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What phylogeny should I use? (Read 2216 times)

anlagers2 YaBB Newbies Offline Curious HyPhy user Posts: 7	What phylogeny should I use? Jul 4^th, 2012 at 4:31am Hello, I am investigating several genes using the Branch-site REL program on datamonkey. If my gene is, e.g., BRCA1, should I construct a phylogeny based on BRCA1 or should I use a true phylogeny (i.e., one which accurately reflects the relatedness of the species)? Thanks.
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Sergei

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Re: What phylogeny should I use?
Reply #1 - Jul 5^th, 2012 at 1:19pm

Hi there,

It depends on whether or not the gene tree mirrors the species tree. I don't know whether or not this is the case for BRCA1. Generally speaking, you are better off using the accurately reconstructed gene tree.

Sergei

anlagers2 wrote on Jul 4^th, 2012 at 4:31am:

Hello,

I am investigating several genes using the Branch-site REL program on datamonkey. If my gene is, e.g., BRCA1, should I construct a phylogeny based on BRCA1 or should I use a true phylogeny (i.e., one which accurately reflects the relatedness of the species)?

Thanks.

Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego

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