makefile

   1 ###################################################
   2 #
   3 # Makefile for mothur
   4 # Creator [Xcode -> Makefile Ver: Feb 14 2007 09:18:41]
   5 # Created: April 16, 2010
   6 #
   7 ###################################################
   8
   9 #
  10 # Macros
  11 #
  12
  13 CC = g++
  14 CC_OPTIONS = -O3
  15
  16 # if you do not want to use the readline library set to no, default yes.
  17 # make sure you have the library installed
  18
  19 64BIT_VERSION ?= yes
  20
  21 ifeq  ($(strip $(64BIT_VERSION)),yes)
  22     CC_OPTIONS += -arch x86_64
  23         LNK_OPTIONS += -arch x86_64
  24 endif
  25
  26 USEREADLINE ?= yes
  27
  28 ifeq  ($(strip $(USEREADLINE)),yes)
  29     CC_OPTIONS += -DUSE_READLINE
  30         LNK_OPTIONS += \
  31       -lreadline\
  32       -lncurses\
  33       -L../readline-6.0
  34 endif
  35
  36 USEMPI ?= no
  37
  38 ifeq  ($(strip $(USEMPI)),yes)
  39         CC = mpic++
  40     CC_OPTIONS += -DUSE_MPI
  41 endif
  42
  43 #
  44 # INCLUDE directories for mothur
  45 #
  46
  47      INCLUDE = -I.
  48
  49 #
  50 # Build mothur
  51 #
  52
  53 mothur : \
  54                 ./sharedutilities.o\
  55                 ./treegroupscommand.o\
  56                 ./bootstrapsharedcommand.o\
  57                 ./matrixoutputcommand.o\
  58                 ./getoturepcommand.o\
  59                 ./screenseqscommand.o\
  60                 ./chimera.o\
  61                 ./decalc.o\
  62                 ./readotucommand.o\
  63                 ./readdistcommand.o\
  64                 ./commandfactory.o\
  65                 ./alignment.o\
  66                 ./alignmentcell.o\
  67                 ./gotohoverlap.o\
  68                 ./overlap.o\
  69                 ./needlemanoverlap.o\
  70                 ./blastalign.o\
  71                 ./noalign.o\
  72                 ./suffixdb.o\
  73                 ./suffixnodes.o\
  74                 ./suffixtree.o\
  75                 ./blastdb.o\
  76                 ./nast.o\
  77                 ./nastreport.o\
  78                 ./boneh.o\
  79                 ./efron.o\
  80                 ./solow.o\
  81                 ./unifracweightedcommand.o\
  82                 ./weighted.o\
  83                 ./unweighted.o\
  84                 ./unifracunweightedcommand.o\
  85                 ./getsabundcommand.o\
  86                 ./getrabundcommand.o\
  87                 ./bellerophon.o\
  88                 ./pintail.o\
  89                 ./sharedanderbergs.o\
  90                 ./venncommand.o\
  91                 ./venn.o\
  92                 ./fullmatrix.o\
  93                 ./heatmap.o\
  94                 ./heatmapcommand.o\
  95                 ./libshuffcommand.o\
  96                 ./nocommands.o\
  97                 ./sharedbraycurtis.o\
  98                 ./sharedkulczynski.o\
  99                 ./sharedlennon.o\
 100                 ./sharedkulczynskicody.o\
 101                 ./sharedmorisitahorn.o\
 102                 ./sharedochiai.o\
 103                 ./readcolumn.o\
 104                 ./readotu.o\
 105                 ./readphylip.o\
 106                 ./consensuscommand.o\
 107                 ./heatmapsimcommand.o\
 108                 ./heatmapsim.o\
 109                 ./optionparser.o\
 110                 ./filterseqscommand.o\
 111                 ./goodscoverage.o\
 112                 ./sequencedb.o\
 113                 ./sharedjackknife.o\
 114                 ./sharedmarczewski.o\
 115                 ./aligncommand.o\
 116                 ./treemap.o\
 117                 ./parsimonycommand.o\
 118                 ./parsimony.o\
 119                 ./seqsummarycommand.o\
 120                 ./chimeraccodecommand.o\
 121                 ./chimerabellerophoncommand.o\
 122                 ./chimeracheckcommand.o\
 123                 ./chimeraslayercommand.o\
 124                 ./chimerapintailcommand.o\
 125                 ./chimeraseqscommand.o\
 126                 ./sharedlistvector.o\
 127                 ./tree.o\
 128                 ./readtree.o\
 129                 ./sharedsobscollectsummary.o\
 130                 ./deconvolutecommand.o\
 131                 ./listseqscommand.o\
 132                 ./getseqscommand.o\
 133                 ./removeseqscommand.o\
 134                 ./systemcommand.o\
 135                 ./binsequencecommand.o\
 136                 ./distancecommand.o\
 137                 ./ace.o\
 138                 ./averagelinkage.o\
 139                 ./bootstrap.o\
 140                 ./calculator.o\
 141                 ./chao1.o\
 142                 ./cluster.o\
 143                 ./clustercommand.o\
 144                 ./collect.o\
 145                 ./collectcommand.o\
 146                 ./collectsharedcommand.o\
 147                 ./commandoptionparser.o\
 148                 ./completelinkage.o\
 149                 ./database.o\
 150                 ./engine.o\
 151                 ./fastamap.o\
 152                 ./fileoutput.o\
 153                 ./globaldata.o\
 154                 ./groupmap.o\
 155                 ./helpcommand.o\
 156                 ./makegroupcommand.o\
 157                 ./chopseqscommand.o\
 158                 ./clearcutcommand.o\
 159                 ./catchallcommand.o\
 160                 ./splitabundcommand.o\
 161                 ./splitmatrix.o\
 162                 ./clustersplitcommand.o\
 163                 ./weightedlinkage.o\
 164                 ./inputdata.o\
 165                 ./jackknife.o\
 166                 ./kmer.o\
 167                 ./kmerdb.o\
 168                 ./listvector.o\
 169                 ./mothur.o\
 170                 ./nameassignment.o\
 171                 ./npshannon.o\
 172                 ./ordervector.o\
 173                 ./progress.o\
 174                 ./quitcommand.o\
 175                 ./rabundvector.o\
 176                 ./rarecalc.o\
 177                 ./raredisplay.o\
 178                 ./rarefact.o\
 179                 ./rarefactcommand.o\
 180                 ./rarefactsharedcommand.o\
 181                 ./sabundvector.o\
 182                 ./sequence.o\
 183                 ./shannon.o\
 184                 ./sharedace.o\
 185                 ./sharedchao1.o\
 186                 ./sharedcommand.o\
 187                 ./sharedjabund.o\
 188                 ./sharedjclass.o\
 189                 ./sharedjest.o\
 190                 ./sharedordervector.o\
 191                 ./sharedrabundvector.o\
 192                 ./sharedsabundvector.o\
 193                 ./sharedsobs.o\
 194                 ./sharedsorabund.o\
 195                 ./sharedsorclass.o\
 196                 ./sharedsorest.o\
 197                 ./sharedthetan.o\
 198                 ./sharedthetayc.o\
 199                 ./simpson.o\
 200                 ./singlelinkage.o\
 201                 ./sparsematrix.o\
 202                 ./summarycommand.o\
 203                 ./summarysharedcommand.o\
 204                 ./uvest.o\
 205                 ./validcalculator.o\
 206                 ./validparameter.o\
 207                 ./treenode.o\
 208                 ./readtreecommand.o\
 209                 ./reversecommand.o\
 210                 ./trimseqscommand.o\
 211                 ./slibshuff.o\
 212                 ./libshuff.o\
 213                 ./dlibshuff.o\
 214                 ./mergefilecommand.o\
 215                 ./coverage.o\
 216                 ./whittaker.o\
 217                 ./preclustercommand.o\
 218                 ./otuhierarchycommand.o\
 219                 ./setdircommand.o\
 220                 ./getgroupcommand.o\
 221                 ./getlabelcommand.o\
