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HyPhy: Hypothesis testing using Phylogenies
http://www.hyphy.org
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Dual Rate-Variation models of HyPhy #1769

Open zhouxp9709 opened 1 week ago

zhouxp9709 commented 1 week ago

Dear professor,

I would like to compare the rate of molecular evolution in different species by calculating the dS value, and one study (https://www.sciencedirect.com/science/article/abs/pii/S0169534710001461) has reported that it is possible to accurately estimate the dS value by using HyPhy's Dual Rate-Variation model. But I didn't find any information about the Dual Rate-Variation model. Can you provide some clues?

Best regards, Xuping

spond commented 1 day ago

Dear @zhouxp9709,

That's an old model; it goes back to this 2005 paper https://pubmed.ncbi.nlm.nih.gov/16107593/

I would suggest you use the BUSTED-S model, which is a more general implementation (https://pubmed.ncbi.nlm.nih.gov/32068869/)

hyphy busted --alignment /path/to/file

Which dS estimates were you interested in? Branch lengths measured in dS?

Best, Sergei

zhouxp9709 commented 1 day ago

Dear Serei,

Thank you for your reply, I am interested in branch lengths measured in dS. My main aim is to convert the estimated dS to the absolute evolutionary rate of the species via r = dS/T.

Best regards, Xuping