augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- 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`
- Incomplete dates are not interpreted as ambiguous by augur filter
- Support compressed alignments
- Developer documentation lacks complete installation instructions
- [BUG] augur mask only supports VCFs with a single "chromosome" entry
- Representation of uncertainty in JSONs
- Improve startup time
- command proposal to stitch together multiple trees
- Docs
- Python not yet supported