diff --git a/src/beastfx/app/treeannotator/TreeAnnotator.java b/src/beastfx/app/treeannotator/TreeAnnotator.java
index d94bd28..4986153 100644
--- a/src/beastfx/app/treeannotator/TreeAnnotator.java
+++ b/src/beastfx/app/treeannotator/TreeAnnotator.java
@@ -36,6 +36,7 @@
 import beast.base.core.Description;
 import beast.base.core.Input;
 import beast.base.core.Log;
+import beast.base.evolution.alignment.TaxonSet;
 import beast.base.evolution.tree.Node;
 import beast.base.evolution.tree.Tree;
 import beast.base.evolution.tree.TreeParser;
@@ -60,7 +61,7 @@ public class TreeAnnotator extends beast.base.inference.Runnable {
     final public Input<Integer> burnInPercentageInput = new Input<>("burnin", "percentage of trees to used as burn-in (and will be ignored)", 10);
     final public Input<Double> limitInput = new Input<>("limit", "the minimum posterior probability for a node to be annotated", 0.0);
     final public Input<String> topologyInput = new Input<> ("topology", "name of the method for determining topology", "MCC");
-    final public Input<String> targetInput = new Input<> ("target", "target_file_name, specifies a user target tree to be annotated", "");
+    final public Input<String> targetInput = new Input<> ("target", "target_file_name, specifies a user target tree to be annotated");
     final public Input<Boolean> forceDiscreteInput = new Input<> ("forceDiscrete", "forces integer traits to be treated as discrete traits.");
     final public Input<Boolean> lowMemInput = new Input<> ("lowMem", "use less memory, which is a bit slower.");
     final public Input<Double> hpd2DInput = new Input<> ("hpd2D", "the HPD interval to be used for the bivariate traits");
@@ -543,6 +544,8 @@ public void run(final int burninPercentage,
                          // HeightsSummary heightsOption,
                          double posteriorLimit,
                          double hpd2D,
+                         // Target targetOption,
+                         String targetTreeFileName,
                          String inputFileName,
                          String outputFileName
     ) throws IOException  {
@@ -550,8 +553,12 @@ public void run(final int burninPercentage,
         topologySettingService = getTopologySettingService();
         nodeHeightSettingService = getNodeHeightSettingService();
 
-        // Get citations, only print if either of them is not empty.
+     // Get citations, only print if eihter of them is not empty.
+        
+
         String nodeCitation = nodeHeightSettingService.getCitations();
+ 
+
         String topoCitation = topologySettingService.getCitations();
  
         if (!nodeCitation.isBlank() || !topoCitation.isBlank()) {
@@ -612,19 +619,11 @@ public void run(final int burninPercentage,
             }
         }
 
-        if (targetInput.get() != null && !targetInput.get().isEmpty()) {
-            String current = topologySettingService.getServiceName();
-            String required = UserTargetTreeTopologyService.SERVICE_NAME;
-            if (!required.equals(current)) {
-                Log.info("Setting topology to be the target tree...");
-                topologyInput.setValue("target", this);
-                topologySettingService = getTopologySettingService();
-            }
-        }
-
         Tree targetTree = topologySettingService.setTopology(treeSet, progressStream, this);
-        cladeSystem = getCladeSystem(targetTree);
 
+     
+        cladeSystem = getCladeSystem(targetTree);
+        
 //        progressStream.println("Collecting node information...");
 //        progressStream.println("0              25             50             75            100");
 //        progressStream.println("|--------------|--------------|--------------|--------------|");
@@ -685,7 +684,7 @@ public void run(final int burninPercentage,
 
         progressStream.println("Writing annotated tree....");
 
-
+        
         processMetaData(targetTree.getRoot());
         try {
             final PrintStream stream = outputFileName != null ?
@@ -693,10 +692,10 @@ public void run(final int burninPercentage,
                     System.out;
             targetTree.init(stream);
             stream.println();
-
-            stream.print("tree TREE_" +
-                        topologySettingService.getServiceName() + "_" +
-                        nodeHeightSettingService.getServiceName() + " = ");
+            
+            stream.print("tree TREE_" + 
+            		topologySettingService.getServiceName() + "_" + 
+            		nodeHeightSettingService.getServiceName() + " = ");
             int[] dummy = new int[1];
             String newick = targetTree.getRoot().toSortedNewick(dummy, true);
             stream.print(newick);
@@ -1176,7 +1175,7 @@ private void annotate2DHPDAttribute(Node node, String preLabel, String postLabel
     private final List<TreeAnnotationPlugin> beastObjects = new ArrayList<>();
 
     Set<String> attributeNames = new HashSet<>();
-//    TaxonSet taxa = null;
+    TaxonSet taxa = null;
 
     static boolean processBivariateAttributes = true;
     
@@ -1388,7 +1387,8 @@ public void run() throws Exception {
     	for (String versionFile : versionFileInput.get()) {
     		BEASTClassLoader.addServices(versionFile);
     	}
-
+    	
+        String targetTreeFileName = null;
         String inputFileName = null;
         String outputFileName = null;
 
@@ -1453,12 +1453,20 @@ public void run() throws Exception {
             hpd2D = hpd2DInput.get();
             if (hpd2D <= 0 || hpd2D >=1) {
             	Log.err.println("hpd2D is a fraction and should be in between 0.0 and 1.0.");
-                System.exit(1);
+            	System.exit(1);            	
             }
             processBivariateAttributes = true;
         }
 
+
+//        Target target = Target.MAX_CLADE_CREDIBILITY;
+//        if (targetInput.get() != null) {
+//            target = Target.USER_TARGET_TREE;
+//            targetTreeFileName = arguments.getStringOption("target");
+//        }
+
         final List<File> args2 = filesInput.get();
+        		
 
         switch (args2.size()) {
             case 2:
@@ -1476,7 +1484,9 @@ public void run() throws Exception {
         }
         
         try {
-            run(burninPercentage, lowMem, posteriorLimit, hpd2D, inputFileName, outputFileName);
+        	run(burninPercentage, lowMem, posteriorLimit, hpd2D, targetTreeFileName, inputFileName, outputFileName);
+        //} catch (IOException e) {
+        //	throw e;
         } catch (Exception e) {
 			e.printStackTrace();
 		}