diff --git a/java/src/org/broadinstitute/sting/bwa/Aligner.java b/java/src/org/broadinstitute/sting/alignment/Aligner.java
similarity index 79%
rename from java/src/org/broadinstitute/sting/bwa/Aligner.java
rename to java/src/org/broadinstitute/sting/alignment/Aligner.java
index b55619e75..78161cf24 100644
--- a/java/src/org/broadinstitute/sting/bwa/Aligner.java
+++ b/java/src/org/broadinstitute/sting/alignment/Aligner.java
@@ -1,10 +1,16 @@
-package org.broadinstitute.sting.bwa;
+package org.broadinstitute.sting.alignment;
 
 import net.sf.samtools.SAMRecord;
 
 import java.io.File;
 import java.util.List;
 
+import org.broadinstitute.sting.alignment.bwa.*;
+import org.broadinstitute.sting.alignment.bwa.bwt.BWT;
+import org.broadinstitute.sting.alignment.bwa.bwt.SuffixArray;
+import org.broadinstitute.sting.alignment.bwa.bwt.BWTReader;
+import org.broadinstitute.sting.alignment.bwa.bwt.SuffixArrayReader;
+
 /**
  * Create perfect alignments from the read to the genome represented by the given BWT / suffix array. 
  *
diff --git a/java/src/org/broadinstitute/sting/bwa/Alignment.java b/java/src/org/broadinstitute/sting/alignment/Alignment.java
similarity index 86%
rename from java/src/org/broadinstitute/sting/bwa/Alignment.java
rename to java/src/org/broadinstitute/sting/alignment/Alignment.java
index c6098464a..4078a1fd3 100644
--- a/java/src/org/broadinstitute/sting/bwa/Alignment.java
+++ b/java/src/org/broadinstitute/sting/alignment/Alignment.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.bwa;
+package org.broadinstitute.sting.alignment;
 
 /**
  * Represents an alignment of a read to a site in the reference genome.
diff --git a/java/src/org/broadinstitute/sting/bwa/BWAAlignment.java b/java/src/org/broadinstitute/sting/alignment/bwa/BWAAlignment.java
similarity index 90%
rename from java/src/org/broadinstitute/sting/bwa/BWAAlignment.java
rename to java/src/org/broadinstitute/sting/alignment/bwa/BWAAlignment.java
index 83f27c307..7e024f5ce 100644
--- a/java/src/org/broadinstitute/sting/bwa/BWAAlignment.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/BWAAlignment.java
@@ -1,4 +1,6 @@
-package org.broadinstitute.sting.bwa;
+package org.broadinstitute.sting.alignment.bwa;
+
+import org.broadinstitute.sting.alignment.Alignment;
 
 /**
  * An alignment object to be used incrementally as the BWA aligner
diff --git a/java/src/org/broadinstitute/sting/bwa/LowerBound.java b/java/src/org/broadinstitute/sting/alignment/bwa/LowerBound.java
similarity index 90%
rename from java/src/org/broadinstitute/sting/bwa/LowerBound.java
rename to java/src/org/broadinstitute/sting/alignment/bwa/LowerBound.java
index 587847ea0..776dc2c5b 100644
--- a/java/src/org/broadinstitute/sting/bwa/LowerBound.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/LowerBound.java
@@ -1,10 +1,13 @@
-package org.broadinstitute.sting.bwa;
+package org.broadinstitute.sting.alignment.bwa;
 
 import net.sf.samtools.SAMRecord;
 
 import java.util.List;
 import java.util.ArrayList;
 
+import org.broadinstitute.sting.alignment.bwa.bwt.Base;
+import org.broadinstitute.sting.alignment.bwa.bwt.BWT;
+
 /**
  * At any point along the given read, what is a good lower bound for the
  * total number of differences?
diff --git a/java/src/org/broadinstitute/sting/bwa/PerfectAlignerTestHarness.java b/java/src/org/broadinstitute/sting/alignment/bwa/PerfectAlignerTestHarness.java
similarity index 95%
rename from java/src/org/broadinstitute/sting/bwa/PerfectAlignerTestHarness.java
rename to java/src/org/broadinstitute/sting/alignment/bwa/PerfectAlignerTestHarness.java
index a6a384510..0991dba37 100644
--- a/java/src/org/broadinstitute/sting/bwa/PerfectAlignerTestHarness.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/PerfectAlignerTestHarness.java
@@ -1,7 +1,9 @@
-package org.broadinstitute.sting.bwa;
+package org.broadinstitute.sting.alignment.bwa;
 
