torchtree 1.0.1

Phylogenetic inference with pytorch

torchtree

Installation

Use an Anaconda environment (Optional)

conda env create -f environment.yml
conda activate torchtree

The easy way

To install the latest stable version, run

pip install torchtree

Using the source code

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

Check install

torchtree --help

Quick start

torchtree will approximate the posterior distribution of an unrooted tree with a JC69 substitution model using variational inference

torchtree examples/advi/fluA.json

The JSON file can be generated using the torchtree CLI

torchtree-cli advi -i data/fluA.fa -t data/fluA.tree > fluA.json