]> git.donarmstrong.com Git - mothur.git/blobdiff - Mothur.xcodeproj/project.pbxproj
started shared utilities, updates to venn and heatmap added tree.groups command
[mothur.git] / Mothur.xcodeproj / project.pbxproj
index a60c51468519eb4acaf570657ee083fcf58b9756..967e8e4be3fc714d822fed1b36f591d3aa1f15e0 100644 (file)
@@ -7,6 +7,40 @@
        objects = {
 
 /* Begin PBXBuildFile section */
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+               372E12960F263D5A0095CF7E /* readdistcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 372E12950F263D5A0095CF7E /* readdistcommand.cpp */; };
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+               374610780F40645300460C57 /* unifracweightedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 374610770F40645300460C57 /* unifracweightedcommand.cpp */; };
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@@ -17,7 +51,6 @@
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@@ -35,7 +68,6 @@
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                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>"; };
                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>"; };
                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>"; };
-               8DD76F6C0486A84900D96B5E /* Mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = Mothur; sourceTree = BUILT_PRODUCTS_DIR; };
+               37E3ED800F4D9D0D00B5DF02 /* mothur.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mothur.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>"; };
+               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 = "<group>"; };
+               A70B53A50F4CD7AD0064797E /* getgroupcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getgroupcommand.h; sourceTree = "<group>"; };
+               A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlabelcommand.cpp; sourceTree = "<group>"; };
+               A70B53A70F4CD7AD0064797E /* getlabelcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlabelcommand.h; sourceTree = "<group>"; };
+               A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlinecommand.cpp; sourceTree = "<group>"; };
+               A70B53A90F4CD7AD0064797E /* getlinecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlinecommand.h; sourceTree = "<group>"; };
                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 = "<group>"; };
+               EB1216870F619B83004A865F /* bergerparker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bergerparker.cpp; sourceTree = "<group>"; };
+               EB1216E30F61ACFB004A865F /* bstick.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bstick.h; sourceTree = "<group>"; };
+               EB1216E40F61ACFB004A865F /* bstick.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bstick.cpp; sourceTree = "<group>"; };
+               EB1217210F61C9AC004A865F /* sharedkstest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedkstest.h; sourceTree = "<group>"; };
+               EB1217220F61C9AC004A865F /* sharedkstest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedkstest.cpp; sourceTree = "<group>"; };
+               EB6E68170F5F1C780044E17B /* qstat.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = qstat.h; sourceTree = "<group>"; };
+               EB6E68180F5F1C780044E17B /* qstat.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = qstat.cpp; sourceTree = "<group>"; };
+               EB6F01590F6AC1670048081A /* sharedbdiversity.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedbdiversity.h; sourceTree = "<group>"; };
+               EB6F015A0F6AC1670048081A /* sharedbdiversity.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedbdiversity.cpp; sourceTree = "<group>"; };
+               EB9303E90F534D9400E8EF26 /* logsd.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = logsd.h; sourceTree = "<group>"; };
+               EB9303EA0F534D9400E8EF26 /* logsd.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = logsd.cpp; sourceTree = "<group>"; };
+               EB9303F70F53517300E8EF26 /* geom.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = geom.h; sourceTree = "<group>"; };
+               EB9303F80F53517300E8EF26 /* geom.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = geom.cpp; sourceTree = "<group>"; };
 /* End PBXFileReference section */
 
 /* Begin PBXFrameworksBuildPhase 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 */,
                                37D928B10F213472001D4494 /* errorcheckor */,
-                               37D927DD0F21331F001D4494 /* fileoutput.cpp */,
                                37D927DE0F21331F001D4494 /* fileoutput.h */,
-                               37D927DF0F21331F001D4494 /* globaldata.cpp */,
+                               37D927DD0F21331F001D4494 /* fileoutput.cpp */,
                                37D927E00F21331F001D4494 /* globaldata.hpp */,
-                               37D927E50F21331F001D4494 /* inputdata.cpp */,
