2 # BioPerl module for Bio::MolEvol::CodonModel
4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
6 # Cared for by Jason Stajich <jason-at-bioperl-dot-org>
8 # Copyright Jason Stajich
10 # You may distribute this module under the same terms as perl itself
12 # POD documentation - main docs before the code
16 Bio::MolEvol::CodonModel - Codon Evolution Models
20 use Bio::MolEvol::CodonModel;
22 my $codon_path = Bio::MolEvol::CodonModel->codon_path;
23 my ($ns, $syn) = $codon_path->{'AATAAC'};
24 print "AAT -> AAC: $ns ns mutations, $syn syn mutations\n";
29 This object is intended to group Codon Evolution Models. Currently it
30 has one method codon_path that returns a hash reference representing
31 the number of mutations it takes to mutate from one codon to another.
32 Some more description of how this is generated will follow later.
33 Additional codon evolution models and substitution matricies could be
34 represented here as well. Some of this may not be optimally named so
35 this can change before the next stable release of the BioPerl code.
41 User feedback is an integral part of the evolution of this and other
42 Bioperl modules. Send your comments and suggestions preferably to
43 the Bioperl mailing list. Your participation is much appreciated.
45 bioperl-l@bioperl.org - General discussion
46 http://bioperl.org/wiki/Mailing_lists - About the mailing lists
50 Please direct usage questions or support issues to the mailing list:
52 I<bioperl-l@bioperl.org>
54 rather than to the module maintainer directly. Many experienced and
55 reponsive experts will be able look at the problem and quickly
56 address it. Please include a thorough description of the problem
57 with code and data examples if at all possible.
61 Report bugs to the Bioperl bug tracking system to help us keep track
62 of the bugs and their resolution. Bug reports can be submitted via
65 https://github.com/bioperl/bioperl-live/issues
67 =head1 AUTHOR - Jason Stajich
69 Email jason-at-bioperl-dot-org
71 This is based on work from Alisha Holloway at UC Davis and Corbin
72 Jones at UNC-Chapel Hill.
76 The rest of the documentation details each of the object methods.
77 Internal methods are usually preceded with a _
81 package Bio
::MolEvol
::CodonModel
;
86 Usage : return a matrix of edit paths between codons
87 Example : my $codon_path = Bio::MolEvol::CodonModel->codon_path;
88 Returns : Hash reference