augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- measurements collection configuration JSON cannot specify "fields" that reference columns used for `--key` or `--value`
- ENH: Add option to mask terminal gaps
- ENH: Warn when exporting large auspice.json, suggest to use `--minify-json`
- ENH: Augur clade "reconstruction from metadata" mode
- Clarify metadata date parsing behavior for un-parsable values
- dates: Consolidate date logic
- Inconsistent behavior when `date` column is missing from metadata
- frequencies: Limit the range of frequency pivots to the observed data when no start and end date are provided
- Update module docstring usage
- Add JSON schema(s) for output of `augur titers {tree,sub}`
- Docs
- Python not yet supported