Question: Can i use consensus phylogenetic tree for calculation of dn/ds via codeml?
gravatar for rprog008
11 months ago by
rprog00850 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 4 months ago • written 11 months ago by rprog00850

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

ADD REPLYlink written 11 months ago by rprog00850
gravatar for Joe
11 months ago by
United Kingdom
Joe16k 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 11 months ago by Joe16k
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