forester/test_data/gene_tree_tax_code_4.xml

   1 <?xml version="1.0" encoding="UTF-8"?>
   2 <phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd" xmlns="http://www.phyloxml.org">
   3 <phylogeny rooted="true">
   4   <clade>
   5     <clade>
   6       <clade>
   7         <clade>
   8           <clade>
   9             <clade>
  10               <clade>
  11                 <clade>
  12                   <clade>
  13                     <clade>
  14                       <clade>
  15                         <clade>
  16                           <clade>
  17                             <clade>
  18                               <clade>
  19                                 <taxonomy>
  20                                   <code>PLAFA</code>
  21                                 </taxonomy>
  22                                 <sequence>
  23                                   <name>A</name>
  24                                 </sequence>
  25                               </clade>
  26                               <clade>
  27                                 <taxonomy>
  28                                   <code>PLAYO</code>
  29                                 </taxonomy>
  30                                 <sequence>
  31                                   <name>A</name>
  32                                 </sequence>
  33                               </clade>
  34                             </clade>
  35                             <clade>
  36                               <taxonomy>
  37                                 <code>PLACH</code>
  38                               </taxonomy>
  39                               <sequence>
  40                                 <name>A</name>
  41                               </sequence>
  42                             </clade>
  43                           </clade>
  44                           <clade>
  45                             <taxonomy>
  46                               <code>PLAYO</code>
  47                             </taxonomy>
  48                             <sequence>
  49                               <name>B</name>
  50                             </sequence>
  51                           </clade>
  52                         </clade>
  53                         <clade>
  54                           <name>i have no species</name>
  55                         </clade>
  56                       </clade>
  57                       <clade>
  58                         <taxonomy>
  59                           <scientific_name>Homo sapiens</scientific_name>
  60                         </taxonomy>
  61                         <sequence>
  62                           <name>X</name>
  63                         </sequence>
  64                       </clade>
  65                     </clade>
  66                     <clade>
  67                       <taxonomy>
  68                         <code>XXXXX</code>
  69                       </taxonomy>
  70                       <sequence>
  71                         <name>X</name>
  72                       </sequence>
  73                     </clade>
  74                   </clade>
  75                   <clade>
  76                     <taxonomy>
  77                       <id provider="ncbi">3093</id>
  78                     </taxonomy>
  79                     <sequence>
  80                       <name>X</name>
  81                     </sequence>
  82                   </clade>
  83                 </clade>
  84                 <clade>
  85                   <clade>
  86                     <clade>
  87                       <clade>
  88                         <taxonomy>
  89                           <code>HUMAN</code>
  90                         </taxonomy>
  91                         <sequence>
  92                           <name>A</name>
  93                         </sequence>
  94                       </clade>
  95                       <clade>
  96                         <taxonomy>
  97                           <code>MOUSE</code>
  98                         </taxonomy>
  99                         <sequence>
 100                           <name>A</name>
 101                         </sequence>
 102                       </clade>
 103                     </clade>
 104                     <clade>
 105                       <taxonomy>
 106                         <code>YEAST</code>
 107                       </taxonomy>
 108                       <sequence>
 109                         <name>A</name>
 110                       </sequence>
 111                     </clade>
 112                   </clade>
 113                   <clade>
 114                     <clade>
 115                       <clade>
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 117                           <code>HUMAN</code>
 118                         </taxonomy>
 119                         <sequence>
 120                           <name>E</name>
 121                         </sequence>
 122                       </clade>
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 125                           <code>YEAST</code>
 126                         </taxonomy>
 127                         <sequence>
 128                           <name>E</name>
 129                         </sequence>
 130                       </clade>
 131                     </clade>
 132                     <clade>
 133                       <taxonomy>
 134                         <code>MOUSE</code>
 135                       </taxonomy>
 136                       <sequence>
 137                         <name>F</name>
 138                       </sequence>
 139                     </clade>
 140                   </clade>
 141                 </clade>
 142               </clade>
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 144                 <clade>
