.780345 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 750 Sequential format.. Reading seq # 1: YOR352W_Sbay Reading seq # 2: YOR352W_Scer Reading seq # 3: YOR352W_Skud Reading seq # 4: YOR352W_Smik Reading seq # 5: YOR352W_Spar Sequences read.. Counting patterns.. # site patterns = 280 Counting frequencies.. 120 bytes for distance 44800 bytes for lkl0 35840 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.046036 0.047794 0.090047 0.162031 0.101747 0.231407 0.230385 0.292559 lnL0 = -3572.963951 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3572.963951 x= 0.04604 0.04779 0.09005 0.16203 0.10175 0.23141 0.23039 0.29256 1 h-lim-p 0.0008 0.0065 105.7560 3571.725254 8 0.0002 43 | 0/8 2 h-lim-p 0.0010 0.0082 15.5583 3571.687997 7 0.0003 75 | 0/8 3 h-lim-p 0.0009 0.0277 5.1744 3571.684447 5 0.0003 101 | 0/8 4 h-lim-p 0.0022 0.1261 0.6843 3571.684333 2 0.0005 118 | 0/8 5 h-lim-p 0.0045 3.8851 0.0744 3571.684331 0 0.0005 140 | 0/8 6 h-lim-p 0.0022 17.2672 0.0166 3571.684331 0 0.0005 161 | 0/8 7 h-lim-p 0.0064 20.0000 0.0012 3571.684331 0 0.0028 181 | 0/8 8 h-lim-p 0.0389 20.0000 0.0001 3571.684330 0 0.6228 205 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3571.684330 0 1.0938 225 | 0/8 10 h-lim-p 0.6674 20.0000 0.0000 3571.684330 0 1.3348 246 | 0/8 11 h-lim-p 0.9383 20.0000 0.0000 3571.684330 0 5.6297 268 | 0/8 12 h-lim-p 0.0116 4.5420 0.0146 3571.684330 0 0.0007 291 | 0/8 13 h-lim-p 0.0006 3.8767 0.0171 3571.684330 0 0.0006 311 | 0/8 14 h-lim-p 0.0006 20.0000 0.0170 3571.684330 0 0.0000 334 | 0/8 15 h-lim-p 0.0002 20.0000 0.0033 3571.684330 0 0.0000 357 | 0/8 16 h-lim-p 0.0001 20.0000 0.0003 3571.684330 0 0.0000 388 | 0/8 17 h-lim-p 0.0000 20.0000 0.0012 | 0/8 18 h-lim-p 0.0000 20.0000 0.0012 Out... lnL = -3571.684330 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3571.684330 Node 7: lnL = -3571.684330 Node 8: lnL = -3571.684330 Node 9: lnL = -3571.684330 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 331 Sequential format.. Reading seq # 1: YOR353C_Sbay Reading seq # 2: YOR353C_Scer Reading seq # 3: YOR353C_Skud Reading seq # 4: YOR353C_Smik Reading seq # 5: YOR353C_Spar Sequences read.. Counting patterns.. # site patterns = 141 Counting frequencies.. 120 bytes for distance 22560 bytes for lkl0 18048 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.026458 0.037855 0.046863 0.107707 0.120377 0.149989 0.194736 0.207621 lnL0 = -1437.071200 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1437.071200 x= 0.02646 0.03786 0.04686 0.10771 0.12038 0.14999 0.19474 0.20762 1 h-lim-p 0.0030 1.2971 97.7301 1435.718824 3 0.0003 30 | 0/8 2 h-lim-p 0.0011 0.0085 11.9924 1435.674891 6 0.0006 58 | 0/8 3 h-lim-p 0.0018 0.0904 4.1195 1435.669570 4 0.0007 78 | 0/8 4 h-lim-p 0.0048 0.2951 0.5890 1435.669454 4 0.0007 102 | 0/8 5 h-lim-p 0.0022 1.5253 0.1801 1435.669442 2 0.0009 126 | 0/8 6 h-lim-p 0.0038 3.9404 0.0407 1435.669441 0 0.0008 147 | 0/8 7 h-lim-p 0.0159 20.0000 0.0021 1435.669441 0 0.0139 167 | 0/8 8 h-lim-p 0.0093 20.0000 0.0032 1435.669392 0 0.0742 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1435.669390 0 1.0938 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1435.669390 0 1.0938 230 | 0/8 11 h-lim-p 1.1240 20.0000 0.0000 1435.669390 0 0.0005 260 | 0/8 12 h-lim-p 0.0002 20.0000 0.0000 1435.669390 0 0.0000 283 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 1435.669390 0 0.0000 315 Out... lnL = -1435.669390 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1435.669390 Node 7: lnL = -1435.669390 Node 8: lnL = -1435.669390 Node 9: lnL = -1435.669390 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 873 Sequential format.. Reading seq # 1: YOR354C_Sbay Reading seq # 2: YOR354C_Scer Reading seq # 3: YOR354C_Skud Reading seq # 4: YOR354C_Smik Reading seq # 5: YOR354C_Spar Sequences read.. Counting patterns.. # site patterns = 393 Counting frequencies.. 120 bytes for distance 62880 bytes for lkl0 50304 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.007828 0.227747 0.056887 0.182955 0.127190 0.251609 0.250374 0.309780 lnL0 = -4160.690965 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4160.690965 x= 0.00783 0.22775 0.05689 0.18296 0.12719 0.25161 0.25037 0.30978 1 h-lim-p 0.0026 0.0207 111.8978 4159.083659 8 0.0003 41 | 0/8 2 h-lim-p 0.0009 0.0072 29.3891 4158.848266 7 0.0006 71 | 0/8 3 h-lim-p 0.0011 0.0268 14.6402 4158.806813 3 0.0005 89 | 0/8 4 h-lim-p 0.0023 0.0976 3.0922 4158.804102 3 0.0006 108 | 0/8 5 h-lim-p 0.0025 0.0466 0.7650 4158.803898 3 0.0007 129 | 0/8 6 h-lim-p 0.0024 1.2975 0.2274 4158.803886 0 0.0005 150 | 0/8 7 h-lim-p 0.0106 3.7036 0.0114 4158.803885 0 0.0047 170 | 0/8 8 h-lim-p 0.0323 20.0000 0.0016 4158.803608 0 0.2587 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4158.803607 0 1.0938 213 | 0/8 10 h-lim-p 1.6833 20.0000 0.0000 4158.803607 0 1.4729 233 | 0/8 11 h-lim-p 2.2085 20.0000 0.0000 4158.803607 0 0.9662 253 | 0/8 12 h-lim-p 0.4410 20.0000 0.0000 4158.803607 0 0.1103 274 | 0/8 13 h-lim-p 0.0113 20.0000 0.0004 4158.803607 0 0.0028 295 | 0/8 14 h-lim-p 0.0002 2.4554 0.0065 4158.803607 0 0.0000 318 | 0/8 15 h-lim-p 0.0003 20.0000 0.0002 4158.803607 0 0.0000 344 | 0/8 16 h-lim-p 0.0005 20.0000 0.0000 4158.803607 0 0.0000 373 Out... lnL = -4158.803607 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4158.803607 Node 7: lnL = -4158.803607 Node 8: lnL = -4158.803607 Node 9: lnL = -4158.803607 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 858 Sequential format.. Reading seq # 1: YOR355W_Sbay Reading seq # 2: YOR355W_Scer Reading seq # 3: YOR355W_Skud Reading seq # 4: YOR355W_Smik Reading seq # 5: YOR355W_Spar Sequences read.. Counting patterns.. # site patterns = 215 Counting frequencies.. 120 bytes for distance 34400 bytes for lkl0 27520 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.010890 0.071223 0.028517 0.070579 0.031759 0.093077 0.126326 0.129562 lnL0 = -3048.534707 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3048.534707 x= 0.01089 0.07122 0.02852 0.07058 0.03176 0.09308 0.12633 0.12956 1 h-lim-p 0.0001 0.0006 247.1195 3046.491150 2 0.0001 26 | 0/8 2 h-lim-p 0.0003 0.0021 51.2117 3046.330933 4 0.0001 46 | 0/8 3 h-lim-p 0.0003 0.0046 23.1399 3046.317196 4 0.0001 66 | 0/8 4 h-lim-p 0.0002 0.0050 6.3782 3046.314786 5 0.0001 90 | 0/8 5 h-lim-p 0.0015 0.2368 0.5686 3046.314748 2 0.0002 109 | 0/8 6 h-lim-p 0.0045 0.7293 0.0303 3046.314746 1 0.0006 133 | 0/8 7 h-lim-p 0.0027 11.0271 0.0063 3046.313705 0 0.0855 158 | 0/8 8 h-lim-p 0.0004 0.0575 1.3774 3046.312171 4 0.0004 188 | 0/8 9 h-lim-p 1.1185 20.0000 0.0005 3046.312157 0 0.9787 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 3046.312157 0 1.0938 220 | 0/8 11 h-lim-p 1.4745 20.0000 0.0001 3046.312157 0 1.4745 240 | 0/8 12 h-lim-p 0.7180 20.0000 0.0001 3046.312157 0 0.0049 266 | 0/8 13 h-lim-p 0.0001 2.6260 0.0064 3046.312157 0 0.0000 303 | 0/8 14 h-lim-p 0.0000 20.0000 0.0039 3046.312157 0 0.0000 336 | 0/8 15 h-lim-p 0.0000 20.0000 0.0037 3046.312157 0 0.0000 366 | 0/8 16 h-lim-p 0.0000 20.0000 0.0010 3046.312157 0 0.0013 393 | 0/8 17 h-lim-p 0.0040 20.0000 0.0003 3046.312157 0 0.0000 423 | 0/8 18 h-lim-p 0.0000 20.0000 0.0014 3046.312157 0 0.0000 447 | 0/8 19 h-lim-p 0.0000 20.0000 0.0010 .. | 0/8 20 h-lim-p 0.0000 20.0000 0.0102 | 0/8 21 h-lim-p 0.0000 20.0000 0.0102 Out... lnL = -3046.312157 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3046.312157 Node 7: lnL = -3046.312157 Node 8: lnL = -3046.312157 Node 9: lnL = -3046.312157 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 606 Sequential format.. Reading seq # 1: YOR356W_Sbay Reading seq # 2: YOR356W_Scer Reading seq # 3: YOR356W_Skud Reading seq # 4: YOR356W_Smik Reading seq # 5: YOR356W_Spar Sequences read.. Counting patterns.. # site patterns = 191 Counting frequencies.. 120 bytes for distance 30560 bytes for lkl0 24448 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.015172 0.070037 0.052730 0.094953 0.072015 0.136071 0.184686 0.176986 lnL0 = -2284.332690 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2284.332690 x= 0.01517 0.07004 0.05273 0.09495 0.07202 0.13607 0.18469 0.17699 1 h-lim-p 0.0058 1.6819 88.7848 2283.546239 8 0.0002 44 | 0/8 2 h-lim-p 0.0006 0.0050 16.1290 2283.508727 2 0.0003 60 | 0/8 3 h-lim-p 0.0011 0.0101 4.3408 2283.506486 2 0.0003 77 | 0/8 4 h-lim-p 0.0014 0.0765 0.7753 2283.506371 3 0.0004 96 | 0/8 5 h-lim-p 0.0011 1.1506 0.2738 2283.506356 1 0.0005 118 | 0/8 6 h-lim-p 0.0047 1.4005 0.0273 2283.506356 0 0.0005 140 | 0/8 7 h-lim-p 0.0066 20.0000 0.0021 2283.506355 0 0.0066 160 | 0/8 8 h-lim-p 0.0048 13.0853 0.0029 2283.506320 0 0.0581 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2283.506320 0 1.0938 203 | 0/8 10 h-lim-p 1.0531 20.0000 0.0000 2283.506320 0 1.5796 223 | 0/8 11 h-lim-p 0.1195 20.0000 0.0005 2283.506320 0 0.0002 251 | 0/8 12 h-lim-p 0.0003 20.0000 0.0004 2283.506320 0 0.0001 271 | 0/8 13 h-lim-p 0.0002 20.0000 0.0003 2283.506320 0 0.0001 291 | 0/8 14 h-lim-p 0.0000 20.0000 0.0058 2283.506320 0 0.0000 320 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 2283.506320 0 0.0000 351 Out... lnL = -2283.506320 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2283.506320 Node 7: lnL = -2283.506320 Node 8: lnL = -2283.506320 Node 9: lnL = -2283.506320 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 472 Sequential format.. Reading seq # 1: YOR357C_Sbay Reading seq # 2: YOR357C_Scer Reading seq # 3: YOR357C_Skud Reading seq # 4: YOR357C_Smik Reading seq # 5: YOR357C_Spar Sequences read.. Counting patterns.. # site patterns = 184 Counting frequencies.. 120 bytes for distance 29440 bytes for lkl0 23552 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.042648 0.073605 0.073187 0.131917 0.132350 0.216698 0.173392 0.263826 lnL0 = -2197.554168 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2197.554168 x= 0.04265 0.07361 0.07319 0.13192 0.13235 0.21670 0.17339 0.26383 1 h-lim-p 0.0023 0.0181 42.9465 2197.217772 8 0.0004 43 | 0/8 2 h-lim-p 0.0014 0.0143 11.5842 2197.181397 3 0.0006 61 | 0/8 3 h-lim-p 0.0021 0.0773 3.2516 2197.178697 3 0.0005 80 | 0/8 4 h-lim-p 0.0029 0.2656 0.6202 2197.178606 3 0.0005 101 | 0/8 5 h-lim-p 0.0040 2.1319 0.0787 2197.178604 1 0.0005 125 | 0/8 6 h-lim-p 0.0019 8.5898 0.0201 2197.178604 0 0.0008 145 | 0/8 7 h-lim-p 0.0082 20.0000 0.0021 2197.178604 0 0.0071 165 | 0/8 8 h-lim-p 0.0225 20.0000 0.0007 2197.178594 0 0.1797 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2197.178593 0 1.0938 208 | 0/8 10 h-lim-p 1.9328 20.0000 0.0000 2197.178593 0 0.8456 228 | 0/8 11 h-lim-p 0.6584 20.0000 0.0000 2197.178593 0 0.0077 254 | 0/8 12 h-lim-p 0.0023 20.0000 0.0001 2197.178593 0 0.0000 279 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 2197.178593 0 0.0000 309 | 0/8 14 h-lim-p 0.0000 20.0000 0.0008 | 0/8 15 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -2197.178593 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2197.178593 Node 7: lnL = -2197.178593 Node 8: lnL = -2197.178593 Node 9: lnL = -2197.178593 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 315 Sequential format.. Reading seq # 1: YOR359W_Sbay Reading seq # 2: YOR359W_Scer Reading seq # 3: YOR359W_Skud Reading seq # 4: YOR359W_Smik Reading seq # 5: YOR359W_Spar Sequences read.. Counting patterns.. # site patterns = 83 Counting frequencies.. 120 bytes for distance 13280 bytes for lkl0 10624 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.019269 0.019303 0.015243 0.046783 0.031487 0.115000 0.079081 0.102848 lnL0 = -1019.672767 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1019.672767 x= 0.01927 0.01930 0.01524 0.04678 0.03149 0.11500 0.07908 0.10285 1 h-lim-p 0.0005 0.0037 192.2098 1018.235293 4 0.0001 31 | 0/8 2 h-lim-p 0.0003 0.0023 30.6427 1018.140966 7 0.0002 59 | 0/8 3 h-lim-p 0.0012 0.0168 5.3427 1018.136985 4 0.0003 80 | 0/8 4 h-lim-p 0.0007 0.0692 2.0584 1018.136507 4 0.0003 103 | 0/8 5 h-lim-p 0.0010 0.1063 0.5054 1018.136470 3 0.0003 123 | 0/8 6 h-lim-p 0.0017 1.4109 0.1000 1018.136468 1 0.0003 146 | 0/8 7 h-lim-p 0.0027 4.5444 0.0124 1018.136468 0 0.0006 167 | 0/8 8 h-lim-p 0.0284 20.0000 0.0003 1018.136357 0 0.9098 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1018.136348 2 0.9644 216 | 0/8 10 h-lim-p 2.1368 20.0000 0.0000 1018.136348 0 0.5342 237 | 0/8 11 h-lim-p 0.3602 20.0000 0.0000 1018.136348 0 0.0028 263 | 0/8 12 h-lim-p 0.0015 20.0000 0.0001 1018.136348 0 0.0000 298 | 0/8 13 h-lim-p 0.0000 20.0000 0.0054 | 0/8 14 h-lim-p 0.0000 20.0000 0.0054 Out... lnL = -1018.136348 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1018.136348 Node 7: lnL = -1018.136348 Node 8: lnL = -1018.136348 Node 9: lnL = -1018.136348 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 562 Sequential format.. Reading seq # 1: YOR360C_Sbay Reading seq # 2: YOR360C_Scer Reading seq # 3: YOR360C_Skud Reading seq # 4: YOR360C_Smik Reading seq # 5: YOR360C_Spar Sequences read.. Counting patterns.. # site patterns = 163 Counting frequencies.. 120 bytes for distance 26080 bytes for lkl0 20864 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.032254 0.037101 0.043965 0.090426 0.054430 0.106251 0.116353 0.159814 lnL0 = -2140.450478 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2140.450478 x= 0.03225 0.03710 0.04397 0.09043 0.05443 0.10625 0.11635 0.15981 1 h-lim-p 0.0002 0.0014 155.6291 2138.933760 8 0.0001 39 | 0/8 2 h-lim-p 0.0007 0.0052 28.5727 2138.845759 7 0.0002 69 | 0/8 3 h-lim-p 0.0005 0.0144 12.2371 2138.835679 6 0.0002 99 | 0/8 4 h-lim-p 0.0006 0.0475 3.3844 2138.834583 4 0.0002 120 | 0/8 5 h-lim-p 0.0011 0.1280 0.6590 2138.834541 2 0.0002 137 | 0/8 6 h-lim-p 0.0013 0.9277 0.1062 2138.834540 0 0.0003 158 | 0/8 7 h-lim-p 0.0437 20.0000 0.0007 2138.834540 0 0.0048 180 | 0/8 8 h-lim-p 0.0058 20.0000 0.0006 2138.834536 0 0.0931 204 | 0/8 9 h-lim-p 1.5713 20.0000 0.0000 2138.834536 0 1.3749 224 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2138.834536 0 2.1875 244 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2138.834536 0 1.0938 264 | 0/8 12 h-lim-p 0.4012 20.0000 0.0000 2138.834536 m20.0000 287 | 0/8 13 h-lim-p 0.0073 0.5693 0.0957 2138.834536 0 0.0109 307 | 0/8 14 h-lim-p 0.0004 0.0207 2.5770 2138.834536 0 0.0000 334 | 0/8 15 h-lim-p 0.2662 20.0000 0.0000 2138.834536 0 2.1297 349 | 0/8 16 h-lim-p 1.7249 20.0000 0.0000 2138.834536 0 0.3773 370 | 0/8 17 h-lim-p 0.4535 20.0000 0.0000 2138.834536 0 0.0142 394 | 0/8 18 h-lim-p 0.0133 20.0000 0.0000 2138.834536 0 0.0000 422 | 0/8 19 h-lim-p 0.0001 20.0000 0.0000 2138.834536 0 0.0000 456 Out... lnL = -2138.834536 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2138.834536 Node 7: lnL = -2138.834536 Node 8: lnL = -2138.834536 Node 9: lnL = -2138.834536 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 374 Sequential format.. Reading seq # 1: YOR361C_Sbay Reading seq # 2: YOR361C_Scer Reading seq # 3: YOR361C_Skud Reading seq # 4: YOR361C_Smik Reading seq # 5: YOR361C_Spar Sequences read.. Counting patterns.. # site patterns = 192 Counting frequencies.. 120 bytes for distance 30720 bytes for lkl0 24576 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.052750 0.056557 0.000060 0.302177 0.215063 0.200744 0.212435 0.307575 lnL0 = -1592.963174 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1592.963174 x= 0.05275 0.05656 0.00006 0.30218 0.21506 0.20074 0.21243 0.30758 1 h-lim-p 0.0029 0.0232 75.9299 1591.472795 8 0.0004 43 | 0/8 2 h-lim-p 0.0008 0.0065 32.1165 1590.961561 0 0.0016 56 | 0/8 3 h-lim-p 0.0047 0.0373 3.4097 1590.955259 2 0.0011 73 | 0/8 4 h-lim-p 0.0025 0.4037 1.4984 1590.953737 4 0.0015 96 | 0/8 5 h-lim-p 0.0049 0.5657 0.4537 1590.953364 2 0.0021 112 | 0/8 6 h-lim-p 0.0073 1.6417 0.1322 1590.948471 0 0.0293 134 | 0/8 7 h-lim-p 0.0049 0.2887 0.7912 1590.921563 0 0.0098 155 | 0/8 8 h-lim-p 0.0027 0.0425 2.8152 1590.890272 0 0.0041 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0027 1590.888109 5 1.0700 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1590.888095 0 1.0938 216 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1590.888095 0 1.0938 236 | 0/8 12 h-lim-p 1.7696 20.0000 0.0000 1590.888095 0 0.7742 256 | 0/8 13 h-lim-p 0.5171 20.0000 0.0000 1590.888095 0 0.0081 281 | 0/8 14 h-lim-p 0.0025 20.0000 0.0000 1590.888095 0 0.0000 307 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 1590.888095 0 0.0000 334 Out... lnL = -1590.888095 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1590.888095 Node 7: lnL = -1590.888095 Node 8: lnL = -1590.888095 Node 9: lnL = -1590.888095 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 975 Sequential format.. Reading seq # 1: YOR362C_Sbay Reading seq # 2: YOR362C_Scer Reading seq # 3: YOR362C_Skud Reading seq # 4: YOR362C_Smik Reading seq # 5: YOR362C_Spar Sequences read.. Counting patterns.. # site patterns = 408 Counting frequencies.. 120 bytes for distance 65280 bytes for lkl0 52224 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.213355 0.131446 0.195824 0.174480 0.281742 0.296301 0.327681 lnL0 = -4806.359371 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4806.359371 x= 0.00006 0.21336 0.13145 0.19582 0.17448 0.28174 0.29630 0.32768 1 h-lim-p 0.0000 0.0000 77.7795 4806.340527 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0067 40.7799 4805.980809 0 0.0006 40 | 1/8 3 h-lim-p 0.0025 0.0468 10.4623 4805.946049 4 0.0007 61 | 1/8 4 h-lim-p 0.0025 0.1145 2.7866 4805.942156 5 0.0007 86 | 1/8 5 h-lim-p 0.0020 0.3449 1.0323 4805.927776 0 0.0061 99 | 1/8 6 h-lim-p 0.0107 2.4987 0.5827 4805.328444 0 0.0430 113 | 1/8 7 h-lim-p 0.0013 0.0250 18.9097 4804.347357 0 0.0026 133 | 1/8 8 h-lim-p 0.0062 0.0832 8.1331 4804.314201 5 0.0010 158 | 0/8 9 h-lim-p 0.0005 0.2179 15.7922 4804.219654 0 0.0010 171 | 0/8 10 h-lim-p 0.7253 5.8027 0.0088 4804.175085 0 1.0880 183 | 0/8 11 h-lim-p 2.5000 20.0000 0.0008 4804.174676 1 1.0938 205 | 0/8 12 h-lim-p 2.5000 20.0000 0.0001 4804.174672 0 1.0938 225 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 4804.174672 0 1.0938 245 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 4804.174672 0 1.0938 265 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 4804.174672 0 3.7500 285 | 0/8 16 h-lim-p 1.7019 20.0000 0.0000 4804.174672 0 0.0000 320 Out... lnL = -4804.174672 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4804.174672 Node 7: lnL = -4804.174672 Node 8: lnL = -4804.174672 Node 9: lnL = -4804.174672 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 169 Sequential format.. Reading seq # 1: YOR363C_Sbay Reading seq # 2: YOR363C_Scer Reading seq # 3: YOR363C_Skud Reading seq # 4: YOR363C_Smik Reading seq # 5: YOR363C_Spar Sequences read.. Counting patterns.. # site patterns = 79 Counting frequencies.. 120 bytes for distance 12640 bytes for lkl0 10112 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.015714 0.118592 0.036353 0.071807 0.075518 0.135901 0.199991 0.187861 lnL0 = -699.751556 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 699.751556 x= 0.01571 0.11859 0.03635 0.07181 0.07552 0.13590 0.19999 0.18786 1 h-lim-p 0.0002 0.0019 29.6610 699.455324 0 0.0007 23 | 0/8 2 h-lim-p 0.0014 0.0376 14.9316 699.384914 7 0.0008 51 | 0/8 3 h-lim-p 0.0018 0.0178 6.3643 699.369756 5 0.0009 73 | 0/8 4 h-lim-p 0.0015 0.0260 3.8444 699.364322 5 0.0010 98 | 0/8 5 h-lim-p 0.0053 0.5146 0.7353 699.364156 2 0.0007 116 | 0/8 6 h-lim-p 0.0024 0.8411 0.1989 699.364133 1 0.0012 138 | 0/8 7 h-lim-p 0.0138 10.3082 0.0176 699.364126 2 0.0091 164 | 0/8 8 h-lim-p 0.0263 10.1035 0.0061 699.363570 0 0.2105 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 699.363502 3 1.0004 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 699.363502 0 2.1875 233 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 699.363502 0 1.0938 253 | 0/8 12 h-lim-p 0.3692 20.0000 0.0000 699.363502 0 4.4299 276 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 699.363502 0 0.0391 301 | 0/8 14 h-lim-p 0.2759 20.0000 0.0000 699.363502 0 0.0043 326 | 0/8 15 h-lim-p 0.0004 20.0000 0.0000 699.363502 0 0.0002 346 | 0/8 16 h-lim-p 0.0002 20.0000 0.0000 699.363502 0 0.0000 384 | 0/8 17 h-lim-p 0.0000 20.0000 0.0021 | 0/8 18 h-lim-p 0.0000 20.0000 0.0021 Out... lnL = -699.363502 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -699.363502 Node 7: lnL = -699.363502 Node 8: lnL = -699.363502 Node 9: lnL = -699.363502 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 457 Sequential format.. Reading seq # 1: YOR365C_Sbay Reading seq # 2: YOR365C_Scer Reading seq # 3: YOR365C_Skud Reading seq # 4: YOR365C_Smik Reading seq # 5: YOR365C_Spar Sequences read.. Counting patterns.. # site patterns = 202 Counting frequencies.. 120 bytes for distance 32320 bytes for lkl0 25856 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.034074 0.098963 0.079394 0.173401 0.082458 0.249536 0.254959 0.286636 lnL0 = -2248.557674 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2248.557674 x= 0.03407 0.09896 0.07939 0.17340 0.08246 0.24954 0.25496 0.28664 1 h-lim-p 0.0007 0.0055 67.8472 2247.401298 4 0.0005 30 | 0/8 2 h-lim-p 0.0009 0.0071 17.9367 2247.316365 7 0.0006 60 | 0/8 3 h-lim-p 0.0010 0.0139 9.4900 2247.299870 5 0.0005 81 | 0/8 4 h-lim-p 0.0020 0.0527 2.1653 2247.297817 2 0.0009 97 | 0/8 5 h-lim-p 0.0036 0.6119 0.5676 2247.297652 4 0.0011 121 | 0/8 6 h-lim-p 0.0074 3.6577 0.0860 2247.297649 0 0.0008 143 | 0/8 7 h-lim-p 0.0135 20.0000 0.0051 2247.297649 0 0.0030 164 | 0/8 8 h-lim-p 0.1176 20.0000 0.0001 2247.297642 0 0.9411 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2247.297642 0 1.0938 207 | 0/8 10 h-lim-p 2.1714 20.0000 0.0000 2247.297642 0 1.9000 227 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2247.297642 0 1.0938 247 | 0/8 12 h-lim-p 0.2729 20.0000 0.0000 2247.297642 0 3.2745 270 | 0/8 13 h-lim-p 0.1271 20.0000 0.0004 2247.297642 0 0.0318 291 | 0/8 14 h-lim-p 0.0084 20.0000 0.0014 2247.297642 0 0.0000 332 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 2247.297642 0 0.0000 356 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 2247.297642 0 0.0000 376 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0004 2247.297642 0 0.0000 440 | 0/8 19 h-lim-p 0.0000 20.0000 0.0004 | 0/8 20 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -2247.297642 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2247.297642 Node 7: lnL = -2247.297642 Node 8: lnL = -2247.297642 Node 9: lnL = -2247.297642 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 424 Sequential format.. Reading seq # 1: YOR367W_Sbay Reading seq # 2: YOR367W_Scer Reading seq # 3: YOR367W_Skud Reading seq # 4: YOR367W_Smik Reading seq # 5: YOR367W_Spar Sequences read.. Counting patterns.. # site patterns = 194 Counting frequencies.. 120 bytes for distance 31040 bytes for lkl0 24832 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.012161 0.159918 0.057549 0.174323 0.096104 0.264944 0.227968 0.268830 lnL0 = -2065.583191 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2065.583191 x= 0.01216 0.15992 0.05755 0.17432 0.09610 0.26494 0.22797 0.26883 1 h-lim-p 0.0035 0.0280 59.8614 2064.739587 9 0.0005 49 | 0/8 2 h-lim-p 0.0008 0.0066 19.9688 2064.613551 3 0.0007 67 | 0/8 3 h-lim-p 0.0012 0.0099 9.3308 2064.589436 7 0.0007 95 | 0/8 4 h-lim-p 0.0031 0.0801 2.0227 2064.587460 4 0.0010 116 | 0/8 5 h-lim-p 0.0058 0.8695 0.3596 2064.587390 2 0.0011 133 | 0/8 6 h-lim-p 0.0055 0.4692 0.0729 2064.587388 1 0.0007 157 | 0/8 7 h-lim-p 0.0046 20.0000 0.0107 2064.587388 0 0.0040 177 | 0/8 8 h-lim-p 0.0792 20.0000 0.0005 2064.587319 0 0.6336 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2064.587311 1 0.9961 222 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2064.587311 0 1.0938 242 | 0/8 11 h-lim-p 1.0058 20.0000 0.0000 2064.587311 0 0.0314 266 | 0/8 12 h-lim-p 0.0003 8.1695 0.0022 2064.587311 0 0.0000 292 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 2064.587311 0 0.0000 325 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -2064.587311 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2064.587311 Node 7: lnL = -2064.587311 Node 8: lnL = -2064.587311 Node 9: lnL = -2064.587311 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 258 Sequential format.. Reading seq # 1: YOR368W_Sbay Reading seq # 2: YOR368W_Scer Reading seq # 3: YOR368W_Skud Reading seq # 4: YOR368W_Smik Reading seq # 5: YOR368W_Spar Sequences read.. Counting patterns.. # site patterns = 126 Counting frequencies.. 120 bytes for distance 20160 bytes for lkl0 16128 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.068322 0.074265 0.050581 0.118710 0.085854 0.289179 0.234555 0.310786 lnL0 = -1201.611012 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1201.611012 x= 0.06832 0.07427 0.05058 0.11871 0.08585 0.28918 0.23456 0.31079 1 h-lim-p 0.0142 0.1139 20.9336 1201.458578 6 0.0007 36 | 0/8 2 h-lim-p 0.0016 0.0169 9.1724 1201.420091 6 0.0011 62 | 0/8 3 h-lim-p 0.0020 0.0261 4.7456 1201.410796 6 0.0011 89 | 0/8 4 h-lim-p 0.0026 0.0975 1.9315 1201.409334 4 0.0010 110 | 0/8 5 h-lim-p 0.0050 0.3901 0.3676 1201.409261 2 0.0012 127 | 0/8 6 h-lim-p 0.0705 20.0000 0.0061 1201.409261 0 0.0039 150 | 0/8 7 h-lim-p 0.0209 20.0000 0.0011 1201.409261 0 0.0209 170 | 0/8 8 h-lim-p 0.0148 20.0000 0.0016 1201.409256 0 0.0886 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1201.409256 0 1.0938 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1201.409256 0 1.0938 232 | 0/8 11 h-lim-p 1.1145 20.0000 0.0000 1201.409256 0 0.1393 254 | 0/8 12 h-lim-p 0.0194 20.0000 0.0000 1201.409256 0 0.0194 274 | 0/8 13 h-lim-p 0.0073 20.0000 0.0001 1201.409256 0 0.0073 294 | 0/8 14 h-lim-p 0.0038 20.0000 0.0002 1201.409256 0 0.0000 320 | 0/8 15 h-lim-p 0.0004 20.0000 0.0000 1201.409256 0 0.0002 340 | 0/8 16 h-lim-p 0.0004 20.0000 0.0000 1201.409256 0 0.0004 360 Out... lnL = -1201.409256 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1201.409256 Node 7: lnL = -1201.409256 Node 8: lnL = -1201.409256 Node 9: lnL = -1201.409256 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 627 Sequential format.. Reading seq # 1: YOR369C_Sbay Reading seq # 2: YOR369C_Scer Reading seq # 3: YOR369C_Skud Reading seq # 4: YOR369C_Smik Reading seq # 5: YOR369C_Spar Sequences read.. Counting patterns.. # site patterns = 238 Counting frequencies.. 120 bytes for distance 38080 bytes for lkl0 30464 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.029329 0.043193 0.067043 0.101263 0.068269 0.201572 0.220734 0.217328 lnL0 = -2738.862198 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2738.862198 x= 0.02933 0.04319 0.06704 0.10126 0.06827 0.20157 0.22073 0.21733 1 h-lim-p 0.0003 0.0024 165.6431 2736.275930 9 0.0002 46 | 0/8 2 h-lim-p 0.0004 0.0034 26.0602 2736.186578 7 0.0003 77 | 0/8 3 h-lim-p 0.0005 0.0209 14.7413 2736.159986 6 0.0003 102 | 0/8 4 h-lim-p 0.0008 0.0350 5.7331 2736.154809 2 0.0004 118 | 0/8 5 h-lim-p 0.0031 0.2208 0.7020 2736.154704 3 0.0005 139 | 0/8 6 h-lim-p 0.0015 0.9372 0.2115 2736.154694 2 0.0005 164 | 0/8 7 h-lim-p 0.0038 7.2073 0.0266 2736.154694 0 0.0008 185 | 0/8 8 h-lim-p 0.1330 20.0000 0.0002 2736.154628 0 1.0640 208 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2736.154628 0 1.0938 228 | 0/8 10 h-lim-p 1.9455 20.0000 0.0000 2736.154628 0 1.7023 248 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2736.154628 0 1.0938 268 | 0/8 12 h-lim-p 0.4055 20.0000 0.0000 2736.154628 0 0.0095 293 | 0/8 13 h-lim-p 0.0004 20.0000 0.0008 2736.154628 0 0.0000 330 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 2736.154628 0 0.0000 365 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -2736.154628 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2736.154628 Node 7: lnL = -2736.154628 Node 8: lnL = -2736.154628 Node 9: lnL = -2736.154628 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 530 Sequential format.. Reading seq # 1: YOR370C_Sbay Reading seq # 2: YOR370C_Scer Reading seq # 3: YOR370C_Skud Reading seq # 4: YOR370C_Smik Reading seq # 5: YOR370C_Spar Sequences read.. Counting patterns.. # site patterns = 172 Counting frequencies.. 120 bytes for distance 27520 bytes for lkl0 22016 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.031177 0.054267 0.065823 0.061190 0.079018 0.145682 0.131897 0.183325 lnL0 = -2071.177799 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2071.177799 x= 0.03118 0.05427 0.06582 0.06119 0.07902 0.14568 0.13190 0.18333 1 h-lim-p 0.0017 0.0137 95.5256 2070.241655 6 0.0002 37 | 0/8 2 h-lim-p 0.0005 0.0044 22.2898 2070.172628 6 0.0003 62 | 0/8 3 h-lim-p 0.0005 0.0151 11.6800 2070.158241 2 0.0003 78 | 0/8 4 h-lim-p 0.0017 0.0680 1.7604 2070.157806 4 0.0003 102 | 0/8 5 h-lim-p 0.0020 0.4359 0.2504 2070.157794 2 0.0004 119 | 0/8 6 h-lim-p 0.0035 6.6426 0.0284 2070.157794 0 0.0004 141 | 0/8 7 h-lim-p 0.0062 20.0000 0.0020 2070.157794 0 0.0055 161 | 0/8 8 h-lim-p 0.0074 20.0000 0.0015 2070.157769 0 0.0883 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2070.157768 0 1.0938 204 | 0/8 10 h-lim-p 0.5520 20.0000 0.0000 2070.157768 0 0.4830 224 | 0/8 11 h-lim-p 0.2240 20.0000 0.0001 2070.157768 0 0.0061 248 | 0/8 12 h-lim-p 0.0024 20.0000 0.0001 2070.157768 0 0.0000 290 | 0/8 13 h-lim-p 0.0000 20.0000 0.0016 | 0/8 14 h-lim-p 0.0000 20.0000 0.0016 Out... lnL = -2070.157768 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2070.157768 Node 7: lnL = -2070.157768 Node 8: lnL = -2070.157768 Node 9: lnL = -2070.157768 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 652 Sequential format.. Reading seq # 1: YOR371C_Sbay Reading seq # 2: YOR371C_Scer Reading seq # 3: YOR371C_Skud Reading seq # 4: YOR371C_Smik Reading seq # 5: YOR371C_Spar Sequences read.. Counting patterns.. # site patterns = 140 Counting frequencies.. 120 bytes for distance 22400 bytes for lkl0 17920 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.117065 0.295364 0.216869 0.220567 0.476864 3.415617 0.677189 lnL0 = -2525.315484 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2525.315484 x= 0.00006 0.11707 0.29536 0.21687 0.22057 0.47686 3.41562 0.67719 1 h-lim-p 0.0000 0.0000 637.2418 2525.072547 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0002 1375.9307 2370.067433 m 0.0002 36 | 2/8 3 h-lim-p 0.0011 0.0087 77.0220 2360.690409 0 0.0022 49 | 2/8 4 h-lim-p 0.0022 0.0179 11.5687 2357.112194 0 0.0090 63 | 2/8 5 h-lim-p 0.0037 0.0298 9.1207 2306.954090 0 0.0223 77 | 1/8 6 h-lim-p 0.0003 0.0023 143.1423 2293.374588 0 0.0009 90 | 1/8 7 h-lim-p 0.0001 0.0010 51.4281 2291.968693 m 0.0010 102 | 2/8 8 h-lim-p 0.1139 0.9110 0.2290 2291.712869 7 0.0821 130 | 2/8 9 h-lim-p 0.3755 3.1922 0.0500 2291.683628 5 0.0810 158 | 2/8 10 h-lim-p 0.8649 20.0000 0.0047 2291.649392 1 1.0811 178 | 2/8 11 h-lim-p 0.5797 20.0000 0.0087 2291.640749 5 0.3057 207 | 2/8 12 h-lim-p 0.6301 20.0000 0.0042 2291.635838 5 0.4412 237 | 1/8 13 h-lim-p 0.0166 16.7749 0.1130 2291.635832 0 0.0010 258 | 1/8 14 h-lim-p 0.1986 1.5890 0.0001 2291.635827 0 0.7945 279 | 0/8 15 h-lim-p 0.0010 0.0083 0.0381 2291.635826 0 0.0009 298 | 0/8 16 h-lim-p 0.0341 0.2726 0.0002 2291.635826 0 0.1363 320 | 0/8 17 h-lim-p 0.0014 0.0115 0.0029 2291.635826 0 0.0000 349 | 0/8 18 h-lim-p 0.0000 0.0012 0.0285 .. | 0/8 19 h-lim-p 0.0000 0.0003 0.1105 2291.635826 0 0.0000 403 | 0/8 20 h-lim-p 0.0000 0.0002 0.2395 2291.635826 0 0.0000 434 | 0/8 21 h-lim-p 0.0000 0.0000 21.7715 .. | 0/8 22 h-lim-p 0.0000 0.0407 0.0204 | 0/8 23 h-lim-p 0.0000 0.0003 0.1079 2291.635826 0 0.0000 519 | 0/8 24 h-lim-p 0.0000 0.0002 0.2431 .. | 0/8 25 h-lim-p 0.0000 0.0003 0.1079 Out... lnL = -2291.635826 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2291.635826 Node 7: lnL = -2291.635826 Node 8: lnL = -2291.635826 Node 9: lnL = -2291.635826 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 384 Sequential format.. Reading seq # 1: YOR372C_Sbay Reading seq # 2: YOR372C_Scer Reading seq # 3: YOR372C_Skud Reading seq # 4: YOR372C_Smik Reading seq # 5: YOR372C_Spar Sequences read.. Counting patterns.. # site patterns = 148 Counting frequencies.. 120 bytes for distance 23680 bytes for lkl0 18944 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.074745 0.024351 0.044309 0.097886 0.072657 0.167296 0.122380 0.231810 lnL0 = -1527.013830 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1527.013830 x= 0.07475 0.02435 0.04431 0.09789 0.07266 0.16730 0.12238 0.23181 1 h-lim-p 0.0020 0.0156 97.1926 1525.862855 8 0.0003 43 | 0/8 2 h-lim-p 0.0003 0.0026 41.4682 1525.513542 0 0.0005 55 | 0/8 3 h-lim-p 0.0010 0.0079 19.6525 1525.467691 7 0.0003 86 | 0/8 4 h-lim-p 0.0035 0.0761 1.6597 1525.467061 4 0.0005 108 | 0/8 5 h-lim-p 0.0011 0.4486 0.6708 1525.466958 2 0.0005 124 | 0/8 6 h-lim-p 0.0012 0.4118 0.2758 1525.466945 2 0.0004 150 | 0/8 7 h-lim-p 0.0100 19.1283 0.0111 1525.466886 0 0.0299 171 | 0/8 8 h-lim-p 0.0080 9.9349 0.0413 1525.465107 0 0.0322 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 1525.464954 2 1.0938 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1525.464951 0 1.2500 237 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1525.464951 0 1.0938 257 | 0/8 12 h-lim-p 1.1515 20.0000 0.0000 1525.464951 0 1.0075 277 | 0/8 13 h-lim-p 0.0932 20.0000 0.0001 1525.464951 0 0.0007 303 | 0/8 14 h-lim-p 0.0000 20.0000 0.0037 1525.464951 0 0.0000 335 | 0/8 15 h-lim-p 0.0004 20.0000 0.0000 1525.464951 0 0.0000 368 Out... lnL = -1525.464951 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1525.464951 Node 7: lnL = -1525.464951 Node 8: lnL = -1525.464951 Node 9: lnL = -1525.464951 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 486 Sequential format.. Reading seq # 1: YOR374W_Sbay Reading seq # 2: YOR374W_Scer Reading seq # 3: YOR374W_Skud Reading seq # 4: YOR374W_Smik Reading seq # 5: YOR374W_Spar Sequences read.. Counting patterns.. # site patterns = 162 Counting frequencies.. 120 bytes for distance 25920 bytes for lkl0 20736 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.072177 0.044134 0.040002 0.050571 0.047970 0.127946 0.117728 0.207661 lnL0 = -1820.263107 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1820.263107 x= 0.07218 0.04413 0.04000 0.05057 0.04797 0.12795 0.11773 0.20766 1 h-lim-p 0.0003 0.0025 65.2365 1819.923939 5 0.0002 33 | 0/8 2 h-lim-p 0.0007 0.0070 15.6262 1819.891528 6 0.0003 56 | 0/8 3 h-lim-p 0.0005 0.0351 9.2367 1819.885358 3 0.0002 74 | 0/8 4 h-lim-p 0.0006 0.0383 2.9922 1819.884564 4 0.0002 95 | 0/8 5 h-lim-p 0.0009 0.1433 0.7128 1819.884510 3 0.0002 114 | 0/8 6 h-lim-p 0.0006 0.7989 0.2504 1819.884500 2 0.0003 139 | 0/8 7 h-lim-p 0.0073 9.2272 0.0118 1819.884500 0 0.0008 161 | 0/8 8 h-lim-p 0.0671 20.0000 0.0001 1819.884467 0 0.8052 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1819.884467 0 1.0938 204 | 0/8 10 h-lim-p 1.8810 20.0000 0.0000 1819.884467 0 1.8810 224 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1819.884467 0 0.1367 247 | 0/8 12 h-lim-p 0.0305 20.0000 0.0000 1819.884467 0 0.0076 268 | 0/8 13 h-lim-p 0.0040 20.0000 0.0000 1819.884467 0 0.0000 297 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 1819.884467 0 0.0000 320 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 1819.884467 0 0.0000 341 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0042 1819.884467 0 0.0000 404 | 0/8 18 h-lim-p 0.0000 20.0000 0.0008 1819.884467 0 0.0006 430 | 0/8 19 h-lim-p 0.0011 20.0000 0.0005 1819.884467 0 0.0000 465 | 0/8 20 h-lim-p 0.0000 20.0000 0.0002 .. | 0/8 21 h-lim-p 0.0000 20.0000 0.0049 1819.884467 0 0.0000 525 | 0/8 22 h-lim-p 0.0000 20.0000 0.0007 1819.884467 0 0.0003 550 | 0/8 23 h-lim-p 0.0008 20.0000 0.0003 1819.884467 0 0.0011 570 | 0/8 24 h-lim-p 0.0034 20.0000 0.0001 1819.884467 0 0.0000 597 | 0/8 25 h-lim-p 0.0000 20.0000 0.0001 1819.884467 0 0.0000 617 | 0/8 26 h-lim-p 0.0000 20.0000 0.0005 .. | 0/8 27 h-lim-p 0.0000 20.0000 0.0050 | 0/8 28 h-lim-p 0.0000 20.0000 0.0050 Out... lnL = -1819.884467 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1819.884467 Node 7: lnL = -1819.884467 Node 8: lnL = -1819.884467 Node 9: lnL = -1819.884467 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 161 Sequential format.. Reading seq # 1: YOR375C_Sbay Reading seq # 2: YOR375C_Scer Reading seq # 3: YOR375C_Skud Reading seq # 4: YOR375C_Smik Reading seq # 5: YOR375C_Spar Sequences read.. Counting patterns.. # site patterns = 91 Counting frequencies.. 120 bytes for distance 14560 bytes for lkl0 11648 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.121737 0.000060 0.138410 0.189892 0.128636 0.294064 0.179550 0.355999 lnL0 = -775.226790 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 775.226790 x= 0.12174 0.00006 0.13841 0.18989 0.12864 0.29406 0.17955 0.35600 1 h-lim-p 0.0006 0.0046 53.9155 772.501335 0 0.0023 24 | 0/8 2 h-lim-p 0.0007 0.0058 22.8964 772.245101 0 0.0015 37 | 0/8 3 h-lim-p 0.0032 0.0253 7.5344 772.187005 7 0.0023 66 | 0/8 4 h-lim-p 0.0174 0.2413 0.9824 772.183339 2 0.0041 83 | 0/8 5 h-lim-p 0.0230 0.4011 0.1741 772.092967 0 0.1378 105 | 0/8 6 h-lim-p 0.0067 0.0538 3.1207 771.934235 0 0.0101 125 | 0/8 7 h-lim-p 0.0024 0.0278 13.0019 771.867595 2 0.0011 141 | 0/8 8 h-lim-p 0.0104 0.1486 1.4194 771.864410 6 0.0032 170 | 0/8 9 h-lim-p 0.9108 20.0000 0.0049 771.860292 4 0.8992 190 | 0/8 10 h-lim-p 2.5000 20.0000 0.0004 771.860257 3 1.0004 216 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 771.860257 0 1.0938 236 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 771.860257 0 1.0938 256 | 0/8 13 h-lim-p 1.6182 20.0000 0.0000 771.860257 0 3.2365 277 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 771.860257 0 0.0293 303 | 0/8 15 h-lim-p 0.0263 20.0000 0.0000 771.860257 0 0.0000 344 Out... lnL = -771.860257 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -771.860257 Node 7: lnL = -771.860257 Node 8: lnL = -771.860257 Node 9: lnL = -771.860257 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 863 Sequential format.. Reading seq # 1: YOR377W_Sbay Reading seq # 2: YOR377W_Scer Reading seq # 3: YOR377W_Skud Reading seq # 4: YOR377W_Smik Reading seq # 5: YOR377W_Spar Sequences read.. Counting patterns.. # site patterns = 440 Counting frequencies.. 120 bytes for distance 70400 bytes for lkl0 56320 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.076505 0.159940 0.073371 0.117375 0.317950 0.299731 0.274714 0.409886 lnL0 = -4288.910088 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4288.910088 x= 0.07651 0.15994 0.07337 0.11737 0.31795 0.29973 0.27471 0.40989 1 h-lim-p 0.0002 0.0013 110.1665 4283.701603 0 0.0010 24 | 0/8 2 h-lim-p 0.0005 0.0039 47.8564 4283.056803 0 0.0007 36 | 0/8 3 h-lim-p 0.0017 0.0265 21.1228 4283.004620 6 0.0003 66 | 0/8 4 h-lim-p 0.0010 0.0139 6.0612 4282.994263 5 0.0006 92 | 0/8 5 h-lim-p 0.0023 0.3306 1.5912 4282.992165 4 0.0015 114 | 0/8 6 h-lim-p 0.0107 2.1817 0.2292 4282.989975 4 0.0092 133 | 0/8 7 h-lim-p 0.0103 1.9018 0.2040 4282.833393 0 0.0827 156 | 0/8 8 h-lim-p 0.0053 0.0420 2.6502 4282.829629 4 0.0010 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 4282.829263 2 0.9961 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4282.829261 0 1.0938 221 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4282.829261 0 1.0938 241 | 0/8 12 h-lim-p 1.2196 20.0000 0.0000 4282.829261 0 1.2196 261 | 0/8 13 h-lim-p 0.6614 20.0000 0.0000 4282.829261 0 0.5787 281 | 0/8 14 h-lim-p 0.0229 20.0000 0.0005 4282.829261 0 0.0002 307 | 0/8 15 h-lim-p 0.0001 20.0000 0.0008 4282.829261 0 0.0001 327 | 0/8 16 h-lim-p 0.0000 20.0000 0.0020 4282.829261 0 0.0000 364 | 0/8 17 h-lim-p 0.0000 20.0000 0.0003 4282.829261 0 0.0000 387 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0003 | 0/8 20 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -4282.829261 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4282.829261 Node 7: lnL = -4282.829261 Node 8: lnL = -4282.829261 Node 9: lnL = -4282.829261 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 837 Sequential format.. Reading seq # 1: YOR378W_Sbay Reading seq # 2: YOR378W_Scer Reading seq # 3: YOR378W_Skud Reading seq # 4: YOR378W_Smik Reading seq # 5: YOR378W_Spar Sequences read.. Counting patterns.. # site patterns = 181 Counting frequencies.. 120 bytes for distance 28960 bytes for lkl0 23168 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.086366 0.041957 0.112749 0.061399 0.125659 0.000060 0.204270 0.257406 lnL0 = -3195.870888 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3195.870888 x= 0.08637 0.04196 0.11275 0.06140 0.12566 0.00006 0.20427 0.25741 1 h-lim-p 0.0000 0.0000 342.6263 3195.318051 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0006 232.9616 3191.167707 0 0.0002 38 | 1/8 3 h-lim-p 0.0004 0.0029 45.3207 3190.809243 4 0.0004 58 | 1/8 4 h-lim-p 0.0003 0.0034 52.0299 3190.180688 0 0.0009 71 | 1/8 5 h-lim-p 0.0002 0.0015 60.1178 3188.940329 m 0.0015 83 | 1/8 6 h-lim-p 0.0000 0.0000 13.7129 h-lim-p: 7.59693963e-20 6.07755170e-19 1.37129259e+01 3188.940329 .. | 1/8 7 h-lim-p 0.0000 0.0035 352.8008 3181.943570 0 0.0002 107 | 1/8 8 h-lim-p 0.0001 0.0010 93.4240 3181.234272 0 0.0002 120 | 1/8 9 h-lim-p 0.0002 0.0018 10.0522 3181.201990 0 0.0009 134 | 1/8 10 h-lim-p 0.0001 0.0007 7.4718 3181.178300 m 0.0007 146 | 2/8 11 h-lim-p 0.0000 0.0000 1489379.3788 3181.178223 2 0.0000 167 | 2/8 12 h-lim-p 0.0002 0.1001 1.2757 3181.090302 0 0.0054 183 | 2/8 13 h-lim-p 0.7172 20.0000 0.0096 3180.936473 1 0.8965 197 | 2/8 14 h-lim-p 2.5000 20.0000 0.0007 3180.935448 3 0.9961 221 | 2/8 15 h-lim-p 2.5000 20.0000 0.0001 3180.935445 1 0.6152 242 | 2/8 16 h-lim-p 2.2726 20.0000 0.0000 3180.935445 0 0.0000 290 | 2/8 17 h-lim-p 0.0000 0.2498 1.9289 3180.934768 0 0.0003 313 | 2/8 18 h-lim-p 0.0014 0.4939 0.4527 3180.934720 2 0.0005 329 | 2/8 19 h-lim-p 0.0013 1.0937 0.1806 3180.934715 0 0.0003 348 | 2/8 20 h-lim-p 0.0028 8.1914 0.0213 3180.934715 0 0.0006 367 | 2/8 21 h-lim-p 0.0007 7.1963 0.0188 3180.934715 0 0.0003 385 | 2/8 22 h-lim-p 0.0421 20.0000 0.0001 3180.934702 0 1.0102 407 | 2/8 23 h-lim-p 2.5000 20.0000 0.0000 3180.934702 0 1.0938 425 | 2/8 24 h-lim-p 2.5000 20.0000 0.0000 3180.934702 0 1.0938 443 | 2/8 25 h-lim-p 0.9663 20.0000 0.0000 3180.934702 0 1.9326 462 | 2/8 26 h-lim-p 0.1589 20.0000 0.0002 3180.934702 0 0.0000 504 | 2/8 27 h-lim-p 0.0000 20.0000 0.0002 | 2/8 28 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -3180.934702 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3180.934702 Node 7: lnL = -3180.934702 Node 8: lnL = -3180.934702 Node 9: lnL = -3180.934702 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 238 Sequential format.. Reading seq # 1: YOR380W_Sbay Reading seq # 2: YOR380W_Scer Reading seq # 3: YOR380W_Skud Reading seq # 4: YOR380W_Smik Reading seq # 5: YOR380W_Spar Sequences read.. Counting patterns.. # site patterns = 111 Counting frequencies.. 120 bytes for distance 17760 bytes for lkl0 14208 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.118203 0.000060 0.190865 0.135469 0.136419 0.425663 0.123570 0.346724 lnL0 = -1142.884682 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1142.884682 x= 0.11820 0.00006 0.19086 0.13547 0.13642 0.42566 0.12357 0.34672 1 h-lim-p 0.0000 0.0000 113.4588 1142.834747 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0061 43.0367 1141.297422 0 0.0019 41 | 1/8 3 h-lim-p 0.0246 0.2379 3.3632 1141.233370 4 0.0047 62 | 1/8 4 h-lim-p 0.0023 0.0479 6.8958 1141.118255 0 0.0035 74 | 1/8 5 h-lim-p 0.0080 0.0720 2.9988 1139.876985 0 0.0320 88 | 1/8 6 h-lim-p 0.0034 0.0272 8.5805 1136.067882 0 0.0136 102 | 0/8 7 h-lim-p 0.0009 0.0071 35.3099 1135.467452 1 0.0011 116 | 0/8 8 h-lim-p 0.0001 0.0011 28.8665 1135.236757 0 0.0008 130 | 0/8 9 h-lim-p 0.3953 3.1620 0.0440 1134.643253 0 0.7905 143 | 0/8 10 h-lim-p 0.0838 0.6701 0.0242 1134.545585 m 0.6701 163 | 1/8 11 h-lim-p 2.5000 20.0000 0.0059 1134.519098 5 1.0583 196 | 1/8 12 h-lim-p 2.5000 20.0000 0.0023 1134.518019 5 0.7228 229 | 1/8 13 h-lim-p 1.5789 20.0000 0.0011 1134.517684 3 0.8486 255 | 1/8 14 h-lim-p 2.5000 20.0000 0.0001 1134.517683 1 0.9961 276 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 1134.517683 0 1.0938 295 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 1134.517683 0 1.0938 314 | 1/8 17 h-lim-p 0.8941 20.0000 0.0000 1134.517683 0 0.0419 337 | 1/8 18 h-lim-p 0.0005 20.0000 0.0005 1134.517683 0 0.0000 370 | 1/8 19 h-lim-p 0.0000 20.0000 0.0000 | 1/8 20 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1134.517683 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1134.517683 Node 7: lnL = -1134.517683 Node 8: lnL = -1134.517683 Node 9: lnL = -1134.517683 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 543 Sequential format.. Reading seq # 1: YOR383C_Sbay Reading seq # 2: YOR383C_Scer Reading seq # 3: YOR383C_Skud Reading seq # 4: YOR383C_Smik Reading seq # 5: YOR383C_Spar Sequences read.. Counting patterns.. # site patterns = 207 Counting frequencies.. 120 bytes for distance 33120 bytes for lkl0 26496 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.018956 0.139733 0.070965 0.070948 0.880693 0.092622 0.270532 lnL0 = -2310.428359 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2310.428359 x= 0.00006 0.01896 0.13973 0.07096 0.07095 0.88069 0.09262 0.27053 1 h-lim-p 0.0000 0.0000 264.8713 2310.320713 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0048 70.7677 2308.302007 0 0.0010 40 | 1/8 3 h-lim-p 0.0002 0.0019 77.9361 2307.397103 0 0.0005 53 | 1/8 4 h-lim-p 0.0007 0.0058 36.2374 2306.846174 0 0.0014 66 | 1/8 5 h-lim-p 0.0012 0.0094 18.7065 2306.720774 5 0.0009 88 | 1/8 6 h-lim-p 0.0011 0.0338 16.1675 2306.417368 0 0.0043 102 | 1/8 7 h-lim-p 0.0048 0.0382 2.5527 2306.389088 3 0.0020 120 | 1/8 8 h-lim-p 0.0116 0.2633 0.4402 2300.098482 0 0.0926 135 | 1/8 9 h-lim-p 0.3132 2.5059 0.0360 2299.631190 0 0.6265 155 | 1/8 10 h-lim-p 1.7167 20.0000 0.0131 2299.615097 2 0.8047 178 | 1/8 11 h-lim-p 2.5000 20.0000 0.0035 2299.614178 4 0.4822 206 | 0/8 12 h-lim-p 0.0246 20.0000 0.0679 2299.614176 0 0.0007 229 | 0/8 13 h-lim-p 0.0529 1.3427 0.0009 2299.614113 2 0.6515 258 | 0/8 14 h-lim-p 0.0533 0.4260 0.0003 2299.614106 m 0.4260 278 | 1/8 15 h-lim-p 2.2637 20.0000 0.0001 2299.614106 0 0.9904 298 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 2299.614106 0 1.0938 317 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 2299.614106 0 2.1875 336 | 1/8 18 h-lim-p 1.9919 20.0000 0.0000 2299.614106 0 0.8714 355 | 1/8 19 h-lim-p 2.5000 20.0000 0.0000 2299.614106 0 0.0049 382 Out... lnL = -2299.614106 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2299.614106 Node 7: lnL = -2299.614106 Node 8: lnL = -2299.614106 Node 9: lnL = -2299.614106 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 526 Sequential format.. Reading seq # 1: YOR384W_Sbay Reading seq # 2: YOR384W_Scer Reading seq # 3: YOR384W_Skud Reading seq # 4: YOR384W_Smik Reading seq # 5: YOR384W_Spar Sequences read.. Counting patterns.. # site patterns = 182 Counting frequencies.. 120 bytes for distance 29120 bytes for lkl0 23296 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.028614 0.107498 0.064383 0.064192 0.862271 0.103697 0.263463 lnL0 = -2163.542462 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2163.542462 x= 0.00006 0.02861 0.10750 0.06438 0.06419 0.86227 0.10370 0.26346 1 h-lim-p 0.0000 0.0000 251.2056 2163.182896 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0020 58.8163 2162.482503 0 0.0004 38 | 1/8 3 h-lim-p 0.0005 0.0040 36.7513 2161.757525 0 0.0015 51 | 1/8 4 h-lim-p 0.0028 0.0224 18.1898 2161.657319 8 0.0008 83 | 1/8 5 h-lim-p 0.0005 0.0081 27.1983 2161.548222 0 0.0008 95 | 1/8 6 h-lim-p 0.0015 0.0245 14.4804 2161.424389 0 0.0029 108 | 1/8 7 h-lim-p 0.0039 0.0309 8.2758 2161.363999 6 0.0020 132 | 1/8 8 h-lim-p 0.1114 0.8911 0.0931 2157.162677 0 0.4456 146 | 1/8 9 h-lim-p 1.0460 8.3682 0.0226 2156.792510 7 0.5215 180 | 0/8 10 h-lim-p 0.0302 20.0000 0.3913 2156.792260 2 0.0019 206 | 0/8 11 h-lim-p 0.0393 0.5784 0.0186 2156.763521 4 0.2861 237 | 0/8 12 h-lim-p 1.3827 20.0000 0.0039 2156.762065 5 0.7995 271 | 0/8 13 h-lim-p 2.5000 20.0000 0.0007 2156.762016 3 0.8059 299 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 2156.762015 0 1.0938 319 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2156.762015 0 1.0938 339 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 2156.762015 0 2.1875 359 | 0/8 17 h-lim-p 1.8597 20.0000 0.0000 2156.762015 0 0.1162 382 | 0/8 18 h-lim-p 0.1313 20.0000 0.0000 2156.762015 0 0.0328 403 | 0/8 19 h-lim-p 0.0338 20.0000 0.0000 2156.762015 0 0.0169 423 | 0/8 20 h-lim-p 0.0171 20.0000 0.0000 2156.762015 0 0.0000 465 Out... lnL = -2156.762015 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2156.762015 Node 7: lnL = -2156.762015 Node 8: lnL = -2156.762015 Node 9: lnL = -2156.762015 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 886 Sequential format.. Reading seq # 1: YOR385W_Sbay Reading seq # 2: YOR385W_Scer Reading seq # 3: YOR385W_Skud Reading seq # 4: YOR385W_Smik Reading seq # 5: YOR385W_Spar Sequences read.. Counting patterns.. # site patterns = 415 Counting frequencies.. 120 bytes for distance 66400 bytes for lkl0 53120 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.151728 0.000060 0.226077 0.175128 0.146817 0.589278 0.262441 0.509035 lnL0 = -4557.709303 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4557.709303 x= 0.15173 0.00006 0.22608 0.17513 0.14682 0.58928 0.26244 0.50904 1 h-lim-p 0.0001 0.0011 168.3167 4553.068874 0 0.0003 23 | 0/8 2 h-lim-p 0.0008 0.0061 58.2154 4551.666100 0 0.0011 35 | 0/8 3 h-lim-p 0.0007 0.0055 38.2210 4551.385092 7 0.0005 61 | 0/8 4 h-lim-p 0.0016 0.0251 12.4512 4551.344641 4 0.0006 81 | 0/8 5 h-lim-p 0.0016 0.1171 4.7626 4551.330760 4 0.0014 100 | 0/8 6 h-lim-p 0.0052 0.3219 1.3200 4551.329446 4 0.0015 123 | 0/8 7 h-lim-p 0.0070 0.2782 0.2864 4551.329020 3 0.0041 144 | 0/8 8 h-lim-p 0.0422 2.7116 0.0280 4551.270815 0 0.3373 167 | 0/8 9 h-lim-p 2.5000 20.0000 0.0015 4551.269999 4 0.8479 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 4551.269994 0 1.0938 218 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4551.269994 0 1.0938 238 | 0/8 12 h-lim-p 1.8141 20.0000 0.0000 4551.269994 0 1.5874 258 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 4551.269994 0 1.0938 278 | 0/8 14 h-lim-p 0.4898 20.0000 0.0000 4551.269994 0 0.2449 298 | 0/8 15 h-lim-p 0.0019 20.0000 0.0015 4551.269994 0 0.0000 335 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 4551.269994 0 0.0001 355 Out... lnL = -4551.269994 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4551.269994 Node 7: lnL = -4551.269994 Node 8: lnL = -4551.269994 Node 9: lnL = -4551.269994 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 925 Sequential format.. Reading seq # 1: YOR386W_Sbay Reading seq # 2: YOR386W_Scer Reading seq # 3: YOR386W_Skud Reading seq # 4: YOR386W_Smik Reading seq # 5: YOR386W_Spar Sequences read.. Counting patterns.. # site patterns = 323 Counting frequencies.. 120 bytes for distance 51680 bytes for lkl0 41344 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.346931 0.000060 0.505660 0.175834 0.170511 0.818245 0.183789 0.864745 lnL0 = -4407.370652 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4407.370652 x= 0.34693 0.00006 0.50566 0.17583 0.17051 0.81825 0.18379 0.86475 1 h-lim-p 0.0000 0.0000 211.2086 4407.155504 m 0.0000 22 | 1/8 2 h-lim-p 0.0001 0.0279 19.0602 4406.229287 0 0.0051 40 | 1/8 3 h-lim-p 0.0123 0.0984 7.6927 4405.849222 3 0.0111 58 | 1/8 4 h-lim-p 0.0103 0.0822 6.2980 4405.500705 1 0.0128 72 | 1/8 5 h-lim-p 0.0060 0.0483 9.3046 4405.016495 0 0.0090 84 | 1/8 6 h-lim-p 0.0328 0.4631 2.5637 4401.795330 0 0.0657 97 | 1/8 7 h-lim-p 0.0098 0.0784 9.9701 4398.664249 0 0.0196 110 | 1/8 8 h-lim-p 2.5000 20.0000 0.0327 4398.483111 6 0.7998 136 | 1/8 9 h-lim-p 2.1292 20.0000 0.0123 4398.476318 5 0.7579 166 | 1/8 10 h-lim-p 2.1006 20.0000 0.0044 4398.475648 3 0.8103 191 | 1/8 11 h-lim-p 2.5000 20.0000 0.0002 4398.475643 0 1.0938 210 | 1/8 12 h-lim-p 2.5000 20.0000 0.0001 4398.475643 0 1.0938 229 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 4398.475643 0 1.0938 248 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 4398.475643 0 1.0938 267 | 1/8 15 h-lim-p 2.2737 20.0000 0.0000 4398.475643 0 0.9948 286 | 1/8 16 h-lim-p 0.9495 20.0000 0.0000 4398.475643 0 0.3561 306 | 1/8 17 h-lim-p 0.0052 20.0000 0.0001 4398.475643 0 0.0052 325 | 1/8 18 h-lim-p 0.0190 20.0000 0.0000 4398.475643 0 0.0000 363 | 1/8 19 h-lim-p 0.0000 20.0000 0.0000 4398.475643 0 0.0000 394 Out... lnL = -4398.475643 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4398.475643 Node 7: lnL = -4398.475643 Node 8: lnL = -4398.475643 Node 9: lnL = -4398.475643 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 293 Sequential format.. Reading seq # 1: YPL001W_Sbay Reading seq # 2: YPL001W_Scer Reading seq # 3: YPL001W_Skud Reading seq # 4: YPL001W_Smik Reading seq # 5: YPL001W_Spar Sequences read.. Counting patterns.. # site patterns = 166 Counting frequencies.. 120 bytes for distance 26560 bytes for lkl0 21248 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.009660 0.301278 0.000060 0.223218 0.173681 0.300403 0.231357 0.303205 lnL0 = -1531.176147 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1531.176147 x= 0.00966 0.30128 0.00006 0.22322 0.17368 0.30040 0.23136 0.30320 1 h-lim-p 0.0002 0.0018 44.7299 1530.211412 0 0.0009 24 | 0/8 2 h-lim-p 0.0001 0.0009 16.9453 1530.035170 m 0.0009 36 | 1/8 3 h-lim-p 0.0020 0.0572 7.5654 1530.000290 6 0.0015 63 | 1/8 4 h-lim-p 0.0111 0.4871 1.0149 1529.998676 3 0.0027 83 | 1/8 5 h-lim-p 0.0066 0.9123 0.4165 1529.997295 4 0.0070 104 | 1/8 6 h-lim-p 0.0189 0.8288 0.1554 1529.983523 0 0.0377 124 | 1/8 7 h-lim-p 0.0045 0.0710 1.2983 1529.935243 0 0.0090 144 | 1/8 8 h-lim-p 0.0063 0.2635 1.8709 1529.929102 2 0.0029 160 | 1/8 9 h-lim-p 0.9591 20.0000 0.0057 1529.922462 2 0.8992 176 | 0/8 10 h-lim-p 0.0854 20.0000 0.0603 1529.922457 0 0.0027 199 | 0/8 11 h-lim-p 0.2499 1.9995 0.0003 1529.922443 0 0.9998 221 | 0/8 12 h-lim-p 0.1053 0.8425 0.0001 1529.922443 0 0.0000 257 | 0/8 13 h-lim-p 0.0000 20.0000 0.0004 1529.922443 0 0.2458 291 | 0/8 14 h-lim-p 0.4569 20.0000 0.0002 1529.922443 0 0.3998 311 | 0/8 15 h-lim-p 0.0140 0.1123 0.0030 1529.922443 0 0.0061 331 | 0/8 16 h-lim-p 0.0938 20.0000 0.0002 1529.922443 0 0.2815 352 | 0/8 17 h-lim-p 0.7473 20.0000 0.0001 1529.922443 0 1.4946 373 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1529.922443 0 1.0938 393 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1529.922443 0 0.5469 414 | 0/8 20 h-lim-p 0.5591 20.0000 0.0000 1529.922443 0 0.2796 434 | 0/8 21 h-lim-p 0.2865 20.0000 0.0000 1529.922443 0 0.0017 461 Out... lnL = -1529.922443 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1529.922443 Node 7: lnL = -1529.922443 Node 8: lnL = -1529.922443 Node 9: lnL = -1529.922443 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 295 Sequential format.. Reading seq # 1: YPL002C_Sbay Reading seq # 2: YPL002C_Scer Reading seq # 3: YPL002C_Skud Reading seq # 4: YPL002C_Smik Reading seq # 5: YPL002C_Spar Sequences read.. Counting patterns.. # site patterns = 169 Counting frequencies.. 120 bytes for distance 27040 bytes for lkl0 21632 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.042807 0.141153 0.012109 0.214898 0.174967 0.245844 0.268620 0.299574 lnL0 = -1431.136407 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1431.136407 x= 0.04281 0.14115 0.01211 0.21490 0.17497 0.24584 0.26862 0.29957 1 h-lim-p 0.0041 0.0326 53.1299 1430.463327 8 0.0005 41 | 0/8 2 h-lim-p 0.0021 0.0242 13.4152 1430.325510 5 0.0016 63 | 0/8 3 h-lim-p 0.0049 0.0769 4.4241 1430.311924 6 0.0015 89 | 0/8 4 h-lim-p 0.0062 0.2373 1.0938 1430.311096 2 0.0015 106 | 0/8 5 h-lim-p 0.0126 1.7722 0.1268 1430.311082 3 0.0019 127 | 0/8 6 h-lim-p 0.0069 8.1790 0.0344 1430.311081 1 0.0017 150 | 0/8 7 h-lim-p 0.0065 11.9596 0.0091 1430.311080 0 0.0028 170 | 0/8 8 h-lim-p 0.1134 20.0000 0.0002 1430.311055 0 0.9075 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1430.311055 0 1.0938 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1430.311055 0 1.0938 233 | 0/8 11 h-lim-p 1.2473 20.0000 0.0000 1430.311055 0 2.4945 254 | 0/8 12 h-lim-p 2.1604 20.0000 0.0000 1430.311055 0 0.9452 274 | 0/8 13 h-lim-p 0.1209 20.0000 0.0001 1430.311055 0 0.0000 305 | 0/8 14 h-lim-p 0.0003 20.0000 0.0000 1430.311055 0 0.0000 336 Out... lnL = -1430.311055 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1430.311055 Node 7: lnL = -1430.311055 Node 8: lnL = -1430.311055 Node 9: lnL = -1430.311055 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 388 Sequential format.. Reading seq # 1: YPL003W_Sbay Reading seq # 2: YPL003W_Scer Reading seq # 3: YPL003W_Skud Reading seq # 4: YPL003W_Smik Reading seq # 5: YPL003W_Spar Sequences read.. Counting patterns.. # site patterns = 149 Counting frequencies.. 120 bytes for distance 23840 bytes for lkl0 19072 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.007633 0.052939 0.087539 0.082768 0.082150 0.137816 0.073450 0.134384 lnL0 = -1475.820087 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1475.820087 x= 0.00763 0.05294 0.08754 0.08277 0.08215 0.13782 0.07345 0.13438 1 h-lim-p 0.0010 0.0137 167.7929 1472.001281 6 0.0003 37 | 0/8 2 h-lim-p 0.0001 0.0004 38.3697 1471.711343 m 0.0004 49 | 0/8 3 h-lim-p 0.0026 0.0251 5.9141 1471.700395 2 0.0006 66 | 0/8 4 h-lim-p 0.0026 0.0789 1.4181 1471.700074 4 0.0003 88 | 0/8 5 h-lim-p 0.0014 0.0278 0.3509 1471.700046 2 0.0004 105 | 0/8 6 h-lim-p 0.0157 14.9519 0.0098 1471.699978 0 0.0314 126 | 0/8 7 h-lim-p 0.0042 3.7021 0.0740 1471.698049 0 0.0166 148 | 0/8 8 h-lim-p 0.0009 0.0080 1.3925 1471.696800 3 0.0008 174 | 0/8 9 h-lim-p 1.8972 20.0000 0.0006 1471.696725 2 0.9338 191 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1471.696725 0 1.0938 211 | 0/8 11 h-lim-p 1.3581 20.0000 0.0000 1471.696725 0 1.1883 231 | 0/8 12 h-lim-p 0.7928 20.0000 0.0000 1471.696725 0 0.7928 251 | 0/8 13 h-lim-p 0.0053 0.1402 0.0067 1471.696725 0 0.0001 276 | 0/8 14 h-lim-p 0.0000 0.0580 0.0162 1471.696725 0 0.0000 296 | 0/8 15 h-lim-p 0.0000 10.8051 0.0166 1471.696725 0 0.0000 318 | 0/8 16 h-lim-p 0.0000 0.2857 0.0033 1471.696725 0 0.0000 353 | 0/8 17 h-lim-p 0.0000 3.3799 0.0006 | 0/8 18 h-lim-p 0.0000 3.3799 0.0006 Out... lnL = -1471.696725 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1471.696725 Node 7: lnL = -1471.696725 Node 8: lnL = -1471.696725 Node 9: lnL = -1471.696725 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 392 Sequential format.. Reading seq # 1: YPL004C_Sbay Reading seq # 2: YPL004C_Scer Reading seq # 3: YPL004C_Skud Reading seq # 4: YPL004C_Smik Reading seq # 5: YPL004C_Spar Sequences read.. Counting patterns.. # site patterns = 144 Counting frequencies.. 120 bytes for distance 23040 bytes for lkl0 18432 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.126626 0.108734 0.100068 0.083158 0.140342 0.092839 0.141078 lnL0 = -1546.000063 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1546.000063 x= 0.00006 0.12663 0.10873 0.10007 0.08316 0.14034 0.09284 0.14108 1 h-lim-p 0.0000 0.0000 54.7258 1545.985503 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0086 21.1014 1545.890056 0 0.0006 39 | 1/8 3 h-lim-p 0.0027 0.0403 4.4797 1545.883642 2 0.0006 56 | 1/8 4 h-lim-p 0.0036 0.4091 0.7891 1545.881980 2 0.0017 72 | 1/8 5 h-lim-p 0.0028 0.2974 0.4748 1545.853167 0 0.0112 93 | 1/8 6 h-lim-p 0.0023 0.0909 2.3444 1545.398364 0 0.0091 114 | 1/8 7 h-lim-p 0.0010 0.0092 21.9214 1545.198065 7 0.0007 144 | 1/8 8 h-lim-p 0.0064 0.0864 2.2310 1545.196555 4 0.0006 166 | 1/8 9 h-lim-p 0.6433 20.0000 0.0021 1545.191978 0 0.9649 178 | 1/8 10 h-lim-p 2.5000 20.0000 0.0002 1545.191958 2 0.9961 201 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 1545.191958 0 1.0938 220 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 1545.191958 0 1.0938 239 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 1545.191958 0 2.1875 258 | 1/8 14 h-lim-p 1.8371 20.0000 0.0000 1545.191958 0 0.8037 277 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 1545.191958 0 0.0781 300 | 1/8 16 h-lim-p 0.0847 20.0000 0.0000 1545.191958 0 0.0010 325 Out... lnL = -1545.191958 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1545.191958 Node 7: lnL = -1545.191958 Node 8: lnL = -1545.191958 Node 9: lnL = -1545.191958 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 383 Sequential format.. Reading seq # 1: YPL005W_Sbay Reading seq # 2: YPL005W_Scer Reading seq # 3: YPL005W_Skud Reading seq # 4: YPL005W_Smik Reading seq # 5: YPL005W_Spar Sequences read.. Counting patterns.. # site patterns = 181 Counting frequencies.. 120 bytes for distance 28960 bytes for lkl0 23168 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.009422 0.179933 0.065660 0.150338 0.100516 0.241338 0.323357 0.262598 lnL0 = -1829.094796 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1829.094796 x= 0.00942 0.17993 0.06566 0.15034 0.10052 0.24134 0.32336 0.26260 1 h-lim-p 0.0004 0.0034 24.1201 1828.933206 0 0.0006 22 | 0/8 2 h-lim-p 0.0007 0.0060 4.9435 1828.925501 3 0.0007 40 | 0/8 3 h-lim-p 0.0022 0.0612 1.4841 1828.924826 5 0.0007 67 | 0/8 4 h-lim-p 0.0013 0.4948 0.7315 1828.924599 3 0.0010 85 | 0/8 5 h-lim-p 0.0078 4.3239 0.0961 1828.924583 3 0.0023 113 | 0/8 6 h-lim-p 0.0028 0.2704 0.0783 1828.924558 1 0.0035 135 | 0/8 7 h-lim-p 0.0087 2.1264 0.0321 1828.923893 0 0.0520 157 | 0/8 8 h-lim-p 0.0061 0.5995 0.2732 1828.921599 1 0.0076 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1828.921564 2 0.9961 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1828.921564 0 1.0938 223 | 0/8 11 h-lim-p 1.1033 20.0000 0.0000 1828.921564 0 0.0172 248 | 0/8 12 h-lim-p 0.0017 20.0000 0.0001 1828.921564 0 0.0000 275 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 1828.921564 0 0.0000 304 | 0/8 14 h-lim-p 0.0000 20.0000 0.0005 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -1828.921564 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1828.921564 Node 7: lnL = -1828.921564 Node 8: lnL = -1828.921564 Node 9: lnL = -1828.921564 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 821 Sequential format.. Reading seq # 1: YPL007C_Sbay Reading seq # 2: YPL007C_Scer Reading seq # 3: YPL007C_Skud Reading seq # 4: YPL007C_Smik Reading seq # 5: YPL007C_Spar Sequences read.. Counting patterns.. # site patterns = 276 Counting frequencies.. 120 bytes for distance 44160 bytes for lkl0 35328 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.034293 0.078644 0.056064 0.131478 0.085793 0.241057 0.272924 0.245185 lnL0 = -3779.950493 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3779.950493 x= 0.03429 0.07864 0.05606 0.13148 0.08579 0.24106 0.27292 0.24518 1 h-lim-p 0.0007 0.0059 67.8947 3779.527119 7 0.0002 39 | 0/8 2 h-lim-p 0.0006 0.0046 19.3880 3779.475795 4 0.0003 60 | 0/8 3 h-lim-p 0.0005 0.0133 10.3110 3779.463376 5 0.0003 83 | 0/8 4 h-lim-p 0.0006 0.0681 4.8697 3779.460087 5 0.0004 108 | 0/8 5 h-lim-p 0.0019 0.2184 0.8893 3779.459911 2 0.0005 125 | 0/8 6 h-lim-p 0.0030 1.1014 0.1401 3779.459906 1 0.0006 148 | 0/8 7 h-lim-p 0.0174 16.2709 0.0049 3779.459906 0 0.0010 171 | 0/8 8 h-lim-p 0.0119 20.0000 0.0004 3779.459874 0 0.3809 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3779.459872 0 1.0938 216 | 0/8 10 h-lim-p 1.5472 20.0000 0.0000 3779.459872 0 1.3538 236 | 0/8 11 h-lim-p 1.7028 20.0000 0.0000 3779.459872 0 0.7450 256 | 0/8 12 h-lim-p 0.3276 20.0000 0.0001 3779.459872 0 0.0102 280 | 0/8 13 h-lim-p 0.0029 20.0000 0.0002 3779.459872 0 0.0001 304 | 0/8 14 h-lim-p 0.0003 20.0000 0.0001 3779.459872 0 0.0003 324 | 0/8 15 h-lim-p 0.0004 20.0000 0.0000 3779.459872 0 0.0002 344 | 0/8 16 h-lim-p 0.0001 20.0000 0.0001 3779.459872 0 0.0001 364 | 0/8 17 h-lim-p 0.0001 20.0000 0.0000 3779.459872 0 0.0000 398 | 0/8 18 h-lim-p 0.0000 20.0000 0.0016 3779.459872 0 0.0000 425 | 0/8 19 h-lim-p 0.0000 20.0000 0.0003 3779.459872 0 0.0000 448 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 21 h-lim-p 0.0000 20.0000 0.0016 | 0/8 22 h-lim-p 0.0000 20.0000 0.0016 Out... lnL = -3779.459872 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3779.459872 Node 7: lnL = -3779.459872 Node 8: lnL = -3779.459872 Node 9: lnL = -3779.459872 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 492 Sequential format.. Reading seq # 1: YPL009C_Sbay Reading seq # 2: YPL009C_Scer Reading seq # 3: YPL009C_Skud Reading seq # 4: YPL009C_Smik Reading seq # 5: YPL009C_Spar Sequences read.. Counting patterns.. # site patterns = 223 Counting frequencies.. 120 bytes for distance 35680 bytes for lkl0 28544 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.022831 0.109312 0.089577 0.120997 0.082109 0.179370 0.273149 0.233244 lnL0 = -2198.157060 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2198.157060 x= 0.02283 0.10931 0.08958 0.12100 0.08211 0.17937 0.27315 0.23324 1 h-lim-p 0.0003 0.0021 58.2525 2197.489724 0 0.0005 23 | 0/8 2 h-lim-p 0.0015 0.0136 20.4777 2197.419463 6 0.0004 49 | 0/8 3 h-lim-p 0.0008 0.0082 9.7849 2197.398438 6 0.0005 76 | 0/8 4 h-lim-p 0.0020 0.0561 2.5939 2197.396787 4 0.0005 97 | 0/8 5 h-lim-p 0.0028 0.2911 0.4844 2197.396582 0 0.0012 109 | 0/8 6 h-lim-p 0.0036 1.2548 0.1685 2197.396173 0 0.0072 130 | 0/8 7 h-lim-p 0.0278 4.3806 0.0434 2197.357726 0 0.1111 152 | 0/8 8 h-lim-p 0.0163 0.8799 0.2952 2197.357703 2 0.0005 180 | 0/8 9 h-lim-p 0.1293 20.0000 0.0012 2197.356099 0 1.0343 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2197.356091 1 0.9961 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2197.356091 0 1.0938 245 | 0/8 12 h-lim-p 0.9471 20.0000 0.0000 2197.356091 0 0.0148 270 | 0/8 13 h-lim-p 0.0000 3.6976 0.0086 2197.356091 0 0.0000 299 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 2197.356091 0 0.0000 322 Out... lnL = -2197.356091 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2197.356091 Node 7: lnL = -2197.356091 Node 8: lnL = -2197.356091 Node 9: lnL = -2197.356091 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 334 Sequential format.. Reading seq # 1: YPL010W_Sbay Reading seq # 2: YPL010W_Scer Reading seq # 3: YPL010W_Skud Reading seq # 4: YPL010W_Smik Reading seq # 5: YPL010W_Spar Sequences read.. Counting patterns.. # site patterns = 126 Counting frequencies.. 120 bytes for distance 20160 bytes for lkl0 16128 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.001056 0.081480 0.027204 0.095465 0.063591 0.166226 0.188495 0.143963 lnL0 = -1353.637208 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1353.637208 x= 0.00106 0.08148 0.02720 0.09547 0.06359 0.16623 0.18849 0.14396 1 h-lim-p 0.0078 0.0763 58.7982 1353.271145 2 0.0002 30 | 0/8 2 h-lim-p 0.0010 0.0132 13.9466 1353.223573 5 0.0005 53 | 0/8 3 h-lim-p 0.0005 0.0040 6.1003 1353.216125 2 0.0005 69 | 0/8 4 h-lim-p 0.0024 0.0188 1.1991 1353.215842 3 0.0004 90 | 0/8 5 h-lim-p 0.0010 0.2270 0.4866 1353.215787 3 0.0005 109 | 0/8 6 h-lim-p 0.0042 2.6278 0.0625 1353.215785 1 0.0008 132 | 0/8 7 h-lim-p 0.0021 8.0479 0.0246 1353.215785 0 0.0009 152 | 0/8 8 h-lim-p 0.0533 20.0000 0.0004 1353.215626 0 0.8522 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1353.215617 1 0.9961 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1353.215617 0 1.2500 218 | 0/8 11 h-lim-p 0.1658 20.0000 0.0002 1353.215617 0 0.0000 264 | 0/8 12 h-lim-p 0.0000 20.0000 0.0002 | 0/8 13 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1353.215617 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1353.215617 Node 7: lnL = -1353.215617 Node 8: lnL = -1353.215617 Node 9: lnL = -1353.215617 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 335 Sequential format.. Reading seq # 1: YPL011C_Sbay Reading seq # 2: YPL011C_Scer Reading seq # 3: YPL011C_Skud Reading seq # 4: YPL011C_Smik Reading seq # 5: YPL011C_Spar Sequences read.. Counting patterns.. # site patterns = 132 Counting frequencies.. 120 bytes for distance 21120 bytes for lkl0 16896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.001208 0.079475 0.021105 0.086059 0.083317 0.197081 0.180657 0.148637 lnL0 = -1380.635595 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1380.635595 x= 0.00121 0.07948 0.02111 0.08606 0.08332 0.19708 0.18066 0.14864 1 h-lim-p 0.0025 0.0287 105.9892 1379.778577 9 0.0002 47 | 0/8 2 h-lim-p 0.0017 0.0144 10.8127 1379.747016 7 0.0005 77 | 0/8 3 h-lim-p 0.0006 0.0047 5.0674 1379.740968 2 0.0005 93 | 0/8 4 h-lim-p 0.0021 0.0549 1.3302 1379.740554 2 0.0005 110 | 0/8 5 h-lim-p 0.0021 0.4746 0.3328 1379.740527 1 0.0005 125 | 0/8 6 h-lim-p 0.0029 0.1533 0.0594 1379.740526 1 0.0004 149 | 0/8 7 h-lim-p 0.0011 14.9841 0.0185 1379.740526 0 0.0010 169 | 0/8 8 h-lim-p 0.1500 20.0000 0.0001 1379.740501 0 1.2001 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1379.740501 0 1.0938 212 | 0/8 10 h-lim-p 1.5501 20.0000 0.0000 1379.740501 0 1.5501 232 | 0/8 11 h-lim-p 0.7430 20.0000 0.0001 1379.740501 0 0.6502 252 | 0/8 12 h-lim-p 0.0201 2.4111 0.0022 1379.740501 0 0.0002 278 | 0/8 13 h-lim-p 0.0000 0.2605 0.0207 1379.740501 0 0.0000 303 | 0/8 14 h-lim-p 0.0001 20.0000 0.0001 1379.740501 0 0.0001 323 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 1379.740501 0 0.0000 357 | 0/8 16 h-lim-p 0.0000 20.0000 0.0015 1379.740501 0 0.0000 384 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 1379.740501 0 0.0013 411 | 0/8 18 h-lim-p 0.0042 20.0000 0.0001 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0018 | 0/8 20 h-lim-p 0.0000 20.0000 0.0018 Out... lnL = -1379.740501 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1379.740501 Node 7: lnL = -1379.740501 Node 8: lnL = -1379.740501 Node 9: lnL = -1379.740501 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 767 Sequential format.. Reading seq # 1: YPL015C_Sbay Reading seq # 2: YPL015C_Scer Reading seq # 3: YPL015C_Skud Reading seq # 4: YPL015C_Smik Reading seq # 5: YPL015C_Spar Sequences read.. Counting patterns.. # site patterns = 238 Counting frequencies.. 