Mothur.xcodeproj/project.pbxproj

   1 // !$*UTF8*$!
   2 {
   3         archiveVersion = 1;
   4         classes = {
   5         };
   6         objectVersion = 44;
   7         objects = {
   8
   9 /* Begin PBXBuildFile section */
  10                 372E12700F26365B0095CF7E /* readotucommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 372E126F0F26365B0095CF7E /* readotucommand.cpp */; };
  11                 372E12960F263D5A0095CF7E /* readdistcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 372E12950F263D5A0095CF7E /* readdistcommand.cpp */; };
  12                 372E12ED0F264D320095CF7E /* commandfactory.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 372E12EC0F264D320095CF7E /* commandfactory.cpp */; };
  13                 374610780F40645300460C57 /* unifracweightedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 374610770F40645300460C57 /* unifracweightedcommand.cpp */; };
  14                 3746107E0F4064D100460C57 /* weighted.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3746107D0F4064D100460C57 /* weighted.cpp */; };
  15                 374610830F40652400460C57 /* unweighted.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 374610820F40652400460C57 /* unweighted.cpp */; };
  16                 3746109D0F40657600460C57 /* unifracunweightedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */; };
  17                 374CD63F0F65832000D90B4A /* libshuffcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 374CD63E0F65832000D90B4A /* libshuffcommand.cpp */; };
  18                 3782163D0F616079008E1F6D /* fullmatrix.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3782163C0F616079008E1F6D /* fullmatrix.cpp */; };
  19                 379293C30F2DE73400B9034A /* treemap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 379293C20F2DE73400B9034A /* treemap.cpp */; };
  20                 379294700F2E191800B9034A /* parsimonycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3792946F0F2E191800B9034A /* parsimonycommand.cpp */; };
  21                 3792948A0F2E258500B9034A /* parsimony.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 379294890F2E258500B9034A /* parsimony.cpp */; };
  22                 37AD4CE40F28AEA300AA2D49 /* sharedlistvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */; };
  23                 37AD4DBB0F28E2FE00AA2D49 /* tree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */; };
  24                 37AD4DCA0F28F3DD00AA2D49 /* readtree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */; };
  25                 37AFC71F0F445386005F492D /* sharedsobscollectsummary.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */; };
  26                 37B28F680F27590100808A62 /* deconvolutecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37B28F670F27590100808A62 /* deconvolutecommand.cpp */; };
  27                 37D928550F21331F001D4494 /* ace.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927B80F21331F001D4494 /* ace.cpp */; };
  28                 37D928560F21331F001D4494 /* averagelinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927BA0F21331F001D4494 /* averagelinkage.cpp */; };
  29                 37D928570F21331F001D4494 /* bootstrap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927BB0F21331F001D4494 /* bootstrap.cpp */; };
  30                 37D928580F21331F001D4494 /* calculator.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927BD0F21331F001D4494 /* calculator.cpp */; };
  31                 37D928590F21331F001D4494 /* chao1.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927BF0F21331F001D4494 /* chao1.cpp */; };
  32                 37D9285A0F21331F001D4494 /* cluster.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927C10F21331F001D4494 /* cluster.cpp */; };
  33                 37D9285B0F21331F001D4494 /* clustercommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927C30F21331F001D4494 /* clustercommand.cpp */; };
  34                 37D9285C0F21331F001D4494 /* collect.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927C50F21331F001D4494 /* collect.cpp */; };
  35                 37D9285D0F21331F001D4494 /* collectcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927C70F21331F001D4494 /* collectcommand.cpp */; };
  36                 37D9285E0F21331F001D4494 /* collectsharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */; };
  37                 37D928600F21331F001D4494 /* commandoptionparser.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927D00F21331F001D4494 /* commandoptionparser.cpp */; };
  38                 37D928610F21331F001D4494 /* completelinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927D20F21331F001D4494 /* completelinkage.cpp */; };
  39                 37D928620F21331F001D4494 /* database.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927D30F21331F001D4494 /* database.cpp */; };
  40                 37D928630F21331F001D4494 /* engine.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927D70F21331F001D4494 /* engine.cpp */; };
  41                 37D928640F21331F001D4494 /* errorchecking.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927D90F21331F001D4494 /* errorchecking.cpp */; };
  42                 37D928650F21331F001D4494 /* fastamap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927DB0F21331F001D4494 /* fastamap.cpp */; };
  43                 37D928660F21331F001D4494 /* fileoutput.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927DD0F21331F001D4494 /* fileoutput.cpp */; };
  44                 37D928670F21331F001D4494 /* globaldata.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927DF0F21331F001D4494 /* globaldata.cpp */; };
  45                 37D928680F21331F001D4494 /* groupmap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927E10F21331F001D4494 /* groupmap.cpp */; };
  46                 37D928690F21331F001D4494 /* helpcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927E30F21331F001D4494 /* helpcommand.cpp */; };
  47                 37D9286A0F21331F001D4494 /* inputdata.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927E50F21331F001D4494 /* inputdata.cpp */; };
  48                 37D9286B0F21331F001D4494 /* jackknife.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927E70F21331F001D4494 /* jackknife.cpp */; };
  49                 37D9286C0F21331F001D4494 /* kmer.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927E90F21331F001D4494 /* kmer.cpp */; };
  50                 37D9286D0F21331F001D4494 /* kmerdb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927EB0F21331F001D4494 /* kmerdb.cpp */; };
  51                 37D9286E0F21331F001D4494 /* listvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927ED0F21331F001D4494 /* listvector.cpp */; };
  52                 37D9286F0F21331F001D4494 /* mothur.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927EF0F21331F001D4494 /* mothur.cpp */; };
  53                 37D928700F21331F001D4494 /* nameassignment.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927F00F21331F001D4494 /* nameassignment.cpp */; };
  54                 37D928710F21331F001D4494 /* nocommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927F20F21331F001D4494 /* nocommand.cpp */; };
  55                 37D928720F21331F001D4494 /* npshannon.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927F40F21331F001D4494 /* npshannon.cpp */; };
  56                 37D928730F21331F001D4494 /* ordervector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927F70F21331F001D4494 /* ordervector.cpp */; };
  57                 37D928740F21331F001D4494 /* parselistcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927F90F21331F001D4494 /* parselistcommand.cpp */; };
  58                 37D928750F21331F001D4494 /* progress.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927FB0F21331F001D4494 /* progress.cpp */; };
  59                 37D928760F21331F001D4494 /* quitcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927FD0F21331F001D4494 /* quitcommand.cpp */; };
  60                 37D928770F21331F001D4494 /* rabundvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927FF0F21331F001D4494 /* rabundvector.cpp */; };
  61                 37D928780F21331F001D4494 /* rarecalc.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928010F21331F001D4494 /* rarecalc.cpp */; };
  62                 37D928790F21331F001D4494 /* raredisplay.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928030F21331F001D4494 /* raredisplay.cpp */; };
  63                 37D9287A0F21331F001D4494 /* rarefact.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928050F21331F001D4494 /* rarefact.cpp */; };
  64                 37D9287B0F21331F001D4494 /* rarefactcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928070F21331F001D4494 /* rarefactcommand.cpp */; };
  65                 37D9287C0F21331F001D4494 /* rarefactsharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */; };
  66                 37D928800F21331F001D4494 /* readmatrix.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928120F21331F001D4494 /* readmatrix.cpp */; };
  67                 37D928840F21331F001D4494 /* sabundvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9281A0F21331F001D4494 /* sabundvector.cpp */; };
  68                 37D928850F21331F001D4494 /* sequence.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9281C0F21331F001D4494 /* sequence.cpp */; };
  69                 37D928860F21331F001D4494 /* shannon.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9281E0F21331F001D4494 /* shannon.cpp */; };
  70                 37D928870F21331F001D4494 /* shared.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928200F21331F001D4494 /* shared.cpp */; };
  71                 37D928880F21331F001D4494 /* sharedace.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928220F21331F001D4494 /* sharedace.cpp */; };
  72                 37D928890F21331F001D4494 /* sharedchao1.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928240F21331F001D4494 /* sharedchao1.cpp */; };
