]> git.donarmstrong.com Git - mothur.git/blobdiff - Mothur.xcodeproj/project.pbxproj
When Pat tried to compile mothur in Ubuntu linux, there were a number of minor proble...
[mothur.git] / Mothur.xcodeproj / project.pbxproj
index a60c51468519eb4acaf570657ee083fcf58b9756..e773981a535e6c8b4d5332e1ce6a87266f1618c4 100644 (file)
@@ -7,6 +7,14 @@
        objects = {
 
 /* Begin PBXBuildFile section */
+               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 */; };
+               379293C30F2DE73400B9034A /* treemap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 379293C20F2DE73400B9034A /* treemap.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 */; };
+               37B28F680F27590100808A62 /* deconvolutecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37B28F670F27590100808A62 /* deconvolutecommand.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 */; };
@@ -17,7 +25,6 @@
                37D9285C0F21331F001D4494 /* collect.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927C50F21331F001D4494 /* collect.cpp */; };
                37D9285D0F21331F001D4494 /* collectcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927C70F21331F001D4494 /* collectcommand.cpp */; };
                37D9285E0F21331F001D4494 /* collectsharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */; };
-               37D9285F0F21331F001D4494 /* commandfactory.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927CE0F21331F001D4494 /* commandfactory.cpp */; };
                37D928600F21331F001D4494 /* commandoptionparser.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927D00F21331F001D4494 /* commandoptionparser.cpp */; };
                37D928610F21331F001D4494 /* completelinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927D20F21331F001D4494 /* completelinkage.cpp */; };
                37D928620F21331F001D4494 /* database.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927D30F21331F001D4494 /* database.cpp */; };
                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 */; };
-               37D9287D0F21331F001D4494 /* readdistcolumnfilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9280C0F21331F001D4494 /* readdistcolumnfilecommand.cpp */; };
-               37D9287E0F21331F001D4494 /* readdistphylipfilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9280E0F21331F001D4494 /* readdistphylipfilecommand.cpp */; };
-               37D9287F0F21331F001D4494 /* readlistfilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928100F21331F001D4494 /* readlistfilecommand.cpp */; };
                37D928800F21331F001D4494 /* readmatrix.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928120F21331F001D4494 /* readmatrix.cpp */; };
-               37D928810F21331F001D4494 /* readrabundfilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928140F21331F001D4494 /* readrabundfilecommand.cpp */; };
-               37D928820F21331F001D4494 /* readsabundfilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928160F21331F001D4494 /* readsabundfilecommand.cpp */; };
-               37D928830F21331F001D4494 /* readsharedfilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928180F21331F001D4494 /* readsharedfilecommand.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 */; };
@@ -82,6 +83,9 @@
                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 */; };
+               7E44EBD10F3235D900B0D45D /* makefile in Sources */ = {isa = PBXBuildFile; fileRef = 7E44EBD00F32358B00B0D45D /* makefile */; };
                8DD76F6A0486A84900D96B5E /* Mothur.1 in CopyFiles */ = {isa = PBXBuildFile; fileRef = C6859E8B029090EE04C91782 /* Mothur.1 */; };
 /* End PBXBuildFile section */
 
 /* End PBXCopyFilesBuildPhase section */
 
 /* Begin PBXFileReference section */
-               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>"; };
-               37D927CE0F21331F001D4494 /* commandfactory.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = commandfactory.cpp; 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>"; };
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-               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>"; };
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-               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>"; };
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+               37D927F90F21331F001D4494 /* parselistcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parselistcommand.cpp; sourceTree = SOURCE_ROOT; };
+               37D927FA0F21331F001D4494 /* parselistcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parselistcommand.h; 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; };
