Mothur.xcodeproj/project.pbxproj

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 231                 373C68BA0FC1C1A600137ACD /* gotohoverlap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = gotohoverlap.cpp; sourceTree = SOURCE_ROOT; };
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 234                 373C68C40FC1C25F00137ACD /* overlap.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = overlap.hpp; sourceTree = SOURCE_ROOT; };
 235                 373C68CD0FC1C2D900137ACD /* needlemanoverlap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = needlemanoverlap.cpp; sourceTree = SOURCE_ROOT; };
 236                 373C68CE0FC1C2D900137ACD /* needlemanoverlap.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = needlemanoverlap.hpp; sourceTree = SOURCE_ROOT; };
 237                 373C68DB0FC1C38D00137ACD /* blastalign.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = blastalign.cpp; sourceTree = SOURCE_ROOT; };
 238                 373C68DC0FC1C38D00137ACD /* blastalign.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = blastalign.hpp; sourceTree = SOURCE_ROOT; };
 239                 373C68E30FC1C4A500137ACD /* noalign.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = noalign.cpp; sourceTree = SOURCE_ROOT; };
 240                 373C68E40FC1C4A500137ACD /* noalign.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = noalign.hpp; sourceTree = SOURCE_ROOT; };
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 242                 373C68F40FC1C6A800137ACD /* suffixdb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixdb.hpp; sourceTree = SOURCE_ROOT; };
 243                 373C68F50FC1C6A800137ACD /* suffixnodes.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixnodes.cpp; sourceTree = SOURCE_ROOT; };
 244                 373C68F60FC1C6A800137ACD /* suffixnodes.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixnodes.hpp; sourceTree = SOURCE_ROOT; };
 245                 373C68F70FC1C6A800137ACD /* suffixtree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixtree.cpp; sourceTree = SOURCE_ROOT; };
 246                 373C68F80FC1C6A800137ACD /* suffixtree.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixtree.hpp; sourceTree = SOURCE_ROOT; };
 247                 373C69160FC1C8AF00137ACD /* blastdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = blastdb.cpp; sourceTree = SOURCE_ROOT; };
 248                 373C69170FC1C8AF00137ACD /* blastdb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = blastdb.hpp; sourceTree = SOURCE_ROOT; };
 249                 373C691D0FC1C98600137ACD /* nast.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nast.cpp; sourceTree = SOURCE_ROOT; };
 250                 373C691E0FC1C98600137ACD /* nast.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = nast.hpp; sourceTree = SOURCE_ROOT; };
 251                 373C69290FC1C9EB00137ACD /* nastreport.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nastreport.cpp; sourceTree = SOURCE_ROOT; };
 252                 373C692A0FC1C9EB00137ACD /* nastreport.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = nastreport.hpp; sourceTree = SOURCE_ROOT; };
 253                 373C69940FC1E63600137ACD /* boneh.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = boneh.cpp; sourceTree = SOURCE_ROOT; };
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 255                 373C69960FC1E63600137ACD /* efron.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = efron.cpp; sourceTree = SOURCE_ROOT; };
 256                 373C69970FC1E63600137ACD /* efron.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = efron.h; sourceTree = SOURCE_ROOT; };
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 258                 373C69990FC1E63600137ACD /* solow.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = solow.h; sourceTree = SOURCE_ROOT; };
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 260                 374610770F40645300460C57 /* unifracweightedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unifracweightedcommand.cpp; sourceTree = SOURCE_ROOT; };
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 306                 375AA1330F9E433D008EF9B8 /* readcolumn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readcolumn.cpp; sourceTree = SOURCE_ROOT; };
 307                 375AA1340F9E433D008EF9B8 /* readcolumn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readcolumn.h; sourceTree = SOURCE_ROOT; };
 308                 375AA1350F9E433D008EF9B8 /* readotu.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readotu.cpp; sourceTree = SOURCE_ROOT; };
 309                 375AA1360F9E433D008EF9B8 /* readotu.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotu.h; sourceTree = SOURCE_ROOT; };
 310                 375AA1370F9E433D008EF9B8 /* readphylip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readphylip.cpp; sourceTree = SOURCE_ROOT; };
 311                 375AA1380F9E433D008EF9B8 /* readphylip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylip.h; sourceTree = SOURCE_ROOT; };
 312                 377326630FAF16E0007ABB8B /* consensuscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = consensuscommand.cpp; sourceTree = SOURCE_ROOT; };
 313                 377326640FAF16E0007ABB8B /* consensuscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = consensuscommand.h; sourceTree = SOURCE_ROOT; };
 314                 378598640FDD497000EF9D03 /* heatmapsimcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapsimcommand.h; sourceTree = SOURCE_ROOT; };
 315                 378598650FDD497000EF9D03 /* heatmapsimcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapsimcommand.cpp; sourceTree = SOURCE_ROOT; };
 316                 378598720FDD4C1500EF9D03 /* heatmapsim.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapsim.h; sourceTree = SOURCE_ROOT; };
 317                 378598730FDD4C1500EF9D03 /* heatmapsim.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapsim.cpp; sourceTree = SOURCE_ROOT; };
 318                 3785990E0FDD7E8E00EF9D03 /* optionparser.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = optionparser.h; sourceTree = SOURCE_ROOT; };
 319                 3785990F0FDD7E8E00EF9D03 /* optionparser.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = optionparser.cpp; sourceTree = SOURCE_ROOT; };
 320                 378C1AEE0FB0644D004D63F5 /* filterseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = filterseqscommand.cpp; sourceTree = SOURCE_ROOT; };
 321                 378C1AEF0FB0644D004D63F5 /* filterseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = filterseqscommand.h; sourceTree = SOURCE_ROOT; };
 322                 378C1AF00FB0644D004D63F5 /* goodscoverage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = goodscoverage.cpp; sourceTree = SOURCE_ROOT; };
 323                 378C1AF10FB0644D004D63F5 /* goodscoverage.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = goodscoverage.h; sourceTree = SOURCE_ROOT; };
 324                 378C1AFD0FB0644D004D63F5 /* sequencedb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sequencedb.cpp; sourceTree = SOURCE_ROOT; };
 325                 378C1AFE0FB0644D004D63F5 /* sequencedb.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sequencedb.h; sourceTree = SOURCE_ROOT; };
 326                 378C1AFF0FB0644D004D63F5 /* sharedjackknife.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjackknife.cpp; sourceTree = SOURCE_ROOT; };
 327                 378C1B000FB0644D004D63F5 /* sharedjackknife.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjackknife.h; sourceTree = SOURCE_ROOT; };
 328                 378C1B010FB0644D004D63F5 /* sharedmarczewski.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedmarczewski.cpp; sourceTree = SOURCE_ROOT; };
 329                 378C1B020FB0644D004D63F5 /* sharedmarczewski.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedmarczewski.h; sourceTree = SOURCE_ROOT; };
 330                 378DC5CD0FBDE1C8003B8607 /* aligncommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = aligncommand.h; sourceTree = SOURCE_ROOT; };
 331                 378DC5CE0FBDE1C8003B8607 /* aligncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = aligncommand.cpp; sourceTree = SOURCE_ROOT; };
 332                 379293C10F2DE73400B9034A /* treemap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treemap.h; sourceTree = SOURCE_ROOT; };
 333                 379293C20F2DE73400B9034A /* treemap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treemap.cpp; sourceTree = SOURCE_ROOT; };
 334                 3792946E0F2E191800B9034A /* parsimonycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimonycommand.h; sourceTree = SOURCE_ROOT; };
 335                 3792946F0F2E191800B9034A /* parsimonycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsimonycommand.cpp; sourceTree = SOURCE_ROOT; };
 336                 379294880F2E258500B9034A /* parsimony.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimony.h; sourceTree = SOURCE_ROOT; };
 337                 379294890F2E258500B9034A /* parsimony.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsimony.cpp; sourceTree = SOURCE_ROOT; };
 338                 3792948D0F2E271100B9034A /* treecalculator.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treecalculator.h; sourceTree = SOURCE_ROOT; };
 339                 3799A94E0FD6A58C00E33EDE /* seqsummarycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = seqsummarycommand.cpp; sourceTree = SOURCE_ROOT; };
 340                 3799A94F0FD6A58C00E33EDE /* seqsummarycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = seqsummarycommand.h; sourceTree = SOURCE_ROOT; };
 341                 379D3D4F0FF90E090068C1C0 /* chimeraseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraseqscommand.h; sourceTree = SOURCE_ROOT; };
 342                 379D3D500FF90E090068C1C0 /* chimeraseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraseqscommand.cpp; sourceTree = SOURCE_ROOT; };
 343                 379D3D6B0FF917F40068C1C0 /* filters.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = filters.h; sourceTree = SOURCE_ROOT; };
 344                 37AD4CE20F28AEA300AA2D49 /* sharedlistvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedlistvector.h; sourceTree = SOURCE_ROOT; };
 345                 37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedlistvector.cpp; sourceTree = SOURCE_ROOT; };
