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                 ./degapseqscommand.o\
 135                 ./systemcommand.o\
 136                 ./binsequencecommand.o\
 137                 ./distancecommand.o\
 138                 ./ace.o\
 139                 ./averagelinkage.o\
 140                 ./bootstrap.o\
 141                 ./calculator.o\
 142                 ./chao1.o\
 143                 ./cluster.o\
 144                 ./clustercommand.o\
 145                 ./collect.o\
 146                 ./collectcommand.o\
 147                 ./collectsharedcommand.o\
 148                 ./commandoptionparser.o\
 149                 ./completelinkage.o\
 150                 ./database.o\
 151                 ./engine.o\
 152                 ./fastamap.o\
 153                 ./fileoutput.o\
 154                 ./globaldata.o\
 155                 ./groupmap.o\
 156                 ./helpcommand.o\
 157                 ./makegroupcommand.o\
 158                 ./chopseqscommand.o\
 159                 ./clearcutcommand.o\
 160                 ./catchallcommand.o\
 161                 ./splitabundcommand.o\
 162                 ./splitmatrix.o\
 163                 ./clustersplitcommand.o\
 164                 ./weightedlinkage.o\
 165                 ./inputdata.o\
 166                 ./jackknife.o\
 167                 ./kmer.o\
 168                 ./kmerdb.o\
 169                 ./listvector.o\
 170                 ./mothur.o\
 171                 ./nameassignment.o\
 172                 ./npshannon.o\
 173                 ./ordervector.o\
 174                 ./progress.o\
 175                 ./quitcommand.o\
 176                 ./rabundvector.o\
 177                 ./rarecalc.o\
 178                 ./raredisplay.o\
 179                 ./rarefact.o\
 180                 ./rarefactcommand.o\
 181                 ./rarefactsharedcommand.o\
 182                 ./sabundvector.o\
 183                 ./sequence.o\
 184                 ./shannon.o\
 185                 ./sharedace.o\
 186                 ./sharedchao1.o\
 187                 ./sharedcommand.o\
 188                 ./sharedjabund.o\
 189                 ./sharedjclass.o\
 190                 ./sharedjest.o\
 191                 ./sharedordervector.o\
 192                 ./sharedrabundvector.o\
 193                 ./sharedsabundvector.o\
 194                 ./sharedsobs.o\
 195                 ./sharedsorabund.o\
 196                 ./sharedsorclass.o\
 197                 ./sharedsorest.o\
 198                 ./sharedthetan.o\
 199                 ./sharedthetayc.o\
 200                 ./simpson.o\
 201                 ./singlelinkage.o\
 202                 ./sparsematrix.o\
 203                 ./summarycommand.o\
 204                 ./summarysharedcommand.o\
 205                 ./uvest.o\
 206                 ./validcalculator.o\
 207                 ./validparameter.o\
 208                 ./treenode.o\
 209                 ./readtreecommand.o\
 210                 ./reversecommand.o\
 211                 ./trimseqscommand.o\
 212                 ./slibshuff.o\
 213                 ./libshuff.o\
 214                 ./dlibshuff.o\
 215                 ./mergefilecommand.o\
 216                 ./coverage.o\
 217                 ./whittaker.o\
 218                 ./preclustercommand.o\
 219                 ./otuhierarchycommand.o\
 220                 ./setdircommand.o\
 221                 ./getgroupcommand.o\
 222                 ./getlabelcommand.o\
 223                 ./secondarystructurecommand.o\
 224                 ./mothurout.o\
 225                 ./parselistscommand.o\
 226                 ./readblast.o\
 227                 ./chimeracheckrdp.o\
 228                 ./hclustercommand.o\
 229                 ./hcluster.o\
 230                 ./getlistcountcommand.o\
 231                 ./getrelabundcommand.o\
 232                 ./readcluster.o\
 233                 ./ccode.o\
 234                 ./taxonomyequalizer.o\
 235                 ./phylotypecommand.o\
 236                 ./classifyseqscommand.o\
 237                 ./classifyotucommand.o\
 238                 ./parsesffcommand.o\
 239                 ./classify.o\
 240                 ./phylotree.o\
 241                 ./phylodiversity.o\
 242                 ./phylodiversitycommand.o\
 243                 ./bayesian.o\
 244                 ./phylosummary.o\
 245                 ./alignmentdb.o\
 246                 ./knn.o\
 247                 ./distancedb.o\
 248                 ./chimeraslayer.o\
 249                 ./slayer.o\
 250                 ./pcacommand.o\
 251                 ./formatcolumn.o\
 252                 ./formatphylip.o\
 253                 ./mgclustercommand.o\
 254                 ./getsharedotucommand.o\
 255                 ./maligner.o\
 256                 ./chimerarealigner.o\
 257                 ./bergerparker.o\
 258                 ./bstick.o\
 259                 ./sharedkstest.o\
 260                 ./qstat.o\
 261                 ./shen.o\
 262                 ./logsd.o\
 263                 ./geom.o\
 264                 ./setlogfilecommand.o
 265         $(CC) $(LNK_OPTIONS) \
 266                 ./sharedutilities.o\
 267                 ./treegroupscommand.o\
 268                 ./bootstrapsharedcommand.o\
 269                 ./matrixoutputcommand.o\
 270                 ./getoturepcommand.o\
 271                 ./screenseqscommand.o\
 272                 ./chimera.o\
 273                 ./decalc.o\
 274                 ./readotucommand.o\
 275                 ./readdistcommand.o\
 276                 ./commandfactory.o\
 277                 ./alignment.o\
 278                 ./alignmentcell.o\
 279                 ./gotohoverlap.o\
 280                 ./overlap.o\
 281                 ./needlemanoverlap.o\
 282                 ./blastalign.o\
 283                 ./noalign.o\
 284                 ./suffixdb.o\
 285                 ./suffixnodes.o\
 286                 ./suffixtree.o\
 287                 ./blastdb.o\
 288                 ./nast.o\
 289                 ./nastreport.o\
 290                 ./boneh.o\
 291                 ./efron.o\
 292                 ./solow.o\
 293                 ./unifracweightedcommand.o\
 294                 ./weighted.o\
 295                 ./unweighted.o\
 296                 ./unifracunweightedcommand.o\
 297                 ./getsabundcommand.o\
 298                 ./getrabundcommand.o\
 299                 ./bellerophon.o\
 300                 ./pintail.o\
 301                 ./sharedanderbergs.o\
 302                 ./venncommand.o\
 303                 ./venn.o\
 304                 ./fullmatrix.o\
 305                 ./heatmap.o\
 306                 ./heatmapcommand.o\
 307                 ./libshuffcommand.o\
 308                 ./nocommands.o\
 309                 ./sharedbraycurtis.o\
 310                 ./sharedkulczynski.o\
 311                 ./sharedlennon.o\
 312                 ./sharedkulczynskicody.o\
 313                 ./sharedmorisitahorn.o\
 314                 ./sharedochiai.o\
 315                 ./readcolumn.o\
 316                 ./readotu.o\
 317                 ./readphylip.o\
 318                 ./consensuscommand.o\
 319                 ./heatmapsimcommand.o\
 320                 ./heatmapsim.o\