+               37D928120F21331F001D4494 /* readmatrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readmatrix.cpp; 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; };
+               37D928200F21331F001D4494 /* shared.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shared.cpp; sourceTree = SOURCE_ROOT; };
+               37D928210F21331F001D4494 /* shared.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shared.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; };
+               37D9284C0F21331F001D4494 /* utilities.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = utilities.hpp; 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; };
+               37D928510F21331F001D4494 /* validcommands.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = validcommands.cpp; sourceTree = SOURCE_ROOT; };
+               37D928520F21331F001D4494 /* validcommands.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = validcommands.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; };
+               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; };
+               7E44EBD00F32358B00B0D45D /* makefile */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.make; path = makefile; sourceTree = "<group>"; };
+               8DD76F6C0486A84900D96B5E /* mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = mothur; sourceTree = BUILT_PRODUCTS_DIR; };
                C6859E8B029090EE04C91782 /* Mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = Mothur.1; sourceTree = "<group>"; };
 /* End PBXFileReference section */
 
                        children = (
                                37D927BA0F21331F001D4494 /* averagelinkage.cpp */,
                                37D928A60F2133C0001D4494 /* calculators */,
-                               37D927C10F21331F001D4494 /* cluster.cpp */,
                                37D927C20F21331F001D4494 /* cluster.hpp */,
+                               37D927C10F21331F001D4494 /* cluster.cpp */,
                                37D928A90F2133E5001D4494 /* commands */,
-                               37D927C50F21331F001D4494 /* collect.cpp */,
                                37D927C60F21331F001D4494 /* collect.h */,
+                               37D927C50F21331F001D4494 /* collect.cpp */,
                                37D927C90F21331F001D4494 /* collectdisplay.h */,
                                37D928AC0F213420001D4494 /* containers */,
                                37D927CA0F21331F001D4494 /* collectorscurvedata.h */,
-                               37D927CE0F21331F001D4494 /* commandfactory.cpp */,
                                37D927CF0F21331F001D4494 /* commandfactory.hpp */,
-                               37D927D00F21331F001D4494 /* commandoptionparser.cpp */,
+                               372E12EC0F264D320095CF7E /* commandfactory.cpp */,
                                37D927D10F21331F001D4494 /* commandoptionparser.hpp */,
+                               37D927D00F21331F001D4494 /* commandoptionparser.cpp */,
                                37D927D20F21331F001D4494 /* completelinkage.cpp */,
-                               37D927D30F21331F001D4494 /* database.cpp */,
                                37D927D40F21331F001D4494 /* database.hpp */,
+                               37D927D30F21331F001D4494 /* database.cpp */,
                                37D927D60F21331F001D4494 /* display.h */,
-                               37D927D70F21331F001D4494 /* engine.cpp */,
                                37D927D80F21331F001D4494 /* engine.hpp */,
+                               37D927D70F21331F001D4494 /* engine.cpp */,
+                               7E44EBD00F32358B00B0D45D /* makefile */,
                                37D928B10F213472001D4494 /* errorcheckor */,
-                               37D927DD0F21331F001D4494 /* fileoutput.cpp */,
                                37D927DE0F21331F001D4494 /* fileoutput.h */,
-                               37D927DF0F21331F001D4494 /* globaldata.cpp */,
+                               37D927DD0F21331F001D4494 /* fileoutput.cpp */,
                                37D927E00F21331F001D4494 /* globaldata.hpp */,
-                               37D927E50F21331F001D4494 /* inputdata.cpp */,
+                               37D927DF0F21331F001D4494 /* globaldata.cpp */,
                                37D927E60F21331F001D4494 /* inputdata.h */,
-                               37D927E90F21331F001D4494 /* kmer.cpp */,
+                               37D927E50F21331F001D4494 /* inputdata.cpp */,
                                37D927EA0F21331F001D4494 /* kmer.hpp */,
-                               37D927EB0F21331F001D4494 /* kmerdb.cpp */,
