augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- ENH: Error or deduplicate alignment in `augur tree` in iqtree mode, to avoid IQtree error
- Dealing with lower case nucleotides: document and potentially auto-convert
- `augur validate` throws an error instead of showing help
- [ancestral] translate genes/CDSs via nuc seq + annotation
- DEV: Failed to build cvxopt during install from source with arm64/Python 3.8
- Augur TreeTime Error. What am i doing wrong?
- ENH: allow export to validate schema for a specific version of auspice
- Export fails validation without useful error message when using key for `metadata-id-column` for coloring as well
- Metadata reader doesn't handle parsing errors: `pandas.errors.ParserError: Error tokenizing data. C error: Expected 57 fields in line 502, saw 58`
- Refine: Date formatted as YYYY-MM (e.g. 2023-08) ignored with neither warning nor error
- Docs
- Python not yet supported