X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=9216cc134d2b406308a78eca23acb81648742e89;hb=902e0fcab76e75009ac43d3f4537e08182628d6f;hp=21dbf8dfbb074de24a0b70e523bd95e56d414695;hpb=f89b6501b7d80e705b6c50ff2c8bdd8bb5d2edf7;p=mothur.git diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index 21dbf8d..9216cc1 100644 --- a/Mothur.xcodeproj/project.pbxproj +++ b/Mothur.xcodeproj/project.pbxproj @@ -3,713 +3,1012 @@ archiveVersion = 1; classes = { }; - objectVersion = 44; + objectVersion = 45; objects = { /* Begin PBXBuildFile section */ - 211C38320F961DD400FEE541 /* sharedutilities.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 211C38300F961DD400FEE541 /* sharedutilities.cpp */; }; - 211C38380F961E1F00FEE541 /* treegroupscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 211C38360F961E1F00FEE541 /* treegroupscommand.cpp */; }; - 21DDC01B0F97A8FE0060691C /* bootstrapsharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 21DDC01A0F97A8FE0060691C /* bootstrapsharedcommand.cpp */; }; - 21E859D80FC4632E005E1A48 /* matrixoutputcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 21E859D70FC4632E005E1A48 /* matrixoutputcommand.cpp */; }; - 370B88070F8A4EE4005AB382 /* getoturepcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */; }; - 371B30B40FD7EE67000414CA /* screenseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 371B30B20FD7EE67000414CA /* screenseqscommand.cpp */; }; - 372095C2103196D70004D347 /* chimera.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 372095C1103196D70004D347 /* chimera.cpp */; }; - 372A55551017922B00C5194B /* decalc.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 372A55541017922B00C5194B /* decalc.cpp */; }; - 372E12700F26365B0095CF7E /* readotucommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 372E126F0F26365B0095CF7E /* readotucommand.cpp */; }; - 372E12960F263D5A0095CF7E /* readdistcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 372E12950F263D5A0095CF7E /* readdistcommand.cpp */; }; - 372E12ED0F264D320095CF7E /* commandfactory.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 372E12EC0F264D320095CF7E /* commandfactory.cpp */; }; - 373C68A40FC1C07D00137ACD /* alignment.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C68A00FC1C07D00137ACD /* alignment.cpp */; }; - 373C68A50FC1C07D00137ACD /* alignmentcell.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C68A20FC1C07D00137ACD /* alignmentcell.cpp */; }; - 373C68BC0FC1C1A600137ACD /* gotohoverlap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C68BA0FC1C1A600137ACD /* gotohoverlap.cpp */; }; - 373C68C50FC1C25F00137ACD /* overlap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C68C30FC1C25F00137ACD /* overlap.cpp */; }; - 373C68CF0FC1C2D900137ACD /* needlemanoverlap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C68CD0FC1C2D900137ACD /* needlemanoverlap.cpp */; }; - 373C68DD0FC1C38D00137ACD /* blastalign.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C68DB0FC1C38D00137ACD /* blastalign.cpp */; }; - 373C68E50FC1C4A500137ACD /* noalign.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C68E30FC1C4A500137ACD /* noalign.cpp */; }; - 373C68F90FC1C6A800137ACD /* suffixdb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C68F30FC1C6A800137ACD /* suffixdb.cpp */; }; - 373C68FA0FC1C6A800137ACD /* suffixnodes.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C68F50FC1C6A800137ACD /* suffixnodes.cpp */; }; - 373C68FB0FC1C6A800137ACD /* suffixtree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C68F70FC1C6A800137ACD /* suffixtree.cpp */; }; - 373C69180FC1C8AF00137ACD /* blastdb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C69160FC1C8AF00137ACD /* blastdb.cpp */; }; - 373C691F0FC1C98600137ACD /* nast.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C691D0FC1C98600137ACD /* nast.cpp */; }; - 373C692B0FC1C9EB00137ACD /* nastreport.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C69290FC1C9EB00137ACD /* nastreport.cpp */; }; - 373C699A0FC1E63600137ACD /* boneh.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C69940FC1E63600137ACD /* boneh.cpp */; }; - 373C699B0FC1E63600137ACD /* efron.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C69960FC1E63600137ACD /* efron.cpp */; }; - 373C699C0FC1E63600137ACD /* solow.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 373C69980FC1E63600137ACD /* solow.cpp */; }; - 374610780F40645300460C57 /* unifracweightedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 374610770F40645300460C57 /* unifracweightedcommand.cpp */; }; - 3746107E0F4064D100460C57 /* weighted.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3746107D0F4064D100460C57 /* weighted.cpp */; }; - 374610830F40652400460C57 /* unweighted.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 374610820F40652400460C57 /* unweighted.cpp */; }; - 3746109D0F40657600460C57 /* unifracunweightedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */; }; - 3749271D0FD58C840031C06B /* getsabundcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3749271C0FD58C840031C06B /* getsabundcommand.cpp */; }; - 3749273F0FD5956B0031C06B /* getrabundcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3749273E0FD5956B0031C06B /* getrabundcommand.cpp */; }; - 374F2FEB100634B600E97C66 /* bellerophon.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 374F2FEA100634B600E97C66 /* bellerophon.cpp */; }; - 374F301310063B6F00E97C66 /* pintail.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 374F301210063B6F00E97C66 /* pintail.cpp */; }; - 37519A6B0F80E6EB00FED5E8 /* sharedanderbergs.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37519A6A0F80E6EB00FED5E8 /* sharedanderbergs.cpp */; }; - 37519AA10F810D0200FED5E8 /* venncommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37519AA00F810D0200FED5E8 /* venncommand.cpp */; }; - 37519AB50F810FAE00FED5E8 /* venn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37519AB40F810FAE00FED5E8 /* venn.cpp */; }; - 375873EC0F7D64520040F377 /* fullmatrix.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873EB0F7D64520040F377 /* fullmatrix.cpp */; }; - 375873EF0F7D646F0040F377 /* heatmap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873EE0F7D646F0040F377 /* heatmap.cpp */; }; - 375873F20F7D64800040F377 /* heatmapcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873F00F7D64800040F377 /* heatmapcommand.cpp */; }; - 375873F50F7D648F0040F377 /* libshuffcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873F30F7D648F0040F377 /* libshuffcommand.cpp */; }; - 375873F80F7D649C0040F377 /* nocommands.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873F60F7D649C0040F377 /* nocommands.cpp */; }; - 375873FD0F7D64DA0040F377 /* sharedbraycurtis.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873FC0F7D64DA0040F377 /* sharedbraycurtis.cpp */; }; - 375874040F7D64EF0040F377 /* sharedkulczynski.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873FE0F7D64EF0040F377 /* sharedkulczynski.cpp */; }; - 375874050F7D64EF0040F377 /* sharedlennon.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873FF0F7D64EF0040F377 /* sharedlennon.cpp */; }; - 375874060F7D64EF0040F377 /* sharedkulczynskicody.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375874020F7D64EF0040F377 /* sharedkulczynskicody.cpp */; }; - 3758740C0F7D64FC0040F377 /* sharedmorisitahorn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375874080F7D64FC0040F377 /* sharedmorisitahorn.cpp */; }; - 3758740D0F7D64FC0040F377 /* sharedochiai.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3758740B0F7D64FC0040F377 /* sharedochiai.cpp */; }; - 375AA1390F9E433D008EF9B8 /* readcolumn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375AA1330F9E433D008EF9B8 /* readcolumn.cpp */; }; - 375AA13A0F9E433D008EF9B8 /* readotu.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375AA1350F9E433D008EF9B8 /* readotu.cpp */; }; - 375AA13B0F9E433D008EF9B8 /* readphylip.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375AA1370F9E433D008EF9B8 /* readphylip.cpp */; }; - 377326650FAF16E0007ABB8B /* consensuscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 377326630FAF16E0007ABB8B /* consensuscommand.cpp */; }; - 378598660FDD497000EF9D03 /* heatmapsimcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378598650FDD497000EF9D03 /* heatmapsimcommand.cpp */; }; - 378598740FDD4C1500EF9D03 /* heatmapsim.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378598730FDD4C1500EF9D03 /* heatmapsim.cpp */; }; - 378599100FDD7E8E00EF9D03 /* optionparser.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3785990F0FDD7E8E00EF9D03 /* optionparser.cpp */; }; - 378C1B030FB0644E004D63F5 /* filterseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378C1AEE0FB0644D004D63F5 /* filterseqscommand.cpp */; }; - 378C1B040FB0644E004D63F5 /* goodscoverage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378C1AF00FB0644D004D63F5 /* goodscoverage.cpp */; }; - 378C1B0A0FB0644E004D63F5 /* sequencedb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378C1AFD0FB0644D004D63F5 /* sequencedb.cpp */; }; - 378C1B0B0FB0644E004D63F5 /* sharedjackknife.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378C1AFF0FB0644D004D63F5 /* sharedjackknife.cpp */; }; - 378C1B0C0FB0644E004D63F5 /* sharedmarczewski.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378C1B010FB0644D004D63F5 /* sharedmarczewski.cpp */; }; - 378DC5CF0FBDE1C8003B8607 /* aligncommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378DC5CE0FBDE1C8003B8607 /* aligncommand.cpp */; }; - 379293C30F2DE73400B9034A /* treemap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 379293C20F2DE73400B9034A /* treemap.cpp */; }; - 379294700F2E191800B9034A /* parsimonycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3792946F0F2E191800B9034A /* parsimonycommand.cpp */; }; - 3792948A0F2E258500B9034A /* parsimony.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 379294890F2E258500B9034A /* parsimony.cpp */; }; - 3799A9510FD6A58C00E33EDE /* seqsummarycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3799A94E0FD6A58C00E33EDE /* seqsummarycommand.cpp */; }; - 379D3D510FF90E090068C1C0 /* chimeraseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 379D3D500FF90E090068C1C0 /* chimeraseqscommand.cpp */; }; - 37AD4CE40F28AEA300AA2D49 /* sharedlistvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */; }; - 37AD4DBB0F28E2FE00AA2D49 /* tree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */; }; - 37AD4DCA0F28F3DD00AA2D49 /* readtree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */; }; - 37AFC71F0F445386005F492D /* sharedsobscollectsummary.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */; }; - 37B28F680F27590100808A62 /* deconvolutecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37B28F670F27590100808A62 /* deconvolutecommand.cpp */; }; - 37B73C761004BEFD008C4B41 /* listseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37B73C751004BEFD008C4B41 /* listseqscommand.cpp */; }; - 37B73CA61004D89A008C4B41 /* getseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37B73CA51004D89A008C4B41 /* getseqscommand.cpp */; }; - 37B73CC01004EB38008C4B41 /* removeseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37B73CBF1004EB38008C4B41 /* removeseqscommand.cpp */; }; - 37B73CCF1004F5E0008C4B41 /* systemcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37B73CCE1004F5E0008C4B41 /* systemcommand.cpp */; }; - 37C1D9730F86506E0059E3F0 /* binsequencecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */; }; - 37C753CE0FB3415200DBD02E /* distancecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37C753CD0FB3415200DBD02E /* distancecommand.cpp */; }; - 37D928550F21331F001D4494 /* ace.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927B80F21331F001D4494 /* ace.cpp */; }; - 37D928560F21331F001D4494 /* averagelinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927BA0F21331F001D4494 /* averagelinkage.cpp */; }; - 37D928570F21331F001D4494 /* bootstrap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927BB0F21331F001D4494 /* bootstrap.cpp */; }; - 37D928580F21331F001D4494 /* calculator.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927BD0F21331F001D4494 /* calculator.cpp */; }; - 37D928590F21331F001D4494 /* chao1.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927BF0F21331F001D4494 /* chao1.cpp */; }; - 37D9285A0F21331F001D4494 /* cluster.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927C10F21331F001D4494 /* cluster.cpp */; }; - 37D9285B0F21331F001D4494 /* clustercommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927C30F21331F001D4494 /* clustercommand.cpp */; }; - 37D9285C0F21331F001D4494 /* collect.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927C50F21331F001D4494 /* collect.cpp */; }; - 37D9285D0F21331F001D4494 /* collectcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927C70F21331F001D4494 /* collectcommand.cpp */; }; - 37D9285E0F21331F001D4494 /* collectsharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */; }; - 37D928600F21331F001D4494 /* commandoptionparser.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927D00F21331F001D4494 /* commandoptionparser.cpp */; }; - 37D928610F21331F001D4494 /* completelinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927D20F21331F001D4494 /* completelinkage.cpp */; }; - 37D928620F21331F001D4494 /* database.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927D30F21331F001D4494 /* database.cpp */; }; - 37D928630F21331F001D4494 /* engine.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927D70F21331F001D4494 /* engine.cpp */; }; - 37D928650F21331F001D4494 /* fastamap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927DB0F21331F001D4494 /* fastamap.cpp */; }; - 37D928660F21331F001D4494 /* fileoutput.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927DD0F21331F001D4494 /* fileoutput.cpp */; }; - 37D928670F21331F001D4494 /* globaldata.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927DF0F21331F001D4494 /* globaldata.cpp */; }; - 37D928680F21331F001D4494 /* groupmap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927E10F21331F001D4494 /* groupmap.cpp */; }; - 37D928690F21331F001D4494 /* helpcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927E30F21331F001D4494 /* helpcommand.cpp */; }; - 37D9286A0F21331F001D4494 /* inputdata.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927E50F21331F001D4494 /* inputdata.cpp */; }; - 37D9286B0F21331F001D4494 /* jackknife.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927E70F21331F001D4494 /* jackknife.cpp */; }; - 37D9286C0F21331F001D4494 /* kmer.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927E90F21331F001D4494 /* kmer.cpp */; }; - 37D9286D0F21331F001D4494 /* kmerdb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927EB0F21331F001D4494 /* kmerdb.cpp */; }; - 37D9286E0F21331F001D4494 /* listvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927ED0F21331F001D4494 /* listvector.cpp */; }; - 37D9286F0F21331F001D4494 /* mothur.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927EF0F21331F001D4494 /* mothur.cpp */; }; - 37D928700F21331F001D4494 /* nameassignment.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927F00F21331F001D4494 /* nameassignment.cpp */; }; - 37D928720F21331F001D4494 /* npshannon.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927F40F21331F001D4494 /* npshannon.cpp */; }; - 37D928730F21331F001D4494 /* ordervector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927F70F21331F001D4494 /* ordervector.cpp */; }; - 37D928750F21331F001D4494 /* progress.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927FB0F21331F001D4494 /* progress.cpp */; }; - 37D928760F21331F001D4494 /* quitcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927FD0F21331F001D4494 /* quitcommand.cpp */; }; - 37D928770F21331F001D4494 /* rabundvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927FF0F21331F001D4494 /* rabundvector.cpp */; }; - 37D928780F21331F001D4494 /* rarecalc.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928010F21331F001D4494 /* rarecalc.cpp */; }; - 37D928790F21331F001D4494 /* raredisplay.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928030F21331F001D4494 /* raredisplay.cpp */; }; - 37D9287A0F21331F001D4494 /* rarefact.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928050F21331F001D4494 /* rarefact.cpp */; }; - 37D9287B0F21331F001D4494 /* rarefactcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928070F21331F001D4494 /* rarefactcommand.cpp */; }; - 37D9287C0F21331F001D4494 /* rarefactsharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */; }; - 37D928840F21331F001D4494 /* sabundvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9281A0F21331F001D4494 /* sabundvector.cpp */; }; - 37D928850F21331F001D4494 /* sequence.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9281C0F21331F001D4494 /* sequence.cpp */; }; - 37D928860F21331F001D4494 /* shannon.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9281E0F21331F001D4494 /* shannon.cpp */; }; - 37D928880F21331F001D4494 /* sharedace.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928220F21331F001D4494 /* sharedace.cpp */; }; - 37D928890F21331F001D4494 /* sharedchao1.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928240F21331F001D4494 /* sharedchao1.cpp */; }; - 37D9288A0F21331F001D4494 /* sharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928260F21331F001D4494 /* sharedcommand.cpp */; }; - 37D9288B0F21331F001D4494 /* sharedjabund.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928280F21331F001D4494 /* sharedjabund.cpp */; }; - 37D9288C0F21331F001D4494 /* sharedjclass.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9282A0F21331F001D4494 /* sharedjclass.cpp */; }; - 37D9288D0F21331F001D4494 /* sharedjest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9282C0F21331F001D4494 /* sharedjest.cpp */; }; - 37D9288E0F21331F001D4494 /* sharedordervector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9282E0F21331F001D4494 /* sharedordervector.cpp */; }; - 37D9288F0F21331F001D4494 /* sharedrabundvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928300F21331F001D4494 /* sharedrabundvector.cpp */; }; - 37D928900F21331F001D4494 /* sharedsabundvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928320F21331F001D4494 /* sharedsabundvector.cpp */; }; - 37D928910F21331F001D4494 /* sharedsobs.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928340F21331F001D4494 /* sharedsobs.cpp */; }; - 37D928920F21331F001D4494 /* sharedsorabund.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928360F21331F001D4494 /* sharedsorabund.cpp */; }; - 37D928930F21331F001D4494 /* sharedsorclass.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928380F21331F001D4494 /* sharedsorclass.cpp */; }; - 37D928940F21331F001D4494 /* sharedsorest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9283A0F21331F001D4494 /* sharedsorest.cpp */; }; - 37D928950F21331F001D4494 /* sharedthetan.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9283C0F21331F001D4494 /* sharedthetan.cpp */; }; - 37D928960F21331F001D4494 /* sharedthetayc.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9283E0F21331F001D4494 /* sharedthetayc.cpp */; }; - 37D928970F21331F001D4494 /* simpson.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928400F21331F001D4494 /* simpson.cpp */; }; - 37D928980F21331F001D4494 /* singlelinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928420F21331F001D4494 /* singlelinkage.cpp */; }; - 37D928990F21331F001D4494 /* sparsematrix.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928440F21331F001D4494 /* sparsematrix.cpp */; }; - 37D9289A0F21331F001D4494 /* summarycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928460F21331F001D4494 /* summarycommand.cpp */; }; - 37D9289B0F21331F001D4494 /* summarysharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */; }; - 37D9289C0F21331F001D4494 /* uvest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9284D0F21331F001D4494 /* uvest.cpp */; }; - 37D9289D0F21331F001D4494 /* validcalculator.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9284F0F21331F001D4494 /* validcalculator.cpp */; }; - 37D9289F0F21331F001D4494 /* validparameter.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928530F21331F001D4494 /* validparameter.cpp */; }; - 37E5F3E30F29FD4200F8D827 /* treenode.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37E5F3E20F29FD4200F8D827 /* treenode.cpp */; }; - 37E5F4920F2A3DA800F8D827 /* readtreecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */; }; - 7E09C5140FDA79C5002ECAE5 /* reversecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E09C5130FDA79C5002ECAE5 /* reversecommand.cpp */; }; - 7E09C5360FDA7F65002ECAE5 /* trimseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E09C5350FDA7F65002ECAE5 /* trimseqscommand.cpp */; }; - 7E412F490F8D21B600381DD0 /* slibshuff.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E412F480F8D21B600381DD0 /* slibshuff.cpp */; }; - 7E412FEA0F8D3E2C00381DD0 /* libshuff.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */; }; - 7E4130F80F8E58FA00381DD0 /* dlibshuff.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E4130F60F8E58FA00381DD0 /* dlibshuff.cpp */; }; - 7E5A17AF0FE57292003C6A03 /* mergefilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E5A17AE0FE57292003C6A03 /* mergefilecommand.cpp */; }; - 7EC3D4550FA0FFF900338DA5 /* coverage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7EC3D4500FA0FFF900338DA5 /* coverage.cpp */; }; - 7EC3D4560FA0FFF900338DA5 /* whittaker.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7EC3D4530FA0FFF900338DA5 /* whittaker.cpp */; }; - 8DD76F6A0486A84900D96B5E /* Mothur.1 in CopyFiles */ = {isa = PBXBuildFile; fileRef = C6859E8B029090EE04C91782 /* Mothur.1 */; }; - A7027F2810DFF86D00BF45FE /* preclustercommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7027F2710DFF86D00BF45FE /* preclustercommand.cpp */; }; - A704E8A31106045D00870157 /* otuhierarchycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A704E8A21106045D00870157 /* otuhierarchycommand.cpp */; }; - A70B00C8110885EB002F453A /* setdircommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70B00C7110885EB002F453A /* setdircommand.cpp */; }; - A70B53AA0F4CD7AD0064797E /* getgroupcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */; }; - A70B53AB0F4CD7AD0064797E /* getlabelcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */; }; - A70DECD91063D8B40057C03C /* secondarystructurecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70DECD81063D8B40057C03C /* secondarystructurecommand.cpp */; }; - A727E84A10D14568001A8432 /* readblast.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A727E84910D14568001A8432 /* readblast.cpp */; }; - A7283FF81056CAE100D0CC69 /* chimeracheckrdp.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7283FF71056CAE100D0CC69 /* chimeracheckrdp.cpp */; }; - A729ACD010848E6100139801 /* hclustercommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A729ACCF10848E6100139801 /* hclustercommand.cpp */; }; - A729ACE410849BBE00139801 /* hcluster.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A729ACE310849BBE00139801 /* hcluster.cpp */; }; - A73329CF1083B3B3003B10C5 /* getlistcountcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A73329CE1083B3B3003B10C5 /* getlistcountcommand.cpp */; }; - A751ACEA1098B283003D0911 /* readcluster.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A751ACE91098B283003D0911 /* readcluster.cpp */; }; - A75B887E104C16860083C454 /* ccode.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A75B887B104C16860083C454 /* ccode.cpp */; }; - A773805F10B6D6FC002A6A61 /* taxonomyequalizer.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A773805E10B6D6FC002A6A61 /* taxonomyequalizer.cpp */; }; - A773809010B6EFD1002A6A61 /* phylotypecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A773808F10B6EFD1002A6A61 /* phylotypecommand.cpp */; }; - A7861478109F5FA00010AAAF /* classifyseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7861477109F5FA00010AAAF /* classifyseqscommand.cpp */; }; - A787810310A06D5D0086103D /* classify.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A787810210A06D5D0086103D /* classify.cpp */; }; - A78781BA10A0813E0086103D /* phylotree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A78781B810A0813D0086103D /* phylotree.cpp */; }; - A787821110A0AAE70086103D /* bayesian.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A787821010A0AAE70086103D /* bayesian.cpp */; }; - A78782AB10A1B1CB0086103D /* alignmentdb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A78782AA10A1B1CB0086103D /* alignmentdb.cpp */; }; - A787844510A1EBDD0086103D /* knn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A787844410A1EBDD0086103D /* knn.cpp */; }; - A794201111107897003AECCD /* distancedb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A794200F11107897003AECCD /* distancedb.cpp */; }; - A7B04493106CC3E60046FC83 /* chimeraslayer.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7B04492106CC3E60046FC83 /* chimeraslayer.cpp */; }; - A7B0450E106CEEC90046FC83 /* slayer.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7B0450D106CEEC90046FC83 /* slayer.cpp */; }; - A7D176CF10F2558500159497 /* pcacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7D176CE10F2558500159497 /* pcacommand.cpp */; }; - A7D86C7D10FE09AB00865661 /* formatcolumn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7D86C7C10FE09AB00865661 /* formatcolumn.cpp */; }; - A7D86C8C10FE09FE00865661 /* formatphylip.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7D86C8B10FE09FE00865661 /* formatphylip.cpp */; }; - A7E0AAB610D2886D00CF407B /* mgclustercommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E0AAB510D2886D00CF407B /* mgclustercommand.cpp */; }; - A7E4A783106913F900688F62 /* getsharedotucommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E4A782106913F900688F62 /* getsharedotucommand.cpp */; }; - A7E4A824106A9AD700688F62 /* maligner.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E4A823106A9AD700688F62 /* maligner.cpp */; }; - A7F5759710CEBC0600E20E47 /* libreadline.a in Frameworks */ = {isa = PBXBuildFile; fileRef = A7F5759610CEBC0600E20E47 /* libreadline.a */; }; - EB1216880F619B83004A865F /* bergerparker.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB1216870F619B83004A865F /* bergerparker.cpp */; }; - EB1216E50F61ACFB004A865F /* bstick.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB1216E40F61ACFB004A865F /* bstick.cpp */; }; - EB1217230F61C9AC004A865F /* sharedkstest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB1217220F61C9AC004A865F /* sharedkstest.cpp */; }; - EB6E68190F5F1C780044E17B /* qstat.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB6E68180F5F1C780044E17B /* qstat.cpp */; }; - EB72FE260FC1F5CA0051AC11 /* shen.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB72FE240FC1F5CA0051AC11 /* shen.cpp */; }; - EB9303EB0F534D9400E8EF26 /* logsd.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB9303EA0F534D9400E8EF26 /* logsd.cpp */; }; - EB9303F90F53517300E8EF26 /* geom.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB9303F80F53517300E8EF26 /* geom.cpp */; }; + 7E6BE10A12F710D8007ADDBE /* refchimeratest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */; }; + 8DD76FB00486AB0100D96B5E /* mothur.1 in CopyFiles */ = {isa = PBXBuildFile; fileRef = C6A0FF2C0290799A04C91782 /* mothur.1 */; }; + A70332B712D3A13400761E33 /* makefile in Sources */ = {isa = PBXBuildFile; fileRef = A70332B512D3A13400761E33 /* makefile */; }; + A713EBAC12DC7613000092AC /* readphylipvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A713EBAB12DC7613000092AC /* readphylipvector.cpp */; }; + A713EBED12DC7C5E000092AC /* nmdscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A713EBEC12DC7C5E000092AC /* nmdscommand.cpp */; }; + A71FE12C12EDF72400963CA7 /* mergegroupscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */; }; + A727864412E9E28C00F86ABA /* removerarecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A727864312E9E28C00F86ABA /* removerarecommand.cpp */; }; + A75790591301749D00A30DAB /* homovacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A75790581301749D00A30DAB /* homovacommand.cpp */; }; + A7A61F2D130062E000E05B6B /* amovacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7A61F2C130062E000E05B6B /* amovacommand.cpp */; }; + A7E9B88112D37EC400DA6239 /* ace.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B64F12D37EC300DA6239 /* ace.cpp */; }; + A7E9B88212D37EC400DA6239 /* aligncommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B65112D37EC300DA6239 /* aligncommand.cpp */; }; + A7E9B88312D37EC400DA6239 /* alignment.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B65312D37EC300DA6239 /* alignment.cpp */; }; + A7E9B88412D37EC400DA6239 /* alignmentcell.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B65512D37EC300DA6239 /* alignmentcell.cpp */; }; + A7E9B88512D37EC400DA6239 /* alignmentdb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B65712D37EC300DA6239 /* alignmentdb.cpp */; }; + A7E9B88612D37EC400DA6239 /* averagelinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B65912D37EC300DA6239 /* averagelinkage.cpp */; }; + A7E9B88712D37EC400DA6239 /* bayesian.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B65A12D37EC300DA6239 /* bayesian.cpp */; }; + A7E9B88812D37EC400DA6239 /* bellerophon.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B65C12D37EC300DA6239 /* bellerophon.cpp */; }; + A7E9B88912D37EC400DA6239 /* bergerparker.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B65E12D37EC300DA6239 /* bergerparker.cpp */; }; + A7E9B88A12D37EC400DA6239 /* binsequencecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B66012D37EC300DA6239 /* binsequencecommand.cpp */; }; + A7E9B88B12D37EC400DA6239 /* blastalign.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B66212D37EC300DA6239 /* blastalign.cpp */; }; + A7E9B88C12D37EC400DA6239 /* blastdb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B66412D37EC400DA6239 /* blastdb.cpp */; }; + A7E9B88D12D37EC400DA6239 /* boneh.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B66612D37EC400DA6239 /* boneh.cpp */; }; + A7E9B88E12D37EC400DA6239 /* bootstrap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B66812D37EC400DA6239 /* bootstrap.cpp */; }; + A7E9B88F12D37EC400DA6239 /* bootstrapsharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B66A12D37EC400DA6239 /* bootstrapsharedcommand.cpp */; }; + A7E9B89012D37EC400DA6239 /* bstick.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B66C12D37EC400DA6239 /* bstick.cpp */; }; + A7E9B89112D37EC400DA6239 /* calculator.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B66E12D37EC400DA6239 /* calculator.cpp */; }; + A7E9B89212D37EC400DA6239 /* canberra.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B67012D37EC400DA6239 /* canberra.cpp */; }; + A7E9B89312D37EC400DA6239 /* catchallcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B67212D37EC400DA6239 /* catchallcommand.cpp */; }; + A7E9B89412D37EC400DA6239 /* ccode.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B67412D37EC400DA6239 /* ccode.cpp */; }; + A7E9B89512D37EC400DA6239 /* chao1.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B67612D37EC400DA6239 /* chao1.cpp */; }; + A7E9B89612D37EC400DA6239 /* chimera.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B67812D37EC400DA6239 /* chimera.cpp */; }; + A7E9B89712D37EC400DA6239 /* chimerabellerophoncommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B67A12D37EC400DA6239 /* chimerabellerophoncommand.cpp */; }; + A7E9B89812D37EC400DA6239 /* chimeraccodecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B67C12D37EC400DA6239 /* chimeraccodecommand.cpp */; }; + A7E9B89912D37EC400DA6239 /* chimeracheckcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B67E12D37EC400DA6239 /* chimeracheckcommand.cpp */; }; + A7E9B89A12D37EC400DA6239 /* chimeracheckrdp.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B68012D37EC400DA6239 /* chimeracheckrdp.cpp */; }; + A7E9B89B12D37EC400DA6239 /* chimerapintailcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B68212D37EC400DA6239 /* chimerapintailcommand.cpp */; }; + A7E9B89C12D37EC400DA6239 /* chimerarealigner.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B68412D37EC400DA6239 /* chimerarealigner.cpp */; }; + A7E9B89D12D37EC400DA6239 /* chimeraseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B68612D37EC400DA6239 /* chimeraseqscommand.cpp */; }; + A7E9B89E12D37EC400DA6239 /* chimeraslayer.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B68812D37EC400DA6239 /* chimeraslayer.cpp */; }; + A7E9B89F12D37EC400DA6239 /* chimeraslayercommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B68A12D37EC400DA6239 /* chimeraslayercommand.cpp */; }; + A7E9B8A012D37EC400DA6239 /* chopseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B68C12D37EC400DA6239 /* chopseqscommand.cpp */; }; + A7E9B8A112D37EC400DA6239 /* classify.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B68E12D37EC400DA6239 /* classify.cpp */; }; + A7E9B8A212D37EC400DA6239 /* classifyotucommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B69012D37EC400DA6239 /* classifyotucommand.cpp */; }; + A7E9B8A312D37EC400DA6239 /* classifyseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B69212D37EC400DA6239 /* classifyseqscommand.cpp */; }; + A7E9B8A412D37EC400DA6239 /* clearcut.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B69412D37EC400DA6239 /* clearcut.cpp */; }; + A7E9B8A512D37EC400DA6239 /* clearcutcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B69612D37EC400DA6239 /* clearcutcommand.cpp */; }; + A7E9B8A612D37EC400DA6239 /* cluster.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B69812D37EC400DA6239 /* cluster.cpp */; }; + A7E9B8A712D37EC400DA6239 /* clusterclassic.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B69A12D37EC400DA6239 /* clusterclassic.cpp */; }; + A7E9B8A812D37EC400DA6239 /* clustercommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B69C12D37EC400DA6239 /* clustercommand.cpp */; }; + A7E9B8A912D37EC400DA6239 /* clusterdoturcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B69E12D37EC400DA6239 /* clusterdoturcommand.cpp */; }; + A7E9B8AA12D37EC400DA6239 /* clusterfragmentscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6A012D37EC400DA6239 /* clusterfragmentscommand.cpp */; }; + A7E9B8AB12D37EC400DA6239 /* clustersplitcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6A212D37EC400DA6239 /* clustersplitcommand.cpp */; }; + A7E9B8AC12D37EC400DA6239 /* cmdargs.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6A412D37EC400DA6239 /* cmdargs.cpp */; }; + A7E9B8AD12D37EC400DA6239 /* collect.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6A612D37EC400DA6239 /* collect.cpp */; }; + A7E9B8AE12D37EC400DA6239 /* collectcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6A812D37EC400DA6239 /* collectcommand.cpp */; }; + A7E9B8AF12D37EC400DA6239 /* collectsharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6AC12D37EC400DA6239 /* collectsharedcommand.cpp */; }; + A7E9B8B012D37EC400DA6239 /* commandfactory.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6AF12D37EC400DA6239 /* commandfactory.cpp */; }; + A7E9B8B112D37EC400DA6239 /* commandoptionparser.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6B112D37EC400DA6239 /* commandoptionparser.cpp */; }; + A7E9B8B212D37EC400DA6239 /* completelinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6B412D37EC400DA6239 /* completelinkage.cpp */; }; + A7E9B8B312D37EC400DA6239 /* consensuscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6B512D37EC400DA6239 /* consensuscommand.cpp */; }; + A7E9B8B412D37EC400DA6239 /* consensusseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6B712D37EC400DA6239 /* consensusseqscommand.cpp */; }; + A7E9B8B512D37EC400DA6239 /* corraxescommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6B912D37EC400DA6239 /* corraxescommand.cpp */; }; + A7E9B8B612D37EC400DA6239 /* coverage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6BB12D37EC400DA6239 /* coverage.cpp */; }; + A7E9B8B712D37EC400DA6239 /* database.