pyani

Application and Python module for whole-genome classification of microbes using Average Nucleotide Identity.

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Contributing

If you would like to contribute code to the pyani project (e.g. a bug fix or new feature), please refer to the CONTRIBUTING.md guide for more details.

pyani is maintained by:

• Leighton Pritchard
• Bailey Harrington

and we are grateful to all who have contributed to this software:

Contributors ✨ (emoji key):

<!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section --> <!-- prettier-ignore-start --> <!-- markdownlint-disable --> <table> <tbody> <tr> <td align="center" valign="top" width="14.28%"><a href="https://www.strath.ac.uk/staff/pritchardleightondr/"><img src="https://avatars.githubusercontent.com/u/63981?v=4?s=100" width="100px;" alt="Leighton Pritchard"/><br />_{<b>Leighton Pritchard</b>}</a><br /><a href="https://github.com/widdowquinn/pyani/commits?author=widdowquinn" title="Documentation">📖</a> <a href="https://github.com/widdowquinn/pyani/commits?author=widdowquinn" title="Code">💻</a> <a href="#design-widdowquinn" title="Design">🎨</a> <a href="#financial-widdowquinn" title="Financial">💵</a> <a href="#ideas-widdowquinn" title="Ideas, Planning, & Feedback">🤔</a> <a href="#infra-widdowquinn" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="#projectManagement-widdowquinn" title="Project Management">📆</a> <a href="#tool-widdowquinn" title="Tools">🔧</a> <a href="https://github.com/widdowquinn/pyani/commits?author=widdowquinn" title="Tests">⚠️</a> <a href="#tutorial-widdowquinn" title="Tutorials">✅</a></td> <td align="center" valign="top" width="14.28%"><a href="https://github.com/baileythegreen"><img src="https://avatars.githubusercontent.com/u/12277715?v=4?s=100" width="100px;" alt="Bailey Harrington"/><br />_{<b>Bailey Harrington</b>}</a><br /><a href="https://github.com/widdowquinn/pyani/commits?author=baileythegreen" title="Code">💻</a> <a href="https://github.com/widdowquinn/pyani/commits?author=baileythegreen" title="Documentation">📖</a> <a href="#design-baileythegreen" title="Design">🎨</a> <a href="#ideas-baileythegreen" title="Ideas, Planning, & Feedback">🤔</a> <a href="#infra-baileythegreen" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="#tool-baileythegreen" title="Tools">🔧</a></td> <td align="center" valign="top" width="14.28%"><a href="http://blastedbio.blogspot.com"><img src="https://avatars.githubusercontent.com/u/63959?v=4?s=100" width="100px;" alt="Peter Cock"/><br />_{<b>Peter Cock</b>}</a><br /><a href="https://github.com/widdowquinn/pyani/commits?author=peterjc" title="Code">💻</a> <a href="#ideas-peterjc" title="Ideas, Planning, & Feedback">🤔</a></td> <td align="center" valign="top" width="14.28%"><a href="http://www.earlham.ac.uk/rob-davey"><img src="https://avatars.githubusercontent.com/u/1872302?v=4?s=100" width="100px;" alt="Robert Davey"/><br />_{<b>Robert Davey</b>}</a><br /><a href="https://github.com/widdowquinn/pyani/commits?author=froggleston" title="Code">💻</a> <a href="#ideas-froggleston" title="Ideas, Planning, & Feedback">🤔</a></td> <td align="center" valign="top" width="14.28%"><a href="https://github.com/nickp60"><img src="https://avatars.githubusercontent.com/u/14367274?v=4?s=100" width="100px;" alt="Nick Waters"/><br />_{<b>Nick Waters</b>}</a><br /><a