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 SUFFIX_FOR_SPECIES_TREE_USED           = "_species_tree_used.xml";
  73     final static private String LOGFILE_SUFFIX                         = "_gsdi_log.txt";
  74     final static private String REMAPPED_SUFFIX                        = "_gsdi_remapped.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                               = "120629";
  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() != 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             out_file = cla.getFile( 2 );
 156             log_file = new File( ForesterUtil.removeSuffix( out_file.toString() ) + LOGFILE_SUFFIX );
 157         }
 158         catch ( final IllegalArgumentException e ) {
 159             ForesterUtil.fatalError( gsdi.PRG_NAME, "error in command line: " + e.getMessage() );
 160         }
 161         if ( ForesterUtil.isReadableFile( gene_tree_file ) != null ) {
 162             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isReadableFile( gene_tree_file ) );
 163         }
 164         if ( ForesterUtil.isReadableFile( species_tree_file ) != null ) {
 165             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isReadableFile( species_tree_file ) );
 166         }
 167         if ( ForesterUtil.isWritableFile( out_file ) != null ) {
 168             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( out_file ) );
 169         }
 170         if ( ForesterUtil.isWritableFile( log_file ) != null ) {
 171             ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( log_file ) );
 172         }
 173         try {
 174             log_writer = ForesterUtil.createEasyWriter( log_file );
 175         }
 176         catch ( final IOException e ) {
 177             ForesterUtil.fatalError( gsdi.PRG_NAME, "Failed to create [" + log_file + "]: " + e.getMessage() );
 178         }
 179         try {
 180             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 181             gene_tree = factory.create( gene_tree_file, new PhyloXmlParser() )[ 0 ];
 182         }
 183         catch ( final IOException e ) {
 184             fatalError( "ERROR",
 185                         "Failed to read gene tree from [" + gene_tree_file + "]: " + e.getMessage(),
 186                         log_writer );
 187         }
 188         try {
 189             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 190             final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( species_tree_file, true );
 191             if ( p instanceof PhyloXmlParser ) {
 192                 species_tree = factory.create( species_tree_file, p )[ 0 ];
 193             }
 194             else {
 195                 if ( REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE && ( p instanceof NHXParser ) ) {
 196                     ( ( NHXParser ) p ).setReplaceUnderscores( true );
 197                 }
 198                 species_tree = factory.create( species_tree_file, p )[ 0 ];
 199                 final TaxonomyComparisonBase comp_base = GSDI.determineTaxonomyComparisonBase( gene_tree );
 200                 switch ( comp_base ) {
 201                     case SCIENTIFIC_NAME:
 202                         try {
 203                             PhylogenyMethods
 204                                     .transferNodeNameToField( species_tree,
 205                                                               PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
 206                                                               true );
 207                         }
 208                         catch ( final PhyloXmlDataFormatException e ) {
 209                             fatalError( "USER ERROR", "Failed to transfer general node name to scientific name, in ["
 210                                     + species_tree_file + "]: " + e.getMessage(), log_writer );
 211                         }
 212                         break;
 213                     case CODE:
 214                         try {
 215                             PhylogenyMethods
 216                                     .transferNodeNameToField( species_tree,
 217                                                               PhylogenyMethods.PhylogenyNodeField.TAXONOMY_CODE,
 218                                                               true );
 219                         }
 220                         catch ( final PhyloXmlDataFormatException e ) {
 221                             fatalError( "USER ERROR", "Failed to transfer general node name to taxonomy code, in ["
 222                                     + species_tree_file + "]: " + e.getMessage(), log_writer );
 223                         }
 224                         break;
 225                     case ID:
 226                         try {
 227                             PhylogenyMethods.transferNodeNameToField( species_tree,
 228                                                                       PhylogenyMethods.PhylogenyNodeField.TAXONOMY_ID,
 229                                                                       true );
 230                         }
 231                         catch ( final PhyloXmlDataFormatException e ) {
 232                             fatalError( "USER ERROR", "Failed to transfer general node name to taxonomy id, in ["
