augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- augur export v2 command line argument for "panels" does not override configuration file values
- ENH: Validate clades.tsv file and provide helpful error message if it doesn't conform to requirements
- `--max-date` with year only is not inclusive
- Installation error with Python 3.9 using `conda`
- Support databases
- Validate root-sequence output
- Move Uppercase after camelCase in parse.prettify
- UFBoot values are parsed incorrectly by refine and interfere with ancestral resulting in odd annotations
- Need for improved documentation for augur clades
- Give more info in `export v2` deprecation warnings about how to update colorings
- Docs
- Python not yet supported