Question: Can i use consensus phylogenetic tree for calculation of dn/ds via codeml?
gravatar for rprog008
20 months ago by
rprog00870 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

ADD COMMENTlink modified 13 months ago • written 20 months ago by rprog00870

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

ADD REPLYlink written 20 months ago by rprog00870
gravatar for Joe
20 months ago by
United Kingdom
Joe18k 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 COMMENTlink written 20 months ago by Joe18k
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