forester/java/src/org/forester/application/gsdi.java

   1 // $Id:
   2 // FORESTER -- software libraries and applications
   3 // for evolutionary biology research and applications.
   4 //
   5 // Copyright (C) 2008-2009 Christian M. Zmasek
   6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   7 // All rights reserved
   8 //
   9 // This library is free software; you can redistribute it and/or
  10 // modify it under the terms of the GNU Lesser General Public
  11 // License as published by the Free Software Foundation; either
  12 // version 2.1 of the License, or (at your option) any later version.
  13 //
  14 // This library is distributed in the hope that it will be useful,
  15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  17 // Lesser General Public License for more details.
  18 //
  19 // You should have received a copy of the GNU Lesser General Public
  20 // License along with this library; if not, write to the Free Software
  21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  22 //
  23 // Contact: phylosoft @ gmail . com
  24 // WWW: www.phylosoft.org/forester
  25
  26 package org.forester.application;
  27
  28 import java.io.File;
  29 import java.io.IOException;
  30 import java.text.SimpleDateFormat;
  31 import java.util.ArrayList;
  32 import java.util.Date;
  33 import java.util.List;
  34 import java.util.SortedMap;
  35 import java.util.SortedSet;
  36 import java.util.TreeMap;
  37 import java.util.TreeSet;
  38
  39 import org.forester.io.parsers.PhylogenyParser;
  40 import org.forester.io.parsers.nhx.NHXParser;
  41 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
  42 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
  43 import org.forester.io.parsers.util.ParserUtils;
  44 import org.forester.io.writers.PhylogenyWriter;
  45 import org.forester.phylogeny.Phylogeny;
  46 import org.forester.phylogeny.PhylogenyMethods;
  47 import org.forester.phylogeny.PhylogenyNode;
  48 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  49 import org.forester.phylogeny.factories.PhylogenyFactory;
  50 import org.forester.sdi.GSDI;
  51 import org.forester.sdi.SDI;
  52 import org.forester.sdi.SDI.TaxonomyComparisonBase;
  53 import org.forester.sdi.SDIException;
  54 import org.forester.sdi.SDIse;
  55 import org.forester.util.CommandLineArguments;
  56 import org.forester.util.EasyWriter;
  57 import org.forester.util.ForesterConstants;
  58 import org.forester.util.ForesterUtil;
  59
  60 public final class gsdi {
  61
  62     private enum BASE_ALGORITHM {
  63         GSDI, SDI
  64     }
  65     final static public boolean REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE = true;
  66     final static private String ALLOW_STRIPPING_OF_GENE_TREE_OPTION    = "g";
  67     final static private String SDISE_OPTION                           = "b";
  68     final static private String MOST_PARSIMONIOUS_OPTION               = "m";
  69     final static private String GUESS_FORMAT_OF_SPECIES_TREE           = "q";
  70     final static private String HELP_OPTION_1                          = "help";
  71     final static private String HELP_OPTION_2                          = "h";
  72     final static private String DEFAULT_OUTFILE_SUFFIX                 = "_gsdi_out.xml";
  73     final static private String SUFFIX_FOR_SPECIES_TREE_USED           = "_species_tree_used.xml";
  74     final static private String LOGFILE_SUFFIX                         = "_gsdi_log.txt";
  75     final static private String PRG_NAME                               = "gsdi";
  76     final static private String PRG_VERSION                            = "1.000";
  77     final static private String PRG_DATE                               = "120608";
  78     final static private String PRG_DESC                               = "general speciation duplication inference";
  79     final static private String E_MAIL                                 = "phylosoft@gmail.com";
  80     final static private String WWW                                    = "www.phylosoft.org/forester";
  81
  82     public static void main( final String args[] ) {
  83         try {
  84             ForesterUtil.printProgramInformation( PRG_NAME,
  85                                                   PRG_DESC,
  86                                                   PRG_VERSION,
  87                                                   PRG_DATE,
  88                                                   E_MAIL,
  89                                                   WWW,
  90                                                   ForesterUtil.getForesterLibraryInformation() );
  91             CommandLineArguments cla = null;
  92             try {
