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syntax: markdown
tags: [tldr, linux]
source: https://github.com/tldr-pages/tldr.git
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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`
