augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- rooting examples in augur refine documentation are out of date
- Genome annotations for segmented CDSs etc
- 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`
- augur clade only partially assigns clade information
- ENH(clades): Validate `clades.tsv`, bad file currently throws uncaught error
- DOC(filter): Surface excellent function level documentation`--exclude-where` for cli help
- filter: Improperly handled `ValueError: not enough values to unpack (expected 2, got 1)` in ` _parse_filter_query`
- Docs
- Python not yet supported