augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- Rollout pandas version 2
- Review Pyright rule exceptions
- filter: Improve speed of `--output-strains` and `--output-metadata`
- Number of Nt changes is different from number of mutations (divergence)
- export: Add option to extend the default lat/longs
- pip/conda dependency version constraints not guaranteed in all environments
- Make command line option headings linkable
- Add docs regarding bootstraps
- export multiple trees
- WIP [refine] unique internal node names
- Docs
- Python not yet supported