tldr/pages/linux/treetime.md

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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