  73                 37D9288A0F21331F001D4494 /* sharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928260F21331F001D4494 /* sharedcommand.cpp */; };
  74                 37D9288B0F21331F001D4494 /* sharedjabund.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928280F21331F001D4494 /* sharedjabund.cpp */; };
  75                 37D9288C0F21331F001D4494 /* sharedjclass.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9282A0F21331F001D4494 /* sharedjclass.cpp */; };
  76                 37D9288D0F21331F001D4494 /* sharedjest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9282C0F21331F001D4494 /* sharedjest.cpp */; };
  77                 37D9288E0F21331F001D4494 /* sharedordervector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9282E0F21331F001D4494 /* sharedordervector.cpp */; };
  78                 37D9288F0F21331F001D4494 /* sharedrabundvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928300F21331F001D4494 /* sharedrabundvector.cpp */; };
  79                 37D928900F21331F001D4494 /* sharedsabundvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928320F21331F001D4494 /* sharedsabundvector.cpp */; };
  80                 37D928910F21331F001D4494 /* sharedsobs.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928340F21331F001D4494 /* sharedsobs.cpp */; };
  81                 37D928920F21331F001D4494 /* sharedsorabund.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928360F21331F001D4494 /* sharedsorabund.cpp */; };
  82                 37D928930F21331F001D4494 /* sharedsorclass.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928380F21331F001D4494 /* sharedsorclass.cpp */; };
  83                 37D928940F21331F001D4494 /* sharedsorest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9283A0F21331F001D4494 /* sharedsorest.cpp */; };
  84                 37D928950F21331F001D4494 /* sharedthetan.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9283C0F21331F001D4494 /* sharedthetan.cpp */; };
  85                 37D928960F21331F001D4494 /* sharedthetayc.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9283E0F21331F001D4494 /* sharedthetayc.cpp */; };
  86                 37D928970F21331F001D4494 /* simpson.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928400F21331F001D4494 /* simpson.cpp */; };
  87                 37D928980F21331F001D4494 /* singlelinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928420F21331F001D4494 /* singlelinkage.cpp */; };
  88                 37D928990F21331F001D4494 /* sparsematrix.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928440F21331F001D4494 /* sparsematrix.cpp */; };
  89                 37D9289A0F21331F001D4494 /* summarycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928460F21331F001D4494 /* summarycommand.cpp */; };
  90                 37D9289B0F21331F001D4494 /* summarysharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */; };
  91                 37D9289C0F21331F001D4494 /* uvest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9284D0F21331F001D4494 /* uvest.cpp */; };
  92                 37D9289D0F21331F001D4494 /* validcalculator.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9284F0F21331F001D4494 /* validcalculator.cpp */; };
  93                 37D9289E0F21331F001D4494 /* validcommands.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928510F21331F001D4494 /* validcommands.cpp */; };
  94                 37D9289F0F21331F001D4494 /* validparameter.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928530F21331F001D4494 /* validparameter.cpp */; };
  95                 37E5F3E30F29FD4200F8D827 /* treenode.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37E5F3E20F29FD4200F8D827 /* treenode.cpp */; };
  96                 37E5F4920F2A3DA800F8D827 /* readtreecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */; };
  97                 8DD76F6A0486A84900D96B5E /* Mothur.1 in CopyFiles */ = {isa = PBXBuildFile; fileRef = C6859E8B029090EE04C91782 /* Mothur.1 */; };
  98                 A70B53AA0F4CD7AD0064797E /* getgroupcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */; };
  99                 A70B53AB0F4CD7AD0064797E /* getlabelcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */; };
 100                 A70B53AC0F4CD7AD0064797E /* getlinecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */; };
 101 /* End PBXBuildFile section */
 102
 103 /* Begin PBXCopyFilesBuildPhase section */
 104                 8DD76F690486A84900D96B5E /* CopyFiles */ = {
 105                         isa = PBXCopyFilesBuildPhase;
 106                         buildActionMask = 8;
 107                         dstPath = /usr/share/man/man1/;
 108                         dstSubfolderSpec = 0;
 109                         files = (
 110                                 8DD76F6A0486A84900D96B5E /* Mothur.1 in CopyFiles */,
 111                         );
 112                         runOnlyForDeploymentPostprocessing = 1;
 113                 };
 114 /* End PBXCopyFilesBuildPhase section */
 115
 116 /* Begin PBXFileReference section */
 117                 372E126E0F26365B0095CF7E /* readotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotucommand.h; sourceTree = "<group>"; };
 118                 372E126F0F26365B0095CF7E /* readotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readotucommand.cpp; sourceTree = "<group>"; };
 119                 372E12940F263D5A0095CF7E /* readdistcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readdistcommand.h; sourceTree = "<group>"; };
 120                 372E12950F263D5A0095CF7E /* readdistcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readdistcommand.cpp; sourceTree = "<group>"; };
 121                 372E12EC0F264D320095CF7E /* commandfactory.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = commandfactory.cpp; sourceTree = "<group>"; };
 122                 374610760F40645300460C57 /* unifracweightedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unifracweightedcommand.h; sourceTree = "<group>"; };
 123                 374610770F40645300460C57 /* unifracweightedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unifracweightedcommand.cpp; sourceTree = "<group>"; };
 124                 3746107C0F4064D100460C57 /* weighted.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = weighted.h; sourceTree = "<group>"; };
 125                 3746107D0F4064D100460C57 /* weighted.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = weighted.cpp; sourceTree = "<group>"; };
 126                 374610810F40652400460C57 /* unweighted.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unweighted.h; sourceTree = "<group>"; };
 127                 374610820F40652400460C57 /* unweighted.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unweighted.cpp; sourceTree = "<group>"; };
 128                 3746109B0F40657600460C57 /* unifracunweightedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unifracunweightedcommand.h; sourceTree = "<group>"; };
 129                 3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unifracunweightedcommand.cpp; sourceTree = "<group>"; };
 130                 374CD63D0F65832000D90B4A /* libshuffcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = libshuffcommand.h; sourceTree = "<group>"; };
 131                 374CD63E0F65832000D90B4A /* libshuffcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = libshuffcommand.cpp; sourceTree = "<group>"; };
 132                 3782163B0F616079008E1F6D /* fullmatrix.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fullmatrix.h; sourceTree = "<group>"; };
 133                 3782163C0F616079008E1F6D /* fullmatrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fullmatrix.cpp; sourceTree = "<group>"; };
 134                 379293C10F2DE73400B9034A /* treemap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treemap.h; sourceTree = "<group>"; };
 135                 379293C20F2DE73400B9034A /* treemap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treemap.cpp; sourceTree = "<group>"; };
 136                 3792946E0F2E191800B9034A /* parsimonycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimonycommand.h; sourceTree = "<group>"; };
 137                 3792946F0F2E191800B9034A /* parsimonycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsimonycommand.cpp; sourceTree = "<group>"; };
 138                 379294880F2E258500B9034A /* parsimony.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimony.h; sourceTree = "<group>"; };
 139                 379294890F2E258500B9034A /* parsimony.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsimony.cpp; sourceTree = "<group>"; };
 140                 3792948D0F2E271100B9034A /* treecalculator.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treecalculator.h; sourceTree = "<group>"; };
 141                 37AD4CE20F28AEA300AA2D49 /* sharedlistvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedlistvector.h; sourceTree = "<group>"; };
 142                 37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedlistvector.cpp; sourceTree = "<group>"; };
 143                 37AD4DB90F28E2FE00AA2D49 /* tree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = tree.h; sourceTree = "<group>"; };
 144                 37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = tree.cpp; sourceTree = "<group>"; };
 145                 37AD4DC80F28F3DD00AA2D49 /* readtree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtree.h; sourceTree = "<group>"; };
 146                 37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtree.cpp; sourceTree = "<group>"; };
 147                 37AFC71D0F445386005F492D /* sharedsobscollectsummary.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsobscollectsummary.h; sourceTree = "<group>"; };
 148                 37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsobscollectsummary.cpp; sourceTree = "<group>"; };
