makefile

   1 ###################################################\r
   2 #\r
   3 # Makefile for mothur\r
   4 # Creator [Xcode -> Makefile Ver: Feb 14 2007 09:18:41]\r
   5 # Created: April 16, 2010\r
   6 #\r
   7 ###################################################\r
   8 \r
   9 #\r
  10 # Macros\r
  11 #\r
  12 \r
  13 CC = g++ \r
  14 CC_OPTIONS = -O3\r
  15 \r
  16 # if you do not want to use the readline library set to no, default yes.\r
  17 # make sure you have the library installed\r
  18 \r
  19 USEREADLINE ?= yes\r
  20 \r
  21 ifeq  ($(strip $(USEREADLINE)),yes)\r
  22     CC_OPTIONS += -DUSE_READLINE\r
  23         LNK_OPTIONS += \\r
  24       -lreadline\\r
  25       -lncurses\\r
  26       -L../readline-6.0\r
  27 endif\r
  28 \r
  29 USEMPI ?= no\r
  30 \r
  31 ifeq  ($(strip $(USEMPI)),yes)\r
  32         CC = mpic++\r
  33     CC_OPTIONS += -DUSE_MPI\r
  34 endif\r
  35 \r
  36 #\r
  37 # INCLUDE directories for mothur\r
  38 #\r
  39 \r
  40      INCLUDE = -I.\r
  41 \r
  42 #\r
  43 # Build mothur\r
  44 #\r
  45 \r
  46 mothur : \\r
  47                 ./sharedutilities.o\\r
  48                 ./treegroupscommand.o\\r
  49                 ./bootstrapsharedcommand.o\\r
  50                 ./matrixoutputcommand.o\\r
  51                 ./getoturepcommand.o\\r
  52                 ./screenseqscommand.o\\r
  53                 ./chimera.o\\r
  54                 ./decalc.o\\r
  55                 ./readotucommand.o\\r
  56                 ./readdistcommand.o\\r
  57                 ./commandfactory.o\\r
  58                 ./alignment.o\\r
  59                 ./alignmentcell.o\\r
  60                 ./gotohoverlap.o\\r
  61                 ./overlap.o\\r
  62                 ./needlemanoverlap.o\\r
  63                 ./blastalign.o\\r
  64                 ./noalign.o\\r
  65                 ./suffixdb.o\\r
  66                 ./suffixnodes.o\\r
  67                 ./suffixtree.o\\r
  68                 ./blastdb.o\\r
  69                 ./nast.o\\r
  70                 ./nastreport.o\\r
  71                 ./boneh.o\\r
  72                 ./efron.o\\r
  73                 ./solow.o\\r
  74                 ./unifracweightedcommand.o\\r
  75                 ./weighted.o\\r
  76                 ./unweighted.o\\r
  77                 ./unifracunweightedcommand.o\\r
  78                 ./getsabundcommand.o\\r
  79                 ./getrabundcommand.o\\r
  80                 ./bellerophon.o\\r
  81                 ./pintail.o\\r
  82                 ./sharedanderbergs.o\\r
  83                 ./venncommand.o\\r
  84                 ./venn.o\\r
  85                 ./fullmatrix.o\\r
  86                 ./heatmap.o\\r
  87                 ./heatmapcommand.o\\r
  88                 ./libshuffcommand.o\\r
  89                 ./nocommands.o\\r
  90                 ./sharedbraycurtis.o\\r
  91                 ./sharedkulczynski.o\\r
  92                 ./sharedlennon.o\\r
  93                 ./sharedkulczynskicody.o\\r
  94                 ./sharedmorisitahorn.o\\r
  95                 ./sharedochiai.o\\r
  96                 ./readcolumn.o\\r
  97                 ./readotu.o\\r
  98                 ./readphylip.o\\r
  99                 ./consensuscommand.o\\r
 100                 ./heatmapsimcommand.o\\r
 101                 ./heatmapsim.o\\r
 102                 ./optionparser.o\\r
 103                 ./filterseqscommand.o\\r
 104                 ./goodscoverage.o\\r
 105                 ./sequencedb.o\\r
 106                 ./sharedjackknife.o\\r
 107                 ./sharedmarczewski.o\\r
 108                 ./aligncommand.o\\r
 109                 ./treemap.o\\r
 110                 ./parsimonycommand.o\\r
 111                 ./parsimony.o\\r
 112                 ./seqsummarycommand.o\\r
 113                 ./chimeraccodecommand.o\\r
 114                 ./chimerabellerophoncommand.o\\r
 115                 ./chimeracheckcommand.o\\r
 116                 ./chimeraslayercommand.o\\r
 117                 ./chimerapintailcommand.o\\r
 118                 ./chimeraseqscommand.o\\r
 119                 ./sharedlistvector.o\\r
 120                 ./tree.o\\r
 121                 ./readtree.o\\r
 122                 ./sharedsobscollectsummary.o\\r
 123                 ./deconvolutecommand.o\\r
 124                 ./listseqscommand.o\\r
 125                 ./getseqscommand.o\\r
 126                 ./removeseqscommand.o\\r
 127                 ./systemcommand.o\\r
 128                 ./binsequencecommand.o\\r
 129                 ./distancecommand.o\\r
 130                 ./ace.o\\r
 131                 ./averagelinkage.o\\r
 132                 ./bootstrap.o\\r
 133                 ./calculator.o\\r
 134                 ./chao1.o\\r
 135                 ./cluster.o\\r
 136                 ./clustercommand.o\\r
 137                 ./collect.o\\r
 138                 ./collectcommand.o\\r
 139                 ./collectsharedcommand.o\\r
 140                 ./commandoptionparser.o\\r
 141                 ./completelinkage.o\\r
 142                 ./database.o\\r
 143                 ./engine.o\\r
 144                 ./fastamap.o\\r
 145                 ./fileoutput.o\\r
 146                 ./globaldata.o\\r
 147                 ./groupmap.o\\r
 148                 ./helpcommand.o\\r
 149                 ./makegroupcommand.o\\r
 150                 ./chopseqscommand.o\\r
 151                 ./clearcutcommand.o\\r
 152                 ./catchallcommand.o\\r
 153                 ./splitabundcommand.o\\r
 154                 ./splitmatrix.o\\r
 155                 ./clustersplitcommand.o\\r
 156                 ./weightedlinkage.o\\r
 157                 ./inputdata.o\\r
 158                 ./jackknife.o\\r
 159                 ./kmer.o\\r
 160                 ./kmerdb.o\\r
 161                 ./listvector.o\\r
 162                 ./mothur.o\\r
 163                 ./nameassignment.o\\r
 164                 ./npshannon.o\\r
 165                 ./ordervector.o\\r
 166                 ./progress.o\\r
 167                 ./quitcommand.o\\r
 168                 ./rabundvector.o\\r
 169                 ./rarecalc.o\\r
 170                 ./raredisplay.o\\r
 171                 ./rarefact.o\\r
 172                 ./rarefactcommand.o\\r
 173                 ./rarefactsharedcommand.o\\r
 174                 ./sabundvector.o\\r
 175                 ./sequence.o\\r
 176                 ./shannon.o\\r
 177                 ./sharedace.o\\r
 178                 ./sharedchao1.o\\r
 179                 ./sharedcommand.o\\r
 180                 ./sharedjabund.o\\r
 181                 ./sharedjclass.o\\r
 182                 ./sharedjest.o\\r
 183                 ./sharedordervector.o\\r
 184                 ./sharedrabundvector.o\\r
 185                 ./sharedsabundvector.o\\r
 186                 ./sharedsobs.o\\r
 187                 ./sharedsorabund.o\\r
 188                 ./sharedsorclass.o\\r
 189                 ./sharedsorest.o\\r
 190                 ./sharedthetan.o\\r
 191                 ./sharedthetayc.o\\r
 192                 ./simpson.o\\r
 193                 ./singlelinkage.o\\r
 194                 ./sparsematrix.o\\r
 195                 ./summarycommand.o\\r
 196                 ./summarysharedcommand.o\\r
 197                 ./uvest.o\\r
 198                 ./validcalculator.o\\r
 199                 ./validparameter.o\\r
 200                 ./treenode.o\\r
 201                 ./readtreecommand.o\\r
 202                 ./reversecommand.o\\r
 203                 ./trimseqscommand.o\\r
 204                 ./slibshuff.o\\r
 205                 ./libshuff.o\\r
 206                 ./dlibshuff.o\\r
 207                 ./mergefilecommand.o\\r
 208                 ./coverage.o\\r
 209                 ./whittaker.o\\r
 210                 ./preclustercommand.o\\r
 211                 ./otuhierarchycommand.o\\r
 212                 ./setdircommand.o\\r
 213                 ./getgroupcommand.o\\r
 214                 ./getlabelcommand.o\\r
 215                 ./secondarystructurecommand.o\\r
 216                 ./mothurout.o\\r
 217                 ./parselistscommand.o\\r
 218                 ./readblast.o\\r
 219                 ./chimeracheckrdp.o\\r
 220                 ./hclustercommand.o\\r
 221                 ./hcluster.o\\r
 222                 ./getlistcountcommand.o\\r
 223                 ./readcluster.o\\r
 224                 ./ccode.o\\r
 225                 ./taxonomyequalizer.o\\r
 226                 ./phylotypecommand.o\\r
 227                 ./classifyseqscommand.o\\r
 228                 ./classifyotucommand.o\\r
 229                 ./parsesffcommand.o\\r
 230                 ./classify.o\\r
 231                 ./phylotree.o\\r
 232                 ./phylodiversity.o\\r
 233                 ./phylodiversitycommand.o\\r
 234                 ./bayesian.o\\r
 235                 ./phylosummary.o\\r
 236                 ./alignmentdb.o\\r
 237                 ./knn.o\\r
 238                 ./distancedb.o\\r
 239                 ./chimeraslayer.o\\r
 240                 ./slayer.o\\r
 241                 ./pcacommand.o\\r
 242                 ./formatcolumn.o\\r
 243                 ./formatphylip.o\\r
 244                 ./mgclustercommand.o\\r
 245                 ./getsharedotucommand.o\\r
 246                 ./maligner.o\\r
 247                 ./chimerarealigner.o\\r
 248                 ./bergerparker.o\\r
 249                 ./bstick.o\\r
 250                 ./sharedkstest.o\\r
 251                 ./qstat.o\\r
 252                 ./shen.o\\r
 253                 ./logsd.o\\r
 254                 ./geom.o\\r
 255                 ./setlogfilecommand.o\r
 256         $(CC) $(LNK_OPTIONS) \\r
 257                 ./sharedutilities.o\\r
 258                 ./treegroupscommand.o\\r
 259                 ./bootstrapsharedcommand.o\\r
 260                 ./matrixoutputcommand.o\\r
 261                 ./getoturepcommand.o\\r
 262                 ./screenseqscommand.o\\r
 263                 ./chimera.o\\r
 264                 ./decalc.o\\r
 265                 ./readotucommand.o\\r
 266                 ./readdistcommand.o\\r
 267                 ./commandfactory.o\\r
 268                 ./alignment.o\\r
 269                 ./alignmentcell.o\\r
 270                 ./gotohoverlap.o\\r
 271                 ./overlap.o\\r
 272                 ./needlemanoverlap.o\\r
 273                 ./blastalign.o\\r
 274                 ./noalign.o\\r
 275                 ./suffixdb.o\\r
 276                 ./suffixnodes.o\\r
 277                 ./suffixtree.o\\r
 278                 ./blastdb.o\\r
 279                 ./nast.o\\r
 280                 ./nastreport.o\\r
 281                 ./boneh.o\\r
 282                 ./efron.o\\r
 283                 ./solow.o\\r
 284                 ./unifracweightedcommand.o\\r
 285                 ./weighted.o\\r
 286                 ./unweighted.o\\r
 287                 ./unifracunweightedcommand.o\\r
 288                 ./getsabundcommand.o\\r
 289                 ./getrabundcommand.o\\r
 290                 ./bellerophon.o\\r
 291                 ./pintail.o\\r
 292                 ./sharedanderbergs.o\\r
 293                 ./venncommand.o\\r
 294                 ./venn.o\\r
 295                 ./fullmatrix.o\\r
 296                 ./heatmap.o\\r
 297                 ./heatmapcommand.o\\r
 298                 ./libshuffcommand.o\\r
 299                 ./nocommands.o\\r
 300                 ./sharedbraycurtis.o\\r
 301                 ./sharedkulczynski.o\\r
 302                 ./sharedlennon.o\\r
 303                 ./sharedkulczynskicody.o\\r
 304                 ./sharedmorisitahorn.o\\r
 305                 ./sharedochiai.o\\r
 306                 ./readcolumn.o\\r
 307                 ./readotu.o\\r
 308                 ./readphylip.o\\r
 309                 ./consensuscommand.o\\r
 310                 ./heatmapsimcommand.o\\r
 311                 ./heatmapsim.o\\r
 312                 ./optionparser.o\\r
 313                 ./filterseqscommand.o\\r
 314                 ./goodscoverage.o\\r
 315                 ./sequencedb.o\\r
 316                 ./sharedjackknife.o\\r
 317                 ./sharedmarczewski.o\\r
 318                 ./aligncommand.o\\r
 319                 ./treemap.o\\r
 320                 ./parsimonycommand.o\\r
 321                 ./parsimony.o\\r
 322                 ./seqsummarycommand.o\\r
 323                 ./chimeraccodecommand.o\\r
 324                 ./chimerabellerophoncommand.o\\r
 325                 ./chimeracheckcommand.o\\r
 326                 ./chimeraslayercommand.o\\r
 327                 ./chimerapintailcommand.o\\r
 328                 ./chimeraseqscommand.o\\r
 329                 ./sharedlistvector.o\\r
 330                 ./tree.o\\r
 331                 ./readtree.o\\r
 332                 ./sharedsobscollectsummary.o\\r
 333                 ./deconvolutecommand.o\\r
 334                 ./listseqscommand.o\\r
 335                 ./getseqscommand.o\\r
 336                 ./removeseqscommand.o\\r
 337                 ./systemcommand.o\\r
 338                 ./binsequencecommand.o\\r
 339                 ./distancecommand.o\\r
 340                 ./ace.o\\r
 341                 ./averagelinkage.o\\r
 342                 ./bootstrap.o\\r
 343                 ./calculator.o\\r
 344                 ./chao1.o\\r
 345                 ./cluster.o\\r
 346                 ./clustercommand.o\\r
 347                 ./collect.o\\r
 348                 ./collectcommand.o\\r
 349                 ./collectsharedcommand.o\\r
 350                 ./commandoptionparser.o\\r
 351                 ./completelinkage.o\\r
 352                 ./database.o\\r
 353                 ./engine.o\\r
 354                 ./fastamap.o\\r
 355                 ./fileoutput.o\\r
 356                 ./globaldata.o\\r
 357                 ./groupmap.o\\r
 358                 ./helpcommand.o\\r
 359                 ./makegroupcommand.o\\r
 360                 ./chopseqscommand.o\\r
 361                 ./clearcutcommand.o\\r
 362                 ./catchallcommand.o\\r
 363                 ./splitabundcommand.o\\r
 364                 ./splitmatrix.o\\r
 365                 ./clustersplitcommand.o\\r
 366                 ./weightedlinkage.o\\r
 367                 ./inputdata.o\\r
 368                 ./jackknife.o\\r
 369                 ./kmer.o\\r
 370                 ./kmerdb.o\\r
 371                 ./listvector.o\\r
 372                 ./mothur.o\\r
 373                 ./nameassignment.o\\r
 374                 ./npshannon.o\\r
 375                 ./ordervector.o\\r
 376                 ./progress.o\\r
 377                 ./quitcommand.o\\r
 378                 ./rabundvector.o\\r
 379                 ./rarecalc.o\\r
 380                 ./raredisplay.o\\r
 381                 ./rarefact.o\\r
 382                 ./rarefactcommand.o\\r
 383                 ./rarefactsharedcommand.o\\r
 384                 ./sabundvector.o\\r
 385                 ./sequence.o\\r
 386                 ./shannon.o\\r
 387                 ./sharedace.o\\r
 388                 ./sharedchao1.o\\r
 389                 ./sharedcommand.o\\r
 390                 ./sharedjabund.o\\r
 391                 ./sharedjclass.o\\r
 392                 ./sharedjest.o\\r
 393                 ./sharedordervector.o\\r
 394                 ./sharedrabundvector.o\\r
 395                 ./sharedsabundvector.o\\r
 396                 ./sharedsobs.o\\r
 397                 ./sharedsorabund.o\\r
 398                 ./sharedsorclass.o\\r
 399                 ./sharedsorest.o\\r
 400                 ./sharedthetan.o\\r
 401                 ./sharedthetayc.o\\r
 402                 ./simpson.o\\r
 403                 ./singlelinkage.o\\r
 404                 ./sparsematrix.o\\r
 405                 ./summarycommand.o\\r
 406                 ./summarysharedcommand.o\\r
 407                 ./uvest.o\\r
 408                 ./validcalculator.o\\r
 409                 ./validparameter.o\\r
 410                 ./treenode.o\\r
 411                 ./readtreecommand.o\\r
 412                 ./reversecommand.o\\r
 413                 ./trimseqscommand.o\\r
 414                 ./slibshuff.o\\r
 415                 ./libshuff.o\\r
 416                 ./dlibshuff.o\\r
 417                 ./mergefilecommand.o\\r
 418                 ./coverage.o\\r
 419                 ./whittaker.o\\r
