augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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Help out
- Issues
- Revisit CI check-docs + `/devel/generate-developer-api-docs`
- curate rename: does not work if some fields do not exist
- curate apply-geolocation-rules: Fails when fields contain `null` values
- Remove export v1
- tree: automatically remove intermediate files with option to disable clean up
- Standardize error handling and console output functions
- Add instructions on adding subcommands
- augur clades should assign clades hierarchically and parsimonously
- curate format-dates : `--expected-date-formats` builtins cannot be overridden
- CI: Add new core pathogens to pathogen-repo-ci
- Docs
- Python not yet supported