 233                                     + species_tree_file + "]: " + e.getMessage(), log_writer );
 234                         }
 235                         break;
 236                     default:
 237                         fatalError( "UNEXPECTED ERROR", "unable to determine comparison base", log_writer );
 238                 }
 239             }
 240         }
 241         catch ( final IOException e ) {
 242             fatalError( "ERROR",
 243                         "Failed to read species tree from [" + species_tree_file + "]: " + e.getMessage(),
 244                         log_writer );
 245         }
 246         gene_tree.setRooted( true );
 247         species_tree.setRooted( true );
 248         if ( !gene_tree.isCompletelyBinary() ) {
 249             fatalError( "user error", "gene tree is not completely binary", log_writer );
 250         }
 251         if ( base_algorithm != BASE_ALGORITHM.GSDI ) {
 252             if ( !species_tree.isCompletelyBinary() ) {
 253                 fatalError( "user error", "species tree is not completely binary, use GSDI instead", log_writer );
 254             }
 255         }
 256         log_writer.println( PRG_NAME + " - " + PRG_DESC );
 257         log_writer.println( "  version         : " + PRG_VERSION );
 258         log_writer.println( "  date            : " + PRG_DATE );
 259         log_writer.println( "  forester version: " + ForesterConstants.FORESTER_VERSION );
 260         log_writer.println();
 261         log_writer.println( "Start time                               : "
 262                 + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) );
 263         System.out.println( "Start time                               : "
 264                 + new SimpleDateFormat( "yyyyMMdd HH:mm:ss" ).format( new Date() ) );
 265         log_writer.println( "Gene tree file                           : " + gene_tree_file.getCanonicalPath() );
 266         System.out.println( "Gene tree file                           : " + gene_tree_file.getCanonicalPath() );
 267         log_writer.println( "Gene tree name                           : "
 268                 + ( ForesterUtil.isEmpty( gene_tree.getName() ) ? "" : gene_tree.getName() ) );
 269         System.out.println( "Gene tree name                           : "
 270                 + ( ForesterUtil.isEmpty( gene_tree.getName() ) ? "" : gene_tree.getName() ) );
 271         log_writer.println( "Species tree file                        : " + species_tree_file.getCanonicalPath() );
 272         System.out.println( "Species tree file                        : " + species_tree_file.getCanonicalPath() );
 273         log_writer.println( "Species tree name                        : "
 274                 + ( ForesterUtil.isEmpty( species_tree.getName() ) ? "" : gene_tree.getName() ) );
 275         System.out.println( "Species tree name                        : "
 276                 + ( ForesterUtil.isEmpty( species_tree.getName() ) ? "" : gene_tree.getName() ) );
 277         SDI sdi = null;
 278         final long start_time = new Date().getTime();
 279         try {
 280             if ( base_algorithm == BASE_ALGORITHM.GSDI ) {
 281                 System.out.println( "Use most parsimonous duplication model   : " + most_parsimonous_duplication_model );
 282                 System.out.println( "Allow stripping of gene tree nodes       : " + allow_stripping_of_gene_tree );
 283                 log_writer.println( "Use most parsimonous duplication model   : " + most_parsimonous_duplication_model );
 284                 log_writer.println( "Allow stripping of gene tree nodes       : " + allow_stripping_of_gene_tree );
 285                 log_writer.flush();
 286                 sdi = new GSDI( gene_tree,
 287                                 species_tree,
 288                                 most_parsimonous_duplication_model,
 289                                 allow_stripping_of_gene_tree,
 290                                 true );
 291             }
 292             else {
 293                 System.out.println();
 294                 System.out.println( "Using SDIse algorithm" );
 295                 log_writer.println( "Using SDIse algorithm" );
 296                 log_writer.flush();
 297                 sdi = new SDIse( gene_tree, species_tree );
 298             }
 299         }
 300         catch ( final SDIException e ) {
 301             fatalError( "user error", e.getLocalizedMessage(), log_writer );
 302         }
 303         catch ( final IOException e ) {
 304             fatalError( "error", e.toString(), log_writer );
 305         }
 306         catch ( final Exception e ) {
 307             e.printStackTrace();
 308             fatalError( "unexpected error", e.toString(), log_writer );
 309         }
 310         System.out.println( "Running time (excluding I/O)             : " + ( new Date().getTime() - start_time )
 311                 + "ms" );
 312         log_writer.println( "Running time (excluding I/O)             : " + ( new Date().getTime() - start_time )
 313                 + "ms" );
 314         if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) ) {
 315             final GSDI gsdi = ( GSDI ) sdi;
 316             System.out.println( "Mapping based on                         : " + gsdi.getTaxCompBase() );
