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 allow_stripping_of_gene_tree = false;
 130         if ( cla.isOptionSet( gsdi.SDISE_OPTION ) ) {
 131             base_algorithm = BASE_ALGORITHM.SDI;
 132         }
 133         if ( cla.isOptionSet( gsdi.MOST_PARSIMONIOUS_OPTION ) ) {
 134             if ( base_algorithm != BASE_ALGORITHM.GSDI ) {
 135                 ForesterUtil.fatalError( gsdi.PRG_NAME, "Can only use most parsimonious duplication mode with GSDI" );
 136             }
 137             most_parsimonous_duplication_model = true;
 138         }
 139         if ( cla.isOptionSet( gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION ) ) {
 140             if ( base_algorithm != BASE_ALGORITHM.GSDI ) {
 141                 ForesterUtil.fatalError( gsdi.PRG_NAME, "Can only allow stripping of gene tree with GSDI" );
 142             }
 143             allow_stripping_of_gene_tree = true;
 144         }
 145         Phylogeny species_tree = null;
 146         Phylogeny gene_tree = null;
 147         File gene_tree_file = null;
 148         File species_tree_file = null;
 149         File out_file = null;
 150         File log_file = null;
 151         EasyWriter log_writer = null;
 152         try {
 153             gene_tree_file = cla.getFile( 0 );
 154             species_tree_file = cla.getFile( 1 );
 155             if ( cla.getNumberOfNames() == 3 ) {
 156                 out_file = cla.getFile( 2 );
 157             }
 158             else {
 159                 out_file = new File( ForesterUtil.removeSuffix( gene_tree_file.toString() ) + DEFAULT_OUTFILE_SUFFIX );
 160             }
 161             log_file = new File( ForesterUtil.removeSuffix( out_file.toString() ) + LOGFILE_SUFFIX );
 162         }
 163         catch ( final IllegalArgumentException e ) {
 164             ForesterUtil.fatalError( gsdi.PRG_NAME, "error in command line: " + e.getMessage() );
 165         }
 166         if ( ForesterUtil.isReadableFile( gene_tree_file ) != null ) {
 167             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isReadableFile( gene_tree_file ) );
 168         }
 169         if ( ForesterUtil.isReadableFile( species_tree_file ) != null ) {
 170             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isReadableFile( species_tree_file ) );
 171         }
 172         if ( ForesterUtil.isWritableFile( out_file ) != null ) {
 173             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( out_file ) );
 174         }
 175         if ( ForesterUtil.isWritableFile( log_file ) != null ) {
 176             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( log_file ) );
 177         }
 178         try {
 179             log_writer = ForesterUtil.createEasyWriter( log_file );
 180         }
 181         catch ( final IOException e ) {
 182             ForesterUtil.fatalError( gsdi.PRG_NAME, "Failed to create [" + log_file + "]: " + e.getMessage() );
 183         }
 184         try {
 185             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 186             gene_tree = factory.create( gene_tree_file, new PhyloXmlParser() )[ 0 ];
 187         }
 188         catch ( final IOException e ) {
 189             ForesterUtil.fatalError( gsdi.PRG_NAME,
 190                                      "Failed to read gene tree from [" + gene_tree_file + "]: " + e.getMessage() );
 191         }
 192         try {
 193             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 194             final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( species_tree_file, true );
 195             if ( p instanceof PhyloXmlParser ) {
 196                 species_tree = factory.create( species_tree_file, p )[ 0 ];
 197             }
 198             else {
 199                 if ( REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE && ( p instanceof NHXParser ) ) {
 200                     ( ( NHXParser ) p ).setReplaceUnderscores( true );
 201                 }
 202                 species_tree = factory.create( species_tree_file, p )[ 0 ];
 203                 final TaxonomyComparisonBase comp_base = GSDI.determineTaxonomyComparisonBase( gene_tree );
 204                 switch ( comp_base ) {
 205                     case SCIENTIFIC_NAME:
 206                         try {
 207                             PhylogenyMethods
 208                                     .transferNodeNameToField( species_tree,
 209                                                               PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
 210                                                               true );
 211                         }
 212                         catch ( final PhyloXmlDataFormatException e ) {
 213                             ForesterUtil.fatalError( gsdi.PRG_NAME,
 214                                                      "Failed to transfer general node name to scientific name, in ["
