diff --git a/build.xml b/build.xml
index 05389ad68..d15a93cf1 100644
--- a/build.xml
+++ b/build.xml
@@ -101,7 +101,10 @@
         </jar>
 
         <jar jarfile="${dist}/GenomeAnalysisTK.jar">
-            <fileset dir="build" includes="**/gatk/**/*.class"/>
+            <fileset dir="build">
+              <include name="**/gatk/**/*.class" />
+              <include name="**/alignment/**/*.class"/>
+            </fileset>
             <manifest>
                 <attribute name="Main-Class" value="org.broadinstitute.sting.gatk.CommandLineGATK"/>
             </manifest>