 420                 ./preclustercommand.o\\r
 421                 ./otuhierarchycommand.o\\r
 422                 ./setdircommand.o\\r
 423                 ./getgroupcommand.o\\r
 424                 ./getlabelcommand.o\\r
 425                 ./secondarystructurecommand.o\\r
 426                 ./mothurout.o\\r
 427                 ./parselistscommand.o\\r
 428                 ./readblast.o\\r
 429                 ./chimeracheckrdp.o\\r
 430                 ./hclustercommand.o\\r
 431                 ./hcluster.o\\r
 432                 ./getlistcountcommand.o\\r
 433                 ./readcluster.o\\r
 434                 ./ccode.o\\r
 435                 ./taxonomyequalizer.o\\r
 436                 ./phylotypecommand.o\\r
 437                 ./classifyseqscommand.o\\r
 438                 ./classifyotucommand.o\\r
 439                 ./parsesffcommand.o\\r
 440                 ./classify.o\\r
 441                 ./phylotree.o\\r
 442                 ./phylodiversity.o\\r
 443                 ./phylodiversitycommand.o\\r
 444                 ./bayesian.o\\r
 445                 ./phylosummary.o\\r
 446                 ./alignmentdb.o\\r
 447                 ./knn.o\\r
 448                 ./distancedb.o\\r
 449                 ./chimeraslayer.o\\r
 450                 ./slayer.o\\r
 451                 ./pcacommand.o\\r
 452                 ./formatcolumn.o\\r
 453                 ./formatphylip.o\\r
 454                 ./mgclustercommand.o\\r
 455                 ./getsharedotucommand.o\\r
 456                 ./maligner.o\\r
 457                 ./chimerarealigner.o\\r
 458                 ./bergerparker.o\\r
 459                 ./bstick.o\\r
 460                 ./sharedkstest.o\\r
 461                 ./qstat.o\\r
 462                 ./shen.o\\r
 463                 ./logsd.o\\r
 464                 ./geom.o\\r
 465                 ./setlogfilecommand.o\\r
 466                 -o ../Release/mothur\r
 467 \r
 468 clean : \r
 469                 rm \\r
 470                 ./sharedutilities.o\\r
 471                 ./treegroupscommand.o\\r
 472                 ./bootstrapsharedcommand.o\\r
 473                 ./matrixoutputcommand.o\\r
 474                 ./getoturepcommand.o\\r
 475                 ./screenseqscommand.o\\r
 476                 ./chimera.o\\r
 477                 ./decalc.o\\r
 478                 ./readotucommand.o\\r
 479                 ./readdistcommand.o\\r
 480                 ./commandfactory.o\\r
 481                 ./alignment.o\\r
 482                 ./alignmentcell.o\\r
 483                 ./gotohoverlap.o\\r
 484                 ./overlap.o\\r
 485                 ./needlemanoverlap.o\\r
 486                 ./blastalign.o\\r
 487                 ./noalign.o\\r
 488                 ./suffixdb.o\\r
 489                 ./suffixnodes.o\\r
 490                 ./suffixtree.o\\r
 491                 ./blastdb.o\\r
 492                 ./nast.o\\r
 493                 ./nastreport.o\\r
 494                 ./boneh.o\\r
 495                 ./efron.o\\r
 496                 ./solow.o\\r
 497                 ./unifracweightedcommand.o\\r
 498                 ./weighted.o\\r
 499                 ./unweighted.o\\r
 500                 ./unifracunweightedcommand.o\\r
 501                 ./getsabundcommand.o\\r
 502                 ./getrabundcommand.o\\r
 503                 ./bellerophon.o\\r
 504                 ./pintail.o\\r
 505                 ./sharedanderbergs.o\\r
 506                 ./venncommand.o\\r
 507                 ./venn.o\\r
 508                 ./fullmatrix.o\\r
 509                 ./heatmap.o\\r
 510                 ./heatmapcommand.o\\r
 511                 ./libshuffcommand.o\\r
 512                 ./nocommands.o\\r
 513                 ./sharedbraycurtis.o\\r
 514                 ./sharedkulczynski.o\\r
 515                 ./sharedlennon.o\\r
 516                 ./sharedkulczynskicody.o\\r
 517                 ./sharedmorisitahorn.o\\r
 518                 ./sharedochiai.o\\r
 519                 ./readcolumn.o\\r
 520                 ./readotu.o\\r
 521                 ./readphylip.o\\r
 522                 ./consensuscommand.o\\r
 523                 ./heatmapsimcommand.o\\r
 524                 ./heatmapsim.o\\r
 525                 ./optionparser.o\\r
 526                 ./filterseqscommand.o\\r
 527                 ./goodscoverage.o\\r
 528                 ./sequencedb.o\\r
 529                 ./sharedjackknife.o\\r
 530                 ./sharedmarczewski.o\\r
 531                 ./aligncommand.o\\r
 532                 ./treemap.o\\r
 533                 ./parsimonycommand.o\\r
 534                 ./parsimony.o\\r
 535                 ./seqsummarycommand.o\\r
 536                 ./chimeraccodecommand.o\\r
 537                 ./chimerabellerophoncommand.o\\r
 538                 ./chimeracheckcommand.o\\r
 539                 ./chimeraslayercommand.o\\r
 540                 ./chimerapintailcommand.o\\r
 541                 ./chimeraseqscommand.o\\r
 542                 ./sharedlistvector.o\\r
 543                 ./tree.o\\r
 544                 ./readtree.o\\r
 545                 ./sharedsobscollectsummary.o\\r
 546                 ./deconvolutecommand.o\\r
 547                 ./listseqscommand.o\\r
 548                 ./getseqscommand.o\\r
 549                 ./removeseqscommand.o\\r
 550                 ./systemcommand.o\\r
 551                 ./binsequencecommand.o\\r
 552                 ./distancecommand.o\\r
 553                 ./ace.o\\r
 554                 ./averagelinkage.o\\r
 555                 ./bootstrap.o\\r
 556                 ./calculator.o\\r
 557                 ./chao1.o\\r
 558                 ./cluster.o\\r
 559                 ./clustercommand.o\\r
 560                 ./collect.o\\r
 561                 ./collectcommand.o\\r
 562                 ./collectsharedcommand.o\\r
 563                 ./commandoptionparser.o\\r
 564                 ./completelinkage.o\\r
 565                 ./database.o\\r
 566                 ./engine.o\\r
 567                 ./fastamap.o\\r
 568                 ./fileoutput.o\\r
 569                 ./globaldata.o\\r
 570                 ./groupmap.o\\r
 571                 ./helpcommand.o\\r
 572                 ./makegroupcommand.o\\r
 573                 ./chopseqscommand.o\\r
 574                 ./clearcutcommand.o\\r
 575                 ./catchallcommand.o\\r
 576                 ./splitabundcommand.o\\r
 577                 ./splitmatrix.o\\r
 578                 ./clustersplitcommand.o\\r
 579                 ./weightedlinkage.o\\r
 580                 ./inputdata.o\\r
 581                 ./jackknife.o\\r
 582                 ./kmer.o\\r
 583                 ./kmerdb.o\\r
 584                 ./listvector.o\\r
 585                 ./mothur.o\\r
 586                 ./nameassignment.o\\r
 587                 ./npshannon.o\\r
 588                 ./ordervector.o\\r
 589                 ./progress.o\\r
 590                 ./quitcommand.o\\r
 591                 ./rabundvector.o\\r
 592                 ./rarecalc.o\\r
 593                 ./raredisplay.o\\r
 594                 ./rarefact.o\\r
 595                 ./rarefactcommand.o\\r
 596                 ./rarefactsharedcommand.o\\r
 597                 ./sabundvector.o\\r
 598                 ./sequence.o\\r
 599                 ./shannon.o\\r
 600                 ./sharedace.o\\r
 601                 ./sharedchao1.o\\r
 602                 ./sharedcommand.o\\r
 603                 ./sharedjabund.o\\r
 604                 ./sharedjclass.o\\r
 605                 ./sharedjest.o\\r
 606                 ./sharedordervector.o\\r
 607                 ./sharedrabundvector.o\\r
 608                 ./sharedsabundvector.o\\r
 609                 ./sharedsobs.o\\r
 610                 ./sharedsorabund.o\\r
 611                 ./sharedsorclass.o\\r
 612                 ./sharedsorest.o\\r
 613                 ./sharedthetan.o\\r
 614                 ./sharedthetayc.o\\r
 615                 ./simpson.o\\r
 616                 ./singlelinkage.o\\r
 617                 ./sparsematrix.o\\r
 618                 ./summarycommand.o\\r
 619                 ./summarysharedcommand.o\\r
