Bio::MolEvol::CodonModel(3) 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 work from Alisha Holloway at UC Davis and Corbin Jones at UNC-Chapel Hill.


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
 Args    : none