 222                 ./secondarystructurecommand.o\
 223                 ./mothurout.o\
 224                 ./parselistscommand.o\
 225                 ./readblast.o\
 226                 ./chimeracheckrdp.o\
 227                 ./hclustercommand.o\
 228                 ./hcluster.o\
 229                 ./getlistcountcommand.o\
 230                 ./readcluster.o\
 231                 ./ccode.o\
 232                 ./taxonomyequalizer.o\
 233                 ./phylotypecommand.o\
 234                 ./classifyseqscommand.o\
 235                 ./classifyotucommand.o\
 236                 ./parsesffcommand.o\
 237                 ./classify.o\
 238                 ./phylotree.o\
 239                 ./phylodiversity.o\
 240                 ./phylodiversitycommand.o\
 241                 ./bayesian.o\
 242                 ./phylosummary.o\
 243                 ./alignmentdb.o\
 244                 ./knn.o\
 245                 ./distancedb.o\
 246                 ./chimeraslayer.o\
 247                 ./slayer.o\
 248                 ./pcacommand.o\
 249                 ./formatcolumn.o\
 250                 ./formatphylip.o\
 251                 ./mgclustercommand.o\
 252                 ./getsharedotucommand.o\
 253                 ./maligner.o\
 254                 ./chimerarealigner.o\
 255                 ./bergerparker.o\
 256                 ./bstick.o\
 257                 ./sharedkstest.o\
 258                 ./qstat.o\
 259                 ./shen.o\
 260                 ./logsd.o\
 261                 ./geom.o\
 262                 ./setlogfilecommand.o
 263         $(CC) $(LNK_OPTIONS) \
 264                 ./sharedutilities.o\
 265                 ./treegroupscommand.o\
 266                 ./bootstrapsharedcommand.o\
 267                 ./matrixoutputcommand.o\
 268                 ./getoturepcommand.o\
 269                 ./screenseqscommand.o\
 270                 ./chimera.o\
 271                 ./decalc.o\
 272                 ./readotucommand.o\
 273                 ./readdistcommand.o\
 274                 ./commandfactory.o\
 275                 ./alignment.o\
 276                 ./alignmentcell.o\
 277                 ./gotohoverlap.o\
 278                 ./overlap.o\
 279                 ./needlemanoverlap.o\
 280                 ./blastalign.o\
 281                 ./noalign.o\
 282                 ./suffixdb.o\
 283                 ./suffixnodes.o\
 284                 ./suffixtree.o\
 285                 ./blastdb.o\
 286                 ./nast.o\
 287                 ./nastreport.o\
 288                 ./boneh.o\
 289                 ./efron.o\
 290                 ./solow.o\
 291                 ./unifracweightedcommand.o\
 292                 ./weighted.o\
 293                 ./unweighted.o\
 294                 ./unifracunweightedcommand.o\
 295                 ./getsabundcommand.o\
 296                 ./getrabundcommand.o\
 297                 ./bellerophon.o\
 298                 ./pintail.o\
 299                 ./sharedanderbergs.o\
 300                 ./venncommand.o\
 301                 ./venn.o\
 302                 ./fullmatrix.o\
 303                 ./heatmap.o\
 304                 ./heatmapcommand.o\
 305                 ./libshuffcommand.o\
 306                 ./nocommands.o\
 307                 ./sharedbraycurtis.o\
 308                 ./sharedkulczynski.o\
 309                 ./sharedlennon.o\
 310                 ./sharedkulczynskicody.o\
 311                 ./sharedmorisitahorn.o\
 312                 ./sharedochiai.o\
 313                 ./readcolumn.o\
 314                 ./readotu.o\
 315                 ./readphylip.o\
 316                 ./consensuscommand.o\
 317                 ./heatmapsimcommand.o\
 318                 ./heatmapsim.o\
 319                 ./optionparser.o\
 320                 ./filterseqscommand.o\
 321                 ./goodscoverage.o\
 322                 ./sequencedb.o\
 323                 ./sharedjackknife.o\
 324                 ./sharedmarczewski.o\
 325                 ./aligncommand.o\
 326                 ./treemap.o\
 327                 ./parsimonycommand.o\
 328                 ./parsimony.o\
 329                 ./seqsummarycommand.o\
 330                 ./chimeraccodecommand.o\
 331                 ./chimerabellerophoncommand.o\
 332                 ./chimeracheckcommand.o\
 333                 ./chimeraslayercommand.o\
 334                 ./chimerapintailcommand.o\
 335                 ./chimeraseqscommand.o\
 336                 ./sharedlistvector.o\
 337                 ./tree.o\
 338                 ./readtree.o\
 339                 ./sharedsobscollectsummary.o\
 340                 ./deconvolutecommand.o\
 341                 ./listseqscommand.o\
 342                 ./getseqscommand.o\
 343                 ./removeseqscommand.o\
 344                 ./systemcommand.o\
 345                 ./binsequencecommand.o\
 346                 ./distancecommand.o\
 347                 ./ace.o\
 348                 ./averagelinkage.o\
 349                 ./bootstrap.o\
 350                 ./calculator.o\
 351                 ./chao1.o\
 352                 ./cluster.o\
 353                 ./clustercommand.o\
 354                 ./collect.o\
 355                 ./collectcommand.o\
 356                 ./collectsharedcommand.o\
 357                 ./commandoptionparser.o\
 358                 ./completelinkage.o\
 359                 ./database.o\
 360                 ./engine.o\
 361                 ./fastamap.o\
 362                 ./fileoutput.o\
 363                 ./globaldata.o\
 364                 ./groupmap.o\
 365                 ./helpcommand.o\
 366                 ./makegroupcommand.o\
 367                 ./chopseqscommand.o\
 368                 ./clearcutcommand.o\
 369                 ./catchallcommand.o\
 370                 ./splitabundcommand.o\
 371                 ./splitmatrix.o\
 372                 ./clustersplitcommand.o\
 373                 ./weightedlinkage.o\
 374                 ./inputdata.o\
 375                 ./jackknife.o\
 376                 ./kmer.o\
 377                 ./kmerdb.o\
 378                 ./listvector.o\
 379                 ./mothur.o\
 380                 ./nameassignment.o\
 381                 ./npshannon.o\
 382                 ./ordervector.o\
 383                 ./progress.o\
 384                 ./quitcommand.o\
 385                 ./rabundvector.o\
 386                 ./rarecalc.o\
 387                 ./raredisplay.o\
 388                 ./rarefact.o\
 389                 ./rarefactcommand.o\
 390                 ./rarefactsharedcommand.o\
 391                 ./sabundvector.o\
 392                 ./sequence.o\
 393                 ./shannon.o\
 394                 ./sharedace.o\
 395                 ./sharedchao1.o\
 396                 ./sharedcommand.o\
 397                 ./sharedjabund.o\
 398                 ./sharedjclass.o\
 399                 ./sharedjest.o\
 400                 ./sharedordervector.o\
 401                 ./sharedrabundvector.o\
 402                 ./sharedsabundvector.o\
 403                 ./sharedsobs.o\
 404                 ./sharedsorabund.o\
 405                 ./sharedsorclass.o\
 406                 ./sharedsorest.o\
 407                 ./sharedthetan.o\
 408                 ./sharedthetayc.o\
 409                 ./simpson.o\
 410                 ./singlelinkage.o\
 411                 ./sparsematrix.o\
 412                 ./summarycommand.o\
 413                 ./summarysharedcommand.o\
 414                 ./uvest.o\
 415                 ./validcalculator.o\
 416                 ./validparameter.o\
 417                 ./treenode.o\
 418                 ./readtreecommand.o\
 419                 ./reversecommand.o\