 321                 ./optionparser.o\
 322                 ./filterseqscommand.o\
 323                 ./goodscoverage.o\
 324                 ./sequencedb.o\
 325                 ./sharedjackknife.o\
 326                 ./sharedmarczewski.o\
 327                 ./aligncommand.o\
 328                 ./treemap.o\
 329                 ./parsimonycommand.o\
 330                 ./parsimony.o\
 331                 ./seqsummarycommand.o\
 332                 ./chimeraccodecommand.o\
 333                 ./chimerabellerophoncommand.o\
 334                 ./chimeracheckcommand.o\
 335                 ./chimeraslayercommand.o\
 336                 ./chimerapintailcommand.o\
 337                 ./chimeraseqscommand.o\
 338                 ./sharedlistvector.o\
 339                 ./tree.o\
 340                 ./readtree.o\
 341                 ./sharedsobscollectsummary.o\
 342                 ./deconvolutecommand.o\
 343                 ./listseqscommand.o\
 344                 ./getseqscommand.o\
 345                 ./removeseqscommand.o\
 346                 ./degapseqscommand.o\
 347                 ./systemcommand.o\
 348                 ./binsequencecommand.o\
 349                 ./distancecommand.o\
 350                 ./ace.o\
 351                 ./averagelinkage.o\
 352                 ./bootstrap.o\
 353                 ./calculator.o\
 354                 ./chao1.o\
 355                 ./cluster.o\
 356                 ./clustercommand.o\
 357                 ./collect.o\
 358                 ./collectcommand.o\
 359                 ./collectsharedcommand.o\
 360                 ./commandoptionparser.o\
 361                 ./completelinkage.o\
 362                 ./database.o\
 363                 ./engine.o\
 364                 ./fastamap.o\
 365                 ./fileoutput.o\
 366                 ./globaldata.o\
 367                 ./groupmap.o\
 368                 ./helpcommand.o\
 369                 ./makegroupcommand.o\
 370                 ./chopseqscommand.o\
 371                 ./clearcutcommand.o\
 372                 ./catchallcommand.o\
 373                 ./splitabundcommand.o\
 374                 ./splitmatrix.o\
 375                 ./clustersplitcommand.o\
 376                 ./weightedlinkage.o\
 377                 ./inputdata.o\
 378                 ./jackknife.o\
 379                 ./kmer.o\
 380                 ./kmerdb.o\
 381                 ./listvector.o\
 382                 ./mothur.o\
 383                 ./nameassignment.o\
 384                 ./npshannon.o\
 385                 ./ordervector.o\
 386                 ./progress.o\
 387                 ./quitcommand.o\
 388                 ./rabundvector.o\
 389                 ./rarecalc.o\
 390                 ./raredisplay.o\
 391                 ./rarefact.o\
 392                 ./rarefactcommand.o\
 393                 ./rarefactsharedcommand.o\
 394                 ./sabundvector.o\
 395                 ./sequence.o\
 396                 ./shannon.o\
 397                 ./sharedace.o\
 398                 ./sharedchao1.o\
 399                 ./sharedcommand.o\
 400                 ./sharedjabund.o\
 401                 ./sharedjclass.o\
 402                 ./sharedjest.o\
 403                 ./sharedordervector.o\
 404                 ./sharedrabundvector.o\
 405                 ./sharedsabundvector.o\
 406                 ./sharedsobs.o\
 407                 ./sharedsorabund.o\
 408                 ./sharedsorclass.o\
 409                 ./sharedsorest.o\
 410                 ./sharedthetan.o\
 411                 ./sharedthetayc.o\
 412                 ./simpson.o\
 413                 ./singlelinkage.o\
 414                 ./sparsematrix.o\
 415                 ./summarycommand.o\
 416                 ./summarysharedcommand.o\
 417                 ./uvest.o\
 418                 ./validcalculator.o\
 419                 ./validparameter.o\
 420                 ./treenode.o\
 421                 ./readtreecommand.o\
 422                 ./reversecommand.o\
 423                 ./trimseqscommand.o\
 424                 ./slibshuff.o\
 425                 ./libshuff.o\
 426                 ./dlibshuff.o\
 427                 ./mergefilecommand.o\
 428                 ./coverage.o\
 429                 ./whittaker.o\
 430                 ./preclustercommand.o\
 431                 ./otuhierarchycommand.o\
 432                 ./setdircommand.o\
 433                 ./getgroupcommand.o\
 434                 ./getlabelcommand.o\
 435                 ./secondarystructurecommand.o\
 436                 ./mothurout.o\
 437                 ./parselistscommand.o\
 438                 ./readblast.o\
 439                 ./chimeracheckrdp.o\
 440                 ./hclustercommand.o\
 441                 ./hcluster.o\
 442                 ./getlistcountcommand.o\
 443                 ./getrelabundcommand.o\
 444                 ./readcluster.o\
 445                 ./ccode.o\
 446                 ./taxonomyequalizer.o\
 447                 ./phylotypecommand.o\
 448                 ./classifyseqscommand.o\
 449                 ./classifyotucommand.o\
 450                 ./parsesffcommand.o\
 451                 ./classify.o\
 452                 ./phylotree.o\
 453                 ./phylodiversity.o\
 454                 ./phylodiversitycommand.o\
 455                 ./bayesian.o\
 456                 ./phylosummary.o\
 457                 ./alignmentdb.o\
 458                 ./knn.o\
 459                 ./distancedb.o\
 460                 ./chimeraslayer.o\
 461                 ./slayer.o\
 462                 ./pcacommand.o\
 463                 ./formatcolumn.o\
 464                 ./formatphylip.o\
 465                 ./mgclustercommand.o\
 466                 ./getsharedotucommand.o\
 467                 ./maligner.o\
 468                 ./chimerarealigner.o\
 469                 ./bergerparker.o\
 470                 ./bstick.o\
 471                 ./sharedkstest.o\
 472                 ./qstat.o\
 473                 ./shen.o\
 474                 ./logsd.o\
 475                 ./geom.o\
 476                 ./setlogfilecommand.o\
 477                 -o ../Release/mothur
 478
 479 clean :
 480                 rm \
 481                 ./sharedutilities.o\
 482                 ./treegroupscommand.o\
 483                 ./bootstrapsharedcommand.o\
 484                 ./matrixoutputcommand.o\
 485                 ./getoturepcommand.o\
 486                 ./screenseqscommand.o\
 487                 ./chimera.o\
 488                 ./decalc.o\
 489                 ./readotucommand.o\
 490                 ./readdistcommand.o\
 491                 ./commandfactory.o\
 492                 ./alignment.o\
 493                 ./alignmentcell.o\
 494                 ./gotohoverlap.o\
 495                 ./overlap.o\
 496                 ./needlemanoverlap.o\
 497                 ./blastalign.o\
 498                 ./noalign.o\
 499                 ./suffixdb.o\
 500                 ./suffixnodes.o\
 501                 ./suffixtree.o\
 502                 ./blastdb.o\
 503                 ./nast.o\
 504                 ./nastreport.o\
 505                 ./boneh.o\
 506                 ./efron.o\
 507                 ./solow.o\
 508                 ./unifracweightedcommand.o\