 import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.alignment.bwa.bwt.SuffixArrayReader;
+import org.broadinstitute.sting.alignment.bwa.bwt.*;
 
 import java.io.File;
 import java.io.FileNotFoundException;
diff --git a/java/src/org/broadinstitute/sting/bwa/BWT.java b/java/src/org/broadinstitute/sting/alignment/bwa/bwt/BWT.java
similarity index 80%
rename from java/src/org/broadinstitute/sting/bwa/BWT.java
rename to java/src/org/broadinstitute/sting/alignment/bwa/bwt/BWT.java
index ffd55dd42..31754d379 100644
--- a/java/src/org/broadinstitute/sting/bwa/BWT.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/bwt/BWT.java
@@ -1,4 +1,6 @@
-package org.broadinstitute.sting.bwa;
+package org.broadinstitute.sting.alignment.bwa.bwt;
+
+import org.broadinstitute.sting.alignment.bwa.packing.PackUtils;
 
 /**
  * Represents the Burrows-Wheeler Transform of a reference sequence.
@@ -128,43 +130,3 @@ public class BWT {
         return sequenceBlocks;
     }
 }
-
-/**
- * Models a block of bases within the BWT.
- */
-class SequenceBlock {
-    /**
-     * Start position of this sequence within the BWT.
-     */
-    public final int sequenceStart;
-
-    /**
-     * Length of this sequence within the BWT.
-     */
-    public final int sequenceLength;
-
-
-    /**
-     * Occurrences of each letter up to this sequence block.
-     */
-    public final Counts occurrences;
-
-    /**
-     * Sequence for this segment.
-     */
-    public final byte[] sequence;
-
-    /**
-     * Create a new block within this BWT.
-     * @param sequenceStart Starting position of this sequence within the BWT.
-     * @param sequenceLength Length of this sequence.
-     * @param occurrences How many of each base has been seen before this sequence began.
-     * @param sequence The actual sequence from the BWT.
-     */
-    SequenceBlock( int sequenceStart, int sequenceLength, Counts occurrences, byte[] sequence ) {
-        this.sequenceStart = sequenceStart;
-        this.sequenceLength = sequenceLength;
-        this.occurrences = occurrences;
-        this.sequence = sequence;
-    }
-}
diff --git a/java/src/org/broadinstitute/sting/bwa/BWTReader.java b/java/src/org/broadinstitute/sting/alignment/bwa/bwt/BWTReader.java
similarity index 88%
rename from java/src/org/broadinstitute/sting/bwa/BWTReader.java
rename to java/src/org/broadinstitute/sting/alignment/bwa/bwt/BWTReader.java
index 413a46fbb..31e25bbb2 100644
--- a/java/src/org/broadinstitute/sting/bwa/BWTReader.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/bwt/BWTReader.java
@@ -1,6 +1,9 @@
-package org.broadinstitute.sting.bwa;
+package org.broadinstitute.sting.alignment.bwa.bwt;
 
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.alignment.bwa.packing.IntPackedInputStream;
+import org.broadinstitute.sting.alignment.bwa.packing.BasePackedInputStream;
+import org.broadinstitute.sting.alignment.bwa.packing.PackUtils;
 
 import java.io.*;
 import java.nio.ByteOrder;
@@ -50,7 +53,7 @@ public class BWTReader {
             sequenceBlocks = new SequenceBlock[PackUtils.numberOfPartitions(bwtSize,BWT.SEQUENCE_BLOCK_SIZE)];
             
             for( int block = 0; block < sequenceBlocks.length; block++ ) {
-                int sequenceStart = block*BWT.SEQUENCE_BLOCK_SIZE;
+                int sequenceStart = block* BWT.SEQUENCE_BLOCK_SIZE;
                 int sequenceLength = Math.min(BWT.SEQUENCE_BLOCK_SIZE,bwtSize-sequenceStart);
 
                 int[] occurrences = new int[PackUtils.ALPHABET_SIZE];
diff --git a/java/src/org/broadinstitute/sting/bwa/BWTWriter.java b/java/src/org/broadinstitute/sting/alignment/bwa/bwt/BWTWriter.java
similarity index 90%
rename from java/src/org/broadinstitute/sting/bwa/BWTWriter.java
rename to java/src/org/broadinstitute/sting/alignment/bwa/bwt/BWTWriter.java
index 1913247d7..a8f810aa7 100644
--- a/java/src/org/broadinstitute/sting/bwa/BWTWriter.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/bwt/BWTWriter.java
@@ -1,6 +1,8 @@
-package org.broadinstitute.sting.bwa;
+package org.broadinstitute.sting.alignment.bwa.bwt;
 
