Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In
Question: Can i use consensus phylogenetic tree for calculation of dn/ds via codeml?
0
gravatar for rprog008
20 months ago by
rprog008 • 70
rprog008 • 70 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 • 358 views
ADD COMMENT • link •
modified 13 months ago • written 20 months ago by rprog008 • 70

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

ADD REPLY • link written 20 months ago by rprog008 • 70
2
gravatar for Joe
20 months ago by
Joe ♦ 18k
United Kingdom
Joe ♦ 18k 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 20 months ago by Joe ♦ 18k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1479 users visited in the last hour