 145                   <taxonomy>
 146                     <code>NEMVE</code>
 147                   </taxonomy>
 148                   <sequence>
 149                     <name>C</name>
 150                   </sequence>
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 154                     <code>PETMA</code>
 155                   </taxonomy>
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 157                     <name>C</name>
 158                   </sequence>
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 160               </clade>
 161             </clade>
 162             <clade>
 163               <clade>
 164                 <clade>
 165                   <taxonomy>
 166                     <code>MYCGR</code>
 167                   </taxonomy>
 168                   <sequence>
 169                     <name>D</name>
 170                   </sequence>
 171                 </clade>
 172                 <clade>
 173                   <taxonomy>
 174                     <code>MYCGR</code>
 175                   </taxonomy>
 176                   <sequence>
 177                     <name>D1</name>
 178                   </sequence>
 179                 </clade>
 180               </clade>
 181               <clade>
 182                 <taxonomy>
 183                   <code>MYCPJ</code>
 184                 </taxonomy>
 185                 <sequence>
 186                   <name>D</name>
 187                 </sequence>
 188               </clade>
 189             </clade>
 190           </clade>
 191           <clade>
 192             <taxonomy>
 193               <code>PYRHO</code>
 194             </taxonomy>
 195             <sequence>
 196               <name>A</name>
 197             </sequence>
 198           </clade>
 199         </clade>
 200         <clade>
 201           <clade>
 202             <clade>
 203               <clade>
 204                 <clade>
 205                   <clade>
 206                     <clade>
 207                       <clade>
 208                         <clade>
 209                           <clade>
 210                             <clade>
 211                               <taxonomy>
 212                                 <code>PLAFA</code>
 213                               </taxonomy>
 214                               <sequence>
 215                                 <name>A</name>
 216                               </sequence>
 217                             </clade>
 218                             <clade>
 219                               <taxonomy>
 220                                 <code>PLAYO</code>
 221                               </taxonomy>
 222                               <sequence>
 223                                 <name>A</name>
 224                               </sequence>
 225                             </clade>
 226                           </clade>
 227                           <clade>
 228                             <taxonomy>
 229                               <code>PLACH</code>
 230                             </taxonomy>
 231                             <sequence>
 232                               <name>A</name>
 233                             </sequence>
 234                           </clade>
 235                         </clade>
 236                         <clade>
 237                           <taxonomy>
 238                             <code>PLAYO</code>
 239                           </taxonomy>
 240                           <sequence>
 241                             <name>B</name>
 242                           </sequence>
 243                         </clade>
 244                       </clade>
 245                       <clade>
 246                         <name>i have no species</name>
 247                       </clade>
 248                     </clade>
 249                     <clade>
 250                       <taxonomy>
 251                         <scientific_name>Homo sapiens</scientific_name>
 252                       </taxonomy>
 253                       <sequence>
 254                         <name>X</name>
 255                       </sequence>
 256                     </clade>
 257                   </clade>
 258                   <clade>
 259                     <taxonomy>
 260                       <code>XXXXX</code>
 261                     </taxonomy>
 262                     <sequence>
 263                       <name>X</name>
 264                     </sequence>
 265                   </clade>
 266                 </clade>
 267                 <clade>
 268                   <taxonomy>
 269                     <id provider="ncbi">3093</id>
 270                   </taxonomy>
 271                   <sequence>
 272                     <name>X</name>
 273                   </sequence>
 274                 </clade>
 275               </clade>
 276               <clade>
 277                 <clade>
 278                   <clade>
 279                     <clade>
 280                       <taxonomy>
 281                         <code>HUMAN</code>
 282                       </taxonomy>
 283                       <sequence>
 284                         <name>A</name>
 285                       </sequence>
 286                     </clade>
 287                     <clade>
 288                       <taxonomy>
 289                         <code>MOUSE</code>
 290                       </taxonomy>
 291                       <sequence>
 292                         <name>A</name>
 293                       </sequence>
 294                     </clade>
 295                   </clade>
 296                   <clade>
 297                     <taxonomy>
 298                       <code>YEAST</code>
 299                     </taxonomy>
 300                     <sequence>
 301                       <name>A</name>