 420                 ./trimseqscommand.o\
 421                 ./slibshuff.o\
 422                 ./libshuff.o\
 423                 ./dlibshuff.o\
 424                 ./mergefilecommand.o\
 425                 ./coverage.o\
 426                 ./whittaker.o\
 427                 ./preclustercommand.o\
 428                 ./otuhierarchycommand.o\
 429                 ./setdircommand.o\
 430                 ./getgroupcommand.o\
 431                 ./getlabelcommand.o\
 432                 ./secondarystructurecommand.o\
 433                 ./mothurout.o\
 434                 ./parselistscommand.o\
 435                 ./readblast.o\
 436                 ./chimeracheckrdp.o\
 437                 ./hclustercommand.o\
 438                 ./hcluster.o\
 439                 ./getlistcountcommand.o\
 440                 ./readcluster.o\
 441                 ./ccode.o\
 442                 ./taxonomyequalizer.o\
 443                 ./phylotypecommand.o\
 444                 ./classifyseqscommand.o\
 445                 ./classifyotucommand.o\
 446                 ./parsesffcommand.o\
 447                 ./classify.o\
 448                 ./phylotree.o\
 449                 ./phylodiversity.o\
 450                 ./phylodiversitycommand.o\
 451                 ./bayesian.o\
 452                 ./phylosummary.o\
 453                 ./alignmentdb.o\
 454                 ./knn.o\
 455                 ./distancedb.o\
 456                 ./chimeraslayer.o\
 457                 ./slayer.o\
 458                 ./pcacommand.o\
 459                 ./formatcolumn.o\
 460                 ./formatphylip.o\
 461                 ./mgclustercommand.o\
 462                 ./getsharedotucommand.o\
 463                 ./maligner.o\
 464                 ./chimerarealigner.o\
 465                 ./bergerparker.o\
 466                 ./bstick.o\
 467                 ./sharedkstest.o\
 468                 ./qstat.o\
 469                 ./shen.o\
 470                 ./logsd.o\
 471                 ./geom.o\
 472                 ./setlogfilecommand.o\
 473                 -o ../Release/mothur
 474
 475 clean :
 476                 rm \
 477                 ./sharedutilities.o\
 478                 ./treegroupscommand.o\
 479                 ./bootstrapsharedcommand.o\
 480                 ./matrixoutputcommand.o\
 481                 ./getoturepcommand.o\
 482                 ./screenseqscommand.o\
 483                 ./chimera.o\
 484                 ./decalc.o\
 485                 ./readotucommand.o\
 486                 ./readdistcommand.o\
 487                 ./commandfactory.o\
 488                 ./alignment.o\
 489                 ./alignmentcell.o\
 490                 ./gotohoverlap.o\
 491                 ./overlap.o\
 492                 ./needlemanoverlap.o\
 493                 ./blastalign.o\
 494                 ./noalign.o\
 495                 ./suffixdb.o\
 496                 ./suffixnodes.o\
 497                 ./suffixtree.o\
 498                 ./blastdb.o\
 499                 ./nast.o\
 500                 ./nastreport.o\
 501                 ./boneh.o\
 502                 ./efron.o\
 503                 ./solow.o\
 504                 ./unifracweightedcommand.o\
 505                 ./weighted.o\
 506                 ./unweighted.o\
 507                 ./unifracunweightedcommand.o\
 508                 ./getsabundcommand.o\
 509                 ./getrabundcommand.o\
 510                 ./bellerophon.o\
 511                 ./pintail.o\
 512                 ./sharedanderbergs.o\
 513                 ./venncommand.o\
 514                 ./venn.o\
 515                 ./fullmatrix.o\
 516                 ./heatmap.o\
 517                 ./heatmapcommand.o\
 518                 ./libshuffcommand.o\
 519                 ./nocommands.o\
 520                 ./sharedbraycurtis.o\
 521                 ./sharedkulczynski.o\
 522                 ./sharedlennon.o\
 523                 ./sharedkulczynskicody.o\
 524                 ./sharedmorisitahorn.o\
 525                 ./sharedochiai.o\
 526                 ./readcolumn.o\
 527                 ./readotu.o\
 528                 ./readphylip.o\
 529                 ./consensuscommand.o\
 530                 ./heatmapsimcommand.o\
 531                 ./heatmapsim.o\
 532                 ./optionparser.o\
 533                 ./filterseqscommand.o\
 534                 ./goodscoverage.o\
 535                 ./sequencedb.o\
 536                 ./sharedjackknife.o\
 537                 ./sharedmarczewski.o\
 538                 ./aligncommand.o\
 539                 ./treemap.o\
 540                 ./parsimonycommand.o\
 541                 ./parsimony.o\
 542                 ./seqsummarycommand.o\
 543                 ./chimeraccodecommand.o\
 544                 ./chimerabellerophoncommand.o\
 545                 ./chimeracheckcommand.o\
 546                 ./chimeraslayercommand.o\
 547                 ./chimerapintailcommand.o\
 548                 ./chimeraseqscommand.o\
 549                 ./sharedlistvector.o\
 550                 ./tree.o\
 551                 ./readtree.o\
 552                 ./sharedsobscollectsummary.o\
 553                 ./deconvolutecommand.o\
 554                 ./listseqscommand.o\
 555                 ./getseqscommand.o\
 556                 ./removeseqscommand.o\
 557                 ./systemcommand.o\
 558                 ./binsequencecommand.o\
 559                 ./distancecommand.o\
 560                 ./ace.o\
 561                 ./averagelinkage.o\
 562                 ./bootstrap.o\
 563                 ./calculator.o\
 564                 ./chao1.o\
 565                 ./cluster.o\
 566                 ./clustercommand.o\
 567                 ./collect.o\
 568                 ./collectcommand.o\
 569                 ./collectsharedcommand.o\
 570                 ./commandoptionparser.o\
 571                 ./completelinkage.o\
 572                 ./database.o\
 573                 ./engine.o\
 574                 ./fastamap.o\
 575                 ./fileoutput.o\
 576                 ./globaldata.o\
 577                 ./groupmap.o\
 578                 ./helpcommand.o\
 579                 ./makegroupcommand.o\
 580                 ./chopseqscommand.o\
 581                 ./clearcutcommand.o\
 582                 ./catchallcommand.o\
 583                 ./splitabundcommand.o\
 584                 ./splitmatrix.o\
 585                 ./clustersplitcommand.o\
 586                 ./weightedlinkage.o\
 587                 ./inputdata.o\
 588                 ./jackknife.o\
 589                 ./kmer.o\
 590                 ./kmerdb.o\
 591                 ./listvector.o\
 592                 ./mothur.o\
 593                 ./nameassignment.o\
 594                 ./npshannon.o\
 595                 ./ordervector.o\
 596                 ./progress.o\
 597                 ./quitcommand.o\
 598                 ./rabundvector.o\
 599                 ./rarecalc.o\
 600                 ./raredisplay.o\
 601                 ./rarefact.o\
 602                 ./rarefactcommand.o\
 603                 ./rarefactsharedcommand.o\
 604                 ./sabundvector.o\
 605                 ./sequence.o\
 606                 ./shannon.o\
 607                 ./sharedace.o\
 608                 ./sharedchao1.o\
 609                 ./sharedcommand.o\
 610                 ./sharedjabund.o\
 611                 ./sharedjclass.o\
 612                 ./sharedjest.o\
 613                 ./sharedordervector.o\
 614                 ./sharedrabundvector.o\
 615                 ./sharedsabundvector.o\
 616                 ./sharedsobs.o\
 617                 ./sharedsorabund.o\
 618                 ./sharedsorclass.o\
 619                 ./sharedsorest.o\
