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:

    godon -h