augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- [resolved] Docs cannot build (entry_points() got an unexpected keyword argument 'group')
- Refine: Date formatted as YYYY-MM (e.g. 2023-08) ignored with neither warning nor error
- rooting examples in augur refine documentation are out of date
- feat(mask): allow empty mask file, warn not error
- feat(mask): Add `--mask-gaps {all,terminals}` option
- Genome annotations for segmented CDSs etc
- Update annotation schema for strand changes
- Feat/parse nextclade annotation
- Remove `export v1`
- Numerical dates support in `augur curate format-dates`
- Docs
- Python not yet supported