 346                 37AD4DB90F28E2FE00AA2D49 /* tree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = tree.h; sourceTree = SOURCE_ROOT; };
 347                 37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = tree.cpp; sourceTree = SOURCE_ROOT; };
 348                 37AD4DC80F28F3DD00AA2D49 /* readtree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtree.h; sourceTree = SOURCE_ROOT; };
 349                 37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtree.cpp; sourceTree = SOURCE_ROOT; };
 350                 37AFC71D0F445386005F492D /* sharedsobscollectsummary.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsobscollectsummary.h; sourceTree = SOURCE_ROOT; };
 351                 37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsobscollectsummary.cpp; sourceTree = SOURCE_ROOT; };
 352                 37B28F660F27590100808A62 /* deconvolutecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = deconvolutecommand.h; sourceTree = SOURCE_ROOT; };
 353                 37B28F670F27590100808A62 /* deconvolutecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = deconvolutecommand.cpp; sourceTree = SOURCE_ROOT; };
 354                 37B73C741004BEFD008C4B41 /* listseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = listseqscommand.h; sourceTree = SOURCE_ROOT; };
 355                 37B73C751004BEFD008C4B41 /* listseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = listseqscommand.cpp; sourceTree = SOURCE_ROOT; };
 356                 37B73CA41004D89A008C4B41 /* getseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getseqscommand.h; sourceTree = SOURCE_ROOT; };
 357                 37B73CA51004D89A008C4B41 /* getseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getseqscommand.cpp; sourceTree = SOURCE_ROOT; };
 358                 37B73CBE1004EB38008C4B41 /* removeseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removeseqscommand.h; sourceTree = SOURCE_ROOT; };
 359                 37B73CBF1004EB38008C4B41 /* removeseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removeseqscommand.cpp; sourceTree = SOURCE_ROOT; };
 360                 37B73CCD1004F5E0008C4B41 /* systemcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = systemcommand.h; sourceTree = SOURCE_ROOT; };
 361                 37B73CCE1004F5E0008C4B41 /* systemcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = systemcommand.cpp; sourceTree = SOURCE_ROOT; };
 362                 37C1D9710F86506E0059E3F0 /* binsequencecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = binsequencecommand.h; sourceTree = SOURCE_ROOT; };
 363                 37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = binsequencecommand.cpp; sourceTree = SOURCE_ROOT; };
 364                 37C753CC0FB3415200DBD02E /* distancecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = distancecommand.h; sourceTree = SOURCE_ROOT; };
 365                 37C753CD0FB3415200DBD02E /* distancecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = distancecommand.cpp; sourceTree = SOURCE_ROOT; };
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 367                 37C753ED0FB34A5700DBD02E /* ignoregaps.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ignoregaps.h; sourceTree = SOURCE_ROOT; };
 368                 37C753F00FB34AE800DBD02E /* eachgapdist.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = eachgapdist.h; sourceTree = SOURCE_ROOT; };
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 370                 37C753F30FB34BBF00DBD02E /* onegapignore.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = onegapignore.h; sourceTree = SOURCE_ROOT; };
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 373                 37D927B90F21331F001D4494 /* ace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ace.h; sourceTree = SOURCE_ROOT; };
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 376                 37D927BC0F21331F001D4494 /* bootstrap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bootstrap.h; sourceTree = SOURCE_ROOT; };
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 380                 37D927C00F21331F001D4494 /* chao1.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chao1.h; sourceTree = SOURCE_ROOT; };
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 393                 37D927CD0F21331F001D4494 /* command.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = command.hpp; sourceTree = SOURCE_ROOT; };
 394                 37D927CF0F21331F001D4494 /* commandfactory.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = commandfactory.hpp; sourceTree = SOURCE_ROOT; };
 395                 37D927D00F21331F001D4494 /* commandoptionparser.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = commandoptionparser.cpp; sourceTree = SOURCE_ROOT; };
 396                 37D927D10F21331F001D4494 /* commandoptionparser.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = commandoptionparser.hpp; sourceTree = SOURCE_ROOT; };
 397                 37D927D20F21331F001D4494 /* completelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = completelinkage.cpp; sourceTree = SOURCE_ROOT; };
 398                 37D927D30F21331F001D4494 /* database.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = database.cpp; sourceTree = SOURCE_ROOT; };
 399                 37D927D40F21331F001D4494 /* database.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = database.hpp; sourceTree = SOURCE_ROOT; };
 400                 37D927D50F21331F001D4494 /* datavector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = datavector.hpp; sourceTree = SOURCE_ROOT; };
 401                 37D927D60F21331F001D4494 /* display.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = display.h; sourceTree = SOURCE_ROOT; };
 402                 37D927D70F21331F001D4494 /* engine.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = engine.cpp; sourceTree = SOURCE_ROOT; };
 403                 37D927D80F21331F001D4494 /* engine.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = engine.hpp; sourceTree = SOURCE_ROOT; };
 404                 37D927DB0F21331F001D4494 /* fastamap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fastamap.cpp; sourceTree = SOURCE_ROOT; };
 405                 37D927DC0F21331F001D4494 /* fastamap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fastamap.h; sourceTree = SOURCE_ROOT; };
 406                 37D927DD0F21331F001D4494 /* fileoutput.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fileoutput.cpp; sourceTree = SOURCE_ROOT; };
 407                 37D927DE0F21331F001D4494 /* fileoutput.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fileoutput.h; sourceTree = SOURCE_ROOT; };
 408                 37D927DF0F21331F001D4494 /* globaldata.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = globaldata.cpp; sourceTree = SOURCE_ROOT; };
 409                 37D927E00F21331F001D4494 /* globaldata.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = globaldata.hpp; sourceTree = SOURCE_ROOT; };
 410                 37D927E10F21331F001D4494 /* groupmap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = groupmap.cpp; sourceTree = SOURCE_ROOT; };
 411                 37D927E20F21331F001D4494 /* groupmap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = groupmap.h; sourceTree = SOURCE_ROOT; };
 412                 37D927E30F21331F001D4494 /* helpcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = helpcommand.cpp; sourceTree = SOURCE_ROOT; };
 413                 37D927E40F21331F001D4494 /* helpcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = helpcommand.h; sourceTree = SOURCE_ROOT; };
 414                 37D927E50F21331F001D4494 /* inputdata.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = inputdata.cpp; sourceTree = SOURCE_ROOT; };
 415                 37D927E60F21331F001D4494 /* inputdata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = inputdata.h; sourceTree = SOURCE_ROOT; };
 416                 37D927E70F21331F001D4494 /* jackknife.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = jackknife.cpp; sourceTree = SOURCE_ROOT; };
 417                 37D927E80F21331F001D4494 /* jackknife.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = jackknife.h; sourceTree = SOURCE_ROOT; };
 418                 37D927E90F21331F001D4494 /* kmer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = kmer.cpp; sourceTree = SOURCE_ROOT; };
 419                 37D927EA0F21331F001D4494 /* kmer.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = kmer.hpp; sourceTree = SOURCE_ROOT; };
 420                 37D927EB0F21331F001D4494 /* kmerdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = kmerdb.cpp; sourceTree = SOURCE_ROOT; };
 421                 37D927EC0F21331F001D4494 /* kmerdb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = kmerdb.hpp; sourceTree = SOURCE_ROOT; };
 422                 37D927ED0F21331F001D4494 /* listvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = listvector.cpp; sourceTree = SOURCE_ROOT; };
 423                 37D927EE0F21331F001D4494 /* listvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = listvector.hpp; sourceTree = SOURCE_ROOT; };
 424                 37D927EF0F21331F001D4494 /* mothur.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mothur.cpp; sourceTree = SOURCE_ROOT; };
 425                 37D927F00F21331F001D4494 /* nameassignment.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nameassignment.cpp; sourceTree = SOURCE_ROOT; };
 426                 37D927F10F21331F001D4494 /* nameassignment.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = nameassignment.hpp; sourceTree = SOURCE_ROOT; };
 427                 37D927F40F21331F001D4494 /* npshannon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = npshannon.cpp; sourceTree = SOURCE_ROOT; };
 428                 37D927F50F21331F001D4494 /* npshannon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = npshannon.h; sourceTree = SOURCE_ROOT; };
 429                 37D927F60F21331F001D4494 /* observable.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = observable.h; sourceTree = SOURCE_ROOT; };
 430                 37D927F70F21331F001D4494 /* ordervector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ordervector.cpp; sourceTree = SOURCE_ROOT; };
