augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- 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
- 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
- Docs
- Python not yet supported