reorder jupyter notebooks

ktmeaton · Feb 23, 2021 · 1ca7bee · 1ca7bee
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diff --git a/auspice/plague-phylogeography_clock-model.json b/auspice/plague-phylogeography_clock-model.json
diff --git a/auspice/plague-phylogeography_parse-tree.json b/auspice/plague-phylogeography_parse-tree.json
diff --git a/docs/notes/Notes_Development.md b/docs/notes/Notes_Development.md
@@ -11,9 +11,14 @@
 1. Confirm pruning consistency between tree, dataframe, and alignment (n=247).
 1. Plot tree comparison.
 1. Checkpoint before clock modelling in BEAST.
+1. Use pickle to save objects of Jupyter notebooks.
+1. New jupyter notebooks for post-phylo.
+
+    - 1_parse_tree
+    - 2_clock_model
+    - 3_mugration_model
 
 ## TO DO
 
 1. Think about snippy_dir in rule ```eager```...
-1. Use pickle to save objects of Jupyter notebooks?
 1. Timetree alters the topology, perhaps run that first?
diff --git a/docs/results/latest/clock_model/clock_model.nexus b/docs/results/latest/clock_model/clock_model.nexus
diff --git a/docs/results/latest/clock_model/clock_model.nwk b/docs/results/latest/clock_model/clock_model.nwk
diff --git a/docs/results/latest/clock_model/clock_model.tsv b/docs/results/latest/clock_model/clock_model.tsv
diff --git a/docs/results/latest/clock_model/clock_model.xml b/docs/results/latest/clock_model/clock_model.xml