adding more error checking for list and group files. outputs missing.names or missin...

[mothur.git] / Mothur.xcodeproj / project.pbxproj

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 93e0e58cf60e16ef5098d680acc14637f59403c0..7f74d48b66e3c8251cfedba52695f71b2457e720 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -7,22 +7,85 @@
        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 */; };
+               3799A9500FD6A58C00E33EDE /* distancedb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3799A94C0FD6A58C00E33EDE /* distancedb.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 */; };
-               37AFC7A30F44703E005F492D /* readsharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37AFC7A20F44703E005F492D /* readsharedcommand.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 */; };
@@ -37,7 +100,6 @@
                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 */; };
-               37D928640F21331F001D4494 /* errorchecking.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927D90F21331F001D4494 /* errorchecking.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 */; };
@@ -50,10 +112,8 @@
                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 */; };
-               37D928710F21331F001D4494 /* nocommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927F20F21331F001D4494 /* nocommand.cpp */; };
                37D928720F21331F001D4494 /* npshannon.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927F40F21331F001D4494 /* npshannon.cpp */; };
                37D928730F21331F001D4494 /* ordervector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927F70F21331F001D4494 /* ordervector.cpp */; };
-               37D928740F21331F001D4494 /* parselistcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927F90F21331F001D4494 /* parselistcommand.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 */; };
@@ -62,11 +122,9 @@
                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 */; };
-               37D928800F21331F001D4494 /* readmatrix.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928120F21331F001D4494 /* readmatrix.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 */; };
-               37D928870F21331F001D4494 /* shared.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928200F21331F001D4494 /* shared.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 */; };
@@ -89,11 +147,31 @@
                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 */; };
-               37D9289E0F21331F001D4494 /* validcommands.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928510F21331F001D4494 /* validcommands.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 */; };
+               A70B53AA0F4CD7AD0064797E /* getgroupcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */; };
+               A70B53AB0F4CD7AD0064797E /* getlabelcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */; };
+               A70B53AC0F4CD7AD0064797E /* getlinecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */; };
+               A70DECD91063D8B40057C03C /* secondarystructurecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70DECD81063D8B40057C03C /* secondarystructurecommand.cpp */; };
+               A7283FF81056CAE100D0CC69 /* chimeracheckrdp.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7283FF71056CAE100D0CC69 /* chimeracheckrdp.cpp */; };
+               A75B887E104C16860083C454 /* ccode.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A75B887B104C16860083C454 /* ccode.cpp */; };
+               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 */; };
 /* End PBXBuildFile section */
 
 /* Begin PBXCopyFilesBuildPhase section */
@@ -110,188 +188,355 @@
 /* End PBXCopyFilesBuildPhase section */
 
 /* Begin PBXFileReference section */
-               372E126E0F26365B0095CF7E /* readotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotucommand.h; sourceTree = "<group>"; };
-               372E126F0F26365B0095CF7E /* readotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readotucommand.cpp; sourceTree = "<group>"; };
-               372E12940F263D5A0095CF7E /* readdistcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readdistcommand.h; sourceTree = "<group>"; };
-               372E12950F263D5A0095CF7E /* readdistcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readdistcommand.cpp; sourceTree = "<group>"; };
-               372E12EC0F264D320095CF7E /* commandfactory.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = commandfactory.cpp; sourceTree = "<group>"; };
-               374610760F40645300460C57 /* unifracweightedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unifracweightedcommand.h; sourceTree = "<group>"; };
-               374610770F40645300460C57 /* unifracweightedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unifracweightedcommand.cpp; sourceTree = "<group>"; };
-               3746107C0F4064D100460C57 /* weighted.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = weighted.h; sourceTree = "<group>"; };
-               3746107D0F4064D100460C57 /* weighted.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = weighted.cpp; sourceTree = "<group>"; };
-               374610810F40652400460C57 /* unweighted.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unweighted.h; sourceTree = "<group>"; };
-               374610820F40652400460C57 /* unweighted.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unweighted.cpp; sourceTree = "<group>"; };
-               3746109B0F40657600460C57 /* unifracunweightedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unifracunweightedcommand.h; sourceTree = "<group>"; };
-               3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unifracunweightedcommand.cpp; sourceTree = "<group>"; };
-               379293C10F2DE73400B9034A /* treemap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treemap.h; sourceTree = "<group>"; };
-               379293C20F2DE73400B9034A /* treemap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treemap.cpp; sourceTree = "<group>"; };
-               3792946E0F2E191800B9034A /* parsimonycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimonycommand.h; sourceTree = "<group>"; };
-               3792946F0F2E191800B9034A /* parsimonycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsimonycommand.cpp; sourceTree = "<group>"; };