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.alignment.bwa.packing.IntPackedOutputStream;
+import org.broadinstitute.sting.alignment.bwa.packing.BasePackedOutputStream;
 
 import java.io.*;
 import java.nio.ByteOrder;
diff --git a/java/src/org/broadinstitute/sting/bwa/Base.java b/java/src/org/broadinstitute/sting/alignment/bwa/bwt/Base.java
similarity index 97%
rename from java/src/org/broadinstitute/sting/bwa/Base.java
rename to java/src/org/broadinstitute/sting/alignment/bwa/bwt/Base.java
index 47e8bff06..f3669864f 100644
--- a/java/src/org/broadinstitute/sting/bwa/Base.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/bwt/Base.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.bwa;
+package org.broadinstitute.sting.alignment.bwa.bwt;
 
 import java.util.EnumSet;
 import java.util.Map;
diff --git a/java/src/org/broadinstitute/sting/bwa/Counts.java b/java/src/org/broadinstitute/sting/alignment/bwa/bwt/Counts.java
similarity index 96%
rename from java/src/org/broadinstitute/sting/bwa/Counts.java
rename to java/src/org/broadinstitute/sting/alignment/bwa/bwt/Counts.java
index 8b8e41933..a92fb30f5 100644
--- a/java/src/org/broadinstitute/sting/bwa/Counts.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/bwt/Counts.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.bwa;
+package org.broadinstitute.sting.alignment.bwa.bwt;
 
 import org.broadinstitute.sting.utils.StingException;
 
@@ -25,7 +25,7 @@ public class Counts implements Cloneable {
      * @param data Count data, broken down by base.
      * @param cumulative Whether the counts are cumulative, (count_G=numA+numC+numG,for example).
      */
-    Counts( int[] data, boolean cumulative ) {
+    public Counts( int[] data, boolean cumulative ) {
         for( Base base: EnumSet.allOf(Base.class))
             counts[base.toPack()] = data[base.toPack()];
 
diff --git a/java/src/org/broadinstitute/sting/bwa/CreateBWTFromReference.java b/java/src/org/broadinstitute/sting/alignment/bwa/bwt/CreateBWTFromReference.java
similarity index 98%
rename from java/src/org/broadinstitute/sting/bwa/CreateBWTFromReference.java
rename to java/src/org/broadinstitute/sting/alignment/bwa/bwt/CreateBWTFromReference.java
index a674f5205..11f413b25 100755
--- a/java/src/org/broadinstitute/sting/bwa/CreateBWTFromReference.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/bwt/CreateBWTFromReference.java
@@ -23,7 +23,7 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.bwa;
+package org.broadinstitute.sting.alignment.bwa.bwt;
 
 import net.sf.picard.reference.ReferenceSequenceFile;
 import net.sf.picard.reference.ReferenceSequenceFileFactory;
@@ -35,6 +35,7 @@ import java.util.TreeSet;
 import java.util.Comparator;
 
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.alignment.bwa.packing.PackUtils;
 