 620                 ./uvest.o\\r
 621                 ./validcalculator.o\\r
 622                 ./validparameter.o\\r
 623                 ./treenode.o\\r
 624                 ./readtreecommand.o\\r
 625                 ./reversecommand.o\\r
 626                 ./trimseqscommand.o\\r
 627                 ./slibshuff.o\\r
 628                 ./libshuff.o\\r
 629                 ./dlibshuff.o\\r
 630                 ./mergefilecommand.o\\r
 631                 ./coverage.o\\r
 632                 ./whittaker.o\\r
 633                 ./preclustercommand.o\\r
 634                 ./otuhierarchycommand.o\\r
 635                 ./setdircommand.o\\r
 636                 ./getgroupcommand.o\\r
 637                 ./getlabelcommand.o\\r
 638                 ./secondarystructurecommand.o\\r
 639                 ./mothurout.o\\r
 640                 ./parselistscommand.o\\r
 641                 ./readblast.o\\r
 642                 ./chimeracheckrdp.o\\r
 643                 ./hclustercommand.o\\r
 644                 ./hcluster.o\\r
 645                 ./getlistcountcommand.o\\r
 646                 ./readcluster.o\\r
 647                 ./ccode.o\\r
 648                 ./taxonomyequalizer.o\\r
 649                 ./phylotypecommand.o\\r
 650                 ./classifyseqscommand.o\\r
 651                 ./classifyotucommand.o\\r
 652                 ./parsesffcommand.o\\r
 653                 ./classify.o\\r
 654                 ./phylotree.o\\r
 655                 ./phylodiversity.o\\r
 656                 ./phylodiversitycommand.o\\r
 657                 ./bayesian.o\\r
 658                 ./phylosummary.o\\r
 659                 ./alignmentdb.o\\r
 660                 ./knn.o\\r
 661                 ./distancedb.o\\r
 662                 ./chimeraslayer.o\\r
 663                 ./slayer.o\\r
 664                 ./pcacommand.o\\r
 665                 ./formatcolumn.o\\r
 666                 ./formatphylip.o\\r
 667                 ./mgclustercommand.o\\r
 668                 ./getsharedotucommand.o\\r
 669                 ./maligner.o\\r
 670                 ./chimerarealigner.o\\r
 671                 ./bergerparker.o\\r
 672                 ./bstick.o\\r
 673                 ./sharedkstest.o\\r
 674                 ./qstat.o\\r
 675                 ./shen.o\\r
 676                 ./logsd.o\\r
 677                 ./geom.o\\r
 678                 ./setlogfilecommand.o\\r
 679                 mothur\r
 680 \r
 681 install : mothur\r
 682                 #cp mothur ../Release/mothur\r
 683 \r
 684 #\r
 685 # Build the parts of mothur\r
 686 #\r
 687 \r
 688 \r
 689 # Item # 1 -- sharedutilities --\r
 690 ./sharedutilities.o : sharedutilities.cpp\r
 691         $(CC) $(CC_OPTIONS) sharedutilities.cpp -c $(INCLUDE) -o ./sharedutilities.o\r
 692 \r
 693 \r
 694 # Item # 2 -- treegroupscommand --\r
 695 ./treegroupscommand.o : treegroupscommand.cpp\r
 696         $(CC) $(CC_OPTIONS) treegroupscommand.cpp -c $(INCLUDE) -o ./treegroupscommand.o\r
 697 \r
 698 \r
 699 # Item # 3 -- bootstrapsharedcommand --\r
 700 ./bootstrapsharedcommand.o : bootstrapsharedcommand.cpp\r
 701         $(CC) $(CC_OPTIONS) bootstrapsharedcommand.cpp -c $(INCLUDE) -o ./bootstrapsharedcommand.o\r
 702 \r
 703 \r
 704 # Item # 4 -- matrixoutputcommand --\r
 705 ./matrixoutputcommand.o : matrixoutputcommand.cpp\r
 706         $(CC) $(CC_OPTIONS) matrixoutputcommand.cpp -c $(INCLUDE) -o ./matrixoutputcommand.o\r
 707 \r
 708 \r
 709 # Item # 5 -- getoturepcommand --\r
 710 ./getoturepcommand.o : getoturepcommand.cpp\r
 711         $(CC) $(CC_OPTIONS) getoturepcommand.cpp -c $(INCLUDE) -o ./getoturepcommand.o\r
 712 \r
 713 \r
 714 # Item # 6 -- screenseqscommand --\r
 715 ./screenseqscommand.o : screenseqscommand.cpp\r
 716         $(CC) $(CC_OPTIONS) screenseqscommand.cpp -c $(INCLUDE) -o ./screenseqscommand.o\r
 717 \r
 718 \r
 719 # Item # 7 -- chimera --\r
 720 ./chimera.o : chimera.cpp\r
 721         $(CC) $(CC_OPTIONS) chimera.cpp -c $(INCLUDE) -o ./chimera.o\r
 722 \r
 723 \r
 724 # Item # 8 -- decalc --\r
 725 ./decalc.o : decalc.cpp\r
 726         $(CC) $(CC_OPTIONS) decalc.cpp -c $(INCLUDE) -o ./decalc.o\r
 727 \r
 728 \r
 729 # Item # 9 -- readotucommand --\r
 730 ./readotucommand.o : readotucommand.cpp\r
 731         $(CC) $(CC_OPTIONS) readotucommand.cpp -c $(INCLUDE) -o ./readotucommand.o\r
 732 \r
 733 \r
 734 # Item # 10 -- readdistcommand --\r
 735 ./readdistcommand.o : readdistcommand.cpp\r
 736         $(CC) $(CC_OPTIONS) readdistcommand.cpp -c $(INCLUDE) -o ./readdistcommand.o\r
 737 \r
 738 \r
 739 # Item # 11 -- commandfactory --\r
 740 ./commandfactory.o : commandfactory.cpp\r
 741         $(CC) $(CC_OPTIONS) commandfactory.cpp -c $(INCLUDE) -o ./commandfactory.o\r
 742 \r
 743 \r
 744 # Item # 12 -- alignment --\r
 745 ./alignment.o : alignment.cpp\r
 746         $(CC) $(CC_OPTIONS) alignment.cpp -c $(INCLUDE) -o ./alignment.o\r
 747 \r
 748 \r
 749 # Item # 13 -- alignmentcell --\r
 750 ./alignmentcell.o : alignmentcell.cpp\r
 751         $(CC) $(CC_OPTIONS) alignmentcell.cpp -c $(INCLUDE) -o ./alignmentcell.o\r
 752 \r
 753 \r
 754 # Item # 14 -- gotohoverlap --\r
 755 ./gotohoverlap.o : gotohoverlap.cpp\r
 756         $(CC) $(CC_OPTIONS) gotohoverlap.cpp -c $(INCLUDE) -o ./gotohoverlap.o\r
 757 \r
 758 \r
 759 # Item # 15 -- overlap --\r
 760 ./overlap.o : overlap.cpp\r
 761         $(CC) $(CC_OPTIONS) overlap.cpp -c $(INCLUDE) -o ./overlap.o\r
 762 \r
 763 \r
 764 # Item # 16 -- needlemanoverlap --\r
 765 ./needlemanoverlap.o : needlemanoverlap.cpp\r
 766         $(CC) $(CC_OPTIONS) needlemanoverlap.cpp -c $(INCLUDE) -o ./needlemanoverlap.o\r
 767 \r
 768 \r
 769 # Item # 17 -- blastalign --\r
 770 ./blastalign.o : blastalign.cpp\r
 771         $(CC) $(CC_OPTIONS) blastalign.cpp -c $(INCLUDE) -o ./blastalign.o\r
 772 \r
 773 \r
 774 # Item # 18 -- noalign --\r
 775 ./noalign.o : noalign.cpp\r
 776         $(CC) $(CC_OPTIONS) noalign.cpp -c $(INCLUDE) -o ./noalign.o\r
 777 \r
 778 \r
 779 # Item # 19 -- suffixdb --\r
 780 ./suffixdb.o : suffixdb.cpp\r
 781         $(CC) $(CC_OPTIONS) suffixdb.cpp -c $(INCLUDE) -o ./suffixdb.o\r
 782 \r
 783 \r
 784 # Item # 20 -- suffixnodes --\r
 785 ./suffixnodes.o : suffixnodes.cpp\r
 786         $(CC) $(CC_OPTIONS) suffixnodes.cpp -c $(INCLUDE) -o ./suffixnodes.o\r
 787 \r
 788 \r
 789 # Item # 21 -- suffixtree --\r
 790 ./suffixtree.o : suffixtree.cpp\r
 791         $(CC) $(CC_OPTIONS) suffixtree.cpp -c $(INCLUDE) -o ./suffixtree.o\r
 792 \r
 793 \r
 794 # Item # 22 -- blastdb --\r
 795 ./blastdb.o : blastdb.cpp\r
 796         $(CC) $(CC_OPTIONS) blastdb.cpp -c $(INCLUDE) -o ./blastdb.o\r
 797 \r
 798 \r
 799 # Item # 23 -- nast --\r
 800 ./nast.o : nast.cpp\r
 801         $(CC) $(CC_OPTIONS) nast.cpp -c $(INCLUDE) -o ./nast.o\r
 802 \r
 803 \r
 804 # Item # 24 -- nastreport --\r
 805 ./nastreport.o : nastreport.cpp\r
 806         $(CC) $(CC_OPTIONS) nastreport.cpp -c $(INCLUDE) -o ./nastreport.o\r
 807 \r
 808 \r
 809 # Item # 25 -- boneh --\r
 810 ./boneh.o : boneh.cpp\r
 811         $(CC) $(CC_OPTIONS) boneh.cpp -c $(INCLUDE) -o ./boneh.o\r
 812 \r
 813 \r
 814 # Item # 26 -- efron --\r
 815 ./efron.o : efron.cpp\r
 816         $(CC) $(CC_OPTIONS) efron.cpp -c $(INCLUDE) -o ./efron.o\r
 817 \r
 818 \r
 819 # Item # 27 -- solow --\r
 820 ./solow.o : solow.cpp\r
 821         $(CC) $(CC_OPTIONS) solow.cpp -c $(INCLUDE) -o ./solow.o\r
 822 \r
 823 \r
 824 # Item # 28 -- unifracweightedcommand --\r
 825 ./unifracweightedcommand.o : unifracweightedcommand.cpp\r
 826         $(CC) $(CC_OPTIONS) unifracweightedcommand.cpp -c $(INCLUDE) -o ./unifracweightedcommand.o\r
 827 \r
 828 \r
 829 # Item # 29 -- weighted --\r
 830 ./weighted.o : weighted.cpp\r
 831         $(CC) $(CC_OPTIONS) weighted.cpp -c $(INCLUDE) -o ./weighted.o\r
 832 \r
 833 \r
 834 # Item # 30 -- unweighted --\r
 835 ./unweighted.o : unweighted.cpp\r
 836         $(CC) $(CC_OPTIONS) unweighted.cpp -c $(INCLUDE) -o ./unweighted.o\r
 837 \r
 838 \r
 839 # Item # 31 -- unifracunweightedcommand --\r
 840 ./unifracunweightedcommand.o : unifracunweightedcommand.cpp\r
 841         $(CC) $(CC_OPTIONS) unifracunweightedcommand.cpp -c $(INCLUDE) -o ./unifracunweightedcommand.o\r
 842 \r
 843 \r
