augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- Add validation of metadata
- Add docs for augur frequencies
- Add support to export distances as pairwise distance matrix
- filter: Remove deprecated `--output` and `-o` options
- Remove workaround for CVXOPT binaries on Python 3.14
- filter: Add remediation option for missing weights error
- Figure out how to make GitHub link checking work consistently
- Unhandled treetime error in ancestral: "ValueError: TreeAnc.sequence can only return reconstructed terminal nodes if TreeAnc.infer_ancestral_sequences was run with this the flag `reconstruct_tip_states`"
- Not very clear error message: "For amino acid sequence reconstruction, you must provide an annotation file, a list of genes, and a template path to amino acid sequences."
- Deprecation warning in curate: "Parsing dates involving a day of month without a year specified is ambiguious"
- Docs
- Python not yet supported