diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/AllelePair.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
similarity index 100%
rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/AllelePair.java
rename to java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/ReadBackedPhasingWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
similarity index 100%
rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/ReadBackedPhasingWalker.java
rename to java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/SNPallelePair.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java
similarity index 100%
rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/SNPallelePair.java
rename to java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/DisjointSet.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/DisjointSet.java
deleted file mode 100644
index a46d423d3..000000000
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/DisjointSet.java
+++ /dev/null
@@ -1,101 +0,0 @@
-package org.broadinstitute.sting.playground.gatk.walkers.phasing;
-
-import java.util.*;
-
-/*
- * Copyright (c) 2010, The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-public class DisjointSet {
-    private ItemNode[] nodes;
-
-    public DisjointSet(int numItems) {
-        this.nodes = new ItemNode[numItems];
-        for (int i = 0; i < numItems; i++)
-            this.nodes[i] = new ItemNode(i);
-    }
-
-    public int findSet(int itemIndex) {
-        // Find itemIndex's root Node:
-        ItemNode curNode = nodes[itemIndex];
-        while (curNode.parent != null)
-          curNode = curNode.parent;
-        ItemNode root = curNode;
-
-        // Perform path compression:
-        curNode = nodes[itemIndex];
-        while (curNode != root) {
-          ItemNode next = curNode.parent;
-          curNode.parent = root;
-          curNode = next;
-        }
-
-        return root.itemIndex;
-    }
-
-    public boolean inSameSet(int x, int y) {
-        return (x == y || nodes[x].parent == nodes[y].parent || findSet(x) == findSet(y));
-    }
-
-    public Set<Integer> inSameSetAs(int x, Collection<Integer> testSet) {
-        Set<Integer> sameSetInds = new TreeSet<Integer>();
-
-        int xSet = findSet(x);
-        for (int t : testSet) {
-            if (findSet(t) == xSet)
-                sameSetInds.add(t);
-        }
-        return sameSetInds;
-    }
-
-    public void setUnion(int x, int y) {
-        link(findSet(x), findSet(y));
-    }
-
-    private void link(int x, int y) {
-        if (x == y)
-            return;
-
-        // Union by rank:
-        if (nodes[x].rank > nodes[y].rank) {
-          nodes[y].parent = nodes[x];
-        }
-        else { // nodes[x].rank <= nodes[y].rank
-          nodes[x].parent = nodes[y];
-          if (nodes[x].rank == nodes[y].rank)
-            nodes[y].rank++;
-        }
-    }
-
-    private class ItemNode {
-        private int itemIndex;
-        private ItemNode parent;
-        private int rank;
-
-        public ItemNode(int itemIndex) {
-            this.itemIndex = itemIndex;
-            this.parent = null;
-            this.rank = 0;
-        }
-    }
-}
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/DoublyLinkedList.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/DoublyLinkedList.java
deleted file mode 100644
index 154fd6f3b..000000000
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/DoublyLinkedList.java
+++ /dev/null
@@ -1,208 +0,0 @@
-package org.broadinstitute.sting.playground.gatk.walkers.phasing;
-
-import java.util.NoSuchElementException;
-
-/*
- * Copyright (c) 2010, The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-public class DoublyLinkedList<E> {
-    private DoublyLinkedNode<E> first;
-    private DoublyLinkedNode<E> last;
-    private int size;
-
-    public DoublyLinkedList() {
-        this.first = null;
-        this.last = null;
-        this.size = 0;
-    }
-
-    public boolean isEmpty() {
-        return first == null;
-    }
-
-    public int size() {
-        return size;
-    }
-
-    public void addFirst(E e) {
-        DoublyLinkedNode<E> newNode = new DoublyLinkedNode<E>(e);
-
-        if (isEmpty())
-            last = newNode;
-        else {
-            first.previous = newNode;
-            newNode.next = first;
-        }
-        first = newNode;
-
-        size++;
-    }
-
-    public void addLast(E e) {
-        DoublyLinkedNode<E> newNode = new DoublyLinkedNode<E>(e);
-
-        if (isEmpty())
-            first = newNode;
-        else {
