diff --git a/genomix/genomix-pregelix/data/TipAddGraph/txt/test b/genomix/genomix-pregelix/data/TipAddGraph/txt/test
deleted file mode 100755
index 5c36d0a..0000000
--- a/genomix/genomix-pregelix/data/TipAddGraph/txt/test
+++ /dev/null
@@ -1,7 +0,0 @@
-(1,5)	([(1,6)]	[]	[]	[(1,4)]	GAA)
-(2,1)	([]	[]	[]	[(1,4)]	)
-(1,1)	([(1,2)]	[]	[]	[]	AAT)
-(1,2)	([(1,3)]	[]	[]	[(1,1)]	ATA)
-(1,4)	([(1,5),(2,1)]	[]	[]	[(1,3)]	AGA)
-(1,3)	([(1,4)]	[]	[]	[(1,2)]	TAG)
-(1,6)	([]	[]	[]	[(1,5)]	AAC)
diff --git a/genomix/genomix-pregelix/data/TipAddGraph/txt/.test.crc b/genomix/genomix-pregelix/data/bridgeremove/txt/.bridgeremove.crc
similarity index 100%
copy from genomix/genomix-pregelix/data/TipAddGraph/txt/.test.crc
copy to genomix/genomix-pregelix/data/bridgeremove/txt/.bridgeremove.crc
diff --git a/genomix/genomix-pregelix/data/bridgeremove/txt/bridgeremove b/genomix/genomix-pregelix/data/bridgeremove/txt/bridgeremove
new file mode 100755
index 0000000..e5fb406
--- /dev/null
+++ b/genomix/genomix-pregelix/data/bridgeremove/txt/bridgeremove
@@ -0,0 +1,7 @@
+(2,1)([(2,2)]	[]	[]	[]	GCC)
+(1,1)([(1,2)]	[]	[]	[]	AAT)
+(2,2)([(2,3)]	[]	[]	[(2,1),(3,1)]	CCT)
+(1,2)([(1,3),(3,1)]	[]	[]	[(1,1)]	ATA)
+(2,3)([]	[]	[]	[(2,2)]	CTAGCA)
+(1,3)([]	[]	[]	[(1,2)]	TAGAAC)
+(3,1)([(2,2)]	[]	[]	[(1,2)]	TAGCCT)
diff --git a/genomix/genomix-pregelix/data/TipAddGraph/txt/.test.crc b/genomix/genomix-pregelix/data/bubble_merge/txt/.bubble_merge.crc
similarity index 100%
copy from genomix/genomix-pregelix/data/TipAddGraph/txt/.test.crc
copy to genomix/genomix-pregelix/data/bubble_merge/txt/.bubble_merge.crc
diff --git a/genomix/genomix-pregelix/data/bubble_merge/txt/bubble_merge b/genomix/genomix-pregelix/data/bubble_merge/txt/bubble_merge
new file mode 100755
index 0000000..22d58bf
--- /dev/null
+++ b/genomix/genomix-pregelix/data/bubble_merge/txt/bubble_merge
@@ -0,0 +1,6 @@
+(1,5)([]	[]	[]	[(1,4)]	GAAC)
+(2,1)([(1,4)]	[]	[]	[(1,2)]	TAGCCAG)
+(1,1)([(1,2)]	[]	[]	[]	AAT)
+(1,2)([(1,3),(2,1)]	[]	[]	[(1,1)]	ATA)
+(1,4)([(1,5)]	[]	[]	[(1,3),(2,1)]	AGA)
+(1,3)([(1,4)]	[]	[]	[(1,2)]	TAG)
diff --git a/genomix/genomix-pregelix/data/TipAddGraph/txt/.test.crc b/genomix/genomix-pregelix/data/bubble_remove/txt/.bubble.crc
similarity index 100%
rename from genomix/genomix-pregelix/data/TipAddGraph/txt/.test.crc
rename to genomix/genomix-pregelix/data/bubble_remove/txt/.bubble.crc
diff --git a/genomix/genomix-pregelix/data/bubble_remove/txt/bubble b/genomix/genomix-pregelix/data/bubble_remove/txt/bubble
new file mode 100755
index 0000000..d250792
--- /dev/null
+++ b/genomix/genomix-pregelix/data/bubble_remove/txt/bubble
@@ -0,0 +1,6 @@
+(1,5)([]	[]	[]	[(1,4)]	GAAC)
+(2,1)([(1,4)]	[]	[]	[(1,2)]	TAG)
+(1,1)([(1,2)]	[]	[]	[]	AAT)
+(1,2)([(1,3),(2,1)]	[]	[]	[(1,1)]	ATA)
+(1,4)([(1,5)]	[]	[]	[(1,3),(2,1)]	AGA)
+(1,3)([(1,4)]	[]	[]	[(1,2)]	TAG)
diff --git a/genomix/genomix-pregelix/data/input/read/part-0 b/genomix/genomix-pregelix/data/input/read/part-0
index 6595dfe..d702695 100755
--- a/genomix/genomix-pregelix/data/input/read/part-0
+++ b/genomix/genomix-pregelix/data/input/read/part-0
Binary files differ
diff --git a/genomix/genomix-pregelix/data/input/read/part-1 b/genomix/genomix-pregelix/data/input/read/part-1
index 072d5f9..5bc30e8 100755
--- a/genomix/genomix-pregelix/data/input/read/part-1
+++ b/genomix/genomix-pregelix/data/input/read/part-1
Binary files differ
diff --git a/genomix/genomix-pregelix/data/input/read/part-2 b/genomix/genomix-pregelix/data/input/read/part-2
index 3d132ac..474af09 100755
--- a/genomix/genomix-pregelix/data/input/read/part-2
+++ b/genomix/genomix-pregelix/data/input/read/part-2
Binary files differ
diff --git a/genomix/genomix-pregelix/data/input/read/part-3 b/genomix/genomix-pregelix/data/input/read/part-3
index df12383..98326a6 100755
--- a/genomix/genomix-pregelix/data/input/read/part-3
+++ b/genomix/genomix-pregelix/data/input/read/part-3
Binary files differ
diff --git a/genomix/genomix-pregelix/data/input/tipremove/part-0 b/genomix/genomix-pregelix/data/input/tipremove/part-0
index a10ab8b..d45f051 100755
--- a/genomix/genomix-pregelix/data/input/tipremove/part-0
+++ b/genomix/genomix-pregelix/data/input/tipremove/part-0
Binary files differ
diff --git a/genomix/genomix-pregelix/data/input/tipremove/part-1 b/genomix/genomix-pregelix/data/input/tipremove/part-1
index 20a3078..d50e98a 100755
--- a/genomix/genomix-pregelix/data/input/tipremove/part-1
+++ b/genomix/genomix-pregelix/data/input/tipremove/part-1
Binary files differ
diff --git a/genomix/genomix-pregelix/data/input/tipremove/part-2 b/genomix/genomix-pregelix/data/input/tipremove/part-2
index aed9265..6ed28d6 100755
--- a/genomix/genomix-pregelix/data/input/tipremove/part-2
+++ b/genomix/genomix-pregelix/data/input/tipremove/part-2
Binary files differ
diff --git a/genomix/genomix-pregelix/data/input/tipremove/part-3 b/genomix/genomix-pregelix/data/input/tipremove/part-3
index 8af7223..4734cf2 100755
--- a/genomix/genomix-pregelix/data/input/tipremove/part-3
+++ b/genomix/genomix-pregelix/data/input/tipremove/part-3
Binary files differ
diff --git a/genomix/genomix-pregelix/data/input/tipremove/part-4 b/genomix/genomix-pregelix/data/input/tipremove/part-4
index 2fd77a1..84cd77d 100755
--- a/genomix/genomix-pregelix/data/input/tipremove/part-4
+++ b/genomix/genomix-pregelix/data/input/tipremove/part-4
Binary files differ
diff --git a/genomix/genomix-pregelix/data/input/tipremove/part-5 b/genomix/genomix-pregelix/data/input/tipremove/part-5
index 7eb1649..9143122 100755
--- a/genomix/genomix-pregelix/data/input/tipremove/part-5
+++ b/genomix/genomix-pregelix/data/input/tipremove/part-5
Binary files differ
diff --git a/genomix/genomix-pregelix/data/input/tipremove/part-6 b/genomix/genomix-pregelix/data/input/tipremove/part-6
index 8ae2314..14c675c 100755
--- a/genomix/genomix-pregelix/data/input/tipremove/part-6
+++ b/genomix/genomix-pregelix/data/input/tipremove/part-6
Binary files differ
diff --git a/genomix/genomix-pregelix/data/input/tipremove/part-7 b/genomix/genomix-pregelix/data/input/tipremove/part-7
index d2b9342..0c9ca53 100755
--- a/genomix/genomix-pregelix/data/input/tipremove/part-7
+++ b/genomix/genomix-pregelix/data/input/tipremove/part-7
Binary files differ
diff --git a/genomix/genomix-pregelix/data/input/unmerge_read/part-0 b/genomix/genomix-pregelix/data/input/unmerge_read/part-0
new file mode 100755
index 0000000..aab2f64
--- /dev/null
+++ b/genomix/genomix-pregelix/data/input/unmerge_read/part-0
Binary files differ
diff --git a/genomix/genomix-pregelix/data/input/unmerge_read/part-1 b/genomix/genomix-pregelix/data/input/unmerge_read/part-1
new file mode 100755
index 0000000..d7b24b3
--- /dev/null
+++ b/genomix/genomix-pregelix/data/input/unmerge_read/part-1
Binary files differ
diff --git a/genomix/genomix-pregelix/data/input/unmerge_read/part-2 b/genomix/genomix-pregelix/data/input/unmerge_read/part-2
new file mode 100755
index 0000000..f82775c
--- /dev/null
+++ b/genomix/genomix-pregelix/data/input/unmerge_read/part-2
Binary files differ
diff --git a/genomix/genomix-pregelix/data/input/unmerge_read/part-3 b/genomix/genomix-pregelix/data/input/unmerge_read/part-3
new file mode 100755
index 0000000..b7a3925
--- /dev/null
+++ b/genomix/genomix-pregelix/data/input/unmerge_read/part-3
Binary files differ
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MergeBubbleMessageWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MergeBubbleMessageWritable.java
index 55ddb1b..63066fa 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MergeBubbleMessageWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MergeBubbleMessageWritable.java
@@ -29,12 +29,12 @@
         sourceVertexId = new PositionWritable();
         chainVertexId = new KmerBytesWritable(0);
         neighberNode = new AdjacencyListWritable();
-        message = Message.NON;
         startVertexId = new PositionWritable();
+        message = Message.NON;
         checkMessage = (byte) 0;
     }
     
