augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- distances: Fails silently on distance to root calculation when the root is not in the alignment
- io: Pass encoding and newline keyword arguments to `open_file`
- Support protein (AA) analyses
- Update schemas with `build_avatar`
- Create docs version of auspice config schema
- distance: Document how to ignore characters and how indels get treated as a single event
- io: Support a larger maximum field size for CSV/TSV files
- io: Raise a more specific exception on missing id columns
- traits: Document when and how to use the `--sampling-bias-correction` argument
- Add option to `augur filter` to produce non-wrapped fasta output
- Docs
- Python not yet supported