3 # BioPerl module for Bio::MolEvol::CodonModel
5 # Cared for by Jason Stajich <jason-at-bioperl-dot-org>
7 # Copyright Jason Stajich
9 # You may distribute this module under the same terms as perl itself
11 # POD documentation - main docs before the code
15 Bio::MolEvol::CodonModel - Codon Evolution Models
19 use Bio::MolEvol::CodonModel;
21 my $codon_path = Bio::MolEvol::CodonModel->codon_path;
22 my ($ns, $syn) = $codon_path->{'AATAAC'};
23 print "AAT -> AAC: $ns ns mutations, $syn syn mutations\n";
28 This object is intended to group Codon Evolution Models. Currently it
29 has one method codon_path that returns a hash reference representing
30 the number of mutations it takes to mutate from one codon to another.
31 Some more description of how this is generated will follow later.
32 Additional codon evolution models and substitution matricies could be
33 represented here as well. Some of this may not be optimally named so
34 this can change before the next stable release of the BioPerl code.
40 User feedback is an integral part of the evolution of this and other
41 Bioperl modules. Send your comments and suggestions preferably to
42 the Bioperl mailing list. Your participation is much appreciated.
44 bioperl-l@bioperl.org - General discussion
45 http://bioperl.org/wiki/Mailing_lists - About the mailing lists
49 Report bugs to the Bioperl bug tracking system to help us keep track
50 of the bugs and their resolution. Bug reports can be submitted via
53 http://bugzilla.open-bio.org/
55 =head1 AUTHOR - Jason Stajich
57 Email jason-at-bioperl-dot-org
59 This is based on work from Alisha Holloway at UC Davis and Corbin
60 Jones at UNC-Chapel Hill.
64 The rest of the documentation details each of the object methods.
65 Internal methods are usually preceded with a _
69 package Bio
::MolEvol
::CodonModel
;
74 Usage : return a matrix of edit paths between codons
75 Example : my $codon_path = Bio::MolEvol::CodonModel->codon_path;
76 Returns : Hash reference