Propinquity is a snakemake-based pipeline for constructing a synthetic tree of life. See https://peerj.com/articles/3058/ for a description and comparison of its performance to the previous tool used to build the Open Tree of Life's summary tree.
It takes as input a collection of phylogenetic trees from the Open Tree of Life datastore and a local copy of the Open Tree of Life Taxonomy. See the collections documentation for input on putting trees into collections.
Using python 3.8 or 3.9 (probably installing in a virtualenv)
pip install -r requirements.txt
python setup.py develop