+                               37D927E90F21331F001D4494 /* kmer.cpp */,
                                37D927EC0F21331F001D4494 /* kmerdb.hpp */,
+                               37D927EB0F21331F001D4494 /* kmerdb.cpp */,
                                37D927EF0F21331F001D4494 /* mothur.cpp */,
-                               37D927F00F21331F001D4494 /* nameassignment.cpp */,
                                37D927F10F21331F001D4494 /* nameassignment.hpp */,
+                               37D927F00F21331F001D4494 /* nameassignment.cpp */,
                                37D927F60F21331F001D4494 /* observable.h */,
-                               37D927FB0F21331F001D4494 /* progress.cpp */,
                                37D927FC0F21331F001D4494 /* progress.hpp */,
-                               37D928030F21331F001D4494 /* raredisplay.cpp */,
+                               37D927FB0F21331F001D4494 /* progress.cpp */,
                                37D928040F21331F001D4494 /* raredisplay.h */,
-                               37D928050F21331F001D4494 /* rarefact.cpp */,
+                               37D928030F21331F001D4494 /* raredisplay.cpp */,
                                37D928060F21331F001D4494 /* rarefact.h */,
+                               37D928050F21331F001D4494 /* rarefact.cpp */,
                                37D928090F21331F001D4494 /* rarefactioncurvedata.h */,
-                               37D928120F21331F001D4494 /* readmatrix.cpp */,
                                37D928130F21331F001D4494 /* readmatrix.hpp */,
-                               37D9281C0F21331F001D4494 /* sequence.cpp */,
+                               37D928120F21331F001D4494 /* readmatrix.cpp */,
+                               37AD4DC80F28F3DD00AA2D49 /* readtree.h */,
+                               37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */,
                                37D9281D0F21331F001D4494 /* sequence.hpp */,
-                               37D928200F21331F001D4494 /* shared.cpp */,
+                               37D9281C0F21331F001D4494 /* sequence.cpp */,
                                37D928210F21331F001D4494 /* shared.h */,
+                               37D928200F21331F001D4494 /* shared.cpp */,
                                37D928420F21331F001D4494 /* singlelinkage.cpp */,
-                               37D928440F21331F001D4494 /* sparsematrix.cpp */,
                                37D928450F21331F001D4494 /* sparsematrix.hpp */,
+                               37D928440F21331F001D4494 /* sparsematrix.cpp */,
                                37D928480F21331F001D4494 /* summarydata.h */,
                                37D928490F21331F001D4494 /* summarydisplay.h */,
                                37D9284C0F21331F001D4494 /* utilities.hpp */,
                        );
                        name = Source;
-                       sourceTree = "<group>";
+                       sourceTree = SOURCE_ROOT;
                };
                1AB674ADFE9D54B511CA2CBB /* Products */ = {
                        isa = PBXGroup;
                        children = (
-                               8DD76F6C0486A84900D96B5E /* Mothur */,
+                               8DD76F6C0486A84900D96B5E /* mothur */,
                        );
                        name = Products;
                        sourceTree = "<group>";
                                37D927BB0F21331F001D4494 /* bootstrap.cpp */,
                                37D927C00F21331F001D4494 /* chao1.h */,
                                37D927BF0F21331F001D4494 /* chao1.cpp */,
-                               37D927E70F21331F001D4494 /* jackknife.cpp */,
                                37D927E80F21331F001D4494 /* jackknife.h */,
-                               37D927F40F21331F001D4494 /* npshannon.cpp */,
+                               37D927E70F21331F001D4494 /* jackknife.cpp */,
                                37D927F50F21331F001D4494 /* npshannon.h */,
-                               37D928010F21331F001D4494 /* rarecalc.cpp */,
+                               37D927F40F21331F001D4494 /* npshannon.cpp */,
                                37D928020F21331F001D4494 /* rarecalc.h */,
-                               37D9281E0F21331F001D4494 /* shannon.cpp */,
+                               37D928010F21331F001D4494 /* rarecalc.cpp */,
                                37D9281F0F21331F001D4494 /* shannon.h */,
-                               37D928220F21331F001D4494 /* sharedace.cpp */,
+                               37D9281E0F21331F001D4494 /* shannon.cpp */,
                                37D928230F21331F001D4494 /* sharedace.h */,
-                               37D928240F21331F001D4494 /* sharedchao1.cpp */,