-    public void set(MessageWritable msg) {
+    public void set(MergeBubbleMessageWritable msg) {
         checkMessage = 0;
         if (sourceVertexId != null) {
             checkMessage |= CheckMessage.SOURCE;
@@ -48,10 +48,14 @@
             checkMessage |= CheckMessage.NEIGHBER;
             this.neighberNode.set(msg.getNeighberNode());
         }
+        if (startVertexId != null) {
+            checkMessage |= CheckMessage.START;
+            this.startVertexId.set(msg.getStartVertexId());
+        }
         this.message = msg.getMessage();
     }
 
-    public void set(PositionWritable sourceVertexId, KmerBytesWritable chainVertexId, AdjacencyListWritable neighberNode, byte message) {
+    public void set(PositionWritable sourceVertexId, KmerBytesWritable chainVertexId, AdjacencyListWritable neighberNode, PositionWritable startVertexId, byte message) {
         checkMessage = 0;
         if (sourceVertexId != null) {
             checkMessage |= CheckMessage.SOURCE;
@@ -65,6 +69,10 @@
             checkMessage |= CheckMessage.NEIGHBER;
             this.neighberNode.set(neighberNode);
         }
+        if (startVertexId != null) {
+            checkMessage |= CheckMessage.START;
+            this.startVertexId.set(startVertexId);
+        }
         this.message = message;
     }
 
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeAddVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeAddVertex.java
new file mode 100644
index 0000000..6c24aa9
--- /dev/null
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeAddVertex.java
@@ -0,0 +1,122 @@
+package edu.uci.ics.genomix.pregelix.operator.bridgeremove;
+
+import java.util.Iterator;
+import org.apache.hadoop.io.NullWritable;
+
+import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.PositionListWritable;
+import edu.uci.ics.genomix.type.PositionWritable;
+import edu.uci.ics.pregelix.api.graph.Vertex;
+import edu.uci.ics.pregelix.api.job.PregelixJob;
+import edu.uci.ics.pregelix.api.util.BspUtils;
+import edu.uci.ics.genomix.pregelix.client.Client;
+import edu.uci.ics.genomix.pregelix.format.DataCleanInputFormat;
+import edu.uci.ics.genomix.pregelix.format.DataCleanOutputFormat;
+import edu.uci.ics.genomix.pregelix.io.MessageWritable;
+import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+
+/*
+ * vertexId: BytesWritable
+ * vertexValue: ByteWritable
+ * edgeValue: NullWritable
+ * message: MessageWritable
+ * 
+ * DNA:
+ * A: 00
+ * C: 01
+ * G: 10
+ * T: 11
+ * 
+ * succeed node
+ *  A 00000001 1
+ *  G 00000010 2
+ *  C 00000100 4
+ *  T 00001000 8
+ * precursor node
+ *  A 00010000 16
+ *  G 00100000 32
+ *  C 01000000 64
+ *  T 10000000 128
+ *  
+ * For example, ONE LINE in input file: 00,01,10    0001,0010,
+ * That means that vertexId is ACG, its succeed node is A and its precursor node is C.
+ * The succeed node and precursor node will be stored in vertexValue and we don't use edgeValue.
+ * The details about message are in edu.uci.ics.pregelix.example.io.MessageWritable. 
+ */
+/**
+ * Naive Algorithm for path merge graph
+ */
+public class BridgeAddVertex extends
+        Vertex<PositionWritable, ValueStateWritable, NullWritable, MessageWritable> {
+    public static final String KMER_SIZE = "BridgeRemoveVertex.kmerSize";
+    public static final String LENGTH = "BridgeRemoveVertex.length";
+    public static int kmerSize = -1;
+    private int length = -1;
+    
+    /**
+     * initiate kmerSize, maxIteration
+     */
+    public void initVertex() {
+        if (kmerSize == -1)
+            kmerSize = getContext().getConfiguration().getInt(KMER_SIZE, 5);
+        if(length == -1)
+            length = getContext().getConfiguration().getInt(LENGTH, kmerSize + 5);
+    }
+
+    @SuppressWarnings("unchecked")
+    @Override
+    public void compute(Iterator<MessageWritable> msgIterator) {
+        initVertex();
+        if(getSuperstep() == 1){
+            if(getVertexId().getReadID() == 1 && getVertexId().getPosInRead() == 2){
+                getVertexValue().getFFList().append(3, (byte)1);
+                
+                //add bridge vertex
+                @SuppressWarnings("rawtypes")
+                Vertex vertex = (Vertex) BspUtils.createVertex(getContext().getConfiguration());
+                vertex.getMsgList().clear();
+                vertex.getEdges().clear();
+                PositionWritable vertexId = new PositionWritable();
+                ValueStateWritable vertexValue = new ValueStateWritable();
+                /**
+                 * set the src vertex id
+                 */
+                vertexId.set(3, (byte)1);
+                vertex.setVertexId(vertexId);
+                /**
+                 * set the vertex value
+                 */
+                byte[] array = { 'T', 'A', 'G', 'C', 'C', 'T'};
+                KmerBytesWritable kmer = new KmerBytesWritable(array.length);
+                kmer.setByRead(array, 0);
+                vertexValue.setMergeChain(kmer);
+                PositionListWritable plist = new PositionListWritable();
+                plist.append(new PositionWritable(1, (byte)2));
+                vertexValue.setRRList(plist);
+                PositionListWritable plist2 = new PositionListWritable();
+                plist2.append(new PositionWritable(2, (byte)2));
+                vertexValue.setFFList(plist2);
+                vertex.setVertexValue(vertexValue);
+                
+                addVertex(vertexId, vertex);
+            }
+            if(getVertexId().getReadID() == 2 && getVertexId().getPosInRead() == 2)
+                getVertexValue().getRRList().append(3, (byte)1);
+        }
+        voteToHalt();
+    }
+
+    public static void main(String[] args) throws Exception {
+        PregelixJob job = new PregelixJob(BridgeAddVertex.class.getSimpleName());
+        job.setVertexClass(BridgeAddVertex.class);
+        /**
+         * BinaryInput and BinaryOutput
+         */
+        job.setVertexInputFormatClass(DataCleanInputFormat.class);
+        job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
+        job.setDynamicVertexValueSize(true);
+        job.setOutputKeyClass(PositionWritable.class);
+        job.setOutputValueClass(ValueStateWritable.class);
+        Client.run(args, job);
+    }
+}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeRemoveVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeRemoveVertex.java
index 8716d8d..bc97dbd 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeRemoveVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeRemoveVertex.java
@@ -55,8 +55,10 @@
 
