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Question: Can i use consensus phylogenetic tree for calculation of dn/ds via codeml?
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gravatar for rprog008
11 months ago by
rprog008 • 50
rprog008 • 50 wrote:

I am trying to calculate dn/ds of about 3000 genes amongst 14 mammalian species via codeml.

Shall i use already established phylogeny tree of these 14 mammalian species or shall i generate phylogenetic tree of each genes separately before codeml analysis

Please help

positive selection codeml phylogenetic tree • 255 views
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modified 4 months ago • written 11 months ago by rprog008 • 50

Thanks. I will generate phylogenetic tree for each gene then :)

ADD REPLY • link written 11 months ago by rprog008 • 50
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gravatar for Joe
11 months ago by
Joe ♦ 16k
United Kingdom
Joe ♦ 16k wrote:

My gut feeling would be that you may want to make new trees for all the genes. As its mammalian you don't have to worry so much about recombination (I would definitely do this for a bacterium for example). But, different genes will be evolving at different rates, and with different pressures, which the overall phylogeny might not capture accurately.
ADD COMMENT • link written 11 months ago by Joe ♦ 16k
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