augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- Grab bag of improvements to augur clades
- Divergence (mutations) on the root node are ignored by augur export
- io: Do not use multiple threads to write compressed files
- Support compression presets for LZMA compression backend
- mask: Support masking terminal gaps
- Support reference alignments by mafft and nextalign
- Support compressed alignments
- More complex 'exclude' allowing a date-check
- Developer documentation lacks complete installation instructions
- Refactor date/time logic for converting between numeric and ISO dates
- Docs
- Python not yet supported