augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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Help out
- Issues
- Document file formats
- Start and end date of augur build intervals are not stored in auspice JSONs
- Update the conda channels list in environment.yml
- Make Sequence Traits work with Fasta Input
- Store titer records in TiterRecord class and export in structured JSON format
- Representation of uncertainty in JSONs
- [BUG] nt_muts.json might miss some variants?
- improve format of help messages
- Want to contribute? Welcome! Please start here.
- Include option to prune outgroup in augur tree or augur refine
- Docs
- Python not yet supported