how to calculate dn/ds in PAML for large amounts of orthologous genes ?
I want to use the Codeml to calculate the Ka/Ks values for each pair of orthologous gene from two species. I have more than 10,000 pairs.
Could you tell me how I can run the Codeml? so I can calculate the Ka/Ks for the 10, 000 pairs of genes quickly (no need to analysis the genes one by one). Maybe, a script?
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