pyani-plus 0.0.1

pyANI-plus is an application and Python module for whole-genome classification of microbes using Average Nucleotide Identity and similar methods.

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

Installation

There are currently no stable releases of pyani-plus. 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 [e-mail]: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

Walkthrough: A First Analysis

Contributing

Please see the CONTRIBUTING.md file for more information

Method and Output Description

Licensing

Unless otherwise indicated, the material in this project is made available under the MIT License.

    (c) The University of Strathclyde 2024-present
    Contact: [e-mail]

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

The MIT License

Copyright (c) 2024-present The James Hutton Institute

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
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