v0.2.2

[ktmeaton]

v0.2.2 - Timetree Joint Parameters

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1. Add entropy to augur.
2. Add mugration models to augur.
3. Add clock model to augur.
4. Add clock lengths to augur.
5. Add date confidence to augur.
6. Scatterplot of taxa vs rtl for treemmer.
7. Prune tree, dataframe, and alignment with treemmer.
8. Confirm pruning consistency between tree, dataframe, and alignment (n=247).
9. Plot tree comparison.
10. Checkpoint before clock modelling in BEAST.
11. Use pickle to save objects of Jupyter notebooks.
12. New jupyter notebooks for post-phylo.
    • 1_parse_tree
    • 2_clock_model
    • 3_mugration_model
13. Put jupyter notebook output into results.