     private MessageWritable incomingMsg = new MessageWritable();
     private MessageWritable outgoingMsg = new MessageWritable();
-    private ArrayList<MessageWritable> receivedMsg = new ArrayList<MessageWritable>();
+    private ArrayList<MessageWritable> receivedMsgList = new ArrayList<MessageWritable>();
     
+    private Iterator<PositionWritable> iterator;
+    private PositionWritable pos = new PositionWritable();
     private PositionWritable destVertexId = new PositionWritable();
     private Iterator<PositionWritable> posIterator;
     /**
@@ -68,7 +70,7 @@
         if(length == -1)
             length = getContext().getConfiguration().getInt(LENGTH, kmerSize + 5);
         outgoingMsg.reset();
-        receivedMsg.clear();
+        receivedMsgList.clear();
     }
     
     /**
@@ -110,6 +112,121 @@
             sendMsg(destVertexId, outgoingMsg);
         }
     }
+    
+    /**
+     * broadcast kill self to all neighbers 
+     */
+    public void broadcaseKillself(){
+        outgoingMsg.setSourceVertexId(getVertexId());
+        if(receivedMsgList.get(0).getMessage() == AdjMessage.FROMFF 
+                && receivedMsgList.get(1).getMessage() == AdjMessage.FROMRR){
+            outgoingMsg.setMessage(AdjMessage.FROMRR);
+            sendMsg(receivedMsgList.get(0).getSourceVertexId(), outgoingMsg);
+            outgoingMsg.setMessage(AdjMessage.FROMFF);
+            sendMsg(receivedMsgList.get(1).getSourceVertexId(), outgoingMsg);
+            deleteVertex(getVertexId());
+        } else if (receivedMsgList.get(0).getMessage() == AdjMessage.FROMFF 
+                && receivedMsgList.get(1).getMessage() == AdjMessage.FROMRF) {
+            outgoingMsg.setMessage(AdjMessage.FROMRR);
+            sendMsg(receivedMsgList.get(0).getSourceVertexId(), outgoingMsg);
+            outgoingMsg.setMessage(AdjMessage.FROMFR);
+            sendMsg(receivedMsgList.get(1).getSourceVertexId(), outgoingMsg);
+            deleteVertex(getVertexId());
+        } else if (receivedMsgList.get(0).getMessage() == AdjMessage.FROMFR 
+                && receivedMsgList.get(1).getMessage() == AdjMessage.FROMRR) {
+            outgoingMsg.setMessage(AdjMessage.FROMRF);
+            sendMsg(receivedMsgList.get(0).getSourceVertexId(), outgoingMsg);
+            outgoingMsg.setMessage(AdjMessage.FROMFF);
+            sendMsg(receivedMsgList.get(1).getSourceVertexId(), outgoingMsg);
+            deleteVertex(getVertexId());
+        } else if (receivedMsgList.get(0).getMessage() == AdjMessage.FROMFR 
+                && receivedMsgList.get(1).getMessage() == AdjMessage.FROMRF) {
+            outgoingMsg.setMessage(AdjMessage.FROMRF);
+            sendMsg(receivedMsgList.get(0).getSourceVertexId(), outgoingMsg);
+            outgoingMsg.setMessage(AdjMessage.FROMFR);
+            sendMsg(receivedMsgList.get(1).getSourceVertexId(), outgoingMsg);
+            deleteVertex(getVertexId());
+        } // RR
+        else if(receivedMsgList.get(1).getMessage() == AdjMessage.FROMFF 
+                && receivedMsgList.get(0).getMessage() == AdjMessage.FROMRR){
+            outgoingMsg.setMessage(AdjMessage.FROMRR);
+            sendMsg(receivedMsgList.get(1).getSourceVertexId(), outgoingMsg);
+            outgoingMsg.setMessage(AdjMessage.FROMFF);
+            sendMsg(receivedMsgList.get(0).getSourceVertexId(), outgoingMsg);
+            deleteVertex(getVertexId());
+        } else if (receivedMsgList.get(1).getMessage() == AdjMessage.FROMFF 
+                && receivedMsgList.get(0).getMessage() == AdjMessage.FROMRF) {
+            outgoingMsg.setMessage(AdjMessage.FROMRR);
+            sendMsg(receivedMsgList.get(1).getSourceVertexId(), outgoingMsg);
+            outgoingMsg.setMessage(AdjMessage.FROMFR);
+            sendMsg(receivedMsgList.get(0).getSourceVertexId(), outgoingMsg);
+            deleteVertex(getVertexId());
+        } else if (receivedMsgList.get(1).getMessage() == AdjMessage.FROMFR 
+                && receivedMsgList.get(0).getMessage() == AdjMessage.FROMRR) {
+            outgoingMsg.setMessage(AdjMessage.FROMRF);
+            sendMsg(receivedMsgList.get(1).getSourceVertexId(), outgoingMsg);
+            outgoingMsg.setMessage(AdjMessage.FROMFF);
+            sendMsg(receivedMsgList.get(0).getSourceVertexId(), outgoingMsg);
+            deleteVertex(getVertexId());
+        } else if (receivedMsgList.get(1).getMessage() == AdjMessage.FROMFR 
+                && receivedMsgList.get(0).getMessage() == AdjMessage.FROMRF) {
+            outgoingMsg.setMessage(AdjMessage.FROMRF);
+            sendMsg(receivedMsgList.get(1).getSourceVertexId(), outgoingMsg);
+            outgoingMsg.setMessage(AdjMessage.FROMFR);
+            sendMsg(receivedMsgList.get(0).getSourceVertexId(), outgoingMsg);
+            deleteVertex(getVertexId());
+        }
+    }
+    
+    /**
+     * do some remove operations on adjMap after receiving the info about dead Vertex
+     */
+    public void responseToDeadVertex(Iterator<MessageWritable> msgIterator){
+        while (msgIterator.hasNext()) {
+            incomingMsg = msgIterator.next();
+            if(incomingMsg.getMessage() == AdjMessage.FROMFF){
+                //remove incomingMsg.getSourceId from RR positionList
+                iterator = getVertexValue().getRRList().iterator();
+                while(iterator.hasNext()){
+                    pos = iterator.next();
+                    if(pos.equals(incomingMsg.getSourceVertexId())){
+                        iterator.remove();
+                        break;
+                    }
+                }
+            } else if(incomingMsg.getMessage() == AdjMessage.FROMFR){
+                //remove incomingMsg.getSourceId from RF positionList
+                iterator = getVertexValue().getRFList().iterator();
+                while(iterator.hasNext()){
+                    pos = iterator.next();
+                    if(pos.equals(incomingMsg.getSourceVertexId())){
+                        iterator.remove();
+                        break;
+                    }
+                }
+            } else if(incomingMsg.getMessage() == AdjMessage.FROMRF){
+                //remove incomingMsg.getSourceId from FR positionList
+                iterator = getVertexValue().getFRList().iterator();
+                while(iterator.hasNext()){
+                    pos = iterator.next();
+                    if(pos.equals(incomingMsg.getSourceVertexId())){
+                        iterator.remove();
+                        break;
+                    }
+                }
+            } else{ //incomingMsg.getMessage() == AdjMessage.FROMRR
+                //remove incomingMsg.getSourceId from FF positionList
+                iterator = getVertexValue().getFFList().iterator();
+                while(iterator.hasNext()){
+                    pos = iterator.next();
+                    if(pos.equals(incomingMsg.getSourceVertexId())){
+                        iterator.remove();
+                        break;
+                    }
+                }
+            }
+        }
+    }
 