120 bytes for distance 38080 bytes for lkl0 30464 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.094596 0.061757 0.084748 0.077768 0.054727 0.136544 0.170959 0.273293 lnL0 = -3138.582596 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3138.582596 x= 0.09460 0.06176 0.08475 0.07777 0.05473 0.13654 0.17096 0.27329 1 h-lim-p 0.0029 0.8554 146.9988 3136.439125 8 0.0002 42 | 0/8 2 h-lim-p 0.0004 0.0035 36.8057 3136.278652 6 0.0002 69 | 0/8 3 h-lim-p 0.0003 0.0076 32.2928 3136.201721 6 0.0002 94 | 0/8 4 h-lim-p 0.0011 0.0299 6.8764 3136.194148 4 0.0004 116 | 0/8 5 h-lim-p 0.0016 0.0952 1.4851 3136.193757 2 0.0004 133 | 0/8 6 h-lim-p 0.0040 0.7737 0.1429 3136.193754 1 0.0002 150 | 0/8 7 h-lim-p 0.0007 3.2154 0.0524 3136.193752 0 0.0007 170 | 0/8 8 h-lim-p 0.0327 20.0000 0.0011 3136.192788 0 0.7850 194 | 0/8 9 h-lim-p 1.2243 20.0000 0.0007 3136.192754 1 0.9756 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3136.192754 0 1.0938 236 | 0/8 11 h-lim-p 1.9986 20.0000 0.0000 3136.192754 0 1.7488 256 | 0/8 12 h-lim-p 1.2293 20.0000 0.0000 3136.192754 0 1.0756 276 | 0/8 13 h-lim-p 0.7192 20.0000 0.0000 3136.192754 0 4.3155 298 | 0/8 14 h-lim-p 0.0939 20.0000 0.0006 3136.192754 0 0.0000 341 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 | 0/8 16 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -3136.192754 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3136.192754 Node 7: lnL = -3136.192754 Node 8: lnL = -3136.192754 Node 9: lnL = -3136.192754 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 684 Sequential format.. Reading seq # 1: YPL019C_Sbay Reading seq # 2: YPL019C_Scer Reading seq # 3: YPL019C_Skud Reading seq # 4: YPL019C_Smik Reading seq # 5: YPL019C_Spar Sequences read.. Counting patterns.. # site patterns = 232 Counting frequencies.. 120 bytes for distance 37120 bytes for lkl0 29696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.037540 0.111412 0.043241 0.171387 0.051567 0.203659 0.185096 0.221994 lnL0 = -2689.320533 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2689.320533 x= 0.03754 0.11141 0.04324 0.17139 0.05157 0.20366 0.18510 0.22199 1 h-lim-p 0.0009 0.0074 86.7440 2688.498140 7 0.0002 36 | 0/8 2 h-lim-p 0.0004 0.0031 42.9251 2688.085174 0 0.0006 48 | 0/8 3 h-lim-p 0.0003 0.0027 70.0144 2687.514048 0 0.0007 61 | 0/8 4 h-lim-p 0.0008 0.0066 26.6767 2687.404061 7 0.0005 90 | 0/8 5 h-lim-p 0.0021 0.0175 6.0934 2687.396423 5 0.0005 112 | 0/8 6 h-lim-p 0.0037 0.2943 0.7568 2687.396221 4 0.0006 136 | 0/8 7 h-lim-p 0.0129 5.4202 0.0331 2687.382048 0 0.2069 160 | 0/8 8 h-lim-p 0.0029 0.0801 2.3719 2687.341935 0 0.0043 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0016 2687.340847 3 1.0449 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2687.340845 0 1.0938 218 | 0/8 11 h-lim-p 2.3844 20.0000 0.0000 2687.340845 0 1.0432 238 | 0/8 12 h-lim-p 0.9280 20.0000 0.0000 2687.340845 0 0.0002 269 | 0/8 13 h-lim-p 0.0000 20.0000 0.0003 2687.340845 0 0.0000 289 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 2687.340845 0 0.0001 310 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 2687.340845 0 0.0000 344 Out... lnL = -2687.340845 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2687.340845 Node 7: lnL = -2687.340845 Node 8: lnL = -2687.340845 Node 9: lnL = -2687.340845 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 371 Sequential format.. Reading seq # 1: YPL020C_Sbay Reading seq # 2: YPL020C_Scer Reading seq # 3: YPL020C_Skud Reading seq # 4: YPL020C_Smik Reading seq # 5: YPL020C_Spar Sequences read.. Counting patterns.. # site patterns = 158 Counting frequencies.. 120 bytes for distance 25280 bytes for lkl0 20224 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.077719 0.014054 0.066877 0.163761 0.063852 0.196027 0.188288 0.256150 lnL0 = -1620.038818 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1620.038818 x= 0.07772 0.01405 0.06688 0.16376 0.06385 0.19603 0.18829 0.25615 1 h-lim-p 0.0019 0.0153 72.6150 1619.423565 6 0.0003 36 | 0/8 2 h-lim-p 0.0014 0.0114 12.6447 1619.382126 7 0.0005 66 | 0/8 3 h-lim-p 0.0012 0.0189 5.6964 1619.375539 3 0.0005 84 | 0/8 4 h-lim-p 0.0019 0.0823 1.4404 1619.375092 2 0.0005 101 | 0/8 5 h-lim-p 0.0015 0.6984 0.4334 1619.375038 1 0.0006 115 | 0/8 6 h-lim-p 0.0087 3.6554 0.0301 1619.375037 0 0.0009 137 | 0/8 7 h-lim-p 0.0076 20.0000 0.0038 1619.375037 0 0.0033 157 | 0/8 8 h-lim-p 0.0822 20.0000 0.0002 1619.375029 0 0.6575 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1619.375028 0 1.0938 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1619.375028 0 2.1875 220 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1619.375028 0 1.0938 240 | 0/8 12 h-lim-p 0.2613 20.0000 0.0000 1619.375028 0 4.1810 264 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1619.375028 0 0.0781 288 | 0/8 14 h-lim-p 0.0119 20.0000 0.0000 1619.375028 0 0.0059 308 | 0/8 15 h-lim-p 0.0021 20.0000 0.0001 1619.375028 0 0.0003 330 | 0/8 16 h-lim-p 0.0001 20.0000 0.0002 1619.375028 0 0.0000 353 | 0/8 17 h-lim-p 0.0002 20.0000 0.0000 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0015 | 0/8 19 h-lim-p 0.0000 20.0000 0.0015 Out... lnL = -1619.375028 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1619.375028 Node 7: lnL = -1619.375028 Node 8: lnL = -1619.375028 Node 9: lnL = -1619.375028 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 869 Sequential format.. Reading seq # 1: YPL021W_Sbay Reading seq # 2: YPL021W_Scer Reading seq # 3: YPL021W_Skud Reading seq # 4: YPL021W_Smik Reading seq # 5: YPL021W_Spar Sequences read.. Counting patterns.. # site patterns = 313 Counting frequencies.. 120 bytes for distance 50080 bytes for lkl0 40064 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.088684 0.138642 0.079354 0.223551 0.057785 0.284783 0.199499 0.343650 lnL0 = -3709.511337 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3709.511337 x= 0.08868 0.13864 0.07935 0.22355 0.05779 0.28478 0.19950 0.34365 1 h-lim-p 0.0012 0.0720 247.1702 3702.921921 8 0.0003 43 | 0/8 2 h-lim-p 0.0006 0.0046 69.4558 3701.056388 0 0.0009 55 | 0/8 3 h-lim-p 0.0019 0.0155 21.3656 3700.720873 3 0.0016 73 | 0/8 4 h-lim-p 0.0036 0.0287 8.1371 3700.670665 4 0.0018 94 | 0/8 5 h-lim-p 0.0022 0.0264 6.4650 3700.661279 5 0.0007 120 | 0/8 6 h-lim-p 0.0019 0.1033 2.3287 3700.658157 5 0.0014 143 | 0/8 7 h-lim-p 0.0189 1.5011 0.1759 3700.658143 2 0.0008 163 | 0/8 8 h-lim-p 0.0962 20.0000 0.0014 3700.654440 0 1.5391 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3700.654412 1 0.9961 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3700.654412 0 1.0938 229 | 0/8 11 h-lim-p 0.9452 20.0000 0.0000 3700.654412 0 0.8270 249 | 0/8 12 h-lim-p 0.4234 20.0000 0.0000 3700.654412 0 0.0008 277 | 0/8 13 h-lim-p 0.0009 20.0000 0.0000 3700.654412 0 0.0000 304 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 3700.654412 0 0.0000 332 Out... lnL = -3700.654412 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3700.654412 Node 7: lnL = -3700.654412 Node 8: lnL = -3700.654412 Node 9: lnL = -3700.654412 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 413 Sequential format.. Reading seq # 1: YPL023C_Sbay Reading seq # 2: YPL023C_Scer Reading seq # 3: YPL023C_Skud Reading seq # 4: YPL023C_Smik Reading seq # 5: YPL023C_Spar Sequences read.. Counting patterns.. # site patterns = 170 Counting frequencies.. 120 bytes for distance 27200 bytes for lkl0 21760 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.079720 0.055884 0.056406 0.112405 0.076081 0.210546 0.164446 0.258671 lnL0 = -1809.786631 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1809.786631 x= 0.07972 0.05588 0.05641 0.11241 0.07608 0.21055 0.16445 0.25867 1 h-lim-p 0.0006 0.0044 51.7589 1809.349510 8 0.0003 46 | 0/8 2 h-lim-p 0.0010 0.0081 16.1933 1809.305157 6 0.0004 72 | 0/8 3 h-lim-p 0.0013 0.0480 4.6415 1809.298379 5 0.0007 95 | 0/8 4 h-lim-p 0.0037 0.1974 0.8609 1809.298222 2 0.0004 113 | 0/8 5 h-lim-p 0.0031 1.5969 0.1215 1809.298218 2 0.0005 139 | 0/8 6 h-lim-p 0.0009 3.0296 0.0672 1809.298217 1 0.0004 162 | 0/8 7 h-lim-p 0.0155 20.0000 0.0019 1809.298203 0 0.0932 184 | 0/8 8 h-lim-p 0.0054 3.8131 0.0327 1809.298052 0 0.0107 205 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1809.298051 0 1.0938 225 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1809.298051 0 1.0938 245 | 0/8 11 h-lim-p 1.0789 20.0000 0.0000 1809.298051 0 0.0084 271 | 0/8 12 h-lim-p 0.0018 20.0000 0.0000 1809.298051 0 0.0002 293 | 0/8 13 h-lim-p 0.0002 20.0000 0.0001 1809.298051 0 0.0000 327 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -1809.298051 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1809.298051 Node 7: lnL = -1809.298051 Node 8: lnL = -1809.298051 Node 9: lnL = -1809.298051 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 510 Sequential format.. Reading seq # 1: YPL024W_Sbay Reading seq # 2: YPL024W_Scer Reading seq # 3: YPL024W_Skud Reading seq # 4: YPL024W_Smik Reading seq # 5: YPL024W_Spar Sequences read.. Counting patterns.. # site patterns = 247 Counting frequencies.. 120 bytes for distance 39520 bytes for lkl0 31616 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.183829 0.019111 0.127119 0.105353 0.111146 0.309323 0.359812 0.479480 lnL0 = -2309.813060 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2309.813060 x= 0.18383 0.01911 0.12712 0.10535 0.11115 0.30932 0.35981 0.47948 1 h-lim-p 0.0006 0.0048 47.4932 2309.089899 7 0.0007 39 | 0/8 2 h-lim-p 0.0019 0.0174 16.7976 2308.979736 2 0.0009 55 | 0/8 3 h-lim-p 0.0005 0.0164 26.8569 2308.864497 0 0.0011 68 | 0/8 4 h-lim-p 0.0026 0.0304 11.3714 2308.799155 7 0.0016 97 | 0/8 5 h-lim-p 0.0035 0.0983 5.1900 2308.786967 6 0.0013 122 | 0/8 6 h-lim-p 0.0020 0.0894 3.1858 2308.781650 4 0.0015 142 | 0/8 7 h-lim-p 0.0117 1.0500 0.4227 2308.781382 2 0.0026 159 | 0/8 8 h-lim-p 0.1035 10.5511 0.0104 2308.764873 0 0.8278 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 2308.764821 2 0.9961 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2308.764821 0 1.0938 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2308.764821 0 1.0938 246 | 0/8 12 h-lim-p 0.9259 20.0000 0.0000 2308.764821 0 0.1157 268 | 0/8 13 h-lim-p 0.0028 20.0000 0.0002 2308.764821 0 0.0004 290 | 0/8 14 h-lim-p 0.0012 20.0000 0.0001 2308.764821 0 0.0000 317 | 0/8 15 h-lim-p 0.0006 20.0000 0.0000 2308.764821 0 0.0001 338 Out... lnL = -2308.764821 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2308.764821 Node 7: lnL = -2308.764821 Node 8: lnL = -2308.764821 Node 9: lnL = -2308.764821 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 310 Sequential format.. Reading seq # 1: YPL026C_Sbay Reading seq # 2: YPL026C_Scer Reading seq # 3: YPL026C_Skud Reading seq # 4: YPL026C_Smik Reading seq # 5: YPL026C_Spar Sequences read.. Counting patterns.. # site patterns = 133 Counting frequencies.. 120 bytes for distance 21280 bytes for lkl0 17024 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.034342 0.040014 0.077731 0.075973 0.074530 0.239372 0.222173 0.206467 lnL0 = -1352.778916 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1352.778916 x= 0.03434 0.04001 0.07773 0.07597 0.07453 0.23937 0.22217 0.20647 1 h-lim-p 0.0021 0.0168 60.4598 1351.992434 3 0.0005 29 | 0/8 2 h-lim-p 0.0005 0.0044 20.2130 1351.859542 0 0.0008 41 | 0/8 3 h-lim-p 0.0031 0.0317 5.3345 1351.849646 4 0.0008 63 | 0/8 4 h-lim-p 0.0010 0.0509 4.1874 1351.846745 4 0.0005 84 | 0/8 5 h-lim-p 0.0022 0.3576 0.9411 1351.846467 4 0.0007 106 | 0/8 6 h-lim-p 0.0025 0.4871 0.2595 1351.846451 2 0.0005 131 | 0/8 7 h-lim-p 0.0485 20.0000 0.0026 1351.843331 0 0.7762 155 | 0/8 8 h-lim-p 0.0044 0.5206 0.4625 1351.843143 4 0.0016 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1351.843124 2 1.3159 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1351.843123 0 1.0938 229 | 0/8 11 h-lim-p 1.4255 20.0000 0.0000 1351.843123 0 1.4255 249 | 0/8 12 h-lim-p 0.7109 20.0000 0.0000 1351.843123 0 0.3555 269 | 0/8 13 h-lim-p 0.0085 20.0000 0.0011 1351.843123 0 0.0085 289 | 0/8 14 h-lim-p 0.0029 15.2320 0.0031 1351.843123 0 0.0007 310 | 0/8 15 h-lim-p 0.0002 3.6858 0.0129 1351.843123 0 0.0000 335 | 0/8 16 h-lim-p 0.0002 20.0000 0.0001 1351.843123 0 0.0000 373 | 0/8 17 h-lim-p 0.0000 20.0000 0.0003 | 0/8 18 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -1351.843123 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1351.843123 Node 7: lnL = -1351.843123 Node 8: lnL = -1351.843123 Node 9: lnL = -1351.843123 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 423 Sequential format.. Reading seq # 1: YPL027W_Sbay Reading seq # 2: YPL027W_Scer Reading seq # 3: YPL027W_Skud Reading seq # 4: YPL027W_Smik Reading seq # 5: YPL027W_Spar Sequences read.. Counting patterns.. # site patterns = 188 Counting frequencies.. 120 bytes for distance 30080 bytes for lkl0 24064 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.090757 0.007562 0.070115 0.147888 0.114367 0.179681 0.242941 0.288089 lnL0 = -1904.318482 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1904.318482 x= 0.09076 0.00756 0.07012 0.14789 0.11437 0.17968 0.24294 0.28809 1 h-lim-p 0.0015 0.8385 157.3092 1901.236172 7 0.0003 38 | 0/8 2 h-lim-p 0.0015 0.0117 22.6604 1901.008551 8 0.0009 71 | 0/8 3 h-lim-p 0.0041 0.0469 4.9206 1901.000305 6 0.0007 100 | 0/8 4 h-lim-p 0.0021 0.1648 1.7097 1900.999085 2 0.0010 116 | 0/8 5 h-lim-p 0.0021 0.4522 0.7848 1900.998910 3 0.0007 135 | 0/8 6 h-lim-p 0.0086 2.5464 0.0627 1900.998907 1 0.0011 159 | 0/8 7 h-lim-p 0.0053 18.1177 0.0125 1900.998901 0 0.0079 179 | 0/8 8 h-lim-p 0.0143 20.0000 0.0070 1900.998088 0 0.1140 202 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1900.998078 1 0.9961 224 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1900.998078 0 1.0938 244 | 0/8 11 h-lim-p 1.2784 20.0000 0.0000 1900.998078 0 1.9176 264 | 0/8 12 h-lim-p 1.4287 20.0000 0.0000 1900.998078 0 0.3572 285 | 0/8 13 h-lim-p 0.0224 20.0000 0.0001 1900.998078 0 0.0336 305 | 0/8 14 h-lim-p 0.0109 20.0000 0.0004 1900.998078 0 0.0001 331 | 0/8 15 h-lim-p 0.0003 20.0000 0.0001 1900.998078 0 0.0000 363 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1900.998078 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1900.998078 Node 7: lnL = -1900.998078 Node 8: lnL = -1900.998078 Node 9: lnL = -1900.998078 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 271 Sequential format.. Reading seq # 1: YPL029W_Sbay Reading seq # 2: YPL029W_Scer Reading seq # 3: YPL029W_Skud Reading seq # 4: YPL029W_Smik Reading seq # 5: YPL029W_Spar Sequences read.. Counting patterns.. # site patterns = 120 Counting frequencies.. 120 bytes for distance 19200 bytes for lkl0 15360 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.047003 0.064514 0.040520 0.126642 0.062678 0.166944 0.231402 0.215488 lnL0 = -1188.452100 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1188.452100 x= 0.04700 0.06451 0.04052 0.12664 0.06268 0.16694 0.23140 0.21549 1 h-lim-p 0.0002 0.0015 71.4107 1187.275139 0 0.0004 23 | 0/8 2 h-lim-p 0.0009 0.0075 20.3844 1187.173321 7 0.0005 54 | 0/8 3 h-lim-p 0.0013 0.0146 8.4277 1187.150392 7 0.0007 85 | 0/8 4 h-lim-p 0.0008 0.0306 7.9630 1187.139668 5 0.0006 109 | 0/8 5 h-lim-p 0.0042 0.1715 1.0973 1187.139136 3 0.0008 128 | 0/8 6 h-lim-p 0.0050 0.4898 0.1812 1187.138592 1 0.0063 142 | 0/8 7 h-lim-p 0.0203 1.9873 0.0562 1187.062573 0 0.1628 165 | 0/8 8 h-lim-p 0.0245 0.4738 0.3726 1187.062493 3 0.0012 194 | 0/8 9 h-lim-p 0.6082 20.0000 0.0007 1187.062102 0 1.2165 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1187.062086 2 0.9961 239 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1187.062086 0 1.0938 259 | 0/8 12 h-lim-p 1.2720 20.0000 0.0000 1187.062086 0 1.2720 279 | 0/8 13 h-lim-p 0.4976 20.0000 0.0000 1187.062086 0 0.2488 299 | 0/8 14 h-lim-p 0.0249 20.0000 0.0002 1187.062086 0 0.0249 319 | 0/8 15 h-lim-p 0.0091 20.0000 0.0005 1187.062086 0 0.0000 346 | 0/8 16 h-lim-p 0.0001 20.0000 0.0002 1187.062086 0 0.0000 380 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 1187.062086 0 0.0000 404 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 1187.062086 0 0.0102 434 | 0/8 19 h-lim-p 0.0217 20.0000 0.0000 1187.062086 0 0.0000 466 | 0/8 20 h-lim-p 0.0000 20.0000 0.0000 1187.062086 0 0.0000 486 | 0/8 21 h-lim-p 0.0000 20.0000 0.0000 1187.062086 0 0.0000 507 | 0/8 22 h-lim-p 0.0000 20.0000 0.0005 1187.062086 0 0.0000 527 | 0/8 23 h-lim-p 0.0000 20.0000 0.0001 1187.062086 0 0.0000 549 | 0/8 24 h-lim-p 0.0000 20.0000 0.0001 1187.062086 0 0.0000 574 | 0/8 25 h-lim-p 0.0000 20.0000 0.0007 1187.062086 0 0.0000 607 | 0/8 26 h-lim-p 0.0000 20.0000 0.0017 1187.062086 0 0.0000 634 | 0/8 27 h-lim-p 0.0000 20.0000 0.0005 1187.062086 0 0.0013 661 | 0/8 28 h-lim-p 0.0049 20.0000 0.0001 1187.062086 0 0.0011 682 | 0/8 29 h-lim-p 0.0022 20.0000 0.0001 1187.062086 0 0.0043 703 | 0/8 30 h-lim-p 0.0096 20.0000 0.0000 1187.062086 0 0.0002 728 | 0/8 31 h-lim-p 0.0000 20.0000 0.0006 1187.062086 0 0.0000 748 | 0/8 32 h-lim-p 0.0000 20.0000 0.0030 1187.062086 0 0.0000 774 | 0/8 33 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 34 h-lim-p 0.0000 20.0000 0.0020 | 0/8 35 h-lim-p 0.0000 20.0000 0.0020 Out... lnL = -1187.062086 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1187.062086 Node 7: lnL = -1187.062086 Node 8: lnL = -1187.062086 Node 9: lnL = -1187.062086 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 532 Sequential format.. Reading seq # 1: YPL030W_Sbay Reading seq # 2: YPL030W_Scer Reading seq # 3: YPL030W_Skud Reading seq # 4: YPL030W_Smik Reading seq # 5: YPL030W_Spar Sequences read.. Counting patterns.. # site patterns = 181 Counting frequencies.. 120 bytes for distance 28960 bytes for lkl0 23168 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.057952 0.066817 0.075524 0.115095 0.052263 0.196795 0.174287 0.232186 lnL0 = -2345.297646 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2345.297646 x= 0.05795 0.06682 0.07552 0.11510 0.05226 0.19680 0.17429 0.23219 1 h-lim-p 0.0175 2.5820 51.8145 2344.937569 5 0.0003 38 | 0/8 2 h-lim-p 0.0010 0.0083 12.2038 2344.913505 5 0.0003 62 | 0/8 3 h-lim-p 0.0004 0.0226 10.3235 2344.903453 6 0.0003 89 | 0/8 4 h-lim-p 0.0021 0.1509 1.4341 2344.903098 3 0.0004 110 | 0/8 5 h-lim-p 0.0038 1.4664 0.1390 2344.903094 0 0.0005 124 | 0/8 6 h-lim-p 0.0019 9.6495 0.0339 2344.903094 0 0.0008 144 | 0/8 7 h-lim-p 0.0103 20.0000 0.0028 2344.903094 0 0.0023 165 | 0/8 8 h-lim-p 0.0274 20.0000 0.0002 2344.903086 0 0.4388 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2344.903085 0 1.0938 209 | 0/8 10 h-lim-p 1.8018 20.0000 0.0000 2344.903085 0 0.7883 229 | 0/8 11 h-lim-p 0.7014 20.0000 0.0000 2344.903085 0 0.0658 252 | 0/8 12 h-lim-p 0.0274 20.0000 0.0000 2344.903085 0 0.0015 275 | 0/8 13 h-lim-p 0.0008 20.0000 0.0001 2344.903085 0 0.0000 305 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 2344.903085 0 0.0000 329 Out... lnL = -2344.903085 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2344.903085 Node 7: lnL = -2344.903085 Node 8: lnL = -2344.903085 Node 9: lnL = -2344.903085 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 759 Sequential format.. Reading seq # 1: YPL033C_Sbay Reading seq # 2: YPL033C_Scer Reading seq # 3: YPL033C_Skud Reading seq # 4: YPL033C_Smik Reading seq # 5: YPL033C_Spar Sequences read.. Counting patterns.. # site patterns = 259 Counting frequencies.. 120 bytes for distance 41440 bytes for lkl0 33152 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.048453 0.084965 0.079330 0.138123 0.083999 0.159602 0.193124 0.232793 lnL0 = -3348.812329 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3348.812329 x= 0.04845 0.08496 0.07933 0.13812 0.08400 0.15960 0.19312 0.23279 1 h-lim-p 0.0003 0.0027 113.0188 3347.400505 9 0.0002 44 | 0/8 2 h-lim-p 0.0014 0.0109 16.1804 3347.355670 2 0.0003 61 | 0/8 3 h-lim-p 0.0008 0.0547 7.0386 3347.350471 5 0.0002 85 | 0/8 4 h-lim-p 0.0007 0.0941 2.6672 3347.349330 5 0.0004 111 | 0/8 5 h-lim-p 0.0030 1.0918 0.3348 3347.349306 2 0.0004 129 | 0/8 6 h-lim-p 0.0071 11.4933 0.0186 3347.349306 0 0.0008 151 | 0/8 7 h-lim-p 0.0034 20.0000 0.0043 3347.349306 0 0.0034 171 | 0/8 8 h-lim-p 0.0049 20.0000 0.0029 3347.349245 0 0.0789 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3347.349245 0 1.0938 215 | 0/8 10 h-lim-p 1.8580 20.0000 0.0000 3347.349245 0 1.6258 235 | 0/8 11 h-lim-p 1.9065 20.0000 0.0000 3347.349245 0 0.8341 255 | 0/8 12 h-lim-p 0.2462 20.0000 0.0001 3347.349245 0 0.0539 276 | 0/8 13 h-lim-p 0.0115 20.0000 0.0003 3347.349245 0 0.0003 301 | 0/8 14 h-lim-p 0.0003 20.0000 0.0003 3347.349245 0 0.0000 323 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 3347.349245 0 0.0000 353 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 3347.349245 0 0.0000 381 Out... lnL = -3347.349245 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3347.349245 Node 7: lnL = -3347.349245 Node 8: lnL = -3347.349245 Node 9: lnL = -3347.349245 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 859 Sequential format.. Reading seq # 1: YPL034W_Sbay Reading seq # 2: YPL034W_Scer Reading seq # 3: YPL034W_Skud Reading seq # 4: YPL034W_Smik Reading seq # 5: YPL034W_Spar Sequences read.. Counting patterns.. # site patterns = 276 Counting frequencies.. 120 bytes for distance 44160 bytes for lkl0 35328 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.044787 0.087778 0.036165 0.078630 0.096027 0.196487 0.186147 0.211978 lnL0 = -3545.312052 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3545.312052 x= 0.04479 0.08778 0.03617 0.07863 0.09603 0.19649 0.18615 0.21198 1 h-lim-p 0.0005 0.0037 199.6036 3542.843999 7 0.0001 39 | 0/8 2 h-lim-p 0.0004 0.0034 59.6543 3542.336081 7 0.0003 68 | 0/8 3 h-lim-p 0.0006 0.0060 31.1565 3542.251817 7 0.0002 98 | 0/8 4 h-lim-p 0.0005 0.0083 13.4507 3542.233609 4 0.0002 120 | 0/8 5 h-lim-p 0.0010 0.0450 3.3656 3542.231907 4 0.0003 142 | 0/8 6 h-lim-p 0.0007 0.1314 1.6936 3542.231469 4 0.0004 164 | 0/8 7 h-lim-p 0.0081 2.6130 0.0806 3542.231467 1 0.0005 181 | 0/8 8 h-lim-p 0.0791 20.0000 0.0005 3542.230949 0 0.9498 204 | 0/8 9 h-lim-p 0.4184 20.0000 0.0011 3542.230936 0 1.2553 225 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 3542.230935 0 1.0938 245 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3542.230935 0 1.0938 265 | 0/8 12 h-lim-p 2.0035 20.0000 0.0000 3542.230935 0 4.0071 286 | 0/8 13 h-lim-p 0.0860 20.0000 0.0011 3542.230935 0 0.0188 307 | 0/8 14 h-lim-p 0.0054 15.9639 0.0039 3542.230935 0 0.0000 341 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 3542.230935 0 0.0000 366 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 3542.230935 0 0.0000 398 Out... lnL = -3542.230935 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3542.230935 Node 7: lnL = -3542.230935 Node 8: lnL = -3542.230935 Node 9: lnL = -3542.230935 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 869 Sequential format.. Reading seq # 1: YPL036W_Sbay Reading seq # 2: YPL036W_Scer Reading seq # 3: YPL036W_Skud Reading seq # 4: YPL036W_Smik Reading seq # 5: YPL036W_Spar Sequences read.. Counting patterns.. # site patterns = 169 Counting frequencies.. 120 bytes for distance 27040 bytes for lkl0 21632 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.218946 0.000060 0.282002 0.134881 0.310139 0.439773 0.065806 0.475849 lnL0 = -3242.972487 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3242.972487 x= 0.21895 0.00006 0.28200 0.13488 0.31014 0.43977 0.06581 0.47585 1 h-lim-p 0.0000 0.0000 602.4248 3242.793511 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0003 1605.7011 3122.791838 0 0.0002 38 | 1/8 3 h-lim-p 0.0001 0.0004 462.3282 3099.778885 m 0.0004 50 | 1/8 4 h-lim-p -0.0000 -0.0000 147.9449 h-lim-p: -9.59692399e-21 -7.67753919e-20 1.47944894e+02 3099.778885 .. | 1/8 5 h-lim-p 0.0000 0.0013 455.3122 3090.407472 0 0.0002 74 | 1/8 6 h-lim-p 0.0001 0.0008 226.7225 3085.223468 0 0.0002 87 | 1/8 7 h-lim-p 0.0006 0.0046 51.1135 3084.689950 7 0.0004 113 | 1/8 8 h-lim-p 0.0008 0.0062 16.2785 3084.484142 0 0.0015 126 | 1/8 9 h-lim-p 0.0003 0.0387 74.3707 3083.173092 0 0.0027 141 | 1/8 10 h-lim-p 0.0004 0.0032 280.1412 3082.260212 1 0.0005 155 | 1/8 11 h-lim-p 1.0377 8.3013 0.0862 3080.927557 0 1.5565 167 | 0/8 12 h-lim-p 0.0064 0.0512 15.8848 3080.912770 6 0.0002 205 | 0/8 13 h-lim-p 0.0868 11.9214 0.0443 3080.699826 0 1.0417 220 | 0/8 14 h-lim-p 1.7155 20.0000 0.0269 3080.670714 0 3.4309 241 | 0/8 15 h-lim-p 2.5000 20.0000 0.0028 3080.668855 2 1.1719 265 | 0/8 16 h-lim-p 2.5000 20.0000 0.0010 3080.668494 0 7.5000 286 | 0/8 17 h-lim-p 0.3862 3.0894 0.0014 3080.666681 m 3.0894 306 | 1/8 18 h-lim-p 0.3647 20.0000 0.0084 3080.666633 1 0.0228 331 | 1/8 19 h-lim-p 0.0317 20.0000 0.0060 3080.666510 0 1.0134 355 | 1/8 20 h-lim-p 2.5000 20.0000 0.0001 3080.666507 0 1.0938 374 | 1/8 21 h-lim-p 1.4689 20.0000 0.0001 3080.666507 0 1.2853 393 | 1/8 22 h-lim-p 2.5000 20.0000 0.0000 3080.666507 0 2.1875 412 | 1/8 23 h-lim-p 0.4615 20.0000 0.0002 3080.666507 0 0.0009 439 | 1/8 24 h-lim-p 0.0002 20.0000 0.0007 3080.666507 0 0.0000 470 | 1/8 25 h-lim-p 0.0000 20.0000 0.0004 | 1/8 26 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -3080.666507 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3080.666507 Node 7: lnL = -3080.666507 Node 8: lnL = -3080.666507 Node 9: lnL = -3080.666507 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 870 Sequential format.. Reading seq # 1: YPL037C_Sbay Reading seq # 2: YPL037C_Scer Reading seq # 3: YPL037C_Skud Reading seq # 4: YPL037C_Smik Reading seq # 5: YPL037C_Spar Sequences read.. Counting patterns.. # site patterns = 190 Counting frequencies.. 120 bytes for distance 30400 bytes for lkl0 24320 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.086195 0.047259 0.027808 0.081475 0.078120 0.106039 0.188509 0.227509 lnL0 = -3137.973832 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3137.973832 x= 0.08619 0.04726 0.02781 0.08148 0.07812 0.10604 0.18851 0.22751 1 h-lim-p 0.0004 0.0035 140.6083 3136.132702 2 0.0002 26 | 0/8 2 h-lim-p 0.0001 0.0010 120.2518 3134.791170 0 0.0002 39 | 0/8 3 h-lim-p 0.0002 0.0018 45.7593 3134.516711 0 0.0004 52 | 0/8 4 h-lim-p 0.0001 0.0011 55.1930 3134.278071 0 0.0003 65 | 0/8 5 h-lim-p 0.0002 0.0014 32.8617 3134.216334 1 0.0002 79 | 0/8 6 h-lim-p 0.0018 0.0369 4.0664 3134.209583 3 0.0009 98 | 0/8 7 h-lim-p 0.0026 0.1681 1.3235 3134.209226 3 0.0004 119 | 0/8 8 h-lim-p 0.0842 15.1297 0.0067 3134.156466 0 1.0104 134 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 3134.155506 3 1.0483 161 | 0/8 10 h-lim-p 2.5000 20.0000 0.0002 3134.155494 0 1.0938 181 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3134.155494 0 1.0938 201 | 0/8 12 h-lim-p 1.6222 20.0000 0.0000 3134.155494 0 0.7097 221 | 0/8 13 h-lim-p 0.3202 20.0000 0.0000 3134.155494 0 0.0300 244 | 0/8 14 h-lim-p 0.0083 20.0000 0.0001 3134.155494 0 0.0001 269 | 0/8 15 h-lim-p 0.0000 2.8186 0.0510 3134.155494 0 0.0000 289 | 0/8 16 h-lim-p 0.0033 20.0000 0.0002 3134.155494 0 0.0000 328 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 3134.155494 0 0.0000 358 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 | 0/8 19 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -3134.155494 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3134.155494 Node 7: lnL = -3134.155494 Node 8: lnL = -3134.155494 Node 9: lnL = -3134.155494 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 406 Sequential format.. Reading seq # 1: YPL038W_Sbay Reading seq # 2: YPL038W_Scer Reading seq # 3: YPL038W_Skud Reading seq # 4: YPL038W_Smik Reading seq # 5: YPL038W_Spar Sequences read.. Counting patterns.. # site patterns = 179 Counting frequencies.. 120 bytes for distance 28640 bytes for lkl0 22912 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.025487 0.070857 0.064554 0.185303 0.086387 0.193020 0.239396 0.208684 lnL0 = -1811.771993 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1811.771993 x= 0.02549 0.07086 0.06455 0.18530 0.08639 0.19302 0.23940 0.20868 1 h-lim-p 0.0011 0.0088 71.7103 1810.738741 4 0.0004 30 | 0/8 2 h-lim-p 0.0010 0.0082 19.3843 1810.623813 7 0.0006 59 | 0/8 3 h-lim-p 0.0013 0.0237 9.8695 1810.602420 5 0.0005 80 | 0/8 4 h-lim-p 0.0028 0.1441 1.9239 1810.600845 4 0.0009 102 | 0/8 5 h-lim-p 0.0029 0.2521 0.5934 1810.600738 2 0.0007 119 | 0/8 6 h-lim-p 0.0065 1.0771 0.0619 1810.600737 1 0.0008 143 | 0/8 7 h-lim-p 0.0102 20.0000 0.0049 1810.600735 0 0.0102 163 | 0/8 8 h-lim-p 0.0124 20.0000 0.0040 1810.600588 0 0.0989 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1810.600588 0 1.0938 206 | 0/8 10 h-lim-p 1.2616 20.0000 0.0000 1810.600588 0 1.2616 226 | 0/8 11 h-lim-p 0.7745 20.0000 0.0000 1810.600588 0 3.0981 248 | 0/8 12 h-lim-p 0.0464 20.0000 0.0016 1810.600588 0 0.0029 271 | 0/8 13 h-lim-p 0.0011 10.8555 0.0042 1810.600588 0 0.0000 295 | 0/8 14 h-lim-p 0.0001 20.0000 0.0011 1810.600588 0 0.0000 334 | 0/8 15 h-lim-p 0.0000 20.0000 0.0007 1810.600588 0 0.0000 357 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0007 | 0/8 18 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -1810.600588 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1810.600588 Node 7: lnL = -1810.600588 Node 8: lnL = -1810.600588 Node 9: lnL = -1810.600588 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 260 Sequential format.. Reading seq # 1: YPL041C_Sbay Reading seq # 2: YPL041C_Scer Reading seq # 3: YPL041C_Skud Reading seq # 4: YPL041C_Smik Reading seq # 5: YPL041C_Spar Sequences read.. Counting patterns.. # site patterns = 68 Counting frequencies.. 120 bytes for distance 10880 bytes for lkl0 8704 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.421319 0.572530 0.317218 0.000060 0.668694 0.323057 2.560139 1.023203 lnL0 = -817.823056 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 817.823056 x= 0.42132 0.57253 0.31722 0.00006 0.66869 0.32306 2.56014 1.02320 1 h-lim-p 0.0000 0.0000 115.0363 817.789758 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0036 186.4579 789.938661 10 0.0024 66 | 1/8 3 h-lim-p 0.0607 0.4856 1.1470 781.752681 m 0.4856 78 | 1/8 4 h-lim-p 0.0000 0.0001 10283.1040 772.944722 0 0.0001 92 | 1/8 5 h-lim-p 0.0321 0.2572 10.2282 766.637442 0 0.1286 106 | 0/8 6 h-lim-p 0.0002 0.0019 689.8260 761.412876 0 0.0010 120 | 0/8 7 h-lim-p 0.2440 1.9517 1.5434 759.776398 0 0.4879 133 | 0/8 8 h-lim-p 0.1176 0.9410 1.3663 759.768386 0 0.2353 146 | 0/8 9 h-lim-p 0.7213 5.7700 0.1544 .. | 0/8 10 h-lim-p 0.0000 0.6181 162.3444 755.114008 0 0.0006 213 | 0/8 11 h-lim-p 0.0004 0.0030 34.9988 754.550475 0 0.0008 226 | 0/8 12 h-lim-p 0.0586 0.5361 0.4549 754.549895 5 0.0025 253 | 0/8 13 h-lim-p 0.0450 5.3147 0.0252 754.348453 0 0.7204 277 | 0/8 14 h-lim-p 1.8148 20.0000 0.0100 754.309398 6 0.9157 313 | 0/8 15 h-lim-p 2.5000 20.0000 0.0010 754.309340 3 0.9482 339 | 0/8 16 h-lim-p 0.9686 20.0000 0.0010 754.309336 0 7.7488 362 | 0/8 17 h-lim-p 0.9996 20.0000 0.0075 754.309189 m20.0000 384 | 0/8 18 h-lim-p 0.0003 0.0023 62.3745 754.309047 m 0.0023 404 | 0/8 19 h-lim-p -0.0000 -0.0000 0.4299 h-lim-p: -5.38289317e-19 -4.30631454e-18 4.29883196e-01 754.309047 .. | 0/8 20 h-lim-p 0.0000 0.2684 0.2735 754.309025 0 0.0006 438 | 0/8 21 h-lim-p 0.0022 16.8195 0.0803 754.309020 1 0.0017 460 | 0/8 22 h-lim-p 0.0000 0.0000 0.0413 754.309020 m 0.0000 480 | 1/8 23 h-lim-p 0.0000 9.6034 0.0221 754.309020 0 0.0007 504 | 1/8 24 h-lim-p 0.0268 20.0000 0.0006 754.309019 0 2.5719 529 | 1/8 25 h-lim-p 1.3017 20.0000 0.0012 754.309016 0 7.8104 550 | 1/8 26 h-lim-p 2.4821 20.0000 0.0038 754.309016 0 0.0000 594 | 1/8 27 h-lim-p 0.0000 5.0424 0.0621 754.309013 0 0.0019 620 | 1/8 28 h-lim-p 0.0071 7.8925 0.0167 754.309013 0 0.0016 640 | 1/8 29 h-lim-p 0.0024 20.0000 0.0107 754.309013 0 0.0011 659 | 1/8 30 h-lim-p 0.0181 20.0000 0.0006 754.309012 0 2.3143 685 | 1/8 31 h-lim-p 0.9140 20.0000 0.0016 754.308993 m20.0000 706 | 1/8 32 h-lim-p 0.0023 0.2619 13.7141 754.203892 0 0.2055 731 | 1/8 33 h-lim-p 0.9922 20.0000 2.8403 .. | 1/8 34 h-lim-p 0.0000 0.1128 2.7314 754.196784 0 0.0019 792 | 1/8 35 h-lim-p 0.0059 0.7753 0.8903 754.196536 2 0.0007 810 | 1/8 36 h-lim-p 0.0019 0.4097 0.3305 754.196480 4 0.0011 840 | 1/8 37 h-lim-p 0.0043 8.8301 0.0875 754.192235 0 1.1047 867 | 1/8 38 h-lim-p 2.5000 20.0000 0.0026 754.192233 2 0.8246 892 | 1/8 39 h-lim-p 2.5000 20.0000 0.0002 754.192233 0 1.0938 911 | 1/8 40 h-lim-p 2.5000 20.0000 0.0000 754.192233 0 1.0938 930 | 1/8 41 h-lim-p 2.5000 20.0000 0.0000 754.192233 0 2.1875 949 | 1/8 42 h-lim-p 1.8425 20.0000 0.0000 754.192233 0 0.4606 969 | 1/8 43 h-lim-p 0.8538 20.0000 0.0000 754.192233 0 0.0067 994 Out... lnL = -754.192233 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -754.192233 Node 7: lnL = -754.192233 Node 8: lnL = -754.192233 Node 9: lnL = -754.192233 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 321 Sequential format.. Reading seq # 1: YPL046C_Sbay Reading seq # 2: YPL046C_Scer Reading seq # 3: YPL046C_Skud Reading seq # 4: YPL046C_Smik Reading seq # 5: YPL046C_Spar Sequences read.. Counting patterns.. # site patterns = 168 Counting frequencies.. 120 bytes for distance 26880 bytes for lkl0 21504 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.088496 0.110382 0.092670 0.093858 0.157099 0.236575 0.172627 0.306781 lnL0 = -1459.762710 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1459.762710 x= 0.08850 0.11038 0.09267 0.09386 0.15710 0.23657 0.17263 0.30678 1 h-lim-p 0.0019 0.0150 34.1095 1459.320599 6 0.0008 36 | 0/8 2 h-lim-p 0.0018 0.0147 14.4651 1459.240798 2 0.0009 52 | 0/8 3 h-lim-p 0.0020 0.0347 6.1395 1459.221108 5 0.0013 78 | 0/8 4 h-lim-p 0.0033 0.1272 2.3693 1459.218506 5 0.0011 103 | 0/8 5 h-lim-p 0.0032 0.3284 0.8090 1459.218049 2 0.0016 119 | 0/8 6 h-lim-p 0.0065 1.6237 0.1974 1459.218029 2 0.0010 145 | 0/8 7 h-lim-p 0.2486 20.0000 0.0008 1459.218021 1 0.1981 167 | 0/8 8 h-lim-p 0.0050 7.6743 0.0331 1459.217987 0 0.0099 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1459.217987 0 1.0938 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1459.217987 0 1.0938 228 | 0/8 11 h-lim-p 1.2665 20.0000 0.0000 1459.217987 0 0.0198 253 | 0/8 12 h-lim-p 0.0060 20.0000 0.0000 1459.217987 0 0.0000 283 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 1459.217987 0 0.0000 305 Out... lnL = -1459.217987 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1459.217987 Node 7: lnL = -1459.217987 Node 8: lnL = -1459.217987 Node 9: lnL = -1459.217987 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 337 Sequential format.. Reading seq # 1: YPL047W_Sbay Reading seq # 2: YPL047W_Scer Reading seq # 3: YPL047W_Skud Reading seq # 4: YPL047W_Smik Reading seq # 5: YPL047W_Spar Sequences read.. Counting patterns.. # site patterns = 170 Counting frequencies.. 120 bytes for distance 27200 bytes for lkl0 21760 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.017620 0.198051 0.039236 0.148541 0.104455 0.190777 0.177654 0.211217 lnL0 = -1466.843809 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1466.843809 x= 0.01762 0.19805 0.03924 0.14854 0.10445 0.19078 0.17765 0.21122 1 h-lim-p 0.0037 1.2342 88.4805 1465.411803 7 0.0004 37 | 0/8 2 h-lim-p 0.0017 0.0133 20.8165 1465.183842 7 0.0011 64 | 0/8 3 h-lim-p 0.0017 0.0132 9.2569 1465.152817 6 0.0009 91 | 0/8 4 h-lim-p 0.0021 0.0183 3.8721 1465.146656 2 0.0010 107 | 0/8 5 h-lim-p 0.0029 0.1864 1.2933 1465.145637 2 0.0014 123 | 0/8 6 h-lim-p 0.0156 1.8051 0.1126 1465.145627 1 0.0015 139 | 0/8 7 h-lim-p 0.0197 20.0000 0.0089 1465.145622 1 0.0097 162 | 0/8 8 h-lim-p 0.0119 20.0000 0.0072 1465.145095 0 0.0955 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1465.145072 2 0.9961 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1465.145072 0 1.0938 229 | 0/8 11 h-lim-p 1.0457 20.0000 0.0000 1465.145072 0 4.1829 251 | 0/8 12 h-lim-p 1.4771 20.0000 0.0000 1465.145072 0 1.2925 271 | 0/8 13 h-lim-p 0.0433 20.0000 0.0009 1465.145072 0 0.0108 292 | 0/8 14 h-lim-p 0.0034 13.4429 0.0027 1465.145072 0 0.0001 316 | 0/8 15 h-lim-p 0.0000 2.2538 0.0163 1465.145072 0 0.0000 336 | 0/8 16 h-lim-p 0.0001 20.0000 0.0011 1465.145072 0 0.0001 356 | 0/8 17 h-lim-p 0.0001 20.0000 0.0009 1465.145072 0 0.0000 376 | 0/8 18 h-lim-p 0.0001 20.0000 0.0002 1465.145072 0 0.0000 407 | 0/8 19 h-lim-p 0.0001 20.0000 0.0000 1465.145072 0 0.0000 437 Out... lnL = -1465.145072 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1465.145072 Node 7: lnL = -1465.145072 Node 8: lnL = -1465.145072 Node 9: lnL = -1465.145072 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 656 Sequential format.. Reading seq # 1: YPL048W_Sbay Reading seq # 2: YPL048W_Scer Reading seq # 3: YPL048W_Skud Reading seq # 4: YPL048W_Smik Reading seq # 5: YPL048W_Spar Sequences read.. Counting patterns.. # site patterns = 189 Counting frequencies.. 120 bytes for distance 30240 bytes for lkl0 24192 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.086534 0.029100 0.070303 0.066513 0.046028 0.100046 0.158316 0.219043 lnL0 = -2464.500681 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2464.500681 x= 0.08653 0.02910 0.07030 0.06651 0.04603 0.10005 0.15832 0.21904 1 h-lim-p 0.0003 0.0025 221.8873 2461.240109 4 0.0002 31 | 0/8 2 h-lim-p 0.0005 0.0043 40.0037 2460.937877 7 0.0004 58 | 0/8 3 h-lim-p 0.0004 0.0059 34.3867 2460.887601 5 0.0001 82 | 0/8 4 h-lim-p 0.0005 0.0131 8.6254 2460.880585 3 0.0002 100 | 0/8 5 h-lim-p 0.0007 0.0611 2.5100 2460.879820 4 0.0003 121 | 0/8 6 h-lim-p 0.0025 0.4069 0.2703 2460.879811 1 0.0002 137 | 0/8 7 h-lim-p 0.0010 2.3034 0.0692 2460.879809 1 0.0008 159 | 0/8 8 h-lim-p 0.0590 20.0000 0.0009 2460.878160 0 0.9437 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 2460.878134 2 0.9644 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2460.878134 0 0.5469 228 | 0/8 11 h-lim-p 0.3041 20.0000 0.0000 2460.878134 0 0.0760 249 | 0/8 12 h-lim-p 0.0446 20.0000 0.0000 2460.878134 0 0.0014 273 | 0/8 13 h-lim-p 0.0008 20.0000 0.0000 2460.878134 0 0.0012 293 | 0/8 14 h-lim-p 0.0011 20.0000 0.0001 2460.878134 0 0.0000 330 | 0/8 15 h-lim-p 0.0000 20.0000 0.0051 | 0/8 16 h-lim-p 0.0000 20.0000 0.0051 Out... lnL = -2460.878134 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2460.878134 Node 7: lnL = -2460.878134 Node 8: lnL = -2460.878134 Node 9: lnL = -2460.878134 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 654 Sequential format.. Reading seq # 1: YPL049C_Sbay Reading seq # 2: YPL049C_Scer Reading seq # 3: YPL049C_Skud Reading seq # 4: YPL049C_Smik Reading seq # 5: YPL049C_Spar Sequences read.. Counting patterns.. # site patterns = 182 Counting frequencies.. 120 bytes for distance 29120 bytes for lkl0 23296 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.073908 0.040280 0.063841 0.068672 0.041778 0.097605 0.153938 0.201238 lnL0 = -2428.818924 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2428.818924 x= 0.07391 0.04028 0.06384 0.06867 0.04178 0.09760 0.15394 0.20124 1 h-lim-p 0.0001 0.0010 191.3731 2426.156499 0 0.0002 22 | 0/8 2 h-lim-p 0.0009 0.0072 31.2830 2426.039331 7 0.0002 51 | 0/8 3 h-lim-p 0.0002 0.0030 34.0420 2425.984813 6 0.0002 77 | 0/8 4 h-lim-p 0.0006 0.0234 8.8825 2425.976914 5 0.0002 99 | 0/8 5 h-lim-p 0.0012 0.0805 1.7108 2425.976520 2 0.0003 116 | 0/8 6 h-lim-p 0.0011 0.2733 0.4318 2425.976487 2 0.0003 133 | 0/8 7 h-lim-p 0.0029 2.9328 0.0422 2425.975913 0 0.0229 156 | 0/8 8 h-lim-p 0.0056 0.4528 0.1732 2425.939418 0 0.0223 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 2425.938632 4 0.9644 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2425.938632 0 1.0938 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2425.938632 0 1.0938 246 | 0/8 12 h-lim-p 0.8684 20.0000 0.0000 2425.938632 0 0.0001 279 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 2425.938632 0 0.0000 299 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 2425.938632 0 0.0000 322 Out... lnL = -2425.938632 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2425.938632 Node 7: lnL = -2425.938632 Node 8: lnL = -2425.938632 Node 9: lnL = -2425.938632 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 543 Sequential format.. Reading seq # 1: YPL050C_Sbay Reading seq # 2: YPL050C_Scer Reading seq # 3: YPL050C_Skud Reading seq # 4: YPL050C_Smik Reading seq # 5: YPL050C_Spar Sequences read.. Counting patterns.. # site patterns = 189 Counting frequencies.. 120 bytes for distance 30240 bytes for lkl0 24192 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.022119 0.025117 0.054804 0.099260 0.100826 0.207787 0.159892 0.162048 lnL0 = -2189.723168 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2189.723168 x= 0.02212 0.02512 0.05480 0.09926 0.10083 0.20779 0.15989 0.16205 1 h-lim-p 0.0008 0.0065 144.1802 2188.247267 8 0.0002 38 | 0/8 2 h-lim-p 0.0006 0.0047 19.7949 2188.185872 6 0.0003 63 | 0/8 3 h-lim-p 0.0019 0.0634 3.2987 2188.183711 4 0.0004 83 | 0/8 4 h-lim-p 0.0013 0.1748 1.0024 2188.183547 3 0.0004 102 | 0/8 5 h-lim-p 0.0016 0.2773 0.2299 2188.183539 1 0.0003 117 | 0/8 6 h-lim-p 0.0015 4.5517 0.0478 2188.183539 0 0.0007 137 | 0/8 7 h-lim-p 0.0050 17.6005 0.0063 2188.183539 0 0.0005 159 | 0/8 8 h-lim-p 0.0655 20.0000 0.0001 2188.183538 0 1.0477 183 | 0/8 9 h-lim-p 2.2277 20.0000 0.0000 2188.183537 0 0.9746 203 | 0/8 10 h-lim-p 0.7643 20.0000 0.0000 2188.183537 0 0.0015 231 | 0/8 11 h-lim-p 0.0004 20.0000 0.0001 2188.183537 0 0.0001 252 | 0/8 12 h-lim-p 0.0001 20.0000 0.0002 2188.183537 0 0.0000 286 | 0/8 13 h-lim-p 0.0000 20.0000 0.0017 | 0/8 14 h-lim-p 0.0000 20.0000 0.0017 Out... lnL = -2188.183537 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2188.183537 Node 7: lnL = -2188.183537 Node 8: lnL = -2188.183537 Node 9: lnL = -2188.183537 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 333 Sequential format.. Reading seq # 1: YPL051W_Sbay Reading seq # 2: YPL051W_Scer Reading seq # 3: YPL051W_Skud Reading seq # 4: YPL051W_Smik Reading seq # 5: YPL051W_Spar Sequences read.. Counting patterns.. # site patterns = 179 Counting frequencies.. 120 bytes for distance 28640 bytes for lkl0 22912 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.007788 0.238006 0.136325 0.125425 0.103531 0.251261 0.177113 0.243793 lnL0 = -1504.532203 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1504.532203 x= 0.00779 0.23801 0.13632 0.12542 0.10353 0.25126 0.17711 0.24379 1 h-lim-p 0.0018 0.0143 32.5730 1504.002986 8 0.0010 42 | 0/8 2 h-lim-p 0.0013 0.0107 12.8662 1503.931044 6 0.0010 69 | 0/8 3 h-lim-p 0.0019 0.0298 6.5513 1503.899120 3 0.0019 87 | 0/8 4 h-lim-p 0.0185 1.6230 0.6674 1503.898706 3 0.0019 107 | 0/8 5 h-lim-p 0.0038 0.0875 0.3393 1503.898652 3 0.0011 136 | 0/8 6 h-lim-p 0.0030 2.5564 0.1269 1503.898643 1 0.0013 158 | 0/8 7 h-lim-p 0.0653 20.0000 0.0025 1503.898643 0 0.0143 179 | 0/8 8 h-lim-p 0.0198 20.0000 0.0018 1503.898619 0 0.1187 201 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1503.898619 0 1.0938 221 | 0/8 10 h-lim-p 1.6753 20.0000 0.0000 1503.898619 0 1.6753 241 | 0/8 11 h-lim-p 0.7117 20.0000 0.0000 1503.898619 0 0.0000 277 | 0/8 12 h-lim-p 0.0000 20.0000 0.0003 1503.898619 0 0.0000 303 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -1503.898619 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1503.898619 Node 7: lnL = -1503.898619 Node 8: lnL = -1503.898619 Node 9: lnL = -1503.898619 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 661 Sequential format.. Reading seq # 1: YPL052W_Sbay Reading seq # 2: YPL052W_Scer Reading seq # 3: YPL052W_Skud Reading seq # 4: YPL052W_Smik Reading seq # 5: YPL052W_Spar Sequences read.. Counting patterns.. # site patterns = 201 Counting frequencies.. 120 bytes for distance 32160 bytes for lkl0 25728 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.062868 0.037349 0.038511 0.085156 0.077938 0.128771 0.181213 0.199110 lnL0 = -2610.368000 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2610.368000 x= 0.06287 0.03735 0.03851 0.08516 0.07794 0.12877 0.18121 0.19911 1 h-lim-p 0.0004 0.0029 204.9764 2607.561766 3 0.0002 28 | 0/8 2 h-lim-p 0.0003 0.0026 55.9271 2607.074653 6 0.0003 55 | 0/8 3 h-lim-p 0.0005 0.0051 37.4673 2606.942379 5 0.0003 78 | 0/8 4 h-lim-p 0.0008 0.0130 12.1959 2606.927660 6 0.0002 105 | 0/8 5 h-lim-p 0.0011 0.0853 2.5932 2606.926555 4 0.0003 127 | 0/8 6 h-lim-p 0.0051 0.8248 0.1758 2606.926551 1 0.0003 144 | 0/8 7 h-lim-p 0.0027 7.2146 0.0166 2606.926551 0 0.0013 164 | 0/8 8 h-lim-p 0.0122 20.0000 0.0018 2606.926173 0 0.2937 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2606.926159 0 1.0938 208 | 0/8 10 h-lim-p 0.8996 20.0000 0.0001 2606.926159 0 0.8996 228 | 0/8 11 h-lim-p 2.4747 20.0000 0.0000 2606.926159 0 2.1654 248 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2606.926159 0 1.0938 268 | 0/8 13 h-lim-p 0.6997 20.0000 0.0000 2606.926159 0 5.5975 291 | 0/8 14 h-lim-p 0.1767 20.0000 0.0007 2606.926159 0 0.1546 311 | 0/8 15 h-lim-p 0.0343 20.0000 0.0033 2606.926159 0 0.0043 333 | 0/8 16 h-lim-p 0.0012 7.2376 0.0120 2606.926159 0 0.0000 357 | 0/8 17 h-lim-p 0.0002 20.0000 0.0023 2606.926159 0 0.0000 389 | 0/8 18 h-lim-p 0.0001 20.0000 0.0000 2606.926159 0 0.0000 409 Out... lnL = -2606.926159 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2606.926159 Node 7: lnL = -2606.926159 Node 8: lnL = -2606.926159 Node 9: lnL = -2606.926159 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 639 Sequential format.. Reading seq # 1: YPL053C_Sbay Reading seq # 2: YPL053C_Scer Reading seq # 3: YPL053C_Skud Reading seq # 4: YPL053C_Smik Reading seq # 5: YPL053C_Spar Sequences read.. Counting patterns.. # site patterns = 165 Counting frequencies.. 120 bytes for distance 26400 bytes for lkl0 21120 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.226749 0.000060 0.318857 0.124146 0.343920 0.395489 0.061147 0.480489 lnL0 = -2541.396258 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2541.396258 x= 0.22675 0.00006 0.31886 0.12415 0.34392 0.39549 0.06115 0.48049 1 h-lim-p 0.0000 0.0000 543.4271 2541.201738 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0002 1922.9860 2398.621997 0 0.0002 38 | 1/8 3 h-lim-p 0.0000 0.0003 548.0588 2378.265760 m 0.0003 50 | 2/8 4 h-lim-p 0.0001 0.0009 354.1867 2370.869041 0 0.0002 63 | 2/8 5 h-lim-p 0.0009 0.0069 53.4704 2368.766826 0 0.0017 76 | 2/8 6 h-lim-p 0.0008 0.0304 114.4056 2363.980457 0 0.0032 90 | 2/8 7 h-lim-p 0.1028 0.8223 0.3026 2359.817110 0 0.3084 103 | 1/8 8 h-lim-p 0.0016 0.0175 58.3019 2358.910898 8 0.0006 140 | 1/8 9 h-lim-p 0.0249 0.1990 0.6195 2353.994625 m 0.1990 152 | 1/8 10 h-lim-p 0.0000 0.0000 0.0362 h-lim-p: 1.02222904e-18 8.17783230e-18 3.61839489e-02 2353.994625 .. | 1/8 11 h-lim-p 0.0000 0.0426 153.6565 2352.748789 0 0.0002 190 | 1/8 12 h-lim-p 0.0005 0.0075 51.8102 2352.346586 8 0.0003 221 | 1/8 13 h-lim-p 0.0000 0.0001 12.3472 2352.331134 m 0.0001 233 | 2/8 14 h-lim-p 0.0008 0.0984 2.0038 2352.329774 4 0.0006 253 | 2/8 15 h-lim-p 0.0004 0.6456 3.1957 2352.317152 0 0.0062 269 | 2/8 16 h-lim-p 0.0012 0.1511 16.5218 2352.290150 0 0.0024 282 | 2/8 17 h-lim-p 0.4601 7.1175 0.0855 2352.274690 4 0.1483 304 | 2/8 18 h-lim-p 0.5331 4.7156 0.0238 2352.201596 7 0.2953 338 | 1/8 19 h-lim-p 0.0812 15.0442 0.0865 2352.201593 1 0.0006 364 | 1/8 20 h-lim-p 0.1051 1.3591 0.0005 2352.201498 1 0.9702 388 | 1/8 21 h-lim-p 0.0392 0.3138 0.0001 2352.201497 m 0.3138 407 | 2/8 22 h-lim-p 0.0403 20.0000 0.0004 2352.201497 0 0.0605 426 | 2/8 23 h-lim-p 1.5438 20.0000 0.0000 2352.201497 0 1.3508 444 | 2/8 24 h-lim-p 2.5000 20.0000 0.0000 2352.201497 0 1.2500 462 | 2/8 25 h-lim-p 2.5000 20.0000 0.0000 2352.201497 0 2.1875 480 | 2/8 26 h-lim-p 2.5000 20.0000 0.0000 2352.201497 0 0.2734 500 | 2/8 27 h-lim-p 0.3771 20.0000 0.0000 2352.201497 0 0.0471 520 | 2/8 28 h-lim-p 0.0494 20.0000 0.0000 2352.201497 0 0.0062 540 Out... lnL = -2352.201497 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2352.201497 Node 7: lnL = -2352.201497 Node 8: lnL = -2352.201497 Node 9: lnL = -2352.201497 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 839 Sequential format.. Reading seq # 1: YPL055C_Sbay Reading seq # 2: YPL055C_Scer Reading seq # 3: YPL055C_Skud Reading seq # 4: YPL055C_Smik Reading seq # 5: YPL055C_Spar Sequences read.. Counting patterns.. # site patterns = 268 Counting frequencies.. 120 bytes for distance 42880 bytes for lkl0 34304 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.090228 0.011259 0.090181 0.097044 0.034177 0.122416 0.191751 0.238974 lnL0 = -3132.949682 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3132.949682 x= 0.09023 0.01126 0.09018 0.09704 0.03418 0.12242 0.19175 0.23897 1 h-lim-p 0.0012 0.4779 224.3619 3129.946970 6 0.0001 35 | 0/8 2 h-lim-p 0.0002 0.0012 81.7869 3129.310913 0 0.0002 47 | 0/8 3 h-lim-p 0.0001 0.0011 88.3138 3129.033556 2 0.0001 63 | 0/8 4 h-lim-p 0.0009 0.0230 12.2789 3129.002697 2 0.0004 79 | 0/8 5 h-lim-p 0.0069 0.2183 0.7861 3129.002581 2 0.0003 98 | 0/8 6 h-lim-p 0.0007 0.4649 0.4119 3129.002547 2 0.0003 123 | 0/8 7 h-lim-p 0.0262 20.0000 0.0055 3128.978924 0 0.6300 147 | 0/8 8 h-lim-p 0.0011 0.1231 3.2702 3128.973771 5 0.0007 181 | 0/8 9 h-lim-p 1.8431 20.0000 0.0012 3128.971478 5 1.3281 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 3128.971458 1 1.0938 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3128.971458 0 2.1875 248 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3128.971458 0 1.0938 268 | 0/8 13 h-lim-p 0.1895 20.0000 0.0000 3128.971458 0 6.0645 293 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 3128.971458 0 0.1367 316 | 0/8 15 h-lim-p 0.1388 20.0000 0.0000 3128.971458 0 0.0694 336 | 0/8 16 h-lim-p 0.0182 20.0000 0.0001 3128.971458 0 0.0091 356 | 0/8 17 h-lim-p 0.0046 20.0000 0.0002 3128.971458 0 0.0000 384 | 0/8 18 h-lim-p 0.0006 20.0000 0.0000 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0055 | 0/8 20 h-lim-p 0.0000 20.0000 0.0055 Out... lnL = -3128.971458 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3128.971458 Node 7: lnL = -3128.971458 Node 8: lnL = -3128.971458 Node 9: lnL = -3128.971458 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 421 Sequential format.. Reading seq # 1: YPL057C_Sbay Reading seq # 2: YPL057C_Scer Reading seq # 3: YPL057C_Skud Reading seq # 4: YPL057C_Smik Reading seq # 5: YPL057C_Spar Sequences read.. Counting patterns.. # site patterns = 141 Counting frequencies.. 120 bytes for distance 22560 bytes for lkl0 18048 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.071828 0.027201 0.042667 0.064222 0.056389 0.143431 0.152989 0.192791 lnL0 = -1593.100404 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1593.100404 x= 0.07183 0.02720 0.04267 0.06422 0.05639 0.14343 0.15299 0.19279 1 h-lim-p 0.0097 0.0782 57.1908 1592.807725 6 0.0002 42 | 0/8 2 h-lim-p 0.0009 0.0214 11.8670 1592.773108 7 0.0005 71 | 0/8 3 h-lim-p 0.0009 0.0148 6.7487 1592.769142 4 0.0002 92 | 0/8 4 h-lim-p 0.0012 0.0532 1.2425 1592.768753 2 0.0005 108 | 0/8 5 h-lim-p 0.0017 0.3210 0.3886 1592.768731 2 0.0003 125 | 0/8 6 h-lim-p 0.0044 5.3549 0.0287 1592.768731 0 0.0003 148 | 0/8 7 h-lim-p 0.0010 20.0000 0.0077 1592.768731 0 0.0009 168 | 0/8 8 h-lim-p 0.1466 20.0000 0.0000 1592.768727 0 1.1727 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1592.768727 0 1.0938 211 | 0/8 10 h-lim-p 1.7434 20.0000 0.0000 1592.768727 0 1.7434 231 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1592.768727 0 0.0391 256 | 0/8 12 h-lim-p 0.0104 20.0000 0.0000 1592.768727 0 0.0045 276 | 0/8 13 h-lim-p 0.0024 20.0000 0.0000 1592.768727 0 0.0006 297 | 0/8 14 h-lim-p 0.0004 20.0000 0.0001 1592.768727 0 0.0000 326 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 1592.768727 0 0.0000 361 Out... lnL = -1592.768727 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1592.768727 Node 7: lnL = -1592.768727 Node 8: lnL = -1592.768727 Node 9: lnL = -1592.768727 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 882 Sequential format.. Reading seq # 1: YPL059W_Sbay Reading seq # 2: YPL059W_Scer Reading seq # 3: YPL059W_Skud Reading seq # 4: YPL059W_Smik Reading seq # 5: YPL059W_Spar Sequences read.. Counting patterns.. # site patterns = 465 Counting frequencies.. 120 bytes for distance 74400 bytes for lkl0 59520 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.073376 0.000060 0.024559 0.419527 0.284324 0.613764 0.546009 0.437363 lnL0 = -5023.472808 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 5023.472808 x= 0.07338 0.00006 0.02456 0.41953 0.28432 0.61376 0.54601 0.43736 1 h-lim-p 0.0004 0.0029 82.0462 5021.123732 0 0.0007 23 | 0/8 2 h-lim-p 0.0001 0.0011 66.0477 5020.147007 0 0.0005 37 | 0/8 3 h-lim-p 0.0009 0.0070 23.9328 5019.854620 0 0.0013 49 | 0/8 4 h-lim-p 0.0014 0.0116 12.4251 5019.781891 5 0.0012 70 | 0/8 5 h-lim-p 0.0033 0.0267 2.6219 5019.775854 6 0.0019 97 | 0/8 6 h-lim-p 0.0171 0.1370 0.2351 5019.775684 2 0.0033 114 | 0/8 7 h-lim-p 0.0308 3.5834 0.0252 5019.764266 0 0.2464 137 | 0/8 8 h-lim-p 0.0036 0.0291 1.1889 5019.754401 0 0.0055 157 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 5019.754234 1 0.9961 171 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 5019.754233 0 1.0938 191 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 5019.754233 0 1.0938 211 | 0/8 12 h-lim-p 1.0517 20.0000 0.0000 5019.754233 0 1.0517 231 | 0/8 13 h-lim-p 0.0048 13.8303 0.0038 5019.754233 0 0.0000 267 | 0/8 14 h-lim-p 0.0003 20.0000 0.0000 5019.754233 0 0.0000 301 Out... lnL = -5019.754233 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -5019.754233 Node 7: lnL = -5019.754233 Node 8: lnL = -5019.754233 Node 9: lnL = -5019.754233 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 473 Sequential format.. Reading seq # 1: YPL060W_Sbay Reading seq # 2: YPL060W_Scer Reading seq # 3: YPL060W_Skud Reading seq # 4: YPL060W_Smik Reading seq # 5: YPL060W_Spar Sequences read.. Counting patterns.. # site patterns = 222 Counting frequencies.. 120 bytes for distance 35520 bytes for lkl0 28416 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.064196 0.042196 0.083670 0.194767 0.107487 0.257169 0.247874 0.268589 lnL0 = -2170.445413 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2170.445413 x= 0.06420 0.04220 0.08367 0.19477 0.10749 0.25717 0.24787 0.26859 1 h-lim-p 0.0048 1.3858 95.2289 2168.826106 8 0.0004 40 | 0/8 2 h-lim-p 0.0010 0.0083 15.2720 2168.750538 7 0.0007 70 | 0/8 3 h-lim-p 0.0014 0.0681 7.1351 2168.732498 6 0.0008 99 | 0/8 4 h-lim-p 0.0033 0.2212 1.8250 2168.730752 5 0.0011 125 | 0/8 5 h-lim-p 0.0097 0.8391 0.2154 2168.730732 2 0.0009 143 | 0/8 6 h-lim-p 0.0055 11.8779 0.0368 2168.730731 1 0.0013 166 | 0/8 7 h-lim-p 0.0076 20.0000 0.0066 2168.730717 0 0.0302 188 | 0/8 8 h-lim-p 0.0108 20.0000 0.0183 2168.730317 0 0.0432 210 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2168.730307 1 0.9961 232 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2168.730307 0 1.2500 252 | 0/8 11 h-lim-p 1.3574 20.0000 0.0000 2168.730307 0 0.3394 273 | 0/8 12 h-lim-p 0.0433 20.0000 0.0001 2168.730307 0 0.0162 294 | 0/8 13 h-lim-p 0.0056 20.0000 0.0002 2168.730307 0 0.0000 335 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 2168.730307 0 0.0000 355 | 0/8 15 h-lim-p 0.0001 20.0000 0.0001 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 | 0/8 17 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -2168.730307 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2168.730307 Node 7: lnL = -2168.730307 Node 8: lnL = -2168.730307 Node 9: lnL = -2168.730307 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 331 Sequential format.. Reading seq # 1: YPL061W_Sbay Reading seq # 2: YPL061W_Scer Reading seq # 3: YPL061W_Skud Reading seq # 4: YPL061W_Smik Reading seq # 5: YPL061W_Spar Sequences read.. Counting patterns.. # site patterns = 137 Counting frequencies.. 120 bytes for distance 21920 bytes for lkl0 17536 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.065216 0.028019 0.080665 0.080633 0.056631 0.139920 0.147939 0.195829 lnL0 = -1288.640281 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1288.640281 x= 0.06522 0.02802 0.08067 0.08063 0.05663 0.13992 0.14794 0.19583 1 h-lim-p 0.0058 0.2815 66.7846 1288.109299 8 0.0003 45 | 0/8 2 h-lim-p 0.0016 0.0150 11.1738 1288.068504 6 0.0007 71 | 0/8 3 h-lim-p 0.0023 0.0978 3.3031 1288.066833 4 0.0003 95 | 0/8 4 h-lim-p 0.0011 0.1369 1.0170 1288.066638 3 0.0004 113 | 0/8 5 h-lim-p 0.0039 2.4987 0.1079 1288.066634 2 0.0006 131 | 0/8 6 h-lim-p 0.0023 6.6797 0.0295 1288.066634 0 0.0005 152 | 0/8 7 h-lim-p 0.0096 20.0000 0.0015 1288.066634 0 0.0042 172 | 0/8 8 h-lim-p 0.0358 20.0000 0.0002 1288.066630 0 0.2861 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1288.066630 0 1.0938 215 | 0/8 10 h-lim-p 1.1449 20.0000 0.0000 1288.066630 0 1.1449 235 | 0/8 11 h-lim-p 1.2250 20.0000 0.0000 1288.066630 0 0.1531 257 | 0/8 12 h-lim-p 0.0171 20.0000 0.0001 1288.066630 0 0.0001 283 | 0/8 13 h-lim-p 0.0000 20.0000 0.0014 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1288.066630 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1288.066630 Node 7: lnL = -1288.066630 Node 8: lnL = -1288.066630 Node 9: lnL = -1288.066630 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 355 Sequential format.. Reading seq # 1: YPL063W_Sbay Reading seq # 2: YPL063W_Scer Reading seq # 3: YPL063W_Skud Reading seq # 4: YPL063W_Smik Reading seq # 5: YPL063W_Spar Sequences read.. Counting patterns.. # site patterns = 157 Counting frequencies.. 120 bytes for distance 25120 bytes for lkl0 20096 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.042302 0.076367 0.062421 0.126894 0.066526 0.246535 0.259085 0.222582 lnL0 = -1569.107599 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1569.107599 x= 0.04230 0.07637 0.06242 0.12689 0.06653 0.24653 0.25909 0.22258 1 h-lim-p 0.0005 0.0040 81.4214 1567.533887 6 0.0005 34 | 0/8 2 h-lim-p 0.0007 0.0057 19.0202 1567.376442 0 0.0011 46 | 0/8 3 h-lim-p 0.0043 0.0489 4.7476 1567.371930 3 0.0004 66 | 0/8 4 h-lim-p 0.0009 0.0703 2.3755 1567.370569 5 0.0006 91 | 0/8 5 h-lim-p 0.0025 0.6760 0.5508 1567.370339 4 0.0016 114 | 0/8 6 h-lim-p 0.0183 1.5567 0.0472 1567.370313 2 0.0043 139 | 0/8 7 h-lim-p 0.0071 16.8486 0.0284 1567.368149 0 0.1136 163 | 0/8 8 h-lim-p 0.0045 0.7589 0.7124 1567.365886 5 0.0034 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0008 1567.365619 3 1.0449 221 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1567.365618 1 1.2305 244 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1567.365618 0 1.0938 264 | 0/8 12 h-lim-p 1.2651 20.0000 0.0000 1567.365618 0 1.2651 284 | 0/8 13 h-lim-p 0.1924 20.0000 0.0001 1567.365618 0 0.0962 304 | 0/8 14 h-lim-p 0.0226 20.0000 0.0003 1567.365618 0 0.0113 324 | 0/8 15 h-lim-p 0.0051 20.0000 0.0007 1567.365618 0 0.0006 346 | 0/8 16 h-lim-p 0.0008 20.0000 0.0005 1567.365618 0 0.0004 366 | 0/8 17 h-lim-p 0.0004 20.0000 0.0005 1567.365618 0 0.0002 386 | 0/8 18 h-lim-p 0.0004 20.0000 0.0003 1567.365618 0 0.0000 421 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1567.365618 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1567.365618 Node 7: lnL = -1567.365618 Node 8: lnL = -1567.365618 Node 9: lnL = -1567.365618 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 349 Sequential format.. Reading seq # 1: YPL064C_Sbay Reading seq # 2: YPL064C_Scer Reading seq # 3: YPL064C_Skud Reading seq # 4: YPL064C_Smik Reading seq # 5: YPL064C_Spar Sequences read.. Counting patterns.. # site patterns = 156 Counting frequencies.. 120 bytes for distance 24960 bytes for lkl0 19968 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.045249 0.153134 0.081557 0.119777 0.073643 0.240422 0.266397 0.252966 lnL0 = -1626.228352 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1626.228352 x= 0.04525 0.15313 0.08156 0.11978 0.07364 0.24042 0.26640 0.25297 1 h-lim-p 0.0005 0.0043 62.9612 1624.888443 0 0.0008 22 | 0/8 2 h-lim-p 0.0012 0.0096 14.6933 1624.771290 2 0.0011 38 | 0/8 3 h-lim-p 0.0010 0.0290 16.9134 1624.732101 4 0.0005 59 | 0/8 4 h-lim-p 0.0021 0.0528 3.9614 1624.725675 5 0.0009 80 | 0/8 5 h-lim-p 0.0056 0.4382 0.6659 1624.725273 3 0.0018 100 | 0/8 6 h-lim-p 0.0062 1.7331 0.1927 1624.725233 2 0.0016 125 | 0/8 7 h-lim-p 0.0399 18.7079 0.0079 1624.720177 0 0.4792 148 | 0/8 8 h-lim-p 0.0039 0.3090 0.9767 1624.716411 4 0.0033 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1624.716395 2 0.9644 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1624.716395 0 1.0938 219 | 0/8 11 h-lim-p 1.2413 20.0000 0.0000 1624.716395 0 2.4825 240 | 0/8 12 h-lim-p 1.6921 20.0000 0.0000 1624.716395 0 0.0004 271 | 0/8 13 h-lim-p 0.0000 20.0000 0.0015 1624.716395 0 0.0000 301 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 1624.716395 0 0.0000 333 Out... lnL = -1624.716395 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1624.716395 Node 7: lnL = -1624.716395 Node 8: lnL = -1624.716395 Node 9: lnL = -1624.716395 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 280 Sequential format.. Reading seq # 1: YPL065W_Sbay Reading seq # 2: YPL065W_Scer Reading seq # 3: YPL065W_Skud Reading seq # 4: YPL065W_Smik Reading seq # 5: YPL065W_Spar Sequences read.. Counting patterns.. # site patterns = 132 Counting frequencies.. 120 bytes for distance 21120 bytes for lkl0 16896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.054551 0.139885 0.199820 0.133757 0.084108 0.350309 0.262865 0.318057 lnL0 = -1132.260646 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1132.260646 x= 0.05455 0.13989 0.19982 0.13376 0.08411 0.35031 0.26287 0.31806 1 h-lim-p 0.0059 0.0473 15.8192 1132.048086 8 0.0018 43 | 0/8 2 h-lim-p 0.0015 0.0180 18.2035 1131.926856 3 0.0013 61 | 0/8 3 h-lim-p 0.0019 0.0300 12.5149 1131.839082 6 0.0020 88 | 0/8 4 h-lim-p 0.0082 0.0659 2.8735 1131.818392 7 0.0057 119 | 0/8 5 h-lim-p 0.0030 0.0291 5.4596 1131.742427 0 0.0120 133 | 0/8 6 h-lim-p 0.0005 0.0039 19.0585 1131.672396 m 0.0039 145 | 0/8 7 h-lim-p 0.1700 1.3597 0.1721 1131.671463 4 0.0548 167 | 0/8 8 h-lim-p 1.4558 20.0000 0.0065 1131.669459 6 0.8344 203 | 0/8 9 h-lim-p 0.5460 4.3683 0.0015 1131.669440 0 1.0921 224 | 0/8 10 h-lim-p 2.5000 20.0000 0.0004 1131.669439 0 1.0938 244 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1131.669439 0 1.0938 264 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1131.669439 0 1.0938 284 | 0/8 13 h-lim-p 1.6184 20.0000 0.0000 1131.669439 0 0.3540 305 | 0/8 14 h-lim-p 0.0153 20.0000 0.0001 1131.669439 0 0.0077 325 | 0/8 15 h-lim-p 0.0031 20.0000 0.0002 1131.669439 0 0.0008 346 | 0/8 16 h-lim-p 0.0007 20.0000 0.0002 1131.669439 0 0.0007 366 | 0/8 17 h-lim-p 0.0003 20.0000 0.0005 1131.669439 0 0.0000 390 | 0/8 18 h-lim-p 0.0006 20.0000 0.0000 1131.669439 0 0.0000 423 Out... lnL = -1131.669439 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1131.669439 Node 7: lnL = -1131.669439 Node 8: lnL = -1131.669439 Node 9: lnL = -1131.669439 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 424 Sequential format.. Reading seq # 1: YPL066W_Sbay Reading seq # 2: YPL066W_Scer Reading seq # 3: YPL066W_Skud Reading seq # 4: YPL066W_Smik Reading seq # 5: YPL066W_Spar Sequences read.. Counting patterns.. # site patterns = 178 Counting frequencies.. 120 bytes for distance 28480 bytes for lkl0 22784 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.036758 0.053776 0.081227 0.124762 0.070070 0.246883 0.237776 0.210437 lnL0 = -1826.952663 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1826.952663 x= 0.03676 0.05378 0.08123 0.12476 0.07007 0.24688 0.23778 0.21044 1 h-lim-p 0.0083 0.0663 51.1944 1826.479060 8 0.0004 45 | 0/8 2 h-lim-p 0.0015 0.0122 11.1698 1826.450026 6 0.0005 71 | 0/8 3 h-lim-p 0.0008 0.0486 6.3920 1826.440571 5 0.0006 95 | 0/8 4 h-lim-p 0.0026 0.0988 1.4718 1826.439516 3 0.0011 113 | 0/8 5 h-lim-p 0.0065 0.7877 0.2450 1826.439499 2 0.0006 131 | 0/8 6 h-lim-p 0.0047 9.6073 0.0322 1826.439498 0 0.0010 152 | 0/8 7 h-lim-p 0.0028 20.0000 0.0118 1826.439498 0 0.0012 172 | 0/8 8 h-lim-p 0.1862 20.0000 0.0001 1826.439492 0 1.1175 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1826.439492 0 1.0938 214 | 0/8 10 h-lim-p 1.3413 20.0000 0.0000 1826.439492 0 1.1737 234 | 0/8 11 h-lim-p 1.0374 20.0000 0.0000 1826.439492 0 6.2245 256 | 0/8 12 h-lim-p 0.0958 20.0000 0.0008 1826.439492 0 0.0045 280 | 0/8 13 h-lim-p 0.0013 20.0000 0.0029 1826.439492 0 0.0000 313 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 1826.439492 0 0.0000 345 Out... lnL = -1826.439492 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1826.439492 Node 7: lnL = -1826.439492 Node 8: lnL = -1826.439492 Node 9: lnL = -1826.439492 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 421 Sequential format.. Reading seq # 1: YPL067C_Sbay Reading seq # 2: YPL067C_Scer Reading seq # 3: YPL067C_Skud Reading seq # 4: YPL067C_Smik Reading seq # 5: YPL067C_Spar Sequences read.. Counting patterns.. # site patterns = 189 Counting frequencies.. 120 bytes for distance 30240 bytes for lkl0 24192 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.052040 0.078618 0.087245 0.129933 0.068383 0.245746 0.221064 0.237078 lnL0 = -1856.365006 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1856.365006 x= 0.05204 0.07862 0.08724 0.12993 0.06838 0.24575 0.22106 0.23708 1 h-lim-p 0.0014 0.0110 46.8078 1855.853344 8 0.0005 38 | 0/8 2 h-lim-p 0.0013 0.0105 10.9508 1855.817100 2 0.0006 54 | 0/8 3 h-lim-p 0.0007 0.0298 9.6639 1855.801387 5 0.0005 76 | 0/8 4 h-lim-p 0.0017 0.0755 2.8968 1855.798935 4 0.0007 96 | 0/8 5 h-lim-p 0.0082 0.8451 0.2428 1855.798909 1 0.0009 112 | 0/8 6 h-lim-p 0.0054 9.1624 0.0399 1855.798909 0 0.0012 133 | 0/8 7 h-lim-p 0.0113 20.0000 0.0042 1855.798908 0 0.0099 153 | 0/8 8 h-lim-p 0.0186 20.0000 0.0022 1855.798850 0 0.1488 176 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1855.798848 0 1.0938 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1855.798848 0 1.0938 216 | 0/8 11 h-lim-p 1.1024 20.0000 0.0000 1855.798848 0 0.0172 241 | 0/8 12 h-lim-p 0.0046 20.0000 0.0000 1855.798848 0 0.0023 261 | 0/8 13 h-lim-p 0.0010 20.0000 0.0001 1855.798848 0 0.0000 295 | 0/8 14 h-lim-p 0.0000 20.0000 0.0005 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -1855.798848 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1855.798848 Node 7: lnL = -1855.798848 Node 8: lnL = -1855.798848 Node 9: lnL = -1855.798848 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 198 Sequential format.. Reading seq # 1: YPL068C_Sbay Reading seq # 2: YPL068C_Scer Reading seq # 3: YPL068C_Skud Reading seq # 4: YPL068C_Smik Reading seq # 5: YPL068C_Spar Sequences read.. Counting patterns.. # site patterns = 104 Counting frequencies.. 120 bytes for distance 16640 bytes for lkl0 13312 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.098781 0.071102 0.035791 0.092016 0.124829 0.251114 0.231119 0.290903 lnL0 = -874.244384 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 874.244384 x= 0.09878 0.07110 0.03579 0.09202 0.12483 0.25111 0.23112 0.29090 1 h-lim-p 0.0025 0.0746 84.2358 872.253296 9 0.0007 44 | 0/8 2 h-lim-p 0.0013 0.0105 20.6152 871.716104 0 0.0026 57 | 0/8 3 h-lim-p 0.0020 0.0157 20.7956 871.584057 7 0.0010 86 | 0/8 4 h-lim-p 0.0076 0.0976 2.8182 871.574380 6 0.0025 112 | 0/8 5 h-lim-p 0.0082 0.3934 0.8718 871.573736 3 0.0019 131 | 0/8 6 h-lim-p 0.0141 2.4969 0.1152 871.573705 2 0.0028 156 | 0/8 7 h-lim-p 0.0253 18.1840 0.0128 871.571914 0 0.2027 179 | 0/8 8 h-lim-p 0.0073 4.1872 0.3564 871.566749 0 0.0145 200 | 0/8 9 h-lim-p 2.4070 20.0000 0.0022 871.565665 4 1.0384 227 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 871.565663 0 1.0938 247 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 871.565663 0 1.0938 267 | 0/8 12 h-lim-p 1.4543 20.0000 0.0000 871.565663 0 1.2725 287 | 0/8 13 h-lim-p 0.5327 20.0000 0.0000 871.565663 0 0.0666 309 | 0/8 14 h-lim-p 0.0061 20.0000 0.0001 871.565663 0 0.0008 331 | 0/8 15 h-lim-p 0.0001 20.0000 0.0005 871.565663 0 0.0000 355 | 0/8 16 h-lim-p 0.0003 20.0000 0.0000 871.565663 0 0.0000 387 Out... lnL = -871.565663 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -871.565663 Node 7: lnL = -871.565663 Node 8: lnL = -871.565663 Node 9: lnL = -871.565663 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 357 Sequential format.. Reading seq # 1: YPL069C_Sbay Reading seq # 2: YPL069C_Scer Reading seq # 3: YPL069C_Skud Reading seq # 4: YPL069C_Smik Reading seq # 5: YPL069C_Spar Sequences read.. Counting patterns.. # site patterns = 154 Counting frequencies.. 120 bytes for distance 24640 bytes for lkl0 19712 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.098716 0.124362 0.071242 0.120457 0.074755 0.182027 0.136775 0.281364 lnL0 = -1596.696066 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1596.696066 x= 0.09872 0.12436 0.07124 0.12046 0.07476 0.18203 0.13678 0.28136 1 h-lim-p 0.0004 0.0033 43.3928 1596.150838 0 0.0006 22 | 0/8 2 h-lim-p 0.0012 0.0156 23.0710 1596.041992 5 0.0005 43 | 0/8 3 h-lim-p 0.0013 0.0259 8.8202 1596.018720 6 0.0007 69 | 0/8 4 h-lim-p 0.0037 0.0739 1.6956 1596.017750 3 0.0007 88 | 0/8 5 h-lim-p 0.0014 0.3479 0.8646 1596.017555 2 0.0007 104 | 0/8 6 h-lim-p 0.0251 6.8207 0.0225 1596.017539 2 0.0062 129 | 0/8 7 h-lim-p 0.0061 9.2960 0.0228 1596.016012 0 0.0730 152 | 0/8 8 h-lim-p 0.0023 0.3713 0.7294 1596.015308 5 0.0016 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1596.015292 1 0.9961 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1596.015292 0 1.0938 228 | 0/8 11 h-lim-p 1.2196 20.0000 0.0000 1596.015292 0 0.0191 253 | 0/8 12 h-lim-p 0.0038 20.0000 0.0000 1596.015292 0 0.0000 284 | 0/8 13 h-lim-p 0.0002 20.0000 0.0000 1596.015292 0 0.0000 318 Out... lnL = -1596.015292 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1596.015292 Node 7: lnL = -1596.015292 Node 8: lnL = -1596.015292 Node 9: lnL = -1596.015292 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 444 Sequential format.. Reading seq # 1: YPL070W_Sbay Reading seq # 2: YPL070W_Scer Reading seq # 3: YPL070W_Skud Reading seq # 4: YPL070W_Smik Reading seq # 5: YPL070W_Spar Sequences read.. Counting patterns.. # site patterns = 136 Counting frequencies.. 