  93                 cla = new CommandLineArguments( args );
  94             }
  95             catch ( final Exception e ) {
  96                 ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
  97             }
  98             if ( cla.isOptionSet( gsdi.HELP_OPTION_1 ) || cla.isOptionSet( gsdi.HELP_OPTION_2 ) ) {
  99                 System.out.println();
 100                 gsdi.print_help();
 101                 System.exit( 0 );
 102             }
 103             else if ( ( args.length < 2 ) || ( cla.getNumberOfNames() < 2 ) || ( cla.getNumberOfNames() > 3 ) ) {
 104                 System.out.println();
 105                 System.out.println( "Wrong number of arguments." );
 106                 System.out.println();
 107                 gsdi.print_help();
 108                 System.exit( -1 );
 109             }
 110             final List<String> allowed_options = new ArrayList<String>();
 111             allowed_options.add( gsdi.SDISE_OPTION );
 112             allowed_options.add( gsdi.GUESS_FORMAT_OF_SPECIES_TREE );
 113             allowed_options.add( gsdi.MOST_PARSIMONIOUS_OPTION );
 114             allowed_options.add( gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION );
 115             final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
 116             if ( dissallowed_options.length() > 0 ) {
 117                 ForesterUtil.fatalError( gsdi.PRG_NAME, "unknown option(s): " + dissallowed_options );
 118             }
 119             execute( cla );
 120         }
 121         catch ( final IOException e ) {
 122             ForesterUtil.fatalError( gsdi.PRG_NAME, e.getMessage() );
 123         }
 124     }
 125
 126     private static void execute( final CommandLineArguments cla ) throws IOException {
 127         BASE_ALGORITHM base_algorithm = BASE_ALGORITHM.GSDI;
 128         boolean most_parsimonous_duplication_model = false;
 129         boolean species_tree_in_phyloxml = true;
 130         boolean allow_stripping_of_gene_tree = false;
 131         if ( cla.isOptionSet( gsdi.SDISE_OPTION ) ) {
 132             base_algorithm = BASE_ALGORITHM.SDI;
 133         }
 134         if ( cla.isOptionSet( gsdi.MOST_PARSIMONIOUS_OPTION ) ) {
 135             if ( base_algorithm != BASE_ALGORITHM.GSDI ) {
 136                 ForesterUtil.fatalError( gsdi.PRG_NAME, "Can only use most parsimonious duplication mode with GSDI" );
 137             }
 138             most_parsimonous_duplication_model = true;
 139         }
 140         if ( cla.isOptionSet( gsdi.GUESS_FORMAT_OF_SPECIES_TREE ) ) {
 141             species_tree_in_phyloxml = false;
 142         }
 143         if ( cla.isOptionSet( gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION ) ) {
 144             if ( base_algorithm != BASE_ALGORITHM.GSDI ) {
 145                 ForesterUtil.fatalError( gsdi.PRG_NAME, "Can only allow stripping of gene tree with GSDI" );
 146             }
 147             allow_stripping_of_gene_tree = true;
 148         }
 149         Phylogeny species_tree = null;
 150         Phylogeny gene_tree = null;
 151         File gene_tree_file = null;
 152         File species_tree_file = null;
 153         File out_file = null;
 154         File log_file = null;
 155         EasyWriter log_writer = null;
 156         try {
 157             gene_tree_file = cla.getFile( 0 );
 158             species_tree_file = cla.getFile( 1 );
 159             if ( cla.getNumberOfNames() == 3 ) {
 160                 out_file = cla.getFile( 2 );
 161             }
 162             else {
 163                 out_file = new File( ForesterUtil.removeSuffix( gene_tree_file.toString() ) + DEFAULT_OUTFILE_SUFFIX );
 164             }
 165             log_file = new File( ForesterUtil.removeSuffix( out_file.toString() ) + LOGFILE_SUFFIX );
 166         }
 167         catch ( final IllegalArgumentException e ) {
 168             ForesterUtil.fatalError( gsdi.PRG_NAME, "error in command line: " + e.getMessage() );
 169         }
 170         if ( ForesterUtil.isReadableFile( gene_tree_file ) != null ) {
 171             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isReadableFile( gene_tree_file ) );
 172         }
 173         if ( ForesterUtil.isReadableFile( species_tree_file ) != null ) {
 174             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isReadableFile( species_tree_file ) );
 175         }
 176         if ( ForesterUtil.isWritableFile( out_file ) != null ) {
 177             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( out_file ) );
 178         }
 179         if ( ForesterUtil.isWritableFile( log_file ) != null ) {
 180             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( log_file ) );