-               379294880F2E258500B9034A /* parsimony.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimony.h; sourceTree = "<group>"; };
-               379294890F2E258500B9034A /* parsimony.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsimony.cpp; sourceTree = "<group>"; };
-               3792948D0F2E271100B9034A /* treecalculator.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treecalculator.h; sourceTree = "<group>"; };
-               37AD4CE20F28AEA300AA2D49 /* sharedlistvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedlistvector.h; sourceTree = "<group>"; };
-               37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedlistvector.cpp; sourceTree = "<group>"; };
-               37AD4DB90F28E2FE00AA2D49 /* tree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = tree.h; sourceTree = "<group>"; };
-               37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = tree.cpp; sourceTree = "<group>"; };
-               37AD4DC80F28F3DD00AA2D49 /* readtree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtree.h; sourceTree = "<group>"; };
-               37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtree.cpp; sourceTree = "<group>"; };
-               37AFC71D0F445386005F492D /* sharedsobscollectsummary.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsobscollectsummary.h; sourceTree = "<group>"; };
-               37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsobscollectsummary.cpp; sourceTree = "<group>"; };
-               37AFC7A10F44703E005F492D /* readsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readsharedcommand.h; sourceTree = "<group>"; };
-               37AFC7A20F44703E005F492D /* readsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readsharedcommand.cpp; sourceTree = "<group>"; };
-               37B28F660F27590100808A62 /* deconvolutecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = deconvolutecommand.h; sourceTree = "<group>"; };
-               37B28F670F27590100808A62 /* deconvolutecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = deconvolutecommand.cpp; sourceTree = "<group>"; };
-               37D927B80F21331F001D4494 /* ace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ace.cpp; sourceTree = "<group>"; };
-               37D927B90F21331F001D4494 /* ace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ace.h; sourceTree = "<group>"; };
-               37D927BA0F21331F001D4494 /* averagelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = averagelinkage.cpp; sourceTree = "<group>"; };
-               37D927BB0F21331F001D4494 /* bootstrap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bootstrap.cpp; sourceTree = "<group>"; };
-               37D927BC0F21331F001D4494 /* bootstrap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bootstrap.h; sourceTree = "<group>"; };
-               37D927BD0F21331F001D4494 /* calculator.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = calculator.cpp; sourceTree = "<group>"; };
-               37D927BE0F21331F001D4494 /* calculator.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = calculator.h; sourceTree = "<group>"; };
-               37D927BF0F21331F001D4494 /* chao1.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chao1.cpp; sourceTree = "<group>"; };
-               37D927C00F21331F001D4494 /* chao1.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chao1.h; sourceTree = "<group>"; };
-               37D927C10F21331F001D4494 /* cluster.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = cluster.cpp; sourceTree = "<group>"; };
-               37D927C20F21331F001D4494 /* cluster.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = cluster.hpp; sourceTree = "<group>"; };
-               37D927C30F21331F001D4494 /* clustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clustercommand.cpp; sourceTree = "<group>"; };
-               37D927C40F21331F001D4494 /* clustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clustercommand.h; sourceTree = "<group>"; };
-               37D927C50F21331F001D4494 /* collect.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = collect.cpp; sourceTree = "<group>"; };
-               37D927C60F21331F001D4494 /* collect.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collect.h; sourceTree = "<group>"; };
-               37D927C70F21331F001D4494 /* collectcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = collectcommand.cpp; sourceTree = "<group>"; };
-               37D927C80F21331F001D4494 /* collectcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectcommand.h; sourceTree = "<group>"; };
-               37D927C90F21331F001D4494 /* collectdisplay.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectdisplay.h; sourceTree = "<group>"; };
-               37D927CA0F21331F001D4494 /* collectorscurvedata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectorscurvedata.h; sourceTree = "<group>"; };
-               37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = collectsharedcommand.cpp; sourceTree = "<group>"; };
-               37D927CC0F21331F001D4494 /* collectsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectsharedcommand.h; sourceTree = "<group>"; };
-               37D927CD0F21331F001D4494 /* command.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = command.hpp; sourceTree = "<group>"; };
-               37D927CF0F21331F001D4494 /* commandfactory.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = commandfactory.hpp; sourceTree = "<group>"; };
-               37D927D00F21331F001D4494 /* commandoptionparser.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = commandoptionparser.cpp; sourceTree = "<group>"; };
-               37D927D10F21331F001D4494 /* commandoptionparser.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = commandoptionparser.hpp; sourceTree = "<group>"; };
-               37D927D20F21331F001D4494 /* completelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = completelinkage.cpp; sourceTree = "<group>"; };
-               37D927D30F21331F001D4494 /* database.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = database.cpp; sourceTree = "<group>"; };
-               37D927D40F21331F001D4494 /* database.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = database.hpp; sourceTree = "<group>"; };
