TreeTime provides routines for ancestral sequence reconstruction and inference of molecular-clock phylogenies. More information: TreeTime command line usage — TreeTime 0.11.1 documentation.
- 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