 620                 ./sharedthetan.o\
 621                 ./sharedthetayc.o\
 622                 ./simpson.o\
 623                 ./singlelinkage.o\
 624                 ./sparsematrix.o\
 625                 ./summarycommand.o\
 626                 ./summarysharedcommand.o\
 627                 ./uvest.o\
 628                 ./validcalculator.o\
 629                 ./validparameter.o\
 630                 ./treenode.o\
 631                 ./readtreecommand.o\
 632                 ./reversecommand.o\
 633                 ./trimseqscommand.o\
 634                 ./slibshuff.o\
 635                 ./libshuff.o\
 636                 ./dlibshuff.o\
 637                 ./mergefilecommand.o\
 638                 ./coverage.o\
 639                 ./whittaker.o\
 640                 ./preclustercommand.o\
 641                 ./otuhierarchycommand.o\
 642                 ./setdircommand.o\
 643                 ./getgroupcommand.o\
 644                 ./getlabelcommand.o\
 645                 ./secondarystructurecommand.o\
 646                 ./mothurout.o\
 647                 ./parselistscommand.o\
 648                 ./readblast.o\
 649                 ./chimeracheckrdp.o\
 650                 ./hclustercommand.o\
 651                 ./hcluster.o\
 652                 ./getlistcountcommand.o\
 653                 ./readcluster.o\
 654                 ./ccode.o\
 655                 ./taxonomyequalizer.o\
 656                 ./phylotypecommand.o\
 657                 ./classifyseqscommand.o\
 658                 ./classifyotucommand.o\
 659                 ./parsesffcommand.o\
 660                 ./classify.o\
 661                 ./phylotree.o\
 662                 ./phylodiversity.o\
 663                 ./phylodiversitycommand.o\
 664                 ./bayesian.o\
 665                 ./phylosummary.o\
 666                 ./alignmentdb.o\
 667                 ./knn.o\
 668                 ./distancedb.o\
 669                 ./chimeraslayer.o\
 670                 ./slayer.o\
 671                 ./pcacommand.o\
 672                 ./formatcolumn.o\
 673                 ./formatphylip.o\
 674                 ./mgclustercommand.o\
 675                 ./getsharedotucommand.o\
 676                 ./maligner.o\
 677                 ./chimerarealigner.o\
 678                 ./bergerparker.o\
 679                 ./bstick.o\
 680                 ./sharedkstest.o\
 681                 ./qstat.o\
 682                 ./shen.o\
 683                 ./logsd.o\
 684                 ./geom.o\
 685                 ./setlogfilecommand.o\
 686                 mothur
 687
 688 install : mothur
 689                 #cp mothur ../Release/mothur
 690
 691 #
 692 # Build the parts of mothur
 693 #
 694
 695
 696 # Item # 1 -- sharedutilities --
 697 ./sharedutilities.o : sharedutilities.cpp
 698         $(CC) $(CC_OPTIONS) sharedutilities.cpp -c $(INCLUDE) -o ./sharedutilities.o
 699
 700
 701 # Item # 2 -- treegroupscommand --
 702 ./treegroupscommand.o : treegroupscommand.cpp
 703         $(CC) $(CC_OPTIONS) treegroupscommand.cpp -c $(INCLUDE) -o ./treegroupscommand.o
 704
 705
 706 # Item # 3 -- bootstrapsharedcommand --
 707 ./bootstrapsharedcommand.o : bootstrapsharedcommand.cpp
 708         $(CC) $(CC_OPTIONS) bootstrapsharedcommand.cpp -c $(INCLUDE) -o ./bootstrapsharedcommand.o
 709
 710
 711 # Item # 4 -- matrixoutputcommand --
 712 ./matrixoutputcommand.o : matrixoutputcommand.cpp
 713         $(CC) $(CC_OPTIONS) matrixoutputcommand.cpp -c $(INCLUDE) -o ./matrixoutputcommand.o
 714
 715
 716 # Item # 5 -- getoturepcommand --
 717 ./getoturepcommand.o : getoturepcommand.cpp
 718         $(CC) $(CC_OPTIONS) getoturepcommand.cpp -c $(INCLUDE) -o ./getoturepcommand.o
 719
 720
 721 # Item # 6 -- screenseqscommand --
 722 ./screenseqscommand.o : screenseqscommand.cpp
 723         $(CC) $(CC_OPTIONS) screenseqscommand.cpp -c $(INCLUDE) -o ./screenseqscommand.o
 724
 725
 726 # Item # 7 -- chimera --
 727 ./chimera.o : chimera.cpp
 728         $(CC) $(CC_OPTIONS) chimera.cpp -c $(INCLUDE) -o ./chimera.o
 729
 730
 731 # Item # 8 -- decalc --
 732 ./decalc.o : decalc.cpp
 733         $(CC) $(CC_OPTIONS) decalc.cpp -c $(INCLUDE) -o ./decalc.o
 734
 735
 736 # Item # 9 -- readotucommand --
 737 ./readotucommand.o : readotucommand.cpp
 738         $(CC) $(CC_OPTIONS) readotucommand.cpp -c $(INCLUDE) -o ./readotucommand.o
 739
 740
 741 # Item # 10 -- readdistcommand --
 742 ./readdistcommand.o : readdistcommand.cpp
 743         $(CC) $(CC_OPTIONS) readdistcommand.cpp -c $(INCLUDE) -o ./readdistcommand.o
 744
 745
 746 # Item # 11 -- commandfactory --
 747 ./commandfactory.o : commandfactory.cpp
 748         $(CC) $(CC_OPTIONS) commandfactory.cpp -c $(INCLUDE) -o ./commandfactory.o
 749
 750
 751 # Item # 12 -- alignment --
 752 ./alignment.o : alignment.cpp
 753         $(CC) $(CC_OPTIONS) alignment.cpp -c $(INCLUDE) -o ./alignment.o
 754
 755
 756 # Item # 13 -- alignmentcell --
 757 ./alignmentcell.o : alignmentcell.cpp
 758         $(CC) $(CC_OPTIONS) alignmentcell.cpp -c $(INCLUDE) -o ./alignmentcell.o
 759
 760
 761 # Item # 14 -- gotohoverlap --
 762 ./gotohoverlap.o : gotohoverlap.cpp
 763         $(CC) $(CC_OPTIONS) gotohoverlap.cpp -c $(INCLUDE) -o ./gotohoverlap.o
 764
 765
 766 # Item # 15 -- overlap --
 767 ./overlap.o : overlap.cpp
 768         $(CC) $(CC_OPTIONS) overlap.cpp -c $(INCLUDE) -o ./overlap.o
 769
 770
 771 # Item # 16 -- needlemanoverlap --
 772 ./needlemanoverlap.o : needlemanoverlap.cpp
 773         $(CC) $(CC_OPTIONS) needlemanoverlap.cpp -c $(INCLUDE) -o ./needlemanoverlap.o
 774
 775
 776 # Item # 17 -- blastalign --
 777 ./blastalign.o : blastalign.cpp
 778         $(CC) $(CC_OPTIONS) blastalign.cpp -c $(INCLUDE) -o ./blastalign.o
 779
 780
 781 # Item # 18 -- noalign --
 782 ./noalign.o : noalign.cpp
 783         $(CC) $(CC_OPTIONS) noalign.cpp -c $(INCLUDE) -o ./noalign.o
 784
 785
 786 # Item # 19 -- suffixdb --
 787 ./suffixdb.o : suffixdb.cpp
 788         $(CC) $(CC_OPTIONS) suffixdb.cpp -c $(INCLUDE) -o ./suffixdb.o
 789
 790
 791 # Item # 20 -- suffixnodes --
 792 ./suffixnodes.o : suffixnodes.cpp
 793         $(CC) $(CC_OPTIONS) suffixnodes.cpp -c $(INCLUDE) -o ./suffixnodes.o
 794
 795
 796 # Item # 21 -- suffixtree --
 797 ./suffixtree.o : suffixtree.cpp
 798         $(CC) $(CC_OPTIONS) suffixtree.cpp -c $(INCLUDE) -o ./suffixtree.o
 799
 800
 801 # Item # 22 -- blastdb --
 802 ./blastdb.o : blastdb.cpp
 803         $(CC) $(CC_OPTIONS) blastdb.cpp -c $(INCLUDE) -o ./blastdb.o
 804
 805
 806 # Item # 23 -- nast --
 807 ./nast.o : nast.cpp
 808         $(CC) $(CC_OPTIONS) nast.cpp -c $(INCLUDE) -o ./nast.o
 809
 810
 811 # Item # 24 -- nastreport --
 812 ./nastreport.o : nastreport.cpp
 813         $(CC) $(CC_OPTIONS) nastreport.cpp -c $(INCLUDE) -o ./nastreport.o
 814
 815
 816 # Item # 25 -- boneh --
 817 ./boneh.o : boneh.cpp
 818         $(CC) $(CC_OPTIONS) boneh.cpp -c $(INCLUDE) -o ./boneh.o
 819
 820
 821 # Item # 26 -- efron --
 822 ./efron.o : efron.cpp
 823         $(CC) $(CC_OPTIONS) efron.cpp -c $(INCLUDE) -o ./efron.o
 824
 825
 826 # Item # 27 -- solow --
 827 ./solow.o : solow.cpp
 828         $(CC) $(CC_OPTIONS) solow.cpp -c $(INCLUDE) -o ./solow.o
 829
 830
 831 # Item # 28 -- unifracweightedcommand --
 832 ./unifracweightedcommand.o : unifracweightedcommand.cpp
 833         $(CC) $(CC_OPTIONS) unifracweightedcommand.cpp -c $(INCLUDE) -o ./unifracweightedcommand.o
 834
 835
 836 # Item # 29 -- weighted --
 837 ./weighted.o : weighted.cpp
 838         $(CC) $(CC_OPTIONS) weighted.cpp -c $(INCLUDE) -o ./weighted.o
 839
 840
 841 # Item # 30 -- unweighted --
 842 ./unweighted.o : unweighted.cpp
 843         $(CC) $(CC_OPTIONS) unweighted.cpp -c $(INCLUDE) -o ./unweighted.o
 844
