Question: Need Help With Understanding Codeml Output
1
gravatar for RT
6.8 years ago by
RT340
European Union
RT340 wrote:

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

codeml • 3.7k views
ADD COMMENTlink modified 6.8 years ago by Biojl1.7k • written 6.8 years ago by RT340
2
gravatar for Biojl
6.8 years ago by
Biojl1.7k
Barcelona
Biojl1.7k wrote:

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.

ADD COMMENTlink modified 6.8 years ago • written 6.8 years ago by Biojl1.7k

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

ADD REPLYlink written 6.8 years ago by RT340

There is an answer in that post...

ADD REPLYlink written 6.8 years ago by Biojl1.7k
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