treelikelihood should set useAmbuguities=true as default #166

LinguaPhylo · Oct 24, 2024 · 16ce13a · 16ce13a
1 parent 087451a
commit 16ce13a
Showing 1 changed file with 1 addition and 0 deletions.
diff --git a/lphybeast/src/main/java/lphybeast/tobeast/generators/PhyloCTMCToBEAST.java b/lphybeast/src/main/java/lphybeast/tobeast/generators/PhyloCTMCToBEAST.java
@@ -149,6 +149,7 @@ private ThreadedTreeLikelihood createThreadedTreeLikelihood(PhyloCTMC phyloCTMC,
         SiteModel siteModel = constructSiteModel(phyloCTMC, context);
         treeLikelihood.setInputValue("siteModel", siteModel);
 
+        treeLikelihood.setInputValue("useAmbiguities", true);
         treeLikelihood.initAndValidate();
         treeLikelihood.setID(alignment.getID() + ".treeLikelihood");
         // logging