120 bytes for distance 21760 bytes for lkl0 17408 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.030269 0.033860 0.066287 0.072385 0.046954 0.122301 0.184010 0.145947 lnL0 = -1754.355700 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1754.355700 x= 0.03027 0.03386 0.06629 0.07239 0.04695 0.12230 0.18401 0.14595 1 h-lim-p 0.0034 0.0275 79.1969 1753.799593 5 0.0002 34 | 0/8 2 h-lim-p 0.0014 0.0110 9.0830 1753.787746 5 0.0003 58 | 0/8 3 h-lim-p 0.0006 0.0530 4.5273 1753.785786 3 0.0002 76 | 0/8 4 h-lim-p 0.0005 0.0958 2.1425 1753.785114 4 0.0004 96 | 0/8 5 h-lim-p 0.0023 0.4338 0.3432 1753.785092 2 0.0004 114 | 0/8 6 h-lim-p 0.0014 1.2965 0.0880 1753.785091 0 0.0003 135 | 0/8 7 h-lim-p 0.0030 14.0337 0.0091 1753.785091 0 0.0004 157 | 0/8 8 h-lim-p 0.0502 20.0000 0.0001 1753.785087 0 1.2044 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1753.785087 0 1.0938 201 | 0/8 10 h-lim-p 1.0572 20.0000 0.0000 1753.785087 0 3.1715 222 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1753.785087 0 0.2734 244 | 0/8 12 h-lim-p 0.0314 20.0000 0.0003 1753.785087 0 0.0005 269 | 0/8 13 h-lim-p 0.0002 20.0000 0.0005 1753.785087 0 0.0001 289 | 0/8 14 h-lim-p 0.0057 20.0000 0.0000 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0033 1753.785087 0 0.0000 357 | 0/8 16 h-lim-p 0.0000 20.0000 0.0007 1753.785087 0 0.0006 383 | 0/8 17 h-lim-p 0.0026 20.0000 0.0002 1753.785087 0 0.0007 404 | 0/8 18 h-lim-p 0.0017 20.0000 0.0001 1753.785087 0 0.0008 424 | 0/8 19 h-lim-p 0.0011 20.0000 0.0001 1753.785087 0 0.0011 444 | 0/8 20 h-lim-p 0.0001 20.0000 0.0005 .. | 0/8 21 h-lim-p 0.0000 20.0000 0.0041 1753.785087 0 0.0000 510 | 0/8 22 h-lim-p 0.0000 20.0000 0.0003 1753.785087 0 0.0000 543 | 0/8 23 h-lim-p 0.0000 20.0000 0.0041 1753.785087 0 0.0000 567 | 0/8 24 h-lim-p 0.0000 20.0000 0.0004 1753.785087 0 0.0000 598 | 0/8 25 h-lim-p 0.0000 20.0000 0.0041 | 0/8 26 h-lim-p 0.0000 20.0000 0.0041 Out... lnL = -1753.785087 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1753.785087 Node 7: lnL = -1753.785087 Node 8: lnL = -1753.785087 Node 9: lnL = -1753.785087 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 444 Sequential format.. Reading seq # 1: YPL071C_Sbay Reading seq # 2: YPL071C_Scer Reading seq # 3: YPL071C_Skud Reading seq # 4: YPL071C_Smik Reading seq # 5: YPL071C_Spar Sequences read.. Counting patterns.. # site patterns = 138 Counting frequencies.. 120 bytes for distance 22080 bytes for lkl0 17664 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.193478 0.071949 0.077965 0.165341 0.176048 0.136637 0.095115 0.000060 lnL0 = -1806.630243 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1806.630243 x= 0.19348 0.07195 0.07796 0.16534 0.17605 0.13664 0.09511 0.00006 1 h-lim-p 0.0000 0.0000 411.5703 1800.117420 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0004 528.3816 1774.596391 9 0.0003 58 | 1/8 3 h-lim-p 0.0001 0.0011 96.1740 1773.811557 0 0.0003 71 | 1/8 4 h-lim-p 0.0008 0.0068 15.1790 1773.758066 4 0.0004 92 | 1/8 5 h-lim-p 0.0055 0.1282 1.2004 1773.648613 0 0.0082 104 | 0/8 6 h-lim-p 0.0003 0.0099 38.4139 1771.693513 0 0.0020 119 | 0/8 7 h-lim-p 0.0001 0.0009 199.3137 1766.895650 m 0.0009 131 | 0/8 8 h-lim-p 0.0000 0.0000 63.0268 h-lim-p: 5.43562130e-21 4.34849704e-20 6.30267773e+01 1766.895650 .. | 0/8 9 h-lim-p 0.0000 0.0015 177.2097 1761.522574 0 0.0003 156 | 0/8 10 h-lim-p 0.0000 0.0002 61.2291 1761.244847 m 0.0002 168 | 0/8 11 h-lim-p 0.0000 0.0000 14.4378 h-lim-p: 1.62339526e-21 1.29871621e-20 1.44378208e+01 1761.244847 .. | 0/8 12 h-lim-p 0.0000 0.0016 42.6652 1761.067961 0 0.0002 192 | 0/8 13 h-lim-p 0.0004 0.0117 19.0729 1760.994957 0 0.0005 204 | 0/8 14 h-lim-p 0.0001 0.0008 3.0512 1760.993698 0 0.0003 217 | 0/8 15 h-lim-p 0.0012 0.0094 0.6893 1760.993620 3 0.0003 236 | 0/8 16 h-lim-p 0.0006 0.0050 0.1623 1760.993608 0 0.0006 256 | 0/8 17 h-lim-p 0.0008 0.0067 0.0634 1760.993517 m 0.0067 276 | 0/8 18 h-lim-p -0.0000 -0.0000 1.3421 h-lim-p: -1.83174143e-21 -1.46539315e-20 1.34212369e+00 1760.993517 .. | 0/8 19 h-lim-p 0.0000 0.0050 11.0348 1760.984461 0 0.0002 308 | 0/8 20 h-lim-p 0.0027 0.1561 0.6568 1760.984404 2 0.0003 326 | 0/8 21 h-lim-p 0.0001 0.0009 0.1572 1760.984401 0 0.0003 347 | 0/8 22 h-lim-p 0.0001 0.0005 0.1241 1760.984401 0 0.0000 370 | 0/8 23 h-lim-p 0.0000 0.0000 2.8453 1760.984401 0 0.0000 392 | 0/8 24 h-lim-p 0.0000 1.9267 0.0781 1760.984400 0 0.0004 409 | 0/8 25 h-lim-p 0.0044 0.0716 0.0064 1760.984400 0 0.0010 430 | 0/8 26 h-lim-p 0.0007 20.0000 0.0094 1760.984400 0 0.0026 452 | 0/8 27 h-lim-p 0.0080 20.0000 0.0031 1760.984348 0 0.0478 474 | 0/8 28 h-lim-p 1.8968 15.1741 0.0000 1760.984347 0 0.8298 494 | 0/8 29 h-lim-p 2.5000 20.0000 0.0000 1760.984347 0 0.3125 516 | 0/8 30 h-lim-p 0.2647 20.0000 0.0000 1760.984347 0 0.0662 537 | 0/8 31 h-lim-p 0.0417 15.2614 0.0000 1760.984347 0 0.0208 557 | 0/8 32 h-lim-p 0.0143 9.2326 0.0000 1760.984347 0 0.0125 577 | 0/8 33 h-lim-p 0.0090 6.1064 0.0000 1760.984347 0 0.0020 598 | 0/8 34 h-lim-p 0.0015 4.3029 0.0000 1760.984347 0 0.0015 618 | 0/8 35 h-lim-p 0.0011 3.1817 0.0000 1760.984347 0 0.0023 639 | 0/8 36 h-lim-p 0.0018 2.4420 0.0000 1760.984347 0 0.0000 677 | 0/8 37 h-lim-p 0.0000 0.0007 0.1031 1760.984347 0 0.0000 697 | 0/8 38 h-lim-p 0.0000 0.0002 0.4571 1760.984347 0 0.0000 731 | 0/8 39 h-lim-p 0.0000 0.0000 60.9886 .. | 0/8 40 h-lim-p 0.0000 0.0921 0.0170 1760.984347 0 0.0000 781 | 0/8 41 h-lim-p 0.0000 0.0007 0.3783 .. | 0/8 42 h-lim-p 0.0000 0.0007 0.1019 | 0/8 43 h-lim-p 0.0000 0.0007 0.1019 Out... lnL = -1760.984347 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1760.984347 Node 7: lnL = -1760.984347 Node 8: lnL = -1760.984347 Node 9: lnL = -1760.984347 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 523 Sequential format.. Reading seq # 1: YPL072W_Sbay Reading seq # 2: YPL072W_Scer Reading seq # 3: YPL072W_Skud Reading seq # 4: YPL072W_Smik Reading seq # 5: YPL072W_Spar Sequences read.. Counting patterns.. # site patterns = 250 Counting frequencies.. 120 bytes for distance 40000 bytes for lkl0 32000 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.381867 0.096146 0.089186 0.244863 0.104751 0.254310 0.287614 0.000060 lnL0 = -2532.527255 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2532.527255 x= 0.38187 0.09615 0.08919 0.24486 0.10475 0.25431 0.28761 0.00006 1 h-lim-p 0.0002 0.0019 76.2213 2531.055610 0 0.0005 23 | 0/8 2 h-lim-p 0.0001 0.0004 19.2652 2530.966344 m 0.0004 35 | 1/8 3 h-lim-p 0.0013 0.0221 6.2842 2530.950322 6 0.0009 61 | 1/8 4 h-lim-p 0.0021 0.1663 2.7081 2530.945814 5 0.0014 87 | 1/8 5 h-lim-p 0.0151 1.4709 0.2575 2530.945545 2 0.0029 104 | 0/8 6 h-lim-p 0.0012 2.2007 0.6033 2530.943947 0 0.0050 125 | 0/8 7 h-lim-p 0.0060 0.0486 0.4968 2530.942925 4 0.0033 154 | 0/8 8 h-lim-p 0.0020 0.0157 0.3858 2530.939084 0 0.0078 176 | 0/8 9 h-lim-p 0.0004 0.0030 1.0951 2530.937455 0 0.0023 198 | 0/8 10 h-lim-p 0.3256 2.6050 0.0023 2530.933637 0 0.9769 211 | 0/8 11 h-lim-p 0.2634 2.1070 0.0001 2530.933634 0 1.0535 233 | 0/8 12 h-lim-p 0.0350 0.2796 0.0005 2530.933634 0 0.0000 268 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 2530.933634 0 0.0000 288 | 0/8 14 h-lim-p 0.0000 0.7762 0.0002 2530.933634 0 0.0000 315 | 0/8 15 h-lim-p 0.0000 0.0466 0.0032 .. | 0/8 16 h-lim-p 0.0000 0.0052 0.0328 2530.933634 0 0.0006 374 | 0/8 17 h-lim-p 0.0001 0.0007 0.1747 2530.933634 0 0.0002 395 | 0/8 18 h-lim-p 0.0000 0.0001 1.7658 2530.933634 0 0.0000 427 | 0/8 19 h-lim-p 0.0000 20.0000 0.0323 2530.933634 0 0.0013 446 | 0/8 20 h-lim-p 0.0113 1.1333 0.0037 2530.933634 0 0.0012 468 | 0/8 21 h-lim-p 0.0036 0.7194 0.0013 2530.933634 0 0.0000 500 | 0/8 22 h-lim-p 0.0000 20.0000 0.0002 .. | 0/8 23 h-lim-p 0.0000 0.0019 0.0361 2530.933634 0 0.0001 556 | 0/8 24 h-lim-p 0.0000 0.0004 0.1660 2530.933634 0 0.0000 585 | 0/8 25 h-lim-p 0.0000 0.0000 1.5814 .. | 0/8 26 h-lim-p 0.0000 0.0924 0.0141 2530.933634 0 0.0001 632 | 0/8 27 h-lim-p 0.0000 0.0015 0.1063 .. | 0/8 28 h-lim-p 0.0000 0.0018 0.0350 2530.933634 0 0.0000 694 | 0/8 29 h-lim-p 0.0000 0.0004 0.1878 2530.933634 0 0.0000 717 | 0/8 30 h-lim-p 0.0000 0.0000 2.8003 2530.933634 0 0.0000 738 | 0/8 31 h-lim-p 0.0002 0.0187 0.0110 2530.933634 0 0.0000 759 | 0/8 32 h-lim-p 0.0000 0.0011 0.1827 2530.933634 0 0.0000 786 | 0/8 33 h-lim-p 0.0000 11.4126 0.0003 2530.933634 0 0.0000 810 | 0/8 34 h-lim-p 0.0000 18.6114 0.0001 2530.933634 0 0.0000 841 | 0/8 35 h-lim-p 0.0000 0.0018 0.0349 | 0/8 36 h-lim-p 0.0000 0.0018 0.0349 Out... lnL = -2530.933634 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2530.933634 Node 7: lnL = -2530.933634 Node 8: lnL = -2530.933634 Node 9: lnL = -2530.933634 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 862 Sequential format.. Reading seq # 1: YPL075W_Sbay Reading seq # 2: YPL075W_Scer Reading seq # 3: YPL075W_Skud Reading seq # 4: YPL075W_Smik Reading seq # 5: YPL075W_Spar Sequences read.. Counting patterns.. # site patterns = 192 Counting frequencies.. 120 bytes for distance 30720 bytes for lkl0 24576 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.324438 0.161280 0.129568 0.475895 0.462034 0.243904 0.019861 0.000060 lnL0 = -3890.299201 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3890.299201 x= 0.32444 0.16128 0.12957 0.47590 0.46203 0.24390 0.01986 0.00006 1 h-lim-p 0.0000 0.0000 1068.6931 3889.895267 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0000 16154.4936 3611.046428 m 0.0000 34 | 2/8 3 h-lim-p 0.0000 0.0002 1638.2622 3449.659222 0 0.0002 48 | 2/8 4 h-lim-p 0.0000 0.0003 460.5939 3440.051565 0 0.0001 62 | 2/8 5 h-lim-p 0.0004 0.0141 141.8057 3430.016294 0 0.0013 75 | 2/8 6 h-lim-p 0.0011 0.0089 22.1829 3429.621419 5 0.0006 98 | 2/8 7 h-lim-p 0.0013 0.0114 10.0148 3424.479830 0 0.0040 111 | 2/8 8 h-lim-p 0.2464 1.9710 0.1094 3420.473691 0 0.4927 124 | 1/8 9 h-lim-p 0.0014 0.0109 26.4153 3420.411561 4 0.0003 151 | 1/8 10 h-lim-p 0.0698 0.5580 0.0477 3419.815550 0 0.2790 165 | 1/8 11 h-lim-p 0.4791 20.0000 0.0278 3419.527128 0 0.9581 185 | 1/8 12 h-lim-p 1.9851 20.0000 0.0134 3419.478641 6 1.1765 219 | 1/8 13 h-lim-p 2.5000 20.0000 0.0005 3419.478075 3 1.0449 244 | 1/8 14 h-lim-p 2.5000 20.0000 0.0001 3419.478062 2 0.6580 268 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 3419.478062 0 1.0938 287 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 3419.478062 0 1.0938 306 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 3419.478062 0 2.1875 325 | 1/8 18 h-lim-p 2.2958 20.0000 0.0000 3419.478062 0 0.0179 350 Out... lnL = -3419.478062 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3419.478062 Node 7: lnL = -3419.478062 Node 8: lnL = -3419.478062 Node 9: lnL = -3419.478062 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 402 Sequential format.. Reading seq # 1: YPL076W_Sbay Reading seq # 2: YPL076W_Scer Reading seq # 3: YPL076W_Skud Reading seq # 4: YPL076W_Smik Reading seq # 5: YPL076W_Spar Sequences read.. Counting patterns.. # site patterns = 168 Counting frequencies.. 120 bytes for distance 26880 bytes for lkl0 21504 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.311168 0.059891 0.126625 0.159992 0.139600 0.203579 0.212539 0.000060 lnL0 = -1829.866837 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1829.866837 x= 0.31117 0.05989 0.12663 0.15999 0.13960 0.20358 0.21254 0.00006 1 h-lim-p 0.0002 0.0015 104.7736 1826.381101 0 0.0006 23 | 0/8 2 h-lim-p 0.0000 0.0002 12.9398 1826.356426 m 0.0002 35 | 1/8 3 h-lim-p 0.0006 0.0866 3.5703 1826.351370 0 0.0009 47 | 1/8 4 h-lim-p 0.0056 0.3257 0.5680 1826.351164 4 0.0010 69 | 1/8 5 h-lim-p 0.0028 20.0000 0.2047 1826.350945 1 0.0028 90 | 1/8 6 h-lim-p 0.0020 0.3070 0.2954 1826.349609 0 0.0059 110 | 1/8 7 h-lim-p 0.0050 1.0456 0.3455 1826.321224 0 0.0202 131 | 1/8 8 h-lim-p 0.0027 0.1254 2.6063 1826.311627 4 0.0021 158 | 1/8 9 h-lim-p 0.8566 17.8694 0.0063 1826.307235 3 0.3413 176 | 1/8 10 h-lim-p 2.5000 20.0000 0.0002 1826.307214 2 0.9644 199 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 1826.307214 0 1.0938 218 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 1826.307214 0 2.1875 237 | 1/8 13 h-lim-p 1.8434 20.0000 0.0000 1826.307214 0 0.2304 258 | 1/8 14 h-lim-p 0.2994 20.0000 0.0000 1826.307214 0 0.0094 281 Out... lnL = -1826.307214 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1826.307214 Node 7: lnL = -1826.307214 Node 8: lnL = -1826.307214 Node 9: lnL = -1826.307214 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 398 Sequential format.. Reading seq # 1: YPL077C_Sbay Reading seq # 2: YPL077C_Scer Reading seq # 3: YPL077C_Skud Reading seq # 4: YPL077C_Smik Reading seq # 5: YPL077C_Spar Sequences read.. Counting patterns.. # site patterns = 187 Counting frequencies.. 120 bytes for distance 29920 bytes for lkl0 23936 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.296335 0.128059 0.123805 0.299099 0.301234 0.209258 0.100581 0.000060 lnL0 = -1801.595273 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1801.595273 x= 0.29634 0.12806 0.12381 0.29910 0.30123 0.20926 0.10058 0.00006 1 h-lim-p 0.0003 0.0021 273.8558 1765.183290 0 0.0011 24 | 0/8 2 h-lim-p 0.0000 0.0001 175.7015 1762.005301 m 0.0001 36 | 1/8 3 h-lim-p 0.0009 0.0071 24.2668 1761.769495 7 0.0008 64 | 1/8 4 h-lim-p 0.0014 0.0235 12.7338 1761.653622 4 0.0013 83 | 1/8 5 h-lim-p 0.0040 0.0979 4.0368 1761.246450 0 0.0080 96 | 1/8 6 h-lim-p 0.0031 0.0399 10.3362 1760.299562 0 0.0047 108 | 1/8 7 h-lim-p 0.0020 0.0158 23.1587 1759.045920 0 0.0030 120 | 1/8 8 h-lim-p 0.0177 0.1413 1.7844 1758.996322 6 0.0057 146 | 1/8 9 h-lim-p 0.0116 0.2039 0.8740 1755.613125 0 0.0926 161 | 0/8 10 h-lim-p -0.0000 -0.0000 1.6658 h-lim-p: -1.29676828e-20 -1.03741463e-19 1.66577856e+00 1755.613125 .. | 0/8 11 h-lim-p 0.0000 0.0452 49.4155 1755.203539 0 0.0003 193 | 0/8 12 h-lim-p 0.0014 0.0254 11.4129 1755.152354 7 0.0008 224 | 0/8 13 h-lim-p 0.0020 0.0160 2.3517 1755.150500 5 0.0007 248 | 0/8 14 h-lim-p 0.0033 2.0933 0.4920 1755.150384 3 0.0010 268 | 0/8 15 h-lim-p 0.0036 0.0304 0.1346 1755.150368 2 0.0012 293 | 0/8 16 h-lim-p 0.0039 7.3025 0.0406 1755.150320 0 0.0077 314 | 0/8 17 h-lim-p 0.0072 4.8851 0.0435 1755.148892 0 0.0288 336 | 0/8 18 h-lim-p 0.0017 0.0176 0.7564 1755.146037 0 0.0025 356 | 0/8 19 h-lim-p 2.5000 20.0000 0.0002 1755.146021 1 0.9961 378 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 1755.146021 0 1.0938 398 | 0/8 21 h-lim-p 1.0198 20.0000 0.0000 1755.146021 0 8.1583 421 | 0/8 22 h-lim-p 0.0096 0.1631 0.0172 1755.146021 0 0.0011 443 | 0/8 23 h-lim-p 0.0001 0.0229 0.1220 1755.146021 0 0.0000 473 | 0/8 24 h-lim-p 0.0002 20.0000 0.0000 1755.146021 0 0.0000 503 | 0/8 25 h-lim-p 0.0000 20.0000 0.0000 1755.146021 0 0.0000 531 Out... lnL = -1755.146021 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1755.146021 Node 7: lnL = -1755.146021 Node 8: lnL = -1755.146021 Node 9: lnL = -1755.146021 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 759 Sequential format.. Reading seq # 1: YPL078C_Sbay Reading seq # 2: YPL078C_Scer Reading seq # 3: YPL078C_Skud Reading seq # 4: YPL078C_Smik Reading seq # 5: YPL078C_Spar Sequences read.. Counting patterns.. # site patterns = 308 Counting frequencies.. 120 bytes for distance 49280 bytes for lkl0 39424 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.376298 0.149663 0.109842 0.336292 0.322298 0.274452 0.185261 0.000060 lnL0 = -3708.739748 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3708.739748 x= 0.37630 0.14966 0.10984 0.33629 0.32230 0.27445 0.18526 0.00006 1 h-lim-p 0.0001 0.0009 402.3700 3652.448158 m 0.0009 22 | 0/8 2 h-lim-p 0.0001 0.0004 366.3104 3648.165643 0 0.0001 35 | 0/8 3 h-lim-p 0.0000 0.0003 87.3745 3646.808108 m 0.0003 47 | 1/8 4 h-lim-p 0.0004 0.0069 54.3128 3646.252331 0 0.0006 59 | 1/8 5 h-lim-p 0.0029 0.0231 7.1407 3646.053384 6 0.0023 83 | 1/8 6 h-lim-p 0.0027 0.0697 6.0245 3644.312848 0 0.0082 96 | 1/8 7 h-lim-p 0.0011 0.0085 43.6374 3641.539382 0 0.0016 108 | 1/8 8 h-lim-p 0.0020 0.0161 30.3929 3640.673893 7 0.0016 137 | 1/8 9 h-lim-p 1.2228 20.0000 0.0406 3636.159628 0 1.8342 149 | 0/8 10 h-lim-p 0.0086 0.9366 8.6665 3636.114405 6 0.0012 183 | 0/8 11 h-lim-p 0.3428 13.7062 0.0306 3635.342385 0 1.3713 197 | 0/8 12 h-lim-p 2.5000 20.0000 0.0054 3635.268915 5 1.9125 227 | 0/8 13 h-lim-p 2.5000 20.0000 0.0023 3635.264650 3 1.1328 253 | 0/8 14 h-lim-p 2.5000 20.0000 0.0003 3635.264537 3 1.3437 280 | 0/8 15 h-lim-p 2.5000 20.0000 0.0001 3635.264533 1 1.2305 303 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 3635.264533 0 1.0938 323 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 3635.264533 0 2.1875 343 | 0/8 18 h-lim-p 2.2566 20.0000 0.0000 3635.264533 0 0.9873 363 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 3635.264533 0 0.4688 385 | 0/8 20 h-lim-p 0.0658 20.0000 0.0000 3635.264533 0 0.0658 405 | 0/8 21 h-lim-p 0.0224 20.0000 0.0000 3635.264533 0 0.0112 425 | 0/8 22 h-lim-p 0.0060 20.0000 0.0000 3635.264533 0 0.0000 453 Out... lnL = -3635.264533 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3635.264533 Node 7: lnL = -3635.264533 Node 8: lnL = -3635.264533 Node 9: lnL = -3635.264533 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 457 Sequential format.. Reading seq # 1: YPL084W_Sbay Reading seq # 2: YPL084W_Scer Reading seq # 3: YPL084W_Skud Reading seq # 4: YPL084W_Smik Reading seq # 5: YPL084W_Spar Sequences read.. Counting patterns.. # site patterns = 207 Counting frequencies.. 120 bytes for distance 33120 bytes for lkl0 26496 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.335540 0.102252 0.093126 0.114151 0.112560 0.204506 0.264733 0.000463 lnL0 = -2036.894684 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2036.894684 x= 0.33554 0.10225 0.09313 0.11415 0.11256 0.20451 0.26473 0.00046 1 h-lim-p 0.0046 0.0369 39.6822 2036.465291 8 0.0006 39 | 0/8 2 h-lim-p 0.0021 0.0200 10.5013 2036.430654 6 0.0007 66 | 0/8 3 h-lim-p 0.0011 0.0476 6.4083 2036.417674 5 0.0008 88 | 0/8 4 h-lim-p 0.0025 0.0203 2.1279 2036.415917 5 0.0009 112 | 0/8 5 h-lim-p 0.0035 0.0652 0.5498 2036.415799 2 0.0008 129 | 0/8 6 h-lim-p 0.0031 2.0592 0.1484 2036.415791 1 0.0008 152 | 0/8 7 h-lim-p 0.0124 5.2099 0.0090 2036.415790 0 0.0027 173 | 0/8 8 h-lim-p 0.1080 20.0000 0.0002 2036.415769 0 0.8643 196 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2036.415769 0 1.0938 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2036.415769 0 1.0938 236 | 0/8 11 h-lim-p 1.1361 20.0000 0.0000 2036.415769 0 2.2723 257 | 0/8 12 h-lim-p 0.5042 20.0000 0.0001 2036.415769 0 0.1260 278 | 0/8 13 h-lim-p 0.0083 17.7581 0.0009 2036.415769 0 0.0000 322 | 0/8 14 h-lim-p 0.0000 20.0000 0.0005 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -2036.415769 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2036.415769 Node 7: lnL = -2036.415769 Node 8: lnL = -2036.415769 Node 9: lnL = -2036.415769 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 650 Sequential format.. Reading seq # 1: YPL086C_Sbay Reading seq # 2: YPL086C_Scer Reading seq # 3: YPL086C_Skud Reading seq # 4: YPL086C_Smik Reading seq # 5: YPL086C_Spar Sequences read.. Counting patterns.. # site patterns = 215 Counting frequencies.. 120 bytes for distance 34400 bytes for lkl0 27520 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.283936 0.098847 0.066524 0.112302 0.054852 0.189872 0.180474 0.010757 lnL0 = -2888.870974 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2888.870974 x= 0.28394 0.09885 0.06652 0.11230 0.05485 0.18987 0.18047 0.01076 1 h-lim-p 0.0001 0.0010 95.6061 2887.814975 0 0.0002 23 | 0/8 2 h-lim-p 0.0007 0.0216 35.2652 2887.712712 7 0.0002 52 | 0/8 3 h-lim-p 0.0004 0.0109 17.4416 2887.673794 5 0.0003 75 | 0/8 4 h-lim-p 0.0010 0.0405 5.6810 2887.668746 5 0.0004 98 | 0/8 5 h-lim-p 0.0021 0.2279 0.9815 2887.668549 3 0.0004 117 | 0/8 6 h-lim-p 0.0023 1.4449 0.1866 2887.668540 1 0.0005 140 | 0/8 7 h-lim-p 0.0046 1.5805 0.0184 2887.668526 0 0.0092 161 | 0/8 8 h-lim-p 0.0111 9.4983 0.0152 2887.666686 0 0.0887 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 2887.666507 2 0.9961 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2887.666507 0 2.1875 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2887.666507 0 1.0938 248 | 0/8 12 h-lim-p 0.0673 20.0000 0.0000 2887.666507 0 8.6183 275 | 0/8 13 h-lim-p 0.1187 6.6370 0.0025 2887.666507 0 0.0519 295 | 0/8 14 h-lim-p 0.0127 1.6054 0.0101 2887.666507 0 0.0004 319 | 0/8 15 h-lim-p 0.0003 1.1357 0.0143 2887.666507 0 0.0000 354 | 0/8 16 h-lim-p 0.0003 20.0000 0.0000 2887.666507 0 0.0000 385 Out... lnL = -2887.666507 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2887.666507 Node 7: lnL = -2887.666507 Node 8: lnL = -2887.666507 Node 9: lnL = -2887.666507 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 488 Sequential format.. Reading seq # 1: YPL087W_Sbay Reading seq # 2: YPL087W_Scer Reading seq # 3: YPL087W_Skud Reading seq # 4: YPL087W_Smik Reading seq # 5: YPL087W_Spar Sequences read.. Counting patterns.. # site patterns = 176 Counting frequencies.. 120 bytes for distance 28160 bytes for lkl0 22528 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.263828 0.027145 0.050208 0.100949 0.072087 0.159389 0.167441 0.033011 lnL0 = -2017.102121 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2017.102121 x= 0.26383 0.02715 0.05021 0.10095 0.07209 0.15939 0.16744 0.03301 1 h-lim-p 0.0022 0.0176 117.6379 2015.902113 8 0.0002 44 | 0/8 2 h-lim-p 0.0007 0.0053 20.7515 2015.809104 7 0.0004 73 | 0/8 3 h-lim-p 0.0009 0.0196 10.5507 2015.793157 5 0.0004 97 | 0/8 4 h-lim-p 0.0015 0.0400 2.4959 2015.792335 3 0.0003 116 | 0/8 5 h-lim-p 0.0010 0.2251 0.7123 2015.792216 2 0.0005 133 | 0/8 6 h-lim-p 0.0025 0.8131 0.1485 2015.792212 1 0.0003 157 | 0/8 7 h-lim-p 0.0037 5.4849 0.0125 2015.792212 0 0.0032 177 | 0/8 8 h-lim-p 0.0296 20.0000 0.0014 2015.791884 0 0.3552 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2015.791878 1 0.9961 222 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2015.791878 0 2.1875 242 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2015.791878 0 1.0938 262 | 0/8 12 h-lim-p 0.1890 20.0000 0.0000 2015.791878 0 0.0052 286 | 0/8 13 h-lim-p 0.0003 20.0000 0.0005 2015.791878 0 0.0000 323 | 0/8 14 h-lim-p 0.0000 20.0000 0.0003 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -2015.791878 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2015.791878 Node 7: lnL = -2015.791878 Node 8: lnL = -2015.791878 Node 9: lnL = -2015.791878 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 1019 Sequential format.. Reading seq # 1: YPL088W_Sbay Reading seq # 2: YPL088W_Scer Reading seq # 3: YPL088W_Skud Reading seq # 4: YPL088W_Smik Reading seq # 5: YPL088W_Spar Sequences read.. Counting patterns.. # site patterns = 338 Counting frequencies.. 120 bytes for distance 54080 bytes for lkl0 43264 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.351967 0.101871 0.087397 0.126284 0.095515 0.229031 0.233297 0.014494 lnL0 = -4255.284888 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4255.284888 x= 0.35197 0.10187 0.08740 0.12628 0.09552 0.22903 0.23330 0.01449 1 h-lim-p 0.0008 0.0063 131.2632 4253.175919 6 0.0003 35 | 0/8 2 h-lim-p 0.0007 0.0052 23.9627 4253.101867 5 0.0003 56 | 0/8 3 h-lim-p 0.0005 0.0218 12.9814 4253.078079 6 0.0004 84 | 0/8 4 h-lim-p 0.0014 0.0415 3.2532 4253.075768 4 0.0005 106 | 0/8 5 h-lim-p 0.0015 0.1651 1.0311 4253.075536 3 0.0005 126 | 0/8 6 h-lim-p 0.0016 1.1494 0.3112 4253.075510 2 0.0006 142 | 0/8 7 h-lim-p 0.0095 1.8767 0.0204 4253.075510 0 0.0010 164 | 0/8 8 h-lim-p 0.1753 20.0000 0.0001 4253.075485 0 1.4028 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4253.075483 0 1.0938 207 | 0/8 10 h-lim-p 1.9117 20.0000 0.0000 4253.075483 0 0.9559 227 | 0/8 11 h-lim-p 0.8504 20.0000 0.0000 4253.075483 0 0.0066 253 | 0/8 12 h-lim-p 0.0009 20.0000 0.0002 4253.075483 0 0.0000 287 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 4253.075483 0 0.0000 316 Out... lnL = -4253.075483 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4253.075483 Node 7: lnL = -4253.075483 Node 8: lnL = -4253.075483 Node 9: lnL = -4253.075483 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 871 Sequential format.. Reading seq # 1: YPL089C_Sbay Reading seq # 2: YPL089C_Scer Reading seq # 3: YPL089C_Skud Reading seq # 4: YPL089C_Smik Reading seq # 5: YPL089C_Spar Sequences read.. Counting patterns.. # site patterns = 397 Counting frequencies.. 120 bytes for distance 63520 bytes for lkl0 50816 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.539440 0.573122 0.322885 0.183469 0.353927 0.447702 0.101492 0.000060 lnL0 = -4344.606134 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4344.606134 x= 0.53944 0.57312 0.32288 0.18347 0.35393 0.44770 0.10149 0.00006 1 h-lim-p 0.0000 0.0000 477.9999 4344.081159 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0003 1596.7144 4224.027839 0 0.0002 38 | 1/8 3 h-lim-p 0.0001 0.0006 480.5807 4176.222026 m 0.0006 50 | 1/8 4 h-lim-p 0.0001 0.0008 264.6424 4164.692330 0 0.0004 64 | 1/8 5 h-lim-p 0.0015 0.0170 68.6394 4162.843846 9 0.0009 99 | 1/8 6 h-lim-p 0.0002 0.0017 20.9309 4162.669386 0 0.0008 113 | 1/8 7 h-lim-p 0.0021 0.0546 8.6264 4162.440230 0 0.0031 125 | 1/8 8 h-lim-p 0.0372 0.3355 0.7163 4135.235432 3 0.2732 145 | 0/8 9 h-lim-p 0.0004 0.0034 45.9408 4134.166216 0 0.0013 165 | 0/8 10 h-lim-p 0.0121 0.0971 0.1723 4131.767906 m 0.0971 177 | 1/8 11 h-lim-p 0.0780 4.1933 0.2139 4113.347043 0 1.2474 201 | 1/8 12 h-lim-p 2.5000 20.0000 0.0821 4111.560353 7 1.2566 237 | 1/8 13 h-lim-p 1.5932 12.7453 0.0509 4111.116364 6 1.0194 270 | 1/8 14 h-lim-p 1.3424 10.7394 0.0285 4110.985600 7 0.9185 307 | 1/8 15 h-lim-p 2.5000 20.0000 0.0042 4110.980995 3 1.2103 333 | 1/8 16 h-lim-p 2.5000 20.0000 0.0004 4110.980940 2 0.7996 357 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 4110.980938 0 1.2500 376 | 1/8 18 h-lim-p 2.5000 20.0000 0.0000 4110.980938 0 1.0938 395 | 1/8 19 h-lim-p 2.5000 20.0000 0.0000 4110.980938 0 2.1875 414 | 1/8 20 h-lim-p 2.1499 20.0000 0.0000 4110.980938 0 0.9406 433 | 1/8 21 h-lim-p 2.5000 20.0000 0.0000 4110.980938 0 0.0146 459 Out... lnL = -4110.980938 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4110.980938 Node 7: lnL = -4110.980938 Node 8: lnL = -4110.980938 Node 9: lnL = -4110.980938 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 397 Sequential format.. Reading seq # 1: YPL091W_Sbay Reading seq # 2: YPL091W_Scer Reading seq # 3: YPL091W_Skud Reading seq # 4: YPL091W_Smik Reading seq # 5: YPL091W_Spar Sequences read.. Counting patterns.. # site patterns = 150 Counting frequencies.. 120 bytes for distance 24000 bytes for lkl0 19200 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.327003 0.066651 0.052667 0.108964 0.091750 0.165368 0.200565 0.038562 lnL0 = -1608.868458 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1608.868458 x= 0.32700 0.06665 0.05267 0.10896 0.09175 0.16537 0.20057 0.03856 1 h-lim-p 0.0007 0.0060 58.0810 1608.202025 7 0.0004 38 | 0/8 2 h-lim-p 0.0011 0.0084 17.6928 1608.127666 2 0.0005 54 | 0/8 3 h-lim-p 0.0016 0.0394 5.4977 1608.120395 6 0.0005 80 | 0/8 4 h-lim-p 0.0018 0.1423 1.6243 1608.119589 4 0.0007 100 | 0/8 5 h-lim-p 0.0026 0.7141 0.4183 1608.119514 3 0.0009 120 | 0/8 6 h-lim-p 0.0038 3.2297 0.1018 1608.119510 1 0.0008 143 | 0/8 7 h-lim-p 0.0029 3.6186 0.0268 1608.119509 1 0.0014 166 | 0/8 8 h-lim-p 0.0862 20.0000 0.0004 1608.119371 0 0.6899 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1608.119369 0 1.0938 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1608.119369 0 1.0938 229 | 0/8 11 h-lim-p 1.0746 20.0000 0.0000 1608.119369 0 4.2983 251 | 0/8 12 h-lim-p 2.1911 20.0000 0.0000 1608.119369 0 0.4793 272 | 0/8 13 h-lim-p 0.0398 20.0000 0.0002 1608.119369 0 0.0003 298 | 0/8 14 h-lim-p 0.0003 20.0000 0.0002 1608.119369 0 0.0000 331 | 0/8 15 h-lim-p 0.0000 20.0000 0.0009 | 0/8 16 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -1608.119369 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1608.119369 Node 7: lnL = -1608.119369 Node 8: lnL = -1608.119369 Node 9: lnL = -1608.119369 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 900 Sequential format.. Reading seq # 1: YPL092W_Sbay Reading seq # 2: YPL092W_Scer Reading seq # 3: YPL092W_Skud Reading seq # 4: YPL092W_Smik Reading seq # 5: YPL092W_Spar Sequences read.. Counting patterns.. # site patterns = 276 Counting frequencies.. 120 bytes for distance 44160 bytes for lkl0 35328 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.257267 0.016105 0.063526 0.095859 0.121111 0.191254 0.177711 0.005862 lnL0 = -3670.868278 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3670.868278 x= 0.25727 0.01610 0.06353 0.09586 0.12111 0.19125 0.17771 0.00586 1 h-lim-p 0.0014 0.0135 227.4117 3668.466617 8 0.0001 42 | 0/8 2 h-lim-p 0.0007 0.0065 32.4404 3668.316185 5 0.0003 64 | 0/8 3 h-lim-p 0.0013 0.0341 7.5241 3668.308626 3 0.0003 83 | 0/8 4 h-lim-p 0.0009 0.0611 2.3025 3668.308129 2 0.0002 100 | 0/8 5 h-lim-p 0.0012 0.0483 0.4012 3668.308107 1 0.0003 115 | 0/8 6 h-lim-p 0.0027 3.5040 0.0424 3668.308106 0 0.0003 137 | 0/8 7 h-lim-p 0.0012 20.0000 0.0102 3668.308106 0 0.0019 157 | 0/8 8 h-lim-p 0.0223 20.0000 0.0008 3668.307936 0 0.3566 181 | 0/8 9 h-lim-p 2.1945 20.0000 0.0001 3668.307926 0 0.9601 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3668.307926 0 1.0938 221 | 0/8 11 h-lim-p 1.1110 20.0000 0.0000 3668.307926 0 8.8877 244 | 0/8 12 h-lim-p 0.0499 2.0059 0.0079 3668.307926 0 0.0094 266 | 0/8 13 h-lim-p 0.0023 0.4972 0.0317 3668.307926 0 0.0000 294 | 0/8 14 h-lim-p 0.0001 20.0000 0.0021 3668.307926 0 0.0000 314 | 0/8 15 h-lim-p 0.0000 9.0286 0.0017 3668.307926 0 0.0000 342 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 3668.307926 0 0.0000 367 Out... lnL = -3668.307926 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3668.307926 Node 7: lnL = -3668.307926 Node 8: lnL = -3668.307926 Node 9: lnL = -3668.307926 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 315 Sequential format.. Reading seq # 1: YPL093W_Sbay Reading seq # 2: YPL093W_Scer Reading seq # 3: YPL093W_Skud Reading seq # 4: YPL093W_Smik Reading seq # 5: YPL093W_Spar Sequences read.. Counting patterns.. # site patterns = 95 Counting frequencies.. 120 bytes for distance 15200 bytes for lkl0 12160 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.195194 0.047130 0.030770 0.056868 0.031796 0.081565 0.118512 0.031156 lnL0 = -1116.548682 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1116.548682 x= 0.19519 0.04713 0.03077 0.05687 0.03180 0.08157 0.11851 0.03116 1 h-lim-p 0.0001 0.0005 109.2048 1115.487332 0 0.0002 24 | 0/8 2 h-lim-p 0.0006 0.0124 40.8002 1115.378697 4 0.0002 45 | 0/8 3 h-lim-p 0.0004 0.0045 16.0998 1115.349936 6 0.0003 73 | 0/8 4 h-lim-p 0.0009 0.0230 4.8561 1115.345115 5 0.0005 96 | 0/8 5 h-lim-p 0.0028 0.2058 0.7812 1115.344955 3 0.0005 117 | 0/8 6 h-lim-p 0.0021 1.2773 0.1681 1115.344750 0 0.0032 137 | 0/8 7 h-lim-p 0.0031 0.6832 0.1716 1115.340599 0 0.0124 159 | 0/8 8 h-lim-p 0.0025 0.0851 0.8586 1115.291295 0 0.0050 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0008 1115.289573 4 1.0519 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1115.289558 2 1.0938 233 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1115.289558 0 1.0938 253 | 0/8 12 h-lim-p 1.2827 20.0000 0.0000 1115.289558 0 1.9240 273 | 0/8 13 h-lim-p 1.4805 20.0000 0.0000 1115.289558 0 1.2955 293 | 0/8 14 h-lim-p 0.1198 20.0000 0.0002 1115.289558 0 0.0000 325 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 1115.289558 0 0.0001 345 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 1115.289558 0 0.0000 365 | 0/8 17 h-lim-p 0.0001 20.0000 0.0000 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0006 1115.289558 0 0.0000 433 | 0/8 19 h-lim-p 0.0000 20.0000 0.0006 1115.289558 0 0.0000 463 | 0/8 20 h-lim-p 0.0000 20.0000 0.0002 1115.289558 0 0.0051 492 | 0/8 21 h-lim-p 0.0134 20.0000 0.0001 1115.289558 0 0.0000 523 | 0/8 22 h-lim-p 0.0000 20.0000 0.0001 1115.289558 0 0.0000 554 | 0/8 23 h-lim-p 0.0000 20.0000 0.0086 | 0/8 24 h-lim-p 0.0000 20.0000 0.0086 Out... lnL = -1115.289558 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1115.289558 Node 7: lnL = -1115.289558 Node 8: lnL = -1115.289558 Node 9: lnL = -1115.289558 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 317 Sequential format.. Reading seq # 1: YPL094C_Sbay Reading seq # 2: YPL094C_Scer Reading seq # 3: YPL094C_Skud Reading seq # 4: YPL094C_Smik Reading seq # 5: YPL094C_Spar Sequences read.. Counting patterns.. # site patterns = 98 Counting frequencies.. 120 bytes for distance 15680 bytes for lkl0 12544 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.197623 0.021309 0.038306 0.054785 0.041763 0.091442 0.109272 0.036480 lnL0 = -1130.935124 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1130.935124 x= 0.19762 0.02131 0.03831 0.05479 0.04176 0.09144 0.10927 0.03648 1 h-lim-p 0.0001 0.0006 136.9877 1129.244887 0 0.0002 23 | 0/8 2 h-lim-p 0.0006 0.0048 21.0151 1129.180415 4 0.0003 43 | 0/8 3 h-lim-p 0.0010 0.0469 6.5952 1129.176575 5 0.0002 65 | 0/8 4 h-lim-p 0.0003 0.0476 3.9158 1129.174345 1 0.0004 79 | 0/8 5 h-lim-p 0.0027 0.1028 0.5906 1129.174264 4 0.0004 101 | 0/8 6 h-lim-p 0.0016 1.0733 0.1354 1129.174034 0 0.0032 122 | 0/8 7 h-lim-p 0.0055 0.7906 0.0782 1129.142417 0 0.0886 146 | 0/8 8 h-lim-p 0.0015 0.0272 4.4731 1129.119110 6 0.0010 180 | 0/8 9 h-lim-p 2.4763 20.0000 0.0018 1129.115587 5 0.9196 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1129.115582 2 0.9644 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1129.115582 0 1.0938 248 | 0/8 12 h-lim-p 1.3516 20.0000 0.0000 1129.115582 0 1.1826 268 | 0/8 13 h-lim-p 0.3140 20.0000 0.0001 1129.115582 0 0.0003 297 | 0/8 14 h-lim-p 0.0026 20.0000 0.0000 1129.115582 0 0.0000 339 Out... lnL = -1129.115582 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1129.115582 Node 7: lnL = -1129.115582 Node 8: lnL = -1129.115582 Node 9: lnL = -1129.115582 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 447 Sequential format.. Reading seq # 1: YPL095C_Sbay Reading seq # 2: YPL095C_Scer Reading seq # 3: YPL095C_Skud Reading seq # 4: YPL095C_Smik Reading seq # 5: YPL095C_Spar Sequences read.. Counting patterns.. # site patterns = 145 Counting frequencies.. 120 bytes for distance 23200 bytes for lkl0 18560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.304131 0.052836 0.064605 0.085188 0.071513 0.123931 0.104748 0.063053 lnL0 = -1788.388840 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1788.388840 x= 0.30413 0.05284 0.06460 0.08519 0.07151 0.12393 0.10475 0.06305 1 h-lim-p 0.0008 0.0068 82.3135 1787.314964 6 0.0003 33 | 0/8 2 h-lim-p 0.0004 0.0033 39.6403 1786.984724 1 0.0005 47 | 0/8 3 h-lim-p 0.0017 0.0212 12.1911 1786.965618 6 0.0003 76 | 0/8 4 h-lim-p 0.0010 0.0593 3.5098 1786.963293 3 0.0004 94 | 0/8 5 h-lim-p 0.0010 0.0963 1.4214 1786.962827 4 0.0005 115 | 0/8 6 h-lim-p 0.0079 1.7749 0.0961 1786.962824 1 0.0005 132 | 0/8 7 h-lim-p 0.0025 9.6438 0.0187 1786.962821 0 0.0025 152 | 0/8 8 h-lim-p 0.0070 20.0000 0.0066 1786.961961 0 0.1121 176 | 0/8 9 h-lim-p 1.3281 20.0000 0.0006 1786.961938 1 1.1620 198 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1786.961938 0 1.0938 218 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1786.961938 0 1.2500 238 | 0/8 12 h-lim-p 0.8762 20.0000 0.0000 1786.961938 0 0.3834 258 | 0/8 13 h-lim-p 0.1144 20.0000 0.0000 1786.961938 0 0.1144 278 | 0/8 14 h-lim-p 0.0441 20.0000 0.0001 1786.961938 0 0.0097 299 | 0/8 15 h-lim-p 0.0049 20.0000 0.0002 1786.961938 0 0.0012 320 | 0/8 16 h-lim-p 0.0005 20.0000 0.0004 1786.961938 0 0.0001 342 | 0/8 17 h-lim-p 0.0001 20.0000 0.0002 1786.961938 0 0.0000 363 | 0/8 18 h-lim-p 0.0004 20.0000 0.0000 1786.961938 0 0.0000 396 | 0/8 19 h-lim-p 0.0000 20.0000 0.0003 | 0/8 20 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -1786.961938 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1786.961938 Node 7: lnL = -1786.961938 Node 8: lnL = -1786.961938 Node 9: lnL = -1786.961938 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 565 Sequential format.. Reading seq # 1: YPL096W_Sbay Reading seq # 2: YPL096W_Scer Reading seq # 3: YPL096W_Skud Reading seq # 4: YPL096W_Smik Reading seq # 5: YPL096W_Spar Sequences read.. Counting patterns.. # site patterns = 138 Counting frequencies.. 120 bytes for distance 22080 bytes for lkl0 17664 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.188568 0.091372 0.088570 0.081362 0.039663 0.120790 0.105294 0.000060 lnL0 = -2079.669702 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2079.669702 x= 0.18857 0.09137 0.08857 0.08136 0.03966 0.12079 0.10529 0.00006 1 h-lim-p 0.0000 0.0000 135.9132 2079.332787 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0008 82.7464 2079.007790 0 0.0001 36 | 1/8 3 h-lim-p 0.0006 0.0066 18.6217 2078.971724 5 0.0002 58 | 1/8 4 h-lim-p 0.0007 0.0358 5.9014 2078.965460 5 0.0003 83 | 1/8 5 h-lim-p 0.0017 0.1613 1.2172 2078.958866 0 0.0025 95 | 0/8 6 h-lim-p 0.0007 0.0687 4.2157 2078.847798 0 0.0088 110 | 0/8 7 h-lim-p 0.0007 0.0057 44.6915 2078.739244 3 0.0006 128 | 0/8 8 h-lim-p 0.0077 0.0615 2.1065 2078.553149 7 0.0057 156 | 0/8 9 h-lim-p 0.0004 0.0034 19.1056 2077.126911 m 0.0034 168 | 0/8 10 h-lim-p 0.0000 0.0000 0.0071 h-lim-p: 1.83019921e-18 1.46415937e-17 7.07089188e-03 2077.126911 .. | 0/8 11 h-lim-p 0.0000 7.0576 21.0112 2077.091616 0 0.0002 200 | 0/8 12 h-lim-p 0.0005 0.0102 6.3680 2077.088769 5 0.0002 226 | 0/8 13 h-lim-p 0.0011 0.1477 0.8510 2077.088664 3 0.0003 245 | 0/8 14 h-lim-p 0.0018 0.3094 0.1394 2077.088661 1 0.0002 269 | 0/8 15 h-lim-p 0.0012 6.4922 0.0262 2077.088661 0 0.0005 289 | 0/8 16 h-lim-p 0.0026 20.0000 0.0053 2077.088661 0 0.0023 309 | 0/8 17 h-lim-p 0.0004 8.9417 0.0301 2077.088661 0 0.0128 334 | 0/8 18 h-lim-p 0.0010 0.6537 0.3736 2077.088660 0 0.0005 354 | 0/8 19 h-lim-p 1.0005 8.0039 0.0001 2077.088660 0 1.0005 374 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 2077.088660 0 2.1875 394 | 0/8 21 h-lim-p 0.1371 12.6886 0.0001 2077.088660 0 0.0003 422 | 0/8 22 h-lim-p 0.0000 0.4501 0.0020 2077.088660 0 0.0000 444 | 0/8 23 h-lim-p 0.0001 20.0000 0.0000 2077.088660 0 0.0000 475 | 0/8 24 h-lim-p 0.0000 12.6223 0.0013 | 0/8 25 h-lim-p 0.0000 12.6223 0.0013 Out... lnL = -2077.088660 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2077.088660 Node 7: lnL = -2077.088660 Node 8: lnL = -2077.088660 Node 9: lnL = -2077.088660 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 226 Sequential format.. Reading seq # 1: YPL097W_Sbay Reading seq # 2: YPL097W_Scer Reading seq # 3: YPL097W_Skud Reading seq # 4: YPL097W_Smik Reading seq # 5: YPL097W_Spar Sequences read.. Counting patterns.. # site patterns = 101 Counting frequencies.. 120 bytes for distance 16160 bytes for lkl0 12928 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.224342 0.069163 0.023444 0.127799 0.091056 0.140288 0.132140 0.002003 lnL0 = -932.743208 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 932.743208 x= 0.22434 0.06916 0.02344 0.12780 0.09106 0.14029 0.13214 0.00200 1 h-lim-p 0.0001 0.0007 46.7916 932.271233 0 0.0004 24 | 0/8 2 h-lim-p 0.0007 0.0281 22.8317 932.191930 7 0.0004 54 | 0/8 3 h-lim-p 0.0037 0.0786 2.2915 932.189810 2 0.0008 71 | 0/8 4 h-lim-p 0.0041 0.2670 0.4539 932.189667 4 0.0012 94 | 0/8 5 h-lim-p 0.0045 1.6544 0.1165 932.189528 2 0.0039 118 | 0/8 6 h-lim-p 0.0035 0.3565 0.1325 932.186879 0 0.0139 140 | 0/8 7 h-lim-p 0.0032 0.0439 0.5801 932.168675 0 0.0063 161 | 0/8 8 h-lim-p 0.0101 0.7938 0.3640 932.168613 3 0.0010 189 | 0/8 9 h-lim-p 0.5452 20.0000 0.0006 932.168201 0 1.0904 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 932.168190 2 0.9644 234 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 932.168190 0 0.5469 255 | 0/8 12 h-lim-p 0.3804 20.0000 0.0000 932.168190 0 0.0000 289 | 0/8 13 h-lim-p 0.0000 20.0000 0.0004 932.168190 0 0.0000 315 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 932.168190 0 0.0000 345 Out... lnL = -932.168190 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -932.168190 Node 7: lnL = -932.168190 Node 8: lnL = -932.168190 Node 9: lnL = -932.168190 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 235 Sequential format.. Reading seq # 1: YPL098C_Sbay Reading seq # 2: YPL098C_Scer Reading seq # 3: YPL098C_Skud Reading seq # 4: YPL098C_Smik Reading seq # 5: YPL098C_Spar Sequences read.. Counting patterns.. # site patterns = 106 Counting frequencies.. 120 bytes for distance 16960 bytes for lkl0 13568 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.227966 0.069558 0.022787 0.131869 0.086985 0.144362 0.147138 0.000284 lnL0 = -953.643620 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 953.643620 x= 0.22797 0.06956 0.02279 0.13187 0.08699 0.14436 0.14714 0.00028 1 h-lim-p 0.0001 0.0008 41.4049 953.249860 0 0.0004 24 | 0/8 2 h-lim-p 0.0007 0.0348 22.5689 953.175948 7 0.0004 54 | 0/8 3 h-lim-p 0.0024 0.0487 3.4892 953.171528 6 0.0007 81 | 0/8 4 h-lim-p 0.0032 0.1399 0.8182 953.171239 5 0.0009 106 | 0/8 5 h-lim-p 0.0044 0.8511 0.1646 953.171205 3 0.0015 133 | 0/8 6 h-lim-p 0.0034 0.5725 0.0747 953.171096 0 0.0068 154 | 0/8 7 h-lim-p 0.0156 0.7717 0.0326 953.163875 0 0.0937 176 | 0/8 8 h-lim-p 0.0030 0.0236 0.7392 953.163588 4 0.0010 206 | 0/8 9 h-lim-p 1.8380 20.0000 0.0004 953.163431 3 0.9675 233 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 953.163431 0 1.0938 253 | 0/8 11 h-lim-p 1.6374 20.0000 0.0000 953.163431 0 0.0448 277 | 0/8 12 h-lim-p 0.0196 20.0000 0.0000 953.163431 0 0.0024 299 | 0/8 13 h-lim-p 0.0014 20.0000 0.0001 953.163431 0 0.0007 319 | 0/8 14 h-lim-p 0.0005 20.0000 0.0001 953.163431 0 0.0002 339 | 0/8 15 h-lim-p 0.0001 20.0000 0.0002 953.163431 0 0.0000 378 | 0/8 16 h-lim-p 0.0000 20.0000 0.0019 | 0/8 17 h-lim-p 0.0000 20.0000 0.0019 Out... lnL = -953.163431 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -953.163431 Node 7: lnL = -953.163431 Node 8: lnL = -953.163431 Node 9: lnL = -953.163431 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 354 Sequential format.. Reading seq # 1: YPL099C_Sbay Reading seq # 2: YPL099C_Scer Reading seq # 3: YPL099C_Skud Reading seq # 4: YPL099C_Smik Reading seq # 5: YPL099C_Spar Sequences read.. Counting patterns.. # site patterns = 122 Counting frequencies.. 120 bytes for distance 19520 bytes for lkl0 15616 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.230936 0.144392 0.130827 0.096795 0.041394 0.181068 0.123630 0.000060 lnL0 = -1459.716822 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1459.716822 x= 0.23094 0.14439 0.13083 0.09679 0.04139 0.18107 0.12363 0.00006 1 h-lim-p 0.0000 0.0000 187.5335 1459.471418 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0004 291.4034 1454.252600 0 0.0002 38 | 1/8 3 h-lim-p 0.0001 0.0007 161.0598 1452.607816 0 0.0002 51 | 1/8 4 h-lim-p 0.0004 0.0029 35.4980 1452.330543 0 0.0005 63 | 1/8 5 h-lim-p 0.0021 0.0631 9.2135 1452.297547 6 0.0007 90 | 1/8 6 h-lim-p 0.0029 0.0879 2.2014 1452.244724 0 0.0044 102 | 0/8 7 h-lim-p 0.0008 0.0287 12.0417 1451.900868 0 0.0032 116 | 0/8 8 h-lim-p 0.0009 0.0071 37.9479 1450.745703 0 0.0036 130 | 0/8 9 h-lim-p 0.0074 0.0595 2.9572 1446.363277 m 0.0595 142 | 0/8 10 h-lim-p 2.5000 20.0000 0.0195 1445.851144 7 0.9378 168 | 0/8 11 h-lim-p 0.2865 2.2920 0.0102 1445.722253 0 1.1460 190 | 0/8 12 h-lim-p 2.5000 20.0000 0.0027 1445.707438 7 1.5197 231 | 0/8 13 h-lim-p 2.2022 20.0000 0.0018 1445.705379 4 1.1559 260 | 0/8 14 h-lim-p 1.0297 8.2377 0.0007 1445.705289 1 1.2871 282 | 0/8 15 h-lim-p 2.5000 20.0000 0.0002 1445.705278 2 1.3159 307 | 0/8 16 h-lim-p 2.5000 20.0000 0.0001 1445.705278 0 1.0938 327 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1445.705278 0 1.0938 347 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1445.705278 0 0.6250 368 | 0/8 19 h-lim-p 0.7297 20.0000 0.0000 1445.705278 0 0.0014 396 Out... lnL = -1445.705278 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1445.705278 Node 7: lnL = -1445.705278 Node 8: lnL = -1445.705278 Node 9: lnL = -1445.705278 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 697 Sequential format.. Reading seq # 1: YPL103C_Sbay Reading seq # 2: YPL103C_Scer Reading seq # 3: YPL103C_Skud Reading seq # 4: YPL103C_Smik Reading seq # 5: YPL103C_Spar Sequences read.. Counting patterns.. # site patterns = 316 Counting frequencies.. 120 bytes for distance 50560 bytes for lkl0 40448 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.360606 0.230716 0.071091 0.273634 0.152414 0.163415 0.253450 0.000060 lnL0 = -3208.530373 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3208.530373 x= 0.36061 0.23072 0.07109 0.27363 0.15241 0.16342 0.25345 0.00006 1 h-lim-p 0.0000 0.0000 74.2670 3208.509981 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0045 32.7672 3208.205956 0 0.0006 40 | 1/8 3 h-lim-p 0.0019 0.0444 10.9808 3208.155083 5 0.0009 64 | 1/8 4 h-lim-p 0.0026 0.0714 3.9625 3208.148475 6 0.0008 93 | 1/8 5 h-lim-p 0.0045 0.1761 0.7097 3208.138063 0 0.0068 105 | 1/8 6 h-lim-p 0.0102 0.9312 0.4731 3207.196035 0 0.0812 127 | 0/8 7 h-lim-p 0.0023 0.0308 16.3636 3206.829656 7 0.0016 164 | 0/8 8 h-lim-p 0.0007 0.0052 4.4824 3206.806046 0 0.0026 178 | 0/8 9 h-lim-p 0.0006 0.0045 3.2549 3206.801870 0 0.0011 191 | 0/8 10 h-lim-p 0.9393 20.0000 0.0039 3206.791192 1 1.1741 205 | 0/8 11 h-lim-p 2.5000 20.0000 0.0002 3206.791181 1 1.0938 227 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3206.791181 0 1.2500 247 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 3206.791181 0 1.0938 267 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 3206.791181 0 2.1875 287 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 3206.791181 0 1.2500 307 | 0/8 16 h-lim-p 1.2286 20.0000 0.0000 3206.791181 0 0.0096 333 Out... lnL = -3206.791181 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3206.791181 Node 7: lnL = -3206.791181 Node 8: lnL = -3206.791181 Node 9: lnL = -3206.791181 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 302 Sequential format.. Reading seq # 1: YPL104W_Sbay Reading seq # 2: YPL104W_Scer Reading seq # 3: YPL104W_Skud Reading seq # 4: YPL104W_Smik Reading seq # 5: YPL104W_Spar Sequences read.. Counting patterns.. # site patterns = 116 Counting frequencies.. 120 bytes for distance 18560 bytes for lkl0 14848 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.286721 0.010318 0.067361 0.114354 0.098499 0.180075 0.233057 0.010004 lnL0 = -1344.709978 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1344.709978 x= 0.28672 0.01032 0.06736 0.11435 0.09850 0.18007 0.23306 0.01000 1 h-lim-p 0.0078 0.3277 58.6749 1344.160210 6 0.0003 39 | 0/8 2 h-lim-p 0.0006 0.0044 13.5170 1344.085521 0 0.0011 52 | 0/8 3 h-lim-p 0.0034 0.0574 4.4023 1344.078873 5 0.0008 74 | 0/8 4 h-lim-p 0.0039 0.1075 0.8532 1344.078495 5 0.0011 98 | 0/8 5 h-lim-p 0.0016 0.1235 0.5758 1344.078417 2 0.0006 122 | 0/8 6 h-lim-p 0.0148 10.7484 0.0241 1344.078348 0 0.0129 142 | 0/8 7 h-lim-p 0.0029 2.4995 0.1073 1344.077359 0 0.0116 164 | 0/8 8 h-lim-p 0.0018 0.0615 0.7010 1344.074037 0 0.0036 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1344.074034 1 0.9961 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1344.074034 0 2.1875 227 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1344.074034 0 1.0938 247 | 0/8 12 h-lim-p 0.2170 20.0000 0.0000 1344.074034 0 0.0025 273 | 0/8 13 h-lim-p 0.0001 20.0000 0.0005 1344.074034 0 0.0000 304 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 1344.074034 0 0.0000 333 Out... lnL = -1344.074034 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1344.074034 Node 7: lnL = -1344.074034 Node 8: lnL = -1344.074034 Node 9: lnL = -1344.074034 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 649 Sequential format.. Reading seq # 1: YPL106C_Sbay Reading seq # 2: YPL106C_Scer Reading seq # 3: YPL106C_Skud Reading seq # 4: YPL106C_Smik Reading seq # 5: YPL106C_Spar Sequences read.. Counting patterns.. # site patterns = 214 Counting frequencies.. 120 bytes for distance 34240 bytes for lkl0 27392 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.266318 0.133892 0.178348 0.136497 0.085684 0.235884 0.132588 0.000060 lnL0 = -2863.754645 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2863.754645 x= 0.26632 0.13389 0.17835 0.13650 0.08568 0.23588 0.13259 0.00006 1 h-lim-p 0.0000 0.0000 284.8343 2863.570371 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0012 205.3953 2857.687559 0 0.0003 39 | 1/8 3 h-lim-p 0.0005 0.0039 52.0088 2856.826473 0 0.0007 51 | 1/8 4 h-lim-p 0.0036 0.0285 9.6076 2856.776539 6 0.0008 79 | 1/8 5 h-lim-p 0.0008 0.0292 9.3419 2856.715206 0 0.0012 91 | 1/8 6 h-lim-p 0.0041 0.0773 2.6674 2855.967877 0 0.0122 104 | 1/8 7 h-lim-p 0.0030 0.0325 10.8705 2845.054379 0 0.0090 117 | 0/8 8 h-lim-p 0.0002 0.0015 134.2841 2842.304604 0 0.0004 130 | 0/8 9 h-lim-p 0.0028 0.0222 13.3463 2842.004423 0 0.0042 142 | 0/8 10 h-lim-p 0.6812 5.4494 0.0354 2840.682264 1 0.8515 156 | 0/8 11 h-lim-p 0.9019 7.2154 0.0299 2840.483695 4 0.9389 184 | 0/8 12 h-lim-p 2.5000 20.0000 0.0096 2840.462109 4 0.8059 214 | 0/8 13 h-lim-p 2.5000 20.0000 0.0007 2840.461636 4 0.9131 243 | 0/8 14 h-lim-p 1.4562 20.0000 0.0004 2840.461588 3 0.7827 270 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2840.461588 0 1.0938 290 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 2840.461588 0 1.0938 310 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 2840.461588 0 0.5469 331 | 0/8 18 h-lim-p 1.5399 20.0000 0.0000 2840.461588 0 0.0962 354 | 0/8 19 h-lim-p 0.1317 20.0000 0.0000 2840.461588 0 0.0005 381 Out... lnL = -2840.461588 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2840.461588 Node 7: lnL = -2840.461588 Node 8: lnL = -2840.461588 Node 9: lnL = -2840.461588 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 191 Sequential format.. Reading seq # 1: YPL107W_Sbay Reading seq # 2: YPL107W_Scer Reading seq # 3: YPL107W_Skud Reading seq # 4: YPL107W_Smik Reading seq # 5: YPL107W_Spar Sequences read.. Counting patterns.. # site patterns = 97 Counting frequencies.. 120 bytes for distance 15520 bytes for lkl0 12416 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.229344 0.154709 0.208343 0.123842 0.076009 0.226031 0.067598 0.000060 lnL0 = -760.614127 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 760.614127 x= 0.22934 0.15471 0.20834 0.12384 0.07601 0.22603 0.06760 0.00006 1 h-lim-p 0.0000 0.0000 110.7557 760.565978 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0022 135.1222 754.983720 0 0.0010 40 | 1/8 3 h-lim-p 0.0011 0.0085 25.0621 754.716472 3 0.0010 58 | 1/8 4 h-lim-p 0.0034 0.0303 7.1484 754.675269 6 0.0014 85 | 1/8 5 h-lim-p 0.0104 0.1660 0.9830 754.525006 0 0.0208 98 | 0/8 6 h-lim-p 0.0039 0.0887 5.2718 753.769264 0 0.0077 118 | 0/8 7 h-lim-p 0.0014 0.0112 20.3143 750.906269 0 0.0056 132 | 0/8 8 h-lim-p 0.0020 0.0160 6.7058 750.805514 0 0.0040 145 | 0/8 9 h-lim-p 0.0014 0.0111 6.0759 750.743066 0 0.0056 159 | 0/8 10 h-lim-p 1.0460 9.3872 0.0323 750.119784 7 1.0753 184 | 0/8 11 h-lim-p 0.9055 7.2441 0.0280 749.996045 0 1.8110 205 | 0/8 12 h-lim-p 0.9461 7.5689 0.0135 749.974629 5 1.0032 235 | 0/8 13 h-lim-p 2.5000 20.0000 0.0008 749.974492 4 0.8479 266 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 749.974491 0 1.0938 286 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 749.974491 0 1.0938 306 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 749.974491 0 1.0938 326 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 749.974491 0 1.0938 346 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 749.974491 0 0.0781 370 | 0/8 19 h-lim-p 0.0249 20.0000 0.0000 749.974491 0 0.0016 393 Out... lnL = -749.974491 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -749.974491 Node 7: lnL = -749.974491 Node 8: lnL = -749.974491 Node 9: lnL = -749.974491 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 872 Sequential format.. Reading seq # 1: YPL108W_Sbay Reading seq # 2: YPL108W_Scer Reading seq # 3: YPL108W_Skud Reading seq # 4: YPL108W_Smik Reading seq # 5: YPL108W_Spar Sequences read.. Counting patterns.. # site patterns = 366 Counting frequencies.. 120 bytes for distance 58560 bytes for lkl0 46848 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.488541 0.275223 0.457669 0.284758 0.171683 0.472331 0.257142 0.000060 lnL0 = -4791.240912 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4791.240912 x= 0.48854 0.27522 0.45767 0.28476 0.17168 0.47233 0.25714 0.00006 1 h-lim-p 0.0000 0.0000 371.5280 4791.074105 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0001 4651.7305 4656.952788 m 0.0001 35 | 1/8 3 h-lim-p 0.0001 0.0008 246.1229 4645.779380 0 0.0004 49 | 1/8 4 h-lim-p 0.0002 0.0017 78.5730 4644.503532 0 0.0004 62 | 1/8 5 h-lim-p 0.0042 0.0372 7.6678 4644.431654 7 0.0013 94 | 0/8 6 h-lim-p 0.0001 0.0205 81.4277 4642.563879 0 0.0007 108 | 0/8 7 h-lim-p 0.0017 0.0139 32.4866 4642.107616 6 0.0009 134 | 0/8 8 h-lim-p 0.0032 0.0485 9.1652 4642.044653 6 0.0009 163 | 0/8 9 h-lim-p 0.0111 0.1762 0.7579 4635.471262 m 0.1762 176 | 0/8 10 h-lim-p 0.6233 4.9865 0.0554 4632.649955 0 1.8699 197 | 0/8 11 h-lim-p 1.1715 9.3721 0.0146 4632.334961 2 1.0983 221 | 0/8 12 h-lim-p 2.2567 20.0000 0.0071 4632.307712 5 1.4564 253 | 0/8 13 h-lim-p 2.5000 20.0000 0.0008 4632.307395 1 1.0938 275 | 0/8 14 h-lim-p 2.5000 20.0000 0.0002 4632.307356 2 1.6492 301 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 4632.307353 0 1.2500 321 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 4632.307353 0 1.0938 341 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 4632.307353 0 1.0938 361 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 4632.307353 0 0.3125 383 | 0/8 19 h-lim-p 0.2014 20.0000 0.0000 4632.307353 0 0.1007 403 | 0/8 20 h-lim-p 0.0571 20.0000 0.0000 4632.307353 0 0.0143 424 Out... lnL = -4632.307353 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4632.307353 Node 7: lnL = -4632.307353 Node 8: lnL = -4632.307353 Node 9: lnL = -4632.307353 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 830 Sequential format.. Reading seq # 1: YPL109C_Sbay Reading seq # 2: YPL109C_Scer Reading seq # 3: YPL109C_Skud Reading seq # 4: YPL109C_Smik Reading seq # 5: YPL109C_Spar Sequences read.. Counting patterns.. # site patterns = 265 Counting frequencies.. 120 bytes for distance 42400 bytes for lkl0 33920 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.374844 0.268813 0.354893 0.252986 0.116628 0.366578 0.122770 0.000060 lnL0 = -3495.943352 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3495.943352 x= 0.37484 0.26881 0.35489 0.25299 0.11663 0.36658 0.12277 0.00006 1 h-lim-p 0.0000 0.0000 354.0385 3495.800164 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0005 1093.5628 3420.749626 9 0.0003 62 | 1/8 3 h-lim-p 0.0001 0.0009 195.2424 3415.145196 0 0.0005 76 | 1/8 4 h-lim-p 0.0008 0.0064 39.4516 3414.729371 7 0.0005 106 | 0/8 5 h-lim-p 0.0002 0.0038 98.6079 3411.587481 0 0.0013 120 | 0/8 6 h-lim-p 0.0001 0.0012 138.9885 3408.924944 m 0.0012 132 | 1/8 7 h-lim-p 0.0037 0.0292 15.6821 3408.831124 5 0.0007 157 | 1/8 8 h-lim-p 0.0323 1.1383 0.3589 3407.829096 0 0.1291 171 | 0/8 9 h-lim-p -0.0000 -0.0000 16.3290 h-lim-p: -7.40461057e-19 -5.92368845e-18 1.63289597e+01 3407.829096 .. | 0/8 10 h-lim-p 0.0000 0.0015 173.4609 3399.266210 0 0.0006 204 | 0/8 11 h-lim-p 0.0000 0.0000 53.5463 3399.217829 m 0.0000 216 | 1/8 12 h-lim-p 0.0001 0.0702 17.3445 3399.170811 0 0.0004 231 | 1/8 13 h-lim-p 0.0013 0.0365 5.7422 3399.162258 4 0.0006 250 | 1/8 14 h-lim-p 0.0024 0.1807 1.3534 3399.160259 5 0.0013 273 | 1/8 15 h-lim-p 0.0093 1.2803 0.1867 3399.100423 0 0.0560 287 | 1/8 16 h-lim-p 0.0019 0.0690 5.4351 3399.019479 5 0.0021 317 | 1/8 17 h-lim-p 0.0130 0.3383 0.8983 3399.006015 3 0.0054 335 | 1/8 18 h-lim-p 0.0064 0.4898 0.7589 3398.514530 0 0.0385 356 | 0/8 19 h-lim-p 0.0229 0.5309 1.2778 3398.513934 4 0.0010 389 | 0/8 20 h-lim-p 0.5668 20.0000 0.0022 3398.510797 0 1.1336 402 | 0/8 21 h-lim-p 2.5000 20.0000 0.0004 3398.510625 2 0.9961 426 | 0/8 22 h-lim-p 2.5000 20.0000 0.0000 3398.510625 0 1.0938 446 | 0/8 23 h-lim-p 2.5000 20.0000 0.0000 3398.510625 0 1.0938 466 | 0/8 24 h-lim-p 2.5000 20.0000 0.0000 3398.510625 0 5.0000 487 | 0/8 25 h-lim-p 1.5169 20.0000 0.0000 3398.510625 0 0.1896 509 | 0/8 26 h-lim-p 0.2443 20.0000 0.0000 3398.510625 0 0.1222 529 | 0/8 27 h-lim-p 0.1239 20.0000 0.0000 3398.510625 0 0.0310 550 | 0/8 28 h-lim-p 0.0252 20.0000 0.0000 3398.510625 0 0.0000 590 Out... lnL = -3398.510625 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3398.510625 Node 7: lnL = -3398.510625 Node 8: lnL = -3398.510625 Node 9: lnL = -3398.510625 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 827 Sequential format.. Reading seq # 1: YPL111W_Sbay Reading seq # 2: YPL111W_Scer Reading seq # 3: YPL111W_Skud Reading seq # 4: YPL111W_Smik Reading seq # 5: YPL111W_Spar Sequences read.. Counting patterns.. # site patterns = 296 Counting frequencies.. 120 bytes for distance 47360 bytes for lkl0 37888 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.572060 0.226748 0.312899 0.347905 0.539877 0.497644 0.158241 0.000060 lnL0 = -3867.494179 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3867.494179 x= 0.57206 0.22675 0.31290 0.34790 0.53988 0.49764 0.15824 0.00006 1 h-lim-p 0.0000 0.0000 332.3235 3866.951266 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0006 832.8678 3797.194670 0 0.0005 39 | 1/8 3 h-lim-p 0.0004 0.0031 62.2752 3793.040914 0 0.0023 53 | 1/8 4 h-lim-p 0.0029 0.0273 48.9550 3789.920442 0 0.0044 65 | 1/8 5 h-lim-p 0.0014 0.0114 53.9217 3787.543927 0 0.0043 78 | 1/8 6 h-lim-p 0.0118 0.0941 5.5581 3787.430752 6 0.0048 104 | 1/8 7 h-lim-p 0.0078 0.0626 3.2578 3786.074636 m 0.0626 116 | 1/8 8 h-lim-p 0.0338 0.2705 1.5594 3781.425944 0 0.1353 130 | 0/8 9 h-lim-p -0.0000 -0.0000 0.1899 h-lim-p: -2.62316873e-21 -2.09853498e-20 1.89910635e-01 3781.425944 .. | 0/8 10 h-lim-p 0.0000 0.0339 36.1156 3780.954808 0 0.0006 164 | 0/8 11 h-lim-p 0.0007 0.0055 17.2989 3780.874445 2 0.0006 180 | 0/8 12 h-lim-p 0.0012 0.0173 8.9674 3780.860324 6 0.0005 206 | 0/8 13 h-lim-p 0.0031 0.3940 1.3353 3780.855233 0 0.0061 219 | 0/8 14 h-lim-p 0.0014 0.0953 5.8702 3780.832704 0 0.0056 233 | 0/8 15 h-lim-p 0.0099 0.2582 3.2995 3780.830609 4 0.0013 255 | 0/8 16 h-lim-p 0.0149 2.7333 0.2807 3780.823716 0 0.1787 270 | 0/8 17 h-lim-p 0.0874 0.6991 0.3260 3780.822594 4 0.0329 298 | 0/8 18 h-lim-p 1.6233 13.8274 0.0066 3780.822115 4 0.9561 328 | 0/8 19 h-lim-p 2.5000 20.0000 0.0003 3780.822114 0 1.0938 348 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 3780.822114 0 1.0938 368 | 0/8 21 h-lim-p 2.5000 20.0000 0.0000 3780.822114 0 1.0938 388 | 0/8 22 h-lim-p 1.7011 20.0000 0.0000 3780.822114 0 0.8506 408 | 0/8 23 h-lim-p 0.0133 20.0000 0.0002 3780.822114 0 0.0000 442 | 0/8 24 h-lim-p 0.0001 20.0000 0.0000 3780.822114 0 0.0000 474 Out... lnL = -3780.822114 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3780.822114 Node 7: lnL = -3780.822114 Node 8: lnL = -3780.822114 Node 9: lnL = -3780.822114 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 934 Sequential format.. Reading seq # 1: YPL112C_Sbay Reading seq # 2: YPL112C_Scer Reading seq # 3: YPL112C_Skud Reading seq # 4: YPL112C_Smik Reading seq # 5: YPL112C_Spar Sequences read.. Counting patterns.. # site patterns = 428 Counting frequencies.. 120 bytes for distance 68480 bytes for lkl0 54784 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.556011 0.068261 0.117619 0.145226 0.197136 0.277563 0.391422 0.050878 lnL0 = -4641.580632 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4641.580632 x= 0.55601 0.06826 0.11762 0.14523 0.19714 0.27756 0.39142 0.05088 1 h-lim-p 0.0037 0.0296 128.6454 4638.512039 6 0.0004 38 | 0/8 2 h-lim-p 0.0008 0.0068 34.3693 4638.230002 6 0.0005 65 | 0/8 3 h-lim-p 0.0013 0.0246 13.4540 4638.157924 6 0.0009 92 | 0/8 4 h-lim-p 0.0019 0.0820 6.5183 4638.139319 6 0.0011 119 | 0/8 5 h-lim-p 0.0030 0.0670 2.3664 4638.135762 2 0.0015 135 | 0/8 6 h-lim-p 0.0047 0.3860 0.7556 4638.135500 2 0.0010 152 | 0/8 7 h-lim-p 0.0123 4.5634 0.0625 4638.135496 1 0.0015 176 | 0/8 8 h-lim-p 0.0954 20.0000 0.0010 4638.134789 0 0.7633 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 4638.134767 1 0.9961 221 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4638.134767 0 1.0938 241 | 0/8 11 h-lim-p 1.1282 20.0000 0.0000 4638.134767 0 1.1282 261 | 0/8 12 h-lim-p 0.0637 20.0000 0.0002 .. | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 4638.134767 0 0.0000 338 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -4638.134767 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4638.134767 Node 7: lnL = -4638.134767 Node 8: lnL = -4638.134767 Node 9: lnL = -4638.134767 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 314 Sequential format.. Reading seq # 1: YPL113C_Sbay Reading seq # 2: YPL113C_Scer Reading seq # 3: YPL113C_Skud Reading seq # 4: YPL113C_Smik Reading seq # 5: YPL113C_Spar Sequences read.. Counting patterns.. # site patterns = 121 Counting frequencies.. 120 bytes for distance 19360 bytes for lkl0 15488 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.998522 0.686627 1.071191 0.518961 0.256546 2.153293 0.098588 0.000060 lnL0 = -1315.846502 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1315.846502 x= 0.99852 0.68663 1.07119 0.51896 0.25655 2.15329 0.09859 0.00006 1 h-lim-p 0.0000 0.0000 159.7078 1315.796117 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0001 1724.0816 1285.119792 m 0.0001 35 | 2/8 3 h-lim-p 0.0014 0.0113 45.0321 1256.278792 m 0.0113 47 | 2/8 4 h-lim-p 0.0010 0.0079 57.6807 1243.163786 0 0.0059 61 | 2/8 5 h-lim-p 0.0007 0.0052 138.1781 1233.527746 0 0.0020 74 | 2/8 6 h-lim-p 0.0853 0.6821 0.4746 1209.366715 m 0.6821 86 | 1/8 7 h-lim-p 0.0000 0.0000 379.0895 h-lim-p: 3.28561715e-21 2.62849372e-20 3.79089508e+02 1209.366715 .. | 1/8 8 h-lim-p 0.0000 0.3838 274.8143 1195.887410 0 0.0006 118 | 1/8 9 h-lim-p 0.0001 0.0005 75.2531 1193.455205 m 0.0005 130 | 2/8 10 h-lim-p 0.0004 0.0071 75.3924 1189.394856 0 0.0024 144 | 2/8 11 h-lim-p 0.0018 0.0147 29.1245 1189.117204 7 0.0009 170 | 2/8 12 h-lim-p 0.0165 0.2299 1.6130 1188.893166 1 0.0206 184 | 2/8 13 h-lim-p 0.0066 0.0776 5.0007 1188.577962 1 0.0083 198 | 2/8 14 h-lim-p 0.0616 0.5192 0.6735 1185.466322 0 0.2464 212 | 1/8 15 h-lim-p 0.0045 0.0362 8.0273 1185.350830 0 0.0068 230 | 0/8 16 h-lim-p 0.0042 0.2268 13.0459 1185.183338 4 0.0020 251 | 0/8 17 h-lim-p 0.4378 3.5021 0.0532 1184.750410 0 0.8755 264 | 0/8 18 h-lim-p 2.0728 16.5821 0.0133 1184.697155 5 1.0134 296 | 0/8 19 h-lim-p 1.7963 20.0000 0.0075 1184.694708 5 0.7267 328 | 0/8 20 h-lim-p 2.5000 20.0000 0.0002 1184.694694 2 1.0938 352 | 0/8 21 h-lim-p 2.5000 20.0000 0.0000 1184.694694 0 1.0938 372 | 0/8 22 h-lim-p 2.5000 20.0000 0.0000 1184.694694 0 1.0938 392 | 0/8 23 h-lim-p 2.5000 20.0000 0.0000 1184.694694 0 2.5000 412 | 0/8 24 h-lim-p 2.5000 20.0000 0.0000 1184.694694 0 0.4688 434 | 0/8 25 h-lim-p 0.0942 20.0000 0.0000 1184.694694 0 0.0000 473 Out... lnL = -1184.694694 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1184.694694 Node 7: lnL = -1184.694694 Node 8: lnL = -1184.694694 Node 9: lnL = -1184.694694 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 495 Sequential format.. Reading seq # 1: YPL115C_Sbay Reading seq # 2: YPL115C_Scer Reading seq # 3: YPL115C_Skud Reading seq # 4: YPL115C_Smik Reading seq # 5: YPL115C_Spar Sequences read.. Counting patterns.. # site patterns = 147 Counting frequencies.. 120 bytes for distance 23520 bytes for lkl0 18816 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.213808 0.055928 0.036792 0.088743 0.060548 0.155486 0.122672 0.004759 lnL0 = -1945.280302 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1945.280302 x= 0.21381 0.05593 0.03679 0.08874 0.06055 0.15549 0.12267 0.00476 1 h-lim-p 0.0046 0.0367 80.1623 1944.761199 8 0.0002 46 | 0/8 2 h-lim-p 0.0005 0.0072 25.3872 1944.649067 6 0.0004 72 | 0/8 3 h-lim-p 0.0015 0.0189 6.5040 1944.643466 4 0.0003 93 | 0/8 4 h-lim-p 0.0009 0.0125 2.0018 1944.642974 5 0.0003 118 | 0/8 5 h-lim-p 0.0010 0.0335 0.5643 1944.642934 3 0.0003 138 | 0/8 6 h-lim-p 0.0101 20.0000 0.0158 1944.642934 0 0.0006 161 | 0/8 7 h-lim-p 0.0022 17.3746 0.0039 1944.642934 0 0.0020 181 | 0/8 8 h-lim-p 0.0147 20.0000 0.0005 1944.642909 0 0.2353 205 | 0/8 9 h-lim-p 2.4408 20.0000 0.0001 1944.642908 0 1.0678 225 | 0/8 10 h-lim-p 1.7026 20.0000 0.0000 1944.642908 0 1.4898 245 | 0/8 11 h-lim-p 1.9657 20.0000 0.0000 1944.642908 0 0.2150 267 | 0/8 12 h-lim-p 0.0596 20.0000 0.0001 1944.642908 0 0.0149 288 | 0/8 13 h-lim-p 0.0063 20.0000 0.0002 1944.642908 0 0.0016 309 | 0/8 14 h-lim-p 0.0008 20.0000 0.0004 1944.642908 0 0.0000 342 | 0/8 15 h-lim-p 0.0000 20.0000 0.0036 | 0/8 16 h-lim-p 0.0000 20.0000 0.0036 Out... lnL = -1944.642908 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1944.642908 Node 7: lnL = -1944.642908 Node 8: lnL = -1944.642908 Node 9: lnL = -1944.642908 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 856 Sequential format.. Reading seq # 1: YPL116W_Sbay Reading seq # 2: YPL116W_Scer Reading seq # 3: YPL116W_Skud Reading seq # 4: YPL116W_Smik Reading seq # 5: YPL116W_Spar Sequences read.. Counting patterns.. # site patterns = 257 Counting frequencies.. 120 bytes for distance 41120 bytes for lkl0 32896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.245131 0.079140 0.047514 0.104799 0.093897 0.169912 0.155029 0.000060 lnL0 = -3611.688329 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3611.688329 x= 0.24513 0.07914 0.04751 0.10480 0.09390 0.16991 0.15503 0.00006 1 h-lim-p 0.0001 0.0006 131.8548 3609.921370 0 0.0002 23 | 0/8 2 h-lim-p 0.0002 0.0017 37.0396 3609.834223 6 0.0001 51 | 0/8 3 h-lim-p 0.0001 0.0005 9.0608 3609.823056 0 0.0002 65 | 0/8 4 h-lim-p 0.0014 0.1253 1.5832 3609.822758 3 0.0002 86 | 0/8 5 h-lim-p 0.0007 0.4263 0.5943 3609.822724 2 0.0002 103 | 0/8 6 h-lim-p 0.0014 0.0194 0.0903 3609.822721 0 0.0007 123 | 0/8 7 h-lim-p 0.0006 0.0143 0.0979 3609.822643 m 0.0143 145 | 1/8 8 h-lim-p 0.0000 0.0000 32683.5670 3609.822472 2 0.0000 174 | 1/8 9 h-lim-p 0.5672 20.0000 0.0008 3609.822074 3 0.6155 194 | 1/8 10 h-lim-p 2.5000 20.0000 0.0001 3609.822066 0 1.0938 213 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 3609.822060 010.0000 234 | 1/8 12 h-lim-p 2.4060 20.0000 0.0000 3609.822050 0 2.4060 253 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 3609.822050 0 1.0938 272 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 3609.822050 0 2.1875 291 | 1/8 15 h-lim-p 1.8463 20.0000 0.0000 3609.822050 0 0.8078 310 | 1/8 16 h-lim-p 2.5000 20.0000 0.0000 3609.822050 0 0.0003 341 Out... lnL = -3609.822050 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3609.822050 Node 7: lnL = -3609.822050 Node 8: lnL = -3609.822050 Node 9: lnL = -3609.822050 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 854 Sequential format.. Reading seq # 1: YPL117C_Sbay Reading seq # 2: YPL117C_Scer Reading seq # 3: YPL117C_Skud Reading seq # 4: YPL117C_Smik Reading seq # 5: YPL117C_Spar Sequences read.. Counting patterns.. # site patterns = 249 Counting frequencies.. 120 bytes for distance 39840 bytes for lkl0 31872 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.249063 0.049588 0.031347 0.098710 0.108309 0.162082 0.166069 0.001458 lnL0 = -3620.571325 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3620.571325 x= 0.24906 0.04959 0.03135 0.09871 0.10831 0.16208 0.16607 0.00146 1 h-lim-p 0.0013 0.5674 233.3433 3617.953244 9 0.0001 48 | 0/8 2 h-lim-p 0.0002 0.0015 48.6797 3617.757154 2 0.0002 64 | 0/8 3 h-lim-p 0.0003 0.0023 5.9116 3617.752356 3 0.0003 82 | 0/8 4 h-lim-p 0.0009 0.0200 1.8813 3617.752007 2 0.0002 99 | 0/8 5 h-lim-p 0.0009 0.5758 0.4614 3617.751978 2 0.0003 117 | 0/8 6 h-lim-p 0.0015 2.4100 0.0883 3617.751977 0 0.0003 138 | 0/8 7 h-lim-p 0.0025 1.4317 0.0117 3617.751976 0 0.0022 158 | 0/8 8 h-lim-p 0.0147 20.0000 0.0018 3617.751629 0 0.1762 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3617.751617 0 1.0938 201 | 0/8 10 h-lim-p 2.0169 20.0000 0.0001 3617.751617 0 0.8824 221 | 0/8 11 h-lim-p 0.8185 20.0000 0.0001 3617.751617 0 0.3581 241 | 0/8 12 h-lim-p 0.1504 20.0000 0.0001 3617.751617 0 0.0023 266 | 0/8 13 h-lim-p 0.0009 16.9422 0.0004 3617.751617 0 0.0009 286 | 0/8 14 h-lim-p 0.0007 12.1600 0.0005 3617.751617 0 0.0007 306 | 0/8 15 h-lim-p 0.0003 4.8813 0.0013 3617.751617 0 0.0001 326 | 0/8 16 h-lim-p 0.0001 20.0000 0.0012 3617.751617 0 0.0000 361 | 0/8 17 h-lim-p 0.0000 20.0000 0.0032 3617.751617 0 0.0000 388 | 0/8 18 h-lim-p 0.0000 20.0000 0.0007 3617.751617 0 0.0005 413 | 0/8 19 h-lim-p 0.0031 20.0000 0.0001 3617.751617 0 0.0000 440 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 3617.751617 0 0.0000 462 | 0/8 21 h-lim-p 0.0000 17.6840 0.0004 .. | 0/8 22 h-lim-p 0.0000 20.0000 0.0038 | 0/8 23 h-lim-p 0.0000 20.0000 0.0038 Out... lnL = -3617.751617 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3617.751617 Node 7: lnL = -3617.751617 Node 8: lnL = -3617.751617 Node 9: lnL = -3617.751617 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 386 Sequential format.. Reading seq # 1: YPL118W_Sbay Reading seq # 2: YPL118W_Scer Reading seq # 3: YPL118W_Skud Reading seq # 4: YPL118W_Smik Reading seq # 5: YPL118W_Spar Sequences read.. Counting patterns.. # site patterns = 178 Counting frequencies.. 120 bytes for distance 28480 bytes for lkl0 22784 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.291676 0.069943 0.095028 0.170158 0.122114 0.229732 0.136120 0.000060 lnL0 = -1744.720663 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1744.720663 x= 0.29168 0.06994 0.09503 0.17016 0.12211 0.22973 0.13612 0.00006 1 h-lim-p 0.0000 0.0000 101.6311 1744.596791 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0028 65.5342 1743.737835 0 0.0006 39 | 1/8 3 h-lim-p 0.0024 0.0197 16.2724 1743.654579 7 0.0007 70 | 1/8 4 h-lim-p 0.0031 0.0649 3.5252 1743.644890 5 0.0010 94 | 1/8 5 h-lim-p 0.0022 0.1306 1.6218 1743.619074 0 0.0044 107 | 1/8 6 h-lim-p 0.0063 0.3739 1.1288 1742.013572 0 0.0505 122 | 0/8 7 h-lim-p 0.0008 0.0068 40.8017 1740.477396 0 0.0013 134 | 0/8 8 h-lim-p 0.0039 0.0315 1.8351 1740.475875 3 0.0008 153 | 0/8 9 h-lim-p 0.0020 0.0683 0.7430 1740.459240 0 0.0325 169 | 0/8 10 h-lim-p 0.9304 17.9887 0.0260 1740.338812 6 0.4565 202 | 0/8 11 h-lim-p 0.8371 6.6965 0.0042 1740.336114 0 1.2556 222 | 0/8 12 h-lim-p 2.5000 20.0000 0.0009 1740.336077 2 1.0889 246 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1740.336077 0 1.0938 266 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1740.336077 0 2.1875 286 | 0/8 15 h-lim-p 1.4783 20.0000 0.0000 1740.336077 0 0.6468 306 | 0/8 16 h-lim-p 0.9640 20.0000 0.0000 1740.336077 0 0.2410 327 | 0/8 17 h-lim-p 0.1765 20.0000 0.0000 1740.336077 0 0.0001 357 Out... lnL = -1740.336077 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1740.336077 Node 7: lnL = -1740.336077 Node 8: lnL = -1740.336077 Node 9: lnL = -1740.336077 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 386 Sequential format.. Reading seq # 1: YPL119C_Sbay Reading seq # 2: YPL119C_Scer Reading seq # 3: YPL119C_Skud Reading seq # 4: YPL119C_Smik Reading seq # 5: YPL119C_Spar Sequences read.. Counting patterns.. # site patterns = 177 Counting frequencies.. 