augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- Add option to `augur filter` to produce non-wrapped fasta output
- [augur tree] input alignment must end in .fasta
- titers: document file input and output formats including examples
- Use str.casefold() instead of str.lower() for case-insensitive comparisons
- augur translate: ValueError("No records found in handle")
- Incomplete dates are not interpreted as ambiguous by augur filter
- Augur filter does not support the integer.float input date format for --min/max-date filtering
- Numerical dates
- frequencies: Validate min and max date before estimating frequencies
- implement composable auspice config file for `augur export v2`
- Docs
- Python not yet supported