Description

The FastSLINK program is the merger of code from FASTLINK version 2.x to the slink program, by Alejandro Schaffer and Dan Weeks. The SLINK package contains a simluation program slink and backend programs unknown, msim, lsim, isim. SLINK generates random replicates, and msim, lsim, isim analyze the replicates.

Version

Type slink on command line

Sample session

% slink
Program SLINK version 2.51

The program constants are set to the following maxima:
8 loci in mapping problem (maxlocus)
11 alleles at a single locus (maxall)
157 recombination probabilities (maxneed)
50000 maximum of censoring array (maxcensor)
180 haplotypes = n1 x n2 x ... where ni = current # alleles at locus i
16290 joint genotypes for a female
16290 joint genotypes for a male
2000 individuals in all pedigrees combined (maxind)
150 pedigrees (maxped)
11 binary codes at a single locus (maxfact)
3 quantitative factor(s) at a single locus
10 liability classes
11 binary codes at a single locus
1.00 base scaling factor for likelihood (scale)
2.00 scale multiplier for each locus (scalemult)
0.00000 frequency for elimination of heterozygotes (minfreq)
*******************************************************
This is SLINK, which is a general simulation program.
The output file pedfile.dat may be analyzed with the
companion programs MSIM, LSIM, and ISIM.
*******************************************************
Reading SIMDATA.DAT
YOU ARE USING LINKAGE/SLINK (V2.51) WITH 2-POINT AUTOSOMAL DATA
Reading SIMPED.DAT
Reading SLINKIN.DAT
The random number seed is: 29876
The number of replications is: 200
The requested proportion of unlinked families is: 0.000
The trait locus is locus number: 1
Summary Statistics about simped.dat
Number of pedigrees 1
Number of people 4
Number of females 2
Number of males 2
There were 0 in category: Marker Unknown; Trait original
There were 0 in category: Marker Available; Trait simulated
There were 4 in category: Marker Available; Trait original
There were 0 in category: Marker Unknown; Trait simulated
-----------------------------------
LINKED ORDER OF LOCI: 1 2
-----------------------------------
-----------------------------------
TRUE THETAS FOR LINKED ORDER 0.010000
-----------------------------------
-----------------------------------
UNLINKED ORDER OF LOCI: 1 2
-----------------------------------
-----------------------------------
TRUE THETAS FOR UNLINKED ORDER 0.500000
-----------------------------------
Beginning simulations...
. Maxneed may be reduced to 7
Maxcensor can be reduced to -32767
Elapsed Time for one replicate = 0.00 seconds
Estimated Time to finish = 0.00 minutes = 0.00 hours
........*.........*.........*.........*.........* 50 replicates generated
.........*.........*.........*.........*.........* 100 replicates generated
.........*.........*.........*.........*.........* 150 replicates generated
.........*.........*.........*.........*.........* 200 replicates generated

Elapsed Time = 0.00 min. or 0.00 hours
-----------------------------------
Actual proportion of unlinked families: 0.000
SLINK has completed 200 replicates.

Documentation

http://watson.hgen.pitt.edu/docs/SLink.html