pairwise_kaks(1) script to calculate pairwise Ka,Ks for a set of sequences


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