Fitting branch models with godon Is it possible to fit branch models (Yang and Nielsen, 1998) in godon? That is, the model which averages over all sites, as opposed to the branch site models?
Branch-models are currently not implemented in godon. In the PAML manual Ziheng Yang writes:

This model is very parameter-rich and its use is discouraged.

This was one of the reasons I did not implement it.
Disclaimer: I am the author of godon.