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.\"
.IX Title "Bio::MolEvol::CodonModel 3pm"
.TH Bio::MolEvol::CodonModel 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::MolEvol::CodonModel \- Codon Evolution Models
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  use Bio::MolEvol::CodonModel;
\&
\&  my $codon_path = Bio::MolEvol::CodonModel\->codon_path;
\&  my ($ns, $syn) = $codon_path\->{\*(AqAATAAC\*(Aq};
\&  print "AAT \-> AAC: $ns ns mutations, $syn syn mutations\en";
.Ve
.SH "DESCRIPTION"
.IX Header "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.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Jason Stajich"
.IX Header "AUTHOR - Jason Stajich"
Email jason-at-bioperl-dot-org
.PP
This is based on code and work from Alisha Holloway at \s-1UC\s0 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/
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "codon_path"
.IX Subsection "codon_path"
.Vb 5
\& 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
.Ve