 181         }
 182         try {
 183             log_writer = ForesterUtil.createEasyWriter( log_file );
 184         }
 185         catch ( final IOException e ) {
 186             ForesterUtil.fatalError( gsdi.PRG_NAME, "Failed to create [" + log_file + "]: " + e.getMessage() );
 187         }
 188         try {
 189             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 190             gene_tree = factory.create( gene_tree_file, new PhyloXmlParser() )[ 0 ];
 191         }
 192         catch ( final IOException e ) {
 193             ForesterUtil.fatalError( gsdi.PRG_NAME,
 194                                      "Failed to read gene tree from [" + gene_tree_file + "]: " + e.getMessage() );
 195         }
 196         try {
 197             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 198             if ( species_tree_in_phyloxml ) {
 199                 species_tree = factory.create( species_tree_file, new PhyloXmlParser() )[ 0 ];
 200             }
 201             else {
 202                 final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( species_tree_file, true );
 203                 if ( REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE && ( p instanceof NHXParser ) ) {
 204                     ( ( NHXParser ) p ).setReplaceUnderscores( true );
 205                 }
 206                 species_tree = factory.create( species_tree_file, p )[ 0 ];
 207                 final TaxonomyComparisonBase comp_base = GSDI.determineTaxonomyComparisonBase( gene_tree );
 208                 switch ( comp_base ) {
 209                     case SCIENTIFIC_NAME:
 210                         try {
 211                             PhylogenyMethods
 212                                     .transferNodeNameToField( species_tree,
 213                                                               PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
 214                                                               true );
 215                         }
 216                         catch ( final PhyloXmlDataFormatException e ) {
 217                             ForesterUtil.fatalError( gsdi.PRG_NAME,
 218                                                      "Failed to transfer general node name to scientific name, in ["
 219                                                              + species_tree_file + "]: " + e.getMessage() );
 220                         }
 221                         break;
 222                     case CODE:
 223                         try {
 224                             PhylogenyMethods
 225                                     .transferNodeNameToField( species_tree,
 226                                                               PhylogenyMethods.PhylogenyNodeField.TAXONOMY_CODE,
 227                                                               true );
 228                         }
 229                         catch ( final PhyloXmlDataFormatException e ) {
 230                             ForesterUtil.fatalError( gsdi.PRG_NAME,
 231                                                      "Failed to transfer general node name to taxonomy code, in ["
 232                                                              + species_tree_file + "]: " + e.getMessage() );
 233                         }
 234                         break;
 235                     case ID:
 236                         try {
 237                             PhylogenyMethods.transferNodeNameToField( species_tree,
 238                                                                       PhylogenyMethods.PhylogenyNodeField.TAXONOMY_ID,
 239                                                                       true );
 240                         }
 241                         catch ( final PhyloXmlDataFormatException e ) {
 242                             ForesterUtil.fatalError( gsdi.PRG_NAME,
 243                                                      "Failed to transfer general node name to taxonomy id, in ["
 244                                                              + species_tree_file + "]: " + e.getMessage() );
 245                         }
 246                         break;
 247                     default:
 248                         ForesterUtil.fatalError( gsdi.PRG_NAME, "unable to determine comparison base" );
 249                 }
 250             }
 251         }
 252         catch ( final IOException e ) {
 253             ForesterUtil.fatalError( gsdi.PRG_NAME, "Failed to read species tree from [" + species_tree_file + "]: "
 254                     + e.getMessage() );
 255         }
 256         gene_tree.setRooted( true );
 257         species_tree.setRooted( true );