 509                 ./weighted.o\
 510                 ./unweighted.o\
 511                 ./unifracunweightedcommand.o\
 512                 ./getsabundcommand.o\
 513                 ./getrabundcommand.o\
 514                 ./bellerophon.o\
 515                 ./pintail.o\
 516                 ./sharedanderbergs.o\
 517                 ./venncommand.o\
 518                 ./venn.o\
 519                 ./fullmatrix.o\
 520                 ./heatmap.o\
 521                 ./heatmapcommand.o\
 522                 ./libshuffcommand.o\
 523                 ./nocommands.o\
 524                 ./sharedbraycurtis.o\
 525                 ./sharedkulczynski.o\
 526                 ./sharedlennon.o\
 527                 ./sharedkulczynskicody.o\
 528                 ./sharedmorisitahorn.o\
 529                 ./sharedochiai.o\
 530                 ./readcolumn.o\
 531                 ./readotu.o\
 532                 ./readphylip.o\
 533                 ./consensuscommand.o\
 534                 ./heatmapsimcommand.o\
 535                 ./heatmapsim.o\
 536                 ./optionparser.o\
 537                 ./filterseqscommand.o\
 538                 ./goodscoverage.o\
 539                 ./sequencedb.o\
 540                 ./sharedjackknife.o\
 541                 ./sharedmarczewski.o\
 542                 ./aligncommand.o\
 543                 ./treemap.o\
 544                 ./parsimonycommand.o\
 545                 ./parsimony.o\
 546                 ./seqsummarycommand.o\
 547                 ./chimeraccodecommand.o\
 548                 ./chimerabellerophoncommand.o\
 549                 ./chimeracheckcommand.o\
 550                 ./chimeraslayercommand.o\
 551                 ./chimerapintailcommand.o\
 552                 ./chimeraseqscommand.o\
 553                 ./sharedlistvector.o\
 554                 ./tree.o\
 555                 ./readtree.o\
 556                 ./sharedsobscollectsummary.o\
 557                 ./deconvolutecommand.o\
 558                 ./listseqscommand.o\
 559                 ./getseqscommand.o\
 560                 ./removeseqscommand.o\
 561                 ./degapseqscommand.o\
 562                 ./systemcommand.o\
 563                 ./binsequencecommand.o\
 564                 ./distancecommand.o\
 565                 ./ace.o\
 566                 ./averagelinkage.o\
 567                 ./bootstrap.o\
 568                 ./calculator.o\
 569                 ./chao1.o\
 570                 ./cluster.o\
 571                 ./clustercommand.o\
 572                 ./collect.o\
 573                 ./collectcommand.o\
 574                 ./collectsharedcommand.o\
 575                 ./commandoptionparser.o\
 576                 ./completelinkage.o\
 577                 ./database.o\
 578                 ./engine.o\
 579                 ./fastamap.o\
 580                 ./fileoutput.o\
 581                 ./globaldata.o\
 582                 ./groupmap.o\
 583                 ./helpcommand.o\
 584                 ./makegroupcommand.o\
 585                 ./chopseqscommand.o\
 586                 ./clearcutcommand.o\
 587                 ./catchallcommand.o\
 588                 ./splitabundcommand.o\
 589                 ./splitmatrix.o\
 590                 ./clustersplitcommand.o\
 591                 ./weightedlinkage.o\
 592                 ./inputdata.o\
 593                 ./jackknife.o\
 594                 ./kmer.o\
 595                 ./kmerdb.o\
 596                 ./listvector.o\
 597                 ./mothur.o\
 598                 ./nameassignment.o\
 599                 ./npshannon.o\
 600                 ./ordervector.o\
 601                 ./progress.o\
 602                 ./quitcommand.o\
 603                 ./rabundvector.o\
 604                 ./rarecalc.o\
 605                 ./raredisplay.o\
 606                 ./rarefact.o\
 607                 ./rarefactcommand.o\
 608                 ./rarefactsharedcommand.o\
 609                 ./sabundvector.o\
 610                 ./sequence.o\
 611                 ./shannon.o\
 612                 ./sharedace.o\
 613                 ./sharedchao1.o\
 614                 ./sharedcommand.o\
 615                 ./sharedjabund.o\
 616                 ./sharedjclass.o\
 617                 ./sharedjest.o\
 618                 ./sharedordervector.o\
 619                 ./sharedrabundvector.o\
 620                 ./sharedsabundvector.o\
 621                 ./sharedsobs.o\
 622                 ./sharedsorabund.o\
 623                 ./sharedsorclass.o\
 624                 ./sharedsorest.o\
 625                 ./sharedthetan.o\
 626                 ./sharedthetayc.o\
 627                 ./simpson.o\
 628                 ./singlelinkage.o\
 629                 ./sparsematrix.o\
 630                 ./summarycommand.o\
 631                 ./summarysharedcommand.o\
 632                 ./uvest.o\
 633                 ./validcalculator.o\
 634                 ./validparameter.o\
 635                 ./treenode.o\
 636                 ./readtreecommand.o\
 637                 ./reversecommand.o\
 638                 ./trimseqscommand.o\
 639                 ./slibshuff.o\
 640                 ./libshuff.o\
 641                 ./dlibshuff.o\
 642                 ./mergefilecommand.o\
 643                 ./coverage.o\
 644                 ./whittaker.o\
 645                 ./preclustercommand.o\
 646                 ./otuhierarchycommand.o\
 647                 ./setdircommand.o\
 648                 ./getgroupcommand.o\
 649                 ./getlabelcommand.o\
 650                 ./secondarystructurecommand.o\
 651                 ./mothurout.o\
 652                 ./parselistscommand.o\
 653                 ./readblast.o\
 654                 ./chimeracheckrdp.o\
 655                 ./hclustercommand.o\
 656                 ./hcluster.o\
 657                 ./getlistcountcommand.o\
 658                 ./getrelabundcommand.o\
 659                 ./readcluster.o\
 660                 ./ccode.o\
 661                 ./taxonomyequalizer.o\
 662                 ./phylotypecommand.o\
 663                 ./classifyseqscommand.o\
 664                 ./classifyotucommand.o\
 665                 ./parsesffcommand.o\
 666                 ./classify.o\
 667                 ./phylotree.o\
 668                 ./phylodiversity.o\
 669                 ./phylodiversitycommand.o\
 670                 ./bayesian.o\
 671                 ./phylosummary.o\
 672                 ./alignmentdb.o\
 673                 ./knn.o\
 674                 ./distancedb.o\
 675                 ./chimeraslayer.o\
 676                 ./slayer.o\
 677                 ./pcacommand.o\
 678                 ./formatcolumn.o\
 679                 ./formatphylip.o\
 680                 ./mgclustercommand.o\
 681                 ./getsharedotucommand.o\
 682                 ./maligner.o\
 683                 ./chimerarealigner.o\
 684                 ./bergerparker.o\
 685                 ./bstick.o\
 686                 ./sharedkstest.o\
 687                 ./qstat.o\
 688                 ./shen.o\
 689                 ./logsd.o\
 690                 ./geom.o\
 691                 ./setlogfilecommand.o\
 692                 mothur
 693
 694 install : mothur
