Provided by: bioperl_1.6.923-1_all bug


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


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


         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.

        * 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.


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        Jason Stajich jason-at-bioperl-dot-org