augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- Replace RAxML with RAxML-NG
- ENH: Allow specification of node_data key that augur clades outputs
- ENH: Allow default clade to be configured for the root
- Export fails if node-data contains unhashable items.
- Replace custom deepdiff wrapper scripts with deepdiff CLI
- Report actual missing filename for index paths
- Refine scope of Augur's Python Development API
- Add functional tests for expected behavior of translate command
- Don't allow conflicting values when parsing metadata
- Ideas for improving how data flows through augur export v2
- Docs
- Python not yet supported