 215                                                              + species_tree_file + "]: " + e.getMessage() );
 216                         }
 217                         break;
 218                     case CODE:
 219                         try {
 220                             PhylogenyMethods
 221                                     .transferNodeNameToField( species_tree,
 222                                                               PhylogenyMethods.PhylogenyNodeField.TAXONOMY_CODE,
 223                                                               true );
 224                         }
 225                         catch ( final PhyloXmlDataFormatException e ) {
 226                             ForesterUtil.fatalError( gsdi.PRG_NAME,
 227                                                      "Failed to transfer general node name to taxonomy code, in ["
 228                                                              + species_tree_file + "]: " + e.getMessage() );
 229                         }
 230                         break;
 231                     case ID:
 232                         try {
 233                             PhylogenyMethods.transferNodeNameToField( species_tree,
 234                                                                       PhylogenyMethods.PhylogenyNodeField.TAXONOMY_ID,
 235                                                                       true );
 236                         }
 237                         catch ( final PhyloXmlDataFormatException e ) {
 238                             ForesterUtil.fatalError( gsdi.PRG_NAME,
 239                                                      "Failed to transfer general node name to taxonomy id, in ["
 240                                                              + species_tree_file + "]: " + e.getMessage() );
 241                         }
 242                         break;
 243                     default:
 244                         ForesterUtil.fatalError( gsdi.PRG_NAME, "unable to determine comparison base" );
 245                 }
 246             }
 247         }
 248         catch ( final IOException e ) {
 249             ForesterUtil.fatalError( gsdi.PRG_NAME, "Failed to read species tree from [" + species_tree_file + "]: "
 250                     + e.getMessage() );
 251         }
 252         gene_tree.setRooted( true );
 253         species_tree.setRooted( true );
 254         if ( !gene_tree.isCompletelyBinary() ) {
 255             log_writer.println( "User Error: gene tree is not completely binary" );
 256             log_writer.close();
 257             ForesterUtil.fatalError( gsdi.PRG_NAME, "gene tree is not completely binary" );
 258         }
 259         if ( base_algorithm != BASE_ALGORITHM.GSDI ) {
 260             if ( !species_tree.isCompletelyBinary() ) {
 261                 log_writer.println( "User Error: species tree is not completely binary, use GSDI instead" );
 262                 log_writer.close();
 263                 ForesterUtil.fatalError( gsdi.PRG_NAME, "species tree is not completely binary, use GSDI instead" );
 264             }
 265         }
 266         log_writer.println( PRG_NAME + " - " + PRG_DESC );
 267         log_writer.println( "  version         : " + PRG_VERSION );
 268         log_writer.println( "  date            : " + PRG_DATE );
 269         log_writer.println( "  forester version: " + ForesterConstants.FORESTER_VERSION );
 270         log_writer.println();
 271         log_writer.println( "Start time                               : "
 272                 + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) );
 273         System.out.println( "Start time                               : "
 274                 + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) );
 275         log_writer.println( "Gene tree file                           : " + gene_tree_file.getCanonicalPath() );
 276         System.out.println( "Gene tree file                           : " + gene_tree_file.getCanonicalPath() );
 277         log_writer.println( "Gene tree name                           : "
 278                 + ( ForesterUtil.isEmpty( gene_tree.getName() ) ? "" : gene_tree.getName() ) );
 279         System.out.println( "Gene tree name                           : "
 280                 + ( ForesterUtil.isEmpty( gene_tree.getName() ) ? "" : gene_tree.getName() ) );
 281         log_writer.println( "Species tree file                        : " + species_tree_file.getCanonicalPath() );
 282         System.out.println( "Species tree file                        : " + species_tree_file.getCanonicalPath() );
 283         log_writer.println( "Species tree name                        : "
 284                 + ( ForesterUtil.isEmpty( species_tree.getName() ) ? "" : gene_tree.getName() ) );
 285         System.out.println( "Species tree name                        : "
