treetime
TreeTime provides routines for ancestral sequence reconstruction and inference of molecular-clock phylogenies.
TLDR
Infer ancestral sequences maximizing the joint or marginal likelihood
$ treetime ancestral
Analyze patterns of recurrent mutations aka homoplasies
$ treetime homoplasy
Estimate molecular clock parameters and reroot the tree
$ treetime clock
Map discrete character such as host or country to the tree
$ treetime mugration