 695                 #cp mothur ../Release/mothur
 696
 697 #
 698 # Build the parts of mothur
 699 #
 700
 701
 702 # Item # 1 -- sharedutilities --
 703 ./sharedutilities.o : sharedutilities.cpp
 704         $(CC) $(CC_OPTIONS) sharedutilities.cpp -c $(INCLUDE) -o ./sharedutilities.o
 705
 706
 707 # Item # 2 -- treegroupscommand --
 708 ./treegroupscommand.o : treegroupscommand.cpp
 709         $(CC) $(CC_OPTIONS) treegroupscommand.cpp -c $(INCLUDE) -o ./treegroupscommand.o
 710
 711
 712 # Item # 3 -- bootstrapsharedcommand --
 713 ./bootstrapsharedcommand.o : bootstrapsharedcommand.cpp
 714         $(CC) $(CC_OPTIONS) bootstrapsharedcommand.cpp -c $(INCLUDE) -o ./bootstrapsharedcommand.o
 715
 716
 717 # Item # 4 -- matrixoutputcommand --
 718 ./matrixoutputcommand.o : matrixoutputcommand.cpp
 719         $(CC) $(CC_OPTIONS) matrixoutputcommand.cpp -c $(INCLUDE) -o ./matrixoutputcommand.o
 720
 721
 722 # Item # 5 -- getoturepcommand --
 723 ./getoturepcommand.o : getoturepcommand.cpp
 724         $(CC) $(CC_OPTIONS) getoturepcommand.cpp -c $(INCLUDE) -o ./getoturepcommand.o
 725
 726
 727 # Item # 6 -- screenseqscommand --
 728 ./screenseqscommand.o : screenseqscommand.cpp
 729         $(CC) $(CC_OPTIONS) screenseqscommand.cpp -c $(INCLUDE) -o ./screenseqscommand.o
 730
 731
 732 # Item # 7 -- chimera --
 733 ./chimera.o : chimera.cpp
 734         $(CC) $(CC_OPTIONS) chimera.cpp -c $(INCLUDE) -o ./chimera.o
 735
 736
 737 # Item # 8 -- decalc --
 738 ./decalc.o : decalc.cpp
 739         $(CC) $(CC_OPTIONS) decalc.cpp -c $(INCLUDE) -o ./decalc.o
 740
 741
 742 # Item # 9 -- readotucommand --
 743 ./readotucommand.o : readotucommand.cpp
 744         $(CC) $(CC_OPTIONS) readotucommand.cpp -c $(INCLUDE) -o ./readotucommand.o
 745
 746
 747 # Item # 10 -- readdistcommand --
 748 ./readdistcommand.o : readdistcommand.cpp
 749         $(CC) $(CC_OPTIONS) readdistcommand.cpp -c $(INCLUDE) -o ./readdistcommand.o
 750
 751
 752 # Item # 11 -- commandfactory --
 753 ./commandfactory.o : commandfactory.cpp
 754         $(CC) $(CC_OPTIONS) commandfactory.cpp -c $(INCLUDE) -o ./commandfactory.o
 755
 756
 757 # Item # 12 -- alignment --
 758 ./alignment.o : alignment.cpp
 759         $(CC) $(CC_OPTIONS) alignment.cpp -c $(INCLUDE) -o ./alignment.o
 760
 761
 762 # Item # 13 -- alignmentcell --
 763 ./alignmentcell.o : alignmentcell.cpp
 764         $(CC) $(CC_OPTIONS) alignmentcell.cpp -c $(INCLUDE) -o ./alignmentcell.o
 765
 766
 767 # Item # 14 -- gotohoverlap --
 768 ./gotohoverlap.o : gotohoverlap.cpp
 769         $(CC) $(CC_OPTIONS) gotohoverlap.cpp -c $(INCLUDE) -o ./gotohoverlap.o
 770
 771
 772 # Item # 15 -- overlap --
 773 ./overlap.o : overlap.cpp
 774         $(CC) $(CC_OPTIONS) overlap.cpp -c $(INCLUDE) -o ./overlap.o
 775
 776
 777 # Item # 16 -- needlemanoverlap --
 778 ./needlemanoverlap.o : needlemanoverlap.cpp
 779         $(CC) $(CC_OPTIONS) needlemanoverlap.cpp -c $(INCLUDE) -o ./needlemanoverlap.o
 780
 781
 782 # Item # 17 -- blastalign --
 783 ./blastalign.o : blastalign.cpp
 784         $(CC) $(CC_OPTIONS) blastalign.cpp -c $(INCLUDE) -o ./blastalign.o
 785
 786
 787 # Item # 18 -- noalign --
 788 ./noalign.o : noalign.cpp
 789         $(CC) $(CC_OPTIONS) noalign.cpp -c $(INCLUDE) -o ./noalign.o
 790
 791
 792 # Item # 19 -- suffixdb --
 793 ./suffixdb.o : suffixdb.cpp
 794         $(CC) $(CC_OPTIONS) suffixdb.cpp -c $(INCLUDE) -o ./suffixdb.o
 795
 796
 797 # Item # 20 -- suffixnodes --
 798 ./suffixnodes.o : suffixnodes.cpp
 799         $(CC) $(CC_OPTIONS) suffixnodes.cpp -c $(INCLUDE) -o ./suffixnodes.o
 800
 801
 802 # Item # 21 -- suffixtree --
 803 ./suffixtree.o : suffixtree.cpp
 804         $(CC) $(CC_OPTIONS) suffixtree.cpp -c $(INCLUDE) -o ./suffixtree.o
 805
 806
 807 # Item # 22 -- blastdb --
 808 ./blastdb.o : blastdb.cpp
 809         $(CC) $(CC_OPTIONS) blastdb.cpp -c $(INCLUDE) -o ./blastdb.o
 810
 811
 812 # Item # 23 -- nast --
 813 ./nast.o : nast.cpp
 814         $(CC) $(CC_OPTIONS) nast.cpp -c $(INCLUDE) -o ./nast.o
 815
 816
 817 # Item # 24 -- nastreport --
 818 ./nastreport.o : nastreport.cpp
 819         $(CC) $(CC_OPTIONS) nastreport.cpp -c $(INCLUDE) -o ./nastreport.o
 820
 821
 822 # Item # 25 -- boneh --
 823 ./boneh.o : boneh.cpp
 824         $(CC) $(CC_OPTIONS) boneh.cpp -c $(INCLUDE) -o ./boneh.o
 825
 826
 827 # Item # 26 -- efron --
 828 ./efron.o : efron.cpp
 829         $(CC) $(CC_OPTIONS) efron.cpp -c $(INCLUDE) -o ./efron.o
 830
 831
 832 # Item # 27 -- solow --
 833 ./solow.o : solow.cpp
 834         $(CC) $(CC_OPTIONS) solow.cpp -c $(INCLUDE) -o ./solow.o
 835
 836
 837 # Item # 28 -- unifracweightedcommand --
 838 ./unifracweightedcommand.o : unifracweightedcommand.cpp
 839         $(CC) $(CC_OPTIONS) unifracweightedcommand.cpp -c $(INCLUDE) -o ./unifracweightedcommand.o
 840
 841
 842 # Item # 29 -- weighted --
 843 ./weighted.o : weighted.cpp
 844         $(CC) $(CC_OPTIONS) weighted.cpp -c $(INCLUDE) -o ./weighted.o
 845
 846
 847 # Item # 30 -- unweighted --
 848 ./unweighted.o : unweighted.cpp
 849         $(CC) $(CC_OPTIONS) unweighted.cpp -c $(INCLUDE) -o ./unweighted.o
 850
 851
 852 # Item # 31 -- unifracunweightedcommand --
 853 ./unifracunweightedcommand.o : unifracunweightedcommand.cpp
 854         $(CC) $(CC_OPTIONS) unifracunweightedcommand.cpp -c $(INCLUDE) -o ./unifracunweightedcommand.o
 855
 856
 857 # Item # 32 -- getsabundcommand --
 858 ./getsabundcommand.o : getsabundcommand.cpp
 859         $(CC) $(CC_OPTIONS) getsabundcommand.cpp -c $(INCLUDE) -o ./getsabundcommand.o
 860
 861
 862 # Item # 33 -- getrabundcommand --
 863 ./getrabundcommand.o : getrabundcommand.cpp
 864         $(CC) $(CC_OPTIONS) getrabundcommand.cpp -c $(INCLUDE) -o ./getrabundcommand.o
 865
 866
 867 # Item # 34 -- bellerophon --
 868 ./bellerophon.o : bellerophon.cpp
 869         $(CC) $(CC_OPTIONS) bellerophon.cpp -c $(INCLUDE) -o ./bellerophon.o
 870
 871
 872 # Item # 35 -- pintail --
 873 ./pintail.o : pintail.cpp
 874         $(CC) $(CC_OPTIONS) pintail.cpp -c $(INCLUDE) -o ./pintail.o
 875
 876
 877 # Item # 36 -- sharedanderbergs --
 878 ./sharedanderbergs.o : sharedanderbergs.cpp
 879         $(CC) $(CC_OPTIONS) sharedanderbergs.cpp -c $(INCLUDE) -o ./sharedanderbergs.o
 880
 881
 882 # Item # 37 -- venncommand --
 883 ./venncommand.o : venncommand.cpp
 884         $(CC) $(CC_OPTIONS) venncommand.cpp -c $(INCLUDE) -o ./venncommand.o
 885
 886
 887 # Item # 38 -- venn --
 888 ./venn.o : venn.cpp
 889         $(CC) $(CC_OPTIONS) venn.cpp -c $(INCLUDE) -o ./venn.o
 890
 891
 892 # Item # 39 -- fullmatrix --
 893 ./fullmatrix.o : fullmatrix.cpp
 894         $(CC) $(CC_OPTIONS) fullmatrix.cpp -c $(INCLUDE) -o ./fullmatrix.o
 895
 896
 897 # Item # 40 -- heatmap --
 898 ./heatmap.o : heatmap.cpp
 899         $(CC) $(CC_OPTIONS) heatmap.cpp -c $(INCLUDE) -o ./heatmap.o
 900
 901
 902 # Item # 41 -- heatmapcommand --
 903 ./heatmapcommand.o : heatmapcommand.cpp
 904         $(CC) $(CC_OPTIONS) heatmapcommand.cpp -c $(INCLUDE) -o ./heatmapcommand.o
 905
 906
 907 # Item # 42 -- libshuffcommand --
 908 ./libshuffcommand.o : libshuffcommand.cpp
 909         $(CC) $(CC_OPTIONS) libshuffcommand.cpp -c $(INCLUDE) -o ./libshuffcommand.o
 910
 911
 912 # Item # 43 -- nocommands --
 913 ./nocommands.o : nocommands.cpp
 914         $(CC) $(CC_OPTIONS) nocommands.cpp -c $(INCLUDE) -o ./nocommands.o
