update analyses, figs, website with new vic alignment

blab · Aug 25, 2023 · 4d1468c · 4d1468c
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Showing 72 changed files with 241 additions and 746 deletions.
diff --git a/adaptive-evolution-analysis/Figure1.ipynb b/adaptive-evolution-analysis/Figure1.ipynb
diff --git a/adaptive-evolution-analysis/Figure2.ipynb b/adaptive-evolution-analysis/Figure2.ipynb
diff --git a/adaptive-evolution-analysis/Figure3.ipynb b/adaptive-evolution-analysis/Figure3.ipynb
diff --git a/adaptive-evolution-analysis/Figure4.ipynb b/adaptive-evolution-analysis/Figure4.ipynb
diff --git a/adaptive-evolution-analysis/Figure5.ipynb b/adaptive-evolution-analysis/Figure5.ipynb
diff --git a/adaptive-evolution-analysis/Supp2_histogramSeqCount.ipynb b/adaptive-evolution-analysis/Supp2_histogramSeqCount.ipynb
diff --git a/adaptive-evolution-analysis/Supp3_SubsVsAdaptation.ipynb b/adaptive-evolution-analysis/Supp3_SubsVsAdaptation.ipynb
diff --git a/adaptive-evolution-analysis/adaptation_results/aasubrates.json b/adaptive-evolution-analysis/adaptation_results/aasubrates.json
@@ -24,7 +24,7 @@
     "rsv_B": 2.350224179101496,
     "influenzaC_Yamagata": 0.26871020167250614,
     "yam": 2.119977566679927,
-    "vic": 1.7959708219688493,
+    "vic": 2.1560641794537654,
     "h1n1pdm": 5.3816050609965504,
     "h3n2": 8.615301227204771
 }
diff --git a/...ution-analysis/adaptation_results/intermediates/input_data_vic_None_NA_3_2_None_None.json b/...ution-analysis/adaptation_results/intermediates/input_data_vic_None_NA_3_2_None_None.json
diff --git a/...ution-analysis/adaptation_results/intermediates/input_data_vic_None_NA_3_3_None_None.json b/...ution-analysis/adaptation_results/intermediates/input_data_vic_None_NA_3_3_None_None.json
diff --git a/...ution-analysis/adaptation_results/intermediates/input_data_vic_None_NA_5_3_None_None.json b/...ution-analysis/adaptation_results/intermediates/input_data_vic_None_NA_5_3_None_None.json
diff --git a/...ion-analysis/adaptation_results/intermediates/input_data_vic_None_NA_all_2_None_None.json b/...ion-analysis/adaptation_results/intermediates/input_data_vic_None_NA_all_2_None_None.json
diff --git a/...ion-analysis/adaptation_results/intermediates/input_data_vic_None_NA_all_3_None_None.json b/...ion-analysis/adaptation_results/intermediates/input_data_vic_None_NA_all_3_None_None.json
diff --git a/...tion-analysis/adaptation_results/intermediates/input_data_vic_None_ha1_3_2_None_None.json b/...tion-analysis/adaptation_results/intermediates/input_data_vic_None_ha1_3_2_None_None.json
diff --git a/...tion-analysis/adaptation_results/intermediates/input_data_vic_None_ha1_3_3_None_None.json b/...tion-analysis/adaptation_results/intermediates/input_data_vic_None_ha1_3_3_None_None.json
diff --git a/...tion-analysis/adaptation_results/intermediates/input_data_vic_None_ha1_5_3_None_None.json b/...tion-analysis/adaptation_results/intermediates/input_data_vic_None_ha1_5_3_None_None.json
diff --git a/...on-analysis/adaptation_results/intermediates/input_data_vic_None_ha1_all_3_None_None.json b/...on-analysis/adaptation_results/intermediates/input_data_vic_None_ha1_all_3_None_None.json
diff --git a/...tion-analysis/adaptation_results/intermediates/input_data_vic_None_ha2_3_2_None_None.json b/...tion-analysis/adaptation_results/intermediates/input_data_vic_None_ha2_3_2_None_None.json
diff --git a/...tion-analysis/adaptation_results/intermediates/input_data_vic_None_ha2_3_3_None_None.json b/...tion-analysis/adaptation_results/intermediates/input_data_vic_None_ha2_3_3_None_None.json
diff --git a/...tion-analysis/adaptation_results/intermediates/input_data_vic_None_ha2_5_3_None_None.json b/...tion-analysis/adaptation_results/intermediates/input_data_vic_None_ha2_5_3_None_None.json