Gene tree or species tree input?

CarineRey / pcoc

Convergent substitution detection tool based on the PCOC model

GNU General Public License v3.0

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Gene tree or species tree input? #18

Closed keren210 closed 4 years ago

keren210 commented 4 years ago

Hi there,

I was wondering whether it's correct to use a gene tree instead of a species tree as input for PCOC?

This issue is a bit confusing to me as I am dealing with some genes under high selection pressure, so the gene tree doesn't really resemble the species tree. I used the former in my analysis, and it creates a bit of a messy situation when trying to flag branches while testing for convergent scenarios.

Thanks in advance for your time, and let me know if you need any more information!

CarineRey commented 4 years ago

Hi, PCOC needs the species tree. Indeed you have to annotate the species tree with the convergent events. In a gene tree, (convergent) evolution can mix branches.

keren210 commented 4 years ago

Great, thank you very much for clarifying this!