]> git.donarmstrong.com Git - mothur.git/blobdiff - Mothur.xcodeproj/project.pbxproj
more calculator edits and added coverage and whittaker
[mothur.git] / Mothur.xcodeproj / project.pbxproj
index a84195d4332a491ff9c0e7f0ff7832f92eccb396..6fd4a0656cc57fa33f0f78be7819368044d31d22 100644 (file)
@@ -7,6 +7,10 @@
        objects = {
 
 /* Begin PBXBuildFile section */
+               211C38320F961DD400FEE541 /* sharedutilities.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 211C38300F961DD400FEE541 /* sharedutilities.cpp */; };
+               211C38380F961E1F00FEE541 /* treegroupscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 211C38360F961E1F00FEE541 /* treegroupscommand.cpp */; };
+               21DDC01B0F97A8FE0060691C /* bootstrapsharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 21DDC01A0F97A8FE0060691C /* bootstrapsharedcommand.cpp */; };
+               370B88070F8A4EE4005AB382 /* getoturepcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */; };
                372E12700F26365B0095CF7E /* readotucommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 372E126F0F26365B0095CF7E /* readotucommand.cpp */; };
                372E12960F263D5A0095CF7E /* readdistcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 372E12950F263D5A0095CF7E /* readdistcommand.cpp */; };
                372E12ED0F264D320095CF7E /* commandfactory.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 372E12EC0F264D320095CF7E /* commandfactory.cpp */; };
                3746107E0F4064D100460C57 /* weighted.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3746107D0F4064D100460C57 /* weighted.cpp */; };
                374610830F40652400460C57 /* unweighted.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 374610820F40652400460C57 /* unweighted.cpp */; };
                3746109D0F40657600460C57 /* unifracunweightedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */; };
-               375873A70F7D61240040F377 /* coverage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3758738B0F7D61240040F377 /* coverage.cpp */; };
-               375873A80F7D61240040F377 /* fullmatrix.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3758738D0F7D61240040F377 /* fullmatrix.cpp */; };
-               375873A90F7D61240040F377 /* heatmap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3758738F0F7D61240040F377 /* heatmap.cpp */; };
-               375873AA0F7D61240040F377 /* heatmapcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873910F7D61240040F377 /* heatmapcommand.cpp */; };
-               375873AB0F7D61240040F377 /* libshuffcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873930F7D61240040F377 /* libshuffcommand.cpp */; };
-               375873AC0F7D61240040F377 /* nocommands.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873950F7D61240040F377 /* nocommands.cpp */; };
-               375873AD0F7D61240040F377 /* sharedanderberg.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873980F7D61240040F377 /* sharedanderberg.cpp */; };
-               375873AE0F7D61240040F377 /* sharedbraycurtis.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3758739A0F7D61240040F377 /* sharedbraycurtis.cpp */; };
-               375873AF0F7D61240040F377 /* sharedkulczynski.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3758739C0F7D61240040F377 /* sharedkulczynski.cpp */; };
-               375873B00F7D61240040F377 /* sharedkulczynskicody.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3758739E0F7D61240040F377 /* sharedkulczynskicody.cpp */; };
-               375873B10F7D61240040F377 /* sharedlennon.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873A00F7D61240040F377 /* sharedlennon.cpp */; };
-               375873B20F7D61240040F377 /* sharedmorisitahorn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873A20F7D61240040F377 /* sharedmorisitahorn.cpp */; };
-               375873B30F7D61240040F377 /* sharedochiai.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873A50F7D61240040F377 /* sharedochiai.cpp */; };
-               375873E30F7D63B50040F377 /* sharedanderberg.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873E20F7D63B50040F377 /* sharedanderberg.cpp */; };
-               375873E70F7D63E90040F377 /* coverage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873E50F7D63E90040F377 /* coverage.cpp */; };
+               37519A6B0F80E6EB00FED5E8 /* sharedanderbergs.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37519A6A0F80E6EB00FED5E8 /* sharedanderbergs.cpp */; };
+               37519AA10F810D0200FED5E8 /* venncommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37519AA00F810D0200FED5E8 /* venncommand.cpp */; };