 431                 37D927F80F21331F001D4494 /* ordervector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = ordervector.hpp; sourceTree = SOURCE_ROOT; };
 432                 37D927FB0F21331F001D4494 /* progress.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = progress.cpp; sourceTree = SOURCE_ROOT; };
 433                 37D927FC0F21331F001D4494 /* progress.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = progress.hpp; sourceTree = SOURCE_ROOT; };
 434                 37D927FD0F21331F001D4494 /* quitcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = quitcommand.cpp; sourceTree = SOURCE_ROOT; };
 435                 37D927FE0F21331F001D4494 /* quitcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = quitcommand.h; sourceTree = SOURCE_ROOT; };
 436                 37D927FF0F21331F001D4494 /* rabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rabundvector.cpp; sourceTree = SOURCE_ROOT; };
 437                 37D928000F21331F001D4494 /* rabundvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = rabundvector.hpp; sourceTree = SOURCE_ROOT; };
 438                 37D928010F21331F001D4494 /* rarecalc.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarecalc.cpp; sourceTree = SOURCE_ROOT; };
 439                 37D928020F21331F001D4494 /* rarecalc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarecalc.h; sourceTree = SOURCE_ROOT; };
 440                 37D928030F21331F001D4494 /* raredisplay.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = raredisplay.cpp; sourceTree = SOURCE_ROOT; };
 441                 37D928040F21331F001D4494 /* raredisplay.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = raredisplay.h; sourceTree = SOURCE_ROOT; };
 442                 37D928050F21331F001D4494 /* rarefact.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefact.cpp; sourceTree = SOURCE_ROOT; };
 443                 37D928060F21331F001D4494 /* rarefact.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefact.h; sourceTree = SOURCE_ROOT; };
 444                 37D928070F21331F001D4494 /* rarefactcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefactcommand.cpp; sourceTree = SOURCE_ROOT; };
 445                 37D928080F21331F001D4494 /* rarefactcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactcommand.h; sourceTree = SOURCE_ROOT; };
 446                 37D928090F21331F001D4494 /* rarefactioncurvedata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactioncurvedata.h; sourceTree = SOURCE_ROOT; };
 447                 37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefactsharedcommand.cpp; sourceTree = SOURCE_ROOT; };
 448                 37D9280B0F21331F001D4494 /* rarefactsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactsharedcommand.h; sourceTree = SOURCE_ROOT; };
 449                 37D928130F21331F001D4494 /* readmatrix.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = readmatrix.hpp; sourceTree = SOURCE_ROOT; };
 450                 37D9281A0F21331F001D4494 /* sabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sabundvector.cpp; sourceTree = SOURCE_ROOT; };
 451                 37D9281B0F21331F001D4494 /* sabundvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sabundvector.hpp; sourceTree = SOURCE_ROOT; };
 452                 37D9281C0F21331F001D4494 /* sequence.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sequence.cpp; sourceTree = SOURCE_ROOT; };
 453                 37D9281D0F21331F001D4494 /* sequence.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sequence.hpp; sourceTree = SOURCE_ROOT; };
 454                 37D9281E0F21331F001D4494 /* shannon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shannon.cpp; sourceTree = SOURCE_ROOT; };
 455                 37D9281F0F21331F001D4494 /* shannon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shannon.h; sourceTree = SOURCE_ROOT; };
 456                 37D928220F21331F001D4494 /* sharedace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedace.cpp; sourceTree = SOURCE_ROOT; };
 457                 37D928230F21331F001D4494 /* sharedace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedace.h; sourceTree = SOURCE_ROOT; };
 458                 37D928240F21331F001D4494 /* sharedchao1.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedchao1.cpp; sourceTree = SOURCE_ROOT; };
 459                 37D928250F21331F001D4494 /* sharedchao1.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedchao1.h; sourceTree = SOURCE_ROOT; };
 460                 37D928260F21331F001D4494 /* sharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedcommand.cpp; sourceTree = SOURCE_ROOT; };
 461                 37D928270F21331F001D4494 /* sharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedcommand.h; sourceTree = SOURCE_ROOT; };
 462                 37D928280F21331F001D4494 /* sharedjabund.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjabund.cpp; sourceTree = SOURCE_ROOT; };
 463                 37D928290F21331F001D4494 /* sharedjabund.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjabund.h; sourceTree = SOURCE_ROOT; };
 464                 37D9282A0F21331F001D4494 /* sharedjclass.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjclass.cpp; sourceTree = SOURCE_ROOT; };
 465                 37D9282B0F21331F001D4494 /* sharedjclass.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjclass.h; sourceTree = SOURCE_ROOT; };
 466                 37D9282C0F21331F001D4494 /* sharedjest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjest.cpp; sourceTree = SOURCE_ROOT; };
 467                 37D9282D0F21331F001D4494 /* sharedjest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjest.h; sourceTree = SOURCE_ROOT; };
 468                 37D9282E0F21331F001D4494 /* sharedordervector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedordervector.cpp; sourceTree = SOURCE_ROOT; };
 469                 37D9282F0F21331F001D4494 /* sharedordervector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedordervector.h; sourceTree = SOURCE_ROOT; };
 470                 37D928300F21331F001D4494 /* sharedrabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedrabundvector.cpp; sourceTree = SOURCE_ROOT; };
 471                 37D928310F21331F001D4494 /* sharedrabundvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedrabundvector.h; sourceTree = SOURCE_ROOT; };
 472                 37D928320F21331F001D4494 /* sharedsabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsabundvector.cpp; sourceTree = SOURCE_ROOT; };
 473                 37D928330F21331F001D4494 /* sharedsabundvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsabundvector.h; sourceTree = SOURCE_ROOT; };
 474                 37D928340F21331F001D4494 /* sharedsobs.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsobs.cpp; sourceTree = SOURCE_ROOT; };
 475                 37D928350F21331F001D4494 /* sharedsobs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsobs.h; sourceTree = SOURCE_ROOT; };
 476                 37D928360F21331F001D4494 /* sharedsorabund.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorabund.cpp; sourceTree = SOURCE_ROOT; };
 477                 37D928370F21331F001D4494 /* sharedsorabund.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsorabund.h; sourceTree = SOURCE_ROOT; };
 478                 37D928380F21331F001D4494 /* sharedsorclass.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorclass.cpp; sourceTree = SOURCE_ROOT; };
 479                 37D928390F21331F001D4494 /* sharedsorclass.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsorclass.h; sourceTree = SOURCE_ROOT; };
 480                 37D9283A0F21331F001D4494 /* sharedsorest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorest.cpp; sourceTree = SOURCE_ROOT; };
 481                 37D9283B0F21331F001D4494 /* sharedsorest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsorest.h; sourceTree = SOURCE_ROOT; };
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 506                 37E5F3E20F29FD4200F8D827 /* treenode.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treenode.cpp; sourceTree = SOURCE_ROOT; };
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 508                 37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtreecommand.cpp; sourceTree = SOURCE_ROOT; };
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 520                 7E5A17AE0FE57292003C6A03 /* mergefilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mergefilecommand.cpp; sourceTree = SOURCE_ROOT; };
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 570                 A7E4A823106A9AD700688F62 /* maligner.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = maligner.cpp; sourceTree = SOURCE_ROOT; };
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 572                 C6859E8B029090EE04C91782 /* Mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = Mothur.1; sourceTree = "<group>"; };
 573                 EB1216860F619B83004A865F /* bergerparker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bergerparker.h; sourceTree = SOURCE_ROOT; };
 574                 EB1216870F619B83004A865F /* bergerparker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bergerparker.cpp; sourceTree = SOURCE_ROOT; };
 575                 EB1216E30F61ACFB004A865F /* bstick.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bstick.h; sourceTree = SOURCE_ROOT; };
 576                 EB1216E40F61ACFB004A865F /* bstick.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bstick.cpp; sourceTree = SOURCE_ROOT; };
 577                 EB1217210F61C9AC004A865F /* sharedkstest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedkstest.h; sourceTree = SOURCE_ROOT; };
 578                 EB1217220F61C9AC004A865F /* sharedkstest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedkstest.cpp; sourceTree = SOURCE_ROOT; };
 579                 EB6E68170F5F1C780044E17B /* qstat.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = qstat.h; sourceTree = SOURCE_ROOT; };
 580                 EB6E68180F5F1C780044E17B /* qstat.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = qstat.cpp; sourceTree = SOURCE_ROOT; };
 581                 EB72FE240FC1F5CA0051AC11 /* shen.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shen.cpp; sourceTree = SOURCE_ROOT; };
 582                 EB72FE250FC1F5CA0051AC11 /* shen.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shen.h; sourceTree = SOURCE_ROOT; };
