TreeTime provides routines for ancestral sequence reconstruction and inference of molecular-clock phylogenies. More information: https://treetime.readthedocs.io/en/latest/tutorials.html.
- Infer ancestral sequences maximizing the joint or marginal likelihood:
- Analyze patterns of recurrent mutations aka homoplasies:
- Estimate molecular clock parameters and reroot the tree:
- Map discrete character such as host or country to the tree: