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TreeTime provides routines for ancestral sequence reconstruction and inference of molecular-clock phylogenies. More information:

  • 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