 845
 846 # Item # 31 -- unifracunweightedcommand --
 847 ./unifracunweightedcommand.o : unifracunweightedcommand.cpp
 848         $(CC) $(CC_OPTIONS) unifracunweightedcommand.cpp -c $(INCLUDE) -o ./unifracunweightedcommand.o
 849
 850
 851 # Item # 32 -- getsabundcommand --
 852 ./getsabundcommand.o : getsabundcommand.cpp
 853         $(CC) $(CC_OPTIONS) getsabundcommand.cpp -c $(INCLUDE) -o ./getsabundcommand.o
 854
 855
 856 # Item # 33 -- getrabundcommand --
 857 ./getrabundcommand.o : getrabundcommand.cpp
 858         $(CC) $(CC_OPTIONS) getrabundcommand.cpp -c $(INCLUDE) -o ./getrabundcommand.o
 859
 860
 861 # Item # 34 -- bellerophon --
 862 ./bellerophon.o : bellerophon.cpp
 863         $(CC) $(CC_OPTIONS) bellerophon.cpp -c $(INCLUDE) -o ./bellerophon.o
 864
 865
 866 # Item # 35 -- pintail --
 867 ./pintail.o : pintail.cpp
 868         $(CC) $(CC_OPTIONS) pintail.cpp -c $(INCLUDE) -o ./pintail.o
 869
 870
 871 # Item # 36 -- sharedanderbergs --
 872 ./sharedanderbergs.o : sharedanderbergs.cpp
 873         $(CC) $(CC_OPTIONS) sharedanderbergs.cpp -c $(INCLUDE) -o ./sharedanderbergs.o
 874
 875
 876 # Item # 37 -- venncommand --
 877 ./venncommand.o : venncommand.cpp
 878         $(CC) $(CC_OPTIONS) venncommand.cpp -c $(INCLUDE) -o ./venncommand.o
 879
 880
 881 # Item # 38 -- venn --
 882 ./venn.o : venn.cpp
 883         $(CC) $(CC_OPTIONS) venn.cpp -c $(INCLUDE) -o ./venn.o
 884
 885
 886 # Item # 39 -- fullmatrix --
 887 ./fullmatrix.o : fullmatrix.cpp
 888         $(CC) $(CC_OPTIONS) fullmatrix.cpp -c $(INCLUDE) -o ./fullmatrix.o
 889
 890
 891 # Item # 40 -- heatmap --
 892 ./heatmap.o : heatmap.cpp
 893         $(CC) $(CC_OPTIONS) heatmap.cpp -c $(INCLUDE) -o ./heatmap.o
 894
 895
 896 # Item # 41 -- heatmapcommand --
 897 ./heatmapcommand.o : heatmapcommand.cpp
 898         $(CC) $(CC_OPTIONS) heatmapcommand.cpp -c $(INCLUDE) -o ./heatmapcommand.o
 899
 900
 901 # Item # 42 -- libshuffcommand --
 902 ./libshuffcommand.o : libshuffcommand.cpp
 903         $(CC) $(CC_OPTIONS) libshuffcommand.cpp -c $(INCLUDE) -o ./libshuffcommand.o
 904
 905
 906 # Item # 43 -- nocommands --
 907 ./nocommands.o : nocommands.cpp
 908         $(CC) $(CC_OPTIONS) nocommands.cpp -c $(INCLUDE) -o ./nocommands.o
 909
 910
 911 # Item # 44 -- sharedbraycurtis --
 912 ./sharedbraycurtis.o : sharedbraycurtis.cpp
 913         $(CC) $(CC_OPTIONS) sharedbraycurtis.cpp -c $(INCLUDE) -o ./sharedbraycurtis.o
 914
 915
 916 # Item # 45 -- sharedkulczynski --
 917 ./sharedkulczynski.o : sharedkulczynski.cpp
 918         $(CC) $(CC_OPTIONS) sharedkulczynski.cpp -c $(INCLUDE) -o ./sharedkulczynski.o
 919
 920
 921 # Item # 46 -- sharedlennon --
 922 ./sharedlennon.o : sharedlennon.cpp
 923         $(CC) $(CC_OPTIONS) sharedlennon.cpp -c $(INCLUDE) -o ./sharedlennon.o
 924
 925
 926 # Item # 47 -- sharedkulczynskicody --
 927 ./sharedkulczynskicody.o : sharedkulczynskicody.cpp
 928         $(CC) $(CC_OPTIONS) sharedkulczynskicody.cpp -c $(INCLUDE) -o ./sharedkulczynskicody.o
 929
 930
 931 # Item # 48 -- sharedmorisitahorn --
 932 ./sharedmorisitahorn.o : sharedmorisitahorn.cpp
 933         $(CC) $(CC_OPTIONS) sharedmorisitahorn.cpp -c $(INCLUDE) -o ./sharedmorisitahorn.o
 934
 935
 936 # Item # 49 -- sharedochiai --
 937 ./sharedochiai.o : sharedochiai.cpp
 938         $(CC) $(CC_OPTIONS) sharedochiai.cpp -c $(INCLUDE) -o ./sharedochiai.o
 939
 940
 941 # Item # 50 -- readcolumn --
 942 ./readcolumn.o : readcolumn.cpp
 943         $(CC) $(CC_OPTIONS) readcolumn.cpp -c $(INCLUDE) -o ./readcolumn.o
 944
 945
 946 # Item # 51 -- readotu --
 947 ./readotu.o : readotu.cpp
 948         $(CC) $(CC_OPTIONS) readotu.cpp -c $(INCLUDE) -o ./readotu.o
 949
 950
 951 # Item # 52 -- readphylip --
 952 ./readphylip.o : readphylip.cpp
 953         $(CC) $(CC_OPTIONS) readphylip.cpp -c $(INCLUDE) -o ./readphylip.o
 954
 955
 956 # Item # 53 -- consensuscommand --
 957 ./consensuscommand.o : consensuscommand.cpp
 958         $(CC) $(CC_OPTIONS) consensuscommand.cpp -c $(INCLUDE) -o ./consensuscommand.o
 959
 960
 961 # Item # 54 -- heatmapsimcommand --
 962 ./heatmapsimcommand.o : heatmapsimcommand.cpp
 963         $(CC) $(CC_OPTIONS) heatmapsimcommand.cpp -c $(INCLUDE) -o ./heatmapsimcommand.o
 964
 965
 966 # Item # 55 -- heatmapsim --
 967 ./heatmapsim.o : heatmapsim.cpp
 968         $(CC) $(CC_OPTIONS) heatmapsim.cpp -c $(INCLUDE) -o ./heatmapsim.o
 969
 970
 971 # Item # 56 -- optionparser --
 972 ./optionparser.o : optionparser.cpp
 973         $(CC) $(CC_OPTIONS) optionparser.cpp -c $(INCLUDE) -o ./optionparser.o
 974
 975
 976 # Item # 57 -- filterseqscommand --
 977 ./filterseqscommand.o : filterseqscommand.cpp
 978         $(CC) $(CC_OPTIONS) filterseqscommand.cpp -c $(INCLUDE) -o ./filterseqscommand.o
 979
 980
 981 # Item # 58 -- goodscoverage --
 982 ./goodscoverage.o : goodscoverage.cpp
 983         $(CC) $(CC_OPTIONS) goodscoverage.cpp -c $(INCLUDE) -o ./goodscoverage.o
 984
 985
 986 # Item # 59 -- sequencedb --
 987 ./sequencedb.o : sequencedb.cpp
 988         $(CC) $(CC_OPTIONS) sequencedb.cpp -c $(INCLUDE) -o ./sequencedb.o
 989
 990
 991 # Item # 60 -- sharedjackknife --
 992 ./sharedjackknife.o : sharedjackknife.cpp
 993         $(CC) $(CC_OPTIONS) sharedjackknife.cpp -c $(INCLUDE) -o ./sharedjackknife.o
 994
 995
 996 # Item # 61 -- sharedmarczewski --
 997 ./sharedmarczewski.o : sharedmarczewski.cpp
 998         $(CC) $(CC_OPTIONS) sharedmarczewski.cpp -c $(INCLUDE) -o ./sharedmarczewski.o
 999
1000
1001 # Item # 62 -- aligncommand --
1002 ./aligncommand.o : aligncommand.cpp
1003         $(CC) $(CC_OPTIONS) aligncommand.cpp -c $(INCLUDE) -o ./aligncommand.o
1004
1005
1006 # Item # 63 -- treemap --
1007 ./treemap.o : treemap.cpp
1008         $(CC) $(CC_OPTIONS) treemap.cpp -c $(INCLUDE) -o ./treemap.o
1009
1010
1011 # Item # 64 -- parsimonycommand --
1012 ./parsimonycommand.o : parsimonycommand.cpp
1013         $(CC) $(CC_OPTIONS) parsimonycommand.cpp -c $(INCLUDE) -o ./parsimonycommand.o
1014
1015
1016 # Item # 65 -- parsimony --
1017 ./parsimony.o : parsimony.cpp
1018         $(CC) $(CC_OPTIONS) parsimony.cpp -c $(INCLUDE) -o ./parsimony.o
1019
1020
1021 # Item # 66 -- seqsummarycommand --
1022 ./seqsummarycommand.o : seqsummarycommand.cpp
1023         $(CC) $(CC_OPTIONS) seqsummarycommand.cpp -c $(INCLUDE) -o ./seqsummarycommand.o
1024
1025
1026 # Item # 67 -- chimeraseqscommand --
1027 ./chimeraseqscommand.o : chimeraseqscommand.cpp
1028         $(CC) $(CC_OPTIONS) chimeraseqscommand.cpp -c $(INCLUDE) -o ./chimeraseqscommand.o
1029
1030
1031 # Item # 68 -- sharedlistvector --
1032 ./sharedlistvector.o : sharedlistvector.cpp
1033         $(CC) $(CC_OPTIONS) sharedlistvector.cpp -c $(INCLUDE) -o ./sharedlistvector.o
1034
1035
1036 # Item # 69 -- tree --
1037 ./tree.o : tree.cpp
1038         $(CC) $(CC_OPTIONS) tree.cpp -c $(INCLUDE) -o ./tree.o
1039
1040
1041 # Item # 70 -- readtree --
1042 ./readtree.o : readtree.cpp
1043         $(CC) $(CC_OPTIONS) readtree.cpp -c $(INCLUDE) -o ./readtree.o
1044
1045
1046 # Item # 71 -- sharedsobscollectsummary --
1047 ./sharedsobscollectsummary.o : sharedsobscollectsummary.cpp
1048         $(CC) $(CC_OPTIONS) sharedsobscollectsummary.cpp -c $(INCLUDE) -o ./sharedsobscollectsummary.o
1049
1050
1051 # Item # 72 -- deconvolutecommand --
1052 ./deconvolutecommand.o : deconvolutecommand.cpp
1053         $(CC) $(CC_OPTIONS) deconvolutecommand.cpp -c $(INCLUDE) -o ./deconvolutecommand.o
1054
1055
1056 # Item # 73 -- listseqscommand --
1057 ./listseqscommand.o : listseqscommand.cpp
1058         $(CC) $(CC_OPTIONS) listseqscommand.cpp -c $(INCLUDE) -o ./listseqscommand.o
1059
1060
1061 # Item # 74 -- getseqscommand --
1062 ./getseqscommand.o : getseqscommand.cpp
1063         $(CC) $(CC_OPTIONS) getseqscommand.cpp -c $(INCLUDE) -o ./getseqscommand.o