-               37D927D50F21331F001D4494 /* datavector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = datavector.hpp; sourceTree = "<group>"; };
-               37D927D60F21331F001D4494 /* display.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = display.h; sourceTree = "<group>"; };
-               37D927D70F21331F001D4494 /* engine.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = engine.cpp; sourceTree = "<group>"; };
-               37D927D80F21331F001D4494 /* engine.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = engine.hpp; sourceTree = "<group>"; };
-               37D927D90F21331F001D4494 /* errorchecking.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = errorchecking.cpp; sourceTree = "<group>"; };
-               37D927DA0F21331F001D4494 /* errorchecking.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = errorchecking.h; sourceTree = "<group>"; };
-               37D927DB0F21331F001D4494 /* fastamap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fastamap.cpp; sourceTree = "<group>"; };
-               37D927DC0F21331F001D4494 /* fastamap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fastamap.h; sourceTree = "<group>"; };
-               37D927DD0F21331F001D4494 /* fileoutput.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fileoutput.cpp; sourceTree = "<group>"; };
-               37D927DE0F21331F001D4494 /* fileoutput.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fileoutput.h; sourceTree = "<group>"; };
-               37D927DF0F21331F001D4494 /* globaldata.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = globaldata.cpp; sourceTree = "<group>"; };
-               37D927E00F21331F001D4494 /* globaldata.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = globaldata.hpp; sourceTree = "<group>"; };
-               37D927E10F21331F001D4494 /* groupmap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = groupmap.cpp; sourceTree = "<group>"; };
-               37D927E20F21331F001D4494 /* groupmap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = groupmap.h; sourceTree = "<group>"; };
-               37D927E30F21331F001D4494 /* helpcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = helpcommand.cpp; sourceTree = "<group>"; };
-               37D927E40F21331F001D4494 /* helpcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = helpcommand.h; sourceTree = "<group>"; };
-               37D927E50F21331F001D4494 /* inputdata.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = inputdata.cpp; sourceTree = "<group>"; };
-               37D927E60F21331F001D4494 /* inputdata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = inputdata.h; sourceTree = "<group>"; };
-               37D927E70F21331F001D4494 /* jackknife.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = jackknife.cpp; sourceTree = "<group>"; };
-               37D927E80F21331F001D4494 /* jackknife.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = jackknife.h; sourceTree = "<group>"; };
-               37D927E90F21331F001D4494 /* kmer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = kmer.cpp; sourceTree = "<group>"; };
-               37D927EA0F21331F001D4494 /* kmer.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = kmer.hpp; sourceTree = "<group>"; };
-               37D927EB0F21331F001D4494 /* kmerdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = kmerdb.cpp; sourceTree = "<group>"; };
-               37D927EC0F21331F001D4494 /* kmerdb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = kmerdb.hpp; sourceTree = "<group>"; };
-               37D927ED0F21331F001D4494 /* listvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = listvector.cpp; sourceTree = "<group>"; };
-               37D927EE0F21331F001D4494 /* listvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = listvector.hpp; sourceTree = "<group>"; };
-               37D927EF0F21331F001D4494 /* mothur.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mothur.cpp; sourceTree = "<group>"; };
-               37D927F00F21331F001D4494 /* nameassignment.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nameassignment.cpp; sourceTree = "<group>"; };
-               37D927F10F21331F001D4494 /* nameassignment.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = nameassignment.hpp; sourceTree = "<group>"; };
-               37D927F20F21331F001D4494 /* nocommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nocommand.cpp; sourceTree = "<group>"; };
-               37D927F30F21331F001D4494 /* nocommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = nocommand.h; sourceTree = "<group>"; };
-               37D927F40F21331F001D4494 /* npshannon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = npshannon.cpp; sourceTree = "<group>"; };
-               37D927F50F21331F001D4494 /* npshannon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = npshannon.h; sourceTree = "<group>"; };
-               37D927F60F21331F001D4494 /* observable.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = observable.h; sourceTree = "<group>"; };
-               37D927F70F21331F001D4494 /* ordervector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ordervector.cpp; sourceTree = "<group>"; };
-               37D927F80F21331F001D4494 /* ordervector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = ordervector.hpp; sourceTree = "<group>"; };
-               37D927F90F21331F001D4494 /* parselistcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parselistcommand.cpp; sourceTree = "<group>"; };
-               37D927FA0F21331F001D4494 /* parselistcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parselistcommand.h; sourceTree = "<group>"; };
-               37D927FB0F21331F001D4494 /* progress.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = progress.cpp; sourceTree = "<group>"; };
-               37D927FC0F21331F001D4494 /* progress.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = progress.hpp; sourceTree = "<group>"; };
-               37D927FD0F21331F001D4494 /* quitcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = quitcommand.cpp; sourceTree = "<group>"; };
-               37D927FE0F21331F001D4494 /* quitcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = quitcommand.h; sourceTree = "<group>"; };
-               37D927FF0F21331F001D4494 /* rabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rabundvector.cpp; sourceTree = "<group>"; };
