diff --git a/src/fr/inrialpes/exmo/align/util/EvalAlign.java b/src/fr/inrialpes/exmo/align/util/EvalAlign.java
index 5afa9255d4fc8c77e19ebee9d0d0f1d247a9dbf7..2ca4e295c67593b555a69b7321cc973d6ebb4d7a 100644
--- a/src/fr/inrialpes/exmo/align/util/EvalAlign.java
+++ b/src/fr/inrialpes/exmo/align/util/EvalAlign.java
@@ -147,11 +147,11 @@ public class EvalAlign {
 	Alignment align1=null, align2 = null;
 	try {
 	    // Load alignments
-	    AlignmentParser aparser1 = new AlignmentParser( debug );
-	    align1 = aparser1.parse( alignName1 );
+	    AlignmentParser aparser = new AlignmentParser( debug );
+	    align1 = aparser.parse( alignName1 );
 	    if ( debug > 0 ) System.err.println(" Alignment structure1 parsed");
-	    AlignmentParser aparser2 = new AlignmentParser( debug );
-	    align2 = aparser2.parse( alignName2 );
+	    aparser.initAlignment( null );
+	    align2 = aparser.parse( alignName2 );
 	    if ( debug > 0 ) System.err.println(" Alignment structure2 parsed");
 	} catch ( Exception ex ) { ex.printStackTrace(); }
 
diff --git a/src/fr/inrialpes/exmo/align/util/ExtGroupEval.java b/src/fr/inrialpes/exmo/align/util/ExtGroupEval.java
index 7850c18820144e5eed7ddf25cf0318f11288eb10..6f096eafcb8a348f69813f5a16b937decfec0898 100644
--- a/src/fr/inrialpes/exmo/align/util/ExtGroupEval.java
+++ b/src/fr/inrialpes/exmo/align/util/ExtGroupEval.java
@@ -233,11 +233,11 @@ public class ExtGroupEval {
 	    if ( debug < 2 ) nextdebug = 0;
 	    else nextdebug = debug - 2;
 	    // Load alignments
-	    AlignmentParser aparser1 = new AlignmentParser( nextdebug );
-	    Alignment align1 = aparser1.parse( alignName1 );
+	    AlignmentParser aparser = new AlignmentParser( nextdebug );
+	    Alignment align1 = aparser.parse( alignName1 );
 	    if ( debug > 1 ) System.err.println(" Alignment structure1 parsed");
-	    AlignmentParser aparser2 = new AlignmentParser( nextdebug );
-	    Alignment align2 = aparser2.parse( alignName2 );
+	    aparser.initAlignment( null );
+	    Alignment align2 = aparser.parse( alignName2 );
 	    if ( debug > 1 ) System.err.println(" Alignment structure2 parsed");
 	    // Create evaluator object
 	    eval = new ExtPREvaluator(ObjectAlignment.toObjectAlignment( (URIAlignment)align1, loaded ), 
diff --git a/src/fr/inrialpes/exmo/align/util/GenPlot.java b/src/fr/inrialpes/exmo/align/util/GenPlot.java
index 71031ab6f1ff307c07f8f00a2be0e103c619ff32..e275bc70cb7aa0785e7ebc18243f3f8a99818d91 100644
--- a/src/fr/inrialpes/exmo/align/util/GenPlot.java
+++ b/src/fr/inrialpes/exmo/align/util/GenPlot.java
@@ -251,11 +251,11 @@ public class GenPlot {
 	    if ( debug < 2 ) nextdebug = 0;
 	    else nextdebug = debug - 2;
 	    // Load alignments
-	    AlignmentParser aparser1 = new AlignmentParser( nextdebug );
-	    Alignment align1 = aparser1.parse( alignName1 );
+	    AlignmentParser aparser = new AlignmentParser( nextdebug );
+	    Alignment align1 = aparser.parse( alignName1 );
 	    if ( debug > 1 ) System.err.println(" Alignment structure1 parsed");
-	    AlignmentParser aparser2 = new AlignmentParser( nextdebug );
-	    Alignment align2 = aparser2.parse( alignName2 );
+	    aparser.initAlignment( null );
+	    Alignment align2 = aparser.parse( alignName2 );
 	    if ( debug > 1 ) System.err.println(" Alignment structure2 parsed");
 	    // Create evaluator object
 	    eval = new PRGraphEvaluator( align1, align2 );
