Question: calculating dn/ds from codeml output
0
gravatar for RT
2.2 years ago by
RT340
European Union
RT340 wrote:

Hi everyone,

I ran branch-site models and made the comparisons of likelihood values modelA vs modelA null and modelA vs m1a. The omega values used are 0,1,2 and 10. I now need to extract dn/ds of my gene. Can someone help me how to extract this from codeml output.

Thanks, RT

codeml • 745 views
ADD COMMENTlink written 2.2 years ago by RT340

Are your running codeml through biopython? Is relatively easy to parse the output: https://github.com/biopython/biopython/blob/master/Bio/Phylo/PAML/codeml.py

ADD REPLYlink written 2.2 years ago by Biojl1.7k

Hi Biojl, thanks for the response. No, I have used a software from a collaborator and now I have to do he dn/ds calculations by hand as part of paper resubmission response. What I understand is fetching W2 values from ModelA where the likelihood score is maximum for different omega starting values (0,1, 2, 10). But not sure, if this is the right way to get the dn/ds estimates. Can someone please elaborate.

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by RT340
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