augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- transform-strain-name: build strain name by concatenating fields
- Branch length units in augur refine output
- [export] format confidence values to save bytes
- Support numpy major version 2
- Extend `augur curate format-dates` to output date ranges
- Curate standard geolocation rules
- Improved subsampling support
- refine: Support rooting with time data without producing a time tree
- relax schema enforcement of `generated_by` in node-data files
- Metadata wrangling prior to merging with existing data
- Docs
- Python not yet supported