TreeFlow

April 10, 2024 ยท View on GitHub

TreeFlow is a library for phylogenetic modelling and inference based on TensorFlow Probability (TFP).

It also includes command line interfaces for fixed-topology phylogenetic inference.

Documentation

Online manual: tutorials, API documentation, CLI description

Installation and getting started

See installation instructions

  • (Optional) Build and install bito for accelerated computations - not used in CLI

Citation

If you want to cite or read about TreeFlow, please see the paper:

Christiaan Swanepoel, Mathieu Fourment, Xiang Ji, Hassan Nasif, Marc A Suchard, Frederick A Matsen IV, Alexei Drummond. "TreeFlow: probabilistic programming and automatic differentiation for phylogenetics". arXiv preprint arXiv:2211.05220 (2022).

Unit tests

  1. pip install -r dev/requirements.txt
  2. pytest

Note tests for acceleration and the benchmark CLI will fail if the extra dependencies for those components are not installed (and bito cannot yet be installed with pip)