1064
1065
1066 # Item # 75 -- removeseqscommand --
1067 ./removeseqscommand.o : removeseqscommand.cpp
1068         $(CC) $(CC_OPTIONS) removeseqscommand.cpp -c $(INCLUDE) -o ./removeseqscommand.o
1069
1070
1071 # Item # 76 -- systemcommand --
1072 ./systemcommand.o : systemcommand.cpp
1073         $(CC) $(CC_OPTIONS) systemcommand.cpp -c $(INCLUDE) -o ./systemcommand.o
1074
1075
1076 # Item # 77 -- binsequencecommand --
1077 ./binsequencecommand.o : binsequencecommand.cpp
1078         $(CC) $(CC_OPTIONS) binsequencecommand.cpp -c $(INCLUDE) -o ./binsequencecommand.o
1079
1080
1081 # Item # 78 -- distancecommand --
1082 ./distancecommand.o : distancecommand.cpp
1083         $(CC) $(CC_OPTIONS) distancecommand.cpp -c $(INCLUDE) -o ./distancecommand.o
1084
1085
1086 # Item # 79 -- ace --
1087 ./ace.o : ace.cpp
1088         $(CC) $(CC_OPTIONS) ace.cpp -c $(INCLUDE) -o ./ace.o
1089
1090
1091 # Item # 80 -- averagelinkage --
1092 ./averagelinkage.o : averagelinkage.cpp
1093         $(CC) $(CC_OPTIONS) averagelinkage.cpp -c $(INCLUDE) -o ./averagelinkage.o
1094
1095
1096 # Item # 81 -- bootstrap --
1097 ./bootstrap.o : bootstrap.cpp
1098         $(CC) $(CC_OPTIONS) bootstrap.cpp -c $(INCLUDE) -o ./bootstrap.o
1099
1100
1101 # Item # 82 -- calculator --
1102 ./calculator.o : calculator.cpp
1103         $(CC) $(CC_OPTIONS) calculator.cpp -c $(INCLUDE) -o ./calculator.o
1104
1105
1106 # Item # 83 -- chao1 --
1107 ./chao1.o : chao1.cpp
1108         $(CC) $(CC_OPTIONS) chao1.cpp -c $(INCLUDE) -o ./chao1.o
1109
1110
1111 # Item # 84 -- cluster --
1112 ./cluster.o : cluster.cpp
1113         $(CC) $(CC_OPTIONS) cluster.cpp -c $(INCLUDE) -o ./cluster.o
1114
1115
1116 # Item # 85 -- clustercommand --
1117 ./clustercommand.o : clustercommand.cpp
1118         $(CC) $(CC_OPTIONS) clustercommand.cpp -c $(INCLUDE) -o ./clustercommand.o
1119
1120
1121 # Item # 86 -- collect --
1122 ./collect.o : collect.cpp
1123         $(CC) $(CC_OPTIONS) collect.cpp -c $(INCLUDE) -o ./collect.o
1124
1125
1126 # Item # 87 -- collectcommand --
1127 ./collectcommand.o : collectcommand.cpp
1128         $(CC) $(CC_OPTIONS) collectcommand.cpp -c $(INCLUDE) -o ./collectcommand.o
1129
1130
1131 # Item # 88 -- collectsharedcommand --
1132 ./collectsharedcommand.o : collectsharedcommand.cpp
1133         $(CC) $(CC_OPTIONS) collectsharedcommand.cpp -c $(INCLUDE) -o ./collectsharedcommand.o
1134
1135
1136 # Item # 89 -- commandoptionparser --
1137 ./commandoptionparser.o : commandoptionparser.cpp
1138         $(CC) $(CC_OPTIONS) commandoptionparser.cpp -c $(INCLUDE) -o ./commandoptionparser.o
1139
1140
1141 # Item # 90 -- completelinkage --
1142 ./completelinkage.o : completelinkage.cpp
1143         $(CC) $(CC_OPTIONS) completelinkage.cpp -c $(INCLUDE) -o ./completelinkage.o
1144
1145
1146 # Item # 91 -- database --
1147 ./database.o : database.cpp
1148         $(CC) $(CC_OPTIONS) database.cpp -c $(INCLUDE) -o ./database.o
1149
1150
1151 # Item # 92 -- engine --
1152 ./engine.o : engine.cpp
1153         $(CC) $(CC_OPTIONS) engine.cpp -c $(INCLUDE) -o ./engine.o
1154
1155
1156 # Item # 93 -- fastamap --
1157 ./fastamap.o : fastamap.cpp
1158         $(CC) $(CC_OPTIONS) fastamap.cpp -c $(INCLUDE) -o ./fastamap.o
1159
1160
1161 # Item # 94 -- fileoutput --
1162 ./fileoutput.o : fileoutput.cpp
1163         $(CC) $(CC_OPTIONS) fileoutput.cpp -c $(INCLUDE) -o ./fileoutput.o
1164
1165
1166 # Item # 95 -- globaldata --
1167 ./globaldata.o : globaldata.cpp
1168         $(CC) $(CC_OPTIONS) globaldata.cpp -c $(INCLUDE) -o ./globaldata.o
1169
1170
1171 # Item # 96 -- groupmap --
1172 ./groupmap.o : groupmap.cpp
1173         $(CC) $(CC_OPTIONS) groupmap.cpp -c $(INCLUDE) -o ./groupmap.o
1174
1175
1176 # Item # 97 -- helpcommand --
1177 ./helpcommand.o : helpcommand.cpp
1178         $(CC) $(CC_OPTIONS) helpcommand.cpp -c $(INCLUDE) -o ./helpcommand.o
1179
1180
1181 # Item # 98 -- inputdata --
1182 ./inputdata.o : inputdata.cpp
1183         $(CC) $(CC_OPTIONS) inputdata.cpp -c $(INCLUDE) -o ./inputdata.o
1184
1185
1186 # Item # 99 -- jackknife --
1187 ./jackknife.o : jackknife.cpp
1188         $(CC) $(CC_OPTIONS) jackknife.cpp -c $(INCLUDE) -o ./jackknife.o
1189
1190
1191 # Item # 100 -- kmer --
1192 ./kmer.o : kmer.cpp
1193         $(CC) $(CC_OPTIONS) kmer.cpp -c $(INCLUDE) -o ./kmer.o
1194
1195
1196 # Item # 101 -- kmerdb --
1197 ./kmerdb.o : kmerdb.cpp
1198         $(CC) $(CC_OPTIONS) kmerdb.cpp -c $(INCLUDE) -o ./kmerdb.o
1199
1200
1201 # Item # 102 -- listvector --
1202 ./listvector.o : listvector.cpp
1203         $(CC) $(CC_OPTIONS) listvector.cpp -c $(INCLUDE) -o ./listvector.o
1204
1205
1206 # Item # 103 -- mothur --
1207 ./mothur.o : mothur.cpp
1208         $(CC) $(CC_OPTIONS) mothur.cpp -c $(INCLUDE) -o ./mothur.o
1209
1210
1211 # Item # 104 -- nameassignment --
1212 ./nameassignment.o : nameassignment.cpp
1213         $(CC) $(CC_OPTIONS) nameassignment.cpp -c $(INCLUDE) -o ./nameassignment.o
1214
1215
1216 # Item # 105 -- npshannon --
1217 ./npshannon.o : npshannon.cpp
1218         $(CC) $(CC_OPTIONS) npshannon.cpp -c $(INCLUDE) -o ./npshannon.o
1219
1220
1221 # Item # 106 -- ordervector --
1222 ./ordervector.o : ordervector.cpp
1223         $(CC) $(CC_OPTIONS) ordervector.cpp -c $(INCLUDE) -o ./ordervector.o
1224
1225
1226 # Item # 107 -- progress --
1227 ./progress.o : progress.cpp
1228         $(CC) $(CC_OPTIONS) progress.cpp -c $(INCLUDE) -o ./progress.o
1229
1230
1231 # Item # 108 -- quitcommand --
1232 ./quitcommand.o : quitcommand.cpp
1233         $(CC) $(CC_OPTIONS) quitcommand.cpp -c $(INCLUDE) -o ./quitcommand.o
1234
1235
1236 # Item # 109 -- rabundvector --
1237 ./rabundvector.o : rabundvector.cpp
1238         $(CC) $(CC_OPTIONS) rabundvector.cpp -c $(INCLUDE) -o ./rabundvector.o
1239
1240
1241 # Item # 110 -- rarecalc --
1242 ./rarecalc.o : rarecalc.cpp
1243         $(CC) $(CC_OPTIONS) rarecalc.cpp -c $(INCLUDE) -o ./rarecalc.o
1244
1245
1246 # Item # 111 -- raredisplay --
1247 ./raredisplay.o : raredisplay.cpp
1248         $(CC) $(CC_OPTIONS) raredisplay.cpp -c $(INCLUDE) -o ./raredisplay.o
1249
1250
1251 # Item # 112 -- rarefact --
1252 ./rarefact.o : rarefact.cpp
1253         $(CC) $(CC_OPTIONS) rarefact.cpp -c $(INCLUDE) -o ./rarefact.o
1254
1255
1256 # Item # 113 -- rarefactcommand --
1257 ./rarefactcommand.o : rarefactcommand.cpp
1258         $(CC) $(CC_OPTIONS) rarefactcommand.cpp -c $(INCLUDE) -o ./rarefactcommand.o
1259
1260
1261 # Item # 114 -- rarefactsharedcommand --
1262 ./rarefactsharedcommand.o : rarefactsharedcommand.cpp
1263         $(CC) $(CC_OPTIONS) rarefactsharedcommand.cpp -c $(INCLUDE) -o ./rarefactsharedcommand.o
1264
1265
1266 # Item # 115 -- sabundvector --
1267 ./sabundvector.o : sabundvector.cpp
1268         $(CC) $(CC_OPTIONS) sabundvector.cpp -c $(INCLUDE) -o ./sabundvector.o
1269
1270
1271 # Item # 116 -- sequence --
1272 ./sequence.o : sequence.cpp
1273         $(CC) $(CC_OPTIONS) sequence.cpp -c $(INCLUDE) -o ./sequence.o
1274
1275
1276 # Item # 117 -- shannon --
1277 ./shannon.o : shannon.cpp
1278         $(CC) $(CC_OPTIONS) shannon.cpp -c $(INCLUDE) -o ./shannon.o
1279
1280
1281 # Item # 118 -- sharedace --
1282 ./sharedace.o : sharedace.cpp
1283         $(CC) $(CC_OPTIONS) sharedace.cpp -c $(INCLUDE) -o ./sharedace.o
1284
1285
1286 # Item # 119 -- sharedchao1 --
1287 ./sharedchao1.o : sharedchao1.cpp
1288         $(CC) $(CC_OPTIONS) sharedchao1.cpp -c $(INCLUDE) -o ./sharedchao1.o
1289
1290
1291 # Item # 120 -- sharedcommand --
1292 ./sharedcommand.o : sharedcommand.cpp
1293         $(CC) $(CC_OPTIONS) sharedcommand.cpp -c $(INCLUDE) -o ./sharedcommand.o
1294
1295
1296 # Item # 121 -- sharedjabund --
1297 ./sharedjabund.o : sharedjabund.cpp
1298         $(CC) $(CC_OPTIONS) sharedjabund.cpp -c $(INCLUDE) -o ./sharedjabund.o