120 bytes for distance 28320 bytes for lkl0 22656 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.310797 0.118128 0.098389 0.210935 0.129608 0.284648 0.128767 0.000060 lnL0 = -1777.579913 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1777.579913 x= 0.31080 0.11813 0.09839 0.21093 0.12961 0.28465 0.12877 0.00006 1 h-lim-p 0.0000 0.0000 177.1147 1777.503632 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0027 124.8304 1773.185178 0 0.0006 40 | 1/8 3 h-lim-p 0.0012 0.0095 53.1257 1772.465860 9 0.0007 74 | 1/8 4 h-lim-p 0.0045 0.0359 6.0484 1772.424284 7 0.0013 104 | 1/8 5 h-lim-p 0.0048 0.1623 1.6960 1772.082514 0 0.0192 118 | 1/8 6 h-lim-p 0.0051 0.0413 6.3951 1767.388544 0 0.0102 131 | 1/8 7 h-lim-p 0.0007 0.0054 45.0215 1764.153301 0 0.0013 144 | 1/8 8 h-lim-p 0.0018 0.0143 19.1464 1763.978046 8 0.0010 176 | 1/8 9 h-lim-p 0.4899 14.1878 0.0391 1762.191525 0 1.4697 189 | 1/8 10 h-lim-p 1.8746 14.9968 0.0225 1762.011406 3 0.7835 214 | 0/8 11 h-lim-p 0.5562 20.0000 0.0317 1762.011337 1 0.0139 239 | 0/8 12 h-lim-p 0.0152 0.1802 0.0290 1762.008084 0 0.0606 261 | 0/8 13 h-lim-p 0.4590 3.6719 0.0007 1762.007816 0 0.9180 282 | 0/8 14 h-lim-p 0.3423 2.7384 0.0001 1762.007814 0 0.6846 303 | 0/8 15 h-lim-p 0.0706 0.5650 0.0003 1762.007814 0 0.0154 324 | 0/8 16 h-lim-p 0.0030 0.1064 0.0017 1762.007814 0 0.0030 344 | 0/8 17 h-lim-p 0.0656 20.0000 0.0001 1762.007814 0 0.2623 366 | 0/8 18 h-lim-p 0.2933 3.6775 0.0001 1762.007814 0 0.0000 401 | 0/8 19 h-lim-p 0.0000 0.5916 0.0004 1762.007814 0 0.0000 428 | 0/8 20 h-lim-p 0.0000 0.0069 0.0389 1762.007814 0 0.0010 454 | 0/8 21 h-lim-p 0.0001 0.0007 0.2562 1762.007814 0 0.0000 490 | 0/8 22 h-lim-p 0.0000 0.0049 0.0406 .. | 0/8 23 h-lim-p 0.0000 0.0043 0.0379 1762.007814 0 0.0000 554 | 0/8 24 h-lim-p 0.0000 0.0004 0.3838 .. | 0/8 25 h-lim-p 0.0000 0.0043 0.0379 | 0/8 26 h-lim-p 0.0000 0.0043 0.0379 Out... lnL = -1762.007814 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1762.007814 Node 7: lnL = -1762.007814 Node 8: lnL = -1762.007814 Node 9: lnL = -1762.007814 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 461 Sequential format.. Reading seq # 1: YPL120W_Sbay Reading seq # 2: YPL120W_Scer Reading seq # 3: YPL120W_Skud Reading seq # 4: YPL120W_Smik Reading seq # 5: YPL120W_Spar Sequences read.. Counting patterns.. # site patterns = 230 Counting frequencies.. 120 bytes for distance 36800 bytes for lkl0 29440 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.378793 0.140460 0.126131 0.292731 0.146248 0.337887 0.124489 0.000060 lnL0 = -2237.516617 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2237.516617 x= 0.37879 0.14046 0.12613 0.29273 0.14625 0.33789 0.12449 0.00006 1 h-lim-p 0.0000 0.0000 165.2598 2237.459487 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0038 124.6101 2233.370390 0 0.0006 40 | 1/8 3 h-lim-p 0.0010 0.0078 64.1445 2231.994869 2 0.0009 56 | 1/8 4 h-lim-p 0.0054 0.0429 4.1778 2231.942737 2 0.0025 72 | 1/8 5 h-lim-p 0.0040 0.1421 2.6048 2231.563891 0 0.0121 85 | 0/8 6 h-lim-p 0.0043 0.0548 7.3011 2226.790868 0 0.0173 99 | 0/8 7 h-lim-p 0.0004 0.0035 58.2136 2223.230640 0 0.0017 113 | 0/8 8 h-lim-p 0.0017 0.0135 9.9914 2222.899808 0 0.0067 127 | 0/8 9 h-lim-p 0.0142 0.1134 1.6066 2222.895718 4 0.0017 151 | 0/8 10 h-lim-p 0.0363 17.6612 0.0768 2221.956782 0 0.5803 167 | 0/8 11 h-lim-p 2.0073 16.0585 0.0168 2221.790631 7 1.3668 204 | 0/8 12 h-lim-p 2.5000 20.0000 0.0065 2221.785617 6 0.8320 238 | 0/8 13 h-lim-p 2.5000 20.0000 0.0013 2221.785243 3 1.0449 264 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 2221.785236 1 0.9961 286 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2221.785236 0 1.0938 306 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 2221.785236 0 1.0938 326 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 2221.785236 0 0.4688 348 | 0/8 18 h-lim-p 0.1195 20.0000 0.0000 2221.785236 0 0.0019 373 Out... lnL = -2221.785236 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2221.785236 Node 7: lnL = -2221.785236 Node 8: lnL = -2221.785236 Node 9: lnL = -2221.785236 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 460 Sequential format.. Reading seq # 1: YPL121C_Sbay Reading seq # 2: YPL121C_Scer Reading seq # 3: YPL121C_Skud Reading seq # 4: YPL121C_Smik Reading seq # 5: YPL121C_Spar Sequences read.. Counting patterns.. # site patterns = 207 Counting frequencies.. 120 bytes for distance 33120 bytes for lkl0 26496 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.741254 0.000060 0.386332 0.500020 0.641718 0.944291 0.121254 0.020370 lnL0 = -2257.052979 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2257.052979 x= 0.74125 0.00006 0.38633 0.50002 0.64172 0.94429 0.12125 0.02037 1 h-lim-p 0.0000 0.0000 201.8894 2257.000958 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0000 3129.7585 2247.814138 m 0.0000 34 | 2/8 3 h-lim-p 0.0005 0.0079 94.8414 2223.097781 0 0.0037 49 | 2/8 4 h-lim-p 0.0023 0.0187 27.5051 2213.045581 0 0.0094 63 | 2/8 5 h-lim-p 0.0042 0.0337 16.0045 2205.750506 0 0.0169 77 | 1/8 6 h-lim-p 0.0012 0.0093 42.7754 2205.247865 7 0.0012 105 | 1/8 7 h-lim-p 0.0141 0.1126 2.9061 .. | 1/8 8 h-lim-p 0.0000 0.0041 340.1030 2174.648642 0 0.0010 159 | 1/8 9 h-lim-p 0.0001 0.0009 232.8398 2152.265255 m 0.0009 171 | 1/8 10 h-lim-p 0.0002 0.0017 246.9743 2132.779711 0 0.0013 185 | 1/8 11 h-lim-p 0.0003 0.0020 172.3587 2128.600856 0 0.0005 198 | 1/8 12 h-lim-p 0.0036 0.0290 13.5965 2126.598078 m 0.0290 210 | 0/8 13 h-lim-p 0.0000 0.0000 63.8360 h-lim-p: 6.20914318e-20 4.96731454e-19 6.38360375e+01 2126.598078 .. | 0/8 14 h-lim-p 0.0000 0.0055 216.2027 2119.145423 0 0.0003 235 | 0/8 15 h-lim-p 0.0006 0.0048 83.5183 2113.079353 0 0.0018 248 | 0/8 16 h-lim-p 0.0023 0.0187 19.4315 2112.926672 6 0.0009 272 | 0/8 17 h-lim-p 0.0023 0.0187 3.6199 2112.918255 6 0.0013 298 | 0/8 18 h-lim-p 0.0012 0.0626 3.9213 2112.892697 0 0.0049 312 | 0/8 19 h-lim-p 0.0017 0.0215 11.2623 2112.865506 0 0.0025 324 | 0/8 20 h-lim-p 0.1002 3.7495 0.2852 2112.846225 0 0.2005 337 | 0/8 21 h-lim-p 0.4623 20.0000 0.1237 2112.782382 6 0.3030 373 | 0/8 22 h-lim-p 2.5000 20.0000 0.0102 2112.768448 5 1.0785 402 | 0/8 23 h-lim-p 2.5000 20.0000 0.0011 2112.768392 1 1.0938 424 | 0/8 24 h-lim-p 2.5000 20.0000 0.0000 2112.768392 0 1.0938 444 | 0/8 25 h-lim-p 1.8835 20.0000 0.0000 2112.768392 0 1.6481 464 | 0/8 26 h-lim-p 1.5138 20.0000 0.0000 2112.768392 0 2.2707 484 | 0/8 27 h-lim-p 0.2547 20.0000 0.0001 2112.768392 0 0.0080 508 | 0/8 28 h-lim-p 0.0010 20.0000 0.0011 2112.768392 0 0.0001 530 | 0/8 29 h-lim-p 0.0002 20.0000 0.0006 2112.768392 0 0.0000 560 | 0/8 30 h-lim-p 0.0002 20.0000 0.0000 2112.768392 0 0.0000 591 Out... lnL = -2112.768392 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2112.768392 Node 7: lnL = -2112.768392 Node 8: lnL = -2112.768392 Node 9: lnL = -2112.768392 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 298 Sequential format.. Reading seq # 1: YPL124W_Sbay Reading seq # 2: YPL124W_Scer Reading seq # 3: YPL124W_Skud Reading seq # 4: YPL124W_Smik Reading seq # 5: YPL124W_Spar Sequences read.. Counting patterns.. # site patterns = 124 Counting frequencies.. 120 bytes for distance 19840 bytes for lkl0 15872 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.294119 0.000060 0.098344 0.166552 0.067674 0.194522 0.138758 0.031469 lnL0 = -1254.045446 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1254.045446 x= 0.29412 0.00006 0.09834 0.16655 0.06767 0.19452 0.13876 0.03147 1 h-lim-p 0.0005 0.0044 75.6077 1252.796104 6 0.0004 35 | 0/8 2 h-lim-p 0.0004 0.0033 41.0163 1252.354963 0 0.0006 47 | 0/8 3 h-lim-p 0.0019 0.0209 13.5544 1252.319289 2 0.0004 64 | 0/8 4 h-lim-p 0.0016 0.0606 3.8614 1252.314325 2 0.0007 80 | 0/8 5 h-lim-p 0.0078 0.5501 0.3611 1252.314266 2 0.0009 98 | 0/8 6 h-lim-p 0.0049 3.2833 0.0631 1252.314245 2 0.0032 124 | 0/8 7 h-lim-p 0.0112 2.1055 0.0182 1252.313013 0 0.0893 147 | 0/8 8 h-lim-p 0.0029 0.1076 0.5694 1252.309805 0 0.0043 167 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 1252.309649 2 0.9961 191 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1252.309649 0 1.0938 211 | 0/8 11 h-lim-p 1.4587 20.0000 0.0000 1252.309649 0 0.6382 231 | 0/8 12 h-lim-p 0.4119 20.0000 0.0000 1252.309649 0 0.0012 259 | 0/8 13 h-lim-p 0.0006 20.0000 0.0000 1252.309649 0 0.0006 279 | 0/8 14 h-lim-p 0.0003 20.0000 0.0001 1252.309649 0 0.0000 317 | 0/8 15 h-lim-p 0.0000 20.0000 0.0010 | 0/8 16 h-lim-p 0.0000 20.0000 0.0010 Out... lnL = -1252.309649 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1252.309649 Node 7: lnL = -1252.309649 Node 8: lnL = -1252.309649 Node 9: lnL = -1252.309649 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 668 Sequential format.. Reading seq # 1: YPL126W_Sbay Reading seq # 2: YPL126W_Scer Reading seq # 3: YPL126W_Skud Reading seq # 4: YPL126W_Smik Reading seq # 5: YPL126W_Spar Sequences read.. Counting patterns.. # site patterns = 242 Counting frequencies.. 120 bytes for distance 38720 bytes for lkl0 30976 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.270382 0.109984 0.049131 0.129421 0.094324 0.190338 0.103539 0.000060 lnL0 = -2797.825671 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2797.825671 x= 0.27038 0.10998 0.04913 0.12942 0.09432 0.19034 0.10354 0.00006 1 h-lim-p 0.0004 0.0034 149.3380 2795.152690 8 0.0003 41 | 0/8 2 h-lim-p 0.0004 0.0031 39.8662 2794.918107 7 0.0003 69 | 0/8 3 h-lim-p 0.0003 0.0026 11.4587 2794.900608 2 0.0003 85 | 0/8 4 h-lim-p 0.0004 0.0030 3.9939 2794.897902 1 0.0004 99 | 0/8 5 h-lim-p 0.0031 0.6066 0.4994 2794.897850 3 0.0004 119 | 0/8 6 h-lim-p 0.0014 1.3832 0.1517 2794.897844 0 0.0006 139 | 0/8 7 h-lim-p 0.0025 9.1651 0.0367 2794.897842 0 0.0025 159 | 0/8 8 h-lim-p 0.0007 2.8570 0.1401 2794.897800 0 0.0208 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 2794.897784 1 0.9961 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2794.897784 0 1.0938 226 | 0/8 11 h-lim-p 2.1284 20.0000 0.0000 2794.897784 0 0.9312 246 | 0/8 12 h-lim-p 0.6107 20.0000 0.0000 2794.897784 0 0.1336 267 | 0/8 13 h-lim-p 0.0169 20.0000 0.0000 2794.897784 0 0.0074 287 | 0/8 14 h-lim-p 0.0028 20.0000 0.0001 2794.897784 0 0.0000 320 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 2794.897784 0 0.0000 352 Out... lnL = -2794.897784 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2794.897784 Node 7: lnL = -2794.897784 Node 8: lnL = -2794.897784 Node 9: lnL = -2794.897784 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 704 Sequential format.. Reading seq # 1: YPL127C_Sbay Reading seq # 2: YPL127C_Scer Reading seq # 3: YPL127C_Skud Reading seq # 4: YPL127C_Smik Reading seq # 5: YPL127C_Spar Sequences read.. Counting patterns.. # site patterns = 259 Counting frequencies.. 120 bytes for distance 41440 bytes for lkl0 33152 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.296488 0.094115 0.050352 0.197072 0.112119 0.340927 0.090242 0.000060 lnL0 = -2790.104934 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2790.104934 x= 0.29649 0.09412 0.05035 0.19707 0.11212 0.34093 0.09024 0.00006 1 h-lim-p 0.0000 0.0000 170.2908 2790.036460 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0038 69.0038 2789.094670 0 0.0005 39 | 1/8 3 h-lim-p 0.0007 0.0101 46.1998 2788.893338 5 0.0003 61 | 1/8 4 h-lim-p 0.0011 0.0159 11.5864 2788.850372 7 0.0006 91 | 1/8 5 h-lim-p 0.0009 0.0422 8.4224 2788.817317 1 0.0011 105 | 1/8 6 h-lim-p 0.0045 0.2180 2.0820 2788.780613 3 0.0038 123 | 1/8 7 h-lim-p 0.0174 0.3962 0.4512 2784.049332 0 0.1394 138 | 0/8 8 h-lim-p 0.0025 0.0196 9.6577 2784.022625 2 0.0006 162 | 0/8 9 h-lim-p 0.0044 0.0749 1.2477 2784.021528 2 0.0010 179 | 0/8 10 h-lim-p 0.0558 20.0000 0.0218 2783.688985 0 0.6691 194 | 0/8 11 h-lim-p 2.5000 20.0000 0.0034 2783.668452 2 1.1719 218 | 0/8 12 h-lim-p 2.5000 20.0000 0.0005 2783.668286 3 0.8855 246 | 0/8 13 h-lim-p 2.5000 20.0000 0.0001 2783.668283 1 0.6152 269 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 2783.668282 0 1.0938 289 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2783.668282 0 1.0938 309 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 2783.668282 0 0.3125 331 | 0/8 17 h-lim-p 0.4839 20.0000 0.0000 2783.668282 0 0.0151 355 Out... lnL = -2783.668282 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2783.668282 Node 7: lnL = -2783.668282 Node 8: lnL = -2783.668282 Node 9: lnL = -2783.668282 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 673 Sequential format.. Reading seq # 1: YPL128C_Sbay Reading seq # 2: YPL128C_Scer Reading seq # 3: YPL128C_Skud Reading seq # 4: YPL128C_Smik Reading seq # 5: YPL128C_Spar Sequences read.. Counting patterns.. # site patterns = 238 Counting frequencies.. 120 bytes for distance 38080 bytes for lkl0 30464 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.270576 0.090179 0.085044 0.161169 0.092631 0.240696 0.123618 0.000060 lnL0 = -2904.818411 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2904.818411 x= 0.27058 0.09018 0.08504 0.16117 0.09263 0.24070 0.12362 0.00006 1 h-lim-p 0.0000 0.0000 237.4830 2904.699673 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0030 90.8918 2903.039976 0 0.0005 39 | 1/8 3 h-lim-p 0.0016 0.0165 27.8747 2902.940056 7 0.0003 68 | 1/8 4 h-lim-p 0.0009 0.0239 9.1116 2902.915279 6 0.0005 98 | 1/8 5 h-lim-p 0.0027 0.1295 1.7473 2902.856316 0 0.0055 111 | 1/8 6 h-lim-p 0.0035 0.0833 2.7323 2900.945611 0 0.0140 125 | 0/8 7 h-lim-p 0.0007 0.0053 52.4277 2895.601444 0 0.0013 138 | 0/8 8 h-lim-p 0.0009 0.0070 42.9245 2895.049390 7 0.0005 166 | 0/8 9 h-lim-p 0.0004 0.0030 18.3619 2894.786285 0 0.0015 180 | 0/8 10 h-lim-p 0.3902 3.1216 0.0199 2894.337113 0 0.7804 193 | 0/8 11 h-lim-p 1.7161 20.0000 0.0090 2894.277006 7 0.9634 231 | 0/8 12 h-lim-p 2.5000 20.0000 0.0023 2894.273803 4 0.6789 260 | 0/8 13 h-lim-p 2.5000 20.0000 0.0003 2894.273694 3 0.9482 286 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 2894.273689 0 1.0938 306 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2894.273689 0 1.0938 326 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 2894.273689 0 0.5469 347 | 0/8 17 h-lim-p 1.2651 20.0000 0.0000 2894.273689 0 0.0198 372 | 0/8 18 h-lim-p 0.0178 20.0000 0.0000 2894.273689 0 0.0001 398 Out... lnL = -2894.273689 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2894.273689 Node 7: lnL = -2894.273689 Node 8: lnL = -2894.273689 Node 9: lnL = -2894.273689 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 418 Sequential format.. Reading seq # 1: YPL130W_Sbay Reading seq # 2: YPL130W_Scer Reading seq # 3: YPL130W_Skud Reading seq # 4: YPL130W_Smik Reading seq # 5: YPL130W_Spar Sequences read.. Counting patterns.. # site patterns = 172 Counting frequencies.. 120 bytes for distance 27520 bytes for lkl0 22016 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.326068 0.047676 0.035312 0.115817 0.108647 0.156622 0.213500 0.032037 lnL0 = -1806.533898 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1806.533898 x= 0.32607 0.04768 0.03531 0.11582 0.10865 0.15662 0.21350 0.03204 1 h-lim-p 0.0014 0.0112 88.0831 1805.625793 8 0.0003 42 | 0/8 2 h-lim-p 0.0007 0.0058 17.9210 1805.559481 6 0.0004 69 | 0/8 3 h-lim-p 0.0019 0.0581 4.0569 1805.554374 5 0.0007 94 | 0/8 4 h-lim-p 0.0011 0.0676 2.3574 1805.552841 5 0.0007 118 | 0/8 5 h-lim-p 0.0091 1.3973 0.1862 1805.552832 0 0.0006 133 | 0/8 6 h-lim-p 0.0029 6.9077 0.0368 1805.552831 1 0.0007 156 | 0/8 7 h-lim-p 0.0060 20.0000 0.0044 1805.552831 0 0.0013 177 | 0/8 8 h-lim-p 0.0502 20.0000 0.0001 1805.552824 0 0.8039 201 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1805.552824 0 1.0938 221 | 0/8 10 h-lim-p 1.4536 20.0000 0.0000 1805.552824 0 1.2719 241 | 0/8 11 h-lim-p 1.2076 20.0000 0.0000 1805.552824 0 1.0566 261 | 0/8 12 h-lim-p 0.1486 20.0000 0.0001 1805.552824 0 0.0003 289 | 0/8 13 h-lim-p 0.0001 20.0000 0.0004 1805.552824 0 0.0000 322 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1805.552824 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1805.552824 Node 7: lnL = -1805.552824 Node 8: lnL = -1805.552824 Node 9: lnL = -1805.552824 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 526 Sequential format.. Reading seq # 1: YPL131W_Sbay Reading seq # 2: YPL131W_Scer Reading seq # 3: YPL131W_Skud Reading seq # 4: YPL131W_Smik Reading seq # 5: YPL131W_Spar Sequences read.. Counting patterns.. # site patterns = 202 Counting frequencies.. 120 bytes for distance 32320 bytes for lkl0 25856 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.293089 0.101661 0.097216 0.104887 0.096559 0.160562 0.207324 0.000060 lnL0 = -2332.961460 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2332.961460 x= 0.29309 0.10166 0.09722 0.10489 0.09656 0.16056 0.20732 0.00006 1 h-lim-p 0.0000 0.0000 126.4277 2332.906749 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0031 55.3692 2332.359671 0 0.0005 39 | 1/8 3 h-lim-p 0.0011 0.0337 23.4621 2332.274341 5 0.0004 64 | 1/8 4 h-lim-p 0.0012 0.0543 7.0443 2332.245064 5 0.0010 89 | 1/8 5 h-lim-p 0.0034 0.1029 2.1460 2332.215937 3 0.0031 107 | 1/8 6 h-lim-p 0.0015 0.1163 4.5542 2332.118076 0 0.0029 120 | 1/8 7 h-lim-p 0.0048 0.0523 2.7542 2328.762774 0 0.0193 134 | 1/8 8 h-lim-p 0.0003 0.0024 50.9260 2327.458274 0 0.0006 147 | 1/8 9 h-lim-p 1.8056 14.4448 0.0168 2327.165498 8 1.1275 180 | 1/8 10 h-lim-p 2.5000 20.0000 0.0026 2327.159161 5 0.8875 210 | 1/8 11 h-lim-p 2.5000 20.0000 0.0006 2327.158883 2 0.9644 233 | 1/8 12 h-lim-p 2.5000 20.0000 0.0002 2327.158861 2 0.9644 256 | 0/8 13 h-lim-p 0.0000 0.0000 0.0041 h-lim-p: 1.84230903e-20 1.47384722e-19 4.05271512e-03 2327.158861 .. | 1/8 14 h-lim-p 0.0000 6.9948 0.0307 2327.158861 0 0.0005 296 | 1/8 15 h-lim-p 0.0011 20.0000 0.0137 2327.158861 0 0.0005 315 | 1/8 16 h-lim-p 0.0010 20.0000 0.0065 2327.158861 0 0.0009 334 | 1/8 17 h-lim-p 0.0022 20.0000 0.0025 2327.158861 0 0.0002 355 | 1/8 18 h-lim-p 0.0009 20.0000 0.0007 2327.158861 0 0.0009 374 | 1/8 19 h-lim-p 0.0145 20.0000 0.0000 2327.158861 0 0.0063 393 | 1/8 20 h-lim-p 0.0012 20.0000 0.0002 2327.158861 0 0.0048 414 | 1/8 21 h-lim-p 0.0044 20.0000 0.0002 2327.158861 0 0.0131 434 | 1/8 22 h-lim-p 2.5000 20.0000 0.0000 2327.158861 0 0.0195 459 | 1/8 23 h-lim-p 0.0199 20.0000 0.0000 2327.158861 0 0.0000 497 Out... lnL = -2327.158861 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2327.158861 Node 7: lnL = -2327.158861 Node 8: lnL = -2327.158861 Node 9: lnL = -2327.158861 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 520 Sequential format.. Reading seq # 1: YPL132W_Sbay Reading seq # 2: YPL132W_Scer Reading seq # 3: YPL132W_Skud Reading seq # 4: YPL132W_Smik Reading seq # 5: YPL132W_Spar Sequences read.. Counting patterns.. # site patterns = 182 Counting frequencies.. 120 bytes for distance 29120 bytes for lkl0 23296 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.316021 0.029393 0.052862 0.099489 0.088108 0.202991 0.170577 0.028290 lnL0 = -2245.785049 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2245.785049 x= 0.31602 0.02939 0.05286 0.09949 0.08811 0.20299 0.17058 0.02829 1 h-lim-p 0.0011 0.0085 61.6967 2245.390533 3 0.0002 29 | 0/8 2 h-lim-p 0.0009 0.0082 15.7930 2245.346954 6 0.0004 52 | 0/8 3 h-lim-p 0.0008 0.0114 7.0391 2245.337651 5 0.0004 75 | 0/8 4 h-lim-p 0.0013 0.0559 2.3641 2245.336900 2 0.0003 92 | 0/8 5 h-lim-p 0.0018 0.6358 0.3996 2245.336861 3 0.0005 111 | 0/8 6 h-lim-p 0.0010 0.4774 0.1920 2245.336855 1 0.0004 133 | 0/8 7 h-lim-p 0.0156 10.2942 0.0050 2245.336850 0 0.0156 153 | 0/8 8 h-lim-p 0.0090 5.5701 0.0088 2245.336544 0 0.0359 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2245.336533 1 0.9961 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2245.336533 0 2.1875 217 | 0/8 11 h-lim-p 1.9181 20.0000 0.0000 2245.336533 0 0.8392 237 | 0/8 12 h-lim-p 0.0735 20.0000 0.0002 2245.336533 0 0.0080 259 | 0/8 13 h-lim-p 0.0026 20.0000 0.0008 2245.336533 0 0.0026 279 | 0/8 14 h-lim-p 0.0009 17.8979 0.0023 2245.336533 0 0.0002 300 | 0/8 15 h-lim-p 0.0001 4.9735 0.0084 2245.336533 0 0.0001 320 | 0/8 16 h-lim-p 0.0005 20.0000 0.0011 2245.336533 0 0.0001 341 | 0/8 17 h-lim-p 0.0003 20.0000 0.0004 2245.336533 0 0.0000 363 | 0/8 18 h-lim-p 0.0002 20.0000 0.0001 2245.336533 0 0.0001 383 | 0/8 19 h-lim-p 0.0001 20.0000 0.0001 2245.336533 0 0.0000 413 | 0/8 20 h-lim-p 0.0000 20.0000 0.0010 | 0/8 21 h-lim-p 0.0000 20.0000 0.0010 Out... lnL = -2245.336533 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2245.336533 Node 7: lnL = -2245.336533 Node 8: lnL = -2245.336533 Node 9: lnL = -2245.336533 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 522 Sequential format.. Reading seq # 1: YPL133C_Sbay Reading seq # 2: YPL133C_Scer Reading seq # 3: YPL133C_Skud Reading seq # 4: YPL133C_Smik Reading seq # 5: YPL133C_Spar Sequences read.. Counting patterns.. # site patterns = 177 Counting frequencies.. 120 bytes for distance 28320 bytes for lkl0 22656 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.300915 0.035628 0.055878 0.105616 0.081981 0.201627 0.173009 0.016521 lnL0 = -2241.578382 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2241.578382 x= 0.30092 0.03563 0.05588 0.10562 0.08198 0.20163 0.17301 0.01652 1 h-lim-p 0.0018 0.0143 57.2278 2241.246062 2 0.0002 28 | 0/8 2 h-lim-p 0.0012 0.0117 10.2398 2241.225577 6 0.0004 57 | 0/8 3 h-lim-p 0.0007 0.0179 5.5649 2241.220625 5 0.0004 80 | 0/8 4 h-lim-p 0.0017 0.0737 1.3185 2241.220412 4 0.0003 103 | 0/8 5 h-lim-p 0.0022 1.8127 0.1643 2241.220403 2 0.0007 121 | 0/8 6 h-lim-p 0.0030 3.5012 0.0389 2241.220402 0 0.0003 143 | 0/8 7 h-lim-p 0.1133 20.0000 0.0001 2241.220402 0 0.2266 164 | 0/8 8 h-lim-p 0.0017 19.4780 0.0152 2241.220400 0 0.0034 185 | 0/8 9 h-lim-p 2.2361 20.0000 0.0000 2241.220400 0 0.9783 205 | 0/8 10 h-lim-p 1.0741 20.0000 0.0000 2241.220400 0 0.0000 253 | 0/8 11 h-lim-p 0.0000 20.0000 0.0009 | 0/8 12 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -2241.220400 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2241.220400 Node 7: lnL = -2241.220400 Node 8: lnL = -2241.220400 Node 9: lnL = -2241.220400 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 423 Sequential format.. Reading seq # 1: YPL134C_Sbay Reading seq # 2: YPL134C_Scer Reading seq # 3: YPL134C_Skud Reading seq # 4: YPL134C_Smik Reading seq # 5: YPL134C_Spar Sequences read.. Counting patterns.. # site patterns = 150 Counting frequencies.. 120 bytes for distance 24000 bytes for lkl0 19200 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.232493 0.048392 0.034035 0.074463 0.055399 0.155350 0.148186 0.009137 lnL0 = -1644.641305 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1644.641305 x= 0.23249 0.04839 0.03404 0.07446 0.05540 0.15535 0.14819 0.00914 1 h-lim-p 0.0007 0.0059 81.8205 1644.031253 7 0.0002 36 | 0/8 2 h-lim-p 0.0006 0.0049 19.8556 1643.969886 5 0.0003 59 | 0/8 3 h-lim-p 0.0011 0.0305 5.8848 1643.964362 6 0.0003 87 | 0/8 4 h-lim-p 0.0007 0.0414 2.9658 1643.963119 4 0.0004 109 | 0/8 5 h-lim-p 0.0017 0.1607 0.6159 1643.963065 3 0.0003 129 | 0/8 6 h-lim-p 0.0017 0.6160 0.1051 1643.963061 1 0.0007 151 | 0/8 7 h-lim-p 0.0075 16.3422 0.0098 1643.963061 0 0.0033 171 | 0/8 8 h-lim-p 0.0409 20.0000 0.0008 1643.962924 0 0.3268 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1643.962923 0 1.0938 214 | 0/8 10 h-lim-p 2.4266 20.0000 0.0000 1643.962923 0 2.1233 234 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1643.962923 0 1.0938 254 | 0/8 12 h-lim-p 0.1550 20.0000 0.0000 1643.962923 0 4.9598 279 | 0/8 13 h-lim-p 0.5314 20.0000 0.0002 1643.962923 0 0.1329 300 | 0/8 14 h-lim-p 0.0072 4.2163 0.0044 1643.962923 0 0.0018 321 | 0/8 15 h-lim-p 0.0005 1.1722 0.0157 1643.962923 0 0.0000 348 | 0/8 16 h-lim-p 0.0001 20.0000 0.0002 1643.962923 0 0.0000 377 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 1643.962923 0 0.0000 409 Out... lnL = -1643.962923 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1643.962923 Node 7: lnL = -1643.962923 Node 8: lnL = -1643.962923 Node 9: lnL = -1643.962923 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 941 Sequential format.. Reading seq # 1: YPL135W_Sbay Reading seq # 2: YPL135W_Scer Reading seq # 3: YPL135W_Skud Reading seq # 4: YPL135W_Smik Reading seq # 5: YPL135W_Spar Sequences read.. Counting patterns.. # site patterns = 282 Counting frequencies.. 120 bytes for distance 45120 bytes for lkl0 36096 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.269051 0.034254 0.051445 0.077612 0.071391 0.110873 0.166512 0.030176 lnL0 = -3665.951467 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3665.951467 x= 0.26905 0.03425 0.05145 0.07761 0.07139 0.11087 0.16651 0.03018 1 h-lim-p 0.0007 0.4203 313.7680 3660.863931 9 0.0001 46 | 0/8 2 h-lim-p 0.0004 0.0035 75.8522 3660.120418 8 0.0003 78 | 0/8 3 h-lim-p 0.0006 0.0077 33.9062 3660.045994 6 0.0002 104 | 0/8 4 h-lim-p 0.0005 0.0203 10.3850 3660.034713 2 0.0002 120 | 0/8 5 h-lim-p 0.0011 0.0656 2.1818 3660.033923 4 0.0003 143 | 0/8 6 h-lim-p 0.0011 0.2479 0.6666 3660.033885 2 0.0002 161 | 0/8 7 h-lim-p 0.0038 3.9849 0.0321 3660.033884 0 0.0004 183 | 0/8 8 h-lim-p 0.0131 20.0000 0.0010 3660.032954 0 0.6301 208 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3660.032948 0 1.0938 228 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3660.032948 0 1.0938 248 | 0/8 11 h-lim-p 1.4060 20.0000 0.0000 3660.032948 0 2.1090 268 | 0/8 12 h-lim-p 0.5324 20.0000 0.0001 3660.032948 0 0.0333 291 | 0/8 13 h-lim-p 0.0014 20.0000 0.0023 3660.032948 0 0.0002 313 | 0/8 14 h-lim-p 0.0006 20.0000 0.0007 3660.032948 0 0.0000 352 | 0/8 15 h-lim-p 0.0000 20.0000 0.0014 | 0/8 16 h-lim-p 0.0000 20.0000 0.0014 Out... lnL = -3660.032948 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3660.032948 Node 7: lnL = -3660.032948 Node 8: lnL = -3660.032948 Node 9: lnL = -3660.032948 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 810 Sequential format.. Reading seq # 1: YPL144W_Sbay Reading seq # 2: YPL144W_Scer Reading seq # 3: YPL144W_Skud Reading seq # 4: YPL144W_Smik Reading seq # 5: YPL144W_Spar Sequences read.. Counting patterns.. # site patterns = 190 Counting frequencies.. 120 bytes for distance 30400 bytes for lkl0 24320 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.178947 0.049935 0.036193 0.059534 0.051813 0.118507 0.129953 0.000060 lnL0 = -3002.617487 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3002.617487 x= 0.17895 0.04993 0.03619 0.05953 0.05181 0.11851 0.12995 0.00006 1 h-lim-p 0.0000 0.0000 148.3691 3002.245501 m 0.0000 22 | 1/8 2 h-lim-p 0.0001 0.0013 48.8425 3002.129390 0 0.0001 35 | 1/8 3 h-lim-p 0.0002 0.0060 27.2452 3002.091012 7 0.0001 65 | 1/8 4 h-lim-p 0.0006 0.0334 5.8395 3002.088585 2 0.0001 82 | 1/8 5 h-lim-p 0.0012 0.2134 0.7040 3002.087326 3 0.0010 100 | 1/8 6 h-lim-p 0.0004 0.0652 1.5922 3002.083628 0 0.0006 119 | 1/8 7 h-lim-p 0.0004 0.1331 2.2809 3001.957313 0 0.0036 134 | 1/8 8 h-lim-p 0.0013 0.0144 6.5096 3001.188828 0 0.0025 147 | 1/8 9 h-lim-p 2.5000 20.0000 0.0022 3001.165443 6 0.8687 174 | 0/8 10 h-lim-p 0.0025 0.6415 0.7482 3001.165346 3 0.0003 201 | 0/8 11 h-lim-p 1.1534 9.2269 0.0002 3001.165206 0 1.0092 221 | 0/8 12 h-lim-p 0.6256 5.0051 0.0001 3001.165205 0 0.6256 241 | 0/8 13 h-lim-p 0.0231 0.1848 0.0014 .. | 0/8 14 h-lim-p 0.0000 0.0035 0.0989 3001.165205 0 0.0001 308 | 0/8 15 h-lim-p 0.0000 0.0006 0.4444 3001.165205 0 0.0000 335 | 0/8 16 h-lim-p 0.0000 0.0001 2.8727 3001.165204 0 0.0000 356 | 0/8 17 h-lim-p 0.0001 0.1470 0.1094 3001.165204 0 0.0002 369 | 0/8 18 h-lim-p 0.0006 6.8438 0.0317 3001.165204 0 0.0003 389 | 0/8 19 h-lim-p 0.0049 2.8524 0.0017 3001.165204 0 0.0000 425 | 0/8 20 h-lim-p 0.0000 1.3707 0.0007 .. | 0/8 21 h-lim-p 0.0000 0.0015 0.1334 3001.165204 0 0.0000 480 | 0/8 22 h-lim-p 0.0000 0.0006 0.3624 3001.165204 0 0.0000 512 | 0/8 23 h-lim-p 0.0000 0.0000 291.8590 .. | 0/8 24 h-lim-p 0.0000 0.0664 0.0754 3001.165204 0 0.0000 551 | 0/8 25 h-lim-p 0.0000 0.0017 0.1800 3001.165204 0 0.0000 582 | 0/8 26 h-lim-p 0.0000 0.2099 0.0103 3001.165204 0 0.0000 603 | 0/8 27 h-lim-p 0.0000 0.4843 0.0069 3001.165204 0 0.0000 624 | 0/8 28 h-lim-p 0.0001 2.1046 0.0005 3001.165204 0 0.0000 658 | 0/8 29 h-lim-p 0.0000 0.3123 0.0045 .. | 0/8 30 h-lim-p 0.0000 0.0015 0.1237 3001.165204 0 0.0000 712 | 0/8 31 h-lim-p 0.0000 0.0003 0.6357 .. | 0/8 32 h-lim-p 0.0000 0.0015 0.1233 | 0/8 33 h-lim-p 0.0000 0.0015 0.1233 Out... lnL = -3001.165204 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3001.165204 Node 7: lnL = -3001.165204 Node 8: lnL = -3001.165204 Node 9: lnL = -3001.165204 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 809 Sequential format.. Reading seq # 1: YPL145C_Sbay Reading seq # 2: YPL145C_Scer Reading seq # 3: YPL145C_Skud Reading seq # 4: YPL145C_Smik Reading seq # 5: YPL145C_Spar Sequences read.. Counting patterns.. # site patterns = 188 Counting frequencies.. 120 bytes for distance 30080 bytes for lkl0 24064 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.182241 0.027779 0.027869 0.061753 0.049150 0.124536 0.144977 0.001207 lnL0 = -3013.735145 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3013.735145 x= 0.18224 0.02778 0.02787 0.06175 0.04915 0.12454 0.14498 0.00121 1 h-lim-p 0.0001 0.0009 284.5806 3011.534954 6 0.0001 34 | 0/8 2 h-lim-p 0.0002 0.0017 46.0663 3011.417416 5 0.0001 57 | 0/8 3 h-lim-p 0.0003 0.0084 20.1586 3011.396614 2 0.0001 73 | 0/8 4 h-lim-p 0.0004 0.0148 6.8000 3011.394303 4 0.0001 95 | 0/8 5 h-lim-p 0.0009 0.0188 0.8612 3011.394232 2 0.0002 112 | 0/8 6 h-lim-p 0.0006 0.1092 0.2780 3011.394227 1 0.0001 135 | 0/8 7 h-lim-p 0.0005 2.3628 0.0866 3011.394226 0 0.0002 155 | 0/8 8 h-lim-p 0.1163 20.0000 0.0002 3011.394038 0 1.3958 178 | 0/8 9 h-lim-p 1.7833 20.0000 0.0001 3011.394036 1 0.8777 201 | 0/8 10 h-lim-p 1.2752 20.0000 0.0001 3011.394036 0 0.6376 221 | 0/8 11 h-lim-p 0.4636 20.0000 0.0001 3011.394036 0 0.0016 248 | 0/8 12 h-lim-p 0.0006 20.0000 0.0003 3011.394036 0 0.0006 268 | 0/8 13 h-lim-p 0.0003 13.0701 0.0006 3011.394036 0 0.0000 306 | 0/8 14 h-lim-p 0.0000 20.0000 0.0088 3011.394036 0 0.0000 334 | 0/8 15 h-lim-p 0.0000 17.5340 0.0016 3011.394036 0 0.0005 359 | 0/8 16 h-lim-p 0.0008 20.0000 0.0010 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0102 3011.394036 0 0.0000 425 | 0/8 18 h-lim-p 0.0000 20.0000 0.0009 3011.394036 0 0.0002 449 | 0/8 19 h-lim-p 0.0003 20.0000 0.0005 3011.394036 0 0.0003 469 | 0/8 20 h-lim-p 0.0010 20.0000 0.0001 3011.394036 0 0.0009 489 | 0/8 21 h-lim-p 0.0002 15.9952 0.0005 3011.394036 0 0.0000 512 | 0/8 22 h-lim-p 0.0000 3.8281 0.0021 3011.394036 0 0.0000 532 | 0/8 23 h-lim-p 0.0000 0.1263 0.0605 3011.394036 0 0.0000 561 | 0/8 24 h-lim-p 0.0000 0.0117 0.6590 3011.394036 0 0.0000 588 | 0/8 25 h-lim-p 0.0003 20.0000 0.0001 .. | 0/8 26 h-lim-p 0.0000 20.0000 0.0102 | 0/8 27 h-lim-p 0.0000 20.0000 0.0102 Out... lnL = -3011.394036 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3011.394036 Node 7: lnL = -3011.394036 Node 8: lnL = -3011.394036 Node 9: lnL = -3011.394036 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 477 Sequential format.. Reading seq # 1: YPL148C_Sbay Reading seq # 2: YPL148C_Scer Reading seq # 3: YPL148C_Skud Reading seq # 4: YPL148C_Smik Reading seq # 5: YPL148C_Spar Sequences read.. Counting patterns.. # site patterns = 202 Counting frequencies.. 120 bytes for distance 32320 bytes for lkl0 25856 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.322026 0.100317 0.075912 0.150279 0.127230 0.170698 0.209585 0.000060 lnL0 = -2192.325839 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2192.325839 x= 0.32203 0.10032 0.07591 0.15028 0.12723 0.17070 0.20959 0.00006 1 h-lim-p 0.0000 0.0000 81.8649 2192.284444 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0059 29.0099 2192.070843 0 0.0006 39 | 1/8 3 h-lim-p 0.0013 0.0232 12.3882 2192.032345 3 0.0006 57 | 1/8 4 h-lim-p 0.0020 0.0517 3.6499 2192.026286 6 0.0007 84 | 1/8 5 h-lim-p 0.0019 0.1982 1.3848 2192.012666 0 0.0038 97 | 1/8 6 h-lim-p 0.0031 0.1908 1.6949 2191.780551 0 0.0124 111 | 0/8 7 h-lim-p 0.0022 0.0412 9.5282 2190.551869 0 0.0088 125 | 0/8 8 h-lim-p 0.0005 0.0041 34.9667 2189.917607 0 0.0010 138 | 0/8 9 h-lim-p 0.0068 0.0543 1.7283 2189.885818 0 0.0272 152 | 0/8 10 h-lim-p 0.3070 2.4563 0.0215 2189.801122 0 0.9211 165 | 0/8 11 h-lim-p 2.5000 20.0000 0.0010 2189.800065 3 0.9961 191 | 0/8 12 h-lim-p 2.5000 20.0000 0.0003 2189.800042 1 0.9961 213 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2189.800041 0 1.0938 233 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 2189.800041 0 1.0938 253 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2189.800041 0 1.0938 273 | 0/8 16 h-lim-p 0.5000 20.0000 0.0000 2189.800041 0 0.2500 293 | 0/8 17 h-lim-p 0.0039 20.0000 0.0001 2189.800041 0 0.0000 329 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 2189.800041 0 0.0000 359 | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -2189.800041 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2189.800041 Node 7: lnL = -2189.800041 Node 8: lnL = -2189.800041 Node 9: lnL = -2189.800041 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 433 Sequential format.. Reading seq # 1: YPL149W_Sbay Reading seq # 2: YPL149W_Scer Reading seq # 3: YPL149W_Skud Reading seq # 4: YPL149W_Smik Reading seq # 5: YPL149W_Spar Sequences read.. Counting patterns.. # site patterns = 208 Counting frequencies.. 120 bytes for distance 33280 bytes for lkl0 26624 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.356782 0.298461 0.045793 0.136446 0.155691 0.205893 0.173115 0.000060 lnL0 = -2121.454985 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2121.454985 x= 0.35678 0.29846 0.04579 0.13645 0.15569 0.20589 0.17312 0.00006 1 h-lim-p 0.0000 0.0000 75.0492 2121.437111 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0116 35.4342 2120.666372 0 0.0013 41 | 1/8 3 h-lim-p 0.0013 0.0101 19.2851 2120.568961 7 0.0007 69 | 1/8 4 h-lim-p 0.0023 0.0407 5.9510 2120.554336 4 0.0009 89 | 1/8 5 h-lim-p 0.0027 0.0980 1.9158 2120.549471 6 0.0017 119 | 1/8 6 h-lim-p 0.0036 0.4998 0.8988 2120.524333 0 0.0143 133 | 1/8 7 h-lim-p 0.0087 0.2207 1.4698 2120.324532 0 0.0131 152 | 1/8 8 h-lim-p 0.0032 0.1760 6.0942 2119.333477 0 0.0063 165 | 1/8 9 h-lim-p 2.5000 20.0000 0.0061 2119.307164 4 1.2130 186 | 1/8 10 h-lim-p 2.5000 20.0000 0.0017 2119.306180 3 1.0004 211 | 0/8 11 h-lim-p 0.0489 15.8826 0.0340 2119.306178 0 0.0053 232 | 0/8 12 h-lim-p 0.1583 1.2666 0.0002 2119.306175 m 1.2666 252 | 1/8 13 h-lim-p 1.9938 20.0000 0.0001 2119.306175 0 0.2181 274 | 0/8 14 h-lim-p -0.0000 -0.0000 0.0010 h-lim-p: -3.91543994e-18 -3.13235195e-17 9.95858136e-04 2119.306175 .. | 1/8 15 h-lim-p 0.0000 11.0519 0.0293 2119.306174 0 0.0006 315 | 1/8 16 h-lim-p 0.0019 20.0000 0.0098 2119.306174 0 0.0017 334 | 1/8 17 h-lim-p 0.0029 20.0000 0.0057 2119.306174 0 0.0006 354 | 1/8 18 h-lim-p 0.0018 20.0000 0.0020 2119.306174 0 0.0016 373 | 1/8 19 h-lim-p 0.0046 20.0000 0.0007 2119.306174 0 0.0011 393 | 1/8 20 h-lim-p 0.0163 20.0000 0.0000 2119.306174 0 0.0142 412 | 1/8 21 h-lim-p 0.0120 20.0000 0.0001 2119.306174 0 0.0240 432 | 1/8 22 h-lim-p 0.0020 20.0000 0.0007 2119.306174 0 0.0059 452 | 1/8 23 h-lim-p 2.5000 20.0000 0.0000 2119.306174 0 1.0938 471 | 1/8 24 h-lim-p 2.5000 20.0000 0.0000 2119.306174 0 2.5000 490 | 1/8 25 h-lim-p 1.6666 20.0000 0.0000 2119.306174 0 0.2083 511 | 1/8 26 h-lim-p 0.2631 20.0000 0.0000 2119.306174 0 0.0000 549 Out... lnL = -2119.306174 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2119.306174 Node 7: lnL = -2119.306174 Node 8: lnL = -2119.306174 Node 9: lnL = -2119.306174 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 684 Sequential format.. Reading seq # 1: YPL151C_Sbay Reading seq # 2: YPL151C_Scer Reading seq # 3: YPL151C_Skud Reading seq # 4: YPL151C_Smik Reading seq # 5: YPL151C_Spar Sequences read.. Counting patterns.. # site patterns = 208 Counting frequencies.. 120 bytes for distance 33280 bytes for lkl0 26624 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.454499 0.090176 0.385595 0.154409 0.217042 0.423352 0.112429 0.000060 lnL0 = -2825.553815 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2825.553815 x= 0.45450 0.09018 0.38560 0.15441 0.21704 0.42335 0.11243 0.00006 1 h-lim-p 0.0000 0.0000 353.7274 2825.429576 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0004 457.9211 2789.708626 m 0.0004 37 | 2/8 3 h-lim-p 0.0006 0.0046 104.1514 2779.839644 0 0.0017 50 | 2/8 4 h-lim-p 0.0011 0.0086 38.4817 2774.900564 0 0.0021 63 | 2/8 5 h-lim-p 0.0007 0.0060 82.3355 2766.136002 0 0.0022 76 | 2/8 6 h-lim-p 0.0098 0.0783 2.8466 2766.116904 5 0.0017 100 | 1/8 7 h-lim-p 0.0002 0.0275 29.2969 2765.792254 0 0.0007 114 | 1/8 8 h-lim-p 0.0209 0.1673 0.4612 2764.075165 0 0.1255 128 | 0/8 9 h-lim-p 0.0000 0.0000 5.9889 h-lim-p: 8.28602182e-20 6.62881745e-19 5.98887790e+00 2764.075165 .. | 0/8 10 h-lim-p 0.0000 0.0097 25.2752 2763.965029 0 0.0003 160 | 0/8 11 h-lim-p 0.0000 0.0003 9.8650 2763.944991 m 0.0003 172 | 1/8 12 h-lim-p 0.0001 0.0378 19.2508 2763.910358 0 0.0008 186 | 1/8 13 h-lim-p 0.0008 0.0323 17.9426 2763.866366 0 0.0012 198 | 1/8 14 h-lim-p 0.0007 0.0223 30.7157 2763.768072 0 0.0014 211 | 1/8 15 h-lim-p 0.0004 0.0035 36.4759 2763.661263 0 0.0013 224 | 1/8 16 h-lim-p 0.0063 0.0505 1.0102 2763.660924 1 0.0006 240 | 1/8 17 h-lim-p 0.0291 20.0000 0.0218 2763.641596 0 0.9310 257 | 1/8 18 h-lim-p 2.5000 20.0000 0.0022 2763.640093 5 1.4877 289 | 1/8 19 h-lim-p 2.5000 20.0000 0.0002 2763.640051 2 0.9961 312 | 1/8 20 h-lim-p 2.5000 20.0000 0.0000 2763.640051 0 1.0938 331 | 1/8 21 h-lim-p 1.4474 20.0000 0.0000 2763.640051 0 1.2665 350 | 1/8 22 h-lim-p 0.4000 20.0000 0.0001 2763.640051 0 0.0008 377 | 1/8 23 h-lim-p 0.0001 17.0333 0.0007 2763.640051 0 0.0000 414 | 1/8 24 h-lim-p 0.0000 20.0000 0.0003 | 1/8 25 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -2763.640051 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2763.640051 Node 7: lnL = -2763.640051 Node 8: lnL = -2763.640051 Node 9: lnL = -2763.640051 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 876 Sequential format.. Reading seq # 1: YPL152W_Sbay Reading seq # 2: YPL152W_Scer Reading seq # 3: YPL152W_Skud Reading seq # 4: YPL152W_Smik Reading seq # 5: YPL152W_Spar Sequences read.. Counting patterns.. # site patterns = 346 Counting frequencies.. 120 bytes for distance 55360 bytes for lkl0 44288 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.396808 0.090647 0.160575 0.148578 0.167585 0.211746 0.243648 0.000060 lnL0 = -4184.476151 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4184.476151 x= 0.39681 0.09065 0.16057 0.14858 0.16759 0.21175 0.24365 0.00006 1 h-lim-p 0.0000 0.0000 113.9877 4184.411098 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0061 46.5537 4183.885525 0 0.0006 39 | 1/8 3 h-lim-p 0.0022 0.0211 12.2224 4183.830489 6 0.0008 67 | 1/8 4 h-lim-p 0.0034 0.2025 2.7547 4183.823672 4 0.0011 89 | 1/8 5 h-lim-p 0.0012 0.1510 2.5911 4183.812931 0 0.0017 101 | 1/8 6 h-lim-p 0.0065 0.3637 0.6984 4183.349031 0 0.0387 115 | 1/8 7 h-lim-p 0.0025 0.0223 10.6408 4181.517862 0 0.0038 134 | 1/8 8 h-lim-p 0.0028 0.0227 13.2492 4181.475884 7 0.0005 164 | 1/8 9 h-lim-p 1.0733 20.0000 0.0058 4181.450651 5 0.8742 187 | 0/8 10 h-lim-p 0.0157 5.9604 0.3249 4181.450596 2 0.0010 213 | 0/8 11 h-lim-p 0.5888 20.0000 0.0006 4181.450392 0 1.1776 234 | 0/8 12 h-lim-p 2.5000 20.0000 0.0001 4181.450367 1 0.9961 256 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 4181.450367 0 1.0938 276 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 4181.450367 0 1.2500 296 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 4181.450367 0 0.0000 345 Out... lnL = -4181.450367 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4181.450367 Node 7: lnL = -4181.450367 Node 8: lnL = -4181.450367 Node 9: lnL = -4181.450367 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 840 Sequential format.. Reading seq # 1: YPL154C_Sbay Reading seq # 2: YPL154C_Scer Reading seq # 3: YPL154C_Skud Reading seq # 4: YPL154C_Smik Reading seq # 5: YPL154C_Spar Sequences read.. Counting patterns.. # site patterns = 307 Counting frequencies.. 120 bytes for distance 49120 bytes for lkl0 39296 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.300736 0.057073 0.090021 0.165522 0.000060 0.198058 0.145084 0.024570 lnL0 = -3554.402084 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3554.402084 x= 0.30074 0.05707 0.09002 0.16552 0.00006 0.19806 0.14508 0.02457 1 h-lim-p 0.0000 0.0745 1341.0092 3532.694183 5 0.0000 32 | 0/8 2 h-lim-p 0.0002 0.0017 124.6096 3530.299367 0 0.0004 45 | 0/8 3 h-lim-p 0.0006 0.0049 37.5855 3529.998127 7 0.0005 71 | 0/8 4 h-lim-p 0.0021 0.0522 8.3820 3529.990177 2 0.0002 89 | 0/8 5 h-lim-p 0.0012 0.1335 1.6724 3529.989224 2 0.0006 105 | 0/8 6 h-lim-p 0.0151 0.8350 0.0629 3529.954461 0 0.0906 119 | 0/8 7 h-lim-p 0.0017 0.0464 3.3534 3529.708395 0 0.0034 140 | 0/8 8 h-lim-p 0.0020 0.0380 5.8030 3529.699831 4 0.0005 161 | 0/8 9 h-lim-p 2.5000 20.0000 0.0012 3529.698275 3 1.0449 179 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 3529.698262 2 1.5991 204 | 0/8 11 h-lim-p 2.0610 20.0000 0.0000 3529.698253 0 4.1220 225 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3529.698252 0 1.0938 245 | 0/8 13 h-lim-p 0.9666 20.0000 0.0000 3529.698252 0 1.4499 265 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 3529.698252 0 0.5469 286 | 0/8 15 h-lim-p 0.1932 20.0000 0.0001 3529.698252 0 0.0060 310 | 0/8 16 h-lim-p 0.0023 20.0000 0.0001 3529.698252 0 0.0003 332 | 0/8 17 h-lim-p 0.0001 20.0000 0.0003 3529.698252 0 0.0001 352 | 0/8 18 h-lim-p 0.0003 20.0000 0.0001 3529.698252 0 0.0000 390 | 0/8 19 h-lim-p 0.0000 20.0000 0.0023 | 0/8 20 h-lim-p 0.0000 20.0000 0.0023 Out... lnL = -3529.698252 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3529.698252 Node 7: lnL = -3529.698252 Node 8: lnL = -3529.698252 Node 9: lnL = -3529.698252 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 508 Sequential format.. Reading seq # 1: YPL156C_Sbay Reading seq # 2: YPL156C_Scer Reading seq # 3: YPL156C_Skud Reading seq # 4: YPL156C_Smik Reading seq # 5: YPL156C_Spar Sequences read.. Counting patterns.. # site patterns = 174 Counting frequencies.. 120 bytes for distance 27840 bytes for lkl0 22272 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.246719 0.054248 0.125828 0.126503 0.097395 0.134311 0.115506 0.000060 lnL0 = -2063.878349 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2063.878349 x= 0.24672 0.05425 0.12583 0.12650 0.09740 0.13431 0.11551 0.00006 1 h-lim-p 0.0000 0.0000 135.5324 2063.767130 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0082 29.0420 2063.592464 0 0.0005 38 | 1/8 3 h-lim-p 0.0016 0.0199 8.4292 2063.574529 6 0.0005 67 | 1/8 4 h-lim-p 0.0013 0.0788 3.0858 2063.566748 6 0.0008 96 | 1/8 5 h-lim-p 0.0020 0.1338 1.2223 2063.404595 0 0.0163 111 | 1/8 6 h-lim-p 0.0026 0.0211 6.4713 2062.388367 0 0.0053 124 | 1/8 7 h-lim-p 0.0009 0.0074 25.3694 2059.940582 0 0.0019 137 | 1/8 8 h-lim-p 0.0033 0.0266 13.9276 2059.897441 5 0.0005 161 | 1/8 9 h-lim-p 0.3818 18.7253 0.0166 2059.768440 0 0.7636 174 | 0/8 10 h-lim-p -0.0000 -0.0000 0.2082 h-lim-p: -2.15736156e-21 -1.72588925e-20 2.08220388e-01 2059.768440 .. | 0/8 11 h-lim-p 0.0000 0.0146 6.2680 2059.764065 0 0.0003 214 | 0/8 12 h-lim-p 0.0021 0.0958 0.9700 2059.763869 3 0.0004 233 | 0/8 13 h-lim-p 0.0003 0.0021 0.1975 2059.763863 0 0.0004 253 | 0/8 14 h-lim-p 0.0001 0.0009 0.1961 2059.763853 m 0.0009 273 | 1/8 15 h-lim-p 0.0010 2.3343 0.1268 2059.763851 0 0.0004 293 | 1/8 16 h-lim-p 0.0005 2.3271 0.1099 2059.763842 0 0.0010 313 | 1/8 17 h-lim-p 0.0320 20.0000 0.0034 2059.763814 0 0.0481 332 | 1/8 18 h-lim-p 0.0026 1.7118 0.0613 2059.763407 0 0.0079 352 | 1/8 19 h-lim-p 0.0031 1.1929 0.1548 2059.763401 2 0.0005 378 | 1/8 20 h-lim-p 1.8696 20.0000 0.0000 2059.763398 1 1.4899 399 | 1/8 21 h-lim-p 2.5000 20.0000 0.0000 2059.763398 0 2.1875 418 | 1/8 22 h-lim-p 2.2373 20.0000 0.0000 2059.763397 0 0.9788 437 | 1/8 23 h-lim-p 2.5000 20.0000 0.0000 2059.763397 0 0.2734 458 | 1/8 24 h-lim-p 0.3637 20.0000 0.0000 2059.763397 0 0.0455 479 | 1/8 25 h-lim-p 0.0476 20.0000 0.0000 2059.763397 0 0.0000 512 Out... lnL = -2059.763397 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2059.763397 Node 7: lnL = -2059.763397 Node 8: lnL = -2059.763397 Node 9: lnL = -2059.763397 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 557 Sequential format.. Reading seq # 1: YPL157W_Sbay Reading seq # 2: YPL157W_Scer Reading seq # 3: YPL157W_Skud Reading seq # 4: YPL157W_Smik Reading seq # 5: YPL157W_Spar Sequences read.. Counting patterns.. # site patterns = 194 Counting frequencies.. 120 bytes for distance 31040 bytes for lkl0 24832 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.283927 0.152990 0.172284 0.110069 0.127677 0.147838 0.105710 0.000060 lnL0 = -2377.679206 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2377.679206 x= 0.28393 0.15299 0.17228 0.11007 0.12768 0.14784 0.10571 0.00006 1 h-lim-p 0.0000 0.0000 245.2841 2377.591727 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0014 170.1007 2371.082752 0 0.0006 40 | 1/8 3 h-lim-p 0.0028 0.0221 36.9760 2370.838771 8 0.0004 74 | 1/8 4 h-lim-p 0.0016 0.0324 8.9488 2370.796181 4 0.0008 95 | 1/8 5 h-lim-p 0.0016 0.0682 4.4282 2370.741268 1 0.0020 109 | 1/8 6 h-lim-p 0.0071 0.1262 1.2740 2367.306195 0 0.0569 124 | 1/8 7 h-lim-p 0.0005 0.0043 40.9542 2358.784526 0 0.0022 138 | 1/8 8 h-lim-p 0.0030 0.0241 8.1272 2358.768587 6 0.0005 169 | 1/8 9 h-lim-p 0.0993 10.8407 0.0376 2357.904761 0 0.5956 183 | 0/8 10 h-lim-p 0.0083 0.4953 2.6845 2357.901864 5 0.0007 215 | 0/8 11 h-lim-p 0.0898 2.3132 0.0222 2357.725531 0 0.5387 229 | 0/8 12 h-lim-p 2.0520 20.0000 0.0058 2357.685291 6 1.0310 264 | 0/8 13 h-lim-p 2.5000 20.0000 0.0013 2357.684053 5 0.7847 298 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 2357.684049 0 1.2500 318 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2357.684049 0 1.0938 338 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 2357.684049 0 1.0938 358 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 2357.684049 0 0.0781 382 | 0/8 18 h-lim-p 0.0124 20.0000 0.0000 2357.684049 0 0.0124 402 | 0/8 19 h-lim-p 0.0049 20.0000 0.0000 2357.684049 0 0.0024 422 Out... lnL = -2357.684049 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2357.684049 Node 7: lnL = -2357.684049 Node 8: lnL = -2357.684049 Node 9: lnL = -2357.684049 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 538 Sequential format.. Reading seq # 1: YPL158C_Sbay Reading seq # 2: YPL158C_Scer Reading seq # 3: YPL158C_Skud Reading seq # 4: YPL158C_Smik Reading seq # 5: YPL158C_Spar Sequences read.. Counting patterns.. # site patterns = 190 Counting frequencies.. 120 bytes for distance 30400 bytes for lkl0 24320 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.285972 0.155298 0.151250 0.116128 0.118635 0.157571 0.098933 0.000060 lnL0 = -2346.040126 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2346.040126 x= 0.28597 0.15530 0.15125 0.11613 0.11863 0.15757 0.09893 0.00006 1 h-lim-p 0.0000 0.0000 230.8414 2345.944393 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0014 147.9146 2341.163442 0 0.0006 40 | 1/8 3 h-lim-p 0.0027 0.0214 27.6738 2341.002114 7 0.0004 70 | 1/8 4 h-lim-p 0.0011 0.0281 10.7018 2340.952112 7 0.0008 102 | 1/8 5 h-lim-p 0.0022 0.0786 3.7435 2340.900188 2 0.0021 118 | 1/8 6 h-lim-p 0.0051 0.1123 1.5248 2338.512014 0 0.0409 133 | 1/8 7 h-lim-p 0.0006 0.0051 30.7627 2330.606359 0 0.0026 147 | 1/8 8 h-lim-p 0.0010 0.0077 26.3114 2330.448152 2 0.0004 163 | 1/8 9 h-lim-p 0.3103 5.8822 0.0381 2329.778277 0 0.6205 176 | 0/8 10 h-lim-p 0.0094 3.5020 2.5264 2329.775709 5 0.0008 209 | 0/8 11 h-lim-p 0.1228 20.0000 0.0155 2329.634992 0 0.7368 223 | 0/8 12 h-lim-p 2.5000 20.0000 0.0036 2329.613654 4 0.9932 251 | 0/8 13 h-lim-p 2.5000 20.0000 0.0008 2329.613218 4 0.8059 281 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 2329.613201 1 0.9961 303 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2329.613201 0 1.0938 323 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 2329.613201 0 0.5469 344 | 0/8 17 h-lim-p 0.8789 20.0000 0.0000 2329.613201 0 0.0137 369 Out... lnL = -2329.613201 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2329.613201 Node 7: lnL = -2329.613201 Node 8: lnL = -2329.613201 Node 9: lnL = -2329.613201 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 375 Sequential format.. Reading seq # 1: YPL159C_Sbay Reading seq # 2: YPL159C_Scer Reading seq # 3: YPL159C_Skud Reading seq # 4: YPL159C_Smik Reading seq # 5: YPL159C_Spar Sequences read.. Counting patterns.. # site patterns = 147 Counting frequencies.. 120 bytes for distance 23520 bytes for lkl0 18816 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.220664 0.047040 0.080498 0.103040 0.117662 0.138580 0.093732 0.000060 lnL0 = -1507.766779 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1507.766779 x= 0.22066 0.04704 0.08050 0.10304 0.11766 0.13858 0.09373 0.00006 1 h-lim-p 0.0000 0.0000 78.0046 1507.730431 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0126 20.6175 1507.652569 0 0.0004 38 | 1/8 3 h-lim-p 0.0011 0.0327 6.6193 1507.641141 4 0.0005 59 | 1/8 4 h-lim-p 0.0017 0.1216 2.1551 1507.637366 4 0.0011 81 | 1/8 5 h-lim-p 0.0026 0.2479 0.8916 1507.626404 0 0.0051 94 | 1/8 6 h-lim-p 0.0058 0.1227 0.7913 1507.133330 0 0.0231 115 | 1/8 7 h-lim-p 0.0005 0.0042 20.9342 1506.478220 0 0.0010 135 | 1/8 8 h-lim-p 0.0073 0.0587 2.5222 1506.476680 4 0.0005 158 | 1/8 9 h-lim-p 0.3433 20.0000 0.0035 1506.463495 0 1.0299 171 | 0/8 10 h-lim-p 0.0273 15.8340 0.1336 1506.463486 2 0.0009 198 | 0/8 11 h-lim-p 0.2009 1.6074 0.0004 1506.463287 0 0.8037 220 | 0/8 12 h-lim-p 0.0818 0.6548 0.0001 1506.463281 m 0.6548 240 | 1/8 13 h-lim-p 0.7459 20.0000 0.0001 1506.463280 1 0.3671 263 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 1506.463280 0 1.0938 282 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 1506.463280 0 1.0938 301 | 1/8 16 h-lim-p 2.3967 20.0000 0.0000 1506.463280 0 1.0485 320 | 1/8 17 h-lim-p 2.5000 20.0000 0.0000 1506.463280 0 0.0146 346 Out... lnL = -1506.463280 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1506.463280 Node 7: lnL = -1506.463280 Node 8: lnL = -1506.463280 Node 9: lnL = -1506.463280 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 887 Sequential format.. Reading seq # 1: YPL160W_Sbay Reading seq # 2: YPL160W_Scer Reading seq # 3: YPL160W_Skud Reading seq # 4: YPL160W_Smik Reading seq # 5: YPL160W_Spar Sequences read.. Counting patterns.. # site patterns = 365 Counting frequencies.. 120 bytes for distance 58400 bytes for lkl0 46720 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.411934 0.060716 0.199474 0.147971 0.109290 0.239012 0.249096 0.000060 lnL0 = -4236.562479 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4236.562479 x= 0.41193 0.06072 0.19947 0.14797 0.10929 0.23901 0.24910 0.00006 1 h-lim-p 0.0000 0.0000 131.3484 4236.065394 m 0.0000 22 | 1/8 2 h-lim-p 0.0001 0.0067 44.6502 4235.602897 0 0.0005 36 | 1/8 3 h-lim-p 0.0020 0.0164 11.3263 4235.564324 7 0.0006 69 | 1/8 4 h-lim-p 0.0019 0.2397 3.6328 4235.559740 5 0.0006 94 | 1/8 5 h-lim-p 0.0011 0.1095 1.9000 4235.552287 0 0.0022 107 | 0/8 6 h-lim-p 0.0012 0.1862 3.4287 4235.405291 0 0.0195 123 | 0/8 7 h-lim-p 0.0020 0.0168 34.1956 4235.240598 6 0.0014 149 | 0/8 8 h-lim-p 0.0103 0.1272 4.5499 4235.192407 6 0.0019 177 | 0/8 9 h-lim-p 0.0029 0.0395 3.0083 4233.908618 0 0.0313 192 | 0/8 10 h-lim-p 0.0942 0.7534 0.0329 4233.859174 m 0.7534 204 | 0/8 11 h-lim-p 0.0000 0.0000 0.0054 h-lim-p: 1.53306535e-17 1.22645228e-16 5.35844082e-03 4233.859174 .. | 0/8 12 h-lim-p 0.0000 0.3177 2.3156 4233.858006 0 0.0005 245 | 0/8 13 h-lim-p 0.0006 0.0881 1.8630 4233.857710 1 0.0002 259 | 0/8 14 h-lim-p 0.0014 0.6956 0.3122 4233.857688 2 0.0005 276 | 0/8 15 h-lim-p 0.0001 0.0005 0.1119 4233.857687 m 0.0005 296 | 1/8 16 h-lim-p 0.0016 20.0000 0.0327 4233.857687 0 0.0014 316 | 1/8 17 h-lim-p 0.0029 15.3864 0.0152 4233.857687 0 0.0006 336 | 1/8 18 h-lim-p 0.0066 20.0000 0.0015 4233.857687 0 0.0099 355 | 1/8 19 h-lim-p 0.0035 20.0000 0.0041 4233.857686 0 0.0035 374 | 1/8 20 h-lim-p 0.0109 20.0000 0.0013 4233.857677 0 0.0869 396 | 1/8 21 h-lim-p 2.5000 20.0000 0.0000 4233.857676 0 1.0938 415 | 1/8 22 h-lim-p 2.5000 20.0000 0.0000 4233.857676 0 1.0938 434 | 1/8 23 h-lim-p 2.5000 20.0000 0.0000 4233.857676 0 0.0391 458 | 1/8 24 h-lim-p 0.0406 20.0000 0.0000 4233.857676 0 0.0102 478 Out... lnL = -4233.857676 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4233.857676 Node 7: lnL = -4233.857676 Node 8: lnL = -4233.857676 Node 9: lnL = -4233.857676 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 307 Sequential format.. Reading seq # 1: YPL162C_Sbay Reading seq # 2: YPL162C_Scer Reading seq # 3: YPL162C_Skud Reading seq # 4: YPL162C_Smik Reading seq # 5: YPL162C_Spar Sequences read.. Counting patterns.. # site patterns = 182 Counting frequencies.. 120 bytes for distance 29120 bytes for lkl0 23296 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.450030 0.275791 0.328559 0.197737 0.242300 0.189044 0.153613 0.000060 lnL0 = -1557.882770 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1557.882770 x= 0.45003 0.27579 0.32856 0.19774 0.24230 0.18904 0.15361 0.00006 1 h-lim-p 0.0000 0.0000 123.0932 1557.852519 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0032 139.3930 1544.708017 0 0.0019 41 | 1/8 3 h-lim-p 0.0007 0.0056 66.2054 1543.052018 0 0.0014 54 | 1/8 4 h-lim-p 0.0053 0.0422 9.7099 1542.953849 8 0.0018 88 | 1/8 5 h-lim-p 0.0083 0.1484 2.1307 1542.751816 0 0.0165 101 | 1/8 6 h-lim-p 0.0209 0.2330 1.6815 1537.974335 0 0.0837 115 | 1/8 7 h-lim-p 0.0012 0.0099 35.1483 1535.262535 0 0.0025 128 | 1/8 8 h-lim-p 0.0055 0.0439 5.7058 1535.220888 5 0.0023 149 | 1/8 9 h-lim-p 0.1830 20.0000 0.0732 1533.955453 0 0.7322 163 | 1/8 10 h-lim-p 0.9934 7.9473 0.0365 1533.791174 7 0.6947 198 | 0/8 11 h-lim-p 0.0055 0.0987 4.6377 1533.766459 7 0.0034 235 | 0/8 12 h-lim-p 0.9570 7.6558 0.0145 1533.716186 2 0.8972 251 | 0/8 13 h-lim-p 2.5000 20.0000 0.0015 1533.715543 3 1.0449 277 | 0/8 14 h-lim-p 2.5000 20.0000 0.0002 1533.715540 1 0.6152 300 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1533.715539 0 1.0938 320 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1533.715539 0 1.0938 340 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1533.715539 0 0.3125 362 | 0/8 18 h-lim-p 0.3612 20.0000 0.0000 1533.715539 0 0.0000 396 Out... lnL = -1533.715539 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1533.715539 Node 7: lnL = -1533.715539 Node 8: lnL = -1533.715539 Node 9: lnL = -1533.715539 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 527 Sequential format.. Reading seq # 1: YPL163C_Sbay Reading seq # 2: YPL163C_Scer Reading seq # 3: YPL163C_Skud Reading seq # 4: YPL163C_Smik Reading seq # 5: YPL163C_Spar Sequences read.. Counting patterns.. # site patterns = 163 Counting frequencies.. 120 bytes for distance 26080 bytes for lkl0 20864 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.231992 0.084501 0.113619 0.093240 0.064108 0.130402 0.096232 0.000060 lnL0 = -2119.493901 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2119.493901 x= 0.23199 0.08450 0.11362 0.09324 0.06411 0.13040 0.09623 0.00006 1 h-lim-p 0.0000 0.0000 167.7685 2119.376855 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0023 64.0681 2118.695900 0 0.0003 39 | 1/8 3 h-lim-p 0.0018 0.0140 12.0226 2118.662838 4 0.0004 60 | 1/8 4 h-lim-p 0.0015 0.0698 3.6252 2118.653992 5 0.0009 84 | 1/8 5 h-lim-p 0.0018 0.0734 1.7546 2118.640957 2 0.0016 100 | 1/8 6 h-lim-p 0.0031 0.2523 0.8902 2117.342936 0 0.0370 115 | 1/8 7 h-lim-p 0.0003 0.0021 40.2745 2115.688426 0 0.0005 135 | 1/8 8 h-lim-p 0.0021 0.0241 10.1566 2115.668891 6 0.0004 163 | 1/8 9 h-lim-p 0.2460 14.9632 0.0153 2115.377663 0 0.9838 177 | 0/8 10 h-lim-p 0.0213 3.6625 0.7042 2115.377498 2 0.0007 204 | 0/8 11 h-lim-p 0.2705 20.0000 0.0017 2115.374036 0 0.8114 225 | 0/8 12 h-lim-p 2.5000 20.0000 0.0002 2115.373993 2 0.9644 249 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2115.373992 0 1.0938 269 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 2115.373992 0 1.0938 289 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2115.373992 0 2.1875 309 | 0/8 16 h-lim-p 1.8383 20.0000 0.0000 2115.373992 0 0.8043 329 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 2115.373992 0 0.0342 354 | 0/8 18 h-lim-p 0.0328 20.0000 0.0000 2115.373992 0 0.0005 379 Out... lnL = -2115.373992 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2115.373992 Node 7: lnL = -2115.373992 Node 8: lnL = -2115.373992 Node 9: lnL = -2115.373992 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 497 Sequential format.. Reading seq # 1: YPL164C_Sbay Reading seq # 2: YPL164C_Scer Reading seq # 3: YPL164C_Skud Reading seq # 4: YPL164C_Smik Reading seq # 5: YPL164C_Spar Sequences read.. Counting patterns.. # site patterns = 245 Counting frequencies.. 120 bytes for distance 39200 bytes for lkl0 31360 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.407795 0.085518 0.115967 0.216170 0.163367 0.224950 0.192058 0.000060 lnL0 = -2321.890134 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2321.890134 x= 0.40779 0.08552 0.11597 0.21617 0.16337 0.22495 0.19206 0.00006 1 h-lim-p 0.0000 0.0000 97.5153 2321.845215 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0046 24.9417 2321.613218 0 0.0009 39 | 1/8 3 h-lim-p 0.0019 0.0548 11.3880 2321.562050 2 0.0009 55 | 1/8 4 h-lim-p 0.0025 0.0646 4.0698 2321.538959 4 0.0019 75 | 1/8 5 h-lim-p 0.0042 0.1885 1.8843 2321.488883 0 0.0063 87 | 1/8 6 h-lim-p 0.0090 0.2145 1.3032 2319.678760 0 0.0362 101 | 0/8 7 h-lim-p 0.0012 0.0093 28.0421 2317.989435 0 0.0023 114 | 0/8 8 h-lim-p 0.0003 0.0026 6.6772 2317.966784 0 0.0013 128 | 0/8 9 h-lim-p 0.0004 0.0030 1.2750 2317.964896 0 0.0022 142 | 0/8 10 h-lim-p 0.1387 1.1863 0.0207 2317.790840 0 0.8325 156 | 0/8 11 h-lim-p 2.5000 20.0000 0.0027 2317.785496 2 1.1719 180 | 0/8 12 h-lim-p 1.4355 11.4841 0.0002 2317.785465 2 1.1075 204 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2317.785465 0 1.0938 224 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 2317.785465 0 1.0938 244 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 2317.785465 0 0.5469 265 | 0/8 16 h-lim-p 1.1136 20.0000 0.0000 2317.785465 0 0.2784 286 | 0/8 17 h-lim-p 0.2843 20.0000 0.0000 2317.785465 0 0.0000 322 Out... lnL = -2317.785465 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2317.785465 Node 7: lnL = -2317.785465 Node 8: lnL = -2317.785465 Node 9: lnL = -2317.785465 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 309 Sequential format.. Reading seq # 1: YPL165C_Sbay Reading seq # 2: YPL165C_Scer Reading seq # 3: YPL165C_Skud Reading seq # 4: YPL165C_Smik Reading seq # 5: YPL165C_Spar Sequences read.. Counting patterns.. # site patterns = 116 Counting frequencies.. 120 bytes for distance 18560 bytes for lkl0 14848 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.265594 0.017902 0.057775 0.075300 0.038362 0.158050 0.183528 0.016311 lnL0 = -1188.100633 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1188.100633 x= 0.26559 0.01790 0.05777 0.07530 0.03836 0.15805 0.18353 0.01631 1 h-lim-p 0.0033 1.7725 84.3937 1187.137326 6 0.0003 37 | 0/8 2 h-lim-p 0.0006 0.0050 16.2002 1187.082209 7 0.0004 66 | 0/8 3 h-lim-p 0.0006 0.0068 11.6390 1187.054685 2 0.0006 82 | 0/8 4 h-lim-p 0.0034 0.0596 1.8999 1187.053738 4 0.0005 105 | 0/8 5 h-lim-p 0.0032 0.6468 0.3247 1187.053684 2 0.0011 123 | 0/8 6 h-lim-p 0.0022 0.4732 0.1596 1187.053677 2 0.0006 148 | 0/8 7 h-lim-p 0.0436 20.0000 0.0021 1187.053672 1 0.0545 170 | 0/8 8 h-lim-p 0.0070 2.9519 0.0162 1187.053566 0 0.0279 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1187.053555 1 0.9961 214 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1187.053555 0 1.0938 234 | 0/8 11 h-lim-p 1.2506 20.0000 0.0000 1187.053555 0 5.0023 256 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1187.053555 0 0.0003 288 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 1187.053555 0 0.0000 310 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 1187.053555 0 0.0001 331 Out... lnL = -1187.053555 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1187.053555 Node 7: lnL = -1187.053555 Node 8: lnL = -1187.053555 Node 9: lnL = -1187.053555 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 259 Sequential format.. Reading seq # 1: YPL166W_Sbay Reading seq # 2: YPL166W_Scer Reading seq # 3: YPL166W_Skud Reading seq # 4: YPL166W_Smik Reading seq # 5: YPL166W_Spar Sequences read.. Counting patterns.. # site patterns = 141 Counting frequencies.. 120 bytes for distance 22560 bytes for lkl0 18048 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.454369 0.134455 0.166205 0.260063 0.213826 0.230978 0.199802 0.000060 lnL0 = -1224.577122 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1224.577122 x= 0.45437 0.13445 0.16621 0.26006 0.21383 0.23098 0.19980 0.00006 1 h-lim-p 0.0000 0.0000 114.2693 1224.546367 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0037 90.7513 1220.378286 0 0.0013 41 | 1/8 3 h-lim-p 0.0023 0.0187 27.6729 1219.457386 1 0.0029 55 | 1/8 4 h-lim-p 0.0065 0.0522 7.6417 1219.298706 8 0.0036 86 | 1/8 5 h-lim-p 0.0053 0.0714 5.1465 1219.089185 3 0.0054 104 | 1/8 6 h-lim-p 0.0131 0.1050 1.6901 1212.687233 0 0.0525 118 | 1/8 7 h-lim-p 0.0011 0.0090 34.0249 1211.334730 0 0.0023 131 | 1/8 8 h-lim-p 0.0151 0.1211 1.4656 1211.311046 2 0.0071 147 | 0/8 9 h-lim-p 0.0012 2.7317 8.5137 1211.203730 0 0.0024 160 | 0/8 10 h-lim-p 0.0256 0.2049 0.2762 1209.284653 m 0.2049 172 | 1/8 11 h-lim-p 1.1089 8.8710 0.0406 1208.734553 6 1.0953 204 | 1/8 12 h-lim-p 1.7919 14.3352 0.0240 1208.641190 4 0.8924 231 | 0/8 13 h-lim-p 0.0515 1.3242 0.4165 1208.640851 2 0.0056 256 | 0/8 14 h-lim-p 0.4993 20.0000 0.0047 1208.636294 0 0.9985 277 | 0/8 15 h-lim-p 2.5000 20.0000 0.0007 1208.636189 3 0.9644 303 | 0/8 16 h-lim-p 2.5000 20.0000 0.0001 1208.636188 0 1.0938 323 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1208.636188 0 2.1875 343 | 0/8 18 h-lim-p 2.5000 20.0000 0.0000 1208.636188 0 1.0938 363 | 0/8 19 h-lim-p 2.5000 20.0000 0.0000 1208.636188 0 1.0938 383 | 0/8 20 h-lim-p 2.5000 20.0000 0.0000 1208.636188 0 2.5000 403 | 0/8 21 h-lim-p 2.5000 20.0000 0.0000 1208.636188 0 0.0391 428 Out... lnL = -1208.636188 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1208.636188 Node 7: lnL = -1208.636188 Node 8: lnL = -1208.636188 Node 9: lnL = -1208.636188 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 861 Sequential format.. Reading seq # 1: YPL170W_Sbay Reading seq # 2: YPL170W_Scer Reading seq # 3: YPL170W_Skud Reading seq # 4: YPL170W_Smik Reading seq # 5: YPL170W_Spar Sequences read.. Counting patterns.. # site patterns = 338 Counting frequencies.. 120 bytes for distance 54080 bytes for lkl0 43264 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.428153 0.097494 0.075667 0.131360 0.099499 0.242986 0.232605 0.015115 lnL0 = -3886.976426 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3886.976426 x= 0.42815 0.09749 0.07567 0.13136 0.09950 0.24299 0.23261 0.01512 1 h-lim-p 0.0005 0.0042 105.6037 3885.494144 5 0.0003 33 | 0/8 2 h-lim-p 0.0010 0.0105 29.1555 3885.265023 8 0.0006 65 | 0/8 3 h-lim-p 0.0007 0.0154 23.5594 3885.215213 4 0.0003 85 | 0/8 4 h-lim-p 0.0007 0.0244 8.7823 3885.204031 3 0.0004 103 | 0/8 5 h-lim-p 0.0013 0.0453 2.3793 3885.202584 3 0.0006 122 | 0/8 6 h-lim-p 0.0019 0.2404 0.7178 3885.202453 3 0.0005 143 | 0/8 7 h-lim-p 0.0158 1.4487 0.0248 3885.202452 0 0.0017 165 | 0/8 8 h-lim-p 0.0456 20.0000 0.0009 3885.202074 0 0.7289 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3885.202031 1 0.9961 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3885.202031 0 1.0938 231 | 0/8 11 h-lim-p 1.0102 20.0000 0.0000 3885.202031 m20.0000 253 | 0/8 12 h-lim-p 0.0061 0.4379 0.0721 3885.202031 0 0.0008 275 | 0/8 13 h-lim-p 0.0001 0.0434 0.7269 3885.202031 0 0.0000 298 | 0/8 14 h-lim-p 0.0000 3.3247 0.1855 3885.202031 0 0.0000 331 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 3885.202031 0 0.0000 364 | 0/8 16 h-lim-p 0.0000 20.0000 0.0007 | 0/8 17 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -3885.202031 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3885.202031 Node 7: lnL = -3885.202031 Node 8: lnL = -3885.202031 Node 9: lnL = -3885.202031 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 457 Sequential format.. Reading seq # 1: YPL172C_Sbay Reading seq # 2: YPL172C_Scer Reading seq # 3: YPL172C_Skud Reading seq # 4: YPL172C_Smik Reading seq # 5: YPL172C_Spar Sequences read.. Counting patterns.. # site patterns = 199 Counting frequencies.. 120 bytes for distance 31840 bytes for lkl0 25472 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.363653 0.042569 0.087909 0.113137 0.061130 0.251260 0.250409 0.001276 lnL0 = -1993.651920 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1993.651920 x= 0.36365 0.04257 0.08791 0.11314 0.06113 0.25126 0.25041 0.00128 1 h-lim-p 0.0007 0.0058 69.9089 1992.694914 7 0.0004 38 | 0/8 2 h-lim-p 0.0007 0.0053 16.1649 1992.620199 2 0.0006 54 | 0/8 3 h-lim-p 0.0003 0.0027 16.1469 1992.590616 5 0.0004 78 | 0/8 4 h-lim-p 0.0009 0.0071 5.3143 1992.581654 5 0.0008 99 | 0/8 5 h-lim-p 0.0038 0.1711 1.0983 1992.581288 4 0.0007 122 | 0/8 6 h-lim-p 0.0015 0.7356 0.4753 1992.581196 3 0.0010 142 | 0/8 7 h-lim-p 0.0078 0.1141 0.0589 1992.581193 0 0.0017 163 | 0/8 8 h-lim-p 0.1149 20.0000 0.0009 1992.580495 0 0.9190 186 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1992.580480 1 1.0938 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1992.580480 0 1.0938 228 | 0/8 11 h-lim-p 1.0922 20.0000 0.0000 1992.580480 0 0.2389 249 | 0/8 12 h-lim-p 0.0862 20.0000 0.0000 1992.580480 0 0.0002 277 | 0/8 13 h-lim-p 0.0001 20.0000 0.0001 1992.580480 0 0.0000 306 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 1992.580480 0 0.0000 339 Out... lnL = -1992.580480 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1992.580480 Node 7: lnL = -1992.580480 Node 8: lnL = -1992.580480 Node 9: lnL = -1992.580480 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 426 Sequential format.. Reading seq # 1: YPL173W_Sbay Reading seq # 2: YPL173W_Scer Reading seq # 3: YPL173W_Skud Reading seq # 4: YPL173W_Smik Reading seq # 5: YPL173W_Spar Sequences read.. Counting patterns.. # site patterns = 185 Counting frequencies.. 120 bytes for distance 29600 bytes for lkl0 23680 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.377046 0.036813 0.103977 0.191172 0.123162 0.237572 0.233976 0.000060 lnL0 = -1929.794668 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1929.794668 x= 0.37705 0.03681 0.10398 0.19117 0.12316 0.23757 0.23398 0.00006 1 h-lim-p 0.0000 0.0000 100.3750 1929.746575 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0051 21.5662 1929.508904 0 0.0014 40 | 1/8 3 h-lim-p 0.0041 0.0340 7.3782 1929.474414 7 0.0012 69 | 1/8 4 h-lim-p 0.0022 0.0212 4.0794 1929.463633 2 0.0010 85 | 1/8 5 h-lim-p 0.0012 0.1542 3.3753 1929.432640 0 0.0023 98 | 1/8 6 h-lim-p 0.0074 0.2073 1.0660 1928.807841 0 0.0295 112 | 1/8 7 h-lim-p 0.0017 0.0133 11.6723 1926.251326 0 0.0050 125 | 1/8 8 h-lim-p 0.0077 0.0617 4.8360 1926.236844 6 0.0012 154 | 1/8 9 h-lim-p 0.4976 20.0000 0.0119 1926.172366 0 0.9952 167 | 0/8 10 h-lim-p 0.0649 20.0000 0.1817 1926.172306 3 0.0024 198 | 0/8 11 h-lim-p 0.1100 5.1647 0.0039 1926.164501 0 0.8796 221 | 0/8 12 h-lim-p 2.5000 20.0000 0.0007 1926.163951 2 0.9644 245 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1926.163951 0 1.0938 265 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1926.163951 0 1.0938 285 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1926.163951 0 1.0938 305 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1926.163951 0 1.0938 325 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1926.163951 0 0.1562 348 | 0/8 18 h-lim-p 0.0327 20.0000 0.0000 1926.163951 0 0.0003 374 Out... lnL = -1926.163951 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1926.163951 Node 7: lnL = -1926.163951 Node 8: lnL = -1926.163951 Node 9: lnL = -1926.163951 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 390 Sequential format.. Reading seq # 1: YPL174C_Sbay Reading seq # 2: YPL174C_Scer Reading seq # 3: YPL174C_Skud Reading seq # 4: YPL174C_Smik Reading seq # 5: YPL174C_Spar Sequences read.. Counting patterns.. # site patterns = 186 Counting frequencies.. 120 bytes for distance 29760 bytes for lkl0 23808 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.373475 0.066581 0.102186 0.201674 0.144480 0.230209 0.199808 0.000060 lnL0 = -1873.855159 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1873.855159 x= 0.37347 0.06658 0.10219 0.20167 0.14448 0.23021 0.19981 0.00006 1 h-lim-p 0.0000 0.0000 137.7353 1873.792435 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0036 32.0508 1873.370125 0 0.0009 40 | 1/8 3 h-lim-p 0.0017 0.0360 16.3909 1873.278178 3 0.0008 58 | 1/8 4 h-lim-p 0.0019 0.0480 6.7451 1873.222600 4 0.0019 78 | 1/8 5 h-lim-p 0.0063 0.1533 2.0391 1873.068460 0 0.0127 91 | 1/8 6 h-lim-p 0.0108 0.1091 2.3890 1868.494376 0 0.0433 105 | 0/8 7 h-lim-p 0.0004 0.0035 42.3879 1866.796338 0 0.0009 118 | 0/8 8 h-lim-p 0.0005 0.0043 9.7549 1866.750784 0 0.0011 131 | 0/8 9 h-lim-p 0.0014 0.0114 0.7297 1866.747083 0 0.0057 145 | 0/8 10 h-lim-p 0.0538 6.3571 0.0772 1866.292546 0 0.4304 168 | 0/8 11 h-lim-p 2.5000 20.0000 0.0081 1866.255509 6 1.0049 199 | 0/8 12 h-lim-p 2.5000 20.0000 0.0012 1866.254876 3 0.8855 227 | 0/8 13 h-lim-p 2.5000 20.0000 0.0002 1866.254862 2 0.9644 251 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1866.254862 0 1.0938 271 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 1866.254862 0 1.0938 291 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 1866.254862 0 1.0938 311 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 1866.254862 0 2.1875 331 | 0/8 18 h-lim-p 2.1202 20.0000 0.0000 1866.254862 0 0.0021 360 Out... lnL = -1866.254862 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1866.254862 Node 7: lnL = -1866.254862 Node 8: lnL = -1866.254862 Node 9: lnL = -1866.254862 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 839 Sequential format.. Reading seq # 1: YPL178W_Sbay Reading seq # 2: YPL178W_Scer Reading seq # 3: YPL178W_Skud Reading seq # 4: YPL178W_Smik Reading seq # 5: YPL178W_Spar Sequences read.. Counting patterns.. # site patterns = 288 Counting frequencies.. 