+               37519AB50F810FAE00FED5E8 /* venn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37519AB40F810FAE00FED5E8 /* venn.cpp */; };
                375873EC0F7D64520040F377 /* fullmatrix.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873EB0F7D64520040F377 /* fullmatrix.cpp */; };
                375873EF0F7D646F0040F377 /* heatmap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873EE0F7D646F0040F377 /* heatmap.cpp */; };
                375873F20F7D64800040F377 /* heatmapcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873F00F7D64800040F377 /* heatmapcommand.cpp */; };
@@ -40,6 +32,9 @@
                375874060F7D64EF0040F377 /* sharedkulczynskicody.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375874020F7D64EF0040F377 /* sharedkulczynskicody.cpp */; };
                3758740C0F7D64FC0040F377 /* sharedmorisitahorn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375874080F7D64FC0040F377 /* sharedmorisitahorn.cpp */; };
                3758740D0F7D64FC0040F377 /* sharedochiai.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3758740B0F7D64FC0040F377 /* sharedochiai.cpp */; };
+               375AA1390F9E433D008EF9B8 /* readcolumn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375AA1330F9E433D008EF9B8 /* readcolumn.cpp */; };
+               375AA13A0F9E433D008EF9B8 /* readotu.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375AA1350F9E433D008EF9B8 /* readotu.cpp */; };
+               375AA13B0F9E433D008EF9B8 /* readphylip.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375AA1370F9E433D008EF9B8 /* readphylip.cpp */; };
                379293C30F2DE73400B9034A /* treemap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 379293C20F2DE73400B9034A /* treemap.cpp */; };
                379294700F2E191800B9034A /* parsimonycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3792946F0F2E191800B9034A /* parsimonycommand.cpp */; };
                3792948A0F2E258500B9034A /* parsimony.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 379294890F2E258500B9034A /* parsimony.cpp */; };
@@ -48,6 +43,7 @@
                37AD4DCA0F28F3DD00AA2D49 /* readtree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */; };
                37AFC71F0F445386005F492D /* sharedsobscollectsummary.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */; };
                37B28F680F27590100808A62 /* deconvolutecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37B28F670F27590100808A62 /* deconvolutecommand.cpp */; };
+               37C1D9730F86506E0059E3F0 /* binsequencecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */; };
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                37D928560F21331F001D4494 /* averagelinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927BA0F21331F001D4494 /* averagelinkage.cpp */; };
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@@ -86,7 +82,6 @@
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                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 */; };
                37D9289F0F21331F001D4494 /* validparameter.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928530F21331F001D4494 /* validparameter.cpp */; };
                37E5F3E30F29FD4200F8D827 /* treenode.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37E5F3E20F29FD4200F8D827 /* treenode.cpp */; };
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+               7E412F490F8D21B600381DD0 /* slibshuff.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E412F480F8D21B600381DD0 /* slibshuff.cpp */; };
+               7E412FEA0F8D3E2C00381DD0 /* libshuff.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */; };
+               7E4130F80F8E58FA00381DD0 /* dlibshuff.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E4130F60F8E58FA00381DD0 /* dlibshuff.cpp */; };
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+               7EC3D4560FA0FFF900338DA5 /* whittaker.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7EC3D4530FA0FFF900338DA5 /* whittaker.cpp */; };
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                A70B53AB0F4CD7AD0064797E /* getlabelcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */; };
                EB1216E50F61ACFB004A865F /* bstick.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB1216E40F61ACFB004A865F /* bstick.cpp */; };
                EB1217230F61C9AC004A865F /* sharedkstest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB1217220F61C9AC004A865F /* sharedkstest.cpp */; };
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 /* End PBXBuildFile section */
 /* End PBXCopyFilesBuildPhase section */
 
 /* Begin PBXFileReference section */