+                               37D927DF0F21331F001D4494 /* globaldata.cpp */,
+                               375873ED0F7D646F0040F377 /* heatmap.h */,
+                               375873EE0F7D646F0040F377 /* heatmap.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 */,
+                               37E3ED800F4D9D0D00B5DF02 /* mothur.h */,
                                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 */,
+                               37C7F3A70F8E90AD00E91C2B /* sharedutilities.h */,
+                               37C7F3A80F8E90AD00E91C2B /* sharedutilities.cpp */,
                                37D928420F21331F001D4494 /* singlelinkage.cpp */,
-                               37D928440F21331F001D4494 /* sparsematrix.cpp */,
-                               37D928450F21331F001D4494 /* sparsematrix.hpp */,
                                37D928480F21331F001D4494 /* summarydata.h */,
                                37D928490F21331F001D4494 /* summarydisplay.h */,
-                               37D9284C0F21331F001D4494 /* utilities.hpp */,
+                               37519AB30F810FAE00FED5E8 /* venn.h */,
+                               37519AB40F810FAE00FED5E8 /* venn.cpp */,
                        );
                        name = Source;
                        sourceTree = "<group>";
                1AB674ADFE9D54B511CA2CBB /* Products */ = {
                        isa = PBXGroup;
                        children = (
-                               8DD76F6C0486A84900D96B5E /* Mothur */,
+                               8DD76F6C0486A84900D96B5E /* mothur */,
                        );
                        name = Products;
                        sourceTree = "<group>";
                        isa = PBXGroup;
                        children = (
                                37D927BE0F21331F001D4494 /* calculator.h */,
+                               3792948D0F2E271100B9034A /* treecalculator.h */,
                                37D927BD0F21331F001D4494 /* calculator.cpp */,
                                37D927B90F21331F001D4494 /* ace.h */,
                                37D927B80F21331F001D4494 /* ace.cpp */,
+                               EB1216860F619B83004A865F /* bergerparker.h */,
+                               EB1216870F619B83004A865F /* bergerparker.cpp */,
                                37D927BC0F21331F001D4494 /* bootstrap.h */,
                                37D927BB0F21331F001D4494 /* bootstrap.cpp */,
+                               EB1216E30F61ACFB004A865F /* bstick.h */,
+                               EB1216E40F61ACFB004A865F /* bstick.cpp */,
                                37D927C00F21331F001D4494 /* chao1.h */,
                                37D927BF0F21331F001D4494 /* chao1.cpp */,
-                               37D927E70F21331F001D4494 /* jackknife.cpp */,
+                               375873E60F7D63E90040F377 /* coverage.h */,
+                               375873E50F7D63E90040F377 /* coverage.cpp */,
+                               EB9303F70F53517300E8EF26 /* geom.h */,
+                               EB9303F80F53517300E8EF26 /* geom.cpp */,
+                               EB9303E90F534D9400E8EF26 /* logsd.h */,
+                               EB9303EA0F534D9400E8EF26 /* logsd.cpp */,
+                               EB6E68170F5F1C780044E17B /* qstat.h */,
+                               EB6E68180F5F1C780044E17B /* qstat.cpp */,
                                37D927E80F21331F001D4494 /* jackknife.h */,
-                               37D927F40F21331F001D4494 /* npshannon.cpp */,
+                               37D927E70F21331F001D4494 /* jackknife.cpp */,
+                               375873F90F7D64AB0040F377 /* nseqs.h */,
                                37D927F50F21331F001D4494 /* npshannon.h */,
-                               37D928010F21331F001D4494 /* rarecalc.cpp */,
+                               37D927F40F21331F001D4494 /* npshannon.cpp */,
+                               379294880F2E258500B9034A /* parsimony.h */,
+                               379294890F2E258500B9034A /* parsimony.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 */,
+                               37519A690F80E6EB00FED5E8 /* sharedanderbergs.h */,
+                               37519A6A0F80E6EB00FED5E8 /* sharedanderbergs.cpp */,
+                               375873FB0F7D64DA0040F377 /* sharedbraycurtis.h */,
+                               375873FC0F7D64DA0040F377 /* sharedbraycurtis.cpp */,
+                               EB6F01590F6AC1670048081A /* sharedbdiversity.h */,
+                               EB6F015A0F6AC1670048081A /* sharedbdiversity.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 */,
+                               EB1217210F61C9AC004A865F /* sharedkstest.h */,
+                               EB1217220F61C9AC004A865F /* sharedkstest.cpp */,
+                               375874000F7D64EF0040F377 /* sharedkulczynski.h */,
+                               375873FE0F7D64EF0040F377 /* sharedkulczynski.cpp */,