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6BD12D37EC400DA6239 /* database.cpp */; }; + A7E9B8B812D37EC400DA6239 /* decalc.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6C112D37EC400DA6239 /* decalc.cpp */; }; + A7E9B8B912D37EC400DA6239 /* deconvolutecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6C312D37EC400DA6239 /* deconvolutecommand.cpp */; }; + A7E9B8BA12D37EC400DA6239 /* degapseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6C512D37EC400DA6239 /* degapseqscommand.cpp */; }; + A7E9B8BB12D37EC400DA6239 /* deuniqueseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6C712D37EC400DA6239 /* deuniqueseqscommand.cpp */; }; + A7E9B8BC12D37EC400DA6239 /* distancecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6CB12D37EC400DA6239 /* distancecommand.cpp */; }; + A7E9B8BD12D37EC400DA6239 /* distancedb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6CD12D37EC400DA6239 /* distancedb.cpp */; }; + A7E9B8BE12D37EC400DA6239 /* distclearcut.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6CF12D37EC400DA6239 /* distclearcut.cpp */; }; + A7E9B8BF12D37EC400DA6239 /* dlibshuff.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6D112D37EC400DA6239 /* dlibshuff.cpp */; }; + A7E9B8C012D37EC400DA6239 /* dmat.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6D312D37EC400DA6239 /* dmat.cpp */; }; + A7E9B8C112D37EC400DA6239 /* efron.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6D712D37EC400DA6239 /* efron.cpp */; }; + A7E9B8C212D37EC400DA6239 /* engine.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6DA12D37EC400DA6239 /* engine.cpp */; }; + A7E9B8C312D37EC400DA6239 /* fasta.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6DC12D37EC400DA6239 /* fasta.cpp */; }; + A7E9B8C412D37EC400DA6239 /* fastamap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6DE12D37EC400DA6239 /* fastamap.cpp */; }; + A7E9B8C512D37EC400DA6239 /* fileoutput.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6E012D37EC400DA6239 /* fileoutput.cpp */; }; + A7E9B8C612D37EC400DA6239 /* filterseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6E312D37EC400DA6239 /* filterseqscommand.cpp */; }; + A7E9B8C712D37EC400DA6239 /* fisher2.c in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6E512D37EC400DA6239 /* fisher2.c */; }; + A7E9B8C812D37EC400DA6239 /* flowdata.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6E712D37EC400DA6239 /* flowdata.cpp */; }; + A7E9B8C912D37EC400DA6239 /* formatcolumn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6E912D37EC400DA6239 /* formatcolumn.cpp */; }; + A7E9B8CA12D37EC400DA6239 /* formatphylip.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6EC12D37EC400DA6239 /* formatphylip.cpp */; }; + A7E9B8CB12D37EC400DA6239 /* fullmatrix.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6EE12D37EC400DA6239 /* fullmatrix.cpp */; }; + A7E9B8CC12D37EC400DA6239 /* geom.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6F012D37EC400DA6239 /* geom.cpp */; }; + A7E9B8CD12D37EC400DA6239 /* getgroupcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6F212D37EC400DA6239 /* getgroupcommand.cpp */; }; + A7E9B8CE12D37EC400DA6239 /* getgroupscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6F412D37EC400DA6239 /* getgroupscommand.cpp */; }; + A7E9B8CF12D37EC400DA6239 /* getlabelcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6F612D37EC400DA6239 /* getlabelcommand.cpp */; }; + A7E9B8D012D37EC400DA6239 /* getlineagecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6F812D37EC400DA6239 /* getlineagecommand.cpp */; }; + A7E9B8D112D37EC400DA6239 /* getlistcountcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6FA12D37EC400DA6239 /* getlistcountcommand.cpp */; }; + A7E9B8D212D37EC400DA6239 /* getopt_long.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6FC12D37EC400DA6239 /* getopt_long.cpp */; }; + A7E9B8D312D37EC400DA6239 /* getoturepcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6FE12D37EC400DA6239 /* getoturepcommand.cpp */; }; + A7E9B8D412D37EC400DA6239 /* getotuscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B70012D37EC400DA6239 /* getotuscommand.cpp */; }; + A7E9B8D512D37EC400DA6239 /* getrabundcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B70212D37EC400DA6239 /* getrabundcommand.cpp */; }; + A7E9B8D612D37EC400DA6239 /* getrelabundcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B70412D37EC400DA6239 /* getrelabundcommand.cpp */; }; + A7E9B8D712D37EC400DA6239 /* getsabundcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B70612D37EC400DA6239 /* getsabundcommand.cpp */; }; + A7E9B8D812D37EC400DA6239 /* getseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B70812D37EC400DA6239 /* getseqscommand.cpp */; }; + A7E9B8D912D37EC400DA6239 /* getsharedotucommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B70A12D37EC400DA6239 /* getsharedotucommand.cpp */; }; + A7E9B8DA12D37EC400DA6239 /* globaldata.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B70C12D37EC400DA6239 /* globaldata.cpp */; }; + A7E9B8DB12D37EC400DA6239 /* goodscoverage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B70E12D37EC400DA6239 /* goodscoverage.cpp */; }; + A7E9B8DC12D37EC400DA6239 /* gotohoverlap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B71012D37EC400DA6239 /* gotohoverlap.cpp */; }; + A7E9B8DD12D37EC400DA6239 /* gower.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B71212D37EC400DA6239 /* gower.cpp */; }; + A7E9B8DE12D37EC400DA6239 /* groupmap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B71412D37EC400DA6239 /* groupmap.cpp */; }; + A7E9B8DF12D37EC400DA6239 /* hamming.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B71612D37EC400DA6239 /* hamming.cpp */; }; + A7E9B8E012D37EC400DA6239 /* hcluster.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B71812D37EC400DA6239 /* hcluster.cpp */; }; + A7E9B8E112D37EC400DA6239 /* hclustercommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B71A12D37EC400DA6239 /* hclustercommand.cpp */; }; + A7E9B8E212D37EC400DA6239 /* heatmap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B71C12D37EC400DA6239 /* heatmap.cpp */; }; + A7E9B8E312D37EC400DA6239 /* heatmapcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B71E12D37EC400DA6239 /* heatmapcommand.cpp */; }; + A7E9B8E412D37EC400DA6239 /* heatmapsim.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B72012D37EC400DA6239 /* heatmapsim.cpp */; }; + A7E9B8E512D37EC400DA6239 /* heatmapsimcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B72212D37EC400DA6239 /* heatmapsimcommand.cpp */; }; + A7E9B8E612D37EC400DA6239 /* heip.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B72412D37EC400DA6239 /* heip.cpp */; }; + A7E9B8E712D37EC400DA6239 /* hellinger.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B72612D37EC400DA6239 /* hellinger.cpp */; }; + A7E9B8E812D37EC400DA6239 /* helpcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B72812D37EC400DA6239 /* helpcommand.cpp */; }; + A7E9B8E912D37EC400DA6239 /* indicatorcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B72B12D37EC400DA6239 /* indicatorcommand.cpp */; }; + A7E9B8EA12D37EC400DA6239 /* inputdata.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B72D12D37EC400DA6239 /* inputdata.cpp */; }; + A7E9B8EB12D37EC400DA6239 /* invsimpson.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B72F12D37EC400DA6239 /* invsimpson.cpp */; }; + A7E9B8EC12D37EC400DA6239 /* jackknife.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B73112D37EC400DA6239 /* jackknife.cpp */; }; + A7E9B8ED12D37EC400DA6239 /* kmer.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B73312D37EC400DA6239 /* kmer.cpp */; }; + A7E9B8EE12D37EC400DA6239 /* kmerdb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B73512D37EC400DA6239 /* kmerdb.cpp */; }; + A7E9B8EF12D37EC400DA6239 /* knn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B73712D37EC400DA6239 /* knn.cpp */; }; + A7E9B8F012D37EC400DA6239 /* libshuff.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B73912D37EC400DA6239 /* libshuff.cpp */; }; + A7E9B8F112D37EC400DA6239 /* libshuffcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B73B12D37EC400DA6239 /* libshuffcommand.cpp */; }; + A7E9B8F212D37EC400DA6239 /* listseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B73D12D37EC400DA6239 /* listseqscommand.cpp */; }; + A7E9B8F312D37EC400DA6239 /* listvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B73F12D37EC400DA6239 /* listvector.cpp */; }; + A7E9B8F412D37EC400DA6239 /* logsd.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B74112D37EC400DA6239 /* logsd.cpp */; }; + A7E9B8F512D37EC400DA6239 /* makegroupcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B74312D37EC400DA6239 /* makegroupcommand.cpp */; }; + A7E9B8F612D37EC400DA6239 /* maligner.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B74512D37EC400DA6239 /* maligner.cpp */; }; + A7E9B8F712D37EC400DA6239 /* manhattan.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B74712D37EC400DA6239 /* manhattan.cpp */; }; + A7E9B8F812D37EC400DA6239 /* matrixoutputcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B74912D37EC400DA6239 /* matrixoutputcommand.cpp */; }; + A7E9B8F912D37EC400DA6239 /* memchi2.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B74B12D37EC400DA6239 /* memchi2.cpp */; }; + A7E9B8FA12D37EC400DA6239 /* memchord.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B74D12D37EC400DA6239 /* memchord.cpp */; }; + A7E9B8FB12D37EC400DA6239 /* memeuclidean.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B74F12D37EC400DA6239 /* memeuclidean.cpp */; }; + A7E9B8FC12D37EC400DA6239 /* mempearson.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B75112D37EC400DA6239 /* mempearson.cpp */; }; + A7E9B8FD12D37EC400DA6239 /* mergefilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B75312D37EC400DA6239 /* mergefilecommand.cpp */; }; + A7E9B8FE12D37EC400DA6239 /* metastats2.c in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B75612D37EC400DA6239 /* metastats2.c */; }; + A7E9B8FF12D37EC400DA6239 /* metastatscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B75712D37EC400DA6239 /* metastatscommand.cpp */; }; + A7E9B90012D37EC400DA6239 /* mgclustercommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B75912D37EC400DA6239 /* mgclustercommand.cpp */; }; + A7E9B90112D37EC400DA6239 /* mothur.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B75B12D37EC400DA6239 /* mothur.cpp */; }; + A7E9B90212D37EC400DA6239 /* mothurout.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B75D12D37EC400DA6239 /* mothurout.cpp */; }; + A7E9B90312D37EC400DA6239 /* nameassignment.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B75F12D37EC400DA6239 /* nameassignment.cpp */; }; + A7E9B90412D37EC400DA6239 /* nast.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B76112D37EC400DA6239 /* nast.cpp */; }; + A7E9B90512D37EC400DA6239 /* nastreport.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B76312D37EC400DA6239 /* nastreport.cpp */; }; + A7E9B90612D37EC400DA6239 /* needlemanoverlap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B76512D37EC400DA6239 /* needlemanoverlap.cpp */; }; + A7E9B90712D37EC400DA6239 /* noalign.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B76712D37EC400DA6239 /* noalign.cpp */; }; + A7E9B90812D37EC400DA6239 /* nocommands.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B76912D37EC400DA6239 /* nocommands.cpp */; }; + A7E9B90912D37EC400DA6239 /* normalizesharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B76B12D37EC400DA6239 /* normalizesharedcommand.cpp */; }; + A7E9B90A12D37EC400DA6239 /* npshannon.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B76D12D37EC400DA6239 /* npshannon.cpp */; }; + A7E9B90B12D37EC400DA6239 /* odum.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B77112D37EC400DA6239 /* odum.cpp */; }; + A7E9B90C12D37EC400DA6239 /* optionparser.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B77512D37EC400DA6239 /* optionparser.cpp */; }; + A7E9B90D12D37EC400DA6239 /* ordervector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B77712D37EC400DA6239 /* ordervector.cpp */; }; + A7E9B90E12D37EC400DA6239 /* otuhierarchycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B77912D37EC400DA6239 /* otuhierarchycommand.cpp */; }; + A7E9B90F12D37EC400DA6239 /* overlap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B77B12D37EC400DA6239 /* overlap.cpp */; }; + A7E9B91012D37EC400DA6239 /* pairwiseseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B77D12D37EC400DA6239 /* pairwiseseqscommand.cpp */; }; + A7E9B91112D37EC400DA6239 /* parsefastaqcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B77F12D37EC400DA6239 /* parsefastaqcommand.cpp */; }; + A7E9B91212D37EC400DA6239 /* parselistscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78112D37EC400DA6239 /* parselistscommand.cpp */; }; + A7E9B91312D37EC400DA6239 /* parsimony.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78312D37EC400DA6239 /* parsimony.cpp */; }; + A7E9B91412D37EC400DA6239 /* parsimonycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78512D37EC400DA6239 /* parsimonycommand.cpp */; }; + A7E9B91512D37EC400DA6239 /* pcoacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */; }; + A7E9B91612D37EC400DA6239 /* phylodiversity.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78912D37EC400DA6239 /* phylodiversity.cpp */; }; + A7E9B91712D37EC400DA6239 /* phylodiversitycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */; }; + A7E9B91812D37EC400DA6239 /* phylosummary.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78D12D37EC400DA6239 /* phylosummary.cpp */; }; + A7E9B91912D37EC400DA6239 /* phylotree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78F12D37EC400DA6239 /* phylotree.cpp */; }; + A7E9B91A12D37EC400DA6239 /* phylotypecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B79112D37EC400DA6239 /* phylotypecommand.cpp */; }; + A7E9B91B12D37EC400DA6239 /* pintail.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B79312D37EC400DA6239 /* pintail.cpp */; }; + A7E9B91C12D37EC400DA6239 /* pipelinepdscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B79512D37EC400DA6239 /* pipelinepdscommand.cpp */; }; + A7E9B91D12D37EC400DA6239 /* preclustercommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B79712D37EC400DA6239 /* preclustercommand.cpp */; }; + A7E9B91E12D37EC400DA6239 /* prng.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B79912D37EC400DA6239 /* prng.cpp */; }; + A7E9B91F12D37EC400DA6239 /* progress.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B79B12D37EC400DA6239 /* progress.cpp */; }; + A7E9B92012D37EC400DA6239 /* qstat.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B79D12D37EC400DA6239 /* qstat.cpp */; }; + A7E9B92112D37EC400DA6239 /* qualityscores.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B79F12D37EC400DA6239 /* qualityscores.cpp */; }; + A7E9B92212D37EC400DA6239 /* quitcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7A112D37EC400DA6239 /* quitcommand.cpp */; }; + A7E9B92312D37EC400DA6239 /* rabundvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7A312D37EC400DA6239 /* rabundvector.cpp */; }; + A7E9B92412D37EC400DA6239 /* rarecalc.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7A512D37EC400DA6239 /* rarecalc.cpp */; }; + A7E9B92512D37EC400DA6239 /* raredisplay.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7A712D37EC400DA6239 /* raredisplay.cpp */; }; + A7E9B92612D37EC400DA6239 /* rarefact.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7A912D37EC400DA6239 /* rarefact.cpp */; }; + A7E9B92712D37EC400DA6239 /* rarefactcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7AB12D37EC400DA6239 /* rarefactcommand.cpp */; }; + A7E9B92812D37EC400DA6239 /* rarefactsharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7AE12D37EC400DA6239 /* rarefactsharedcommand.cpp */; }; + A7E9B92912D37EC400DA6239 /* readblast.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7B012D37EC400DA6239 /* readblast.cpp */; }; + A7E9B92A12D37EC400DA6239 /* readcluster.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7B212D37EC400DA6239 /* readcluster.cpp */; }; + A7E9B92B12D37EC400DA6239 /* readcolumn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7B412D37EC400DA6239 /* readcolumn.cpp */; }; + A7E9B92C12D37EC400DA6239 /* readdistcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7B612D37EC400DA6239 /* readdistcommand.cpp */; }; + A7E9B92D12D37EC400DA6239 /* readotu.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7B912D37EC400DA6239 /* readotu.cpp */; }; + A7E9B92E12D37EC400DA6239 /* readotucommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7BB12D37EC400DA6239 /* readotucommand.cpp */; }; + A7E9B92F12D37EC400DA6239 /* readphylip.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7BD12D37EC400DA6239 /* readphylip.cpp */; }; + A7E9B93012D37EC400DA6239 /* readtree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7BF12D37EC400DA6239 /* readtree.cpp */; }; + A7E9B93112D37EC400DA6239 /* readtreecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7C112D37EC400DA6239 /* readtreecommand.cpp */; }; + A7E9B93212D37EC400DA6239 /* removegroupscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7C312D37EC400DA6239 /* removegroupscommand.cpp */; }; + A7E9B93312D37EC400DA6239 /* removelineagecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7C512D37EC400DA6239 /* removelineagecommand.cpp */; }; + A7E9B93412D37EC400DA6239 /* removeotuscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7C712D37EC400DA6239 /* removeotuscommand.cpp */; }; + A7E9B93512D37EC400DA6239 /* removeseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7C912D37EC400DA6239 /* removeseqscommand.cpp */; }; + A7E9B93612D37EC400DA6239 /* reportfile.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7CB12D37EC400DA6239 /* reportfile.cpp */; }; + A7E9B93712D37EC400DA6239 /* reversecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7CD12D37EC400DA6239 /* reversecommand.cpp */; }; + A7E9B93812D37EC400DA6239 /* sabundvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7CF12D37EC400DA6239 /* sabundvector.cpp */; }; + A7E9B93912D37EC400DA6239 /* screenseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7D112D37EC400DA6239 /* screenseqscommand.cpp */; }; + A7E9B93A12D37EC400DA6239 /* secondarystructurecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7D312D37EC400DA6239 /* secondarystructurecommand.cpp */; }; + A7E9B93B12D37EC400DA6239 /* sensspeccommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7D512D37EC400DA6239 /* sensspeccommand.cpp */; }; + A7E9B93C12D37EC400DA6239 /* seqerrorcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7D712D37EC400DA6239 /* seqerrorcommand.cpp */; }; + A7E9B93D12D37EC400DA6239 /* seqsummarycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7D912D37EC400DA6239 /* seqsummarycommand.cpp */; }; + A7E9B93E12D37EC400DA6239 /* sequence.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7DB12D37EC400DA6239 /* sequence.cpp */; }; + A7E9B93F12D37EC400DA6239 /* sequencedb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7DD12D37EC400DA6239 /* sequencedb.cpp */; }; + A7E9B94012D37EC400DA6239 /* setdircommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7DF12D37EC400DA6239 /* setdircommand.cpp */; }; + A7E9B94112D37EC400DA6239 /* setlogfilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7E112D37EC400DA6239 /* setlogfilecommand.cpp */; }; + A7E9B94212D37EC400DA6239 /* sffinfocommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7E312D37EC400DA6239 /* sffinfocommand.cpp */; }; + A7E9B94312D37EC400DA6239 /* shannon.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7E512D37EC400DA6239 /* shannon.cpp */; }; + A7E9B94412D37EC400DA6239 /* shannoneven.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7E712D37EC400DA6239 /* shannoneven.cpp */; }; + A7E9B94512D37EC400DA6239 /* sharedace.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7E912D37EC400DA6239 /* sharedace.cpp */; }; + A7E9B94612D37EC400DA6239 /* sharedanderbergs.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7EC12D37EC400DA6239 /* sharedanderbergs.cpp */; }; + A7E9B94712D37EC400DA6239 /* sharedbraycurtis.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7EE12D37EC400DA6239 /* sharedbraycurtis.cpp */; }; + A7E9B94812D37EC400DA6239 /* sharedchao1.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7F012D37EC400DA6239 /* sharedchao1.cpp */; }; + A7E9B94912D37EC400DA6239 /* sharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7F212D37EC400DA6239 /* sharedcommand.cpp */; }; + A7E9B94A12D37EC400DA6239 /* sharedjabund.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7F412D37EC400DA6239 /* sharedjabund.cpp */; }; + A7E9B94B12D37EC400DA6239 /* sharedjackknife.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7F612D37EC400DA6239 /* sharedjackknife.cpp */; }; + A7E9B94C12D37EC400DA6239 /* sharedjclass.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7F812D37EC400DA6239 /* sharedjclass.cpp */; }; + A7E9B94D12D37EC400DA6239 /* sharedjest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7FA12D37EC400DA6239 /* sharedjest.cpp */; }; + A7E9B94E12D37EC400DA6239 /* sharedkstest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7FC12D37EC400DA6239 /* sharedkstest.cpp */; }; + A7E9B94F12D37EC400DA6239 /* sharedkulczynski.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7FE12D37EC400DA6239 /* sharedkulczynski.cpp */; }; + A7E9B95012D37EC400DA6239 /* sharedkulczynskicody.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B80012D37EC400DA6239 /* sharedkulczynskicody.cpp */; }; + A7E9B95112D37EC400DA6239 /* sharedlennon.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B80212D37EC400DA6239 /* sharedlennon.cpp */; }; + A7E9B95212D37EC400DA6239 /* sharedlistvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B80412D37EC400DA6239 /* sharedlistvector.cpp */; }; + A7E9B95312D37EC400DA6239 /* sharedmarczewski.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B80612D37EC400DA6239 /* sharedmarczewski.cpp */; }; + A7E9B95412D37EC400DA6239 /* sharedmorisitahorn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B80812D37EC400DA6239 /* sharedmorisitahorn.cpp */; }; + A7E9B95512D37EC400DA6239 /* sharedochiai.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B80B12D37EC400DA6239 /* sharedochiai.cpp */; }; + A7E9B95612D37EC400DA6239 /* sharedordervector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B80D12D37EC400DA6239 /* sharedordervector.cpp */; }; + A7E9B95712D37EC400DA6239 /* sharedrabundfloatvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B80F12D37EC400DA6239 /* sharedrabundfloatvector.cpp */; }; + A7E9B95812D37EC400DA6239 /* sharedrabundvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B81112D37EC400DA6239 /* sharedrabundvector.cpp */; }; + A7E9B95912D37EC400DA6239 /* sharedsabundvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B81312D37EC400DA6239 /* sharedsabundvector.cpp */; }; + A7E9B95A12D37EC400DA6239 /* sharedsobs.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B81512D37EC400DA6239 /* sharedsobs.cpp */; }; + A7E9B95B12D37EC400DA6239 /* sharedsobscollectsummary.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B81712D37EC400DA6239 /* sharedsobscollectsummary.cpp */; }; + A7E9B95C12D37EC400DA6239 /* sharedsorabund.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B81912D37EC400DA6239 /* sharedsorabund.cpp */; }; + A7E9B95D12D37EC400DA6239 /* sharedsorclass.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B81B12D37EC400DA6239 /* sharedsorclass.cpp */; }; + A7E9B95E12D37EC400DA6239 /* sharedsorest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B81D12D37EC400DA6239 /* sharedsorest.cpp */; }; + A7E9B95F12D37EC400DA6239 /* sharedthetan.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B81F12D37EC400DA6239 /* sharedthetan.cpp */; }; + A7E9B96012D37EC400DA6239 /* sharedthetayc.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B82112D37EC400DA6239 /* sharedthetayc.cpp */; }; + A7E9B96112D37EC400DA6239 /* sharedutilities.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B82312D37EC400DA6239 /* sharedutilities.cpp */; }; + A7E9B96212D37EC400DA6239 /* shen.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B82512D37EC400DA6239 /* shen.cpp */; }; + A7E9B96312D37EC400DA6239 /* shhhercommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B82712D37EC400DA6239 /* shhhercommand.cpp */; }; + A7E9B96412D37EC400DA6239 /* simpson.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B82912D37EC400DA6239 /* simpson.cpp */; }; + A7E9B96512D37EC400DA6239 /* simpsoneven.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B82B12D37EC400DA6239 /* simpsoneven.cpp */; }; + A7E9B96612D37EC400DA6239 /* singlelinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B82D12D37EC400DA6239 /* singlelinkage.cpp */; }; + A7E9B96712D37EC400DA6239 /* slayer.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B82E12D37EC400DA6239 /* slayer.cpp */; }; + A7E9B96812D37EC400DA6239 /* slibshuff.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B83012D37EC400DA6239 /* slibshuff.cpp */; }; + A7E9B96912D37EC400DA6239 /* smithwilson.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B83212D37EC400DA6239 /* smithwilson.cpp */; }; + A7E9B96A12D37EC400DA6239 /* soergel.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B83512D37EC400DA6239 /* soergel.cpp */; }; + A7E9B96B12D37EC400DA6239 /* solow.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B83712D37EC400DA6239 /* solow.cpp */; }; + A7E9B96C12D37EC400DA6239 /* sparsematrix.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B83912D37EC400DA6239 /* sparsematrix.cpp */; }; + A7E9B96D12D37EC400DA6239 /* spearman.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B83B12D37EC400DA6239 /* spearman.cpp */; }; + A7E9B96E12D37EC400DA6239 /* speciesprofile.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B83D12D37EC400DA6239 /* speciesprofile.cpp */; }; + A7E9B96F12D37EC400DA6239 /* splitabundcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B83F12D37EC400DA6239 /* splitabundcommand.cpp */; }; + A7E9B97012D37EC400DA6239 /* splitgroupscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B84112D37EC400DA6239 /* splitgroupscommand.cpp */; }; + A7E9B97112D37EC400DA6239 /* splitmatrix.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B84312D37EC400DA6239 /* splitmatrix.cpp */; }; + A7E9B97212D37EC400DA6239 /* structchi2.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B84512D37EC400DA6239 /* structchi2.cpp */; }; + A7E9B97312D37EC400DA6239 /* structchord.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B84712D37EC400DA6239 /* structchord.cpp */; }; + A7E9B97412D37EC400DA6239 /* structeuclidean.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B84912D37EC400DA6239 /* structeuclidean.cpp */; }; + A7E9B97512D37EC400DA6239 /* structkulczynski.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B84B12D37EC400DA6239 /* structkulczynski.cpp */; }; + A7E9B97612D37EC400DA6239 /* structpearson.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B84D12D37EC400DA6239 /* structpearson.cpp */; }; + A7E9B97712D37EC400DA6239 /* subsamplecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B84F12D37EC400DA6239 /* subsamplecommand.cpp */; }; + A7E9B97812D37EC400DA6239 /* suffixdb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B85112D37EC400DA6239 /* suffixdb.cpp */; }; + A7E9B97912D37EC400DA6239 /* suffixnodes.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B85312D37EC400DA6239 /* suffixnodes.cpp */; }; + A7E9B97A12D37EC400DA6239 /* suffixtree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B85512D37EC400DA6239 /* suffixtree.cpp */; }; + A7E9B97B12D37EC400DA6239 /* summarycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B85712D37EC400DA6239 /* summarycommand.cpp */; }; + A7E9B97C12D37EC400DA6239 /* summarysharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B85912D37EC400DA6239 /* summarysharedcommand.cpp */; }; + A7E9B97D12D37EC400DA6239 /* systemcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B85B12D37EC400DA6239 /* systemcommand.cpp */; }; + A7E9B97E12D37EC400DA6239 /* taxonomyequalizer.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B85D12D37EC400DA6239 /* taxonomyequalizer.cpp */; }; + A7E9B97F12D37EC400DA6239 /* tree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B85F12D37EC400DA6239 /* tree.cpp */; }; + A7E9B98012D37EC400DA6239 /* treegroupscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B86212D37EC400DA6239 /* treegroupscommand.cpp */; }; + A7E9B98112D37EC400DA6239 /* treemap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B86412D37EC400DA6239 /* treemap.cpp */; }; + A7E9B98212D37EC400DA6239 /* treenode.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B86612D37EC400DA6239 /* treenode.cpp */; }; + A7E9B98312D37EC400DA6239 /* trimflowscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B86812D37EC400DA6239 /* trimflowscommand.cpp */; }; + A7E9B98412D37EC400DA6239 /* trimseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B86A12D37EC400DA6239 /* trimseqscommand.cpp */; }; + A7E9B98512D37EC400DA6239 /* unifracunweightedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B86C12D37EC400DA6239 /* unifracunweightedcommand.cpp */; }; + A7E9B98612D37EC400DA6239 /* unifracweightedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B86E12D37EC400DA6239 /* unifracweightedcommand.cpp */; }; + A7E9B98712D37EC400DA6239 /* unweighted.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B87012D37EC400DA6239 /* unweighted.cpp */; }; + A7E9B98812D37EC400DA6239 /* uvest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B87212D37EC400DA6239 /* uvest.cpp */; }; + A7E9B98912D37EC400DA6239 /* validcalculator.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B87412D37EC400DA6239 /* validcalculator.cpp */; }; + A7E9B98A12D37EC400DA6239 /* validparameter.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B87612D37EC400DA6239 /* validparameter.cpp */; }; + A7E9B98B12D37EC400DA6239 /* venn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B87812D37EC400DA6239 /* venn.cpp */; }; + A7E9B98C12D37EC400DA6239 /* venncommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B87A12D37EC400DA6239 /* venncommand.cpp */; }; + A7E9B98D12D37EC400DA6239 /* weighted.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B87C12D37EC400DA6239 /* weighted.cpp */; }; + A7E9B98E12D37EC400DA6239 /* weightedlinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B87E12D37EC400DA6239 /* weightedlinkage.cpp */; }; + A7E9B98F12D37EC400DA6239 /* whittaker.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B87F12D37EC400DA6239 /* whittaker.cpp */; }; + A7FC480E12D788F20055BC5C /* linearalgebra.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7FC480D12D788F20055BC5C /* linearalgebra.cpp */; }; + A7FC486712D795D60055BC5C /* pcacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7FC486612D795D60055BC5C /* pcacommand.cpp */; }; /* End PBXBuildFile section */ /* Begin PBXCopyFilesBuildPhase section */ - 8DD76F690486A84900D96B5E /* CopyFiles */ = { + 8DD76FAF0486AB0100D96B5E /* CopyFiles */ = { isa = PBXCopyFilesBuildPhase; buildActionMask = 8; dstPath = /usr/share/man/man1/; dstSubfolderSpec = 0; files = ( - 8DD76F6A0486A84900D96B5E /* Mothur.1 in CopyFiles */, + 8DD76FB00486AB0100D96B5E /* mothur.1 in CopyFiles */, ); runOnlyForDeploymentPostprocessing = 1; }; /* End PBXCopyFilesBuildPhase section */ /* Begin PBXFileReference section */ - 211C38300F961DD400FEE541 /* sharedutilities.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedutilities.cpp; sourceTree = SOURCE_ROOT; }; - 211C38310F961DD400FEE541 /* sharedutilities.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedutilities.h; sourceTree = SOURCE_ROOT; }; - 211C38360F961E1F00FEE541 /* treegroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treegroupscommand.cpp; sourceTree = SOURCE_ROOT; }; - 211C38370F961E1F00FEE541 /* treegroupscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treegroupscommand.h; sourceTree = SOURCE_ROOT; }; - 21DDC0190F97A8FE0060691C /* bootstrapsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bootstrapsharedcommand.h; sourceTree = SOURCE_ROOT; }; - 21DDC01A0F97A8FE0060691C /* bootstrapsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bootstrapsharedcommand.cpp; sourceTree = SOURCE_ROOT; }; - 21E859D60FC4632E005E1A48 /* matrixoutputcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = matrixoutputcommand.h; sourceTree = SOURCE_ROOT; }; - 21E859D70FC4632E005E1A48 /* matrixoutputcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = matrixoutputcommand.cpp; sourceTree = SOURCE_ROOT; }; - 370B88050F8A4EE4005AB382 /* getoturepcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getoturepcommand.h; sourceTree = SOURCE_ROOT; }; - 370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getoturepcommand.cpp; sourceTree = SOURCE_ROOT; }; - 371B30B20FD7EE67000414CA /* screenseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = screenseqscommand.cpp; sourceTree = SOURCE_ROOT; }; - 371B30B30FD7EE67000414CA /* screenseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = screenseqscommand.h; sourceTree = SOURCE_ROOT; }; - 372095C1103196D70004D347 /* chimera.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimera.cpp; sourceTree = SOURCE_ROOT; }; - 372A55531017922B00C5194B /* decalc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = decalc.h; sourceTree = SOURCE_ROOT; }; - 372A55541017922B00C5194B /* decalc.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = decalc.cpp; sourceTree = SOURCE_ROOT; }; - 372E126E0F26365B0095CF7E /* readotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotucommand.h; sourceTree = SOURCE_ROOT; }; - 372E126F0F26365B0095CF7E /* readotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readotucommand.cpp; sourceTree = SOURCE_ROOT; }; - 372E12940F263D5A0095CF7E /* readdistcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readdistcommand.h; sourceTree = SOURCE_ROOT; }; - 372E12950F263D5A0095CF7E /* readdistcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readdistcommand.cpp; sourceTree = SOURCE_ROOT; }; - 372E12EC0F264D320095CF7E /* commandfactory.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = commandfactory.cpp; sourceTree = SOURCE_ROOT; }; - 373C68A00FC1C07D00137ACD /* alignment.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = alignment.cpp; sourceTree = SOURCE_ROOT; }; - 373C68A10FC1C07D00137ACD /* alignment.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = alignment.hpp; sourceTree = SOURCE_ROOT; }; - 373C68A20FC1C07D00137ACD /* alignmentcell.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = alignmentcell.cpp; sourceTree = SOURCE_ROOT; }; - 373C68A30FC1C07D00137ACD /* alignmentcell.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = alignmentcell.hpp; sourceTree = SOURCE_ROOT; }; - 373C68BA0FC1C1A600137ACD /* gotohoverlap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = gotohoverlap.cpp; sourceTree = SOURCE_ROOT; }; - 373C68BB0FC1C1A600137ACD /* gotohoverlap.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = gotohoverlap.hpp; sourceTree = SOURCE_ROOT; }; - 373C68C30FC1C25F00137ACD /* overlap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = overlap.cpp; sourceTree = SOURCE_ROOT; }; - 373C68C40FC1C25F00137ACD /* overlap.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = overlap.hpp; sourceTree = SOURCE_ROOT; }; - 373C68CD0FC1C2D900137ACD /* needlemanoverlap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = needlemanoverlap.cpp; sourceTree = SOURCE_ROOT; }; - 373C68CE0FC1C2D900137ACD /* needlemanoverlap.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = needlemanoverlap.hpp; sourceTree = SOURCE_ROOT; }; - 373C68DB0FC1C38D00137ACD /* blastalign.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = blastalign.cpp; sourceTree = SOURCE_ROOT; }; - 373C68DC0FC1C38D00137ACD /* blastalign.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = blastalign.hpp; sourceTree = SOURCE_ROOT; }; - 373C68E30FC1C4A500137ACD /* noalign.