diff -urN clustalx-2.1/AlignOutputFileNames.cpp clustalx-2.1-bak/AlignOutputFileNames.cpp
--- clustalx-2.1/AlignOutputFileNames.cpp	2010-11-17 11:12:30.000000000 +0100
+++ clustalx-2.1-bak/AlignOutputFileNames.cpp	2015-09-18 18:59:38.582405761 +0200
@@ -13,6 +13,7 @@
  * 18-06-07,Nigel Brown(EMBL): Made the 'ok' button in each dialogue be the
  * default instead of a Browse button.
  */
+#include <QtGui>
 #include <QPushButton>
 #include <QGroupBox>
 #include <QCheckBox>
@@ -20,8 +21,8 @@
 #include <QGridLayout>
 #include <QSizePolicy>
 #include <QComboBox>
-#include <QtGui>
 #include <QLabel>
+#include <QLineEdit>
 #include <iostream>
 #include "AlignOutputFileNames.h"
 #include "clustalW/general/userparams.h"
diff -urN clustalx-2.1/AlignmentViewerWidget.cpp clustalx-2.1-bak/AlignmentViewerWidget.cpp
--- clustalx-2.1/AlignmentViewerWidget.cpp	2010-11-17 11:12:30.000000000 +0100
+++ clustalx-2.1-bak/AlignmentViewerWidget.cpp	2015-09-18 18:50:09.762563103 +0200
@@ -69,6 +69,11 @@
 #include "PSPrinter.h"
 #include "FileDialog.h"
 #include <QFontMetrics>
+#include <QVBoxLayout>
+#include <QScrollBar>
+#include <QScrollArea>
+#include <QMessageBox>
+#include <QGroupBox>
 
 AlignmentViewerWidget::AlignmentViewerWidget(QWidget *parent)
  : QWidget(parent),
diff -urN clustalx-2.1/AlignmentWidget.cpp clustalx-2.1-bak/AlignmentWidget.cpp
--- clustalx-2.1/AlignmentWidget.cpp	2010-11-17 11:12:30.000000000 +0100
+++ clustalx-2.1-bak/AlignmentWidget.cpp	2015-09-18 18:58:36.656119118 +0200
@@ -46,6 +46,7 @@
  ****************************************************************************/
 
 #include <QtGui>
+#include <QScrollArea>
 #include "AlignmentWidget.h"
 #include "clustalW/general/userparams.h"
 #include "ClustalQtParams.h"
diff -urN clustalx-2.1/BootstrapTreeDialog.cpp clustalx-2.1-bak/BootstrapTreeDialog.cpp
--- clustalx-2.1/BootstrapTreeDialog.cpp	2010-11-17 11:12:30.000000000 +0100
+++ clustalx-2.1-bak/BootstrapTreeDialog.cpp	2015-09-18 19:00:09.782214298 +0200
@@ -5,6 +5,7 @@
  * 12-4-07, Mark Larkin, Removed destructor. No need to delete QObjects. Also removed
  * setAllPtrsToNull function. 
  */
+#include <QtGui>
 #include <QPushButton>
 #include <QGroupBox>
 #include <QCheckBox>
@@ -12,8 +13,8 @@
 #include <QGridLayout>
 #include <QSizePolicy>
 #include <QComboBox>
-#include <QtGui>
 #include <QLabel>
+#include <QLineEdit>
 #include <iostream>
 #include "BootstrapTreeDialog.h"
 #include "clustalW/general/userparams.h"
diff -urN clustalx-2.1/ColorFileXmlParser.cpp clustalx-2.1-bak/ColorFileXmlParser.cpp
--- clustalx-2.1/ColorFileXmlParser.cpp	2010-11-17 11:12:30.000000000 +0100
+++ clustalx-2.1-bak/ColorFileXmlParser.cpp	2015-09-18 19:00:42.695345653 +0200
@@ -1,4 +1,5 @@
 #include <QtGui>
+#include <QMessageBox>
 
 #include "ColorFileXmlParser.h"
 #include "ClustalQtParams.h"
@@ -202,4 +203,4 @@
         rule = rule.nextSiblingElement("resrule");
     }  
     return numOfRules;  
-}
\ No newline at end of file
+}
diff -urN clustalx-2.1/HelpDisplayWidget.cpp clustalx-2.1-bak/HelpDisplayWidget.cpp
--- clustalx-2.1/HelpDisplayWidget.cpp	2010-11-17 11:12:30.000000000 +0100
+++ clustalx-2.1-bak/HelpDisplayWidget.cpp	2015-09-18 19:34:51.692771579 +0200
@@ -16,6 +16,8 @@
 #include <QTextEdit>
 #include <iostream>
 #include <fstream>
+#include <QPushButton>
+#include <QVBoxLayout>
 #include <QtGui>
 #include "Resources.h"
 
