augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- WIP: New clades subcommand that works like traits, using labeled tips rather than clades.tsv
- Allow precise date ranges
- feat(mask): Add `--mask-gaps {all,terminals}` option
- dates: Consolidate date logic
- `augur db` with import/export of metadata
- Refine throw `ValueError: x and y arrays must have at least 2 entries`
- Odd pandas error coming from augur export
- export: allow users to define gene order in genotype color-by
- BUG in mask: empty (header only) .bed file causes unhandled error
- Installation error with Python 3.9 using `conda`
- Docs
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