 844 # Item # 32 -- getsabundcommand --\r
 845 ./getsabundcommand.o : getsabundcommand.cpp\r
 846         $(CC) $(CC_OPTIONS) getsabundcommand.cpp -c $(INCLUDE) -o ./getsabundcommand.o\r
 847 \r
 848 \r
 849 # Item # 33 -- getrabundcommand --\r
 850 ./getrabundcommand.o : getrabundcommand.cpp\r
 851         $(CC) $(CC_OPTIONS) getrabundcommand.cpp -c $(INCLUDE) -o ./getrabundcommand.o\r
 852 \r
 853 \r
 854 # Item # 34 -- bellerophon --\r
 855 ./bellerophon.o : bellerophon.cpp\r
 856         $(CC) $(CC_OPTIONS) bellerophon.cpp -c $(INCLUDE) -o ./bellerophon.o\r
 857 \r
 858 \r
 859 # Item # 35 -- pintail --\r
 860 ./pintail.o : pintail.cpp\r
 861         $(CC) $(CC_OPTIONS) pintail.cpp -c $(INCLUDE) -o ./pintail.o\r
 862 \r
 863 \r
 864 # Item # 36 -- sharedanderbergs --\r
 865 ./sharedanderbergs.o : sharedanderbergs.cpp\r
 866         $(CC) $(CC_OPTIONS) sharedanderbergs.cpp -c $(INCLUDE) -o ./sharedanderbergs.o\r
 867 \r
 868 \r
 869 # Item # 37 -- venncommand --\r
 870 ./venncommand.o : venncommand.cpp\r
 871         $(CC) $(CC_OPTIONS) venncommand.cpp -c $(INCLUDE) -o ./venncommand.o\r
 872 \r
 873 \r
 874 # Item # 38 -- venn --\r
 875 ./venn.o : venn.cpp\r
 876         $(CC) $(CC_OPTIONS) venn.cpp -c $(INCLUDE) -o ./venn.o\r
 877 \r
 878 \r
 879 # Item # 39 -- fullmatrix --\r
 880 ./fullmatrix.o : fullmatrix.cpp\r
 881         $(CC) $(CC_OPTIONS) fullmatrix.cpp -c $(INCLUDE) -o ./fullmatrix.o\r
 882 \r
 883 \r
 884 # Item # 40 -- heatmap --\r
 885 ./heatmap.o : heatmap.cpp\r
 886         $(CC) $(CC_OPTIONS) heatmap.cpp -c $(INCLUDE) -o ./heatmap.o\r
 887 \r
 888 \r
 889 # Item # 41 -- heatmapcommand --\r
 890 ./heatmapcommand.o : heatmapcommand.cpp\r
 891         $(CC) $(CC_OPTIONS) heatmapcommand.cpp -c $(INCLUDE) -o ./heatmapcommand.o\r
 892 \r
 893 \r
 894 # Item # 42 -- libshuffcommand --\r
 895 ./libshuffcommand.o : libshuffcommand.cpp\r
 896         $(CC) $(CC_OPTIONS) libshuffcommand.cpp -c $(INCLUDE) -o ./libshuffcommand.o\r
 897 \r
 898 \r
 899 # Item # 43 -- nocommands --\r
 900 ./nocommands.o : nocommands.cpp\r
 901         $(CC) $(CC_OPTIONS) nocommands.cpp -c $(INCLUDE) -o ./nocommands.o\r
 902 \r
 903 \r
 904 # Item # 44 -- sharedbraycurtis --\r
 905 ./sharedbraycurtis.o : sharedbraycurtis.cpp\r
 906         $(CC) $(CC_OPTIONS) sharedbraycurtis.cpp -c $(INCLUDE) -o ./sharedbraycurtis.o\r
 907 \r
 908 \r
 909 # Item # 45 -- sharedkulczynski --\r
 910 ./sharedkulczynski.o : sharedkulczynski.cpp\r
 911         $(CC) $(CC_OPTIONS) sharedkulczynski.cpp -c $(INCLUDE) -o ./sharedkulczynski.o\r
 912 \r
 913 \r
 914 # Item # 46 -- sharedlennon --\r
 915 ./sharedlennon.o : sharedlennon.cpp\r
 916         $(CC) $(CC_OPTIONS) sharedlennon.cpp -c $(INCLUDE) -o ./sharedlennon.o\r
 917 \r
 918 \r
 919 # Item # 47 -- sharedkulczynskicody --\r
 920 ./sharedkulczynskicody.o : sharedkulczynskicody.cpp\r
 921         $(CC) $(CC_OPTIONS) sharedkulczynskicody.cpp -c $(INCLUDE) -o ./sharedkulczynskicody.o\r
 922 \r
 923 \r
 924 # Item # 48 -- sharedmorisitahorn --\r
 925 ./sharedmorisitahorn.o : sharedmorisitahorn.cpp\r
 926         $(CC) $(CC_OPTIONS) sharedmorisitahorn.cpp -c $(INCLUDE) -o ./sharedmorisitahorn.o\r
 927 \r
 928 \r
 929 # Item # 49 -- sharedochiai --\r
 930 ./sharedochiai.o : sharedochiai.cpp\r
 931         $(CC) $(CC_OPTIONS) sharedochiai.cpp -c $(INCLUDE) -o ./sharedochiai.o\r
 932 \r
 933 \r
 934 # Item # 50 -- readcolumn --\r
 935 ./readcolumn.o : readcolumn.cpp\r
 936         $(CC) $(CC_OPTIONS) readcolumn.cpp -c $(INCLUDE) -o ./readcolumn.o\r
 937 \r
 938 \r
 939 # Item # 51 -- readotu --\r
 940 ./readotu.o : readotu.cpp\r
 941         $(CC) $(CC_OPTIONS) readotu.cpp -c $(INCLUDE) -o ./readotu.o\r
 942 \r
 943 \r
 944 # Item # 52 -- readphylip --\r
 945 ./readphylip.o : readphylip.cpp\r
 946         $(CC) $(CC_OPTIONS) readphylip.cpp -c $(INCLUDE) -o ./readphylip.o\r
 947 \r
 948 \r
 949 # Item # 53 -- consensuscommand --\r
 950 ./consensuscommand.o : consensuscommand.cpp\r
 951         $(CC) $(CC_OPTIONS) consensuscommand.cpp -c $(INCLUDE) -o ./consensuscommand.o\r
 952 \r
 953 \r
 954 # Item # 54 -- heatmapsimcommand --\r
 955 ./heatmapsimcommand.o : heatmapsimcommand.cpp\r
 956         $(CC) $(CC_OPTIONS) heatmapsimcommand.cpp -c $(INCLUDE) -o ./heatmapsimcommand.o\r
 957 \r
 958 \r
 959 # Item # 55 -- heatmapsim --\r
 960 ./heatmapsim.o : heatmapsim.cpp\r
 961         $(CC) $(CC_OPTIONS) heatmapsim.cpp -c $(INCLUDE) -o ./heatmapsim.o\r
 962 \r
 963 \r
 964 # Item # 56 -- optionparser --\r
 965 ./optionparser.o : optionparser.cpp\r
 966         $(CC) $(CC_OPTIONS) optionparser.cpp -c $(INCLUDE) -o ./optionparser.o\r
 967 \r
 968 \r
 969 # Item # 57 -- filterseqscommand --\r
 970 ./filterseqscommand.o : filterseqscommand.cpp\r
 971         $(CC) $(CC_OPTIONS) filterseqscommand.cpp -c $(INCLUDE) -o ./filterseqscommand.o\r
 972 \r
 973 \r
 974 # Item # 58 -- goodscoverage --\r
 975 ./goodscoverage.o : goodscoverage.cpp\r
 976         $(CC) $(CC_OPTIONS) goodscoverage.cpp -c $(INCLUDE) -o ./goodscoverage.o\r
 977 \r
 978 \r
 979 # Item # 59 -- sequencedb --\r
 980 ./sequencedb.o : sequencedb.cpp\r
 981         $(CC) $(CC_OPTIONS) sequencedb.cpp -c $(INCLUDE) -o ./sequencedb.o\r
 982 \r
 983 \r
 984 # Item # 60 -- sharedjackknife --\r
 985 ./sharedjackknife.o : sharedjackknife.cpp\r
 986         $(CC) $(CC_OPTIONS) sharedjackknife.cpp -c $(INCLUDE) -o ./sharedjackknife.o\r
 987 \r
 988 \r
 989 # Item # 61 -- sharedmarczewski --\r
 990 ./sharedmarczewski.o : sharedmarczewski.cpp\r
 991         $(CC) $(CC_OPTIONS) sharedmarczewski.cpp -c $(INCLUDE) -o ./sharedmarczewski.o\r
 992 \r
 993 \r
 994 # Item # 62 -- aligncommand --\r
 995 ./aligncommand.o : aligncommand.cpp\r
 996         $(CC) $(CC_OPTIONS) aligncommand.cpp -c $(INCLUDE) -o ./aligncommand.o\r
 997 \r
 998 \r
 999 # Item # 63 -- treemap --\r
1000 ./treemap.o : treemap.cpp\r
1001         $(CC) $(CC_OPTIONS) treemap.cpp -c $(INCLUDE) -o ./treemap.o\r
1002 \r
1003 \r
1004 # Item # 64 -- parsimonycommand --\r
1005 ./parsimonycommand.o : parsimonycommand.cpp\r
1006         $(CC) $(CC_OPTIONS) parsimonycommand.cpp -c $(INCLUDE) -o ./parsimonycommand.o\r
1007 \r
1008 \r
1009 # Item # 65 -- parsimony --\r
1010 ./parsimony.o : parsimony.cpp\r
1011         $(CC) $(CC_OPTIONS) parsimony.cpp -c $(INCLUDE) -o ./parsimony.o\r
1012 \r
1013 \r
1014 # Item # 66 -- seqsummarycommand --\r
1015 ./seqsummarycommand.o : seqsummarycommand.cpp\r
1016         $(CC) $(CC_OPTIONS) seqsummarycommand.cpp -c $(INCLUDE) -o ./seqsummarycommand.o\r
1017 \r
1018 \r
1019 # Item # 67 -- chimeraseqscommand --\r
1020 ./chimeraseqscommand.o : chimeraseqscommand.cpp\r
1021         $(CC) $(CC_OPTIONS) chimeraseqscommand.cpp -c $(INCLUDE) -o ./chimeraseqscommand.o\r
1022 \r
1023 \r
1024 # Item # 68 -- sharedlistvector --\r
1025 ./sharedlistvector.o : sharedlistvector.cpp\r
1026         $(CC) $(CC_OPTIONS) sharedlistvector.cpp -c $(INCLUDE) -o ./sharedlistvector.o\r
1027 \r
1028 \r
1029 # Item # 69 -- tree --\r
1030 ./tree.o : tree.cpp\r
1031         $(CC) $(CC_OPTIONS) tree.cpp -c $(INCLUDE) -o ./tree.o\r
1032 \r
1033 \r
1034 # Item # 70 -- readtree --\r
1035 ./readtree.o : readtree.cpp\r
1036         $(CC) $(CC_OPTIONS) readtree.cpp -c $(INCLUDE) -o ./readtree.o\r
1037 \r
1038 \r
1039 # Item # 71 -- sharedsobscollectsummary --\r
1040 ./sharedsobscollectsummary.o : sharedsobscollectsummary.cpp\r
1041         $(CC) $(CC_OPTIONS) sharedsobscollectsummary.cpp -c $(INCLUDE) -o ./sharedsobscollectsummary.o\r
1042 \r
1043 \r
1044 # Item # 72 -- deconvolutecommand --\r
1045 ./deconvolutecommand.o : deconvolutecommand.cpp\r
1046         $(CC) $(CC_OPTIONS) deconvolutecommand.cpp -c $(INCLUDE) -o ./deconvolutecommand.o\r
1047 \r
1048 \r
1049 # Item # 73 -- listseqscommand --\r
1050 ./listseqscommand.o : listseqscommand.cpp\r
1051         $(CC) $(CC_OPTIONS) listseqscommand.cpp -c $(INCLUDE) -o ./listseqscommand.o\r
1052 \r
1053 \r
1054 # Item # 74 -- getseqscommand --\r
1055 ./getseqscommand.o : getseqscommand.cpp\r
1056         $(CC) $(CC_OPTIONS) getseqscommand.cpp -c $(INCLUDE) -o ./getseqscommand.o\r
1057 \r
1058 \r
1059 # Item # 75 -- removeseqscommand --\r
1060 ./removeseqscommand.o : removeseqscommand.cpp\r
1061         $(CC) $(CC_OPTIONS) removeseqscommand.cpp -c $(INCLUDE) -o ./removeseqscommand.o\r