-               37D928000F21331F001D4494 /* rabundvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = rabundvector.hpp; sourceTree = "<group>"; };
-               37D928010F21331F001D4494 /* rarecalc.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarecalc.cpp; sourceTree = "<group>"; };
-               37D928020F21331F001D4494 /* rarecalc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarecalc.h; sourceTree = "<group>"; };
-               37D928030F21331F001D4494 /* raredisplay.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = raredisplay.cpp; sourceTree = "<group>"; };
-               37D928040F21331F001D4494 /* raredisplay.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = raredisplay.h; sourceTree = "<group>"; };
-               37D928050F21331F001D4494 /* rarefact.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefact.cpp; sourceTree = "<group>"; };
-               37D928060F21331F001D4494 /* rarefact.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefact.h; sourceTree = "<group>"; };
-               37D928070F21331F001D4494 /* rarefactcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefactcommand.cpp; sourceTree = "<group>"; };
-               37D928080F21331F001D4494 /* rarefactcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactcommand.h; sourceTree = "<group>"; };
-               37D928090F21331F001D4494 /* rarefactioncurvedata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactioncurvedata.h; sourceTree = "<group>"; };
-               37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefactsharedcommand.cpp; sourceTree = "<group>"; };
-               37D9280B0F21331F001D4494 /* rarefactsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactsharedcommand.h; sourceTree = "<group>"; };
-               37D928120F21331F001D4494 /* readmatrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readmatrix.cpp; sourceTree = "<group>"; };
-               37D928130F21331F001D4494 /* readmatrix.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = readmatrix.hpp; sourceTree = "<group>"; };
-               37D9281A0F21331F001D4494 /* sabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sabundvector.cpp; sourceTree = "<group>"; };
-               37D9281B0F21331F001D4494 /* sabundvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sabundvector.hpp; sourceTree = "<group>"; };
-               37D9281C0F21331F001D4494 /* sequence.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sequence.cpp; sourceTree = "<group>"; };
-               37D9281D0F21331F001D4494 /* sequence.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sequence.hpp; sourceTree = "<group>"; };
-               37D9281E0F21331F001D4494 /* shannon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shannon.cpp; sourceTree = "<group>"; };
-               37D9281F0F21331F001D4494 /* shannon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shannon.h; sourceTree = "<group>"; };
-               37D928200F21331F001D4494 /* shared.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shared.cpp; sourceTree = "<group>"; };
-               37D928210F21331F001D4494 /* shared.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shared.h; sourceTree = "<group>"; };
-               37D928220F21331F001D4494 /* sharedace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedace.cpp; sourceTree = "<group>"; };
-               37D928230F21331F001D4494 /* sharedace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedace.h; sourceTree = "<group>"; };
-               37D928240F21331F001D4494 /* sharedchao1.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedchao1.cpp; sourceTree = "<group>"; };
-               37D928250F21331F001D4494 /* sharedchao1.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedchao1.h; sourceTree = "<group>"; };
-               37D928260F21331F001D4494 /* sharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedcommand.cpp; sourceTree = "<group>"; };
-               37D928270F21331F001D4494 /* sharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedcommand.h; sourceTree = "<group>"; };
-               37D928280F21331F001D4494 /* sharedjabund.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjabund.cpp; sourceTree = "<group>"; };
-               37D928290F21331F001D4494 /* sharedjabund.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjabund.h; sourceTree = "<group>"; };
-               37D9282A0F21331F001D4494 /* sharedjclass.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjclass.cpp; sourceTree = "<group>"; };
-               37D9282B0F21331F001D4494 /* sharedjclass.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjclass.h; sourceTree = "<group>"; };
-               37D9282C0F21331F001D4494 /* sharedjest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjest.cpp; sourceTree = "<group>"; };
-               37D9282D0F21331F001D4494 /* sharedjest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjest.h; sourceTree = "<group>"; };
-               37D9282E0F21331F001D4494 /* sharedordervector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedordervector.cpp; sourceTree = "<group>"; };
-               37D9282F0F21331F001D4494 /* sharedordervector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedordervector.h; sourceTree = "<group>"; };
-               37D928300F21331F001D4494 /* sharedrabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedrabundvector.cpp; sourceTree = "<group>"; };
-               37D928310F21331F001D4494 /* sharedrabundvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedrabundvector.h; sourceTree = "<group>"; };
-               37D928320F21331F001D4494 /* sharedsabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsabundvector.cpp; sourceTree = "<group>"; };
-               37D928330F21331F001D4494 /* sharedsabundvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsabundvector.h; sourceTree = "<group>"; };
-               37D928340F21331F001D4494 /* sharedsobs.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsobs.cpp; sourceTree = "<group>"; };
-               37D928350F21331F001D4494 /* sharedsobs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsobs.h; sourceTree = "<group>"; };
-               37D928360F21331F001D4494 /* sharedsorabund.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorabund.cpp; sourceTree = "<group>"; };
