Table of Contents

treetime

Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction.

TreeTime provides routines for ancestral sequence reconstruction and inference of molecular-clock phylogenies, i.e., a tree where all branches are scaled such that the positions of terminal nodes correspond to their sampling times and internal nodes are placed at the most likely time of divergence.

Information

Usage

See versions that are available:

$ module avail treetime

Load one version into your environment and run it:

$ module load treetime/0.11.3
$ treetime

Installation

Notes from the sysadmin during installation.

$ sudo mkdir -p /export/apps/treetime/0.11.3
$ sudo chown aorth /export/apps/treetime/0.11.3
$ module load python/3.9
$ python3 -m venv /export/apps/treetime/0.11.3
$ source /export/apps/treetime/0.11.3/bin/activate
$ pip install --upgrade pip wheel setuptools
$ python3 -m pip install phylo-treetime==0.11.3
$ sudo chown -R root:root /export/apps/treetime/0.11.3