Provided by: libbio-perl-perl_1.7.2-3_all bug


       Bio::MolEvol::CodonModel - Codon Evolution Models


         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";


       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.


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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


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

        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