-            last.next = newNode;
-            newNode.previous = last;
-        }
-        last = newNode;
-
-        size++;
-    }
-
-    public E removeFirst() {
-        if (isEmpty())
-            throw new NoSuchElementException();
-        E e = first.element;
-
-        if (first.next == null)
-            last = null;
-        else
-            first.next.previous = null;
-        first = first.next;
-
-        size--;
-        return e;
-    }
-
-    public E removeLast() {
-        if (isEmpty())
-            throw new NoSuchElementException();
-        E e = last.element;
-
-        if (last.previous == null)
-            first = null;
-        else
-            last.previous.next = null;
-        last = last.previous;
-
-        size--;
-        return e;
-    }
-
-    public E getFirst() {
-        if (isEmpty())
-            throw new NoSuchElementException();
-
-        return first.element;
-    }
-
-    public E getLast() {
-        if (isEmpty())
-            throw new NoSuchElementException();
-
-        return last.element;
-    }
-
-    public E peek() {
-        if (isEmpty())
-            return null;
-
-        return getFirst();
-    }
-
-    public E remove() {
-        return removeFirst();
-    }
-
-    public boolean add(E e) {
-    	addLast(e);
-        return true;
-    }
-
-    public BidirectionalIterator<E> iterator() {
-        return new BidirectionalIterator<E>(this);
-    }
-
-
-    private static class DoublyLinkedNode<E> {
-        private E element = null;
-        private DoublyLinkedNode<E> next = null;
-        private DoublyLinkedNode<E> previous = null;
-
-        public DoublyLinkedNode(E element) {
-            this.element = element;
-            this.next = null;
-            this.previous = null;
-        }
-    }
-
-
-    public static class BidirectionalIterator<E> implements Cloneable {
-        private DoublyLinkedNode<E> nextNode;
-        private DoublyLinkedNode<E> lastNode;
-
-        private BidirectionalIterator(DoublyLinkedNode<E> nextNode, DoublyLinkedNode<E> lastNode) {
-            this.nextNode = nextNode;
-            this.lastNode = lastNode;
-        }
-
-        private BidirectionalIterator(DoublyLinkedList<E> list) {
-            this(list.first, list.last);
-        }
-
-        public boolean hasNext() {
-            return nextNode != null;
-        }
-
-        public E next() {
-            if (!hasNext())
-                throw new NoSuchElementException();
-
-            E e = nextNode.element;
-            nextNode = nextNode.next;
-            return e;
-        }
-
-        public boolean hasPrevious() {
-            if (nextNode != null)
-                return nextNode.previous != null;
-
-            return lastNode != null;
-        }
-
-        public E previous() {
-            if (!hasPrevious())
-                throw new NoSuchElementException();
-
-            if (nextNode != null)
-                nextNode = nextNode.previous;
-            else
-                nextNode = lastNode;
-
-            return nextNode.element;
-        }
-
-        public BidirectionalIterator<E> clone() {
-            try {
-                super.clone();
-            } catch (CloneNotSupportedException e) {
-                e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
-            }
-            return new BidirectionalIterator<E>(nextNode, lastNode);
-        }
-    }
-}
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/Graph.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/Graph.java
deleted file mode 100644
index dc1389be0..000000000
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/Graph.java
+++ /dev/null
@@ -1,168 +0,0 @@
-package org.broadinstitute.sting.playground.gatk.walkers.phasing;
-
-import java.util.*;
-
-/*
- * Copyright (c) 2010, The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-// Represents an undirected graph with no self-edges:
-public class Graph implements Iterable<GraphEdge> {
-    private Neighbors[] adj;
-
-    public Graph(int numVertices) {
-        adj = new Neighbors[numVertices];
-        for (int i = 0; i < numVertices; i++)
-            adj[i] = new Neighbors();
-    }
-
-    public void addEdge(GraphEdge e) {
-        if (e.v1 == e.v2) // do not permit self-edges
-            return;
-
-        adj[e.v1].addNeighbor(e);
-        adj[e.v2].addNeighbor(e);
-    }
-
-    public void addEdges(Collection<GraphEdge> edges) {
-        for (GraphEdge e : edges)
-            addEdge(e);
-    }
-
-    public void removeEdge(GraphEdge e) {
-        adj[e.v1].removeNeighbor(e);
