The Cogent3 Team is passionate about science, the role of computing in science and the necessity of making high-quality scientific tools freely available to everyone. Arguably the greatest pleasure in doing science is the opportunity to share the experience through collaboration with others.

Our mission is to produce high quality, sophisticated scientific software that addresses the incredible pace of change in genomics. We are rewarded when users choose cogent3 and get value from it. Even better is when those users make suggestions on how we can improve it. And best yet is when those users feel enthusiastic about making contributions at any level. All contribution are gratefully received.

Because we value the open and inclusive nature of our community, we have adopted a code of conduct so newcomers understand the standards we adhere to in our interactions with each other. Please read it and help us ensure our positive community culture remains as we grow.


If you would like to contribute (and we hope you do!), we have created a companion c3dev repo which provides technical details on how to contribute and some useful tools for doing so.

Asking for help#

If you can’t figure out how to use cogent3 to solve a problem, create a new discussion and the community will give you a hand.

Posting bugs#

If you discover a bug please post a ticket at the issues page!


We are grateful to Chan-Zuckerberg Initiative for funding continued development of cogent3.

We acknowledge the provision by Wingware of free licenses for their professional IDE. Their commitment, over more than a decade, to supporting our development of Open Source software for science is greatly appreciated. (The port of PyCogent to cogent3 was made much easier by using Wing’s refactor tools!)


If you use this software for published work please cite – Knight et al., 2007, Genome Biol, 8, R171.