-               37D928370F21331F001D4494 /* sharedsorabund.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsorabund.h; sourceTree = "<group>"; };
-               37D928380F21331F001D4494 /* sharedsorclass.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorclass.cpp; sourceTree = "<group>"; };
-               37D928390F21331F001D4494 /* sharedsorclass.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsorclass.h; sourceTree = "<group>"; };
-               37D9283A0F21331F001D4494 /* sharedsorest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorest.cpp; sourceTree = "<group>"; };
-               37D9283B0F21331F001D4494 /* sharedsorest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsorest.h; sourceTree = "<group>"; };
-               37D9283C0F21331F001D4494 /* sharedthetan.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedthetan.cpp; sourceTree = "<group>"; };
-               37D9283D0F21331F001D4494 /* sharedthetan.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedthetan.h; sourceTree = "<group>"; };
-               37D9283E0F21331F001D4494 /* sharedthetayc.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedthetayc.cpp; sourceTree = "<group>"; };
-               37D9283F0F21331F001D4494 /* sharedthetayc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedthetayc.h; sourceTree = "<group>"; };
-               37D928400F21331F001D4494 /* simpson.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = simpson.cpp; sourceTree = "<group>"; };
-               37D928410F21331F001D4494 /* simpson.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = simpson.h; sourceTree = "<group>"; };
-               37D928420F21331F001D4494 /* singlelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = singlelinkage.cpp; sourceTree = "<group>"; };
-               37D928430F21331F001D4494 /* sobs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sobs.h; sourceTree = "<group>"; };
-               37D928440F21331F001D4494 /* sparsematrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sparsematrix.cpp; sourceTree = "<group>"; };
-               37D928450F21331F001D4494 /* sparsematrix.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sparsematrix.hpp; sourceTree = "<group>"; };
-               37D928460F21331F001D4494 /* summarycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summarycommand.cpp; sourceTree = "<group>"; };
-               37D928470F21331F001D4494 /* summarycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarycommand.h; sourceTree = "<group>"; };
-               37D928480F21331F001D4494 /* summarydata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarydata.h; sourceTree = "<group>"; };
-               37D928490F21331F001D4494 /* summarydisplay.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarydisplay.h; sourceTree = "<group>"; };
-               37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summarysharedcommand.cpp; sourceTree = "<group>"; };
-               37D9284B0F21331F001D4494 /* summarysharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarysharedcommand.h; sourceTree = "<group>"; };
-               37D9284C0F21331F001D4494 /* utilities.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = utilities.hpp; sourceTree = "<group>"; };
-               37D9284D0F21331F001D4494 /* uvest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = uvest.cpp; sourceTree = "<group>"; };
-               37D9284E0F21331F001D4494 /* uvest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = uvest.h; sourceTree = "<group>"; };
-               37D9284F0F21331F001D4494 /* validcalculator.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = validcalculator.cpp; sourceTree = "<group>"; };
-               37D928500F21331F001D4494 /* validcalculator.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = validcalculator.h; sourceTree = "<group>"; };
-               37D928510F21331F001D4494 /* validcommands.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = validcommands.cpp; sourceTree = "<group>"; };
-               37D928520F21331F001D4494 /* validcommands.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = validcommands.h; sourceTree = "<group>"; };
-               37D928530F21331F001D4494 /* validparameter.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = validparameter.cpp; sourceTree = "<group>"; };
-               37D928540F21331F001D4494 /* validparameter.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = validparameter.h; sourceTree = "<group>"; };
-               37E5F3E10F29FD4200F8D827 /* treenode.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treenode.h; sourceTree = "<group>"; };
-               37E5F3E20F29FD4200F8D827 /* treenode.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treenode.cpp; sourceTree = "<group>"; };
-               37E5F4900F2A3DA800F8D827 /* readtreecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtreecommand.h; sourceTree = "<group>"; };
-               37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtreecommand.cpp; sourceTree = "<group>"; };
+               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; };
+               3799A94C0FD6A58C00E33EDE /* distancedb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = distancedb.cpp; sourceTree = SOURCE_ROOT; };
+               3799A94D0FD6A58C00E33EDE /* distancedb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = distancedb.hpp; 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; };
+               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; };
+               A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlinecommand.cpp; sourceTree = SOURCE_ROOT; };
+               A70B53A90F4CD7AD0064797E /* getlinecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlinecommand.h; sourceTree = SOURCE_ROOT; };
+               A70DECD71063D8B40057C03C /* secondarystructurecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = secondarystructurecommand.h; sourceTree = "<group>"; };
+               A70DECD81063D8B40057C03C /* secondarystructurecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = secondarystructurecommand.cpp; sourceTree = "<group>"; };
+               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; };
+               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; };
                C6859E8B029090EE04C91782 /* Mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = Mothur.1; sourceTree = "<group>"; };
