I have over 1000 files each having 30 sequences.
Manually aligning, removing stop codons and then calculating avarage dN/dS for each file is impossible for me.
Are there ways to perform this via command drive.
(I know PAML, but no tool known for aligning in paml format and for removing stop codons)
Even 3 different tools for each step will do, the thing is just that I should be able to do it from command prompt.
(I'm on Win7)
Thanks in advance.