treetime

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:
  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