Question: How can the node distances affect to the omega values on the site model performed by codeml?
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gravatar for DR
4.0 years ago by
DR10
European Union
DR10 wrote:

Hi! I'm performing a site positive selection test with codeml. I used the p-distance for obtaining the tree topology that then I used in order to contrast the different models for detecting positive selection. In spite of obtaining the same tree typology, could you give me an idea about how can the underestimated distance values affect to the dN/dS estimates?

Thanks!!

codeml paml phylogeny • 1.3k views
ADD COMMENTlink modified 4.0 years ago by Brice Sarver2.5k • written 4.0 years ago by DR10
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gravatar for Brice Sarver
4.0 years ago by
Brice Sarver2.5k
United States
Brice Sarver2.5k wrote:

I used the p-distance for obtaining the tree topology that then I used in order to contrast the different models for detecting positive selection.

If you are fixing the tree (i.e., not letting codeml optimize topology/branch lengths), I would recommend using a more sophisticated means of estimating the tree. I would expect to see, at the very least, corrected p-distances if I was a reviewer. Likelihood-based approaches are better. Remember to transform your tree from units of substitutions/site to substitutions/codon.

Think of the branch lengths as your data for these analyses. The longer the branch lengths among your taxa, the more power you will have to infer positive selection; this is why it's hard to confidently infer positive selection acting on codons in closely-related lineages. Therefore, if your branch lengths are problematic, you might be drawing incorrect conclusions.

ADD COMMENTlink written 4.0 years ago by Brice Sarver2.5k
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