diff --git a/src/fr/inrialpes/exmo/align/util/GenTriangle.java b/src/fr/inrialpes/exmo/align/util/GenTriangle.java
index bf6cece475084279c0eb33d61c5b6940d5378c8b..b5ac61b2fa3ea3a00e7ca83fceff7b1eff82d64f 100644
--- a/src/fr/inrialpes/exmo/align/util/GenTriangle.java
+++ b/src/fr/inrialpes/exmo/align/util/GenTriangle.java
@@ -253,11 +253,11 @@ public class GenTriangle {
 	    if ( debug < 2 ) nextdebug = 0;
 	    else nextdebug = debug - 2;
 	    // Load alignments
-	    AlignmentParser aparser1 = new AlignmentParser( nextdebug );
-	    Alignment align1 = aparser1.parse( alignName1 );
+	    AlignmentParser aparser = new AlignmentParser( nextdebug );
+	    Alignment align1 = aparser.parse( alignName1 );
 	    if ( debug > 2 ) System.err.println(" Alignment structure1 parsed");
-	    AlignmentParser aparser2 = new AlignmentParser( nextdebug );
-	    Alignment align2 = aparser2.parse( alignName2 );
+	    aparser.initAlignment( null );
+	    Alignment align2 = aparser.parse( alignName2 );
 	    if ( debug > 2 ) System.err.println(" Alignment structure2 parsed");
 	    // Create evaluator object
 	    eval = new PRecEvaluator( align1, align2 );
diff --git a/src/fr/inrialpes/exmo/align/util/GroupEval.java b/src/fr/inrialpes/exmo/align/util/GroupEval.java
index 1fab84473ea6de216397eeaa23ea965812a4bb58..266420bf6edc076ef480295cc061042519f0d4e8 100644
--- a/src/fr/inrialpes/exmo/align/util/GroupEval.java
+++ b/src/fr/inrialpes/exmo/align/util/GroupEval.java
@@ -254,11 +254,11 @@ public class GroupEval {
 	    if ( debug < 2 ) nextdebug = 0;
 	    else nextdebug = debug - 2;
 	    // Load alignments
-	    AlignmentParser aparser1 = new AlignmentParser( nextdebug );
-	    Alignment align1 = aparser1.parse( alignName1 );
+	    AlignmentParser aparser = new AlignmentParser( nextdebug );
+	    Alignment align1 = aparser.parse( alignName1 );
 	    if ( debug > 2 ) System.err.println(" Alignment structure1 parsed");
-	    AlignmentParser aparser2 = new AlignmentParser( nextdebug );
-	    Alignment align2 = aparser2.parse( alignName2 );
+	    aparser.initAlignment( null );
+	    Alignment align2 = aparser.parse( alignName2 );
 	    if ( debug > 2 ) System.err.println(" Alignment structure2 parsed");
 	    // Create evaluator object
 	    eval = new PRecEvaluator( align1, align2 );
diff --git a/src/fr/inrialpes/exmo/align/util/GroupOutput.java b/src/fr/inrialpes/exmo/align/util/GroupOutput.java
index dbf7e80ac56822797e255c6140e4e6e8a441e9dd..57c700516d738e618bb18aaa066290236a729359 100644
--- a/src/fr/inrialpes/exmo/align/util/GroupOutput.java
+++ b/src/fr/inrialpes/exmo/align/util/GroupOutput.java
@@ -264,11 +264,11 @@ public class GroupOutput {
 	// Load alignments
 	Alignment align1=null, align2=null;
 	try {
-	    AlignmentParser aparser1 = new AlignmentParser( nextdebug );
-	    align1 = aparser1.parse( alignName1 );
+	    AlignmentParser aparser = new AlignmentParser( nextdebug );
+	    align1 = aparser.parse( alignName1 );
 	    if ( debug > 2 ) System.err.println(" Alignment structure1 parsed");
-	    AlignmentParser aparser2 = new AlignmentParser( nextdebug );
-	    align2 = aparser2.parse( alignName2 );
+	    aparser.initAlignment( null );
+	    align2 = aparser.parse( alignName2 );
 	    if ( debug > 2 ) System.err.println(" Alignment structure2 parsed");
 	} catch (Exception ex) {
 	    throw new AlignmentException( "Cannot parse ", ex );