augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- 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
- Review Pyright rule exceptions
- filter: Improve speed of `--output-strains` and `--output-metadata`
- Number of Nt changes is different from number of mutations (divergence)
- pip/conda dependency version constraints not guaranteed in all environments
- Make command line option headings linkable
- Add docs regarding bootstraps
- Docs
- Python not yet supported