| Bio::MolEvol::CodonModel(3pm) | User Contributed Perl Documentation | Bio::MolEvol::CodonModel(3pm) |
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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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/
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
| 2018-10-27 | perl v5.26.2 |