 149                 37B28F660F27590100808A62 /* deconvolutecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = deconvolutecommand.h; sourceTree = "<group>"; };
 150                 37B28F670F27590100808A62 /* deconvolutecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = deconvolutecommand.cpp; sourceTree = "<group>"; };
 151                 37D927B80F21331F001D4494 /* ace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ace.cpp; sourceTree = "<group>"; };
 152                 37D927B90F21331F001D4494 /* ace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ace.h; sourceTree = "<group>"; };
 153                 37D927BA0F21331F001D4494 /* averagelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = averagelinkage.cpp; sourceTree = "<group>"; };
 154                 37D927BB0F21331F001D4494 /* bootstrap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bootstrap.cpp; sourceTree = "<group>"; };
 155                 37D927BC0F21331F001D4494 /* bootstrap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bootstrap.h; sourceTree = "<group>"; };
 156                 37D927BD0F21331F001D4494 /* calculator.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = calculator.cpp; sourceTree = "<group>"; };
 157                 37D927BE0F21331F001D4494 /* calculator.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = calculator.h; sourceTree = "<group>"; };
 158                 37D927BF0F21331F001D4494 /* chao1.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chao1.cpp; sourceTree = "<group>"; };
 159                 37D927C00F21331F001D4494 /* chao1.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chao1.h; sourceTree = "<group>"; };
 160                 37D927C10F21331F001D4494 /* cluster.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = cluster.cpp; sourceTree = "<group>"; };
 161                 37D927C20F21331F001D4494 /* cluster.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = cluster.hpp; sourceTree = "<group>"; };
 162                 37D927C30F21331F001D4494 /* clustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clustercommand.cpp; sourceTree = "<group>"; };
 163                 37D927C40F21331F001D4494 /* clustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clustercommand.h; sourceTree = "<group>"; };
 164                 37D927C50F21331F001D4494 /* collect.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = collect.cpp; sourceTree = "<group>"; };
 165                 37D927C60F21331F001D4494 /* collect.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collect.h; sourceTree = "<group>"; };
 166                 37D927C70F21331F001D4494 /* collectcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = collectcommand.cpp; sourceTree = "<group>"; };
 167                 37D927C80F21331F001D4494 /* collectcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectcommand.h; sourceTree = "<group>"; };
 168                 37D927C90F21331F001D4494 /* collectdisplay.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectdisplay.h; sourceTree = "<group>"; };
 169                 37D927CA0F21331F001D4494 /* collectorscurvedata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectorscurvedata.h; sourceTree = "<group>"; };
 170                 37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = collectsharedcommand.cpp; sourceTree = "<group>"; };
 171                 37D927CC0F21331F001D4494 /* collectsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectsharedcommand.h; sourceTree = "<group>"; };
 172                 37D927CD0F21331F001D4494 /* command.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = command.hpp; sourceTree = "<group>"; };
 173                 37D927CF0F21331F001D4494 /* commandfactory.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = commandfactory.hpp; sourceTree = "<group>"; };
 174                 37D927D00F21331F001D4494 /* commandoptionparser.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = commandoptionparser.cpp; sourceTree = "<group>"; };
 175                 37D927D10F21331F001D4494 /* commandoptionparser.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = commandoptionparser.hpp; sourceTree = "<group>"; };
 176                 37D927D20F21331F001D4494 /* completelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = completelinkage.cpp; sourceTree = "<group>"; };
 177                 37D927D30F21331F001D4494 /* database.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = database.cpp; sourceTree = "<group>"; };
 178                 37D927D40F21331F001D4494 /* database.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = database.hpp; sourceTree = "<group>"; };
 179                 37D927D50F21331F001D4494 /* datavector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = datavector.hpp; sourceTree = "<group>"; };
 180                 37D927D60F21331F001D4494 /* display.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = display.h; sourceTree = "<group>"; };
 181                 37D927D70F21331F001D4494 /* engine.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = engine.cpp; sourceTree = "<group>"; };
 182                 37D927D80F21331F001D4494 /* engine.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = engine.hpp; sourceTree = "<group>"; };
 183                 37D927D90F21331F001D4494 /* errorchecking.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = errorchecking.cpp; sourceTree = "<group>"; };
 184                 37D927DA0F21331F001D4494 /* errorchecking.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = errorchecking.h; sourceTree = "<group>"; };
 185                 37D927DB0F21331F001D4494 /* fastamap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fastamap.cpp; sourceTree = "<group>"; };
 186                 37D927DC0F21331F001D4494 /* fastamap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fastamap.h; sourceTree = "<group>"; };
 187                 37D927DD0F21331F001D4494 /* fileoutput.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fileoutput.cpp; sourceTree = "<group>"; };
 188                 37D927DE0F21331F001D4494 /* fileoutput.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fileoutput.h; sourceTree = "<group>"; };
 189                 37D927DF0F21331F001D4494 /* globaldata.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = globaldata.cpp; sourceTree = "<group>"; };
 190                 37D927E00F21331F001D4494 /* globaldata.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = globaldata.hpp; sourceTree = "<group>"; };
 191                 37D927E10F21331F001D4494 /* groupmap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = groupmap.cpp; sourceTree = "<group>"; };
 192                 37D927E20F21331F001D4494 /* groupmap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = groupmap.h; sourceTree = "<group>"; };
 193                 37D927E30F21331F001D4494 /* helpcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = helpcommand.cpp; sourceTree = "<group>"; };
 194                 37D927E40F21331F001D4494 /* helpcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = helpcommand.h; sourceTree = "<group>"; };
 195                 37D927E50F21331F001D4494 /* inputdata.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = inputdata.cpp; sourceTree = "<group>"; };
 196                 37D927E60F21331F001D4494 /* inputdata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = inputdata.h; sourceTree = "<group>"; };
 197                 37D927E70F21331F001D4494 /* jackknife.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = jackknife.cpp; sourceTree = "<group>"; };
 198                 37D927E80F21331F001D4494 /* jackknife.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = jackknife.h; sourceTree = "<group>"; };
 199                 37D927E90F21331F001D4494 /* kmer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = kmer.cpp; sourceTree = "<group>"; };
 200                 37D927EA0F21331F001D4494 /* kmer.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = kmer.hpp; sourceTree = "<group>"; };
 201                 37D927EB0F21331F001D4494 /* kmerdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = kmerdb.cpp; sourceTree = "<group>"; };
 202                 37D927EC0F21331F001D4494 /* kmerdb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = kmerdb.hpp; sourceTree = "<group>"; };
 203                 37D927ED0F21331F001D4494 /* listvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = listvector.cpp; sourceTree = "<group>"; };
 204                 37D927EE0F21331F001D4494 /* listvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = listvector.hpp; sourceTree = "<group>"; };
 205                 37D927EF0F21331F001D4494 /* mothur.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mothur.cpp; sourceTree = "<group>"; };
 206                 37D927F00F21331F001D4494 /* nameassignment.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nameassignment.cpp; sourceTree = "<group>"; };
 207                 37D927F10F21331F001D4494 /* nameassignment.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = nameassignment.hpp; sourceTree = "<group>"; };
 208                 37D927F20F21331F001D4494 /* nocommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nocommand.cpp; sourceTree = "<group>"; };
 209                 37D927F30F21331F001D4494 /* nocommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = nocommand.h; sourceTree = "<group>"; };
 210                 37D927F40F21331F001D4494 /* npshannon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = npshannon.cpp; sourceTree = "<group>"; };
 211                 37D927F50F21331F001D4494 /* npshannon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = npshannon.h; sourceTree = "<group>"; };
 212                 37D927F60F21331F001D4494 /* observable.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = observable.h; sourceTree = "<group>"; };
 213                 37D927F70F21331F001D4494 /* ordervector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ordervector.cpp; sourceTree = "<group>"; };
