diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/pmcommon/PathNodeInitial.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/pmcommon/PathNodeInitial.java
new file mode 100644
index 0000000..97563de
--- /dev/null
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/pmcommon/PathNodeInitial.java
@@ -0,0 +1,209 @@
+/*
+ * Copyright 2009-2012 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package edu.uci.ics.genomix.hadoop.pmcommon;
+
+import java.io.IOException;
+import java.util.Iterator;
+
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.conf.Configured;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.io.NullWritable;
+import org.apache.hadoop.mapred.FileInputFormat;
+import org.apache.hadoop.mapred.FileOutputFormat;
+import org.apache.hadoop.mapred.JobClient;
+import org.apache.hadoop.mapred.JobConf;
+import org.apache.hadoop.mapred.MapReduceBase;
+import org.apache.hadoop.mapred.Mapper;
+import org.apache.hadoop.mapred.OutputCollector;
+import org.apache.hadoop.mapred.Reducer;
+import org.apache.hadoop.mapred.Reporter;
+import org.apache.hadoop.mapred.RunningJob;
+import org.apache.hadoop.mapred.SequenceFileInputFormat;
+import org.apache.hadoop.mapred.SequenceFileOutputFormat;
+import org.apache.hadoop.util.Tool;
+import org.apache.hadoop.util.ToolRunner;
+
+import edu.uci.ics.genomix.hadoop.graphclean.mergepaths.h3.MergePathsH3.MessageFlag;
+import edu.uci.ics.genomix.type.NodeWritable;
+import edu.uci.ics.genomix.type.PositionWritable;
+
+/*
+ * A map-reduce job to find all nodes that are part of a simple path and the mark the nodes that
+ * form their heads and tails.
+ */
+@SuppressWarnings("deprecation")
+public class PathNodeInitial extends Configured implements Tool {
+
+    public static class PathNodeInitialMapper extends MapReduceBase implements
+            Mapper<NodeWritable, NullWritable, PositionWritable, MessageWritableNodeWithFlag> {
+
+        private int KMER_SIZE;
+        private PositionWritable outputKey;
+        private MessageWritableNodeWithFlag outputValue;
+        private int inDegree;
+        private int outDegree;
+        private NodeWritable emptyNode;
+        
+        public PathNodeInitialMapper() {
+            
+        }
+
+        public void configure(JobConf conf) {
+            KMER_SIZE = conf.getInt("sizeKmer", 0);
+            outputValue = new MessageWritableNodeWithFlag(KMER_SIZE);
+            outputKey = new PositionWritable();
+            emptyNode = new NodeWritable();
+        }
+
+        @Override
+        public void map(NodeWritable key, NullWritable value,
+                OutputCollector<PositionWritable, MessageWritableNodeWithFlag> output, Reporter reporter)
+                throws IOException {
+            inDegree = key.inDegree();
+            outDegree = key.outDegree();
+            if (inDegree == 1 && outDegree == 1) {
+                // simple path nodes map themselves
+                outputValue.set(MessageFlag.FROM_SELF, key);
+                output.collect(key.getNodeID(), outputValue);
+                reporter.incrCounter("genomix", "path_nodes", 1);
+            } else if (outDegree == 1) {
+                // Not a path myself, but my successor might be one. Map forward successor
+                outputValue.set(MessageFlag.FROM_PREDECESSOR, emptyNode);
+                if (key.getFFList().getCountOfPosition() > 0) {
+                    outputKey.set(key.getFFList().getPosition(0));
+                } else {
+                    outputKey.set(key.getFRList().getPosition(0));
+                }
+                output.collect(outputKey, outputValue);
+            } else if (inDegree == 1) {
+                // Not a path myself, but my predecessor might be one.
+                outputValue.set(MessageFlag.FROM_SUCCESSOR, emptyNode);
+                if (key.getRRList().getCountOfPosition() > 0) {
+                    outputKey.set(key.getRRList().getPosition(0));
+                } else {
+                    outputKey.set(key.getRFList().getPosition(0));
+                }
+                output.collect(outputKey, outputValue);
+            }
+            else {
+                // TODO: all other nodes will not participate-- should they be collected in a "complete" output?
