Bio::MolEvol::CodonModel(3pm) User Contributed Perl Documentation Bio::MolEvol::CodonModel(3pm)
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
";
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://redmine.open-bio.org/projects/bioperl/
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.
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
Args : none
perl v5.14.2 2012-03-02 Bio::MolEvol::CodonModel(3pm)