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diff --git a/forester/java/src/org/forester/application/dom_dup.java b/forester/java/src/org/forester/application/dom_dup.java
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+++ b/forester/java/src/org/forester/application/dom_dup.java
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+
+package org.forester.application;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.SortedMap;
+import java.util.SortedSet;
+import java.util.TreeMap;
+import java.util.TreeSet;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.forester.io.parsers.phyloxml.PhyloXmlParser;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+import org.forester.util.CommandLineArguments;
+import org.forester.util.ForesterUtil;
+
+public class dom_dup {
+
+    // HUMAN MOUSE
+    // ARATH SOYBN VOLCA CYAME PARTE THAPS EMIHU NAEGR 
+    final static private String HELP_OPTION_1 = "help";
+    final static private String HELP_OPTION_2 = "h";
+    final static private String PRG_NAME      = "dom_dup";
+    final static private String PRG_DESC      = "";
+    final static private String PRG_VERSION   = "0.90";
+    final static private String PRG_DATE      = "2013.03.12";
+    final static private String E_MAIL        = "phylosoft@gmail.com";
+    final static private String WWW           = "sites.google.com/site/cmzmasek/home/software/forester";
+
+    public static void main( final String args[] ) {
+        try {
+            final CommandLineArguments cla = new CommandLineArguments( args );
+            if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( cla.getNumberOfNames() != 3 ) ) {
+                printHelp();
+                System.exit( 0 );
+            }
+            final String pattern_str = cla.getName( 0 );
+            final File intree_file = cla.getFile( 2 );
+            final File species_groups_file = cla.getFile( 1 );
+            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+            final Phylogeny phy = factory.create( intree_file, new PhyloXmlParser() )[ 0 ];
+            ForesterUtil.programMessage( PRG_NAME, "Pattern string: " + pattern_str );
+            final Pattern pattern = Pattern.compile( pattern_str );
+            ForesterUtil.programMessage( PRG_NAME, "Pattern is: " + pattern );
+            final SortedSet<String> set_a = new TreeSet<String>();
+            final SortedSet<String> set_b = new TreeSet<String>();
+            read( species_groups_file, set_a, set_b );
+            print_set( set_a, "Set a:" );
+            print_set( set_b, "Set b:" );
+            final SortedSet<String> matching_names = obtainMatchingNames( phy, pattern );
+            ForesterUtil.programMessage( PRG_NAME, "Found names: " );
+            final SortedMap<String, List<String>> pairs = obtainPairs( matching_names );
+            int lca_counter = 0;
+            int non_lca_counter = 0;
+            int missing_counter = 0;
+            int total_counter = 0;
+            final Iterator<Entry<String, List<String>>> it = pairs.entrySet().iterator();
+            while ( it.hasNext() ) {
+                final Map.Entry<String, List<String>> x = it.next();
+                total_counter++;
+                if ( x.getValue().size() == 2 ) {
+                    final String a = x.getValue().get( 0 );
+                    final String b = x.getValue().get( 1 );
+                    System.out.print( a + " - " + b );
+                    final PhylogenyNode lca = PhylogenyMethods.calculateLCA( phy.getNode( a ), phy.getNode( b ) );
+                    final List<PhylogenyNode> external_descs = lca.getAllExternalDescendants();
+                    boolean in_a = false;
+                    boolean in_b = false;
+                    for( final PhylogenyNode external_desc : external_descs ) {
+                        final String tc = external_desc.getNodeData().getTaxonomy().getTaxonomyCode();
+                        if ( set_a.contains( tc ) ) {
+                            in_a = true;
+                        }
+                        if ( set_b.contains( tc ) ) {
+                            in_b = true;
+                        }
+                    }
+                    if ( in_a && in_b ) {
+                        System.out.print( " => LCA " );
+                        lca_counter++;
+                    }
+                    else {
+                        non_lca_counter++;
+                    }
+                    System.out.println();
+                }
+                else if ( x.getValue().size() == 1 ) {
+                    System.out.println( x.getValue().get( 0 ) + " => no partner in current tree!" );
+                    missing_counter++;
+                }
+                else {
+                    System.out.println( "error" );
+                    System.exit( -1 );
+                }
+            }
+            System.out.println( "Total       : " + total_counter );
+            System.out.println( "LCA         : " + lca_counter );
+            System.out.println( "Non-LCA     : " + non_lca_counter );
+            System.out.println( "With missing: " + missing_counter );
+        }
+        catch ( final Exception e ) {
+            e.printStackTrace();
+            ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+        }
+    }
+
+    private static SortedMap<String, List<String>> obtainPairs( final SortedSet<String> matching_names ) {
+        final SortedMap<String, List<String>> pairs = new TreeMap<String, List<String>>();
+        for( final String m : matching_names ) {
+            final String short_m = m.substring( 0, m.indexOf( '~' ) );
+            if ( !pairs.containsKey( short_m ) ) {
+                final List<String> p = new ArrayList<String>();
+                p.add( m );
+                pairs.put( short_m, p );
+            }
+            else {
+                pairs.get( short_m ).add( m );
+            }
+        }
+        return pairs;
+    }
+
+    private static SortedSet<String> obtainMatchingNames( final Phylogeny phy, final Pattern pattern ) {
+        final SortedSet<String> matching_names = new TreeSet<String>();
+        for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
+            final PhylogenyNode n = it.next();
+            final Matcher m = pattern.matcher( n.getName() );
+            if ( m.find() ) {
+                matching_names.add( n.getName() );
+            }
+        }
+        return matching_names;
+    }
+
+    private static void print_set( final Set<String> set_a, final String l ) {
+        ForesterUtil.programMessage( PRG_NAME, l );
+        for( final String s : set_a ) {
+            System.out.print( s + " " );
+        }
+        System.out.println();
+    }
+
+    private static void read( final File species_groups_file, final Set<String> set_a, final Set<String> set_b )
+            throws IOException {
+        final BufferedReader reader = ForesterUtil.obtainReader( species_groups_file );
+        String line;
+        boolean first_line = true;
+        while ( ( line = reader.readLine() ) != null ) {
+            line = line.trim();
+            if ( !ForesterUtil.isEmpty( line ) ) {
+                final String s[] = line.split( " " );
+                for( final String name : s ) {
+                    if ( first_line ) {
+                        set_a.add( name );
+                    }
+                    else {
+                        set_b.add( name );
+                    }
+                }
+                if ( first_line ) {
+                    first_line = false;
+                }
+            }
+        }
+    }
+
+    private static void printHelp() {
+        ForesterUtil.printProgramInformation( PRG_NAME,
+                                              PRG_DESC,
+                                              PRG_VERSION,
+                                              PRG_DATE,
+                                              E_MAIL,
+                                              WWW,
+                                              ForesterUtil.getForesterLibraryInformation() );
+        System.out.println( "Usage:" );
+        System.out.println();
+        System.out.println( PRG_NAME + "" );
+        System.out.println();
+        System.out.println( " exmple: " );
+        System.out.println();
+        System.out
+                .println( "dom_dup \"HUMAN~[12]-2\" groups.txt RRMa_ALL_plus_RRMa_ee3_50_hmmalign_05_40_fme_gsdi.phylo.xml" );
+        System.out.println();
+        System.out.println();
+    }
+}