augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- distance: Add option to calculate the cumulative distance from the root node to each tip instead of the pairwise distance
- docs: Fix numpy types for Python 3.12
- io/metadata: increase `csv.field_size_limit`
- [export] Allow warning text in auspice-config JSON
- refine: simplify node data JSON output
- tests: Cram to Prysk
- Write alignment file in temporary directory
- Config based Augur commands
- Augur proximity follow-ups
- [refine] ? allow substitution model selection
- Docs
- Python not yet supported