augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- Resolve all input file paths
- distance: error on missing root sequence instead of reporting zeros
- Add generic get_referenced_files()
- Read color odering directly in `augur export v2`
- Implement --config for various commands
- refine: Implement --config
- 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
- Docs
- Python not yet supported