Godon implements number of codon models (including M0 and branch-site). It includes various likelihood optimizers as well as Metropolis-Hastings sampler.
The basic usage of godon looks like this:
godon M0 alignment.fst tree.nwk
, this will run M0 model with a default optimizer (LBFGS-B).
You can change a model and an optimizer:
godon -m simplex BS alignment.fst tree.nwk
The above will use the branch-site model and downhill simplex optimizer.
To see all the options run: