augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- [ancestral] translate genes/CDSs via nuc seq + annotation
- feat: treat CDS as a valid feature for GFFs in `load_features`
- feat: complex CDSs within augur ancestral
- WIP: New clades subcommand that works like traits, using labeled tips rather than clades.tsv
- DEV: Failed to build cvxopt during install from source with arm64/Python 3.8
- Augur TreeTime Error. What am i doing wrong?
- ENH: allow export to validate schema for a specific version of auspice
- fix: upper case root sequence for ancestral reconstruction
- Export fails validation without useful error message when using key for `metadata-id-column` for coloring as well
- Improved ancestral translation validation
- Docs
- Python not yet supported