+               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; };
 /* End PBXFileReference section */
 
 /* Begin PBXFrameworksBuildPhase section */
@@ -319,7 +564,10 @@
                        isa = PBXGroup;
                        children = (
                                37D927BA0F21331F001D4494 /* averagelinkage.cpp */,
+                               373C68DC0FC1C38D00137ACD /* blastalign.hpp */,
+                               373C68DB0FC1C38D00137ACD /* blastalign.cpp */,
                                37D928A60F2133C0001D4494 /* calculators */,
+                               374F2FE81006346600E97C66 /* chimera */,
                                37D927C20F21331F001D4494 /* cluster.hpp */,
                                37D927C10F21331F001D4494 /* cluster.cpp */,
                                37D928A90F2133E5001D4494 /* commands */,
@@ -333,8 +581,8 @@
                                37D927D10F21331F001D4494 /* commandoptionparser.hpp */,
                                37D927D00F21331F001D4494 /* commandoptionparser.cpp */,
                                37D927D20F21331F001D4494 /* completelinkage.cpp */,
-                               37D927D40F21331F001D4494 /* database.hpp */,
-                               37D927D30F21331F001D4494 /* database.cpp */,
+                               7E4130F70F8E58FA00381DD0 /* dlibshuff.h */,
+                               7E4130F60F8E58FA00381DD0 /* dlibshuff.cpp */,
                                37D927D60F21331F001D4494 /* display.h */,
                                37D927D80F21331F001D4494 /* engine.hpp */,
                                37D927D70F21331F001D4494 /* engine.cpp */,
@@ -343,16 +591,33 @@
                                37D927DD0F21331F001D4494 /* fileoutput.cpp */,
                                37D927E00F21331F001D4494 /* globaldata.hpp */,
                                37D927DF0F21331F001D4494 /* globaldata.cpp */,
+                               373C68BB0FC1C1A600137ACD /* gotohoverlap.hpp */,
+                               373C68BA0FC1C1A600137ACD /* gotohoverlap.cpp */,
+                               375873ED0F7D646F0040F377 /* heatmap.h */,
+                               375873EE0F7D646F0040F377 /* heatmap.cpp */,
+                               378598720FDD4C1500EF9D03 /* heatmapsim.h */,
+                               378598730FDD4C1500EF9D03 /* heatmapsim.cpp */,
                                37D927E60F21331F001D4494 /* inputdata.h */,
                                37D927E50F21331F001D4494 /* inputdata.cpp */,
-                               37D927EA0F21331F001D4494 /* kmer.hpp */,
-                               37D927E90F21331F001D4494 /* kmer.cpp */,
-                               37D927EC0F21331F001D4494 /* kmerdb.hpp */,
-                               37D927EB0F21331F001D4494 /* kmerdb.cpp */,
+                               7E412F420F8D213C00381DD0 /* libshuff.h */,
+                               7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */,
+                               37E3ED800F4D9D0D00B5DF02 /* mothur.h */,
                                37D927EF0F21331F001D4494 /* mothur.cpp */,
                                37D927F10F21331F001D4494 /* nameassignment.hpp */,
                                37D927F00F21331F001D4494 /* nameassignment.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 */,
@@ -360,20 +625,16 @@
                                37D928060F21331F001D4494 /* rarefact.h */,
                                37D928050F21331F001D4494 /* rarefact.cpp */,
                                37D928090F21331F001D4494 /* rarefactioncurvedata.h */,
-                               37D928130F21331F001D4494 /* readmatrix.hpp */,
-                               37D928120F21331F001D4494 /* readmatrix.cpp */,
-                               37AD4DC80F28F3DD00AA2D49 /* readtree.h */,
-                               37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */,
-                               37D9281D0F21331F001D4494 /* sequence.hpp */,
-                               37D9281C0F21331F001D4494 /* sequence.cpp */,
-                               37D928210F21331F001D4494 /* shared.h */,
-                               37D928200F21331F001D4494 /* shared.cpp */,
+                               3796441D0FB9B9650081FDB6 /* read */,
+                               211C38310F961DD400FEE541 /* sharedutilities.h */,
+                               211C38300F961DD400FEE541 /* sharedutilities.cpp */,
                                37D928420F21331F001D4494 /* singlelinkage.cpp */,
-                               37D928450F21331F001D4494 /* sparsematrix.hpp */,
-                               37D928440F21331F001D4494 /* sparsematrix.cpp */,
+                               7E412F470F8D21B600381DD0 /* slibshuff.h */,
+                               7E412F480F8D21B600381DD0 /* slibshuff.cpp */,
                                37D928480F21331F001D4494 /* summarydata.h */,
                                37D928490F21331F001D4494 /* summarydisplay.h */,
-                               37D9284C0F21331F001D4494 /* utilities.hpp */,
+                               37519AB30F810FAE00FED5E8 /* venn.h */,
+                               37519AB40F810FAE00FED5E8 /* venn.cpp */,
                        );
                        name = Source;
                        sourceTree = "<group>";
@@ -386,38 +647,121 @@
                        name = Products;
                        sourceTree = "<group>";
                };
+               374F2FE81006346600E97C66 /* chimera */ = {
+                       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 */,
+                               372A55531017922B00C5194B /* decalc.h */,
+                               372A55541017922B00C5194B /* decalc.cpp */,
+                               374F301110063B6F00E97C66 /* pintail.h */,
+                               374F301210063B6F00E97C66 /* pintail.cpp */,
+                       );
+                       name = chimera;
+                       sourceTree = "<group>";
+               };
+               3796441D0FB9B9650081FDB6 /* read */ = {
+                       isa = PBXGroup;
+                       children = (
+                               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 */,
+                       );
