diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
index aa99d82ee..99d9c98a9 100644
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
@@ -21,10 +21,10 @@ import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.gatk.traversals.*;
 import org.broadinstitute.sting.gatk.executive.MicroManager;
-import org.broadinstitute.sting.utils.FastaSequenceFile2;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;
+import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
 
 import java.io.File;
 import java.io.PrintStream;
diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/ReadDataSource.java b/java/src/org/broadinstitute/sting/gatk/dataSources/ReadDataSource.java
index 2f463a958..996fee83c 100644
--- a/java/src/org/broadinstitute/sting/gatk/dataSources/ReadDataSource.java
+++ b/java/src/org/broadinstitute/sting/gatk/dataSources/ReadDataSource.java
@@ -8,7 +8,7 @@ import java.io.File;
 
 import org.broadinstitute.sting.gatk.iterators.VerifyingSamIterator;
 import org.broadinstitute.sting.gatk.iterators.ReferenceIterator;
-import org.broadinstitute.sting.utils.FastaSequenceFile2;
+import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
 
 /**
  * User: aaron
diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/ReferenceDataSource.java b/java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/ReferenceDataSource.java
index ccde116d4..540a7f358 100644
--- a/java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/ReferenceDataSource.java
+++ b/java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/ReferenceDataSource.java
@@ -2,8 +2,8 @@ package org.broadinstitute.sting.gatk.dataSources.simpleDataSources;
 
 import org.broadinstitute.sting.gatk.iterators.BoundedReferenceIterator;
 import org.broadinstitute.sting.gatk.iterators.ReferenceIterator;
-import org.broadinstitute.sting.utils.FastaSequenceFile2;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
 
 import java.io.File;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/executive/MicroManager.java b/java/src/org/broadinstitute/sting/gatk/executive/MicroManager.java
index 4dea622b9..c4ce0de6e 100644
--- a/java/src/org/broadinstitute/sting/gatk/executive/MicroManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/executive/MicroManager.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.gatk.executive;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.FastaSequenceFile2;
+import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategy;
diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/BoundedReferenceIterator.java b/java/src/org/broadinstitute/sting/gatk/iterators/BoundedReferenceIterator.java
index 9083f14c3..c916439f3 100644
--- a/java/src/org/broadinstitute/sting/gatk/iterators/BoundedReferenceIterator.java
+++ b/java/src/org/broadinstitute/sting/gatk/iterators/BoundedReferenceIterator.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.gatk.iterators;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.FastaSequenceFile2;
+import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
 
 import java.util.Iterator;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/ReferenceIterator.java b/java/src/org/broadinstitute/sting/gatk/iterators/ReferenceIterator.java
index 6f4fe14ee..6b381e1f8 100755
--- a/java/src/org/broadinstitute/sting/gatk/iterators/ReferenceIterator.java
+++ b/java/src/org/broadinstitute/sting/gatk/iterators/ReferenceIterator.java
@@ -4,8 +4,8 @@ import edu.mit.broad.picard.reference.ReferenceSequence;
 import net.sf.samtools.util.RuntimeIOException;
 import net.sf.samtools.util.StringUtil;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.FastaSequenceFile2;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
 
 import java.util.Iterator;
 import java.util.NoSuchElementException;
diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
index 30c295e0e..9630757e2 100755
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
@@ -17,6 +17,7 @@ import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
 
 import java.io.*;
 import java.util.*;
diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReads.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReads.java
index 593e9dd54..11a9d7aed 100644
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReads.java
+++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReads.java
@@ -8,7 +8,7 @@ import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.iterators.ReferenceIterator;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.FastaSequenceFile2;
+import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
 
 import java.util.List;
 import java.util.Arrays;
diff --git a/java/src/org/broadinstitute/sting/utils/FastaSequenceFile2.java b/java/src/org/broadinstitute/sting/utils/fasta/FastaSequenceFile2.java
similarity index 99%
rename from java/src/org/broadinstitute/sting/utils/FastaSequenceFile2.java
rename to java/src/org/broadinstitute/sting/utils/fasta/FastaSequenceFile2.java
index 7cea61732..bf6bc6d36 100644
--- a/java/src/org/broadinstitute/sting/utils/FastaSequenceFile2.java
+++ b/java/src/org/broadinstitute/sting/utils/fasta/FastaSequenceFile2.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.sting.utils.fasta;
 