href="https://github.com/widdowquinn/pyani/commits?author=nickp60" title="Documentation">📖</a></td> <td align="center" valign="top" width="14.28%"><a href="https://github.com/ytanizaw"><img src="https://avatars.githubusercontent.com/u/2227458?v=4?s=100" width="100px;" alt="YT"/><br />_<b>YT</b></a><br /><a href="https://github.com/widdowquinn/pyani/commits?author=ytanizaw" title="Code">💻</a> <a href="#ideas-ytanizaw" title="Ideas, Planning, & Feedback">🤔</a></td> <td align="center" valign="top" width="14.28%"><a href="https://github.com/ozcan"><img src="https://avatars.githubusercontent.com/u/940884?v=4?s=100" width="100px;" alt="Özcan Esen"/><br />_{<b>Özcan Esen</b>}</a><br /><a href="https://github.com/widdowquinn/pyani/commits?author=ozcan" title="Code">💻</a> <a href="https://github.com/widdowquinn/pyani/issues?q=author%3Aozcan" title="Bug reports">🐛</a></td> </tr> <tr> <td align="center" valign="top" width="14.28%"><a href="https://b-brankovics.github.io"><img src="https://avatars.githubusercontent.com/u/6728856?v=4?s=100" width="100px;" alt="Balázs Brankovics"/><br />_{<b>Balázs Brankovics</b>}</a><br /><a href="https://github.com/widdowquinn/pyani/commits?author=b-brankovics" title="Code">💻</a> <a href="https://github.com/widdowquinn/pyani/issues?q=author%3Ab-brankovics" title="Bug reports">🐛</a></td> <td align="center" valign="top" width="14.28%"><a href="https://github.com/sammywinchester19"><img src="https://avatars.githubusercontent.com/u/67588791?v=4?s=100" width="100px;" alt="sammywinchester19"/><br />_{<b>sammywinchester19</b>}</a><br /><a href="https://github.com/widdowquinn/pyani/issues?q=author%3Asammywinchester19" title="Bug reports">🐛</a></td> <td align="center" valign="top" width="14.28%"><a href="https://github.com/TSL-RamKrishna"><img src="https://avatars.githubusercontent.com/u/20773891?v=4?s=100" width="100px;" alt="Ram Krishna Shrestha"/><br />_{<b>Ram Krishna Shrestha</b>}</a><br /><a href="https://github.com/widdowquinn/pyani/commits?author=TSL-RamKrishna" title="Tests">⚠️</a> <a href="https://github.com/widdowquinn/pyani/commits?author=TSL-RamKrishna" title="Code">💻</a> <a href="#ideas-TSL-RamKrishna" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/widdowquinn/pyani/issues?q=author%3ATSL-RamKrishna" title="Bug reports">🐛</a></td> <td align="center" valign="top" width="14.28%"><a href="https://github.com/dparks1134"><img src="https://avatars.githubusercontent.com/u/3688336?v=4?s=100" width="100px;" alt="Donovan Parks"/><br />_{<b>Donovan Parks</b>}</a><br /><a href="https://github.com/widdowquinn/pyani/issues?q=author%3Adparks1134" title="Bug reports">🐛</a></td> <td align="center" valign="top" width="14.28%"><a href="https://www.researchgate.net/profile/Zaki-Saati-Santamaria"><img src="https://avatars.githubusercontent.com/u/50806485?v=4?s=100" width="100px;" alt="Zaki Saati Santamaría"/><br />_{<b>Zaki Saati Santamaría</b>}</a><br /><a href="https://github.com/widdowquinn/pyani/issues?q=author%3Azakisaati" title="Bug reports">🐛</a></td> <td align="center" valign="top" width="14.28%"><a href="https://github.com/neelam19051"><img src="https://avatars.githubusercontent.com/u/97612372?v=4?s=100" width="100px;" alt="neelam19051"/><br />_{<b>neelam19051</b>}</a><br /><a href="https://github.com/widdowquinn/pyani/issues?q=author%3Aneelam19051" title="Bug reports">🐛</a></td> <td