NAME

       bp_pairwise_kaks - script to calculate pairwise Ka,Ks for a set of sequences

SYNOPSIS

       bp_pairwise_kaks.PLS -i t/data/worm_fam_2785.cdna [-f fasta/genbank/embl...] [-msa
       tcoffee/clustal] [-kaks yn00/codeml]

DESCRIPTION

         This script will take as input a dataset of cDNA sequences verify
        that they contain no stop codons, align them in protein space,
        project the alignment back into cDNA and estimate the Ka
        (non-synonymous) and Ks (synonymous) substitutions based on the ML
        method of Yang with the PAML package.

        Requires:
        * bioperl-run package
        * PAML program codeml or yn00
        * Multiple sequence alignment programs Clustalw OR T-Coffee

        Often there are specific specific parameters you want to run when you
        a computing Ka/Ks ratios so consider this script a starting point and
        do not rely it on for every situation.

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

   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://github.com/bioperl/bioperl-live/issues

AUTHOR

        Jason Stajich jason-at-bioperl-dot-org