augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- fix(tests): Fix false negative cram tests
- tests: add cram wrapper parallel_cram.sh that runs cram tests in parallel
- feat(ancestral): Add optional Nextclade GFF3 compatibility mode
- merge: Support sequences without cross-checking
- merge: Support sequences
- Uncaught error when root not in tree.
- Pick a meaning of TSV and use it consistently
- No standard test environment
- filter: Improve speed of `--output-strains` and `--output-metadata`
- export multiple trees
- Docs
- Python not yet supported