augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- 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
- filter: Rewrite priority queue logic with pandas functions
- Can the software do phylogenetic trees based on protein multiple sequence alignment data
- Update schemas with `build_avatar`
- Create docs version of auspice config schema
- Provide notebook or script to parse exported JSON into a tree object for downstream analysis
- Docs
- Python not yet supported