Need Help With Understanding Codeml Output

Question

[GR]

Dear All,

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.

RT

Answer 1

[Biojl]

I would recommend you look for a parser written in the programming language of your choice, there's no point in reinventing the wheel. I usually use python:

http://biopython.org/wiki/PAML

In this case you get all the results in a dictionary structure, which is very easy to work with and you'll have to select the branches you're interested in.

[GR]

Hi Biojl, This is very helpful. Can you please let me know how these branches are labelled. There is another post here on biostar without any solution How does CodeML assign internal branch numbers to phylogenetic trees?. Do you now if codeml provides somewhere in output files a labelled tree?

Thanks, RT

[Biojl]

There is an answer in that post...