 583                 EB9303E90F534D9400E8EF26 /* logsd.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = logsd.h; sourceTree = SOURCE_ROOT; };
 584                 EB9303EA0F534D9400E8EF26 /* logsd.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = logsd.cpp; sourceTree = SOURCE_ROOT; };
 585                 EB9303F70F53517300E8EF26 /* geom.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = geom.h; sourceTree = SOURCE_ROOT; };
 586                 EB9303F80F53517300E8EF26 /* geom.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = geom.cpp; sourceTree = SOURCE_ROOT; };
 587 /* End PBXFileReference section */
 588
 589 /* Begin PBXFrameworksBuildPhase section */
 590                 8DD76F660486A84900D96B5E /* Frameworks */ = {
 591                         isa = PBXFrameworksBuildPhase;
 592                         buildActionMask = 2147483647;
 593                         files = (
 594                                 A7F5759710CEBC0600E20E47 /* libreadline.a in Frameworks */,
 595                         );
 596                         runOnlyForDeploymentPostprocessing = 0;
 597                 };
 598 /* End PBXFrameworksBuildPhase section */
 599
 600 /* Begin PBXGroup section */
 601                 08FB7794FE84155DC02AAC07 /* Mothur */ = {
 602                         isa = PBXGroup;
 603                         children = (
 604                                 08FB7795FE84155DC02AAC07 /* Source */,
 605                                 C6859E8C029090F304C91782 /* Documentation */,
 606                                 1AB674ADFE9D54B511CA2CBB /* Products */,
 607                         );
 608                         name = Mothur;
 609                         sourceTree = "<group>";
 610                 };
 611                 08FB7795FE84155DC02AAC07 /* Source */ = {
 612                         isa = PBXGroup;
 613                         children = (
 614                                 37D927BA0F21331F001D4494 /* averagelinkage.cpp */,
 615                                 373C68DC0FC1C38D00137ACD /* blastalign.hpp */,
 616                                 373C68DB0FC1C38D00137ACD /* blastalign.cpp */,
 617                                 37D928A60F2133C0001D4494 /* calculators */,
 618                                 374F2FE81006346600E97C66 /* chimera */,
 619                                 A787811210A073F40086103D /* classifiers */,
 620                                 37D927C20F21331F001D4494 /* cluster.hpp */,
 621                                 37D927C10F21331F001D4494 /* cluster.cpp */,
 622                                 37D928A90F2133E5001D4494 /* commands */,
 623                                 37D927C60F21331F001D4494 /* collect.h */,
 624                                 37D927C50F21331F001D4494 /* collect.cpp */,
 625                                 37D927C90F21331F001D4494 /* collectdisplay.h */,
 626                                 37D928AC0F213420001D4494 /* containers */,
 627                                 37D927CA0F21331F001D4494 /* collectorscurvedata.h */,
 628                                 37D927CF0F21331F001D4494 /* commandfactory.hpp */,
 629                                 372E12EC0F264D320095CF7E /* commandfactory.cpp */,
 630                                 37D927D10F21331F001D4494 /* commandoptionparser.hpp */,
 631                                 37D927D00F21331F001D4494 /* commandoptionparser.cpp */,
 632                                 37D927D20F21331F001D4494 /* completelinkage.cpp */,
 633                                 7E4130F70F8E58FA00381DD0 /* dlibshuff.h */,
 634                                 7E4130F60F8E58FA00381DD0 /* dlibshuff.cpp */,
 635                                 37D927D60F21331F001D4494 /* display.h */,
 636                                 37D927D80F21331F001D4494 /* engine.hpp */,
 637                                 37D927D70F21331F001D4494 /* engine.cpp */,
 638                                 37D928B10F213472001D4494 /* errorcheckor */,
 639                                 37D927DE0F21331F001D4494 /* fileoutput.h */,
 640                                 37D927DD0F21331F001D4494 /* fileoutput.cpp */,
 641                                 37D927E00F21331F001D4494 /* globaldata.hpp */,
 642                                 37D927DF0F21331F001D4494 /* globaldata.cpp */,
 643                                 373C68BB0FC1C1A600137ACD /* gotohoverlap.hpp */,
 644                                 373C68BA0FC1C1A600137ACD /* gotohoverlap.cpp */,
 645                                 A729ACE210849BBE00139801 /* hcluster.h */,
 646                                 A729ACE310849BBE00139801 /* hcluster.cpp */,
 647                                 375873ED0F7D646F0040F377 /* heatmap.h */,
 648                                 375873EE0F7D646F0040F377 /* heatmap.cpp */,
 649                                 378598720FDD4C1500EF9D03 /* heatmapsim.h */,
 650                                 378598730FDD4C1500EF9D03 /* heatmapsim.cpp */,
 651                                 37D927E60F21331F001D4494 /* inputdata.h */,
 652                                 37D927E50F21331F001D4494 /* inputdata.cpp */,
 653                                 7E412F420F8D213C00381DD0 /* libshuff.h */,
 654                                 7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */,
 655                                 37E3ED800F4D9D0D00B5DF02 /* mothur.h */,
 656                                 37D927EF0F21331F001D4494 /* mothur.cpp */,
 657                                 373C691E0FC1C98600137ACD /* nast.hpp */,
 658                                 373C691D0FC1C98600137ACD /* nast.cpp */,
 659                                 373C692A0FC1C9EB00137ACD /* nastreport.hpp */,
 660                                 373C69290FC1C9EB00137ACD /* nastreport.cpp */,
 661                                 373C68CE0FC1C2D900137ACD /* needlemanoverlap.hpp */,
 662                                 373C68CD0FC1C2D900137ACD /* needlemanoverlap.cpp */,
 663                                 373C68E40FC1C4A500137ACD /* noalign.hpp */,
 664                                 373C68E30FC1C4A500137ACD /* noalign.cpp */,
 665                                 37D927F60F21331F001D4494 /* observable.h */,
 666                                 3785990E0FDD7E8E00EF9D03 /* optionparser.h */,
 667                                 3785990F0FDD7E8E00EF9D03 /* optionparser.cpp */,
 668                                 373C68C40FC1C25F00137ACD /* overlap.hpp */,
 669                                 373C68C30FC1C25F00137ACD /* overlap.cpp */,
 670                                 37D927FC0F21331F001D4494 /* progress.hpp */,
 671                                 37D927FB0F21331F001D4494 /* progress.cpp */,
 672                                 37D928040F21331F001D4494 /* raredisplay.h */,
 673                                 37D928030F21331F001D4494 /* raredisplay.cpp */,
 674                                 37D928060F21331F001D4494 /* rarefact.h */,
 675                                 37D928050F21331F001D4494 /* rarefact.cpp */,
 676                                 37D928090F21331F001D4494 /* rarefactioncurvedata.h */,
 677                                 3796441D0FB9B9650081FDB6 /* read */,
 678                                 211C38310F961DD400FEE541 /* sharedutilities.h */,
 679                                 211C38300F961DD400FEE541 /* sharedutilities.cpp */,
 680                                 37D928420F21331F001D4494 /* singlelinkage.cpp */,
 681                                 7E412F470F8D21B600381DD0 /* slibshuff.h */,
 682                                 7E412F480F8D21B600381DD0 /* slibshuff.cpp */,
 683                                 37D928480F21331F001D4494 /* summarydata.h */,
 684                                 37D928490F21331F001D4494 /* summarydisplay.h */,
 685                                 37519AB30F810FAE00FED5E8 /* venn.h */,
 686                                 37519AB40F810FAE00FED5E8 /* venn.cpp */,
 687                                 A7F5759610CEBC0600E20E47 /* libreadline.a */,
 688                         );
 689                         name = Source;
 690                         sourceTree = "<group>";
 691                 };
 692                 1AB674ADFE9D54B511CA2CBB /* Products */ = {
 693                         isa = PBXGroup;
 694                         children = (
 695                                 8DD76F6C0486A84900D96B5E /* mothur */,
 696                         );
 697                         name = Products;
 698                         sourceTree = "<group>";
 699                 };
 700                 374F2FE81006346600E97C66 /* chimera */ = {
 701                         isa = PBXGroup;
 702                         children = (
 703                                 374F2FD51006320200E97C66 /* chimera.h */,
 704                                 372095C1103196D70004D347 /* chimera.cpp */,
 705                                 374F2FE9100634B600E97C66 /* bellerophon.h */,
 706                                 374F2FEA100634B600E97C66 /* bellerophon.cpp */,
 707                                 A75B887C104C16860083C454 /* ccode.h */,
 708                                 A75B887B104C16860083C454 /* ccode.cpp */,
 709                                 A7283FF61056CAE100D0CC69 /* chimeracheckrdp.h */,
 710                                 A7283FF71056CAE100D0CC69 /* chimeracheckrdp.cpp */,
 711                                 A7B04491106CC3E60046FC83 /* chimeraslayer.h */,
 712                                 A7B04492106CC3E60046FC83 /* chimeraslayer.cpp */,
 713                                 372A55531017922B00C5194B /* decalc.h */,
 714                                 372A55541017922B00C5194B /* decalc.cpp */,
 715                                 A7E4A822106A9AD700688F62 /* maligner.h */,
 716                                 A7E4A823106A9AD700688F62 /* maligner.cpp */,
 717                                 374F301110063B6F00E97C66 /* pintail.h */,
 718                                 374F301210063B6F00E97C66 /* pintail.cpp */,
 719                                 A7B0450C106CEEC90046FC83 /* slayer.h */,
 720                                 A7B0450D106CEEC90046FC83 /* slayer.cpp */,
 721                         );
 722                         name = chimera;
 723                         sourceTree = "<group>";
 724                 };
 725                 3796441D0FB9B9650081FDB6 /* read */ = {
