augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- Add instructions on adding subcommands
- augur clades should assign clades hierarchically and parsimonously
- Speed up CI run times
- Fix silent parse bug
- Help text injected by `CustomHelpFormatter` is not included in rendered docs
- curate format-dates : `--expected-date-formats` builtins cannot be overridden
- Use `ExtendOverwriteDefault` for all multi-value options
- CI: Add new core pathogens to pathogen-repo-ci
- Rename `master` to `main`
- Remove `authors` hard-coding in `augur export`
- Docs
- Python not yet supported