 317             log_writer.println( "Mapping based on                         : " + gsdi.getTaxCompBase() );
 318         }
 319         try {
 320             final PhylogenyWriter writer = new PhylogenyWriter();
 321             writer.toPhyloXML( out_file, gene_tree, 0 );
 322         }
 323         catch ( final IOException e ) {
 324             ForesterUtil.fatalError( PRG_NAME,
 325                                      "Failed to write to [" + out_file.getCanonicalPath() + "]: " + e.getMessage() );
 326         }
 327         System.out.println( "Wrote resulting gene tree to             : " + out_file.getCanonicalPath() );
 328         log_writer.println( "Wrote resulting gene tree to             : " + out_file.getCanonicalPath() );
 329         if ( base_algorithm == BASE_ALGORITHM.SDI ) {
 330             sdi.computeMappingCostL();
 331             System.out.println( "Mapping cost                             : " + sdi.computeMappingCostL() );
 332             log_writer.println( "Mapping cost                             : " + sdi.computeMappingCostL() );
 333         }
 334         else if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) ) {
 335             final GSDI gsdi = ( GSDI ) sdi;
 336             final File species_tree_used_file = new File( ForesterUtil.removeSuffix( out_file.toString() )
 337                     + SUFFIX_FOR_SPECIES_TREE_USED );
 338             try {
 339                 final PhylogenyWriter writer = new PhylogenyWriter();
 340                 writer.toPhyloXML( species_tree_used_file, gsdi.getSpeciesTree(), 0 );
 341             }
 342             catch ( final IOException e ) {
 343                 ForesterUtil.fatalError( PRG_NAME, "Failed to write to [" + species_tree_used_file.getCanonicalPath()
 344                         + "]: " + e.getMessage() );
 345             }
 346             System.out.println( "Wrote (stripped) species tree to         : "
 347                     + species_tree_used_file.getCanonicalPath() );
 348             log_writer.println( "Wrote (stripped) species tree to         : "
 349                     + species_tree_used_file.getCanonicalPath() );
 350             if ( ( gsdi.getReMappedScientificNamesFromGeneTree() != null )
 351                     && !gsdi.getReMappedScientificNamesFromGeneTree().isEmpty() ) {
 352                 System.out.println( "Number of gene tree species remapped     : "
 353                         + gsdi.getReMappedScientificNamesFromGeneTree().size() );
 354                 log_writer.println( "Number of gene tree species remapped     : "
 355                         + gsdi.getReMappedScientificNamesFromGeneTree().size() );
 356                 writeToRemappedFile( out_file, gsdi.getReMappedScientificNamesFromGeneTree(), log_writer );
 357             }
 358         }
 359         System.out.println( "Number of external nodes in gene tree    : " + gene_tree.getNumberOfExternalNodes() );
 360         log_writer.println( "Number of external nodes in gene tree    : " + gene_tree.getNumberOfExternalNodes() );
 361         System.out.println( "Number of external nodes in species tree : "
 362                 + sdi.getSpeciesTree().getNumberOfExternalNodes() );
 363         log_writer.println( "Number of external nodes in species tree : "
 364                 + sdi.getSpeciesTree().getNumberOfExternalNodes() );
 365         if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) ) {
 366             final GSDI gsdi = ( GSDI ) sdi;
 367             final int poly = PhylogenyMethods.countNumberOfPolytomies( gsdi.getSpeciesTree() );
 368             System.out.println( "Number of polytomies in species tree     : " + poly );
 369             log_writer.println( "Number of polytomies in species tree     : " + poly );
 370             System.out.println( "External nodes stripped from gene tree   : "
 371                     + gsdi.getStrippedExternalGeneTreeNodes().size() );
 372             log_writer.println( "External nodes stripped from gene tree   : "
 373                     + gsdi.getStrippedExternalGeneTreeNodes().size() );
 374             System.out.println( "External nodes stripped from species tree: "
 375                     + gsdi.getStrippedSpeciesTreeNodes().size() );
 376             log_writer.println( "External nodes stripped from species tree: "
 377                     + gsdi.getStrippedSpeciesTreeNodes().size() );
 378         }
 379         System.out.println();
 380         System.out.println( "Number of duplications                   : " + sdi.getDuplicationsSum() );
 381         log_writer.println( "Number of duplications                   : " + sdi.getDuplicationsSum() );
 382         if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) ) {
 383             final GSDI gsdi = ( GSDI ) sdi;
 384             if ( !most_parsimonous_duplication_model ) {
 385                 final int u = gsdi.getSpeciationOrDuplicationEventsSum();
 386                 System.out.println( "Number of potential duplications         : " + u );
 387                 log_writer.println( "Number of potential duplications         : " + u );
 388             }
 389             System.out.println( "Number of speciations                    : " + gsdi.getSpeciationsSum() );