 915
 916
 917 # Item # 44 -- sharedbraycurtis --
 918 ./sharedbraycurtis.o : sharedbraycurtis.cpp
 919         $(CC) $(CC_OPTIONS) sharedbraycurtis.cpp -c $(INCLUDE) -o ./sharedbraycurtis.o
 920
 921
 922 # Item # 45 -- sharedkulczynski --
 923 ./sharedkulczynski.o : sharedkulczynski.cpp
 924         $(CC) $(CC_OPTIONS) sharedkulczynski.cpp -c $(INCLUDE) -o ./sharedkulczynski.o
 925
 926
 927 # Item # 46 -- sharedlennon --
 928 ./sharedlennon.o : sharedlennon.cpp
 929         $(CC) $(CC_OPTIONS) sharedlennon.cpp -c $(INCLUDE) -o ./sharedlennon.o
 930
 931
 932 # Item # 47 -- sharedkulczynskicody --
 933 ./sharedkulczynskicody.o : sharedkulczynskicody.cpp
 934         $(CC) $(CC_OPTIONS) sharedkulczynskicody.cpp -c $(INCLUDE) -o ./sharedkulczynskicody.o
 935
 936
 937 # Item # 48 -- sharedmorisitahorn --
 938 ./sharedmorisitahorn.o : sharedmorisitahorn.cpp
 939         $(CC) $(CC_OPTIONS) sharedmorisitahorn.cpp -c $(INCLUDE) -o ./sharedmorisitahorn.o
 940
 941
 942 # Item # 49 -- sharedochiai --
 943 ./sharedochiai.o : sharedochiai.cpp
 944         $(CC) $(CC_OPTIONS) sharedochiai.cpp -c $(INCLUDE) -o ./sharedochiai.o
 945
 946
 947 # Item # 50 -- readcolumn --
 948 ./readcolumn.o : readcolumn.cpp
 949         $(CC) $(CC_OPTIONS) readcolumn.cpp -c $(INCLUDE) -o ./readcolumn.o
 950
 951
 952 # Item # 51 -- readotu --
 953 ./readotu.o : readotu.cpp
 954         $(CC) $(CC_OPTIONS) readotu.cpp -c $(INCLUDE) -o ./readotu.o
 955
 956
 957 # Item # 52 -- readphylip --
 958 ./readphylip.o : readphylip.cpp
 959         $(CC) $(CC_OPTIONS) readphylip.cpp -c $(INCLUDE) -o ./readphylip.o
 960
 961
 962 # Item # 53 -- consensuscommand --
 963 ./consensuscommand.o : consensuscommand.cpp
 964         $(CC) $(CC_OPTIONS) consensuscommand.cpp -c $(INCLUDE) -o ./consensuscommand.o
 965
 966
 967 # Item # 54 -- heatmapsimcommand --
 968 ./heatmapsimcommand.o : heatmapsimcommand.cpp
 969         $(CC) $(CC_OPTIONS) heatmapsimcommand.cpp -c $(INCLUDE) -o ./heatmapsimcommand.o
 970
 971
 972 # Item # 55 -- heatmapsim --
 973 ./heatmapsim.o : heatmapsim.cpp
 974         $(CC) $(CC_OPTIONS) heatmapsim.cpp -c $(INCLUDE) -o ./heatmapsim.o
 975
 976
 977 # Item # 56 -- optionparser --
 978 ./optionparser.o : optionparser.cpp
 979         $(CC) $(CC_OPTIONS) optionparser.cpp -c $(INCLUDE) -o ./optionparser.o
 980
 981
 982 # Item # 57 -- filterseqscommand --
 983 ./filterseqscommand.o : filterseqscommand.cpp
 984         $(CC) $(CC_OPTIONS) filterseqscommand.cpp -c $(INCLUDE) -o ./filterseqscommand.o
 985
 986
 987 # Item # 58 -- goodscoverage --
 988 ./goodscoverage.o : goodscoverage.cpp
 989         $(CC) $(CC_OPTIONS) goodscoverage.cpp -c $(INCLUDE) -o ./goodscoverage.o
 990
 991
 992 # Item # 59 -- sequencedb --
 993 ./sequencedb.o : sequencedb.cpp
 994         $(CC) $(CC_OPTIONS) sequencedb.cpp -c $(INCLUDE) -o ./sequencedb.o
 995
 996
 997 # Item # 60 -- sharedjackknife --
 998 ./sharedjackknife.o : sharedjackknife.cpp
 999         $(CC) $(CC_OPTIONS) sharedjackknife.cpp -c $(INCLUDE) -o ./sharedjackknife.o
1000
1001
1002 # Item # 61 -- sharedmarczewski --
1003 ./sharedmarczewski.o : sharedmarczewski.cpp
1004         $(CC) $(CC_OPTIONS) sharedmarczewski.cpp -c $(INCLUDE) -o ./sharedmarczewski.o
1005
1006
1007 # Item # 62 -- aligncommand --
1008 ./aligncommand.o : aligncommand.cpp
1009         $(CC) $(CC_OPTIONS) aligncommand.cpp -c $(INCLUDE) -o ./aligncommand.o
1010
1011
1012 # Item # 63 -- treemap --
1013 ./treemap.o : treemap.cpp
1014         $(CC) $(CC_OPTIONS) treemap.cpp -c $(INCLUDE) -o ./treemap.o
1015
1016
1017 # Item # 64 -- parsimonycommand --
1018 ./parsimonycommand.o : parsimonycommand.cpp
1019         $(CC) $(CC_OPTIONS) parsimonycommand.cpp -c $(INCLUDE) -o ./parsimonycommand.o
1020
1021
1022 # Item # 65 -- parsimony --
1023 ./parsimony.o : parsimony.cpp
1024         $(CC) $(CC_OPTIONS) parsimony.cpp -c $(INCLUDE) -o ./parsimony.o
1025
1026
1027 # Item # 66 -- seqsummarycommand --
1028 ./seqsummarycommand.o : seqsummarycommand.cpp
1029         $(CC) $(CC_OPTIONS) seqsummarycommand.cpp -c $(INCLUDE) -o ./seqsummarycommand.o
1030
1031
1032 # Item # 67 -- chimeraseqscommand --
1033 ./chimeraseqscommand.o : chimeraseqscommand.cpp
1034         $(CC) $(CC_OPTIONS) chimeraseqscommand.cpp -c $(INCLUDE) -o ./chimeraseqscommand.o
1035
1036
1037 # Item # 68 -- sharedlistvector --
1038 ./sharedlistvector.o : sharedlistvector.cpp
1039         $(CC) $(CC_OPTIONS) sharedlistvector.cpp -c $(INCLUDE) -o ./sharedlistvector.o
1040
1041
1042 # Item # 69 -- tree --
1043 ./tree.o : tree.cpp
1044         $(CC) $(CC_OPTIONS) tree.cpp -c $(INCLUDE) -o ./tree.o
1045
1046
1047 # Item # 70 -- readtree --
1048 ./readtree.o : readtree.cpp
1049         $(CC) $(CC_OPTIONS) readtree.cpp -c $(INCLUDE) -o ./readtree.o
1050
1051
1052 # Item # 71 -- sharedsobscollectsummary --
1053 ./sharedsobscollectsummary.o : sharedsobscollectsummary.cpp
1054         $(CC) $(CC_OPTIONS) sharedsobscollectsummary.cpp -c $(INCLUDE) -o ./sharedsobscollectsummary.o
1055
1056
1057 # Item # 72 -- deconvolutecommand --
1058 ./deconvolutecommand.o : deconvolutecommand.cpp
1059         $(CC) $(CC_OPTIONS) deconvolutecommand.cpp -c $(INCLUDE) -o ./deconvolutecommand.o
1060
1061
1062 # Item # 73 -- listseqscommand --
1063 ./listseqscommand.o : listseqscommand.cpp
1064         $(CC) $(CC_OPTIONS) listseqscommand.cpp -c $(INCLUDE) -o ./listseqscommand.o
1065
1066
1067 # Item # 74 -- getseqscommand --
1068 ./getseqscommand.o : getseqscommand.cpp
1069         $(CC) $(CC_OPTIONS) getseqscommand.cpp -c $(INCLUDE) -o ./getseqscommand.o
1070
1071
1072 # Item # 75 -- removeseqscommand --
1073 ./removeseqscommand.o : removeseqscommand.cpp
1074         $(CC) $(CC_OPTIONS) removeseqscommand.cpp -c $(INCLUDE) -o ./removeseqscommand.o
1075
1076
1077 # Item # 76 -- systemcommand --
1078 ./systemcommand.o : systemcommand.cpp
1079         $(CC) $(CC_OPTIONS) systemcommand.cpp -c $(INCLUDE) -o ./systemcommand.o
1080
1081
1082 # Item # 77 -- binsequencecommand --
1083 ./binsequencecommand.o : binsequencecommand.cpp
1084         $(CC) $(CC_OPTIONS) binsequencecommand.cpp -c $(INCLUDE) -o ./binsequencecommand.o
1085
1086
1087 # Item # 78 -- distancecommand --
1088 ./distancecommand.o : distancecommand.cpp
1089         $(CC) $(CC_OPTIONS) distancecommand.cpp -c $(INCLUDE) -o ./distancecommand.o
1090
1091
1092 # Item # 79 -- ace --
1093 ./ace.o : ace.cpp
1094         $(CC) $(CC_OPTIONS) ace.cpp -c $(INCLUDE) -o ./ace.o
1095
1096
1097 # Item # 80 -- averagelinkage --
1098 ./averagelinkage.o : averagelinkage.cpp
1099         $(CC) $(CC_OPTIONS) averagelinkage.cpp -c $(INCLUDE) -o ./averagelinkage.o
1100
1101
1102 # Item # 81 -- bootstrap --
1103 ./bootstrap.o : bootstrap.cpp
1104         $(CC) $(CC_OPTIONS) bootstrap.cpp -c $(INCLUDE) -o ./bootstrap.o
1105
1106
1107 # Item # 82 -- calculator --
1108 ./calculator.o : calculator.cpp
1109         $(CC) $(CC_OPTIONS) calculator.cpp -c $(INCLUDE) -o ./calculator.o
1110
1111
1112 # Item # 83 -- chao1 --
1113 ./chao1.o : chao1.cpp
1114         $(CC) $(CC_OPTIONS) chao1.cpp -c $(INCLUDE) -o ./chao1.o
1115
1116
1117 # Item # 84 -- cluster --
1118 ./cluster.o : cluster.cpp
1119         $(CC) $(CC_OPTIONS) cluster.cpp -c $(INCLUDE) -o ./cluster.o
1120
1121
1122 # Item # 85 -- clustercommand --