 /**
  * Create a suffix array data structure.
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/bwt/SequenceBlock.java b/java/src/org/broadinstitute/sting/alignment/bwa/bwt/SequenceBlock.java
new file mode 100644
index 000000000..ba41d92f3
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/bwt/SequenceBlock.java
@@ -0,0 +1,41 @@
+package org.broadinstitute.sting.alignment.bwa.bwt;
+
+/**
+ * Models a block of bases within the BWT.
+ */
+public class SequenceBlock {
+    /**
+     * Start position of this sequence within the BWT.
+     */
+    public final int sequenceStart;
+
+    /**
+     * Length of this sequence within the BWT.
+     */
+    public final int sequenceLength;
+
+
+    /**
+     * Occurrences of each letter up to this sequence block.
+     */
+    public final Counts occurrences;
+
+    /**
+     * Sequence for this segment.
+     */
+    public final byte[] sequence;
+
+    /**
+     * Create a new block within this BWT.
+     * @param sequenceStart Starting position of this sequence within the BWT.
+     * @param sequenceLength Length of this sequence.
+     * @param occurrences How many of each base has been seen before this sequence began.
+     * @param sequence The actual sequence from the BWT.
+     */
+    public SequenceBlock( int sequenceStart, int sequenceLength, Counts occurrences, byte[] sequence ) {
+        this.sequenceStart = sequenceStart;
+        this.sequenceLength = sequenceLength;
+        this.occurrences = occurrences;
+        this.sequence = sequence;
+    }
+}
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/bwa/SuffixArray.java b/java/src/org/broadinstitute/sting/alignment/bwa/bwt/SuffixArray.java
similarity index 94%
rename from java/src/org/broadinstitute/sting/bwa/SuffixArray.java
rename to java/src/org/broadinstitute/sting/alignment/bwa/bwt/SuffixArray.java
index fffec0657..7451fc894 100644
--- a/java/src/org/broadinstitute/sting/bwa/SuffixArray.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/bwt/SuffixArray.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.bwa;
+package org.broadinstitute.sting.alignment.bwa.bwt;
 
 /**
  * An in-memory representation of a suffix array.
diff --git a/java/src/org/broadinstitute/sting/bwa/SuffixArrayReader.java b/java/src/org/broadinstitute/sting/alignment/bwa/bwt/SuffixArrayReader.java
similarity index 91%
rename from java/src/org/broadinstitute/sting/bwa/SuffixArrayReader.java
rename to java/src/org/broadinstitute/sting/alignment/bwa/bwt/SuffixArrayReader.java
index 591f4125a..8d7ea797c 100644
--- a/java/src/org/broadinstitute/sting/bwa/SuffixArrayReader.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/bwt/SuffixArrayReader.java
@@ -1,6 +1,8 @@
-package org.broadinstitute.sting.bwa;
+package org.broadinstitute.sting.alignment.bwa.bwt;
 
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.alignment.bwa.packing.IntPackedInputStream;
+import org.broadinstitute.sting.alignment.bwa.packing.PackUtils;
 
 import java.io.*;
 import java.nio.ByteOrder;
diff --git a/java/src/org/broadinstitute/sting/bwa/SuffixArrayWriter.java b/java/src/org/broadinstitute/sting/alignment/bwa/bwt/SuffixArrayWriter.java
similarity index 93%
rename from java/src/org/broadinstitute/sting/bwa/SuffixArrayWriter.java
rename to java/src/org/broadinstitute/sting/alignment/bwa/bwt/SuffixArrayWriter.java
index edc3a0821..c0dabd04b 100644
--- a/java/src/org/broadinstitute/sting/bwa/SuffixArrayWriter.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/bwt/SuffixArrayWriter.java
@@ -1,6 +1,7 @@
-package org.broadinstitute.sting.bwa;
+package org.broadinstitute.sting.alignment.bwa.bwt;
 
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.alignment.bwa.packing.IntPackedOutputStream;
 
 import java.io.*;
 import java.nio.ByteOrder;
diff --git a/java/src/org/broadinstitute/sting/bwa/BasePackedInputStream.java b/java/src/org/broadinstitute/sting/alignment/bwa/packing/BasePackedInputStream.java
similarity index 96%
rename from java/src/org/broadinstitute/sting/bwa/BasePackedInputStream.java
rename to java/src/org/broadinstitute/sting/alignment/bwa/packing/BasePackedInputStream.java
index 9a6abda94..40b5b581e 100644
--- a/java/src/org/broadinstitute/sting/bwa/BasePackedInputStream.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/packing/BasePackedInputStream.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.bwa;
+package org.broadinstitute.sting.alignment.bwa.packing;
 
 import org.broadinstitute.sting.utils.StingException;
 
@@ -38,7 +38,7 @@ public class BasePackedInputStream<T> {
 
         this.targetInputStream = inputStream;
         this.type = type;
-        this.buffer = ByteBuffer.allocate(PackUtils.bitsInType(type)/PackUtils.BITS_PER_BYTE).order(byteOrder);
+        this.buffer = ByteBuffer.allocate(PackUtils.bitsInType(type)/ PackUtils.BITS_PER_BYTE).order(byteOrder);
     }
 
