diff --git a/.classpath b/.classpath
index 996cad79ef..e405ad1237 100644
--- a/.classpath
+++ b/.classpath
@@ -15,6 +15,6 @@
 	<classpathentry kind="lib" path="lib/options.jar"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
 	<classpathentry kind="lib" path="lib/commons-math-2.2.jar"/>
+	<classpathentry kind="lib" path="lib/freemarker.jar"/>
 	<classpathentry kind="output" path="bin"/>
 </classpath>
-
diff --git a/.gitignore b/.gitignore
index 7413f970fb..72793f877d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,4 @@
 *.iml
 *.ipr
 *.iws
+bin/
diff --git a/src/dr/app/beagle/evomodel/branchmodel/RandomBranchAssignmentModel.java b/src/dr/app/beagle/evomodel/branchmodel/RandomBranchAssignmentModel.java
index 5ab7c6f80b..d5e38c98d3 100644
--- a/src/dr/app/beagle/evomodel/branchmodel/RandomBranchAssignmentModel.java
+++ b/src/dr/app/beagle/evomodel/branchmodel/RandomBranchAssignmentModel.java
@@ -16,6 +16,8 @@
 @SuppressWarnings("serial")
 public class RandomBranchAssignmentModel extends AbstractModel implements BranchModel {
 
+	public static final boolean DEBUG = true;
+	
     public static final String RANDOM_BRANCH_ASSIGNMENT_MODEL = "randomBranchAssignmentModel";
     private final TreeModel treeModel;
     private final List<SubstitutionModel> substitutionModels;
@@ -40,9 +42,28 @@ public RandomBranchAssignmentModel(TreeModel treeModel,
 		for (int i = 0; i < nodeCount; i++) {
 
 			NodeRef node = treeModel.getNode(i);
-			int branchClass = MathUtils.nextInt(nModels);
+			int branchClass = Integer.MAX_VALUE; //MathUtils.nextInt(nModels);
+			
+			if(DEBUG) {
+				
+//				System.out.println(node.toString());
+				
+				// hack to get fixed indexing
+				if(node.toString().equalsIgnoreCase("node 0, height=0.0: SimSeq1") || 
+						node.toString().equalsIgnoreCase("node 1, height=0.0: SimSeq2") ||
+						node.toString().equalsIgnoreCase("node 4, height=22.0")
+						) {
+					branchClass = 0; // 5
+				} else {
+					branchClass = 1; // 10
+				}//END: node check
+				
+			} else {
+				branchClass = MathUtils.nextInt(nModels);
+			}//END: DEBUG check
+			
 			branchAssignmentMap.put(node, branchClass);
-
+			
 		}// END: nodes loop		
 		
 	}//END: Constructor
diff --git a/src/dr/app/beagle/evomodel/branchmodel/lineagespecific/BeagleBranchLikelihood.java b/src/dr/app/beagle/evomodel/branchmodel/lineagespecific/BeagleBranchLikelihood.java
index 90a6dfa41c..06698cd06f 100644
--- a/src/dr/app/beagle/evomodel/branchmodel/lineagespecific/BeagleBranchLikelihood.java
+++ b/src/dr/app/beagle/evomodel/branchmodel/lineagespecific/BeagleBranchLikelihood.java
@@ -45,8 +45,8 @@ public BeagleBranchLikelihood(TreeModel treeModel,
 
 		if(this.treeModel != null) {
 			
-		this.categoriesProvider = new CountableBranchCategoryProvider.IndependentBranchCategoryModel( treeModel, categoriesParameter);
-//		this.categoriesProvider = new CountableBranchCategoryProvider.CladeBranchCategoryModel(treeModel, categoriesParameter);
+//		this.categoriesProvider = new CountableBranchCategoryProvider.IndependentBranchCategoryModel( treeModel, categoriesParameter);
+		this.categoriesProvider = new CountableBranchCategoryProvider.CladeBranchCategoryModel(treeModel, categoriesParameter);
 		
 		}
 		
diff --git a/src/dr/app/bss/BeagleSequenceSimulatorConsoleApp.java b/src/dr/app/bss/BeagleSequenceSimulatorConsoleApp.java
index c7639d0e94..2991585b55 100644
--- a/src/dr/app/bss/BeagleSequenceSimulatorConsoleApp.java
+++ b/src/dr/app/bss/BeagleSequenceSimulatorConsoleApp.java
@@ -28,13 +28,16 @@
 import dr.app.beagle.tools.BeagleSequenceSimulator;
 import dr.app.beagle.tools.Partition;
 import dr.app.util.Arguments;
+import dr.app.util.Arguments.ArgumentException;
 import dr.evolution.alignment.SimpleAlignment;
+import dr.evolution.io.Importer.ImportException;
 import dr.evolution.tree.Tree;
 import dr.evolution.util.Taxa;
 import dr.math.MathUtils;
 
 import java.io.File;
 import java.io.FileWriter;
+import java.io.IOException;
 import java.io.PrintWriter;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -623,16 +626,34 @@ public void simulate(String[] args) {
             writer.println(alignment.toString());
             writer.close();
 
-        } catch (Exception e) {
-
-            System.out.println();
-            printUsage(arguments);
-            System.out.println();
-            System.out.println(e.getMessage());
-            e.printStackTrace();
-            System.exit(1);
-
-        }// END: try-catch block
+		} catch (ArgumentException e) {
+
+			System.out.println();
+			printUsage(arguments);
+			System.out.println();
+			System.out.println(e.getMessage());
+			e.printStackTrace();
+			System.exit(1);
+
+		} catch (IOException e) {
+			
+			System.out.println();
+			printUsage(arguments);
+			System.out.println();
+			System.out.println(e.getMessage());
+			e.printStackTrace();
+			System.exit(1);
+			
+		} catch (ImportException e) {
+		
+			System.out.println();
+			printUsage(arguments);
+			System.out.println();
+			System.out.println(e.getMessage());
+			e.printStackTrace();
+			System.exit(1);
+		
+		}// END: try-catch block
 
     }// END: simulate