Index: branches/autoquest-ui-core-alignment/src/main/java/de/ugoe/cs/autoquest/commands/usability/CMDgenerateTaskTree.java
===================================================================
--- branches/autoquest-ui-core-alignment/src/main/java/de/ugoe/cs/autoquest/commands/usability/CMDgenerateTaskTree.java	(revision 1708)
+++ branches/autoquest-ui-core-alignment/src/main/java/de/ugoe/cs/autoquest/commands/usability/CMDgenerateTaskTree.java	(revision 1710)
@@ -45,5 +45,5 @@
 	@Override
 	public String help() {
-		return "generateTaskTree <sequences> {<tasktree>} {<boolean: harmonize sequences or not (true or false)>} {<integer: number of threads>}";
+		return "generateTaskTree <sequences> {<tasktree>} {<boolean: harmonize sequences or not (true or false)>} {boolean: load substitutionmatrix} {<integer: number of threads>}";
 	}
 
@@ -71,12 +71,17 @@
 			String harmonize = (String) parameters.get(2);
 			de.ugoe.cs.autoquest.tasktrees.temporalrelation.SequenceForTaskDetectionRuleAlignment.harmonizeSequences = true;
-			System.out.println(harmonize);
-			if (harmonize.equals("false")) {
-				System.out.println("Not harmonizing");
+			if (harmonize.equals("false")) {	
 				de.ugoe.cs.autoquest.tasktrees.temporalrelation.SequenceForTaskDetectionRuleAlignment.harmonizeSequences = false;
 			}
 		}
 		if (parameters.size() > 3) {
-			String threadCount = (String) parameters.get(3);
+			String loadSubMat = (String) parameters.get(3);
+			de.ugoe.cs.autoquest.tasktrees.temporalrelation.SequenceForTaskDetectionRuleAlignment.loadSubstutionMatrix = false;
+			if (loadSubMat.equals("true")) {
+				de.ugoe.cs.autoquest.tasktrees.temporalrelation.SequenceForTaskDetectionRuleAlignment.loadSubstutionMatrix = true;
+			}
+		}
+		if (parameters.size() > 4) {
+			String threadCount = (String) parameters.get(4);
 			de.ugoe.cs.autoquest.tasktrees.temporalrelation.SequenceForTaskDetectionRuleAlignment.nThreads = 1;
 			try {
@@ -85,7 +90,9 @@
 			} catch (Exception e) {
 				throw new IllegalArgumentException(
-						"The fourth parameter must be an integer. Did you forget to name the tasktree?");
+						"The fifth parameter must be an integer. Did you forget to name the tasktree?");
 			}
 		}
+		
+		de.ugoe.cs.autoquest.tasktrees.temporalrelation.SequenceForTaskDetectionRuleAlignment.loadSubstutionMatrix=false;
 
 		Collection<List<Event>> sequences = null;