PAML branch-site output

[sp24]

Hi All,

I'm trying to understand PAML output for branch-site models. I specified Model A with have nssites=2 and model=2 and the null model is the same but with fixomega=1 and omega =1. I set a specific lineage in the foreground.

The results do not indicate significance after performing a LRT between ModelA and the Null model, so what is the meaning of the BEB output that lists positively selected sites? Does this mean that those sites are still undergoing positive selection in the specified lineage?

Thanks,
Shikha

[ymc]

I am running model=3, nssites=2, ie model C and labeled two branches with $1 and $2. How do I interpret this result? Branch $1 is more positively selected than branch $2?

dN/dS (w) for site classes (K=3)

site class 0 1 2
proportion 0.00000 0.03762 0.96238
branch type 0: 0.00000 1.00000 0.01578
branch type 1: 0.00000 1.00000 0.04130
branch type 2: 0.00000 1.00000 0.00010