torchtree 1.0.2

Phylogenetic inference with pytorch

torchtree

torchtree is a program designed for inferring phylogenetic trees from molecular sequences. Implemented in Python, it leverages PyTorch for automatic differentiation. The suite of inference algorithms encompasses variational inference, Hamiltonian Monte Carlo, maximum a posteriori, and Markov chain Monte Carlo.

• Getting Started
  • Dependencies
  • Installation
• Quick start
• Plug-ins

Getting Started

Dependencies

• DendroPy
• PyTorch

Installation

Use an Anaconda environment (Optional)

conda env create -f environment.yml
conda activate torchtree

To install the latest stable version you can run

pip install torchtree

To build torchtree from source you can run

git clone https://github.com/4ment/torchtree
pip install torchtree/

Check install

torchtree --help

Quick start

torchtree requires a JSON file containing models and algorithms. A configuration file can be generated using torchtree-cli, a command line-based tool. This two-step process allows the user to adjust values in the configuration file, such as hyperparameters.

1 - Generating a configuration file

Some examples of models using variational inference:

Unrooted tree with GTR+W4 model

W4 refers to a site model with 4 rates categories coming from a discretized Weibull distribution. This is similar to the more commonly used discretized Gamma distribution site model.

torchtree-cli advi -i data/fluA.fa -t data/fluA.tree -m GTR -C 4 > fluA.json

Time tree with strict clock and constant coalescent model

torchtree-cli advi -i data/fluA.fa -t data/fluA.tree -m JC69 --clock strict --coalescent constant > fluA.json

2 - Running torchtree

This will generate sample.csv and sample.trees files containing parameter and tree samples drawn from the variational distribution

torchtree fluA.json

torchtree plug-in

torchtree can be easily extended without modifying the code base thanks its modular implementation. Some examples of external packages

• torchtree-bito
• torchtree-physher
• torchtree-scipy
• torchtree-tensorflow

License

Distributed under the GPLv3 License. See LICENSE for more information.

Acknowledgements

torchtree makes use of the following libraries and tools, which are under their own respective licenses:

• PyTorch
• DendroPy