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-               375873970F7D61240040F377 /* nseqs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = nseqs.h; sourceTree = "<group>"; };
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-               375873990F7D61240040F377 /* sharedanderberg.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedanderberg.h; sourceTree = "<group>"; };
-               3758739A0F7D61240040F377 /* sharedbraycurtis.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedbraycurtis.cpp; sourceTree = "<group>"; };
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-               3758739C0F7D61240040F377 /* sharedkulczynski.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedkulczynski.cpp; sourceTree = "<group>"; };
-               3758739D0F7D61240040F377 /* sharedkulczynski.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedkulczynski.h; sourceTree = "<group>"; };
-               3758739E0F7D61240040F377 /* sharedkulczynskicody.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedkulczynskicody.cpp; sourceTree = "<group>"; };
-               3758739F0F7D61240040F377 /* sharedkulczynskicody.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedkulczynskicody.h; sourceTree = "<group>"; };
-               375873A00F7D61240040F377 /* sharedlennon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedlennon.cpp; sourceTree = "<group>"; };
-               375873A10F7D61240040F377 /* sharedlennon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedlennon.h; sourceTree = "<group>"; };
-               375873A20F7D61240040F377 /* sharedmorisitahorn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedmorisitahorn.cpp; sourceTree = "<group>"; };
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-               375873A40F7D61240040F377 /* sharednseqs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharednseqs.h; sourceTree = "<group>"; };
-               375873A50F7D61240040F377 /* sharedochiai.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedochiai.cpp; sourceTree = "<group>"; };
-               375873A60F7D61240040F377 /* sharedochiai.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedochiai.h; sourceTree = "<group>"; };
-               375873E20F7D63B50040F377 /* sharedanderberg.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedanderberg.cpp; sourceTree = "<group>"; };
-               375873E50F7D63E90040F377 /* coverage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = coverage.cpp; sourceTree = "<group>"; };
-               375873E60F7D63E90040F377 /* coverage.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = coverage.h; sourceTree = "<group>"; };
+               37519A690F80E6EB00FED5E8 /* sharedanderbergs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedanderbergs.h; sourceTree = "<group>"; };
+               37519A6A0F80E6EB00FED5E8 /* sharedanderbergs.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedanderbergs.cpp; sourceTree = "<group>"; };
+               37519A9F0F810D0200FED5E8 /* venncommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = venncommand.h; sourceTree = "<group>"; };
+               37519AA00F810D0200FED5E8 /* venncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = venncommand.cpp; sourceTree = "<group>"; };
+               37519AB30F810FAE00FED5E8 /* venn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = venn.h; sourceTree = "<group>"; };
+               37519AB40F810FAE00FED5E8 /* venn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = venn.cpp; sourceTree = "<group>"; };
                375873EA0F7D64520040F377 /* fullmatrix.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fullmatrix.h; sourceTree = "<group>"; };
                375873EB0F7D64520040F377 /* fullmatrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fullmatrix.cpp; sourceTree = "<group>"; };
                375873ED0F7D646F0040F377 /* heatmap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmap.h; sourceTree = "<group>"; };
                375873F60F7D649C0040F377 /* nocommands.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nocommands.cpp; sourceTree = "<group>"; };
                375873F70F7D649C0040F377 /* nocommands.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = nocommands.h; sourceTree = "<group>"; };
                375873F90F7D64AB0040F377 /* nseqs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = nseqs.h; sourceTree = "<group>"; };
-               375873FA0F7D64D20040F377 /* sharedanderberg.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedanderberg.h; sourceTree = "<group>"; };
