augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- filter: Remove deprecated `--output` and `-o` options
- 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"
- When we switch to Python 3.14, collect coverage with `COVERAGE_CORE=sysmon`
- subsample: Improve --output-log
- Uncaught error in `curate transform-strain-name`
- Optionally error if not all clades defined in clades.tsv are found in tree
- Handle ambiguity in --min-date and --max-date
- Docs
- Python not yet supported