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = noalign.cpp; sourceTree = SOURCE_ROOT; }; - 373C68E40FC1C4A500137ACD /* noalign.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = noalign.hpp; sourceTree = SOURCE_ROOT; }; - 373C68F30FC1C6A800137ACD /* suffixdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixdb.cpp; sourceTree = SOURCE_ROOT; }; - 373C68F40FC1C6A800137ACD /* suffixdb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixdb.hpp; sourceTree = SOURCE_ROOT; }; - 373C68F50FC1C6A800137ACD /* suffixnodes.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixnodes.cpp; sourceTree = SOURCE_ROOT; }; - 373C68F60FC1C6A800137ACD /* suffixnodes.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixnodes.hpp; sourceTree = SOURCE_ROOT; }; - 373C68F70FC1C6A800137ACD /* suffixtree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixtree.cpp; sourceTree = SOURCE_ROOT; }; - 373C68F80FC1C6A800137ACD /* suffixtree.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixtree.hpp; sourceTree = SOURCE_ROOT; }; - 373C69160FC1C8AF00137ACD /* blastdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = blastdb.cpp; sourceTree = SOURCE_ROOT; }; - 373C69170FC1C8AF00137ACD /* blastdb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = blastdb.hpp; sourceTree = SOURCE_ROOT; }; - 373C691D0FC1C98600137ACD /* nast.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nast.cpp; sourceTree = SOURCE_ROOT; }; - 373C691E0FC1C98600137ACD /* nast.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = nast.hpp; sourceTree = SOURCE_ROOT; }; - 373C69290FC1C9EB00137ACD /* nastreport.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nastreport.cpp; sourceTree = SOURCE_ROOT; }; - 373C692A0FC1C9EB00137ACD /* nastreport.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = nastreport.hpp; sourceTree = SOURCE_ROOT; }; - 373C69940FC1E63600137ACD /* boneh.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = boneh.cpp; sourceTree = SOURCE_ROOT; }; - 373C69950FC1E63600137ACD /* boneh.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = boneh.h; sourceTree = SOURCE_ROOT; }; - 373C69960FC1E63600137ACD /* efron.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = efron.cpp; sourceTree = SOURCE_ROOT; }; - 373C69970FC1E63600137ACD /* efron.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = efron.h; sourceTree = SOURCE_ROOT; }; - 373C69980FC1E63600137ACD /* solow.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = solow.cpp; sourceTree = SOURCE_ROOT; }; - 373C69990FC1E63600137ACD /* solow.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = solow.h; sourceTree = SOURCE_ROOT; }; - 374610760F40645300460C57 /* unifracweightedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unifracweightedcommand.h; sourceTree = SOURCE_ROOT; }; - 374610770F40645300460C57 /* unifracweightedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unifracweightedcommand.cpp; sourceTree = SOURCE_ROOT; }; - 3746107C0F4064D100460C57 /* weighted.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = weighted.h; sourceTree = SOURCE_ROOT; }; - 3746107D0F4064D100460C57 /* weighted.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = weighted.cpp; sourceTree = SOURCE_ROOT; }; - 374610810F40652400460C57 /* unweighted.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unweighted.h; sourceTree = SOURCE_ROOT; }; - 374610820F40652400460C57 /* unweighted.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unweighted.cpp; sourceTree = SOURCE_ROOT; }; - 3746109B0F40657600460C57 /* unifracunweightedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unifracunweightedcommand.h; sourceTree = SOURCE_ROOT; }; - 3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unifracunweightedcommand.cpp; sourceTree = SOURCE_ROOT; }; - 3749271B0FD58C840031C06B /* getsabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getsabundcommand.h; sourceTree = SOURCE_ROOT; }; - 3749271C0FD58C840031C06B /* getsabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getsabundcommand.cpp; sourceTree = SOURCE_ROOT; }; - 3749273D0FD5956B0031C06B /* getrabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getrabundcommand.h; sourceTree = SOURCE_ROOT; }; - 3749273E0FD5956B0031C06B /* getrabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getrabundcommand.cpp; sourceTree = SOURCE_ROOT; }; - 374F2FD51006320200E97C66 /* chimera.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimera.h; sourceTree = SOURCE_ROOT; }; - 374F2FE9100634B600E97C66 /* bellerophon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bellerophon.h; sourceTree = SOURCE_ROOT; }; - 374F2FEA100634B600E97C66 /* bellerophon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bellerophon.cpp; sourceTree = SOURCE_ROOT; }; - 374F301110063B6F00E97C66 /* pintail.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pintail.h; sourceTree = SOURCE_ROOT; }; - 374F301210063B6F00E97C66 /* pintail.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pintail.cpp; sourceTree = SOURCE_ROOT; }; - 37519A690F80E6EB00FED5E8 /* sharedanderbergs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedanderbergs.h; sourceTree = SOURCE_ROOT; }; - 37519A6A0F80E6EB00FED5E8 /* sharedanderbergs.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedanderbergs.cpp; sourceTree = SOURCE_ROOT; }; - 37519A9F0F810D0200FED5E8 /* venncommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = venncommand.h; sourceTree = SOURCE_ROOT; }; - 37519AA00F810D0200FED5E8 /* venncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = venncommand.cpp; sourceTree = SOURCE_ROOT; }; - 37519AB30F810FAE00FED5E8 /* venn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = venn.h; sourceTree = SOURCE_ROOT; }; - 37519AB40F810FAE00FED5E8 /* venn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = venn.cpp; sourceTree = SOURCE_ROOT; }; - 375873EA0F7D64520040F377 /* fullmatrix.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fullmatrix.h; sourceTree = SOURCE_ROOT; }; - 375873EB0F7D64520040F377 /* fullmatrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fullmatrix.cpp; sourceTree = SOURCE_ROOT; }; - 375873ED0F7D646F0040F377 /* heatmap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmap.h; sourceTree = SOURCE_ROOT; }; - 375873EE0F7D646F0040F377 /* heatmap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmap.cpp; sourceTree = SOURCE_ROOT; }; - 375873F00F7D64800040F377 /* heatmapcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapcommand.cpp; sourceTree = SOURCE_ROOT; }; - 375873F10F7D64800040F377 /* heatmapcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapcommand.h; sourceTree = SOURCE_ROOT; }; - 375873F30F7D648F0040F377 /* libshuffcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = libshuffcommand.cpp; sourceTree = SOURCE_ROOT; }; - 375873F40F7D648F0040F377 /* libshuffcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = libshuffcommand.h; sourceTree = SOURCE_ROOT; }; - 375873F60F7D649C0040F377 /* nocommands.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nocommands.cpp; sourceTree = SOURCE_ROOT; }; - 375873F70F7D649C0040F377 /* nocommands.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = nocommands.h; sourceTree = SOURCE_ROOT; }; - 375873F90F7D64AB0040F377 /* nseqs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = nseqs.h; sourceTree = SOURCE_ROOT; }; - 375873FB0F7D64DA0040F377 /* sharedbraycurtis.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedbraycurtis.h; sourceTree = SOURCE_ROOT; }; - 375873FC0F7D64DA0040F377 /* sharedbraycurtis.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedbraycurtis.cpp; sourceTree = SOURCE_ROOT; }; - 375873FE0F7D64EF0040F377 /* sharedkulczynski.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedkulczynski.cpp; sourceTree = SOURCE_ROOT; }; - 375873FF0F7D64EF0040F377 /* sharedlennon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedlennon.cpp; sourceTree = SOURCE_ROOT; }; - 375874000F7D64EF0040F377 /* sharedkulczynski.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedkulczynski.h; sourceTree = SOURCE_ROOT; }; - 375874010F7D64EF0040F377 /* sharedlennon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedlennon.h; sourceTree = SOURCE_ROOT; }; - 375874020F7D64EF0040F377 /* sharedkulczynskicody.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedkulczynskicody.cpp; sourceTree = SOURCE_ROOT; }; - 375874030F7D64EF0040F377 /* sharedkulczynskicody.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedkulczynskicody.h; sourceTree = SOURCE_ROOT; }; - 375874070F7D64FC0040F377 /* sharedmorisitahorn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedmorisitahorn.h; sourceTree = SOURCE_ROOT; }; - 375874080F7D64FC0040F377 /* sharedmorisitahorn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedmorisitahorn.cpp; sourceTree = SOURCE_ROOT; }; - 375874090F7D64FC0040F377 /* sharedochiai.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedochiai.h; sourceTree = SOURCE_ROOT; }; - 3758740A0F7D64FC0040F377 /* sharednseqs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharednseqs.h; sourceTree = SOURCE_ROOT; }; - 3758740B0F7D64FC0040F377 /* sharedochiai.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedochiai.cpp; sourceTree = SOURCE_ROOT; }; - 375AA1330F9E433D008EF9B8 /* readcolumn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readcolumn.cpp; sourceTree = SOURCE_ROOT; }; - 375AA1340F9E433D008EF9B8 /* readcolumn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readcolumn.h; sourceTree = SOURCE_ROOT; }; - 375AA1350F9E433D008EF9B8 /* readotu.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readotu.cpp; sourceTree = SOURCE_ROOT; }; - 375AA1360F9E433D008EF9B8 /* readotu.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotu.h; sourceTree = SOURCE_ROOT; }; - 375AA1370F9E433D008EF9B8 /* readphylip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readphylip.cpp; sourceTree = SOURCE_ROOT; }; - 375AA1380F9E433D008EF9B8 /* readphylip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylip.h; sourceTree = SOURCE_ROOT; }; - 377326630FAF16E0007ABB8B /* consensuscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = consensuscommand.cpp; sourceTree = SOURCE_ROOT; }; - 377326640FAF16E0007ABB8B /* consensuscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = consensuscommand.h; sourceTree = SOURCE_ROOT; }; - 378598640FDD497000EF9D03 /* heatmapsimcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapsimcommand.h; sourceTree = SOURCE_ROOT; }; - 378598650FDD497000EF9D03 /* heatmapsimcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapsimcommand.cpp; sourceTree = SOURCE_ROOT; }; - 378598720FDD4C1500EF9D03 /* heatmapsim.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapsim.h; sourceTree = SOURCE_ROOT; }; - 378598730FDD4C1500EF9D03 /* heatmapsim.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapsim.cpp; sourceTree = SOURCE_ROOT; }; - 3785990E0FDD7E8E00EF9D03 /* optionparser.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = optionparser.h; sourceTree = SOURCE_ROOT; }; - 3785990F0FDD7E8E00EF9D03 /* optionparser.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = optionparser.cpp; sourceTree = SOURCE_ROOT; }; - 378C1AEE0FB0644D004D63F5 /* filterseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = filterseqscommand.cpp; sourceTree = SOURCE_ROOT; }; - 378C1AEF0FB0644D004D63F5 /* filterseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = filterseqscommand.h; sourceTree = SOURCE_ROOT; }; - 378C1AF00FB0644D004D63F5 /* goodscoverage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = goodscoverage.cpp; sourceTree = SOURCE_ROOT; }; - 378C1AF10FB0644D004D63F5 /* goodscoverage.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = goodscoverage.h; sourceTree = SOURCE_ROOT; }; - 378C1AFD0FB0644D004D63F5 /* sequencedb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sequencedb.cpp; sourceTree = SOURCE_ROOT; }; - 378C1AFE0FB0644D004D63F5 /* sequencedb.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sequencedb.h; sourceTree = SOURCE_ROOT; }; - 378C1AFF0FB0644D004D63F5 /* sharedjackknife.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjackknife.cpp; sourceTree = SOURCE_ROOT; }; - 378C1B000FB0644D004D63F5 /* sharedjackknife.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjackknife.h; sourceTree = SOURCE_ROOT; }; - 378C1B010FB0644D004D63F5 /* sharedmarczewski.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedmarczewski.cpp; sourceTree = SOURCE_ROOT; }; - 378C1B020FB0644D004D63F5 /* sharedmarczewski.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedmarczewski.h; sourceTree = SOURCE_ROOT; }; - 378DC5CD0FBDE1C8003B8607 /* aligncommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = aligncommand.h; sourceTree = SOURCE_ROOT; }; - 378DC5CE0FBDE1C8003B8607 /* aligncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = aligncommand.cpp; sourceTree = SOURCE_ROOT; }; - 379293C10F2DE73400B9034A /* treemap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treemap.h; sourceTree = SOURCE_ROOT; }; - 379293C20F2DE73400B9034A /* treemap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treemap.cpp; sourceTree = SOURCE_ROOT; }; - 3792946E0F2E191800B9034A /* parsimonycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimonycommand.h; sourceTree = SOURCE_ROOT; }; - 3792946F0F2E191800B9034A /* parsimonycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsimonycommand.cpp; sourceTree = SOURCE_ROOT; }; - 379294880F2E258500B9034A /* parsimony.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimony.h; sourceTree = SOURCE_ROOT; }; - 379294890F2E258500B9034A /* parsimony.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsimony.cpp; sourceTree = SOURCE_ROOT; }; - 3792948D0F2E271100B9034A /* treecalculator.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treecalculator.h; sourceTree = SOURCE_ROOT; }; - 3799A94E0FD6A58C00E33EDE /* seqsummarycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = seqsummarycommand.cpp; sourceTree = SOURCE_ROOT; }; - 3799A94F0FD6A58C00E33EDE /* seqsummarycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = seqsummarycommand.h; sourceTree = SOURCE_ROOT; }; - 379D3D4F0FF90E090068C1C0 /* chimeraseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraseqscommand.h; sourceTree = SOURCE_ROOT; }; - 379D3D500FF90E090068C1C0 /* chimeraseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraseqscommand.cpp; sourceTree = SOURCE_ROOT; }; - 379D3D6B0FF917F40068C1C0 /* filters.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = filters.h; sourceTree = SOURCE_ROOT; }; - 37AD4CE20F28AEA300AA2D49 /* sharedlistvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedlistvector.h; sourceTree = SOURCE_ROOT; }; - 37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedlistvector.cpp; sourceTree = SOURCE_ROOT; }; - 37AD4DB90F28E2FE00AA2D49 /* tree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = tree.h; sourceTree = SOURCE_ROOT; }; - 37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = tree.cpp; sourceTree = SOURCE_ROOT; }; - 37AD4DC80F28F3DD00AA2D49 /* readtree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtree.h; sourceTree = SOURCE_ROOT; }; - 37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtree.cpp; sourceTree = SOURCE_ROOT; }; - 37AFC71D0F445386005F492D /* sharedsobscollectsummary.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsobscollectsummary.h; sourceTree = SOURCE_ROOT; }; - 37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsobscollectsummary.cpp; sourceTree = SOURCE_ROOT; }; - 37B28F660F27590100808A62 /* deconvolutecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = deconvolutecommand.h; sourceTree = SOURCE_ROOT; }; - 37B28F670F27590100808A62 /* deconvolutecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = deconvolutecommand.cpp; sourceTree = SOURCE_ROOT; }; - 37B73C741004BEFD008C4B41 /* listseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = listseqscommand.h; sourceTree = SOURCE_ROOT; }; - 37B73C751004BEFD008C4B41 /* listseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = listseqscommand.cpp; sourceTree = SOURCE_ROOT; }; - 37B73CA41004D89A008C4B41 /* getseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getseqscommand.h; sourceTree = SOURCE_ROOT; }; - 37B73CA51004D89A008C4B41 /* getseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getseqscommand.cpp; sourceTree = SOURCE_ROOT; }; - 37B73CBE1004EB38008C4B41 /* removeseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removeseqscommand.h; sourceTree = SOURCE_ROOT; }; - 37B73CBF1004EB38008C4B41 /* removeseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removeseqscommand.cpp; sourceTree = SOURCE_ROOT; }; - 37B73CCD1004F5E0008C4B41 /* systemcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = systemcommand.h; sourceTree = SOURCE_ROOT; }; - 37B73CCE1004F5E0008C4B41 /* systemcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = systemcommand.cpp; sourceTree = SOURCE_ROOT; }; - 37C1D9710F86506E0059E3F0 /* binsequencecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = binsequencecommand.h; sourceTree = SOURCE_ROOT; }; - 37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = binsequencecommand.cpp; sourceTree = SOURCE_ROOT; }; - 37C753CC0FB3415200DBD02E /* distancecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = distancecommand.h; sourceTree = SOURCE_ROOT; }; - 37C753CD0FB3415200DBD02E /* distancecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = distancecommand.cpp; sourceTree = SOURCE_ROOT; }; - 37C753DF0FB3492400DBD02E /* dist.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = dist.h; sourceTree = SOURCE_ROOT; }; - 37C753ED0FB34A5700DBD02E /* ignoregaps.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ignoregaps.h; sourceTree = SOURCE_ROOT; }; - 37C753F00FB34AE800DBD02E /* eachgapdist.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = eachgapdist.h; sourceTree = SOURCE_ROOT; }; - 37C753F10FB34B4700DBD02E /* onegapdist.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = onegapdist.h; sourceTree = SOURCE_ROOT; }; - 37C753F30FB34BBF00DBD02E /* onegapignore.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = onegapignore.h; sourceTree = SOURCE_ROOT; }; - 37C753F40FB34C0300DBD02E /* eachgapignore.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = eachgapignore.h; sourceTree = SOURCE_ROOT; }; - 37D927B80F21331F001D4494 /* ace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ace.cpp; sourceTree = SOURCE_ROOT; }; - 37D927B90F21331F001D4494 /* ace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ace.h; sourceTree = SOURCE_ROOT; }; - 37D927BA0F21331F001D4494 /* averagelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = averagelinkage.cpp; sourceTree = SOURCE_ROOT; }; - 37D927BB0F21331F001D4494 /* bootstrap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bootstrap.cpp; sourceTree = SOURCE_ROOT; }; - 37D927BC0F21331F001D4494 /* bootstrap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bootstrap.h; sourceTree = SOURCE_ROOT; }; - 37D927BD0F21331F001D4494 /* calculator.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = calculator.cpp; sourceTree = SOURCE_ROOT; }; - 37D927BE0F21331F001D4494 /* calculator.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = calculator.h; sourceTree = SOURCE_ROOT; }; - 37D927BF0F21331F001D4494 /* chao1.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chao1.cpp; sourceTree = SOURCE_ROOT; }; - 37D927C00F21331F001D4494 /* chao1.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chao1.h; sourceTree = SOURCE_ROOT; }; - 37D927C10F21331F001D4494 /* cluster.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = cluster.cpp; sourceTree = SOURCE_ROOT; }; - 37D927C20F21331F001D4494 /* cluster.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = cluster.hpp; sourceTree = SOURCE_ROOT; }; - 37D927C30F21331F001D4494 /* clustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clustercommand.cpp; sourceTree = SOURCE_ROOT; }; - 37D927C40F21331F001D4494 /* clustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clustercommand.h; sourceTree = SOURCE_ROOT; }; - 37D927C50F21331F001D4494 /* collect.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = collect.cpp; sourceTree = SOURCE_ROOT; }; - 37D927C60F21331F001D4494 /* collect.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collect.h; sourceTree = SOURCE_ROOT; }; - 37D927C70F21331F001D4494 /* collectcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = collectcommand.cpp; sourceTree = SOURCE_ROOT; }; - 37D927C80F21331F001D4494 /* collectcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectcommand.h; sourceTree = SOURCE_ROOT; }; - 37D927C90F21331F001D4494 /* collectdisplay.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectdisplay.h; sourceTree = SOURCE_ROOT; }; - 37D927CA0F21331F001D4494 /* collectorscurvedata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectorscurvedata.h; sourceTree = SOURCE_ROOT; }; - 37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = collectsharedcommand.cpp; sourceTree = SOURCE_ROOT; }; - 37D927CC0F21331F001D4494 /* collectsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectsharedcommand.h; sourceTree = SOURCE_ROOT; }; - 37D927CD0F21331F001D4494 /* command.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = command.hpp; sourceTree = SOURCE_ROOT; }; - 37D927CF0F21331F001D4494 /* commandfactory.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = commandfactory.hpp; sourceTree = SOURCE_ROOT; }; - 37D927D00F21331F001D4494 /* commandoptionparser.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = commandoptionparser.cpp; sourceTree = SOURCE_ROOT; }; - 37D927D10F21331F001D4494 /* commandoptionparser.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = commandoptionparser.hpp; sourceTree = SOURCE_ROOT; }; - 37D927D20F21331F001D4494 /* completelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = completelinkage.cpp; sourceTree = SOURCE_ROOT; }; - 37D927D30F21331F001D4494 /* database.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = database.cpp; sourceTree = SOURCE_ROOT; }; - 37D927D40F21331F001D4494 /* database.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = database.hpp; sourceTree = SOURCE_ROOT; }; - 37D927D50F21331F001D4494 /* datavector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = datavector.hpp; sourceTree = SOURCE_ROOT; }; - 37D927D60F21331F001D4494 /* display.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = display.h; sourceTree = SOURCE_ROOT; }; - 37D927D70F21331F001D4494 /* engine.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = engine.cpp; sourceTree = SOURCE_ROOT; }; - 37D927D80F21331F001D4494 /* engine.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = engine.hpp; sourceTree = SOURCE_ROOT; }; - 37D927DB0F21331F001D4494 /* fastamap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fastamap.cpp; sourceTree = SOURCE_ROOT; }; - 37D927DC0F21331F001D4494 /* fastamap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fastamap.h; sourceTree = SOURCE_ROOT; }; - 37D927DD0F21331F001D4494 /* fileoutput.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fileoutput.cpp; sourceTree = SOURCE_ROOT; }; - 37D927DE0F21331F001D4494 /* fileoutput.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fileoutput.h; sourceTree = SOURCE_ROOT; }; - 37D927DF0F21331F001D4494 /* globaldata.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = globaldata.cpp; sourceTree = SOURCE_ROOT; }; - 37D927E00F21331F001D4494 /* globaldata.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = globaldata.hpp; sourceTree = SOURCE_ROOT; }; - 37D927E10F21331F001D4494 /* groupmap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = groupmap.cpp; sourceTree = SOURCE_ROOT; }; - 37D927E20F21331F001D4494 /* groupmap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = groupmap.h; sourceTree = SOURCE_ROOT; }; - 37D927E30F21331F001D4494 /* helpcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = helpcommand.cpp; sourceTree = SOURCE_ROOT; }; - 37D927E40F21331F001D4494 /* helpcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = helpcommand.h; sourceTree = SOURCE_ROOT; }; - 37D927E50F21331F001D4494 /* inputdata.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = inputdata.cpp; sourceTree = SOURCE_ROOT; }; - 37D927E60F21331F001D4494 /* inputdata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = inputdata.h; sourceTree = SOURCE_ROOT; }; - 37D927E70F21331F001D4494 /* jackknife.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = jackknife.cpp; sourceTree = SOURCE_ROOT; }; - 37D927E80F21331F001D4494 /* jackknife.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = jackknife.h; sourceTree = SOURCE_ROOT; }; - 37D927E90F21331F001D4494 /* kmer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = kmer.cpp; sourceTree = SOURCE_ROOT; }; - 37D927EA0F21331F001D4494 /* kmer.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = kmer.hpp; sourceTree = SOURCE_ROOT; }; - 37D927EB0F21331F001D4494 /* kmerdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = kmerdb.cpp; sourceTree = SOURCE_ROOT; }; - 37D927EC0F21331F001D4494 /* kmerdb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = kmerdb.hpp; sourceTree = SOURCE_ROOT; }; - 37D927ED0F21331F001D4494 /* listvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = listvector.cpp; sourceTree = SOURCE_ROOT; }; - 37D927EE0F21331F001D4494 /* listvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = listvector.hpp; sourceTree = SOURCE_ROOT; }; - 37D927EF0F21331F001D4494 /* mothur.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mothur.cpp; sourceTree = SOURCE_ROOT; }; - 37D927F00F21331F001D4494 /* nameassignment.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nameassignment.cpp; sourceTree = SOURCE_ROOT; }; - 37D927F10F21331F001D4494 /* nameassignment.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = nameassignment.hpp; sourceTree = SOURCE_ROOT; }; - 37D927F40F21331F001D4494 /* npshannon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = npshannon.cpp; sourceTree = SOURCE_ROOT; }; - 37D927F50F21331F001D4494 /* npshannon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = npshannon.h; sourceTree = SOURCE_ROOT; }; - 37D927F60F21331F001D4494 /* observable.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = observable.h; sourceTree = SOURCE_ROOT; }; - 37D927F70F21331F001D4494 /* ordervector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ordervector.cpp; sourceTree = SOURCE_ROOT; }; - 37D927F80F21331F001D4494 /* ordervector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = ordervector.hpp; sourceTree = SOURCE_ROOT; }; - 37D927FB0F21331F001D4494 /* progress.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = progress.cpp; sourceTree = SOURCE_ROOT; }; - 37D927FC0F21331F001D4494 /* progress.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = progress.hpp; sourceTree = SOURCE_ROOT; }; - 37D927FD0F21331F001D4494 /* quitcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = quitcommand.cpp; sourceTree = SOURCE_ROOT; }; - 37D927FE0F21331F001D4494 /* quitcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = quitcommand.h; sourceTree = SOURCE_ROOT; }; - 37D927FF0F21331F001D4494 /* rabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rabundvector.cpp; sourceTree = SOURCE_ROOT; }; - 37D928000F21331F001D4494 /* rabundvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = rabundvector.hpp; sourceTree = SOURCE_ROOT; }; - 37D928010F21331F001D4494 /* rarecalc.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarecalc.cpp; sourceTree = SOURCE_ROOT; }; - 37D928020F21331F001D4494 /* rarecalc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarecalc.h; sourceTree = SOURCE_ROOT; }; - 37D928030F21331F001D4494 /* raredisplay.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = raredisplay.cpp; sourceTree = SOURCE_ROOT; }; - 37D928040F21331F001D4494 /* raredisplay.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = raredisplay.h; sourceTree = SOURCE_ROOT; }; - 37D928050F21331F001D4494 /* rarefact.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefact.cpp; sourceTree = SOURCE_ROOT; }; - 37D928060F21331F001D4494 /* rarefact.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefact.h; sourceTree = SOURCE_ROOT; }; - 37D928070F21331F001D4494 /* rarefactcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefactcommand.cpp; sourceTree = SOURCE_ROOT; }; - 37D928080F21331F001D4494 /* rarefactcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactcommand.h; sourceTree = SOURCE_ROOT; }; - 37D928090F21331F001D4494 /* rarefactioncurvedata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactioncurvedata.h; sourceTree = SOURCE_ROOT; }; - 37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefactsharedcommand.cpp; sourceTree = SOURCE_ROOT; }; - 37D9280B0F21331F001D4494 /* rarefactsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactsharedcommand.h; sourceTree = SOURCE_ROOT; }; - 37D928130F21331F001D4494 /* readmatrix.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = readmatrix.hpp; sourceTree = SOURCE_ROOT; }; - 37D9281A0F21331F001D4494 /* sabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sabundvector.cpp; sourceTree = SOURCE_ROOT; }; - 37D9281B0F21331F001D4494 /* sabundvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sabundvector.hpp; sourceTree = SOURCE_ROOT; }; - 37D9281C0F21331F001D4494 /* sequence.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sequence.cpp; sourceTree = SOURCE_ROOT; }; - 37D9281D0F21331F001D4494 /* sequence.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sequence.hpp; sourceTree = SOURCE_ROOT; }; - 37D9281E0F21331F001D4494 /* shannon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shannon.cpp; sourceTree = SOURCE_ROOT; }; - 37D9281F0F21331F001D4494 /* shannon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shannon.h; sourceTree = SOURCE_ROOT; }; - 37D928220F21331F001D4494 /* sharedace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedace.cpp; sourceTree = SOURCE_ROOT; }; - 37D928230F21331F001D4494 /* sharedace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedace.h; sourceTree = SOURCE_ROOT; }; - 37D928240F21331F001D4494 /* sharedchao1.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedchao1.cpp; sourceTree = SOURCE_ROOT; }; - 37D928250F21331F001D4494 /* sharedchao1.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedchao1.h; sourceTree = SOURCE_ROOT; }; - 37D928260F21331F001D4494 /* sharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedcommand.cpp; sourceTree = SOURCE_ROOT; }; - 37D928270F21331F001D4494 /* sharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedcommand.h; sourceTree = SOURCE_ROOT; }; - 37D928280F21331F001D4494 /* sharedjabund.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjabund.cpp; sourceTree = SOURCE_ROOT; }; - 37D928290F21331F001D4494 /* sharedjabund.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjabund.h; sourceTree = SOURCE_ROOT; }; - 37D9282A0F21331F001D4494 /* sharedjclass.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjclass.cpp; sourceTree = SOURCE_ROOT; }; - 37D9282B0F21331F001D4494 /* sharedjclass.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjclass.h; sourceTree = SOURCE_ROOT; }; - 37D9282C0F21331F001D4494 /* sharedjest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjest.cpp; sourceTree = SOURCE_ROOT; }; - 37D9282D0F21331F001D4494 /* sharedjest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjest.h; sourceTree = SOURCE_ROOT; }; - 37D9282E0F21331F001D4494 /* sharedordervector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedordervector.cpp; sourceTree = SOURCE_ROOT; }; - 37D9282F0F21331F001D4494 /* sharedordervector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedordervector.h; sourceTree = SOURCE_ROOT; }; - 37D928300F21331F001D4494 /* sharedrabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedrabundvector.cpp; sourceTree = SOURCE_ROOT; }; - 37D928310F21331F001D4494 /* sharedrabundvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedrabundvector.h; sourceTree = SOURCE_ROOT; }; - 37D928320F21331F001D4494 /* sharedsabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsabundvector.cpp; sourceTree = SOURCE_ROOT; }; - 37D928330F21331F001D4494 /* sharedsabundvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsabundvector.h; sourceTree = SOURCE_ROOT; }; - 37D928340F21331F001D4494 /* sharedsobs.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsobs.cpp; sourceTree = SOURCE_ROOT; }; - 37D928350F21331F001D4494 /* sharedsobs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsobs.h; sourceTree = SOURCE_ROOT; }; - 37D928360F21331F001D4494 /* sharedsorabund.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorabund.cpp; sourceTree = SOURCE_ROOT; }; - 37D928370F21331F001D4494 /* sharedsorabund.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsorabund.h; sourceTree = SOURCE_ROOT; }; - 37D928380F21331F001D4494 /* sharedsorclass.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorclass.cpp; sourceTree = SOURCE_ROOT; }; - 37D928390F21331F001D4494 /* sharedsorclass.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsorclass.h; sourceTree = SOURCE_ROOT; }; - 37D9283A0F21331F001D4494 /* sharedsorest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorest.cpp; sourceTree = SOURCE_ROOT; }; - 37D9283B0F21331F001D4494 /* sharedsorest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsorest.h; sourceTree = SOURCE_ROOT; }; - 37D9283C0F21331F001D4494 /* sharedthetan.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedthetan.cpp; sourceTree = SOURCE_ROOT; }; - 37D9283D0F21331F001D4494 /* sharedthetan.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedthetan.h; sourceTree = SOURCE_ROOT; }; - 37D9283E0F21331F001D4494 /* sharedthetayc.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedthetayc.cpp; sourceTree = SOURCE_ROOT; }; - 37D9283F0F21331F001D4494 /* sharedthetayc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedthetayc.h; sourceTree = SOURCE_ROOT; }; - 37D928400F21331F001D4494 /* simpson.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = simpson.cpp; sourceTree = SOURCE_ROOT; }; - 37D928410F21331F001D4494 /* simpson.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = simpson.h; sourceTree = SOURCE_ROOT; }; - 37D928420F21331F001D4494 /* singlelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = singlelinkage.cpp; sourceTree = SOURCE_ROOT; }; - 37D928430F21331F001D4494 /* sobs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sobs.h; sourceTree = SOURCE_ROOT; }; - 37D928440F21331F001D4494 /* sparsematrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sparsematrix.cpp; sourceTree = SOURCE_ROOT; }; - 37D928450F21331F001D4494 /* sparsematrix.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sparsematrix.hpp; sourceTree = SOURCE_ROOT; }; - 37D928460F21331F001D4494 /* summarycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summarycommand.cpp; sourceTree = SOURCE_ROOT; }; - 37D928470F21331F001D4494 /* summarycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarycommand.h; sourceTree = SOURCE_ROOT; }; - 37D928480F21331F001D4494 /* summarydata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarydata.h; sourceTree = SOURCE_ROOT; }; - 37D928490F21331F001D4494 /* summarydisplay.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarydisplay.h; sourceTree = SOURCE_ROOT; }; - 37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summarysharedcommand.cpp; sourceTree = SOURCE_ROOT; }; - 37D9284B0F21331F001D4494 /* summarysharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarysharedcommand.h; sourceTree = SOURCE_ROOT; }; - 37D9284D0F21331F001D4494 /* uvest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = uvest.cpp; sourceTree = SOURCE_ROOT; }; - 37D9284E0F21331F001D4494 /* uvest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = uvest.h; sourceTree = SOURCE_ROOT; }; - 37D9284F0F21331F001D4494 /* validcalculator.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = validcalculator.cpp; sourceTree = SOURCE_ROOT; }; - 37D928500F21331F001D4494 /* validcalculator.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = validcalculator.h; sourceTree = SOURCE_ROOT; }; - 37D928530F21331F001D4494 /* validparameter.