 286                 + ( ForesterUtil.isEmpty( species_tree.getName() ) ? "" : gene_tree.getName() ) );
 287         SDI sdi = null;
 288         final long start_time = new Date().getTime();
 289         try {
 290             if ( base_algorithm == BASE_ALGORITHM.GSDI ) {
 291                 System.out.println( "Use most parsimonous duplication model   : " + most_parsimonous_duplication_model );
 292                 System.out.println( "Allow stripping of gene tree nodes       : " + allow_stripping_of_gene_tree );
 293                 log_writer.println( "Use most parsimonous duplication model   : " + most_parsimonous_duplication_model );
 294                 log_writer.println( "Allow stripping of gene tree nodes       : " + allow_stripping_of_gene_tree );
 295                 log_writer.flush();
 296                 sdi = new GSDI( gene_tree,
 297                                 species_tree,
 298                                 most_parsimonous_duplication_model,
 299                                 allow_stripping_of_gene_tree,
 300                                 true );
 301             }
 302             else {
 303                 System.out.println();
 304                 System.out.println( "Using SDIse algorithm" );
 305                 log_writer.println( "Using SDIse algorithm" );
 306                 log_writer.flush();
 307                 sdi = new SDIse( gene_tree, species_tree );
 308             }
 309         }
 310         catch ( final SDIException e ) {
 311             log_writer.println( "User Error: " + e.getLocalizedMessage() );
 312             log_writer.close();
 313             ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
 314         }
 315         catch ( final IOException e ) {
 316             log_writer.println( "Error: " + e );
 317             log_writer.close();
 318             ForesterUtil.fatalError( PRG_NAME, e.toString() );
 319         }
 320         catch ( final Exception e ) {
 321             log_writer.println( "Error: " + e );
 322             log_writer.close();
 323             e.printStackTrace();
 324             System.exit( -1 );
 325         }
 326         System.out.println( "Running time (excluding I/O)             : " + ( new Date().getTime() - start_time )
 327                 + "ms" );
 328         log_writer.println( "Running time (excluding I/O)             : " + ( new Date().getTime() - start_time )
 329                 + "ms" );
 330         if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) ) {
 331             final GSDI gsdi = ( GSDI ) sdi;
 332             System.out.println( "Mapping based on                         : " + gsdi.getTaxCompBase() );
 333             log_writer.println( "Mapping based on                         : " + gsdi.getTaxCompBase() );
 334         }
 335         try {
 336             final PhylogenyWriter writer = new PhylogenyWriter();
 337             writer.toPhyloXML( out_file, gene_tree, 0 );
 338         }
 339         catch ( final IOException e ) {
 340             ForesterUtil.fatalError( PRG_NAME,
 341                                      "Failed to write to [" + out_file.getCanonicalPath() + "]: " + e.getMessage() );
 342         }
 343         System.out.println( "Wrote resulting gene tree to             : " + out_file.getCanonicalPath() );
 344         log_writer.println( "Wrote resulting gene tree to             : " + out_file.getCanonicalPath() );
 345         if ( base_algorithm == BASE_ALGORITHM.SDI ) {
 346             sdi.computeMappingCostL();
 347             System.out.println( "Mapping cost                             : " + sdi.computeMappingCostL() );
 348             log_writer.println( "Mapping cost                             : " + sdi.computeMappingCostL() );
 349         }
 350         else if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) ) {
 351             final GSDI gsdi = ( GSDI ) sdi;
 352             final File species_tree_used_file = new File( ForesterUtil.removeSuffix( out_file.toString() )
 353                     + SUFFIX_FOR_SPECIES_TREE_USED );
 354             try {
 355                 final PhylogenyWriter writer = new PhylogenyWriter();
 356                 writer.toPhyloXML( species_tree_used_file, gsdi.getSpeciesTree(), 0 );
 357             }
 358             catch ( final IOException e ) {
 359                 ForesterUtil.fatalError( PRG_NAME, "Failed to write to [" + species_tree_used_file.getCanonicalPath()
 360                         + "]: " + e.getMessage() );
 361             }
 362             System.out.println( "Wrote (stripped) species tree to         : "
 363                     + species_tree_used_file.getCanonicalPath() );
 364             log_writer.println( "Wrote (stripped) species tree to         : "
 365                     + species_tree_used_file.getCanonicalPath() );
 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.getCanonicalPath() );
 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 }