diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
index 70ef13f..245fe85 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
@@ -9,7 +9,9 @@
 import edu.uci.ics.genomix.type.VKmerBytesWritable;
 import edu.uci.ics.genomix.type.VKmerListWritable;
 
-public class VertexValueWritable implements WritableComparable<VertexValueWritable> {
+public class VertexValueWritable implements WritableComparable<VertexValueWritable>, Serializable {
+
+    private static final long serialVersionUID = 1L;
 
     public static class State extends VertexStateFlag{            
         public static final byte NO_MERGE = 0b00 << 3;
@@ -18,10 +20,12 @@
         public static final byte SHOULD_MERGE_MASK = 0b11 << 3;
         public static final byte SHOULD_MERGE_CLEAR = 0b1100111;
         
+        public static final byte UNCHANGE = 0b0 << 3;
         public static final byte KILL = 0b1 << 3;
         public static final byte KILL_MASK = 0b1 << 3;
         
         public static final byte DIR_FROM_DEADVERTEX = 0b10 << 3;
+        public static final byte DEAD_MASK = 0b10 << 3;
     }
     
     public static class VertexStateFlag extends FakeFlag {
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java
index 83686fb..c92148f 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java
@@ -3,8 +3,10 @@
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.Iterator;
 import java.util.Map;
+import java.util.Set;
 
 import edu.uci.ics.genomix.type.VKmerBytesWritable;
 import edu.uci.ics.pregelix.api.job.PregelixJob;
@@ -22,10 +24,12 @@
  */
 public class BubbleMergeVertex extends
     BasicGraphCleanVertex {
-
+    public static final String DISSIMILARITY_THRESHOLD = "BubbleMergeVertex.dissimilarThreshold";
+    private float dissimilarThreshold = -1;
+    
     private Map<VKmerBytesWritable, ArrayList<MessageWritable>> receivedMsgMap = new HashMap<VKmerBytesWritable, ArrayList<MessageWritable>>();
     private ArrayList<MessageWritable> receivedMsgList = new ArrayList<MessageWritable>();
-    
+
     /**
      * initiate kmerSize, maxIteration
      */
@@ -34,6 +38,8 @@
             kmerSize = getContext().getConfiguration().getInt(KMER_SIZE, 5);
         if (maxIteration < 0)
             maxIteration = getContext().getConfiguration().getInt(ITERATIONS, 1000000);
+        if(dissimilarThreshold == -1)
+            dissimilarThreshold = getContext().getConfiguration().getFloat(DISSIMILARITY_THRESHOLD, (float) 0.05);
         if(incomingMsg == null)
             incomingMsg = new MessageWritable();
         if(outgoingMsg == null)
@@ -42,6 +48,7 @@
             outgoingMsg.reset(kmerSize);
         if(destVertexId == null)
             destVertexId = new VKmerBytesWritable();
+        outFlag = 0;
     }
     
     public void sendBubbleAndMajorVertexMsgToMinorVertex(){
@@ -109,18 +116,47 @@
             /** aggregate bubble nodes and grouped by major vertex **/ 
             aggregateBubbleNodesByMajorNode(msgIterator);
             
+            Set<MessageWritable> unchangedSet = new HashSet<MessageWritable>();
+            Set<MessageWritable> deletedSet = new HashSet<MessageWritable>();
             for(VKmerBytesWritable prevId : receivedMsgMap.keySet()){
                 if(receivedMsgList.size() > 1){ // filter bubble
                     /** for each startVertex, sort the node by decreasing order of coverage **/
                     receivedMsgList = receivedMsgMap.get(prevId);
                     Collections.sort(receivedMsgList, new MessageWritable.SortByCoverage());
-                    System.out.println("");
-                    
                     
                     /** process similarSet, keep the unchanged set and deleted set & add coverage to unchange node **/
+                    MessageWritable topCoverageMessage = new MessageWritable();
+                    MessageWritable tmpMessage = new MessageWritable();
+                    Iterator<MessageWritable> it;
+                    while(!receivedMsgList.isEmpty()){
+                        it = receivedMsgList.iterator();
+                        topCoverageMessage.set(it.next());
+                        it.remove(); //delete topCoverage node
+                        while(it.hasNext()){
+                            tmpMessage.set(it.next());
+                            //compute the similarity  
+                            float fracDissimilar = (float) 0.02;
+                            if(fracDissimilar < dissimilarThreshold){ //If similar with top node, delete this node and put it in deletedSet 
+                                //TODO add coverage to top node
+                                deletedSet.add(tmpMessage);
+                                it.remove();
+                            }
+                        }
+                        unchangedSet.add(topCoverageMessage);
+                    }
                     
