Mothur.xcodeproj/project.pbxproj

   1 // !$*UTF8*$!
   2 {
   3         archiveVersion = 1;
   4         classes = {
   5         };
   6         objectVersion = 44;
   7         objects = {
   8
   9 /* Begin PBXBuildFile section */
  10                 211C38320F961DD400FEE541 /* sharedutilities.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 211C38300F961DD400FEE541 /* sharedutilities.cpp */; };
  11                 211C38380F961E1F00FEE541 /* treegroupscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 211C38360F961E1F00FEE541 /* treegroupscommand.cpp */; };
  12                 21DDC01B0F97A8FE0060691C /* bootstrapsharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 21DDC01A0F97A8FE0060691C /* bootstrapsharedcommand.cpp */; };
  13                 21E859D80FC4632E005E1A48 /* matrixoutputcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 21E859D70FC4632E005E1A48 /* matrixoutputcommand.cpp */; };
  14                 370B88070F8A4EE4005AB382 /* getoturepcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */; };
  15                 371B30B40FD7EE67000414CA /* screenseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 371B30B20FD7EE67000414CA /* screenseqscommand.cpp */; };
  16                 372095C2103196D70004D347 /* chimera.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 372095C1103196D70004D347 /* chimera.cpp */; };
  17                 372A55551017922B00C5194B /* decalc.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 372A55541017922B00C5194B /* decalc.cpp */; };
  18                 372E12700F26365B0095CF7E /* readotucommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 372E126F0F26365B0095CF7E /* readotucommand.cpp */; };
  19                 372E12960F263D5A0095CF7E /* readdistcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 372E12950F263D5A0095CF7E /* readdistcommand.cpp */; };
  20                 372E12ED0F264D320095CF7E /* commandfactory.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 372E12EC0F264D320095CF7E /* commandfactory.cpp */; };
  21                 373C68A40FC1C07D00137ACD /* alignment.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C68A00FC1C07D00137ACD /* alignment.cpp */; };
  22                 373C68A50FC1C07D00137ACD /* alignmentcell.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C68A20FC1C07D00137ACD /* alignmentcell.cpp */; };
  23                 373C68BC0FC1C1A600137ACD /* gotohoverlap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C68BA0FC1C1A600137ACD /* gotohoverlap.cpp */; };
  24                 373C68C50FC1C25F00137ACD /* overlap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C68C30FC1C25F00137ACD /* overlap.cpp */; };
  25                 373C68CF0FC1C2D900137ACD /* needlemanoverlap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C68CD0FC1C2D900137ACD /* needlemanoverlap.cpp */; };
  26                 373C68DD0FC1C38D00137ACD /* blastalign.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C68DB0FC1C38D00137ACD /* blastalign.cpp */; };
  27                 373C68E50FC1C4A500137ACD /* noalign.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C68E30FC1C4A500137ACD /* noalign.cpp */; };
  28                 373C68F90FC1C6A800137ACD /* suffixdb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C68F30FC1C6A800137ACD /* suffixdb.cpp */; };
  29                 373C68FA0FC1C6A800137ACD /* suffixnodes.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C68F50FC1C6A800137ACD /* suffixnodes.cpp */; };
  30                 373C68FB0FC1C6A800137ACD /* suffixtree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C68F70FC1C6A800137ACD /* suffixtree.cpp */; };
  31                 373C69180FC1C8AF00137ACD /* blastdb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C69160FC1C8AF00137ACD /* blastdb.cpp */; };
  32                 373C691F0FC1C98600137ACD /* nast.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C691D0FC1C98600137ACD /* nast.cpp */; };
  33                 373C692B0FC1C9EB00137ACD /* nastreport.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C69290FC1C9EB00137ACD /* nastreport.cpp */; };
  34                 373C699A0FC1E63600137ACD /* boneh.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C69940FC1E63600137ACD /* boneh.cpp */; };
  35                 373C699B0FC1E63600137ACD /* efron.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C69960FC1E63600137ACD /* efron.cpp */; };
  36                 373C699C0FC1E63600137ACD /* solow.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C69980FC1E63600137ACD /* solow.cpp */; };
  37                 374610780F40645300460C57 /* unifracweightedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 374610770F40645300460C57 /* unifracweightedcommand.cpp */; };
  38                 3746107E0F4064D100460C57 /* weighted.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3746107D0F4064D100460C57 /* weighted.cpp */; };
  39                 374610830F40652400460C57 /* unweighted.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 374610820F40652400460C57 /* unweighted.cpp */; };
  40                 3746109D0F40657600460C57 /* unifracunweightedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */; };
  41                 3749271D0FD58C840031C06B /* getsabundcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3749271C0FD58C840031C06B /* getsabundcommand.cpp */; };
  42                 3749273F0FD5956B0031C06B /* getrabundcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3749273E0FD5956B0031C06B /* getrabundcommand.cpp */; };
  43                 374F2FEB100634B600E97C66 /* bellerophon.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 374F2FEA100634B600E97C66 /* bellerophon.cpp */; };
  44                 374F301310063B6F00E97C66 /* pintail.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 374F301210063B6F00E97C66 /* pintail.cpp */; };
  45                 37519A6B0F80E6EB00FED5E8 /* sharedanderbergs.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37519A6A0F80E6EB00FED5E8 /* sharedanderbergs.cpp */; };
  46                 37519AA10F810D0200FED5E8 /* venncommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37519AA00F810D0200FED5E8 /* venncommand.cpp */; };
  47                 37519AB50F810FAE00FED5E8 /* venn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37519AB40F810FAE00FED5E8 /* venn.cpp */; };
  48                 375873EC0F7D64520040F377 /* fullmatrix.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873EB0F7D64520040F377 /* fullmatrix.cpp */; };
  49                 375873EF0F7D646F0040F377 /* heatmap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873EE0F7D646F0040F377 /* heatmap.cpp */; };
  50                 375873F20F7D64800040F377 /* heatmapcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873F00F7D64800040F377 /* heatmapcommand.cpp */; };
  51                 375873F50F7D648F0040F377 /* libshuffcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873F30F7D648F0040F377 /* libshuffcommand.cpp */; };
  52                 375873F80F7D649C0040F377 /* nocommands.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873F60F7D649C0040F377 /* nocommands.cpp */; };
  53                 375873FD0F7D64DA0040F377 /* sharedbraycurtis.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873FC0F7D64DA0040F377 /* sharedbraycurtis.cpp */; };
  54                 375874040F7D64EF0040F377 /* sharedkulczynski.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873FE0F7D64EF0040F377 /* sharedkulczynski.cpp */; };
  55                 375874050F7D64EF0040F377 /* sharedlennon.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873FF0F7D64EF0040F377 /* sharedlennon.cpp */; };
  56                 375874060F7D64EF0040F377 /* sharedkulczynskicody.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375874020F7D64EF0040F377 /* sharedkulczynskicody.cpp */; };
  57                 3758740C0F7D64FC0040F377 /* sharedmorisitahorn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375874080F7D64FC0040F377 /* sharedmorisitahorn.cpp */; };
  58                 3758740D0F7D64FC0040F377 /* sharedochiai.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3758740B0F7D64FC0040F377 /* sharedochiai.cpp */; };
  59                 375AA1390F9E433D008EF9B8 /* readcolumn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375AA1330F9E433D008EF9B8 /* readcolumn.cpp */; };
  60                 375AA13A0F9E433D008EF9B8 /* readotu.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375AA1350F9E433D008EF9B8 /* readotu.cpp */; };
  61                 375AA13B0F9E433D008EF9B8 /* readphylip.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375AA1370F9E433D008EF9B8 /* readphylip.cpp */; };
  62                 377326650FAF16E0007ABB8B /* consensuscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 377326630FAF16E0007ABB8B /* consensuscommand.cpp */; };
  63                 378598660FDD497000EF9D03 /* heatmapsimcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378598650FDD497000EF9D03 /* heatmapsimcommand.cpp */; };
  64                 378598740FDD4C1500EF9D03 /* heatmapsim.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378598730FDD4C1500EF9D03 /* heatmapsim.cpp */; };
  65                 378599100FDD7E8E00EF9D03 /* optionparser.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3785990F0FDD7E8E00EF9D03 /* optionparser.cpp */; };
  66                 378C1B030FB0644E004D63F5 /* filterseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378C1AEE0FB0644D004D63F5 /* filterseqscommand.cpp */; };
  67                 378C1B040FB0644E004D63F5 /* goodscoverage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378C1AF00FB0644D004D63F5 /* goodscoverage.cpp */; };
  68                 378C1B0A0FB0644E004D63F5 /* sequencedb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378C1AFD0FB0644D004D63F5 /* sequencedb.cpp */; };
  69                 378C1B0B0FB0644E004D63F5 /* sharedjackknife.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378C1AFF0FB0644D004D63F5 /* sharedjackknife.cpp */; };
  70                 378C1B0C0FB0644E004D63F5 /* sharedmarczewski.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378C1B010FB0644D004D63F5 /* sharedmarczewski.cpp */; };
  71                 378DC5CF0FBDE1C8003B8607 /* aligncommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378DC5CE0FBDE1C8003B8607 /* aligncommand.cpp */; };
  72                 379293C30F2DE73400B9034A /* treemap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 379293C20F2DE73400B9034A /* treemap.cpp */; };
  73                 379294700F2E191800B9034A /* parsimonycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3792946F0F2E191800B9034A /* parsimonycommand.cpp */; };
  74                 3792948A0F2E258500B9034A /* parsimony.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 379294890F2E258500B9034A /* parsimony.cpp */; };
  75                 3799A9510FD6A58C00E33EDE /* seqsummarycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3799A94E0FD6A58C00E33EDE /* seqsummarycommand.cpp */; };
  76                 379D3D510FF90E090068C1C0 /* chimeraseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 379D3D500FF90E090068C1C0 /* chimeraseqscommand.cpp */; };
  77                 37AD4CE40F28AEA300AA2D49 /* sharedlistvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */; };
  78                 37AD4DBB0F28E2FE00AA2D49 /* tree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */; };
  79                 37AD4DCA0F28F3DD00AA2D49 /* readtree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */; };
  80                 37AFC71F0F445386005F492D /* sharedsobscollectsummary.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */; };
  81                 37B28F680F27590100808A62 /* deconvolutecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37B28F670F27590100808A62 /* deconvolutecommand.cpp */; };
  82                 37B73C761004BEFD008C4B41 /* listseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37B73C751004BEFD008C4B41 /* listseqscommand.cpp */; };
  83                 37B73CA61004D89A008C4B41 /* getseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37B73CA51004D89A008C4B41 /* getseqscommand.cpp */; };
  84                 37B73CC01004EB38008C4B41 /* removeseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37B73CBF1004EB38008C4B41 /* removeseqscommand.cpp */; };
  85                 37B73CCF1004F5E0008C4B41 /* systemcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37B73CCE1004F5E0008C4B41 /* systemcommand.cpp */; };
  86                 37C1D9730F86506E0059E3F0 /* binsequencecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */; };
  87                 37C753CE0FB3415200DBD02E /* distancecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37C753CD0FB3415200DBD02E /* distancecommand.cpp */; };
  88                 37D928550F21331F001D4494 /* ace.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927B80F21331F001D4494 /* ace.cpp */; };
  89                 37D928560F21331F001D4494 /* averagelinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927BA0F21331F001D4494 /* averagelinkage.cpp */; };
  90                 37D928570F21331F001D4494 /* bootstrap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927BB0F21331F001D4494 /* bootstrap.cpp */; };
  91                 37D928580F21331F001D4494 /* calculator.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927BD0F21331F001D4494 /* calculator.cpp */; };
  92                 37D928590F21331F001D4494 /* chao1.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927BF0F21331F001D4494 /* chao1.cpp */; };
  93                 37D9285A0F21331F001D4494 /* cluster.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927C10F21331F001D4494 /* cluster.cpp */; };
  94                 37D9285B0F21331F001D4494 /* clustercommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927C30F21331F001D4494 /* clustercommand.cpp */; };
  95                 37D9285C0F21331F001D4494 /* collect.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927C50F21331F001D4494 /* collect.cpp */; };
  96                 37D9285D0F21331F001D4494 /* collectcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927C70F21331F001D4494 /* collectcommand.cpp */; };
  97                 37D9285E0F21331F001D4494 /* collectsharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */; };
  98                 37D928600F21331F001D4494 /* commandoptionparser.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927D00F21331F001D4494 /* commandoptionparser.cpp */; };
  99                 37D928610F21331F001D4494 /* completelinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927D20F21331F001D4494 /* completelinkage.cpp */; };
 100                 37D928620F21331F001D4494 /* database.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927D30F21331F001D4494 /* database.cpp */; };
 101                 37D928630F21331F001D4494 /* engine.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927D70F21331F001D4494 /* engine.cpp */; };
 102                 37D928650F21331F001D4494 /* fastamap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927DB0F21331F001D4494 /* fastamap.cpp */; };
 103                 37D928660F21331F001D4494 /* fileoutput.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927DD0F21331F001D4494 /* fileoutput.cpp */; };
 104                 37D928670F21331F001D4494 /* globaldata.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927DF0F21331F001D4494 /* globaldata.cpp */; };
 105                 37D928680F21331F001D4494 /* groupmap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927E10F21331F001D4494 /* groupmap.cpp */; };
 106                 37D928690F21331F001D4494 /* helpcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927E30F21331F001D4494 /* helpcommand.cpp */; };
 107                 37D9286A0F21331F001D4494 /* inputdata.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927E50F21331F001D4494 /* inputdata.cpp */; };
 108                 37D9286B0F21331F001D4494 /* jackknife.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927E70F21331F001D4494 /* jackknife.cpp */; };
 109                 37D9286C0F21331F001D4494 /* kmer.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927E90F21331F001D4494 /* kmer.cpp */; };
 110                 37D9286D0F21331F001D4494 /* kmerdb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927EB0F21331F001D4494 /* kmerdb.cpp */; };
 111                 37D9286E0F21331F001D4494 /* listvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927ED0F21331F001D4494 /* listvector.cpp */; };
 112                 37D9286F0F21331F001D4494 /* mothur.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927EF0F21331F001D4494 /* mothur.cpp */; };
 113                 37D928700F21331F001D4494 /* nameassignment.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927F00F21331F001D4494 /* nameassignment.cpp */; };
 114                 37D928720F21331F001D4494 /* npshannon.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927F40F21331F001D4494 /* npshannon.cpp */; };
 115                 37D928730F21331F001D4494 /* ordervector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927F70F21331F001D4494 /* ordervector.cpp */; };
 116                 37D928750F21331F001D4494 /* progress.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927FB0F21331F001D4494 /* progress.cpp */; };
 117                 37D928760F21331F001D4494 /* quitcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927FD0F21331F001D4494 /* quitcommand.cpp */; };
 118                 37D928770F21331F001D4494 /* rabundvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927FF0F21331F001D4494 /* rabundvector.cpp */; };
 119                 37D928780F21331F001D4494 /* rarecalc.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928010F21331F001D4494 /* rarecalc.cpp */; };
 120                 37D928790F21331F001D4494 /* raredisplay.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928030F21331F001D4494 /* raredisplay.cpp */; };
 121                 37D9287A0F21331F001D4494 /* rarefact.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928050F21331F001D4494 /* rarefact.cpp */; };
 122                 37D9287B0F21331F001D4494 /* rarefactcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928070F21331F001D4494 /* rarefactcommand.cpp */; };
 123                 37D9287C0F21331F001D4494 /* rarefactsharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */; };
 124                 37D928840F21331F001D4494 /* sabundvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9281A0F21331F001D4494 /* sabundvector.cpp */; };
 125                 37D928850F21331F001D4494 /* sequence.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9281C0F21331F001D4494 /* sequence.cpp */; };
 126                 37D928860F21331F001D4494 /* shannon.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9281E0F21331F001D4494 /* shannon.cpp */; };
 127                 37D928880F21331F001D4494 /* sharedace.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928220F21331F001D4494 /* sharedace.cpp */; };
 128                 37D928890F21331F001D4494 /* sharedchao1.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928240F21331F001D4494 /* sharedchao1.cpp */; };
 129                 37D9288A0F21331F001D4494 /* sharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928260F21331F001D4494 /* sharedcommand.cpp */; };
 130                 37D9288B0F21331F001D4494 /* sharedjabund.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928280F21331F001D4494 /* sharedjabund.cpp */; };
 131                 37D9288C0F21331F001D4494 /* sharedjclass.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9282A0F21331F001D4494 /* sharedjclass.cpp */; };
 132                 37D9288D0F21331F001D4494 /* sharedjest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9282C0F21331F001D4494 /* sharedjest.cpp */; };
 133                 37D9288E0F21331F001D4494 /* sharedordervector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9282E0F21331F001D4494 /* sharedordervector.cpp */; };
 134                 37D9288F0F21331F001D4494 /* sharedrabundvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928300F21331F001D4494 /* sharedrabundvector.cpp */; };