 214                 37D927F80F21331F001D4494 /* ordervector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = ordervector.hpp; sourceTree = "<group>"; };
 215                 37D927F90F21331F001D4494 /* parselistcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parselistcommand.cpp; sourceTree = "<group>"; };
 216                 37D927FA0F21331F001D4494 /* parselistcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parselistcommand.h; sourceTree = "<group>"; };
 217                 37D927FB0F21331F001D4494 /* progress.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = progress.cpp; sourceTree = "<group>"; };
 218                 37D927FC0F21331F001D4494 /* progress.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = progress.hpp; sourceTree = "<group>"; };
 219                 37D927FD0F21331F001D4494 /* quitcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = quitcommand.cpp; sourceTree = "<group>"; };
 220                 37D927FE0F21331F001D4494 /* quitcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = quitcommand.h; sourceTree = "<group>"; };
 221                 37D927FF0F21331F001D4494 /* rabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rabundvector.cpp; sourceTree = "<group>"; };
 222                 37D928000F21331F001D4494 /* rabundvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = rabundvector.hpp; sourceTree = "<group>"; };
 223                 37D928010F21331F001D4494 /* rarecalc.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarecalc.cpp; sourceTree = "<group>"; };
 224                 37D928020F21331F001D4494 /* rarecalc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarecalc.h; sourceTree = "<group>"; };
 225                 37D928030F21331F001D4494 /* raredisplay.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = raredisplay.cpp; sourceTree = "<group>"; };
 226                 37D928040F21331F001D4494 /* raredisplay.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = raredisplay.h; sourceTree = "<group>"; };
 227                 37D928050F21331F001D4494 /* rarefact.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefact.cpp; sourceTree = "<group>"; };
 228                 37D928060F21331F001D4494 /* rarefact.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefact.h; sourceTree = "<group>"; };
 229                 37D928070F21331F001D4494 /* rarefactcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefactcommand.cpp; sourceTree = "<group>"; };
 230                 37D928080F21331F001D4494 /* rarefactcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactcommand.h; sourceTree = "<group>"; };
 231                 37D928090F21331F001D4494 /* rarefactioncurvedata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactioncurvedata.h; sourceTree = "<group>"; };
 232                 37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefactsharedcommand.cpp; sourceTree = "<group>"; };
 233                 37D9280B0F21331F001D4494 /* rarefactsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactsharedcommand.h; sourceTree = "<group>"; };
 234                 37D928120F21331F001D4494 /* readmatrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readmatrix.cpp; sourceTree = "<group>"; };
 235                 37D928130F21331F001D4494 /* readmatrix.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = readmatrix.hpp; sourceTree = "<group>"; };
 236                 37D9281A0F21331F001D4494 /* sabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sabundvector.cpp; sourceTree = "<group>"; };
 237                 37D9281B0F21331F001D4494 /* sabundvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sabundvector.hpp; sourceTree = "<group>"; };
 238                 37D9281C0F21331F001D4494 /* sequence.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sequence.cpp; sourceTree = "<group>"; };
 239                 37D9281D0F21331F001D4494 /* sequence.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sequence.hpp; sourceTree = "<group>"; };
 240                 37D9281E0F21331F001D4494 /* shannon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shannon.cpp; sourceTree = "<group>"; };
 241                 37D9281F0F21331F001D4494 /* shannon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shannon.h; sourceTree = "<group>"; };
 242                 37D928200F21331F001D4494 /* shared.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shared.cpp; sourceTree = "<group>"; };
 243                 37D928210F21331F001D4494 /* shared.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shared.h; sourceTree = "<group>"; };
 244                 37D928220F21331F001D4494 /* sharedace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedace.cpp; sourceTree = "<group>"; };
 245                 37D928230F21331F001D4494 /* sharedace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedace.h; sourceTree = "<group>"; };
 246                 37D928240F21331F001D4494 /* sharedchao1.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedchao1.cpp; sourceTree = "<group>"; };
 247                 37D928250F21331F001D4494 /* sharedchao1.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedchao1.h; sourceTree = "<group>"; };
 248                 37D928260F21331F001D4494 /* sharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedcommand.cpp; sourceTree = "<group>"; };
 249                 37D928270F21331F001D4494 /* sharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedcommand.h; sourceTree = "<group>"; };
 250                 37D928280F21331F001D4494 /* sharedjabund.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjabund.cpp; sourceTree = "<group>"; };
 251                 37D928290F21331F001D4494 /* sharedjabund.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjabund.h; sourceTree = "<group>"; };
 252                 37D9282A0F21331F001D4494 /* sharedjclass.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjclass.cpp; sourceTree = "<group>"; };
 253                 37D9282B0F21331F001D4494 /* sharedjclass.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjclass.h; sourceTree = "<group>"; };
 254                 37D9282C0F21331F001D4494 /* sharedjest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjest.cpp; sourceTree = "<group>"; };
 255                 37D9282D0F21331F001D4494 /* sharedjest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjest.h; sourceTree = "<group>"; };
 256                 37D9282E0F21331F001D4494 /* sharedordervector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedordervector.cpp; sourceTree = "<group>"; };
 257                 37D9282F0F21331F001D4494 /* sharedordervector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedordervector.h; sourceTree = "<group>"; };
 258                 37D928300F21331F001D4494 /* sharedrabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedrabundvector.cpp; sourceTree = "<group>"; };
 259                 37D928310F21331F001D4494 /* sharedrabundvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedrabundvector.h; sourceTree = "<group>"; };
 260                 37D928320F21331F001D4494 /* sharedsabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsabundvector.cpp; sourceTree = "<group>"; };
 261                 37D928330F21331F001D4494 /* sharedsabundvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsabundvector.h; sourceTree = "<group>"; };
 262                 37D928340F21331F001D4494 /* sharedsobs.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsobs.cpp; sourceTree = "<group>"; };
 263                 37D928350F21331F001D4494 /* sharedsobs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsobs.h; sourceTree = "<group>"; };
 264                 37D928360F21331F001D4494 /* sharedsorabund.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorabund.cpp; sourceTree = "<group>"; };
 265                 37D928370F21331F001D4494 /* sharedsorabund.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsorabund.h; sourceTree = "<group>"; };
 266                 37D928380F21331F001D4494 /* sharedsorclass.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorclass.cpp; sourceTree = "<group>"; };
 267                 37D928390F21331F001D4494 /* sharedsorclass.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsorclass.h; sourceTree = "<group>"; };
 268                 37D9283A0F21331F001D4494 /* sharedsorest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorest.cpp; sourceTree = "<group>"; };
 269                 37D9283B0F21331F001D4494 /* sharedsorest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsorest.h; sourceTree = "<group>"; };
 270                 37D9283C0F21331F001D4494 /* sharedthetan.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedthetan.cpp; sourceTree = "<group>"; };
 271                 37D9283D0F21331F001D4494 /* sharedthetan.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedthetan.h; sourceTree = "<group>"; };
 272                 37D9283E0F21331F001D4494 /* sharedthetayc.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedthetayc.cpp; sourceTree = "<group>"; };
 273                 37D9283F0F21331F001D4494 /* sharedthetayc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedthetayc.h; sourceTree = "<group>"; };
 274                 37D928400F21331F001D4494 /* simpson.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = simpson.cpp; sourceTree = "<group>"; };
 275                 37D928410F21331F001D4494 /* simpson.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = simpson.h; sourceTree = "<group>"; };
 276                 37D928420F21331F001D4494 /* singlelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = singlelinkage.cpp; sourceTree = "<group>"; };
 277                 37D928430F21331F001D4494 /* sobs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sobs.h; sourceTree = "<group>"; };
 278                 37D928440F21331F001D4494 /* sparsematrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sparsematrix.cpp; sourceTree = "<group>"; };
