Nextclade: analysis of viral genetic sequences


If you are migrating from Nextclade v2 to Nextclade v3, please read our Nextclade v3 migration guide

Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement.

Nextclade consists of a set of related tools:

  • Nextclade Web - a web application available online at

  • Nextclade CLI - a command-line tool

Both tools are powered by the same algorithms, they consume the same inputs and produce the same outputs, but they differ in the user interface, the features included, and the degree of customization. It is recommended to start with Nextclade Web and later proceed to CLI tools if you have more advanced use-cases (for example, repeated batch processing, bioinformatics pipelines).

Nextclade is a part of Nextstrain, an open-source project to harness the scientific and public health potential of pathogen genome data. All source code is available on GitHub.


Referring to Nextclade in a publication

If you use results obtained with Nextclade in a publication, please


Do you find Nextclade useful? Tell us about your use-case and experience with it.

For a general conversation, feel free to join Nextstrain Discussion at

If you want to report an error or request a new feature, please open a new Github Issue (despite the name, “Github Issues” can be about anything, not only problems).

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