augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
Triage Issues!
When you volunteer to triage issues, you'll receive an email each day with a link to an open issue that needs help in this project. You'll also receive instructions on how to triage issues.
Triage Docs!
Receive a documented method or class from your favorite GitHub repos in your inbox every day. If you're really pro, receive undocumented methods or classes and supercharge your commit history.
Python not yet supported38 Subscribers
Add a CodeTriage badge to augur
Help out
- Issues
- Replace sequence indexing
- Deprecation warning in export.py: "Nesting mutually exclusive groups is deprecated."
- merge: Unhelpful error message with named sequence inputs
- merge: Support inner join
- Add validation of metadata
- Add docs for augur frequencies
- Add support to export distances as pairwise distance matrix
- filter: Remove deprecated `--output` and `-o` options
- Figure out how to make GitHub link checking work consistently
- Unhandled treetime error in ancestral: "ValueError: TreeAnc.sequence can only return reconstructed terminal nodes if TreeAnc.infer_ancestral_sequences was run with this the flag `reconstruct_tip_states`"
- Docs
- Python not yet supported