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = validparameter.cpp; sourceTree = SOURCE_ROOT; }; - 37D928540F21331F001D4494 /* validparameter.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = validparameter.h; sourceTree = SOURCE_ROOT; }; - 37E3ED800F4D9D0D00B5DF02 /* mothur.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mothur.h; sourceTree = SOURCE_ROOT; }; - 37E5F3E10F29FD4200F8D827 /* treenode.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treenode.h; sourceTree = SOURCE_ROOT; }; - 37E5F3E20F29FD4200F8D827 /* treenode.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treenode.cpp; sourceTree = SOURCE_ROOT; }; - 37E5F4900F2A3DA800F8D827 /* readtreecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtreecommand.h; sourceTree = SOURCE_ROOT; }; - 37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtreecommand.cpp; sourceTree = SOURCE_ROOT; }; - 7E09C5120FDA79C5002ECAE5 /* reversecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = reversecommand.h; sourceTree = SOURCE_ROOT; }; - 7E09C5130FDA79C5002ECAE5 /* reversecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = reversecommand.cpp; sourceTree = SOURCE_ROOT; }; - 7E09C5340FDA7F65002ECAE5 /* trimseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = trimseqscommand.h; sourceTree = SOURCE_ROOT; }; - 7E09C5350FDA7F65002ECAE5 /* trimseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = trimseqscommand.cpp; sourceTree = SOURCE_ROOT; }; - 7E412F420F8D213C00381DD0 /* libshuff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = libshuff.h; sourceTree = SOURCE_ROOT; }; - 7E412F470F8D21B600381DD0 /* slibshuff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = slibshuff.h; sourceTree = SOURCE_ROOT; }; - 7E412F480F8D21B600381DD0 /* slibshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = slibshuff.cpp; sourceTree = SOURCE_ROOT; }; - 7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = libshuff.cpp; sourceTree = SOURCE_ROOT; }; - 7E4130F60F8E58FA00381DD0 /* dlibshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = dlibshuff.cpp; sourceTree = SOURCE_ROOT; }; - 7E4130F70F8E58FA00381DD0 /* dlibshuff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = dlibshuff.h; sourceTree = SOURCE_ROOT; }; - 7E5A17AD0FE57292003C6A03 /* mergefilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mergefilecommand.h; sourceTree = SOURCE_ROOT; }; - 7E5A17AE0FE57292003C6A03 /* mergefilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mergefilecommand.cpp; sourceTree = SOURCE_ROOT; }; - 7EC3D4500FA0FFF900338DA5 /* coverage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = coverage.cpp; sourceTree = SOURCE_ROOT; }; - 7EC3D4510FA0FFF900338DA5 /* coverage.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = coverage.h; sourceTree = SOURCE_ROOT; }; - 7EC3D4520FA0FFF900338DA5 /* sharedanderberg.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedanderberg.h; sourceTree = SOURCE_ROOT; }; - 7EC3D4530FA0FFF900338DA5 /* whittaker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = whittaker.cpp; sourceTree = SOURCE_ROOT; }; - 7EC3D4540FA0FFF900338DA5 /* whittaker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = whittaker.h; sourceTree = SOURCE_ROOT; }; - 8DD76F6C0486A84900D96B5E /* mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = mothur; sourceTree = BUILT_PRODUCTS_DIR; }; - A7027F2610DFF86D00BF45FE /* preclustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = preclustercommand.h; sourceTree = SOURCE_ROOT; }; - A7027F2710DFF86D00BF45FE /* preclustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = preclustercommand.cpp; sourceTree = SOURCE_ROOT; }; - A704E8A11106045D00870157 /* otuhierarchycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = otuhierarchycommand.h; sourceTree = SOURCE_ROOT; }; - A704E8A21106045D00870157 /* otuhierarchycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = otuhierarchycommand.cpp; sourceTree = SOURCE_ROOT; }; - A70B00C6110885EB002F453A /* setdircommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = setdircommand.h; sourceTree = SOURCE_ROOT; }; - A70B00C7110885EB002F453A /* setdircommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = setdircommand.cpp; sourceTree = SOURCE_ROOT; }; - A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getgroupcommand.cpp; sourceTree = SOURCE_ROOT; }; - A70B53A50F4CD7AD0064797E /* getgroupcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getgroupcommand.h; sourceTree = SOURCE_ROOT; }; - A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlabelcommand.cpp; sourceTree = SOURCE_ROOT; }; - A70B53A70F4CD7AD0064797E /* getlabelcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlabelcommand.h; sourceTree = SOURCE_ROOT; }; - A70DECD71063D8B40057C03C /* secondarystructurecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = secondarystructurecommand.h; sourceTree = SOURCE_ROOT; }; - A70DECD81063D8B40057C03C /* secondarystructurecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = secondarystructurecommand.cpp; sourceTree = SOURCE_ROOT; }; - A727E84810D14568001A8432 /* readblast.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readblast.h; sourceTree = SOURCE_ROOT; }; - A727E84910D14568001A8432 /* readblast.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readblast.cpp; sourceTree = SOURCE_ROOT; }; - A7283FF61056CAE100D0CC69 /* chimeracheckrdp.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeracheckrdp.h; sourceTree = SOURCE_ROOT; }; - A7283FF71056CAE100D0CC69 /* chimeracheckrdp.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeracheckrdp.cpp; sourceTree = SOURCE_ROOT; }; - A729ACCE10848E6100139801 /* hclustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = hclustercommand.h; sourceTree = SOURCE_ROOT; }; - A729ACCF10848E6100139801 /* hclustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = hclustercommand.cpp; sourceTree = SOURCE_ROOT; }; - A729ACE210849BBE00139801 /* hcluster.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = hcluster.h; sourceTree = SOURCE_ROOT; }; - A729ACE310849BBE00139801 /* hcluster.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = hcluster.cpp; sourceTree = SOURCE_ROOT; }; - A73329CD1083B3B3003B10C5 /* getlistcountcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlistcountcommand.h; sourceTree = SOURCE_ROOT; }; - A73329CE1083B3B3003B10C5 /* getlistcountcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlistcountcommand.cpp; sourceTree = SOURCE_ROOT; }; - A751ACE81098B283003D0911 /* readcluster.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readcluster.h; sourceTree = SOURCE_ROOT; }; - A751ACE91098B283003D0911 /* readcluster.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readcluster.cpp; sourceTree = SOURCE_ROOT; }; - A75B887B104C16860083C454 /* ccode.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ccode.cpp; sourceTree = SOURCE_ROOT; }; - A75B887C104C16860083C454 /* ccode.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ccode.h; sourceTree = SOURCE_ROOT; }; - A773805D10B6D6FC002A6A61 /* taxonomyequalizer.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = taxonomyequalizer.h; sourceTree = SOURCE_ROOT; }; - A773805E10B6D6FC002A6A61 /* taxonomyequalizer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = taxonomyequalizer.cpp; sourceTree = SOURCE_ROOT; }; - A773808E10B6EFD1002A6A61 /* phylotypecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylotypecommand.h; sourceTree = SOURCE_ROOT; }; - A773808F10B6EFD1002A6A61 /* phylotypecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylotypecommand.cpp; sourceTree = SOURCE_ROOT; }; - A7861476109F5FA00010AAAF /* classifyseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = classifyseqscommand.h; sourceTree = SOURCE_ROOT; }; - A7861477109F5FA00010AAAF /* classifyseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = classifyseqscommand.cpp; sourceTree = SOURCE_ROOT; }; - A78780FE10A06B8B0086103D /* classify.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = classify.h; sourceTree = SOURCE_ROOT; }; - A787810210A06D5D0086103D /* classify.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = classify.cpp; sourceTree = SOURCE_ROOT; }; - A78781B810A0813D0086103D /* phylotree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylotree.cpp; sourceTree = SOURCE_ROOT; }; - A78781B910A0813D0086103D /* phylotree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylotree.h; sourceTree = SOURCE_ROOT; }; - A787820F10A0AAE70086103D /* bayesian.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bayesian.h; sourceTree = SOURCE_ROOT; }; - A787821010A0AAE70086103D /* bayesian.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bayesian.cpp; sourceTree = SOURCE_ROOT; }; - A78782A910A1B1CB0086103D /* alignmentdb.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = alignmentdb.h; sourceTree = SOURCE_ROOT; }; - A78782AA10A1B1CB0086103D /* alignmentdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = alignmentdb.cpp; sourceTree = SOURCE_ROOT; }; - A787844310A1EBDD0086103D /* knn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = knn.h; sourceTree = SOURCE_ROOT; }; - A787844410A1EBDD0086103D /* knn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = knn.cpp; sourceTree = SOURCE_ROOT; }; - A794200F11107897003AECCD /* distancedb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = distancedb.cpp; sourceTree = SOURCE_ROOT; }; - A794201011107897003AECCD /* distancedb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = distancedb.hpp; sourceTree = SOURCE_ROOT; }; - A7B04491106CC3E60046FC83 /* chimeraslayer.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraslayer.h; sourceTree = SOURCE_ROOT; }; - A7B04492106CC3E60046FC83 /* chimeraslayer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraslayer.cpp; sourceTree = SOURCE_ROOT; }; - A7B0450C106CEEC90046FC83 /* slayer.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = slayer.h; sourceTree = SOURCE_ROOT; }; - A7B0450D106CEEC90046FC83 /* slayer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = slayer.cpp; sourceTree = SOURCE_ROOT; }; - A7D176CD10F2558500159497 /* pcacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pcacommand.h; sourceTree = SOURCE_ROOT; }; - A7D176CE10F2558500159497 /* pcacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pcacommand.cpp; sourceTree = SOURCE_ROOT; }; - A7D86C6A10FE084300865661 /* formatmatrix.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = formatmatrix.h; sourceTree = SOURCE_ROOT; }; - A7D86C7B10FE09AB00865661 /* formatcolumn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = formatcolumn.h; sourceTree = SOURCE_ROOT; }; - A7D86C7C10FE09AB00865661 /* formatcolumn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = formatcolumn.cpp; sourceTree = SOURCE_ROOT; }; - A7D86C8A10FE09FE00865661 /* formatphylip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = formatphylip.h; sourceTree = SOURCE_ROOT; }; - A7D86C8B10FE09FE00865661 /* formatphylip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = formatphylip.cpp; sourceTree = SOURCE_ROOT; }; - A7E0AAB410D2886D00CF407B /* mgclustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mgclustercommand.h; sourceTree = SOURCE_ROOT; }; - A7E0AAB510D2886D00CF407B /* mgclustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mgclustercommand.cpp; sourceTree = SOURCE_ROOT; }; - A7E4A781106913F900688F62 /* getsharedotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getsharedotucommand.h; sourceTree = SOURCE_ROOT; }; - A7E4A782106913F900688F62 /* getsharedotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getsharedotucommand.cpp; sourceTree = SOURCE_ROOT; }; - A7E4A822106A9AD700688F62 /* maligner.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = maligner.h; sourceTree = SOURCE_ROOT; }; - A7E4A823106A9AD700688F62 /* maligner.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = maligner.cpp; sourceTree = SOURCE_ROOT; }; - A7F5759610CEBC0600E20E47 /* libreadline.a */ = {isa = PBXFileReference; lastKnownFileType = archive.ar; name = libreadline.a; path = "../readline-6.0/libreadline.a"; sourceTree = SOURCE_ROOT; }; - C6859E8B029090EE04C91782 /* Mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = Mothur.1; sourceTree = ""; }; - EB1216860F619B83004A865F /* bergerparker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bergerparker.h; sourceTree = SOURCE_ROOT; }; - EB1216870F619B83004A865F /* bergerparker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bergerparker.cpp; sourceTree = SOURCE_ROOT; }; - EB1216E30F61ACFB004A865F /* bstick.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bstick.h; sourceTree = SOURCE_ROOT; }; - EB1216E40F61ACFB004A865F /* bstick.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bstick.cpp; sourceTree = SOURCE_ROOT; }; - EB1217210F61C9AC004A865F /* sharedkstest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedkstest.h; sourceTree = SOURCE_ROOT; }; - EB1217220F61C9AC004A865F /* sharedkstest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedkstest.cpp; sourceTree = SOURCE_ROOT; }; - EB6E68170F5F1C780044E17B /* qstat.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = qstat.h; sourceTree = SOURCE_ROOT; }; - EB6E68180F5F1C780044E17B /* qstat.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = qstat.cpp; sourceTree = SOURCE_ROOT; }; - EB72FE240FC1F5CA0051AC11 /* shen.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shen.cpp; sourceTree = SOURCE_ROOT; }; - EB72FE250FC1F5CA0051AC11 /* shen.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shen.h; sourceTree = SOURCE_ROOT; }; - EB9303E90F534D9400E8EF26 /* logsd.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = logsd.h; sourceTree = SOURCE_ROOT; }; - EB9303EA0F534D9400E8EF26 /* logsd.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = logsd.cpp; sourceTree = SOURCE_ROOT; }; - EB9303F70F53517300E8EF26 /* geom.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = geom.h; sourceTree = SOURCE_ROOT; }; - EB9303F80F53517300E8EF26 /* geom.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = geom.cpp; sourceTree = SOURCE_ROOT; }; + 7E6BE10812F710D8007ADDBE /* refchimeratest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = refchimeratest.h; sourceTree = ""; }; + 7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = refchimeratest.cpp; sourceTree = ""; }; + 8DD76FB20486AB0100D96B5E /* Mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = Mothur; sourceTree = BUILT_PRODUCTS_DIR; }; + A70332B512D3A13400761E33 /* makefile */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.make; path = makefile; sourceTree = ""; }; + A713EBAA12DC7613000092AC /* readphylipvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylipvector.h; sourceTree = ""; }; + A713EBAB12DC7613000092AC /* readphylipvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readphylipvector.cpp; sourceTree = ""; }; + A713EBEB12DC7C5E000092AC /* nmdscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = nmdscommand.h; sourceTree = ""; }; + A713EBEC12DC7C5E000092AC /* nmdscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nmdscommand.cpp; sourceTree = ""; }; + A71FE12A12EDF72400963CA7 /* mergegroupscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mergegroupscommand.h; sourceTree = ""; }; + A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mergegroupscommand.cpp; sourceTree = ""; }; + A727864212E9E28C00F86ABA /* removerarecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removerarecommand.h; sourceTree = ""; }; + A727864312E9E28C00F86ABA /* removerarecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removerarecommand.cpp; sourceTree = ""; }; + A75790571301749D00A30DAB /* homovacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = homovacommand.h; sourceTree = ""; }; + A75790581301749D00A30DAB /* homovacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = homovacommand.cpp; sourceTree = ""; }; + A7A61F1A130035C800E05B6B /* LICENSE */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = LICENSE; sourceTree = ""; }; + A7A61F2B130062E000E05B6B /* amovacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = amovacommand.h; sourceTree = ""; }; + A7A61F2C130062E000E05B6B /* amovacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = amovacommand.cpp; sourceTree = ""; }; + A7E9B64F12D37EC300DA6239 /* ace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ace.cpp; sourceTree = ""; }; + A7E9B65012D37EC300DA6239 /* ace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ace.h; sourceTree = ""; }; + A7E9B65112D37EC300DA6239 /* aligncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = aligncommand.cpp; sourceTree = ""; }; + A7E9B65212D37EC300DA6239 /* aligncommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = aligncommand.h; sourceTree = ""; }; + A7E9B65312D37EC300DA6239 /* alignment.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = alignment.cpp; sourceTree = ""; }; + A7E9B65412D37EC300DA6239 /* alignment.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = alignment.hpp; sourceTree = ""; }; + A7E9B65512D37EC300DA6239 /* alignmentcell.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = alignmentcell.cpp; sourceTree = ""; }; + A7E9B65612D37EC300DA6239 /* alignmentcell.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = alignmentcell.hpp; sourceTree = ""; }; + A7E9B65712D37EC300DA6239 /* alignmentdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = alignmentdb.cpp; sourceTree = ""; }; + A7E9B65812D37EC300DA6239 /* alignmentdb.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = alignmentdb.h; sourceTree = ""; }; + A7E9B65912D37EC300DA6239 /* averagelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = averagelinkage.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B65A12D37EC300DA6239 /* bayesian.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bayesian.cpp; sourceTree = ""; }; + A7E9B65B12D37EC300DA6239 /* bayesian.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bayesian.h; sourceTree = ""; }; + A7E9B65C12D37EC300DA6239 /* bellerophon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bellerophon.cpp; sourceTree = ""; }; + A7E9B65D12D37EC300DA6239 /* bellerophon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bellerophon.h; sourceTree = ""; }; + A7E9B65E12D37EC300DA6239 /* bergerparker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bergerparker.cpp; sourceTree = ""; }; + A7E9B65F12D37EC300DA6239 /* bergerparker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bergerparker.h; sourceTree = ""; }; + A7E9B66012D37EC300DA6239 /* binsequencecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = binsequencecommand.cpp; sourceTree = ""; }; + A7E9B66112D37EC300DA6239 /* binsequencecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = binsequencecommand.h; sourceTree = ""; }; + A7E9B66212D37EC300DA6239 /* blastalign.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = blastalign.cpp; sourceTree = ""; }; + A7E9B66312D37EC400DA6239 /* blastalign.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = blastalign.hpp; sourceTree = ""; }; + A7E9B66412D37EC400DA6239 /* blastdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = blastdb.cpp; sourceTree = ""; }; + A7E9B66512D37EC400DA6239 /* blastdb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = blastdb.hpp; sourceTree = ""; }; + A7E9B66612D37EC400DA6239 /* boneh.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = boneh.cpp; sourceTree = ""; }; + A7E9B66712D37EC400DA6239 /* boneh.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = boneh.h; sourceTree = ""; }; + A7E9B66812D37EC400DA6239 /* bootstrap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bootstrap.cpp; sourceTree = ""; }; + A7E9B66912D37EC400DA6239 /* bootstrap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bootstrap.h; sourceTree = ""; }; + A7E9B66A12D37EC400DA6239 /* bootstrapsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bootstrapsharedcommand.cpp; sourceTree = ""; }; + A7E9B66B12D37EC400DA6239 /* bootstrapsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bootstrapsharedcommand.h; sourceTree = ""; }; + A7E9B66C12D37EC400DA6239 /* bstick.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bstick.cpp; sourceTree = ""; }; + A7E9B66D12D37EC400DA6239 /* bstick.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bstick.h; sourceTree = ""; }; + A7E9B66E12D37EC400DA6239 /* calculator.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = calculator.cpp; sourceTree = ""; }; + A7E9B66F12D37EC400DA6239 /* calculator.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = calculator.h; sourceTree = ""; }; + A7E9B67012D37EC400DA6239 /* canberra.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = canberra.cpp; sourceTree = ""; }; + A7E9B67112D37EC400DA6239 /* canberra.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = canberra.h; sourceTree = ""; }; + A7E9B67212D37EC400DA6239 /* catchallcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = catchallcommand.cpp; sourceTree = ""; }; + A7E9B67312D37EC400DA6239 /* catchallcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = catchallcommand.h; sourceTree = ""; }; + A7E9B67412D37EC400DA6239 /* ccode.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ccode.cpp; sourceTree = ""; }; + A7E9B67512D37EC400DA6239 /* ccode.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ccode.h; sourceTree = ""; }; + A7E9B67612D37EC400DA6239 /* chao1.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chao1.cpp; sourceTree = ""; }; + A7E9B67712D37EC400DA6239 /* chao1.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chao1.h; sourceTree = ""; }; + A7E9B67812D37EC400DA6239 /* chimera.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimera.cpp; sourceTree = ""; }; + A7E9B67912D37EC400DA6239 /* chimera.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimera.h; sourceTree = ""; }; + A7E9B67A12D37EC400DA6239 /* chimerabellerophoncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimerabellerophoncommand.cpp; sourceTree = ""; }; + A7E9B67B12D37EC400DA6239 /* chimerabellerophoncommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimerabellerophoncommand.h; sourceTree = ""; }; + A7E9B67C12D37EC400DA6239 /* chimeraccodecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraccodecommand.cpp; sourceTree = ""; }; + A7E9B67D12D37EC400DA6239 /* chimeraccodecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraccodecommand.h; sourceTree = ""; }; + A7E9B67E12D37EC400DA6239 /* chimeracheckcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeracheckcommand.cpp; sourceTree = ""; }; + A7E9B67F12D37EC400DA6239 /* chimeracheckcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeracheckcommand.h; sourceTree = ""; }; + A7E9B68012D37EC400DA6239 /* chimeracheckrdp.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeracheckrdp.cpp; sourceTree = ""; }; + A7E9B68112D37EC400DA6239 /* chimeracheckrdp.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeracheckrdp.h; sourceTree = ""; }; + A7E9B68212D37EC400DA6239 /* chimerapintailcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimerapintailcommand.cpp; sourceTree = ""; }; + A7E9B68312D37EC400DA6239 /* chimerapintailcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimerapintailcommand.h; sourceTree = ""; }; + A7E9B68412D37EC400DA6239 /* chimerarealigner.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimerarealigner.cpp; sourceTree = ""; }; + A7E9B68512D37EC400DA6239 /* chimerarealigner.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimerarealigner.h; sourceTree = ""; }; + A7E9B68612D37EC400DA6239 /* chimeraseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraseqscommand.cpp; sourceTree = ""; }; + A7E9B68712D37EC400DA6239 /* chimeraseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraseqscommand.h; sourceTree = ""; }; + A7E9B68812D37EC400DA6239 /* chimeraslayer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraslayer.cpp; sourceTree = ""; }; + A7E9B68912D37EC400DA6239 /* chimeraslayer.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraslayer.h; sourceTree = ""; }; + A7E9B68A12D37EC400DA6239 /* chimeraslayercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraslayercommand.cpp; sourceTree = ""; }; + A7E9B68B12D37EC400DA6239 /* chimeraslayercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraslayercommand.h; sourceTree = ""; }; + A7E9B68C12D37EC400DA6239 /* chopseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chopseqscommand.cpp; sourceTree = ""; }; + A7E9B68D12D37EC400DA6239 /* chopseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chopseqscommand.h; sourceTree = ""; }; + A7E9B68E12D37EC400DA6239 /* classify.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = classify.cpp; sourceTree = ""; }; + A7E9B68F12D37EC400DA6239 /* classify.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = classify.h; sourceTree = ""; }; + A7E9B69012D37EC400DA6239 /* classifyotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = classifyotucommand.cpp; sourceTree = ""; }; + A7E9B69112D37EC400DA6239 /* classifyotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = classifyotucommand.h; sourceTree = ""; }; + A7E9B69212D37EC400DA6239 /* classifyseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = classifyseqscommand.cpp; sourceTree = ""; }; + A7E9B69312D37EC400DA6239 /* classifyseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = classifyseqscommand.h; sourceTree = ""; }; + A7E9B69412D37EC400DA6239 /* clearcut.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clearcut.cpp; sourceTree = ""; }; + A7E9B69512D37EC400DA6239 /* clearcut.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clearcut.h; sourceTree = ""; }; + A7E9B69612D37EC400DA6239 /* clearcutcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clearcutcommand.cpp; sourceTree = ""; }; + A7E9B69712D37EC400DA6239 /* clearcutcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clearcutcommand.h; sourceTree = ""; }; + A7E9B69812D37EC400DA6239 /* cluster.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = cluster.cpp; sourceTree = ""; }; + A7E9B69912D37EC400DA6239 /* cluster.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = cluster.hpp; sourceTree = ""; }; + A7E9B69A12D37EC400DA6239 /* clusterclassic.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clusterclassic.cpp; sourceTree = ""; }; + A7E9B69B12D37EC400DA6239 /* clusterclassic.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clusterclassic.h; sourceTree = ""; }; + A7E9B69C12D37EC400DA6239 /* clustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clustercommand.cpp; sourceTree = ""; }; + A7E9B69D12D37EC400DA6239 /* clustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clustercommand.h; sourceTree = ""; }; + A7E9B69E12D37EC400DA6239 /* clusterdoturcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clusterdoturcommand.cpp; sourceTree = ""; }; + A7E9B69F12D37EC400DA6239 /* clusterdoturcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clusterdoturcommand.h; sourceTree = ""; }; + A7E9B6A012D37EC400DA6239 /* clusterfragmentscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clusterfragmentscommand.cpp; sourceTree = ""; }; + A7E9B6A112D37EC400DA6239 /* clusterfragmentscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clusterfragmentscommand.h; sourceTree = ""; }; + A7E9B6A212D37EC400DA6239 /* clustersplitcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clustersplitcommand.cpp; sourceTree = ""; }; + A7E9B6A312D37EC400DA6239 /* clustersplitcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clustersplitcommand.h; sourceTree = ""; }; + A7E9B6A412D37EC400DA6239 /* cmdargs.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = cmdargs.cpp; sourceTree = ""; }; + A7E9B6A512D37EC400DA6239 /* cmdargs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cmdargs.h; sourceTree = ""; }; + A7E9B6A612D37EC400DA6239 /* collect.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = collect.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B6A712D37EC400DA6239 /* collect.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collect.h; sourceTree = SOURCE_ROOT; }; + A7E9B6A812D37EC400DA6239 /* collectcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = collectcommand.cpp; sourceTree = ""; }; + A7E9B6A912D37EC400DA6239 /* collectcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectcommand.h; sourceTree = ""; }; + A7E9B6AA12D37EC400DA6239 /* collectdisplay.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectdisplay.h; sourceTree = SOURCE_ROOT; }; + A7E9B6AB12D37EC400DA6239 /* collectorscurvedata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectorscurvedata.h; sourceTree = SOURCE_ROOT; }; + A7E9B6AC12D37EC400DA6239 /* collectsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = collectsharedcommand.cpp; sourceTree = ""; }; + A7E9B6AD12D37EC400DA6239 /* collectsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectsharedcommand.h; sourceTree = ""; }; + A7E9B6AE12D37EC400DA6239 /* command.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = command.hpp; sourceTree = ""; }; + A7E9B6AF12D37EC400DA6239 /* commandfactory.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = commandfactory.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B6B012D37EC400DA6239 /* commandfactory.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = commandfactory.hpp; sourceTree = SOURCE_ROOT; }; + A7E9B6B112D37EC400DA6239 /* commandoptionparser.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = commandoptionparser.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B6B212D37EC400DA6239 /* commandoptionparser.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = commandoptionparser.hpp; sourceTree = SOURCE_ROOT; }; + A7E9B6B312D37EC400DA6239 /* common.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = common.h; sourceTree = ""; }; + A7E9B6B412D37EC400DA6239 /* completelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = completelinkage.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B6B512D37EC400DA6239 /* consensuscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = consensuscommand.cpp; sourceTree = ""; }; + A7E9B6B612D37EC400DA6239 /* consensuscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = consensuscommand.h; sourceTree = ""; }; + A7E9B6B712D37EC400DA6239 /* consensusseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = consensusseqscommand.cpp; sourceTree = ""; }; + A7E9B6B812D37EC400DA6239 /* consensusseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = consensusseqscommand.h; sourceTree = ""; }; + A7E9B6B912D37EC400DA6239 /* corraxescommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = corraxescommand.cpp; sourceTree = ""; }; + A7E9B6BA12D37EC400DA6239 /* corraxescommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = corraxescommand.h; sourceTree = ""; }; + A7E9B6BB12D37EC400DA6239 /* coverage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = coverage.cpp; sourceTree = ""; }; + A7E9B6BC12D37EC400DA6239 /* coverage.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = coverage.h; sourceTree = ""; }; + A7E9B6BD12D37EC400DA6239 /* database.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = database.cpp; sourceTree = ""; }; + A7E9B6BE12D37EC400DA6239 /* database.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = database.hpp; sourceTree = ""; }; + A7E9B6BF12D37EC400DA6239 /* datavector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = datavector.hpp; sourceTree = ""; }; + A7E9B6C012D37EC400DA6239 /* dayhoff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = dayhoff.h; sourceTree = ""; }; + A7E9B6C112D37EC400DA6239 /* decalc.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = decalc.cpp; sourceTree = ""; }; + A7E9B6C212D37EC400DA6239 /* decalc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = decalc.h; sourceTree = ""; }; + A7E9B6C312D37EC400DA6239 /* deconvolutecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = deconvolutecommand.cpp; sourceTree = ""; }; + A7E9B6C412D37EC400DA6239 /* deconvolutecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = deconvolutecommand.h; sourceTree = ""; }; + A7E9B6C512D37EC400DA6239 /* degapseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = degapseqscommand.cpp; sourceTree = ""; }; + A7E9B6C612D37EC400DA6239 /* degapseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = degapseqscommand.h; sourceTree = ""; }; + A7E9B6C712D37EC400DA6239 /* deuniqueseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = deuniqueseqscommand.cpp; sourceTree = ""; }; + A7E9B6C812D37EC400DA6239 /* deuniqueseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = deuniqueseqscommand.h; sourceTree = ""; }; + A7E9B6C912D37EC400DA6239 /* display.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = display.h; sourceTree = SOURCE_ROOT; }; + A7E9B6CA12D37EC400DA6239 /* dist.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = dist.h; sourceTree = ""; }; + A7E9B6CB12D37EC400DA6239 /* distancecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = distancecommand.cpp; sourceTree = ""; }; + A7E9B6CC12D37EC400DA6239 /* distancecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = distancecommand.h; sourceTree = ""; }; + A7E9B6CD12D37EC400DA6239 /* distancedb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = distancedb.cpp; sourceTree = ""; }; + A7E9B6CE12D37EC400DA6239 /* distancedb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = distancedb.hpp; sourceTree = ""; }; + A7E9B6CF12D37EC400DA6239 /* distclearcut.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = distclearcut.cpp; sourceTree = ""; }; + A7E9B6D012D37EC400DA6239 /* distclearcut.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = distclearcut.h; sourceTree = ""; }; + A7E9B6D112D37EC400DA6239 /* dlibshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = dlibshuff.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B6D212D37EC400DA6239 /* dlibshuff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = dlibshuff.h; sourceTree = SOURCE_ROOT; }; + A7E9B6D312D37EC400DA6239 /* dmat.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = dmat.cpp; sourceTree = ""; }; + A7E9B6D412D37EC400DA6239 /* dmat.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = dmat.h; sourceTree = ""; }; + A7E9B6D512D37EC400DA6239 /* eachgapdist.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = eachgapdist.h; sourceTree = ""; }; + A7E9B6D612D37EC400DA6239 /* eachgapignore.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = eachgapignore.h; sourceTree = ""; }; + A7E9B6D712D37EC400DA6239 /* efron.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = efron.cpp; sourceTree = ""; }; + A7E9B6D812D37EC400DA6239 /* efron.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = efron.h; sourceTree = ""; }; + A7E9B6D912D37EC400DA6239 /* endiannessmacros.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = endiannessmacros.h; sourceTree = SOURCE_ROOT; }; + A7E9B6DA12D37EC400DA6239 /* engine.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = engine.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B6DB12D37EC400DA6239 /* engine.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = engine.hpp; sourceTree = SOURCE_ROOT; }; + A7E9B6DC12D37EC400DA6239 /* fasta.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fasta.cpp; sourceTree = ""; }; + A7E9B6DD12D37EC400DA6239 /* fasta.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fasta.h; sourceTree = ""; }; + A7E9B6DE12D37EC400DA6239 /* fastamap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fastamap.cpp; sourceTree = ""; }; + A7E9B6DF12D37EC400DA6239 /* fastamap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fastamap.h; sourceTree = ""; }; + A7E9B6E012D37EC400DA6239 /* fileoutput.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fileoutput.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B6E112D37EC400DA6239 /* fileoutput.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fileoutput.h; sourceTree = SOURCE_ROOT; }; + A7E9B6E212D37EC400DA6239 /* filters.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = filters.h; sourceTree = ""; }; + A7E9B6E312D37EC400DA6239 /* filterseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = filterseqscommand.cpp; sourceTree = ""; }; + A7E9B6E412D37EC400DA6239 /* filterseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = filterseqscommand.h; sourceTree = ""; }; + A7E9B6E512D37EC400DA6239 /* fisher2.c */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.c; path = fisher2.c; sourceTree = ""; }; + A7E9B6E612D37EC400DA6239 /* fisher2.