pyANI-plus

pyani-plus is an application and Python module for whole-genome classification of microbes using Average Nucleotide Identity and similar methods. It is a reimplemented version of pyani with support for additional schedulers and methods.

Citing pyANI-plus

A complete guide to citing pyani is included in the file CITATIONS. Please cite the following manuscript in your work, if you have found pyani useful:

Pritchard et al. (2016) "Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens" Anal. Methods 8, 12-24 DOI: 10.1039/C5AY02550H

Documentation

See pyANI-plus documentation including Walkthrough: A First Analysis.

Installation

See our full installation instructions for more details. In brief, if you are using conda we recommend pyani-plus from the BioConda channel, which will include all the dependencies. Otherwise, we recommend installing pyani-plus from the Python Package Index (PyPI), and install the non-python tools as needed.

If you would like to use the in-progress development version, please follow the usual installation procedure for GitHub repositories, e.g.

1. Clone the repository: git clone git@github.com:pyani-plus/pyani-plus.git
2. Change directory to the repository: cd pyani-plus
3. Create a new conda environment called pyani-plus_py312 using the command make setup_conda_env (there is a corresponding remove_conda_env target)
4. Activate the conda environment with the command conda activate pyani-plus_py312
5. Install using one of the following methods:
   1. pip, e.g.: pip install -U -e .
   2. Make, e.g.: make install_macos or make install_linux

Contributing

Please see the CONTRIBUTING.md file for more information, including installing additional development-only dependencies like pytest and ruff.

Changes

Please see the CHANGELOG.md file recording changes of note in each release.

Licensing

Unless otherwise indicated, the material in this project is made available under the MIT License, and copyright The University of Strathclyde 2024 to present. See the LICENSE file.

Contact: leighton.pritchard@strath.ac.uk

Address: Dr Leighton Pritchard, Strathclyde Institute of Pharmacy and Biomedical Sciences 161 Cathedral Street Glasgow G4 0RE, Scotland, UK