 726                         isa = PBXGroup;
 727                         children = (
 728                                 A751ACE81098B283003D0911 /* readcluster.h */,
 729                                 A751ACE91098B283003D0911 /* readcluster.cpp */,
 730                                 375AA1340F9E433D008EF9B8 /* readcolumn.h */,
 731                                 375AA1330F9E433D008EF9B8 /* readcolumn.cpp */,
 732                                 37D928130F21331F001D4494 /* readmatrix.hpp */,
 733                                 375AA1360F9E433D008EF9B8 /* readotu.h */,
 734                                 375AA1350F9E433D008EF9B8 /* readotu.cpp */,
 735                                 375AA1380F9E433D008EF9B8 /* readphylip.h */,
 736                                 375AA1370F9E433D008EF9B8 /* readphylip.cpp */,
 737                                 37AD4DC80F28F3DD00AA2D49 /* readtree.h */,
 738                                 37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */,
 739                         );
 740                         name = read;
 741                         sourceTree = "<group>";
 742                 };
 743                 37D928A60F2133C0001D4494 /* calculators */ = {
 744                         isa = PBXGroup;
 745                         children = (
 746                                 37D927BE0F21331F001D4494 /* calculator.h */,
 747                                 37D927BD0F21331F001D4494 /* calculator.cpp */,
 748                                 3792948D0F2E271100B9034A /* treecalculator.h */,
 749                                 37D927B90F21331F001D4494 /* ace.h */,
 750                                 37D927B80F21331F001D4494 /* ace.cpp */,
 751                                 EB1216860F619B83004A865F /* bergerparker.h */,
 752                                 EB1216870F619B83004A865F /* bergerparker.cpp */,
 753                                 373C69950FC1E63600137ACD /* boneh.h */,
 754                                 373C69940FC1E63600137ACD /* boneh.cpp */,
 755                                 37D927BC0F21331F001D4494 /* bootstrap.h */,
 756                                 37D927BB0F21331F001D4494 /* bootstrap.cpp */,
 757                                 EB1216E30F61ACFB004A865F /* bstick.h */,
 758                                 EB1216E40F61ACFB004A865F /* bstick.cpp */,
 759                                 37D927C00F21331F001D4494 /* chao1.h */,
 760                                 37D927BF0F21331F001D4494 /* chao1.cpp */,
 761                                 7EC3D4510FA0FFF900338DA5 /* coverage.h */,
 762                                 7EC3D4500FA0FFF900338DA5 /* coverage.cpp */,
 763                                 37C753DF0FB3492400DBD02E /* dist.h */,
 764                                 37C753F00FB34AE800DBD02E /* eachgapdist.h */,
 765                                 37C753F40FB34C0300DBD02E /* eachgapignore.h */,
 766                                 373C69960FC1E63600137ACD /* efron.cpp */,
 767                                 373C69970FC1E63600137ACD /* efron.h */,
 768                                 379D3D6B0FF917F40068C1C0 /* filters.h */,
 769                                 EB9303F70F53517300E8EF26 /* geom.h */,
 770                                 EB9303F80F53517300E8EF26 /* geom.cpp */,
 771                                 378C1AF10FB0644D004D63F5 /* goodscoverage.h */,
 772                                 378C1AF00FB0644D004D63F5 /* goodscoverage.cpp */,
 773                                 37C753ED0FB34A5700DBD02E /* ignoregaps.h */,
 774                                 37D927E80F21331F001D4494 /* jackknife.h */,
 775                                 37D927E70F21331F001D4494 /* jackknife.cpp */,
 776                                 EB9303E90F534D9400E8EF26 /* logsd.h */,
 777                                 EB9303EA0F534D9400E8EF26 /* logsd.cpp */,
 778                                 375873F90F7D64AB0040F377 /* nseqs.h */,
 779                                 37D927F50F21331F001D4494 /* npshannon.h */,
 780                                 37D927F40F21331F001D4494 /* npshannon.cpp */,
 781                                 37C753F10FB34B4700DBD02E /* onegapdist.h */,
 782                                 37C753F30FB34BBF00DBD02E /* onegapignore.h */,
 783                                 379294880F2E258500B9034A /* parsimony.h */,
 784                                 379294890F2E258500B9034A /* parsimony.cpp */,
 785                                 EB6E68170F5F1C780044E17B /* qstat.h */,
 786                                 EB6E68180F5F1C780044E17B /* qstat.cpp */,
 787                                 37D928020F21331F001D4494 /* rarecalc.h */,
 788                                 37D928010F21331F001D4494 /* rarecalc.cpp */,
 789                                 37D9281F0F21331F001D4494 /* shannon.h */,
 790                                 37D9281E0F21331F001D4494 /* shannon.cpp */,
 791                                 37D928230F21331F001D4494 /* sharedace.h */,
 792                                 37D928220F21331F001D4494 /* sharedace.cpp */,
 793                                 37519A690F80E6EB00FED5E8 /* sharedanderbergs.h */,
 794                                 37519A6A0F80E6EB00FED5E8 /* sharedanderbergs.cpp */,
 795                                 7EC3D4520FA0FFF900338DA5 /* sharedanderberg.h */,
 796                                 375873FB0F7D64DA0040F377 /* sharedbraycurtis.h */,
 797                                 375873FC0F7D64DA0040F377 /* sharedbraycurtis.cpp */,
 798                                 37D928250F21331F001D4494 /* sharedchao1.h */,
 799                                 37D928240F21331F001D4494 /* sharedchao1.cpp */,
 800                                 37D928290F21331F001D4494 /* sharedjabund.h */,
 801                                 37D928280F21331F001D4494 /* sharedjabund.cpp */,
 802                                 378C1B000FB0644D004D63F5 /* sharedjackknife.h */,
 803                                 378C1AFF0FB0644D004D63F5 /* sharedjackknife.cpp */,
 804                                 37D9282B0F21331F001D4494 /* sharedjclass.h */,
 805                                 37D9282A0F21331F001D4494 /* sharedjclass.cpp */,
 806                                 37D9282D0F21331F001D4494 /* sharedjest.h */,
 807                                 37D9282C0F21331F001D4494 /* sharedjest.cpp */,
 808                                 EB1217210F61C9AC004A865F /* sharedkstest.h */,
 809                                 EB1217220F61C9AC004A865F /* sharedkstest.cpp */,
 810                                 375874000F7D64EF0040F377 /* sharedkulczynski.h */,
 811                                 375873FE0F7D64EF0040F377 /* sharedkulczynski.cpp */,
 812                                 375874030F7D64EF0040F377 /* sharedkulczynskicody.h */,
 813                                 375874020F7D64EF0040F377 /* sharedkulczynskicody.cpp */,
 814                                 375874010F7D64EF0040F377 /* sharedlennon.h */,
 815                                 375873FF0F7D64EF0040F377 /* sharedlennon.cpp */,
 816                                 378C1B020FB0644D004D63F5 /* sharedmarczewski.h */,
 817                                 378C1B010FB0644D004D63F5 /* sharedmarczewski.cpp */,
 818                                 375874070F7D64FC0040F377 /* sharedmorisitahorn.h */,
 819                                 375874080F7D64FC0040F377 /* sharedmorisitahorn.cpp */,
 820                                 375874090F7D64FC0040F377 /* sharedochiai.h */,
 821                                 3758740B0F7D64FC0040F377 /* sharedochiai.cpp */,
 822                                 3758740A0F7D64FC0040F377 /* sharednseqs.h */,
 823                                 37D928350F21331F001D4494 /* sharedsobs.h */,
 824                                 37D928340F21331F001D4494 /* sharedsobs.cpp */,
 825                                 37AFC71D0F445386005F492D /* sharedsobscollectsummary.h */,
 826                                 37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */,
 827                                 37D928370F21331F001D4494 /* sharedsorabund.h */,
 828                                 37D928360F21331F001D4494 /* sharedsorabund.cpp */,
 829                                 37D928390F21331F001D4494 /* sharedsorclass.h */,
 830                                 37D928380F21331F001D4494 /* sharedsorclass.cpp */,
 831                                 37D9283B0F21331F001D4494 /* sharedsorest.h */,
 832                                 37D9283A0F21331F001D4494 /* sharedsorest.cpp */,
 833                                 37D9283D0F21331F001D4494 /* sharedthetan.h */,
 834                                 37D9283C0F21331F001D4494 /* sharedthetan.cpp */,
 835                                 37D9283F0F21331F001D4494 /* sharedthetayc.h */,
 836                                 37D9283E0F21331F001D4494 /* sharedthetayc.cpp */,
 837                                 EB72FE250FC1F5CA0051AC11 /* shen.h */,
 838                                 EB72FE240FC1F5CA0051AC11 /* shen.cpp */,
 839                                 37D928410F21331F001D4494 /* simpson.h */,
 840                                 37D928400F21331F001D4494 /* simpson.cpp */,
 841                                 37D928430F21331F001D4494 /* sobs.h */,
 842                                 373C69980FC1E63600137ACD /* solow.cpp */,
 843                                 373C69990FC1E63600137ACD /* solow.h */,
 844                                 374610810F40652400460C57 /* unweighted.h */,
 845                                 374610820F40652400460C57 /* unweighted.cpp */,
 846                                 37D9284E0F21331F001D4494 /* uvest.h */,
 847                                 37D9284D0F21331F001D4494 /* uvest.cpp */,
 848                                 3746107C0F4064D100460C57 /* weighted.h */,
 849                                 3746107D0F4064D100460C57 /* weighted.cpp */,
 850                                 7EC3D4540FA0FFF900338DA5 /* whittaker.h */,
 851                                 7EC3D4530FA0FFF900338DA5 /* whittaker.cpp */,
 852                         );
 853                         name = calculators;
 854                         sourceTree = "<group>";
 855                 };
 856                 37D928A90F2133E5001D4494 /* commands */ = {