 135                 37D928900F21331F001D4494 /* sharedsabundvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928320F21331F001D4494 /* sharedsabundvector.cpp */; };
 136                 37D928910F21331F001D4494 /* sharedsobs.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928340F21331F001D4494 /* sharedsobs.cpp */; };
 137                 37D928920F21331F001D4494 /* sharedsorabund.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928360F21331F001D4494 /* sharedsorabund.cpp */; };
 138                 37D928930F21331F001D4494 /* sharedsorclass.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928380F21331F001D4494 /* sharedsorclass.cpp */; };
 139                 37D928940F21331F001D4494 /* sharedsorest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9283A0F21331F001D4494 /* sharedsorest.cpp */; };
 140                 37D928950F21331F001D4494 /* sharedthetan.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9283C0F21331F001D4494 /* sharedthetan.cpp */; };
 141                 37D928960F21331F001D4494 /* sharedthetayc.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9283E0F21331F001D4494 /* sharedthetayc.cpp */; };
 142                 37D928970F21331F001D4494 /* simpson.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928400F21331F001D4494 /* simpson.cpp */; };
 143                 37D928980F21331F001D4494 /* singlelinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928420F21331F001D4494 /* singlelinkage.cpp */; };
 144                 37D928990F21331F001D4494 /* sparsematrix.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928440F21331F001D4494 /* sparsematrix.cpp */; };
 145                 37D9289A0F21331F001D4494 /* summarycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928460F21331F001D4494 /* summarycommand.cpp */; };
 146                 37D9289B0F21331F001D4494 /* summarysharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */; };
 147                 37D9289C0F21331F001D4494 /* uvest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9284D0F21331F001D4494 /* uvest.cpp */; };
 148                 37D9289D0F21331F001D4494 /* validcalculator.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9284F0F21331F001D4494 /* validcalculator.cpp */; };
 149                 37D9289F0F21331F001D4494 /* validparameter.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928530F21331F001D4494 /* validparameter.cpp */; };
 150                 37E5F3E30F29FD4200F8D827 /* treenode.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37E5F3E20F29FD4200F8D827 /* treenode.cpp */; };
 151                 37E5F4920F2A3DA800F8D827 /* readtreecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */; };
 152                 7E09C5140FDA79C5002ECAE5 /* reversecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E09C5130FDA79C5002ECAE5 /* reversecommand.cpp */; };
 153                 7E09C5360FDA7F65002ECAE5 /* trimseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E09C5350FDA7F65002ECAE5 /* trimseqscommand.cpp */; };
 154                 7E412F490F8D21B600381DD0 /* slibshuff.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E412F480F8D21B600381DD0 /* slibshuff.cpp */; };
 155                 7E412FEA0F8D3E2C00381DD0 /* libshuff.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */; };
 156                 7E4130F80F8E58FA00381DD0 /* dlibshuff.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E4130F60F8E58FA00381DD0 /* dlibshuff.cpp */; };
 157                 7E5A17AF0FE57292003C6A03 /* mergefilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E5A17AE0FE57292003C6A03 /* mergefilecommand.cpp */; };
 158                 7EC3D4550FA0FFF900338DA5 /* coverage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7EC3D4500FA0FFF900338DA5 /* coverage.cpp */; };
 159                 7EC3D4560FA0FFF900338DA5 /* whittaker.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7EC3D4530FA0FFF900338DA5 /* whittaker.cpp */; };
 160                 8DD76F6A0486A84900D96B5E /* Mothur.1 in CopyFiles */ = {isa = PBXBuildFile; fileRef = C6859E8B029090EE04C91782 /* Mothur.1 */; };
 161                 A7027F2810DFF86D00BF45FE /* preclustercommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7027F2710DFF86D00BF45FE /* preclustercommand.cpp */; };
 162                 A704E8A31106045D00870157 /* otuhierarchycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A704E8A21106045D00870157 /* otuhierarchycommand.cpp */; };
 163                 A70B00C8110885EB002F453A /* setdircommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70B00C7110885EB002F453A /* setdircommand.cpp */; };
 164                 A70B53AA0F4CD7AD0064797E /* getgroupcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */; };
 165                 A70B53AB0F4CD7AD0064797E /* getlabelcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */; };
 166                 A70DECD91063D8B40057C03C /* secondarystructurecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70DECD81063D8B40057C03C /* secondarystructurecommand.cpp */; };
 167                 A70F3FD01136E391004FDC52 /* mothurout.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70F3FCF1136E391004FDC52 /* mothurout.cpp */; };
 168                 A71CB8A311354B9F00848EF7 /* parselistscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A71CB8A211354B9F00848EF7 /* parselistscommand.cpp */; };
 169                 A727E84A10D14568001A8432 /* readblast.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A727E84910D14568001A8432 /* readblast.cpp */; };
 170                 A7283FF81056CAE100D0CC69 /* chimeracheckrdp.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7283FF71056CAE100D0CC69 /* chimeracheckrdp.cpp */; };
 171                 A729ACD010848E6100139801 /* hclustercommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A729ACCF10848E6100139801 /* hclustercommand.cpp */; };
 172                 A729ACE410849BBE00139801 /* hcluster.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A729ACE310849BBE00139801 /* hcluster.cpp */; };
 173                 A73329CF1083B3B3003B10C5 /* getlistcountcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A73329CE1083B3B3003B10C5 /* getlistcountcommand.cpp */; };
 174                 A751ACEA1098B283003D0911 /* readcluster.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A751ACE91098B283003D0911 /* readcluster.cpp */; };
 175                 A75B887E104C16860083C454 /* ccode.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A75B887B104C16860083C454 /* ccode.cpp */; };
 176                 A773805F10B6D6FC002A6A61 /* taxonomyequalizer.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A773805E10B6D6FC002A6A61 /* taxonomyequalizer.cpp */; };
 177                 A773809010B6EFD1002A6A61 /* phylotypecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A773808F10B6EFD1002A6A61 /* phylotypecommand.cpp */; };
 178                 A7861478109F5FA00010AAAF /* classifyseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7861477109F5FA00010AAAF /* classifyseqscommand.cpp */; };
 179                 A787810310A06D5D0086103D /* classify.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A787810210A06D5D0086103D /* classify.cpp */; };
 180                 A78781BA10A0813E0086103D /* phylotree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A78781B810A0813D0086103D /* phylotree.cpp */; };
 181                 A787821110A0AAE70086103D /* bayesian.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A787821010A0AAE70086103D /* bayesian.cpp */; };
 182                 A78782AB10A1B1CB0086103D /* alignmentdb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A78782AA10A1B1CB0086103D /* alignmentdb.cpp */; };
 183                 A787844510A1EBDD0086103D /* knn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A787844410A1EBDD0086103D /* knn.cpp */; };
 184                 A794201111107897003AECCD /* distancedb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A794200F11107897003AECCD /* distancedb.cpp */; };
 185                 A7B04493106CC3E60046FC83 /* chimeraslayer.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7B04492106CC3E60046FC83 /* chimeraslayer.cpp */; };
 186                 A7B0450E106CEEC90046FC83 /* slayer.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7B0450D106CEEC90046FC83 /* slayer.cpp */; };
 187                 A7D176CF10F2558500159497 /* pcacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7D176CE10F2558500159497 /* pcacommand.cpp */; };
 188                 A7D86C7D10FE09AB00865661 /* formatcolumn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7D86C7C10FE09AB00865661 /* formatcolumn.cpp */; };
 189                 A7D86C8C10FE09FE00865661 /* formatphylip.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7D86C8B10FE09FE00865661 /* formatphylip.cpp */; };
 190                 A7E0AAB610D2886D00CF407B /* mgclustercommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E0AAB510D2886D00CF407B /* mgclustercommand.cpp */; };
 191                 A7E4A783106913F900688F62 /* getsharedotucommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E4A782106913F900688F62 /* getsharedotucommand.cpp */; };
 192                 A7E4A824106A9AD700688F62 /* maligner.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E4A823106A9AD700688F62 /* maligner.cpp */; };
 193                 A7E8A22F1125939F0011D39C /* chimerarealigner.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E8A22E1125939F0011D39C /* chimerarealigner.cpp */; };
 194                 A7F5759710CEBC0600E20E47 /* libreadline.a in Frameworks */ = {isa = PBXBuildFile; fileRef = A7F5759610CEBC0600E20E47 /* libreadline.a */; };
 195                 EB1216880F619B83004A865F /* bergerparker.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB1216870F619B83004A865F /* bergerparker.cpp */; };
 196                 EB1216E50F61ACFB004A865F /* bstick.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB1216E40F61ACFB004A865F /* bstick.cpp */; };
 197                 EB1217230F61C9AC004A865F /* sharedkstest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB1217220F61C9AC004A865F /* sharedkstest.cpp */; };
 198                 EB6E68190F5F1C780044E17B /* qstat.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB6E68180F5F1C780044E17B /* qstat.cpp */; };
 199                 EB72FE260FC1F5CA0051AC11 /* shen.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB72FE240FC1F5CA0051AC11 /* shen.cpp */; };
 200                 EB9303EB0F534D9400E8EF26 /* logsd.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB9303EA0F534D9400E8EF26 /* logsd.cpp */; };
 201                 EB9303F90F53517300E8EF26 /* geom.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB9303F80F53517300E8EF26 /* geom.cpp */; };
 202 /* End PBXBuildFile section */
 203
 204 /* Begin PBXCopyFilesBuildPhase section */
 205                 8DD76F690486A84900D96B5E /* CopyFiles */ = {
 206                         isa = PBXCopyFilesBuildPhase;
 207                         buildActionMask = 8;
 208                         dstPath = /usr/share/man/man1/;
 209                         dstSubfolderSpec = 0;
 210                         files = (
 211                                 8DD76F6A0486A84900D96B5E /* Mothur.1 in CopyFiles */,
 212                         );
 213                         runOnlyForDeploymentPostprocessing = 1;
 214                 };
 215 /* End PBXCopyFilesBuildPhase section */
 216
 217 /* Begin PBXFileReference section */
 218                 211C38300F961DD400FEE541 /* sharedutilities.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedutilities.cpp; sourceTree = SOURCE_ROOT; };
 219                 211C38310F961DD400FEE541 /* sharedutilities.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedutilities.h; sourceTree = SOURCE_ROOT; };
 220                 211C38360F961E1F00FEE541 /* treegroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treegroupscommand.cpp; sourceTree = SOURCE_ROOT; };
 221                 211C38370F961E1F00FEE541 /* treegroupscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treegroupscommand.h; sourceTree = SOURCE_ROOT; };
 222                 21DDC0190F97A8FE0060691C /* bootstrapsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bootstrapsharedcommand.h; sourceTree = SOURCE_ROOT; };
 223                 21DDC01A0F97A8FE0060691C /* bootstrapsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bootstrapsharedcommand.cpp; sourceTree = SOURCE_ROOT; };
 224                 21E859D60FC4632E005E1A48 /* matrixoutputcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = matrixoutputcommand.h; sourceTree = SOURCE_ROOT; };
 225                 21E859D70FC4632E005E1A48 /* matrixoutputcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = matrixoutputcommand.cpp; sourceTree = SOURCE_ROOT; };
 226                 370B88050F8A4EE4005AB382 /* getoturepcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getoturepcommand.h; sourceTree = SOURCE_ROOT; };
 227                 370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getoturepcommand.cpp; sourceTree = SOURCE_ROOT; };
 228                 371B30B20FD7EE67000414CA /* screenseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = screenseqscommand.cpp; sourceTree = SOURCE_ROOT; };
 229                 371B30B30FD7EE67000414CA /* screenseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = screenseqscommand.h; sourceTree = SOURCE_ROOT; };
 230                 372095C1103196D70004D347 /* chimera.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimera.cpp; sourceTree = SOURCE_ROOT; };
 231                 372A55531017922B00C5194B /* decalc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = decalc.h; sourceTree = SOURCE_ROOT; };
 232                 372A55541017922B00C5194B /* decalc.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = decalc.cpp; sourceTree = SOURCE_ROOT; };
 233                 372E126E0F26365B0095CF7E /* readotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotucommand.h; sourceTree = SOURCE_ROOT; };
 234                 372E126F0F26365B0095CF7E /* readotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readotucommand.cpp; sourceTree = SOURCE_ROOT; };
 235                 372E12940F263D5A0095CF7E /* readdistcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readdistcommand.h; sourceTree = SOURCE_ROOT; };
 236                 372E12950F263D5A0095CF7E /* readdistcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readdistcommand.cpp; sourceTree = SOURCE_ROOT; };
 237                 372E12EC0F264D320095CF7E /* commandfactory.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = commandfactory.cpp; sourceTree = SOURCE_ROOT; };
 238                 373C68A00FC1C07D00137ACD /* alignment.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = alignment.cpp; sourceTree = SOURCE_ROOT; };
 239                 373C68A10FC1C07D00137ACD /* alignment.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = alignment.hpp; sourceTree = SOURCE_ROOT; };
 240                 373C68A20FC1C07D00137ACD /* alignmentcell.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = alignmentcell.cpp; sourceTree = SOURCE_ROOT; };
 241                 373C68A30FC1C07D00137ACD /* alignmentcell.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = alignmentcell.hpp; sourceTree = SOURCE_ROOT; };
 242                 373C68BA0FC1C1A600137ACD /* gotohoverlap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = gotohoverlap.cpp; sourceTree = SOURCE_ROOT; };
 243                 373C68BB0FC1C1A600137ACD /* gotohoverlap.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = gotohoverlap.hpp; sourceTree = SOURCE_ROOT; };
 244                 373C68C30FC1C25F00137ACD /* overlap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = overlap.cpp; sourceTree = SOURCE_ROOT; };
 245                 373C68C40FC1C25F00137ACD /* overlap.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = overlap.hpp; sourceTree = SOURCE_ROOT; };
 246                 373C68CD0FC1C2D900137ACD /* needlemanoverlap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = needlemanoverlap.cpp; sourceTree = SOURCE_ROOT; };
 247                 373C68CE0FC1C2D900137ACD /* needlemanoverlap.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = needlemanoverlap.hpp; sourceTree = SOURCE_ROOT; };
 248                 373C68DB0FC1C38D00137ACD /* blastalign.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = blastalign.cpp; sourceTree = SOURCE_ROOT; };
 249                 373C68DC0FC1C38D00137ACD /* blastalign.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = blastalign.hpp; sourceTree = SOURCE_ROOT; };
 250                 373C68E30FC1C4A500137ACD /* noalign.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = noalign.cpp; sourceTree = SOURCE_ROOT; };
 251                 373C68E40FC1C4A500137ACD /* noalign.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = noalign.hpp; sourceTree = SOURCE_ROOT; };
 252                 373C68F30FC1C6A800137ACD /* suffixdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixdb.cpp; sourceTree = SOURCE_ROOT; };
 253                 373C68F40FC1C6A800137ACD /* suffixdb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixdb.hpp; sourceTree = SOURCE_ROOT; };
 254                 373C68F50FC1C6A800137ACD /* suffixnodes.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixnodes.cpp; sourceTree = SOURCE_ROOT; };
 255                 373C68F60FC1C6A800137ACD /* suffixnodes.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixnodes.hpp; sourceTree = SOURCE_ROOT; };
 256                 373C68F70FC1C6A800137ACD /* suffixtree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixtree.cpp; sourceTree = SOURCE_ROOT; };
 257                 373C68F80FC1C6A800137ACD /* suffixtree.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixtree.hpp; sourceTree = SOURCE_ROOT; };
 258                 373C69160FC1C8AF00137ACD /* blastdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = blastdb.cpp; sourceTree = SOURCE_ROOT; };
 259                 373C69170FC1C8AF00137ACD /* blastdb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = blastdb.hpp; sourceTree = SOURCE_ROOT; };
 260                 373C691D0FC1C98600137ACD /* nast.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nast.cpp; sourceTree = SOURCE_ROOT; };
 261                 373C691E0FC1C98600137ACD /* nast.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = nast.hpp; sourceTree = SOURCE_ROOT; };
 262                 373C69290FC1C9EB00137ACD /* nastreport.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nastreport.cpp; sourceTree = SOURCE_ROOT; };
 263                 373C692A0FC1C9EB00137ACD /* nastreport.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = nastreport.hpp; sourceTree = SOURCE_ROOT; };
 264                 373C69940FC1E63600137ACD /* boneh.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = boneh.cpp; sourceTree = SOURCE_ROOT; };
 265                 373C69950FC1E63600137ACD /* boneh.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = boneh.h; sourceTree = SOURCE_ROOT; };
 266                 373C69960FC1E63600137ACD /* efron.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = efron.cpp; sourceTree = SOURCE_ROOT; };
 267                 373C69970FC1E63600137ACD /* efron.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = efron.h; sourceTree = SOURCE_ROOT; };
 268                 373C69980FC1E63600137ACD /* solow.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = solow.cpp; sourceTree = SOURCE_ROOT; };
 269                 373C69990FC1E63600137ACD /* solow.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = solow.h; sourceTree = SOURCE_ROOT; };
 270                 374610760F40645300460C57 /* unifracweightedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unifracweightedcommand.h; sourceTree = SOURCE_ROOT; };
 271                 374610770F40645300460C57 /* unifracweightedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unifracweightedcommand.cpp; sourceTree = SOURCE_ROOT; };
 272                 3746107C0F4064D100460C57 /* weighted.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = weighted.h; sourceTree = SOURCE_ROOT; };
