augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- Run CI against blab/veme-2022 and zika-tutorial
- ENH: Error or deduplicate alignment in `augur tree` in iqtree mode, to avoid IQtree error
- Dealing with lower case nucleotides: document and potentially auto-convert
- refine throws error "TypeError: '<' not supported between instances of 'NoneType' and 'str'"
- `augur validate` throws an error instead of showing help
- Can't install with Python ~3.11~ 3.12 on Conda
- [ancestral] translate genes/CDSs via nuc seq + annotation
- 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
- Docs
- Python not yet supported