align="center" valign="top" width="14.28%"><a href="https://github.com/jthomp28"><img src="https://avatars.githubusercontent.com/u/73444930?v=4?s=100" width="100px;" alt="jthomp28"/><br />_{<b>jthomp28</b>}</a><br /><a href="https://github.com/widdowquinn/pyani/issues?q=author%3Ajthomp28" title="Bug reports">🐛</a></td> </tr> <tr> <td align="center" valign="top" width="14.28%"><a href="https://github.com/louellette"><img src="https://avatars.githubusercontent.com/u/24635515?v=4?s=100" width="100px;" alt="louellette"/><br />_{<b>louellette</b>}</a><br /><a href="#ideas-louellette" title="Ideas, Planning, & Feedback">🤔</a></td> <td align="center" valign="top" width="14.28%"><a href="https://github.com/sbridel"><img src="https://avatars.githubusercontent.com/u/7995272?v=4?s=100" width="100px;" alt="Seb."/><br />_<b>Seb.</b></a><br /><a href="#ideas-sbridel" title="Ideas, Planning, & Feedback">🤔</a></td> <td align="center" valign="top" width="14.28%"><a href="https://github.com/ninjatacoshell"><img src="https://avatars.githubusercontent.com/u/17790858?v=4?s=100" width="100px;" alt="ninjatacoshell"/><br />_{<b>ninjatacoshell</b>}</a><br /><a href="#ideas-ninjatacoshell" title="Ideas, Planning, & Feedback">🤔</a></td> <td align="center" valign="top" width="14.28%"><a href="https://github.com/phbrito"><img src="https://avatars.githubusercontent.com/u/20931119?v=4?s=100" width="100px;" alt="Patricia H. Brito"/><br />_{<b>Patricia H. Brito</b>}</a><br /><a href="#ideas-phbrito" title="Ideas, Planning, & Feedback">🤔</a></td> <td align="center" valign="top" width="14.28%"><a href="https://github.com/ZiliaMR"><img src="https://avatars.githubusercontent.com/u/17069965?v=4?s=100" width="100px;" alt="Zilia Y. Muñoz Ramirez"/><br />_{<b>Zilia Y. Muñoz Ramirez</b>}</a><br /><a href="https://github.com/widdowquinn/pyani/issues?q=author%3AZiliaMR" title="Bug reports">🐛</a></td> <td align="center" valign="top" width="14.28%"><a href="https://github.com/nclaesnacw"><img src="https://avatars.githubusercontent.com/u/14940823?v=4?s=100" width="100px;" alt="nclaesnacw"/><br />_{<b>nclaesnacw</b>}</a><br /><a href="#ideas-nclaesnacw" title="Ideas, Planning, & Feedback">🤔</a></td> <td align="center" valign="top" width="14.28%"><a href="https://github.com/EricDeveaud"><img src="https://avatars.githubusercontent.com/u/6849075?v=4?s=100" width="100px;" alt="Eric Deveaud"/><br />_{<b>Eric Deveaud</b>}</a><br /><a href="https://github.com/widdowquinn/pyani/issues?q=author%3AEricDeveaud" title="Bug reports">🐛</a></td> </tr> <tr> <td align="center" valign="top" width="14.28%"><a href="https://github.com/kiepczi"><img src="https://avatars.githubusercontent.com/u/72203476?v=4?s=100" width="100px;" alt="Angelika Kiepas"/><br />_{<b>Angelika Kiepas</b>}</a><br /><a href="https://github.com/widdowquinn/pyani/commits?author=kiepczi" title="Code">💻</a> <a href="#design-kiepczi" title="Design">🎨</a> <a href="https://github.com/widdowquinn/pyani/commits?author=kiepczi" title="Tests">⚠️</a></td> </tr> </tbody> </table> <!-- markdownlint-restore --> <!-- prettier-ignore-end --> <!-- ALL-CONTRIBUTORS-LIST:END -->

(This project follows the all-contributors specification. Contributions of any kind welcome!)

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Citing pyani

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

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