 273                 3746107D0F4064D100460C57 /* weighted.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = weighted.cpp; sourceTree = SOURCE_ROOT; };
 274                 374610810F40652400460C57 /* unweighted.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unweighted.h; sourceTree = SOURCE_ROOT; };
 275                 374610820F40652400460C57 /* unweighted.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unweighted.cpp; sourceTree = SOURCE_ROOT; };
 276                 3746109B0F40657600460C57 /* unifracunweightedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unifracunweightedcommand.h; sourceTree = SOURCE_ROOT; };
 277                 3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unifracunweightedcommand.cpp; sourceTree = SOURCE_ROOT; };
 278                 3749271B0FD58C840031C06B /* getsabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getsabundcommand.h; sourceTree = SOURCE_ROOT; };
 279                 3749271C0FD58C840031C06B /* getsabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getsabundcommand.cpp; sourceTree = SOURCE_ROOT; };
 280                 3749273D0FD5956B0031C06B /* getrabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getrabundcommand.h; sourceTree = SOURCE_ROOT; };
 281                 3749273E0FD5956B0031C06B /* getrabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getrabundcommand.cpp; sourceTree = SOURCE_ROOT; };
 282                 374F2FD51006320200E97C66 /* chimera.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimera.h; sourceTree = SOURCE_ROOT; };
 283                 374F2FE9100634B600E97C66 /* bellerophon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bellerophon.h; sourceTree = SOURCE_ROOT; };
 284                 374F2FEA100634B600E97C66 /* bellerophon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bellerophon.cpp; sourceTree = SOURCE_ROOT; };
 285                 374F301110063B6F00E97C66 /* pintail.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pintail.h; sourceTree = SOURCE_ROOT; };
 286                 374F301210063B6F00E97C66 /* pintail.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pintail.cpp; sourceTree = SOURCE_ROOT; };
 287                 37519A690F80E6EB00FED5E8 /* sharedanderbergs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedanderbergs.h; sourceTree = SOURCE_ROOT; };
 288                 37519A6A0F80E6EB00FED5E8 /* sharedanderbergs.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedanderbergs.cpp; sourceTree = SOURCE_ROOT; };
 289                 37519A9F0F810D0200FED5E8 /* venncommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = venncommand.h; sourceTree = SOURCE_ROOT; };
 290                 37519AA00F810D0200FED5E8 /* venncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = venncommand.cpp; sourceTree = SOURCE_ROOT; };
 291                 37519AB30F810FAE00FED5E8 /* venn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = venn.h; sourceTree = SOURCE_ROOT; };
 292                 37519AB40F810FAE00FED5E8 /* venn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = venn.cpp; sourceTree = SOURCE_ROOT; };
 293                 375873EA0F7D64520040F377 /* fullmatrix.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fullmatrix.h; sourceTree = SOURCE_ROOT; };
 294                 375873EB0F7D64520040F377 /* fullmatrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fullmatrix.cpp; sourceTree = SOURCE_ROOT; };
 295                 375873ED0F7D646F0040F377 /* heatmap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmap.h; sourceTree = SOURCE_ROOT; };
 296                 375873EE0F7D646F0040F377 /* heatmap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmap.cpp; sourceTree = SOURCE_ROOT; };
 297                 375873F00F7D64800040F377 /* heatmapcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapcommand.cpp; sourceTree = SOURCE_ROOT; };
 298                 375873F10F7D64800040F377 /* heatmapcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapcommand.h; sourceTree = SOURCE_ROOT; };
 299                 375873F30F7D648F0040F377 /* libshuffcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = libshuffcommand.cpp; sourceTree = SOURCE_ROOT; };
 300                 375873F40F7D648F0040F377 /* libshuffcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = libshuffcommand.h; sourceTree = SOURCE_ROOT; };
 301                 375873F60F7D649C0040F377 /* nocommands.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nocommands.cpp; sourceTree = SOURCE_ROOT; };
 302                 375873F70F7D649C0040F377 /* nocommands.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = nocommands.h; sourceTree = SOURCE_ROOT; };
 303                 375873F90F7D64AB0040F377 /* nseqs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = nseqs.h; sourceTree = SOURCE_ROOT; };
 304                 375873FB0F7D64DA0040F377 /* sharedbraycurtis.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedbraycurtis.h; sourceTree = SOURCE_ROOT; };
 305                 375873FC0F7D64DA0040F377 /* sharedbraycurtis.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedbraycurtis.cpp; sourceTree = SOURCE_ROOT; };
 306                 375873FE0F7D64EF0040F377 /* sharedkulczynski.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedkulczynski.cpp; sourceTree = SOURCE_ROOT; };
 307                 375873FF0F7D64EF0040F377 /* sharedlennon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedlennon.cpp; sourceTree = SOURCE_ROOT; };
 308                 375874000F7D64EF0040F377 /* sharedkulczynski.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedkulczynski.h; sourceTree = SOURCE_ROOT; };
 309                 375874010F7D64EF0040F377 /* sharedlennon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedlennon.h; sourceTree = SOURCE_ROOT; };
 310                 375874020F7D64EF0040F377 /* sharedkulczynskicody.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedkulczynskicody.cpp; sourceTree = SOURCE_ROOT; };
 311                 375874030F7D64EF0040F377 /* sharedkulczynskicody.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedkulczynskicody.h; sourceTree = SOURCE_ROOT; };
 312                 375874070F7D64FC0040F377 /* sharedmorisitahorn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedmorisitahorn.h; sourceTree = SOURCE_ROOT; };
 313                 375874080F7D64FC0040F377 /* sharedmorisitahorn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedmorisitahorn.cpp; sourceTree = SOURCE_ROOT; };
 314                 375874090F7D64FC0040F377 /* sharedochiai.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedochiai.h; sourceTree = SOURCE_ROOT; };
 315                 3758740A0F7D64FC0040F377 /* sharednseqs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharednseqs.h; sourceTree = SOURCE_ROOT; };
 316                 3758740B0F7D64FC0040F377 /* sharedochiai.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedochiai.cpp; sourceTree = SOURCE_ROOT; };
 317                 375AA1330F9E433D008EF9B8 /* readcolumn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readcolumn.cpp; sourceTree = SOURCE_ROOT; };
 318                 375AA1340F9E433D008EF9B8 /* readcolumn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readcolumn.h; sourceTree = SOURCE_ROOT; };
 319                 375AA1350F9E433D008EF9B8 /* readotu.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readotu.cpp; sourceTree = SOURCE_ROOT; };
 320                 375AA1360F9E433D008EF9B8 /* readotu.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotu.h; sourceTree = SOURCE_ROOT; };
 321                 375AA1370F9E433D008EF9B8 /* readphylip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readphylip.cpp; sourceTree = SOURCE_ROOT; };
 322                 375AA1380F9E433D008EF9B8 /* readphylip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylip.h; sourceTree = SOURCE_ROOT; };
 323                 377326630FAF16E0007ABB8B /* consensuscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = consensuscommand.cpp; sourceTree = SOURCE_ROOT; };
 324                 377326640FAF16E0007ABB8B /* consensuscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = consensuscommand.h; sourceTree = SOURCE_ROOT; };
 325                 378598640FDD497000EF9D03 /* heatmapsimcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapsimcommand.h; sourceTree = SOURCE_ROOT; };
 326                 378598650FDD497000EF9D03 /* heatmapsimcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapsimcommand.cpp; sourceTree = SOURCE_ROOT; };
 327                 378598720FDD4C1500EF9D03 /* heatmapsim.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapsim.h; sourceTree = SOURCE_ROOT; };
 328                 378598730FDD4C1500EF9D03 /* heatmapsim.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapsim.cpp; sourceTree = SOURCE_ROOT; };
 329                 3785990E0FDD7E8E00EF9D03 /* optionparser.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = optionparser.h; sourceTree = SOURCE_ROOT; };
 330                 3785990F0FDD7E8E00EF9D03 /* optionparser.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = optionparser.cpp; sourceTree = SOURCE_ROOT; };
 331                 378C1AEE0FB0644D004D63F5 /* filterseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = filterseqscommand.cpp; sourceTree = SOURCE_ROOT; };
 332                 378C1AEF0FB0644D004D63F5 /* filterseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = filterseqscommand.h; sourceTree = SOURCE_ROOT; };
 333                 378C1AF00FB0644D004D63F5 /* goodscoverage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = goodscoverage.cpp; sourceTree = SOURCE_ROOT; };
 334                 378C1AF10FB0644D004D63F5 /* goodscoverage.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = goodscoverage.h; sourceTree = SOURCE_ROOT; };
 335                 378C1AFD0FB0644D004D63F5 /* sequencedb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sequencedb.cpp; sourceTree = SOURCE_ROOT; };
 336                 378C1AFE0FB0644D004D63F5 /* sequencedb.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sequencedb.h; sourceTree = SOURCE_ROOT; };
 337                 378C1AFF0FB0644D004D63F5 /* sharedjackknife.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjackknife.cpp; sourceTree = SOURCE_ROOT; };
 338                 378C1B000FB0644D004D63F5 /* sharedjackknife.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjackknife.h; sourceTree = SOURCE_ROOT; };
 339                 378C1B010FB0644D004D63F5 /* sharedmarczewski.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedmarczewski.cpp; sourceTree = SOURCE_ROOT; };
 340                 378C1B020FB0644D004D63F5 /* sharedmarczewski.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedmarczewski.h; sourceTree = SOURCE_ROOT; };
 341                 378DC5CD0FBDE1C8003B8607 /* aligncommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = aligncommand.h; sourceTree = SOURCE_ROOT; };
 342                 378DC5CE0FBDE1C8003B8607 /* aligncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = aligncommand.cpp; sourceTree = SOURCE_ROOT; };
 343                 379293C10F2DE73400B9034A /* treemap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treemap.h; sourceTree = SOURCE_ROOT; };
 344                 379293C20F2DE73400B9034A /* treemap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treemap.cpp; sourceTree = SOURCE_ROOT; };
 345                 3792946E0F2E191800B9034A /* parsimonycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimonycommand.h; sourceTree = SOURCE_ROOT; };
 346                 3792946F0F2E191800B9034A /* parsimonycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsimonycommand.cpp; sourceTree = SOURCE_ROOT; };
 347                 379294880F2E258500B9034A /* parsimony.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimony.h; sourceTree = SOURCE_ROOT; };
 348                 379294890F2E258500B9034A /* parsimony.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsimony.cpp; sourceTree = SOURCE_ROOT; };
 349                 3792948D0F2E271100B9034A /* treecalculator.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treecalculator.h; sourceTree = SOURCE_ROOT; };
 350                 3799A94E0FD6A58C00E33EDE /* seqsummarycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = seqsummarycommand.cpp; sourceTree = SOURCE_ROOT; };
 351                 3799A94F0FD6A58C00E33EDE /* seqsummarycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = seqsummarycommand.h; sourceTree = SOURCE_ROOT; };
 352                 379D3D4F0FF90E090068C1C0 /* chimeraseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraseqscommand.h; sourceTree = SOURCE_ROOT; };
 353                 379D3D500FF90E090068C1C0 /* chimeraseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraseqscommand.cpp; sourceTree = SOURCE_ROOT; };
 354                 379D3D6B0FF917F40068C1C0 /* filters.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = filters.h; sourceTree = SOURCE_ROOT; };
 355                 37AD4CE20F28AEA300AA2D49 /* sharedlistvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedlistvector.h; sourceTree = SOURCE_ROOT; };
 356                 37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedlistvector.cpp; sourceTree = SOURCE_ROOT; };
 357                 37AD4DB90F28E2FE00AA2D49 /* tree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = tree.h; sourceTree = SOURCE_ROOT; };
 358                 37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = tree.cpp; sourceTree = SOURCE_ROOT; };
 359                 37AD4DC80F28F3DD00AA2D49 /* readtree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtree.h; sourceTree = SOURCE_ROOT; };
 360                 37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtree.cpp; sourceTree = SOURCE_ROOT; };
 361                 37AFC71D0F445386005F492D /* sharedsobscollectsummary.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsobscollectsummary.h; sourceTree = SOURCE_ROOT; };
 362                 37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsobscollectsummary.cpp; sourceTree = SOURCE_ROOT; };
 363                 37B28F660F27590100808A62 /* deconvolutecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = deconvolutecommand.h; sourceTree = SOURCE_ROOT; };
 364                 37B28F670F27590100808A62 /* deconvolutecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = deconvolutecommand.cpp; sourceTree = SOURCE_ROOT; };
 365                 37B73C741004BEFD008C4B41 /* listseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = listseqscommand.h; sourceTree = SOURCE_ROOT; };
 366                 37B73C751004BEFD008C4B41 /* listseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = listseqscommand.cpp; sourceTree = SOURCE_ROOT; };
 367                 37B73CA41004D89A008C4B41 /* getseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getseqscommand.h; sourceTree = SOURCE_ROOT; };
 368                 37B73CA51004D89A008C4B41 /* getseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getseqscommand.cpp; sourceTree = SOURCE_ROOT; };
 369                 37B73CBE1004EB38008C4B41 /* removeseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removeseqscommand.h; sourceTree = SOURCE_ROOT; };
 370                 37B73CBF1004EB38008C4B41 /* removeseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removeseqscommand.cpp; sourceTree = SOURCE_ROOT; };
 371                 37B73CCD1004F5E0008C4B41 /* systemcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = systemcommand.h; sourceTree = SOURCE_ROOT; };
 372                 37B73CCE1004F5E0008C4B41 /* systemcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = systemcommand.cpp; sourceTree = SOURCE_ROOT; };
 373                 37C1D9710F86506E0059E3F0 /* binsequencecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = binsequencecommand.h; sourceTree = SOURCE_ROOT; };
 374                 37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = binsequencecommand.cpp; sourceTree = SOURCE_ROOT; };
 375                 37C753CC0FB3415200DBD02E /* distancecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = distancecommand.h; sourceTree = SOURCE_ROOT; };
 376                 37C753CD0FB3415200DBD02E /* distancecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = distancecommand.cpp; sourceTree = SOURCE_ROOT; };
 377                 37C753DF0FB3492400DBD02E /* dist.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = dist.h; sourceTree = SOURCE_ROOT; };
 378                 37C753ED0FB34A5700DBD02E /* ignoregaps.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ignoregaps.h; sourceTree = SOURCE_ROOT; };
 379                 37C753F00FB34AE800DBD02E /* eachgapdist.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = eachgapdist.h; sourceTree = SOURCE_ROOT; };
 380                 37C753F10FB34B4700DBD02E /* onegapdist.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = onegapdist.h; sourceTree = SOURCE_ROOT; };
 381                 37C753F30FB34BBF00DBD02E /* onegapignore.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = onegapignore.h; sourceTree = SOURCE_ROOT; };
 382                 37C753F40FB34C0300DBD02E /* eachgapignore.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = eachgapignore.h; sourceTree = SOURCE_ROOT; };
 383                 37D927B80F21331F001D4494 /* ace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ace.cpp; sourceTree = SOURCE_ROOT; };
 384                 37D927B90F21331F001D4494 /* ace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ace.h; sourceTree = SOURCE_ROOT; };
 385                 37D927BA0F21331F001D4494 /* averagelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = averagelinkage.cpp; sourceTree = SOURCE_ROOT; };
 386                 37D927BB0F21331F001D4494 /* bootstrap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bootstrap.cpp; sourceTree = SOURCE_ROOT; };
 387                 37D927BC0F21331F001D4494 /* bootstrap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bootstrap.h; sourceTree = SOURCE_ROOT; };
 388                 37D927BD0F21331F001D4494 /* calculator.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = calculator.cpp; sourceTree = SOURCE_ROOT; };
 389                 37D927BE0F21331F001D4494 /* calculator.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = calculator.h; sourceTree = SOURCE_ROOT; };
 390                 37D927BF0F21331F001D4494 /* chao1.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chao1.cpp; sourceTree = SOURCE_ROOT; };
 391                 37D927C00F21331F001D4494 /* chao1.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chao1.h; sourceTree = SOURCE_ROOT; };
 392                 37D927C10F21331F001D4494 /* cluster.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = cluster.cpp; sourceTree = SOURCE_ROOT; };
 393                 37D927C20F21331F001D4494 /* cluster.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = cluster.hpp; sourceTree = SOURCE_ROOT; };
 394                 37D927C30F21331F001D4494 /* clustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clustercommand.cpp; sourceTree = SOURCE_ROOT; };
 395                 37D927C40F21331F001D4494 /* clustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clustercommand.h; sourceTree = SOURCE_ROOT; };
 396                 37D927C50F21331F001D4494 /* collect.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = collect.cpp; sourceTree = SOURCE_ROOT; };
 397                 37D927C60F21331F001D4494 /* collect.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collect.h; sourceTree = SOURCE_ROOT; };
 398                 37D927C70F21331F001D4494 /* collectcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = collectcommand.cpp; sourceTree = SOURCE_ROOT; };
 399                 37D927C80F21331F001D4494 /* collectcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectcommand.h; sourceTree = SOURCE_ROOT; };
 400                 37D927C90F21331F001D4494 /* collectdisplay.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectdisplay.h; sourceTree = SOURCE_ROOT; };
 401                 37D927CA0F21331F001D4494 /* collectorscurvedata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectorscurvedata.h; sourceTree = SOURCE_ROOT; };
