augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- merge: Import metadata files concurrently?
- Release: changelog can be out-of-sync
- Align fractional sequences per group conversion methods
- Legacy editable installs are deprecated
- Revise docs for v25 features to add `versionadded` directives
- filter: Prefer "output sequences" over "output"?
- merge: Support sequences with cross-checking
- augur ancestral - IndexError when using wrong (shorter) reference
- Use identical help text for shared options
- filter: Make under-sampling more apparent
- Docs
- Python not yet supported