augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- Subcommand for data de-duplication
- Replace `sys.exit()` calls with `raise AugurError`
- Omit duplicate sequences in filter output
- augur export v2 command line argument for "panels" does not override configuration file values
- ENH: Validate clades.tsv file and provide helpful error message if it doesn't conform to requirements
- filter: `--max-date` with year only is not inclusive
- Add documentation page on supported date formats
- Cannot install under python 3.9 due to datrie
- Standardize naming of strains/sequences/records
- tree: Unable to use IQ-TREE `-g` option if strain name contains certain characters
- Docs
- Python not yet supported