                375873FB0F7D64DA0040F377 /* sharedbraycurtis.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedbraycurtis.h; sourceTree = "<group>"; };
                375873FC0F7D64DA0040F377 /* sharedbraycurtis.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedbraycurtis.cpp; sourceTree = "<group>"; };
                375873FE0F7D64EF0040F377 /* sharedkulczynski.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedkulczynski.cpp; sourceTree = "<group>"; };
                375874090F7D64FC0040F377 /* sharedochiai.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedochiai.h; sourceTree = "<group>"; };
                3758740A0F7D64FC0040F377 /* sharednseqs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharednseqs.h; sourceTree = "<group>"; };
                3758740B0F7D64FC0040F377 /* sharedochiai.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedochiai.cpp; sourceTree = "<group>"; };
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+               375AA1340F9E433D008EF9B8 /* readcolumn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readcolumn.h; sourceTree = "<group>"; };
+               375AA1350F9E433D008EF9B8 /* readotu.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readotu.cpp; sourceTree = "<group>"; };
+               375AA1360F9E433D008EF9B8 /* readotu.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotu.h; sourceTree = "<group>"; };
+               375AA1370F9E433D008EF9B8 /* readphylip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readphylip.cpp; sourceTree = "<group>"; };
+               375AA1380F9E433D008EF9B8 /* readphylip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylip.h; sourceTree = "<group>"; };
                379293C10F2DE73400B9034A /* treemap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treemap.h; sourceTree = "<group>"; };
                379293C20F2DE73400B9034A /* treemap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treemap.cpp; sourceTree = "<group>"; };
                3792946E0F2E191800B9034A /* parsimonycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimonycommand.h; sourceTree = "<group>"; };
                37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsobscollectsummary.cpp; sourceTree = "<group>"; };
                37B28F660F27590100808A62 /* deconvolutecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = deconvolutecommand.h; sourceTree = "<group>"; };
                37B28F670F27590100808A62 /* deconvolutecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = deconvolutecommand.cpp; sourceTree = "<group>"; };
+               37C1D9710F86506E0059E3F0 /* binsequencecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = binsequencecommand.h; sourceTree = "<group>"; };
+               37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = binsequencecommand.cpp; sourceTree = "<group>"; };
                37D927B80F21331F001D4494 /* ace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ace.cpp; sourceTree = "<group>"; };
                37D927B90F21331F001D4494 /* ace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ace.h; sourceTree = "<group>"; };
                37D927BA0F21331F001D4494 /* averagelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = averagelinkage.cpp; sourceTree = "<group>"; };
                37D928090F21331F001D4494 /* rarefactioncurvedata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactioncurvedata.h; sourceTree = "<group>"; };
                37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefactsharedcommand.cpp; sourceTree = "<group>"; };
                37D9280B0F21331F001D4494 /* rarefactsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactsharedcommand.h; sourceTree = "<group>"; };
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                37D928130F21331F001D4494 /* readmatrix.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = readmatrix.hpp; sourceTree = "<group>"; };
                37D9281A0F21331F001D4494 /* sabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sabundvector.cpp; sourceTree = "<group>"; };
                37D9281B0F21331F001D4494 /* sabundvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sabundvector.hpp; sourceTree = "<group>"; };
                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>"; };
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                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>"; };
                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>"; };
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                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>"; };
                08FB7795FE84155DC02AAC07 /* Source */ = {
                        isa = PBXGroup;