                     /** send message to the unchanged set for updating coverage & send kill message to the deleted set **/ 
-                    
+                    for(MessageWritable msg : unchangedSet){
+                        outFlag = MessageFlag.UNCHANGE;
+                        outgoingMsg.setFlag(outFlag);
+                        outgoingMsg.setAverageCoverage(msg.getAverageCoverage());
+                        sendMsg(msg.getSourceVertexId(), outgoingMsg);
+                    }
+                    for(MessageWritable msg : deletedSet){
+                        outFlag = MessageFlag.KILL;
+                        outgoingMsg.setFlag(outFlag);
+                        sendMsg(msg.getSourceVertexId(), outgoingMsg);
+                    }
                 }
             }
         } else if (getSuperstep() == 4){
@@ -128,12 +164,14 @@
                 incomingMsg = msgIterator.next();
                 if(incomingMsg.getFlag() == MessageFlag.KILL){
                     broadcaseKillself();
-                } 
+                } else if(incomingMsg.getFlag() == MessageFlag.UNCHANGE){
+                    getVertexValue().setAverageCoverage(incomingMsg.getAverageCoverage());
+                }
             }
         } else if(getSuperstep() == 5){
             if(msgIterator.hasNext()) {
                 incomingMsg = msgIterator.next();
-                if(incomingMsg.getFlag() == MessageFlag.KILL){
+                if(isResponseKillMsg()){
                     responseToDeadVertex();
                 }
             }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicGraphCleanVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicGraphCleanVertex.java
index 080cf35..58ef4d6 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicGraphCleanVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicGraphCleanVertex.java
@@ -22,14 +22,14 @@
     public static final String KMER_SIZE = "BasicGraphCleanVertex.kmerSize";
     public static final String ITERATIONS = "BasicGraphCleanVertex.iteration";
     public static int kmerSize = -1;
-    protected int maxIteration = -1;
+    public static int maxIteration = -1;
     
     protected MessageWritable incomingMsg = null; 
     protected MessageWritable outgoingMsg = null; 
     protected VKmerBytesWritable destVertexId = null;
     protected Iterator<VKmerBytesWritable> kmerIterator;
-    protected VKmerBytesWritable tmpKmer = new VKmerBytesWritable(kmerSize);
-    byte headFlag;
+    protected VKmerBytesWritable tmpKmer = null;
+    protected byte headFlag;
     protected byte outFlag;
     protected byte inFlag;
     protected byte selfFlag;
@@ -814,9 +814,16 @@
         }
     }
     
-    public boolean isKillMsg(){
+    public boolean isReceiveKillMsg(){
         byte killFlag = (byte) (incomingMsg.getFlag() & MessageFlag.KILL_MASK);
-        return killFlag == MessageFlag.KILL;
+        byte deadFlag = (byte) (incomingMsg.getFlag() & MessageFlag.DEAD_MASK);
+        return killFlag == MessageFlag.KILL & deadFlag != MessageFlag.DIR_FROM_DEADVERTEX;
+    }
+    
+    public boolean isResponseKillMsg(){
+        byte killFlag = (byte) (incomingMsg.getFlag() & MessageFlag.KILL_MASK);
+        byte deadFlag = (byte) (incomingMsg.getFlag() & MessageFlag.DEAD_MASK);
+        return killFlag == MessageFlag.KILL & deadFlag == MessageFlag.DIR_FROM_DEADVERTEX; 
     }
     
     @Override
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/MapReduceVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/MapReduceVertex.java
index 10137da..5baf492 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/MapReduceVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/MapReduceVertex.java
@@ -171,7 +171,7 @@
         } else if(getSuperstep() == 5){
             while (msgIterator.hasNext()) {
                 incomingMsg = msgIterator.next();
-                if(isKillMsg())
+                if(isReceiveKillMsg())
                     responseToDeadVertex();
             }
         }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P2ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P2ForPathMergeVertex.java
index 6b7ad1f..c042f49 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P2ForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P2ForPathMergeVertex.java
@@ -249,7 +249,7 @@
                         processFinalMerge(incomingMsg);
                         /** NON-FAKE and Final vertice send msg to FAKE vertex **/
                         sendMsgToFakeVertex();
-                    } else if(isKillMsg()){
+                    } else if(isReceiveKillMsg()){
                         responseToDeadVertex();
                     }
                 }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/MessageFlag.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/MessageFlag.java
index 9468681..3ce6c5a 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/MessageFlag.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/MessageFlag.java
@@ -2,11 +2,6 @@
 
 public class MessageFlag extends DirectionFlag {
     
-    //public static final byte FLIP = 1 << 6;
-    public static final byte HEAD_SHOULD_MERGEWITHPREV = 0b101 << 0;
-    public static final byte HEAD_SHOULD_MERGEWITHNEXT = 0b111 << 0;
-
-    
     public static String getFlagAsString(byte code) {
         // TODO: allow multiple flags to be set
         return "ERROR_BAD_MESSAGE";
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
index fb51e52..fe82add 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
@@ -13,6 +13,7 @@
 import edu.uci.ics.genomix.pregelix.operator.bridgeremove.BridgeRemoveVertex;
 import edu.uci.ics.genomix.pregelix.operator.bubblemerge.BubbleAddVertex;
 import edu.uci.ics.genomix.pregelix.operator.bubblemerge.BubbleMergeVertex;
+import edu.uci.ics.genomix.pregelix.operator.pathmerge.BasicGraphCleanVertex;
 import edu.uci.ics.genomix.pregelix.operator.pathmerge.P2ForPathMergeVertex;
 import edu.uci.ics.genomix.pregelix.operator.pathmerge.MapReduceVertex;
 import edu.uci.ics.genomix.pregelix.operator.pathmerge.P3ForPathMergeVertex;