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fisher2.h; sourceTree = ""; }; + A7E9B6E712D37EC400DA6239 /* flowdata.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = flowdata.cpp; sourceTree = ""; }; + A7E9B6E812D37EC400DA6239 /* flowdata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = flowdata.h; sourceTree = ""; }; + A7E9B6E912D37EC400DA6239 /* formatcolumn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = formatcolumn.cpp; sourceTree = ""; }; + A7E9B6EA12D37EC400DA6239 /* formatcolumn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = formatcolumn.h; sourceTree = ""; }; + A7E9B6EB12D37EC400DA6239 /* formatmatrix.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = formatmatrix.h; sourceTree = ""; }; + A7E9B6EC12D37EC400DA6239 /* formatphylip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = formatphylip.cpp; sourceTree = ""; }; + A7E9B6ED12D37EC400DA6239 /* formatphylip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = formatphylip.h; sourceTree = ""; }; + A7E9B6EE12D37EC400DA6239 /* fullmatrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fullmatrix.cpp; sourceTree = ""; }; + A7E9B6EF12D37EC400DA6239 /* fullmatrix.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fullmatrix.h; sourceTree = ""; }; + A7E9B6F012D37EC400DA6239 /* geom.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = geom.cpp; sourceTree = ""; }; + A7E9B6F112D37EC400DA6239 /* geom.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = geom.h; sourceTree = ""; }; + A7E9B6F212D37EC400DA6239 /* getgroupcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getgroupcommand.cpp; sourceTree = ""; }; + A7E9B6F312D37EC400DA6239 /* getgroupcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getgroupcommand.h; sourceTree = ""; }; + A7E9B6F412D37EC400DA6239 /* getgroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getgroupscommand.cpp; sourceTree = ""; }; + A7E9B6F512D37EC400DA6239 /* getgroupscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getgroupscommand.h; sourceTree = ""; }; + A7E9B6F612D37EC400DA6239 /* getlabelcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlabelcommand.cpp; sourceTree = ""; }; + A7E9B6F712D37EC400DA6239 /* getlabelcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlabelcommand.h; sourceTree = ""; }; + A7E9B6F812D37EC400DA6239 /* getlineagecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlineagecommand.cpp; sourceTree = ""; }; + A7E9B6F912D37EC400DA6239 /* getlineagecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlineagecommand.h; sourceTree = ""; }; + A7E9B6FA12D37EC400DA6239 /* getlistcountcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlistcountcommand.cpp; sourceTree = ""; }; + A7E9B6FB12D37EC400DA6239 /* getlistcountcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlistcountcommand.h; sourceTree = ""; }; + A7E9B6FC12D37EC400DA6239 /* getopt_long.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getopt_long.cpp; sourceTree = ""; }; + A7E9B6FD12D37EC400DA6239 /* getopt_long.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getopt_long.h; sourceTree = ""; }; + A7E9B6FE12D37EC400DA6239 /* getoturepcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getoturepcommand.cpp; sourceTree = ""; }; + A7E9B6FF12D37EC400DA6239 /* getoturepcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getoturepcommand.h; sourceTree = ""; }; + A7E9B70012D37EC400DA6239 /* getotuscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getotuscommand.cpp; sourceTree = ""; }; + A7E9B70112D37EC400DA6239 /* getotuscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getotuscommand.h; sourceTree = ""; }; + A7E9B70212D37EC400DA6239 /* getrabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getrabundcommand.cpp; sourceTree = ""; }; + A7E9B70312D37EC400DA6239 /* getrabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getrabundcommand.h; sourceTree = ""; }; + A7E9B70412D37EC400DA6239 /* getrelabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getrelabundcommand.cpp; sourceTree = ""; }; + A7E9B70512D37EC400DA6239 /* getrelabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getrelabundcommand.h; sourceTree = ""; }; + A7E9B70612D37EC400DA6239 /* getsabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getsabundcommand.cpp; sourceTree = ""; }; + A7E9B70712D37EC400DA6239 /* getsabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getsabundcommand.h; sourceTree = ""; }; + A7E9B70812D37EC400DA6239 /* getseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getseqscommand.cpp; sourceTree = ""; }; + A7E9B70912D37EC400DA6239 /* getseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getseqscommand.h; sourceTree = ""; }; + A7E9B70A12D37EC400DA6239 /* getsharedotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getsharedotucommand.cpp; sourceTree = ""; }; + A7E9B70B12D37EC400DA6239 /* getsharedotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getsharedotucommand.h; sourceTree = ""; }; + A7E9B70C12D37EC400DA6239 /* globaldata.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = globaldata.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B70D12D37EC400DA6239 /* globaldata.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = globaldata.hpp; sourceTree = SOURCE_ROOT; }; + A7E9B70E12D37EC400DA6239 /* goodscoverage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = goodscoverage.cpp; sourceTree = ""; }; + A7E9B70F12D37EC400DA6239 /* goodscoverage.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = goodscoverage.h; sourceTree = ""; }; + A7E9B71012D37EC400DA6239 /* gotohoverlap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = gotohoverlap.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B71112D37EC400DA6239 /* gotohoverlap.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = gotohoverlap.hpp; sourceTree = SOURCE_ROOT; }; + A7E9B71212D37EC400DA6239 /* gower.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = gower.cpp; sourceTree = ""; }; + A7E9B71312D37EC400DA6239 /* gower.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = gower.h; sourceTree = ""; }; + A7E9B71412D37EC400DA6239 /* groupmap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = groupmap.cpp; sourceTree = ""; }; + A7E9B71512D37EC400DA6239 /* groupmap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = groupmap.h; sourceTree = ""; }; + A7E9B71612D37EC400DA6239 /* hamming.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = hamming.cpp; sourceTree = ""; }; + A7E9B71712D37EC400DA6239 /* hamming.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = hamming.h; sourceTree = ""; }; + A7E9B71812D37EC400DA6239 /* hcluster.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = hcluster.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B71912D37EC400DA6239 /* hcluster.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = hcluster.h; sourceTree = SOURCE_ROOT; }; + A7E9B71A12D37EC400DA6239 /* hclustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = hclustercommand.cpp; sourceTree = ""; }; + A7E9B71B12D37EC400DA6239 /* hclustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = hclustercommand.h; sourceTree = ""; }; + A7E9B71C12D37EC400DA6239 /* heatmap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmap.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B71D12D37EC400DA6239 /* heatmap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmap.h; sourceTree = SOURCE_ROOT; }; + A7E9B71E12D37EC400DA6239 /* heatmapcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapcommand.cpp; sourceTree = ""; }; + A7E9B71F12D37EC400DA6239 /* heatmapcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapcommand.h; sourceTree = ""; }; + A7E9B72012D37EC400DA6239 /* heatmapsim.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapsim.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B72112D37EC400DA6239 /* heatmapsim.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapsim.h; sourceTree = SOURCE_ROOT; }; + A7E9B72212D37EC400DA6239 /* heatmapsimcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapsimcommand.cpp; sourceTree = ""; }; + A7E9B72312D37EC400DA6239 /* heatmapsimcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapsimcommand.h; sourceTree = ""; }; + A7E9B72412D37EC400DA6239 /* heip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heip.cpp; sourceTree = ""; }; + A7E9B72512D37EC400DA6239 /* heip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heip.h; sourceTree = ""; }; + A7E9B72612D37EC400DA6239 /* hellinger.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = hellinger.cpp; sourceTree = ""; }; + A7E9B72712D37EC400DA6239 /* hellinger.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = hellinger.h; sourceTree = ""; }; + A7E9B72812D37EC400DA6239 /* helpcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = helpcommand.cpp; sourceTree = ""; }; + A7E9B72912D37EC400DA6239 /* helpcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = helpcommand.h; sourceTree = ""; }; + A7E9B72A12D37EC400DA6239 /* ignoregaps.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ignoregaps.h; sourceTree = ""; }; + A7E9B72B12D37EC400DA6239 /* indicatorcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = indicatorcommand.cpp; sourceTree = ""; }; + A7E9B72C12D37EC400DA6239 /* indicatorcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = indicatorcommand.h; sourceTree = ""; }; + A7E9B72D12D37EC400DA6239 /* inputdata.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = inputdata.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B72E12D37EC400DA6239 /* inputdata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = inputdata.h; sourceTree = SOURCE_ROOT; }; + A7E9B72F12D37EC400DA6239 /* invsimpson.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = invsimpson.cpp; sourceTree = ""; }; + A7E9B73012D37EC400DA6239 /* invsimpson.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = invsimpson.h; sourceTree = ""; }; + A7E9B73112D37EC400DA6239 /* jackknife.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = jackknife.cpp; sourceTree = ""; }; + A7E9B73212D37EC400DA6239 /* jackknife.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = jackknife.h; sourceTree = ""; }; + A7E9B73312D37EC400DA6239 /* kmer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = kmer.cpp; sourceTree = ""; }; + A7E9B73412D37EC400DA6239 /* kmer.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = kmer.hpp; sourceTree = ""; }; + A7E9B73512D37EC400DA6239 /* kmerdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = kmerdb.cpp; sourceTree = ""; }; + A7E9B73612D37EC400DA6239 /* kmerdb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = kmerdb.hpp; sourceTree = ""; }; + A7E9B73712D37EC400DA6239 /* knn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = knn.cpp; sourceTree = ""; }; + A7E9B73812D37EC400DA6239 /* knn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = knn.h; sourceTree = ""; }; + A7E9B73912D37EC400DA6239 /* libshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = libshuff.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B73A12D37EC400DA6239 /* libshuff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = libshuff.h; sourceTree = SOURCE_ROOT; }; + A7E9B73B12D37EC400DA6239 /* libshuffcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = libshuffcommand.cpp; sourceTree = ""; }; + A7E9B73C12D37EC400DA6239 /* libshuffcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = libshuffcommand.h; sourceTree = ""; }; + A7E9B73D12D37EC400DA6239 /* listseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = listseqscommand.cpp; sourceTree = ""; }; + A7E9B73E12D37EC400DA6239 /* listseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = listseqscommand.h; sourceTree = ""; }; + A7E9B73F12D37EC400DA6239 /* listvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = listvector.cpp; sourceTree = ""; }; + A7E9B74012D37EC400DA6239 /* listvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = listvector.hpp; sourceTree = ""; }; + A7E9B74112D37EC400DA6239 /* logsd.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = logsd.cpp; sourceTree = ""; }; + A7E9B74212D37EC400DA6239 /* logsd.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = logsd.h; sourceTree = ""; }; + A7E9B74312D37EC400DA6239 /* makegroupcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = makegroupcommand.cpp; sourceTree = ""; }; + A7E9B74412D37EC400DA6239 /* makegroupcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = makegroupcommand.h; sourceTree = ""; }; + A7E9B74512D37EC400DA6239 /* maligner.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = maligner.cpp; sourceTree = ""; }; + A7E9B74612D37EC400DA6239 /* maligner.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = maligner.h; sourceTree = ""; }; + A7E9B74712D37EC400DA6239 /* manhattan.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = manhattan.cpp; sourceTree = ""; }; + A7E9B74812D37EC400DA6239 /* manhattan.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = manhattan.h; sourceTree = ""; }; + A7E9B74912D37EC400DA6239 /* matrixoutputcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = matrixoutputcommand.cpp; sourceTree = ""; }; + A7E9B74A12D37EC400DA6239 /* matrixoutputcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = matrixoutputcommand.h; sourceTree = ""; }; + A7E9B74B12D37EC400DA6239 /* memchi2.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = memchi2.cpp; sourceTree = ""; }; + A7E9B74C12D37EC400DA6239 /* memchi2.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = memchi2.h; sourceTree = ""; }; + A7E9B74D12D37EC400DA6239 /* memchord.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = memchord.cpp; sourceTree = ""; }; + A7E9B74E12D37EC400DA6239 /* memchord.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = memchord.h; sourceTree = ""; }; + A7E9B74F12D37EC400DA6239 /* memeuclidean.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = memeuclidean.cpp; sourceTree = ""; }; + A7E9B75012D37EC400DA6239 /* memeuclidean.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = memeuclidean.h; sourceTree = ""; }; + A7E9B75112D37EC400DA6239 /* mempearson.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mempearson.cpp; sourceTree = ""; }; + A7E9B75212D37EC400DA6239 /* mempearson.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mempearson.h; sourceTree = ""; }; + A7E9B75312D37EC400DA6239 /* mergefilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mergefilecommand.cpp; sourceTree = ""; }; + A7E9B75412D37EC400DA6239 /* mergefilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mergefilecommand.h; sourceTree = ""; }; + A7E9B75512D37EC400DA6239 /* metastats.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = metastats.h; sourceTree = ""; }; + A7E9B75612D37EC400DA6239 /* metastats2.c */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.c; path = metastats2.c; sourceTree = ""; }; + A7E9B75712D37EC400DA6239 /* metastatscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = metastatscommand.cpp; sourceTree = ""; }; + A7E9B75812D37EC400DA6239 /* metastatscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = metastatscommand.h; sourceTree = ""; }; + A7E9B75912D37EC400DA6239 /* mgclustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mgclustercommand.cpp; sourceTree = ""; }; + A7E9B75A12D37EC400DA6239 /* mgclustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mgclustercommand.h; sourceTree = ""; }; + A7E9B75B12D37EC400DA6239 /* mothur.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mothur.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B75C12D37EC400DA6239 /* mothur.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mothur.h; sourceTree = SOURCE_ROOT; }; + A7E9B75D12D37EC400DA6239 /* mothurout.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mothurout.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B75E12D37EC400DA6239 /* mothurout.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mothurout.h; sourceTree = SOURCE_ROOT; }; + A7E9B75F12D37EC400DA6239 /* nameassignment.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nameassignment.cpp; sourceTree = ""; }; + A7E9B76012D37EC400DA6239 /* nameassignment.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = nameassignment.hpp; sourceTree = ""; }; + A7E9B76112D37EC400DA6239 /* nast.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nast.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B76212D37EC400DA6239 /* nast.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = nast.hpp; sourceTree = SOURCE_ROOT; }; + A7E9B76312D37EC400DA6239 /* nastreport.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nastreport.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B76412D37EC400DA6239 /* nastreport.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = nastreport.hpp; sourceTree = SOURCE_ROOT; }; + A7E9B76512D37EC400DA6239 /* needlemanoverlap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = needlemanoverlap.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B76612D37EC400DA6239 /* needlemanoverlap.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = needlemanoverlap.hpp; sourceTree = SOURCE_ROOT; }; + A7E9B76712D37EC400DA6239 /* noalign.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = noalign.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B76812D37EC400DA6239 /* noalign.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = noalign.hpp; sourceTree = SOURCE_ROOT; }; + A7E9B76912D37EC400DA6239 /* nocommands.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nocommands.cpp; sourceTree = ""; }; + A7E9B76A12D37EC400DA6239 /* nocommands.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = nocommands.h; sourceTree = ""; }; + A7E9B76B12D37EC400DA6239 /* normalizesharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = normalizesharedcommand.cpp; sourceTree = ""; }; + A7E9B76C12D37EC400DA6239 /* normalizesharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = normalizesharedcommand.h; sourceTree = ""; }; + A7E9B76D12D37EC400DA6239 /* npshannon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = npshannon.cpp; sourceTree = ""; }; + A7E9B76E12D37EC400DA6239 /* npshannon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = npshannon.h; sourceTree = ""; }; + A7E9B76F12D37EC400DA6239 /* nseqs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = nseqs.h; sourceTree = ""; }; + A7E9B77012D37EC400DA6239 /* observable.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = observable.h; sourceTree = SOURCE_ROOT; }; + A7E9B77112D37EC400DA6239 /* odum.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = odum.cpp; sourceTree = ""; }; + A7E9B77212D37EC400DA6239 /* odum.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = odum.h; sourceTree = ""; }; + A7E9B77312D37EC400DA6239 /* onegapdist.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = onegapdist.h; sourceTree = ""; }; + A7E9B77412D37EC400DA6239 /* onegapignore.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = onegapignore.h; sourceTree = ""; }; + A7E9B77512D37EC400DA6239 /* optionparser.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = optionparser.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B77612D37EC400DA6239 /* optionparser.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = optionparser.h; sourceTree = SOURCE_ROOT; }; + A7E9B77712D37EC400DA6239 /* ordervector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ordervector.cpp; sourceTree = ""; }; + A7E9B77812D37EC400DA6239 /* ordervector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = ordervector.hpp; sourceTree = ""; }; + A7E9B77912D37EC400DA6239 /* otuhierarchycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = otuhierarchycommand.cpp; sourceTree = ""; }; + A7E9B77A12D37EC400DA6239 /* otuhierarchycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = otuhierarchycommand.h; sourceTree = ""; }; + A7E9B77B12D37EC400DA6239 /* overlap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = overlap.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B77C12D37EC400DA6239 /* overlap.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = overlap.hpp; sourceTree = SOURCE_ROOT; }; + A7E9B77D12D37EC400DA6239 /* pairwiseseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pairwiseseqscommand.cpp; sourceTree = ""; }; + A7E9B77E12D37EC400DA6239 /* pairwiseseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pairwiseseqscommand.h; sourceTree = ""; }; + A7E9B77F12D37EC400DA6239 /* parsefastaqcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsefastaqcommand.cpp; sourceTree = ""; }; + A7E9B78012D37EC400DA6239 /* parsefastaqcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsefastaqcommand.h; sourceTree = ""; }; + A7E9B78112D37EC400DA6239 /* parselistscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parselistscommand.cpp; sourceTree = ""; }; + A7E9B78212D37EC400DA6239 /* parselistscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parselistscommand.h; sourceTree = ""; }; + A7E9B78312D37EC400DA6239 /* parsimony.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsimony.cpp; sourceTree = ""; }; + A7E9B78412D37EC400DA6239 /* parsimony.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimony.h; sourceTree = ""; }; + A7E9B78512D37EC400DA6239 /* parsimonycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsimonycommand.cpp; sourceTree = ""; }; + A7E9B78612D37EC400DA6239 /* parsimonycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimonycommand.h; sourceTree = ""; }; + A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pcoacommand.cpp; sourceTree = ""; }; + A7E9B78812D37EC400DA6239 /* pcoacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pcoacommand.h; sourceTree = ""; }; + A7E9B78912D37EC400DA6239 /* phylodiversity.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylodiversity.cpp; sourceTree = ""; }; + A7E9B78A12D37EC400DA6239 /* phylodiversity.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylodiversity.h; sourceTree = ""; }; + A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylodiversitycommand.cpp; sourceTree = ""; }; + A7E9B78C12D37EC400DA6239 /* phylodiversitycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylodiversitycommand.h; sourceTree = ""; }; + A7E9B78D12D37EC400DA6239 /* phylosummary.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylosummary.cpp; sourceTree = ""; }; + A7E9B78E12D37EC400DA6239 /* phylosummary.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylosummary.h; sourceTree = ""; }; + A7E9B78F12D37EC400DA6239 /* phylotree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylotree.cpp; sourceTree = ""; }; + A7E9B79012D37EC400DA6239 /* phylotree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylotree.h; sourceTree = ""; }; + A7E9B79112D37EC400DA6239 /* phylotypecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylotypecommand.cpp; sourceTree = ""; }; + A7E9B79212D37EC400DA6239 /* phylotypecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylotypecommand.h; sourceTree = ""; }; + A7E9B79312D37EC400DA6239 /* pintail.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pintail.cpp; sourceTree = ""; }; + A7E9B79412D37EC400DA6239 /* pintail.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pintail.h; sourceTree = ""; }; + A7E9B79512D37EC400DA6239 /* pipelinepdscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pipelinepdscommand.cpp; sourceTree = ""; }; + A7E9B79612D37EC400DA6239 /* pipelinepdscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pipelinepdscommand.h; sourceTree = ""; }; + A7E9B79712D37EC400DA6239 /* preclustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = preclustercommand.cpp; sourceTree = ""; }; + A7E9B79812D37EC400DA6239 /* preclustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = preclustercommand.h; sourceTree = ""; }; + A7E9B79912D37EC400DA6239 /* prng.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = prng.cpp; sourceTree = ""; }; + A7E9B79A12D37EC400DA6239 /* prng.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = prng.h; sourceTree = ""; }; + A7E9B79B12D37EC400DA6239 /* progress.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = progress.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B79C12D37EC400DA6239 /* progress.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = progress.hpp; sourceTree = SOURCE_ROOT; }; + A7E9B79D12D37EC400DA6239 /* qstat.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = qstat.cpp; sourceTree = ""; }; + A7E9B79E12D37EC400DA6239 /* qstat.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = qstat.h; sourceTree = ""; }; + A7E9B79F12D37EC400DA6239 /* qualityscores.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = qualityscores.cpp; sourceTree = ""; }; + A7E9B7A012D37EC400DA6239 /* qualityscores.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = qualityscores.h; sourceTree = ""; }; + A7E9B7A112D37EC400DA6239 /* quitcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = quitcommand.cpp; sourceTree = ""; }; + A7E9B7A212D37EC400DA6239 /* quitcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = quitcommand.h; sourceTree = ""; }; + A7E9B7A312D37EC400DA6239 /* rabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rabundvector.cpp; sourceTree = ""; }; + A7E9B7A412D37EC400DA6239 /* rabundvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = rabundvector.hpp; sourceTree = ""; }; + A7E9B7A512D37EC400DA6239 /* rarecalc.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarecalc.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B7A612D37EC400DA6239 /* rarecalc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarecalc.h; sourceTree = SOURCE_ROOT; }; + A7E9B7A712D37EC400DA6239 /* raredisplay.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = raredisplay.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B7A812D37EC400DA6239 /* raredisplay.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = raredisplay.h; sourceTree = SOURCE_ROOT; }; + A7E9B7A912D37EC400DA6239 /* rarefact.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefact.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B7AA12D37EC400DA6239 /* rarefact.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefact.h; sourceTree = SOURCE_ROOT; }; + A7E9B7AB12D37EC400DA6239 /* rarefactcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefactcommand.cpp; sourceTree = ""; }; + A7E9B7AC12D37EC400DA6239 /* rarefactcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactcommand.h; sourceTree = ""; }; + A7E9B7AD12D37EC400DA6239 /* rarefactioncurvedata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactioncurvedata.h; sourceTree = SOURCE_ROOT; }; + A7E9B7AE12D37EC400DA6239 /* rarefactsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefactsharedcommand.cpp; sourceTree = ""; }; + A7E9B7AF12D37EC400DA6239 /* rarefactsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactsharedcommand.h; sourceTree = ""; }; + A7E9B7B012D37EC400DA6239 /* readblast.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readblast.cpp; sourceTree = ""; }; + A7E9B7B112D37EC400DA6239 /* readblast.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readblast.h; sourceTree = ""; }; + A7E9B7B212D37EC400DA6239 /* readcluster.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readcluster.cpp; sourceTree = ""; }; + A7E9B7B312D37EC400DA6239 /* readcluster.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readcluster.h; sourceTree = ""; }; + A7E9B7B412D37EC400DA6239 /* readcolumn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readcolumn.cpp; sourceTree = ""; }; + A7E9B7B512D37EC400DA6239 /* readcolumn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readcolumn.h; sourceTree = ""; }; + A7E9B7B612D37EC400DA6239 /* readdistcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readdistcommand.cpp; sourceTree = ""; }; + A7E9B7B712D37EC400DA6239 /* readdistcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readdistcommand.h; sourceTree = ""; }; + A7E9B7B812D37EC400DA6239 /* readmatrix.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = readmatrix.hpp; sourceTree = ""; }; + A7E9B7B912D37EC400DA6239 /* readotu.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readotu.cpp; sourceTree = ""; }; + A7E9B7BA12D37EC400DA6239 /* readotu.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotu.h; sourceTree = ""; }; + A7E9B7BB12D37EC400DA6239 /* readotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readotucommand.cpp; sourceTree = ""; }; + A7E9B7BC12D37EC400DA6239 /* readotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotucommand.h; sourceTree = ""; }; + A7E9B7BD12D37EC400DA6239 /* readphylip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readphylip.cpp; sourceTree = ""; }; + A7E9B7BE12D37EC400DA6239 /* readphylip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylip.h; sourceTree = ""; }; + A7E9B7BF12D37EC400DA6239 /* readtree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtree.cpp; sourceTree = ""; }; + A7E9B7C012D37EC400DA6239 /* readtree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtree.h; sourceTree = ""; }; + A7E9B7C112D37EC400DA6239 /* readtreecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtreecommand.cpp; sourceTree = ""; }; + A7E9B7C212D37EC400DA6239 /* readtreecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtreecommand.h; sourceTree = ""; }; + A7E9B7C312D37EC400DA6239 /* removegroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removegroupscommand.cpp; sourceTree = ""; }; + A7E9B7C412D37EC400DA6239 /* removegroupscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removegroupscommand.h; sourceTree = ""; }; + A7E9B7C512D37EC400DA6239 /* removelineagecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removelineagecommand.cpp; sourceTree = ""; }; + A7E9B7C612D37EC400DA6239 /* removelineagecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removelineagecommand.h; sourceTree = ""; }; + A7E9B7C712D37EC400DA6239 /* removeotuscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removeotuscommand.cpp; sourceTree = ""; }; + A7E9B7C812D37EC400DA6239 /* removeotuscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removeotuscommand.h; sourceTree = ""; }; + A7E9B7C912D37EC400DA6239 /* removeseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removeseqscommand.cpp; sourceTree = ""; }; + A7E9B7CA12D37EC400DA6239 /* removeseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removeseqscommand.h; sourceTree = ""; }; + A7E9B7CB12D37EC400DA6239 /* reportfile.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = reportfile.cpp; sourceTree = ""; }; + A7E9B7CC12D37EC400DA6239 /* reportfile.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = reportfile.h; sourceTree = ""; }; + A7E9B7CD12D37EC400DA6239 /* reversecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = reversecommand.cpp; sourceTree = ""; }; + A7E9B7CE12D37EC400DA6239 /* reversecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = reversecommand.h; sourceTree = ""; }; + A7E9B7CF12D37EC400DA6239 /* sabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sabundvector.cpp; sourceTree = ""; }; + A7E9B7D012D37EC400DA6239 /* sabundvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sabundvector.hpp; sourceTree = ""; }; + A7E9B7D112D37EC400DA6239 /* screenseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = screenseqscommand.cpp; sourceTree = ""; }; + A7E9B7D212D37EC400DA6239 /* screenseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = screenseqscommand.h; sourceTree = ""; }; + A7E9B7D312D37EC400DA6239 /* secondarystructurecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = secondarystructurecommand.cpp; sourceTree = ""; }; + A7E9B7D412D37EC400DA6239 /* secondarystructurecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = secondarystructurecommand.h; sourceTree = ""; }; + A7E9B7D512D37EC400DA6239 /* sensspeccommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sensspeccommand.cpp; sourceTree = ""; }; + A7E9B7D612D37EC400DA6239 /* sensspeccommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sensspeccommand.h; sourceTree = ""; }; + A7E9B7D712D37EC400DA6239 /* seqerrorcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = seqerrorcommand.cpp; sourceTree = ""; }; + A7E9B7D812D37EC400DA6239 /* seqerrorcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = seqerrorcommand.h; sourceTree = ""; }; + A7E9B7D912D37EC400DA6239 /* seqsummarycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = seqsummarycommand.cpp; sourceTree = ""; }; + A7E9B7DA12D37EC400DA6239 /* seqsummarycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = seqsummarycommand.h; sourceTree = ""; }; + A7E9B7DB12D37EC400DA6239 /* sequence.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sequence.cpp; sourceTree = ""; }; + A7E9B7DC12D37EC400DA6239 /* sequence.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sequence.hpp; sourceTree = ""; }; + A7E9B7DD12D37EC400DA6239 /* sequencedb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sequencedb.cpp; sourceTree = ""; }; + A7E9B7DE12D37EC400DA6239 /* sequencedb.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sequencedb.h; sourceTree = ""; }; + A7E9B7DF12D37EC400DA6239 /* setdircommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = setdircommand.cpp; sourceTree = ""; }; + A7E9B7E012D37EC400DA6239 /* setdircommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = setdircommand.h; sourceTree = ""; }; + A7E9B7E112D37EC400DA6239 /* setlogfilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = setlogfilecommand.cpp; sourceTree = ""; }; + A7E9B7E212D37EC400DA6239 /* setlogfilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = setlogfilecommand.h; sourceTree = ""; }; + A7E9B7E312D37EC400DA6239 /* sffinfocommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sffinfocommand.cpp; sourceTree = ""; }; + A7E9B7E412D37EC400DA6239 /* sffinfocommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sffinfocommand.h; sourceTree = ""; }; + A7E9B7E512D37EC400DA6239 /* shannon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shannon.cpp; sourceTree = ""; }; + A7E9B7E612D37EC400DA6239 /* shannon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shannon.h; sourceTree = ""; }; + A7E9B7E712D37EC400DA6239 /* shannoneven.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shannoneven.cpp; sourceTree = ""; }; + A7E9B7E812D37EC400DA6239 /* shannoneven.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shannoneven.h; sourceTree = ""; }; + A7E9B7E912D37EC400DA6239 /* sharedace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedace.cpp; sourceTree = ""; }; + A7E9B7EA12D37EC400DA6239 /* sharedace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedace.h; sourceTree = ""; }; + A7E9B7EB12D37EC400DA6239 /* sharedanderberg.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedanderberg.h; sourceTree = ""; }; + A7E9B7EC12D37EC400DA6239 /* sharedanderbergs.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedanderbergs.cpp; sourceTree = ""; }; + A7E9B7ED12D37EC400DA6239 /* sharedanderbergs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedanderbergs.h; sourceTree = ""; }; + A7E9B7EE12D37EC400DA6239 /* sharedbraycurtis.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedbraycurtis.cpp; sourceTree = ""; }; + A7E9B7EF12D37EC400DA6239 /* sharedbraycurtis.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedbraycurtis.h; sourceTree = ""; }; + A7E9B7F012D37EC400DA6239 /* sharedchao1.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedchao1.cpp; sourceTree = ""; }; + A7E9B7F112D37EC400DA6239 /* sharedchao1.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedchao1.h; sourceTree = ""; }; + A7E9B7F212D37EC400DA6239 /* sharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedcommand.cpp; sourceTree = ""; }; + A7E9B7F312D37EC400DA6239 /* sharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedcommand.h; sourceTree = ""; }; + A7E9B7F412D37EC400DA6239 /* sharedjabund.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjabund.cpp; sourceTree = ""; }; + A7E9B7F512D37EC400DA6239 /* sharedjabund.