I need some help to understand and fetch some information from codeml output. This question has been asked before but I have few specific questions that I could not find in previous posts. I ran codeml for my set of genes and to infer the positive selection I did likelihood ratio tests to compare different codeml models. Now I want to extract simply ds values for my genes to see whether the high dn/ds is the results of low ds not because of the positive selection. I check the output of the free-ratio model (i.e. M1Neutral). But there is ds calculated for each branch of the tree under different w parameters. I am not sure how to extract ds from this output. Can anyone help me please.
Thanks a lot.