1123 ./clustercommand.o : clustercommand.cpp
1124         $(CC) $(CC_OPTIONS) clustercommand.cpp -c $(INCLUDE) -o ./clustercommand.o
1125
1126
1127 # Item # 86 -- collect --
1128 ./collect.o : collect.cpp
1129         $(CC) $(CC_OPTIONS) collect.cpp -c $(INCLUDE) -o ./collect.o
1130
1131
1132 # Item # 87 -- collectcommand --
1133 ./collectcommand.o : collectcommand.cpp
1134         $(CC) $(CC_OPTIONS) collectcommand.cpp -c $(INCLUDE) -o ./collectcommand.o
1135
1136
1137 # Item # 88 -- collectsharedcommand --
1138 ./collectsharedcommand.o : collectsharedcommand.cpp
1139         $(CC) $(CC_OPTIONS) collectsharedcommand.cpp -c $(INCLUDE) -o ./collectsharedcommand.o
1140
1141
1142 # Item # 89 -- commandoptionparser --
1143 ./commandoptionparser.o : commandoptionparser.cpp
1144         $(CC) $(CC_OPTIONS) commandoptionparser.cpp -c $(INCLUDE) -o ./commandoptionparser.o
1145
1146
1147 # Item # 90 -- completelinkage --
1148 ./completelinkage.o : completelinkage.cpp
1149         $(CC) $(CC_OPTIONS) completelinkage.cpp -c $(INCLUDE) -o ./completelinkage.o
1150
1151
1152 # Item # 91 -- database --
1153 ./database.o : database.cpp
1154         $(CC) $(CC_OPTIONS) database.cpp -c $(INCLUDE) -o ./database.o
1155
1156
1157 # Item # 92 -- engine --
1158 ./engine.o : engine.cpp
1159         $(CC) $(CC_OPTIONS) engine.cpp -c $(INCLUDE) -o ./engine.o
1160
1161
1162 # Item # 93 -- fastamap --
1163 ./fastamap.o : fastamap.cpp
1164         $(CC) $(CC_OPTIONS) fastamap.cpp -c $(INCLUDE) -o ./fastamap.o
1165
1166
1167 # Item # 94 -- fileoutput --
1168 ./fileoutput.o : fileoutput.cpp
1169         $(CC) $(CC_OPTIONS) fileoutput.cpp -c $(INCLUDE) -o ./fileoutput.o
1170
1171
1172 # Item # 95 -- globaldata --
1173 ./globaldata.o : globaldata.cpp
1174         $(CC) $(CC_OPTIONS) globaldata.cpp -c $(INCLUDE) -o ./globaldata.o
1175
1176
1177 # Item # 96 -- groupmap --
1178 ./groupmap.o : groupmap.cpp
1179         $(CC) $(CC_OPTIONS) groupmap.cpp -c $(INCLUDE) -o ./groupmap.o
1180
1181
1182 # Item # 97 -- helpcommand --
1183 ./helpcommand.o : helpcommand.cpp
1184         $(CC) $(CC_OPTIONS) helpcommand.cpp -c $(INCLUDE) -o ./helpcommand.o
1185
1186
1187 # Item # 98 -- inputdata --
1188 ./inputdata.o : inputdata.cpp
1189         $(CC) $(CC_OPTIONS) inputdata.cpp -c $(INCLUDE) -o ./inputdata.o
1190
1191
1192 # Item # 99 -- jackknife --
1193 ./jackknife.o : jackknife.cpp
1194         $(CC) $(CC_OPTIONS) jackknife.cpp -c $(INCLUDE) -o ./jackknife.o
1195
1196
1197 # Item # 100 -- kmer --
1198 ./kmer.o : kmer.cpp
1199         $(CC) $(CC_OPTIONS) kmer.cpp -c $(INCLUDE) -o ./kmer.o
1200
1201
1202 # Item # 101 -- kmerdb --
1203 ./kmerdb.o : kmerdb.cpp
1204         $(CC) $(CC_OPTIONS) kmerdb.cpp -c $(INCLUDE) -o ./kmerdb.o
1205
1206
1207 # Item # 102 -- listvector --
1208 ./listvector.o : listvector.cpp
1209         $(CC) $(CC_OPTIONS) listvector.cpp -c $(INCLUDE) -o ./listvector.o
1210
1211
1212 # Item # 103 -- mothur --
1213 ./mothur.o : mothur.cpp
1214         $(CC) $(CC_OPTIONS) mothur.cpp -c $(INCLUDE) -o ./mothur.o
1215
1216
1217 # Item # 104 -- nameassignment --
1218 ./nameassignment.o : nameassignment.cpp
1219         $(CC) $(CC_OPTIONS) nameassignment.cpp -c $(INCLUDE) -o ./nameassignment.o
1220
1221
1222 # Item # 105 -- npshannon --
1223 ./npshannon.o : npshannon.cpp
1224         $(CC) $(CC_OPTIONS) npshannon.cpp -c $(INCLUDE) -o ./npshannon.o
1225
1226
1227 # Item # 106 -- ordervector --
1228 ./ordervector.o : ordervector.cpp
1229         $(CC) $(CC_OPTIONS) ordervector.cpp -c $(INCLUDE) -o ./ordervector.o
1230
1231
1232 # Item # 107 -- progress --
1233 ./progress.o : progress.cpp
1234         $(CC) $(CC_OPTIONS) progress.cpp -c $(INCLUDE) -o ./progress.o
1235
1236
1237 # Item # 108 -- quitcommand --
1238 ./quitcommand.o : quitcommand.cpp
1239         $(CC) $(CC_OPTIONS) quitcommand.cpp -c $(INCLUDE) -o ./quitcommand.o
1240
1241
1242 # Item # 109 -- rabundvector --
1243 ./rabundvector.o : rabundvector.cpp
1244         $(CC) $(CC_OPTIONS) rabundvector.cpp -c $(INCLUDE) -o ./rabundvector.o
1245
1246
1247 # Item # 110 -- rarecalc --
1248 ./rarecalc.o : rarecalc.cpp
1249         $(CC) $(CC_OPTIONS) rarecalc.cpp -c $(INCLUDE) -o ./rarecalc.o
1250
1251
1252 # Item # 111 -- raredisplay --
1253 ./raredisplay.o : raredisplay.cpp
1254         $(CC) $(CC_OPTIONS) raredisplay.cpp -c $(INCLUDE) -o ./raredisplay.o
1255
1256
1257 # Item # 112 -- rarefact --
1258 ./rarefact.o : rarefact.cpp
1259         $(CC) $(CC_OPTIONS) rarefact.cpp -c $(INCLUDE) -o ./rarefact.o
1260
1261
1262 # Item # 113 -- rarefactcommand --
1263 ./rarefactcommand.o : rarefactcommand.cpp
1264         $(CC) $(CC_OPTIONS) rarefactcommand.cpp -c $(INCLUDE) -o ./rarefactcommand.o
1265
1266
1267 # Item # 114 -- rarefactsharedcommand --
1268 ./rarefactsharedcommand.o : rarefactsharedcommand.cpp
1269         $(CC) $(CC_OPTIONS) rarefactsharedcommand.cpp -c $(INCLUDE) -o ./rarefactsharedcommand.o
1270
1271
1272 # Item # 115 -- sabundvector --
1273 ./sabundvector.o : sabundvector.cpp
1274         $(CC) $(CC_OPTIONS) sabundvector.cpp -c $(INCLUDE) -o ./sabundvector.o
1275
1276
1277 # Item # 116 -- sequence --
1278 ./sequence.o : sequence.cpp
1279         $(CC) $(CC_OPTIONS) sequence.cpp -c $(INCLUDE) -o ./sequence.o
1280
1281
1282 # Item # 117 -- shannon --
1283 ./shannon.o : shannon.cpp
1284         $(CC) $(CC_OPTIONS) shannon.cpp -c $(INCLUDE) -o ./shannon.o
1285
1286
1287 # Item # 118 -- sharedace --
1288 ./sharedace.o : sharedace.cpp
1289         $(CC) $(CC_OPTIONS) sharedace.cpp -c $(INCLUDE) -o ./sharedace.o
1290
1291
1292 # Item # 119 -- sharedchao1 --
1293 ./sharedchao1.o : sharedchao1.cpp
1294         $(CC) $(CC_OPTIONS) sharedchao1.cpp -c $(INCLUDE) -o ./sharedchao1.o
1295
1296
1297 # Item # 120 -- sharedcommand --
1298 ./sharedcommand.o : sharedcommand.cpp
1299         $(CC) $(CC_OPTIONS) sharedcommand.cpp -c $(INCLUDE) -o ./sharedcommand.o
1300
1301
1302 # Item # 121 -- sharedjabund --
1303 ./sharedjabund.o : sharedjabund.cpp
1304         $(CC) $(CC_OPTIONS) sharedjabund.cpp -c $(INCLUDE) -o ./sharedjabund.o
1305
1306
1307 # Item # 122 -- sharedjclass --
1308 ./sharedjclass.o : sharedjclass.cpp
1309         $(CC) $(CC_OPTIONS) sharedjclass.cpp -c $(INCLUDE) -o ./sharedjclass.o
1310
1311
1312 # Item # 123 -- sharedjest --
1313 ./sharedjest.o : sharedjest.cpp
1314         $(CC) $(CC_OPTIONS) sharedjest.cpp -c $(INCLUDE) -o ./sharedjest.o
1315
1316
1317 # Item # 124 -- sharedordervector --
1318 ./sharedordervector.o : sharedordervector.cpp
1319         $(CC) $(CC_OPTIONS) sharedordervector.cpp -c $(INCLUDE) -o ./sharedordervector.o
1320
1321
1322 # Item # 125 -- sharedrabundvector --
1323 ./sharedrabundvector.o : sharedrabundvector.cpp
1324         $(CC) $(CC_OPTIONS) sharedrabundvector.cpp -c $(INCLUDE) -o ./sharedrabundvector.o
1325
1326
1327 # Item # 126 -- sharedsabundvector --
1328 ./sharedsabundvector.o : sharedsabundvector.cpp
1329         $(CC) $(CC_OPTIONS) sharedsabundvector.cpp -c $(INCLUDE) -o ./sharedsabundvector.o
1330
1331
1332 # Item # 127 -- sharedsobs --
1333 ./sharedsobs.o : sharedsobs.cpp
1334         $(CC) $(CC_OPTIONS) sharedsobs.cpp -c $(INCLUDE) -o ./sharedsobs.o
1335
1336
1337 # Item # 128 -- sharedsorabund --
1338 ./sharedsorabund.o : sharedsorabund.cpp
1339         $(CC) $(CC_OPTIONS) sharedsorabund.cpp -c $(INCLUDE) -o ./sharedsorabund.o
1340
1341