120 bytes for distance 46080 bytes for lkl0 36864 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 1.098927 0.034671 0.155297 0.655924 3.330584 0.461277 0.366116 0.000060 lnL0 = -3944.710534 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3944.710534 x= 1.09893 0.03467 0.15530 0.65592 3.33058 0.46128 0.36612 0.00006 1 h-lim-p 0.0000 0.0000 118.0502 3944.665839 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0055 62.0763 3937.169109 4 0.0041 50 | 1/8 3 h-lim-p 0.0004 0.0029 39.0452 3934.817773 m 0.0029 62 | 2/8 4 h-lim-p 0.0021 0.0167 33.7055 3930.320903 0 0.0042 75 | 2/8 5 h-lim-p 0.0062 0.0493 3.4978 3930.308636 4 0.0023 95 | 2/8 6 h-lim-p 0.1057 11.6290 0.0768 3930.048760 0 0.8459 110 | 1/8 7 h-lim-p 0.5133 10.8014 0.1265 3930.045002 5 0.1551 143 | 1/8 8 h-lim-p 0.0356 0.2849 0.1084 3930.032076 m 0.2849 162 | 2/8 9 h-lim-p 2.5000 20.0000 0.0038 3930.031612 2 0.5469 186 | 1/8 10 h-lim-p 0.0227 20.0000 0.0914 3930.031576 0 0.0099 204 | 1/8 11 h-lim-p 2.3266 20.0000 0.0004 3930.031550 2 0.7441 228 | 1/8 12 h-lim-p 2.5000 20.0000 0.0001 3930.031549 0 1.0938 247 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 3930.031549 0 1.0938 266 | 1/8 14 h-lim-p 2.4204 20.0000 0.0000 3930.031549 0 1.0589 285 | 1/8 15 h-lim-p 1.0444 20.0000 0.0000 3930.031549 0 1.5666 304 | 1/8 16 h-lim-p 0.1977 20.0000 0.0001 3930.031549 0 0.0062 327 | 1/8 17 h-lim-p 0.0006 20.0000 0.0009 3930.031549 0 0.0000 361 | 1/8 18 h-lim-p 0.0000 20.0000 0.0000 3930.031549 0 0.0000 388 Out... lnL = -3930.031549 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3930.031549 Node 7: lnL = -3930.031549 Node 8: lnL = -3930.031549 Node 9: lnL = -3930.031549 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 546 Sequential format.. Reading seq # 1: YPL179W_Sbay Reading seq # 2: YPL179W_Scer Reading seq # 3: YPL179W_Skud Reading seq # 4: YPL179W_Smik Reading seq # 5: YPL179W_Spar Sequences read.. Counting patterns.. # site patterns = 190 Counting frequencies.. 120 bytes for distance 30400 bytes for lkl0 24320 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.266818 0.016266 0.074526 0.065136 0.071003 0.182982 0.157771 0.006934 lnL0 = -2302.503163 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2302.503163 x= 0.26682 0.01627 0.07453 0.06514 0.07100 0.18298 0.15777 0.00693 1 h-lim-p 0.0009 0.4778 225.2172 2299.550966 9 0.0001 48 | 0/8 2 h-lim-p 0.0012 0.0094 12.9219 2299.516390 5 0.0004 72 | 0/8 3 h-lim-p 0.0007 0.0379 8.0766 2299.510898 5 0.0002 95 | 0/8 4 h-lim-p 0.0009 0.0505 1.9429 2299.510351 4 0.0003 117 | 0/8 5 h-lim-p 0.0044 1.0485 0.1409 2299.510348 1 0.0003 134 | 0/8 6 h-lim-p 0.0007 3.2889 0.0564 2299.510348 0 0.0006 154 | 0/8 7 h-lim-p 0.0181 20.0000 0.0018 2299.510348 0 0.0020 176 | 0/8 8 h-lim-p 0.0095 20.0000 0.0004 2299.510343 0 0.4562 201 | 0/8 9 h-lim-p 1.6783 20.0000 0.0001 2299.510343 0 1.4685 221 | 0/8 10 h-lim-p 1.9995 20.0000 0.0001 2299.510343 0 0.9997 241 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2299.510343 0 2.1875 261 | 0/8 12 h-lim-p 0.0319 6.8903 0.0019 2299.510343 0 0.0005 286 | 0/8 13 h-lim-p 0.0001 1.7815 0.0072 2299.510343 0 0.0003 307 | 0/8 14 h-lim-p 0.0001 0.6771 0.0189 2299.510343 0 0.0000 333 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 2299.510343 0 0.0000 363 | 0/8 16 h-lim-p 0.0001 20.0000 0.0000 2299.510343 0 0.0000 395 Out... lnL = -2299.510343 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2299.510343 Node 7: lnL = -2299.510343 Node 8: lnL = -2299.510343 Node 9: lnL = -2299.510343 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 822 Sequential format.. Reading seq # 1: YPL181W_Sbay Reading seq # 2: YPL181W_Scer Reading seq # 3: YPL181W_Skud Reading seq # 4: YPL181W_Smik Reading seq # 5: YPL181W_Spar Sequences read.. Counting patterns.. # site patterns = 255 Counting frequencies.. 120 bytes for distance 40800 bytes for lkl0 32640 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.288041 0.041564 0.078328 0.148977 0.110945 0.118016 0.194728 0.000060 lnL0 = -3230.806303 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3230.806303 x= 0.28804 0.04156 0.07833 0.14898 0.11094 0.11802 0.19473 0.00006 1 h-lim-p 0.0000 0.0000 163.4076 3230.367847 m 0.0000 22 | 1/8 2 h-lim-p 0.0001 0.0025 53.5156 3230.061968 0 0.0002 36 | 1/8 3 h-lim-p 0.0004 0.0121 31.1981 3229.892155 0 0.0005 48 | 1/8 4 h-lim-p 0.0022 0.0431 7.6650 3229.873384 6 0.0006 76 | 1/8 5 h-lim-p 0.0030 0.1836 1.6243 3229.864588 5 0.0020 100 | 0/8 6 h-lim-p 0.0006 0.0876 5.7258 3229.839821 0 0.0011 113 | 0/8 7 h-lim-p 0.0007 0.0433 9.5400 3229.525978 0 0.0082 128 | 0/8 8 h-lim-p 0.0033 0.0268 5.2459 3229.438297 7 0.0023 158 | 0/8 9 h-lim-p 0.0041 0.0332 2.8816 3227.217507 4 0.0264 180 | 0/8 10 h-lim-p 0.1528 1.2223 0.0157 3227.156167 m 1.2223 192 | 0/8 11 h-lim-p 0.0000 0.0000 0.0041 h-lim-p: 2.58116175e-17 2.06492940e-16 4.14796152e-03 3227.156167 .. | 0/8 12 h-lim-p 0.0000 0.0169 6.4076 3227.152577 0 0.0002 232 | 0/8 13 h-lim-p 0.0012 0.5291 0.8219 3227.152473 1 0.0003 247 | 0/8 14 h-lim-p 0.0006 0.4052 0.4646 3227.152441 2 0.0004 272 | 0/8 15 h-lim-p 0.0003 0.0023 0.1639 3227.152437 0 0.0004 292 | 0/8 16 h-lim-p 0.0003 0.0027 0.0948 3227.152436 0 0.0005 312 | 0/8 17 h-lim-p 0.0002 0.0016 0.1004 3227.152436 0 0.0000 350 | 0/8 18 h-lim-p 0.0000 0.0004 0.2903 .. | 0/8 19 h-lim-p 0.0000 0.0012 0.5622 3227.152411 0 0.0002 407 | 0/8 20 h-lim-p 0.0001 0.0012 0.0900 3227.152411 0 0.0001 427 | 0/8 21 h-lim-p 0.0000 0.0001 1.1879 3227.152411 0 0.0000 460 | 0/8 22 h-lim-p 0.0000 20.0000 0.0699 3227.152410 0 0.0005 477 | 0/8 23 h-lim-p 0.0027 0.4779 0.0126 3227.152410 0 0.0012 497 | 0/8 24 h-lim-p 0.0024 20.0000 0.0061 3227.152410 0 0.0011 517 | 0/8 25 h-lim-p 0.0029 20.0000 0.0022 3227.152410 0 0.0013 537 | 0/8 26 h-lim-p 0.0304 20.0000 0.0001 3227.152410 0 0.0304 557 | 0/8 27 h-lim-p 0.0058 1.0558 0.0005 3227.152410 0 0.0116 578 | 0/8 28 h-lim-p 1.1762 20.0000 0.0000 3227.152410 0 0.1286 600 | 0/8 29 h-lim-p 0.1472 20.0000 0.0000 3227.152410 0 0.0000 637 Out... lnL = -3227.152410 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3227.152410 Node 7: lnL = -3227.152410 Node 8: lnL = -3227.152410 Node 9: lnL = -3227.152410 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 793 Sequential format.. Reading seq # 1: YPL183C_Sbay Reading seq # 2: YPL183C_Scer Reading seq # 3: YPL183C_Skud Reading seq # 4: YPL183C_Smik Reading seq # 5: YPL183C_Spar Sequences read.. Counting patterns.. # site patterns = 277 Counting frequencies.. 120 bytes for distance 44320 bytes for lkl0 35456 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.423743 0.000060 0.172631 0.215093 0.200648 0.268610 0.231876 0.019289 lnL0 = -3053.743872 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3053.743872 x= 0.42374 0.00006 0.17263 0.21509 0.20065 0.26861 0.23188 0.01929 1 h-lim-p 0.0000 0.0000 445.7106 3053.457704 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0004 134.4381 3048.331899 m 0.0004 37 | 2/8 3 h-lim-p 0.0011 0.0087 35.5634 3007.540361 0 0.0065 51 | 1/8 4 h-lim-p 0.0002 0.0013 165.5062 3003.279309 0 0.0003 64 | 1/8 5 h-lim-p 0.0002 0.0017 72.8455 3001.685410 0 0.0009 78 | 1/8 6 h-lim-p 0.0007 0.0054 74.6471 3000.806715 6 0.0005 103 | 1/8 7 h-lim-p 0.0012 0.0096 23.2620 3000.677600 2 0.0006 119 | 1/8 8 h-lim-p 0.0009 0.0075 8.7094 3000.631601 0 0.0014 131 | 0/8 9 h-lim-p 0.0007 0.0556 18.0088 3000.517178 1 0.0009 145 | 0/8 10 h-lim-p 0.0528 0.4225 0.1488 2995.785010 m 0.4225 157 | 0/8 11 h-lim-p -0.0000 -0.0000 0.0567 h-lim-p: -4.46315641e-17 -3.57052513e-16 5.66677663e-02 2995.785010 .. | 0/8 12 h-lim-p 0.0000 0.0093 49.4558 2995.351218 0 0.0003 198 | 0/8 13 h-lim-p 0.0000 0.0000 41.5375 2995.350960 m 0.0000 210 | 1/8 14 h-lim-p 0.0000 0.0580 34.1513 2995.163143 0 0.0006 228 | 1/8 15 h-lim-p 0.0008 0.0126 26.7153 2995.104496 6 0.0003 255 | 1/8 16 h-lim-p 0.0008 0.0102 11.7104 2995.080782 6 0.0005 281 | 1/8 17 h-lim-p 0.0013 0.0107 2.5595 2995.076918 2 0.0012 297 | 1/8 18 h-lim-p 0.0067 0.2034 0.4452 2995.074228 4 0.0057 316 | 1/8 19 h-lim-p 0.0099 0.2582 0.2589 2995.060527 0 0.0198 336 | 1/8 20 h-lim-p 0.0133 0.7301 0.3838 2994.727066 0 0.0800 357 | 0/8 21 h-lim-p 0.0256 0.3116 1.1964 2994.726485 2 0.0015 383 | 0/8 22 h-lim-p 0.9466 20.0000 0.0019 2994.723718 1 0.9466 397 | 0/8 23 h-lim-p 2.5000 20.0000 0.0001 2994.723715 0 1.0938 417 | 0/8 24 h-lim-p 2.5000 20.0000 0.0000 2994.723715 0 1.0938 437 | 0/8 25 h-lim-p 2.5000 20.0000 0.0000 2994.723715 0 2.1875 457 | 0/8 26 h-lim-p 1.9172 20.0000 0.0000 2994.723715 0 0.8388 477 | 0/8 27 h-lim-p 2.5000 20.0000 0.0000 2994.723715 0 0.0003 509 Out... lnL = -2994.723715 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2994.723715 Node 7: lnL = -2994.723715 Node 8: lnL = -2994.723715 Node 9: lnL = -2994.723715 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 866 Sequential format.. Reading seq # 1: YPL183W-A_Sbay Reading seq # 2: YPL183W-A_Scer Reading seq # 3: YPL183W-A_Skud Reading seq # 4: YPL183W-A_Smik Reading seq # 5: YPL183W-A_Spar Sequences read.. Counting patterns.. # site patterns = 281 Counting frequencies.. 120 bytes for distance 44960 bytes for lkl0 35968 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.109542 0.080714 0.049715 0.109924 0.085365 0.200405 0.201572 0.222310 lnL0 = -3845.581288 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3845.581288 x= 0.10954 0.08071 0.04972 0.10992 0.08536 0.20041 0.20157 0.22231 1 h-lim-p 0.0004 0.0033 190.3892 3843.155804 8 0.0001 41 | 0/8 2 h-lim-p 0.0005 0.0039 36.1621 3842.982212 7 0.0003 71 | 0/8 3 h-lim-p 0.0004 0.0133 22.0350 3842.938115 5 0.0002 94 | 0/8 4 h-lim-p 0.0008 0.0244 6.9033 3842.932388 5 0.0003 118 | 0/8 5 h-lim-p 0.0014 0.1852 1.3194 3842.932000 3 0.0005 138 | 0/8 6 h-lim-p 0.0024 0.9729 0.2559 3842.931990 1 0.0003 154 | 0/8 7 h-lim-p 0.0105 20.0000 0.0072 3842.931990 0 0.0012 176 | 0/8 8 h-lim-p 0.0625 20.0000 0.0001 3842.931972 0 1.0007 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3842.931971 0 1.0938 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3842.931971 0 1.0938 240 | 0/8 11 h-lim-p 1.3564 20.0000 0.0000 3842.931971 0 2.7128 261 | 0/8 12 h-lim-p 2.0220 20.0000 0.0000 3842.931971 0 0.1264 284 | 0/8 13 h-lim-p 0.0132 20.0000 0.0001 3842.931971 0 0.0132 304 | 0/8 14 h-lim-p 0.0045 20.0000 0.0004 3842.931971 0 0.0000 331 | 0/8 15 h-lim-p 0.0001 20.0000 0.0001 3842.931971 0 0.0000 360 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 3842.931971 0 0.0000 390 Out... lnL = -3842.931971 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3842.931971 Node 7: lnL = -3842.931971 Node 8: lnL = -3842.931971 Node 9: lnL = -3842.931971 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 550 Sequential format.. Reading seq # 1: YPL186C_Sbay Reading seq # 2: YPL186C_Scer Reading seq # 3: YPL186C_Skud Reading seq # 4: YPL186C_Smik Reading seq # 5: YPL186C_Spar Sequences read.. Counting patterns.. # site patterns = 198 Counting frequencies.. 120 bytes for distance 31680 bytes for lkl0 25344 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.051208 0.080078 0.052551 0.089908 0.079857 0.132480 0.163922 0.136735 lnL0 = -2193.400314 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2193.400314 x= 0.05121 0.08008 0.05255 0.08991 0.07986 0.13248 0.16392 0.13673 1 h-lim-p 0.0043 1.3555 101.1595 2192.278781 7 0.0002 37 | 0/8 2 h-lim-p 0.0006 0.0051 25.9771 2192.176212 6 0.0003 64 | 0/8 3 h-lim-p 0.0014 0.0223 6.0981 2192.172023 5 0.0002 89 | 0/8 4 h-lim-p 0.0023 0.1926 0.6368 2192.171936 2 0.0004 106 | 0/8 5 h-lim-p 0.0011 1.2790 0.2538 2192.171924 1 0.0004 128 | 0/8 6 h-lim-p 0.0111 19.0651 0.0101 2192.171923 0 0.0012 150 | 0/8 7 h-lim-p 0.0017 20.0000 0.0073 2192.171920 0 0.0067 172 | 0/8 8 h-lim-p 0.0038 20.0000 0.0130 2192.171785 0 0.0228 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2192.171784 0 1.0938 214 | 0/8 10 h-lim-p 1.3850 20.0000 0.0000 2192.171784 0 1.2119 234 | 0/8 11 h-lim-p 1.3555 20.0000 0.0000 2192.171784 0 2.7111 255 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2192.171784 0 0.5469 276 | 0/8 13 h-lim-p 0.0929 20.0000 0.0001 2192.171784 0 0.0058 299 | 0/8 14 h-lim-p 0.0017 20.0000 0.0003 2192.171784 0 0.0001 322 | 0/8 15 h-lim-p 0.0000 4.0323 0.0172 2192.171784 0 0.0000 344 | 0/8 16 h-lim-p 0.0001 20.0000 0.0002 2192.171784 0 0.0000 379 | 0/8 17 h-lim-p 0.0000 20.0000 0.0016 2192.171784 0 0.0000 409 | 0/8 18 h-lim-p 0.0000 20.0000 0.0004 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0016 | 0/8 20 h-lim-p 0.0000 20.0000 0.0016 Out... lnL = -2192.171784 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2192.171784 Node 7: lnL = -2192.171784 Node 8: lnL = -2192.171784 Node 9: lnL = -2192.171784 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 893 Sequential format.. Reading seq # 1: YPL187W_Sbay Reading seq # 2: YPL187W_Scer Reading seq # 3: YPL187W_Skud Reading seq # 4: YPL187W_Smik Reading seq # 5: YPL187W_Spar Sequences read.. Counting patterns.. # site patterns = 294 Counting frequencies.. 120 bytes for distance 47040 bytes for lkl0 37632 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.093475 0.066458 0.068432 0.129234 0.095026 0.188721 0.243400 0.209995 lnL0 = -3983.055566 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3983.055566 x= 0.09348 0.06646 0.06843 0.12923 0.09503 0.18872 0.24340 0.21000 1 h-lim-p 0.0021 0.0166 158.9328 3980.955524 9 0.0002 49 | 0/8 2 h-lim-p 0.0006 0.0052 23.9980 3980.882318 5 0.0003 72 | 0/8 3 h-lim-p 0.0006 0.0287 10.0628 3980.869532 2 0.0003 88 | 0/8 4 h-lim-p 0.0009 0.0858 3.0652 3980.867785 2 0.0004 104 | 0/8 5 h-lim-p 0.0017 0.4811 0.7367 3980.867674 2 0.0004 121 | 0/8 6 h-lim-p 0.0197 18.6771 0.0158 3980.867674 0 0.0005 145 | 0/8 7 h-lim-p 0.0025 20.0000 0.0034 3980.867674 0 0.0022 165 | 0/8 8 h-lim-p 0.0166 20.0000 0.0004 3980.867659 0 0.2655 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3980.867659 0 1.0938 209 | 0/8 10 h-lim-p 1.2390 20.0000 0.0000 3980.867659 0 1.0842 229 | 0/8 11 h-lim-p 0.6994 20.0000 0.0000 3980.867659 0 0.0000 262 | 0/8 12 h-lim-p 0.0006 20.0000 0.0000 3980.867659 0 0.0006 282 Out... lnL = -3980.867659 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3980.867659 Node 7: lnL = -3980.867659 Node 8: lnL = -3980.867659 Node 9: lnL = -3980.867659 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 836 Sequential format.. Reading seq # 1: YPL190C_Sbay Reading seq # 2: YPL190C_Scer Reading seq # 3: YPL190C_Skud Reading seq # 4: YPL190C_Smik Reading seq # 5: YPL190C_Spar Sequences read.. Counting patterns.. # site patterns = 257 Counting frequencies.. 120 bytes for distance 41120 bytes for lkl0 32896 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.088637 0.047058 0.055486 0.119127 0.054642 0.191927 0.178079 0.186124 lnL0 = -3636.287705 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3636.287705 x= 0.08864 0.04706 0.05549 0.11913 0.05464 0.19193 0.17808 0.18612 1 h-lim-p 0.0001 0.0004 227.3842 3633.035436 0 0.0001 23 | 0/8 2 h-lim-p 0.0005 0.0056 49.7712 3632.857910 7 0.0002 53 | 0/8 3 h-lim-p 0.0003 0.0050 23.2087 3632.824056 2 0.0002 69 | 0/8 4 h-lim-p 0.0004 0.0195 10.0905 3632.813133 5 0.0003 93 | 0/8 5 h-lim-p 0.0010 0.0610 2.5983 3632.812382 2 0.0002 110 | 0/8 6 h-lim-p 0.0016 0.4691 0.3888 3632.812251 2 0.0007 126 | 0/8 7 h-lim-p 0.0055 8.9580 0.0527 3632.799532 0 0.0660 149 | 0/8 8 h-lim-p 0.0018 0.0608 1.9553 3632.705746 0 0.0036 170 | 0/8 9 h-lim-p 2.5000 20.0000 0.0009 3632.702892 3 0.9961 188 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3632.702886 0 1.0938 208 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3632.702886 0 1.0938 228 | 0/8 12 h-lim-p 1.2760 20.0000 0.0000 3632.702886 0 2.5520 249 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 3632.702886 0 0.0098 276 | 0/8 14 h-lim-p 0.0004 20.0000 0.0000 3632.702886 0 0.0000 312 | 0/8 15 h-lim-p 0.0000 20.0000 0.0049 | 0/8 16 h-lim-p 0.0000 20.0000 0.0049 Out... lnL = -3632.702886 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3632.702886 Node 7: lnL = -3632.702886 Node 8: lnL = -3632.702886 Node 9: lnL = -3632.702886 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 445 Sequential format.. Reading seq # 1: YPL199C_Sbay Reading seq # 2: YPL199C_Scer Reading seq # 3: YPL199C_Skud Reading seq # 4: YPL199C_Smik Reading seq # 5: YPL199C_Spar Sequences read.. Counting patterns.. # site patterns = 229 Counting frequencies.. 120 bytes for distance 36640 bytes for lkl0 29312 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.072376 0.119405 0.032113 0.170629 0.155976 0.347723 0.225155 0.214063 lnL0 = -2148.775977 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2148.775977 x= 0.07238 0.11940 0.03211 0.17063 0.15598 0.34772 0.22516 0.21406 1 h-lim-p 0.0040 1.1264 104.2638 2147.033225 8 0.0004 42 | 0/8 2 h-lim-p 0.0029 0.0249 13.0040 2146.946587 6 0.0010 69 | 0/8 3 h-lim-p 0.0023 0.0508 5.9519 2146.933930 5 0.0008 93 | 0/8 4 h-lim-p 0.0069 0.2802 0.7294 2146.933664 3 0.0010 115 | 0/8 5 h-lim-p 0.0027 0.6840 0.2722 2146.933626 1 0.0012 137 | 0/8 6 h-lim-p 0.0038 4.5022 0.0846 2146.933622 1 0.0015 159 | 0/8 7 h-lim-p 0.0145 20.0000 0.0089 2146.933622 0 0.0032 180 | 0/8 8 h-lim-p 0.0546 20.0000 0.0005 2146.933547 0 0.4368 203 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2146.933544 0 1.0938 223 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2146.933544 0 1.0938 243 | 0/8 11 h-lim-p 1.2637 20.0000 0.0000 2146.933544 0 1.2637 263 | 0/8 12 h-lim-p 1.0879 20.0000 0.0000 2146.933544 0 0.1360 285 | 0/8 13 h-lim-p 0.0033 20.0000 0.0004 2146.933544 0 0.0002 308 | 0/8 14 h-lim-p 0.0006 20.0000 0.0001 2146.933544 0 0.0001 330 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 2146.933544 0 0.0000 356 | 0/8 16 h-lim-p 0.0008 20.0000 0.0000 2146.933544 0 0.0000 383 Out... lnL = -2146.933544 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2146.933544 Node 7: lnL = -2146.933544 Node 8: lnL = -2146.933544 Node 9: lnL = -2146.933544 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 393 Sequential format.. Reading seq # 1: YPL200W_Sbay Reading seq # 2: YPL200W_Scer Reading seq # 3: YPL200W_Skud Reading seq # 4: YPL200W_Smik Reading seq # 5: YPL200W_Spar Sequences read.. Counting patterns.. # site patterns = 163 Counting frequencies.. 120 bytes for distance 26080 bytes for lkl0 20864 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.096706 0.090226 0.076814 0.146202 0.059789 0.171033 0.214189 0.212058 lnL0 = -1656.040677 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1656.040677 x= 0.09671 0.09023 0.07681 0.14620 0.05979 0.17103 0.21419 0.21206 1 h-lim-p 0.0181 3.8996 42.8202 1655.660102 7 0.0004 42 | 0/8 2 h-lim-p 0.0011 0.0102 17.3549 1655.584813 5 0.0006 65 | 0/8 3 h-lim-p 0.0021 0.0208 4.8088 1655.578126 6 0.0006 94 | 0/8 4 h-lim-p 0.0037 0.2576 0.8165 1655.577860 2 0.0008 111 | 0/8 5 h-lim-p 0.0066 5.1609 0.1006 1655.577855 2 0.0011 138 | 0/8 6 h-lim-p 0.0083 20.0000 0.0131 1655.577854 0 0.0018 159 | 0/8 7 h-lim-p 0.0035 20.0000 0.0068 1655.577854 0 0.0031 179 | 0/8 8 h-lim-p 0.0292 20.0000 0.0007 1655.577825 0 0.2338 202 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1655.577824 0 1.0938 222 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1655.577824 0 1.0938 242 | 0/8 11 h-lim-p 1.3079 20.0000 0.0000 1655.577824 0 0.0613 266 | 0/8 12 h-lim-p 0.0252 20.0000 0.0000 1655.577824 0 0.0008 290 | 0/8 13 h-lim-p 0.0005 20.0000 0.0000 1655.577824 0 0.0000 327 | 0/8 14 h-lim-p 0.0000 20.0000 0.0005 1655.577824 0 0.0000 353 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0005 | 0/8 17 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -1655.577824 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1655.577824 Node 7: lnL = -1655.577824 Node 8: lnL = -1655.577824 Node 9: lnL = -1655.577824 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 359 Sequential format.. Reading seq # 1: YPL201C_Sbay Reading seq # 2: YPL201C_Scer Reading seq # 3: YPL201C_Skud Reading seq # 4: YPL201C_Smik Reading seq # 5: YPL201C_Spar Sequences read.. Counting patterns.. # site patterns = 159 Counting frequencies.. 120 bytes for distance 25440 bytes for lkl0 20352 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.115269 0.035682 0.070967 0.129199 0.068662 0.188407 0.253149 0.230035 lnL0 = -1614.430392 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1614.430392 x= 0.11527 0.03568 0.07097 0.12920 0.06866 0.18841 0.25315 0.23004 1 h-lim-p 0.0052 0.1985 79.0388 1613.270805 9 0.0004 46 | 0/8 2 h-lim-p 0.0008 0.0062 21.9527 1613.102417 2 0.0007 62 | 0/8 3 h-lim-p 0.0013 0.0240 12.6111 1613.060745 5 0.0007 85 | 0/8 4 h-lim-p 0.0016 0.0347 5.3428 1613.053411 4 0.0006 105 | 0/8 5 h-lim-p 0.0033 0.2528 1.0511 1613.052851 4 0.0011 126 | 0/8 6 h-lim-p 0.0078 1.0703 0.1450 1613.052843 2 0.0006 145 | 0/8 7 h-lim-p 0.0073 15.0320 0.0123 1613.052840 0 0.0073 165 | 0/8 8 h-lim-p 0.0206 20.0000 0.0044 1613.052301 0 0.1647 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1613.052293 1 0.9961 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1613.052293 0 1.0938 230 | 0/8 11 h-lim-p 1.0231 20.0000 0.0000 1613.052293 0 3.0693 251 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1613.052293 0 0.0781 275 | 0/8 13 h-lim-p 0.0477 20.0000 0.0000 1613.052293 0 0.0238 295 | 0/8 14 h-lim-p 0.0088 20.0000 0.0000 1613.052293 0 0.0000 322 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 1613.052293 0 0.0000 356 | 0/8 16 h-lim-p 0.0000 20.0000 0.0010 1613.052293 0 0.0000 382 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0010 1613.052293 0 0.0000 443 | 0/8 19 h-lim-p 0.0000 20.0000 0.0002 .. | 0/8 20 h-lim-p 0.0000 20.0000 0.0010 | 0/8 21 h-lim-p 0.0000 20.0000 0.0010 Out... lnL = -1613.052293 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1613.052293 Node 7: lnL = -1613.052293 Node 8: lnL = -1613.052293 Node 9: lnL = -1613.052293 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 486 Sequential format.. Reading seq # 1: YPL202C_Sbay Reading seq # 2: YPL202C_Scer Reading seq # 3: YPL202C_Skud Reading seq # 4: YPL202C_Smik Reading seq # 5: YPL202C_Spar Sequences read.. Counting patterns.. # site patterns = 205 Counting frequencies.. 120 bytes for distance 32800 bytes for lkl0 26240 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.139746 0.096363 0.042081 0.119749 0.070349 0.187878 0.183154 0.256558 lnL0 = -2024.379411 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2024.379411 x= 0.13975 0.09636 0.04208 0.11975 0.07035 0.18788 0.18315 0.25656 1 h-lim-p 0.0064 1.8291 79.2541 2023.479268 6 0.0003 37 | 0/8 2 h-lim-p 0.0007 0.0053 22.2773 2023.371382 8 0.0005 70 | 0/8 3 h-lim-p 0.0011 0.0109 9.3796 2023.354096 5 0.0005 93 | 0/8 4 h-lim-p 0.0014 0.0842 3.1702 2023.350357 6 0.0008 120 | 0/8 5 h-lim-p 0.0030 0.2489 0.8882 2023.350107 2 0.0007 137 | 0/8 6 h-lim-p 0.0029 1.1709 0.2153 2023.350088 2 0.0010 163 | 0/8 7 h-lim-p 0.0235 20.0000 0.0088 2023.350088 0 0.0026 185 | 0/8 8 h-lim-p 0.0807 20.0000 0.0003 2023.350059 0 0.6455 208 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2023.350058 0 1.0938 228 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2023.350058 0 1.2500 248 | 0/8 11 h-lim-p 1.6393 20.0000 0.0000 2023.350058 0 0.3586 269 | 0/8 12 h-lim-p 0.1831 20.0000 0.0000 2023.350058 0 0.0057 293 | 0/8 13 h-lim-p 0.0035 20.0000 0.0000 2023.350058 0 0.0009 314 | 0/8 14 h-lim-p 0.0003 20.0000 0.0000 2023.350058 0 0.0000 352 | 0/8 15 h-lim-p 0.0000 20.0000 0.0009 | 0/8 16 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -2023.350058 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2023.350058 Node 7: lnL = -2023.350058 Node 8: lnL = -2023.350058 Node 9: lnL = -2023.350058 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 527 Sequential format.. Reading seq # 1: YPL203W_Sbay Reading seq # 2: YPL203W_Scer Reading seq # 3: YPL203W_Skud Reading seq # 4: YPL203W_Smik Reading seq # 5: YPL203W_Spar Sequences read.. Counting patterns.. # site patterns = 152 Counting frequencies.. 120 bytes for distance 24320 bytes for lkl0 19456 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.085047 0.028553 0.060263 0.066697 0.060272 0.097650 0.108880 0.156008 lnL0 = -1941.302424 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1941.302424 x= 0.08505 0.02855 0.06026 0.06670 0.06027 0.09765 0.10888 0.15601 1 h-lim-p 0.0034 1.0476 106.9356 1940.539785 7 0.0001 42 | 0/8 2 h-lim-p 0.0008 0.0079 19.2391 1940.476882 5 0.0003 64 | 0/8 3 h-lim-p 0.0019 0.0615 3.4818 1940.475626 4 0.0002 85 | 0/8 4 h-lim-p 0.0007 0.1499 1.0121 1940.475511 3 0.0002 104 | 0/8 5 h-lim-p 0.0011 1.0377 0.2223 1940.475507 2 0.0002 122 | 0/8 6 h-lim-p 0.0044 20.0000 0.0087 1940.475507 0 0.0005 144 | 0/8 7 h-lim-p 0.0022 20.0000 0.0020 1940.475507 0 0.0019 164 | 0/8 8 h-lim-p 0.0054 20.0000 0.0007 1940.475494 0 0.1292 188 | 0/8 9 h-lim-p 2.4181 20.0000 0.0000 1940.475493 0 1.0579 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1940.475493 0 0.5469 229 | 0/8 11 h-lim-p 0.4312 20.0000 0.0000 1940.475493 0 0.0004 258 | 0/8 12 h-lim-p 0.0003 20.0000 0.0000 1940.475493 0 0.0001 278 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 1940.475493 0 0.0000 316 | 0/8 14 h-lim-p 0.0000 20.0000 0.0035 1940.475493 0 0.0000 348 | 0/8 15 h-lim-p 0.0000 20.0000 0.0015 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0035 | 0/8 17 h-lim-p 0.0000 20.0000 0.0035 Out... lnL = -1940.475493 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1940.475493 Node 7: lnL = -1940.475493 Node 8: lnL = -1940.475493 Node 9: lnL = -1940.475493 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 279 Sequential format.. Reading seq # 1: YPL210C_Sbay Reading seq # 2: YPL210C_Scer Reading seq # 3: YPL210C_Skud Reading seq # 4: YPL210C_Smik Reading seq # 5: YPL210C_Spar Sequences read.. Counting patterns.. # site patterns = 109 Counting frequencies.. 120 bytes for distance 17440 bytes for lkl0 13952 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.045288 0.043004 0.067972 0.138384 0.076405 0.168572 0.158273 0.134285 lnL0 = -1167.591167 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1167.591167 x= 0.04529 0.04300 0.06797 0.13838 0.07641 0.16857 0.15827 0.13429 1 h-lim-p 0.0006 0.0046 76.4459 1166.584273 8 0.0004 38 | 0/8 2 h-lim-p 0.0008 0.0060 15.1256 1166.521984 7 0.0006 66 | 0/8 3 h-lim-p 0.0015 0.0672 5.5473 1166.513792 4 0.0006 86 | 0/8 4 h-lim-p 0.0029 0.1669 1.1738 1166.513274 5 0.0008 111 | 0/8 5 h-lim-p 0.0026 0.3380 0.3532 1166.513223 3 0.0009 131 | 0/8 6 h-lim-p 0.0057 2.3567 0.0574 1166.513221 1 0.0007 155 | 0/8 7 h-lim-p 0.0038 18.7603 0.0107 1166.513221 0 0.0008 176 | 0/8 8 h-lim-p 0.0679 20.0000 0.0001 1166.513207 0 1.0871 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1166.513206 0 1.0938 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1166.513206 0 1.2500 240 | 0/8 11 h-lim-p 1.4788 20.0000 0.0000 1166.513206 0 0.1848 262 | 0/8 12 h-lim-p 0.0748 20.0000 0.0000 1166.513206 0 0.0023 286 | 0/8 13 h-lim-p 0.0012 20.0000 0.0000 1166.513206 0 0.0000 323 | 0/8 14 h-lim-p 0.0000 20.0000 0.0010 | 0/8 15 h-lim-p 0.0000 20.0000 0.0010 Out... lnL = -1166.513206 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1166.513206 Node 7: lnL = -1166.513206 Node 8: lnL = -1166.513206 Node 9: lnL = -1166.513206 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 354 Sequential format.. Reading seq # 1: YPL211W_Sbay Reading seq # 2: YPL211W_Scer Reading seq # 3: YPL211W_Skud Reading seq # 4: YPL211W_Smik Reading seq # 5: YPL211W_Spar Sequences read.. Counting patterns.. # site patterns = 130 Counting frequencies.. 120 bytes for distance 20800 bytes for lkl0 16640 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.080150 0.055220 0.083929 0.075636 0.051233 0.155781 0.222377 0.170373 lnL0 = -1483.414731 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1483.414731 x= 0.08015 0.05522 0.08393 0.07564 0.05123 0.15578 0.22238 0.17037 1 h-lim-p 0.0002 0.0016 71.6872 1482.503710 0 0.0004 23 | 0/8 2 h-lim-p 0.0017 0.0360 16.4000 1482.474973 5 0.0002 47 | 0/8 3 h-lim-p 0.0007 0.0352 5.3074 1482.466084 4 0.0007 67 | 0/8 4 h-lim-p 0.0025 0.1944 1.4639 1482.465448 4 0.0006 88 | 0/8 5 h-lim-p 0.0016 0.3957 0.5844 1482.465350 3 0.0007 106 | 0/8 6 h-lim-p 0.0017 0.6904 0.2268 1482.465331 2 0.0008 130 | 0/8 7 h-lim-p 0.0345 20.0000 0.0050 1482.464933 0 0.1379 152 | 0/8 8 h-lim-p 0.0023 0.3021 0.2944 1482.462705 0 0.0047 173 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1482.462671 2 0.9961 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1482.462671 0 1.0938 217 | 0/8 11 h-lim-p 1.1837 20.0000 0.0000 1482.462671 0 7.1021 239 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1482.462671 0 0.1562 262 | 0/8 13 h-lim-p 0.3436 20.0000 0.0000 1482.462671 0 0.0002 292 Out... lnL = -1482.462671 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1482.462671 Node 7: lnL = -1482.462671 Node 8: lnL = -1482.462671 Node 9: lnL = -1482.462671 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 355 Sequential format.. Reading seq # 1: YPL212C_Sbay Reading seq # 2: YPL212C_Scer Reading seq # 3: YPL212C_Skud Reading seq # 4: YPL212C_Smik Reading seq # 5: YPL212C_Spar Sequences read.. Counting patterns.. # site patterns = 128 Counting frequencies.. 120 bytes for distance 20480 bytes for lkl0 16384 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.061957 0.079257 0.079451 0.080791 0.046079 0.157976 0.216754 0.151099 lnL0 = -1477.213037 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1477.213037 x= 0.06196 0.07926 0.07945 0.08079 0.04608 0.15798 0.21675 0.15110 1 h-lim-p 0.0002 0.0017 65.8560 1476.406298 0 0.0004 23 | 0/8 2 h-lim-p 0.0014 0.0489 19.8140 1476.368346 7 0.0002 54 | 0/8 3 h-lim-p 0.0007 0.0402 5.9340 1476.357610 2 0.0007 70 | 0/8 4 h-lim-p 0.0047 0.1506 0.8426 1476.357418 0 0.0005 84 | 0/8 5 h-lim-p 0.0026 1.0076 0.1677 1476.357408 2 0.0007 109 | 0/8 6 h-lim-p 0.0016 3.8509 0.0713 1476.357396 0 0.0024 129 | 0/8 7 h-lim-p 0.0049 7.8460 0.0347 1476.357272 0 0.0148 150 | 0/8 8 h-lim-p 0.0075 1.8960 0.0682 1476.354368 0 0.0301 172 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1476.354267 2 0.9961 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1476.354267 0 1.0938 216 | 0/8 11 h-lim-p 1.1144 20.0000 0.0000 1476.354267 0 1.1144 236 | 0/8 12 h-lim-p 0.1206 20.0000 0.0001 1476.354267 0 0.0016 261 | 0/8 13 h-lim-p 0.0004 20.0000 0.0003 1476.354267 0 0.0000 288 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 1476.354267 0 0.0000 318 Out... lnL = -1476.354267 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1476.354267 Node 7: lnL = -1476.354267 Node 8: lnL = -1476.354267 Node 9: lnL = -1476.354267 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 447 Sequential format.. Reading seq # 1: YPL213W_Sbay Reading seq # 2: YPL213W_Scer Reading seq # 3: YPL213W_Skud Reading seq # 4: YPL213W_Smik Reading seq # 5: YPL213W_Spar Sequences read.. Counting patterns.. # site patterns = 182 Counting frequencies.. 120 bytes for distance 29120 bytes for lkl0 23296 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.060015 0.102658 0.059403 0.185291 0.115245 0.237217 0.196122 0.173252 lnL0 = -2128.876416 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2128.876416 x= 0.06002 0.10266 0.05940 0.18529 0.11525 0.23722 0.19612 0.17325 1 h-lim-p 0.0019 0.0153 69.9522 2128.065843 8 0.0004 41 | 0/8 2 h-lim-p 0.0012 0.0100 14.2570 2128.008288 2 0.0006 57 | 0/8 3 h-lim-p 0.0016 0.0674 5.1059 2128.000784 4 0.0006 77 | 0/8 4 h-lim-p 0.0040 0.3713 0.8277 2128.000509 3 0.0008 96 | 0/8 5 h-lim-p 0.0046 0.7396 0.1507 2128.000503 0 0.0005 118 | 0/8 6 h-lim-p 0.0034 16.3444 0.0222 2128.000503 0 0.0015 138 | 0/8 7 h-lim-p 0.0620 20.0000 0.0005 2128.000503 0 0.0271 158 | 0/8 8 h-lim-p 0.0076 20.0000 0.0019 2128.000498 0 0.0304 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2128.000498 0 1.0938 200 | 0/8 10 h-lim-p 1.7718 20.0000 0.0000 2128.000498 0 1.5504 220 | 0/8 11 h-lim-p 2.1716 20.0000 0.0000 2128.000498 0 0.9501 240 | 0/8 12 h-lim-p 0.3567 20.0000 0.0000 2128.000498 0 0.0028 266 | 0/8 13 h-lim-p 0.0005 20.0000 0.0001 2128.000498 0 0.0000 301 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -2128.000498 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2128.000498 Node 7: lnL = -2128.000498 Node 8: lnL = -2128.000498 Node 9: lnL = -2128.000498 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 446 Sequential format.. Reading seq # 1: YPL214C_Sbay Reading seq # 2: YPL214C_Scer Reading seq # 3: YPL214C_Skud Reading seq # 4: YPL214C_Smik Reading seq # 5: YPL214C_Spar Sequences read.. Counting patterns.. # site patterns = 174 Counting frequencies.. 120 bytes for distance 27840 bytes for lkl0 22272 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.091627 0.063150 0.053093 0.196885 0.103651 0.218922 0.232876 0.206201 lnL0 = -2135.129006 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2135.129006 x= 0.09163 0.06315 0.05309 0.19688 0.10365 0.21892 0.23288 0.20620 1 h-lim-p 0.0012 0.0094 82.3390 2134.241344 6 0.0003 34 | 0/8 2 h-lim-p 0.0009 0.0074 15.6835 2134.186496 5 0.0005 56 | 0/8 3 h-lim-p 0.0016 0.1069 4.4511 2134.180511 4 0.0007 77 | 0/8 4 h-lim-p 0.0033 0.5377 0.8807 2134.180267 2 0.0007 94 | 0/8 5 h-lim-p 0.0018 0.8910 0.3259 2134.180234 2 0.0007 118 | 0/8 6 h-lim-p 0.0116 14.2251 0.0200 2134.180233 0 0.0013 140 | 0/8 7 h-lim-p 0.0131 20.0000 0.0019 2134.180233 0 0.0029 161 | 0/8 8 h-lim-p 0.0250 20.0000 0.0002 2134.180228 0 0.3997 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2134.180228 0 1.0938 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2134.180228 0 1.0938 225 | 0/8 11 h-lim-p 1.0984 20.0000 0.0000 2134.180228 0 0.8238 245 | 0/8 12 h-lim-p 0.1096 20.0000 0.0001 2134.180228 0 0.0000 289 | 0/8 13 h-lim-p 0.0000 20.0000 0.0001 | 0/8 14 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -2134.180228 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2134.180228 Node 7: lnL = -2134.180228 Node 8: lnL = -2134.180228 Node 9: lnL = -2134.180228 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 303 Sequential format.. Reading seq # 1: YPL215W_Sbay Reading seq # 2: YPL215W_Scer Reading seq # 3: YPL215W_Skud Reading seq # 4: YPL215W_Smik Reading seq # 5: YPL215W_Spar Sequences read.. Counting patterns.. # site patterns = 159 Counting frequencies.. 120 bytes for distance 25440 bytes for lkl0 20352 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.095093 0.082874 0.122972 0.188048 0.088146 0.283969 0.204639 0.225543 lnL0 = -1490.860107 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1490.860107 x= 0.09509 0.08287 0.12297 0.18805 0.08815 0.28397 0.20464 0.22554 1 h-lim-p 0.0099 0.0791 36.3310 1490.378562 8 0.0008 47 | 0/8 2 h-lim-p 0.0031 0.0250 8.7792 1490.334322 4 0.0012 67 | 0/8 3 h-lim-p 0.0020 0.0473 5.2883 1490.326724 5 0.0007 90 | 0/8 4 h-lim-p 0.0087 0.8149 0.4351 1490.326585 4 0.0015 114 | 0/8 5 h-lim-p 0.0051 2.7870 0.1249 1490.326573 2 0.0017 140 | 0/8 6 h-lim-p 0.0209 20.0000 0.0101 1490.326573 0 0.0026 162 | 0/8 7 h-lim-p 0.0179 20.0000 0.0015 1490.326558 0 0.1435 185 | 0/8 8 h-lim-p 0.0041 20.0000 0.0519 1490.326511 0 0.0061 205 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1490.326511 0 1.0938 225 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1490.326511 0 1.0938 245 | 0/8 11 h-lim-p 1.4648 20.0000 0.0000 1490.326511 0 2.1972 265 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1490.326511 0 0.5469 286 | 0/8 13 h-lim-p 0.1043 20.0000 0.0000 1490.326511 0 0.0522 306 | 0/8 14 h-lim-p 0.0172 20.0000 0.0000 1490.326511 0 0.0086 326 | 0/8 15 h-lim-p 0.0035 20.0000 0.0001 1490.326511 0 0.0002 349 | 0/8 16 h-lim-p 0.0002 20.0000 0.0001 1490.326511 0 0.0001 370 | 0/8 17 h-lim-p 0.0003 20.0000 0.0000 1490.326511 0 0.0000 393 | 0/8 18 h-lim-p 0.0004 20.0000 0.0000 1490.326511 0 0.0002 413 Out... lnL = -1490.326511 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1490.326511 Node 7: lnL = -1490.326511 Node 8: lnL = -1490.326511 Node 9: lnL = -1490.326511 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 713 Sequential format.. Reading seq # 1: YPL216W_Sbay Reading seq # 2: YPL216W_Scer Reading seq # 3: YPL216W_Skud Reading seq # 4: YPL216W_Smik Reading seq # 5: YPL216W_Spar Sequences read.. Counting patterns.. # site patterns = 293 Counting frequencies.. 120 bytes for distance 46880 bytes for lkl0 37504 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.144403 0.069462 0.050742 0.195852 0.121825 0.314486 0.312254 0.290312 lnL0 = -3628.194547 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3628.194547 x= 0.14440 0.06946 0.05074 0.19585 0.12182 0.31449 0.31225 0.29031 1 h-lim-p 0.0006 0.0052 81.7991 3626.738578 7 0.0005 37 | 0/8 2 h-lim-p 0.0002 0.0019 38.9593 3626.389486 0 0.0005 50 | 0/8 3 h-lim-p 0.0008 0.0221 22.1543 3626.302680 7 0.0005 79 | 0/8 4 h-lim-p 0.0011 0.0265 9.4053 3626.288051 6 0.0004 106 | 0/8 5 h-lim-p 0.0035 0.4117 1.1119 3626.287351 3 0.0011 126 | 0/8 6 h-lim-p 0.0385 4.2175 0.0327 3626.287252 2 0.0101 143 | 0/8 7 h-lim-p 0.0045 0.9775 0.0729 3626.278793 0 0.0545 166 | 0/8 8 h-lim-p 0.0047 0.2248 0.8517 3626.278470 4 0.0009 196 | 0/8 9 h-lim-p 1.8792 20.0000 0.0004 3626.278264 4 1.0655 226 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3626.278263 0 1.0938 246 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3626.278263 0 0.5469 267 | 0/8 12 h-lim-p 0.3308 20.0000 0.0000 3626.278263 0 0.0006 295 | 0/8 13 h-lim-p 0.0015 20.0000 0.0000 3626.278263 0 0.0000 330 Out... lnL = -3626.278263 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3626.278263 Node 7: lnL = -3626.278263 Node 8: lnL = -3626.278263 Node 9: lnL = -3626.278263 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 425 Sequential format.. Reading seq # 1: YPL219W_Sbay Reading seq # 2: YPL219W_Scer Reading seq # 3: YPL219W_Skud Reading seq # 4: YPL219W_Smik Reading seq # 5: YPL219W_Spar Sequences read.. Counting patterns.. # site patterns = 135 Counting frequencies.. 120 bytes for distance 21600 bytes for lkl0 17280 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.087493 0.003868 0.062260 0.052529 0.064731 0.120003 0.204892 0.161436 lnL0 = -1546.231273 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1546.231273 x= 0.08749 0.00387 0.06226 0.05253 0.06473 0.12000 0.20489 0.16144 1 h-lim-p 0.0003 0.2967 349.8040 1540.593713 8 0.0001 38 | 0/8 2 h-lim-p 0.0005 0.0043 41.8701 1540.251917 6 0.0004 62 | 0/8 3 h-lim-p 0.0010 0.0100 17.0349 1540.195521 5 0.0004 83 | 0/8 4 h-lim-p 0.0008 0.0285 9.0978 1540.183860 4 0.0004 102 | 0/8 5 h-lim-p 0.0011 0.0785 2.9371 1540.181081 4 0.0007 124 | 0/8 6 h-lim-p 0.0032 0.2565 0.6858 1540.180977 3 0.0005 146 | 0/8 7 h-lim-p 0.0039 2.6788 0.0834 1540.180975 1 0.0005 170 | 0/8 8 h-lim-p 0.0839 20.0000 0.0005 1540.180648 0 1.3430 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1540.180594 3 1.4879 222 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1540.180584 2 1.6492 248 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1540.180584 0 1.0938 268 | 0/8 12 h-lim-p 1.5432 20.0000 0.0000 1540.180584 0 0.7716 288 | 0/8 13 h-lim-p 0.5489 20.0000 0.0000 1540.180584 0 0.0686 310 | 0/8 14 h-lim-p 0.0244 20.0000 0.0000 1540.180584 0 0.0107 330 | 0/8 15 h-lim-p 0.0048 20.0000 0.0001 1540.180584 0 0.0000 369 | 0/8 16 h-lim-p 0.0000 20.0000 0.0004 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1540.180584 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1540.180584 Node 7: lnL = -1540.180584 Node 8: lnL = -1540.180584 Node 9: lnL = -1540.180584 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 862 Sequential format.. Reading seq # 1: YPL222W_Sbay Reading seq # 2: YPL222W_Scer Reading seq # 3: YPL222W_Skud Reading seq # 4: YPL222W_Smik Reading seq # 5: YPL222W_Spar Sequences read.. Counting patterns.. # site patterns = 346 Counting frequencies.. 120 bytes for distance 55360 bytes for lkl0 44288 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.128251 0.034253 0.073842 0.116074 0.084334 0.234138 0.277497 0.244965 lnL0 = -3890.932560 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3890.932560 x= 0.12825 0.03425 0.07384 0.11607 0.08433 0.23414 0.27750 0.24496 1 h-lim-p 0.0036 0.0288 122.2788 3889.464327 2 0.0002 29 | 0/8 2 h-lim-p 0.0004 0.0029 34.2386 3889.337771 7 0.0002 60 | 0/8 3 h-lim-p 0.0006 0.0053 13.0617 3889.306116 6 0.0004 85 | 0/8 4 h-lim-p 0.0007 0.0202 7.5579 3889.297426 6 0.0004 112 | 0/8 5 h-lim-p 0.0019 0.1776 1.5878 3889.296615 4 0.0007 133 | 0/8 6 h-lim-p 0.0074 0.3782 0.1467 3889.296611 0 0.0004 148 | 0/8 7 h-lim-p 0.0024 12.6485 0.0249 3889.296609 0 0.0021 168 | 0/8 8 h-lim-p 0.0272 20.0000 0.0019 3889.295840 0 0.3261 191 | 0/8 9 h-lim-p 2.2435 20.0000 0.0003 3889.295829 0 0.9815 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3889.295829 0 1.0938 231 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3889.295829 0 1.0938 251 | 0/8 12 h-lim-p 0.7726 20.0000 0.0000 3889.295829 0 1.5453 272 | 0/8 13 h-lim-p 0.0139 20.0000 0.0011 3889.295829 0 0.0000 317 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -3889.295829 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3889.295829 Node 7: lnL = -3889.295829 Node 8: lnL = -3889.295829 Node 9: lnL = -3889.295829 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 890 Sequential format.. Reading seq # 1: YPL223C_Sbay Reading seq # 2: YPL223C_Scer Reading seq # 3: YPL223C_Skud Reading seq # 4: YPL223C_Smik Reading seq # 5: YPL223C_Spar Sequences read.. Counting patterns.. # site patterns = 359 Counting frequencies.. 120 bytes for distance 57440 bytes for lkl0 45952 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.130899 0.071661 0.065728 0.109456 0.087091 0.220897 0.273567 0.250524 lnL0 = -4045.350622 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4045.350622 x= 0.13090 0.07166 0.06573 0.10946 0.08709 0.22090 0.27357 0.25052 1 h-lim-p 0.0047 0.9232 131.2473 4043.898026 8 0.0002 47 | 0/8 2 h-lim-p 0.0004 0.0036 28.3446 4043.810841 4 0.0002 67 | 0/8 3 h-lim-p 0.0009 0.0235 7.0922 4043.801184 2 0.0004 83 | 0/8 4 h-lim-p 0.0009 0.0722 3.3584 4043.799331 3 0.0004 101 | 0/8 5 h-lim-p 0.0013 0.3969 1.0008 4043.799060 2 0.0006 117 | 0/8 6 h-lim-p 0.0027 0.4410 0.2210 4043.799051 1 0.0003 133 | 0/8 7 h-lim-p 0.0087 20.0000 0.0083 4043.799050 1 0.0043 156 | 0/8 8 h-lim-p 0.0137 20.0000 0.0026 4043.798767 0 0.1647 179 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4043.798757 1 0.9961 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4043.798757 0 1.0938 221 | 0/8 11 h-lim-p 0.9939 20.0000 0.0000 4043.798757 0 1.4908 241 | 0/8 12 h-lim-p 0.9598 20.0000 0.0000 4043.798757 0 0.8398 261 | 0/8 13 h-lim-p 0.0030 20.0000 0.0037 4043.798757 0 0.0011 282 | 0/8 14 h-lim-p 0.0008 20.0000 0.0049 4043.798757 0 0.0000 319 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 4043.798757 0 0.0000 351 Out... lnL = -4043.798757 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4043.798757 Node 7: lnL = -4043.798757 Node 8: lnL = -4043.798757 Node 9: lnL = -4043.798757 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 586 Sequential format.. Reading seq # 1: YPL224C_Sbay Reading seq # 2: YPL224C_Scer Reading seq # 3: YPL224C_Skud Reading seq # 4: YPL224C_Smik Reading seq # 5: YPL224C_Spar Sequences read.. Counting patterns.. # site patterns = 208 Counting frequencies.. 120 bytes for distance 33280 bytes for lkl0 26624 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.105619 0.000381 0.054161 0.078263 0.063927 0.177768 0.228754 0.192509 lnL0 = -2398.916801 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2398.916801 x= 0.10562 0.00038 0.05416 0.07826 0.06393 0.17777 0.22875 0.19251 1 h-lim-p 0.0010 0.4723 218.3071 2396.628438 3 0.0001 30 | 0/8 2 h-lim-p 0.0003 0.0027 23.2953 2396.554225 6 0.0003 53 | 0/8 3 h-lim-p 0.0007 0.0486 9.1034 2396.537970 5 0.0004 77 | 0/8 4 h-lim-p 0.0014 0.0418 2.8699 2396.537131 4 0.0002 100 | 0/8 5 h-lim-p 0.0005 0.1965 1.3981 2396.536765 2 0.0005 116 | 0/8 6 h-lim-p 0.0008 0.1689 0.7991 2396.536712 3 0.0002 135 | 0/8 7 h-lim-p 0.0259 20.0000 0.0067 2396.536712 0 0.0028 157 | 0/8 8 h-lim-p 0.0343 20.0000 0.0006 2396.536611 0 0.5495 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2396.536600 1 0.9961 203 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2396.536600 0 1.2500 223 | 0/8 11 h-lim-p 1.4791 20.0000 0.0000 2396.536600 0 0.0025 251 | 0/8 12 h-lim-p 0.0008 20.0000 0.0000 2396.536600 0 0.0000 280 | 0/8 13 h-lim-p 0.0000 20.0000 0.0013 2396.536600 0 0.0000 315 | 0/8 14 h-lim-p 0.0000 20.0000 0.0013 2396.536600 0 0.0000 340 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 .. | 0/8 16 h-lim-p 0.0000 20.0000 0.0013 2396.536600 0 0.0000 403 | 0/8 17 h-lim-p 0.0000 20.0000 0.0006 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0013 | 0/8 19 h-lim-p 0.0000 20.0000 0.0013 Out... lnL = -2396.536600 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2396.536600 Node 7: lnL = -2396.536600 Node 8: lnL = -2396.536600 Node 9: lnL = -2396.536600 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 709 Sequential format.. Reading seq # 1: YPL225W_Sbay Reading seq # 2: YPL225W_Scer Reading seq # 3: YPL225W_Skud Reading seq # 4: YPL225W_Smik Reading seq # 5: YPL225W_Spar Sequences read.. Counting patterns.. # site patterns = 225 Counting frequencies.. 120 bytes for distance 36000 bytes for lkl0 28800 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.080806 0.048256 0.051622 0.120440 0.063079 0.220778 0.207283 0.176082 lnL0 = -3119.494954 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3119.494954 x= 0.08081 0.04826 0.05162 0.12044 0.06308 0.22078 0.20728 0.17608 1 h-lim-p 0.0003 0.0024 149.1944 3117.915828 7 0.0002 39 | 0/8 2 h-lim-p 0.0005 0.0037 22.0205 3117.867045 5 0.0002 60 | 0/8 3 h-lim-p 0.0004 0.0354 10.2601 3117.857297 4 0.0002 82 | 0/8 4 h-lim-p 0.0008 0.0866 2.8758 3117.855691 4 0.0004 103 | 0/8 5 h-lim-p 0.0037 2.0131 0.3344 3117.855671 1 0.0004 119 | 0/8 6 h-lim-p 0.0021 2.1093 0.0593 3117.855670 0 0.0005 140 | 0/8 7 h-lim-p 0.0016 15.2800 0.0169 3117.855670 0 0.0007 160 | 0/8 8 h-lim-p 0.2164 20.0000 0.0001 3117.855661 0 0.8657 182 | 0/8 9 h-lim-p 1.5362 20.0000 0.0000 3117.855661 0 1.3442 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3117.855661 0 1.0938 222 | 0/8 11 h-lim-p 0.5317 20.0000 0.0000 3117.855661 0 2.1266 244 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3117.855661 0 0.0085 271 | 0/8 13 h-lim-p 0.0014 20.0000 0.0001 3117.855661 0 0.0014 291 | 0/8 14 h-lim-p 0.0003 20.0000 0.0003 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0021 | 0/8 16 h-lim-p 0.0000 20.0000 0.0021 Out... lnL = -3117.855661 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3117.855661 Node 7: lnL = -3117.855661 Node 8: lnL = -3117.855661 Node 9: lnL = -3117.855661 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 629 Sequential format.. Reading seq # 1: YPL227C_Sbay Reading seq # 2: YPL227C_Scer Reading seq # 3: YPL227C_Skud Reading seq # 4: YPL227C_Smik Reading seq # 5: YPL227C_Spar Sequences read.. Counting patterns.. # site patterns = 176 Counting frequencies.. 120 bytes for distance 28160 bytes for lkl0 22528 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.053958 0.044412 0.071831 0.064443 0.067524 0.120102 0.137814 0.123341 lnL0 = -2454.369480 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2454.369480 x= 0.05396 0.04441 0.07183 0.06444 0.06752 0.12010 0.13781 0.12334 1 h-lim-p 0.0008 0.0062 159.6449 2452.544688 7 0.0002 36 | 0/8 2 h-lim-p 0.0008 0.0063 24.1048 2452.463911 6 0.0003 61 | 0/8 3 h-lim-p 0.0005 0.0125 13.4380 2452.451543 6 0.0002 89 | 0/8 4 h-lim-p 0.0011 0.0509 2.1772 2452.451082 3 0.0002 108 | 0/8 5 h-lim-p 0.0012 0.3000 0.3650 2452.451068 2 0.0002 125 | 0/8 6 h-lim-p 0.0019 5.9691 0.0458 2452.451067 0 0.0004 146 | 0/8 7 h-lim-p 0.0026 20.0000 0.0072 2452.451067 0 0.0006 167 | 0/8 8 h-lim-p 0.0448 20.0000 0.0001 2452.451057 0 0.7175 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2452.451056 0 1.0938 211 | 0/8 10 h-lim-p 0.6277 20.0000 0.0000 2452.451056 0 1.8832 232 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2452.451056 0 0.5469 253 | 0/8 12 h-lim-p 0.1037 20.0000 0.0001 2452.451056 0 0.0049 277 | 0/8 13 h-lim-p 0.0014 20.0000 0.0002 2452.451056 0 0.0000 305 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 2452.451056 0 0.0000 336 Out... lnL = -2452.451056 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2452.451056 Node 7: lnL = -2452.451056 Node 8: lnL = -2452.451056 Node 9: lnL = -2452.451056 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 770 Sequential format.. Reading seq # 1: YPL228W_Sbay Reading seq # 2: YPL228W_Scer Reading seq # 3: YPL228W_Skud Reading seq # 4: YPL228W_Smik Reading seq # 5: YPL228W_Spar Sequences read.. Counting patterns.. # site patterns = 239 Counting frequencies.. 120 bytes for distance 38240 bytes for lkl0 30592 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.075035 0.093296 0.048770 0.085318 0.122375 0.322173 0.243646 0.183175 lnL0 = -3016.571799 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3016.571799 x= 0.07504 0.09330 0.04877 0.08532 0.12237 0.32217 0.24365 0.18318 1 h-lim-p 0.0005 0.0037 93.5775 3015.506134 9 0.0003 42 | 0/8 2 h-lim-p 0.0004 0.0033 41.1080 3015.199959 6 0.0004 68 | 0/8 3 h-lim-p 0.0003 0.0026 39.5879 3014.893094 0 0.0006 81 | 0/8 4 h-lim-p 0.0010 0.0089 24.3234 3014.836909 7 0.0003 114 | 0/8 5 h-lim-p 0.0014 0.0592 5.3543 3014.805920 0 0.0029 127 | 0/8 6 h-lim-p 0.0034 0.0857 4.6099 3014.802084 5 0.0006 153 | 0/8 7 h-lim-p 0.0018 0.2091 1.4677 3014.801600 4 0.0006 177 | 0/8 8 h-lim-p 0.2965 20.0000 0.0027 3014.797398 0 1.1858 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0006 3014.797291 1 0.9961 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3014.797290 0 1.0938 233 | 0/8 11 h-lim-p 2.2280 20.0000 0.0000 3014.797290 0 0.9747 253 | 0/8 12 h-lim-p 0.8519 20.0000 0.0000 3014.797290 0 0.0058 279 | 0/8 13 h-lim-p 0.0008 20.0000 0.0001 3014.797290 0 0.0000 302 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 3014.797290 0 0.0000 329 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 3014.797290 0 0.0000 364 Out... lnL = -3014.797290 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3014.797290 Node 7: lnL = -3014.797290 Node 8: lnL = -3014.797290 Node 9: lnL = -3014.797290 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 871 Sequential format.. Reading seq # 1: YPL230W_Sbay Reading seq # 2: YPL230W_Scer Reading seq # 3: YPL230W_Skud Reading seq # 4: YPL230W_Smik Reading seq # 5: YPL230W_Spar Sequences read.. Counting patterns.. # site patterns = 226 Counting frequencies.. 120 bytes for distance 36160 bytes for lkl0 28928 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.113370 0.047983 0.047542 0.051442 0.050821 0.132091 0.122024 0.182477 lnL0 = -3325.758492 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3325.758492 x= 0.11337 0.04798 0.04754 0.05144 0.05082 0.13209 0.12202 0.18248 1 h-lim-p 0.0003 0.0024 158.8940 3324.415024 7 0.0001 37 | 0/8 2 h-lim-p 0.0003 0.0026 34.5734 3324.344699 6 0.0001 63 | 0/8 3 h-lim-p 0.0003 0.0074 16.5642 3324.330587 4 0.0001 85 | 0/8 4 h-lim-p 0.0003 0.0266 7.0571 3324.326902 5 0.0002 111 | 0/8 5 h-lim-p 0.0016 0.2628 0.8143 3324.326844 0 0.0002 125 | 0/8 6 h-lim-p 0.0003 0.3142 0.4330 3324.326832 0 0.0002 145 | 0/8 7 h-lim-p 0.0022 5.0283 0.0320 3324.326832 0 0.0005 166 | 0/8 8 h-lim-p 0.0888 20.0000 0.0002 3324.326728 0 1.0662 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3324.326727 0 1.0938 209 | 0/8 10 h-lim-p 1.5514 20.0000 0.0000 3324.326727 0 0.6787 229 | 0/8 11 h-lim-p 0.5239 20.0000 0.0000 3324.326727 0 0.0015 257 | 0/8 12 h-lim-p 0.0008 20.0000 0.0000 3324.326727 0 0.0000 287 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0041 3324.326727 0 0.0000 348 | 0/8 15 h-lim-p 0.0000 20.0000 0.0011 3324.326727 0 0.0005 373 | 0/8 16 h-lim-p 0.0012 20.0000 0.0004 3324.326727 0 0.0000 398 | 0/8 17 h-lim-p 0.0001 20.0000 0.0001 3324.326727 0 0.0027 423 | 0/8 18 h-lim-p 0.0036 20.0000 0.0001 3324.326727 0 0.0001 448 | 0/8 19 h-lim-p 0.0000 20.0000 0.0021 3324.326727 0 0.0006 474 | 0/8 20 h-lim-p 0.0002 20.0000 0.0065 3324.326727 0 0.0000 500 | 0/8 21 h-lim-p 0.0002 20.0000 0.0001 .. | 0/8 22 h-lim-p 0.0000 20.0000 0.0061 3324.326727 0 0.0000 570 | 0/8 23 h-lim-p 0.0000 20.0000 0.0023 .. | 0/8 24 h-lim-p 0.0000 20.0000 0.0061 3324.326727 0 0.0000 634 | 0/8 25 h-lim-p 0.0000 20.0000 0.0011 .. | 0/8 26 h-lim-p 0.0000 20.0000 0.0061 | 0/8 27 h-lim-p 0.0000 20.0000 0.0061 Out... lnL = -3324.326727 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3324.326727 Node 7: lnL = -3324.326727 Node 8: lnL = -3324.326727 Node 9: lnL = -3324.326727 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 480 Sequential format.. Reading seq # 1: YPL232W_Sbay Reading seq # 2: YPL232W_Scer Reading seq # 3: YPL232W_Skud Reading seq # 4: YPL232W_Smik Reading seq # 5: YPL232W_Spar Sequences read.. Counting patterns.. # site patterns = 155 Counting frequencies.. 120 bytes for distance 24800 bytes for lkl0 19840 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.082755 0.045057 0.036616 0.068342 0.065345 0.091958 0.124301 0.143449 lnL0 = -1771.177835 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1771.177835 x= 0.08276 0.04506 0.03662 0.06834 0.06534 0.09196 0.12430 0.14345 1 h-lim-p 0.0004 0.0033 134.0627 1769.421928 4 0.0002 31 | 0/8 2 h-lim-p 0.0002 0.0017 29.5416 1769.326577 6 0.0002 57 | 0/8 3 h-lim-p 0.0008 0.0206 7.7291 1769.316731 3 0.0004 75 | 0/8 4 h-lim-p 0.0008 0.0380 3.3458 1769.315526 5 0.0003 100 | 0/8 5 h-lim-p 0.0007 0.1510 1.1319 1769.315311 2 0.0004 117 | 0/8 6 h-lim-p 0.0030 0.6591 0.1475 1769.315308 1 0.0003 133 | 0/8 7 h-lim-p 0.0020 5.9294 0.0224 1769.315308 0 0.0009 153 | 0/8 8 h-lim-p 0.0550 20.0000 0.0004 1769.315160 0 0.8807 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1769.315159 0 1.0938 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1769.315159 0 1.0938 217 | 0/8 11 h-lim-p 1.7488 20.0000 0.0000 1769.315159 0 2.6231 237 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1769.315159 0 0.1367 260 | 0/8 13 h-lim-p 0.0275 20.0000 0.0000 1769.315159 0 0.0003 286 Out... lnL = -1769.315159 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1769.315159 Node 7: lnL = -1769.315159 Node 8: lnL = -1769.315159 Node 9: lnL = -1769.315159 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 579 Sequential format.. Reading seq # 1: YPL236C_Sbay Reading seq # 2: YPL236C_Scer Reading seq # 3: YPL236C_Skud Reading seq # 4: YPL236C_Smik Reading seq # 5: YPL236C_Spar Sequences read.. Counting patterns.. # site patterns = 224 Counting frequencies.. 120 bytes for distance 35840 bytes for lkl0 28672 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.035494 0.139177 0.076052 0.139270 0.089698 0.150578 0.168528 0.125104 lnL0 = -2517.344743 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2517.344743 x= 0.03549 0.13918 0.07605 0.13927 0.08970 0.15058 0.16853 0.12510 1 h-lim-p 0.0013 0.0106 90.2956 2516.320634 5 0.0003 33 | 0/8 2 h-lim-p 0.0012 0.0113 19.2241 2516.241847 6 0.0004 58 | 0/8 3 h-lim-p 0.0014 0.0496 6.0197 2516.235122 5 0.0004 83 | 0/8 4 h-lim-p 0.0034 0.4243 0.7196 2516.234977 3 0.0006 103 | 0/8 5 h-lim-p 0.0114 3.3818 0.0351 2516.234977 0 0.0006 126 | 0/8 6 h-lim-p 0.0021 15.6183 0.0102 2516.234977 0 0.0005 147 | 0/8 7 h-lim-p 0.0123 20.0000 0.0004 2516.234976 0 0.0736 169 | 0/8 8 h-lim-p 0.0024 20.0000 0.0119 2516.234967 0 0.0072 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2516.234967 0 1.0938 210 | 0/8 10 h-lim-p 1.0485 20.0000 0.0000 2516.234967 0 0.9174 230 | 0/8 11 h-lim-p 0.1428 20.0000 0.0001 2516.234967 0 0.0045 254 | 0/8 12 h-lim-p 0.0012 20.0000 0.0006 2516.234967 0 0.0006 274 | 0/8 13 h-lim-p 0.0002 20.0000 0.0014 2516.234967 0 0.0001 295 | 0/8 14 h-lim-p 0.0002 20.0000 0.0004 2516.234967 0 0.0000 331 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 2516.234967 0 0.0000 351 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 2516.234967 0 0.0000 377 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 2516.234967 0 0.0000 401 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 2516.234967 0 0.0000 436 | 0/8 19 h-lim-p 0.0000 20.0000 0.0002 | 0/8 20 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -2516.234967 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2516.234967 Node 7: lnL = -2516.234967 Node 8: lnL = -2516.234967 Node 9: lnL = -2516.234967 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 829 Sequential format.. Reading seq # 1: YPL239W_Sbay Reading seq # 2: YPL239W_Scer Reading seq # 3: YPL239W_Skud Reading seq # 4: YPL239W_Smik Reading seq # 5: YPL239W_Spar Sequences read.. Counting patterns.. # site patterns = 332 Counting frequencies.. 120 bytes for distance 53120 bytes for lkl0 42496 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.120247 0.034474 0.075057 0.153002 0.074143 0.245686 0.281952 0.230565 lnL0 = -3956.905490 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3956.905490 x= 0.12025 0.03447 0.07506 0.15300 0.07414 0.24569 0.28195 0.23057 1 h-lim-p 0.0023 0.0768 186.1888 3953.944352 5 0.0002 36 | 0/8 2 h-lim-p 0.0007 0.0058 36.1300 3953.745739 6 0.0003 59 | 0/8 3 h-lim-p 0.0005 0.0088 22.1461 3953.676171 6 0.0004 86 | 0/8 4 h-lim-p 0.0010 0.0335 8.2042 3953.665092 4 0.0004 106 | 0/8 5 h-lim-p 0.0026 0.2870 1.2593 3953.664570 3 0.0007 125 | 0/8 6 h-lim-p 0.0065 1.5413 0.1320 3953.664567 0 0.0004 140 | 0/8 7 h-lim-p 0.0046 19.9869 0.0102 3953.664559 0 0.0093 161 | 0/8 8 h-lim-p 0.0093 20.0000 0.0102 3953.663583 0 0.0743 184 | 0/8 9 h-lim-p 1.9907 20.0000 0.0004 3953.663567 0 0.9954 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3953.663566 0 1.0938 224 | 0/8 11 h-lim-p 1.1842 20.0000 0.0000 3953.663566 0 1.0362 244 | 0/8 12 h-lim-p 0.7775 20.0000 0.0000 3953.663566 0 0.0364 268 | 0/8 13 h-lim-p 0.0000 0.3236 0.5532 3953.663566 0 0.0000 295 | 0/8 14 h-lim-p 0.0007 20.0000 0.0000 3953.663566 0 0.0000 318 | 0/8 15 h-lim-p 0.0012 20.0000 0.0000 3953.663566 0 0.0000 350 Out... lnL = -3953.663566 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3953.663566 Node 7: lnL = -3953.663566 Node 8: lnL = -3953.663566 Node 9: lnL = -3953.663566 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 279 Sequential format.. Reading seq # 1: YPL242C_Sbay Reading seq # 2: YPL242C_Scer Reading seq # 3: YPL242C_Skud Reading seq # 4: YPL242C_Smik Reading seq # 5: YPL242C_Spar Sequences read.. Counting patterns.. # site patterns = 127 Counting frequencies.. 120 bytes for distance 20320 bytes for lkl0 16256 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.060231 0.035914 0.072845 0.121654 0.066005 0.198021 0.150703 0.138242 lnL0 = -1178.069688 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1178.069688 x= 0.06023 0.03591 0.07285 0.12165 0.06601 0.19802 0.15070 0.13824 1 h-lim-p 0.0004 0.0034 91.0081 1176.703138 7 0.0004 36 | 0/8 2 h-lim-p 0.0009 0.0070 18.0266 1176.603820 7 0.0006 64 | 0/8 3 h-lim-p 0.0019 0.0921 5.9094 1176.595750 5 0.0005 87 | 0/8 4 h-lim-p 0.0010 0.0827 3.1209 1176.592941 5 0.0007 109 | 0/8 5 h-lim-p 0.0037 0.2665 0.6215 1176.592807 3 0.0007 128 | 0/8 6 h-lim-p 0.0056 1.8323 0.0813 1176.592803 1 0.0011 151 | 0/8 7 h-lim-p 0.0056 16.0207 0.0162 1176.592801 1 0.0028 174 | 0/8 8 h-lim-p 0.0235 20.0000 0.0019 1176.592385 0 0.3760 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1176.592379 1 0.9961 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1176.592379 0 2.1875 240 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1176.592379 0 0.5469 261 | 0/8 12 h-lim-p 0.0631 20.0000 0.0000 1176.592379 0 0.0138 282 | 0/8 13 h-lim-p 0.0045 20.0000 0.0000 1176.592379 0 0.0045 302 | 0/8 14 h-lim-p 0.0026 20.0000 0.0001 1176.592379 0 0.0000 337 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 1176.592379 0 0.0000 365 Out... lnL = -1176.592379 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1176.592379 Node 7: lnL = -1176.592379 Node 8: lnL = -1176.592379 Node 9: lnL = -1176.592379 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 514 Sequential format.. Reading seq # 1: YPL243W_Sbay Reading seq # 2: YPL243W_Scer Reading seq # 3: YPL243W_Skud Reading seq # 4: YPL243W_Smik Reading seq # 5: YPL243W_Spar Sequences read.. Counting patterns.. # site patterns = 169 Counting frequencies.. 120 bytes for distance 27040 bytes for lkl0 21632 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.099002 0.043979 0.059944 0.102173 0.076093 0.134314 0.172052 0.178776 lnL0 = -2161.432209 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2161.432209 x= 0.09900 0.04398 0.05994 0.10217 0.07609 0.13431 0.17205 0.17878 1 h-lim-p 0.0003 0.0027 89.9277 2160.546722 9 0.0002 45 | 0/8 2 h-lim-p 0.0013 0.0111 15.4105 2160.511490 3 0.0003 64 | 0/8 3 h-lim-p 0.0009 0.0447 5.0056 2160.508470 5 0.0003 89 | 0/8 4 h-lim-p 0.0009 0.1166 1.4475 2160.508153 4 0.0003 111 | 0/8 5 h-lim-p 0.0016 0.7425 0.3020 2160.508131 2 0.0005 129 | 0/8 6 h-lim-p 0.0022 1.3288 0.0725 2160.508130 0 0.0005 150 | 0/8 7 h-lim-p 0.0016 13.1070 0.0218 2160.508130 0 0.0007 170 | 0/8 8 h-lim-p 0.1065 20.0000 0.0001 2160.508093 0 0.8517 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2160.508092 0 1.0938 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2160.508092 0 1.0938 233 | 0/8 11 h-lim-p 0.9808 20.0000 0.0000 2160.508092 0 1.9617 254 | 0/8 12 h-lim-p 1.3128 20.0000 0.0000 2160.508092 0 0.0205 279 | 0/8 13 h-lim-p 0.0004 20.0000 0.0005 2160.508092 0 0.0000 317 | 0/8 14 h-lim-p 0.0000 20.0000 0.0005 | 0/8 15 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -2160.508092 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2160.508092 Node 7: lnL = -2160.508092 Node 8: lnL = -2160.508092 Node 9: lnL = -2160.508092 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 334 Sequential format.. Reading seq # 1: YPL245W_Sbay Reading seq # 2: YPL245W_Scer Reading seq # 3: YPL245W_Skud Reading seq # 4: YPL245W_Smik Reading seq # 5: YPL245W_Spar Sequences read.. Counting patterns.. # site patterns = 124 Counting frequencies.. 120 bytes for distance 19840 bytes for lkl0 15872 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.110872 0.039624 0.062983 0.103109 0.058508 0.148104 0.125262 0.187993 lnL0 = -1304.589308 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1304.589308 x= 0.11087 0.03962 0.06298 0.10311 0.05851 0.14810 0.12526 0.18799 1 h-lim-p 0.0004 0.0028 84.4847 1303.356352 8 0.0004 43 | 0/8 2 h-lim-p 0.0005 0.0044 28.2073 1303.156282 5 0.0005 65 | 0/8 3 h-lim-p 0.0016 0.0199 9.7955 1303.139759 6 0.0004 93 | 0/8 4 h-lim-p 0.0020 0.0699 1.9523 1303.139055 3 0.0004 112 | 0/8 5 h-lim-p 0.0009 0.2850 0.8448 1303.138928 2 0.0004 128 | 0/8 6 h-lim-p 0.0019 1.4428 0.1854 1303.138917 2 0.0007 152 | 0/8 7 h-lim-p 0.0126 20.0000 0.0110 1303.138916 1 0.0031 175 | 0/8 8 h-lim-p 0.0190 20.0000 0.0018 1303.138643 0 0.3032 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1303.138643 0 1.0938 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1303.138643 0 2.1875 239 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1303.138643 0 1.0938 259 | 0/8 12 h-lim-p 0.4100 20.0000 0.0000 1303.138643 0 3.2802 282 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1303.138643 0 0.0586 307 | 0/8 14 h-lim-p 0.0033 20.0000 0.0000 1303.138643 0 0.0016 327 | 0/8 15 h-lim-p 0.0007 20.0000 0.0000 1303.138643 0 0.0003 347 | 0/8 16 h-lim-p 0.0001 20.0000 0.0001 1303.138643 0 0.0000 369 | 0/8 17 h-lim-p 0.0004 20.0000 0.0000 1303.138643 0 0.0000 402 Out... lnL = -1303.138643 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1303.138643 Node 7: lnL = -1303.138643 Node 8: lnL = -1303.138643 Node 9: lnL = -1303.138643 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 364 Sequential format.. Reading seq # 1: YPL247C_Sbay Reading seq # 2: YPL247C_Scer Reading seq # 3: YPL247C_Skud Reading seq # 4: YPL247C_Smik Reading seq # 5: YPL247C_Spar Sequences read.. Counting patterns.. # site patterns = 120 Counting frequencies.. 120 bytes for distance 19200 bytes for lkl0 15360 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.064282 0.055909 0.031573 0.064244 0.072498 0.103882 0.131093 0.124361 lnL0 = -1314.029632 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1314.029632 x= 0.06428 0.05591 0.03157 0.06424 0.07250 0.10388 0.13109 0.12436 1 h-lim-p 0.0007 0.0059 125.5098 1312.600040 9 0.0002 43 | 0/8 2 h-lim-p 0.0006 0.0050 29.4904 1312.428854 8 0.0004 73 | 0/8 3 h-lim-p 0.0018 0.0291 6.6932 1312.420772 5 0.0004 97 | 0/8 4 h-lim-p 0.0011 0.0608 2.2598 1312.419847 5 0.0004 120 | 0/8 5 h-lim-p 0.0014 0.2483 0.6268 1312.419740 3 0.0006 138 | 0/8 6 h-lim-p 0.0075 3.1440 0.0483 1312.419740 0 0.0005 161 | 0/8 7 h-lim-p 0.0042 20.0000 0.0054 1312.419739 0 0.0042 181 | 0/8 8 h-lim-p 0.0100 20.0000 0.0023 1312.419596 0 0.1605 205 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1312.419582 2 0.9961 229 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1312.419582 0 1.0938 249 | 0/8 11 h-lim-p 1.0821 20.0000 0.0000 1312.419582 015.4852 273 | 0/8 12 h-lim-p 0.1537 20.0000 0.0010 1312.419582 0 0.0384 294 | 0/8 13 h-lim-p 0.0077 18.2808 0.0049 1312.419582 0 0.0019 315 | 0/8 14 h-lim-p 0.0009 8.2880 0.0107 1312.419582 0 0.0000 339 | 0/8 15 h-lim-p 0.0004 20.0000 0.0007 1312.419582 0 0.0001 360 | 0/8 16 h-lim-p 0.0004 20.0000 0.0002 1312.419582 0 0.0001 381 | 0/8 17 h-lim-p 0.0004 20.0000 0.0000 1312.419582 0 0.0000 413 | 0/8 18 h-lim-p 0.0000 20.0000 0.0010 1312.419582 0 0.0000 439 | 0/8 19 h-lim-p 0.0000 20.0000 0.0004 1312.419582 0 0.0019 466 | 0/8 20 h-lim-p 0.0084 20.0000 0.0001 1312.419582 0 0.0000 500 | 0/8 21 h-lim-p 0.0000 20.0000 0.0000 1312.419582 0 0.0000 526 | 0/8 22 h-lim-p 0.0000 20.0000 0.0019 | 0/8 23 h-lim-p 0.0000 20.0000 0.0019 Out... lnL = -1312.419582 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1312.419582 Node 7: lnL = -1312.419582 Node 8: lnL = -1312.419582 Node 9: lnL = -1312.419582 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 467 Sequential format.. Reading seq # 1: YPL249C-A_Sbay Reading seq # 2: YPL249C-A_Scer Reading seq # 3: YPL249C-A_Skud Reading seq # 4: YPL249C-A_Smik Reading seq # 5: YPL249C-A_Spar Sequences read.. Counting patterns.. # site patterns = 218 Counting frequencies.. 120 bytes for distance 34880 bytes for lkl0 27904 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.050313 0.010605 0.000060 0.957728 0.204935 0.236419 0.104007 0.205619 lnL0 = -2076.876457 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2076.876457 x= 0.05031 0.01060 0.00006 0.95773 0.20494 0.23642 0.10401 0.20562 1 h-lim-p 0.0000 0.0000 170.3173 2076.809402 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0002 326.4951 2071.499440 m 0.0002 36 | 1/8 3 h-lim-p 0.0002 0.0015 148.3261 2068.677214 0 0.0004 49 | 1/8 4 h-lim-p 0.0018 0.0176 30.9511 2067.721305 0 0.0027 61 | 1/8 5 h-lim-p 0.0011 0.0163 77.2987 2065.103945 0 0.0032 74 | 1/8 6 h-lim-p 0.0013 0.0105 11.4136 2065.058250 7 0.0007 103 | 1/8 7 h-lim-p 0.0392 1.3336 0.2102 2060.491268 0 0.4708 118 | 0/8 8 h-lim-p 0.0231 0.2093 4.2821 2060.484131 2 0.0007 145 | 0/8 9 h-lim-p 0.0347 0.3010 0.0836 2059.603978 m 0.3010 158 | 0/8 10 h-lim-p -0.0000 -0.0000 0.0433 h-lim-p: -3.88388221e-18 -3.10710577e-17 4.32908410e-02 2059.603978 .. | 0/8 11 h-lim-p 0.0000 0.6569 78.7119 2058.917369 0 0.0003 199 | 0/8 12 h-lim-p 0.0000 0.0000 14.1990 2058.916723 m 0.0000 211 | 1/8 13 h-lim-p 0.0000 0.0174 12.1934 2058.905395 0 0.0003 228 | 1/8 14 h-lim-p 0.0018 0.0538 2.1380 2058.869880 0 0.0037 241 | 1/8 15 h-lim-p 0.0012 0.0221 6.7587 2058.851250 6 0.0007 269 | 1/8 16 h-lim-p 0.0019 0.0710 2.3463 2058.848981 2 0.0009 285 | 1/8 17 h-lim-p 0.0014 0.8311 1.4778 2058.840645 0 0.0115 300 | 1/8 18 h-lim-p 2.5000 20.0000 0.0019 2058.832714 6 1.7375 327 | 1/8 19 h-lim-p 2.5000 20.0000 0.0013 2058.831665 3 1.2341 352 | 1/8 20 h-lim-p 2.5000 20.0000 0.0000 2058.831664 0 1.0938 371 | 1/8 21 h-lim-p 2.0409 20.0000 0.0000 2058.831664 0 1.0205 390 | 1/8 22 h-lim-p 0.8852 20.0000 0.0000 2058.831664 0 0.8852 409 | 1/8 23 h-lim-p 0.0019 11.1084 0.0070 2058.831664 0 0.0005 429 | 1/8 24 h-lim-p 0.0005 20.0000 0.0068 2058.831664 0 0.0004 448 | 1/8 25 h-lim-p 0.0005 20.0000 0.0063 2058.831664 0 0.0002 467 | 1/8 26 h-lim-p 0.0003 20.0000 0.0037 2058.831664 0 0.0000 489 | 1/8 27 h-lim-p 0.0001 20.0000 0.0010 2058.831664 0 0.0000 516 | 1/8 28 h-lim-p 0.0002 20.0000 0.0000 2058.831664 0 0.0000 547 Out... lnL = -2058.831664 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2058.831664 Node 7: lnL = -2058.831664 Node 8: lnL = -2058.831664 Node 9: lnL = -2058.831664 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 921 Sequential format.. Reading seq # 1: YPL250C_Sbay Reading seq # 2: YPL250C_Scer Reading seq # 3: YPL250C_Skud Reading seq # 4: YPL250C_Smik Reading seq # 5: YPL250C_Spar Sequences read.. Counting patterns.. # site patterns = 320 Counting frequencies.. 