augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- Simplify configuration of `accession` as metadata id column
- Fix year-weighted sampling
- Pandas error when weights file has year column and that column contains "default"
- Weighted sampling stdout/err is very verbose: multiple screens of warnings
- Use standard date parsing logic for subsampling
- Use standard date parsing logic for subsampling (and general improvements)
- curate format-dates: Add support for date intervals
- align: Remove insertion sequence print statements
- Support precise date ranges
- Allow user to exclude specific strains from refine's clock filter
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- Python not yet supported