 857                         isa = PBXGroup;
 858                         children = (
 859                                 37D927CD0F21331F001D4494 /* command.hpp */,
 860                                 378DC5CD0FBDE1C8003B8607 /* aligncommand.h */,
 861                                 378DC5CE0FBDE1C8003B8607 /* aligncommand.cpp */,
 862                                 37C1D9710F86506E0059E3F0 /* binsequencecommand.h */,
 863                                 37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */,
 864                                 21DDC0190F97A8FE0060691C /* bootstrapsharedcommand.h */,
 865                                 21DDC01A0F97A8FE0060691C /* bootstrapsharedcommand.cpp */,
 866                                 37D927C40F21331F001D4494 /* clustercommand.h */,
 867                                 37D927C30F21331F001D4494 /* clustercommand.cpp */,
 868                                 37D927C80F21331F001D4494 /* collectcommand.h */,
 869                                 37D927C70F21331F001D4494 /* collectcommand.cpp */,
 870                                 37D927CC0F21331F001D4494 /* collectsharedcommand.h */,
 871                                 37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */,
 872                                 377326640FAF16E0007ABB8B /* consensuscommand.h */,
 873                                 377326630FAF16E0007ABB8B /* consensuscommand.cpp */,
 874                                 379D3D4F0FF90E090068C1C0 /* chimeraseqscommand.h */,
 875                                 379D3D500FF90E090068C1C0 /* chimeraseqscommand.cpp */,
 876                                 A7861476109F5FA00010AAAF /* classifyseqscommand.h */,
 877                                 A7861477109F5FA00010AAAF /* classifyseqscommand.cpp */,
 878                                 37B28F660F27590100808A62 /* deconvolutecommand.h */,
 879                                 37B28F670F27590100808A62 /* deconvolutecommand.cpp */,
 880                                 37C753CC0FB3415200DBD02E /* distancecommand.h */,
 881                                 37C753CD0FB3415200DBD02E /* distancecommand.cpp */,
 882                                 378C1AEF0FB0644D004D63F5 /* filterseqscommand.h */,
 883                                 378C1AEE0FB0644D004D63F5 /* filterseqscommand.cpp */,
 884                                 A70B53A50F4CD7AD0064797E /* getgroupcommand.h */,
 885                                 A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */,
 886                                 A70B53A70F4CD7AD0064797E /* getlabelcommand.h */,
 887                                 A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */,
 888                                 A70B53A90F4CD7AD0064797E /* getlinecommand.h */,
 889                                 A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */,
 890                                 A73329CD1083B3B3003B10C5 /* getlistcountcommand.h */,
 891                                 A73329CE1083B3B3003B10C5 /* getlistcountcommand.cpp */,
 892                                 370B88050F8A4EE4005AB382 /* getoturepcommand.h */,
 893                                 370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */,
 894                                 3749273D0FD5956B0031C06B /* getrabundcommand.h */,
 895                                 3749273E0FD5956B0031C06B /* getrabundcommand.cpp */,
 896                                 3749271B0FD58C840031C06B /* getsabundcommand.h */,
 897                                 3749271C0FD58C840031C06B /* getsabundcommand.cpp */,
 898                                 37B73CA41004D89A008C4B41 /* getseqscommand.h */,
 899                                 37B73CA51004D89A008C4B41 /* getseqscommand.cpp */,
 900                                 A7E4A781106913F900688F62 /* getsharedotucommand.h */,
 901                                 A7E4A782106913F900688F62 /* getsharedotucommand.cpp */,
 902                                 A729ACCE10848E6100139801 /* hclustercommand.h */,
 903                                 A729ACCF10848E6100139801 /* hclustercommand.cpp */,
 904                                 375873F10F7D64800040F377 /* heatmapcommand.h */,
 905                                 375873F00F7D64800040F377 /* heatmapcommand.cpp */,
 906                                 378598640FDD497000EF9D03 /* heatmapsimcommand.h */,
 907                                 378598650FDD497000EF9D03 /* heatmapsimcommand.cpp */,
 908                                 37D927E40F21331F001D4494 /* helpcommand.h */,
 909                                 37D927E30F21331F001D4494 /* helpcommand.cpp */,
 910                                 375873F40F7D648F0040F377 /* libshuffcommand.h */,
 911                                 375873F30F7D648F0040F377 /* libshuffcommand.cpp */,
 912                                 37B73C741004BEFD008C4B41 /* listseqscommand.h */,
 913                                 37B73C751004BEFD008C4B41 /* listseqscommand.cpp */,
 914                                 21E859D60FC4632E005E1A48 /* matrixoutputcommand.h */,
 915                                 21E859D70FC4632E005E1A48 /* matrixoutputcommand.cpp */,
 916                                 7E5A17AD0FE57292003C6A03 /* mergefilecommand.h */,
 917                                 7E5A17AE0FE57292003C6A03 /* mergefilecommand.cpp */,
 918                                 375873F70F7D649C0040F377 /* nocommands.h */,
 919                                 375873F60F7D649C0040F377 /* nocommands.cpp */,
 920                                 3792946E0F2E191800B9034A /* parsimonycommand.h */,
 921                                 3792946F0F2E191800B9034A /* parsimonycommand.cpp */,
 922                                 A773808E10B6EFD1002A6A61 /* phylotypecommand.h */,
 923                                 A773808F10B6EFD1002A6A61 /* phylotypecommand.cpp */,
 924                                 37D927FE0F21331F001D4494 /* quitcommand.h */,
 925                                 37D927FD0F21331F001D4494 /* quitcommand.cpp */,
 926                                 37D928080F21331F001D4494 /* rarefactcommand.h */,
 927                                 37D928070F21331F001D4494 /* rarefactcommand.cpp */,
 928                                 37D9280B0F21331F001D4494 /* rarefactsharedcommand.h */,
 929                                 37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */,
 930                                 372E12940F263D5A0095CF7E /* readdistcommand.h */,
 931                                 372E12950F263D5A0095CF7E /* readdistcommand.cpp */,
 932                                 372E126E0F26365B0095CF7E /* readotucommand.h */,
 933                                 372E126F0F26365B0095CF7E /* readotucommand.cpp */,
 934                                 37E5F4900F2A3DA800F8D827 /* readtreecommand.h */,
 935                                 37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */,
 936                                 37B73CBE1004EB38008C4B41 /* removeseqscommand.h */,
 937                                 37B73CBF1004EB38008C4B41 /* removeseqscommand.cpp */,
 938                                 7E09C5120FDA79C5002ECAE5 /* reversecommand.h */,
 939                                 7E09C5130FDA79C5002ECAE5 /* reversecommand.cpp */,
 940                                 A70DECD71063D8B40057C03C /* secondarystructurecommand.h */,
 941                                 A70DECD81063D8B40057C03C /* secondarystructurecommand.cpp */,
 942                                 371B30B30FD7EE67000414CA /* screenseqscommand.h */,
 943                                 371B30B20FD7EE67000414CA /* screenseqscommand.cpp */,
 944                                 3799A94F0FD6A58C00E33EDE /* seqsummarycommand.h */,
 945                                 3799A94E0FD6A58C00E33EDE /* seqsummarycommand.cpp */,
 946                                 37D928270F21331F001D4494 /* sharedcommand.h */,
 947                                 37D928260F21331F001D4494 /* sharedcommand.cpp */,
 948                                 37D928470F21331F001D4494 /* summarycommand.h */,
 949                                 37D928460F21331F001D4494 /* summarycommand.cpp */,
 950                                 37D9284B0F21331F001D4494 /* summarysharedcommand.h */,
 951                                 37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */,
 952                                 37B73CCD1004F5E0008C4B41 /* systemcommand.h */,
 953                                 37B73CCE1004F5E0008C4B41 /* systemcommand.cpp */,
 954                                 211C38370F961E1F00FEE541 /* treegroupscommand.h */,
 955                                 211C38360F961E1F00FEE541 /* treegroupscommand.cpp */,
 956                                 7E09C5340FDA7F65002ECAE5 /* trimseqscommand.h */,
 957                                 7E09C5350FDA7F65002ECAE5 /* trimseqscommand.cpp */,
 958                                 3746109B0F40657600460C57 /* unifracunweightedcommand.h */,
 959                                 3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */,
 960                                 374610760F40645300460C57 /* unifracweightedcommand.h */,
 961                                 374610770F40645300460C57 /* unifracweightedcommand.cpp */,
 962                                 37519A9F0F810D0200FED5E8 /* venncommand.h */,
 963                                 37519AA00F810D0200FED5E8 /* venncommand.cpp */,
 964                         );
 965                         name = commands;
 966                         sourceTree = "<group>";
 967                 };
 968                 37D928AC0F213420001D4494 /* containers */ = {
 969                         isa = PBXGroup;
 970                         children = (
 971                                 373C68A10FC1C07D00137ACD /* alignment.hpp */,
 972                                 373C68A00FC1C07D00137ACD /* alignment.cpp */,
 973                                 373C68A30FC1C07D00137ACD /* alignmentcell.hpp */,
 974                                 373C68A20FC1C07D00137ACD /* alignmentcell.cpp */,
 975                                 A78782A910A1B1CB0086103D /* alignmentdb.h */,
 976                                 A78782AA10A1B1CB0086103D /* alignmentdb.cpp */,
 977                                 373C69170FC1C8AF00137ACD /* blastdb.hpp */,
