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