120 bytes for distance 51200 bytes for lkl0 40960 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.128096 0.011331 0.061615 0.087413 0.065008 0.152232 0.154193 0.206532 lnL0 = -3597.526690 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3597.526690 x= 0.12810 0.01133 0.06161 0.08741 0.06501 0.15223 0.15419 0.20653 1 h-lim-p 0.0007 0.0295 329.0516 3593.298587 9 0.0001 44 | 0/8 2 h-lim-p 0.0003 0.0025 42.2538 3593.103187 6 0.0002 69 | 0/8 3 h-lim-p 0.0006 0.0280 16.3889 3593.073880 3 0.0002 87 | 0/8 4 h-lim-p 0.0018 0.1025 2.2409 3593.073191 4 0.0003 111 | 0/8 5 h-lim-p 0.0005 0.2413 1.3475 3593.073075 3 0.0002 131 | 0/8 6 h-lim-p 0.0105 9.4618 0.0211 3593.073075 0 0.0006 146 | 0/8 7 h-lim-p 0.0008 6.9349 0.0160 3593.073075 0 0.0003 166 | 0/8 8 h-lim-p 0.0392 20.0000 0.0001 3593.073059 0 0.9415 190 | 0/8 9 h-lim-p 1.6362 20.0000 0.0001 3593.073058 0 1.4317 210 | 0/8 10 h-lim-p 0.8201 20.0000 0.0001 3593.073058 0 0.7176 230 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3593.073058 0 1.0938 250 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3593.073058 0 2.1875 270 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 3593.073058 0 0.2734 292 | 0/8 14 h-lim-p 0.0303 20.0000 0.0000 3593.073058 0 0.0076 313 | 0/8 15 h-lim-p 0.0035 20.0000 0.0000 3593.073058 0 0.0013 334 | 0/8 16 h-lim-p 0.0006 20.0000 0.0000 3593.073058 0 0.0000 362 | 0/8 17 h-lim-p 0.0001 20.0000 0.0000 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0018 | 0/8 19 h-lim-p 0.0000 20.0000 0.0018 Out... lnL = -3593.073058 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3593.073058 Node 7: lnL = -3593.073058 Node 8: lnL = -3593.073058 Node 9: lnL = -3593.073058 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 458 Sequential format.. Reading seq # 1: YPL252C_Sbay Reading seq # 2: YPL252C_Scer Reading seq # 3: YPL252C_Skud Reading seq # 4: YPL252C_Smik Reading seq # 5: YPL252C_Spar Sequences read.. Counting patterns.. # site patterns = 178 Counting frequencies.. 120 bytes for distance 28480 bytes for lkl0 22784 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.083876 0.068869 0.001163 0.108616 0.077792 0.162437 0.115675 0.148146 lnL0 = -1749.090858 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1749.090858 x= 0.08388 0.06887 0.00116 0.10862 0.07779 0.16244 0.11568 0.14815 1 h-lim-p 0.0006 0.4043 250.5194 1747.757332 6 0.0001 35 | 0/8 2 h-lim-p 0.0005 0.0054 28.3963 1747.602776 4 0.0004 55 | 0/8 3 h-lim-p 0.0015 0.0211 7.1856 1747.594702 2 0.0003 72 | 0/8 4 h-lim-p 0.0011 0.0615 2.1434 1747.593866 4 0.0004 93 | 0/8 5 h-lim-p 0.0035 0.7523 0.2420 1747.593853 0 0.0004 107 | 0/8 6 h-lim-p 0.0021 2.5589 0.0501 1747.593853 0 0.0005 128 | 0/8 7 h-lim-p 0.0244 20.0000 0.0010 1747.593842 0 0.0974 150 | 0/8 8 h-lim-p 0.0027 0.8975 0.0349 1747.593718 0 0.0080 171 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1747.593702 2 1.2305 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1747.593702 0 1.2500 216 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1747.593702 0 0.5469 237 | 0/8 12 h-lim-p 0.3161 20.0000 0.0000 1747.593702 0 0.0025 263 | 0/8 13 h-lim-p 0.0014 20.0000 0.0000 1747.593702 0 0.0003 284 | 0/8 14 h-lim-p 0.0003 20.0000 0.0000 1747.593702 0 0.0000 318 | 0/8 15 h-lim-p 0.0000 20.0000 0.0044 | 0/8 16 h-lim-p 0.0000 20.0000 0.0044 Out... lnL = -1747.593702 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1747.593702 Node 7: lnL = -1747.593702 Node 8: lnL = -1747.593702 Node 9: lnL = -1747.593702 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 389 Sequential format.. Reading seq # 1: YPL253C_Sbay Reading seq # 2: YPL253C_Scer Reading seq # 3: YPL253C_Skud Reading seq # 4: YPL253C_Smik Reading seq # 5: YPL253C_Spar Sequences read.. Counting patterns.. # site patterns = 172 Counting frequencies.. 120 bytes for distance 27520 bytes for lkl0 22016 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.103541 0.072533 0.071306 0.131893 0.100723 0.256297 0.196778 0.200169 lnL0 = -1680.247487 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1680.247487 x= 0.10354 0.07253 0.07131 0.13189 0.10072 0.25630 0.19678 0.20017 1 h-lim-p 0.0005 0.0039 72.1353 1678.922927 1 0.0006 24 | 0/8 2 h-lim-p 0.0016 0.0126 18.9327 1678.753897 7 0.0010 54 | 0/8 3 h-lim-p 0.0019 0.0237 9.8371 1678.730777 7 0.0006 83 | 0/8 4 h-lim-p 0.0013 0.0462 4.4238 1678.725860 2 0.0006 99 | 0/8 5 h-lim-p 0.0298 1.5227 0.0924 1678.725823 2 0.0029 117 | 0/8 6 h-lim-p 0.0044 4.4336 0.0602 1678.725320 0 0.0176 139 | 0/8 7 h-lim-p 0.0044 0.6113 0.2421 1678.720699 0 0.0176 161 | 0/8 8 h-lim-p 0.0034 0.2415 1.2365 1678.716011 5 0.0026 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0010 1678.715468 2 0.9644 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1678.715468 0 1.0938 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1678.715468 0 1.0938 249 | 0/8 12 h-lim-p 1.1848 20.0000 0.0000 1678.715468 0 0.1481 271 | 0/8 13 h-lim-p 0.0452 20.0000 0.0000 1678.715468 0 0.0113 292 | 0/8 14 h-lim-p 0.0053 20.0000 0.0000 1678.715468 0 0.0002 316 | 0/8 15 h-lim-p 0.0004 20.0000 0.0000 1678.715468 0 0.0000 347 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1678.715468 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1678.715468 Node 7: lnL = -1678.715468 Node 8: lnL = -1678.715468 Node 9: lnL = -1678.715468 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 637 Sequential format.. Reading seq # 1: YPL254W_Sbay Reading seq # 2: YPL254W_Scer Reading seq # 3: YPL254W_Skud Reading seq # 4: YPL254W_Smik Reading seq # 5: YPL254W_Spar Sequences read.. Counting patterns.. # site patterns = 181 Counting frequencies.. 120 bytes for distance 28960 bytes for lkl0 23168 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.045749 0.113827 0.050497 0.086378 0.072104 0.135318 0.114760 0.110823 lnL0 = -2501.815309 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2501.815309 x= 0.04575 0.11383 0.05050 0.08638 0.07210 0.13532 0.11476 0.11082 1 h-lim-p 0.0002 0.0014 84.7049 2501.152611 6 0.0002 33 | 0/8 2 h-lim-p 0.0008 0.0062 13.2292 2501.132559 6 0.0002 61 | 0/8 3 h-lim-p 0.0007 0.0654 4.5645 2501.129818 4 0.0003 80 | 0/8 4 h-lim-p 0.0010 0.0813 1.3153 2501.129695 4 0.0002 104 | 0/8 5 h-lim-p 0.0009 0.7562 0.2289 2501.129688 2 0.0003 122 | 0/8 6 h-lim-p 0.0024 4.0271 0.0280 2501.129688 0 0.0003 144 | 0/8 7 h-lim-p 0.0024 20.0000 0.0031 2501.129688 0 0.0005 165 | 0/8 8 h-lim-p 0.1283 20.0000 0.0000 2501.129688 0 1.0263 188 | 0/8 9 h-lim-p 0.5496 20.0000 0.0000 2501.129688 0 0.4809 208 | 0/8 10 h-lim-p 0.2701 20.0000 0.0000 2501.129688 0 0.0084 232 | 0/8 11 h-lim-p 0.0036 20.0000 0.0001 2501.129688 0 0.0002 255 | 0/8 12 h-lim-p 0.0000 20.0000 0.0033 .. | 0/8 13 h-lim-p 0.0000 20.0000 0.0024 | 0/8 14 h-lim-p 0.0000 20.0000 0.0024 Out... lnL = -2501.129688 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2501.129688 Node 7: lnL = -2501.129688 Node 8: lnL = -2501.129688 Node 9: lnL = -2501.129688 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 836 Sequential format.. Reading seq # 1: YPL256C_Sbay Reading seq # 2: YPL256C_Scer Reading seq # 3: YPL256C_Skud Reading seq # 4: YPL256C_Smik Reading seq # 5: YPL256C_Spar Sequences read.. Counting patterns.. # site patterns = 209 Counting frequencies.. 120 bytes for distance 33440 bytes for lkl0 26752 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.061542 0.052990 0.052091 0.074386 0.046362 0.112959 0.140419 0.118622 lnL0 = -3212.604914 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3212.604914 x= 0.06154 0.05299 0.05209 0.07439 0.04636 0.11296 0.14042 0.11862 1 h-lim-p 0.0002 0.0014 165.8011 3211.230612 9 0.0001 46 | 0/8 2 h-lim-p 0.0008 0.0077 22.7247 3211.189305 5 0.0002 70 | 0/8 3 h-lim-p 0.0004 0.0085 9.4835 3211.185202 5 0.0001 93 | 0/8 4 h-lim-p 0.0002 0.0421 4.2212 3211.184164 4 0.0001 116 | 0/8 5 h-lim-p 0.0007 0.2549 0.8185 3211.184104 2 0.0002 133 | 0/8 6 h-lim-p 0.0008 0.6583 0.2002 3211.184101 0 0.0002 154 | 0/8 7 h-lim-p 0.0380 20.0000 0.0009 3211.184101 0 0.0166 174 | 0/8 8 h-lim-p 0.0017 20.0000 0.0088 3211.184057 0 0.0137 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3211.184056 0 1.0938 217 | 0/8 10 h-lim-p 0.9327 20.0000 0.0000 3211.184056 0 0.8162 237 | 0/8 11 h-lim-p 0.5914 20.0000 0.0000 3211.184056 0 0.0012 265 | 0/8 12 h-lim-p 0.0003 20.0000 0.0001 3211.184056 0 0.0001 285 | 0/8 13 h-lim-p 0.0001 20.0000 0.0002 3211.184056 0 0.0000 305 | 0/8 14 h-lim-p 0.0002 20.0000 0.0000 3211.184056 0 0.0000 336 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 3211.184056 0 0.0000 366 Out... lnL = -3211.184056 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3211.184056 Node 7: lnL = -3211.184056 Node 8: lnL = -3211.184056 Node 9: lnL = -3211.184056 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 1004 Sequential format.. Reading seq # 1: YPL258C_Sbay Reading seq # 2: YPL258C_Scer Reading seq # 3: YPL258C_Skud Reading seq # 4: YPL258C_Smik Reading seq # 5: YPL258C_Spar Sequences read.. Counting patterns.. # site patterns = 400 Counting frequencies.. 120 bytes for distance 64000 bytes for lkl0 51200 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.087084 0.000060 0.357108 0.060418 0.072447 0.385150 0.327004 0.219197 lnL0 = -4889.781835 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4889.781835 x= 0.08708 0.00006 0.35711 0.06042 0.07245 0.38515 0.32700 0.21920 1 h-lim-p 0.0001 0.0006 129.2367 4888.153221 0 0.0002 23 | 0/8 2 h-lim-p 0.0002 0.0025 92.1908 4887.716345 5 0.0001 47 | 0/8 3 h-lim-p 0.0008 0.0328 16.3354 4887.626310 4 0.0007 66 | 0/8 4 h-lim-p 0.0004 0.0031 10.0472 4887.612742 2 0.0004 82 | 0/8 5 h-lim-p 0.0012 0.0257 2.9423 4887.611025 5 0.0004 106 | 0/8 6 h-lim-p 0.0026 0.7404 0.5069 4887.610905 3 0.0009 126 | 0/8 7 h-lim-p 0.0168 17.5467 0.0278 4887.610693 0 0.0252 146 | 0/8 8 h-lim-p 0.0130 1.0387 0.0541 4887.603869 0 0.0389 167 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4887.603861 1 0.9961 189 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4887.603861 0 2.1875 209 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4887.603861 0 0.5469 230 | 0/8 12 h-lim-p 0.0413 20.0000 0.0000 4887.603861 0 0.0207 250 | 0/8 13 h-lim-p 0.0083 20.0000 0.0000 4887.603861 0 0.0000 291 | 0/8 14 h-lim-p 0.0000 20.0000 0.0030 | 0/8 15 h-lim-p 0.0000 20.0000 0.0030 Out... lnL = -4887.603861 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4887.603861 Node 7: lnL = -4887.603861 Node 8: lnL = -4887.603861 Node 9: lnL = -4887.603861 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 878 Sequential format.. Reading seq # 1: YPL259C_Sbay Reading seq # 2: YPL259C_Scer Reading seq # 3: YPL259C_Skud Reading seq # 4: YPL259C_Smik Reading seq # 5: YPL259C_Spar Sequences read.. Counting patterns.. # site patterns = 367 Counting frequencies.. 120 bytes for distance 58720 bytes for lkl0 46976 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.212073 0.000060 0.319991 0.102889 0.058900 0.406502 0.357821 0.364517 lnL0 = -4490.515491 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4490.515491 x= 0.21207 0.00006 0.31999 0.10289 0.05890 0.40650 0.35782 0.36452 1 h-lim-p 0.0001 0.0006 178.6318 4488.325748 0 0.0001 23 | 0/8 2 h-lim-p 0.0004 0.0032 64.9110 4487.472971 1 0.0005 37 | 0/8 3 h-lim-p 0.0006 0.0069 50.2136 4486.798886 0 0.0009 49 | 0/8 4 h-lim-p 0.0003 0.0021 13.8131 4486.760606 0 0.0005 62 | 0/8 5 h-lim-p 0.0021 0.1949 3.4600 4486.751497 4 0.0016 82 | 0/8 6 h-lim-p 0.0102 0.8718 0.5536 4486.751191 3 0.0016 103 | 0/8 7 h-lim-p 0.0818 20.0000 0.0111 4486.725007 0 0.6545 126 | 0/8 8 h-lim-p 0.0029 0.0480 2.4795 4486.718650 5 0.0015 159 | 0/8 9 h-lim-p 2.5000 20.0000 0.0009 4486.717643 3 1.0004 177 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4486.717642 0 1.0938 197 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4486.717642 0 1.0938 217 | 0/8 12 h-lim-p 1.5116 20.0000 0.0000 4486.717642 0 2.2674 237 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 4486.717642 0 0.5469 258 | 0/8 14 h-lim-p 0.0692 20.0000 0.0000 4486.717642 0 0.0022 282 | 0/8 15 h-lim-p 0.0022 20.0000 0.0000 4486.717642 0 0.0000 313 Out... lnL = -4486.717642 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4486.717642 Node 7: lnL = -4486.717642 Node 8: lnL = -4486.717642 Node 9: lnL = -4486.717642 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 553 Sequential format.. Reading seq # 1: YPL260W_Sbay Reading seq # 2: YPL260W_Scer Reading seq # 3: YPL260W_Skud Reading seq # 4: YPL260W_Smik Reading seq # 5: YPL260W_Spar Sequences read.. Counting patterns.. # site patterns = 232 Counting frequencies.. 120 bytes for distance 37120 bytes for lkl0 29696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.135144 0.003288 0.036064 0.133345 0.111417 0.224521 0.252372 0.226754 lnL0 = -2498.478472 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2498.478472 x= 0.13514 0.00329 0.03606 0.13335 0.11142 0.22452 0.25237 0.22675 1 h-lim-p 0.0007 0.4443 259.9435 2493.873203 7 0.0002 36 | 0/8 2 h-lim-p 0.0006 0.0048 26.9954 2493.707767 6 0.0004 60 | 0/8 3 h-lim-p 0.0017 0.0602 7.2412 2493.695828 6 0.0005 87 | 0/8 4 h-lim-p 0.0014 0.1396 2.4756 2493.693922 3 0.0007 105 | 0/8 5 h-lim-p 0.0018 0.0927 0.9738 2493.693717 4 0.0005 127 | 0/8 6 h-lim-p 0.0018 1.2146 0.2801 2493.693692 1 0.0007 149 | 0/8 7 h-lim-p 0.0523 20.0000 0.0038 2493.693687 0 0.0229 169 | 0/8 8 h-lim-p 0.0100 20.0000 0.0086 2493.693355 0 0.0600 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2493.693350 1 0.9961 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2493.693350 0 1.2500 233 | 0/8 11 h-lim-p 1.6887 20.0000 0.0000 2493.693350 0 0.1847 255 | 0/8 12 h-lim-p 0.0800 20.0000 0.0000 2493.693350 0 0.0350 275 | 0/8 13 h-lim-p 0.0201 20.0000 0.0000 2493.693350 0 0.0050 296 | 0/8 14 h-lim-p 0.0035 20.0000 0.0000 2493.693350 0 0.0000 336 | 0/8 15 h-lim-p 0.0000 20.0000 0.0009 2493.693350 0 0.0000 365 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0009 | 0/8 18 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -2493.693350 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2493.693350 Node 7: lnL = -2493.693350 Node 8: lnL = -2493.693350 Node 9: lnL = -2493.693350 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 824 Sequential format.. Reading seq # 1: YPL262W_Sbay Reading seq # 2: YPL262W_Scer Reading seq # 3: YPL262W_Skud Reading seq # 4: YPL262W_Smik Reading seq # 5: YPL262W_Spar Sequences read.. Counting patterns.. # site patterns = 280 Counting frequencies.. 120 bytes for distance 44800 bytes for lkl0 35840 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.102431 0.027888 0.055373 0.154271 0.072101 0.197500 0.173803 0.183272 lnL0 = -3648.799933 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3648.799933 x= 0.10243 0.02789 0.05537 0.15427 0.07210 0.19750 0.17380 0.18327 1 h-lim-p 0.0008 0.0347 294.3537 3644.265679 8 0.0001 43 | 0/8 2 h-lim-p 0.0004 0.0033 53.5159 3643.874133 7 0.0003 72 | 0/8 3 h-lim-p 0.0004 0.0062 32.9980 3643.781506 4 0.0002 92 | 0/8 4 h-lim-p 0.0012 0.0457 6.0093 3643.777619 5 0.0002 117 | 0/8 5 h-lim-p 0.0011 0.1482 1.2716 3643.777374 3 0.0003 138 | 0/8 6 h-lim-p 0.0030 2.3140 0.1323 3643.777369 1 0.0004 154 | 0/8 7 h-lim-p 0.0087 20.0000 0.0057 3643.776945 0 0.1384 178 | 0/8 8 h-lim-p 0.0025 1.8565 0.3122 3643.772686 0 0.0051 199 | 0/8 9 h-lim-p 1.9914 20.0000 0.0008 3643.772530 2 0.9879 223 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 3643.772530 0 1.0938 243 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3643.772530 0 1.0938 263 | 0/8 12 h-lim-p 0.3323 20.0000 0.0000 3643.772530 0 0.3323 283 | 0/8 13 h-lim-p 0.1288 20.0000 0.0000 3643.772530 0 0.0322 304 | 0/8 14 h-lim-p 0.0148 20.0000 0.0001 3643.772530 0 0.0001 331 | 0/8 15 h-lim-p 0.0004 20.0000 0.0000 3643.772530 0 0.0000 362 Out... lnL = -3643.772530 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3643.772530 Node 7: lnL = -3643.772530 Node 8: lnL = -3643.772530 Node 9: lnL = -3643.772530 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 355 Sequential format.. Reading seq # 1: YPL267W_Sbay Reading seq # 2: YPL267W_Scer Reading seq # 3: YPL267W_Skud Reading seq # 4: YPL267W_Smik Reading seq # 5: YPL267W_Spar Sequences read.. Counting patterns.. # site patterns = 164 Counting frequencies.. 120 bytes for distance 26240 bytes for lkl0 20992 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.023166 0.223303 0.080939 0.128116 0.075676 0.192392 0.210867 0.119899 lnL0 = -1546.422078 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1546.422078 x= 0.02317 0.22330 0.08094 0.12812 0.07568 0.19239 0.21087 0.11990 1 h-lim-p 0.0024 0.0195 47.1151 1545.941637 8 0.0005 41 | 0/8 2 h-lim-p 0.0015 0.0162 13.8701 1545.867553 5 0.0008 64 | 0/8 3 h-lim-p 0.0019 0.0402 5.9638 1545.854717 3 0.0009 82 | 0/8 4 h-lim-p 0.0039 0.1596 1.3308 1545.854284 4 0.0005 104 | 0/8 5 h-lim-p 0.0037 1.3345 0.1863 1545.854269 0 0.0008 117 | 0/8 6 h-lim-p 0.0024 3.4370 0.0637 1545.854267 0 0.0010 137 | 0/8 7 h-lim-p 0.0092 20.0000 0.0072 1545.854267 0 0.0020 158 | 0/8 8 h-lim-p 0.0848 20.0000 0.0002 1545.854258 0 0.6787 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1545.854258 0 1.0938 201 | 0/8 10 h-lim-p 2.2017 20.0000 0.0000 1545.854258 0 0.9632 221 | 0/8 11 h-lim-p 0.7840 20.0000 0.0000 1545.854258 0 0.0000 256 | 0/8 12 h-lim-p 0.0000 20.0000 0.0000 1545.854258 0 0.0000 285 Out... lnL = -1545.854258 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1545.854258 Node 7: lnL = -1545.854258 Node 8: lnL = -1545.854258 Node 9: lnL = -1545.854258 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 223 Sequential format.. Reading seq # 1: YPL269W_Sbay Reading seq # 2: YPL269W_Scer Reading seq # 3: YPL269W_Skud Reading seq # 4: YPL269W_Smik Reading seq # 5: YPL269W_Spar Sequences read.. Counting patterns.. # site patterns = 99 Counting frequencies.. 120 bytes for distance 15840 bytes for lkl0 12672 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.065916 0.003319 0.049106 0.128340 0.042609 0.094611 0.107146 0.116750 lnL0 = -796.348209 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 796.348209 x= 0.06592 0.00332 0.04911 0.12834 0.04261 0.09461 0.10715 0.11675 1 h-lim-p 0.0003 0.4841 217.7938 794.075746 4 0.0001 31 | 0/8 2 h-lim-p 0.0004 0.0030 31.6570 793.835122 0 0.0006 43 | 0/8 3 h-lim-p 0.0017 0.0133 4.6360 793.829278 6 0.0006 69 | 0/8 4 h-lim-p 0.0020 0.1424 1.2921 793.828797 4 0.0006 93 | 0/8 5 h-lim-p 0.0044 1.1284 0.1816 793.828774 2 0.0011 110 | 0/8 6 h-lim-p 0.0116 8.0118 0.0168 793.828556 0 0.0466 132 | 0/8 7 h-lim-p 0.0077 0.7660 0.1012 793.823554 0 0.0309 154 | 0/8 8 h-lim-p 0.0035 0.1304 0.8898 793.823269 3 0.0007 181 | 0/8 9 h-lim-p 0.7376 20.0000 0.0008 793.822066 0 1.4752 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0003 793.821891 4 1.4126 233 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 793.821891 0 1.0938 253 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 793.821891 0 1.0938 273 | 0/8 13 h-lim-p 1.1519 20.0000 0.0000 793.821891 0 2.3038 294 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 793.821891 0 0.0781 318 | 0/8 15 h-lim-p 0.0137 20.0000 0.0000 793.821891 0 0.0000 363 | 0/8 16 h-lim-p 0.0000 20.0000 0.0005 | 0/8 17 h-lim-p 0.0000 20.0000 0.0005 Out... lnL = -793.821891 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -793.821891 Node 7: lnL = -793.821891 Node 8: lnL = -793.821891 Node 9: lnL = -793.821891 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 864 Sequential format.. Reading seq # 1: YPL271W_Sbay Reading seq # 2: YPL271W_Scer Reading seq # 3: YPL271W_Skud Reading seq # 4: YPL271W_Smik Reading seq # 5: YPL271W_Spar Sequences read.. Counting patterns.. # site patterns = 370 Counting frequencies.. 120 bytes for distance 59200 bytes for lkl0 47360 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.191022 0.082040 0.070814 0.180445 0.141403 0.307569 0.364858 0.318366 lnL0 = -4496.664499 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4496.664499 x= 0.19102 0.08204 0.07081 0.18045 0.14140 0.30757 0.36486 0.31837 1 h-lim-p 0.0010 0.0080 92.6408 4495.272055 7 0.0003 40 | 0/8 2 h-lim-p 0.0008 0.0066 24.3352 4495.155166 3 0.0004 58 | 0/8 3 h-lim-p 0.0010 0.0155 10.1680 4495.133129 6 0.0005 82 | 0/8 4 h-lim-p 0.0009 0.0987 5.4679 4495.123018 2 0.0009 98 | 0/8 5 h-lim-p 0.0030 0.3213 1.5881 4495.122077 4 0.0008 120 | 0/8 6 h-lim-p 0.0024 0.7147 0.5624 4495.121964 3 0.0008 140 | 0/8 7 h-lim-p 0.0140 12.3313 0.0342 4495.121963 0 0.0015 162 | 0/8 8 h-lim-p 0.3059 20.0000 0.0002 4495.121925 0 1.2236 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4495.121924 0 1.0938 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4495.121924 0 1.0938 224 | 0/8 11 h-lim-p 1.2374 20.0000 0.0000 4495.121924 0 2.4747 245 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 4495.121924 0 0.5469 266 | 0/8 13 h-lim-p 0.0260 20.0000 0.0000 4495.121924 0 0.0000 303 Out... lnL = -4495.121924 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4495.121924 Node 7: lnL = -4495.121924 Node 8: lnL = -4495.121924 Node 9: lnL = -4495.121924 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 831 Sequential format.. Reading seq # 1: YPL272C_Sbay Reading seq # 2: YPL272C_Scer Reading seq # 3: YPL272C_Skud Reading seq # 4: YPL272C_Smik Reading seq # 5: YPL272C_Spar Sequences read.. Counting patterns.. # site patterns = 222 Counting frequencies.. 120 bytes for distance 35520 bytes for lkl0 28416 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.060291 0.043869 0.053236 0.069490 0.062720 0.133735 0.160099 0.115197 lnL0 = -3259.895703 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3259.895703 x= 0.06029 0.04387 0.05324 0.06949 0.06272 0.13374 0.16010 0.11520 1 h-lim-p 0.0002 0.0020 151.7417 3258.728066 5 0.0001 31 | 0/8 2 h-lim-p 0.0007 0.0060 15.3689 3258.712668 5 0.0001 56 | 0/8 3 h-lim-p 0.0004 0.0451 5.0875 3258.710794 3 0.0002 74 | 0/8 4 h-lim-p 0.0004 0.0731 2.0942 3258.710507 3 0.0002 92 | 0/8 5 h-lim-p 0.0011 0.4596 0.2905 3258.710496 0 0.0003 105 | 0/8 6 h-lim-p 0.0010 2.5999 0.0790 3258.710495 0 0.0002 126 | 0/8 7 h-lim-p 0.0011 6.5344 0.0155 3258.710495 0 0.0002 147 | 0/8 8 h-lim-p 0.0559 20.0000 0.0001 3258.710477 0 0.8952 171 | 0/8 9 h-lim-p 1.0987 20.0000 0.0001 3258.710476 0 0.9613 191 | 0/8 10 h-lim-p 2.2829 20.0000 0.0000 3258.710476 0 2.2829 211 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3258.710476 0 0.0391 236 | 0/8 12 h-lim-p 0.0029 20.0000 0.0000 3258.710476 0 0.0000 270 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 3258.710476 0 0.0000 302 Out... lnL = -3258.710476 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3258.710476 Node 7: lnL = -3258.710476 Node 8: lnL = -3258.710476 Node 9: lnL = -3258.710476 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 408 Sequential format.. Reading seq # 1: YPL273W_Sbay Reading seq # 2: YPL273W_Scer Reading seq # 3: YPL273W_Skud Reading seq # 4: YPL273W_Smik Reading seq # 5: YPL273W_Spar Sequences read.. Counting patterns.. # site patterns = 128 Counting frequencies.. 120 bytes for distance 20480 bytes for lkl0 16384 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.184804 0.230511 0.439890 0.117002 0.108735 1.012352 0.000060 0.334461 lnL0 = -1502.120750 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1502.120750 x= 0.18480 0.23051 0.43989 0.11700 0.10873 1.01235 0.00006 0.33446 1 h-lim-p 0.0000 0.0000 284.8906 1502.027182 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0003 837.7701 1451.755210 m 0.0003 36 | 1/8 3 h-lim-p 0.0001 0.0004 253.3735 1442.964217 m 0.0004 48 | 1/8 4 h-lim-p -0.0000 -0.0000 4.2107 h-lim-p: -2.16009386e-19 -1.72807509e-18 4.21065400e+00 1442.964217 .. | 0/8 5 h-lim-p 0.0000 0.0005 342.5392 1433.843759 0 0.0002 72 | 0/8 6 h-lim-p 0.0000 0.0000 140.8415 1433.565840 m 0.0000 84 | 1/8 7 h-lim-p 0.0000 0.0012 289.5330 1431.057091 0 0.0002 100 | 1/8 8 h-lim-p 0.0009 0.0071 36.4858 1430.525071 2 0.0008 116 | 1/8 9 h-lim-p 0.0061 0.0485 2.8821 1430.126022 0 0.0121 129 | 1/8 10 h-lim-p 0.0050 0.0396 6.5439 1430.097259 2 0.0012 146 | 1/8 11 h-lim-p 0.0039 2.5352 1.9320 1427.687878 0 0.5031 165 | 1/8 12 h-lim-p 0.2895 2.3162 0.6367 1426.641192 0 0.8686 178 | 0/8 13 h-lim-p 0.0060 0.0483 19.9929 1426.635741 2 0.0007 203 | 0/8 14 h-lim-p 0.0318 3.4983 0.4129 1426.449640 0 0.7640 219 | 0/8 15 h-lim-p 0.2825 2.2597 0.2253 1426.406759 0 0.5649 240 | 0/8 16 h-lim-p 0.3897 3.1175 0.0220 1426.401192 0 1.1691 261 | 0/8 17 h-lim-p 0.2948 2.3581 0.0041 1426.399471 m 2.3581 281 | 1/8 18 h-lim-p 2.5000 20.0000 0.0028 1426.399029 2 0.2930 307 | 1/8 19 h-lim-p 0.1483 20.0000 0.0055 1426.398357 0 0.5931 328 | 1/8 20 h-lim-p 1.5447 20.0000 0.0021 1426.398310 3 0.9194 355 | 1/8 21 h-lim-p 2.5000 20.0000 0.0001 1426.398310 0 1.0938 374 | 1/8 22 h-lim-p 2.5000 20.0000 0.0000 1426.398310 0 1.0938 393 | 1/8 23 h-lim-p 1.7214 20.0000 0.0000 1426.398310 0 2.5821 412 | 1/8 24 h-lim-p 2.5000 20.0000 0.0000 1426.398310 0 0.2734 433 | 1/8 25 h-lim-p 0.1205 20.0000 0.0000 1426.398310 0 0.0151 454 | 1/8 26 h-lim-p 0.0063 20.0000 0.0000 1426.398310 0 0.0002 477 | 1/8 27 h-lim-p 0.0001 20.0000 0.0000 1426.398310 0 0.0001 496 | 1/8 28 h-lim-p 0.0000 20.0000 0.0001 1426.398310 0 0.0000 527 | 1/8 29 h-lim-p 0.0000 20.0000 0.0026 | 1/8 30 h-lim-p 0.0000 20.0000 0.0026 Out... lnL = -1426.398310 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1426.398310 Node 7: lnL = -1426.398310 Node 8: lnL = -1426.398310 Node 9: lnL = -1426.398310 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 868 Sequential format.. Reading seq # 1: YPL274W_Sbay Reading seq # 2: YPL274W_Scer Reading seq # 3: YPL274W_Skud Reading seq # 4: YPL274W_Smik Reading seq # 5: YPL274W_Spar Sequences read.. Counting patterns.. # site patterns = 443 Counting frequencies.. 120 bytes for distance 70880 bytes for lkl0 56704 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.339213 0.000060 0.285561 0.190922 0.131908 0.804302 0.360516 0.527577 lnL0 = -4880.412332 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4880.412332 x= 0.33921 0.00006 0.28556 0.19092 0.13191 0.80430 0.36052 0.52758 1 h-lim-p 0.0000 0.0000 103.2988 4880.393047 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0055 70.2746 4879.482804 0 0.0006 40 | 1/8 3 h-lim-p 0.0011 0.0101 39.7186 4878.548019 0 0.0023 53 | 1/8 4 h-lim-p 0.0058 0.0461 5.6064 4878.523354 2 0.0013 70 | 1/8 5 h-lim-p 0.0114 1.1427 0.6651 4878.242427 0 0.0682 84 | 1/8 6 h-lim-p 0.0109 0.1567 4.1562 4876.544268 0 0.0218 104 | 1/8 7 h-lim-p 0.0073 0.0737 12.4942 4875.220679 6 0.0071 130 | 1/8 8 h-lim-p 2.5000 20.0000 0.0295 4875.094855 7 0.7320 158 | 1/8 9 h-lim-p 2.5000 20.0000 0.0023 4875.093827 4 0.8228 186 | 1/8 10 h-lim-p 2.5000 20.0000 0.0002 4875.093817 1 0.6152 208 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 4875.093817 0 1.0938 227 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 4875.093817 0 1.0938 246 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 4875.093817 0 1.2500 265 | 1/8 14 h-lim-p 1.7192 20.0000 0.0000 4875.093817 0 0.8596 284 | 1/8 15 h-lim-p 0.6042 20.0000 0.0000 4875.093817 0 0.3021 303 | 1/8 16 h-lim-p 0.0920 20.0000 0.0000 4875.093817 0 0.0000 332 Out... lnL = -4875.093817 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4875.093817 Node 7: lnL = -4875.093817 Node 8: lnL = -4875.093817 Node 9: lnL = -4875.093817 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 667 Sequential format.. Reading seq # 1: YPR001W_Sbay Reading seq # 2: YPR001W_Scer Reading seq # 3: YPR001W_Skud Reading seq # 4: YPR001W_Smik Reading seq # 5: YPR001W_Spar Sequences read.. Counting patterns.. # site patterns = 304 Counting frequencies.. 120 bytes for distance 48640 bytes for lkl0 38912 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.093260 0.111228 0.000060 0.241791 0.359427 0.352832 0.302794 0.215190 lnL0 = -3123.212766 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3123.212766 x= 0.09326 0.11123 0.00006 0.24179 0.35943 0.35283 0.30279 0.21519 1 h-lim-p 0.0004 0.0031 62.9361 3121.452736 0 0.0008 23 | 0/8 2 h-lim-p 0.0014 0.0151 36.0856 3120.924436 5 0.0011 46 | 0/8 3 h-lim-p 0.0001 0.0006 11.1910 3120.905316 0 0.0004 60 | 0/8 4 h-lim-p 0.0010 0.1290 4.6390 3120.893775 0 0.0015 72 | 0/8 5 h-lim-p 0.0009 0.0070 0.7331 3120.893421 0 0.0017 85 | 0/8 6 h-lim-p 0.0491 0.4024 0.0261 3120.891009 0 0.0983 106 | 0/8 7 h-lim-p 0.0039 0.1983 0.6569 3120.875778 0 0.0078 127 | 0/8 8 h-lim-p 0.0027 0.0693 1.9054 3120.870854 5 0.0020 158 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 3120.870831 1 0.9961 172 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3120.870831 0 1.0938 192 | 0/8 11 h-lim-p 1.3115 20.0000 0.0000 3120.870831 0 1.9672 212 | 0/8 12 h-lim-p 1.3090 20.0000 0.0000 3120.870831 0 0.0003 243 | 0/8 13 h-lim-p 0.0010 20.0000 0.0000 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0007 | 0/8 15 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -3120.870831 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3120.870831 Node 7: lnL = -3120.870831 Node 8: lnL = -3120.870831 Node 9: lnL = -3120.870831 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 596 Sequential format.. Reading seq # 1: YPR002W_Sbay Reading seq # 2: YPR002W_Scer Reading seq # 3: YPR002W_Skud Reading seq # 4: YPR002W_Smik Reading seq # 5: YPR002W_Spar Sequences read.. Counting patterns.. # site patterns = 190 Counting frequencies.. 120 bytes for distance 30400 bytes for lkl0 24320 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.000060 0.145849 0.283640 0.184830 0.168240 4.406287 0.263952 0.275567 lnL0 = -2418.821162 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2418.821162 x= 0.00006 0.14585 0.28364 0.18483 0.16824 4.40629 0.26395 0.27557 1 h-lim-p 0.0000 0.0000 95.6257 2418.799666 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0048 61.5420 2417.379116 0 0.0013 41 | 1/8 3 h-lim-p 0.0036 0.0292 21.0339 2417.164143 6 0.0011 69 | 1/8 4 h-lim-p 0.0043 0.0617 5.4579 2417.118181 7 0.0026 99 | 1/8 5 h-lim-p 0.0944 1.8458 0.1518 2414.856591 0 0.3776 113 | 1/8 6 h-lim-p 0.0017 0.0137 24.2077 2413.910750 6 0.0019 145 | 1/8 7 h-lim-p 1.6045 13.1408 0.0280 2413.711451 2 0.7521 161 | 1/8 8 h-lim-p 2.5000 20.0000 0.0027 2413.709528 5 0.7695 194 | 0/8 9 h-lim-p 0.0350 12.7268 0.0585 2413.709526 1 0.0017 218 | 0/8 10 h-lim-p 0.1485 1.1876 0.0002 2413.709521 0 0.8907 240 | 0/8 11 h-lim-p 0.0158 0.1265 0.0002 2413.709521 0 0.0000 272 | 0/8 12 h-lim-p 0.0000 0.0026 0.0244 2413.709521 0 0.0000 301 | 0/8 13 h-lim-p 0.0000 0.0037 0.0085 2413.709521 0 0.0000 331 | 0/8 14 h-lim-p 0.0000 0.0004 0.0649 | 0/8 15 h-lim-p 0.0000 0.0004 0.0649 Out... lnL = -2413.709521 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2413.709521 Node 7: lnL = -2413.709521 Node 8: lnL = -2413.709521 Node 9: lnL = -2413.709521 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 809 Sequential format.. Reading seq # 1: YPR004C_Sbay Reading seq # 2: YPR004C_Scer Reading seq # 3: YPR004C_Skud Reading seq # 4: YPR004C_Smik Reading seq # 5: YPR004C_Spar Sequences read.. Counting patterns.. # site patterns = 360 Counting frequencies.. 120 bytes for distance 57600 bytes for lkl0 46080 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.184279 0.084843 0.047171 0.217305 0.184305 0.228800 0.284882 0.301810 lnL0 = -4104.585614 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4104.585614 x= 0.18428 0.08484 0.04717 0.21730 0.18431 0.22880 0.28488 0.30181 1 h-lim-p 0.0012 0.0098 81.4280 4103.668854 2 0.0003 27 | 0/8 2 h-lim-p 0.0007 0.0063 32.7594 4103.446025 6 0.0005 52 | 0/8 3 h-lim-p 0.0011 0.0226 13.5996 4103.384700 7 0.0008 83 | 0/8 4 h-lim-p 0.0024 0.0696 4.4014 4103.379409 4 0.0006 104 | 0/8 5 h-lim-p 0.0038 0.2579 0.7146 4103.379253 3 0.0006 124 | 0/8 6 h-lim-p 0.0022 1.4575 0.2042 4103.379240 2 0.0007 150 | 0/8 7 h-lim-p 0.1047 20.0000 0.0014 4103.379129 0 0.3141 171 | 0/8 8 h-lim-p 0.0022 5.1733 0.1965 4103.378780 0 0.0033 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 4103.378763 1 0.9961 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4103.378763 0 1.2500 233 | 0/8 11 h-lim-p 1.7118 20.0000 0.0000 4103.378763 0 0.4279 254 | 0/8 12 h-lim-p 0.1827 20.0000 0.0000 4103.378763 0 0.0457 275 | 0/8 13 h-lim-p 0.0193 20.0000 0.0000 4103.378763 0 0.0006 299 | 0/8 14 h-lim-p 0.0000 7.9032 0.0338 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -4103.378763 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4103.378763 Node 7: lnL = -4103.378763 Node 8: lnL = -4103.378763 Node 9: lnL = -4103.378763 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 728 Sequential format.. Reading seq # 1: YPR005C_Sbay Reading seq # 2: YPR005C_Scer Reading seq # 3: YPR005C_Skud Reading seq # 4: YPR005C_Smik Reading seq # 5: YPR005C_Spar Sequences read.. Counting patterns.. # site patterns = 229 Counting frequencies.. 120 bytes for distance 36640 bytes for lkl0 29312 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.085784 0.080722 0.074797 0.114380 0.087645 0.187098 0.161772 0.161586 lnL0 = -2871.986471 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2871.986471 x= 0.08578 0.08072 0.07480 0.11438 0.08764 0.18710 0.16177 0.16159 1 h-lim-p 0.0025 0.0198 93.3326 2870.824970 2 0.0003 28 | 0/8 2 h-lim-p 0.0005 0.0043 22.0667 2870.734653 5 0.0004 51 | 0/8 3 h-lim-p 0.0015 0.0647 5.7429 2870.729547 3 0.0003 70 | 0/8 4 h-lim-p 0.0007 0.0704 2.6271 2870.728603 2 0.0003 86 | 0/8 5 h-lim-p 0.0015 0.3934 0.5668 2870.728544 2 0.0004 103 | 0/8 6 h-lim-p 0.0062 11.1547 0.0359 2870.728544 0 0.0007 125 | 0/8 7 h-lim-p 0.0093 20.0000 0.0026 2870.728544 0 0.0020 146 | 0/8 8 h-lim-p 0.0180 20.0000 0.0003 2870.728532 0 0.2875 170 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2870.728532 0 1.0938 190 | 0/8 10 h-lim-p 1.9028 20.0000 0.0000 2870.728532 0 1.6649 210 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2870.728532 0 0.3125 232 | 0/8 12 h-lim-p 0.0938 20.0000 0.0000 2870.728532 0 0.0000 274 | 0/8 13 h-lim-p 0.0000 20.0000 0.0011 | 0/8 14 h-lim-p 0.0000 20.0000 0.0011 Out... lnL = -2870.728532 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2870.728532 Node 7: lnL = -2870.728532 Node 8: lnL = -2870.728532 Node 9: lnL = -2870.728532 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 884 Sequential format.. Reading seq # 1: YPR008W_Sbay Reading seq # 2: YPR008W_Scer Reading seq # 3: YPR008W_Skud Reading seq # 4: YPR008W_Smik Reading seq # 5: YPR008W_Spar Sequences read.. Counting patterns.. # site patterns = 224 Counting frequencies.. 120 bytes for distance 35840 bytes for lkl0 28672 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.054711 0.030619 0.021057 0.072904 0.061950 0.101780 0.099589 0.096204 lnL0 = -3064.641734 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3064.641734 x= 0.05471 0.03062 0.02106 0.07290 0.06195 0.10178 0.09959 0.09620 1 h-lim-p 0.0005 0.3634 366.0485 3061.484256 3 0.0001 30 | 0/8 2 h-lim-p 0.0002 0.0014 52.5424 3061.350798 8 0.0001 62 | 0/8 3 h-lim-p 0.0008 0.0206 6.7816 3061.347789 5 0.0001 88 | 0/8 4 h-lim-p 0.0009 0.1456 0.9881 3061.347718 3 0.0001 108 | 0/8 5 h-lim-p 0.0007 0.8952 0.2186 3061.347715 1 0.0001 131 | 0/8 6 h-lim-p 0.0007 2.6656 0.0445 3061.347715 0 0.0001 152 | 0/8 7 h-lim-p 0.0015 20.0000 0.0042 3061.347715 0 0.0003 173 | 0/8 8 h-lim-p 0.0211 20.0000 0.0001 3061.347708 0 0.6747 198 | 0/8 9 h-lim-p 1.6910 20.0000 0.0000 3061.347707 0 1.4796 218 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3061.347707 0 1.2500 238 | 0/8 11 h-lim-p 0.7293 20.0000 0.0000 3061.347707 0 0.0456 261 | 0/8 12 h-lim-p 0.0204 20.0000 0.0000 3061.347707 0 0.0045 282 | 0/8 13 h-lim-p 0.0026 20.0000 0.0001 3061.347707 0 0.0006 303 | 0/8 14 h-lim-p 0.0003 20.0000 0.0002 3061.347707 0 0.0001 324 | 0/8 15 h-lim-p 0.0004 20.0000 0.0000 3061.347707 0 0.0000 364 | 0/8 16 h-lim-p 0.0000 20.0000 0.0097 | 0/8 17 h-lim-p 0.0000 20.0000 0.0097 Out... lnL = -3061.347707 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3061.347707 Node 7: lnL = -3061.347707 Node 8: lnL = -3061.347707 Node 9: lnL = -3061.347707 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 852 Sequential format.. Reading seq # 1: YPR009W_Sbay Reading seq # 2: YPR009W_Scer Reading seq # 3: YPR009W_Skud Reading seq # 4: YPR009W_Smik Reading seq # 5: YPR009W_Spar Sequences read.. Counting patterns.. # site patterns = 280 Counting frequencies.. 120 bytes for distance 44800 bytes for lkl0 35840 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.111501 0.014120 0.057080 0.072141 0.016197 0.146062 0.195552 0.165877 lnL0 = -3375.190500 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3375.190500 x= 0.11150 0.01412 0.05708 0.07214 0.01620 0.14606 0.19555 0.16588 1 h-lim-p 0.0001 0.0007 956.5622 3359.587390 10 0.0001 47 | 0/8 2 h-lim-p 0.0001 0.0004 232.0726 3355.827938 0 0.0002 60 | 0/8 3 h-lim-p 0.0007 0.0053 40.3576 3355.615111 3 0.0003 78 | 0/8 4 h-lim-p 0.0010 0.0111 11.1811 3355.604795 5 0.0002 102 | 0/8 5 h-lim-p 0.0004 0.0453 5.6299 3355.602378 5 0.0002 125 | 0/8 6 h-lim-p 0.0008 0.1676 1.2738 3355.602052 2 0.0004 141 | 0/8 7 h-lim-p 0.0048 1.6495 0.1078 3355.601913 3 0.0029 161 | 0/8 8 h-lim-p 0.0097 2.2403 0.0320 3355.560327 0 0.1557 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0012 3355.548382 6 1.3994 221 | 0/8 10 h-lim-p 2.5000 20.0000 0.0005 3355.546927 5 1.3631 252 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3355.546925 0 1.0938 272 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3355.546925 0 1.2500 292 | 0/8 13 h-lim-p 1.3226 20.0000 0.0000 3355.546925 0 0.2893 313 | 0/8 14 h-lim-p 0.1413 20.0000 0.0000 3355.546925 0 0.0000 354 | 0/8 15 h-lim-p 0.0000 20.0000 0.0024 | 0/8 16 h-lim-p 0.0000 20.0000 0.0024 Out... lnL = -3355.546925 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3355.546925 Node 7: lnL = -3355.546925 Node 8: lnL = -3355.546925 Node 9: lnL = -3355.546925 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 295 Sequential format.. Reading seq # 1: YPR011C_Sbay Reading seq # 2: YPR011C_Scer Reading seq # 3: YPR011C_Skud Reading seq # 4: YPR011C_Smik Reading seq # 5: YPR011C_Spar Sequences read.. Counting patterns.. # site patterns = 138 Counting frequencies.. 120 bytes for distance 22080 bytes for lkl0 17664 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.088833 0.126091 0.053613 0.108184 0.119882 0.213593 0.221673 0.168317 lnL0 = -1317.648661 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1317.648661 x= 0.08883 0.12609 0.05361 0.10818 0.11988 0.21359 0.22167 0.16832 1 h-lim-p 0.0110 0.3603 48.8644 1316.816591 5 0.0007 35 | 0/8 2 h-lim-p 0.0012 0.0093 16.7894 1316.693048 3 0.0010 53 | 0/8 3 h-lim-p 0.0022 0.0342 7.3847 1316.662927 6 0.0013 80 | 0/8 4 h-lim-p 0.0094 0.1654 1.0338 1316.662431 3 0.0009 100 | 0/8 5 h-lim-p 0.0079 2.3369 0.1231 1316.662421 2 0.0013 119 | 0/8 6 h-lim-p 0.0044 6.2033 0.0360 1316.662418 0 0.0019 139 | 0/8 7 h-lim-p 0.0243 20.0000 0.0029 1316.661916 0 0.3880 163 | 0/8 8 h-lim-p 0.0033 0.8994 0.3351 1316.661695 4 0.0023 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1316.661684 1 0.9961 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1316.661684 0 1.0938 235 | 0/8 11 h-lim-p 1.5301 20.0000 0.0000 1316.661684 0 0.0478 259 | 0/8 12 h-lim-p 0.0184 20.0000 0.0000 1316.661684 0 0.0092 279 | 0/8 13 h-lim-p 0.0045 20.0000 0.0000 1316.661684 0 0.0022 299 | 0/8 14 h-lim-p 0.0017 20.0000 0.0000 1316.661684 0 0.0000 332 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 1316.661684 0 0.0000 357 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0002 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -1316.661684 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1316.661684 Node 7: lnL = -1316.661684 Node 8: lnL = -1316.661684 Node 9: lnL = -1316.661684 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 822 Sequential format.. Reading seq # 1: YPR013C_Sbay Reading seq # 2: YPR013C_Scer Reading seq # 3: YPR013C_Skud Reading seq # 4: YPR013C_Smik Reading seq # 5: YPR013C_Spar Sequences read.. Counting patterns.. # site patterns = 143 Counting frequencies.. 120 bytes for distance 22880 bytes for lkl0 18304 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.057360 0.033244 0.019960 0.043884 0.018652 0.067544 0.078374 0.086202 lnL0 = -2569.674995 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2569.674995 x= 0.05736 0.03324 0.01996 0.04388 0.01865 0.06754 0.07837 0.08620 1 h-lim-p 0.0002 0.0014 113.0805 2569.370121 8 0.0000 44 | 0/8 2 h-lim-p 0.0001 0.0010 33.4743 2569.342299 3 0.0001 62 | 0/8 3 h-lim-p 0.0003 0.0278 5.2623 2569.341012 4 0.0001 84 | 0/8 4 h-lim-p 0.0003 0.2354 1.7700 2569.340967 1 0.0000 100 | 0/8 5 h-lim-p 0.0004 0.8975 0.1364 2569.340966 0 0.0001 113 | 0/8 6 h-lim-p 0.0002 3.5014 0.0736 2569.340966 0 0.0001 133 | 0/8 7 h-lim-p 0.0021 20.0000 0.0029 2569.340966 0 0.0003 155 | 0/8 8 h-lim-p 0.0135 20.0000 0.0001 2569.340962 0 0.4321 180 | 0/8 9 h-lim-p 0.1565 20.0000 0.0002 2569.340961 0 0.9387 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2569.340961 0 1.0938 222 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2569.340961 0 0.0000 257 Out... lnL = -2569.340961 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2569.340961 Node 7: lnL = -2569.340961 Node 8: lnL = -2569.340961 Node 9: lnL = -2569.340961 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 29 Sequential format.. Reading seq # 1: YPR016C_Sbay Reading seq # 2: YPR016C_Scer Reading seq # 3: YPR016C_Skud Reading seq # 4: YPR016C_Smik Reading seq # 5: YPR016C_Spar Sequences read.. Counting patterns.. # site patterns = 16 Counting frequencies.. 120 bytes for distance 2560 bytes for lkl0 2048 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.014071 0.035099 0.108116 0.102837 0.000060 0.066151 0.128874 0.053653 lnL0 = -98.785706 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 98.785706 x= 0.01407 0.03510 0.10812 0.10284 0.00006 0.06615 0.12887 0.05365 1 h-lim-p 0.0000 0.0000 22.0467 98.783294 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0067 8.1693 98.701557 0 0.0026 42 | 1/8 3 h-lim-p 0.0028 0.0222 6.1578 98.677444 7 0.0019 70 | 1/8 4 h-lim-p 0.0127 0.1513 0.9473 98.671867 6 0.0078 97 | 1/8 5 h-lim-p 0.0037 0.0300 1.1160 98.667457 1 0.0047 118 | 1/8 6 h-lim-p 0.0252 0.6389 0.2071 98.517632 0 0.2019 133 | 1/8 7 h-lim-p 0.0024 0.0193 4.4849 98.418977 0 0.0048 153 | 1/8 8 h-lim-p 1.0361 15.1947 0.0209 98.370808 9 0.7143 189 | 1/8 9 h-lim-p 2.5000 20.0000 0.0040 98.368213 5 1.2177 221 | 1/8 10 h-lim-p 2.5000 20.0000 0.0009 98.368134 4 0.9802 248 | 1/8 11 h-lim-p 2.5000 20.0000 0.0002 98.368128 2 1.0938 271 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 98.368128 1 0.9961 292 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 98.368128 0 1.0938 311 | 1/8 14 h-lim-p 1.1443 20.0000 0.0000 98.368128 0 0.0003 341 Out... lnL = -98.368128 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -98.368128 Node 7: lnL = -98.368128 Node 8: lnL = -98.368128 Node 9: lnL = -98.368128 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 630 Sequential format.. Reading seq # 1: YPR017C_Sbay Reading seq # 2: YPR017C_Scer Reading seq # 3: YPR017C_Skud Reading seq # 4: YPR017C_Smik Reading seq # 5: YPR017C_Spar Sequences read.. Counting patterns.. # site patterns = 252 Counting frequencies.. 120 bytes for distance 40320 bytes for lkl0 32256 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.092342 0.167137 0.054353 0.181927 0.124209 0.267862 0.251919 0.188450 lnL0 = -3047.518005 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3047.518005 x= 0.09234 0.16714 0.05435 0.18193 0.12421 0.26786 0.25192 0.18845 1 h-lim-p 0.0050 0.0401 90.8778 3046.354692 7 0.0003 38 | 0/8 2 h-lim-p 0.0012 0.0095 16.8234 3046.282285 5 0.0005 59 | 0/8 3 h-lim-p 0.0013 0.0663 6.8289 3046.270244 2 0.0006 75 | 0/8 4 h-lim-p 0.0024 0.1691 1.6813 3046.269269 5 0.0007 102 | 0/8 5 h-lim-p 0.0082 2.5039 0.1517 3046.269258 0 0.0009 116 | 0/8 6 h-lim-p 0.0021 3.7429 0.0655 3046.269257 0 0.0009 136 | 0/8 7 h-lim-p 0.4874 20.0000 0.0001 3046.269240 0 0.9749 157 | 0/8 8 h-lim-p 0.0021 6.1687 0.0559 3046.269238 0 0.0009 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3046.269237 0 1.0938 197 | 0/8 10 h-lim-p 2.4872 20.0000 0.0000 3046.269237 0 1.2436 217 | 0/8 11 h-lim-p 1.2834 20.0000 0.0000 3046.269237 0 0.3209 238 | 0/8 12 h-lim-p 0.1040 20.0000 0.0000 3046.269237 0 0.0520 258 | 0/8 13 h-lim-p 0.0224 20.0000 0.0001 3046.269237 0 0.0003 283 | 0/8 14 h-lim-p 0.0010 20.0000 0.0000 3046.269237 0 0.0000 314 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 3046.269237 0 0.0000 341 Out... lnL = -3046.269237 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3046.269237 Node 7: lnL = -3046.269237 Node 8: lnL = -3046.269237 Node 9: lnL = -3046.269237 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 636 Sequential format.. Reading seq # 1: YPR018W_Sbay Reading seq # 2: YPR018W_Scer Reading seq # 3: YPR018W_Skud Reading seq # 4: YPR018W_Smik Reading seq # 5: YPR018W_Spar Sequences read.. Counting patterns.. # site patterns = 255 Counting frequencies.. 120 bytes for distance 40800 bytes for lkl0 32640 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.115068 0.135314 0.077992 0.161579 0.110600 0.272189 0.196027 0.207429 lnL0 = -3003.125823 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3003.125823 x= 0.11507 0.13531 0.07799 0.16158 0.11060 0.27219 0.19603 0.20743 1 h-lim-p 0.0005 0.0037 74.9310 3001.926378 2 0.0004 26 | 0/8 2 h-lim-p 0.0012 0.0092 21.1697 3001.791356 6 0.0006 53 | 0/8 3 h-lim-p 0.0014 0.0343 9.7487 3001.775147 5 0.0004 78 | 0/8 4 h-lim-p 0.0011 0.0613 3.7204 3001.772166 2 0.0005 94 | 0/8 5 h-lim-p 0.0049 0.4914 0.3809 3001.772112 3 0.0007 116 | 0/8 6 h-lim-p 0.0032 3.5664 0.0852 3001.772108 1 0.0008 139 | 0/8 7 h-lim-p 0.0028 13.4722 0.0243 3001.772105 0 0.0028 159 | 0/8 8 h-lim-p 0.0178 20.0000 0.0038 3001.771396 0 0.2844 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 3001.771344 2 0.9961 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3001.771344 0 1.0938 227 | 0/8 11 h-lim-p 1.3367 20.0000 0.0000 3001.771344 0 1.1696 247 | 0/8 12 h-lim-p 0.5179 20.0000 0.0000 3001.771344 0 0.0000 291 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 3001.771344 0 0.0000 322 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -3001.771344 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3001.771344 Node 7: lnL = -3001.771344 Node 8: lnL = -3001.771344 Node 9: lnL = -3001.771344 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 502 Sequential format.. Reading seq # 1: YPR019W_Sbay Reading seq # 2: YPR019W_Scer Reading seq # 3: YPR019W_Skud Reading seq # 4: YPR019W_Smik Reading seq # 5: YPR019W_Spar Sequences read.. Counting patterns.. # site patterns = 191 Counting frequencies.. 120 bytes for distance 30560 bytes for lkl0 24448 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.123789 0.150513 0.074859 0.138980 0.125272 0.122249 0.175933 0.205957 lnL0 = -2289.431622 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2289.431622 x= 0.12379 0.15051 0.07486 0.13898 0.12527 0.12225 0.17593 0.20596 1 h-lim-p 0.0014 0.0114 70.5684 2288.582212 7 0.0004 38 | 0/8 2 h-lim-p 0.0007 0.0060 22.0673 2288.477103 6 0.0005 66 | 0/8 3 h-lim-p 0.0025 0.1017 4.0493 2288.470708 5 0.0008 90 | 0/8 4 h-lim-p 0.0019 0.1500 1.7518 2288.470070 4 0.0005 111 | 0/8 5 h-lim-p 0.0035 0.8354 0.2496 2288.470052 2 0.0006 129 | 0/8 6 h-lim-p 0.0061 20.0000 0.0227 2288.470052 0 0.0007 151 | 0/8 7 h-lim-p 0.0071 20.0000 0.0021 2288.470052 0 0.0008 173 | 0/8 8 h-lim-p 0.0625 20.0000 0.0000 2288.470052 0 1.0006 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2288.470052 0 1.0938 217 | 0/8 10 h-lim-p 1.1991 20.0000 0.0000 2288.470052 0 0.0375 241 | 0/8 11 h-lim-p 0.0167 20.0000 0.0000 2288.470052 0 0.0000 279 | 0/8 12 h-lim-p 0.0000 20.0000 0.0009 2288.470052 0 0.0000 307 | 0/8 13 h-lim-p 0.0000 20.0000 0.0002 .. | 0/8 14 h-lim-p 0.0000 20.0000 0.0009 | 0/8 15 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -2288.470052 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2288.470052 Node 7: lnL = -2288.470052 Node 8: lnL = -2288.470052 Node 9: lnL = -2288.470052 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 335 Sequential format.. Reading seq # 1: YPR020W_Sbay Reading seq # 2: YPR020W_Scer Reading seq # 3: YPR020W_Skud Reading seq # 4: YPR020W_Smik Reading seq # 5: YPR020W_Spar Sequences read.. Counting patterns.. # site patterns = 122 Counting frequencies.. 120 bytes for distance 19520 bytes for lkl0 15616 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.060031 0.061480 0.058076 0.077890 0.071539 0.160017 0.095179 0.110419 lnL0 = -1295.761316 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1295.761316 x= 0.06003 0.06148 0.05808 0.07789 0.07154 0.16002 0.09518 0.11042 1 h-lim-p 0.0005 0.0042 87.2868 1294.516176 9 0.0004 47 | 0/8 2 h-lim-p 0.0006 0.0044 24.4181 1294.402093 6 0.0004 74 | 0/8 3 h-lim-p 0.0035 0.0786 2.7830 1294.400772 4 0.0003 96 | 0/8 4 h-lim-p 0.0012 0.3501 0.7696 1294.400630 3 0.0005 114 | 0/8 5 h-lim-p 0.0018 0.7293 0.2243 1294.400616 2 0.0006 140 | 0/8 6 h-lim-p 0.0051 5.4788 0.0256 1294.400616 0 0.0006 162 | 0/8 7 h-lim-p 0.0184 20.0000 0.0008 1294.400616 0 0.0080 182 | 0/8 8 h-lim-p 0.0058 20.0000 0.0011 1294.400610 0 0.0934 206 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1294.400610 0 1.0938 226 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1294.400610 0 1.0938 246 | 0/8 11 h-lim-p 1.1234 20.0000 0.0000 1294.400610 0 2.2468 267 | 0/8 12 h-lim-p 0.8404 20.0000 0.0000 1294.400610 0 0.0131 292 | 0/8 13 h-lim-p 0.0000 2.9278 0.0329 1294.400610 0 0.0000 312 | 0/8 14 h-lim-p 0.0002 20.0000 0.0008 1294.400610 0 0.0002 332 | 0/8 15 h-lim-p 0.0000 0.1747 0.5517 1294.400610 0 0.0000 352 | 0/8 16 h-lim-p 0.0004 7.4943 0.0129 1294.400610 0 0.0001 373 | 0/8 17 h-lim-p 0.0003 20.0000 0.0052 1294.400610 0 0.0000 412 | 0/8 18 h-lim-p 0.0000 20.0000 0.0004 | 0/8 19 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -1294.400610 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1294.400610 Node 7: lnL = -1294.400610 Node 8: lnL = -1294.400610 Node 9: lnL = -1294.400610 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 567 Sequential format.. Reading seq # 1: YPR021C_Sbay Reading seq # 2: YPR021C_Scer Reading seq # 3: YPR021C_Skud Reading seq # 4: YPR021C_Smik Reading seq # 5: YPR021C_Spar Sequences read.. Counting patterns.. # site patterns = 184 Counting frequencies.. 120 bytes for distance 29440 bytes for lkl0 23552 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.397668 0.000060 0.072468 0.093971 0.070544 0.132858 0.224737 0.500471 lnL0 = -2532.828143 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2532.828143 x= 0.39767 0.00006 0.07247 0.09397 0.07054 0.13286 0.22474 0.50047 1 h-lim-p 0.0001 0.0009 125.4802 2530.657671 0 0.0002 23 | 0/8 2 h-lim-p 0.0005 0.0060 59.7663 2530.292663 8 0.0003 54 | 0/8 3 h-lim-p 0.0005 0.0105 28.4017 2530.047831 0 0.0008 66 | 0/8 4 h-lim-p 0.0006 0.0075 37.0759 2529.889756 3 0.0005 84 | 0/8 5 h-lim-p 0.0021 0.0204 9.0824 2529.876596 4 0.0004 105 | 0/8 6 h-lim-p 0.0009 0.0810 3.8399 2529.874792 5 0.0003 129 | 0/8 7 h-lim-p 0.0007 0.0740 1.6254 2529.871190 0 0.0028 143 | 0/8 8 h-lim-p 0.4021 20.0000 0.0113 2529.802671 0 0.8042 156 | 0/8 9 h-lim-p 2.5000 20.0000 0.0007 2529.801737 3 1.0449 182 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2529.801736 0 1.0938 202 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2529.801736 0 1.0938 222 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2529.801736 0 0.5469 243 | 0/8 13 h-lim-p 0.3718 20.0000 0.0000 2529.801736 0 0.0004 272 Out... lnL = -2529.801736 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2529.801736 Node 7: lnL = -2529.801736 Node 8: lnL = -2529.801736 Node 9: lnL = -2529.801736 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 460 Sequential format.. Reading seq # 1: YPR023C_Sbay Reading seq # 2: YPR023C_Scer Reading seq # 3: YPR023C_Skud Reading seq # 4: YPR023C_Smik Reading seq # 5: YPR023C_Spar Sequences read.. Counting patterns.. # site patterns = 136 Counting frequencies.. 120 bytes for distance 21760 bytes for lkl0 17408 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.087665 0.062157 0.058650 0.087038 0.039680 0.103539 0.115365 0.137919 lnL0 = -1799.236454 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1799.236454 x= 0.08766 0.06216 0.05865 0.08704 0.03968 0.10354 0.11536 0.13792 1 h-lim-p 0.0002 0.0015 54.5046 1798.935884 7 0.0002 39 | 0/8 2 h-lim-p 0.0005 0.0157 20.7225 1798.907771 6 0.0001 67 | 0/8 3 h-lim-p 0.0005 0.0258 6.2471 1798.903058 5 0.0003 90 | 0/8 4 h-lim-p 0.0010 0.0985 1.5896 1798.902741 4 0.0003 111 | 0/8 5 h-lim-p 0.0018 0.5733 0.2350 1798.902732 2 0.0003 128 | 0/8 6 h-lim-p 0.0044 11.3219 0.0186 1798.902732 0 0.0010 149 | 0/8 7 h-lim-p 0.0039 20.0000 0.0046 1798.902730 0 0.0077 170 | 0/8 8 h-lim-p 0.0037 7.5910 0.0098 1798.902594 0 0.0292 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1798.902590 1 0.9961 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1798.902590 0 1.0938 235 | 0/8 11 h-lim-p 0.6729 20.0000 0.0000 1798.902590 0 5.3835 258 | 0/8 12 h-lim-p 0.7949 20.0000 0.0001 1798.902590 0 0.0497 281 | 0/8 13 h-lim-p 0.0013 20.0000 0.0036 1798.902590 0 0.0013 301 | 0/8 14 h-lim-p 0.0000 0.0491 2.5231 1798.902590 0 0.0000 327 | 0/8 15 h-lim-p 0.0019 20.0000 0.0001 1798.902590 0 1.9257 349 | 0/8 16 h-lim-p 1.9796 20.0000 0.0001 1798.902590 0 0.0039 377 | 0/8 17 h-lim-p 0.0038 20.0000 0.0001 1798.902590 0 0.0000 412 | 0/8 18 h-lim-p 0.0000 20.0000 0.0051 1798.902590 0 0.0000 445 | 0/8 19 h-lim-p 0.0000 20.0000 0.0029 1798.902590 0 0.0001 468 | 0/8 20 h-lim-p 0.0006 20.0000 0.0006 1798.902590 0 0.0000 495 | 0/8 21 h-lim-p 0.0000 20.0000 0.0009 1798.902590 0 0.0000 516 | 0/8 22 h-lim-p 0.0000 20.0000 0.0030 1798.902590 0 0.0000 541 | 0/8 23 h-lim-p 0.0000 20.0000 0.0005 1798.902590 0 0.0000 561 | 0/8 24 h-lim-p 0.0001 20.0000 0.0001 1798.902590 0 0.0000 586 | 0/8 25 h-lim-p 0.0000 20.0000 0.0000 1798.902590 0 0.0000 608 | 0/8 26 h-lim-p 0.0000 20.0000 0.0034 .. | 0/8 27 h-lim-p 0.0000 20.0000 0.0047 | 0/8 28 h-lim-p 0.0000 20.0000 0.0047 Out... lnL = -1798.902590 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1798.902590 Node 7: lnL = -1798.902590 Node 8: lnL = -1798.902590 Node 9: lnL = -1798.902590 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 460 Sequential format.. Reading seq # 1: YPR024W_Sbay Reading seq # 2: YPR024W_Scer Reading seq # 3: YPR024W_Skud Reading seq # 4: YPR024W_Smik Reading seq # 5: YPR024W_Spar Sequences read.. Counting patterns.. # site patterns = 134 Counting frequencies.. 120 bytes for distance 21440 bytes for lkl0 17152 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.090354 0.058515 0.053738 0.085620 0.041098 0.110255 0.111317 0.140266 lnL0 = -1799.470353 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1799.470353 x= 0.09035 0.05851 0.05374 0.08562 0.04110 0.11026 0.11132 0.14027 1 h-lim-p 0.0002 0.0014 73.9239 1798.914043 1 0.0002 24 | 0/8 2 h-lim-p 0.0008 0.0085 20.9996 1798.879301 2 0.0002 41 | 0/8 3 h-lim-p 0.0004 0.0146 9.4503 1798.871830 4 0.0002 63 | 0/8 4 h-lim-p 0.0011 0.1047 1.7837 1798.871428 3 0.0003 82 | 0/8 5 h-lim-p 0.0020 0.6748 0.2368 1798.871418 2 0.0003 100 | 0/8 6 h-lim-p 0.0035 8.2244 0.0211 1798.871418 0 0.0008 121 | 0/8 7 h-lim-p 0.0019 20.0000 0.0087 1798.871414 0 0.0075 143 | 0/8 8 h-lim-p 0.0047 6.8576 0.0139 1798.871137 0 0.0282 165 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1798.871136 0 1.0938 185 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1798.871136 0 1.2500 205 | 0/8 11 h-lim-p 0.7283 20.0000 0.0000 1798.871136 0 0.3186 225 | 0/8 12 h-lim-p 0.1813 20.0000 0.0000 1798.871136 0 0.0397 246 | 0/8 13 h-lim-p 0.0244 20.0000 0.0000 1798.871136 0 0.0000 290 | 0/8 14 h-lim-p 0.0000 20.0000 0.0029 | 0/8 15 h-lim-p 0.0000 20.0000 0.0029 Out... lnL = -1798.871136 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1798.871136 Node 7: lnL = -1798.871136 Node 8: lnL = -1798.871136 Node 9: lnL = -1798.871136 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 867 Sequential format.. Reading seq # 1: YPR026W_Sbay Reading seq # 2: YPR026W_Scer Reading seq # 3: YPR026W_Skud Reading seq # 4: YPR026W_Smik Reading seq # 5: YPR026W_Spar Sequences read.. Counting patterns.. # site patterns = 276 Counting frequencies.. 120 bytes for distance 44160 bytes for lkl0 35328 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.111039 0.095378 0.050156 0.107095 0.091347 0.189304 0.189695 0.183885 lnL0 = -3822.115296 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3822.115296 x= 0.11104 0.09538 0.05016 0.10709 0.09135 0.18930 0.18970 0.18388 1 h-lim-p 0.0009 0.0069 158.4828 3820.342191 6 0.0002 38 | 0/8 2 h-lim-p 0.0005 0.0044 39.0657 3820.132778 6 0.0003 63 | 0/8 3 h-lim-p 0.0006 0.0169 18.3951 3820.098423 4 0.0002 83 | 0/8 4 h-lim-p 0.0007 0.0335 6.4436 3820.093498 4 0.0003 103 | 0/8 5 h-lim-p 0.0018 0.3019 0.9699 3820.093355 3 0.0003 124 | 0/8 6 h-lim-p 0.0014 1.3134 0.2272 3820.093347 0 0.0003 145 | 0/8 7 h-lim-p 0.0179 20.0000 0.0044 3820.093347 0 0.0010 168 | 0/8 8 h-lim-p 0.0294 20.0000 0.0001 3820.093336 0 0.4702 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3820.093336 0 1.0938 212 | 0/8 10 h-lim-p 1.4667 20.0000 0.0000 3820.093336 0 0.6417 232 | 0/8 11 h-lim-p 0.4226 20.0000 0.0000 3820.093336 0 0.0004 261 | 0/8 12 h-lim-p 0.0000 20.0000 0.0017 3820.093336 0 0.0000 281 | 0/8 13 h-lim-p 0.0002 20.0000 0.0000 3820.093336 0 0.0000 319 | 0/8 14 h-lim-p 0.0000 20.0000 0.0016 3820.093336 0 0.0000 343 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 3820.093336 0 0.0013 370 | 0/8 16 h-lim-p 0.0090 20.0000 0.0000 3820.093336 0 0.0040 390 | 0/8 17 h-lim-p 0.0065 20.0000 0.0000 3820.093336 0 0.0000 417 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 3820.093336 0 0.0000 452 | 0/8 19 h-lim-p 0.0000 20.0000 0.0021 | 0/8 20 h-lim-p 0.0000 20.0000 0.0021 Out... lnL = -3820.093336 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3820.093336 Node 7: lnL = -3820.093336 Node 8: lnL = -3820.093336 Node 9: lnL = -3820.093336 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 840 Sequential format.. Reading seq # 1: YPR027C_Sbay Reading seq # 2: YPR027C_Scer Reading seq # 3: YPR027C_Skud Reading seq # 4: YPR027C_Smik Reading seq # 5: YPR027C_Spar Sequences read.. Counting patterns.. # site patterns = 481 Counting frequencies.. 120 bytes for distance 76960 bytes for lkl0 61568 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.035363 0.383534 0.038972 0.393375 0.286042 0.544725 0.734351 0.205632 lnL0 = -5014.996952 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 5014.996952 x= 0.03536 0.38353 0.03897 0.39337 0.28604 0.54472 0.73435 0.20563 1 h-lim-p 0.0050 0.0400 58.1431 5013.827557 8 0.0007 43 | 0/8 2 h-lim-p 0.0007 0.0058 21.6673 5013.572254 0 0.0014 56 | 0/8 3 h-lim-p 0.0039 0.0698 7.9464 5013.536710 6 0.0013 81 | 0/8 4 h-lim-p 0.0030 0.1447 3.3692 5013.528517 5 0.0017 106 | 0/8 5 h-lim-p 0.0042 0.1813 1.3867 5013.526721 3 0.0022 125 | 0/8 6 h-lim-p 0.0177 3.4814 0.1728 5013.526583 2 0.0057 142 | 0/8 7 h-lim-p 0.0765 20.0000 0.0128 5013.520413 0 0.4590 164 | 0/8 8 h-lim-p 0.0107 1.2797 0.5481 5013.518213 3 0.0085 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 5013.518166 1 1.0938 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 5013.518166 0 1.0938 232 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 5013.518166 0 1.0938 252 | 0/8 12 h-lim-p 1.0153 20.0000 0.0000 5013.518166 0 3.0458 273 | 0/8 13 h-lim-p 0.0017 3.2713 0.0147 5013.518166 0 0.0000 305 | 0/8 14 h-lim-p 0.0024 20.0000 0.0000 5013.518166 0 0.0000 340 Out... lnL = -5013.518166 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -5013.518166 Node 7: lnL = -5013.518166 Node 8: lnL = -5013.518166 Node 9: lnL = -5013.518166 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 900 Sequential format.. Reading seq # 1: YPR029C_Sbay Reading seq # 2: YPR029C_Scer Reading seq # 3: YPR029C_Skud Reading seq # 4: YPR029C_Smik Reading seq # 5: YPR029C_Spar Sequences read.. Counting patterns.. # site patterns = 376 Counting frequencies.. 120 bytes for distance 60160 bytes for lkl0 48128 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.152622 0.063877 0.098846 0.125989 0.115905 0.191272 0.294513 0.234273 lnL0 = -4185.317005 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4185.317005 x= 0.15262 0.06388 0.09885 0.12599 0.11590 0.19127 0.29451 0.23427 1 h-lim-p 0.0027 0.7219 177.0187 4181.599657 8 0.0003 43 | 0/8 2 h-lim-p 0.0008 0.0062 29.6635 4181.447459 2 0.0004 59 | 0/8 3 h-lim-p 0.0005 0.0117 19.8218 4181.380038 6 0.0005 83 | 0/8 4 h-lim-p 0.0012 0.0443 7.4878 4181.368257 3 0.0005 101 | 0/8 5 h-lim-p 0.0029 0.2830 1.3321 4181.367733 2 0.0006 118 | 0/8 6 h-lim-p 0.0023 0.7608 0.3641 4181.367705 1 0.0005 133 | 0/8 7 h-lim-p 0.0143 20.0000 0.0116 4181.367684 0 0.0143 153 | 0/8 8 h-lim-p 0.0095 20.0000 0.0174 4181.366051 0 0.0571 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 4181.366026 1 0.9961 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4181.366026 0 1.0938 217 | 0/8 11 h-lim-p 1.8732 20.0000 0.0000 4181.366026 0 0.8195 237 | 0/8 12 h-lim-p 0.5918 20.0000 0.0000 4181.366026 0 0.0046 263 | 0/8 13 h-lim-p 0.0002 20.0000 0.0002 4181.366026 0 0.0001 283 | 0/8 14 h-lim-p 0.0010 20.0000 0.0000 4181.366026 0 0.0000 312 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 4181.366026 0 0.0000 342 Out... lnL = -4181.366026 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4181.366026 Node 7: lnL = -4181.366026 Node 8: lnL = -4181.366026 Node 9: lnL = -4181.366026 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 879 Sequential format.. Reading seq # 1: YPR030W_Sbay Reading seq # 2: YPR030W_Scer Reading seq # 3: YPR030W_Skud Reading seq # 4: YPR030W_Smik Reading seq # 5: YPR030W_Spar Sequences read.. Counting patterns.. # site patterns = 367 Counting frequencies.. 120 bytes for distance 58720 bytes for lkl0 46976 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.159647 0.046384 0.098765 0.148788 0.140459 0.163843 0.289815 0.241484 lnL0 = -4241.973293 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4241.973293 x= 0.15965 0.04638 0.09876 0.14879 0.14046 0.16384 0.28982 0.24148 1 h-lim-p 0.0016 0.5356 232.2403 4236.370816 9 0.0002 45 | 0/8 2 h-lim-p 0.0014 0.0115 28.4313 4236.191340 7 0.0004 76 | 0/8 3 h-lim-p 0.0010 0.0320 12.9726 4236.153246 5 0.0005 99 | 0/8 4 h-lim-p 0.0012 0.0682 5.6987 4236.147121 4 0.0005 119 | 0/8 5 h-lim-p 0.0019 0.1540 1.3744 4236.146516 4 0.0007 140 | 0/8 6 h-lim-p 0.0048 1.3558 0.1949 4236.146504 0 0.0006 154 | 0/8 7 h-lim-p 0.0037 12.6143 0.0313 4236.146481 0 0.0056 174 | 0/8 8 h-lim-p 0.0125 20.0000 0.0140 4236.141982 0 0.1496 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 4236.141822 2 0.9961 221 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4236.141822 0 1.0938 241 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4236.141822 0 1.0938 261 | 0/8 12 h-lim-p 0.9519 20.0000 0.0000 4236.141822 0 1.4279 281 | 0/8 13 h-lim-p 0.2203 20.0000 0.0000 4236.141822 0 0.0034 306 | 0/8 14 h-lim-p 0.0003 20.0000 0.0004 4236.141822 0 0.0000 339 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 4236.141822 0 0.0000 364 Out... lnL = -4236.141822 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4236.141822 Node 7: lnL = -4236.141822 Node 8: lnL = -4236.141822 Node 9: lnL = -4236.141822 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 309 Sequential format.. Reading seq # 1: YPR031W_Sbay Reading seq # 2: YPR031W_Scer Reading seq # 3: YPR031W_Skud Reading seq # 4: YPR031W_Smik Reading seq # 5: YPR031W_Spar Sequences read.. Counting patterns.. # site patterns = 148 Counting frequencies.. 120 bytes for distance 23680 bytes for lkl0 18944 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.078223 0.123625 0.111632 0.135446 0.080942 0.191050 0.151128 0.146504 lnL0 = -1348.717812 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1348.717812 x= 0.07822 0.12362 0.11163 0.13545 0.08094 0.19105 0.15113 0.14650 1 h-lim-p 0.0011 0.0091 26.9161 1348.449363 8 0.0008 40 | 0/8 2 h-lim-p 0.0035 0.0498 5.7919 1348.439311 6 0.0006 66 | 0/8 3 h-lim-p 0.0014 0.0651 2.5394 1348.437192 4 0.0008 87 | 0/8 4 h-lim-p 0.0032 0.6682 0.6150 1348.437062 2 0.0007 104 | 0/8 5 h-lim-p 0.0044 1.8612 0.1043 1348.437057 0 0.0010 125 | 0/8 6 h-lim-p 0.0055 16.9093 0.0183 1348.437056 0 0.0012 146 | 0/8 7 h-lim-p 0.0071 20.0000 0.0031 1348.437056 0 0.0107 166 | 0/8 8 h-lim-p 0.0184 20.0000 0.0018 1348.437028 0 0.1470 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1348.437027 0 1.0938 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1348.437027 0 1.0938 229 | 0/8 11 h-lim-p 1.3511 20.0000 0.0000 1348.437027 0 1.1822 249 | 0/8 12 h-lim-p 0.8632 20.0000 0.0000 1348.437027 0 0.4316 269 | 0/8 13 h-lim-p 0.0012 20.0000 0.0026 1348.437027 0 0.0012 289 | 0/8 14 h-lim-p 0.0001 4.0465 0.0261 1348.437027 0 0.0000 319 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 1348.437027 0 0.0000 348 Out... lnL = -1348.437027 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1348.437027 Node 7: lnL = -1348.437027 Node 8: lnL = -1348.437027 Node 9: lnL = -1348.437027 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 540 Sequential format.. Reading seq # 1: YPR033C_Sbay Reading seq # 2: YPR033C_Scer Reading seq # 3: YPR033C_Skud Reading seq # 4: YPR033C_Smik Reading seq # 5: YPR033C_Spar Sequences read.. Counting patterns.. # site patterns = 207 Counting frequencies.. 120 bytes for distance 33120 bytes for lkl0 26496 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.103121 0.098106 0.038786 0.097220 0.086538 0.192777 0.213845 0.167185 lnL0 = -2396.961333 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2396.961333 x= 0.10312 0.09811 0.03879 0.09722 0.08654 0.19278 0.21385 0.16719 1 h-lim-p 0.0005 0.0040 116.7647 2395.579848 6 0.0002 33 | 0/8 2 h-lim-p 0.0006 0.0045 31.6736 2395.417664 7 0.0003 65 | 0/8 3 h-lim-p 0.0010 0.0174 10.8655 2395.398681 6 0.0004 92 | 0/8 4 h-lim-p 0.0008 0.0469 5.2131 2395.393187 5 0.0005 115 | 0/8 5 h-lim-p 0.0019 0.1954 1.3650 2395.392800 2 0.0004 132 | 0/8 6 h-lim-p 0.0031 2.0347 0.1951 2395.392788 1 0.0006 147 | 0/8 7 h-lim-p 0.0117 20.0000 0.0104 2395.392788 1 0.0029 170 | 0/8 8 h-lim-p 0.0206 20.0000 0.0014 2395.392548 0 0.2472 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2395.392544 0 1.0938 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2395.392543 0 1.0938 233 | 0/8 11 h-lim-p 1.0022 20.0000 0.0000 2395.392543 0 0.0020 261 | 0/8 12 h-lim-p 0.0008 20.0000 0.0000 2395.392543 0 0.0001 283 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 2395.392543 0 0.0000 303 | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 2395.392543 0 0.0000 337 | 0/8 15 h-lim-p 0.0000 20.0000 0.0014 2395.392543 0 0.0000 367 | 0/8 16 h-lim-p 0.0000 20.0000 0.0010 2395.392543 0 0.0001 390 | 0/8 17 h-lim-p 0.0003 20.0000 0.0003 2395.392543 0 0.0004 410 | 0/8 18 h-lim-p 0.0009 20.0000 0.0001 2395.392543 0 0.0009 430 | 0/8 19 h-lim-p 0.0015 20.0000 0.0001 2395.392543 0 0.0001 453 | 0/8 20 h-lim-p 0.0000 20.0000 0.0003 2395.392543 0 0.0000 474 | 0/8 21 h-lim-p 0.0000 20.0000 0.0018 2395.392543 0 0.0000 502 | 0/8 22 h-lim-p 0.0000 20.0000 0.0000 2395.392543 0 0.0000 525 | 0/8 23 h-lim-p 0.0000 20.0000 0.0000 2395.392543 0 0.0000 558 Out... lnL = -2395.392543 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2395.392543 Node 7: lnL = -2395.392543 Node 8: lnL = -2395.392543 Node 9: lnL = -2395.392543 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 541 Sequential format.. Reading seq # 1: YPR034W_Sbay Reading seq # 2: YPR034W_Scer Reading seq # 3: YPR034W_Skud Reading seq # 4: YPR034W_Smik Reading seq # 5: YPR034W_Spar Sequences read.. Counting patterns.. # site patterns = 203 Counting frequencies.. 120 bytes for distance 32480 bytes for lkl0 25984 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.093488 0.102761 0.040569 0.092222 0.091536 0.188320 0.210482 0.156439 lnL0 = -2380.520148 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2380.520148 x= 0.09349 0.10276 0.04057 0.09222 0.09154 0.18832 0.21048 0.15644 1 h-lim-p 0.0004 0.0029 111.4132 2379.193689 9 0.0002 47 | 0/8 2 h-lim-p 0.0005 0.0039 30.6227 2379.060422 7 0.0003 78 | 0/8 3 h-lim-p 0.0011 0.0197 8.0222 2379.050371 4 0.0003 101 | 0/8 4 h-lim-p 0.0009 0.0763 3.0061 2379.048505 4 0.0005 122 | 0/8 5 h-lim-p 0.0017 0.2906 0.8182 2379.048340 4 0.0005 145 | 0/8 6 h-lim-p 0.0020 1.5761 0.2143 2379.048328 2 0.0005 170 | 0/8 7 h-lim-p 0.0113 20.0000 0.0101 2379.048327 0 0.0050 190 | 0/8 8 h-lim-p 0.0186 20.0000 0.0027 2379.047964 0 0.1491 213 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2379.047961 0 1.0938 233 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2379.047961 0 1.0938 253 | 0/8 11 h-lim-p 1.2622 20.0000 0.0000 2379.047961 0 1.2622 273 | 0/8 12 h-lim-p 1.2193 20.0000 0.0000 2379.047961 0 0.0762 296 | 0/8 13 h-lim-p 0.0064 20.0000 0.0001 2379.047961 0 0.0032 316 | 0/8 14 h-lim-p 0.0010 20.0000 0.0003 2379.047961 0 0.0000 341 | 0/8 15 h-lim-p 0.0001 20.0000 0.0001 2379.047961 0 0.0000 374 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 | 0/8 17 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -2379.047961 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2379.047961 Node 7: lnL = -2379.047961 Node 8: lnL = -2379.047961 Node 9: lnL = -2379.047961 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 580 Sequential format.. Reading seq # 1: YPR036W_Sbay Reading seq # 2: YPR036W_Scer Reading seq # 3: YPR036W_Skud Reading seq # 4: YPR036W_Smik Reading seq # 5: YPR036W_Spar Sequences read.. Counting patterns.. # site patterns = 183 Counting frequencies.. 120 bytes for distance 29280 bytes for lkl0 23424 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.098446 0.020372 0.054140 0.074515 0.027553 0.110553 0.157620 0.141854 lnL0 = -2134.770434 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2134.770434 x= 0.09845 0.02037 0.05414 0.07451 0.02755 0.11055 0.15762 0.14185 1 h-lim-p 0.0004 0.3320 326.9417 2129.085195 6 0.0001 35 | 0/8 2 h-lim-p 0.0001 0.0011 48.9395 2128.901324 1 0.0002 49 | 0/8 3 h-lim-p 0.0002 0.0030 35.4116 2128.790870 5 0.0002 70 | 0/8 4 h-lim-p 0.0011 0.0245 8.0710 2128.781416 5 0.0003 95 | 0/8 5 h-lim-p 0.0010 0.0822 2.4683 2128.780232 3 0.0004 113 | 0/8 6 h-lim-p 0.0015 0.2511 0.7146 2128.780176 3 0.0002 134 | 0/8 7 h-lim-p 0.0055 9.3439 0.0313 2128.780159 2 0.0043 158 | 0/8 8 h-lim-p 0.0151 20.0000 0.0088 2128.775409 0 0.1207 181 | 0/8 9 h-lim-p 2.3474 20.0000 0.0005 2128.774789 4 1.3264 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2128.774776 0 1.0938 232 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2128.774776 0 2.1875 252 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2128.774776 0 0.5469 273 | 0/8 13 h-lim-p 0.1983 20.0000 0.0000 2128.774776 0 0.0000 304 Out... lnL = -2128.774776 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2128.774776 Node 7: lnL = -2128.774776 Node 8: lnL = -2128.774776 Node 9: lnL = -2128.774776 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 286 Sequential format.. Reading seq # 1: YPR037C_Sbay Reading seq # 2: YPR037C_Scer Reading seq # 3: YPR037C_Skud Reading seq # 4: YPR037C_Smik Reading seq # 5: YPR037C_Spar Sequences read.. Counting patterns.. # site patterns = 150 Counting frequencies.. 