augur
https://github.com/nextstrain/augur
Python
Pipeline components for real-time phylodynamic analysis
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- Issues
- ENH: Allow export of clock deviation from refine
- Refine throw `ValueError: x and y arrays must have at least 2 entries`
- Refine throws: `ERROR: 'NoneType' object has no attribute 'shape'`
- Odd pandas error coming from augur export
- BUG(refine): With `--use-fft`, refine occasionally fails with `ERROR: No module named 'ipdb'`
- export: allow users to define gene order in genotype color-by
- ENH: Clades should only require aa mutations if aa mutations occur in clade definitions
- ENH: Mention `--skip-validation` flag when augur export fails validation as workaround for users
- Replace RAxML with RAxML-NG
- ENH: Allow specification of node_data key that augur clades outputs
- Docs
- Python not yet supported