diff --git a/java/src/org/broadinstitute/sting/bwa/Aligner.java b/java/src/org/broadinstitute/sting/bwa/Aligner.java
new file mode 100644
index 000000000..b55619e75
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/bwa/Aligner.java
@@ -0,0 +1,53 @@
+package org.broadinstitute.sting.bwa;
+
+import net.sf.samtools.SAMRecord;
+
+import java.io.File;
+import java.util.List;
+
+/**
+ * Create perfect alignments from the read to the genome represented by the given BWT / suffix array. 
+ *
+ * @author mhanna
+ * @version 0.1
+ */
+public class Aligner {
+    /**
+     * BWT in the forward direction.
+     */
+    private BWT forwardBWT;
+
+    /**
+     * Suffix array in the forward direction.
+     */
+    private SuffixArray forwardSuffixArray;
+
+    /**
+     * BWT in the reverse direction.
+     */
+    private BWT reverseBWT;
+
+    /**
+     * Suffix array in the reverse direction.
+     */
+    private SuffixArray reverseSuffixArray;
+
+    public Aligner( File forwardBWTFile, File forwardSuffixArrayFile, File reverseBWTFile, File reverseSuffixArrayFile ) {
+        forwardBWT = new BWTReader(forwardBWTFile).read();
+        forwardSuffixArray = new SuffixArrayReader(forwardSuffixArrayFile).read();
+
+        reverseBWT = new BWTReader(reverseBWTFile).read();
+        reverseSuffixArray = new SuffixArrayReader(reverseSuffixArrayFile).read();
+    }
+
+    /**
+     * Align the read to the given reference.
+     * @param read Read to align.
+     * @return A list of the alignments.
+     */
+    public List<Alignment> align( SAMRecord read ) {
+        List<LowerBound> lowerBounds = LowerBound.create(read,reverseBWT);
+        return null;    
+    }
+}
+
diff --git a/java/src/org/broadinstitute/sting/bwa/Alignment.java b/java/src/org/broadinstitute/sting/bwa/Alignment.java
new file mode 100644
index 000000000..c6098464a
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/bwa/Alignment.java
@@ -0,0 +1,15 @@
+package org.broadinstitute.sting.bwa;
+
+/**
+ * Represents an alignment of a read to a site in the reference genome.
+ *
+ * @author mhanna
+ * @version 0.1
+ */
+public interface Alignment extends Comparable<Alignment> {
+    /**
+     * Gets the score of this alignment.
+     * @return The score.
+     */
+    public int getScore();
+}
diff --git a/java/src/org/broadinstitute/sting/bwa/BWAAlignment.java b/java/src/org/broadinstitute/sting/bwa/BWAAlignment.java
new file mode 100644
index 000000000..83f27c307
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/bwa/BWAAlignment.java
@@ -0,0 +1,42 @@
+package org.broadinstitute.sting.bwa;
+
+/**
+ * An alignment object to be used incrementally as the BWA aligner
+ * inspects the read.
+ *
+ * @author mhanna
+ * @version 0.1
+ */
+public class BWAAlignment implements Alignment {
+    /**
+     * Working variable.  The lower bound of the alignment within the BWT.
+     */
+    protected int loBound;
+
+    /**
+     * Working variable.  The upper bound of the alignment within the BWT.
+     */
+    protected int hiBound;
+
+    /**
+     * Current score for this alignment.
+     */
+    protected int score;
+
+    /**
+     * Gets the BWA score of this alignment.
+     * @return BWA-style scores.  0 is best.
+     */
+    public int getScore() {
+        return score;
+    }
+
+    /**
+     * Compare this alignment to another alignment.
+     * @param other Other alignment to which to compare.
+     * @return < 0 if this < other, == 0 if this == other, > 0 if this > other
+     */
+    public int compareTo( Alignment other ) {
+        return Integer.valueOf(score).compareTo(other.getScore());
+    }
+}
diff --git a/java/src/org/broadinstitute/sting/bwa/LowerBound.java b/java/src/org/broadinstitute/sting/bwa/LowerBound.java
new file mode 100644
index 000000000..587847ea0
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/bwa/LowerBound.java
@@ -0,0 +1,50 @@
+package org.broadinstitute.sting.bwa;
+
+import net.sf.samtools.SAMRecord;
+
+import java.util.List;
+import java.util.ArrayList;
+
+/**
+ * At any point along the given read, what is a good lower bound for the
+ * total number of differences?
+ *
+ * @author mhanna
+ * @version 0.1
+ */
+public class LowerBound {
+    /**
+     * The lower bound at the given point.
+     */
+    public final int value;
+
+    /**
+     * Create a new lower bound with the given value.
+     * @param value Value for the lower bound at this site.
+     */
+    private LowerBound(int value) {
+        this.value = value;
+    }
+
+    /**
+     * Create a non-optimal bound according to the algorithm specified in Figure 3 of the BWA paper.
+     */
+    public static List<LowerBound> create( SAMRecord read, BWT reverseBWT ) {
+        List<LowerBound> bounds = new ArrayList<LowerBound>();
+
+        int loIndex = 0, hiIndex = reverseBWT.length(), mismatches = 0;
+        for( int i = 0; i < read.getReadBases().length; i++ ) {
+            Base base = Base.fromASCII(read.getReadBases()[i]);
+            loIndex = reverseBWT.counts(base) + reverseBWT.occurrences(base,loIndex-1) + 1;
+            hiIndex = reverseBWT.counts(base) + reverseBWT.occurrences(base,hiIndex);
+            if( loIndex > hiIndex ) {
+                loIndex = 0;
+                hiIndex = reverseBWT.length();
+                mismatches++;
+            }
+            bounds.add(new LowerBound(mismatches));
+        }
+
+        return bounds;
+    }
+}