-        adj[e.v2].removeNeighbor(e);
-    }
-
-    public Collection<GraphEdge> removeAllIncidentEdges(int vertexIndex) {
-        Collection<GraphEdge> incidentEdges = new TreeSet<GraphEdge>(adj[vertexIndex].neighbors); // implemented GraphEdge.compareTo()
-
-        for (GraphEdge neighbEdge : incidentEdges) {
-            if (vertexIndex != neighbEdge.v1) // vertexIndex == neighbEdge.v2
-                adj[neighbEdge.v1].removeNeighbor(neighbEdge);
-            else if (vertexIndex != neighbEdge.v2) // vertexIndex == neighbEdge.v1
-                adj[neighbEdge.v2].removeNeighbor(neighbEdge);
-        }
-        adj[vertexIndex].clearAllNeighbors();
-
-        return incidentEdges;
-    }
-
-    public DisjointSet getConnectedComponents() {
-        DisjointSet cc = new DisjointSet(adj.length);
-
-        for (GraphEdge e : this)
-            cc.setUnion(e.v1, e.v2);
-
-        return cc;
-    }
-
-    public Iterator<GraphEdge> iterator() {
-        return new AllEdgesIterator();
-    }
-
-    public String toString() {
-        StringBuilder sb = new StringBuilder();
-
-        for (int i = 0; i < adj.length; i++) {
-            sb.append(i + ":");
-            for (GraphEdge e : adj[i]) {
-                sb.append(" " + (e.v1 == i ? e.v2 : e.v1));
-            }
-            sb.append("\n");
-        }
-
-        return sb.toString();
-    }
-
-    private class AllEdgesIterator implements Iterator<GraphEdge> {
-        private int curInd;
-        private Iterator<GraphEdge> innerIt;
-        private GraphEdge nextEdge;
-
-        public AllEdgesIterator() {
-            curInd = 0;
-            innerIt = null;
-            nextEdge = null;
-        }
-
-        public boolean hasNext() {
-            if (nextEdge != null)
-                return true;
-
-            for (; curInd < adj.length; curInd++) {
-                if (innerIt == null)
-                    innerIt = adj[curInd].iterator();
-
-                while (innerIt.hasNext()) {
-                    GraphEdge e = innerIt.next();
-                    if (e.v1 == curInd) { // only want to see each edge once
-                        nextEdge = e;
-                        return true;
-                    }
-                }
-
-                innerIt = null;
-            }
-
-            return false;
-        }
-
-        public GraphEdge next() {
-            if (!hasNext())
-                throw new NoSuchElementException();
-
-            GraphEdge tmpEdge = nextEdge;
-            nextEdge = null;
-            return tmpEdge;
-        }
-
-        public void remove() {
-            throw new UnsupportedOperationException();
-        }
-    }
-
-    private class Neighbors implements Iterable<GraphEdge> {
-        private Set<GraphEdge> neighbors;
-
-        public Neighbors() {
-            this.neighbors = new TreeSet<GraphEdge>(); // implemented GraphEdge.compareTo()
-        }
-
-        public void addNeighbor(GraphEdge e) {
-            neighbors.add(e);
-        }
-
-        public void removeNeighbor(GraphEdge e) {
-            neighbors.remove(e);
-        }
-
-        public Iterator<GraphEdge> iterator() {
-            return neighbors.iterator();
-        }
-
-        public void clearAllNeighbors() {
-            neighbors.clear();
-        }
-    }
-}
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/GraphEdge.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/GraphEdge.java
deleted file mode 100644
index 0170d476d..000000000
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/GraphEdge.java
+++ /dev/null
@@ -1,61 +0,0 @@
-package org.broadinstitute.sting.playground.gatk.walkers.phasing;
-
-/*
- * Copyright (c) 2010, The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-public class GraphEdge implements Comparable<GraphEdge> {
-    protected int v1;
-    protected int v2;
-
-    public GraphEdge(int v1, int v2) {
-        this.v1 = v1;
-        this.v2 = v2;
-    }
-
-    public int getV1() {
-        return v1;
-    }
-
-    public int getV2() {
-        return v2;
-    }
-
-    public int compareTo(GraphEdge that) {
-        if (this.v1 != that.v1)
-            return (this.v1 - that.v1);
-
-        // this.v1 == that.v1:
-        return (this.v2 - that.v2);
-    }
-
-    public boolean equals(GraphEdge other) {
-        return (this.compareTo(other) == 0);
-    }
-
-    public String toString() {
-        StringBuilder sb = new StringBuilder();
-        sb.append("(").append(v1).append(", ").append(v2).append(")");
-        return sb.toString();
-    }
-}