                        children = (
+                               7E4130F60F8E58FA00381DD0 /* dlibshuff.cpp */,
+                               7E4130F70F8E58FA00381DD0 /* dlibshuff.h */,
                                37D927BA0F21331F001D4494 /* averagelinkage.cpp */,
                                37D928A60F2133C0001D4494 /* calculators */,
                                37D927C20F21331F001D4494 /* cluster.hpp */,
                                37D927C10F21331F001D4494 /* cluster.cpp */,
+                               7E412F470F8D21B600381DD0 /* slibshuff.h */,
+                               7E412F480F8D21B600381DD0 /* slibshuff.cpp */,
+                               7E412F420F8D213C00381DD0 /* libshuff.h */,
+                               7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */,
                                37D928A90F2133E5001D4494 /* commands */,
                                37D927C60F21331F001D4494 /* collect.h */,
                                37D927C50F21331F001D4494 /* collect.cpp */,
                                37D927EF0F21331F001D4494 /* mothur.cpp */,
                                37D927F10F21331F001D4494 /* nameassignment.hpp */,
                                37D927F00F21331F001D4494 /* nameassignment.cpp */,
-                               3758738B0F7D61240040F377 /* coverage.cpp */,
-                               3758738C0F7D61240040F377 /* coverage.h */,
-                               3758738D0F7D61240040F377 /* fullmatrix.cpp */,
-                               3758738E0F7D61240040F377 /* fullmatrix.h */,
-                               3758738F0F7D61240040F377 /* heatmap.cpp */,
-                               375873900F7D61240040F377 /* heatmap.h */,
-                               375873910F7D61240040F377 /* heatmapcommand.cpp */,
-                               375873920F7D61240040F377 /* heatmapcommand.h */,
-                               375873930F7D61240040F377 /* libshuffcommand.cpp */,
-                               375873940F7D61240040F377 /* libshuffcommand.h */,
-                               375873950F7D61240040F377 /* nocommands.cpp */,
-                               375873960F7D61240040F377 /* nocommands.h */,
-                               375873970F7D61240040F377 /* nseqs.h */,
-                               375873980F7D61240040F377 /* sharedanderberg.cpp */,
-                               375873990F7D61240040F377 /* sharedanderberg.h */,
-                               3758739A0F7D61240040F377 /* sharedbraycurtis.cpp */,
-                               3758739B0F7D61240040F377 /* sharedbraycurtis.h */,
-                               3758739C0F7D61240040F377 /* sharedkulczynski.cpp */,
-                               3758739D0F7D61240040F377 /* sharedkulczynski.h */,
-                               3758739E0F7D61240040F377 /* sharedkulczynskicody.cpp */,
-                               3758739F0F7D61240040F377 /* sharedkulczynskicody.h */,
-                               375873A00F7D61240040F377 /* sharedlennon.cpp */,
-                               375873A10F7D61240040F377 /* sharedlennon.h */,
-                               375873A20F7D61240040F377 /* sharedmorisitahorn.cpp */,
-                               375873A30F7D61240040F377 /* sharedmorisitahorn.h */,
-                               375873A40F7D61240040F377 /* sharednseqs.h */,
-                               375873A50F7D61240040F377 /* sharedochiai.cpp */,
-                               375873A60F7D61240040F377 /* sharedochiai.h */,
                                37D927F60F21331F001D4494 /* observable.h */,
                                37D927FC0F21331F001D4494 /* progress.hpp */,
                                37D927FB0F21331F001D4494 /* progress.cpp */,
                                37D928060F21331F001D4494 /* rarefact.h */,
                                37D928050F21331F001D4494 /* rarefact.cpp */,
                                37D928090F21331F001D4494 /* rarefactioncurvedata.h */,
+                               375AA1340F9E433D008EF9B8 /* readcolumn.h */,
+                               375AA1330F9E433D008EF9B8 /* readcolumn.cpp */,
                                37D928130F21331F001D4494 /* readmatrix.hpp */,
-                               37D928120F21331F001D4494 /* readmatrix.cpp */,
+                               375AA1360F9E433D008EF9B8 /* readotu.h */,
+                               375AA1350F9E433D008EF9B8 /* readotu.cpp */,
+                               375AA1380F9E433D008EF9B8 /* readphylip.h */,
+                               375AA1370F9E433D008EF9B8 /* readphylip.cpp */,