 390             log_writer.println( "Number of speciations                    : " + gsdi.getSpeciationsSum() );
 391             log_writer.println();
 392             printMappedNodesToLog( log_writer, gsdi );
 393             log_writer.println();
 394             printStrippedGeneTreeNodesToLog( log_writer, gsdi );
 395         }
 396         System.out.println();
 397         System.out.println( "Wrote log to                             : " + log_file.getCanonicalPath() );
 398         System.out.println();
 399         log_writer.close();
 400     }
 401
 402     private static void writeToRemappedFile( final File out_file,
 403                                              final SortedSet<String> remapped,
 404                                              final EasyWriter log_writer ) throws IOException {
 405         final File file = new File( ForesterUtil.removeSuffix( out_file.toString() ) + REMAPPED_SUFFIX );
 406         final EasyWriter remapped_writer = ForesterUtil.createEasyWriter( file );
 407         for( final String s : remapped ) {
 408             remapped_writer.println( s );
 409         }
 410         remapped_writer.close();
 411         System.out.println( "Wrote remapped gene tree species to      : " + file.getCanonicalPath() );
 412         log_writer.println( "Wrote remapped gene tree species to      : " + file.getCanonicalPath() );
 413     }
 414
 415     private static void printMappedNodesToLog( final EasyWriter log_writer, final GSDI gsdi ) throws IOException {
 416         final SortedSet<String> ss = new TreeSet<String>();
 417         for( final PhylogenyNode n : gsdi.getMappedExternalSpeciesTreeNodes() ) {
 418             ss.add( n.toString() );
 419         }
 420         log_writer.println( "The following " + ss.size() + " species were used: " );
 421         for( final String s : ss ) {
 422             log_writer.println( "  " + s );
 423         }
 424     }
 425
 426     private static void fatalError( final String type, final String msg, final EasyWriter log_writer ) {
 427         try {
 428             log_writer.flush();
 429             log_writer.println();
 430             log_writer.print( type.toUpperCase() + ": " );
 431             log_writer.println( msg );
 432             log_writer.close();
 433         }
 434         catch ( final IOException e ) {
 435             e.printStackTrace();
 436         }
 437         ForesterUtil.fatalError( gsdi.PRG_NAME, msg );
 438     }
 439
 440     private static void printStrippedGeneTreeNodesToLog( final EasyWriter log_writer, final GSDI gsdi )
 441             throws IOException {
 442         final SortedMap<String, Integer> sm = new TreeMap<String, Integer>();
 443         for( final PhylogenyNode n : gsdi.getStrippedExternalGeneTreeNodes() ) {
 444             final String s = n.toString();
 445             if ( sm.containsKey( s ) ) {
 446                 sm.put( s, sm.get( s ) + 1 );
 447             }
 448             else {
 449                 sm.put( s, 1 );
 450             }
 451         }
 452         log_writer.println( "The following " + sm.size() + " nodes were stripped from the gene tree: " );
 453         for( final String s : sm.keySet() ) {
 454             final int count = sm.get( s );
 455             if ( count == 1 ) {
 456                 log_writer.println( "  " + s );
 457             }
 458             else {
 459                 log_writer.println( "  " + s + " [" + count + "]" );
 460             }
 461         }
 462     }
 463
 464     private static void print_help() {
 465         System.out.println( "Usage: " + gsdi.PRG_NAME
 466                 + " [-options] <gene tree in phyloXML format> <species tree> <outfile>" );
 467         System.out.println();
 468         System.out.println( "Options:" );
 469         System.out.println( " -" + gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION
 470                 + ": to allow stripping of gene tree nodes without a matching species" );
 471         System.out.println( " -" + gsdi.MOST_PARSIMONIOUS_OPTION
 472                 + ": use most parimonious duplication model for GSDI: " );
 473         System.out.println( "     assign nodes as speciations which would otherwise be assiged" );
 474         System.out.println( "     as potential duplications due to polytomies in the species tree" );
 475         System.out.println( " -" + gsdi.GUESS_FORMAT_OF_SPECIES_TREE
 476                 + ": to allow species tree in other formats than phyloXML (i.e. Newick, NHX, Nexus)" );
 477         System.out.println( " -" + gsdi.SDISE_OPTION
 478                 + ": to use SDIse algorithm instead of GSDI algorithm (for binary species trees)" );
 479         System.out.println();
 480         System.out.println( "Gene tree:" );
 481         System.out.println( " in phyloXM format, with taxonomy and sequence data in appropriate fields" );
 482         System.out.println();
 483         System.out.println( "Species tree:" );
 484         System.out.println( " in phyloXML format (unless option -" + gsdi.GUESS_FORMAT_OF_SPECIES_TREE + " is used)" );
 485         System.out.println();
 486         System.out.println( "Example: gsdi -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION
 487                 + "  gene_tree.xml tree_of_life.xml out.xml" );
 488         System.out.println();
 489     }
 490 }