1062 \r
1063 \r
1064 # Item # 76 -- systemcommand --\r
1065 ./systemcommand.o : systemcommand.cpp\r
1066         $(CC) $(CC_OPTIONS) systemcommand.cpp -c $(INCLUDE) -o ./systemcommand.o\r
1067 \r
1068 \r
1069 # Item # 77 -- binsequencecommand --\r
1070 ./binsequencecommand.o : binsequencecommand.cpp\r
1071         $(CC) $(CC_OPTIONS) binsequencecommand.cpp -c $(INCLUDE) -o ./binsequencecommand.o\r
1072 \r
1073 \r
1074 # Item # 78 -- distancecommand --\r
1075 ./distancecommand.o : distancecommand.cpp\r
1076         $(CC) $(CC_OPTIONS) distancecommand.cpp -c $(INCLUDE) -o ./distancecommand.o\r
1077 \r
1078 \r
1079 # Item # 79 -- ace --\r
1080 ./ace.o : ace.cpp\r
1081         $(CC) $(CC_OPTIONS) ace.cpp -c $(INCLUDE) -o ./ace.o\r
1082 \r
1083 \r
1084 # Item # 80 -- averagelinkage --\r
1085 ./averagelinkage.o : averagelinkage.cpp\r
1086         $(CC) $(CC_OPTIONS) averagelinkage.cpp -c $(INCLUDE) -o ./averagelinkage.o\r
1087 \r
1088 \r
1089 # Item # 81 -- bootstrap --\r
1090 ./bootstrap.o : bootstrap.cpp\r
1091         $(CC) $(CC_OPTIONS) bootstrap.cpp -c $(INCLUDE) -o ./bootstrap.o\r
1092 \r
1093 \r
1094 # Item # 82 -- calculator --\r
1095 ./calculator.o : calculator.cpp\r
1096         $(CC) $(CC_OPTIONS) calculator.cpp -c $(INCLUDE) -o ./calculator.o\r
1097 \r
1098 \r
1099 # Item # 83 -- chao1 --\r
1100 ./chao1.o : chao1.cpp\r
1101         $(CC) $(CC_OPTIONS) chao1.cpp -c $(INCLUDE) -o ./chao1.o\r
1102 \r
1103 \r
1104 # Item # 84 -- cluster --\r
1105 ./cluster.o : cluster.cpp\r
1106         $(CC) $(CC_OPTIONS) cluster.cpp -c $(INCLUDE) -o ./cluster.o\r
1107 \r
1108 \r
1109 # Item # 85 -- clustercommand --\r
1110 ./clustercommand.o : clustercommand.cpp\r
1111         $(CC) $(CC_OPTIONS) clustercommand.cpp -c $(INCLUDE) -o ./clustercommand.o\r
1112 \r
1113 \r
1114 # Item # 86 -- collect --\r
1115 ./collect.o : collect.cpp\r
1116         $(CC) $(CC_OPTIONS) collect.cpp -c $(INCLUDE) -o ./collect.o\r
1117 \r
1118 \r
1119 # Item # 87 -- collectcommand --\r
1120 ./collectcommand.o : collectcommand.cpp\r
1121         $(CC) $(CC_OPTIONS) collectcommand.cpp -c $(INCLUDE) -o ./collectcommand.o\r
1122 \r
1123 \r
1124 # Item # 88 -- collectsharedcommand --\r
1125 ./collectsharedcommand.o : collectsharedcommand.cpp\r
1126         $(CC) $(CC_OPTIONS) collectsharedcommand.cpp -c $(INCLUDE) -o ./collectsharedcommand.o\r
1127 \r
1128 \r
1129 # Item # 89 -- commandoptionparser --\r
1130 ./commandoptionparser.o : commandoptionparser.cpp\r
1131         $(CC) $(CC_OPTIONS) commandoptionparser.cpp -c $(INCLUDE) -o ./commandoptionparser.o\r
1132 \r
1133 \r
1134 # Item # 90 -- completelinkage --\r
1135 ./completelinkage.o : completelinkage.cpp\r
1136         $(CC) $(CC_OPTIONS) completelinkage.cpp -c $(INCLUDE) -o ./completelinkage.o\r
1137 \r
1138 \r
1139 # Item # 91 -- database --\r
1140 ./database.o : database.cpp\r
1141         $(CC) $(CC_OPTIONS) database.cpp -c $(INCLUDE) -o ./database.o\r
1142 \r
1143 \r
1144 # Item # 92 -- engine --\r
1145 ./engine.o : engine.cpp\r
1146         $(CC) $(CC_OPTIONS) engine.cpp -c $(INCLUDE) -o ./engine.o\r
1147 \r
1148 \r
1149 # Item # 93 -- fastamap --\r
1150 ./fastamap.o : fastamap.cpp\r
1151         $(CC) $(CC_OPTIONS) fastamap.cpp -c $(INCLUDE) -o ./fastamap.o\r
1152 \r
1153 \r
1154 # Item # 94 -- fileoutput --\r
1155 ./fileoutput.o : fileoutput.cpp\r
1156         $(CC) $(CC_OPTIONS) fileoutput.cpp -c $(INCLUDE) -o ./fileoutput.o\r
1157 \r
1158 \r
1159 # Item # 95 -- globaldata --\r
1160 ./globaldata.o : globaldata.cpp\r
1161         $(CC) $(CC_OPTIONS) globaldata.cpp -c $(INCLUDE) -o ./globaldata.o\r
1162 \r
1163 \r
1164 # Item # 96 -- groupmap --\r
1165 ./groupmap.o : groupmap.cpp\r
1166         $(CC) $(CC_OPTIONS) groupmap.cpp -c $(INCLUDE) -o ./groupmap.o\r
1167 \r
1168 \r
1169 # Item # 97 -- helpcommand --\r
1170 ./helpcommand.o : helpcommand.cpp\r
1171         $(CC) $(CC_OPTIONS) helpcommand.cpp -c $(INCLUDE) -o ./helpcommand.o\r
1172 \r
1173 \r
1174 # Item # 98 -- inputdata --\r
1175 ./inputdata.o : inputdata.cpp\r
1176         $(CC) $(CC_OPTIONS) inputdata.cpp -c $(INCLUDE) -o ./inputdata.o\r
1177 \r
1178 \r
1179 # Item # 99 -- jackknife --\r
1180 ./jackknife.o : jackknife.cpp\r
1181         $(CC) $(CC_OPTIONS) jackknife.cpp -c $(INCLUDE) -o ./jackknife.o\r
1182 \r
1183 \r
1184 # Item # 100 -- kmer --\r
1185 ./kmer.o : kmer.cpp\r
1186         $(CC) $(CC_OPTIONS) kmer.cpp -c $(INCLUDE) -o ./kmer.o\r
1187 \r
1188 \r
1189 # Item # 101 -- kmerdb --\r
1190 ./kmerdb.o : kmerdb.cpp\r
1191         $(CC) $(CC_OPTIONS) kmerdb.cpp -c $(INCLUDE) -o ./kmerdb.o\r
1192 \r
1193 \r
1194 # Item # 102 -- listvector --\r
1195 ./listvector.o : listvector.cpp\r
1196         $(CC) $(CC_OPTIONS) listvector.cpp -c $(INCLUDE) -o ./listvector.o\r
1197 \r
1198 \r
1199 # Item # 103 -- mothur --\r
1200 ./mothur.o : mothur.cpp\r
1201         $(CC) $(CC_OPTIONS) mothur.cpp -c $(INCLUDE) -o ./mothur.o\r
1202 \r
1203 \r
1204 # Item # 104 -- nameassignment --\r
1205 ./nameassignment.o : nameassignment.cpp\r
1206         $(CC) $(CC_OPTIONS) nameassignment.cpp -c $(INCLUDE) -o ./nameassignment.o\r
1207 \r
1208 \r
1209 # Item # 105 -- npshannon --\r
1210 ./npshannon.o : npshannon.cpp\r
1211         $(CC) $(CC_OPTIONS) npshannon.cpp -c $(INCLUDE) -o ./npshannon.o\r
1212 \r
1213 \r
1214 # Item # 106 -- ordervector --\r
1215 ./ordervector.o : ordervector.cpp\r
1216         $(CC) $(CC_OPTIONS) ordervector.cpp -c $(INCLUDE) -o ./ordervector.o\r
1217 \r
1218 \r
1219 # Item # 107 -- progress --\r
1220 ./progress.o : progress.cpp\r
1221         $(CC) $(CC_OPTIONS) progress.cpp -c $(INCLUDE) -o ./progress.o\r
1222 \r
1223 \r
1224 # Item # 108 -- quitcommand --\r
1225 ./quitcommand.o : quitcommand.cpp\r
1226         $(CC) $(CC_OPTIONS) quitcommand.cpp -c $(INCLUDE) -o ./quitcommand.o\r
1227 \r
1228 \r
1229 # Item # 109 -- rabundvector --\r
1230 ./rabundvector.o : rabundvector.cpp\r
1231         $(CC) $(CC_OPTIONS) rabundvector.cpp -c $(INCLUDE) -o ./rabundvector.o\r
1232 \r
1233 \r
1234 # Item # 110 -- rarecalc --\r
1235 ./rarecalc.o : rarecalc.cpp\r
1236         $(CC) $(CC_OPTIONS) rarecalc.cpp -c $(INCLUDE) -o ./rarecalc.o\r
1237 \r
1238 \r
1239 # Item # 111 -- raredisplay --\r
1240 ./raredisplay.o : raredisplay.cpp\r
1241         $(CC) $(CC_OPTIONS) raredisplay.cpp -c $(INCLUDE) -o ./raredisplay.o\r
1242 \r
1243 \r
1244 # Item # 112 -- rarefact --\r
1245 ./rarefact.o : rarefact.cpp\r
1246         $(CC) $(CC_OPTIONS) rarefact.cpp -c $(INCLUDE) -o ./rarefact.o\r
1247 \r
1248 \r
1249 # Item # 113 -- rarefactcommand --\r
1250 ./rarefactcommand.o : rarefactcommand.cpp\r
1251         $(CC) $(CC_OPTIONS) rarefactcommand.cpp -c $(INCLUDE) -o ./rarefactcommand.o\r
1252 \r
1253 \r
1254 # Item # 114 -- rarefactsharedcommand --\r
1255 ./rarefactsharedcommand.o : rarefactsharedcommand.cpp\r
1256         $(CC) $(CC_OPTIONS) rarefactsharedcommand.cpp -c $(INCLUDE) -o ./rarefactsharedcommand.o\r
1257 \r
1258 \r
1259 # Item # 115 -- sabundvector --\r
1260 ./sabundvector.o : sabundvector.cpp\r
1261         $(CC) $(CC_OPTIONS) sabundvector.cpp -c $(INCLUDE) -o ./sabundvector.o\r
1262 \r
1263 \r
1264 # Item # 116 -- sequence --\r
1265 ./sequence.o : sequence.cpp\r
1266         $(CC) $(CC_OPTIONS) sequence.cpp -c $(INCLUDE) -o ./sequence.o\r
1267 \r
1268 \r
1269 # Item # 117 -- shannon --\r
1270 ./shannon.o : shannon.cpp\r
1271         $(CC) $(CC_OPTIONS) shannon.cpp -c $(INCLUDE) -o ./shannon.o\r
1272 \r
1273 \r
1274 # Item # 118 -- sharedace --\r
1275 ./sharedace.o : sharedace.cpp\r
1276         $(CC) $(CC_OPTIONS) sharedace.cpp -c $(INCLUDE) -o ./sharedace.o\r
1277 \r
1278 \r
1279 # Item # 119 -- sharedchao1 --\r
1280 ./sharedchao1.o : sharedchao1.cpp\r
1281         $(CC) $(CC_OPTIONS) sharedchao1.cpp -c $(INCLUDE) -o ./sharedchao1.o\r
1282 \r
1283 \r
1284 # Item # 120 -- sharedcommand --\r
1285 ./sharedcommand.o : sharedcommand.cpp\r
1286         $(CC) $(CC_OPTIONS) sharedcommand.cpp -c $(INCLUDE) -o ./sharedcommand.o\r
1287 \r
1288 \r
1289 # Item # 121 -- sharedjabund --\r
1290 ./sharedjabund.o : sharedjabund.cpp\r
1291         $(CC) $(CC_OPTIONS) sharedjabund.cpp -c $(INCLUDE) -o ./sharedjabund.o\r
1292 \r
1293 \r
1294 # Item # 122 -- sharedjclass --\r
1295 ./sharedjclass.o : sharedjclass.cpp\r