+                               37D928220F21331F001D4494 /* sharedace.cpp */,
                                37D928250F21331F001D4494 /* sharedchao1.h */,
-                               37D928280F21331F001D4494 /* sharedjabund.cpp */,
+                               37D928240F21331F001D4494 /* sharedchao1.cpp */,
                                37D928290F21331F001D4494 /* sharedjabund.h */,
-                               37D9282A0F21331F001D4494 /* sharedjclass.cpp */,
+                               37D928280F21331F001D4494 /* sharedjabund.cpp */,
                                37D9282B0F21331F001D4494 /* sharedjclass.h */,
-                               37D9282C0F21331F001D4494 /* sharedjest.cpp */,
+                               37D9282A0F21331F001D4494 /* sharedjclass.cpp */,
                                37D9282D0F21331F001D4494 /* sharedjest.h */,
-                               37D928340F21331F001D4494 /* sharedsobs.cpp */,
+                               37D9282C0F21331F001D4494 /* sharedjest.cpp */,
                                37D928350F21331F001D4494 /* sharedsobs.h */,
-                               37D928360F21331F001D4494 /* sharedsorabund.cpp */,
+                               37D928340F21331F001D4494 /* sharedsobs.cpp */,
                                37D928370F21331F001D4494 /* sharedsorabund.h */,
-                               37D928380F21331F001D4494 /* sharedsorclass.cpp */,
+                               37D928360F21331F001D4494 /* sharedsorabund.cpp */,
                                37D928390F21331F001D4494 /* sharedsorclass.h */,
-                               37D9283A0F21331F001D4494 /* sharedsorest.cpp */,
+                               37D928380F21331F001D4494 /* sharedsorclass.cpp */,
                                37D9283B0F21331F001D4494 /* sharedsorest.h */,
+                               37D9283A0F21331F001D4494 /* sharedsorest.cpp */,
                                37D9283C0F21331F001D4494 /* sharedthetan.cpp */,
                                37D9283D0F21331F001D4494 /* sharedthetan.h */,
-                               37D9283E0F21331F001D4494 /* sharedthetayc.cpp */,
                                37D9283F0F21331F001D4494 /* sharedthetayc.h */,
-                               37D928400F21331F001D4494 /* simpson.cpp */,
+                               37D9283E0F21331F001D4494 /* sharedthetayc.cpp */,
                                37D928410F21331F001D4494 /* simpson.h */,
+                               37D928400F21331F001D4494 /* simpson.cpp */,
                                37D928430F21331F001D4494 /* sobs.h */,
-                               37D9284D0F21331F001D4494 /* uvest.cpp */,
                                37D9284E0F21331F001D4494 /* uvest.h */,
+                               37D9284D0F21331F001D4494 /* uvest.cpp */,
                        );
                        name = calculators;
-                       sourceTree = "<group>";
+                       sourceTree = SOURCE_ROOT;
                };
                37D928A90F2133E5001D4494 /* commands */ = {
                        isa = PBXGroup;
                                37D927C30F21331F001D4494 /* clustercommand.cpp */,
                                37D927C80F21331F001D4494 /* collectcommand.h */,
                                37D927C70F21331F001D4494 /* collectcommand.cpp */,
-                               37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */,
                                37D927CC0F21331F001D4494 /* collectsharedcommand.h */,
-                               37D927E30F21331F001D4494 /* helpcommand.cpp */,
+                               37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */,
+                               37B28F660F27590100808A62 /* deconvolutecommand.h */,
+                               37B28F670F27590100808A62 /* deconvolutecommand.cpp */,
                                37D927E40F21331F001D4494 /* helpcommand.h */,
+                               37D927E30F21331F001D4494 /* helpcommand.cpp */,
                                37D927F20F21331F001D4494 /* nocommand.cpp */,
                                37D927F30F21331F001D4494 /* nocommand.h */,
-                               37D927F90F21331F001D4494 /* parselistcommand.cpp */,
                                37D927FA0F21331F001D4494 /* parselistcommand.h */,
-                               37D927FD0F21331F001D4494 /* quitcommand.cpp */,
-                               37D927FE0F21331F001D4494 /* quitcommand.h */,
-                               37D928070F21331F001D4494 /* rarefactcommand.cpp */,
+                               37D927F90F21331F001D4494 /* parselistcommand.cpp */,