1299
1300
1301 # Item # 122 -- sharedjclass --
1302 ./sharedjclass.o : sharedjclass.cpp
1303         $(CC) $(CC_OPTIONS) sharedjclass.cpp -c $(INCLUDE) -o ./sharedjclass.o
1304
1305
1306 # Item # 123 -- sharedjest --
1307 ./sharedjest.o : sharedjest.cpp
1308         $(CC) $(CC_OPTIONS) sharedjest.cpp -c $(INCLUDE) -o ./sharedjest.o
1309
1310
1311 # Item # 124 -- sharedordervector --
1312 ./sharedordervector.o : sharedordervector.cpp
1313         $(CC) $(CC_OPTIONS) sharedordervector.cpp -c $(INCLUDE) -o ./sharedordervector.o
1314
1315
1316 # Item # 125 -- sharedrabundvector --
1317 ./sharedrabundvector.o : sharedrabundvector.cpp
1318         $(CC) $(CC_OPTIONS) sharedrabundvector.cpp -c $(INCLUDE) -o ./sharedrabundvector.o
1319
1320
1321 # Item # 126 -- sharedsabundvector --
1322 ./sharedsabundvector.o : sharedsabundvector.cpp
1323         $(CC) $(CC_OPTIONS) sharedsabundvector.cpp -c $(INCLUDE) -o ./sharedsabundvector.o
1324
1325
1326 # Item # 127 -- sharedsobs --
1327 ./sharedsobs.o : sharedsobs.cpp
1328         $(CC) $(CC_OPTIONS) sharedsobs.cpp -c $(INCLUDE) -o ./sharedsobs.o
1329
1330
1331 # Item # 128 -- sharedsorabund --
1332 ./sharedsorabund.o : sharedsorabund.cpp
1333         $(CC) $(CC_OPTIONS) sharedsorabund.cpp -c $(INCLUDE) -o ./sharedsorabund.o
1334
1335
1336 # Item # 129 -- sharedsorclass --
1337 ./sharedsorclass.o : sharedsorclass.cpp
1338         $(CC) $(CC_OPTIONS) sharedsorclass.cpp -c $(INCLUDE) -o ./sharedsorclass.o
1339
1340
1341 # Item # 130 -- sharedsorest --
1342 ./sharedsorest.o : sharedsorest.cpp
1343         $(CC) $(CC_OPTIONS) sharedsorest.cpp -c $(INCLUDE) -o ./sharedsorest.o
1344
1345
1346 # Item # 131 -- sharedthetan --
1347 ./sharedthetan.o : sharedthetan.cpp
1348         $(CC) $(CC_OPTIONS) sharedthetan.cpp -c $(INCLUDE) -o ./sharedthetan.o
1349
1350
1351 # Item # 132 -- sharedthetayc --
1352 ./sharedthetayc.o : sharedthetayc.cpp
1353         $(CC) $(CC_OPTIONS) sharedthetayc.cpp -c $(INCLUDE) -o ./sharedthetayc.o
1354
1355
1356 # Item # 133 -- simpson --
1357 ./simpson.o : simpson.cpp
1358         $(CC) $(CC_OPTIONS) simpson.cpp -c $(INCLUDE) -o ./simpson.o
1359
1360
1361 # Item # 134 -- singlelinkage --
1362 ./singlelinkage.o : singlelinkage.cpp
1363         $(CC) $(CC_OPTIONS) singlelinkage.cpp -c $(INCLUDE) -o ./singlelinkage.o
1364
1365
1366 # Item # 135 -- sparsematrix --
1367 ./sparsematrix.o : sparsematrix.cpp
1368         $(CC) $(CC_OPTIONS) sparsematrix.cpp -c $(INCLUDE) -o ./sparsematrix.o
1369
1370
1371 # Item # 136 -- summarycommand --
1372 ./summarycommand.o : summarycommand.cpp
1373         $(CC) $(CC_OPTIONS) summarycommand.cpp -c $(INCLUDE) -o ./summarycommand.o
1374
1375
1376 # Item # 137 -- summarysharedcommand --
1377 ./summarysharedcommand.o : summarysharedcommand.cpp
1378         $(CC) $(CC_OPTIONS) summarysharedcommand.cpp -c $(INCLUDE) -o ./summarysharedcommand.o
1379
1380
1381 # Item # 138 -- uvest --
1382 ./uvest.o : uvest.cpp
1383         $(CC) $(CC_OPTIONS) uvest.cpp -c $(INCLUDE) -o ./uvest.o
1384
1385
1386 # Item # 139 -- validcalculator --
1387 ./validcalculator.o : validcalculator.cpp
1388         $(CC) $(CC_OPTIONS) validcalculator.cpp -c $(INCLUDE) -o ./validcalculator.o
1389
1390
1391 # Item # 140 -- validparameter --
1392 ./validparameter.o : validparameter.cpp
1393         $(CC) $(CC_OPTIONS) validparameter.cpp -c $(INCLUDE) -o ./validparameter.o
1394
1395
1396 # Item # 141 -- treenode --
1397 ./treenode.o : treenode.cpp
1398         $(CC) $(CC_OPTIONS) treenode.cpp -c $(INCLUDE) -o ./treenode.o
1399
1400
1401 # Item # 142 -- readtreecommand --
1402 ./readtreecommand.o : readtreecommand.cpp
1403         $(CC) $(CC_OPTIONS) readtreecommand.cpp -c $(INCLUDE) -o ./readtreecommand.o
1404
1405
1406 # Item # 143 -- reversecommand --
1407 ./reversecommand.o : reversecommand.cpp
1408         $(CC) $(CC_OPTIONS) reversecommand.cpp -c $(INCLUDE) -o ./reversecommand.o
1409
1410
1411 # Item # 144 -- trimseqscommand --
1412 ./trimseqscommand.o : trimseqscommand.cpp
1413         $(CC) $(CC_OPTIONS) trimseqscommand.cpp -c $(INCLUDE) -o ./trimseqscommand.o
1414
1415
1416 # Item # 145 -- slibshuff --
1417 ./slibshuff.o : slibshuff.cpp
1418         $(CC) $(CC_OPTIONS) slibshuff.cpp -c $(INCLUDE) -o ./slibshuff.o
1419
1420
1421 # Item # 146 -- libshuff --
1422 ./libshuff.o : libshuff.cpp
1423         $(CC) $(CC_OPTIONS) libshuff.cpp -c $(INCLUDE) -o ./libshuff.o
1424
1425
1426 # Item # 147 -- dlibshuff --
1427 ./dlibshuff.o : dlibshuff.cpp
1428         $(CC) $(CC_OPTIONS) dlibshuff.cpp -c $(INCLUDE) -o ./dlibshuff.o
1429
1430
1431 # Item # 148 -- mergefilecommand --
1432 ./mergefilecommand.o : mergefilecommand.cpp
1433         $(CC) $(CC_OPTIONS) mergefilecommand.cpp -c $(INCLUDE) -o ./mergefilecommand.o
1434
1435
1436 # Item # 149 -- coverage --
1437 ./coverage.o : coverage.cpp
1438         $(CC) $(CC_OPTIONS) coverage.cpp -c $(INCLUDE) -o ./coverage.o
1439
1440
1441 # Item # 150 -- whittaker --
1442 ./whittaker.o : whittaker.cpp
1443         $(CC) $(CC_OPTIONS) whittaker.cpp -c $(INCLUDE) -o ./whittaker.o
1444
1445
1446 # Item # 151 -- preclustercommand --
1447 ./preclustercommand.o : preclustercommand.cpp
1448         $(CC) $(CC_OPTIONS) preclustercommand.cpp -c $(INCLUDE) -o ./preclustercommand.o
1449
1450
1451 # Item # 152 -- otuhierarchycommand --
1452 ./otuhierarchycommand.o : otuhierarchycommand.cpp
1453         $(CC) $(CC_OPTIONS) otuhierarchycommand.cpp -c $(INCLUDE) -o ./otuhierarchycommand.o
1454
1455
1456 # Item # 153 -- setdircommand --
1457 ./setdircommand.o : setdircommand.cpp
1458         $(CC) $(CC_OPTIONS) setdircommand.cpp -c $(INCLUDE) -o ./setdircommand.o
1459
1460
1461 # Item # 154 -- getgroupcommand --
1462 ./getgroupcommand.o : getgroupcommand.cpp
1463         $(CC) $(CC_OPTIONS) getgroupcommand.cpp -c $(INCLUDE) -o ./getgroupcommand.o
1464
1465
1466 # Item # 155 -- getlabelcommand --
1467 ./getlabelcommand.o : getlabelcommand.cpp
1468         $(CC) $(CC_OPTIONS) getlabelcommand.cpp -c $(INCLUDE) -o ./getlabelcommand.o
1469
1470
1471 # Item # 156 -- secondarystructurecommand --
1472 ./secondarystructurecommand.o : secondarystructurecommand.cpp
1473         $(CC) $(CC_OPTIONS) secondarystructurecommand.cpp -c $(INCLUDE) -o ./secondarystructurecommand.o
1474
1475
1476 # Item # 157 -- mothurout --
1477 ./mothurout.o : mothurout.cpp
1478         $(CC) $(CC_OPTIONS) mothurout.cpp -c $(INCLUDE) -o ./mothurout.o
1479
1480
1481 # Item # 158 -- parselistscommand --
1482 ./parselistscommand.o : parselistscommand.cpp
1483         $(CC) $(CC_OPTIONS) parselistscommand.cpp -c $(INCLUDE) -o ./parselistscommand.o
1484
1485
1486 # Item # 159 -- readblast --
1487 ./readblast.o : readblast.cpp
1488         $(CC) $(CC_OPTIONS) readblast.cpp -c $(INCLUDE) -o ./readblast.o
1489
1490
1491 # Item # 160 -- chimeracheckrdp --
1492 ./chimeracheckrdp.o : chimeracheckrdp.cpp
1493         $(CC) $(CC_OPTIONS) chimeracheckrdp.cpp -c $(INCLUDE) -o ./chimeracheckrdp.o
1494
1495
1496 # Item # 161 -- hclustercommand --
1497 ./hclustercommand.o : hclustercommand.cpp
1498         $(CC) $(CC_OPTIONS) hclustercommand.cpp -c $(INCLUDE) -o ./hclustercommand.o
1499
1500
1501 # Item # 162 -- hcluster --
1502 ./hcluster.o : hcluster.cpp
1503         $(CC) $(CC_OPTIONS) hcluster.cpp -c $(INCLUDE) -o ./hcluster.o
1504
1505
1506 # Item # 163 -- getlistcountcommand --
1507 ./getlistcountcommand.o : getlistcountcommand.cpp
1508         $(CC) $(CC_OPTIONS) getlistcountcommand.cpp -c $(INCLUDE) -o ./getlistcountcommand.o
1509
1510
1511 # Item # 164 -- readcluster --
1512 ./readcluster.o : readcluster.cpp
1513         $(CC) $(CC_OPTIONS) readcluster.cpp -c $(INCLUDE) -o ./readcluster.o
1514
1515
1516 # Item # 165 -- ccode --
1517 ./ccode.o : ccode.cpp
1518         $(CC) $(CC_OPTIONS) ccode.cpp -c $(INCLUDE) -o ./ccode.o
