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 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