pairwise_kaks - 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. 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.
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