                                37D928080F21331F001D4494 /* rarefactcommand.h */,
-                               37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */,
+                               37D928070F21331F001D4494 /* rarefactcommand.cpp */,
                                37D9280B0F21331F001D4494 /* rarefactsharedcommand.h */,
-                               37D9280C0F21331F001D4494 /* readdistcolumnfilecommand.cpp */,
-                               37D9280D0F21331F001D4494 /* readdistcolumnfilecommand.h */,
-                               37D9280E0F21331F001D4494 /* readdistphylipfilecommand.cpp */,
-                               37D9280F0F21331F001D4494 /* readdistphylipfilecommand.h */,
-                               37D928100F21331F001D4494 /* readlistfilecommand.cpp */,
-                               37D928110F21331F001D4494 /* readlistfilecommand.h */,
-                               37D928140F21331F001D4494 /* readrabundfilecommand.cpp */,
-                               37D928150F21331F001D4494 /* readrabundfilecommand.h */,
-                               37D928160F21331F001D4494 /* readsabundfilecommand.cpp */,
-                               37D928170F21331F001D4494 /* readsabundfilecommand.h */,
-                               37D928180F21331F001D4494 /* readsharedfilecommand.cpp */,
-                               37D928190F21331F001D4494 /* readsharedfilecommand.h */,
-                               37D928260F21331F001D4494 /* sharedcommand.cpp */,
+                               37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */,
+                               372E12940F263D5A0095CF7E /* readdistcommand.h */,
+                               372E12950F263D5A0095CF7E /* readdistcommand.cpp */,
+                               372E126E0F26365B0095CF7E /* readotucommand.h */,
+                               372E126F0F26365B0095CF7E /* readotucommand.cpp */,
+                               37E5F4900F2A3DA800F8D827 /* readtreecommand.h */,
+                               37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */,
                                37D928270F21331F001D4494 /* sharedcommand.h */,
-                               37D928460F21331F001D4494 /* summarycommand.cpp */,
+                               37D928260F21331F001D4494 /* sharedcommand.cpp */,
                                37D928470F21331F001D4494 /* summarycommand.h */,
-                               37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */,
+                               37D928460F21331F001D4494 /* summarycommand.cpp */,
                                37D9284B0F21331F001D4494 /* summarysharedcommand.h */,
+                               37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */,
+                               37D927FE0F21331F001D4494 /* quitcommand.h */,
+                               37D927FD0F21331F001D4494 /* quitcommand.cpp */,
                        );
                        name = commands;
-                       sourceTree = "<group>";
+                       sourceTree = SOURCE_ROOT;
                };
                37D928AC0F213420001D4494 /* containers */ = {
                        isa = PBXGroup;
                        children = (
                                37D927D50F21331F001D4494 /* datavector.hpp */,
-                               37D927DB0F21331F001D4494 /* fastamap.cpp */,
                                37D927DC0F21331F001D4494 /* fastamap.h */,
-                               37D927E10F21331F001D4494 /* groupmap.cpp */,
+                               37D927DB0F21331F001D4494 /* fastamap.cpp */,
                                37D927E20F21331F001D4494 /* groupmap.h */,
-                               37D927ED0F21331F001D4494 /* listvector.cpp */,
+                               37D927E10F21331F001D4494 /* groupmap.cpp */,
                                37D927EE0F21331F001D4494 /* listvector.hpp */,
-                               37D927F70F21331F001D4494 /* ordervector.cpp */,
+                               37D927ED0F21331F001D4494 /* listvector.cpp */,
                                37D927F80F21331F001D4494 /* ordervector.hpp */,
-                               37D927FF0F21331F001D4494 /* rabundvector.cpp */,
+                               37D927F70F21331F001D4494 /* ordervector.cpp */,
                                37D928000F21331F001D4494 /* rabundvector.hpp */,
-                               37D9281A0F21331F001D4494 /* sabundvector.cpp */,
+                               37D927FF0F21331F001D4494 /* rabundvector.cpp */,
                                37D9281B0F21331F001D4494 /* sabundvector.hpp */,
