augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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Help out
- Issues
- 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
- Augur Traits - Problems with assigning concrete traits
- distance: Document how to ignore characters and how indels get treated as a single event
- io: Support a larger maximum field size for CSV/TSV files
- io: Raise a more specific exception on missing id columns
- traits: Document when and how to use the `--sampling-bias-correction` argument
- Docs
- Python not yet supported