120 bytes for distance 24000 bytes for lkl0 19200 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.128709 0.000060 0.199045 0.128368 0.073683 0.158309 0.232102 0.198029 lnL0 = -1208.536077 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1208.536077 x= 0.12871 0.00006 0.19905 0.12837 0.07368 0.15831 0.23210 0.19803 1 h-lim-p 0.0004 0.0031 55.2958 1207.595262 0 0.0008 23 | 0/8 2 h-lim-p 0.0014 0.0265 29.7548 1207.347319 8 0.0007 55 | 0/8 3 h-lim-p 0.0001 0.0009 11.0959 1207.313511 m 0.0009 67 | 0/8 4 h-lim-p 0.0054 0.1046 1.8398 1207.312211 5 0.0008 94 | 0/8 5 h-lim-p 0.0034 0.5569 0.4292 1207.311933 4 0.0025 115 | 0/8 6 h-lim-p 0.0638 1.3766 0.0166 1207.301406 0 0.3826 137 | 0/8 7 h-lim-p 0.0046 0.2617 1.3923 1207.287172 3 0.0047 163 | 0/8 8 h-lim-p 0.0135 0.1553 0.4853 1207.286997 2 0.0015 181 | 0/8 9 h-lim-p 1.0180 17.3085 0.0007 1207.286842 2 0.9544 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1207.286842 0 1.0938 225 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1207.286842 0 1.0938 245 | 0/8 12 h-lim-p 1.4912 20.0000 0.0000 1207.286842 0 2.9825 266 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1207.286842 0 0.0098 293 | 0/8 14 h-lim-p 0.0032 20.0000 0.0000 1207.286842 0 0.0000 329 Out... lnL = -1207.286842 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1207.286842 Node 7: lnL = -1207.286842 Node 8: lnL = -1207.286842 Node 9: lnL = -1207.286842 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 124 Sequential format.. Reading seq # 1: YPR040W_Sbay Reading seq # 2: YPR040W_Scer Reading seq # 3: YPR040W_Skud Reading seq # 4: YPR040W_Smik Reading seq # 5: YPR040W_Spar Sequences read.. Counting patterns.. # site patterns = 70 Counting frequencies.. 120 bytes for distance 11200 bytes for lkl0 8960 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.114144 0.000060 0.103686 0.167887 0.083409 0.080559 0.292212 0.173501 lnL0 = -515.454165 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 515.454165 x= 0.11414 0.00006 0.10369 0.16789 0.08341 0.08056 0.29221 0.17350 1 h-lim-p 0.0007 0.0057 23.5791 515.067145 0 0.0014 23 | 0/8 2 h-lim-p 0.0001 0.0011 11.7115 514.960209 m 0.0011 35 | 1/8 3 h-lim-p 0.0048 0.0650 2.6867 514.949121 6 0.0032 62 | 1/8 4 h-lim-p 0.0061 0.1091 1.4092 514.947942 2 0.0013 79 | 1/8 5 h-lim-p 0.0066 0.6033 0.2829 514.947159 3 0.0067 97 | 1/8 6 h-lim-p 0.0170 8.4324 0.1126 514.939308 0 0.0339 117 | 1/8 7 h-lim-p 0.0196 0.7871 0.1949 514.899722 0 0.0784 138 | 1/8 8 h-lim-p 0.0062 0.0798 2.4448 514.891315 4 0.0026 166 | 1/8 9 h-lim-p 2.5000 20.0000 0.0020 514.890654 3 1.0483 185 | 1/8 10 h-lim-p 2.5000 20.0000 0.0000 514.890654 0 1.0938 204 | 1/8 11 h-lim-p 2.5000 20.0000 0.0000 514.890654 0 1.0938 223 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 514.890654 0 0.5469 243 | 1/8 13 h-lim-p 0.3655 20.0000 0.0000 514.890654 0 0.0086 267 | 1/8 14 h-lim-p 0.0048 20.0000 0.0000 514.890654 0 0.0012 287 Out... lnL = -514.890654 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -514.890654 Node 7: lnL = -514.890654 Node 8: lnL = -514.890654 Node 9: lnL = -514.890654 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 543 Sequential format.. Reading seq # 1: YPR042C_Sbay Reading seq # 2: YPR042C_Scer Reading seq # 3: YPR042C_Skud Reading seq # 4: YPR042C_Smik Reading seq # 5: YPR042C_Spar Sequences read.. Counting patterns.. # site patterns = 205 Counting frequencies.. 120 bytes for distance 32800 bytes for lkl0 26240 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.051944 0.060931 0.106582 0.117406 0.085975 0.162585 0.174519 0.109211 lnL0 = -2316.595912 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2316.595912 x= 0.05194 0.06093 0.10658 0.11741 0.08597 0.16259 0.17452 0.10921 1 h-lim-p 0.0032 1.0017 121.2109 2314.867633 6 0.0003 38 | 0/8 2 h-lim-p 0.0008 0.0064 17.8585 2314.806738 5 0.0004 61 | 0/8 3 h-lim-p 0.0015 0.0415 4.5373 2314.801971 5 0.0005 85 | 0/8 4 h-lim-p 0.0018 0.1525 1.2197 2314.801765 3 0.0003 106 | 0/8 5 h-lim-p 0.0015 1.0182 0.2450 2314.801752 2 0.0005 124 | 0/8 6 h-lim-p 0.0020 4.9582 0.0596 2314.801751 1 0.0005 147 | 0/8 7 h-lim-p 0.0043 20.0000 0.0069 2314.801749 0 0.0087 168 | 0/8 8 h-lim-p 0.0108 20.0000 0.0055 2314.801437 0 0.0862 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2314.801436 0 1.0938 211 | 0/8 10 h-lim-p 2.4368 20.0000 0.0000 2314.801436 0 1.0661 231 | 0/8 11 h-lim-p 1.3777 20.0000 0.0000 2314.801436 0 2.7555 252 | 0/8 12 h-lim-p 1.0446 20.0000 0.0000 2314.801436 0 0.0326 276 | 0/8 13 h-lim-p 0.0001 4.4035 0.0175 2314.801436 0 0.0001 296 | 0/8 14 h-lim-p 0.0003 20.0000 0.0035 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0010 2314.801436 0 0.0000 356 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 2314.801436 0 0.0000 376 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0010 | 0/8 19 h-lim-p 0.0000 20.0000 0.0010 Out... lnL = -2314.801436 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2314.801436 Node 7: lnL = -2314.801436 Node 8: lnL = -2314.801436 Node 9: lnL = -2314.801436 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 259 Sequential format.. Reading seq # 1: YPR045C_Sbay Reading seq # 2: YPR045C_Scer Reading seq # 3: YPR045C_Skud Reading seq # 4: YPR045C_Smik Reading seq # 5: YPR045C_Spar Sequences read.. Counting patterns.. # site patterns = 131 Counting frequencies.. 120 bytes for distance 20960 bytes for lkl0 16768 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.169976 0.044819 0.078412 0.106859 0.064921 0.253302 0.270481 0.238824 lnL0 = -1211.025111 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1211.025111 x= 0.16998 0.04482 0.07841 0.10686 0.06492 0.25330 0.27048 0.23882 1 h-lim-p 0.0008 0.0067 22.5338 1210.854224 3 0.0007 28 | 0/8 2 h-lim-p 0.0020 0.0543 7.8033 1210.841600 2 0.0005 45 | 0/8 3 h-lim-p 0.0015 0.0516 2.5061 1210.839332 5 0.0008 68 | 0/8 4 h-lim-p 0.0023 0.3649 0.8815 1210.838862 5 0.0014 94 | 0/8 5 h-lim-p 0.0053 1.2035 0.2297 1210.838843 3 0.0008 124 | 0/8 6 h-lim-p 0.0022 3.7344 0.0800 1210.838836 1 0.0023 146 | 0/8 7 h-lim-p 0.0281 20.0000 0.0066 1210.838836 0 0.0031 168 | 0/8 8 h-lim-p 0.0902 20.0000 0.0002 1210.838823 0 0.7212 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1210.838823 0 1.0938 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1210.838823 0 2.1875 231 | 0/8 11 h-lim-p 2.4224 20.0000 0.0000 1210.838823 0 1.0598 251 | 0/8 12 h-lim-p 1.3495 20.0000 0.0000 1210.838823 0 5.3979 273 | 0/8 13 h-lim-p 1.7212 20.0000 0.0000 1210.838823 0 0.0941 296 | 0/8 14 h-lim-p 0.1698 20.0000 0.0000 1210.838823 0 0.0424 317 | 0/8 15 h-lim-p 0.1222 20.0000 0.0000 1210.838823 0 0.0000 363 Out... lnL = -1210.838823 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1210.838823 Node 7: lnL = -1210.838823 Node 8: lnL = -1210.838823 Node 9: lnL = -1210.838823 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 260 Sequential format.. Reading seq # 1: YPR046W_Sbay Reading seq # 2: YPR046W_Scer Reading seq # 3: YPR046W_Skud Reading seq # 4: YPR046W_Smik Reading seq # 5: YPR046W_Spar Sequences read.. Counting patterns.. # site patterns = 129 Counting frequencies.. 120 bytes for distance 20640 bytes for lkl0 16512 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.175560 0.038247 0.076231 0.104142 0.067637 0.244487 0.260485 0.243236 lnL0 = -1207.951093 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1207.951093 x= 0.17556 0.03825 0.07623 0.10414 0.06764 0.24449 0.26049 0.24324 1 h-lim-p 0.0006 0.0050 33.6247 1207.597787 4 0.0006 30 | 0/8 2 h-lim-p 0.0027 0.0277 7.9481 1207.583557 5 0.0005 55 | 0/8 3 h-lim-p 0.0012 0.0301 3.0850 1207.580465 6 0.0007 84 | 0/8 4 h-lim-p 0.0021 0.3029 1.0966 1207.579609 4 0.0016 104 | 0/8 5 h-lim-p 0.0032 0.5421 0.5651 1207.579502 3 0.0009 123 | 0/8 6 h-lim-p 0.0033 3.1096 0.1450 1207.579482 3 0.0019 152 | 0/8 7 h-lim-p 0.0588 20.0000 0.0048 1207.579476 2 0.0309 177 | 0/8 8 h-lim-p 0.0177 20.0000 0.0084 1207.579273 0 0.0709 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1207.579273 0 1.0938 219 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1207.579273 0 1.0938 239 | 0/8 11 h-lim-p 2.4094 20.0000 0.0000 1207.579273 0 0.5271 260 | 0/8 12 h-lim-p 0.3307 20.0000 0.0000 1207.579273 0 0.0827 281 | 0/8 13 h-lim-p 0.0452 20.0000 0.0000 1207.579273 0 0.0452 301 | 0/8 14 h-lim-p 0.0298 20.0000 0.0000 1207.579273 0 0.0000 340 Out... lnL = -1207.579273 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1207.579273 Node 7: lnL = -1207.579273 Node 8: lnL = -1207.579273 Node 9: lnL = -1207.579273 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 304 Sequential format.. Reading seq # 1: YPR049C_Sbay Reading seq # 2: YPR049C_Scer Reading seq # 3: YPR049C_Skud Reading seq # 4: YPR049C_Smik Reading seq # 5: YPR049C_Spar Sequences read.. Counting patterns.. # site patterns = 130 Counting frequencies.. 120 bytes for distance 20800 bytes for lkl0 16640 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.042464 0.088082 0.077906 0.093713 0.097081 0.141474 0.171891 0.089744 lnL0 = -1257.442536 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1257.442536 x= 0.04246 0.08808 0.07791 0.09371 0.09708 0.14147 0.17189 0.08974 1 h-lim-p 0.0011 0.0085 33.9346 1257.129662 5 0.0006 33 | 0/8 2 h-lim-p 0.0012 0.0098 9.6987 1257.108524 4 0.0005 53 | 0/8 3 h-lim-p 0.0020 0.0741 2.2732 1257.107265 4 0.0005 75 | 0/8 4 h-lim-p 0.0029 0.7331 0.4074 1257.107210 2 0.0007 92 | 0/8 5 h-lim-p 0.0051 6.6074 0.0540 1257.107209 0 0.0006 114 | 0/8 6 h-lim-p 0.0024 15.7380 0.0123 1257.107209 0 0.0011 134 | 0/8 7 h-lim-p 0.0051 20.0000 0.0026 1257.107209 0 0.0006 156 | 0/8 8 h-lim-p 0.0150 20.0000 0.0001 1257.107206 0 0.4794 181 | 0/8 9 h-lim-p 2.4839 20.0000 0.0000 1257.107206 0 1.0867 201 | 0/8 10 h-lim-p 1.9461 20.0000 0.0000 1257.107206 0 0.8514 221 | 0/8 11 h-lim-p 0.5871 20.0000 0.0000 1257.107206 0 0.0092 246 | 0/8 12 h-lim-p 0.0017 20.0000 0.0001 1257.107206 0 0.0009 266 | 0/8 13 h-lim-p 0.0005 20.0000 0.0001 1257.107206 0 0.0001 287 | 0/8 14 h-lim-p 0.0001 20.0000 0.0002 1257.107206 0 0.0000 310 | 0/8 15 h-lim-p 0.0001 20.0000 0.0000 1257.107206 0 0.0000 339 Out... lnL = -1257.107206 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1257.107206 Node 7: lnL = -1257.107206 Node 8: lnL = -1257.107206 Node 9: lnL = -1257.107206 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 311 Sequential format.. Reading seq # 1: YPR051W_Sbay Reading seq # 2: YPR051W_Scer Reading seq # 3: YPR051W_Skud Reading seq # 4: YPR051W_Smik Reading seq # 5: YPR051W_Spar Sequences read.. Counting patterns.. # site patterns = 128 Counting frequencies.. 120 bytes for distance 20480 bytes for lkl0 16384 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.044212 0.093260 0.067453 0.094443 0.095543 0.151548 0.164621 0.091356 lnL0 = -1288.276559 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1288.276559 x= 0.04421 0.09326 0.06745 0.09444 0.09554 0.15155 0.16462 0.09136 1 h-lim-p 0.0011 0.0084 46.8199 1287.676141 7 0.0006 37 | 0/8 2 h-lim-p 0.0015 0.0117 14.2816 1287.624740 7 0.0005 65 | 0/8 3 h-lim-p 0.0025 0.0757 3.0324 1287.622704 4 0.0005 88 | 0/8 4 h-lim-p 0.0027 0.3615 0.5207 1287.622630 1 0.0006 103 | 0/8 5 h-lim-p 0.0024 2.1849 0.1294 1287.622626 2 0.0005 128 | 0/8 6 h-lim-p 0.0025 10.1613 0.0239 1287.622626 0 0.0011 148 | 0/8 7 h-lim-p 0.0054 20.0000 0.0048 1287.622624 0 0.0109 169 | 0/8 8 h-lim-p 0.0077 20.0000 0.0068 1287.622510 0 0.0618 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1287.622510 0 1.0938 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1287.622510 0 1.0938 232 | 0/8 11 h-lim-p 1.0937 20.0000 0.0000 1287.622510 0 0.9570 252 | 0/8 12 h-lim-p 0.2177 20.0000 0.0001 1287.622510 0 0.0060 276 | 0/8 13 h-lim-p 0.0014 20.0000 0.0002 1287.622510 0 0.0000 307 | 0/8 14 h-lim-p 0.0001 20.0000 0.0000 1287.622510 0 0.0000 339 Out... lnL = -1287.622510 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1287.622510 Node 7: lnL = -1287.622510 Node 8: lnL = -1287.622510 Node 9: lnL = -1287.622510 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 309 Sequential format.. Reading seq # 1: YPR052C_Sbay Reading seq # 2: YPR052C_Scer Reading seq # 3: YPR052C_Skud Reading seq # 4: YPR052C_Smik Reading seq # 5: YPR052C_Spar Sequences read.. Counting patterns.. # site patterns = 66 Counting frequencies.. 120 bytes for distance 10560 bytes for lkl0 8448 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.059628 0.002349 0.031616 0.035322 0.029713 0.054630 0.080036 0.080496 lnL0 = -954.641000 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 954.641000 x= 0.05963 0.00235 0.03162 0.03532 0.02971 0.05463 0.08004 0.08050 1 h-lim-p 0.0001 0.0008 529.4917 951.900421 3 0.0000 29 | 0/8 2 h-lim-p 0.0002 0.0015 33.1522 951.811979 5 0.0002 50 | 0/8 3 h-lim-p 0.0004 0.0057 15.0444 951.792327 7 0.0002 81 | 0/8 4 h-lim-p 0.0005 0.0105 6.6999 951.789602 5 0.0001 105 | 0/8 5 h-lim-p 0.0014 0.2389 0.7219 951.789543 3 0.0002 125 | 0/8 6 h-lim-p 0.0032 1.4311 0.0516 951.789543 0 0.0002 148 | 0/8 7 h-lim-p 0.0006 8.1604 0.0170 951.789542 0 0.0012 169 | 0/8 8 h-lim-p 0.0326 20.0000 0.0006 951.788661 0 0.7823 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 951.788633 2 0.9644 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 951.788633 0 1.0938 237 | 0/8 11 h-lim-p 1.4065 20.0000 0.0000 951.788633 0 1.2307 257 | 0/8 12 h-lim-p 1.0792 20.0000 0.0000 951.788633 0 8.6339 280 | 0/8 13 h-lim-p 0.3669 20.0000 0.0002 951.788633 0 0.1605 300 | 0/8 14 h-lim-p 0.0149 20.0000 0.0017 951.788633 0 0.0000 331 | 0/8 15 h-lim-p 0.0002 20.0000 0.0000 951.788633 0 0.0000 370 | 0/8 16 h-lim-p 0.0000 20.0000 0.0012 | 0/8 17 h-lim-p 0.0000 20.0000 0.0012 Out... lnL = -951.788633 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -951.788633 Node 7: lnL = -951.788633 Node 8: lnL = -951.788633 Node 9: lnL = -951.788633 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 46 Sequential format.. Reading seq # 1: YPR054W_Sbay Reading seq # 2: YPR054W_Scer Reading seq # 3: YPR054W_Skud Reading seq # 4: YPR054W_Smik Reading seq # 5: YPR054W_Spar Sequences read.. Counting patterns.. # site patterns = 21 Counting frequencies.. 120 bytes for distance 3360 bytes for lkl0 2688 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.154359 0.008363 0.102480 0.034553 0.000060 0.122538 0.086370 0.194907 lnL0 = -149.603483 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 149.603483 x= 0.15436 0.00836 0.10248 0.03455 0.00006 0.12254 0.08637 0.19491 1 h-lim-p 0.0000 0.0000 36.7158 149.598854 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0068 19.0466 149.226019 0 0.0026 42 | 1/8 3 h-lim-p 0.0007 0.0054 19.8039 149.143601 0 0.0010 54 | 1/8 4 h-lim-p 0.0040 0.0318 2.4023 149.134339 7 0.0029 83 | 1/8 5 h-lim-p 0.0261 0.8153 0.2660 149.098427 0 0.1043 97 | 1/8 6 h-lim-p 0.0161 20.0000 1.7223 149.015379 2 0.0151 120 | 1/8 7 h-lim-p 0.0141 0.1649 1.8436 148.671051 0 0.0282 133 | 1/8 8 h-lim-p 2.5000 20.0000 0.0141 148.623021 6 1.6399 158 | 1/8 9 h-lim-p 2.5000 20.0000 0.0052 148.615791 7 1.5309 197 | 1/8 10 h-lim-p 2.5000 20.0000 0.0011 148.615623 2 1.0889 220 | 1/8 11 h-lim-p 2.5000 20.0000 0.0001 148.615622 2 1.0938 243 | 1/8 12 h-lim-p 2.5000 20.0000 0.0000 148.615622 0 0.6250 263 | 1/8 13 h-lim-p 1.4876 20.0000 0.0000 148.615622 0 0.0007 292 Out... lnL = -148.615622 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -148.615622 Node 7: lnL = -148.615622 Node 8: lnL = -148.615622 Node 9: lnL = -148.615622 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 267 Sequential format.. Reading seq # 1: YPR056W_Sbay Reading seq # 2: YPR056W_Scer Reading seq # 3: YPR056W_Skud Reading seq # 4: YPR056W_Smik Reading seq # 5: YPR056W_Spar Sequences read.. Counting patterns.. # site patterns = 139 Counting frequencies.. 120 bytes for distance 22240 bytes for lkl0 17792 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.115703 0.097891 0.131999 0.096344 0.109484 0.192613 0.193744 0.181621 lnL0 = -1261.276161 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1261.276161 x= 0.11570 0.09789 0.13200 0.09634 0.10948 0.19261 0.19374 0.18162 1 h-lim-p 0.0007 0.0056 57.7604 1259.843024 0 0.0011 22 | 0/8 2 h-lim-p 0.0011 0.0085 16.9470 1259.717368 4 0.0009 41 | 0/8 3 h-lim-p 0.0011 0.0208 14.1113 1259.646068 6 0.0011 66 | 0/8 4 h-lim-p 0.0109 0.1368 1.4086 1259.645093 5 0.0010 92 | 0/8 5 h-lim-p 0.0106 2.1417 0.1317 1259.644998 3 0.0044 110 | 0/8 6 h-lim-p 0.0093 4.8889 0.0632 1259.644268 0 0.0186 131 | 0/8 7 h-lim-p 0.0050 0.9005 0.2336 1259.630442 0 0.0301 153 | 0/8 8 h-lim-p 0.0064 0.2393 1.1051 1259.629358 4 0.0016 183 | 0/8 9 h-lim-p 1.8279 20.0000 0.0010 1259.628975 3 0.9825 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1259.628975 0 1.0938 222 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1259.628975 0 1.0938 242 | 0/8 12 h-lim-p 1.3193 20.0000 0.0000 1259.628975 0 1.3193 262 | 0/8 13 h-lim-p 0.6842 20.0000 0.0000 1259.628975 0 0.1711 283 | 0/8 14 h-lim-p 0.0047 20.0000 0.0002 1259.628975 0 0.0012 304 | 0/8 15 h-lim-p 0.0003 20.0000 0.0006 1259.628975 0 0.0000 329 | 0/8 16 h-lim-p 0.0004 20.0000 0.0000 1259.628975 0 0.0000 360 Out... lnL = -1259.628975 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1259.628975 Node 7: lnL = -1259.628975 Node 8: lnL = -1259.628975 Node 9: lnL = -1259.628975 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 345 Sequential format.. Reading seq # 1: YPR057W_Sbay Reading seq # 2: YPR057W_Scer Reading seq # 3: YPR057W_Skud Reading seq # 4: YPR057W_Smik Reading seq # 5: YPR057W_Spar Sequences read.. Counting patterns.. # site patterns = 195 Counting frequencies.. 120 bytes for distance 31200 bytes for lkl0 24960 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.119494 0.126135 0.127026 0.218224 0.179506 0.272852 0.262198 0.207024 lnL0 = -1767.360237 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1767.360237 x= 0.11949 0.12613 0.12703 0.21822 0.17951 0.27285 0.26220 0.20702 1 h-lim-p 0.0184 0.1475 26.1911 1767.053473 5 0.0009 34 | 0/8 2 h-lim-p 0.0042 0.0608 5.7805 1767.026872 5 0.0017 56 | 0/8 3 h-lim-p 0.0057 0.2580 1.6826 1767.024983 4 0.0014 78 | 0/8 4 h-lim-p 0.0071 0.8487 0.3442 1767.024906 2 0.0014 95 | 0/8 5 h-lim-p 0.0061 3.3973 0.0767 1767.024902 0 0.0013 116 | 0/8 6 h-lim-p 0.0177 20.0000 0.0058 1767.024902 0 0.0044 137 | 0/8 7 h-lim-p 0.0229 20.0000 0.0011 1767.024889 0 0.1834 160 | 0/8 8 h-lim-p 0.0044 10.4871 0.0467 1767.024872 1 0.0045 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1767.024872 0 1.0938 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1767.024872 0 1.0938 222 | 0/8 11 h-lim-p 1.3071 20.0000 0.0000 1767.024872 0 0.5719 242 | 0/8 12 h-lim-p 0.2097 20.0000 0.0000 1767.024872 0 0.0001 273 Out... lnL = -1767.024872 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1767.024872 Node 7: lnL = -1767.024872 Node 8: lnL = -1767.024872 Node 9: lnL = -1767.024872 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 400 Sequential format.. Reading seq # 1: YPR060C_Sbay Reading seq # 2: YPR060C_Scer Reading seq # 3: YPR060C_Skud Reading seq # 4: YPR060C_Smik Reading seq # 5: YPR060C_Spar Sequences read.. Counting patterns.. # site patterns = 174 Counting frequencies.. 120 bytes for distance 27840 bytes for lkl0 22272 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.122310 0.079809 0.101974 0.132567 0.071833 0.197035 0.279697 0.189921 lnL0 = -1773.486763 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1773.486763 x= 0.12231 0.07981 0.10197 0.13257 0.07183 0.19703 0.27970 0.18992 1 h-lim-p 0.0007 0.0056 41.1695 1772.962183 3 0.0006 28 | 0/8 2 h-lim-p 0.0029 0.0231 6.6513 1772.947009 2 0.0007 45 | 0/8 3 h-lim-p 0.0012 0.0654 3.8296 1772.944215 3 0.0005 63 | 0/8 4 h-lim-p 0.0015 0.2374 1.2552 1772.943597 5 0.0009 89 | 0/8 5 h-lim-p 0.0034 0.9036 0.3351 1772.943530 2 0.0013 105 | 0/8 6 h-lim-p 0.0073 6.9105 0.0602 1772.943528 1 0.0009 129 | 0/8 7 h-lim-p 0.0060 20.0000 0.0091 1772.943528 0 0.0013 150 | 0/8 8 h-lim-p 0.0614 20.0000 0.0002 1772.943513 0 0.7364 173 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1772.943513 0 1.0938 193 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1772.943513 0 2.1875 213 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1772.943513 0 0.6250 234 | 0/8 12 h-lim-p 0.1535 20.0000 0.0000 1772.943513 0 0.0768 254 | 0/8 13 h-lim-p 0.0371 20.0000 0.0000 1772.943513 0 0.0000 296 Out... lnL = -1772.943513 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1772.943513 Node 7: lnL = -1772.943513 Node 8: lnL = -1772.943513 Node 9: lnL = -1772.943513 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 316 Sequential format.. Reading seq # 1: YPR061C_Sbay Reading seq # 2: YPR061C_Scer Reading seq # 3: YPR061C_Skud Reading seq # 4: YPR061C_Smik Reading seq # 5: YPR061C_Spar Sequences read.. Counting patterns.. # site patterns = 144 Counting frequencies.. 120 bytes for distance 23040 bytes for lkl0 18432 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.107926 0.094138 0.000060 0.122101 0.128451 0.181562 0.157637 0.161418 lnL0 = -1338.810239 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1338.810239 x= 0.10793 0.09414 0.00006 0.12210 0.12845 0.18156 0.15764 0.16142 1 h-lim-p 0.0025 0.0511 102.8928 1337.038394 6 0.0003 35 | 0/8 2 h-lim-p 0.0003 0.0024 25.9551 1336.783303 0 0.0009 48 | 0/8 3 h-lim-p 0.0051 0.0470 4.5187 1336.773820 5 0.0010 71 | 0/8 4 h-lim-p 0.0040 0.2498 1.0864 1336.773266 2 0.0010 88 | 0/8 5 h-lim-p 0.0050 0.4522 0.2155 1336.773242 3 0.0009 109 | 0/8 6 h-lim-p 0.0044 4.7261 0.0434 1336.773204 0 0.0087 130 | 0/8 7 h-lim-p 0.0066 5.9462 0.0574 1336.772512 0 0.0198 151 | 0/8 8 h-lim-p 0.0034 0.7503 0.3398 1336.769089 0 0.0067 172 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1336.769035 1 1.0938 194 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1336.769035 0 1.0938 214 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1336.769035 0 1.0938 234 | 0/8 12 h-lim-p 1.1695 20.0000 0.0000 1336.769035 0 0.0183 259 | 0/8 13 h-lim-p 0.0021 20.0000 0.0000 1336.769035 0 0.0001 282 | 0/8 14 h-lim-p 0.0003 20.0000 0.0000 1336.769035 0 0.0000 312 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1336.769035 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1336.769035 Node 7: lnL = -1336.769035 Node 8: lnL = -1336.769035 Node 9: lnL = -1336.769035 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 485 Sequential format.. Reading seq # 1: YPR066W_Sbay Reading seq # 2: YPR066W_Scer Reading seq # 3: YPR066W_Skud Reading seq # 4: YPR066W_Smik Reading seq # 5: YPR066W_Spar Sequences read.. Counting patterns.. # site patterns = 197 Counting frequencies.. 120 bytes for distance 31520 bytes for lkl0 25216 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.093925 0.061815 0.076023 0.066875 0.103277 0.240934 0.320234 0.157445 lnL0 = -2099.936306 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2099.936306 x= 0.09393 0.06182 0.07602 0.06687 0.10328 0.24093 0.32023 0.15745 1 h-lim-p 0.0052 1.6456 90.2437 2098.620365 5 0.0003 35 | 0/8 2 h-lim-p 0.0005 0.0040 19.8656 2098.554006 7 0.0003 66 | 0/8 3 h-lim-p 0.0013 0.0336 5.2983 2098.545874 2 0.0006 82 | 0/8 4 h-lim-p 0.0020 0.1521 1.6201 2098.544920 3 0.0008 100 | 0/8 5 h-lim-p 0.0024 0.6785 0.5435 2098.544780 2 0.0010 116 | 0/8 6 h-lim-p 0.0029 1.1542 0.1947 2098.544767 2 0.0008 141 | 0/8 7 h-lim-p 0.0078 14.4162 0.0190 2098.544766 0 0.0034 161 | 0/8 8 h-lim-p 0.0540 20.0000 0.0012 2098.544435 0 0.4324 184 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2098.544433 0 1.0938 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2098.544433 0 1.0938 224 | 0/8 11 h-lim-p 1.5051 20.0000 0.0000 2098.544433 0 0.6585 244 | 0/8 12 h-lim-p 0.4105 20.0000 0.0000 2098.544433 0 0.0064 269 | 0/8 13 h-lim-p 0.0022 20.0000 0.0000 2098.544433 0 0.0011 289 | 0/8 14 h-lim-p 0.0005 20.0000 0.0001 2098.544433 0 0.0005 309 | 0/8 15 h-lim-p 0.0015 20.0000 0.0000 2098.544433 0 0.0000 337 | 0/8 16 h-lim-p 0.0006 20.0000 0.0000 2098.544433 0 0.0000 373 Out... lnL = -2098.544433 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2098.544433 Node 7: lnL = -2098.544433 Node 8: lnL = -2098.544433 Node 9: lnL = -2098.544433 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 129 Sequential format.. Reading seq # 1: YPR067W_Sbay Reading seq # 2: YPR067W_Scer Reading seq # 3: YPR067W_Skud Reading seq # 4: YPR067W_Smik Reading seq # 5: YPR067W_Spar Sequences read.. Counting patterns.. # site patterns = 76 Counting frequencies.. 120 bytes for distance 12160 bytes for lkl0 9728 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.139576 0.182183 0.015953 0.113460 0.114075 0.201461 0.283604 0.212293 lnL0 = -558.200131 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 558.200131 x= 0.13958 0.18218 0.01595 0.11346 0.11408 0.20146 0.28360 0.21229 1 h-lim-p 0.0023 0.0181 24.2365 557.947994 6 0.0010 33 | 0/8 2 h-lim-p 0.0021 0.0165 9.7651 557.861574 6 0.0020 58 | 0/8 3 h-lim-p 0.0066 0.1080 2.9730 557.850825 6 0.0027 83 | 0/8 4 h-lim-p 0.0055 0.1483 1.4485 557.849134 6 0.0020 109 | 0/8 5 h-lim-p 0.0105 0.7071 0.2747 557.848974 2 0.0046 125 | 0/8 6 h-lim-p 0.0238 7.5718 0.0529 557.848967 1 0.0059 148 | 0/8 7 h-lim-p 0.0180 13.3956 0.0174 557.848966 0 0.0045 169 | 0/8 8 h-lim-p 0.3333 20.0000 0.0002 557.848938 0 1.3334 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 557.848935 1 0.9961 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 557.848935 0 1.0938 233 | 0/8 11 h-lim-p 1.7003 20.0000 0.0000 557.848935 0 3.4007 254 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 557.848935 0 0.5469 275 | 0/8 13 h-lim-p 0.1193 20.0000 0.0000 557.848935 0 0.0002 303 Out... lnL = -557.848935 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -557.848935 Node 7: lnL = -557.848935 Node 8: lnL = -557.848935 Node 9: lnL = -557.848935 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 221 Sequential format.. Reading seq # 1: YPR068C_Sbay Reading seq # 2: YPR068C_Scer Reading seq # 3: YPR068C_Skud Reading seq # 4: YPR068C_Smik Reading seq # 5: YPR068C_Spar Sequences read.. Counting patterns.. # site patterns = 127 Counting frequencies.. 120 bytes for distance 20320 bytes for lkl0 16256 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.144850 0.086950 0.125734 0.159285 0.105945 0.196899 0.279947 0.221057 lnL0 = -1047.640955 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1047.640955 x= 0.14485 0.08695 0.12573 0.15929 0.10594 0.19690 0.27995 0.22106 1 h-lim-p 0.0010 0.0076 36.2129 1046.818352 0 0.0014 22 | 0/8 2 h-lim-p 0.0082 0.0655 5.6618 1046.782685 7 0.0023 50 | 0/8 3 h-lim-p 0.0048 0.1333 2.6762 1046.774653 7 0.0027 79 | 0/8 4 h-lim-p 0.0113 1.0297 0.6316 1046.774460 4 0.0010 102 | 0/8 5 h-lim-p 0.0024 1.0831 0.2651 1046.774388 2 0.0022 126 | 0/8 6 h-lim-p 0.0132 6.2911 0.0451 1046.774351 3 0.0086 153 | 0/8 7 h-lim-p 0.0267 10.2228 0.0145 1046.771284 0 0.2137 176 | 0/8 8 h-lim-p 0.0074 0.5434 0.4185 1046.771002 4 0.0028 204 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1046.770986 2 0.9961 228 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1046.770986 0 1.0938 248 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1046.770986 0 2.1875 268 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1046.770986 0 1.0938 288 | 0/8 13 h-lim-p 0.3767 20.0000 0.0000 1046.770986 0 6.0279 312 | 0/8 14 h-lim-p 0.8733 20.0000 0.0000 1046.770986 0 0.1910 333 | 0/8 15 h-lim-p 0.0004 20.0000 0.0053 1046.770986 0 0.0000 359 | 0/8 16 h-lim-p 0.0002 20.0000 0.0001 1046.770986 0 0.0000 392 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 1046.770986 0 0.0000 418 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 19 h-lim-p 0.0000 20.0000 0.0001 | 0/8 20 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -1046.770986 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1046.770986 Node 7: lnL = -1046.770986 Node 8: lnL = -1046.770986 Node 9: lnL = -1046.770986 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 496 Sequential format.. Reading seq # 1: YPR069C_Sbay Reading seq # 2: YPR069C_Scer Reading seq # 3: YPR069C_Skud Reading seq # 4: YPR069C_Smik Reading seq # 5: YPR069C_Spar Sequences read.. Counting patterns.. # site patterns = 143 Counting frequencies.. 120 bytes for distance 22880 bytes for lkl0 18304 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.098578 0.049417 0.037266 0.073825 0.056422 0.148158 0.132075 0.140194 lnL0 = -1948.367891 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1948.367891 x= 0.09858 0.04942 0.03727 0.07383 0.05642 0.14816 0.13207 0.14019 1 h-lim-p 0.0016 0.0128 113.8153 1947.333266 8 0.0002 39 | 0/8 2 h-lim-p 0.0004 0.0029 24.0886 1947.256745 7 0.0003 67 | 0/8 3 h-lim-p 0.0008 0.0370 7.9281 1947.249526 6 0.0003 95 | 0/8 4 h-lim-p 0.0005 0.0420 3.7555 1947.248097 2 0.0003 111 | 0/8 5 h-lim-p 0.0016 0.7516 0.5822 1947.248033 0 0.0004 124 | 0/8 6 h-lim-p 0.0015 0.6845 0.1596 1947.248030 1 0.0003 147 | 0/8 7 h-lim-p 0.0495 20.0000 0.0010 1947.248029 0 0.0433 167 | 0/8 8 h-lim-p 0.0045 20.0000 0.0092 1947.247988 0 0.0179 189 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1947.247986 0 1.0938 209 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1947.247986 0 1.0938 229 | 0/8 11 h-lim-p 1.1815 20.0000 0.0000 1947.247986 0 4.7261 251 | 0/8 12 h-lim-p 2.1037 20.0000 0.0000 1947.247986 0 0.2301 273 | 0/8 13 h-lim-p 1.1173 20.0000 0.0000 1947.247986 0 0.0011 302 Out... lnL = -1947.247986 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1947.247986 Node 7: lnL = -1947.247986 Node 8: lnL = -1947.247986 Node 9: lnL = -1947.247986 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 952 Sequential format.. Reading seq # 1: YPR072W_Sbay Reading seq # 2: YPR072W_Scer Reading seq # 3: YPR072W_Skud Reading seq # 4: YPR072W_Smik Reading seq # 5: YPR072W_Spar Sequences read.. Counting patterns.. # site patterns = 401 Counting frequencies.. 120 bytes for distance 64160 bytes for lkl0 51328 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.105752 0.091214 0.105854 0.185298 0.186234 0.273520 0.210709 0.182640 lnL0 = -4629.239022 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4629.239022 x= 0.10575 0.09121 0.10585 0.18530 0.18623 0.27352 0.21071 0.18264 1 h-lim-p 0.0023 0.3042 199.0758 4624.176232 3 0.0003 30 | 0/8 2 h-lim-p 0.0008 0.0065 43.8715 4623.635091 6 0.0006 55 | 0/8 3 h-lim-p 0.0019 0.0336 13.2900 4623.598514 2 0.0004 72 | 0/8 4 h-lim-p 0.0019 0.1091 3.1287 4623.596016 5 0.0005 98 | 0/8 5 h-lim-p 0.0020 0.4229 0.8748 4623.595853 2 0.0005 115 | 0/8 6 h-lim-p 0.0044 4.0102 0.0906 4623.595822 0 0.0022 135 | 0/8 7 h-lim-p 0.0107 20.0000 0.0187 4623.591814 0 0.1284 158 | 0/8 8 h-lim-p 0.0017 0.4396 1.3995 4623.582780 1 0.0021 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 4623.582724 2 0.9961 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4623.582724 0 1.0938 216 | 0/8 11 h-lim-p 1.6489 20.0000 0.0000 4623.582724 0 1.4428 236 | 0/8 12 h-lim-p 1.9727 20.0000 0.0000 4623.582724 0 0.8631 256 | 0/8 13 h-lim-p 0.3974 20.0000 0.0000 4623.582724 0 0.0497 278 | 0/8 14 h-lim-p 0.0077 20.0000 0.0001 4623.582724 0 0.0039 298 | 0/8 15 h-lim-p 0.0030 20.0000 0.0001 4623.582724 0 0.0000 324 | 0/8 16 h-lim-p 0.0003 20.0000 0.0000 4623.582724 0 0.0000 352 | 0/8 17 h-lim-p 0.0002 20.0000 0.0000 4623.582724 0 0.0000 377 Out... lnL = -4623.582724 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4623.582724 Node 7: lnL = -4623.582724 Node 8: lnL = -4623.582724 Node 9: lnL = -4623.582724 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 472 Sequential format.. Reading seq # 1: YPR073C_Sbay Reading seq # 2: YPR073C_Scer Reading seq # 3: YPR073C_Skud Reading seq # 4: YPR073C_Smik Reading seq # 5: YPR073C_Spar Sequences read.. Counting patterns.. # site patterns = 181 Counting frequencies.. 120 bytes for distance 28960 bytes for lkl0 23168 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.049592 0.116825 0.080017 0.126692 0.071325 0.198279 0.142316 0.102231 lnL0 = -1848.538728 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1848.538728 x= 0.04959 0.11683 0.08002 0.12669 0.07133 0.19828 0.14232 0.10223 1 h-lim-p 0.0024 0.0195 70.2845 1847.545703 8 0.0004 43 | 0/8 2 h-lim-p 0.0007 0.0057 22.8293 1847.435242 6 0.0005 69 | 0/8 3 h-lim-p 0.0013 0.0251 8.1104 1847.420676 4 0.0005 89 | 0/8 4 h-lim-p 0.0015 0.0833 2.7352 1847.419437 2 0.0004 106 | 0/8 5 h-lim-p 0.0021 0.4575 0.4800 1847.419371 3 0.0006 125 | 0/8 6 h-lim-p 0.0028 2.8755 0.0973 1847.419368 1 0.0007 148 | 0/8 7 h-lim-p 0.0051 18.9435 0.0132 1847.419366 1 0.0025 171 | 0/8 8 h-lim-p 0.0120 20.0000 0.0028 1847.419004 0 0.1913 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1847.418994 1 0.9961 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1847.418994 0 0.5469 238 | 0/8 11 h-lim-p 0.3347 20.0000 0.0000 1847.418994 0 0.0105 262 | 0/8 12 h-lim-p 0.0046 20.0000 0.0000 1847.418994 0 0.0000 288 | 0/8 13 h-lim-p 0.0005 20.0000 0.0000 1847.418994 0 0.0000 321 Out... lnL = -1847.418994 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1847.418994 Node 7: lnL = -1847.418994 Node 8: lnL = -1847.418994 Node 9: lnL = -1847.418994 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 344 Sequential format.. Reading seq # 1: YPR075C_Sbay Reading seq # 2: YPR075C_Scer Reading seq # 3: YPR075C_Skud Reading seq # 4: YPR075C_Smik Reading seq # 5: YPR075C_Spar Sequences read.. Counting patterns.. # site patterns = 164 Counting frequencies.. 120 bytes for distance 26240 bytes for lkl0 20992 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.075801 0.047996 0.098510 0.138204 0.011760 0.230583 0.177374 0.128228 lnL0 = -1406.066272 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1406.066272 x= 0.07580 0.04800 0.09851 0.13820 0.01176 0.23058 0.17737 0.12823 1 h-lim-p 0.0003 0.0299 293.0120 1402.525071 8 0.0001 39 | 0/8 2 h-lim-p 0.0010 0.0081 31.5240 1402.202933 8 0.0007 69 | 0/8 3 h-lim-p 0.0015 0.0119 11.1296 1402.166988 5 0.0006 90 | 0/8 4 h-lim-p 0.0022 0.0413 3.2191 1402.163182 6 0.0008 117 | 0/8 5 h-lim-p 0.0053 0.4649 0.4863 1402.163107 2 0.0006 135 | 0/8 6 h-lim-p 0.0038 3.3485 0.0797 1402.163103 2 0.0012 160 | 0/8 7 h-lim-p 0.0166 20.0000 0.0058 1402.163099 0 0.0166 180 | 0/8 8 h-lim-p 0.0149 16.2412 0.0065 1402.162864 0 0.1191 203 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 1402.162789 3 1.4879 231 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1402.162777 2 1.6492 257 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1402.162777 0 1.0938 277 | 0/8 12 h-lim-p 2.4882 20.0000 0.0000 1402.162777 0 2.1772 297 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1402.162777 0 0.6250 318 | 0/8 14 h-lim-p 0.1290 20.0000 0.0000 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0009 | 0/8 16 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -1402.162777 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1402.162777 Node 7: lnL = -1402.162777 Node 8: lnL = -1402.162777 Node 9: lnL = -1402.162777 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 672 Sequential format.. Reading seq # 1: YPR078C_Sbay Reading seq # 2: YPR078C_Scer Reading seq # 3: YPR078C_Skud Reading seq # 4: YPR078C_Smik Reading seq # 5: YPR078C_Spar Sequences read.. Counting patterns.. # site patterns = 244 Counting frequencies.. 120 bytes for distance 39040 bytes for lkl0 31232 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.143470 0.077515 0.070094 0.109832 0.096974 0.229610 0.301726 0.204546 lnL0 = -3082.834721 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3082.834721 x= 0.14347 0.07752 0.07009 0.10983 0.09697 0.22961 0.30173 0.20455 1 h-lim-p 0.0018 0.0145 83.0049 3081.862191 6 0.0003 36 | 0/8 2 h-lim-p 0.0012 0.0117 21.3198 3081.773419 7 0.0004 63 | 0/8 3 h-lim-p 0.0007 0.0314 12.6376 3081.750851 5 0.0004 86 | 0/8 4 h-lim-p 0.0009 0.0727 5.1252 3081.744550 5 0.0006 110 | 0/8 5 h-lim-p 0.0016 0.2062 1.8856 3081.743698 4 0.0006 132 | 0/8 6 h-lim-p 0.0013 0.3751 0.8175 3081.743563 3 0.0005 150 | 0/8 7 h-lim-p 0.1625 20.0000 0.0025 3081.743558 0 0.0355 171 | 0/8 8 h-lim-p 0.0067 20.0000 0.0131 3081.743398 0 0.0268 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3081.743397 0 1.0938 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3081.743397 0 1.0938 233 | 0/8 11 h-lim-p 1.3058 20.0000 0.0000 3081.743397 0 2.6116 254 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3081.743397 0 0.0098 281 | 0/8 13 h-lim-p 0.0020 20.0000 0.0000 3081.743397 0 0.0015 301 | 0/8 14 h-lim-p 0.0004 20.0000 0.0000 3081.743397 0 0.0000 332 | 0/8 15 h-lim-p 0.0000 20.0000 0.0009 | 0/8 16 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -3081.743397 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3081.743397 Node 7: lnL = -3081.743397 Node 8: lnL = -3081.743397 Node 9: lnL = -3081.743397 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 217 Sequential format.. Reading seq # 1: YPR082C_Sbay Reading seq # 2: YPR082C_Scer Reading seq # 3: YPR082C_Skud Reading seq # 4: YPR082C_Smik Reading seq # 5: YPR082C_Spar Sequences read.. Counting patterns.. # site patterns = 85 Counting frequencies.. 120 bytes for distance 13600 bytes for lkl0 10880 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.041952 0.093081 0.083351 0.053462 0.043972 0.133495 0.120916 0.076270 lnL0 = -830.271332 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 830.271332 x= 0.04195 0.09308 0.08335 0.05346 0.04397 0.13349 0.12092 0.07627 1 h-lim-p 0.0036 0.0289 31.4755 830.039655 5 0.0005 34 | 0/8 2 h-lim-p 0.0010 0.0077 10.8624 830.015567 2 0.0005 50 | 0/8 3 h-lim-p 0.0013 0.0361 3.8642 830.012566 5 0.0005 75 | 0/8 4 h-lim-p 0.0015 0.1505 1.1398 830.012073 4 0.0008 96 | 0/8 5 h-lim-p 0.0047 1.4569 0.2053 830.012057 2 0.0007 114 | 0/8 6 h-lim-p 0.0028 1.5722 0.0542 830.012056 1 0.0006 137 | 0/8 7 h-lim-p 0.0066 20.0000 0.0046 830.012056 0 0.0029 157 | 0/8 8 h-lim-p 0.0328 20.0000 0.0004 830.012035 0 0.3939 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 830.012035 0 1.0938 200 | 0/8 10 h-lim-p 1.6546 20.0000 0.0000 830.012035 0 0.7239 220 | 0/8 11 h-lim-p 0.5386 20.0000 0.0000 830.012035 0 0.0000 253 | 0/8 12 h-lim-p 0.0000 20.0000 0.0000 830.012035 0 0.0000 275 | 0/8 13 h-lim-p 0.0000 20.0000 0.0006 830.012035 0 0.0000 306 | 0/8 14 h-lim-p 0.0000 20.0000 0.0006 830.012035 0 0.0000 338 | 0/8 15 h-lim-p 0.0000 20.0000 0.0006 | 0/8 16 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -830.012035 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -830.012035 Node 7: lnL = -830.012035 Node 8: lnL = -830.012035 Node 9: lnL = -830.012035 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 217 Sequential format.. Reading seq # 1: YPR083W_Sbay Reading seq # 2: YPR083W_Scer Reading seq # 3: YPR083W_Skud Reading seq # 4: YPR083W_Smik Reading seq # 5: YPR083W_Spar Sequences read.. Counting patterns.. # site patterns = 82 Counting frequencies.. 120 bytes for distance 13120 bytes for lkl0 10496 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.040120 0.067695 0.032044 0.054840 0.042594 0.163148 0.134840 0.070757 lnL0 = -808.202667 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 808.202667 x= 0.04012 0.06770 0.03204 0.05484 0.04259 0.16315 0.13484 0.07076 1 h-lim-p 0.0006 0.0045 62.7339 807.617467 9 0.0003 44 | 0/8 2 h-lim-p 0.0014 0.0111 14.1933 807.549001 3 0.0007 62 | 0/8 3 h-lim-p 0.0013 0.0245 7.7342 807.541584 5 0.0003 88 | 0/8 4 h-lim-p 0.0013 0.0518 1.8005 807.540983 5 0.0004 113 | 0/8 5 h-lim-p 0.0016 0.5119 0.4661 807.540880 3 0.0010 133 | 0/8 6 h-lim-p 0.0060 1.5881 0.0778 807.540878 1 0.0006 157 | 0/8 7 h-lim-p 0.0021 5.9611 0.0226 807.540877 1 0.0010 180 | 0/8 8 h-lim-p 0.0298 20.0000 0.0008 807.540637 0 0.4767 204 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 807.540627 2 0.9961 228 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 807.540627 0 0.5469 249 | 0/8 11 h-lim-p 0.3618 20.0000 0.0000 807.540627 0 0.0057 274 | 0/8 12 h-lim-p 0.0026 20.0000 0.0000 807.540627 0 0.0000 312 | 0/8 13 h-lim-p 0.0000 20.0000 0.0006 807.540627 0 0.0000 340 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 807.540627 0 0.0038 368 | 0/8 15 h-lim-p 0.0075 20.0000 0.0001 807.540627 0 0.0000 398 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 807.540627 0 0.0000 431 | 0/8 17 h-lim-p 0.0000 20.0000 0.0022 807.540627 0 0.0000 463 | 0/8 18 h-lim-p 0.0000 20.0000 0.0008 807.540627 0 0.0005 488 | 0/8 19 h-lim-p 0.0014 20.0000 0.0003 807.540627 0 0.0012 508 | 0/8 20 h-lim-p 0.0015 20.0000 0.0002 807.540627 0 0.0000 550 | 0/8 21 h-lim-p 0.0000 20.0000 0.0019 | 0/8 22 h-lim-p 0.0000 20.0000 0.0019 Out... lnL = -807.540627 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -807.540627 Node 7: lnL = -807.540627 Node 8: lnL = -807.540627 Node 9: lnL = -807.540627 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 410 Sequential format.. Reading seq # 1: YPR084W_Sbay Reading seq # 2: YPR084W_Scer Reading seq # 3: YPR084W_Skud Reading seq # 4: YPR084W_Smik Reading seq # 5: YPR084W_Spar Sequences read.. Counting patterns.. # site patterns = 208 Counting frequencies.. 120 bytes for distance 33280 bytes for lkl0 26624 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.101013 0.042428 0.151507 0.133065 0.090805 0.249415 0.248896 0.160551 lnL0 = -1900.737403 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1900.737403 x= 0.10101 0.04243 0.15151 0.13306 0.09081 0.24942 0.24890 0.16055 1 h-lim-p 0.0017 0.0137 70.4274 1899.599638 9 0.0005 44 | 0/8 2 h-lim-p 0.0010 0.0081 13.7181 1899.544179 7 0.0006 74 | 0/8 3 h-lim-p 0.0015 0.0874 5.5874 1899.537167 5 0.0005 98 | 0/8 4 h-lim-p 0.0022 0.2539 1.3267 1899.536168 5 0.0012 123 | 0/8 5 h-lim-p 0.0147 1.8104 0.1096 1899.536161 2 0.0010 142 | 0/8 6 h-lim-p 0.0033 7.5195 0.0325 1899.536161 0 0.0014 162 | 0/8 7 h-lim-p 0.0121 20.0000 0.0038 1899.536161 0 0.0026 183 | 0/8 8 h-lim-p 0.0911 20.0000 0.0001 1899.536157 0 0.7289 206 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1899.536157 0 1.0938 226 | 0/8 10 h-lim-p 2.2433 20.0000 0.0000 1899.536157 0 0.9814 246 | 0/8 11 h-lim-p 0.8299 20.0000 0.0000 1899.536157 0 0.0519 269 | 0/8 12 h-lim-p 0.0081 20.0000 0.0000 1899.536157 0 0.0001 295 | 0/8 13 h-lim-p 0.0011 20.0000 0.0000 1899.536157 0 0.0000 332 Out... lnL = -1899.536157 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1899.536157 Node 7: lnL = -1899.536157 Node 8: lnL = -1899.536157 Node 9: lnL = -1899.536157 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 278 Sequential format.. Reading seq # 1: YPR085C_Sbay Reading seq # 2: YPR085C_Scer Reading seq # 3: YPR085C_Skud Reading seq # 4: YPR085C_Smik Reading seq # 5: YPR085C_Spar Sequences read.. Counting patterns.. # site patterns = 119 Counting frequencies.. 120 bytes for distance 19040 bytes for lkl0 15232 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.069262 0.087980 0.062486 0.115379 0.084918 0.143291 0.209516 0.114209 lnL0 = -1194.198982 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1194.198982 x= 0.06926 0.08798 0.06249 0.11538 0.08492 0.14329 0.20952 0.11421 1 h-lim-p 0.0007 0.0054 67.1346 1193.009207 6 0.0006 35 | 0/8 2 h-lim-p 0.0011 0.0088 14.4756 1192.933089 6 0.0007 61 | 0/8 3 h-lim-p 0.0019 0.0687 5.5889 1192.925042 6 0.0006 91 | 0/8 4 h-lim-p 0.0016 0.1107 2.0149 1192.923513 4 0.0009 112 | 0/8 5 h-lim-p 0.0029 0.5092 0.5910 1192.923369 4 0.0009 136 | 0/8 6 h-lim-p 0.0070 2.6637 0.0773 1192.923367 0 0.0008 158 | 0/8 7 h-lim-p 0.0107 20.0000 0.0055 1192.923355 0 0.0322 179 | 0/8 8 h-lim-p 0.0098 20.0000 0.0180 1192.922951 0 0.0394 201 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1192.922947 1 0.9961 223 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1192.922947 0 0.5469 244 | 0/8 11 h-lim-p 0.3826 20.0000 0.0000 1192.922947 0 0.0000 288 Out... lnL = -1192.922947 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1192.922947 Node 7: lnL = -1192.922947 Node 8: lnL = -1192.922947 Node 9: lnL = -1192.922947 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 278 Sequential format.. Reading seq # 1: YPR086W_Sbay Reading seq # 2: YPR086W_Scer Reading seq # 3: YPR086W_Skud Reading seq # 4: YPR086W_Smik Reading seq # 5: YPR086W_Spar Sequences read.. Counting patterns.. # site patterns = 107 Counting frequencies.. 120 bytes for distance 17120 bytes for lkl0 13696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.079546 0.081690 0.050904 0.122609 0.074361 0.294426 0.180830 0.130024 lnL0 = -1046.404628 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1046.404628 x= 0.07955 0.08169 0.05090 0.12261 0.07436 0.29443 0.18083 0.13002 1 h-lim-p 0.0012 0.0094 36.7102 1045.995840 7 0.0006 38 | 0/8 2 h-lim-p 0.0005 0.0038 19.2766 1045.830941 0 0.0009 51 | 0/8 3 h-lim-p 0.0005 0.0036 17.3097 1045.717473 0 0.0014 64 | 0/8 4 h-lim-p 0.0021 0.0172 9.0735 1045.699301 6 0.0007 92 | 0/8 5 h-lim-p 0.0031 0.1609 1.9907 1045.693739 3 0.0031 110 | 0/8 6 h-lim-p 0.0021 0.0963 2.9642 1045.687655 0 0.0042 123 | 0/8 7 h-lim-p 0.0157 0.2290 0.7883 1045.687462 3 0.0008 144 | 0/8 8 h-lim-p 0.1709 20.0000 0.0036 1045.685775 0 1.0256 166 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 1045.685750 2 0.9644 190 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1045.685749 0 1.0938 210 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1045.685749 0 1.0938 230 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1045.685749 0 0.0049 258 | 0/8 13 h-lim-p 0.0022 20.0000 0.0000 1045.685749 0 0.0000 297 Out... lnL = -1045.685749 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1045.685749 Node 7: lnL = -1045.685749 Node 8: lnL = -1045.685749 Node 9: lnL = -1045.685749 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 252 Sequential format.. Reading seq # 1: YPR088C_Sbay Reading seq # 2: YPR088C_Scer Reading seq # 3: YPR088C_Skud Reading seq # 4: YPR088C_Smik Reading seq # 5: YPR088C_Spar Sequences read.. Counting patterns.. # site patterns = 96 Counting frequencies.. 120 bytes for distance 15360 bytes for lkl0 12288 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.055676 0.090364 0.038929 0.087159 0.047732 0.137572 0.140755 0.090882 lnL0 = -995.101693 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 995.101693 x= 0.05568 0.09036 0.03893 0.08716 0.04773 0.13757 0.14075 0.09088 1 h-lim-p 0.0331 0.3553 24.5169 995.010651 8 0.0003 49 | 0/8 2 h-lim-p 0.0010 0.0194 7.3457 994.996595 6 0.0006 74 | 0/8 3 h-lim-p 0.0012 0.0307 3.5331 994.994727 6 0.0004 102 | 0/8 4 h-lim-p 0.0025 0.2387 0.5227 994.994667 3 0.0005 121 | 0/8 5 h-lim-p 0.0044 2.4591 0.0560 994.994666 1 0.0005 145 | 0/8 6 h-lim-p 0.0036 13.8888 0.0084 994.994666 0 0.0008 166 | 0/8 7 h-lim-p 0.0057 20.0000 0.0012 994.994666 0 0.0025 186 | 0/8 8 h-lim-p 0.0405 20.0000 0.0001 994.994665 0 0.3240 209 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 994.994665 0 1.2500 229 | 0/8 10 h-lim-p 2.0849 20.0000 0.0000 994.994665 0 0.2280 251 | 0/8 11 h-lim-p 0.1051 20.0000 0.0000 994.994665 0 0.0000 288 | 0/8 12 h-lim-p 0.0000 20.0000 0.0022 | 0/8 13 h-lim-p 0.0000 20.0000 0.0022 Out... lnL = -994.994665 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -994.994665 Node 7: lnL = -994.994665 Node 8: lnL = -994.994665 Node 9: lnL = -994.994665 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 894 Sequential format.. Reading seq # 1: YPR091C_Sbay Reading seq # 2: YPR091C_Scer Reading seq # 3: YPR091C_Skud Reading seq # 4: YPR091C_Smik Reading seq # 5: YPR091C_Spar Sequences read.. Counting patterns.. # site patterns = 184 Counting frequencies.. 120 bytes for distance 29440 bytes for lkl0 23552 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.050670 0.008083 0.043334 0.066361 0.036876 0.099105 0.113290 0.074880 lnL0 = -2990.318020 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2990.318020 x= 0.05067 0.00808 0.04333 0.06636 0.03688 0.09911 0.11329 0.07488 1 h-lim-p 0.0001 0.1509 689.1093 2984.393426 6 0.0000 35 | 0/8 2 h-lim-p 0.0004 0.0030 54.7300 2984.244803 5 0.0001 58 | 0/8 3 h-lim-p 0.0010 0.0356 5.6746 2984.242792 4 0.0001 80 | 0/8 4 h-lim-p 0.0002 0.0212 3.2120 2984.242433 3 0.0001 98 | 0/8 5 h-lim-p 0.0003 0.1533 1.0071 2984.242379 2 0.0001 114 | 0/8 6 h-lim-p 0.0031 3.4823 0.0392 2984.242378 0 0.0003 128 | 0/8 7 h-lim-p 0.0006 5.8529 0.0214 2984.242377 0 0.0013 149 | 0/8 8 h-lim-p 0.0062 7.8621 0.0044 2984.241026 0 0.0985 173 | 0/8 9 h-lim-p 0.1184 20.0000 0.0036 2984.240841 0 0.9475 196 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 2984.240790 0 1.0938 216 | 0/8 11 h-lim-p 0.3084 20.0000 0.0004 2984.240787 0 1.2335 238 | 0/8 12 h-lim-p 2.5000 20.0000 0.0001 2984.240787 0 1.0938 258 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2984.240787 0 0.0000 307 | 0/8 14 h-lim-p 0.0000 20.0000 0.0028 2984.240787 0 0.0000 337 | 0/8 15 h-lim-p 0.0000 20.0000 0.0007 2984.240787 0 0.0013 364 | 0/8 16 h-lim-p 0.0026 20.0000 0.0004 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0101 | 0/8 18 h-lim-p 0.0000 20.0000 0.0101 Out... lnL = -2984.240787 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2984.240787 Node 7: lnL = -2984.240787 Node 8: lnL = -2984.240787 Node 9: lnL = -2984.240787 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 149 Sequential format.. Reading seq # 1: YPR093C_Sbay Reading seq # 2: YPR093C_Scer Reading seq # 3: YPR093C_Skud Reading seq # 4: YPR093C_Smik Reading seq # 5: YPR093C_Spar Sequences read.. Counting patterns.. # site patterns = 87 Counting frequencies.. 120 bytes for distance 13920 bytes for lkl0 11136 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.108468 0.146960 0.198388 0.024359 0.142999 0.052268 0.622190 0.185726 lnL0 = -681.456379 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 681.456379 x= 0.10847 0.14696 0.19839 0.02436 0.14300 0.05227 0.62219 0.18573 1 h-lim-p 0.0011 0.0205 111.4087 676.929962 3 0.0009 28 | 0/8 2 h-lim-p 0.0015 0.0122 37.3224 674.328342 0 0.0061 42 | 0/8 3 h-lim-p 0.0008 0.0061 31.0366 673.559589 0 0.0030 56 | 0/8 4 h-lim-p 0.0045 0.0359 4.3864 673.503896 1 0.0056 70 | 0/8 5 h-lim-p 0.0043 0.0344 4.6162 673.465872 1 0.0054 84 | 0/8 6 h-lim-p 0.0209 0.1674 0.7863 673.422463 0 0.0314 96 | 0/8 7 h-lim-p 0.0060 0.1285 4.1134 673.364990 3 0.0061 122 | 0/8 8 h-lim-p 0.0252 0.4950 0.9930 672.737177 0 0.1010 136 | 0/8 9 h-lim-p 1.3637 10.9098 0.0260 672.670671 7 1.0371 172 | 0/8 10 h-lim-p 2.5000 20.0000 0.0072 672.664067 6 1.4650 206 | 0/8 11 h-lim-p 2.5000 20.0000 0.0022 672.663106 5 1.4675 238 | 0/8 12 h-lim-p 2.5000 20.0000 0.0004 672.663085 1 1.2500 260 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 672.663084 0 1.2500 280 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 672.663084 0 2.1875 300 | 0/8 15 h-lim-p 2.3311 20.0000 0.0000 672.663084 0 1.0199 320 | 0/8 16 h-lim-p 2.5000 20.0000 0.0000 672.663084 0 0.0012 350 Out... lnL = -672.663084 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -672.663084 Node 7: lnL = -672.663084 Node 8: lnL = -672.663084 Node 9: lnL = -672.663084 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 172 Sequential format.. Reading seq # 1: YPR094W_Sbay Reading seq # 2: YPR094W_Scer Reading seq # 3: YPR094W_Skud Reading seq # 4: YPR094W_Smik Reading seq # 5: YPR094W_Spar Sequences read.. Counting patterns.. # site patterns = 97 Counting frequencies.. 120 bytes for distance 15520 bytes for lkl0 12416 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.041816 0.328005 0.048343 0.085995 0.093614 0.285552 0.426060 0.117243 lnL0 = -783.322924 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 783.322924 x= 0.04182 0.32801 0.04834 0.08600 0.09361 0.28555 0.42606 0.11724 1 h-lim-p 0.0007 0.0054 36.6918 782.410518 0 0.0013 23 | 0/8 2 h-lim-p 0.0011 0.0091 10.7058 782.349381 6 0.0011 48 | 0/8 3 h-lim-p 0.0014 0.0364 8.7444 782.262306 0 0.0041 61 | 0/8 4 h-lim-p 0.0089 0.0879 4.0096 782.250751 4 0.0020 81 | 0/8 5 h-lim-p 0.0048 0.2218 1.6374 782.244785 1 0.0060 95 | 0/8 6 h-lim-p 0.0102 0.2215 0.9578 782.244120 3 0.0019 114 | 0/8 7 h-lim-p 0.0649 17.6270 0.0286 782.243259 0 0.1298 135 | 0/8 8 h-lim-p 0.0295 3.2135 0.1262 782.236640 0 0.0589 156 | 0/8 9 h-lim-p 2.5000 20.0000 0.0015 782.236387 2 1.0889 180 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 782.236387 0 1.0938 200 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 782.236387 0 1.0938 220 | 0/8 12 h-lim-p 1.5490 20.0000 0.0000 782.236387 0 0.0061 247 | 0/8 13 h-lim-p 0.0027 20.0000 0.0000 782.236387 0 0.0000 287 Out... lnL = -782.236387 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -782.236387 Node 7: lnL = -782.236387 Node 8: lnL = -782.236387 Node 9: lnL = -782.236387 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 541 Sequential format.. Reading seq # 1: YPR100W_Sbay Reading seq # 2: YPR100W_Scer Reading seq # 3: YPR100W_Skud Reading seq # 4: YPR100W_Smik Reading seq # 5: YPR100W_Spar Sequences read.. Counting patterns.. # site patterns = 181 Counting frequencies.. 120 bytes for distance 28960 bytes for lkl0 23168 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.077096 0.056269 0.072262 0.101692 0.070678 0.195928 0.159471 0.119958 lnL0 = -2319.925210 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2319.925210 x= 0.07710 0.05627 0.07226 0.10169 0.07068 0.19593 0.15947 0.11996 1 h-lim-p 0.0019 0.0152 113.5929 2318.633234 2 0.0002 28 | 0/8 2 h-lim-p 0.0020 0.0159 11.5026 2318.607541 4 0.0004 49 | 0/8 3 h-lim-p 0.0008 0.0387 5.8367 2318.604063 5 0.0002 73 | 0/8 4 h-lim-p 0.0011 0.1717 1.3698 2318.603758 4 0.0003 94 | 0/8 5 h-lim-p 0.0023 1.3769 0.2031 2318.603750 2 0.0004 113 | 0/8 6 h-lim-p 0.0024 6.5239 0.0331 2318.603748 0 0.0012 133 | 0/8 7 h-lim-p 0.0138 20.0000 0.0028 2318.603663 0 0.1105 156 | 0/8 8 h-lim-p 0.0012 0.4018 0.2544 2318.603096 0 0.0025 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2318.603080 1 0.9961 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2318.603080 0 1.0938 219 | 0/8 11 h-lim-p 1.0560 20.0000 0.0000 2318.603080 0 0.2640 240 | 0/8 12 h-lim-p 0.1238 20.0000 0.0000 2318.603080 0 0.0155 262 | 0/8 13 h-lim-p 0.0077 20.0000 0.0000 2318.603080 0 0.0010 284 | 0/8 14 h-lim-p 0.0005 20.0000 0.0001 2318.603080 0 0.0001 305 | 0/8 15 h-lim-p 0.0008 20.0000 0.0000 2318.603080 0 0.0000 341 | 0/8 16 h-lim-p 0.0000 20.0000 0.0010 2318.603080 0 0.0000 370 | 0/8 17 h-lim-p 0.0000 20.0000 0.0004 2318.603080 0 0.0000 390 | 0/8 18 h-lim-p 0.0000 20.0000 0.0002 2318.603080 0 0.0000 413 | 0/8 19 h-lim-p 0.0000 20.0000 0.0003 2318.603080 0 0.0000 434 | 0/8 20 h-lim-p 0.0000 20.0000 0.0009 2318.603080 0 0.0000 455 | 0/8 21 h-lim-p 0.0000 20.0000 0.0006 2318.603080 0 0.0000 475 | 0/8 22 h-lim-p 0.0001 20.0000 0.0000 2318.603080 0 0.0000 496 | 0/8 23 h-lim-p 0.0001 20.0000 0.0000 2318.603080 0 0.0000 520 | 0/8 24 h-lim-p 0.0000 20.0000 0.0000 2318.603080 0 0.0000 550 Out... lnL = -2318.603080 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2318.603080 Node 7: lnL = -2318.603080 Node 8: lnL = -2318.603080 Node 9: lnL = -2318.603080 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 302 Sequential format.. Reading seq # 1: YPR101W_Sbay Reading seq # 2: YPR101W_Scer Reading seq # 3: YPR101W_Skud Reading seq # 4: YPR101W_Smik Reading seq # 5: YPR101W_Spar Sequences read.. Counting patterns.. # site patterns = 150 Counting frequencies.. 120 bytes for distance 24000 bytes for lkl0 19200 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.100759 0.128809 0.108798 0.170975 0.085064 0.213601 0.169384 0.159408 lnL0 = -1292.208419 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1292.208419 x= 0.10076 0.12881 0.10880 0.17098 0.08506 0.21360 0.16938 0.15941 1 h-lim-p 0.0040 0.0317 38.7560 1291.479434 4 0.0010 31 | 0/8 2 h-lim-p 0.0021 0.0171 11.5166 1291.403607 8 0.0012 65 | 0/8 3 h-lim-p 0.0021 0.0453 6.8413 1291.390380 6 0.0007 93 | 0/8 4 h-lim-p 0.0026 0.1160 1.9493 1291.387530 4 0.0017 115 | 0/8 5 h-lim-p 0.0096 0.7802 0.3413 1291.387436 3 0.0017 136 | 0/8 6 h-lim-p 0.0124 5.5839 0.0467 1291.387433 1 0.0015 160 | 0/8 7 h-lim-p 0.0056 17.4780 0.0128 1291.387430 0 0.0112 181 | 0/8 8 h-lim-p 0.0330 20.0000 0.0043 1291.387157 0 0.1978 203 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1291.387157 0 1.0938 223 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1291.387157 0 1.0938 243 | 0/8 11 h-lim-p 1.7437 20.0000 0.0000 1291.387157 0 1.7437 263 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1291.387157 0 0.0001 297 Out... lnL = -1291.387157 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1291.387157 Node 7: lnL = -1291.387157 Node 8: lnL = -1291.387157 Node 9: lnL = -1291.387157 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 642 Sequential format.. Reading seq # 1: YPR103W_Sbay Reading seq # 2: YPR103W_Scer Reading seq # 3: YPR103W_Skud Reading seq # 4: YPR103W_Smik Reading seq # 5: YPR103W_Spar Sequences read.. Counting patterns.. # site patterns = 255 Counting frequencies.. 120 bytes for distance 40800 bytes for lkl0 32640 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.098577 0.144386 0.087321 0.119499 0.090765 0.199630 0.198703 0.155087 lnL0 = -2973.942878 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2973.942878 x= 0.09858 0.14439 0.08732 0.11950 0.09077 0.19963 0.19870 0.15509 1 h-lim-p 0.0031 0.8580 137.4518 2971.160057 3 0.0003 30 | 0/8 2 h-lim-p 0.0007 0.0054 37.3775 2970.871056 5 0.0004 54 | 0/8 3 h-lim-p 0.0007 0.0097 24.4701 2970.789322 7 0.0004 85 | 0/8 4 h-lim-p 0.0034 0.0828 2.6784 2970.787411 4 0.0005 108 | 0/8 5 h-lim-p 0.0018 0.2606 0.8319 2970.787198 2 0.0007 124 | 0/8 6 h-lim-p 0.0066 3.4939 0.0850 2970.787196 1 0.0004 149 | 0/8 7 h-lim-p 0.0016 14.0452 0.0220 2970.787196 0 0.0007 169 | 0/8 8 h-lim-p 0.0979 20.0000 0.0002 2970.787155 0 1.1749 192 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2970.787154 0 1.0938 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2970.787154 0 1.0938 232 | 0/8 11 h-lim-p 1.2024 20.0000 0.0000 2970.787154 0 2.4049 253 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2970.787154 0 0.0195 279 | 0/8 13 h-lim-p 0.0032 20.0000 0.0000 2970.787154 0 0.0008 300 | 0/8 14 h-lim-p 0.0003 20.0000 0.0001 2970.787154 0 0.0000 340 | 0/8 15 h-lim-p 0.0000 20.0000 0.0007 | 0/8 16 h-lim-p 0.0000 20.0000 0.0007 Out... lnL = -2970.787154 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2970.787154 Node 7: lnL = -2970.787154 Node 8: lnL = -2970.787154 Node 9: lnL = -2970.787154 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 580 Sequential format.. Reading seq # 1: YPR104C_Sbay Reading seq # 2: YPR104C_Scer Reading seq # 3: YPR104C_Skud Reading seq # 4: YPR104C_Smik Reading seq # 5: YPR104C_Spar Sequences read.. Counting patterns.. # site patterns = 172 Counting frequencies.. 120 bytes for distance 27520 bytes for lkl0 22016 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.069459 0.091800 0.007088 0.082115 0.057399 0.132013 0.170758 0.105204 lnL0 = -2251.566949 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2251.566949 x= 0.06946 0.09180 0.00709 0.08212 0.05740 0.13201 0.17076 0.10520 1 h-lim-p 0.0006 0.0048 229.3775 2250.441492 8 0.0001 46 | 0/8 2 h-lim-p 0.0002 0.0026 47.4908 2250.183055 2 0.0002 62 | 0/8 3 h-lim-p 0.0007 0.0156 16.9813 2250.152654 6 0.0002 88 | 0/8 4 h-lim-p 0.0004 0.0207 9.0258 2250.145198 6 0.0002 112 | 0/8 5 h-lim-p 0.0012 0.1010 1.7782 2250.144695 4 0.0003 135 | 0/8 6 h-lim-p 0.0019 0.8570 0.3178 2250.144683 2 0.0002 153 | 0/8 7 h-lim-p 0.0206 20.0000 0.0038 2250.144668 0 0.0310 173 | 0/8 8 h-lim-p 0.0038 1.1012 0.0310 2250.143998 0 0.0152 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2250.143964 2 1.3159 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2250.143963 0 1.0938 240 | 0/8 11 h-lim-p 1.1420 20.0000 0.0000 2250.143963 0 0.9992 260 | 0/8 12 h-lim-p 0.9137 20.0000 0.0000 2250.143963 0 3.6549 282 | 0/8 13 h-lim-p 0.0583 20.0000 0.0007 2250.143963 0 0.0128 303 | 0/8 14 h-lim-p 0.0032 20.0000 0.0028 2250.143963 0 0.0008 324 | 0/8 15 h-lim-p 0.0008 20.0000 0.0027 2250.143963 0 0.0000 360 | 0/8 16 h-lim-p 0.0000 20.0000 0.0005 2250.143963 0 0.0006 386 | 0/8 17 h-lim-p 0.0024 20.0000 0.0001 2250.143963 0 0.0000 415 | 0/8 18 h-lim-p 0.0000 20.0000 0.0001 2250.143963 0 0.0051 444 | 0/8 19 h-lim-p 0.0303 20.0000 0.0000 2250.143963 0 0.0019 467 | 0/8 20 h-lim-p 0.0001 20.0000 0.0002 2250.143963 0 0.0000 489 | 0/8 21 h-lim-p 0.0000 20.0000 0.0023 2250.143963 0 0.0000 509 | 0/8 22 h-lim-p 0.0000 20.0000 0.0046 2250.143963 0 0.0000 531 | 0/8 23 h-lim-p 0.0000 20.0000 0.0017 2250.143963 0 0.0000 552 | 0/8 24 h-lim-p 0.0001 20.0000 0.0000 2250.143963 0 0.0000 585 | 0/8 25 h-lim-p 0.0000 20.0000 0.0019 2250.143963 0 0.0000 617 | 0/8 26 h-lim-p 0.0000 20.0000 0.0010 2250.143963 0 0.0013 644 | 0/8 27 h-lim-p 0.0025 20.0000 0.0005 2250.143963 0 0.0000 675 | 0/8 28 h-lim-p 0.0000 20.0000 0.0010 2250.143963 0 0.0000 698 | 0/8 29 h-lim-p 0.0000 20.0000 0.0011 2250.143963 0 0.0006 724 | 0/8 30 h-lim-p 0.0023 20.0000 0.0003 2250.143963 0 0.0000 752 | 0/8 31 h-lim-p 0.0000 20.0000 0.0001 2250.143963 0 0.0044 779 | 0/8 32 h-lim-p 0.0157 20.0000 0.0000 2250.143963 0 0.0000 810 | 0/8 33 h-lim-p 0.0000 20.0000 0.0000 2250.143963 0 0.0000 831 | 0/8 34 h-lim-p 0.0001 20.0000 0.0000 2250.143963 0 0.0000 855 Out... lnL = -2250.143963 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2250.143963 Node 7: lnL = -2250.143963 Node 8: lnL = -2250.143963 Node 9: lnL = -2250.143963 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 537 Sequential format.. Reading seq # 1: YPR106W_Sbay Reading seq # 2: YPR106W_Scer Reading seq # 3: YPR106W_Skud Reading seq # 4: YPR106W_Smik Reading seq # 5: YPR106W_Spar Sequences read.. Counting patterns.. # site patterns = 208 Counting frequencies.. 120 bytes for distance 33280 bytes for lkl0 26624 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.138133 0.025852 0.153314 0.109942 0.080302 0.175566 0.251417 0.186580 lnL0 = -2455.520796 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2455.520796 x= 0.13813 0.02585 0.15331 0.10994 0.08030 0.17557 0.25142 0.18658 1 h-lim-p 0.0054 1.1181 95.0583 2454.431052 4 0.0003 33 | 0/8 2 h-lim-p 0.0025 0.0241 10.0048 2454.403181 5 0.0006 55 | 0/8 3 h-lim-p 0.0010 0.0532 5.3984 2454.399731 5 0.0003 79 | 0/8 4 h-lim-p 0.0022 0.2777 0.7307 2454.399570 4 0.0006 102 | 0/8 5 h-lim-p 0.0012 0.5300 0.3871 2454.399529 3 0.0007 131 | 0/8 6 h-lim-p 0.0047 3.5702 0.0562 2454.399528 1 0.0006 155 | 0/8 7 h-lim-p 0.0034 20.0000 0.0096 2454.399528 0 0.0007 176 | 0/8 8 h-lim-p 0.4117 20.0000 0.0000 2454.399527 0 0.8233 197 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2454.399527 0 1.0938 217 | 0/8 10 h-lim-p 1.6990 20.0000 0.0000 2454.399527 0 1.4866 237 | 0/8 11 h-lim-p 1.6482 20.0000 0.0000 2454.399527 0 0.0451 261 | 0/8 12 h-lim-p 0.0101 20.0000 0.0000 2454.399527 0 0.0050 281 | 0/8 13 h-lim-p 0.0038 20.0000 0.0000 2454.399527 0 0.0000 317 | 0/8 14 h-lim-p 0.0000 20.0000 0.0002 | 0/8 15 h-lim-p 0.0000 20.0000 0.0002 Out... lnL = -2454.399527 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2454.399527 Node 7: lnL = -2454.399527 Node 8: lnL = -2454.399527 Node 9: lnL = -2454.399527 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 437 Sequential format.. Reading seq # 1: YPR107C_Sbay Reading seq # 2: YPR107C_Scer Reading seq # 3: YPR107C_Skud Reading seq # 4: YPR107C_Smik Reading seq # 5: YPR107C_Spar Sequences read.. Counting patterns.. # site patterns = 191 Counting frequencies.. 120 bytes for distance 30560 bytes for lkl0 24448 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.097918 0.115825 0.066000 0.181300 0.111289 0.208829 0.210678 0.147133 lnL0 = -2035.467203 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2035.467203 x= 0.09792 0.11583 0.06600 0.18130 0.11129 0.20883 0.21068 0.14713 1 h-lim-p 0.0102 0.0816 49.6510 2035.012352 9 0.0004 51 | 0/8 2 h-lim-p 0.0021 0.0204 9.2038 2034.983233 6 0.0007 79 | 0/8 3 h-lim-p 0.0016 0.0682 4.0357 2034.978565 3 0.0007 97 | 0/8 4 h-lim-p 0.0073 0.6730 0.3727 2034.978510 2 0.0008 115 | 0/8 5 h-lim-p 0.0089 10.9477 0.0332 2034.978509 0 0.0010 137 | 0/8 6 h-lim-p 0.0113 20.0000 0.0029 2034.978509 0 0.0025 158 | 0/8 7 h-lim-p 0.0059 20.0000 0.0012 2034.978509 0 0.0088 178 | 0/8 8 h-lim-p 0.0077 20.0000 0.0014 2034.978505 0 0.0614 201 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2034.978505 0 1.0938 221 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2034.978505 0 1.0938 241 | 0/8 11 h-lim-p 1.2449 20.0000 0.0000 2034.978505 0 2.4897 262 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2034.978505 0 0.0098 289 | 0/8 13 h-lim-p 0.0011 20.0000 0.0000 2034.978505 0 0.0022 310 | 0/8 14 h-lim-p 0.0013 20.0000 0.0000 2034.978505 0 0.0000 347 | 0/8 15 h-lim-p 0.0000 20.0000 0.0006 2034.978505 0 0.0000 372 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 17 h-lim-p 0.0000 20.0000 0.0006 | 0/8 18 h-lim-p 0.0000 20.0000 0.0006 Out... lnL = -2034.978505 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2034.978505 Node 7: lnL = -2034.978505 Node 8: lnL = -2034.978505 Node 9: lnL = -2034.978505 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 440 Sequential format.. Reading seq # 1: YPR108W_Sbay Reading seq # 2: YPR108W_Scer Reading seq # 3: YPR108W_Skud Reading seq # 4: YPR108W_Smik Reading seq # 5: YPR108W_Spar Sequences read.. Counting patterns.. # site patterns = 191 Counting frequencies.. 120 bytes for distance 30560 bytes for lkl0 24448 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.144519 0.025243 0.066250 0.179375 0.113215 0.208579 0.248231 0.193525 lnL0 = -2053.442947 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2053.442947 x= 0.14452 0.02524 0.06625 0.17937 0.11321 0.20858 0.24823 0.19353 1 h-lim-p 0.0091 0.0731 65.8235 2052.793558 9 0.0003 49 | 0/8 2 h-lim-p 0.0014 0.0158 14.4755 2052.713519 6 0.0008 74 | 0/8 3 h-lim-p 0.0018 0.0463 6.4147 2052.702142 5 0.0007 97 | 0/8 4 h-lim-p 0.0024 0.1162 1.7679 2052.701235 4 0.0006 118 | 0/8 5 h-lim-p 0.0026 0.6877 0.4335 2052.701177 2 0.0007 135 | 0/8 6 h-lim-p 0.0064 7.1701 0.0467 2052.701176 1 0.0008 159 | 0/8 7 h-lim-p 0.0102 20.0000 0.0036 2052.701176 0 0.0022 180 | 0/8 8 h-lim-p 0.0459 20.0000 0.0002 2052.701168 0 0.5507 203 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2052.701168 0 1.0938 223 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2052.701168 0 1.0938 243 | 0/8 11 h-lim-p 1.2603 20.0000 0.0000 2052.701168 0 5.0411 265 | 0/8 12 h-lim-p 2.2608 20.0000 0.0000 2052.701168 0 0.4946 286 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 2052.701168 0 0.0195 312 | 0/8 14 h-lim-p 0.0031 20.0000 0.0000 2052.701168 0 0.0000 342 Out... lnL = -2052.701168 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2052.701168 Node 7: lnL = -2052.701168 Node 8: lnL = -2052.701168 Node 9: lnL = -2052.701168 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 862 Sequential format.. Reading seq # 1: YPR109W_Sbay Reading seq # 2: YPR109W_Scer Reading seq # 3: YPR109W_Skud Reading seq # 4: YPR109W_Smik Reading seq # 5: YPR109W_Spar Sequences read.. Counting patterns.. # site patterns = 406 Counting frequencies.. 120 bytes for distance 64960 bytes for lkl0 51968 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.168544 0.086494 0.131955 0.198070 0.181830 0.304830 0.308907 0.237673 lnL0 = -4612.954666 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4612.954666 x= 0.16854 0.08649 0.13196 0.19807 0.18183 0.30483 0.30891 0.23767 1 h-lim-p 0.0043 0.8513 147.3225 4609.339661 8 0.0004 44 | 0/8 2 h-lim-p 0.0022 0.0185 23.6035 4609.143516 7 0.0007 72 | 0/8 3 h-lim-p 0.0011 0.0301 15.0305 4609.090137 6 0.0006 99 | 0/8 4 h-lim-p 0.0037 0.1706 2.4988 4609.087421 3 0.0009 119 | 0/8 5 h-lim-p 0.0081 1.1433 0.2806 4609.087391 2 0.0008 137 | 0/8 6 h-lim-p 0.0102 20.0000 0.0213 4609.087359 1 0.0128 159 | 0/8 7 h-lim-p 0.0041 6.8021 0.0663 4609.087043 0 0.0124 180 | 0/8 8 h-lim-p 0.0034 20.0000 0.2404 4609.084316 0 0.0068 201 | 0/8 9 h-lim-p 2.5000 20.0000 0.0002 4609.084295 1 0.9961 223 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4609.084295 0 1.0938 243 | 0/8 11 h-lim-p 1.7434 20.0000 0.0000 4609.084295 0 1.5255 263 | 0/8 12 h-lim-p 1.8103 20.0000 0.0000 4609.084295 0 0.0000 305 Out... lnL = -4609.084295 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4609.084295 Node 7: lnL = -4609.084295 Node 8: lnL = -4609.084295 Node 9: lnL = -4609.084295 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 487 Sequential format.. Reading seq # 1: YPR110C_Sbay Reading seq # 2: YPR110C_Scer Reading seq # 3: YPR110C_Skud Reading seq # 4: YPR110C_Smik Reading seq # 5: YPR110C_Spar Sequences read.. Counting patterns.. # site patterns = 201 Counting frequencies.. 120 bytes for distance 32160 bytes for lkl0 25728 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.106922 0.143392 0.088727 0.144086 0.131225 0.196082 0.230200 0.159595 lnL0 = -2394.862126 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2394.862126 x= 0.10692 0.14339 0.08873 0.14409 0.13123 0.19608 0.23020 0.15959 1 h-lim-p 0.0023 0.0187 27.8317 2394.650785 2 0.0005 27 | 0/8 2 h-lim-p 0.0017 0.0320 8.7532 2394.629310 6 0.0006 53 | 0/8 3 h-lim-p 0.0026 0.1404 2.0183 2394.628332 3 0.0005 72 | 0/8 4 h-lim-p 0.0015 0.3946 0.6672 2394.628192 2 0.0007 88 | 0/8 5 h-lim-p 0.0016 1.0611 0.2928 2394.628170 2 0.0006 112 | 0/8 6 h-lim-p 0.0299 20.0000 0.0062 2394.628170 0 0.0033 134 | 0/8 7 h-lim-p 0.0050 20.0000 0.0041 2394.628168 0 0.0100 155 | 0/8 8 h-lim-p 0.0036 20.0000 0.0113 2394.628127 0 0.0217 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2394.628127 0 1.0938 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2394.628127 0 1.0938 217 | 0/8 11 h-lim-p 1.1885 20.0000 0.0000 2394.628127 0 2.3770 238 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2394.628127 0 0.5469 259 | 0/8 13 h-lim-p 0.1002 20.0000 0.0000 2394.628127 0 0.0016 284 | 0/8 14 h-lim-p 0.0006 20.0000 0.0000 2394.628127 0 0.0000 319 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 | 0/8 16 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -2394.628127 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2394.628127 Node 7: lnL = -2394.628127 Node 8: lnL = -2394.628127 Node 9: lnL = -2394.628127 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 372 Sequential format.. Reading seq # 1: YPR113W_Sbay Reading seq # 2: YPR113W_Scer Reading seq # 3: YPR113W_Skud Reading seq # 4: YPR113W_Smik Reading seq # 5: YPR113W_Spar Sequences read.. Counting patterns.. # site patterns = 140 Counting frequencies.. 