After exploring little bit about PAML for calculating dN/dS rate two files are required, as an input codeml.ctl file
1) MSA in phylip format 2) Tree file.
My question is, already I know the phylogeny of my genome data. I'm interested in calculating only dN/dS rate among the each genome. How I do it ?
How to write a tree file manually, is it possible to write a tree file by looking in to the previous phylogeny ? Else, Is it possible to run codeml program with out tree file ?