augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- [export] Mismatch between default footer filters and Auspice sidebar filters
- Add `jq` to dev dependency
- [ancestral] error when writing gzipped VCF output
- [ancestral] VCF REF != reference base resulting in missing variation
- Extend `augur import` with `auspice` mode that imports from `auspice.json`
- [ancestral] reference seq may be reference or inferred tree root
- Incompatabilities between augur tree and augur ancestral
- Augur errors when jsonschema version 4 is installed
- [vcf] Replace `write_VCF_translation` with treetime's `write_vcf`
- [vcf] replace VCF reading with TreeTime's `read_vcf`
- Docs
- Python not yet supported