 402                 37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = collectsharedcommand.cpp; sourceTree = SOURCE_ROOT; };
 403                 37D927CC0F21331F001D4494 /* collectsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectsharedcommand.h; sourceTree = SOURCE_ROOT; };
 404                 37D927CD0F21331F001D4494 /* command.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = command.hpp; sourceTree = SOURCE_ROOT; };
 405                 37D927CF0F21331F001D4494 /* commandfactory.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = commandfactory.hpp; sourceTree = SOURCE_ROOT; };
 406                 37D927D00F21331F001D4494 /* commandoptionparser.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = commandoptionparser.cpp; sourceTree = SOURCE_ROOT; };
 407                 37D927D10F21331F001D4494 /* commandoptionparser.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = commandoptionparser.hpp; sourceTree = SOURCE_ROOT; };
 408                 37D927D20F21331F001D4494 /* completelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = completelinkage.cpp; sourceTree = SOURCE_ROOT; };
 409                 37D927D30F21331F001D4494 /* database.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = database.cpp; sourceTree = SOURCE_ROOT; };
 410                 37D927D40F21331F001D4494 /* database.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = database.hpp; sourceTree = SOURCE_ROOT; };
 411                 37D927D50F21331F001D4494 /* datavector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = datavector.hpp; sourceTree = SOURCE_ROOT; };
 412                 37D927D60F21331F001D4494 /* display.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = display.h; sourceTree = SOURCE_ROOT; };
 413                 37D927D70F21331F001D4494 /* engine.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = engine.cpp; sourceTree = SOURCE_ROOT; };
 414                 37D927D80F21331F001D4494 /* engine.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = engine.hpp; sourceTree = SOURCE_ROOT; };
 415                 37D927DB0F21331F001D4494 /* fastamap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fastamap.cpp; sourceTree = SOURCE_ROOT; };
 416                 37D927DC0F21331F001D4494 /* fastamap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fastamap.h; sourceTree = SOURCE_ROOT; };
 417                 37D927DD0F21331F001D4494 /* fileoutput.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fileoutput.cpp; sourceTree = SOURCE_ROOT; };
 418                 37D927DE0F21331F001D4494 /* fileoutput.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fileoutput.h; sourceTree = SOURCE_ROOT; };
 419                 37D927DF0F21331F001D4494 /* globaldata.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = globaldata.cpp; sourceTree = SOURCE_ROOT; };
 420                 37D927E00F21331F001D4494 /* globaldata.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = globaldata.hpp; sourceTree = SOURCE_ROOT; };
 421                 37D927E10F21331F001D4494 /* groupmap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = groupmap.cpp; sourceTree = SOURCE_ROOT; };
 422                 37D927E20F21331F001D4494 /* groupmap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = groupmap.h; sourceTree = SOURCE_ROOT; };
 423                 37D927E30F21331F001D4494 /* helpcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = helpcommand.cpp; sourceTree = SOURCE_ROOT; };
 424                 37D927E40F21331F001D4494 /* helpcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = helpcommand.h; sourceTree = SOURCE_ROOT; };
 425                 37D927E50F21331F001D4494 /* inputdata.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = inputdata.cpp; sourceTree = SOURCE_ROOT; };
 426                 37D927E60F21331F001D4494 /* inputdata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = inputdata.h; sourceTree = SOURCE_ROOT; };
 427                 37D927E70F21331F001D4494 /* jackknife.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = jackknife.cpp; sourceTree = SOURCE_ROOT; };
 428                 37D927E80F21331F001D4494 /* jackknife.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = jackknife.h; sourceTree = SOURCE_ROOT; };
 429                 37D927E90F21331F001D4494 /* kmer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = kmer.cpp; sourceTree = SOURCE_ROOT; };
 430                 37D927EA0F21331F001D4494 /* kmer.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = kmer.hpp; sourceTree = SOURCE_ROOT; };
 431                 37D927EB0F21331F001D4494 /* kmerdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = kmerdb.cpp; sourceTree = SOURCE_ROOT; };
 432                 37D927EC0F21331F001D4494 /* kmerdb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = kmerdb.hpp; sourceTree = SOURCE_ROOT; };
 433                 37D927ED0F21331F001D4494 /* listvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = listvector.cpp; sourceTree = SOURCE_ROOT; };
 434                 37D927EE0F21331F001D4494 /* listvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = listvector.hpp; sourceTree = SOURCE_ROOT; };
 435                 37D927EF0F21331F001D4494 /* mothur.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mothur.cpp; sourceTree = SOURCE_ROOT; };
 436                 37D927F00F21331F001D4494 /* nameassignment.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nameassignment.cpp; sourceTree = SOURCE_ROOT; };
 437                 37D927F10F21331F001D4494 /* nameassignment.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = nameassignment.hpp; sourceTree = SOURCE_ROOT; };
 438                 37D927F40F21331F001D4494 /* npshannon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = npshannon.cpp; sourceTree = SOURCE_ROOT; };
 439                 37D927F50F21331F001D4494 /* npshannon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = npshannon.h; sourceTree = SOURCE_ROOT; };
 440                 37D927F60F21331F001D4494 /* observable.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = observable.h; sourceTree = SOURCE_ROOT; };
 441                 37D927F70F21331F001D4494 /* ordervector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ordervector.cpp; sourceTree = SOURCE_ROOT; };
 442                 37D927F80F21331F001D4494 /* ordervector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = ordervector.hpp; sourceTree = SOURCE_ROOT; };
 443                 37D927FB0F21331F001D4494 /* progress.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = progress.cpp; sourceTree = SOURCE_ROOT; };
 444                 37D927FC0F21331F001D4494 /* progress.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = progress.hpp; sourceTree = SOURCE_ROOT; };
 445                 37D927FD0F21331F001D4494 /* quitcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = quitcommand.cpp; sourceTree = SOURCE_ROOT; };
 446                 37D927FE0F21331F001D4494 /* quitcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = quitcommand.h; sourceTree = SOURCE_ROOT; };
 447                 37D927FF0F21331F001D4494 /* rabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rabundvector.cpp; sourceTree = SOURCE_ROOT; };
 448                 37D928000F21331F001D4494 /* rabundvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = rabundvector.hpp; sourceTree = SOURCE_ROOT; };
 449                 37D928010F21331F001D4494 /* rarecalc.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarecalc.cpp; sourceTree = SOURCE_ROOT; };
 450                 37D928020F21331F001D4494 /* rarecalc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarecalc.h; sourceTree = SOURCE_ROOT; };
 451                 37D928030F21331F001D4494 /* raredisplay.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = raredisplay.cpp; sourceTree = SOURCE_ROOT; };
 452                 37D928040F21331F001D4494 /* raredisplay.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = raredisplay.h; sourceTree = SOURCE_ROOT; };
 453                 37D928050F21331F001D4494 /* rarefact.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefact.cpp; sourceTree = SOURCE_ROOT; };
 454                 37D928060F21331F001D4494 /* rarefact.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefact.h; sourceTree = SOURCE_ROOT; };
 455                 37D928070F21331F001D4494 /* rarefactcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefactcommand.cpp; sourceTree = SOURCE_ROOT; };
 456                 37D928080F21331F001D4494 /* rarefactcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactcommand.h; sourceTree = SOURCE_ROOT; };
 457                 37D928090F21331F001D4494 /* rarefactioncurvedata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactioncurvedata.h; sourceTree = SOURCE_ROOT; };
 458                 37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefactsharedcommand.cpp; sourceTree = SOURCE_ROOT; };
 459                 37D9280B0F21331F001D4494 /* rarefactsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactsharedcommand.h; sourceTree = SOURCE_ROOT; };
 460                 37D928130F21331F001D4494 /* readmatrix.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = readmatrix.hpp; sourceTree = SOURCE_ROOT; };
 461                 37D9281A0F21331F001D4494 /* sabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sabundvector.cpp; sourceTree = SOURCE_ROOT; };
 462                 37D9281B0F21331F001D4494 /* sabundvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sabundvector.hpp; sourceTree = SOURCE_ROOT; };
 463                 37D9281C0F21331F001D4494 /* sequence.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sequence.cpp; sourceTree = SOURCE_ROOT; };
 464                 37D9281D0F21331F001D4494 /* sequence.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sequence.hpp; sourceTree = SOURCE_ROOT; };
 465                 37D9281E0F21331F001D4494 /* shannon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shannon.cpp; sourceTree = SOURCE_ROOT; };
 466                 37D9281F0F21331F001D4494 /* shannon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shannon.h; sourceTree = SOURCE_ROOT; };
 467                 37D928220F21331F001D4494 /* sharedace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedace.cpp; sourceTree = SOURCE_ROOT; };
 468                 37D928230F21331F001D4494 /* sharedace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedace.h; sourceTree = SOURCE_ROOT; };
 469                 37D928240F21331F001D4494 /* sharedchao1.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedchao1.cpp; sourceTree = SOURCE_ROOT; };
 470                 37D928250F21331F001D4494 /* sharedchao1.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedchao1.h; sourceTree = SOURCE_ROOT; };
 471                 37D928260F21331F001D4494 /* sharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedcommand.cpp; sourceTree = SOURCE_ROOT; };
 472                 37D928270F21331F001D4494 /* sharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedcommand.h; sourceTree = SOURCE_ROOT; };
 473                 37D928280F21331F001D4494 /* sharedjabund.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjabund.cpp; sourceTree = SOURCE_ROOT; };
 474                 37D928290F21331F001D4494 /* sharedjabund.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjabund.h; sourceTree = SOURCE_ROOT; };
 475                 37D9282A0F21331F001D4494 /* sharedjclass.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjclass.cpp; sourceTree = SOURCE_ROOT; };
 476                 37D9282B0F21331F001D4494 /* sharedjclass.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjclass.h; sourceTree = SOURCE_ROOT; };
 477                 37D9282C0F21331F001D4494 /* sharedjest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjest.cpp; sourceTree = SOURCE_ROOT; };
 478                 37D9282D0F21331F001D4494 /* sharedjest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjest.h; sourceTree = SOURCE_ROOT; };
 479                 37D9282E0F21331F001D4494 /* sharedordervector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedordervector.cpp; sourceTree = SOURCE_ROOT; };
 480                 37D9282F0F21331F001D4494 /* sharedordervector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedordervector.h; sourceTree = SOURCE_ROOT; };
 481                 37D928300F21331F001D4494 /* sharedrabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedrabundvector.cpp; sourceTree = SOURCE_ROOT; };
 482                 37D928310F21331F001D4494 /* sharedrabundvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedrabundvector.h; sourceTree = SOURCE_ROOT; };
 483                 37D928320F21331F001D4494 /* sharedsabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsabundvector.cpp; sourceTree = SOURCE_ROOT; };
 484                 37D928330F21331F001D4494 /* sharedsabundvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsabundvector.h; sourceTree = SOURCE_ROOT; };
 485                 37D928340F21331F001D4494 /* sharedsobs.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsobs.cpp; sourceTree = SOURCE_ROOT; };
 486                 37D928350F21331F001D4494 /* sharedsobs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsobs.h; sourceTree = SOURCE_ROOT; };
 487                 37D928360F21331F001D4494 /* sharedsorabund.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorabund.cpp; sourceTree = SOURCE_ROOT; };
 488                 37D928370F21331F001D4494 /* sharedsorabund.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsorabund.h; sourceTree = SOURCE_ROOT; };
 489                 37D928380F21331F001D4494 /* sharedsorclass.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorclass.cpp; sourceTree = SOURCE_ROOT; };
 490                 37D928390F21331F001D4494 /* sharedsorclass.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsorclass.h; sourceTree = SOURCE_ROOT; };
 491                 37D9283A0F21331F001D4494 /* sharedsorest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorest.cpp; sourceTree = SOURCE_ROOT; };
 492                 37D9283B0F21331F001D4494 /* sharedsorest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsorest.h; sourceTree = SOURCE_ROOT; };
 493                 37D9283C0F21331F001D4494 /* sharedthetan.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedthetan.cpp; sourceTree = SOURCE_ROOT; };
 494                 37D9283D0F21331F001D4494 /* sharedthetan.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedthetan.h; sourceTree = SOURCE_ROOT; };
 495                 37D9283E0F21331F001D4494 /* sharedthetayc.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedthetayc.cpp; sourceTree = SOURCE_ROOT; };
 496                 37D9283F0F21331F001D4494 /* sharedthetayc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedthetayc.h; sourceTree = SOURCE_ROOT; };
 497                 37D928400F21331F001D4494 /* simpson.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = simpson.cpp; sourceTree = SOURCE_ROOT; };
 498                 37D928410F21331F001D4494 /* simpson.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = simpson.h; sourceTree = SOURCE_ROOT; };
 499                 37D928420F21331F001D4494 /* singlelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = singlelinkage.cpp; sourceTree = SOURCE_ROOT; };
 500                 37D928430F21331F001D4494 /* sobs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sobs.h; sourceTree = SOURCE_ROOT; };
 501                 37D928440F21331F001D4494 /* sparsematrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sparsematrix.cpp; sourceTree = SOURCE_ROOT; };
 502                 37D928450F21331F001D4494 /* sparsematrix.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sparsematrix.hpp; sourceTree = SOURCE_ROOT; };
 503                 37D928460F21331F001D4494 /* summarycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summarycommand.cpp; sourceTree = SOURCE_ROOT; };
 504                 37D928470F21331F001D4494 /* summarycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarycommand.h; sourceTree = SOURCE_ROOT; };
 505                 37D928480F21331F001D4494 /* summarydata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarydata.h; sourceTree = SOURCE_ROOT; };
 506                 37D928490F21331F001D4494 /* summarydisplay.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarydisplay.h; sourceTree = SOURCE_ROOT; };
 507                 37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summarysharedcommand.cpp; sourceTree = SOURCE_ROOT; };
 508                 37D9284B0F21331F001D4494 /* summarysharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarysharedcommand.h; sourceTree = SOURCE_ROOT; };
 509                 37D9284D0F21331F001D4494 /* uvest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = uvest.cpp; sourceTree = SOURCE_ROOT; };
 510                 37D9284E0F21331F001D4494 /* uvest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = uvest.h; sourceTree = SOURCE_ROOT; };
 511                 37D9284F0F21331F001D4494 /* validcalculator.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = validcalculator.cpp; sourceTree = SOURCE_ROOT; };
 512                 37D928500F21331F001D4494 /* validcalculator.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = validcalculator.h; sourceTree = SOURCE_ROOT; };
 513                 37D928530F21331F001D4494 /* validparameter.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = validparameter.cpp; sourceTree = SOURCE_ROOT; };
 514                 37D928540F21331F001D4494 /* validparameter.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = validparameter.h; sourceTree = SOURCE_ROOT; };
 515                 37E3ED800F4D9D0D00B5DF02 /* mothur.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mothur.h; sourceTree = SOURCE_ROOT; };
 516                 37E5F3E10F29FD4200F8D827 /* treenode.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treenode.h; sourceTree = SOURCE_ROOT; };
 517                 37E5F3E20F29FD4200F8D827 /* treenode.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treenode.cpp; sourceTree = SOURCE_ROOT; };
 518                 37E5F4900F2A3DA800F8D827 /* readtreecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtreecommand.h; sourceTree = SOURCE_ROOT; };
 519                 37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtreecommand.cpp; sourceTree = SOURCE_ROOT; };
 520                 7E09C5120FDA79C5002ECAE5 /* reversecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = reversecommand.h; sourceTree = SOURCE_ROOT; };
 521                 7E09C5130FDA79C5002ECAE5 /* reversecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = reversecommand.cpp; sourceTree = SOURCE_ROOT; };
 522                 7E09C5340FDA7F65002ECAE5 /* trimseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = trimseqscommand.h; sourceTree = SOURCE_ROOT; };
 523                 7E09C5350FDA7F65002ECAE5 /* trimseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = trimseqscommand.cpp; sourceTree = SOURCE_ROOT; };
 524                 7E412F420F8D213C00381DD0 /* libshuff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = libshuff.h; sourceTree = SOURCE_ROOT; };
 525                 7E412F470F8D21B600381DD0 /* slibshuff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = slibshuff.h; sourceTree = SOURCE_ROOT; };
 526                 7E412F480F8D21B600381DD0 /* slibshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = slibshuff.cpp; sourceTree = SOURCE_ROOT; };
 527                 7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = libshuff.cpp; sourceTree = SOURCE_ROOT; };
 528                 7E4130F60F8E58FA00381DD0 /* dlibshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = dlibshuff.cpp; sourceTree = SOURCE_ROOT; };
 529                 7E4130F70F8E58FA00381DD0 /* dlibshuff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = dlibshuff.h; sourceTree = SOURCE_ROOT; };
 530                 7E5A17AD0FE57292003C6A03 /* mergefilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mergefilecommand.h; sourceTree = SOURCE_ROOT; };
 531                 7E5A17AE0FE57292003C6A03 /* mergefilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mergefilecommand.cpp; sourceTree = SOURCE_ROOT; };