 978                                 373C69160FC1C8AF00137ACD /* blastdb.cpp */,
 979                                 37D927D40F21331F001D4494 /* database.hpp */,
 980                                 37D927D30F21331F001D4494 /* database.cpp */,
 981                                 37D927D50F21331F001D4494 /* datavector.hpp */,
 982                                 37D927DC0F21331F001D4494 /* fastamap.h */,
 983                                 37D927DB0F21331F001D4494 /* fastamap.cpp */,
 984                                 375873EA0F7D64520040F377 /* fullmatrix.h */,
 985                                 375873EB0F7D64520040F377 /* fullmatrix.cpp */,
 986                                 37D927E20F21331F001D4494 /* groupmap.h */,
 987                                 37D927E10F21331F001D4494 /* groupmap.cpp */,
 988                                 37D927EA0F21331F001D4494 /* kmer.hpp */,
 989                                 37D927E90F21331F001D4494 /* kmer.cpp */,
 990                                 37D927EC0F21331F001D4494 /* kmerdb.hpp */,
 991                                 37D927EB0F21331F001D4494 /* kmerdb.cpp */,
 992                                 37D927EE0F21331F001D4494 /* listvector.hpp */,
 993                                 37D927ED0F21331F001D4494 /* listvector.cpp */,
 994                                 37D927F10F21331F001D4494 /* nameassignment.hpp */,
 995                                 37D927F00F21331F001D4494 /* nameassignment.cpp */,
 996                                 37D927F80F21331F001D4494 /* ordervector.hpp */,
 997                                 37D927F70F21331F001D4494 /* ordervector.cpp */,
 998                                 37D928000F21331F001D4494 /* rabundvector.hpp */,
 999                                 37D927FF0F21331F001D4494 /* rabundvector.cpp */,
1000                                 37D9281B0F21331F001D4494 /* sabundvector.hpp */,
1001                                 37D9281A0F21331F001D4494 /* sabundvector.cpp */,
1002                                 37D9281D0F21331F001D4494 /* sequence.hpp */,
1003                                 37D9281C0F21331F001D4494 /* sequence.cpp */,
1004                                 378C1AFE0FB0644D004D63F5 /* sequencedb.h */,
1005                                 378C1AFD0FB0644D004D63F5 /* sequencedb.cpp */,
1006                                 37AD4CE20F28AEA300AA2D49 /* sharedlistvector.h */,
1007                                 37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */,
1008                                 37D9282F0F21331F001D4494 /* sharedordervector.h */,
1009                                 37D9282E0F21331F001D4494 /* sharedordervector.cpp */,
1010                                 37D928310F21331F001D4494 /* sharedrabundvector.h */,
1011                                 37D928300F21331F001D4494 /* sharedrabundvector.cpp */,
1012                                 37D928330F21331F001D4494 /* sharedsabundvector.h */,
1013                                 37D928320F21331F001D4494 /* sharedsabundvector.cpp */,
1014                                 37D928450F21331F001D4494 /* sparsematrix.hpp */,
1015                                 37D928440F21331F001D4494 /* sparsematrix.cpp */,
1016                                 373C68F40FC1C6A800137ACD /* suffixdb.hpp */,
1017                                 373C68F30FC1C6A800137ACD /* suffixdb.cpp */,
1018                                 373C68F60FC1C6A800137ACD /* suffixnodes.hpp */,
1019                                 373C68F50FC1C6A800137ACD /* suffixnodes.cpp */,
1020                                 373C68F80FC1C6A800137ACD /* suffixtree.hpp */,
1021                                 373C68F70FC1C6A800137ACD /* suffixtree.cpp */,
1022                                 37AD4DB90F28E2FE00AA2D49 /* tree.h */,
1023                                 37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */,
1024                                 379293C10F2DE73400B9034A /* treemap.h */,
1025                                 379293C20F2DE73400B9034A /* treemap.cpp */,
1026                                 37E5F3E10F29FD4200F8D827 /* treenode.h */,
1027                                 37E5F3E20F29FD4200F8D827 /* treenode.cpp */,
1028                         );
1029                         name = containers;
1030                         sourceTree = "<group>";
1031                 };
1032                 37D928B10F213472001D4494 /* errorcheckor */ = {
1033                         isa = PBXGroup;
1034                         children = (
1035                                 37D928500F21331F001D4494 /* validcalculator.h */,
1036                                 37D9284F0F21331F001D4494 /* validcalculator.cpp */,
1037                                 37D928540F21331F001D4494 /* validparameter.h */,
1038                                 37D928530F21331F001D4494 /* validparameter.cpp */,
1039                         );
1040                         name = errorcheckor;
1041                         sourceTree = "<group>";
1042                 };
1043                 A787811210A073F40086103D /* classifiers */ = {
1044                         isa = PBXGroup;
1045                         children = (
1046                                 A78780FE10A06B8B0086103D /* classify.h */,
1047                                 A787810210A06D5D0086103D /* classify.cpp */,
1048                                 A787820F10A0AAE70086103D /* bayesian.h */,
1049                                 A787821010A0AAE70086103D /* bayesian.cpp */,
1050                                 A773805D10B6D6FC002A6A61 /* taxonomyequalizer.h */,
1051                                 A773805E10B6D6FC002A6A61 /* taxonomyequalizer.cpp */,
1052                                 A78781B910A0813D0086103D /* phylotree.h */,
1053                                 A78781B810A0813D0086103D /* phylotree.cpp */,
1054                                 A787844310A1EBDD0086103D /* knn.h */,
1055                                 A787844410A1EBDD0086103D /* knn.cpp */,
1056                         );
1057                         name = classifiers;
1058                         sourceTree = "<group>";
1059                 };
1060                 C6859E8C029090F304C91782 /* Documentation */ = {
1061                         isa = PBXGroup;
1062                         children = (
1063                                 C6859E8B029090EE04C91782 /* Mothur.1 */,
1064                         );
1065                         name = Documentation;
1066                         sourceTree = "<group>";
1067                 };
1068 /* End PBXGroup section */
1069
1070 /* Begin PBXNativeTarget section */
1071                 8DD76F620486A84900D96B5E /* mothur */ = {
1072                         isa = PBXNativeTarget;
1073                         buildConfigurationList = 1DEB923108733DC60010E9CD /* Build configuration list for PBXNativeTarget "mothur" */;
1074                         buildPhases = (
1075                                 8DD76F640486A84900D96B5E /* Sources */,
1076                                 8DD76F660486A84900D96B5E /* Frameworks */,
1077                                 8DD76F690486A84900D96B5E /* CopyFiles */,
1078                         );
1079                         buildRules = (
1080                         );
1081                         dependencies = (
1082                         );
1083                         name = mothur;
1084                         productInstallPath = "$(HOME)/bin";
1085                         productName = Mothur;
1086                         productReference = 8DD76F6C0486A84900D96B5E /* mothur */;
1087                         productType = "com.apple.product-type.tool";
1088                 };
1089 /* End PBXNativeTarget section */
1090
1091 /* Begin PBXProject section */
1092                 08FB7793FE84155DC02AAC07 /* Project object */ = {
1093                         isa = PBXProject;
1094                         buildConfigurationList = 1DEB923508733DC60010E9CD /* Build configuration list for PBXProject "Mothur" */;
1095                         compatibilityVersion = "Xcode 3.0";
1096                         hasScannedForEncodings = 1;
1097                         mainGroup = 08FB7794FE84155DC02AAC07 /* Mothur */;
1098                         projectDirPath = "";
1099                         projectRoot = "";
1100                         targets = (
1101                                 8DD76F620486A84900D96B5E /* mothur */,
1102                         );
1103                 };
1104 /* End PBXProject section */
1105
1106 /* Begin PBXSourcesBuildPhase section */
1107                 8DD76F640486A84900D96B5E /* Sources */ = {
1108                         isa = PBXSourcesBuildPhase;
1109                         buildActionMask = 2147483647;
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1114                                 37D928580F21331F001D4494 /* calculator.cpp in Sources */,
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1118                                 37D9285C0F21331F001D4494 /* collect.cpp in Sources */,
1119                                 37D9285D0F21331F001D4494 /* collectcommand.cpp in Sources */,
1120                                 37D9285E0F21331F001D4494 /* collectsharedcommand.cpp in Sources */,
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1124                                 37D928630F21331F001D4494 /* engine.cpp in Sources */,
1125                                 37D928650F21331F001D4494 /* fastamap.cpp in Sources */,
1126                                 37D928660F21331F001D4494 /* fileoutput.cpp in Sources */,
1127                                 37D928670F21331F001D4494 /* globaldata.cpp in Sources */,
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1148                                 37D928850F21331F001D4494 /* sequence.cpp in Sources */,
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1151                                 37D928890F21331F001D4494 /* sharedchao1.cpp in Sources */,
1152                                 37D9288A0F21331F001D4494 /* sharedcommand.cpp in Sources */,
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1154                                 37D9288C0F21331F001D4494 /* sharedjclass.cpp in Sources */,
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1156                                 37D9288E0F21331F001D4494 /* sharedordervector.cpp in Sources */,