1296         $(CC) $(CC_OPTIONS) sharedjclass.cpp -c $(INCLUDE) -o ./sharedjclass.o\r
1297 \r
1298 \r
1299 # Item # 123 -- sharedjest --\r
1300 ./sharedjest.o : sharedjest.cpp\r
1301         $(CC) $(CC_OPTIONS) sharedjest.cpp -c $(INCLUDE) -o ./sharedjest.o\r
1302 \r
1303 \r
1304 # Item # 124 -- sharedordervector --\r
1305 ./sharedordervector.o : sharedordervector.cpp\r
1306         $(CC) $(CC_OPTIONS) sharedordervector.cpp -c $(INCLUDE) -o ./sharedordervector.o\r
1307 \r
1308 \r
1309 # Item # 125 -- sharedrabundvector --\r
1310 ./sharedrabundvector.o : sharedrabundvector.cpp\r
1311         $(CC) $(CC_OPTIONS) sharedrabundvector.cpp -c $(INCLUDE) -o ./sharedrabundvector.o\r
1312 \r
1313 \r
1314 # Item # 126 -- sharedsabundvector --\r
1315 ./sharedsabundvector.o : sharedsabundvector.cpp\r
1316         $(CC) $(CC_OPTIONS) sharedsabundvector.cpp -c $(INCLUDE) -o ./sharedsabundvector.o\r
1317 \r
1318 \r
1319 # Item # 127 -- sharedsobs --\r
1320 ./sharedsobs.o : sharedsobs.cpp\r
1321         $(CC) $(CC_OPTIONS) sharedsobs.cpp -c $(INCLUDE) -o ./sharedsobs.o\r
1322 \r
1323 \r
1324 # Item # 128 -- sharedsorabund --\r
1325 ./sharedsorabund.o : sharedsorabund.cpp\r
1326         $(CC) $(CC_OPTIONS) sharedsorabund.cpp -c $(INCLUDE) -o ./sharedsorabund.o\r
1327 \r
1328 \r
1329 # Item # 129 -- sharedsorclass --\r
1330 ./sharedsorclass.o : sharedsorclass.cpp\r
1331         $(CC) $(CC_OPTIONS) sharedsorclass.cpp -c $(INCLUDE) -o ./sharedsorclass.o\r
1332 \r
1333 \r
1334 # Item # 130 -- sharedsorest --\r
1335 ./sharedsorest.o : sharedsorest.cpp\r
1336         $(CC) $(CC_OPTIONS) sharedsorest.cpp -c $(INCLUDE) -o ./sharedsorest.o\r
1337 \r
1338 \r
1339 # Item # 131 -- sharedthetan --\r
1340 ./sharedthetan.o : sharedthetan.cpp\r
1341         $(CC) $(CC_OPTIONS) sharedthetan.cpp -c $(INCLUDE) -o ./sharedthetan.o\r
1342 \r
1343 \r
1344 # Item # 132 -- sharedthetayc --\r
1345 ./sharedthetayc.o : sharedthetayc.cpp\r
1346         $(CC) $(CC_OPTIONS) sharedthetayc.cpp -c $(INCLUDE) -o ./sharedthetayc.o\r
1347 \r
1348 \r
1349 # Item # 133 -- simpson --\r
1350 ./simpson.o : simpson.cpp\r
1351         $(CC) $(CC_OPTIONS) simpson.cpp -c $(INCLUDE) -o ./simpson.o\r
1352 \r
1353 \r
1354 # Item # 134 -- singlelinkage --\r
1355 ./singlelinkage.o : singlelinkage.cpp\r
1356         $(CC) $(CC_OPTIONS) singlelinkage.cpp -c $(INCLUDE) -o ./singlelinkage.o\r
1357 \r
1358 \r
1359 # Item # 135 -- sparsematrix --\r
1360 ./sparsematrix.o : sparsematrix.cpp\r
1361         $(CC) $(CC_OPTIONS) sparsematrix.cpp -c $(INCLUDE) -o ./sparsematrix.o\r
1362 \r
1363 \r
1364 # Item # 136 -- summarycommand --\r
1365 ./summarycommand.o : summarycommand.cpp\r
1366         $(CC) $(CC_OPTIONS) summarycommand.cpp -c $(INCLUDE) -o ./summarycommand.o\r
1367 \r
1368 \r
1369 # Item # 137 -- summarysharedcommand --\r
1370 ./summarysharedcommand.o : summarysharedcommand.cpp\r
1371         $(CC) $(CC_OPTIONS) summarysharedcommand.cpp -c $(INCLUDE) -o ./summarysharedcommand.o\r
1372 \r
1373 \r
1374 # Item # 138 -- uvest --\r
1375 ./uvest.o : uvest.cpp\r
1376         $(CC) $(CC_OPTIONS) uvest.cpp -c $(INCLUDE) -o ./uvest.o\r
1377 \r
1378 \r
1379 # Item # 139 -- validcalculator --\r
1380 ./validcalculator.o : validcalculator.cpp\r
1381         $(CC) $(CC_OPTIONS) validcalculator.cpp -c $(INCLUDE) -o ./validcalculator.o\r
1382 \r
1383 \r
1384 # Item # 140 -- validparameter --\r
1385 ./validparameter.o : validparameter.cpp\r
1386         $(CC) $(CC_OPTIONS) validparameter.cpp -c $(INCLUDE) -o ./validparameter.o\r
1387 \r
1388 \r
1389 # Item # 141 -- treenode --\r
1390 ./treenode.o : treenode.cpp\r
1391         $(CC) $(CC_OPTIONS) treenode.cpp -c $(INCLUDE) -o ./treenode.o\r
1392 \r
1393 \r
1394 # Item # 142 -- readtreecommand --\r
1395 ./readtreecommand.o : readtreecommand.cpp\r
1396         $(CC) $(CC_OPTIONS) readtreecommand.cpp -c $(INCLUDE) -o ./readtreecommand.o\r
1397 \r
1398 \r
1399 # Item # 143 -- reversecommand --\r
1400 ./reversecommand.o : reversecommand.cpp\r
1401         $(CC) $(CC_OPTIONS) reversecommand.cpp -c $(INCLUDE) -o ./reversecommand.o\r
1402 \r
1403 \r
1404 # Item # 144 -- trimseqscommand --\r
1405 ./trimseqscommand.o : trimseqscommand.cpp\r
1406         $(CC) $(CC_OPTIONS) trimseqscommand.cpp -c $(INCLUDE) -o ./trimseqscommand.o\r
1407 \r
1408 \r
1409 # Item # 145 -- slibshuff --\r
1410 ./slibshuff.o : slibshuff.cpp\r
1411         $(CC) $(CC_OPTIONS) slibshuff.cpp -c $(INCLUDE) -o ./slibshuff.o\r
1412 \r
1413 \r
1414 # Item # 146 -- libshuff --\r
1415 ./libshuff.o : libshuff.cpp\r
1416         $(CC) $(CC_OPTIONS) libshuff.cpp -c $(INCLUDE) -o ./libshuff.o\r
1417 \r
1418 \r
1419 # Item # 147 -- dlibshuff --\r
1420 ./dlibshuff.o : dlibshuff.cpp\r
1421         $(CC) $(CC_OPTIONS) dlibshuff.cpp -c $(INCLUDE) -o ./dlibshuff.o\r
1422 \r
1423 \r
1424 # Item # 148 -- mergefilecommand --\r
1425 ./mergefilecommand.o : mergefilecommand.cpp\r
1426         $(CC) $(CC_OPTIONS) mergefilecommand.cpp -c $(INCLUDE) -o ./mergefilecommand.o\r
1427 \r
1428 \r
1429 # Item # 149 -- coverage --\r
1430 ./coverage.o : coverage.cpp\r
1431         $(CC) $(CC_OPTIONS) coverage.cpp -c $(INCLUDE) -o ./coverage.o\r
1432 \r
1433 \r
1434 # Item # 150 -- whittaker --\r
1435 ./whittaker.o : whittaker.cpp\r
1436         $(CC) $(CC_OPTIONS) whittaker.cpp -c $(INCLUDE) -o ./whittaker.o\r
1437 \r
1438 \r
1439 # Item # 151 -- preclustercommand --\r
1440 ./preclustercommand.o : preclustercommand.cpp\r
1441         $(CC) $(CC_OPTIONS) preclustercommand.cpp -c $(INCLUDE) -o ./preclustercommand.o\r
1442 \r
1443 \r
1444 # Item # 152 -- otuhierarchycommand --\r
1445 ./otuhierarchycommand.o : otuhierarchycommand.cpp\r
1446         $(CC) $(CC_OPTIONS) otuhierarchycommand.cpp -c $(INCLUDE) -o ./otuhierarchycommand.o\r
1447 \r
1448 \r
1449 # Item # 153 -- setdircommand --\r
1450 ./setdircommand.o : setdircommand.cpp\r
1451         $(CC) $(CC_OPTIONS) setdircommand.cpp -c $(INCLUDE) -o ./setdircommand.o\r
1452 \r
1453 \r
1454 # Item # 154 -- getgroupcommand --\r
1455 ./getgroupcommand.o : getgroupcommand.cpp\r
1456         $(CC) $(CC_OPTIONS) getgroupcommand.cpp -c $(INCLUDE) -o ./getgroupcommand.o\r
1457 \r
1458 \r
1459 # Item # 155 -- getlabelcommand --\r
1460 ./getlabelcommand.o : getlabelcommand.cpp\r
1461         $(CC) $(CC_OPTIONS) getlabelcommand.cpp -c $(INCLUDE) -o ./getlabelcommand.o\r
1462 \r
1463 \r
1464 # Item # 156 -- secondarystructurecommand --\r
1465 ./secondarystructurecommand.o : secondarystructurecommand.cpp\r
1466         $(CC) $(CC_OPTIONS) secondarystructurecommand.cpp -c $(INCLUDE) -o ./secondarystructurecommand.o\r
1467 \r
1468 \r
1469 # Item # 157 -- mothurout --\r
1470 ./mothurout.o : mothurout.cpp\r
1471         $(CC) $(CC_OPTIONS) mothurout.cpp -c $(INCLUDE) -o ./mothurout.o\r
1472 \r
1473 \r
1474 # Item # 158 -- parselistscommand --\r
1475 ./parselistscommand.o : parselistscommand.cpp\r
1476         $(CC) $(CC_OPTIONS) parselistscommand.cpp -c $(INCLUDE) -o ./parselistscommand.o\r
1477 \r
1478 \r
1479 # Item # 159 -- readblast --\r
1480 ./readblast.o : readblast.cpp\r
1481         $(CC) $(CC_OPTIONS) readblast.cpp -c $(INCLUDE) -o ./readblast.o\r
1482 \r
1483 \r
1484 # Item # 160 -- chimeracheckrdp --\r
1485 ./chimeracheckrdp.o : chimeracheckrdp.cpp\r
1486         $(CC) $(CC_OPTIONS) chimeracheckrdp.cpp -c $(INCLUDE) -o ./chimeracheckrdp.o\r
1487 \r
1488 \r
1489 # Item # 161 -- hclustercommand --\r
1490 ./hclustercommand.o : hclustercommand.cpp\r
1491         $(CC) $(CC_OPTIONS) hclustercommand.cpp -c $(INCLUDE) -o ./hclustercommand.o\r
1492 \r
1493 \r
1494 # Item # 162 -- hcluster --\r
1495 ./hcluster.o : hcluster.cpp\r
1496         $(CC) $(CC_OPTIONS) hcluster.cpp -c $(INCLUDE) -o ./hcluster.o\r
1497 \r
1498 \r
1499 # Item # 163 -- getlistcountcommand --\r
1500 ./getlistcountcommand.o : getlistcountcommand.cpp\r
1501         $(CC) $(CC_OPTIONS) getlistcountcommand.cpp -c $(INCLUDE) -o ./getlistcountcommand.o\r
1502 \r
1503 \r
1504 # Item # 164 -- readcluster --\r
1505 ./readcluster.o : readcluster.cpp\r
1506         $(CC) $(CC_OPTIONS) readcluster.cpp -c $(INCLUDE) -o ./readcluster.o\r
1507 \r
1508 \r
1509 # Item # 165 -- ccode --\r
1510 ./ccode.o : ccode.cpp\r
1511         $(CC) $(CC_OPTIONS) ccode.cpp -c $(INCLUDE) -o ./ccode.o\r
1512 \r
1513 \r