 532                 7EC3D4500FA0FFF900338DA5 /* coverage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = coverage.cpp; sourceTree = SOURCE_ROOT; };
 533                 7EC3D4510FA0FFF900338DA5 /* coverage.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = coverage.h; sourceTree = SOURCE_ROOT; };
 534                 7EC3D4520FA0FFF900338DA5 /* sharedanderberg.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedanderberg.h; sourceTree = SOURCE_ROOT; };
 535                 7EC3D4530FA0FFF900338DA5 /* whittaker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = whittaker.cpp; sourceTree = SOURCE_ROOT; };
 536                 7EC3D4540FA0FFF900338DA5 /* whittaker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = whittaker.h; sourceTree = SOURCE_ROOT; };
 537                 8DD76F6C0486A84900D96B5E /* mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = mothur; sourceTree = BUILT_PRODUCTS_DIR; };
 538                 A7027F2610DFF86D00BF45FE /* preclustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = preclustercommand.h; sourceTree = SOURCE_ROOT; };
 539                 A7027F2710DFF86D00BF45FE /* preclustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = preclustercommand.cpp; sourceTree = SOURCE_ROOT; };
 540                 A704E8A11106045D00870157 /* otuhierarchycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = otuhierarchycommand.h; sourceTree = SOURCE_ROOT; };
 541                 A704E8A21106045D00870157 /* otuhierarchycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = otuhierarchycommand.cpp; sourceTree = SOURCE_ROOT; };
 542                 A70B00C6110885EB002F453A /* setdircommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = setdircommand.h; sourceTree = SOURCE_ROOT; };
 543                 A70B00C7110885EB002F453A /* setdircommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = setdircommand.cpp; sourceTree = SOURCE_ROOT; };
 544                 A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getgroupcommand.cpp; sourceTree = SOURCE_ROOT; };
 545                 A70B53A50F4CD7AD0064797E /* getgroupcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getgroupcommand.h; sourceTree = SOURCE_ROOT; };
 546                 A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlabelcommand.cpp; sourceTree = SOURCE_ROOT; };
 547                 A70B53A70F4CD7AD0064797E /* getlabelcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlabelcommand.h; sourceTree = SOURCE_ROOT; };
 548                 A70DECD71063D8B40057C03C /* secondarystructurecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = secondarystructurecommand.h; sourceTree = SOURCE_ROOT; };
 549                 A70DECD81063D8B40057C03C /* secondarystructurecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = secondarystructurecommand.cpp; sourceTree = SOURCE_ROOT; };
 550                 A70F3FCE1136E391004FDC52 /* mothurout.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mothurout.h; sourceTree = SOURCE_ROOT; };
 551                 A70F3FCF1136E391004FDC52 /* mothurout.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mothurout.cpp; sourceTree = SOURCE_ROOT; };
 552                 A71CB8A111354B9F00848EF7 /* parselistscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parselistscommand.h; sourceTree = SOURCE_ROOT; };
 553                 A71CB8A211354B9F00848EF7 /* parselistscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parselistscommand.cpp; sourceTree = SOURCE_ROOT; };
 554                 A727E84810D14568001A8432 /* readblast.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readblast.h; sourceTree = SOURCE_ROOT; };
 555                 A727E84910D14568001A8432 /* readblast.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readblast.cpp; sourceTree = SOURCE_ROOT; };
 556                 A7283FF61056CAE100D0CC69 /* chimeracheckrdp.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeracheckrdp.h; sourceTree = SOURCE_ROOT; };
 557                 A7283FF71056CAE100D0CC69 /* chimeracheckrdp.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeracheckrdp.cpp; sourceTree = SOURCE_ROOT; };
 558                 A729ACCE10848E6100139801 /* hclustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = hclustercommand.h; sourceTree = SOURCE_ROOT; };
 559                 A729ACCF10848E6100139801 /* hclustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = hclustercommand.cpp; sourceTree = SOURCE_ROOT; };
 560                 A729ACE210849BBE00139801 /* hcluster.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = hcluster.h; sourceTree = SOURCE_ROOT; };
 561                 A729ACE310849BBE00139801 /* hcluster.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = hcluster.cpp; sourceTree = SOURCE_ROOT; };
 562                 A73329CD1083B3B3003B10C5 /* getlistcountcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlistcountcommand.h; sourceTree = SOURCE_ROOT; };
 563                 A73329CE1083B3B3003B10C5 /* getlistcountcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlistcountcommand.cpp; sourceTree = SOURCE_ROOT; };
 564                 A751ACE81098B283003D0911 /* readcluster.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readcluster.h; sourceTree = SOURCE_ROOT; };
 565                 A751ACE91098B283003D0911 /* readcluster.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readcluster.cpp; sourceTree = SOURCE_ROOT; };
 566                 A75B887B104C16860083C454 /* ccode.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ccode.cpp; sourceTree = SOURCE_ROOT; };
 567                 A75B887C104C16860083C454 /* ccode.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ccode.h; sourceTree = SOURCE_ROOT; };
 568                 A773805D10B6D6FC002A6A61 /* taxonomyequalizer.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = taxonomyequalizer.h; sourceTree = SOURCE_ROOT; };
 569                 A773805E10B6D6FC002A6A61 /* taxonomyequalizer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = taxonomyequalizer.cpp; sourceTree = SOURCE_ROOT; };
 570                 A773808E10B6EFD1002A6A61 /* phylotypecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylotypecommand.h; sourceTree = SOURCE_ROOT; };
 571                 A773808F10B6EFD1002A6A61 /* phylotypecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylotypecommand.cpp; sourceTree = SOURCE_ROOT; };
 572                 A7861476109F5FA00010AAAF /* classifyseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = classifyseqscommand.h; sourceTree = SOURCE_ROOT; };
 573                 A7861477109F5FA00010AAAF /* classifyseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = classifyseqscommand.cpp; sourceTree = SOURCE_ROOT; };
 574                 A78780FE10A06B8B0086103D /* classify.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = classify.h; sourceTree = SOURCE_ROOT; };
 575                 A787810210A06D5D0086103D /* classify.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = classify.cpp; sourceTree = SOURCE_ROOT; };
 576                 A78781B810A0813D0086103D /* phylotree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylotree.cpp; sourceTree = SOURCE_ROOT; };
 577                 A78781B910A0813D0086103D /* phylotree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylotree.h; sourceTree = SOURCE_ROOT; };
 578                 A787820F10A0AAE70086103D /* bayesian.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bayesian.h; sourceTree = SOURCE_ROOT; };
 579                 A787821010A0AAE70086103D /* bayesian.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bayesian.cpp; sourceTree = SOURCE_ROOT; };
 580                 A78782A910A1B1CB0086103D /* alignmentdb.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = alignmentdb.h; sourceTree = SOURCE_ROOT; };
 581                 A78782AA10A1B1CB0086103D /* alignmentdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = alignmentdb.cpp; sourceTree = SOURCE_ROOT; };
 582                 A787844310A1EBDD0086103D /* knn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = knn.h; sourceTree = SOURCE_ROOT; };
 583                 A787844410A1EBDD0086103D /* knn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = knn.cpp; sourceTree = SOURCE_ROOT; };
 584                 A794200F11107897003AECCD /* distancedb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = distancedb.cpp; sourceTree = SOURCE_ROOT; };
 585                 A794201011107897003AECCD /* distancedb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = distancedb.hpp; sourceTree = SOURCE_ROOT; };
 586                 A7B04491106CC3E60046FC83 /* chimeraslayer.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraslayer.h; sourceTree = SOURCE_ROOT; };
 587                 A7B04492106CC3E60046FC83 /* chimeraslayer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraslayer.cpp; sourceTree = SOURCE_ROOT; };
 588                 A7B0450C106CEEC90046FC83 /* slayer.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = slayer.h; sourceTree = SOURCE_ROOT; };
 589                 A7B0450D106CEEC90046FC83 /* slayer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = slayer.cpp; sourceTree = SOURCE_ROOT; };
 590                 A7D176CD10F2558500159497 /* pcacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pcacommand.h; sourceTree = SOURCE_ROOT; };
 591                 A7D176CE10F2558500159497 /* pcacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pcacommand.cpp; sourceTree = SOURCE_ROOT; };
 592                 A7D86C6A10FE084300865661 /* formatmatrix.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = formatmatrix.h; sourceTree = SOURCE_ROOT; };
 593                 A7D86C7B10FE09AB00865661 /* formatcolumn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = formatcolumn.h; sourceTree = SOURCE_ROOT; };
 594                 A7D86C7C10FE09AB00865661 /* formatcolumn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = formatcolumn.cpp; sourceTree = SOURCE_ROOT; };
 595                 A7D86C8A10FE09FE00865661 /* formatphylip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = formatphylip.h; sourceTree = SOURCE_ROOT; };
 596                 A7D86C8B10FE09FE00865661 /* formatphylip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = formatphylip.cpp; sourceTree = SOURCE_ROOT; };
 597                 A7E0AAB410D2886D00CF407B /* mgclustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mgclustercommand.h; sourceTree = SOURCE_ROOT; };
 598                 A7E0AAB510D2886D00CF407B /* mgclustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mgclustercommand.cpp; sourceTree = SOURCE_ROOT; };
 599                 A7E4A781106913F900688F62 /* getsharedotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getsharedotucommand.h; sourceTree = SOURCE_ROOT; };
 600                 A7E4A782106913F900688F62 /* getsharedotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getsharedotucommand.cpp; sourceTree = SOURCE_ROOT; };
 601                 A7E4A822106A9AD700688F62 /* maligner.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = maligner.h; sourceTree = SOURCE_ROOT; };
 602                 A7E4A823106A9AD700688F62 /* maligner.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = maligner.cpp; sourceTree = SOURCE_ROOT; };
 603                 A7E8A22D1125939F0011D39C /* chimerarealigner.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimerarealigner.h; sourceTree = SOURCE_ROOT; };
 604                 A7E8A22E1125939F0011D39C /* chimerarealigner.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimerarealigner.cpp; sourceTree = SOURCE_ROOT; };
 605                 A7F5759610CEBC0600E20E47 /* libreadline.a */ = {isa = PBXFileReference; lastKnownFileType = archive.ar; name = libreadline.a; path = "../readline-6.0/libreadline.a"; sourceTree = SOURCE_ROOT; };
 606                 C6859E8B029090EE04C91782 /* Mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = Mothur.1; sourceTree = "<group>"; };
 607                 EB1216860F619B83004A865F /* bergerparker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bergerparker.h; sourceTree = SOURCE_ROOT; };
 608                 EB1216870F619B83004A865F /* bergerparker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bergerparker.cpp; sourceTree = SOURCE_ROOT; };
 609                 EB1216E30F61ACFB004A865F /* bstick.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bstick.h; sourceTree = SOURCE_ROOT; };
 610                 EB1216E40F61ACFB004A865F /* bstick.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bstick.cpp; sourceTree = SOURCE_ROOT; };
 611                 EB1217210F61C9AC004A865F /* sharedkstest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedkstest.h; sourceTree = SOURCE_ROOT; };
 612                 EB1217220F61C9AC004A865F /* sharedkstest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedkstest.cpp; sourceTree = SOURCE_ROOT; };
 613                 EB6E68170F5F1C780044E17B /* qstat.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = qstat.h; sourceTree = SOURCE_ROOT; };
 614                 EB6E68180F5F1C780044E17B /* qstat.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = qstat.cpp; sourceTree = SOURCE_ROOT; };
 615                 EB72FE240FC1F5CA0051AC11 /* shen.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shen.cpp; sourceTree = SOURCE_ROOT; };
 616                 EB72FE250FC1F5CA0051AC11 /* shen.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shen.h; sourceTree = SOURCE_ROOT; };
 617                 EB9303E90F534D9400E8EF26 /* logsd.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = logsd.h; sourceTree = SOURCE_ROOT; };
 618                 EB9303EA0F534D9400E8EF26 /* logsd.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = logsd.cpp; sourceTree = SOURCE_ROOT; };
 619                 EB9303F70F53517300E8EF26 /* geom.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = geom.h; sourceTree = SOURCE_ROOT; };
 620                 EB9303F80F53517300E8EF26 /* geom.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = geom.cpp; sourceTree = SOURCE_ROOT; };
 621 /* End PBXFileReference section */
 622
 623 /* Begin PBXFrameworksBuildPhase section */
 624                 8DD76F660486A84900D96B5E /* Frameworks */ = {
 625                         isa = PBXFrameworksBuildPhase;
 626                         buildActionMask = 2147483647;
 627                         files = (
 628                                 A7F5759710CEBC0600E20E47 /* libreadline.a in Frameworks */,
 629                         );
 630                         runOnlyForDeploymentPostprocessing = 0;
 631                 };
 632 /* End PBXFrameworksBuildPhase section */
 633
 634 /* Begin PBXGroup section */
 635                 08FB7794FE84155DC02AAC07 /* Mothur */ = {
 636                         isa = PBXGroup;
 637                         children = (
 638                                 08FB7795FE84155DC02AAC07 /* Source */,
 639                                 C6859E8C029090F304C91782 /* Documentation */,
 640                                 1AB674ADFE9D54B511CA2CBB /* Products */,
 641                         );
 642                         name = Mothur;
 643                         sourceTree = "<group>";
 644                 };
 645                 08FB7795FE84155DC02AAC07 /* Source */ = {
 646                         isa = PBXGroup;
 647                         children = (
 648                                 37D927BA0F21331F001D4494 /* averagelinkage.cpp */,
 649                                 373C68DC0FC1C38D00137ACD /* blastalign.hpp */,
 650                                 373C68DB0FC1C38D00137ACD /* blastalign.cpp */,
 651                                 37D928A60F2133C0001D4494 /* calculators */,
 652                                 374F2FE81006346600E97C66 /* chimera */,
 653                                 A787811210A073F40086103D /* classifiers */,
 654                                 37D927C20F21331F001D4494 /* cluster.hpp */,
 655                                 37D927C10F21331F001D4494 /* cluster.cpp */,
 656                                 37D928A90F2133E5001D4494 /* commands */,
 657                                 37D927C60F21331F001D4494 /* collect.h */,
 658                                 37D927C50F21331F001D4494 /* collect.cpp */,
 659                                 37D927C90F21331F001D4494 /* collectdisplay.h */,
 660                                 37D928AC0F213420001D4494 /* containers */,
 661                                 37D927CA0F21331F001D4494 /* collectorscurvedata.h */,
 662                                 37D927CF0F21331F001D4494 /* commandfactory.hpp */,
 663                                 372E12EC0F264D320095CF7E /* commandfactory.cpp */,
 664                                 37D927D10F21331F001D4494 /* commandoptionparser.hpp */,
 665                                 37D927D00F21331F001D4494 /* commandoptionparser.cpp */,
 666                                 37D927D20F21331F001D4494 /* completelinkage.cpp */,
 667                                 7E4130F70F8E58FA00381DD0 /* dlibshuff.h */,
 668                                 7E4130F60F8E58FA00381DD0 /* dlibshuff.cpp */,
 669                                 37D927D60F21331F001D4494 /* display.h */,
 670                                 37D927D80F21331F001D4494 /* engine.hpp */,
 671                                 37D927D70F21331F001D4494 /* engine.cpp */,
 672                                 37D928B10F213472001D4494 /* errorcheckor */,
 673                                 37D927DE0F21331F001D4494 /* fileoutput.h */,
 674                                 37D927DD0F21331F001D4494 /* fileoutput.cpp */,
 675                                 37D927E00F21331F001D4494 /* globaldata.hpp */,
 676                                 37D927DF0F21331F001D4494 /* globaldata.cpp */,
 677                                 373C68BB0FC1C1A600137ACD /* gotohoverlap.hpp */,
 678                                 373C68BA0FC1C1A600137ACD /* gotohoverlap.cpp */,
 679                                 A729ACE210849BBE00139801 /* hcluster.h */,
 680                                 A729ACE310849BBE00139801 /* hcluster.cpp */,
 681                                 375873ED0F7D646F0040F377 /* heatmap.h */,
 682                                 375873EE0F7D646F0040F377 /* heatmap.cpp */,
 683                                 378598720FDD4C1500EF9D03 /* heatmapsim.h */,
 684                                 378598730FDD4C1500EF9D03 /* heatmapsim.cpp */,
 685                                 37D927E60F21331F001D4494 /* inputdata.h */,
 686                                 37D927E50F21331F001D4494 /* inputdata.cpp */,
 687                                 7E412F420F8D213C00381DD0 /* libshuff.h */,
 688                                 7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */,
 689                                 37E3ED800F4D9D0D00B5DF02 /* mothur.h */,
 690                                 37D927EF0F21331F001D4494 /* mothur.cpp */,
 691                                 A70F3FCE1136E391004FDC52 /* mothurout.h */,
 692                                 A70F3FCF1136E391004FDC52 /* mothurout.cpp */,
 693                                 373C691E0FC1C98600137ACD /* nast.hpp */,
 694                                 373C691D0FC1C98600137ACD /* nast.cpp */,
 695                                 373C692A0FC1C9EB00137ACD /* nastreport.hpp */,
 696                                 373C69290FC1C9EB00137ACD /* nastreport.cpp */,
 697                                 373C68CE0FC1C2D900137ACD /* needlemanoverlap.hpp */,
 698                                 373C68CD0FC1C2D900137ACD /* needlemanoverlap.cpp */,
 699                                 373C68E40FC1C4A500137ACD /* noalign.hpp */,
 700                                 373C68E30FC1C4A500137ACD /* noalign.cpp */,
 701                                 37D927F60F21331F001D4494 /* observable.h */,
 702                                 3785990E0FDD7E8E00EF9D03 /* optionparser.h */,
 703                                 3785990F0FDD7E8E00EF9D03 /* optionparser.cpp */,
 704                                 373C68C40FC1C25F00137ACD /* overlap.hpp */,
