diff --git a/.classpath b/.classpath
index 63f429de8e5c2b1df6b03b0a2ab22b301a90fa95..cb5e8f1662a4ab1bf1efbb8d36630e30a315f919 100644
--- a/.classpath
+++ b/.classpath
@@ -30,8 +30,6 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="lib" path="lib/jemAlign.jar"/>
-	<classpathentry kind="lib" path="lib/biojava.jar"/>
 	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>