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)