 705                                 373C68C30FC1C25F00137ACD /* overlap.cpp */,
 706                                 37D927FC0F21331F001D4494 /* progress.hpp */,
 707                                 37D927FB0F21331F001D4494 /* progress.cpp */,
 708                                 37D928040F21331F001D4494 /* raredisplay.h */,
 709                                 37D928030F21331F001D4494 /* raredisplay.cpp */,
 710                                 37D928060F21331F001D4494 /* rarefact.h */,
 711                                 37D928050F21331F001D4494 /* rarefact.cpp */,
 712                                 37D928090F21331F001D4494 /* rarefactioncurvedata.h */,
 713                                 3796441D0FB9B9650081FDB6 /* read */,
 714                                 211C38310F961DD400FEE541 /* sharedutilities.h */,
 715                                 211C38300F961DD400FEE541 /* sharedutilities.cpp */,
 716                                 37D928420F21331F001D4494 /* singlelinkage.cpp */,
 717                                 7E412F470F8D21B600381DD0 /* slibshuff.h */,
 718                                 7E412F480F8D21B600381DD0 /* slibshuff.cpp */,
 719                                 37D928480F21331F001D4494 /* summarydata.h */,
 720                                 37D928490F21331F001D4494 /* summarydisplay.h */,
 721                                 37519AB30F810FAE00FED5E8 /* venn.h */,
 722                                 37519AB40F810FAE00FED5E8 /* venn.cpp */,
 723                                 A7F5759610CEBC0600E20E47 /* libreadline.a */,
 724                         );
 725                         name = Source;
 726                         sourceTree = "<group>";
 727                 };
 728                 1AB674ADFE9D54B511CA2CBB /* Products */ = {
 729                         isa = PBXGroup;
 730                         children = (
 731                                 8DD76F6C0486A84900D96B5E /* mothur */,
 732                         );
 733                         name = Products;
 734                         sourceTree = "<group>";
 735                 };
 736                 374F2FE81006346600E97C66 /* chimera */ = {
 737                         isa = PBXGroup;
 738                         children = (
 739                                 374F2FD51006320200E97C66 /* chimera.h */,
 740                                 372095C1103196D70004D347 /* chimera.cpp */,
 741                                 374F2FE9100634B600E97C66 /* bellerophon.h */,
 742                                 374F2FEA100634B600E97C66 /* bellerophon.cpp */,
 743                                 A75B887C104C16860083C454 /* ccode.h */,
 744                                 A75B887B104C16860083C454 /* ccode.cpp */,
 745                                 A7283FF61056CAE100D0CC69 /* chimeracheckrdp.h */,
 746                                 A7283FF71056CAE100D0CC69 /* chimeracheckrdp.cpp */,
 747                                 A7E8A22D1125939F0011D39C /* chimerarealigner.h */,
 748                                 A7E8A22E1125939F0011D39C /* chimerarealigner.cpp */,
 749                                 A7B04491106CC3E60046FC83 /* chimeraslayer.h */,
 750                                 A7B04492106CC3E60046FC83 /* chimeraslayer.cpp */,
 751                                 372A55531017922B00C5194B /* decalc.h */,
 752                                 372A55541017922B00C5194B /* decalc.cpp */,
 753                                 A7E4A822106A9AD700688F62 /* maligner.h */,
 754                                 A7E4A823106A9AD700688F62 /* maligner.cpp */,
 755                                 374F301110063B6F00E97C66 /* pintail.h */,
 756                                 374F301210063B6F00E97C66 /* pintail.cpp */,
 757                                 A7B0450C106CEEC90046FC83 /* slayer.h */,
 758                                 A7B0450D106CEEC90046FC83 /* slayer.cpp */,
 759                         );
 760                         name = chimera;
 761                         sourceTree = "<group>";
 762                 };
 763                 3796441D0FB9B9650081FDB6 /* read */ = {
 764                         isa = PBXGroup;
 765                         children = (
 766                                 A7D86C6A10FE084300865661 /* formatmatrix.h */,
 767                                 A7D86C7B10FE09AB00865661 /* formatcolumn.h */,
 768                                 A7D86C7C10FE09AB00865661 /* formatcolumn.cpp */,
 769                                 A7D86C8A10FE09FE00865661 /* formatphylip.h */,
 770                                 A7D86C8B10FE09FE00865661 /* formatphylip.cpp */,
 771                                 A727E84810D14568001A8432 /* readblast.h */,
 772                                 A727E84910D14568001A8432 /* readblast.cpp */,
 773                                 A751ACE81098B283003D0911 /* readcluster.h */,
 774                                 A751ACE91098B283003D0911 /* readcluster.cpp */,
 775                                 375AA1340F9E433D008EF9B8 /* readcolumn.h */,
 776                                 375AA1330F9E433D008EF9B8 /* readcolumn.cpp */,
 777                                 37D928130F21331F001D4494 /* readmatrix.hpp */,
 778                                 375AA1360F9E433D008EF9B8 /* readotu.h */,
 779                                 375AA1350F9E433D008EF9B8 /* readotu.cpp */,
 780                                 375AA1380F9E433D008EF9B8 /* readphylip.h */,
 781                                 375AA1370F9E433D008EF9B8 /* readphylip.cpp */,
 782                                 37AD4DC80F28F3DD00AA2D49 /* readtree.h */,
 783                                 37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */,
 784                         );
 785                         name = read;
 786                         sourceTree = "<group>";
 787                 };
 788                 37D928A60F2133C0001D4494 /* calculators */ = {
 789                         isa = PBXGroup;
 790                         children = (
 791                                 37D927BE0F21331F001D4494 /* calculator.h */,
 792                                 37D927BD0F21331F001D4494 /* calculator.cpp */,
 793                                 3792948D0F2E271100B9034A /* treecalculator.h */,
 794                                 37D927B90F21331F001D4494 /* ace.h */,
 795                                 37D927B80F21331F001D4494 /* ace.cpp */,
 796                                 EB1216860F619B83004A865F /* bergerparker.h */,
 797                                 EB1216870F619B83004A865F /* bergerparker.cpp */,
 798                                 373C69950FC1E63600137ACD /* boneh.h */,
 799                                 373C69940FC1E63600137ACD /* boneh.cpp */,
 800                                 37D927BC0F21331F001D4494 /* bootstrap.h */,
 801                                 37D927BB0F21331F001D4494 /* bootstrap.cpp */,
 802                                 EB1216E30F61ACFB004A865F /* bstick.h */,
 803                                 EB1216E40F61ACFB004A865F /* bstick.cpp */,
 804                                 37D927C00F21331F001D4494 /* chao1.h */,
 805                                 37D927BF0F21331F001D4494 /* chao1.cpp */,
 806                                 7EC3D4510FA0FFF900338DA5 /* coverage.h */,
 807                                 7EC3D4500FA0FFF900338DA5 /* coverage.cpp */,
 808                                 37C753DF0FB3492400DBD02E /* dist.h */,
 809                                 37C753F00FB34AE800DBD02E /* eachgapdist.h */,
 810                                 37C753F40FB34C0300DBD02E /* eachgapignore.h */,
 811                                 373C69960FC1E63600137ACD /* efron.cpp */,
 812                                 373C69970FC1E63600137ACD /* efron.h */,
 813                                 379D3D6B0FF917F40068C1C0 /* filters.h */,
 814                                 EB9303F70F53517300E8EF26 /* geom.h */,
 815                                 EB9303F80F53517300E8EF26 /* geom.cpp */,
 816                                 378C1AF10FB0644D004D63F5 /* goodscoverage.h */,
 817                                 378C1AF00FB0644D004D63F5 /* goodscoverage.cpp */,
 818                                 37C753ED0FB34A5700DBD02E /* ignoregaps.h */,
 819                                 37D927E80F21331F001D4494 /* jackknife.h */,
 820                                 37D927E70F21331F001D4494 /* jackknife.cpp */,
 821                                 EB9303E90F534D9400E8EF26 /* logsd.h */,
 822                                 EB9303EA0F534D9400E8EF26 /* logsd.cpp */,
 823                                 375873F90F7D64AB0040F377 /* nseqs.h */,
 824                                 37D927F50F21331F001D4494 /* npshannon.h */,
 825                                 37D927F40F21331F001D4494 /* npshannon.cpp */,
 826                                 37C753F10FB34B4700DBD02E /* onegapdist.h */,
 827                                 37C753F30FB34BBF00DBD02E /* onegapignore.h */,
 828                                 379294880F2E258500B9034A /* parsimony.h */,
 829                                 379294890F2E258500B9034A /* parsimony.cpp */,
 830                                 EB6E68170F5F1C780044E17B /* qstat.h */,
 831                                 EB6E68180F5F1C780044E17B /* qstat.cpp */,
 832                                 37D928020F21331F001D4494 /* rarecalc.h */,
 833                                 37D928010F21331F001D4494 /* rarecalc.cpp */,
 834                                 37D9281F0F21331F001D4494 /* shannon.h */,
 835                                 37D9281E0F21331F001D4494 /* shannon.cpp */,
 836                                 37D928230F21331F001D4494 /* sharedace.h */,
 837                                 37D928220F21331F001D4494 /* sharedace.cpp */,
 838                                 37519A690F80E6EB00FED5E8 /* sharedanderbergs.h */,
 839                                 37519A6A0F80E6EB00FED5E8 /* sharedanderbergs.cpp */,
 840                                 7EC3D4520FA0FFF900338DA5 /* sharedanderberg.h */,
 841                                 375873FB0F7D64DA0040F377 /* sharedbraycurtis.h */,
 842                                 375873FC0F7D64DA0040F377 /* sharedbraycurtis.cpp */,
 843                                 37D928250F21331F001D4494 /* sharedchao1.h */,
 844                                 37D928240F21331F001D4494 /* sharedchao1.cpp */,
 845                                 37D928290F21331F001D4494 /* sharedjabund.h */,
 846                                 37D928280F21331F001D4494 /* sharedjabund.cpp */,
 847                                 378C1B000FB0644D004D63F5 /* sharedjackknife.h */,
 848                                 378C1AFF0FB0644D004D63F5 /* sharedjackknife.cpp */,
 849                                 37D9282B0F21331F001D4494 /* sharedjclass.h */,
 850                                 37D9282A0F21331F001D4494 /* sharedjclass.cpp */,
 851                                 37D9282D0F21331F001D4494 /* sharedjest.h */,
 852                                 37D9282C0F21331F001D4494 /* sharedjest.cpp */,
 853                                 EB1217210F61C9AC004A865F /* sharedkstest.h */,
 854                                 EB1217220F61C9AC004A865F /* sharedkstest.cpp */,
 855                                 375874000F7D64EF0040F377 /* sharedkulczynski.h */,
 856                                 375873FE0F7D64EF0040F377 /* sharedkulczynski.cpp */,
 857                                 375874030F7D64EF0040F377 /* sharedkulczynskicody.h */,
 858                                 375874020F7D64EF0040F377 /* sharedkulczynskicody.cpp */,
 859                                 375874010F7D64EF0040F377 /* sharedlennon.h */,
 860                                 375873FF0F7D64EF0040F377 /* sharedlennon.cpp */,
 861                                 378C1B020FB0644D004D63F5 /* sharedmarczewski.h */,
 862                                 378C1B010FB0644D004D63F5 /* sharedmarczewski.cpp */,
 863                                 375874070F7D64FC0040F377 /* sharedmorisitahorn.h */,
 864                                 375874080F7D64FC0040F377 /* sharedmorisitahorn.cpp */,
 865                                 375874090F7D64FC0040F377 /* sharedochiai.h */,
 866                                 3758740B0F7D64FC0040F377 /* sharedochiai.cpp */,
 867                                 3758740A0F7D64FC0040F377 /* sharednseqs.h */,
 868                                 37D928350F21331F001D4494 /* sharedsobs.h */,
 869                                 37D928340F21331F001D4494 /* sharedsobs.cpp */,
 870                                 37AFC71D0F445386005F492D /* sharedsobscollectsummary.h */,
 871                                 37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */,
 872                                 37D928370F21331F001D4494 /* sharedsorabund.h */,
 873                                 37D928360F21331F001D4494 /* sharedsorabund.cpp */,
 874                                 37D928390F21331F001D4494 /* sharedsorclass.h */,
 875                                 37D928380F21331F001D4494 /* sharedsorclass.cpp */,
 876                                 37D9283B0F21331F001D4494 /* sharedsorest.h */,
 877                                 37D9283A0F21331F001D4494 /* sharedsorest.cpp */,
 878                                 37D9283D0F21331F001D4494 /* sharedthetan.h */,
 879                                 37D9283C0F21331F001D4494 /* sharedthetan.cpp */,
 880                                 37D9283F0F21331F001D4494 /* sharedthetayc.h */,
 881                                 37D9283E0F21331F001D4494 /* sharedthetayc.cpp */,
 882                                 EB72FE250FC1F5CA0051AC11 /* shen.h */,
 883                                 EB72FE240FC1F5CA0051AC11 /* shen.cpp */,
 884                                 37D928410F21331F001D4494 /* simpson.h */,
 885                                 37D928400F21331F001D4494 /* simpson.cpp */,
 886                                 37D928430F21331F001D4494 /* sobs.h */,
 887                                 373C69980FC1E63600137ACD /* solow.cpp */,
 888                                 373C69990FC1E63600137ACD /* solow.h */,
 889                                 374610810F40652400460C57 /* unweighted.h */,
 890                                 374610820F40652400460C57 /* unweighted.cpp */,
 891                                 37D9284E0F21331F001D4494 /* uvest.h */,
 892                                 37D9284D0F21331F001D4494 /* uvest.cpp */,
 893                                 3746107C0F4064D100460C57 /* weighted.h */,
 894                                 3746107D0F4064D100460C57 /* weighted.cpp */,
 895                                 7EC3D4540FA0FFF900338DA5 /* whittaker.h */,
 896                                 7EC3D4530FA0FFF900338DA5 /* whittaker.cpp */,
 897                         );
 898                         name = calculators;
 899                         sourceTree = "<group>";
 900                 };
 901                 37D928A90F2133E5001D4494 /* commands */ = {
 902                         isa = PBXGroup;
 903                         children = (
 904                                 37D927CD0F21331F001D4494 /* command.hpp */,
 905                                 378DC5CD0FBDE1C8003B8607 /* aligncommand.h */,
 906                                 378DC5CE0FBDE1C8003B8607 /* aligncommand.cpp */,
 907                                 37C1D9710F86506E0059E3F0 /* binsequencecommand.h */,
 908                                 37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */,
 909                                 21DDC0190F97A8FE0060691C /* bootstrapsharedcommand.h */,
 910                                 21DDC01A0F97A8FE0060691C /* bootstrapsharedcommand.cpp */,
 911                                 37D927C40F21331F001D4494 /* clustercommand.h */,
 912                                 37D927C30F21331F001D4494 /* clustercommand.cpp */,
 913                                 37D927C80F21331F001D4494 /* collectcommand.h */,
 914                                 37D927C70F21331F001D4494 /* collectcommand.cpp */,
 915                                 37D927CC0F21331F001D4494 /* collectsharedcommand.h */,
 916                                 37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */,
 917                                 377326640FAF16E0007ABB8B /* consensuscommand.h */,
 918                                 377326630FAF16E0007ABB8B /* consensuscommand.cpp */,
 919                                 379D3D4F0FF90E090068C1C0 /* chimeraseqscommand.h */,
 920                                 379D3D500FF90E090068C1C0 /* chimeraseqscommand.cpp */,
 921                                 A7861476109F5FA00010AAAF /* classifyseqscommand.h */,
 922                                 A7861477109F5FA00010AAAF /* classifyseqscommand.cpp */,
 923                                 37B28F660F27590100808A62 /* deconvolutecommand.h */,
 924                                 37B28F670F27590100808A62 /* deconvolutecommand.cpp */,
 925                                 37C753CC0FB3415200DBD02E /* distancecommand.h */,
 926                                 37C753CD0FB3415200DBD02E /* distancecommand.cpp */,
 927                                 378C1AEF0FB0644D004D63F5 /* filterseqscommand.h */,
 928                                 378C1AEE0FB0644D004D63F5 /* filterseqscommand.cpp */,
 929                                 A70B53A50F4CD7AD0064797E /* getgroupcommand.h */,
 930                                 A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */,
 931                                 A70B53A70F4CD7AD0064797E /* getlabelcommand.h */,
 932                                 A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */,
 933                                 A73329CD1083B3B3003B10C5 /* getlistcountcommand.h */,
 934                                 A73329CE1083B3B3003B10C5 /* getlistcountcommand.cpp */,
 935                                 370B88050F8A4EE4005AB382 /* getoturepcommand.h */,
 936                                 370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */,
 937                                 3749273D0FD5956B0031C06B /* getrabundcommand.h */,
 938                                 3749273E0FD5956B0031C06B /* getrabundcommand.cpp */,
 939                                 3749271B0FD58C840031C06B /* getsabundcommand.h */,
 940                                 3749271C0FD58C840031C06B /* getsabundcommand.cpp */,
 941                                 37B73CA41004D89A008C4B41 /* getseqscommand.h */,
 942                                 37B73CA51004D89A008C4B41 /* getseqscommand.cpp */,
 943                                 A7E4A781106913F900688F62 /* getsharedotucommand.h */,
 944                                 A7E4A782106913F900688F62 /* getsharedotucommand.cpp */,
 945                                 A729ACCE10848E6100139801 /* hclustercommand.h */,
 946                                 A729ACCF10848E6100139801 /* hclustercommand.cpp */,
 947                                 375873F10F7D64800040F377 /* heatmapcommand.h */,
 948                                 375873F00F7D64800040F377 /* heatmapcommand.cpp */,
 949                                 378598640FDD497000EF9D03 /* heatmapsimcommand.h */,
 950                                 378598650FDD497000EF9D03 /* heatmapsimcommand.cpp */,
 951                                 37D927E40F21331F001D4494 /* helpcommand.h */,
 952                                 37D927E30F21331F001D4494 /* helpcommand.cpp */,
 953                                 375873F40F7D648F0040F377 /* libshuffcommand.h */,
 954                                 375873F30F7D648F0040F377 /* libshuffcommand.cpp */,
 955                                 37B73C741004BEFD008C4B41 /* listseqscommand.h */,
 956                                 37B73C751004BEFD008C4B41 /* listseqscommand.cpp */,
 957                                 21E859D60FC4632E005E1A48 /* matrixoutputcommand.h */,
 958                                 21E859D70FC4632E005E1A48 /* matrixoutputcommand.cpp */,
 959                                 7E5A17AD0FE57292003C6A03 /* mergefilecommand.h */,
