augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- Unhelpful error message from treetime when `augur ancestral` fails to load translation alignment
- Update pandas requirement from <3,>=1.4.0 to >=1.4.0,<4
- subsample: Print errors from get_referenced_files
- augur align: inserted Ns are reported incorrectly
- align: Improve handling of duplicate reference sequence
- Unhandled error in `curate apply-geolocation-rules`
- fix: When JSON dump with sort_key fails, retry without sorting
- augur clades inheritance doesn't enforce inheritance
- Allow passing arguments to augur align
- read-file is slow with concurrent runs
- Docs
- Python not yet supported