                                37AD4DC80F28F3DD00AA2D49 /* readtree.h */,
                                37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */,
                                37D9281D0F21331F001D4494 /* sequence.hpp */,
                                37D9281C0F21331F001D4494 /* sequence.cpp */,
                                37D928210F21331F001D4494 /* shared.h */,
                                37D928200F21331F001D4494 /* shared.cpp */,
+                               211C38310F961DD400FEE541 /* sharedutilities.h */,
+                               211C38300F961DD400FEE541 /* sharedutilities.cpp */,
                                37D928420F21331F001D4494 /* singlelinkage.cpp */,
-                               37D928450F21331F001D4494 /* sparsematrix.hpp */,
-                               37D928440F21331F001D4494 /* sparsematrix.cpp */,
                                37D928480F21331F001D4494 /* summarydata.h */,
                                37D928490F21331F001D4494 /* summarydisplay.h */,
-                               37D9284C0F21331F001D4494 /* utilities.hpp */,
+                               37519AB30F810FAE00FED5E8 /* venn.h */,
+                               37519AB40F810FAE00FED5E8 /* venn.cpp */,
                        );
                        name = Source;
                        sourceTree = "<group>";
                                EB1216E40F61ACFB004A865F /* bstick.cpp */,
                                37D927C00F21331F001D4494 /* chao1.h */,
                                37D927BF0F21331F001D4494 /* chao1.cpp */,
-                               375873E60F7D63E90040F377 /* coverage.h */,
-                               375873E50F7D63E90040F377 /* coverage.cpp */,
                                EB9303F70F53517300E8EF26 /* geom.h */,
                                EB9303F80F53517300E8EF26 /* geom.cpp */,
                                EB9303E90F534D9400E8EF26 /* logsd.h */,
                                37D9281E0F21331F001D4494 /* shannon.cpp */,
                                37D928230F21331F001D4494 /* sharedace.h */,
                                37D928220F21331F001D4494 /* sharedace.cpp */,
-                               375873FA0F7D64D20040F377 /* sharedanderberg.h */,
-                               375873E20F7D63B50040F377 /* sharedanderberg.cpp */,
+                               37519A690F80E6EB00FED5E8 /* sharedanderbergs.h */,
+                               37519A6A0F80E6EB00FED5E8 /* sharedanderbergs.cpp */,
+                               7EC3D4500FA0FFF900338DA5 /* coverage.cpp */,
+                               7EC3D4510FA0FFF900338DA5 /* coverage.h */,
+                               7EC3D4520FA0FFF900338DA5 /* sharedanderberg.h */,
+                               7EC3D4530FA0FFF900338DA5 /* whittaker.cpp */,
+                               7EC3D4540FA0FFF900338DA5 /* whittaker.h */,
                                375873FB0F7D64DA0040F377 /* sharedbraycurtis.h */,
                                375873FC0F7D64DA0040F377 /* sharedbraycurtis.cpp */,
-                               EB6F01590F6AC1670048081A /* sharedbdiversity.h */,
-                               EB6F015A0F6AC1670048081A /* sharedbdiversity.cpp */,
                                37D928250F21331F001D4494 /* sharedchao1.h */,
                                37D928240F21331F001D4494 /* sharedchao1.cpp */,
                                37D928290F21331F001D4494 /* sharedjabund.h */,
                                37D9282C0F21331F001D4494 /* sharedjest.cpp */,
                                EB1217210F61C9AC004A865F /* sharedkstest.h */,
                                EB1217220F61C9AC004A865F /* sharedkstest.cpp */,
-                               375873FE0F7D64EF0040F377 /* sharedkulczynski.cpp */,
-                               375873FF0F7D64EF0040F377 /* sharedlennon.cpp */,
                                375874000F7D64EF0040F377 /* sharedkulczynski.h */,
-                               375874010F7D64EF0040F377 /* sharedlennon.h */,
-                               375874020F7D64EF0040F377 /* sharedkulczynskicody.cpp */,
+                               375873FE0F7D64EF0040F377 /* sharedkulczynski.cpp */,
                                375874030F7D64EF0040F377 /* sharedkulczynskicody.h */,
+                               375874020F7D64EF0040F377 /* sharedkulczynskicody.cpp */,
+                               375874010F7D64EF0040F377 /* sharedlennon.h */,
+                               375873FF0F7D64EF0040F377 /* sharedlennon.cpp */,
                                375874070F7D64FC0040F377 /* sharedmorisitahorn.h */,