+                       name = read;
+                       sourceTree = "<group>";
+               };
                37D928A60F2133C0001D4494 /* calculators */ = {
                        isa = PBXGroup;
                        children = (
                                37D927BE0F21331F001D4494 /* calculator.h */,
-                               3792948D0F2E271100B9034A /* treecalculator.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 */,
@@ -428,19 +772,25 @@
                                37D928380F21331F001D4494 /* sharedsorclass.cpp */,
                                37D9283B0F21331F001D4494 /* sharedsorest.h */,
                                37D9283A0F21331F001D4494 /* sharedsorest.cpp */,
-                               37D9283C0F21331F001D4494 /* sharedthetan.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 */,
                        );
                        name = calculators;
                        sourceTree = "<group>";
@@ -449,20 +799,58 @@
                        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 */,
                                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 */,
+                               A70B53A90F4CD7AD0064797E /* getlinecommand.h */,
+                               A70B53A80F4CD7AD0064797E /* getlinecommand.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 */,
+                               375873F10F7D64800040F377 /* heatmapcommand.h */,
+                               375873F00F7D64800040F377 /* heatmapcommand.cpp */,
+                               378598640FDD497000EF9D03 /* heatmapsimcommand.h */,
+                               378598650FDD497000EF9D03 /* heatmapsimcommand.cpp */,
                                37D927E40F21331F001D4494 /* helpcommand.h */,
                                37D927E30F21331F001D4494 /* helpcommand.cpp */,
-                               37D927F20F21331F001D4494 /* nocommand.cpp */,
-                               37D927F30F21331F001D4494 /* nocommand.h */,
-                               37D927FA0F21331F001D4494 /* parselistcommand.h */,
-                               37D927F90F21331F001D4494 /* parselistcommand.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 */,
+                               375873F70F7D649C0040F377 /* nocommands.h */,
+                               375873F60F7D649C0040F377 /* nocommands.cpp */,
                                3792946E0F2E191800B9034A /* parsimonycommand.h */,
                                3792946F0F2E191800B9034A /* parsimonycommand.cpp */,
                                37D927FE0F21331F001D4494 /* quitcommand.h */,
@@ -475,20 +863,36 @@
                                372E12950F263D5A0095CF7E /* readdistcommand.cpp */,
                                372E126E0F26365B0095CF7E /* readotucommand.h */,
                                372E126F0F26365B0095CF7E /* readotucommand.cpp */,
-                               37AFC7A10F44703E005F492D /* readsharedcommand.h */,
-                               37AFC7A20F44703E005F492D /* readsharedcommand.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 */,
                                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 */,
                        );
                        name = commands;
                        sourceTree = "<group>";
@@ -496,11 +900,27 @@
                37D928AC0F213420001D4494 /* containers */ = {
                        isa = PBXGroup;
                        children = (
+                               373C68A10FC1C07D00137ACD /* alignment.hpp */,
+                               373C68A00FC1C07D00137ACD /* alignment.cpp */,
+                               373C68A30FC1C07D00137ACD /* alignmentcell.hpp */,
+                               373C68A20FC1C07D00137ACD /* alignmentcell.cpp */,
+                               373C69170FC1C8AF00137ACD /* blastdb.hpp */,
+                               373C69160FC1C8AF00137ACD /* blastdb.cpp */,
+                               37D927D40F21331F001D4494 /* database.hpp */,
+                               37D927D30F21331F001D4494 /* database.cpp */,
                                37D927D50F21331F001D4494 /* datavector.hpp */,
+                               3799A94D0FD6A58C00E33EDE /* distancedb.hpp */,
+                               3799A94C0FD6A58C00E33EDE /* 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 */,
                                37D927F80F21331F001D4494 /* ordervector.hpp */,
@@ -509,6 +929,10 @@
                                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 */,
@@ -517,6 +941,14 @@
                                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 */,
@@ -530,12 +962,8 @@
                37D928B10F213472001D4494 /* errorcheckor */ = {
                        isa = PBXGroup;
                        children = (
-                               37D927DA0F21331F001D4494 /* errorchecking.h */,
-                               37D927D90F21331F001D4494 /* errorchecking.cpp */,
                                37D928500F21331F001D4494 /* validcalculator.h */,
                                37D9284F0F21331F001D4494 /* validcalculator.cpp */,
-                               37D928520F21331F001D4494 /* validcommands.h */,
-                               37D928510F21331F001D4494 /* validcommands.cpp */,
                                37D928540F21331F001D4494 /* validparameter.h */,
                                37D928530F21331F001D4494 /* validparameter.cpp */,
                        );
@@ -607,7 +1035,6 @@
                                37D928610F21331F001D4494 /* completelinkage.cpp in Sources */,
                                37D928620F21331F001D4494 /* database.cpp in Sources */,
                                37D928630F21331F001D4494 /* engine.cpp in Sources */,
-                               37D928640F21331F001D4494 /* errorchecking.cpp in Sources */,
                                37D928650F21331F001D4494 /* fastamap.cpp in Sources */,
                                37D928660F21331F001D4494 /* fileoutput.cpp in Sources */,
                                37D928670F21331F001D4494 /* globaldata.cpp in Sources */,
@@ -620,10 +1047,8 @@
                                37D9286E0F21331F001D4494 /* listvector.cpp in Sources */,
                                37D9286F0F21331F001D4494 /* mothur.cpp in Sources */,