120 bytes for distance 22400 bytes for lkl0 17920 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.125039 0.039435 0.046856 0.110304 0.059857 0.145409 0.132636 0.159541 lnL0 = -1531.947240 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1531.947240 x= 0.12504 0.03944 0.04686 0.11030 0.05986 0.14541 0.13264 0.15954 1 h-lim-p 0.0002 0.0020 155.7802 1529.220474 6 0.0003 35 | 0/8 2 h-lim-p 0.0004 0.0028 33.0472 1528.989049 0 0.0005 47 | 0/8 3 h-lim-p 0.0010 0.0140 16.9780 1528.955355 6 0.0003 74 | 0/8 4 h-lim-p 0.0013 0.0591 3.8668 1528.951841 4 0.0005 94 | 0/8 5 h-lim-p 0.0028 0.2369 0.6961 1528.951717 3 0.0005 114 | 0/8 6 h-lim-p 0.0128 6.2407 0.0270 1528.951590 1 0.0160 136 | 0/8 7 h-lim-p 0.0066 5.1195 0.0654 1528.945183 0 0.0527 159 | 0/8 8 h-lim-p 0.0060 0.3052 0.5787 1528.945059 2 0.0007 185 | 0/8 9 h-lim-p 0.4936 20.0000 0.0009 1528.944288 0 0.9872 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1528.944286 1 1.2305 229 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1528.944286 0 1.0938 249 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1528.944286 0 0.0006 280 Out... lnL = -1528.944286 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1528.944286 Node 7: lnL = -1528.944286 Node 8: lnL = -1528.944286 Node 9: lnL = -1528.944286 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 412 Sequential format.. Reading seq # 1: YPR114W_Sbay Reading seq # 2: YPR114W_Scer Reading seq # 3: YPR114W_Skud Reading seq # 4: YPR114W_Smik Reading seq # 5: YPR114W_Spar Sequences read.. Counting patterns.. # site patterns = 134 Counting frequencies.. 120 bytes for distance 21440 bytes for lkl0 17152 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.073639 0.052187 0.044405 0.064837 0.064483 0.111933 0.102028 0.100127 lnL0 = -1479.051228 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1479.051228 x= 0.07364 0.05219 0.04441 0.06484 0.06448 0.11193 0.10203 0.10013 1 h-lim-p 0.0024 0.9712 110.2339 1477.726279 6 0.0002 36 | 0/8 2 h-lim-p 0.0004 0.0035 20.1315 1477.666924 7 0.0003 65 | 0/8 3 h-lim-p 0.0008 0.0154 7.2596 1477.659027 5 0.0003 88 | 0/8 4 h-lim-p 0.0026 0.0812 0.9393 1477.658922 3 0.0002 108 | 0/8 5 h-lim-p 0.0015 1.0058 0.1561 1477.658918 0 0.0004 129 | 0/8 6 h-lim-p 0.0013 2.3593 0.0446 1477.658918 0 0.0006 149 | 0/8 7 h-lim-p 0.0046 20.0000 0.0055 1477.658916 0 0.0092 170 | 0/8 8 h-lim-p 0.0076 20.0000 0.0067 1477.658651 0 0.0608 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1477.658650 0 1.0938 213 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1477.658650 0 1.0938 233 | 0/8 11 h-lim-p 1.3021 20.0000 0.0000 1477.658650 0 1.1394 253 | 0/8 12 h-lim-p 0.9187 20.0000 0.0000 1477.658650 0 0.0000 293 Out... lnL = -1477.658650 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1477.658650 Node 7: lnL = -1477.658650 Node 8: lnL = -1477.658650 Node 9: lnL = -1477.658650 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 541 Sequential format.. Reading seq # 1: YPR116W_Sbay Reading seq # 2: YPR116W_Scer Reading seq # 3: YPR116W_Skud Reading seq # 4: YPR116W_Smik Reading seq # 5: YPR116W_Spar Sequences read.. Counting patterns.. # site patterns = 227 Counting frequencies.. 120 bytes for distance 36320 bytes for lkl0 29056 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.090870 0.088352 0.087973 0.172872 0.103793 0.214292 0.240986 0.139981 lnL0 = -2548.811240 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2548.811240 x= 0.09087 0.08835 0.08797 0.17287 0.10379 0.21429 0.24099 0.13998 1 h-lim-p 0.0009 0.0069 48.2344 2548.342730 2 0.0004 26 | 0/8 2 h-lim-p 0.0017 0.0180 11.2046 2548.313435 6 0.0005 52 | 0/8 3 h-lim-p 0.0019 0.1295 2.8650 2548.311724 2 0.0004 69 | 0/8 4 h-lim-p 0.0009 0.2013 1.4623 2548.311259 4 0.0005 93 | 0/8 5 h-lim-p 0.0031 0.6481 0.2535 2548.311243 2 0.0005 112 | 0/8 6 h-lim-p 0.0026 12.6180 0.0506 2548.311241 0 0.0011 132 | 0/8 7 h-lim-p 0.0069 20.0000 0.0083 2548.311236 0 0.0104 152 | 0/8 8 h-lim-p 0.0074 20.0000 0.0116 2548.310839 0 0.0592 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2548.310831 1 0.9961 197 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2548.310831 0 1.0938 217 | 0/8 11 h-lim-p 1.1461 20.0000 0.0000 2548.310831 0 4.5846 239 | 0/8 12 h-lim-p 0.5524 20.0000 0.0000 2548.310831 0 0.1381 260 | 0/8 13 h-lim-p 0.0062 20.0000 0.0011 2548.310831 0 0.0008 282 | 0/8 14 h-lim-p 0.0003 20.0000 0.0027 2548.310831 0 0.0000 316 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 2548.310831 0 0.0000 349 Out... lnL = -2548.310831 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2548.310831 Node 7: lnL = -2548.310831 Node 8: lnL = -2548.310831 Node 9: lnL = -2548.310831 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 829 Sequential format.. Reading seq # 1: YPR122W_Sbay Reading seq # 2: YPR122W_Scer Reading seq # 3: YPR122W_Skud Reading seq # 4: YPR122W_Smik Reading seq # 5: YPR122W_Spar Sequences read.. Counting patterns.. # site patterns = 378 Counting frequencies.. 120 bytes for distance 60480 bytes for lkl0 48384 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.173152 0.115143 0.105752 0.216955 0.217772 0.299542 0.351112 0.246642 lnL0 = -4570.088156 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4570.088156 x= 0.17315 0.11514 0.10575 0.21695 0.21777 0.29954 0.35111 0.24664 1 h-lim-p 0.0089 1.5336 101.2306 4568.174516 6 0.0004 39 | 0/8 2 h-lim-p 0.0030 0.0339 13.2750 4568.120045 3 0.0006 59 | 0/8 3 h-lim-p 0.0014 0.0825 5.9659 4568.104676 6 0.0010 87 | 0/8 4 h-lim-p 0.0042 0.2697 1.4522 4568.103731 2 0.0010 104 | 0/8 5 h-lim-p 0.0037 1.0835 0.3890 4568.103671 0 0.0008 117 | 0/8 6 h-lim-p 0.0101 10.3408 0.0308 4568.103671 0 0.0022 138 | 0/8 7 h-lim-p 0.0194 20.0000 0.0035 4568.103669 0 0.0169 158 | 0/8 8 h-lim-p 0.0093 20.0000 0.0064 4568.103563 0 0.0560 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 4568.103562 0 1.0938 200 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4568.103562 0 1.0938 220 | 0/8 11 h-lim-p 1.5960 20.0000 0.0000 4568.103562 0 1.5960 240 | 0/8 12 h-lim-p 2.3678 20.0000 0.0000 4568.103562 0 0.0185 266 | 0/8 13 h-lim-p 0.0045 20.0000 0.0000 4568.103562 0 0.0011 287 | 0/8 14 h-lim-p 0.0017 20.0000 0.0000 4568.103562 0 0.0000 318 Out... lnL = -4568.103562 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4568.103562 Node 7: lnL = -4568.103562 Node 8: lnL = -4568.103562 Node 9: lnL = -4568.103562 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 531 Sequential format.. Reading seq # 1: YPR129W_Sbay Reading seq # 2: YPR129W_Scer Reading seq # 3: YPR129W_Skud Reading seq # 4: YPR129W_Smik Reading seq # 5: YPR129W_Spar Sequences read.. Counting patterns.. # site patterns = 210 Counting frequencies.. 120 bytes for distance 33600 bytes for lkl0 26880 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.075286 0.109886 0.072441 0.153577 0.080757 0.252165 0.205116 0.121792 lnL0 = -2409.121151 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2409.121151 x= 0.07529 0.10989 0.07244 0.15358 0.08076 0.25217 0.20512 0.12179 1 h-lim-p 0.0002 0.0018 116.8673 2406.880406 0 0.0004 23 | 0/8 2 h-lim-p 0.0018 0.0144 22.1345 2406.745277 7 0.0006 51 | 0/8 3 h-lim-p 0.0026 0.0405 4.9361 2406.737675 5 0.0007 75 | 0/8 4 h-lim-p 0.0019 0.1595 1.7389 2406.736833 4 0.0006 97 | 0/8 5 h-lim-p 0.0056 3.8492 0.1839 2406.736676 3 0.0015 116 | 0/8 6 h-lim-p 0.0009 0.9854 0.3036 2406.730926 0 0.0109 139 | 0/8 7 h-lim-p 0.0040 0.1674 0.8205 2406.655523 0 0.0121 160 | 0/8 8 h-lim-p 0.0022 0.0645 4.4950 2406.638998 6 0.0012 193 | 0/8 9 h-lim-p 2.5000 20.0000 0.0009 2406.638284 3 0.9482 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2406.638284 0 1.0938 231 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2406.638284 0 1.0938 251 | 0/8 12 h-lim-p 1.0770 20.0000 0.0000 2406.638284 0 0.0337 275 | 0/8 13 h-lim-p 0.0088 20.0000 0.0000 2406.638284 0 0.0000 311 | 0/8 14 h-lim-p 0.0000 20.0000 0.0004 | 0/8 15 h-lim-p 0.0000 20.0000 0.0004 Out... lnL = -2406.638284 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2406.638284 Node 7: lnL = -2406.638284 Node 8: lnL = -2406.638284 Node 9: lnL = -2406.638284 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 686 Sequential format.. Reading seq # 1: YPR133C_Sbay Reading seq # 2: YPR133C_Scer Reading seq # 3: YPR133C_Skud Reading seq # 4: YPR133C_Smik Reading seq # 5: YPR133C_Spar Sequences read.. Counting patterns.. # site patterns = 164 Counting frequencies.. 120 bytes for distance 26240 bytes for lkl0 20992 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.079395 0.073337 0.061455 0.118010 0.086754 0.216343 0.281833 0.123743 lnL0 = -2133.995049 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2133.995049 x= 0.07939 0.07334 0.06146 0.11801 0.08675 0.21634 0.28183 0.12374 1 h-lim-p 0.0049 0.0390 67.2404 2133.059724 8 0.0004 42 | 0/8 2 h-lim-p 0.0007 0.0054 21.1349 2132.944450 3 0.0006 60 | 0/8 3 h-lim-p 0.0036 0.0494 3.3307 2132.942149 2 0.0004 78 | 0/8 4 h-lim-p 0.0018 0.1976 0.7742 2132.941992 4 0.0006 102 | 0/8 5 h-lim-p 0.0012 1.9976 0.3498 2132.941932 0 0.0012 122 | 0/8 6 h-lim-p 0.0065 2.3700 0.0663 2132.941930 0 0.0007 144 | 0/8 7 h-lim-p 0.0024 12.3050 0.0201 2132.941926 0 0.0047 165 | 0/8 8 h-lim-p 0.0275 20.0000 0.0034 2132.941292 0 0.2203 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2132.941282 1 0.9961 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2132.941282 0 1.0938 230 | 0/8 11 h-lim-p 1.3508 20.0000 0.0000 2132.941282 0 0.0000 268 Out... lnL = -2132.941282 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2132.941282 Node 7: lnL = -2132.941282 Node 8: lnL = -2132.941282 Node 9: lnL = -2132.941282 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 353 Sequential format.. Reading seq # 1: YPR134W_Sbay Reading seq # 2: YPR134W_Scer Reading seq # 3: YPR134W_Skud Reading seq # 4: YPR134W_Smik Reading seq # 5: YPR134W_Spar Sequences read.. Counting patterns.. # site patterns = 148 Counting frequencies.. 120 bytes for distance 23680 bytes for lkl0 18944 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.119008 0.060856 0.064001 0.114711 0.058942 0.176346 0.128891 0.156698 lnL0 = -1465.946319 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1465.946319 x= 0.11901 0.06086 0.06400 0.11471 0.05894 0.17635 0.12889 0.15670 1 h-lim-p 0.0003 0.0022 86.1451 1464.664896 0 0.0004 22 | 0/8 2 h-lim-p 0.0025 0.0201 14.6429 1464.601270 5 0.0006 45 | 0/8 3 h-lim-p 0.0012 0.0114 7.1669 1464.594417 4 0.0003 66 | 0/8 4 h-lim-p 0.0008 0.0848 2.7656 1464.592702 4 0.0005 88 | 0/8 5 h-lim-p 0.0090 1.0080 0.1613 1464.592665 3 0.0015 109 | 0/8 6 h-lim-p 0.0046 4.6225 0.0514 1464.592287 0 0.0183 131 | 0/8 7 h-lim-p 0.0065 0.8709 0.1452 1464.577310 0 0.0259 153 | 0/8 8 h-lim-p 0.0029 0.1873 1.2841 1464.576481 4 0.0009 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1464.576425 2 0.9644 199 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1464.576425 0 1.0938 219 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1464.576425 0 2.1875 239 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1464.576425 0 0.5469 260 | 0/8 13 h-lim-p 0.2542 20.0000 0.0000 1464.576425 0 0.0278 282 | 0/8 14 h-lim-p 0.0143 20.0000 0.0000 1464.576425 0 0.0000 310 Out... lnL = -1464.576425 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1464.576425 Node 7: lnL = -1464.576425 Node 8: lnL = -1464.576425 Node 9: lnL = -1464.576425 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 355 Sequential format.. Reading seq # 1: YPR137W_Sbay Reading seq # 2: YPR137W_Scer Reading seq # 3: YPR137W_Skud Reading seq # 4: YPR137W_Smik Reading seq # 5: YPR137W_Spar Sequences read.. Counting patterns.. # site patterns = 154 Counting frequencies.. 120 bytes for distance 24640 bytes for lkl0 19712 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.100595 0.030399 0.084557 0.120830 0.064219 0.213140 0.182685 0.133498 lnL0 = -1552.506038 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1552.506038 x= 0.10060 0.03040 0.08456 0.12083 0.06422 0.21314 0.18269 0.13350 1 h-lim-p 0.0038 1.3449 90.3632 1551.375082 6 0.0003 38 | 0/8 2 h-lim-p 0.0017 0.0135 8.9380 1551.354131 6 0.0005 65 | 0/8 3 h-lim-p 0.0012 0.0405 4.0752 1551.351025 5 0.0004 87 | 0/8 4 h-lim-p 0.0026 0.3232 0.6884 1551.350814 3 0.0009 107 | 0/8 5 h-lim-p 0.0043 1.4935 0.1493 1551.350807 2 0.0007 134 | 0/8 6 h-lim-p 0.0188 20.0000 0.0056 1551.350807 0 0.0021 156 | 0/8 7 h-lim-p 0.0028 20.0000 0.0041 1551.350806 0 0.0056 177 | 0/8 8 h-lim-p 0.0123 20.0000 0.0019 1551.350782 0 0.0987 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1551.350780 0 1.0938 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1551.350780 0 1.0938 240 | 0/8 11 h-lim-p 2.0340 20.0000 0.0000 1551.350780 0 0.0000 284 Out... lnL = -1551.350780 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1551.350780 Node 7: lnL = -1551.350780 Node 8: lnL = -1551.350780 Node 9: lnL = -1551.350780 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 784 Sequential format.. Reading seq # 1: YPR138C_Sbay Reading seq # 2: YPR138C_Scer Reading seq # 3: YPR138C_Skud Reading seq # 4: YPR138C_Smik Reading seq # 5: YPR138C_Spar Sequences read.. Counting patterns.. # site patterns = 237 Counting frequencies.. 120 bytes for distance 37920 bytes for lkl0 30336 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.111570 0.000823 0.033918 0.057265 0.059938 0.151285 0.175182 0.136351 lnL0 = -3027.851282 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3027.851282 x= 0.11157 0.00082 0.03392 0.05726 0.05994 0.15129 0.17518 0.13635 1 h-lim-p 0.0003 0.0054 471.7591 3022.951066 7 0.0001 38 | 0/8 2 h-lim-p 0.0002 0.0013 36.5941 3022.854129 5 0.0001 59 | 0/8 3 h-lim-p 0.0004 0.0156 12.0929 3022.835216 6 0.0003 85 | 0/8 4 h-lim-p 0.0012 0.0552 2.9034 3022.834557 4 0.0002 108 | 0/8 5 h-lim-p 0.0002 0.1303 1.9704 3022.834257 2 0.0002 124 | 0/8 6 h-lim-p 0.0138 6.3136 0.0308 3022.834256 0 0.0009 139 | 0/8 7 h-lim-p 0.0004 1.9886 0.0638 3022.834252 0 0.0008 160 | 0/8 8 h-lim-p 0.0104 4.4721 0.0051 3022.832390 0 0.1668 184 | 0/8 9 h-lim-p 1.0312 20.0000 0.0008 3022.832084 2 0.9667 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3022.832079 1 0.9961 230 | 0/8 11 h-lim-p 1.4247 20.0000 0.0000 3022.832079 0 1.2466 250 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 3022.832079 0 0.5469 271 | 0/8 13 h-lim-p 0.1667 20.0000 0.0000 3022.832079 0 0.0078 295 | 0/8 14 h-lim-p 0.0048 20.0000 0.0000 3022.832079 0 0.0000 326 Out... lnL = -3022.832079 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3022.832079 Node 7: lnL = -3022.832079 Node 8: lnL = -3022.832079 Node 9: lnL = -3022.832079 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 356 Sequential format.. Reading seq # 1: YPR139C_Sbay Reading seq # 2: YPR139C_Scer Reading seq # 3: YPR139C_Skud Reading seq # 4: YPR139C_Smik Reading seq # 5: YPR139C_Spar Sequences read.. Counting patterns.. # site patterns = 190 Counting frequencies.. 120 bytes for distance 30400 bytes for lkl0 24320 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.172813 0.056933 0.107039 0.149855 0.122896 0.200658 0.253259 0.218254 lnL0 = -1715.940280 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1715.940280 x= 0.17281 0.05693 0.10704 0.14985 0.12290 0.20066 0.25326 0.21825 1 h-lim-p 0.0019 0.0151 56.1849 1714.986779 8 0.0006 40 | 0/8 2 h-lim-p 0.0018 0.0146 10.7800 1714.941801 5 0.0008 61 | 0/8 3 h-lim-p 0.0020 0.0716 4.2216 1714.934984 3 0.0009 79 | 0/8 4 h-lim-p 0.0033 0.2144 1.1298 1714.934386 5 0.0010 105 | 0/8 5 h-lim-p 0.0081 2.2041 0.1430 1714.934365 2 0.0021 122 | 0/8 6 h-lim-p 0.0129 19.1915 0.0236 1714.934365 0 0.0014 144 | 0/8 7 h-lim-p 0.0078 20.0000 0.0042 1714.934365 0 0.0034 164 | 0/8 8 h-lim-p 0.0890 20.0000 0.0002 1714.934357 0 0.7117 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1714.934357 0 1.0938 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1714.934357 0 1.0938 227 | 0/8 11 h-lim-p 1.2876 20.0000 0.0000 1714.934357 0 2.5752 248 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1714.934357 0 0.0049 276 Out... lnL = -1714.934357 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1714.934357 Node 7: lnL = -1714.934357 Node 8: lnL = -1714.934357 Node 9: lnL = -1714.934357 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 356 Sequential format.. Reading seq # 1: YPR140W_Sbay Reading seq # 2: YPR140W_Scer Reading seq # 3: YPR140W_Skud Reading seq # 4: YPR140W_Smik Reading seq # 5: YPR140W_Spar Sequences read.. Counting patterns.. # site patterns = 194 Counting frequencies.. 120 bytes for distance 31040 bytes for lkl0 24832 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.173655 0.049490 0.117099 0.157446 0.119704 0.272567 0.227775 0.221041 lnL0 = -1735.046408 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1735.046408 x= 0.17366 0.04949 0.11710 0.15745 0.11970 0.27257 0.22778 0.22104 1 h-lim-p 0.0006 0.0048 55.5256 1734.049473 1 0.0007 24 | 0/8 2 h-lim-p 0.0027 0.0217 9.9925 1734.008372 7 0.0008 55 | 0/8 3 h-lim-p 0.0033 0.2191 2.5689 1734.006162 2 0.0007 72 | 0/8 4 h-lim-p 0.0014 0.2856 1.3503 1734.005171 2 0.0014 88 | 0/8 5 h-lim-p 0.0174 3.9888 0.1050 1734.005126 2 0.0035 105 | 0/8 6 h-lim-p 0.0102 8.9406 0.0355 1734.004497 0 0.0409 127 | 0/8 7 h-lim-p 0.0048 0.5099 0.3059 1734.000913 0 0.0095 148 | 0/8 8 h-lim-p 0.0027 0.0880 1.0723 1733.997151 4 0.0030 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1733.997111 2 0.9961 194 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1733.997111 0 1.0938 214 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1733.997111 0 2.1875 234 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1733.997111 0 0.5469 255 | 0/8 13 h-lim-p 0.2843 20.0000 0.0000 1733.997111 0 0.0011 282 Out... lnL = -1733.997111 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1733.997111 Node 7: lnL = -1733.997111 Node 8: lnL = -1733.997111 Node 9: lnL = -1733.997111 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 236 Sequential format.. Reading seq # 1: YPR141C_Sbay Reading seq # 2: YPR141C_Scer Reading seq # 3: YPR141C_Skud Reading seq # 4: YPR141C_Smik Reading seq # 5: YPR141C_Spar Sequences read.. Counting patterns.. # site patterns = 104 Counting frequencies.. 120 bytes for distance 16640 bytes for lkl0 13312 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.129985 0.152651 0.075686 0.111772 0.081959 0.246819 0.160369 0.171467 lnL0 = -1051.174018 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1051.174018 x= 0.12998 0.15265 0.07569 0.11177 0.08196 0.24682 0.16037 0.17147 1 h-lim-p 0.0008 0.0064 36.1760 1050.670884 3 0.0008 28 | 0/8 2 h-lim-p 0.0051 0.0428 5.7471 1050.647133 7 0.0015 60 | 0/8 3 h-lim-p 0.0033 0.0770 2.5753 1050.644802 5 0.0008 85 | 0/8 4 h-lim-p 0.0018 0.2478 1.2125 1050.644277 3 0.0009 104 | 0/8 5 h-lim-p 0.0048 2.7506 0.2183 1050.644239 3 0.0017 124 | 0/8 6 h-lim-p 0.0137 8.2145 0.0272 1050.644238 0 0.0015 146 | 0/8 7 h-lim-p 0.0065 20.0000 0.0063 1050.644237 0 0.0097 166 | 0/8 8 h-lim-p 0.0506 20.0000 0.0012 1050.644181 0 0.3034 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1050.644180 0 1.0938 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1050.644180 0 1.0938 228 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1050.644180 0 2.1875 248 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1050.644180 0 1.0938 268 | 0/8 13 h-lim-p 0.3030 20.0000 0.0000 1050.644180 0 4.8482 292 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1050.644180 0 0.1562 315 | 0/8 15 h-lim-p 0.0156 20.0000 0.0000 1050.644180 0 0.0156 335 | 0/8 16 h-lim-p 0.0057 20.0000 0.0000 1050.644180 0 0.0001 360 | 0/8 17 h-lim-p 0.0003 20.0000 0.0000 1050.644180 0 0.0001 381 Out... lnL = -1050.644180 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1050.644180 Node 7: lnL = -1050.644180 Node 8: lnL = -1050.644180 Node 9: lnL = -1050.644180 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 434 Sequential format.. Reading seq # 1: YPR143W_Sbay Reading seq # 2: YPR143W_Scer Reading seq # 3: YPR143W_Skud Reading seq # 4: YPR143W_Smik Reading seq # 5: YPR143W_Spar Sequences read.. Counting patterns.. # site patterns = 147 Counting frequencies.. 120 bytes for distance 23520 bytes for lkl0 18816 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.081440 0.113240 0.057116 0.092366 0.075934 0.190585 0.162626 0.113840 lnL0 = -1836.115326 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1836.115326 x= 0.08144 0.11324 0.05712 0.09237 0.07593 0.19058 0.16263 0.11384 1 h-lim-p 0.0004 0.0029 77.7544 1835.259302 3 0.0003 28 | 0/8 2 h-lim-p 0.0013 0.0108 10.3143 1835.237764 7 0.0004 60 | 0/8 3 h-lim-p 0.0010 0.0539 4.3071 1835.234684 4 0.0004 80 | 0/8 4 h-lim-p 0.0008 0.0919 2.0520 1835.233926 5 0.0004 105 | 0/8 5 h-lim-p 0.0055 1.5887 0.1659 1835.233917 1 0.0007 121 | 0/8 6 h-lim-p 0.0056 20.0000 0.0202 1835.233917 0 0.0006 143 | 0/8 7 h-lim-p 0.0021 20.0000 0.0059 1835.233916 0 0.0042 164 | 0/8 8 h-lim-p 0.0101 20.0000 0.0024 1835.233822 0 0.1218 187 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1835.233821 0 1.0938 207 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1835.233821 0 1.0938 227 | 0/8 11 h-lim-p 1.2111 20.0000 0.0000 1835.233821 0 0.0189 252 | 0/8 12 h-lim-p 0.0085 20.0000 0.0000 1835.233821 0 0.0003 276 | 0/8 13 h-lim-p 0.0001 20.0000 0.0000 1835.233821 0 0.0000 309 | 0/8 14 h-lim-p 0.0000 20.0000 0.0009 | 0/8 15 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -1835.233821 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1835.233821 Node 7: lnL = -1835.233821 Node 8: lnL = -1835.233821 Node 9: lnL = -1835.233821 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 854 Sequential format.. Reading seq # 1: YPR145W_Sbay Reading seq # 2: YPR145W_Scer Reading seq # 3: YPR145W_Skud Reading seq # 4: YPR145W_Smik Reading seq # 5: YPR145W_Spar Sequences read.. Counting patterns.. # site patterns = 271 Counting frequencies.. 120 bytes for distance 43360 bytes for lkl0 34688 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.174958 0.050525 0.050390 0.094593 0.078206 0.153255 0.153274 0.208761 lnL0 = -3656.882782 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3656.882782 x= 0.17496 0.05053 0.05039 0.09459 0.07821 0.15325 0.15327 0.20876 1 h-lim-p 0.0013 0.0105 180.4426 3654.237138 5 0.0002 34 | 0/8 2 h-lim-p 0.0002 0.0012 61.5008 3653.859352 0 0.0002 46 | 0/8 3 h-lim-p 0.0004 0.0056 34.0651 3653.747554 6 0.0002 74 | 0/8 4 h-lim-p 0.0013 0.0316 6.4508 3653.742987 4 0.0002 96 | 0/8 5 h-lim-p 0.0004 0.0664 3.6986 3653.741808 4 0.0002 117 | 0/8 6 h-lim-p 0.0059 0.9579 0.1390 3653.741805 0 0.0003 132 | 0/8 7 h-lim-p 0.0069 20.0000 0.0064 3653.740993 0 0.1111 156 | 0/8 8 h-lim-p 0.0016 2.7232 0.4596 3653.737722 0 0.0031 177 | 0/8 9 h-lim-p 2.5000 20.0000 0.0005 3653.737378 2 1.0889 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3653.737375 0 1.0938 221 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 3653.737375 0 1.0938 241 | 0/8 12 h-lim-p 1.2040 20.0000 0.0000 3653.737375 0 1.0535 261 | 0/8 13 h-lim-p 1.0709 20.0000 0.0000 3653.737375 017.1343 285 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 3653.737375 0 0.6250 306 | 0/8 15 h-lim-p 0.0560 20.0000 0.0001 3653.737375 0 0.0002 333 | 0/8 16 h-lim-p 0.0010 20.0000 0.0000 3653.737375 0 0.0000 370 | 0/8 17 h-lim-p 0.0000 20.0000 0.0008 | 0/8 18 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -3653.737375 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3653.737375 Node 7: lnL = -3653.737375 Node 8: lnL = -3653.737375 Node 9: lnL = -3653.737375 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 305 Sequential format.. Reading seq # 1: YPR147C_Sbay Reading seq # 2: YPR147C_Scer Reading seq # 3: YPR147C_Skud Reading seq # 4: YPR147C_Smik Reading seq # 5: YPR147C_Spar Sequences read.. Counting patterns.. # site patterns = 158 Counting frequencies.. 120 bytes for distance 25280 bytes for lkl0 20224 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.201973 0.000060 0.164948 0.107311 0.115969 0.184412 0.310307 0.249067 lnL0 = -1468.087069 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1468.087069 x= 0.20197 0.00006 0.16495 0.10731 0.11597 0.18441 0.31031 0.24907 1 h-lim-p 0.0005 0.0041 52.9479 1466.903317 0 0.0010 23 | 0/8 2 h-lim-p 0.0048 0.0383 8.5501 1466.856509 6 0.0013 48 | 0/8 3 h-lim-p 0.0028 0.1085 3.9756 1466.851526 3 0.0007 67 | 0/8 4 h-lim-p 0.0015 0.1721 1.9295 1466.849926 5 0.0010 91 | 0/8 5 h-lim-p 0.0047 0.2594 0.4162 1466.849457 3 0.0023 110 | 0/8 6 h-lim-p 0.0024 0.9444 0.4010 1466.845488 0 0.0096 132 | 0/8 7 h-lim-p 0.0107 0.5486 0.3589 1466.804336 0 0.0322 153 | 0/8 8 h-lim-p 0.0033 0.0263 2.8328 1466.742185 1 0.0041 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0015 1466.741244 4 0.9422 195 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1466.741243 0 1.0938 215 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1466.741243 0 1.0938 235 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1466.741243 0 1.0938 255 | 0/8 13 h-lim-p 1.2272 20.0000 0.0000 1466.741243 0 2.4545 276 | 0/8 14 h-lim-p 2.5000 20.0000 0.0000 1466.741243 0 0.6250 297 | 0/8 15 h-lim-p 0.1139 20.0000 0.0000 1466.741243 0 0.0498 317 | 0/8 16 h-lim-p 0.0131 20.0000 0.0000 1466.741243 0 0.0000 359 | 0/8 17 h-lim-p 0.0000 20.0000 0.0000 | 0/8 18 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1466.741243 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1466.741243 Node 7: lnL = -1466.741243 Node 8: lnL = -1466.741243 Node 9: lnL = -1466.741243 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 913 Sequential format.. Reading seq # 1: YPR148C_Sbay Reading seq # 2: YPR148C_Scer Reading seq # 3: YPR148C_Skud Reading seq # 4: YPR148C_Smik Reading seq # 5: YPR148C_Spar Sequences read.. Counting patterns.. # site patterns = 327 Counting frequencies.. 120 bytes for distance 52320 bytes for lkl0 41856 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.118168 0.061169 0.093034 0.144193 0.083569 0.171116 0.310280 0.158733 lnL0 = -4008.191400 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4008.191400 x= 0.11817 0.06117 0.09303 0.14419 0.08357 0.17112 0.31028 0.15873 1 h-lim-p 0.0049 0.9244 127.7310 4006.529105 7 0.0002 41 | 0/8 2 h-lim-p 0.0007 0.0059 29.5431 4006.391659 5 0.0003 62 | 0/8 3 h-lim-p 0.0005 0.0144 19.1086 4006.356776 5 0.0003 86 | 0/8 4 h-lim-p 0.0010 0.0675 4.8903 4006.349866 5 0.0006 110 | 0/8 5 h-lim-p 0.0017 0.1998 1.8680 4006.349324 2 0.0004 127 | 0/8 6 h-lim-p 0.0068 2.9095 0.1006 4006.349321 1 0.0004 144 | 0/8 7 h-lim-p 0.0037 12.2105 0.0114 4006.349319 0 0.0032 164 | 0/8 8 h-lim-p 0.0078 20.0000 0.0047 4006.348752 0 0.1245 188 | 0/8 9 h-lim-p 1.8661 20.0000 0.0003 4006.348736 1 0.9185 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 4006.348736 0 1.0938 231 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 4006.348736 0 1.0938 251 | 0/8 12 h-lim-p 1.1441 20.0000 0.0000 4006.348736 0 1.7161 271 | 0/8 13 h-lim-p 0.3742 20.0000 0.0000 4006.348736 0 0.0044 297 | 0/8 14 h-lim-p 0.0012 20.0000 0.0001 4006.348736 0 0.0003 318 | 0/8 15 h-lim-p 0.0011 20.0000 0.0000 4006.348736 0 0.0000 343 | 0/8 16 h-lim-p 0.0014 20.0000 0.0000 4006.348736 0 0.0000 377 Out... lnL = -4006.348736 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4006.348736 Node 7: lnL = -4006.348736 Node 8: lnL = -4006.348736 Node 9: lnL = -4006.348736 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 844 Sequential format.. Reading seq # 1: YPR149W_Sbay Reading seq # 2: YPR149W_Scer Reading seq # 3: YPR149W_Skud Reading seq # 4: YPR149W_Smik Reading seq # 5: YPR149W_Spar Sequences read.. Counting patterns.. # site patterns = 196 Counting frequencies.. 120 bytes for distance 31360 bytes for lkl0 25088 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.076097 0.027686 0.042633 0.049643 0.037043 0.103113 0.132407 0.096086 lnL0 = -2998.746113 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2998.746113 x= 0.07610 0.02769 0.04263 0.04964 0.03704 0.10311 0.13241 0.09609 1 h-lim-p 0.0006 0.0057 315.4031 2995.440108 8 0.0001 41 | 0/8 2 h-lim-p 0.0002 0.0013 47.2449 2995.286705 5 0.0001 64 | 0/8 3 h-lim-p 0.0003 0.0081 24.2974 2995.267663 5 0.0001 89 | 0/8 4 h-lim-p 0.0002 0.0212 9.6843 2995.263225 5 0.0001 114 | 0/8 5 h-lim-p 0.0008 0.1539 1.3632 2995.263090 3 0.0002 133 | 0/8 6 h-lim-p 0.0003 0.1507 0.7428 2995.263064 1 0.0001 147 | 0/8 7 h-lim-p 0.0007 1.3274 0.1310 2995.263062 1 0.0002 170 | 0/8 8 h-lim-p 0.1090 20.0000 0.0002 2995.262754 0 1.7432 194 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2995.262737 1 0.9961 216 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2995.262737 0 1.0938 236 | 0/8 11 h-lim-p 0.9033 20.0000 0.0000 2995.262737 0 0.0018 264 | 0/8 12 h-lim-p 0.0005 20.0000 0.0000 2995.262737 0 0.0005 284 | 0/8 13 h-lim-p 0.0007 20.0000 0.0000 2995.262737 0 0.0000 316 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 2995.262737 0 0.0000 350 Out... lnL = -2995.262737 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2995.262737 Node 7: lnL = -2995.262737 Node 8: lnL = -2995.262737 Node 9: lnL = -2995.262737 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 331 Sequential format.. Reading seq # 1: YPR154W_Sbay Reading seq # 2: YPR154W_Scer Reading seq # 3: YPR154W_Skud Reading seq # 4: YPR154W_Smik Reading seq # 5: YPR154W_Spar Sequences read.. Counting patterns.. # site patterns = 127 Counting frequencies.. 120 bytes for distance 20320 bytes for lkl0 16256 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.279337 0.000060 0.125241 0.290911 0.236538 0.150439 0.384987 0.330312 lnL0 = -1226.072508 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1226.072508 x= 0.27934 0.00006 0.12524 0.29091 0.23654 0.15044 0.38499 0.33031 1 h-lim-p 0.0000 0.0000 151.2381 1225.740387 m 0.0000 22 | 1/8 2 h-lim-p 0.0001 0.0389 27.9008 1224.040018 0 0.0050 40 | 1/8 3 h-lim-p 0.0095 0.0763 6.8984 1222.748136 0 0.0191 53 | 1/8 4 h-lim-p 0.0329 0.2635 1.7686 1208.142697 0 0.1318 67 | 1/8 5 h-lim-p 0.0024 0.0194 20.9747 1206.807575 0 0.0049 80 | 1/8 6 h-lim-p 0.0011 0.0088 27.1798 1205.744842 0 0.0044 94 | 1/8 7 h-lim-p 0.0029 0.0230 6.9155 1205.663882 0 0.0043 106 | 1/8 8 h-lim-p 0.3707 3.4602 0.0805 1205.309415 0 0.5561 118 | 1/8 9 h-lim-p 2.5000 20.0000 0.0088 1205.304177 6 0.7851 152 | 1/8 10 h-lim-p 2.5000 20.0000 0.0025 1205.303605 5 0.6926 184 | 1/8 11 h-lim-p 2.5000 20.0000 0.0003 1205.303595 1 1.2500 205 | 1/8 12 h-lim-p 2.5000 20.0000 0.0001 1205.303595 0 1.0938 224 | 1/8 13 h-lim-p 2.5000 20.0000 0.0000 1205.303595 0 1.0938 243 | 1/8 14 h-lim-p 2.5000 20.0000 0.0000 1205.303595 0 1.0938 262 | 1/8 15 h-lim-p 2.5000 20.0000 0.0000 1205.303595 0 0.2734 283 | 1/8 16 h-lim-p 0.1453 20.0000 0.0000 1205.303595 0 0.0182 304 | 1/8 17 h-lim-p 0.0115 20.0000 0.0000 1205.303595 0 0.0000 339 Out... lnL = -1205.303595 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1205.303595 Node 7: lnL = -1205.303595 Node 8: lnL = -1205.303595 Node 9: lnL = -1205.303595 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 850 Sequential format.. Reading seq # 1: YPR156C_Sbay Reading seq # 2: YPR156C_Scer Reading seq # 3: YPR156C_Skud Reading seq # 4: YPR156C_Smik Reading seq # 5: YPR156C_Spar Sequences read.. Counting patterns.. # site patterns = 185 Counting frequencies.. 120 bytes for distance 29600 bytes for lkl0 23680 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.093822 0.035759 0.037577 0.053841 0.029346 0.097450 0.113068 0.114206 lnL0 = -2986.231343 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2986.231343 x= 0.09382 0.03576 0.03758 0.05384 0.02935 0.09745 0.11307 0.11421 1 h-lim-p 0.0001 0.0010 236.3907 2984.416317 7 0.0001 37 | 0/8 2 h-lim-p 0.0001 0.0010 73.0583 2984.196507 6 0.0001 62 | 0/8 3 h-lim-p 0.0002 0.0045 35.3879 2984.127440 7 0.0001 92 | 0/8 4 h-lim-p 0.0005 0.0150 8.7202 2984.123507 3 0.0001 111 | 0/8 5 h-lim-p 0.0008 0.0886 1.3046 2984.123381 2 0.0002 128 | 0/8 6 h-lim-p 0.0007 0.3689 0.3047 2984.123376 1 0.0001 144 | 0/8 7 h-lim-p 0.0005 3.6523 0.0466 2984.123376 0 0.0002 164 | 0/8 8 h-lim-p 0.0681 20.0000 0.0002 2984.123251 0 1.0892 188 | 0/8 9 h-lim-p 1.6280 20.0000 0.0001 2984.123248 1 0.8013 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2984.123247 0 1.0938 231 | 0/8 11 h-lim-p 2.0720 20.0000 0.0000 2984.123247 0 1.8130 251 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 2984.123247 0 0.1367 274 | 0/8 13 h-lim-p 0.0149 20.0000 0.0000 2984.123247 0 0.0037 295 | 0/8 14 h-lim-p 0.0020 20.0000 0.0000 2984.123247 0 0.0005 316 | 0/8 15 h-lim-p 0.0003 20.0000 0.0000 2984.123247 0 0.0000 347 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 2984.123247 0 0.0000 367 Out... lnL = -2984.123247 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2984.123247 Node 7: lnL = -2984.123247 Node 8: lnL = -2984.123247 Node 9: lnL = -2984.123247 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 639 Sequential format.. Reading seq # 1: YPR158W_Sbay Reading seq # 2: YPR158W_Scer Reading seq # 3: YPR158W_Skud Reading seq # 4: YPR158W_Smik Reading seq # 5: YPR158W_Spar Sequences read.. Counting patterns.. # site patterns = 284 Counting frequencies.. 120 bytes for distance 45440 bytes for lkl0 36352 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.156438 0.114121 0.066261 0.147223 0.112012 0.305141 0.330676 0.207403 lnL0 = -3121.895942 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3121.895942 x= 0.15644 0.11412 0.06626 0.14722 0.11201 0.30514 0.33068 0.20740 1 h-lim-p 0.0047 0.0375 105.8900 3120.213588 9 0.0003 46 | 0/8 2 h-lim-p 0.0015 0.0122 15.2098 3120.168445 5 0.0004 70 | 0/8 3 h-lim-p 0.0009 0.0646 6.8250 3120.152254 2 0.0008 86 | 0/8 4 h-lim-p 0.0020 0.0965 2.8253 3120.149745 4 0.0008 106 | 0/8 5 h-lim-p 0.0038 0.3539 0.5545 3120.149519 3 0.0015 124 | 0/8 6 h-lim-p 0.0135 4.2039 0.0633 3120.149517 0 0.0007 147 | 0/8 7 h-lim-p 0.0053 20.0000 0.0089 3120.149517 0 0.0046 167 | 0/8 8 h-lim-p 0.0409 20.0000 0.0010 3120.149390 0 0.3270 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3120.149390 0 1.0938 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3120.149390 0 1.2500 230 | 0/8 11 h-lim-p 1.7361 20.0000 0.0000 3120.149390 0 0.3798 251 | 0/8 12 h-lim-p 0.1938 20.0000 0.0000 3120.149390 0 0.0242 273 | 0/8 13 h-lim-p 0.0127 20.0000 0.0000 3120.149390 0 0.0008 296 | 0/8 14 h-lim-p 0.0001 20.0000 0.0001 3120.149390 0 0.0000 333 | 0/8 15 h-lim-p 0.0000 20.0000 0.0003 3120.149390 0 0.0000 358 | 0/8 16 h-lim-p 0.0000 20.0000 0.0002 3120.149390 0 0.0000 379 | 0/8 17 h-lim-p 0.0000 20.0000 0.0001 .. | 0/8 18 h-lim-p 0.0000 20.0000 0.0003 3120.149390 0 0.0000 439 | 0/8 19 h-lim-p 0.0000 20.0000 0.0003 .. | 0/8 20 h-lim-p 0.0000 20.0000 0.0003 | 0/8 21 h-lim-p 0.0000 20.0000 0.0003 Out... lnL = -3120.149390 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3120.149390 Node 7: lnL = -3120.149390 Node 8: lnL = -3120.149390 Node 9: lnL = -3120.149390 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 866 Sequential format.. Reading seq # 1: YPR159W_Sbay Reading seq # 2: YPR159W_Scer Reading seq # 3: YPR159W_Skud Reading seq # 4: YPR159W_Smik Reading seq # 5: YPR159W_Spar Sequences read.. Counting patterns.. # site patterns = 265 Counting frequencies.. 120 bytes for distance 42400 bytes for lkl0 33920 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.109284 0.018160 0.036268 0.087480 0.070311 0.156500 0.154928 0.130333 lnL0 = -3495.664636 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3495.664636 x= 0.10928 0.01816 0.03627 0.08748 0.07031 0.15650 0.15493 0.13033 1 h-lim-p 0.0003 0.2360 511.1070 3487.585297 10 0.0001 44 | 0/8 2 h-lim-p 0.0006 0.0045 43.9151 3487.313618 4 0.0003 65 | 0/8 3 h-lim-p 0.0007 0.0164 17.4866 3487.290268 4 0.0002 86 | 0/8 4 h-lim-p 0.0006 0.0210 5.5733 3487.287665 4 0.0002 109 | 0/8 5 h-lim-p 0.0012 0.1347 0.8944 3487.287572 1 0.0002 124 | 0/8 6 h-lim-p 0.0009 0.7937 0.2351 3487.287567 0 0.0002 145 | 0/8 7 h-lim-p 0.0015 9.1486 0.0310 3487.287567 0 0.0003 166 | 0/8 8 h-lim-p 0.0855 20.0000 0.0001 3487.287492 0 1.3681 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3487.287488 0 1.2500 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3487.287488 0 1.0938 230 | 0/8 11 h-lim-p 1.4188 20.0000 0.0000 3487.287488 0 0.2660 252 | 0/8 12 h-lim-p 0.1369 20.0000 0.0000 3487.287488 0 0.0086 275 | 0/8 13 h-lim-p 0.0054 20.0000 0.0000 3487.287488 0 0.0000 315 | 0/8 14 h-lim-p 0.0000 20.0000 0.0008 | 0/8 15 h-lim-p 0.0000 20.0000 0.0008 Out... lnL = -3487.287488 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3487.287488 Node 7: lnL = -3487.287488 Node 8: lnL = -3487.287488 Node 9: lnL = -3487.287488 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 882 Sequential format.. Reading seq # 1: YPR160W_Sbay Reading seq # 2: YPR160W_Scer Reading seq # 3: YPR160W_Skud Reading seq # 4: YPR160W_Smik Reading seq # 5: YPR160W_Spar Sequences read.. Counting patterns.. # site patterns = 268 Counting frequencies.. 120 bytes for distance 42880 bytes for lkl0 34304 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.095780 0.034922 0.056554 0.085389 0.051161 0.166554 0.175792 0.117875 lnL0 = -3483.847281 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3483.847281 x= 0.09578 0.03492 0.05655 0.08539 0.05116 0.16655 0.17579 0.11788 1 h-lim-p 0.0001 0.0011 227.2622 3481.210368 3 0.0001 28 | 0/8 2 h-lim-p 0.0005 0.0038 27.8275 3481.142759 6 0.0002 52 | 0/8 3 h-lim-p 0.0004 0.0298 11.5774 3481.134918 5 0.0001 76 | 0/8 4 h-lim-p 0.0002 0.0292 6.5867 3481.132176 4 0.0002 98 | 0/8 5 h-lim-p 0.0013 0.1855 0.8844 3481.132082 2 0.0002 115 | 0/8 6 h-lim-p 0.0026 1.2435 0.0813 3481.132081 0 0.0003 137 | 0/8 7 h-lim-p 0.0010 10.5527 0.0235 3481.132081 0 0.0010 157 | 0/8 8 h-lim-p 0.0224 20.0000 0.0010 3481.131509 0 0.3588 181 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3481.131503 0 1.0938 201 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3481.131503 0 1.0938 221 | 0/8 11 h-lim-p 1.2850 20.0000 0.0000 3481.131503 0 1.2850 241 | 0/8 12 h-lim-p 1.4851 20.0000 0.0000 3481.131503 0 0.0928 264 | 0/8 13 h-lim-p 0.0261 20.0000 0.0000 3481.131503 0 0.0002 290 | 0/8 14 h-lim-p 0.0010 20.0000 0.0000 3481.131503 0 0.0000 330 Out... lnL = -3481.131503 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3481.131503 Node 7: lnL = -3481.131503 Node 8: lnL = -3481.131503 Node 9: lnL = -3481.131503 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 378 Sequential format.. Reading seq # 1: YPR162C_Sbay Reading seq # 2: YPR162C_Scer Reading seq # 3: YPR162C_Skud Reading seq # 4: YPR162C_Smik Reading seq # 5: YPR162C_Spar Sequences read.. Counting patterns.. # site patterns = 139 Counting frequencies.. 120 bytes for distance 22240 bytes for lkl0 17792 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.097554 0.073771 0.056313 0.090390 0.100636 0.120910 0.176159 0.121582 lnL0 = -1556.056551 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1556.056551 x= 0.09755 0.07377 0.05631 0.09039 0.10064 0.12091 0.17616 0.12158 1 h-lim-p 0.0005 0.0043 70.8508 1555.215698 7 0.0004 37 | 0/8 2 h-lim-p 0.0009 0.0075 20.2683 1555.135299 5 0.0004 58 | 0/8 3 h-lim-p 0.0023 0.0530 3.6621 1555.132607 5 0.0004 84 | 0/8 4 h-lim-p 0.0021 0.2130 0.7078 1555.132485 2 0.0005 101 | 0/8 5 h-lim-p 0.0019 1.0892 0.1858 1555.132473 2 0.0007 125 | 0/8 6 h-lim-p 0.0067 6.7368 0.0204 1555.132473 0 0.0007 147 | 0/8 7 h-lim-p 0.0063 20.0000 0.0024 1555.132472 0 0.0126 168 | 0/8 8 h-lim-p 0.0070 20.0000 0.0043 1555.132422 0 0.0557 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1555.132420 0 1.0938 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1555.132420 0 1.0938 231 | 0/8 11 h-lim-p 1.7564 20.0000 0.0000 1555.132420 0 0.0034 259 | 0/8 12 h-lim-p 0.0014 20.0000 0.0000 1555.132420 0 0.0000 294 Out... lnL = -1555.132420 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1555.132420 Node 7: lnL = -1555.132420 Node 8: lnL = -1555.132420 Node 9: lnL = -1555.132420 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 847 Sequential format.. Reading seq # 1: YPR163C_Sbay Reading seq # 2: YPR163C_Scer Reading seq # 3: YPR163C_Skud Reading seq # 4: YPR163C_Smik Reading seq # 5: YPR163C_Spar Sequences read.. Counting patterns.. # site patterns = 292 Counting frequencies.. 120 bytes for distance 46720 bytes for lkl0 37376 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.089305 0.202954 0.063683 0.153666 0.123175 0.176280 0.209987 0.123273 lnL0 = -3863.735686 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3863.735686 x= 0.08931 0.20295 0.06368 0.15367 0.12317 0.17628 0.20999 0.12327 1 h-lim-p 0.0035 0.0280 119.3305 3862.265963 8 0.0002 43 | 0/8 2 h-lim-p 0.0010 0.0169 26.5818 3862.100676 4 0.0005 63 | 0/8 3 h-lim-p 0.0010 0.0309 12.4933 3862.079934 6 0.0003 91 | 0/8 4 h-lim-p 0.0029 0.2542 1.3802 3862.079389 3 0.0006 110 | 0/8 5 h-lim-p 0.0021 0.5963 0.3906 3862.079367 2 0.0003 129 | 0/8 6 h-lim-p 0.0013 2.6453 0.0995 3862.079365 1 0.0003 152 | 0/8 7 h-lim-p 0.0025 18.9830 0.0133 3862.079365 0 0.0011 172 | 0/8 8 h-lim-p 0.0904 20.0000 0.0002 3862.079341 0 1.0844 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 3862.079340 0 1.0938 215 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3862.079340 0 1.0938 235 | 0/8 11 h-lim-p 1.1084 20.0000 0.0000 3862.079340 0 1.1084 255 | 0/8 12 h-lim-p 0.4841 20.0000 0.0000 3862.079340 0 0.0132 279 | 0/8 13 h-lim-p 0.0010 20.0000 0.0002 3862.079340 0 0.0003 300 | 0/8 14 h-lim-p 0.0009 20.0000 0.0001 3862.079340 0 0.0000 337 | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -3862.079340 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3862.079340 Node 7: lnL = -3862.079340 Node 8: lnL = -3862.079340 Node 9: lnL = -3862.079340 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 817 Sequential format.. Reading seq # 1: YPR164W_Sbay Reading seq # 2: YPR164W_Scer Reading seq # 3: YPR164W_Skud Reading seq # 4: YPR164W_Smik Reading seq # 5: YPR164W_Spar Sequences read.. Counting patterns.. # site patterns = 287 Counting frequencies.. 120 bytes for distance 45920 bytes for lkl0 36736 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.086301 0.203113 0.054405 0.150574 0.126267 0.194337 0.218174 0.120449 lnL0 = -3841.255094 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 3841.255094 x= 0.08630 0.20311 0.05441 0.15057 0.12627 0.19434 0.21817 0.12045 1 h-lim-p 0.0038 0.3014 141.7291 3839.269840 3 0.0002 31 | 0/8 2 h-lim-p 0.0010 0.0115 31.7860 3839.025889 6 0.0005 56 | 0/8 3 h-lim-p 0.0010 0.0203 15.8342 3838.993268 6 0.0003 84 | 0/8 4 h-lim-p 0.0025 0.1261 2.0279 3838.992287 2 0.0005 101 | 0/8 5 h-lim-p 0.0018 0.5829 0.5351 3838.992226 2 0.0004 118 | 0/8 6 h-lim-p 0.0012 2.6334 0.2083 3838.992220 1 0.0003 141 | 0/8 7 h-lim-p 0.0024 10.4385 0.0242 3838.992219 0 0.0011 161 | 0/8 8 h-lim-p 0.0461 20.0000 0.0006 3838.991962 0 0.7383 185 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 3838.991956 0 1.0938 205 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 3838.991956 0 1.0938 225 | 0/8 11 h-lim-p 1.2831 20.0000 0.0000 3838.991956 0 0.2807 246 | 0/8 12 h-lim-p 0.1405 20.0000 0.0000 3838.991956 0 0.0351 267 | 0/8 13 h-lim-p 0.0191 20.0000 0.0000 3838.991956 0 0.0191 287 | 0/8 14 h-lim-p 0.0125 20.0000 0.0000 3838.991956 0 0.0003 311 | 0/8 15 h-lim-p 0.0000 20.0000 0.0006 3838.991956 0 0.0000 335 | 0/8 16 h-lim-p 0.0005 20.0000 0.0000 3838.991956 0 0.0000 373 Out... lnL = -3838.991956 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -3838.991956 Node 7: lnL = -3838.991956 Node 8: lnL = -3838.991956 Node 9: lnL = -3838.991956 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 453 Sequential format.. Reading seq # 1: YPR165W_Sbay Reading seq # 2: YPR165W_Scer Reading seq # 3: YPR165W_Skud Reading seq # 4: YPR165W_Smik Reading seq # 5: YPR165W_Spar Sequences read.. Counting patterns.. # site patterns = 106 Counting frequencies.. 120 bytes for distance 16960 bytes for lkl0 13568 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.061566 0.014053 0.006433 0.049156 0.041567 0.107776 0.117996 0.074433 lnL0 = -1514.889819 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1514.889819 x= 0.06157 0.01405 0.00643 0.04916 0.04157 0.10778 0.11800 0.07443 1 h-lim-p 0.0002 0.0015 370.5001 1512.921519 9 0.0000 39 | 0/8 2 h-lim-p 0.0001 0.0006 92.1397 1512.525343 0 0.0001 52 | 0/8 3 h-lim-p 0.0004 0.0038 30.6798 1512.440056 2 0.0002 68 | 0/8 4 h-lim-p 0.0006 0.0213 10.2989 1512.428383 5 0.0002 91 | 0/8 5 h-lim-p 0.0006 0.0126 4.5709 1512.427244 2 0.0001 108 | 0/8 6 h-lim-p 0.0006 0.2353 0.9583 1512.427160 4 0.0002 131 | 0/8 7 h-lim-p 0.0023 1.5257 0.0724 1512.426980 0 0.0047 152 | 0/8 8 h-lim-p 0.0075 0.8436 0.0448 1512.391886 0 0.0604 175 | 0/8 9 h-lim-p 2.5000 20.0000 0.0003 1512.391144 3 1.3159 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0001 1512.391085 2 1.3159 227 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1512.391084 0 1.0938 247 | 0/8 12 h-lim-p 1.4344 20.0000 0.0000 1512.391084 0 2.8687 268 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1512.391084 0 0.1562 291 | 0/8 14 h-lim-p 0.2560 20.0000 0.0000 1512.391084 0 0.0035 316 | 0/8 15 h-lim-p 0.0011 20.0000 0.0000 1512.391084 0 0.0000 349 Out... lnL = -1512.391084 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1512.391084 Node 7: lnL = -1512.391084 Node 8: lnL = -1512.391084 Node 9: lnL = -1512.391084 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 271 Sequential format.. Reading seq # 1: YPR166C_Sbay Reading seq # 2: YPR166C_Scer Reading seq # 3: YPR166C_Skud Reading seq # 4: YPR166C_Smik Reading seq # 5: YPR166C_Spar Sequences read.. Counting patterns.. # site patterns = 134 Counting frequencies.. 120 bytes for distance 21440 bytes for lkl0 17152 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.124649 0.119506 0.018203 0.140734 0.134548 0.207657 0.303643 0.158639 lnL0 = -1225.951059 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1225.951059 x= 0.12465 0.11951 0.01820 0.14073 0.13455 0.20766 0.30364 0.15864 1 h-lim-p 0.0014 0.0112 67.8814 1224.587610 3 0.0006 29 | 0/8 2 h-lim-p 0.0004 0.0033 26.9362 1224.209074 0 0.0012 42 | 0/8 3 h-lim-p 0.0014 0.0114 10.1226 1224.141138 6 0.0015 70 | 0/8 4 h-lim-p 0.0029 0.0723 5.3049 1224.127773 3 0.0012 88 | 0/8 5 h-lim-p 0.0083 0.5119 0.7879 1224.127101 4 0.0022 109 | 0/8 6 h-lim-p 0.0364 6.1089 0.0481 1224.127086 2 0.0048 135 | 0/8 7 h-lim-p 0.0070 11.7681 0.0328 1224.126997 0 0.0141 156 | 0/8 8 h-lim-p 0.0087 13.0768 0.0532 1224.125266 0 0.0347 178 | 0/8 9 h-lim-p 2.5000 20.0000 0.0004 1224.125191 2 1.0889 202 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1224.125190 0 1.0938 222 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1224.125190 0 1.0938 242 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1224.125190 0 2.1875 262 | 0/8 13 h-lim-p 2.5000 20.0000 0.0000 1224.125190 0 0.1367 285 | 0/8 14 h-lim-p 0.0404 20.0000 0.0000 1224.125190 0 0.0202 305 | 0/8 15 h-lim-p 0.0098 20.0000 0.0000 1224.125190 0 0.0012 327 Out... lnL = -1224.125190 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1224.125190 Node 7: lnL = -1224.125190 Node 8: lnL = -1224.125190 Node 9: lnL = -1224.125190 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 471 Sequential format.. Reading seq # 1: YPR167C_Sbay Reading seq # 2: YPR167C_Scer Reading seq # 3: YPR167C_Skud Reading seq # 4: YPR167C_Smik Reading seq # 5: YPR167C_Spar Sequences read.. Counting patterns.. # site patterns = 200 Counting frequencies.. 120 bytes for distance 32000 bytes for lkl0 25600 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.111681 0.108044 0.077288 0.140881 0.123401 0.161415 0.160208 0.141425 lnL0 = -2135.932373 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2135.932373 x= 0.11168 0.10804 0.07729 0.14088 0.12340 0.16142 0.16021 0.14142 1 h-lim-p 0.0045 0.0359 66.5763 2135.189354 8 0.0004 43 | 0/8 2 h-lim-p 0.0024 0.0295 9.8717 2135.163501 2 0.0006 60 | 0/8 3 h-lim-p 0.0016 0.0656 3.5284 2135.160164 4 0.0006 80 | 0/8 4 h-lim-p 0.0032 0.3828 0.6694 2135.160042 3 0.0006 100 | 0/8 5 h-lim-p 0.0036 1.8377 0.1050 2135.160039 1 0.0004 124 | 0/8 6 h-lim-p 0.0038 20.0000 0.0121 2135.160039 0 0.0008 145 | 0/8 7 h-lim-p 0.0442 20.0000 0.0002 2135.160026 0 0.7067 169 | 0/8 8 h-lim-p 0.0017 3.1816 0.0953 2135.160021 1 0.0008 192 | 0/8 9 h-lim-p 2.1750 20.0000 0.0000 2135.160019 0 0.9516 212 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2135.160019 0 1.0938 232 | 0/8 11 h-lim-p 1.4575 20.0000 0.0000 2135.160019 0 0.0228 257 | 0/8 12 h-lim-p 0.0094 20.0000 0.0000 2135.160019 0 0.0001 283 Out... lnL = -2135.160019 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2135.160019 Node 7: lnL = -2135.160019 Node 8: lnL = -2135.160019 Node 9: lnL = -2135.160019 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 470 Sequential format.. Reading seq # 1: YPR168W_Sbay Reading seq # 2: YPR168W_Scer Reading seq # 3: YPR168W_Skud Reading seq # 4: YPR168W_Smik Reading seq # 5: YPR168W_Spar Sequences read.. Counting patterns.. # site patterns = 187 Counting frequencies.. 120 bytes for distance 29920 bytes for lkl0 23936 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.119740 0.091991 0.075265 0.140095 0.124187 0.163375 0.168828 0.149473 lnL0 = -2137.050795 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2137.050795 x= 0.11974 0.09199 0.07527 0.14009 0.12419 0.16337 0.16883 0.14947 1 h-lim-p 0.0097 1.8743 66.3026 2136.336286 8 0.0003 43 | 0/8 2 h-lim-p 0.0022 0.0267 10.2055 2136.305773 5 0.0006 66 | 0/8 3 h-lim-p 0.0016 0.0544 3.9183 2136.302099 5 0.0005 90 | 0/8 4 h-lim-p 0.0036 0.4646 0.5870 2136.301998 3 0.0006 110 | 0/8 5 h-lim-p 0.0097 4.8130 0.0361 2136.301997 0 0.0005 133 | 0/8 6 h-lim-p 0.0098 20.0000 0.0020 2136.301997 0 0.0011 155 | 0/8 7 h-lim-p 0.0080 20.0000 0.0003 2136.301997 0 0.0240 176 | 0/8 8 h-lim-p 0.0060 20.0000 0.0010 2136.301996 0 0.0239 198 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2136.301996 0 1.0938 218 | 0/8 10 h-lim-p 1.6938 20.0000 0.0000 2136.301996 0 2.5408 238 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2136.301996 0 0.2734 260 | 0/8 12 h-lim-p 0.0867 20.0000 0.0000 2136.301996 0 0.0650 280 | 0/8 13 h-lim-p 0.0286 20.0000 0.0000 2136.301996 0 0.0286 300 | 0/8 14 h-lim-p 0.0167 20.0000 0.0000 2136.301996 0 0.0000 334 Out... lnL = -2136.301996 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2136.301996 Node 7: lnL = -2136.301996 Node 8: lnL = -2136.301996 Node 9: lnL = -2136.301996 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 147 Sequential format.. Reading seq # 1: YPR169W_Sbay Reading seq # 2: YPR169W_Scer Reading seq # 3: YPR169W_Skud Reading seq # 4: YPR169W_Smik Reading seq # 5: YPR169W_Spar Sequences read.. Counting patterns.. # site patterns = 79 Counting frequencies.. 120 bytes for distance 12640 bytes for lkl0 10112 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.059205 0.086361 0.057329 0.141301 0.117934 0.172690 0.132021 0.083769 lnL0 = -597.159176 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 597.159176 x= 0.05921 0.08636 0.05733 0.14130 0.11793 0.17269 0.13202 0.08377 1 h-lim-p 0.0069 0.0548 41.2152 596.452849 5 0.0009 34 | 0/8 2 h-lim-p 0.0019 0.0155 10.0591 596.379118 5 0.0015 56 | 0/8 3 h-lim-p 0.0043 0.0536 3.5143 596.373546 2 0.0010 73 | 0/8 4 h-lim-p 0.0041 0.1805 0.8586 596.372907 3 0.0019 91 | 0/8 5 h-lim-p 0.0112 1.1383 0.1436 596.372882 2 0.0025 116 | 0/8 6 h-lim-p 0.0376 20.0000 0.0094 596.372877 1 0.0150 138 | 0/8 7 h-lim-p 0.0131 15.9832 0.0108 596.372820 0 0.0522 160 | 0/8 8 h-lim-p 0.0055 20.0000 0.1020 596.372578 0 0.0083 180 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 596.372568 2 0.9961 204 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 596.372568 0 1.0938 224 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 596.372568 0 2.1875 244 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 596.372568 0 1.0938 264 | 0/8 13 h-lim-p 0.3194 20.0000 0.0000 596.372568 0 5.1102 288 | 0/8 14 h-lim-p 1.0612 20.0000 0.0000 596.372568 0 0.0000 327 | 0/8 15 h-lim-p 0.0000 20.0000 0.0001 | 0/8 16 h-lim-p 0.0000 20.0000 0.0001 Out... lnL = -596.372568 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -596.372568 Node 7: lnL = -596.372568 Node 8: lnL = -596.372568 Node 9: lnL = -596.372568 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 263 Sequential format.. Reading seq # 1: YPR172W_Sbay Reading seq # 2: YPR172W_Scer Reading seq # 3: YPR172W_Skud Reading seq # 4: YPR172W_Smik Reading seq # 5: YPR172W_Spar Sequences read.. Counting patterns.. # site patterns = 130 Counting frequencies.. 120 bytes for distance 20800 bytes for lkl0 16640 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.131644 0.097286 0.068112 0.083448 0.121705 0.126267 0.129815 0.158252 lnL0 = -1113.332008 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1113.332008 x= 0.13164 0.09729 0.06811 0.08345 0.12170 0.12627 0.12982 0.15825 1 h-lim-p 0.0025 0.0198 67.7444 1112.110220 3 0.0006 29 | 0/8 2 h-lim-p 0.0009 0.0074 21.9142 1111.901419 4 0.0009 49 | 0/8 3 h-lim-p 0.0041 0.0519 4.9631 1111.892881 6 0.0007 77 | 0/8 4 h-lim-p 0.0023 0.1129 1.5851 1111.891676 2 0.0011 93 | 0/8 5 h-lim-p 0.0105 2.9926 0.1629 1111.891661 2 0.0010 111 | 0/8 6 h-lim-p 0.0072 10.4249 0.0235 1111.891655 2 0.0048 137 | 0/8 7 h-lim-p 0.0125 20.0000 0.0090 1111.891095 0 0.1001 160 | 0/8 8 h-lim-p 0.0017 0.4998 0.5417 1111.890370 1 0.0021 182 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 1111.890360 2 0.9961 206 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1111.890360 0 1.0938 226 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1111.890360 0 2.1875 246 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 1111.890360 0 1.0938 266 | 0/8 13 h-lim-p 0.8645 20.0000 0.0000 1111.890360 0 5.1868 288 | 0/8 14 h-lim-p 1.8219 20.0000 0.0000 1111.890360 0 0.2277 310 | 0/8 15 h-lim-p 0.6106 20.0000 0.0000 1111.890360 0 0.0083 335 | 0/8 16 h-lim-p 0.0244 20.0000 0.0000 1111.890360 0 0.0000 376 Out... lnL = -1111.890360 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1111.890360 Node 7: lnL = -1111.890360 Node 8: lnL = -1111.890360 Node 9: lnL = -1111.890360 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 217 Sequential format.. Reading seq # 1: YPR173C_Sbay Reading seq # 2: YPR173C_Scer Reading seq # 3: YPR173C_Skud Reading seq # 4: YPR173C_Smik Reading seq # 5: YPR173C_Spar Sequences read.. Counting patterns.. # site patterns = 64 Counting frequencies.. 120 bytes for distance 10240 bytes for lkl0 8192 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.003774 0.029958 0.048420 0.096004 0.067872 4.869642 0.093394 0.103631 lnL0 = -659.527085 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 659.527085 x= 0.00377 0.02996 0.04842 0.09600 0.06787 4.86964 0.09339 0.10363 1 h-lim-p 0.0012 0.0093 30.3103 659.330629 7 0.0004 38 | 0/8 2 h-lim-p 0.0004 0.0030 12.7456 659.294871 0 0.0006 50 | 0/8 3 h-lim-p 0.0009 0.0070 1.9670 659.293905 5 0.0005 74 | 0/8 4 h-lim-p 0.0019 0.3510 0.5224 659.293841 2 0.0005 91 | 0/8 5 h-lim-p 0.0043 0.2445 0.0618 659.293839 1 0.0005 115 | 0/8 6 h-lim-p 0.0388 20.0000 0.0008 659.293406 0 0.9316 139 | 0/8 7 h-lim-p 2.5000 20.0000 0.0001 659.293390 2 0.9961 163 | 0/8 8 h-lim-p 2.5000 20.0000 0.0000 659.293390 0 2.1875 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 659.293390 0 1.0938 203 | 0/8 10 h-lim-p 0.2054 20.0000 0.0001 659.293390 0 0.0002 232 | 0/8 11 h-lim-p 0.0000 13.1444 0.0005 659.293390 0 0.0000 255 | 0/8 12 h-lim-p 0.0000 20.0000 0.0001 659.293390 0 0.0000 276 | 0/8 13 h-lim-p 0.0000 17.7889 0.0007 659.293390 0 0.0000 297 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 659.293390 0 0.0000 328 | 0/8 15 h-lim-p 0.0000 20.0000 0.0009 | 0/8 16 h-lim-p 0.0000 20.0000 0.0009 Out... lnL = -659.293390 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -659.293390 Node 7: lnL = -659.293390 Node 8: lnL = -659.293390 Node 9: lnL = -659.293390 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 275 Sequential format.. Reading seq # 1: YPR174C_Sbay Reading seq # 2: YPR174C_Scer Reading seq # 3: YPR174C_Skud Reading seq # 4: YPR174C_Smik Reading seq # 5: YPR174C_Spar Sequences read.. Counting patterns.. # site patterns = 113 Counting frequencies.. 120 bytes for distance 18080 bytes for lkl0 14464 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.111646 0.056901 0.043564 0.074470 0.082624 0.138935 0.193914 0.135280 lnL0 = -1151.660414 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1151.660414 x= 0.11165 0.05690 0.04356 0.07447 0.08262 0.13894 0.19391 0.13528 1 h-lim-p 0.0005 0.0038 83.0991 1150.374345 6 0.0004 33 | 0/8 2 h-lim-p 0.0007 0.0060 17.8864 1150.296281 7 0.0005 62 | 0/8 3 h-lim-p 0.0014 0.0357 6.2293 1150.286701 4 0.0006 82 | 0/8 4 h-lim-p 0.0021 0.1228 1.6085 1150.285993 5 0.0006 105 | 0/8 5 h-lim-p 0.0020 0.3766 0.4606 1150.285904 2 0.0009 121 | 0/8 6 h-lim-p 0.0020 1.3766 0.2107 1150.285891 2 0.0008 145 | 0/8 7 h-lim-p 0.0357 20.0000 0.0044 1150.285891 0 0.0020 168 | 0/8 8 h-lim-p 0.1630 20.0000 0.0001 1150.285888 0 0.9780 190 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1150.285888 0 1.0938 210 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1150.285888 0 1.0938 230 | 0/8 11 h-lim-p 1.1751 20.0000 0.0000 1150.285888 0 0.0184 255 | 0/8 12 h-lim-p 0.0014 20.0000 0.0000 1150.285888 0 0.0000 297 | 0/8 13 h-lim-p 0.0000 20.0000 0.0000 1150.285888 0 0.0000 322 | 0/8 14 h-lim-p 0.0000 20.0000 0.0000 .. | 0/8 15 h-lim-p 0.0000 20.0000 0.0000 | 0/8 16 h-lim-p 0.0000 20.0000 0.0000 Out... lnL = -1150.285888 convergence? Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1150.285888 Node 7: lnL = -1150.285888 Node 8: lnL = -1150.285888 Node 9: lnL = -1150.285888 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 227 Sequential format.. Reading seq # 1: YPR180W_Sbay Reading seq # 2: YPR180W_Scer Reading seq # 3: YPR180W_Skud Reading seq # 4: YPR180W_Smik Reading seq # 5: YPR180W_Spar Sequences read.. Counting patterns.. # site patterns = 97 Counting frequencies.. 120 bytes for distance 15520 bytes for lkl0 12416 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.134964 0.001276 0.027188 0.055484 0.124217 0.153839 0.251334 0.159517 lnL0 = -901.032731 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 901.032731 x= 0.13496 0.00128 0.02719 0.05548 0.12422 0.15384 0.25133 0.15952 1 h-lim-p 0.0012 0.0092 67.7846 900.497403 3 0.0003 29 | 0/8 2 h-lim-p 0.0010 0.0079 12.9042 900.438309 7 0.0007 59 | 0/8 3 h-lim-p 0.0010 0.0185 9.1889 900.421029 6 0.0006 85 | 0/8 4 h-lim-p 0.0068 0.7535 0.7681 900.420522 4 0.0017 106 | 0/8 5 h-lim-p 0.0033 0.0407 0.4049 900.420480 2 0.0006 131 | 0/8 6 h-lim-p 0.0013 0.9345 0.2041 900.420464 2 0.0010 155 | 0/8 7 h-lim-p 0.0059 1.5703 0.0348 900.420463 0 0.0013 176 | 0/8 8 h-lim-p 0.1296 20.0000 0.0003 900.420291 0 1.0372 199 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 900.420290 1 0.9961 221 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 900.420290 0 1.0938 241 | 0/8 11 h-lim-p 2.4429 20.0000 0.0000 900.420290 0 2.1375 261 | 0/8 12 h-lim-p 2.5000 20.0000 0.0000 900.420290 0 0.1562 284 | 0/8 13 h-lim-p 0.0329 20.0000 0.0000 900.420290 0 0.0000 321 Out... lnL = -900.420290 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -900.420290 Node 7: lnL = -900.420290 Node 8: lnL = -900.420290 Node 9: lnL = -900.420290 err or end of tree file. Time used: 00:00:01  Reading options from ./baseml.ctl.. ns = 5 ls = 580 Sequential format.. Reading seq # 1: YPR182W_Sbay Reading seq # 2: YPR182W_Scer Reading seq # 3: YPR182W_Skud Reading seq # 4: YPR182W_Smik Reading seq # 5: YPR182W_Spar Sequences read.. Counting patterns.. # site patterns = 228 Counting frequencies.. 120 bytes for distance 36480 bytes for lkl0 29184 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.141495 0.023291 0.078176 0.094648 0.079203 0.213246 0.258588 0.163480 lnL0 = -2554.889038 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2554.889038 x= 0.14149 0.02329 0.07818 0.09465 0.07920 0.21325 0.25859 0.16348 1 h-lim-p 0.0013 0.5644 195.6261 2551.097667 9 0.0002 46 | 0/8 2 h-lim-p 0.0006 0.0049 28.3922 2550.881304 6 0.0005 69 | 0/8 3 h-lim-p 0.0006 0.0108 23.7849 2550.818763 4 0.0003 90 | 0/8 4 h-lim-p 0.0008 0.0304 9.4665 2550.803243 5 0.0004 113 | 0/8 5 h-lim-p 0.0024 0.1702 1.7177 2550.802383 3 0.0006 132 | 0/8 6 h-lim-p 0.0010 0.2738 0.9970 2550.802201 2 0.0005 148 | 0/8 7 h-lim-p 0.0163 12.9915 0.0298 2550.802195 1 0.0032 171 | 0/8 8 h-lim-p 0.0238 20.0000 0.0041 2550.799727 0 0.3803 195 | 0/8 9 h-lim-p 2.5000 20.0000 0.0001 2550.799701 1 0.9961 217 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 2550.799701 0 1.0938 237 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 2550.799701 0 1.0938 257 | 0/8 12 h-lim-p 1.1187 20.0000 0.0000 2550.799701 0 1.6781 277 | 0/8 13 h-lim-p 0.7938 20.0000 0.0000 2550.799701 0 0.0496 300 | 0/8 14 h-lim-p 0.0000 20.0000 0.0066 2550.799701 0 0.0000 320 | 0/8 15 h-lim-p 0.0035 20.0000 0.0000 2550.799701 0 0.0000 349 | 0/8 16 h-lim-p 0.0059 20.0000 0.0000 2550.799701 0 0.0004 372 Out... lnL = -2550.799701 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2550.799701 Node 7: lnL = -2550.799701 Node 8: lnL = -2550.799701 Node 9: lnL = -2550.799701 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 332 Sequential format.. Reading seq # 1: YPR183W_Sbay Reading seq # 2: YPR183W_Scer Reading seq # 3: YPR183W_Skud Reading seq # 4: YPR183W_Smik Reading seq # 5: YPR183W_Spar Sequences read.. Counting patterns.. # site patterns = 136 Counting frequencies.. 120 bytes for distance 21760 bytes for lkl0 17408 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.088965 0.058709 0.041435 0.068663 0.095278 0.163565 0.139873 0.105146 lnL0 = -1262.664970 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1262.664970 x= 0.08896 0.05871 0.04143 0.06866 0.09528 0.16356 0.13987 0.10515 1 h-lim-p 0.0040 1.8272 79.8293 1261.742183 8 0.0003 44 | 0/8 2 h-lim-p 0.0012 0.0094 14.3586 1261.692672 6 0.0005 69 | 0/8 3 h-lim-p 0.0015 0.0468 4.7887 1261.687825 6 0.0005 96 | 0/8 4 h-lim-p 0.0013 0.1283 1.7799 1261.686992 2 0.0006 112 | 0/8 5 h-lim-p 0.0061 1.3768 0.1721 1261.686981 0 0.0008 126 | 0/8 6 h-lim-p 0.0098 15.7345 0.0134 1261.686981 0 0.0011 148 | 0/8 7 h-lim-p 0.0026 20.0000 0.0055 1261.686981 0 0.0039 168 | 0/8 8 h-lim-p 0.0161 20.0000 0.0013 1261.686929 0 0.1290 191 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1261.686928 0 1.0938 211 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1261.686928 0 1.0938 231 | 0/8 11 h-lim-p 2.5000 20.0000 0.0000 1261.686928 0 0.0195 257 | 0/8 12 h-lim-p 0.0088 20.0000 0.0000 1261.686928 0 0.0088 277 | 0/8 13 h-lim-p 0.0063 20.0000 0.0000 1261.686928 0 0.0007 299 | 0/8 14 h-lim-p 0.0003 20.0000 0.0000 1261.686928 0 0.0003 319 | 0/8 15 h-lim-p 0.0005 20.0000 0.0000 1261.686928 0 0.0001 340 Out... lnL = -1261.686928 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1261.686928 Node 7: lnL = -1261.686928 Node 8: lnL = -1261.686928 Node 9: lnL = -1261.686928 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 572 Sequential format.. Reading seq # 1: YPR185W_Sbay Reading seq # 2: YPR185W_Scer Reading seq # 3: YPR185W_Skud Reading seq # 4: YPR185W_Smik Reading seq # 5: YPR185W_Spar Sequences read.. Counting patterns.. # site patterns = 145 Counting frequencies.. 120 bytes for distance 23200 bytes for lkl0 18560 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.112672 0.048487 0.046619 0.067784 0.032958 0.150688 0.089559 0.127093 lnL0 = -2161.875758 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 2161.875758 x= 0.11267 0.04849 0.04662 0.06778 0.03296 0.15069 0.08956 0.12709 1 h-lim-p 0.0002 0.0013 109.5318 2161.115996 6 0.0001 33 | 0/8 2 h-lim-p 0.0011 0.0188 13.0921 2161.103045 6 0.0002 61 | 0/8 3 h-lim-p 0.0002 0.0077 9.2100 2161.098790 5 0.0001 86 | 0/8 4 h-lim-p 0.0005 0.0547 2.6051 2161.098173 2 0.0002 102 | 0/8 5 h-lim-p 0.0022 0.3441 0.2485 2161.098166 0 0.0002 116 | 0/8 6 h-lim-p 0.0009 4.1653 0.0690 2161.098165 0 0.0004 136 | 0/8 7 h-lim-p 0.0084 20.0000 0.0031 2161.098165 0 0.0005 159 | 0/8 8 h-lim-p 0.0521 20.0000 0.0000 2161.098164 0 0.8330 183 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 2161.098164 0 1.0938 203 | 0/8 10 h-lim-p 1.1225 20.0000 0.0000 2161.098164 0 0.0001 235 Out... lnL = -2161.098164 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -2161.098164 Node 7: lnL = -2161.098164 Node 8: lnL = -2161.098164 Node 9: lnL = -2161.098164 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 247 Sequential format.. Reading seq # 1: YPR186C_Sbay Reading seq # 2: YPR186C_Scer Reading seq # 3: YPR186C_Skud Reading seq # 4: YPR186C_Smik Reading seq # 5: YPR186C_Spar Sequences read.. Counting patterns.. # site patterns = 107 Counting frequencies.. 120 bytes for distance 17120 bytes for lkl0 13696 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.067369 0.112668 0.002699 0.101343 0.093780 0.166579 0.199219 0.085038 lnL0 = -1029.344186 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 1029.344186 x= 0.06737 0.11267 0.00270 0.10134 0.09378 0.16658 0.19922 0.08504 1 h-lim-p 0.0003 0.0174 279.5393 1026.477570 7 0.0001 36 | 0/8 2 h-lim-p 0.0017 0.0135 12.4442 1026.425162 6 0.0007 62 | 0/8 3 h-lim-p 0.0015 0.0371 5.4999 1026.413334 7 0.0009 92 | 0/8 4 h-lim-p 0.0074 0.3154 0.6816 1026.413170 3 0.0007 112 | 0/8 5 h-lim-p 0.0017 0.9546 0.2809 1026.413141 1 0.0009 134 | 0/8 6 h-lim-p 0.0055 4.7016 0.0440 1026.413140 1 0.0007 158 | 0/8 7 h-lim-p 0.0035 20.0000 0.0086 1026.413140 0 0.0015 178 | 0/8 8 h-lim-p 0.4327 20.0000 0.0000 1026.413137 0 1.7307 200 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 1026.413136 0 1.2500 220 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 1026.413136 0 1.0938 240 | 0/8 11 h-lim-p 1.5231 20.0000 0.0000 1026.413136 0 1.3327 260 | 0/8 12 h-lim-p 1.0783 20.0000 0.0000 1026.413136 0 0.5392 280 | 0/8 13 h-lim-p 0.0053 20.0000 0.0004 1026.413136 0 0.0000 310 | 0/8 14 h-lim-p 0.0003 20.0000 0.0000 1026.413136 0 0.0000 339 Out... lnL = -1026.413136 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -1026.413136 Node 7: lnL = -1026.413136 Node 8: lnL = -1026.413136 Node 9: lnL = -1026.413136 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 190 Sequential format.. Reading seq # 1: YPR188C_Sbay Reading seq # 2: YPR188C_Scer Reading seq # 3: YPR188C_Skud Reading seq # 4: YPR188C_Smik Reading seq # 5: YPR188C_Spar Sequences read.. Counting patterns.. # site patterns = 100 Counting frequencies.. 120 bytes for distance 16000 bytes for lkl0 12800 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.157861 0.068291 0.100071 0.156910 0.069636 0.152715 0.226997 0.181751 lnL0 = -871.500827 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 871.500827 x= 0.15786 0.06829 0.10007 0.15691 0.06964 0.15271 0.22700 0.18175 1 h-lim-p 0.0082 0.0658 7.0130 871.471176 6 0.0012 38 | 0/8 2 h-lim-p 0.0032 0.0977 2.6834 871.467176 4 0.0012 58 | 0/8 3 h-lim-p 0.0036 0.4311 0.9358 871.466903 3 0.0007 77 | 0/8 4 h-lim-p 0.0053 0.9963 0.1251 871.466891 3 0.0016 105 | 0/8 5 h-lim-p 0.0043 8.0076 0.0464 871.466890 0 0.0019 125 | 0/8 6 h-lim-p 0.0268 20.0000 0.0032 871.466890 0 0.0029 147 | 0/8 7 h-lim-p 0.0845 20.0000 0.0001 871.466889 0 0.1267 167 | 0/8 8 h-lim-p 0.0043 20.0000 0.0033 871.466889 0 0.0086 188 | 0/8 9 h-lim-p 2.5000 20.0000 0.0000 871.466889 0 1.0938 208 | 0/8 10 h-lim-p 2.5000 20.0000 0.0000 871.466889 0 0.3125 230 | 0/8 11 h-lim-p 0.2159 20.0000 0.0000 871.466889 0 0.0540 251 | 0/8 12 h-lim-p 0.0355 20.0000 0.0000 871.466889 0 0.0022 274 Out... lnL = -871.466889 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -871.466889 Node 7: lnL = -871.466889 Node 8: lnL = -871.466889 Node 9: lnL = -871.466889 err or end of tree file. Time used: 00:00:00  Reading options from ./baseml.ctl.. ns = 5 ls = 866 Sequential format.. Reading seq # 1: YPR193C_Sbay Reading seq # 2: YPR193C_Scer Reading seq # 3: YPR193C_Skud Reading seq # 4: YPR193C_Smik Reading seq # 5: YPR193C_Spar Sequences read.. Counting patterns.. # site patterns = 326 Counting frequencies.. 120 bytes for distance 52160 bytes for lkl0 41728 bytes for lkl1 0 bytes for fhK 800000 bytes for space TREE # 1: ((((2, 5), 4), 3), 1); MP score: -1.00 This is a rooted tree, without clock. Check. ntime & nrate & np: 8 0 8 6..7 7..8 8..9 9..2 9..5 8..4 7..3 6..1 0.341660 0.242435 0.000060 0.230873 0.138744 0.195958 0.381820 0.378923 lnL0 = -4302.662757 Bounds (np=8): 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 Iterating by ming2 Initial: fx= 4302.662757 x= 0.34166 0.24243 0.00006 0.23087 0.13874 0.19596 0.38182 0.37892 1 h-lim-p 0.0000 0.0000 421.1554 4302.576364 m 0.0000 22 | 1/8 2 h-lim-p 0.0000 0.0166 134.6679 4297.148930 0 0.0006 40 | 1/8 3 h-lim-p 0.0013 0.0102 65.6964 4295.455168 8 0.0009 70 | 1/8 4 h-lim-p 0.0024 0.0261 25.4570 4294.694539 2 0.0023 86 | 1/8 5 h-lim-p 0.0016 0.0129 31.4485 4294.340310 8 0.0011 117 | 1/8 6 h-lim-p 0.0052 0.0954 6.6799 4293.555644 0 0.0103 130 | 1/8 7 h-lim-p 0.0238 0.1900 1.3594 4270.511956 0 0.0950 144 | 0/8 8 h-lim-p 0.0002 0.0016 112.7974 4270.163796 7 0.0001 174 | 0/8 9 h-lim-p 0.0985 3.7611 0.1310 4268.136322 0 0.5908 188 | 0/8 10 h-lim-p 0.5560 4.4482 0.0418 4267.946831 3 0.4648 214 | 0/8 11 h-lim-p 1.5986 20.0000 0.0122 4267.897606 5 0.7847 246 | 0/8 12 h-lim-p 2.1598 20.0000 0.0044 4267.895295 4 0.6910 276 | 0/8 13 h-lim-p 2.5000 20.0000 0.0007 4267.895088 2 0.9644 300 | 0/8 14 h-lim-p 2.5000 20.0000 0.0001 4267.895086 0 1.0938 320 | 0/8 15 h-lim-p 2.5000 20.0000 0.0000 4267.895086 0 2.1875 340 | 0/8 16 h-lim-p 1.9626 20.0000 0.0000 4267.895086 0 0.8586 360 | 0/8 17 h-lim-p 2.5000 20.0000 0.0000 4267.895086 0 0.0000 403 Out... lnL = -4267.895086 Reconstructed ancestral states go into file rst. Marginal reconstruction.. Node 6: lnL = -4267.895086 Node 7: lnL = -4267.895086 Node 8: lnL = -4267.895086 Node 9: lnL = -4267.895086 err or end of tree file. Time used: 00:00:00