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
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
torchtree-1.0.0.post3.tar.gz
(118.8 kB
view details)
Built Distribution
File details
Details for the file torchtree-1.0.0.post3.tar.gz.
File metadata
- Download URL: torchtree-1.0.0.post3.tar.gz
- Upload date:
- Size: 118.8 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/3.8.0 pkginfo/1.8.2 readme-renderer/32.0 requests/2.27.1 requests-toolbelt/0.9.1 urllib3/1.26.8 tqdm/4.63.0 importlib-metadata/4.2.0 keyring/23.5.0 rfc3986/2.0.0 colorama/0.4.4 CPython/3.9.10
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 00e3d66a3faf548de1b9cfd08242f2323624a7089b395b05106aedf18a938626 |
|
| MD5 | db0d84b76413f45b13fc4ee13bd8c65d |
|
| BLAKE2b-256 | 33e785b9fe46e6941234544be8d0f01e6d5e8c030e73829dbcda64256d568784 |
File details
Details for the file torchtree-1.0.0.post3-py3-none-any.whl.
File metadata
- Download URL: torchtree-1.0.0.post3-py3-none-any.whl
- Upload date:
- Size: 137.3 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/3.8.0 pkginfo/1.8.2 readme-renderer/32.0 requests/2.27.1 requests-toolbelt/0.9.1 urllib3/1.26.8 tqdm/4.63.0 importlib-metadata/4.2.0 keyring/23.5.0 rfc3986/2.0.0 colorama/0.4.4 CPython/3.9.10
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | ba7682b3d97bbbc6f22718bf91f586c84f3c45fe0cdd4566737ec45e4e8c5211 |
|
| MD5 | cfdf385b13772bdeffd8de953cee1b96 |
|
| BLAKE2b-256 | 34ee08ae3034f766be0933d13365585bfa424a7ec6f1ef93d94e3cdf70cf177c |