     /**
diff --git a/java/src/org/broadinstitute/sting/bwa/BasePackedOutputStream.java b/java/src/org/broadinstitute/sting/alignment/bwa/packing/BasePackedOutputStream.java
similarity index 98%
rename from java/src/org/broadinstitute/sting/bwa/BasePackedOutputStream.java
rename to java/src/org/broadinstitute/sting/alignment/bwa/packing/BasePackedOutputStream.java
index 0ba98693b..cc6294a99 100644
--- a/java/src/org/broadinstitute/sting/bwa/BasePackedOutputStream.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/packing/BasePackedOutputStream.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.bwa;
+package org.broadinstitute.sting.alignment.bwa.packing;
 
 import org.broadinstitute.sting.utils.StingException;
 
diff --git a/java/src/org/broadinstitute/sting/bwa/CreatePACFromReference.java b/java/src/org/broadinstitute/sting/alignment/bwa/packing/CreatePACFromReference.java
similarity index 98%
rename from java/src/org/broadinstitute/sting/bwa/CreatePACFromReference.java
rename to java/src/org/broadinstitute/sting/alignment/bwa/packing/CreatePACFromReference.java
index 1ce2925d3..05bc1fe61 100755
--- a/java/src/org/broadinstitute/sting/bwa/CreatePACFromReference.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/packing/CreatePACFromReference.java
@@ -23,7 +23,7 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.bwa;
+package org.broadinstitute.sting.alignment.bwa.packing;
 
 import net.sf.picard.reference.ReferenceSequenceFile;
 import net.sf.picard.reference.ReferenceSequenceFileFactory;
diff --git a/java/src/org/broadinstitute/sting/bwa/IntPackedInputStream.java b/java/src/org/broadinstitute/sting/alignment/bwa/packing/IntPackedInputStream.java
similarity index 95%
rename from java/src/org/broadinstitute/sting/bwa/IntPackedInputStream.java
rename to java/src/org/broadinstitute/sting/alignment/bwa/packing/IntPackedInputStream.java
index 8de0ca8d6..bdc04d7e2 100644
--- a/java/src/org/broadinstitute/sting/bwa/IntPackedInputStream.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/packing/IntPackedInputStream.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.bwa;
+package org.broadinstitute.sting.alignment.bwa.packing;
 
 import java.io.*;
 import java.nio.ByteBuffer;
@@ -38,7 +38,7 @@ public class IntPackedInputStream {
      */
     public IntPackedInputStream(InputStream inputStream, ByteOrder byteOrder) {
         this.targetInputStream = inputStream;
-        this.buffer = ByteBuffer.allocate(PackUtils.bitsInType(Integer.class)/PackUtils.BITS_PER_BYTE).order(byteOrder);        
+        this.buffer = ByteBuffer.allocate(PackUtils.bitsInType(Integer.class)/ PackUtils.BITS_PER_BYTE).order(byteOrder);
     }
 
     /**
diff --git a/java/src/org/broadinstitute/sting/bwa/IntPackedOutputStream.java b/java/src/org/broadinstitute/sting/alignment/bwa/packing/IntPackedOutputStream.java
similarity index 98%
rename from java/src/org/broadinstitute/sting/bwa/IntPackedOutputStream.java
rename to java/src/org/broadinstitute/sting/alignment/bwa/packing/IntPackedOutputStream.java
index e9386de37..3933f6b5c 100755
--- a/java/src/org/broadinstitute/sting/bwa/IntPackedOutputStream.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/packing/IntPackedOutputStream.java
@@ -23,7 +23,7 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.bwa;
+package org.broadinstitute.sting.alignment.bwa.packing;
 
 import java.io.*;
 import java.nio.ByteBuffer;
diff --git a/java/src/org/broadinstitute/sting/bwa/PackUtils.java b/java/src/org/broadinstitute/sting/alignment/bwa/packing/PackUtils.java
similarity index 98%
rename from java/src/org/broadinstitute/sting/bwa/PackUtils.java
rename to java/src/org/broadinstitute/sting/alignment/bwa/packing/PackUtils.java
index c3313f9e4..6fd175652 100644
--- a/java/src/org/broadinstitute/sting/bwa/PackUtils.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/packing/PackUtils.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.bwa;
+package org.broadinstitute.sting.alignment.bwa.packing;
 
 import org.broadinstitute.sting.utils.StingException;