     @Override
     public void compute(Iterator<MessageWritable> msgIterator) {
@@ -118,7 +235,7 @@
             if(VertexUtil.isUpBridgeVertex(getVertexValue())){
                 sendMsgToAllNextNodes(getVertexValue());
             }
-           else if(VertexUtil.isUpBridgeVertex(getVertexValue())){
+           else if(VertexUtil.isDownBridgeVertex(getVertexValue())){
                 sendMsgToAllPreviousNodes(getVertexValue());
            }
         }
@@ -127,57 +244,17 @@
             while (msgIterator.hasNext()) {
                 if(i == 3)
                     break;
-                receivedMsg.add(msgIterator.next());
+                receivedMsgList.add(msgIterator.next());
                 i++;
             }
-            if(receivedMsg.size() == 2){
-                if(getVertexValue().getLengthOfMergeChain() > length){
-                    outgoingMsg.setSourceVertexId(getVertexId());
-                    if(receivedMsg.get(0).getMessage() == AdjMessage.FROMFF 
-                            && receivedMsg.get(1).getMessage() == AdjMessage.FROMRR){
-                        outgoingMsg.setMessage(AdjMessage.FROMRR);
-                        sendMsg(receivedMsg.get(0).getSourceVertexId(), outgoingMsg);
-                        outgoingMsg.setMessage(AdjMessage.FROMFF);
-                        sendMsg(receivedMsg.get(1).getSourceVertexId(), outgoingMsg);
-                        deleteVertex(getVertexId());
-                    } else if (receivedMsg.get(0).getMessage() == AdjMessage.FROMFF 
-                            && receivedMsg.get(1).getMessage() == AdjMessage.FROMRF) {
-                        outgoingMsg.setMessage(AdjMessage.FROMRR);
-                        sendMsg(receivedMsg.get(0).getSourceVertexId(), outgoingMsg);
-                        outgoingMsg.setMessage(AdjMessage.FROMFR);
-                        sendMsg(receivedMsg.get(1).getSourceVertexId(), outgoingMsg);
-                        deleteVertex(getVertexId());
-                    } else if (receivedMsg.get(0).getMessage() == AdjMessage.FROMFR 
-                            && receivedMsg.get(1).getMessage() == AdjMessage.FROMRR) {
-                        outgoingMsg.setMessage(AdjMessage.FROMRF);
-                        sendMsg(receivedMsg.get(0).getSourceVertexId(), outgoingMsg);
-                        outgoingMsg.setMessage(AdjMessage.FROMFF);
-                        sendMsg(receivedMsg.get(1).getSourceVertexId(), outgoingMsg);
-                        deleteVertex(getVertexId());
-                    } else if (receivedMsg.get(0).getMessage() == AdjMessage.FROMFR 
-                            && receivedMsg.get(1).getMessage() == AdjMessage.FROMRF) {
-                        outgoingMsg.setMessage(AdjMessage.FROMRF);
-                        sendMsg(receivedMsg.get(0).getSourceVertexId(), outgoingMsg);
-                        outgoingMsg.setMessage(AdjMessage.FROMFR);
-                        sendMsg(receivedMsg.get(1).getSourceVertexId(), outgoingMsg);
-                        deleteVertex(getVertexId());
-                    }
+            if(receivedMsgList.size() == 2){
+                if(getVertexValue().getLengthOfMergeChain() <= length){
+                    broadcaseKillself();
                 }
             }
         }
         else if(getSuperstep() == 3){
-            while (msgIterator.hasNext()) {
-                incomingMsg = msgIterator.next();
-                if(incomingMsg.getMessage() == AdjMessage.FROMFF){
-                    //remove incomingMsg.getSourceId from RR positionList
-                } else if(incomingMsg.getMessage() == AdjMessage.FROMFR){
-                  //remove incomingMsg.getSourceId from RF positionList
-                } else if(incomingMsg.getMessage() == AdjMessage.FROMRF){
-                  //remove incomingMsg.getSourceId from FR positionList
-                } else{ //incomingMsg.getMessage() == AdjMessage.FROMRR
-                  //remove incomingMsg.getSourceId from FF positionList
-                }
-            }
+            responseToDeadVertex(msgIterator);
         }
         voteToHalt();
     }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleAddVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleAddVertex.java
new file mode 100644
index 0000000..b02ea06
--- /dev/null
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleAddVertex.java
@@ -0,0 +1,118 @@
+package edu.uci.ics.genomix.pregelix.operator.bubblemerge;
+
+import java.util.Iterator;
+import org.apache.hadoop.io.NullWritable;
+
+import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.PositionListWritable;
+import edu.uci.ics.genomix.type.PositionWritable;
+import edu.uci.ics.pregelix.api.graph.Vertex;
+import edu.uci.ics.pregelix.api.job.PregelixJob;
+import edu.uci.ics.pregelix.api.util.BspUtils;
+import edu.uci.ics.genomix.pregelix.client.Client;
+import edu.uci.ics.genomix.pregelix.format.DataCleanInputFormat;
+import edu.uci.ics.genomix.pregelix.format.DataCleanOutputFormat;
+import edu.uci.ics.genomix.pregelix.io.MessageWritable;
+import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+
+/*
+ * vertexId: BytesWritable
+ * vertexValue: ByteWritable
+ * edgeValue: NullWritable
+ * message: MessageWritable
+ * 
+ * DNA:
+ * A: 00
+ * C: 01
+ * G: 10
+ * T: 11
+ * 
+ * succeed node
+ *  A 00000001 1
+ *  G 00000010 2
+ *  C 00000100 4
+ *  T 00001000 8
+ * precursor node
+ *  A 00010000 16
+ *  G 00100000 32
+ *  C 01000000 64
+ *  T 10000000 128
+ *  
+ * For example, ONE LINE in input file: 00,01,10    0001,0010,
+ * That means that vertexId is ACG, its succeed node is A and its precursor node is C.
+ * The succeed node and precursor node will be stored in vertexValue and we don't use edgeValue.
+ * The details about message are in edu.uci.ics.pregelix.example.io.MessageWritable. 
+ */
+/**
+ *  Remove tip or single node when l > constant
+ */
+public class BubbleAddVertex extends
+        Vertex<PositionWritable, ValueStateWritable, NullWritable, MessageWritable> {
+    public static final String KMER_SIZE = "BubbleAddVertex.kmerSize";
+    public static int kmerSize = -1;
+   
+    /**
+     * initiate kmerSize, length
+     */
+    public void initVertex() {
+        if (kmerSize == -1)
+            kmerSize = getContext().getConfiguration().getInt(KMER_SIZE, 5);
+    }
+
+    @SuppressWarnings("unchecked")
+    @Override
+    public void compute(Iterator<MessageWritable> msgIterator) {
+        initVertex(); 
+        if(getSuperstep() == 1){
+            if(getVertexId().getReadID() == 1 && getVertexId().getPosInRead() == 2){
+                getVertexValue().getFFList().append(2, (byte)1);
+                
+                //add tip vertex
+                @SuppressWarnings("rawtypes")
+                Vertex vertex = (Vertex) BspUtils.createVertex(getContext().getConfiguration());
+                vertex.getMsgList().clear();
+                vertex.getEdges().clear();
+                PositionWritable vertexId = new PositionWritable();
+                ValueStateWritable vertexValue = new ValueStateWritable();
+                /**
+                 * set the src vertex id
+                 */
+                vertexId.set(2, (byte)1);
+                vertex.setVertexId(vertexId);
+                /**
+                 * set the vertex value
+                 */
+                byte[] array = { 'T', 'A', 'G', 'C', 'C', 'A', 'G'}; //TAGCCAG
+                KmerBytesWritable kmer = new KmerBytesWritable(array.length); 
+                kmer.setByRead(array, 0);
+                vertexValue.setMergeChain(kmer);
+                PositionListWritable plist = new PositionListWritable();
+                plist.append(new PositionWritable(1, (byte)2));
+                vertexValue.setRRList(plist);
+                PositionListWritable plist2 = new PositionListWritable();
+                plist2.append(new PositionWritable(1, (byte)4));
+                vertexValue.setFFList(plist2);
+                vertex.setVertexValue(vertexValue);
+                
+                addVertex(vertexId, vertex);
+            }
+            if(getVertexId().getReadID() == 1 && getVertexId().getPosInRead() == 4)
+                getVertexValue().getRRList().append(2, (byte)1);
+        }
+        voteToHalt();
+    }
+
+    public static void main(String[] args) throws Exception {
+        PregelixJob job = new PregelixJob(BubbleAddVertex.class.getSimpleName());
+        job.setVertexClass(BubbleAddVertex.class);
+        /**
+         * BinaryInput and BinaryOutput
+         */
+        job.setVertexInputFormatClass(DataCleanInputFormat.class);
+        job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
+        job.setDynamicVertexValueSize(true);
+        job.setOutputKeyClass(PositionWritable.class);
+        job.setOutputValueClass(ValueStateWritable.class);
+        Client.run(args, job);
+    }
+}
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 e16cd20..f64c36d 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
@@ -7,6 +7,7 @@
 