 279                 37D928450F21331F001D4494 /* sparsematrix.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sparsematrix.hpp; sourceTree = "<group>"; };
 280                 37D928460F21331F001D4494 /* summarycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summarycommand.cpp; sourceTree = "<group>"; };
 281                 37D928470F21331F001D4494 /* summarycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarycommand.h; sourceTree = "<group>"; };
 282                 37D928480F21331F001D4494 /* summarydata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarydata.h; sourceTree = "<group>"; };
 283                 37D928490F21331F001D4494 /* summarydisplay.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarydisplay.h; sourceTree = "<group>"; };
 284                 37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summarysharedcommand.cpp; sourceTree = "<group>"; };
 285                 37D9284B0F21331F001D4494 /* summarysharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarysharedcommand.h; sourceTree = "<group>"; };
 286                 37D9284C0F21331F001D4494 /* utilities.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = utilities.hpp; sourceTree = "<group>"; };
 287                 37D9284D0F21331F001D4494 /* uvest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = uvest.cpp; sourceTree = "<group>"; };
 288                 37D9284E0F21331F001D4494 /* uvest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = uvest.h; sourceTree = "<group>"; };
 289                 37D9284F0F21331F001D4494 /* validcalculator.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = validcalculator.cpp; sourceTree = "<group>"; };
 290                 37D928500F21331F001D4494 /* validcalculator.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = validcalculator.h; sourceTree = "<group>"; };
 291                 37D928510F21331F001D4494 /* validcommands.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = validcommands.cpp; sourceTree = "<group>"; };
 292                 37D928520F21331F001D4494 /* validcommands.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = validcommands.h; sourceTree = "<group>"; };
 293                 37D928530F21331F001D4494 /* validparameter.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = validparameter.cpp; sourceTree = "<group>"; };
 294                 37D928540F21331F001D4494 /* validparameter.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = validparameter.h; sourceTree = "<group>"; };
 295                 37E3ED800F4D9D0D00B5DF02 /* mothur.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mothur.h; sourceTree = "<group>"; };
 296                 37E5F3E10F29FD4200F8D827 /* treenode.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treenode.h; sourceTree = "<group>"; };
 297                 37E5F3E20F29FD4200F8D827 /* treenode.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treenode.cpp; sourceTree = "<group>"; };
 298                 37E5F4900F2A3DA800F8D827 /* readtreecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtreecommand.h; sourceTree = "<group>"; };
 299                 37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtreecommand.cpp; sourceTree = "<group>"; };
 300                 8DD76F6C0486A84900D96B5E /* mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = mothur; sourceTree = BUILT_PRODUCTS_DIR; };
 301                 A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getgroupcommand.cpp; sourceTree = "<group>"; };
 302                 A70B53A50F4CD7AD0064797E /* getgroupcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getgroupcommand.h; sourceTree = "<group>"; };
 303                 A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlabelcommand.cpp; sourceTree = "<group>"; };
 304                 A70B53A70F4CD7AD0064797E /* getlabelcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlabelcommand.h; sourceTree = "<group>"; };
 305                 A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlinecommand.cpp; sourceTree = "<group>"; };
 306                 A70B53A90F4CD7AD0064797E /* getlinecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlinecommand.h; sourceTree = "<group>"; };
 307                 C6859E8B029090EE04C91782 /* Mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = Mothur.1; sourceTree = "<group>"; };
 308 /* End PBXFileReference section */
 309
 310 /* Begin PBXFrameworksBuildPhase section */
 311                 8DD76F660486A84900D96B5E /* Frameworks */ = {
 312                         isa = PBXFrameworksBuildPhase;
 313                         buildActionMask = 2147483647;
 314                         files = (
 315                         );
 316                         runOnlyForDeploymentPostprocessing = 0;
 317                 };
 318 /* End PBXFrameworksBuildPhase section */
 319
 320 /* Begin PBXGroup section */
 321                 08FB7794FE84155DC02AAC07 /* Mothur */ = {
 322                         isa = PBXGroup;
 323                         children = (
 324                                 08FB7795FE84155DC02AAC07 /* Source */,
 325                                 C6859E8C029090F304C91782 /* Documentation */,
 326                                 1AB674ADFE9D54B511CA2CBB /* Products */,
 327                         );
 328                         name = Mothur;
 329                         sourceTree = "<group>";
 330                 };
 331                 08FB7795FE84155DC02AAC07 /* Source */ = {
 332                         isa = PBXGroup;
 333                         children = (
 334                                 37D927BA0F21331F001D4494 /* averagelinkage.cpp */,
 335                                 37D928A60F2133C0001D4494 /* calculators */,
 336                                 37D927C20F21331F001D4494 /* cluster.hpp */,
 337                                 37D927C10F21331F001D4494 /* cluster.cpp */,
 338                                 37D928A90F2133E5001D4494 /* commands */,
 339                                 37D927C60F21331F001D4494 /* collect.h */,
 340                                 37D927C50F21331F001D4494 /* collect.cpp */,
 341                                 37D927C90F21331F001D4494 /* collectdisplay.h */,
 342                                 37D928AC0F213420001D4494 /* containers */,
 343                                 37D927CA0F21331F001D4494 /* collectorscurvedata.h */,
 344                                 37D927CF0F21331F001D4494 /* commandfactory.hpp */,
 345                                 372E12EC0F264D320095CF7E /* commandfactory.cpp */,
 346                                 37D927D10F21331F001D4494 /* commandoptionparser.hpp */,
 347                                 37D927D00F21331F001D4494 /* commandoptionparser.cpp */,
 348                                 37D927D20F21331F001D4494 /* completelinkage.cpp */,
 349                                 37D927D40F21331F001D4494 /* database.hpp */,
 350                                 37D927D30F21331F001D4494 /* database.cpp */,
 351                                 37D927D60F21331F001D4494 /* display.h */,
 352                                 37D927D80F21331F001D4494 /* engine.hpp */,
 353                                 37D927D70F21331F001D4494 /* engine.cpp */,
 354                                 37D928B10F213472001D4494 /* errorcheckor */,
 355                                 37D927DE0F21331F001D4494 /* fileoutput.h */,
 356                                 37D927DD0F21331F001D4494 /* fileoutput.cpp */,
 357                                 37D927E00F21331F001D4494 /* globaldata.hpp */,
 358                                 37D927DF0F21331F001D4494 /* globaldata.cpp */,
 359                                 37D927E60F21331F001D4494 /* inputdata.h */,
 360                                 37D927E50F21331F001D4494 /* inputdata.cpp */,
 361                                 37D927EA0F21331F001D4494 /* kmer.hpp */,
 362                                 37D927E90F21331F001D4494 /* kmer.cpp */,
 363                                 37D927EC0F21331F001D4494 /* kmerdb.hpp */,
 364                                 37D927EB0F21331F001D4494 /* kmerdb.cpp */,
 365                                 37E3ED800F4D9D0D00B5DF02 /* mothur.h */,
 366                                 37D927EF0F21331F001D4494 /* mothur.cpp */,
 367                                 37D927F10F21331F001D4494 /* nameassignment.hpp */,
 368                                 37D927F00F21331F001D4494 /* nameassignment.cpp */,
 369                                 37D927F60F21331F001D4494 /* observable.h */,
 370                                 37D927FC0F21331F001D4494 /* progress.hpp */,
 371                                 37D927FB0F21331F001D4494 /* progress.cpp */,
 372                                 37D928040F21331F001D4494 /* raredisplay.h */,
 373                                 37D928030F21331F001D4494 /* raredisplay.cpp */,
 374                                 37D928060F21331F001D4494 /* rarefact.h */,
 375                                 37D928050F21331F001D4494 /* rarefact.cpp */,
 376                                 37D928090F21331F001D4494 /* rarefactioncurvedata.h */,
 377                                 37D928130F21331F001D4494 /* readmatrix.hpp */,
 378                                 37D928120F21331F001D4494 /* readmatrix.cpp */,
 379                                 37AD4DC80F28F3DD00AA2D49 /* readtree.h */,
 380                                 37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */,
 381                                 37D9281D0F21331F001D4494 /* sequence.hpp */,
 382                                 37D9281C0F21331F001D4494 /* sequence.cpp */,
 383                                 37D928210F21331F001D4494 /* shared.h */,
 384                                 37D928200F21331F001D4494 /* shared.cpp */,
 385                                 37D928420F21331F001D4494 /* singlelinkage.cpp */,
 386                                 37D928480F21331F001D4494 /* summarydata.h */,
