augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- is there a way to give protein sites non-sequential numbering?
- multiple inputs: include source attribution
- subsample: Add helper function for setting --nthreads
- augur proximity
- [WIP] allow protein analyses
- get_numerical_date_from_value inconsistently handles nonstandard date values
- Use `[0-9]` instead of `\d` to match numbers in regex
- merge: Support datasets with multiple sequence files
- filter: No sequence index mismatch warning when `--sequence` has additional entries
- Clade definition inheritance
- Docs
- Python not yet supported