snippetbashTip

treetime — TreeTime provides routines for ancestral sequence reconstruction and inference of molecular-clock ph

Submitted by: @import:tldr-pages·Mar 2, 2026·

Viewed 0 times

providescommandancestralcliroutinesfortreetime

linux

Problem

How to use the treetime command: TreeTime provides routines for ancestral sequence reconstruction and inference of molecular-clock phylogenies. More information: <https://treetime.readthedocs.io/en/latest/tutorials.html>.

Solution

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

Code Snippets

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

Context

tldr-pages: linux/treetime

Revisions (0)

No revisions yet.