 258         if ( !gene_tree.isCompletelyBinary() ) {
 259             log_writer.println( "User Error: gene tree is not completely binary" );
 260             log_writer.close();
 261             ForesterUtil.fatalError( gsdi.PRG_NAME, "gene tree is not completely binary" );
 262         }
 263         if ( base_algorithm != BASE_ALGORITHM.GSDI ) {
 264             if ( !species_tree.isCompletelyBinary() ) {
 265                 log_writer.println( "User Error: species tree is not completely binary, use GSDI instead" );
 266                 log_writer.close();
 267                 ForesterUtil.fatalError( gsdi.PRG_NAME, "species tree is not completely binary, use GSDI instead" );
 268             }
 269         }
 270         log_writer.println( PRG_NAME + " - " + PRG_DESC );
 271         log_writer.println( "  version         : " + PRG_VERSION );
 272         log_writer.println( "  date            : " + PRG_DATE );
 273         log_writer.println( "  forester version: " + ForesterConstants.FORESTER_VERSION );
 274         log_writer.println();
 275         log_writer.println( "Start time                               : "
 276                 + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) );
 277         System.out.println( "Start time                               : "
 278                 + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) );
 279         log_writer.println( "Gene tree file                           : " + gene_tree_file.getCanonicalPath() );
 280         System.out.println( "Gene tree file                           : " + gene_tree_file.getCanonicalPath() );
 281         log_writer.println( "Gene tree name                           : "
 282                 + ( ForesterUtil.isEmpty( gene_tree.getName() ) ? "" : gene_tree.getName() ) );
 283         System.out.println( "Gene tree name                           : "
 284                 + ( ForesterUtil.isEmpty( gene_tree.getName() ) ? "" : gene_tree.getName() ) );
 285         log_writer.println( "Species tree file                        : " + species_tree_file.getCanonicalPath() );
 286         System.out.println( "Species tree file                        : " + species_tree_file.getCanonicalPath() );
 287         log_writer.println( "Species tree name                        : "
 288                 + ( ForesterUtil.isEmpty( species_tree.getName() ) ? "" : gene_tree.getName() ) );
 289         System.out.println( "Species tree name                        : "
 290                 + ( ForesterUtil.isEmpty( species_tree.getName() ) ? "" : gene_tree.getName() ) );
 291         SDI sdi = null;
 292         final long start_time = new Date().getTime();
 293         try {
 294             if ( base_algorithm == BASE_ALGORITHM.GSDI ) {
 295                 System.out.println( "Use most parsimonous duplication model   : " + most_parsimonous_duplication_model );
 296                 System.out.println( "Allow stripping of gene tree nodes       : " + allow_stripping_of_gene_tree );
 297                 log_writer.println( "Use most parsimonous duplication model   : " + most_parsimonous_duplication_model );
 298                 log_writer.println( "Allow stripping of gene tree nodes       : " + allow_stripping_of_gene_tree );
 299                 log_writer.flush();
 300                 sdi = new GSDI( gene_tree,
 301                                 species_tree,
 302                                 most_parsimonous_duplication_model,
 303                                 allow_stripping_of_gene_tree,
 304                                 true );
 305             }
 306             else {
 307                 System.out.println();
 308                 System.out.println( "Using SDIse algorithm" );
 309                 log_writer.println( "Using SDIse algorithm" );
 310                 log_writer.flush();
 311                 sdi = new SDIse( gene_tree, species_tree );
 312             }
 313         }
 314         catch ( final SDIException e ) {
 315             log_writer.println( "User Error: " + e.getLocalizedMessage() );
 316             log_writer.close();
 317             ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
 318         }
 319         catch ( final IOException e ) {
 320             log_writer.println( "Error: " + e );
 321             log_writer.close();
 322             ForesterUtil.fatalError( PRG_NAME, e.toString() );
 323         }
 324         catch ( final Exception e ) {
 325             log_writer.println( "Error: " + e );
 326             log_writer.close();
 327             e.printStackTrace();
 328             System.exit( -1 );
 329         }
 330         System.out.println( "Running time (excluding I/O)             : " + ( new Date().getTime() - start_time )
