++ed by:

8 PAUSE users
10 non-PAUSE users.

Christopher Fields
and 1 contributors


Bio::MolEvol::CodonModel - Codon Evolution Models


  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";


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.


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


Please direct usage questions or support issues to the mailing list:


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:


AUTHOR - Jason Stajich

Email jason-at-bioperl-dot-org

This is based on code and work from Alisha Holloway at UC 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/


The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 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