https://github.com/4ment/torchtree-bito
https://github.com/4ment/torchtree-bito
beagle bito phylogenetics pybind11 python torchtree
Last synced: 7 months ago
JSON representation
- Host: GitHub
- URL: https://github.com/4ment/torchtree-bito
- Owner: 4ment
- License: gpl-3.0
- Created: 2021-10-22T00:12:00.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2023-08-23T02:56:40.000Z (almost 3 years ago)
- Last Synced: 2024-12-27T04:42:26.061Z (over 1 year ago)
- Topics: beagle, bito, phylogenetics, pybind11, python, torchtree
- Language: Python
- Homepage:
- Size: 66.4 KB
- Stars: 2
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# torchtree-bito
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
```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
```
[torchtree]: https://github.com/4ment/torchtree
[BITO]: https://github.com/phylovi/bito