augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- feat(ancestral): make --genes optional when reconstructing translations, if omitted, translate all genes in annotation
- feat(ancestral): Add optional Nextclade GFF3 compatibility mode
- Validation regex pattern for `branch_label` display default values in Auspice config JSON is too strict
- CLI help text can't contain rST section headings
- Gff3 file: differences between nextclade datasets and augur ancestral
- curate apply-geolocation-rules: Allow rule overrides
- Add examples for weighted sampling with multiple columns including month/week
- Register subparsers recursively
- CLI: Use raw descriptions
- Improve rendering of CLI documentation
- Docs
- Python not yet supported