How to retrieve single Ka and Ks values from a whole multiple sequence alignment using PAML (codeml)? · Biostar

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How to retrieve single Ka and Ks values from a whole multiple sequence alignment using PAML (codeml)?

I am able to retrieve ka/ks ratio for a multiple sequence alignment using the model=0 and NSsites=0 in the .ctl file of PAML. But, I also require the individual ka and ks values for the whole alignment. Is it possible to retrieve this from PAML? If yes, then what parameter should I change in the .ctl file?

alignment substitutions evolutionary constraints

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updated 10.9 years ago by Biostar

• written 11.0 years ago by tigeradab

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