augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- 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
- How to have more control over the contents of the maintainers section?
- [WIP] add initial tests for reconstruct_sequences.py
- Docs
- Python not yet supported