augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- merge: Support sequences
- Uncaught error when root not in tree.
- Pick a meaning of TSV and use it consistently
- No standard test environment
- filter: Improve speed of `--output-strains` and `--output-metadata`
- export multiple trees
- WIP: New clades subcommand that works like traits, using labeled tips rather than clades.tsv
- Allow precise date ranges
- feat(mask): Add `--mask-gaps {all,terminals}` option
- dates: Consolidate date logic
- Docs
- Python not yet supported