 387                                 37D928490F21331F001D4494 /* summarydisplay.h */,
 388                                 37D9284C0F21331F001D4494 /* utilities.hpp */,
 389                         );
 390                         name = Source;
 391                         sourceTree = "<group>";
 392                 };
 393                 1AB674ADFE9D54B511CA2CBB /* Products */ = {
 394                         isa = PBXGroup;
 395                         children = (
 396                                 8DD76F6C0486A84900D96B5E /* mothur */,
 397                         );
 398                         name = Products;
 399                         sourceTree = "<group>";
 400                 };
 401                 37D928A60F2133C0001D4494 /* calculators */ = {
 402                         isa = PBXGroup;
 403                         children = (
 404                                 37D927BE0F21331F001D4494 /* calculator.h */,
 405                                 3792948D0F2E271100B9034A /* treecalculator.h */,
 406                                 37D927BD0F21331F001D4494 /* calculator.cpp */,
 407                                 37D927B90F21331F001D4494 /* ace.h */,
 408                                 37D927B80F21331F001D4494 /* ace.cpp */,
 409                                 37D927BC0F21331F001D4494 /* bootstrap.h */,
 410                                 37D927BB0F21331F001D4494 /* bootstrap.cpp */,
 411                                 37D927C00F21331F001D4494 /* chao1.h */,
 412                                 37D927BF0F21331F001D4494 /* chao1.cpp */,
 413                                 37D927E80F21331F001D4494 /* jackknife.h */,
 414                                 37D927E70F21331F001D4494 /* jackknife.cpp */,
 415                                 37D927F50F21331F001D4494 /* npshannon.h */,
 416                                 37D927F40F21331F001D4494 /* npshannon.cpp */,
 417                                 379294880F2E258500B9034A /* parsimony.h */,
 418                                 379294890F2E258500B9034A /* parsimony.cpp */,
 419                                 37D928020F21331F001D4494 /* rarecalc.h */,
 420                                 37D928010F21331F001D4494 /* rarecalc.cpp */,
 421                                 37D9281F0F21331F001D4494 /* shannon.h */,
 422                                 37D9281E0F21331F001D4494 /* shannon.cpp */,
 423                                 37D928230F21331F001D4494 /* sharedace.h */,
 424                                 37D928220F21331F001D4494 /* sharedace.cpp */,
 425                                 37D928250F21331F001D4494 /* sharedchao1.h */,
 426                                 37D928240F21331F001D4494 /* sharedchao1.cpp */,
 427                                 37D928290F21331F001D4494 /* sharedjabund.h */,
 428                                 37D928280F21331F001D4494 /* sharedjabund.cpp */,
 429                                 37D9282B0F21331F001D4494 /* sharedjclass.h */,
 430                                 37D9282A0F21331F001D4494 /* sharedjclass.cpp */,
 431                                 37D9282D0F21331F001D4494 /* sharedjest.h */,
 432                                 37D9282C0F21331F001D4494 /* sharedjest.cpp */,
 433                                 37D928350F21331F001D4494 /* sharedsobs.h */,
 434                                 37D928340F21331F001D4494 /* sharedsobs.cpp */,
 435                                 37AFC71D0F445386005F492D /* sharedsobscollectsummary.h */,
 436                                 37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */,
 437                                 37D928370F21331F001D4494 /* sharedsorabund.h */,
 438                                 37D928360F21331F001D4494 /* sharedsorabund.cpp */,
 439                                 37D928390F21331F001D4494 /* sharedsorclass.h */,
 440                                 37D928380F21331F001D4494 /* sharedsorclass.cpp */,
 441                                 37D9283B0F21331F001D4494 /* sharedsorest.h */,
 442                                 37D9283A0F21331F001D4494 /* sharedsorest.cpp */,
 443                                 37D9283D0F21331F001D4494 /* sharedthetan.h */,
 444                                 37D9283C0F21331F001D4494 /* sharedthetan.cpp */,
 445                                 37D9283F0F21331F001D4494 /* sharedthetayc.h */,
 446                                 37D9283E0F21331F001D4494 /* sharedthetayc.cpp */,
 447                                 37D928410F21331F001D4494 /* simpson.h */,
 448                                 37D928400F21331F001D4494 /* simpson.cpp */,
 449                                 37D928430F21331F001D4494 /* sobs.h */,
 450                                 374610810F40652400460C57 /* unweighted.h */,
 451                                 374610820F40652400460C57 /* unweighted.cpp */,
 452                                 37D9284E0F21331F001D4494 /* uvest.h */,
 453                                 37D9284D0F21331F001D4494 /* uvest.cpp */,
 454                                 3746107C0F4064D100460C57 /* weighted.h */,
 455                                 3746107D0F4064D100460C57 /* weighted.cpp */,
 456                         );
 457                         name = calculators;
 458                         sourceTree = "<group>";
 459                 };
 460                 37D928A90F2133E5001D4494 /* commands */ = {
 461                         isa = PBXGroup;
 462                         children = (
 463                                 37D927CD0F21331F001D4494 /* command.hpp */,
 464                                 37D927C40F21331F001D4494 /* clustercommand.h */,
 465                                 37D927C30F21331F001D4494 /* clustercommand.cpp */,
 466                                 37D927C80F21331F001D4494 /* collectcommand.h */,
 467                                 37D927C70F21331F001D4494 /* collectcommand.cpp */,
 468                                 37D927CC0F21331F001D4494 /* collectsharedcommand.h */,
 469                                 37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */,
 470                                 37B28F660F27590100808A62 /* deconvolutecommand.h */,
 471                                 37B28F670F27590100808A62 /* deconvolutecommand.cpp */,
 472                                 A70B53A50F4CD7AD0064797E /* getgroupcommand.h */,
 473                                 A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */,
 474                                 A70B53A70F4CD7AD0064797E /* getlabelcommand.h */,
 475                                 A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */,
 476                                 A70B53A90F4CD7AD0064797E /* getlinecommand.h */,
 477                                 A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */,
 478                                 37D927E40F21331F001D4494 /* helpcommand.h */,
 479                                 37D927E30F21331F001D4494 /* helpcommand.cpp */,
 480                                 374CD63D0F65832000D90B4A /* libshuffcommand.h */,
 481                                 374CD63E0F65832000D90B4A /* libshuffcommand.cpp */,
 482                                 37D927F30F21331F001D4494 /* nocommand.h */,
 483                                 37D927F20F21331F001D4494 /* nocommand.cpp */,
 484                                 37D927FA0F21331F001D4494 /* parselistcommand.h */,
 485                                 37D927F90F21331F001D4494 /* parselistcommand.cpp */,
 486                                 3792946E0F2E191800B9034A /* parsimonycommand.h */,
 487                                 3792946F0F2E191800B9034A /* parsimonycommand.cpp */,
 488                                 37D927FE0F21331F001D4494 /* quitcommand.h */,
 489                                 37D927FD0F21331F001D4494 /* quitcommand.cpp */,
 490                                 37D928080F21331F001D4494 /* rarefactcommand.h */,
 491                                 37D928070F21331F001D4494 /* rarefactcommand.cpp */,
 492                                 37D9280B0F21331F001D4494 /* rarefactsharedcommand.h */,
 493                                 37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */,
 494                                 372E12940F263D5A0095CF7E /* readdistcommand.h */,
 495                                 372E12950F263D5A0095CF7E /* readdistcommand.cpp */,
 496                                 372E126E0F26365B0095CF7E /* readotucommand.h */,
 497                                 372E126F0F26365B0095CF7E /* readotucommand.cpp */,
 498                                 37E5F4900F2A3DA800F8D827 /* readtreecommand.h */,
 499                                 37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */,
 500                                 37D928270F21331F001D4494 /* sharedcommand.h */,
 501                                 37D928260F21331F001D4494 /* sharedcommand.cpp */,
 502                                 37D928470F21331F001D4494 /* summarycommand.h */,
 503                                 37D928460F21331F001D4494 /* summarycommand.cpp */,
 504                                 37D9284B0F21331F001D4494 /* summarysharedcommand.h */,
 505                                 37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */,
 506                                 3746109B0F40657600460C57 /* unifracunweightedcommand.h */,
 507                                 3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */,
 508                                 374610760F40645300460C57 /* unifracweightedcommand.h */,
 509                                 374610770F40645300460C57 /* unifracweightedcommand.cpp */,
 510                         );
 511                         name = commands;
 512                         sourceTree = "<group>";
 513                 };
 514                 37D928AC0F213420001D4494 /* containers */ = {
 515                         isa = PBXGroup;
 516                         children = (
