makefile

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