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.
Online manual: tutorials, API documentation, CLI description
- (Optional) Build and install
bitofor accelerated computations - not used in CLI
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).
pip install -r dev/requirements.txtpytest
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)