-                               37D9282E0F21331F001D4494 /* sharedordervector.cpp */,
+                               37D9281A0F21331F001D4494 /* sabundvector.cpp */,
+                               37AD4CE20F28AEA300AA2D49 /* sharedlistvector.h */,
+                               37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */,
                                37D9282F0F21331F001D4494 /* sharedordervector.h */,
-                               37D928300F21331F001D4494 /* sharedrabundvector.cpp */,
+                               37D9282E0F21331F001D4494 /* sharedordervector.cpp */,
                                37D928310F21331F001D4494 /* sharedrabundvector.h */,
-                               37D928320F21331F001D4494 /* sharedsabundvector.cpp */,
+                               37D928300F21331F001D4494 /* sharedrabundvector.cpp */,
                                37D928330F21331F001D4494 /* sharedsabundvector.h */,
+                               37D928320F21331F001D4494 /* sharedsabundvector.cpp */,
+                               37AD4DB90F28E2FE00AA2D49 /* tree.h */,
+                               37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */,
+                               379293C10F2DE73400B9034A /* treemap.h */,
+                               379293C20F2DE73400B9034A /* treemap.cpp */,
+                               37E5F3E10F29FD4200F8D827 /* treenode.h */,
+                               37E5F3E20F29FD4200F8D827 /* treenode.cpp */,
                        );
                        name = containers;
-                       sourceTree = "<group>";
+                       sourceTree = SOURCE_ROOT;
                };
                37D928B10F213472001D4494 /* errorcheckor */ = {
                        isa = PBXGroup;
                        children = (
-                               37D927D90F21331F001D4494 /* errorchecking.cpp */,
                                37D927DA0F21331F001D4494 /* errorchecking.h */,
-                               37D9284F0F21331F001D4494 /* validcalculator.cpp */,
+                               37D927D90F21331F001D4494 /* errorchecking.cpp */,
                                37D928500F21331F001D4494 /* validcalculator.h */,
-                               37D928510F21331F001D4494 /* validcommands.cpp */,
+                               37D9284F0F21331F001D4494 /* validcalculator.cpp */,
                                37D928520F21331F001D4494 /* validcommands.h */,
-                               37D928530F21331F001D4494 /* validparameter.cpp */,
+                               37D928510F21331F001D4494 /* validcommands.cpp */,
                                37D928540F21331F001D4494 /* validparameter.h */,
+                               37D928530F21331F001D4494 /* validparameter.cpp */,
                        );
                        name = errorcheckor;
-                       sourceTree = "<group>";
+                       sourceTree = SOURCE_ROOT;
                };
                C6859E8C029090F304C91782 /* Documentation */ = {
                        isa = PBXGroup;
 /* End PBXGroup section */
 
 /* Begin PBXNativeTarget section */
-               8DD76F620486A84900D96B5E /* Mothur */ = {
+               8DD76F620486A84900D96B5E /* mothur */ = {
                        isa = PBXNativeTarget;
-                       buildConfigurationList = 1DEB923108733DC60010E9CD /* Build configuration list for PBXNativeTarget "Mothur" */;
+                       buildConfigurationList = 1DEB923108733DC60010E9CD /* Build configuration list for PBXNativeTarget "mothur" */;
                        buildPhases = (
                                8DD76F640486A84900D96B5E /* Sources */,
                                8DD76F660486A84900D96B5E /* Frameworks */,
                        );
                        dependencies = (
                        );
-                       name = Mothur;
+                       name = mothur;
                        productInstallPath = "$(HOME)/bin";
                        productName = Mothur;
-                       productReference = 8DD76F6C0486A84900D96B5E /* Mothur */;
+                       productReference = 8DD76F6C0486A84900D96B5E /* mothur */;
                        productType = "com.apple.product-type.tool";
                };
 /* End PBXNativeTarget section */
                        projectDirPath = "";
                        projectRoot = "";
                        targets = (
-                               8DD76F620486A84900D96B5E /* Mothur */,
+                               8DD76F620486A84900D96B5E /* mothur */,
                        );
                };
 /* End PBXProject section */
                                37D9285C0F21331F001D4494 /* collect.cpp in Sources */,