                                375874080F7D64FC0040F377 /* sharedmorisitahorn.cpp */,
                                375874090F7D64FC0040F377 /* sharedochiai.h */,
-                               3758740A0F7D64FC0040F377 /* sharednseqs.h */,
                                3758740B0F7D64FC0040F377 /* sharedochiai.cpp */,
+                               3758740A0F7D64FC0040F377 /* sharednseqs.h */,
                                37D928350F21331F001D4494 /* sharedsobs.h */,
                                37D928340F21331F001D4494 /* sharedsobs.cpp */,
                                37AFC71D0F445386005F492D /* sharedsobscollectsummary.h */,
                        isa = PBXGroup;
                        children = (
                                37D927CD0F21331F001D4494 /* command.hpp */,
+                               37C1D9710F86506E0059E3F0 /* binsequencecommand.h */,
+                               37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */,
+                               21DDC0190F97A8FE0060691C /* bootstrapsharedcommand.h */,
+                               21DDC01A0F97A8FE0060691C /* bootstrapsharedcommand.cpp */,
                                37D927C40F21331F001D4494 /* clustercommand.h */,
                                37D927C30F21331F001D4494 /* clustercommand.cpp */,
                                37D927C80F21331F001D4494 /* collectcommand.h */,
                                A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */,
                                A70B53A90F4CD7AD0064797E /* getlinecommand.h */,
                                A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */,
-                               375873F00F7D64800040F377 /* heatmapcommand.cpp */,
+                               370B88050F8A4EE4005AB382 /* getoturepcommand.h */,
+                               370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */,
                                375873F10F7D64800040F377 /* heatmapcommand.h */,
+                               375873F00F7D64800040F377 /* heatmapcommand.cpp */,
                                37D927E40F21331F001D4494 /* helpcommand.h */,
                                37D927E30F21331F001D4494 /* helpcommand.cpp */,
-                               375873F30F7D648F0040F377 /* libshuffcommand.cpp */,
                                375873F40F7D648F0040F377 /* libshuffcommand.h */,
+                               375873F30F7D648F0040F377 /* libshuffcommand.cpp */,
                                375873F60F7D649C0040F377 /* nocommands.cpp */,
                                375873F70F7D649C0040F377 /* nocommands.h */,
                                37D927FA0F21331F001D4494 /* parselistcommand.h */,
                                37D928460F21331F001D4494 /* summarycommand.cpp */,
                                37D9284B0F21331F001D4494 /* summarysharedcommand.h */,
                                37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */,
+                               211C38370F961E1F00FEE541 /* treegroupscommand.h */,
+                               211C38360F961E1F00FEE541 /* treegroupscommand.cpp */,
                                3746109B0F40657600460C57 /* unifracunweightedcommand.h */,
                                3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */,
                                374610760F40645300460C57 /* unifracweightedcommand.h */,
                                374610770F40645300460C57 /* unifracweightedcommand.cpp */,
+                               37519A9F0F810D0200FED5E8 /* venncommand.h */,
+                               37519AA00F810D0200FED5E8 /* venncommand.cpp */,
                        );
                        name = commands;
                        sourceTree = "<group>";
                                37D928300F21331F001D4494 /* sharedrabundvector.cpp */,
                                37D928330F21331F001D4494 /* sharedsabundvector.h */,
                                37D928320F21331F001D4494 /* sharedsabundvector.cpp */,
+                               37D928450F21331F001D4494 /* sparsematrix.hpp */,
+                               37D928440F21331F001D4494 /* sparsematrix.cpp */,
                                37AD4DB90F28E2FE00AA2D49 /* tree.h */,
                                37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */,
                                379293C10F2DE73400B9034A /* treemap.h */,
                                37D9287A0F21331F001D4494 /* rarefact.cpp in Sources */,
                                37D9287B0F21331F001D4494 /* rarefactcommand.cpp in Sources */,
                                37D9287C0F21331F001D4494 /* rarefactsharedcommand.cpp in Sources */,