1157                                 37D9288F0F21331F001D4494 /* sharedrabundvector.cpp in Sources */,
1158                                 37D928900F21331F001D4494 /* sharedsabundvector.cpp in Sources */,
1159                                 37D928910F21331F001D4494 /* sharedsobs.cpp in Sources */,
1160                                 37D928920F21331F001D4494 /* sharedsorabund.cpp in Sources */,
1161                                 37D928930F21331F001D4494 /* sharedsorclass.cpp in Sources */,
1162                                 37D928940F21331F001D4494 /* sharedsorest.cpp in Sources */,
1163                                 37D928950F21331F001D4494 /* sharedthetan.cpp in Sources */,
1164                                 37D928960F21331F001D4494 /* sharedthetayc.cpp in Sources */,
1165                                 37D928970F21331F001D4494 /* simpson.cpp in Sources */,
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1167                                 37D928990F21331F001D4494 /* sparsematrix.cpp in Sources */,
1168                                 37D9289A0F21331F001D4494 /* summarycommand.cpp in Sources */,
1169                                 37D9289B0F21331F001D4494 /* summarysharedcommand.cpp in Sources */,
1170                                 37D9289C0F21331F001D4494 /* uvest.cpp in Sources */,
1171                                 37D9289D0F21331F001D4494 /* validcalculator.cpp in Sources */,
1172                                 37D9289F0F21331F001D4494 /* validparameter.cpp in Sources */,
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1177                                 37AD4CE40F28AEA300AA2D49 /* sharedlistvector.cpp in Sources */,
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1179                                 37AD4DCA0F28F3DD00AA2D49 /* readtree.cpp in Sources */,
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1185                                 374610780F40645300460C57 /* unifracweightedcommand.cpp in Sources */,
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1192                                 A70B53AC0F4CD7AD0064797E /* getlinecommand.cpp in Sources */,
1193                                 EB9303EB0F534D9400E8EF26 /* logsd.cpp in Sources */,
1194                                 EB9303F90F53517300E8EF26 /* geom.cpp in Sources */,
1195                                 EB6E68190F5F1C780044E17B /* qstat.cpp in Sources */,
1196                                 EB1216880F619B83004A865F /* bergerparker.cpp in Sources */,
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1199                                 375873EC0F7D64520040F377 /* fullmatrix.cpp in Sources */,
1200                                 375873EF0F7D646F0040F377 /* heatmap.cpp in Sources */,
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1279                                 A729ACD010848E6100139801 /* hclustercommand.cpp in Sources */,
1280                                 A729ACE410849BBE00139801 /* hcluster.cpp in Sources */,
1281                                 A751ACEA1098B283003D0911 /* readcluster.cpp in Sources */,
1282                                 A7861478109F5FA00010AAAF /* classifyseqscommand.cpp in Sources */,
1283                                 A787810310A06D5D0086103D /* classify.cpp in Sources */,
1284                                 A78781BA10A0813E0086103D /* phylotree.cpp in Sources */,
1285                                 A787821110A0AAE70086103D /* bayesian.cpp in Sources */,
1286                                 A78782AB10A1B1CB0086103D /* alignmentdb.cpp in Sources */,
1287                                 A787844510A1EBDD0086103D /* knn.cpp in Sources */,
1288                                 A773805F10B6D6FC002A6A61 /* taxonomyequalizer.cpp in Sources */,
1289                                 A773809010B6EFD1002A6A61 /* phylotypecommand.cpp in Sources */,
1290                         );
1291                         runOnlyForDeploymentPostprocessing = 0;
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1293 /* End PBXSourcesBuildPhase section */
1294
1295 /* Begin XCBuildConfiguration section */
1296                 1DEB923208733DC60010E9CD /* Debug */ = {
1297                         isa = XCBuildConfiguration;
1298                         buildSettings = {
1299                                 COPY_PHASE_STRIP = NO;
1300                                 GCC_DYNAMIC_NO_PIC = NO;
1301                                 GCC_ENABLE_FIX_AND_CONTINUE = YES;
1302                                 GCC_MODEL_TUNING = G5;
1303                                 GCC_OPTIMIZATION_LEVEL = 0;
1304                                 GCC_PREPROCESSOR_DEFINITIONS = (
1305                                         "_GLIBCXX_DEBUG=1",
1306                                         "_GLIBCXX_DEBUG_PEDANTIC=1",
1307                                 );
1308                                 INSTALL_PATH = /usr/local/bin;
1309                                 LIBRARY_SEARCH_PATHS = (
1310                                         "$(inherited)",
1311                                         "\"$(SRCROOT)/../readline-6.0\"",
1312                                 );
1313                                 PRODUCT_NAME = mothur;
1314                                 ZERO_LINK = YES;
1315                         };
1316                         name = Debug;
1317                 };
1318                 1DEB923308733DC60010E9CD /* Release */ = {
1319                         isa = XCBuildConfiguration;
1320                         buildSettings = {
1321                                 DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym";
1322                                 GCC_MODEL_TUNING = G5;
1323                                 INSTALL_PATH = /usr/local/bin;
1324                                 LIBRARY_SEARCH_PATHS = (
1325                                         "$(inherited)",
1326                                         "\"$(SRCROOT)/../readline-6.0\"",
1327                                 );
1328                                 PRODUCT_NAME = mothur;
1329                         };
1330                         name = Release;
1331                 };
1332                 1DEB923608733DC60010E9CD /* Debug */ = {
1333                         isa = XCBuildConfiguration;
1334                         buildSettings = {
1335                                 GCC_OPTIMIZATION_LEVEL = 3;
1336                                 GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
1337                                 GCC_WARN_ABOUT_RETURN_TYPE = YES;
1338                                 GCC_WARN_ALLOW_INCOMPLETE_PROTOCOL = NO;
1339                                 GCC_WARN_PEDANTIC = NO;
1340                                 GCC_WARN_UNUSED_VARIABLE = YES;
1341                                 OTHER_CPLUSPLUSFLAGS = "";
1342                                 PREBINDING = NO;
1343                                 SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
1344                                 WARNING_CFLAGS = "";
1345                         };
1346                         name = Debug;
1347                 };
1348                 1DEB923708733DC60010E9CD /* Release */ = {
1349                         isa = XCBuildConfiguration;
1350                         buildSettings = {
1351                                 ARCHS = (
1352                                         ppc,
1353                                         i386,
1354                                 );
1355                                 GCC_OPTIMIZATION_LEVEL = 3;
1356                                 GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
1357                                 GCC_WARN_ABOUT_MISSING_PROTOTYPES = YES;
1358                                 GCC_WARN_ABOUT_RETURN_TYPE = YES;
1359                                 GCC_WARN_ALLOW_INCOMPLETE_PROTOCOL = NO;
1360                                 GCC_WARN_MISSING_PARENTHESES = YES;
1361                                 GCC_WARN_PEDANTIC = YES;
1362                                 GCC_WARN_UNUSED_FUNCTION = YES;
1363                                 GCC_WARN_UNUSED_PARAMETER = NO;
1364                                 GCC_WARN_UNUSED_VALUE = YES;
1365                                 GCC_WARN_UNUSED_VARIABLE = YES;
1366                                 OTHER_CPLUSPLUSFLAGS = (
1367                                         "-ansi",
1368                                         "-pedantic",
1369                                         "-wall",
1370                                         "-lreadline",
1371                                         "-DUSE_READLINE",
1372                                 );
1373                                 PREBINDING = NO;
1374                                 SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
1375                                 SYMROOT = /Users/johnwestcott/Desktop;
1376                                 WARNING_CFLAGS = "";
1377                         };
1378                         name = Release;
1379                 };
1380 /* End XCBuildConfiguration section */
1381
1382 /* Begin XCConfigurationList section */
1383                 1DEB923108733DC60010E9CD /* Build configuration list for PBXNativeTarget "mothur" */ = {
1384                         isa = XCConfigurationList;
1385                         buildConfigurations = (
1386                                 1DEB923208733DC60010E9CD /* Debug */,
1387                                 1DEB923308733DC60010E9CD /* Release */,
1388                         );
1389                         defaultConfigurationIsVisible = 0;
1390                         defaultConfigurationName = Release;
1391                 };
1392                 1DEB923508733DC60010E9CD /* Build configuration list for PBXProject "Mothur" */ = {
1393                         isa = XCConfigurationList;
1394                         buildConfigurations = (
1395                                 1DEB923608733DC60010E9CD /* Debug */,
1396                                 1DEB923708733DC60010E9CD /* Release */,
1397                         );
1398                         defaultConfigurationIsVisible = 0;
1399                         defaultConfigurationName = Release;
1400                 };
1401 /* End XCConfigurationList section */
1402         };
1403         rootObject = 08FB7793FE84155DC02AAC07 /* Project object */;
1404 }