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https://github.com/4ment/torchtree-bito

https://github.com/4ment/torchtree-bito

Science Score: 13.0%

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Keywords

beagle bito phylogenetics pybind11 python torchtree
Last synced: 6 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: 4ment
  • License: gpl-3.0
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 66.4 KB
Statistics
  • Stars: 2
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Topics
beagle bito phylogenetics pybind11 python torchtree
Created over 4 years ago · Last pushed over 2 years ago
Metadata Files
Readme License

README.md

torchtree-bito

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

Dependencies

Installation

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

Get the source code

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

Install using pip

bash pip install .

Check install

bash python -c "import bito"

bash torchtree --help

Command line arguments

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

bash 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 bash torchtree examples/advi/fluA-HKY.json

The JSON file can be generated by providing an alignment and a tree to the torchtree CLI: bash torchtree-cli advi -i foo.fa -t foo.tree -m HKY --bito > foo.json

Owner

  • Name: Mathieu Fourment
  • Login: 4ment
  • Kind: user
  • Location: Australia
  • Company: University of Technology Sydney

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