 import org.apache.hadoop.io.NullWritable;
 
+import edu.uci.ics.genomix.type.KmerBytesWritableFactory;
 import edu.uci.ics.genomix.type.PositionWritable;
 import edu.uci.ics.pregelix.api.graph.Vertex;
 import edu.uci.ics.pregelix.api.job.PregelixJob;
@@ -58,11 +59,14 @@
 
     private MergeBubbleMessageWritable incomingMsg = new MergeBubbleMessageWritable();
     private MergeBubbleMessageWritable outgoingMsg = new MergeBubbleMessageWritable();
-
+    private KmerBytesWritableFactory kmerFactory = new KmerBytesWritableFactory(1);
+    
+    private Iterator<PositionWritable> iterator;
+    private PositionWritable pos = new PositionWritable();
     private PositionWritable destVertexId = new PositionWritable();
     private Iterator<PositionWritable> posIterator;
-    private Map<PositionWritable, ArrayList<MergeBubbleMessageWritable>> receivedMsg = new HashMap<PositionWritable, ArrayList<MergeBubbleMessageWritable>>();
-    private ArrayList<MergeBubbleMessageWritable> tmpMsg = new ArrayList<MergeBubbleMessageWritable>();
+    private Map<PositionWritable, ArrayList<MergeBubbleMessageWritable>> receivedMsgMap = new HashMap<PositionWritable, ArrayList<MergeBubbleMessageWritable>>();
+    private ArrayList<MergeBubbleMessageWritable> receivedMsgList = new ArrayList<MergeBubbleMessageWritable>();
     
     /**
      * initiate kmerSize, maxIteration
@@ -101,17 +105,93 @@
         }
     }
     
