Phylogenetic inference with pytorch
Project description
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
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