augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- Allow custom date column name to be specified in `refine` - similar to `metadata-id-column`
- Add schema for node-data JSONs
- align: error message when reading a reference sequence does not completely explain the root issue
- DRAFT: add 'gene' feature capture when reading genbank files
- filter: Split filtering and subsampling
- filter: Improve help text
- `measurements export` does not consistently allow the strain column to be used as a grouping column
- `parse` silently removes spaces from record ids in the sequence output but not in the metadata output
- Improve validation output to identify problematic nodes / properties
- frequencies: Validate arguments
- Docs
- Python not yet supported