augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- 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`
- Consolidate dates logic between `curate/format_dates` and `dates/ambiguous_date`
- Support partial ambiguity in `augur curate format-dates`
- filter: Rewrite using SQLite3
- Docs
- Python not yet supported