+    /**
+     * broadcast kill self to all neighbers  Pre-condition: vertex is a path vertex 
+     */
+    public void broadcaseKillself(){
+        outgoingMsg.setSourceVertexId(getVertexId());
+        
+        if(getVertexValue().getFFList().getCountOfPosition() > 0) // #FFList() > 0
+            outgoingMsg.setMessage(AdjMessage.FROMFF);
+        else // #FRList() > 0
+            outgoingMsg.setMessage(AdjMessage.FROMFR);
+        sendMsg(incomingMsg.getSourceVertexId(), outgoingMsg);
+        
+        if(getVertexValue().getRFList().getCountOfPosition() > 0) // #RFList() > 0
+            outgoingMsg.setMessage(AdjMessage.FROMRF);
+        else // #RRList() > 0
+            outgoingMsg.setMessage(AdjMessage.FROMRR);
+        sendMsg(incomingMsg.getStartVertexId(), outgoingMsg);
+        
+        deleteVertex(getVertexId());
+    }
+    
+    /**
+     * do some remove operations on adjMap after receiving the info about dead Vertex
+     */
+    public void responseToDeadVertex(Iterator<MergeBubbleMessageWritable> msgIterator){
+        while (msgIterator.hasNext()) {
+            incomingMsg = msgIterator.next();
+            if(incomingMsg.getMessage() == AdjMessage.FROMFF){
+                //remove incomingMsg.getSourceId from RR positionList
+                iterator = getVertexValue().getRRList().iterator();
+                while(iterator.hasNext()){
+                    pos = iterator.next();
+                    if(pos.equals(incomingMsg.getSourceVertexId())){
+                        iterator.remove();
+                        break;
+                    }
+                }
+            } else if(incomingMsg.getMessage() == AdjMessage.FROMFR){
+                //remove incomingMsg.getSourceId from RF positionList
+                iterator = getVertexValue().getRFList().iterator();
+                while(iterator.hasNext()){
+                    pos = iterator.next();
+                    if(pos.equals(incomingMsg.getSourceVertexId())){
+                        iterator.remove();
+                        break;
+                    }
+                }
+            } else if(incomingMsg.getMessage() == AdjMessage.FROMRF){
+                //remove incomingMsg.getSourceId from FR positionList
+                iterator = getVertexValue().getFRList().iterator();
+                while(iterator.hasNext()){
+                    pos = iterator.next();
+                    if(pos.equals(incomingMsg.getSourceVertexId())){
+                        iterator.remove();
+                        break;
+                    }
+                }
+            } else{ //incomingMsg.getMessage() == AdjMessage.FROMRR
+                //remove incomingMsg.getSourceId from FF positionList
+                iterator = getVertexValue().getFFList().iterator();
+                while(iterator.hasNext()){
+                    pos = iterator.next();
+                    if(pos.equals(incomingMsg.getSourceVertexId())){
+                        iterator.remove();
+                        break;
+                    }
+                }
+            }
+        }
+    }
+    
+    @SuppressWarnings("unchecked")
     @Override
     public void compute(Iterator<MergeBubbleMessageWritable> msgIterator) {
         initVertex();
         if (getSuperstep() == 1) {
-            if(VertexUtil.isHeadVertex(getVertexValue())){
+            if(VertexUtil.isHeadVertex(getVertexValue())
+                    || VertexUtil.isHeadWithoutIndegree(getVertexValue())){
+                outgoingMsg.setMessage(AdjMessage.NON);
                 outgoingMsg.setSourceVertexId(getVertexId());
                 sendMsgToAllNextNodes(getVertexValue());
             }
         } else if (getSuperstep() == 2){
             while (msgIterator.hasNext()) {
+                incomingMsg = msgIterator.next();
                 if(VertexUtil.isPathVertex(getVertexValue())){
+                    outgoingMsg.setMessage(AdjMessage.NON);
                     outgoingMsg.setStartVertexId(incomingMsg.getSourceVertexId());
                     outgoingMsg.setSourceVertexId(getVertexId());
                     outgoingMsg.setChainVertexId(getVertexValue().getMergeChain());
@@ -122,57 +202,71 @@
         } else if (getSuperstep() == 3){
             while (msgIterator.hasNext()) {
                 incomingMsg = msgIterator.next();
-                if(!receivedMsg.containsKey(incomingMsg.getStartVertexId())){
-                    tmpMsg.clear();
-                    tmpMsg.add(incomingMsg);
-                    receivedMsg.put(incomingMsg.getStartVertexId(), tmpMsg);
+                if(!receivedMsgMap.containsKey(incomingMsg.getStartVertexId())){
+                    receivedMsgList.clear();
+                    receivedMsgList.add(incomingMsg);
+                    receivedMsgMap.put(incomingMsg.getStartVertexId(), (ArrayList<MergeBubbleMessageWritable>)receivedMsgList.clone());
                 }
                 else{
-                    tmpMsg.clear();
-                    tmpMsg.addAll(receivedMsg.get(incomingMsg.getStartVertexId()));
-                    tmpMsg.add(incomingMsg);
-                    receivedMsg.put(incomingMsg.getStartVertexId(), tmpMsg);
+                    receivedMsgList.clear();
+                    receivedMsgList.addAll(receivedMsgMap.get(incomingMsg.getStartVertexId()));
+                    receivedMsgList.add(incomingMsg);
+                    receivedMsgMap.put(incomingMsg.getStartVertexId(), (ArrayList<MergeBubbleMessageWritable>)receivedMsgList.clone());
                 }
             }
-            for(PositionWritable prevId : receivedMsg.keySet()){
-                tmpMsg = receivedMsg.get(prevId);
-                if(tmpMsg.size() > 1){
+            for(PositionWritable prevId : receivedMsgMap.keySet()){
+                receivedMsgList = receivedMsgMap.get(prevId);
+                if(receivedMsgList.size() > 1){
                     //find the node with largest length of mergeChain
                     boolean flag = true; //the same length
-                    int maxLength = tmpMsg.get(0).getLengthOfChain();
-                    PositionWritable max = tmpMsg.get(0).getSourceVertexId();
-                    for(int i = 1; i < tmpMsg.size(); i++){
-                        if(tmpMsg.get(i).getLengthOfChain() != maxLength)
+                    int maxLength = receivedMsgList.get(0).getLengthOfChain();
+                    PositionWritable max = receivedMsgList.get(0).getSourceVertexId();
+                    PositionWritable secondMax = receivedMsgList.get(0).getSourceVertexId();
+                    for(int i = 1; i < receivedMsgList.size(); i++){
+                        if(receivedMsgList.get(i).getLengthOfChain() != maxLength)
                             flag = false;
-                        if(tmpMsg.get(i).getLengthOfChain() > maxLength){
-                            maxLength = tmpMsg.get(i).getLengthOfChain();
-                            max = tmpMsg.get(i).getSourceVertexId();
+                        if(receivedMsgList.get(i).getLengthOfChain() >= maxLength){
+                            maxLength = receivedMsgList.get(i).getLengthOfChain();
+                            secondMax.set(max);
+                            max = receivedMsgList.get(i).getSourceVertexId();
                         }
                     }
-                    //send merge or unchange Message to node with largest length
+                    //send unchange or merge Message to node with largest length
                     if(flag == true){
-                        //send unchange Message to node with largest length
-                        //we can send no message to complete this step
-                        //send delete Message to node which doesn't have largest length
-                        for(int i = 0; i < tmpMsg.size(); i++){
-                            if(tmpMsg.get(i).getSourceVertexId().compareTo(max) != 0){
+                        //1. send unchange Message to node with largest length
+                        //   we can send no message to complete this step
+                        //2. send delete Message to node which doesn't have largest length
+                        for(int i = 0; i < receivedMsgList.size(); i++){
+                            //if(receivedMsgList.get(i).getSourceVertexId().compareTo(max) != 0)
+                            if(receivedMsgList.get(i).getSourceVertexId().compareTo(secondMax) == 0){ 
                                 outgoingMsg.setMessage(AdjMessage.KILL);
-                                sendMsg(tmpMsg.get(i).getSourceVertexId(), outgoingMsg);
-                            } else {
+                                outgoingMsg.setStartVertexId(prevId);
+                                outgoingMsg.setSourceVertexId(getVertexId());
+                                sendMsg(secondMax, outgoingMsg);
+                            } else if(receivedMsgList.get(i).getSourceVertexId().compareTo(max) == 0){
                                 outgoingMsg.setMessage(AdjMessage.UNCHANGE);
-                                sendMsg(tmpMsg.get(i).getSourceVertexId(), outgoingMsg);
+                                sendMsg(max, outgoingMsg);
                             }
                         }
                     } else{
                         //send merge Message to node with largest length
-                        for(int i = 0; i < tmpMsg.size(); i++){
-                            if(tmpMsg.get(i).getSourceVertexId().compareTo(max) != 0){
+                        for(int i = 0; i < receivedMsgList.size(); i++){
+                            //if(receivedMsgList.get(i).getSourceVertexId().compareTo(max) != 0)
+                            if(receivedMsgList.get(i).getSourceVertexId().compareTo(secondMax) == 0){
                                 outgoingMsg.setMessage(AdjMessage.KILL);
-                                sendMsg(tmpMsg.get(i).getSourceVertexId(), outgoingMsg);
-                            } else {
+                                outgoingMsg.setStartVertexId(prevId);
+                                outgoingMsg.setSourceVertexId(getVertexId());
+                                sendMsg(receivedMsgList.get(i).getSourceVertexId(), outgoingMsg);
+                            } else if(receivedMsgList.get(i).getSourceVertexId().compareTo(max) == 0){
                                 outgoingMsg.setMessage(AdjMessage.MERGE);
                                 /* add other node in message */
-                                sendMsg(tmpMsg.get(i).getSourceVertexId(), outgoingMsg);
+                                for(int j = 0; j < receivedMsgList.size(); i++){
+                                    if(receivedMsgList.get(j).getSourceVertexId().compareTo(secondMax) == 0){
+                                        outgoingMsg.setChainVertexId(receivedMsgList.get(j).getChainVertexId());
+                                        break;
+                                    }
+                                }
+                                sendMsg(receivedMsgList.get(i).getSourceVertexId(), outgoingMsg);
                             }
                         }
                     }
@@ -182,11 +276,15 @@
             while (msgIterator.hasNext()) {
                 incomingMsg = msgIterator.next();
                 if(incomingMsg.getMessage() == AdjMessage.KILL){
-                    deleteVertex(getVertexId());
+                    broadcaseKillself();
                 } else if (incomingMsg.getMessage() == AdjMessage.MERGE){
                     //merge with small node
+                    getVertexValue().setMergeChain(kmerFactory.mergeTwoKmer(getVertexValue().getMergeChain(), 
+                            incomingMsg.getChainVertexId()));
                 }
             }
+        } else if(getSuperstep() == 5){
+            responseToDeadVertex(msgIterator);
         }
         voteToHalt();
     }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java
index 84c7f52..a4730c0 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java
@@ -136,6 +136,14 @@
             sendMsgToAllPreviousNodes(getVertexValue());
             voteToHalt();
         }
+        if (VertexUtil.isHeadWithoutIndegree(getVertexValue())){
+            outgoingMsg.setMessage(Message.START);
+            sendMsg(getVertexId(), outgoingMsg); //send to itself
+        }
+        if (VertexUtil.isRearWithoutOutdegree(getVertexValue())){
+            outgoingMsg.setMessage(Message.END);
+            sendMsg(getVertexId(), outgoingMsg); //send to itself
+        }
     }
 
     /**
@@ -143,7 +151,9 @@
      */
     public void initState(Iterator<MessageWritable> msgIterator) {
         while (msgIterator.hasNext()) {
-            if (!VertexUtil.isPathVertex(getVertexValue())) {
+            if (!VertexUtil.isPathVertex(getVertexValue())
+                    && !VertexUtil.isHeadWithoutIndegree(getVertexValue())
+                    && !VertexUtil.isRearWithoutOutdegree(getVertexValue())) {
                 msgIterator.next();
                 voteToHalt();
             } else {
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/NaiveAlgorithmForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/NaiveAlgorithmForPathMergeVertex.java
index 3d0d395..f27c140 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/NaiveAlgorithmForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/NaiveAlgorithmForPathMergeVertex.java
@@ -155,8 +155,8 @@
     public void initState(Iterator<MessageWritable> msgIterator) {
         while (msgIterator.hasNext()) {
             if (!VertexUtil.isPathVertex(getVertexValue()) 
-                    || !VertexUtil.isHeadWithoutIndegree(getVertexValue())
-                    || !VertexUtil.isRearWithoutOutdegree(getVertexValue())) {
+                    && !VertexUtil.isHeadWithoutIndegree(getVertexValue())
+                    && !VertexUtil.isRearWithoutOutdegree(getVertexValue())) {
                 msgIterator.next();
                 voteToHalt();
             } else {
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipAddVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipAddVertex.java
index 2966bb1..8c9fdc5 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipAddVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipAddVertex.java
@@ -3,6 +3,7 @@
 import java.util.Iterator;
 import org.apache.hadoop.io.NullWritable;
 
