augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- filter: `--max-date` with year only is not inclusive
- Add documentation page on supported date formats
- Cannot install under python 3.9 due to datrie
- Standardize naming of strains/sequences/records
- tree: Unable to use IQ-TREE `-g` option if strain name contains certain characters
- 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
- Docs
- Python not yet supported