Glossary of major routines and variables used in the RNAGA
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Major routines:

  pop1st - Call "gtstr" to obtain initial set of structures for each
           sequence.

  maturation - Apply GA iteration to the initial population until every
               strucure in the population reach to the desired stability.
                  
  gtcnfrm -  Generate 2n new structures by performing crossover and mutation 
             operations on current populationof n structures. Mutate every 
             structure in the population to obtain n new structures. Select 
             n pair of structures based on the structure conservation score. 
             Do crossover for each pair to obtain another n new structures.
             
  hmlgy - Compute conservation score for each structure. A structure is
          represented as a set of stems. Each stem assign a weight. A stem
          get full credit if there is an equivalent stem (see manuscript) 
          in another sequence, otherwise, no credit to the stem. The 
          conservation score of a structure is the sum of its stem scores.

  hmlgyy - Compute the adjusted conservation score for each structure. The
           computation is similar to hmlgy except a stem may get partial
           credit of weight.

  gtwt - Compute the weight for each stem in a structure. Called by
         hmlgy and hmlgyy.

  nodcmpr - Determine whether a stem has an equivalent stem in another
            sequence, and also compute the score for the stem. Called
            by hmlgy and hmlgyy.

  fndcmstr - Find potential common structures that satisfy certain conditions
             in structural conservation score and stability.

  gtpopH - Select next generation based on structural conservation scores
           and also the diversity of structures.

  ritcmstr - Write out the predicted common structures. The structure is
             represented as a set of stems (region table).

  mutat - Perform mutation operation. The stem with low conservation score
          has better chance to be selected to mutate.

  xovr - Perform uniform crossover operation. The structure with high 
         conservation has better chance to be a parental structure.


Global variables:

  mxnseq - maximum number of sequences in sequence file

  lmax - maximum length of sequence

  mxnp - maximum number of stuctures in a population

  mxnp2 - maximum number of structures generated during GA iteration which
          is 3*mxnp

  mxnr - maximum number of regions (stems) in a structure

  Hcrtval - minimum conservation score for a structure to be considered as
            a potential common structure

  Hcrtval2 - minimum conservation score for a structure to be a common 
             structure

  mseq(mxnseq,lmax) - original multiple sequences returned from gtmseq

  lenseq(mxnseq) - array for the length of sequences

  seq(lmax) - hold single sequence 1st structure information

  ireg(mxnseq,mxnp2,mxnr) - array for the 5' of stem of structures generated
                            during GA iteration

  jreg(mxnseq,mxnp2,mxnr) - array for the 3' of stem of structures generated
                            during GA iteration

  rsz(mxnseq,mxnp2,mxnr) - array for the length of stem of structures 
                           generated during GA iteration

  struc(mxnseq,mxnp2,2) - array for the number of stems and the energy of
                          structures generated during GA iteration

  irHm(mxnseq,mxnp5,mxnr) - array for the 5' of stem of predicted common
                            structures

  jrHm(mxnseq,mxnp5,mxnr) - array for the 3' of stem of predicted common
                            structures

  rszHm(mxnseq,mxnp5,mxnr) - array for the length of stem of predicted common
                            structures

  strHm(mxnseq,mxnp5,2) - array for the number of stems and the energy of
                          predicted common structures

  nstrHm(mxnseq) - array for the number of predicted common structures 

  regscr(mxnseq,mxnp5,mxnr) - array for the stem conservation score

  Hscore(mxnseq,mxnp2) - array for the structural conservation score in which
                         a stem get either full credir of weight or none

  Hmscr(mxnseq,mxnp) - array for the structural conservation score in which
                       a stem may get partialcredir of weight