Hi,

Is it possible to implement in HyPhy a 2-ratio model for the analysis of substitution rates in two clades of a tree (analogous to that implemented in PAML with model=2)?

I have been able to implement a “3-ratio model” with Compartmentalization.bf, with a ratio for each of the clades of interest and a third one for the branch separating them, but I have not been able to implement a model with just 2 ratios.

Thanks a lot in advance for your help,

Benja