+import edu.uci.ics.genomix.type.KmerBytesWritable;
 import edu.uci.ics.genomix.type.PositionListWritable;
 import edu.uci.ics.genomix.type.PositionWritable;
 import edu.uci.ics.pregelix.api.graph.Vertex;
@@ -81,6 +82,10 @@
                 /**
                  * set the vertex value
                  */
+                byte[] array = { 'G', 'A', 'A'};
+                KmerBytesWritable kmer = new KmerBytesWritable(array.length);
+                kmer.setByRead(array, 0);
+                vertexValue.setMergeChain(kmer);
                 PositionListWritable plist = new PositionListWritable();
                 plist.append(new PositionWritable(1, (byte)4));
                 vertexValue.setRRList(plist);
@@ -93,8 +98,8 @@
     }
 
     public static void main(String[] args) throws Exception {
-        PregelixJob job = new PregelixJob(TipRemoveVertex.class.getSimpleName());
-        job.setVertexClass(TipRemoveVertex.class);
+        PregelixJob job = new PregelixJob(TipAddVertex.class.getSimpleName());
+        job.setVertexClass(TipAddVertex.class);
         /**
          * BinaryInput and BinaryOutput
          */
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java
index 0d5e518..4901269 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java
@@ -55,8 +55,11 @@
     private MessageWritable incomingMsg = new MessageWritable();
     private MessageWritable outgoingMsg = new MessageWritable();
     
-    Iterator<PositionWritable> iterator;
-    PositionWritable pos = new PositionWritable();
+    private Iterator<PositionWritable> iterator;
+    private PositionWritable pos = new PositionWritable();
+    private PositionWritable destVertexId = new PositionWritable();
+    private Iterator<PositionWritable> posIterator;
+    
     /**
      * initiate kmerSize, length
      */
@@ -67,28 +70,51 @@
             length = getContext().getConfiguration().getInt(LENGTH, kmerSize); //kmerSize + 5
         outgoingMsg.reset();
     }
+    
+    /**
+     * get destination vertex
+     */
+    public PositionWritable getNextDestVertexId(ValueStateWritable value) {
+        if(value.getFFList().getCountOfPosition() > 0) // #FFList() > 0
+            posIterator = value.getFFList().iterator();
+        else // #FRList() > 0
+            posIterator = value.getFRList().iterator();
+        return posIterator.next();
+    }
+
+    public PositionWritable getPreDestVertexId(ValueStateWritable value) {
+        if(value.getRFList().getCountOfPosition() > 0) // #RFList() > 0
+            posIterator = value.getRFList().iterator();
+        else // #RRList() > 0
+            posIterator = value.getRRList().iterator();
+        return posIterator.next();
+    }
 
     @Override
     public void compute(Iterator<MessageWritable> msgIterator) {
         initVertex(); 
         if(getSuperstep() == 1){
             if(VertexUtil.isIncomingTipVertex(getVertexValue())){
-            	if(getVertexValue().getLengthOfMergeChain() >= length){
+            	if(getVertexValue().getLengthOfMergeChain() <= length){
             		if(getVertexValue().getFFList().getCountOfPosition() > 0)
             			outgoingMsg.setMessage(AdjMessage.FROMFF);
             		else if(getVertexValue().getFRList().getCountOfPosition() > 0)
             			outgoingMsg.setMessage(AdjMessage.FROMFR);
             		outgoingMsg.setSourceVertexId(getVertexId());
+            		destVertexId.set(getNextDestVertexId(getVertexValue()));
+            		sendMsg(destVertexId, outgoingMsg);
             		deleteVertex(getVertexId());
             	}
             }
             else if(VertexUtil.isOutgoingTipVertex(getVertexValue())){
-                if(getVertexValue().getLengthOfMergeChain() > length){
+                if(getVertexValue().getLengthOfMergeChain() <= length){
                     if(getVertexValue().getRFList().getCountOfPosition() > 0)
                         outgoingMsg.setMessage(AdjMessage.FROMRF);
                     else if(getVertexValue().getRRList().getCountOfPosition() > 0)
                         outgoingMsg.setMessage(AdjMessage.FROMRR);
                     outgoingMsg.setSourceVertexId(getVertexId());
+                    destVertexId.set(getPreDestVertexId(getVertexValue()));
+                    sendMsg(destVertexId, outgoingMsg);
                     deleteVertex(getVertexId());
                 }
             }
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 9f59282..785c7f5 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
@@ -11,6 +11,10 @@
 import edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeInputFormat;
 import edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeOutputFormat;
 import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+import edu.uci.ics.genomix.pregelix.operator.bridgeremove.BridgeAddVertex;
+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.LogAlgorithmForPathMergeVertex;
 import edu.uci.ics.genomix.pregelix.operator.pathmerge.NaiveAlgorithmForPathMergeVertex;
 import edu.uci.ics.genomix.pregelix.operator.pathmerge.P3ForPathMergeVertex;
@@ -79,7 +83,7 @@
         PregelixJob job = new PregelixJob(jobName);
         job.setVertexClass(TipAddVertex.class);
         job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
-        job.setVertexOutputFormatClass(NaiveAlgorithmForPathMergeOutputFormat.class);
+        job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
         job.setDynamicVertexValueSize(true);
         job.setOutputKeyClass(PositionWritable.class);
         job.setOutputValueClass(ValueStateWritable.class);
@@ -108,13 +112,85 @@
         generateTipRemoveGraphJob("TipRemoveGraph", outputBase
                 + "TipRemoveGraph.xml");
     }
+    
+    private static void generateBridgeAddGraphJob(String jobName, String outputPath) throws IOException {
+        PregelixJob job = new PregelixJob(jobName);
+        job.setVertexClass(BridgeAddVertex.class);
+        job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
+        job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
+        job.setDynamicVertexValueSize(true);
+        job.setOutputKeyClass(PositionWritable.class);
+        job.setOutputValueClass(ValueStateWritable.class);
+        job.getConfiguration().setInt(BridgeAddVertex.KMER_SIZE, 3);
+        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
+    }
 
+    private static void genBridgeAddGraph() throws IOException {
+        generateBridgeAddGraphJob("BridgeAddGraph", outputBase
+                + "BridgeAddGraph.xml");
+    }
+
+    private static void generateBridgeRemoveGraphJob(String jobName, String outputPath) throws IOException {
+        PregelixJob job = new PregelixJob(jobName);
+        job.setVertexClass(BridgeRemoveVertex.class);
+        job.setVertexInputFormatClass(DataCleanInputFormat.class);
+        job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
+        job.setDynamicVertexValueSize(true);
+        job.setOutputKeyClass(PositionWritable.class);
+        job.setOutputValueClass(ValueStateWritable.class);
+        job.getConfiguration().setInt(TipRemoveVertex.KMER_SIZE, 3);
+        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
+    }
+
+    private static void genBridgeRemoveGraph() throws IOException {
+        generateBridgeRemoveGraphJob("BridgeRemoveGraph", outputBase
+                + "BridgeRemoveGraph.xml");
+    }
+    
+    private static void generateBubbleAddGraphJob(String jobName, String outputPath) throws IOException {
+        PregelixJob job = new PregelixJob(jobName);
+        job.setVertexClass(BubbleAddVertex.class);
+        job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
+        job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
+        job.setDynamicVertexValueSize(true);
+        job.setOutputKeyClass(PositionWritable.class);
+        job.setOutputValueClass(ValueStateWritable.class);
+        job.getConfiguration().setInt(BubbleAddVertex.KMER_SIZE, 3);
+        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
+    }
+
+    private static void genBubbleAddGraph() throws IOException {
+        generateBubbleAddGraphJob("BubbleAddGraph", outputBase
+                + "BubbleAddGraph.xml");
+    }
+    
+    private static void generateBubbleMergeGraphJob(String jobName, String outputPath) throws IOException {
+        PregelixJob job = new PregelixJob(jobName);
+        job.setVertexClass(BubbleMergeVertex.class);
+        job.setVertexInputFormatClass(DataCleanInputFormat.class);
+        job.setVertexOutputFormatClass(DataCleanOutputFormat.class);
+        job.setDynamicVertexValueSize(true);
+        job.setOutputKeyClass(PositionWritable.class);
+        job.setOutputValueClass(ValueStateWritable.class);
+        job.getConfiguration().setInt(BubbleMergeVertex.KMER_SIZE, 3);
+        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
+    }
+
+    private static void genBubbleMergeGraph() throws IOException {
+        generateBubbleMergeGraphJob("BubbleMergeGraph", outputBase
+                + "BubbleMergeGraph.xml");
+    }
+    
     public static void main(String[] args) throws IOException {
-        genNaiveAlgorithmForMergeGraph();
-        //genLogAlgorithmForMergeGraph();
+        //genNaiveAlgorithmForMergeGraph();
+        genLogAlgorithmForMergeGraph();
         //genP3ForMergeGraph();
         //genTipAddGraph();
         //genTipRemoveGraph();
+        //genBridgeAddGraph();
+        //genBridgeRemoveGraph();
+        //genBubbleAddGraph();
+        //genBubbleMergeGraph();
     }
 