                                37D928700F21331F001D4494 /* nameassignment.cpp in Sources */,
-                               37D928710F21331F001D4494 /* nocommand.cpp in Sources */,
                                37D928720F21331F001D4494 /* npshannon.cpp in Sources */,
                                37D928730F21331F001D4494 /* ordervector.cpp in Sources */,
-                               37D928740F21331F001D4494 /* parselistcommand.cpp in Sources */,
                                37D928750F21331F001D4494 /* progress.cpp in Sources */,
                                37D928760F21331F001D4494 /* quitcommand.cpp in Sources */,
                                37D928770F21331F001D4494 /* rabundvector.cpp in Sources */,
@@ -632,11 +1057,9 @@
                                37D9287A0F21331F001D4494 /* rarefact.cpp in Sources */,
                                37D9287B0F21331F001D4494 /* rarefactcommand.cpp in Sources */,
                                37D9287C0F21331F001D4494 /* rarefactsharedcommand.cpp in Sources */,
-                               37D928800F21331F001D4494 /* readmatrix.cpp in Sources */,
                                37D928840F21331F001D4494 /* sabundvector.cpp in Sources */,
                                37D928850F21331F001D4494 /* sequence.cpp in Sources */,
                                37D928860F21331F001D4494 /* shannon.cpp in Sources */,
-                               37D928870F21331F001D4494 /* shared.cpp in Sources */,
                                37D928880F21331F001D4494 /* sharedace.cpp in Sources */,
                                37D928890F21331F001D4494 /* sharedchao1.cpp in Sources */,
                                37D9288A0F21331F001D4494 /* sharedcommand.cpp in Sources */,
@@ -659,7 +1082,6 @@
                                37D9289B0F21331F001D4494 /* summarysharedcommand.cpp in Sources */,
                                37D9289C0F21331F001D4494 /* uvest.cpp in Sources */,
                                37D9289D0F21331F001D4494 /* validcalculator.cpp in Sources */,
-                               37D9289E0F21331F001D4494 /* validcommands.cpp in Sources */,
                                37D9289F0F21331F001D4494 /* validparameter.cpp in Sources */,
                                372E12700F26365B0095CF7E /* readotucommand.cpp in Sources */,
                                372E12960F263D5A0095CF7E /* readdistcommand.cpp in Sources */,
@@ -678,7 +1100,91 @@
                                374610830F40652400460C57 /* unweighted.cpp in Sources */,
                                3746109D0F40657600460C57 /* unifracunweightedcommand.cpp in Sources */,
                                37AFC71F0F445386005F492D /* sharedsobscollectsummary.cpp in Sources */,
-                               37AFC7A30F44703E005F492D /* readsharedcommand.cpp in Sources */,
+                               A70B53AA0F4CD7AD0064797E /* getgroupcommand.cpp in Sources */,
+                               A70B53AB0F4CD7AD0064797E /* getlabelcommand.cpp in Sources */,
+                               A70B53AC0F4CD7AD0064797E /* getlinecommand.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 */,
+                               3799A9500FD6A58C00E33EDE /* distancedb.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 */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };
@@ -692,7 +1198,7 @@
                                GCC_DYNAMIC_NO_PIC = NO;
                                GCC_ENABLE_FIX_AND_CONTINUE = YES;
                                GCC_MODEL_TUNING = G5;
-                               GCC_OPTIMIZATION_LEVEL = 3;
+                               GCC_OPTIMIZATION_LEVEL = 0;
                                GCC_PREPROCESSOR_DEFINITIONS = (
                                        "_GLIBCXX_DEBUG=1",
                                        "_GLIBCXX_DEBUG_PEDANTIC=1",
@@ -708,7 +1214,6 @@
                        buildSettings = {
                                DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym";
                                GCC_MODEL_TUNING = G5;
-                               GCC_OPTIMIZATION_LEVEL = 3;
                                INSTALL_PATH = /usr/local/bin;
                                PRODUCT_NAME = mothur;
                        };
@@ -718,10 +1223,15 @@
                        isa = XCBuildConfiguration;
                        buildSettings = {
                                GCC_OPTIMIZATION_LEVEL = 3;
+                               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 = "";
                                PREBINDING = NO;
                                SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
+                               WARNING_CFLAGS = "";
                        };
                        name = Debug;
                };
@@ -732,11 +1242,26 @@
                                        ppc,
                                        i386,
                                );
-                               GCC_OPTIMIZATION_LEVEL = 0;
+                               GCC_OPTIMIZATION_LEVEL = 3;
+                               GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
+                               GCC_WARN_ABOUT_MISSING_PROTOTYPES = YES;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
+                               GCC_WARN_ALLOW_INCOMPLETE_PROTOCOL = NO;
+                               GCC_WARN_MISSING_PARENTHESES = YES;
+                               GCC_WARN_PEDANTIC = YES;
+                               GCC_WARN_UNUSED_FUNCTION = YES;
+                               GCC_WARN_UNUSED_PARAMETER = NO;
+                               GCC_WARN_UNUSED_VALUE = YES;
                                GCC_WARN_UNUSED_VARIABLE = YES;
+                               OTHER_CPLUSPLUSFLAGS = (
+                                       "-ansi",
+                                       "-pedantic",
+                                       "-wall",
+                               );
                                PREBINDING = NO;
                                SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
+                               SYMROOT = /Users/johnwestcott/Desktop;
+                               WARNING_CFLAGS = "";
                        };
                        name = Release;
                };