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-1.0.1.tar.gz
(109.8 kB
view details)
Built Distribution
torchtree-1.0.1-py3-none-any.whl
(130.3 kB
view details)
File details
Details for the file torchtree-1.0.1.tar.gz.
File metadata
- Download URL: torchtree-1.0.1.tar.gz
- Upload date:
- Size: 109.8 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/4.0.0 CPython/3.9.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 282d11ea2608ca46622d07920652b7a46a7064ca3078e1c1d2f511b7ceb55c5d |
|
| MD5 | 4de81e7954b325e03209f95c7c1d4bb3 |
|
| BLAKE2b-256 | 0759a7a2d417c67307286522120f39a67b4142e095fd06984cc4e85331973ae0 |
File details
Details for the file torchtree-1.0.1-py3-none-any.whl.
File metadata
- Download URL: torchtree-1.0.1-py3-none-any.whl
- Upload date:
- Size: 130.3 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/4.0.0 CPython/3.9.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 02a05db1af453efd1097d866d6e7f58487db13a066c8c819c627b48e6f625fc6 |
|
| MD5 | 71894ddc28bddf476711e5c6bc125445 |
|
| BLAKE2b-256 | e8df2f952faed626abb53e0f528082f996290c275a7665d26bdbadc8c19c741e |