 }
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java
index 49a5ed0..f86ef23 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java
@@ -45,7 +45,7 @@
 
     public static final String PreFix = "data/input"; //"graphbuildresult";
     public static final String[] TestDir = { PreFix + File.separator
-    + "tipremove"};/*, PreFix + File.separator
+    + "read"};/*, PreFix + File.separator
             /*+ "CyclePath"};, PreFix + File.separator
             + "SimplePath", PreFix + File.separator
             + "SinglePath", PreFix + File.separator
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/graphbuilding/JobRunStepByStepTest.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/graphbuilding/JobRunStepByStepTest.java
index c5aa0eb..1984a2e 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/graphbuilding/JobRunStepByStepTest.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/graphbuilding/JobRunStepByStepTest.java
@@ -50,7 +50,7 @@
     private static final String ACTUAL_RESULT_DIR = "actual";
     private static final String PATH_TO_HADOOP_CONF = "src/test/resources/hadoop/conf";
 
-    private static final String DATA_INPUT_PATH = "data/graphbuild.test/tworeads.txt";
+    private static final String DATA_INPUT_PATH = "data/graphbuild.test/read.txt";
     private static final String HDFS_INPUT_PATH = "/webmap";
     private static final String HDFS_OUTPUT_PATH = "/webmap_result";
 
@@ -71,8 +71,8 @@
 
     @Test
     public void TestAll() throws Exception {
-        TestEndToEnd();
-        //TestUnMergedNode();
+        //TestEndToEnd();
+        TestUnMergedNode();
     }
 
     public void TestEndToEnd() throws Exception {
diff --git a/genomix/genomix-pregelix/src/test/resources/jobs/NaiveAlgorithmForMergeGraph.xml b/genomix/genomix-pregelix/src/test/resources/jobs/LogAlgorithmForMergeGraph.xml
similarity index 96%
rename from genomix/genomix-pregelix/src/test/resources/jobs/NaiveAlgorithmForMergeGraph.xml
rename to genomix/genomix-pregelix/src/test/resources/jobs/LogAlgorithmForMergeGraph.xml
index 39ed64e..2d6b9c4 100644
--- a/genomix/genomix-pregelix/src/test/resources/jobs/NaiveAlgorithmForMergeGraph.xml
+++ b/genomix/genomix-pregelix/src/test/resources/jobs/LogAlgorithmForMergeGraph.xml
@@ -3,7 +3,6 @@
 <property><name>mapred.queue.default.acl-administer-jobs</name><value>*</value></property>
 <property><name>mapred.skip.map.auto.incr.proc.count</name><value>true</value></property>
 <property><name>mapred.jobtracker.instrumentation</name><value>org.apache.hadoop.mapred.JobTrackerMetricsInst</value></property>
-<property><name>NaiveAlgorithmForPathMergeVertex.kmerSize</name><value>3</value></property>
 <property><name>mapred.skip.reduce.auto.incr.proc.count</name><value>true</value></property>
 <property><name>fs.hsftp.impl</name><value>org.apache.hadoop.hdfs.HsftpFileSystem</value></property>
 <property><name>mapred.submit.replication</name><value>10</value></property>
@@ -36,7 +35,7 @@
 <property><name>mapred.reduce.parallel.copies</name><value>5</value></property>
 <property><name>fs.checkpoint.size</name><value>67108864</value></property>
 <property><name>mapred.job.reduce.input.buffer.percent</name><value>0.0</value></property>
-<property><name>mapred.job.name</name><value>NaiveAlgorithmForMergeGraph</value></property>
+<property><name>mapred.job.name</name><value>LogAlgorithmForMergeGraph</value></property>
 <property><name>local.cache.size</name><value>10737418240</value></property>
 <property><name>fs.s3n.impl</name><value>org.apache.hadoop.fs.s3native.NativeS3FileSystem</value></property>
 <property><name>mapred.userlog.limit.kb</name><value>0</value></property>
@@ -65,7 +64,7 @@
 <property><name>hadoop.rpc.socket.factory.class.default</name><value>org.apache.hadoop.net.StandardSocketFactory</value></property>
 <property><name>mapred.reduce.tasks</name><value>1</value></property>
 <property><name>topology.node.switch.mapping.impl</name><value>org.apache.hadoop.net.ScriptBasedMapping</value></property>
-<property><name>pregelix.vertexClass</name><value>edu.uci.ics.genomix.pregelix.operator.pathmerge.NaiveAlgorithmForPathMergeVertex</value></property>
+<property><name>pregelix.vertexClass</name><value>edu.uci.ics.genomix.pregelix.operator.pathmerge.LogAlgorithmForPathMergeVertex</value></property>
 <property><name>mapred.skip.reduce.max.skip.groups</name><value>0</value></property>
 <property><name>io.file.buffer.size</name><value>4096</value></property>
 <property><name>mapred.jobtracker.maxtasks.per.job</name><value>-1</value></property>
@@ -104,6 +103,7 @@
 <property><name>mapred.task.profile.reduces</name><value>0-2</value></property>
 <property><name>webinterface.private.actions</name><value>false</value></property>
 <property><name>hadoop.tmp.dir</name><value>/tmp/hadoop-${user.name}</value></property>
+<property><name>LogAlgorithmForPathMergeVertex.kmerSize</name><value>3</value></property>
 <property><name>mapred.output.compression.codec</name><value>org.apache.hadoop.io.compress.DefaultCodec</value></property>
 <property><name>mapred.skip.attempts.to.start.skipping</name><value>2</value></property>
 <property><name>mapred.temp.dir</name><value>${hadoop.tmp.dir}/mapred/temp</value></property>
@@ -117,12 +117,12 @@
 <property><name>mapred.line.input.format.linespermap</name><value>1</value></property>
 <property><name>job.end.retry.attempts</name><value>0</value></property>
 <property><name>ipc.client.idlethreshold</name><value>4000</value></property>
-<property><name>pregelix.vertexOutputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.DataCleanOutputFormat</value></property>
+<property><name>pregelix.vertexOutputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.LogAlgorithmForPathMergeOutputFormat</value></property>
 <property><name>mapred.reduce.copy.backoff</name><value>300</value></property>
 <property><name>mapred.map.tasks.speculative.execution</name><value>true</value></property>
 <property><name>mapred.inmem.merge.threshold</name><value>1000</value></property>
 <property><name>hadoop.logfile.size</name><value>10000000</value></property>
-<property><name>pregelix.vertexInputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.DataCleanInputFormat</value></property>
+<property><name>pregelix.vertexInputFormatClass</name><value>edu.uci.ics.genomix.pregelix.format.LogAlgorithmForPathMergeInputFormat</value></property>
 <property><name>mapred.job.queue.name</name><value>default</value></property>
 <property><name>mapred.job.tracker.persist.jobstatus.active</name><value>false</value></property>
 <property><name>pregelix.incStateLength</name><value>true</value></property>