diff --git a/lphybeast/src/main/java/lphybeast/tobeast/values/TimeTreeToBEAST.java b/lphybeast/src/main/java/lphybeast/tobeast/values/TimeTreeToBEAST.java index 1164e96..df62d07 100644 --- a/lphybeast/src/main/java/lphybeast/tobeast/values/TimeTreeToBEAST.java +++ b/lphybeast/src/main/java/lphybeast/tobeast/values/TimeTreeToBEAST.java @@ -30,7 +30,10 @@ public TreeParser valueToBEAST(Value timeTreeValue, BEASTContext conte TreeParser tree = new TreeParser(); tree.setInputValue("newick", timeTree.toNewick(false)); + // TODO seems IsLabelledNewick="true" causes the trouble when cares internal node index tree.setInputValue("IsLabelledNewick", true); + // IsLabelledNewick="true" Is the Newick tree labelled (alternatively contains node numbers). +// tree.setInputValue("IsLabelledNewick", false); TaxonSet taxa = new TaxonSet(); List taxonList = context.createTaxonList(getTaxaNames(timeTree));