Hello, I have been using normally PAML to infer omega per branch (Free-ratio), however I think that synonymous rate varies across lineages (Paml assumes synonymous rate is constant), so I would like to test if syn rate is constant.

Initially, I wanted to try to replicate my analysis done in PAML using Hyphy (using GY94_3x4?) and then compare such results with a model that allows variation in the synonymous rates across lineages. However, I can´t get the exact same results using Hyphy and PAML, I believe you can´t because PAML and Hyphy work differently … or maybe I am using the wrong codon model.

How can I know if there are different syn rates among my lineages? Is it possible to use the same model I used in PAML in Hyphy, but allowing variation for syn rates?

I would like, apart from obtaining the omega values, to obtain also the dN and dS values to compare with those from PAML, because what I obtain are the parameters: synRate and non-synRate. I know that the batch file dSdN.bf allows me to do that but for model  MG94custom, when I try to change the model in the batch file I get an error.

Thank you on advance