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjabund.h; sourceTree = ""; }; + A7E9B7F612D37EC400DA6239 /* sharedjackknife.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjackknife.cpp; sourceTree = ""; }; + A7E9B7F712D37EC400DA6239 /* sharedjackknife.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjackknife.h; sourceTree = ""; }; + A7E9B7F812D37EC400DA6239 /* sharedjclass.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjclass.cpp; sourceTree = ""; }; + A7E9B7F912D37EC400DA6239 /* sharedjclass.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjclass.h; sourceTree = ""; }; + A7E9B7FA12D37EC400DA6239 /* sharedjest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjest.cpp; sourceTree = ""; }; + A7E9B7FB12D37EC400DA6239 /* sharedjest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjest.h; sourceTree = ""; }; + A7E9B7FC12D37EC400DA6239 /* sharedkstest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedkstest.cpp; sourceTree = ""; }; + A7E9B7FD12D37EC400DA6239 /* sharedkstest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedkstest.h; sourceTree = ""; }; + A7E9B7FE12D37EC400DA6239 /* sharedkulczynski.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedkulczynski.cpp; sourceTree = ""; }; + A7E9B7FF12D37EC400DA6239 /* sharedkulczynski.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedkulczynski.h; sourceTree = ""; }; + A7E9B80012D37EC400DA6239 /* sharedkulczynskicody.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedkulczynskicody.cpp; sourceTree = ""; }; + A7E9B80112D37EC400DA6239 /* sharedkulczynskicody.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedkulczynskicody.h; sourceTree = ""; }; + A7E9B80212D37EC400DA6239 /* sharedlennon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedlennon.cpp; sourceTree = ""; }; + A7E9B80312D37EC400DA6239 /* sharedlennon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedlennon.h; sourceTree = ""; }; + A7E9B80412D37EC400DA6239 /* sharedlistvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedlistvector.cpp; sourceTree = ""; }; + A7E9B80512D37EC400DA6239 /* sharedlistvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedlistvector.h; sourceTree = ""; }; + A7E9B80612D37EC400DA6239 /* sharedmarczewski.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedmarczewski.cpp; sourceTree = ""; }; + A7E9B80712D37EC400DA6239 /* sharedmarczewski.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedmarczewski.h; sourceTree = ""; }; + A7E9B80812D37EC400DA6239 /* sharedmorisitahorn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedmorisitahorn.cpp; sourceTree = ""; }; + A7E9B80912D37EC400DA6239 /* sharedmorisitahorn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedmorisitahorn.h; sourceTree = ""; }; + A7E9B80A12D37EC400DA6239 /* sharednseqs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharednseqs.h; sourceTree = ""; }; + A7E9B80B12D37EC400DA6239 /* sharedochiai.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedochiai.cpp; sourceTree = ""; }; + A7E9B80C12D37EC400DA6239 /* sharedochiai.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedochiai.h; sourceTree = ""; }; + A7E9B80D12D37EC400DA6239 /* sharedordervector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedordervector.cpp; sourceTree = ""; }; + A7E9B80E12D37EC400DA6239 /* sharedordervector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedordervector.h; sourceTree = ""; }; + A7E9B80F12D37EC400DA6239 /* sharedrabundfloatvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedrabundfloatvector.cpp; sourceTree = ""; }; + A7E9B81012D37EC400DA6239 /* sharedrabundfloatvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedrabundfloatvector.h; sourceTree = ""; }; + A7E9B81112D37EC400DA6239 /* sharedrabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedrabundvector.cpp; sourceTree = ""; }; + A7E9B81212D37EC400DA6239 /* sharedrabundvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedrabundvector.h; sourceTree = ""; }; + A7E9B81312D37EC400DA6239 /* sharedsabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsabundvector.cpp; sourceTree = ""; }; + A7E9B81412D37EC400DA6239 /* sharedsabundvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsabundvector.h; sourceTree = ""; }; + A7E9B81512D37EC400DA6239 /* sharedsobs.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsobs.cpp; sourceTree = ""; }; + A7E9B81612D37EC400DA6239 /* sharedsobs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsobs.h; sourceTree = ""; }; + A7E9B81712D37EC400DA6239 /* sharedsobscollectsummary.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsobscollectsummary.cpp; sourceTree = ""; }; + A7E9B81812D37EC400DA6239 /* sharedsobscollectsummary.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsobscollectsummary.h; sourceTree = ""; }; + A7E9B81912D37EC400DA6239 /* sharedsorabund.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorabund.cpp; sourceTree = ""; }; + A7E9B81A12D37EC400DA6239 /* sharedsorabund.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsorabund.h; sourceTree = ""; }; + A7E9B81B12D37EC400DA6239 /* sharedsorclass.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorclass.cpp; sourceTree = ""; }; + A7E9B81C12D37EC400DA6239 /* sharedsorclass.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsorclass.h; sourceTree = ""; }; + A7E9B81D12D37EC400DA6239 /* sharedsorest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorest.cpp; sourceTree = ""; }; + A7E9B81E12D37EC400DA6239 /* sharedsorest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsorest.h; sourceTree = ""; }; + A7E9B81F12D37EC400DA6239 /* sharedthetan.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedthetan.cpp; sourceTree = ""; }; + A7E9B82012D37EC400DA6239 /* sharedthetan.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedthetan.h; sourceTree = ""; }; + A7E9B82112D37EC400DA6239 /* sharedthetayc.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedthetayc.cpp; sourceTree = ""; }; + A7E9B82212D37EC400DA6239 /* sharedthetayc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedthetayc.h; sourceTree = ""; }; + A7E9B82312D37EC400DA6239 /* sharedutilities.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedutilities.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B82412D37EC400DA6239 /* sharedutilities.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedutilities.h; sourceTree = SOURCE_ROOT; }; + A7E9B82512D37EC400DA6239 /* shen.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shen.cpp; sourceTree = ""; }; + A7E9B82612D37EC400DA6239 /* shen.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shen.h; sourceTree = ""; }; + A7E9B82712D37EC400DA6239 /* shhhercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shhhercommand.cpp; sourceTree = ""; }; + A7E9B82812D37EC400DA6239 /* shhhercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shhhercommand.h; sourceTree = ""; }; + A7E9B82912D37EC400DA6239 /* simpson.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = simpson.cpp; sourceTree = ""; }; + A7E9B82A12D37EC400DA6239 /* simpson.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = simpson.h; sourceTree = ""; }; + A7E9B82B12D37EC400DA6239 /* simpsoneven.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = simpsoneven.cpp; sourceTree = ""; }; + A7E9B82C12D37EC400DA6239 /* simpsoneven.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = simpsoneven.h; sourceTree = ""; }; + A7E9B82D12D37EC400DA6239 /* singlelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = singlelinkage.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B82E12D37EC400DA6239 /* slayer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = slayer.cpp; sourceTree = ""; }; + A7E9B82F12D37EC400DA6239 /* slayer.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = slayer.h; sourceTree = ""; }; + A7E9B83012D37EC400DA6239 /* slibshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = slibshuff.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B83112D37EC400DA6239 /* slibshuff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = slibshuff.h; sourceTree = SOURCE_ROOT; }; + A7E9B83212D37EC400DA6239 /* smithwilson.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = smithwilson.cpp; sourceTree = ""; }; + A7E9B83312D37EC400DA6239 /* smithwilson.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = smithwilson.h; sourceTree = ""; }; + A7E9B83412D37EC400DA6239 /* sobs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sobs.h; sourceTree = ""; }; + A7E9B83512D37EC400DA6239 /* soergel.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = soergel.cpp; sourceTree = ""; }; + A7E9B83612D37EC400DA6239 /* soergel.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = soergel.h; sourceTree = ""; }; + A7E9B83712D37EC400DA6239 /* solow.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = solow.cpp; sourceTree = ""; }; + A7E9B83812D37EC400DA6239 /* solow.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = solow.h; sourceTree = ""; }; + A7E9B83912D37EC400DA6239 /* sparsematrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sparsematrix.cpp; sourceTree = ""; }; + A7E9B83A12D37EC400DA6239 /* sparsematrix.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sparsematrix.hpp; sourceTree = ""; }; + A7E9B83B12D37EC400DA6239 /* spearman.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = spearman.cpp; sourceTree = ""; }; + A7E9B83C12D37EC400DA6239 /* spearman.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = spearman.h; sourceTree = ""; }; + A7E9B83D12D37EC400DA6239 /* speciesprofile.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = speciesprofile.cpp; sourceTree = ""; }; + A7E9B83E12D37EC400DA6239 /* speciesprofile.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = speciesprofile.h; sourceTree = ""; }; + A7E9B83F12D37EC400DA6239 /* splitabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = splitabundcommand.cpp; sourceTree = ""; }; + A7E9B84012D37EC400DA6239 /* splitabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = splitabundcommand.h; sourceTree = ""; }; + A7E9B84112D37EC400DA6239 /* splitgroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = splitgroupscommand.cpp; sourceTree = ""; }; + A7E9B84212D37EC400DA6239 /* splitgroupscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = splitgroupscommand.h; sourceTree = ""; }; + A7E9B84312D37EC400DA6239 /* splitmatrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = splitmatrix.cpp; sourceTree = ""; }; + A7E9B84412D37EC400DA6239 /* splitmatrix.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = splitmatrix.h; sourceTree = ""; }; + A7E9B84512D37EC400DA6239 /* structchi2.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = structchi2.cpp; sourceTree = ""; }; + A7E9B84612D37EC400DA6239 /* structchi2.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = structchi2.h; sourceTree = ""; }; + A7E9B84712D37EC400DA6239 /* structchord.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = structchord.cpp; sourceTree = ""; }; + A7E9B84812D37EC400DA6239 /* structchord.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = structchord.h; sourceTree = ""; }; + A7E9B84912D37EC400DA6239 /* structeuclidean.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = structeuclidean.cpp; sourceTree = ""; }; + A7E9B84A12D37EC400DA6239 /* structeuclidean.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = structeuclidean.h; sourceTree = ""; }; + A7E9B84B12D37EC400DA6239 /* structkulczynski.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = structkulczynski.cpp; sourceTree = ""; }; + A7E9B84C12D37EC400DA6239 /* structkulczynski.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = structkulczynski.h; sourceTree = ""; }; + A7E9B84D12D37EC400DA6239 /* structpearson.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = structpearson.cpp; sourceTree = ""; }; + A7E9B84E12D37EC400DA6239 /* structpearson.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = structpearson.h; sourceTree = ""; }; + A7E9B84F12D37EC400DA6239 /* subsamplecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = subsamplecommand.cpp; sourceTree = ""; }; + A7E9B85012D37EC400DA6239 /* subsamplecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = subsamplecommand.h; sourceTree = ""; }; + A7E9B85112D37EC400DA6239 /* suffixdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixdb.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B85212D37EC400DA6239 /* suffixdb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixdb.hpp; sourceTree = SOURCE_ROOT; }; + A7E9B85312D37EC400DA6239 /* suffixnodes.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixnodes.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B85412D37EC400DA6239 /* suffixnodes.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixnodes.hpp; sourceTree = SOURCE_ROOT; }; + A7E9B85512D37EC400DA6239 /* suffixtree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixtree.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B85612D37EC400DA6239 /* suffixtree.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixtree.hpp; sourceTree = SOURCE_ROOT; }; + A7E9B85712D37EC400DA6239 /* summarycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summarycommand.cpp; sourceTree = ""; }; + A7E9B85812D37EC400DA6239 /* summarycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarycommand.h; sourceTree = ""; }; + A7E9B85912D37EC400DA6239 /* summarysharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summarysharedcommand.cpp; sourceTree = ""; }; + A7E9B85A12D37EC400DA6239 /* summarysharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarysharedcommand.h; sourceTree = ""; }; + A7E9B85B12D37EC400DA6239 /* systemcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = systemcommand.cpp; sourceTree = ""; }; + A7E9B85C12D37EC400DA6239 /* systemcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = systemcommand.h; sourceTree = ""; }; + A7E9B85D12D37EC400DA6239 /* taxonomyequalizer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = taxonomyequalizer.cpp; sourceTree = ""; }; + A7E9B85E12D37EC400DA6239 /* taxonomyequalizer.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = taxonomyequalizer.h; sourceTree = ""; }; + A7E9B85F12D37EC400DA6239 /* tree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = tree.cpp; sourceTree = ""; }; + A7E9B86012D37EC400DA6239 /* tree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = tree.h; sourceTree = ""; }; + A7E9B86112D37EC400DA6239 /* treecalculator.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treecalculator.h; sourceTree = ""; }; + A7E9B86212D37EC400DA6239 /* treegroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treegroupscommand.cpp; sourceTree = ""; }; + A7E9B86312D37EC400DA6239 /* treegroupscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treegroupscommand.h; sourceTree = ""; }; + A7E9B86412D37EC400DA6239 /* treemap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treemap.cpp; sourceTree = ""; }; + A7E9B86512D37EC400DA6239 /* treemap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treemap.h; sourceTree = ""; }; + A7E9B86612D37EC400DA6239 /* treenode.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treenode.cpp; sourceTree = ""; }; + A7E9B86712D37EC400DA6239 /* treenode.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treenode.h; sourceTree = ""; }; + A7E9B86812D37EC400DA6239 /* trimflowscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = trimflowscommand.cpp; sourceTree = ""; }; + A7E9B86912D37EC400DA6239 /* trimflowscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = trimflowscommand.h; sourceTree = ""; }; + A7E9B86A12D37EC400DA6239 /* trimseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = trimseqscommand.cpp; sourceTree = ""; }; + A7E9B86B12D37EC400DA6239 /* trimseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = trimseqscommand.h; sourceTree = ""; }; + A7E9B86C12D37EC400DA6239 /* unifracunweightedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unifracunweightedcommand.cpp; sourceTree = ""; }; + A7E9B86D12D37EC400DA6239 /* unifracunweightedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unifracunweightedcommand.h; sourceTree = ""; }; + A7E9B86E12D37EC400DA6239 /* unifracweightedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unifracweightedcommand.cpp; sourceTree = ""; }; + A7E9B86F12D37EC400DA6239 /* unifracweightedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unifracweightedcommand.h; sourceTree = ""; }; + A7E9B87012D37EC400DA6239 /* unweighted.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unweighted.cpp; sourceTree = ""; }; + A7E9B87112D37EC400DA6239 /* unweighted.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unweighted.h; sourceTree = ""; }; + A7E9B87212D37EC400DA6239 /* uvest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = uvest.cpp; sourceTree = ""; }; + A7E9B87312D37EC400DA6239 /* uvest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = uvest.h; sourceTree = ""; }; + A7E9B87412D37EC400DA6239 /* validcalculator.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = validcalculator.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B87512D37EC400DA6239 /* validcalculator.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = validcalculator.h; sourceTree = SOURCE_ROOT; }; + A7E9B87612D37EC400DA6239 /* validparameter.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = validparameter.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B87712D37EC400DA6239 /* validparameter.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = validparameter.h; sourceTree = SOURCE_ROOT; }; + A7E9B87812D37EC400DA6239 /* venn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = venn.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B87912D37EC400DA6239 /* venn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = venn.h; sourceTree = SOURCE_ROOT; }; + A7E9B87A12D37EC400DA6239 /* venncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = venncommand.cpp; sourceTree = ""; }; + A7E9B87B12D37EC400DA6239 /* venncommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = venncommand.h; sourceTree = ""; }; + A7E9B87C12D37EC400DA6239 /* weighted.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = weighted.cpp; sourceTree = ""; }; + A7E9B87D12D37EC400DA6239 /* weighted.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = weighted.h; sourceTree = ""; }; + A7E9B87E12D37EC400DA6239 /* weightedlinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = weightedlinkage.cpp; sourceTree = SOURCE_ROOT; }; + A7E9B87F12D37EC400DA6239 /* whittaker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = whittaker.cpp; sourceTree = ""; }; + A7E9B88012D37EC400DA6239 /* whittaker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = whittaker.h; sourceTree = ""; }; + A7FC480C12D788F20055BC5C /* linearalgebra.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = linearalgebra.h; sourceTree = ""; }; + A7FC480D12D788F20055BC5C /* linearalgebra.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = linearalgebra.cpp; sourceTree = ""; }; + A7FC486512D795D60055BC5C /* pcacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pcacommand.h; sourceTree = ""; }; + A7FC486612D795D60055BC5C /* pcacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pcacommand.cpp; sourceTree = ""; }; + C6A0FF2C0290799A04C91782 /* mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = mothur.1; sourceTree = ""; }; /* End PBXFileReference section */ /* Begin PBXFrameworksBuildPhase section */ - 8DD76F660486A84900D96B5E /* Frameworks */ = { + 8DD76FAD0486AB0100D96B5E /* Frameworks */ = { isa = PBXFrameworksBuildPhase; buildActionMask = 2147483647; files = ( - A7F5759710CEBC0600E20E47 /* libreadline.a in Frameworks */, ); runOnlyForDeploymentPostprocessing = 0; }; /* End PBXFrameworksBuildPhase section */ /* Begin PBXGroup section */ - 08FB7794FE84155DC02AAC07 /* Mothur */ = { + 08FB7794FE84155DC02AAC07 /* mothur */ = { isa = PBXGroup; children = ( 08FB7795FE84155DC02AAC07 /* Source */, - C6859E8C029090F304C91782 /* Documentation */, + C6A0FF2B0290797F04C91782 /* Documentation */, 1AB674ADFE9D54B511CA2CBB /* Products */, ); - name = Mothur; + name = mothur; sourceTree = ""; }; 08FB7795FE84155DC02AAC07 /* Source */ = { isa = PBXGroup; children = ( - 37D927BA0F21331F001D4494 /* averagelinkage.cpp */, - 373C68DC0FC1C38D00137ACD /* blastalign.hpp */, - 373C68DB0FC1C38D00137ACD /* blastalign.cpp */, - 37D928A60F2133C0001D4494 /* calculators */, - 374F2FE81006346600E97C66 /* chimera */, - A787811210A073F40086103D /* classifiers */, - 37D927C20F21331F001D4494 /* cluster.hpp */, - 37D927C10F21331F001D4494 /* cluster.cpp */, - 37D928A90F2133E5001D4494 /* commands */, - 37D927C60F21331F001D4494 /* collect.h */, - 37D927C50F21331F001D4494 /* collect.cpp */, - 37D927C90F21331F001D4494 /* collectdisplay.h */, - 37D928AC0F213420001D4494 /* containers */, - 37D927CA0F21331F001D4494 /* collectorscurvedata.h */, - 37D927CF0F21331F001D4494 /* commandfactory.hpp */, - 372E12EC0F264D320095CF7E /* commandfactory.cpp */, - 37D927D10F21331F001D4494 /* commandoptionparser.hpp */, - 37D927D00F21331F001D4494 /* commandoptionparser.cpp */, - 37D927D20F21331F001D4494 /* completelinkage.cpp */, - 7E4130F70F8E58FA00381DD0 /* dlibshuff.h */, - 7E4130F60F8E58FA00381DD0 /* dlibshuff.cpp */, - 37D927D60F21331F001D4494 /* display.h */, - 37D927D80F21331F001D4494 /* engine.hpp */, - 37D927D70F21331F001D4494 /* engine.cpp */, - 37D928B10F213472001D4494 /* errorcheckor */, - 37D927DE0F21331F001D4494 /* fileoutput.h */, - 37D927DD0F21331F001D4494 /* fileoutput.cpp */, - 37D927E00F21331F001D4494 /* globaldata.hpp */, - 37D927DF0F21331F001D4494 /* globaldata.cpp */, - 373C68BB0FC1C1A600137ACD /* gotohoverlap.hpp */, - 373C68BA0FC1C1A600137ACD /* gotohoverlap.cpp */, - A729ACE210849BBE00139801 /* hcluster.h */, - A729ACE310849BBE00139801 /* hcluster.cpp */, - 375873ED0F7D646F0040F377 /* heatmap.h */, - 375873EE0F7D646F0040F377 /* heatmap.cpp */, - 378598720FDD4C1500EF9D03 /* heatmapsim.h */, - 378598730FDD4C1500EF9D03 /* heatmapsim.cpp */, - 37D927E60F21331F001D4494 /* inputdata.h */, - 37D927E50F21331F001D4494 /* inputdata.cpp */, - 7E412F420F8D213C00381DD0 /* libshuff.h */, - 7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */, - 37E3ED800F4D9D0D00B5DF02 /* mothur.h */, - 37D927EF0F21331F001D4494 /* mothur.cpp */, - 373C691E0FC1C98600137ACD /* nast.hpp */, - 373C691D0FC1C98600137ACD /* nast.cpp */, - 373C692A0FC1C9EB00137ACD /* nastreport.hpp */, - 373C69290FC1C9EB00137ACD /* nastreport.cpp */, - 373C68CE0FC1C2D900137ACD /* needlemanoverlap.hpp */, - 373C68CD0FC1C2D900137ACD /* needlemanoverlap.cpp */, - 373C68E40FC1C4A500137ACD /* noalign.hpp */, - 373C68E30FC1C4A500137ACD /* noalign.cpp */, - 37D927F60F21331F001D4494 /* observable.h */, - 3785990E0FDD7E8E00EF9D03 /* optionparser.h */, - 3785990F0FDD7E8E00EF9D03 /* optionparser.cpp */, - 373C68C40FC1C25F00137ACD /* overlap.hpp */, - 373C68C30FC1C25F00137ACD /* overlap.cpp */, - 37D927FC0F21331F001D4494 /* progress.hpp */, - 37D927FB0F21331F001D4494 /* progress.cpp */, - 37D928040F21331F001D4494 /* raredisplay.h */, - 37D928030F21331F001D4494 /* raredisplay.cpp */, - 37D928060F21331F001D4494 /* rarefact.h */, - 37D928050F21331F001D4494 /* rarefact.cpp */, - 37D928090F21331F001D4494 /* rarefactioncurvedata.h */, - 3796441D0FB9B9650081FDB6 /* read */, - 211C38310F961DD400FEE541 /* sharedutilities.h */, - 211C38300F961DD400FEE541 /* sharedutilities.cpp */, - 37D928420F21331F001D4494 /* singlelinkage.cpp */, - 7E412F470F8D21B600381DD0 /* slibshuff.h */, - 7E412F480F8D21B600381DD0 /* slibshuff.cpp */, - 37D928480F21331F001D4494 /* summarydata.h */, - 37D928490F21331F001D4494 /* summarydisplay.h */, - 37519AB30F810FAE00FED5E8 /* venn.h */, - 37519AB40F810FAE00FED5E8 /* venn.cpp */, - A7F5759610CEBC0600E20E47 /* libreadline.a */, + A7A61F1A130035C800E05B6B /* LICENSE */, + A70332B512D3A13400761E33 /* makefile */, + A7E9B65912D37EC300DA6239 /* averagelinkage.cpp */, + A7E9BA4F12D398D700DA6239 /* clearcut */, + A7E9B69812D37EC400DA6239 /* cluster.cpp */, + A7E9B69912D37EC400DA6239 /* cluster.hpp */, + A7E9B69A12D37EC400DA6239 /* clusterclassic.cpp */, + A7E9B69B12D37EC400DA6239 /* clusterclassic.h */, + A7E9BA3F12D395F700DA6239 /* calculators */, + A7E9BA4512D3965600DA6239 /* chimera */, + A7E9BA4B12D3966900DA6239 /* classifier */, + A7E9B6A612D37EC400DA6239 /* collect.cpp */, + A7E9B6A712D37EC400DA6239 /* collect.h */, + A7E9B6AA12D37EC400DA6239 /* collectdisplay.h */, + A7E9B6AB12D37EC400DA6239 /* collectorscurvedata.h */, + A7E9BA3812D3956100DA6239 /* commands */, + A7E9B6AF12D37EC400DA6239 /* commandfactory.cpp */, + A7E9B6B012D37EC400DA6239 /* commandfactory.hpp */, + A7E9B6B112D37EC400DA6239 /* commandoptionparser.cpp */, + A7E9B6B212D37EC400DA6239 /* commandoptionparser.hpp */, + A7E9B6B412D37EC400DA6239 /* completelinkage.cpp */, + A7E9BA4212D3960D00DA6239 /* containers */, + A7E9B6C912D37EC400DA6239 /* display.h */, + A7E9B6D112D37EC400DA6239 /* dlibshuff.cpp */, + A7E9B6D212D37EC400DA6239 /* dlibshuff.h */, + A7E9B6D912D37EC400DA6239 /* endiannessmacros.h */, + A7E9B6DA12D37EC400DA6239 /* engine.cpp */, + A7E9B6DB12D37EC400DA6239 /* engine.hpp */, + A7E9B6E012D37EC400DA6239 /* fileoutput.cpp */, + A7E9B6E112D37EC400DA6239 /* fileoutput.h */, + A7E9B70C12D37EC400DA6239 /* globaldata.cpp */, + A7E9B70D12D37EC400DA6239 /* globaldata.hpp */, + A7E9B71112D37EC400DA6239 /* gotohoverlap.hpp */, + A7E9B71012D37EC400DA6239 /* gotohoverlap.cpp */, + A7E9B71812D37EC400DA6239 /* hcluster.cpp */, + A7E9B71912D37EC400DA6239 /* hcluster.h */, + A7E9B71C12D37EC400DA6239 /* heatmap.cpp */, + A7E9B71D12D37EC400DA6239 /* heatmap.h */, + A7E9B72012D37EC400DA6239 /* heatmapsim.cpp */, + A7E9B72112D37EC400DA6239 /* heatmapsim.h */, + A7E9B72E12D37EC400DA6239 /* inputdata.h */, + A7E9B72D12D37EC400DA6239 /* inputdata.cpp */, + A7E9B73912D37EC400DA6239 /* libshuff.cpp */, + A7E9B73A12D37EC400DA6239 /* libshuff.h */, + A7FC480C12D788F20055BC5C /* linearalgebra.h */, + A7FC480D12D788F20055BC5C /* linearalgebra.cpp */, + A7E9BA5612D39BD800DA6239 /* metastats */, + A7E9B75B12D37EC400DA6239 /* mothur.cpp */, + A7E9B75C12D37EC400DA6239 /* mothur.h */, + A7E9B75D12D37EC400DA6239 /* mothurout.cpp */, + A7E9B75E12D37EC400DA6239 /* mothurout.h */, + A7E9B76112D37EC400DA6239 /* nast.cpp */, + A7E9B76212D37EC400DA6239 /* nast.hpp */, + A7E9B76312D37EC400DA6239 /* nastreport.cpp */, + A7E9B76412D37EC400DA6239 /* nastreport.hpp */, + A7E9B76712D37EC400DA6239 /* noalign.cpp */, + A7E9B76812D37EC400DA6239 /* noalign.hpp */, + A7E9B76512D37EC400DA6239 /* needlemanoverlap.cpp */, + A7E9B76612D37EC400DA6239 /* needlemanoverlap.hpp */, + A7E9B77012D37EC400DA6239 /* observable.h */, + A7E9B77512D37EC400DA6239 /* optionparser.cpp */, + A7E9B77612D37EC400DA6239 /* optionparser.h */, + A7E9B77B12D37EC400DA6239 /* overlap.cpp */, + A7E9B77C12D37EC400DA6239 /* overlap.hpp */, + A7E9B79B12D37EC400DA6239 /* progress.cpp */, + A7E9B79C12D37EC400DA6239 /* progress.hpp */, + A7E9B7A512D37EC400DA6239 /* rarecalc.cpp */, + A7E9B7A612D37EC400DA6239 /* rarecalc.h */, + A7E9B7A712D37EC400DA6239 /* raredisplay.cpp */, + A7E9B7A812D37EC400DA6239 /* raredisplay.h */, + A7E9B7A912D37EC400DA6239 /* rarefact.cpp */, + A7E9B7AA12D37EC400DA6239 /* rarefact.h */, + A7E9B7AD12D37EC400DA6239 /* rarefactioncurvedata.h */, + 7E6BE10812F710D8007ADDBE /* refchimeratest.h */, + 7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */, + A7E9BA5312D39A5E00DA6239 /* read */, + A7E9B82312D37EC400DA6239 /* sharedutilities.cpp */, + A7E9B82412D37EC400DA6239 /* sharedutilities.h */, + A7E9B82D12D37EC400DA6239 /* singlelinkage.cpp */, + A7E9B83012D37EC400DA6239 /* slibshuff.cpp */, + A7E9B83112D37EC400DA6239 /* slibshuff.h */, + A7E9B85112D37EC400DA6239 /* suffixdb.cpp */, + A7E9B85212D37EC400DA6239 /* suffixdb.hpp */, + A7E9B85312D37EC400DA6239 /* suffixnodes.cpp */, + A7E9B85412D37EC400DA6239 /* suffixnodes.hpp */, + A7E9B85512D37EC400DA6239 /* suffixtree.cpp */, + A7E9B85612D37EC400DA6239 /* suffixtree.hpp */, + A7E9B87412D37EC400DA6239 /* validcalculator.cpp */, + A7E9B87512D37EC400DA6239 /* validcalculator.h */, + A7E9B87612D37EC400DA6239 /* validparameter.cpp */, + A7E9B87712D37EC400DA6239 /* validparameter.h */, + A7E9B87812D37EC400DA6239 /* venn.cpp */, + A7E9B87912D37EC400DA6239 /* venn.h */, + A7E9B87E12D37EC400DA6239 /* weightedlinkage.cpp */, ); name = Source; sourceTree = ""; @@ -717,392 +1016,567 @@ 1AB674ADFE9D54B511CA2CBB /* Products */ = { isa = PBXGroup; children = ( - 8DD76F6C0486A84900D96B5E /* mothur */, + 8DD76FB20486AB0100D96B5E /* Mothur */, ); name = Products; sourceTree = ""; }; - 374F2FE81006346600E97C66 /* chimera */ = { + A7E9BA3812D3956100DA6239 /* commands */ = { isa = PBXGroup; children = ( - 374F2FD51006320200E97C66 /* chimera.h */, - 372095C1103196D70004D347 /* chimera.cpp */, - 374F2FE9100634B600E97C66 /* bellerophon.h */, - 374F2FEA100634B600E97C66 /* bellerophon.cpp */, - A75B887C104C16860083C454 /* ccode.h */, - A75B887B104C16860083C454 /* ccode.cpp */, - A7283FF61056CAE100D0CC69 /* chimeracheckrdp.h */, - A7283FF71056CAE100D0CC69 /* chimeracheckrdp.cpp */, - A7B04491106CC3E60046FC83 /* chimeraslayer.h */, - A7B04492106CC3E60046FC83 /* chimeraslayer.cpp */, - 372A55531017922B00C5194B /* decalc.h */, - 372A55541017922B00C5194B /* decalc.cpp */, - A7E4A822106A9AD700688F62 /* maligner.h */, - A7E4A823106A9AD700688F62 /* maligner.cpp */, - 374F301110063B6F00E97C66 /* pintail.h */, - 374F301210063B6F00E97C66 /* pintail.cpp */, - A7B0450C106CEEC90046FC83 /* slayer.h */, - A7B0450D106CEEC90046FC83 /* slayer.cpp */, + A7E9B6AE12D37EC400DA6239 /* command.hpp */, + A7E9B65112D37EC300DA6239 /* aligncommand.cpp */, + A7E9B65212D37EC300DA6239 /* aligncommand.h */, + A7A61F2B130062E000E05B6B /* amovacommand.h */, + A7A61F2C130062E000E05B6B /* amovacommand.cpp */, + A7E9B66012D37EC300DA6239 /* binsequencecommand.cpp */, + A7E9B66112D37EC300DA6239 /* binsequencecommand.h */, + A7E9B66A12D37EC400DA6239 /* bootstrapsharedcommand.cpp */, + A7E9B66B12D37EC400DA6239 /* bootstrapsharedcommand.h */, + A7E9B67212D37EC400DA6239 /* catchallcommand.cpp */, + A7E9B67312D37EC400DA6239 /* catchallcommand.h */, + A7E9B67A12D37EC400DA6239 /* chimerabellerophoncommand.cpp */, + A7E9B67B12D37EC400DA6239 /* chimerabellerophoncommand.h */, + A7E9B67C12D37EC400DA6239 /* chimeraccodecommand.cpp */, + A7E9B67D12D37EC400DA6239 /* chimeraccodecommand.h */, + A7E9B67E12D37EC400DA6239 /* chimeracheckcommand.cpp */, + A7E9B67F12D37EC400DA6239 /* chimeracheckcommand.h */, + A7E9B68212D37EC400DA6239 /* chimerapintailcommand.cpp */, + A7E9B68312D37EC400DA6239 /* chimerapintailcommand.h */, + A7E9B68612D37EC400DA6239 /* chimeraseqscommand.cpp */, + A7E9B68712D37EC400DA6239 /* chimeraseqscommand.h */, + A7E9B68A12D37EC400DA6239 /* chimeraslayercommand.cpp */, + A7E9B68B12D37EC400DA6239 /* chimeraslayercommand.h */, + A7E9B68C12D37EC400DA6239 /* chopseqscommand.cpp */, + A7E9B68D12D37EC400DA6239 /* chopseqscommand.h */, + A7E9B69012D37EC400DA6239 /* classifyotucommand.cpp */, + A7E9B69112D37EC400DA6239 /* classifyotucommand.h */, + A7E9B69212D37EC400DA6239 /* classifyseqscommand.cpp */, + A7E9B69312D37EC400DA6239 /* classifyseqscommand.h */, + A7E9B69612D37EC400DA6239 /* clearcutcommand.cpp */, + A7E9B69712D37EC400DA6239 /* clearcutcommand.h */, + A7E9B69C12D37EC400DA6239 /* clustercommand.cpp */, + A7E9B69D12D37EC400DA6239 /* clustercommand.h */, + A7E9B69E12D37EC400DA6239 /* clusterdoturcommand.cpp */, + A7E9B69F12D37EC400DA6239 /* clusterdoturcommand.h */, + A7E9B6A012D37EC400DA6239 /* clusterfragmentscommand.cpp */, + A7E9B6A112D37EC400DA6239 /* clusterfragmentscommand.h */, + A7E9B6A212D37EC400DA6239 /* clustersplitcommand.cpp */, + A7E9B6A312D37EC400DA6239 /* clustersplitcommand.h */, + A7E9B6A812D37EC400DA6239 /* collectcommand.cpp */, + A7E9B6A912D37EC400DA6239 /* collectcommand.h */, + A7E9B6AC12D37EC400DA6239 /* collectsharedcommand.cpp */, + A7E9B6AD12D37EC400DA6239 /* collectsharedcommand.h */, + A7E9B6B512D37EC400DA6239 /* consensuscommand.cpp */, + A7E9B6B612D37EC400DA6239 /* consensuscommand.h */, + A7E9B6B712D37EC400DA6239 /* consensusseqscommand.cpp */, + A7E9B6B812D37EC400DA6239 /* consensusseqscommand.h */, + A7E9B6B912D37EC400DA6239 /* corraxescommand.cpp */, + A7E9B6BA12D37EC400DA6239 /* corraxescommand.h */, + A7E9B6C312D37EC400DA6239 /* deconvolutecommand.cpp */, + A7E9B6C412D37EC400DA6239 /* deconvolutecommand.h */, + A7E9B6C512D37EC400DA6239 /* degapseqscommand.cpp */, + A7E9B6C612D37EC400DA6239 /* degapseqscommand.h */, + A7E9B6C712D37EC400DA6239 /* deuniqueseqscommand.cpp */, + A7E9B6C812D37EC400DA6239 /* deuniqueseqscommand.h */, + A7E9B6CB12D37EC400DA6239 /* distancecommand.cpp */, + A7E9B6CC12D37EC400DA6239 /* distancecommand.h */, + A7E9B6E312D37EC400DA6239 /* filterseqscommand.cpp */, + A7E9B6E412D37EC400DA6239 /* filterseqscommand.h */, + A7E9B6F212D37EC400DA6239 /* getgroupcommand.cpp */, + A7E9B6F312D37EC400DA6239 /* getgroupcommand.h */, + A7E9B6F412D37EC400DA6239 /* getgroupscommand.cpp */, + A7E9B6F512D37EC400DA6239 /* getgroupscommand.h */, + A7E9B6F612D37EC400DA6239 /* getlabelcommand.cpp */, + A7E9B6F712D37EC400DA6239 /* getlabelcommand.h */, + A7E9B6F812D37EC400DA6239 /* getlineagecommand.cpp */, + A7E9B6F912D37EC400DA6239 /* getlineagecommand.h */, + A7E9B6FA12D37EC400DA6239 /* getlistcountcommand.cpp */, + A7E9B6FB12D37EC400DA6239 /* getlistcountcommand.h */, + A7E9B6FE12D37EC400DA6239 /* getoturepcommand.cpp */, + A7E9B6FF12D37EC400DA6239 /* getoturepcommand.h */, + A7E9B70012D37EC400DA6239 /* getotuscommand.cpp */, + A7E9B70112D37EC400DA6239 /* getotuscommand.h */, + A7E9B70212D37EC400DA6239 /* getrabundcommand.cpp */, + A7E9B70312D37EC400DA6239 /* getrabundcommand.h */, + A7E9B70412D37EC400DA6239 /* getrelabundcommand.cpp */, + A7E9B70512D37EC400DA6239 /* getrelabundcommand.h */, + A7E9B70612D37EC400DA6239 /* getsabundcommand.cpp */, + A7E9B70712D37EC400DA6239 /* getsabundcommand.h */, + A7E9B70812D37EC400DA6239 /* getseqscommand.cpp */, + A7E9B70912D37EC400DA6239 /* getseqscommand.h */, + A7E9B70A12D37EC400DA6239 /* getsharedotucommand.cpp */, + A7E9B70B12D37EC400DA6239 /* getsharedotucommand.h */, + A7E9B71A12D37EC400DA6239 /* hclustercommand.cpp */, + A7E9B71B12D37EC400DA6239 /* hclustercommand.h */, + A7E9B71E12D37EC400DA6239 /* heatmapcommand.cpp */, + A7E9B71F12D37EC400DA6239 /* heatmapcommand.h */, + A7E9B72212D37EC400DA6239 /* heatmapsimcommand.cpp */, + A7E9B72312D37EC400DA6239 /* heatmapsimcommand.h */, + A7E9B72812D37EC400DA6239 /* helpcommand.cpp */, + A7E9B72912D37EC400DA6239 /* helpcommand.h */, + A75790571301749D00A30DAB /* homovacommand.h */, + A75790581301749D00A30DAB /* homovacommand.cpp */, + A7E9B72B12D37EC400DA6239 /* indicatorcommand.cpp */, + A7E9B72C12D37EC400DA6239 /* indicatorcommand.h */, + A7E9B73B12D37EC400DA6239 /* libshuffcommand.cpp */, + A7E9B73C12D37EC400DA6239 /* libshuffcommand.h */, + A7E9B73D12D37EC400DA6239 /* listseqscommand.cpp */, + A7E9B73E12D37EC400DA6239 /* listseqscommand.h */, + A7E9B74312D37EC400DA6239 /* makegroupcommand.cpp */, + A7E9B74412D37EC400DA6239 /* makegroupcommand.h */, + A7E9B74912D37EC400DA6239 /* matrixoutputcommand.cpp */, + A7E9B74A12D37EC400DA6239 /* matrixoutputcommand.h */, + A7E9B75312D37EC400DA6239 /* mergefilecommand.cpp */, + A7E9B75412D37EC400DA6239 /* mergefilecommand.h */, + A71FE12A12EDF72400963CA7 /* mergegroupscommand.h */, + A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */, + A7E9B75712D37EC400DA6239 /* metastatscommand.cpp */, + A7E9B75812D37EC400DA6239 /* metastatscommand.h */, + A7E9B75912D37EC400DA6239 /* mgclustercommand.cpp */, + A7E9B75A12D37EC400DA6239 /* mgclustercommand.h */, + A7E9B76A12D37EC400DA6239 /* nocommands.h */, + A7E9B76912D37EC400DA6239 /* nocommands.cpp */, + A7E9B76B12D37EC400DA6239 /* normalizesharedcommand.cpp */, + A7E9B76C12D37EC400DA6239 /* normalizesharedcommand.h */, + A713EBEB12DC7C5E000092AC /* nmdscommand.h */, + A713EBEC12DC7C5E000092AC /* nmdscommand.cpp */, + A7E9B77912D37EC400DA6239 /* otuhierarchycommand.cpp */, + A7E9B77A12D37EC400DA6239 /* otuhierarchycommand.h */, + A7E9B77D12D37EC400DA6239 /* pairwiseseqscommand.cpp */, + A7E9B77E12D37EC400DA6239 /* pairwiseseqscommand.h */, + A7E9B77F12D37EC400DA6239 /* parsefastaqcommand.cpp */, + A7E9B78012D37EC400DA6239 /* parsefastaqcommand.h */, + A7E9B78112D37EC400DA6239 /* parselistscommand.cpp */, + A7E9B78212D37EC400DA6239 /* parselistscommand.h */, + A7E9B78512D37EC400DA6239 /* parsimonycommand.cpp */, + A7E9B78612D37EC400DA6239 /* parsimonycommand.h */, + A7FC486512D795D60055BC5C /* pcacommand.h */, + A7FC486612D795D60055BC5C /* pcacommand.cpp */, + A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */, + A7E9B78812D37EC400DA6239 /* pcoacommand.h */, + A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */, + A7E9B78C12D37EC400DA6239 /* phylodiversitycommand.h */, + A7E9B79112D37EC400DA6239 /* phylotypecommand.cpp */, + A7E9B79212D37EC400DA6239 /* phylotypecommand.h */, + A7E9B79512D37EC400DA6239 /* pipelinepdscommand.cpp */, + A7E9B79612D37EC400DA6239 /* pipelinepdscommand.h */, + A7E9B79712D37EC400DA6239 /* preclustercommand.cpp */, + A7E9B79812D37EC400DA6239 /* preclustercommand.h */, + A7E9B7A112D37EC400DA6239 /* quitcommand.cpp */, + A7E9B7A212D37EC400DA6239 /* quitcommand.h */, + A7E9B7AB12D37EC400DA6239 /* rarefactcommand.cpp */, + A7E9B7AC12D37EC400DA6239 /* rarefactcommand.h */, + A7E9B7AE12D37EC400DA6239 /* rarefactsharedcommand.cpp */, + A7E9B7AF12D37EC400DA6239 /* rarefactsharedcommand.h */, + A7E9B7B612D37EC400DA6239 /* readdistcommand.cpp */, + A7E9B7B712D37EC400DA6239 /* readdistcommand.h */, + A7E9B7BB12D37EC400DA6239 /* readotucommand.cpp */, + A7E9B7BC12D37EC400DA6239 /* readotucommand.h */, + A7E9B7C112D37EC400DA6239 /* readtreecommand.cpp */, + A7E9B7C212D37EC400DA6239 /* readtreecommand.h */, + A7E9B7C312D37EC400DA6239 /* removegroupscommand.cpp */, + A7E9B7C412D37EC400DA6239 /* removegroupscommand.h */, + A7E9B7C512D37EC400DA6239 /* removelineagecommand.cpp */, + A7E9B7C612D37EC400DA6239 /* removelineagecommand.h */, + A7E9B7C712D37EC400DA6239 /* removeotuscommand.cpp */, + A7E9B7C812D37EC400DA6239 /* removeotuscommand.h */, + A727864212E9E28C00F86ABA /* removerarecommand.h */, + A727864312E9E28C00F86ABA /* removerarecommand.cpp */, + A7E9B7C912D37EC400DA6239 /* removeseqscommand.cpp */, + A7E9B7CA12D37EC400DA6239 /* removeseqscommand.h */, + A7E9B7CD12D37EC400DA6239 /* reversecommand.cpp */, + A7E9B7CE12D37EC400DA6239 /* reversecommand.h */, + A7E9B7D112D37EC400DA6239 /* screenseqscommand.cpp */, + A7E9B7D212D37EC400DA6239 /* screenseqscommand.h */, + A7E9B7D312D37EC400DA6239 /* secondarystructurecommand.cpp */, + A7E9B7D412D37EC400DA6239 /* secondarystructurecommand.h */, + A7E9B7D512D37EC400DA6239 /* sensspeccommand.cpp */, + A7E9B7D612D37EC400DA6239 /* sensspeccommand.h */, + A7E9B7D712D37EC400DA6239 /* seqerrorcommand.cpp */, + A7E9B7D812D37EC400DA6239 /* seqerrorcommand.h */, + A7E9B7D912D37EC400DA6239 /* seqsummarycommand.cpp */, + A7E9B7DA12D37EC400DA6239 /* seqsummarycommand.h */, + A7E9B7DF12D37EC400DA6239 /* setdircommand.cpp */, + A7E9B7E012D37EC400DA6239 /* setdircommand.h */, + A7E9B7E112D37EC400DA6239 /* setlogfilecommand.cpp */, + A7E9B7E212D37EC400DA6239 /* setlogfilecommand.h */, + A7E9B7E312D37EC400DA6239 /* sffinfocommand.cpp */, + A7E9B7E412D37EC400DA6239 /* sffinfocommand.h */, + A7E9B7F212D37EC400DA6239 /* sharedcommand.cpp */, + A7E9B7F312D37EC400DA6239 /* sharedcommand.h */, + A7E9B82712D37EC400DA6239 /* shhhercommand.cpp */, + A7E9B82812D37EC400DA6239 /* shhhercommand.h */, + A7E9B83F12D37EC400DA6239 /* splitabundcommand.cpp */, + A7E9B84012D37EC400DA6239 /* splitabundcommand.h */, + A7E9B84112D37EC400DA6239 /* splitgroupscommand.cpp */, + A7E9B84212D37EC400DA6239 /* splitgroupscommand.h */, + A7E9B84F12D37EC400DA6239 /* subsamplecommand.cpp */, + A7E9B85012D37EC400DA6239 /* subsamplecommand.h */, + A7E9B85712D37EC400DA6239 /* summarycommand.cpp */, + A7E9B85812D37EC400DA6239 /* summarycommand.h */, + A7E9B85912D37EC400DA6239 /* summarysharedcommand.cpp */, + A7E9B85A12D37EC400DA6239 /* summarysharedcommand.h */, + A7E9B85B12D37EC400DA6239 /* systemcommand.cpp */, + A7E9B85C12D37EC400DA6239 /* systemcommand.h */, + A7E9B86212D37EC400DA6239 /* treegroupscommand.cpp */, + A7E9B86312D37EC400DA6239 /* treegroupscommand.h */, + A7E9B86812D37EC400DA6239 /* trimflowscommand.cpp */, + A7E9B86912D37EC400DA6239 /* trimflowscommand.h */, + A7E9B86A12D37EC400DA6239 /* trimseqscommand.cpp */, + A7E9B86B12D37EC400DA6239 /* trimseqscommand.h */, + A7E9B86C12D37EC400DA6239 /* unifracunweightedcommand.cpp */, + A7E9B86D12D37EC400DA6239 /* unifracunweightedcommand.h */, + A7E9B86E12D37EC400DA6239 /* unifracweightedcommand.cpp */, + A7E9B86F12D37EC400DA6239 /* unifracweightedcommand.h */, + A7E9B87A12D37EC400DA6239 /* venncommand.cpp */, + A7E9B87B12D37EC400DA6239 /* venncommand.h */, ); - name = chimera; + name = commands; sourceTree = ""; }; - 3796441D0FB9B9650081FDB6 /* read */ = { + A7E9BA3F12D395F700DA6239 /* calculators */ = { isa = PBXGroup; children = ( - A7D86C6A10FE084300865661 /* formatmatrix.h */, - A7D86C7B10FE09AB00865661 /* formatcolumn.h */, - A7D86C7C10FE09AB00865661 /* formatcolumn.cpp */, - A7D86C8A10FE09FE00865661 /* formatphylip.h */, - A7D86C8B10FE09FE00865661 /* formatphylip.cpp */, - A727E84810D14568001A8432 /* readblast.h */, - A727E84910D14568001A8432 /* readblast.cpp */, - A751ACE81098B283003D0911 /* readcluster.h */, - A751ACE91098B283003D0911 /* readcluster.cpp */, - 375AA1340F9E433D008EF9B8 /* readcolumn.h */, - 375AA1330F9E433D008EF9B8 /* readcolumn.cpp */, - 37D928130F21331F001D4494 /* readmatrix.hpp */, - 375AA1360F9E433D008EF9B8 /* readotu.h */, - 375AA1350F9E433D008EF9B8 /* readotu.cpp */, - 375AA1380F9E433D008EF9B8 /* readphylip.h */, - 375AA1370F9E433D008EF9B8 /* readphylip.cpp */, - 37AD4DC80F28F3DD00AA2D49 /* readtree.h */, - 37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */, + A7E9B64F12D37EC300DA6239 /* ace.cpp */, + A7E9B65012D37EC300DA6239 /* ace.h */, + A7E9B65E12D37EC300DA6239 /* bergerparker.cpp */, + A7E9B65F12D37EC300DA6239 /* bergerparker.h */, + A7E9B66612D37EC400DA6239 /* boneh.cpp */, + A7E9B66712D37EC400DA6239 /* boneh.h */, + A7E9B66812D37EC400DA6239 /* bootstrap.cpp */, + A7E9B66912D37EC400DA6239 /* bootstrap.h */, + A7E9B66C12D37EC400DA6239 /* bstick.cpp */, + A7E9B66D12D37EC400DA6239 /* bstick.h */, + A7E9B66E12D37EC400DA6239 /* calculator.cpp */, + A7E9B66F12D37EC400DA6239 /* calculator.h */, + A7E9B67012D37EC400DA6239 /* canberra.cpp */, + A7E9B67112D37EC400DA6239 /* canberra.h */, + A7E9B67612D37EC400DA6239 /* chao1.cpp */, + A7E9B67712D37EC400DA6239 /* chao1.h */, + A7E9B6A412D37EC400DA6239 /* cmdargs.cpp */, + A7E9B6A512D37EC400DA6239 /* cmdargs.h */, + A7E9B6BB12D37EC400DA6239 /* coverage.cpp */, + A7E9B6BC12D37EC400DA6239 /* coverage.h */, + A7E9B6CA12D37EC400DA6239 /* dist.h */, + A7E9B6C012D37EC400DA6239 /* dayhoff.h */, + A7E9B6D512D37EC400DA6239 /* eachgapdist.h */, + A7E9B6D612D37EC400DA6239 /* eachgapignore.h */, + A7E9B6D712D37EC400DA6239 /* efron.cpp */, + A7E9B6D812D37EC400DA6239 /* efron.h */, + A7E9B6E212D37EC400DA6239 /* filters.h */, + A7E9B6E512D37EC400DA6239 /* fisher2.c */, + A7E9B6E612D37EC400DA6239 /* fisher2.h */, + A7E9B6F012D37EC400DA6239 /* geom.cpp */, + A7E9B6F112D37EC400DA6239 /* geom.h */, + A7E9B70E12D37EC400DA6239 /* goodscoverage.cpp */, + A7E9B70F12D37EC400DA6239 /* goodscoverage.h */, + A7E9B71212D37EC400DA6239 /* gower.cpp */, + A7E9B71312D37EC400DA6239 /* gower.h */, + A7E9B71612D37EC400DA6239 /* hamming.cpp */, + A7E9B71712D37EC400DA6239 /* hamming.h */, + A7E9B72412D37EC400DA6239 /* heip.cpp */, + A7E9B72512D37EC400DA6239 /* heip.h */, + A7E9B72612D37EC400DA6239 /* hellinger.cpp */, + A7E9B72712D37EC400DA6239 /* hellinger.h */, + A7E9B72A12D37EC400DA6239 /* ignoregaps.h */, + A7E9B72F12D37EC400DA6239 /* invsimpson.cpp */, + A7E9B73012D37EC400DA6239 /* invsimpson.h */, + A7E9B73112D37EC400DA6239 /* jackknife.cpp */, + A7E9B73212D37EC400DA6239 /* jackknife.h */, + A7E9B74112D37EC400DA6239 /* logsd.cpp */, + A7E9B74212D37EC400DA6239 /* logsd.h */, + A7E9B74712D37EC400DA6239 /* manhattan.cpp */, + A7E9B74812D37EC400DA6239 /* manhattan.h */, + A7E9B74B12D37EC400DA6239 /* memchi2.cpp */, + A7E9B74C12D37EC400DA6239 /* memchi2.h */, + A7E9B74D12D37EC400DA6239 /* memchord.cpp */, + A7E9B74E12D37EC400DA6239 /* memchord.h */, + A7E9B74F12D37EC400DA6239 /* memeuclidean.cpp */, + A7E9B75012D37EC400DA6239 /* memeuclidean.h */, + A7E9B75112D37EC400DA6239 /* mempearson.cpp */, + A7E9B75212D37EC400DA6239 /* mempearson.h */, + A7E9B76D12D37EC400DA6239 /* npshannon.cpp */, + A7E9B76E12D37EC400DA6239 /* npshannon.h */, + A7E9B76F12D37EC400DA6239 /* nseqs.h */, + A7E9B77112D37EC400DA6239 /* odum.cpp */, + A7E9B77212D37EC400DA6239 /* odum.h */, + A7E9B77312D37EC400DA6239 /* onegapdist.h */, + A7E9B77412D37EC400DA6239 /* onegapignore.h */, + A7E9B78412D37EC400DA6239 /* parsimony.h */, + A7E9B78312D37EC400DA6239 /* parsimony.cpp */, + A7E9B79912D37EC400DA6239 /* prng.cpp */, + A7E9B79A12D37EC400DA6239 /* prng.h */, + A7E9B79D12D37EC400DA6239 /* qstat.cpp */, + A7E9B79E12D37EC400DA6239 /* qstat.h */, + A7E9B7E512D37EC400DA6239 /* shannon.cpp */, + A7E9B7E612D37EC400DA6239 /* shannon.h */, + A7E9B7E712D37EC400DA6239 /* shannoneven.cpp */, + A7E9B7E812D37EC400DA6239 /* shannoneven.h */, + A7E9B7E912D37EC400DA6239 /* sharedace.cpp */, + A7E9B7EA12D37EC400DA6239 /* sharedace.h */, + A7E9B7EB12D37EC400DA6239 /* sharedanderberg.h */, + A7E9B7EC12D37EC400DA6239 /* sharedanderbergs.cpp */, + A7E9B7ED12D37EC400DA6239 /* sharedanderbergs.h */, + A7E9B7EE12D37EC400DA6239 /* sharedbraycurtis.cpp */, + A7E9B7EF12D37EC400DA6239 /* sharedbraycurtis.h */, + A7E9B7F012D37EC400DA6239 /* sharedchao1.cpp */, + A7E9B7F112D37EC400DA6239 /* sharedchao1.h */, + A7E9B7F412D37EC400DA6239 /* sharedjabund.cpp */, + A7E9B7F512D37EC400DA6239 /* sharedjabund.h */, + A7E9B7F612D37EC400DA6239 /* sharedjackknife.cpp */, + A7E9B7F712D37EC400DA6239 /* sharedjackknife.h */, + A7E9B7F812D37EC400DA6239 /* sharedjclass.cpp */, + A7E9B7F912D37EC400DA6239 /* sharedjclass.h */, + A7E9B7FA12D37EC400DA6239 /* sharedjest.cpp */, + A7E9B7FB12D37EC400DA6239 /* sharedjest.h */, + A7E9B7FC12D37EC400DA6239 /* sharedkstest.cpp */, + A7E9B7FD12D37EC400DA6239 /* sharedkstest.h */, + A7E9B7FE12D37EC400DA6239 /* sharedkulczynski.cpp */, + A7E9B7FF12D37EC400DA6239 /* sharedkulczynski.h */, + A7E9B80012D37EC400DA6239 /* sharedkulczynskicody.cpp */, + A7E9B80112D37EC400DA6239 /* sharedkulczynskicody.h */, + A7E9B80212D37EC400DA6239 /* sharedlennon.cpp */, + A7E9B80312D37EC400DA6239 /* sharedlennon.h */, + A7E9B80612D37EC400DA6239 /* sharedmarczewski.cpp */, + A7E9B80712D37EC400DA6239 /* sharedmarczewski.h */, + A7E9B80812D37EC400DA6239 /* sharedmorisitahorn.cpp */, + A7E9B80912D37EC400DA6239 /* sharedmorisitahorn.h */, + A7E9B80A12D37EC400DA6239 /* sharednseqs.h */, + A7E9B80B12D37EC400DA6239 /* sharedochiai.cpp */, + A7E9B80C12D37EC400DA6239 /* sharedochiai.h */, + A7E9B81512D37EC400DA6239 /* sharedsobs.cpp */, + A7E9B81612D37EC400DA6239 /* sharedsobs.h */, + A7E9B81712D37EC400DA6239 /* sharedsobscollectsummary.cpp */, + A7E9B81812D37EC400DA6239 /* sharedsobscollectsummary.h */, + A7E9B81912D37EC400DA6239 /* sharedsorabund.cpp */, + A7E9B81A12D37EC400DA6239 /* sharedsorabund.h */, + A7E9B81B12D37EC400DA6239 /* sharedsorclass.cpp */, + A7E9B81C12D37EC400DA6239 /* sharedsorclass.h */, + A7E9B81D12D37EC400DA6239 /* sharedsorest.cpp */, + A7E9B81E12D37EC400DA6239 /* sharedsorest.h */, + A7E9B81F12D37EC400DA6239 /* sharedthetan.cpp */, + A7E9B82012D37EC400DA6239 /* sharedthetan.h */, + A7E9B82112D37EC400DA6239 /* sharedthetayc.cpp */, + A7E9B82212D37EC400DA6239 /* sharedthetayc.h */, + A7E9B82512D37EC400DA6239 /* shen.cpp */, + A7E9B82612D37EC400DA6239 /* shen.h */, + A7E9B82912D37EC400DA6239 /* simpson.cpp */, + A7E9B82A12D37EC400DA6239 /* simpson.h */, + A7E9B82B12D37EC400DA6239 /* simpsoneven.cpp */, + A7E9B82C12D37EC400DA6239 /* simpsoneven.h */, + A7E9B83212D37EC400DA6239 /* smithwilson.cpp */, + A7E9B83312D37EC400DA6239 /* smithwilson.h */, + A7E9B83412D37EC400DA6239 /* sobs.h */, + A7E9B83512D37EC400DA6239 /* soergel.cpp */, + A7E9B83612D37EC400DA6239 /* soergel.h */, + A7E9B83712D37EC400DA6239 /* solow.cpp */, + A7E9B83812D37EC400DA6239 /* solow.h */, + A7E9B83B12D37EC400DA6239 /* spearman.cpp */, + A7E9B83C12D37EC400DA6239 /* spearman.h */, + A7E9B83D12D37EC400DA6239 /* speciesprofile.cpp */, + A7E9B83E12D37EC400DA6239 /* speciesprofile.h */, + A7E9B84512D37EC400DA6239 /* structchi2.cpp */, + A7E9B84612D37EC400DA6239 /* structchi2.h */, + A7E9B84712D37EC400DA6239 /* structchord.cpp */, + A7E9B84812D37EC400DA6239 /* structchord.h */, + A7E9B84912D37EC400DA6239 /* structeuclidean.cpp */, + A7E9B84A12D37EC400DA6239 /* structeuclidean.h */, + A7E9B84B12D37EC400DA6239 /* structkulczynski.cpp */, + A7E9B84C12D37EC400DA6239 /* structkulczynski.h */, + A7E9B84D12D37EC400DA6239 /* structpearson.cpp */, + A7E9B84E12D37EC400DA6239 /* structpearson.h */, + A7E9B86112D37EC400DA6239 /* treecalculator.h */, + A7E9B87012D37EC400DA6239 /* unweighted.cpp */, + A7E9B87112D37EC400DA6239 /* unweighted.h */, + A7E9B87212D37EC400DA6239 /* uvest.cpp */, + A7E9B87312D37EC400DA6239 /* uvest.h */, + A7E9B87C12D37EC400DA6239 /* weighted.cpp */, + A7E9B87D12D37EC400DA6239 /* weighted.h */, + A7E9B87F12D37EC400DA6239 /* whittaker.cpp */, + A7E9B88012D37EC400DA6239 /* whittaker.h */, ); - name = read; + name = calculators; sourceTree = ""; }; - 37D928A60F2133C0001D4494 /* calculators */ = { + A7E9BA4212D3960D00DA6239 /* containers */ = { isa = PBXGroup; children = ( - 37D927BE0F21331F001D4494 /* calculator.h */, - 37D927BD0F21331F001D4494 /* calculator.cpp */, - 3792948D0F2E271100B9034A /* treecalculator.h */, - 37D927B90F21331F001D4494 /* ace.h */, - 37D927B80F21331F001D4494 /* ace.cpp */, - EB1216860F619B83004A865F /* bergerparker.h */, - EB1216870F619B83004A865F /* bergerparker.cpp */, - 373C69950FC1E63600137ACD /* boneh.h */, - 373C69940FC1E63600137ACD /* boneh.cpp */, - 37D927BC0F21331F001D4494 /* bootstrap.h */, - 37D927BB0F21331F001D4494 /* bootstrap.cpp */, - EB1216E30F61ACFB004A865F /* bstick.h */, - EB1216E40F61ACFB004A865F /* bstick.cpp */, - 37D927C00F21331F001D4494 /* chao1.h */, - 37D927BF0F21331F001D4494 /* chao1.cpp */, - 7EC3D4510FA0FFF900338DA5 /* coverage.h */, - 7EC3D4500FA0FFF900338DA5 /* coverage.cpp */, - 37C753DF0FB3492400DBD02E /* dist.h */, - 37C753F00FB34AE800DBD02E /* eachgapdist.h */, - 37C753F40FB34C0300DBD02E /* eachgapignore.h */, - 373C69960FC1E63600137ACD /* efron.cpp */, - 373C69970FC1E63600137ACD /* efron.h */, - 379D3D6B0FF917F40068C1C0 /* filters.h */, - EB9303F70F53517300E8EF26 /* geom.h */, - EB9303F80F53517300E8EF26 /* geom.cpp */, - 378C1AF10FB0644D004D63F5 /* goodscoverage.h */, - 378C1AF00FB0644D004D63F5 /* goodscoverage.cpp */, - 37C753ED0FB34A5700DBD02E /* ignoregaps.h */, - 37D927E80F21331F001D4494 /* jackknife.h */, - 37D927E70F21331F001D4494 /* jackknife.cpp */, - EB9303E90F534D9400E8EF26 /* logsd.h */, - EB9303EA0F534D9400E8EF26 /* logsd.cpp */, - 375873F90F7D64AB0040F377 /* nseqs.h */, - 37D927F50F21331F001D4494 /* npshannon.h */, - 37D927F40F21331F001D4494 /* npshannon.cpp */, - 37C753F10FB34B4700DBD02E /* onegapdist.h */, - 37C753F30FB34BBF00DBD02E /* onegapignore.h */, - 379294880F2E258500B9034A /* parsimony.h */, - 379294890F2E258500B9034A /* parsimony.cpp */, - EB6E68170F5F1C780044E17B /* qstat.h */, - EB6E68180F5F1C780044E17B /* qstat.cpp */, - 37D928020F21331F001D4494 /* rarecalc.h */, - 37D928010F21331F001D4494 /* rarecalc.cpp */, - 37D9281F0F21331F001D4494 /* shannon.h */, - 37D9281E0F21331F001D4494 /* shannon.cpp */, - 37D928230F21331F001D4494 /* sharedace.h */, - 37D928220F21331F001D4494 /* sharedace.cpp */, - 37519A690F80E6EB00FED5E8 /* sharedanderbergs.h */, - 37519A6A0F80E6EB00FED5E8 /* sharedanderbergs.cpp */, - 7EC3D4520FA0FFF900338DA5 /* sharedanderberg.h */, - 375873FB0F7D64DA0040F377 /* sharedbraycurtis.h */, - 375873FC0F7D64DA0040F377 /* sharedbraycurtis.cpp */, - 37D928250F21331F001D4494 /* sharedchao1.h */, - 37D928240F21331F001D4494 /* sharedchao1.cpp */, - 37D928290F21331F001D4494 /* sharedjabund.h */, - 37D928280F21331F001D4494 /* sharedjabund.cpp */, - 378C1B000FB0644D004D63F5 /* sharedjackknife.h */, - 378C1AFF0FB0644D004D63F5 /* sharedjackknife.cpp */, - 37D9282B0F21331F001D4494 /* sharedjclass.h */, - 37D9282A0F21331F001D4494 /* sharedjclass.cpp */, - 37D9282D0F21331F001D4494 /* sharedjest.h */, - 37D9282C0F21331F001D4494 /* sharedjest.cpp */, - EB1217210F61C9AC004A865F /* sharedkstest.h */, - EB1217220F61C9AC004A865F /* sharedkstest.cpp */, - 375874000F7D64EF0040F377 /* sharedkulczynski.h */, - 375873FE0F7D64EF0040F377 /* sharedkulczynski.cpp */, - 375874030F7D64EF0040F377 /* sharedkulczynskicody.h */, - 375874020F7D64EF0040F377 /* sharedkulczynskicody.cpp */, - 375874010F7D64EF0040F377 /* sharedlennon.h */, - 375873FF0F7D64EF0040F377 /* sharedlennon.cpp */, - 378C1B020FB0644D004D63F5 /* sharedmarczewski.h */, - 378C1B010FB0644D004D63F5 /* sharedmarczewski.cpp */, - 375874070F7D64FC0040F377 /* sharedmorisitahorn.h */, - 375874080F7D64FC0040F377 /* sharedmorisitahorn.cpp */, - 375874090F7D64FC0040F377 /* sharedochiai.h */, - 3758740B0F7D64FC0040F377 /* sharedochiai.cpp */, - 3758740A0F7D64FC0040F377 /* sharednseqs.h */, - 37D928350F21331F001D4494 /* sharedsobs.h */, - 37D928340F21331F001D4494 /* sharedsobs.cpp */, - 37AFC71D0F445386005F492D /* sharedsobscollectsummary.h */, - 37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */, - 37D928370F21331F001D4494 /* sharedsorabund.h */, - 37D928360F21331F001D4494 /* sharedsorabund.cpp */, - 37D928390F21331F001D4494 /* sharedsorclass.h */, - 37D928380F21331F001D4494 /* sharedsorclass.cpp */, - 37D9283B0F21331F001D4494 /* sharedsorest.h */, - 37D9283A0F21331F001D4494 /* sharedsorest.cpp */, - 37D9283D0F21331F001D4494 /* sharedthetan.h */, - 37D9283C0F21331F001D4494 /* sharedthetan.cpp */, - 37D9283F0F21331F001D4494 /* sharedthetayc.h */, - 37D9283E0F21331F001D4494 /* sharedthetayc.cpp */, - EB72FE250FC1F5CA0051AC11 /* shen.h */, - EB72FE240FC1F5CA0051AC11 /* shen.cpp */, - 37D928410F21331F001D4494 /* simpson.h */, - 37D928400F21331F001D4494 /* simpson.cpp */, - 37D928430F21331F001D4494 /* sobs.h */, - 373C69980FC1E63600137ACD /* solow.cpp */, - 373C69990FC1E63600137ACD /* solow.h */, - 374610810F40652400460C57 /* unweighted.h */, - 374610820F40652400460C57 /* unweighted.cpp */, - 37D9284E0F21331F001D4494 /* uvest.h */, - 37D9284D0F21331F001D4494 /* uvest.cpp */, - 3746107C0F4064D100460C57 /* weighted.h */, - 3746107D0F4064D100460C57 /* weighted.cpp */, - 7EC3D4540FA0FFF900338DA5 /* whittaker.h */, - 7EC3D4530FA0FFF900338DA5 /* whittaker.cpp */, + A7E9B65312D37EC300DA6239 /* alignment.cpp */, + A7E9B65412D37EC300DA6239 /* alignment.hpp */, + A7E9B65512D37EC300DA6239 /* alignmentcell.cpp */, + A7E9B65612D37EC300DA6239 /* alignmentcell.hpp */, + A7E9B65712D37EC300DA6239 /* alignmentdb.cpp */, + A7E9B65812D37EC300DA6239 /* alignmentdb.h */, + A7E9B66212D37EC300DA6239 /* blastalign.cpp */, + A7E9B66312D37EC400DA6239 /* blastalign.hpp */, + A7E9B66412D37EC400DA6239 /* blastdb.cpp */, + A7E9B66512D37EC400DA6239 /* blastdb.hpp */, + A7E9B6BD12D37EC400DA6239 /* database.cpp */, + A7E9B6BE12D37EC400DA6239 /* database.hpp */, + A7E9B6BF12D37EC400DA6239 /* datavector.hpp */, + A7E9B6CD12D37EC400DA6239 /* distancedb.cpp */, + A7E9B6CE12D37EC400DA6239 /* distancedb.hpp */, + A7E9B6DE12D37EC400DA6239 /* fastamap.cpp */, + A7E9B6DF12D37EC400DA6239 /* fastamap.h */, + A7E9B6E812D37EC400DA6239 /* flowdata.h */, + A7E9B6E712D37EC400DA6239 /* flowdata.cpp */, + A7E9B6EE12D37EC400DA6239 /* fullmatrix.cpp */, + A7E9B6EF12D37EC400DA6239 /* fullmatrix.h */, + A7E9B71412D37EC400DA6239 /* groupmap.cpp */, + A7E9B71512D37EC400DA6239 /* groupmap.h */, + A7E9B73312D37EC400DA6239 /* kmer.cpp */, + A7E9B73412D37EC400DA6239 /* kmer.hpp */, + A7E9B73512D37EC400DA6239 /* kmerdb.cpp */, + A7E9B73612D37EC400DA6239 /* kmerdb.hpp */, + A7E9B73F12D37EC400DA6239 /* listvector.cpp */, + A7E9B74012D37EC400DA6239 /* listvector.hpp */, + A7E9B75F12D37EC400DA6239 /* nameassignment.cpp */, + A7E9B76012D37EC400DA6239 /* nameassignment.hpp */, + A7E9B77712D37EC400DA6239 /* ordervector.cpp */, + A7E9B77812D37EC400DA6239 /* ordervector.hpp */, + A7E9B79F12D37EC400DA6239 /* qualityscores.cpp */, + A7E9B7A012D37EC400DA6239 /* qualityscores.h */, + A7E9B7A312D37EC400DA6239 /* rabundvector.cpp */, + A7E9B7A412D37EC400DA6239 /* rabundvector.hpp */, + A7E9B7CB12D37EC400DA6239 /* reportfile.cpp */, + A7E9B7CC12D37EC400DA6239 /* reportfile.h */, + A7E9B7CF12D37EC400DA6239 /* sabundvector.cpp */, + A7E9B7D012D37EC400DA6239 /* sabundvector.hpp */, + A7E9B7DB12D37EC400DA6239 /* sequence.cpp */, + A7E9B7DC12D37EC400DA6239 /* sequence.hpp */, + A7E9B7DD12D37EC400DA6239 /* sequencedb.cpp */, + A7E9B7DE12D37EC400DA6239 /* sequencedb.h */, + A7E9B80412D37EC400DA6239 /* sharedlistvector.cpp */, + A7E9B80512D37EC400DA6239 /* sharedlistvector.h */, + A7E9B80D12D37EC400DA6239 /* sharedordervector.cpp */, + A7E9B80E12D37EC400DA6239 /* sharedordervector.h */, + A7E9B80F12D37EC400DA6239 /* sharedrabundfloatvector.cpp */, + A7E9B81012D37EC400DA6239 /* sharedrabundfloatvector.h */, + A7E9B81112D37EC400DA6239 /* sharedrabundvector.cpp */, + A7E9B81212D37EC400DA6239 /* sharedrabundvector.h */, + A7E9B81312D37EC400DA6239 /* sharedsabundvector.cpp */, + A7E9B81412D37EC400DA6239 /* sharedsabundvector.h */, + A7E9B83912D37EC400DA6239 /* sparsematrix.cpp */, + A7E9B83A12D37EC400DA6239 /* sparsematrix.hpp */, + A7E9B85F12D37EC400DA6239 /* tree.cpp */, + A7E9B86012D37EC400DA6239 /* tree.h */, + A7E9B86412D37EC400DA6239 /* treemap.cpp */, + A7E9B86512D37EC400DA6239 /* treemap.h */, + A7E9B86612D37EC400DA6239 /* treenode.cpp */, + A7E9B86712D37EC400DA6239 /* treenode.h */, ); - name = calculators; + name = containers; sourceTree = ""; }; - 37D928A90F2133E5001D4494 /* commands */ = { + A7E9BA4512D3965600DA6239 /* chimera */ = { isa = PBXGroup; children = ( - 37D927CD0F21331F001D4494 /* command.hpp */, - 378DC5CD0FBDE1C8003B8607 /* aligncommand.h */, - 378DC5CE0FBDE1C8003B8607 /* aligncommand.cpp */, - 37C1D9710F86506E0059E3F0 /* binsequencecommand.h */, - 37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */, - 21DDC0190F97A8FE0060691C /* bootstrapsharedcommand.h */, - 21DDC01A0F97A8FE0060691C /* bootstrapsharedcommand.cpp */, - 37D927C40F21331F001D4494 /* clustercommand.h */, - 37D927C30F21331F001D4494 /* clustercommand.cpp */, - 37D927C80F21331F001D4494 /* collectcommand.h */, - 37D927C70F21331F001D4494 /* collectcommand.cpp */, - 37D927CC0F21331F001D4494 /* collectsharedcommand.h */, - 37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */, - 377326640FAF16E0007ABB8B /* consensuscommand.h */, - 377326630FAF16E0007ABB8B /* consensuscommand.cpp */, - 379D3D4F0FF90E090068C1C0 /* chimeraseqscommand.h */, - 379D3D500FF90E090068C1C0 /* chimeraseqscommand.cpp */, - A7861476109F5FA00010AAAF /* classifyseqscommand.h */, - A7861477109F5FA00010AAAF /* classifyseqscommand.cpp */, - 37B28F660F27590100808A62 /* deconvolutecommand.h */, - 37B28F670F27590100808A62 /* deconvolutecommand.cpp */, - 37C753CC0FB3415200DBD02E /* distancecommand.h */, - 37C753CD0FB3415200DBD02E /* distancecommand.cpp */, - 378C1AEF0FB0644D004D63F5 /* filterseqscommand.h */, - 378C1AEE0FB0644D004D63F5 /* filterseqscommand.cpp */, - A70B53A50F4CD7AD0064797E /* getgroupcommand.h */, - A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */, - A70B53A70F4CD7AD0064797E /* getlabelcommand.h */, - A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */, - A73329CD1083B3B3003B10C5 /* getlistcountcommand.h */, - A73329CE1083B3B3003B10C5 /* getlistcountcommand.cpp */, - 370B88050F8A4EE4005AB382 /* getoturepcommand.h */, - 370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */, - 3749273D0FD5956B0031C06B /* getrabundcommand.h */, - 3749273E0FD5956B0031C06B /* getrabundcommand.cpp */, - 3749271B0FD58C840031C06B /* getsabundcommand.h */, - 3749271C0FD58C840031C06B /* getsabundcommand.cpp */, - 37B73CA41004D89A008C4B41 /* getseqscommand.h */, - 37B73CA51004D89A008C4B41 /* getseqscommand.cpp */, - A7E4A781106913F900688F62 /* getsharedotucommand.h */, - A7E4A782106913F900688F62 /* getsharedotucommand.cpp */, - A729ACCE10848E6100139801 /* hclustercommand.h */, - A729ACCF10848E6100139801 /* hclustercommand.cpp */, - 375873F10F7D64800040F377 /* heatmapcommand.h */, - 375873F00F7D64800040F377 /* heatmapcommand.cpp */, - 378598640FDD497000EF9D03 /* heatmapsimcommand.h */, - 378598650FDD497000EF9D03 /* heatmapsimcommand.cpp */, - 37D927E40F21331F001D4494 /* helpcommand.h */, - 37D927E30F21331F001D4494 /* helpcommand.cpp */, - 375873F40F7D648F0040F377 /* libshuffcommand.h */, - 375873F30F7D648F0040F377 /* libshuffcommand.cpp */, - 37B73C741004BEFD008C4B41 /* listseqscommand.h */, - 37B73C751004BEFD008C4B41 /* listseqscommand.cpp */, - 21E859D60FC4632E005E1A48 /* matrixoutputcommand.h */, - 21E859D70FC4632E005E1A48 /* matrixoutputcommand.cpp */, - 7E5A17AD0FE57292003C6A03 /* mergefilecommand.h */, - 7E5A17AE0FE57292003C6A03 /* mergefilecommand.cpp */, - A7E0AAB410D2886D00CF407B /* mgclustercommand.h */, - A7E0AAB510D2886D00CF407B /* mgclustercommand.cpp */, - 375873F70F7D649C0040F377 /* nocommands.h */, - 375873F60F7D649C0040F377 /* nocommands.cpp */, - A704E8A11106045D00870157 /* otuhierarchycommand.h */, - A704E8A21106045D00870157 /* otuhierarchycommand.cpp */, - 3792946E0F2E191800B9034A /* parsimonycommand.h */, - 3792946F0F2E191800B9034A /* parsimonycommand.cpp */, - A7D176CD10F2558500159497 /* pcacommand.h */, - A7D176CE10F2558500159497 /* pcacommand.cpp */, - A773808E10B6EFD1002A6A61 /* phylotypecommand.h */, - A773808F10B6EFD1002A6A61 /* phylotypecommand.cpp */, - A7027F2610DFF86D00BF45FE /* preclustercommand.h */, - A7027F2710DFF86D00BF45FE /* preclustercommand.cpp */, - 37D927FE0F21331F001D4494 /* quitcommand.h */, - 37D927FD0F21331F001D4494 /* quitcommand.cpp */, - 37D928080F21331F001D4494 /* rarefactcommand.h */, - 37D928070F21331F001D4494 /* rarefactcommand.cpp */, - 37D9280B0F21331F001D4494 /* rarefactsharedcommand.h */, - 37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */, - 372E12940F263D5A0095CF7E /* readdistcommand.h */, - 372E12950F263D5A0095CF7E /* readdistcommand.cpp */, - 372E126E0F26365B0095CF7E /* readotucommand.h */, - 372E126F0F26365B0095CF7E /* readotucommand.cpp */, - 37E5F4900F2A3DA800F8D827 /* readtreecommand.h */, - 37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */, - 37B73CBE1004EB38008C4B41 /* removeseqscommand.h */, - 37B73CBF1004EB38008C4B41 /* removeseqscommand.cpp */, - 7E09C5120FDA79C5002ECAE5 /* reversecommand.h */, - 7E09C5130FDA79C5002ECAE5 /* reversecommand.cpp */, - A70DECD71063D8B40057C03C /* secondarystructurecommand.h */, - A70DECD81063D8B40057C03C /* secondarystructurecommand.cpp */, - 371B30B30FD7EE67000414CA /* screenseqscommand.h */, - 371B30B20FD7EE67000414CA /* screenseqscommand.cpp */, - 3799A94F0FD6A58C00E33EDE /* seqsummarycommand.h */, - 3799A94E0FD6A58C00E33EDE /* seqsummarycommand.cpp */, - A70B00C6110885EB002F453A /* setdircommand.h */, - A70B00C7110885EB002F453A /* setdircommand.cpp */, - 37D928270F21331F001D4494 /* sharedcommand.h */, - 37D928260F21331F001D4494 /* sharedcommand.cpp */, - 37D928470F21331F001D4494 /* summarycommand.h */, - 37D928460F21331F001D4494 /* summarycommand.cpp */, - 37D9284B0F21331F001D4494 /* summarysharedcommand.h */, - 37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */, - 37B73CCD1004F5E0008C4B41 /* systemcommand.h */, - 37B73CCE1004F5E0008C4B41 /* systemcommand.cpp */, - 211C38370F961E1F00FEE541 /* treegroupscommand.h */, - 211C38360F961E1F00FEE541 /* treegroupscommand.cpp */, - 7E09C5340FDA7F65002ECAE5 /* trimseqscommand.h */, - 7E09C5350FDA7F65002ECAE5 /* trimseqscommand.cpp */, - 3746109B0F40657600460C57 /* unifracunweightedcommand.h */, - 3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */, - 374610760F40645300460C57 /* unifracweightedcommand.h */, - 374610770F40645300460C57 /* unifracweightedcommand.cpp */, - 37519A9F0F810D0200FED5E8 /* venncommand.h */, - 37519AA00F810D0200FED5E8 /* venncommand.cpp */, + A7E9B65C12D37EC300DA6239 /* bellerophon.cpp */, + A7E9B65D12D37EC300DA6239 /* bellerophon.h */, + A7E9B67412D37EC400DA6239 /* ccode.cpp */, + A7E9B67512D37EC400DA6239 /* ccode.h */, + A7E9B67812D37EC400DA6239 /* chimera.cpp */, + A7E9B67912D37EC400DA6239 /* chimera.h */, + A7E9B68012D37EC400DA6239 /* chimeracheckrdp.cpp */, + A7E9B68112D37EC400DA6239 /* chimeracheckrdp.h */, + A7E9B68412D37EC400DA6239 /* chimerarealigner.cpp */, + A7E9B68512D37EC400DA6239 /* chimerarealigner.h */, + A7E9B68812D37EC400DA6239 /* chimeraslayer.cpp */, + A7E9B68912D37EC400DA6239 /* chimeraslayer.h */, + A7E9B6C112D37EC400DA6239 /* decalc.cpp */, + A7E9B6C212D37EC400DA6239 /* decalc.h */, + A7E9B74612D37EC400DA6239 /* maligner.h */, + A7E9B74512D37EC400DA6239 /* maligner.cpp */, + A7E9B79312D37EC400DA6239 /* pintail.cpp */, + A7E9B79412D37EC400DA6239 /* pintail.h */, + A7E9B82E12D37EC400DA6239 /* slayer.cpp */, + A7E9B82F12D37EC400DA6239 /* slayer.h */, ); - name = commands; + name = chimera; sourceTree = ""; }; - 37D928AC0F213420001D4494 /* containers */ = { + A7E9BA4B12D3966900DA6239 /* classifier */ = { isa = PBXGroup; children = ( - 373C68A10FC1C07D00137ACD /* alignment.hpp */, - 373C68A00FC1C07D00137ACD /* alignment.cpp */, - 373C68A30FC1C07D00137ACD /* alignmentcell.hpp */, - 373C68A20FC1C07D00137ACD /* alignmentcell.cpp */, - A78782A910A1B1CB0086103D /* alignmentdb.h */, - A78782AA10A1B1CB0086103D /* alignmentdb.cpp */, - 373C69170FC1C8AF00137ACD /* blastdb.hpp */, - 373C69160FC1C8AF00137ACD /* blastdb.cpp */, - 37D927D40F21331F001D4494 /* database.hpp */, - 37D927D30F21331F001D4494 /* database.cpp */, - 37D927D50F21331F001D4494 /* datavector.hpp */, - A794201011107897003AECCD /* distancedb.hpp */, - A794200F11107897003AECCD /* distancedb.cpp */, - 37D927DC0F21331F001D4494 /* fastamap.h */, - 37D927DB0F21331F001D4494 /* fastamap.cpp */, - 375873EA0F7D64520040F377 /* fullmatrix.h */, - 375873EB0F7D64520040F377 /* fullmatrix.cpp */, - 37D927E20F21331F001D4494 /* groupmap.h */, - 37D927E10F21331F001D4494 /* groupmap.cpp */, - 37D927EA0F21331F001D4494 /* kmer.hpp */, - 37D927E90F21331F001D4494 /* kmer.cpp */, - 37D927EC0F21331F001D4494 /* kmerdb.hpp */, - 37D927EB0F21331F001D4494 /* kmerdb.cpp */, - 37D927EE0F21331F001D4494 /* listvector.hpp */, - 37D927ED0F21331F001D4494 /* listvector.cpp */, - 37D927F10F21331F001D4494 /* nameassignment.hpp */, - 37D927F00F21331F001D4494 /* nameassignment.cpp */, - 37D927F80F21331F001D4494 /* ordervector.hpp */, - 37D927F70F21331F001D4494 /* ordervector.cpp */, - 37D928000F21331F001D4494 /* rabundvector.hpp */, - 37D927FF0F21331F001D4494 /* rabundvector.cpp */, - 37D9281B0F21331F001D4494 /* sabundvector.hpp */, - 37D9281A0F21331F001D4494 /* sabundvector.cpp */, - 37D9281D0F21331F001D4494 /* sequence.hpp */, - 37D9281C0F21331F001D4494 /* sequence.cpp */, - 378C1AFE0FB0644D004D63F5 /* sequencedb.h */, - 378C1AFD0FB0644D004D63F5 /* sequencedb.cpp */, - 37AD4CE20F28AEA300AA2D49 /* sharedlistvector.h */, - 37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */, - 37D9282F0F21331F001D4494 /* sharedordervector.h */, - 37D9282E0F21331F001D4494 /* sharedordervector.cpp */, - 37D928310F21331F001D4494 /* sharedrabundvector.h */, - 37D928300F21331F001D4494 /* sharedrabundvector.cpp */, - 37D928330F21331F001D4494 /* sharedsabundvector.h */, - 37D928320F21331F001D4494 /* sharedsabundvector.cpp */, - 37D928450F21331F001D4494 /* sparsematrix.hpp */, - 37D928440F21331F001D4494 /* sparsematrix.cpp */, - 373C68F40FC1C6A800137ACD /* suffixdb.hpp */, - 373C68F30FC1C6A800137ACD /* suffixdb.cpp */, - 373C68F60FC1C6A800137ACD /* suffixnodes.hpp */, - 373C68F50FC1C6A800137ACD /* suffixnodes.cpp */, - 373C68F80FC1C6A800137ACD /* suffixtree.hpp */, - 373C68F70FC1C6A800137ACD /* suffixtree.cpp */, - 37AD4DB90F28E2FE00AA2D49 /* tree.h */, - 37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */, - 379293C10F2DE73400B9034A /* treemap.h */, - 379293C20F2DE73400B9034A /* treemap.cpp */, - 37E5F3E10F29FD4200F8D827 /* treenode.h */, - 37E5F3E20F29FD4200F8D827 /* treenode.cpp */, + A7E9B65A12D37EC300DA6239 /* bayesian.cpp */, + A7E9B65B12D37EC300DA6239 /* bayesian.h */, + A7E9B68E12D37EC400DA6239 /* classify.cpp */, + A7E9B68F12D37EC400DA6239 /* classify.h */, + A7E9B73812D37EC400DA6239 /* knn.h */, + A7E9B73712D37EC400DA6239 /* knn.cpp */, + A7E9B78912D37EC400DA6239 /* phylodiversity.cpp */, + A7E9B78A12D37EC400DA6239 /* phylodiversity.h */, + A7E9B78D12D37EC400DA6239 /* phylosummary.cpp */, + A7E9B78E12D37EC400DA6239 /* phylosummary.h */, + A7E9B78F12D37EC400DA6239 /* phylotree.cpp */, + A7E9B79012D37EC400DA6239 /* phylotree.h */, + A7E9B85D12D37EC400DA6239 /* taxonomyequalizer.cpp */, + A7E9B85E12D37EC400DA6239 /* taxonomyequalizer.h */, ); - name = containers; + name = classifier; + sourceTree = ""; + }; + A7E9BA4F12D398D700DA6239 /* clearcut */ = { + isa = PBXGroup; + children = ( + A7E9B69412D37EC400DA6239 /* clearcut.cpp */, + A7E9B69512D37EC400DA6239 /* clearcut.h */, + A7E9B6B312D37EC400DA6239 /* common.h */, + A7E9B6CF12D37EC400DA6239 /* distclearcut.cpp */, + A7E9B6D012D37EC400DA6239 /* distclearcut.h */, + A7E9B6D312D37EC400DA6239 /* dmat.cpp */, + A7E9B6D412D37EC400DA6239 /* dmat.h */, + A7E9B6DC12D37EC400DA6239 /* fasta.cpp */, + A7E9B6DD12D37EC400DA6239 /* fasta.h */, + A7E9B6FD12D37EC400DA6239 /* getopt_long.h */, + A7E9B6FC12D37EC400DA6239 /* getopt_long.cpp */, + ); + name = clearcut; sourceTree = ""; }; - 37D928B10F213472001D4494 /* errorcheckor */ = { + A7E9BA5312D39A5E00DA6239 /* read */ = { isa = PBXGroup; children = ( - 37D928500F21331F001D4494 /* validcalculator.h */, - 37D9284F0F21331F001D4494 /* validcalculator.cpp */, - 37D928540F21331F001D4494 /* validparameter.h */, - 37D928530F21331F001D4494 /* validparameter.cpp */, + A7E9B6E912D37EC400DA6239 /* formatcolumn.cpp */, + A7E9B6EA12D37EC400DA6239 /* formatcolumn.h */, + A7E9B6EB12D37EC400DA6239 /* formatmatrix.h */, + A7E9B6EC12D37EC400DA6239 /* formatphylip.cpp */, + A7E9B6ED12D37EC400DA6239 /* formatphylip.h */, + A7E9B7B012D37EC400DA6239 /* readblast.cpp */, + A7E9B7B112D37EC400DA6239 /* readblast.h */, + A7E9B7B212D37EC400DA6239 /* readcluster.cpp */, + A7E9B7B312D37EC400DA6239 /* readcluster.h */, + A7E9B7B412D37EC400DA6239 /* readcolumn.cpp */, + A7E9B7B512D37EC400DA6239 /* readcolumn.h */, + A7E9B7B812D37EC400DA6239 /* readmatrix.hpp */, + A7E9B7B912D37EC400DA6239 /* readotu.cpp */, + A7E9B7BA12D37EC400DA6239 /* readotu.h */, + A7E9B7BD12D37EC400DA6239 /* readphylip.cpp */, + A7E9B7BE12D37EC400DA6239 /* readphylip.h */, + A7E9B7BF12D37EC400DA6239 /* readtree.cpp */, + A7E9B7C012D37EC400DA6239 /* readtree.h */, + A713EBAA12DC7613000092AC /* readphylipvector.h */, + A713EBAB12DC7613000092AC /* readphylipvector.cpp */, + A7E9B84312D37EC400DA6239 /* splitmatrix.cpp */, + A7E9B84412D37EC400DA6239 /* splitmatrix.h */, ); - name = errorcheckor; + name = read; sourceTree = ""; }; - A787811210A073F40086103D /* classifiers */ = { + A7E9BA5612D39BD800DA6239 /* metastats */ = { isa = PBXGroup; children = ( - A78780FE10A06B8B0086103D /* classify.h */, - A787810210A06D5D0086103D /* classify.cpp */, - A787820F10A0AAE70086103D /* bayesian.h */, - A787821010A0AAE70086103D /* bayesian.cpp */, - A773805D10B6D6FC002A6A61 /* taxonomyequalizer.h */, - A773805E10B6D6FC002A6A61 /* taxonomyequalizer.cpp */, - A78781B910A0813D0086103D /* phylotree.h */, - A78781B810A0813D0086103D /* phylotree.cpp */, - A787844310A1EBDD0086103D /* knn.h */, - A787844410A1EBDD0086103D /* knn.cpp */, + A7E9B75512D37EC400DA6239 /* metastats.h */, + A7E9B75612D37EC400DA6239 /* metastats2.c */, ); - name = classifiers; + name = metastats; sourceTree = ""; }; - C6859E8C029090F304C91782 /* Documentation */ = { + C6A0FF2B0290797F04C91782 /* Documentation */ = { isa = PBXGroup; children = ( - C6859E8B029090EE04C91782 /* Mothur.1 */, + C6A0FF2C0290799A04C91782 /* mothur.1 */, ); name = Documentation; sourceTree = ""; @@ -1110,22 +1584,22 @@ /* End PBXGroup section */ /* Begin PBXNativeTarget section */ - 8DD76F620486A84900D96B5E /* mothur */ = { + 8DD76FA90486AB0100D96B5E /* Mothur */ = { isa = PBXNativeTarget; - buildConfigurationList = 1DEB923108733DC60010E9CD /* Build configuration list for PBXNativeTarget "mothur" */; + buildConfigurationList = 1DEB928508733DD80010E9CD /* Build configuration list for PBXNativeTarget "Mothur" */; buildPhases = ( - 8DD76F640486A84900D96B5E /* Sources */, - 8DD76F660486A84900D96B5E /* Frameworks */, - 8DD76F690486A84900D96B5E /* CopyFiles */, + 8DD76FAB0486AB0100D96B5E /* Sources */, + 8DD76FAD0486AB0100D96B5E /* Frameworks */, + 8DD76FAF0486AB0100D96B5E /* CopyFiles */, ); buildRules = ( ); dependencies = ( ); - name = mothur; + name = Mothur; productInstallPath = "$(HOME)/bin"; - productName = Mothur; - productReference = 8DD76F6C0486A84900D96B5E /* mothur */; + productName = mothur; + productReference = 8DD76FB20486AB0100D96B5E /* Mothur */; productType = "com.apple.product-type.tool"; }; /* End PBXNativeTarget section */ @@ -1133,317 +1607,434 @@ /* Begin PBXProject section */ 08FB7793FE84155DC02AAC07 /* Project object */ = { isa = PBXProject; - buildConfigurationList = 1DEB923508733DC60010E9CD /* Build configuration list for PBXProject "Mothur" */; - compatibilityVersion = "Xcode 3.0"; + attributes = { + ORGANIZATIONNAME = "Schloss Lab"; + }; + buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */; + compatibilityVersion = "Xcode 3.1"; + developmentRegion = English; hasScannedForEncodings = 1; - mainGroup = 08FB7794FE84155DC02AAC07 /* Mothur */; + knownRegions = ( + English, + Japanese, + French, + German, + ); + mainGroup = 08FB7794FE84155DC02AAC07 /* mothur */; projectDirPath = ""; projectRoot = ""; targets = ( - 8DD76F620486A84900D96B5E /* mothur */, + 8DD76FA90486AB0100D96B5E /* Mothur */, ); }; /* End PBXProject section */ /* Begin PBXSourcesBuildPhase section */ - 8DD76F640486A84900D96B5E /* Sources */ = { + 8DD76FAB0486AB0100D96B5E /* Sources */ = { isa = PBXSourcesBuildPhase; buildActionMask = 2147483647; files = ( - 37D928550F21331F001D4494 /* ace.cpp in Sources */, - 37D928560F21331F001D4494 /* averagelinkage.cpp in Sources */, - 37D928570F21331F001D4494 /* bootstrap.cpp in Sources */, - 37D928580F21331F001D4494 /* calculator.cpp in Sources */, - 37D928590F21331F001D4494 /* chao1.cpp in Sources */, - 37D9285A0F21331F001D4494 /* cluster.cpp in Sources */, - 37D9285B0F21331F001D4494 /* clustercommand.cpp in Sources */, - 37D9285C0F21331F001D4494 /* collect.cpp in Sources */, - 37D9285D0F21331F001D4494 /* collectcommand.cpp in Sources */, - 37D9285E0F21331F001D4494 /* collectsharedcommand.cpp in Sources */, - 37D928600F21331F001D4494 /* commandoptionparser.cpp in Sources */, - 37D928610F21331F001D4494 /* completelinkage.cpp in Sources */, - 37D928620F21331F001D4494 /* database.cpp in Sources */, - 37D928630F21331F001D4494 /* engine.cpp in Sources */, - 37D928650F21331F001D4494 /* fastamap.cpp in Sources */, - 37D928660F21331F001D4494 /* fileoutput.cpp in Sources */, - 37D928670F21331F001D4494 /* globaldata.cpp in Sources */, - 37D928680F21331F001D4494 /* groupmap.cpp in Sources */, - 37D928690F21331F001D4494 /* helpcommand.cpp in Sources */, - 37D9286A0F21331F001D4494 /* inputdata.cpp in Sources */, - 37D9286B0F21331F001D4494 /* jackknife.cpp in Sources */, - 37D9286C0F21331F001D4494 /* kmer.cpp in Sources */, - 37D9286D0F21331F001D4494 /* kmerdb.cpp in Sources */, - 37D9286E0F21331F001D4494 /* listvector.cpp in Sources */, - 37D9286F0F21331F001D4494 /* mothur.cpp in Sources */, - 37D928700F21331F001D4494 /* nameassignment.cpp in Sources */, - 37D928720F21331F001D4494 /* npshannon.cpp in Sources */, - 37D928730F21331F001D4494 /* ordervector.cpp in Sources */, - 37D928750F21331F001D4494 /* progress.cpp in Sources */, - 37D928760F21331F001D4494 /* quitcommand.cpp in Sources */, - 37D928770F21331F001D4494 /* rabundvector.cpp in Sources */, - 37D928780F21331F001D4494 /* rarecalc.cpp in Sources */, - 37D928790F21331F001D4494 /* raredisplay.cpp in Sources */, - 37D9287A0F21331F001D4494 /* rarefact.cpp in Sources */, - 37D9287B0F21331F001D4494 /* rarefactcommand.cpp in Sources */, - 37D9287C0F21331F001D4494 /* rarefactsharedcommand.cpp in Sources */, - 37D928840F21331F001D4494 /* sabundvector.cpp in Sources */, - 37D928850F21331F001D4494 /* sequence.cpp in Sources */, - 37D928860F21331F001D4494 /* shannon.cpp in Sources */, - 37D928880F21331F001D4494 /* sharedace.cpp in Sources */, - 37D928890F21331F001D4494 /* sharedchao1.cpp in Sources */, - 37D9288A0F21331F001D4494 /* sharedcommand.cpp in Sources */, - 37D9288B0F21331F001D4494 /* sharedjabund.cpp in Sources */, - 37D9288C0F21331F001D4494 /* sharedjclass.cpp in Sources */, - 37D9288D0F21331F001D4494 /* sharedjest.cpp in Sources */, - 37D9288E0F21331F001D4494 /* sharedordervector.cpp in Sources */, - 37D9288F0F21331F001D4494 /* sharedrabundvector.cpp in Sources */, - 37D928900F21331F001D4494 /* sharedsabundvector.cpp in Sources */, - 37D928910F21331F001D4494 /* sharedsobs.cpp in Sources */, - 37D928920F21331F001D4494 /* sharedsorabund.cpp in Sources */, - 37D928930F21331F001D4494 /* sharedsorclass.cpp in Sources */, - 37D928940F21331F001D4494 /* sharedsorest.cpp in Sources */, - 37D928950F21331F001D4494 /* sharedthetan.cpp in Sources */, - 37D928960F21331F001D4494 /* sharedthetayc.cpp in Sources */, - 37D928970F21331F001D4494 /* simpson.cpp in Sources */, - 37D928980F21331F001D4494 /* singlelinkage.cpp in Sources */, - 37D928990F21331F001D4494 /* sparsematrix.cpp in Sources */, - 37D9289A0F21331F001D4494 /* summarycommand.cpp in Sources */, - 37D9289B0F21331F001D4494 /* summarysharedcommand.cpp in Sources */, - 37D9289C0F21331F001D4494 /* uvest.cpp in Sources */, - 37D9289D0F21331F001D4494 /* validcalculator.cpp in Sources */, - 37D9289F0F21331F001D4494 /* validparameter.cpp in Sources */, - 372E12700F26365B0095CF7E /* readotucommand.cpp in Sources */, - 372E12960F263D5A0095CF7E /* readdistcommand.cpp in Sources */, - 372E12ED0F264D320095CF7E /* commandfactory.cpp in Sources */, - 37B28F680F27590100808A62 /* deconvolutecommand.cpp in Sources */, - 37AD4CE40F28AEA300AA2D49 /* sharedlistvector.cpp in Sources */, - 37AD4DBB0F28E2FE00AA2D49 /* tree.cpp in Sources */, - 37AD4DCA0F28F3DD00AA2D49 /* readtree.cpp in Sources */, - 37E5F3E30F29FD4200F8D827 /* treenode.cpp in Sources */, - 37E5F4920F2A3DA800F8D827 /* readtreecommand.cpp in Sources */, - 379293C30F2DE73400B9034A /* treemap.cpp in Sources */, - 379294700F2E191800B9034A /* parsimonycommand.cpp in Sources */, - 3792948A0F2E258500B9034A /* parsimony.cpp in Sources */, - 374610780F40645300460C57 /* unifracweightedcommand.cpp in Sources */, - 3746107E0F4064D100460C57 /* weighted.cpp in Sources */, - 374610830F40652400460C57 /* unweighted.cpp in Sources */, - 3746109D0F40657600460C57 /* unifracunweightedcommand.cpp in Sources */, - 37AFC71F0F445386005F492D /* sharedsobscollectsummary.cpp in Sources */, - A70B53AA0F4CD7AD0064797E /* getgroupcommand.cpp in Sources */, - A70B53AB0F4CD7AD0064797E /* getlabelcommand.cpp in Sources */, - EB9303EB0F534D9400E8EF26 /* logsd.cpp in Sources */, - EB9303F90F53517300E8EF26 /* geom.cpp in Sources */, - EB6E68190F5F1C780044E17B /* qstat.cpp in Sources */, - EB1216880F619B83004A865F /* bergerparker.cpp in Sources */, - EB1216E50F61ACFB004A865F /* bstick.cpp in Sources */, - EB1217230F61C9AC004A865F /* sharedkstest.cpp in Sources */, - 375873EC0F7D64520040F377 /* fullmatrix.cpp in Sources */, - 375873EF0F7D646F0040F377 /* heatmap.cpp in Sources */, - 375873F20F7D64800040F377 /* heatmapcommand.cpp in Sources */, - 375873F50F7D648F0040F377 /* libshuffcommand.cpp in Sources */, - 375873F80F7D649C0040F377 /* nocommands.cpp in Sources */, - 375873FD0F7D64DA0040F377 /* sharedbraycurtis.cpp in Sources */, - 375874040F7D64EF0040F377 /* sharedkulczynski.cpp in Sources */, - 375874050F7D64EF0040F377 /* sharedlennon.cpp in Sources */, - 375874060F7D64EF0040F377 /* sharedkulczynskicody.cpp in Sources */, - 3758740C0F7D64FC0040F377 /* sharedmorisitahorn.cpp in Sources */, - 3758740D0F7D64FC0040F377 /* sharedochiai.cpp in Sources */, - 37519A6B0F80E6EB00FED5E8 /* sharedanderbergs.cpp in Sources */, - 37519AA10F810D0200FED5E8 /* venncommand.cpp in Sources */, - 37519AB50F810FAE00FED5E8 /* venn.cpp in Sources */, - 37C1D9730F86506E0059E3F0 /* binsequencecommand.cpp in Sources */, - 370B88070F8A4EE4005AB382 /* getoturepcommand.cpp in Sources */, - 7E412F490F8D21B600381DD0 /* slibshuff.cpp in Sources */, - 7E412FEA0F8D3E2C00381DD0 /* libshuff.cpp in Sources */, - 7E4130F80F8E58FA00381DD0 /* dlibshuff.cpp in Sources */, - 211C38320F961DD400FEE541 /* sharedutilities.cpp in Sources */, - 211C38380F961E1F00FEE541 /* treegroupscommand.cpp in Sources */, - 21DDC01B0F97A8FE0060691C /* bootstrapsharedcommand.cpp in Sources */, - 375AA1390F9E433D008EF9B8 /* readcolumn.cpp in Sources */, - 375AA13A0F9E433D008EF9B8 /* readotu.cpp in Sources */, - 375AA13B0F9E433D008EF9B8 /* readphylip.cpp in Sources */, - 7EC3D4550FA0FFF900338DA5 /* coverage.cpp in Sources */, - 7EC3D4560FA0FFF900338DA5 /* whittaker.cpp in Sources */, - 377326650FAF16E0007ABB8B /* consensuscommand.cpp in Sources */, - 378C1B030FB0644E004D63F5 /* filterseqscommand.cpp in Sources */, - 378C1B040FB0644E004D63F5 /* goodscoverage.cpp in Sources */, - 378C1B0A0FB0644E004D63F5 /* sequencedb.cpp in Sources */, - 378C1B0B0FB0644E004D63F5 /* sharedjackknife.cpp in Sources */, - 378C1B0C0FB0644E004D63F5 /* sharedmarczewski.cpp in Sources */, - 37C753CE0FB3415200DBD02E /* distancecommand.cpp in Sources */, - 378DC5CF0FBDE1C8003B8607 /* aligncommand.cpp in Sources */, - 373C68A40FC1C07D00137ACD /* alignment.cpp in Sources */, - 373C68A50FC1C07D00137ACD /* alignmentcell.cpp in Sources */, - 373C68BC0FC1C1A600137ACD /* gotohoverlap.cpp in Sources */, - 373C68C50FC1C25F00137ACD /* overlap.cpp in Sources */, - 373C68CF0FC1C2D900137ACD /* needlemanoverlap.cpp in Sources */, - 373C68DD0FC1C38D00137ACD /* blastalign.cpp in Sources */, - 373C68E50FC1C4A500137ACD /* noalign.cpp in Sources */, - 373C68F90FC1C6A800137ACD /* suffixdb.cpp in Sources */, - 373C68FA0FC1C6A800137ACD /* suffixnodes.cpp in Sources */, - 373C68FB0FC1C6A800137ACD /* suffixtree.cpp in Sources */, - 373C69180FC1C8AF00137ACD /* blastdb.cpp in Sources */, - 373C691F0FC1C98600137ACD /* nast.cpp in Sources */, - 373C692B0FC1C9EB00137ACD /* nastreport.cpp in Sources */, - 373C699A0FC1E63600137ACD /* boneh.cpp in Sources */, - 373C699B0FC1E63600137ACD /* efron.cpp in Sources */, - 373C699C0FC1E63600137ACD /* solow.cpp in Sources */, - EB72FE260FC1F5CA0051AC11 /* shen.cpp in Sources */, - 21E859D80FC4632E005E1A48 /* matrixoutputcommand.cpp in Sources */, - 3749271D0FD58C840031C06B /* getsabundcommand.cpp in Sources */, - 3749273F0FD5956B0031C06B /* getrabundcommand.cpp in Sources */, - 3799A9510FD6A58C00E33EDE /* seqsummarycommand.cpp in Sources */, - 371B30B40FD7EE67000414CA /* screenseqscommand.cpp in Sources */, - 7E09C5140FDA79C5002ECAE5 /* reversecommand.cpp in Sources */, - 7E09C5360FDA7F65002ECAE5 /* trimseqscommand.cpp in Sources */, - 378598660FDD497000EF9D03 /* heatmapsimcommand.cpp in Sources */, - 378598740FDD4C1500EF9D03 /* heatmapsim.cpp in Sources */, - 378599100FDD7E8E00EF9D03 /* optionparser.cpp in Sources */, - 7E5A17AF0FE57292003C6A03 /* mergefilecommand.cpp in Sources */, - 379D3D510FF90E090068C1C0 /* chimeraseqscommand.cpp in Sources */, - 37B73C761004BEFD008C4B41 /* listseqscommand.cpp in Sources */, - 37B73CA61004D89A008C4B41 /* getseqscommand.cpp in Sources */, - 37B73CC01004EB38008C4B41 /* removeseqscommand.cpp in Sources */, - 37B73CCF1004F5E0008C4B41 /* systemcommand.cpp in Sources */, - 374F2FEB100634B600E97C66 /* bellerophon.cpp in Sources */, - 374F301310063B6F00E97C66 /* pintail.cpp in Sources */, - 372A55551017922B00C5194B /* decalc.cpp in Sources */, - 372095C2103196D70004D347 /* chimera.cpp in Sources */, - A75B887E104C16860083C454 /* ccode.cpp in Sources */, - A7283FF81056CAE100D0CC69 /* chimeracheckrdp.cpp in Sources */, - A70DECD91063D8B40057C03C /* secondarystructurecommand.cpp in Sources */, - A7E4A783106913F900688F62 /* getsharedotucommand.cpp in Sources */, - A7E4A824106A9AD700688F62 /* maligner.cpp in Sources */, - A7B04493106CC3E60046FC83 /* chimeraslayer.cpp in Sources */, - A7B0450E106CEEC90046FC83 /* slayer.cpp in Sources */, - A73329CF1083B3B3003B10C5 /* getlistcountcommand.cpp in Sources */, - A729ACD010848E6100139801 /* hclustercommand.cpp in Sources */, - A729ACE410849BBE00139801 /* hcluster.cpp in Sources */, - A751ACEA1098B283003D0911 /* readcluster.cpp in Sources */, - A7861478109F5FA00010AAAF /* classifyseqscommand.cpp in Sources */, - A787810310A06D5D0086103D /* classify.cpp in Sources */, - A78781BA10A0813E0086103D /* phylotree.cpp in Sources */, - A787821110A0AAE70086103D /* bayesian.cpp in Sources */, - A78782AB10A1B1CB0086103D /* alignmentdb.cpp in Sources */, - A787844510A1EBDD0086103D /* knn.cpp in Sources */, - A773805F10B6D6FC002A6A61 /* taxonomyequalizer.cpp in Sources */, - A773809010B6EFD1002A6A61 /* phylotypecommand.cpp in Sources */, - A727E84A10D14568001A8432 /* readblast.cpp in Sources */, - A7E0AAB610D2886D00CF407B /* mgclustercommand.cpp in Sources */, - A7027F2810DFF86D00BF45FE /* preclustercommand.cpp in Sources */, - A7D176CF10F2558500159497 /* pcacommand.cpp in Sources */, - A7D86C7D10FE09AB00865661 /* formatcolumn.cpp in Sources */, - A7D86C8C10FE09FE00865661 /* formatphylip.cpp in Sources */, - A704E8A31106045D00870157 /* otuhierarchycommand.cpp in Sources */, - A70B00C8110885EB002F453A /* setdircommand.cpp in Sources */, - A794201111107897003AECCD /* distancedb.cpp in Sources */, + A7E9B88112D37EC400DA6239 /* ace.cpp in Sources */, + A7E9B88212D37EC400DA6239 /* aligncommand.cpp in Sources */, + A7E9B88312D37EC400DA6239 /* alignment.cpp in Sources */, + A7E9B88412D37EC400DA6239 /* alignmentcell.cpp in Sources */, + A7E9B88512D37EC400DA6239 /* alignmentdb.cpp in Sources */, + A7E9B88612D37EC400DA6239 /* averagelinkage.cpp in Sources */, + A7E9B88712D37EC400DA6239 /* bayesian.cpp in Sources */, + A7E9B88812D37EC400DA6239 /* bellerophon.cpp in Sources */, + A7E9B88912D37EC400DA6239 /* bergerparker.cpp in Sources */, + A7E9B88A12D37EC400DA6239 /* binsequencecommand.cpp in Sources */, + A7E9B88B12D37EC400DA6239 /* blastalign.cpp in Sources */, + A7E9B88C12D37EC400DA6239 /* blastdb.cpp in Sources */, + A7E9B88D12D37EC400DA6239 /* boneh.cpp in Sources */, + A7E9B88E12D37EC400DA6239 /* bootstrap.cpp in Sources */, + A7E9B88F12D37EC400DA6239 /* bootstrapsharedcommand.cpp in Sources */, + A7E9B89012D37EC400DA6239 /* bstick.cpp in Sources */, + A7E9B89112D37EC400DA6239 /* calculator.cpp in Sources */, + A7E9B89212D37EC400DA6239 /* canberra.cpp in Sources */, + A7E9B89312D37EC400DA6239 /* catchallcommand.cpp in Sources */, + A7E9B89412D37EC400DA6239 /* ccode.cpp in Sources */, + A7E9B89512D37EC400DA6239 /* chao1.cpp in Sources */, + A7E9B89612D37EC400DA6239 /* chimera.cpp in Sources */, + A7E9B89712D37EC400DA6239 /* chimerabellerophoncommand.cpp in Sources */, + A7E9B89812D37EC400DA6239 /* chimeraccodecommand.cpp in Sources */, + A7E9B89912D37EC400DA6239 /* chimeracheckcommand.cpp in Sources */, + A7E9B89A12D37EC400DA6239 /* chimeracheckrdp.cpp in Sources */, + A7E9B89B12D37EC400DA6239 /* chimerapintailcommand.cpp in Sources */, + A7E9B89C12D37EC400DA6239 /* chimerarealigner.cpp in Sources */, + A7E9B89D12D37EC400DA6239 /* chimeraseqscommand.cpp in Sources */, + A7E9B89E12D37EC400DA6239 /* chimeraslayer.cpp in Sources */, + A7E9B89F12D37EC400DA6239 /* chimeraslayercommand.cpp in Sources */, + A7E9B8A012D37EC400DA6239 /* chopseqscommand.cpp in Sources */, + A7E9B8A112D37EC400DA6239 /* classify.cpp in Sources */, + A7E9B8A212D37EC400DA6239 /* classifyotucommand.cpp in Sources */, + A7E9B8A312D37EC400DA6239 /* classifyseqscommand.cpp in Sources */, + A7E9B8A412D37EC400DA6239 /* clearcut.cpp in Sources */, + A7E9B8A512D37EC400DA6239 /* clearcutcommand.cpp in Sources */, + A7E9B8A612D37EC400DA6239 /* cluster.cpp in Sources */, + A7E9B8A712D37EC400DA6239 /* clusterclassic.cpp in Sources */, + A7E9B8A812D37EC400DA6239 /* clustercommand.cpp in Sources */, + A7E9B8A912D37EC400DA6239 /* clusterdoturcommand.cpp in Sources */, + A7E9B8AA12D37EC400DA6239 /* clusterfragmentscommand.cpp in Sources */, + A7E9B8AB12D37EC400DA6239 /* clustersplitcommand.cpp in Sources */, + A7E9B8AC12D37EC400DA6239 /* cmdargs.cpp in Sources */, + A7E9B8AD12D37EC400DA6239 /* collect.cpp in Sources */, + A7E9B8AE12D37EC400DA6239 /* collectcommand.cpp in Sources */, + A7E9B8AF12D37EC400DA6239 /* collectsharedcommand.cpp in Sources */, + A7E9B8B012D37EC400DA6239 /* commandfactory.cpp in Sources */, + A7E9B8B112D37EC400DA6239 /* commandoptionparser.cpp in Sources */, + A7E9B8B212D37EC400DA6239 /* completelinkage.cpp in Sources */, + A7E9B8B312D37EC400DA6239 /* consensuscommand.cpp in Sources */, + A7E9B8B412D37EC400DA6239 /* consensusseqscommand.cpp in Sources */, + A7E9B8B512D37EC400DA6239 /* corraxescommand.cpp in Sources */, + A7E9B8B612D37EC400DA6239 /* coverage.cpp in Sources */, + A7E9B8B712D37EC400DA6239 /* database.cpp in Sources */, + A7E9B8B812D37EC400DA6239 /* decalc.cpp in Sources */, + A7E9B8B912D37EC400DA6239 /* deconvolutecommand.cpp in Sources */, + A7E9B8BA12D37EC400DA6239 /* degapseqscommand.cpp in Sources */, + A7E9B8BB12D37EC400DA6239 /* deuniqueseqscommand.cpp in Sources */, + A7E9B8BC12D37EC400DA6239 /* distancecommand.cpp in Sources */, + A7E9B8BD12D37EC400DA6239 /* distancedb.cpp in Sources */, + A7E9B8BE12D37EC400DA6239 /* distclearcut.cpp in Sources */, + A7E9B8BF12D37EC400DA6239 /* dlibshuff.cpp in Sources */, + A7E9B8C012D37EC400DA6239 /* dmat.cpp in Sources */, + A7E9B8C112D37EC400DA6239 /* efron.cpp in Sources */, + A7E9B8C212D37EC400DA6239 /* engine.cpp in Sources */, + A7E9B8C312D37EC400DA6239 /* fasta.cpp in Sources */, + A7E9B8C412D37EC400DA6239 /* fastamap.cpp in Sources */, + A7E9B8C512D37EC400DA6239 /* fileoutput.cpp in Sources */, + A7E9B8C612D37EC400DA6239 /* filterseqscommand.cpp in Sources */, + A7E9B8C712D37EC400DA6239 /* fisher2.c in Sources */, + A7E9B8C812D37EC400DA6239 /* flowdata.cpp in Sources */, + A7E9B8C912D37EC400DA6239 /* formatcolumn.cpp in Sources */, + A7E9B8CA12D37EC400DA6239 /* formatphylip.cpp in Sources */, + A7E9B8CB12D37EC400DA6239 /* fullmatrix.cpp in Sources */, + A7E9B8CC12D37EC400DA6239 /* geom.cpp in Sources */, + A7E9B8CD12D37EC400DA6239 /* getgroupcommand.cpp in Sources */, + A7E9B8CE12D37EC400DA6239 /* getgroupscommand.cpp in Sources */, + A7E9B8CF12D37EC400DA6239 /* getlabelcommand.cpp in Sources */, + A7E9B8D012D37EC400DA6239 /* getlineagecommand.cpp in Sources */, + A7E9B8D112D37EC400DA6239 /* getlistcountcommand.cpp in Sources */, + A7E9B8D212D37EC400DA6239 /* getopt_long.cpp in Sources */, + A7E9B8D312D37EC400DA6239 /* getoturepcommand.cpp in Sources */, + A7E9B8D412D37EC400DA6239 /* getotuscommand.cpp in Sources */, + A7E9B8D512D37EC400DA6239 /* getrabundcommand.cpp in Sources */, + A7E9B8D612D37EC400DA6239 /* getrelabundcommand.cpp in Sources */, + A7E9B8D712D37EC400DA6239 /* getsabundcommand.cpp in Sources */, + A7E9B8D812D37EC400DA6239 /* getseqscommand.cpp in Sources */, + A7E9B8D912D37EC400DA6239 /* getsharedotucommand.cpp in Sources */, + A7E9B8DA12D37EC400DA6239 /* globaldata.cpp in Sources */, + A7E9B8DB12D37EC400DA6239 /* goodscoverage.cpp in Sources */, + A7E9B8DC12D37EC400DA6239 /* gotohoverlap.cpp in Sources */, + A7E9B8DD12D37EC400DA6239 /* gower.cpp in Sources */, + A7E9B8DE12D37EC400DA6239 /* groupmap.cpp in Sources */, + A7E9B8DF12D37EC400DA6239 /* hamming.cpp in Sources */, + A7E9B8E012D37EC400DA6239 /* hcluster.cpp in Sources */, + A7E9B8E112D37EC400DA6239 /* hclustercommand.cpp in Sources */, + A7E9B8E212D37EC400DA6239 /* heatmap.cpp in Sources */, + A7E9B8E312D37EC400DA6239 /* heatmapcommand.cpp in Sources */, + A7E9B8E412D37EC400DA6239 /* heatmapsim.cpp in Sources */, + A7E9B8E512D37EC400DA6239 /* heatmapsimcommand.cpp in Sources */, + A7E9B8E612D37EC400DA6239 /* heip.cpp in Sources */, + A7E9B8E712D37EC400DA6239 /* hellinger.cpp in Sources */, + A7E9B8E812D37EC400DA6239 /* helpcommand.cpp in Sources */, + A7E9B8E912D37EC400DA6239 /* indicatorcommand.cpp in Sources */, + A7E9B8EA12D37EC400DA6239 /* inputdata.cpp in Sources */, + A7E9B8EB12D37EC400DA6239 /* invsimpson.cpp in Sources */, + A7E9B8EC12D37EC400DA6239 /* jackknife.cpp in Sources */, + A7E9B8ED12D37EC400DA6239 /* kmer.cpp in Sources */, + A7E9B8EE12D37EC400DA6239 /* kmerdb.cpp in Sources */, + A7E9B8EF12D37EC400DA6239 /* knn.cpp in Sources */, + A7E9B8F012D37EC400DA6239 /* libshuff.cpp in Sources */, + A7E9B8F112D37EC400DA6239 /* libshuffcommand.cpp in Sources */, + A7E9B8F212D37EC400DA6239 /* listseqscommand.cpp in Sources */, + A7E9B8F312D37EC400DA6239 /* listvector.cpp in Sources */, + A7E9B8F412D37EC400DA6239 /* logsd.cpp in Sources */, + A7E9B8F512D37EC400DA6239 /* makegroupcommand.cpp in Sources */, + A7E9B8F612D37EC400DA6239 /* maligner.cpp in Sources */, + A7E9B8F712D37EC400DA6239 /* manhattan.cpp in Sources */, + A7E9B8F812D37EC400DA6239 /* matrixoutputcommand.cpp in Sources */, + A7E9B8F912D37EC400DA6239 /* memchi2.cpp in Sources */, + A7E9B8FA12D37EC400DA6239 /* memchord.cpp in Sources */, + A7E9B8FB12D37EC400DA6239 /* memeuclidean.cpp in Sources */, + A7E9B8FC12D37EC400DA6239 /* mempearson.cpp in Sources */, + A7E9B8FD12D37EC400DA6239 /* mergefilecommand.cpp in Sources */, + A7E9B8FE12D37EC400DA6239 /* metastats2.c in Sources */, + A7E9B8FF12D37EC400DA6239 /* metastatscommand.cpp in Sources */, + A7E9B90012D37EC400DA6239 /* mgclustercommand.cpp in Sources */, + A7E9B90112D37EC400DA6239 /* mothur.cpp in Sources */, + A7E9B90212D37EC400DA6239 /* mothurout.cpp in Sources */, + A7E9B90312D37EC400DA6239 /* nameassignment.cpp in Sources */, + A7E9B90412D37EC400DA6239 /* nast.cpp in Sources */, + A7E9B90512D37EC400DA6239 /* nastreport.cpp in Sources */, + A7E9B90612D37EC400DA6239 /* needlemanoverlap.cpp in Sources */, + A7E9B90712D37EC400DA6239 /* noalign.cpp in Sources */, + A7E9B90812D37EC400DA6239 /* nocommands.cpp in Sources */, + A7E9B90912D37EC400DA6239 /* normalizesharedcommand.cpp in Sources */, + A7E9B90A12D37EC400DA6239 /* npshannon.cpp in Sources */, + A7E9B90B12D37EC400DA6239 /* odum.cpp in Sources */, + A7E9B90C12D37EC400DA6239 /* optionparser.cpp in Sources */, + A7E9B90D12D37EC400DA6239 /* ordervector.cpp in Sources */, + A7E9B90E12D37EC400DA6239 /* otuhierarchycommand.cpp in Sources */, + A7E9B90F12D37EC400DA6239 /* overlap.cpp in Sources */, + A7E9B91012D37EC400DA6239 /* pairwiseseqscommand.cpp in Sources */, + A7E9B91112D37EC400DA6239 /* parsefastaqcommand.cpp in Sources */, + A7E9B91212D37EC400DA6239 /* parselistscommand.cpp in Sources */, + A7E9B91312D37EC400DA6239 /* parsimony.cpp in Sources */, + A7E9B91412D37EC400DA6239 /* parsimonycommand.cpp in Sources */, + A7E9B91512D37EC400DA6239 /* pcoacommand.cpp in Sources */, + A7E9B91612D37EC400DA6239 /* phylodiversity.cpp in Sources */, + A7E9B91712D37EC400DA6239 /* phylodiversitycommand.cpp in Sources */, + A7E9B91812D37EC400DA6239 /* phylosummary.cpp in Sources */, + A7E9B91912D37EC400DA6239 /* phylotree.cpp in Sources */, + A7E9B91A12D37EC400DA6239 /* phylotypecommand.cpp in Sources */, + A7E9B91B12D37EC400DA6239 /* pintail.cpp in Sources */, + A7E9B91C12D37EC400DA6239 /* pipelinepdscommand.cpp in Sources */, + A7E9B91D12D37EC400DA6239 /* preclustercommand.cpp in Sources */, + A7E9B91E12D37EC400DA6239 /* prng.cpp in Sources */, + A7E9B91F12D37EC400DA6239 /* progress.cpp in Sources */, + A7E9B92012D37EC400DA6239 /* qstat.cpp in Sources */, + A7E9B92112D37EC400DA6239 /* qualityscores.cpp in Sources */, + A7E9B92212D37EC400DA6239 /* quitcommand.cpp in Sources */, + A7E9B92312D37EC400DA6239 /* rabundvector.cpp in Sources */, + A7E9B92412D37EC400DA6239 /* rarecalc.cpp in Sources */, + A7E9B92512D37EC400DA6239 /* raredisplay.cpp in Sources */, + A7E9B92612D37EC400DA6239 /* rarefact.cpp in Sources */, + A7E9B92712D37EC400DA6239 /* rarefactcommand.cpp in Sources */, + A7E9B92812D37EC400DA6239 /* rarefactsharedcommand.cpp in Sources */, + A7E9B92912D37EC400DA6239 /* readblast.cpp in Sources */, + A7E9B92A12D37EC400DA6239 /* readcluster.cpp in Sources */, + A7E9B92B12D37EC400DA6239 /* readcolumn.cpp in Sources */, + A7E9B92C12D37EC400DA6239 /* readdistcommand.cpp in Sources */, + A7E9B92D12D37EC400DA6239 /* readotu.cpp in Sources */, + A7E9B92E12D37EC400DA6239 /* readotucommand.cpp in Sources */, + A7E9B92F12D37EC400DA6239 /* readphylip.cpp in Sources */, + A7E9B93012D37EC400DA6239 /* readtree.cpp in Sources */, + A7E9B93112D37EC400DA6239 /* readtreecommand.cpp in Sources */, + A7E9B93212D37EC400DA6239 /* removegroupscommand.cpp in Sources */, + A7E9B93312D37EC400DA6239 /* removelineagecommand.cpp in Sources */, + A7E9B93412D37EC400DA6239 /* removeotuscommand.cpp in Sources */, + A7E9B93512D37EC400DA6239 /* removeseqscommand.cpp in Sources */, + A7E9B93612D37EC400DA6239 /* reportfile.cpp in Sources */, + A7E9B93712D37EC400DA6239 /* reversecommand.cpp in Sources */, + A7E9B93812D37EC400DA6239 /* sabundvector.cpp in Sources */, + A7E9B93912D37EC400DA6239 /* screenseqscommand.cpp in Sources */, + A7E9B93A12D37EC400DA6239 /* secondarystructurecommand.cpp in Sources */, + A7E9B93B12D37EC400DA6239 /* sensspeccommand.cpp in Sources */, + A7E9B93C12D37EC400DA6239 /* seqerrorcommand.cpp in Sources */, + A7E9B93D12D37EC400DA6239 /* seqsummarycommand.cpp in Sources */, + A7E9B93E12D37EC400DA6239 /* sequence.cpp in Sources */, + A7E9B93F12D37EC400DA6239 /* sequencedb.cpp in Sources */, + A7E9B94012D37EC400DA6239 /* setdircommand.cpp in Sources */, + A7E9B94112D37EC400DA6239 /* setlogfilecommand.cpp in Sources */, + A7E9B94212D37EC400DA6239 /* sffinfocommand.cpp in Sources */, + A7E9B94312D37EC400DA6239 /* shannon.cpp in Sources */, + A7E9B94412D37EC400DA6239 /* shannoneven.cpp in Sources */, + A7E9B94512D37EC400DA6239 /* sharedace.cpp in Sources */, + A7E9B94612D37EC400DA6239 /* sharedanderbergs.cpp in Sources */, + A7E9B94712D37EC400DA6239 /* sharedbraycurtis.cpp in Sources */, + A7E9B94812D37EC400DA6239 /* sharedchao1.cpp in Sources */, + A7E9B94912D37EC400DA6239 /* sharedcommand.cpp in Sources */, + A7E9B94A12D37EC400DA6239 /* sharedjabund.cpp in Sources */, + A7E9B94B12D37EC400DA6239 /* sharedjackknife.cpp in Sources */, + A7E9B94C12D37EC400DA6239 /* sharedjclass.cpp in Sources */, + A7E9B94D12D37EC400DA6239 /* sharedjest.cpp in Sources */, + A7E9B94E12D37EC400DA6239 /* sharedkstest.cpp in Sources */, + A7E9B94F12D37EC400DA6239 /* sharedkulczynski.cpp in Sources */, + A7E9B95012D37EC400DA6239 /* sharedkulczynskicody.cpp in Sources */, + A7E9B95112D37EC400DA6239 /* sharedlennon.cpp in Sources */, + A7E9B95212D37EC400DA6239 /* sharedlistvector.cpp in Sources */, + A7E9B95312D37EC400DA6239 /* sharedmarczewski.cpp in Sources */, + A7E9B95412D37EC400DA6239 /* sharedmorisitahorn.cpp in Sources */, + A7E9B95512D37EC400DA6239 /* sharedochiai.cpp in Sources */, + A7E9B95612D37EC400DA6239 /* sharedordervector.cpp in Sources */, + A7E9B95712D37EC400DA6239 /* sharedrabundfloatvector.cpp in Sources */, + A7E9B95812D37EC400DA6239 /* sharedrabundvector.cpp in Sources */, + A7E9B95912D37EC400DA6239 /* sharedsabundvector.cpp in Sources */, + A7E9B95A12D37EC400DA6239 /* sharedsobs.cpp in Sources */, + A7E9B95B12D37EC400DA6239 /* sharedsobscollectsummary.cpp in Sources */, + A7E9B95C12D37EC400DA6239 /* sharedsorabund.cpp in Sources */, + A7E9B95D12D37EC400DA6239 /* sharedsorclass.cpp in Sources */, + A7E9B95E12D37EC400DA6239 /* sharedsorest.cpp in Sources */, + A7E9B95F12D37EC400DA6239 /* sharedthetan.cpp in Sources */, + A7E9B96012D37EC400DA6239 /* sharedthetayc.cpp in Sources */, + A7E9B96112D37EC400DA6239 /* sharedutilities.cpp in Sources */, + A7E9B96212D37EC400DA6239 /* shen.cpp in Sources */, + A7E9B96312D37EC400DA6239 /* shhhercommand.cpp in Sources */, + A7E9B96412D37EC400DA6239 /* simpson.cpp in Sources */, + A7E9B96512D37EC400DA6239 /* simpsoneven.cpp in Sources */, + A7E9B96612D37EC400DA6239 /* singlelinkage.cpp in Sources */, + A7E9B96712D37EC400DA6239 /* slayer.cpp in Sources */, + A7E9B96812D37EC400DA6239 /* slibshuff.cpp in Sources */, + A7E9B96912D37EC400DA6239 /* smithwilson.cpp in Sources */, + A7E9B96A12D37EC400DA6239 /* soergel.cpp in Sources */, + A7E9B96B12D37EC400DA6239 /* solow.cpp in Sources */, + A7E9B96C12D37EC400DA6239 /* sparsematrix.cpp in Sources */, + A7E9B96D12D37EC400DA6239 /* spearman.cpp in Sources */, + A7E9B96E12D37EC400DA6239 /* speciesprofile.cpp in Sources */, + A7E9B96F12D37EC400DA6239 /* splitabundcommand.cpp in Sources */, + A7E9B97012D37EC400DA6239 /* splitgroupscommand.cpp in Sources */, + A7E9B97112D37EC400DA6239 /* splitmatrix.cpp in Sources */, + A7E9B97212D37EC400DA6239 /* structchi2.cpp in Sources */, + A7E9B97312D37EC400DA6239 /* structchord.cpp in Sources */, + A7E9B97412D37EC400DA6239 /* structeuclidean.cpp in Sources */, + A7E9B97512D37EC400DA6239 /* structkulczynski.cpp in Sources */, + A7E9B97612D37EC400DA6239 /* structpearson.cpp in Sources */, + A7E9B97712D37EC400DA6239 /* subsamplecommand.cpp in Sources */, + A7E9B97812D37EC400DA6239 /* suffixdb.cpp in Sources */, + A7E9B97912D37EC400DA6239 /* suffixnodes.cpp in Sources */, + A7E9B97A12D37EC400DA6239 /* suffixtree.cpp in Sources */, + A7E9B97B12D37EC400DA6239 /* summarycommand.cpp in Sources */, + A7E9B97C12D37EC400DA6239 /* summarysharedcommand.cpp in Sources */, + A7E9B97D12D37EC400DA6239 /* systemcommand.cpp in Sources */, + A7E9B97E12D37EC400DA6239 /* taxonomyequalizer.cpp in Sources */, + A7E9B97F12D37EC400DA6239 /* tree.cpp in Sources */, + A7E9B98012D37EC400DA6239 /* treegroupscommand.cpp in Sources */, + A7E9B98112D37EC400DA6239 /* treemap.cpp in Sources */, + A7E9B98212D37EC400DA6239 /* treenode.cpp in Sources */, + A7E9B98312D37EC400DA6239 /* trimflowscommand.cpp in Sources */, + A7E9B98412D37EC400DA6239 /* trimseqscommand.cpp in Sources */, + A7E9B98512D37EC400DA6239 /* unifracunweightedcommand.cpp in Sources */, + A7E9B98612D37EC400DA6239 /* unifracweightedcommand.cpp in Sources */, + A7E9B98712D37EC400DA6239 /* unweighted.cpp in Sources */, + A7E9B98812D37EC400DA6239 /* uvest.cpp in Sources */, + A7E9B98912D37EC400DA6239 /* validcalculator.cpp in Sources */, + A7E9B98A12D37EC400DA6239 /* validparameter.cpp in Sources */, + A7E9B98B12D37EC400DA6239 /* venn.cpp in Sources */, + A7E9B98C12D37EC400DA6239 /* venncommand.cpp in Sources */, + A7E9B98D12D37EC400DA6239 /* weighted.cpp in Sources */, + A7E9B98E12D37EC400DA6239 /* weightedlinkage.cpp in Sources */, + A7E9B98F12D37EC400DA6239 /* whittaker.cpp in Sources */, + A70332B712D3A13400761E33 /* makefile in Sources */, + A7FC480E12D788F20055BC5C /* linearalgebra.cpp in Sources */, + A7FC486712D795D60055BC5C /* pcacommand.cpp in Sources */, + A713EBAC12DC7613000092AC /* readphylipvector.cpp in Sources */, + A713EBED12DC7C5E000092AC /* nmdscommand.cpp in Sources */, + A727864412E9E28C00F86ABA /* removerarecommand.cpp in Sources */, + A71FE12C12EDF72400963CA7 /* mergegroupscommand.cpp in Sources */, + 7E6BE10A12F710D8007ADDBE /* refchimeratest.cpp in Sources */, + A7A61F2D130062E000E05B6B /* amovacommand.cpp in Sources */, + A75790591301749D00A30DAB /* homovacommand.cpp in Sources */, ); runOnlyForDeploymentPostprocessing = 0; }; /* End PBXSourcesBuildPhase section */ /* Begin XCBuildConfiguration section */ - 1DEB923208733DC60010E9CD /* Debug */ = { + 1DEB928608733DD80010E9CD /* Debug */ = { isa = XCBuildConfiguration; buildSettings = { + ALWAYS_SEARCH_USER_PATHS = NO; COPY_PHASE_STRIP = NO; GCC_DYNAMIC_NO_PIC = NO; GCC_ENABLE_FIX_AND_CONTINUE = YES; GCC_MODEL_TUNING = G5; GCC_OPTIMIZATION_LEVEL = 0; - GCC_PREPROCESSOR_DEFINITIONS = ( - "_GLIBCXX_DEBUG=1", - "_GLIBCXX_DEBUG_PEDANTIC=1", - ); INSTALL_PATH = /usr/local/bin; - LIBRARY_SEARCH_PATHS = ( - "$(inherited)", - "\"$(SRCROOT)/../readline-6.0\"", - ); - PRODUCT_NAME = mothur; - ZERO_LINK = YES; + PRODUCT_NAME = Mothur; }; name = Debug; }; - 1DEB923308733DC60010E9CD /* Release */ = { + 1DEB928708733DD80010E9CD /* Release */ = { isa = XCBuildConfiguration; buildSettings = { + ALWAYS_SEARCH_USER_PATHS = NO; DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym"; + DEPLOYMENT_LOCATION = YES; GCC_MODEL_TUNING = G5; - INSTALL_PATH = /usr/local/bin; - LIBRARY_SEARCH_PATHS = ( - "$(inherited)", - "\"$(SRCROOT)/../readline-6.0\"", - ); - PRODUCT_NAME = mothur; + GCC_WARN_UNUSED_VALUE = YES; + INSTALL_PATH = ./; + PRODUCT_NAME = Mothur; }; name = Release; }; - 1DEB923608733DC60010E9CD /* Debug */ = { + 1DEB928A08733DD80010E9CD /* Debug */ = { isa = XCBuildConfiguration; buildSettings = { - ARCHS = "$(ARCHS_STANDARD_64_BIT_PRE_XCODE_3_1)"; - ARCHS_STANDARD_64_BIT_PRE_XCODE_3_1 = x86_64; + ARCHS = "$(ARCHS_STANDARD_32_64_BIT)"; + DEPLOYMENT_LOCATION = NO; + GCC_C_LANGUAGE_STANDARD = gnu99; GCC_OPTIMIZATION_LEVEL = 3; + GCC_PREPROCESSOR_DEFINITIONS = ( + "MOTHUR_FILES=\"\\\"../release\\\"\"", + "VERSION=\"\\\"1.16.0\\\"\"", + "RELEASE_DATE=\"\\\"2/7/2011\\\"\"", + ); GCC_WARN_ABOUT_MISSING_NEWLINE = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES; - GCC_WARN_ALLOW_INCOMPLETE_PROTOCOL = NO; - GCC_WARN_PEDANTIC = NO; GCC_WARN_UNUSED_VARIABLE = YES; - OTHER_CPLUSPLUSFLAGS = ""; + INSTALL_PATH = ""; + MACH_O_TYPE = mh_execute; + ONLY_ACTIVE_ARCH = YES; + OTHER_CPLUSPLUSFLAGS = ( + "-DUSE_READLINE", + "-DBIT_VERSION", + "$(OTHER_CFLAGS)", + ); + OTHER_LDFLAGS = ( + "-lncurses", + "-lreadline", + ); PREBINDING = NO; - SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk"; - WARNING_CFLAGS = ""; + SDKROOT = macosx10.5; }; name = Debug; }; - 1DEB923708733DC60010E9CD /* Release */ = { + 1DEB928B08733DD80010E9CD /* Release */ = { isa = XCBuildConfiguration; buildSettings = { - ARCHS = "$(ARCHS_STANDARD_64_BIT_PRE_XCODE_3_1)"; - ARCHS_STANDARD_64_BIT_PRE_XCODE_3_1 = x86_64; + ARCHS = "$(ARCHS_STANDARD_32_64_BIT)"; + DEPLOYMENT_LOCATION = NO; + GCC_C_LANGUAGE_STANDARD = gnu99; + GCC_GENERATE_DEBUGGING_SYMBOLS = NO; + GCC_MODEL_TUNING = ""; GCC_OPTIMIZATION_LEVEL = 3; + GCC_PREPROCESSOR_DEFINITIONS = ( + "MOTHUR_FILES=\"\\\"../release\\\"\"", + "VERSION=\"\\\"1.15.0\\\"\"", + "RELEASE_DATE=\"\\\"12/10/2010\\\"\"", + ); GCC_WARN_ABOUT_MISSING_NEWLINE = YES; - GCC_WARN_ABOUT_MISSING_PROTOTYPES = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES; - GCC_WARN_ALLOW_INCOMPLETE_PROTOCOL = NO; GCC_WARN_MISSING_PARENTHESES = YES; - GCC_WARN_PEDANTIC = YES; + GCC_WARN_MULTIPLE_DEFINITION_TYPES_FOR_SELECTOR = YES; GCC_WARN_UNUSED_FUNCTION = YES; - GCC_WARN_UNUSED_PARAMETER = NO; + GCC_WARN_UNUSED_PARAMETER = YES; GCC_WARN_UNUSED_VALUE = YES; GCC_WARN_UNUSED_VARIABLE = YES; + INSTALL_PATH = ""; + MACH_O_TYPE = mh_execute; OTHER_CPLUSPLUSFLAGS = ( - "-ansi", - "-pedantic", - "-wall", - "-lreadline", "-DUSE_READLINE", + "-DBIT_VERSION", + "$(OTHER_CFLAGS)", + ); + OTHER_LDFLAGS = ( + "-lncurses", + "-lreadline", ); PREBINDING = NO; - SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk"; - SYMROOT = /Users/johnwestcott/Desktop; - WARNING_CFLAGS = ""; + SDKROOT = macosx10.5; }; name = Release; }; /* End XCBuildConfiguration section */ /* Begin XCConfigurationList section */ - 1DEB923108733DC60010E9CD /* Build configuration list for PBXNativeTarget "mothur" */ = { + 1DEB928508733DD80010E9CD /* Build configuration list for PBXNativeTarget "Mothur" */ = { isa = XCConfigurationList; buildConfigurations = ( - 1DEB923208733DC60010E9CD /* Debug */, - 1DEB923308733DC60010E9CD /* Release */, + 1DEB928608733DD80010E9CD /* Debug */, + 1DEB928708733DD80010E9CD /* Release */, ); defaultConfigurationIsVisible = 0; defaultConfigurationName = Release; }; - 1DEB923508733DC60010E9CD /* Build configuration list for PBXProject "Mothur" */ = { + 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */ = { isa = XCConfigurationList; buildConfigurations = ( - 1DEB923608733DC60010E9CD /* Debug */, - 1DEB923708733DC60010E9CD /* Release */, + 1DEB928A08733DD80010E9CD /* Debug */, + 1DEB928B08733DD80010E9CD /* Release */, ); defaultConfigurationIsVisible = 0; defaultConfigurationName = Release;