pyani

We have deprecated pyani. Please use pyani-plus.

As part of the genomeRxiv project, we developed a new and improved implementation of average nucleotide identity methods that scales better on a wider range of computing environments. Please use pyani-plus in place of pyani.

You can download pyani-plus and find instructions for using it at the links below.

• pyani-plus repository
• pyani-plus documentation

The pyani program and package has now reached the end of its useful life. It will no longer be maintained, and this repository is now archived.

I would like to take this opportunity to thank everyone who has used, worked on, or in any way improved pyani in its previous incarnations. It proved to be a popular and powerful software tool, used in over 1000 publications, and downloaded over 40,000 times. It's been great, but it's time to move on to better things (i.e. pyani-plus).

What happens next?

Hopefully, you become an active and enthusiastic user of pyani-plus.

We archived this repository on 1st July 2025. All issues and pull requests have been closed, and the repository is read-only.

What to do next

• I am happy using this version of pyani
  • If you are happy using this version of pyani, then by all means continue using it. But please be aware we will not be fixing bugs, or improving the codebase from this point on. The repository was archived on 1st July 2025.
• pyani is no longer working for me
• There is a bug in pyani that I can't live with
• I would like to try the new improved pyani-plus
  • pyani-plus does the same job but is better in pretty much every relevant way, so please do visit the links below to download/install, and to read the documentation.
    • pyani-plus repository
    • pyani-plus documentation

But what if we don't want pyani to die?

I'm sorry. pyani has had its time. If you would like to fork the project and maintain that fork, you are always free to do so. But I don't think anyone wants pyani to live on any more than I do myself and, if I'm letting go, you may want to question whether using your finite time on this planet to keep this software alive is worth it.

Roll of Honour

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> <a href="https://github.com/widdowquinn/pyani/issues?q=author%3Apeterjc" title="Bug reports">🐛</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