+            }
+        }
+    }
+
+    public static class PathNodeInitialReducer extends MapReduceBase implements
+            Reducer<PositionWritable, MessageWritableNodeWithFlag, PositionWritable, MessageWritableNodeWithFlag> {
+
+        private int KMER_SIZE;
+        private MessageWritableNodeWithFlag inputValue;
+        private MessageWritableNodeWithFlag outputValue;
+        private NodeWritable nodeToKeep;
+        private int count;
+        private byte flag;
+
+        public void configure(JobConf conf) {
+            KMER_SIZE = conf.getInt("sizeKmer", 0);
+            inputValue = new MessageWritableNodeWithFlag(KMER_SIZE);
+            outputValue = new MessageWritableNodeWithFlag(KMER_SIZE);
+            nodeToKeep = new NodeWritable(KMER_SIZE);
+        }
+
+        @Override
+        public void reduce(PositionWritable key, Iterator<MessageWritableNodeWithFlag> values,
+                OutputCollector<PositionWritable, MessageWritableNodeWithFlag> output, Reporter reporter)
+                throws IOException {
+
+            inputValue.set(values.next());
+            if (!values.hasNext()) {
+                if ((inputValue.getFlag() & MessageFlag.FROM_SELF) == MessageFlag.FROM_SELF) {
+                    // FROM_SELF => need to keep this PATH node
+                    output.collect(key, inputValue);
+                }
+            } else {
+                // multiple inputs => possible HEAD or TAIL to a path node. note if HEAD or TAIL node 
+                count = 0;
+                flag = MessageFlag.EMPTY_MESSAGE;
+                while (true) { // process values; break when no more
+                    count++;
+                    if ((inputValue.getFlag() & MessageFlag.FROM_SELF) == MessageFlag.FROM_SELF) {
+                        // SELF -> keep this node
+                        nodeToKeep.set(inputValue.getNode());
+                    } else if ((inputValue.getFlag() & MessageFlag.FROM_SUCCESSOR) == MessageFlag.FROM_SUCCESSOR) {
+                        flag |= MessageFlag.IS_TAIL;
+                        reporter.incrCounter("genomix", "path_nodes_tails", 1);
+                    } else if ((inputValue.getFlag() & MessageFlag.FROM_PREDECESSOR) == MessageFlag.FROM_PREDECESSOR) {
+                        flag |= MessageFlag.IS_HEAD;
+                        reporter.incrCounter("genomix", "path_nodes_heads", 1);
+                    }
+                    if (!values.hasNext()) {
+                        break;
+                    } else {
+                        inputValue = values.next();
+                    }
+                }
+                if (count < 2) {
+                    throw new IOException("Expected at least two nodes in PathNodeInitial reduce; saw "
+                            + String.valueOf(count));
+                }
+                if ((flag & MessageFlag.FROM_SELF) == MessageFlag.FROM_SELF) {
+                    // only map simple path nodes
+                    outputValue.set(flag, nodeToKeep);
+                    output.collect(key, outputValue);
+                    reporter.incrCounter("genomix", "path_nodes", 1);
+                }
+            }
+        }
+    }
+
+    /*
+     * Mark the head, tail, and simple path nodes in one map-reduce job.
+     */
+    public RunningJob run(String inputPath, String outputPath, JobConf baseConf) throws IOException {
+        JobConf conf = new JobConf(baseConf);
+        conf.setJarByClass(PathNodeInitial.class);
+        conf.setJobName("PathNodeInitial " + inputPath);
+
+        FileInputFormat.addInputPath(conf, new Path(inputPath));
+        FileOutputFormat.setOutputPath(conf, new Path(outputPath));
+
+        conf.setInputFormat(SequenceFileInputFormat.class);
+        conf.setOutputFormat(SequenceFileOutputFormat.class);
+
+        conf.setMapOutputKeyClass(PositionWritable.class);
+        conf.setMapOutputValueClass(MessageWritableNodeWithFlag.class);
+        conf.setOutputKeyClass(PositionWritable.class);
+        conf.setOutputValueClass(MessageWritableNodeWithFlag.class);
+
+        conf.setMapperClass(PathNodeInitialMapper.class);
+        conf.setReducerClass(PathNodeInitialReducer.class);
+
+        FileSystem.get(conf).delete(new Path(outputPath), true);