 960                                 7E5A17AE0FE57292003C6A03 /* mergefilecommand.cpp */,
 961                                 A7E0AAB410D2886D00CF407B /* mgclustercommand.h */,
 962                                 A7E0AAB510D2886D00CF407B /* mgclustercommand.cpp */,
 963                                 375873F70F7D649C0040F377 /* nocommands.h */,
 964                                 375873F60F7D649C0040F377 /* nocommands.cpp */,
 965                                 A704E8A11106045D00870157 /* otuhierarchycommand.h */,
 966                                 A704E8A21106045D00870157 /* otuhierarchycommand.cpp */,
 967                                 A71CB8A111354B9F00848EF7 /* parselistscommand.h */,
 968                                 A71CB8A211354B9F00848EF7 /* parselistscommand.cpp */,
 969                                 3792946E0F2E191800B9034A /* parsimonycommand.h */,
 970                                 3792946F0F2E191800B9034A /* parsimonycommand.cpp */,
 971                                 A7D176CD10F2558500159497 /* pcacommand.h */,
 972                                 A7D176CE10F2558500159497 /* pcacommand.cpp */,
 973                                 A773808E10B6EFD1002A6A61 /* phylotypecommand.h */,
 974                                 A773808F10B6EFD1002A6A61 /* phylotypecommand.cpp */,
 975                                 A7027F2610DFF86D00BF45FE /* preclustercommand.h */,
 976                                 A7027F2710DFF86D00BF45FE /* preclustercommand.cpp */,
 977                                 37D927FE0F21331F001D4494 /* quitcommand.h */,
 978                                 37D927FD0F21331F001D4494 /* quitcommand.cpp */,
 979                                 37D928080F21331F001D4494 /* rarefactcommand.h */,
 980                                 37D928070F21331F001D4494 /* rarefactcommand.cpp */,
 981                                 37D9280B0F21331F001D4494 /* rarefactsharedcommand.h */,
 982                                 37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */,
 983                                 372E12940F263D5A0095CF7E /* readdistcommand.h */,
 984                                 372E12950F263D5A0095CF7E /* readdistcommand.cpp */,
 985                                 372E126E0F26365B0095CF7E /* readotucommand.h */,
 986                                 372E126F0F26365B0095CF7E /* readotucommand.cpp */,
 987                                 37E5F4900F2A3DA800F8D827 /* readtreecommand.h */,
 988                                 37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */,
 989                                 37B73CBE1004EB38008C4B41 /* removeseqscommand.h */,
 990                                 37B73CBF1004EB38008C4B41 /* removeseqscommand.cpp */,
 991                                 7E09C5120FDA79C5002ECAE5 /* reversecommand.h */,
 992                                 7E09C5130FDA79C5002ECAE5 /* reversecommand.cpp */,
 993                                 A70DECD71063D8B40057C03C /* secondarystructurecommand.h */,
 994                                 A70DECD81063D8B40057C03C /* secondarystructurecommand.cpp */,
 995                                 371B30B30FD7EE67000414CA /* screenseqscommand.h */,
 996                                 371B30B20FD7EE67000414CA /* screenseqscommand.cpp */,
 997                                 3799A94F0FD6A58C00E33EDE /* seqsummarycommand.h */,
 998                                 3799A94E0FD6A58C00E33EDE /* seqsummarycommand.cpp */,
 999                                 A70B00C6110885EB002F453A /* setdircommand.h */,
1000                                 A70B00C7110885EB002F453A /* setdircommand.cpp */,
1001                                 37D928270F21331F001D4494 /* sharedcommand.h */,
1002                                 37D928260F21331F001D4494 /* sharedcommand.cpp */,
1003                                 37D928470F21331F001D4494 /* summarycommand.h */,
1004                                 37D928460F21331F001D4494 /* summarycommand.cpp */,
1005                                 37D9284B0F21331F001D4494 /* summarysharedcommand.h */,
1006                                 37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */,
1007                                 37B73CCD1004F5E0008C4B41 /* systemcommand.h */,
1008                                 37B73CCE1004F5E0008C4B41 /* systemcommand.cpp */,
1009                                 211C38370F961E1F00FEE541 /* treegroupscommand.h */,
1010                                 211C38360F961E1F00FEE541 /* treegroupscommand.cpp */,
1011                                 7E09C5340FDA7F65002ECAE5 /* trimseqscommand.h */,
1012                                 7E09C5350FDA7F65002ECAE5 /* trimseqscommand.cpp */,
1013                                 3746109B0F40657600460C57 /* unifracunweightedcommand.h */,
1014                                 3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */,
1015                                 374610760F40645300460C57 /* unifracweightedcommand.h */,
1016                                 374610770F40645300460C57 /* unifracweightedcommand.cpp */,
1017                                 37519A9F0F810D0200FED5E8 /* venncommand.h */,
1018                                 37519AA00F810D0200FED5E8 /* venncommand.cpp */,
1019                         );
1020                         name = commands;
1021                         sourceTree = "<group>";
1022                 };
1023                 37D928AC0F213420001D4494 /* containers */ = {
1024                         isa = PBXGroup;
1025                         children = (
1026                                 373C68A10FC1C07D00137ACD /* alignment.hpp */,
1027                                 373C68A00FC1C07D00137ACD /* alignment.cpp */,
1028                                 373C68A30FC1C07D00137ACD /* alignmentcell.hpp */,
1029                                 373C68A20FC1C07D00137ACD /* alignmentcell.cpp */,
1030                                 A78782A910A1B1CB0086103D /* alignmentdb.h */,
1031                                 A78782AA10A1B1CB0086103D /* alignmentdb.cpp */,
1032                                 373C69170FC1C8AF00137ACD /* blastdb.hpp */,
1033                                 373C69160FC1C8AF00137ACD /* blastdb.cpp */,
1034                                 37D927D40F21331F001D4494 /* database.hpp */,
1035                                 37D927D30F21331F001D4494 /* database.cpp */,
1036                                 37D927D50F21331F001D4494 /* datavector.hpp */,
1037                                 A794201011107897003AECCD /* distancedb.hpp */,
1038                                 A794200F11107897003AECCD /* distancedb.cpp */,
1039                                 37D927DC0F21331F001D4494 /* fastamap.h */,
1040                                 37D927DB0F21331F001D4494 /* fastamap.cpp */,
1041                                 375873EA0F7D64520040F377 /* fullmatrix.h */,
1042                                 375873EB0F7D64520040F377 /* fullmatrix.cpp */,
1043                                 37D927E20F21331F001D4494 /* groupmap.h */,
1044                                 37D927E10F21331F001D4494 /* groupmap.cpp */,
1045                                 37D927EA0F21331F001D4494 /* kmer.hpp */,
1046                                 37D927E90F21331F001D4494 /* kmer.cpp */,
1047                                 37D927EC0F21331F001D4494 /* kmerdb.hpp */,
1048                                 37D927EB0F21331F001D4494 /* kmerdb.cpp */,
1049                                 37D927EE0F21331F001D4494 /* listvector.hpp */,
1050                                 37D927ED0F21331F001D4494 /* listvector.cpp */,
1051                                 37D927F10F21331F001D4494 /* nameassignment.hpp */,
1052                                 37D927F00F21331F001D4494 /* nameassignment.cpp */,
1053                                 37D927F80F21331F001D4494 /* ordervector.hpp */,
1054                                 37D927F70F21331F001D4494 /* ordervector.cpp */,
1055                                 37D928000F21331F001D4494 /* rabundvector.hpp */,
1056                                 37D927FF0F21331F001D4494 /* rabundvector.cpp */,
1057                                 37D9281B0F21331F001D4494 /* sabundvector.hpp */,
1058                                 37D9281A0F21331F001D4494 /* sabundvector.cpp */,
1059                                 37D9281D0F21331F001D4494 /* sequence.hpp */,
1060                                 37D9281C0F21331F001D4494 /* sequence.cpp */,
1061                                 378C1AFE0FB0644D004D63F5 /* sequencedb.h */,
1062                                 378C1AFD0FB0644D004D63F5 /* sequencedb.cpp */,
1063                                 37AD4CE20F28AEA300AA2D49 /* sharedlistvector.h */,
1064                                 37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */,
1065                                 37D9282F0F21331F001D4494 /* sharedordervector.h */,
1066                                 37D9282E0F21331F001D4494 /* sharedordervector.cpp */,
1067                                 37D928310F21331F001D4494 /* sharedrabundvector.h */,
1068                                 37D928300F21331F001D4494 /* sharedrabundvector.cpp */,
1069                                 37D928330F21331F001D4494 /* sharedsabundvector.h */,
1070                                 37D928320F21331F001D4494 /* sharedsabundvector.cpp */,
1071                                 37D928450F21331F001D4494 /* sparsematrix.hpp */,
1072                                 37D928440F21331F001D4494 /* sparsematrix.cpp */,
1073                                 373C68F40FC1C6A800137ACD /* suffixdb.hpp */,
1074                                 373C68F30FC1C6A800137ACD /* suffixdb.cpp */,
1075                                 373C68F60FC1C6A800137ACD /* suffixnodes.hpp */,
1076                                 373C68F50FC1C6A800137ACD /* suffixnodes.cpp */,
1077                                 373C68F80FC1C6A800137ACD /* suffixtree.hpp */,
1078                                 373C68F70FC1C6A800137ACD /* suffixtree.cpp */,
1079                                 37AD4DB90F28E2FE00AA2D49 /* tree.h */,
1080                                 37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */,
1081                                 379293C10F2DE73400B9034A /* treemap.h */,
1082                                 379293C20F2DE73400B9034A /* treemap.cpp */,
1083                                 37E5F3E10F29FD4200F8D827 /* treenode.h */,
1084                                 37E5F3E20F29FD4200F8D827 /* treenode.cpp */,
1085                         );
1086                         name = containers;
1087                         sourceTree = "<group>";
1088                 };
1089                 37D928B10F213472001D4494 /* errorcheckor */ = {
1090                         isa = PBXGroup;
1091                         children = (
1092                                 37D928500F21331F001D4494 /* validcalculator.h */,
1093                                 37D9284F0F21331F001D4494 /* validcalculator.cpp */,
1094                                 37D928540F21331F001D4494 /* validparameter.h */,
1095                                 37D928530F21331F001D4494 /* validparameter.cpp */,
1096                         );
1097                         name = errorcheckor;
1098                         sourceTree = "<group>";
1099                 };
1100                 A787811210A073F40086103D /* classifiers */ = {
1101                         isa = PBXGroup;
1102                         children = (
1103                                 A78780FE10A06B8B0086103D /* classify.h */,
1104                                 A787810210A06D5D0086103D /* classify.cpp */,
1105                                 A787820F10A0AAE70086103D /* bayesian.h */,
1106                                 A787821010A0AAE70086103D /* bayesian.cpp */,
1107                                 A773805D10B6D6FC002A6A61 /* taxonomyequalizer.h */,
1108                                 A773805E10B6D6FC002A6A61 /* taxonomyequalizer.cpp */,
1109                                 A78781B910A0813D0086103D /* phylotree.h */,
1110                                 A78781B810A0813D0086103D /* phylotree.cpp */,
1111                                 A787844310A1EBDD0086103D /* knn.h */,
1112                                 A787844410A1EBDD0086103D /* knn.cpp */,
1113                         );
1114                         name = classifiers;
1115                         sourceTree = "<group>";
1116                 };
1117                 C6859E8C029090F304C91782 /* Documentation */ = {
1118                         isa = PBXGroup;
1119                         children = (
1120                                 C6859E8B029090EE04C91782 /* Mothur.1 */,
1121                         );
1122                         name = Documentation;
1123                         sourceTree = "<group>";
1124                 };
1125 /* End PBXGroup section */
1126
1127 /* Begin PBXNativeTarget section */
1128                 8DD76F620486A84900D96B5E /* mothur */ = {
1129                         isa = PBXNativeTarget;
1130                         buildConfigurationList = 1DEB923108733DC60010E9CD /* Build configuration list for PBXNativeTarget "mothur" */;
1131                         buildPhases = (
1132                                 8DD76F640486A84900D96B5E /* Sources */,
1133                                 8DD76F660486A84900D96B5E /* Frameworks */,
1134                                 8DD76F690486A84900D96B5E /* CopyFiles */,
1135                         );
1136                         buildRules = (
1137                         );
1138                         dependencies = (
1139                         );
1140                         name = mothur;
1141                         productInstallPath = "$(HOME)/bin";
1142                         productName = Mothur;
1143                         productReference = 8DD76F6C0486A84900D96B5E /* mothur */;
1144                         productType = "com.apple.product-type.tool";
1145                 };
1146 /* End PBXNativeTarget section */
1147
1148 /* Begin PBXProject section */
1149                 08FB7793FE84155DC02AAC07 /* Project object */ = {
1150                         isa = PBXProject;
1151                         buildConfigurationList = 1DEB923508733DC60010E9CD /* Build configuration list for PBXProject "Mothur" */;
1152                         compatibilityVersion = "Xcode 3.0";
1153                         hasScannedForEncodings = 1;
1154                         mainGroup = 08FB7794FE84155DC02AAC07 /* Mothur */;
1155                         projectDirPath = "";
1156                         projectRoot = "";
1157                         targets = (
1158                                 8DD76F620486A84900D96B5E /* mothur */,
1159                         );
1160                 };
1161 /* End PBXProject section */
1162
1163 /* Begin PBXSourcesBuildPhase section */
1164                 8DD76F640486A84900D96B5E /* Sources */ = {
1165                         isa = PBXSourcesBuildPhase;
1166                         buildActionMask = 2147483647;
1167                         files = (
1168                                 37D928550F21331F001D4494 /* ace.cpp in Sources */,
1169                                 37D928560F21331F001D4494 /* averagelinkage.cpp in Sources */,
1170                                 37D928570F21331F001D4494 /* bootstrap.cpp in Sources */,
1171                                 37D928580F21331F001D4494 /* calculator.cpp in Sources */,
1172                                 37D928590F21331F001D4494 /* chao1.cpp in Sources */,
1173                                 37D9285A0F21331F001D4494 /* cluster.cpp in Sources */,
1174                                 37D9285B0F21331F001D4494 /* clustercommand.cpp in Sources */,
1175                                 37D9285C0F21331F001D4494 /* collect.cpp in Sources */,
1176                                 37D9285D0F21331F001D4494 /* collectcommand.cpp in Sources */,
1177                                 37D9285E0F21331F001D4494 /* collectsharedcommand.cpp in Sources */,
1178                                 37D928600F21331F001D4494 /* commandoptionparser.cpp in Sources */,
1179                                 37D928610F21331F001D4494 /* completelinkage.cpp in Sources */,
1180                                 37D928620F21331F001D4494 /* database.cpp in Sources */,
1181                                 37D928630F21331F001D4494 /* engine.cpp in Sources */,
1182                                 37D928650F21331F001D4494 /* fastamap.cpp in Sources */,
1183                                 37D928660F21331F001D4494 /* fileoutput.cpp in Sources */,
1184                                 37D928670F21331F001D4494 /* globaldata.cpp in Sources */,
1185                                 37D928680F21331F001D4494 /* groupmap.cpp in Sources */,
1186                                 37D928690F21331F001D4494 /* helpcommand.cpp in Sources */,
1187                                 37D9286A0F21331F001D4494 /* inputdata.cpp in Sources */,
1188                                 37D9286B0F21331F001D4494 /* jackknife.cpp in Sources */,
1189                                 37D9286C0F21331F001D4494 /* kmer.cpp in Sources */,
1190                                 37D9286D0F21331F001D4494 /* kmerdb.cpp in Sources */,
1191                                 37D9286E0F21331F001D4494 /* listvector.cpp in Sources */,
1192                                 37D9286F0F21331F001D4494 /* mothur.cpp in Sources */,
1193                                 37D928700F21331F001D4494 /* nameassignment.cpp in Sources */,
1194                                 37D928720F21331F001D4494 /* npshannon.cpp in Sources */,
1195                                 37D928730F21331F001D4494 /* ordervector.cpp in Sources */,
1196                                 37D928750F21331F001D4494 /* progress.cpp in Sources */,
1197                                 37D928760F21331F001D4494 /* quitcommand.cpp in Sources */,
1198                                 37D928770F21331F001D4494 /* rabundvector.cpp in Sources */,
1199                                 37D928780F21331F001D4494 /* rarecalc.cpp in Sources */,
1200                                 37D928790F21331F001D4494 /* raredisplay.cpp in Sources */,
1201                                 37D9287A0F21331F001D4494 /* rarefact.cpp in Sources */,
1202                                 37D9287B0F21331F001D4494 /* rarefactcommand.cpp in Sources */,
1203                                 37D9287C0F21331F001D4494 /* rarefactsharedcommand.cpp in Sources */,
1204                                 37D928840F21331F001D4494 /* sabundvector.cpp in Sources */,
1205                                 37D928850F21331F001D4494 /* sequence.cpp in Sources */,
1206                                 37D928860F21331F001D4494 /* shannon.cpp in Sources */,
1207                                 37D928880F21331F001D4494 /* sharedace.cpp in Sources */,
1208                                 37D928890F21331F001D4494 /* sharedchao1.cpp in Sources */,
1209                                 37D9288A0F21331F001D4494 /* sharedcommand.cpp in Sources */,
1210                                 37D9288B0F21331F001D4494 /* sharedjabund.cpp in Sources */,
1211                                 37D9288C0F21331F001D4494 /* sharedjclass.cpp in Sources */,
1212                                 37D9288D0F21331F001D4494 /* sharedjest.cpp in Sources */,
1213                                 37D9288E0F21331F001D4494 /* sharedordervector.cpp in Sources */,
1214                                 37D9288F0F21331F001D4494 /* sharedrabundvector.cpp in Sources */,
1215                                 37D928900F21331F001D4494 /* sharedsabundvector.cpp in Sources */,
1216                                 37D928910F21331F001D4494 /* sharedsobs.cpp in Sources */,
1217                                 37D928920F21331F001D4494 /* sharedsorabund.cpp in Sources */,
1218                                 37D928930F21331F001D4494 /* sharedsorclass.cpp in Sources */,
1219                                 37D928940F21331F001D4494 /* sharedsorest.cpp in Sources */,
