augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- Support reference alignments by mafft and nextalign
- Support compressed alignments
- More complex 'exclude' allowing a date-check
- Developer documentation lacks complete installation instructions
- Refactor date/time logic for converting between numeric and ISO dates
- Improve Augur error handling
- augur subsample command
- Add warning to docs fetched by docs.nextstrain.org
- Format metadata in a tagged data format (e.g., JSON-LD)
- RFC: separating CLI and library code
- Docs
- Python not yet supported