+
+        return JobClient.runJob(conf);
+    }
+
+    @Override
+    public int run(String[] arg0) throws Exception {
+        // TODO Auto-generated method stub
+        return 0;
+    }
+
+    public static void main(String[] args) throws Exception {
+        int res = ToolRunner.run(new Configuration(), new PathNodeInitial(), args);
+        System.exit(res);
+    }
+}
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h3/TestPathMergeH3.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h3/TestPathMergeH3.java
new file mode 100644
index 0000000..17c6b16
--- /dev/null
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h3/TestPathMergeH3.java
@@ -0,0 +1,79 @@
+package edu.uci.ics.genomix.hadoop.graphclean.mergepaths.h3;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.mapred.FileInputFormat;
+import org.apache.hadoop.mapred.FileOutputFormat;
+import org.apache.hadoop.mapred.JobConf;
+import org.junit.Test;
+
+import edu.uci.ics.genomix.hadoop.pmcommon.GenomixMiniClusterTest;
+import edu.uci.ics.genomix.hadoop.pmcommon.PathNodeInitial;
+import edu.uci.ics.genomix.hyracks.driver.Driver.Plan;
+import edu.uci.ics.genomix.hyracks.job.GenomixJobConf;
+
+@SuppressWarnings("deprecation")
+public class TestPathMergeH3 extends GenomixMiniClusterTest {
+    protected String LOCAL_SEQUENCE_FILE = "src/test/resources/data/webmap/text.txt";
+    protected String HDFS_SEQUENCE = "/00-sequence/";
+    protected String HDFS_GRAPHBUILD = "/01-graphbuild/";
+    protected String HDFS_MARKPATHS = "/02-pathmark/";
+    protected String HDFS_MERGED = "/03-pathmerge/";
+    
+    protected String GRAPHBUILD_FILE = "result.graphbuild.txt";
+    protected String PATHMARKS_FILE = "result.markpaths.txt";
+    protected String PATHMERGE_FILE = "result.mergepath.txt";
+    protected boolean regenerateGraph = false;
+    
+    {
+        KMER_LENGTH = 5;
+        READ_LENGTH = 8;
+        HDFS_PATHS = new ArrayList<String>(Arrays.asList(HDFS_SEQUENCE, HDFS_GRAPHBUILD, HDFS_MARKPATHS, HDFS_MERGED));
+        conf.setInt(GenomixJobConf.KMER_LENGTH, KMER_LENGTH);
+        conf.setInt(GenomixJobConf.READ_LENGTH, READ_LENGTH);
+    }
+
+    @Test
+    public void TestBuildGraph() throws Exception {
+        cleanUpOutput();
+        copyLocalToDFS(LOCAL_SEQUENCE_FILE, HDFS_SEQUENCE);
+        buildGraph();
+    }
+
+    @Test
+    public void TestMergeOneIteration() throws Exception {
+        cleanUpOutput();
+        if (regenerateGraph) {
+            copyLocalToDFS(LOCAL_SEQUENCE_FILE, HDFS_SEQUENCE);
+            buildGraph();
+            copyLocalToDFS(ACTUAL_ROOT + GRAPHBUILD_FILE + ".binmerge", HDFS_GRAPHBUILD);
+        } else {
+            copyLocalToDFS(EXPECTED_ROOT + GRAPHBUILD_FILE + ".binmerge", HDFS_GRAPHBUILD);
+        }
+        
+        PathNodeInitial inith3 = new PathNodeInitial();
+        inith3.run(HDFS_GRAPHBUILD, HDFS_MARKPATHS, conf);
+        copyResultsToLocal(HDFS_MARKPATHS, ACTUAL_ROOT + PATHMARKS_FILE, false, conf);
+
+        MergePathsH3Driver h3 = new MergePathsH3Driver();
+//        h3.run(HDFS_GRAPHBUILD, HDFS_MERGED, 2, KMER_LENGTH, 1, HADOOP_CONF_ROOT + "conf.xml", conf);
+        h3.run(HDFS_MARKPATHS, HDFS_MERGED, 2, KMER_LENGTH, 10, HADOOP_CONF_ROOT + "conf.xml", null);
+        copyResultsToLocal(HDFS_MERGED, ACTUAL_ROOT + PATHMERGE_FILE, false, conf);
+    }
+
+
+
+    public void buildGraph() throws Exception {
+        JobConf buildConf = new JobConf(conf);  // use a separate conf so we don't interfere with other jobs 
+        FileInputFormat.setInputPaths(buildConf, HDFS_SEQUENCE);
+        FileOutputFormat.setOutputPath(buildConf, new Path(HDFS_GRAPHBUILD));
+        buildConf.set(GenomixJobConf.OUTPUT_FORMAT, GenomixJobConf.OUTPUT_FORMAT_BINARY);
+        buildConf.set(GenomixJobConf.GROUPBY_TYPE, GenomixJobConf.GROUPBY_TYPE_PRECLUSTER);
+        driver.runJob(new GenomixJobConf(buildConf), Plan.BUILD_DEBRUJIN_GRAPH, true);
+        String fileFormat = buildConf.get(GenomixJobConf.OUTPUT_FORMAT);
+        boolean resultsAreText = GenomixJobConf.OUTPUT_FORMAT_TEXT.equalsIgnoreCase(fileFormat);
+        copyResultsToLocal(HDFS_GRAPHBUILD, ACTUAL_ROOT + GRAPHBUILD_FILE, resultsAreText, buildConf);
+    }
+}