+                               375874030F7D64EF0040F377 /* sharedkulczynskicody.h */,
+                               375874020F7D64EF0040F377 /* sharedkulczynskicody.cpp */,
+                               375874010F7D64EF0040F377 /* sharedlennon.h */,
+                               375873FF0F7D64EF0040F377 /* sharedlennon.cpp */,
+                               375874070F7D64FC0040F377 /* sharedmorisitahorn.h */,
+                               375874080F7D64FC0040F377 /* sharedmorisitahorn.cpp */,
+                               375874090F7D64FC0040F377 /* sharedochiai.h */,
+                               3758740B0F7D64FC0040F377 /* sharedochiai.cpp */,
+                               3758740A0F7D64FC0040F377 /* sharednseqs.h */,
                                37D928350F21331F001D4494 /* sharedsobs.h */,
-                               37D928360F21331F001D4494 /* sharedsorabund.cpp */,
+                               37D928340F21331F001D4494 /* sharedsobs.cpp */,
+                               37AFC71D0F445386005F492D /* sharedsobscollectsummary.h */,
+                               37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */,
                                37D928370F21331F001D4494 /* sharedsorabund.h */,
-                               37D928380F21331F001D4494 /* sharedsorclass.cpp */,
+                               37D928360F21331F001D4494 /* sharedsorabund.cpp */,
                                37D928390F21331F001D4494 /* sharedsorclass.h */,
-                               37D9283A0F21331F001D4494 /* sharedsorest.cpp */,
+                               37D928380F21331F001D4494 /* sharedsorclass.cpp */,
                                37D9283B0F21331F001D4494 /* sharedsorest.h */,
-                               37D9283C0F21331F001D4494 /* sharedthetan.cpp */,
+                               37D9283A0F21331F001D4494 /* sharedsorest.cpp */,
                                37D9283D0F21331F001D4494 /* sharedthetan.h */,
-                               37D9283E0F21331F001D4494 /* sharedthetayc.cpp */,
+                               37D9283C0F21331F001D4494 /* sharedthetan.cpp */,
                                37D9283F0F21331F001D4494 /* sharedthetayc.h */,
-                               37D928400F21331F001D4494 /* simpson.cpp */,
+                               37D9283E0F21331F001D4494 /* sharedthetayc.cpp */,
                                37D928410F21331F001D4494 /* simpson.h */,
+                               37D928400F21331F001D4494 /* simpson.cpp */,
                                37D928430F21331F001D4494 /* sobs.h */,
-                               37D9284D0F21331F001D4494 /* uvest.cpp */,
+                               374610810F40652400460C57 /* unweighted.h */,
+                               374610820F40652400460C57 /* unweighted.cpp */,
                                37D9284E0F21331F001D4494 /* uvest.h */,
+                               37D9284D0F21331F001D4494 /* uvest.cpp */,
+                               3746107C0F4064D100460C57 /* weighted.h */,
+                               3746107D0F4064D100460C57 /* weighted.cpp */,
                        );
                        name = calculators;
                        sourceTree = "<group>";
                        isa = PBXGroup;
                        children = (
                                37D927CD0F21331F001D4494 /* command.hpp */,
+                               37C1D9710F86506E0059E3F0 /* binsequencecommand.h */,
+                               37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */,
                                37D927C40F21331F001D4494 /* clustercommand.h */,
                                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 */,
+                               A70B53A50F4CD7AD0064797E /* getgroupcommand.h */,
+                               A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */,
+                               A70B53A70F4CD7AD0064797E /* getlabelcommand.h */,
+                               A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */,
+                               A70B53A90F4CD7AD0064797E /* getlinecommand.h */,
+                               A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */,
+                               370B88050F8A4EE4005AB382 /* getoturepcommand.h */,
+                               370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */,
+                               375873F10F7D64800040F377 /* heatmapcommand.h */,
+                               375873F00F7D64800040F377 /* heatmapcommand.cpp */,
                                37D927E40F21331F001D4494 /* helpcommand.h */,
-                               37D927F20F21331F001D4494 /* nocommand.cpp */,
-                               37D927F30F21331F001D4494 /* nocommand.h */,
-                               37D927F90F21331F001D4494 /* parselistcommand.cpp */,
+                               37D927E30F21331F001D4494 /* helpcommand.cpp */,