diff -urN clustalx-2.1/PSPrinter.cpp clustalx-2.1-bak/PSPrinter.cpp
--- clustalx-2.1/PSPrinter.cpp	2010-11-17 11:12:30.000000000 +0100
+++ clustalx-2.1-bak/PSPrinter.cpp	2015-09-18 19:20:36.528019466 +0200
@@ -17,6 +17,7 @@
 #include <iomanip>
 #include <sstream>
 #include <QtGui>
+#include <QMessageBox>
 #include "PSPrinter.h"
 #include "ColorFileXmlParser.h"
 #include "clustalW/general/userparams.h"
diff -urN clustalx-2.1/ProteinGapParameters.cpp clustalx-2.1-bak/ProteinGapParameters.cpp
--- clustalx-2.1/ProteinGapParameters.cpp	2010-11-17 11:12:30.000000000 +0100
+++ clustalx-2.1-bak/ProteinGapParameters.cpp	2015-09-18 19:20:07.311532091 +0200
@@ -9,6 +9,7 @@
 #include <QLabel>
 #include <QString>
 #include <QMessageBox>
+#include <QLineEdit>
 #include "ProteinGapParameters.h"
 #include "clustalW/general/userparams.h"
 
diff -urN clustalx-2.1/SaveSeqFile.cpp clustalx-2.1-bak/SaveSeqFile.cpp
--- clustalx-2.1/SaveSeqFile.cpp	2010-11-17 11:12:30.000000000 +0100
+++ clustalx-2.1-bak/SaveSeqFile.cpp	2015-09-18 19:21:28.231035513 +0200
@@ -20,6 +20,8 @@
 #include <QComboBox>
 #include <QtGui>
 #include <QLabel>
+#include <QMessageBox>
+#include <QLineEdit>
 #include "SaveSeqFile.h"
 #include "clustalW/general/userparams.h"
 #include "clustalW/general/utils.h"
diff -urN clustalx-2.1/SeqNameWidget.cpp clustalx-2.1-bak/SeqNameWidget.cpp
--- clustalx-2.1/SeqNameWidget.cpp	2010-11-17 11:12:30.000000000 +0100
+++ clustalx-2.1-bak/SeqNameWidget.cpp	2015-09-18 19:22:48.903873782 +0200
@@ -56,6 +56,7 @@
  ****************************************************************************/
 
 #include <QtGui>
+#include <QScrollArea>
 #include "SeqNameWidget.h"
 #include "KeyController.h" //- nige
 #include "clustalW/alignment/Alignment.h"
diff -urN clustalx-2.1/TreeOutputFileNames.cpp clustalx-2.1-bak/TreeOutputFileNames.cpp
--- clustalx-2.1/TreeOutputFileNames.cpp	2010-11-17 11:12:30.000000000 +0100
+++ clustalx-2.1-bak/TreeOutputFileNames.cpp	2015-09-18 19:23:37.006911921 +0200
@@ -13,6 +13,7 @@
 #include <QComboBox>
 #include <QtGui>
 #include <QLabel>
+#include <QLineEdit>
 #include <iostream>
 #include "TreeOutputFileNames.h"
 #include "clustalW/general/userparams.h"
diff -urN clustalx-2.1/WritePostscriptFile.cpp clustalx-2.1-bak/WritePostscriptFile.cpp
--- clustalx-2.1/WritePostscriptFile.cpp	2010-11-17 11:12:30.000000000 +0100
+++ clustalx-2.1-bak/WritePostscriptFile.cpp	2015-09-18 19:24:30.429917414 +0200
@@ -20,6 +20,8 @@
 #include <QComboBox>
 #include <QtGui>
 #include <QLabel>
+#include <QLineEdit>
+#include <QMessageBox>
 #include <iostream>
 #include "WritePostscriptFile.h"
 #include "clustalW/general/userparams.h"
Binary files clustalx-2.1/clustalx and clustalx-2.1-bak/clustalx differ
diff -urN clustalx-2.1/clustalx.pro clustalx-2.1-bak/clustalx.pro
--- clustalx-2.1/clustalx.pro	2010-11-17 11:12:30.000000000 +0100
+++ clustalx-2.1-bak/clustalx.pro	2015-09-18 19:14:42.666857671 +0200
@@ -4,8 +4,11 @@
 
 TEMPLATE = app
 TARGET = clustalx
-CONFIG += release static
+CONFIG += release 
 QT += xml
+QT += widgets
+DEFINES += QT_DISABLE_DEPRECATED_BEFORE=0x000000
+
 VERSION = 2.1
 win32 {
    DEFINES += OS_WINDOWS
diff -urN clustalx-2.1/mainwindow.cpp clustalx-2.1-bak/mainwindow.cpp
--- clustalx-2.1/mainwindow.cpp	2010-11-17 11:12:30.000000000 +0100
+++ clustalx-2.1-bak/mainwindow.cpp	2015-09-18 19:19:03.545256739 +0200
@@ -94,6 +94,15 @@
 #include <cstdlib>
 #include <QCheckBox>
 #include <QStringList>
+#include <QMenu>
+#include <QMenuBar>
+#include <QAction>
+#include <QMessageBox>
+#include <QApplication>
+#include <QScrollBar>
+#include <QHBoxLayout>
+#include <QGroupBox>
+#include <QVBoxLayout>
 #include "SecStructOptions.h"
 #include "mainwindow.h"
 #include "WritePostscriptFile.h"