augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- Update phylo-treetime requirement from <0.12,>=0.11.2 to >=0.11.2,<0.13
- Augur proximity follow-ups
- [refine] ? allow substitution model selection
- merge: Support single inputs
- is there a way to give protein sites non-sequential numbering?
- multiple inputs: include source attribution
- subsample: Add helper function for setting --nthreads
- allow protein analyses
- get_numerical_date_from_value inconsistently handles nonstandard date values
- Use `[0-9]` instead of `\d` to match numbers in regex
- Docs
- Python not yet supported