 517                                 37D927D50F21331F001D4494 /* datavector.hpp */,
 518                                 37D927DC0F21331F001D4494 /* fastamap.h */,
 519                                 37D927DB0F21331F001D4494 /* fastamap.cpp */,
 520                                 3782163B0F616079008E1F6D /* fullmatrix.h */,
 521                                 3782163C0F616079008E1F6D /* fullmatrix.cpp */,
 522                                 37D927E20F21331F001D4494 /* groupmap.h */,
 523                                 37D927E10F21331F001D4494 /* groupmap.cpp */,
 524                                 37D927EE0F21331F001D4494 /* listvector.hpp */,
 525                                 37D927ED0F21331F001D4494 /* listvector.cpp */,
 526                                 37D927F80F21331F001D4494 /* ordervector.hpp */,
 527                                 37D927F70F21331F001D4494 /* ordervector.cpp */,
 528                                 37D928000F21331F001D4494 /* rabundvector.hpp */,
 529                                 37D927FF0F21331F001D4494 /* rabundvector.cpp */,
 530                                 37D9281B0F21331F001D4494 /* sabundvector.hpp */,
 531                                 37D9281A0F21331F001D4494 /* sabundvector.cpp */,
 532                                 37AD4CE20F28AEA300AA2D49 /* sharedlistvector.h */,
 533                                 37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */,
 534                                 37D9282F0F21331F001D4494 /* sharedordervector.h */,
 535                                 37D9282E0F21331F001D4494 /* sharedordervector.cpp */,
 536                                 37D928310F21331F001D4494 /* sharedrabundvector.h */,
 537                                 37D928300F21331F001D4494 /* sharedrabundvector.cpp */,
 538                                 37D928330F21331F001D4494 /* sharedsabundvector.h */,
 539                                 37D928320F21331F001D4494 /* sharedsabundvector.cpp */,
 540                                 37D928450F21331F001D4494 /* sparsematrix.hpp */,
 541                                 37D928440F21331F001D4494 /* sparsematrix.cpp */,
 542                                 37AD4DB90F28E2FE00AA2D49 /* tree.h */,
 543                                 37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */,
 544                                 379293C10F2DE73400B9034A /* treemap.h */,
 545                                 379293C20F2DE73400B9034A /* treemap.cpp */,
 546                                 37E5F3E10F29FD4200F8D827 /* treenode.h */,
 547                                 37E5F3E20F29FD4200F8D827 /* treenode.cpp */,
 548                         );
 549                         name = containers;
 550                         sourceTree = "<group>";
 551                 };
 552                 37D928B10F213472001D4494 /* errorcheckor */ = {
 553                         isa = PBXGroup;
 554                         children = (
 555                                 37D927DA0F21331F001D4494 /* errorchecking.h */,
 556                                 37D927D90F21331F001D4494 /* errorchecking.cpp */,
 557                                 37D928500F21331F001D4494 /* validcalculator.h */,
 558                                 37D9284F0F21331F001D4494 /* validcalculator.cpp */,
 559                                 37D928520F21331F001D4494 /* validcommands.h */,
 560                                 37D928510F21331F001D4494 /* validcommands.cpp */,
 561                                 37D928540F21331F001D4494 /* validparameter.h */,
 562                                 37D928530F21331F001D4494 /* validparameter.cpp */,
 563                         );
 564                         name = errorcheckor;
 565                         sourceTree = "<group>";
 566                 };
 567                 C6859E8C029090F304C91782 /* Documentation */ = {
 568                         isa = PBXGroup;
 569                         children = (
 570                                 C6859E8B029090EE04C91782 /* Mothur.1 */,
 571                         );
 572                         name = Documentation;
 573                         sourceTree = "<group>";
 574                 };
 575 /* End PBXGroup section */
 576
 577 /* Begin PBXNativeTarget section */
 578                 8DD76F620486A84900D96B5E /* mothur */ = {
 579                         isa = PBXNativeTarget;
 580                         buildConfigurationList = 1DEB923108733DC60010E9CD /* Build configuration list for PBXNativeTarget "mothur" */;
 581                         buildPhases = (
 582                                 8DD76F640486A84900D96B5E /* Sources */,
 583                                 8DD76F660486A84900D96B5E /* Frameworks */,
 584                                 8DD76F690486A84900D96B5E /* CopyFiles */,
 585                         );
 586                         buildRules = (
 587                         );
 588                         dependencies = (
 589                         );
 590                         name = mothur;
 591                         productInstallPath = "$(HOME)/bin";
 592                         productName = Mothur;
 593                         productReference = 8DD76F6C0486A84900D96B5E /* mothur */;
 594                         productType = "com.apple.product-type.tool";
 595                 };
 596 /* End PBXNativeTarget section */
 597
 598 /* Begin PBXProject section */
 599                 08FB7793FE84155DC02AAC07 /* Project object */ = {
 600                         isa = PBXProject;
 601                         buildConfigurationList = 1DEB923508733DC60010E9CD /* Build configuration list for PBXProject "Mothur" */;
 602                         compatibilityVersion = "Xcode 3.0";
 603                         hasScannedForEncodings = 1;
 604                         mainGroup = 08FB7794FE84155DC02AAC07 /* Mothur */;
 605                         projectDirPath = "";
 606                         projectRoot = "";
 607                         targets = (
 608                                 8DD76F620486A84900D96B5E /* mothur */,
 609                         );
 610                 };
 611 /* End PBXProject section */
 612
 613 /* Begin PBXSourcesBuildPhase section */
 614                 8DD76F640486A84900D96B5E /* Sources */ = {
 615                         isa = PBXSourcesBuildPhase;
 616                         buildActionMask = 2147483647;
 617                         files = (
 618                                 37D928550F21331F001D4494 /* ace.cpp in Sources */,
 619                                 37D928560F21331F001D4494 /* averagelinkage.cpp in Sources */,
 620                                 37D928570F21331F001D4494 /* bootstrap.cpp in Sources */,
 621                                 37D928580F21331F001D4494 /* calculator.cpp in Sources */,
 622                                 37D928590F21331F001D4494 /* chao1.cpp in Sources */,
 623                                 37D9285A0F21331F001D4494 /* cluster.cpp in Sources */,
 624                                 37D9285B0F21331F001D4494 /* clustercommand.cpp in Sources */,
 625                                 37D9285C0F21331F001D4494 /* collect.cpp in Sources */,
 626                                 37D9285D0F21331F001D4494 /* collectcommand.cpp in Sources */,
 627                                 37D9285E0F21331F001D4494 /* collectsharedcommand.cpp in Sources */,
 628                                 37D928600F21331F001D4494 /* commandoptionparser.cpp in Sources */,
 629                                 37D928610F21331F001D4494 /* completelinkage.cpp in Sources */,
 630                                 37D928620F21331F001D4494 /* database.cpp in Sources */,
 631                                 37D928630F21331F001D4494 /* engine.cpp in Sources */,
 632                                 37D928640F21331F001D4494 /* errorchecking.cpp in Sources */,
 633                                 37D928650F21331F001D4494 /* fastamap.cpp in Sources */,
 634                                 37D928660F21331F001D4494 /* fileoutput.cpp in Sources */,
 635                                 37D928670F21331F001D4494 /* globaldata.cpp in Sources */,
 636                                 37D928680F21331F001D4494 /* groupmap.cpp in Sources */,
 637                                 37D928690F21331F001D4494 /* helpcommand.cpp in Sources */,
 638                                 37D9286A0F21331F001D4494 /* inputdata.cpp in Sources */,
 639                                 37D9286B0F21331F001D4494 /* jackknife.cpp in Sources */,
 640                                 37D9286C0F21331F001D4494 /* kmer.cpp in Sources */,
 641                                 37D9286D0F21331F001D4494 /* kmerdb.cpp in Sources */,
 642                                 37D9286E0F21331F001D4494 /* listvector.cpp in Sources */,
 643                                 37D9286F0F21331F001D4494 /* mothur.cpp in Sources */,
 644                                 37D928700F21331F001D4494 /* nameassignment.cpp in Sources */,
 645                                 37D928710F21331F001D4494 /* nocommand.cpp in Sources */,
 646                                 37D928720F21331F001D4494 /* npshannon.cpp in Sources */,
 647                                 37D928730F21331F001D4494 /* ordervector.cpp in Sources */,
 648                                 37D928740F21331F001D4494 /* parselistcommand.cpp in Sources */,
 649                                 37D928750F21331F001D4494 /* progress.cpp in Sources */,
 650                                 37D928760F21331F001D4494 /* quitcommand.cpp in Sources */,
 651                                 37D928770F21331F001D4494 /* rabundvector.cpp in Sources */,
 652                                 37D928780F21331F001D4494 /* rarecalc.cpp in Sources */,
 653                                 37D928790F21331F001D4494 /* raredisplay.cpp in Sources */,
 654                                 37D9287A0F21331F001D4494 /* rarefact.cpp in Sources */,