1519
1520
1521 # Item # 166 -- taxonomyequalizer --
1522 ./taxonomyequalizer.o : taxonomyequalizer.cpp
1523         $(CC) $(CC_OPTIONS) taxonomyequalizer.cpp -c $(INCLUDE) -o ./taxonomyequalizer.o
1524
1525
1526 # Item # 167 -- phylotypecommand --
1527 ./phylotypecommand.o : phylotypecommand.cpp
1528         $(CC) $(CC_OPTIONS) phylotypecommand.cpp -c $(INCLUDE) -o ./phylotypecommand.o
1529
1530
1531 # Item # 168 -- classifyseqscommand --
1532 ./classifyseqscommand.o : classifyseqscommand.cpp
1533         $(CC) $(CC_OPTIONS) classifyseqscommand.cpp -c $(INCLUDE) -o ./classifyseqscommand.o
1534
1535
1536 # Item # 169 -- classify --
1537 ./classify.o : classify.cpp
1538         $(CC) $(CC_OPTIONS) classify.cpp -c $(INCLUDE) -o ./classify.o
1539
1540
1541 # Item # 170 -- phylotree --
1542 ./phylotree.o : phylotree.cpp
1543         $(CC) $(CC_OPTIONS) phylotree.cpp -c $(INCLUDE) -o ./phylotree.o
1544
1545
1546 # Item # 171 -- bayesian --
1547 ./bayesian.o : bayesian.cpp
1548         $(CC) $(CC_OPTIONS) bayesian.cpp -c $(INCLUDE) -o ./bayesian.o
1549
1550
1551 # Item # 172 -- alignmentdb --
1552 ./alignmentdb.o : alignmentdb.cpp
1553         $(CC) $(CC_OPTIONS) alignmentdb.cpp -c $(INCLUDE) -o ./alignmentdb.o
1554
1555
1556 # Item # 173 -- knn --
1557 ./knn.o : knn.cpp
1558         $(CC) $(CC_OPTIONS) knn.cpp -c $(INCLUDE) -o ./knn.o
1559
1560
1561 # Item # 174 -- distancedb --
1562 ./distancedb.o : distancedb.cpp
1563         $(CC) $(CC_OPTIONS) distancedb.cpp -c $(INCLUDE) -o ./distancedb.o
1564
1565
1566 # Item # 175 -- chimeraslayer --
1567 ./chimeraslayer.o : chimeraslayer.cpp
1568         $(CC) $(CC_OPTIONS) chimeraslayer.cpp -c $(INCLUDE) -o ./chimeraslayer.o
1569
1570
1571 # Item # 176 -- slayer --
1572 ./slayer.o : slayer.cpp
1573         $(CC) $(CC_OPTIONS) slayer.cpp -c $(INCLUDE) -o ./slayer.o
1574
1575
1576 # Item # 177 -- pcacommand --
1577 ./pcacommand.o : pcacommand.cpp
1578         $(CC) $(CC_OPTIONS) pcacommand.cpp -c $(INCLUDE) -o ./pcacommand.o
1579
1580
1581 # Item # 178 -- formatcolumn --
1582 ./formatcolumn.o : formatcolumn.cpp
1583         $(CC) $(CC_OPTIONS) formatcolumn.cpp -c $(INCLUDE) -o ./formatcolumn.o
1584
1585
1586 # Item # 179 -- formatphylip --
1587 ./formatphylip.o : formatphylip.cpp
1588         $(CC) $(CC_OPTIONS) formatphylip.cpp -c $(INCLUDE) -o ./formatphylip.o
1589
1590
1591 # Item # 180 -- mgclustercommand --
1592 ./mgclustercommand.o : mgclustercommand.cpp
1593         $(CC) $(CC_OPTIONS) mgclustercommand.cpp -c $(INCLUDE) -o ./mgclustercommand.o
1594
1595
1596 # Item # 181 -- getsharedotucommand --
1597 ./getsharedotucommand.o : getsharedotucommand.cpp
1598         $(CC) $(CC_OPTIONS) getsharedotucommand.cpp -c $(INCLUDE) -o ./getsharedotucommand.o
1599
1600
1601 # Item # 182 -- maligner --
1602 ./maligner.o : maligner.cpp
1603         $(CC) $(CC_OPTIONS) maligner.cpp -c $(INCLUDE) -o ./maligner.o
1604
1605
1606 # Item # 183 -- chimerarealigner --
1607 ./chimerarealigner.o : chimerarealigner.cpp
1608         $(CC) $(CC_OPTIONS) chimerarealigner.cpp -c $(INCLUDE) -o ./chimerarealigner.o
1609
1610
1611 # Item # 184 -- bergerparker --
1612 ./bergerparker.o : bergerparker.cpp
1613         $(CC) $(CC_OPTIONS) bergerparker.cpp -c $(INCLUDE) -o ./bergerparker.o
1614
1615
1616 # Item # 185 -- bstick --
1617 ./bstick.o : bstick.cpp
1618         $(CC) $(CC_OPTIONS) bstick.cpp -c $(INCLUDE) -o ./bstick.o
1619
1620
1621 # Item # 186 -- sharedkstest --
1622 ./sharedkstest.o : sharedkstest.cpp
1623         $(CC) $(CC_OPTIONS) sharedkstest.cpp -c $(INCLUDE) -o ./sharedkstest.o
1624
1625
1626 # Item # 187 -- qstat --
1627 ./qstat.o : qstat.cpp
1628         $(CC) $(CC_OPTIONS) qstat.cpp -c $(INCLUDE) -o ./qstat.o
1629
1630
1631 # Item # 188 -- shen --
1632 ./shen.o : shen.cpp
1633         $(CC) $(CC_OPTIONS) shen.cpp -c $(INCLUDE) -o ./shen.o
1634
1635
1636 # Item # 189 -- logsd --
1637 ./logsd.o : logsd.cpp
1638         $(CC) $(CC_OPTIONS) logsd.cpp -c $(INCLUDE) -o ./logsd.o
1639
1640
1641 # Item # 190 -- geom --
1642 ./geom.o : geom.cpp
1643         $(CC) $(CC_OPTIONS) geom.cpp -c $(INCLUDE) -o ./geom.o
1644
1645 # Item # 191 -- parsesffcommand --
1646 ./parsesffcommand.o : parsesffcommand.cpp
1647         $(CC) $(CC_OPTIONS) parsesffcommand.cpp -c $(INCLUDE) -o ./parsesffcommand.o
1648
1649 # Item # 192 -- chimeraccodecommand --
1650 ./chimeraccodecommand.o : chimeraccodecommand.cpp
1651         $(CC) $(CC_OPTIONS) chimeraccodecommand.cpp -c $(INCLUDE) -o ./chimeraccodecommand.o
1652
1653 # Item # 193 -- chimeracheckcommand --
1654 ./chimeracheckcommand.o : chimeracheckcommand.cpp
1655         $(CC) $(CC_OPTIONS) chimeracheckcommand.cpp -c $(INCLUDE) -o ./chimeracheckcommand.o
1656
1657
1658 # Item # 194 -- chimeraslayercommand --
1659 ./chimeraslayercommand.o : chimeraslayercommand.cpp
1660         $(CC) $(CC_OPTIONS) chimeraslayercommand.cpp -c $(INCLUDE) -o ./chimeraslayercommand.o
1661
1662 # Item # 195 -- chimerapintailcommand --
1663 ./chimerapintailcommand.o : chimerapintailcommand.cpp
1664         $(CC) $(CC_OPTIONS) chimerapintailcommand.cpp -c $(INCLUDE) -o ./chimerapintailcommand.o
1665
1666 # Item # 196 -- chimerabellerophoncommand --
1667 ./chimerabellerophoncommand.o : chimerabellerophoncommand.cpp
1668         $(CC) $(CC_OPTIONS) chimerabellerophoncommand.cpp -c $(INCLUDE) -o ./chimerabellerophoncommand.o
1669
1670 # Item # 197 -- phylosummary --
1671 ./phylosummary.o : phylosummary.cpp
1672         $(CC) $(CC_OPTIONS) phylosummary.cpp -c $(INCLUDE) -o ./phylosummary.o
1673
1674 # Item # 198 -- setlogfilecommand --
1675 ./setlogfilecommand.o : setlogfilecommand.cpp
1676         $(CC) $(CC_OPTIONS) setlogfilecommand.cpp -c $(INCLUDE) -o ./setlogfilecommand.o
1677
1678 # Item # 199 -- phylodiversity --
1679 ./phylodiversity.o : phylodiversity.cpp
1680         $(CC) $(CC_OPTIONS) phylodiversity.cpp -c $(INCLUDE) -o ./phylodiversity.o
1681
1682 # Item # 200 -- phylodiversitycommand --
1683 ./phylodiversitycommand.o : phylodiversitycommand.cpp
1684         $(CC) $(CC_OPTIONS) phylodiversitycommand.cpp -c $(INCLUDE) -o ./phylodiversitycommand.o
1685
1686 # Item # 201 -- makegroupcommand --
1687 ./makegroupcommand.o : makegroupcommand.cpp
1688         $(CC) $(CC_OPTIONS) makegroupcommand.cpp -c $(INCLUDE) -o ./makegroupcommand.o
1689
1690 # Item # 202 -- chopseqscommand --
1691 ./chopseqscommand.o : chopseqscommand.cpp
1692         $(CC) $(CC_OPTIONS) chopseqscommand.cpp -c $(INCLUDE) -o ./chopseqscommand.o
1693
1694 # Item # 203 -- clearcutcommand --
1695 ./clearcutcommand.o : clearcutcommand.cpp
1696         $(CC) $(CC_OPTIONS) clearcutcommand.cpp -c $(INCLUDE) -o ./clearcutcommand.o
1697
1698 # Item # 204 -- catchallcommand --
1699 ./catchallcommand.o : catchallcommand.cpp
1700         $(CC) $(CC_OPTIONS) catchallcommand.cpp -c $(INCLUDE) -o ./catchallcommand.o
1701
1702 # Item # 205 -- splitabundcommand --
1703 ./splitabundcommand.o : splitabundcommand.cpp
1704         $(CC) $(CC_OPTIONS) splitabundcommand.cpp -c $(INCLUDE) -o ./splitabundcommand.o
1705
1706 # Item # 206 -- splitmatrix --
1707 ./splitmatrix.o : splitmatrix.cpp
1708         $(CC) $(CC_OPTIONS) splitmatrix.cpp -c $(INCLUDE) -o ./splitmatrix.o
1709
1710 # Item # 207 -- clustersplit --
1711 ./clustersplitcommand.o : clustersplitcommand.cpp
1712         $(CC) $(CC_OPTIONS) clustersplitcommand.cpp -c $(INCLUDE) -o ./clustersplitcommand.o
1713
1714 # Item # 208 -- classifyotu --
1715 ./classifyotucommand.o : classifyotucommand.cpp
1716         $(CC) $(CC_OPTIONS) classifyotucommand.cpp -c $(INCLUDE) -o ./classifyotucommand.o
1717
1718 # Item # 209 -- weightedlinkage --
1719 ./weightedlinkage.o : weightedlinkage.cpp
1720         $(CC) $(CC_OPTIONS) weightedlinkage.cpp -c $(INCLUDE) -o ./weightedlinkage.o
1721
1722 ##### END RUN ####