 import edu.mit.broad.picard.PicardException;
 import edu.mit.broad.picard.reference.ReferenceSequenceFile;
@@ -469,4 +469,4 @@ public class FastaSequenceFile2 implements ReferenceSequenceFile {
     public String toString() {
         return this.file.getAbsolutePath();
     }
-}
\ No newline at end of file
+}
diff --git a/java/src/org/broadinstitute/sting/utils/FastaSequenceIndex.java b/java/src/org/broadinstitute/sting/utils/fasta/FastaSequenceIndex.java
similarity index 99%
rename from java/src/org/broadinstitute/sting/utils/FastaSequenceIndex.java
rename to java/src/org/broadinstitute/sting/utils/fasta/FastaSequenceIndex.java
index a6221b3f8..7f33e2dba 100755
--- a/java/src/org/broadinstitute/sting/utils/FastaSequenceIndex.java
+++ b/java/src/org/broadinstitute/sting/utils/fasta/FastaSequenceIndex.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.sting.utils.fasta;
 
 import edu.mit.broad.picard.PicardException;
 
@@ -145,4 +145,4 @@ class FastaSequenceIndexEntry {
                                                                                                   basesPerLine,
                                                                                                   bytesPerLine );
     }
-}
\ No newline at end of file
+}
diff --git a/java/test/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategyFactoryTest.java b/java/test/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategyFactoryTest.java
index 7b9f797eb..44877a8c0 100755
--- a/java/test/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategyFactoryTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategyFactoryTest.java
@@ -5,8 +5,8 @@ import static junit.framework.Assert.fail;
 import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.samtools.SAMSequenceRecord;
 import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.FastaSequenceFile2;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
 import org.junit.*;
 
 import java.io.File;
diff --git a/java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMBAMDataSourceTest.java b/java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMBAMDataSourceTest.java
index 2b3cef898..9523374d0 100755
--- a/java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMBAMDataSourceTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMBAMDataSourceTest.java
@@ -7,8 +7,8 @@ import org.broadinstitute.sting.gatk.dataSources.shards.Shard;
 import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategy;
 import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategyFactory;
 import org.broadinstitute.sting.gatk.iterators.MergingSamRecordIterator2;
-import org.broadinstitute.sting.utils.FastaSequenceFile2;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
diff --git a/java/test/org/broadinstitute/sting/utils/GenomeLocTest.java b/java/test/org/broadinstitute/sting/utils/GenomeLocTest.java
index 5e7eb603d..4f4a64616 100644
--- a/java/test/org/broadinstitute/sting/utils/GenomeLocTest.java
+++ b/java/test/org/broadinstitute/sting/utils/GenomeLocTest.java
@@ -8,6 +8,7 @@ import org.junit.*;
 import static org.junit.Assert.*;
 import org.apache.commons.cli.ParseException;
 import org.broadinstitute.sting.utils.cmdLine.ArgumentParser;
+import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
 
 import java.util.ArrayList;
 import java.io.File;
diff --git a/java/test/org/broadinstitute/sting/utils/FastaSequenceFile2Test.java b/java/test/org/broadinstitute/sting/utils/fasta/FastaSequenceFile2Test.java
similarity index 99%
rename from java/test/org/broadinstitute/sting/utils/FastaSequenceFile2Test.java
rename to java/test/org/broadinstitute/sting/utils/fasta/FastaSequenceFile2Test.java
index 2c220a1ae..2d6264cab 100755
--- a/java/test/org/broadinstitute/sting/utils/FastaSequenceFile2Test.java
+++ b/java/test/org/broadinstitute/sting/utils/fasta/FastaSequenceFile2Test.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.sting.utils.fasta;
 
 import edu.mit.broad.picard.reference.ReferenceSequence;
 import net.sf.samtools.util.StringUtil;
diff --git a/java/test/org/broadinstitute/sting/utils/FastaSequenceIndexTest.java b/java/test/org/broadinstitute/sting/utils/fasta/FastaSequenceIndexTest.java
similarity index 99%
rename from java/test/org/broadinstitute/sting/utils/FastaSequenceIndexTest.java
rename to java/test/org/broadinstitute/sting/utils/fasta/FastaSequenceIndexTest.java
index 423d2d3dc..afb304c1d 100755
--- a/java/test/org/broadinstitute/sting/utils/FastaSequenceIndexTest.java
+++ b/java/test/org/broadinstitute/sting/utils/fasta/FastaSequenceIndexTest.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.sting.utils.fasta;
 
 import org.junit.BeforeClass;
 import org.junit.Before;