augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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Help out
- Issues
- Fix flake errors
- Add documentation for frequencies methods and interface
- Understand mutations produced by augur
- Frequency estimation fails with missing data.
- Allow multiple file inputs for `lat_longs`, etc. via a deep merge
- Execute Cram via pytest
- [RFC] Functional tests with Cram
- Get path and list of mutations between to strains?
- Adding a full example to the tests data directory
- WIP/RFC: Add tests for ancestral.py
- Docs
- Python not yet supported