torchtree-bito

February 3, 2023 · View on GitHub

torchtree-bito is a package providing an interface to BITO for torchtree

Dependencies

torchtree
BITO

Installation

Instructions about installing BITO can be found on the BITO website.

Get the source code

git clone https://github.com/4ment/torchtree-bito
cd torchtree-bito

Install using pip

pip install .

Check install

python -c "import bito"

torchtree --help

Command line arguments

The torchtree-bito plugin adds these arguments to the torchtree CLI:

torchtree-cli advi --help
  ...
  --bito                use bito
  --bito_gpu            use GPU in bito/BEAGLE
  --bito_disable_sse    disable SSE in bito/BEAGLE

Quick start

torchtree will approximate the posterior distribution of an unrooted tree with an HKY substitution model using variational

torchtree examples/advi/fluA-HKY.json

The JSON file can be generated by providing an alignment and a tree to the torchtree CLI:

torchtree-cli advi -i foo.fa -t foo.tree -m HKY --bito > foo.json