1514 # Item # 166 -- taxonomyequalizer --\r
1515 ./taxonomyequalizer.o : taxonomyequalizer.cpp\r
1516         $(CC) $(CC_OPTIONS) taxonomyequalizer.cpp -c $(INCLUDE) -o ./taxonomyequalizer.o\r
1517 \r
1518 \r
1519 # Item # 167 -- phylotypecommand --\r
1520 ./phylotypecommand.o : phylotypecommand.cpp\r
1521         $(CC) $(CC_OPTIONS) phylotypecommand.cpp -c $(INCLUDE) -o ./phylotypecommand.o\r
1522 \r
1523 \r
1524 # Item # 168 -- classifyseqscommand --\r
1525 ./classifyseqscommand.o : classifyseqscommand.cpp\r
1526         $(CC) $(CC_OPTIONS) classifyseqscommand.cpp -c $(INCLUDE) -o ./classifyseqscommand.o\r
1527 \r
1528 \r
1529 # Item # 169 -- classify --\r
1530 ./classify.o : classify.cpp\r
1531         $(CC) $(CC_OPTIONS) classify.cpp -c $(INCLUDE) -o ./classify.o\r
1532 \r
1533 \r
1534 # Item # 170 -- phylotree --\r
1535 ./phylotree.o : phylotree.cpp\r
1536         $(CC) $(CC_OPTIONS) phylotree.cpp -c $(INCLUDE) -o ./phylotree.o\r
1537 \r
1538 \r
1539 # Item # 171 -- bayesian --\r
1540 ./bayesian.o : bayesian.cpp\r
1541         $(CC) $(CC_OPTIONS) bayesian.cpp -c $(INCLUDE) -o ./bayesian.o\r
1542 \r
1543 \r
1544 # Item # 172 -- alignmentdb --\r
1545 ./alignmentdb.o : alignmentdb.cpp\r
1546         $(CC) $(CC_OPTIONS) alignmentdb.cpp -c $(INCLUDE) -o ./alignmentdb.o\r
1547 \r
1548 \r
1549 # Item # 173 -- knn --\r
1550 ./knn.o : knn.cpp\r
1551         $(CC) $(CC_OPTIONS) knn.cpp -c $(INCLUDE) -o ./knn.o\r
1552 \r
1553 \r
1554 # Item # 174 -- distancedb --\r
1555 ./distancedb.o : distancedb.cpp\r
1556         $(CC) $(CC_OPTIONS) distancedb.cpp -c $(INCLUDE) -o ./distancedb.o\r
1557 \r
1558 \r
1559 # Item # 175 -- chimeraslayer --\r
1560 ./chimeraslayer.o : chimeraslayer.cpp\r
1561         $(CC) $(CC_OPTIONS) chimeraslayer.cpp -c $(INCLUDE) -o ./chimeraslayer.o\r
1562 \r
1563 \r
1564 # Item # 176 -- slayer --\r
1565 ./slayer.o : slayer.cpp\r
1566         $(CC) $(CC_OPTIONS) slayer.cpp -c $(INCLUDE) -o ./slayer.o\r
1567 \r
1568 \r
1569 # Item # 177 -- pcacommand --\r
1570 ./pcacommand.o : pcacommand.cpp\r
1571         $(CC) $(CC_OPTIONS) pcacommand.cpp -c $(INCLUDE) -o ./pcacommand.o\r
1572 \r
1573 \r
1574 # Item # 178 -- formatcolumn --\r
1575 ./formatcolumn.o : formatcolumn.cpp\r
1576         $(CC) $(CC_OPTIONS) formatcolumn.cpp -c $(INCLUDE) -o ./formatcolumn.o\r
1577 \r
1578 \r
1579 # Item # 179 -- formatphylip --\r
1580 ./formatphylip.o : formatphylip.cpp\r
1581         $(CC) $(CC_OPTIONS) formatphylip.cpp -c $(INCLUDE) -o ./formatphylip.o\r
1582 \r
1583 \r
1584 # Item # 180 -- mgclustercommand --\r
1585 ./mgclustercommand.o : mgclustercommand.cpp\r
1586         $(CC) $(CC_OPTIONS) mgclustercommand.cpp -c $(INCLUDE) -o ./mgclustercommand.o\r
1587 \r
1588 \r
1589 # Item # 181 -- getsharedotucommand --\r
1590 ./getsharedotucommand.o : getsharedotucommand.cpp\r
1591         $(CC) $(CC_OPTIONS) getsharedotucommand.cpp -c $(INCLUDE) -o ./getsharedotucommand.o\r
1592 \r
1593 \r
1594 # Item # 182 -- maligner --\r
1595 ./maligner.o : maligner.cpp\r
1596         $(CC) $(CC_OPTIONS) maligner.cpp -c $(INCLUDE) -o ./maligner.o\r
1597 \r
1598 \r
1599 # Item # 183 -- chimerarealigner --\r
1600 ./chimerarealigner.o : chimerarealigner.cpp\r
1601         $(CC) $(CC_OPTIONS) chimerarealigner.cpp -c $(INCLUDE) -o ./chimerarealigner.o\r
1602 \r
1603 \r
1604 # Item # 184 -- bergerparker --\r
1605 ./bergerparker.o : bergerparker.cpp\r
1606         $(CC) $(CC_OPTIONS) bergerparker.cpp -c $(INCLUDE) -o ./bergerparker.o\r
1607 \r
1608 \r
1609 # Item # 185 -- bstick --\r
1610 ./bstick.o : bstick.cpp\r
1611         $(CC) $(CC_OPTIONS) bstick.cpp -c $(INCLUDE) -o ./bstick.o\r
1612 \r
1613 \r
1614 # Item # 186 -- sharedkstest --\r
1615 ./sharedkstest.o : sharedkstest.cpp\r
1616         $(CC) $(CC_OPTIONS) sharedkstest.cpp -c $(INCLUDE) -o ./sharedkstest.o\r
1617 \r
1618 \r
1619 # Item # 187 -- qstat --\r
1620 ./qstat.o : qstat.cpp\r
1621         $(CC) $(CC_OPTIONS) qstat.cpp -c $(INCLUDE) -o ./qstat.o\r
1622 \r
1623 \r
1624 # Item # 188 -- shen --\r
1625 ./shen.o : shen.cpp\r
1626         $(CC) $(CC_OPTIONS) shen.cpp -c $(INCLUDE) -o ./shen.o\r
1627 \r
1628 \r
1629 # Item # 189 -- logsd --\r
1630 ./logsd.o : logsd.cpp\r
1631         $(CC) $(CC_OPTIONS) logsd.cpp -c $(INCLUDE) -o ./logsd.o\r
1632 \r
1633 \r
1634 # Item # 190 -- geom --\r
1635 ./geom.o : geom.cpp\r
1636         $(CC) $(CC_OPTIONS) geom.cpp -c $(INCLUDE) -o ./geom.o\r
1637 \r
1638 # Item # 191 -- parsesffcommand --\r
1639 ./parsesffcommand.o : parsesffcommand.cpp\r
1640         $(CC) $(CC_OPTIONS) parsesffcommand.cpp -c $(INCLUDE) -o ./parsesffcommand.o\r
1641 \r
1642 # Item # 192 -- chimeraccodecommand --\r
1643 ./chimeraccodecommand.o : chimeraccodecommand.cpp\r
1644         $(CC) $(CC_OPTIONS) chimeraccodecommand.cpp -c $(INCLUDE) -o ./chimeraccodecommand.o\r
1645 \r
1646 # Item # 193 -- chimeracheckcommand --\r
1647 ./chimeracheckcommand.o : chimeracheckcommand.cpp\r
1648         $(CC) $(CC_OPTIONS) chimeracheckcommand.cpp -c $(INCLUDE) -o ./chimeracheckcommand.o\r
1649 \r
1650 \r
1651 # Item # 194 -- chimeraslayercommand --\r
1652 ./chimeraslayercommand.o : chimeraslayercommand.cpp\r
1653         $(CC) $(CC_OPTIONS) chimeraslayercommand.cpp -c $(INCLUDE) -o ./chimeraslayercommand.o\r
1654 \r
1655 # Item # 195 -- chimerapintailcommand --\r
1656 ./chimerapintailcommand.o : chimerapintailcommand.cpp\r
1657         $(CC) $(CC_OPTIONS) chimerapintailcommand.cpp -c $(INCLUDE) -o ./chimerapintailcommand.o\r
1658 \r
1659 # Item # 196 -- chimerabellerophoncommand --\r
1660 ./chimerabellerophoncommand.o : chimerabellerophoncommand.cpp\r
1661         $(CC) $(CC_OPTIONS) chimerabellerophoncommand.cpp -c $(INCLUDE) -o ./chimerabellerophoncommand.o\r
1662 \r
1663 # Item # 197 -- phylosummary --\r
1664 ./phylosummary.o : phylosummary.cpp\r
1665         $(CC) $(CC_OPTIONS) phylosummary.cpp -c $(INCLUDE) -o ./phylosummary.o\r
1666 \r
1667 # Item # 198 -- setlogfilecommand --\r
1668 ./setlogfilecommand.o : setlogfilecommand.cpp\r
1669         $(CC) $(CC_OPTIONS) setlogfilecommand.cpp -c $(INCLUDE) -o ./setlogfilecommand.o\r
1670 \r
1671 # Item # 199 -- phylodiversity --\r
1672 ./phylodiversity.o : phylodiversity.cpp\r
1673         $(CC) $(CC_OPTIONS) phylodiversity.cpp -c $(INCLUDE) -o ./phylodiversity.o\r
1674 \r
1675 # Item # 200 -- phylodiversitycommand --\r
1676 ./phylodiversitycommand.o : phylodiversitycommand.cpp\r
1677         $(CC) $(CC_OPTIONS) phylodiversitycommand.cpp -c $(INCLUDE) -o ./phylodiversitycommand.o\r
1678 \r
1679 # Item # 201 -- makegroupcommand --\r
1680 ./makegroupcommand.o : makegroupcommand.cpp\r
1681         $(CC) $(CC_OPTIONS) makegroupcommand.cpp -c $(INCLUDE) -o ./makegroupcommand.o\r
1682 \r
1683 # Item # 202 -- chopseqscommand --\r
1684 ./chopseqscommand.o : chopseqscommand.cpp\r
1685         $(CC) $(CC_OPTIONS) chopseqscommand.cpp -c $(INCLUDE) -o ./chopseqscommand.o\r
1686 \r
1687 # Item # 203 -- clearcutcommand --\r
1688 ./clearcutcommand.o : clearcutcommand.cpp\r
1689         $(CC) $(CC_OPTIONS) clearcutcommand.cpp -c $(INCLUDE) -o ./clearcutcommand.o\r
1690 \r
1691 # Item # 204 -- catchallcommand --\r
1692 ./catchallcommand.o : catchallcommand.cpp\r
1693         $(CC) $(CC_OPTIONS) catchallcommand.cpp -c $(INCLUDE) -o ./catchallcommand.o\r
1694 \r
1695 # Item # 205 -- splitabundcommand --\r
1696 ./splitabundcommand.o : splitabundcommand.cpp\r
1697         $(CC) $(CC_OPTIONS) splitabundcommand.cpp -c $(INCLUDE) -o ./splitabundcommand.o\r
1698         \r
1699 # Item # 206 -- splitmatrix --\r
1700 ./splitmatrix.o : splitmatrix.cpp\r
1701         $(CC) $(CC_OPTIONS) splitmatrix.cpp -c $(INCLUDE) -o ./splitmatrix.o\r
1702         \r
1703 # Item # 207 -- clustersplit --\r
1704 ./clustersplitcommand.o : clustersplitcommand.cpp\r
1705         $(CC) $(CC_OPTIONS) clustersplitcommand.cpp -c $(INCLUDE) -o ./clustersplitcommand.o\r
1706         \r
1707 # Item # 208 -- classifyotu --\r
1708 ./classifyotucommand.o : classifyotucommand.cpp\r
1709         $(CC) $(CC_OPTIONS) classifyotucommand.cpp -c $(INCLUDE) -o ./classifyotucommand.o\r
1710 \r
1711 # Item # 209 -- weightedlinkage --\r
1712 ./weightedlinkage.o : weightedlinkage.cpp\r
1713         $(CC) $(CC_OPTIONS) weightedlinkage.cpp -c $(INCLUDE) -o ./weightedlinkage.o\r
1714 \r
1715 ##### END RUN ####\r