tldr/pages/linux/treetime.md

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2022-10-24 08:58:33 +01:00
# 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`