+                               375873F40F7D648F0040F377 /* libshuffcommand.h */,
+                               375873F30F7D648F0040F377 /* libshuffcommand.cpp */,
+                               375873F60F7D649C0040F377 /* nocommands.cpp */,
+                               375873F70F7D649C0040F377 /* nocommands.h */,
                                37D927FA0F21331F001D4494 /* parselistcommand.h */,
-                               37D927FD0F21331F001D4494 /* quitcommand.cpp */,
+                               37D927F90F21331F001D4494 /* parselistcommand.cpp */,
+                               3792946E0F2E191800B9034A /* parsimonycommand.h */,
+                               3792946F0F2E191800B9034A /* parsimonycommand.cpp */,
                                37D927FE0F21331F001D4494 /* quitcommand.h */,
-                               37D928070F21331F001D4494 /* rarefactcommand.cpp */,
+                               37D927FD0F21331F001D4494 /* quitcommand.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 */,
+                               3731C1F10F8CFC0A0065A2AD /* treegroupscommand.h */,
+                               3731C1F20F8CFC0A0065A2AD /* treegroupscommand.cpp */,
+                               3746109B0F40657600460C57 /* unifracunweightedcommand.h */,
+                               3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */,
+                               374610760F40645300460C57 /* unifracweightedcommand.h */,
+                               374610770F40645300460C57 /* unifracweightedcommand.cpp */,
+                               37519A9F0F810D0200FED5E8 /* venncommand.h */,
+                               37519AA00F810D0200FED5E8 /* venncommand.cpp */,
                        );
                        name = commands;
                        sourceTree = "<group>";
                        isa = PBXGroup;
                        children = (
                                37D927D50F21331F001D4494 /* datavector.hpp */,
-                               37D927DB0F21331F001D4494 /* fastamap.cpp */,
                                37D927DC0F21331F001D4494 /* fastamap.h */,
-                               37D927E10F21331F001D4494 /* groupmap.cpp */,
+                               37D927DB0F21331F001D4494 /* fastamap.cpp */,
+                               375873EA0F7D64520040F377 /* fullmatrix.h */,
+                               375873EB0F7D64520040F377 /* fullmatrix.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 */,
+                               37D928450F21331F001D4494 /* sparsematrix.hpp */,
+                               37D928440F21331F001D4494 /* sparsematrix.cpp */,
+                               37AD4DB90F28E2FE00AA2D49 /* tree.h */,
+                               37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */,
+                               379293C10F2DE73400B9034A /* treemap.h */,
+                               379293C20F2DE73400B9034A /* treemap.cpp */,
+                               37E5F3E10F29FD4200F8D827 /* treenode.h */,
+                               37E5F3E20F29FD4200F8D827 /* treenode.cpp */,
                        );
                        name = containers;
                        sourceTree = "<group>";
                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>";
 /* 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 */,
                                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 */,
                                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 */,
+                               379294700F2E191800B9034A /* parsimonycommand.cpp in Sources */,
+                               3792948A0F2E258500B9034A /* parsimony.cpp in Sources */,
+                               374610780F40645300460C57 /* unifracweightedcommand.cpp in Sources */,
+                               3746107E0F4064D100460C57 /* weighted.cpp in Sources */,
+                               374610830F40652400460C57 /* unweighted.cpp in Sources */,
+                               3746109D0F40657600460C57 /* unifracunweightedcommand.cpp in Sources */,
+                               37AFC71F0F445386005F492D /* sharedsobscollectsummary.cpp in Sources */,
+                               A70B53AA0F4CD7AD0064797E /* getgroupcommand.cpp in Sources */,
+                               A70B53AB0F4CD7AD0064797E /* getlabelcommand.cpp in Sources */,
+                               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 */,
+                               EB6F015B0F6AC1670048081A /* sharedbdiversity.cpp in Sources */,
+                               375873E70F7D63E90040F377 /* coverage.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 */,
+                               3731C1F30F8CFC0A0065A2AD /* treegroupscommand.cpp in Sources */,
+                               37C7F3A90F8E90AD00E91C2B /* sharedutilities.cpp 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 = 0;
                                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 */,