Welcome to Nextstrain’s documentation!

Nextstrain is a project to harness the scientific and public health potential of pathogen genome data. It’s made up of many different parts that all work together. Through our website, nextstrain.org, we provide a continually-updated view of publicly available data with powerful analyses and visualizations showing pathogen evolution and epidemic spread. Through our open-source software tools, we aim to help you analyze and visualize your own data in the same way. Our goal is to aid epidemiological understanding and improve outbreak response.

Our intent for this documentation site is to cover all parts of Nextstrain, from viewing the website to producing your own analyses to contributing to Nextstrain’s development.


If you’re new to Nextstrain, start with What is Nextstrain?.

If you’re interested in how to interpret what you see on nextstrain.org, start with Interpreting analyses.

If you’re ready to go beyond viewing the website (or just plain curious!), start with Parts of a whole.

If you have questions, need help, or simply want to say hi, post to our discussion forum where the Nextstrain team and other Nextstrain users provide assistance. For private inquiries, email the Nextstrain team.