If you are a developer, curious about how Nextclade and Nextalign work, want to modify it or contribute new features or fixes, check out out developer guide in docs/dev/developer-guide.md!
If you are looking for how to use Nextclade or Nextalign, check out user documentation:
- Documentation for Nextclade: https://docs.nextstrain.org/projects/nextclade
- Documentation for the parent project, Nextstrain: https://docs.nextstrain.org