-                               37D928800F21331F001D4494 /* readmatrix.cpp in Sources */,
                                37D928840F21331F001D4494 /* sabundvector.cpp in Sources */,
                                37D928850F21331F001D4494 /* sequence.cpp in Sources */,
                                37D928860F21331F001D4494 /* shannon.cpp in Sources */,
                                EB1216880F619B83004A865F /* bergerparker.cpp in Sources */,
                                EB1216E50F61ACFB004A865F /* bstick.cpp in Sources */,
                                EB1217230F61C9AC004A865F /* sharedkstest.cpp in Sources */,
-                               EB6F015B0F6AC1670048081A /* sharedbdiversity.cpp in Sources */,
-                               375873A70F7D61240040F377 /* coverage.cpp in Sources */,
-                               375873A80F7D61240040F377 /* fullmatrix.cpp in Sources */,
-                               375873A90F7D61240040F377 /* heatmap.cpp in Sources */,
-                               375873AA0F7D61240040F377 /* heatmapcommand.cpp in Sources */,
-                               375873AB0F7D61240040F377 /* libshuffcommand.cpp in Sources */,
-                               375873AC0F7D61240040F377 /* nocommands.cpp in Sources */,
-                               375873AD0F7D61240040F377 /* sharedanderberg.cpp in Sources */,
-                               375873AE0F7D61240040F377 /* sharedbraycurtis.cpp in Sources */,
-                               375873AF0F7D61240040F377 /* sharedkulczynski.cpp in Sources */,
-                               375873B00F7D61240040F377 /* sharedkulczynskicody.cpp in Sources */,
-                               375873B10F7D61240040F377 /* sharedlennon.cpp in Sources */,
-                               375873B20F7D61240040F377 /* sharedmorisitahorn.cpp in Sources */,
-                               375873B30F7D61240040F377 /* sharedochiai.cpp in Sources */,
-                               375873E30F7D63B50040F377 /* sharedanderberg.cpp in Sources */,
-                               375873E70F7D63E90040F377 /* coverage.cpp in Sources */,
                                375873EC0F7D64520040F377 /* fullmatrix.cpp in Sources */,
                                375873EF0F7D646F0040F377 /* heatmap.cpp in Sources */,
                                375873F20F7D64800040F377 /* heatmapcommand.cpp in Sources */,
                                375874060F7D64EF0040F377 /* sharedkulczynskicody.cpp in Sources */,
                                3758740C0F7D64FC0040F377 /* sharedmorisitahorn.cpp in Sources */,
                                3758740D0F7D64FC0040F377 /* sharedochiai.cpp in Sources */,
+                               37519A6B0F80E6EB00FED5E8 /* sharedanderbergs.cpp in Sources */,
+                               37519AA10F810D0200FED5E8 /* venncommand.cpp in Sources */,
+                               37519AB50F810FAE00FED5E8 /* venn.cpp in Sources */,
+                               37C1D9730F86506E0059E3F0 /* binsequencecommand.cpp in Sources */,
+                               370B88070F8A4EE4005AB382 /* getoturepcommand.cpp in Sources */,
+                               7E412F490F8D21B600381DD0 /* slibshuff.cpp in Sources */,
+                               7E412FEA0F8D3E2C00381DD0 /* libshuff.cpp in Sources */,
+                               7E4130F80F8E58FA00381DD0 /* dlibshuff.cpp in Sources */,
+                               211C38320F961DD400FEE541 /* sharedutilities.cpp in Sources */,
+                               211C38380F961E1F00FEE541 /* treegroupscommand.cpp in Sources */,
+                               21DDC01B0F97A8FE0060691C /* bootstrapsharedcommand.cpp in Sources */,
+                               375AA1390F9E433D008EF9B8 /* readcolumn.cpp in Sources */,
+                               375AA13A0F9E433D008EF9B8 /* readotu.cpp in Sources */,
+                               375AA13B0F9E433D008EF9B8 /* readphylip.cpp in Sources */,
+                               7EC3D4550FA0FFF900338DA5 /* coverage.cpp in Sources */,
+                               7EC3D4560FA0FFF900338DA5 /* whittaker.cpp in Sources */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };
                                        ppc,
                                        i386,
                                );
-                               GCC_OPTIMIZATION_LEVEL = 0;
+                               GCC_OPTIMIZATION_LEVEL = 3;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
                                GCC_WARN_UNUSED_VARIABLE = YES;
                                PREBINDING = NO;