 331                 + "ms" );
 332         log_writer.println( "Running time (excluding I/O)             : " + ( new Date().getTime() - start_time )
 333                 + "ms" );
 334         if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) ) {
 335             final GSDI gsdi = ( GSDI ) sdi;
 336             System.out.println( "Mapping based on                         : " + gsdi.getTaxCompBase() );
 337             log_writer.println( "Mapping based on                         : " + gsdi.getTaxCompBase() );
 338         }
 339         try {
 340             final PhylogenyWriter writer = new PhylogenyWriter();
 341             writer.toPhyloXML( out_file, gene_tree, 0 );
 342         }
 343         catch ( final IOException e ) {
 344             ForesterUtil.fatalError( PRG_NAME, "Failed to write to [" + out_file + "]: " + e.getMessage() );
 345         }
 346         System.out.println( "Wrote resulting gene tree to             : " + out_file );
 347         log_writer.println( "Wrote resulting gene tree to             : " + out_file );
 348         if ( base_algorithm == BASE_ALGORITHM.SDI ) {
 349             sdi.computeMappingCostL();
 350             System.out.println( "Mapping cost                             : " + sdi.computeMappingCostL() );
 351             log_writer.println( "Mapping cost                             : " + sdi.computeMappingCostL() );
 352         }
 353         else if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) ) {
 354             final GSDI gsdi = ( GSDI ) sdi;
 355             final File species_tree_used_file = new File( out_file + SUFFIX_FOR_SPECIES_TREE_USED );
 356             try {
 357                 final PhylogenyWriter writer = new PhylogenyWriter();
 358                 writer.toPhyloXML( species_tree_used_file, gsdi.getSpeciesTree(), 0 );
 359             }
 360             catch ( final IOException e ) {
 361                 ForesterUtil.fatalError( PRG_NAME,
 362                                          "Failed to write to [" + species_tree_used_file + "]: " + e.getMessage() );
 363             }
 364             System.out.println( "Wrote (stripped) species tree to         : " + species_tree_used_file );
 365             log_writer.println( "Wrote (stripped) species tree to         : " + species_tree_used_file );
 366         }
 367         System.out.println( "Number of external nodes in gene tree    : " + gene_tree.getNumberOfExternalNodes() );
 368         log_writer.println( "Number of external nodes in gene tree    : " + gene_tree.getNumberOfExternalNodes() );
 369         System.out.println( "Number of external nodes in species tree : "
 370                 + sdi.getSpeciesTree().getNumberOfExternalNodes() );
 371         log_writer.println( "Number of external nodes in species tree : "
 372                 + sdi.getSpeciesTree().getNumberOfExternalNodes() );
 373         if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) ) {
 374             final GSDI gsdi = ( GSDI ) sdi;
 375             final int poly = PhylogenyMethods.countNumberOfPolytomies( gsdi.getSpeciesTree() );
 376             System.out.println( "Number of polytomies in species tree     : " + poly );
 377             log_writer.println( "Number of polytomies in species tree     : " + poly );
 378             System.out.println( "External nodes stripped from gene tree   : "
 379                     + gsdi.getStrippedExternalGeneTreeNodes().size() );
 380             log_writer.println( "External nodes stripped from gene tree   : "
 381                     + gsdi.getStrippedExternalGeneTreeNodes().size() );
 382             System.out.println( "External nodes stripped from species tree: "
 383                     + gsdi.getStrippedSpeciesTreeNodes().size() );
 384             log_writer.println( "External nodes stripped from species tree: "
 385                     + gsdi.getStrippedSpeciesTreeNodes().size() );
 386         }
 387         System.out.println();
 388         System.out.println( "Number of duplications                   : " + sdi.getDuplicationsSum() );
 389         log_writer.println( "Number of duplications                   : " + sdi.getDuplicationsSum() );
 390         if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) ) {
 391             final GSDI gsdi = ( GSDI ) sdi;
 392             if ( !most_parsimonous_duplication_model ) {
 393                 final int u = gsdi.getSpeciationOrDuplicationEventsSum();
 394                 System.out.println( "Number of potential duplications         : " + u );
 395                 log_writer.println( "Number of potential duplications         : " + u );
 396             }
 397             System.out.println( "Number of speciations                    : " + gsdi.getSpeciationsSum() );
