diff -urN clustalx-2.1/ClustalQtParams.h clustalx-2.1a/ClustalQtParams.h
--- clustalx-2.1/ClustalQtParams.h	2010-11-17 05:12:30.000000000 -0500
+++ clustalx-2.1a/ClustalQtParams.h	2010-11-18 12:19:42.450866697 -0500
@@ -13,9 +13,9 @@
 #include "clustalW/alignment/Alignment.h"
 #include <vector>
 
-static QString psColorFile = "colprot.xml";
-static QString psDNAFile = "coldna.xml";
-static QString psPrintFile = "colprint.xml";
+static QString psColorFile = "/usr/share/clustalx/colprot.xml";
+static QString psDNAFile = "/usr/share/clustalx/coldna.xml";
+static QString psPrintFile = "/usr/share/clustalx/colprint.xml";
 
 static const int BlackAndWhite = 1;
 static const int ColorsBackGround = 2;
diff -urN clustalx-2.1/HelpDisplayWidget.cpp clustalx-2.1a/HelpDisplayWidget.cpp
--- clustalx-2.1/HelpDisplayWidget.cpp	2010-11-17 05:12:30.000000000 -0500
+++ clustalx-2.1a/HelpDisplayWidget.cpp	2010-11-18 12:20:34.727866697 -0500
@@ -19,7 +19,7 @@
 #include <QtGui>
 #include "Resources.h"
 
-const string HelpDisplayWidget::helpFileName = "clustalx.hlp";
+const string HelpDisplayWidget::helpFileName = "/usr/share/clustalx/clustalx.hlp";
 
 HelpDisplayWidget::HelpDisplayWidget(char helpPointer)
 {