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HYPHY Package >> HyPhy feedback >> BS-REL Datamonkey vs HyPhy
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Message started by Vinny Lynch on Mar 11th, 2014 at 12:25pm

Title: BS-REL Datamonkey vs HyPhy
Post by Vinny Lynch on Mar 11th, 2014 at 12:25pm
Hi Sergei,

What is the difference between the implantation of BS-REL in Datamonkey and HyPhy. In HyPhy v2.22 it looks like BS-REL estimates how many rate classes to have while in Datamonkey there are three.

If HyPhy BS-REL does infer the number of rate categories to have I'm curious how I should interpret the situation where (and albeit relatively short branch) has Mean_dNdS=1.3, OmegaOver1=1.28, WtOmegaOver1=1? Note that only 1 rate class is inferred for all branches, and the dN/dS for this particular lineage with OmegaOver1=1.28 is not significant.

Is the dN/dS inference reliable when with WtOmegaOver1=1?

Best,
Vinny

Title: Re: BS-REL Datamonkey vs HyPhy
Post by Vinny Lynch on Mar 12th, 2014 at 5:22am
And on a sort of related note, is there a way to get confidence intervals on the dN/dS estimates from BS-REL?

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