ILRI Research Computing

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====== 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 =====

  * Version: 0.11.3
  * Added: May, 2024
  * Link: https://github.com/neherlab/treetime

===== Usage =====

See versions that are available:
<code>$ module avail treetime</code>

Load one version into your environment and run it:
<code>$ module load treetime/0.11.3
$ treetime</code>


===== Installation ======
Notes from the sysadmin during installation.

<code>$ 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</code>