                                37D9285D0F21331F001D4494 /* collectcommand.cpp in Sources */,
                                37D9285E0F21331F001D4494 /* collectsharedcommand.cpp in Sources */,
-                               37D9285F0F21331F001D4494 /* commandfactory.cpp in Sources */,
                                37D928600F21331F001D4494 /* commandoptionparser.cpp in Sources */,
                                37D928610F21331F001D4494 /* completelinkage.cpp in Sources */,
                                37D928620F21331F001D4494 /* database.cpp in Sources */,
                                37D9287A0F21331F001D4494 /* rarefact.cpp in Sources */,
                                37D9287B0F21331F001D4494 /* rarefactcommand.cpp in Sources */,
                                37D9287C0F21331F001D4494 /* rarefactsharedcommand.cpp in Sources */,
-                               37D9287D0F21331F001D4494 /* readdistcolumnfilecommand.cpp in Sources */,
-                               37D9287E0F21331F001D4494 /* readdistphylipfilecommand.cpp in Sources */,
-                               37D9287F0F21331F001D4494 /* readlistfilecommand.cpp in Sources */,
                                37D928800F21331F001D4494 /* readmatrix.cpp in Sources */,
-                               37D928810F21331F001D4494 /* readrabundfilecommand.cpp in Sources */,
-                               37D928820F21331F001D4494 /* readsabundfilecommand.cpp in Sources */,
-                               37D928830F21331F001D4494 /* readsharedfilecommand.cpp in Sources */,
                                37D928840F21331F001D4494 /* sabundvector.cpp in Sources */,
                                37D928850F21331F001D4494 /* sequence.cpp in Sources */,
                                37D928860F21331F001D4494 /* shannon.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 */,
+                               372E12ED0F264D320095CF7E /* commandfactory.cpp in Sources */,
+                               37B28F680F27590100808A62 /* deconvolutecommand.cpp in Sources */,
+                               37AD4CE40F28AEA300AA2D49 /* sharedlistvector.cpp in Sources */,
+                               37AD4DBB0F28E2FE00AA2D49 /* tree.cpp in Sources */,
+                               37AD4DCA0F28F3DD00AA2D49 /* readtree.cpp in Sources */,
+                               37E5F3E30F29FD4200F8D827 /* treenode.cpp in Sources */,
+                               37E5F4920F2A3DA800F8D827 /* readtreecommand.cpp in Sources */,
+                               379293C30F2DE73400B9034A /* treemap.cpp in Sources */,
+                               7E44EBD10F3235D900B0D45D /* makefile in Sources */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };
                                        "_GLIBCXX_DEBUG_PEDANTIC=1",
                                );
                                INSTALL_PATH = /usr/local/bin;
-                               PRODUCT_NAME = Mothur;
+                               PRODUCT_NAME = mothur;
                                ZERO_LINK = YES;
                        };
                        name = Debug;
                                DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym";
                                GCC_MODEL_TUNING = G5;
                                INSTALL_PATH = /usr/local/bin;
-                               PRODUCT_NAME = Mothur;
+                               PRODUCT_NAME = mothur;
                        };
                        name = Release;
                };
                1DEB923608733DC60010E9CD /* Debug */ = {
                        isa = XCBuildConfiguration;
                        buildSettings = {
+                               GCC_OPTIMIZATION_LEVEL = 3;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
                                GCC_WARN_UNUSED_VARIABLE = YES;
                                PREBINDING = NO;
                                        ppc,
                                        i386,
                                );
+                               GCC_OPTIMIZATION_LEVEL = 3;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
                                GCC_WARN_UNUSED_VARIABLE = YES;
                                PREBINDING = NO;
 /* End XCBuildConfiguration section */
 
 /* Begin XCConfigurationList section */
-               1DEB923108733DC60010E9CD /* Build configuration list for PBXNativeTarget "Mothur" */ = {
+               1DEB923108733DC60010E9CD /* Build configuration list for PBXNativeTarget "mothur" */ = {
                        isa = XCConfigurationList;
                        buildConfigurations = (
                                1DEB923208733DC60010E9CD /* Debug */,