1220                                 37D928950F21331F001D4494 /* sharedthetan.cpp in Sources */,
1221                                 37D928960F21331F001D4494 /* sharedthetayc.cpp in Sources */,
1222                                 37D928970F21331F001D4494 /* simpson.cpp in Sources */,
1223                                 37D928980F21331F001D4494 /* singlelinkage.cpp in Sources */,
1224                                 37D928990F21331F001D4494 /* sparsematrix.cpp in Sources */,
1225                                 37D9289A0F21331F001D4494 /* summarycommand.cpp in Sources */,
1226                                 37D9289B0F21331F001D4494 /* summarysharedcommand.cpp in Sources */,
1227                                 37D9289C0F21331F001D4494 /* uvest.cpp in Sources */,
1228                                 37D9289D0F21331F001D4494 /* validcalculator.cpp in Sources */,
1229                                 37D9289F0F21331F001D4494 /* validparameter.cpp in Sources */,
1230                                 372E12700F26365B0095CF7E /* readotucommand.cpp in Sources */,
1231                                 372E12960F263D5A0095CF7E /* readdistcommand.cpp in Sources */,
1232                                 372E12ED0F264D320095CF7E /* commandfactory.cpp in Sources */,
1233                                 37B28F680F27590100808A62 /* deconvolutecommand.cpp in Sources */,
1234                                 37AD4CE40F28AEA300AA2D49 /* sharedlistvector.cpp in Sources */,
1235                                 37AD4DBB0F28E2FE00AA2D49 /* tree.cpp in Sources */,
1236                                 37AD4DCA0F28F3DD00AA2D49 /* readtree.cpp in Sources */,
1237                                 37E5F3E30F29FD4200F8D827 /* treenode.cpp in Sources */,
1238                                 37E5F4920F2A3DA800F8D827 /* readtreecommand.cpp in Sources */,
1239                                 379293C30F2DE73400B9034A /* treemap.cpp in Sources */,
1240                                 379294700F2E191800B9034A /* parsimonycommand.cpp in Sources */,
1241                                 3792948A0F2E258500B9034A /* parsimony.cpp in Sources */,
1242                                 374610780F40645300460C57 /* unifracweightedcommand.cpp in Sources */,
1243                                 3746107E0F4064D100460C57 /* weighted.cpp in Sources */,
1244                                 374610830F40652400460C57 /* unweighted.cpp in Sources */,
1245                                 3746109D0F40657600460C57 /* unifracunweightedcommand.cpp in Sources */,
1246                                 37AFC71F0F445386005F492D /* sharedsobscollectsummary.cpp in Sources */,
1247                                 A70B53AA0F4CD7AD0064797E /* getgroupcommand.cpp in Sources */,
1248                                 A70B53AB0F4CD7AD0064797E /* getlabelcommand.cpp in Sources */,
1249                                 EB9303EB0F534D9400E8EF26 /* logsd.cpp in Sources */,
1250                                 EB9303F90F53517300E8EF26 /* geom.cpp in Sources */,
1251                                 EB6E68190F5F1C780044E17B /* qstat.cpp in Sources */,
1252                                 EB1216880F619B83004A865F /* bergerparker.cpp in Sources */,
1253                                 EB1216E50F61ACFB004A865F /* bstick.cpp in Sources */,
1254                                 EB1217230F61C9AC004A865F /* sharedkstest.cpp in Sources */,
1255                                 375873EC0F7D64520040F377 /* fullmatrix.cpp in Sources */,
1256                                 375873EF0F7D646F0040F377 /* heatmap.cpp in Sources */,
1257                                 375873F20F7D64800040F377 /* heatmapcommand.cpp in Sources */,
1258                                 375873F50F7D648F0040F377 /* libshuffcommand.cpp in Sources */,
1259                                 375873F80F7D649C0040F377 /* nocommands.cpp in Sources */,
1260                                 375873FD0F7D64DA0040F377 /* sharedbraycurtis.cpp in Sources */,
1261                                 375874040F7D64EF0040F377 /* sharedkulczynski.cpp in Sources */,
1262                                 375874050F7D64EF0040F377 /* sharedlennon.cpp in Sources */,
1263                                 375874060F7D64EF0040F377 /* sharedkulczynskicody.cpp in Sources */,
1264                                 3758740C0F7D64FC0040F377 /* sharedmorisitahorn.cpp in Sources */,
1265                                 3758740D0F7D64FC0040F377 /* sharedochiai.cpp in Sources */,
1266                                 37519A6B0F80E6EB00FED5E8 /* sharedanderbergs.cpp in Sources */,
1267                                 37519AA10F810D0200FED5E8 /* venncommand.cpp in Sources */,
1268                                 37519AB50F810FAE00FED5E8 /* venn.cpp in Sources */,
1269                                 37C1D9730F86506E0059E3F0 /* binsequencecommand.cpp in Sources */,
1270                                 370B88070F8A4EE4005AB382 /* getoturepcommand.cpp in Sources */,
1271                                 7E412F490F8D21B600381DD0 /* slibshuff.cpp in Sources */,
1272                                 7E412FEA0F8D3E2C00381DD0 /* libshuff.cpp in Sources */,
1273                                 7E4130F80F8E58FA00381DD0 /* dlibshuff.cpp in Sources */,
1274                                 211C38320F961DD400FEE541 /* sharedutilities.cpp in Sources */,
1275                                 211C38380F961E1F00FEE541 /* treegroupscommand.cpp in Sources */,
1276                                 21DDC01B0F97A8FE0060691C /* bootstrapsharedcommand.cpp in Sources */,
1277                                 375AA1390F9E433D008EF9B8 /* readcolumn.cpp in Sources */,
1278                                 375AA13A0F9E433D008EF9B8 /* readotu.cpp in Sources */,
1279                                 375AA13B0F9E433D008EF9B8 /* readphylip.cpp in Sources */,
1280                                 7EC3D4550FA0FFF900338DA5 /* coverage.cpp in Sources */,
1281                                 7EC3D4560FA0FFF900338DA5 /* whittaker.cpp in Sources */,
1282                                 377326650FAF16E0007ABB8B /* consensuscommand.cpp in Sources */,
1283                                 378C1B030FB0644E004D63F5 /* filterseqscommand.cpp in Sources */,
1284                                 378C1B040FB0644E004D63F5 /* goodscoverage.cpp in Sources */,
1285                                 378C1B0A0FB0644E004D63F5 /* sequencedb.cpp in Sources */,
1286                                 378C1B0B0FB0644E004D63F5 /* sharedjackknife.cpp in Sources */,
1287                                 378C1B0C0FB0644E004D63F5 /* sharedmarczewski.cpp in Sources */,
1288                                 37C753CE0FB3415200DBD02E /* distancecommand.cpp in Sources */,
1289                                 378DC5CF0FBDE1C8003B8607 /* aligncommand.cpp in Sources */,
1290                                 373C68A40FC1C07D00137ACD /* alignment.cpp in Sources */,
1291                                 373C68A50FC1C07D00137ACD /* alignmentcell.cpp in Sources */,
1292                                 373C68BC0FC1C1A600137ACD /* gotohoverlap.cpp in Sources */,
1293                                 373C68C50FC1C25F00137ACD /* overlap.cpp in Sources */,
1294                                 373C68CF0FC1C2D900137ACD /* needlemanoverlap.cpp in Sources */,
1295                                 373C68DD0FC1C38D00137ACD /* blastalign.cpp in Sources */,
1296                                 373C68E50FC1C4A500137ACD /* noalign.cpp in Sources */,
1297                                 373C68F90FC1C6A800137ACD /* suffixdb.cpp in Sources */,
1298                                 373C68FA0FC1C6A800137ACD /* suffixnodes.cpp in Sources */,
1299                                 373C68FB0FC1C6A800137ACD /* suffixtree.cpp in Sources */,
1300                                 373C69180FC1C8AF00137ACD /* blastdb.cpp in Sources */,
1301                                 373C691F0FC1C98600137ACD /* nast.cpp in Sources */,
1302                                 373C692B0FC1C9EB00137ACD /* nastreport.cpp in Sources */,
1303                                 373C699A0FC1E63600137ACD /* boneh.cpp in Sources */,
1304                                 373C699B0FC1E63600137ACD /* efron.cpp in Sources */,
1305                                 373C699C0FC1E63600137ACD /* solow.cpp in Sources */,
1306                                 EB72FE260FC1F5CA0051AC11 /* shen.cpp in Sources */,
1307                                 21E859D80FC4632E005E1A48 /* matrixoutputcommand.cpp in Sources */,
1308                                 3749271D0FD58C840031C06B /* getsabundcommand.cpp in Sources */,
1309                                 3749273F0FD5956B0031C06B /* getrabundcommand.cpp in Sources */,
1310                                 3799A9510FD6A58C00E33EDE /* seqsummarycommand.cpp in Sources */,
1311                                 371B30B40FD7EE67000414CA /* screenseqscommand.cpp in Sources */,
1312                                 7E09C5140FDA79C5002ECAE5 /* reversecommand.cpp in Sources */,
1313                                 7E09C5360FDA7F65002ECAE5 /* trimseqscommand.cpp in Sources */,
1314                                 378598660FDD497000EF9D03 /* heatmapsimcommand.cpp in Sources */,
1315                                 378598740FDD4C1500EF9D03 /* heatmapsim.cpp in Sources */,
1316                                 378599100FDD7E8E00EF9D03 /* optionparser.cpp in Sources */,
1317                                 7E5A17AF0FE57292003C6A03 /* mergefilecommand.cpp in Sources */,
1318                                 379D3D510FF90E090068C1C0 /* chimeraseqscommand.cpp in Sources */,
1319                                 37B73C761004BEFD008C4B41 /* listseqscommand.cpp in Sources */,
1320                                 37B73CA61004D89A008C4B41 /* getseqscommand.cpp in Sources */,
1321                                 37B73CC01004EB38008C4B41 /* removeseqscommand.cpp in Sources */,
1322                                 37B73CCF1004F5E0008C4B41 /* systemcommand.cpp in Sources */,
1323                                 374F2FEB100634B600E97C66 /* bellerophon.cpp in Sources */,
1324                                 374F301310063B6F00E97C66 /* pintail.cpp in Sources */,
1325                                 372A55551017922B00C5194B /* decalc.cpp in Sources */,
1326                                 372095C2103196D70004D347 /* chimera.cpp in Sources */,
1327                                 A75B887E104C16860083C454 /* ccode.cpp in Sources */,
1328                                 A7283FF81056CAE100D0CC69 /* chimeracheckrdp.cpp in Sources */,
1329                                 A70DECD91063D8B40057C03C /* secondarystructurecommand.cpp in Sources */,
1330                                 A7E4A783106913F900688F62 /* getsharedotucommand.cpp in Sources */,
1331                                 A7E4A824106A9AD700688F62 /* maligner.cpp in Sources */,
1332                                 A7B04493106CC3E60046FC83 /* chimeraslayer.cpp in Sources */,
1333                                 A7B0450E106CEEC90046FC83 /* slayer.cpp in Sources */,
1334                                 A73329CF1083B3B3003B10C5 /* getlistcountcommand.cpp in Sources */,
1335                                 A729ACD010848E6100139801 /* hclustercommand.cpp in Sources */,
1336                                 A729ACE410849BBE00139801 /* hcluster.cpp in Sources */,
1337                                 A751ACEA1098B283003D0911 /* readcluster.cpp in Sources */,
1338                                 A7861478109F5FA00010AAAF /* classifyseqscommand.cpp in Sources */,
1339                                 A787810310A06D5D0086103D /* classify.cpp in Sources */,
1340                                 A78781BA10A0813E0086103D /* phylotree.cpp in Sources */,
1341                                 A787821110A0AAE70086103D /* bayesian.cpp in Sources */,
1342                                 A78782AB10A1B1CB0086103D /* alignmentdb.cpp in Sources */,
1343                                 A787844510A1EBDD0086103D /* knn.cpp in Sources */,
1344                                 A773805F10B6D6FC002A6A61 /* taxonomyequalizer.cpp in Sources */,
1345                                 A773809010B6EFD1002A6A61 /* phylotypecommand.cpp in Sources */,
1346                                 A727E84A10D14568001A8432 /* readblast.cpp in Sources */,
1347                                 A7E0AAB610D2886D00CF407B /* mgclustercommand.cpp in Sources */,
1348                                 A7027F2810DFF86D00BF45FE /* preclustercommand.cpp in Sources */,
1349                                 A7D176CF10F2558500159497 /* pcacommand.cpp in Sources */,
1350                                 A7D86C7D10FE09AB00865661 /* formatcolumn.cpp in Sources */,
1351                                 A7D86C8C10FE09FE00865661 /* formatphylip.cpp in Sources */,
1352                                 A704E8A31106045D00870157 /* otuhierarchycommand.cpp in Sources */,
1353                                 A70B00C8110885EB002F453A /* setdircommand.cpp in Sources */,
1354                                 A794201111107897003AECCD /* distancedb.cpp in Sources */,
1355                                 A7E8A22F1125939F0011D39C /* chimerarealigner.cpp in Sources */,
1356                                 A71CB8A311354B9F00848EF7 /* parselistscommand.cpp in Sources */,
1357                                 A70F3FD01136E391004FDC52 /* mothurout.cpp in Sources */,
1358                         );
1359                         runOnlyForDeploymentPostprocessing = 0;
1360                 };
1361 /* End PBXSourcesBuildPhase section */
1362
1363 /* Begin XCBuildConfiguration section */
1364                 1DEB923208733DC60010E9CD /* Debug */ = {
1365                         isa = XCBuildConfiguration;
1366                         buildSettings = {
1367                                 COPY_PHASE_STRIP = NO;
1368                                 GCC_DYNAMIC_NO_PIC = NO;
1369                                 GCC_ENABLE_FIX_AND_CONTINUE = YES;
1370                                 GCC_MODEL_TUNING = G5;
1371                                 GCC_OPTIMIZATION_LEVEL = 0;
1372                                 GCC_PREPROCESSOR_DEFINITIONS = (
1373                                         "_GLIBCXX_DEBUG=1",
1374                                         "_GLIBCXX_DEBUG_PEDANTIC=1",
1375                                 );
1376                                 INSTALL_PATH = /usr/local/bin;
1377                                 LIBRARY_SEARCH_PATHS = (
1378                                         "$(inherited)",
1379                                         "\"$(SRCROOT)/../readline-6.0\"",
1380                                 );
1381                                 PRODUCT_NAME = mothur;
1382                                 ZERO_LINK = YES;
1383                         };
1384                         name = Debug;
1385                 };
1386                 1DEB923308733DC60010E9CD /* Release */ = {
1387                         isa = XCBuildConfiguration;
1388                         buildSettings = {
1389                                 DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym";
1390                                 GCC_MODEL_TUNING = G5;
1391                                 INSTALL_PATH = /usr/local/bin;
1392                                 LIBRARY_SEARCH_PATHS = (
1393                                         "$(inherited)",
1394                                         "\"$(SRCROOT)/../readline-6.0\"",
1395                                 );
1396                                 PRODUCT_NAME = mothur;
1397                         };
1398                         name = Release;
1399                 };
1400                 1DEB923608733DC60010E9CD /* Debug */ = {
1401                         isa = XCBuildConfiguration;
1402                         buildSettings = {
1403                                 ARCHS = "$(ARCHS_STANDARD_64_BIT_PRE_XCODE_3_1)";
1404                                 ARCHS_STANDARD_64_BIT_PRE_XCODE_3_1 = x86_64;
1405                                 GCC_OPTIMIZATION_LEVEL = 3;
1406                                 GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
1407                                 GCC_WARN_ABOUT_RETURN_TYPE = YES;
1408                                 GCC_WARN_ALLOW_INCOMPLETE_PROTOCOL = NO;
1409                                 GCC_WARN_PEDANTIC = NO;
1410                                 GCC_WARN_UNUSED_VARIABLE = YES;
1411                                 OTHER_CPLUSPLUSFLAGS = "";
1412                                 PREBINDING = NO;
1413                                 SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
1414                                 WARNING_CFLAGS = "";
1415                         };
1416                         name = Debug;
1417                 };
1418                 1DEB923708733DC60010E9CD /* Release */ = {
1419                         isa = XCBuildConfiguration;
1420                         buildSettings = {
1421                                 ARCHS = "$(ARCHS_STANDARD_64_BIT_PRE_XCODE_3_1)";
1422                                 ARCHS_STANDARD_64_BIT_PRE_XCODE_3_1 = x86_64;
1423                                 GCC_OPTIMIZATION_LEVEL = 3;
1424                                 GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
1425                                 GCC_WARN_ABOUT_MISSING_PROTOTYPES = YES;
1426                                 GCC_WARN_ABOUT_RETURN_TYPE = YES;
1427                                 GCC_WARN_ALLOW_INCOMPLETE_PROTOCOL = NO;
1428                                 GCC_WARN_MISSING_PARENTHESES = YES;
1429                                 GCC_WARN_PEDANTIC = YES;
1430                                 GCC_WARN_UNUSED_FUNCTION = YES;
1431                                 GCC_WARN_UNUSED_PARAMETER = NO;
1432                                 GCC_WARN_UNUSED_VALUE = YES;
1433                                 GCC_WARN_UNUSED_VARIABLE = YES;
1434                                 OTHER_CPLUSPLUSFLAGS = (
1435                                         "-ansi",
1436                                         "-pedantic",
1437                                         "-wall",
1438                                         "-lreadline",
1439                                         "-DUSE_READLINE",
1440                                 );
1441                                 PREBINDING = NO;
1442                                 SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
1443                                 SYMROOT = /Users/johnwestcott/Desktop;
1444                                 WARNING_CFLAGS = "";
1445                         };
1446                         name = Release;
1447                 };
1448 /* End XCBuildConfiguration section */
1449
1450 /* Begin XCConfigurationList section */
1451                 1DEB923108733DC60010E9CD /* Build configuration list for PBXNativeTarget "mothur" */ = {
1452                         isa = XCConfigurationList;
1453                         buildConfigurations = (
1454                                 1DEB923208733DC60010E9CD /* Debug */,
1455                                 1DEB923308733DC60010E9CD /* Release */,
1456                         );
1457                         defaultConfigurationIsVisible = 0;
1458                         defaultConfigurationName = Release;
1459                 };
1460                 1DEB923508733DC60010E9CD /* Build configuration list for PBXProject "Mothur" */ = {
1461                         isa = XCConfigurationList;
1462                         buildConfigurations = (
1463                                 1DEB923608733DC60010E9CD /* Debug */,
1464                                 1DEB923708733DC60010E9CD /* Release */,
1465                         );
1466                         defaultConfigurationIsVisible = 0;
1467                         defaultConfigurationName = Release;
1468                 };
1469 /* End XCConfigurationList section */
1470         };
1471         rootObject = 08FB7793FE84155DC02AAC07 /* Project object */;
1472 }