 302                     </sequence>
 303                   </clade>
 304                 </clade>
 305                 <clade>
 306                   <clade>
 307                     <clade>
 308                       <taxonomy>
 309                         <code>HUMAN</code>
 310                       </taxonomy>
 311                       <sequence>
 312                         <name>E</name>
 313                       </sequence>
 314                     </clade>
 315                     <clade>
 316                       <taxonomy>
 317                         <code>YEAST</code>
 318                       </taxonomy>
 319                       <sequence>
 320                         <name>E</name>
 321                       </sequence>
 322                     </clade>
 323                   </clade>
 324                   <clade>
 325                     <taxonomy>
 326                       <code>MOUSE</code>
 327                     </taxonomy>
 328                     <sequence>
 329                       <name>F</name>
 330                     </sequence>
 331                   </clade>
 332                 </clade>
 333               </clade>
 334             </clade>
 335             <clade>
 336               <clade>
 337                 <taxonomy>
 338                   <code>NEMVE</code>
 339                 </taxonomy>
 340                 <sequence>
 341                   <name>C</name>
 342                 </sequence>
 343               </clade>
 344               <clade>
 345                 <taxonomy>
 346                   <code>PETMA</code>
 347                 </taxonomy>
 348                 <sequence>
 349                   <name>C</name>
 350                 </sequence>
 351               </clade>
 352             </clade>
 353           </clade>
 354           <clade>
 355             <clade>
 356               <clade>
 357                 <taxonomy>
 358                   <code>MYCGR</code>
 359                 </taxonomy>
 360                 <sequence>
 361                   <name>D</name>
 362                 </sequence>
 363               </clade>
 364               <clade>
 365                 <taxonomy>
 366                   <code>MYCGR</code>
 367                 </taxonomy>
 368                 <sequence>
 369                   <name>D1</name>
 370                 </sequence>
 371               </clade>
 372             </clade>
 373             <clade>
 374               <taxonomy>
 375                 <code>MYCPJ</code>
 376               </taxonomy>
 377               <sequence>
 378                 <name>D</name>
 379               </sequence>
 380             </clade>
 381           </clade>
 382         </clade>
 383       </clade>
 384       <clade>
 385         <clade>
 386           <clade>
 387             <clade>
 388               <clade>
 389                 <clade>
 390                   <clade>
 391                     <clade>
 392                       <clade>
 393                         <clade>
 394                           <clade>
 395                             <taxonomy>
 396                               <code>PLAFA</code>
 397                             </taxonomy>
 398                             <sequence>
 399                               <name>A</name>
 400                             </sequence>
 401                           </clade>
 402                           <clade>
 403                             <taxonomy>
 404                               <code>PLAYO</code>
 405                             </taxonomy>
 406                             <sequence>
 407                               <name>A</name>
 408                             </sequence>
 409                           </clade>
 410                         </clade>
 411                         <clade>
 412                           <taxonomy>
 413                             <code>PLACH</code>
 414                           </taxonomy>
 415                           <sequence>
 416                             <name>A</name>
 417                           </sequence>
 418                         </clade>
 419                       </clade>
 420                       <clade>
 421                         <taxonomy>
 422                           <code>PLAYO</code>
 423                         </taxonomy>
 424                         <sequence>
 425                           <name>B</name>
 426                         </sequence>
 427                       </clade>
 428                     </clade>
 429                     <clade>
 430                       <name>i have no species</name>
 431                     </clade>
 432                   </clade>
 433                   <clade>
 434                     <taxonomy>
 435                       <scientific_name>Homo sapiens</scientific_name>
 436                     </taxonomy>
 437                     <sequence>
 438                       <name>X</name>
 439                     </sequence>
 440                   </clade>
 441                 </clade>
 442                 <clade>
 443                   <taxonomy>
 444                     <code>XXXXX</code>
 445                   </taxonomy>
 446                   <sequence>
 447                     <name>X</name>
 448                   </sequence>
 449                 </clade>
 450               </clade>
 451               <clade>
 452                 <taxonomy>
 453                   <id provider="ncbi">3093</id>
 454                 </taxonomy>
 455                 <sequence>
 456                   <name>X</name>
 457                 </sequence>
 458               </clade>
 459             </clade>
 460             <clade>
 461               <clade>
 462                 <clade>
 463                   <clade>
 464                     <taxonomy>
 465                       <code>HUMAN</code>
 466                     </taxonomy>
