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