dated-complete-tree

Code that takes the Open Tree of Life, resolves all polytomies, and interpolates dates for all nodes. For a full explanation of the algorithms and the results of using them, see this preprint.

Resolution and interpolation can be performed repeatedly to generate distributions of dated complete trees. Dates can be sampled from available date sources in the Open Tree phylesystem.

Optionally, you can also compute a distribution of evolutionary distinctiveness scores (you can choose ED/EDGE or ED2/EDGE2) for each leaf node.

Pre-computed median trees and tree distributions can be found at the accompanying Zenodo dataset.

Prerequisites:

• The Open Tree of Life. By default we look for a folder ./opentree16.1_tree/ containing the files annotations.json and labelled_supertree/labelled_supertree_ottnames.tre.

• The Open Tree Taxonomy. By default we look for a folder called ./ott3.7.3/ containing taxonomy.tsv.

• The Python library chronosynth, available at https://github.com/OpenTreeOfLife/chronosynth/. This should be available in your PYTHONPATH.

• A folder to cache the chronosynth output. By default we use ./chronosynth_date_info/.

Usage:

There are three options:

1. The file main.py can be run from the command line. For available options run: python main.py --help. For example: python main.py --num_trees=10 --pd_clades=pd_clades.txt will produce 10 trees with different topologies and a text file with phylogenetic diversity (PD) distributions for the clades specified in your text file ./pd_clades.txt (one Open Tree node name per line, e.g. Eukaryota_ott304358). The default output folder for the Newick-format trees and the PD file is ./output/.

2. The file main_non_exec.py contains code you can edit and run from your favourite Python IDE.

3. A Jupyter notebook edge2_notebook.ipynb is included, which will open a Jupyter (IPython) notebook to step through the process of loading trees and computes EDGE2 scores.

Subtrees

If you want to work with only a subtree or subset of species, see the notebook getting_a_subtree.ipynb.

Reproducing the pre-computed tree distributions

Should you wish to reproduce the distributions of trees used in the paper, you can use the following commands:

• equal_splits_topo.tar.gz: python main.py --num_trees=501 --pd_clades=pd_clades.txt

• equal_splits_both.tar.gz: python main.py --num_trees=501 --num_date_samples=3 --pd_clades=pd_clades.txt

• birth_model_topo.tar.gz: python main.py --use_birth_model --num_trees=101 --pd_clades=pd_clades.txt

• birth_model_both.tar.gz: python main.py --use_birth_model --num_trees=101 --num_date_samples=3 --pd_clades=pd_clades.txt