diff --git a/src/master/BeastTreeFromMaster.java b/src/master/BeastTreeFromMaster.java
index 504bba0..9856358 100644
--- a/src/master/BeastTreeFromMaster.java
+++ b/src/master/BeastTreeFromMaster.java
@@ -399,6 +399,11 @@ public void initNodeNumbers(beast.evolution.tree.Node beastRoot) {
                     throw new IllegalArgumentException("Alignment does not contain taxon named " + leaf.getID());
 
                 leaf.setNr(alignmentInput.get().getTaxonIndex(leaf.getID()));
+            } else if (m_taxonset.get() != null) {
+                if (!m_taxonset.get().getTaxaNames().contains(leaf.getID()))
+                    throw new IllegalArgumentException("TaxonSet does not contain taxon named " + leaf.getID());
+
+                leaf.setNr(m_taxonset.get().getTaxonIndex(leaf.getID()));
             } else {
                 leaf.setNr(nodeNr);
                 nodeNr += 1;
diff --git a/version.xml b/version.xml
index 3dda4ae..954f30c 100644
--- a/version.xml
+++ b/version.xml
@@ -1,3 +1,3 @@
-<addon name="MASTER" version="6.1.1">
+<addon name="MASTER" version="6.1.2">
     <depends on="BEAST" atleast="2.5.0" atmost="2.6.9"/>
 </addon>