1342 # Item # 129 -- sharedsorclass --
1343 ./sharedsorclass.o : sharedsorclass.cpp
1344         $(CC) $(CC_OPTIONS) sharedsorclass.cpp -c $(INCLUDE) -o ./sharedsorclass.o
1345
1346
1347 # Item # 130 -- sharedsorest --
1348 ./sharedsorest.o : sharedsorest.cpp
1349         $(CC) $(CC_OPTIONS) sharedsorest.cpp -c $(INCLUDE) -o ./sharedsorest.o
1350
1351
1352 # Item # 131 -- sharedthetan --
1353 ./sharedthetan.o : sharedthetan.cpp
1354         $(CC) $(CC_OPTIONS) sharedthetan.cpp -c $(INCLUDE) -o ./sharedthetan.o
1355
1356
1357 # Item # 132 -- sharedthetayc --
1358 ./sharedthetayc.o : sharedthetayc.cpp
1359         $(CC) $(CC_OPTIONS) sharedthetayc.cpp -c $(INCLUDE) -o ./sharedthetayc.o
1360
1361
1362 # Item # 133 -- simpson --
1363 ./simpson.o : simpson.cpp
1364         $(CC) $(CC_OPTIONS) simpson.cpp -c $(INCLUDE) -o ./simpson.o
1365
1366
1367 # Item # 134 -- singlelinkage --
1368 ./singlelinkage.o : singlelinkage.cpp
1369         $(CC) $(CC_OPTIONS) singlelinkage.cpp -c $(INCLUDE) -o ./singlelinkage.o
1370
1371
1372 # Item # 135 -- sparsematrix --
1373 ./sparsematrix.o : sparsematrix.cpp
1374         $(CC) $(CC_OPTIONS) sparsematrix.cpp -c $(INCLUDE) -o ./sparsematrix.o
1375
1376
1377 # Item # 136 -- summarycommand --
1378 ./summarycommand.o : summarycommand.cpp
1379         $(CC) $(CC_OPTIONS) summarycommand.cpp -c $(INCLUDE) -o ./summarycommand.o
1380
1381
1382 # Item # 137 -- summarysharedcommand --
1383 ./summarysharedcommand.o : summarysharedcommand.cpp
1384         $(CC) $(CC_OPTIONS) summarysharedcommand.cpp -c $(INCLUDE) -o ./summarysharedcommand.o
1385
1386
1387 # Item # 138 -- uvest --
1388 ./uvest.o : uvest.cpp
1389         $(CC) $(CC_OPTIONS) uvest.cpp -c $(INCLUDE) -o ./uvest.o
1390
1391
1392 # Item # 139 -- validcalculator --
1393 ./validcalculator.o : validcalculator.cpp
1394         $(CC) $(CC_OPTIONS) validcalculator.cpp -c $(INCLUDE) -o ./validcalculator.o
1395
1396
1397 # Item # 140 -- validparameter --
1398 ./validparameter.o : validparameter.cpp
1399         $(CC) $(CC_OPTIONS) validparameter.cpp -c $(INCLUDE) -o ./validparameter.o
1400
1401
1402 # Item # 141 -- treenode --
1403 ./treenode.o : treenode.cpp
1404         $(CC) $(CC_OPTIONS) treenode.cpp -c $(INCLUDE) -o ./treenode.o
1405
1406
1407 # Item # 142 -- readtreecommand --
1408 ./readtreecommand.o : readtreecommand.cpp
1409         $(CC) $(CC_OPTIONS) readtreecommand.cpp -c $(INCLUDE) -o ./readtreecommand.o
1410
1411
1412 # Item # 143 -- reversecommand --
1413 ./reversecommand.o : reversecommand.cpp
1414         $(CC) $(CC_OPTIONS) reversecommand.cpp -c $(INCLUDE) -o ./reversecommand.o
1415
1416
1417 # Item # 144 -- trimseqscommand --
1418 ./trimseqscommand.o : trimseqscommand.cpp
1419         $(CC) $(CC_OPTIONS) trimseqscommand.cpp -c $(INCLUDE) -o ./trimseqscommand.o
1420
1421
1422 # Item # 145 -- slibshuff --
1423 ./slibshuff.o : slibshuff.cpp
1424         $(CC) $(CC_OPTIONS) slibshuff.cpp -c $(INCLUDE) -o ./slibshuff.o
1425
1426
1427 # Item # 146 -- libshuff --
1428 ./libshuff.o : libshuff.cpp
1429         $(CC) $(CC_OPTIONS) libshuff.cpp -c $(INCLUDE) -o ./libshuff.o
1430
1431
1432 # Item # 147 -- dlibshuff --
1433 ./dlibshuff.o : dlibshuff.cpp
1434         $(CC) $(CC_OPTIONS) dlibshuff.cpp -c $(INCLUDE) -o ./dlibshuff.o
1435
1436
1437 # Item # 148 -- mergefilecommand --
1438 ./mergefilecommand.o : mergefilecommand.cpp
1439         $(CC) $(CC_OPTIONS) mergefilecommand.cpp -c $(INCLUDE) -o ./mergefilecommand.o
1440
1441
1442 # Item # 149 -- coverage --
1443 ./coverage.o : coverage.cpp
1444         $(CC) $(CC_OPTIONS) coverage.cpp -c $(INCLUDE) -o ./coverage.o
1445
1446
1447 # Item # 150 -- whittaker --
1448 ./whittaker.o : whittaker.cpp
1449         $(CC) $(CC_OPTIONS) whittaker.cpp -c $(INCLUDE) -o ./whittaker.o
1450
1451
1452 # Item # 151 -- preclustercommand --
1453 ./preclustercommand.o : preclustercommand.cpp
1454         $(CC) $(CC_OPTIONS) preclustercommand.cpp -c $(INCLUDE) -o ./preclustercommand.o
1455
1456
1457 # Item # 152 -- otuhierarchycommand --
1458 ./otuhierarchycommand.o : otuhierarchycommand.cpp
1459         $(CC) $(CC_OPTIONS) otuhierarchycommand.cpp -c $(INCLUDE) -o ./otuhierarchycommand.o
1460
1461
1462 # Item # 153 -- setdircommand --
1463 ./setdircommand.o : setdircommand.cpp
1464         $(CC) $(CC_OPTIONS) setdircommand.cpp -c $(INCLUDE) -o ./setdircommand.o
1465
1466
1467 # Item # 154 -- getgroupcommand --
1468 ./getgroupcommand.o : getgroupcommand.cpp
1469         $(CC) $(CC_OPTIONS) getgroupcommand.cpp -c $(INCLUDE) -o ./getgroupcommand.o
1470
1471
1472 # Item # 155 -- getlabelcommand --
1473 ./getlabelcommand.o : getlabelcommand.cpp
1474         $(CC) $(CC_OPTIONS) getlabelcommand.cpp -c $(INCLUDE) -o ./getlabelcommand.o
1475
1476
1477 # Item # 156 -- secondarystructurecommand --
1478 ./secondarystructurecommand.o : secondarystructurecommand.cpp
1479         $(CC) $(CC_OPTIONS) secondarystructurecommand.cpp -c $(INCLUDE) -o ./secondarystructurecommand.o
1480
1481
1482 # Item # 157 -- mothurout --
1483 ./mothurout.o : mothurout.cpp
1484         $(CC) $(CC_OPTIONS) mothurout.cpp -c $(INCLUDE) -o ./mothurout.o
1485
1486
1487 # Item # 158 -- parselistscommand --
1488 ./parselistscommand.o : parselistscommand.cpp
1489         $(CC) $(CC_OPTIONS) parselistscommand.cpp -c $(INCLUDE) -o ./parselistscommand.o
1490
1491
1492 # Item # 159 -- readblast --
1493 ./readblast.o : readblast.cpp
1494         $(CC) $(CC_OPTIONS) readblast.cpp -c $(INCLUDE) -o ./readblast.o
1495
1496
1497 # Item # 160 -- chimeracheckrdp --
1498 ./chimeracheckrdp.o : chimeracheckrdp.cpp
1499         $(CC) $(CC_OPTIONS) chimeracheckrdp.cpp -c $(INCLUDE) -o ./chimeracheckrdp.o
1500
1501
1502 # Item # 161 -- hclustercommand --
1503 ./hclustercommand.o : hclustercommand.cpp
1504         $(CC) $(CC_OPTIONS) hclustercommand.cpp -c $(INCLUDE) -o ./hclustercommand.o
1505
1506
1507 # Item # 162 -- hcluster --
1508 ./hcluster.o : hcluster.cpp
1509         $(CC) $(CC_OPTIONS) hcluster.cpp -c $(INCLUDE) -o ./hcluster.o
1510
1511
1512 # Item # 163 -- getlistcountcommand --
1513 ./getlistcountcommand.o : getlistcountcommand.cpp
1514         $(CC) $(CC_OPTIONS) getlistcountcommand.cpp -c $(INCLUDE) -o ./getlistcountcommand.o
1515
1516
1517 # Item # 164 -- readcluster --
1518 ./readcluster.o : readcluster.cpp
1519         $(CC) $(CC_OPTIONS) readcluster.cpp -c $(INCLUDE) -o ./readcluster.o
1520
1521
1522 # Item # 165 -- ccode --
1523 ./ccode.o : ccode.cpp
1524         $(CC) $(CC_OPTIONS) ccode.cpp -c $(INCLUDE) -o ./ccode.o
1525
1526
1527 # Item # 166 -- taxonomyequalizer --
1528 ./taxonomyequalizer.o : taxonomyequalizer.cpp
1529         $(CC) $(CC_OPTIONS) taxonomyequalizer.cpp -c $(INCLUDE) -o ./taxonomyequalizer.o
1530
1531
1532 # Item # 167 -- phylotypecommand --
1533 ./phylotypecommand.o : phylotypecommand.cpp
1534         $(CC) $(CC_OPTIONS) phylotypecommand.cpp -c $(INCLUDE) -o ./phylotypecommand.o
1535
1536
1537 # Item # 168 -- classifyseqscommand --
1538 ./classifyseqscommand.o : classifyseqscommand.cpp
1539         $(CC) $(CC_OPTIONS) classifyseqscommand.cpp -c $(INCLUDE) -o ./classifyseqscommand.o
1540
1541
1542 # Item # 169 -- classify --
1543 ./classify.o : classify.cpp
1544         $(CC) $(CC_OPTIONS) classify.cpp -c $(INCLUDE) -o ./classify.o
1545
1546
1547 # Item # 170 -- phylotree --
1548 ./phylotree.o : phylotree.cpp