 655                                 37D9287B0F21331F001D4494 /* rarefactcommand.cpp in Sources */,
 656                                 37D9287C0F21331F001D4494 /* rarefactsharedcommand.cpp in Sources */,
 657                                 37D928800F21331F001D4494 /* readmatrix.cpp in Sources */,
 658                                 37D928840F21331F001D4494 /* sabundvector.cpp in Sources */,
 659                                 37D928850F21331F001D4494 /* sequence.cpp in Sources */,
 660                                 37D928860F21331F001D4494 /* shannon.cpp in Sources */,
 661                                 37D928870F21331F001D4494 /* shared.cpp in Sources */,
 662                                 37D928880F21331F001D4494 /* sharedace.cpp in Sources */,
 663                                 37D928890F21331F001D4494 /* sharedchao1.cpp in Sources */,
 664                                 37D9288A0F21331F001D4494 /* sharedcommand.cpp in Sources */,
 665                                 37D9288B0F21331F001D4494 /* sharedjabund.cpp in Sources */,
 666                                 37D9288C0F21331F001D4494 /* sharedjclass.cpp in Sources */,
 667                                 37D9288D0F21331F001D4494 /* sharedjest.cpp in Sources */,
 668                                 37D9288E0F21331F001D4494 /* sharedordervector.cpp in Sources */,
 669                                 37D9288F0F21331F001D4494 /* sharedrabundvector.cpp in Sources */,
 670                                 37D928900F21331F001D4494 /* sharedsabundvector.cpp in Sources */,
 671                                 37D928910F21331F001D4494 /* sharedsobs.cpp in Sources */,
 672                                 37D928920F21331F001D4494 /* sharedsorabund.cpp in Sources */,
 673                                 37D928930F21331F001D4494 /* sharedsorclass.cpp in Sources */,
 674                                 37D928940F21331F001D4494 /* sharedsorest.cpp in Sources */,
 675                                 37D928950F21331F001D4494 /* sharedthetan.cpp in Sources */,
 676                                 37D928960F21331F001D4494 /* sharedthetayc.cpp in Sources */,
 677                                 37D928970F21331F001D4494 /* simpson.cpp in Sources */,
 678                                 37D928980F21331F001D4494 /* singlelinkage.cpp in Sources */,
 679                                 37D928990F21331F001D4494 /* sparsematrix.cpp in Sources */,
 680                                 37D9289A0F21331F001D4494 /* summarycommand.cpp in Sources */,
 681                                 37D9289B0F21331F001D4494 /* summarysharedcommand.cpp in Sources */,
 682                                 37D9289C0F21331F001D4494 /* uvest.cpp in Sources */,
 683                                 37D9289D0F21331F001D4494 /* validcalculator.cpp in Sources */,
 684                                 37D9289E0F21331F001D4494 /* validcommands.cpp in Sources */,
 685                                 37D9289F0F21331F001D4494 /* validparameter.cpp in Sources */,
 686                                 372E12700F26365B0095CF7E /* readotucommand.cpp in Sources */,
 687                                 372E12960F263D5A0095CF7E /* readdistcommand.cpp in Sources */,
 688                                 372E12ED0F264D320095CF7E /* commandfactory.cpp in Sources */,
 689                                 37B28F680F27590100808A62 /* deconvolutecommand.cpp in Sources */,
 690                                 37AD4CE40F28AEA300AA2D49 /* sharedlistvector.cpp in Sources */,
 691                                 37AD4DBB0F28E2FE00AA2D49 /* tree.cpp in Sources */,
 692                                 37AD4DCA0F28F3DD00AA2D49 /* readtree.cpp in Sources */,
 693                                 37E5F3E30F29FD4200F8D827 /* treenode.cpp in Sources */,
 694                                 37E5F4920F2A3DA800F8D827 /* readtreecommand.cpp in Sources */,
 695                                 379293C30F2DE73400B9034A /* treemap.cpp in Sources */,
 696                                 379294700F2E191800B9034A /* parsimonycommand.cpp in Sources */,
 697                                 3792948A0F2E258500B9034A /* parsimony.cpp in Sources */,
 698                                 374610780F40645300460C57 /* unifracweightedcommand.cpp in Sources */,
 699                                 3746107E0F4064D100460C57 /* weighted.cpp in Sources */,
 700                                 374610830F40652400460C57 /* unweighted.cpp in Sources */,
 701                                 3746109D0F40657600460C57 /* unifracunweightedcommand.cpp in Sources */,
 702                                 37AFC71F0F445386005F492D /* sharedsobscollectsummary.cpp in Sources */,
 703                                 A70B53AA0F4CD7AD0064797E /* getgroupcommand.cpp in Sources */,
 704                                 A70B53AB0F4CD7AD0064797E /* getlabelcommand.cpp in Sources */,
 705                                 A70B53AC0F4CD7AD0064797E /* getlinecommand.cpp in Sources */,
 706                                 3782163D0F616079008E1F6D /* fullmatrix.cpp in Sources */,
 707                                 374CD63F0F65832000D90B4A /* libshuffcommand.cpp in Sources */,
 708                         );
 709                         runOnlyForDeploymentPostprocessing = 0;
 710                 };
 711 /* End PBXSourcesBuildPhase section */
 712
 713 /* Begin XCBuildConfiguration section */
 714                 1DEB923208733DC60010E9CD /* Debug */ = {
 715                         isa = XCBuildConfiguration;
 716                         buildSettings = {
 717                                 COPY_PHASE_STRIP = NO;
 718                                 GCC_DYNAMIC_NO_PIC = NO;
 719                                 GCC_ENABLE_FIX_AND_CONTINUE = YES;
 720                                 GCC_MODEL_TUNING = G5;
 721                                 GCC_OPTIMIZATION_LEVEL = 3;
 722                                 GCC_PREPROCESSOR_DEFINITIONS = (
 723                                         "_GLIBCXX_DEBUG=1",
 724                                         "_GLIBCXX_DEBUG_PEDANTIC=1",
 725                                 );
 726                                 INSTALL_PATH = /usr/local/bin;
 727                                 PRODUCT_NAME = mothur;
 728                                 ZERO_LINK = YES;
 729                         };
 730                         name = Debug;
 731                 };
 732                 1DEB923308733DC60010E9CD /* Release */ = {
 733                         isa = XCBuildConfiguration;
 734                         buildSettings = {
 735                                 DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym";
 736                                 GCC_MODEL_TUNING = G5;
 737                                 GCC_OPTIMIZATION_LEVEL = 3;
 738                                 INSTALL_PATH = /usr/local/bin;
 739                                 PRODUCT_NAME = mothur;
 740                         };
 741                         name = Release;
 742                 };
 743                 1DEB923608733DC60010E9CD /* Debug */ = {
 744                         isa = XCBuildConfiguration;
 745                         buildSettings = {
 746                                 GCC_OPTIMIZATION_LEVEL = 3;
 747                                 GCC_WARN_ABOUT_RETURN_TYPE = YES;
 748                                 GCC_WARN_UNUSED_VARIABLE = YES;
 749                                 INSTALL_MODE_FLAG = "a-w,a+rX";
 750                                 PREBINDING = NO;
 751                                 SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
 752                         };
 753                         name = Debug;
 754                 };
 755                 1DEB923708733DC60010E9CD /* Release */ = {
 756                         isa = XCBuildConfiguration;
 757                         buildSettings = {
 758                                 ARCHS = (
 759                                         ppc,
 760                                         i386,
 761                                 );
 762                                 GCC_OPTIMIZATION_LEVEL = 0;
 763                                 GCC_WARN_ABOUT_RETURN_TYPE = YES;
 764                                 GCC_WARN_UNUSED_VARIABLE = YES;
 765                                 INSTALL_MODE_FLAG = "a-w,a+rX";
 766                                 PREBINDING = NO;
 767                                 SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
 768                         };
 769                         name = Release;
 770                 };
 771 /* End XCBuildConfiguration section */
 772
 773 /* Begin XCConfigurationList section */
 774                 1DEB923108733DC60010E9CD /* Build configuration list for PBXNativeTarget "mothur" */ = {
 775                         isa = XCConfigurationList;
 776                         buildConfigurations = (
 777                                 1DEB923208733DC60010E9CD /* Debug */,
 778                                 1DEB923308733DC60010E9CD /* Release */,
 779                         );
 780                         defaultConfigurationIsVisible = 0;
 781                         defaultConfigurationName = Release;
 782                 };
 783                 1DEB923508733DC60010E9CD /* Build configuration list for PBXProject "Mothur" */ = {
 784                         isa = XCConfigurationList;
 785                         buildConfigurations = (
 786                                 1DEB923608733DC60010E9CD /* Debug */,
 787                                 1DEB923708733DC60010E9CD /* Release */,
 788                         );
 789                         defaultConfigurationIsVisible = 0;
 790                         defaultConfigurationName = Release;
 791                 };
 792 /* End XCConfigurationList section */
 793         };
 794         rootObject = 08FB7793FE84155DC02AAC07 /* Project object */;
 795 }