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