CODEML: Ideal setting for generating dn/ds values for a gene family within a species.
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8 months ago
venura ▴ 70

Hi,

I have a couple of questions regarding obtaining dn/ds values for a gene family within a species using codeml. In my case, I have 67 genes and hoping to calculate dn/ds for each gene (not site) to identify which genes are under selection. Most of the tutorials and papers I read talk about genes belong to multiple spp. So I would appreciate it if someone can help me to come up with the ideal setting to run codeml for this specific scenario. I already have codon aligned seq alignment and ML tree (protein) of the genes of interest. I use PAML4.9j on pamIX frontend. Thanks in advance.

codeml PAML • 240 views
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I don't see any immediate reasons why you would have to use a different approach for a within species or between species analysis. Those values are calculated on a per gene basis, regardless of where those genes come from.

This does not mean you might get more reliable results when you include some more species. Reasoning here is that when adding more species you could get a useful 'outgroup' gene, resembling the ancestral state of the genes.

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