1549         $(CC) $(CC_OPTIONS) phylotree.cpp -c $(INCLUDE) -o ./phylotree.o
1550
1551
1552 # Item # 171 -- bayesian --
1553 ./bayesian.o : bayesian.cpp
1554         $(CC) $(CC_OPTIONS) bayesian.cpp -c $(INCLUDE) -o ./bayesian.o
1555
1556
1557 # Item # 172 -- alignmentdb --
1558 ./alignmentdb.o : alignmentdb.cpp
1559         $(CC) $(CC_OPTIONS) alignmentdb.cpp -c $(INCLUDE) -o ./alignmentdb.o
1560
1561
1562 # Item # 173 -- knn --
1563 ./knn.o : knn.cpp
1564         $(CC) $(CC_OPTIONS) knn.cpp -c $(INCLUDE) -o ./knn.o
1565
1566
1567 # Item # 174 -- distancedb --
1568 ./distancedb.o : distancedb.cpp
1569         $(CC) $(CC_OPTIONS) distancedb.cpp -c $(INCLUDE) -o ./distancedb.o
1570
1571
1572 # Item # 175 -- chimeraslayer --
1573 ./chimeraslayer.o : chimeraslayer.cpp
1574         $(CC) $(CC_OPTIONS) chimeraslayer.cpp -c $(INCLUDE) -o ./chimeraslayer.o
1575
1576
1577 # Item # 176 -- slayer --
1578 ./slayer.o : slayer.cpp
1579         $(CC) $(CC_OPTIONS) slayer.cpp -c $(INCLUDE) -o ./slayer.o
1580
1581
1582 # Item # 177 -- pcacommand --
1583 ./pcacommand.o : pcacommand.cpp
1584         $(CC) $(CC_OPTIONS) pcacommand.cpp -c $(INCLUDE) -o ./pcacommand.o
1585
1586
1587 # Item # 178 -- formatcolumn --
1588 ./formatcolumn.o : formatcolumn.cpp
1589         $(CC) $(CC_OPTIONS) formatcolumn.cpp -c $(INCLUDE) -o ./formatcolumn.o
1590
1591
1592 # Item # 179 -- formatphylip --
1593 ./formatphylip.o : formatphylip.cpp
1594         $(CC) $(CC_OPTIONS) formatphylip.cpp -c $(INCLUDE) -o ./formatphylip.o
1595
1596
1597 # Item # 180 -- mgclustercommand --
1598 ./mgclustercommand.o : mgclustercommand.cpp
1599         $(CC) $(CC_OPTIONS) mgclustercommand.cpp -c $(INCLUDE) -o ./mgclustercommand.o
1600
1601
1602 # Item # 181 -- getsharedotucommand --
1603 ./getsharedotucommand.o : getsharedotucommand.cpp
1604         $(CC) $(CC_OPTIONS) getsharedotucommand.cpp -c $(INCLUDE) -o ./getsharedotucommand.o
1605
1606
1607 # Item # 182 -- maligner --
1608 ./maligner.o : maligner.cpp
1609         $(CC) $(CC_OPTIONS) maligner.cpp -c $(INCLUDE) -o ./maligner.o
1610
1611
1612 # Item # 183 -- chimerarealigner --
1613 ./chimerarealigner.o : chimerarealigner.cpp
1614         $(CC) $(CC_OPTIONS) chimerarealigner.cpp -c $(INCLUDE) -o ./chimerarealigner.o
1615
1616
1617 # Item # 184 -- bergerparker --
1618 ./bergerparker.o : bergerparker.cpp
1619         $(CC) $(CC_OPTIONS) bergerparker.cpp -c $(INCLUDE) -o ./bergerparker.o
1620
1621
1622 # Item # 185 -- bstick --
1623 ./bstick.o : bstick.cpp
1624         $(CC) $(CC_OPTIONS) bstick.cpp -c $(INCLUDE) -o ./bstick.o
1625
1626
1627 # Item # 186 -- sharedkstest --
1628 ./sharedkstest.o : sharedkstest.cpp
1629         $(CC) $(CC_OPTIONS) sharedkstest.cpp -c $(INCLUDE) -o ./sharedkstest.o
1630
1631
1632 # Item # 187 -- qstat --
1633 ./qstat.o : qstat.cpp
1634         $(CC) $(CC_OPTIONS) qstat.cpp -c $(INCLUDE) -o ./qstat.o
1635
1636
1637 # Item # 188 -- shen --
1638 ./shen.o : shen.cpp
1639         $(CC) $(CC_OPTIONS) shen.cpp -c $(INCLUDE) -o ./shen.o
1640
1641
1642 # Item # 189 -- logsd --
1643 ./logsd.o : logsd.cpp
1644         $(CC) $(CC_OPTIONS) logsd.cpp -c $(INCLUDE) -o ./logsd.o
1645
1646
1647 # Item # 190 -- geom --
1648 ./geom.o : geom.cpp
1649         $(CC) $(CC_OPTIONS) geom.cpp -c $(INCLUDE) -o ./geom.o
1650
1651 # Item # 191 -- parsesffcommand --
1652 ./parsesffcommand.o : parsesffcommand.cpp
1653         $(CC) $(CC_OPTIONS) parsesffcommand.cpp -c $(INCLUDE) -o ./parsesffcommand.o
1654
1655 # Item # 192 -- chimeraccodecommand --
1656 ./chimeraccodecommand.o : chimeraccodecommand.cpp
1657         $(CC) $(CC_OPTIONS) chimeraccodecommand.cpp -c $(INCLUDE) -o ./chimeraccodecommand.o
1658
1659 # Item # 193 -- chimeracheckcommand --
1660 ./chimeracheckcommand.o : chimeracheckcommand.cpp
1661         $(CC) $(CC_OPTIONS) chimeracheckcommand.cpp -c $(INCLUDE) -o ./chimeracheckcommand.o
1662
1663
1664 # Item # 194 -- chimeraslayercommand --
1665 ./chimeraslayercommand.o : chimeraslayercommand.cpp
1666         $(CC) $(CC_OPTIONS) chimeraslayercommand.cpp -c $(INCLUDE) -o ./chimeraslayercommand.o
1667
1668 # Item # 195 -- chimerapintailcommand --
1669 ./chimerapintailcommand.o : chimerapintailcommand.cpp
1670         $(CC) $(CC_OPTIONS) chimerapintailcommand.cpp -c $(INCLUDE) -o ./chimerapintailcommand.o
1671
1672 # Item # 196 -- chimerabellerophoncommand --
1673 ./chimerabellerophoncommand.o : chimerabellerophoncommand.cpp
1674         $(CC) $(CC_OPTIONS) chimerabellerophoncommand.cpp -c $(INCLUDE) -o ./chimerabellerophoncommand.o
1675
1676 # Item # 197 -- phylosummary --
1677 ./phylosummary.o : phylosummary.cpp
1678         $(CC) $(CC_OPTIONS) phylosummary.cpp -c $(INCLUDE) -o ./phylosummary.o
1679
1680 # Item # 198 -- setlogfilecommand --
1681 ./setlogfilecommand.o : setlogfilecommand.cpp
1682         $(CC) $(CC_OPTIONS) setlogfilecommand.cpp -c $(INCLUDE) -o ./setlogfilecommand.o
1683
1684 # Item # 199 -- phylodiversity --
1685 ./phylodiversity.o : phylodiversity.cpp
1686         $(CC) $(CC_OPTIONS) phylodiversity.cpp -c $(INCLUDE) -o ./phylodiversity.o
1687
1688 # Item # 200 -- phylodiversitycommand --
1689 ./phylodiversitycommand.o : phylodiversitycommand.cpp
1690         $(CC) $(CC_OPTIONS) phylodiversitycommand.cpp -c $(INCLUDE) -o ./phylodiversitycommand.o
1691
1692 # Item # 201 -- makegroupcommand --
1693 ./makegroupcommand.o : makegroupcommand.cpp
1694         $(CC) $(CC_OPTIONS) makegroupcommand.cpp -c $(INCLUDE) -o ./makegroupcommand.o
1695
1696 # Item # 202 -- chopseqscommand --
1697 ./chopseqscommand.o : chopseqscommand.cpp
1698         $(CC) $(CC_OPTIONS) chopseqscommand.cpp -c $(INCLUDE) -o ./chopseqscommand.o
1699
1700 # Item # 203 -- clearcutcommand --
1701 ./clearcutcommand.o : clearcutcommand.cpp
1702         $(CC) $(CC_OPTIONS) clearcutcommand.cpp -c $(INCLUDE) -o ./clearcutcommand.o
1703
1704 # Item # 204 -- catchallcommand --
1705 ./catchallcommand.o : catchallcommand.cpp
1706         $(CC) $(CC_OPTIONS) catchallcommand.cpp -c $(INCLUDE) -o ./catchallcommand.o
1707
1708 # Item # 205 -- splitabundcommand --
1709 ./splitabundcommand.o : splitabundcommand.cpp
1710         $(CC) $(CC_OPTIONS) splitabundcommand.cpp -c $(INCLUDE) -o ./splitabundcommand.o
1711
1712 # Item # 206 -- splitmatrix --
1713 ./splitmatrix.o : splitmatrix.cpp
1714         $(CC) $(CC_OPTIONS) splitmatrix.cpp -c $(INCLUDE) -o ./splitmatrix.o
1715
1716 # Item # 207 -- clustersplit --
1717 ./clustersplitcommand.o : clustersplitcommand.cpp
1718         $(CC) $(CC_OPTIONS) clustersplitcommand.cpp -c $(INCLUDE) -o ./clustersplitcommand.o
1719
1720 # Item # 208 -- classifyotu --
1721 ./classifyotucommand.o : classifyotucommand.cpp
1722         $(CC) $(CC_OPTIONS) classifyotucommand.cpp -c $(INCLUDE) -o ./classifyotucommand.o
1723
1724 # Item # 209 -- weightedlinkage --
1725 ./weightedlinkage.o : weightedlinkage.cpp
1726         $(CC) $(CC_OPTIONS) weightedlinkage.cpp -c $(INCLUDE) -o ./weightedlinkage.o
1727
1728 # Item # 210 -- degapseqscommand --
1729 ./degapseqscommand.o : degapseqscommand.cpp
1730         $(CC) $(CC_OPTIONS) degapseqscommand.cpp -c $(INCLUDE) -o ./degapseqscommand.o
1731
1732 # Item # 211 -- getrelabundcommand --
1733 ./getrelabundcommand.o : getrelabundcommand.cpp
1734         $(CC) $(CC_OPTIONS) getrelabundcommand.cpp -c $(INCLUDE) -o ./getrelabundcommand.o
1735
1736 ##### END RUN ####