augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- Support databases
- Validate root-sequence output
- Move Uppercase after camelCase in parse.prettify
- UFBoot values are parsed incorrectly by refine and interfere with ancestral resulting in odd annotations
- Need for improved documentation for augur clades
- Give more info in `export v2` deprecation warnings about how to update colorings
- distances: Fails silently on distance to root calculation when the root is not in the alignment
- filter: Subsampling crashes on numeric dates
- io: Pass encoding and newline keyword arguments to `open_file`
- Add notebook for parsing json to ete tree objects for downstream analysis
- Docs
- Python not yet supported