 467                     <sequence>
 468                       <name>A</name>
 469                     </sequence>
 470                   </clade>
 471                   <clade>
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 473                       <code>MOUSE</code>
 474                     </taxonomy>
 475                     <sequence>
 476                       <name>A</name>
 477                     </sequence>
 478                   </clade>
 479                 </clade>
 480                 <clade>
 481                   <taxonomy>
 482                     <code>YEAST</code>
 483                   </taxonomy>
 484                   <sequence>
 485                     <name>A</name>
 486                   </sequence>
 487                 </clade>
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 489               <clade>
 490                 <clade>
 491                   <clade>
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 501                       <code>YEAST</code>
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 504                       <name>E</name>
 505                     </sequence>
 506                   </clade>
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 508                 <clade>
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 510                     <code>MOUSE</code>
 511                   </taxonomy>
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 518           </clade>
 519           <clade>
 520             <clade>
 521               <clade>
 522                 <clade>
 523                   <clade>
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 536                       <name>A</name>
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 539                 </clade>
 540                 <clade>
 541                   <taxonomy>
 542                     <code>PLACH</code>
 543                   </taxonomy>
 544                   <sequence>
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 546                   </sequence>
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 550                 <taxonomy>
 551                   <code>PLAYO</code>
 552                 </taxonomy>
 553                 <sequence>
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 555                 </sequence>
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 557             </clade>
 558             <clade>
 559               <clade>
 560                 <taxonomy>
 561                   <code>NEMVE</code>
 562                 </taxonomy>
 563                 <sequence>
 564                   <name>C</name>
 565                 </sequence>
 566               </clade>
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 569                   <code>PETMA</code>
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 571                 <sequence>
 572                   <name>C</name>
 573                 </sequence>
 574               </clade>
 575             </clade>
 576           </clade>
 577         </clade>
 578         <clade>
 579           <clade>
 580             <clade>
 581               <taxonomy>
 582                 <code>MYCGR</code>
 583               </taxonomy>
 584               <sequence>
 585                 <name>D</name>
 586               </sequence>
 587             </clade>
 588             <clade>
 589               <taxonomy>
 590                 <code>MYCGR</code>
 591               </taxonomy>
 592               <sequence>
 593                 <name>D1</name>
 594               </sequence>
 595             </clade>
 596           </clade>
 597           <clade>
 598             <taxonomy>
 599               <code>MYCPJ</code>
 600             </taxonomy>
 601             <sequence>
 602               <name>D</name>
 603             </sequence>
 604           </clade>
 605         </clade>
 606       </clade>
 607     </clade>
 608     <clade>
 609       <clade>
 610         <clade>
 611           <clade>
 612             <clade>
 613               <taxonomy>
 614                 <id provider="uniprot">266940</id>
 615                 <code>KINRD</code>
 616                 <scientific_name>Kineococcus radiotolerans</scientific_name>
 617               </taxonomy>
 618               <sequence>
 619                 <name>A</name>
 620               </sequence>
 621             </clade>
 622             <clade>
 623               <taxonomy>
 624                 <id provider="uniprot">378753</id>
 625                 <code>KOCRD</code>
 626                 <scientific_name>Kocuria rhizophila</scientific_name>
 627               </taxonomy>
 628               <sequence>
 629                 <name>A</name>
 630               </sequence>
 631             </clade>
 632           </clade>
 633           <clade>
 634             <clade>
 635               <taxonomy>
 636                 <code>MICPN</code>
 637               </taxonomy>
 638               <sequence>
 639                 <name>A</name>
 640               </sequence>
 641             </clade>
 642             <clade>
 643               <taxonomy>
 644                 <code>THEFY</code>
 645               </taxonomy>
 646               <sequence>
 647                 <name>A</name>
 648               </sequence>
 649             </clade>
 650           </clade>
 651         </clade>
 652         <clade>
 653           <taxonomy>
 654             <code>STRCO</code>
 655           </taxonomy>
 656           <sequence>
 657             <name>A</name>
 658           </sequence>
 659         </clade>
 660       </clade>
 661       <clade>
 662         <taxonomy>
 663           <code>BACTN</code>
 664         </taxonomy>
 665         <sequence>
 666           <name>A</name>
 667         </sequence>
 668       </clade>
 669     </clade>
 670   </clade>
 671 </phylogeny>
 672 </phyloxml>