 398             log_writer.println( "Number of speciations                    : " + gsdi.getSpeciationsSum() );
 399             log_writer.println();
 400             printMappedNodesToLog( log_writer, gsdi );
 401             log_writer.println();
 402             printStrippedGeneTreeNodesToLog( log_writer, gsdi );
 403             log_writer.println();
 404             printStrippedSpeciesTreeNodesToLog( log_writer, gsdi );
 405         }
 406         System.out.println();
 407         System.out.println( "Wrote log to                             : " + log_file );
 408         System.out.println();
 409         log_writer.close();
 410     }
 411
 412     private static void printMappedNodesToLog( final EasyWriter log_writer, final GSDI gsdi ) throws IOException {
 413         final SortedSet<String> ss = new TreeSet<String>();
 414         for( final PhylogenyNode n : gsdi.getMappedExternalSpeciesTreeNodes() ) {
 415             ss.add( n.toString() );
 416         }
 417         log_writer.println( "The following " + ss.size() + " species were used: " );
 418         for( final String s : ss ) {
 419             log_writer.println( "  " + s );
 420         }
 421     }
 422
 423     private static void printStrippedGeneTreeNodesToLog( final EasyWriter log_writer, final GSDI gsdi )
 424             throws IOException {
 425         final SortedMap<String, Integer> sm = new TreeMap<String, Integer>();
 426         for( final PhylogenyNode n : gsdi.getStrippedExternalGeneTreeNodes() ) {
 427             final String s = n.toString();
 428             if ( sm.containsKey( s ) ) {
 429                 sm.put( s, sm.get( s ) + 1 );
 430             }
 431             else {
 432                 sm.put( s, 1 );
 433             }
 434         }
 435         log_writer.println( "The following " + sm.size() + " nodes were stripped from the gene tree: " );
 436         for( final String s : sm.keySet() ) {
 437             final int count = sm.get( s );
 438             if ( count == 1 ) {
 439                 log_writer.println( "  " + s );
 440             }
 441             else {
 442                 log_writer.println( "  " + s + " [" + count + "]" );
 443             }
 444         }
 445     }
 446
 447     private static void printStrippedSpeciesTreeNodesToLog( final EasyWriter log_writer, final GSDI gsdi )
 448             throws IOException {
 449         final SortedSet<String> ss = new TreeSet<String>();
 450         for( final PhylogenyNode n : gsdi.getStrippedSpeciesTreeNodes() ) {
 451             ss.add( n.toString() );
 452         }
 453         log_writer.println( "The following " + ss.size() + " nodes were stripped from the species tree: " );
 454         for( final String n : ss ) {
 455             log_writer.println( "  " + n );
 456         }
 457     }
 458
 459     private static void print_help() {
 460         System.out.println( "Usage: " + gsdi.PRG_NAME
 461                 + " [-options] <gene tree in phyloXML format> <species tree> [outfile]" );
 462         System.out.println();
 463         System.out.println( "Options:" );
 464         System.out.println( " -" + gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION
 465                 + ": to allow stripping of gene tree nodes without a matching species" );
 466         System.out.println( " -" + gsdi.MOST_PARSIMONIOUS_OPTION
 467                 + ": use most parimonious duplication model for GSDI: " );
 468         System.out.println( "     assign nodes as speciations which would otherwise be assiged" );
 469         System.out.println( "     as potential duplications dueof polytomies in the species tree" );
 470         System.out.println( " -" + gsdi.GUESS_FORMAT_OF_SPECIES_TREE
 471                 + ": to allow species tree in other formats than phyloXML (i.e. Newick, NHX, Nexus)" );
 472         System.out.println( " -" + gsdi.SDISE_OPTION
 473                 + ": to use SDIse algorithm instead of GSDI algorithm (for binary species trees)" );
 474         System.out.println();
 475         System.out.println( "Gene tree:" );
 476         System.out.println( " in phyloXM format, with taxonomy and sequence data in appropriate fields" );
 477         System.out.println();
 478         System.out.println( "Species tree:" );
 479         System.out.println( " in phyloXML format (unless option -" + gsdi.GUESS_FORMAT_OF_SPECIES_TREE + " is used)" );
 480         System.out.println();
 481         System.out.println( "Example: gsdi -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION
 482                 + "  gene_tree.xml tree_of_life.xml out.xml" );
 483         System.out.println();
 484     }
 485 }