bionic (3) Bio::MolEvol::CodonModel.3pm.gz

NAME

       Bio::MolEvol::CodonModel - Codon Evolution Models

SYNOPSIS

         use Bio::MolEvol::CodonModel;

         my $codon_path = Bio::MolEvol::CodonModel->codon_path;
         my ($ns, $syn) = $codon_path->{'AATAAC'};
         print "AAT -> AAC: $ns ns mutations, $syn syn mutations\n";

DESCRIPTION

       This object is intended to group Codon Evolution Models.  Currently it has one method codon_path that
       returns a hash reference representing the number of mutations it takes to mutate from one codon to
       another.  Some more description of how this is generated will follow later.  Additional codon evolution
       models and substitution matricies could be represented here as well.  Some of this may not be optimally
       named so this can change before the next stable release of the BioPerl code.

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments
       and suggestions preferably to the Bioperl mailing list.  Your participation is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will be able look
       at the problem and quickly address it. Please include a thorough description of the problem with code and
       data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution.
       Bug reports can be submitted via the web:

         https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

       Email jason-at-bioperl-dot-org

       This is based on code and work from Alisha Holloway at UC Davis and Corbin Jones at UNC-Chapel Hill. See
       Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans
       http://dx.doi.org/http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0050310 and
       http://www.dpgp.org/

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are usually preceded
       with a _

   codon_path
        Title   : codon_path
        Usage   : return a matrix of edit paths between codons
        Example : my $codon_path = Bio::MolEvol::CodonModel->codon_path;
        Returns : Hash reference, the array values for each codon path are num of Nonsyn & syn changes respectively.
        Args    : none